#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_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	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_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_Mutation_Status	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	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_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
SGK1	6446	hgsc.bcm.edu	37	6	134494703	134494703	+	Splice_Site	DEL	G	G	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134494703delG	ENST00000237305.7	-	4	318	c.230delC	c.(229-231)cca>ca	p.P77fs	SGK1_ENST00000367858.5_Splice_Site_p.P172fs|SGK1_ENST00000367857.5_Splice_Site_p.P67fs|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000475719.2_Splice_Site_p.P77fs|SGK1_ENST00000413996.3_Splice_Site_p.P91fs|SGK1_ENST00000528577.1_Splice_Site_p.P105fs	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	77					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		AGAAGGACTTGGCTAGAAAAA	0.368																																					p.P172fs		Atlas-Indel	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,-2,6	SGK1	387	6	0			c.516delA						PASS	.						46.0	49.0	48.0					6																	134494703		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon6			.	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.229-1C>-	6.37:g.134494703delG		Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	68	13	0.191176	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Frame_Shift_Del	DEL	ENST00000237305.7	37	CCDS5170.1																																																																																			.	.	none		0.368	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Frame_Shift_Del
IRF2BPL	64207	hgsc.bcm.edu	37	14	77493762	77493767	+	In_Frame_Del	DEL	TGCTGC	TGCTGC	-	rs553703325|rs556445214|rs200317113	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	TGCTGC	TGCTGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:77493762_77493767delTGCTGC	ENST00000238647.3	-	1	1267_1272	c.369_374delGCAGCA	c.(367-375)cagcagcaa>caa	p.123_125QQQ>Q		NM_024496.3	NP_078772.1	Q9H1B7	I2BPL_HUMAN	interferon regulatory factor 2 binding protein-like	123	Poly-Gln.				development of secondary female sexual characteristics (GO:0046543)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	extracellular space (GO:0005615)|nucleus (GO:0005634)	metal ion binding (GO:0046872)			endometrium(2)|kidney(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(2)	11						GAgctgttgttgctgctgctgctgct	0.714														4658	0.930112	0.9297	0.9769	5008	,	,		7189	0.872		0.9712	False		,,,				2504	0.9151				p.124_125del		Atlas-Indel	.											.	IRF2BPL	40	.	0			c.370_375del						PASS	.																																			SO:0001651	inframe_deletion	64207	exon1			.	AJ277365	CCDS9854.1	14q24.3	2011-02-23	2011-02-23	2011-02-23	ENSG00000119669	ENSG00000119669			14282	protein-coding gene	gene with protein product	"""enhanced at puberty 1"""	611720	"""chromosome 14 open reading frame 4"""	C14orf4		11095982, 17627301	Standard	NM_024496		Approved	EAP1, KIAA1865	uc001xsy.4	Q9H1B7		ENST00000238647.3:c.369_374delGCAGCA	14.37:g.77493768_77493773delTGCTGC	ENSP00000238647:p.Gln125_Gln126del	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	25	10	0.4	NM_024496	Q8NDQ2|Q96JG2|Q9H3I7	In_Frame_Del	DEL	ENST00000238647.3	37	CCDS9854.1																																																																																			TGCTGC|0.190;-|0.810	0.810	strong		0.714	IRF2BPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414298.1	NM_024496	
TOP2B	7155	hgsc.bcm.edu	37	3	25674218	25674218	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:25674218delT	ENST00000264331.4	-	9	1093	c.1094delA	c.(1093-1095)aagfs	p.K365fs	TOP2B_ENST00000435706.2_Frame_Shift_Del_p.K360fs	NM_001068.2	NP_001059.2	Q02880	TOP2B_HUMAN	topoisomerase (DNA) II beta 180kDa	365	Interaction with DNA. {ECO:0000250}.				ATP catabolic process (GO:0006200)|axonogenesis (GO:0007409)|DNA topological change (GO:0006265)|DNA unwinding involved in DNA replication (GO:0006268)|forebrain development (GO:0030900)|mitotic DNA integrity checkpoint (GO:0044774)|mitotic recombination (GO:0006312)|neuron migration (GO:0001764)|resolution of meiotic recombination intermediates (GO:0000712)|sister chromatid segregation (GO:0000819)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|DNA topoisomerase complex (ATP-hydrolyzing) (GO:0009330)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding, bending (GO:0008301)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein kinase C binding (GO:0005080)			breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|skin(2)|stomach(1)	36					Dactinomycin(DB00970)|Daunorubicin(DB00694)|Dexrazoxane(DB00380)|Etoposide(DB00773)	AGCTTTGTTCTTTTTCTTAAC	0.313																																					p.K360fs		Pindel,Atlas-Indel	.											.	TOP2B	98	.	0			c.1080delG						PASS	.						141.0	142.0	141.0					3																	25674218		1859	4100	5959	SO:0001589	frameshift_variant	7155	exon9			.	X68060	CCDS46776.1	3p24.2	2012-08-30	2002-08-29		ENSG00000077097	ENSG00000077097	5.99.1.3		11990	protein-coding gene	gene with protein product		126431	"""topoisomerase (DNA) II beta (180kD)"""			1309226, 1333583	Standard	NM_001068		Approved		uc003cdj.3	Q02880	OTTHUMG00000155596	ENST00000264331.4:c.1094delA	3.37:g.25674218delT	ENSP00000264331:p.Lys365fs	Somatic	204	.	.		WXS	Illumina HiSeq	Phase_I	261	42	0.161	NM_001068	Q13600|Q9UMG8|Q9UQP8	Frame_Shift_Del	DEL	ENST00000264331.4	37																																																																																				.	.	none		0.313	TOP2B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding			
ITPKB	3707	hgsc.bcm.edu	37	1	226836447	226836447	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:226836447delT	ENST00000272117.3	-	2	1957	c.1958delA	c.(1957-1959)aacfs	p.N653fs	ITPKB_ENST00000429204.1_Frame_Shift_Del_p.N653fs			P27987	IP3KB_HUMAN	inositol-trisphosphate 3-kinase B	653					cell surface receptor signaling pathway (GO:0007166)|inositol phosphate metabolic process (GO:0043647)|MAPK cascade (GO:0000165)|positive regulation of alpha-beta T cell differentiation (GO:0046638)|positive regulation of Ras protein signal transduction (GO:0046579)|positive thymic T cell selection (GO:0045059)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|inositol-1,4,5-trisphosphate 3-kinase activity (GO:0008440)			central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(4)|prostate(1)|skin(1)	30		Prostate(94;0.0773)				GTGCACCATGTTTTTTATCTT	0.438																																					p.N653fs	Colon(84;110 1851 5306 33547)	Pindel,Atlas-Indel	.											.	ITPKB	158	.	0			c.1959delC						PASS	.						164.0	163.0	164.0					1																	226836447		2203	4300	6503	SO:0001589	frameshift_variant	3707	exon3			.	AJ242780	CCDS1555.1	1q42.12	2011-04-28	2011-04-28		ENSG00000143772	ENSG00000143772	2.7.1.127		6179	protein-coding gene	gene with protein product		147522	"""inositol 1,4,5-trisphosphate 3-kinase B"""			1654894, 1330886	Standard	NM_002221		Approved	IP3KB, IP3-3KB	uc010pvo.2	P27987	OTTHUMG00000037582	ENST00000272117.3:c.1958delA	1.37:g.226836447delT	ENSP00000272117:p.Asn653fs	Somatic	171	.	.		WXS	Illumina HiSeq	Phase_I	169	32	0.189	NM_002221	Q5VWL9|Q5VWM0|Q96BZ2|Q96JS1|Q9UH47	Frame_Shift_Del	DEL	ENST00000272117.3	37	CCDS1555.1																																																																																			.	.	none		0.438	ITPKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091632.1	NM_002221	
BNC2	54796	hgsc.bcm.edu	37	9	16436374	16436375	+	Frame_Shift_Ins	INS	-	-	G	rs116528562|rs142872531	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:16436374_16436375insG	ENST00000380672.4	-	6	1874_1875	c.1817_1818insC	c.(1816-1818)ccgfs	p.P606fs	BNC2_ENST00000380667.2_Frame_Shift_Ins_p.P539fs|BNC2_ENST00000380666.2_Frame_Shift_Ins_p.P606fs|BNC2_ENST00000545497.1_Frame_Shift_Ins_p.P511fs	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		CAGAGGGTGGCGGGGGGTGCTG	0.564																																					p.P606fs		Pindel,Atlas-Indel	.											.	BNC2	166	.	0			c.1818_1819insC						PASS	.																																			SO:0001589	frameshift_variant	54796	exon6			.	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.1818dupC	9.37:g.16436380_16436380dupG	ENSP00000370047:p.Pro606fs	Somatic	99	.	.		WXS	Illumina HiSeq	Phase_I	96	17	0.177	NM_017637		Frame_Shift_Ins	INS	ENST00000380672.4	37	CCDS6482.2																																																																																			.	.	none		0.564	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	
CCDC7	79741	hgsc.bcm.edu	37	10	33018277	33018277	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:33018277delA	ENST00000375030.2	+	13	1360	c.742delA	c.(742-744)aaafs	p.K250fs	C10orf68_ENST00000375025.4_Frame_Shift_Del_p.K242fs|C10orf68_ENST00000375028.3_Frame_Shift_Del_p.K218fs			Q9H943	CJ068_HUMAN		242										breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(15)|ovary(1)|skin(4)	29						TTTAGAAATCAAAAAAAAGGA	0.323																																					p.I239fs		Pindel,Atlas-Indel	.											.	C10orf68	75	.	0			c.717delC						PASS	.						49.0	52.0	51.0					10																	33018277		2200	4293	6493	SO:0001589	frameshift_variant	79741	exon10			.																												ENST00000375030.2:c.742delA	10.37:g.33018277delA	ENSP00000364170:p.Lys250fs	Somatic	99	.	.		WXS	Illumina HiSeq	Phase_I	107	16	0.150	NM_024688	B0QZ71|Q08AN7|Q8N7T7	Frame_Shift_Del	DEL	ENST00000375030.2	37																																																																																				.	.	none		0.323	C10orf68-001	PUTATIVE	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000313999.2		
TET2	54790	hgsc.bcm.edu	37	4	106196908	106196908	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:106196908delA	ENST00000540549.1	+	11	6101	c.5241delA	c.(5239-5241)ccafs	p.P1747fs	TET2_ENST00000513237.1_Frame_Shift_Del_p.P1768fs|TET2_ENST00000545826.1_3'UTR|TET2_ENST00000380013.4_Frame_Shift_Del_p.P1747fs			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1747					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		TGAGCAATCCAAACATGGACT	0.458			"""Mis N, F"""		MDS																																p.P1747fs		Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.5240delC						PASS	.						37.0	29.0	31.0					4																	106196908		692	1591	2283	SO:0001589	frameshift_variant	54790	exon11			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5241delA	4.37:g.106196908delA	ENSP00000442788:p.Pro1747fs	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	110	18	0.163636	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.458	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
NF1	4763	hgsc.bcm.edu	37	17	29661926	29661927	+	Frame_Shift_Ins	INS	-	-	C	rs144808600	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:29661926_29661927insC	ENST00000358273.4	+	40	6266_6267	c.5883_5884insC	c.(5884-5886)catfs	p.H1962fs	NF1_ENST00000356175.3_Frame_Shift_Ins_p.H1941fs|NF1_ENST00000417592.2_5'Flank|NF1_ENST00000581113.2_3'UTR|NF1_ENST00000444181.2_5'Flank	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1962					actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		GTTTTTGCAAGCATAATGATGA	0.351			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																											p.K1961fs		Pindel,Atlas-Indel	.	yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	neurofibromatosis type 1 gene		O	.	NF1	1586	.	11	Whole gene deletion(8)|Unknown(3)	soft_tissue(7)|autonomic_ganglia(2)|lung(1)|central_nervous_system(1)	c.5883_5884insC						PASS	.																																			SO:0001589	frameshift_variant	4763	exon40	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	.		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.5884dupC	17.37:g.29661927_29661927dupC	ENSP00000351015:p.His1962fs	Somatic	125	.	.		WXS	Illumina HiSeq	Phase_I	145	24	0.166	NM_001042492	O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Ins	INS	ENST00000358273.4	37	CCDS42292.1																																																																																			.	.	none		0.351	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789313	117789327	+	In_Frame_Del	DEL	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	-	rs577467360|rs201746372|rs200205086|rs61900346|rs371814093|rs58754377|rs201983451|rs368164118|rs201369736	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:117789313_117789327delGGGCTGGAGATGCCT	ENST00000430170.2	-	2	335_349	c.248_262delAGGCATCTCCAGCCC	c.(247-264)caggcatctccagcccgg>cgg	p.QASPA83del	TMPRSS13_ENST00000524993.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000445164.2_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000526090.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000528626.1_In_Frame_Del_p.QASPA83del	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	83	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGAGATGCCCGGGCTGGAGATGCCTGGGCTGGAGA	0.66																																					p.83_88del		Atlas-Indel	.											TMPRSS13_ENST00000445164,NS,NS,0,3	TMPRSS13	75	3	1	Deletion - In frame(1)	urinary_tract(1)	c.249_263del						PASS	.		,,	2974,624		1262,450,87					,,	0.0	0.0		dbSNP_126	58	5904,1944		2214,1476,234	no	coding,coding,coding	TMPRSS13	NM_001206790.1,NM_001206789.1,NM_001077263.2	,,	3476,1926,321	A1A1,A1R,RR		24.7706,17.343,22.4358	,,	,,		8878,2568				SO:0001651	inframe_deletion	84000	exon2			.	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.248_262delAGGCATCTCCAGCCC	11.37:g.117789313_117789327delGGGCTGGAGATGCCT	ENSP00000387702:p.Gln83_Ala87del	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	111	25	0.225225	NM_001206789	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	In_Frame_Del	DEL	ENST00000430170.2	37	CCDS58185.1																																																																																			GGGCTGGAGATGCCT|0.257;-|0.743	0.743	strong		0.660	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
ABCB1	5243	hgsc.bcm.edu	37	7	87195445	87195445	+	Frame_Shift_Del	DEL	T	T	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:87195445delT	ENST00000265724.3	-	8	1060	c.643delA	c.(643-645)accfs	p.T215fs	ABCB1_ENST00000543898.1_Frame_Shift_Del_p.T151fs	NM_000927.4	NP_000918.2	P08183	MDR1_HUMAN	ATP-binding cassette, sub-family B (MDR/TAP), member 1	215	ABC transmembrane type-1 1. {ECO:0000255|PROSITE-ProRule:PRU00441}.				drug transmembrane transport (GO:0006855)|G2/M transition of mitotic cell cycle (GO:0000086)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)|stem cell proliferation (GO:0072089)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)|xenobiotic-transporting ATPase activity (GO:0008559)			NS(1)|breast(6)|central_nervous_system(2)|endometrium(14)|kidney(9)|large_intestine(14)|lung(48)|ovary(4)|prostate(6)|skin(6)|upper_aerodigestive_tract(1)	111	Esophageal squamous(14;0.00164)				Acebutolol(DB01193)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Adenosine triphosphate(DB00171)|ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Albendazole(DB00518)|Alfentanil(DB00802)|Alitretinoin(DB00523)|Amantadine(DB00915)|Aminohippurate(DB00345)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Amsacrine(DB00276)|Apixaban(DB06605)|Arsenic trioxide(DB01169)|Astemizole(DB00637)|Atazanavir(DB01072)|Atenolol(DB00335)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzocaine(DB01086)|Bepridil(DB01244)|Betamethasone(DB00443)|Biperiden(DB00810)|Boceprevir(DB08873)|Bosutinib(DB06616)|Brentuximab vedotin(DB08870)|Bromocriptine(DB01200)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Canagliflozin(DB08907)|Candesartan(DB00796)|Captopril(DB01197)|Carbamazepine(DB00564)|Carfilzomib(DB08889)|Carvedilol(DB01136)|Caspofungin(DB00520)|Chloroquine(DB00608)|Chlorpromazine(DB00477)|Chlorpropamide(DB00672)|Chlorprothixene(DB01239)|Cilazapril(DB01340)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisplatin(DB00515)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clobazam(DB00349)|Clofazimine(DB00845)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Colchicine(DB01394)|Conjugated Estrogens(DB00286)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dabigatran etexilate(DB06695)|Dabrafenib(DB08912)|Dactinomycin(DB00970)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diclofenac(DB00586)|Diethylstilbestrol(DB00255)|Digitoxin(DB01396)|Digoxin(DB00390)|Dihydroergotamine(DB00320)|Diltiazem(DB00343)|Dipyridamole(DB00975)|Docetaxel(DB01248)|Domperidone(DB01184)|Doxazosin(DB00590)|Doxepin(DB01142)|Doxorubicin(DB00997)|Dronabinol(DB00470)|Dronedarone(DB04855)|Eletriptan(DB00216)|Enalapril(DB00584)|Enzalutamide(DB08899)|Epinastine(DB00751)|Ergonovine(DB01253)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estramustine(DB01196)|Estriol(DB04573)|Estrone(DB00655)|Ethinyl Estradiol(DB00977)|Etoposide(DB00773)|Etravirine(DB06414)|Ezetimibe(DB00973)|Felodipine(DB01023)|Fentanyl(DB00813)|Fesoterodine(DB06702)|Fexofenadine(DB00950)|Fidaxomicin(DB08874)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Flurazepam(DB00690)|Fluticasone furoate(DB08906)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gemcitabine(DB00441)|Glyburide(DB01016)|Gramicidin D(DB00027)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ibuprofen(DB01050)|Imatinib(DB00619)|Imipramine(DB00458)|Indacaterol(DB05039)|Indinavir(DB00224)|Indomethacin(DB00328)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ivacaftor(DB08820)|Ivermectin(DB00602)|Ketamine(DB01221)|Ketazolam(DB01587)|Ketoconazole(DB01026)|Lamivudine(DB00709)|Lamotrigine(DB00555)|Lansoprazole(DB00448)|Lapatinib(DB01259)|Lenalidomide(DB00480)|Levetiracetam(DB01202)|Levofloxacin(DB01137)|Levomilnacipran(DB08918)|Levothyroxine(DB00451)|Lidocaine(DB00281)|Linagliptin(DB08882)|Liothyronine(DB00279)|Liotrix(DB01583)|Lisinopril(DB00722)|Lomitapide(DB08827)|Loperamide(DB00836)|Lopinavir(DB01601)|Loratadine(DB00455)|Losartan(DB00678)|Lovastatin(DB00227)|Mannitol(DB00742)|Maprotiline(DB00934)|Mebendazole(DB00643)|Mefloquine(DB00358)|Megestrol acetate(DB00351)|Meprobamate(DB00371)|Methadone(DB00333)|Methotrexate(DB00563)|Methylprednisolone(DB00959)|Metoprolol(DB00264)|Miconazole(DB01110)|Midazolam(DB00683)|Mifepristone(DB00834)|Mirabegron(DB08893)|Mitomycin(DB00305)|Mitoxantrone(DB01204)|Morphine(DB00295)|Mycophenolate mofetil(DB00688)|Nadolol(DB01203)|Naloxone(DB01183)|Naltrexone(DB00704)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Neostigmine(DB01400)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nisoldipine(DB00401)|Nitrazepam(DB01595)|Nitrendipine(DB01054)|Nizatidine(DB00585)|Norethindrone(DB00717)|Olanzapine(DB00334)|Omeprazole(DB00338)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paroxetine(DB00715)|Pazopanib(DB06589)|Perindopril(DB00790)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Pitavastatin(DB08860)|Pomalidomide(DB08910)|Ponatinib(DB08901)|Posaconazole(DB01263)|Pravastatin(DB00175)|Prazosin(DB00457)|Prednisolone(DB00860)|Prednisone(DB00635)|Probenecid(DB01032)|Progesterone(DB00396)|Promethazine(DB01069)|Propafenone(DB01182)|Propranolol(DB00571)|Protriptyline(DB00344)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinidine(DB00908)|Quinine(DB00468)|Ranitidine(DB00863)|Reboxetine(DB00234)|Regorafenib(DB08896)|Reserpine(DB00206)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Roxithromycin(DB00778)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Scopolamine(DB00747)|Selegiline(DB01037)|Sertraline(DB01104)|Silodosin(DB06207)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sitagliptin(DB01261)|SOFOSBUVIR(DB08934)|Sorafenib(DB00398)|Sparfloxacin(DB01208)|Spironolactone(DB00421)|Streptozocin(DB00428)|Sulfinpyrazone(DB01138)|Sumatriptan(DB00669)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telaprevir(DB05521)|Telmisartan(DB00966)|Temsirolimus(DB06287)|Terazosin(DB01162)|Testosterone(DB00624)|Ticagrelor(DB08816)|Timolol(DB00373)|Tolvaptan(DB06212)|Topotecan(DB01030)|Toremifene(DB00539)|Trazodone(DB00656)|Trifluoperazine(DB00831)|Triflupromazine(DB00508)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Vecuronium(DB01339)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vinblastine(DB00570)|Vincristine(DB00541)|Vinorelbine(DB00361)|Vismodegib(DB08828)|Voacamine(DB04877)|Zidovudine(DB00495)	ATCACAAGGGTTAGCTTCCAA	0.428																																					p.T215fs		Pindel,Atlas-Indel	.											.	ABCB1	263	.	0			c.644delC						PASS	.						150.0	134.0	139.0					7																	87195445		2203	4300	6503	SO:0001589	frameshift_variant	5243	exon8			.	M14758	CCDS5608.1	7q21.12	2012-03-14	2004-05-12		ENSG00000085563	ENSG00000085563		"""CD molecules"", ""ATP binding cassette transporters / subfamily B"""	40	protein-coding gene	gene with protein product	"""multidrug resistance protein 1"""	171050	"""colchicin sensitivity"""	PGY1, MDR1, CLCS		3027054	Standard	NM_000927		Approved	P-gp, CD243, GP170, ABC20	uc003uiz.2	P08183	OTTHUMG00000023393	ENST00000265724.3:c.643delA	7.37:g.87195445delT	ENSP00000265724:p.Thr215fs	Somatic	144	.	.		WXS	Illumina HiSeq	Phase_I	198	33	0.167	NM_000927	A8K294|B5AK60|Q12755|Q14812	Frame_Shift_Del	DEL	ENST00000265724.3	37	CCDS5608.1																																																																																			.	.	none		0.428	ABCB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335444.2	NM_000927	
GLI2	2736	hgsc.bcm.edu	37	2	121708820	121708820	+	Splice_Site	DEL	C	C	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:121708820delC	ENST00000452319.1	+	4	316	c.256delC	c.(256-258)ccc>cc	p.P87fs	GLI2_ENST00000435313.2_3'UTR|GLI2_ENST00000314490.11_5'UTR|GLI2_ENST00000361492.4_Splice_Site_p.P87fs					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)				TCTCTGCAGGCCCCCTGCCCT	0.622																																					p.G85fs		Pindel,Atlas-Indel	.											.	GLI2	187	.	0			c.255delG						PASS	.						99.0	112.0	107.0					2																	121708820		2203	4299	6502	SO:0001630	splice_region_variant	2736	exon3			.		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.255-1C>-	2.37:g.121708820delC		Somatic	241	.	.		WXS	Illumina HiSeq	Phase_I	221	36	0.163	NM_005270		Frame_Shift_Del	DEL	ENST00000452319.1	37	CCDS33283.1																																																																																			.	.	none		0.622	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	Frame_Shift_Del
EGFL6	25975	hgsc.bcm.edu	37	X	13636081	13636082	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chrX:13636081_13636082insA	ENST00000361306.1	+	8	1268_1269	c.1011_1012insA	c.(1012-1014)aaafs	p.K338fs	EGFL6_ENST00000380602.3_Frame_Shift_Ins_p.K338fs	NM_001167890.1|NM_015507.3	NP_001161362.1|NP_056322.2	Q8IUX8	EGFL6_HUMAN	EGF-like-domain, multiple 6	338					cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)			breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(7)|prostate(1)|skin(3)	23						GGAATGAAGAGAAAATGAAAGA	0.465																																					p.E337fs		Pindel,Atlas-Indel	.											.	EGFL6	111	.	0			c.1011_1012insA						PASS	.																																			SO:0001589	frameshift_variant	25975	exon8			.	AF186084	CCDS14155.1, CCDS55370.1	Xp22	2008-02-05	2002-10-09		ENSG00000198759	ENSG00000198759			3235	protein-coding gene	gene with protein product		300239	"""MAM and EGF domain containing"""	MAEG		10610727	Standard	NM_015507		Approved		uc004cvj.3	Q8IUX8	OTTHUMG00000021155	ENST00000361306.1:c.1015dupA	X.37:g.13636085_13636085dupA	ENSP00000355126:p.Lys338fs	Somatic	74	.	.		WXS	Illumina HiSeq	Phase_I	79	22	0.278	NM_001167890	B2RCB1|Q6UXJ1|Q8NBV0|Q8WYG3|Q9NY67|Q9NZL7|Q9UFK6	Frame_Shift_Ins	INS	ENST00000361306.1	37	CCDS14155.1																																																																																			.	.	none		0.465	EGFL6-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055800.1	NM_015507	
REST	5978	hgsc.bcm.edu	37	4	57777675	57777676	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:57777675_57777676insA	ENST00000309042.7	+	2	1185_1186	c.871_872insA	c.(871-873)tatfs	p.Y291fs	REST_ENST00000514063.1_3'UTR	NM_001193508.1|NM_005612.4	NP_001180437.1|NP_005603.3	Q13127	REST_HUMAN	RE1-silencing transcription factor	291					cardiac muscle cell myoblast differentiation (GO:0060379)|cellular response to drug (GO:0035690)|cellular response to electrical stimulus (GO:0071257)|cellular response to glucocorticoid stimulus (GO:0071385)|hematopoietic progenitor cell differentiation (GO:0002244)|histone H4 deacetylation (GO:0070933)|negative regulation by host of viral transcription (GO:0043922)|negative regulation of aldosterone biosynthetic process (GO:0032348)|negative regulation of amniotic stem cell differentiation (GO:2000798)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cortisol biosynthetic process (GO:2000065)|negative regulation of dense core granule biogenesis (GO:2000706)|negative regulation of gene expression (GO:0010629)|negative regulation of insulin secretion (GO:0046676)|negative regulation of mesenchymal stem cell differentiation (GO:2000740)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of transcription, DNA-templated (GO:0045893)|potassium ion transmembrane transport (GO:0071805)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|outward rectifier potassium channel activity (GO:0015271)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(2)|lung(22)|ovary(1)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	50	Glioma(25;0.08)|all_neural(26;0.181)					AAAAAACAATTATGTTCAGCAT	0.351																																					p.Y291_V292delinsX		Pindel,Atlas-Indel	.											.	REST	104	.	0			c.871_872insA						PASS	.																																			SO:0001589	frameshift_variant	5978	exon2			.	U13879	CCDS3509.1	4q12	2008-02-05			ENSG00000084093	ENSG00000084093			9966	protein-coding gene	gene with protein product		600571				7871435, 7697725	Standard	NM_005612		Approved	NRSF, XBR	uc003hci.3	Q13127	OTTHUMG00000128770	ENST00000309042.7:c.872dupA	4.37:g.57777676_57777676dupA	ENSP00000311816:p.Tyr291fs	Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	89	14	0.157	NM_001193508	A2RUE0|B9EGJ0|Q12956|Q12957|Q13134|Q59ER1|Q8IWI3	Frame_Shift_Ins	INS	ENST00000309042.7	37	CCDS3509.1																																																																																			.	.	none		0.351	REST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250691.2	NM_005612	
GRIA2	2891	hgsc.bcm.edu	37	4	158254497	158254497	+	Frame_Shift_Del	DEL	C	C	-			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:158254497delC	ENST00000264426.9	+	8	1426	c.1147delC	c.(1147-1149)cccfs	p.P383fs	GRIA2_ENST00000296526.7_Frame_Shift_Del_p.P383fs|GRIA2_ENST00000449365.1_Frame_Shift_Del_p.P336fs|GRIA2_ENST00000507898.1_Frame_Shift_Del_p.P336fs|GRIA2_ENST00000393815.2_Frame_Shift_Del_p.P336fs	NM_001083619.1	NP_001077088	P42262	GRIA2_HUMAN	glutamate receptor, ionotropic, AMPA 2	383					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(2)|lung(32)|ovary(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	79	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0294)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	AACTAATGGGCCCCGGAAGGT	0.398																																					p.G382fs		Atlas-Indel	.											.	GRIA2	358	.	0			c.1146delG						PASS	.						34.0	36.0	35.0					4																	158254497		2198	4294	6492	SO:0001589	frameshift_variant	2891	exon8			.		CCDS3797.1, CCDS43274.1, CCDS43275.1	4q32.1	2012-08-29			ENSG00000120251	ENSG00000120251		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4572	protein-coding gene	gene with protein product		138247		GLUR2		1311100	Standard	NM_001083619		Approved	GluA2, GLURB	uc003ipl.4	P42262	OTTHUMG00000133836	ENST00000264426.9:c.1147delC	4.37:g.158254497delC	ENSP00000264426:p.Pro383fs	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	68	11	0.161765	NM_001083619	A8MT92|I6L997|Q96FP6	Frame_Shift_Del	DEL	ENST00000264426.9	37	CCDS43274.1																																																																																			.	.	none		0.398	GRIA2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000258367.2		
DRICH1	51233	hgsc.bcm.edu	37	22	23956338	23956340	+	In_Frame_Del	DEL	TCT	TCT	-	rs117546628	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	TCT	TCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23956338_23956340delTCT	ENST00000317749.5	-	9	900_902	c.603_605delAGA	c.(601-606)gaagat>gat	p.E201del		NM_016449.3	NP_057533.2	Q6PGQ1	DRIC1_HUMAN		201	Asp-rich.									endometrium(1)|large_intestine(3)|lung(5)|pancreas(1)|skin(1)	11						GTCATCATCATCTTCTTCTTCTT	0.384																																					p.202_202del		Pindel,Atlas-Indel	.											.	C22orf43	18	.	0			c.604_606del						PASS	.																																			SO:0001651	inframe_deletion	51233	exon9			.																												ENST00000317749.5:c.603_605delAGA	22.37:g.23956347_23956349delTCT	ENSP00000316137:p.Glu201del	Somatic	236	.	.		WXS	Illumina HiSeq	Phase_I	306	52	0.170	NM_016449	Q6ICJ8|Q6P4I3|Q9NU31	In_Frame_Del	DEL	ENST00000317749.5	37	CCDS42985.1																																																																																			.	.	none		0.384	C22orf43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319708.2		
CNKSR1	10256	hgsc.bcm.edu	37	1	26510311	26510311	+	Frame_Shift_Del	DEL	C	C	-	rs201305445	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:26510311delC	ENST00000374253.5	+	9	905	c.866delC	c.(865-867)accfs	p.T289fs	CNKSR1_ENST00000361530.6_Frame_Shift_Del_p.T282fs|CNKSR1_ENST00000531191.1_Frame_Shift_Del_p.T24fs	NM_006314.2	NP_006305.2	Q969H4	CNKR1_HUMAN	connector enhancer of kinase suppressor of Ras 1	289	Pro-rich.				Ras protein signal transduction (GO:0007265)|Rho protein signal transduction (GO:0007266)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell cortex (GO:0005938)|cell-cell junction (GO:0005911)|plasma membrane (GO:0005886)	protein binding, bridging (GO:0030674)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	28		Colorectal(325;3.46e-05)|all_lung(284;0.000116)|Lung NSC(340;0.000154)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0133)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;2.72e-26)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00072)|BRCA - Breast invasive adenocarcinoma(304;0.000959)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00823)|READ - Rectum adenocarcinoma(331;0.0649)		ATACCGGAGACCCCCCCACAG	0.667														59	0.0117812	0.0008	0.0202	5008	,	,		6575	0.001		0.0348	False		,,,				2504	0.0082				p.T282fs	NSCLC(180;1396 2109 28270 30756 34275)	Pindel	.											.	CNKSR1	66	.	0			c.844delA						PASS	.			5,37,4224		0,0,5,0,37,2091	44.0	46.0	45.0			-0.5	0.0	1		47	1,431,7822		0,0,1,13,405,3708	no	codingComplex	CNKSR1	NM_006314.2		0,0,6,13,442,5799	A1A1,A1A2,A1R,A2A2,A2R,RR		5.2338,0.9845,3.7859			26510311	6,468,12046	2203	4300	6503	SO:0001589	frameshift_variant	10256	exon9			.	AF100153	CCDS276.1, CCDS72732.1	1p35.3	2013-01-10			ENSG00000142675	ENSG00000142675		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	19700	protein-coding gene	gene with protein product		603272				9814705	Standard	NM_006314		Approved	CNK1, KSR, CNK	uc001blm.4	Q969H4	OTTHUMG00000007541	ENST00000374253.5:c.866delC	1.37:g.26510311delC	ENSP00000363371:p.Thr289fs	Somatic	49	.	.		WXS	Illumina HiSeq	Phase_I	59	12	0.203	NM_006314	B1AMW9|O95381	Frame_Shift_Del	DEL	ENST00000374253.5	37																																																																																				C|0.980;-|0.020	0.020	strong		0.667	CNKSR1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000089943.2	NM_006314	
TCEB3CL2	100506888	hgsc.bcm.edu	37	18	44543098	44543099	+	Frame_Shift_Ins	INS	-	-	GC	rs373334809		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:44543098_44543099insGC	ENST00000591973.2	-	1	1508_1509	c.1273_1274insGC	c.(1273-1275)cagfs	p.Q425fs	KATNAL2_ENST00000356157.7_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000245121.5_Intron	NM_001242907.1	NP_001229836.1	A6NLF2	EA3L2_HUMAN	transcription elongation factor B polypeptide 3C-like 2	425	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)										TCGCAGCCGCTGCTCTCGGGCG	0.554																																					p.Q425fs		Pindel	.											.	.	.	.	0			c.1274_1275insGC						PASS	.																																			SO:0001589	frameshift_variant	100506888	exon1			.		CCDS59316.1	18q21.1	2012-10-25			ENSG00000266996	ENSG00000274744			33511	protein-coding gene	gene with protein product							Standard	NM_001242907		Approved		uc021ujk.1	A6NLF2	OTTHUMG00000180382	ENST00000591973.2:c.1272_1273dupGC	18.37:g.44543099_44543100dupGC	ENSP00000468046:p.Gln425fs	Somatic	623	.	.		WXS	Illumina HiSeq	Phase_I	621	95	0.153	NM_001242907		Frame_Shift_Ins	INS	ENST00000591973.2	37	CCDS59316.1																																																																																			.	.	weak		0.554	TCEB3CL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451070.1	XM_929328	
ASPM	259266	hgsc.bcm.edu	37	1	197070009	197070009	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:197070009C>A	ENST00000367409.4	-	18	8628	c.8372G>T	c.(8371-8373)gGt>gTt	p.G2791V	ASPM_ENST00000294732.7_Intron|ASPM_ENST00000367408.1_Intron	NM_018136.4	NP_060606.3	Q8IZT6	ASPM_HUMAN	asp (abnormal spindle) homolog, microcephaly associated (Drosophila)	2791					developmental growth (GO:0048589)|forebrain neuroblast division (GO:0021873)|maintenance of centrosome location (GO:0051661)|mitotic nuclear division (GO:0007067)|negative regulation of asymmetric cell division (GO:0045769)|negative regulation of neuron differentiation (GO:0045665)|neuron migration (GO:0001764)|oogenesis (GO:0048477)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of neuroblast proliferation (GO:0002052)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|midbody (GO:0030496)|nucleus (GO:0005634)|spindle pole (GO:0000922)				breast(6)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(9)|large_intestine(28)|liver(1)|lung(87)|ovary(5)|pancreas(2)|prostate(6)|skin(4)|urinary_tract(3)	165						AATCATAACACCTTCACTTTG	0.393																																					p.G2791V		Atlas-SNP	.											ASPM,right_upper_lobe,carcinoma,0,1	ASPM	444	1	0			c.G8372T						PASS	.						133.0	133.0	133.0					1																	197070009		2203	4300	6503	SO:0001583	missense	259266	exon18			ATAACACCTTCAC	AY367065	CCDS1389.1, CCDS55672.1	1q31	2008-02-05	2006-09-12		ENSG00000066279	ENSG00000066279			19048	protein-coding gene	gene with protein product		605481	"""microcephaly, primary autosomal recessive 5"", ""asp (abnormal spindle)-like, microcephaly associated (Drosophila)"""	MCPH5		11078481	Standard	NM_018136		Approved	Calmbp1, ASP, FLJ10517, FLJ10549	uc001gtu.3	Q8IZT6	OTTHUMG00000036277	ENST00000367409.4:c.8372G>T	1.37:g.197070009C>A	ENSP00000356379:p.Gly2791Val	Somatic	115	0	0		WXS	Illumina HiSeq	Phase_I	157	33	0.210191	NM_018136	Q4G1H1|Q5VYL3|Q86UX4|Q8IUL2|Q8IZJ7|Q8IZJ8|Q8IZJ9|Q8N4D1|Q9NVS1|Q9NVT6	Missense_Mutation	SNP	ENST00000367409.4	37	CCDS1389.1	.	.	.	.	.	.	.	.	.	.	C	10.19	1.280914	0.23392	.	.	ENSG00000066279	ENST00000367409;ENST00000367406	T	0.56611	0.45	4.66	-1.47	0.08772	.	1.296170	0.05105	N	0.487807	T	0.55689	0.1936	L	0.36672	1.1	0.09310	N	1	D;B	0.89917	1.0;0.112	D;B	0.87578	0.998;0.057	T	0.46034	-0.9220	10	0.23891	T	0.37	.	2.4063	0.04414	0.1324:0.1431:0.3433:0.3813	.	777;2791	E7EQ84;Q8IZT6	.;ASPM_HUMAN	V	2791;777	ENSP00000356379:G2791V	ENSP00000356376:G777V	G	-	2	0	ASPM	195336632	0.001000	0.12720	0.000000	0.03702	0.073000	0.16967	0.619000	0.24388	-0.532000	0.06332	-0.379000	0.06801	GGT	.	.	none		0.393	ASPM-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000088256.1	NM_018136	
UNC80	285175	hgsc.bcm.edu	37	2	210783352	210783352	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:210783352G>A	ENST00000439458.1	+	32	5190	c.5110G>A	c.(5110-5112)Ggg>Agg	p.G1704R	UNC80_ENST00000272845.6_Missense_Mutation_p.G1699R	NM_032504.1	NP_115893.1	Q8N2C7	UNC80_HUMAN	unc-80 homolog (C. elegans)	1704					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(9)|ovary(1)|prostate(1)	20						TCAGTGCAGCGGGAGTGTCCA	0.502																																					p.G1704R		Atlas-SNP	.											.	UNC80	280	.	0			c.G5110A						PASS	.						69.0	63.0	65.0					2																	210783352		692	1591	2283	SO:0001583	missense	285175	exon32			TGCAGCGGGAGTG	AK090815	CCDS2387.1, CCDS46504.1, CCDS2387.2	2q35	2009-08-17	2009-08-17	2009-08-17	ENSG00000144406	ENSG00000144406			26582	protein-coding gene	gene with protein product		612636	"""chromosome 2 open reading frame 21"""	C2orf21		19092807	Standard	NM_032504		Approved	FLJ33496, KIAA1843, UNC-80	uc010zjc.1	Q8N2C7	OTTHUMG00000132963	ENST00000439458.1:c.5110G>A	2.37:g.210783352G>A	ENSP00000391088:p.Gly1704Arg	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	167	39	0.233533	NM_032504	B2RN50|B4DQY9|B4DZB3|C4IXS8|C9J1U3|Q96JI4|Q96SS0	Missense_Mutation	SNP	ENST00000439458.1	37	CCDS46504.1	.	.	.	.	.	.	.	.	.	.	G	31	5.081141	0.94050	.	.	ENSG00000144406	ENST00000439458;ENST00000272845	T;T	0.29655	1.56;1.56	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.36608	0.0973	N	0.22421	0.69	0.80722	D	1	D	0.67145	0.996	P	0.57679	0.825	T	0.04991	-1.0913	10	0.21014	T	0.42	-20.4916	18.9863	0.92771	0.0:0.0:1.0:0.0	.	1704	Q8N2C7	UNC80_HUMAN	R	1704;1699	ENSP00000391088:G1704R;ENSP00000272845:G1699R	ENSP00000272845:G1699R	G	+	1	0	UNC80	210491597	1.000000	0.71417	0.999000	0.59377	0.987000	0.75469	9.869000	0.99810	2.502000	0.84385	0.555000	0.69702	GGG	.	.	none		0.502	UNC80-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_182587	
AHNAK2	113146	hgsc.bcm.edu	37	14	105418119	105418119	+	Missense_Mutation	SNP	G	G	C	rs201187390	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:105418119G>C	ENST00000333244.5	-	7	3788	c.3669C>G	c.(3667-3669)caC>caG	p.H1223Q	AHNAK2_ENST00000557457.1_Intron	NM_138420.2	NP_612429.2	Q8IVF2	AHNK2_HUMAN	AHNAK nucleoprotein 2	1223						costamere (GO:0043034)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)				cervix(4)|endometrium(4)|large_intestine(3)|lung(14)|ovary(2)|prostate(2)|skin(1)|stomach(3)	33		all_cancers(154;0.115)|Melanoma(154;0.155)|all_epithelial(191;0.183)	all cancers(16;0.000479)|OV - Ovarian serous cystadenocarcinoma(23;0.00659)|Epithelial(46;0.0151)|GBM - Glioblastoma multiforme(11;0.116)			CCTGGCCAGCGTGGACCTCCA	0.632													.|||	963	0.192292	0.0787	0.2334	5008	,	,		14203	0.0585		0.3439	False		,,,				2504	0.2986				p.H1223Q		Atlas-SNP	.											AHNAK2_ENST00000333244,NS,carcinoma,0,1	AHNAK2	719	1	0			c.C3669G						scavenged	.						81.0	58.0	66.0					14																	105418119		1913	3852	5765	SO:0001583	missense	113146	exon7			GCCAGCGTGGACC	AB095939	CCDS45177.1	14q32.33	2010-04-01	2007-03-26	2007-03-26	ENSG00000185567	ENSG00000185567			20125	protein-coding gene	gene with protein product		608570	"""chromosome 14 open reading frame 78"""	C14orf78		15007166	Standard	NM_138420		Approved		uc010axc.1	Q8IVF2		ENST00000333244.5:c.3669C>G	14.37:g.105418119G>C	ENSP00000353114:p.His1223Gln	Somatic	4	4	1		WXS	Illumina HiSeq	Phase_I	9	9	1	NM_138420	Q5BKX7|Q7Z343|Q7Z358|Q7Z394|Q7Z3G0|Q86WQ6|Q8IYY1|Q8N3G4|Q96EX9	Missense_Mutation	SNP	ENST00000333244.5	37	CCDS45177.1	.	.	.	.	.	.	.	.	.	.	c	3.891	-0.024009	0.07634	.	.	ENSG00000185567	ENST00000333244	T	0.00664	5.92	4.55	0.472	0.16758	.	.	.	.	.	T	0.00241	0.0007	N	0.00099	-2.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.40289	-0.9571	9	0.12766	T	0.61	.	4.3186	0.11005	0.0:0.3151:0.3178:0.3671	.	1223	Q8IVF2	AHNK2_HUMAN	Q	1223	ENSP00000353114:H1223Q	ENSP00000353114:H1223Q	H	-	3	2	AHNAK2	104489164	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.576000	0.02129	0.044000	0.15775	-0.322000	0.08575	CAC	.	.	weak		0.632	AHNAK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000410300.1	NM_138420	
RAB8A	4218	hgsc.bcm.edu	37	19	16222712	16222712	+	Start_Codon_SNP	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:16222712A>C	ENST00000300935.3	+	1	274	c.1A>C	c.(1-3)Atg>Ctg	p.M1L	RAB8A_ENST00000588105.1_3'UTR|RAB8A_ENST00000586682.1_Start_Codon_SNP_p.M1L	NM_005370.4	NP_005361.2	P61006	RAB8A_HUMAN	RAB8A, member RAS oncogene family	1					axonogenesis (GO:0007409)|cellular response to insulin stimulus (GO:0032869)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi vesicle fusion to target membrane (GO:0048210)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of protein transport (GO:0051223)|small GTPase mediated signal transduction (GO:0007264)|vesicle docking involved in exocytosis (GO:0006904)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|neuronal cell body (GO:0043025)|nonmotile primary cilium (GO:0031513)|phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)|recycling endosome membrane (GO:0055038)|trans-Golgi network transport vesicle (GO:0030140)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)|Rab GTPase binding (GO:0017137)			endometrium(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)	8						AGAGTGTAATATGGCGAAGAC	0.627																																					p.M1L		Atlas-SNP	.											.	RAB8A	19	.	0			c.A1C						PASS	.						175.0	175.0	175.0					19																	16222712		2203	4300	6503	SO:0001582	initiator_codon_variant	4218	exon1			TGTAATATGGCGA		CCDS12339.1	19p13.2-p13.1	2008-05-14	2004-01-30	2004-01-30		ENSG00000167461		"""RAB, member RAS oncogene"""	7007	protein-coding gene	gene with protein product		165040	"""mel transforming oncogene (derived from cell line NK14)"""	MEL		1886711, 8408203	Standard	NM_005370		Approved	RAB8	uc002ndn.4	P61006		ENST00000300935.3:c.1A>C	19.37:g.16222712A>C	ENSP00000300935:p.Met1Leu	Somatic	41	0	0		WXS	Illumina HiSeq	Phase_I	102	13	0.127451	NM_005370	B4DEK7|P24407|Q6FHV5	Missense_Mutation	SNP	ENST00000300935.3	37	CCDS12339.1	.	.	.	.	.	.	.	.	.	.	A	31	5.088240	0.94100	.	.	ENSG00000167461	ENST00000300935	T	0.61040	0.14	4.54	4.54	0.55810	.	0.000000	0.85682	D	0.000000	T	0.74928	0.3781	.	.	.	0.80722	D	1	D;D	0.67145	0.996;0.992	D;D	0.77004	0.989;0.989	T	0.78590	-0.2145	9	0.66056	D	0.02	.	13.478	0.61320	1.0:0.0:0.0:0.0	.	1;1	B4DEK7;P61006	.;RAB8A_HUMAN	L	1	ENSP00000300935:M1L	ENSP00000300935:M1L	M	+	1	0	RAB8A	16083712	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.560000	0.90712	2.034000	0.60081	0.402000	0.26972	ATG	.	.	none		0.627	RAB8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460186.1	NM_005370	Missense_Mutation
VGLL3	389136	hgsc.bcm.edu	37	3	87018229	87018229	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:87018229A>C	ENST00000398399.2	-	3	811	c.448T>G	c.(448-450)Ttt>Gtt	p.F150V	VGLL3_ENST00000383698.3_Missense_Mutation_p.F150V	NM_016206.2	NP_057290.2			vestigial-like family member 3											NS(1)|breast(1)|endometrium(4)|large_intestine(2)|lung(11)	19	all_cancers(8;0.109)|Lung SC(3;0.184)	Lung NSC(201;0.0777)		LUSC - Lung squamous cell carcinoma(29;0.00241)|Lung(72;0.00712)		CTGGTCCAAAAGGAAGTTGGG	0.483																																					p.F150V		Atlas-SNP	.											.	VGLL3	62	.	0			c.T448G						PASS	.						85.0	86.0	86.0					3																	87018229		1910	4132	6042	SO:0001583	missense	389136	exon3			TCCAAAAGGAAGT	AF099505	CCDS43110.1	3p12.1	2014-03-03	2014-03-03		ENSG00000206538	ENSG00000206538			24327	protein-coding gene	gene with protein product		609980	"""vestigial like 3 (Drosophila)"""			12376544	Standard	NM_016206		Approved	VGL-3	uc003dqn.3	A8MV65	OTTHUMG00000158984	ENST00000398399.2:c.448T>G	3.37:g.87018229A>C	ENSP00000381436:p.Phe150Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	58	14	0.241379	NM_016206		Missense_Mutation	SNP	ENST00000398399.2	37	CCDS43110.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	20.4|20.4	3.991213|3.991213	0.74703|0.74703	.|.	.|.	ENSG00000206538|ENSG00000206538	ENST00000398399;ENST00000383698|ENST00000494229	T;T|.	0.50277|.	0.76;0.75|.	5.88|5.88	5.88|5.88	0.94601|0.94601	.|.	0.204155|.	0.43260|.	D|.	0.000595|.	T|T	0.68026|0.68026	0.2956|0.2956	M|M	0.74881|0.74881	2.28|2.28	0.41670|0.41670	D|D	0.989238|0.989238	B|.	0.23806|.	0.091|.	B|.	0.17098|.	0.017|.	T|T	0.69892|0.69892	-0.5022|-0.5022	10|5	0.52906|.	T|.	0.07|.	-8.6808|-8.6808	10.3235|10.3235	0.43780|0.43780	0.9261:0.0:0.0739:0.0|0.9261:0.0:0.0739:0.0	.|.	150|.	A8MV65|.	VGLL3_HUMAN|.	V|R	150|83	ENSP00000381436:F150V;ENSP00000373199:F150V|.	ENSP00000373199:F150V|.	F|L	-|-	1|2	0|0	VGLL3|VGLL3	87100919|87100919	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	5.414000|5.414000	0.66405|0.66405	2.252000|2.252000	0.74401|0.74401	0.459000|0.459000	0.35465|0.35465	TTT|CTT	.	.	none		0.483	VGLL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352805.1	NM_016206	
SFTPD	6441	hgsc.bcm.edu	37	10	81702261	81702261	+	Splice_Site	SNP	C	C	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:81702261C>A	ENST00000372292.3	-	4	357		c.e4-1			NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D						defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			CCTGGAGGTCCTGAGCAAAAG	0.572																																					.		Atlas-SNP	.											.	SFTPD	43	.	0			c.317-1G>T						PASS	.						57.0	56.0	56.0					10																	81702261		2203	4300	6503	SO:0001630	splice_region_variant	6441	exon5			GAGGTCCTGAGCA	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"""Collectins"""	10803	protein-coding gene	gene with protein product		178635	"""surfactant, pulmonary-associated protein D"""	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.317-1G>T	10.37:g.81702261C>A		Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	61	8	0.131148	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Splice_Site	SNP	ENST00000372292.3	37	CCDS7362.1	.	.	.	.	.	.	.	.	.	.	c	13.45	2.241591	0.39598	.	.	ENSG00000133661	ENST00000372292;ENST00000444384	.	.	.	5.02	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8133	0.63276	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SFTPD	81692241	1.000000	0.71417	0.938000	0.37757	0.374000	0.29953	4.668000	0.61568	2.311000	0.77944	0.457000	0.33378	.	.	.	none		0.572	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		Intron
ZFC3H1	196441	hgsc.bcm.edu	37	12	72022729	72022729	+	Silent	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:72022729A>G	ENST00000378743.3	-	20	4273	c.3915T>C	c.(3913-3915)gaT>gaC	p.D1305D		NM_144982.4	NP_659419.3	O60293	ZC3H1_HUMAN	zinc finger, C3H1-type containing	1305					RNA processing (GO:0006396)	extracellular space (GO:0005615)|intracellular (GO:0005622)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(31)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	69						ACTGTTCCTCATCACTACTGA	0.323																																					p.D1305D		Atlas-SNP	.											.	ZFC3H1	172	.	0			c.T3915C						PASS	.						147.0	134.0	138.0					12																	72022729		1824	4077	5901	SO:0001819	synonymous_variant	196441	exon20			TTCCTCATCACTA	AB011118	CCDS41813.1	12q21.1	2013-01-25	2008-10-01	2008-10-01		ENSG00000133858		"""Zinc finger, C3H1-type containing"""	28328	protein-coding gene	gene with protein product			"""proline/serine-rich coiled-coil 2"", ""coiled-coil domain containing 131"""	PSRC2, CCDC131		9628581	Standard	NM_144982		Approved	MGC23401, KIAA0546	uc001swo.2	O60293	OTTHUMG00000169545	ENST00000378743.3:c.3915T>C	12.37:g.72022729A>G		Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	87	36	0.413793	NM_144982	Q6GMU1|Q6P2S9|Q6ZV36|Q96BE7	Silent	SNP	ENST00000378743.3	37	CCDS41813.1																																																																																			.	.	none		0.323	ZFC3H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404751.1	NM_144982	
SH2D4B	387694	hgsc.bcm.edu	37	10	82329986	82329986	+	Silent	SNP	T	T	C	rs192169537		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:82329986T>C	ENST00000470604.2	+	2	258	c.258T>C	c.(256-258)ccT>ccC	p.P86P	SH2D4B_ENST00000339284.2_Silent_p.P87P|SH2D4B_ENST00000313455.4_Silent_p.P38P			Q5SQS7	SH24B_HUMAN	SH2 domain containing 4B	86										endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|lung(6)	13			Colorectal(32;0.229)			GAGAAGGCCCTGGTGACAAGC	0.572																																					p.P87P		Atlas-SNP	.											.	SH2D4B	44	.	0			c.T261C						PASS	.						99.0	97.0	98.0					10																	82329986		2203	4300	6503	SO:0001819	synonymous_variant	387694	exon2			AGGCCCTGGTGAC		CCDS7370.1, CCDS44449.1	10q23.1	2013-02-14			ENSG00000178217	ENSG00000178217		"""SH2 domain containing"""	31440	protein-coding gene	gene with protein product							Standard	NM_207372		Approved		uc001kck.1	Q5SQS7	OTTHUMG00000018617	ENST00000470604.2:c.258T>C	10.37:g.82329986T>C		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	127	22	0.173228	NM_207372	Q5SQS5|Q6ZVW9|Q6ZVZ3	Silent	SNP	ENST00000470604.2	37																																																																																				T|1.000;A|0.000	.	alt		0.572	SH2D4B-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_351984	
ADAMTS10	81794	hgsc.bcm.edu	37	19	8651562	8651562	+	Silent	SNP	A	A	G	rs4476282	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:8651562A>G	ENST00000597188.1	-	20	2553	c.2283T>C	c.(2281-2283)ccT>ccC	p.P761P	ADAMTS10_ENST00000270328.4_Silent_p.P761P|ADAMTS10_ENST00000595838.1_Silent_p.P248P	NM_030957.2	NP_112219.3	Q9H324	ATS10_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 10	761	Spacer.					extracellular matrix (GO:0031012)|microfibril (GO:0001527)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(16)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(3)|skin(10)|urinary_tract(1)	53						GGGGGGTCCCAGGCAGCCCCT	0.642											OREG0025221	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	925	0.184704	0.2322	0.2061	5008	,	,		14798	0.125		0.2097	False		,,,				2504	0.1411				p.P761P		Atlas-SNP	.											ADAMTS10,NS,carcinoma,0,2	ADAMTS10	132	2	0			c.T2283C						PASS	.	G		962,3444	699.5+/-406.5	101,760,1342	45.0	53.0	51.0		2283	-9.9	0.5	19	dbSNP_111	51	1864,6736	706.5+/-405.5	201,1462,2637	no	coding-synonymous	ADAMTS10	NM_030957.2		302,2222,3979	GG,GA,AA		21.6744,21.8339,21.7284		761/1104	8651562	2826,10180	2203	4300	6503	SO:0001819	synonymous_variant	81794	exon20			GGTCCCAGGCAGC	AF163762	CCDS12206.1, CCDS62529.1	19p13.2	2014-08-12	2005-08-19		ENSG00000142303	ENSG00000142303		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13201	protein-coding gene	gene with protein product		608990	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 10"""				Standard	XM_005272499		Approved	ADAM-TS10	uc002mkj.1	Q9H324	OTTHUMG00000182216	ENST00000597188.1:c.2283T>C	19.37:g.8651562A>G		Somatic	66	0	0	81	WXS	Illumina HiSeq	Phase_I	73	5	0.0684932	NM_030957	M0QZE4	Silent	SNP	ENST00000597188.1	37	CCDS12206.1																																																																																			A|0.790;G|0.210	0.210	strong		0.642	ADAMTS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460085.3	NM_030957	
PCDH17	27253	hgsc.bcm.edu	37	13	58208119	58208119	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:58208119A>G	ENST00000377918.3	+	1	1465	c.1439A>G	c.(1438-1440)cAg>cGg	p.Q480R		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	480	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		TACGTGCTTCAGGTGCACGAG	0.602																																					p.Q480R	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.A1439G						PASS	.						48.0	44.0	46.0					13																	58208119		2203	4300	6503	SO:0001583	missense	27253	exon1			TGCTTCAGGTGCA	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1439A>G	13.37:g.58208119A>G	ENSP00000367151:p.Gln480Arg	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	94	12	0.12766	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	.	.	.	.	.	.	.	.	.	.	A	19.56	3.850826	0.71719	.	.	ENSG00000118946	ENST00000377918	T	0.51071	0.72	5.68	5.68	0.88126	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	T	0.55097	0.1899	L	0.31065	0.9	0.58432	D	0.999996	D;D	0.61697	0.988;0.99	P;D	0.64877	0.775;0.93	T	0.52155	-0.8613	9	.	.	.	.	15.9249	0.79609	1.0:0.0:0.0:0.0	.	480;480	O14917-2;O14917	.;PCD17_HUMAN	R	480	ENSP00000367151:Q480R	.	Q	+	2	0	PCDH17	57106120	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.576000	0.82467	2.170000	0.68504	0.459000	0.35465	CAG	.	.	none		0.602	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
MYH1	4619	hgsc.bcm.edu	37	17	10399321	10399321	+	Silent	SNP	G	G	T	rs145122906		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:10399321G>T	ENST00000226207.5	-	35	5209	c.5115C>A	c.(5113-5115)atC>atA	p.I1705I	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	1705					muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)	p.I1705I(1)		NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CCTGTTCTGCGATTTTCCTGC	0.532																																					p.I1705I		Atlas-SNP	.											MYH1,nipple,malignant_melanoma,0,1	MYH1	403	1	1	Substitution - coding silent(1)	skin(1)	c.C5115A						scavenged	.						101.0	92.0	95.0					17																	10399321		2203	4300	6503	SO:0001819	synonymous_variant	4619	exon35			TTCTGCGATTTTC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.5115C>A	17.37:g.10399321G>T		Somatic	170	1	0.00588235		WXS	Illumina HiSeq	Phase_I	180	5	0.0277778	NM_005963	Q14CA4|Q9Y622	Silent	SNP	ENST00000226207.5	37	CCDS11155.1																																																																																			.	.	alt		0.532	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
SFTPD	6441	hgsc.bcm.edu	37	10	81702260	81702260	+	Splice_Site	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:81702260C>T	ENST00000372292.3	-	4	357	c.317G>A	c.(316-318)gGa>gAa	p.G106E		NM_003019.4	NP_003010.4	P35247	SFTPD_HUMAN	surfactant protein D	106	Collagen-like.				defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|lung alveolus development (GO:0048286)|macrophage chemotaxis (GO:0048246)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of phagocytosis (GO:0050766)|reactive oxygen species metabolic process (GO:0072593)|receptor-mediated endocytosis (GO:0006898)|regulation of cytokine production (GO:0001817)|respiratory gaseous exchange (GO:0007585)|surfactant homeostasis (GO:0043129)	collagen trimer (GO:0005581)|endocytic vesicle (GO:0030139)|extracellular region (GO:0005576)|lysosome (GO:0005764)|proteinaceous extracellular matrix (GO:0005578)	carbohydrate binding (GO:0030246)			endometrium(1)|kidney(3)|large_intestine(5)|lung(3)|skin(4)|urinary_tract(1)	17	Breast(12;0.000615)|Prostate(51;0.0095)|all_epithelial(25;0.027)		Epithelial(14;0.0244)|all cancers(16;0.0558)|Colorectal(32;0.109)			TCCTGGAGGTCCTGAGCAAAA	0.567																																					p.G106E		Atlas-SNP	.											.	SFTPD	43	.	0			c.G317A						PASS	.						58.0	57.0	57.0					10																	81702260		2203	4300	6503	SO:0001630	splice_region_variant	6441	exon4			GGAGGTCCTGAGC	L05485	CCDS7362.1	10q22.2-q23.1	2012-11-02	2008-08-26		ENSG00000133661	ENSG00000133661		"""Collectins"""	10803	protein-coding gene	gene with protein product		178635	"""surfactant, pulmonary-associated protein D"""	SFTP4		1898081, 1339284	Standard	NM_003019		Approved	SP-D, COLEC7	uc001kbh.3	P35247	OTTHUMG00000018590	ENST00000372292.3:c.317-1G>A	10.37:g.81702260C>T		Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	61	8	0.131148	NM_003019	Q5T0M3|Q6FH08|Q86YK9|Q8TCD8|Q9UCJ2|Q9UCJ3	Missense_Mutation	SNP	ENST00000372292.3	37	CCDS7362.1	.	.	.	.	.	.	.	.	.	.	C	15.84	2.951636	0.53186	.	.	ENSG00000133661	ENST00000372292;ENST00000444384	D;D	0.99353	-4.61;-5.77	5.02	4.1	0.47936	.	0.000000	0.56097	D	0.000031	D	0.98883	0.9622	H	0.96889	3.9	0.39145	D	0.96211	P	0.38711	0.643	B	0.34489	0.184	D	0.98750	1.0720	10	0.87932	D	0	.	9.683	0.40080	0.0:0.9007:0.0:0.0993	.	106	P35247	SFTPD_HUMAN	E	106;119	ENSP00000361366:G106E;ENSP00000394325:G119E	ENSP00000361366:G106E	G	-	2	0	SFTPD	81692240	1.000000	0.71417	0.948000	0.38648	0.427000	0.31564	2.235000	0.43044	1.068000	0.40764	0.457000	0.33378	GGA	.	.	none		0.567	SFTPD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049011.1		Missense_Mutation
CD300LB	124599	hgsc.bcm.edu	37	17	72522004	72522004	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:72522004G>A	ENST00000392621.1	-	2	368	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	CD300LB_ENST00000314401.3_Missense_Mutation_p.R122C	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	85					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						GTGAACGTGCGGTCTTTCTGA	0.527																																					p.R122C		Atlas-SNP	.											CD300LB,lower_third,carcinoma,0,1	CD300LB	38	1	0			c.C364T						PASS	.						256.0	225.0	235.0					17																	72522004		2203	4300	6503	SO:0001583	missense	124599	exon2			ACGTGCGGTCTTT	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"""Immunoglobulin superfamily / V-set domain containing"""	30811	protein-coding gene	gene with protein product	"""triggering receptor expressed on myeloid cells 5"""	610705	"""CD300 antigen like family member B"""			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.364C>T	17.37:g.72522004G>A	ENSP00000376397:p.Arg122Cys	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	280	64	0.228571	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	37	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	G	6.311	0.425440	0.11987	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	T	0.04502	3.61	5.17	2.03	0.26663	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.216860	0.05978	N	0.643733	T	0.07324	0.0185	M	0.73319	2.225	0.09310	N	1	B;P	0.35242	0.077;0.492	B;B	0.23716	0.019;0.048	T	0.40961	-0.9535	10	0.38643	T	0.18	-16.1436	8.9441	0.35747	0.1487:0.0:0.7281:0.1232	.	122;85	B4DQ71;A8K4G0	.;CLM7_HUMAN	C	85;122	ENSP00000317337:R122C	ENSP00000317337:R122C	R	-	1	0	CD300LB	70033599	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.013000	0.13310	0.022000	0.15160	-1.119000	0.02030	CGC	.	.	none		0.527	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892	
FLG	2312	hgsc.bcm.edu	37	1	152280900	152280900	+	Missense_Mutation	SNP	T	T	G	rs74129452	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:152280900T>G	ENST00000368799.1	-	3	6497	c.6462A>C	c.(6460-6462)caA>caC	p.Q2154H	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2154	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCGATTGCTCTTGGTGGGACC	0.592									Ichthyosis				-|||	1722	0.34385	0.3843	0.3487	5008	,	,		25148	0.4444		0.1541	False		,,,				2504	0.3773				p.Q2154H		Atlas-SNP	.											FLG,right_upper_lobe,carcinoma,-2,1	FLG	900	1	0			c.A6462C						scavenged	.						380.0	322.0	342.0					1																	152280900		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	TTGCTCTTGGTGG	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.6462A>C	1.37:g.152280900T>G	ENSP00000357789:p.Gln2154His	Somatic	377	1	0.00265252		WXS	Illumina HiSeq	Phase_I	477	6	0.0125786	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	g	2.361	-0.346581	0.05208	.	.	ENSG00000143631	ENST00000368799	T	0.03524	3.9	2.59	-5.18	0.02840	.	.	.	.	.	T	0.00178	0.0005	N	0.00074	-2.255	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.49943	-0.8885	9	0.38643	T	0.18	.	0.1659	0.00108	0.2732:0.2266:0.1592:0.341	.	2154	P20930	FILA_HUMAN	H	2154	ENSP00000357789:Q2154H	ENSP00000357789:Q2154H	Q	-	3	2	FLG	150547524	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-3.334000	0.00508	-3.813000	0.00104	-2.053000	0.00404	CAA	T|0.872;G|0.128	0.128	strong		0.592	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
GLI2	2736	hgsc.bcm.edu	37	2	121747495	121747495	+	Missense_Mutation	SNP	G	G	C	rs570401582		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:121747495G>C	ENST00000452319.1	+	14	4065	c.4005G>C	c.(4003-4005)gaG>gaC	p.E1335D	GLI2_ENST00000314490.11_Intron|GLI2_ENST00000361492.4_Missense_Mutation_p.E1335D					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)				TGAGCCAGGAGGGCTACCACC	0.657																																					p.E1335D		Atlas-SNP	.											.	GLI2	187	.	0			c.G4005C						PASS	.						17.0	18.0	18.0					2																	121747495		2200	4295	6495	SO:0001583	missense	2736	exon13			CCAGGAGGGCTAC		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.4005G>C	2.37:g.121747495G>C	ENSP00000390436:p.Glu1335Asp	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	79	19	0.240506	NM_005270		Missense_Mutation	SNP	ENST00000452319.1	37	CCDS33283.1	.	.	.	.	.	.	.	.	.	.	G	6.282	0.420101	0.11928	.	.	ENSG00000074047	ENST00000452319;ENST00000361492	T;T	0.14516	2.5;2.5	4.55	-0.643	0.11482	.	0.579611	0.18288	N	0.145806	T	0.06508	0.0167	N	0.25647	0.755	0.09310	N	0.999998	B;B	0.09022	0.0;0.002	B;B	0.06405	0.001;0.002	T	0.32134	-0.9918	9	.	.	.	.	1.8185	0.03105	0.2117:0.2668:0.3922:0.1293	.	1335;990	P10070;P10070-2	GLI2_HUMAN;.	D	1335	ENSP00000390436:E1335D;ENSP00000354586:E1335D	.	E	+	3	2	GLI2	121463965	0.923000	0.31300	0.210000	0.23637	0.895000	0.52256	0.437000	0.21543	-0.051000	0.13334	0.455000	0.32223	GAG	.	.	none		0.657	GLI2-009	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332293.3	NM_005270	
GBP3	2635	hgsc.bcm.edu	37	1	89476655	89476655	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:89476655A>G	ENST00000370481.4	-	8	1514	c.1294T>C	c.(1294-1296)Tgt>Cgt	p.C432R		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		ATAAAGAGACAATAGCCCCCT	0.423																																					p.C432R		Atlas-SNP	.											.	GBP3	53	.	0			c.T1294C						PASS	.						202.0	169.0	181.0					1																	89476655		2191	3988	6179	SO:0001583	missense	2635	exon8			AGAGACAATAGCC	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.1294T>C	1.37:g.89476655A>G	ENSP00000359512:p.Cys432Arg	Somatic	339	0	0		WXS	Illumina HiSeq	Phase_I	333	64	0.192192	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.185169	0.00305	.	.	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000235878	T	0.01821	4.62	3.79	-1.98	0.07480	Guanylate-binding protein, C-terminal (3);	0.843353	0.10841	N	0.628203	T	0.00109	0.0003	N	0.00258	-1.755	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31223	-0.9951	10	0.02654	T	1	.	5.3138	0.15845	0.2643:0.0:0.5065:0.2292	.	298;432	F6X827;Q9H0R5	.;GBP3_HUMAN	R	400;432;432	ENSP00000359512:C432R	ENSP00000235878:C432R	C	-	1	0	GBP3	89249243	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.521000	0.02239	-0.900000	0.03896	-2.405000	0.00223	TGT	.	.	none		0.423	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
ZG16	653808	hgsc.bcm.edu	37	16	29791721	29791721	+	Missense_Mutation	SNP	G	G	C	rs235638	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:29791721G>C	ENST00000400752.4	+	4	559	c.485G>C	c.(484-486)aGt>aCt	p.S162T	AC009133.21_ENST00000572964.1_lincRNA	NM_152338.3	NP_689551	O60844	ZG16_HUMAN	zymogen granule protein 16	162			S -> T (in dbSNP:rs235638).		protein transport (GO:0015031)	extracellular matrix (GO:0031012)|Golgi lumen (GO:0005796)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	carbohydrate binding (GO:0030246)			endometrium(1)	1						GTTTACCCCAGTAGCTGCAGC	0.552													G|||	4442	0.886981	0.6407	0.9625	5008	,	,		18876	0.9405		0.998	False		,,,				2504	0.9969				p.S162T		Atlas-SNP	.											.	ZG16	14	.	0			c.G485C						PASS	.	G	THR/SER	920,464		313,294,85	75.0	66.0	69.0		485	2.2	0.4	16	dbSNP_79	69	3178,4		1587,4,0	yes	missense	ZG16	NM_152338.3	58	1900,298,85	CC,CG,GG		0.1257,33.526,10.2497	benign	162/168	29791721	4098,468	692	1591	2283	SO:0001583	missense	653808	exon4			ACCCCAGTAGCTG	AK125559	CCDS54000.1	16p11.2	2012-12-07	2012-12-07	2009-03-11	ENSG00000174992	ENSG00000174992			30961	protein-coding gene	gene with protein product			"""jacalin-like lectin domain containing"", ""zymogen granule protein 16 homolog (rat)"""	JCLN		12477932	Standard	NM_152338		Approved	hZG16, JCLN1, ZG16A	uc002dtr.4	O60844		ENST00000400752.4:c.485G>C	16.37:g.29791721G>C	ENSP00000383563:p.Ser162Thr	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	7	7	1	NM_152338	B2R4Z3|B9EK72	Missense_Mutation	SNP	ENST00000400752.4	37	CCDS54000.1	1973	0.9033882783882784	323	0.6565040650406504	348	0.9613259668508287	545	0.9527972027972028	757	0.9986807387862797	G	11.98	1.799397	0.31869	0.66474	0.998743	ENSG00000174992	ENST00000400752	T	0.24151	1.87	5.33	2.15	0.27550	.	0.774363	0.12322	N	0.479207	T	0.00012	0.0000	.	.	.	0.53688	P	2.8999999999945736E-5	.	.	.	.	.	.	T	0.43065	-0.9414	6	0.13470	T	0.59	.	7.4081	0.27001	0.0884:0.322:0.5896:0.0	rs235638;rs17856826;rs52829584;rs235638	.	.	.	T	162	ENSP00000383563:S162T	ENSP00000383563:S162T	S	+	2	0	ZG16	29699222	0.897000	0.30589	0.429000	0.26710	0.859000	0.49053	1.196000	0.32198	0.810000	0.34279	0.655000	0.94253	AGT	G|0.120;C|0.880	0.880	strong		0.552	ZG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435523.2	NM_152338	
SLIT1	6585	hgsc.bcm.edu	37	10	98802756	98802756	+	Missense_Mutation	SNP	C	C	T	rs144930720		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:98802756C>T	ENST00000266058.4	-	20	2311	c.2066G>A	c.(2065-2067)cGc>cAc	p.R689H	ARHGAP19-SLIT1_ENST00000453547.2_3'UTR|SLIT1_ENST00000371070.4_Missense_Mutation_p.R689H	NM_003061.2	NP_003052.2	O75093	SLIT1_HUMAN	slit homolog 1 (Drosophila)	689	LRRCT 3.				axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|dorsal/ventral axon guidance (GO:0033563)|establishment of nucleus localization (GO:0040023)|forebrain morphogenesis (GO:0048853)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of synapse assembly (GO:0051964)|retinal ganglion cell axon guidance (GO:0031290)|spinal cord development (GO:0021510)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)	extracellular space (GO:0005615)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(37)|ovary(5)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	78		Colorectal(252;0.162)		Epithelial(162;2.02e-08)|all cancers(201;1.5e-06)		CACGATCTTGCGCTTCCGTAG	0.612													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20013	0.0		0.0	False		,,,				2504	0.0				p.R689H		Atlas-SNP	.											SLIT1,NS,lymphoid_neoplasm,0,1	SLIT1	154	1	0			c.G2066A						scavenged	.						65.0	60.0	62.0					10																	98802756		2203	4300	6503	SO:0001583	missense	6585	exon20			ATCTTGCGCTTCC	AB011537	CCDS7453.1	10q23.3-q24	2008-08-01	2001-11-28		ENSG00000187122	ENSG00000187122			11085	protein-coding gene	gene with protein product		603742	"""slit (Drosophila) homolog 1"""	SLIL1		9693030, 9813312	Standard	NM_003061		Approved	slit1, MEGF4, Slit-1, SLIT3	uc001kmw.2	O75093	OTTHUMG00000018843	ENST00000266058.4:c.2066G>A	10.37:g.98802756C>T	ENSP00000266058:p.Arg689His	Somatic	155	2	0.0129032		WXS	Illumina HiSeq	Phase_I	119	3	0.0252101	NM_003061	Q5T0V1|Q8WWZ2|Q9UIL7	Missense_Mutation	SNP	ENST00000266058.4	37	CCDS7453.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	22.4	4.278640	0.80692	.	.	ENSG00000187122	ENST00000266058;ENST00000371057;ENST00000371070;ENST00000314867	T;T;T	0.81163	-1.46;-1.46;0.47	4.73	3.83	0.44106	Cysteine-rich flanking region, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.86653	0.5984	L	0.58583	1.82	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.91;0.997	D	0.86950	0.2085	10	0.56958	D	0.05	.	12.8219	0.57698	0.0:0.9211:0.0:0.0789	.	699;689	E7EWQ8;O75093	.;SLIT1_HUMAN	H	689;699;689;682	ENSP00000266058:R689H;ENSP00000360109:R689H;ENSP00000315005:R682H	ENSP00000266058:R689H	R	-	2	0	SLIT1	98792746	1.000000	0.71417	0.965000	0.40720	0.698000	0.40448	4.479000	0.60236	1.209000	0.43321	0.561000	0.74099	CGC	C|1.000;T|0.000	0.000	strong		0.612	SLIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049636.1	NM_003061	
ANKLE1	126549	hgsc.bcm.edu	37	19	17393015	17393015	+	Missense_Mutation	SNP	C	C	T	rs1864116	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:17393015C>T	ENST00000394458.3	+	2	488	c.212C>T	c.(211-213)gCt>gTt	p.A71V	ANKLE1_ENST00000404085.1_Missense_Mutation_p.A93V|ANKLE1_ENST00000594072.1_Missense_Mutation_p.A60V|ANKLE1_ENST00000598347.1_Missense_Mutation_p.A71V|ANKLE1_ENST00000433424.2_Missense_Mutation_p.A125V|CTD-2278I10.6_ENST00000596542.1_3'UTR	NM_152363.4	NP_689576	Q8NAG6	ANKL1_HUMAN	ankyrin repeat and LEM domain containing 1	71			A -> V (in dbSNP:rs1864116). {ECO:0000269|PubMed:14702039, ECO:0000269|Ref.1}.							large_intestine(1)|lung(3)|prostate(1)|skin(1)|urinary_tract(1)	7						GACCCCAACGCTCGGTAAGAT	0.741													C|||	3182	0.635383	0.798	0.5533	5008	,	,		8910	0.3125		0.834	False		,,,				2504	0.6022				p.A71V		Atlas-SNP	.											.	ANKLE1	27	.	0			c.C212T						PASS	.	C	VAL/ALA	2161,339		925,311,14	2.0	2.0	2.0		212	0.8	0.5	19	dbSNP_92	2	4508,662		1957,594,34	yes	missense	ANKLE1	NM_152363.4	64	2882,905,48	TT,TC,CC		12.8046,13.56,13.0508	probably-damaging	71/616	17393015	6669,1001	1250	2585	3835	SO:0001583	missense	126549	exon2			CCAACGCTCGGTA	AK096688	CCDS12354.2, CCDS12354.3	19p13.11	2013-01-10	2008-03-25	2008-03-25	ENSG00000160117	ENSG00000160117		"""Ankyrin repeat domain containing"""	26812	protein-coding gene	gene with protein product	"""LEM domain containing 6"""		"""ankyrin repeat domain 41"""	ANKRD41			Standard	NM_152363		Approved	FLJ39369, LEMD6	uc002nga.2	Q8NAG6	OTTHUMG00000150839	ENST00000394458.3:c.212C>T	19.37:g.17393015C>T	ENSP00000377971:p.Ala71Val	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_152363	A8VU82|Q8N8J8	Missense_Mutation	SNP	ENST00000394458.3	37	CCDS12354.2	1399	0.6405677655677655	380	0.7723577235772358	218	0.6022099447513812	164	0.2867132867132867	637	0.8403693931398417	C	16.19	3.054076	0.55218	0.8644	0.871954	ENSG00000160117	ENST00000404261;ENST00000433424;ENST00000404085;ENST00000394458;ENST00000438921	T;T;T	0.67865	-0.29;-0.29;-0.29	4.15	0.796	0.18648	Ankyrin repeat-containing domain (4);	0.432303	0.19437	N	0.114285	T	0.00012	0.0000	N	0.20807	0.61	0.80722	P	0.0	B;B;B	0.15930	0.005;0.015;0.002	B;B;B	0.17722	0.016;0.015;0.019	T	0.27606	-1.0069	9	0.18710	T	0.47	-20.551	6.1339	0.20221	0.0:0.667:0.0:0.333	rs1864116;rs17238816;rs59648740;rs1864116	71;57;71	E7ETZ9;Q8NAG6-1;Q8NAG6	.;.;ANKL1_HUMAN	V	71;125;93;60;71	ENSP00000384753:A71V;ENSP00000394460:A125V;ENSP00000384008:A93V	ENSP00000377971:A60V	A	+	2	0	ANKLE1	17254015	0.002000	0.14202	0.527000	0.27925	0.842000	0.47809	0.606000	0.24194	0.078000	0.16900	0.555000	0.69702	GCT	C|0.362;T|0.638	0.638	strong		0.741	ANKLE1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000325392.2	NM_152363	
ZNF181	339318	hgsc.bcm.edu	37	19	35232469	35232469	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:35232469C>T	ENST00000492450.1	+	4	1272	c.1183C>T	c.(1183-1185)Cat>Tat	p.H395Y	ZNF181_ENST00000392232.3_Missense_Mutation_p.H439Y|ZNF181_ENST00000459757.2_Missense_Mutation_p.H394Y			Q2M3W8	ZN181_HUMAN	zinc finger protein 181	395					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(6)|kidney(2)|large_intestine(1)|lung(7)|ovary(2)|prostate(3)|skin(1)	22	all_lung(56;1.13e-07)|Lung NSC(56;1.81e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.138)			CCTTACTCGACATCAAAGAAT	0.388																																					p.H395Y		Atlas-SNP	.											.	ZNF181	65	.	0			c.C1183T						PASS	.						72.0	67.0	68.0					19																	35232469		2203	4298	6501	SO:0001583	missense	339318	exon4			ACTCGACATCAAA	BC104759, H54888	CCDS32990.2, CCDS46043.1	19q13.13	2013-01-08	2006-04-27		ENSG00000197841	ENSG00000197841		"""Zinc fingers, C2H2-type"", ""-"""	12971	protein-coding gene	gene with protein product		606741	"""zinc finger protein 181 (HHZ181)"""				Standard	NM_001029997		Approved	HHZ181, MGC44316	uc002nvu.3	Q2M3W8	OTTHUMG00000157508	ENST00000492450.1:c.1183C>T	19.37:g.35232469C>T	ENSP00000420727:p.His395Tyr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	122	19	0.155738	NM_001029997	B7ZKX3|Q49A75	Missense_Mutation	SNP	ENST00000492450.1	37	CCDS32990.2	.	.	.	.	.	.	.	.	.	.	C	17.03	3.285590	0.59867	.	.	ENSG00000197841	ENST00000392232;ENST00000425140;ENST00000492450;ENST00000459757	D;D;D	0.86769	-2.17;-2.17;-2.17	2.84	2.84	0.33178	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	D	0.95098	0.8412	H	0.97611	4.04	0.34829	D	0.739442	D;P	0.71674	0.998;0.95	D;D	0.66847	0.944;0.947	D	0.97572	1.0105	9	0.87932	D	0	.	11.88	0.52568	0.0:1.0:0.0:0.0	.	394;395	B7ZKX3;Q2M3W8	.;ZN181_HUMAN	Y	439;394;395;394	ENSP00000376065:H439Y;ENSP00000420727:H395Y;ENSP00000419435:H394Y	ENSP00000376065:H439Y	H	+	1	0	ZNF181	39924309	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.481000	0.73608	1.876000	0.54355	0.561000	0.74099	CAT	.	.	none		0.388	ZNF181-002	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349005.3	NM_001029997	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970774	45970774	+	Missense_Mutation	SNP	G	G	A	rs76536096|rs67692969|rs71199610	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:45970774G>A	ENST00000391621.1	-	1	614	c.568C>T	c.(568-570)Cct>Tct	p.P190S	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						CAGCAGACAGGCTTGCAGCAG	0.607																																					p.P190S		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.C568T						PASS	.						110.0	112.0	111.0					21																	45970774		2192	4279	6471	SO:0001583	missense	386679	exon1			AGACAGGCTTGCA	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.568C>T	21.37:g.45970774G>A	ENSP00000375479:p.Pro190Ser	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	119	12	0.10084	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	g	9.523	1.108901	0.20714	.	.	ENSG00000205445	ENST00000391621	T	0.01705	4.68	3.28	0.222	0.15288	.	.	.	.	.	T	0.02083	0.0065	L	0.49455	1.56	0.09310	N	1	B	0.26672	0.156	B	0.24394	0.053	T	0.42310	-0.9459	9	0.62326	D	0.03	.	4.9369	0.13944	0.2108:0.1755:0.6137:0.0	.	190	P60368	KR102_HUMAN	S	190	ENSP00000375479:P190S	ENSP00000375479:P190S	P	-	1	0	KRTAP10-2	44795202	0.105000	0.21958	0.000000	0.03702	0.002000	0.02628	1.284000	0.33249	-0.177000	0.10690	0.462000	0.41574	CCT	G|0.917;A|0.083	0.083	strong		0.607	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
NFASC	23114	hgsc.bcm.edu	37	1	204943936	204943936	+	Missense_Mutation	SNP	C	C	T	rs149731085		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:204943936C>T	ENST00000401399.1	+	13	1742	c.1543C>T	c.(1543-1545)Cgc>Tgc	p.R515C	NFASC_ENST00000513543.1_Missense_Mutation_p.R526C|NFASC_ENST00000404076.1_Missense_Mutation_p.R509C|NFASC_ENST00000367171.4_Missense_Mutation_p.R515C|NFASC_ENST00000367172.4_Missense_Mutation_p.R515C|NFASC_ENST00000403080.1_Missense_Mutation_p.R515C|NFASC_ENST00000339876.6_Missense_Mutation_p.R515C|NFASC_ENST00000367170.4_Missense_Mutation_p.R515C|NFASC_ENST00000360049.4_Missense_Mutation_p.R526C|NFASC_ENST00000367169.4_Missense_Mutation_p.R515C|NFASC_ENST00000539706.1_Missense_Mutation_p.R526C|NFASC_ENST00000338586.6_Missense_Mutation_p.R515C|NFASC_ENST00000338515.6_Missense_Mutation_p.R515C|NFASC_ENST00000404907.1_Missense_Mutation_p.R526C			O94856	NFASC_HUMAN	neurofascin	515	Ig-like C2-type 5.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			AAACCAAGTCCGCCTGGAGGT	0.512													C|||	1	0.000199681	0.0	0.0	5008	,	,		21343	0.0		0.001	False		,,,				2504	0.0				p.R526C		Atlas-SNP	.											.	NFASC	396	.	0			c.C1576T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	0,4406		0,0,2203	99.0	92.0	95.0		1543,1543,1576,1576,1525,1576	5.8	1.0	1	dbSNP_134	95	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense,missense,missense	NFASC	NM_001005388.2,NM_001005389.1,NM_001160331.1,NM_001160332.1,NM_001160333.1,NM_015090.3	180,180,180,180,180,180	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	515/1241,515/620,526/1190,526/1175,509/614,526/1170	204943936	2,13004	2203	4300	6503	SO:0001583	missense	23114	exon14			CAAGTCCGCCTGG	AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000401399.1:c.1543C>T	1.37:g.204943936C>T	ENSP00000385637:p.Arg515Cys	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	116	30	0.258621	NM_015090	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Missense_Mutation	SNP	ENST00000401399.1	37	CCDS53460.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	34	5.399757	0.96030	0.0	2.33E-4	ENSG00000163531	ENST00000367172;ENST00000367171;ENST00000367170;ENST00000338515;ENST00000339876;ENST00000338586;ENST00000295776;ENST00000539706;ENST00000360049;ENST00000367169;ENST00000403080;ENST00000404076;ENST00000401399;ENST00000404907;ENST00000513543;ENST00000430393	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.68025	-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3;-0.3	5.8	5.8	0.92144	Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.237674	0.29822	N	0.011105	T	0.80105	0.4562	L	0.61387	1.9	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.962;0.999;1.0;1.0;0.998;0.995	D;P;P;D;P;P;P	0.66497	0.943;0.501;0.905;0.944;0.648;0.814;0.804	T	0.78816	-0.2055	10	0.49607	T	0.09	.	19.7118	0.96099	0.0:1.0:0.0:0.0	.	515;526;526;515;515;526;515	O94856;O94856-11;O94856-8;F8W791;O94856-9;O94856-3;O94856-2	NFASC_HUMAN;.;.;.;.;.;.	C	515;515;515;515;515;515;526;526;526;515;515;509;515;526;526;502	ENSP00000356140:R515C;ENSP00000356139:R515C;ENSP00000356138:R515C;ENSP00000342128:R515C;ENSP00000344786:R515C;ENSP00000343509:R515C;ENSP00000438614:R526C;ENSP00000353154:R526C;ENSP00000356137:R515C;ENSP00000384875:R515C;ENSP00000385676:R509C;ENSP00000385637:R515C;ENSP00000384061:R526C;ENSP00000425908:R526C;ENSP00000415031:R502C	ENSP00000295776:R526C	R	+	1	0	NFASC	203210559	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.975000	0.70475	2.764000	0.94973	0.485000	0.47835	CGC	C|1.000;T|0.000	0.000	strong		0.512	NFASC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000131237.1	NM_001005388	
TMPRSS2	7113	hgsc.bcm.edu	37	21	42851153	42851153	+	Missense_Mutation	SNP	A	A	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:42851153A>T	ENST00000332149.5	-	7	763	c.629T>A	c.(628-630)aTg>aAg	p.M210K	TMPRSS2_ENST00000398585.3_Missense_Mutation_p.M247K|TMPRSS2_ENST00000458356.1_Missense_Mutation_p.M210K	NM_005656.3	NP_005647.3	O15393	TMPS2_HUMAN	transmembrane protease, serine 2	210	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				positive regulation of viral entry into host cell (GO:0046598)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)		TMPRSS2/ETV1(34)|TMPRSS2/ETV5_ENST00000306376(5)|TMPRSS2/ERG(3582)|TMPRSS2/ETV4(13)	central_nervous_system(1)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	4		Prostate(19;4.48e-07)|all_epithelial(19;0.031)				GTTCAGTTTCATAAAGCTGGT	0.353			T	"""ERG, ETV1, ETV4, ETV5"""	prostate																																p.M247K		Atlas-SNP	.		Dom	yes		21	21q22.3	7113	"""transmembrane protease, serine 2"""		E	.	TMPRSS2	148	.	0			c.T740A						PASS	.						146.0	145.0	146.0					21																	42851153		2203	4300	6503	SO:0001583	missense	7113	exon7			AGTTTCATAAAGC	U75329	CCDS33564.1, CCDS54486.1	21q22.3	2010-04-13			ENSG00000184012	ENSG00000184012		"""Serine peptidases / Transmembrane"""	11876	protein-coding gene	gene with protein product		602060				9325052	Standard	NM_005656		Approved	PRSS10	uc010gor.3	O15393	OTTHUMG00000086762	ENST00000332149.5:c.629T>A	21.37:g.42851153A>T	ENSP00000330330:p.Met210Lys	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_001135099	A8K6Z8|B2R8E5|B7Z459|D3DSJ2|F8WES1|Q6GTK7|Q9BXX1	Missense_Mutation	SNP	ENST00000332149.5	37	CCDS33564.1	.	.	.	.	.	.	.	.	.	.	A	13.10	2.137229	0.37728	.	.	ENSG00000184012	ENST00000332149;ENST00000398585;ENST00000458356;ENST00000454499;ENST00000424093	T;T;T;T;T	0.60171	0.21;0.21;0.21;0.21;0.21	5.43	4.25	0.50352	Speract/scavenger receptor (1);Speract/scavenger receptor-related (2);	0.065677	0.64402	D	0.000007	T	0.62527	0.2435	M	0.72479	2.2	0.39156	D	0.962314	D;P	0.55800	0.973;0.85	P;P	0.54174	0.735;0.744	T	0.62324	-0.6878	10	0.12766	T	0.61	.	9.4178	0.38532	0.8205:0.1795:0.0:0.0	.	247;210	F8WES1;O15393	.;TMPS2_HUMAN	K	210;247;210;210;170	ENSP00000330330:M210K;ENSP00000381588:M247K;ENSP00000391216:M210K;ENSP00000389006:M210K;ENSP00000397846:M170K	ENSP00000330330:M210K	M	-	2	0	TMPRSS2	41773023	1.000000	0.71417	0.597000	0.28824	0.032000	0.12392	4.796000	0.62496	0.872000	0.35775	0.448000	0.29417	ATG	.	.	none		0.353	TMPRSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195189.1		
GABRA4	2557	hgsc.bcm.edu	37	4	46995366	46995366	+	Missense_Mutation	SNP	G	G	T	rs2229940	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:46995366G>T	ENST00000264318.3	-	1	1058	c.76C>A	c.(76-78)Ctg>Atg	p.L26M	GABRA4_ENST00000509316.1_5'UTR	NM_000809.3|NM_001204266.1|NM_001204267.1	NP_000800.2|NP_001191195.1|NP_001191196.1	P48169	GBRA4_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 4	26			L -> M (in dbSNP:rs2229940).		central nervous system development (GO:0007417)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|regulation of response to drug (GO:2001023)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)	p.L26M(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45					Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	CAAACCGCCAGGCACAGGAAG	0.607													G|||	1506	0.300719	0.2526	0.2968	5008	,	,		16875	0.3879		0.3668	False		,,,				2504	0.2106				p.L26M	Ovarian(6;283 369 8234 12290 33402)	Atlas-SNP	.											GABRA4,NS,carcinoma,0,1	GABRA4	129	1	1	Substitution - Missense(1)	prostate(1)	c.C76A						scavenged	.	G	MET/LEU,,	1132,3274	403.5+/-332.8	127,878,1198	109.0	105.0	106.0		76,,	3.0	1.0	4	dbSNP_98	106	3154,5446	479.1+/-370.0	599,1956,1745	yes	missense,intron,intron	GABRA4	NM_000809.3,NM_001204266.1,NM_001204267.1	15,,	726,2834,2943	TT,TG,GG		36.6744,25.6922,32.954	probably-damaging,,	26/555,,	46995366	4286,8720	2203	4300	6503	SO:0001583	missense	2557	exon1			CCGCCAGGCACAG		CCDS3473.1	4p12	2012-06-22			ENSG00000109158	ENSG00000109158		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4078	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 4"""	137141				7607683	Standard	NM_000809		Approved		uc021xnz.1	P48169	OTTHUMG00000099431	ENST00000264318.3:c.76C>A	4.37:g.46995366G>T	ENSP00000264318:p.Leu26Met	Somatic	218	2	0.00917431		WXS	Illumina HiSeq	Phase_I	220	5	0.0227273	NM_000809	Q8IYR7	Missense_Mutation	SNP	ENST00000264318.3	37	CCDS3473.1	742	0.33974358974358976	138	0.2804878048780488	107	0.2955801104972376	214	0.3741258741258741	283	0.3733509234828496	G	13.24	2.178732	0.38511	0.256922	0.366744	ENSG00000109158	ENST00000264318	D	0.81996	-1.56	4.72	2.98	0.34508	.	0.473208	0.19701	N	0.108022	T	0.00012	0.0000	N	0.24115	0.695	0.35598	P	0.19235199999999997	B	0.23806	0.091	B	0.29524	0.103	T	0.13045	-1.0524	9	0.49607	T	0.09	.	6.8007	0.23750	0.2113:0.0:0.7887:0.0	rs2229940;rs2280071;rs16859834;rs52790560;rs2229940	26	P48169	GBRA4_HUMAN	M	26	ENSP00000264318:L26M	ENSP00000264318:L26M	L	-	1	2	GABRA4	46690123	1.000000	0.71417	0.998000	0.56505	0.930000	0.56654	2.533000	0.45667	0.588000	0.29660	0.585000	0.79938	CTG	G|0.672;T|0.328	0.328	strong		0.607	GABRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216893.1		
LTB	4050	hgsc.bcm.edu	37	6	31549632	31549632	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:31549632G>A	ENST00000429299.2	-	2	174	c.167C>T	c.(166-168)aCg>aTg	p.T56M	LTB_ENST00000483972.1_Intron|LTB_ENST00000446745.2_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	56					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GGCCGTCTCCGTTACCTGGTT	0.627																																					p.T56M		Atlas-SNP	.											.	LTB	19	.	0			c.C167T						PASS	.						80.0	89.0	86.0					6																	31549632		1509	2709	4218	SO:0001583	missense	4050	exon2			GTCTCCGTTACCT	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.167C>T	6.37:g.31549632G>A	ENSP00000410481:p.Thr56Met	Somatic	99	0	0		WXS	Illumina HiSeq	Phase_I	82	13	0.158537	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	G	11.08	1.534745	0.27475	.	.	ENSG00000227507	ENST00000429299	T	0.21932	1.98	5.45	-0.999	0.10208	.	1.156080	0.06349	N	0.709538	T	0.03871	0.0109	N	0.22421	0.69	0.09310	N	0.999997	B	0.13145	0.007	B	0.08055	0.003	T	0.42732	-0.9434	10	0.44086	T	0.13	-0.0223	3.3408	0.07118	0.3298:0.0:0.3705:0.2997	.	56	Q06643	TNFC_HUMAN	M	56	ENSP00000410481:T56M	ENSP00000410481:T56M	T	-	2	0	LTB	31657611	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.359000	0.20233	-0.203000	0.10251	-0.742000	0.03525	ACG	.	.	none		0.627	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		
GNAT3	346562	hgsc.bcm.edu	37	7	80117974	80117974	+	Silent	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:80117974A>C	ENST00000398291.3	-	3	273	c.180T>G	c.(178-180)ggT>ggG	p.G60G	CD36_ENST00000435819.1_Intron	NM_001102386.1	NP_001095856.1	A8MTJ3	GNAT3_HUMAN	guanine nucleotide binding protein, alpha transducing 3	60					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of visible light (GO:0009584)|platelet activation (GO:0030168)|response to nicotine (GO:0035094)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|synaptic transmission (GO:0007268)	acrosomal vesicle (GO:0001669)|apical plasma membrane (GO:0016324)|axoneme (GO:0005930)|heterotrimeric G-protein complex (GO:0005834)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled photoreceptor activity (GO:0008020)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)	9						GCTCACTGTAACCATTCTTAT	0.343																																					p.G60G		Atlas-SNP	.											.	GNAT3	65	.	0			c.T180G						PASS	.						119.0	100.0	106.0					7																	80117974		1847	4095	5942	SO:0001819	synonymous_variant	346562	exon3			ACTGTAACCATTC		CCDS47625.1	7q21.11	2007-06-13			ENSG00000214415	ENSG00000214415			22800	protein-coding gene	gene with protein product		139395					Standard	NM_001102386		Approved	gustducin, GDCA	uc011kgu.2	A8MTJ3	OTTHUMG00000155401	ENST00000398291.3:c.180T>G	7.37:g.80117974A>C		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	143	26	0.181818	NM_001102386	A4D1B2|A4D1B3|B9EJG5	Silent	SNP	ENST00000398291.3	37	CCDS47625.1																																																																																			.	.	none		0.343	GNAT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339909.3	XM_294370	
PTCD1	26024	hgsc.bcm.edu	37	7	99017681	99017681	+	Missense_Mutation	SNP	G	G	T	rs568698296	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:99017681G>T	ENST00000292478.4	-	8	2262	c.2012C>A	c.(2011-2013)cCg>cAg	p.P671Q	ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.P720Q|PTCD1_ENST00000555673.1_Missense_Mutation_p.P720Q	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	671					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)		STAD - Stomach adenocarcinoma(171;0.215)			CCAGGGGTGCGGGGTTTCCTC	0.592																																					p.P720Q		Atlas-SNP	.											PTCD1,colon,carcinoma,+1,1	.	.	1	0			c.C2159A						scavenged	.						137.0	137.0	137.0					7																	99017681		2203	4300	6503	SO:0001583	missense	100526740	exon9			GGGTGCGGGGTTT	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.2012C>A	7.37:g.99017681G>T	ENSP00000292478:p.Pro671Gln	Somatic	134	0	0		WXS	Illumina HiSeq	Phase_I	130	3	0.0230769	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990837	0.54041	.	.	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000438524;ENST00000555673;ENST00000413834	T;T;T	0.66995	-0.24;-0.21;-0.21	5.82	4.94	0.65067	.	0.379952	0.31210	N	0.008053	T	0.78672	0.4320	M	0.68317	2.08	0.40810	D	0.983417	D;P	0.59357	0.985;0.938	P;P	0.59288	0.855;0.605	T	0.80171	-0.1493	10	0.54805	T	0.06	-18.8575	18.0718	0.89410	0.0639:0.0:0.9361:0.0	.	720;671	G3V325;O75127	.;PTCD1_HUMAN	Q	671;453;720;720	ENSP00000292478:P671Q;ENSP00000450995:P720Q;ENSP00000400168:P720Q	ENSP00000400168:P720Q	P	-	2	0	ATP5J2-PTCD1;PTCD1	98855617	1.000000	0.71417	1.000000	0.80357	0.338000	0.28826	4.522000	0.60539	0.811000	0.34303	-1.134000	0.01955	CCG	.	.	none		0.592	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
PCDH7	5099	hgsc.bcm.edu	37	4	30723952	30723952	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:30723952A>C	ENST00000361762.2	+	1	1916	c.908A>C	c.(907-909)gAc>gCc	p.D303A	PCDH7_ENST00000543491.1_Missense_Mutation_p.D303A	NM_002589.2	NP_002580.2	O60245	PCDH7_HUMAN	protocadherin 7	303	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(8)|liver(1)|lung(26)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	55						GACGTGAACGACAACAGCCCC	0.682																																					p.D303A		Atlas-SNP	.											.	PCDH7	215	.	0			c.A908C						PASS	.						11.0	14.0	13.0					4																	30723952		2196	4284	6480	SO:0001583	missense	5099	exon1			TGAACGACAACAG	AB006755	CCDS33971.1, CCDS75116.1	4p15	2014-06-13	2007-02-12			ENSG00000169851		"""Cadherins / Protocadherins : Non-clustered"""	8659	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 120"""	602988	"""BH-protocadherin (brain-heart)"""			9615233	Standard	NM_002589		Approved	BH-Pcdh, PPP1R120	uc021xnd.1	O60245		ENST00000361762.2:c.908A>C	4.37:g.30723952A>C	ENSP00000355243:p.Asp303Ala	Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	64	6	0.09375	NM_032457	O60246|O60247|Q4W5C4	Missense_Mutation	SNP	ENST00000361762.2	37	CCDS33971.1	.	.	.	.	.	.	.	.	.	.	A	22.3	4.270608	0.80469	.	.	ENSG00000169851	ENST00000361762;ENST00000543491	T;T	0.71579	-0.58;-0.58	5.18	5.18	0.71444	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	D	0.88250	0.6386	H	0.94964	3.605	0.54753	D	0.999988	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	D	0.91602	0.5296	9	0.87932	D	0	.	15.0142	0.71570	1.0:0.0:0.0:0.0	.	303;303	F5GWJ1;O60245	.;PCDH7_HUMAN	A	303	ENSP00000355243:D303A;ENSP00000441802:D303A	ENSP00000355243:D303A	D	+	2	0	PCDH7	30333050	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.322000	0.96357	1.934000	0.56057	0.459000	0.35465	GAC	.	.	none		0.682	PCDH7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360366.1	NM_032457, NM_002589	
MUC12	10071	hgsc.bcm.edu	37	7	100648117	100648117	+	Missense_Mutation	SNP	C	C	G	rs11766125	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:100648117C>G	ENST00000379442.3	+	5	14702	c.14702C>G	c.(14701-14703)aCa>aGa	p.T4901R	MUC12_ENST00000536621.1_Missense_Mutation_p.T4758R			Q9UKN1	MUC12_HUMAN	mucin 12, cell surface associated	4901	Ser-rich.			T -> R (in Ref. 2; AAD55678). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|regulation of cell growth (GO:0001558)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)		p.T4758R(1)		breast(6)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)|stomach(13)	25						GCCAGCATGACAAGCTCCAGC	0.537													-|||	2353	0.469848	0.3449	0.366	5008	,	,		22309	0.6111		0.5129	False		,,,				2504	0.5225				p.T4758R		Atlas-SNP	.											MUC12,NS,carcinoma,0,1	MUC12	140	1	1	Substitution - Missense(1)	stomach(1)	c.C14273G						scavenged	.	C	ARG/THR	560,824		100,360,232	177.0	162.0	166.0		14273	-1.0	0.0	7	dbSNP_120	166	1634,1548		435,764,392	yes	missense	MUC12	NM_001164462.1	71	535,1124,624	GG,GC,CC		48.6486,40.4624,48.0508		4758/5336	100648117	2194,2372	692	1591	2283	SO:0001583	missense	10071	exon2			GCATGACAAGCTC	AF147790, AF147791	CCDS55139.1	7q22	2007-01-17	2006-03-14		ENSG00000205277	ENSG00000205277		"""Mucins"""	7510	protein-coding gene	gene with protein product		604609	"""mucin 11"""	MUC11		10463611	Standard	NM_001164462		Approved		uc003uxo.3	Q9UKN1	OTTHUMG00000157042	ENST00000379442.3:c.14702C>G	7.37:g.100648117C>G	ENSP00000368755:p.Thr4901Arg	Somatic	4	1	0.25		WXS	Illumina HiSeq	Phase_I	11	4	0.363636	NM_001164462	A6ND38|F5GWV9|Q9UKN0	Missense_Mutation	SNP	ENST00000379442.3	37		1060	0.48534798534798534	193	0.39227642276422764	143	0.39502762430939226	332	0.5804195804195804	392	0.5171503957783641	c	0.012	-1.654591	0.00779	0.404624	0.513514	ENSG00000205277	ENST00000379442;ENST00000536621	T;T	0.09538	2.97;2.97	0.49	-0.979	0.10276	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.36841	-0.9731	5	0.19147	T	0.46	.	.	.	.	rs11766125;rs52795737;rs11766125	.	.	.	R	4901;4758	ENSP00000368755:T4901R;ENSP00000441929:T4758R	ENSP00000368755:T4901R	T	+	2	0	MUC12	100434837	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-1.538000	0.02204	-1.413000	0.02027	-1.296000	0.01341	ACA	C|0.499;G|0.501	0.501	strong		0.537	MUC12-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347234.1	XM_379904	
