#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_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_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_Chromosome_hg18	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_End_position_hg18	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_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_Start_position_hg18	i_TranscriptID	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
CRB1	23418	hgsc.bcm.edu	37	1	197391010	197391011	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	-	-	-	-	-	-	Unknown	Wildtype	None	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:197391010_197391011insG	ENST00000367400.3	+	6	2187_2188	c.2052_2053insG	c.(2053-2055)ggafs	p.G685fs	CRB1_ENST00000544212.1_Frame_Shift_Ins_p.G166fs|CRB1_ENST00000535699.1_Frame_Shift_Ins_p.G616fs|CRB1_ENST00000538660.1_Frame_Shift_Ins_p.G685fs|CRB1_ENST00000367397.1_Frame_Shift_Ins_p.G66fs|CRB1_ENST00000543483.1_3'UTR|CRB1_ENST00000367399.2_Frame_Shift_Ins_p.G573fs	NM_201253.2	NP_957705.1	P82279	CRUM1_HUMAN	crumbs family member 1, photoreceptor morphogenesis associated	685	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|plasma membrane organization (GO:0007009)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(13)|kidney(4)|large_intestine(21)|lung(58)|ovary(7)|prostate(3)|skin(10)|upper_aerodigestive_tract(4)|urinary_tract(2)	132						GTCAAAGCAGAGGACGCTGCAT	0.505																																					p.R684fs												.	.	0			c.2052_2053insG	1						.																																			195657634	SO:0001589	frameshift_variant	23418	exon6				CCDS1390.1, CCDS53454.1, CCDS58052.1, CCDS58053.1	1q31-q32.1	2014-02-06	2014-02-06		ENSG00000134376	ENSG00000134376			2343	protein-coding gene	gene with protein product		604210	"""crumbs (Drosophila) homolog 1"", ""crumbs homolog 1 (Drosophila)"""	RP12		10373321, 10508521	Standard	NM_201253		Approved	LCA8	uc001gtz.3	P82279	OTTHUMG00000035663	ENST00000367400.3:c.2054dupG	1.37:g.197391012_197391012dupG	ENSP00000356370:p.Gly685fs		195657633	NM_201253	A2A308|B7Z5T2|B9EG71|Q5K3A6|Q5TC28|Q5VUT1|Q6N027|Q8WWY0|Q8WWY1	Frame_Shift_Ins	INS	ENST00000367400.3	37	CCDS1390.1																																																																																				0.505	CRB1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086565.2	NM_201253	
CDCP2	200008	hgsc.bcm.edu	37	1	54605319	54605320	+	Frame_Shift_Ins	INS	-	-	C	rs77544356|rs66812916|rs36013100|rs66537746|rs75306471|rs549857682	byFrequency	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	-	-	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:54605319_54605320insC	ENST00000371330.1	-	4	2070_2071	c.1223_1224insG	c.(1222-1224)cccfs	p.P408fs	RP11-446E24.4_ENST00000525949.1_5'Flank|CDCP2_ENST00000530059.1_Intron	NM_201546.2	NP_963840.2	Q5VXM1	CDCP2_HUMAN	CUB domain containing protein 2	408						extracellular region (GO:0005576)		p.M409fs*>42(1)		kidney(1)|large_intestine(6)|lung(13)|ovary(1)|prostate(2)|stomach(1)	24						GACCATTCATGGGGGGGGCAGG	0.594													?|-|C|unsure	2403	0.479832	0.3631	0.6614	5008	,	,		16583	0.3889		0.6521	False		,,,				2504	0.4254				p.P408fs												.	.	1	Insertion - Frameshift(1)	large_intestine(1)	c.1224_1225insG	1						.																																			54377908	SO:0001589	frameshift_variant	200008	exon4				CCDS588.2	1p32.3	2011-02-10			ENSG00000157211	ENSG00000157211			27297	protein-coding gene	gene with protein product		612320				12477932	Standard	NM_201546		Approved		uc001cwv.2	Q5VXM1	OTTHUMG00000155307	ENST00000371330.1:c.1223_1224insG	1.37:g.54605319_54605320insC	ENSP00000360381:p.Pro408fs		54377907	NM_201546	Q6ZWJ3	Frame_Shift_Ins	INS	ENST00000371330.1	37	CCDS588.2																																																																																				0.594	CDCP2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000022209.2	NM_201546	
PDE1C	5137	hgsc.bcm.edu	37	7	31864484	31864484	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr7:31864484G>T	ENST00000396191.1	-	13	1858	c.1403C>A	c.(1402-1404)tCg>tAg	p.S468*	PDE1C_ENST00000396182.2_Nonsense_Mutation_p.S468*|PDE1C_ENST00000321453.7_Nonsense_Mutation_p.S468*|PDE1C_ENST00000396193.1_Nonsense_Mutation_p.S528*|PDE1C_ENST00000396184.3_Nonsense_Mutation_p.S468*	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	468	Catalytic. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)	p.S468*(2)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	CACTGACCTCGAACGCCTCTG	0.512																																					p.S468X												.	.	2	Substitution - Nonsense(2)	large_intestine(2)	c.C1403A	7						.						167.0	141.0	150.0					7																	31864484		2203	4300	6503	31831009	SO:0001587	stop_gained	5137	exon13			U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.1403C>A	7.37:g.31864484G>T	ENSP00000379494:p.Ser468*		31831009	NM_001191056	B3KPC6|E9PE92|Q14124|Q8NB10	Nonsense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	G	39	7.344738	0.98224	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453;ENST00000396184;ENST00000396182	.	.	.	5.82	5.82	0.92795	.	0.460721	0.21290	N	0.076982	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.6844	0.95976	0.0:0.0:1.0:0.0	.	.	.	.	X	528;468;468;468;468	.	ENSP00000318105:S468X	S	-	2	0	PDE1C	31831009	1.000000	0.71417	0.927000	0.36925	0.466000	0.32739	9.085000	0.94083	2.761000	0.94854	0.655000	0.94253	TCG		0.512	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
AKAP9	10142	hgsc.bcm.edu	37	7	91603212	91603212	+	Missense_Mutation	SNP	C	C	G			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr7:91603212C>G	ENST00000359028.2	+	3	497	c.272C>G	c.(271-273)cCt>cGt	p.P91R	AKAP9_ENST00000358100.2_Missense_Mutation_p.P91R|AKAP9_ENST00000356239.3_Missense_Mutation_p.P79R|AKAP9_ENST00000394564.1_Missense_Mutation_p.P79R			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	91					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.P91R(1)|p.P79R(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			ACTGTGATTCCTGAATCTACA	0.348			T	BRAF	papillary thyroid																																p.P79R			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	.	2	Substitution - Missense(2)	large_intestine(2)	c.C236G	7						.						72.0	69.0	70.0					7																	91603212		2203	4300	6503	91441148	SO:0001583	missense	10142	exon2			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.272C>G	7.37:g.91603212C>G	ENSP00000351922:p.Pro91Arg		91441148	NM_147185	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	C	11.63	1.694485	0.30052	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564;ENST00000438114	T;T;T;T;T	0.63913	2.61;2.61;2.61;-0.07;-0.07	4.37	4.37	0.52481	.	0.000000	0.36303	N	0.002664	T	0.73313	0.3571	L	0.47716	1.5	0.33866	D	0.634364	D;D;D;D	0.89917	0.998;0.999;0.996;1.0	D;D;D;D	0.91635	0.934;0.983;0.931;0.999	T	0.81263	-0.1012	10	0.72032	D	0.01	.	15.6366	0.76961	0.0:1.0:0.0:0.0	.	79;79;91;79	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	R	79;91;91;91;91;79;48	ENSP00000348573:P79R;ENSP00000351922:P91R;ENSP00000350813:P91R;ENSP00000378065:P79R;ENSP00000391704:P48R	ENSP00000348573:P79R	P	+	2	0	AKAP9	91441148	1.000000	0.71417	0.981000	0.43875	0.354000	0.29330	4.750000	0.62162	2.410000	0.81850	0.637000	0.83480	CCT		0.348	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
RELN	5649	hgsc.bcm.edu	37	7	103243887	103243887	+	Missense_Mutation	SNP	G	G	A	rs116225248		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr7:103243887G>A	ENST00000428762.1	-	24	3356	c.3197C>T	c.(3196-3198)cCg>cTg	p.P1066L	RELN_ENST00000424685.2_Missense_Mutation_p.P1066L|RELN_ENST00000343529.5_Missense_Mutation_p.P1066L	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1066					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)	p.P1066L(1)		NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		AATTGTGGACGGAAGGGCAGC	0.517													G|||	1	0.000199681	0.0	0.0	5008	,	,		19576	0.001		0.0	False		,,,				2504	0.0				p.P1066L	NSCLC(146;835 1944 15585 22231 52158)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3197T	7						.						95.0	92.0	93.0					7																	103243887		2203	4300	6503	103031123	SO:0001583	missense	5649	exon24				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.3197C>T	7.37:g.103243887G>A	ENSP00000392423:p.Pro1066Leu		103031123	NM_005045	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	37	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.640404	0.87859	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.25749	2.09;2.2;1.78	5.45	5.45	0.79879	.	0.060232	0.64402	D	0.000002	T	0.52141	0.1716	M	0.66939	2.045	0.80722	D	1	D;D	0.89917	0.996;1.0	P;D	0.79108	0.823;0.992	T	0.53620	-0.8413	10	0.87932	D	0	.	19.3079	0.94171	0.0:0.0:1.0:0.0	.	1066;1066	P78509-2;P78509	.;RELN_HUMAN	L	1066	ENSP00000392423:P1066L;ENSP00000345694:P1066L;ENSP00000388446:P1066L	ENSP00000345694:P1066L	P	-	2	0	RELN	103031123	1.000000	0.71417	0.995000	0.50966	0.911000	0.54048	9.199000	0.95003	2.550000	0.86006	0.655000	0.94253	CCG		0.517	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
FLRT2	23768	hgsc.bcm.edu	37	14	86089366	86089366	+	Missense_Mutation	SNP	C	C	T	rs190071329		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr14:86089366C>T	ENST00000330753.4	+	2	2275	c.1508C>T	c.(1507-1509)gCg>gTg	p.A503V	FLRT2_ENST00000554746.1_Missense_Mutation_p.A503V	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	503	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)	p.A503V(1)		NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		AACTACCGCGCGGTAGAAGAC	0.537																																					p.A503V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1508T	14						.						131.0	119.0	123.0					14																	86089366		2203	4300	6503	85159119	SO:0001583	missense	23768	exon2			AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1508C>T	14.37:g.86089366C>T	ENSP00000332879:p.Ala503Val		85159119	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	105	0.04807692307692308	28	0.056910569105691054	12	0.03314917127071823	23	0.04020979020979021	42	0.055408970976253295	C	7.482	0.648807	0.14516	.	.	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.56444	0.46;0.46	6.17	6.17	0.99709	Fibronectin, type III (1);	0.164767	0.56097	D	0.000039	T	0.06962	0.0177	L	0.38175	1.15	0.34329	D	0.687504	B	0.09022	0.002	B	0.04013	0.001	T	0.22382	-1.0218	10	0.20519	T	0.43	-6.2272	14.9567	0.71120	0.0:0.9326:0.0:0.0674	.	503	O43155	FLRT2_HUMAN	V	503;503;156	ENSP00000332879:A503V;ENSP00000451050:A503V	ENSP00000332879:A503V	A	+	2	0	FLRT2	85159119	0.998000	0.40836	0.301000	0.25044	0.108000	0.19459	4.031000	0.57267	2.941000	0.99782	0.655000	0.94253	GCG		0.537	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
MOK	5891	hgsc.bcm.edu	37	14	102717311	102717311	+	Nonsense_Mutation	SNP	A	A	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr14:102717311A>T	ENST00000361847.2	-	7	659	c.428T>A	c.(427-429)tTa>tAa	p.L143*	MOK_ENST00000193029.6_5'UTR|MOK_ENST00000522874.1_Nonsense_Mutation_p.L142*|MOK_ENST00000524214.1_Nonsense_Mutation_p.L113*	NM_014226.1	NP_055041.1	Q9UQ07	MOK_HUMAN	MOK protein kinase	143	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.L143*(1)									AAAGTCCCCTAATTTCAGGAC	0.502																																					p.L143X												.	.	1	Substitution - Nonsense(1)	large_intestine(1)	c.T428A	14						.						59.0	64.0	62.0					14																	102717311		2203	4300	6503	101787064	SO:0001587	stop_gained	5891	exon7			AB022694	CCDS9971.1, CCDS61552.1	14q32	2014-04-23	2011-09-06	2011-09-06	ENSG00000080823	ENSG00000080823			9833	protein-coding gene	gene with protein product		605762	"""renal tumor antigen"""	RAGE		8781117, 10421840	Standard	NM_014226		Approved	RAGE1, STK30	uc001ylm.4	Q9UQ07	OTTHUMG00000164896	ENST00000361847.2:c.428T>A	14.37:g.102717311A>T	ENSP00000355304:p.Leu143*		101787064	NM_014226	B2R6Z4|B7Z7P6|E7ER76|E7ERR8|Q92790|Q93067	Nonsense_Mutation	SNP	ENST00000361847.2	37	CCDS9971.1	.	.	.	.	.	.	.	.	.	.	.	15.61	2.884952	0.51908	.	.	ENSG00000080823	ENST00000522874;ENST00000361847;ENST00000524214	.	.	.	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.6057	0.76668	1.0:0.0:0.0:0.0	.	.	.	.	X	142;143;113	.	ENSP00000355304:L143X	L	-	2	0	RAGE	101787064	0.996000	0.38824	0.010000	0.14722	0.625000	0.37756	8.317000	0.89987	2.166000	0.68216	0.533000	0.62120	TTA		0.502	MOK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380848.3		
