#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_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_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	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_dbSNPPopFreq	i_dbSNP_AF	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
RPS6KA1	6195	hgsc.bcm.edu	37	1	26881119	26881119	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr1:26881119G>A	ENST00000374168.2	+	9	800	c.646G>A	c.(646-648)Gag>Aag	p.E216K	MIR1976_ENST00000459548.1_RNA|RPS6KA1_ENST00000530003.1_Missense_Mutation_p.E200K|RPS6KA1_ENST00000374166.4_Missense_Mutation_p.E216K|RPS6KA1_ENST00000374162.2_Missense_Mutation_p.E124K|RPS6KA1_ENST00000526792.1_Missense_Mutation_p.E124K|RPS6KA1_ENST00000531382.1_Missense_Mutation_p.E225K	NM_002953.3	NP_002944.2	Q15418	KS6A1_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 1	216	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|cell cycle (GO:0007049)|innate immune response (GO:0045087)|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 cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell growth (GO:0030307)|positive regulation of hepatic stellate cell activation (GO:2000491)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of DNA-templated transcription in response to stress (GO:0043620)|regulation of translation in response to stress (GO:0043555)|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)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			lung(1)	1		all_cancers(24;2.49e-24)|Colorectal(325;3.46e-05)|all_lung(284;4.76e-05)|Lung NSC(340;5.83e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.00571)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Epithelial(14;1.12e-50)|OV - Ovarian serous cystadenocarcinoma(117;2.89e-29)|Colorectal(126;1.4e-08)|COAD - Colon adenocarcinoma(152;9.31e-07)|BRCA - Breast invasive adenocarcinoma(304;0.000537)|KIRC - Kidney renal clear cell carcinoma(1967;0.000759)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.0361)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.161)|LUSC - Lung squamous cell carcinoma(448;0.234)		CATTGACCACGAGAAGAAGGC	0.587																																					p.E225K		Atlas-SNP	.											.	RPS6KA1	65	.	0			c.G673A						.						171.0	170.0	170.0					1																	26881119		2203	4300	6503	SO:0001583	missense	6195	exon8			GACCACGAGAAGA	BC014966	CCDS284.1, CCDS30649.1	1p	2011-04-05	2002-08-29		ENSG00000117676	ENSG00000117676			10430	protein-coding gene	gene with protein product		601684	"""ribosomal protein S6 kinase, 90kD, polypeptide 1"""			8141249	Standard	NM_001006665		Approved	RSK, RSK1, HU-1	uc001bms.1	Q15418	OTTHUMG00000004003	ENST00000374168.2:c.646G>A	chr1.hg19:g.26881119G>A	ENSP00000363283:p.Glu216Lys	150.0	0.0		232.0	75.0	NM_001006665	A6NGG4|A8K9K7|B2RDY8|B7Z5J0|Q5SVM5|Q5SVM8|Q5SVM9|Q96C05|Q9BQK2	Missense_Mutation	SNP	ENST00000374168.2	hg19	CCDS284.1	.	.	.	.	.	.	.	.	.	.	G	36	5.845293	0.97016	.	.	ENSG00000117676	ENST00000374168;ENST00000374166;ENST00000526792;ENST00000374162;ENST00000530003;ENST00000531382	T;T;T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1;-0.1;-0.1	5.65	5.65	0.86999	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	0.71953	0.3401	L	0.33137	0.985	0.80722	D	1	P;P;D	0.67145	0.824;0.76;0.996	P;B;D	0.74348	0.531;0.144;0.983	T	0.74093	-0.3776	10	0.72032	D	0.01	.	18.6893	0.91577	0.0:0.0:1.0:0.0	.	200;225;216	B7Z2K7;Q15418-2;Q15418	.;.;KS6A1_HUMAN	K	216;216;124;124;200;225	ENSP00000363283:E216K;ENSP00000363281:E216K;ENSP00000431651:E124K;ENSP00000363277:E124K;ENSP00000432281:E200K;ENSP00000435412:E225K	ENSP00000363277:E124K	E	+	1	0	RPS6KA1	26753706	1.000000	0.71417	0.978000	0.43139	0.994000	0.84299	9.869000	0.99810	2.655000	0.90218	0.563000	0.77884	GAG	.	.		0.587	RPS6KA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011431.1	NM_002953	
TMEM79	84283	hgsc.bcm.edu	37	1	156255146	156255146	+	Silent	SNP	A	A	C			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr1:156255146A>C	ENST00000405535.2	+	2	300	c.129A>C	c.(127-129)ggA>ggC	p.G43G	SMG5_ENST00000361813.5_5'Flank|SMG5_ENST00000368267.5_5'Flank|TMEM79_ENST00000357501.2_Intron|TMEM79_ENST00000295694.5_Silent_p.G43G|TMEM79_ENST00000495881.1_3'UTR	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	43					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					AATCCCCGGGAGCTGAGTCCC	0.607																																					p.G43G		Atlas-SNP	.											.	TMEM79	43	.	0			c.A129C						.						35.0	40.0	39.0					1																	156255146		2203	4300	6503	SO:0001819	synonymous_variant	84283	exon2			CCCGGGAGCTGAG	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"""mattrin"""	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.129A>C	chr1.hg19:g.156255146A>C		92.0	0.0		121.0	38.0	NM_032323	B2RE22|D3DVB8	Silent	SNP	ENST00000405535.2	hg19	CCDS1138.1																																																																																			.	.		0.607	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323	
PPP1R12B	4660	hgsc.bcm.edu	37	1	202462434	202462434	+	Missense_Mutation	SNP	C	C	A			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr1:202462434C>A	ENST00000608999.1	+	15	2287	c.2134C>A	c.(2134-2136)Ctg>Atg	p.L712M	PPP1R12B_ENST00000367270.4_5'UTR|PPP1R12B_ENST00000336894.4_Missense_Mutation_p.L712M|PPP1R12B_ENST00000290419.5_3'UTR|PPP1R12B_ENST00000391959.3_5'UTR	NM_001197131.1|NM_002481.3	NP_001184060.1|NP_002472.2	O60237	MYPT2_HUMAN	protein phosphatase 1, regulatory subunit 12B	712					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)|regulation of muscle contraction (GO:0006937)|signal transduction (GO:0007165)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	enzyme activator activity (GO:0008047)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(7)|lung(17)|ovary(4)|skin(3)|urinary_tract(1)	41			BRCA - Breast invasive adenocarcinoma(75;0.166)			GGGCAGGAGTCTGGATGAAGA	0.537																																					p.L712M		Atlas-SNP	.											.	PPP1R12B	100	.	0			c.C2134A						.						