GLYR1	84656	hgsc.bcm.edu	37	16	4882161	4882161	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:4882161C>T	ENST00000321919.9	-	5	432	c.356G>A	c.(355-357)aGg>aAg	p.R119K	GLYR1_ENST00000436648.5_Intron|GLYR1_ENST00000591451.1_Missense_Mutation_p.R119K|GLYR1_ENST00000586901.1_5'UTR|GLYR1_ENST00000381983.3_Missense_Mutation_p.R119K	NM_032569.3	NP_115958	Q49A26	GLYR1_HUMAN	glyoxylate reductase 1 homolog (Arabidopsis)	119					pentose-phosphate shunt (GO:0006098)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	DNA binding (GO:0003677)|methylated histone binding (GO:0035064)|NAD binding (GO:0051287)|phosphogluconate dehydrogenase (decarboxylating) activity (GO:0004616)			endometrium(1)|kidney(1)|large_intestine(7)|lung(6)|prostate(2)|skin(1)|urinary_tract(1)	19						TGAGTTTGGCCTACTTCTCTC	0.433																																					p.R119K		Atlas-SNP	.											.	GLYR1	49	.	0			c.G356A						PASS	.						177.0	156.0	163.0					16																	4882161		2197	4300	6497	SO:0001583	missense	84656	exon5			TTTGGCCTACTTC	AF244907	CCDS10524.1	16p13.3	2010-02-17			ENSG00000140632	ENSG00000140632			24434	protein-coding gene	gene with protein product	"""nuclear protein 60kDa"""	610660				16352664	Standard	NM_032569		Approved	BM045, HIBDL, NP60, N-PAC	uc002cxx.4	Q49A26	OTTHUMG00000129530	ENST00000321919.9:c.356G>A	16.37:g.4882161C>T	ENSP00000322716:p.Arg119Lys	Somatic	257	0	0		WXS	Illumina HiSeq	Phase_I	255	43	0.168627	NM_032569	B4DL47|C9JJ40|C9JJ60|Q5U632|Q6P1Q2|Q6V3W7|Q9BTI1|Q9BXK2	Missense_Mutation	SNP	ENST00000321919.9	37	CCDS10524.1	.	.	.	.	.	.	.	.	.	.	C	11.48	1.651816	0.29336	.	.	ENSG00000140632	ENST00000321919;ENST00000381983	T;T	0.61742	0.08;0.08	5.29	4.32	0.51571	.	0.300170	0.38326	N	0.001739	T	0.33673	0.0871	N	0.08118	0	0.28988	N	0.888228	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.13045	-1.0524	10	0.37606	T	0.19	-24.4605	8.8028	0.34918	0.0:0.8427:0.0:0.1573	.	119;119;119	Q49A26-3;Q49A26-2;Q49A26	.;.;GLYR1_HUMAN	K	119	ENSP00000322716:R119K;ENSP00000371413:R119K	ENSP00000322716:R119K	R	-	2	0	GLYR1	4822162	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.203000	0.42752	2.634000	0.89283	0.650000	0.86243	AGG	.	.	none		0.433	GLYR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251717.2	NM_032569	
MUC4	4585	hgsc.bcm.edu	37	3	195513521	195513521	+	Missense_Mutation	SNP	C	C	G	rs111334497	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195513521C>G	ENST00000463781.3	-	2	5389	c.4930G>C	c.(4930-4932)Ggt>Cgt	p.G1644R	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.G1644R|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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.N1637_T1652delNASSLSTGHATPLHVT(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)		GTGGCGTGACCTGTGGATAAT	0.577																																					p.G1644R		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+2,1	MUC4	1505	1	2	Deletion - In frame(2)	stomach(2)	c.G4930C						scavenged	.						31.0	38.0	36.0					3																	195513521		690	1580	2270	SO:0001583	missense	4585	exon2			CGTGACCTGTGGA	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.4930G>C	3.37:g.195513521C>G	ENSP00000417498:p.Gly1644Arg	Somatic	1183	11	0.00929839		WXS	Illumina HiSeq	Phase_I	1145	14	0.0122271	NM_018406	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	.	.	.	.	.	.	.	.	.	.	-	4.040	0.005027	0.07866	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.5	0.423	-0.846	0.10734	.	.	.	.	.	T	0.26955	0.0660	N	0.19112	0.55	0.09310	N	1	D	0.59357	0.985	P	0.58013	0.831	T	0.14172	-1.0482	8	.	.	.	.	4.1233	0.10116	0.651:0.3489:1.0E-4:0.0	.	1644	E7ESK3	.	R	1644	ENSP00000417498:G1644R;ENSP00000420243:G1644R	.	G	-	1	0	MUC4	196997916	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	-0.948000	0.03897	-0.784000	0.04528	0.089000	0.15464	GGT	C|0.995;G|0.005	0.005	strong		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NRG3	10718	hgsc.bcm.edu	37	10	84498369	84498369	+	Silent	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:84498369A>G	ENST00000404547.1	+	3	990	c.990A>G	c.(988-990)caA>caG	p.Q330Q	NRG3_ENST00000556918.1_Silent_p.Q160Q|NRG3_ENST00000372141.2_Silent_p.Q330Q|NRG3_ENST00000372142.2_Silent_p.Q109Q|NRG3_ENST00000404576.2_Silent_p.Q134Q			P56975	NRG3_HUMAN	neuregulin 3	330					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|intracellular signal transduction (GO:0035556)|mammary placode formation (GO:0060596)|pattern specification process (GO:0007389)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	growth factor activity (GO:0008083)|receptor tyrosine kinase binding (GO:0030971)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(41)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	69				GBM - Glioblastoma multiforme(1;2.5e-18)|all cancers(1;2.85e-09)		GTTGTGATCAATTTCTGCCGA	0.398																																					p.Q330Q		Atlas-SNP	.											.	NRG3	301	.	0			c.A990G						PASS	.						161.0	142.0	149.0					10																	84498369		2203	4300	6503	SO:0001819	synonymous_variant	10718	exon3			TGATCAATTTCTG	AK098823	CCDS31233.1, CCDS53547.1	10q22-q23	2003-09-09			ENSG00000185737	ENSG00000185737			7999	protein-coding gene	gene with protein product		605533				9275162	Standard	NM_001010848		Approved		uc001kco.2	P56975	OTTHUMG00000018626	ENST00000404547.1:c.990A>G	10.37:g.84498369A>G		Somatic	191	0	0		WXS	Illumina HiSeq	Phase_I	213	40	0.187793	NM_001165972	A4D7U1|Q0PEH2|Q5VYH3	Silent	SNP	ENST00000404547.1	37	CCDS31233.1																																																																																			.	.	none		0.398	NRG3-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412262.1	XM_166086	
SEL1L3	23231	hgsc.bcm.edu	37	4	25783964	25783964	+	Missense_Mutation	SNP	T	T	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:25783964T>A	ENST00000399878.3	-	15	2479	c.2357A>T	c.(2356-2358)tAc>tTc	p.Y786F	SEL1L3_ENST00000502949.1_Missense_Mutation_p.Y633F|SEL1L3_ENST00000264868.5_Missense_Mutation_p.Y751F	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	786						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						TTTTAACCAGTACTTTGCTGC	0.433																																					p.Y786F		Atlas-SNP	.											SEL1L3,NS,carcinoma,+1,2	SEL1L3	62	2	0			c.A2357T						scavenged	.						207.0	190.0	195.0					4																	25783964		1870	4113	5983	SO:0001583	missense	23231	exon15			AACCAGTACTTTG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.2357A>T	4.37:g.25783964T>A	ENSP00000382767:p.Tyr786Phe	Somatic	184	1	0.00543478		WXS	Illumina HiSeq	Phase_I	175	45	0.257143	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	37	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	T	22.6	4.316857	0.81469	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.55930	0.49;0.49;0.49	5.66	5.66	0.87406	Tetratricopeptide-like helical (1);	0.414434	0.25291	N	0.031738	T	0.60573	0.2279	L	0.27053	0.805	0.43103	D	0.99479	P;D	0.67145	0.924;0.996	P;D	0.67725	0.652;0.953	T	0.65274	-0.6208	10	0.72032	D	0.01	-18.4383	15.9017	0.79384	0.0:0.0:0.0:1.0	.	193;786	B4DTH5;Q68CR1	.;SE1L3_HUMAN	F	786;751;633	ENSP00000382767:Y786F;ENSP00000264868:Y751F;ENSP00000425438:Y633F	ENSP00000264868:Y751F	Y	-	2	0	SEL1L3	25393062	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.721000	0.61951	2.153000	0.67306	0.460000	0.39030	TAC	.	.	none		0.433	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
ARHGAP31	57514	hgsc.bcm.edu	37	3	119109676	119109676	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:119109676C>A	ENST00000264245.4	+	7	1259	c.727C>A	c.(727-729)Ctg>Atg	p.L243M		NM_020754.2	NP_065805.2	Q2M1Z3	RHG31_HUMAN	Rho GTPase activating protein 31	243					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(3)|large_intestine(11)|lung(29)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	67						AGCCCTCTCCCTGCCCATGAA	0.577																																					p.L243M	Pancreas(7;176 297 5394 51128 51241)	Atlas-SNP	.											ARHGAP31,NS,carcinoma,-2,1	ARHGAP31	175	1	0			c.C727A						scavenged	.						61.0	66.0	64.0					3																	119109676		1982	4156	6138	SO:0001583	missense	57514	exon7			CTCTCCCTGCCCA		CCDS43135.1	3q13.33	2011-06-29			ENSG00000031081	ENSG00000031081		"""Rho GTPase activating proteins"""	29216	protein-coding gene	gene with protein product		610911				9786927, 12819203, 16519628	Standard	NM_020754		Approved	CDGAP	uc003ecj.4	Q2M1Z3	OTTHUMG00000159362	ENST00000264245.4:c.727C>A	3.37:g.119109676C>A	ENSP00000264245:p.Leu243Met	Somatic	94	0	0		WXS	Illumina HiSeq	Phase_I	85	3	0.0352941	NM_020754	Q9ULL6	Missense_Mutation	SNP	ENST00000264245.4	37	CCDS43135.1	.	.	.	.	.	.	.	.	.	.	C	17.19	3.327434	0.60743	.	.	ENSG00000031081	ENST00000264245;ENST00000543280	T	0.07567	3.18	4.99	2.24	0.28232	.	0.134298	0.33895	N	0.004445	T	0.11153	0.0272	L	0.40543	1.245	0.34273	D	0.681191	P	0.43412	0.806	P	0.48901	0.594	T	0.14282	-1.0478	10	0.56958	D	0.05	.	9.2111	0.37320	0.0:0.7648:0.0:0.2352	.	243	Q2M1Z3	RHG31_HUMAN	M	243	ENSP00000264245:L243M	ENSP00000264245:L243M	L	+	1	2	ARHGAP31	120592366	0.970000	0.33590	1.000000	0.80357	0.989000	0.77384	0.827000	0.27421	0.302000	0.22762	-0.350000	0.07774	CTG	.	.	none		0.577	ARHGAP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354942.2		
SOCS3	9021	hgsc.bcm.edu	37	17	76354959	76354959	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:76354959C>T	ENST00000330871.2	-	2	633	c.218G>A	c.(217-219)aGc>aAc	p.S73N	RP11-806H10.4_ENST00000592569.1_lincRNA	NM_003955.3	NP_003946.3	O14543	SOCS3_HUMAN	suppressor of cytokine signaling 3	73	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				branching involved in labyrinthine layer morphogenesis (GO:0060670)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of protein kinase activity (GO:0006469)|placenta blood vessel development (GO:0060674)|positive regulation of cell differentiation (GO:0045597)|protein ubiquitination (GO:0016567)|regulation of growth (GO:0040008)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|spongiotrophoblast differentiation (GO:0060708)|trophoblast giant cell differentiation (GO:0060707)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)	protein kinase inhibitor activity (GO:0004860)			kidney(1)|lung(2)|ovary(1)|pancreas(1)|skin(1)	6			BRCA - Breast invasive adenocarcinoma(99;0.000688)|OV - Ovarian serous cystadenocarcinoma(97;0.0554)			CTGGTCCGAGCTGTCGCGGAT	0.647																																					p.S73N		Atlas-SNP	.											.	SOCS3	16	.	0			c.G218A						PASS	.						31.0	28.0	29.0					17																	76354959		2203	4300	6503	SO:0001583	missense	9021	exon2			TCCGAGCTGTCGC	AB004904	CCDS11756.1	17q25.3	2014-09-17						"""Suppressors of cytokine signaling"", ""SH2 domain containing"""	19391	protein-coding gene	gene with protein product		604176				9266833, 9344848	Standard	NM_003955		Approved	SSI-3, CIS3, SOCS-3, Cish3	uc002jvl.2	O14543		ENST00000330871.2:c.218G>A	17.37:g.76354959C>T	ENSP00000330341:p.Ser73Asn	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	84	20	0.238095	NM_003955	O14509	Missense_Mutation	SNP	ENST00000330871.2	37	CCDS11756.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.046512	0.75846	.	.	ENSG00000184557	ENST00000330871	D	0.95069	-3.6	4.13	4.13	0.48395	SH2 motif (4);	0.200591	0.51477	D	0.000091	D	0.98140	0.9386	H	0.96208	3.785	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	D	0.99847	1.1067	10	0.87932	D	0	-16.133	16.3864	0.83505	0.0:1.0:0.0:0.0	.	73	O14543	SOCS3_HUMAN	N	73	ENSP00000330341:S73N	ENSP00000330341:S73N	S	-	2	0	SOCS3	73866554	1.000000	0.71417	1.000000	0.80357	0.629000	0.37895	3.837000	0.55820	1.845000	0.53610	0.313000	0.20887	AGC	.	.	none		0.647	SOCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437300.1		
VCAN	1462	hgsc.bcm.edu	37	5	82816658	82816658	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:82816658A>C	ENST00000265077.3	+	7	3098	c.2533A>C	c.(2533-2535)Agt>Cgt	p.S845R	VCAN_ENST00000512590.2_Missense_Mutation_p.S797R|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.S845R|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	845	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	AGACATCCCAAGTTTCACTGA	0.428																																					p.S845R		Atlas-SNP	.											.	VCAN	498	.	0			c.A2533C						PASS	.						105.0	105.0	105.0					5																	82816658		2203	4300	6503	SO:0001583	missense	1462	exon7			ATCCCAAGTTTCA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2533A>C	5.37:g.82816658A>C	ENSP00000265077:p.Ser845Arg	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	84	22	0.261905	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	A	2.468	-0.322533	0.05350	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.24538	1.85;1.85;1.85	5.76	-2.5	0.06384	.	0.320753	0.31589	N	0.007394	T	0.17023	0.0409	L	0.48362	1.52	0.20926	N	0.999821	B;B	0.12630	0.005;0.006	B;B	0.12156	0.007;0.006	T	0.15037	-1.0451	10	0.44086	T	0.13	.	6.2271	0.20714	0.4327:0.1508:0.4164:0.0	.	845;845	P13611-3;P13611	.;CSPG2_HUMAN	R	845;845;797	ENSP00000265077:S845R;ENSP00000342768:S845R;ENSP00000425959:S797R	ENSP00000265077:S845R	S	+	1	0	VCAN	82852414	0.073000	0.21202	0.880000	0.34516	0.109000	0.19521	0.804000	0.27098	-0.051000	0.13334	0.528000	0.53228	AGT	.	.	none		0.428	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
HDDC2	51020	hgsc.bcm.edu	37	6	125621684	125621684	+	Splice_Site	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:125621684C>T	ENST00000398153.2	-	2	248	c.206G>A	c.(205-207)cGa>cAa	p.R69Q	HDDC2_ENST00000608284.1_Splice_Site_p.R69Q|HDDC2_ENST00000368377.4_Splice_Site_p.R69Q|HDDC2_ENST00000608295.1_Splice_Site_p.R69Q	NM_016063.2	NP_057147.2	Q7Z4H3	HDDC2_HUMAN	HD domain containing 2	69	HD.			R -> P (in Ref. 2; AAD34125). {ECO:0000305}.		extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(4)	6			LUSC - Lung squamous cell carcinoma(4;0.0263)|Lung(4;0.0828)	GBM - Glioblastoma multiforme(226;0.0186)		CTCAGCTTACCGGTCTTTGTT	0.468																																					p.R69Q		Atlas-SNP	.											.	HDDC2	21	.	0			c.G206A						PASS	.						87.0	93.0	91.0					6																	125621684		1978	4164	6142	SO:0001630	splice_region_variant	51020	exon2			GCTTACCGGTCTT	AF151888	CCDS43503.1	6q13-q24.3	2008-02-05	2005-08-22	2005-08-22	ENSG00000111906	ENSG00000111906			21078	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 74"""	C6orf74		10810093	Standard	NM_016063		Approved	CGI-130, dJ167O5.2	uc003qaa.1	Q7Z4H3	OTTHUMG00000015506	ENST00000398153.2:c.206+1G>A	6.37:g.125621684C>T		Somatic	193	0	0		WXS	Illumina HiSeq	Phase_I	186	40	0.215054	NM_016063	Q5TDQ4|Q6NZ49|Q9BTT2|Q9BV31|Q9Y3D1	Missense_Mutation	SNP	ENST00000398153.2	37	CCDS43503.1	.	.	.	.	.	.	.	.	.	.	C	23.3	4.402058	0.83120	.	.	ENSG00000111906	ENST00000318787;ENST00000398153;ENST00000368377	T;T;T	0.53857	1.01;0.6;1.01	5.53	5.53	0.82687	Metal-dependent phosphohydrolase, HD domain (1);Metal-dependent phosphohydrolase, HD subdomain (1);HD domain (1);	0.045026	0.85682	D	0.000000	T	0.63640	0.2528	M	0.87682	2.9	0.42936	D	0.994335	D	0.62365	0.991	P	0.56612	0.802	T	0.63659	-0.6587	10	0.19147	T	0.46	.	18.2254	0.89915	0.0:1.0:0.0:0.0	.	69	Q7Z4H3	HDDC2_HUMAN	Q	69	ENSP00000316242:R69Q;ENSP00000381220:R69Q;ENSP00000357361:R69Q	ENSP00000316242:R69Q	R	-	2	0	HDDC2	125663383	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	5.636000	0.67848	2.593000	0.87608	0.655000	0.94253	CGG;CGA;CGA	.	.	none		0.468	HDDC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472493.1	NM_016063	Missense_Mutation
MPZL1	9019	hgsc.bcm.edu	37	1	167741720	167741720	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:167741720A>G	ENST00000359523.2	+	3	669	c.467A>G	c.(466-468)gAa>gGa	p.E156G	MPZL1_ENST00000392121.3_Intron|MPZL1_ENST00000474859.1_Missense_Mutation_p.E156G	NM_003953.5|NM_024569.4	NP_003944.1|NP_078845.3	O95297	MPZL1_HUMAN	myelin protein zero-like 1	156					cell-cell signaling (GO:0007267)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)	structural molecule activity (GO:0005198)			breast(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(2)	15	all_hematologic(923;0.215)					TATGTCGTAGAAAAAGGTACT	0.408																																					p.E156G		Atlas-SNP	.											.	MPZL1	25	.	0			c.A467G						PASS	.						83.0	74.0	77.0					1																	167741720		2203	4300	6503	SO:0001583	missense	9019	exon3			TCGTAGAAAAAGG	AF087020	CCDS1264.1, CCDS44273.1, CCDS53425.1	1q24.2	2013-01-11			ENSG00000197965	ENSG00000197965		"""Immunoglobulin superfamily / V-set domain containing"""	7226	protein-coding gene	gene with protein product		604376				9792637	Standard	NM_003953		Approved	PZR, FLJ21047	uc001geo.3	O95297	OTTHUMG00000034571	ENST00000359523.2:c.467A>G	1.37:g.167741720A>G	ENSP00000352513:p.Glu156Gly	Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	186	30	0.16129	NM_024569	B2REB9|B2REC0|Q5R332|Q8IX11|Q9BWZ3|Q9NYK4|Q9UL20	Missense_Mutation	SNP	ENST00000359523.2	37	CCDS1264.1	.	.	.	.	.	.	.	.	.	.	A	19.55	3.848702	0.71603	.	.	ENSG00000197965	ENST00000359523;ENST00000474859;ENST00000367853	D;D;D	0.97850	-4.15;-4.57;-4.55	4.81	4.81	0.61882	.	0.224105	0.45867	D	0.000339	D	0.95236	0.8455	L	0.32530	0.975	0.35992	D	0.836794	D;P	0.53462	0.96;0.651	P;B	0.51229	0.663;0.273	D	0.94779	0.7952	9	0.34782	T	0.22	.	15.0743	0.72066	1.0:0.0:0.0:0.0	.	156;156	O95297-3;O95297	.;MPZL1_HUMAN	G	156;156;130	ENSP00000352513:E156G;ENSP00000420455:E156G;ENSP00000356827:E130G	ENSP00000352513:E156G	E	+	2	0	MPZL1	166008344	1.000000	0.71417	0.995000	0.50966	0.910000	0.53928	2.674000	0.46867	2.116000	0.64780	0.455000	0.32223	GAA	.	.	none		0.408	MPZL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083655.2	NM_024569	
NOX4	50507	hgsc.bcm.edu	37	11	89182653	89182653	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:89182653T>C	ENST00000263317.4	-	4	542	c.304A>G	c.(304-306)Aga>Gga	p.R102G	NOX4_ENST00000527626.1_Intron|NOX4_ENST00000424319.1_Missense_Mutation_p.R78G|NOX4_ENST00000343727.5_Missense_Mutation_p.R78G|NOX4_ENST00000413594.2_Missense_Mutation_p.R123G|NOX4_ENST00000525196.1_Missense_Mutation_p.R102G|NOX4_ENST00000375979.3_Intron|NOX4_ENST00000532825.1_Missense_Mutation_p.R78G|NOX4_ENST00000542487.1_Missense_Mutation_p.R78G|NOX4_ENST00000527956.1_Missense_Mutation_p.R78G|NOX4_ENST00000531342.1_Intron|NOX4_ENST00000535633.1_Missense_Mutation_p.R78G|NOX4_ENST00000528341.1_Missense_Mutation_p.R77G|NOX4_ENST00000534731.1_Missense_Mutation_p.R102G			Q9NPH5	NOX4_HUMAN	NADPH oxidase 4	102	Ferric oxidoreductase.				bone resorption (GO:0045453)|cardiac muscle cell differentiation (GO:0055007)|cell aging (GO:0007569)|cell morphogenesis (GO:0000902)|cellular response to cAMP (GO:0071320)|cellular response to gamma radiation (GO:0071480)|cellular response to glucose stimulus (GO:0071333)|cellular response to transforming growth factor beta stimulus (GO:0071560)|homocysteine metabolic process (GO:0050667)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|oxidation-reduction process (GO:0055114)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of smooth muscle cell migration (GO:0014911)|positive regulation of stress fiber assembly (GO:0051496)|reactive oxygen species metabolic process (GO:0072593)|response to hypoxia (GO:0001666)|superoxide anion generation (GO:0042554)	apical plasma membrane (GO:0016324)|endoplasmic reticulum (GO:0005783)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|NADPH oxidase complex (GO:0043020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|modified amino acid binding (GO:0072341)|NAD(P)H oxidase activity (GO:0016174)|nucleotide binding (GO:0000166)|oxygen sensor activity (GO:0019826)|superoxide-generating NADPH oxidase activity (GO:0016175)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(20)|ovary(2)|prostate(3)|skin(2)	44		Acute lymphoblastic leukemia(157;2.26e-05)|all_hematologic(158;0.011)				TGGAATGTTCTGCTTTTATCC	0.299																																					p.R102G		Atlas-SNP	.											.	NOX4	101	.	0			c.A304G						PASS	.						88.0	85.0	86.0					11																	89182653		2201	4295	6496	SO:0001583	missense	50507	exon4			ATGTTCTGCTTTT	AF254621	CCDS8285.1, CCDS44695.1, CCDS44696.1, CCDS73361.1, CCDS73362.1	11q14.2-q21	2008-02-05			ENSG00000086991	ENSG00000086991			7891	protein-coding gene	gene with protein product		605261					Standard	NM_001143837		Approved	KOX-1, KOX	uc001pct.3	Q9NPH5	OTTHUMG00000167298	ENST00000263317.4:c.304A>G	11.37:g.89182653T>C	ENSP00000263317:p.Arg102Gly	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	120	28	0.233333	NM_001143836	A8K715|B7Z520|E7EMD7|Q5K3R4|Q5K3R5|Q5K3R6|Q5K3R8|Q7Z7G3|Q86V92	Missense_Mutation	SNP	ENST00000263317.4	37	CCDS8285.1	.	.	.	.	.	.	.	.	.	.	T	14.99	2.701251	0.48307	.	.	ENSG00000086991	ENST00000424319;ENST00000535633;ENST00000343727;ENST00000534731;ENST00000525196;ENST00000263317;ENST00000532825;ENST00000527956;ENST00000542487;ENST00000528341;ENST00000413594	D;D;D;D;D;D;D;D;D;D;D	0.90955	-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76;-2.76	5.42	4.22	0.49857	Flavoprotein transmembrane component (1);	0.105540	0.64402	D	0.000010	D	0.88321	0.6405	L	0.47716	1.5	0.29673	N	0.842284	B;P;B;B;B	0.43287	0.154;0.802;0.049;0.077;0.154	B;P;B;B;B	0.45577	0.102;0.486;0.025;0.259;0.175	D	0.84793	0.0780	9	.	.	.	-8.7869	11.2298	0.48905	0.0:0.0:0.1532:0.8468	.	78;77;102;102;102	E9PMY6;E9PPP2;E9PI95;Q9NPH5-6;Q9NPH5	.;.;.;.;NOX4_HUMAN	G	78;78;78;102;102;102;78;78;78;77;123	ENSP00000412446:R78G;ENSP00000440172:R78G;ENSP00000344747:R78G;ENSP00000436892:R102G;ENSP00000436716:R102G;ENSP00000263317:R102G;ENSP00000434924:R78G;ENSP00000433797:R78G;ENSP00000439373:R78G;ENSP00000436970:R77G;ENSP00000405705:R123G	.	R	-	1	2	NOX4	88822301	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.714000	0.47202	2.043000	0.60533	0.533000	0.62120	AGA	.	.	none		0.299	NOX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394054.1	NM_016931	
KIF16B	55614	hgsc.bcm.edu	37	20	16348090	16348090	+	Intron	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:16348090G>A	ENST00000354981.2	-	22	3656				KIF16B_ENST00000355755.3_Intron|KIF16B_ENST00000378003.2_Intron|KIF16B_ENST00000408042.1_Missense_Mutation_p.P1294S	NM_001199865.1|NM_024704.4	NP_001186794.1|NP_078980.3	Q96L93	KI16B_HUMAN	kinesin family member 16B						ATP catabolic process (GO:0006200)|early endosome to late endosome transport (GO:0045022)|endoderm development (GO:0007492)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|formation of primary germ layer (GO:0001704)|Golgi to endosome transport (GO:0006895)|microtubule-based movement (GO:0007018)|receptor catabolic process (GO:0032801)|regulation of receptor recycling (GO:0001919)	early endosome (GO:0005769)|endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|plus-end-directed microtubule motor activity (GO:0008574)			NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(24)|ovary(1)|prostate(15)|skin(3)|upper_aerodigestive_tract(2)	74						GCACCCGGAGGAGGTATGTTT	0.438																																					p.P1294S		Atlas-SNP	.											.	KIF16B	305	.	0			c.C3880T						PASS	.						226.0	208.0	214.0					20																	16348090		876	1991	2867	SO:0001627	intron_variant	55614	exon23			CCGGAGGAGGTAT	AK000142	CCDS13122.1, CCDS56178.1	20p11.23	2008-03-03	2008-03-03	2008-03-03	ENSG00000089177	ENSG00000089177		"""Kinesins"""	15869	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 23"""	C20orf23		16084724, 16782399	Standard	NM_024704		Approved	FLJ20135, dJ971B4.1, SNX23	uc010gci.2	Q96L93	OTTHUMG00000031927	ENST00000354981.2:c.3498+3140C>T	20.37:g.16348090G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	188	25	0.132979	NM_001199866	A6NKJ9|A7E2A8|B1AKG3|B1AKT7|C9JDN5|C9JI52|C9JSM8|C9JWJ7|Q2TBF5|Q5HYC0|Q5HYK1|Q5JWW3|Q5TFK5|Q86VL9|Q86YS5|Q8IYU0|Q9BQJ8|Q9BQM0|Q9BQM1|Q9BQM5|Q9H5U0|Q9HCI2|Q9NXN9	Missense_Mutation	SNP	ENST00000354981.2	37	CCDS13122.1	.	.	.	.	.	.	.	.	.	.	G	13.00	2.106630	0.37145	.	.	ENSG00000089177	ENST00000408042	T	0.70516	-0.49	5.62	3.43	0.39272	.	0.835806	0.10985	N	0.612294	T	0.56485	0.1988	.	.	.	0.09310	N	0.999999	B	0.17667	0.023	B	0.14578	0.011	T	0.49615	-0.8921	9	0.54805	T	0.06	.	3.8299	0.08870	0.3117:0.0:0.5246:0.1636	.	1294	Q96L93-2	.	S	1294	ENSP00000384164:P1294S	ENSP00000384164:P1294S	P	-	1	0	KIF16B	16296090	0.044000	0.20184	0.004000	0.12327	0.647000	0.38526	1.008000	0.29872	0.540000	0.28808	0.544000	0.68410	CCT	.	.	none		0.438	KIF16B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078104.2	NM_017683	
KBTBD6	89890	hgsc.bcm.edu	37	13	41705897	41705897	+	Missense_Mutation	SNP	G	G	C	rs150633583	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:41705897G>C	ENST00000379485.1	-	1	985	c.751C>G	c.(751-753)Ccc>Gcc	p.P251A	KBTBD6_ENST00000499385.2_Missense_Mutation_p.P185A	NM_152903.4	NP_690867.3	Q86V97	KBTB6_HUMAN	kelch repeat and BTB (POZ) domain containing 6	251								p.P251A(1)		NS(1)|breast(1)|endometrium(8)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|skin(4)|urinary_tract(4)	43		Lung NSC(96;4.52e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;4.08e-09)|Epithelial(112;4.74e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000131)|GBM - Glioblastoma multiforme(144;0.000876)|BRCA - Breast invasive adenocarcinoma(63;0.0673)		CGCTCTTTGGGAGCAGCCTCC	0.587													G|||	4	0.000798722	0.003	0.0	5008	,	,		19033	0.0		0.0	False		,,,				2504	0.0				p.P251A		Atlas-SNP	.											KBTBD6,trunk,malignant_melanoma,0,2	KBTBD6	83	2	1	Substitution - Missense(1)	skin(1)	c.C751G						scavenged	.	G	ALA/PRO	14,4392	19.1+/-41.9	0,14,2189	64.0	65.0	65.0		751	3.7	1.0	13	dbSNP_134	65	0,8600		0,0,4300	yes	missense	KBTBD6	NM_152903.4	27	0,14,6489	CC,CG,GG		0.0,0.3177,0.1076	benign	251/675	41705897	14,12992	2203	4300	6503	SO:0001583	missense	89890	exon1			CTTTGGGAGCAGC	AK056633	CCDS9376.1	13q13.3	2013-01-08			ENSG00000165572	ENSG00000165572		"""BTB/POZ domain containing"""	25340	protein-coding gene	gene with protein product						12477932	Standard	NM_152903		Approved	DKFZp547E1912	uc001uxu.1	Q86V97	OTTHUMG00000016786	ENST00000379485.1:c.751C>G	13.37:g.41705897G>C	ENSP00000368799:p.Pro251Ala	Somatic	320	1	0.003125		WXS	Illumina HiSeq	Phase_I	395	4	0.0101266	NM_152903	Q5T6Y8|Q8N8L0|Q8NDM5|Q96MP6	Missense_Mutation	SNP	ENST00000379485.1	37	CCDS9376.1	.	.	.	.	.	.	.	.	.	.	g	3.422	-0.117976	0.06838	0.003177	0.0	ENSG00000165572	ENST00000379485;ENST00000499385	T;T	0.67523	-0.27;-0.27	3.68	3.68	0.42216	BTB/Kelch-associated (2);	0.074945	0.53938	D	0.000048	T	0.51193	0.1660	L	0.31926	0.97	0.38217	D	0.940638	B;B	0.10296	0.003;0.001	B;B	0.15052	0.012;0.006	T	0.48328	-0.9045	10	0.08837	T	0.75	.	13.263	0.60117	0.0:0.0:1.0:0.0	.	185;251	F5GZN7;Q86V97	.;KBTB6_HUMAN	A	251;185	ENSP00000368799:P251A;ENSP00000444326:P185A	ENSP00000368799:P251A	P	-	1	0	KBTBD6	40603897	0.817000	0.29147	0.996000	0.52242	0.966000	0.64601	1.519000	0.35888	2.060000	0.61445	0.455000	0.32223	CCC	G|0.998;C|0.002	0.002	strong		0.587	KBTBD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044657.1	NM_152903	
EPS8L1	54869	hgsc.bcm.edu	37	19	55598724	55598724	+	Missense_Mutation	SNP	A	A	G	rs1054940	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:55598724A>G	ENST00000201647.6	+	19	2062	c.2006A>G	c.(2005-2007)aAg>aGg	p.K669R	EPS8L1_ENST00000586329.1_Intron|EPS8L1_ENST00000588359.1_Missense_Mutation_p.K355R|EPS8L1_ENST00000540810.1_Missense_Mutation_p.K605R|EPS8L1_ENST00000245618.5_Missense_Mutation_p.K542R	NM_133180.2	NP_573441.2	Q8TE68	ES8L1_HUMAN	EPS8-like 1	669			K -> R (in dbSNP:rs1054940). {ECO:0000269|PubMed:12620401, ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:15498874}.		positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of ruffle assembly (GO:1900029)|regulation of Rho protein signal transduction (GO:0035023)|Rho protein signal transduction (GO:0007266)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|T cell receptor binding (GO:0042608)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(3)|ovary(1)|prostate(1)	12			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.044)		TCGCTGCAGAAGGAGGAGCTG	0.731													A|||	2342	0.467652	0.3419	0.4597	5008	,	,		13706	0.4514		0.506	False		,,,				2504	0.6207				p.K669R	Ovarian(149;255 1863 3636 27051 29647)	Atlas-SNP	.											EPS8L1_ENST00000245618,NS,carcinoma,0,2	EPS8L1	122	2	0			c.A2006G						scavenged	.	A	ARG/LYS,ARG/LYS	1592,2812		310,972,920	26.0	28.0	27.0		1625,2006	4.0	1.0	19	dbSNP_86	27	4241,4353		1078,2085,1134	yes	missense,missense	EPS8L1	NM_017729.3,NM_133180.2	26,26	1388,3057,2054	GG,GA,AA		49.3484,36.149,44.8761	probably-damaging,probably-damaging	542/597,669/724	55598724	5833,7165	2202	4297	6499	SO:0001583	missense	54869	exon19			TGCAGAAGGAGGA	AK057052	CCDS12914.1, CCDS12915.1	19q13.42	2008-02-05				ENSG00000131037			21295	protein-coding gene	gene with protein product		614987				12620401	Standard	NM_133180		Approved	FLJ20258, DRC3, MGC23164, MGC4642	uc002qis.4	Q8TE68		ENST00000201647.6:c.2006A>G	19.37:g.55598724A>G	ENSP00000201647:p.Lys669Arg	Somatic	7	1	0.142857		WXS	Illumina HiSeq	Phase_I	4	3	0.75	NM_133180	Q71RE2|Q8NC10|Q96BB7|Q9BSQ2|Q9GZQ2|Q9NXH0	Missense_Mutation	SNP	ENST00000201647.6	37	CCDS12914.1	983	0.4500915750915751	171	0.3475609756097561	170	0.4696132596685083	260	0.45454545454545453	382	0.503957783641161	A	27.8	4.868341	0.91587	0.36149	0.493484	ENSG00000131037	ENST00000201647;ENST00000540810;ENST00000245618;ENST00000539118	T;T;T	0.25250	1.81;1.81;1.81	4.02	4.02	0.46733	.	0.121108	0.53938	D	0.000057	T	0.00012	0.0000	L	0.54908	1.71	0.09310	P	0.99999486196	D;D;P	0.89917	1.0;0.991;0.863	D;D;P	0.87578	0.998;0.927;0.73	T	0.50440	-0.8828	9	0.34782	T	0.22	-35.624	11.4935	0.50394	1.0:0.0:0.0:0.0	rs1054940;rs3195458;rs58630253;rs1054940	448;542;669	Q8TE68-4;Q8TE68-2;Q8TE68	.;.;ES8L1_HUMAN	R	669;605;542;355	ENSP00000201647:K669R;ENSP00000437541:K605R;ENSP00000245618:K542R	ENSP00000201647:K669R	K	+	2	0	EPS8L1	60290536	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	5.360000	0.66086	1.768000	0.52137	0.260000	0.18958	AAG	A|0.559;G|0.441	0.441	strong		0.731	EPS8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451713.1	NM_017729	
ZSWIM8	23053	hgsc.bcm.edu	37	10	75558867	75558867	+	Silent	SNP	G	G	A	rs2271271	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:75558867G>A	ENST00000605216.1	+	21	4486	c.4269G>A	c.(4267-4269)ctG>ctA	p.L1423L	ZSWIM8_ENST00000604524.1_Intron|RP11-574K11.31_ENST00000603027.1_Intron|ZSWIM8_ENST00000603114.1_Silent_p.L1390L|ZSWIM8_ENST00000604729.1_Silent_p.L1428L|ZSWIM8_ENST00000398706.2_Silent_p.L1428L|ZSWIM8-AS1_ENST00000456638.2_RNA	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	1423							zinc ion binding (GO:0008270)	p.L1428L(1)									GGTTCTGGCTGTATGAGCAAA	0.587													A|||	2443	0.487819	0.4887	0.4755	5008	,	,		19612	0.2351		0.7575	False		,,,				2504	0.4785				p.L1428L		Atlas-SNP	.											KIAA0913_ENST00000398706,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	stomach(1)	c.G4284A						scavenged	.	A	,,	2251,1787		629,993,397	70.0	77.0	75.0		4269,4269,4284	-7.4	0.8	10	dbSNP_100	75	6280,2072		2374,1532,270	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA0913	NM_001242487.1,NM_001242488.1,NM_015037.3	,,	3003,2525,667	AA,AG,GG		24.8084,44.2546,31.1461	,,	1423/1838,1423/1893,1428/1843	75558867	8531,3859	2019	4176	6195	SO:0001819	synonymous_variant	23053	exon21			CTGGCTGTATGAG	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"""Zinc fingers, SWIM-type"""	23528	protein-coding gene	gene with protein product			"""KIAA0913"""	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.4269G>A	10.37:g.75558867G>A		Somatic	225	2	0.00888889		WXS	Illumina HiSeq	Phase_I	230	6	0.026087	NM_015037	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	37		1133|1133	0.5187728937728938|0.5187728937728938	242|242	0.491869918699187|0.491869918699187	199|199	0.5497237569060773|0.5497237569060773	134|134	0.23426573426573427|0.23426573426573427	558|558	0.7361477572559367|0.7361477572559367	A|A	6.766|6.766	0.510148|0.510148	0.12883|0.12883	0.557454|0.557454	0.751916|0.751916	ENSG00000214655|ENSG00000214655	ENST00000412198|ENST00000433366	.|.	.|.	.|.	5.59|5.59	-7.37|-7.37	0.01412|0.01412	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999095434|0.9999999999095434	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.26087|0.26087	-1.0113|-1.0113	3|3	.|.	.|.	.|.	-3.31|-3.31	7.2207|7.2207	0.25985|0.25985	0.1379:0.0839:0.5369:0.2413|0.1379:0.0839:0.5369:0.2413	rs2271271;rs58670385;rs2271271|rs2271271;rs58670385;rs2271271	.|.	.|.	.|.	Y|I	698|1139	.|.	.|.	C|V	+|+	2|1	0|0	KIAA0913|KIAA0913	75228873|75228873	0.217000|0.217000	0.23597|0.23597	0.814000|0.814000	0.32528|0.32528	0.981000|0.981000	0.71138|0.71138	-0.488000|-0.488000	0.06497|0.06497	-1.254000|-1.254000	0.02485|0.02485	-0.982000|-0.982000	0.02568|0.02568	TGT|GTA	G|0.465;A|0.535	0.535	strong		0.587	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487	
DUSP5	1847	hgsc.bcm.edu	37	10	112266771	112266771	+	Silent	SNP	C	C	T	rs1889567	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:112266771C>T	ENST00000369583.3	+	3	891	c.607C>T	c.(607-609)Ctg>Ttg	p.L203L	DUSP5_ENST00000468749.1_3'UTR	NM_004419.3	NP_004410.3	Q16690	DUS5_HUMAN	dual specificity phosphatase 5	203	Tyrosine-protein phosphatase.				endoderm formation (GO:0001706)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.L203L(1)		kidney(2)|large_intestine(3)|lung(5)|ovary(1)|upper_aerodigestive_tract(2)	13		Breast(234;0.0848)		Epithelial(162;0.000276)|all cancers(201;0.00465)|BRCA - Breast invasive adenocarcinoma(275;0.12)		CCTCGCCAACCTGCACATCAC	0.582													C|||	1420	0.283546	0.2753	0.2406	5008	,	,		19623	0.376		0.2853	False		,,,				2504	0.228				p.L203L		Atlas-SNP	.											DUSP5_ENST00000369583,NS,carcinoma,0,1	DUSP5	62	1	1	Substitution - coding silent(1)	stomach(1)	c.C607T						scavenged	.	C		1321,3085	444.7+/-347.4	211,899,1093	214.0	208.0	210.0		607	3.4	1.0	10	dbSNP_92	210	2757,5843	439.7+/-359.3	457,1843,2000	no	coding-synonymous	DUSP5	NM_004419.3		668,2742,3093	TT,TC,CC		32.0581,29.9818,31.3548		203/385	112266771	4078,8928	2203	4300	6503	SO:0001819	synonymous_variant	1847	exon3			GCCAACCTGCACA	U16996	CCDS7566.1	10q25	2011-06-09			ENSG00000138166	ENSG00000138166		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3071	protein-coding gene	gene with protein product		603069				7806236	Standard	NM_004419		Approved	HVH3	uc001kzd.3	Q16690	OTTHUMG00000019040	ENST00000369583.3:c.607C>T	10.37:g.112266771C>T		Somatic	235	1	0.00425532		WXS	Illumina HiSeq	Phase_I	271	4	0.0147601	NM_004419	Q12997|Q5T603	Silent	SNP	ENST00000369583.3	37	CCDS7566.1																																																																																			C|0.692;T|0.308	0.308	strong		0.582	DUSP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050333.1	NM_004419	
CLCA2	9635	hgsc.bcm.edu	37	1	86920904	86920904	+	Silent	SNP	A	A	G	rs2390057	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:86920904A>G	ENST00000370565.4	+	14	2688	c.2526A>G	c.(2524-2526)caA>caG	p.Q842Q		NM_006536.5	NP_006527.1	Q9UQC9	CLCA2_HUMAN	chloride channel accessory 2	842					cell adhesion (GO:0007155)|transport (GO:0006810)	cell junction (GO:0030054)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	chloride channel activity (GO:0005254)|ligand-gated ion channel activity (GO:0015276)	p.Q842Q(1)		NS(2)|breast(1)|endometrium(1)|kidney(3)|large_intestine(9)|lung(18)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|stomach(1)	42		Lung NSC(277;0.238)		all cancers(265;0.0233)|Epithelial(280;0.0452)		TCTCACCCCAAATTTCCACGA	0.393													A|||	1647	0.328874	0.2057	0.2435	5008	,	,		17291	0.4405		0.335	False		,,,				2504	0.4346				p.Q842Q	Melanoma(157;1000 1898 5363 5664 48018)|Ovarian(88;135 1366 2838 28875 34642)	Atlas-SNP	.											CLCA2,NS,carcinoma,0,1	CLCA2	102	1	1	Substitution - coding silent(1)	stomach(1)	c.A2526G						scavenged	.	A		1085,3321	393.5+/-328.9	142,801,1260	110.0	104.0	106.0		2526	-1.1	0.0	1	dbSNP_100	106	2876,5724	451.3+/-362.6	470,1936,1894	no	coding-synonymous	CLCA2	NM_006536.5		612,2737,3154	GG,GA,AA		33.4419,24.6255,30.4552		842/944	86920904	3961,9045	2203	4300	6503	SO:0001819	synonymous_variant	9635	exon14			ACCCCAAATTTCC		CCDS708.1	1p22.3	2012-02-26	2009-01-29		ENSG00000137975	ENSG00000137975			2016	protein-coding gene	gene with protein product		604003	"""chloride channel, calcium activated, family member 2"", ""chloride channel regulator 2"""				Standard	NM_006536		Approved	CLCRG2	uc001dlr.4	Q9UQC9	OTTHUMG00000010256	ENST00000370565.4:c.2526A>G	1.37:g.86920904A>G		Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	126	2	0.015873	NM_006536	A8K2T3|Q9Y6N2	Silent	SNP	ENST00000370565.4	37	CCDS708.1																																																																																			A|0.686;G|0.314	0.314	strong		0.393	CLCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028284.1	NM_006536	
CHTF18	63922	hgsc.bcm.edu	37	16	847932	847932	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:847932C>G	ENST00000262315.9	+	22	2948	c.2885C>G	c.(2884-2886)tCc>tGc	p.S962C	CHTF18_ENST00000317063.6_Missense_Mutation_p.S1171C|CHTF18_ENST00000455171.2_Missense_Mutation_p.S990C	NM_022092.2	NP_071375.1	Q8WVB6	CTF18_HUMAN	CTF18, chromosome transmission fidelity factor 18 homolog (S. cerevisiae)	962					cell cycle (GO:0007049)|DNA replication (GO:0006260)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			endometrium(1)|kidney(3)|liver(2)|lung(4)|prostate(1)	11		Hepatocellular(780;0.00335)				GAGGGTGTCTCCAACGCCGTG	0.657																																					p.S962C		Atlas-SNP	.											.	CHTF18	52	.	0			c.C2885G						PASS	.						33.0	40.0	38.0					16																	847932		2120	4231	6351	SO:0001583	missense	63922	exon22			GTGTCTCCAACGC	BC018184	CCDS45371.1	16p13.3	2010-04-21	2003-12-09		ENSG00000127586	ENSG00000127586		"""ATPases / AAA-type"""	18435	protein-coding gene	gene with protein product		613201	"""chromosome 16 open reading frame 41"""	C16orf41		12171929	Standard	NM_022092		Approved	CHL12, C321D2.4, Ctf18	uc002cke.4	Q8WVB6	OTTHUMG00000047838	ENST00000262315.9:c.2885C>G	16.37:g.847932C>G	ENSP00000262315:p.Ser962Cys	Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	81	7	0.0864198	NM_022092	B7ZBA2|D3DU68|Q7Z6Y4|Q7Z6Y6|Q9BR83|Q9BRG5|Q9H7K3	Missense_Mutation	SNP	ENST00000262315.9	37	CCDS45371.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.196489	0.58126	.	.	ENSG00000127586	ENST00000317063;ENST00000455171;ENST00000262315	T;T;T	0.22134	1.97;2.11;2.08	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.51890	0.1701	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.57711	-0.7764	10	0.87932	D	0	-42.161	17.6563	0.88179	0.0:1.0:0.0:0.0	.	990;962	Q8WVB6-2;Q8WVB6	.;CTF18_HUMAN	C	1171;990;962	ENSP00000313029:S1171C;ENSP00000406252:S990C;ENSP00000262315:S962C	ENSP00000262315:S962C	S	+	2	0	CHTF18	787933	1.000000	0.71417	0.996000	0.52242	0.334000	0.28698	7.419000	0.80179	2.529000	0.85273	0.561000	0.74099	TCC	.	.	none		0.657	CHTF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109061.3	NM_022092	
SLC18A1	6570	hgsc.bcm.edu	37	8	20031913	20031913	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:20031913C>T	ENST00000276373.5	-	5	856	c.590G>A	c.(589-591)cGa>cAa	p.R197Q	SLC18A1_ENST00000524272.1_5'UTR|SLC18A1_ENST00000265808.7_Missense_Mutation_p.R197Q|SLC18A1_ENST00000519026.1_Missense_Mutation_p.R197Q|SLC18A1_ENST00000437980.1_Missense_Mutation_p.R197Q|SLC18A1_ENST00000381608.4_Missense_Mutation_p.R197Q|SLC18A1_ENST00000440926.1_Missense_Mutation_p.R197Q	NM_003053.3	NP_003044.1	P54219	VMAT1_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 1	197					monoamine transport (GO:0015844)|neurotransmitter transport (GO:0006836)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	drug transmembrane transporter activity (GO:0015238)|monoamine transmembrane transporter activity (GO:0008504)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)	29				Colorectal(74;0.0747)	Ephedra(DB01363)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Reserpine(DB00206)	TTGAAGGGTTCGGGCCACAAA	0.468																																					p.R197Q		Atlas-SNP	.											SLC18A1,NS,carcinoma,-1,1	SLC18A1	68	1	0			c.G590A						PASS	.						159.0	137.0	145.0					8																	20031913		2203	4300	6503	SO:0001583	missense	6570	exon6			AGGGTTCGGGCCA		CCDS6013.1, CCDS47814.1, CCDS47815.1	8p21.3	2013-07-18	2013-07-18		ENSG00000036565	ENSG00000036565		"""Solute carriers"""	10934	protein-coding gene	gene with protein product		193002		VMAT1, VAT1			Standard	NM_003053		Approved	CGAT	uc003wzm.3	P54219	OTTHUMG00000097017	ENST00000276373.5:c.590G>A	8.37:g.20031913C>T	ENSP00000276373:p.Arg197Gln	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	139	24	0.172662	NM_001142324	E9PDJ5|Q9BRE4	Missense_Mutation	SNP	ENST00000276373.5	37	CCDS6013.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.107635	0.77096	.	.	ENSG00000036565	ENST00000265808;ENST00000276373;ENST00000440926;ENST00000437980;ENST00000519026;ENST00000381608	T;T;T;T;T;T	0.70164	-0.46;-0.46;-0.46;-0.46;-0.46;-0.46	5.6	4.73	0.59995	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.054237	0.85682	N	0.000000	D	0.85974	0.5822	H	0.94345	3.525	0.58432	D	0.999995	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.89609	0.3840	10	0.87932	D	0	-8.6207	13.4319	0.61059	0.0:0.9232:0.0:0.0768	.	197;197;197	E9PB33;E9PDJ5;P54219	.;.;VMAT1_HUMAN	Q	197	ENSP00000265808:R197Q;ENSP00000276373:R197Q;ENSP00000387549:R197Q;ENSP00000413361:R197Q;ENSP00000429664:R197Q;ENSP00000371021:R197Q	ENSP00000265808:R197Q	R	-	2	0	SLC18A1	20076193	0.965000	0.33210	0.695000	0.30226	0.332000	0.28634	5.733000	0.68571	1.487000	0.48415	0.655000	0.94253	CGA	.	.	none		0.468	SLC18A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214106.1		
NCAPD3	23310	hgsc.bcm.edu	37	11	134076494	134076494	+	Splice_Site	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:134076494C>T	ENST00000534548.2	-	8	1080	c.1016G>A	c.(1015-1017)aGc>aAc	p.S339N		NM_015261.2	NP_056076.1	P42695	CNDD3_HUMAN	non-SMC condensin II complex, subunit D3	339					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	germinal vesicle (GO:0042585)|membrane (GO:0016020)|nuclear condensin complex (GO:0000799)|nuclear pericentric heterochromatin (GO:0031618)|nucleoplasm (GO:0005654)	methylated histone binding (GO:0035064)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(10)|kidney(5)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_hematologic(175;0.127)	all_cancers(12;1.68e-21)|all_epithelial(12;5.86e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;8.74e-10)|BRCA - Breast invasive adenocarcinoma(10;1e-08)|all cancers(11;1.46e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00345)|Lung(977;0.227)		TGTGCTTCACCTGATAAACTG	0.453																																					p.S339N		Atlas-SNP	.											.	NCAPD3	141	.	0			c.G1016A						PASS	.						136.0	122.0	127.0					11																	134076494		2201	4297	6498	SO:0001630	splice_region_variant	23310	exon8			CTTCACCTGATAA	AK124878	CCDS31723.1	11q25	2008-02-04			ENSG00000151503	ENSG00000151503			28952	protein-coding gene	gene with protein product		609276				7584044, 8619474, 14532007	Standard	NM_015261		Approved	hCAP-D3, CAP-D3, hHCP-6, KIAA0056, FLJ42888, hcp-6	uc001qhd.1	P42695	OTTHUMG00000167172	ENST00000534548.2:c.1016+1G>A	11.37:g.134076494C>T		Somatic	259	0	0		WXS	Illumina HiSeq	Phase_I	284	63	0.221831	NM_015261	A6NFS2|Q4KMQ9	Missense_Mutation	SNP	ENST00000534548.2	37	CCDS31723.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.240992	0.79912	.	.	ENSG00000151503	ENST00000534548	T	0.08546	3.08	5.67	5.67	0.87782	Armadillo-type fold (1);	0.116016	0.85682	D	0.000000	T	0.18467	0.0443	M	0.66939	2.045	0.80722	D	1	P	0.48764	0.915	P	0.47251	0.542	T	0.00206	-1.1920	9	.	.	.	-11.7273	20.1313	0.98000	0.0:1.0:0.0:0.0	.	339	P42695	CNDD3_HUMAN	N	339	ENSP00000433681:S339N	.	S	-	2	0	NCAPD3	133581704	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	5.469000	0.66749	2.837000	0.97791	0.655000	0.94253	AGC	.	.	none		0.453	NCAPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393575.2	NM_015261	Missense_Mutation
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970772	45970772	+	Silent	SNP	A	A	G	rs76021731|rs67692969|rs71199610	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:45970772A>G	ENST00000391621.1	-	1	616	c.570T>C	c.(568-570)ccT>ccC	p.P190P	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	190	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						TGCAGCAGACAGGCTTGCAGC	0.607																																					p.P190P		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.T570C						PASS	.						111.0	112.0	112.0					21																	45970772		2192	4282	6474	SO:0001819	synonymous_variant	386679	exon1			GCAGACAGGCTTG	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.570T>C	21.37:g.45970772A>G		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	120	14	0.116667	NM_198693	Q70LJ5	Silent	SNP	ENST00000391621.1	37	CCDS42955.1																																																																																			A|0.908;G|0.092	0.092	strong		0.607	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
DPY19L2	283417	hgsc.bcm.edu	37	12	63954304	63954304	+	Silent	SNP	T	T	C	rs1054891	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:63954304T>C	ENST00000324472.4	-	22	2448	c.2265A>G	c.(2263-2265)ttA>ttG	p.L755L	DPY19L2_ENST00000413230.2_Silent_p.L202L	NM_173812.4	NP_776173.3	Q6NUT2	D19L2_HUMAN	dpy-19-like 2 (C. elegans)	755					multicellular organismal development (GO:0007275)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|nuclear inner membrane (GO:0005637)|nucleus (GO:0005634)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(19)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	45			GBM - Glioblastoma multiforme(1;2.77e-05)	GBM - Glioblastoma multiforme(28;0.044)		AGTTAACCTTTAATACTCTGT	0.418													N|||	2174	0.434105	0.7057	0.4568	5008	,	,		16369	0.2857		0.4245	False		,,,				2504	0.2137				p.L755L		Atlas-SNP	.											DPY19L2,colon,carcinoma,0,1	DPY19L2	97	1	0			c.A2265G						scavenged	.	C		2776,1630	500.0+/-364.6	884,1008,311	85.0	80.0	82.0		2265	-1.3	0.3	12	dbSNP_86	82	3491,5109	633.6+/-398.7	694,2103,1503	no	coding-synonymous	DPY19L2	NM_173812.4		1578,3111,1814	CC,CT,TT		40.593,36.995,48.1855		755/759	63954304	6267,6739	2203	4300	6503	SO:0001819	synonymous_variant	283417	exon22			AACCTTTAATACT		CCDS31851.1	12q14.2	2012-11-14			ENSG00000177990	ENSG00000177990			19414	protein-coding gene	gene with protein product	"""spermatogenesis associated 34"""	613893				12975309	Standard	XM_006719348		Approved	FLJ32949, SPATA34	uc001srp.1	Q6NUT2	OTTHUMG00000168712	ENST00000324472.4:c.2265A>G	12.37:g.63954304T>C		Somatic	216	2	0.00925926		WXS	Illumina HiSeq	Phase_I	222	3	0.0135135	NM_173812	A4FVC1|B4E191|Q3ZCX2|Q6UWG8|Q96LZ9	Silent	SNP	ENST00000324472.4	37	CCDS31851.1																																																																																			T|0.532;C|0.468	0.468	strong		0.418	DPY19L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400689.2	NM_173812	
DPY19L1	23333	hgsc.bcm.edu	37	7	35009120	35009120	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:35009120G>A	ENST00000310974.4	-	9	864	c.720C>T	c.(718-720)agC>agT	p.S240S	DPY19L1_ENST00000462134.2_5'UTR	NM_015283.1	NP_056098.1	Q2PZI1	D19L1_HUMAN	dpy-19-like 1 (C. elegans)	240						integral component of membrane (GO:0016021)|membrane (GO:0016020)	transferase activity, transferring glycosyl groups (GO:0016757)	p.S240S(2)		endometrium(3)|kidney(5)|large_intestine(8)|lung(8)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(4)	31						GTGCAATCAAGCTTCCTCTAT	0.358																																					p.S240S		Atlas-SNP	.											DPY19L1,NS,carcinoma,0,2	DPY19L1	56	2	2	Substitution - coding silent(2)	kidney(2)	c.C720T						scavenged	.						81.0	76.0	77.0					7																	35009120		1833	4097	5930	SO:0001819	synonymous_variant	23333	exon9			AATCAAGCTTCCT	AB020684	CCDS43567.1	7p14.3-p14.2	2006-04-26			ENSG00000173852	ENSG00000173852			22205	protein-coding gene	gene with protein product		613892					Standard	NM_015283		Approved	KIAA0877	uc003tem.4	Q2PZI1	OTTHUMG00000154888	ENST00000310974.4:c.720C>T	7.37:g.35009120G>A		Somatic	458	9	0.0196507		WXS	Illumina HiSeq	Phase_I	439	12	0.0273349	NM_015283	O94954|Q4G151	Silent	SNP	ENST00000310974.4	37	CCDS43567.1																																																																																			.	.	none		0.358	DPY19L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337506.1		
CYSRT1	375791	hgsc.bcm.edu	37	9	140120215	140120215	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:140120215G>A	ENST00000359069.2	+	2	192	c.142G>A	c.(142-144)Ggg>Agg	p.G48R	RNF224_ENST00000445101.2_5'Flank|C9orf169_ENST00000409414.1_Missense_Mutation_p.G88R	NM_199001.2	NP_945352.2	A8MQ03	CRTP1_HUMAN		48						extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)	1						CCTGCCAGTGGGGCCCTGTGC	0.677																																					p.G48R		Atlas-SNP	.											.	C9orf169	6	.	0			c.G142A						PASS	.						19.0	25.0	23.0					9																	140120215		692	1587	2279	SO:0001583	missense	375791	exon2			CCAGTGGGGCCCT																												ENST00000359069.2:c.142G>A	9.37:g.140120215G>A	ENSP00000351967:p.Gly48Arg	Somatic	69	0	0		WXS	Illumina HiSeq	Phase_I	56	13	0.232143	NM_199001	Q86UY7	Missense_Mutation	SNP	ENST00000359069.2	37	CCDS48064.1	.	.	.	.	.	.	.	.	.	.	G	10.06	1.246913	0.22796	.	.	ENSG00000197191	ENST00000409414;ENST00000359069	.	.	.	3.18	2.27	0.28462	.	.	.	.	.	T	0.34745	0.0908	N	0.19112	0.55	0.09310	N	1	D	0.63046	0.992	P	0.60415	0.874	T	0.10064	-1.0646	8	0.36615	T	0.2	.	5.8886	0.18896	0.1497:0.0:0.8503:0.0	.	48	A8MQ03	CI169_HUMAN	R	88;48	.	ENSP00000351967:G48R	G	+	1	0	C9orf169	139240036	0.008000	0.16893	0.001000	0.08648	0.107000	0.19398	1.496000	0.35638	0.550000	0.28991	0.462000	0.41574	GGG	.	.	none		0.677	C9orf169-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
AMICA1	120425	hgsc.bcm.edu	37	11	118085545	118085545	+	Silent	SNP	A	A	G	rs553861053	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:118085545A>G	ENST00000356289.5	-	2	210	c.37T>C	c.(37-39)Tta>Cta	p.L13L	AMICA1_ENST00000533261.1_Silent_p.L13L|AMICA1_ENST00000526620.1_Intron|AMICA1_ENST00000292067.7_5'Flank	NM_001098526.1	NP_001091996.1	Q86YT9	JAML1_HUMAN	adhesion molecule, interacts with CXADR antigen 1	13					blood coagulation (GO:0007596)|gamma-delta T cell activation (GO:0046629)|heterophilic cell-cell adhesion (GO:0007157)|leukocyte migration (GO:0050900)|monocyte extravasation (GO:0035696)|neutrophil chemotaxis (GO:0030593)|neutrophil extravasation (GO:0072672)|positive regulation of epithelial cell proliferation involved in wound healing (GO:0060054)|regulation of immune response (GO:0050776)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|stomach(2)	20	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		TTACCCAGTAACACTGGCAGC	0.383													A|||	12	0.00239617	0.0	0.0	5008	,	,		20342	0.0		0.0	False		,,,				2504	0.0123				p.L13L		Atlas-SNP	.											.	AMICA1	49	.	0			c.T37C						PASS	.						124.0	119.0	120.0					11																	118085545		1843	4089	5932	SO:0001819	synonymous_variant	120425	exon2			CCAGTAACACTGG	AY138965, AY358362	CCDS8391.1, CCDS41723.1, CCDS66240.1	11q23.3	2013-01-11				ENSG00000160593		"""Immunoglobulin superfamily / V-set domain containing"""	19084	protein-coding gene	gene with protein product		609770				12975309	Standard	NM_001098526		Approved	Gm638, AMICA	uc001psk.2	Q86YT9		ENST00000356289.5:c.37T>C	11.37:g.118085545A>G		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	46	7	0.152174	NM_001098526	B0YIV1|B0YIV2|Q496M1|Q5DTC6|Q7Z499|Q8N9I7|Q8NF70	Silent	SNP	ENST00000356289.5	37	CCDS41723.1																																																																																			.	.	none		0.383	AMICA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392105.2	NM_153206	
BCAR1	9564	hgsc.bcm.edu	37	16	75276775	75276775	+	Missense_Mutation	SNP	G	G	A	rs1035539	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:75276775G>A	ENST00000162330.5	-	2	352	c.226C>T	c.(226-228)Ccc>Tcc	p.P76S	BCAR1_ENST00000546196.1_Missense_Mutation_p.P47S|BCAR1_ENST00000418647.3_Missense_Mutation_p.P122S|BCAR1_ENST00000393420.6_Missense_Mutation_p.P76S|BCAR1_ENST00000420641.3_Missense_Mutation_p.P94S|BCAR1_ENST00000393422.2_Missense_Mutation_p.P94S|BCAR1_ENST00000535626.2_Intron|BCAR1_ENST00000542031.2_Missense_Mutation_p.P74S|BCAR1_ENST00000538440.2_Missense_Mutation_p.P76S	NM_001170717.1|NM_014567.3	NP_001164188.1|NP_055382.2	P56945	BCAR1_HUMAN	breast cancer anti-estrogen resistance 1	76	Pro-rich.		P -> S (in dbSNP:rs1035539). {ECO:0000269|PubMed:10639512, ECO:0000269|PubMed:14702039, ECO:0000269|Ref.2, ECO:0000269|Ref.3}.		actin filament organization (GO:0007015)|antigen receptor-mediated signaling pathway (GO:0050851)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell division (GO:0051301)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|epidermal growth factor receptor signaling pathway (GO:0007173)|G-protein coupled receptor signaling pathway (GO:0007186)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell migration (GO:0010595)|regulation of apoptotic process (GO:0042981)|regulation of cell growth (GO:0001558)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(5)|endometrium(1)|kidney(6)|large_intestine(1)|liver(1)|lung(13)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)	35				BRCA - Breast invasive adenocarcinoma(221;0.169)		GGAGGGCCGGGGCCAGGCCCT	0.692													G|||	2974	0.59385	0.3427	0.7622	5008	,	,		14078	0.629		0.6769	False		,,,				2504	0.6922				p.P122S		Atlas-SNP	.											BCAR1_ENST00000418647,rectum,carcinoma,0,6	BCAR1	184	6	0			c.C364T						scavenged	.	G	SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,SER/PRO,,SER/PRO	1768,2620		372,1024,798	19.0	22.0	21.0		364,280,280,226,226,220,,226	4.0	0.1	16	dbSNP_86	21	5721,2867		1915,1891,488	no	missense,missense,missense,missense,missense,missense,intron,missense	BCAR1	NM_001170714.1,NM_001170715.1,NM_001170716.1,NM_001170717.1,NM_001170718.1,NM_001170719.1,NM_001170720.1,NM_014567.3	74,74,74,74,74,74,,74	2287,2915,1286	AA,AG,GG		33.3838,40.2917,42.2858	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,,probably-damaging	122/917,94/889,94/889,76/889,76/871,74/869,,76/871	75276775	7489,5487	2194	4294	6488	SO:0001583	missense	9564	exon3			GGCCGGGGCCAGG	AJ242987	CCDS10915.1, CCDS54037.1, CCDS54038.1, CCDS54039.1, CCDS54040.1, CCDS54041.1, CCDS54042.1, CCDS54043.1	16q22-q23	2011-04-13			ENSG00000050820	ENSG00000050820		"""Cas scaffolding proteins"""	971	protein-coding gene	gene with protein product	"""Crk-associated substrate"", ""Cas scaffolding protein family member 1"""	602941				8413311, 10639512	Standard	NM_001170714		Approved	P130Cas, Crkas, CAS, CASS1	uc010vnb.2	P56945	OTTHUMG00000137604	ENST00000162330.5:c.226C>T	16.37:g.75276775G>A	ENSP00000162330:p.Pro76Ser	Somatic	6	1	0.166667		WXS	Illumina HiSeq	Phase_I	12	9	0.75	NM_001170714	B3KWD7|B4DEV4|B4DGB5|B4DIW5|B7Z7X7|E9PCL5|E9PCV2|F5GXA2|F5GXV6|F5H7Z0|F8WA69|Q6QEF7	Missense_Mutation	SNP	ENST00000162330.5	37	CCDS10915.1	1313	0.6011904761904762	190	0.3861788617886179	265	0.7320441988950276	345	0.6031468531468531	513	0.6767810026385225	G	4.260	0.047302	0.08243	0.402917	0.666162	ENSG00000050820	ENST00000162330;ENST00000393422;ENST00000420641;ENST00000538440;ENST00000418647;ENST00000393420;ENST00000542031;ENST00000546196	T;T;T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51;0.51;0.51	4.97	3.99	0.46301	Src homology-3 domain (1);	1.655160	0.04132	N	0.318187	T	0.00012	0.0000	L	0.36672	1.1	0.58432	P	1.999999999946489E-6	B;B;B;B;B;B;B	0.13594	0.0;0.008;0.003;0.001;0.0;0.003;0.0	B;B;B;B;B;B;B	0.12156	0.002;0.003;0.004;0.006;0.001;0.007;0.001	T	0.42682	-0.9437	9	0.17369	T	0.5	-8.8335	9.9141	0.41423	0.1013:0.0:0.8987:0.0	rs1035539;rs17855754;rs61029671	94;122;74;76;94;76;76	B4DIW5;E9PCL5;F5GXA2;F8WA69;E9PCV2;F5H7Z0;P56945	.;.;.;.;.;.;BCAR1_HUMAN	S	76;94;94;76;122;76;74;47	ENSP00000162330:P76S;ENSP00000377074:P94S;ENSP00000392708:P94S;ENSP00000443841:P76S;ENSP00000391669:P122S;ENSP00000377072:P76S;ENSP00000440415:P74S;ENSP00000442161:P47S	ENSP00000162330:P76S	P	-	1	0	BCAR1	73834276	0.726000	0.28059	0.109000	0.21407	0.115000	0.19883	3.618000	0.54188	1.200000	0.43188	0.655000	0.94253	CCC	G|0.447;A|0.553	0.553	strong		0.692	BCAR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269017.1	NM_014567	
MAN2A1	4124	hgsc.bcm.edu	37	5	109202627	109202627	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:109202627C>T	ENST00000261483.4	+	22	4415	c.3363C>T	c.(3361-3363)ccC>ccT	p.P1121P		NM_002372.2	NP_002363.2	Q16706	MA2A1_HUMAN	mannosidase, alpha, class 2A, member 1	1121					cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|liver development (GO:0001889)|lung alveolus development (GO:0048286)|mannose metabolic process (GO:0006013)|mitochondrion organization (GO:0007005)|N-glycan processing (GO:0006491)|positive regulation of neurogenesis (GO:0050769)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|respiratory gaseous exchange (GO:0007585)|retina morphogenesis in camera-type eye (GO:0060042)|vacuole organization (GO:0007033)	cis-Golgi network (GO:0005801)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|hydrolase activity, hydrolyzing N-glycosyl compounds (GO:0016799)|mannosyl-oligosaccharide 1,3-1,6-alpha-mannosidase activity (GO:0004572)|zinc ion binding (GO:0008270)	p.P1121P(1)		breast(2)|central_nervous_system(2)|endometrium(7)|kidney(2)|large_intestine(13)|lung(20)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_cancers(142;8.66e-07)|all_epithelial(76;7.73e-09)|Prostate(80;0.000303)|Lung NSC(167;0.0186)|all_lung(232;0.0241)|Ovarian(225;0.0444)|Colorectal(57;0.0959)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;2.17e-10)|Epithelial(69;1.37e-09)|COAD - Colon adenocarcinoma(37;0.141)		ATTCACCTCCCGGCACTCAGA	0.373																																					p.P1121P		Atlas-SNP	.											MAN2A1,NS,NS,0,1	MAN2A1	136	1	1	Substitution - coding silent(1)	pancreas(1)	c.C3363T						scavenged	.						123.0	113.0	116.0					5																	109202627		2202	4300	6502	SO:0001819	synonymous_variant	4124	exon22			ACCTCCCGGCACT		CCDS34209.1	5q21.3	2013-09-20			ENSG00000112893	ENSG00000112893	3.2.1.114		6824	protein-coding gene	gene with protein product	"""golgi integral membrane protein 7"""	154582		MANA2		1757461, 15004235	Standard	NM_002372		Approved	GOLIM7	uc003kou.1	Q16706	OTTHUMG00000162834	ENST00000261483.4:c.3363C>T	5.37:g.109202627C>T		Somatic	547	2	0.00365631		WXS	Illumina HiSeq	Phase_I	552	7	0.0126812	NM_002372	Q16767	Silent	SNP	ENST00000261483.4	37	CCDS34209.1																																																																																			.	.	none		0.373	MAN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370680.1		
FLG2	388698	hgsc.bcm.edu	37	1	152328295	152328295	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:152328295C>G	ENST00000388718.5	-	3	2039	c.1967G>C	c.(1966-1968)gGc>gCc	p.G656A	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	656	Ser-rich.				establishment of skin barrier (GO:0061436)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			NS(2)|breast(7)|cervix(3)|endometrium(11)|kidney(9)|large_intestine(24)|liver(1)|lung(85)|ovary(12)|pancreas(1)|prostate(6)|skin(17)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	188	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TCCATATTGGCCAAAGCCAGT	0.498																																					p.G656A		Atlas-SNP	.											.	FLG2	431	.	0			c.G1967C						PASS	.						213.0	228.0	223.0					1																	152328295		2203	4300	6503	SO:0001583	missense	388698	exon3			TATTGGCCAAAGC	AY827490	CCDS30861.1	1q21.3	2013-01-10			ENSG00000143520	ENSG00000143520		"""EF-hand domain containing"""	33276	protein-coding gene	gene with protein product						12477932	Standard	NM_001014342		Approved	IFPS	uc001ezw.4	Q5D862	OTTHUMG00000012245	ENST00000388718.5:c.1967G>C	1.37:g.152328295C>G	ENSP00000373370:p.Gly656Ala	Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	185	10	0.0540541	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	c	10.12	1.261737	0.23051	.	.	ENSG00000143520	ENST00000388718	T	0.17213	2.29	4.55	3.56	0.40772	.	.	.	.	.	T	0.11281	0.0275	M	0.73962	2.25	0.09310	N	1	D	0.56968	0.978	P	0.52856	0.711	T	0.17258	-1.0375	9	0.08599	T	0.76	-1.6533	4.9448	0.13984	0.2112:0.6799:0.0:0.109	.	656	Q5D862	FILA2_HUMAN	A	656	ENSP00000373370:G656A	ENSP00000373370:G656A	G	-	2	0	FLG2	150594919	0.004000	0.15560	0.014000	0.15608	0.046000	0.14306	1.621000	0.36986	2.083000	0.62718	0.561000	0.74099	GGC	.	.	none		0.498	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
SLC19A1	6573	hgsc.bcm.edu	37	21	46935613	46935613	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:46935613G>A	ENST00000311124.4	-	6	1887	c.1735C>T	c.(1735-1737)Cag>Tag	p.Q579*	SLC19A1_ENST00000567670.1_Intron|SLC19A1_ENST00000485649.2_Nonsense_Mutation_p.Q539*|SLC19A1_ENST00000380010.4_Intron|SLC19A1_ENST00000468508.1_5'Flank	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	579					folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|methotrexate transporter activity (GO:0015350)			endometrium(4)|kidney(1)|large_intestine(1)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	10				Colorectal(79;0.0569)|READ - Rectum adenocarcinoma(84;0.172)	Methotrexate(DB00563)|Pralatrexate(DB06813)	GGAAGACACTGCAAACCCAGC	0.612																																					p.Q579X		Atlas-SNP	.											.	SLC19A1	53	.	0			c.C1735T						PASS	.						68.0	65.0	66.0					21																	46935613		2203	4300	6503	SO:0001587	stop_gained	6573	exon6			GACACTGCAAACC	U15939	CCDS13725.1, CCDS56217.1, CCDS56218.1	21q22.3	2013-05-22			ENSG00000173638	ENSG00000173638		"""Solute carriers"""	10937	protein-coding gene	gene with protein product		600424				9570943	Standard	NM_194255		Approved	FOLT	uc002zhl.2	P41440	OTTHUMG00000090397	ENST00000311124.4:c.1735C>T	21.37:g.46935613G>A	ENSP00000308895:p.Gln579*	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	86	4	0.0465116	NM_194255	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Nonsense_Mutation	SNP	ENST00000311124.4	37	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.905088	0.92035	.	.	ENSG00000173638	ENST00000311124;ENST00000485649	.	.	.	2.8	-1.34	0.09143	.	.	.	.	.	.	.	.	.	.	.	0.30402	N	0.779886	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	6.3474	0.21357	0.5305:0.0:0.4695:0.0	.	.	.	.	X	579;539	.	ENSP00000308895:Q579X	Q	-	1	0	SLC19A1	45760041	0.000000	0.05858	0.000000	0.03702	0.026000	0.11368	-1.359000	0.02602	-0.337000	0.08426	0.467000	0.42956	CAG	.	.	none		0.612	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
DTX2	113878	hgsc.bcm.edu	37	7	76132841	76132841	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:76132841G>A	ENST00000324432.5	+	10	1998	c.1488G>A	c.(1486-1488)tcG>tcA	p.S496S	DTX2_ENST00000430490.2_Silent_p.S496S|DTX2_ENST00000413936.2_Silent_p.S496S|DTX2_ENST00000446600.1_Silent_p.S405S|DTX2_ENST00000446820.2_Silent_p.S449S|DTX2_ENST00000307569.8_Silent_p.S449S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	496					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						TCCAGATGTCGCTCCCCGGCC	0.577																																					p.S496S		Atlas-SNP	.											.	DTX2	64	.	0			c.G1488A						PASS	.						68.0	61.0	63.0					7																	76132841		2199	4293	6492	SO:0001819	synonymous_variant	113878	exon9			GATGTCGCTCCCC		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.1488G>A	7.37:g.76132841G>A		Somatic	203	0	0		WXS	Illumina HiSeq	Phase_I	219	51	0.232877	NM_001102594	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Silent	SNP	ENST00000324432.5	37	CCDS5587.1																																																																																			.	.	none		0.577	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
GBP3	2635	hgsc.bcm.edu	37	1	89476646	89476646	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:89476646T>C	ENST00000370481.4	-	8	1523	c.1303A>G	c.(1303-1305)Att>Gtt	p.I435V		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		AGCTTCTGAATAAAGAGACAA	0.433																																					p.I435V		Atlas-SNP	.											.	GBP3	53	.	0			c.A1303G						PASS	.						203.0	170.0	182.0					1																	89476646		2191	3984	6175	SO:0001583	missense	2635	exon8			TCTGAATAAAGAG	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.1303A>G	1.37:g.89476646T>C	ENSP00000359512:p.Ile435Val	Somatic	321	0	0		WXS	Illumina HiSeq	Phase_I	341	73	0.214076	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Missense_Mutation	SNP	ENST00000370481.4	37	CCDS717.2	.	.	.	.	.	.	.	.	.	.	T	7.103	0.574507	0.13623	.	.	ENSG00000117226	ENST00000370482;ENST00000370481;ENST00000235878	T	0.01887	4.58	3.57	-1.8	0.07907	Guanylate-binding protein, C-terminal (3);	1.033460	0.07626	N	0.927902	T	0.00412	0.0013	N	0.16478	0.41	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.12837	0.008;0.006	T	0.47235	-0.9133	10	0.20519	T	0.43	.	0.9257	0.01324	0.1662:0.3148:0.1708:0.3482	.	301;435	F6X827;Q9H0R5	.;GBP3_HUMAN	V	403;435;435	ENSP00000359512:I435V	ENSP00000235878:I435V	I	-	1	0	GBP3	89249234	0.000000	0.05858	0.000000	0.03702	0.128000	0.20619	-2.842000	0.00737	-0.211000	0.10124	0.491000	0.48974	ATT	.	.	none		0.433	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28306970	28306970	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:28306970C>T	ENST00000284987.5	-	4	1625	c.1504G>A	c.(1504-1506)Ggg>Agg	p.G502R	AP001601.2_ENST00000426771.1_RNA	NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	502	Disintegrin.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						TACTCAGGCCCGAATGTCAGG	0.592																																					p.G502R	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											ADAMTS5,NS,carcinoma,+1,1	ADAMTS5	184	1	0			c.G1504A						scavenged	.						106.0	85.0	92.0					21																	28306970		2203	4300	6503	SO:0001583	missense	11096	exon4			CAGGCCCGAATGT	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1504G>A	21.37:g.28306970C>T	ENSP00000284987:p.Gly502Arg	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	218	4	0.0183486	NM_007038	Q52LV4|Q9UKP2	Missense_Mutation	SNP	ENST00000284987.5	37	CCDS13579.1	.	.	.	.	.	.	.	.	.	.	C	32	5.129729	0.94473	.	.	ENSG00000154736	ENST00000284987	T	0.12465	2.68	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.44371	0.1290	M	0.83118	2.625	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.45145	-0.9281	10	0.87932	D	0	.	19.4665	0.94945	0.0:1.0:0.0:0.0	.	502	Q9UNA0	ATS5_HUMAN	R	502	ENSP00000284987:G502R	ENSP00000284987:G502R	G	-	1	0	ADAMTS5	27228841	1.000000	0.71417	0.905000	0.35620	0.825000	0.46686	7.433000	0.80362	2.624000	0.88883	0.557000	0.71058	GGG	.	.	none		0.592	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
CDH3	1001	hgsc.bcm.edu	37	16	68719113	68719113	+	Missense_Mutation	SNP	G	G	A	rs34494880	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:68719113G>A	ENST00000264012.4	+	11	1974	c.1430G>A	c.(1429-1431)cGc>cAc	p.R477H	CDH3_ENST00000581171.1_Missense_Mutation_p.R422H|CDH3_ENST00000429102.2_Missense_Mutation_p.R477H	NM_001793.4	NP_001784.2	P22223	CADH3_HUMAN	cadherin 3, type 1, P-cadherin (placental)	477	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.		R -> H (in dbSNP:rs34494880).		adherens junction organization (GO:0034332)|canonical Wnt signaling pathway (GO:0060070)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|hair cycle process (GO:0022405)|homophilic cell adhesion (GO:0007156)|keratinization (GO:0031424)|negative regulation of catagen (GO:0051796)|negative regulation of transforming growth factor beta2 production (GO:0032912)|positive regulation of gene expression (GO:0010628)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of keratinocyte proliferation (GO:0010838)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanosome transport (GO:1902910)|positive regulation of monophenol monooxygenase activity (GO:0032773)|regulation of hair cycle by canonical Wnt signaling pathway (GO:0060901)|response to drug (GO:0042493)|retina homeostasis (GO:0001895)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)|wound healing (GO:0042060)	cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.?(2)		NS(1)|breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(4)|ovary(3)|skin(1)|urinary_tract(1)	25		Ovarian(137;0.0564)		OV - Ovarian serous cystadenocarcinoma(108;0.000782)|Epithelial(162;0.0054)|all cancers(182;0.0384)		TCCAGCTACCGCATCCTGAGA	0.542													G|||	130	0.0259585	0.0023	0.0173	5008	,	,		20212	0.0		0.0596	False		,,,				2504	0.0562				p.R477H		Atlas-SNP	.											.	CDH3	68	.	2	Unknown(2)	breast(2)	c.G1430A						PASS	.	G	HIS/ARG	65,4331	61.1+/-98.1	0,65,2133	80.0	70.0	73.0		1430	0.6	1.0	16	dbSNP_126	73	645,7955	166.1+/-218.1	26,593,3681	yes	missense	CDH3	NM_001793.4	29	26,658,5814	AA,AG,GG		7.5,1.4786,5.4632	benign	477/830	68719113	710,12286	2198	4300	6498	SO:0001583	missense	1001	exon11			GCTACCGCATCCT	X63629	CCDS10868.1	16q22.1	2013-01-08	2001-12-04		ENSG00000062038	ENSG00000062038		"""Cadherins / Major cadherins"""	1762	protein-coding gene	gene with protein product		114021	"""cadherin 3, P-cadherin (placental)"""			1427864	Standard	NM_001793		Approved	CDHP, PCAD	uc002ewf.2	P22223	OTTHUMG00000137560	ENST00000264012.4:c.1430G>A	16.37:g.68719113G>A	ENSP00000264012:p.Arg477His	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	94	4	0.0425532	NM_001793	B2R6F4|Q05DI6	Missense_Mutation	SNP	ENST00000264012.4	37	CCDS10868.1	63	0.028846153846153848	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	55	0.07255936675461741	G	11.26	1.584836	0.28268	0.014786	0.075	ENSG00000062038	ENST00000429102;ENST00000264012;ENST00000542274	T;T	0.53640	0.61;0.61	5.58	0.567	0.17325	Cadherin (4);Cadherin-like (1);	0.911629	0.09141	N	0.842988	T	0.02193	0.0068	L	0.28014	0.82	0.24544	N	0.994051	B	0.13145	0.007	B	0.12837	0.008	T	0.13548	-1.0505	10	0.35671	T	0.21	.	0.9118	0.01296	0.4382:0.1566:0.2544:0.1508	rs34494880	477	P22223	CADH3_HUMAN	H	477;477;422	ENSP00000398485:R477H;ENSP00000264012:R477H	ENSP00000264012:R477H	R	+	2	0	CDH3	67276614	0.000000	0.05858	0.999000	0.59377	0.725000	0.41563	-0.843000	0.04350	0.072000	0.16694	-0.672000	0.03802	CGC	G|0.953;A|0.047	0.047	strong		0.542	CDH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268896.2	NM_001793	
MAGI2	9863	hgsc.bcm.edu	37	7	78636484	78636484	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:78636484A>C	ENST00000354212.4	-	2	593	c.340T>G	c.(340-342)Tta>Gta	p.L114V	MAGI2_ENST00000419488.1_Missense_Mutation_p.L114V|MAGI2_ENST00000522391.1_Missense_Mutation_p.L114V|MAGI2-AS2_ENST00000411616.1_RNA	NM_012301.3	NP_036433.2	Q86UL8	MAGI2_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 2	114	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				cellular response to nerve growth factor stimulus (GO:1990090)|cytoplasmic transport (GO:0016482)|glomerular visceral epithelial cell development (GO:0072015)|mitotic cell cycle arrest (GO:0071850)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of protein kinase B signaling (GO:0051898)|nerve growth factor signaling pathway (GO:0038180)|planar cell polarity pathway involved in axis elongation (GO:0003402)|positive regulation of neuron projection development (GO:0010976)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of receptor internalization (GO:0002092)|protein heterooligomerization (GO:0051291)|receptor clustering (GO:0043113)|SMAD protein signal transduction (GO:0060395)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|late endosome (GO:0005770)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)|synapse (GO:0045202)|tight junction (GO:0005923)	beta-1 adrenergic receptor binding (GO:0031697)|phosphatase binding (GO:0019902)|receptor signaling complex scaffold activity (GO:0030159)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|type II activin receptor binding (GO:0070699)	p.L114V(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(37)|ovary(5)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(3)	84		all_cancers(73;0.0064)|all_epithelial(88;0.087)|all_neural(109;0.0936)|Medulloblastoma(109;0.166)|Melanoma(862;0.236)				TGAAATCGTAAGTTGAGGTAG	0.388																																					p.L114V		Atlas-SNP	.											MAGI2,caecum,carcinoma,0,1	MAGI2	246	1	1	Substitution - Missense(1)	large_intestine(1)	c.T340G						PASS	.						147.0	126.0	133.0					7																	78636484		2203	4300	6503	SO:0001583	missense	9863	exon2			ATCGTAAGTTGAG	AB014605	CCDS5594.1, CCDS75623.1	7q21	2005-08-09			ENSG00000187391	ENSG00000187391			18957	protein-coding gene	gene with protein product		606382				10681527, 9734811	Standard	XM_005250725		Approved	AIP1, ARIP1, KIAA0705, ACVRIP1, MAGI-2	uc003ugx.3	Q86UL8	OTTHUMG00000130697	ENST00000354212.4:c.340T>G	7.37:g.78636484A>C	ENSP00000346151:p.Leu114Val	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	148	22	0.148649	NM_012301	A4D1C1|A7E2C3|O60434|O60510|Q86UI7|Q9NP44|Q9UDQ5|Q9UDU1	Missense_Mutation	SNP	ENST00000354212.4	37	CCDS5594.1	.	.	.	.	.	.	.	.	.	.	A	20.5	3.994850	0.74703	.	.	ENSG00000187391	ENST00000419488;ENST00000354212;ENST00000536298;ENST00000522391	T;T;T	0.11277	2.89;2.89;2.79	5.29	4.1	0.47936	Guanylate kinase/L-type calcium channel (1);Guanylate kinase (1);	.	.	.	.	T	0.23492	0.0568	L	0.52573	1.65	0.80722	D	1	D;D	0.89917	1.0;0.996	D;P	0.91635	0.999;0.82	T	0.00647	-1.1628	9	0.35671	T	0.21	.	9.4432	0.38681	0.8477:0.0:0.1523:0.0	.	114;114	Q86UL8-2;Q86UL8	.;MAGI2_HUMAN	V	114	ENSP00000405766:L114V;ENSP00000346151:L114V;ENSP00000428389:L114V	ENSP00000346151:L114V	L	-	1	2	MAGI2	78474420	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.746000	0.55127	0.802000	0.34089	0.519000	0.50382	TTA	.	.	none		0.388	MAGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253197.3	NM_012301	
NLGN1	22871	hgsc.bcm.edu	37	3	173322630	173322630	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:173322630T>C	ENST00000457714.1	+	3	671	c.242T>C	c.(241-243)cTt>cCt	p.L81P	NLGN1_ENST00000361589.4_Missense_Mutation_p.L81P|NLGN1_ENST00000545397.1_Missense_Mutation_p.L81P|NLGN1_ENST00000401917.3_Missense_Mutation_p.L81P	NM_014932.2	NP_055747.1	Q8N2Q7	NLGN1_HUMAN	neuroligin 1	81					alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|calcium-dependent cell-cell adhesion (GO:0016339)|cytoskeletal matrix organization at active zone (GO:0048789)|establishment of protein localization (GO:0045184)|heterophilic cell-cell adhesion (GO:0007157)|N-methyl-D-aspartate receptor clustering (GO:0097114)|nervous system development (GO:0007399)|neurexin clustering (GO:0097115)|neuron cell-cell adhesion (GO:0007158)|neuronal signal transduction (GO:0023041)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of synaptic vesicle endocytosis (GO:1900244)|positive regulation of synaptic vesicle exocytosis (GO:2000302)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein heterotetramerization (GO:0051290)|protein homooligomerization (GO:0051260)|protein localization to synapse (GO:0035418)|protein targeting (GO:0006605)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuron differentiation (GO:0045664)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|synapse assembly (GO:0007416)|synaptic vesicle clustering (GO:0097091)|synaptic vesicle targeting (GO:0016080)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|filopodium tip (GO:0032433)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuronal postsynaptic density (GO:0097481)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|PDZ domain binding (GO:0030165)|protein dimerization activity (GO:0046983)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|liver(2)|lung(54)|ovary(1)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	83	Ovarian(172;0.0025)		LUSC - Lung squamous cell carcinoma(14;5.36e-13)|Lung(28;9.49e-13)			ATTCAATTTCTTGGGGTTCCA	0.458																																					p.L81P		Atlas-SNP	.											NLGN1,NS,carcinoma,+1,1	NLGN1	209	1	0			c.T242C						PASS	.						102.0	108.0	106.0					3																	173322630		2203	4300	6503	SO:0001583	missense	22871	exon3			AATTTCTTGGGGT	AB028993	CCDS3222.1	3q26.32	2008-07-18			ENSG00000169760	ENSG00000169760			14291	protein-coding gene	gene with protein product		600568				10767552, 10819331	Standard	NM_014932		Approved	KIAA1070	uc003fio.1	Q8N2Q7	OTTHUMG00000157005	ENST00000457714.1:c.242T>C	3.37:g.173322630T>C	ENSP00000392500:p.Leu81Pro	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	64	11	0.171875	NM_014932	Q9UPT2	Missense_Mutation	SNP	ENST00000457714.1	37	CCDS3222.1	.	.	.	.	.	.	.	.	.	.	T	18.42	3.620055	0.66787	.	.	ENSG00000169760	ENST00000457714;ENST00000361589;ENST00000415045;ENST00000545397;ENST00000401917	T;T;T;T;T	0.71934	-0.08;-0.08;-0.61;-0.08;-0.08	5.62	5.62	0.85841	.	0.000000	0.64402	D	0.000005	D	0.90202	0.6937	H	0.98089	4.145	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.992;0.997	D	0.93761	0.7067	10	0.87932	D	0	.	16.1135	0.81278	0.0:0.0:0.0:1.0	.	81;81	D2X2H5;Q8N2Q7-2	.;.	P	81	ENSP00000392500:L81P;ENSP00000354541:L81P;ENSP00000410374:L81P;ENSP00000441108:L81P;ENSP00000385750:L81P	ENSP00000354541:L81P	L	+	2	0	NLGN1	174805324	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.655000	0.83696	2.267000	0.75376	0.383000	0.25322	CTT	.	.	none		0.458	NLGN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347054.3	NM_014932	
MAP3K12	7786	hgsc.bcm.edu	37	12	53880795	53880795	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:53880795G>A	ENST00000267079.2	-	3	507	c.282C>T	c.(280-282)tgC>tgT	p.C94C	MAP3K12_ENST00000547035.1_Silent_p.C127C|MAP3K12_ENST00000547488.1_Silent_p.C127C|MAP3K12_ENST00000547151.1_5'UTR	NM_001193511.1|NM_006301.3	NP_001180440.1|NP_006292.3	Q12852	M3K12_HUMAN	mitogen-activated protein kinase kinase kinase 12	94					histone phosphorylation (GO:0016572)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|pancreas(1)|prostate(1)|skin(3)	37						CAGGGCGCAGGCAGCCAAAGA	0.602																																					p.C127C		Atlas-SNP	.											.	MAP3K12	160	.	0			c.C381T						PASS	.						80.0	66.0	71.0					12																	53880795		2203	4300	6503	SO:0001819	synonymous_variant	7786	exon2			GCGCAGGCAGCCA	U07358	CCDS8860.1, CCDS55831.1	12q13.13	2013-10-30			ENSG00000139625	ENSG00000139625		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6851	protein-coding gene	gene with protein product	"""dual leucine zipper kinase DLK"""	600447		ZPK		8037767	Standard	NM_006301		Approved	MUK, DLK, ZPKP1, MEKK12	uc001sdn.2	Q12852	OTTHUMG00000169854	ENST00000267079.2:c.282C>T	12.37:g.53880795G>A		Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	147	39	0.265306	NM_001193511	B3KSS9|G3V1Y2|Q86VQ5|Q8WY25	Silent	SNP	ENST00000267079.2	37	CCDS8860.1	.	.	.	.	.	.	.	.	.	.	G	7.742	0.701512	0.15172	.	.	ENSG00000139625	ENST00000547151	.	.	.	4.73	1.91	0.25777	.	.	.	.	.	T	0.63177	0.2489	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61681	-0.7013	5	0.87932	D	0	.	7.939	0.29946	0.3359:0.0:0.6641:0.0	.	.	.	.	V	91	.	ENSP00000446800:A91V	A	-	2	0	MAP3K12	52167062	0.968000	0.33430	1.000000	0.80357	0.987000	0.75469	0.040000	0.13905	0.183000	0.20059	-0.448000	0.05591	GCC	.	.	none		0.602	MAP3K12-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406267.1	NM_006301	
OR8J1	219477	hgsc.bcm.edu	37	11	56128081	56128081	+	Missense_Mutation	SNP	A	A	G	rs10896290	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:56128081A>G	ENST00000303039.3	+	1	391	c.359A>G	c.(358-360)tAt>tGt	p.Y120C		NM_001005205.2	NP_001005205.2	Q8NGP2	OR8J1_HUMAN	olfactory receptor, family 8, subfamily J, member 1	120			Y -> C (in dbSNP:rs10896290). {ECO:0000269|PubMed:12213199, ECO:0000269|PubMed:14983052, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.1}.			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(30)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	47	Esophageal squamous(21;0.00448)					TTGATGGCCTATGACCGCTAT	0.488													A|||	1103	0.220248	0.2542	0.1873	5008	,	,		18213	0.1369		0.328	False		,,,				2504	0.1728				p.Y120C		Atlas-SNP	.											OR8J1,head_neck,carcinoma,0,1	OR8J1	87	1	0			c.A359G						scavenged	.	A	CYS/TYR	1238,3164	425.5+/-340.8	183,872,1146	149.0	137.0	141.0		359	4.8	1.0	11	dbSNP_120	141	2939,5653	458.5+/-364.6	521,1897,1878	yes	missense	OR8J1	NM_001005205.2	194	704,2769,3024	GG,GA,AA		34.2062,28.1236,32.1456	benign	120/317	56128081	4177,8817	2201	4296	6497	SO:0001583	missense	219477	exon1			TGGCCTATGACCG	AB065748	CCDS31529.1	11q11	2012-08-09			ENSG00000172487	ENSG00000172487		"""GPCR / Class A : Olfactory receptors"""	14855	protein-coding gene	gene with protein product							Standard	NM_001005205		Approved		uc010rjh.2	Q8NGP2	OTTHUMG00000166859	ENST00000303039.3:c.359A>G	11.37:g.56128081A>G	ENSP00000304060:p.Tyr120Cys	Somatic	223	0	0		WXS	Illumina HiSeq	Phase_I	266	4	0.0150376	NM_001005205	B2RNQ6|B9EH63|Q6IFC2|Q96RC3	Missense_Mutation	SNP	ENST00000303039.3	37	CCDS31529.1	524	0.23992673992673993	112	0.22764227642276422	68	0.1878453038674033	88	0.15384615384615385	256	0.33773087071240104	A	12.19	1.863321	0.32884	0.281236	0.342062	ENSG00000172487	ENST00000303039	T	0.00490	7.03	4.76	4.76	0.60689	GPCR, rhodopsin-like superfamily (1);	0.000000	0.56097	D	0.000031	T	0.00012	0.0000	M	0.91196	3.185	0.33499	P	0.41034099999999996	B	0.24651	0.108	B	0.29942	0.109	T	0.39014	-0.9634	9	0.72032	D	0.01	.	13.3744	0.60730	1.0:0.0:0.0:0.0	rs10896290;rs52824219;rs59409905;rs10896290	120	Q8NGP2	OR8J1_HUMAN	C	120	ENSP00000304060:Y120C	ENSP00000304060:Y120C	Y	+	2	0	OR8J1	55884657	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.624000	0.54231	1.910000	0.55303	0.523000	0.50628	TAT	A|0.712;G|0.288	0.288	strong		0.488	OR8J1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391606.2	NM_001005205	
ENPEP	2028	hgsc.bcm.edu	37	4	111397599	111397599	+	Missense_Mutation	SNP	A	A	C	rs564550794		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:111397599A>C	ENST00000265162.5	+	1	371	c.29A>C	c.(28-30)aAg>aCg	p.K10T		NM_001977.3	NP_001968.3	Q07075	AMPE_HUMAN	glutamyl aminopeptidase (aminopeptidase A)	10					angiogenesis (GO:0001525)|angiotensin catabolic process in blood (GO:0002005)|angiotensin maturation (GO:0002003)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular protein metabolic process (GO:0044267)|glomerulus development (GO:0032835)|regulation of systemic arterial blood pressure by renin-angiotensin (GO:0003081)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|brush border (GO:0005903)|cytoplasmic vesicle (GO:0031410)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloaminopeptidase activity (GO:0070006)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|prostate(3)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(1)	54		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.0031)		GAGGGCTCTAAGAGATACTGC	0.438																																					p.K10T		Atlas-SNP	.											.	ENPEP	149	.	0			c.A29C						PASS	.						171.0	163.0	166.0					4																	111397599		2203	4300	6503	SO:0001583	missense	2028	exon1			GCTCTAAGAGATA	L12468	CCDS3691.1	4q25	2008-02-05			ENSG00000138792	ENSG00000138792	3.4.11.7	"""CD molecules"""	3355	protein-coding gene	gene with protein product		138297				9268642	Standard	NM_001977		Approved	gp160, CD249	uc003iab.4	Q07075	OTTHUMG00000132546	ENST00000265162.5:c.29A>C	4.37:g.111397599A>C	ENSP00000265162:p.Lys10Thr	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	212	31	0.146226	NM_001977	Q504U2	Missense_Mutation	SNP	ENST00000265162.5	37	CCDS3691.1	.	.	.	.	.	.	.	.	.	.	A	25.8	4.679199	0.88542	.	.	ENSG00000138792	ENST00000265162	T	0.01347	4.99	5.42	3.04	0.35103	.	0.352416	0.31279	N	0.007939	T	0.02848	0.0085	M	0.66939	2.045	0.48040	D	0.99957	D	0.57899	0.981	P	0.46629	0.522	T	0.55685	-0.8102	10	0.51188	T	0.08	.	9.0788	0.36538	0.8513:0.0:0.1487:0.0	.	10	Q07075	AMPE_HUMAN	T	10	ENSP00000265162:K10T	ENSP00000265162:K10T	K	+	2	0	ENPEP	111617048	1.000000	0.71417	0.278000	0.24718	0.723000	0.41478	4.877000	0.63086	0.912000	0.36772	0.260000	0.18958	AAG	.	.	none		0.438	ENPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255747.2		
CNOT1	23019	hgsc.bcm.edu	37	16	58577327	58577327	+	Intron	SNP	A	A	C	rs556592424		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:58577327A>C	ENST00000317147.5	-	31	4767				CNOT1_ENST00000441024.2_Missense_Mutation_p.F1540V|CNOT1_ENST00000569240.1_Intron|CNOT1_ENST00000245138.4_Intron	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1						gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		aaaaaaaaaaaacacacagac	0.299													A|||	1	0.000199681	0.0	0.0	5008	,	,		18548	0.0		0.001	False		,,,				2504	0.0				p.F1540V		Atlas-SNP	.											CNOT1_ENST00000441024,caecum,carcinoma,0,1	CNOT1	359	1	0			c.T4618G						scavenged	.						20.0	20.0	20.0					16																	58577327		1013	2122	3135	SO:0001627	intron_variant	23019	exon31			AAAAAAAACACAC	AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.4434+183T>G	16.37:g.58577327A>C		Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	83	3	0.0361446	NM_206999	Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Missense_Mutation	SNP	ENST00000317147.5	37	CCDS10799.1	.	.	.	.	.	.	.	.	.	.	A	4.645	0.119968	0.08881	.	.	ENSG00000125107	ENST00000441024	T	0.44482	0.92	1.6	-3.2	0.05156	.	.	.	.	.	T	0.28499	0.0705	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12400	-1.0549	8	0.87932	D	0	.	5.872	0.18809	0.2548:0.5872:0.158:0.0	.	1540	A5YKK6-4	.	V	1540	ENSP00000413113:F1540V	ENSP00000413113:F1540V	F	-	1	0	CNOT1	57134828	0.004000	0.15560	0.000000	0.03702	0.000000	0.00434	0.507000	0.22675	-2.105000	0.00842	-1.344000	0.01245	TTT	.	.	none		0.299	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3	NM_016284	
CDC27	996	hgsc.bcm.edu	37	17	45214528	45214528	+	Missense_Mutation	SNP	A	A	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:45214528A>T	ENST00000066544.3	-	14	1996	c.1903T>A	c.(1903-1905)Tat>Aat	p.Y635N	CDC27_ENST00000531206.1_Missense_Mutation_p.Y641N|CDC27_ENST00000446365.2_Missense_Mutation_p.Y574N|CDC27_ENST00000527547.1_Missense_Mutation_p.Y634N	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	635					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CATGCATTATAATGTCTAGGA	0.338																																					p.Y641N		Atlas-SNP	.											CDC27_ENST00000531206,colon,carcinoma,0,2	CDC27	337	2	0			c.T1921A						scavenged	.						36.0	36.0	36.0					17																	45214528		2203	4300	6503	SO:0001583	missense	996	exon14			CATTATAATGTCT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1903T>A	17.37:g.45214528A>T	ENSP00000066544:p.Tyr635Asn	Somatic	44	3	0.0681818		WXS	Illumina HiSeq	Phase_I	54	4	0.0740741	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	32	5.126360	0.94429	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	5.98	5.98	0.97165	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	D	0.83825	0.5338	H	0.96943	3.91	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.85130	0.997;0.995;0.995;0.996	D	0.89008	0.3426	10	0.87932	D	0	-24.5847	14.4087	0.67101	1.0:0.0:0.0:0.0	.	574;634;641;635	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	N	635;641;574;634	ENSP00000066544:Y635N;ENSP00000434614:Y641N;ENSP00000392802:Y574N;ENSP00000437339:Y634N	ENSP00000066544:Y635N	Y	-	1	0	CDC27	42569527	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.293000	0.77203	0.477000	0.44152	TAT	.	.	none		0.338	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
OR2T2	401992	hgsc.bcm.edu	37	1	248616749	248616749	+	Silent	SNP	C	C	G	rs151176830		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:248616749C>G	ENST00000342927.3	+	1	673	c.651C>G	c.(649-651)gtC>gtG	p.V217V		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	217						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TCATCTCTGTCTCCTACACGC	0.542																																					p.V217V		Atlas-SNP	.											OR2T2,NS,carcinoma,0,1	OR2T2	73	1	0			c.C651G						scavenged	.						255.0	173.0	201.0					1																	248616749		2189	4267	6456	SO:0001819	synonymous_variant	401992	exon1			CTCTGTCTCCTAC	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.651C>G	1.37:g.248616749C>G		Somatic	373	0	0		WXS	Illumina HiSeq	Phase_I	480	6	0.0125	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			C|0.500;G|0.500	0.500	strong		0.542	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
BIRC8	112401	hgsc.bcm.edu	37	19	53793122	53793122	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:53793122G>T	ENST00000426466.1	-	1	1753	c.506C>A	c.(505-507)tCa>tAa	p.S169*		NM_033341.4	NP_203127.3	Q96P09	BIRC8_HUMAN	baculoviral IAP repeat containing 8	169					apoptotic process (GO:0006915)	cytoplasm (GO:0005737)	zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(10)|urinary_tract(1)	19				GBM - Glioblastoma multiforme(134;0.00304)		TCTCTGCAATGAAGTCTGATT	0.418																																					p.S169X		Atlas-SNP	.											.	BIRC8	54	.	0			c.C506A						PASS	.						87.0	86.0	86.0					19																	53793122		2203	4300	6503	SO:0001587	stop_gained	112401	exon1			TGCAATGAAGTCT	AF164682	CCDS12863.1	19q13.3-q13.4	2011-01-25	2011-01-25			ENSG00000163098		"""Baculoviral IAP repeat containing"""	14878	protein-coding gene	gene with protein product	"""IAP-like protein 2"", ""inhibitor of apoptosis-like protein 2"""		"""baculoviral IAP repeat-containing 8"""			11390657	Standard	NM_033341		Approved	ILP-2, hILP2	uc002qbk.3	Q96P09		ENST00000426466.1:c.506C>A	19.37:g.53793122G>T	ENSP00000412957:p.Ser169*	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	110	17	0.154545	NM_033341	Q6IPY1|Q96RW5	Nonsense_Mutation	SNP	ENST00000426466.1	37	CCDS12863.1	.	.	.	.	.	.	.	.	.	.	G	43	10.235541	0.99365	.	.	ENSG00000163098	ENST00000426466	.	.	.	0.637	-0.588	0.11687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-6.1522	4.9292	0.13909	0.2589:0.0:0.7411:0.0	.	.	.	.	X	169	.	ENSP00000412957:S169X	S	-	2	0	BIRC8	58484934	0.007000	0.16637	0.010000	0.14722	0.003000	0.03518	0.299000	0.19138	-0.140000	0.11394	-0.347000	0.07816	TCA	.	.	none		0.418	BIRC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464357.1	NM_033341	
OSCAR	126014	hgsc.bcm.edu	37	19	54599222	54599222	+	Silent	SNP	G	G	T	rs61742144	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:54599222G>T	ENST00000284648.6	-	5	767	c.570C>A	c.(568-570)ccC>ccA	p.P190P	OSCAR_ENST00000358375.4_Silent_p.P190P|OSCAR_ENST00000359649.4_Silent_p.P194P|OSCAR_ENST00000391761.1_Silent_p.P179P|OSCAR_ENST00000351806.4_Silent_p.P179P|OSCAR_ENST00000391760.1_Silent_p.R133R|OSCAR_ENST00000356532.3_Silent_p.P194P			Q8IYS5	OSCAR_HUMAN	osteoclast associated, immunoglobulin-like receptor	190	Ig-like 2.					extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				large_intestine(1)|skin(1)	2	all_cancers(19;0.0128)|all_epithelial(19;0.00564)|all_lung(19;0.031)|Lung NSC(19;0.0358)|Ovarian(34;0.19)					TGTAGGTGCCGGGGGCGCGGG	0.711													g|||	640	0.127796	0.1831	0.1182	5008	,	,		11804	0.0526		0.1113	False		,,,				2504	0.1544				p.P194P		Atlas-SNP	.											OSCAR_ENST00000356532,NS,carcinoma,0,2	OSCAR	22	2	0			c.C582A						scavenged	.	T	,,,	640,3676		47,546,1565	7.0	8.0	8.0		582,537,570,582	-8.1	0.0	19	dbSNP_129	8	968,7474		66,836,3319	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OSCAR	NM_130771.3,NM_133168.3,NM_133169.3,NM_206818.1	,,,	113,1382,4884	TT,TG,GG		11.4665,14.8285,12.6039	,,,	194/268,179/253,190/264,194/287	54599222	1608,11150	2158	4221	6379	SO:0001819	synonymous_variant	126014	exon5			GGTGCCGGGGGCG	AK130199	CCDS12873.1, CCDS12874.1, CCDS12875.1, CCDS12876.1, CCDS62789.1, CCDS74444.1	19q13.42	2013-01-29			ENSG00000170909	ENSG00000170909		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29960	protein-coding gene	gene with protein product		606862				11805147	Standard	NM_206818		Approved		uc002qda.3	Q8IYS5	OTTHUMG00000064966	ENST00000284648.6:c.570C>A	19.37:g.54599222G>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	9	2	0.222222	NM_130771	B7WNS2|Q5GRG5|Q8N763|Q8NHL4|Q8WXQ0|Q8WXQ1|Q8WXQ2	Silent	SNP	ENST00000284648.6	37																																																																																				G|0.886;T|0.114	0.114	strong		0.711	OSCAR-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000139493.4	NM_133169	