CCDC116	164592	hgsc.bcm.edu	37	22	21990806	21990806	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr22:21990806G>A	ENST00000292779.3	+	5	1450	c.1289G>A	c.(1288-1290)cGc>cAc	p.R430H		NM_152612.2	NP_689825.2	Q8IYX3	CC116_HUMAN	coiled-coil domain containing 116	430								p.R430H(1)		endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(2)|skin(5)	22	Colorectal(54;0.105)					TTCTCCAACCGCCTTTATGAG	0.587																																					p.R430H												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1289A	22						.						62.0	56.0	58.0					22																	21990806		2203	4300	6503	20320806	SO:0001583	missense	164592	exon5			BC033499	CCDS13791.1	22q11.21	2006-06-27			ENSG00000161180	ENSG00000161180			26688	protein-coding gene	gene with protein product						12477932	Standard	NM_152612		Approved	FLJ36046	uc002zve.3	Q8IYX3	OTTHUMG00000150821	ENST00000292779.3:c.1289G>A	22.37:g.21990806G>A	ENSP00000292779:p.Arg430His		20320806	NM_152612	Q8N9Y9	Missense_Mutation	SNP	ENST00000292779.3	37	CCDS13791.1	.	.	.	.	.	.	.	.	.	.	G	12.88	2.071988	0.36566	.	.	ENSG00000161180	ENST00000292779	T	0.12569	2.67	4.68	3.65	0.41850	.	0.251684	0.28624	N	0.014682	T	0.06781	0.0173	N	0.08118	0	0.09310	N	1	P	0.48350	0.909	B	0.38562	0.276	T	0.20042	-1.0287	10	0.52906	T	0.07	-32.305	10.8237	0.46620	0.0:0.7969:0.2031:0.0	.	430	Q8IYX3-2	.	H	430	ENSP00000292779:R430H	ENSP00000292779:R430H	R	+	2	0	CCDC116	20320806	0.029000	0.19370	0.009000	0.14445	0.000000	0.00434	0.848000	0.27710	1.330000	0.45394	-0.353000	0.07706	CGC		0.587	CCDC116-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320199.1	NM_152612	
TBCB	1155	hgsc.bcm.edu	37	19	36616597	36616597	+	Silent	SNP	C	C	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr19:36616597C>T	ENST00000221855.3	+	6	1223	c.648C>T	c.(646-648)tgC>tgT	p.C216C	TBCB_ENST00000586868.1_3'UTR|TBCB_ENST00000589996.1_3'UTR|TBCB_ENST00000585746.1_Silent_p.C165C	NM_001281.2	NP_001272.2	Q99426	TBCB_HUMAN	tubulin folding cofactor B	216	CAP-Gly. {ECO:0000255|PROSITE- ProRule:PRU00045}.				'de novo' posttranslational protein folding (GO:0051084)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)		p.C216C(1)		large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	5	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			ACTTCGAATGCCAGGCCAAGT	0.562																																					p.C216C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C648T	19						.						260.0	251.0	254.0					19																	36616597		2203	4300	6503	41308437	SO:0001819	synonymous_variant	1155	exon6			AF013488	CCDS12488.1, CCDS74344.1	19q13.11-q13.12	2008-02-05	2006-11-22	2006-11-22	ENSG00000105254	ENSG00000105254			1989	protein-coding gene	gene with protein product		601303	"""cytoskeleton-associated protein 1"", ""cytoskeleton associated protein 1"""	CKAP1		8978778	Standard	NM_001281		Approved	CG22, CKAPI	uc002odg.1	Q99426	OTTHUMG00000048143	ENST00000221855.3:c.648C>T	19.37:g.36616597C>T			41308437	NM_001281	O00111|O00674|O14728|Q6FGY5	Silent	SNP	ENST00000221855.3	37	CCDS12488.1																																																																																				0.562	TBCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000156291.2	NM_001281	
NLRP8	126205	hgsc.bcm.edu	37	19	56465979	56465979	+	Silent	SNP	C	C	T	rs112109260	byFrequency	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr19:56465979C>T	ENST00000291971.3	+	3	626	c.555C>T	c.(553-555)caC>caT	p.H185H	NLRP8_ENST00000590542.1_Silent_p.H185H	NM_176811.2	NP_789781.2	Q86W28	NALP8_HUMAN	NLR family, pyrin domain containing 8	185					neuron death (GO:0070997)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)	p.H185H(1)		breast(4)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|ovary(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)	35		Colorectal(82;0.000147)|Ovarian(87;0.17)		GBM - Glioblastoma multiforme(193;0.0695)		TACACAGGCACGAGGAGTACT	0.502																																					p.H185H												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C555T	19						.						103.0	96.0	99.0					19																	56465979		2203	4300	6503	61157791	SO:0001819	synonymous_variant	126205	exon3			AY154463	CCDS12937.1	19q13.43	2008-02-05	2006-12-08	2006-12-08		ENSG00000179709		"""Nucleotide-binding domain and leucine rich repeat containing"""	22940	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 8"""	609659	"""NACHT, leucine rich repeat and PYD containing 8"""	NALP8		12563287	Standard	NM_176811		Approved	NOD16, PAN4, CLR19.2	uc002qmh.3	Q86W28		ENST00000291971.3:c.555C>T	19.37:g.56465979C>T			61157791	NM_176811	Q7RTR4	Silent	SNP	ENST00000291971.3	37	CCDS12937.1																																																																																				0.502	NLRP8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457462.1	NM_176811	
RGS20	8601	hgsc.bcm.edu	37	8	54852159	54852159	+	Silent	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr8:54852159G>A	ENST00000297313.3	+	3	626	c.534G>A	c.(532-534)gaG>gaA	p.E178E	RGS20_ENST00000344277.6_Silent_p.E63E|RGS20_ENST00000522225.1_Intron|RGS20_ENST00000276500.4_Silent_p.E31E	NM_170587.2	NP_733466.1	O76081	RGS20_HUMAN	regulator of G-protein signaling 20	178					positive regulation of GTPase activity (GO:0043547)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.E178E(1)		breast(2)|endometrium(1)|large_intestine(6)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	21			OV - Ovarian serous cystadenocarcinoma(7;1.37e-06)|Epithelial(17;0.000126)|all cancers(17;0.0009)			AGCGGATGGAGATGCGGAAGC	0.667																																					p.E178E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G534A	8						.						16.0	21.0	19.0					8																	54852159		2199	4298	6497	55014712	SO:0001819	synonymous_variant	8601	exon3			AF074979	CCDS6155.1, CCDS6156.1, CCDS69482.1	8q11.23	2008-07-25	2007-08-14		ENSG00000147509	ENSG00000147509		"""Regulators of G-protein signaling"""	14600	protein-coding gene	gene with protein product		607193	"""regulator of G-protein signalling 20"""			9748279, 9748280	Standard	NM_003702		Approved	RGSZ1, ZGAP1	uc003xrp.3	O76081	OTTHUMG00000164750	ENST00000297313.3:c.534G>A	8.37:g.54852159G>A			55014712	NM_170587	Q96BG9	Silent	SNP	ENST00000297313.3	37	CCDS6155.1																																																																																				0.667	RGS20-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000380058.1		
AMPD2	271	hgsc.bcm.edu	37	1	110170090	110170090	+	Silent	SNP	A	A	G			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:110170090A>G	ENST00000256578.3	+	8	1422	c.1062A>G	c.(1060-1062)gaA>gaG	p.E354E	AMPD2_ENST00000342115.4_Silent_p.E273E|AMPD2_ENST00000358729.4_Silent_p.E279E|AMPD2_ENST00000393688.3_Silent_p.E235E|AMPD2_ENST00000528667.1_Silent_p.E354E|AMPD2_ENST00000528454.1_Silent_p.E236E|AMPD2_ENST00000526301.1_3'UTR|RP5-1160K1.6_ENST00000369843.3_RNA	NM_004037.7	NP_004028.3	Q01433	AMPD2_HUMAN	adenosine monophosphate deaminase 2	354					cell death (GO:0008219)|cyclic purine nucleotide metabolic process (GO:0052652)|energy homeostasis (GO:0097009)|IMP biosynthetic process (GO:0006188)|IMP salvage (GO:0032264)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	AMP deaminase activity (GO:0003876)|metal ion binding (GO:0046872)	p.E354E(1)		breast(1)|large_intestine(3)|ovary(2)|skin(1)	7		all_epithelial(167;2.5e-05)|all_lung(203;0.000135)|Lung NSC(277;0.000269)|Breast(1374;0.244)		Lung(183;0.0425)|all cancers(265;0.0884)|Colorectal(144;0.109)|Epithelial(280;0.111)|LUSC - Lung squamous cell carcinoma(189;0.228)		ACCTGCAGGAATTTGTGGCTG	0.597																																					p.E354E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1062G	1						.						169.0	163.0	165.0					1																	110170090		2203	4300	6503	109971613	SO:0001819	synonymous_variant	271	exon8			S47833	CCDS804.1, CCDS805.1, CCDS30796.1, CCDS58016.1	1p13.3	2014-03-03	2010-02-10		ENSG00000116337	ENSG00000116337	3.5.4.6		469	protein-coding gene	gene with protein product	"""AMPD isoform L"""	102771	"""adenosine monophosphate deaminase 2 (isoform L)"""			1400401, 24482476	Standard	NM_004037		Approved	SPG63	uc009wfh.2	Q01433	OTTHUMG00000011649	ENST00000256578.3:c.1062A>G	1.37:g.110170090A>G			109971613	NM_004037	B4DK50|B4DZI5|E9PNG0|Q14856|Q14857|Q16686|Q16687|Q16688|Q16729|Q5T693|Q5T695|Q96IA1|Q9UDX8|Q9UDX9|Q9UMU4	Silent	SNP	ENST00000256578.3	37	CCDS805.1	.	.	.	.	.	.	.	.	.	.	A	9.659	1.143722	0.21205	.	.	ENSG00000116337	ENST00000369840	.	.	.	4.98	-0.0898	0.13667	.	.	.	.	.	T	0.42832	0.1220	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.38845	-0.9642	4	.	.	.	-18.702	9.7524	0.40483	0.4249:0.0:0.5751:0.0	.	.	.	.	V	325	.	.	I	+	1	0	AMPD2	109971613	1.000000	0.71417	0.997000	0.53966	0.993000	0.82548	0.949000	0.29109	-0.123000	0.11745	0.379000	0.24179	ATT		0.597	AMPD2-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000390615.1		
SIKE1	80143	hgsc.bcm.edu	37	1	115323085	115323085	+	Silent	SNP	T	T	C			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	T	T	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:115323085T>C	ENST00000060969.5	-	1	213	c.144A>G	c.(142-144)acA>acG	p.T48T	SIKE1_ENST00000506320.1_5'UTR|SIKE1_ENST00000369528.5_Silent_p.T48T			Q9BRV8	SIKE1_HUMAN	suppressor of IKBKE 1	48					innate immune response (GO:0045087)	cytosol (GO:0005829)				endometrium(1)|kidney(2)|large_intestine(1)|lung(2)	6						CCGGAAGCGCTGTCCCCGCCT	0.667																																					p.T48T												.	.	0			c.A144G	1						.						32.0	39.0	37.0					1																	115323085		2203	4300	6503	115124608	SO:0001819	synonymous_variant	80143	exon1			AK024821	CCDS878.1, CCDS41371.1	1p13.1	2009-08-13			ENSG00000052723	ENSG00000052723			26119	protein-coding gene	gene with protein product	"""suppressor of IKK epsilon"""	611656				16281057	Standard	NM_025073		Approved	FLJ21168, SIKE	uc001efp.4	Q9BRV8	OTTHUMG00000012061	ENST00000060969.5:c.144A>G	1.37:g.115323085T>C			115124608	NM_025073	Q5TEZ7|Q5TEZ9|Q68DZ4|Q9H778	Silent	SNP	ENST00000060969.5	37	CCDS878.1																																																																																				0.667	SIKE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033401.1	NM_025073	
FLG2	388698	hgsc.bcm.edu	37	1	152323648	152323648	+	Missense_Mutation	SNP	C	C	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:152323648C>A	ENST00000388718.5	-	3	6686	c.6614G>T	c.(6613-6615)gGa>gTa	p.G2205V	FLG-AS1_ENST00000392688.2_RNA|FLG-AS1_ENST00000445097.1_RNA	NM_001014342.2	NP_001014364.1	Q5D862	FILA2_HUMAN	filaggrin family member 2	2205					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)	p.G2205V(1)		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)			ATGTCGAGATCCGGCTTGGCT	0.507																																					p.G2205V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G6614T	1						.						400.0	349.0	366.0					1																	152323648		2203	4300	6503	150590272	SO:0001583	missense	388698	exon3			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.6614G>T	1.37:g.152323648C>A	ENSP00000373370:p.Gly2205Val		150590272	NM_001014342	Q9H4U1	Missense_Mutation	SNP	ENST00000388718.5	37	CCDS30861.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.005689	0.35415	.	.	ENSG00000143520	ENST00000388718	T	0.52983	0.64	4.0	0.865	0.19074	.	.	.	.	.	T	0.47911	0.1471	M	0.79926	2.475	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.23261	-1.0193	9	0.37606	T	0.19	-0.1979	4.2172	0.10540	0.0:0.5874:0.1907:0.2219	.	2205	Q5D862	FILA2_HUMAN	V	2205	ENSP00000373370:G2205V	ENSP00000373370:G2205V	G	-	2	0	FLG2	150590272	0.090000	0.21635	0.001000	0.08648	0.005000	0.04900	0.878000	0.28126	0.091000	0.17302	0.551000	0.68910	GGA		0.507	FLG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034018.5	NM_001014342	
