#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
RHBDL2	54933	hgsc.bcm.edu	37	1	39352191	39352191	+	Silent	SNP	T	T	C			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:39352191T>C	ENST00000289248.2	-	8	1905	c.897A>G	c.(895-897)ctA>ctG	p.L299L	RHBDL2_ENST00000372985.3_Silent_p.L379L|RHBDL2_ENST00000538156.1_Silent_p.L366L|RP5-864K19.4_ENST00000433671.2_RNA|RHBDL2_ENST00000372990.1_Silent_p.L299L			Q9NX52	RHBL2_HUMAN	rhomboid, veinlet-like 2 (Drosophila)	299						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(3)	8	Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;8.23e-17)			TTGCTGGAGATAGGAAAATGT	0.363																																					p.L299L		Atlas-SNP	.											.	RHBDL2	28	.	0			c.A897G						.						77.0	71.0	73.0					1																	39352191		2203	4300	6503	SO:0001819	synonymous_variant	54933	exon8			TGGAGATAGGAAA	AK000442	CCDS30680.1	1p35.1	2014-01-28	2001-11-28		ENSG00000158315	ENSG00000158315			16083	protein-coding gene	gene with protein product		608962	"""rhomboid (veinlet, Drosophila)-like 2"""				Standard	NM_017821		Approved	FLJ20435	uc001ccu.1	Q9NX52	OTTHUMG00000000487	ENST00000289248.2:c.897A>G	chr1.hg19:g.39352191T>C		76.0	0.0		66.0	38.0	NM_017821	B2RNT3|B9EH75|Q6P175|Q8NER8|Q96E02	Silent	SNP	ENST00000289248.2	hg19	CCDS30680.1																																																																																			.	.		0.363	RHBDL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001216.1	NM_017821	
NASP	4678	hgsc.bcm.edu	37	1	46080777	46080777	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:46080777C>T	ENST00000350030.3	+	10	1846	c.1759C>T	c.(1759-1761)Cac>Tac	p.H587Y	NASP_ENST00000530073.1_3'UTR|NASP_ENST00000351223.3_Missense_Mutation_p.H248Y|NASP_ENST00000372052.4_Missense_Mutation_p.H221Y|NASP_ENST00000537798.1_Missense_Mutation_p.H523Y|NASP_ENST00000402363.3_Missense_Mutation_p.H589Y	NM_002482.3	NP_002473.2	P49321	NASP_HUMAN	nuclear autoantigenic sperm protein (histone-binding)	587	Glu-rich (acidic).				blastocyst development (GO:0001824)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone exchange (GO:0043486)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)	Hsp90 protein binding (GO:0051879)			breast(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	17	Acute lymphoblastic leukemia(166;0.155)|Lung SC(450;0.211)					TGCAGAGACCCACTACCAGCT	0.493																																					p.H587Y		Atlas-SNP	.											.	NASP	77	.	0			c.C1759T						.						84.0	79.0	81.0					1																	46080777		2203	4300	6503	SO:0001583	missense	4678	exon10			GAGACCCACTACC	M97856	CCDS524.1, CCDS525.1, CCDS55597.1	1p34.1	2013-01-10			ENSG00000132780	ENSG00000132780		"""Tetratricopeptide (TTC) repeat domain containing"""	7644	protein-coding gene	gene with protein product		603185				1426632	Standard	NM_002482		Approved	FLB7527, FLJ31599, FLJ35510, MGC19722, MGC20372, MGC2297, DKFZp547F162, PRO1999	uc001coi.2	P49321	OTTHUMG00000007826	ENST00000350030.3:c.1759C>T	chr1.hg19:g.46080777C>T	ENSP00000255120:p.His587Tyr	138.0	0.0		159.0	74.0	NM_002482	A8K6H2|B4DQP3|D3DQ07|F5H3J2|Q53GW5|Q5T622|Q5T625|Q96A69|Q9BTW2	Missense_Mutation	SNP	ENST00000350030.3	hg19	CCDS524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	24.6|24.6	4.551819|4.551819	0.86127|0.86127	.