SPATA31A6	389730	hgsc.bcm.edu	37	9	43626759	43626759	+	Missense_Mutation	SNP	G	G	A	rs574727392	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:43626759G>A	ENST00000332857.6	-	4	1956	c.1928C>T	c.(1927-1929)aCg>aTg	p.T643M	SPATA31A6_ENST00000496386.1_5'Flank	NM_001145196.1	NP_001138668.1	Q5VVP1	S31A6_HUMAN	SPATA31 subfamily A, member 6	643					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.T643M(1)									ACCTGTGGACGTGGAGGACTG	0.572													A|||	1567	0.312899	0.2292	0.2795	5008	,	,		8461	0.5516		0.3052	False		,,,				2504	0.2117				p.T643M		Atlas-SNP	.											FAM75A6,NS,carcinoma,+1,2	.	.	2	1	Substitution - Missense(1)	breast(1)	c.C1928T						scavenged	.						8.0	7.0	7.0					9																	43626759		454	1111	1565	SO:0001583	missense	389730	exon4			GTGGACGTGGAGG		CCDS75837.1	9p11.2	2012-10-15	2012-10-12	2012-10-12	ENSG00000185775	ENSG00000185775			32006	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A6"""	FAM75A6		20850414	Standard	NM_001145196		Approved	OTTHUMG00000013224	uc011lrb.2	Q5VVP1	OTTHUMG00000013224	ENST00000332857.6:c.1928C>T	9.37:g.43626759G>A	ENSP00000329825:p.Thr643Met	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_001145196		Missense_Mutation	SNP	ENST00000332857.6	37	CCDS47973.1	.	.	.	.	.	.	.	.	.	.	A	2.502	-0.314968	0.05422	.	.	ENSG00000185775	ENST00000332857	T	0.06142	3.34	2.36	-4.38	0.03622	.	2.118030	0.02377	N	0.078485	T	0.03390	0.0098	N	0.11427	0.14	0.80722	P	0.0	B	0.02656	0.0	B	0.04013	0.001	T	0.39035	-0.9633	9	0.28530	T	0.3	0.4794	4.5079	0.11898	0.5468:0.1745:0.2787:0.0	.	643	Q5VVP1	F75A6_HUMAN	M	643	ENSP00000329825:T643M	ENSP00000329825:T643M	T	-	2	0	FAM75A6	43566755	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.736000	0.04882	-1.194000	0.02684	-3.677000	0.00025	ACG	A|1.000;|0.000	1.000	weak		0.572	SPATA31A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036987.1	NM_001145196	
PROX1	5629	hgsc.bcm.edu	37	1	214171399	214171399	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:214171399A>C	ENST00000366958.4	+	2	2129	c.1521A>C	c.(1519-1521)aaA>aaC	p.K507N	PROX1_ENST00000261454.4_Missense_Mutation_p.K507N|PROX1_ENST00000498508.2_Missense_Mutation_p.K507N|PROX1_ENST00000435016.1_Missense_Mutation_p.K507N	NM_001270616.1	NP_001257545.1	Q92786	PROX1_HUMAN	prospero homeobox 1	507					aorta smooth muscle tissue morphogenesis (GO:0060414)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|brain development (GO:0007420)|cell fate determination (GO:0001709)|cerebellar granule cell differentiation (GO:0021707)|dentate gyrus development (GO:0021542)|dorsal spinal cord development (GO:0021516)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocardium formation (GO:0060214)|hepatocyte cell migration (GO:0002194)|hepatocyte differentiation (GO:0070365)|hepatocyte proliferation (GO:0072574)|kidney development (GO:0001822)|lens development in camera-type eye (GO:0002088)|lens fiber cell morphogenesis (GO:0070309)|liver development (GO:0001889)|lung development (GO:0030324)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|negative regulation of bile acid biosynthetic process (GO:0070858)|negative regulation of cell proliferation (GO:0008285)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral genome replication (GO:0045071)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|olfactory placode formation (GO:0030910)|optic placode formation involved in camera-type eye formation (GO:0046619)|otic placode formation (GO:0043049)|pancreas development (GO:0031016)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell cycle checkpoint (GO:1901978)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of forebrain neuron differentiation (GO:2000979)|positive regulation of heart growth (GO:0060421)|positive regulation of neural precursor cell proliferation (GO:2000179)|positive regulation of sarcomere organization (GO:0060298)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of gene expression (GO:0010468)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to nutrient levels (GO:0031667)|retina morphogenesis in camera-type eye (GO:0060042)|skeletal muscle thin filament assembly (GO:0030240)|venous blood vessel morphogenesis (GO:0048845)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular cardiac myofibril assembly (GO:0055005)|ventricular septum morphogenesis (GO:0060412)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|DBD domain binding (GO:0050692)|DNA binding (GO:0003677)|LBD domain binding (GO:0050693)|ligand-dependent nuclear receptor binding (GO:0016922)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(3)|prostate(2)|skin(4)	47				OV - Ovarian serous cystadenocarcinoma(81;0.0179)|all cancers(67;0.0488)|GBM - Glioblastoma multiforme(131;0.188)|Epithelial(68;0.219)		TCTCTGGAAAAGACAGAGCCT	0.552																																					p.K507N		Atlas-SNP	.											.	PROX1	124	.	0			c.A1521C						PASS	.						78.0	85.0	82.0					1																	214171399		2203	4300	6503	SO:0001583	missense	5629	exon2			TGGAAAAGACAGA	U44060	CCDS31021.1	1q41	2011-06-20	2007-06-01		ENSG00000117707	ENSG00000117707		"""Homeoboxes / PROS class"""	9459	protein-coding gene	gene with protein product		601546	"""prospero-related homeobox 1"""			8812486	Standard	NM_002763		Approved		uc001hkg.2	Q92786	OTTHUMG00000036946	ENST00000366958.4:c.1521A>C	1.37:g.214171399A>C	ENSP00000355925:p.Lys507Asn	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	65	18	0.276923	NM_001270616	A6NK29|A8K2B1|Q5SW76|Q8TB91	Missense_Mutation	SNP	ENST00000366958.4	37	CCDS31021.1	.	.	.	.	.	.	.	.	.	.	A	11.80	1.748020	0.30955	.	.	ENSG00000117707	ENST00000541470;ENST00000498508;ENST00000366958;ENST00000435016;ENST00000261454	T;T;T;T	0.48836	0.81;0.8;0.81;0.81	5.71	1.66	0.24008	.	0.000000	0.85682	D	0.000000	T	0.59032	0.2164	M	0.62723	1.935	0.52501	D	0.999953	D	0.76494	0.999	D	0.85130	0.997	T	0.52223	-0.8604	10	0.22109	T	0.4	-5.3341	9.702	0.40192	0.6316:0.0:0.3684:0.0	.	507	Q92786	PROX1_HUMAN	N	79;507;507;507;507	ENSP00000420283:K507N;ENSP00000355925:K507N;ENSP00000400694:K507N;ENSP00000261454:K507N	ENSP00000261454:K507N	K	+	3	2	PROX1	212238022	1.000000	0.71417	0.995000	0.50966	0.997000	0.91878	1.513000	0.35823	0.026000	0.15269	0.533000	0.62120	AAA	.	.	none		0.552	PROX1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089727.6	NM_002763	
CEP89	84902	hgsc.bcm.edu	37	19	33444556	33444556	+	Missense_Mutation	SNP	T	T	C	rs73579706	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:33444556T>C	ENST00000305768.5	-	4	545	c.457A>G	c.(457-459)Agt>Ggt	p.S153G	CEP89_ENST00000590597.2_Missense_Mutation_p.S153G	NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	153					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						AGGTCATCACTGTGGCCTCCT	0.483																																					p.S153G		Atlas-SNP	.											CEP89,NS,carcinoma,+1,1	CEP89	82	1	0			c.A457G						scavenged	.						401.0	426.0	418.0					19																	33444556		2203	4300	6503	SO:0001583	missense	84902	exon4			CATCACTGTGGCC	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.457A>G	19.37:g.33444556T>C	ENSP00000306105:p.Ser153Gly	Somatic	79	2	0.0253165		WXS	Illumina HiSeq	Phase_I	89	5	0.0561798	NM_032816	B9EGA6|Q8N5J8	Missense_Mutation	SNP	ENST00000305768.5	37	CCDS32987.1	.	.	.	.	.	.	.	.	.	.	T	3.578	-0.086165	0.07097	.	.	ENSG00000121289	ENST00000305768	T	0.31510	1.49	5.12	-10.2	0.00374	.	3.796690	0.00695	N	0.000748	T	0.07234	0.0183	N	0.01048	-1.04	0.09310	N	1	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.08055	0.003;0.0;0.0	T	0.34725	-0.9817	10	0.22706	T	0.39	7.6155	0.6143	0.00767	0.2371:0.2982:0.1712:0.2935	.	124;153;153	Q8WUL5;Q96ST8-3;Q96ST8	.;.;CEP89_HUMAN	G	153	ENSP00000306105:S153G	ENSP00000306105:S153G	S	-	1	0	CEP89	38136396	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.650000	0.01991	-4.026000	0.00080	-0.951000	0.02657	AGT	T|0.500;C|0.500	0.500	strong		0.483	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
SRSF1	6426	hgsc.bcm.edu	37	17	56083867	56083867	+	Nonsense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:56083867A>C	ENST00000258962.4	-	2	424	c.216T>G	c.(214-216)taT>taG	p.Y72*	SRSF1_ENST00000585096.1_Intron|SRSF1_ENST00000581497.1_5'Flank|SRSF1_ENST00000582730.2_Nonsense_Mutation_p.Y72*|RP11-159D12.5_ENST00000578794.1_5'Flank|SRSF1_ENST00000584773.1_Nonsense_Mutation_p.Y72*	NM_006924.4	NP_008855.1	Q07955	SRSF1_HUMAN	serine/arginine-rich splicing factor 1	72	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cardiac muscle contraction (GO:0060048)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|mRNA 3'-end processing (GO:0031124)|mRNA 5'-splice site recognition (GO:0000395)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splice site selection (GO:0006376)|mRNA splicing, via spliceosome (GO:0000398)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(1)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						CGTCGCGACCATACACCGCGT	0.627																																					p.Y72X		Atlas-SNP	.											.	SRSF1	41	.	0			c.T216G						PASS	.						28.0	25.0	26.0					17																	56083867		2202	4288	6490	SO:0001587	stop_gained	6426	exon2			GCGACCATACACC		CCDS11600.1, CCDS58580.1	17q22	2013-02-12	2010-06-22	2010-06-22	ENSG00000136450	ENSG00000136450		"""Serine/arginine-rich splicing factors"", ""RNA binding motif (RRM) containing"""	10780	protein-coding gene	gene with protein product	"""splicing factor 2"", ""pre-mRNA-splicing factor SF2, P33 subunit"", ""alternate splicing factor"", ""SR splicing factor 1"""	600812	"""splicing factor, arginine/serine-rich 1"""	SFRS1		8530103, 20516191	Standard	NM_006924		Approved	ASF, SF2, SRp30a, SF2p33, MGC5228	uc002ivi.3	Q07955		ENST00000258962.4:c.216T>G	17.37:g.56083867A>C	ENSP00000258962:p.Tyr72*	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	174	42	0.241379	NM_006924	B2R6Z7|D3DTZ3|Q13809	Nonsense_Mutation	SNP	ENST00000258962.4	37	CCDS11600.1	.	.	.	.	.	.	.	.	.	.	A	23.2	4.381974	0.82792	.	.	ENSG00000136450	ENST00000258962	.	.	.	5.96	-3.56	0.04626	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.7599	0.62959	0.5977:0.0:0.4023:0.0	.	.	.	.	X	72	.	ENSP00000258962:Y72X	Y	-	3	2	SRSF1	53438866	0.877000	0.30153	0.866000	0.34008	0.984000	0.73092	0.001000	0.13038	-0.941000	0.03700	-0.899000	0.02877	TAT	.	.	none		0.627	SRSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443335.1	NM_006924	
LTB	4050	hgsc.bcm.edu	37	6	31549636	31549636	+	Splice_Site	SNP	C	C	G	rs571318566	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:31549636C>G	ENST00000429299.2	-	2	170	c.163G>C	c.(163-165)Gta>Cta	p.V55L	LTB_ENST00000483972.1_Intron|LTB_ENST00000446745.2_Intron	NM_002341.1	NP_002332.1	Q06643	TNFC_HUMAN	lymphotoxin beta (TNF superfamily, member 3)	55					cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|signal transduction (GO:0007165)|skin development (GO:0043588)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(1)	9						GTCTCCGTTACCTGGTTGGGT	0.622																																					p.V55L		Atlas-SNP	.											.	LTB	19	.	0			c.G163C						PASS	.						78.0	87.0	84.0					6																	31549636		1509	2709	4218	SO:0001630	splice_region_variant	4050	exon2			CCGTTACCTGGTT	L11015	CCDS4703.1, CCDS4704.1	6p21.3	2013-05-22			ENSG00000227507	ENSG00000227507		"""Tumor necrosis factor (ligand) superfamily"""	6711	protein-coding gene	gene with protein product		600978		TNFC		7916655, 1714477	Standard	NM_002341		Approved	p33, TNFSF3	uc003nuk.3	Q06643	OTTHUMG00000031136	ENST00000429299.2:c.163-1G>C	6.37:g.31549636C>G		Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	79	11	0.139241	NM_002341	P78370|Q52LU8|Q99761	Missense_Mutation	SNP	ENST00000429299.2	37	CCDS4703.1	.	.	.	.	.	.	.	.	.	.	C	17.12	3.307743	0.60305	.	.	ENSG00000227507	ENST00000429299	T	0.21361	2.01	5.45	5.45	0.79879	.	0.715933	0.12594	N	0.455328	T	0.22627	0.0546	L	0.49126	1.545	0.80722	D	1	D	0.67145	0.996	P	0.55161	0.77	T	0.00915	-1.1516	10	0.27082	T	0.32	-17.783	14.7884	0.69821	0.0:1.0:0.0:0.0	.	55	Q06643	TNFC_HUMAN	L	55	ENSP00000410481:V55L	ENSP00000410481:V55L	V	-	1	0	LTB	31657615	0.998000	0.40836	0.993000	0.49108	0.049000	0.14656	1.506000	0.35747	2.555000	0.86185	0.655000	0.94253	GTA	.	.	none		0.622	LTB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076239.3		Missense_Mutation
NMBR	4829	hgsc.bcm.edu	37	6	142399929	142399929	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:142399929T>C	ENST00000258042.1	-	2	674	c.534A>G	c.(532-534)gaA>gaG	p.E178E	NMBR_ENST00000480652.1_5'Flank	NM_002511.2	NP_002502.2	P28336	NMBR_HUMAN	neuromedin B receptor	178					G-protein coupled receptor signaling pathway (GO:0007186)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	bombesin receptor activity (GO:0004946)			breast(2)|central_nervous_system(3)|endometrium(3)|large_intestine(3)|lung(8)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	23	Breast(32;0.155)			OV - Ovarian serous cystadenocarcinoma(155;9.93e-06)|GBM - Glioblastoma multiforme(68;0.0013)		AAAACACCGCTTCGGGAACTG	0.512																																					p.E178E		Atlas-SNP	.											NMBR,NS,carcinoma,-2,1	NMBR	62	1	0			c.A534G						PASS	.						117.0	107.0	110.0					6																	142399929		2203	4300	6503	SO:0001819	synonymous_variant	4829	exon2			CACCGCTTCGGGA		CCDS5196.1	6q24.1	2014-02-21			ENSG00000135577	ENSG00000135577		"""GPCR / Class A : Bombesin receptors"""	7843	protein-coding gene	gene with protein product	"""bombesin receptor 1"""	162341					Standard	NM_002511		Approved	BB1	uc003qiu.3	P28336	OTTHUMG00000015704	ENST00000258042.1:c.534A>G	6.37:g.142399929T>C		Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	176	37	0.210227	NM_002511	E9KL38|Q5VUK8	Silent	SNP	ENST00000258042.1	37	CCDS5196.1																																																																																			.	.	none		0.512	NMBR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042479.1		
LOXL3	84695	hgsc.bcm.edu	37	2	74761669	74761669	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:74761669G>A	ENST00000264094.3	-	10	1883	c.1812C>T	c.(1810-1812)caC>caT	p.H604H	LOXL3_ENST00000393937.2_Silent_p.H459H|LOXL3_ENST00000409986.1_Silent_p.H459H|LOXL3_ENST00000409249.1_Intron|LOXL3_ENST00000409549.1_Silent_p.H548H	NM_032603.2	NP_115992.1	P58215	LOXL3_HUMAN	lysyl oxidase-like 3	604	Lysyl-oxidase like.				epithelial to mesenchymal transition (GO:0001837)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|nucleus (GO:0005634)	copper ion binding (GO:0005507)|protein-lysine 6-oxidase activity (GO:0004720)|scavenger receptor activity (GO:0005044)			endometrium(7)|kidney(2)|large_intestine(9)|lung(9)|ovary(1)|prostate(1)|urinary_tract(1)	30						CATGGCACTCGTGCCACACCC	0.607																																					p.H604H		Atlas-SNP	.											.	LOXL3	73	.	0			c.C1812T						PASS	.						41.0	42.0	42.0					2																	74761669		2203	4300	6503	SO:0001819	synonymous_variant	84695	exon10			GCACTCGTGCCAC	AF282619	CCDS1953.1, CCDS74527.1	2p13	2008-05-23			ENSG00000115318	ENSG00000115318			13869	protein-coding gene	gene with protein product		607163				11386757	Standard	NM_032603		Approved		uc002smp.1	P58215	OTTHUMG00000129953	ENST00000264094.3:c.1812C>T	2.37:g.74761669G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	114	6	0.0526316	NM_032603	D6W5J1|Q2EHP2|Q6IPL7|Q96RS1	Silent	SNP	ENST00000264094.3	37	CCDS1953.1																																																																																			.	.	none		0.607	LOXL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252215.1	NM_032603	
TOX3	27324	hgsc.bcm.edu	37	16	52478202	52478202	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:52478202T>C	ENST00000219746.9	-	6	1257	c.973A>G	c.(973-975)Agc>Ggc	p.S325G	TOX3_ENST00000407228.3_Missense_Mutation_p.S320G	NM_001080430.2	NP_001073899.2	O15405	TOX3_HUMAN	TOX high mobility group box family member 3	325					apoptotic process (GO:0006915)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|estrogen response element binding (GO:0034056)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)			NS(2)|endometrium(6)|kidney(1)|lung(8)|prostate(3)|stomach(3)|upper_aerodigestive_tract(1)	24						GAAACGAGGCTGGCCCTGTAT	0.478																																					p.S325G		Atlas-SNP	.											.	TOX3	121	.	0			c.A973G						PASS	.						44.0	43.0	43.0					16																	52478202		1826	4090	5916	SO:0001583	missense	27324	exon6			CGAGGCTGGCCCT	U80736	CCDS54008.1, CCDS54009.1	16q12.1	2008-02-05	2007-03-20	2007-03-20		ENSG00000103460		"""Trinucleotide (CAG) repeat containing"""	11972	protein-coding gene	gene with protein product		611416	"""trinucleotide repeat containing 9"""	TNRC9		9225980	Standard	NM_001080430		Approved	CAGF9	uc002egw.2	O15405		ENST00000219746.9:c.973A>G	16.37:g.52478202T>C	ENSP00000219746:p.Ser325Gly	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	63	7	0.111111	NM_001080430	B4DRD0|B5MCW4	Missense_Mutation	SNP	ENST00000219746.9	37	CCDS54009.1	.	.	.	.	.	.	.	.	.	.	T	19.68	3.873421	0.72180	.	.	ENSG00000103460	ENST00000219746;ENST00000407228	T;T	0.45668	0.89;0.89	5.35	5.35	0.76521	High mobility group, HMG1/HMG2, subgroup (1);High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (1);	0.000000	0.85682	D	0.000000	T	0.39627	0.1085	L	0.27053	0.805	0.58432	D	0.999997	P;P	0.35612	0.512;0.512	B;B	0.42522	0.39;0.39	T	0.37865	-0.9687	10	0.59425	D	0.04	.	15.6388	0.76977	0.0:0.0:0.0:1.0	.	320;325	B4DRD0;O15405	.;TOX3_HUMAN	G	325;320	ENSP00000219746:S325G;ENSP00000385705:S320G	ENSP00000219746:S325G	S	-	1	0	TOX3	51035703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.232000	0.72313	2.169000	0.68431	0.528000	0.53228	AGC	.	.	none		0.478	TOX3-003	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000422534.1	XM_049037	
RPS6KA2	6196	hgsc.bcm.edu	37	6	166862233	166862233	+	Silent	SNP	T	T	C	rs2230730	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:166862233T>C	ENST00000265678.4	-	14	1534	c.1311A>G	c.(1309-1311)acA>acG	p.T437T	RPS6KA2_ENST00000503859.1_Silent_p.T445T|RPS6KA2_ENST00000481261.2_Silent_p.T348T|RPS6KA2_ENST00000510118.1_Silent_p.T462T|RPS6KA2_ENST00000405189.3_Silent_p.T348T	NM_021135.4	NP_066958.2	Q15349	KS6A2_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 2	437	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|brain renin-angiotensin system (GO:0002035)|cardiac muscle cell apoptotic process (GO:0010659)|cellular response to carbohydrate stimulus (GO:0071322)|heart contraction (GO:0060047)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of meiosis (GO:0045835)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of apoptotic process (GO:0043065)|positive regulation of gene expression (GO:0010628)|regulation of protein processing (GO:0070613)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|synaptic transmission (GO:0007268)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|ribosomal protein S6 kinase activity (GO:0004711)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		Breast(66;2.04e-05)|Ovarian(120;0.0652)|Prostate(117;0.105)		OV - Ovarian serous cystadenocarcinoma(33;2.76e-18)|GBM - Glioblastoma multiforme(31;9.94e-06)|BRCA - Breast invasive adenocarcinoma(81;1.36e-05)		ACTCGGTGTCTGTGGCTTTAT	0.582													C|||	996	0.198882	0.1876	0.2723	5008	,	,		24814	0.0764		0.3082	False		,,,				2504	0.1759				p.T445T		Atlas-SNP	.											RPS6KA2_ENST00000503859,NS,carcinoma,-1,2	RPS6KA2	212	2	0			c.A1335G						scavenged	.	C	,	931,3475	736.1+/-410.7	99,733,1371	238.0	158.0	185.0		1335,1311	-8.8	0.6	6	dbSNP_120	185	2587,6013	688.1+/-404.3	387,1813,2100	no	coding-synonymous,coding-synonymous	RPS6KA2	NM_001006932.1,NM_021135.4	,	486,2546,3471	CC,CT,TT		30.0814,21.1303,27.0491	,	445/742,437/734	166862233	3518,9488	2203	4300	6503	SO:0001819	synonymous_variant	6196	exon15			GGTGTCTGTGGCT	L07598	CCDS5294.1, CCDS34570.1	6q27	2011-04-05	2002-08-29		ENSG00000071242	ENSG00000071242			10431	protein-coding gene	gene with protein product		601685	"""ribosomal protein S6 kinase, 90kD, polypeptide 2"""			8141249	Standard	NM_001006932		Approved	RSK, RSK3, HU-2	uc003qvc.1	Q15349	OTTHUMG00000016007	ENST00000265678.4:c.1311A>G	6.37:g.166862233T>C		Somatic	337	1	0.00296736		WXS	Illumina HiSeq	Phase_I	319	5	0.015674	NM_001006932	B3KTK9|Q15419|Q59GJ3|Q5TI68|Q96J38|Q9UJN5	Silent	SNP	ENST00000265678.4	37	CCDS5294.1																																																																																			T|0.764;C|0.236;A|0.000	0.236	strong		0.582	RPS6KA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043075.3	NM_021135	
RPAP3	79657	hgsc.bcm.edu	37	12	48090083	48090083	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:48090083G>T	ENST00000005386.3	-	5	636	c.521C>A	c.(520-522)gCg>gAg	p.A174E	RPAP3_ENST00000432584.3_Missense_Mutation_p.A15E|RPAP3_ENST00000380650.4_Missense_Mutation_p.A174E	NM_024604.2	NP_078880.2	Q9H6T3	RPAP3_HUMAN	RNA polymerase II associated protein 3	174										endometrium(2)|large_intestine(4)|liver(1)|lung(6)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	16	Lung SC(27;0.192)					ATATGCTGACGCTCTGTTCGT	0.358																																					p.A174E		Atlas-SNP	.											RPAP3,caecum,carcinoma,-1,1	RPAP3	45	1	0			c.C521A						scavenged	.						161.0	142.0	148.0					12																	48090083		2203	4300	6503	SO:0001583	missense	79657	exon5			GCTGACGCTCTGT	AK025561	CCDS8753.1, CCDS53782.1, CCDS53783.1	12q13.11	2013-01-10				ENSG00000005175		"""Tetratricopeptide (TTC) repeat domain containing"""	26151	protein-coding gene	gene with protein product		611477				17643375	Standard	NM_024604		Approved	FLJ21908, spag	uc001rpr.3	Q9H6T3	OTTHUMG00000169668	ENST00000005386.3:c.521C>A	12.37:g.48090083G>T	ENSP00000005386:p.Ala174Glu	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	171	5	0.0292398	NM_024604	B4DRW9|Q6PHR5	Missense_Mutation	SNP	ENST00000005386.3	37	CCDS8753.1	.	.	.	.	.	.	.	.	.	.	G	16.83	3.231151	0.58777	.	.	ENSG00000005175	ENST00000005386;ENST00000432584;ENST00000380650	T;T;T	0.74002	-0.8;-0.13;-0.8	6.02	4.22	0.49857	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.047393	0.85682	D	0.000000	D	0.91222	0.7234	H	0.98738	4.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.993;0.996	D	0.92935	0.6367	10	0.87932	D	0	.	12.086	0.53698	0.1375:0.0:0.8625:0.0	.	174;174	Q9H6T3-2;Q9H6T3	.;RPAP3_HUMAN	E	174;15;174	ENSP00000005386:A174E;ENSP00000401823:A15E;ENSP00000370024:A174E	ENSP00000005386:A174E	A	-	2	0	RPAP3	46376350	1.000000	0.71417	0.750000	0.31169	0.083000	0.17756	9.420000	0.97426	0.894000	0.36317	-0.143000	0.13931	GCG	.	.	none		0.358	RPAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405340.1	NM_024604	
CCDC64B	146439	hgsc.bcm.edu	37	16	3078165	3078165	+	Missense_Mutation	SNP	A	A	G	rs12448103	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:3078165A>G	ENST00000572449.1	-	10	1531	c.1469T>C	c.(1468-1470)cTg>cCg	p.L490P	CCDC64B_ENST00000573514.1_Missense_Mutation_p.L283P|CCDC64B_ENST00000389347.4_Missense_Mutation_p.L490P			A1A5D9	BICR2_HUMAN	coiled-coil domain containing 64B	490										breast(1)|endometrium(2)|large_intestine(1)	4						GCCCAGGCGCAGCGAGAAGCG	0.716													A|||	909	0.18151	0.0492	0.2925	5008	,	,		10148	0.128		0.2356	False		,,,				2504	0.2812				p.L490P		Atlas-SNP	.											CCDC64B,NS,carcinoma,0,1	CCDC64B	19	1	0			c.T1469C						scavenged	.	A	PRO/LEU	205,3283		5,195,1544	4.0	5.0	5.0		1469	5.2	0.8	16	dbSNP_120	5	1331,6363		97,1137,2613	yes	missense	CCDC64B	NM_001103175.1	98	102,1332,4157	GG,GA,AA		17.2992,5.8773,13.7364	probably-damaging	490/509	3078165	1536,9646	1744	3847	5591	SO:0001583	missense	146439	exon9			AGGCGCAGCGAGA	BC128602	CCDS45393.1	16p13.3	2008-07-04				ENSG00000162069			33584	protein-coding gene	gene with protein product							Standard	NM_001103175		Approved		uc002ctf.4	A1A5D9		ENST00000572449.1:c.1469T>C	16.37:g.3078165A>G	ENSP00000459043:p.Leu490Pro	Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	3	0.75	NM_001103175	Q658L9	Missense_Mutation	SNP	ENST00000572449.1	37	CCDS45393.1	382	0.1749084249084249	26	0.052845528455284556	112	0.30939226519337015	64	0.11188811188811189	180	0.23746701846965698	a	17.73	3.462111	0.63513	0.058773	0.172992	ENSG00000162069	ENST00000389347	T	0.36157	1.27	5.15	5.15	0.70609	.	0.119688	0.34879	N	0.003617	T	0.00012	0.0000	M	0.68952	2.095	0.23473	P	0.99760263	D	0.89917	1.0	D	0.91635	0.999	T	0.26018	-1.0115	9	0.30854	T	0.27	-7.2384	11.3817	0.49761	1.0:0.0:0.0:0.0	rs12448103	490	A1A5D9	BICR2_HUMAN	P	490	ENSP00000373998:L490P	ENSP00000373998:L490P	L	-	2	0	CCDC64B	3018166	0.249000	0.23941	0.820000	0.32676	0.129000	0.20672	0.546000	0.23284	1.957000	0.56846	0.454000	0.30748	CTG	A|0.823;G|0.177	0.177	strong		0.716	CCDC64B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436991.1		
KIRREL3	84623	hgsc.bcm.edu	37	11	126294687	126294687	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:126294687G>A	ENST00000525144.2	-	17	2374	c.2125C>T	c.(2125-2127)Cgg>Tgg	p.R709W	KIRREL3_ENST00000529097.2_Missense_Mutation_p.R697W|KIRREL3_ENST00000416561.2_Missense_Mutation_p.R176W	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	709	Ser-rich.				hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		TGGAACTCCCGCTCACAAAGC	0.627																																					p.R709W		Atlas-SNP	.											KIRREL3_ENST00000525144,NS,carcinoma,0,2	KIRREL3	183	2	0			c.C2125T						PASS	.						64.0	72.0	69.0					11																	126294687		2161	4274	6435	SO:0001583	missense	84623	exon17			ACTCCCGCTCACA	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.2125C>T	11.37:g.126294687G>A	ENSP00000435466:p.Arg709Trp	Somatic	144	0	0		WXS	Illumina HiSeq	Phase_I	122	31	0.254098	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Missense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.353005	0.82132	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000416561	T;T;T	0.53423	0.62;0.62;0.62	4.88	3.96	0.45880	.	0.000000	0.85682	D	0.000000	T	0.57961	0.2089	L	0.36672	1.1	0.58432	D	0.999993	D;D	0.89917	1.0;1.0	D;D	0.74023	0.982;0.982	T	0.62115	-0.6922	10	0.72032	D	0.01	-11.0324	14.353	0.66716	0.0:0.0:0.8508:0.1492	.	697;709	E9PRX9;Q8IZU9	.;KIRR3_HUMAN	W	709;697;176	ENSP00000435466:R709W;ENSP00000434081:R697W;ENSP00000408692:R176W	ENSP00000408692:R176W	R	-	1	2	KIRREL3	125799897	1.000000	0.71417	0.987000	0.45799	0.993000	0.82548	6.135000	0.71696	1.271000	0.44313	0.655000	0.94253	CGG	.	.	none		0.627	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
PRG4	10216	hgsc.bcm.edu	37	1	186276291	186276291	+	Silent	SNP	A	A	G	rs151267614	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:186276291A>G	ENST00000445192.2	+	7	1485	c.1440A>G	c.(1438-1440)aaA>aaG	p.K480K	PRG4_ENST00000367485.4_Silent_p.K387K|PRG4_ENST00000367483.4_Silent_p.K439K|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Silent_p.K437K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	480	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.K480K(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CCACTCCCAAAGAGCCTGCAC	0.662													-|||	610	0.121805	0.1051	0.072	5008	,	,		8182	0.1319		0.1541	False		,,,				2504	0.136				p.K480K		Atlas-SNP	.											PRG4,NS,carcinoma,0,1	PRG4	259	1	1	Substitution - coding silent(1)	prostate(1)	c.A1440G						scavenged	.						89.0	94.0	92.0					1																	186276291		2198	4275	6473	SO:0001819	synonymous_variant	10216	exon7			TCCCAAAGAGCCT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1440A>G	1.37:g.186276291A>G		Somatic	46	7	0.152174		WXS	Illumina HiSeq	Phase_I	45	15	0.333333	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			A|0.906;G|0.094	0.094	strong		0.662	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230404	23230404	+	Silent	SNP	A	A	G	rs115653109	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230404A>G	ENST00000526893.1	+	1	445	c.171A>G	c.(169-171)ggA>ggG	p.G57G	IGLL5_ENST00000531372.1_Silent_p.G57G|IGLL5_ENST00000532223.2_Silent_p.G57G|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	57						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCTCAGTTGGAAGCAGCCGAT	0.662													A|||	2	0.000399361	0.0015	0.0	5008	,	,		10542	0.0		0.0	False		,,,				2504	0.0				p.E22G		Atlas-SNP	.											.	IGLL5	26	.	0			c.A65G						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			AGTTGGAAGCAGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.171A>G	22.37:g.23230404A>G		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	59	14	0.237288	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			A|0.999;G|0.001	0.001	strong		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
OBSCN	84033	hgsc.bcm.edu	37	1	228482059	228482059	+	Missense_Mutation	SNP	G	G	T	rs56218706	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:228482059G>T	ENST00000422127.1	+	42	11382	c.11338G>T	c.(11338-11340)Ggg>Tgg	p.G3780W	RP5-1139B12.4_ENST00000602778.1_RNA|OBSCN_ENST00000284548.11_Missense_Mutation_p.G3780W|OBSCN_ENST00000366707.4_Missense_Mutation_p.G899W|OBSCN_ENST00000366709.4_Missense_Mutation_p.G899W|OBSCN_ENST00000570156.2_Missense_Mutation_p.G4209W|OBSCN_ENST00000359599.6_Missense_Mutation_p.G2627W	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3780	Ig-like 38.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGTGGATGCCGGGGAGTACTC	0.602																																					p.G4209W		Atlas-SNP	.											OBSCN_ENST00000570156,NS,carcinoma,-2,4	OBSCN	2142	4	0			c.G12625T						scavenged	.						140.0	144.0	143.0					1																	228482059		2160	4259	6419	SO:0001583	missense	84033	exon47			GATGCCGGGGAGT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.11338G>T	1.37:g.228482059G>T	ENSP00000409493:p.Gly3780Trp	Somatic	386	3	0.00777202		WXS	Illumina HiSeq	Phase_I	356	4	0.011236	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.	.	.	.	.	.	.	.	.	.	G	18.30	3.594671	0.66219	.	.	ENSG00000154358	ENST00000284548;ENST00000422127;ENST00000366707;ENST00000366709;ENST00000359599	T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26	4.98	4.05	0.47172	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.180214	0.35555	N	0.003125	T	0.64438	0.2598	H	0.99863	4.86	0.51012	D	0.999902	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.83351	-0.0003	10	0.87932	D	0	.	15.6657	0.77227	0.0:0.1373:0.8627:0.0	.	3780;3780	Q5VST9;Q5VST9-3	OBSCN_HUMAN;.	W	3780;3780;899;899;2627	ENSP00000284548:G3780W;ENSP00000409493:G3780W;ENSP00000355668:G899W;ENSP00000355670:G899W;ENSP00000352613:G2627W	ENSP00000284548:G3780W	G	+	1	0	OBSCN	226548682	1.000000	0.71417	0.903000	0.35520	0.190000	0.23558	5.384000	0.66225	1.314000	0.45095	0.508000	0.49915	GGG	G|0.979;A|0.021	.	alt		0.602	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
HSP90AA1	3320	hgsc.bcm.edu	37	14	102552577	102552577	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:102552577C>G	ENST00000216281.8	-	2	344	c.139G>C	c.(139-141)Gag>Cag	p.E47Q	HSP90AA1_ENST00000334701.7_Missense_Mutation_p.E169Q|HSP90AA1_ENST00000441629.2_5'UTR	NM_005348.3	NP_005339.3	P07900	HS90A_HUMAN	heat shock protein 90kDa alpha (cytosolic), class A member 1	47					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone-mediated protein complex assembly (GO:0051131)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|mitochondrial transport (GO:0006839)|mitotic cell cycle (GO:0000278)|nitric oxide metabolic process (GO:0046209)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|protein import into mitochondrial outer membrane (GO:0045040)|protein refolding (GO:0042026)|regulation of nitric-oxide synthase activity (GO:0050999)|response to unfolded protein (GO:0006986)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle lumen (GO:0071682)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|identical protein binding (GO:0042802)|MHC class II protein complex binding (GO:0023026)|nitric-oxide synthase regulator activity (GO:0030235)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(6)|large_intestine(3)|liver(1)|lung(10)|ovary(2)|prostate(1)	28					Nedocromil(DB00716)|Rifabutin(DB00615)	GAAATGAGCTCTCTCAGAAAG	0.403																																					p.E169Q		Atlas-SNP	.											.	HSP90AA1	65	.	0			c.G505C						PASS	.						51.0	53.0	52.0					14																	102552577		2203	4300	6503	SO:0001583	missense	3320	exon3			TGAGCTCTCTCAG	M27024	CCDS9967.1, CCDS32160.1	14q32.33	2011-09-02	2006-02-24	2006-02-24	ENSG00000080824	ENSG00000080824		"""Heat shock proteins / HSPC"""	5253	protein-coding gene	gene with protein product		140571	"""heat shock 90kD protein 1, alpha"", ""heat shock 90kDa protein 1, alpha"""	HSPC1, HSPCA		2527334, 16269234	Standard	NM_001017963		Approved	Hsp89, Hsp90, FLJ31884, HSP90N	uc001ykv.4	P07900		ENST00000216281.8:c.139G>C	14.37:g.102552577C>G	ENSP00000216281:p.Glu47Gln	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	117	30	0.25641	NM_001017963	A8K500|B3KPJ9|Q2PP14|Q5CAQ6|Q5CAQ7|Q9BVQ5	Missense_Mutation	SNP	ENST00000216281.8	37	CCDS9967.1	.	.	.	.	.	.	.	.	.	.	C	8.396	0.840777	0.16891	.	.	ENSG00000080824	ENST00000216281;ENST00000334701;ENST00000553585	D;D;D	0.85411	-1.98;-1.98;-1.98	3.79	2.88	0.33553	Heat shock protein Hsp90, conserved site (1);Heat shock protein Hsp90, N-terminal (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	U	0.000000	D	0.96522	0.8865	H	0.99993	5.365	0.80722	D	1	D;D	0.69078	0.997;0.992	D;D	0.78314	0.99;0.991	D	0.96129	0.9091	10	0.87932	D	0	.	12.6451	0.56729	0.1672:0.8328:0.0:0.0	.	169;47	P07900-2;P07900	.;HS90A_HUMAN	Q	47;169;47	ENSP00000216281:E47Q;ENSP00000335153:E169Q;ENSP00000450712:E47Q	ENSP00000216281:E47Q	E	-	1	0	HSP90AA1	101622330	1.000000	0.71417	0.999000	0.59377	0.175000	0.22909	7.473000	0.81007	0.694000	0.31654	-0.312000	0.09012	GAG	.	.	none		0.403	HSP90AA1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414952.2	NM_005348	
DOCK5	80005	hgsc.bcm.edu	37	8	25198452	25198452	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:25198452T>C	ENST00000276440.7	+	23	2431	c.2387T>C	c.(2386-2388)cTt>cCt	p.L796P		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	796					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		CAGTTATTTCTTGCTTTCAAT	0.423																																					p.L796P	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.T2387C						PASS	.						85.0	81.0	82.0					8																	25198452		2203	4300	6503	SO:0001583	missense	80005	exon23			TATTTCTTGCTTT		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.2387T>C	8.37:g.25198452T>C	ENSP00000276440:p.Leu796Pro	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	87	13	0.149425	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Missense_Mutation	SNP	ENST00000276440.7	37	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	T	11.20	1.567446	0.28003	.	.	ENSG00000147459	ENST00000276440	T	0.27890	1.64	4.99	4.99	0.66335	Armadillo-type fold (1);	0.222771	0.39210	N	0.001427	T	0.28665	0.0710	L	0.40543	1.245	0.80722	D	1	B;B;B	0.30664	0.186;0.289;0.186	B;B;B	0.33339	0.162;0.162;0.162	T	0.05954	-1.0854	10	0.36615	T	0.2	.	14.8781	0.70510	0.0:0.0:0.0:1.0	.	786;571;796	D3DSS6;Q68DL4;Q9H7D0	.;.;DOCK5_HUMAN	P	796	ENSP00000276440:L796P	ENSP00000276440:L796P	L	+	2	0	DOCK5	25254369	1.000000	0.71417	0.892000	0.35008	0.266000	0.26442	7.525000	0.81892	2.095000	0.63458	0.528000	0.53228	CTT	.	.	none		0.423	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
NPAP1	23742	hgsc.bcm.edu	37	15	24921512	24921512	+	Silent	SNP	G	G	A	rs35737140	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:24921512G>A	ENST00000329468.2	+	1	972	c.498G>A	c.(496-498)ccG>ccA	p.P166P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	166					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)		p.P166P(1)									ATGAGGATCCGGTGCAGATCG	0.627													G|||	13	0.00259585	0.0	0.0014	5008	,	,		15046	0.0		0.005	False		,,,				2504	0.0072				p.P166P		Atlas-SNP	.											C15orf2,colon,carcinoma,0,5	.	.	5	1	Substitution - coding silent(1)	central_nervous_system(1)	c.G498A						scavenged	.	G		1,4405		0,1,2202	43.0	37.0	39.0		498	-3.2	0.0	15	dbSNP_126	39	38,8562		0,38,4262	no	coding-synonymous	C15orf2	NM_018958.2		0,39,6464	AA,AG,GG		0.4419,0.0227,0.2999		166/1157	24921512	39,12967	2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			GGATCCGGTGCAG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.498G>A	15.37:g.24921512G>A		Somatic	46	0	0		WXS	Illumina HiSeq	Phase_I	62	2	0.0322581	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			G|0.997;A|0.003	0.003	strong		0.627	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
LRP1B	53353	hgsc.bcm.edu	37	2	141356256	141356256	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:141356256A>G	ENST00000389484.3	-	43	8109	c.7138T>C	c.(7138-7140)Tca>Cca	p.S2380P		NM_018557.2	NP_061027.2	Q9NZR2	LRP1B_HUMAN	low density lipoprotein receptor-related protein 1B	2380					protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)	integral component of membrane (GO:0016021)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|low-density lipoprotein receptor activity (GO:0005041)			NS(5)|autonomic_ganglia(1)|biliary_tract(1)|breast(3)|central_nervous_system(7)|endometrium(25)|haematopoietic_and_lymphoid_tissue(10)|kidney(27)|large_intestine(98)|liver(4)|lung(337)|ovary(15)|pancreas(6)|prostate(11)|skin(30)|stomach(2)|upper_aerodigestive_tract(19)|urinary_tract(5)	606		all_cancers(3;1.1e-60)|all_epithelial(3;1.94e-59)|all_lung(3;1.09e-24)|Lung NSC(3;5.65e-24)|Esophageal squamous(3;5.41e-13)|Renal(3;0.000147)|Breast(3;0.000527)|Hepatocellular(3;0.011)|all_neural(3;0.014)|Colorectal(150;0.101)		UCEC - Uterine corpus endometrioid carcinoma (2;0.00139)|Epithelial(1;1.25e-24)|all cancers(1;8.86e-24)|OV - Ovarian serous cystadenocarcinoma(1;2.45e-12)|LUSC - Lung squamous cell carcinoma(1;2.97e-10)|Lung(1;6.05e-09)|BRCA - Breast invasive adenocarcinoma(221;0.0103)		CTGCCATCTGAGAAATACAGC	0.398										TSP Lung(27;0.18)																											p.S2380P	Colon(99;50 2074 2507 20106)	Atlas-SNP	.											LRP1B,NS,carcinoma,+1,3	LRP1B	1315	3	0			c.T7138C						PASS	.						165.0	147.0	153.0					2																	141356256		2203	4300	6503	SO:0001583	missense	53353	exon43			CATCTGAGAAATA	AF176832	CCDS2182.1	2q21.2	2013-05-29	2010-01-26		ENSG00000168702	ENSG00000168702		"""Low density lipoprotein receptors"""	6693	protein-coding gene	gene with protein product	"""LRP-deleted in tumors"""	608766				10766186	Standard	NM_018557		Approved	LRP-DIT, LRPDIT	uc002tvj.1	Q9NZR2	OTTHUMG00000131799	ENST00000389484.3:c.7138T>C	2.37:g.141356256A>G	ENSP00000374135:p.Ser2380Pro	Somatic	246	0	0		WXS	Illumina HiSeq	Phase_I	295	58	0.19661	NM_018557	Q8WY29|Q8WY30|Q8WY31	Missense_Mutation	SNP	ENST00000389484.3	37	CCDS2182.1	.	.	.	.	.	.	.	.	.	.	A	19.53	3.845113	0.71603	.	.	ENSG00000168702	ENST00000389484;ENST00000544579	D	0.92249	-3.0	5.64	4.42	0.53409	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.64402	U	0.000003	D	0.94594	0.8258	M	0.88570	2.965	0.51233	D	0.999919	D	0.57899	0.981	P	0.52109	0.69	D	0.94914	0.8067	10	0.56958	D	0.05	.	12.4181	0.55504	0.8599:0.1401:0.0:0.0	.	2380	Q9NZR2	LRP1B_HUMAN	P	2380;2318	ENSP00000374135:S2380P	ENSP00000374135:S2380P	S	-	1	0	LRP1B	141072726	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.291000	0.78721	2.156000	0.67533	0.377000	0.23210	TCA	.	.	none		0.398	LRP1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254736.2	NM_018557	
USP44	84101	hgsc.bcm.edu	37	12	95926864	95926864	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:95926864T>C	ENST00000258499.3	-	2	1457	c.1169A>G	c.(1168-1170)cAa>cGa	p.Q390R	USP44_ENST00000393091.2_Missense_Mutation_p.Q390R|USP44_ENST00000537435.2_Missense_Mutation_p.Q390R|USP44_ENST00000552440.1_Missense_Mutation_p.Q390R	NM_001278393.1|NM_032147.2	NP_001265322.1|NP_115523.2	Q9H0E7	UBP44_HUMAN	ubiquitin specific peptidase 44	390	USP.				mitotic nuclear division (GO:0007067)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deubiquitination (GO:0016579)|regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090266)|regulation of spindle checkpoint (GO:0090231)	nucleus (GO:0005634)	ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(5)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	36						CCACATGACTTGGAACAAAGT	0.453																																					p.Q390R		Atlas-SNP	.											.	USP44	83	.	0			c.A1169G						PASS	.						140.0	127.0	131.0					12																	95926864		2203	4300	6503	SO:0001583	missense	84101	exon2			ATGACTTGGAACA	AK027434	CCDS9053.1	12q21.33	2005-08-08	2005-08-08			ENSG00000136014		"""Ubiquitin-specific peptidases"""	20064	protein-coding gene	gene with protein product		610993	"""ubiquitin specific protease 44"""			12838346	Standard	NM_001278393		Approved	FLJ14528	uc001teg.3	Q9H0E7		ENST00000258499.3:c.1169A>G	12.37:g.95926864T>C	ENSP00000258499:p.Gln390Arg	Somatic	195	0	0		WXS	Illumina HiSeq	Phase_I	250	62	0.248	NM_032147	B2RDW3	Missense_Mutation	SNP	ENST00000258499.3	37	CCDS9053.1	.	.	.	.	.	.	.	.	.	.	T	1.962	-0.438603	0.04636	.	.	ENSG00000136014	ENST00000258499;ENST00000393091;ENST00000552440;ENST00000537435	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.1	5.1	0.69264	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.100708	0.64402	D	0.000001	T	0.14270	0.0345	N	0.04090	-0.28	0.53688	D	0.999972	B	0.11235	0.004	B	0.18871	0.023	T	0.08973	-1.0696	10	0.05833	T	0.94	.	15.189	0.73028	0.0:0.0:0.0:1.0	.	390	Q9H0E7	UBP44_HUMAN	R	390	ENSP00000258499:Q390R;ENSP00000376806:Q390R;ENSP00000448670:Q390R;ENSP00000442629:Q390R	ENSP00000258499:Q390R	Q	-	2	0	USP44	94450995	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.495000	0.53280	2.049000	0.60858	0.454000	0.30748	CAA	.	.	none		0.453	USP44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408312.1	NM_032147	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386300	7386300	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:7386300G>A	ENST00000412468.2	+	2	1112	c.997G>A	c.(997-999)Gaa>Aaa	p.E333K	POLR2A_ENST00000572844.1_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000322644.6_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	333						integral component of membrane (GO:0016021)											CTGTGAGAGGGAAGGGAAGGT	0.557																																					p.E333K		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,-1,1	.	.	1	0			c.G997A						scavenged	.						60.0	59.0	59.0					17																	7386300		2203	4300	6503	SO:0001583	missense	643664	exon2			GAGAGGGAAGGGA		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.997G>A	17.37:g.7386300G>A	ENSP00000396523:p.Glu333Lys	Somatic	160	1	0.00625		WXS	Illumina HiSeq	Phase_I	111	3	0.027027	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	0.033	-1.322479	0.01320	.	.	ENSG00000181222	ENST00000412468	T	0.26518	1.73	4.69	1.44	0.22558	.	.	.	.	.	T	0.14056	0.0340	L	0.36672	1.1	0.09310	N	1	B	0.18013	0.025	B	0.15870	0.014	T	0.37526	-0.9702	9	0.02654	T	1	-0.2286	4.7772	0.13185	0.2637:0.1728:0.5636:0.0	.	333	P0C7Q6	S35G6_HUMAN	K	333	ENSP00000396523:E333K	ENSP00000396523:E333K	E	+	1	0	SLC35G6	7327024	1.000000	0.71417	0.321000	0.25320	0.451000	0.32288	4.403000	0.59729	0.499000	0.27970	-0.225000	0.12378	GAA	.	.	none		0.557	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
PRG4	10216	hgsc.bcm.edu	37	1	186277277	186277277	+	Missense_Mutation	SNP	G	G	A	rs113308576		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:186277277G>A	ENST00000445192.2	+	7	2471	c.2426G>A	c.(2425-2427)gGg>gAg	p.G809E	PRG4_ENST00000367485.4_Missense_Mutation_p.G716E|PRG4_ENST00000367483.4_Missense_Mutation_p.G768E|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Missense_Mutation_p.G766E	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	809	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.G809E(2)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						ACCACCAAGGGGCCCACATCC	0.597																																					p.G809E		Atlas-SNP	.											PRG4,NS,carcinoma,0,2	PRG4	259	2	2	Substitution - Missense(2)	large_intestine(1)|prostate(1)	c.G2426A						scavenged	.						215.0	240.0	232.0					1																	186277277		2203	4300	6503	SO:0001583	missense	10216	exon7			CCAAGGGGCCCAC	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2426G>A	1.37:g.186277277G>A	ENSP00000399679:p.Gly809Glu	Somatic	218	8	0.0366972		WXS	Illumina HiSeq	Phase_I	289	11	0.0380623	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Missense_Mutation	SNP	ENST00000445192.2	37	CCDS1369.1	.	.	.	.	.	.	.	.	.	.	A	4.604	0.112258	0.08831	.	.	ENSG00000116690	ENST00000367486;ENST00000367482;ENST00000367483;ENST00000367485;ENST00000445192	T;T;T;T	0.04809	3.56;3.66;3.55;3.67	2.72	-2.01	0.07410	.	.	.	.	.	T	0.01661	0.0053	N	0.03115	-0.41	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.47947	-0.9077	8	.	.	.	0.0864	1.0004	0.01475	0.3795:0.2548:0.23:0.1358	.	675;716;809;768	Q92954-4;Q92954-3;Q92954;Q92954-2	.;.;PRG4_HUMAN;.	E	766;675;768;716;809	ENSP00000356456:G766E;ENSP00000356453:G768E;ENSP00000356455:G716E;ENSP00000399679:G809E	.	G	+	2	0	PRG4	184543900	0.001000	0.12720	0.000000	0.03702	0.039000	0.13416	0.727000	0.25999	-0.259000	0.09432	-1.958000	0.00481	GGG	G|0.500;A|0.500	0.500	weak		0.597	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
DCAF12	25853	hgsc.bcm.edu	37	9	34107505	34107505	+	Missense_Mutation	SNP	C	C	T	rs11557154	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:34107505C>T	ENST00000361264.4	-	3	733	c.392G>A	c.(391-393)cGg>cAg	p.R131Q	DCAF12_ENST00000463286.1_5'UTR	NM_015397.3	NP_056212.1	Q5T6F0	DCA12_HUMAN	DDB1 and CUL4 associated factor 12	131			R -> Q (in dbSNP:rs11557154). {ECO:0000269|PubMed:15489334}.		protein ubiquitination (GO:0016567)	centrosome (GO:0005813)|Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)				breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)	11						TCCAGGCTCCCGGTCTTTCAG	0.483													C|||	1137	0.227037	0.0106	0.2147	5008	,	,		19495	0.6012		0.1372	False		,,,				2504	0.2352				p.R131Q		Atlas-SNP	.											DCAF12,colon,carcinoma,+1,1	DCAF12	37	1	0			c.G392A						scavenged	.	C	GLN/ARG	151,4255	103.8+/-142.4	3,145,2055	104.0	100.0	102.0		392	4.2	1.0	9	dbSNP_120	102	1064,7536	222.9+/-259.8	78,908,3314	yes	missense	DCAF12	NM_015397.3	43	81,1053,5369	TT,TC,CC		12.3721,3.4271,9.3418	probably-damaging	131/454	34107505	1215,11791	2203	4300	6503	SO:0001583	missense	25853	exon3			GGCTCCCGGTCTT	AB067479	CCDS6549.1	9p11.2	2013-01-09	2009-07-17	2009-07-17	ENSG00000198876	ENSG00000198876		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	19911	protein-coding gene	gene with protein product	"""cancer/testis antigen 102"""		"""KIAA1892"", ""WD repeat domain 40A"""	KIAA1892, WDR40A		11572484, 9110174	Standard	NM_015397		Approved	DKFZP434O125, MGC1058, CT102, TCC52	uc003ztt.2	Q5T6F0	OTTHUMG00000019806	ENST00000361264.4:c.392G>A	9.37:g.34107505C>T	ENSP00000355114:p.Arg131Gln	Somatic	155	1	0.00645161		WXS	Illumina HiSeq	Phase_I	144	3	0.0208333	NM_015397	A8KA70|D3DRL6|Q5T6E9|Q5T6F1|Q6P3V0|Q7L4F8|Q96PZ5|Q9NXA9|Q9UFJ1	Missense_Mutation	SNP	ENST00000361264.4	37	CCDS6549.1	532	0.24358974358974358	10	0.02032520325203252	76	0.20994475138121546	335	0.5856643356643356	111	0.14643799472295516	C	22.7	4.325631	0.81580	0.034271	0.123721	ENSG00000198876	ENST00000361264;ENST00000396990;ENST00000450964	T;T;T	0.30182	1.54;1.54;1.54	5.07	4.17	0.49024	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	L	0.58101	1.795	0.20489	P	0.999890017	D	0.64830	0.994	P	0.47376	0.545	T	0.46735	-0.9170	9	0.31617	T	0.26	-22.0702	11.837	0.52330	0.0:0.9192:0.0:0.0808	rs11557154;rs17855881;rs11557154	131	Q5T6F0	DCA12_HUMAN	Q	131;113;110	ENSP00000355114:R131Q;ENSP00000380187:R113Q;ENSP00000415833:R110Q	ENSP00000355114:R131Q	R	-	2	0	DCAF12	34097505	1.000000	0.71417	0.976000	0.42696	0.769000	0.43574	7.287000	0.78681	1.368000	0.46115	0.655000	0.94253	CGG	C|0.846;T|0.154	0.154	strong		0.483	DCAF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052133.2	NM_015397	
NEFH	4744	hgsc.bcm.edu	37	22	29885823	29885823	+	Missense_Mutation	SNP	A	A	T	rs145125701		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:29885823A>T	ENST00000310624.6	+	4	2227	c.2194A>T	c.(2194-2196)Acc>Tcc	p.T732S		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	738	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.				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						AGAAGCAAAGACCCCCGAGAA	0.542																																					p.T732S		Atlas-SNP	.											NEFH,NS,lymphoid_neoplasm,0,2	NEFH	178	2	0			c.A2194T						scavenged	.						105.0	109.0	108.0					22																	29885823		2203	4300	6503	SO:0001583	missense	4744	exon4			GCAAAGACCCCCG		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	ENST00000310624.6:c.2194A>T	22.37:g.29885823A>T	ENSP00000311997:p.Thr732Ser	Somatic	189	4	0.021164		WXS	Illumina HiSeq	Phase_I	231	7	0.030303	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	a	0.001	-3.519686	0.00010	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	T	0.80033	-1.33	3.79	0.344	0.16006	.	0.265420	0.27315	N	0.019939	T	0.34803	0.0910	N	0.00185	-1.9	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.50939	-0.8768	10	0.02654	T	1	.	4.2709	0.10785	0.1831:0.1132:0.0:0.7037	.	738	P12036	NFH_HUMAN	S	732	ENSP00000311997:T732S	ENSP00000311997:T732S	T	+	1	0	NEFH	28215823	0.000000	0.05858	0.661000	0.29709	0.007000	0.05969	-2.683000	0.00835	-0.106000	0.12110	-2.653000	0.00148	ACC	.	.	weak		0.542	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
MUC4	4585	hgsc.bcm.edu	37	3	195509843	195509843	+	Missense_Mutation	SNP	C	C	T	rs200739317		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195509843C>T	ENST00000463781.3	-	2	9067	c.8608G>A	c.(8608-8610)Gct>Act	p.A2870T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2870T|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)		ACTGAGGAAGCGTCGGTGACA	0.597																																					p.A2870T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G8608A						scavenged	.						24.0	21.0	22.0					3																	195509843		675	1566	2241	SO:0001583	missense	4585	exon2			AGGAAGCGTCGGT	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.8608G>A	3.37:g.195509843C>T	ENSP00000417498:p.Ala2870Thr	Somatic	448	16	0.0357143		WXS	Illumina HiSeq	Phase_I	489	29	0.0593047	NM_018406	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	15.45	2.838365	0.51057	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31769	1.48;1.48	.	.	.	.	.	.	.	.	T	0.28499	0.0705	N	0.14661	0.345	0.20821	N	0.999847	D	0.69078	0.997	D	0.65573	0.936	T	0.15925	-1.0420	7	.	.	.	.	4.8018	0.13301	0.3429:0.657:0.0:1.0E-4	.	2742	E7ESK3	.	T	2870	ENSP00000417498:A2870T;ENSP00000420243:A2870T	.	A	-	1	0	MUC4	196994622	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.830000	0.00355	-0.000000	0.14550	0.000000	0.15137	GCT	.	.	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
RBMXL2	27288	hgsc.bcm.edu	37	11	7111451	7111451	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:7111451G>T	ENST00000306904.5	+	1	1287	c.1100G>T	c.(1099-1101)cGg>cTg	p.R367L		NM_014469.4	NP_055284.3	O75526	RMXL2_HUMAN	RNA binding motif protein, X-linked-like 2	367	Arg/Gly/Pro-rich.					nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15				Epithelial(150;5.14e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		TCTTACAGCCGGTCAGGCTGC	0.652																																					p.R367L		Atlas-SNP	.											.	RBMXL2	47	.	0			c.G1100T						PASS	.						12.0	14.0	14.0					11																	7111451		2198	4295	6493	SO:0001583	missense	27288	exon1			ACAGCCGGTCAGG	AF069682	CCDS7777.1	11p15	2013-07-16				ENSG00000170748		"""RNA binding motif (RRM) containing"""	17886	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G T"""	605444				10958650	Standard	NM_014469		Approved	HNRNPG-T, HNRPGT	uc001mfc.2	O75526		ENST00000306904.5:c.1100G>T	11.37:g.7111451G>T	ENSP00000304139:p.Arg367Leu	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	67	14	0.208955	NM_014469	Q6PEZ2|Q9NQU0	Missense_Mutation	SNP	ENST00000306904.5	37	CCDS7777.1	.	.	.	.	.	.	.	.	.	.	G	13.21	2.170468	0.38315	.	.	ENSG00000170748	ENST00000306904	T	0.76448	-1.02	3.97	3.97	0.46021	.	0.162448	0.51477	U	0.000087	T	0.69931	0.3166	L	0.47716	1.5	0.29826	N	0.830395	P	0.48764	0.915	B	0.38712	0.28	T	0.74509	-0.3642	10	0.66056	D	0.02	.	14.3415	0.66630	0.0:0.0:1.0:0.0	.	367	O75526	HNRGT_HUMAN	L	367	ENSP00000304139:R367L	ENSP00000304139:R367L	R	+	2	0	RBMXL2	7068027	1.000000	0.71417	0.920000	0.36463	0.112000	0.19704	6.007000	0.70731	2.492000	0.84095	0.655000	0.94253	CGG	.	.	none		0.652	RBMXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384552.1	NM_014469	
ENTPD5	957	hgsc.bcm.edu	37	14	74441684	74441684	+	Silent	SNP	G	G	A	rs2074932	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:74441684G>A	ENST00000334696.6	-	11	1046	c.727C>T	c.(727-729)Ctg>Ttg	p.L243L	ENTPD5_ENST00000557325.1_Silent_p.L243L	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	243					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		CCAAATCCCAGGTAACTGTAA	0.483													A|||	2442	0.48762	0.3707	0.6787	5008	,	,		19267	0.2649		0.6123	False		,,,				2504	0.6115				p.L243L		Atlas-SNP	.											ENTPD5,NS,carcinoma,+1,1	ENTPD5	26	1	0			c.C727T						PASS	.	A		1737,2669	647.9+/-398.6	361,1015,827	139.0	129.0	132.0		727	5.3	1.0	14	dbSNP_96	132	5360,3240	486.5+/-371.9	1674,2012,614	no	coding-synonymous	ENTPD5	NM_001249.2		2035,3027,1441	AA,AG,GG		37.6744,39.4235,45.4329		243/429	74441684	7097,5909	2203	4300	6503	SO:0001819	synonymous_variant	957	exon11			ATCCCAGGTAACT	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"""proto-oncogene CPH"""	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.727C>T	14.37:g.74441684G>A		Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	116	7	0.0603448	NM_001249	A1L4C5|Q96RX0	Silent	SNP	ENST00000334696.6	37	CCDS9825.1																																																																																			G|0.494;A|0.506	0.506	strong		0.483	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
IGSF9B	22997	hgsc.bcm.edu	37	11	133790483	133790483	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:133790483G>A	ENST00000321016.8	-	18	3367	c.3137C>T	c.(3136-3138)cCc>cTc	p.P1046L	IGSF9B_ENST00000533871.2_Missense_Mutation_p.P1046L			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	1046	Pro-rich.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		CCCCCCGAAGGGGAATTCTGG	0.662																																					p.P1046L		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C3137T						PASS	.						45.0	54.0	51.0					11																	133790483		1935	4142	6077	SO:0001583	missense	22997	exon18			CCGAAGGGGAATT	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.3137C>T	11.37:g.133790483G>A	ENSP00000317980:p.Pro1046Leu	Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	151	39	0.258278	NM_014987	G5EA26	Missense_Mutation	SNP	ENST00000321016.8	37		.	.	.	.	.	.	.	.	.	.	G	17.22	3.335293	0.60853	.	.	ENSG00000080854	ENST00000321016;ENST00000533871	T;T	0.69561	-0.09;-0.41	4.82	4.82	0.62117	.	0.159476	0.29737	N	0.011322	T	0.71341	0.3328	N	0.19112	0.55	0.58432	D	0.999997	D	0.89917	1.0	D	0.80764	0.994	T	0.75045	-0.3456	10	0.51188	T	0.08	.	17.5246	0.87796	0.0:0.0:1.0:0.0	.	1046	Q9UPX0	TUTLB_HUMAN	L	1046;888	ENSP00000317980:P1046L;ENSP00000436552:P888L	ENSP00000317980:P1046L	P	-	2	0	IGSF9B	133295693	1.000000	0.71417	1.000000	0.80357	0.937000	0.57800	7.551000	0.82182	2.220000	0.72140	0.455000	0.32223	CCC	.	.	none		0.662	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887149	9887149	+	Missense_Mutation	SNP	G	G	C	rs11662946	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:9887149G>C	ENST00000306084.6	+	2	872	c.673G>C	c.(673-675)Gcc>Ccc	p.A225P	TXNDC2_ENST00000536353.2_Intron|TXNDC2_ENST00000357775.5_Missense_Mutation_p.A158P	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	225	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.		A -> P (in dbSNP:rs11662946).		cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						GGGCAATATTGCCAAGACCTC	0.572													g|||	327	0.0652955	0.0477	0.0591	5008	,	,		22613	0.0228		0.0716	False		,,,				2504	0.1309				p.A225P		Atlas-SNP	.											TXNDC2_ENST00000306084,colon,carcinoma,-1,2	TXNDC2	168	2	0			c.G673C						scavenged	.	G	PRO/ALA,PRO/ALA	218,4188	131.8+/-168.3	4,210,1989	130.0	132.0	131.0		673,472	-2.8	0.0	18	dbSNP_120	131	668,7932	167.1+/-218.9	29,610,3661	no	missense,missense	TXNDC2	NM_001098529.1,NM_032243.5	27,27	33,820,5650	CC,CG,GG		7.7674,4.9478,6.8122	benign,benign	225/554,158/487	9887149	886,12120	2203	4300	6503	SO:0001583	missense	84203	exon2			AATATTGCCAAGA	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.673G>C	18.37:g.9887149G>C	ENSP00000304908:p.Ala225Pro	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	145	8	0.0551724	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	105	0.04807692307692308	14	0.028455284552845527	20	0.055248618784530384	16	0.027972027972027972	55	0.07255936675461741	g	0.015	-1.566545	0.00903	0.049478	0.077674	ENSG00000168454	ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.11604	2.76;2.76	3.14	-2.78	0.05859	.	2.212560	0.02264	N	0.067858	T	0.00144	0.0004	N	0.00377	-1.585	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.35375	-0.9791	9	.	.	.	.	2.2647	0.04076	0.1466:0.2121:0.4354:0.2058	rs11662946;rs11662946	225	Q86VQ3	TXND2_HUMAN	P	158;225;225	ENSP00000350419:A158P;ENSP00000304908:A225P	.	A	+	1	0	TXNDC2	9877149	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.313000	0.08103	-0.458000	0.07023	-0.266000	0.10368	GCC	G|0.937;C|0.063	0.063	strong		0.572	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
CPXCR1	53336	hgsc.bcm.edu	37	X	88008609	88008609	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chrX:88008609A>G	ENST00000276127.4	+	3	453	c.194A>G	c.(193-195)cAa>cGa	p.Q65R	CPXCR1_ENST00000373111.1_Missense_Mutation_p.Q65R	NM_033048.5	NP_149037	Q8N123	CPXCR_HUMAN	CPX chromosome region, candidate 1	65							metal ion binding (GO:0046872)			NS(1)|cervix(1)|kidney(1)|large_intestine(11)|liver(1)|lung(20)|ovary(3)|upper_aerodigestive_tract(2)	40						GTTGTTCCTCAAGCAGCAGAA	0.463																																					p.Q65R		Atlas-SNP	.											.	CPXCR1	83	.	0			c.A194G						PASS	.						44.0	42.0	43.0					X																	88008609		2203	4300	6503	SO:0001583	missense	53336	exon3			TTCCTCAAGCAGC	AL031116	CCDS14458.1	Xq21.3	2009-08-06			ENSG00000147183	ENSG00000147183			2332	protein-coding gene	gene with protein product	"""cancer/testis antigen 77"""					11499681	Standard	NM_033048		Approved	CT77	uc004efc.4	Q8N123	OTTHUMG00000021950	ENST00000276127.4:c.194A>G	X.37:g.88008609A>G	ENSP00000276127:p.Gln65Arg	Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	57	17	0.298246	NM_001184771	B2R9F9|D3DTE7|Q96RS3	Missense_Mutation	SNP	ENST00000276127.4	37	CCDS14458.1	.	.	.	.	.	.	.	.	.	.	A	9.947	1.219144	0.22373	.	.	ENSG00000147183	ENST00000276127;ENST00000373111	T;T	0.32515	1.45;1.45	3.43	2.22	0.28083	.	0.415062	0.17767	N	0.162708	T	0.28699	0.0711	L	0.29908	0.895	0.09310	N	1	D	0.61697	0.99	P	0.54174	0.744	T	0.06092	-1.0846	9	.	.	.	.	5.9873	0.19442	0.7342:0.2658:0.0:0.0	.	65	Q8N123	CPXCR_HUMAN	R	65	ENSP00000276127:Q65R;ENSP00000362203:Q65R	.	Q	+	2	0	CPXCR1	87895265	0.000000	0.05858	0.004000	0.12327	0.089000	0.18198	-0.008000	0.12788	0.511000	0.28236	-0.387000	0.06579	CAA	.	.	none		0.463	CPXCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057418.1	NM_033048	
MYH1	4619	hgsc.bcm.edu	37	17	10409204	10409204	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:10409204T>G	ENST00000226207.5	-	19	2193	c.2099A>C	c.(2098-2100)aAc>aCc	p.N700T	CTC-297N7.11_ENST00000587182.2_RNA|RP11-799N11.1_ENST00000581304.1_RNA|RP11-799N11.1_ENST00000399342.2_RNA	NM_005963.3	NP_005954.3	P12882	MYH1_HUMAN	myosin, heavy chain 1, skeletal muscle, adult	700	Myosin motor.				muscle contraction (GO:0006936)	A band (GO:0031672)|cytoplasmic ribonucleoprotein granule (GO:0036464)|intercalated disc (GO:0014704)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(7)|breast(4)|central_nervous_system(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(22)|lung(78)|ovary(11)|pancreas(1)|prostate(3)|skin(13)|upper_aerodigestive_tract(4)|urinary_tract(5)	176						CAGCACACCGTTACACCTCAG	0.468																																					p.N700T		Atlas-SNP	.											MYH1,NS,carcinoma,+1,1	MYH1	403	1	0			c.A2099C						PASS	.						76.0	64.0	68.0					17																	10409204		2203	4298	6501	SO:0001583	missense	4619	exon19			ACACCGTTACACC		CCDS11155.1	17p13.1	2013-09-19	2006-09-29		ENSG00000109061	ENSG00000109061		"""Myosins / Myosin superfamily : Class II"""	7567	protein-coding gene	gene with protein product	"""myosin heavy chain IIx/d"""	160730	"""myosin, heavy polypeptide 1, skeletal muscle, adult"""			6304733	Standard	NM_005963		Approved	MYHSA1, MYHa, MyHC-2X/D, MGC133384	uc002gmo.3	P12882	OTTHUMG00000130362	ENST00000226207.5:c.2099A>C	17.37:g.10409204T>G	ENSP00000226207:p.Asn700Thr	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	521	88	0.168906	NM_005963	Q14CA4|Q9Y622	Missense_Mutation	SNP	ENST00000226207.5	37	CCDS11155.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381448	0.61845	.	.	ENSG00000109061	ENST00000226207	T	0.71579	-0.58	4.94	4.94	0.65067	Myosin head, motor domain (2);	0.000000	0.46442	U	0.000282	T	0.77418	0.4127	M	0.82132	2.575	0.58432	D	0.999997	P	0.38078	0.617	B	0.44085	0.44	T	0.81516	-0.0897	10	0.87932	D	0	.	15.0655	0.71992	0.0:0.0:0.0:1.0	.	700	P12882	MYH1_HUMAN	T	700	ENSP00000226207:N700T	ENSP00000226207:N700T	N	-	2	0	MYH1	10349929	1.000000	0.71417	0.896000	0.35187	0.920000	0.55202	7.698000	0.84413	2.216000	0.71823	0.528000	0.53228	AAC	.	.	none		0.468	MYH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252725.1	NM_005963	
RSBN1	54665	hgsc.bcm.edu	37	1	114354654	114354654	+	Silent	SNP	T	T	C	rs3195954	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:114354654T>C	ENST00000261441.5	-	1	444	c.381A>G	c.(379-381)ccA>ccG	p.P127P	RP5-1073O3.2_ENST00000418238.1_RNA|RP5-1073O3.2_ENST00000429398.1_RNA	NM_018364.3	NP_060834.2	Q5VWQ0	RSBN1_HUMAN	round spermatid basic protein 1	127	Pro-rich.					nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|prostate(3)|urinary_tract(2)	29	Lung SC(450;0.184)	all_cancers(81;3.78e-08)|all_epithelial(167;5.56e-08)|all_lung(203;6.97e-06)|Lung NSC(69;1.18e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTGCATTCGTTGGCGGCAGCG	0.746													T|||	610	0.121805	0.0045	0.1311	5008	,	,		11529	0.2282		0.1869	False		,,,				2504	0.0971				p.P127P		Atlas-SNP	.											RSBN1,colon,carcinoma,0,2	RSBN1	71	2	0			c.A381G						PASS	.	T		149,4053		2,145,1954	13.0	24.0	21.0		381	-4.9	0.5	1	dbSNP_105	21	1412,6854		115,1182,2836	no	coding-synonymous	RSBN1	NM_018364.3		117,1327,4790	CC,CT,TT		17.082,3.5459,12.5201		127/803	114354654	1561,10907	2101	4133	6234	SO:0001819	synonymous_variant	54665	exon1			ATTCGTTGGCGGC	AK002082	CCDS862.1	1p13.1	2008-02-05			ENSG00000081019	ENSG00000081019			25642	protein-coding gene	gene with protein product		615858				12477932	Standard	NM_018364		Approved	FLJ11220, ROSBIN	uc001edq.3	Q5VWQ0	OTTHUMG00000011938	ENST00000261441.5:c.381A>G	1.37:g.114354654T>C		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	7	6	0.857143	NM_018364	A8K937|Q6AI21|Q8TC33|Q9HA80|Q9NUP6	Silent	SNP	ENST00000261441.5	37	CCDS862.1																																																																																			T|0.861;C|0.139	0.139	strong		0.746	RSBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033022.2	NM_018364	
SPATA31A3	727830	hgsc.bcm.edu	37	9	40702760	40702760	+	Missense_Mutation	SNP	T	T	G	rs192661010	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:40702760T>G	ENST00000356699.5	+	4	446	c.417T>G	c.(415-417)caT>caG	p.H139Q	RP11-395E19.5_ENST00000432614.1_lincRNA|SPATA31A3_ENST00000463536.1_3'UTR	NM_001083124.1	NP_001076593.1	Q5VYP0	S31A3_HUMAN	SPATA31 subfamily A, member 3	139	Pro-rich.				cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											AGTCCTCTCATGAGCCTATGG	0.597													T|||	514	0.102636	0.0885	0.1009	5008	,	,		20141	0.003		0.2286	False		,,,				2504	0.0961				p.H139Q		Atlas-SNP	.											FAM75A3_ENST00000356699,NS,carcinoma,+2,2	.	.	2	0			c.T417G						scavenged	.	T	GLN/HIS	382,3416		13,356,1530	53.0	63.0	60.0		417	-3.7	0.0	9	dbSNP_134	60	1741,6417		82,1577,2420	no	missense	FAM75A3	NM_001083124.1	24	95,1933,3950	GG,GT,TT		21.341,10.0579,17.7568	possibly-damaging	139/1348	40702760	2123,9833	1899	4079	5978	SO:0001583	missense	727830	exon4			CTCTCATGAGCCT			9p12	2012-10-15	2012-10-12	2012-10-12	ENSG00000147926				32003	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member A3"""	FAM75A3		20850414	Standard	NM_001083124		Approved	OTTHUMG00000013164, DKFZp434B204	uc010mmj.3	Q5VYP0	OTTHUMG00000013164	ENST00000356699.5:c.417T>G	9.37:g.40702760T>G	ENSP00000349132:p.His139Gln	Somatic	676	6	0.00887574		WXS	Illumina HiSeq	Phase_I	793	8	0.0100883	NM_001083124		Missense_Mutation	SNP	ENST00000356699.5	37	CCDS47969.1	.	.	.	.	.	.	.	.	.	.	T	1.786	-0.480697	0.04383	0.100579	0.21341	ENSG00000147926	ENST00000356699	T	0.03889	3.77	1.86	-3.73	0.04398	.	1.943840	0.02631	N	0.104336	T	0.00012	0.0000	N	0.02916	-0.46	0.80722	P	0.0	B	0.12013	0.005	B	0.11329	0.006	T	0.45760	-0.9239	9	0.25106	T	0.35	0.3542	0.1983	0.00142	0.2674:0.2166:0.2878:0.2282	.	139	Q5VYP0	F75A3_HUMAN	Q	139	ENSP00000349132:H139Q	ENSP00000349132:H139Q	H	+	3	2	FAM75A3	40692760	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.285000	0.02791	-1.013000	0.03383	-0.836000	0.03065	CAT	T|0.744;G|0.256	0.256	strong		0.597	SPATA31A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036919.1	NM_001083124	
SLC22A25	387601	hgsc.bcm.edu	37	11	62997098	62997098	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:62997098T>G	ENST00000306494.6	-	1	26	c.27A>C	c.(25-27)caA>caC	p.Q9H	SLC22A25_ENST00000403374.2_5'Flank|SLC22A10_ENST00000535888.1_Intron|SLC22A10_ENST00000525620.1_Intron	NM_199352.3	NP_955384.3			solute carrier family 22, member 25											NS(2)|breast(2)|endometrium(4)|kidney(2)|large_intestine(7)|lung(7)|ovary(3)|skin(7)	34						GGCCTCCAACTTGATCTAGGA	0.438																																					p.Q9H		Atlas-SNP	.											SLC22A25,right_upper_lobe,carcinoma,-2,1	SLC22A25	87	1	0			c.A27C						PASS	.						47.0	51.0	50.0					11																	62997098		2201	4298	6499	SO:0001583	missense	387601	exon1			TCCAACTTGATCT	AY437532	CCDS31592.1	11q12.3	2014-05-20			ENSG00000196600	ENSG00000196600		"""Solute carriers"""	32935	protein-coding gene	gene with protein product		610792	"""MGI:2442751, MGI:2385316, MGI:3042283, MGI:3645714, MGI:3605624, MGI:2442750"""			17714910	Standard	NM_199352		Approved	UST6, HIMTP, MGC120420	uc001nwr.1	Q6T423	OTTHUMG00000165340	ENST00000306494.6:c.27A>C	11.37:g.62997098T>G	ENSP00000307443:p.Gln9His	Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	54	13	0.240741	NM_199352		Missense_Mutation	SNP	ENST00000306494.6	37	CCDS31592.1	.	.	.	.	.	.	.	.	.	.	T	2.589	-0.295687	0.05532	.	.	ENSG00000196600	ENST00000306494;ENST00000451441	T	0.36157	1.27	3.98	0.0938	0.14478	.	0.474947	0.22983	N	0.053281	T	0.28995	0.0720	M	0.65677	2.01	0.24828	N	0.992545	B;B	0.20671	0.01;0.047	B;B	0.23419	0.019;0.046	T	0.17531	-1.0366	10	0.30854	T	0.27	.	3.2687	0.06874	0.1778:0.3193:0.0:0.503	.	7;9	A4IF29;Q6T423	.;S22AP_HUMAN	H	9	ENSP00000307443:Q9H	ENSP00000307443:Q9H	Q	-	3	2	SLC22A25	62753674	0.256000	0.24012	0.031000	0.17742	0.131000	0.20780	1.426000	0.34870	0.062000	0.16340	0.386000	0.25728	CAA	.	.	none		0.438	SLC22A25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383519.3	NM_199352	
CSHL1	1444	hgsc.bcm.edu	37	17	61987570	61987570	+	Missense_Mutation	SNP	G	G	T	rs2727307	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:61987570G>T	ENST00000309894.5	-	4	422	c.423C>A	c.(421-423)gaC>gaA	p.D141E	CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000561003.1_Missense_Mutation_p.D58E|CSHL1_ENST00000259003.10_Missense_Mutation_p.D79E|CSHL1_ENST00000346606.6_Missense_Mutation_p.D47E|CSHL1_ENST00000438387.2_Missense_Mutation_p.D58E|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000450719.3_Missense_Mutation_p.D47E	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	141			D -> E (in dbSNP:rs2727307). {ECO:0000269|PubMed:15489334}.			extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						GGAGGTGATAGTCATCGCTGT	0.592													G|||	1392	0.277955	0.059	0.3256	5008	,	,		19686	0.4196		0.4185	False		,,,				2504	0.2495				p.D141E		Atlas-SNP	.											CSHL1_ENST00000561003,bladder,carcinoma,-2,4	CSHL1	42	4	0			c.C423A						scavenged	.	G	GLU/ASP,GLU/ASP,GLU/ASP,GLU/ASP	555,3851	249.3+/-256.8	32,491,1680	90.0	78.0	82.0		141,423,174,354	3.1	0.2	17	dbSNP_100	82	3562,5038	516.7+/-378.9	747,2068,1485	no	missense,missense,missense,missense	CSHL1	NM_001318.2,NM_022579.1,NM_022580.1,NM_022581.1	45,45,45,45	779,2559,3165	TT,TG,GG		41.4186,12.5965,31.6546	benign,benign,benign,benign	47/129,141/223,58/140,118/200	61987570	4117,8889	2203	4300	6503	SO:0001583	missense	1444	exon4			GTGATAGTCATCG	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"""chorionic somatomammotropin CS-5"""	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.423C>A	17.37:g.61987570G>T	ENSP00000309524:p.Asp141Glu	Somatic	696	4	0.00574713		WXS	Illumina HiSeq	Phase_I	684	10	0.0146199	NM_022579	D3DU26|D3DU27|Q0VDB2	Missense_Mutation	SNP	ENST00000309894.5	37	CCDS11652.1	708	0.3241758241758242	38	0.07723577235772358	135	0.3729281767955801	217	0.3793706293706294	318	0.41952506596306066	g	8.404	0.842563	0.16963	0.125965	0.414186	ENSG00000204414	ENST00000309894;ENST00000438387;ENST00000259003;ENST00000346606;ENST00000450719	D;D;D	0.90261	-2.64;-2.64;-2.64	3.07	3.07	0.35406	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.304551	0.31145	N	0.008174	T	0.00012	0.0000	L	0.29908	0.895	0.09310	P	0.99999999455923	B;B;B;B	0.32893	0.007;0.337;0.389;0.337	B;B;B;B	0.38156	0.007;0.173;0.266;0.253	T	0.08411	-1.0723	9	0.87932	D	0	.	8.2735	0.31857	0.0:0.2465:0.7534:0.0	rs2727307;rs57082825	47;58;141;118	Q14406-4;Q14406-3;Q14406;Q14406-2	.;.;CSHL_HUMAN;.	E	141;58;136;47;136	ENSP00000309524:D141E;ENSP00000402632:D58E;ENSP00000316360:D47E	ENSP00000259003:D136E	D	-	3	2	GH1	59341302	1.000000	0.71417	0.247000	0.24249	0.002000	0.02628	1.431000	0.34925	1.730000	0.51580	0.305000	0.20034	GAC	G|0.670;T|0.330	0.330	strong		0.592	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579	
MAML2	84441	hgsc.bcm.edu	37	11	95825407	95825407	+	Silent	SNP	C	C	T	rs61901862		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:95825407C>T	ENST00000524717.1	-	2	3072	c.1788G>A	c.(1786-1788)caG>caA	p.Q596Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	596					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q596Q(1)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgctgctgctgctgctgtt	0.532			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q596Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,rectum,carcinoma,0,2	MAML2	94	2	1	Substitution - coding silent(1)	kidney(1)	c.G1788A						PASS	.						28.0	35.0	33.0					11																	95825407		2119	4148	6267	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1788G>A	11.37:g.95825407C>T		Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	180	23	0.127778	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			C|0.250;T|0.750	0.750	weak		0.532	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
CDH9	1007	hgsc.bcm.edu	37	5	26890585	26890585	+	Missense_Mutation	SNP	G	G	A	rs148731332		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:26890585G>A	ENST00000231021.4	-	8	1514	c.1342C>T	c.(1342-1344)Cgg>Tgg	p.R448W		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	448	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						GATGATTCCCGGTCAAGGGCT	0.418													G|||	1	0.000199681	0.0	0.0	5008	,	,		14536	0.0		0.001	False		,,,				2504	0.0				p.R448W	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											CDH9,colon,carcinoma,+1,1	CDH9	305	1	0			c.C1342T						scavenged	.	G	TRP/ARG	0,4406		0,0,2203	110.0	110.0	110.0		1342	3.2	1.0	5	dbSNP_134	110	2,8598	2.2+/-6.3	1,0,4299	yes	missense	CDH9	NM_016279.3	101	1,0,6502	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	448/790	26890585	2,13004	2203	4300	6503	SO:0001583	missense	1007	exon8			ATTCCCGGTCAAG	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1342C>T	5.37:g.26890585G>A	ENSP00000231021:p.Arg448Trp	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	163	4	0.0245399	NM_016279	Q3B7I5	Missense_Mutation	SNP	ENST00000231021.4	37	CCDS3893.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	19.62	3.861225	0.71949	0.0	2.33E-4	ENSG00000113100	ENST00000231021	T	0.60299	0.2	5.09	3.21	0.36854	Cadherin (4);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.83008	0.5161	H	0.97587	4.035	0.51233	D	0.999917	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.88151	0.2851	9	.	.	.	.	12.832	0.57750	0.0:0.0:0.7038:0.2962	.	41;448	B4DFP0;Q9ULB4	.;CADH9_HUMAN	W	448	ENSP00000231021:R448W	.	R	-	1	2	CDH9	26926342	1.000000	0.71417	0.993000	0.49108	0.915000	0.54546	1.935000	0.40173	1.138000	0.42230	0.453000	0.30009	CGG	G|1.000;A|0.000	0.000	strong		0.418	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
SLMO2	51012	hgsc.bcm.edu	37	20	57613585	57613585	+	Missense_Mutation	SNP	G	G	C	rs80245608		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:57613585G>C	ENST00000355937.4	-	2	315	c.137C>G	c.(136-138)tCt>tGt	p.S46C	SLMO2_ENST00000371033.5_Missense_Mutation_p.S46C	NM_016045.2	NP_057129.2	Q9Y3B1	SLMO2_HUMAN	slowmo homolog 2 (Drosophila)	46	PRELI/MSF1. {ECO:0000255|PROSITE- ProRule:PRU00158}.				phospholipid transport (GO:0015914)	mitochondrial intermembrane space (GO:0005758)	phosphatidic acid transporter activity (GO:1990050)	p.S46C(1)		endometrium(1)|lung(2)|skin(2)	5	all_lung(29;0.00711)		Colorectal(105;0.109)			CAACTTTCCAGAGGGATCTAT	0.478																																					p.S46C		Atlas-SNP	.											SLMO2,hand,malignant_melanoma,0,1	SLMO2	10	1	1	Substitution - Missense(1)	skin(1)	c.C137G						scavenged	.	G	CYS/SER	7,3841		0,7,1917	115.0	109.0	111.0		137	4.3	0.8	20	dbSNP_131	111	4,8264		0,4,4130	no	missense	SLMO2	NM_016045.2	112	0,11,6047	CC,CG,GG		0.0484,0.1819,0.0908	benign	46/195	57613585	11,12105	1924	4134	6058	SO:0001583	missense	51012	exon2			TTTCCAGAGGGAT	AF151865	CCDS42893.1, CCDS58783.1	20q13.32	2008-10-22	2007-02-06	2007-02-06	ENSG00000101166	ENSG00000101166			15892	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 45"""	C20orf45			Standard	NM_016045		Approved	dJ543J19.5, PRELID3B	uc002yam.3	Q9Y3B1	OTTHUMG00000032856	ENST00000355937.4:c.137C>G	20.37:g.57613585G>C	ENSP00000348206:p.Ser46Cys	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	180	2	0.0111111	NM_001256403	E1P5I8|Q5JX17|Q9NUL0	Missense_Mutation	SNP	ENST00000355937.4	37	CCDS42893.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.930106	0.34096	0.001819	4.84E-4	ENSG00000101166	ENST00000355937;ENST00000371033	T;T	0.18502	2.21;2.21	5.36	4.35	0.52113	PRELI/MSF1 (2);	0.813932	0.11853	N	0.523114	T	0.25005	0.0607	M	0.68317	2.08	0.24807	N	0.992666	P;B	0.37955	0.612;0.002	B;B	0.43536	0.423;0.012	T	0.14364	-1.0475	10	0.72032	D	0.01	-11.7417	8.2385	0.31640	0.0:0.1548:0.5815:0.2638	.	46;46	Q5JX17;Q9Y3B1	.;SLMO2_HUMAN	C	46	ENSP00000348206:S46C;ENSP00000360072:S46C	ENSP00000348206:S46C	S	-	2	0	SLMO2	57046980	0.099000	0.21834	0.789000	0.31954	0.847000	0.48162	2.659000	0.46741	2.665000	0.90641	0.655000	0.94253	TCT	.	.	weak		0.478	SLMO2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079897.2	NM_016045	
ZNF546	339327	hgsc.bcm.edu	37	19	40504295	40504295	+	Missense_Mutation	SNP	C	C	T	rs139751800	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:40504295C>T	ENST00000347077.4	+	3	278	c.62C>T	c.(61-63)cCt>cTt	p.P21L	ZNF546_ENST00000600094.1_Intron|ZNF546_ENST00000596894.1_Intron	NM_178544.3	NP_848639.2	Q86UE3	ZN546_HUMAN	zinc finger protein 546	21					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(15)|lung(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(3)	34	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					CAAATCATTCCTCTGCACTCA	0.403													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18331	0.0		0.0	False		,,,				2504	0.0				p.P21L		Atlas-SNP	.											.	ZNF546	93	.	0			c.C62T						PASS	.	C	LEU/PRO	4,4402	8.1+/-20.4	0,4,2199	95.0	92.0	93.0		62	-0.7	0.0	19	dbSNP_134	93	0,8600		0,0,4300	no	missense	ZNF546	NM_178544.3	98	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	benign	21/837	40504295	4,13002	2203	4300	6503	SO:0001583	missense	339327	exon3			TCATTCCTCTGCA	BC045649	CCDS12548.1	19q13.2	2013-01-08				ENSG00000187187		"""Zinc fingers, C2H2-type"", ""-"""	28671	protein-coding gene	gene with protein product				ZNF49		12477932	Standard	XM_005258853		Approved	MGC43537	uc002oms.2	Q86UE3		ENST00000347077.4:c.62C>T	19.37:g.40504295C>T	ENSP00000339823:p.Pro21Leu	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	103	31	0.300971	NM_178544	A8K913	Missense_Mutation	SNP	ENST00000347077.4	37	CCDS12548.1	.	.	.	.	.	.	.	.	.	.	c	6.834	0.523083	0.13066	9.08E-4	0.0	ENSG00000187187	ENST00000347077	T	0.06528	3.29	1.66	-0.677	0.11357	.	.	.	.	.	T	0.02807	0.0084	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43048	-0.9415	9	0.49607	T	0.09	.	2.2331	0.04002	0.3012:0.5036:0.0:0.1953	.	21	Q86UE3	ZN546_HUMAN	L	21	ENSP00000339823:P21L	ENSP00000339823:P21L	P	+	2	0	ZNF546	45196135	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-0.414000	0.07114	-0.099000	0.12263	-0.145000	0.13849	CCT	C|1.000;T|0.000	0.000	weak		0.403	ZNF546-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462495.2	NM_178544	
ZBTB17	7709	hgsc.bcm.edu	37	1	16272337	16272337	+	Splice_Site	SNP	T	T	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:16272337T>A	ENST00000375743.4	-	6	768		c.e6-2		ZBTB17_ENST00000448462.2_Splice_Site|ZBTB17_ENST00000479282.1_5'Flank|ZBTB17_ENST00000375733.2_Splice_Site|ZBTB17_ENST00000537142.1_Splice_Site	NM_003443.2	NP_003434.2	Q13105	ZBT17_HUMAN	zinc finger and BTB domain containing 17						activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|ectoderm development (GO:0007398)|endoplasmic reticulum unfolded protein response (GO:0030968)|gastrulation with mouth forming second (GO:0001702)|negative regulation of cell cycle (GO:0045786)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(4)|large_intestine(1)|lung(4)|ovary(2)|prostate(2)	15		Colorectal(325;0.000257)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|Colorectal(212;4.12e-07)|COAD - Colon adenocarcinoma(227;2.43e-05)|BRCA - Breast invasive adenocarcinoma(304;9.97e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0649)		GCTCTGCACCTGGGTGGGGGA	0.672																																					.		Atlas-SNP	.											.	ZBTB17	45	.	0			c.536-2A>T						PASS	.						41.0	48.0	46.0					1																	16272337		2203	4300	6503	SO:0001630	splice_region_variant	7709	exon7			TGCACCTGGGTGG	U20647	CCDS165.1, CCDS55576.1, CCDS72712.1	1p36.13	2013-01-08	2004-07-16	2004-07-16	ENSG00000116809	ENSG00000116809		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12936	protein-coding gene	gene with protein product		604084	"""zinc finger protein 151 (pHZ-67)"", ""zinc finger protein 60"""	ZNF151, ZNF60			Standard	NM_003443		Approved	MIZ1, pHZ-67	uc001axl.4	Q13105	OTTHUMG00000009377	ENST00000375743.4:c.536-2A>T	1.37:g.16272337T>A		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	16	5	0.3125	NM_003443	A0AV07|B4DXB4|B7ZLQ9|F5H411|Q15932|Q5JYB2|Q9NUC9	Splice_Site	SNP	ENST00000375743.4	37	CCDS165.1	.	.	.	.	.	.	.	.	.	.	T	13.78	2.340713	0.41498	.	.	ENSG00000116809	ENST00000375743;ENST00000375733;ENST00000537142;ENST00000448462	.	.	.	4.39	4.39	0.52855	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	8.584	0.33646	0.0:0.0:0.1946:0.8054	.	.	.	.	.	-1	.	.	.	-	.	.	ZBTB17	16144924	1.000000	0.71417	0.910000	0.35882	0.676000	0.39594	3.477000	0.53151	1.918000	0.55548	0.379000	0.24179	.	.	.	none		0.672	ZBTB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025998.1	NM_003443	Intron
GAK	2580	hgsc.bcm.edu	37	4	843695	843695	+	Silent	SNP	A	A	G	rs76111882|rs8093	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:843695A>G	ENST00000314167.4	-	27	3929	c.3819T>C	c.(3817-3819)gcT>gcC	p.A1273A	GAK_ENST00000509566.1_5'UTR|GAK_ENST00000511163.1_Silent_p.A1194A	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	1273	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		CGGGGTGCACAGCCAGCACCG	0.726													a|||	4010	0.800719	0.8918	0.6369	5008	,	,		11851	0.877		0.671	False		,,,				2504	0.8487				p.A1273A		Atlas-SNP	.											.	GAK	104	.	0			c.T3819C						PASS	.	G		3856,542		1696,464,39	17.0	18.0	18.0		3819	-9.1	0.1	4	dbSNP_52	18	5883,2711		2028,1827,442	no	coding-synonymous	GAK	NM_005255.2		3724,2291,481	GG,GA,AA		31.5453,12.3238,25.0385		1273/1312	843695	9739,3253	2199	4297	6496	SO:0001819	synonymous_variant	2580	exon27			GTGCACAGCCAGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.3819T>C	4.37:g.843695A>G		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_005255	Q5U4P5|Q9BVY6	Silent	SNP	ENST00000314167.4	37	CCDS3340.1	1636	0.7490842490842491	420	0.8536585365853658	226	0.6243093922651933	484	0.8461538461538461	506	0.6675461741424802	a	0.556	-0.847528	0.02651	0.876762	0.684547	ENSG00000178950	ENST00000511980	.	.	.	4.56	-9.13	0.00704	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.99999999880066	.	.	.	.	.	.	T	0.16512	-1.0400	3	.	.	.	-19.8857	2.0039	0.03473	0.429:0.2136:0.2148:0.1425	rs8093;rs1134910;rs3197278;rs3816672;rs17359324;rs60405968;rs8093	.	.	.	P	429	.	.	L	-	2	0	GAK	833695	0.000000	0.05858	0.094000	0.20943	0.014000	0.08584	-4.755000	0.00190	-2.434000	0.00554	-1.578000	0.00866	CTG	A|0.228;G|0.772	0.772	strong		0.726	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
POTEF	728378	hgsc.bcm.edu	37	2	130877892	130877892	+	Missense_Mutation	SNP	C	C	T	rs11889701	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:130877892C>T	ENST00000409914.2	-	3	596	c.197G>A	c.(196-198)cGc>cAc	p.R66H	POTEF_ENST00000360967.5_Missense_Mutation_p.R66H|POTEF_ENST00000361163.4_Missense_Mutation_p.R66H|POTEF_ENST00000357462.5_Missense_Mutation_p.R66H	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	66					retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GAAGCAGTGGCGGCACCACTT	0.602													.|||	37	0.00738818	0.0272	0.0	5008	,	,		15114	0.0		0.0	False		,,,				2504	0.001				p.R66H		Atlas-SNP	.											POTEF,NS,carcinoma,-1,12	POTEF	140	12	0			c.G197A						scavenged	.						91.0	126.0	114.0					2																	130877892		2167	4294	6461	SO:0001583	missense	728378	exon3			CAGTGGCGGCACC	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.197G>A	2.37:g.130877892C>T	ENSP00000386786:p.Arg66His	Somatic	396	19	0.0479798		WXS	Illumina HiSeq	Phase_I	492	32	0.0650406	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	.	.	.	.	.	.	.	.	.	.	.	0.014	-1.587100	0.00872	.	.	ENSG00000196604	ENST00000357462;ENST00000409914;ENST00000360967;ENST00000361163	T;T;T;T	0.77358	-1.09;-1.09;1.74;1.76	.	.	.	.	.	.	.	.	T	0.47469	0.1447	N	0.01109	-1.01	0.09310	N	1	D	0.56521	0.976	P	0.46629	0.522	T	0.47509	-0.9112	7	0.12766	T	0.61	.	.	.	.	.	66	A5A3E0	POTEF_HUMAN	H	66	ENSP00000350052:R66H;ENSP00000386786:R66H;ENSP00000354232:R66H;ENSP00000355012:R66H	ENSP00000350052:R66H	R	-	2	0	POTEF	130594362	0.005000	0.15991	0.077000	0.20336	0.096000	0.18686	-1.080000	0.03407	0.149000	0.19098	0.152000	0.16155	CGC	C|0.500;T|0.500	0.500	weak		0.602	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
MAML2	84441	hgsc.bcm.edu	37	11	95825362	95825362	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:95825362C>T	ENST00000524717.1	-	2	3117	c.1833G>A	c.(1831-1833)caG>caA	p.Q611Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	611					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)	p.Q611Q(2)	CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gctgttgctgctgctgctgct	0.542			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q611Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,NS,carcinoma,0,4	MAML2	94	4	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)	c.G1833A						scavenged	.						39.0	44.0	42.0					11																	95825362		2057	4042	6099	SO:0001819	synonymous_variant	84441	exon2			TTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1833G>A	11.37:g.95825362C>T		Somatic	177	3	0.0169492		WXS	Illumina HiSeq	Phase_I	169	7	0.0414201	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			.	.	none		0.542	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
ARHGEF18	23370	hgsc.bcm.edu	37	19	7533850	7533850	+	Missense_Mutation	SNP	A	A	G	rs9329368	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:7533850A>G	ENST00000359920.6	+	17	3309	c.3056A>G	c.(3055-3057)aAc>aGc	p.N1019S	ARHGEF18_ENST00000319670.9_Missense_Mutation_p.N861S|CTD-2207O23.3_ENST00000593531.1_Missense_Mutation_p.T977A	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	1019			N -> S (in dbSNP:rs9329368). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9628581}.		actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				CCCACCGAGAACCGGCTGGCC	0.706													G|||	4178	0.834265	0.9523	0.7608	5008	,	,		14876	0.8433		0.7445	False		,,,				2504	0.8098				p.N1019S		Atlas-SNP	.											ARHGEF18_ENST00000359920,NS,carcinoma,0,2	ARHGEF18	129	2	0			c.A3056G						scavenged	.	G	SER/ASN,SER/ASN	4023,309		1872,279,15	15.0	14.0	15.0		3056,2582	3.2	0.4	19	dbSNP_119	15	6415,2105		2417,1581,262	yes	missense,missense	ARHGEF18	NM_001130955.1,NM_015318.3	46,46	4289,1860,277	GG,GA,AA		24.7066,7.133,18.7831	benign,benign	1019/1174,861/1016	7533850	10438,2414	2166	4260	6426	SO:0001583	missense	23370	exon17			CCGAGAACCGGCT	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.3056A>G	19.37:g.7533850A>G	ENSP00000352995:p.Asn1019Ser	Somatic	3	1	0.333333		WXS	Illumina HiSeq	Phase_I	4	2	0.5	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	1777	0.8136446886446886	468	0.9512195121951219	261	0.7209944751381215	485	0.8479020979020979	563	0.7427440633245382	G	0.013	-1.634801	0.00806	0.92867	0.752934	ENSG00000104880	ENST00000319670;ENST00000359920	T;T	0.27890	1.66;1.64	4.24	3.16	0.36331	.	0.960980	0.08586	N	0.923776	T	0.00012	0.0000	N	0.01705	-0.755	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.30765	-0.9967	9	0.07325	T	0.83	-3.5407	3.0267	0.06094	0.1009:0.1765:0.5409:0.1816	rs9329368	861;1019	Q6ZSZ5-2;Q6ZSZ5	.;ARHGI_HUMAN	S	861;1019	ENSP00000319200:N861S;ENSP00000352995:N1019S	ENSP00000319200:N861S	N	+	2	0	ARHGEF18	7439850	0.159000	0.22864	0.394000	0.26270	0.182000	0.23217	0.158000	0.16422	0.252000	0.21531	-0.213000	0.12676	AAC	A|0.184;G|0.816	0.816	strong		0.706	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
CDK5RAP2	55755	hgsc.bcm.edu	37	9	123342220	123342220	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:123342220G>T	ENST00000349780.4	-	1	216	c.37C>A	c.(37-39)Cct>Act	p.P13T	CDK5RAP2_ENST00000359309.3_Missense_Mutation_p.P13T|CDK5RAP2_ENST00000360822.3_Missense_Mutation_p.P13T|CDK5RAP2_ENST00000360190.4_Missense_Mutation_p.P13T	NM_018249.4	NP_060719.4	Q96SN8	CK5P2_HUMAN	CDK5 regulatory subunit associated protein 2	13					brain development (GO:0007420)|centrosome organization (GO:0051297)|chromosome segregation (GO:0007059)|establishment of mitotic spindle orientation (GO:0000132)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|negative regulation of centriole replication (GO:0046600)|negative regulation of neuron differentiation (GO:0045665)|neurogenesis (GO:0022008)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of neuron differentiation (GO:0045664)|regulation of spindle checkpoint (GO:0090231)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|pericentriolar material (GO:0000242)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	calmodulin binding (GO:0005516)|microtubule binding (GO:0008017)|protein kinase binding (GO:0019901)|transcription regulatory region DNA binding (GO:0044212)|tubulin binding (GO:0015631)	p.P13S(1)		breast(6)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(12)|lung(21)|ovary(2)|prostate(2)|skin(6)|urinary_tract(1)	58						AGCGTCCCAGGGACGGTGACG	0.652																																					p.P13T		Atlas-SNP	.											CDK5RAP2,NS,carcinoma,0,1	CDK5RAP2	157	1	1	Substitution - Missense(1)	lung(1)	c.C37A						scavenged	.						44.0	35.0	38.0					9																	123342220		2203	4300	6503	SO:0001583	missense	55755	exon1			TCCCAGGGACGGT	BK005504	CCDS6823.1, CCDS43871.1, CCDS75888.1	9q33.3	2014-02-21			ENSG00000136861	ENSG00000136861			18672	protein-coding gene	gene with protein product	"""centrosomin"""	608201	"""microcephaly, primary autosomal recessive 3"""	MCPH3		10721722, 17764569, 24466316	Standard	NM_018249		Approved	C48, FLJ10867, CEP215	uc004bkf.4	Q96SN8	OTTHUMG00000021043	ENST00000349780.4:c.37C>A	9.37:g.123342220G>T	ENSP00000343818:p.Pro13Thr	Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	185	4	0.0216216	NM_018249	Q5JV18|Q7Z3L4|Q7Z3U1|Q7Z7I6|Q9BSW0|Q9H6J6|Q9HCD9|Q9NV90|Q9UIW9	Missense_Mutation	SNP	ENST00000349780.4	37	CCDS6823.1	.	.	.	.	.	.	.	.	.	.	G	19.02	3.745705	0.69418	.	.	ENSG00000136861	ENST00000360822;ENST00000359309;ENST00000349780;ENST00000360190;ENST00000345313	T;T;T;T	0.05081	3.67;3.5;3.62;3.52	4.99	4.1	0.47936	.	0.454240	0.18929	N	0.127278	T	0.06872	0.0175	L	0.27053	0.805	0.26883	N	0.967492	B;B;B	0.28552	0.215;0.184;0.137	B;B;B	0.37047	0.24;0.227;0.121	T	0.25916	-1.0118	10	0.51188	T	0.08	.	9.563	0.39380	0.0958:0.0:0.9042:0.0	.	13;13;13	Q96SN8-2;Q96SN8-4;Q96SN8	.;.;CK5P2_HUMAN	T	13	ENSP00000354065:P13T;ENSP00000352258:P13T;ENSP00000343818:P13T;ENSP00000353317:P13T	ENSP00000341695:P13T	P	-	1	0	CDK5RAP2	122382041	1.000000	0.71417	0.995000	0.50966	0.585000	0.36419	2.306000	0.43673	1.462000	0.47948	0.655000	0.94253	CCT	.	.	none		0.652	CDK5RAP2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055535.1	NM_018249	
TEKT4	150483	hgsc.bcm.edu	37	2	95542364	95542364	+	Silent	SNP	G	G	A	rs113812263	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:95542364G>A	ENST00000295201.4	+	6	1295	c.1158G>A	c.(1156-1158)gcG>gcA	p.A386A	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	386					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						TTCTAGAAGCGGAGCAGTCCC	0.597																																					p.A386A		Atlas-SNP	.											TEKT4,caecum,carcinoma,0,3	TEKT4	72	3	0			c.G1158A						scavenged	.						63.0	50.0	54.0					2																	95542364		2203	4300	6503	SO:0001819	synonymous_variant	150483	exon6			AGAAGCGGAGCAG	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.1158G>A	2.37:g.95542364G>A		Somatic	65	2	0.0307692		WXS	Illumina HiSeq	Phase_I	82	5	0.0609756	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			G|0.972;A|0.028	0.028	strong		0.597	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
HLA-B	3106	hgsc.bcm.edu	37	6	31322910	31322910	+	Missense_Mutation	SNP	G	G	A	rs74189305		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:31322910G>A	ENST00000412585.2	-	5	1014	c.986C>T	c.(985-987)gCt>gTt	p.A329V		NM_005514.6	NP_005505.2	P30486	1B48_HUMAN	major histocompatibility complex, class I, B	329			A -> T (in dbSNP:rs1051488).		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|immune response (GO:0006955)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|viral process (GO:0016032)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|MHC class I protein complex (GO:0042612)	peptide antigen binding (GO:0042605)	p.A329V(4)		endometrium(4)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(4)|lung(4)|prostate(1)|upper_aerodigestive_tract(2)	27						ACACATCACAGCAGCGACCAC	0.587									Melanoma, Familial Clustering of;Lichen Sclerosis et Atrophicus, Familial Clustering of																												p.A329V		Atlas-SNP	.											HLA-B,NS,carcinoma,-1,7	HLA-B	54	7	4	Substitution - Missense(4)	kidney(4)	c.C986T						scavenged	.						102.0	101.0	101.0					6																	31322910		1511	2709	4220	SO:0001583	missense	3106	exon5	Familial Cancer Database	;Lichen Sclerosis, Familial	ATCACAGCAGCGA	M15470	CCDS34394.1	6p21.3	2013-01-11			ENSG00000234745	ENSG00000234745		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4932	protein-coding gene	gene with protein product		142830	"""ankylosing spondylitis"""	AS		3459708	Standard	NM_005514		Approved		uc011imz.2	P01889	OTTHUMG00000031153	ENST00000412585.2:c.986C>T	6.37:g.31322910G>A	ENSP00000399168:p.Ala329Val	Somatic	179	5	0.027933		WXS	Illumina HiSeq	Phase_I	196	7	0.0357143	NM_005514	Q29764	Missense_Mutation	SNP	ENST00000412585.2	37	CCDS34394.1	.	.	.	.	.	.	.	.	.	.	N	9.051	0.992087	0.18966	.	.	ENSG00000234745	ENST00000412585;ENST00000428231	T	0.00622	6.16	3.73	-3.02	0.05446	.	.	.	.	.	T	0.00109	0.0003	N	0.00729	-1.24	0.09310	N	1	B	0.20052	0.041	B	0.29077	0.098	T	0.22906	-1.0203	9	0.49607	T	0.09	.	5.2273	0.15401	0.4363:0.3516:0.2121:0.0	.	329	P01889	1B07_HUMAN	V	329;208	ENSP00000399168:A329V	ENSP00000399168:A329V	A	-	2	0	HLA-B	31430889	0.000000	0.05858	0.128000	0.21923	0.021000	0.10359	0.033000	0.13754	-0.241000	0.09681	0.448000	0.29417	GCT	.	.	weak		0.587	HLA-B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076280.4	NM_005514	