PKLR	5313	hgsc.bcm.edu	37	1	155263259	155263259	+	Silent	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:155263259G>A	ENST00000342741.4	-	8	1277	c.1239C>T	c.(1237-1239)ttC>ttT	p.F413F	PKLR_ENST00000392414.3_Silent_p.F382F	NM_000298.5	NP_000289.1	P30613	KPYR_HUMAN	pyruvate kinase, liver and RBC	413					ATP biosynthetic process (GO:0006754)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|endocrine pancreas development (GO:0031018)|energy reserve metabolic process (GO:0006112)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|positive regulation of cellular metabolic process (GO:0031325)|pyruvate biosynthetic process (GO:0042866)|response to ATP (GO:0033198)|response to cAMP (GO:0051591)|response to glucose (GO:0009749)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to lithium ion (GO:0010226)|response to nutrient (GO:0007584)|response to other organism (GO:0051707)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|potassium ion binding (GO:0030955)|pyruvate kinase activity (GO:0004743)	p.F413F(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	35	all_lung(78;6.99e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;3.18e-10)|all cancers(21;7.9e-10)|BRCA - Breast invasive adenocarcinoma(34;0.00116)|LUSC - Lung squamous cell carcinoma(543;0.127)		Pyruvic acid(DB00119)	CTTCCACAGGGAAGTTGCCCT	0.587																																					p.F413F												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C1239T	1						.						81.0	70.0	74.0					1																	155263259		2203	4300	6503	153529883	SO:0001819	synonymous_variant	5313	exon8			BC025737, M15465	CCDS1109.1, CCDS44240.1	1q22	2012-10-02			ENSG00000143627	ENSG00000143627	2.7.1.40		9020	protein-coding gene	gene with protein product		609712				3566732	Standard	NM_000298		Approved		uc001fkb.4	P30613	OTTHUMG00000035875	ENST00000342741.4:c.1239C>T	1.37:g.155263259G>A			153529883	NM_000298	O75758|P11973	Silent	SNP	ENST00000342741.4	37	CCDS1109.1																																																																																				0.587	PKLR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000087407.2	NM_000298	
EXTL1	2134	hgsc.bcm.edu	37	1	26349888	26349888	+	Missense_Mutation	SNP	C	C	T	rs116675357		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:26349888C>T	ENST00000374280.3	+	1	1618	c.751C>T	c.(751-753)Cgc>Tgc	p.R251C	EXTL1_ENST00000484339.1_3'UTR	NM_004455.2	NP_004446.2	Q92935	EXTL1_HUMAN	exostosin-like glycosyltransferase 1	251					protein glycosylation (GO:0006486)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)	p.R251C(1)		central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(1)|stomach(1)|urinary_tract(1)	23		Colorectal(325;3.46e-05)|Lung NSC(340;6.18e-05)|all_lung(284;9.43e-05)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0298)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|OV - Ovarian serous cystadenocarcinoma(117;6.44e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|BRCA - Breast invasive adenocarcinoma(304;0.000954)|STAD - Stomach adenocarcinoma(196;0.00151)|GBM - Glioblastoma multiforme(114;0.00594)|READ - Rectum adenocarcinoma(331;0.0649)		CTGGGATGGGCGCTGTGAGCA	0.642													C|||	1	0.000199681	0.0	0.0	5008	,	,		17299	0.0		0.001	False		,,,				2504	0.0				p.R251C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C751T	1						.	C	CYS/ARG	1,4265		0,1,2132	11.0	8.0	9.0		751	3.2	0.2	1	dbSNP_132	9	0,8354		0,0,4177	no	missense	EXTL1	NM_004455.2	180	0,1,6309	TT,TC,CC		0.0,0.0234,0.0079	probably-damaging	251/677	26349888	1,12619	2133	4177	6310	26222475	SO:0001583	missense	2134	exon1			U67191	CCDS271.1	1p36.1	2013-03-01	2013-03-01		ENSG00000158008	ENSG00000158008	2.4.1.224	"""Exostosin glycosyltransferase family"""	3515	protein-coding gene	gene with protein product	"""glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""alpha-N-acetylglucosaminyltransferase II"", ""glucuronyl-N-acetylglucosaminylproteoglycan alpha-1,4-N- acetylglucosaminyltransferase"", ""exostosin-L"""	601738	"""exostoses (multiple)-like 1"""			9037597	Standard	NM_004455		Approved	EXTL, MGC70794	uc001blf.3	Q92935	OTTHUMG00000007509	ENST00000374280.3:c.751C>T	1.37:g.26349888C>T	ENSP00000363398:p.Arg251Cys		26222475	NM_004455	Q6GSC1	Missense_Mutation	SNP	ENST00000374280.3	37	CCDS271.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	13.22	2.170783	0.38315	2.34E-4	0.0	ENSG00000158008	ENST00000374280	D	0.97688	-4.49	5.08	3.15	0.36227	.	0.590841	0.17965	N	0.156049	D	0.98523	0.9507	M	0.82517	2.595	0.42012	D	0.990943	D	0.89917	1.0	D	0.76575	0.988	D	0.98735	1.0714	10	0.87932	D	0	-2.2911	12.6713	0.56868	0.2986:0.7014:0.0:0.0	.	251	Q92935	EXTL1_HUMAN	C	251	ENSP00000363398:R251C	ENSP00000363398:R251C	R	+	1	0	EXTL1	26222475	0.600000	0.26899	0.212000	0.23672	0.078000	0.17371	0.993000	0.29680	0.786000	0.33708	0.655000	0.94253	CGC		0.642	EXTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019749.1	NM_004455	
NFIA	4774	hgsc.bcm.edu	37	1	61872295	61872295	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:61872295C>T	ENST00000403491.3	+	9	1800	c.1316C>T	c.(1315-1317)cCg>cTg	p.P439L	NFIA_ENST00000371184.2_Missense_Mutation_p.P310L|NFIA_ENST00000357977.5_Missense_Mutation_p.P87L|NFIA_ENST00000407417.3_Missense_Mutation_p.P431L|NFIA_ENST00000371189.4_Missense_Mutation_p.P484L|NFIA_ENST00000371185.2_Missense_Mutation_p.P417L|NFIA_ENST00000479364.1_3'UTR|NFIA_ENST00000371191.1_Missense_Mutation_p.P462L|NFIA_ENST00000371187.3_Missense_Mutation_p.P439L|NFIA_ENST00000485903.2_Missense_Mutation_p.P396L	NM_001134673.3|NM_005595.4	NP_001128145.1|NP_005586.1	Q12857	NFIA_HUMAN	nuclear factor I/A	439					DNA replication (GO:0006260)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to organic cyclic compound (GO:0014070)|viral genome replication (GO:0019079)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.P439L(1)	NFIA/EHF(2)	endometrium(1)|kidney(2)|large_intestine(8)|lung(20)|pancreas(1)|prostate(1)|skin(1)	34						ATGTTGCCACCGCCACCGCCA	0.632																																					p.P484L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C1451T	1						.						56.0	42.0	47.0					1																	61872295		2203	4300	6503	61644883	SO:0001583	missense	4774	exon10			U07809	CCDS615.1, CCDS44156.1, CCDS53322.1, CCDS53321.1	1p31.3-p31.2	2008-02-05			ENSG00000162599	ENSG00000162599			7784	protein-coding gene	gene with protein product		600727				7590749	Standard	NM_001134673		Approved	NFI-L, KIAA1439	uc010oos.2	Q12857	OTTHUMG00000008618	ENST00000403491.3:c.1316C>T	1.37:g.61872295C>T	ENSP00000384523:p.Pro439Leu		61644883	NM_001145512	B4DRJ3|B4DS53|F5H0R0|F8W8W3|Q8TA97|Q9H3X9|Q9P2A9	Missense_Mutation	SNP	ENST00000403491.3	37	CCDS44156.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221034	0.79464	.	.	ENSG00000162599	ENST00000371191;ENST00000407417;ENST00000371189;ENST00000403491;ENST00000485903;ENST00000371185;ENST00000371184;ENST00000371187	T;T;T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;0.74;-0.04;-0.04	5.99	5.99	0.97316	.	0.049314	0.85682	D	0.000000	T	0.78181	0.4243	L	0.58510	1.815	0.80722	D	1	P;B;D;B;D	0.89917	0.883;0.158;1.0;0.158;0.999	B;B;D;B;D	0.81914	0.285;0.066;0.995;0.105;0.992	T	0.77262	-0.2653	10	0.62326	D	0.03	-18.5814	20.4756	0.99175	0.0:1.0:0.0:0.0	.	484;462;417;439;439	F8W8W3;B1AKN8;B1AKN5;Q12857;Q12857-2	.;.;.;NFIA_HUMAN;.	L	462;431;484;439;439;417;310;396	ENSP00000360233:P462L;ENSP00000384680:P431L;ENSP00000360231:P484L;ENSP00000384523:P439L;ENSP00000419785:P439L;ENSP00000360227:P417L;ENSP00000360226:P310L	ENSP00000360226:P310L	P	+	2	0	NFIA	61644883	1.000000	0.71417	0.992000	0.48379	0.957000	0.61999	7.298000	0.78815	2.847000	0.97988	0.655000	0.94253	CCG		0.632	NFIA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023799.3	NM_005595	
GBP6	163351	hgsc.bcm.edu	37	1	89844132	89844134	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	AGA	AGA	AGA	-	AGA	AGA	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:89844132_89844134delAGA	ENST00000370456.4	+	5	678_680	c.585_587delAGA	c.(583-588)acagaa>aca	p.E196del	GBP6_ENST00000535065.1_In_Frame_Del_p.E66del	NM_198460.2	NP_940862.2	Q6ZN66	GBP6_HUMAN	guanylate binding protein family, member 6	196	GB1/RHD3-type G.|GTPase domain (Globular). {ECO:0000250}.				cellular response to interferon-gamma (GO:0071346)|defense response to bacterium (GO:0042742)|immune response (GO:0006955)	extracellular vesicular exosome (GO:0070062)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)	p.E196delE(1)		breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(8)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42		Lung NSC(277;0.0908)		all cancers(265;0.0108)|Epithelial(280;0.0398)		ACCCTATCACAGAAGATGAATAC	0.483																																					p.195_196del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.585_587del	1						.																																			89616722	SO:0001651	inframe_deletion	163351	exon5			BX537949	CCDS723.1	1p22	2008-02-05			ENSG00000183347	ENSG00000183347			25395	protein-coding gene	gene with protein product		612467					Standard	NM_198460		Approved	DKFZp686G0786	uc001dnf.2	Q6ZN66	OTTHUMG00000010123	ENST00000370456.4:c.585_587delAGA	1.37:g.89844135_89844137delAGA	ENSP00000359485:p.Glu196del		89616720	NM_198460	A2RRM3|Q6ZN86|Q7Z3F0	In_Frame_Del	DEL	ENST00000370456.4	37	CCDS723.1																																																																																				0.483	GBP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028001.1	NM_198460	
SERPINC1	462	hgsc.bcm.edu	37	1	173878723	173878723	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr1:173878723C>T	ENST00000367698.3	-	5	1238	c.1120G>A	c.(1120-1122)Gat>Aat	p.D374N	SERPINC1_ENST00000494024.1_5'Flank	NM_000488.3	NP_000479.1	P01008	ANT3_HUMAN	serpin peptidase inhibitor, clade C (antithrombin), member 1	374					blood coagulation (GO:0007596)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of inflammatory response (GO:0050728)|regulation of blood coagulation, intrinsic pathway (GO:2000266)|regulation of proteolysis (GO:0030162)|response to nutrient (GO:0007584)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protease binding (GO:0002020)|serine-type endopeptidase inhibitor activity (GO:0004867)	p.D374N(1)		NS(1)|endometrium(2)|large_intestine(5)|liver(1)|lung(15)|ovary(1)	25					Ardeparin(DB00407)|Dalteparin(DB06779)|Enoxaparin(DB01225)|Fondaparinux sodium(DB00569)|Heparin(DB01109)|Nadroparin(DB08813)|Sulodexide(DB06271)|Tinzaparin(DB06822)	CTGAACAGATCGACAAGGCCC	0.527																																					p.D374N												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1120A	1						.						76.0	78.0	77.0					1																	173878723		2203	4300	6503	172145346	SO:0001583	missense	462	exon5			X68793	CCDS1313.1	1q25.1	2014-02-18	2005-08-18		ENSG00000117601	ENSG00000117601		"""Serine (or cysteine) peptidase inhibitors"""	775	protein-coding gene	gene with protein product	"""antithrombin III"", ""signal peptide antithrombin part 1"", ""coding sequence signal peptide antithrombin part 1"", ""antithrombin (aa 375-432)"""	107300	"""serine (or cysteine) proteinase inhibitor, clade C (antithrombin), member 1"""	AT3		3979120, 24172014	Standard	NM_000488		Approved	ATIII, MGC22579	uc001gjt.3	P01008	OTTHUMG00000037276	ENST00000367698.3:c.1120G>A	1.37:g.173878723C>T	ENSP00000356671:p.Asp374Asn		172145346	NM_000488	B2R6P0|P78439|P78447|Q13815|Q5TC78|Q7KZ43|Q7KZ97|Q9UC78	Missense_Mutation	SNP	ENST00000367698.3	37	CCDS1313.1	.	.	.	.	.	.	.	.	.	.	C	27.3	4.815362	0.90790	.	.	ENSG00000117601	ENST00000367698	D	0.84223	-1.82	5.32	5.32	0.75619	Serpin domain (3);	0.000000	0.85682	D	0.000000	D	0.91768	0.7396	M	0.83118	2.625	0.80722	D	1	D	0.76494	0.999	D	0.68483	0.958	D	0.91912	0.5540	10	0.54805	T	0.06	.	18.6879	0.91571	0.0:1.0:0.0:0.0	.	374	P01008	ANT3_HUMAN	N	374	ENSP00000356671:D374N	ENSP00000356671:D374N	D	-	1	0	SERPINC1	172145346	1.000000	0.71417	0.681000	0.30009	0.709000	0.40893	5.638000	0.67861	2.512000	0.84698	0.650000	0.86243	GAT		0.527	SERPINC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090734.1	NM_000488	