|.	.|.	ENSG00000132780|ENSG00000132780	ENST00000437901;ENST00000537798;ENST00000402363;ENST00000341288;ENST00000528238;ENST00000350030;ENST00000372052;ENST00000351223|ENST00000534450	T;T;T;T;T;T;T|.	0.71461|.	-0.57;0.29;0.29;0.29;0.29;0.29;0.29|.	5.3|5.3	5.3|5.3	0.74995|0.74995	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);|.	0.042533|.	0.85682|.	D|.	0.000000|.	T|T	0.63283|0.63283	0.2498|0.2498	L|L	0.52126|0.52126	1.63|1.63	0.58432|0.58432	D|D	0.999998|0.999998	D;D;B;B|.	0.76494|.	0.958;0.999;0.268;0.006|.	P;D;P;B|.	0.67548|.	0.781;0.952;0.488;0.03|.	T|T	0.59847|0.59847	-0.7377|-0.7377	10|5	0.87932|.	D|.	0|.	-5.2361|-5.2361	14.1917|14.1917	0.65641|0.65641	0.1495:0.8504:0.0:0.0|0.1495:0.8504:0.0:0.0	.|.	523;248;587;589|.	F5H3J2;Q5T626;P49321;P49321-3|.	.;.;NASP_HUMAN;.|.	Y|L	248;523;589;487;184;587;221;248|16	ENSP00000400792:H248Y;ENSP00000438871:H523Y;ENSP00000384529:H589Y;ENSP00000432289:H184Y;ENSP00000255120:H587Y;ENSP00000361122:H221Y;ENSP00000255121:H248Y|.	ENSP00000345532:H487Y|.	H|P	+|+	1|2	0|0	NASP|NASP	45853364|45853364	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.377000|5.377000	0.66184|0.66184	2.635000|2.635000	0.89317|0.89317	0.655000|0.655000	0.94253|0.94253	CAC|CCA	.	.		0.493	NASP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000021533.2	NM_002482	
CCDC18	343099	hgsc.bcm.edu	37	1	93649646	93649646	+	Silent	SNP	A	A	G			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:93649646A>G	ENST00000343253.7	+	3	748	c.246A>G	c.(244-246)gaA>gaG	p.E82E	CCDC18_ENST00000557479.1_Silent_p.E200E|CCDC18_ENST00000401026.3_Silent_p.E82E|CCDC18_ENST00000338949.4_5'UTR|CCDC18_ENST00000334652.5_5'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	82										breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		CACCTTATGAAAACGTCTGTA	0.348																																					p.E82E		Atlas-SNP	.											.	CCDC18	93	.	0			c.A246G						.						85.0	77.0	80.0					1																	93649646		1808	4075	5883	SO:0001819	synonymous_variant	343099	exon3			TTATGAAAACGTC			1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.246A>G	chr1.hg19:g.93649646A>G		89.0	0.0		118.0	48.0	NM_206886	Q6ZU17	Silent	SNP	ENST00000343253.7	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	2.242|2.242	-0.373521|-0.373521	0.05034|0.05034	.|.	.|.	ENSG00000122483|ENSG00000122483	ENST00000448243|ENST00000370276	.|.	.|.	.|.	5.75|5.75	0.14|0.14	0.14804|0.14804	.|.	.|.	.|.	.|.	.|.	T|T	0.34077|0.34077	0.0885|0.0885	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.22277|0.22277	-1.0221|-1.0221	4|4	.|.	.|.	.|.	.|.	4.5408|4.5408	0.12056|0.12056	0.4817:0.3081:0.2102:0.0|0.4817:0.3081:0.2102:0.0	.|.	.|.	.|.	.|.	E|R	129|136	.|.	.|.	K|K	+|+	1|2	0|0	CCDC18|CCDC18	93422234|93422234	0.999000|0.999000	0.42202|0.42202	0.848000|0.848000	0.33437|0.33437	0.332000|0.332000	0.28634|0.28634	0.495000|0.495000	0.22483|0.22483	-0.001000|-0.001000	0.14495|0.14495	0.482000|0.482000	0.46254|0.46254	AAA|AAA	.	.		0.348	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1	NM_206886	