SLC43A2	124935	hgsc.bcm.edu	37	17	1494567	1494567	+	Silent	SNP	G	G	A	rs12953268	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:1494567G>A	ENST00000301335.5	-	8	1015	c.927C>T	c.(925-927)gcC>gcT	p.A309A	SLC43A2_ENST00000574274.1_5'UTR|SLC43A2_ENST00000382147.4_Silent_p.A309A|SLC43A2_ENST00000412517.3_Silent_p.A172A|SLC43A2_ENST00000571650.1_Silent_p.A309A	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	309					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		GGGTACCTGCGGCATCCGGCT	0.682													G|||	1399	0.279353	0.0832	0.3127	5008	,	,		11580	0.1508		0.5388	False		,,,				2504	0.3865				p.A309A		Atlas-SNP	.											SLC43A2,NS,carcinoma,0,1	SLC43A2	37	1	0			c.C927T						scavenged	.	G		726,3680	287.2+/-279.2	55,616,1532	42.0	43.0	43.0		927	-5.5	0.1	17	dbSNP_121	43	4715,3885	595.2+/-393.4	1297,2121,882	no	coding-synonymous	SLC43A2	NM_152346.1		1352,2737,2414	AA,AG,GG		45.1744,16.4775,41.8345		309/570	1494567	5441,7565	2203	4300	6503	SO:0001819	synonymous_variant	124935	exon8			ACCTGCGGCATCC	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.927C>T	17.37:g.1494567G>A		Somatic	4	1	0.25		WXS	Illumina HiSeq	Phase_I	9	7	0.777778	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Silent	SNP	ENST00000301335.5	37	CCDS11006.1																																																																																			A|0.422;C|0.000;G|0.578	0.422	strong		0.682	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
P2RX7	5027	hgsc.bcm.edu	37	12	121615103	121615103	+	Missense_Mutation	SNP	G	G	A	rs1718119	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:121615103G>A	ENST00000546057.1	+	11	1185	c.1042G>A	c.(1042-1044)Gct>Act	p.A348T	P2RX7_ENST00000328963.5_Missense_Mutation_p.A178T|P2RX7_ENST00000541446.1_Missense_Mutation_p.A59T|P2RX7_ENST00000535250.1_Missense_Mutation_p.A258T|P2RX7_ENST00000443520.3_3'UTR	NM_002562.5	NP_002553	Q99572	P2RX7_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 7	348			A -> T (in dbSNP:rs1718119). {ECO:0000269|PubMed:9826911}.		apoptotic signaling pathway (GO:0097190)|bleb assembly (GO:0032060)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cell surface receptor signaling pathway (GO:0007166)|innate immune response (GO:0045087)|membrane depolarization (GO:0051899)|negative regulation of bone resorption (GO:0045779)|negative regulation of MAPK cascade (GO:0043409)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|pore complex assembly (GO:0046931)|positive regulation of bone mineralization (GO:0030501)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cytolysis (GO:0045919)|positive regulation of cytoskeleton organization (GO:0051495)|positive regulation of interleukin-1 beta secretion (GO:0050718)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of killing of cells of other organism (GO:0051709)|regulation of sodium ion transport (GO:0002028)|response to ATP (GO:0033198)|sensory perception of pain (GO:0019233)	bleb (GO:0032059)|cytoplasm (GO:0005737)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|lipopolysaccharide binding (GO:0001530)|protein homodimerization activity (GO:0042803)|purinergic nucleotide receptor activity (GO:0001614)|receptor binding (GO:0005102)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(9)|skin(1)|stomach(1)	19	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TCCCCAGGCCGCTGTGTTCAT	0.498													A|||	1615	0.322484	0.4599	0.2003	5008	,	,		20159	0.1419		0.3827	False		,,,				2504	0.3476				p.A348T		Atlas-SNP	.											P2RX7,NS,carcinoma,0,1	P2RX7	53	1	0			c.G1042A						scavenged	.	A	THR/ALA	2007,2399	614.4+/-392.4	454,1099,650	138.0	121.0	127.0		1042	5.6	1.0	12	dbSNP_89	127	3418,5182	639.4+/-399.5	723,1972,1605	yes	missense	P2RX7	NM_002562.5	58	1177,3071,2255	AA,AG,GG		39.7442,45.5515,41.7115	benign	348/596	121615103	5425,7581	2203	4300	6503	SO:0001583	missense	5027	exon11			CAGGCCGCTGTGT	Y09561	CCDS9213.1	12q24	2012-01-17			ENSG00000089041	ENSG00000089041		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8537	protein-coding gene	gene with protein product		602566				9038151, 9826911	Standard	NM_002562		Approved	P2X7, MGC20089	uc001tzm.3	Q99572	OTTHUMG00000169153	ENST00000546057.1:c.1042G>A	12.37:g.121615103G>A	ENSP00000442349:p.Ala348Thr	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	194	2	0.0103093	NM_002562	A8K2Z0|E7EMK6|F5H6P2|F5H7E8|F8W951|O14991|Q4VKH8|Q4VKH9|Q4VKI0|Q4VKI1|Q4VKI2|Q4VKI3|Q4VKI4|Q7Z771|Q96EV7	Missense_Mutation	SNP	ENST00000546057.1	37	CCDS9213.1	673	0.30815018315018317	231	0.4695121951219512	76	0.20994475138121546	73	0.12762237762237763	293	0.3865435356200528	A	6.616	0.482145	0.12581	0.455515	0.397442	ENSG00000089041	ENST00000546057;ENST00000328963;ENST00000535250;ENST00000541446	T;T;T;T	0.03580	3.88;3.88;3.88;3.88	5.62	5.62	0.85841	.	0.382952	0.23821	N	0.044240	T	0.00012	0.0000	N	0.00112	-2.095	0.52501	P	4.199999999998649E-5	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.38887	-0.9640	9	0.02654	T	1	.	7.4513	0.27240	0.8325:0.0:0.1675:0.0	rs1718119;rs2230910;rs17525154;rs52812840;rs58430687;rs1718119	178;59;258;348	F8W951;F5H6P2;F5H7E8;Q99572	.;.;.;P2RX7_HUMAN	T	348;178;258;59	ENSP00000442349:A348T;ENSP00000330696:A178T;ENSP00000442572:A258T;ENSP00000437471:A59T	ENSP00000330696:A178T	A	+	1	0	P2RX7	120099486	0.976000	0.34144	0.978000	0.43139	0.854000	0.48673	0.672000	0.25187	0.980000	0.38523	-0.332000	0.08345	GCT	G|0.628;N|0.001	.	strong		0.498	P2RX7-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402532.1	NM_002562	
UNC45B	146862	hgsc.bcm.edu	37	17	33497208	33497208	+	Silent	SNP	C	C	T	rs531660473		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:33497208C>T	ENST00000268876.5	+	12	1720	c.1623C>T	c.(1621-1623)gaC>gaT	p.D541D	UNC45B_ENST00000378449.1_Intron|UNC45B_ENST00000394570.2_Silent_p.D541D|UNC45B_ENST00000433649.1_Silent_p.D541D|UNC45B_ENST00000591048.1_Intron	NM_173167.2	NP_775259.1	Q8IWX7	UN45B_HUMAN	unc-45 homolog B (C. elegans)	541					cell differentiation (GO:0030154)|chaperone-mediated protein folding (GO:0061077)|muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(1)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(10)|lung(24)|ovary(3)|prostate(2)|skin(1)|stomach(1)|urinary_tract(3)	59		Ovarian(249;0.17)				TCACGCTGGACGCTGATGTGA	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18902	0.0		0.0	False		,,,				2504	0.0				p.D541D		Atlas-SNP	.											.	UNC45B	133	.	0			c.C1623T						PASS	.						77.0	62.0	67.0					17																	33497208		2203	4300	6503	SO:0001819	synonymous_variant	146862	exon12			GCTGGACGCTGAT	AW755253	CCDS11292.1, CCDS45648.1	17q12	2008-02-05	2005-11-17	2005-11-17	ENSG00000141161	ENSG00000141161			14304	protein-coding gene	gene with protein product		611220	"""cardiomyopathy associated 4"""	CMYA4		12356907	Standard	NM_001267052		Approved	UNC45	uc002hja.3	Q8IWX7	OTTHUMG00000132931	ENST00000268876.5:c.1623C>T	17.37:g.33497208C>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	150	23	0.153333	NM_001267052	Q495Q8|Q495Q9	Silent	SNP	ENST00000268876.5	37	CCDS11292.1																																																																																			.	.	none		0.617	UNC45B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256458.2	NM_173167	
TTLL1	25809	hgsc.bcm.edu	37	22	43447891	43447891	+	Silent	SNP	C	C	T	rs9607998	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:43447891C>T	ENST00000266254.7	-	9	1134	c.894G>A	c.(892-894)ccG>ccA	p.P298P	AL022476.2_ENST00000443063.1_RNA|TTLL1_ENST00000331018.7_Intron	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	298	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		TGTTCATCACCGGCTGGAGAG	0.577													C|||	78	0.0155751	0.0068	0.0216	5008	,	,		21914	0.0		0.0497	False		,,,				2504	0.0041				p.P298P		Atlas-SNP	.											TTLL1,NS,carcinoma,-2,1	TTLL1	41	1	0			c.G894A						scavenged	.	C		46,4360	48.2+/-83.0	3,40,2160	263.0	185.0	212.0		894	-3.7	1.0	22	dbSNP_119	212	419,8181	130.0+/-188.0	10,399,3891	no	coding-synonymous	TTLL1	NM_012263.4		13,439,6051	TT,TC,CC		4.8721,1.044,3.5753		298/424	43447891	465,12541	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon9			CATCACCGGCTGG	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.894G>A	22.37:g.43447891C>T		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	210	6	0.0285714	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	52	0.023809523809523808	6	0.012195121951219513	10	0.027624309392265192	0	0.0	36	0.047493403693931395	C	9.531	1.110796	0.20714	0.01044	0.048721	ENSG00000100271	ENST00000495814	.	.	.	5.97	-3.65	0.04502	.	.	.	.	.	T	0.07503	0.0189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29941	-0.9995	4	.	.	.	.	0.9386	0.01351	0.3008:0.1773:0.3147:0.2072	rs9607998;rs52827145;rs9607998	.	.	.	Q	224	.	.	R	-	2	0	TTLL1	41777835	0.001000	0.12720	0.987000	0.45799	0.774000	0.43823	-1.617000	0.02051	-0.307000	0.08804	-0.126000	0.14955	CGG	C|0.971;T|0.029	0.029	strong		0.577	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
AGAP1	116987	hgsc.bcm.edu	37	2	236715883	236715883	+	Splice_Site	SNP	T	T	C	rs202230563	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:236715883T>C	ENST00000304032.8	+	9	1538	c.958T>C	c.(958-960)Tct>Cct	p.S320P	AGAP1_ENST00000336665.5_Splice_Site_p.S320P|AGAP1_ENST00000428334.2_Splice_Site_p.S159P|AGAP1_ENST00000409538.1_Splice_Site_p.S585P|AGAP1_ENST00000409457.1_Splice_Site_p.S320P	NM_001037131.2	NP_001032208.1	Q9UPQ3	AGAP1_HUMAN	ArfGAP with GTPase domain, ankyrin repeat and PH domain 1	320					protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	ARF GTPase activator activity (GO:0008060)|GTP binding (GO:0005525)|phospholipid binding (GO:0005543)|zinc ion binding (GO:0008270)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						TGCTTTGCAGTCTCGGAAAGG	0.532																																					p.S320P		Atlas-SNP	.											.	AGAP1	95	.	0			c.T958C						PASS	.	T	PRO/SER,PRO/SER	0,4406		0,0,2203	80.0	88.0	86.0		958,958	5.1	1.0	2		86	4,8596	3.7+/-12.6	0,4,4296	yes	missense-near-splice,missense-near-splice	AGAP1	NM_001037131.2,NM_014914.4	74,74	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	probably-damaging,probably-damaging	320/858,320/805	236715883	4,13002	2203	4300	6503	SO:0001630	splice_region_variant	116987	exon9			TTGCAGTCTCGGA	AF413078	CCDS2514.1, CCDS33408.1, CCDS58756.1	2q37	2013-01-10	2008-09-22	2008-09-22	ENSG00000157985	ENSG00000157985		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16922	protein-coding gene	gene with protein product		608651	"""centaurin, gamma 2"""	CENTG2			Standard	NM_001037131		Approved	KIAA1099, GGAP1	uc002vvs.3	Q9UPQ3	OTTHUMG00000133293	ENST00000304032.8:c.958-1T>C	2.37:g.236715883T>C		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	57	5	0.0877193	NM_014914	B2RTX7|Q541S5|Q6P9D7|Q9NV93	Missense_Mutation	SNP	ENST00000304032.8	37	CCDS33408.1	.	.	.	.	.	.	.	.	.	.	T	13.77	2.336551	0.41398	0.0	4.65E-4	ENSG00000157985	ENST00000409457;ENST00000304032;ENST00000336665;ENST00000409538;ENST00000428334	T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51	5.12	5.12	0.69794	.	0.000000	0.85682	D	0.000000	T	0.48003	0.1476	L	0.46157	1.445	0.80722	D	1	D;D	0.69078	0.997;0.992	D;D	0.78314	0.991;0.98	T	0.36456	-0.9747	9	.	.	.	.	15.2676	0.73675	0.0:0.0:0.0:1.0	.	320;320	Q9UPQ3-2;Q9UPQ3	.;AGAP1_HUMAN	P	320;320;320;585;159	ENSP00000387174:S320P;ENSP00000307634:S320P;ENSP00000338378:S320P;ENSP00000386897:S585P;ENSP00000411824:S159P	.	S	+	1	0	AGAP1	236380622	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.731000	0.84895	2.064000	0.61679	0.533000	0.62120	TCT	T|0.998;C|0.002	0.002	strong		0.532	AGAP1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000257076.2	NM_014914	Missense_Mutation
CEPT1	10390	hgsc.bcm.edu	37	1	111724864	111724864	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:111724864G>A	ENST00000545121.1	+	6	978	c.770G>A	c.(769-771)gGg>gAg	p.G257E	CEPT1_ENST00000357172.4_Missense_Mutation_p.G257E|RP5-1180E21.4_ENST00000607951.1_RNA|RP5-1180E21.5_ENST00000610049.1_RNA|CEPT1_ENST00000467362.1_3'UTR	NM_001007794.1	NP_001007795.1	Q9Y6K0	CEPT1_HUMAN	choline/ethanolamine phosphotransferase 1	257					CDP-choline pathway (GO:0006657)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	diacylglycerol cholinephosphotransferase activity (GO:0004142)|ethanolaminephosphotransferase activity (GO:0004307)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	8		all_cancers(81;2.27e-05)|all_epithelial(167;7.36e-06)|all_lung(203;0.00018)|Lung NSC(277;0.000359)		Lung(183;0.0173)|Colorectal(144;0.0375)|all cancers(265;0.0701)|LUSC - Lung squamous cell carcinoma(189;0.0888)|Epithelial(280;0.103)|COAD - Colon adenocarcinoma(174;0.141)	Choline(DB00122)	ACTGTAGCAGGGACCATATTT	0.333																																					p.G257E		Atlas-SNP	.											.	CEPT1	25	.	0			c.G770A						PASS	.						84.0	80.0	82.0					1																	111724864		2203	4300	6503	SO:0001583	missense	10390	exon6			TAGCAGGGACCAT	AF068302	CCDS830.1	1p13	2010-07-08			ENSG00000134255	ENSG00000134255	2.7.8.1, 2.7.8.2		24289	protein-coding gene	gene with protein product						10191259, 12216837	Standard	XM_005270353		Approved		uc001eah.1	Q9Y6K0	OTTHUMG00000012357	ENST00000545121.1:c.770G>A	1.37:g.111724864G>A	ENSP00000441980:p.Gly257Glu	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	137	36	0.262774	NM_006090	Q69YJ9|Q9P0Y8	Missense_Mutation	SNP	ENST00000545121.1	37	CCDS830.1	.	.	.	.	.	.	.	.	.	.	G	29.8	5.039564	0.93630	.	.	ENSG00000134255	ENST00000545121;ENST00000357172	T;T	0.51325	0.71;0.71	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.67249	0.2873	M	0.85462	2.755	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.63139	-0.6704	10	0.30854	T	0.27	-5.595	18.3537	0.90348	0.0:0.0:1.0:0.0	.	257	Q9Y6K0	CEPT1_HUMAN	E	257	ENSP00000441980:G257E;ENSP00000349696:G257E	ENSP00000349696:G257E	G	+	2	0	CEPT1	111526387	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.434000	0.97515	2.937000	0.99478	0.650000	0.86243	GGG	.	.	none		0.333	CEPT1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034462.2	NM_006090	
KRTAP10-2	386679	hgsc.bcm.edu	37	21	45970771	45970771	+	Missense_Mutation	SNP	C	C	T	rs200215960|rs67692969|rs71199610	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:45970771C>T	ENST00000391621.1	-	1	617	c.571G>A	c.(571-573)Gtc>Atc	p.V191I	KRTAP10-2_ENST00000498210.1_Intron|TSPEAR_ENST00000323084.4_Intron|TSPEAR_ENST00000397916.1_Intron	NM_198693.2	NP_941966.1	P60368	KR102_HUMAN	keratin associated protein 10-2	191	22 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				large_intestine(1)|lung(4)|skin(1)	6						TTGCAGCAGACAGGCTTGCAG	0.612																																					p.V191I		Atlas-SNP	.											.	KRTAP10-2	21	.	0			c.G571A						PASS	.						114.0	116.0	115.0					21																	45970771		2203	4299	6502	SO:0001583	missense	386679	exon1			AGCAGACAGGCTT	AJ566381	CCDS42955.1	21q22.3	2007-10-05			ENSG00000205445	ENSG00000205445		"""Keratin associated proteins"""	22967	protein-coding gene	gene with protein product				KRTAP18-2			Standard	NM_198693		Approved	KAP10.2, KAP18.2	uc002zfi.1	P60368	OTTHUMG00000057625	ENST00000391621.1:c.571G>A	21.37:g.45970771C>T	ENSP00000375479:p.Val191Ile	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	125	12	0.096	NM_198693	Q70LJ5	Missense_Mutation	SNP	ENST00000391621.1	37	CCDS42955.1	.	.	.	.	.	.	.	.	.	.	c	9.177	1.022646	0.19433	.	.	ENSG00000205445	ENST00000391621	T	0.01430	4.9	3.28	-6.57	0.01842	.	.	.	.	.	T	0.01627	0.0052	L	0.60904	1.88	0.09310	N	1	B	0.22604	0.072	B	0.26614	0.071	T	0.44697	-0.9311	9	0.62326	D	0.03	.	3.2055	0.06665	0.2595:0.2667:0.3822:0.0916	.	191	P60368	KR102_HUMAN	I	191	ENSP00000375479:V191I	ENSP00000375479:V191I	V	-	1	0	KRTAP10-2	44795199	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.395000	0.02516	-1.216000	0.02607	0.462000	0.41574	GTC	C|0.956;T|0.044	0.044	strong		0.612	KRTAP10-2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128027.1		
DOCK1	1793	hgsc.bcm.edu	37	10	128807004	128807004	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:128807004G>A	ENST00000280333.6	+	11	1103	c.994G>A	c.(994-996)Gta>Ata	p.V332I	RP11-223P11.3_ENST00000601242.1_RNA|RP11-223P11.3_ENST00000595456.1_RNA|RP11-223P11.3_ENST00000594559.1_RNA|RP11-223P11.3_ENST00000594614.1_RNA|RP11-223P11.3_ENST00000601826.1_RNA	NM_001380.3	NP_001371.1	Q14185	DOCK1_HUMAN	dedicator of cytokinesis 1	332					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|hematopoietic progenitor cell differentiation (GO:0002244)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|phagocytosis, engulfment (GO:0006911)|positive regulation of GTPase activity (GO:0043547)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)			NS(2)|breast(1)|central_nervous_system(7)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(10)|lung(15)|ovary(4)|prostate(3)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	72		all_epithelial(44;2.3e-07)|all_lung(145;0.00466)|Lung NSC(174;0.00685)|Colorectal(57;0.0107)|Renal(717;0.0113)|Breast(234;0.0492)|all_neural(114;0.108)|all_hematologic(284;0.14)		BRCA - Breast invasive adenocarcinoma(275;0.0221)|Colorectal(40;0.115)		AGTGATGGATGTAACAGATAT	0.353																																					p.V332I		Atlas-SNP	.											.	DOCK1	188	.	0			c.G994A						PASS	.						77.0	76.0	76.0					10																	128807004		1953	4194	6147	SO:0001583	missense	1793	exon11			ATGGATGTAACAG	D50857	CCDS73222.1	10q26.13-q26.3	2009-10-28			ENSG00000150760	ENSG00000150760			2987	protein-coding gene	gene with protein product	"""DOwnstream of CrK"""	601403	"""dedicator of cyto-kinesis 1"""			8657152, 8661160	Standard	XM_006717681		Approved	DOCK180, ced5	uc001ljt.3	Q14185	OTTHUMG00000019249	ENST00000280333.6:c.994G>A	10.37:g.128807004G>A	ENSP00000280333:p.Val332Ile	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	107	14	0.130841	NM_001380	A9Z1Z5	Missense_Mutation	SNP	ENST00000280333.6	37		.	.	.	.	.	.	.	.	.	.	G	7.557	0.663827	0.14710	.	.	ENSG00000150760	ENST00000280333	T	0.16457	2.34	5.03	5.03	0.67393	.	0.000000	0.85682	D	0.000000	T	0.04363	0.0120	N	0.00280	-1.71	0.54753	D	0.999984	B;B	0.16166	0.008;0.016	B;B	0.14023	0.01;0.01	T	0.40905	-0.9538	10	0.02654	T	1	.	18.5603	0.91097	0.0:0.0:1.0:0.0	.	332;332	B2RUU3;Q14185	.;DOCK1_HUMAN	I	332	ENSP00000280333:V332I	ENSP00000280333:V332I	V	+	1	0	DOCK1	128696994	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.530000	0.81962	2.624000	0.88883	0.650000	0.86243	GTA	.	.	none		0.353	DOCK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050979.2	NM_001380	
TARDBP	23435	hgsc.bcm.edu	37	1	11073808	11073808	+	Silent	SNP	C	C	T	rs72870030	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:11073808C>T	ENST00000240185.3	+	2	138	c.24C>T	c.(22-24)acC>acT	p.T8T	TARDBP_ENST00000439080.2_5'UTR|TARDBP_ENST00000315091.3_Silent_p.T8T	NM_007375.3	NP_031401.1	Q13148	TADBP_HUMAN	TAR DNA binding protein	8					3'-UTR-mediated mRNA stabilization (GO:0070935)|cell death (GO:0008219)|mRNA processing (GO:0006397)|negative regulation by host of viral transcription (GO:0043922)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|mRNA 3'-UTR binding (GO:0003730)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(3)|ovary(2)	11	Ovarian(185;0.249)	Lung NSC(185;1.04e-05)|all_lung(284;1.31e-05)|Renal(390;0.000147)|Colorectal(325;0.00205)|Breast(348;0.00262)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0578)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;3.37e-07)|COAD - Colon adenocarcinoma(227;7.38e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|Kidney(185;0.000754)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|READ - Rectum adenocarcinoma(331;0.0487)		TTCGGGTAACCGAAGATGAGA	0.428													C|||	7	0.00139776	0.0045	0.0014	5008	,	,		23229	0.0		0.0	False		,,,				2504	0.0				p.T8T		Atlas-SNP	.											TARDBP,caecum,carcinoma,0,1	TARDBP	31	1	0			c.C24T						scavenged	.	C		9,4397	14.3+/-33.2	0,9,2194	34.0	31.0	32.0		24	-10.6	0.2	1	dbSNP_131	32	0,8598		0,0,4299	no	coding-synonymous	TARDBP	NM_007375.3		0,9,6493	TT,TC,CC		0.0,0.2043,0.0692		8/415	11073808	9,12995	2203	4299	6502	SO:0001819	synonymous_variant	23435	exon2			GGTAACCGAAGAT	U23731	CCDS122.1	1p36.22	2014-09-17			ENSG00000120948	ENSG00000120948		"""RNA binding motif (RRM) containing"""	11571	protein-coding gene	gene with protein product		605078				7745706	Standard	NM_007375		Approved	TDP-43, ALS10	uc001art.3	Q13148	OTTHUMG00000002120	ENST00000240185.3:c.24C>T	1.37:g.11073808C>T		Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	148	2	0.0135135	NM_007375	A4GUK4|A4GUK5|A4GUK6|B2R629|B4DJ45|E2PU12|Q53H27|Q6FI92|Q96DJ0	Silent	SNP	ENST00000240185.3	37	CCDS122.1																																																																																			C|0.999;T|0.001	0.001	strong		0.428	TARDBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006063.1	NM_007375	
ARHGAP44	9912	hgsc.bcm.edu	37	17	12859254	12859254	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:12859254G>A	ENST00000379672.5	+	14	1507	c.1207G>A	c.(1207-1209)Gca>Aca	p.A403T	ARHGAP44_ENST00000340825.3_Missense_Mutation_p.A403T|ARHGAP44_ENST00000262444.9_Missense_Mutation_p.A403T	NM_014859.4	NP_055674.4	Q17R89	RHG44_HUMAN	Rho GTPase activating protein 44	403	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				exocytosis (GO:0006887)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell junction (GO:0030054)|cell projection (GO:0042995)|cytosol (GO:0005829)|endosome (GO:0005768)|leading edge membrane (GO:0031256)|synapse (GO:0045202)	GTPase activator activity (GO:0005096)|phospholipid binding (GO:0005543)			NS(2)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|urinary_tract(1)	31						CAGTAATATGGCAATTGTTTT	0.428																																					p.A403T		Atlas-SNP	.											.	ARHGAP44	55	.	0			c.G1207A						PASS	.						72.0	69.0	70.0					17																	12859254		1959	4140	6099	SO:0001583	missense	9912	exon14			AATATGGCAATTG		CCDS45616.1	17p12	2011-06-29			ENSG00000006740	ENSG00000006740		"""Rho GTPase activating proteins"""	29096	protein-coding gene	gene with protein product						19273615	Standard	NM_014859		Approved	KIAA0672, RICH-2, RICH2	uc002gnr.4	Q17R89	OTTHUMG00000058765	ENST00000379672.5:c.1207G>A	17.37:g.12859254G>A	ENSP00000368994:p.Ala403Thr	Somatic	236	0	0		WXS	Illumina HiSeq	Phase_I	210	38	0.180952	NM_014859	A6NCP5|A8MQB2|O75160|Q7Z5Z7|Q9Y4Q4	Missense_Mutation	SNP	ENST00000379672.5	37	CCDS45616.1	.	.	.	.	.	.	.	.	.	.	G	17.50	3.406245	0.62288	.	.	ENSG00000006740	ENST00000379672;ENST00000544416;ENST00000340825	T;T	0.25250	1.81;1.81	5.89	5.89	0.94794	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.67906	0.2943	H	0.97564	4.03	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;0.999	D;D;D;D	0.91635	0.999;0.998;0.997;0.992	T	0.79415	-0.1813	10	0.87932	D	0	.	17.7556	0.88447	0.0:0.0:1.0:0.0	.	403;48;65;403	A6NCP5;Q9Y4Q4;F5H6L3;Q17R89	.;.;.;RHG44_HUMAN	T	403;65;403	ENSP00000368994:A403T;ENSP00000342566:A403T	ENSP00000342566:A403T	A	+	1	0	ARHGAP44	12799979	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.420000	0.97426	2.793000	0.96121	0.655000	0.94253	GCA	.	.	none		0.428	ARHGAP44-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441566.1	NM_014859	
NBPF10	100132406	hgsc.bcm.edu	37	1	145296403	145296403	+	Silent	SNP	C	C	T	rs4996269	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:145296403C>T	ENST00000342960.5	+	3	360	c.325C>T	c.(325-327)Cta>Tta	p.L109L	NBPF10_ENST00000369338.1_Intron|NBPF10_ENST00000369339.3_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	109						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCTGACCCAGCTAAGGGAGAA	0.517																																					p.L109L		Atlas-SNP	.											NBPF10,NS,carcinoma,0,1	NBPF10	221	1	0			c.C325T						scavenged	.																																			SO:0001819	synonymous_variant	100132406	exon3			ACCCAGCTAAGGG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.325C>T	1.37:g.145296403C>T		Somatic	146	1	0.00684932		WXS	Illumina HiSeq	Phase_I	162	4	0.0246914	NM_001039703	Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	CCDS53355.1																																																																																			T|0.001;G|0.956	0.001	strong		0.517	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
RNF216	54476	hgsc.bcm.edu	37	7	5662542	5662542	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:5662542C>T	ENST00000425013.2	-	17	2774	c.2550G>A	c.(2548-2550)ctG>ctA	p.L850L	RNF216_ENST00000469375.1_5'Flank|RNF216_ENST00000389902.3_Silent_p.L907L	NM_207111.3|NM_207116.2	NP_996994.1|NP_996999.1	Q9NWF9	RN216_HUMAN	ring finger protein 216	850	Pro-rich.				apoptotic process (GO:0006915)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|regulation of defense response to virus by host (GO:0050691)|regulation of interferon-beta production (GO:0032648)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)		FBXL18/RNF216(2)	breast(3)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|prostate(1)|skin(1)|urinary_tract(4)	33		Ovarian(82;0.07)		UCEC - Uterine corpus endometrioid carcinoma (126;0.135)|OV - Ovarian serous cystadenocarcinoma(56;2.69e-13)		GGTTGTGCTCCAGGGGCATGT	0.617																																					p.L907L		Atlas-SNP	.											.	RNF216	71	.	0			c.G2721A						PASS	.						108.0	118.0	114.0					7																	5662542		2203	4300	6503	SO:0001819	synonymous_variant	54476	exon17			GTGCTCCAGGGGC	AY062174	CCDS34594.1, CCDS34595.1	7p22.1	2014-02-12	2007-08-20		ENSG00000011275	ENSG00000011275		"""RING-type (C3HC4) zinc fingers"""	21698	protein-coding gene	gene with protein product		609948					Standard	NM_207111		Approved	TRIAD3, UBCE7IP1, ZIN	uc003sox.2	Q9NWF9	OTTHUMG00000155500	ENST00000425013.2:c.2550G>A	7.37:g.5662542C>T		Somatic	47	0	0		WXS	Illumina HiSeq	Phase_I	51	8	0.156863	NM_207111	Q6Y691|Q75ML7|Q7Z2H7|Q7Z7C1|Q8NHW7|Q9NYT1	Silent	SNP	ENST00000425013.2	37	CCDS34595.1																																																																																			.	.	none		0.617	RNF216-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000340374.1	NM_207111	
MUC4	4585	hgsc.bcm.edu	37	3	195507064	195507064	+	Missense_Mutation	SNP	G	G	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195507064G>C	ENST00000463781.3	-	2	11846	c.11387C>G	c.(11386-11388)aCc>aGc	p.T3796S	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3796S|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.T3796S(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)		GGAAGTGTCGGTGACAGGAAG	0.602																																					p.T3796S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	endometrium(1)	c.C11387G						scavenged	.						7.0	7.0	7.0					3																	195507064		638	1493	2131	SO:0001583	missense	4585	exon2			GTGTCGGTGACAG	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.11387C>G	3.37:g.195507064G>C	ENSP00000417498:p.Thr3796Ser	Somatic	296	5	0.0168919		WXS	Illumina HiSeq	Phase_I	307	13	0.0423453	NM_018406	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	.	.	.	.	.	.	.	.	.	.	g	5.869	0.344521	0.11126	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37752	1.26;1.18	.	.	.	.	1.826270	0.06000	U	0.647533	T	0.22475	0.0542	N	0.19112	0.55	0.19300	N	0.999973	P	0.42584	0.784	B	0.39706	0.307	T	0.19451	-1.0305	8	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3668	E7ESK3	.	S	3796	ENSP00000417498:T3796S;ENSP00000420243:T3796S	.	T	-	2	0	MUC4	196991843	0.000000	0.05858	0.066000	0.19879	0.066000	0.16364	-0.667000	0.05274	0.064000	0.16427	0.064000	0.15345	ACC	.	.	none		0.602	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR5AP2	338675	hgsc.bcm.edu	37	11	56409697	56409697	+	Silent	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:56409697A>C	ENST00000302981.1	-	1	218	c.219T>G	c.(217-219)tcT>tcG	p.S73S	OR5AP2_ENST00000544374.1_Silent_p.S74S	NM_001002925.1	NP_001002925.1	Q8NGF4	O5AP2_HUMAN	olfactory receptor, family 5, subfamily AP, member 2	73						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(2)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	29						CATCTACAAAAGAGAGGCTAC	0.443																																					p.S73S		Atlas-SNP	.											.	OR5AP2	69	.	0			c.T219G						PASS	.						65.0	64.0	65.0					11																	56409697		2201	4296	6497	SO:0001819	synonymous_variant	338675	exon1			TACAAAAGAGAGG	AB065854	CCDS31534.1	11q11	2012-08-09			ENSG00000172464	ENSG00000172464		"""GPCR / Class A : Olfactory receptors"""	15258	protein-coding gene	gene with protein product							Standard	NM_001002925		Approved		uc001njb.1	Q8NGF4	OTTHUMG00000166865	ENST00000302981.1:c.219T>G	11.37:g.56409697A>C		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	102	15	0.147059	NM_001002925	B2RNM8	Silent	SNP	ENST00000302981.1	37	CCDS31534.1																																																																																			.	.	none		0.443	OR5AP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391613.1	NM_001002925	
GNL2	29889	hgsc.bcm.edu	37	1	38032563	38032563	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:38032563G>A	ENST00000373062.3	-	16	2187	c.2089C>T	c.(2089-2091)Cgc>Tgc	p.R697C	GNL2_ENST00000462812.1_5'UTR	NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	697					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				TCATAGTAGCGCACACCAACT	0.403																																					p.R697C		Atlas-SNP	.											.	GNL2	58	.	0			c.C2089T						PASS	.						188.0	170.0	176.0					1																	38032563		2203	4300	6503	SO:0001583	missense	29889	exon16			AGTAGCGCACACC	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.2089C>T	1.37:g.38032563G>A	ENSP00000362153:p.Arg697Cys	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	133	27	0.203008	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	37	CCDS421.1	.	.	.	.	.	.	.	.	.	.	G	32	5.138938	0.94560	.	.	ENSG00000134697	ENST00000373062	T	0.25579	1.79	5.38	5.38	0.77491	.	0.000000	0.85682	D	0.000000	T	0.52386	0.1731	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.52503	-0.8567	10	0.72032	D	0.01	-9.6294	19.4985	0.95083	0.0:0.0:1.0:0.0	.	697	Q13823	NOG2_HUMAN	C	697	ENSP00000362153:R697C	ENSP00000362153:R697C	R	-	1	0	GNL2	37805150	1.000000	0.71417	0.994000	0.49952	0.963000	0.63663	7.721000	0.84768	2.698000	0.92095	0.561000	0.74099	CGC	.	.	none		0.403	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285	
DNAJB1	3337	hgsc.bcm.edu	37	19	14627500	14627500	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:14627500T>C	ENST00000254322.2	-	2	640	c.570A>G	c.(568-570)ctA>ctG	p.L190L	DNAJB1_ENST00000396969.4_Silent_p.L90L	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	190					chaperone cofactor-dependent protein refolding (GO:0070389)|chaperone mediated protein folding requiring cofactor (GO:0051085)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|unfolded protein binding (GO:0051082)	p.L190L(1)		NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		CGTCGGGGTTTAGCCGCTTGT	0.483																																					p.L190L		Atlas-SNP	.											DNAJB1,NS,carcinoma,0,1	DNAJB1	38	1	1	Substitution - coding silent(1)	prostate(1)	c.A570G						scavenged	.						168.0	167.0	168.0					19																	14627500		2203	4300	6503	SO:0001819	synonymous_variant	3337	exon2			GGGGTTTAGCCGC	D49547	CCDS12312.1, CCDS74295.1	19p13.12	2014-08-12			ENSG00000132002	ENSG00000132002		"""Heat shock proteins / DNAJ (HSP40)"""	5270	protein-coding gene	gene with protein product	"""radial spoke 16 homolog B (Chlamydomonas)"""	604572		HSPF1		8975727, 8250930	Standard	XM_006722733		Approved	Hsp40, Sis1, RSPH16B	uc002myz.1	P25685	OTTHUMG00000183289	ENST00000254322.2:c.570A>G	19.37:g.14627500T>C		Somatic	160	0	0		WXS	Illumina HiSeq	Phase_I	165	3	0.0181818	NM_006145	B4DX52	Silent	SNP	ENST00000254322.2	37	CCDS12312.1																																																																																			.	.	none		0.483	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145	
PKHD1	5314	hgsc.bcm.edu	37	6	51909826	51909826	+	Missense_Mutation	SNP	C	C	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:51909826C>A	ENST00000371117.3	-	25	2928	c.2653G>T	c.(2653-2655)Ggt>Tgt	p.G885C	PKHD1_ENST00000340994.4_Missense_Mutation_p.G885C	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	885					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AAAACTCCACCATCATATACC	0.478																																					p.G885C		Atlas-SNP	.											PKHD1_ENST00000340994,scalp,malignant_melanoma,0,2	PKHD1	927	2	0			c.G2653T						scavenged	.						119.0	103.0	108.0					6																	51909826		2203	4299	6502	SO:0001583	missense	5314	exon25			CTCCACCATCATA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.2653G>T	6.37:g.51909826C>A	ENSP00000360158:p.Gly885Cys	Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	122	3	0.0245902	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	C	21.5	4.158377	0.78114	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.96073	-3.68;-3.9	5.25	5.25	0.73442	.	0.072878	0.56097	D	0.000025	D	0.97711	0.9249	M	0.85710	2.77	0.40959	D	0.984606	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.98539	1.0631	10	0.87932	D	0	.	16.704	0.85367	0.0:1.0:0.0:0.0	.	885;885	P08F94-2;P08F94	.;PKHD1_HUMAN	C	885	ENSP00000360158:G885C;ENSP00000341097:G885C	ENSP00000341097:G885C	G	-	1	0	PKHD1	52017785	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.027000	0.64109	2.619000	0.88677	0.655000	0.94253	GGT	.	.	none		0.478	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
DDX42	11325	hgsc.bcm.edu	37	17	61895140	61895140	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:61895140T>C	ENST00000578681.1	+	19	2800	c.2199T>C	c.(2197-2199)agT>agC	p.S733S	DDX42_ENST00000389924.2_Silent_p.S733S|DDX42_ENST00000583590.1_Silent_p.S733S|DDX42_ENST00000359353.5_Silent_p.S614S|DDX42_ENST00000582985.1_Intron|DDX42_ENST00000457800.2_Silent_p.S733S	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42	733					protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						GGTGGACTAGTGCAGGGAGCT	0.517																																					p.S733S		Atlas-SNP	.											.	DDX42	86	.	0			c.T2199C						PASS	.						105.0	98.0	100.0					17																	61895140		2203	4300	6503	SO:0001819	synonymous_variant	11325	exon18			GACTAGTGCAGGG	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3		ENST00000578681.1:c.2199T>C	17.37:g.61895140T>C		Somatic	208	0	0		WXS	Illumina HiSeq	Phase_I	215	44	0.204651	NM_203499	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Silent	SNP	ENST00000578681.1	37	CCDS32704.1																																																																																			.	.	none		0.517	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
TBC1D14	57533	hgsc.bcm.edu	37	4	7008366	7008366	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:7008366T>C	ENST00000409757.4	+	9	1483	c.1359T>C	c.(1357-1359)ggT>ggC	p.G453G	TBC1D14_ENST00000446947.2_Silent_p.G66G|TBC1D14_ENST00000448507.1_Silent_p.G453G|TBC1D14_ENST00000451522.2_Silent_p.G173G|TBC1D14_ENST00000410031.1_Silent_p.G225G	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	453	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						CAGATGCTGGTTTTTCAGCAG	0.403																																					p.G453G		Atlas-SNP	.											.	TBC1D14	110	.	0			c.T1359C						PASS	.						90.0	89.0	90.0					4																	7008366		2203	4300	6503	SO:0001819	synonymous_variant	57533	exon9			TGCTGGTTTTTCA	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.1359T>C	4.37:g.7008366T>C		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	125	26	0.208	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Silent	SNP	ENST00000409757.4	37	CCDS3394.2																																																																																			.	.	none		0.403	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773	
OR2T2	401992	hgsc.bcm.edu	37	1	248616764	248616764	+	Silent	SNP	C	C	T	rs376553658		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:248616764C>T	ENST00000342927.3	+	1	688	c.666C>T	c.(664-666)atC>atT	p.I222I		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	222						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			ACACGCACATCCTCCTGACTG	0.542																																					p.I222I		Atlas-SNP	.											OR2T2,NS,carcinoma,0,1	OR2T2	73	1	0			c.C666T						scavenged	.						182.0	125.0	144.0					1																	248616764		2186	4264	6450	SO:0001819	synonymous_variant	401992	exon1			GCACATCCTCCTG	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.666C>T	1.37:g.248616764C>T		Somatic	409	8	0.0195599		WXS	Illumina HiSeq	Phase_I	509	28	0.0550098	NM_001004136	B2RNM1|B9EH01	Silent	SNP	ENST00000342927.3	37	CCDS31116.1																																																																																			C|0.500;T|0.500	0.500	strong		0.542	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
SGK1	6446	hgsc.bcm.edu	37	6	134494704	134494704	+	Splice_Site	SNP	G	G	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134494704G>C	ENST00000237305.7	-	4	317	c.229C>G	c.(229-231)Cca>Gca	p.P77A	SGK1_ENST00000367858.5_Splice_Site_p.P172A|SGK1_ENST00000367857.5_Splice_Site_p.P67A|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000475719.2_Splice_Site_p.P77A|SGK1_ENST00000413996.3_Splice_Site_p.P91A|SGK1_ENST00000528577.1_Splice_Site_p.P105A	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	77					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)	p.P172S(1)|p.P77S(1)		central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GAAGGACTTGGCTAGAAAAAA	0.368																																					p.P172A		Atlas-SNP	.											SGK1_ENST00000528577,NS,lymphoid_neoplasm,0,6	SGK1	387	6	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.C514G						PASS	.						44.0	48.0	47.0					6																	134494704		2203	4300	6503	SO:0001630	splice_region_variant	6446	exon6			GACTTGGCTAGAA	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.229-1C>G	6.37:g.134494704G>C		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	50	5	0.1	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	14.64	2.594913	0.46318	.	.	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72394	3.18;3.18;3.18;3.18;3.18;-0.65	6.02	6.02	0.97574	Protein kinase-like domain (1);	0.050195	0.85682	D	0.000000	T	0.56558	0.1993	M	0.62723	1.935	0.80722	D	1	B;P;B;B;B;B	0.42871	0.065;0.792;0.014;0.05;0.232;0.008	B;B;B;B;B;B	0.34138	0.064;0.121;0.028;0.061;0.176;0.011	T	0.59359	-0.7469	10	0.21014	T	0.42	.	20.5407	0.99260	0.0:0.0:1.0:0.0	.	105;91;77;67;172;77	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	A	172;91;77;67;105;77;141	ENSP00000356832:P172A;ENSP00000396242:P91A;ENSP00000237305:P77A;ENSP00000356831:P67A;ENSP00000434450:P105A;ENSP00000434302:P77A	ENSP00000237305:P77A	P	-	1	0	SGK1	134536397	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	7.563000	0.82314	2.865000	0.98341	0.655000	0.94253	CCA	.	.	none		0.368	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		Missense_Mutation
KALRN	8997	hgsc.bcm.edu	37	3	124103697	124103697	+	Silent	SNP	G	G	A	rs574174504	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:124103697G>A	ENST00000240874.3	+	11	1927	c.1770G>A	c.(1768-1770)acG>acA	p.T590T	KALRN_ENST00000460856.1_Silent_p.T590T|KALRN_ENST00000360013.3_Silent_p.T590T	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	590					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GGCAGAATACGTACACCAATG	0.612													G|||	2	0.000399361	0.0	0.0029	5008	,	,		17008	0.0		0.0	False		,,,				2504	0.0				p.T590T		Atlas-SNP	.											KALRN_ENST00000360013,NS,carcinoma,+1,4	KALRN	556	4	0			c.G1770A						PASS	.						83.0	71.0	75.0					3																	124103697		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon11			GAATACGTACACC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.1770G>A	3.37:g.124103697G>A		Somatic	277	0	0		WXS	Illumina HiSeq	Phase_I	279	52	0.18638	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	G	7.665	0.685732	0.14973	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.35	-10.7	0.00240	.	.	.	.	.	T	0.40398	0.1115	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50816	-0.8783	4	.	.	.	.	4.2215	0.10559	0.1084:0.3716:0.3202:0.1998	.	.	.	.	H	568	.	.	R	+	2	0	KALRN	125586387	0.000000	0.05858	0.080000	0.20451	0.960000	0.62799	-4.083000	0.00298	-3.444000	0.00162	-0.878000	0.02970	CGT	.	.	none		0.612	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
PLOD2	5352	hgsc.bcm.edu	37	3	145841964	145841964	+	Silent	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:145841964T>G	ENST00000360060.3	-	2	339	c.162A>C	c.(160-162)cgA>cgC	p.R54R	PLOD2_ENST00000494950.1_5'UTR|PLOD2_ENST00000282903.5_Silent_p.R54R	NM_000935.2	NP_000926.2	O00469	PLOD2_HUMAN	procollagen-lysine, 2-oxoglutarate 5-dioxygenase 2	54					cellular protein modification process (GO:0006464)|extracellular matrix organization (GO:0030198)|response to hypoxia (GO:0001666)	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-lysine 5-dioxygenase activity (GO:0008475)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29					Vitamin C(DB00126)	ACTGCATAAATCGATGGAATC	0.313																																					p.R54R		Atlas-SNP	.											PLOD2,colon,carcinoma,-2,5	PLOD2	81	5	0			c.A162C						PASS	.						154.0	151.0	152.0					3																	145841964		2202	4299	6501	SO:0001819	synonymous_variant	5352	exon2			CATAAATCGATGG	U84573	CCDS3131.1, CCDS3132.1	3q24	2011-08-24	2005-01-04		ENSG00000152952	ENSG00000152952			9082	protein-coding gene	gene with protein product	"""lysyl hydroxlase 2"""	601865	"""procollagen-lysine, 2-oxoglutarate 5-dioxygenase (lysine hydroxylase) 2"""			9054364	Standard	XM_005247535		Approved	LH2	uc003evr.1	O00469	OTTHUMG00000159417	ENST00000360060.3:c.162A>C	3.37:g.145841964T>G		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	97	16	0.164948	NM_182943	B3KWS3|Q59ED2|Q8N170	Silent	SNP	ENST00000360060.3	37	CCDS3131.1																																																																																			.	.	none		0.313	PLOD2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355185.1	NM_000935	
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:16285491C>T	ENST00000395837.1	+	2	451	c.270C>T	c.(268-270)acC>acT	p.T90T	UBB_ENST00000395839.1_Silent_p.T90T|UBB_ENST00000535788.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Silent_p.T90T|UBB_ENST00000578649.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	90	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCATCACCCTGGAAGTGG	0.552																																					p.T90T	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,bladder,carcinoma,0,2	UBB	30	2	0			c.C270T						scavenged	.						75.0	76.0	75.0					17																	16285491		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			CATCACCCTGGAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.270C>T	17.37:g.16285491C>T		Somatic	313	2	0.00638978		WXS	Illumina HiSeq	Phase_I	388	4	0.0103093	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
RHOA	387	hgsc.bcm.edu	37	3	49413009	49413009	+	Missense_Mutation	SNP	C	C	T	rs11552758		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:49413009C>T	ENST00000418115.1	-	2	398	c.14G>A	c.(13-15)cGg>cAg	p.R5Q	RHOA_ENST00000422781.1_Missense_Mutation_p.R5Q|RHOA_ENST00000454011.2_Missense_Mutation_p.R5Q	NM_001664.2	NP_001655.1	P61586	RHOA_HUMAN	ras homolog family member A	5					actin cytoskeleton organization (GO:0030036)|androgen receptor signaling pathway (GO:0030521)|apical junction assembly (GO:0043297)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|cerebral cortex cell migration (GO:0021795)|cleavage furrow formation (GO:0036089)|forebrain radial glial cell differentiation (GO:0021861)|negative chemotaxis (GO:0050919)|negative regulation of axonogenesis (GO:0050771)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intracellular steroid hormone receptor signaling pathway (GO:0033144)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neuron differentiation (GO:0045665)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification involved in bone maturation (GO:0043931)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of axonogenesis (GO:0050772)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of cell migration (GO:0030335)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytokinesis (GO:0032467)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of podosome assembly (GO:0071803)|positive regulation of smooth muscle contraction (GO:0045987)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of translation (GO:0045727)|positive regulation of vasoconstriction (GO:0045907)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion transport (GO:0051924)|regulation of cell migration (GO:0030334)|regulation of dendrite development (GO:0050773)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of osteoblast proliferation (GO:0033688)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to amino acid (GO:0043200)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to glucocorticoid (GO:0051384)|response to glucose (GO:0009749)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|Rho protein signal transduction (GO:0007266)|skeletal muscle tissue development (GO:0007519)|small GTPase mediated signal transduction (GO:0007264)|spindle assembly involved in mitosis (GO:0090307)|stress fiber assembly (GO:0043149)|stress-activated protein kinase signaling cascade (GO:0031098)|substantia nigra development (GO:0021762)|trabecula morphogenesis (GO:0061383)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	apical junction complex (GO:0043296)|axon (GO:0030424)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin binding (GO:0017022)	p.R5Q(1)		cervix(1)|kidney(1)|large_intestine(5)|lung(1)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	12				BRCA - Breast invasive adenocarcinoma(193;8.58e-05)|Kidney(197;0.0023)|KIRC - Kidney renal clear cell carcinoma(197;0.00258)		CAGTTTCTTCCGGATGGCAGC	0.473																																					p.R5Q		Atlas-SNP	.											RHOA,NS,lymphoid_neoplasm,0,7	RHOA	46	7	1	Substitution - Missense(1)	large_intestine(1)	c.G14A						PASS	.						106.0	97.0	100.0					3																	49413009		2203	4300	6503	SO:0001583	missense	387	exon2			TTCTTCCGGATGG	BC001360	CCDS2795.1	3p21.3	2012-02-27	2012-02-27	2004-03-23	ENSG00000067560	ENSG00000067560			667	protein-coding gene	gene with protein product		165390	"""ras homolog gene family, member A"""	ARH12, ARHA		9605859	Standard	NM_001664		Approved	RhoA, Rho12, RHOH12	uc003cwu.3	P61586	OTTHUMG00000156838	ENST00000418115.1:c.14G>A	3.37:g.49413009C>T	ENSP00000400175:p.Arg5Gln	Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	171	51	0.298246	NM_001664	P06749|Q53HM4|Q5U024|Q9UDJ0|Q9UEJ4	Missense_Mutation	SNP	ENST00000418115.1	37	CCDS2795.1	.	.	.	.	.	.	.	.	.	.	C	33	5.291209	0.95546	.	.	ENSG00000067560	ENST00000418115;ENST00000454011;ENST00000422781;ENST00000445425;ENST00000431929	T;T;T;T;T	0.70399	-0.3;1.78;-0.33;-0.48;2.14	5.89	5.89	0.94794	Small GTP-binding protein domain (1);	0.000000	0.64402	D	0.000001	T	0.65943	0.2740	L	0.38175	1.15	0.80722	D	1	B	0.18166	0.026	B	0.20184	0.028	T	0.61926	-0.6962	10	0.87932	D	0	.	18.8947	0.92419	0.0:1.0:0.0:0.0	.	5	P61586	RHOA_HUMAN	Q	5	ENSP00000400175:R5Q;ENSP00000394483:R5Q;ENSP00000413587:R5Q;ENSP00000408402:R5Q;ENSP00000400747:R5Q	ENSP00000400175:R5Q	R	-	2	0	RHOA	49388013	1.000000	0.71417	0.999000	0.59377	0.896000	0.52359	7.652000	0.83633	2.809000	0.96659	0.558000	0.71614	CGG	.	.	weak		0.473	RHOA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346157.3	NM_001664	
USH2A	7399	hgsc.bcm.edu	37	1	216221971	216221971	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:216221971A>G	ENST00000307340.3	-	31	6454	c.6068T>C	c.(6067-6069)cTa>cCa	p.L2023P	USH2A_ENST00000366943.2_Missense_Mutation_p.L2023P	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	2023	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		TTTGAAGGGTAGCAAGCCTGT	0.413										HNSCC(13;0.011)																											p.L2023P		Atlas-SNP	.											.	USH2A	1168	.	0			c.T6068C						PASS	.						161.0	158.0	159.0					1																	216221971		2203	4300	6503	SO:0001583	missense	7399	exon31			AAGGGTAGCAAGC	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.6068T>C	1.37:g.216221971A>G	ENSP00000305941:p.Leu2023Pro	Somatic	167	0	0		WXS	Illumina HiSeq	Phase_I	175	50	0.285714	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	37	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	A	11.46	1.644095	0.29246	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.57907	0.37;0.37	6.16	3.75	0.43078	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.558741	0.13626	N	0.374070	T	0.64000	0.2559	M	0.70275	2.135	0.34933	D	0.749578	D	0.53885	0.963	P	0.60541	0.876	T	0.65010	-0.6272	10	0.30854	T	0.27	.	6.883	0.24183	0.4969:0.1739:0.0:0.3292	.	2023	O75445	USH2A_HUMAN	P	2023	ENSP00000305941:L2023P;ENSP00000355910:L2023P	ENSP00000305941:L2023P	L	-	2	0	USH2A	214288594	0.218000	0.23608	0.304000	0.25085	0.998000	0.95712	0.502000	0.22594	0.491000	0.27793	0.528000	0.53228	CTA	.	.	none		0.413	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
PDE2A	5138	hgsc.bcm.edu	37	11	72301503	72301503	+	Missense_Mutation	SNP	G	G	A	rs341047	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:72301503G>A	ENST00000334456.5	-	8	916	c.671C>T	c.(670-672)aCc>aTc	p.T224I	PDE2A_ENST00000418754.2_Missense_Mutation_p.T109I|PDE2A_ENST00000376450.3_Intron|RP11-169D4.2_ENST00000545254.1_RNA|PDE2A_ENST00000444035.2_Missense_Mutation_p.T215I|PDE2A_ENST00000540345.1_Missense_Mutation_p.T215I|PDE2A_ENST00000544570.1_Missense_Mutation_p.T217I	NM_002599.4	NP_002590.1	O00408	PDE2A_HUMAN	phosphodiesterase 2A, cGMP-stimulated	224			T -> I (in dbSNP:rs341047).		blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cAMP catabolic process (GO:0006198)|cAMP-mediated signaling (GO:0019933)|cellular response to cGMP (GO:0071321)|cellular response to drug (GO:0035690)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cellular response to mechanical stimulus (GO:0071260)|cellular response to transforming growth factor beta stimulus (GO:0071560)|cGMP catabolic process (GO:0046069)|cGMP-mediated signaling (GO:0019934)|establishment of endothelial barrier (GO:0061028)|metabolic process (GO:0008152)|monocyte differentiation (GO:0030224)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of protein import into nucleus, translocation (GO:0033159)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vascular permeability (GO:0043116)|positive regulation of inflammatory response (GO:0050729)|positive regulation of vascular permeability (GO:0043117)|protein targeting to mitochondrion (GO:0006626)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	calcium channel activity (GO:0005262)|cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|cGMP-stimulated cyclic-nucleotide phosphodiesterase activity (GO:0004118)|cyclic-nucleotide phosphodiesterase activity (GO:0004112)|drug binding (GO:0008144)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|TPR domain binding (GO:0030911)	p.T224I(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(2)|lung(21)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	36			BRCA - Breast invasive adenocarcinoma(5;3.55e-05)		Caffeine(DB00201)|Tofisopam(DB08811)	GTCGCGGTCGGTGTACGCCGC	0.736													G|||	353	0.0704872	0.003	0.0937	5008	,	,		12179	0.0784		0.1044	False		,,,				2504	0.1022				p.T224I		Atlas-SNP	.											PDE2A,colon,carcinoma,0,2	PDE2A	156	2	1	Substitution - Missense(1)	prostate(1)	c.C671T						scavenged	.	G	ILE/THR,ILE/THR,ILE/THR	107,4261		1,105,2078	11.0	14.0	13.0		650,644,671	2.1	0.3	11	dbSNP_79	13	937,7615		47,843,3386	yes	missense,missense,missense	PDE2A	NM_001143839.3,NM_001146209.2,NM_002599.4	89,89,89	48,948,5464	AA,AG,GG		10.9565,2.4496,8.0805	possibly-damaging,possibly-damaging,possibly-damaging	217/935,215/933,224/942	72301503	1044,11876	2184	4276	6460	SO:0001583	missense	5138	exon8			CGGTCGGTGTACG	U67733	CCDS8216.1, CCDS44670.1, CCDS53678.1, CCDS73345.1	11q13.1-q14.1	2008-05-14			ENSG00000186642	ENSG00000186642	3.1.4.17	"""Phosphodiesterases"""	8777	protein-coding gene	gene with protein product		602658				9210593	Standard	NM_002599		Approved		uc010rrc.2	O00408	OTTHUMG00000102045	ENST00000334456.5:c.671C>T	11.37:g.72301503G>A	ENSP00000334910:p.Thr224Ile	Somatic	2	2	1		WXS	Illumina HiSeq	Phase_I	3	3	1	NM_002599	B2R646|B3KRV5|E9PGI1|F6W5Z0|Q5J791|Q5J792|Q5J793|Q6ZMR1	Missense_Mutation	SNP	ENST00000334456.5	37	CCDS8216.1	186	0.08516483516483517	14	0.028455284552845527	34	0.09392265193370165	49	0.08566433566433566	89	0.11741424802110818	G	11.61	1.689892	0.29962	0.024496	0.109565	ENSG00000186642	ENST00000334456;ENST00000444035;ENST00000429363;ENST00000544570;ENST00000418754;ENST00000540345	T;T;T;T;T	0.66280	-0.2;-0.2;-0.19;-0.17;-0.2	4.21	2.11	0.27256	.	2.363610	0.01332	N	0.011285	T	0.00906	0.0030	N	0.19112	0.55	0.51767	P	6.60000000000105E-5	B;B;B;B;B	0.24092	0.01;0.059;0.059;0.097;0.073	B;B;B;B;B	0.15052	0.001;0.005;0.008;0.012;0.007	T	0.07558	-1.0766	9	0.36615	T	0.2	.	9.7098	0.40238	0.0:0.454:0.546:0.0	rs341047;rs56918155	109;224;215;217;224	E9PEF1;O00408;E9PGI1;F6W5Z0;B2R646	.;PDE2A_HUMAN;.;.;.	I	224;215;293;217;109;215	ENSP00000334910:T224I;ENSP00000411657:T215I;ENSP00000442256:T217I;ENSP00000410310:T109I;ENSP00000446399:T215I	ENSP00000334910:T224I	T	-	2	0	PDE2A	71979151	0.006000	0.16342	0.319000	0.25293	0.074000	0.17049	0.019000	0.13444	0.938000	0.37419	0.313000	0.20887	ACC	G|0.921;A|0.079	0.079	strong		0.736	PDE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219839.2	NM_002599	
CLPTM1	1209	hgsc.bcm.edu	37	19	45495643	45495643	+	Missense_Mutation	SNP	G	G	A	rs548487634		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:45495643G>A	ENST00000337392.5	+	13	1858	c.1708G>A	c.(1708-1710)Ggc>Agc	p.G570S	CLPTM1_ENST00000541297.2_Missense_Mutation_p.G556S|CLPTM1_ENST00000546079.1_Missense_Mutation_p.G468S	NM_001282175.1|NM_001282176.1|NM_001294.2	NP_001269104.1|NP_001269105.1|NP_001285.1	O96005	CLPT1_HUMAN	cleft lip and palate associated transmembrane protein 1	570					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of T cell differentiation in thymus (GO:0033081)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(266;0.224)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00354)|Epithelial(262;0.187)		GTACCGGATCGGCTGCCTGCG	0.647													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17297	0.0		0.0	False		,,,				2504	0.0				p.G570S		Atlas-SNP	.											CLPTM1_ENST00000347493,colon,carcinoma,0,2	CLPTM1	109	2	0			c.G1708A						scavenged	.						162.0	151.0	154.0					19																	45495643		2203	4300	6503	SO:0001583	missense	1209	exon13			CGGATCGGCTGCC	AF037339	CCDS12651.1, CCDS74394.1, CCDS74395.1	19q13.3	2008-02-05				ENSG00000104853			2087	protein-coding gene	gene with protein product		604783				9828125	Standard	NM_001294		Approved		uc002pai.3	O96005		ENST00000337392.5:c.1708G>A	19.37:g.45495643G>A	ENSP00000336994:p.Gly570Ser	Somatic	136	1	0.00735294		WXS	Illumina HiSeq	Phase_I	134	4	0.0298507	NM_001294	B3KQH2|B4DDS3|B4E2X9|B7Z9X9|F5H8J3|Q53ET6|Q9BSS5	Missense_Mutation	SNP	ENST00000337392.5	37	CCDS12651.1	.	.	.	.	.	.	.	.	.	.	G	27.1	4.798279	0.90538	.	.	ENSG00000104853	ENST00000546079;ENST00000541297;ENST00000337392;ENST00000347493	.	.	.	5.21	5.21	0.72293	.	0.057551	0.64402	D	0.000002	T	0.46619	0.1402	N	0.03983	-0.305	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.71656	0.974;0.942	T	0.46359	-0.9197	9	0.17832	T	0.49	-48.0596	14.1849	0.65598	0.0:0.0:1.0:0.0	.	556;570	F5H8J3;O96005	.;CLPT1_HUMAN	S	468;556;570;570	.	ENSP00000336994:G570S	G	+	1	0	CLPTM1	50187483	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.891000	0.92485	2.727000	0.93392	0.650000	0.86243	GGC	.	.	none		0.647	CLPTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453267.1	NM_001294	
CD274	29126	hgsc.bcm.edu	37	9	5457196	5457196	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:5457196G>A	ENST00000381577.3	+	3	256	c.170G>A	c.(169-171)tGg>tAg	p.W57*	CD274_ENST00000381573.4_Intron|CD274_ENST00000498261.1_3'UTR	NM_014143.3	NP_054862.1	Q9NZQ7	PD1L1_HUMAN	CD274 molecule	57	Ig-like V-type.				cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)	11	all_hematologic(13;0.158)	Acute lymphoblastic leukemia(23;0.154)		GBM - Glioblastoma multiforme(50;0.000742)|Lung(218;0.111)		ATTGTCTATTGGGAAATGGAG	0.428			T	CIITA	"""PMBL, Hodgkin Lymphona, """																																p.W57X		Atlas-SNP	.		Dom	yes		9	9p24	29126	CD274 molecule		L	CD274,spleen,lymphoid_neoplasm,-1,1	CD274	26	1	0			c.G170A						PASS	.						94.0	94.0	94.0					9																	5457196		2203	4300	6503	SO:0001587	stop_gained	29126	exon3			TCTATTGGGAAAT	AF177937	CCDS6464.1, CCDS59118.1	9p24.1	2014-01-30	2006-03-28	2005-02-25	ENSG00000120217	ENSG00000120217		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Endogenous ligands"""	17635	protein-coding gene	gene with protein product	"""B7 homolog 1"""	605402	"""programmed cell death 1 ligand 1"", ""CD274 antigen"""	PDCD1LG1		11015443, 10581077	Standard	NM_014143		Approved	B7-H, B7H1, PD-L1, PDL1, B7-H1	uc003zje.3	Q9NZQ7	OTTHUMG00000019503	ENST00000381577.3:c.170G>A	9.37:g.5457196G>A	ENSP00000370989:p.Trp57*	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	130	20	0.153846	NM_014143	B2RBA2|B4DU27|Q14CJ2|Q2V8D5|Q66RK1|Q6WEX4|Q9NUZ5	Nonsense_Mutation	SNP	ENST00000381577.3	37	CCDS6464.1	.	.	.	.	.	.	.	.	.	.	G	37	6.439266	0.97568	.	.	ENSG00000120217	ENST00000381577	.	.	.	5.87	5.87	0.94306	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.29301	T	0.29	-5.8249	18.3892	0.90477	0.0:0.0:1.0:0.0	.	.	.	.	X	57	.	ENSP00000370989:W57X	W	+	2	0	CD274	5447196	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	6.301000	0.72782	2.791000	0.96007	0.655000	0.94253	TGG	.	.	none		0.428	CD274-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051631.2	NM_014143	
TNFRSF18	8784	hgsc.bcm.edu	37	1	1139804	1139804	+	Nonsense_Mutation	SNP	C	C	A	rs531486834		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:1139804C>A	ENST00000379268.2	-	3	492	c.373G>T	c.(373-375)Gaa>Taa	p.E125*	TNFRSF18_ENST00000379265.5_Nonsense_Mutation_p.E125*|TNFRSF18_ENST00000328596.6_Nonsense_Mutation_p.E125*|TNFRSF18_ENST00000486728.1_Nonsense_Mutation_p.E53*	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	125					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)	p.E125K(2)		lung(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CAGTGGCCTTCGTGGCCCCCG	0.647																																					p.E125X	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											TNFRSF18_ENST00000379268,NS,carcinoma,0,2	TNFRSF18	13	2	2	Substitution - Missense(2)	lung(2)	c.G373T						scavenged	.						34.0	38.0	37.0					1																	1139804		2197	4294	6491	SO:0001587	stop_gained	8784	exon3			GGCCTTCGTGGCC	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.373G>T	1.37:g.1139804C>A	ENSP00000368570:p.Glu125*	Somatic	128	0	0		WXS	Illumina HiSeq	Phase_I	123	4	0.0325203	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Nonsense_Mutation	SNP	ENST00000379268.2	37	CCDS10.1	.	.	.	.	.	.	.	.	.	.	C	10.56	1.385542	0.25031	.	.	ENSG00000186891	ENST00000328596;ENST00000379268;ENST00000379265	.	.	.	3.55	2.6	0.31112	.	0.678176	0.13361	N	0.393645	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-9.6217	10.9468	0.47306	0.0:0.8076:0.1924:0.0	.	.	.	.	X	125	.	ENSP00000328207:E125X	E	-	1	0	TNFRSF18	1129667	0.001000	0.12720	0.099000	0.21106	0.009000	0.06853	1.116000	0.31221	1.035000	0.39972	0.655000	0.94253	GAA	.	.	none		0.647	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195	
UBB	7314	hgsc.bcm.edu	37	17	16285497	16285497	+	Silent	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:16285497A>G	ENST00000395837.1	+	2	457	c.276A>G	c.(274-276)gaA>gaG	p.E92E	UBB_ENST00000395839.1_Silent_p.E92E|UBB_ENST00000535788.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Silent_p.E92E|UBB_ENST00000578649.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	92	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.E92E(2)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		TCACCCTGGAAGTGGAGCCCA	0.557																																					p.E92E	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,bladder,carcinoma,0,6	UBB	30	6	2	Substitution - coding silent(2)	endometrium(1)|central_nervous_system(1)	c.A276G						scavenged	.																																			SO:0001819	synonymous_variant	7314	exon2			CCTGGAAGTGGAG		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.276A>G	17.37:g.16285497A>G		Somatic	332	2	0.0060241		WXS	Illumina HiSeq	Phase_I	400	12	0.03	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			G|1.000;|0.000	1.000	weak		0.557	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
PTCH1	5727	hgsc.bcm.edu	37	9	98231221	98231221	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:98231221G>T	ENST00000331920.6	-	14	2361	c.2062C>A	c.(2062-2064)Cag>Aag	p.Q688K	PTCH1_ENST00000430669.2_Missense_Mutation_p.Q622K|PTCH1_ENST00000418258.1_Missense_Mutation_p.Q537K|PTCH1_ENST00000429896.2_Missense_Mutation_p.Q537K|PTCH1_ENST00000375274.2_Missense_Mutation_p.Q687K|PTCH1_ENST00000437951.1_Missense_Mutation_p.Q622K|PTCH1_ENST00000421141.1_Missense_Mutation_p.Q537K	NM_000264.3	NP_000255.2	Q13635	PTC1_HUMAN	patched 1	688					brain development (GO:0007420)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation involved in kidney development (GO:0061005)|cell proliferation involved in metanephros development (GO:0072203)|cellular response to cholesterol (GO:0071397)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|embryonic organ development (GO:0048568)|epidermis development (GO:0008544)|glucose homeostasis (GO:0042593)|heart morphogenesis (GO:0003007)|hindlimb morphogenesis (GO:0035137)|in utero embryonic development (GO:0001701)|keratinocyte proliferation (GO:0043616)|limb morphogenesis (GO:0035108)|mammary gland duct morphogenesis (GO:0060603)|mammary gland epithelial cell differentiation (GO:0060644)|negative regulation of cell division (GO:0051782)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate axis specification (GO:0021997)|neural tube closure (GO:0001843)|neural tube patterning (GO:0021532)|organ morphogenesis (GO:0009887)|pharyngeal system development (GO:0060037)|positive regulation of cholesterol efflux (GO:0010875)|protein processing (GO:0016485)|protein targeting to plasma membrane (GO:0072661)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein localization (GO:0032880)|regulation of smoothened signaling pathway (GO:0008589)|renal system development (GO:0072001)|response to chlorate (GO:0010157)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to mechanical stimulus (GO:0009612)|response to retinoic acid (GO:0032526)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)|somite development (GO:0061053)|spinal cord motor neuron differentiation (GO:0021522)	axonal growth cone (GO:0044295)|caveola (GO:0005901)|dendritic growth cone (GO:0044294)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|midbody (GO:0030496)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|primary cilium (GO:0072372)	cholesterol binding (GO:0015485)|cyclin binding (GO:0030332)|hedgehog family protein binding (GO:0097108)|hedgehog receptor activity (GO:0008158)|heparin binding (GO:0008201)|smoothened binding (GO:0005119)	p.Q688*(1)|p.Q688K(1)		NS(8)|bone(33)|breast(10)|central_nervous_system(95)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(8)|kidney(2)|large_intestine(18)|lung(22)|meninges(1)|oesophagus(3)|ovary(6)|prostate(2)|skin(262)|upper_aerodigestive_tract(11)|urinary_tract(2)|vulva(1)	490		Medulloblastoma(1;7.87e-06)|all_neural(1;0.000555)|Acute lymphoblastic leukemia(62;0.136)				GTGACGGGCTGCACAGAGATC	0.632																																					p.Q688K		Atlas-SNP	.											PTCH1_ENST00000430669,colon,carcinoma,+1,18	PTCH1	1850	18	2	Substitution - Missense(1)|Substitution - Nonsense(1)	lung(1)|skin(1)	c.C2062A	GRCh37	CM971262	PTCH1	M		scavenged	.						125.0	118.0	121.0					9																	98231221		2203	4300	6503	SO:0001583	missense	5727	exon14			CGGGCTGCACAGA	AI494442	CCDS6714.1, CCDS43851.1, CCDS47995.1, CCDS47996.1	9q22.1-q31	2014-09-17	2010-06-24	2006-09-26	ENSG00000185920	ENSG00000185920			9585	protein-coding gene	gene with protein product		601309	"""patched (Drosophila) homolog"", ""patched homolog (Drosophila)"", ""patched homolog 1 (Drosophila)"""	NBCCS, PTCH		8658145	Standard	NM_001083603		Approved	BCNS	uc004avk.4	Q13635	OTTHUMG00000020280	ENST00000331920.6:c.2062C>A	9.37:g.98231221G>T	ENSP00000332353:p.Gln688Lys	Somatic	122	0	0		WXS	Illumina HiSeq	Phase_I	119	4	0.0336134	NM_000264	A3KBI9|E9PEJ8|Q13463|Q5R1U7|Q5R1U9|Q5R1V0|Q5VZC0|Q5VZC2|Q86XG7	Missense_Mutation	SNP	ENST00000331920.6	37	CCDS6714.1	.	.	.	.	.	.	.	.	.	.	G	13.12	2.143313	0.37825	.	.	ENSG00000185920	ENST00000331920;ENST00000437951;ENST00000421141;ENST00000418258;ENST00000375275;ENST00000430669;ENST00000429896;ENST00000375274	D;D;D;D;D;D;D	0.89939	-2.59;-2.58;-2.56;-2.56;-2.58;-2.56;-2.59	4.84	4.84	0.62591	.	0.000000	0.85682	D	0.000000	D	0.84902	0.5575	L	0.50333	1.59	0.80722	D	1	B;B;B;B	0.24368	0.034;0.054;0.102;0.007	B;B;B;B	0.24394	0.053;0.047;0.031;0.005	T	0.80228	-0.1469	10	0.06625	T	0.88	-19.7364	18.1325	0.89606	0.0:0.0:1.0:0.0	.	537;622;687;688	Q13635-4;Q13635-3;Q13635-2;Q13635	.;.;.;PTC1_HUMAN	K	688;622;537;537;124;622;537;687	ENSP00000332353:Q688K;ENSP00000389744:Q622K;ENSP00000399981:Q537K;ENSP00000396135:Q537K;ENSP00000410287:Q622K;ENSP00000414823:Q537K;ENSP00000364423:Q687K	ENSP00000332353:Q688K	Q	-	1	0	PTCH1	97271042	1.000000	0.71417	1.000000	0.80357	0.954000	0.61252	9.096000	0.94182	2.505000	0.84491	0.557000	0.71058	CAG	.	.	none		0.632	PTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053229.2	NM_000264	
PRAMEF1	65121	hgsc.bcm.edu	37	1	12855752	12855752	+	Silent	SNP	G	G	A	rs80197258	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:12855752G>A	ENST00000332296.7	+	4	1135	c.1032G>A	c.(1030-1032)ctG>ctA	p.L344L	PRAMEF1_ENST00000400814.3_Silent_p.L99L	NM_023013.2	NP_075389.1	O95521	PRAM1_HUMAN	PRAME family member 1	344					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)			p.L344L(2)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(6)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00812)|Colorectal(212;4.88e-06)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000194)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAGCTCTGCTGGAGAAAATTG	0.557																																					p.L344L		Atlas-SNP	.											PRAMEF1,NS,carcinoma,0,2	PRAMEF1	78	2	2	Substitution - coding silent(2)	prostate(2)	c.G1032A						scavenged	.						188.0	192.0	191.0					1																	12855752		2203	4300	6503	SO:0001819	synonymous_variant	65121	exon4			TCTGCTGGAGAAA	AL049686	CCDS148.1	1p36.21	2013-01-17			ENSG00000116721	ENSG00000116721		"""-"""	28840	protein-coding gene	gene with protein product							Standard	NM_023013		Approved		uc001auj.2	O95521	OTTHUMG00000001928	ENST00000332296.7:c.1032G>A	1.37:g.12855752G>A		Somatic	533	5	0.00938086		WXS	Illumina HiSeq	Phase_I	581	13	0.0223752	NM_023013	Q9UQP2	Silent	SNP	ENST00000332296.7	37	CCDS148.1																																																																																			G|0.997;A|0.003	0.003	strong		0.557	PRAMEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005458.1	NM_023013	
MTNR1A	4543	hgsc.bcm.edu	37	4	187455075	187455075	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:187455075T>C	ENST00000307161.5	-	2	1022	c.821A>G	c.(820-822)gAg>gGg	p.E274G	RP11-215A19.2_ENST00000509111.1_Intron	NM_005958.3	NP_005949.1	P48039	MTR1A_HUMAN	melatonin receptor 1A	274					circadian rhythm (GO:0007623)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|mating behavior (GO:0007617)|positive regulation of cGMP biosynthetic process (GO:0030828)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	hormone binding (GO:0042562)|melatonin receptor activity (GO:0008502)|organic cyclic compound binding (GO:0097159)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	14		all_cancers(14;6.39e-56)|all_epithelial(14;1.48e-41)|all_lung(41;2.45e-15)|Lung NSC(41;7.26e-15)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00335)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|Renal(120;0.0183)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;7.63e-12)|BRCA - Breast invasive adenocarcinoma(30;6.68e-07)|GBM - Glioblastoma multiforme(59;3.44e-05)|LUSC - Lung squamous cell carcinoma(40;0.000106)|STAD - Stomach adenocarcinoma(60;0.000279)|READ - Rectum adenocarcinoma(43;0.159)	Agomelatine(DB06594)|Melatonin(DB01065)|Ramelteon(DB00980)	AAACAGCCACTCTGGGATCCT	0.502																																					p.E274G		Atlas-SNP	.											.	MTNR1A	46	.	0			c.A821G						PASS	.						73.0	79.0	77.0					4																	187455075		2203	4300	6503	SO:0001583	missense	4543	exon2			AGCCACTCTGGGA		CCDS3848.1	4q35	2012-08-08				ENSG00000168412		"""GPCR / Class A : Melatonin receptors"""	7463	protein-coding gene	gene with protein product		600665				7558006	Standard	NM_005958		Approved	MEL-1A-R	uc003izd.1	P48039		ENST00000307161.5:c.821A>G	4.37:g.187455075T>C	ENSP00000302811:p.Glu274Gly	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	137	14	0.10219	NM_005958	A0AVC5|B0M0L2	Missense_Mutation	SNP	ENST00000307161.5	37	CCDS3848.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.224502	0.79576	.	.	ENSG00000168412	ENST00000307161	T	0.73047	-0.71	4.96	4.96	0.65561	GPCR, rhodopsin-like superfamily (1);	0.049677	0.85682	D	0.000000	T	0.77398	0.4124	M	0.89353	3.025	0.80722	D	1	B	0.29909	0.261	B	0.36378	0.223	T	0.76963	-0.2764	10	0.33940	T	0.23	-23.224	14.6218	0.68592	0.0:0.0:0.0:1.0	.	274	P48039	MTR1A_HUMAN	G	274	ENSP00000302811:E274G	ENSP00000302811:E274G	E	-	2	0	MTNR1A	187692069	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	6.145000	0.71769	1.860000	0.53959	0.533000	0.62120	GAG	.	.	none		0.502	MTNR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360189.1		
MANSC1	54682	hgsc.bcm.edu	37	12	12483713	12483713	+	Silent	SNP	A	A	G	rs4763282	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:12483713A>G	ENST00000535902.1	-	4	1107	c.544T>C	c.(544-546)Ttg>Ctg	p.L182L	MANSC1_ENST00000396349.3_Silent_p.L148L|MANSC1_ENST00000545735.1_Silent_p.L101L			Q9H8J5	MANS1_HUMAN	MANSC domain containing 1	182						integral component of membrane (GO:0016021)		p.L182L(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(4)|lung(9)|skin(1)|stomach(4)	23		Prostate(47;0.0865)		BRCA - Breast invasive adenocarcinoma(232;0.185)		AGTTTCTCCAAGTGATCTGAG	0.428													A|||	2914	0.581869	0.4894	0.6614	5008	,	,		21284	0.375		0.7306	False		,,,				2504	0.7106				p.L182L		Atlas-SNP	.											MANSC1,NS,carcinoma,0,1	MANSC1	38	1	1	Substitution - coding silent(1)	stomach(1)	c.T544C						scavenged	.	A		2313,2093	603.1+/-390.1	595,1123,485	74.0	75.0	75.0		544	2.4	0.6	12	dbSNP_111	75	6493,2107	716.5+/-406.1	2467,1559,274	no	coding-synonymous	MANSC1	NM_018050.2		3062,2682,759	GG,GA,AA		24.5,47.5034,32.2928		182/432	12483713	8806,4200	2203	4300	6503	SO:0001819	synonymous_variant	54682	exon4			TCTCCAAGTGATC	AK001160	CCDS8648.1	12p13.2	2006-04-12				ENSG00000111261			25505	protein-coding gene	gene with protein product						12975309	Standard	NM_018050		Approved	FLJ10298, LOH12CR3	uc001rai.1	Q9H8J5		ENST00000535902.1:c.544T>C	12.37:g.12483713A>G		Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	165	3	0.0181818	NM_018050	Q8NEC1|Q9NW60	Silent	SNP	ENST00000535902.1	37	CCDS8648.1																																																																																			A|0.380;G|0.620	0.620	strong		0.428	MANSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400144.1	NM_018050	
C1orf87	127795	hgsc.bcm.edu	37	1	60491072	60491072	+	Splice_Site	SNP	C	C	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:60491072C>G	ENST00000371201.3	-	8	1235		c.e8+1		C1orf87_ENST00000450089.2_Splice_Site	NM_152377.2	NP_689590.1	Q8N0U7	CA087_HUMAN	chromosome 1 open reading frame 87								calcium ion binding (GO:0005509)			breast(2)|endometrium(2)|large_intestine(6)|lung(19)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	33						AGTTGACTTACTTTATTTCAT	0.388																																					.	NSCLC(75;811 1386 4923 13371 51772)	Atlas-SNP	.											.	C1orf87	55	.	0			c.1127+1G>C						PASS	.						120.0	121.0	121.0					1																	60491072		2203	4300	6503	SO:0001630	splice_region_variant	127795	exon9			GACTTACTTTATT	AK124828	CCDS614.1	1p32.1	2014-04-03			ENSG00000162598	ENSG00000162598			28547	protein-coding gene	gene with protein product	"""carcinoma-related EF-hand protein"""					12477932	Standard	NM_152377		Approved	MGC34837, CREF	uc001czs.2	Q8N0U7	OTTHUMG00000008992	ENST00000371201.3:c.1127+1G>C	1.37:g.60491072C>G		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	79	20	0.253165	NM_152377	Q6ZU07|Q8IVS0	Splice_Site	SNP	ENST00000371201.3	37	CCDS614.1	.	.	.	.	.	.	.	.	.	.	C	16.22	3.060848	0.55432	.	.	ENSG00000162598	ENST00000371201;ENST00000450089	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.851	0.63496	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	C1orf87	60263660	1.000000	0.71417	1.000000	0.80357	0.715000	0.41141	3.775000	0.55349	2.648000	0.89879	0.555000	0.69702	.	.	.	none		0.388	C1orf87-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024943.1	NM_152377	Intron
SPRR3	6707	hgsc.bcm.edu	37	1	152975715	152975715	+	Silent	SNP	C	C	T	rs28989168	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:152975715C>T	ENST00000295367.4	+	2	261	c.219C>T	c.(217-219)ggC>ggT	p.G73G	SPRR3_ENST00000331860.3_Silent_p.G73G|SPRR3_ENST00000542696.1_Silent_p.G73G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	73	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)			endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGCTGTACCAAGG	0.577													T|||	2	0.000399361	0.0015	0.0	5008	,	,		14904	0.0		0.0	False		,,,				2504	0.0				p.G73G		Atlas-SNP	.											SPRR3,colon,carcinoma,0,3	SPRR3	45	3	0			c.C219T						PASS	.						42.0	39.0	40.0					1																	152975715		2182	4268	6450	SO:0001819	synonymous_variant	6707	exon2			GCCAGGCTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.219C>T	1.37:g.152975715C>T		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	101	26	0.257426	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			.	.	none		0.577	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
POTEG	404785	hgsc.bcm.edu	37	14	19553680	19553680	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:19553680C>T	ENST00000409832.3	+	1	316	c.264C>T	c.(262-264)gaC>gaT	p.D88D		NM_001005356.2	NP_001005356.1	Q6S5H5	POTEG_HUMAN	POTE ankyrin domain family, member G	88										cervix(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(31)|ovary(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	47						ACCACGACGACTCTGCTATGA	0.617																																					p.D88D		Atlas-SNP	.											POTEG,bladder,carcinoma,0,1	POTEG	118	1	0			c.C264T						scavenged	.						67.0	87.0	80.0					14																	19553680		1966	4009	5975	SO:0001819	synonymous_variant	404785	exon1			CGACGACTCTGCT		CCDS73610.1	14q11.2	2013-01-10	2008-11-26	2008-11-26	ENSG00000222036	ENSG00000222036		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33896	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 4"""	608916	"""ANKRD26-like family C, member 2"""	A26C2			Standard	NR_027480		Approved	POTE14, POTE-14, POTE14alpha, CT104.4	uc001vuz.1	Q6S5H5	OTTHUMG00000170340	ENST00000409832.3:c.264C>T	14.37:g.19553680C>T		Somatic	777	15	0.019305		WXS	Illumina HiSeq	Phase_I	754	16	0.0212202	NM_001005356	A1L153|A6NMI9|Q6S5H6|Q6S8J2	Silent	SNP	ENST00000409832.3	37	CCDS32018.1																																																																																			.	.	weak		0.617	POTEG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408579.1	NM_001005356	
HIST1H2BL	8340	hgsc.bcm.edu	37	6	27775641	27775641	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:27775641G>A	ENST00000377401.2	-	1	68	c.44C>T	c.(43-45)tCc>tTc	p.S15F	HIST1H2AI_ENST00000358739.3_5'Flank|HIST1H3H_ENST00000369163.2_5'Flank	NM_003519.3	NP_003510.1	Q99880	H2B1L_HUMAN	histone cluster 1, H2bl	15					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)			cervix(1)|endometrium(1)|large_intestine(2)|lung(7)|urinary_tract(1)	12						CGCCTTCTTGGAGCCCTTCTT	0.527																																					p.S15F		Atlas-SNP	.											.	HIST1H2BL	48	.	0			c.C44T						PASS	.						98.0	99.0	99.0					6																	27775641		2203	4300	6503	SO:0001583	missense	8340	exon1			TTCTTGGAGCCCT	Z83740	CCDS4625.1	6p22.1	2011-01-27	2006-10-11	2003-02-28	ENSG00000185130	ENSG00000185130		"""Histones / Replication-dependent"""	4748	protein-coding gene	gene with protein product		602800	"""H2B histone family, member C"", ""histone 1, H2bl"""	H2BFC		9439656, 12408966	Standard	NM_003519		Approved	H2B/c, dJ97D16.4	uc003njl.3	Q99880	OTTHUMG00000014485	ENST00000377401.2:c.44C>T	6.37:g.27775641G>A	ENSP00000366618:p.Ser15Phe	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	286	71	0.248252	NM_003519	B2R5A3|Q52LW9	Missense_Mutation	SNP	ENST00000377401.2	37	CCDS4625.1	.	.	.	.	.	.	.	.	.	.	.	24.0	4.484608	0.84854	.	.	ENSG00000185130	ENST00000377401	T	0.22945	1.93	4.35	4.35	0.52113	Histone-fold (2);	.	.	.	.	T	0.33177	0.0854	L	0.45228	1.405	0.58432	D	0.999991	D	0.69078	0.997	D	0.71656	0.974	T	0.05022	-1.0911	9	0.46703	T	0.11	.	16.7381	0.85452	0.0:0.0:1.0:0.0	.	15	Q99880	H2B1L_HUMAN	F	15	ENSP00000366618:S15F	ENSP00000366618:S15F	S	-	2	0	HIST1H2BL	27883620	1.000000	0.71417	0.997000	0.53966	0.633000	0.38033	4.668000	0.61568	2.331000	0.79229	0.650000	0.86243	TCC	.	.	none		0.527	HIST1H2BL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040153.1	NM_003519	
EPPK1	83481	hgsc.bcm.edu	37	8	144941419	144941419	+	Silent	SNP	C	C	T	rs12681478	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:144941419C>T	ENST00000525985.1	-	2	6074	c.6003G>A	c.(6001-6003)gcG>gcA	p.A2001A				P58107	EPIPL_HUMAN	epiplakin 1	2001						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TCAGTGCCTCCGCCTTCTCGA	0.642													C|||	1066	0.212859	0.0113	0.33	5008	,	,		18060	0.1399		0.3708	False		,,,				2504	0.3149				p.A2001A		Atlas-SNP	.											EPPK1,NS,carcinoma,0,1	EPPK1	199	1	0			c.G6003A						scavenged	.	C		369,3945		22,325,1810	35.0	39.0	37.0		6003	-3.7	0.0	8	dbSNP_120	37	3411,5111		676,2059,1526	no	coding-synonymous	EPPK1	NM_031308.1		698,2384,3336	TT,TC,CC		40.0258,8.5535,29.4484		2001/2420	144941419	3780,9056	2157	4261	6418	SO:0001819	synonymous_variant	83481	exon1			TGCCTCCGCCTTC	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.6003G>A	8.37:g.144941419C>T		Somatic	103	1	0.00970874		WXS	Illumina HiSeq	Phase_I	108	4	0.037037	NM_031308	Q76E58|Q9NSU9	Silent	SNP	ENST00000525985.1	37																																																																																				C|0.740;T|0.260	0.260	strong		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
ABR	29	hgsc.bcm.edu	37	17	970326	970326	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:970326G>A	ENST00000302538.5	-	10	1319	c.1173C>T	c.(1171-1173)atC>atT	p.I391I	ABR_ENST00000291107.2_Silent_p.I354I|ABR_ENST00000544583.2_Silent_p.I345I|ABR_ENST00000574437.1_Silent_p.I345I|ABR_ENST00000536794.2_Silent_p.I173I	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	391	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CCTCCTTCTGGATTTCACTCT	0.572																																					p.I391I	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.C1173T						PASS	.						55.0	43.0	47.0					17																	970326		2203	4300	6503	SO:0001819	synonymous_variant	29	exon10			CTTCTGGATTTCA	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	81	protein-coding gene	gene with protein product		600365	"""active BCR-related gene"""			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.1173C>T	17.37:g.970326G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	76	21	0.276316	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Silent	SNP	ENST00000302538.5	37	CCDS10999.1																																																																																			.	.	none		0.572	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		
MYO9B	4650	hgsc.bcm.edu	37	19	17316782	17316782	+	Missense_Mutation	SNP	T	T	C	rs7248508	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:17316782T>C	ENST00000594824.1	+	32	5225	c.5078T>C	c.(5077-5079)gTt>gCt	p.V1693A	MYO9B_ENST00000595618.1_Missense_Mutation_p.V1693A|MYO9B_ENST00000397274.2_Missense_Mutation_p.V1693A|CTD-3032J10.3_ENST00000601929.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	1693	Tail.			V -> A (in Ref. 1; AAC50402). {ECO:0000305}.	actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						GAGCCAGGCGTTGAGCCTGGC	0.667													C|||	3163	0.631589	0.708	0.6772	5008	,	,		12871	0.746		0.3917	False		,,,				2504	0.6247				p.V1693A		Atlas-SNP	.											MYO9B_ENST00000319396,NS,carcinoma,0,2	MYO9B	264	2	0			c.T5078C						scavenged	.	C	ALA/VAL,ALA/VAL	2660,1460		885,890,285	21.0	27.0	25.0		5078,5078	4.7	0.0	19	dbSNP_116	25	3346,5022		710,1926,1548	yes	missense,missense	MYO9B	NM_001130065.1,NM_004145.3	64,64	1595,2816,1833	CC,CT,TT		39.9857,35.4369,48.0942	benign,benign	1693/2023,1693/2158	17316782	6006,6482	2060	4184	6244	SO:0001583	missense	4650	exon32			CAGGCGTTGAGCC		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.5078T>C	19.37:g.17316782T>C	ENSP00000471367:p.Val1693Ala	Somatic	6	1	0.166667		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		1311	0.6002747252747253	331	0.6727642276422764	232	0.6408839779005525	445	0.777972027972028	303	0.3997361477572559	C	2.673	-0.277158	0.05679	0.645631	0.399857	ENSG00000099331	ENST00000397274;ENST00000319396	D	0.84442	-1.85	4.74	4.74	0.60224	.	0.234317	0.29676	N	0.011484	T	0.00012	0.0000	N	0.00436	-1.5	0.80722	P	0.0	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.41142	-0.9525	9	0.05959	T	0.93	.	10.8777	0.46921	0.0:0.9112:0.0:0.0888	rs7248508;rs11545735;rs7248508	1693;1693;1699	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	A	1693;38	ENSP00000380444:V1693A	ENSP00000314032:V38A	V	+	2	0	MYO9B	17177782	0.001000	0.12720	0.039000	0.18376	0.005000	0.04900	1.204000	0.32296	1.136000	0.42199	-0.215000	0.12644	GTT	T|0.406;C|0.594	0.594	strong		0.667	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
MUC4	4585	hgsc.bcm.edu	37	3	195512262	195512262	+	Silent	SNP	C	C	G	rs199610666	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195512262C>G	ENST00000463781.3	-	2	6648	c.6189G>C	c.(6187-6189)acG>acC	p.T2063T	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2063T|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)		CAGGAAGAGGCGTGGTGTCAC	0.577																																					p.T2063T		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,0,1	MUC4	1505	1	0			c.G6189C						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			AAGAGGCGTGGTG	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.6189G>C	3.37:g.195512262C>G		Somatic	471	56	0.118896		WXS	Illumina HiSeq	Phase_I	554	64	0.115523	NM_018406	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																																																																																			C|0.500;G|0.500	0.500	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CTTNBP2	83992	hgsc.bcm.edu	37	7	117368154	117368154	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:117368154T>C	ENST00000160373.3	-	17	4135	c.4044A>G	c.(4042-4044)caA>caG	p.Q1348Q		NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	1348					brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		TCACTGTCACTTGGGCATGCC	0.498																																					p.Q1348Q		Atlas-SNP	.											.	CTTNBP2	200	.	0			c.A4044G						PASS	.						78.0	83.0	82.0					7																	117368154		2203	4300	6503	SO:0001819	synonymous_variant	83992	exon17			TGTCACTTGGGCA		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.4044A>G	7.37:g.117368154T>C		Somatic	182	0	0		WXS	Illumina HiSeq	Phase_I	177	33	0.186441	NM_033427	O43389|Q7LG11|Q9C0A5	Silent	SNP	ENST00000160373.3	37	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	T	8.983	0.975850	0.18736	.	.	ENSG00000077063	ENST00000446636	.	.	.	5.43	0.0764	0.14403	.	.	.	.	.	T	0.44623	0.1302	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.28554	-1.0040	4	.	.	.	3.8122	4.251	0.10695	0.2507:0.22:0.0:0.5293	.	.	.	.	G	836	.	.	S	-	1	0	CTTNBP2	117155390	0.004000	0.15560	0.997000	0.53966	0.975000	0.68041	-0.307000	0.08167	0.414000	0.25790	0.528000	0.53228	AGT	.	.	none		0.498	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
SEC62	7095	hgsc.bcm.edu	37	3	169684611	169684611	+	Start_Codon_SNP	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:169684611A>G	ENST00000337002.4	+	1	59	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	RP11-379K17.4_ENST00000600502.1_RNA|RP11-379K17.4_ENST00000483289.2_RNA|RP11-379K17.4_ENST00000487580.1_RNA|RP11-379K17.4_ENST00000469301.1_RNA|SEC62_ENST00000480708.1_Start_Codon_SNP_p.M1V	NM_003262.3	NP_003253.1	Q99442	SEC62_HUMAN	SEC62 homolog (S. cerevisiae)	1					cotranslational protein targeting to membrane (GO:0006613)|posttranslational protein targeting to membrane (GO:0006620)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|rough endoplasmic reticulum (GO:0005791)	protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)	9						AGCGGCCAACATGGCGGAACG	0.672																																					p.M1V		Atlas-SNP	.											.	SEC62	27	.	0			c.A1G						PASS	.						26.0	23.0	24.0					3																	169684611		2137	4176	6313	SO:0001582	initiator_codon_variant	7095	exon1			GCCAACATGGCGG	D87127	CCDS3210.1	3q26.2	2008-04-22	2008-04-22	2008-04-22	ENSG00000008952	ENSG00000008952			11846	protein-coding gene	gene with protein product		602173	"""translocation protein 1"""	TLOC1		9020021, 10799540	Standard	NM_003262		Approved	Dtrp1, HTP1	uc003fgh.3	Q99442	OTTHUMG00000158753	ENST00000337002.4:c.1A>G	3.37:g.169684611A>G	ENSP00000337688:p.Met1Val	Somatic	214	0	0		WXS	Illumina HiSeq	Phase_I	173	33	0.190751	NM_003262	D3DNQ0|O00682|O00729	Missense_Mutation	SNP	ENST00000337002.4	37	CCDS3210.1	.	.	.	.	.	.	.	.	.	.	A	17.41	3.382105	0.61845	.	.	ENSG00000008952	ENST00000337002;ENST00000537426;ENST00000544081;ENST00000480708	.	.	.	4.92	4.92	0.64577	.	0.095017	0.64402	D	0.000001	T	0.60996	0.2312	.	.	.	0.80722	D	1	B	0.31435	0.323	B	0.38194	0.267	T	0.65294	-0.6203	8	0.87932	D	0	-9.7133	12.5634	0.56295	1.0:0.0:0.0:0.0	.	1	Q99442	SEC62_HUMAN	V	1	.	ENSP00000337688:M1V	M	+	1	0	SEC62	171167305	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	6.666000	0.74446	2.052000	0.61016	0.460000	0.39030	ATG	.	.	none		0.672	SEC62-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352043.1		Missense_Mutation
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907275	12907275	+	Missense_Mutation	SNP	G	G	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:12907275G>C	ENST00000317869.6	-	2	1093	c.868C>G	c.(868-870)Cag>Gag	p.Q290E		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	290						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						GAGTCATCCTGGCCATTGGTG	0.443																																					p.Q290E		Atlas-SNP	.											HNRNPCL1,NS,neuroblastoma,0,1	HNRNPCL1	68	1	0			c.C868G						scavenged	.						125.0	135.0	132.0					1																	12907275		2203	4299	6502	SO:0001583	missense	343069	exon2			CATCCTGGCCATT	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.868C>G	1.37:g.12907275G>C	ENSP00000365370:p.Gln290Glu	Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	313	4	0.0127796	NM_001013631	B2RP44	Missense_Mutation	SNP	ENST00000317869.6	37	CCDS30591.1	.	.	.	.	.	.	.	.	.	.	.	0.001	-4.135616	0.00001	.	.	ENSG00000179172	ENST00000317869	T	0.07216	3.21	1.09	-2.18	0.07037	.	0.420350	0.20880	N	0.084017	T	0.01353	0.0044	N	0.00583	-1.355	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.31971	-0.9924	10	0.02654	T	1	.	2.6632	0.05032	0.0:0.3331:0.2756:0.3913	.	290	O60812	HNRCL_HUMAN	E	290	ENSP00000365370:Q290E	ENSP00000365370:Q290E	Q	-	1	0	HNRNPCL1	12829862	0.994000	0.37717	0.016000	0.15963	0.063000	0.16089	-0.019000	0.12546	-1.068000	0.03156	-0.786000	0.03341	CAG	.	.	none		0.443	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
ZNF471	57573	hgsc.bcm.edu	37	19	57036891	57036891	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:57036891A>C	ENST00000308031.5	+	5	1588	c.1455A>C	c.(1453-1455)aaA>aaC	p.K485N	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_3'UTR	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	485					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		CTGGTGAAAAACCCTATGAAT	0.383																																					p.K485N	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A1455C						PASS	.						55.0	56.0	55.0					19																	57036891		2203	4300	6503	SO:0001583	missense	57573	exon5			TGAAAAACCCTAT	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.1455A>C	19.37:g.57036891A>C	ENSP00000309161:p.Lys485Asn	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	61	7	0.114754	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	37	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	A	15.71	2.913227	0.52439	.	.	ENSG00000196263	ENST00000308031	T	0.26067	1.76	3.66	2.59	0.31030	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.43166	0.1235	M	0.76727	2.345	0.80722	D	1	D	0.76494	0.999	D	0.65684	0.937	T	0.27434	-1.0074	9	0.72032	D	0.01	.	5.8421	0.18639	0.8355:0.0:0.1645:0.0	.	485	Q9BX82	ZN471_HUMAN	N	485	ENSP00000309161:K485N	ENSP00000309161:K485N	K	+	3	2	ZNF471	61728703	0.004000	0.15560	0.997000	0.53966	0.985000	0.73830	-0.726000	0.04936	0.497000	0.27926	0.379000	0.24179	AAA	.	.	none		0.383	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