CD44	960	hgsc.bcm.edu	37	11	35198160	35198160	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr11:35198160G>A	ENST00000428726.2	+	2	229	c.106G>A	c.(106-108)Gtg>Atg	p.V36M	CD44_ENST00000437706.2_Missense_Mutation_p.V36M|CD44_ENST00000433354.2_Missense_Mutation_p.V36M|CD44_ENST00000263398.6_Missense_Mutation_p.V36M|CD44_ENST00000352818.4_Missense_Mutation_p.V36M|CD44_ENST00000433892.2_Missense_Mutation_p.V36M|CD44_ENST00000415148.2_Missense_Mutation_p.V36M|CD44_ENST00000449691.2_Missense_Mutation_p.V36M|CD44_ENST00000526669.2_Missense_Mutation_p.V36M|CD44_ENST00000434472.2_Missense_Mutation_p.V36M|CD44_ENST00000360158.4_Missense_Mutation_p.V36M|CD44_ENST00000526025.1_Missense_Mutation_p.V36M|CD44_ENST00000278386.6_Missense_Mutation_p.V36M	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	36	Link. {ECO:0000255|PROSITE- ProRule:PRU00323}.				blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)	p.V36M(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	TGTATTCCACGTGGAGAAAAA	0.443																																					p.V36M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G106A	11						.						47.0	47.0	47.0					11																	35198160		2202	4298	6500	35154736	SO:0001583	missense	960	exon2			M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.106G>A	11.37:g.35198160G>A	ENSP00000398632:p.Val36Met		35154736	NM_001001389	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	37	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.8|20.8	4.051856|4.051856	0.75960|0.75960	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000442151|ENST00000263398;ENST00000526025;ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000360158;ENST00000428726;ENST00000433892;ENST00000278386;ENST00000434472;ENST00000352818;ENST00000525211;ENST00000526669;ENST00000526000	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.10573	.|2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86;2.86	5.85|5.85	5.85|5.85	0.93711|0.93711	.|C-type lectin fold (1);Link (3);C-type lectin-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.37785|0.37785	0.1016|0.1016	M|M	0.82056|0.82056	2.57|2.57	0.58432|0.58432	D|D	0.999996|0.999996	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;0.999;1.0	.|D;D;D;D;D;D;D	.|0.97110	.|1.0;0.999;1.0;1.0;0.999;0.993;0.996	T|T	0.09037|0.09037	-1.0693|-1.0693	5|10	.|0.87932	.|D	.|0	-22.4765|-22.4765	17.6713|17.6713	0.88218|0.88218	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|36;36;36;36;36;36;36	.|B6EAT9;P16070-11;O95370;P16070-12;P16070-10;P16070-4;P16070	.|.;.;.;.;.;.;CD44_HUMAN	H|M	35|36;36;36;36;36;36;36;36;36;36;36;36;15;15;14	.|ENSP00000263398:V36M;ENSP00000435377:V36M;ENSP00000389830:V36M;ENSP00000414567:V36M;ENSP00000391008:V36M;ENSP00000403990:V36M;ENSP00000353280:V36M;ENSP00000398632:V36M;ENSP00000392331:V36M;ENSP00000278386:V36M;ENSP00000404447:V36M;ENSP00000309732:V36M;ENSP00000432405:V15M;ENSP00000434465:V14M	.|ENSP00000263398:V36M	R|V	+|+	2|1	0|0	CD44|CD44	35154736|35154736	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.750000|0.750000	0.42670|0.42670	6.305000|6.305000	0.72805|0.72805	2.771000|2.771000	0.95319|0.95319	0.561000|0.561000	0.74099|0.74099	CGT|GTG		0.443	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
KRTAP5-5	439915	hgsc.bcm.edu	37	11	1651120	1651120	+	Missense_Mutation	SNP	G	G	T	rs66665994		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr11:1651120G>T	ENST00000399676.2	+	1	88	c.50G>T	c.(49-51)cGt>cTt	p.R17L		NM_001001480.2	NP_001001480.2	Q701N2	KRA55_HUMAN	keratin associated protein 5-5	17				R -> L (in Ref. 1; BAD20201 and 2; CAF31639). {ECO:0000305}.		keratin filament (GO:0045095)		p.R17L(2)		endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(17)|ovary(2)|prostate(5)|urinary_tract(1)	33		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		tgtggaggccgtggctccggc	0.697																																					p.R17L												KRTAP5-5,lung,NS,Substitution - Missense,+1	.	2	Substitution - Missense(2)	ovary(1)|large_intestine(1)	c.G50T	11						.						49.0	62.0	58.0					11																	1651120		2185	4288	6473	1607696	SO:0001583	missense	439915	exon1			AB125074	CCDS41592.1	11p15.5	2008-10-30			ENSG00000185940	ENSG00000185940		"""Keratin associated proteins"""	23601	protein-coding gene	gene with protein product						15144888	Standard	NM_001001480		Approved	KRTAP5.5, KRTAP5-11	uc001lty.3	Q701N2	OTTHUMG00000057554	ENST00000399676.2:c.50G>T	11.37:g.1651120G>T	ENSP00000382584:p.Arg17Leu		1607696	NM_001001480	A8MWN2	Missense_Mutation	SNP	ENST00000399676.2	37	CCDS41592.1	1029	0.47115384615384615	280	0.5691056910569106	162	0.44751381215469616	221	0.38636363636363635	366	0.48284960422163586	G	7.595	0.671480	0.14776	.	.	ENSG00000185940	ENST00000399676;ENST00000422553	T	0.01005	5.45	2.63	2.63	0.31362	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.49389	P	2.1099999999996122E-4	B	0.24963	0.115	B	0.14023	0.01	T	0.01504	-1.1338	8	0.44086	T	0.13	.	9.323	0.37975	0.0:0.0:1.0:0.0	.	17	Q701N2	KRA55_HUMAN	L	17;15	ENSP00000382584:R17L	ENSP00000382584:R17L	R	+	2	0	KRTAP5-5	1607696	1.000000	0.71417	0.817000	0.32601	0.004000	0.04260	3.925000	0.56484	1.420000	0.47138	0.442000	0.29010	CGT		0.697	KRTAP5-5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000127919.1		
MYRF	745	hgsc.bcm.edu	37	11	61547731	61547731	+	Missense_Mutation	SNP	C	C	T	rs150031578		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr11:61547731C>T	ENST00000278836.5	+	18	2470	c.2374C>T	c.(2374-2376)Cgc>Tgc	p.R792C	MYRF_ENST00000389602.4_Missense_Mutation_p.R183C|MYRF_ENST00000265460.5_Missense_Mutation_p.R783C|TMEM258_ENST00000535042.1_Intron|MYRF_ENST00000327797.1_Missense_Mutation_p.A474V	NM_001127392.1	NP_001120864.1	Q9Y2G1	MRF_HUMAN	myelin regulatory factor	792					central nervous system myelin maintenance (GO:0032286)|central nervous system myelination (GO:0022010)|oligodendrocyte development (GO:0014003)|oligodendrocyte differentiation (GO:0048709)|positive regulation of myelination (GO:0031643)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R783C(1)									GCTGAGCCTGCGCACAGAGGA	0.612																																					p.R783C												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C2347T	11						.	C	CYS/ARG,CYS/ARG	1,4403	2.1+/-5.4	0,1,2201	88.0	70.0	76.0		2374,2347	4.9	1.0	11	dbSNP_134	76	0,8598		0,0,4299	no	missense,missense	C11orf9	NM_001127392.1,NM_013279.2	180,180	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	probably-damaging,probably-damaging	792/1152,783/1112	61547731	1,13001	2202	4299	6501	61304307	SO:0001583	missense	745	exon18				CCDS31579.1, CCDS44622.1	11q12-q13.1	2012-12-19	2012-12-19	2012-12-19	ENSG00000124920	ENSG00000124920			1181	protein-coding gene	gene with protein product	"""myelin gene regulatory factor"""	608329	"""chromosome 11 open reading frame 9"""	C11orf9		10828591, 12384578	Standard	NM_001127392		Approved	Ndt80, pqn-47, MRF	uc001nsc.1	Q9Y2G1	OTTHUMG00000168161	ENST00000278836.5:c.2374C>T	11.37:g.61547731C>T	ENSP00000278836:p.Arg792Cys		61304307	NM_013279	O43582|Q9P1Q6	Missense_Mutation	SNP	ENST00000278836.5	37	CCDS44622.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	34|34	5.366121|5.366121	0.95900|0.95900	2.27E-4|2.27E-4	0.0|0.0	ENSG00000124920|ENSG00000124920	ENST00000327797|ENST00000278836;ENST00000265460;ENST00000389602	T|T;T;T	0.47177|0.36520	0.85|1.26;1.31;1.25	4.86|4.86	4.86|4.86	0.63082|0.63082	.|.	.|0.053510	.|0.85682	.|D	.|0.000000	T|T	0.59142|0.59142	0.2172|0.2172	M|M	0.62723|0.62723	1.935|1.935	0.37236|0.37236	D|D	0.905908|0.905908	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.77557	.|0.983;0.99;0.973	T|T	0.67373|0.67373	-0.5687|-0.5687	7|10	0.87932|0.87932	D|D	0|0	-29.3023|-29.3023	18.3723|18.3723	0.90411|0.90411	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|183;783;792	.|B4DHB2;Q9Y2G1-2;Q9Y2G1	.|.;.;MRF_HUMAN	V|C	474|792;783;183	ENSP00000333261:A474V|ENSP00000278836:R792C;ENSP00000265460:R783C;ENSP00000374253:R183C	ENSP00000333261:A474V|ENSP00000265460:R783C	A|R	+|+	2|1	0|0	C11orf9|C11orf9	61304307|61304307	1.000000|1.000000	0.71417|0.71417	0.997000|0.997000	0.53966|0.53966	0.962000|0.962000	0.63368|0.63368	6.672000|6.672000	0.74477|0.74477	2.410000|2.410000	0.81850|0.81850	0.561000|0.561000	0.74099|0.74099	GCG|CGC		0.612	MYRF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398519.2	NM_013279	
JARID2	3720	hgsc.bcm.edu	37	6	15487585	15487585	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr6:15487585A>C	ENST00000341776.2	+	6	962	c.718A>C	c.(718-720)Aaa>Caa	p.K240Q	JARID2_ENST00000397311.3_Missense_Mutation_p.K68Q|JARID2_ENST00000541660.1_Missense_Mutation_p.K202Q	NM_004973.3	NP_004964.2	Q92833	JARD2_HUMAN	jumonji, AT rich interactive domain 2	240					central nervous system development (GO:0007417)|chromatin modification (GO:0016568)|liver development (GO:0001889)|negative regulation of cell proliferation (GO:0008285)|negative regulation of histone methylation (GO:0031061)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K9 methylation (GO:0051574)|spleen development (GO:0048536)|stem cell differentiation (GO:0048863)|thymus development (GO:0048538)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.K240Q(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(10)|kidney(2)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	59	Breast(50;0.0142)|Ovarian(93;0.103)	all_hematologic(90;0.00612)				ACCTGTTCAAAAACACAAAAG	0.532																																					p.K240Q												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.A718C	6						.						111.0	100.0	104.0					6																	15487585		2203	4300	6503	15595564	SO:0001583	missense	3720	exon6			U57592	CCDS4533.1, CCDS58996.1	6p24-p23	2008-02-05	2006-10-06	2004-01-30	ENSG00000008083	ENSG00000008083			6196	protein-coding gene	gene with protein product		601594	"""jumonji (mouse) homolog"", ""Jumonji, AT rich interactive domain 2"""	JMJ		8894700	Standard	NM_001267040		Approved		uc003nbj.4	Q92833	OTTHUMG00000014293	ENST00000341776.2:c.718A>C	6.37:g.15487585A>C	ENSP00000341280:p.Lys240Gln		15595564	NM_004973	A8K9Z6|B7Z5S5|B7Z8L0|Q5U5L5|Q86X63	Missense_Mutation	SNP	ENST00000341776.2	37	CCDS4533.1	.	.	.	.	.	.	.	.	.	.	A	17.30	3.353562	0.61293	.	.	ENSG00000008083	ENST00000538175;ENST00000341776;ENST00000397311;ENST00000541660	T;T;T	0.35421	1.31;1.31;1.31	5.42	5.42	0.78866	.	0.141453	0.52532	D	0.000073	T	0.15782	0.0380	N	0.24115	0.695	0.37120	D	0.90078	P;P;B	0.40431	0.617;0.717;0.335	B;B;B	0.39738	0.308;0.291;0.116	T	0.04255	-1.0965	10	0.30078	T	0.28	-9.8087	15.7416	0.77901	1.0:0.0:0.0:0.0	.	202;104;240	F5H590;B7Z7X9;Q92833	.;.;JARD2_HUMAN	Q	104;240;68;202	ENSP00000341280:K240Q;ENSP00000380478:K68Q;ENSP00000444623:K202Q	ENSP00000341280:K240Q	K	+	1	0	JARID2	15595564	1.000000	0.71417	0.951000	0.38953	0.996000	0.88848	7.121000	0.77160	2.168000	0.68352	0.533000	0.62120	AAA		0.532	JARID2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039926.1	NM_004973	