VCAM1	7412	hgsc.bcm.edu	37	1	101194785	101194785	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:101194785A>G	ENST00000294728.2	+	5	1152	c.1051A>G	c.(1051-1053)Ata>Gta	p.I351V	VCAM1_ENST00000370115.1_Intron|VCAM1_ENST00000370119.4_Missense_Mutation_p.I289V|VCAM1_ENST00000347652.2_Intron	NM_001078.3	NP_001069.1	P19320	VCAM1_HUMAN	vascular cell adhesion molecule 1	351	Ig-like C2-type 4.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|amine metabolic process (GO:0009308)|B cell differentiation (GO:0030183)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-matrix adhesion (GO:0007160)|cellular response to glucose stimulus (GO:0071333)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|chorio-allantoic fusion (GO:0060710)|chronic inflammatory response (GO:0002544)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte tethering or rolling (GO:0050901)|membrane to membrane docking (GO:0022614)|oxidation-reduction process (GO:0055114)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|response to lipopolysaccharide (GO:0032496)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|viral process (GO:0016032)	alpha9-beta1 integrin-vascular cell adhesion molecule-1 complex (GO:0071065)|apical part of cell (GO:0045177)|cell surface (GO:0009986)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|podosome (GO:0002102)|sarcolemma (GO:0042383)	cell adhesion molecule binding (GO:0050839)|integrin binding (GO:0005178)|primary amine oxidase activity (GO:0008131)			central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(11)|liver(1)|lung(27)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	56		all_epithelial(167;3.83e-06)|all_lung(203;0.000485)|Lung NSC(277;0.0011)		Epithelial(280;0.0227)|all cancers(265;0.0276)|COAD - Colon adenocarcinoma(174;0.149)|Colorectal(144;0.169)|Lung(183;0.196)	Carvedilol(DB01136)	GAGAACCCAGATAGACAGCCC	0.542																																					p.I351V		Atlas-SNP	.											.	VCAM1	111	.	0			c.A1051G						.						107.0	109.0	108.0					1																	101194785		2203	4300	6503	SO:0001583	missense	7412	exon5			ACCCAGATAGACA	M60335	CCDS773.1, CCDS774.1, CCDS55617.1	1p32-p31	2014-01-30			ENSG00000162692	ENSG00000162692		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	12663	protein-coding gene	gene with protein product		192225					Standard	NM_080682		Approved	CD106	uc001dti.3	P19320	OTTHUMG00000010982	ENST00000294728.2:c.1051A>G	chr1.hg19:g.101194785A>G	ENSP00000294728:p.Ile351Val	163.0	0.0		198.0	73.0	NM_001078	A8K6R7|B4DKS4|E9PDD1|Q6NUP8	Missense_Mutation	SNP	ENST00000294728.2	hg19	CCDS773.1	.	.	.	.	.	.	.	.	.	.	A	6.714	0.500487	0.12822	.	.	ENSG00000162692	ENST00000370119;ENST00000294728	T;T	0.53423	0.62;2.96	5.41	3.07	0.35406	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.864402	0.10744	N	0.639117	T	0.27594	0.0678	M	0.81341	2.54	0.80722	D	1	B;B	0.22414	0.032;0.069	B;B	0.25614	0.062;0.062	T	0.19976	-1.0289	10	0.22706	T	0.39	-4.5994	4.2123	0.10517	0.677:0.1302:0.0681:0.1247	.	289;351	E9PDD1;P19320	.;VCAM1_HUMAN	V	289;351	ENSP00000359137:I289V;ENSP00000294728:I351V	ENSP00000294728:I351V	I	+	1	0	VCAM1	100967373	0.997000	0.39634	0.839000	0.33178	0.249000	0.25844	0.929000	0.28844	0.489000	0.27749	0.533000	0.62120	ATA	.	.		0.542	VCAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030213.1	NM_001078	