20.0	22.0	21.0					1																	202462434		2203	4299	6502	SO:0001583	missense	4660	exon15			AGGAGTCTGGATG	AB003062	CCDS1426.1, CCDS44294.1, CCDS44295.1, CCDS53458.1, CCDS53459.1, CCDS73005.1	1q32.1	2013-01-10	2011-10-04	2001-08-10	ENSG00000077157	ENSG00000077157		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	7619	protein-coding gene	gene with protein product	"""myosin phosphatase regulatory subunit"", ""myosin phosphatase, target subunit 2"""	603768	"""protein phosphatase 1, regulatory (inhibitor) subunit 12B"""	MYPT2		9570949	Standard	NM_002481		Approved	MGC87886, MGC131980, PP1bp55	uc001gya.2	O60237	OTTHUMG00000041393	ENST00000608999.1:c.2134C>A	chr1.hg19:g.202462434C>A	ENSP00000476755:p.Leu712Met	277.0	0.0		394.0	144.0	NM_002481	A8MYF5|B7ZMN6|Q2TAI8|Q5T506|Q5VUK2|Q8N179|Q9HCB7|Q9HCB8	Missense_Mutation	SNP	ENST00000608999.1	hg19	CCDS1426.1	.	.	.	.	.	.	.	.	.	.	C	13.87	2.364616	0.41902	.	.	ENSG00000077157	ENST00000406302;ENST00000336894	T;T	0.03358	3.96;3.96	5.47	2.22	0.28083	.	0.785958	0.11171	N	0.592005	T	0.08492	0.0211	L	0.56769	1.78	0.20563	N	0.999881	P;P	0.47484	0.761;0.896	B;P	0.53988	0.275;0.739	T	0.29243	-1.0018	10	0.36615	T	0.2	.	5.2635	0.15586	0.0:0.5498:0.0:0.4502	.	712;712	O60237;F8W8M3	MYPT2_HUMAN;.	M	712	ENSP00000384496:L712M;ENSP00000337897:L712M	ENSP00000337897:L712M	L	+	1	2	PPP1R12B	200729057	0.000000	0.05858	0.016000	0.15963	0.965000	0.64279	0.034000	0.13776	0.692000	0.31613	-0.136000	0.14681	CTG	.	.		0.537	PPP1R12B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000099166.3	NM_032105	
SP9	100131390	hgsc.bcm.edu	37	2	175200968	175200968	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr2:175200968G>T	ENST00000394967.2	+	2	302	c.155G>T	c.(154-156)cGc>cTc	p.R52L	AC018470.1_ENST00000595354.1_Missense_Mutation_p.A395E	NM_001145250.1	NP_001138722.1	P0CG40	SP9_HUMAN	Sp9 transcription factor	52					embryonic limb morphogenesis (GO:0030326)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			lung(1)	1						CCCTGGAAGCGCTCCTCGTCC	0.726																																					p.R52L		Atlas-SNP	.											.	SP9	15	.	0			c.G155T						.						16.0	16.0	16.0					2																	175200968		692	1591	2283	SO:0001583	missense	100131390	exon2			GGAAGCGCTCCTC		CCDS46453.1	2q31.1	2013-01-08	2012-12-07		ENSG00000217236	ENSG00000217236		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	30690	protein-coding gene	gene with protein product	"""zinc finger protein 990"""		"""Sp9 transcription factor homolog (mouse)"""				Standard	NM_001145250		Approved	ZNF990	uc010zem.1	P0CG40	OTTHUMG00000150371	ENST00000394967.2:c.155G>T	chr2.hg19:g.175200968G>T	ENSP00000378418:p.Arg52Leu	60.0	0.0		100.0	4.0	NM_001145250		Missense_Mutation	SNP	ENST00000394967.2	hg19	CCDS46453.1	.	.	.	.	.	.	.	.	.	.	G	18.89	3.718770	0.68844	.	.	ENSG00000217236	ENST00000394967	T	0.11495	2.77	3.92	3.92	0.45320	.	.	.	.	.	T	0.21761	0.0524	M	0.69823	2.125	0.47778	D	0.999514	P	0.52842	0.956	P	0.49276	0.605	T	0.07309	-1.0779	9	0.72032	D	0.01	.	15.7269	0.77766	0.0:0.0:1.0:0.0	.	52	P0CG40	SP9_HUMAN	L	52	ENSP00000378418:R52L	ENSP00000378418:R52L	R	+	2	0	SP9	174909214	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.536000	0.67180	2.024000	0.59613	0.591000	0.81541	CGC	.	.		0.726	SP9-001	NOVEL	not_organism_supported|not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317878.1	NM_001145250	
SCN10A	6336	hgsc.bcm.edu	37	3	38791583	38791583	+	Silent	SNP	G	G	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr3:38791583G>T	ENST00000449082.2	-	12	1847	c.1848C>A	c.(1846-1848)atC>atA	p.I616I		NM_006514.2	NP_006505.2	Q9Y5Y9	SCNAA_HUMAN	sodium channel, voltage-gated, type X, alpha subunit	616					AV node cell to bundle of His cell communication (GO:0086067)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of cardiac muscle contraction (GO:0055117)|regulation of heart rate (GO:0002027)|regulation of ion transmembrane transport (GO:0034765)|sensory perception (GO:0007600)|sensory perception of pain (GO:0019233)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	C-fiber (GO:0044299)|extracellular vesicular exosome (GO:0070062)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			NS(5)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(14)|kidney(5)|large_intestine(33)|lung(54)|ovary(5)|pancreas(1)|prostate(5)|skin(13)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	150				KIRC - Kidney renal clear cell carcinoma(284;0.0769)|Kidney(284;0.0945)	Benzocaine(DB01086)|Bupivacaine(DB00297)|Chloroprocaine(DB01161)|Cinchocaine(DB00527)|Cocaine(DB00907)|Dyclonine(DB00645)|Hexylcaine(DB00473)|Lacosamide(DB06218)|Levobupivacaine(DB01002)|Lidocaine(DB00281)|Mepivacaine(DB00961)|Orphenadrine(DB01173)|Oxybuprocaine(DB00892)|Procaine(DB00721)|Proparacaine(DB00807)|Ropivacaine(DB00296)|Valproic Acid(DB00313)	CGGAGGTTATGATACTGACAA	0.463																																					p.I616I		Atlas-SNP	.											.	SCN10A	359	.	0			c.C1848A						.						178.0	148.0	158.0					3																	38791583		2203	4300	6503	SO:0001819	synonymous_variant	6336	exon12			GGTTATGATACTG	AF117907	CCDS33736.1	3p22.2	2012-02-26	2007-01-23		ENSG00000185313	ENSG00000185313		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10582	protein-coding gene	gene with protein product		604427	"""sodium channel, voltage-gated, type X, alpha polypeptide"""			9839820, 10198179, 16382098	Standard	NM_006514		Approved	Nav1.8, hPN3, SNS, PN3	uc003ciq.3	Q9Y5Y9	OTTHUMG00000048245	ENST00000449082.2:c.1848C>A	chr3.hg19:g.38791583G>T		105.0	0.0		134.0	38.0	NM_006514	A6NDQ1	Silent	SNP	ENST00000449082.2	hg19	CCDS33736.1																																																																																			.	.		0.463	SCN10A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109745.3	NM_006514	
APC	324	hgsc.bcm.edu	37	5	112111324	112111324	+	Splice_Site	SNP	A	A	G			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr5:112111324A>G	ENST00000457016.1	+	5	802		c.e5-1		APC_ENST00000257430.4_Splice_Site|RNU6-482P_ENST00000391068.1_RNA|APC_ENST00000508376.2_Splice_Site			P25054	APC_HUMAN	adenomatous polyposis coli						anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)			NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		aaaaaaaaataGGTCATTGCT	0.313		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)																											.	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,colon,carcinoma,0,1	APC	4158	.	0			c.453-2A>G	GRCh37	CS043351|CS051678	APC	S		.						47.0	53.0	51.0					5																	112111324		2202	4288	6490	SO:0001630	splice_region_variant	324	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AAAAATAGGTCAT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.423-1A>G	chr5.hg19:g.112111324A>G		49.0	0.0		49.0	21.0	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Splice_Site	SNP	ENST00000457016.1	hg19	CCDS4107.1																																																																																			.	.		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Intron