BTN2A1	11120	hgsc.bcm.edu	37	6	26465488	26465488	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr6:26465488C>T	ENST00000312541.5	+	5	1036	c.788C>T	c.(787-789)gCc>gTc	p.A263V	BTN2A1_ENST00000541522.1_Missense_Mutation_p.A202V|BTN2A1_ENST00000429381.1_Missense_Mutation_p.A263V|BTN2A1_ENST00000469185.1_Missense_Mutation_p.A263V	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	263					lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)		p.A263V(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						ATACCCATTGCCGTATGCATC	0.428																																					p.A263V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C788T	6						.						157.0	155.0	156.0					6																	26465488		2203	4300	6503	26573467	SO:0001583	missense	11120	exon5			U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.788C>T	6.37:g.26465488C>T	ENSP00000312158:p.Ala263Val		26573467	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.50|14.50	2.553849|2.553849	0.45487|0.45487	.|.	.|.	ENSG00000112763|ENSG00000112763	ENST00000312541;ENST00000541522;ENST00000429381;ENST00000265424;ENST00000469185|ENST00000480218	T;T;T;T|.	0.78003|.	-0.5;1.09;-1.13;-1.14|.	3.64|3.64	-0.299|-0.299	0.12808|0.12808	.|.	0.503907|.	0.16592|.	N|.	0.207727|.	T|T	0.26882|0.26882	0.0658|0.0658	M|M	0.69823|0.69823	2.125|2.125	0.09310|0.09310	N|N	1|1	B;D;P|.	0.53745|.	0.047;0.962;0.952|.	B;P;P|.	0.51974|.	0.024;0.686;0.678|.	T|T	0.30937|0.30937	-0.9961|-0.9961	10|5	0.02654|.	T|.	1|.	.|.	5.964|5.964	0.19315|0.19315	0.0:0.4836:0.0:0.5164|0.0:0.4836:0.0:0.5164	.|.	202;263;263|.	B4DLP9;Q96AV7;Q7KYR7|.	.;.;BT2A1_HUMAN|.	V|S	263;202;263;249;263|12	ENSP00000312158:A263V;ENSP00000443909:A202V;ENSP00000416945:A263V;ENSP00000419043:A263V|.	ENSP00000265424:A249V|.	A|P	+|+	2|1	0|0	BTN2A1|BTN2A1	26573467|26573467	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.003000|0.003000	0.03518|0.03518	-0.083000|-0.083000	0.11286|0.11286	0.008000|0.008000	0.14787|0.14787	0.455000|0.455000	0.32223|0.32223	GCC|CCG		0.428	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
P2RX1	5023	hgsc.bcm.edu	37	17	3819435	3819435	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr17:3819435C>T	ENST00000225538.3	-	1	359	c.85G>A	c.(85-87)Gtg>Atg	p.V29M		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	29					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)	p.V29M(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		ATAACGCCCACCTTCTTATTA	0.667																																					p.V29M												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G85A	17						.						110.0	99.0	103.0					17																	3819435		2203	4300	6503	3766184	SO:0001583	missense	5023	exon1			X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.85G>A	17.37:g.3819435C>T	ENSP00000225538:p.Val29Met		3766184	NM_002558	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	37	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	C	22.5	4.300256	0.81136	.	.	ENSG00000108405	ENST00000225538	T	0.06294	3.32	4.7	4.7	0.59300	.	0.000000	0.64402	D	0.000001	T	0.30510	0.0767	M	0.86502	2.82	0.58432	D	0.999991	D	0.89917	1.0	D	0.91635	0.999	T	0.19289	-1.0310	10	0.87932	D	0	-25.1762	16.5811	0.84715	0.0:1.0:0.0:0.0	.	29	P51575	P2RX1_HUMAN	M	29	ENSP00000225538:V29M	ENSP00000225538:V29M	V	-	1	0	P2RX1	3766184	1.000000	0.71417	1.000000	0.80357	0.444000	0.32077	5.115000	0.64655	2.323000	0.78572	0.491000	0.48974	GTG		0.667	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1	NM_002558	
CETP	1071	hgsc.bcm.edu	37	16	57016114	57016114	+	Missense_Mutation	SNP	T	T	C			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr16:57016114T>C	ENST00000566128.1	+	14	1358	c.1091T>C	c.(1090-1092)aTg>aCg	p.M364T	CETP_ENST00000200676.3_Missense_Mutation_p.M429T|CETP_ENST00000379780.2_Missense_Mutation_p.M369T					cholesteryl ester transfer protein, plasma									p.M429T(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(4)|skin(3)	23						CTGCAGTCAATGATCACCGCT	0.577																																					p.M429T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T1286C	16						.						153.0	120.0	131.0					16																	57016114		2198	4300	6498	55573615	SO:0001583	missense	1071	exon14			M30185	CCDS10772.1, CCDS67032.1	16q13	2012-10-02			ENSG00000087237	ENSG00000087237		"""BPI fold containing"""	1869	protein-coding gene	gene with protein product	"""BPI fold containing family F"""	118470				3600759, 2334701	Standard	NM_000078		Approved	BPIFF	uc002eki.2	P11597	OTTHUMG00000133279	ENST00000566128.1:c.1091T>C	16.37:g.57016114T>C	ENSP00000456276:p.Met364Thr		55573615	NM_000078		Missense_Mutation	SNP	ENST00000566128.1	37		.	.	.	.	.	.	.	.	.	.	t	6.206	0.406095	0.11754	.	.	ENSG00000087237	ENST00000200676;ENST00000379780	T;T	0.10763	2.84;2.84	3.56	1.21	0.21127	Lipid-binding serum glycoprotein, C-terminal (2);Bactericidal permeability-increasing protein, alpha/beta domain (1);	1.152170	0.06352	U	0.710148	T	0.06462	0.0166	N	0.12182	0.205	0.09310	N	1	B;B	0.14012	0.002;0.009	B;B	0.19666	0.005;0.026	T	0.42498	-0.9448	10	0.37606	T	0.19	-9.673	4.4885	0.11801	0.0:0.112:0.2128:0.6752	.	369;429	P11597-2;P11597	.;CETP_HUMAN	T	429;369	ENSP00000200676:M429T;ENSP00000369106:M369T	ENSP00000200676:M429T	M	+	2	0	CETP	55573615	0.000000	0.05858	0.001000	0.08648	0.272000	0.26649	0.478000	0.22212	0.115000	0.18071	0.375000	0.23000	ATG		0.577	CETP-003	PUTATIVE	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000432305.1	NM_000078	
ANKRD12	23253	hgsc.bcm.edu	37	18	9258903	9258903	+	Missense_Mutation	SNP	C	C	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr18:9258903C>T	ENST00000262126.4	+	9	5878	c.5638C>T	c.(5638-5640)Ccc>Tcc	p.P1880S	ANKRD12_ENST00000400020.3_Missense_Mutation_p.P1857S|ANKRD12_ENST00000383440.2_Missense_Mutation_p.P1857S|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1880						cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.P1880S(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						GGATGGAAACCCCTTAAGCAA	0.383																																					p.P1880S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C5638T	18						.						97.0	95.0	96.0					18																	9258903		2202	4297	6499	9248903	SO:0001583	missense	23253	exon9			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.5638C>T	18.37:g.9258903C>T	ENSP00000262126:p.Pro1880Ser		9248903	NM_015208	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	ENST00000262126.4	37	CCDS11843.1	.	.	.	.	.	.	.	.	.	.	C	28.1	4.889236	0.91889	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.67698	-0.28;-0.28	5.44	5.44	0.79542	.	0.116868	0.64402	D	0.000015	T	0.78168	0.4241	L	0.43923	1.385	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.996	T	0.79165	-0.1916	10	0.72032	D	0.01	-8.3714	19.6223	0.95663	0.0:1.0:0.0:0.0	.	1857;1880	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	S	1857;1880	ENSP00000372932:P1857S;ENSP00000262126:P1880S	ENSP00000262126:P1880S	P	+	1	0	ANKRD12	9248903	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.776000	0.85560	2.707000	0.92482	0.655000	0.94253	CCC		0.383	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254478.2	NM_015208	
TMPPE	643853	hgsc.bcm.edu	37	3	33134871	33134871	+	Missense_Mutation	SNP	A	A	C			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr3:33134871A>C	ENST00000342462.4	-	2	1007	c.817T>G	c.(817-819)Ttc>Gtc	p.F273V	GLB1_ENST00000399402.3_Intron|GLB1_ENST00000307377.8_Intron|GLB1_ENST00000445488.2_Intron|GLB1_ENST00000307363.5_Intron|TMPPE_ENST00000416695.2_Missense_Mutation_p.F136V	NM_001039770.2	NP_001034859.2	Q6ZT21	TMPPE_HUMAN	transmembrane protein with metallophosphoesterase domain	273						integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)	p.F273V(1)		breast(1)|large_intestine(5)|lung(6)|prostate(1)	13						CCTGTGACGAAGTAGGCACCG	0.537																																					p.F136V												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T406G	3						.						93.0	84.0	87.0					3																	33134871		2203	4300	6503	33109875	SO:0001583	missense	643853	exon2			AK126979	CCDS33732.1, CCDS46786.1	3p22.3	2014-02-12	2009-02-24		ENSG00000188167	ENSG00000188167			33865	protein-coding gene	gene with protein product							Standard	NM_001039770		Approved	FLJ45032	uc003cfk.2	Q6ZT21	OTTHUMG00000155779	ENST00000342462.4:c.817T>G	3.37:g.33134871A>C	ENSP00000343398:p.Phe273Val		33109875	NM_001136238	B2RNG5|Q6ZRG1	Missense_Mutation	SNP	ENST00000342462.4	37	CCDS33732.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.416734	0.83449	.	.	ENSG00000188167	ENST00000416695;ENST00000342462	D;D	0.83837	-1.77;-1.77	6.05	6.05	0.98169	Metallophosphoesterase domain (1);	0.000000	0.64402	D	0.000004	D	0.87617	0.6222	L	0.46670	1.46	0.53688	D	0.999972	D	0.89917	1.0	D	0.81914	0.995	D	0.85784	0.1363	10	0.30854	T	0.27	-22.3097	14.823	0.70087	1.0:0.0:0.0:0.0	.	273	Q6ZT21	TMPPE_HUMAN	V	136;273	ENSP00000400715:F136V;ENSP00000343398:F273V	ENSP00000343398:F273V	F	-	1	0	TMPPE	33109875	1.000000	0.71417	0.999000	0.59377	0.973000	0.67179	7.134000	0.77268	2.320000	0.78422	0.528000	0.53228	TTC		0.537	TMPPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341566.1	NM_001039770	
CLSTN2	64084	hgsc.bcm.edu	37	3	140281149	140281149	+	Splice_Site	SNP	C	C	T	rs148317543		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr3:140281149C>T	ENST00000458420.3	+	13	2401	c.2211C>T	c.(2209-2211)taC>taT	p.Y737Y		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	737					homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)	p.Y737Y(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						ACTCCATCTACGGTAAGGCCA	0.552										HNSCC(16;0.037)																											p.Y737Y	GBM(45;858 913 3709 36904 37282)											.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C2211T	3						.	C		1,4405	2.1+/-5.4	0,1,2202	100.0	92.0	95.0		2211	-2.6	1.0	3	dbSNP_134	95	0,8600		0,0,4300	no	coding-synonymous-near-splice	CLSTN2	NM_022131.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		737/956	140281149	1,13005	2203	4300	6503	141763839	SO:0001630	splice_region_variant	64084	exon13			AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.2212+1C>T	3.37:g.140281149C>T			141763839	NM_022131	B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Silent	SNP	ENST00000458420.3	37	CCDS3112.1																																																																																				0.552	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131	Silent
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	T	rs121913529		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr12:25398284C>T	ENST00000256078.4	-	2	98	c.35G>A	c.(34-36)gGt>gAt	p.G12D	KRAS_ENST00000556131.1_Missense_Mutation_p.G12D|KRAS_ENST00000311936.3_Missense_Mutation_p.G12D|KRAS_ENST00000557334.1_Missense_Mutation_p.G12D	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12D	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS,haematopoietic_and_lymphoid_tissue,NS,Substitution - Missense,0	.	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35A	12						.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	25289551	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>A	12.37:g.25398284C>T	ENSP00000256078:p.Gly12Asp		25289551	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	23.4	4.409094	0.83340	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78595	-1.19;-1.19;-1.19;-1.19	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.85919	0.5809	M	0.91818	3.245	0.80722	D	1	B;P	0.35714	0.385;0.517	B;B	0.41619	0.257;0.361	D	0.87870	0.2670	10	0.87932	D	0	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	D	12	ENSP00000308495:G12D;ENSP00000452512:G12D;ENSP00000256078:G12D;ENSP00000451856:G12D	ENSP00000256078:G12D	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