COL4A3	1285	hgsc.bcm.edu	37	2	228173618	228173618	+	Missense_Mutation	SNP	C	C	A	rs200818438		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:228173618C>A	ENST00000396578.3	+	49	4628	c.4466C>A	c.(4465-4467)aCt>aAt	p.T1489N	AC097662.2_ENST00000433324.1_RNA|AC097662.2_ENST00000439598.2_RNA|AC097662.2_ENST00000396588.2_RNA	NM_000091.4	NP_000082.2	Q01955	CO4A3_HUMAN	collagen, type IV, alpha 3 (Goodpasture antigen)	1489	Collagen IV NC1. {ECO:0000255|PROSITE- ProRule:PRU00736}.|Required for the anti-angiogenic activity of tumstatin.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|axon guidance (GO:0007411)|blood circulation (GO:0008015)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|collagen catabolic process (GO:0030574)|endothelial cell apoptotic process (GO:0072577)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|sensory perception of sound (GO:0007605)	basement membrane (GO:0005604)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metalloendopeptidase inhibitor activity (GO:0008191)|structural molecule activity (GO:0005198)			NS(4)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	55		all_lung(227;0.00101)|Lung NSC(271;0.00278)|Renal(207;0.0112)|Ovarian(221;0.0129)|all_hematologic(139;0.211)|Esophageal squamous(248;0.247)		Epithelial(121;1.17e-46)|all cancers(144;6.87e-42)|Lung(261;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0187)		TCATTAGGAACTCTTGGCAGC	0.363																																					p.T1489N		Atlas-SNP	.											.	COL4A3	293	.	0			c.C4466A						PASS	.						104.0	93.0	97.0					2																	228173618		1903	4123	6026	SO:0001583	missense	1285	exon49			TAGGAACTCTTGG		CCDS42829.1	2q36-q37	2014-09-17			ENSG00000169031	ENSG00000169031		"""Collagens"""	2204	protein-coding gene	gene with protein product	"""tumstatin"""	120070				1737849	Standard	NM_000091		Approved		uc002vom.2	Q01955	OTTHUMG00000149891	ENST00000396578.3:c.4466C>A	2.37:g.228173618C>A	ENSP00000379823:p.Thr1489Asn	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	105	33	0.314286	NM_000091	Q53QQ1|Q53R14|Q53RW8|Q9BQT2|Q9NYC4|Q9UDJ9|Q9UDK9|Q9UDL0|Q9UDL1	Missense_Mutation	SNP	ENST00000396578.3	37	CCDS42829.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.948596	0.73787	.	.	ENSG00000169031	ENST00000396578;ENST00000328380	D	0.94280	-3.39	5.97	5.97	0.96955	C-type lectin fold (1);	0.102311	0.43260	D	0.000584	D	0.96756	0.8941	M	0.86178	2.8	0.80722	D	1	D;D	0.63046	0.992;0.979	P;P	0.62740	0.906;0.884	D	0.95139	0.8262	10	0.31617	T	0.26	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	1489;1489	Q01955-2;Q01955	.;CO4A3_HUMAN	N	1489	ENSP00000379823:T1489N	ENSP00000327594:T1489N	T	+	2	0	COL4A3	227881862	1.000000	0.71417	0.998000	0.56505	0.927000	0.56198	7.487000	0.81328	2.836000	0.97738	0.655000	0.94253	ACT	.	.	alt		0.363	COL4A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331409.2	NM_000091	
SPATA31E1	286234	hgsc.bcm.edu	37	9	90499849	90499849	+	Silent	SNP	C	C	T	rs148586576		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:90499849C>T	ENST00000325643.5	+	4	513	c.447C>T	c.(445-447)ggC>ggT	p.G149G		NM_178828.4	NP_849150.3	Q6ZUB1	S31E1_HUMAN	SPATA31 subfamily E, member 1	149					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.G149G(1)									AGCTCGCTGGCGAAGGCAGCT	0.657																																					p.G149G		Atlas-SNP	.											C9orf79,colon,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C447T						PASS	.	C		7,4399		0,7,2196	28.0	29.0	29.0		447	-1.0	0.0	9	dbSNP_134	29	1,8597		0,1,4298	no	coding-synonymous	C9orf79	NM_178828.4		0,8,6494	TT,TC,CC		0.0116,0.1589,0.0615		149/1446	90499849	8,12996	2203	4299	6502	SO:0001819	synonymous_variant	286234	exon4			CGCTGGCGAAGGC	AK093185	CCDS6676.1	9q22.1-q22.2	2012-10-12	2012-10-12	2012-10-12	ENSG00000177992	ENSG00000177992			26672	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 79"", ""family with sequence similarity 75, member E1"""	C9orf79, FAM75E1			Standard	NM_178828		Approved	FLJ35866	uc004app.4	Q6ZUB1	OTTHUMG00000020157	ENST00000325643.5:c.447C>T	9.37:g.90499849C>T		Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	71	8	0.112676	NM_178828	B2RPB1|Q5SQC9|Q8NA41|Q8ND27	Silent	SNP	ENST00000325643.5	37	CCDS6676.1																																																																																			C|1.000;T|0.000	0.000	weak		0.657	SPATA31E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052954.2	NM_178828	
PDCL3	79031	hgsc.bcm.edu	37	2	101188050	101188050	+	Splice_Site	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:101188050A>G	ENST00000264254.6	+	5	746		c.e5-1			NM_024065.4	NP_076970.1	Q9H2J4	PDCL3_HUMAN	phosducin-like 3						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell proliferation (GO:0001938)|protein folding (GO:0006457)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|viral process (GO:0016032)	cytoplasm (GO:0005737)	protein binding involved in protein folding (GO:0044183)	p.?(1)		endometrium(3)|large_intestine(2)|liver(1)|lung(6)	12						TGTGTTTTATAGAATTCCCCT	0.388																																					.		Atlas-SNP	.											PDCL3,NS,carcinoma,0,1	PDCL3	27	1	1	Unknown(1)	lung(1)	c.369-2A>G						PASS	.						129.0	129.0	129.0					2																	101188050		2203	4300	6503	SO:0001630	splice_region_variant	79031	exon5			TTTTATAGAATTC	AF267853	CCDS33261.1	2q12	2008-02-05			ENSG00000115539	ENSG00000115539			28860	protein-coding gene	gene with protein product		611678					Standard	NM_024065		Approved	VIAF1	uc002tao.2	Q9H2J4	OTTHUMG00000153141	ENST00000264254.6:c.369-1A>G	2.37:g.101188050A>G		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	29	7	0.241379	NM_024065	B2RA00|Q53S68	Splice_Site	SNP	ENST00000264254.6	37	CCDS33261.1	.	.	.	.	.	.	.	.	.	.	a	17.13	3.311619	0.60414	.	.	ENSG00000115539	ENST00000264254;ENST00000416255;ENST00000450127	.	.	.	5.59	5.59	0.84812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8181	0.78621	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PDCL3	100554482	1.000000	0.71417	0.985000	0.45067	0.633000	0.38033	8.950000	0.93019	2.150000	0.67090	0.514000	0.50259	.	.	.	none		0.388	PDCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329734.1	NM_024065	Intron
GABRG3	2567	hgsc.bcm.edu	37	15	27765242	27765242	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:27765242A>C	ENST00000333743.6	+	7	1091	c.837A>C	c.(835-837)aaA>aaC	p.K279N	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	279					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGATCAAAAAAGATGCTACGC	0.348																																					p.K279N	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											.	GABRG3	115	.	0			c.A837C						PASS	.						65.0	61.0	62.0					15																	27765242		1844	4105	5949	SO:0001583	missense	2567	exon7			CAAAAAAGATGCT		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.837A>C	15.37:g.27765242A>C	ENSP00000331912:p.Lys279Asn	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	26	0.209677	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.47|18.47	3.630222|3.630222	0.67015|0.67015	.|.	.|.	ENSG00000182256|ENSG00000182256	ENST00000333743;ENST00000554696|ENST00000451330	D;D|D	0.86097|0.86030	-2.07;-2.07|-2.06	5.3|5.3	1.55|1.55	0.23275|0.23275	Neurotransmitter-gated ion-channel transmembrane domain (2);|.	0.208504|0.208504	0.49916|0.49916	D|D	0.000133|0.000133	D|D	0.83982|0.83982	0.5372|0.5372	L|L	0.49350|0.49350	1.555|1.555	0.80722|0.80722	D|D	1|1	D|.	0.56521|.	0.976|.	P|.	0.62560|.	0.904|.	T|T	0.80908|0.80908	-0.1172|-0.1172	10|8	0.66056|0.54805	D|T	0.02|0.06	.|.	8.4792|8.4792	0.33032|0.33032	0.6971:0.0:0.3029:0.0|0.6971:0.0:0.3029:0.0	.|.	279|.	Q99928|.	GBRG3_HUMAN|.	N|T	279;221|42	ENSP00000331912:K279N;ENSP00000451862:K221N|ENSP00000390708:K42T	ENSP00000331912:K279N|ENSP00000390708:K88T	K|K	+|+	3|2	2|0	GABRG3|GABRG3	25438837|25438837	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	1.094000|1.094000	0.30951|0.30951	0.430000|0.430000	0.26230|0.26230	0.528000|0.528000	0.53228|0.53228	AAA|AAG	.	.	none		0.348	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
ZNF729	100287226	hgsc.bcm.edu	37	19	22496574	22496574	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:22496574A>G	ENST00000601693.1	+	4	473	c.355A>G	c.(355-357)Aat>Gat	p.N119D	ZNF729_ENST00000357491.6_Missense_Mutation_p.N119D			A6NN14	ZN729_HUMAN	zinc finger protein 729	119					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(1)|lung(32)|ovary(3)	41						TGGACATAAGAATTTACGATT	0.363																																					p.N119D		Atlas-SNP	.											.	ZNF729	78	.	0			c.A355G						PASS	.																																			SO:0001583	missense	100287226	exon4			CATAAGAATTTAC		CCDS59368.1	19p12	2014-02-14			ENSG00000196350	ENSG00000196350		"""Zinc fingers, C2H2-type"", ""-"""	32464	protein-coding gene	gene with protein product							Standard	NM_001242680		Approved		uc021urs.1	A6NN14	OTTHUMG00000182938	ENST00000601693.1:c.355A>G	19.37:g.22496574A>G	ENSP00000469582:p.Asn119Asp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	71	16	0.225352	NM_001242680	M0QY45	Missense_Mutation	SNP	ENST00000601693.1	37	CCDS59368.1	.	.	.	.	.	.	.	.	.	.	.	5.888	0.347981	0.11126	.	.	ENSG00000196350	ENST00000357491	T	0.06371	3.31	1.55	0.414	0.16406	.	.	.	.	.	T	0.04998	0.0134	L	0.38175	1.15	.	.	.	.	.	.	.	.	.	T	0.41662	-0.9496	6	0.10377	T	0.69	.	5.2286	0.15410	0.8235:0.0:0.1765:0.0	.	.	.	.	D	119	ENSP00000350085:N119D	ENSP00000350085:N119D	N	+	1	0	ZNF729	22288414	0.001000	0.12720	0.001000	0.08648	0.016000	0.09150	0.308000	0.19314	-0.099000	0.12263	0.397000	0.26171	AAT	.	.	none		0.363	ZNF729-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464396.1	XM_496301	
FRG1	2483	hgsc.bcm.edu	37	4	190876224	190876224	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:190876224T>G	ENST00000226798.4	+	5	572	c.350T>G	c.(349-351)cTt>cGt	p.L117R	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	117					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		GGAAAATATCTTGGTATAAAT	0.353																																					p.L117R		Atlas-SNP	.											FRG1,NS,carcinoma,0,1	FRG1	76	1	0			c.T350G						scavenged	.						62.0	61.0	61.0					4																	190876224		2203	4300	6503	SO:0001583	missense	2483	exon5			AATATCTTGGTAT	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.350T>G	4.37:g.190876224T>G	ENSP00000226798:p.Leu117Arg	Somatic	387	0	0		WXS	Illumina HiSeq	Phase_I	444	5	0.0112613	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	20.4	3.991897	0.74703	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.58210	0.91;0.35	4.04	4.04	0.47022	Actin cross-linking (1);	0.000000	0.85682	D	0.000000	T	0.74465	0.3720	M	0.88704	2.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79347	-0.1841	10	0.87932	D	0	-8.6377	11.3071	0.49342	0.0:0.0:0.0:1.0	.	117	Q14331	FRG1_HUMAN	R	117;54	ENSP00000226798:L117R;ENSP00000435943:L54R	ENSP00000226798:L117R	L	+	2	0	FRG1	191113218	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	7.497000	0.81536	1.599000	0.50093	0.462000	0.41574	CTT	.	.	none		0.353	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
SGK1	6446	hgsc.bcm.edu	37	6	134495169	134495169	+	Missense_Mutation	SNP	G	G	C	rs141028225		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134495169G>C	ENST00000237305.7	-	3	290	c.202C>G	c.(202-204)Ctt>Gtt	p.L68V	SGK1_ENST00000367858.5_Missense_Mutation_p.L163V|SGK1_ENST00000367857.5_Missense_Mutation_p.L58V|SGK1_ENST00000489458.2_5'UTR|SGK1_ENST00000475719.2_Missense_Mutation_p.L68V|SGK1_ENST00000413996.3_Missense_Mutation_p.L82V|SGK1_ENST00000528577.1_Missense_Mutation_p.L96V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	68					apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		GCATTCATAAGCTCAGGCTCC	0.478																																					p.L163V		Atlas-SNP	.											.	SGK1	387	.	0			c.C487G						PASS	.	G	VAL/LEU,VAL/LEU,VAL/LEU,VAL/LEU	0,4406		0,0,2203	151.0	144.0	146.0		487,286,244,202	5.0	1.0	6	dbSNP_134	146	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	SGK1	NM_001143676.1,NM_001143677.1,NM_001143678.1,NM_005627.3	32,32,32,32	0,1,6502	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	163/527,96/460,82/446,68/432	134495169	1,13005	2203	4300	6503	SO:0001583	missense	6446	exon5			TCATAAGCTCAGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.202C>G	6.37:g.134495169G>C	ENSP00000237305:p.Leu68Val	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	110	22	0.2	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	12.84	2.057170	0.36277	0.0	1.16E-4	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T	0.72282	-0.64;-0.63;-0.62;-0.62;-0.62;-0.63	5.99	5.04	0.67666	.	0.000000	0.85682	D	0.000000	T	0.51210	0.1661	L	0.54323	1.7	0.80722	D	1	B;B;B;B;B;B	0.28605	0.008;0.008;0.0;0.073;0.217;0.002	B;B;B;B;B;B	0.31946	0.012;0.002;0.001;0.088;0.138;0.004	T	0.53092	-0.8487	10	0.30854	T	0.27	.	11.0283	0.47757	0.1506:0.0:0.8494:0.0	.	96;82;68;58;163;68	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	163;82;68;58;96;68;132	ENSP00000356832:L163V;ENSP00000396242:L82V;ENSP00000237305:L68V;ENSP00000356831:L58V;ENSP00000434450:L96V;ENSP00000434302:L68V	ENSP00000237305:L68V	L	-	1	0	SGK1	134536862	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.307000	0.51888	1.377000	0.46286	0.655000	0.94253	CTT	G|1.000;C|0.000	0.000	weak		0.478	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
OR10G2	26534	hgsc.bcm.edu	37	14	22102293	22102293	+	Missense_Mutation	SNP	C	C	T	rs41307110	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:22102293C>T	ENST00000542433.1	-	1	803	c.706G>A	c.(706-708)Gct>Act	p.A236T		NM_001005466.1	NP_001005466.1	Q8NGC3	O10G2_HUMAN	olfactory receptor, family 10, subfamily G, member 2	236						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)|stomach(2)	22	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0142)		CTCCCATCAGCGGTGCGTATC	0.542																																					p.A236T		Atlas-SNP	.											OR10G2,NS,carcinoma,0,1	OR10G2	35	1	0			c.G706A						scavenged	.						39.0	41.0	40.0					14																	22102293		2179	4246	6425	SO:0001583	missense	26534	exon1			CATCAGCGGTGCG		CCDS32047.1	14q11.2	2013-09-24			ENSG00000255582	ENSG00000255582		"""GPCR / Class A : Olfactory receptors"""	8170	protein-coding gene	gene with protein product						8188290	Standard	NM_001005466		Approved		uc010tmc.2	Q8NGC3	OTTHUMG00000168890	ENST00000542433.1:c.706G>A	14.37:g.22102293C>T	ENSP00000445383:p.Ala236Thr	Somatic	223	8	0.0358744		WXS	Illumina HiSeq	Phase_I	290	8	0.0275862	NM_001005466	B2RPD0	Missense_Mutation	SNP	ENST00000542433.1	37	CCDS32047.1	347	0.15888278388278387	55	0.11178861788617886	40	0.11049723756906077	137	0.2395104895104895	115	0.1517150395778364	c	2.861	-0.236170	0.05944	.	.	ENSG00000255582	ENST00000542433	T	0.00174	8.62	3.92	2.07	0.26955	GPCR, rhodopsin-like superfamily (1);	0.146443	0.31134	N	0.008190	T	0.00012	0.0000	L	0.41236	1.265	0.80722	P	0.0	B	0.29378	0.243	B	0.25506	0.061	T	0.41305	-0.9516	9	0.41790	T	0.15	-5.7356	13.1106	0.59270	0.0:0.9007:0.0:0.0993	rs41307110;rs41428047;rs61753936;rs41307110	236	Q8NGC3	O10G2_HUMAN	T	236	ENSP00000445383:A236T	ENSP00000445383:A236T	A	-	1	0	OR10G2	21172133	0.000000	0.05858	0.819000	0.32651	0.005000	0.04900	-0.178000	0.09782	0.045000	0.15804	-2.571000	0.00171	GCT	C|0.750;T|0.250	0.250	weak		0.542	OR10G2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401525.1		
INSC	387755	hgsc.bcm.edu	37	11	15267551	15267551	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:15267551T>G	ENST00000379554.3	+	13	1751	c.1705T>G	c.(1705-1707)Tta>Gta	p.L569V	INSC_ENST00000379556.3_Missense_Mutation_p.L522V|INSC_ENST00000530161.1_Missense_Mutation_p.L522V|INSC_ENST00000447214.2_3'UTR|INSC_ENST00000528567.1_3'UTR|INSC_ENST00000525218.1_Missense_Mutation_p.L480V|INSC_ENST00000424273.1_Missense_Mutation_p.L480V	NM_001031853.3	NP_001027024.3	Q1MX18	INSC_HUMAN	inscuteable homolog (Drosophila)	569					establishment of mitotic spindle orientation (GO:0000132)|lung epithelial cell differentiation (GO:0060487)|nervous system development (GO:0007399)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)				NS(2)|breast(1)|central_nervous_system(2)|endometrium(6)|kidney(4)|large_intestine(3)|lung(24)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49						GGACTCCTTCTTACTCTGCAG	0.547																																					p.L569V		Atlas-SNP	.											.	INSC	104	.	0			c.T1705G						PASS	.						122.0	124.0	123.0					11																	15267551		1986	4160	6146	SO:0001583	missense	387755	exon13			TCCTTCTTACTCT	AB231744	CCDS41621.1, CCDS41622.1, CCDS60735.1, CCDS60736.1	11p15.2	2014-02-05			ENSG00000188487	ENSG00000188487			33116	protein-coding gene	gene with protein product	"""inscuteable spindle orientation adaptor protein"""	610668				16458856	Standard	NM_001031853		Approved		uc001mly.4	Q1MX18	OTTHUMG00000165838	ENST00000379554.3:c.1705T>G	11.37:g.15267551T>G	ENSP00000368872:p.Leu569Val	Somatic	199	0	0		WXS	Illumina HiSeq	Phase_I	214	40	0.186916	NM_001031853	A0PJX5|Q1MX19|Q3C1V6|Q4AC95|Q4AC96|Q4AC97|Q4AC98	Missense_Mutation	SNP	ENST00000379554.3	37	CCDS41621.1	.	.	.	.	.	.	.	.	.	.	T	22.7	4.320930	0.81580	.	.	ENSG00000188487	ENST00000379554;ENST00000379556;ENST00000424273;ENST00000530161;ENST00000525218	T;T;T;T;T	0.50277	0.75;0.79;0.94;0.79;0.94	6.17	3.57	0.40892	Armadillo-type fold (1);	0.000000	0.64402	D	0.000004	T	0.58566	0.2131	L	0.53249	1.67	0.38663	D	0.952138	D;D;D	0.89917	1.0;0.996;1.0	D;D;D	0.87578	0.998;0.986;0.996	T	0.61950	-0.6957	10	0.66056	D	0.02	-7.5535	6.8426	0.23971	0.0:0.2948:0.0:0.7052	.	557;480;569	Q1MX18-5;Q1MX18-4;Q1MX18	.;.;INSC_HUMAN	V	569;522;480;522;480	ENSP00000368872:L569V;ENSP00000368874:L522V;ENSP00000389161:L480V;ENSP00000436194:L522V;ENSP00000436113:L480V	ENSP00000368872:L569V	L	+	1	2	INSC	15224127	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.660000	0.37397	1.158000	0.42547	0.533000	0.62120	TTA	.	.	none		0.547	INSC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386590.1	NM_001031853	
RABGEF1	27342	hgsc.bcm.edu	37	7	66270294	66270294	+	Missense_Mutation	SNP	C	C	T	rs558434519		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:66270294C>T	ENST00000284957.5	+	8	1065	c.988C>T	c.(988-990)Cgc>Tgc	p.R330C	RABGEF1_ENST00000450873.2_Missense_Mutation_p.R330C|RABGEF1_ENST00000484547.2_3'UTR|KCTD7_ENST00000380828.2_Missense_Mutation_p.R370C|RABGEF1_ENST00000437078.2_Missense_Mutation_p.R344C|KCTD7_ENST00000510829.2_Missense_Mutation_p.R330C|KCTD7_ENST00000451741.2_Missense_Mutation_p.R330C|RABGEF1_ENST00000439720.2_Missense_Mutation_p.R343C			Q9UJ41	RABX5_HUMAN	RAB guanine nucleotide exchange factor (GEF) 1	547					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein targeting to membrane (GO:0006612)	early endosome (GO:0005769)	DNA binding (GO:0003677)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|lung(9)|ovary(1)|stomach(1)	27						CAACCCCCCACGCCTTCAGTC	0.502													c|||	1	0.000199681	0.0008	0.0	5008	,	,		20067	0.0		0.0	False		,,,				2504	0.0				p.R330C		Atlas-SNP	.											RABGEF1,NS,carcinoma,-1,1	RABGEF1	56	1	0			c.C988T						scavenged	.						119.0	100.0	106.0					7																	66270294		2203	4300	6503	SO:0001583	missense	27342	exon8			CCCCCACGCCTTC	AJ250042	CCDS5535.1, CCDS69308.1, CCDS75610.1	7q11.21	2010-07-09			ENSG00000154710	ENSG00000154710			17676	protein-coding gene	gene with protein product		609700				12505986, 11098082	Standard	NM_014504		Approved	rabex-5, RABEX5	uc003tvh.3	Q9UJ41	OTTHUMG00000129547	ENST00000284957.5:c.988C>T	7.37:g.66270294C>T	ENSP00000284957:p.Arg330Cys	Somatic	200	0	0		WXS	Illumina HiSeq	Phase_I	200	2	0.01	NM_014504	B4DZM7|Q3HKR2|Q3HKR3|Q53FG0	Missense_Mutation	SNP	ENST00000284957.5	37	CCDS5535.1	.	.	.	.	.	.	.	.	.	.	C	28.4	4.912936	0.92178	.	.	ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000243335;ENSG00000154710;ENSG00000154710;ENSG00000154710;ENSG00000154710	ENST00000380827;ENST00000380828;ENST00000510829;ENST00000451741;ENST00000539561;ENST00000284957;ENST00000450873;ENST00000439720;ENST00000437078	T;T;T;T;T;T;T	0.30981	1.51;1.51;1.51;1.51;1.51;1.51;1.51	5.6	5.6	0.85130	Vacuolar sorting protein 9, subgroup (1);Vacuolar sorting protein 9 (2);	0.047247	0.85682	D	0.000000	T	0.61198	0.2328	M	0.83118	2.625	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.81914	0.989;0.994;0.995	T	0.65492	-0.6155	10	0.72032	D	0.01	-5.7146	18.602	0.91250	0.0:1.0:0.0:0.0	.	344;164;547	B4DZM7;B3KMF1;Q9UJ41	.;.;RABX5_HUMAN	C	414;370;330;330;246;330;330;343;344	ENSP00000370208:R370C;ENSP00000421124:R330C;ENSP00000398177:R330C;ENSP00000284957:R330C;ENSP00000415815:R330C;ENSP00000403429:R343C;ENSP00000390480:R344C	ENSP00000370207:R414C	R	+	1	0	RABGEF1;KCTD7	65907729	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.411000	0.59781	2.643000	0.89663	0.655000	0.94253	CGC	.	.	none		0.502	RABGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251737.3	NM_014504	
SLIT2	9353	hgsc.bcm.edu	37	4	20619095	20619095	+	Silent	SNP	G	G	A	rs61746361	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:20619095G>A	ENST00000504154.1	+	36	4422	c.4170G>A	c.(4168-4170)gcG>gcA	p.A1390A	SLIT2_ENST00000503823.1_Silent_p.A1382A|SLIT2_ENST00000273739.5_Silent_p.A1403A|SLIT2_ENST00000503837.1_Silent_p.A1386A	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	1390					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						CCATCAATGCGTTCTCCTACA	0.522													G|||	22	0.00439297	0.0166	0.0	5008	,	,		16502	0.0		0.0	False		,,,				2504	0.0				p.A1390A		Atlas-SNP	.											.	SLIT2	290	.	0			c.G4170A						PASS	.	G		54,4352	54.9+/-90.9	0,54,2149	106.0	92.0	97.0		4170	-11.8	0.0	4	dbSNP_129	97	0,8600		0,0,4300	no	coding-synonymous	SLIT2	NM_004787.1		0,54,6449	AA,AG,GG		0.0,1.2256,0.4152		1390/1530	20619095	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	9353	exon36			CAATGCGTTCTCC	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.4170G>A	4.37:g.20619095G>A		Somatic	330	0	0		WXS	Illumina HiSeq	Phase_I	261	54	0.206897	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			G|0.996;A|0.004	0.004	strong		0.522	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
ZNF57	126295	hgsc.bcm.edu	37	19	2917857	2917857	+	Missense_Mutation	SNP	C	C	T	rs148390269		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:2917857C>T	ENST00000306908.5	+	4	1386	c.1238C>T	c.(1237-1239)aCg>aTg	p.T413M	AC006277.2_ENST00000520090.2_RNA|ZNF57_ENST00000523428.1_Missense_Mutation_p.T381M	NM_173480.2	NP_775751.1	Q68EA5	ZNF57_HUMAN	zinc finger protein 57	413					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				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)|GBM - Glioblastoma multiforme(1328;0.00161)|STAD - Stomach adenocarcinoma(1328;0.18)		CATTTGAGGACGCACACTGGA	0.438													C|||	1	0.000199681	0.0	0.0014	5008	,	,		22852	0.0		0.0	False		,,,				2504	0.0				p.T413M	NSCLC(150;910 1964 4303 10464 26498)	Atlas-SNP	.											ZNF57,NS,carcinoma,0,1	ZNF57	57	1	0			c.C1238T						scavenged	.						100.0	90.0	93.0					19																	2917857		2203	4300	6503	SO:0001583	missense	126295	exon4			TGAGGACGCACAC	M88368	CCDS12098.1	19p13.3	2013-01-08			ENSG00000171970	ENSG00000171970		"""Zinc fingers, C2H2-type"", ""-"""	13125	protein-coding gene	gene with protein product			"""zinc finger protein 424"""	ZNF424		1505991	Standard	NM_173480		Approved		uc002lwr.3	Q68EA5	OTTHUMG00000164485	ENST00000306908.5:c.1238C>T	19.37:g.2917857C>T	ENSP00000303696:p.Thr413Met	Somatic	243	3	0.0123457		WXS	Illumina HiSeq	Phase_I	221	5	0.0226244	NM_173480	Q8N6R9	Missense_Mutation	SNP	ENST00000306908.5	37	CCDS12098.1	.	.	.	.	.	.	.	.	.	.	C	9.937	1.216517	0.22373	.	.	ENSG00000171970	ENST00000306908;ENST00000395204;ENST00000523428	T;T	0.13089	2.62;2.62	2.08	-2.04	0.07343	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.17577	0.0422	L	0.50847	1.595	0.09310	N	1	D	0.57899	0.981	P	0.52343	0.696	T	0.15665	-1.0429	9	0.52906	T	0.07	.	6.5785	0.22581	0.0:0.5038:0.0:0.4962	.	413	Q68EA5	ZNF57_HUMAN	M	413;415;381	ENSP00000303696:T413M;ENSP00000430223:T381M	ENSP00000303696:T413M	T	+	2	0	ZNF57	2868857	0.000000	0.05858	0.001000	0.08648	0.023000	0.10783	-4.310000	0.00255	-0.255000	0.09486	-0.424000	0.05967	ACG	C|0.999;T|0.001	0.001	weak		0.438	ZNF57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378969.1	NM_173480	
NASP	4678	hgsc.bcm.edu	37	1	46073299	46073299	+	Missense_Mutation	SNP	C	C	T	rs140271488		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:46073299C>T	ENST00000350030.3	+	6	803	c.716C>T	c.(715-717)gCt>gTt	p.A239V	NASP_ENST00000402363.3_Missense_Mutation_p.A241V|NASP_ENST00000372052.4_Intron|NASP_ENST00000351223.3_Intron|NASP_ENST00000537798.1_Missense_Mutation_p.A175V	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	239	Glu-rich (acidic).|Histone-binding.				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)	p.A241V(1)		breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					GTACCAGATGCTGAGGAAGAA	0.478																																					p.A239V		Atlas-SNP	.											NASP,NS,carcinoma,0,1	NASP	77	1	1	Substitution - Missense(1)	lung(1)	c.C716T						scavenged	.						40.0	42.0	41.0					1																	46073299		2203	4298	6501	SO:0001583	missense	4678	exon6			CAGATGCTGAGGA	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.716C>T	1.37:g.46073299C>T	ENSP00000255120:p.Ala239Val	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	113	4	0.0353982	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	37	CCDS524.1	.	.	.	.	.	.	.	.	.	.	C	8.758	0.922910	0.18056	.	.	ENSG00000132780	ENST00000537798;ENST00000402363;ENST00000341288;ENST00000350030;ENST00000470768	D;D;D;D	0.94793	-3.52;-3.52;-3.52;-3.52	4.39	4.39	0.52855	.	0.605538	0.17715	N	0.164452	D	0.90293	0.6964	L	0.29908	0.895	0.23063	N	0.998351	B;B;B;B;B	0.25312	0.037;0.077;0.123;0.022;0.037	B;B;B;B;B	0.21360	0.021;0.034;0.034;0.009;0.033	T	0.77925	-0.2405	9	.	.	.	0.3497	18.274	0.90077	0.0:1.0:0.0:0.0	.	175;239;139;239;241	F5H3J2;Q53H03;B4DS57;P49321;P49321-3	.;.;.;NASP_HUMAN;.	V	175;241;139;239;202	ENSP00000438871:A175V;ENSP00000384529:A241V;ENSP00000255120:A239V;ENSP00000436924:A202V	.	A	+	2	0	NASP	45845886	0.002000	0.14202	0.629000	0.29254	0.680000	0.39746	0.731000	0.26058	2.713000	0.92767	0.650000	0.86243	GCT	C|0.998;T|0.002	0.002	weak		0.478	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
RFPL3	10738	hgsc.bcm.edu	37	22	32754250	32754250	+	Silent	SNP	C	C	T	rs376474772	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:32754250C>T	ENST00000249007.4	+	1	397	c.192C>T	c.(190-192)atC>atT	p.I64I	RFPL3_ENST00000382088.3_Silent_p.I35I|RFPL3S_ENST00000461833.1_5'Flank|RFPL3_ENST00000397468.1_Silent_p.I35I	NM_001098535.1	NP_001092005.1	O75679	RFPL3_HUMAN	ret finger protein-like 3	64							zinc ion binding (GO:0008270)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(2)|stomach(1)	15						TCAAGTGCATCAATTCGCTGC	0.532													c|||	6	0.00119808	0.0038	0.0014	5008	,	,		19944	0.0		0.0	False		,,,				2504	0.0				p.I64I		Atlas-SNP	.											RFPL3_ENST00000249007,NS,carcinoma,+2,2	RFPL3	91	2	0			c.C192T						scavenged	.						122.0	115.0	117.0					22																	32754250		2203	4300	6503	SO:0001819	synonymous_variant	10738	exon1			GTGCATCAATTCG	AJ010232	CCDS13904.1, CCDS43011.1	22q12	2006-04-25			ENSG00000128276	ENSG00000128276			9980	protein-coding gene	gene with protein product		605970				10508838	Standard	NM_006604		Approved		uc010gwn.3	O75679	OTTHUMG00000030290	ENST00000249007.4:c.192C>T	22.37:g.32754250C>T		Somatic	326	3	0.00920245		WXS	Illumina HiSeq	Phase_I	321	10	0.0311526	NM_001098535	A2A279|Q6IC03|Q6IC04|Q6NSX3|Q8N5R4	Silent	SNP	ENST00000249007.4	37	CCDS43011.1																																																																																			.	.	weak		0.532	RFPL3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000075172.3	NM_006604	
SLC35G5	83650	hgsc.bcm.edu	37	8	11188922	11188922	+	Missense_Mutation	SNP	T	T	C	rs76944947	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:11188922T>C	ENST00000382435.4	+	1	526	c.307T>C	c.(307-309)Tgg>Cgg	p.W103R		NM_001282300.1|NM_054028.1	NP_001269229.1|NP_473369.1	Q96KT7	S35G5_HUMAN	solute carrier family 35, member G5	103	EamA 1.					integral component of membrane (GO:0016021)		p.W103R(1)									CATCCGAGGCTGGGCCTGCTT	0.602																																					p.W103R		Atlas-SNP	.											AMAC1L2,colon,carcinoma,0,2	.	.	2	1	Substitution - Missense(1)	pancreas(1)	c.T307C						scavenged	.						216.0	216.0	216.0					8																	11188922		2203	4300	6503	SO:0001583	missense	83650	exon1			CGAGGCTGGGCCT	AJ291677	CCDS5980.1	8p23.1	2013-05-22	2011-08-03	2011-08-03	ENSG00000177710	ENSG00000177710		"""Solute carriers"""	15546	protein-coding gene	gene with protein product		615199	"""acyl-malonyl condensing enzyme 1-like 2"""	AMAC, AMAC1L2			Standard	NM_054028		Approved		uc003wtp.1	Q96KT7	OTTHUMG00000090653	ENST00000382435.4:c.307T>C	8.37:g.11188922T>C	ENSP00000371872:p.Trp103Arg	Somatic	220	4	0.0181818		WXS	Illumina HiSeq	Phase_I	305	11	0.0360656	NM_054028	A2RRL6	Missense_Mutation	SNP	ENST00000382435.4	37	CCDS5980.1	.	.	.	.	.	.	.	.	.	.	t	0	-2.642709	0.00112	.	.	ENSG00000177710	ENST00000382435	T	0.69306	-0.39	0.34	-0.68	0.11346	.	0.244821	0.21560	N	0.072582	T	0.30665	0.0772	N	0.01168	-0.975	0.18873	N	0.999984	B	0.02656	0.0	B	0.01281	0.0	T	0.14062	-1.0486	10	0.23891	T	0.37	-0.4591	6.793	0.23709	0.0:0.7448:0.0:0.2552	.	103	Q96KT7	S35G5_HUMAN	R	103	ENSP00000371872:W103R	ENSP00000371872:W103R	W	+	1	0	SLC35G5	11226332	0.010000	0.17322	0.030000	0.17652	0.042000	0.13812	0.106000	0.15354	-2.178000	0.00768	-2.006000	0.00442	TGG	T|0.754;C|0.246	0.246	strong		0.602	SLC35G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207313.2	NM_054028	
PPP1R15A	23645	hgsc.bcm.edu	37	19	49377187	49377187	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:49377187G>T	ENST00000200453.5	+	2	966	c.697G>T	c.(697-699)Gag>Tag	p.E233*		NM_014330.3	NP_055145.3	O75807	PR15A_HUMAN	protein phosphatase 1, regulatory subunit 15A	233	Glu-rich.				apoptotic process (GO:0006915)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of translation (GO:0006417)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)	protein kinase binding (GO:0019901)	p.E233K(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(8)|skin(2)|urinary_tract(1)	23		all_epithelial(76;5.29e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000244)|all cancers(93;0.000694)|GBM - Glioblastoma multiforme(486;0.0222)|Epithelial(262;0.033)		TCAAGCCACGGAGGATAAAAG	0.537																																					p.E233X		Atlas-SNP	.											PPP1R15A,caecum,carcinoma,0,1	PPP1R15A	48	1	1	Substitution - Missense(1)	large_intestine(1)	c.G697T						scavenged	.						75.0	84.0	81.0					19																	49377187		2203	4300	6503	SO:0001587	stop_gained	23645	exon2			GCCACGGAGGATA	U83981	CCDS12738.1	19q13.2	2012-04-17	2011-10-04		ENSG00000087074	ENSG00000087074		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14375	protein-coding gene	gene with protein product	"""growth arrest and DNA-damage-inducible 34"""	611048	"""protein phosphatase 1, regulatory (inhibitor) subunit 15A"""			9153226, 9413226	Standard	NM_014330		Approved	GADD34	uc002pky.4	O75807		ENST00000200453.5:c.697G>T	19.37:g.49377187G>T	ENSP00000200453:p.Glu233*	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	81	3	0.037037	NM_014330	B4DKQ3|Q6IA96|Q9NVU6	Nonsense_Mutation	SNP	ENST00000200453.5	37	CCDS12738.1	.	.	.	.	.	.	.	.	.	.	G	37	6.434933	0.97564	.	.	ENSG00000087074	ENST00000200453;ENST00000540695;ENST00000544084	.	.	.	4.04	4.04	0.47022	.	0.896444	0.09522	N	0.790754	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-7.8722	11.8954	0.52654	0.0:0.0:1.0:0.0	.	.	.	.	X	233;73;191	.	ENSP00000200453:E233X	E	+	1	0	PPP1R15A	54068999	0.279000	0.24239	0.226000	0.23910	0.136000	0.21042	0.802000	0.27069	2.276000	0.75962	0.561000	0.74099	GAG	.	.	none		0.537	PPP1R15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466226.1	NM_014330	
CHRM3	1131	hgsc.bcm.edu	37	1	240071117	240071117	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:240071117G>T	ENST00000255380.4	+	5	1145	c.366G>T	c.(364-366)atG>atT	p.M122I		NM_000740.2	NP_000731.1	P20309	ACM3_HUMAN	cholinergic receptor, muscarinic 3	122					cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|energy reserve metabolic process (GO:0006112)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|nervous system development (GO:0007399)|positive regulation of smooth muscle contraction (GO:0045987)|regulation of insulin secretion (GO:0050796)|regulation of vascular smooth muscle contraction (GO:0003056)|saliva secretion (GO:0046541)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|smooth muscle contraction (GO:0006939)	asymmetric synapse (GO:0032279)|axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|drug binding (GO:0008144)|G-protein coupled acetylcholine receptor activity (GO:0016907)|phosphatidylinositol phospholipase C activity (GO:0004435)|receptor activity (GO:0004872)	p.M122I(1)		breast(3)|endometrium(5)|kidney(2)|large_intestine(4)|lung(19)|ovary(4)|prostate(1)|skin(12)|upper_aerodigestive_tract(1)	51	Ovarian(103;0.127)	all_cancers(173;0.00567)|all_neural(198;0.203)	OV - Ovarian serous cystadenocarcinoma(106;0.00989)		Aclidinium(DB08897)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Anisotropine Methylbromide(DB00517)|Aripiprazole(DB01238)|Atropine(DB00572)|Brompheniramine(DB00835)|Cevimeline(DB00185)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Cryptenamine(DB00785)|Cyproheptadine(DB00434)|Darifenacin(DB00496)|Desipramine(DB01151)|Diphemanil Methylsulfate(DB00729)|Diphenidol(DB01231)|Disopyramide(DB00280)|Doxepin(DB01142)|Fesoterodine(DB06702)|Glycopyrrolate(DB00986)|Homatropine Methylbromide(DB00725)|Hyoscyamine(DB00424)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|Isopropamide(DB01625)|Ketamine(DB01221)|Loxapine(DB00408)|Maprotiline(DB00934)|Mepenzolate(DB04843)|Methacholine(DB06709)|Methotrimeprazine(DB01403)|Methylscopolamine bromide(DB00462)|Metixene(DB00340)|Mivacurium(DB01226)|Nicardipine(DB00622)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxybutynin(DB01062)|Oxyphencyclimine(DB00383)|Pancuronium(DB01337)|Paroxetine(DB00715)|Pethidine(DB00454)|Pilocarpine(DB01085)|Pipecuronium(DB01338)|Procyclidine(DB00387)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Scopolamine(DB00747)|Solifenacin(DB01591)|Succinylcholine(DB00202)|Tiotropium(DB01409)|Tolterodine(DB01036)|Tramadol(DB00193)|Trihexyphenidyl(DB00376)|Trimipramine(DB00726)|Tropicamide(DB00809)|Ziprasidone(DB00246)	TCATTTCAATGAATCTGTTTA	0.473																																					p.M122I		Atlas-SNP	.											CHRM3,NS,carcinoma,0,1	CHRM3	118	1	1	Substitution - Missense(1)	breast(1)	c.G366T						scavenged	.						106.0	91.0	96.0					1																	240071117		2203	4300	6503	SO:0001583	missense	1131	exon5			TTCAATGAATCTG	U29589	CCDS1616.1	1q43	2012-09-20			ENSG00000133019	ENSG00000133019		"""Cholinergic receptors"", ""GPCR / Class A : Cholinergic receptors, muscarinic"""	1952	protein-coding gene	gene with protein product	"""acetylcholine receptor, muscarinic 3"""	118494					Standard	XM_005273032		Approved		uc001hyp.3	P20309	OTTHUMG00000039649	ENST00000255380.4:c.366G>T	1.37:g.240071117G>T	ENSP00000255380:p.Met122Ile	Somatic	377	1	0.00265252		WXS	Illumina HiSeq	Phase_I	349	58	0.166189	NM_000740	Q0VAJ8|Q4QRI3|Q5VXY2|Q9HB60	Missense_Mutation	SNP	ENST00000255380.4	37	CCDS1616.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.331523	0.81690	.	.	ENSG00000133019	ENST00000255380	T	0.17213	2.29	5.9	5.9	0.94986	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.40522	0.1120	L	0.52126	1.63	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.05338	-1.0891	10	0.87932	D	0	-30.8099	20.2789	0.98501	0.0:0.0:1.0:0.0	.	122	P20309	ACM3_HUMAN	I	122	ENSP00000255380:M122I	ENSP00000255380:M122I	M	+	3	0	CHRM3	238137740	1.000000	0.71417	1.000000	0.80357	0.871000	0.50021	9.869000	0.99810	2.788000	0.95919	0.650000	0.86243	ATG	.	.	none		0.473	CHRM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095644.2	NM_000740	
PBX2	5089	hgsc.bcm.edu	37	6	32155509	32155509	+	Missense_Mutation	SNP	T	T	A	rs202223627		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:32155509T>A	ENST00000375050.4	-	5	1055	c.785A>T	c.(784-786)tAt>tTt	p.Y262F	XXbac-BPG300A18.13_ENST00000559458.1_RNA	NM_002586.4	NP_002577.2	P40425	PBX2_HUMAN	pre-B-cell leukemia homeobox 2	262					embryonic limb morphogenesis (GO:0030326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.Y262F(3)		endometrium(1)|kidney(1)|lung(9)|ovary(1)|prostate(2)	14						GGAGTAGAAATACTCATTTAG	0.517																																					p.Y262F		Atlas-SNP	.											PBX2,NS,carcinoma,0,4	PBX2	29	4	3	Substitution - Missense(3)	lung(3)	c.A785T						scavenged	.																																			SO:0001583	missense	5089	exon5			TAGAAATACTCAT		CCDS4748.1	6p21.32	2011-06-20	2007-01-30		ENSG00000204304	ENSG00000204304		"""Homeoboxes / TALE class"""	8633	protein-coding gene	gene with protein product		176311	"""pre-B-cell leukemia transcription factor 2"""			7835890	Standard	NM_002586		Approved	G17, HOX12, PBX2MHC	uc003oav.1	P40425	OTTHUMG00000031116	ENST00000375050.4:c.785A>T	6.37:g.32155509T>A	ENSP00000364190:p.Tyr262Phe	Somatic	223	2	0.00896861		WXS	Illumina HiSeq	Phase_I	212	14	0.0660377	NM_002586	A2BFJ2	Missense_Mutation	SNP	ENST00000375050.4	37	CCDS4748.1	.	.	.	.	.	.	.	.	.	.	T	19.51	3.841111	0.71488	.	.	ENSG00000204304	ENST00000375050	D	0.83673	-1.75	4.63	4.63	0.57726	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.201957	0.34435	N	0.003969	T	0.61837	0.2379	N	0.10629	0.01	0.80722	D	1	P;P	0.42337	0.776;0.502	P;P	0.45232	0.474;0.458	T	0.71314	-0.4630	10	0.49607	T	0.09	-0.8351	12.0363	0.53427	0.0:0.0:0.0:1.0	.	262;262	Q7KZE5;P40425	.;PBX2_HUMAN	F	262	ENSP00000364190:Y262F	ENSP00000364190:Y262F	Y	-	2	0	PBX2	32263487	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.505000	0.81655	1.943000	0.56356	0.459000	0.35465	TAT	T|0.999;A|0.001	0.001	weak		0.517	PBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076194.4		
PRPH2	5961	hgsc.bcm.edu	37	6	42690015	42690015	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:42690015G>T	ENST00000230381.5	-	1	297	c.58C>A	c.(58-60)Ctc>Atc	p.L20I		NM_000322.4	NP_000313.2	P23942	PRPH2_HUMAN	peripherin 2 (retinal degeneration, slow)	20					cell adhesion (GO:0007155)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)				NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|ovary(4)|prostate(1)|skin(1)|urinary_tract(1)	18	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|all cancers(41;0.00178)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|Kidney(15;0.0388)|OV - Ovarian serous cystadenocarcinoma(102;0.0904)			ATGAGCCAGAGCCCTTGGGCC	0.527																																					p.L20I		Atlas-SNP	.											.	PRPH2	47	.	0			c.C58A						PASS	.						81.0	78.0	79.0					6																	42690015		2203	4300	6503	SO:0001583	missense	5961	exon1			GCCAGAGCCCTTG		CCDS4871.1	6p21.1	2013-09-20	2006-11-23	2006-11-23	ENSG00000112619	ENSG00000112619		"""Tetraspanins"""	9942	protein-coding gene	gene with protein product	retinal peripherin	179605	"""retinal degeneration, slow (retinitis pigmentosa 7)"", ""retinal degeneration, slow"""	RP7, RDS		1749427	Standard	NM_000322		Approved	TSPAN22, rd2, CACD2	uc003osk.3	P23942	OTTHUMG00000014701	ENST00000230381.5:c.58C>A	6.37:g.42690015G>T	ENSP00000230381:p.Leu20Ile	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	133	38	0.285714	NM_000322	Q5TFH5|Q6DK65	Missense_Mutation	SNP	ENST00000230381.5	37	CCDS4871.1	.	.	.	.	.	.	.	.	.	.	G	19.18	3.778382	0.70107	.	.	ENSG00000112619	ENST00000230381	D	0.82526	-1.62	5.61	5.61	0.85477	.	0.057622	0.64402	D	0.000001	D	0.89203	0.6648	M	0.84585	2.705	0.51233	D	0.999911	P	0.51791	0.948	P	0.56700	0.804	D	0.88512	0.3090	10	0.44086	T	0.13	.	19.6248	0.95674	0.0:0.0:1.0:0.0	.	20	P23942	PRPH2_HUMAN	I	20	ENSP00000230381:L20I	ENSP00000230381:L20I	L	-	1	0	PRPH2	42797993	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.685000	0.54678	2.631000	0.89168	0.655000	0.94253	CTC	.	.	none		0.527	PRPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040556.1	NM_000322	
BPIFB3	359710	hgsc.bcm.edu	37	20	31656632	31656632	+	Missense_Mutation	SNP	C	C	G	rs6057717	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:31656632C>G	ENST00000375494.3	+	10	1002	c.1002C>G	c.(1000-1002)caC>caG	p.H334Q		NM_182658.1	NP_872599.1	P59826	BPIB3_HUMAN	BPI fold containing family B, member 3	334			H -> Q (in dbSNP:rs6057717).		innate immune response (GO:0045087)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)	lipid binding (GO:0008289)										TGCCCCTGCACCAGCAACTCC	0.562													C|||	2414	0.482029	0.3086	0.4741	5008	,	,		17133	0.7698		0.3837	False		,,,				2504	0.5266				p.H334Q		Atlas-SNP	.											C20orf185,NS,carcinoma,0,1	.	.	1	0			c.C1002G						scavenged	.	C	GLN/HIS	1307,3099	442.3+/-346.6	202,903,1098	89.0	66.0	74.0		1002	2.3	0.6	20	dbSNP_114	74	3124,5476	475.9+/-369.2	578,1968,1754	yes	missense	BPIFB3	NM_182658.1	24	780,2871,2852	GG,GC,CC		36.3256,29.6641,34.0689	benign	334/477	31656632	4431,8575	2203	4300	6503	SO:0001583	missense	359710	exon10			CCTGCACCAGCAA	AF549189	CCDS13212.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000186190	ENSG00000186190		"""BPI fold containing"""	16178	protein-coding gene	gene with protein product		615717	"""chromosome 20 open reading frame 185"""	C20orf185		11971875, 21787333	Standard	NM_182658		Approved	dJ726C3.4, LPLUNC3, RYA3	uc002wym.1	P59826	OTTHUMG00000032234	ENST00000375494.3:c.1002C>G	20.37:g.31656632C>G	ENSP00000364643:p.His334Gln	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	79	2	0.0253165	NM_182658	Q5TDX7	Missense_Mutation	SNP	ENST00000375494.3	37	CCDS13212.1	1051	0.48122710622710624	163	0.3313008130081301	160	0.4419889502762431	438	0.7657342657342657	290	0.38258575197889183	C	2.285	-0.363791	0.05103	0.296641	0.363256	ENSG00000186190	ENST00000375494	T	0.08193	3.12	4.25	2.26	0.28386	.	2.005100	0.02461	N	0.086613	T	0.00012	0.0000	N	0.22421	0.69	0.58432	P	9.99999999995449E-6	B	0.26635	0.155	B	0.29785	0.107	T	0.28332	-1.0047	9	0.13853	T	0.58	0.2314	6.1232	0.20164	0.0:0.7579:0.0:0.2421	rs6057717;rs6057717	334	P59826	BPIB3_HUMAN	Q	334	ENSP00000364643:H334Q	ENSP00000364643:H334Q	H	+	3	2	BPIFB3	31120293	0.019000	0.18553	0.644000	0.29465	0.068000	0.16541	0.094000	0.15107	0.519000	0.28406	0.591000	0.81541	CAC	C|0.625;G|0.375	0.375	strong		0.562	BPIFB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078654.2	NM_182658	
OR8D4	338662	hgsc.bcm.edu	37	11	123777861	123777861	+	Silent	SNP	T	T	C	rs61748875	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:123777861T>C	ENST00000321355.2	+	1	753	c.723T>C	c.(721-723)tgT>tgC	p.C241C		NM_001005197.1	NP_001005197.1	Q8NGM9	OR8D4_HUMAN	olfactory receptor, family 8, subfamily D, member 4	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.C241C(1)		large_intestine(1)|lung(16)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.93e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0409)		TTAGCACCTGTAGCTCCCACC	0.458													T|||	818	0.163339	0.2005	0.1398	5008	,	,		18173	0.0933		0.1819	False		,,,				2504	0.183				p.C241C		Atlas-SNP	.											OR8D4,NS,carcinoma,0,1	OR8D4	62	1	1	Substitution - coding silent(1)	stomach(1)	c.T723C						scavenged	.	T		857,3547	336.5+/-304.4	88,681,1433	114.0	114.0	114.0		723	3.6	1.0	11	dbSNP_129	114	1634,6964	303.0+/-306.2	164,1306,2829	no	coding-synonymous	OR8D4	NM_001005197.1		252,1987,4262	CC,CT,TT		19.0044,19.4596,19.1586		241/315	123777861	2491,10511	2202	4299	6501	SO:0001819	synonymous_variant	338662	exon1			CACCTGTAGCTCC	AB065761	CCDS31698.1	11q24.1	2012-08-09			ENSG00000181518	ENSG00000181518		"""GPCR / Class A : Olfactory receptors"""	14840	protein-coding gene	gene with protein product							Standard	NM_001005197		Approved		uc010saa.2	Q8NGM9	OTTHUMG00000165960	ENST00000321355.2:c.723T>C	11.37:g.123777861T>C		Somatic	201	1	0.00497512		WXS	Illumina HiSeq	Phase_I	253	7	0.027668	NM_001005197	Q6IFE9	Silent	SNP	ENST00000321355.2	37	CCDS31698.1																																																																																			T|0.815;C|0.185	0.185	strong		0.458	OR8D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387262.1	NM_001005197	
EIF4EBP3	8637	hgsc.bcm.edu	37	5	139931629	139931629	+	IGR	SNP	C	C	G	rs5871740|rs368142622|rs202193903	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:139931629C>G	ENST00000310331.2	+	0	691				SRA1_ENST00000520427.1_5'UTR|SRA1_ENST00000336283.6_Missense_Mutation_p.V110L	NM_003732.2	NP_003723.1	O60516	4EBP3_HUMAN	eukaryotic translation initiation factor 4E binding protein 3						negative regulation of translational initiation (GO:0045947)	eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	translation repressor activity (GO:0030371)			endometrium(1)|ovary(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCTCCATCACAGCCTCAGAC	0.592																																					p.V110L		Atlas-SNP	.											SRA1,NS,carcinoma,+1,2	SRA1	24	2	0			c.G328C						scavenged	.						82.0	59.0	67.0					5																	139931629		2202	4295	6497	SO:0001628	intergenic_variant	10011	exon3			CCATCACAGCCTC	AF038869	CCDS4226.1	5q31.3	2007-07-18			ENSG00000243056	ENSG00000243056			3290	protein-coding gene	gene with protein product		603483				9593750	Standard	NM_003732		Approved	4E-BP3	uc003lfy.1	O60516	OTTHUMG00000129498		5.37:g.139931629C>G		Somatic	213	74	0.347418		WXS	Illumina HiSeq	Phase_I	184	69	0.375	NM_001035235		Missense_Mutation	SNP	ENST00000310331.2	37	CCDS4226.1	.	.	.	.	.	.	.	.	.	.	C	4.980	0.181983	0.09495	.	.	ENSG00000213523	ENST00000336283;ENST00000520427	T	0.40476	1.03	5.75	1.75	0.24633	.	0.938709	0.08826	N	0.888002	T	0.11196	0.0273	N	0.00560	-1.38	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.32052	-0.9921	9	.	.	.	.	3.3903	0.07286	0.0902:0.3003:0.4378:0.1718	.	110	Q9HD15	SRA1_HUMAN	L	110;36	ENSP00000337513:V110L	.	V	-	1	0	SRA1	139911813	0.037000	0.19845	0.998000	0.56505	0.973000	0.67179	-0.239000	0.08965	0.800000	0.34041	-0.211000	0.12701	GTG	.	.	alt		0.592	EIF4EBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251668.2	NM_003732	
IVL	3713	hgsc.bcm.edu	37	1	152883856	152883856	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:152883856G>A	ENST00000368764.3	+	2	1647	c.1583G>A	c.(1582-1584)gGg>gAg	p.G528E	IVL_ENST00000392667.2_Missense_Mutation_p.G382E			P07476	INVO_HUMAN	involucrin	528	39 X 10 AA approximate tandem repeats of [LP]-[EKG]-[LHVYQEK]-[PLSQE]-[EQDV]- [QHEKRGA]-Q-[EMVQLP]-[GKLE]-[QHVNLD].				isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|response to UV-B (GO:0010224)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(1)|endometrium(6)|kidney(1)|large_intestine(5)|lung(11)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	29	Lung NSC(65;3.97e-29)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			cagcaggaggggcagctgaag	0.597																																					p.G528E		Atlas-SNP	.											.	IVL	100	.	0			c.G1583A						PASS	.						70.0	66.0	67.0					1																	152883856		2203	4300	6503	SO:0001583	missense	3713	exon2			AGGAGGGGCAGCT	BC046391	CCDS1030.1	1q21	2008-02-05			ENSG00000163207	ENSG00000163207			6187	protein-coding gene	gene with protein product		147360				2873896	Standard	NM_005547		Approved		uc001fau.3	P07476	OTTHUMG00000012451	ENST00000368764.3:c.1583G>A	1.37:g.152883856G>A	ENSP00000357753:p.Gly528Glu	Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	96	21	0.21875	NM_005547	Q5T7P4	Missense_Mutation	SNP	ENST00000368764.3	37	CCDS1030.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.070892	0.36566	.	.	ENSG00000163207	ENST00000368764;ENST00000392667	T;T	0.47177	1.77;0.85	3.34	-1.01	0.10169	.	.	.	.	.	T	0.07234	0.0183	N	0.21545	0.675	0.09310	N	1	B	0.21905	0.062	B	0.18561	0.022	T	0.34403	-0.9830	9	0.02654	T	1	.	3.2393	0.06776	0.3377:0.0:0.447:0.2153	.	528	P07476	INVO_HUMAN	E	528;382	ENSP00000357753:G528E;ENSP00000376435:G382E	ENSP00000357753:G528E	G	+	2	0	IVL	151150480	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.649000	0.05384	-0.022000	0.13986	-0.274000	0.10170	GGG	.	.	none		0.597	IVL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034664.1	NM_005547	
TRIOBP	11078	hgsc.bcm.edu	37	22	38120006	38120006	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:38120006T>C	ENST00000406386.3	+	7	1698	c.1443T>C	c.(1441-1443)tgT>tgC	p.C481C		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	481					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.C481C(3)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					GAACATCCTGTGCCCAGCGGG	0.592																																					p.C481C		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,5	TRIOBP	262	5	3	Substitution - coding silent(3)	kidney(2)|large_intestine(1)	c.T1443C						scavenged	.						52.0	51.0	51.0					22																	38120006		1899	4072	5971	SO:0001819	synonymous_variant	11078	exon7			ATCCTGTGCCCAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1443T>C	22.37:g.38120006T>C		Somatic	227	5	0.0220264		WXS	Illumina HiSeq	Phase_I	206	7	0.0339806	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Silent	SNP	ENST00000406386.3	37	CCDS43015.1																																																																																			.	.	none		0.592	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
USP31	57478	hgsc.bcm.edu	37	16	23117736	23117736	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:23117736A>C	ENST00000219689.7	-	3	843	c.844T>G	c.(844-846)Ttt>Gtt	p.F282V		NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	213	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		TGCGCTTGAAAGAGTTCTTGT	0.388																																					p.F282V		Atlas-SNP	.											.	USP31	122	.	0			c.T844G						PASS	.						79.0	72.0	75.0					16																	23117736		2197	4300	6497	SO:0001583	missense	57478	exon3			CTTGAAAGAGTTC	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.844T>G	16.37:g.23117736A>C	ENSP00000219689:p.Phe282Val	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	249	40	0.160643	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	.	.	.	.	.	.	.	.	.	.	A	24.7	4.559863	0.86335	.	.	ENSG00000103404	ENST00000219689	T	0.48522	0.81	5.5	5.5	0.81552	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.060995	0.64402	D	0.000003	T	0.74824	0.3767	M	0.92026	3.265	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	T	0.81360	-0.0968	10	0.87932	D	0	-20.3252	15.0849	0.72145	1.0:0.0:0.0:0.0	.	282	Q70CQ4	UBP31_HUMAN	V	282	ENSP00000219689:F282V	ENSP00000219689:F282V	F	-	1	0	USP31	23025237	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.851000	0.92205	2.214000	0.71695	0.523000	0.50628	TTT	.	.	none		0.388	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
OR52I2	143502	hgsc.bcm.edu	37	11	4608396	4608396	+	Silent	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:4608396A>C	ENST00000312614.4	+	1	376	c.354A>C	c.(352-354)ggA>ggC	p.G118G		NM_001005170.2	NP_001005170.1	Q8NH67	O52I2_HUMAN	olfactory receptor, family 52, subfamily I, member 2	118						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|pancreas(1)|skin(1)	19		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TCTGCTCAGGAGACAGCTCAA	0.512																																					p.G118G		Atlas-SNP	.											.	OR52I2	50	.	0			c.A354C						PASS	.						201.0	189.0	193.0					11																	4608396		2201	4298	6499	SO:0001819	synonymous_variant	143502	exon1			CTCAGGAGACAGC	BK004264	CCDS31355.1	11p15.4	2012-08-09			ENSG00000226288	ENSG00000226288		"""GPCR / Class A : Olfactory receptors"""	15221	protein-coding gene	gene with protein product							Standard	NM_001005170		Approved		uc010qyh.2	Q8NH67	OTTHUMG00000165721	ENST00000312614.4:c.354A>C	11.37:g.4608396A>C		Somatic	503	1	0.00198807		WXS	Illumina HiSeq	Phase_I	572	149	0.26049	NM_001005170	B2RNJ5|B9EKV8|Q6IFJ8	Silent	SNP	ENST00000312614.4	37	CCDS31355.1																																																																																			.	.	none		0.512	OR52I2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385946.1	NM_001005170	
WHSC1	7468	hgsc.bcm.edu	37	4	1957912	1957912	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:1957912A>C	ENST00000382895.3	+	17	3309	c.2878A>C	c.(2878-2880)Aac>Cac	p.N960H	WHSC1_ENST00000382892.2_Missense_Mutation_p.N960H|WHSC1_ENST00000382888.3_Missense_Mutation_p.N308H|WHSC1_ENST00000382891.5_Missense_Mutation_p.N960H|WHSC1_ENST00000508803.1_Missense_Mutation_p.N960H|WHSC1_ENST00000482415.2_3'UTR	NM_133330.2	NP_579877.1	O96028	NSD2_HUMAN	Wolf-Hirschhorn syndrome candidate 1	960					anatomical structure morphogenesis (GO:0009653)|atrial septum primum morphogenesis (GO:0003289)|atrial septum secundum morphogenesis (GO:0003290)|bone development (GO:0060348)|membranous septum morphogenesis (GO:0003149)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(14)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|urinary_tract(3)	48		all_epithelial(65;1.34e-05)	OV - Ovarian serous cystadenocarcinoma(23;0.00606)	STAD - Stomach adenocarcinoma(129;0.232)		AGTCTTCAAAAACGGTACGGA	0.458			T	IGH@	MM																																p.N960H		Atlas-SNP	.		Dom	yes		4	4p16.3	7468	Wolf-Hirschhorn syndrome candidate 1(MMSET)		L	.	WHSC1	180	.	0			c.A2878C						PASS	.						54.0	64.0	61.0					4																	1957912		2199	4300	6499	SO:0001583	missense	7468	exon15			TTCAAAAACGGTA	AF083386	CCDS3356.1, CCDS33940.1, CCDS46999.1	4p16.3	2013-05-20			ENSG00000109685	ENSG00000109685		"""Zinc fingers, PHD-type"""	12766	protein-coding gene	gene with protein product		602952				9618163, 9787135	Standard	NM_133334		Approved	MMSET, NSD2	uc003gdz.4	O96028	OTTHUMG00000121147	ENST00000382895.3:c.2878A>C	4.37:g.1957912A>C	ENSP00000372351:p.Asn960His	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	18	6	0.333333	NM_133335	A2A2T2|A2A2T3|A2A2T4|A7MCZ1|D3DVQ2|O96031|Q4VBY8|Q672J1|Q6IS00|Q86V01|Q9BZB4|Q9UI92|Q9UPR2	Missense_Mutation	SNP	ENST00000382895.3	37	CCDS33940.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.80|14.80	2.643251|2.643251	0.47153|0.47153	.|.	.|.	ENSG00000109685|ENSG00000109685	ENST00000514329|ENST00000508803;ENST00000382891;ENST00000382892;ENST00000382895;ENST00000382888	D|T;T;T;T;T	0.98105|0.70749	-4.72|-0.51;-0.51;-0.51;-0.51;-0.51	5.43|5.43	5.43|5.43	0.79202|0.79202	.|.	.|0.000000	.|0.64402	.|D	.|0.000017	T|T	0.56093|0.56093	0.1962|0.1962	N|N	0.15975|0.15975	0.35|0.35	0.80722|0.80722	D|D	1|1	.|B;B	.|0.25850	.|0.005;0.136	.|B;B	.|0.22753	.|0.006;0.041	T|T	0.57505|0.57505	-0.7800|-0.7800	7|10	0.87932|0.62326	D|D	0|0.03	.|.	15.4756|15.4756	0.75478|0.75478	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|308;960	.|A2A2T2;O96028	.|.;NSD2_HUMAN	T|H	283|960;960;960;960;308	ENSP00000425094:K283T|ENSP00000423972:N960H;ENSP00000372347:N960H;ENSP00000372348:N960H;ENSP00000372351:N960H;ENSP00000372344:N308H	ENSP00000425094:K283T|ENSP00000372344:N308H	K|N	+|+	2|1	0|0	WHSC1|WHSC1	1927710|1927710	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.949000|0.949000	0.60115|0.60115	5.838000|5.838000	0.69388|0.69388	2.062000|2.062000	0.61559|0.61559	0.533000|0.533000	0.62120|0.62120	AAA|AAC	.	.	none		0.458	WHSC1-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366269.2	NM_133330	
TIAM1	7074	hgsc.bcm.edu	37	21	32554842	32554842	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr21:32554842G>T	ENST00000286827.3	-	16	3254	c.2783C>A	c.(2782-2784)cCc>cAc	p.P928H	TIAM1_ENST00000541036.1_Missense_Mutation_p.P868H	NM_003253.2	NP_003244.2	Q13009	TIAM1_HUMAN	T-cell lymphoma invasion and metastasis 1	928					apoptotic signaling pathway (GO:0097190)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|ephrin receptor signaling pathway (GO:0048013)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell contact zone (GO:0044291)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)	phospholipid binding (GO:0005543)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|receptor signaling protein activity (GO:0005057)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			autonomic_ganglia(3)|breast(7)|central_nervous_system(2)|endometrium(13)|kidney(4)|large_intestine(33)|lung(44)|ovary(2)|prostate(3)|skin(2)|urinary_tract(2)	115						CTCCAGCTCGGGGTAGGTCCT	0.602																																					p.P928H		Atlas-SNP	.											.	TIAM1	522	.	0			c.C2783A						PASS	.						43.0	43.0	43.0					21																	32554842		2203	4300	6503	SO:0001583	missense	7074	exon16			AGCTCGGGGTAGG		CCDS13609.1	21q22.1	2013-01-10			ENSG00000156299	ENSG00000156299		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11805	protein-coding gene	gene with protein product		600687				8595894, 15340013	Standard	NM_003253		Approved		uc002yow.1	Q13009	OTTHUMG00000084869	ENST00000286827.3:c.2783C>A	21.37:g.32554842G>T	ENSP00000286827:p.Pro928His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	95	25	0.263158	NM_003253	B7ZLR6|F5GZ53|Q17RT7	Missense_Mutation	SNP	ENST00000286827.3	37	CCDS13609.1	.	.	.	.	.	.	.	.	.	.	G	19.69	3.873912	0.72180	.	.	ENSG00000156299	ENST00000286827;ENST00000399841;ENST00000541036	T;T	0.49139	0.79;0.82	4.24	4.24	0.50183	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.62624	0.2443	L	0.55481	1.735	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.64807	-0.6320	10	0.56958	D	0.05	.	13.6799	0.62476	0.0:0.0:1.0:0.0	.	868;868;928	F5GZ53;B7ZLR6;Q13009	.;.;TIAM1_HUMAN	H	928;769;868	ENSP00000286827:P928H;ENSP00000441570:P868H	ENSP00000286827:P928H	P	-	2	0	TIAM1	31476713	1.000000	0.71417	0.937000	0.37676	0.985000	0.73830	5.349000	0.66010	2.193000	0.70182	0.555000	0.69702	CCC	.	.	none		0.602	TIAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192552.1	NM_003253	
IRF5	3663	hgsc.bcm.edu	37	7	128587374	128587374	+	Missense_Mutation	SNP	G	G	A	rs199508964|rs113806178|rs60344245	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:128587374G>A	ENST00000402030.2	+	6	596	c.524G>A	c.(523-525)cGg>cAg	p.R175Q	IRF5_ENST00000477535.1_Intron|IRF5_ENST00000473745.1_Missense_Mutation_p.R175Q|IRF5_ENST00000249375.4_Missense_Mutation_p.R175Q|IRF5_ENST00000357234.5_Missense_Mutation_p.R191Q	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	175					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						CCCACTCTGCGGCCGCCTACT	0.657																																					p.R191Q		Atlas-SNP	.											IRF5,NS,haematopoietic_neoplasm,0,2	IRF5	40	2	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.G572A						PASS	.						6.0	8.0	7.0					7																	128587374		1947	3850	5797	SO:0001583	missense	3663	exon6			CTCTGCGGCCGCC		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.524G>A	7.37:g.128587374G>A	ENSP00000385352:p.Arg175Gln	Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	45	16	0.355556	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	37	CCDS5808.1	628|628	0.2875457875457875|0.2875457875457875	155|155	0.3150406504065041|0.3150406504065041	88|88	0.2430939226519337|0.2430939226519337	148|148	0.25874125874125875|0.25874125874125875	237|237	0.31266490765171506|0.31266490765171506	G|G	0.019|0.019	-1.454282|-1.454282	0.01071|0.01071	.|.	.|.	ENSG00000128604|ENSG00000128604	ENST00000430204|ENST00000357234;ENST00000402030;ENST00000249375;ENST00000473745	.|D;D;D;D	.|0.97256	.|-4.25;-4.31;-4.31;-4.31	.|.	.|.	.|.	.|.	.|5.726080	.|0.00166	.|N	.|0.000000	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.80722|0.80722	P|P	0.0|0.0	.|B;.	.|0.02656	.|0.0;.	.|B;.	.|0.01281	.|0.0;.	T|T	0.62562|0.62562	-0.6828|-0.6828	3|7	0.06757|0.13470	T|T	0.87|0.59	.|.	.|.	.|.	.|.	.|.	164|175;191	E9PC81|Q13568;Q13568-2	.|IRF5_HUMAN;.	S|Q	164|191;175;175;175	.|ENSP00000349770:R191Q;ENSP00000385352:R175Q;ENSP00000249375:R175Q;ENSP00000419149:R175Q	ENSP00000409106:G164S|ENSP00000249375:R175Q	G|R	+|+	1|2	0|0	IRF5|IRF5	128374610|128374610	0.019000|0.019000	0.18553|0.18553	0.128000|0.128000	0.21923|0.21923	0.042000|0.042000	0.13812|0.13812	-1.450000|-1.450000	0.02390|0.02390	-1.505000|-1.505000	0.01807|0.01807	-1.490000|-1.490000	0.00973|0.00973	GGC|CGG	G|0.714;A|0.286	0.286	strong		0.657	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
B2M	567	hgsc.bcm.edu	37	15	45003745	45003745	+	Start_Codon_SNP	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:45003745A>G	ENST00000558401.1	+	1	71	c.1A>G	c.(1-3)Atg>Gtg	p.M1V	B2M_ENST00000544417.1_Start_Codon_SNP_p.M1V|B2M_ENST00000559916.1_Start_Codon_SNP_p.M1V|PATL2_ENST00000558573.1_5'Flank	NM_004048.2	NP_004039.1	P61769	B2MG_HUMAN	beta-2-microglobulin	1					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent (GO:0002481)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|innate immune response (GO:0045087)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein refolding (GO:0042026)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to molecule of bacterial origin (GO:0002237)|retina homeostasis (GO:0001895)|T cell differentiation in thymus (GO:0033077)|viral process (GO:0016032)	cytoplasm (GO:0005737)|early endosome lumen (GO:0031905)|early endosome membrane (GO:0031901)|endoplasmic reticulum lumen (GO:0005788)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)	p.M1L(3)|p.M1V(2)|p.?(1)		breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(30)|kidney(8)|large_intestine(6)|lung(6)|ovary(2)|skin(2)|urinary_tract(1)	59		all_cancers(109;1.88e-13)|all_epithelial(112;2.13e-11)|Lung NSC(122;2.22e-07)|all_lung(180;1.81e-06)|Melanoma(134;0.0122)		all cancers(107;4.16e-21)|GBM - Glioblastoma multiforme(94;8.97e-07)|COAD - Colon adenocarcinoma(120;0.0357)|Colorectal(105;0.0377)|Lung(196;0.0903)|LUSC - Lung squamous cell carcinoma(244;0.192)		TCGGGCCGAGATGTCTCGCTC	0.612																																					p.M1V		Atlas-SNP	.											B2M,caecum,carcinoma,-2,17	B2M	99	17	6	Substitution - Missense(5)|Unknown(1)	ovary(2)|haematopoietic_and_lymphoid_tissue(2)|lung(1)|large_intestine(1)	c.A1G						scavenged	.						126.0	92.0	104.0					15																	45003745		2198	4298	6496	SO:0001582	initiator_codon_variant	567	exon1			GCCGAGATGTCTC	AB021288	CCDS10113.1	15q21-q22.2	2013-01-11			ENSG00000166710	ENSG00000166710		"""Immunoglobulin superfamily / C1-set domain containing"""	914	protein-coding gene	gene with protein product		109700					Standard	NM_004048		Approved		uc001zuc.3	P61769	OTTHUMG00000131247	ENST00000558401.1:c.1A>G	15.37:g.45003745A>G	ENSP00000452780:p.Met1Val	Somatic	140	1	0.00714286		WXS	Illumina HiSeq	Phase_I	169	49	0.289941	NM_004048	P01884|Q540F8|Q6IAT8|Q9UCK0|Q9UD48|Q9UDF4	Missense_Mutation	SNP	ENST00000558401.1	37	CCDS10113.1	.	.	.	.	.	.	.	.	.	.	A	19.48	3.836331	0.71373	.	.	ENSG00000166710	ENST00000349264;ENST00000544417;ENST00000396754	T	0.01228	5.14	5.35	5.35	0.76521	.	.	.	.	.	T	0.02119	0.0066	.	.	.	0.80722	D	1	P;P;P	0.48407	0.86;0.91;0.78	B;B;B	0.41271	0.352;0.294;0.192	T	0.58912	-0.7552	8	0.87932	D	0	.	11.9	0.52678	1.0:0.0:0.0:0.0	.	1;1;1	F5H6I0;A6XMH4;P61769	.;.;B2MG_HUMAN	V	1	ENSP00000437604:M1V	ENSP00000340858:M1V	M	+	1	0	B2M	42791037	0.891000	0.30450	0.406000	0.26421	0.024000	0.10985	1.849000	0.39318	2.371000	0.80710	0.533000	0.62120	ATG	.	.	none		0.612	B2M-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254007.2	NM_004048	Missense_Mutation
LAMP5	24141	hgsc.bcm.edu	37	20	9498795	9498795	+	Missense_Mutation	SNP	C	C	T	rs137866690		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:9498795C>T	ENST00000246070.2	+	5	1076	c.584C>T	c.(583-585)cCg>cTg	p.P195L	LAMP5_ENST00000427562.2_Missense_Mutation_p.P151L	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	195						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)											TCTAGTGATCCGCAGAAGACG	0.512																																					p.P195L		Atlas-SNP	.											.	.	.	.	0			c.C584T						PASS	.	T	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	129.0	104.0	112.0		452,584	2.6	0.3	20	dbSNP_134	112	0,8600		0,0,4300	no	missense,missense	C20orf103	NM_001199897.1,NM_012261.3	98,98	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign,benign	151/237,195/281	9498795	1,13005	2203	4300	6503	SO:0001583	missense	24141	exon5			GTGATCCGCAGAA	AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"""brain and dendritic cell associated LAMP"""	614641	"""chromosome 20 open reading frame 103"""	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.584C>T	20.37:g.9498795C>T	ENSP00000246070:p.Pro195Leu	Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	303	72	0.237624	NM_012261	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	c	10.44	1.351081	0.24512	2.27E-4	0.0	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.31510	1.49;1.49	5.84	2.59	0.31030	.	0.274631	0.40908	N	0.000994	T	0.12646	0.0307	N	0.14661	0.345	0.42298	D	0.992169	P;B	0.35192	0.489;0.004	B;B	0.22152	0.038;0.002	T	0.13764	-1.0497	9	.	.	.	-2.5454	7.7449	0.28862	0.5288:0.3877:0.0:0.0835	.	151;195	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	L	195;151	ENSP00000246070:P195L;ENSP00000406360:P151L	.	P	+	2	0	C20orf103	9446795	0.999000	0.42202	0.335000	0.25508	0.363000	0.29612	4.323000	0.59221	0.800000	0.34041	-0.119000	0.15052	CCG	C|1.000;T|0.000	0.000	weak		0.512	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2	NM_012261	
UBB	7314	hgsc.bcm.edu	37	17	16285542	16285542	+	Silent	SNP	G	G	A	rs17052364	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:16285542G>A	ENST00000395837.1	+	2	502	c.321G>A	c.(319-321)caG>caA	p.Q107Q	UBB_ENST00000395839.1_Silent_p.Q107Q|UBB_ENST00000535788.1_Intron|RP11-138I1.4_ENST00000583934.1_RNA|UBB_ENST00000302182.3_Silent_p.Q107Q|UBB_ENST00000578649.1_Intron	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	107	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.Q107Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CCAAGATCCAGGATAAAGAAG	0.537																																					p.Q107Q	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,NS,carcinoma,0,1	UBB	30	1	1	Substitution - coding silent(1)	lung(1)	c.G321A						scavenged	.						114.0	110.0	112.0					17																	16285542		2203	4300	6503	SO:0001819	synonymous_variant	7314	exon2			GATCCAGGATAAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.321G>A	17.37:g.16285542G>A		Somatic	440	3	0.00681818		WXS	Illumina HiSeq	Phase_I	492	6	0.0121951	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			G|0.540;A|0.460	0.460	strong		0.537	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
CRYZ	1429	hgsc.bcm.edu	37	1	75184932	75184932	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:75184932C>T	ENST00000340866.5	-	4	476	c.389G>A	c.(388-390)gGc>gAc	p.G130D	CRYZ_ENST00000417775.1_Missense_Mutation_p.G130D|CRYZ_ENST00000370872.3_Intron|CRYZ_ENST00000370871.3_Missense_Mutation_p.G130D	NM_001889.3	NP_001880.2	Q08257	QOR_HUMAN	crystallin, zeta (quinone reductase)	130					protein homotetramerization (GO:0051289)|visual perception (GO:0007601)|xenobiotic catabolic process (GO:0042178)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	mRNA 3'-UTR binding (GO:0003730)|NADPH binding (GO:0070402)|NADPH:quinone reductase activity (GO:0003960)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)	10					Dicoumarol(DB00266)	ATATGGAATGCCGATGGCAGC	0.438																																					p.G130D		Atlas-SNP	.											CRYZ,colon,carcinoma,-1,1	CRYZ	28	1	0			c.G389A						scavenged	.						150.0	140.0	143.0					1																	75184932		2203	4300	6503	SO:0001583	missense	1429	exon4			GGAATGCCGATGG		CCDS665.1, CCDS44162.1, CCDS44163.1	1p31.1	2013-02-14			ENSG00000116791	ENSG00000116791			2419	protein-coding gene	gene with protein product		123691					Standard	NM_001889		Approved		uc001dgj.3	Q08257	OTTHUMG00000009620	ENST00000340866.5:c.389G>A	1.37:g.75184932C>T	ENSP00000339399:p.Gly130Asp	Somatic	185	0	0		WXS	Illumina HiSeq	Phase_I	231	4	0.017316	NM_001130043	A6NN60|D3DQ76|Q53FT0|Q59EU7|Q5HYE7|Q6NSK9	Missense_Mutation	SNP	ENST00000340866.5	37	CCDS665.1	.	.	.	.	.	.	.	.	.	.	C	10.82	1.457699	0.26161	.	.	ENSG00000116791	ENST00000340866;ENST00000417775;ENST00000370871;ENST00000370870;ENST00000441120	T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8	5.16	4.22	0.49857	GroES-like (1);	0.207171	0.49916	D	0.000128	T	0.62073	0.2398	M	0.87038	2.855	0.48632	D	0.999688	D;D	0.76494	0.999;0.976	D;P	0.74023	0.982;0.85	T	0.69566	-0.5111	10	0.72032	D	0.01	.	10.578	0.45238	0.1498:0.7057:0.1444:0.0	.	130;130	A6NN60;Q08257	.;QOR_HUMAN	D	130	ENSP00000339399:G130D;ENSP00000399805:G130D;ENSP00000359908:G130D;ENSP00000359907:G130D;ENSP00000404289:G130D	ENSP00000339399:G130D	G	-	2	0	CRYZ	74957520	0.985000	0.35326	0.699000	0.30290	0.029000	0.11900	3.243000	0.51392	1.265000	0.44215	0.460000	0.39030	GGC	.	.	none		0.438	CRYZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026514.1		
SYT16	83851	hgsc.bcm.edu	37	14	62536400	62536400	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:62536400C>T	ENST00000430451.2	+	2	800	c.603C>T	c.(601-603)tcC>tcT	p.S201S	SYT16_ENST00000446982.2_Silent_p.S201S|RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	201					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		TTGAGATTTCCGTGTCCCGGT	0.483																																					p.S201S		Atlas-SNP	.											.	SYT16	144	.	0			c.C603T						PASS	.						169.0	159.0	162.0					14																	62536400		1932	4125	6057	SO:0001819	synonymous_variant	83851	exon2			GATTTCCGTGTCC	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.603C>T	14.37:g.62536400C>T		Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	227	50	0.220264	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	37	CCDS45121.1																																																																																			.	.	none		0.483	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
HIPK1	204851	hgsc.bcm.edu	37	1	114495495	114495495	+	Missense_Mutation	SNP	C	C	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:114495495C>G	ENST00000369558.1	+	3	1416	c.1184C>G	c.(1183-1185)gCt>gGt	p.A395G	HIPK1_ENST00000426820.2_Missense_Mutation_p.A395G|HIPK1_ENST00000369559.4_Missense_Mutation_p.A395G|HIPK1_ENST00000369553.1_5'Flank|HIPK1_ENST00000340480.4_Missense_Mutation_p.A21G|HIPK1_ENST00000369555.2_Missense_Mutation_p.A395G|HIPK1_ENST00000369554.2_Missense_Mutation_p.A395G|HIPK1_ENST00000369561.4_Missense_Mutation_p.A395G|HIPK1_ENST00000406344.1_5'Flank			Q86Z02	HIPK1_HUMAN	homeodomain interacting protein kinase 1	395	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				anterior/posterior pattern specification (GO:0009952)|definitive hemopoiesis (GO:0060216)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endothelial cell apoptotic process (GO:0072577)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|iris morphogenesis (GO:0061072)|lens induction in camera-type eye (GO:0060235)|neuron differentiation (GO:0030182)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tumor necrosis factor-mediated signaling pathway (GO:0010803)|retina layer formation (GO:0010842)|smoothened signaling pathway (GO:0007224)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|PML body (GO:0016605)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(15)|ovary(4)|prostate(2)	39	Lung SC(450;0.184)	all_cancers(81;4.5e-08)|all_epithelial(167;1.09e-07)|all_lung(203;1.53e-05)|Lung NSC(69;2.76e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TATCCTGGTGCTTCAGAATAT	0.373																																					p.A395G		Atlas-SNP	.											.	HIPK1	195	.	0			c.C1184G						PASS	.						178.0	164.0	169.0					1																	114495495		2203	4300	6503	SO:0001583	missense	204851	exon3			CTGGTGCTTCAGA	AB089957	CCDS867.1, CCDS868.1, CCDS869.1, CCDS41370.1	1p13.1	2008-02-05			ENSG00000163349	ENSG00000163349			19006	protein-coding gene	gene with protein product		608003					Standard	NM_198268		Approved	KIAA0630, Myak, MGC26642, Nbak2, MGC33446, MGC33548	uc001eem.3	Q86Z02	OTTHUMG00000011983	ENST00000369558.1:c.1184C>G	1.37:g.114495495C>G	ENSP00000358571:p.Ala395Gly	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	144	27	0.1875	NM_198268	A6NJ34|O75125|Q5SQL2|Q5SQL4|Q5SQL5|Q8IYD7|Q8NDN5|Q8NEB6|Q8TBZ1	Missense_Mutation	SNP	ENST00000369558.1	37	CCDS867.1	.	.	.	.	.	.	.	.	.	.	C	32	5.145198	0.94603	.	.	ENSG00000163349	ENST00000426820;ENST00000369559;ENST00000443627;ENST00000369554;ENST00000369555;ENST00000369558;ENST00000369561;ENST00000340480	T;T;T;T;T;T;T;T	0.66280	-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2;-0.2	5.36	5.36	0.76844	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000003	T	0.60431	0.2268	N	0.17800	0.525	0.80722	D	1	D;D	0.57571	0.98;0.975	D;P	0.63488	0.915;0.904	T	0.67348	-0.5693	10	0.66056	D	0.02	.	19.0806	0.93180	0.0:1.0:0.0:0.0	.	395;395	Q86Z02;Q86Z02-2	HIPK1_HUMAN;.	G	466;395;395;395;395;395;395;21	ENSP00000407442:A466G;ENSP00000358572:A395G;ENSP00000409673:A395G;ENSP00000358567:A395G;ENSP00000358568:A395G;ENSP00000358571:A395G;ENSP00000358574:A395G;ENSP00000340956:A21G	ENSP00000340956:A21G	A	+	2	0	HIPK1	114297018	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.792000	0.85828	2.509000	0.84616	0.650000	0.86243	GCT	.	.	none		0.373	HIPK1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000033127.1	NM_198268	
FRAS1	80144	hgsc.bcm.edu	37	4	79399181	79399181	+	Silent	SNP	C	C	T	rs371145937		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:79399181C>T	ENST00000264895.6	+	55	8504	c.8064C>T	c.(8062-8064)agC>agT	p.S2688S		NM_025074.6	NP_079350.5	Q86XX4	FRAS1_HUMAN	Fraser extracellular matrix complex subunit 1	2684	Calx-beta 2.				cell communication (GO:0007154)|embryonic limb morphogenesis (GO:0030326)|metanephros morphogenesis (GO:0003338)|morphogenesis of an epithelium (GO:0002009)|palate development (GO:0060021)|protein transport (GO:0015031)|skin development (GO:0043588)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sublamina densa (GO:0061618)	metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(5)|lung(54)|prostate(7)|skin(2)|urinary_tract(4)	103						TTAACGAGAGCGCTGGTTTTC	0.418													C|||	1	0.000199681	0.0	0.0	5008	,	,		21744	0.0		0.001	False		,,,				2504	0.0				p.S2688S		Atlas-SNP	.											.	FRAS1	779	.	0			c.C8064T						PASS	.	C		1,3763		0,1,1881	79.0	79.0	79.0		8064	-9.0	0.8	4		79	0,8244		0,0,4122	no	coding-synonymous	FRAS1	NM_025074.6		0,1,6003	TT,TC,CC		0.0,0.0266,0.0083		2688/4013	79399181	1,12007	1882	4122	6004	SO:0001819	synonymous_variant	80144	exon55			CGAGAGCGCTGGT	AB040933	CCDS54772.1	4q21.21	2014-06-25	2014-06-25		ENSG00000138759	ENSG00000138759			19185	protein-coding gene	gene with protein product		607830	"""Fraser syndrome 1"""			12766769, 3118036	Standard	NM_025074		Approved	FLJ22031, FLJ14927, KIAA1500	uc003hlb.2	Q86XX4	OTTHUMG00000160856	ENST00000264895.6:c.8064C>T	4.37:g.79399181C>T		Somatic	274	0	0		WXS	Illumina HiSeq	Phase_I	322	80	0.248447	NM_025074	A2RRR8|Q86UZ4|Q8N3U9|Q8NAU7|Q96JW7|Q9H6N9|Q9P228	Silent	SNP	ENST00000264895.6	37	CCDS54771.1	.	.	.	.	.	.	.	.	.	.	C	0.046	-1.265514	0.01433	2.66E-4	0.0	ENSG00000138759	ENST00000512123	.	.	.	5.69	-8.98	0.00754	.	.	.	.	.	T	0.63414	0.2509	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71300	-0.4634	4	.	.	.	.	17.9308	0.88996	0.0:0.524:0.0:0.476	.	.	.	.	C	917	.	.	R	+	1	0	FRAS1	79618205	0.024000	0.19004	0.770000	0.31555	0.041000	0.13682	-0.890000	0.04140	-1.654000	0.01499	-1.152000	0.01820	CGC	.	.	weak		0.418	FRAS1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ACSM6	142827	hgsc.bcm.edu	37	10	96971738	96971738	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:96971738G>T	ENST00000394005.3	+	5	868	c.859G>T	c.(859-861)Gcc>Tcc	p.A287S	C10orf129_ENST00000341686.3_Missense_Mutation_p.A287S|C10orf129_ENST00000430183.1_Missense_Mutation_p.A132S			Q6P461	ACSM6_HUMAN		287					fatty acid metabolic process (GO:0006631)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|GTP binding (GO:0005525)|metal ion binding (GO:0046872)	p.A287S(1)|p.A132S(1)		breast(1)|kidney(2)|lung(1)|pancreas(1)|prostate(1)|skin(1)	7		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		GTTCCAAGGAGCCTGTGTGTT	0.498																																					p.A287S		Atlas-SNP	.											C10orf129_ENST00000341686,extremity,malignant_melanoma,0,2	C10orf129	52	2	2	Substitution - Missense(2)	skin(2)	c.G859T						scavenged	.						199.0	171.0	180.0					10																	96971738		2203	4300	6503	SO:0001583	missense	142827	exon6			CAAGGAGCCTGTG																												ENST00000394005.3:c.859G>T	10.37:g.96971738G>T	ENSP00000377573:p.Ala287Ser	Somatic	478	29	0.0606695		WXS	Illumina HiSeq	Phase_I	514	26	0.0505837	NM_207321	A4FU95|A4IF38|Q5VZX2|Q6ZTX1	Missense_Mutation	SNP	ENST00000394005.3	37	CCDS7440.2	.	.	.	.	.	.	.	.	.	.	G	16.01	3.001602	0.54254	.	.	ENSG00000173124	ENST00000539707;ENST00000341686;ENST00000430183;ENST00000394005	T;T;T	0.50277	0.75;0.75;0.75	1.84	-0.578	0.11724	AMP-dependent synthetase/ligase (1);	.	.	.	.	T	0.49064	0.1535	L	0.48986	1.54	0.20563	N	0.999889	P	0.50710	0.938	P	0.59115	0.852	T	0.35822	-0.9773	9	0.32370	T	0.25	.	2.6332	0.04950	0.3173:0.0:0.46:0.2227	.	287	Q6P461	ACSM6_HUMAN	S	313;287;132;287	ENSP00000340296:A287S;ENSP00000400368:A132S;ENSP00000377573:A287S	ENSP00000340296:A287S	A	+	1	0	C10orf129	96961728	0.226000	0.23696	0.175000	0.22980	0.964000	0.63967	0.127000	0.15790	-0.304000	0.08843	0.454000	0.30748	GCC	.	.	none		0.498	C10orf129-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049506.2		
MUC4	4585	hgsc.bcm.edu	37	3	195505819	195505819	+	Missense_Mutation	SNP	A	A	T	rs425588		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195505819A>T	ENST00000463781.3	-	2	13091	c.12632T>A	c.(12631-12633)gTc>gAc	p.V4211D	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V4211D|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.V4211D(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)		AGTGTCGGTGACAGGAAGAGG	0.597																																					p.V4211D		Atlas-SNP	.											MUC4_ENST00000463781,trunk,malignant_melanoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	skin(1)	c.T12632A						scavenged	.						19.0	17.0	18.0					3																	195505819		688	1573	2261	SO:0001583	missense	4585	exon2			TCGGTGACAGGAA	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.12632T>A	3.37:g.195505819A>T	ENSP00000417498:p.Val4211Asp	Somatic	407	3	0.00737101		WXS	Illumina HiSeq	Phase_I	405	5	0.0123457	NM_018406	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	.	.	.	.	.	.	.	.	.	.	a	6.103	0.387345	0.11581	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37584	1.36;1.19	.	.	.	.	.	.	.	.	T	0.34803	0.0910	N	0.19112	0.55	0.21290	N	0.999739	D	0.65815	0.995	D	0.66497	0.944	T	0.16988	-1.0384	7	.	.	.	.	4.5176	0.11943	0.9993:0.0:7.0E-4:0.0	.	4083	E7ESK3	.	D	4211	ENSP00000417498:V4211D;ENSP00000420243:V4211D	.	V	-	2	0	MUC4	196990598	.	.	0.016000	0.15963	0.019000	0.09904	.	.	0.077000	0.16863	0.076000	0.15429	GTC	.	.	alt		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LTA4H	4048	hgsc.bcm.edu	37	12	96409429	96409429	+	Nonsense_Mutation	SNP	C	C	A	rs138184255	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:96409429C>A	ENST00000228740.2	-	11	1132	c.991G>T	c.(991-993)Gga>Tga	p.G331*	LTA4H_ENST00000413268.2_Nonsense_Mutation_p.G307*|LTA4H_ENST00000552789.1_Nonsense_Mutation_p.G307*|LTA4H_ENST00000548375.1_5'Flank	NM_000895.2	NP_000886.1	P09960	LKHA4_HUMAN	leukotriene A4 hydrolase	331					arachidonic acid metabolic process (GO:0019369)|inflammatory response (GO:0006954)|leukotriene biosynthetic process (GO:0019370)|leukotriene metabolic process (GO:0006691)|peptide catabolic process (GO:0043171)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|epoxide hydrolase activity (GO:0004301)|leukotriene-A4 hydrolase activity (GO:0004463)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(3)|lung(4)|skin(2)|stomach(1)	12					Captopril(DB01197)	AACAATCGTCCGCAAATGTGG	0.373											OREG0022040	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G331X		Atlas-SNP	.											.	LTA4H	38	.	0			c.G991T						PASS	.						130.0	126.0	127.0					12																	96409429		2203	4300	6503	SO:0001587	stop_gained	4048	exon11			ATCGTCCGCAAAT	BC032528	CCDS9059.1, CCDS58266.1, CCDS58267.1	12q22	2005-10-06				ENSG00000111144	3.3.2.6		6710	protein-coding gene	gene with protein product		151570				7628486	Standard	NM_000895		Approved		uc001ten.2	P09960	OTTHUMG00000170355	ENST00000228740.2:c.991G>T	12.37:g.96409429C>A	ENSP00000228740:p.Gly331*	Somatic	61	0	0	1320	WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	NM_000895	B4DNQ9|F8VV40|Q6IAT6|Q9UCT7	Nonsense_Mutation	SNP	ENST00000228740.2	37	CCDS9059.1	.	.	.	.	.	.	.	.	.	.	C	39	7.747344	0.98468	.	.	ENSG00000111144	ENST00000228740;ENST00000552789;ENST00000413268	.	.	.	6.17	6.17	0.99709	.	0.044184	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.25751	T	0.34	-23.289	20.8794	0.99867	0.0:1.0:0.0:0.0	.	.	.	.	X	331;307;307	.	ENSP00000228740:G331X	G	-	1	0	LTA4H	94933560	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.426000	0.59882	2.941000	0.99782	0.655000	0.94253	GGA	C|0.999;T|0.001	.	alt		0.373	LTA4H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408655.1	NM_000895	
RFC5	5985	hgsc.bcm.edu	37	12	118458748	118458748	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:118458748G>A	ENST00000454402.2	+	4	423	c.305G>A	c.(304-306)cGa>cAa	p.R102Q	RFC5_ENST00000392542.2_Missense_Mutation_p.R81Q|RFC5_ENST00000229043.3_Missense_Mutation_p.R17Q	NM_001206801.1|NM_007370.5	NP_001193730.1|NP_031396.1	P40937	RFC5_HUMAN	replication factor C (activator 1) 5, 36.5kDa	102					DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	DNA replication factor C complex (GO:0005663)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|endometrium(1)|large_intestine(3)|lung(3)	9	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GACATCATTCGAGGACCGATC	0.388																																					p.R102Q		Atlas-SNP	.											.	RFC5	35	.	0			c.G305A						PASS	.						149.0	135.0	140.0					12																	118458748		2203	4300	6503	SO:0001583	missense	5985	exon4			TCATTCGAGGACC		CCDS9185.1, CCDS41843.2	12q24.3	2010-04-21	2002-08-29		ENSG00000111445	ENSG00000111445		"""ATPases / AAA-type"""	9973	protein-coding gene	gene with protein product		600407	"""replication factor C (activator 1) 5 (36.5kD)"""			7774928	Standard	NM_007370		Approved	RFC36	uc001twq.3	P40937	OTTHUMG00000156438	ENST00000454402.2:c.305G>A	12.37:g.118458748G>A	ENSP00000408295:p.Arg102Gln	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	83	19	0.228916	NM_007370	A8MZ62|B3KSX8	Missense_Mutation	SNP	ENST00000454402.2	37	CCDS9185.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.488169	0.84854	.	.	ENSG00000111445	ENST00000449641;ENST00000537315;ENST00000229043;ENST00000484086;ENST00000420967;ENST00000454402;ENST00000392542	T;T;T;T;T	0.51817	0.96;0.69;0.69;0.69;1.39	5.38	4.49	0.54785	ATPase, AAA-type, core (1);ATPase, AAA+ type, core (1);	0.000000	0.85682	D	0.000000	T	0.69459	0.3113	M	0.83774	2.66	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.75020	0.978;0.985;0.985	T	0.74751	-0.3559	10	0.87932	D	0	0.7778	13.1853	0.59677	0.0783:0.0:0.9217:0.0	.	81;116;102	A8MZ62;Q59GW7;P40937	.;.;RFC5_HUMAN	Q	17;17;17;134;81;102;81	ENSP00000229043:R17Q;ENSP00000445917:R134Q;ENSP00000390340:R81Q;ENSP00000408295:R102Q;ENSP00000376325:R81Q	ENSP00000229043:R17Q	R	+	2	0	RFC5	116943131	1.000000	0.71417	0.998000	0.56505	0.461000	0.32589	9.691000	0.98679	1.270000	0.44297	-0.150000	0.13652	CGA	.	.	none		0.388	RFC5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344196.2	NM_007370	
PIWIL1	9271	hgsc.bcm.edu	37	12	130855827	130855827	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:130855827C>T	ENST00000245255.3	+	20	2700	c.2428C>T	c.(2428-2430)Cgc>Tgc	p.R810C	PIWIL1_ENST00000541480.1_3'UTR	NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	810	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				gene silencing by RNA (GO:0031047)|meiotic nuclear division (GO:0007126)|multicellular organismal development (GO:0007275)|piRNA metabolic process (GO:0034587)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		CCACATACAGCGCTTGACCTA	0.428																																					p.R810C		Atlas-SNP	.											.	PIWIL1	157	.	0			c.C2428T						PASS	.						192.0	164.0	174.0					12																	130855827		2203	4300	6503	SO:0001583	missense	9271	exon20			ATACAGCGCTTGA	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"""Argonaute/PIWI family"""	9007	protein-coding gene	gene with protein product		605571	"""piwi (Drosophila)-like 1"", ""piwi-like 1 (Drosophila)"""			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.2428C>T	12.37:g.130855827C>T	ENSP00000245255:p.Arg810Cys	Somatic	187	0	0		WXS	Illumina HiSeq	Phase_I	202	39	0.193069	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	C	17.89	3.499927	0.64298	.	.	ENSG00000125207	ENST00000245255	T	0.32515	1.45	5.45	3.49	0.39957	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.053233	0.85682	D	0.000000	T	0.52108	0.1714	M	0.81112	2.525	0.80722	D	1	P;D	0.89917	0.602;1.0	B;D	0.87578	0.178;0.998	T	0.52946	-0.8507	10	0.59425	D	0.04	-29.512	7.1092	0.25380	0.3786:0.5358:0.0:0.0856	.	810;810	Q96J94;Q96J94-2	PIWL1_HUMAN;.	C	810	ENSP00000245255:R810C	ENSP00000245255:R810C	R	+	1	0	PIWIL1	129421780	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	2.059000	0.41384	1.154000	0.42482	0.561000	0.74099	CGC	.	.	none		0.428	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1		
PBRM1	55193	hgsc.bcm.edu	37	3	52584787	52584787	+	Silent	SNP	T	T	C	rs2251219	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:52584787T>C	ENST00000296302.7	-	28	4657	c.4656A>G	c.(4654-4656)ccA>ccG	p.P1552P	SMIM4_ENST00000476842.1_Intron|PBRM1_ENST00000356770.4_Silent_p.P1465P|PBRM1_ENST00000337303.4_Silent_p.P1445P|PBRM1_ENST00000409114.3_Silent_p.P1515P|RNU6-856P_ENST00000516959.1_RNA|PBRM1_ENST00000409057.1_Silent_p.P1497P|PBRM1_ENST00000410007.1_Silent_p.P1472P|PBRM1_ENST00000409767.1_Silent_p.P1460P|PBRM1_ENST00000394830.3_Silent_p.P1445P			Q86U86	PB1_HUMAN	polybromo 1	1552	Pro-rich.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		GACTTCCACCTGGTGCTGGAG	0.468			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""								T|||	1618	0.323083	0.1452	0.4654	5008	,	,		20114	0.4296		0.4195	False		,,,				2504	0.2536				p.P1445P		Atlas-SNP	.		Rec	yes		3	3p21	55193	polybromo 1		E	.	PBRM1	1252	.	0			c.A4335G						PASS	.	T	,,	766,3640	313.0+/-292.9	65,636,1502	80.0	74.0	76.0	http://www.ncbi.nlm.nih.gov/pubmed?term	4395,4335,4335	3.5	1.0	3	dbSNP_100	76	3517,5083	512.3+/-377.9	740,2037,1523	yes	coding-synonymous,coding-synonymous,coding-synonymous	PBRM1	NM_018165.4,NM_018313.4,NM_181042.3	,,	805,2673,3025	CC,CT,TT	http://www.ncbi.nlm.nih.gov/pubmed?term	40.8953,17.3854,32.931	,,	1465/1603,1445/1583,1445/1583	52584787	4283,8723	2203	4300	6503	SO:0001819	synonymous_variant	55193	exon28			TCCACCTGGTGCT	BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.4656A>G	3.37:g.52584787T>C		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	101	5	0.049505	NM_018313	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Silent	SNP	ENST00000296302.7	37																																																																																				T|0.654;C|0.346	0.346	strong		0.468	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1	NM_018165	
SPRR3	6707	hgsc.bcm.edu	37	1	152975739	152975739	+	Silent	SNP	T	T	A	rs17851565	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:152975739T>A	ENST00000295367.4	+	2	285	c.243T>A	c.(241-243)ggT>ggA	p.G81G	SPRR3_ENST00000331860.3_Silent_p.G81G|SPRR3_ENST00000542696.1_Silent_p.G81G	NM_001097589.1	NP_001091058.1	Q9UBC9	SPRR3_HUMAN	small proline-rich protein 3	81	14 X 8 AA approximate tandem repeats.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	structural molecule activity (GO:0005198)	p.G81G(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	11	Lung NSC(65;1.49e-28)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			CTGAGCCAGGTTGTACCAAGG	0.592																																					p.G81G		Atlas-SNP	.											SPRR3,colon,carcinoma,0,4	SPRR3	45	4	1	Substitution - coding silent(1)	prostate(1)	c.T243A						scavenged	.						61.0	52.0	55.0					1																	152975739		2203	4299	6502	SO:0001819	synonymous_variant	6707	exon2			GCCAGGTTGTACC	AY118269	CCDS1033.1	1q21-q22	2008-02-05			ENSG00000163209	ENSG00000163209			11268	protein-coding gene	gene with protein product		182271				8325635	Standard	NM_005416		Approved		uc001faz.4	Q9UBC9	OTTHUMG00000013872	ENST00000295367.4:c.243T>A	1.37:g.152975739T>A		Somatic	119	1	0.00840336		WXS	Illumina HiSeq	Phase_I	90	7	0.0777778	NM_001097589	A5YKK8|B2R4G8|D3DV32|O75597|Q4ZGI7|Q5T525|Q8NET7|Q9UDG3	Silent	SNP	ENST00000295367.4	37	CCDS1033.1																																																																																			A|0.010;C|0.001;T|0.988	0.010	strong		0.592	SPRR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000038910.1	NM_005416	
CDH20	28316	hgsc.bcm.edu	37	18	59195219	59195219	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:59195219A>G	ENST00000262717.4	+	7	1435	c.1037A>G	c.(1036-1038)aAg>aGg	p.K346R	CDH20_ENST00000536675.2_Missense_Mutation_p.K346R|CDH20_ENST00000538374.1_Missense_Mutation_p.K346R			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	346	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				TTTGAAAGCAAGAAAAGCTAC	0.438																																					p.K346R		Atlas-SNP	.											.	CDH20	117	.	0			c.A1037G						PASS	.						73.0	69.0	70.0					18																	59195219		2203	4300	6503	SO:0001583	missense	28316	exon6			AAAGCAAGAAAAG	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1037A>G	18.37:g.59195219A>G	ENSP00000262717:p.Lys346Arg	Somatic	180	0	0		WXS	Illumina HiSeq	Phase_I	179	28	0.156425	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.104904	0.77096	.	.	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.49720	0.77;0.77;0.77	5.92	5.92	0.95590	Cadherin (5);Cadherin-like (1);	0.190290	0.53938	D	0.000052	T	0.54919	0.1888	L	0.45422	1.42	0.58432	D	0.999996	P	0.40476	0.718	P	0.51415	0.669	T	0.49952	-0.8884	10	0.35671	T	0.21	.	16.3526	0.83220	1.0:0.0:0.0:0.0	.	346	Q9HBT6	CAD20_HUMAN	R	346	ENSP00000444767:K346R;ENSP00000442226:K346R;ENSP00000262717:K346R	ENSP00000262717:K346R	K	+	2	0	CDH20	57346199	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.932000	0.92897	2.255000	0.74692	0.533000	0.62120	AAG	.	.	none		0.438	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
AOX1	316	hgsc.bcm.edu	37	2	201478599	201478599	+	Silent	SNP	G	G	T	rs200716526		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:201478599G>T	ENST00000374700.2	+	15	1762	c.1521G>T	c.(1519-1521)gcG>gcT	p.A507A	AOX1_ENST00000485106.1_3'UTR	NM_001159.3	NP_001150.3	Q06278	AOXA_HUMAN	aldehyde oxidase 1	507					inflammatory response (GO:0006954)|reactive oxygen species metabolic process (GO:0072593)|small molecule metabolic process (GO:0044281)|vitamin B6 metabolic process (GO:0042816)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	2 iron, 2 sulfur cluster binding (GO:0051537)|aldehyde oxidase activity (GO:0004031)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|NAD binding (GO:0051287)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)	p.A507A(1)		breast(5)|endometrium(3)|kidney(4)|large_intestine(13)|lung(38)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	81					Allopurinol(DB00437)|Aminocaproic Acid(DB00513)|Brimonidine(DB00484)|Famciclovir(DB00426)|Menadione(DB00170)|Mercaptopurine(DB01033)|Methotrexate(DB00563)|Pyrazinamide(DB00339)|Raloxifene(DB00481)|Zaleplon(DB00962)|Zonisamide(DB00909)	TGGGCTCGGCGCCAGGTGGGA	0.468													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19816	0.0		0.0	False		,,,				2504	0.0				p.A507A		Atlas-SNP	.											AOX1,NS,carcinoma,+1,3	AOX1	152	3	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G1521T						scavenged	.						95.0	92.0	93.0					2																	201478599		2203	4300	6503	SO:0001819	synonymous_variant	316	exon15			CTCGGCGCCAGGT	AF017060	CCDS33360.1	2q33	2008-05-20			ENSG00000138356	ENSG00000138356			553	protein-coding gene	gene with protein product		602841				7570184	Standard	NM_001159		Approved	AO, AOH1	uc002uvx.3	Q06278	OTTHUMG00000154536	ENST00000374700.2:c.1521G>T	2.37:g.201478599G>T		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	124	3	0.0241935	NM_001159	O14765|Q53RR8|Q53TV3|Q9BYF0|Q9UPG6	Silent	SNP	ENST00000374700.2	37	CCDS33360.1																																																																																			G|1.000;T|0.000	0.000	strong		0.468	AOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335844.1	NM_001159	