ZNF451	26036	hgsc.bcm.edu	37	6	57012123	57012123	+	Missense_Mutation	SNP	G	G	A			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr6:57012123G>A	ENST00000370706.4	+	10	1484	c.1240G>A	c.(1240-1242)Gac>Aac	p.D414N	RP11-203B9.4_ENST00000591553.1_RNA|RP11-203B9.4_ENST00000586432.1_RNA|RP11-203B9.4_ENST00000585792.1_RNA|RP11-203B9.4_ENST00000588811.1_RNA|ZNF451_ENST00000491832.2_Missense_Mutation_p.D414N|RP11-203B9.4_ENST00000416069.2_RNA|RP11-203B9.4_ENST00000587815.1_RNA|RP11-203B9.4_ENST00000592500.1_RNA|ZNF451_ENST00000357489.3_Missense_Mutation_p.D414N|RP11-203B9.4_ENST00000586668.1_RNA|RP11-203B9.4_ENST00000592038.1_RNA|RP11-203B9.4_ENST00000589549.1_RNA|RP11-203B9.4_ENST00000586053.1_RNA	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451	414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			TCCTTCTTCTGACTTGCATTT	0.383																																					p.D414N		Atlas-SNP	.											.	ZNF451	181	.	0			c.G1240A						.						64.0	67.0	66.0					6																	57012123		2203	4300	6503	SO:0001583	missense	26036	exon10			TCTTCTGACTTGC	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"""Zinc fingers, C2H2-type"""	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.1240G>A	chr6.hg19:g.57012123G>A	ENSP00000359740:p.Asp414Asn	65.0	0.0		82.0	7.0	NM_001031623	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	hg19	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784441	0.49997	.	.	ENSG00000112200	ENST00000370706;ENST00000357489;ENST00000491832	T;T;T	0.06687	3.27;3.27;3.27	5.2	5.2	0.72013	.	0.265926	0.37906	N	0.001894	T	0.14614	0.0353	M	0.72118	2.19	0.80722	D	1	D;D;P;D	0.71674	0.998;0.963;0.536;0.963	D;P;B;P	0.65573	0.936;0.704;0.152;0.704	T	0.10359	-1.0633	10	0.16896	T	0.51	-16.8979	14.7166	0.69275	0.0:0.1883:0.8117:0.0	.	414;414;414;414	Q9Y4E5-2;Q9Y4E5;E9PH99;Q4KMR5	.;ZN451_HUMAN;.;.	N	414	ENSP00000359740:D414N;ENSP00000350083:D414N;ENSP00000421645:D414N	ENSP00000350083:D414N	D	+	1	0	ZNF451	57120082	1.000000	0.71417	0.988000	0.46212	0.765000	0.43378	3.019000	0.49635	2.419000	0.82065	0.650000	0.86243	GAC	.	.		0.383	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555	
BET1	10282	hgsc.bcm.edu	37	7	93628605	93628605	+	Splice_Site	SNP	A	A	G			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr7:93628605A>G	ENST00000222547.3	-	2	179	c.21T>C	c.(19-21)ggT>ggC	p.G7G	BET1_ENST00000425626.1_Splice_Site_p.G7G|BET1_ENST00000471446.1_5'Flank|AC006378.2_ENST00000426193.2_RNA|AC006378.2_ENST00000426634.1_RNA|BET1_ENST00000433727.1_Splice_Site_p.G7G	NM_005868.4	NP_005859.1	O15155	BET1_HUMAN	Bet1 golgi vesicular membrane trafficking protein	7					ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)|vesicle fusion with Golgi apparatus (GO:0048280)	cis-Golgi network (GO:0005801)|endoplasmic reticulum (GO:0005783)|Golgi cisterna (GO:0031985)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				large_intestine(2)|lung(1)|prostate(1)|skin(1)	5	all_cancers(62;2.22e-10)|all_epithelial(64;1.38e-09)|Lung NSC(181;0.218)	Breast(660;0.000162)|Ovarian(593;0.000626)	STAD - Stomach adenocarcinoma(171;0.000967)			GTACTCCTTCACCTGCAAGGA	0.453																																					p.G7G		Atlas-SNP	.											.	BET1	12	.	0			c.T21C						.						63.0	57.0	59.0					7																	93628605		2203	4300	6503	SO:0001630	splice_region_variant	10282	exon2			TCCTTCACCTGCA	AF007551	CCDS5635.1	7q21.1-q22	2013-03-08	2013-03-08		ENSG00000105829	ENSG00000105829			14562	protein-coding gene	gene with protein product	"""Golgi vesicular membrane trafficking protein p18"", ""Bet1p homolog"""	605456	"""Bet1 (S. cerevisiae) homolog"", ""BET1 homolog (S. cerevisiae)"", ""blocked early in transport 1 homolog (S. cerevisiae)"""			9382863, 10449330	Standard	XM_005250109		Approved	hbet1	uc003unf.1	O15155	OTTHUMG00000023487	ENST00000222547.3:c.20-1T>C	chr7.hg19:g.93628605A>G		40.0	0.0		46.0	16.0	NM_005868	Q96EA0	Silent	SNP	ENST00000222547.3	hg19	CCDS5635.1	.	.	.	.	.	.	.	.	.	.	A	14.25	2.478612	0.44044	.	.	ENSG00000105829	ENST00000457139	.	.	.	5.35	4.18	0.49190	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.354	0.43954	0.8534:0.0:0.0:0.1466	.	.	.	.	R	22	.	.	X	-	1	0	BET1	93466541	1.000000	0.71417	1.000000	0.80357	0.811000	0.45836	3.650000	0.54424	0.964000	0.38108	0.533000	0.62120	TGA	.	.		0.453	BET1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255181.2	NM_005868	Silent
ZNF800	168850	hgsc.bcm.edu	37	7	127026146	127026146	+	Missense_Mutation	SNP	C	C	G			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr7:127026146C>G	ENST00000393313.1	-	3	716	c.125G>C	c.(124-126)gGt>gCt	p.G42A	ZNF800_ENST00000265827.3_Missense_Mutation_p.G42A|ZNF800_ENST00000393312.1_Missense_Mutation_p.G42A			Q2TB10	ZN800_HUMAN	zinc finger protein 800	42					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)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(8)|ovary(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	32						TTGTTGAATACCAGATTTGGA	0.378																																					p.G42A		Atlas-SNP	.											ZNF800,NS,carcinoma,0,2	ZNF800	78	.	0			c.G125C						.						112.0	106.0	108.0					7																	127026146		2203	4300	6503	SO:0001583	missense	168850	exon3			TGAATACCAGATT	AF218032	CCDS5795.1	7q31.33	2008-05-02			ENSG00000048405	ENSG00000048405		"""Zinc fingers, C2H2-type"""	27267	protein-coding gene	gene with protein product						12477932	Standard	NM_176814		Approved		uc003vly.1	Q2TB10	OTTHUMG00000023456	ENST00000393313.1:c.125G>C	chr7.hg19:g.127026146C>G	ENSP00000376989:p.Gly42Ala	34.0	0.0		41.0	10.0	NM_176814	Q9HBN0	Missense_Mutation	SNP	ENST00000393313.1	hg19	CCDS5795.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.821552	0.90873	.	.	ENSG00000048405	ENST00000393313;ENST00000265827;ENST00000393312;ENST00000434602;ENST00000436992;ENST00000439506	T;T;T;T;T;T	0.54675	2.08;2.08;2.08;0.56;0.69;1.28	5.43	5.43	0.79202	.	0.000000	0.85682	D	0.000000	T	0.61689	0.2367	N	0.24115	0.695	0.38778	D	0.954700	D	0.76494	0.999	D	0.80764	0.994	T	0.66941	-0.5796	9	0.72032	D	0.01	-6.8906	18.2091	0.89864	0.0:1.0:0.0:0.0	.	42	Q2TB10	ZN800_HUMAN	A	42	ENSP00000376989:G42A;ENSP00000265827:G42A;ENSP00000376988:G42A;ENSP00000403945:G42A;ENSP00000401109:G42A;ENSP00000389776:G42A	ENSP00000265827:G42A	G	-	2	0	ZNF800	126813382	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.240000	0.78192	2.546000	0.85860	0.655000	0.94253	GGT	.	.		0.378	ZNF800-002	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000141823.1	NM_176814	