CERS5	91012	hgsc.bcm.edu	37	12	50529767	50529767	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr12:50529767G>A	ENST00000317551.6	-	7	846	c.722C>T	c.(721-723)aCt>aTt	p.T241I	CERS5_ENST00000422340.2_Missense_Mutation_p.T183I	NM_147190.2	NP_671723.1	Q8N5B7	CERS5_HUMAN	ceramide synthase 5	241	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.T241I(1)									CATGATCAGAGTTCCCACTCG	0.428																																					p.T241I												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C722T	12						.						137.0	126.0	130.0					12																	50529767		2203	4300	6503	48816034	SO:0001583	missense	91012	exon7				CCDS8801.1, CCDS61120.1	12q13.12	2014-09-04	2011-07-08	2011-07-08	ENSG00000139624			"""Homeoboxes / CERS class"""	23749	protein-coding gene	gene with protein product		615335	"""LAG1 longevity assurance homolog 5 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 5"""	LASS5			Standard	NM_147190		Approved	Trh4, MGC45411, FLJ25304	uc001rwd.4	Q8N5B7	OTTHUMG00000169819	ENST00000317551.6:c.722C>T	12.37:g.50529767G>A	ENSP00000325485:p.Thr241Ile		48816034	NM_147190	B4DV54	Missense_Mutation	SNP	ENST00000317551.6	37	CCDS8801.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.04|18.04	3.535552|3.535552	0.64972|0.64972	.|.	.|.	ENSG00000139624|ENSG00000139624	ENST00000550547;ENST00000547800|ENST00000551005;ENST00000317551;ENST00000422340	.|D;D;D	.|0.84442	.|-1.85;-1.85;-1.85	4.35|4.35	4.35|4.35	0.52113|0.52113	.|TRAM/LAG1/CLN8 homology domain (3);	.|0.096875	.|0.64402	.|D	.|0.000001	D|D	0.89952|0.89952	0.6864|0.6864	M|M	0.64676|0.64676	1.99|1.99	0.46203|0.46203	D|D	0.998921|0.998921	.|D;P;D	.|0.67145	.|0.958;0.784;0.996	.|P;P;P	.|0.62885	.|0.876;0.507;0.908	D|D	0.89071|0.89071	0.3469|0.3469	5|10	.|0.36615	.|T	.|0.2	-6.162|-6.162	17.4728|17.4728	0.87650|0.87650	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|183;241;160	.|B4DV54;Q8N5B7;F8W0U5	.|.;CERS5_HUMAN;.	F|I	43;145|160;241;183	.|ENSP00000447556:T160I;ENSP00000325485:T241I;ENSP00000389050:T183I	.|ENSP00000325485:T241I	L|T	-|-	1|2	0|0	CERS5|CERS5	48816034|48816034	0.998000|0.998000	0.40836|0.40836	0.998000|0.998000	0.56505|0.56505	0.856000|0.856000	0.48823|0.48823	2.838000|2.838000	0.48199|0.48199	2.426000|2.426000	0.82243|0.82243	0.655000|0.655000	0.94253|0.94253	CTC|ACT		0.428	CERS5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406069.3	NM_147190	
DCUN1D4	23142	hgsc.bcm.edu	37	4	52779714	52779714	+	Silent	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr4:52779714G>A	ENST00000334635.5	+	11	1023	c.843G>A	c.(841-843)gaG>gaA	p.E281E	DCUN1D4_ENST00000381441.3_Silent_p.E246E|DCUN1D4_ENST00000381437.4_Silent_p.E221E|DCUN1D4_ENST00000451288.2_Silent_p.E325E	NM_001040402.1	NP_001035492.1	Q92564	DCNL4_HUMAN	DCN1, defective in cullin neddylation 1, domain containing 4	281	DCUN1. {ECO:0000255|PROSITE- ProRule:PRU00574}.					nucleus (GO:0005634)		p.E281E(1)		endometrium(2)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	9			GBM - Glioblastoma multiforme(4;1.93e-11)|LUSC - Lung squamous cell carcinoma(32;0.00654)			TGTTGGACGAGTTTGTGGAGT	0.373																																					p.E281E												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G843A	4						.						104.0	102.0	103.0					4																	52779714		2203	4300	6503	52474471	SO:0001819	synonymous_variant	23142	exon11			D87466	CCDS3487.2, CCDS33982.1, CCDS75123.1	4q11	2013-06-10	2013-06-10		ENSG00000109184	ENSG00000109184			28998	protein-coding gene	gene with protein product		612977	"""DCN1, defective in cullin neddylation 1, domain containing 4 (S. cerevisiae)"""			15988528	Standard	XM_005265731		Approved	KIAA0276	uc003gze.3	Q92564	OTTHUMG00000128700	ENST00000334635.5:c.843G>A	4.37:g.52779714G>A			52474471	NM_001040402	B4DH25|Q7Z3F3|Q7Z6B8	Silent	SNP	ENST00000334635.5	37	CCDS33982.1																																																																																				0.373	DCUN1D4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250599.2	NM_015115	
KIT	3815	hgsc.bcm.edu	37	4	55599268	55599268	+	Silent	SNP	C	C	T	rs55789615	byFrequency	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr4:55599268C>T	ENST00000288135.5	+	17	2491	c.2394C>T	c.(2392-2394)atC>atT	p.I798I		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	798	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.I798I(12)		NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CCAGAAATATCCTCCTTACTC	0.363		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors				C|||	57	0.0113818	0.0023	0.0231	5008	,	,		16853	0.0		0.0358	False		,,,				2504	0.002				p.I798I		yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	KIT,haematopoietic_and_lymphoid_tissue,NS,Substitution - coding silent,0	.	12	Substitution - coding silent(12)	bone(3)|testis(2)|haematopoietic_and_lymphoid_tissue(2)|autonomic_ganglia(1)|soft_tissue(1)|genital_tract(1)|large_intestine(1)|NS(1)	c.C2394T	4						.	C	,	39,4367	42.3+/-75.8	0,39,2164	112.0	111.0	112.0		2394,2382	3.6	1.0	4	dbSNP_129	112	284,8316	106.2+/-167.1	10,264,4026	no	coding-synonymous,coding-synonymous	KIT	NM_000222.2,NM_001093772.1	,	10,303,6190	TT,TC,CC		3.3023,0.8852,2.4835	,	798/977,794/973	55599268	323,12683	2203	4300	6503	55294025	SO:0001819	synonymous_variant	3815	exon17	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.2394C>T	4.37:g.55599268C>T			55294025	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	37	CCDS3496.1																																																																																				0.363	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
PRSS12	8492	hgsc.bcm.edu	37	4	119204036	119204037	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	CT	CT	CT	-	CT	CT	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr4:119204036_119204037delCT	ENST00000296498.3	-	12	2551_2552	c.2269_2270delAG	c.(2269-2271)aggfs	p.R757fs	PRSS12_ENST00000510903.1_5'Flank	NM_003619.3	NP_003610.2	P56730	NETR_HUMAN	protease, serine, 12 (neurotrypsin, motopsin)	757	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				exocytosis (GO:0006887)|zymogen activation (GO:0031638)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)|terminal bouton (GO:0043195)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.R757fs*15(1)		endometrium(3)|kidney(1)|large_intestine(9)|lung(11)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	29						TTTCTGTGGCCTCTCTCTCCAG	0.45																																					p.757_757del												.	.	1	Deletion - Frameshift(1)	large_intestine(1)	c.2269_2270del	4						.																																			119423485	SO:0001589	frameshift_variant	8492	exon12			AJ001531	CCDS3709.1	4q25-q26	2010-05-07			ENSG00000164099	ENSG00000164099		"""Serine peptidases / Serine peptidases"""	9477	protein-coding gene	gene with protein product		606709				9540828, 9245503	Standard	NM_003619		Approved	BSSP-3, MRT1	uc003ica.2	P56730	OTTHUMG00000161166	ENST00000296498.3:c.2269_2270delAG	4.37:g.119204042_119204043delCT	ENSP00000296498:p.Arg757fs		119423484	NM_003619	Q9UP16	Frame_Shift_Del	DEL	ENST00000296498.3	37	CCDS3709.1																																																																																				0.450	PRSS12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256516.2		
DCHS2	54798	hgsc.bcm.edu	37	4	155241937	155241937	+	Missense_Mutation	SNP	G	G	T	rs146199349		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr4:155241937G>T	ENST00000357232.4	-	14	3248	c.3249C>A	c.(3247-3249)gaC>gaA	p.D1083E		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1083	Cadherin 9. {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)	p.D1083E(1)		NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		AAAAACTGCCGTCATCATCTT	0.448																																					p.D1083E												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C3249A	4						.						238.0	257.0	250.0					4																	155241937		2203	4300	6503	155461387	SO:0001583	missense	54798	exon14			BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.3249C>A	4.37:g.155241937G>T	ENSP00000349768:p.Asp1083Glu		155461387	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	.	.	.	.	.	.	.	.	.	.	G	12.54	1.969999	0.34754	.	.	ENSG00000197410	ENST00000357232	T	0.73789	-0.78	5.69	-8.67	0.00863	Cadherin (4);Cadherin-like (1);	0.000000	0.64402	D	0.000002	D	0.88991	0.6588	H	0.98612	4.28	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.91522	0.5235	10	0.59425	D	0.04	.	16.6243	0.84952	0.4372:0.0:0.5628:0.0	.	1083	Q6V1P9	PCD23_HUMAN	E	1083	ENSP00000349768:D1083E	ENSP00000349768:D1083E	D	-	3	2	DCHS2	155461387	0.595000	0.26857	0.064000	0.19789	0.227000	0.25037	-0.042000	0.12063	-2.217000	0.00731	-2.010000	0.00438	GAC		0.448	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
HNRNPH2	3188	hgsc.bcm.edu	37	X	100667024	100667024	+	Silent	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chrX:100667024G>A	ENST00000316594.5	+	2	126	c.48G>A	c.(46-48)agG>agA	p.R16R	RPL36A-HNRNPH2_ENST00000409170.3_3'UTR	NM_001032393.2|NM_001199973.1|NM_001199974.1|NM_019597.4	NP_001027565.1|NP_001186902.1|NP_001186903.1|NP_062543.1	P55795	HNRH2_HUMAN	heterogeneous nuclear ribonucleoprotein H2 (H')	16	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)	membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.R16R(1)		breast(3)|large_intestine(2)|lung(6)|skin(1)	12						TGAAGGTCAGGGGCCTACCCT	0.517																																					p.R16R												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.G48A	X						.						144.0	115.0	125.0					X																	100667024		2203	4300	6503	100553680	SO:0001819	synonymous_variant	3188	exon2			U01923	CCDS14485.1	Xq22	2013-02-12		2008-04-18	ENSG00000126945	ENSG00000126945		"""RNA binding motif (RRM) containing"""	5042	protein-coding gene	gene with protein product		300610		HNRPH2		7499401	Standard	NM_019597		Approved	hnRNPH', FTP3, HNRPH'	uc004ehn.3	P55795	OTTHUMG00000022029	ENST00000316594.5:c.48G>A	X.37:g.100667024G>A			100553680	NM_019597	A1L400|Q9HHA7	Silent	SNP	ENST00000316594.5	37	CCDS14485.1																																																																																				0.517	HNRNPH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057556.1	NM_019597	