BRAF	673	hgsc.bcm.edu	37	7	140453134	140453134	+	Missense_Mutation	SNP	T	T	C	rs397516897|rs121913364|rs121913226|rs121913377		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:140453134T>C	ENST00000288602.6	-	15	1861	c.1801A>G	c.(1801-1803)Aaa>Gaa	p.K601E		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	601	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in CRC). {ECO:0000269|PubMed:12198537}.|K -> Q (in CFC1). {ECO:0000269|PubMed:19206169}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.K601E(40)|p.V600_K601>E(12)|p.T599_R603>I(2)|p.K601del(1)|p.V600_S605>EK(1)|p.V600_S605>DV(1)|p.V600_S605>D(1)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	CATCGAGATTTCACTGTAGCT	0.368		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.K601E	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,NS,malignant_melanoma,0,81	BRAF	36346	81	58	Substitution - Missense(40)|Complex - deletion inframe(17)|Deletion - In frame(1)	thyroid(30)|skin(15)|large_intestine(5)|ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|endometrium(1)|lung(1)|NS(1)	c.A1801G						PASS	.						111.0	103.0	106.0					7																	140453134		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	GAGATTTCACTGT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1801A>G	7.37:g.140453134T>C	ENSP00000288602:p.Lys601Glu	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	115	19	0.165217	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.8|23.8	4.454487|4.454487	0.84209|0.84209	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000288602|ENST00000496384	D|.	0.82711|.	-1.64|.	5.65|5.65	5.65|5.65	0.86999|0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.54464|.	0.1860|.	N|N	0.25380|0.25380	0.74|0.74	0.80722|0.80722	D|D	1|1	P|.	0.42584|.	0.784|.	P|.	0.49922|.	0.626|.	T|.	0.51108|.	-0.8747|.	10|.	0.87932|.	D|.	0|.	.|.	15.9326|15.9326	0.79675|0.79675	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	601|.	P15056|.	BRAF_HUMAN|.	E|W	601|208	ENSP00000288602:K601E|.	ENSP00000288602:K601E|.	K|X	-|-	1|3	0|0	BRAF|BRAF	140099603|140099603	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.921000|7.921000	0.87530|0.87530	2.169000|2.169000	0.68431|0.68431	0.529000|0.529000	0.55759|0.55759	AAA|TGA	.	.	weak		0.368	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
TMEM8A	58986	hgsc.bcm.edu	37	16	427516	427516	+	Silent	SNP	T	T	C	rs11649031	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:427516T>C	ENST00000431232.2	-	3	529	c.369A>G	c.(367-369)gtA>gtG	p.V123V	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	123					cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						AGGAGGGCTGTACCGCGGTGT	0.692											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2859	0.570887	0.736	0.4885	5008	,	,		15299	0.3036		0.5437	False		,,,				2504	0.7096				p.V123V		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,2	TMEM8A	49	2	0			c.A369G						scavenged	.	C		3129,1243		1125,879,182	19.0	19.0	19.0		369	-0.5	0.0	16	dbSNP_120	19	4870,3712		1419,2032,840	no	coding-synonymous	TMEM8A	NM_021259.2		2544,2911,1022	CC,CT,TT		43.2533,28.4309,38.2507		123/772	427516	7999,4955	2186	4291	6477	SO:0001819	synonymous_variant	58986	exon3			GGGCTGTACCGCG	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.369A>G	16.37:g.427516T>C		Somatic	22	1	0.0454545	588	WXS	Illumina HiSeq	Phase_I	37	15	0.405405	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Silent	SNP	ENST00000431232.2	37	CCDS10407.1																																																																																			T|0.429;C|0.571	0.571	strong		0.692	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
IGSF3	3321	hgsc.bcm.edu	37	1	117122285	117122285	+	Missense_Mutation	SNP	G	G	C	rs576658823|rs114915440	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:117122285G>C	ENST00000369486.3	-	10	3828	c.3063C>G	c.(3061-3063)gaC>gaG	p.D1021E	IGSF3_ENST00000318837.6_Missense_Mutation_p.D1041E|IGSF3_ENST00000369483.1_Missense_Mutation_p.D1041E	NM_001007237.1	NP_001007238.1	O75054	IGSF3_HUMAN	immunoglobulin superfamily, member 3	1021	Ig-like C2-type 8.				lacrimal gland development (GO:0032808)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)		p.D1041D(1)|p.D1021D(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(31)|ovary(4)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	62	Lung SC(450;0.225)	all_cancers(81;1.24e-06)|all_epithelial(167;4.85e-07)|all_lung(203;1.66e-06)|Lung NSC(69;1.11e-05)		Lung(183;0.0142)|Colorectal(144;0.0929)|LUSC - Lung squamous cell carcinoma(189;0.108)|COAD - Colon adenocarcinoma(174;0.139)|all cancers(265;0.159)|Epithelial(280;0.166)		cgtcgtcgtcgtcgtcctcct	0.632																																					p.D1041E		Atlas-SNP	.											IGSF3_ENST00000369483,NS,carcinoma,0,4	IGSF3	294	4	2	Substitution - coding silent(2)	prostate(2)	c.C3123G						scavenged	.						28.0	28.0	28.0					1																	117122285		2203	4300	6503	SO:0001583	missense	3321	exon11			GTCGTCGTCGTCC	AF031174	CCDS30813.1, CCDS30814.1	1p13	2013-01-29			ENSG00000143061	ENSG00000143061		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5950	protein-coding gene	gene with protein product		603491				9790749	Standard	NM_001007237		Approved	V8, EWI-3, MGC117164	uc031pnr.1	O75054	OTTHUMG00000022751	ENST00000369486.3:c.3063C>G	1.37:g.117122285G>C	ENSP00000358498:p.Asp1021Glu	Somatic	104	3	0.0288462		WXS	Illumina HiSeq	Phase_I	117	8	0.0683761	NM_001542	A6NJZ6|A6NMC7	Missense_Mutation	SNP	ENST00000369486.3	37	CCDS30813.1	.	.	.	.	.	.	.	.	.	.	g	0.001	-3.470330	0.00011	.	.	ENSG00000143061	ENST00000369486;ENST00000369483;ENST00000318837	T;T;T	0.02890	4.12;4.12;4.12	0.329	0.329	0.15924	Immunoglobulin subtype (1);Immunoglobulin-like (1);	0.329841	0.23883	N	0.043632	T	0.00468	0.0015	N	0.22421	0.69	0.80722	P	0.0	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.46925	-0.9156	8	0.02654	T	1	-2.9576	.	.	.	.	1021;1041	O75054;A6NJZ6	IGSF3_HUMAN;.	E	1021;1041;1041	ENSP00000358498:D1021E;ENSP00000358495:D1041E;ENSP00000321184:D1041E	ENSP00000321184:D1041E	D	-	3	2	IGSF3	116923808	0.026000	0.19158	0.036000	0.18154	0.121000	0.20230	-1.340000	0.02650	-0.471000	0.06891	-0.473000	0.04963	GAC	.	.	weak		0.632	IGSF3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000059040.1	NM_001542	
FAT3	120114	hgsc.bcm.edu	37	11	92577819	92577819	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:92577819C>T	ENST00000298047.6	+	18	11303	c.11286C>T	c.(11284-11286)caC>caT	p.H3762H	FAT3_ENST00000525166.1_Silent_p.H3612H|FAT3_ENST00000409404.2_Silent_p.H3762H|FAT3_ENST00000533797.1_Silent_p.H97H			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	3762					homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				TCGATTCCCACGCGCTCATGA	0.527										TCGA Ovarian(4;0.039)																											p.H3762H		Atlas-SNP	.											FAT3_ENST00000409404,colon,carcinoma,0,6	FAT3	1822	6	0			c.C11286T						PASS	.						101.0	100.0	101.0					11																	92577819		2143	4249	6392	SO:0001819	synonymous_variant	120114	exon18			TTCCCACGCGCTC	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.11286C>T	11.37:g.92577819C>T		Somatic	399	0	0		WXS	Illumina HiSeq	Phase_I	451	80	0.177384	NM_001008781	B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37																																																																																				.	.	none		0.527	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
MUC4	4585	hgsc.bcm.edu	37	3	195515244	195515244	+	Silent	SNP	G	G	A	rs368817935	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195515244G>A	ENST00000463781.3	-	2	3666	c.3207C>T	c.(3205-3207)caC>caT	p.H1069H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.H1069H|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	502					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.H1069H(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)		GAGGGGTGACGTGACCTGTGG	0.572													.|||	33	0.00658946	0.0008	0.0043	5008	,	,		16900	0.0188		0.005	False		,,,				2504	0.0051				p.H1069H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.C3207T						scavenged	.						30.0	20.0	23.0					3																	195515244		691	1589	2280	SO:0001819	synonymous_variant	4585	exon2			GGTGACGTGACCT	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.3207C>T	3.37:g.195515244G>A		Somatic	412	3	0.00728155		WXS	Illumina HiSeq	Phase_I	401	9	0.0224439	NM_018406	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																																																																																			.	.	weak		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
OR56B4	196335	hgsc.bcm.edu	37	11	6129720	6129720	+	Nonsense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:6129720G>T	ENST00000316529.3	+	1	807	c.712G>T	c.(712-714)Gaa>Taa	p.E238*	RP11-290F24.3_ENST00000529961.1_RNA	NM_001005181.1	NP_001005181.1	Q8NH76	O56B4_HUMAN	olfactory receptor, family 56, subfamily B, member 4	238						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.E238*(1)		NS(1)|central_nervous_system(1)|endometrium(1)|lung(10)|skin(6)|urinary_tract(2)	21		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;1.31e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GAACTCAGCAGAAGCAATGTC	0.493																																					p.E238X		Atlas-SNP	.											OR56B4,bladder,carcinoma,0,1	OR56B4	50	1	1	Substitution - Nonsense(1)	urinary_tract(1)	c.G712T						scavenged	.						175.0	157.0	163.0					11																	6129720		2201	4296	6497	SO:0001587	stop_gained	196335	exon1			TCAGCAGAAGCAA	AB065513	CCDS31406.1	11p15.4	2012-08-09			ENSG00000180919	ENSG00000180919		"""GPCR / Class A : Olfactory receptors"""	15248	protein-coding gene	gene with protein product							Standard	NM_001005181		Approved		uc010qzx.2	Q8NH76	OTTHUMG00000165531	ENST00000316529.3:c.712G>T	11.37:g.6129720G>T	ENSP00000321196:p.Glu238*	Somatic	154	0	0		WXS	Illumina HiSeq	Phase_I	153	3	0.0196078	NM_001005181	Q6IFD7	Nonsense_Mutation	SNP	ENST00000316529.3	37	CCDS31406.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.380020	0.42207	.	.	ENSG00000180919	ENST00000316529	.	.	.	4.06	3.15	0.36227	.	0.000000	0.37857	U	0.001904	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	.	12.3722	0.55261	0.0868:0.0:0.9132:0.0	.	.	.	.	X	238	.	ENSP00000321196:E238X	E	+	1	0	OR56B4	6086296	0.853000	0.29707	0.648000	0.29521	0.004000	0.04260	2.090000	0.41682	0.997000	0.38969	-0.347000	0.07816	GAA	.	.	none		0.493	OR56B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384668.1	NM_001005181	
ASUN	55726	hgsc.bcm.edu	37	12	27070328	27070328	+	Silent	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:27070328T>G	ENST00000261191.7	-	10	1562	c.1026A>C	c.(1024-1026)gtA>gtC	p.V342V	ASUN_ENST00000539625.1_Silent_p.V241V	NM_018164.2	NP_060634.2	Q9NVM9	ASUN_HUMAN	asunder spermatogenesis regulator	342					centrosome localization (GO:0051642)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|protein localization to nuclear envelope (GO:0090435)|regulation of fertilization (GO:0080154)|regulation of mitotic cell cycle (GO:0007346)|sperm motility (GO:0030317)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											GTCTACTATTTACATCTACAG	0.269																																					p.V342V		Atlas-SNP	.											.	.	.	.	0			c.A1026C						PASS	.						47.0	50.0	49.0					12																	27070328		2199	4289	6488	SO:0001819	synonymous_variant	55726	exon10			ACTATTTACATCT	AK001222	CCDS8708.1	12p12.3	2013-05-08	2013-05-08	2011-12-09	ENSG00000064102	ENSG00000064102			20174	protein-coding gene	gene with protein product	"""spermatogenesis associated 30"""	615079	"""chromosome 12 open reading frame 11"", ""asunder, spermatogenesis regulator homolog (Drosphila)"""	C12orf11		12414650, 19357193, 23097494	Standard	NM_018164		Approved	FLJ10637, NET48, Mat89Bb, SPATA30	uc001rhk.4	Q9NVM9	OTTHUMG00000169193	ENST00000261191.7:c.1026A>C	12.37:g.27070328T>G		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	168	40	0.238095	NM_018164	B4DNK1|Q86WE2|Q96HM2|Q9BTX2|Q9NTB6|Q9NVM5	Silent	SNP	ENST00000261191.7	37	CCDS8708.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.949|9.949	1.219491|1.219491	0.22373|0.22373	.|.	.|.	ENSG00000064102|ENSG00000064102	ENST00000542392|ENST00000536232	.|.	.|.	.|.	5.39|5.39	2.92|2.92	0.33932|0.33932	.|.	.|.	.|.	.|.	.|.	T|.	0.56645|.	0.1999|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.51608|.	-0.8684|.	4|.	.|.	.|.	.|.	-15.2582|-15.2582	8.0783|8.0783	0.30729|0.30729	0.0:0.0698:0.2529:0.6773|0.0:0.0698:0.2529:0.6773	.|.	.|.	.|.	.|.	Q|S	56|70	.|.	.|.	K|X	-|-	1|2	0|2	C12orf11|C12orf11	26961595|26961595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	1.034000|1.034000	0.30204|0.30204	0.948000|0.948000	0.37687|0.37687	0.477000|0.477000	0.44152|0.44152	AAA|TAA	.	.	none		0.269	ASUN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402819.1	NM_018164	
WDR18	57418	hgsc.bcm.edu	37	19	984533	984533	+	Silent	SNP	T	T	C	rs2301810	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:984533T>C	ENST00000251289.5	+	1	203	c.180T>C	c.(178-180)aaT>aaC	p.N60N	WDR18_ENST00000591997.1_Intron|WDR18_ENST00000587001.2_Silent_p.N60N	NM_024100.3	NP_077005.2	Q9BV38	WDR18_HUMAN	WD repeat domain 18	60					multicellular organismal development (GO:0007275)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|kidney(2)|lung(2)|skin(2)	7		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		TGGGCAAGAATTACATCAGCG	0.711													.|||	2246	0.448482	0.4667	0.438	5008	,	,		11366	0.3899		0.5577	False		,,,				2504	0.3793				p.N60N		Atlas-SNP	.											.	WDR18	20	.	0			c.T180C						PASS	.	C		1857,2351		456,945,703	7.0	9.0	9.0		180	3.3	1.0	19	dbSNP_100	9	4066,4176		1101,1864,1156	no	coding-synonymous	WDR18	NM_024100.3		1557,2809,1859	CC,CT,TT		49.3327,44.1302,47.5743		60/433	984533	5923,6527	2104	4121	6225	SO:0001819	synonymous_variant	57418	exon1			CAAGAATTACATC		CCDS12051.1	19p13.3	2013-01-09				ENSG00000065268		"""WD repeat domain containing"""	17956	protein-coding gene	gene with protein product	"""Involved in Processing ITS2 3 homolog (S. cerevisiae)"""					22190735	Standard	NM_024100		Approved	Ipi3	uc002lqm.1	Q9BV38		ENST00000251289.5:c.180T>C	19.37:g.984533T>C		Somatic	9	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_024100	O60390|Q9BWR2	Silent	SNP	ENST00000251289.5	37	CCDS12051.1																																																																																			T|0.552;C|0.448	0.448	strong		0.711	WDR18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458225.2		
FAM135B	51059	hgsc.bcm.edu	37	8	139164570	139164570	+	Silent	SNP	C	C	T	rs3750307	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:139164570C>T	ENST00000395297.1	-	13	2318	c.2148G>A	c.(2146-2148)ccG>ccA	p.P716P		NM_015912.3	NP_056996.2	Q49AJ0	F135B_HUMAN	family with sequence similarity 135, member B	716										NS(3)|breast(9)|endometrium(21)|kidney(5)|large_intestine(28)|liver(1)|lung(135)|ovary(9)|pancreas(1)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	238	all_epithelial(106;8.29e-14)|Lung NSC(106;6.88e-06)|all_lung(105;1.44e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0805)			TTCGAACAAACGGGTGCAAGA	0.562										HNSCC(54;0.14)			C|||	1070	0.213658	0.2057	0.1931	5008	,	,		18235	0.2321		0.173	False		,,,				2504	0.2618				p.P716P		Atlas-SNP	.											LOC51059,caecum,carcinoma,0,2	FAM135B	423	2	0			c.G2148A						scavenged	.	C		758,3178		87,584,1297	45.0	46.0	46.0		2148	-4.7	0.0	8	dbSNP_107	46	1511,6779		131,1249,2765	no	coding-synonymous	FAM135B	NM_015912.3		218,1833,4062	TT,TC,CC		18.2268,19.2581,18.5588		716/1407	139164570	2269,9957	1968	4145	6113	SO:0001819	synonymous_variant	51059	exon13			AACAAACGGGTGC	AB196635	CCDS6375.2	8q24.23	2008-11-05			ENSG00000147724	ENSG00000147724			28029	protein-coding gene	gene with protein product						8619474, 9110174	Standard	NM_015912		Approved	C8ORFK32	uc003yuy.3	Q49AJ0	OTTHUMG00000149864	ENST00000395297.1:c.2148G>A	8.37:g.139164570C>T		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	151	2	0.013245	NM_015912	B5MDB3|O95879|Q2WGJ7|Q3KP46	Silent	SNP	ENST00000395297.1	37	CCDS6375.2																																																																																			C|0.791;N|0.000	.	strong		0.562	FAM135B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313590.3	NM_015912	
TRIOBP	11078	hgsc.bcm.edu	37	22	38119902	38119902	+	Missense_Mutation	SNP	A	A	G	rs537300122	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:38119902A>G	ENST00000406386.3	+	7	1594	c.1339A>G	c.(1339-1341)Aca>Gca	p.T447A		NM_001039141.2	NP_001034230.1	Q9H2D6	TARA_HUMAN	TRIO and F-actin binding protein	447					actin modification (GO:0030047)|barbed-end actin filament capping (GO:0051016)|mitotic nuclear division (GO:0007067)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	actin filament binding (GO:0051015)|GTP-Rho binding (GO:0017049)|myosin II binding (GO:0045159)|ubiquitin protein ligase binding (GO:0031625)	p.T447A(3)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12	Melanoma(58;0.0574)					CAGTAGAGCTACACGAGACAA	0.587													A|||	50	0.00998403	0.0	0.0029	5008	,	,		19561	0.0337		0.0119	False		,,,				2504	0.002				p.T447A		Atlas-SNP	.											TRIOBP_ENST00000344404,NS,carcinoma,0,4	TRIOBP	262	4	3	Substitution - Missense(3)	prostate(2)|skin(1)	c.A1339G						scavenged	.						60.0	64.0	63.0					22																	38119902		1870	4095	5965	SO:0001583	missense	11078	exon7			AGAGCTACACGAG	AB051449	CCDS33644.1, CCDS43015.1, CCDS43016.1	22q13.1	2014-06-03			ENSG00000100106	ENSG00000100106		"""Pleckstrin homology (PH) domain containing"""	17009	protein-coding gene	gene with protein product		609761		DFNB28		11148140, 16385457, 16385458	Standard	NM_001039141		Approved	HRIHFB2122, KIAA1662, Tara, TAP68	uc003atr.3	Q9H2D6	OTTHUMG00000150657	ENST00000406386.3:c.1339A>G	22.37:g.38119902A>G	ENSP00000384312:p.Thr447Ala	Somatic	238	1	0.00420168		WXS	Illumina HiSeq	Phase_I	296	4	0.0135135	NM_001039141	B1AHD4|B1AHD7|F2Z2W0|F8W6V6|O94797|Q2PZW8|Q2Q3Z9|Q2Q400|Q5R3M6|Q96DW1|Q9BT77|Q9BTL7|Q9BY98|Q9Y3L4	Missense_Mutation	SNP	ENST00000406386.3	37	CCDS43015.1	.	.	.	.	.	.	.	.	.	.	A	5.040	0.193024	0.09599	.	.	ENSG00000100106	ENST00000406386;ENST00000417174	T	0.19806	2.12	2.54	2.54	0.30619	.	.	.	.	.	T	0.23727	0.0574	L	0.36672	1.1	0.19945	N	0.999945	P	0.52463	0.953	P	0.53988	0.739	T	0.07558	-1.0766	9	0.30854	T	0.27	.	6.7436	0.23449	1.0:0.0:0.0:0.0	.	447	Q9H2D6	TARA_HUMAN	A	447	ENSP00000384312:T447A	ENSP00000384312:T447A	T	+	1	0	TRIOBP	36449848	0.000000	0.05858	0.003000	0.11579	0.005000	0.04900	-0.062000	0.11674	1.059000	0.40554	0.113000	0.15668	ACA	.	.	none		0.587	TRIOBP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319439.2		
SCUBE1	80274	hgsc.bcm.edu	37	22	43600118	43600118	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:43600118G>A	ENST00000360835.4	-	22	2978	c.2852C>T	c.(2851-2853)gCg>gTg	p.A951V		NM_173050.3	NP_766638.2	Q8IWY4	SCUB1_HUMAN	signal peptide, CUB domain, EGF-like 1	951					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|post-embryonic development (GO:0009791)|protein homooligomerization (GO:0051260)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extrinsic component of plasma membrane (GO:0019897)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|protein heterodimerization activity (GO:0046982)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(4)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31		all_neural(38;0.0414)|Ovarian(80;0.07)				CTGGGGATGCGCCAGCACGTC	0.567																																					p.A951V		Atlas-SNP	.											.	SCUBE1	105	.	0			c.C2852T						PASS	.						157.0	140.0	146.0					22																	43600118		2203	4300	6503	SO:0001583	missense	80274	exon22			GGATGCGCCAGCA		CCDS14048.1	22q13	2008-07-01			ENSG00000159307	ENSG00000159307			13441	protein-coding gene	gene with protein product		611746				11087664	Standard	NM_173050		Approved		uc003bdt.2	Q8IWY4	OTTHUMG00000150679	ENST00000360835.4:c.2852C>T	22.37:g.43600118G>A	ENSP00000354080:p.Ala951Val	Somatic	212	0	0		WXS	Illumina HiSeq	Phase_I	192	46	0.239583	NM_173050	Q5R336	Missense_Mutation	SNP	ENST00000360835.4	37	CCDS14048.1	.	.	.	.	.	.	.	.	.	.	G	31	5.082468	0.94050	.	.	ENSG00000159307	ENST00000360835;ENST00000381243	D	0.88586	-2.4	3.95	3.95	0.45737	.	0.000000	0.85682	D	0.000000	D	0.90584	0.7048	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92328	0.5871	10	0.87932	D	0	.	16.5437	0.84408	0.0:0.0:1.0:0.0	.	951	Q8IWY4	SCUB1_HUMAN	V	951;581	ENSP00000354080:A951V	ENSP00000354080:A951V	A	-	2	0	SCUBE1	41930062	1.000000	0.71417	0.948000	0.38648	0.976000	0.68499	9.514000	0.98013	2.204000	0.70986	0.591000	0.81541	GCG	.	.	none		0.567	SCUBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319582.3	NM_173050	
SLX4IP	128710	hgsc.bcm.edu	37	20	10603706	10603706	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:10603706G>A	ENST00000334534.5	+	8	1086	c.906G>A	c.(904-906)gcG>gcA	p.A302A		NM_001009608.1	NP_001009608.1	Q5VYV7	SLX4I_HUMAN	SLX4 interacting protein	302																	GCAGCTCTGCGGAAGACTTCG	0.507																																					p.A302A		Atlas-SNP	.											.	.	.	.	0			c.G906A						PASS	.						89.0	99.0	96.0					20																	10603706		2203	4300	6503	SO:0001819	synonymous_variant	128710	exon8			CTCTGCGGAAGAC	AL035456	CCDS33439.1	20p12	2012-10-30	2012-10-30	2012-10-30	ENSG00000149346	ENSG00000149346			16225	protein-coding gene	gene with protein product		615958	"""chromosome 20 open reading frame 94"""	C20orf94		19596235	Standard	XM_005260664		Approved	dJ1099D15.3	uc010zre.2	Q5VYV7	OTTHUMG00000031873	ENST00000334534.5:c.906G>A	20.37:g.10603706G>A		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	71	11	0.15493	NM_001009608	Q05CG2|Q05CT9	Silent	SNP	ENST00000334534.5	37	CCDS33439.1																																																																																			.	.	none		0.507	SLX4IP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078000.3	NM_001009608	
CROCC	9696	hgsc.bcm.edu	37	1	17265560	17265560	+	Missense_Mutation	SNP	C	C	T	rs9435793	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:17265560C>T	ENST00000375541.5	+	12	1600	c.1531C>T	c.(1531-1533)Ccc>Tcc	p.P511S	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		CCGCCGAGGCCCCTCCCCGGC	0.731																																					p.P511S		Atlas-SNP	.											CROCC,NS,carcinoma,0,1	CROCC	185	1	0			c.C1531T						scavenged	.						6.0	6.0	6.0					1																	17265560		2007	3902	5909	SO:0001583	missense	9696	exon12			CGAGGCCCCTCCC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1531C>T	1.37:g.17265560C>T	ENSP00000364691:p.Pro511Ser	Somatic	3	1	0.333333		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_014675		Missense_Mutation	SNP	ENST00000375541.5	37	CCDS30616.1	781	0.3576007326007326	171	0.3475609756097561	123	0.3397790055248619	240	0.4195804195804196	247	0.3258575197889182	C	11.08	1.532985	0.27387	.	.	ENSG00000058453	ENST00000375541;ENST00000445545	T	0.09255	3.0	5.39	4.42	0.53409	.	.	.	.	.	T	0.00012	0.0000	N	0.24115	0.695	0.28995	N	0.887822	B;B;P	0.38504	0.007;0.001;0.634	B;B;B	0.41813	0.013;0.002;0.367	T	0.40213	-0.9575	9	0.07644	T	0.81	.	8.3381	0.32228	0.0:0.7587:0.1582:0.0831	rs9435793;rs58724462	374;374;511	A1L0S8;A1L0S9;Q5TZA2	.;.;CROCC_HUMAN	S	511;392	ENSP00000364691:P511S	ENSP00000364691:P511S	P	+	1	0	CROCC	17138147	0.959000	0.32827	1.000000	0.80357	0.963000	0.63663	1.779000	0.38624	2.702000	0.92279	0.561000	0.74099	CCC	C|0.643;T|0.357	0.357	strong		0.731	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
UBA6	55236	hgsc.bcm.edu	37	4	68514904	68514904	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:68514904T>C	ENST00000322244.5	-	14	1189	c.1130A>G	c.(1129-1131)cAt>cGt	p.H377R		NM_018227.5	NP_060697.4	A0AVT1	UBA6_HUMAN	ubiquitin-like modifier activating enzyme 6	377					protein ubiquitination (GO:0016567)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|FAT10 activating enzyme activity (GO:0019780)|ligase activity (GO:0016874)			central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(6)|liver(1)|lung(23)|skin(2)|upper_aerodigestive_tract(2)	44						AGAGAGCCAATGCACAATGTC	0.388																																					p.H377R		Atlas-SNP	.											.	UBA6	98	.	0			c.A1130G						PASS	.						94.0	95.0	95.0					4																	68514904		2203	4300	6503	SO:0001583	missense	55236	exon14			AGCCAATGCACAA	AK094164	CCDS3516.1	4q13.2	2008-02-05	2007-11-30	2007-11-30	ENSG00000033178	ENSG00000033178		"""Ubiquitin-like modifier activating enzymes"""	25581	protein-coding gene	gene with protein product	"""UBA6, ubiquitin-activating enzyme E1"""	611361	"""ubiquitin-activating enzyme E1-like 2"""	UBE1L2		17580310	Standard	NM_018227		Approved	FLJ10808	uc003hdg.4	A0AVT1	OTTHUMG00000129299	ENST00000322244.5:c.1130A>G	4.37:g.68514904T>C	ENSP00000313454:p.His377Arg	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	197	55	0.279188	NM_018227	A6N8M7|B2RAV3|Q4W5K0|Q6UV21|Q86T78|Q86TC7|Q8N5T3|Q8N9E4|Q9H3T7|Q9NVC9	Missense_Mutation	SNP	ENST00000322244.5	37	CCDS3516.1	.	.	.	.	.	.	.	.	.	.	T	0.007	-1.995347	0.00435	.	.	ENSG00000033178	ENST00000322244	T	0.54866	0.55	5.08	-3.06	0.05379	Molybdenum cofactor biosynthesis, MoeB (1);NAD(P)-binding domain (1);	0.635180	0.16937	N	0.193439	T	0.13500	0.0327	N	0.00272	-1.73	0.58432	D	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.46665	-0.9175	10	0.02654	T	1	-0.5102	14.018	0.64536	0.0:0.1147:0.0:0.8853	.	377	A0AVT1	UBA6_HUMAN	R	377	ENSP00000313454:H377R	ENSP00000313454:H377R	H	-	2	0	UBA6	68197499	0.396000	0.25262	0.545000	0.28153	0.083000	0.17756	0.448000	0.21726	-0.758000	0.04690	-0.425000	0.05940	CAT	.	.	none		0.388	UBA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251429.2	NM_018227	
PRDM16	63976	hgsc.bcm.edu	37	1	3328358	3328358	+	Missense_Mutation	SNP	T	T	C	rs870124	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:3328358T>C	ENST00000270722.5	+	9	1646	c.1597T>C	c.(1597-1599)Tcg>Ccg	p.S533P	PRDM16_ENST00000378391.2_Missense_Mutation_p.S533P|PRDM16_ENST00000442529.2_Missense_Mutation_p.S533P|PRDM16_ENST00000511072.1_Missense_Mutation_p.S534P|PRDM16_ENST00000378398.3_Missense_Mutation_p.S534P|PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000441472.2_Missense_Mutation_p.S533P|PRDM16_ENST00000514189.1_Missense_Mutation_p.S534P			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	533	Pro-rich.		S -> P (in dbSNP:rs870124). {ECO:0000269|PubMed:11050005, ECO:0000269|PubMed:11214970, ECO:0000269|PubMed:15489334}.		brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		ACCTCCCACATCGCTGCTCAA	0.687			T	EVI1	"""MDS, AML"""								C|||	4733	0.945088	0.9924	0.9006	5008	,	,		12650	0.998		0.8419	False		,,,				2504	0.9642				p.S533P		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	.	PRDM16	147	.	0			c.T1597C						PASS	.	C	PRO/SER,PRO/SER	3759,127		1817,125,1	63.0	80.0	75.0		1597,1597	5.3	0.9	1	dbSNP_86	75	6902,1358		2895,1112,123	yes	missense,missense	PRDM16	NM_199454.2,NM_022114.3	74,74	4712,1237,124	CC,CT,TT		16.4407,3.2681,12.2262	benign,benign	533/1258,533/1277	3328358	10661,1485	1943	4130	6073	SO:0001583	missense	63976	exon9			CCCACATCGCTGC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.1597T>C	1.37:g.3328358T>C	ENSP00000270722:p.Ser533Pro	Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	10	6	0.6	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	2025	0.9271978021978022	489	0.9939024390243902	315	0.8701657458563536	572	1.0	649	0.8562005277044855	C	2.636	-0.285273	0.05605	0.967319	0.835593	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.06068	3.38;3.4;3.41;3.42;3.42;3.4;3.41;3.35;3.35	5.33	5.33	0.75918	.	0.128883	0.33023	N	0.005363	T	0.00012	0.0000	N	0.02539	-0.55	0.37301	P	0.09128199999999997	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.40646	-0.9552	9	0.15952	T	0.53	.	14.274	0.66167	0.0:0.928:0.0:0.072	rs870124;rs58280858;rs870124	533;533;533;533	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	P	534;534;533;533;533;534;533;349;349;342	ENSP00000426975:S534P;ENSP00000367651:S534P;ENSP00000407968:S533P;ENSP00000405253:S533P;ENSP00000367643:S533P;ENSP00000421400:S534P;ENSP00000270722:S533P;ENSP00000422504:S349P;ENSP00000425796:S342P	ENSP00000270722:S533P	S	+	1	0	PRDM16	3318218	0.373000	0.25073	0.893000	0.35052	0.878000	0.50629	1.977000	0.40589	1.290000	0.44636	-0.172000	0.13284	TCG	T|0.095;G|0.001	.	strong		0.687	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
TROAP	10024	hgsc.bcm.edu	37	12	49724403	49724403	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:49724403A>G	ENST00000257909.3	+	13	1851	c.1775A>G	c.(1774-1776)tAc>tGc	p.Y592C	TROAP_ENST00000547923.1_Intron|TROAP_ENST00000551245.1_Missense_Mutation_p.Y592C	NM_005480.3	NP_005471.3	Q12815	TROAP_HUMAN	trophinin associated protein	592	4 X 33 AA approximate tandem repeats.|Cys-rich.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(14)|ovary(1)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	32						CTAGAGTCCTACTGTAGGATT	0.617																																					p.Y592C		Atlas-SNP	.											TROAP,bladder,carcinoma,0,3	TROAP	80	3	0			c.A1775G						scavenged	.						72.0	70.0	71.0					12																	49724403		2203	4300	6503	SO:0001583	missense	10024	exon13			AGTCCTACTGTAG	U04810	CCDS8784.1, CCDS41779.1, CCDS61117.1	12q13.12	2012-10-17	2012-10-17		ENSG00000135451	ENSG00000135451			12327	protein-coding gene	gene with protein product	"""tastin"""	603872				7758945	Standard	NM_005480		Approved	TASTIN	uc001rtx.4	Q12815	OTTHUMG00000169486	ENST00000257909.3:c.1775A>G	12.37:g.49724403A>G	ENSP00000257909:p.Tyr592Cys	Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	150	5	0.0333333	NM_005480	F8VSF9|Q6PJU7|Q8N5B2	Missense_Mutation	SNP	ENST00000257909.3	37	CCDS8784.1	.	.	.	.	.	.	.	.	.	.	a	5.880	0.346480	0.11126	.	.	ENSG00000135451	ENST00000551245;ENST00000257909	.	.	.	3.34	-3.85	0.04243	.	1.490010	0.03952	N	0.288732	T	0.09069	0.0224	N	0.00841	-1.15	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18272	-1.0342	9	0.28530	T	0.3	7.0657	4.9225	0.13876	0.4025:0.2764:0.321:0.0	.	592;592	F8W130;Q12815	.;TROAP_HUMAN	C	592	.	ENSP00000257909:Y592C	Y	+	2	0	TROAP	48010670	0.904000	0.30761	0.000000	0.03702	0.008000	0.06430	-0.239000	0.08965	-0.648000	0.05437	-1.237000	0.01550	TAC	.	.	none		0.617	TROAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404300.1	NM_005480	
IL3	3562	hgsc.bcm.edu	37	5	131396478	131396478	+	Missense_Mutation	SNP	C	C	T	rs40401	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:131396478C>T	ENST00000296870.2	+	1	257	c.79C>T	c.(79-81)Ccc>Tcc	p.P27S		NM_000588.3	NP_000579.2	P08700	IL3_HUMAN	interleukin 3	27			P -> S (in dbSNP:rs40401). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:2544122, ECO:0000269|Ref.4}.		cell-cell signaling (GO:0007267)|embryonic hemopoiesis (GO:0035162)|immune response (GO:0006955)|nervous system development (GO:0007399)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-3 receptor binding (GO:0005135)			central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)	10		all_cancers(142;7.42e-12)|Lung NSC(810;4.25e-07)|all_lung(232;1.93e-06)|Prostate(281;0.00741)|Breast(839;0.0544)|Lung SC(612;0.122)|Ovarian(839;0.223)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	GBM - Glioblastoma multiforme(465;0.0161)|Lung(113;0.105)	Amlexanox(DB01025)	CCAGACAACGCCCTTGAAGAC	0.537													T|||	2101	0.419529	0.5703	0.3156	5008	,	,		21475	0.5714		0.2515	False		,,,				2504	0.3057				p.P27S		Atlas-SNP	.											IL3,NS,carcinoma,0,1	IL3	28	1	0			c.C79T						scavenged	.	T	SER/PRO	2268,2138	578.4+/-384.7	588,1092,523	100.0	97.0	98.0		79	1.2	0.0	5	dbSNP_76	98	1951,6649	725.2+/-406.5	226,1499,2575	yes	missense	IL3	NM_000588.3	74	814,2591,3098	TT,TC,CC		22.686,48.5247,32.4389	benign	27/153	131396478	4219,8787	2203	4300	6503	SO:0001583	missense	3562	exon1			ACAACGCCCTTGA	M14743	CCDS4149.1	5q23-q31	2014-04-04	2014-04-04		ENSG00000164399	ENSG00000164399		"""Interleukins and interleukin receptors"""	6011	protein-coding gene	gene with protein product	"""multilineage-colony-stimulating factor"", ""hematopoietic growth factor"", ""P-cell stimulating factor"", ""mast-cell growth factor"", ""colony-stimulating factor, multiple"""	147740	"""interleukin 3 (colony-stimulating factor, multiple)"""			3489530	Standard	NM_000588		Approved	IL-3, MULTI-CSF, MCGF, MGC79398, MGC79399	uc003kwe.1	P08700	OTTHUMG00000059640	ENST00000296870.2:c.79C>T	5.37:g.131396478C>T	ENSP00000296870:p.Pro27Ser	Somatic	189	1	0.00529101		WXS	Illumina HiSeq	Phase_I	207	5	0.0241546	NM_000588	Q6GS87	Missense_Mutation	SNP	ENST00000296870.2	37	CCDS4149.1	911	0.41712454212454214	291	0.5914634146341463	100	0.27624309392265195	319	0.5576923076923077	201	0.26517150395778366	T	0.343	-0.949559	0.02304	0.514753	0.22686	ENSG00000164399	ENST00000296870	T	0.26373	1.74	3.24	1.18	0.20946	.	1.255760	0.05782	N	0.608778	T	0.00012	0.0000	N	0.24115	0.695	0.80722	P	0.0	B	0.18968	0.032	B	0.20577	0.03	T	0.43766	-0.9371	9	0.07644	T	0.81	-2.5392	6.6006	0.22699	0.0:0.6449:0.2355:0.1196	rs40401;rs657709;rs3181636;rs52803049;rs59548569;rs40401	27	P08700	IL3_HUMAN	S	27	ENSP00000296870:P27S	ENSP00000296870:P27S	P	+	1	0	IL3	131424377	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-5.640000	0.00108	0.009000	0.14813	-0.834000	0.03071	CCC	C|0.616;N|0.000	.	strong		0.537	IL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132639.1	NM_000588	
FGGY	55277	hgsc.bcm.edu	37	1	60223665	60223665	+	Splice_Site	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:60223665G>T	ENST00000303721.7	+	15	1748		c.e15+1		FGGY_ENST00000371210.1_Splice_Site|FGGY_ENST00000371218.4_Splice_Site|FGGY_ENST00000371212.1_Splice_Site|RP4-782L23.2_ENST00000443012.1_RNA	NM_018291.3	NP_060761.3	Q96C11	FGGY_HUMAN	FGGY carbohydrate kinase domain containing						carbohydrate metabolic process (GO:0005975)|cell death (GO:0008219)|neuron cellular homeostasis (GO:0070050)		kinase activity (GO:0016301)|phosphotransferase activity, alcohol group as acceptor (GO:0016773)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	22	all_cancers(7;7.36e-05)					AGGATAAAAAGTAAGTGTGTA	0.378																																					.		Atlas-SNP	.											.	FGGY	99	.	0			c.1646+1G>T						PASS	.						95.0	91.0	92.0					1																	60223665		2203	4300	6503	SO:0001630	splice_region_variant	55277	exon16			TAAAAAGTAAGTG		CCDS611.2, CCDS44155.1, CCDS58003.1, CCDS60155.1	1p32.1	2008-10-23			ENSG00000172456	ENSG00000172456			25610	protein-coding gene	gene with protein product		611370				17671248	Standard	NM_018291		Approved	FLJ10986	uc009wac.3	Q96C11	OTTHUMG00000008424	ENST00000303721.7:c.1574+1G>T	1.37:g.60223665G>T		Somatic	80	0	0		WXS	Illumina HiSeq	Phase_I	73	9	0.123288	NM_001113411	B1AK92|B1AK93|B1AK94|B2RDR8|D3DQ56|Q9HA63|Q9NV20	Splice_Site	SNP	ENST00000303721.7	37	CCDS611.2	.	.	.	.	.	.	.	.	.	.	G	11.53	1.665493	0.29604	.	.	ENSG00000172456	ENST00000371218;ENST00000303721;ENST00000371212;ENST00000371210	.	.	.	5.09	5.09	0.68999	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3446	0.74327	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	FGGY	59996253	1.000000	0.71417	1.000000	0.80357	0.229000	0.25112	5.100000	0.64560	2.646000	0.89796	0.563000	0.77884	.	.	.	none		0.378	FGGY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023210.2	NM_001113411	Intron
COL6A5	256076	hgsc.bcm.edu	37	3	130128909	130128909	+	Missense_Mutation	SNP	A	A	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:130128909A>T	ENST00000432398.2	+	19	5093	c.4599A>T	c.(4597-4599)caA>caT	p.Q1533H	COL6A5_ENST00000265379.6_Missense_Mutation_p.Q1533H	NM_153264.5	NP_694996.5	A8TX70	CO6A5_HUMAN	collagen, type VI, alpha 5	1533	Triple-helical region.				cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				endometrium(6)|kidney(4)|large_intestine(8)|lung(19)|pancreas(2)|prostate(3)|stomach(1)|urinary_tract(1)	44						AAGGAGAACAAGGAAGACAAG	0.308																																					p.Q1533H		Atlas-SNP	.											.	COL6A5	205	.	0			c.A4599T						PASS	.						209.0	209.0	209.0					3																	130128909		692	1591	2283	SO:0001583	missense	256076	exon19			AGAACAAGGAAGA	AK093199		3q21.3	2013-01-16	2010-05-24	2010-05-24	ENSG00000172752	ENSG00000172752		"""Collagens"""	26674	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 4"""	611916	"""collagen, type XXIX, alpha 1"""	COL29A1		17850181	Standard	NM_153264		Approved	FLJ35880, VWA4	uc010htk.2	A8TX70	OTTHUMG00000159712	ENST00000432398.2:c.4599A>T	3.37:g.130128909A>T	ENSP00000390895:p.Gln1533His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	78	16	0.205128	NM_153264	A9J6L2|A9J6L4|A9J6L6|A9J6L7|A9J6M0|A9J6M1|A9J6M2|B5MEA7|Q6ZW26|Q8NA36	Missense_Mutation	SNP	ENST00000432398.2	37		.	.	.	.	.	.	.	.	.	.	A	12.46	1.945999	0.34377	.	.	ENSG00000172752	ENST00000432398;ENST00000265379	D;D	0.93307	-3.2;-3.2	5.52	5.52	0.82312	.	.	.	.	.	D	0.92192	0.7524	M	0.68728	2.09	0.27514	N	0.951595	B	0.23540	0.087	B	0.23852	0.049	D	0.86368	0.1721	9	0.45353	T	0.12	.	13.4845	0.61357	1.0:0.0:0.0:0.0	.	1533	A8TX70-2	.	H	1533	ENSP00000390895:Q1533H;ENSP00000265379:Q1533H	ENSP00000265379:Q1533H	Q	+	3	2	COL6A5	131611599	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	2.344000	0.44010	2.236000	0.73375	0.528000	0.53228	CAA	.	.	none		0.308	COL6A5-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_153264	
CHST9	83539	hgsc.bcm.edu	37	18	24496569	24496569	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:24496569T>C	ENST00000284224.8	-	6	1263	c.986A>G	c.(985-987)aAg>aGg	p.K329R	CHST9_ENST00000580774.1_3'UTR|AQP4-AS1_ENST00000579964.1_RNA|AQP4-AS1_ENST00000568797.1_RNA|AQP4-AS1_ENST00000582605.1_RNA|CHST9_ENST00000581714.1_Missense_Mutation_p.K329R|AQP4-AS1_ENST00000578701.1_RNA	NM_031422.5	NP_113610.2	Q7L1S5	CHST9_HUMAN	carbohydrate (N-acetylgalactosamine 4-0) sulfotransferase 9	329					carbohydrate biosynthetic process (GO:0016051)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|hormone biosynthetic process (GO:0042446)|proteoglycan biosynthetic process (GO:0030166)|small molecule metabolic process (GO:0044281)|sulfur compound metabolic process (GO:0006790)	extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	N-acetylgalactosamine 4-O-sulfotransferase activity (GO:0001537)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(7)|ovary(2)|pancreas(1)|skin(3)	28	all_lung(6;0.0145)|Ovarian(20;0.124)					CTCTTTGAACTTGACTCCAGA	0.418																																					p.K329R		Atlas-SNP	.											CHST9_ENST00000284224,NS,carcinoma,0,2	CHST9	114	2	0			c.A986G						scavenged	.						142.0	137.0	138.0					18																	24496569		1904	4110	6014	SO:0001583	missense	83539	exon6			TTGAACTTGACTC	AF239821	CCDS42422.1, CCDS58618.1	18q11.2	2011-04-28			ENSG00000154080	ENSG00000154080		"""Sulfotransferases, membrane-bound"""	19898	protein-coding gene	gene with protein product		610191				11139592, 11445554	Standard	NM_031422		Approved	GALNAC4ST-2, GALNAC-4-ST2	uc002kwe.4	Q7L1S5		ENST00000284224.8:c.986A>G	18.37:g.24496569T>C	ENSP00000284224:p.Lys329Arg	Somatic	148	1	0.00675676		WXS	Illumina HiSeq	Phase_I	209	47	0.22488	NM_031422	Q6UX69|Q9BXH3|Q9BXH4|Q9BZW9	Missense_Mutation	SNP	ENST00000284224.8	37	CCDS42422.1	.	.	.	.	.	.	.	.	.	.	T	1.905	-0.452082	0.04540	.	.	ENSG00000154080	ENST00000284224	T	0.73258	-0.73	6.17	2.49	0.30216	.	0.214382	0.41938	N	0.000787	T	0.49321	0.1550	N	0.13043	0.29	0.80722	D	1	B	0.06786	0.001	B	0.15052	0.012	T	0.30119	-0.9989	10	0.07813	T	0.8	-12.2193	13.2521	0.60057	0.0:0.1491:0.0:0.8509	.	329	Q7L1S5	CHST9_HUMAN	R	329	ENSP00000284224:K329R	ENSP00000284224:K329R	K	-	2	0	CHST9	22750567	0.999000	0.42202	0.993000	0.49108	0.700000	0.40528	1.620000	0.36976	-0.021000	0.14009	-1.715000	0.00711	AAG	.	.	none		0.418	CHST9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446549.1	NM_031422	
MUC4	4585	hgsc.bcm.edu	37	3	195475799	195475799	+	Silent	SNP	C	C	T	rs3205933	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195475799C>T	ENST00000346145.4	-	23	3339	c.3300G>A	c.(3298-3300)caG>caA	p.Q1100Q	MUC4_ENST00000349607.4_Silent_p.Q1049Q|MUC4_ENST00000463781.3_Silent_p.Q5336Q|MUC4_ENST00000475231.1_Silent_p.Q5284Q	NM_004532.5	NP_004523.3	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	2093					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)		TGGGCAGGTGCTGGCACTGGC	0.652													.|||	266	0.053115	0.0151	0.072	5008	,	,		26136	0.001		0.1382	False		,,,				2504	0.0573				p.Q5336Q		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,0,3	MUC4	1505	3	0			c.G16008A						scavenged	.	C	,,	128,4278		0,128,2075	57.0	54.0	55.0		3300,16008,3147	3.2	1.0	3	dbSNP_105	55	1093,7507		7,1079,3214	no	coding-synonymous,coding-synonymous,coding-synonymous	MUC4	NM_004532.5,NM_018406.6,NM_138297.4	,,	7,1207,5289	TT,TC,CC		12.7093,2.9051,9.388	,,	1100/1177,5336/5413,1049/1126	195475799	1221,11785	2203	4300	6503	SO:0001819	synonymous_variant	4585	exon24			CAGGTGCTGGCAC	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	ENST00000346145.4:c.3300G>A	3.37:g.195475799C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	65	3	0.0461538	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000346145.4	37	CCDS3310.1																																																																																			C|0.917;T|0.083	0.083	strong		0.652	MUC4-015	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341862.1	NM_018406	
MUC6	4588	hgsc.bcm.edu	37	11	1017316	1017316	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:1017316G>T	ENST00000421673.2	-	31	5535	c.5485C>A	c.(5485-5487)Cca>Aca	p.P1829T		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1829	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GGGTGTGATGGGGTTGGATAG	0.547																																					p.P1829T		Atlas-SNP	.											MUC6_ENST00000421673,right_upper_lobe,carcinoma,+1,2	MUC6	408	2	0			c.C5485A						scavenged	.																																			SO:0001583	missense	4588	exon31			GTGATGGGGTTGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5485C>A	11.37:g.1017316G>T	ENSP00000406861:p.Pro1829Thr	Somatic	1645	57	0.0346505		WXS	Illumina HiSeq	Phase_I	1796	82	0.045657	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	10.38	1.335327	0.24253	.	.	ENSG00000184956	ENST00000421673	T	0.24723	1.84	3.21	-0.343	0.12632	.	.	.	.	.	T	0.30355	0.0762	L	0.52126	1.63	0.09310	N	1	D	0.54964	0.969	P	0.61477	0.889	T	0.17531	-1.0366	9	0.02654	T	1	.	7.2552	0.26173	0.0:0.2939:0.4065:0.2996	.	1829	Q6W4X9	MUC6_HUMAN	T	1829	ENSP00000406861:P1829T	ENSP00000406861:P1829T	P	-	1	0	MUC6	1007316	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	-0.664000	0.05292	-0.177000	0.10690	0.313000	0.20887	CCA	.	.	none		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
OR4E2	26686	hgsc.bcm.edu	37	14	22134018	22134018	+	Missense_Mutation	SNP	C	C	T	rs61732411	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:22134018C>T	ENST00000408935.1	+	1	722	c.722C>T	c.(721-723)tCg>tTg	p.S241L		NM_001001912.1	NP_001001912.1	Q8NGC2	OR4E2_HUMAN	olfactory receptor, family 4, subfamily E, member 2	241						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	15	all_cancers(95;0.00113)	Acute lymphoblastic leukemia(2;0.0279)		GBM - Glioblastoma multiforme(265;0.0137)		TCTACCTGCTCGGCCCACTTC	0.527													C|||	699	0.139577	0.2526	0.1628	5008	,	,		21318	0.005		0.2038	False		,,,				2504	0.0429				p.S241L		Atlas-SNP	.											OR4E2,NS,carcinoma,-1,1	OR4E2	44	1	0			c.C722T						scavenged	.	C	LEU/SER	921,2999		109,703,1148	96.0	93.0	94.0		722	4.8	1.0	14	dbSNP_129	94	1719,6581		190,1339,2621	yes	missense	OR4E2	NM_001001912.1	145	299,2042,3769	TT,TC,CC		20.7108,23.4949,21.6039	benign	241/314	22134018	2640,9580	1960	4150	6110	SO:0001583	missense	26686	exon1			CCTGCTCGGCCCA		CCDS41916.1	14q11.2	2013-09-23			ENSG00000221977	ENSG00000221977		"""GPCR / Class A : Olfactory receptors"""	8297	protein-coding gene	gene with protein product							Standard	NM_001001912		Approved		uc010tmd.2	Q8NGC2	OTTHUMG00000168979	ENST00000408935.1:c.722C>T	14.37:g.22134018C>T	ENSP00000386195:p.Ser241Leu	Somatic	307	2	0.00651466		WXS	Illumina HiSeq	Phase_I	326	7	0.0214724	NM_001001912	Q6IET6|Q96R62	Missense_Mutation	SNP	ENST00000408935.1	37	CCDS41916.1	311	0.1423992673992674	106	0.21544715447154472	59	0.16298342541436464	2	0.0034965034965034965	144	0.18997361477572558	C	12.41	1.928415	0.34002	0.234949	0.207108	ENSG00000221977	ENST00000408935	T	0.35789	1.29	5.68	4.79	0.61399	GPCR, rhodopsin-like superfamily (1);	0.255127	0.19259	U	0.118721	T	0.00012	0.0000	L	0.59967	1.855	0.39721	P	0.02852600000000005	P	0.35363	0.497	B	0.33254	0.16	T	0.10474	-1.0628	9	0.54805	T	0.06	.	13.0304	0.58839	0.0:0.9212:0.0:0.0788	rs61732411	241	Q8NGC2	OR4E2_HUMAN	L	241	ENSP00000386195:S241L	ENSP00000386195:S241L	S	+	2	0	OR4E2	21203858	0.000000	0.05858	0.997000	0.53966	0.487000	0.33371	0.099000	0.15210	1.534000	0.49203	0.655000	0.94253	TCG	C|0.830;T|0.170	0.170	strong		0.527	OR4E2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401874.1		
FAT2	2196	hgsc.bcm.edu	37	5	150922050	150922050	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:150922050G>T	ENST00000261800.5	-	9	8650	c.8638C>A	c.(8638-8640)Cac>Aac	p.H2880N		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	2880	Cadherin 25. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			GTCTGTCCGTGGTCATAGGCC	0.502																																					p.H2880N		Atlas-SNP	.											FAT2,NS,carcinoma,+2,1	FAT2	465	1	0			c.C8638A						scavenged	.						163.0	153.0	157.0					5																	150922050		2203	4300	6503	SO:0001583	missense	2196	exon9			GTCCGTGGTCATA	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.8638C>A	5.37:g.150922050G>T	ENSP00000261800:p.His2880Asn	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	185	3	0.0162162	NM_001447	O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	CCDS4317.1	.	.	.	.	.	.	.	.	.	.	G	13.52	2.262837	0.39995	.	.	ENSG00000086570	ENST00000261800	T	0.01665	4.7	6.05	5.17	0.71159	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000004	T	0.02119	0.0066	N	0.10760	0.04	0.51482	D	0.999922	P	0.37612	0.602	P	0.46917	0.531	T	0.71374	-0.4612	10	0.13108	T	0.6	.	16.7973	0.85605	0.0:0.0:0.8701:0.1299	.	2880	Q9NYQ8	FAT2_HUMAN	N	2880	ENSP00000261800:H2880N	ENSP00000261800:H2880N	H	-	1	0	FAT2	150902243	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	6.620000	0.74224	1.547000	0.49401	0.650000	0.86243	CAC	.	.	none		0.502	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
DDX25	29118	hgsc.bcm.edu	37	11	125775114	125775114	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:125775114A>G	ENST00000263576.6	+	2	226	c.71A>G	c.(70-72)aAc>aGc	p.N24S	PUS3_ENST00000227474.3_5'Flank|RP11-680F20.9_ENST00000533033.2_RNA|DDX25_ENST00000525943.1_3'UTR	NM_013264.4	NP_037396.3	Q9UHL0	DDX25_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 25	24					mRNA export from nucleus (GO:0006406)|multicellular organismal development (GO:0007275)|regulation of translation (GO:0006417)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|RNA binding (GO:0003723)			breast(2)|endometrium(2)|kidney(1)|large_intestine(2)|ovary(2)|upper_aerodigestive_tract(1)	10	all_hematologic(175;0.177)	Breast(109;0.0021)|all_lung(97;0.0203)|Lung NSC(97;0.0203)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.14e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.046)		TAGTTTTCAAACCTCAGCCAA	0.493																																					p.N24S		Atlas-SNP	.											DDX25_ENST00000263576,caecum,carcinoma,+1,1	DDX25	65	1	0			c.A71G						scavenged	.						138.0	127.0	131.0					11																	125775114		692	1591	2283	SO:0001583	missense	29118	exon2			TTTCAAACCTCAG	AF155140	CCDS44766.1	11q24	2012-02-23	2012-02-23		ENSG00000109832	ENSG00000109832		"""DEAD-boxes"""	18698	protein-coding gene	gene with protein product	"""gonadotropin-regulated testicular RNA helicase"""	607663	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 25"", ""DEAD (Asp-Glu-Ala-Asp) box polypeptide 25"""			10608860, 15096601	Standard	NM_013264		Approved	GRTH	uc001qcz.5	Q9UHL0	OTTHUMG00000165859	ENST00000263576.6:c.71A>G	11.37:g.125775114A>G	ENSP00000263576:p.Asn24Ser	Somatic	142	0	0		WXS	Illumina HiSeq	Phase_I	146	3	0.0205479	NM_013264	B2R6Z0|Q5XVN2|Q86W81|Q8IYP1	Missense_Mutation	SNP	ENST00000263576.6	37	CCDS44766.1	.	.	.	.	.	.	.	.	.	.	A	11.76	1.735153	0.30774	.	.	ENSG00000109832	ENST00000263576	T	0.02974	4.09	5.2	5.2	0.72013	.	0.253893	0.34133	N	0.004234	T	0.05227	0.0139	N	0.14661	0.345	0.37370	D	0.911605	P;P	0.52842	0.956;0.956	D;D	0.65010	0.931;0.931	T	0.60969	-0.7157	10	0.24483	T	0.36	-0.7007	11.3873	0.49793	1.0:0.0:0.0:0.0	.	24;24	B4DHI6;Q9UHL0	.;DDX25_HUMAN	S	24	ENSP00000263576:N24S	ENSP00000263576:N24S	N	+	2	0	DDX25	125280324	1.000000	0.71417	1.000000	0.80357	0.825000	0.46686	3.912000	0.56386	2.174000	0.68829	0.533000	0.62120	AAC	.	.	none		0.493	DDX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386736.3	NM_013264	
HIST1H1E	3008	hgsc.bcm.edu	37	6	26157012	26157012	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:26157012G>A	ENST00000304218.3	+	1	454	c.394G>A	c.(394-396)Gca>Aca	p.A132T	HIST1H2BD_ENST00000289316.2_5'Flank|HIST1H2BD_ENST00000377777.4_5'Flank	NM_005321.2	NP_005312.1	P10412	H14_HUMAN	histone cluster 1, H1e	132					nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	extracellular vesicular exosome (GO:0070062)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)			NS(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|liver(1)|lung(9)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	26						CAAGAAGCCAGCAGGAGCGGC	0.637																																					p.A132T		Atlas-SNP	.											.	HIST1H1E	69	.	0			c.G394A						PASS	.						15.0	22.0	19.0					6																	26157012		2201	4297	6498	SO:0001583	missense	3008	exon1			AAGCCAGCAGGAG	M60748	CCDS4586.1	6p22.1	2012-05-04	2006-10-11	2003-02-21	ENSG00000168298	ENSG00000168298		"""Histones / Replication-dependent"""	4718	protein-coding gene	gene with protein product		142220	"""H1 histone family, member 4"", ""histone 1, H1e"""	H1F4		1916825, 12408966	Standard	NM_005321		Approved	H1.4, H1e, H1s-4	uc003ngq.3	P10412	OTTHUMG00000014422	ENST00000304218.3:c.394G>A	6.37:g.26157012G>A	ENSP00000307705:p.Ala132Thr	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	73	15	0.205479	NM_005321	Q4VB25	Missense_Mutation	SNP	ENST00000304218.3	37	CCDS4586.1	.	.	.	.	.	.	.	.	.	.	.	5.354	0.250648	0.10130	.	.	ENSG00000168298	ENST00000304218	T	0.26957	1.7	5.51	1.63	0.23807	.	0.267468	0.34628	N	0.003817	T	0.05135	0.0137	L	0.27053	0.805	0.32693	N	0.513953	B	0.02656	0.0	B	0.04013	0.001	T	0.40194	-0.9576	10	0.14656	T	0.56	-0.2098	9.6047	0.39626	0.1402:0.0:0.7406:0.1192	.	132	P10412	H14_HUMAN	T	132	ENSP00000307705:A132T	ENSP00000307705:A132T	A	+	1	0	HIST1H1E	26264991	0.944000	0.32072	0.001000	0.08648	0.032000	0.12392	2.034000	0.41145	0.070000	0.16634	-1.300000	0.01332	GCA	.	.	none		0.637	HIST1H1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040084.1	NM_005321	
AGO4	192670	hgsc.bcm.edu	37	1	36307020	36307020	+	Missense_Mutation	SNP	G	G	T	rs146736735		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:36307020G>T	ENST00000373210.3	+	14	2224	c.1979G>T	c.(1978-1980)cGc>cTc	p.R660L		NM_017629.3	NP_060099.2	Q9HCK5	AGO4_HUMAN	argonaute RISC catalytic component 4	660	Piwi. {ECO:0000255|HAMAP-Rule:MF_03033}.				epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|mRNA catabolic process (GO:0006402)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|phosphatidylinositol-mediated signaling (GO:0048015)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)|micro-ribonucleoprotein complex (GO:0035068)|RISC complex (GO:0016442)	miRNA binding (GO:0035198)										AAATCCACACGCTTCAAACCC	0.517																																					p.R660L		Atlas-SNP	.											EIF2C4,NS,carcinoma,+1,1	.	.	1	0			c.G1979T						scavenged	.						77.0	75.0	76.0					1																	36307020		2203	4300	6503	SO:0001583	missense	192670	exon14			CCACACGCTTCAA	AB046787	CCDS397.1	1p34	2013-02-15	2013-02-15	2013-02-15	ENSG00000134698	ENSG00000134698		"""Argonaute/PIWI family"""	18424	protein-coding gene	gene with protein product	"""argonaute 4"""	607356	"""eukaryotic translation initiation factor 2C, 4"""	EIF2C4		12906857	Standard	NM_017629		Approved	hAGO4, KIAA1567, FLJ20033	uc001bzj.2	Q9HCK5	OTTHUMG00000004243	ENST00000373210.3:c.1979G>T	1.37:g.36307020G>T	ENSP00000362306:p.Arg660Leu	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	281	5	0.0177936	NM_017629	A7MD27	Missense_Mutation	SNP	ENST00000373210.3	37	CCDS397.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.047883	0.93740	.	.	ENSG00000134698	ENST00000373210	T	0.32023	1.47	6.01	6.01	0.97437	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.000000	0.85682	D	0.000000	T	0.55369	0.1916	M	0.90019	3.08	0.80722	D	1	P	0.42908	0.793	P	0.47376	0.545	T	0.60682	-0.7215	10	0.52906	T	0.07	-11.5748	20.5211	0.99222	0.0:0.0:1.0:0.0	.	660	Q9HCK5	AGO4_HUMAN	L	660	ENSP00000362306:R660L	ENSP00000362306:R660L	R	+	2	0	EIF2C4	36079607	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.737000	0.98831	2.861000	0.98227	0.650000	0.86243	CGC	G|1.000;A|0.000	.	alt		0.517	AGO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012213.3	NM_017629	
CACNA1C	775	hgsc.bcm.edu	37	12	2794937	2794937	+	Missense_Mutation	SNP	C	C	T	rs201777030		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:2794937C>T	ENST00000347598.4	+	46	5753	c.5753C>T	c.(5752-5754)aCg>aTg	p.T1918M	CACNA1C_ENST00000335762.5_Missense_Mutation_p.T1895M|CACNA1C_ENST00000327702.7_Missense_Mutation_p.T1905M|CACNA1C_ENST00000399601.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399655.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399641.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399629.1_Missense_Mutation_p.T1887M|CACNA1C_ENST00000399621.1_Missense_Mutation_p.T1889M|CACNA1C_ENST00000399591.1_Missense_Mutation_p.T1878M|CACNA1C_ENST00000399644.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000402845.3_Missense_Mutation_p.T1889M|CACNA1C_ENST00000399617.1_Missense_Mutation_p.T1905M|CACNA1C_ENST00000399603.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000399597.1_Missense_Mutation_p.T1870M|CACNA1C_ENST00000344100.3_Missense_Mutation_p.T1911M|CACNA1C_ENST00000399595.1_Missense_Mutation_p.T1878M|CACNA1C_ENST00000399638.1_Missense_Mutation_p.T1898M|CACNA1C_ENST00000406454.3_Missense_Mutation_p.T1941M|CACNA1C_ENST00000399637.1_Missense_Mutation_p.T1889M|CACNA1C-AS1_ENST00000501371.1_RNA|CACNA1C_ENST00000399606.1_Missense_Mutation_p.T1890M|CACNA1C_ENST00000399634.1_Missense_Mutation_p.T1941M|CACNA1C_ENST00000399649.1_Missense_Mutation_p.T1876M	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1953					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.T1911M(1)|p.T1983M(1)|p.T1405M(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CGGCAACTGACGCTCCCAGAG	0.582																																					p.T1953M		Atlas-SNP	.											Q6YL47_HUMAN,trunk,malignant_melanoma,0,3	CACNA1C	1023	3	3	Substitution - Missense(3)	skin(3)	c.C5858T						scavenged	.						49.0	49.0	49.0					12																	2794937		2012	4159	6171	SO:0001583	missense	775	exon47			AACTGACGCTCCC	AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.5753C>T	12.37:g.2794937C>T	ENSP00000266376:p.Thr1918Met	Somatic	195	9	0.0461538		WXS	Illumina HiSeq	Phase_I	194	11	0.056701	NM_199460	B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.802724	0.50315	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.54866	0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55;0.55	4.26	4.26	0.50523	.	29.029300	0.00550	N	0.000258	T	0.70133	0.3189	L	0.56769	1.78	0.34775	D	0.734153	P;P;D;P;P;D;D;P;P;D;P;D;P;P;D;P;P;B;P;P;D;P;P;D;D	0.65815	0.863;0.922;0.995;0.664;0.934;0.988;0.992;0.869;0.638;0.966;0.922;0.989;0.927;0.783;0.992;0.677;0.927;0.317;0.922;0.485;0.985;0.869;0.869;0.981;0.995	B;P;P;B;P;P;P;P;B;P;P;P;P;P;P;B;P;B;P;B;P;P;P;P;P	0.56916	0.238;0.595;0.809;0.146;0.756;0.647;0.795;0.595;0.282;0.553;0.595;0.736;0.521;0.595;0.65;0.391;0.521;0.299;0.595;0.229;0.542;0.595;0.595;0.46;0.809	T	0.60281	-0.7294	10	0.38643	T	0.18	.	16.9179	0.86156	0.0:1.0:0.0:0.0	.	561;1911;1867;1953;1905;1889;1870;1887;1898;1870;1890;1870;1901;1918;1870;1905;1941;1878;1876;1878;1859;1889;1889;1870;1870	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	M	1895;1870;1870;1898;1870;1889;1889;1878;1870;1918;1890;1870;1911;1887;1905;1876;1889;1870;1941;1905;1941;1878;1771	ENSP00000336982:T1895M;ENSP00000382563:T1870M;ENSP00000382552:T1870M;ENSP00000382547:T1898M;ENSP00000382506:T1870M;ENSP00000382530:T1889M;ENSP00000382546:T1889M;ENSP00000382500:T1878M;ENSP00000382549:T1870M;ENSP00000266376:T1918M;ENSP00000382515:T1890M;ENSP00000382510:T1870M;ENSP00000341092:T1911M;ENSP00000382537:T1887M;ENSP00000329877:T1905M;ENSP00000382557:T1876M;ENSP00000385724:T1889M;ENSP00000382512:T1870M;ENSP00000382542:T1941M;ENSP00000382526:T1905M;ENSP00000385896:T1941M;ENSP00000382504:T1878M	ENSP00000323129:T1771M	T	+	2	0	CACNA1C	2665198	1.000000	0.71417	0.106000	0.21319	0.488000	0.33401	5.733000	0.68571	2.202000	0.70862	0.449000	0.29647	ACG	.	.	weak		0.582	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1	NM_000719	
DRD5	1816	hgsc.bcm.edu	37	4	9783982	9783982	+	Missense_Mutation	SNP	G	G	A	rs2227849	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:9783982G>A	ENST00000304374.2	+	1	725	c.329G>A	c.(328-330)gGa>gAa	p.G110E		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	110			G -> E (in dbSNP:rs2227849).		activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)	p.G110E(1)		NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	TGGCCCTTTGGAGCGTTCTGC	0.612																																					p.G110E		Atlas-SNP	.											DRD5,NS,carcinoma,0,2	DRD5	119	2	1	Substitution - Missense(1)	prostate(1)	c.G329A						scavenged	.						49.0	47.0	48.0					4																	9783982		2203	4300	6503	SO:0001583	missense	1816	exon1			CCTTTGGAGCGTT	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.329G>A	4.37:g.9783982G>A	ENSP00000306129:p.Gly110Glu	Somatic	137	5	0.0364963		WXS	Illumina HiSeq	Phase_I	127	15	0.11811	NM_000798	B2R9S3|Q8NEQ8	Missense_Mutation	SNP	ENST00000304374.2	37	CCDS3405.1	.	.	.	.	.	.	.	.	.	.	g	22.5	4.294138	0.81025	.	.	ENSG00000169676	ENST00000304374	T	0.49720	0.77	4.11	4.11	0.48088	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.65954	0.2741	H	0.94925	3.6	0.80722	D	1	P	0.43750	0.816	P	0.45343	0.477	T	0.78902	-0.2021	10	0.87932	D	0	.	15.5246	0.75894	0.0:0.0:1.0:0.0	rs2227849	110	P21918	DRD5_HUMAN	E	110	ENSP00000306129:G110E	ENSP00000306129:G110E	G	+	2	0	DRD5	9393080	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.199000	0.95003	2.130000	0.65690	0.305000	0.20034	GGA	G|0.916;A|0.084	0.084	strong		0.612	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
PDHA2	5161	hgsc.bcm.edu	37	4	96761615	96761615	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:96761615G>A	ENST00000295266.4	+	1	377	c.314G>A	c.(313-315)gGc>gAc	p.G105D		NM_005390.4	NP_005381.1	P29803	ODPAT_HUMAN	pyruvate dehydrogenase (lipoamide) alpha 2	105					glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	pyruvate dehydrogenase (acetyl-transferring) activity (GO:0004739)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(23)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	46		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;1.23e-06)		CTTGAGGCCGGCATAAACCCC	0.517																																					p.G105D		Atlas-SNP	.											PDHA2,NS,carcinoma,0,1	PDHA2	118	1	0			c.G314A						scavenged	.						129.0	113.0	119.0					4																	96761615		2203	4300	6503	SO:0001583	missense	5161	exon1			AGGCCGGCATAAA		CCDS3644.1	4q22-q23	2009-11-09			ENSG00000163114	ENSG00000163114	1.2.4.1		8807	protein-coding gene	gene with protein product		179061		PDHAL			Standard	NM_005390		Approved		uc003htr.4	P29803	OTTHUMG00000130990	ENST00000295266.4:c.314G>A	4.37:g.96761615G>A	ENSP00000295266:p.Gly105Asp	Somatic	336	0	0		WXS	Illumina HiSeq	Phase_I	436	7	0.016055	NM_005390	B2R9Q3|Q0VDI5|Q4VC02|Q6NXQ1	Missense_Mutation	SNP	ENST00000295266.4	37	CCDS3644.1	.	.	.	.	.	.	.	.	.	.	G	10.75	1.439043	0.25900	.	.	ENSG00000163114	ENST00000295266	D	0.97114	-4.25	4.91	4.05	0.47172	Dehydrogenase, E1 component (1);	0.263878	0.35179	N	0.003394	D	0.97408	0.9152	L	0.56124	1.755	0.21220	N	0.999757	D	0.61697	0.99	D	0.69824	0.966	D	0.92952	0.6381	10	0.87932	D	0	-17.1313	11.773	0.51970	0.0:0.3428:0.6572:0.0	.	105	P29803	ODPAT_HUMAN	D	105	ENSP00000295266:G105D	ENSP00000295266:G105D	G	+	2	0	PDHA2	96980638	1.000000	0.71417	0.093000	0.20910	0.022000	0.10575	3.757000	0.55212	1.408000	0.46895	0.467000	0.42956	GGC	.	.	none		0.517	PDHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253608.1		
CSHL1	1444	hgsc.bcm.edu	37	17	61987576	61987576	+	Silent	SNP	G	G	A	rs2246207	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:61987576G>A	ENST00000309894.5	-	4	416	c.417C>T	c.(415-417)agC>agT	p.S139S	CSHL1_ENST00000392824.4_3'UTR|CSHL1_ENST00000561003.1_Silent_p.S56S|CSHL1_ENST00000259003.10_Silent_p.S77S|CSHL1_ENST00000346606.6_Silent_p.S45S|CSHL1_ENST00000438387.2_Silent_p.S56S|CSHL1_ENST00000558099.1_5'UTR|CSHL1_ENST00000450719.3_Silent_p.S45S	NM_022579.1	NP_072101.1	Q14406	CSHL_HUMAN	chorionic somatomammotropin hormone-like 1	139						extracellular region (GO:0005576)	hormone activity (GO:0005179)|metal ion binding (GO:0046872)			endometrium(3)|lung(6)	9						GATAGTCATCGCTGTCCGAGG	0.587													G|||	1952	0.389776	0.4637	0.3501	5008	,	,		19398	0.4196		0.4225	False		,,,				2504	0.2536				p.S139S		Atlas-SNP	.											CSHL1_ENST00000561003,NS,adenoma,0,2	CSHL1	42	2	0			c.C417T						scavenged	.	G	,,,	2165,2241	583.4+/-385.8	538,1089,576	88.0	76.0	80.0		135,417,168,348	-4.3	0.0	17	dbSNP_100	80	3571,5029	517.8+/-379.1	751,2069,1480	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CSHL1	NM_001318.2,NM_022579.1,NM_022580.1,NM_022581.1	,,,	1289,3158,2056	AA,AG,GG		41.5233,49.1375,44.1027	,,,	45/129,139/223,56/140,116/200	61987576	5736,7270	2203	4300	6503	SO:0001819	synonymous_variant	1444	exon4			GTCATCGCTGTCC	BC029365	CCDS11652.1, CCDS42370.1, CCDS45759.1	17q22-q24	2012-10-02							2442	protein-coding gene	gene with protein product	"""chorionic somatomammotropin CS-5"""	603515		CSHP1		8083227	Standard	NM_001318		Approved	hCS-L, CSL, CS-5, MGC149868	uc002jda.1	Q14406		ENST00000309894.5:c.417C>T	17.37:g.61987576G>A		Somatic	687	6	0.00873362		WXS	Illumina HiSeq	Phase_I	658	8	0.0121581	NM_022579	D3DU26|D3DU27|Q0VDB2	Silent	SNP	ENST00000309894.5	37	CCDS11652.1																																																																																			G|0.566;A|0.434	0.434	strong		0.587	CSHL1-009	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444557.1	NM_022579	
LTBP2	4053	hgsc.bcm.edu	37	14	74971792	74971792	+	Silent	SNP	C	C	T	rs61738017	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:74971792C>T	ENST00000261978.4	-	29	4649	c.4263G>A	c.(4261-4263)gcG>gcA	p.A1421A	LTBP2_ENST00000556690.1_Silent_p.A1377A	NM_000428.2	NP_000419.1	Q14767	LTBP2_HUMAN	latent transforming growth factor beta binding protein 2	1421	TB 3.				protein secretion (GO:0009306)|protein targeting (GO:0006605)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(9)|liver(1)|lung(29)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	58				BRCA - Breast invasive adenocarcinoma(234;0.00219)|READ - Rectum adenocarcinoma(1;0.0649)		TGGAGCAGGGCGCATGGCCCT	0.662													C|||	101	0.0201677	0.0703	0.0101	5008	,	,		17322	0.0		0.0	False		,,,				2504	0.001				p.A1421A		Atlas-SNP	.											LTBP2,colon,carcinoma,-1,1	LTBP2	158	1	0			c.G4263A						PASS	.	C		268,4138	150.7+/-184.7	12,244,1947	48.0	48.0	48.0		4263	-7.4	0.0	14	dbSNP_129	48	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	LTBP2	NM_000428.2		12,256,6235	TT,TC,CC		0.1395,6.0826,2.1529		1421/1822	74971792	280,12726	2203	4300	6503	SO:0001819	synonymous_variant	4053	exon29			GCAGGGCGCATGG		CCDS9831.1	14q24.3	2011-10-20	2001-12-04			ENSG00000119681		"""Latent transforming growth factor, beta binding proteins"""	6715	protein-coding gene	gene with protein product		602091	"""chromosome 14 open reading frame 141"""	LTBP3, C14orf141		7798248	Standard	NM_000428		Approved		uc001xqa.3	Q14767		ENST00000261978.4:c.4263G>A	14.37:g.74971792C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	49	22	0.44898	NM_000428	Q99907|Q9NS51	Silent	SNP	ENST00000261978.4	37	CCDS9831.1																																																																																			C|0.979;T|0.021	0.021	strong		0.662	LTBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413595.1	NM_000428	
LAMA1	284217	hgsc.bcm.edu	37	18	6978290	6978290	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:6978290A>G	ENST00000389658.3	-	43	6188	c.6095T>C	c.(6094-6096)cTg>cCg	p.L2032P		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2032	Domain II and I.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTCCTGGCTCAGCCCCGCCAC	0.562																																					p.L2032P		Atlas-SNP	.											LAMA1,colon,carcinoma,+1,1	LAMA1	458	1	0			c.T6095C						scavenged	.						136.0	119.0	125.0					18																	6978290		2203	4300	6503	SO:0001583	missense	284217	exon43			TGGCTCAGCCCCG	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.6095T>C	18.37:g.6978290A>G	ENSP00000374309:p.Leu2032Pro	Somatic	195	1	0.00512821		WXS	Illumina HiSeq	Phase_I	255	3	0.0117647	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	A	11.99	1.803406	0.31869	.	.	ENSG00000101680	ENST00000389658	T	0.55760	0.5	5.4	2.94	0.34122	Laminin II (1);	0.402501	0.24285	N	0.039866	T	0.65428	0.2690	L	0.59436	1.845	0.52099	D	0.999941	D	0.63046	0.992	D	0.65573	0.936	T	0.65730	-0.6097	10	0.66056	D	0.02	.	12.538	0.56152	0.7364:0.2636:0.0:0.0	.	2032	P25391	LAMA1_HUMAN	P	2032	ENSP00000374309:L2032P	ENSP00000374309:L2032P	L	-	2	0	LAMA1	6968290	0.931000	0.31567	0.165000	0.22776	0.002000	0.02628	3.526000	0.53509	0.420000	0.25954	-0.323000	0.08544	CTG	.	.	none		0.562	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
PGM1	5236	hgsc.bcm.edu	37	1	64104389	64104389	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:64104389G>A	ENST00000371084.3	+	7	1275	c.1062G>A	c.(1060-1062)gaG>gaA	p.E354E	PGM1_ENST00000371083.4_Silent_p.E372E|PGM1_ENST00000540265.1_Silent_p.E157E	NM_002633.2	NP_002624.2	P36871	PGM1_HUMAN	phosphoglucomutase 1	354					carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|glycolytic process (GO:0006096)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	magnesium ion binding (GO:0000287)|phosphoglucomutase activity (GO:0004614)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	20						CTTTGTATGAGACCCCAACTG	0.502																																					p.E372E		Atlas-SNP	.											.	PGM1	75	.	0			c.G1116A						PASS	.						179.0	169.0	172.0					1																	64104389		2203	4300	6503	SO:0001819	synonymous_variant	5236	exon7			GTATGAGACCCCA	BC019920	CCDS625.1, CCDS53323.1, CCDS53324.1	1p22.1	2012-10-02			ENSG00000079739	ENSG00000079739	5.4.2.2		8905	protein-coding gene	gene with protein product		171900				4517931, 1530890	Standard	NM_002633		Approved		uc010ooz.2	P36871	OTTHUMG00000008968	ENST00000371084.3:c.1062G>A	1.37:g.64104389G>A		Somatic	368	0	0		WXS	Illumina HiSeq	Phase_I	302	18	0.0596026	NM_001172818	B2R5N9|B4DPV0|Q16105|Q16106|Q5BKZ9|Q6NW22|Q86U74|Q96J40|Q9NTY4	Silent	SNP	ENST00000371084.3	37	CCDS625.1																																																																																			.	.	none		0.502	PGM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024868.1	NM_002633	
GOLGA6L1	283767	hgsc.bcm.edu	37	15	22743235	22743235	+	Silent	SNP	A	A	G	rs371649333		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:22743235A>G	ENST00000560659.2	+	8	1470	c.1470A>G	c.(1468-1470)cgA>cgG	p.R490R	GOLGA6L1_ENST00000316397.3_Silent_p.R540R			Q8N7Z2	GG6L1_HUMAN	golgin A6 family-like 1	534								p.R540R(1)		NS(1)|breast(2)|endometrium(5)|large_intestine(1)|lung(1)|skin(1)	11						agaagatacgagagcaggagg	0.532																																					p.R540R		Atlas-SNP	.											GOLGA6L1,NS,carcinoma,0,5	GOLGA6L1	20	5	1	Substitution - coding silent(1)	endometrium(1)	c.A1620G						scavenged	.						2.0	1.0	1.0					15																	22743235		605	798	1403	SO:0001819	synonymous_variant	283767	exon8			GATACGAGAGCAG	AK097517	CCDS73699.1	15q11.2	2012-10-05	2010-02-12		ENSG00000197414	ENSG00000277865			37444	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 1"""				Standard	NM_001001413		Approved		uc010tzx.1	Q8N7Z2	OTTHUMG00000171883	ENST00000560659.2:c.1470A>G	15.37:g.22743235A>G		Somatic	59	2	0.0338983		WXS	Illumina HiSeq	Phase_I	54	4	0.0740741	NM_001001413		Silent	SNP	ENST00000560659.2	37																																																																																				.	.	weak		0.532	GOLGA6L1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000415616.2	NM_001001413	
RGPD8	727851	hgsc.bcm.edu	37	2	113147238	113147238	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:113147238A>G	ENST00000302558.3	-	20	3475	c.3284T>C	c.(3283-3285)cTa>cCa	p.L1095P	RGPD8_ENST00000409750.1_Missense_Mutation_p.L955P	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	1095	RanBD1 1. {ECO:0000255|PROSITE- ProRule:PRU00164}.				protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						CAGCATTCTTAGTTTGCCATT	0.418																																					p.L1095P		Atlas-SNP	.											RGPD8_ENST00000302558,NS,carcinoma,0,2	RGPD8	81	2	0			c.T3284C						scavenged	.						1.0	1.0	1.0					2																	113147238		3	5	8	SO:0001583	missense	727851	exon20			ATTCTTAGTTTGC	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.3284T>C	2.37:g.113147238A>G	ENSP00000306637:p.Leu1095Pro	Somatic	47	3	0.0638298		WXS	Illumina HiSeq	Phase_I	57	6	0.105263	NM_001164463	Q5CZA8	Missense_Mutation	SNP	ENST00000302558.3	37	CCDS46394.1	.	.	.	.	.	.	.	.	.	.	-	0.070	-1.203988	0.01581	.	.	ENSG00000169629	ENST00000302558;ENST00000409750	T;T	0.44083	0.93;0.93	2.3	2.3	0.28687	Pleckstrin homology-type (1);Ran binding protein 1 (3);	.	.	.	.	T	0.39682	0.1087	M	0.70595	2.14	0.80722	D	1	B	0.06786	0.001	B	0.12156	0.007	T	0.36890	-0.9729	9	0.48119	T	0.1	-0.3282	8.205	0.31449	1.0:0.0:0.0:0.0	.	1095	O14715	RGPD8_HUMAN	P	1095;955	ENSP00000306637:L1095P;ENSP00000386511:L955P	ENSP00000306637:L1095P	L	-	2	0	RGPD8	112863709	1.000000	0.71417	0.884000	0.34674	0.576000	0.36127	7.271000	0.78506	1.068000	0.40764	0.128000	0.15822	CTA	.	.	weak		0.418	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
EPB41L5	57669	hgsc.bcm.edu	37	2	120799656	120799656	+	Silent	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:120799656T>G	ENST00000263713.5	+	3	469	c.255T>G	c.(253-255)ggT>ggG	p.G85G	EPB41L5_ENST00000452780.1_Silent_p.G85G|EPB41L5_ENST00000443902.2_Silent_p.G85G|EPB41L5_ENST00000443124.1_Silent_p.G85G|EPB41L5_ENST00000331393.4_Silent_p.G85G	NM_020909.3	NP_065960.2	Q9HCM4	E41L5_HUMAN	erythrocyte membrane protein band 4.1 like 5	85	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				actomyosin structure organization (GO:0031032)|apical constriction (GO:0003383)|axial mesoderm morphogenesis (GO:0048319)|cellular response to transforming growth factor beta stimulus (GO:0071560)|ectoderm development (GO:0007398)|embryonic foregut morphogenesis (GO:0048617)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|in utero embryonic development (GO:0001701)|left/right axis specification (GO:0070986)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of protein binding (GO:0032091)|neural plate morphogenesis (GO:0001839)|paraxial mesoderm development (GO:0048339)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein binding (GO:0032092)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of establishment of protein localization (GO:0070201)|somite rostral/caudal axis specification (GO:0032525)|substrate-dependent cell migration, cell attachment to substrate (GO:0006931)|unidimensional cell growth (GO:0009826)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)				breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(12)|ovary(1)	26						ACTATTTTGGTCTGAGATTTA	0.343																																					p.G85G		Atlas-SNP	.											.	EPB41L5	98	.	0			c.T255G						PASS	.						156.0	147.0	150.0					2																	120799656		2203	4300	6503	SO:0001819	synonymous_variant	57669	exon3			TTTTGGTCTGAGA	AK023019	CCDS2130.1, CCDS54392.1, CCDS54393.1	2q14.2	2009-07-28			ENSG00000115109	ENSG00000115109			19819	protein-coding gene	gene with protein product		611730					Standard	NM_001184937		Approved	KIAA1548, FLJ12957, BE37, YMO1	uc002tmg.3	Q9HCM4	OTTHUMG00000131433	ENST00000263713.5:c.255T>G	2.37:g.120799656T>G		Somatic	219	0	0		WXS	Illumina HiSeq	Phase_I	241	36	0.149378	NM_020909	Q7Z5S1|Q8IZ12|Q9H975	Silent	SNP	ENST00000263713.5	37	CCDS2130.1																																																																																			.	.	none		0.343	EPB41L5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254230.2	NM_020909	
OR2T33	391195	hgsc.bcm.edu	37	1	248436963	248436963	+	Silent	SNP	G	G	T	rs560438352	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:248436963G>T	ENST00000318021.2	-	1	175	c.154C>A	c.(154-156)Cgg>Agg	p.R52R		NM_001004695.1	NP_001004695.1	Q8NG76	O2T33_HUMAN	olfactory receptor, family 2, subfamily T, member 33	52						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(41)|ovary(1)|prostate(1)|skin(4)	67	all_cancers(71;0.000124)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0245)			GTGTGGAGCCGGTGGTCCCAG	0.527													t|||	74	0.0147764	0.0545	0.0029	5008	,	,		16409	0.0		0.0	False		,,,				2504	0.0				p.R52R		Atlas-SNP	.											OR2T33,NS,carcinoma,0,1	OR2T33	133	1	0			c.C154A						scavenged	.						58.0	56.0	57.0					1																	248436963		2195	4288	6483	SO:0001819	synonymous_variant	391195	exon1			GGAGCCGGTGGTC		CCDS31109.1	1q44	2012-08-09			ENSG00000177212	ENSG00000177212		"""GPCR / Class A : Olfactory receptors"""	31255	protein-coding gene	gene with protein product							Standard	NM_001004695		Approved		uc010pzi.2	Q8NG76	OTTHUMG00000040458	ENST00000318021.2:c.154C>A	1.37:g.248436963G>T		Somatic	769	28	0.0364109		WXS	Illumina HiSeq	Phase_I	940	37	0.0393617	NM_001004695	B2RNN0	Silent	SNP	ENST00000318021.2	37	CCDS31109.1																																																																																			.	.	none		0.527	OR2T33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097354.1	NM_001004695	
BIRC6	57448	hgsc.bcm.edu	37	2	32724813	32724813	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:32724813C>T	ENST00000421745.2	+	46	8802	c.8668C>T	c.(8668-8670)Cga>Tga	p.R2890*		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	2890					apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CGTGGGTGCTCGAGCATGCTT	0.438																																					p.R2890X	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,NS,carcinoma,-1,4	BIRC6	838	4	0			c.C8668T						scavenged	.						216.0	211.0	213.0					2																	32724813		2203	4300	6503	SO:0001587	stop_gained	57448	exon46			GGTGCTCGAGCAT	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.8668C>T	2.37:g.32724813C>T	ENSP00000393596:p.Arg2890*	Somatic	210	2	0.00952381		WXS	Illumina HiSeq	Phase_I	286	65	0.227273	NM_016252	Q9ULD1	Nonsense_Mutation	SNP	ENST00000421745.2	37	CCDS33175.2	.	.	.	.	.	.	.	.	.	.	C	51	17.445868	0.99886	.	.	ENSG00000115760	ENST00000421745	.	.	.	5.42	4.53	0.55603	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07030	T	0.85	.	14.7907	0.69841	0.2614:0.7386:0.0:0.0	.	.	.	.	X	2890	.	ENSP00000393596:R2890X	R	+	1	2	BIRC6	32578317	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.557000	0.45871	1.370000	0.46153	0.655000	0.94253	CGA	.	.	none		0.438	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
TRPC3	7222	hgsc.bcm.edu	37	4	122846198	122846198	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:122846198A>C	ENST00000379645.3	-	3	1224	c.1151T>G	c.(1150-1152)cTt>cGt	p.L384R	TRPC3_ENST00000264811.5_Missense_Mutation_p.L311R|TRPC3_ENST00000513531.1_Missense_Mutation_p.L311R	NM_001130698.1	NP_001124170.1	Q13507	TRPC3_HUMAN	transient receptor potential cation channel, subfamily C, member 3	299					axon guidance (GO:0007411)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|phototransduction (GO:0007602)|platelet activation (GO:0030168)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of cardiac muscle hypertrophy in response to stress (GO:1903244)|response to ATP (GO:0033198)|response to calcium ion (GO:0051592)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(12)|lung(13)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	51						CTTAATGGCAAGTTTGACACG	0.418																																					p.L384R		Atlas-SNP	.											.	TRPC3	201	.	0			c.T1151G						PASS	.						208.0	185.0	192.0					4																	122846198		2203	4300	6503	SO:0001583	missense	7222	exon3			ATGGCAAGTTTGA	Y13758	CCDS3725.1, CCDS47130.1	4q27	2011-12-14			ENSG00000138741	ENSG00000138741		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	12335	protein-coding gene	gene with protein product		602345				8646775, 16382100	Standard	NM_003305		Approved		uc003ieg.2	Q13507	OTTHUMG00000133069	ENST00000379645.3:c.1151T>G	4.37:g.122846198A>C	ENSP00000368966:p.Leu384Arg	Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	212	11	0.0518868	NM_001130698	A7VJS1|E9PCJ9|O00593|Q15660|Q52M35|Q5G1L5	Missense_Mutation	SNP	ENST00000379645.3	37	CCDS47130.1	.	.	.	.	.	.	.	.	.	.	A	28.5	4.923161	0.92319	.	.	ENSG00000138741	ENST00000264811;ENST00000379645;ENST00000513531	T;T;T	0.71103	-0.54;-0.54;-0.54	5.92	5.92	0.95590	.	0.141093	0.39341	N	0.001390	D	0.85682	0.5753	M	0.87456	2.885	0.30473	N	0.773102	P;D;P	0.71674	0.852;0.998;0.911	P;D;P	0.67725	0.736;0.953;0.821	D	0.86427	0.1758	10	0.87932	D	0	-16.0118	16.3526	0.83220	1.0:0.0:0.0:0.0	.	299;311;384	Q13507;E9PCJ9;Q5G1L5	TRPC3_HUMAN;.;.	R	311;384;311	ENSP00000264811:L311R;ENSP00000368966:L384R;ENSP00000426899:L311R	ENSP00000264811:L311R	L	-	2	0	TRPC3	123065648	1.000000	0.71417	0.990000	0.47175	0.998000	0.95712	9.262000	0.95591	2.255000	0.74692	0.533000	0.62120	CTT	.	.	none		0.418	TRPC3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364252.1	NM_003305	
SPG11	80208	hgsc.bcm.edu	37	15	44943757	44943757	+	Missense_Mutation	SNP	A	A	G	rs3759871	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:44943757A>G	ENST00000261866.7	-	6	1404	c.1388T>C	c.(1387-1389)tTt>tCt	p.F463S	SPG11_ENST00000558319.1_Missense_Mutation_p.F463S|SPG11_ENST00000559193.1_Missense_Mutation_p.F463S|SPG11_ENST00000535302.2_Missense_Mutation_p.F463S|SPG11_ENST00000427534.2_Missense_Mutation_p.F463S	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	463			F -> S (in dbSNP:rs3759871). {ECO:0000269|PubMed:11347906, ECO:0000269|PubMed:15489334}.		cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)		p.F463S(1)		autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GCCAAGGGAAAAACACTGCAT	0.463													A|||	2378	0.47484	0.5234	0.5893	5008	,	,		20546	0.4653		0.4513	False		,,,				2504	0.362				p.F463S		Atlas-SNP	.											SPG11,NS,carcinoma,0,1	SPG11	207	1	1	Substitution - Missense(1)	stomach(1)	c.T1388C						scavenged	.	A	SER/PHE,SER/PHE	2310,2086	603.0+/-390.0	609,1092,497	118.0	110.0	113.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1388,1388	4.9	0.9	15	dbSNP_107	113	3917,4679	547.6+/-385.2	924,2069,1305	yes	missense,missense	SPG11	NM_001160227.1,NM_025137.3	155,155	1533,3161,1802	GG,GA,AA		45.5677,47.4522,47.9295	benign,benign	463/2331,463/2444	44943757	6227,6765	2198	4298	6496	SO:0001583	missense	80208	exon6			AGGGAAAAACACT		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.1388T>C	15.37:g.44943757A>G	ENSP00000261866:p.Phe463Ser	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	166	3	0.0180723	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	1075	0.49221611721611724	254	0.516260162601626	206	0.569060773480663	283	0.49475524475524474	332	0.43799472295514513	A	10.01	1.234381	0.22626	0.525478	0.455677	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.76060	-0.99;-0.73;-0.73	6.06	4.93	0.64822	.	0.209291	0.42053	D	0.000773	T	0.00012	0.0000	L	0.51422	1.61	0.80722	P	0.0	B;B;B;B	0.22211	0.021;0.066;0.053;0.021	B;B;B;B	0.18561	0.009;0.02;0.022;0.008	T	0.48514	-0.9029	9	0.26408	T	0.33	.	3.1014	0.06327	0.6352:0.1486:0.0744:0.1418	rs3759871;rs52807288;rs59538210;rs3759871	463;463;463;463	C4B7M2;F5H3N6;B9EK60;Q96JI7	.;.;.;SPTCS_HUMAN	S	463	ENSP00000261866:F463S;ENSP00000445278:F463S;ENSP00000396110:F463S	ENSP00000261866:F463S	F	-	2	0	SPG11	42731049	0.042000	0.20092	0.856000	0.33681	0.991000	0.79684	1.226000	0.32563	1.092000	0.41356	0.533000	0.62120	TTT	A|0.523;G|0.477	0.477	strong		0.463	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
WDR72	256764	hgsc.bcm.edu	37	15	54025345	54025345	+	Start_Codon_SNP	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:54025345A>C	ENST00000396328.1	-	2	241	c.2T>G	c.(1-3)aTg>aGg	p.M1R	WDR72_ENST00000557913.1_Start_Codon_SNP_p.M1R|WDR72_ENST00000360509.5_Start_Codon_SNP_p.M1R|WDR72_ENST00000559418.1_Start_Codon_SNP_p.M1R	NM_001277176.1|NM_182758.2	NP_001264105.1|NP_877435.3	Q3MJ13	WDR72_HUMAN	WD repeat domain 72	1										NS(1)|breast(1)|endometrium(4)|kidney(4)|large_intestine(18)|lung(29)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	71				all cancers(107;0.0511)		GGAAGTCCTCATTTTGGGCGA	0.463																																					p.M1R		Atlas-SNP	.											.	WDR72	177	.	0			c.T2G						PASS	.						71.0	66.0	68.0					15																	54025345		2194	4293	6487	SO:0001582	initiator_codon_variant	256764	exon2			GTCCTCATTTTGG	BX537884	CCDS10151.1, CCDS73730.1	15q21.3	2013-01-09			ENSG00000166415	ENSG00000166415		"""WD repeat domain containing"""	26790	protein-coding gene	gene with protein product		613214					Standard	NM_182758		Approved	FLJ38736	uc002acj.2	Q3MJ13	OTTHUMG00000131939	ENST00000396328.1:c.2T>G	15.37:g.54025345A>C	ENSP00000379619:p.Met1Arg	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	67	14	0.208955	NM_182758	Q7Z3I3|Q8N8X2	Missense_Mutation	SNP	ENST00000396328.1	37	CCDS10151.1	.	.	.	.	.	.	.	.	.	.	A	19.26	3.794156	0.70452	.	.	ENSG00000166415	ENST00000396328;ENST00000360509	T;T	0.45276	0.9;0.9	4.42	4.42	0.53409	.	0.000000	0.85682	D	0.000000	T	0.63248	0.2495	.	.	.	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	T	0.68202	-0.5471	9	0.87932	D	0	.	11.9358	0.52872	1.0:0.0:0.0:0.0	.	1	Q3MJ13	WDR72_HUMAN	R	1	ENSP00000379619:M1R;ENSP00000353699:M1R	ENSP00000353699:M1R	M	-	2	0	WDR72	51812637	1.000000	0.71417	0.611000	0.29010	0.474000	0.32979	5.692000	0.68256	2.002000	0.58637	0.533000	0.62120	ATG	.	.	none		0.463	WDR72-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254893.2	NM_182758	Missense_Mutation
MAN2B1	4125	hgsc.bcm.edu	37	19	12772090	12772090	+	Missense_Mutation	SNP	C	C	T	rs1133330	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:12772090C>T	ENST00000456935.2	-	7	1050	c.1010G>A	c.(1009-1011)cGg>cAg	p.R337Q	MAN2B1_ENST00000495617.1_5'Flank|MAN2B1_ENST00000221363.4_Missense_Mutation_p.R337Q	NM_000528.3|NM_001173498.1	NP_000519.2|NP_001166969.1	O00754	MA2B1_HUMAN	mannosidase, alpha, class 2B, member 1	337			R -> Q (in dbSNP:rs1133330). {ECO:0000269|PubMed:22161967, ECO:0000269|PubMed:9915946}.		cellular protein modification process (GO:0006464)|mannose metabolic process (GO:0006013)|protein deglycosylation (GO:0006517)	extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)	alpha-mannosidase activity (GO:0004559)|carbohydrate binding (GO:0030246)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(10)|ovary(4)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	33						ATTTACCAGCCGGATGAGCTT	0.552													C|||	1244	0.248403	0.3086	0.255	5008	,	,		20976	0.0615		0.3926	False		,,,				2504	0.2065				p.R337Q		Atlas-SNP	.											MAN2B1,NS,meningioma,0,1	MAN2B1	91	1	0			c.G1010A						scavenged	.	C	GLN/ARG,GLN/ARG	1379,3027	455.9+/-351.1	215,949,1039	221.0	174.0	190.0		1010,1010	-5.3	0.3	19	dbSNP_86	190	3431,5169	504.3+/-376.1	668,2095,1537	yes	missense,missense	MAN2B1	NM_000528.3,NM_001173498.1	43,43	883,3044,2576	TT,TC,CC		39.8953,31.2982,36.9829	benign,benign	337/1012,337/1011	12772090	4810,8196	2203	4300	6503	SO:0001583	missense	4125	exon7			ACCAGCCGGATGA		CCDS32919.1, CCDS54224.1	19p13.2	2013-09-20			ENSG00000104774	ENSG00000104774	3.2.1.24		6826	protein-coding gene	gene with protein product		609458		MANB			Standard	NM_000528		Approved	LAMAN	uc002mub.2	O00754	OTTHUMG00000156397	ENST00000456935.2:c.1010G>A	19.37:g.12772090C>T	ENSP00000395473:p.Arg337Gln	Somatic	285	1	0.00350877		WXS	Illumina HiSeq	Phase_I	345	5	0.0144928	NM_001173498	G5E928|O15330|Q16680|Q93094|Q9BW13	Missense_Mutation	SNP	ENST00000456935.2	37	CCDS32919.1	566	0.2591575091575092	140	0.2845528455284553	106	0.292817679558011	30	0.05244755244755245	290	0.38258575197889183	C	12.08	1.830324	0.32329	0.312982	0.398953	ENSG00000104774	ENST00000456935;ENST00000536796;ENST00000221363	T;T	0.79454	-1.27;-1.27	5.51	-5.32	0.02722	Glycoside hydrolase/deacetylase, beta/alpha-barrel (1);Glycoside hydrolase, family 38, core (2);	1.735930	0.03031	N	0.152116	T	0.00012	0.0000	N	0.05510	-0.035	0.46849	P	7.770000000000277E-4	B;B	0.20550	0.022;0.046	B;B	0.15052	0.007;0.012	T	0.03840	-1.0999	9	0.29301	T	0.29	-13.1141	13.4528	0.61180	0.0:0.3494:0.0:0.6506	rs1133330;rs2070087;rs3195023;rs17421598;rs56909861;rs1133330	337;337	G5E928;O00754	.;MA2B1_HUMAN	Q	337;276;337	ENSP00000395473:R337Q;ENSP00000221363:R337Q	ENSP00000221363:R337Q	R	-	2	0	MAN2B1	12633090	0.013000	0.17824	0.311000	0.25182	0.842000	0.47809	-0.041000	0.12084	-0.929000	0.03757	-0.291000	0.09656	CGG	C|0.675;T|0.325	0.325	strong		0.552	MAN2B1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000344062.1		
HSD3B7	80270	hgsc.bcm.edu	37	16	30997460	30997460	+	Missense_Mutation	SNP	C	C	T	rs371576756		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:30997460C>T	ENST00000297679.5	+	3	350	c.257C>T	c.(256-258)aCg>aTg	p.T86M	HSD3B7_ENST00000262520.6_Missense_Mutation_p.T86M|HSD3B7_ENST00000353250.5_Missense_Mutation_p.T86M|AC135048.1_ENST00000602217.1_Missense_Mutation_p.R25H	NM_025193.3	NP_079469.2	Q9H2F3	3BHS7_HUMAN	hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 7	86					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)|cholest-5-ene-3-beta,7-alpha-diol 3-beta-dehydrogenase activity (GO:0047016)			central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	12						GTCATCCACACGGCTGGGCTG	0.652																																					p.T86M		Atlas-SNP	.											.	HSD3B7	33	.	0			c.C257T						PASS	.	C	MET/THR,MET/THR,MET/THR	1,4393	2.1+/-5.4	0,1,2196	56.0	48.0	51.0		257,257,257	0.2	0.9	16		51	0,8600		0,0,4300	no	missense,missense,missense	HSD3B7	NM_001142777.1,NM_001142778.1,NM_025193.3	81,81,81	0,1,6496	TT,TC,CC		0.0,0.0228,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	86/197,86/197,86/370	30997460	1,12993	2197	4300	6497	SO:0001583	missense	80270	exon3			TCCACACGGCTGG	AF277719	CCDS10698.1, CCDS45466.1	16p11.2	2011-09-14			ENSG00000099377	ENSG00000099377	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	18324	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 11E, member 3"""	607764				11067870, 19027726	Standard	NM_001142777		Approved	C(27)-3BETA-HSD, SDR11E3	uc002eaf.2	Q9H2F3	OTTHUMG00000132417	ENST00000297679.5:c.257C>T	16.37:g.30997460C>T	ENSP00000297679:p.Thr86Met	Somatic	318	0	0		WXS	Illumina HiSeq	Phase_I	355	74	0.208451	NM_025193	Q96M28|Q9BSN9	Missense_Mutation	SNP	ENST00000297679.5	37	CCDS10698.1	.	.	.	.	.	.	.	.	.	.	C	17.65	3.442073	0.63067	2.28E-4	0.0	ENSG00000099377	ENST00000262520;ENST00000353250;ENST00000297679	D;D;D	0.88586	-2.4;-2.4;-2.03	4.84	0.206	0.15208	3-beta hydroxysteroid dehydrogenase/isomerase (1);NAD(P)-binding domain (1);	0.448337	0.25391	N	0.031012	D	0.86222	0.5881	L	0.53617	1.68	0.27401	N	0.954856	P;P	0.51057	0.941;0.895	P;P	0.46850	0.473;0.529	T	0.80193	-0.1484	10	0.62326	D	0.03	-0.1907	9.4723	0.38851	0.0:0.6139:0.0:0.3861	.	86;86	Q96M28;Q9H2F3	.;3BHS7_HUMAN	M	86	ENSP00000262520:T86M;ENSP00000370662:T86M;ENSP00000297679:T86M	ENSP00000262520:T86M	T	+	2	0	HSD3B7	30904961	0.025000	0.19082	0.859000	0.33776	0.922000	0.55478	1.024000	0.30077	0.198000	0.20407	-0.377000	0.06932	ACG	.	.	weak		0.652	HSD3B7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255554.2		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230315	23230315	+	Silent	SNP	C	C	T	rs148489860	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230315C>T	ENST00000526893.1	+	1	356	c.82C>T	c.(82-84)Ctg>Ttg	p.L28L	IGLL5_ENST00000531372.1_Silent_p.L28L|IGLL5_ENST00000532223.2_Silent_p.L28L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	28						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCCCCTGCTGCTGCTGGGTCT	0.662													C|||	11	0.00219649	0.0045	0.0	5008	,	,		12566	0.003		0.001	False		,,,				2504	0.001				p.L28L		Atlas-SNP	.											.	IGLL5	26	.	0			c.C82T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CTGCTGCTGCTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.82C>T	22.37:g.23230315C>T		Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	68	20	0.294118	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			C|1.000;T|0.000	0.000	strong		0.662	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
WNK2	65268	hgsc.bcm.edu	37	9	96055063	96055063	+	Silent	SNP	C	C	T	rs41278286	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:96055063C>T	ENST00000297954.4	+	23	5427	c.5427C>T	c.(5425-5427)gaC>gaT	p.D1809D	WNK2_ENST00000356055.3_Silent_p.D136D|WNK2_ENST00000395477.2_Silent_p.D1772D|WNK2_ENST00000349097.3_Silent_p.D1421D|WNK2_ENST00000395475.2_3'UTR|WNK2_ENST00000427277.2_Silent_p.D1384D	NM_001282394.1	NP_001269323.1	Q9Y3S1	WNK2_HUMAN	WNK lysine deficient protein kinase 2	1809					intracellular signal transduction (GO:0035556)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of ion homeostasis (GO:2000021)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|central_nervous_system(1)|endometrium(11)|kidney(4)|large_intestine(5)|lung(17)|ovary(2)|prostate(3)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)	54						CCCCACCCGACGTCTACCTGG	0.692													C|||	1965	0.392372	0.3487	0.2954	5008	,	,		13856	0.4206		0.3131	False		,,,				2504	0.5726				p.D1772D		Atlas-SNP	.											WNK2_ENST00000297954,colon,carcinoma,+2,4	WNK2	277	4	0			c.C5316T						scavenged	.	C		1467,2891		252,963,964	15.0	15.0	15.0		5316	-1.8	0.9	9	dbSNP_127	15	2457,6027		393,1671,2178	no	coding-synonymous	WNK2	NM_006648.3		645,2634,3142	TT,TC,CC		28.9604,33.6622,30.556		1772/2218	96055063	3924,8918	2179	4242	6421	SO:0001819	synonymous_variant	65268	exon22			ACCCGACGTCTAC	AJ242724	CCDS75858.1	9q22.3	2008-02-05	2003-06-23	2005-01-22	ENSG00000165238	ENSG00000165238			14542	protein-coding gene	gene with protein product		606249	"""serologically defined colon cancer antigen 43"""	SDCCAG43, PRKWNK2		9610721, 11571656	Standard	NM_006648		Approved	NY-CO-43, KIAA1760	uc004atj.3	Q9Y3S1	OTTHUMG00000020247	ENST00000297954.4:c.5427C>T	9.37:g.96055063C>T		Somatic	94	1	0.0106383		WXS	Illumina HiSeq	Phase_I	98	2	0.0204082	NM_006648	Q5VWF1|Q5VWF2|Q8IY36|Q9C0A3|Q9H3P4	Silent	SNP	ENST00000297954.4	37		777|777	0.3557692307692308|0.3557692307692308	176|176	0.35772357723577236|0.35772357723577236	105|105	0.2900552486187845|0.2900552486187845	256|256	0.44755244755244755|0.44755244755244755	240|240	0.316622691292876|0.316622691292876	C|C	0.625|0.625	-0.819743|-0.819743	0.02776|0.02776	0.336622|0.336622	0.289604|0.289604	ENSG00000165238|ENSG00000165238	ENST00000411624|ENST00000432730;ENST00000448251;ENST00000453718	.|.	.|.	.|.	5.39|5.39	-1.75|-1.75	0.08031|0.08031	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.09310|0.09310	P|P	0.9999999999996005|0.9999999999996005	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.46005|0.46005	-0.9222|-0.9222	3|3	.|.	.|.	.|.	.|.	11.3977|11.3977	0.49851|0.49851	0.0:0.3577:0.0:0.6423|0.0:0.3577:0.0:0.6423	rs41278286;rs57682323;rs61738874|rs41278286;rs57682323;rs61738874	.|.	.|.	.|.	C|M	1376|1768;569;294	.|.	.|.	R|T	+|+	1|2	0|0	WNK2|WNK2	95094884|95094884	0.000000|0.000000	0.05858|0.05858	0.908000|0.908000	0.35775|0.35775	0.064000|0.064000	0.16182|0.16182	-2.297000|-2.297000	0.01141|0.01141	-0.195000|-0.195000	0.10382|0.10382	-1.010000|-1.010000	0.02471|0.02471	CGT|ACG	C|0.672;T|0.328	0.328	strong		0.692	WNK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317359.1	NM_006648	