PTN	5764	hgsc.bcm.edu	37	7	136938301	136938301	+	Silent	SNP	G	G	T	rs149012204		TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr7:136938301G>T	ENST00000348225.2	-	3	626	c.199C>A	c.(199-201)Cgg>Agg	p.R67R	PTN_ENST00000393083.2_Silent_p.R67R	NM_002825.5	NP_002816.1	P21246	PTN_HUMAN	pleiotrophin	67					bone mineralization (GO:0030282)|learning (GO:0007612)|negative regulation of catalytic activity (GO:0043086)|nervous system development (GO:0007399)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	heparin binding (GO:0008201)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23						GTGCCCTCCCGTGTGCCCAGC	0.522																																					p.R67R		Atlas-SNP	.											.	PTN	38	.	0			c.C199A						.						105.0	88.0	94.0					7																	136938301		2203	4300	6503	SO:0001819	synonymous_variant	5764	exon3			CCTCCCGTGTGCC	M57399	CCDS5844.1	7q33	2014-01-30	2008-07-31		ENSG00000105894	ENSG00000105894		"""Endogenous ligands"""	9630	protein-coding gene	gene with protein product	"""heparin binding growth factor 8"""	162095	"""neurite growth-promoting factor 1"""	NEGF1		1457401, 1768439	Standard	NM_002825		Approved	HBNF, HBGF8	uc003vtq.2	P21246	OTTHUMG00000155709	ENST00000348225.2:c.199C>A	chr7.hg19:g.136938301G>T		60.0	0.0		82.0	4.0	NM_002825	Q5U0B0|Q6ICQ5|Q9UCC6	Silent	SNP	ENST00000348225.2	hg19	CCDS5844.1																																																																																			.	G|1.000;A|0.000		0.522	PTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341339.1	NM_002825	
WHSC1L1	54904	hgsc.bcm.edu	37	8	38133282	38133282	+	Silent	SNP	A	A	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr8:38133282A>T	ENST00000317025.8	-	24	4708	c.4191T>A	c.(4189-4191)tcT>tcA	p.S1397S	RP11-513D5.5_ENST00000529325.1_RNA|WHSC1L1_ENST00000433384.2_Silent_p.S1348S|WHSC1L1_ENST00000527502.1_Silent_p.S1386S	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1	1397					histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			CTTCCAGTGCAGAGGGAACCA	0.498			T	NUP98	AML																																p.S1397S		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.T4191A						.						81.0	76.0	77.0					8																	38133282		1917	4153	6070	SO:0001819	synonymous_variant	54904	exon24			CAGTGCAGAGGGA	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.4191T>A	chr8.hg19:g.38133282A>T		45.0	0.0		70.0	23.0	NM_023034	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Silent	SNP	ENST00000317025.8	hg19	CCDS43729.1																																																																																			.	.		0.498	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
LRRTM3	347731	hgsc.bcm.edu	37	10	68686847	68686847	+	Missense_Mutation	SNP	G	G	C			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr10:68686847G>C	ENST00000361320.4	+	2	751	c.173G>C	c.(172-174)aGt>aCt	p.S58T	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	58	LRRNT.				positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						ATACCCTCAAGTATATCTGCT	0.423																																					p.S58T		Atlas-SNP	.											.	LRRTM3	241	.	0			c.G173C						.						126.0	129.0	128.0					10																	68686847		2203	4300	6503	SO:0001583	missense	347731	exon2			CCTCAAGTATATC	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.173G>C	chr10.hg19:g.68686847G>C	ENSP00000355187:p.Ser58Thr	48.0	0.0		59.0	21.0	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	hg19	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.916752	0.33815	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	D	0.95949	-3.86	5.53	5.53	0.82687	Leucine-rich repeat-containing N-terminal (2);	0.000000	0.85682	D	0.000000	D	0.93471	0.7917	L	0.39085	1.19	0.43761	D	0.996272	B;B	0.34200	0.441;0.387	B;B	0.41723	0.365;0.196	D	0.92422	0.5946	10	0.44086	T	0.13	.	13.9266	0.63966	0.0:0.1526:0.8474:0.0	.	58;58	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	T	58	ENSP00000355187:S58T	ENSP00000355187:S58T	S	+	2	0	LRRTM3	68356853	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.912000	0.56386	2.613000	0.88420	0.655000	0.94253	AGT	.	.		0.423	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011	
NRAP	4892	hgsc.bcm.edu	37	10	115374663	115374663	+	Missense_Mutation	SNP	A	A	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr10:115374663A>T	ENST00000359988.3	-	28	3365	c.3121T>A	c.(3121-3123)Tat>Aat	p.Y1041N	NRAP_ENST00000369360.3_Missense_Mutation_p.Y1014N|NRAP_ENST00000369358.4_Missense_Mutation_p.Y1049N|NRAP_ENST00000360478.3_Missense_Mutation_p.Y1006N	NM_001261463.1|NM_198060.3	NP_001248392.1|NP_932326.2			nebulin-related anchoring protein											autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(18)|lung(39)|ovary(6)|prostate(3)|skin(1)|stomach(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Colorectal(252;0.0233)|Breast(234;0.188)		Epithelial(162;0.00392)|all cancers(201;0.00569)		CTCAGTTTATAGCCACCATCT	0.458																																					p.Y1041N		Atlas-SNP	.											.	NRAP	208	.	0			c.T3121A						.						190.0	168.0	175.0					10																	115374663		2203	4300	6503	SO:0001583	missense	4892	exon28			GTTTATAGCCACC		CCDS7578.1, CCDS7579.1, CCDS73199.1	10q24-q26	2008-08-01			ENSG00000197893	ENSG00000197893			7988	protein-coding gene	gene with protein product		602873				12789664, 10320340	Standard	NM_006175		Approved		uc001lal.4	Q86VF7	OTTHUMG00000019072	ENST00000359988.3:c.3121T>A	chr10.hg19:g.115374663A>T	ENSP00000353078:p.Tyr1041Asn	146.0	0.0		235.0	73.0	NM_001261463		Missense_Mutation	SNP	ENST00000359988.3	hg19	CCDS7579.1	.	.	.	.	.	.	.	.	.	.	A	14.24	2.476461	0.44044	.	.	ENSG00000197893	ENST00000369358;ENST00000369360;ENST00000359988;ENST00000360478	T;T;T;T	0.35048	2.01;2.13;1.38;1.33	5.56	5.56	0.83823	.	0.000000	0.85682	D	0.000000	T	0.64549	0.2608	M	0.86502	2.82	0.46701	D	0.99916	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.80764	0.987;0.994;0.99	T	0.67201	-0.5730	10	0.34782	T	0.22	.	15.7107	0.77626	1.0:0.0:0.0:0.0	.	1041;1006;1041	A0AVL2;Q86VF7-4;Q86VF7	.;.;NRAP_HUMAN	N	1049;1014;1041;1006	ENSP00000358365:Y1049N;ENSP00000358367:Y1014N;ENSP00000353078:Y1041N;ENSP00000353666:Y1006N	ENSP00000353078:Y1041N	Y	-	1	0	NRAP	115364653	1.000000	0.71417	0.155000	0.22561	0.331000	0.28603	8.551000	0.90678	2.112000	0.64535	0.533000	0.62120	TAT	.	.		0.458	NRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050425.2	NM_006175	