DMD	1756	hgsc.bcm.edu	37	X	32482738	32482738	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chrX:32482738A>T	ENST00000357033.4	-	24	3447	c.3241T>A	c.(3241-3243)Tca>Aca	p.S1081T	DMD_ENST00000378677.2_Missense_Mutation_p.S1077T	NM_000109.3|NM_004006.2|NM_004011.3|NM_004012.3|NM_004014.2	NP_000100.2|NP_003997|NP_004002.2|NP_004003.1|NP_004005.1	P11532	DMD_HUMAN	dystrophin	1081					cardiac muscle cell action potential (GO:0086001)|cardiac muscle contraction (GO:0060048)|cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|extracellular matrix organization (GO:0030198)|motile cilium assembly (GO:0044458)|muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|negative regulation of peptidyl-cysteine S-nitrosylation (GO:1902083)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|peptide biosynthetic process (GO:0043043)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of cellular response to growth factor stimulus (GO:0090287)|regulation of heart rate (GO:0002027)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)|regulation of skeletal muscle contraction (GO:0014819)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|regulation of voltage-gated calcium channel activity (GO:1901385)	cell junction (GO:0030054)|cell surface (GO:0009986)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dystrophin-associated glycoprotein complex (GO:0016010)|filopodium (GO:0030175)|filopodium membrane (GO:0031527)|membrane raft (GO:0045121)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|syntrophin complex (GO:0016013)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|dystroglycan binding (GO:0002162)|myosin binding (GO:0017022)|nitric-oxide synthase binding (GO:0050998)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)|vinculin binding (GO:0017166)|zinc ion binding (GO:0008270)	p.S1076T(1)		NS(2)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(17)|liver(1)|lung(25)|ovary(3)|pancreas(3)|prostate(2)|skin(1)|urinary_tract(2)	77		all_cancers(2;1.22e-16)|Acute lymphoblastic leukemia(2;4.65e-06)|all_hematologic(2;0.00108)|all_epithelial(3;0.00626)|all_neural(2;0.0189)|all_lung(315;0.182)|Glioma(3;0.203)				AGAATTTCTGAATCCCCAAGG	0.358																																					p.S1081T												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T3241A	X						.						114.0	98.0	103.0					X																	32482738		2202	4300	6502	32392659	SO:0001583	missense	1756	exon24			AF047505	CCDS14231.1, CCDS14232.1, CCDS14233.1, CCDS14234.1, CCDS48091.1, CCDS55394.1, CCDS55395.1, CCDS75965.1	Xp21.2	2014-09-17	2008-08-01		ENSG00000198947	ENSG00000198947			2928	protein-coding gene	gene with protein product	"""muscular dystrophy, Duchenne and Becker types"""	300377	"""dystrophin (muscular dystrophy, Duchenne and Becker types), includes DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272"", ""mental retardation, X-linked 85"""	MRX85		3282674, 3607877, 23900271	Standard	NM_004019		Approved	BMD, DXS142, DXS164, DXS206, DXS230, DXS239, DXS268, DXS269, DXS270, DXS272	uc004dda.1	P11532	OTTHUMG00000021336	ENST00000357033.4:c.3241T>A	X.37:g.32482738A>T	ENSP00000354923:p.Ser1081Thr		32392659	NM_004006	E9PDN1|Q02295|Q14169|Q14170|Q5JYU0|Q6NSJ9|Q7KZ48|Q8N754|Q9UCW3|Q9UCW4	Missense_Mutation	SNP	ENST00000357033.4	37	CCDS14233.1	.	.	.	.	.	.	.	.	.	.	A	6.960	0.546991	0.13312	.	.	ENSG00000198947	ENST00000534884;ENST00000378677;ENST00000357033;ENST00000542849;ENST00000535280	T;T	0.49139	0.79;0.79	4.8	0.932	0.19466	.	0.293789	0.18014	U	0.154447	T	0.30916	0.0780	L	0.41236	1.265	0.80722	D	1	B;B;B	0.19583	0.03;0.013;0.037	B;B;B	0.22152	0.022;0.033;0.038	T	0.07809	-1.0753	10	0.11182	T	0.66	.	5.618	0.17442	0.6942:0.1458:0.1599:0.0	.	1073;1081;1077	P11532-4;P11532;E9PDN5	.;DMD_HUMAN;.	T	1073;1077;1081;1081;958	ENSP00000367948:S1077T;ENSP00000354923:S1081T	ENSP00000354923:S1081T	S	-	1	0	DMD	32392659	1.000000	0.71417	0.990000	0.47175	0.762000	0.43233	2.370000	0.44240	-0.106000	0.12110	0.376000	0.23039	TCA		0.358	DMD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056182.2	NM_004006	
TFE3	7030	hgsc.bcm.edu	37	X	48896802	48896802	+	Missense_Mutation	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chrX:48896802G>A	ENST00000315869.7	-	3	623	c.364C>T	c.(364-366)Cgg>Tgg	p.R122W	TFE3_ENST00000487451.1_5'UTR	NM_006521.4	NP_006512.2	P19532	TFE3_HUMAN	transcription factor binding to IGHM enhancer 3	122					humoral immune response (GO:0006959)|positive regulation of cell adhesion (GO:0045785)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of osteoclast differentiation (GO:0045670)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)	p.R122W(1)	NONO/TFE3(2)|PRCC/TFE3(25)|SFPQ/TFE3(6)|CLTC/TFE3(2)|ASPSCR1/TFE3(167)	central_nervous_system(1)	1						GCCTGGGCCCGCATTAGCTGC	0.652			T	"""SFPQ, ASPSCR1, PRCC, NONO, CLTC"""	"""papillary renal, alveolar soft part sarcoma, renal"""																																p.R122W			Dom	yes		X	Xp11.22	7030	transcription factor binding to IGHM enhancer 3		E	.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C364T	X						.						20.0	18.0	19.0					X																	48896802		2201	4298	6499	48783746	SO:0001583	missense	7030	exon3			X96717	CCDS14315.3	Xp11.22	2013-05-21			ENSG00000068323	ENSG00000068323		"""Basic helix-loop-helix proteins"""	11752	protein-coding gene	gene with protein product	transcription factor E family, member A	314310				1672758, 1685140	Standard	NM_006521		Approved	TFEA, bHLHe33	uc004dmb.3	P19532	OTTHUMG00000022690	ENST00000315869.7:c.364C>T	X.37:g.48896802G>A	ENSP00000314129:p.Arg122Trp		48783746	NM_006521	A8MZL6|Q5JU74|Q92757|Q92758|Q99964	Missense_Mutation	SNP	ENST00000315869.7	37	CCDS14315.3	.	.	.	.	.	.	.	.	.	.	G	14.17	2.454032	0.43634	.	.	ENSG00000068323	ENST00000315869	T	0.35048	1.33	5.21	1.92	0.25849	.	0.000000	0.64402	D	0.000001	T	0.45994	0.1370	L	0.56396	1.775	0.48452	D	0.999655	D	0.76494	0.999	P	0.54815	0.761	T	0.48328	-0.9045	10	0.87932	D	0	-16.7957	12.2662	0.54679	0.0:0.0:0.5478:0.4522	.	122	P19532	TFE3_HUMAN	W	122	ENSP00000314129:R122W	ENSP00000314129:R122W	R	-	1	2	TFE3	48783746	1.000000	0.71417	0.999000	0.59377	0.613000	0.37349	1.683000	0.37638	0.361000	0.24292	0.513000	0.50165	CGG		0.652	TFE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058872.2	NM_006521	
PFKFB1	5207	hgsc.bcm.edu	37	X	54987295	54987295	+	Missense_Mutation	SNP	G	G	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chrX:54987295G>T	ENST00000375006.3	-	3	349	c.279C>A	c.(277-279)ttC>ttA	p.F93L	PFKFB1_ENST00000545676.1_Missense_Mutation_p.F28L|PFKFB1_ENST00000374992.2_Intron	NM_002625.2	NP_002616.2	P16118	F261_HUMAN	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1	93	6-phosphofructo-2-kinase.				carbohydrate metabolic process (GO:0005975)|dephosphorylation (GO:0016311)|energy reserve metabolic process (GO:0006112)|fructose 2,6-bisphosphate metabolic process (GO:0006003)|fructose metabolic process (GO:0006000)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|intracellular signal transduction (GO:0035556)|organ regeneration (GO:0031100)|positive regulation of glucokinase activity (GO:0033133)|response to cAMP (GO:0051591)|response to glucagon (GO:0033762)|response to glucocorticoid (GO:0051384)|response to insulin (GO:0032868)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	6-phosphofructo-2-kinase/fructose-2,6-biphosphatase complex (GO:0043540)|cytosol (GO:0005829)	6-phosphofructo-2-kinase activity (GO:0003873)|ATP binding (GO:0005524)|fructose-2,6-bisphosphate 2-phosphatase activity (GO:0004331)|fructose-6-phosphate binding (GO:0070095)	p.F93L(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(11)|ovary(1)	24						CTGGAAGAAAGAATTCATAGT	0.458																																					p.F93L												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.C279A	X						.						134.0	111.0	119.0					X																	54987295		2203	4300	6503	55004020	SO:0001583	missense	5207	exon3				CCDS14364.1, CCDS65273.1	Xp11.21	2012-07-13			ENSG00000158571	ENSG00000158571	2.7.1.105, 3.1.3.46		8872	protein-coding gene	gene with protein product		311790		PFRX		9119406	Standard	NM_002625		Approved		uc004dty.2	P16118	OTTHUMG00000021643	ENST00000375006.3:c.279C>A	X.37:g.54987295G>T	ENSP00000364145:p.Phe93Leu		55004020	NM_002625	B2RA88|B4DUN5|Q5JXS5|Q99951	Missense_Mutation	SNP	ENST00000375006.3	37	CCDS14364.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.126215	0.77549	.	.	ENSG00000158571	ENST00000375006;ENST00000545676	.	.	.	4.89	3.12	0.35913	6-phosphofructo-2-kinase (1);	0.000000	0.85682	D	0.000000	T	0.71151	0.3306	M	0.78223	2.4	0.80722	D	1	D;D	0.76494	0.995;0.999	D;D	0.75020	0.968;0.985	T	0.69803	-0.5046	9	0.87932	D	0	-20.8028	6.6213	0.22804	0.394:0.0:0.606:0.0	.	28;93	B4DUN5;P16118	.;F261_HUMAN	L	93;28	.	ENSP00000364145:F93L	F	-	3	2	PFKFB1	55004020	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.567000	0.36407	0.435000	0.26365	0.594000	0.82650	TTC		0.458	PFKFB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056847.1		
ESX1	80712	hgsc.bcm.edu	37	X	103499520	103499520	+	Missense_Mutation	SNP	A	A	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chrX:103499520A>T	ENST00000372588.4	-	1	94	c.11T>A	c.(10-12)cTt>cAt	p.L4H		NM_153448.3	NP_703149.1	Q8N693	ESX1_HUMAN	ESX homeobox 1	4					labyrinthine layer blood vessel development (GO:0060716)|labyrinthine layer morphogenesis (GO:0060713)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|regulation of cell cycle (GO:0051726)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	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 negative regulation of transcription (GO:0001227)|sequence-specific DNA binding (GO:0043565)	p.L4H(1)		endometrium(2)|large_intestine(10)|lung(12)|ovary(1)|skin(2)	27						GTACCCGCGAAGAGACTCCAT	0.587																																					p.L4H	Pancreas(200;1705 2227 25194 28471 45274)											.	.	1	Substitution - Missense(1)	large_intestine(1)	c.T11A	X						.						166.0	134.0	145.0					X																	103499520		2203	4300	6503	103386176	SO:0001583	missense	80712	exon1			AL049631	CCDS14516.1	Xq22.2	2011-06-20	2007-07-11	2006-02-08	ENSG00000123576	ENSG00000123576		"""Homeoboxes / PRD class"""	14865	protein-coding gene	gene with protein product		300154	"""extraembryonic, spermatogenesis, homeobox 1 homolog (mouse)"""	ESX1L		11374906, 17242862	Standard	NM_153448		Approved	ESXR1	uc004ely.3	Q8N693	OTTHUMG00000022125	ENST00000372588.4:c.11T>A	X.37:g.103499520A>T	ENSP00000361669:p.Leu4His		103386176	NM_153448	B0QYU3|Q7Z6K7	Missense_Mutation	SNP	ENST00000372588.4	37	CCDS14516.1	.	.	.	.	.	.	.	.	.	.	a	9.901	1.206814	0.22205	.	.	ENSG00000123576	ENST00000372588	D	0.91521	-2.86	3.45	-6.91	0.01649	POU (1);	.	.	.	.	T	0.73536	0.3599	N	0.08118	0	0.09310	N	1	D	0.53462	0.96	B	0.40565	0.333	T	0.71748	-0.4499	9	0.56958	D	0.05	5.1864	2.5901	0.04840	0.3064:0.1693:0.402:0.1223	.	4	Q8N693	ESX1_HUMAN	H	4	ENSP00000361669:L4H	ENSP00000361669:L4H	L	-	2	0	ESX1	103386176	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.372000	0.01073	-4.208000	0.00065	-2.590000	0.00165	CTT		0.587	ESX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057763.2	NM_153448	
CLHC1	130162	hgsc.bcm.edu	37	2	55436540	55436540	+	Splice_Site	SNP	C	C	T	rs200240456		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr2:55436540C>T	ENST00000401408.1	-	7	1159	c.814G>A	c.(814-816)Ggt>Agt	p.G272S	CLHC1_ENST00000406437.2_Intron|CLHC1_ENST00000406076.1_Splice_Site_p.G150S|CLHC1_ENST00000407122.1_Splice_Site_p.G272S|CLHC1_ENST00000494539.1_Intron	NM_152385.2	NP_689598.2	Q8NHS4	CLHC1_HUMAN	clathrin heavy chain linker domain containing 1	272								p.G272S(2)									GATAATCTACCTTGTAAATAT	0.328													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15485	0.0		0.0	False		,,,				2504	0.0				p.G272S												.	.	2	Substitution - Missense(2)	large_intestine(2)	c.G814A	2						.						54.0	59.0	57.0					2																	55436540		2201	4300	6501	55290044	SO:0001630	splice_region_variant	130162	exon7				CCDS33201.1, CCDS46287.1	2p16.1	2012-08-03	2012-08-03	2012-08-03	ENSG00000162994	ENSG00000162994			26453	protein-coding gene	gene with protein product			"""chromosome 2 open reading frame 63"""	C2orf63			Standard	NM_152385		Approved	FLJ31438	uc002ryi.2	Q8NHS4	OTTHUMG00000151918	ENST00000401408.1:c.814+1G>A	2.37:g.55436540C>T			55290044	NM_152385	B2RDV1|Q53R93|Q8N403	Missense_Mutation	SNP	ENST00000401408.1	37	CCDS33201.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	11.93	1.786029	0.31593	.	.	ENSG00000162994	ENST00000407122;ENST00000401408;ENST00000406076	T;T;T	0.16597	2.33;2.33;2.33	5.48	5.48	0.80851	.	0.407672	0.22495	N	0.059311	T	0.18467	0.0443	L	0.53249	1.67	0.80722	D	1	P	0.42871	0.792	B	0.37650	0.255	T	0.01729	-1.1286	9	.	.	.	-0.3112	14.8626	0.70392	0.0:1.0:0.0:0.0	.	272	Q8NHS4	CB063_HUMAN	S	272;272;150	ENSP00000385778:G272S;ENSP00000384869:G272S;ENSP00000385512:G150S	.	G	-	1	0	C2orf63	55290044	0.993000	0.37304	0.923000	0.36655	0.009000	0.06853	4.065000	0.57513	2.567000	0.86603	0.655000	0.94253	GGT		0.328	CLHC1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324412.4	NM_152385	Missense_Mutation