GALNT8	26290	hgsc.bcm.edu	37	12	4873163	4873163	+	Missense_Mutation	SNP	G	G	T	rs1468556	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:4873163G>T	ENST00000252318.2	+	9	1880	c.1543G>T	c.(1543-1545)Gtt>Ttt	p.V515F		NM_017417.1	NP_059113.1	Q9NY28	GALT8_HUMAN	polypeptide N-acetylgalactosaminyltransferase 8	515	Ricin B-type lectin. {ECO:0000255|PROSITE-ProRule:PRU00174}.		V -> F (in dbSNP:rs1468556). {ECO:0000269|PubMed:10767557}.		cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|pancreas(1)|prostate(4)|skin(2)|urinary_tract(1)	35						TCAGGGACCCGTTCCAGGCAA	0.502													G|||	1651	0.329673	0.2466	0.4251	5008	,	,		19640	0.3611		0.4225	False		,,,				2504	0.2464				p.V515F	Colon(108;631 1558 7270 20097 39846)	Atlas-SNP	.											GALNT8,NS,adenoma,0,1	GALNT8	89	1	0			c.G1543T						scavenged	.	G	PHE/VAL	1305,3101	442.3+/-346.6	207,891,1105	196.0	174.0	182.0		1543	-7.6	0.0	12	dbSNP_88	182	3609,4991	521.6+/-379.9	761,2087,1452	yes	missense	GALNT8	NM_017417.1	50	968,2978,2557	TT,TG,GG		41.9651,29.6187,37.7826	possibly-damaging	515/638	4873163	4914,8092	2203	4300	6503	SO:0001583	missense	26290	exon9			GGACCCGTTCCAG	AJ271385	CCDS8533.1	12p13.32	2014-03-13	2014-03-13		ENSG00000130035	ENSG00000130035	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4130	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 8"""	606250	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 8 (GalNAc-T8)"""			10767557	Standard	NM_017417		Approved	GALNAC-T8	uc001qne.1	Q9NY28	OTTHUMG00000166188	ENST00000252318.2:c.1543G>T	12.37:g.4873163G>T	ENSP00000252318:p.Val515Phe	Somatic	306	1	0.00326797		WXS	Illumina HiSeq	Phase_I	329	6	0.0182371	NM_017417	B2RU02	Missense_Mutation	SNP	ENST00000252318.2	37	CCDS8533.1	814	0.3727106227106227	124	0.25203252032520324	150	0.4143646408839779	223	0.38986013986013984	317	0.4182058047493404	G	8.342	0.828853	0.16749	0.296187	0.419651	ENSG00000130035	ENST00000252318	T	0.26957	1.7	4.43	-7.55	0.01327	Ricin B-related lectin (1);Ricin B lectin (3);	1.667950	0.02954	N	0.142084	T	0.00012	0.0000	L	0.31926	0.97	0.80722	P	0.0	B	0.31383	0.321	B	0.29716	0.106	T	0.18935	-1.0321	9	0.56958	D	0.05	.	8.9706	0.35903	0.596:0.0:0.3027:0.1014	rs1468556;rs17783619;rs59456221;rs1468556	515	Q9NY28	GALT8_HUMAN	F	515	ENSP00000252318:V515F	ENSP00000252318:V515F	V	+	1	0	GALNT8	4743424	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.158000	0.10070	-1.811000	0.01229	-0.751000	0.03497	GTT	G|0.627;T|0.373	0.373	strong		0.502	GALNT8-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388277.2	NM_017417	
SEMG1	6406	hgsc.bcm.edu	37	20	43837052	43837052	+	Missense_Mutation	SNP	C	C	A	rs199672858	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:43837052C>A	ENST00000372781.3	+	2	1171	c.1114C>A	c.(1114-1116)Cgc>Agc	p.R372S	SEMG1_ENST00000244069.6_Missense_Mutation_p.R312S	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	372	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.		R -> L (in dbSNP:rs2233887). {ECO:0000269|PubMed:14629036}.		insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				TGTATCCCAACGCAGTATTTA	0.418																																					p.R372S		Atlas-SNP	.											SEMG1,bladder,carcinoma,0,3	SEMG1	71	3	0			c.C1114A						scavenged	.						77.0	71.0	73.0					20																	43837052		2203	4300	6503	SO:0001583	missense	6406	exon2			TCCCAACGCAGTA		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.1114C>A	20.37:g.43837052C>A	ENSP00000361867:p.Arg372Ser	Somatic	200	1	0.005		WXS	Illumina HiSeq	Phase_I	158	5	0.0316456	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Missense_Mutation	SNP	ENST00000372781.3	37	CCDS13345.1	.	.	.	.	.	.	.	.	.	.	A	0.011	-1.712711	0.00712	.	.	ENSG00000124233	ENST00000244069;ENST00000372781	T;T	0.03951	3.75;3.75	0.951	-1.9	0.07665	.	.	.	.	.	T	0.00754	0.0025	N	0.00082	-2.215	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.34079	-0.9843	9	0.09590	T	0.72	.	0.297	0.00267	0.2228:0.2395:0.2981:0.2396	.	312;372	P04279-2;P04279	.;SEMG1_HUMAN	S	312;372	ENSP00000244069:R312S;ENSP00000361867:R372S	ENSP00000244069:R312S	R	+	1	0	SEMG1	43270466	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.965000	0.03829	-2.064000	0.00888	-1.625000	0.00788	CGC	C|1.000;T|0.000	.	alt		0.418	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
NYNRIN	57523	hgsc.bcm.edu	37	14	24878537	24878537	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:24878537G>A	ENST00000382554.3	+	4	1855	c.1537G>A	c.(1537-1539)Gct>Act	p.A513T		NM_025081.2	NP_079357.2	Q9P2P1	NYNRI_HUMAN	NYN domain and retroviral integrase containing	513					DNA integration (GO:0015074)	integral component of membrane (GO:0016021)	nucleic acid binding (GO:0003676)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(8)|lung(21)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	56						AGAGGGACCCGCTCCAGTGCT	0.572																																					p.A513T		Atlas-SNP	.											.	NYNRIN	120	.	0			c.G1537A						PASS	.						39.0	42.0	41.0					14																	24878537		1934	4128	6062	SO:0001583	missense	57523	exon4			GGACCCGCTCCAG	AB037726	CCDS45090.1	14q11.2	2009-10-14	2009-10-14	2009-10-14		ENSG00000205978			20165	protein-coding gene	gene with protein product	"""Cousin of GIN1"""		"""KIAA1305"""	KIAA1305		19561090, 17114934	Standard	NM_025081		Approved	FLJ11811, CGIN1	uc001wpf.4	Q9P2P1		ENST00000382554.3:c.1537G>A	14.37:g.24878537G>A	ENSP00000371994:p.Ala513Thr	Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	102	13	0.127451	NM_025081	Q6P153|Q86TR3|Q9HAC4	Missense_Mutation	SNP	ENST00000382554.3	37	CCDS45090.1	.	.	.	.	.	.	.	.	.	.	g	7.747	0.702554	0.15172	.	.	ENSG00000205978	ENST00000382554	T	0.09817	2.94	4.63	-3.59	0.04583	.	.	.	.	.	T	0.03348	0.0097	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.44314	-0.9336	9	0.07990	T	0.79	.	2.4094	0.04420	0.2503:0.0823:0.4134:0.2539	.	513	Q9P2P1	NYNRI_HUMAN	T	513	ENSP00000371994:A513T	ENSP00000371994:A513T	A	+	1	0	NYNRIN	23948377	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.413000	0.07123	-0.640000	0.05495	-2.194000	0.00310	GCT	.	.	none		0.572	NYNRIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412939.1		
POU2AF1	5450	hgsc.bcm.edu	37	11	111249896	111249896	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:111249896A>G	ENST00000393067.3	-	1	521	c.7T>C	c.(7-9)Tgg>Cgg	p.W3R		NM_006235.2	NP_006226.2	Q16633	OBF1_HUMAN	POU class 2 associating factor 1	3					humoral immune response (GO:0006959)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(2)|lung(2)	5		all_cancers(61;1.36e-12)|all_epithelial(67;1.87e-07)|Melanoma(852;1.46e-05)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|all_neural(223;0.0146)|Medulloblastoma(222;0.0245)|Breast(348;0.0389)		Epithelial(105;1.01e-06)|BRCA - Breast invasive adenocarcinoma(274;3.12e-06)|all cancers(92;1.8e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.0364)		CGTTTTTGCCAGAGCATGGCC	0.557			T	BCL6	NHL																																p.W3R		Atlas-SNP	.		Dom	yes		11	11q23.1	5450	"""POU domain, class 2, associating factor 1 (OBF1)"""		L	.	POU2AF1	23	.	0			c.T7C						PASS	.						211.0	202.0	205.0					11																	111249896		2201	4297	6498	SO:0001583	missense	5450	exon1			TTTGCCAGAGCAT		CCDS31675.1	11q23.1	2011-06-01	2007-07-13			ENSG00000110777			9211	protein-coding gene	gene with protein product		601206	"""POU domain class 2, associating factor 1"""			8617501	Standard	NM_006235		Approved	OBF1	uc001plg.4	Q16633		ENST00000393067.3:c.7T>C	11.37:g.111249896A>G	ENSP00000376786:p.Trp3Arg	Somatic	313	0	0		WXS	Illumina HiSeq	Phase_I	366	82	0.224044	NM_006235	B2R8Z9|Q14983	Missense_Mutation	SNP	ENST00000393067.3	37	CCDS31675.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.211438	0.79240	.	.	ENSG00000110777	ENST00000393067	T	0.31510	1.49	5.3	5.3	0.74995	.	0.572674	0.16592	N	0.207726	T	0.46073	0.1374	L	0.38175	1.15	0.45118	D	0.998132	D	0.76494	0.999	D	0.87578	0.998	T	0.40403	-0.9565	10	0.87932	D	0	.	13.2379	0.59979	1.0:0.0:0.0:0.0	.	3	Q16633	OBF1_HUMAN	R	3	ENSP00000376786:W3R	ENSP00000376786:W3R	W	-	1	0	POU2AF1	110755106	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.293000	0.65680	2.225000	0.72522	0.533000	0.62120	TGG	.	.	none		0.557	POU2AF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391002.1	NM_006235	
SACS	26278	hgsc.bcm.edu	37	13	23907902	23907902	+	Silent	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:23907902A>C	ENST00000382292.3	-	9	10386	c.10113T>G	c.(10111-10113)acT>acG	p.T3371T	SACS_ENST00000402364.1_Silent_p.T2621T|SACS_ENST00000382298.3_Silent_p.T3371T			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	3371					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TAAATGTTGAAGTTTGGACCA	0.353																																					p.T3371T		Atlas-SNP	.											SACS_ENST00000382298,NS,carcinoma,0,2	SACS	871	2	0			c.T10113G						PASS	.						75.0	73.0	74.0					13																	23907902		2203	4299	6502	SO:0001819	synonymous_variant	26278	exon10			TGTTGAAGTTTGG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.10113T>G	13.37:g.23907902A>C		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	96	20	0.208333	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	37	CCDS9300.2																																																																																			.	.	none		0.353	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
ST7L	54879	hgsc.bcm.edu	37	1	113153627	113153627	+	Splice_Site	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:113153627T>C	ENST00000358039.4	-	3	593		c.e3-2		ST7L_ENST00000369666.1_Splice_Site|ST7L_ENST00000490067.1_Splice_Site|ST7L_ENST00000360743.4_Splice_Site|ST7L_ENST00000463235.1_Splice_Site|ST7L_ENST00000369668.2_Splice_Site|ST7L_ENST00000544629.1_Splice_Site|ST7L_ENST00000543570.1_Splice_Site|ST7L_ENST00000343210.7_Splice_Site|ST7L_ENST00000538187.1_Splice_Site|ST7L_ENST00000369669.1_Splice_Site	NM_017744.4|NM_138727.3	NP_060214.2|NP_620055.1	Q8TDW4	ST7L_HUMAN	suppression of tumorigenicity 7 like						negative regulation of cell growth (GO:0030308)	integral component of membrane (GO:0016021)				endometrium(1)|kidney(4)|large_intestine(3)|lung(1)|prostate(2)|stomach(1)|urinary_tract(3)	15	Lung SC(450;0.246)	all_cancers(81;1.44e-07)|all_epithelial(167;7.64e-07)|all_lung(203;2.16e-05)|Lung NSC(69;3.86e-05)		Lung(183;0.0234)|all cancers(265;0.0246)|Epithelial(280;0.0342)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTCAAATATCTATGACAAACA	0.383																																					.		Atlas-SNP	.											.	ST7L	31	.	0			c.289-2A>G						PASS	.						93.0	88.0	90.0					1																	113153627		2203	4300	6503	SO:0001630	splice_region_variant	54879	exon4			AATATCTATGACA	AB081317	CCDS848.1, CCDS849.1, CCDS850.1, CCDS852.1	1p13.1	2008-06-06			ENSG00000007341	ENSG00000007341			18441	protein-coding gene	gene with protein product						12012006	Standard	NM_138729		Approved	FLJ20284, STLR, ST7R, FAM4B	uc001ecd.3	Q8TDW4	OTTHUMG00000011753	ENST00000358039.4:c.289-2A>G	1.37:g.113153627T>C		Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	92	20	0.217391	NM_138728	A8K4S7|Q49AH6|Q5TEI4|Q5U5K6|Q6N067|Q7Z2Z0|Q7Z3C2|Q8N7P8|Q8TDW1|Q8TDW2|Q8TDW3|Q9NXF3	Splice_Site	SNP	ENST00000358039.4	37	CCDS848.1	.	.	.	.	.	.	.	.	.	.	T	19.02	3.746023	0.69418	.	.	ENSG00000007341	ENST00000358039;ENST00000360743;ENST00000544629;ENST00000490067;ENST00000369668;ENST00000343210;ENST00000369666;ENST00000538187;ENST00000543570;ENST00000369664	.	.	.	5.9	5.9	0.94986	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3058	0.73990	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	ST7L	112955150	1.000000	0.71417	0.970000	0.41538	0.839000	0.47603	7.606000	0.82863	2.254000	0.74563	0.482000	0.46254	.	.	.	none		0.383	ST7L-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000032504.3		Intron
KEAP1	9817	hgsc.bcm.edu	37	19	10600442	10600442	+	Silent	SNP	G	G	C	rs1048290	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:10600442G>C	ENST00000171111.5	-	4	1960	c.1413C>G	c.(1411-1413)ctC>ctG	p.L471L	KEAP1_ENST00000588024.1_5'Flank|KEAP1_ENST00000393623.2_Silent_p.L471L|CTC-429L19.3_ENST00000592671.1_RNA	NM_203500.1	NP_987096.1	Q14145	KEAP1_HUMAN	kelch-like ECH-associated protein 1	471					cellular response to interleukin-4 (GO:0071353)|in utero embryonic development (GO:0001701)|proteasomal ubiquitin-independent protein catabolic process (GO:0010499)|protein ubiquitination (GO:0016567)|regulation of epidermal cell differentiation (GO:0045604)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|nucleus (GO:0005634)		p.L471L(1)		breast(3)|endometrium(2)|kidney(4)|large_intestine(4)|liver(2)|lung(69)|ovary(2)|pancreas(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	92			OV - Ovarian serous cystadenocarcinoma(20;2.71e-09)|Epithelial(33;2.32e-06)|all cancers(31;1.42e-05)		Dimethyl fumarate(DB08908)	CGGCATAAAGGAGACGATTGA	0.562													C|||	2545	0.508187	0.7534	0.2983	5008	,	,		14922	0.5337		0.3549	False		,,,				2504	0.4571				p.L471L		Atlas-SNP	.											KEAP1,NS,carcinoma,0,1	KEAP1	182	1	1	Substitution - coding silent(1)	stomach(1)	c.C1413G						scavenged	.	C	,	3017,1389	455.9+/-351.1	1037,943,223	77.0	63.0	68.0		1413,1413	0.6	1.0	19	dbSNP_86	68	3200,5400	653.2+/-401.0	612,1976,1712	no	coding-synonymous,coding-synonymous	KEAP1	NM_012289.3,NM_203500.1	,	1649,2919,1935	CC,CG,GG		37.2093,31.5252,47.801	,	471/625,471/625	10600442	6217,6789	2203	4300	6503	SO:0001819	synonymous_variant	9817	exon4			ATAAAGGAGACGA	AF361886	CCDS12239.1	19p13.2	2013-01-30				ENSG00000079999		"""Kelch-like"", ""BTB/POZ domain containing"""	23177	protein-coding gene	gene with protein product	"""kelch-like family member 19"""	606016					Standard	NM_012289		Approved	KIAA0132, MGC10630, MGC1114, MGC20887, MGC4407, MGC9454, INrf2, KLHL19	uc002mor.1	Q14145		ENST00000171111.5:c.1413C>G	19.37:g.10600442G>C		Somatic	217	1	0.00460829		WXS	Illumina HiSeq	Phase_I	217	3	0.0138249	NM_012289	B3KPD5|Q6LEP0|Q8WTX1|Q9BPY9	Silent	SNP	ENST00000171111.5	37	CCDS12239.1																																																																																			G|0.511;C|0.489	0.489	strong		0.562	KEAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452000.1	NM_012289	
DMBT1	1755	hgsc.bcm.edu	37	10	124340397	124340397	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:124340397C>T	ENST00000338354.3	+	11	1125	c.1019C>T	c.(1018-1020)cCg>cTg	p.P340L	DMBT1_ENST00000368955.3_Missense_Mutation_p.P340L|DMBT1_ENST00000368909.3_Missense_Mutation_p.P340L|DMBT1_ENST00000330163.4_Missense_Mutation_p.P340L|DMBT1_ENST00000359586.6_Missense_Mutation_p.P208L|DMBT1_ENST00000368956.2_Missense_Mutation_p.P340L|DMBT1_ENST00000344338.3_Missense_Mutation_p.P340L			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	340					defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CAGTCCCGGCCGACACCCAGC	0.532																																					p.P340L	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											DMBT1_ENST00000368915,NS,carcinoma,-1,13	DMBT1	677	13	0			c.C1019T						scavenged	.						449.0	390.0	409.0					10																	124340397		1913	4113	6026	SO:0001583	missense	1755	exon11			CCCGGCCGACACC		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.1019C>T	10.37:g.124340397C>T	ENSP00000342210:p.Pro340Leu	Somatic	726	2	0.00275482		WXS	Illumina HiSeq	Phase_I	784	158	0.201531	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		.	.	.	.	.	.	.	.	.	.	C	5.419	0.262446	0.10294	.	.	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.25579	1.82;1.83;1.81;1.82;1.83;1.81;1.79	1.45	1.45	0.22620	Speract/scavenger receptor-related (1);	.	.	.	.	T	0.12008	0.0292	N	0.08118	0	0.09310	N	1	B;B;P;B;D;B	0.55800	0.11;0.036;0.704;0.001;0.973;0.293	B;B;B;B;P;B	0.45343	0.018;0.004;0.041;0.001;0.477;0.034	T	0.08106	-1.0738	9	0.11182	T	0.66	.	6.398	0.21622	0.0:1.0:0.0:0.0	.	208;340;340;340;340;340	F8WEF7;Q9UGM3-4;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;.;DMBT1_HUMAN	L	340;340;340;340;340;340;340;340;340;340;340;340;340;208	ENSP00000342210:P340L;ENSP00000343175:P340L;ENSP00000327747:P340L;ENSP00000357905:P340L;ENSP00000357951:P340L;ENSP00000357952:P340L;ENSP00000352593:P208L	ENSP00000331522:P340L	P	+	2	0	DMBT1	124330387	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.841000	0.27613	1.165000	0.42670	0.194000	0.17425	CCG	.	.	none		0.532	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230318	23230318	+	Missense_Mutation	SNP	C	C	G	rs567537853		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230318C>G	ENST00000526893.1	+	1	359	c.85C>G	c.(85-87)Ctg>Gtg	p.L29V	IGLL5_ENST00000531372.1_Missense_Mutation_p.L29V|IGLL5_ENST00000532223.2_Missense_Mutation_p.L29V|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	29						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCTGCTGCTGCTGGGTCTGGC	0.657																																					p.L29V		Atlas-SNP	.											.	IGLL5	26	.	0			c.C85G						PASS	.																																			SO:0001583	missense	100423062	exon1			CTGCTGCTGGGTC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.85C>G	22.37:g.23230318C>G	ENSP00000431254:p.Leu29Val	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	62	18	0.290323	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	C	17.27	3.347544	0.61183	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00717	5.79;5.8	3.82	3.82	0.43975	.	.	.	.	.	T	0.02193	0.0068	L	0.32530	0.975	0.24893	N	0.992151	D	0.76494	0.999	D	0.75484	0.986	T	0.54159	-0.8335	9	0.66056	D	0.02	.	11.5007	0.50435	0.0:1.0:0.0:0.0	.	29	B9A064	IGLL5_HUMAN	V	29	ENSP00000436353:L29V;ENSP00000431254:L29V	ENSP00000431254:L29V	L	+	1	2	IGLL5	21560318	0.000000	0.05858	0.815000	0.32552	0.079000	0.17450	0.026000	0.13599	2.423000	0.82170	0.643000	0.83706	CTG	.	.	none		0.657	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
NECAP1	25977	hgsc.bcm.edu	37	12	8245311	8245311	+	Silent	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:8245311A>G	ENST00000339754.5	+	5	501	c.423A>G	c.(421-423)caA>caG	p.Q141Q		NM_015509.3	NP_056324.2	Q8NC96	NECP1_HUMAN	NECAP endocytosis associated 1	141					endocytosis (GO:0006897)|protein transport (GO:0015031)	clathrin vesicle coat (GO:0030125)|coated pit (GO:0005905)|plasma membrane (GO:0005886)				cervix(1)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	10				Kidney(36;0.0915)		AGGAATCTCAAGAAATGGATG	0.408																																					p.Q141Q		Atlas-SNP	.											.	NECAP1	21	.	0			c.A423G						PASS	.						70.0	71.0	71.0					12																	8245311		2203	4300	6503	SO:0001819	synonymous_variant	25977	exon5			ATCTCAAGAAATG	AK074923	CCDS8589.1	12p13.31	2012-05-02			ENSG00000089818	ENSG00000089818			24539	protein-coding gene	gene with protein product		611623				14555962, 15494011	Standard	NM_015509		Approved	DKFZP566B183	uc001qtx.2	Q8NC96	OTTHUMG00000168568	ENST00000339754.5:c.423A>G	12.37:g.8245311A>G		Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	138	40	0.289855	NM_015509	Q2NL73|Q5XG95|Q6NWY6|Q8N153|Q8NCB0|Q9BU52|Q9Y407	Silent	SNP	ENST00000339754.5	37	CCDS8589.1																																																																																			.	.	none		0.408	NECAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400244.1	NM_015509	
PI4KA	5297	hgsc.bcm.edu	37	22	21167787	21167787	+	Silent	SNP	G	G	A	rs165854	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:21167787G>A	ENST00000572273.1	-	8	920	c.690C>T	c.(688-690)tgC>tgT	p.C230C	PI4KA_ENST00000255882.6_Silent_p.C288C			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	230					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)	p.C230C(1)		breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)			CATCGGGCAAGCAGGAGGCTG	0.522													G|||	2461	0.491414	0.6036	0.5144	5008	,	,		16352	0.5486		0.4254	False		,,,				2504	0.3323				p.C288C	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											PI4KA_ENST00000255882,NS,carcinoma,0,1	PI4KA	313	1	1	Substitution - coding silent(1)	stomach(1)	c.C864T						scavenged	.	G		2509,1897	628.1+/-395.0	717,1075,411	58.0	60.0	59.0		690	5.3	0.1	22	dbSNP_79	59	3494,5106	510.8+/-377.6	718,2058,1524	no	coding-synonymous	PI4KA	NM_058004.3		1435,3133,1935	AA,AG,GG		40.6279,43.0549,46.1556		230/2045	21167787	6003,7003	2203	4300	6503	SO:0001819	synonymous_variant	5297	exon8			GGGCAAGCAGGAG	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.690C>T	22.37:g.21167787G>A		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	117	3	0.025641	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				G|0.526;A|0.474	0.474	strong		0.522	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
GPR98	84059	hgsc.bcm.edu	37	5	89948249	89948249	+	Missense_Mutation	SNP	A	A	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:89948249A>T	ENST00000405460.2	+	19	3599	c.3503A>T	c.(3502-3504)gAg>gTg	p.E1168V		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	1168	Calx-beta 9. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		CCTGGGCAGGAGTTCTATGAA	0.388																																					p.E1168V		Atlas-SNP	.											.	GPR98	605	.	0			c.A3503T						PASS	.						134.0	128.0	130.0					5																	89948249		1908	4144	6052	SO:0001583	missense	84059	exon19			GGCAGGAGTTCTA	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.3503A>T	5.37:g.89948249A>T	ENSP00000384582:p.Glu1168Val	Somatic	168	0	0		WXS	Illumina HiSeq	Phase_I	153	31	0.202614	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	A	33	5.230671	0.95207	.	.	ENSG00000164199	ENST00000405460;ENST00000296619;ENST00000399043	T	0.29917	1.55	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	T	0.47637	0.1456	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.76071	0.987	T	0.45789	-0.9237	10	0.87932	D	0	.	16.635	0.85050	1.0:0.0:0.0:0.0	.	1168	Q8WXG9	GPR98_HUMAN	V	1168	ENSP00000384582:E1168V	ENSP00000296619:E1168V	E	+	2	0	GPR98	89984005	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	9.078000	0.94023	2.330000	0.79161	0.477000	0.44152	GAG	.	.	none		0.388	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230283	23230283	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:23230283G>A	ENST00000526893.1	+	1	324	c.50G>A	c.(49-51)gGc>gAc	p.G17D	IGLL5_ENST00000531372.1_Missense_Mutation_p.G17D|IGLL5_ENST00000532223.2_Missense_Mutation_p.G17D|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	17						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GAGGAGCTGGGCCCTGGTCCC	0.672																																					p.G17D		Atlas-SNP	.											.	IGLL5	26	.	0			c.G50A						PASS	.																																			SO:0001583	missense	100423062	exon1			AGCTGGGCCCTGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.50G>A	22.37:g.23230283G>A	ENSP00000431254:p.Gly17Asp	Somatic	107	0	0		WXS	Illumina HiSeq	Phase_I	142	38	0.267606	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.81	1.455202	0.26161	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00614	6.21;6.22	3.24	-0.78	0.10969	.	.	.	.	.	T	0.00580	0.0019	L	0.29908	0.895	0.09310	N	1	B	0.15930	0.015	B	0.10450	0.005	T	0.45425	-0.9262	9	0.52906	T	0.07	.	3.2568	0.06835	0.325:0.2123:0.4627:0.0	.	17	B9A064	IGLL5_HUMAN	D	17	ENSP00000436353:G17D;ENSP00000431254:G17D	ENSP00000431254:G17D	G	+	2	0	IGLL5	21560283	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.154000	0.16343	-0.051000	0.13334	0.643000	0.83706	GGC	.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
SLC35G6	643664	hgsc.bcm.edu	37	17	7386301	7386301	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:7386301A>C	ENST00000412468.2	+	2	1113	c.998A>C	c.(997-999)gAa>gCa	p.E333A	POLR2A_ENST00000572844.1_5'Flank|ZBTB4_ENST00000311403.4_Intron|POLR2A_ENST00000322644.6_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	333						integral component of membrane (GO:0016021)		p.E333A(1)									TGTGAGAGGGAAGGGAAGGTG	0.557																																					p.E333A		Atlas-SNP	.											POLR2A_ENST00000412468,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	prostate(1)	c.A998C						scavenged	.						60.0	58.0	59.0					17																	7386301		2203	4300	6503	SO:0001583	missense	643664	exon2			AGAGGGAAGGGAA		CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.998A>C	17.37:g.7386301A>C	ENSP00000396523:p.Glu333Ala	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	107	3	0.0280374	NM_001102614		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	A	2.913	-0.225018	0.06022	.	.	ENSG00000181222	ENST00000412468	T	0.26067	1.76	4.69	1.0	0.19881	.	.	.	.	.	T	0.15609	0.0376	N	0.25647	0.755	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.22626	-1.0211	9	0.36615	T	0.2	-0.2286	5.7938	0.18375	0.4278:0.471:0.1012:0.0	.	333	P0C7Q6	S35G6_HUMAN	A	333	ENSP00000396523:E333A	ENSP00000396523:E333A	E	+	2	0	SLC35G6	7327025	0.886000	0.30341	0.428000	0.26697	0.484000	0.33280	1.649000	0.37281	0.732000	0.32470	0.477000	0.44152	GAA	.	.	none		0.557	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001102614	
RABEP2	79874	hgsc.bcm.edu	37	16	28935738	28935738	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:28935738T>C	ENST00000358201.4	-	2	848	c.260A>G	c.(259-261)cAg>cGg	p.Q87R	RABEP2_ENST00000561803.1_5'UTR|RABEP2_ENST00000357573.6_Missense_Mutation_p.Q87R|RABEP2_ENST00000544477.1_Intron	NM_024816.2	NP_079092.2	Q9H5N1	RABE2_HUMAN	rabaptin, RAB GTPase binding effector protein 2	87					endocytosis (GO:0006897)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			breast(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(1)	16						CAGGATGGCCTGCAGCGAGGC	0.607																																					p.Q87R	Pancreas(66;639 1284 10093 31061 49099)	Atlas-SNP	.											.	RABEP2	48	.	0			c.A260G						PASS	.						47.0	49.0	48.0					16																	28935738		2102	4240	6342	SO:0001583	missense	79874	exon2			ATGGCCTGCAGCG	AK026935	CCDS42140.1	16p11.2	2014-09-11			ENSG00000177548	ENSG00000177548			24817	protein-coding gene	gene with protein product		611869				12477932	Standard	NM_024816		Approved	FRA, FLJ23282	uc002drq.3	Q9H5N1	OTTHUMG00000176593	ENST00000358201.4:c.260A>G	16.37:g.28935738T>C	ENSP00000350934:p.Gln87Arg	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	81	10	0.123457	NM_024816		Missense_Mutation	SNP	ENST00000358201.4	37	CCDS42140.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.637917	0.47049	.	.	ENSG00000177548	ENST00000358201;ENST00000357573	T;T	0.58210	0.39;0.35	4.29	4.29	0.51040	Rabaptin coiled-coil domain (1);	0.000000	0.85682	D	0.000000	T	0.67097	0.2857	L	0.58810	1.83	0.80722	D	1	D;D;D	0.69078	0.992;0.997;0.994	D;D;D	0.81914	0.979;0.995;0.988	T	0.70461	-0.4865	10	0.72032	D	0.01	-26.7142	12.7364	0.57228	0.0:0.0:0.0:1.0	.	87;87;87	Q9H5N1-2;Q49AT6;Q9H5N1	.;.;RABE2_HUMAN	R	87	ENSP00000350934:Q87R;ENSP00000350186:Q87R	ENSP00000350186:Q87R	Q	-	2	0	RABEP2	28843239	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	7.284000	0.78650	1.711000	0.51337	0.454000	0.30748	CAG	.	.	none		0.607	RABEP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432691.1	NM_024816	
RERE	473	hgsc.bcm.edu	37	1	8421203	8421203	+	Silent	SNP	T	T	C	rs13596	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:8421203T>C	ENST00000337907.3	-	19	2998	c.2364A>G	c.(2362-2364)ccA>ccG	p.P788P	RERE_ENST00000476556.1_Silent_p.P234P|RERE_ENST00000400907.2_Intron|RERE_ENST00000377464.1_Silent_p.P520P|RERE_ENST00000400908.2_Silent_p.P788P	NM_012102.3	NP_036234.3	Q9P2R6	RERE_HUMAN	arginine-glutamic acid dipeptide (RE) repeats	788	Pro-rich.				chromatin remodeling (GO:0006338)|multicellular organismal development (GO:0007275)|NLS-bearing protein import into nucleus (GO:0006607)|transcription, DNA-templated (GO:0006351)	histone deacetylase complex (GO:0000118)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|poly-glutamine tract binding (GO:0008267)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|liver(1)|lung(16)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	49	Ovarian(185;0.0661)	all_epithelial(116;1.17e-21)|all_lung(118;1.4e-06)|Lung NSC(185;3.06e-06)|Renal(390;0.000147)|Breast(348;0.000206)|Colorectal(325;0.00187)|Hepatocellular(190;0.00825)|Ovarian(437;0.0253)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|all cancers(8;9.64e-67)|GBM - Glioblastoma multiforme(8;9.89e-33)|Colorectal(212;1.45e-07)|COAD - Colon adenocarcinoma(227;3.42e-05)|Kidney(185;6e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000533)|KIRC - Kidney renal clear cell carcinoma(229;0.00106)|STAD - Stomach adenocarcinoma(132;0.00118)|READ - Rectum adenocarcinoma(331;0.0419)|Lung(427;0.195)		TGGGAGCCTGTGGCTGGTTAG	0.731													t|||	4006	0.79992	0.8411	0.7925	5008	,	,		12992	0.9206		0.6819	False		,,,				2504	0.7464				p.P788P		Atlas-SNP	.											RERE,NS,carcinoma,0,4	RERE	129	4	0			c.A2364G						PASS	.	T	,,	3390,752		1409,572,90	6.0	7.0	7.0		2364,702,2364	-10.0	0.0	1	dbSNP_52	7	5605,2589		1942,1721,434	no	coding-synonymous,coding-synonymous,coding-synonymous	RERE	NM_001042681.1,NM_001042682.1,NM_012102.3	,,	3351,2293,524	CC,CT,TT		31.5963,18.1555,27.0833	,,	788/1567,234/1013,788/1567	8421203	8995,3341	2071	4097	6168	SO:0001819	synonymous_variant	473	exon19			AGCCTGTGGCTGG	AF016005	CCDS95.1, CCDS41243.1	1p36.23	2013-01-25			ENSG00000142599	ENSG00000142599		"""GATA zinc finger domain containing"""	9965	protein-coding gene	gene with protein product		605226		ATN1L		10814707, 10729226	Standard	NM_012102		Approved	KIAA0458, ARP, ARG, DNB1	uc001apf.3	Q9P2R6	OTTHUMG00000001765	ENST00000337907.3:c.2364A>G	1.37:g.8421203T>C		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_012102	O43393|O75046|O75359|Q5VXL9|Q6P6B9|Q9Y2W4	Silent	SNP	ENST00000337907.3	37	CCDS95.1																																																																																			T|0.214;C|0.786	0.786	strong		0.731	RERE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000004916.1		
PRG4	10216	hgsc.bcm.edu	37	1	186276981	186276981	+	Silent	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:186276981A>G	ENST00000445192.2	+	7	2175	c.2130A>G	c.(2128-2130)aaA>aaG	p.K710K	PRG4_ENST00000367485.4_Silent_p.K617K|PRG4_ENST00000367483.4_Silent_p.K669K|PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Silent_p.K667K	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	710	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CTACCCCTAAAGGGACTGCTC	0.582																																					p.K710K		Atlas-SNP	.											PRG4,NS,carcinoma,0,6	PRG4	259	6	0			c.A2130G						scavenged	.						162.0	175.0	171.0					1																	186276981		2203	4300	6503	SO:0001819	synonymous_variant	10216	exon7			CCCTAAAGGGACT	U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.2130A>G	1.37:g.186276981A>G		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	118	5	0.0423729	NM_005807	Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																			.	.	none		0.582	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1	NM_005807	
DUSP2	1844	hgsc.bcm.edu	37	2	96809580	96809580	+	Silent	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:96809580G>T	ENST00000288943.4	-	4	1012	c.927C>A	c.(925-927)acC>acA	p.T309T	AC012307.2_ENST00000449242.1_lincRNA	NM_004418.3	NP_004409.1	Q05923	DUS2_HUMAN	dual specificity phosphatase 2	309					endoderm formation (GO:0001706)|inactivation of MAPK activity (GO:0000188)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			NS(1)|breast(1)|lung(2)|skin(1)	5		Ovarian(717;0.0228)				ACAGCACCTGGGTCTCAAACT	0.642																																					p.T309T		Atlas-SNP	.											DUSP2,NS,NS,-2,2	DUSP2	20	2	0			c.C927A						scavenged	.						42.0	41.0	41.0					2																	96809580		2203	4300	6503	SO:0001819	synonymous_variant	1844	exon4			CACCTGGGTCTCA	L11329	CCDS2016.1	2q11	2011-06-09			ENSG00000158050	ENSG00000158050		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3068	protein-coding gene	gene with protein product		603068				7806236, 7590752, 12673251	Standard	NM_004418		Approved	PAC-1	uc002svk.4	Q05923	OTTHUMG00000130456	ENST00000288943.4:c.927C>A	2.37:g.96809580G>T		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	201	3	0.0149254	NM_004418	Q53T45	Silent	SNP	ENST00000288943.4	37	CCDS2016.1																																																																																			.	.	none		0.642	DUSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252847.1	NM_004418	
SCN1A	6323	hgsc.bcm.edu	37	2	166847770	166847770	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:166847770T>G	ENST00000303395.4	-	26	6014	c.6015A>C	c.(6013-6015)aaA>aaC	p.K2005N	SCN1A_ENST00000375405.3_Missense_Mutation_p.K1994N|SCN1A_ENST00000423058.2_Missense_Mutation_p.K2005N|AC010127.3_ENST00000595647.1_RNA|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000409050.1_Missense_Mutation_p.K1977N			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	2005					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	tCCCTTTGGCTTTTTCATCTT	0.383																																					p.K2005N		Atlas-SNP	.											SCN1A_ENST00000303395,NS,carcinoma,-1,2	SCN1A	641	2	0			c.A6015C						PASS	.						75.0	70.0	72.0					2																	166847770		2201	4300	6501	SO:0001583	missense	6323	exon26			TTTGGCTTTTTCA	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.6015A>C	2.37:g.166847770T>G	ENSP00000303540:p.Lys2005Asn	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	55	16	0.290909	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	9.523	1.108698	0.20714	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.96168	-3.93;-3.93;-3.89;-3.86	5.67	3.33	0.38152	.	0.462954	0.22275	N	0.062216	D	0.86535	0.5956	N	0.08118	0	0.34054	D	0.656484	B	0.15473	0.013	B	0.19391	0.025	T	0.81959	-0.0694	10	0.62326	D	0.03	.	2.4206	0.04447	0.2292:0.3772:0.0:0.3937	.	1994	P35498-2	.	N	2005;2005;1994;1977	ENSP00000407030:K2005N;ENSP00000303540:K2005N;ENSP00000364554:K1994N;ENSP00000386312:K1977N	ENSP00000303540:K2005N	K	-	3	2	SCN1A	166556016	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	1.969000	0.40510	0.980000	0.38523	0.397000	0.26171	AAA	.	.	none		0.383	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
DYRK2	8445	hgsc.bcm.edu	37	12	68051819	68051819	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:68051819C>T	ENST00000344096.3	+	3	1545	c.1132C>T	c.(1132-1134)Cgt>Tgt	p.R378C	RP11-335O4.3_ENST00000425371.2_RNA|DYRK2_ENST00000393555.3_Missense_Mutation_p.R305C	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	378	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		CGAGCATCAGCGTGTCTACAC	0.483																																					p.R378C		Atlas-SNP	.											DYRK2,colon,carcinoma,-1,2	DYRK2	63	2	0			c.C1132T						scavenged	.						110.0	105.0	107.0					12																	68051819		2203	4300	6503	SO:0001583	missense	8445	exon3			CATCAGCGTGTCT	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.1132C>T	12.37:g.68051819C>T	ENSP00000342105:p.Arg378Cys	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	285	3	0.0105263	NM_006482	B2R9V9|Q9BRB5	Missense_Mutation	SNP	ENST00000344096.3	37	CCDS8978.1	.	.	.	.	.	.	.	.	.	.	C	16.60	3.169037	0.57584	.	.	ENSG00000127334	ENST00000344096;ENST00000393555	T;T	0.20738	2.05;2.05	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.43986	0.1272	L	0.54908	1.71	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	T	0.06197	-1.0840	9	.	.	.	.	19.6624	0.95878	0.0:1.0:0.0:0.0	.	378	Q92630	DYRK2_HUMAN	C	378;305	ENSP00000342105:R378C;ENSP00000377186:R305C	.	R	+	1	0	DYRK2	66338086	1.000000	0.71417	0.998000	0.56505	0.902000	0.53008	4.997000	0.63921	2.736000	0.93811	0.305000	0.20034	CGT	.	.	none		0.483	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
PCDHA7	56141	hgsc.bcm.edu	37	5	140215022	140215022	+	Missense_Mutation	SNP	C	C	A	rs150063888		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:140215022C>A	ENST00000525929.1	+	1	1054	c.1054C>A	c.(1054-1056)Ctc>Atc	p.L352I	PCDHA7_ENST00000378125.3_Missense_Mutation_p.L352I|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron	NM_018910.2	NP_061733.1	Q9UN72	PCDA7_HUMAN	protocadherin alpha 7	352	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)	p.L352F(1)		NS(2)|biliary_tract(1)|breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(3)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	63			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAGTTGACTCTCACTTCCCT	0.507																																					p.L352I	NSCLC(160;258 2013 5070 22440 28951)	Atlas-SNP	.											PCDHA7,shoulder,malignant_melanoma,0,1	PCDHA7	367	1	1	Substitution - Missense(1)	skin(1)	c.C1054A						scavenged	.						181.0	157.0	165.0					5																	140215022		2203	4299	6502	SO:0001583	missense	56141	exon1			TTGACTCTCACTT	AF152485	CCDS54918.1	5q31	2010-11-26				ENSG00000204963		"""Cadherins / Protocadherins : Clustered"""	8673	other	complex locus constituent	"""KIAA0345-like 7"", ""ortholog to mouse CNR4"""	606313		CNRS4		10380929, 10662547	Standard	NM_018910		Approved	CNR4, CRNR4		Q9UN72		ENST00000525929.1:c.1054C>A	5.37:g.140215022C>A	ENSP00000436426:p.Leu352Ile	Somatic	490	4	0.00816326		WXS	Illumina HiSeq	Phase_I	577	9	0.0155979	NM_031852	O75282	Missense_Mutation	SNP	ENST00000525929.1	37	CCDS54918.1	.	.	.	.	.	.	.	.	.	.	C	0.413	-0.912035	0.02415	.	.	ENSG00000204963	ENST00000525929;ENST00000378125	T;T	0.61274	0.12;0.26	4.04	-1.41	0.08941	Cadherin (2);Cadherin-like (1);	0.343115	0.15286	N	0.270413	T	0.21347	0.0514	N	0.03268	-0.37	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.001	T	0.19877	-1.0292	10	0.05833	T	0.94	.	2.2003	0.03921	0.3512:0.1209:0.4122:0.1158	.	352;352	Q9UN72-2;Q9UN72	.;PCDA7_HUMAN	I	352	ENSP00000436426:L352I;ENSP00000367365:L352I	ENSP00000367365:L352I	L	+	1	0	PCDHA7	140195206	0.000000	0.05858	0.000000	0.03702	0.882000	0.50991	-3.197000	0.00562	-0.656000	0.05380	0.305000	0.20034	CTC	.	.	alt		0.507	PCDHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372887.2	NM_018910	
WASF3	10810	hgsc.bcm.edu	37	13	27239258	27239258	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:27239258T>C	ENST00000335327.5	+	4	405	c.227T>C	c.(226-228)cTt>cCt	p.L76P	WASF3_ENST00000496788.1_3'UTR|WASF3_ENST00000361042.4_Missense_Mutation_p.L76P	NM_006646.5	NP_006637.2	Q9UPY6	WASF3_HUMAN	WAS protein family, member 3	76					actin filament polymerization (GO:0030041)|cytoskeleton organization (GO:0007010)|lamellipodium assembly (GO:0030032)|oligodendrocyte development (GO:0014003)|positive regulation of myelination (GO:0031643)|protein complex assembly (GO:0006461)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)				breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|pancreas(1)|prostate(2)|skin(2)	22	Colorectal(5;0.000247)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0114)|Epithelial(112;0.046)|OV - Ovarian serous cystadenocarcinoma(117;0.0547)|Lung(94;0.105)|LUSC - Lung squamous cell carcinoma(192;0.155)		ATTGATCGCCTTGCTGTCAAA	0.413																																					p.L76P		Atlas-SNP	.											.	WASF3	68	.	0			c.T227C						PASS	.						92.0	85.0	88.0					13																	27239258		2203	4300	6503	SO:0001583	missense	10810	exon4			ATCGCCTTGCTGT	AB020707	CCDS9318.1	13q12	2008-06-23			ENSG00000132970	ENSG00000132970			12734	protein-coding gene	gene with protein product		605068				10381382	Standard	NM_006646		Approved	WAVE3, SCAR3, KIAA0900	uc001uqv.3	Q9UPY6	OTTHUMG00000016621	ENST00000335327.5:c.227T>C	13.37:g.27239258T>C	ENSP00000335055:p.Leu76Pro	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	110	34	0.309091	NM_006646	O94974|Q86VQ2	Missense_Mutation	SNP	ENST00000335327.5	37	CCDS9318.1	.	.	.	.	.	.	.	.	.	.	T	22.0	4.230247	0.79688	.	.	ENSG00000132970	ENST00000361042;ENST00000335327	T;T	0.69040	-0.37;-0.37	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	D	0.85062	0.5611	M	0.90650	3.135	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.88329	0.2967	10	0.87932	D	0	-27.7935	15.8529	0.78947	0.0:0.0:0.0:1.0	.	76;76	Q86VQ2;Q9UPY6	.;WASF3_HUMAN	P	76	ENSP00000354325:L76P;ENSP00000335055:L76P	ENSP00000335055:L76P	L	+	2	0	WASF3	26137258	1.000000	0.71417	0.922000	0.36590	0.865000	0.49528	7.562000	0.82300	2.147000	0.66899	0.528000	0.53228	CTT	.	.	none		0.413	WASF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044258.1		
ATG2B	55102	hgsc.bcm.edu	37	14	96771961	96771961	+	Silent	SNP	T	T	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:96771961T>A	ENST00000359933.4	-	31	5591	c.4698A>T	c.(4696-4698)ggA>ggT	p.G1566G	ATG2B_ENST00000261834.5_5'UTR	NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	1566					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		GAGGGACTATTCCAAAATCCT	0.383																																					p.G1566G		Atlas-SNP	.											.	ATG2B	169	.	0			c.A4698T						PASS	.						67.0	63.0	64.0					14																	96771961		2203	4300	6503	SO:0001819	synonymous_variant	55102	exon31			GACTATTCCAAAA	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.4698A>T	14.37:g.96771961T>A		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	51	18	0.352941	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Silent	SNP	ENST00000359933.4	37	CCDS9944.2																																																																																			.	.	none		0.383	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
FAM131C	348487	hgsc.bcm.edu	37	1	16385042	16385042	+	Missense_Mutation	SNP	G	G	A	rs77667563	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:16385042G>A	ENST00000375662.4	-	7	916	c.733C>T	c.(733-735)Cgg>Tgg	p.R245W	FAM131C_ENST00000494078.1_5'UTR	NM_182623.2	NP_872429.2	Q96AQ9	F131C_HUMAN	family with sequence similarity 131, member C	245	Pro-rich.									large_intestine(2)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	8		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.32e-08)|COAD - Colon adenocarcinoma(227;5.56e-06)|BRCA - Breast invasive adenocarcinoma(304;9.12e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00656)|READ - Rectum adenocarcinoma(331;0.0649)		GGCAGCCGCCGCCGATGCTGC	0.741																																					p.R245W		Atlas-SNP	.											FAM131C,NS,other,0,1	FAM131C	21	1	0			c.C733T						scavenged	.						2.0	2.0	2.0					1																	16385042		1409	3130	4539	SO:0001583	missense	348487	exon7			GCCGCCGCCGATG		CCDS41270.1	1p36.13	2008-02-05	2007-03-20	2007-03-20	ENSG00000185519	ENSG00000185519			26717	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 117"""	C1orf117		12477932	Standard	NM_182623		Approved	FLJ36766	uc001axz.4	Q96AQ9	OTTHUMG00000009525	ENST00000375662.4:c.733C>T	1.37:g.16385042G>A	ENSP00000364814:p.Arg245Trp	Somatic	3	1	0.333333		WXS	Illumina HiSeq	Phase_I	5	2	0.4	NM_182623	Q5T5Q5|Q8N3X3|Q8N9P9	Missense_Mutation	SNP	ENST00000375662.4	37	CCDS41270.1	773	0.35393772893772896	210	0.4268292682926829	106	0.292817679558011	224	0.3916083916083916	233	0.3073878627968338	G	11.88	1.771185	0.31320	.	.	ENSG00000185519	ENST00000375662	T	0.15487	2.42	4.8	-0.971	0.10303	.	2.839240	0.01092	N	0.005214	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	D	0.65815	0.995	P	0.46825	0.528	T	0.32428	-0.9907	9	0.54805	T	0.06	-7.4813	4.4045	0.11402	0.1749:0.0:0.3887:0.4365	.	245	Q96AQ9	F131C_HUMAN	W	245	ENSP00000364814:R245W	ENSP00000364814:R245W	R	-	1	2	FAM131C	16257629	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.080000	0.11339	-0.172000	0.10779	0.549000	0.68633	CGG	G|0.646;A|0.354	0.354	strong		0.741	FAM131C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026319.1	NM_182623	
FREM2	341640	hgsc.bcm.edu	37	13	39262561	39262561	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr13:39262561T>C	ENST00000280481.7	+	1	1296	c.1080T>C	c.(1078-1080)acT>acC	p.T360T		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	360					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TCAACCTTACTTCTCCATTCC	0.572																																					p.T360T		Atlas-SNP	.											.	FREM2	385	.	0			c.T1080C						PASS	.						124.0	113.0	117.0					13																	39262561		2203	4300	6503	SO:0001819	synonymous_variant	341640	exon1			CCTTACTTCTCCA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.1080T>C	13.37:g.39262561T>C		Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	132	28	0.212121	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			.	.	none		0.572	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
CPNE6	9362	hgsc.bcm.edu	37	14	24544773	24544773	+	Silent	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr14:24544773A>C	ENST00000397016.2	+	10	1148	c.837A>C	c.(835-837)tcA>tcC	p.S279S	CPNE6_ENST00000216775.2_Silent_p.S279S|CPNE6_ENST00000537691.1_Silent_p.S334S	NM_001280558.1	NP_001267487.1	O95741	CPNE6_HUMAN	copine VI (neuronal)	279					lipid metabolic process (GO:0006629)|nervous system development (GO:0007399)|synaptic transmission (GO:0007268)|vesicle-mediated transport (GO:0016192)	axon (GO:0030424)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|phosphatidylserine binding (GO:0001786)|transporter activity (GO:0005215)			endometrium(4)|large_intestine(3)|liver(2)|lung(5)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(265;0.0184)		ACAAGAGCTCAGGGACGGTAG	0.552																																					p.S279S		Atlas-SNP	.											CPNE6,mouth,carcinoma,+1,1	CPNE6	40	1	0			c.A837C						PASS	.						104.0	89.0	94.0					14																	24544773		2203	4300	6503	SO:0001819	synonymous_variant	9362	exon9			GAGCTCAGGGACG	AB009288	CCDS9607.1, CCDS61413.1	14q11.2	2008-07-09			ENSG00000100884	ENSG00000100884			2319	protein-coding gene	gene with protein product		605688				9645480	Standard	NM_001280558		Approved		uc001wll.3	O95741	OTTHUMG00000028781	ENST00000397016.2:c.837A>C	14.37:g.24544773A>C		Somatic	162	0	0		WXS	Illumina HiSeq	Phase_I	191	32	0.167539	NM_006032	B2RAG6|B7Z1M3|D3DS55|F5GXN1|Q53HA6|Q8WVG1	Silent	SNP	ENST00000397016.2	37	CCDS9607.1																																																																																			.	.	none		0.552	CPNE6-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071869.5		
STRC	161497	hgsc.bcm.edu	37	15	43892847	43892847	+	Silent	SNP	G	G	C	rs12438025	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:43892847G>C	ENST00000450892.2	-	26	4955	c.4878C>G	c.(4876-4878)ctC>ctG	p.L1626L	RNU6-554P_ENST00000410466.1_RNA|STRC_ENST00000541030.1_Silent_p.L853L	NM_153700.2	NP_714544.1	Q7RTU9	STRC_HUMAN	stereocilin	1626					auditory receptor cell stereocilium organization (GO:0060088)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)	kinocilium (GO:0060091)|stereocilium bundle tip (GO:0032426)				skin(4)	4		all_cancers(109;3.26e-15)|all_epithelial(112;1.48e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.56e-07)		CAGAGCACTGGAGATGCAGGG	0.532													G|||	1475	0.294529	0.556	0.2032	5008	,	,		20056	0.2718		0.0994	False		,,,				2504	0.2301				p.L1626L		Atlas-SNP	.											STRC_ENST00000450892,colon,carcinoma,0,1	STRC	58	1	0			c.C4878G						scavenged	.	G		2041,2359	541.9+/-375.9	485,1071,644	55.0	64.0	61.0		4878	2.9	1.0	15	dbSNP_120	61	846,7748	189.1+/-236.0	50,746,3501	no	coding-synonymous	STRC	NM_153700.2		535,1817,4145	CC,CG,GG		9.8441,46.3864,22.2179		1626/1776	43892847	2887,10107	2200	4297	6497	SO:0001819	synonymous_variant	161497	exon26			GCACTGGAGATGC	BK000138	CCDS10098.1	15q15.3	2010-02-26			ENSG00000242866	ENSG00000242866			16035	protein-coding gene	gene with protein product		606440		DFNB16		11687802, 9429146	Standard	NM_153700		Approved		uc001zsf.3	Q7RTU9	OTTHUMG00000059899	ENST00000450892.2:c.4878C>G	15.37:g.43892847G>C		Somatic	346	2	0.00578035		WXS	Illumina HiSeq	Phase_I	272	3	0.0110294	NM_153700		Silent	SNP	ENST00000450892.2	37	CCDS10098.1																																																																																			G|0.784;C|0.216	0.216	strong		0.532	STRC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000133140.1	NM_153700	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318698	21318698	+	Missense_Mutation	SNP	C	C	T	rs1657738	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:21318698C>T	ENST00000583088.1	+	3	939	c.44C>T	c.(43-45)tCg>tTg	p.S15L	KCNJ12_ENST00000331718.5_Missense_Mutation_p.S15L	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	15			S -> L (in dbSNP:rs1657738).		muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	ATCGTGTCATCGGAGGAGGAC	0.711										Prostate(3;0.18)																											p.S15L		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	0			c.C44T						scavenged	.																																			SO:0001583	missense	100134444	exon3			TGTCATCGGAGGA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.44C>T	17.37:g.21318698C>T	ENSP00000463778:p.Ser15Leu	Somatic	11	1	0.0909091		WXS	Illumina HiSeq	Phase_I	6	5	0.833333	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	1092	0.5	246	0.5	181	0.5	286	0.5	379	0.5	C	16.91	3.253602	0.59212	.	.	ENSG00000184185	ENST00000331718	T	0.35605	1.3	5.33	4.37	0.52481	Potassium channel, inwardly rectifying, Kir, N-terminal (1);	0.060531	0.64402	D	0.000002	T	0.00012	0.0000	L	0.55481	1.735	0.53005	D	0.999966	P	0.46578	0.88	B	0.34301	0.179	T	0.56408	-0.7984	10	0.45353	T	0.12	.	13.6407	0.62249	0.0:0.9242:0.0:0.0758	rs1657738;rs59809956	15	Q14500	IRK12_HUMAN	L	15	ENSP00000328150:S15L	ENSP00000328150:S15L	S	+	2	0	KCNJ12	21259291	1.000000	0.71417	0.117000	0.21633	0.983000	0.72400	5.954000	0.70298	1.257000	0.44085	0.591000	0.81541	TCG	C|0.500;T|0.500	0.500	strong		0.711	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
ZNF454	285676	hgsc.bcm.edu	37	5	178392474	178392474	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:178392474G>A	ENST00000320129.3	+	5	1372	c.1069G>A	c.(1069-1071)Gaa>Aaa	p.E357K	ZNF454_ENST00000519564.1_Missense_Mutation_p.E357K	NM_001178090.1|NM_182594.2	NP_001171561.1|NP_872400.2	Q8N9F8	ZN454_HUMAN	zinc finger protein 454	357					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(11)|lung(18)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)	46	all_cancers(89;0.000904)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.225)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.234)		GAAACCCTTTGAATGTAATGA	0.393																																					p.E357K		Atlas-SNP	.											.	ZNF454	99	.	0			c.G1069A						PASS	.						40.0	44.0	43.0					5																	178392474		2203	4300	6503	SO:0001583	missense	285676	exon5			CCCTTTGAATGTA	AK094763	CCDS4441.1	5q35.3	2013-01-08			ENSG00000178187	ENSG00000178187		"""Zinc fingers, C2H2-type"", ""-"""	21200	protein-coding gene	gene with protein product							Standard	NM_182594		Approved	FLJ37444	uc021yjc.1	Q8N9F8	OTTHUMG00000130891	ENST00000320129.3:c.1069G>A	5.37:g.178392474G>A	ENSP00000326249:p.Glu357Lys	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	49	5	0.102041	NM_001178089	Q2M1P2|Q2M323	Missense_Mutation	SNP	ENST00000320129.3	37	CCDS4441.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.716785	0.48622	.	.	ENSG00000178187	ENST00000320129;ENST00000519564	T;T	0.06608	3.28;3.28	4.21	4.21	0.49690	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.40818	N	0.001005	T	0.04452	0.0122	N	0.01188	-0.97	0.28822	N	0.897625	P	0.51791	0.948	P	0.51866	0.682	T	0.44050	-0.9353	10	0.34782	T	0.22	-18.4194	14.4348	0.67274	0.0:0.0:1.0:0.0	.	357	Q8N9F8	ZN454_HUMAN	K	357	ENSP00000326249:E357K;ENSP00000430354:E357K	ENSP00000326249:E357K	E	+	1	0	ZNF454	178325080	0.000000	0.05858	1.000000	0.80357	0.992000	0.81027	-0.128000	0.10531	2.344000	0.79699	0.650000	0.86243	GAA	.	.	none		0.393	ZNF454-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253476.2	XM_209718	
BRD1	23774	hgsc.bcm.edu	37	22	50170766	50170766	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr22:50170766G>A	ENST00000216267.8	-	9	3130	c.2644C>T	c.(2644-2646)Cga>Tga	p.R882*	BRD1_ENST00000404034.1_Nonsense_Mutation_p.R882*|BRD1_ENST00000542442.1_Nonsense_Mutation_p.R570*|BRD1_ENST00000457780.2_Silent_p.C985C|BRD1_ENST00000342989.5_Nonsense_Mutation_p.R608*|BRD1_ENST00000404760.1_Nonsense_Mutation_p.R1013*	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	882					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GTGTGCCGTCGCACAAGAGCC	0.652																																					p.R882X		Atlas-SNP	.											BRD1_ENST00000342989,NS,carcinoma,+1,2	BRD1	144	2	0			c.C2644T						scavenged	.						75.0	75.0	75.0					22																	50170766		2203	4300	6503	SO:0001587	stop_gained	23774	exon9			GCCGTCGCACAAG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2644C>T	22.37:g.50170766G>A	ENSP00000216267:p.Arg882*	Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	161	4	0.0248447	NM_014577	A6ZJA4	Nonsense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	.	.	.	.	.	.	.	.	.	.	G	39	7.353829	0.98231	.	.	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000542442;ENST00000342989;ENST00000419212	.	.	.	4.98	4.98	0.66077	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.245	0.89982	0.0:0.0:1.0:0.0	.	.	.	.	X	882;882;1013;570;608;473	.	ENSP00000216267:R882X	R	-	1	2	BRD1	48556770	1.000000	0.71417	0.975000	0.42487	0.847000	0.48162	7.293000	0.78740	2.300000	0.77407	0.655000	0.94253	CGA	.	.	none		0.652	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
ZNF727	442319	hgsc.bcm.edu	37	7	63538777	63538777	+	Silent	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:63538777G>A	ENST00000550760.3	+	4	1529	c.1350G>A	c.(1348-1350)aaG>aaA	p.K450K	RP11-3N2.13_ENST00000445978.1_RNA	NM_001159522.1	NP_001152994.1	A8MUV8	ZN727_HUMAN	zinc finger protein 727	450					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(3)|kidney(2)|skin(1)|stomach(1)|urinary_tract(1)	8						CTGGAGAGAAGCCCTACAAAT	0.408																																					p.K450K		Atlas-SNP	.											ZNF727,NS,carcinoma,0,1	ZNF727	35	1	0			c.G1350A						scavenged	.						47.0	44.0	45.0					7																	63538777		692	1591	2283	SO:0001819	synonymous_variant	442319	exon4			AGAGAAGCCCTAC			7q11.21	2014-09-09	2014-09-09	2014-09-09	ENSG00000214652	ENSG00000214652		"""Zinc fingers, C2H2-type"", ""-"""	22785	pseudogene	pseudogene			"""zinc finger protein 727, pseudogene"""	ZNF727P			Standard	NM_001159522		Approved		uc011kdm.2	A8MUV8	OTTHUMG00000156536	ENST00000550760.3:c.1350G>A	7.37:g.63538777G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	90	3	0.0333333	NM_001159522		Silent	SNP	ENST00000550760.3	37	CCDS55113.1																																																																																			.	.	none		0.408	ZNF727-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001159522	
TXNDC2	84203	hgsc.bcm.edu	37	18	9887155	9887155	+	Missense_Mutation	SNP	A	A	G	rs200725516		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr18:9887155A>G	ENST00000306084.6	+	2	878	c.679A>G	c.(679-681)Acc>Gcc	p.T227A	TXNDC2_ENST00000536353.2_Intron|TXNDC2_ENST00000357775.5_Missense_Mutation_p.T160A	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	227	22 X 15 AA approximate tandem repeat of Q-P-K-X-G-D-I-P-K-S-[PS]-E-[KE]-X-I.				cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						TATTGCCAAGACCTCAGTGAA	0.562																																					p.T227A		Atlas-SNP	.											TXNDC2_ENST00000306084,NS,carcinoma,0,2	TXNDC2	168	2	0			c.A679G						PASS	.						131.0	132.0	132.0					18																	9887155		2203	4300	6503	SO:0001583	missense	84203	exon2			GCCAAGACCTCAG	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.679A>G	18.37:g.9887155A>G	ENSP00000304908:p.Thr227Ala	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	137	9	0.0656934	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	a	9.538	1.112696	0.20795	.	.	ENSG00000168454	ENST00000536353;ENST00000357775;ENST00000306084;ENST00000426718	T;T	0.15952	2.38;2.38	3.14	-4.09	0.03951	.	3.297290	0.00964	N	0.003154	T	0.06096	0.0158	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.22695	-1.0209	9	.	.	.	-0.4193	2.0291	0.03525	0.1619:0.1351:0.4638:0.2392	.	227	Q86VQ3	TXND2_HUMAN	A	100;160;227;227	ENSP00000350419:T160A;ENSP00000304908:T227A	.	T	+	1	0	TXNDC2	9877155	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-3.570000	0.00427	-0.337000	0.08426	-0.528000	0.04320	ACC	A|1.000;G|0.000	0.000	strong		0.562	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
MMP15	4324	hgsc.bcm.edu	37	16	58079165	58079165	+	Missense_Mutation	SNP	G	G	A	rs3743563	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:58079165G>A	ENST00000219271.3	+	10	2610	c.1825G>A	c.(1825-1827)Ggg>Agg	p.G609R		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	609			G -> R (in dbSNP:rs3743563). {ECO:0000269|PubMed:9119382, ECO:0000269|Ref.2}.		cellular protein modification process (GO:0006464)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)|response to estradiol (GO:0032355)	extracellular matrix (GO:0031012)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)	p.G609R(2)		breast(1)|central_nervous_system(2)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	18					Marimastat(DB00786)	CAACAAGGACGGGGGCAGCCG	0.701													G|||	996	0.198882	0.0318	0.3963	5008	,	,		11871	0.3462		0.1829	False		,,,				2504	0.1493				p.G609R		Atlas-SNP	.											MMP15,hand,carcinoma,0,3	MMP15	58	3	2	Substitution - Missense(2)	central_nervous_system(1)|skin(1)	c.G1825A						scavenged	.	G	ARG/GLY	308,4086	156.6+/-189.7	15,278,1904	105.0	117.0	113.0		1825	3.7	1.0	16	dbSNP_107	113	1645,6955	282.4+/-295.5	161,1323,2816	yes	missense	MMP15	NM_002428.2	125	176,1601,4720	AA,AG,GG		19.1279,7.0096,15.03	possibly-damaging	609/670	58079165	1953,11041	2197	4300	6497	SO:0001583	missense	4324	exon10			AAGGACGGGGGCA	Z48482	CCDS10792.1	16q13	2008-05-14	2005-08-08		ENSG00000102996	ENSG00000102996			7161	protein-coding gene	gene with protein product		602261	"""matrix metalloproteinase 15 (membrane-inserted)"""			9070935, 9119382	Standard	NM_002428		Approved	MT2-MMP, MTMMP2, SMCP-2	uc002ena.3	P51511	OTTHUMG00000133466	ENST00000219271.3:c.1825G>A	16.37:g.58079165G>A	ENSP00000219271:p.Gly609Arg	Somatic	7	1	0.142857		WXS	Illumina HiSeq	Phase_I	13	6	0.461538	NM_002428	A0A2U6|Q14111	Missense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	482	0.2206959706959707	24	0.04878048780487805	111	0.30662983425414364	199	0.3479020979020979	148	0.19525065963060687	G	13.06	2.125616	0.37533	0.070096	0.191279	ENSG00000102996	ENST00000219271	T	0.28069	1.63	4.65	3.69	0.42338	Peptidase M10A, matrix metallopeptidase, C-terminal (1);	0.368453	0.32081	N	0.006618	T	0.00012	0.0000	N	0.21448	0.665	0.35109	P	0.23400299999999996	B	0.23854	0.092	B	0.19946	0.027	T	0.45804	-0.9236	9	0.17369	T	0.5	.	8.5638	0.33527	0.1046:0.0:0.8954:0.0	rs3743563;rs3743563	609	P51511	MMP15_HUMAN	R	609	ENSP00000219271:G609R	ENSP00000219271:G609R	G	+	1	0	MMP15	56636666	1.000000	0.71417	0.982000	0.44146	0.606000	0.37113	6.421000	0.73353	1.184000	0.42957	0.555000	0.69702	GGG	G|0.829;A|0.171	0.171	strong		0.701	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428	
IL7R	3575	hgsc.bcm.edu	37	5	35861068	35861068	+	Missense_Mutation	SNP	T	T	C	rs1494558	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:35861068T>C	ENST00000303115.3	+	2	326	c.197T>C	c.(196-198)aTc>aCc	p.I66T	IL7R_ENST00000343305.4_Missense_Mutation_p.I66T|IL7R_ENST00000511982.1_Missense_Mutation_p.I66T|IL7R_ENST00000506850.1_Missense_Mutation_p.I66T|IL7R_ENST00000511031.1_3'UTR	NM_002185.3	NP_002176.2	P16871	IL7RA_HUMAN	interleukin 7 receptor	66			T -> I (in T(-)/B(+)/NK(+) SCID; dbSNP:rs1494558). {ECO:0000269|PubMed:15372022, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9843216, ECO:0000269|Ref.5}.		B cell proliferation (GO:0042100)|cell growth (GO:0016049)|cell morphogenesis (GO:0000902)|cell surface receptor signaling pathway (GO:0007166)|homeostasis of number of cells (GO:0048872)|immune response (GO:0006955)|immunoglobulin production (GO:0002377)|interleukin-7-mediated signaling pathway (GO:0038111)|lymph node development (GO:0048535)|negative regulation of T cell mediated cytotoxicity (GO:0001915)|positive regulation of gene expression (GO:0010628)|positive regulation of T cell differentiation in thymus (GO:0033089)|regulation of cell size (GO:0008361)|regulation of DNA recombination (GO:0000018)|signal transduction (GO:0007165)|T cell differentiation (GO:0030217)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|interleukin-7 receptor activity (GO:0004917)	p.I66T(1)		NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(78)|kidney(2)|large_intestine(6)|lung(25)|ovary(3)|pancreas(1)|skin(5)|stomach(3)	126	all_lung(31;0.00015)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Epithelial(62;0.187)|Colorectal(62;0.202)			GATGTCAACATCACCAATCTG	0.428			"""Mis, O"""		"""ALL, ETP ALL"""		Severe combined immune deficiency						C|||	3004	0.59984	0.7625	0.5418	5008	,	,		18968	0.4256		0.6978	False		,,,				2504	0.5				p.I66T		Atlas-SNP	.		Dom	yes		5	5p13	146661	interleukin 7 receptor	yes	L	IL7R,NS,carcinoma,0,1	IL7R	200	1	1	Substitution - Missense(1)	stomach(1)	c.T197C						scavenged	.	C	THR/ILE	3323,1083	393.5+/-328.9	1254,815,134	199.0	185.0	190.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	197	2.2	1.0	5	dbSNP_88	190	5793,2807	445.1+/-360.9	1936,1921,443	yes	missense	IL7R	NM_002185.2	89	3190,2736,577	CC,CT,TT		32.6395,24.5801,29.9093	possibly-damaging	66/460	35861068	9116,3890	2203	4300	6503	SO:0001583	missense	3575	exon2			TCAACATCACCAA	M29696	CCDS3911.1	5p13	2014-09-17			ENSG00000168685	ENSG00000168685		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6024	protein-coding gene	gene with protein product		146661				2317865	Standard	NM_002185		Approved	CD127	uc003jjs.4	P16871	OTTHUMG00000090791	ENST00000303115.3:c.197T>C	5.37:g.35861068T>C	ENSP00000306157:p.Ile66Thr	Somatic	321	2	0.00623053		WXS	Illumina HiSeq	Phase_I	412	6	0.0145631	NM_002185	B2RCS6|B4DVT1|Q05CU8|Q6NSP4|Q6NWM0|Q6NWM1|Q6NWM2|Q6NWM3|Q6SV45|Q9UPC1	Missense_Mutation	SNP	ENST00000303115.3	37	CCDS3911.1	1339	0.6130952380952381	367	0.7459349593495935	208	0.574585635359116	231	0.40384615384615385	533	0.7031662269129287	C	0.016	-1.521583	0.00967	0.754199	0.673605	ENSG00000168685	ENST00000303115;ENST00000343305;ENST00000506850;ENST00000511982	T;T;T;T	0.73575	-0.76;-0.76;-0.76;-0.76	5.97	2.16	0.27623	.	0.786211	0.12045	N	0.504638	T	0.00012	0.0000	.	.	.	0.58432	P	1.0000000000287557E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.41142	-0.9525	7	.	.	.	-20.4536	3.6783	0.08301	0.0777:0.3334:0.3331:0.2558	rs1494558;rs17668036;rs52799522;rs59370393;rs1494558	66	D6RGV2	.	T	66	ENSP00000306157:I66T;ENSP00000345819:I66T;ENSP00000421207:I66T;ENSP00000425309:I66T	.	I	+	2	0	IL7R	35896825	0.993000	0.37304	0.999000	0.59377	0.013000	0.08279	0.337000	0.19841	0.111000	0.17947	-2.304000	0.00258	ATC	T|0.349;C|0.651	0.651	strong		0.428	IL7R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207577.2		
OR4C3	256144	hgsc.bcm.edu	37	11	48347041	48347041	+	Silent	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:48347041T>C	ENST00000319856.4	+	1	570	c.549T>C	c.(547-549)gtT>gtC	p.V183V		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	156						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						ATTCATTGGTTCAGCTCCTCC	0.527																																					p.V183V		Atlas-SNP	.											.	OR4C3	75	.	0			c.T549C						PASS	.						155.0	144.0	148.0					11																	48347041		2201	4298	6499	SO:0001819	synonymous_variant	256144	exon1			ATTGGTTCAGCTC	AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"""GPCR / Class A : Olfactory receptors"""	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.549T>C	11.37:g.48347041T>C		Somatic	347	0	0		WXS	Illumina HiSeq	Phase_I	361	26	0.0720222	NM_001004702	B2RNF2|Q6IFB3	Silent	SNP	ENST00000319856.4	37	CCDS31489.1																																																																																			.	.	none		0.527	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702	
MAML2	84441	hgsc.bcm.edu	37	11	95825383	95825383	+	Silent	SNP	C	C	T	rs113349418|rs141671766|rs60727839	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:95825383C>T	ENST00000524717.1	-	2	3096	c.1812G>A	c.(1810-1812)caG>caA	p.Q604Q		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	604					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				gttgctgctgctgctgctgct	0.527			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid																																p.Q604Q		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	MAML2,rectum,carcinoma,0,1	MAML2	94	1	0			c.G1812A						scavenged	.						19.0	23.0	22.0					11																	95825383		1910	3681	5591	SO:0001819	synonymous_variant	84441	exon2			CTGCTGCTGCTGC	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.1812G>A	11.37:g.95825383C>T		Somatic	122	2	0.0163934		WXS	Illumina HiSeq	Phase_I	154	24	0.155844	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Silent	SNP	ENST00000524717.1	37	CCDS44714.1																																																																																			C|0.500;T|0.500	0.500	weak		0.527	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
PDLIM1	9124	hgsc.bcm.edu	37	10	96998439	96998439	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:96998439T>C	ENST00000329399.6	-	6	797	c.689A>G	c.(688-690)gAt>gGt	p.D230G	PDLIM1_ENST00000477757.1_5'UTR	NM_020992.2	NP_066272.1	O00151	PDLI1_HUMAN	PDZ and LIM domain 1	230					regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)			endometrium(1)|large_intestine(5)|lung(1)|ovary(1)|skin(2)	10		Colorectal(252;0.083)		Epithelial(162;1.64e-06)|all cancers(201;3.71e-05)		CTTGTTGGGATCCCCTGAAAT	0.433																																					p.D230G		Atlas-SNP	.											.	PDLIM1	33	.	0			c.A689G						PASS	.						80.0	72.0	74.0					10																	96998439		2203	4300	6503	SO:0001583	missense	9124	exon6			TTGGGATCCCCTG	U90878	CCDS7441.1	10q23.1	2008-07-29	2008-07-29		ENSG00000107438	ENSG00000107438			2067	protein-coding gene	gene with protein product	"""carboxyl terminal LIM domain protein 1"", ""elfin"""	605900	"""PDZ and LIM domain 1 (elfin)"""	CLIM1		10861853	Standard	NM_020992		Approved	CLP-36, hCLIM1, CLP36	uc001kkh.4	O00151	OTTHUMG00000018810	ENST00000329399.6:c.689A>G	10.37:g.96998439T>C	ENSP00000360305:p.Asp230Gly	Somatic	248	0	0		WXS	Illumina HiSeq	Phase_I	225	46	0.204444	NM_020992	B2RBS6|Q5VZH5|Q9BPZ9	Missense_Mutation	SNP	ENST00000329399.6	37	CCDS7441.1	.	.	.	.	.	.	.	.	.	.	T	23.3	4.399588	0.83120	.	.	ENSG00000107438	ENST00000329399	T	0.21734	1.99	5.23	5.23	0.72850	.	0.088256	0.85682	D	0.000000	T	0.37183	0.0994	M	0.68317	2.08	0.80722	D	1	D	0.61080	0.989	P	0.55749	0.783	T	0.09907	-1.0653	10	0.37606	T	0.19	-18.4018	14.2967	0.66318	0.0:0.0:0.0:1.0	.	230	O00151	PDLI1_HUMAN	G	230	ENSP00000360305:D230G	ENSP00000360305:D230G	D	-	2	0	PDLIM1	96988429	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.491000	0.81471	1.978000	0.57642	0.454000	0.30748	GAT	.	.	none		0.433	PDLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049508.1		
PRDM6	93166	hgsc.bcm.edu	37	5	122425832	122425832	+	Silent	SNP	G	G	T	rs13182369	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:122425832G>T	ENST00000407847.4	+	2	537	c.123G>T	c.(121-123)gcG>gcT	p.A41A	AC106786.1_ENST00000442777.2_RNA|AC106786.1_ENST00000458103.2_RNA	NM_001136239.1	NP_001129711.1	Q9NQX0	PRDM6_HUMAN	PR domain containing 6	41					negative regulation of smooth muscle cell differentiation (GO:0051151)|negative regulation of transcription, DNA-templated (GO:0045892)|neurogenesis (GO:0022008)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)	p.A41A(1)		NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|skin(1)	7						GCGGCGCCGCGGGTCTCCTGA	0.761													G|||	1111	0.221845	0.2753	0.2622	5008	,	,		8018	0.0337		0.3966	False		,,,				2504	0.135				p.A41A		Atlas-SNP	.											PRDM6,NS,NS,0,1	PRDM6	26	1	1	Substitution - coding silent(1)	NS(1)	c.G123T						scavenged	.						1.0	2.0	2.0					5																	122425832		394	1099	1493	SO:0001819	synonymous_variant	93166	exon2			CGCCGCGGGTCTC	AF272898	CCDS47259.1	5q21-q23	2013-01-08			ENSG00000061455	ENSG00000061455		"""Zinc fingers, C2H2-type"""	9350	protein-coding gene	gene with protein product							Standard	NM_001136239		Approved		uc003kti.3	Q9NQX0	OTTHUMG00000150469	ENST00000407847.4:c.123G>T	5.37:g.122425832G>T		Somatic	1	1	1		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001136239	B5MCJ4|Q9NQW9	Silent	SNP	ENST00000407847.4	37	CCDS47259.1																																																																																			G|0.741;T|0.259	0.259	strong		0.761	PRDM6-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318226.2	XM_049619	
TSPAN19	144448	hgsc.bcm.edu	37	12	85421763	85421763	+	Missense_Mutation	SNP	A	A	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:85421763A>C	ENST00000532498.2	-	4	258	c.178T>G	c.(178-180)Ttg>Gtg	p.L60V	TSPAN19_ENST00000547403.2_Intron	NM_001100917.1	NP_001094387.1	P0C672	TSN19_HUMAN	tetraspanin 19	60						integral component of membrane (GO:0016021)				ovary(1)	1						ATTCCAATCAAAATTTGAGAA	0.294																																					p.L60V		Atlas-SNP	.											TSPAN19_ENST00000532498,NS,carcinoma,+2,2	TSPAN19	23	2	0			c.T178G						PASS	.						58.0	54.0	55.0					12																	85421763		1806	4063	5869	SO:0001583	missense	144448	exon4			CAATCAAAATTTG		CCDS44949.1	12q21.31	2013-02-14			ENSG00000231738	ENSG00000231738		"""Tetraspanins"""	31886	protein-coding gene	gene with protein product							Standard	NM_001100917		Approved		uc009zsj.3	P0C672	OTTHUMG00000166181	ENST00000532498.2:c.178T>G	12.37:g.85421763A>C	ENSP00000433816:p.Leu60Val	Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	119	22	0.184874	NM_001100917		Missense_Mutation	SNP	ENST00000532498.2	37	CCDS44949.1	.	.	.	.	.	.	.	.	.	.	A	10.04	1.241688	0.22711	.	.	ENSG00000231738	ENST00000532498;ENST00000547836	T;T	0.80738	-1.41;-1.41	4.4	0.887	0.19200	.	.	.	.	.	T	0.70885	0.3275	L	0.29908	0.895	0.09310	N	1	P	0.45348	0.856	P	0.45753	0.492	T	0.60342	-0.7282	9	0.51188	T	0.08	.	5.6138	0.17420	0.5677:0.0:0.4323:0.0	.	60	P0C672	TSN19_HUMAN	V	60	ENSP00000433816:L60V;ENSP00000446898:L60V	ENSP00000433816:L60V	L	-	1	2	TSPAN19	83945894	0.109000	0.22037	0.001000	0.08648	0.131000	0.20780	0.497000	0.22514	0.302000	0.22762	0.533000	0.62120	TTG	.	.	none		0.294	TSPAN19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388240.2	NM_001100917	
PENK	5179	hgsc.bcm.edu	37	8	57354094	57354094	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:57354094C>T	ENST00000314922.3	-	2	617	c.541G>A	c.(541-543)Gaa>Aaa	p.E181K	PENK_ENST00000523274.1_5'UTR|PENK_ENST00000451791.2_Missense_Mutation_p.E181K	NM_006211.3	NP_006202.1	P01210	PENK_HUMAN	proenkephalin	181					aggressive behavior (GO:0002118)|behavioral fear response (GO:0001662)|locomotory behavior (GO:0007626)|neuropeptide signaling pathway (GO:0007218)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|startle response (GO:0001964)	extracellular region (GO:0005576)	neuropeptide hormone activity (GO:0005184)	p.E181K(1)		central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|liver(1)|lung(5)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	21		all_lung(136;0.229)	Epithelial(17;0.000873)|all cancers(17;0.0069)			TTGCTCACTTCTTCCTCATTA	0.522																																					p.E181K		Atlas-SNP	.											PENK,NS,carcinoma,0,1	PENK	59	1	1	Substitution - Missense(1)	lung(1)	c.G541A						PASS	.						136.0	140.0	138.0					8																	57354094		2203	4300	6503	SO:0001583	missense	5179	exon4			TCACTTCTTCCTC		CCDS6168.1	8q23-q24	2013-02-26				ENSG00000181195		"""Endogenous ligands"""	8831	protein-coding gene	gene with protein product	"""preproenkephalin"""	131330				6281660	Standard	NM_006211		Approved		uc003xsz.2	P01210		ENST00000314922.3:c.541G>A	8.37:g.57354094C>T	ENSP00000324248:p.Glu181Lys	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	116	20	0.172414	NM_001135690	B2RC23|Q6FHC6|Q6FHE6	Missense_Mutation	SNP	ENST00000314922.3	37	CCDS6168.1	.	.	.	.	.	.	.	.	.	.	C	18.30	3.593512	0.66219	.	.	ENSG00000181195	ENST00000539312;ENST00000314922;ENST00000451791	T;T	0.17691	2.26;2.26	5.81	4.92	0.64577	.	0.472244	0.22308	N	0.061779	T	0.19967	0.0480	L	0.55990	1.75	0.80722	D	1	P	0.42078	0.77	B	0.38803	0.282	T	0.01630	-1.1308	10	0.41790	T	0.15	-3.0444	15.9707	0.80013	0.0:0.8651:0.1349:0.0	.	181	P01210	PENK_HUMAN	K	181	ENSP00000324248:E181K;ENSP00000400894:E181K	ENSP00000324248:E181K	E	-	1	0	PENK	57516648	0.997000	0.39634	0.064000	0.19789	0.904000	0.53231	7.035000	0.76517	1.429000	0.47314	0.655000	0.94253	GAA	.	.	none		0.522	PENK-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378645.1		
ZNF629	23361	hgsc.bcm.edu	37	16	30795076	30795076	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:30795076C>T	ENST00000262525.4	-	3	780	c.573G>A	c.(571-573)tcG>tcA	p.S191S		NM_001080417.1	NP_001073886.1	Q9UEG4	ZN629_HUMAN	zinc finger protein 629	191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(3)|urinary_tract(1)	22			Colorectal(24;0.198)			GCACCAGGTGCGAGCTCTGCG	0.662																																					p.S191S		Atlas-SNP	.											ZNF629,colon,carcinoma,-1,1	ZNF629	44	1	0			c.G573A						PASS	.						45.0	47.0	46.0					16																	30795076		2197	4300	6497	SO:0001819	synonymous_variant	23361	exon3			CAGGTGCGAGCTC	AB002324	CCDS45463.1	16p11.2	2013-01-08				ENSG00000102870		"""Zinc fingers, C2H2-type"""	29008	protein-coding gene	gene with protein product			"""zinc finger protein 65"""	ZNF65		9205841	Standard	NM_001080417		Approved	KIAA0326	uc002dzs.1	Q9UEG4		ENST00000262525.4:c.573G>A	16.37:g.30795076C>T		Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	20	7	0.35	NM_001080417	Q15938	Silent	SNP	ENST00000262525.4	37	CCDS45463.1																																																																																			.	.	none		0.662	ZNF629-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434291.1	NM_015309	
LRP11	84918	hgsc.bcm.edu	37	6	150174287	150174287	+	Missense_Mutation	SNP	G	G	T	rs150922217	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:150174287G>T	ENST00000239367.2	-	2	628	c.623C>A	c.(622-624)gCg>gAg	p.A208E	LRP11_ENST00000546019.1_5'UTR|LRP11_ENST00000367368.2_Missense_Mutation_p.A208E|RP11-350J20.12_ENST00000472053.2_RNA	NM_032832.5	NP_116221.3	Q86VZ4	LRP11_HUMAN	low density lipoprotein receptor-related protein 11	208						integral component of membrane (GO:0016021)				cervix(1)|kidney(5)|large_intestine(1)|lung(1)	8		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;4.56e-12)|GBM - Glioblastoma multiforme(68;0.225)		AAGTGGAGGCGCATCCTTTTC	0.438																																					p.A208E		Atlas-SNP	.											LRP11,NS,carcinoma,0,2	LRP11	27	2	0			c.C623A						scavenged	.						57.0	52.0	53.0					6																	150174287		2203	4300	6503	SO:0001583	missense	84918	exon2			GGAGGCGCATCCT	AK027641	CCDS5220.1	6q24.3	2013-02-27			ENSG00000120256	ENSG00000120256		"""Low density lipoprotein receptors"""	16936	protein-coding gene	gene with protein product							Standard	NM_032832		Approved	bA350J20.3, MANSC3	uc003qng.2	Q86VZ4	OTTHUMG00000015801	ENST00000239367.2:c.623C>A	6.37:g.150174287G>T	ENSP00000239367:p.Ala208Glu	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	123	2	0.0162602	NM_032832	Q5VYC0|Q96SN6	Missense_Mutation	SNP	ENST00000239367.2	37	CCDS5220.1	.	.	.	.	.	.	.	.	.	.	G	4.619	0.115107	0.08831	.	.	ENSG00000120256	ENST00000239367;ENST00000367368	T;T	0.14022	2.54;2.54	5.54	3.09	0.35607	PKD domain (1);	0.264933	0.42821	N	0.000651	T	0.01287	0.0042	N	0.01152	-0.98	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.001	T	0.44421	-0.9329	10	0.12430	T	0.62	-13.944	10.7567	0.46241	0.0:0.0:0.363:0.637	.	208;208	Q5VYB9;Q86VZ4	.;LRP11_HUMAN	E	208	ENSP00000239367:A208E;ENSP00000356338:A208E	ENSP00000239367:A208E	A	-	2	0	LRP11	150215980	1.000000	0.71417	0.981000	0.43875	0.538000	0.34931	3.589000	0.53972	0.359000	0.24239	-0.274000	0.10170	GCG	G|1.000;A|0.000	.	alt		0.438	LRP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042664.1	NM_032832	
ADAM29	11086	hgsc.bcm.edu	37	4	175898913	175898913	+	Missense_Mutation	SNP	C	C	T	rs142711835		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:175898913C>T	ENST00000359240.3	+	5	2907	c.2237C>T	c.(2236-2238)aCg>aTg	p.T746M	RP13-577H12.2_ENST00000507525.1_RNA|ADAM29_ENST00000445694.1_Missense_Mutation_p.T746M|ADAM29_ENST00000514159.1_Missense_Mutation_p.T746M|ADAM29_ENST00000404450.4_Missense_Mutation_p.T746M	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	746	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T746M(2)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTCCTGTGACGCCTTCCCAG	0.537																																					p.T746M	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,rectum,carcinoma,0,22	ADAM29	262	22	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	c.C2237T						scavenged	.						149.0	132.0	138.0					4																	175898913		2203	4300	6503	SO:0001583	missense	11086	exon4			CTGTGACGCCTTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2237C>T	4.37:g.175898913C>T	ENSP00000352177:p.Thr746Met	Somatic	118	8	0.0677966		WXS	Illumina HiSeq	Phase_I	144	7	0.0486111	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	8.511	0.866447	0.17250	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.02015	4.5;4.5;4.5;4.5	1.54	0.582	0.17412	.	.	.	.	.	T	0.01558	0.0050	N	0.08118	0	0.09310	N	1	D	0.62365	0.991	P	0.45998	0.5	T	0.53005	-0.8499	8	.	.	.	.	6.1783	0.20457	0.0:0.802:0.0:0.198	.	746	Q9UKF5	ADA29_HUMAN	M	746	ENSP00000352177:T746M;ENSP00000414544:T746M;ENSP00000384229:T746M;ENSP00000423517:T746M	.	T	+	2	0	ADAM29	176135488	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.798000	0.04565	-0.059000	0.13154	0.478000	0.44815	ACG	.	.	weak		0.537	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
DDX11	1663	hgsc.bcm.edu	37	12	31250830	31250830	+	Missense_Mutation	SNP	C	C	G	rs2911826		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:31250830C>G	ENST00000407793.2	+	18	2025	c.1774C>G	c.(1774-1776)Cag>Gag	p.Q592E	DDX11_ENST00000350437.4_Missense_Mutation_p.Q592E|DDX11_ENST00000542838.1_Missense_Mutation_p.Q592E|DDX11_ENST00000545668.1_Missense_Mutation_p.Q592E|DDX11_ENST00000228264.6_Missense_Mutation_p.Q566E|DDX11_ENST00000251758.5_3'UTR|DDX11_ENST00000539673.1_3'UTR	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	592					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)	p.Q592E(1)		breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CAGCCTCAGTCAGAGCACCCT	0.582										Multiple Myeloma(12;0.14)																											p.Q592E		Atlas-SNP	.											DDX11,extremity,malignant_melanoma,0,1	DDX11	188	1	1	Substitution - Missense(1)	skin(1)	c.C1774G						scavenged	.						81.0	80.0	81.0					12																	31250830		2203	4300	6503	SO:0001583	missense	1663	exon18			CTCAGTCAGAGCA	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.1774C>G	12.37:g.31250830C>G	ENSP00000384703:p.Gln592Glu	Somatic	395	17	0.043038		WXS	Illumina HiSeq	Phase_I	404	25	0.0618812	NM_030653	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	C	5.933	0.356089	0.11239	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000404673;ENST00000228264;ENST00000545668;ENST00000350437	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	3.23	3.23	0.37069	.	0.250227	0.40728	N	0.001040	T	0.21550	0.0519	L	0.54965	1.715	0.80722	D	1	B;B;B;B	0.22909	0.048;0.077;0.023;0.048	B;B;B;B	0.18871	0.023;0.017;0.015;0.023	T	0.04481	-1.0948	10	0.11794	T	0.64	.	12.0234	0.53356	0.0:1.0:0.0:0.0	rs2911826	566;592;592;592	Q96FC9-3;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	E	592;592;317;566;592;592	ENSP00000443426:Q592E;ENSP00000384703:Q592E;ENSP00000228264:Q566E;ENSP00000440402:Q592E;ENSP00000309965:Q592E	ENSP00000228264:Q566E	Q	+	1	0	DDX11	31142097	1.000000	0.71417	0.998000	0.56505	0.511000	0.34104	3.091000	0.50199	1.632000	0.50472	0.505000	0.49811	CAG	.	.	weak		0.582	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
KCND2	3751	hgsc.bcm.edu	37	7	120373050	120373050	+	Silent	SNP	G	G	T	rs139984469		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:120373050G>T	ENST00000331113.4	+	2	2174	c.1209G>T	c.(1207-1209)ccG>ccT	p.P403P		NM_012281.2	NP_036413.1	Q9NZV8	KCND2_HUMAN	potassium voltage-gated channel, Shal-related subfamily, member 2	403					action potential (GO:0001508)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	dendritic spine (GO:0043197)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	A-type (transient outward) potassium channel activity (GO:0005250)|metal ion binding (GO:0046872)|voltage-gated potassium channel activity (GO:0005249)			NS(2)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(2)|large_intestine(11)|lung(35)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	75	all_neural(327;0.117)				Amitriptyline(DB00321)|Dalfampridine(DB06637)|Disopyramide(DB00280)|Imipramine(DB00458)	TACCTGTTCCGGTGATTGTAT	0.473																																					p.P403P		Atlas-SNP	.											KCND2,NS,carcinoma,+1,2	KCND2	194	2	0			c.G1209T						scavenged	.						187.0	157.0	167.0					7																	120373050		2203	4300	6503	SO:0001819	synonymous_variant	3751	exon2			TGTTCCGGTGATT	AJ010969	CCDS5776.1	7q31	2012-07-05			ENSG00000184408	ENSG00000184408		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6238	protein-coding gene	gene with protein product		605410				10551270, 16382104	Standard	NM_012281		Approved	Kv4.2, RK5, KIAA1044	uc003vjj.1	Q9NZV8	OTTHUMG00000156989	ENST00000331113.4:c.1209G>T	7.37:g.120373050G>T		Somatic	328	0	0		WXS	Illumina HiSeq	Phase_I	347	5	0.0144092	NM_012281	O95012|O95021|Q2TBD3|Q9UBY7|Q9UN98|Q9UNH9	Silent	SNP	ENST00000331113.4	37	CCDS5776.1																																																																																			G|1.000;A|0.000	.	alt		0.473	KCND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346996.1	NM_012281	
FREM1	158326	hgsc.bcm.edu	37	9	14859353	14859353	+	Silent	SNP	C	C	T	rs562673690	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:14859353C>T	ENST00000380880.3	-	4	1242	c.459G>A	c.(457-459)gcG>gcA	p.A153A	FREM1_ENST00000380881.4_Silent_p.A153A|FREM1_ENST00000422223.2_Silent_p.A153A			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	153					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TTTTATCAATCGCTTGGGACA	0.488																																					p.A153A		Atlas-SNP	.											.	FREM1	261	.	0			c.G459A						PASS	.						132.0	130.0	131.0					9																	14859353		1898	4126	6024	SO:0001819	synonymous_variant	158326	exon5			ATCAATCGCTTGG	AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.459G>A	9.37:g.14859353C>T		Somatic	125	0	0		WXS	Illumina HiSeq	Phase_I	130	25	0.192308	NM_144966	B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Silent	SNP	ENST00000380880.3	37	CCDS47952.1																																																																																			.	.	none		0.488	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2	NM_144966	
LYN	4067	hgsc.bcm.edu	37	8	56910951	56910951	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr8:56910951G>A	ENST00000519728.1	+	11	1393	c.1097G>A	c.(1096-1098)cGg>cAg	p.R366Q	LYN_ENST00000420292.1_3'UTR|LYN_ENST00000520220.2_Missense_Mutation_p.R345Q	NM_002350.3	NP_002341.1	P07948	LYN_HUMAN	LYN proto-oncogene, Src family tyrosine kinase	366	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				B cell homeostasis (GO:0001782)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to heat (GO:0034605)|cellular response to retinoic acid (GO:0071300)|cytokine secretion (GO:0050663)|dendritic cell differentiation (GO:0097028)|erythrocyte differentiation (GO:0030218)|Fc receptor mediated inhibitory signaling pathway (GO:0002774)|Fc receptor mediated stimulatory signaling pathway (GO:0002431)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|histamine secretion by mast cell (GO:0002553)|immune response-regulating cell surface receptor signaling pathway (GO:0002768)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|leukocyte migration (GO:0050900)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of immune response (GO:0050777)|negative regulation of intracellular signal transduction (GO:1902532)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mast cell proliferation (GO:0070667)|negative regulation of myeloid leukocyte differentiation (GO:0002762)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|neuron projection development (GO:0031175)|oligodendrocyte development (GO:0014003)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular component movement (GO:0051272)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060369)|positive regulation of glial cell proliferation (GO:0060252)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of neuron projection development (GO:0010976)|positive regulation of oligodendrocyte progenitor proliferation (GO:0070447)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of stress-activated protein kinase signaling cascade (GO:0070304)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of B cell apoptotic process (GO:0002902)|regulation of B cell receptor signaling pathway (GO:0050855)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cytokine production (GO:0001817)|regulation of cytokine secretion (GO:0050707)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of erythrocyte differentiation (GO:0045646)|regulation of inflammatory response (GO:0050727)|regulation of mast cell activation (GO:0033003)|regulation of mast cell degranulation (GO:0043304)|regulation of monocyte chemotaxis (GO:0090025)|regulation of platelet aggregation (GO:0090330)|regulation of protein phosphorylation (GO:0001932)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|response to amino acid (GO:0043200)|response to axon injury (GO:0048678)|response to carbohydrate (GO:0009743)|response to drug (GO:0042493)|response to hormone (GO:0009725)|response to insulin (GO:0032868)|response to organic cyclic compound (GO:0014070)|response to sterol depletion (GO:0006991)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|T cell costimulation (GO:0031295)|tolerance induction to self antigen (GO:0002513)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integrin alpha2-beta1 complex (GO:0034666)|mast cell granule (GO:0042629)|membrane raft (GO:0045121)|mitochondrial crista (GO:0030061)|mitochondrial intermembrane space (GO:0005758)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	ATP binding (GO:0005524)|enzyme binding (GO:0019899)|glycosphingolipid binding (GO:0043208)|ion channel binding (GO:0044325)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)			breast(4)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)	22		all_lung(136;0.0555)|Lung NSC(129;0.0726)|all_epithelial(80;0.0772)	Epithelial(17;0.000834)|all cancers(17;0.00598)		Bosutinib(DB06616)|Ponatinib(DB08901)	TACATTCACCGGGACCTGCGA	0.448																																					p.R366Q		Atlas-SNP	.											.	LYN	54	.	0			c.G1097A						PASS	.						115.0	110.0	112.0					8																	56910951		2203	4300	6503	SO:0001583	missense	4067	exon11			TTCACCGGGACCT	M16038	CCDS6162.1, CCDS47859.1	8q13	2014-06-25	2014-06-25		ENSG00000254087	ENSG00000254087		"""SH2 domain containing"""	6735	protein-coding gene	gene with protein product		165120	"""v-yes-1 Yamaguchi sarcoma viral related oncogene homolog"""			3561390	Standard	NM_002350		Approved	JTK8	uc003xsk.4	P07948	OTTHUMG00000044345	ENST00000519728.1:c.1097G>A	8.37:g.56910951G>A	ENSP00000428924:p.Arg366Gln	Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	287	73	0.254355	NM_002350	A0AVQ5	Missense_Mutation	SNP	ENST00000519728.1	37	CCDS6162.1	.	.	.	.	.	.	.	.	.	.	G	36	5.851905	0.97023	.	.	ENSG00000254087	ENST00000519728;ENST00000520220	D;D	0.88354	-2.37;-2.37	5.52	5.52	0.82312	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.97099	0.9052	H	0.98507	4.25	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.99	D	0.98468	1.0599	10	0.87932	D	0	.	19.4505	0.94865	0.0:0.0:1.0:0.0	.	436;366	Q6NUK7;P07948	.;LYN_HUMAN	Q	366;345	ENSP00000428924:R366Q;ENSP00000428424:R345Q	ENSP00000428924:R366Q	R	+	2	0	LYN	57073505	1.000000	0.71417	0.688000	0.30117	0.945000	0.59286	9.869000	0.99810	2.597000	0.87782	0.655000	0.94253	CGG	.	.	none		0.448	LYN-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378155.1	NM_002350	
QPCTL	54814	hgsc.bcm.edu	37	19	46206262	46206262	+	Silent	SNP	G	G	A	rs17850756	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:46206262G>A	ENST00000012049.5	+	7	1325	c.1104G>A	c.(1102-1104)ttG>ttA	p.L368L	QPCTL_ENST00000366382.4_Silent_p.L274L	NM_017659.3	NP_060129.2	Q9NXS2	QPCTL_HUMAN	glutaminyl-peptide cyclotransferase-like	368					peptidyl-pyroglutamic acid biosynthetic process, using glutaminyl-peptide cyclotransferase (GO:0017186)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glutaminyl-peptide cyclotransferase activity (GO:0016603)|zinc ion binding (GO:0008270)	p.L368L(1)		breast(1)|cervix(2)|endometrium(1)|lung(5)|skin(1)|stomach(1)	11		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0059)|GBM - Glioblastoma multiforme(486;0.0882)|Epithelial(262;0.208)		TACACAACTTGTGCCGCATTC	0.612													G|||	1178	0.235224	0.2163	0.1744	5008	,	,		18926	0.2133		0.2853	False		,,,				2504	0.2751				p.L368L		Atlas-SNP	.											QPCTL,NS,carcinoma,0,1	QPCTL	24	1	1	Substitution - coding silent(1)	stomach(1)	c.G1104A						scavenged	.	G	,	973,3433	366.4+/-317.8	114,745,1344	171.0	125.0	140.0		822,1104	-8.7	0.8	19	dbSNP_123	140	2781,5819	441.0+/-359.7	472,1837,1991	no	coding-synonymous,coding-synonymous	QPCTL	NM_001163377.1,NM_017659.3	,	586,2582,3335	AA,AG,GG		32.3372,22.0835,28.8636	,	274/289,368/383	46206262	3754,9252	2203	4300	6503	SO:0001819	synonymous_variant	54814	exon7			CAACTTGTGCCGC	AK000091	CCDS12672.1, CCDS54282.1	19q13.32	2014-09-04			ENSG00000011478	ENSG00000011478			25952	protein-coding gene	gene with protein product	"""glutaminyl cyclase-like"""						Standard	NM_017659		Approved	FLJ20084	uc010xxr.2	Q9NXS2	OTTHUMG00000182131	ENST00000012049.5:c.1104G>A	19.37:g.46206262G>A		Somatic	427	3	0.00702576		WXS	Illumina HiSeq	Phase_I	383	7	0.0182768	NM_017659	Q53HE4|Q96F74	Silent	SNP	ENST00000012049.5	37	CCDS12672.1																																																																																			G|0.727;A|0.273	0.273	strong		0.612	QPCTL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459656.1	NM_017659	
ALX1	8092	hgsc.bcm.edu	37	12	85674196	85674196	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:85674196T>G	ENST00000316824.3	+	1	312	c.157T>G	c.(157-159)Ttc>Gtc	p.F53V		NM_006982.2	NP_008913.2	Q15699	ALX1_HUMAN	ALX homeobox 1	53					anterior/posterior pattern specification (GO:0009952)|brain development (GO:0007420)|cartilage condensation (GO:0001502)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|mesenchymal cell development (GO:0014031)|multicellular organismal development (GO:0007275)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural tube closure (GO:0001843)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|ovary(1)	26				GBM - Glioblastoma multiforme(134;0.134)		CGTGCAGGCCTTCGGACCCCT	0.637																																					p.F53V		Atlas-SNP	.											ALX1,lower_third,carcinoma,-2,1	ALX1	61	1	0			c.T157G						scavenged	.						43.0	44.0	44.0					12																	85674196		2203	4300	6503	SO:0001583	missense	8092	exon1			CAGGCCTTCGGAC	U31986	CCDS9028.1	12q21.31	2011-06-20	2007-07-26	2007-07-26		ENSG00000180318		"""Homeoboxes / PRD class"""	1494	protein-coding gene	gene with protein product		601527	"""cartilage paired-class homeoprotein 1"""	CART1		8756334, 7592751	Standard	NM_006982		Approved		uc001tae.4	Q15699	OTTHUMG00000169820	ENST00000316824.3:c.157T>G	12.37:g.85674196T>G	ENSP00000315417:p.Phe53Val	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	66	12	0.181818	NM_006982	Q546C8|Q96FH4	Missense_Mutation	SNP	ENST00000316824.3	37	CCDS9028.1	.	.	.	.	.	.	.	.	.	.	T	17.81	3.481878	0.63849	.	.	ENSG00000180318	ENST00000316824	D	0.91843	-2.92	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	D	0.91794	0.7404	N	0.24115	0.695	0.80722	D	1	D	0.57899	0.981	D	0.65140	0.932	D	0.90594	0.4539	10	0.27082	T	0.32	.	14.7384	0.69434	0.0:0.0:0.0:1.0	.	53	Q15699	ALX1_HUMAN	V	53	ENSP00000315417:F53V	ENSP00000315417:F53V	F	+	1	0	ALX1	84198327	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	5.290000	0.65661	2.069000	0.61940	0.528000	0.53228	TTC	.	.	none		0.637	ALX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406072.1	NM_006982	