STT3A	3703	hgsc.bcm.edu	37	11	125476211	125476211	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr11:125476211G>T	ENST00000529196.1	+	9	837	c.631G>T	c.(631-633)Ggt>Tgt	p.G211C	STT3A_ENST00000531491.1_Missense_Mutation_p.G119C|STT3A_ENST00000392708.4_Missense_Mutation_p.G211C			P46977	STT3A_HUMAN	STT3A, subunit of the oligosaccharyltransferase complex (catalytic)	211					cellular protein metabolic process (GO:0044267)|co-translational protein modification (GO:0043686)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			NS(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(3)|lung(15)|skin(1)	33	all_hematologic(175;0.228)	Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.0919)|all_lung(97;0.0994)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.13e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0996)		GTCATGGGGAGGTTATGTGTT	0.468																																					p.G211C		Atlas-SNP	.											.	STT3A	52	.	0			c.G631T						.						368.0	320.0	337.0					11																	125476211		2201	4299	6500	SO:0001583	missense	3703	exon8			TGGGGAGGTTATG	BC020965	CCDS8458.1, CCDS60998.1	11q23.3	2013-03-06	2013-03-06	2006-02-07	ENSG00000134910	ENSG00000134910	2.4.99.18		6172	protein-coding gene	gene with protein product	"""dolichyl-diphosphooligosaccharide protein glycotransferase"""	601134	"""integral membrane protein 1"", ""STT3, subunit of the oligosaccharyltransferase complex, homolog A (S. cerevisiae)"", ""STT3A, cataylic subunit of the oligosaccharyltransferase complex"""	ITM1		8941377, 8634329, 10234787	Standard	NM_152713		Approved	TMC, MGC9042, STT3-A	uc001qcd.2	P46977	OTTHUMG00000165852	ENST00000529196.1:c.631G>T	chr11.hg19:g.125476211G>T	ENSP00000436962:p.Gly211Cys	63.0	0.0		99.0	4.0	NM_152713	B4DJ24|E9PNQ1|Q86XU9|Q8TE35|Q8WUB4	Missense_Mutation	SNP	ENST00000529196.1	hg19	CCDS8458.1	.	.	.	.	.	.	.	.	.	.	G	34	5.308801	0.95629	.	.	ENSG00000134910	ENST00000392708;ENST00000529196;ENST00000531491	.	.	.	6.03	6.03	0.97812	.	0.000000	0.85682	D	0.000000	D	0.90089	0.6904	H	0.96460	3.825	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92186	0.5755	9	0.87932	D	0	-15.9493	20.177	0.98182	0.0:0.0:1.0:0.0	.	119;211	E9PNQ1;P46977	.;STT3A_HUMAN	C	211;211;119	.	ENSP00000376472:G211C	G	+	1	0	STT3A	124981421	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.869000	0.99810	2.854000	0.98071	0.655000	0.94253	GGT	.	.		0.468	STT3A-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000386691.1	NM_152713	
WNT1	7471	hgsc.bcm.edu	37	12	49374348	49374348	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:49374348G>T	ENST00000293549.3	+	3	536	c.500G>T	c.(499-501)tGg>tTg	p.W167L		NM_005430.3	NP_005421.1	P04628	WNT1_HUMAN	wingless-type MMTV integration site family, member 1	167					bone development (GO:0060348)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|cellular response to peptide hormone stimulus (GO:0071375)|central nervous system morphogenesis (GO:0021551)|cerebellum formation (GO:0021588)|diencephalon development (GO:0021536)|embryonic axis specification (GO:0000578)|forebrain anterior/posterior pattern specification (GO:0021797)|hematopoietic stem cell proliferation (GO:0071425)|hepatocyte differentiation (GO:0070365)|inner ear morphogenesis (GO:0042472)|midbrain development (GO:0030901)|midbrain-hindbrain boundary maturation during brain development (GO:0022004)|myoblast fusion (GO:0007520)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of cell aging (GO:0090344)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000059)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron differentiation (GO:0030182)|neuron fate determination (GO:0048664)|organ regeneration (GO:0031100)|positive regulation of cell proliferation (GO:0008284)|positive regulation of dermatome development (GO:0061184)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of insulin-like growth factor receptor signaling pathway (GO:0043568)|positive regulation of lamellipodium assembly (GO:0010592)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|response to wounding (GO:0009611)|signal transduction in response to DNA damage (GO:0042770)|Spemann organizer formation (GO:0060061)|spinal cord association neuron differentiation (GO:0021527)|T cell differentiation in thymus (GO:0033077)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)|transcription regulatory region DNA binding (GO:0044212)	p.G169fs*30(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(7)|prostate(1)	11				BRCA - Breast invasive adenocarcinoma(357;0.244)		gACTGGCACTGGGGGGGCTGC	0.682																																					p.W167L		Atlas-SNP	.											.,1	WNT1	13	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.G500T						.						9.0	11.0	11.0					12																	49374348		2195	4281	6476	SO:0001583	missense	7471	exon3			GGCACTGGGGGGG	X03072	CCDS8776.1	12q13	2013-02-28				ENSG00000125084		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12774	protein-coding gene	gene with protein product		164820		INT1		2998762, 3281802	Standard	NM_005430		Approved		uc001rsu.3	P04628	OTTHUMG00000170403	ENST00000293549.3:c.500G>T	chr12.hg19:g.49374348G>T	ENSP00000293549:p.Trp167Leu	92.0	0.0		145.0	52.0	NM_005430	Q5U0N2	Missense_Mutation	SNP	ENST00000293549.3	hg19	CCDS8776.1	.	.	.	.	.	.	.	.	.	.	G	34	5.389170	0.95988	.	.	ENSG00000125084	ENST00000293549;ENST00000380414	D	0.81739	-1.53	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	D	0.92792	0.7708	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.94755	0.7931	10	0.87932	D	0	.	17.1121	0.86678	0.0:0.0:1.0:0.0	.	167	P04628	WNT1_HUMAN	L	167;3	ENSP00000293549:W167L	ENSP00000293549:W167L	W	+	2	0	WNT1	47660615	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.816000	0.86201	2.574000	0.86865	0.655000	0.94253	TGG	.	.		0.682	WNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408937.1		