RIF1	55183	hgsc.bcm.edu	37	2	152292057	152292057	+	Silent	SNP	A	A	G			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	A	A	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr2:152292057A>G	ENST00000243326.5	+	10	1641	c.1158A>G	c.(1156-1158)acA>acG	p.T386T	RIF1_ENST00000428287.2_Silent_p.T386T|RIF1_ENST00000444746.2_Silent_p.T386T|RIF1_ENST00000453091.2_Silent_p.T386T|RIF1_ENST00000433166.2_Intron|RIF1_ENST00000430328.2_Silent_p.T386T			Q9Y581	INSL6_HUMAN	replication timing regulatory factor 1	0					fertilization (GO:0009566)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|sperm motility (GO:0030317)|spermatid development (GO:0007286)	extracellular region (GO:0005576)	hormone activity (GO:0005179)	p.T386T(1)		NS(2)|breast(8)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(19)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	97				BRCA - Breast invasive adenocarcinoma(221;0.0429)		ATGTAGCTACATCTCCAGGTT	0.383																																					p.T386T												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.A1158G	2						.						239.0	228.0	232.0					2																	152292057		2203	4300	6503	152000303	SO:0001819	synonymous_variant	55183	exon11			AK022932	CCDS2194.1, CCDS54406.1	2q23.3	2014-06-02	2014-06-02		ENSG00000080345	ENSG00000080345			23207	protein-coding gene	gene with protein product		608952	"""RAP1 interacting factor homolog (yeast)"""			15342490, 15042697, 22850674	Standard	NM_018151		Approved	FLJ12870, FLJ10599	uc002txm.3	Q5UIP0	OTTHUMG00000131886	ENST00000243326.5:c.1158A>G	2.37:g.152292057A>G			152000303	NM_001177664	A0AVS0|Q9NS16	Silent	SNP	ENST00000243326.5	37	CCDS2194.1	.	.	.	.	.	.	.	.	.	.	A	0.133	-1.111389	0.01813	.	.	ENSG00000080345	ENST00000414861	.	.	.	4.96	2.3	0.28687	.	.	.	.	.	T	0.47488	0.1448	.	.	.	0.35676	D	0.813708	.	.	.	.	.	.	T	0.49011	-0.8983	4	.	.	.	-0.7972	5.8161	0.18494	0.1953:0.0792:0.0:0.7255	.	.	.	.	V	378	.	.	I	+	1	0	RIF1	152000303	0.000000	0.05858	0.115000	0.21578	0.134000	0.20937	-0.190000	0.09615	0.155000	0.19261	-1.804000	0.00617	ATC		0.383	RIF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254836.3		
ZCCHC6	79670	hgsc.bcm.edu	37	9	88937851	88937853	+	In_Frame_Del	DEL	ATT	ATT	-	rs58050565|rs200402481|rs397759922	byFrequency	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	ATT	ATT	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr9:88937851_88937853delATT	ENST00000375963.3	-	13	2984_2986	c.2812_2814delAAT	c.(2812-2814)aatdel	p.N938del	ZCCHC6_ENST00000469004.1_5'Flank|ZCCHC6_ENST00000375961.2_In_Frame_Del_p.N938del|ZCCHC6_ENST00000375960.2_In_Frame_Del_p.N815del|ZCCHC6_ENST00000277141.6_In_Frame_Del_p.N227del	NM_001185059.1|NM_024617.3	NP_001171988.1|NP_078893.2	Q5VYS8	TUT7_HUMAN	zinc finger, CCHC domain containing 6	938					RNA 3'-end processing (GO:0031123)		poly(A) RNA binding (GO:0044822)|RNA uridylyltransferase activity (GO:0050265)|zinc ion binding (GO:0008270)	p.N938delN(1)		breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|liver(1)|lung(14)|ovary(2)|prostate(1)|skin(2)|urinary_tract(1)	46						CCACAGGTGAATTTTTTTCTTCA	0.35																																					p.938_938del												.	.	1	Deletion - In frame(1)	large_intestine(1)	c.2812_2814del	9						.																																			88127673	SO:0001651	inframe_deletion	79670	exon13			AL832026	CCDS35057.1, CCDS55323.1	9q21	2014-03-05			ENSG00000083223	ENSG00000083223		"""Zinc fingers, CCHC domain containing"""	25817	protein-coding gene	gene with protein product	"""TUTase7"""					11214970	Standard	NM_001185059		Approved	KIAA1711, FLJ13409, PAPD6, TUT7	uc004aoq.3	Q5VYS8	OTTHUMG00000020137	ENST00000375963.3:c.2812_2814delAAT	9.37:g.88937851_88937853delATT	ENSP00000365130:p.Asn938del		88127671	NM_024617	Q5H9T0|Q5VYS5|Q5VYS7|Q658Z9|Q659A2|Q6MZJ3|Q8N5F0|Q96N57|Q96NE8|Q9C0F2|Q9H8M6	In_Frame_Del	DEL	ENST00000375963.3	37	CCDS35057.1																																																																																				0.350	ZCCHC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052918.1	NM_024617	
FRMPD2	143162	hgsc.bcm.edu	37	10	49450381	49450381	+	Silent	SNP	G	G	A			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr10:49450381G>A	ENST00000374201.3	-	5	692	c.390C>T	c.(388-390)tgC>tgT	p.C130C	FRMPD2_ENST00000305531.3_Silent_p.C106C|FRMPD2_ENST00000407470.4_Silent_p.C99C	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	130	KIND. {ECO:0000255|PROSITE- ProRule:PRU00709}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)	p.C130C(1)		NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		GCAGGGGCTCGCAGAGCTGCA	0.622																																					p.C130C												.	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C390T	10						.						47.0	48.0	48.0					10																	49450381		2203	4300	6503	49120387	SO:0001819	synonymous_variant	143162	exon5			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.390C>T	10.37:g.49450381G>A			49120387	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Silent	SNP	ENST00000374201.3	37	CCDS31195.1																																																																																				0.622	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
DPYSL4	10570	hgsc.bcm.edu	37	10	134013906	134013906	+	Silent	SNP	C	C	T	rs56326856	byFrequency	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	.	.	.	.	Unknown	Unknown	Somatic	Phase_I	Capture	.			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr10:134013906C>T	ENST00000338492.4	+	9	1022	c.858C>T	c.(856-858)gaC>gaT	p.D286D	DPYSL4_ENST00000368629.1_Silent_p.D186D|DPYSL4_ENST00000368627.1_Silent_p.D186D	NM_006426.2	NP_006417.2	O14531	DPYL4_HUMAN	dihydropyrimidinase-like 4	286					axon guidance (GO:0007411)|nervous system development (GO:0007399)|pyrimidine nucleobase catabolic process (GO:0006208)	cytosol (GO:0005829)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.D286D(3)		NS(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		all_cancers(35;4.33e-08)|all_epithelial(44;6.75e-06)|Lung NSC(174;0.0108)|all_lung(145;0.0173)|all_neural(114;0.0726)|Glioma(114;0.172)|Melanoma(40;0.175)|Colorectal(31;0.19)		OV - Ovarian serous cystadenocarcinoma(35;7.21e-05)|Epithelial(32;8.01e-05)|all cancers(32;9.29e-05)|BRCA - Breast invasive adenocarcinoma(275;0.206)		TGGGCACCGACGGTTCACACT	0.672													T|||	751	0.14996	0.2708	0.098	5008	,	,		15549	0.001		0.159	False		,,,				2504	0.1677				p.D286D												DPYSL4,central_nervous_system,brain,Substitution - Missense,0	.	3	Substitution - Missense(3)	central_nervous_system(2)|endometrium(1)	c.C858T	10						.	T		1004,3402	727.6+/-409.9	119,766,1318	119.0	107.0	112.0		858	-3.2	0.1	10	dbSNP_129	112	1324,7276	756.8+/-407.5	92,1140,3068	no	coding-synonymous	DPYSL4	NM_006426.2		211,1906,4386	TT,TC,CC		15.3953,22.7871,17.8994		286/573	134013906	2328,10678	2203	4300	6503	133863896	SO:0001819	synonymous_variant	10570	exon9			AB006713	CCDS7665.1	10q25.2-q26	2008-05-14			ENSG00000151640	ENSG00000151640			3016	protein-coding gene	gene with protein product		608407				8973361, 9652388	Standard	NM_006426		Approved	ULIP4, DRP-4	uc009ybb.3	O14531	OTTHUMG00000019283	ENST00000338492.4:c.858C>T	10.37:g.134013906C>T			133863896	NM_006426	B2RMQ1|D3DRG5|O00240|Q5T0Q7	Silent	SNP	ENST00000338492.4	37	CCDS7665.1																																																																																				0.672	DPYSL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051050.2		
APC	324	hgsc.bcm.edu	37	5	112173251	112173251	+	Splice_Site	SNP	C	C	T			TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr5:112173251C>T	ENST00000457016.1	+	16	2340	c.1960C>T	c.(1960-1962)Caa>Taa	p.Q654*	APC_ENST00000257430.4_Splice_Site_p.Q654*|APC_ENST00000508376.2_Splice_Site_p.Q654*|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	654	Leu-rich.				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)	p.Q654*(1)|p.?(1)		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)		TTATTTCAGGCAAATCCTAAG	0.318		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)																											p.Q636X	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	.	2	Substitution - Nonsense(1)|Unknown(1)	large_intestine(1)|skin(1)	c.C1906T	5	GRCh37	CM045038	APC	M		.						46.0	48.0	47.0					5																	112173251		2202	4300	6502	112201150	SO:0001630	splice_region_variant	324	exon14	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	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.1959-1C>T	5.37:g.112173251C>T			112201150	NM_001127511	D3DT03|Q15162|Q15163|Q93042	Nonsense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	.	.	.	.	.	.	.	.	.	.	C	36	5.697731	0.96802	.	.	ENSG00000134982	ENST00000457016;ENST00000507379;ENST00000257430;ENST00000508376;ENST00000512211	.	.	.	5.88	5.88	0.94601	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	-14.7537	20.2422	0.98381	0.0:1.0:0.0:0.0	.	.	.	.	X	654;636;654;654;654	.	ENSP00000257430:Q654X	Q	+	1	0	APC	112201150	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.487000	0.81328	2.782000	0.95742	0.655000	0.94253	CAA		0.318	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	Nonsense_Mutation
GRM6	2916	hgsc.bcm.edu	37	5	178408795	178408795	+	Missense_Mutation	SNP	C	C	T	rs373757775		TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	Capture	454			SOLID	TCGA-AA-3532-01A-01W-0831-10	TCGA-AA-3532-10A-01W-0831-10	g.chr5:178408795C>T	ENST00000517717.1	-	11	2535	c.2497G>A	c.(2497-2499)Ggc>Agc	p.G833S	GRM6_ENST00000231188.5_Missense_Mutation_p.G833S|RP11-281O15.4_ENST00000519491.1_RNA			O15303	GRM6_HUMAN	glutamate receptor, metabotropic 6	833					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|detection of light stimulus involved in visual perception (GO:0050908)|detection of visible light (GO:0009584)|G-protein coupled glutamate receptor signaling pathway (GO:0007216)|locomotory behavior (GO:0007626)|positive regulation of calcium ion import (GO:0090280)|regulation of synaptic transmission, glutamatergic (GO:0051966)|retina development in camera-type eye (GO:0060041)|synaptic transmission (GO:0007268)	cell projection (GO:0042995)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|new growing cell tip (GO:0035841)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	G-protein coupled receptor activity (GO:0004930)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|protein homodimerization activity (GO:0042803)	p.G833S(1)		NS(2)|breast(4)|endometrium(9)|large_intestine(12)|lung(21)|ovary(2)|pancreas(1)|prostate(3)|urinary_tract(1)	55	all_cancers(89;0.000828)|Renal(175;0.000159)|all_epithelial(37;0.000167)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_cancers(40;0.0156)|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)	all cancers(165;0.245)		TAGAGCATGCCGAGGGACACC	0.582																																					p.G833S												.	.	1	Substitution - Missense(1)	large_intestine(1)	c.G2497A	5						.						178.0	157.0	164.0					5																	178408795		2203	4300	6503	178341401	SO:0001583	missense	2916	exon10			U82083	CCDS4442.1	5q35	2014-01-28						"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4598	protein-coding gene	gene with protein product		604096				9215706	Standard	NM_000843		Approved	GPRC1F, mGlu6, MGLUR6, CSNB1B	uc003mjr.3	O15303	OTTHUMG00000130889	ENST00000517717.1:c.2497G>A	5.37:g.178408795C>T	ENSP00000430767:p.Gly833Ser		178341401	NM_000843		Missense_Mutation	SNP	ENST00000517717.1	37	CCDS4442.1	.	.	.	.	.	.	.	.	.	.	C	28.8	4.951815	0.92660	.	.	ENSG00000113262	ENST00000319065;ENST00000231188;ENST00000517717	D;D	0.88586	-2.4;-2.4	5.28	5.28	0.74379	GPCR, family 3, C-terminal (2);	.	.	.	.	D	0.92407	0.7590	L	0.51422	1.61	0.58432	D	0.999999	D;D	0.89917	1.0;0.999	D;D	0.72982	0.97;0.979	D	0.91692	0.5367	9	0.42905	T	0.14	.	16.7914	0.85590	0.0:1.0:0.0:0.0	.	833;127	O15303;Q5HYM4	GRM6_HUMAN;.	S	907;833;833	ENSP00000231188:G833S;ENSP00000430767:G833S	ENSP00000231188:G833S	G	-	1	0	GRM6	178341401	1.000000	0.71417	0.999000	0.59377	0.547000	0.35210	5.906000	0.69900	2.643000	0.89663	0.462000	0.41574	GGC		0.582	GRM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253474.2		