MUC12	10071	hgsc.bcm.edu	37	7	100635679	100635679	+	Missense_Mutation	SNP	C	C	G	rs10953314	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:100635679C>G	ENST00000379442.3	+	5	2264	c.2264C>G	c.(2263-2265)aCc>aGc	p.T755S	MUC12_ENST00000536621.1_Missense_Mutation_p.T612S			Q9UKN1	MUC12_HUMAN	mucin 12, cell surface associated	755	28 X 19 AA approximate tandem repeats of E-E-S-X-X-X-H-X-X-P-X-X-T-X-T-X-X-X-P.|Ser-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|regulation of cell growth (GO:0001558)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)				breast(6)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|prostate(1)|stomach(13)	25						CACAGCAGCACCAGATCGCCA	0.562													-|||	2362	0.471645	0.3457	0.3718	5008	,	,		31418	0.6111		0.5149	False		,,,				2504	0.5245				p.T612S		Atlas-SNP	.											.	MUC12	140	.	0			c.C1835G						PASS	.	C	SER/THR	560,824		100,360,232	309.0	331.0	325.0		1835	-1.4	0.0	7	dbSNP_120	325	1634,1548		435,764,392	no	missense	MUC12	NM_001164462.1	58	535,1124,624	GG,GC,CC		48.6486,40.4624,48.0508		612/5336	100635679	2194,2372	692	1591	2283	SO:0001583	missense	10071	exon2			GCAGCACCAGATC	AF147790, AF147791	CCDS55139.1	7q22	2007-01-17	2006-03-14		ENSG00000205277	ENSG00000205277		"""Mucins"""	7510	protein-coding gene	gene with protein product		604609	"""mucin 11"""	MUC11		10463611	Standard	NM_001164462		Approved		uc003uxo.3	Q9UKN1	OTTHUMG00000157042	ENST00000379442.3:c.2264C>G	7.37:g.100635679C>G	ENSP00000368755:p.Thr755Ser	Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	5	4	0.8	NM_001164462	A6ND38|F5GWV9|Q9UKN0	Missense_Mutation	SNP	ENST00000379442.3	37		1060	0.48534798534798534	193	0.39227642276422764	144	0.39779005524861877	331	0.5786713286713286	392	0.5171503957783641	-	0.699	-0.791553	0.02884	0.404624	0.513514	ENSG00000205277	ENST00000379442;ENST00000536621	T;T	0.11385	2.79;2.78	0.695	-1.39	0.08997	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	.	.	.	.	.	.	T	0.36962	-0.9726	6	0.08599	T	0.76	.	3.6015	0.08026	0.2554:0.4889:0.2557:0.0	rs10953314;rs61247694	.	.	.	S	755;612	ENSP00000368755:T755S;ENSP00000441929:T612S	ENSP00000368755:T755S	T	+	2	0	MUC12	100422399	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.139000	0.10358	-1.094000	0.03054	0.162000	0.16502	ACC	C|0.505;G|0.495	0.495	strong		0.562	MUC12-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347234.1	XM_379904	
PRSS3	5646	hgsc.bcm.edu	37	9	33797861	33797861	+	Missense_Mutation	SNP	A	A	G	rs151192741		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:33797861A>G	ENST00000361005.5	+	3	406	c.406A>G	c.(406-408)Aaa>Gaa	p.K136E	PRSS3_ENST00000429677.3_Missense_Mutation_p.K72E|PRSS3_ENST00000342836.4_Missense_Mutation_p.K93E|PRSS3_ENST00000379405.3_Missense_Mutation_p.K79E|RP11-133O22.6_ENST00000454429.2_RNA	NM_007343.3	NP_031369	P35030	TRY3_HUMAN	protease, serine, 3	136	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				cobalamin metabolic process (GO:0009235)|digestion (GO:0007586)|endothelial cell migration (GO:0043542)|innate immune response (GO:0045087)|proteolysis (GO:0006508)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			large_intestine(3)|lung(4)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(2)	13			LUSC - Lung squamous cell carcinoma(29;0.0176)			GCACAACATCAAAGTCCTGGA	0.562																																					p.K136E		Atlas-SNP	.											PRSS3_ENST00000361005,NS,carcinoma,-2,3	PRSS3	79	3	0			c.A406G						scavenged	.						162.0	140.0	147.0					9																	33797861		2203	4300	6503	SO:0001583	missense	5646	exon3			AACATCAAAGTCC		CCDS6545.1, CCDS47958.1, CCDS56570.1, CCDS56571.1	9p13	2010-05-07	2008-03-11		ENSG00000010438	ENSG00000010438	3.4.21.4	"""Serine peptidases / Serine peptidases"""	9486	protein-coding gene	gene with protein product	"""mesotrypsin"""	613578	"""protease, serine, 4 (trypsin 4, brain)"", ""protease, serine, 3 (mesotrypsin)"""	PRSS4		2326201, 8294000	Standard	NM_002771		Approved	TRY3, TRY4	uc003ztj.4	P35030	OTTHUMG00000019798	ENST00000361005.5:c.406A>G	9.37:g.33797861A>G	ENSP00000354280:p.Lys136Glu	Somatic	257	11	0.0428016		WXS	Illumina HiSeq	Phase_I	310	11	0.0354839	NM_007343	A8CED1|A8CED3|A9Z1Y4|E7ES07|F8W7P3|P15951|Q15665|Q5VXV0|Q6ISJ4|Q9UQV3	Missense_Mutation	SNP	ENST00000361005.5	37	CCDS47958.1	.	.	.	.	.	.	.	.	.	.	A	2.299	-0.360659	0.05103	.	.	ENSG00000010438	ENST00000361005;ENST00000457896;ENST00000342836;ENST00000429677;ENST00000379405	D;D;D;D;D	0.88664	-2.41;-2.41;-2.41;-2.41;-2.41	3.62	-3.56	0.04626	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.762692	0.13361	N	0.393640	T	0.71668	0.3367	N	0.13140	0.3	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.60801	-0.7191	10	0.05620	T	0.96	.	8.866	0.35286	0.4937:0.0:0.5063:0.0	.	79;136;93	P35030-3;P35030;P35030-4	.;TRY3_HUMAN;.	E	136;91;93;72;79	ENSP00000354280:K136E;ENSP00000401249:K91E;ENSP00000340889:K93E;ENSP00000401828:K72E;ENSP00000368715:K79E	ENSP00000340889:K93E	K	+	1	0	PRSS3	33787861	0.007000	0.16637	0.044000	0.18714	0.056000	0.15407	1.581000	0.36558	-0.349000	0.08274	-1.351000	0.01236	AAA	.	.	weak		0.562	PRSS3-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052121.1	NM_002771	
GOLGA4	2803	hgsc.bcm.edu	37	3	37368928	37368928	+	Missense_Mutation	SNP	A	A	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:37368928A>T	ENST00000361924.2	+	14	5925	c.5551A>T	c.(5551-5553)Att>Ttt	p.I1851F	GOLGA4_ENST00000444882.1_Intron|GOLGA4_ENST00000356847.4_Missense_Mutation_p.I1873F	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1851	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						AACCTGTCAGATTTTGGAGCA	0.368																																					p.I1873F		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A5617T						PASS	.						56.0	58.0	57.0					3																	37368928		2203	4298	6501	SO:0001583	missense	2803	exon15			TGTCAGATTTTGG	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5551A>T	3.37:g.37368928A>T	ENSP00000354486:p.Ile1851Phe	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	71	18	0.253521	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	10.50	1.367946	0.24771	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.23147	1.92;1.92;1.92	4.81	-1.98	0.07480	.	1.321480	0.05575	N	0.571778	T	0.23492	0.0568	L	0.57536	1.79	0.09310	N	1	B;B;B;B	0.26744	0.001;0.001;0.001;0.158	B;B;B;B	0.23574	0.003;0.002;0.002;0.047	T	0.39860	-0.9593	10	0.56958	D	0.05	.	5.1342	0.14926	0.445:0.0:0.36:0.1949	.	1851;1851;1873;1851	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	F	1851;1873;1722	ENSP00000354486:I1851F;ENSP00000349305:I1873F;ENSP00000405842:I1722F	ENSP00000349305:I1873F	I	+	1	0	GOLGA4	37343932	0.000000	0.05858	0.452000	0.26994	0.653000	0.38743	-0.420000	0.07062	0.009000	0.14813	-0.463000	0.05309	ATT	.	.	none		0.368	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
SGK1	6446	hgsc.bcm.edu	37	6	134495658	134495658	+	Missense_Mutation	SNP	G	G	A	rs375777416		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:134495658G>A	ENST00000237305.7	-	2	231	c.143C>T	c.(142-144)gCa>gTa	p.A48V	SGK1_ENST00000367858.5_Missense_Mutation_p.A143V|SGK1_ENST00000367857.5_Missense_Mutation_p.A38V|SGK1_ENST00000489458.2_5'Flank|SGK1_ENST00000475719.2_Missense_Mutation_p.A48V|SGK1_ENST00000413996.3_Missense_Mutation_p.A62V|SGK1_ENST00000528577.1_Missense_Mutation_p.A76V	NM_005627.3	NP_005618.2	O00141	SGK1_HUMAN	serum/glucocorticoid regulated kinase 1	48	Necessary for localization to the mitochondria.				apoptotic process (GO:0006915)|cellular response to DNA damage stimulus (GO:0006974)|ion transmembrane transport (GO:0034220)|long-term memory (GO:0007616)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of catalytic activity (GO:0050790)|regulation of cell growth (GO:0001558)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of gastric acid secretion (GO:0060453)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|renal sodium ion absorption (GO:0070294)|response to stress (GO:0006950)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chloride channel regulator activity (GO:0017081)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|sodium channel regulator activity (GO:0017080)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(21)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(4)|stomach(1)	46	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.00317)|GBM - Glioblastoma multiforme(68;0.00847)		CTGTTTGCATGCATAGGAGTT	0.413											OREG0017675	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.A143V		Atlas-SNP	.											.	SGK1	387	.	0			c.C428T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA,VAL/ALA	0,4406		0,0,2203	88.0	85.0	86.0		143,185,227,428	5.9	1.0	6		86	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	SGK1	NM_005627.3,NM_001143678.1,NM_001143677.1,NM_001143676.1	64,64,64,64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign,benign,benign,benign	48/432,62/446,76/460,143/527	134495658	1,13005	2203	4300	6503	SO:0001583	missense	6446	exon4			TTGCATGCATAGG	AJ000512	CCDS5170.1, CCDS47476.1, CCDS47477.1, CCDS47478.1	6q23	2008-02-05	2007-12-05	2007-12-05	ENSG00000118515	ENSG00000118515			10810	protein-coding gene	gene with protein product		602958	"""serum/glucocorticoid regulated kinase"""	SGK		9114008, 9722955	Standard	NM_005627		Approved		uc003qeo.4	O00141	OTTHUMG00000015613	ENST00000237305.7:c.143C>T	6.37:g.134495658G>A	ENSP00000237305:p.Ala48Val	Somatic	86	0	0	1611	WXS	Illumina HiSeq	Phase_I	88	14	0.159091	NM_001143676	B7UUP7|B7UUP8|B7UUP9|B7Z5B2|E1P583|Q5TCN2|Q5TCN3|Q5TCN4|Q5VY65|Q9UN56	Missense_Mutation	SNP	ENST00000237305.7	37	CCDS5170.1	.	.	.	.	.	.	.	.	.	.	G	11.90	1.778015	0.31502	0.0	1.16E-4	ENSG00000118515	ENST00000367858;ENST00000413996;ENST00000237305;ENST00000367857;ENST00000528577;ENST00000475719;ENST00000461976	T;T;T;T;T;T;T	0.38240	1.67;1.67;1.67;1.67;1.67;1.67;1.15	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.19005	0.0456	L	0.42245	1.32	0.80722	D	1	B;B;B;B;B;B	0.29988	0.001;0.264;0.0;0.004;0.013;0.001	B;B;B;B;B;B	0.24269	0.004;0.052;0.001;0.005;0.022;0.002	T	0.06267	-1.0836	10	0.15066	T	0.55	.	20.2576	0.98430	0.0:0.0:1.0:0.0	.	76;62;48;38;143;48	O00141-5;O00141-3;E9PR89;O00141-4;O00141-2;O00141	.;.;.;.;.;SGK1_HUMAN	V	143;62;48;38;76;48;112	ENSP00000356832:A143V;ENSP00000396242:A62V;ENSP00000237305:A48V;ENSP00000356831:A38V;ENSP00000434450:A76V;ENSP00000434302:A48V;ENSP00000435577:A112V	ENSP00000237305:A48V	A	-	2	0	SGK1	134537351	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	8.062000	0.89475	2.783000	0.95769	0.655000	0.94253	GCA	.	.	weak		0.413	SGK1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042312.2		
TMX4	56255	hgsc.bcm.edu	37	20	8000141	8000141	+	Silent	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:8000141C>T	ENST00000246024.2	-	1	335	c.120G>A	c.(118-120)caG>caA	p.Q40Q	RP5-971N18.3_ENST00000607924.1_RNA|RP5-971N18.3_ENST00000457707.1_RNA	NM_021156.2	NP_066979.2	Q9H1E5	TMX4_HUMAN	thioredoxin-related transmembrane protein 4	40	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				cell redox homeostasis (GO:0045454)|oxidation-reduction process (GO:0055114)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein disulfide isomerase activity (GO:0003756)			endometrium(3)|large_intestine(2)|lung(11)|skin(1)	17						CGGTCATGGGCTGGACCCGGC	0.736																																					p.Q40Q		Atlas-SNP	.											.	TMX4	39	.	0			c.G120A						PASS	.						13.0	14.0	14.0					20																	8000141		1935	3764	5699	SO:0001819	synonymous_variant	56255	exon1			CATGGGCTGGACC		CCDS13101.1	20p12	2011-10-19	2009-02-23	2009-02-23	ENSG00000125827	ENSG00000125827		"""Protein disulfide isomerases"""	25237	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 14"""		"""thioredoxin domain containing 13"""	TXNDC13			Standard	NM_021156		Approved	DJ971N18.2, KIAA1162, PDIA14	uc002wmx.1	Q9H1E5	OTTHUMG00000031843	ENST00000246024.2:c.120G>A	20.37:g.8000141C>T		Somatic	14	0	0		WXS	Illumina HiSeq	Phase_I	40	11	0.275	NM_021156	Q8N4P7|Q8NCC1|Q9UJA1|Q9ULQ8	Silent	SNP	ENST00000246024.2	37	CCDS13101.1																																																																																			.	.	none		0.736	TMX4-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000077928.2	NM_021156	
PAX1	5075	hgsc.bcm.edu	37	20	21687153	21687153	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:21687153C>T	ENST00000398485.2	+	2	418	c.364C>T	c.(364-366)Cgc>Tgc	p.R122C	PAX1_ENST00000460221.1_Intron|PAX1_ENST00000444366.2_Missense_Mutation_p.R98C	NM_001257096.1|NM_006192.4	NP_001244025.1|NP_006183.2	P15863	PAX1_HUMAN	paired box 1	122	Paired. {ECO:0000255|PROSITE- ProRule:PRU00381}.				bone morphogenesis (GO:0060349)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|CD8-positive, alpha-beta T cell differentiation (GO:0043374)|cell proliferation (GO:0008283)|parathyroid gland development (GO:0060017)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|sclerotome development (GO:0061056)|skeletal system development (GO:0001501)|somitogenesis (GO:0001756)|thymus development (GO:0048538)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)			autonomic_ganglia(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(21)|prostate(3)|skin(1)|upper_aerodigestive_tract(3)	38						CATCCGCTTGCGCATTGTGGA	0.647																																					p.R122C		Atlas-SNP	.											.	PAX1	152	.	0			c.C364T						PASS	.						32.0	35.0	34.0					20																	21687153		2203	4299	6502	SO:0001583	missense	5075	exon2			CGCTTGCGCATTG		CCDS13146.2, CCDS74709.1	20p11.22	2007-07-12	2007-07-12		ENSG00000125813	ENSG00000125813		"""Paired boxes"""	8615	protein-coding gene	gene with protein product		167411	"""paired box gene 1"""			1358810	Standard	NM_006192		Approved		uc002wsj.3	P15863	OTTHUMG00000032034	ENST00000398485.2:c.364C>T	20.37:g.21687153C>T	ENSP00000381499:p.Arg122Cys	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	27	8	0.296296	NM_006192	B4E0D6|Q642X9|Q6NTC0|Q9Y558	Missense_Mutation	SNP	ENST00000398485.2	37	CCDS13146.2	.	.	.	.	.	.	.	.	.	.	C	15.94	2.981240	0.53827	.	.	ENSG00000125813	ENST00000398485;ENST00000444366	D;D	0.99479	-5.98;-5.98	5.14	5.14	0.70334	Paired box protein, N-terminal (4);Winged helix-turn-helix transcription repressor DNA-binding (1);Homeodomain-like (1);	0.000000	0.85682	D	0.000000	D	0.99510	0.9825	M	0.80422	2.495	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.98521	1.0623	10	0.87932	D	0	.	18.2175	0.89890	0.0:1.0:0.0:0.0	.	98;28;122	P15863-2;C9J775;P15863	.;.;PAX1_HUMAN	C	122;98	ENSP00000381499:R122C;ENSP00000410355:R98C	ENSP00000381499:R122C	R	+	1	0	PAX1	21635153	1.000000	0.71417	0.998000	0.56505	0.015000	0.08874	2.369000	0.44231	2.382000	0.81193	0.655000	0.94253	CGC	.	.	none		0.647	PAX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078282.3		
MUC4	4585	hgsc.bcm.edu	37	3	195505810	195505810	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195505810G>T	ENST00000463781.3	-	2	13100	c.12641C>A	c.(12640-12642)aCt>aAt	p.T4214N	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T4214N|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)		TGCTGAGGAAGTGTCGGTGAC	0.592																																					p.T4214N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,3	MUC4	1505	3	0			c.C12641A						scavenged	.																																			SO:0001583	missense	4585	exon2			GAGGAAGTGTCGG	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.12641C>A	3.37:g.195505810G>T	ENSP00000417498:p.Thr4214Asn	Somatic	389	5	0.0128535		WXS	Illumina HiSeq	Phase_I	390	8	0.0205128	NM_018406	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	.	.	.	.	.	.	.	.	.	.	g	0.534	-0.856375	0.02630	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.31510	1.49;1.5	0.42	-0.784	0.10954	.	.	.	.	.	T	0.13415	0.0325	N	0.14661	0.345	0.09310	N	1	B	0.22909	0.077	B	0.04013	0.001	T	0.28106	-1.0054	7	.	.	.	.	.	.	.	.	4086	E7ESK3	.	N	4214	ENSP00000417498:T4214N;ENSP00000420243:T4214N	.	T	-	2	0	MUC4	196990589	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-0.373000	0.07979	-0.379000	0.06801	ACT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRTAP4-12	83755	hgsc.bcm.edu	37	17	39280162	39280162	+	Silent	SNP	A	A	G	rs28515113	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:39280162A>G	ENST00000394014.1	-	1	257	c.213T>C	c.(211-213)tgT>tgC	p.C71C		NM_031854.2	NP_114060.1	Q9BQ66	KR412_HUMAN	keratin associated protein 4-12	71	31 X 5 AA repeats of C-C-[GRQVIL]-[SPTR]- [VSTQPC].					keratin filament (GO:0045095)		p.C71C(3)		endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			AGGTGGTCCTACAGCAGGTGG	0.677													A|||	863	0.172324	0.4357	0.1138	5008	,	,		14227	0.1389		0.0477	False		,,,				2504	0.0204				p.C71C		Atlas-SNP	.											KRTAP4-12,colon,carcinoma,0,3	KRTAP4-12	32	3	3	Substitution - coding silent(3)	large_intestine(3)	c.T213C						scavenged	.	A		192,3702		9,174,1764	31.0	55.0	47.0		213	-2.0	0.0	17	dbSNP_125	47	5,8543		0,5,4269	no	coding-synonymous	KRTAP4-12	NM_031854.2		9,179,6033	GG,GA,AA		0.0585,4.9307,1.5833		71/202	39280162	197,12245	1947	4274	6221	SO:0001819	synonymous_variant	83755	exon1			GGTCCTACAGCAG	AJ406943	CCDS32649.1	17q21.2	2013-06-25			ENSG00000213416	ENSG00000213416		"""Keratin associated proteins"""	16776	protein-coding gene	gene with protein product						11279113	Standard	NM_031854		Approved	KAP4.12	uc002hwa.3	Q9BQ66	OTTHUMG00000133632	ENST00000394014.1:c.213T>C	17.37:g.39280162A>G		Somatic	12	1	0.0833333		WXS	Illumina HiSeq	Phase_I	16	4	0.25	NM_031854	A3KMC5|Q495I0	Silent	SNP	ENST00000394014.1	37	CCDS32649.1																																																																																			A|0.891;G|0.109	0.109	strong		0.677	KRTAP4-12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257777.1		
CHAT	1103	hgsc.bcm.edu	37	10	50824117	50824117	+	Intron	SNP	G	G	A	rs1880676	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr10:50824117G>A	ENST00000337653.2	+	2	439				CHAT_ENST00000351556.3_Intron|CHAT_ENST00000339797.1_Intron|CHAT_ENST00000460699.1_Intron|CHAT_ENST00000395559.2_Intron|CHAT_ENST00000455728.2_Intron|CHAT_ENST00000395562.2_Missense_Mutation_p.D7N	NM_001142929.1|NM_020549.4	NP_001136401.1|NP_065574	P28329	CLAT_HUMAN	choline O-acetyltransferase						adult walking behavior (GO:0007628)|dendrite development (GO:0016358)|establishment of synaptic specificity at neuromuscular junction (GO:0007529)|glycerophospholipid biosynthetic process (GO:0046474)|muscle organ development (GO:0007517)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter biosynthetic process (GO:0042136)|neurotransmitter secretion (GO:0007269)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|rhythmic behavior (GO:0007622)|rhythmic excitation (GO:0043179)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	choline O-acetyltransferase activity (GO:0004102)			central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(11)|lung(34)|prostate(3)|urinary_tract(1)	56		all_neural(218;0.107)		GBM - Glioblastoma multiforme(2;0.000585)	Choline(DB00122)|Nicotine(DB00184)	GGAATGCAGAGATGAAGCACT	0.502													G|||	809	0.161542	0.0061	0.1686	5008	,	,		23013	0.1716		0.2316	False		,,,				2504	0.2843				p.D7N		Atlas-SNP	.											CHAT_ENST00000395562,NS,meningioma,0,1	CHAT	162	1	0			c.G19A						scavenged	.	G	,ASN/ASP,,,,,	157,2979		6,145,1417	205.0	171.0	181.0		,19,,,,,	3.2	0.0	10	dbSNP_92	181	1775,5389		221,1333,2028	yes	intron,missense,utr-5,intron,intron,intron,intron	CHAT	NM_001142929.1,NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3,NM_020985.3,NM_020986.3	,23,,,,,	227,1478,3445	AA,AG,GG		24.7767,5.0064,18.7573	,,,,,,	,7/667,,,,,	50824117	1932,8368	1568	3582	5150	SO:0001627	intron_variant	1103	exon2			TGCAGAGATGAAG	AF305907	CCDS7232.1, CCDS7233.1, CCDS44389.1	10q11.2	2010-05-11	2010-05-11		ENSG00000070748	ENSG00000070748	2.3.1.6		1912	protein-coding gene	gene with protein product		118490	"""choline acetyltransferase"""			1840566	Standard	NM_020984		Approved		uc001jhz.2	P28329	OTTHUMG00000018198	ENST00000337653.2:c.287-431G>A	10.37:g.50824117G>A		Somatic	235	2	0.00851064		WXS	Illumina HiSeq	Phase_I	189	3	0.015873	NM_001142933	A2BDF4|A2BDF5|Q16488|Q9BQ23|Q9BQ35|Q9BQE1	Missense_Mutation	SNP	ENST00000337653.2	37	CCDS7232.1	334	0.15293040293040294	5	0.01016260162601626	77	0.212707182320442	89	0.1555944055944056	163	0.21503957783641162	G	13.30	2.197365	0.38806	0.050064	0.247767	ENSG00000070748	ENST00000395562	D	0.85088	-1.94	3.16	3.16	0.36331	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.36813	P	0.11398900000000001	.	.	.	.	.	.	T	0.00984	-1.1491	5	0.87932	D	0	.	10.0691	0.42322	0.0:0.0:1.0:0.0	rs1880676;rs56499801;rs59491670;rs1880676	.	.	.	N	7	ENSP00000378929:D7N	ENSP00000378929:D7N	D	+	1	0	CHAT	50494123	0.004000	0.15560	0.013000	0.15412	0.005000	0.04900	1.413000	0.34725	2.090000	0.63153	0.655000	0.94253	GAT	G|0.836;A|0.164	0.164	strong		0.502	CHAT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047997.1	NM_020549	
ROPN1B	152015	hgsc.bcm.edu	37	3	125702141	125702141	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:125702141A>G	ENST00000514116.1	+	7	932	c.617A>G	c.(616-618)aAc>aGc	p.N206S	ROPN1B_ENST00000251776.4_Missense_Mutation_p.N206S|ROPN1B_ENST00000505382.1_Missense_Mutation_p.N114S|ROPN1B_ENST00000511082.1_Missense_Mutation_p.N114S			Q9BZX4	ROP1B_HUMAN	rhophilin associated tail protein 1B	206					acrosome reaction (GO:0007340)|cytokinesis (GO:0000910)|fusion of sperm to egg plasma membrane (GO:0007342)|Rho protein signal transduction (GO:0007266)|single organismal cell-cell adhesion (GO:0016337)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)	protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor signaling complex scaffold activity (GO:0030159)			endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|stomach(1)	8				GBM - Glioblastoma multiforme(114;0.151)		TTTACCCAAAACCCCAGGGTT	0.373																																					p.N206S		Atlas-SNP	.											.	ROPN1B	16	.	0			c.A617G						PASS	.						119.0	110.0	113.0					3																	125702141		2203	4300	6503	SO:0001583	missense	152015	exon6			CCCAAAACCCCAG	AF231410	CCDS33841.1	3q21.2	2011-01-20	2011-01-20		ENSG00000114547	ENSG00000114547			31927	protein-coding gene	gene with protein product			"""ropporin, rhophilin associated protein 1B"""				Standard	XM_005247137		Approved		uc003eih.3	Q9BZX4	OTTHUMG00000162651	ENST00000514116.1:c.617A>G	3.37:g.125702141A>G	ENSP00000426271:p.Asn206Ser	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	137	19	0.138686	NM_001012337	D3DNA6|Q96BM7	Missense_Mutation	SNP	ENST00000514116.1	37	CCDS33841.1	.	.	.	.	.	.	.	.	.	.	A	11.26	1.585762	0.28268	.	.	ENSG00000114547	ENST00000514116;ENST00000251776;ENST00000505382;ENST00000511082	T;T;T;T	0.22539	1.95;1.95;1.96;1.96	2.16	2.16	0.27623	.	0.000000	0.85682	D	0.000000	T	0.20941	0.0504	N	0.22421	0.69	0.27471	N	0.95288	D	0.56035	0.974	D	0.67725	0.953	T	0.10636	-1.0621	10	0.07990	T	0.79	-14.4117	6.3386	0.21310	1.0:0.0:0.0:0.0	.	206	Q9BZX4	ROP1B_HUMAN	S	206;206;114;114	ENSP00000426271:N206S;ENSP00000251776:N206S;ENSP00000421662:N114S;ENSP00000424447:N114S	ENSP00000251776:N206S	N	+	2	0	ROPN1B	127184831	1.000000	0.71417	0.999000	0.59377	0.750000	0.42670	4.669000	0.61575	1.241000	0.43820	0.373000	0.22412	AAC	.	.	none		0.373	ROPN1B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369931.1	NM_001012337	
FAM83E	54854	hgsc.bcm.edu	37	19	49116555	49116555	+	Silent	SNP	A	A	G	rs368654	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:49116555A>G	ENST00000263266.3	-	1	264	c.75T>C	c.(73-75)ttT>ttC	p.F25F	FAM83E_ENST00000595110.1_5'Flank	NM_017708.3	NP_060178.2	Q2M2I3	FA83E_HUMAN	family with sequence similarity 83, member E	25										NS(1)|endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|urinary_tract(2)	10		all_epithelial(76;2.38e-06)|all_lung(116;4.89e-06)|Lung NSC(112;9.34e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000102)|all cancers(93;0.000117)|GBM - Glioblastoma multiforme(486;0.00627)|Epithelial(262;0.0158)		CGGAATATAGAAAGCCGGGGC	0.701													G|||	4442	0.886981	0.9887	0.8401	5008	,	,		13823	0.997		0.7137	False		,,,				2504	0.8476				p.F25F		Atlas-SNP	.											FAM83E,NS,carcinoma,0,1	FAM83E	34	1	0			c.T75C						scavenged	.	G		3176,174		1515,146,14	8.0	10.0	9.0		75	2.9	0.0	19	dbSNP_80	9	5522,2104		2021,1480,312	no	coding-synonymous	FAM83E	NM_017708.3		3536,1626,326	GG,GA,AA		27.5898,5.194,20.7544		25/479	49116555	8698,2278	1675	3813	5488	SO:0001819	synonymous_variant	54854	exon1			ATATAGAAAGCCG	AK000207	CCDS42587.1	19q13.33	2013-10-24			ENSG00000105523	ENSG00000105523			25972	protein-coding gene	gene with protein product							Standard	NM_017708		Approved	FLJ20200	uc002pjn.2	Q2M2I3	OTTHUMG00000183315	ENST00000263266.3:c.75T>C	19.37:g.49116555A>G		Somatic	4	1	0.25		WXS	Illumina HiSeq	Phase_I	6	4	0.666667	NM_017708	Q9NXK1	Silent	SNP	ENST00000263266.3	37	CCDS42587.1																																																																																			A|0.144;G|0.856	0.856	strong		0.701	FAM83E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466145.1	NM_017708	
ASIC1	41	hgsc.bcm.edu	37	12	50467769	50467769	+	Intron	SNP	G	G	A	rs706793	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr12:50467769G>A	ENST00000447966.2	+	4	787				ASIC1_ENST00000552438.1_Silent_p.P134P|ASIC1_ENST00000228468.4_Intron	NM_001095.3	NP_001086.2	P78348	ASIC1_HUMAN	acid-sensing (proton-gated) ion channel 1						associative learning (GO:0008306)|calcium ion transmembrane transport (GO:0070588)|cellular response to pH (GO:0071467)|ion transmembrane transport (GO:0034220)|memory (GO:0007613)|negative regulation of neurotransmitter secretion (GO:0046929)|protein homotrimerization (GO:0070207)|regulation of membrane potential (GO:0042391)|response to acidic pH (GO:0010447)|response to pH (GO:0009268)|sensory perception of sour taste (GO:0050915)|signal transduction (GO:0007165)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acid-sensing ion channel activity (GO:0044736)|ion gated channel activity (GO:0022839)|ligand-gated sodium channel activity (GO:0015280)									Amiloride(DB00594)|Diclofenac(DB00586)	TGGCCTTCCCGGCAGTCACCC	0.577													G|||	1142	0.228035	0.1021	0.3112	5008	,	,		17370	0.0913		0.4364	False		,,,				2504	0.2658				p.P134P		Atlas-SNP	.											.	.	.	.	0			c.G402A						PASS	.																																			SO:0001627	intron_variant	41	exon1			CTTCCCGGCAGTC	U78181	CCDS8796.1, CCDS44876.1, CCDS58228.1	12q12	2012-02-23	2012-02-22	2012-02-22		ENSG00000110881		"""Ion channels / Acid-sensing (proton-gated) ion channels"""	100	protein-coding gene	gene with protein product		602866	"""amiloride-sensitive cation channel 2, neuronal"""	ACCN2		9037075	Standard	NM_001095		Approved	BNaC2, hBNaC2	uc001rvv.4	P78348	OTTHUMG00000169812	ENST00000447966.2:c.559-3227G>A	12.37:g.50467769G>A		Somatic	2	0	0		WXS	Illumina HiSeq	Phase_I	4	4	1	NM_001256830	A3KN86|E5KBL7|P78349|Q96CV2	Silent	SNP	ENST00000447966.2	37	CCDS44876.1																																																																																			G|0.753;A|0.247	0.247	strong		0.577	ASIC1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406004.2	NM_020039	
HRH1	3269	hgsc.bcm.edu	37	3	11301217	11301217	+	Missense_Mutation	SNP	G	G	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:11301217G>T	ENST00000397056.1	+	3	685	c.494G>T	c.(493-495)tGg>tTg	p.W165L	HRH1_ENST00000438284.2_Missense_Mutation_p.W165L|HRH1_ENST00000431010.2_Missense_Mutation_p.W165L	NM_000861.3|NM_001098211.1	NP_000852.1|NP_001091681.1	P35367	HRH1_HUMAN	histamine receptor H1	165					cellular response to histamine (GO:0071420)|eosinophil chemotaxis (GO:0048245)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|inositol phosphate-mediated signaling (GO:0048016)|memory (GO:0007613)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of vasoconstriction (GO:0045907)|regulation of synaptic plasticity (GO:0048167)|regulation of vascular permeability (GO:0043114)|visual learning (GO:0008542)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|histamine receptor activity (GO:0004969)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25					Aceprometazine(DB01615)|Alcaftadine(DB06766)|Alimemazine(DB01246)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Antazoline(DB08799)|Aripiprazole(DB01238)|Asenapine(DB06216)|Astemizole(DB00637)|Azatadine(DB00719)|Azelastine(DB00972)|Benzatropine(DB00245)|Bepotastine(DB04890)|Betahistine(DB06698)|Bromodiphenhydramine(DB01237)|Brompheniramine(DB00835)|Buclizine(DB00354)|Carbinoxamine(DB00748)|Cetirizine(DB00341)|Chlorcyclizine(DB08936)|Chloropyramine(DB08800)|Chlorphenamine(DB01114)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Citalopram(DB00215)|Clemastine(DB00283)|Clofedanol(DB04837)|Clozapine(DB00363)|Cyclizine(DB01176)|Cyproheptadine(DB00434)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexbrompheniramine(DB00405)|Dimenhydrinate(DB00985)|Dimetindene(DB08801)|Diphenhydramine(DB01075)|Diphenylpyraline(DB01146)|Doxepin(DB01142)|Doxylamine(DB00366)|Emedastine(DB01084)|Epinastine(DB00751)|Escitalopram(DB01175)|Fexofenadine(DB00950)|Flunarizine(DB04841)|Histamine Phosphate(DB00667)|Hydroxyzine(DB00557)|Iloperidone(DB04946)|Imipramine(DB00458)|Isothipendyl(DB08802)|Ketotifen(DB00920)|Levocabastine(DB01106)|Loratadine(DB00455)|Loxapine(DB00408)|Maprotiline(DB00934)|Meclizine(DB00737)|Mepyramine(DB06691)|Mequitazine(DB01071)|Methdilazine(DB00902)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Olopatadine(DB00768)|Orphenadrine(DB01173)|Paliperidone(DB01267)|Phenindamine(DB01619)|Pheniramine(DB01620)|Promazine(DB00420)|Promethazine(DB01069)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Tolazoline(DB00797)|Trazodone(DB00656)|Trimipramine(DB00726)|Tripelennamine(DB00792)|Triprolidine(DB00427)|Ziprasidone(DB00246)	ATTCTAGGCTGGAATCACTTC	0.527																																					p.W165L		Atlas-SNP	.											HRH1,NS,carcinoma,-1,1	HRH1	58	1	0			c.G494T						scavenged	.						101.0	96.0	97.0					3																	11301217		2203	4300	6503	SO:0001583	missense	3269	exon3			TAGGCTGGAATCA		CCDS2604.1	3p25	2012-11-12			ENSG00000196639	ENSG00000196639		"""GPCR / Class A : Histamine receptors"""	5182	protein-coding gene	gene with protein product		600167				8003029	Standard	NM_001098211		Approved		uc010hds.3	P35367	OTTHUMG00000129719	ENST00000397056.1:c.494G>T	3.37:g.11301217G>T	ENSP00000380247:p.Trp165Leu	Somatic	142	1	0.00704225		WXS	Illumina HiSeq	Phase_I	134	2	0.0149254	NM_000861	A8K047|Q6P9E5	Missense_Mutation	SNP	ENST00000397056.1	37	CCDS2604.1	.	.	.	.	.	.	.	.	.	.	G	29.5	5.007825	0.93287	.	.	ENSG00000196639	ENST00000438284;ENST00000431010;ENST00000397056	T;T;T	0.70869	-0.52;-0.52;-0.52	5.98	5.98	0.97165	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.84215	0.5423	M	0.66560	2.04	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83958	0.0320	10	0.66056	D	0.02	-19.6705	20.4434	0.99119	0.0:0.0:1.0:0.0	.	165	P35367	HRH1_HUMAN	L	165	ENSP00000406705:W165L;ENSP00000397028:W165L;ENSP00000380247:W165L	ENSP00000380247:W165L	W	+	2	0	HRH1	11276217	1.000000	0.71417	0.997000	0.53966	0.923000	0.55619	9.731000	0.98807	2.838000	0.97847	0.655000	0.94253	TGG	.	.	none		0.527	HRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251928.2		
SCN9A	6335	hgsc.bcm.edu	37	2	167168208	167168208	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:167168208A>G	ENST00000409435.1	-	1	58	c.59T>C	c.(58-60)cTt>cCt	p.L20P	SCN9A_ENST00000303354.6_Missense_Mutation_p.L20P|SCN9A_ENST00000409672.1_Missense_Mutation_p.L20P|SCN9A_ENST00000375387.4_Missense_Mutation_p.L20P			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	20					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AATGAGGGCAAGAGACTGTTT	0.428																																					p.L20P		Atlas-SNP	.											SCN9A,colon,carcinoma,+1,2	SCN9A	296	2	0			c.T59C						PASS	.						97.0	95.0	96.0					2																	167168208		1908	4140	6048	SO:0001583	missense	6335	exon2			AGGGCAAGAGACT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.59T>C	2.37:g.167168208A>G	ENSP00000386330:p.Leu20Pro	Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	81	19	0.234568	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	a	22.4	4.283973	0.80803	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.98012	-4.65;-4.66;-4.66;-4.66	5.43	5.43	0.79202	.	0.235814	0.30227	N	0.010109	D	0.99180	0.9716	H	0.96943	3.91	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99100	1.0843	10	0.87932	D	0	.	15.1326	0.72536	1.0:0.0:0.0:0.0	.	20	E7EUN6	.	P	20	ENSP00000386306:L20P;ENSP00000364536:L20P;ENSP00000304748:L20P;ENSP00000386330:L20P	ENSP00000304748:L20P	L	-	2	0	SCN9A	166876454	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	9.307000	0.96226	2.055000	0.61198	0.533000	0.62120	CTT	.	.	none		0.428	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
SEC23B	10483	hgsc.bcm.edu	37	20	18513372	18513372	+	Missense_Mutation	SNP	C	C	T	rs17807673	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:18513372C>T	ENST00000336714.3	+	11	1730	c.1298C>T	c.(1297-1299)cCg>cTg	p.P433L	SEC23B_ENST00000377465.1_Missense_Mutation_p.P433L|SEC23B_ENST00000262544.2_Missense_Mutation_p.P433L|SEC23B_ENST00000377475.3_Missense_Mutation_p.P433L	NM_006363.4|NM_032985.4|NM_032986.3	NP_006354.2|NP_116780.1|NP_116781.1	Q15437	SC23B_HUMAN	Sec23 homolog B (S. cerevisiae)	433			P -> L (in dbSNP:rs17807673). {ECO:0000269|PubMed:15489334}.		ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	COPII vesicle coat (GO:0030127)|endomembrane system (GO:0012505)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|large_intestine(6)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	32						GTGAAAGGACCGTGTGTGTCA	0.453													C|||	307	0.0613019	0.0061	0.1095	5008	,	,		22089	0.003		0.1302	False		,,,				2504	0.091				p.P433L		Atlas-SNP	.											SEC23B,NS,carcinoma,-1,1	SEC23B	70	1	0			c.C1298T						scavenged	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	133,4273	95.3+/-134.0	4,125,2074	135.0	128.0	130.0		1298,1244,1298,1298,1298	4.8	1.0	20	dbSNP_123	130	1235,7365	248.6+/-276.2	95,1045,3160	yes	missense,missense,missense,missense,missense	SEC23B	NM_001172745.1,NM_001172746.1,NM_006363.4,NM_032985.4,NM_032986.3	98,98,98,98,98	99,1170,5234	TT,TC,CC		14.3605,3.0186,10.5182	benign,benign,benign,benign,benign	433/768,415/750,433/768,433/768,433/768	18513372	1368,11638	2203	4300	6503	SO:0001583	missense	10483	exon11			AAGGACCGTGTGT	X97065	CCDS13137.1	20p11.23	2010-02-09	2001-11-28		ENSG00000101310	ENSG00000101310			10702	protein-coding gene	gene with protein product		610512	"""Sec23 (S. cerevisiae) homolog B"", ""congenital dyserythropoietic anemia, type II"""	CDAN2		8898360, 10329445, 19621418	Standard	NM_032985		Approved	CDA-II, CDAII, HEMPAS	uc002wrb.2	Q15437	OTTHUMG00000031976	ENST00000336714.3:c.1298C>T	20.37:g.18513372C>T	ENSP00000338844:p.Pro433Leu	Somatic	219	2	0.00913242		WXS	Illumina HiSeq	Phase_I	251	4	0.0159363	NM_032985	D3DW33|Q503A9|Q5W183|Q9BS15|Q9BSI2|Q9H1D7	Missense_Mutation	SNP	ENST00000336714.3	37	CCDS13137.1	133	0.060897435897435896	6	0.012195121951219513	31	0.0856353591160221	1	0.0017482517482517483	95	0.12532981530343007	C	19.62	3.860872	0.71834	0.030186	0.143605	ENSG00000101310	ENST00000336714;ENST00000262544;ENST00000377475;ENST00000377465	T;T;T;T	0.75154	-0.91;-0.91;-0.91;-0.91	4.75	4.75	0.60458	Sec23/Sec24 beta-sandwich (1);	0.217145	0.48767	D	0.000178	T	0.02929	0.0087	M	0.90595	3.13	0.09310	P	0.9999999999602158	P	0.35411	0.5	B	0.42282	0.382	T	0.57837	-0.7742	9	0.72032	D	0.01	-11.4113	17.2702	0.87099	0.0:1.0:0.0:0.0	rs17807673;rs17849993;rs56617302;rs17807673	433	Q15437	SC23B_HUMAN	L	433	ENSP00000338844:P433L;ENSP00000262544:P433L;ENSP00000366695:P433L;ENSP00000366685:P433L	ENSP00000262544:P433L	P	+	2	0	SEC23B	18461372	0.998000	0.40836	0.977000	0.42913	0.989000	0.77384	7.109000	0.77062	2.631000	0.89168	0.655000	0.94253	CCG	C|0.909;T|0.091	0.091	strong		0.453	SEC23B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078184.5		
PTPRT	11122	hgsc.bcm.edu	37	20	40709537	40709537	+	Missense_Mutation	SNP	T	T	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr20:40709537T>A	ENST00000373187.1	-	31	4307	c.4308A>T	c.(4306-4308)gaA>gaT	p.E1436D	PTPRT_ENST00000373201.1_Missense_Mutation_p.E1426D|PTPRT_ENST00000373193.3_Missense_Mutation_p.E1439D|PTPRT_ENST00000373198.4_Missense_Mutation_p.E1455D|PTPRT_ENST00000373184.1_Missense_Mutation_p.E1446D|PTPRT_ENST00000356100.2_Missense_Mutation_p.E1445D|PTPRT_ENST00000373190.1_Missense_Mutation_p.E1435D			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	1436	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				AGCTTAAATATTCCAGTGCCA	0.507																																					p.E1455D		Atlas-SNP	.											PTPRT,upper_back,malignant_melanoma,-2,1	PTPRT	372	1	0			c.A4365T						PASS	.						56.0	60.0	59.0					20																	40709537		2084	4243	6327	SO:0001583	missense	11122	exon32			TAAATATTCCAGT	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.4308A>T	20.37:g.40709537T>A	ENSP00000362283:p.Glu1436Asp	Somatic	39	0	0		WXS	Illumina HiSeq	Phase_I	31	7	0.225806	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	.	.	.	.	.	.	.	.	.	.	T	26.5	4.740476	0.89573	.	.	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	D;D;D;D;D;D;D	0.84516	-1.86;-1.86;-1.86;-1.86;-1.86;-1.86;-1.86	6.08	6.08	0.98989	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.92047	0.7480	M	0.83012	2.62	0.58432	D	0.999999	D;D	0.76494	0.999;0.999	D;D	0.87578	0.997;0.998	D	0.92777	0.6237	10	0.87932	D	0	.	10.9027	0.47062	0.0:0.0695:0.0:0.9305	.	1458;1436	O14522-1;O14522	.;PTPRT_HUMAN	D	1435;1436;1439;1445;1458;1446;1426	ENSP00000362286:E1435D;ENSP00000362283:E1436D;ENSP00000362289:E1439D;ENSP00000348408:E1445D;ENSP00000362294:E1458D;ENSP00000362280:E1446D;ENSP00000362297:E1426D	ENSP00000348408:E1445D	E	-	3	2	PTPRT	40142951	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	2.782000	0.47758	2.333000	0.79357	0.533000	0.62120	GAA	.	.	none		0.507	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
KIRREL3	84623	hgsc.bcm.edu	37	11	126299148	126299148	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:126299148G>A	ENST00000525144.2	-	15	1981	c.1732C>T	c.(1732-1734)Cga>Tga	p.R578*	KIRREL3_ENST00000529097.2_Nonsense_Mutation_p.R566*|KIRREL3_ENST00000416561.2_Nonsense_Mutation_p.R45*	NM_032531.3	NP_115920.1	Q8IZU9	KIRR3_HUMAN	kin of IRRE like 3 (Drosophila)	578					hemopoiesis (GO:0030097)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				central_nervous_system(1)|endometrium(5)|large_intestine(11)|lung(8)|ovary(3)|prostate(1)	29	all_hematologic(175;0.145)	Lung NSC(97;0.0484)|all_lung(97;0.0522)|Medulloblastoma(222;0.0523)|Breast(109;0.0949)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;6.03e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.12)		ATTTCCACTCGGATATCATTT	0.458																																					p.R578X		Atlas-SNP	.											.	KIRREL3	183	.	0			c.C1732T						PASS	.						96.0	99.0	98.0					11																	126299148		1942	4138	6080	SO:0001587	stop_gained	84623	exon15			CCACTCGGATATC	AB058770	CCDS53723.1, CCDS55796.1, CCDS73413.1	11q24	2013-01-29			ENSG00000149571	ENSG00000149571		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	23204	protein-coding gene	gene with protein product		607761				12424224, 11347906	Standard	NM_032531		Approved	NEPH2, KIAA1867, KIRRE	uc001qea.3	Q8IZU9	OTTHUMG00000165831	ENST00000525144.2:c.1732C>T	11.37:g.126299148G>A	ENSP00000435466:p.Arg578*	Somatic	158	0	0		WXS	Illumina HiSeq	Phase_I	108	36	0.333333	NM_032531	Q3MIJ7|Q6UWJ9|Q6UWL5|Q96JG0	Nonsense_Mutation	SNP	ENST00000525144.2	37	CCDS53723.1	.	.	.	.	.	.	.	.	.	.	G	37	6.421659	0.97555	.	.	ENSG00000149571	ENST00000525144;ENST00000529097;ENST00000416561	.	.	.	5.66	4.71	0.59529	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.7594	15.9821	0.80116	0.0:0.0:0.8647:0.1353	.	.	.	.	X	578;566;45	.	ENSP00000408692:R45X	R	-	1	2	KIRREL3	125804358	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.330000	0.65899	2.668000	0.90789	0.561000	0.74099	CGA	.	.	none		0.458	KIRREL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386479.2	NM_032531	
TARS	6897	hgsc.bcm.edu	37	5	33461355	33461355	+	Silent	SNP	G	G	A	rs2270905	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:33461355G>A	ENST00000265112.3	+	13	1817	c.1506G>A	c.(1504-1506)ccG>ccA	p.P502P	TARS_ENST00000455217.2_Silent_p.P535P|TARS_ENST00000414361.2_Silent_p.P381P|TARS_ENST00000502553.1_Silent_p.P502P|TARS_ENST00000541634.1_Silent_p.P398P|TARS_ENST00000509410.1_3'UTR	NM_152295.4	NP_689508.3	P26639	SYTC_HUMAN	threonyl-tRNA synthetase	502					gene expression (GO:0010467)|threonyl-tRNA aminoacylation (GO:0006435)|translation (GO:0006412)|tRNA aminoacylation for protein translation (GO:0006418)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|threonine-tRNA ligase activity (GO:0004829)			NS(1)|biliary_tract(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|lung(11)|ovary(2)|prostate(1)	29					L-Threonine(DB00156)	CTACTCGCCCGGAAAAATTCC	0.353													G|||	692	0.138179	0.1256	0.1441	5008	,	,		18644	0.127		0.2356	False		,,,				2504	0.0624				p.P535P		Atlas-SNP	.											TARS,NS,carcinoma,+1,1	TARS	66	1	0			c.G1605A						scavenged	.	G		624,3782	262.5+/-264.9	43,538,1622	85.0	91.0	89.0		1506	-4.8	1.0	5	dbSNP_100	89	1892,6708	331.8+/-319.8	201,1490,2609	no	coding-synonymous	TARS	NM_152295.3		244,2028,4231	AA,AG,GG		22.0,14.1625,19.3449		502/724	33461355	2516,10490	2203	4300	6503	SO:0001819	synonymous_variant	6897	exon14			TCGCCCGGAAAAA	AK095852	CCDS3899.1, CCDS58943.1	5p13.2	2012-10-02			ENSG00000113407	ENSG00000113407	6.1.1.3	"""Aminoacyl tRNA synthetases / Class II"""	11572	protein-coding gene	gene with protein product	"""threonine tRNA ligase 1, cytoplasmic"""	187790					Standard	NM_152295		Approved		uc011coc.3	P26639	OTTHUMG00000090683	ENST00000265112.3:c.1506G>A	5.37:g.33461355G>A		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	97	4	0.0412371	NM_001258438	A8K8I1|B4DEG8|Q96FP5|Q9BWA6	Silent	SNP	ENST00000265112.3	37	CCDS3899.1																																																																																			G|0.816;A|0.184	0.184	strong		0.353	TARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207367.1	NM_152295	
MAP2K3	5606	hgsc.bcm.edu	37	17	21206529	21206529	+	Missense_Mutation	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:21206529T>C	ENST00000342679.4	+	7	800	c.551T>C	c.(550-552)cTg>cCg	p.L184P	MAP2K3_ENST00000361818.5_Missense_Mutation_p.L155P|MAP2K3_ENST00000316920.6_Missense_Mutation_p.L155P	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	184	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		CACAGCAAGCTGTCGGTGATC	0.632																																					p.L184P		Atlas-SNP	.											.	MAP2K3	135	.	0			c.T551C						PASS	.						50.0	42.0	45.0					17																	21206529		2203	4300	6503	SO:0001583	missense	5606	exon7			GCAAGCTGTCGGT	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.551T>C	17.37:g.21206529T>C	ENSP00000345083:p.Leu184Pro	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	98	12	0.122449	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	T	14.32	2.501712	0.44455	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.40756	1.02;1.02	5.45	5.45	0.79879	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.52532	D	0.000069	T	0.63534	0.2519	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.67325	-0.5699	10	0.87932	D	0	-29.8457	15.5058	0.75739	0.0:0.0:0.0:1.0	.	184	P46734	MP2K3_HUMAN	P	184;155;155;188	ENSP00000345083:L184P;ENSP00000355081:L155P	ENSP00000319139:L188P	L	+	2	0	MAP2K3	21147122	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.679000	0.84048	2.077000	0.62373	0.459000	0.35465	CTG	.	.	none		0.632	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	
GRK6	2870	hgsc.bcm.edu	37	5	176863212	176863212	+	Missense_Mutation	SNP	G	G	A	rs200870863		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:176863212G>A	ENST00000355472.5	+	12	1364	c.1196G>A	c.(1195-1197)cGg>cAg	p.R399Q	GRK6_ENST00000528793.1_Missense_Mutation_p.R399Q|GRK6_ENST00000393576.3_Missense_Mutation_p.R365Q|GRK6_ENST00000355958.5_Missense_Mutation_p.R399Q|GRK6_ENST00000507633.1_Missense_Mutation_p.R399Q|PRR7-AS1_ENST00000425316.3_RNA	NM_001004106.2|NM_002082.3	NP_001004106.1|NP_002073.2	P43250	GRK6_HUMAN	G protein-coupled receptor kinase 6	399	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway (GO:0016055)	membrane (GO:0016020)	ATP binding (GO:0005524)|G-protein coupled receptor kinase activity (GO:0004703)	p.R399Q(2)		breast(1)|endometrium(4)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(5)|stomach(1)	25	all_cancers(89;1.15e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GAGGTGGAGCGGCTGGTGAAG	0.637																																					p.R399Q		Atlas-SNP	.											GRK6,NS,carcinoma,0,1	GRK6	48	1	2	Substitution - Missense(2)	prostate(2)	c.G1196A						scavenged	.						64.0	78.0	73.0					5																	176863212		2203	4300	6503	SO:0001583	missense	2870	exon12			TGGAGCGGCTGGT		CCDS34303.1, CCDS43406.1, CCDS47348.1	5q35	2011-01-14	2004-02-04	2004-02-06	ENSG00000198055	ENSG00000198055			4545	protein-coding gene	gene with protein product		600869		GPRK6		8415712	Standard	NM_002082		Approved		uc021yiu.1	P43250	OTTHUMG00000163401	ENST00000355472.5:c.1196G>A	5.37:g.176863212G>A	ENSP00000347655:p.Arg399Gln	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	122	6	0.0491803	NM_002082	O60541|Q13652	Missense_Mutation	SNP	ENST00000355472.5	37	CCDS34303.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.481147	0.63849	.	.	ENSG00000198055	ENST00000355472;ENST00000507633;ENST00000393576;ENST00000355958;ENST00000528793	T;T;T;T;T	0.65364	-0.15;-0.15;-0.15;-0.15;-0.15	5.9	5.9	0.94986	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.061068	0.64402	D	0.000007	T	0.41143	0.1146	N	0.11106	0.095	0.80722	D	1	P;P;B;B	0.39535	0.598;0.677;0.139;0.28	B;B;B;B	0.26094	0.026;0.066;0.016;0.007	T	0.38134	-0.9675	10	0.25751	T	0.34	-30.4439	20.2768	0.98488	0.0:0.0:1.0:0.0	.	399;369;399;399	P43250;B3KPS5;P43250-2;D6RHX8	GRK6_HUMAN;.;.;.	Q	399;399;365;399;399	ENSP00000347655:R399Q;ENSP00000427581:R399Q;ENSP00000377204:R365Q;ENSP00000348230:R399Q;ENSP00000433511:R399Q	ENSP00000347655:R399Q	R	+	2	0	GRK6	176795818	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.675000	0.74493	2.808000	0.96608	0.650000	0.86243	CGG	.	.	weak		0.637	GRK6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000373204.1	NM_002082	
CDC27	996	hgsc.bcm.edu	37	17	45234327	45234327	+	Missense_Mutation	SNP	C	C	T	rs7350889		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:45234327C>T	ENST00000066544.3	-	7	887	c.794G>A	c.(793-795)gGt>gAt	p.G265D	CDC27_ENST00000531206.1_Missense_Mutation_p.G265D|CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000446365.2_Missense_Mutation_p.G204D|CDC27_ENST00000527547.1_Missense_Mutation_p.G265D	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	265					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.G265D(2)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAACTTCGACCAGTTTTTGG	0.368																																					p.G265D		Atlas-SNP	.											CDC27_ENST00000531206,NS,adenoma,0,4	CDC27	337	4	2	Substitution - Missense(2)	skin(2)	c.G794A						scavenged	.						60.0	65.0	63.0					17																	45234327		2201	4295	6496	SO:0001583	missense	996	exon7			CTTCGACCAGTTT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.794G>A	17.37:g.45234327C>T	ENSP00000066544:p.Gly265Asp	Somatic	61	1	0.0163934		WXS	Illumina HiSeq	Phase_I	55	6	0.109091	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.725453	0.48833	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.11;-0.31;0.86	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.52853	0.1760	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.32350	0.251;0.366;0.247;0.251	B;B;B;B	0.27076	0.045;0.056;0.076;0.055	T	0.51694	-0.8673	10	0.33141	T	0.24	1.6987	17.2083	0.86924	0.0:1.0:0.0:0.0	rs7350889;rs7350889	204;265;265;265	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	D	265;265;204;265;265	ENSP00000066544:G265D;ENSP00000434614:G265D;ENSP00000392802:G204D;ENSP00000437339:G265D;ENSP00000432105:G265D	ENSP00000066544:G265D	G	-	2	0	CDC27	42589326	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.618000	0.67722	2.665000	0.90641	0.460000	0.39030	GGT	C|1.000;|0.000	.	weak		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
VCAN	1462	hgsc.bcm.edu	37	5	82833506	82833506	+	Missense_Mutation	SNP	T	T	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:82833506T>G	ENST00000265077.3	+	8	5249	c.4684T>G	c.(4684-4686)Ttt>Gtt	p.F1562V	VCAN-AS1_ENST00000512090.1_RNA|VCAN_ENST00000512590.2_Intron|VCAN_ENST00000513016.1_3'UTR|VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Intron|VCAN_ENST00000343200.5_Missense_Mutation_p.F575V	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1562	GAG-beta.				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	GAAAATAGCCTTTGCAAGGGC	0.413																																					p.F1562V		Atlas-SNP	.											.	VCAN	498	.	0			c.T4684G						PASS	.						72.0	74.0	73.0					5																	82833506		2203	4300	6503	SO:0001583	missense	1462	exon8			ATAGCCTTTGCAA	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.4684T>G	5.37:g.82833506T>G	ENSP00000265077:p.Phe1562Val	Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	73	16	0.219178	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	T	5.696	0.312954	0.10789	.	.	ENSG00000038427	ENST00000265077;ENST00000343200;ENST00000513960	D;D;T	0.86769	-2.17;-2.17;2.95	5.78	1.85	0.25348	.	0.656922	0.14873	N	0.293408	T	0.81503	0.4836	M	0.61703	1.905	0.09310	N	0.999999	B;B	0.23806	0.091;0.055	B;B	0.19946	0.027;0.012	T	0.64334	-0.6432	10	0.18276	T	0.48	.	6.8329	0.23921	0.2407:0.0:0.2497:0.5096	.	575;1562	P13611-2;P13611	.;CSPG2_HUMAN	V	1562;575;575	ENSP00000265077:F1562V;ENSP00000340062:F575V;ENSP00000426251:F575V	ENSP00000265077:F1562V	F	+	1	0	VCAN	82869262	0.055000	0.20627	0.001000	0.08648	0.056000	0.15407	1.323000	0.33701	0.436000	0.26393	0.533000	0.62120	TTT	.	.	none		0.413	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
POTEE	445582	hgsc.bcm.edu	37	2	132021817	132021817	+	Missense_Mutation	SNP	C	C	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:132021817C>T	ENST00000356920.5	+	15	2883	c.2789C>T	c.(2788-2790)gCg>gTg	p.A930V	PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	930	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)		p.A930V(1)									ATGGCCACGGCGGCCTCCAGC	0.617																																					p.A930V		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,0,1	.	.	1	1	Substitution - Missense(1)	endometrium(1)	c.C2789T						scavenged	.						142.0	158.0	152.0					2																	132021817		2201	4297	6498	SO:0001583	missense	445582	exon15			CCACGGCGGCCTC	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2789C>T	2.37:g.132021817C>T	ENSP00000439189:p.Ala930Val	Somatic	244	4	0.0163934		WXS	Illumina HiSeq	Phase_I	303	7	0.0231023	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	13.30	2.195218	0.38806	.	.	ENSG00000188219	ENST00000356920	D	0.94650	-3.48	.	.	.	.	.	.	.	.	D	0.92721	0.7686	M	0.85945	2.785	0.80722	D	1	B	0.17465	0.022	B	0.09377	0.004	D	0.86962	0.2092	8	0.49607	T	0.09	.	5.9051	0.18992	0.0:0.9992:0.0:8.0E-4	.	930	Q6S8J3	POTEE_HUMAN	V	930	ENSP00000439189:A930V	ENSP00000439189:A930V	A	+	2	0	AC131180.1	131738287	1.000000	0.71417	0.549000	0.28204	0.554000	0.35429	5.240000	0.65378	0.119000	0.18210	0.121000	0.15741	GCG	C|1.000;|0.000	.	weak		0.617	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
ABCE1	6059	hgsc.bcm.edu	37	4	146033391	146033391	+	Splice_Site	SNP	T	T	C			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr4:146033391T>C	ENST00000296577.4	+	9	1226	c.711T>C	c.(709-711)atT>atC	p.I237I	OTUD4_ENST00000455611.2_Intron|ABCE1_ENST00000502803.1_Intron	NM_001040876.1|NM_002940.2	NP_001035809.1|NP_002931.2	P61221	ABCE1_HUMAN	ATP-binding cassette, sub-family E (OABP), member 1	237	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				negative regulation of catalytic activity (GO:0043086)|response to virus (GO:0009615)|RNA catabolic process (GO:0006401)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|iron-sulfur cluster binding (GO:0051536)|ribonuclease inhibitor activity (GO:0008428)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|lung(5)|prostate(2)|skin(3)	18	all_hematologic(180;0.151)					TTTTTCATAGTTTCATGTTTG	0.313																																					p.I237I		Atlas-SNP	.											.	ABCE1	47	.	0			c.T711C						PASS	.						30.0	29.0	29.0					4																	146033391		2202	4297	6499	SO:0001630	splice_region_variant	6059	exon9			TCATAGTTTCATG	X74987	CCDS34071.1	4q31	2012-03-14			ENSG00000164163	ENSG00000164163		"""ATP binding cassette transporters / subfamily E"""	69	protein-coding gene	gene with protein product		601213		RNASEL1, RNASELI, RNS4I		7539425	Standard	NM_002940		Approved	RLI, OABP	uc003ijy.3	P61221	OTTHUMG00000161478	ENST00000296577.4:c.711-1T>C	4.37:g.146033391T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	101	12	0.118812	NM_002940	O88793|Q13181|Q13864|Q6NR76|Q96AL0|Q96B10|Q99K66	Silent	SNP	ENST00000296577.4	37	CCDS34071.1																																																																																			.	.	none		0.313	ABCE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365104.1	NM_002940	Silent
POTEE	445582	hgsc.bcm.edu	37	2	132021684	132021684	+	Missense_Mutation	SNP	C	C	A	rs2672150		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr2:132021684C>A	ENST00000356920.5	+	15	2750	c.2656C>A	c.(2656-2658)Cct>Act	p.P886T	PLEKHB2_ENST00000303908.3_Intron|PLEKHB2_ENST00000404460.1_Intron|POTEE_ENST00000358087.5_3'UTR	NM_001083538.1	NP_001077007.1	Q6S8J3	POTEE_HUMAN	POTE ankyrin domain family, member E	886	Actin-like.				retina homeostasis (GO:0001895)|substantia nigra development (GO:0021762)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)											GCGGGAACTGCCTGACTACCT	0.592																																					p.P886T		Atlas-SNP	.											ENSG00000188219,NS,carcinoma,-1,1	.	.	1	0			c.C2656A						scavenged	.						46.0	47.0	47.0					2																	132021684		2203	4281	6484	SO:0001583	missense	445582	exon15			GAACTGCCTGACT	AY462868	CCDS46414.1	2q21.1	2014-04-10	2008-11-26	2008-11-26	ENSG00000188219	ENSG00000188219		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33895	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 2"""	608914	"""ANKRD26-like family C, member 1A"""	A26C1A			Standard	NM_001083538		Approved	POTE2, POTE-2, A26C1, POTE2gamma, CT104.2	uc002tsn.2	Q6S8J3	OTTHUMG00000186974	ENST00000356920.5:c.2656C>A	2.37:g.132021684C>A	ENSP00000439189:p.Pro886Thr	Somatic	644	6	0.00931677		WXS	Illumina HiSeq	Phase_I	749	11	0.0146862	NM_001083538	Q6S8J4|Q6S8J5|Q6S8J8	Missense_Mutation	SNP	ENST00000356920.5	37	CCDS46414.1	.	.	.	.	.	.	.	.	.	.	.	3.880	-0.026136	0.07589	.	.	ENSG00000188219	ENST00000356920	T	0.04360	3.64	.	.	.	.	.	.	.	.	T	0.00241	0.0007	N	0.00000	-5.39	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59606	-0.7423	8	0.02654	T	1	.	4.0636	0.09849	0.6406:0.3593:1.0E-4:0.0	.	886	Q6S8J3	POTEE_HUMAN	T	886	ENSP00000439189:P886T	ENSP00000439189:P886T	P	+	1	0	AC131180.1	131738154	1.000000	0.71417	0.081000	0.20488	0.082000	0.17680	4.531000	0.60602	-2.143000	0.00803	-2.210000	0.00300	CCT	.	.	weak		0.592	POTEE-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001083538	
IRF5	3663	hgsc.bcm.edu	37	7	128587381	128587381	+	Silent	SNP	T	T	C	rs199508964|rs79724471|rs60344245	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr7:128587381T>C	ENST00000402030.2	+	6	603	c.531T>C	c.(529-531)ccT>ccC	p.P177P	IRF5_ENST00000477535.1_Intron|IRF5_ENST00000473745.1_Silent_p.P177P|IRF5_ENST00000249375.4_Silent_p.P177P|IRF5_ENST00000357234.5_Silent_p.P193P	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	177					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.?(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						TGCGGCCGCCTACTCTGCAGC	0.657																																					p.P193P		Atlas-SNP	.											.	IRF5	40	.	1	Unknown(1)	haematopoietic_and_lymphoid_tissue(1)	c.T579C						PASS	.	T	,,,,	881,2925		144,593,1166	5.0	7.0	6.0		531,579,531,,531		0.1	7	dbSNP_131	6	1628,6000		358,912,2544	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous	IRF5	NM_001098627.2,NM_001098629.1,NM_001098630.1,NM_001242452.1,NM_032643.3	,,,,	502,1505,3710	CC,CT,TT		21.3424,23.1477,21.9433	,,,,	177/499,193/515,177/499,,177/499	128587381	2509,8925	1903	3814	5717	SO:0001819	synonymous_variant	3663	exon6			GCCGCCTACTCTG		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.531T>C	7.37:g.128587381T>C		Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	25	15	0.6	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Silent	SNP	ENST00000402030.2	37	CCDS5808.1	740	0.33882783882783885	191	0.3882113821138211	85	0.23480662983425415	170	0.2972027972027972	294	0.38786279683377306	T	2.949	-0.217149	0.06101	0.231477	0.213424	ENSG00000128604	ENST00000430204	.	.	.	.	.	.	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.58432	P	2.9999999999752447E-6	.	.	.	.	.	.	T	0.44667	-0.9313	1	.	.	.	.	.	.	.	.	166	E9PC81	.	P	166	.	.	L	+	2	0	IRF5	128374617	0.027000	0.19231	0.110000	0.21437	0.055000	0.15305	0.056000	0.14256	0.056000	0.16144	0.055000	0.15244	CTA	T|0.661;C|0.339	0.339	strong		0.657	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
MCC	4163	hgsc.bcm.edu	37	5	112406832	112406832	+	Nonsense_Mutation	SNP	G	G	T	rs140633829		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr5:112406832G>T	ENST00000302475.4	-	10	1877	c.1314C>A	c.(1312-1314)taC>taA	p.Y438*	MCC_ENST00000514701.3_5'UTR|MCC_ENST00000515367.2_Nonsense_Mutation_p.Y375*|MCC_ENST00000408903.3_Nonsense_Mutation_p.Y628*	NM_002387.2	NP_002378	P23508	CRCM_HUMAN	mutated in colorectal cancers	438					negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|signal transduction (GO:0007165)|Wnt signaling pathway (GO:0016055)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			endometrium(4)|kidney(3)|large_intestine(15)|liver(2)|lung(8)|ovary(2)|pancreas(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	42		all_cancers(142;5.89e-08)|all_epithelial(76;3.57e-11)|all_lung(232;0.000605)|Lung NSC(810;0.000697)|Colorectal(10;0.00146)|Prostate(80;0.00174)|Ovarian(225;0.0175)|Breast(839;0.198)		OV - Ovarian serous cystadenocarcinoma(64;2.04e-54)|Epithelial(69;9.69e-49)|all cancers(49;6.25e-44)|COAD - Colon adenocarcinoma(37;0.0432)|Colorectal(14;0.0766)		CATTGGATTCGTATTTTCCCA	0.512																																					p.Y628X		Atlas-SNP	.											MCC_ENST00000408903,NS,carcinoma,-1,2	MCC	234	2	0			c.C1884A						scavenged	.						267.0	214.0	232.0					5																	112406832		2202	4300	6502	SO:0001587	stop_gained	4163	exon12			GGATTCGTATTTT		CCDS4111.1, CCDS43351.1	5q21-q22	2013-01-10			ENSG00000171444	ENSG00000171444		"""EF-hand domain containing"""	6935	protein-coding gene	gene with protein product		159350				1848370	Standard	NM_002387		Approved		uc003kql.4	P23508	OTTHUMG00000128804	ENST00000302475.4:c.1314C>A	5.37:g.112406832G>T	ENSP00000305617:p.Tyr438*	Somatic	308	1	0.00324675		WXS	Illumina HiSeq	Phase_I	364	4	0.010989	NM_001085377	D3DT05|Q6ZR04	Nonsense_Mutation	SNP	ENST00000302475.4	37	CCDS4111.1	.	.	.	.	.	.	.	.	.	.	G	41	9.122106	0.99073	.	.	ENSG00000171444	ENST00000302475;ENST00000515367;ENST00000408903	.	.	.	5.15	-1.8	0.07907	.	0.000000	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.23302	T	0.38	-20.1983	13.186	0.59682	0.6038:0.0:0.3962:0.0	.	.	.	.	X	438;375;628	.	ENSP00000305617:Y438X	Y	-	3	2	MCC	112434731	0.441000	0.25626	0.971000	0.41717	0.979000	0.70002	-0.312000	0.08113	-0.313000	0.08728	0.591000	0.81541	TAC	G|1.000;A|0.000	.	alt		0.512	MCC-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250736.3	NM_001085377	
TNXB	7148	hgsc.bcm.edu	37	6	32020562	32020562	+	Silent	SNP	G	G	A	rs375459891		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr6:32020562G>A	ENST00000375244.3	-	26	9201	c.9000C>T	c.(8998-9000)ggC>ggT	p.G3000G	TNXB_ENST00000375247.2_Silent_p.G2998G			P22105	TENX_HUMAN	tenascin XB	3045	Fibronectin type-III 22. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						CGCTCTCCTCGCCCCTGACAC	0.687													g|||	1	0.000199681	0.0	0.0	5008	,	,		14923	0.001		0.0	False		,,,				2504	0.0				p.G2998G		Atlas-SNP	.											.	TNXB	553	.	0			c.C8994T						PASS	.						40.0	44.0	43.0					6																	32020562		1251	2548	3799	SO:0001819	synonymous_variant	7148	exon26			CTCCTCGCCCCTG	X71923	CCDS4736.1	6p21.3	2013-02-11			ENSG00000168477	ENSG00000168477		"""Fibrinogen C domain containing"", ""Fibronectin type III domain containing"""	11976	protein-coding gene	gene with protein product		600985		TNXB1, TNXB2		8530023	Standard	NM_019105		Approved	TNXBS, XBS, XB	uc021yvf.2	P22105	OTTHUMG00000031088	ENST00000375244.3:c.9000C>T	6.37:g.32020562G>A		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	41	5	0.121951	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				.	.	weak		0.687	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
CDHR5	53841	hgsc.bcm.edu	37	11	618683	618683	+	Missense_Mutation	SNP	T	T	C	rs200124815		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:618683T>C	ENST00000358353.3	-	14	2198	c.1876A>G	c.(1876-1878)Acc>Gcc	p.T626A	IRF7_ENST00000397570.1_5'Flank|IRF7_ENST00000397562.3_5'Flank|CDHR5_ENST00000397542.2_Missense_Mutation_p.T626A|CDHR5_ENST00000349570.7_Intron|IRF7_ENST00000330243.5_5'Flank|IRF7_ENST00000397574.2_5'Flank|IRF7_ENST00000397566.1_5'Flank			Q9HBB8	CDHR5_HUMAN	cadherin-related family member 5	626	4 X 31 AA approximate tandem repeats.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|calcium ion binding (GO:0005509)	p.T626A(1)		NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(7)|ovary(1)|skin(2)	23						CCGGGTGTGGTTGGTTGGTGG	0.652																																					p.T626A		Atlas-SNP	.											CDHR5,NS,malignant_melanoma,0,1	CDHR5	77	1	1	Substitution - Missense(1)	NS(1)	c.A1876G						scavenged	.						140.0	141.0	141.0					11																	618683		2203	4300	6503	SO:0001583	missense	53841	exon13			GTGTGGTTGGTTG	AF258675	CCDS7707.1, CCDS7708.1	11p15.5	2011-07-01	2010-01-25	2010-01-25	ENSG00000099834	ENSG00000099834		"""Cadherins / Cadherin-related"""	7521	protein-coding gene	gene with protein product		606839	"""mucin and cadherin-like"", ""mucin-like protocadherin"""	MUCDHL, MUPCDH		11031102, 10801787	Standard	NM_021924		Approved	FLJ20219, MU-PCDH	uc001lqj.3	Q9HBB8	OTTHUMG00000132018	ENST00000358353.3:c.1876A>G	11.37:g.618683T>C	ENSP00000351118:p.Thr626Ala	Somatic	191	3	0.0157068		WXS	Illumina HiSeq	Phase_I	272	12	0.0441176	NM_021924	C9J7X1|Q9H746|Q9HAU3|Q9HBB5|Q9HBB6|Q9HBB7|Q9NX86|Q9NXI9	Missense_Mutation	SNP	ENST00000358353.3	37	CCDS7707.1	.	.	.	.	.	.	.	.	.	.	N	1.980	-0.434457	0.04669	.	.	ENSG00000099834	ENST00000397542;ENST00000358353	T;T	0.44083	0.93;0.93	2.57	0.592	0.17471	.	.	.	.	.	T	0.14184	0.0343	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.31251	-0.9950	9	0.02654	T	1	.	5.0186	0.14349	0.0:0.5128:0.0:0.4872	.	620;626	Q9HBB8-4;Q9HBB8	.;CDHR5_HUMAN	A	626	ENSP00000380676:T626A;ENSP00000351118:T626A	ENSP00000351118:T626A	T	-	1	0	CDHR5	608683	0.005000	0.15991	0.025000	0.17156	0.045000	0.14185	-0.293000	0.08320	0.026000	0.15269	-0.511000	0.04467	ACC	.	.	weak		0.652	CDHR5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255023.2	NM_021924	
MUC4	4585	hgsc.bcm.edu	37	3	195508959	195508959	+	Silent	SNP	A	A	T			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195508959A>T	ENST00000463781.3	-	2	9951	c.9492T>A	c.(9490-9492)ggT>ggA	p.G3164G	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.G3164G|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.G3164G(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)		GGGTGGCCTGACCTGTGGATG	0.592																																					p.G3164G		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.T9492A						scavenged	.						5.0	3.0	3.0					3																	195508959		542	1229	1771	SO:0001819	synonymous_variant	4585	exon2			GGCCTGACCTGTG	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.9492T>A	3.37:g.195508959A>T		Somatic	361	7	0.0193906		WXS	Illumina HiSeq	Phase_I	359	9	0.0250696	NM_018406	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																																																																																			.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CACNA1B	774	hgsc.bcm.edu	37	9	140773504	140773504	+	Splice_Site	SNP	A	A	C	rs140008467|rs77221813		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:140773504A>C	ENST00000371372.1	+	2	429		c.e2-1		CACNA1B_ENST00000277551.2_Splice_Site|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371363.1_Splice_Site|CACNA1B_ENST00000371355.4_Intron|CACNA1B_ENST00000371357.1_Splice_Site|CACNA1B_ENST00000277549.5_Splice_Site	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit						calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TAACTCACGCACTCCATTCGA	0.632																																					.		Atlas-SNP	.											CACNA1B,colon,carcinoma,0,1	CACNA1B	266	1	0			c.285-2A>C						scavenged	.						34.0	38.0	37.0					9																	140773504		2144	4242	6386	SO:0001630	splice_region_variant	774	exon2			TCACGCACTCCAT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.285-1A>C	9.37:g.140773504A>C		Somatic	65	4	0.0615385		WXS	Illumina HiSeq	Phase_I	86	6	0.0697674	NM_001243812	B1AQK5	Splice_Site	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	A	9.642	1.139206	0.21205	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357	.	.	.	4.52	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8471	0.41034	0.9182:0.0:0.0818:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1B	139893325	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	8.392000	0.90180	0.597000	0.29811	-0.379000	0.06801	.	.	.	weak		0.632	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	Intron
ZBBX	79740	hgsc.bcm.edu	37	3	167023655	167023655	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:167023655A>G	ENST00000392766.2	-	17	1841	c.1501T>C	c.(1501-1503)Tcc>Ccc	p.S501P	ZBBX_ENST00000392764.1_Missense_Mutation_p.S472P|ZBBX_ENST00000455345.2_Missense_Mutation_p.S501P|ZBBX_ENST00000307529.5_Missense_Mutation_p.S501P|ZBBX_ENST00000392767.2_Missense_Mutation_p.S501P	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	501						intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						CTTTCAAAGGAGGTGCTTTCC	0.348																																					p.S501P		Atlas-SNP	.											.	ZBBX	299	.	0			c.T1501C						PASS	.						54.0	48.0	49.0					3																	167023655		1798	4072	5870	SO:0001583	missense	79740	exon17			CAAAGGAGGTGCT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1501T>C	3.37:g.167023655A>G	ENSP00000376519:p.Ser501Pro	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	42	9	0.214286	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	.	.	.	.	.	.	.	.	.	.	A	10.90	1.480260	0.26598	.	.	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.10573	3.03;3.03;3.03;3.03;2.86	5.54	-3.07	0.05363	.	1.376370	0.04080	N	0.309527	T	0.05868	0.0153	N	0.19112	0.55	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.04013	0.001;0.0	T	0.36040	-0.9764	10	0.33141	T	0.24	0.0641	0.6	0.00743	0.3168:0.135:0.1556:0.3926	.	501;501	A8MT70-2;A8MT70	.;ZBBX_HUMAN	P	501;501;501;501;472	ENSP00000376519:S501P;ENSP00000376520:S501P;ENSP00000390232:S501P;ENSP00000305065:S501P;ENSP00000376517:S472P	ENSP00000305065:S501P	S	-	1	0	ZBBX	168506349	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.094000	0.15107	-0.425000	0.07371	-1.159000	0.01794	TCC	.	.	none		0.348	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
TMEM8A	58986	hgsc.bcm.edu	37	16	427479	427479	+	Missense_Mutation	SNP	T	T	C	rs11248931	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:427479T>C	ENST00000431232.2	-	3	566	c.406A>G	c.(406-408)Aca>Gca	p.T136A	TMEM8A_ENST00000476735.1_5'UTR|TMEM8A_ENST00000250930.3_5'UTR	NM_021259.2	NP_067082.2	Q9HCN3	TMM8A_HUMAN	transmembrane protein 8A	136			T -> A (in dbSNP:rs11248931). {ECO:0000269|PubMed:11006113, ECO:0000269|PubMed:15489334, ECO:0000269|Ref.3}.		cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)				central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)|prostate(1)	14						CTTCTCGGTGTGGTGCTCAGC	0.682											OREG0003703	type=REGULATORY REGION|Gene=TMEM8|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	C|||	2677	0.534545	0.6188	0.4755	5008	,	,		15166	0.3006		0.5408	False		,,,				2504	0.6973				p.T136A		Atlas-SNP	.											TMEM8A,colon,carcinoma,0,1	TMEM8A	49	1	0			c.A406G						scavenged	.	C	ALA/THR	2729,1649		847,1035,307	22.0	22.0	22.0		406	1.0	0.0	16	dbSNP_120	22	4876,3718		1417,2042,838	yes	missense	TMEM8A	NM_021259.2	58	2264,3077,1145	CC,CT,TT		43.2627,37.6656,41.3737	benign	136/772	427479	7605,5367	2189	4297	6486	SO:0001583	missense	58986	exon3			TCGGTGTGGTGCT	AB045292	CCDS10407.1	16p13.3	2009-06-12	2009-06-12	2009-06-12	ENSG00000129925	ENSG00000129925			17205	protein-coding gene	gene with protein product			"""transmembrane protein 6"", ""transmembrane protein 8 (five membrane-spanning domains)"""	TMEM6, TMEM8		11006113	Standard	NM_021259		Approved	M83	uc002cgu.4	Q9HCN3	OTTHUMG00000047996	ENST00000431232.2:c.406A>G	16.37:g.427479T>C	ENSP00000401338:p.Thr136Ala	Somatic	22	2	0.0909091	588	WXS	Illumina HiSeq	Phase_I	43	15	0.348837	NM_021259	D3DU49|Q4TT35|Q8WU24|Q96S25|Q9BR03|Q9BT97|Q9H7B9	Missense_Mutation	SNP	ENST00000431232.2	37	CCDS10407.1	1089	0.49862637362637363	335	0.6808943089430894	181	0.5	163	0.28496503496503495	410	0.5408970976253298	C	0.003	-2.441316	0.00180	0.623344	0.567373	ENSG00000129925	ENST00000431232	T	0.23147	1.92	3.34	0.981	0.19756	.	3.558320	0.02310	N	0.072046	T	0.00012	0.0000	N	0.01352	-0.895	0.58432	P	2.9999999999752447E-6	B	0.02656	0.0	B	0.01281	0.0	T	0.40590	-0.9555	9	0.06099	T	0.92	-8.0545	4.5877	0.12291	0.15:0.2114:0.0:0.6386	rs11248931;rs17845652;rs17858586;rs57237473;rs11248931	136	Q9HCN3	TMM8A_HUMAN	A	136	ENSP00000401338:T136A	ENSP00000401338:T136A	T	-	1	0	TMEM8A	367480	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-1.411000	0.02478	-0.100000	0.12241	-1.309000	0.01313	ACA	T|0.463;C|0.537	0.537	strong		0.682	TMEM8A-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000109257.2	NM_021259	
FCN2	2220	hgsc.bcm.edu	37	9	137779176	137779176	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:137779176G>A	ENST00000291744.6	+	8	867	c.857G>A	c.(856-858)aGc>aAc	p.S286N	FCN2_ENST00000350339.2_Missense_Mutation_p.S248N	NM_004108.2	NP_004099.2	Q15485	FCN2_HUMAN	ficolin (collagen/fibrinogen domain containing lectin) 2	286	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)|opsonization (GO:0008228)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	antigen binding (GO:0003823)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(2)|urinary_tract(2)	20		Myeloproliferative disorder(178;0.0333)		OV - Ovarian serous cystadenocarcinoma(145;3.58e-08)|Epithelial(140;6.41e-08)|all cancers(34;3.96e-07)		ACTCATGGCAGCTTTGCAAAT	0.512																																					p.S286N		Atlas-SNP	.											.	FCN2	55	.	0			c.G857A						PASS	.						85.0	83.0	83.0					9																	137779176		2203	4300	6503	SO:0001583	missense	2220	exon8			ATGGCAGCTTTGC	D49353	CCDS6983.1	9q34	2013-09-12	2013-09-12		ENSG00000160339	ENSG00000160339		"""Fibrinogen C domain containing"""	3624	protein-coding gene	gene with protein product	"""hucolin"", ""collagen/fibrinogen domain-containing protein 2"", ""ficolin B"", ""serum lectin p35"", ""L-ficolin"""	601624	"""ficolin (collagen/fibrinogen domain-containing lectin) 2 (hucolin)"""			8884275	Standard	XM_006717015		Approved	P35, FCNL, EBP-37, ficolin-2	uc004cfg.1	Q15485	OTTHUMG00000020892	ENST00000291744.6:c.857G>A	9.37:g.137779176G>A	ENSP00000291744:p.Ser286Asn	Somatic	149	0	0		WXS	Illumina HiSeq	Phase_I	164	19	0.115854	NM_004108	A6NFG7|A8K478|Q6IS69|Q7M4P4|Q9UC57	Missense_Mutation	SNP	ENST00000291744.6	37	CCDS6983.1	.	.	.	.	.	.	.	.	.	.	G	16.19	3.052816	0.55218	.	.	ENSG00000160339	ENST00000350339;ENST00000291744	T;T	0.21361	2.01;2.01	4.05	4.05	0.47172	Fibrinogen, alpha/beta/gamma chain, C-terminal globular (4);Fibrinogen, alpha/beta/gamma chain, C-terminal globular, subdomain 2 (1);	0.000000	0.50627	D	0.000110	T	0.26304	0.0642	M	0.66297	2.02	0.22796	N	0.998726	B;B	0.29835	0.258;0.144	B;B	0.32724	0.064;0.151	T	0.19976	-1.0289	10	0.52906	T	0.07	.	13.7007	0.62606	0.0:0.0:1.0:0.0	.	248;286	Q15485-2;Q15485	.;FCN2_HUMAN	N	248;286	ENSP00000291741:S248N;ENSP00000291744:S286N	ENSP00000291744:S286N	S	+	2	0	FCN2	136918997	0.171000	0.23029	0.279000	0.24732	0.456000	0.32438	0.609000	0.24238	1.791000	0.52520	0.563000	0.77884	AGC	.	.	none		0.512	FCN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054960.1	NM_004108	
PPFIA1	8500	hgsc.bcm.edu	37	11	70171055	70171055	+	Missense_Mutation	SNP	G	G	A			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:70171055G>A	ENST00000253925.7	+	4	684	c.469G>A	c.(469-471)Gaa>Aaa	p.E157K	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.E157K|CTA-797E19.2_ENST00000526017.1_RNA	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	157					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			CGTGTCCAGCGAAGTGGAAGT	0.507																																					p.E157K		Atlas-SNP	.											.	PPFIA1	114	.	0			c.G469A						PASS	.						95.0	96.0	96.0					11																	70171055		2200	4294	6494	SO:0001583	missense	8500	exon4			TCCAGCGAAGTGG	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.469G>A	11.37:g.70171055G>A	ENSP00000253925:p.Glu157Lys	Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	95	22	0.231579	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	.	.	.	.	.	.	.	.	.	.	G	36	5.665691	0.96745	.	.	ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000530746	T;T;T	0.46451	0.87;0.87;0.87	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.56702	0.2003	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	T	0.59804	-0.7385	10	0.87932	D	0	.	19.2525	0.93930	0.0:0.0:1.0:0.0	.	157;157	Q13136;Q13136-2	LIPA1_HUMAN;.	K	157	ENSP00000253925:E157K;ENSP00000374198:E157K;ENSP00000432722:E157K	ENSP00000253925:E157K	E	+	1	0	PPFIA1	69848703	1.000000	0.71417	0.791000	0.31998	0.687000	0.40016	9.522000	0.98032	2.617000	0.88574	0.650000	0.86243	GAA	.	.	none		0.507	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
MAZ	4150	hgsc.bcm.edu	37	16	29821438	29821438	+	Silent	SNP	G	G	A	rs199924629|rs374878500		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr16:29821438G>A	ENST00000322945.6	+	5	1485	c.1320G>A	c.(1318-1320)gcG>gcA	p.A440A	MAZ_ENST00000563402.1_Missense_Mutation_p.G97S|PRRT2_ENST00000358758.7_5'Flank|AC009133.15_ENST00000566537.1_RNA|AC009133.14_ENST00000563806.1_RNA|AC009133.20_ENST00000569039.1_RNA|MAZ_ENST00000562337.1_Silent_p.A135A|AC009133.14_ENST00000569981.1_RNA|MAZ_ENST00000219782.6_3'UTR|MAZ_ENST00000568544.1_Silent_p.A41A|MAZ_ENST00000545521.1_Silent_p.A417A|PRRT2_ENST00000567659.1_5'Flank|MAZ_ENST00000568282.1_3'UTR|MAZ_ENST00000566906.2_Splice_Site_p.G95S|PRRT2_ENST00000300797.6_5'Flank	NM_002383.2	NP_002374.2	P56270	MAZ_HUMAN	MYC-associated zinc finger protein (purine-binding transcription factor)	440	Poly-Ala.				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|termination of RNA polymerase II transcription (GO:0006369)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			endometrium(3)|lung(4)|ovary(2)|upper_aerodigestive_tract(1)	10						cagcggcagcggcggcagcgg	0.662																																					p.A440A	Colon(72;875 1167 15364 30899 37091)	Atlas-SNP	.											MAZ_ENST00000322945,caecum,carcinoma,0,2	MAZ	48	2	0			c.G1320A						scavenged	.	A	,	29,4087		0,29,2029	16.0	21.0	19.0		,1320	-7.8	0.0	16		19	32,8282		0,32,4125	no	utr-3,coding-synonymous	MAZ	NM_001042539.1,NM_002383.2	,	0,61,6154	AA,AG,GG		0.3849,0.7046,0.4907	,	,440/478	29821438	61,12369	2058	4157	6215	SO:0001819	synonymous_variant	4150	exon5			GGCAGCGGCGGCA	M93339	CCDS42143.1, CCDS42144.1, CCDS61902.1, CCDS61903.1	16p11.2	2013-01-08			ENSG00000103495	ENSG00000103495		"""Zinc fingers, C2H2-type"""	6914	protein-coding gene	gene with protein product		600999				1567856, 1502157	Standard	NM_001276275		Approved	ZF87, Pur-1, Zif87, ZNF801	uc002dtx.4	P56270	OTTHUMG00000132119	ENST00000322945.6:c.1320G>A	16.37:g.29821438G>A		Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	69	3	0.0434783	NM_002383	A8QJL9|C6G496|G5E927|H3BQD6|Q15703|Q8NFN7|Q99443	Silent	SNP	ENST00000322945.6	37	CCDS42143.1																																																																																			G|0.993;A|0.007	0.007	strong		0.662	MAZ-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000435536.1	NM_002383	
OR10G4	390264	hgsc.bcm.edu	37	11	123887164	123887164	+	Missense_Mutation	SNP	A	A	C	rs4936881	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr11:123887164A>C	ENST00000320891.4	+	1	883	c.883A>C	c.(883-885)Aag>Cag	p.K295Q		NM_001004462.1	NP_001004462.1	Q8NGN3	O10G4_HUMAN	olfactory receptor, family 10, subfamily G, member 4	295			K -> Q (in dbSNP:rs4936881).			integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.K295Q(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)|skin(4)|stomach(6)|upper_aerodigestive_tract(1)	48		Breast(109;0.00867)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.22)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0401)		CAAGGAGGTGAAGAAAGCTGT	0.413													a|||	2142	0.427716	0.469	0.5029	5008	,	,		20676	0.3591		0.4404	False		,,,				2504	0.3763				p.K295Q		Atlas-SNP	.											OR10G4,NS,carcinoma,-2,2	OR10G4	77	2	1	Substitution - Missense(1)	stomach(1)	c.A883C						scavenged	.	A	GLN/LYS	2107,2295	574.0+/-383.7	510,1087,604	78.0	73.0	75.0		883	3.4	0.9	11	dbSNP_111	75	3918,4678	545.6+/-384.8	872,2174,1252	yes	missense	OR10G4	NM_001004462.1	53	1382,3261,1856	CC,CA,AA		45.5793,47.8646,46.3533	benign	295/312	123887164	6025,6973	2201	4298	6499	SO:0001583	missense	390264	exon1			GAGGTGAAGAAAG	AB065757	CCDS31702.1	11q24.1	2012-08-09			ENSG00000254737	ENSG00000254737		"""GPCR / Class A : Olfactory receptors"""	14809	protein-coding gene	gene with protein product							Standard	NM_001004462		Approved		uc010sac.2	Q8NGN3	OTTHUMG00000165966	ENST00000320891.4:c.883A>C	11.37:g.123887164A>C	ENSP00000325076:p.Lys295Gln	Somatic	232	0	0		WXS	Illumina HiSeq	Phase_I	167	4	0.0239521	NM_001004462	Q6IEW0	Missense_Mutation	SNP	ENST00000320891.4	37	CCDS31702.1	977	0.44734432234432236	223	0.4532520325203252	192	0.5303867403314917	231	0.40384615384615385	331	0.4366754617414248	a	13.05	2.121331	0.37436	0.478646	0.455793	ENSG00000254737	ENST00000320891	T	0.39406	1.08	3.38	3.38	0.38709	.	0.162599	0.28772	N	0.014191	T	0.00012	0.0000	L	0.42632	1.34	0.41583	P	0.011248000000000036	B	0.30021	0.265	B	0.31337	0.128	T	0.48317	-0.9046	9	0.72032	D	0.01	.	11.9412	0.52903	1.0:0.0:0.0:0.0	rs4936881;rs4936881	295	Q8NGN3	O10G4_HUMAN	Q	295	ENSP00000325076:K295Q	ENSP00000325076:K295Q	K	+	1	0	OR10G4	123392374	0.772000	0.28567	0.943000	0.38184	0.941000	0.58515	3.532000	0.53553	1.547000	0.49401	0.473000	0.43528	AAG	A|0.539;C|0.461	0.461	strong		0.413	OR10G4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387268.1	NM_001004462	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51920498	51920498	+	Silent	SNP	G	G	T	rs201146870		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr19:51920498G>T	ENST00000339313.5	-	2	375	c.259C>A	c.(259-261)Cgg>Agg	p.R87R	SIGLEC10_ENST00000353836.5_Silent_p.R87R|SIGLEC10_ENST00000439889.2_Silent_p.R87R|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000442846.3_Silent_p.R87R|SIGLEC10_ENST00000525998.1_Silent_p.R87R|CTD-2616J11.3_ENST00000532473.1_RNA|SIGLEC10_ENST00000436984.2_Silent_p.R87R|SIGLEC10_ENST00000441969.3_Silent_p.R87R|SIGLEC10_ENST00000432469.2_Silent_p.R87R|SIGLEC10_ENST00000356298.5_Silent_p.R87R|CTD-2616J11.2_ENST00000526996.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	87	Ig-like V-type.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.R87W(2)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		AATCGGCCCCGGGTGCTCATT	0.567																																					p.R87R		Atlas-SNP	.											SIGLEC12_ENST00000439889,NS,carcinoma,0,5	SIGLEC10	112	5	2	Substitution - Missense(2)	endometrium(2)	c.C259A						scavenged	.						56.0	55.0	55.0					19																	51920498		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon2			GGCCCCGGGTGCT	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.259C>A	19.37:g.51920498G>T		Somatic	227	0	0		WXS	Illumina HiSeq	Phase_I	258	3	0.0116279	NM_001171161	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			G|0.999;A|0.001	.	alt		0.567	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
ARHGAP29	9411	hgsc.bcm.edu	37	1	94670633	94670633	+	Missense_Mutation	SNP	T	T	G	rs201001778		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:94670633T>G	ENST00000260526.6	-	7	863	c.681A>C	c.(679-681)gaA>gaC	p.E227D	ARHGAP29_ENST00000370217.3_Missense_Mutation_p.E227D	NM_004815.3	NP_004806.3	Q52LW3	RHG29_HUMAN	Rho GTPase activating protein 29	227					positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|Rho GTPase activator activity (GO:0005100)			NS(1)|breast(5)|endometrium(6)|kidney(2)|large_intestine(9)|lung(19)|ovary(1)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	54		all_lung(203;0.000732)|Lung NSC(277;0.00328)		all cancers(265;0.0187)|Epithelial(280;0.159)		TAAGCTTTTTTTCAACCCATG	0.318																																					p.E227D		Atlas-SNP	.											.	ARHGAP29	132	.	0			c.A681C						PASS	.						83.0	84.0	83.0					1																	94670633		2202	4298	6500	SO:0001583	missense	9411	exon7			CTTTTTTTCAACC		CCDS748.1	1p22.1	2011-06-29			ENSG00000137962	ENSG00000137962		"""Rho GTPase activating proteins"""	30207	protein-coding gene	gene with protein product		610496				9305890	Standard	NM_004815		Approved	PARG1	uc001dqj.4	Q52LW3	OTTHUMG00000010643	ENST00000260526.6:c.681A>C	1.37:g.94670633T>G	ENSP00000260526:p.Glu227Asp	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	140	18	0.128571	NM_004815	O15463|Q59H86|Q5VYZ0|Q6NVX2|Q8TBI6	Missense_Mutation	SNP	ENST00000260526.6	37	CCDS748.1	.	.	.	.	.	.	.	.	.	.	T	19.12	3.766355	0.69878	.	.	ENSG00000137962	ENST00000260526;ENST00000370217	T;T	0.46451	0.87;0.87	5.87	2.48	0.30137	.	0.000000	0.37053	N	0.002263	T	0.25531	0.0621	L	0.53671	1.685	0.45066	D	0.998081	P;P	0.46784	0.884;0.849	P;B	0.45610	0.487;0.318	T	0.02975	-1.1087	10	0.45353	T	0.12	-29.8012	8.1775	0.31292	0.0:0.3743:0.0:0.6257	.	227;227	Q52LW3-2;Q52LW3	.;RHG29_HUMAN	D	227	ENSP00000260526:E227D;ENSP00000359237:E227D	ENSP00000260526:E227D	E	-	3	2	ARHGAP29	94443221	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.684000	0.25364	0.603000	0.29913	0.533000	0.62120	GAA	T|1.000;C|0.000	.	alt		0.318	ARHGAP29-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029376.2	NM_004815	
OR2M5	127059	hgsc.bcm.edu	37	1	248309020	248309020	+	Missense_Mutation	SNP	G	G	A	rs139290187	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr1:248309020G>A	ENST00000366476.1	+	1	571	c.571G>A	c.(571-573)Gac>Aac	p.D191N		NM_001004690.1	NP_001004690.1	A3KFT3	OR2M5_HUMAN	olfactory receptor, family 2, subfamily M, member 5	191						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|endometrium(5)|kidney(2)|large_intestine(7)|liver(1)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	49	all_cancers(71;0.000149)|all_epithelial(71;1.27e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0388)			CTCATGCAATGACACATCAAT	0.418																																					p.D191N		Atlas-SNP	.											OR2M5,NS,carcinoma,0,2	OR2M5	117	2	0			c.G571A						scavenged	.						284.0	272.0	276.0					1																	248309020		2203	4300	6503	SO:0001583	missense	127059	exon1			TGCAATGACACAT		CCDS31105.1	1q44	2012-08-09		2004-03-10	ENSG00000162727	ENSG00000162727		"""GPCR / Class A : Olfactory receptors"""	19576	protein-coding gene	gene with protein product				OR2M5P			Standard	NM_001004690		Approved		uc010pze.2	A3KFT3	OTTHUMG00000040447	ENST00000366476.1:c.571G>A	1.37:g.248309020G>A	ENSP00000355432:p.Asp191Asn	Somatic	429	5	0.011655		WXS	Illumina HiSeq	Phase_I	454	5	0.0110132	NM_001004690		Missense_Mutation	SNP	ENST00000366476.1	37	CCDS31105.1	.	.	.	.	.	.	.	.	.	.	g	13.27	2.186763	0.38609	.	.	ENSG00000162727	ENST00000366476	T	0.00231	8.49	3.05	-0.584	0.11702	GPCR, rhodopsin-like superfamily (1);	0.000000	0.33691	U	0.004660	T	0.00178	0.0005	M	0.63843	1.955	0.09310	N	1	B	0.20052	0.041	B	0.25405	0.06	T	0.40739	-0.9547	10	0.52906	T	0.07	.	6.3472	0.21355	0.2028:0.2355:0.5617:0.0	.	191	A3KFT3	OR2M5_HUMAN	N	191	ENSP00000355432:D191N	ENSP00000355432:D191N	D	+	1	0	OR2M5	246375643	0.002000	0.14202	0.001000	0.08648	0.566000	0.35808	0.608000	0.24223	-0.004000	0.14419	0.492000	0.49549	GAC	G|0.996;A|0.004	0.004	strong		0.418	OR2M5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097343.1	NM_001004690	
ZNF592	9640	hgsc.bcm.edu	37	15	85328068	85328068	+	Missense_Mutation	SNP	G	G	A	rs549731730		TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr15:85328068G>A	ENST00000560079.2	+	4	2450	c.2162G>A	c.(2161-2163)cGg>cAg	p.R721Q	ZNF592_ENST00000299927.3_Missense_Mutation_p.R721Q	NM_014630.2	NP_055445.2	Q92610	ZN592_HUMAN	zinc finger protein 592	721					cell death (GO:0008219)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|kidney(1)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AAGCAGATGCGGGACTACATG	0.582																																					p.R721Q		Atlas-SNP	.											.	ZNF592	95	.	0			c.G2162A						PASS	.						77.0	71.0	73.0					15																	85328068		2203	4299	6502	SO:0001583	missense	9640	exon4			AGATGCGGGACTA	D86966	CCDS32317.1	15q25.2	2011-03-15				ENSG00000166716		"""Zinc fingers, C2H2-type"""	28986	protein-coding gene	gene with protein product		613624	"""spinocerebellar ataxia, autosomal recessive 5"""	SCAR5		9039502, 12030328, 20531441	Standard	NM_014630		Approved	KIAA0211, CAMOS	uc002bld.3	Q92610		ENST00000560079.2:c.2162G>A	15.37:g.85328068G>A	ENSP00000452877:p.Arg721Gln	Somatic	250	0	0		WXS	Illumina HiSeq	Phase_I	286	54	0.188811	NM_014630	Q2M1T2|Q504Y9	Missense_Mutation	SNP	ENST00000560079.2	37	CCDS32317.1	.	.	.	.	.	.	.	.	.	.	G	5.267	0.234764	0.09969	.	.	ENSG00000166716	ENST00000299927	T	0.28454	1.61	6.07	1.72	0.24424	Zinc finger, C2H2-like (1);	0.573110	0.19945	N	0.102543	T	0.19127	0.0459	L	0.45581	1.43	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35475	-0.9787	10	0.02654	T	1	-6.9559	6.7387	0.23422	0.4709:0.0:0.5291:0.0	.	721	Q92610	ZN592_HUMAN	Q	721	ENSP00000299927:R721Q	ENSP00000299927:R721Q	R	+	2	0	ZNF592	83129072	0.011000	0.17503	0.647000	0.29507	0.998000	0.95712	0.820000	0.27323	0.467000	0.27218	0.655000	0.94253	CGG	.	.	none		0.582	ZNF592-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418779.2	NM_014630	
TAF1L	138474	hgsc.bcm.edu	37	9	32631369	32631369	+	Silent	SNP	C	C	T	rs10971047	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr9:32631369C>T	ENST00000242310.4	-	1	4298	c.4209G>A	c.(4207-4209)acG>acA	p.T1403T	RP11-555J4.4_ENST00000430787.1_RNA	NM_153809.2	NP_722516.1	Q8IZX4	TAF1L_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa-like	1403					DNA-templated transcription, initiation (GO:0006352)|histone acetylation (GO:0016573)|male meiosis (GO:0007140)|positive regulation of transcription, DNA-templated (GO:0045893)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	transcription factor TFIID complex (GO:0005669)	DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|protein serine/threonine kinase activity (GO:0004674)|TBP-class protein binding (GO:0017025)			breast(6)|central_nervous_system(4)|endometrium(14)|kidney(11)|large_intestine(32)|liver(2)|lung(68)|ovary(2)|pancreas(2)|prostate(7)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	159			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.00301)		TGGATGACAGCGTCACCATAG	0.458													C|||	809	0.161542	0.1097	0.1182	5008	,	,		21985	0.3095		0.1034	False		,,,				2504	0.1697				p.T1403T		Atlas-SNP	.											TAF1L,NS,carcinoma,-1,1	TAF1L	382	1	0			c.G4209A						scavenged	.	C		374,4032	188.5+/-214.9	13,348,1842	297.0	272.0	280.0		4209	-0.9	0.9	9	dbSNP_120	280	893,7707	201.1+/-244.7	44,805,3451	no	coding-synonymous	TAF1L	NM_153809.2		57,1153,5293	TT,TC,CC		10.3837,8.4884,9.7417		1403/1827	32631369	1267,11739	2203	4300	6503	SO:0001819	synonymous_variant	138474	exon1			TGACAGCGTCACC	AF390562	CCDS35003.1	9p12	2007-07-27	2007-07-27		ENSG00000122728	ENSG00000122728			18056	protein-coding gene	gene with protein product		607798	"""TAF1-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 210kDa"""			12217962	Standard	NM_153809		Approved		uc003zrg.1	Q8IZX4	OTTHUMG00000019747	ENST00000242310.4:c.4209G>A	9.37:g.32631369C>T		Somatic	423	3	0.0070922		WXS	Illumina HiSeq	Phase_I	492	5	0.0101626	NM_153809	Q0VG57	Silent	SNP	ENST00000242310.4	37	CCDS35003.1																																																																																			C|0.873;T|0.127	0.127	strong		0.458	TAF1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052012.2		
GSDMA	284110	hgsc.bcm.edu	37	17	38122591	38122591	+	Missense_Mutation	SNP	C	C	T	rs140044904	byFrequency	TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr17:38122591C>T	ENST00000301659.4	+	3	411	c.293C>T	c.(292-294)aCg>aTg	p.T98M		NM_178171.4	NP_835465.2	Q96QA5	GSDMA_HUMAN	gasdermin A	98					apoptotic process (GO:0006915)	perinuclear region of cytoplasm (GO:0048471)				NS(1)|endometrium(2)|large_intestine(3)|lung(1)	7						GTACCAAAGACGGTGAAGGTG	0.552													C|||	33	0.00658946	0.0242	0.0014	5008	,	,		18543	0.0		0.0	False		,,,				2504	0.0				p.T98M		Atlas-SNP	.											.	GSDMA	26	.	0			c.C293T						PASS	.	C	MET/THR	42,3964		0,42,1961	107.0	111.0	110.0		293	5.5	1.0	17	dbSNP_134	110	0,8332		0,0,4166	yes	missense	GSDMA	NM_178171.4	81	0,42,6127	TT,TC,CC		0.0,1.0484,0.3404	benign	98/446	38122591	42,12296	2003	4166	6169	SO:0001583	missense	284110	exon3			CAAAGACGGTGAA	AB093591	CCDS45669.1	17q21.2	2008-07-31	2008-07-31	2008-07-31		ENSG00000167914			13311	protein-coding gene	gene with protein product		611218	"""gasdermin"", ""gasdermin 1"""	GSDM, GSDM1		12883658, 15010812, 17350798	Standard	NM_178171		Approved	FLJ39120	uc002htl.1	Q96QA5		ENST00000301659.4:c.293C>T	17.37:g.38122591C>T	ENSP00000301659:p.Thr98Met	Somatic	298	0	0		WXS	Illumina HiSeq	Phase_I	278	54	0.194245	NM_178171	Q32MC5|Q86VE7|Q8N1M6	Missense_Mutation	SNP	ENST00000301659.4	37	CCDS45669.1	20	0.009157509157509158	19	0.03861788617886179	1	0.0027624309392265192	0	0.0	0	0.0	C	11.66	1.704373	0.30232	0.010484	0.0	ENSG00000167914	ENST00000301659	T	0.23147	1.92	5.5	5.5	0.81552	.	0.442749	0.21282	N	0.077127	T	0.04318	0.0119	L	0.36672	1.1	0.35397	D	0.791245	P	0.39404	0.672	B	0.27887	0.084	T	0.14531	-1.0469	10	0.48119	T	0.1	-0.926	14.8824	0.70542	0.0:1.0:0.0:0.0	.	98	Q96QA5	GSDMA_HUMAN	M	98	ENSP00000301659:T98M	ENSP00000301659:T98M	T	+	2	0	GSDMA	35376117	0.987000	0.35691	0.972000	0.41901	0.744000	0.42396	3.521000	0.53472	2.581000	0.87130	0.563000	0.77884	ACG	C|0.991;T|0.009	0.009	strong		0.552	GSDMA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446847.1	NM_178171	
MUC4	4585	hgsc.bcm.edu	37	3	195507985	195507985	+	Missense_Mutation	SNP	A	A	G			TCGA-FA-8693-01A-11D-2397-10	TCGA-FA-8693-10A-01D-2397-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	62ff5bc5-21ea-47e2-bade-812ba5a9d8a2	9800e9ed-3710-40d0-b01e-c5ee272234c7	g.chr3:195507985A>G	ENST00000463781.3	-	2	10925	c.10466T>C	c.(10465-10467)cTt>cCt	p.L3489P	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.L3489P|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)		GGTGACATGAAGAGGGGTGGT	0.592																																					p.L3489P		Atlas-SNP	.											.	MUC4	1505	.	0			c.T10466C						PASS	.						28.0	25.0	26.0					3																	195507985		657	1575	2232	SO:0001583	missense	4585	exon2			ACATGAAGAGGGG	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.10466T>C	3.37:g.195507985A>G	ENSP00000417498:p.Leu3489Pro	Somatic	538	0	0		WXS	Illumina HiSeq	Phase_I	536	29	0.0541045	NM_018406	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	.	.	.	.	.	.	.	.	.	.	A	2.458	-0.324778	0.05350	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37058	1.25;1.22	.	.	.	.	.	.	.	.	T	0.34308	0.0893	N	0.19112	0.55	0.09310	N	0.999995	D	0.57571	0.98	D	0.64321	0.924	T	0.16689	-1.0394	7	.	.	.	.	4.5052	0.11883	0.9993:0.0:7.0E-4:0.0	.	3361	E7ESK3	.	P	3489	ENSP00000417498:L3489P;ENSP00000420243:L3489P	.	L	-	2	0	MUC4	196992764	0.000000	0.05858	0.026000	0.17262	0.027000	0.11550	0.158000	0.16422	0.064000	0.16427	0.063000	0.15292	CTT	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