HOXC6	3223	hgsc.bcm.edu	37	12	54423712	54423712	+	Missense_Mutation	SNP	G	G	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:54423712G>T	ENST00000243108.4	+	2	838	c.674G>T	c.(673-675)cGg>cTg	p.R225L	RP11-834C11.12_ENST00000513209.1_Intron|HOXC5_ENST00000312492.2_5'Flank|HOXC4_ENST00000303406.4_Intron|HOXC6_ENST00000394331.3_Missense_Mutation_p.R143L|RP11-834C11.14_ENST00000512206.1_RNA	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	225	Glu/Lys-rich.				anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GAGGAAAAGCGGGAAGAGACA	0.587																																					p.R225L		Atlas-SNP	.											.	HOXC6	30	.	0			c.G674T						.						130.0	158.0	149.0					12																	54423712		2202	4300	6502	SO:0001583	missense	3223	exon2			AAAAGCGGGAAGA		CCDS8871.1, CCDS41792.1	12q13.13	2011-06-20	2005-12-22		ENSG00000197757	ENSG00000197757		"""Homeoboxes / ANTP class : HOXL subclass"""	5128	protein-coding gene	gene with protein product		142972	"""homeo box C6"""	HOX3C, HOX3		1973146, 1358459	Standard	NM_153693		Approved		uc001sev.3	P09630	OTTHUMG00000160027	ENST00000243108.4:c.674G>T	chr12.hg19:g.54423712G>T	ENSP00000243108:p.Arg225Leu	90.0	0.0		84.0	4.0	NM_004503	B2RBV2|Q6DK09	Missense_Mutation	SNP	ENST00000243108.4	hg19	CCDS8871.1	.	.	.	.	.	.	.	.	.	.	G	13.57	2.277602	0.40294	.	.	ENSG00000197757	ENST00000394331;ENST00000243108	D;D	0.92699	-3.09;-3.03	4.96	4.96	0.65561	.	0.233443	0.37304	N	0.002155	D	0.84115	0.5401	N	0.08118	0	0.80722	D	1	B	0.14012	0.009	B	0.06405	0.002	T	0.79448	-0.1799	10	0.42905	T	0.14	.	17.1341	0.86734	0.0:0.0:1.0:0.0	.	225	P09630	HXC6_HUMAN	L	143;225	ENSP00000377864:R143L;ENSP00000243108:R225L	ENSP00000243108:R225L	R	+	2	0	HOXC6	52709979	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.396000	0.59684	2.584000	0.87258	0.561000	0.74099	CGG	.	.		0.587	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2		
SART3	9733	hgsc.bcm.edu	37	12	108929239	108929239	+	Silent	SNP	T	T	C			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:108929239T>C	ENST00000228284.3	-	12	1686	c.1452A>G	c.(1450-1452)cgA>cgG	p.R484R	SART3_ENST00000431469.2_Silent_p.R448R	NM_014706.3	NP_055521.1	Q15020	SART3_HUMAN	squamous cell carcinoma antigen recognized by T cells 3	484					cell morphogenesis (GO:0000902)|hematopoietic stem cell proliferation (GO:0071425)|homeostasis of number of cells (GO:0048872)|regulation of gene expression (GO:0010468)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|endometrium(8)|kidney(1)|large_intestine(4)|lung(8)|pancreas(1)|stomach(1)	25						TATTGCACAGTCGAGCCTAAA	0.478									Porokeratosis																												p.R484R		Atlas-SNP	.											.	SART3	64	.	0			c.A1452G						.						231.0	210.0	217.0					12																	108929239		2203	4300	6503	SO:0001819	synonymous_variant	9733	exon12	Familial Cancer Database	incl.: Porokeratosis of Mibelli, Disseminated Superficial Actinic Porokertosis, Porokeratosis Palmaris Plantaris et Disseminata, Porokeratosis Punctata Palmaris et Plantaris, Linear Porokeratosis	GCACAGTCGAGCC	AB020880	CCDS9117.1	12q24.11	2013-02-12	2006-12-07			ENSG00000075856		"""RNA binding motif (RRM) containing"""	16860	protein-coding gene	gene with protein product		611684	"""squamous cell carcinoma antigen recognised by T cells 3"""			12032085, 15840095, 20595234	Standard	NM_014706		Approved	KIAA0156, RP11-13G14, TIP110, p110	uc001tmz.1	Q15020	OTTHUMG00000169449	ENST00000228284.3:c.1452A>G	chr12.hg19:g.108929239T>C		99.0	0.0		163.0	25.0	NM_014706	A8K2E4|Q2M2H0|Q58F06|Q8IUS1|Q96J95	Silent	SNP	ENST00000228284.3	hg19	CCDS9117.1																																																																																			.	.		0.478	SART3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404094.1		
SBNO1	55206	hgsc.bcm.edu	37	12	123815842	123815842	+	Silent	SNP	C	C	T	rs74679372	byFrequency	TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr12:123815842C>T	ENST00000602398.1	-	8	1117	c.990G>A	c.(988-990)acG>acA	p.T330T	SBNO1_ENST00000602750.1_Silent_p.T329T|SBNO1_ENST00000420886.2_Silent_p.T330T|SBNO1_ENST00000267176.4_Silent_p.T329T			A3KN83	SBNO1_HUMAN	strawberry notch homolog 1 (Drosophila)	330					regulation of transcription, DNA-templated (GO:0006355)					NS(2)|breast(6)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(11)|lung(18)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(2)	62	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000701)|Epithelial(86;0.00197)		TTCCTGCTATCGTCCTTCCTT	0.443																																					p.T330T		Atlas-SNP	.											.	SBNO1	138	.	0			c.G990A						.						158.0	142.0	148.0					12																	123815842		2203	4300	6503	SO:0001819	synonymous_variant	55206	exon7			TGCTATCGTCCTT	AK001563	CCDS9246.1, CCDS53844.1	12q24.31	2006-10-06	2006-10-06			ENSG00000139697			22973	protein-coding gene	gene with protein product		614274	"""sno, strawberry notch homolog 1 (Drosophila)"""				Standard	NM_018183		Approved	MOP3, FLJ10701, FLJ10833, Sno	uc010tap.2	A3KN83		ENST00000602398.1:c.990G>A	chr12.hg19:g.123815842C>T		63.0	0.0		104.0	39.0	NM_001167856	Q05C06|Q3ZTS3|Q9H3T8|Q9NVB2	Silent	SNP	ENST00000602398.1	hg19	CCDS53844.1																																																																																			.	C|0.999;A|0.001		0.443	SBNO1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000467684.1	NM_018183	
OR4M2	390538	hgsc.bcm.edu	37	15	22369299	22369299	+	Missense_Mutation	SNP	T	T	A			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr15:22369299T>A	ENST00000332663.2	+	1	822	c.724T>A	c.(724-726)Tgc>Agc	p.C242S	RP11-69H14.6_ENST00000558896.1_RNA	NM_001004719.2	NP_001004719.2	Q8NGB6	OR4M2_HUMAN	olfactory receptor, family 4, subfamily M, member 2	242						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|endometrium(2)|kidney(4)|large_intestine(6)|lung(38)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	63		all_cancers(20;1.94e-20)|all_epithelial(15;3.94e-18)|Lung NSC(15;8.53e-15)|all_lung(15;2.87e-14)|Breast(32;0.00519)|Colorectal(260;0.101)	GBM - Glioblastoma multiforme(6;0.124)	all cancers(64;1.64e-11)|Epithelial(43;5.81e-10)|BRCA - Breast invasive adenocarcinoma(123;0.000255)|Kidney(6;0.00736)|KIRC - Kidney renal clear cell carcinoma(6;0.0135)|GBM - Glioblastoma multiforme(186;0.0963)		CATGTCCACCTGCTATTCCCA	0.458																																					p.C242S		Atlas-SNP	.											.	OR4M2	140	.	0			c.T724A						.						276.0	196.0	223.0					15																	22369299		2203	4300	6503	SO:0001583	missense	390538	exon1			TCCACCTGCTATT	AC060768	CCDS32172.1	15q11.2	2013-09-23			ENSG00000182974	ENSG00000182974		"""GPCR / Class A : Olfactory receptors"""	15373	protein-coding gene	gene with protein product							Standard	NM_001004719		Approved		uc010tzu.2	Q8NGB6	OTTHUMG00000171738	ENST00000332663.2:c.724T>A	chr15.hg19:g.22369299T>A	ENSP00000329467:p.Cys242Ser	272.0	0.0		333.0	69.0	NM_001004719	B9EH16|Q6IEY2	Missense_Mutation	SNP	ENST00000332663.2	hg19	CCDS32172.1	.	.	.	.	.	.	.	.	.	.	.	17.54	3.413917	0.62511	.	.	ENSG00000182974	ENST00000332663	T	0.00369	7.74	2.28	2.28	0.28536	GPCR, rhodopsin-like superfamily (1);	0.000000	0.53938	D	0.000046	T	0.01320	0.0043	H	0.96111	3.77	0.43632	D	0.996026	D	0.89917	1.0	D	0.97110	1.0	T	0.41324	-0.9515	10	0.87932	D	0	-12.2555	8.1829	0.31322	0.0:0.0:0.0:1.0	.	242	Q8NGB6	OR4M2_HUMAN	S	242	ENSP00000329467:C242S	ENSP00000329467:C242S	C	+	1	0	OR4M2	19870663	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.243000	0.78219	1.068000	0.40764	0.368000	0.22195	TGC	.	.		0.458	OR4M2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414921.1		
MYH14	79784	hgsc.bcm.edu	37	19	50794186	50794186	+	Missense_Mutation	SNP	C	C	T	rs369826983		TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr19:50794186C>T	ENST00000596571.1	+	33	4885	c.4885C>T	c.(4885-4887)Cgc>Tgc	p.R1629C	MYH14_ENST00000425460.1_Missense_Mutation_p.R1637C|MYH14_ENST00000440075.2_Missense_Mutation_p.R1670C|MYH14_ENST00000262269.8_Missense_Mutation_p.R1670C|MYH14_ENST00000376970.2_Missense_Mutation_p.R1662C|MYH14_ENST00000601313.1_Missense_Mutation_p.R1670C|MYH14_ENST00000598205.1_Missense_Mutation_p.R1637C			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	1629					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		GCGGAAGCAGCGCACTCTGGC	0.657																																					p.R1670C		Atlas-SNP	.											.	MYH14	261	.	0			c.C5008T						.	C	CYS/ARG,CYS/ARG,CYS/ARG	1,4141		0,1,2070	19.0	25.0	23.0		4909,5008,4885	0.7	1.0	19		23	0,8398		0,0,4199	no	missense,missense,missense	MYH14	NM_001077186.1,NM_001145809.1,NM_024729.3	180,180,180	0,1,6269	TT,TC,CC		0.0,0.0241,0.0080	probably-damaging,probably-damaging,probably-damaging	1637/2004,1670/2037,1629/1996	50794186	1,12539	2071	4199	6270	SO:0001583	missense	79784	exon36			AAGCAGCGCACTC	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.4885C>T	chr19.hg19:g.50794186C>T	ENSP00000472819:p.Arg1629Cys	165.0	0.0		270.0	86.0	NM_001145809	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Missense_Mutation	SNP	ENST00000596571.1	hg19	CCDS59411.1	.	.	.	.	.	.	.	.	.	.	C	14.42	2.530049	0.45073	2.41E-4	0.0	ENSG00000105357	ENST00000440075;ENST00000376970;ENST00000425460;ENST00000376965;ENST00000262269	D;D;D;D	0.81499	-1.5;-1.5;-1.5;-1.5	4.42	0.697	0.18081	Myosin tail (1);	.	.	.	.	D	0.88804	0.6536	M	0.84773	2.715	0.54753	D	0.99998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.88589	0.3142	9	0.87932	D	0	.	11.0492	0.47876	0.68:0.32:0.0:0.0	.	1670;1629;1637	Q7Z406-2;Q7Z406;Q7Z406-6	.;MYH14_HUMAN;.	C	1670;1662;1637;1413;1670	ENSP00000406273:R1670C;ENSP00000366169:R1662C;ENSP00000407879:R1637C;ENSP00000262269:R1670C	ENSP00000262269:R1670C	R	+	1	0	MYH14	55485998	0.405000	0.25336	1.000000	0.80357	0.358000	0.29455	-0.374000	0.07484	0.493000	0.27837	0.491000	0.48974	CGC	.	.		0.657	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000464710.2	NM_024729	
SLC19A1	6573	hgsc.bcm.edu	37	21	46951887	46951887	+	Missense_Mutation	SNP	A	A	G			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr21:46951887A>G	ENST00000311124.4	-	3	517	c.365T>C	c.(364-366)aTg>aCg	p.M122T	SLC19A1_ENST00000485649.2_Missense_Mutation_p.M82T|SLC19A1_ENST00000380010.4_Missense_Mutation_p.M122T|SLC19A1_ENST00000567670.1_Missense_Mutation_p.M122T	NM_194255.2	NP_919231.1	P41440	S19A1_HUMAN	solute carrier family 19 (folate transporter), member 1	122					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)	GAAGAGCTCCATGAGCTGCAT	0.657																																					p.M122T		Atlas-SNP	.											.	SLC19A1	53	.	0			c.T365C						.						23.0	25.0	25.0					21																	46951887		2198	4300	6498	SO:0001583	missense	6573	exon3			AGCTCCATGAGCT	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.365T>C	chr21.hg19:g.46951887A>G	ENSP00000308895:p.Met122Thr	40.0	0.0		55.0	7.0	NM_001205206	B2R7U8|B7Z8C3|E9PFY4|O00553|O60227|Q13026|Q9BTX8	Missense_Mutation	SNP	ENST00000311124.4	hg19	CCDS13725.1	.	.	.	.	.	.	.	.	.	.	A	14.37	2.513930	0.44763	.	.	ENSG00000173638	ENST00000311124;ENST00000380010;ENST00000485649;ENST00000427839;ENST00000443742	T;T;T;T;T	0.80214	-1.35;-1.35;-1.35;0.36;0.36	4.95	4.95	0.65309	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.90484	0.7019	M	0.90814	3.15	0.58432	D	0.999998	D;D;D;D	0.67145	0.996;0.996;0.996;0.996	D;D;D;D	0.67725	0.953;0.953;0.936;0.953	D	0.92332	0.5874	10	0.72032	D	0.01	-67.9873	13.7172	0.62705	1.0:0.0:0.0:0.0	.	82;144;122;122	B7Z8C3;D3DSM6;E9PFY4;P41440	.;.;.;S19A1_HUMAN	T	122;122;82;122;122	ENSP00000308895:M122T;ENSP00000369347:M122T;ENSP00000441772:M82T;ENSP00000401850:M122T;ENSP00000411345:M122T	ENSP00000308895:M122T	M	-	2	0	SLC19A1	45776315	1.000000	0.71417	0.993000	0.49108	0.006000	0.05464	8.830000	0.92063	1.989000	0.58080	0.379000	0.24179	ATG	.	.		0.657	SLC19A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206796.1		
LIF	3976	hgsc.bcm.edu	37	22	30640773	30640773	+	Missense_Mutation	SNP	C	C	T			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr22:30640773C>T	ENST00000249075.3	-	2	324	c.169G>A	c.(169-171)Ggc>Agc	p.G57S	RP1-102K2.8_ENST00000593843.1_RNA|LIF_ENST00000403987.3_Intron|RP1-102K2.8_ENST00000608354.1_RNA	NM_002309.4	NP_002300.1	P15018	LIF_HUMAN	leukemia inhibitory factor	57					blood vessel remodeling (GO:0001974)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|immune response (GO:0006955)|leukemia inhibitory factor signaling pathway (GO:0048861)|lung alveolus development (GO:0048286)|lung lobe morphogenesis (GO:0060463)|lung vasculature development (GO:0060426)|multicellular organismal development (GO:0007275)|muscle organ morphogenesis (GO:0048644)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of hormone secretion (GO:0046888)|negative regulation of meiosis (GO:0045835)|neuron development (GO:0048666)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cell proliferation (GO:0008284)|positive regulation of histone H3-K27 acetylation (GO:1901676)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0072108)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-serine phosphorylation of STAT protein (GO:0033141)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein localization to nucleus (GO:1900182)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|spongiotrophoblast differentiation (GO:0060708)|stem cell maintenance (GO:0019827)|transcription from RNA polymerase II promoter (GO:0006366)|trophoblast giant cell differentiation (GO:0060707)|tyrosine phosphorylation of Stat3 protein (GO:0042503)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	cytokine activity (GO:0005125)|growth factor activity (GO:0008083)|leukemia inhibitory factor receptor binding (GO:0005146)|receptor binding (GO:0005102)|RNA polymerase II transcription factor recruiting transcription factor activity (GO:0001135)			breast(1)|lung(3)|skin(3)	7			Epithelial(10;0.171)			TTGGCACTGCCATTGAGCTGT	0.542																																					p.G57S		Atlas-SNP	.											.	LIF	18	.	0			c.G169A						.						176.0	150.0	159.0					22																	30640773		2203	4300	6503	SO:0001583	missense	3976	exon2			CACTGCCATTGAG		CCDS13872.1, CCDS58799.1	22q12.2	2012-02-09	2012-02-09		ENSG00000128342	ENSG00000128342			6596	protein-coding gene	gene with protein product	"""differentiation inhibitory activity"", ""differentiation-inducing factor"", ""hepatocyte-stimulating factor III"", ""cholinergic differentiation factor"", ""human interleukin in DA cells"""	159540				1714745, 8058719	Standard	NM_002309		Approved	CDF, DIA, HILDA	uc003agz.3	P15018	OTTHUMG00000150910	ENST00000249075.3:c.169G>A	chr22.hg19:g.30640773C>T	ENSP00000249075:p.Gly57Ser	157.0	0.0		221.0	11.0	NM_002309	B2RCW7|B5MC23|Q52LZ2	Missense_Mutation	SNP	ENST00000249075.3	hg19	CCDS13872.1	.	.	.	.	.	.	.	.	.	.	C	5.385	0.256288	0.10185	.	.	ENSG00000128342	ENST00000249075	T	0.74842	-0.88	4.56	-0.535	0.11879	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	0.637394	0.14132	N	0.339333	T	0.51415	0.1673	N	0.14661	0.345	0.52099	D	0.999949	B	0.17038	0.02	B	0.19946	0.027	T	0.17715	-1.0360	10	0.16896	T	0.51	-3.3473	7.6763	0.28488	0.0:0.4459:0.0:0.5541	.	57	P15018	LIF_HUMAN	S	57	ENSP00000249075:G57S	ENSP00000249075:G57S	G	-	1	0	LIF	28970773	0.003000	0.15002	0.768000	0.31515	0.974000	0.67602	-0.678000	0.05209	-0.253000	0.09514	0.563000	0.77884	GGC	.	.		0.542	LIF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320508.1	NM_002309	
IL6ST	3572	hgsc.bcm.edu	37	5	55260044	55260049	+	In_Frame_Del	DEL	GACTTC	GACTTC	-			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	GACTTC	GACTTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr5:55260044_55260049delGACTTC	ENST00000381298.2	-	6	895_900	c.583_588delGAAGTC	c.(583-588)gaagtcdel	p.EV195del	IL6ST_ENST00000536319.1_In_Frame_Del_p.EV195del|IL6ST_ENST00000502326.3_In_Frame_Del_p.EV195del|IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000522633.2_In_Frame_Del_p.EV195del|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000381287.4_In_Frame_Del_p.EV195del|IL6ST_ENST00000396816.1_In_Frame_Del_p.52_54LKS>F|IL6ST_ENST00000336909.5_In_Frame_Del_p.EV195del|IL6ST_ENST00000381294.3_In_Frame_Del_p.EV195del	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	195	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				CTTCTACCCAGACTTCAATGTTGACA	0.379			O		hepatocellular ca																																p.195_197del		Atlas-Indel,Pindel	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.584_589del						.																																			SO:0001651	inframe_deletion	3572	exon6			.	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.583_588delGAAGTC	chr5.hg19:g.55260044_55260049delGACTTC	ENSP00000370698:p.Glu195_Val196del	112.0	0.0		125.0	14.0	NM_001190981	A0N0L4|Q5FC04|Q9UQ41	In_Frame_Del	DEL	ENST00000381298.2	hg19	CCDS3971.1																																																																																			.	.		0.379	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
TUBB2A	7280	hgsc.bcm.edu	37	6	3154966	3154966	+	Frame_Shift_Del	DEL	C	C	-			TCGA-DD-A4NP-01A-11D-A28X-10	TCGA-DD-A4NP-10A-01D-A28X-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0e6e1c91-c07f-404f-9f9c-0fc66616a63e	563ad2ed-2b5a-43e0-9e0d-3f875800b598	g.chr6:3154966delC	ENST00000333628.3	-	4	531	c.469delG	c.(469-471)gaafs	p.E158fs	TUBB2A_ENST00000489942.1_5'UTR|RP1-40E16.11_ENST00000447644.1_RNA	NM_001069.2	NP_001060.1	Q13885	TBB2A_HUMAN	tubulin, beta 2A class IIa	158					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|nucleus (GO:0005634)|vesicle (GO:0031982)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|large_intestine(4)|lung(2)|skin(1)	9	Ovarian(93;0.0386)	all_hematologic(90;0.0895)				GGGTACTCTTCCCGGATCTTG	0.622																																					p.E157fs		Atlas-INDEL	.											.	TUBB2A	23	.	0			c.470delA						.						33.0	23.0	26.0					6																	3154966		2202	4276	6478	SO:0001589	frameshift_variant	7280	exon4			.	AY159127	CCDS4484.1	6p25.2	2012-10-02	2011-10-10	2005-11-03	ENSG00000137267	ENSG00000137267		"""Tubulins"""	12412	protein-coding gene	gene with protein product	"""class IIa beta-tubulin"""	615101	"""tubulin, beta polypeptide"", ""tubulin, beta 2"", ""tubulin, beta 2A"""	TUBB, TUBB2		14574404	Standard	NM_001069		Approved	dJ40E16.7	uc003mvc.3	Q13885	OTTHUMG00000014135	ENST00000333628.3:c.469delG	chr6.hg19:g.3154966delC	ENSP00000369703:p.Glu158fs	222.0	0.0		320.0	69.0	NM_001069	Q6FGZ8|Q8IWR2	Frame_Shift_Del	DEL	ENST00000333628.3	hg19	CCDS4484.1																																																																																			.	.		0.622	TUBB2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039662.1	NM_001069	