SPAG17	200162	hgsc.bcm.edu	37	1	118584651	118584651	+	Silent	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:118584651C>T	ENST00000336338.5	-	21	2894	c.2829G>A	c.(2827-2829)gaG>gaA	p.E943E		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	943						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ATCGATGTTGCTCTTCTTTCC	0.358																																					p.E943E		Atlas-SNP	.											.	SPAG17	263	.	0			c.G2829A						.						169.0	162.0	164.0					1																	118584651		2203	4300	6503	SO:0001819	synonymous_variant	200162	exon21			ATGTTGCTCTTCT		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.2829G>A	chr1.hg19:g.118584651C>T		82.0	0.0		97.0	28.0	NM_206996	Q8NAZ1|Q9NT21	Silent	SNP	ENST00000336338.5	hg19	CCDS899.1																																																																																			.	.		0.358	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
ATF3	467	hgsc.bcm.edu	37	1	212792748	212792748	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:212792748G>A	ENST00000341491.4	+	4	662	c.397G>A	c.(397-399)Gag>Aag	p.E133K	ATF3_ENST00000492118.1_3'UTR|ATF3_ENST00000366987.2_Missense_Mutation_p.E133K|ATF3_ENST00000366985.1_Missense_Mutation_p.E76K|ATF3_ENST00000366983.1_3'UTR	NM_001040619.2|NM_001206488.2|NM_001674.3	NP_001035709.1|NP_001193417.2|NP_001665.1	P18847	ATF3_HUMAN	activating transcription factor 3	133	Leucine-zipper. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|gluconeogenesis (GO:0006094)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle cell differentiation (GO:0035914)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|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 negative regulation of transcription (GO:0001078)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	6				OV - Ovarian serous cystadenocarcinoma(81;0.00628)|all cancers(67;0.0097)|GBM - Glioblastoma multiforme(131;0.0388)|Epithelial(68;0.0933)	Pseudoephedrine(DB00852)	GGCTCAGATTGAGGAGCTCAA	0.517																																					p.E133K		Atlas-SNP	.											.	ATF3	22	.	0			c.G397A						.						114.0	100.0	105.0					1																	212792748		2203	4300	6503	SO:0001583	missense	467	exon4			CAGATTGAGGAGC	L19871	CCDS1506.1, CCDS41464.1, CCDS55688.1, CCDS58059.1	1q32.3	2013-01-10			ENSG00000162772	ENSG00000162772		"""basic leucine zipper proteins"""	785	protein-coding gene	gene with protein product		603148				7515060	Standard	NM_001674		Approved		uc021pit.1	P18847	OTTHUMG00000036747	ENST00000341491.4:c.397G>A	chr1.hg19:g.212792748G>A	ENSP00000344352:p.Glu133Lys	79.0	0.0		124.0	41.0	NM_001674	Q5VTZ2|Q6ICQ9|Q7Z566|Q8WYM6	Missense_Mutation	SNP	ENST00000341491.4	hg19	CCDS1506.1	.	.	.	.	.	.	.	.	.	.	G	28.8	4.948807	0.92660	.	.	ENSG00000162772	ENST00000366981;ENST00000366987;ENST00000341491;ENST00000366985	T;T;T;T	0.55588	0.51;0.51;0.51;0.51	6.17	5.26	0.73747	Basic-leucine zipper (bZIP) transcription factor (2);bZIP transcription factor, bZIP-1 (1);	0.042570	0.85682	D	0.000000	T	0.55162	0.1903	L	0.49513	1.565	0.80722	D	1	P	0.35328	0.495	B	0.42555	0.391	T	0.50224	-0.8853	10	0.23891	T	0.37	-0.2071	17.6945	0.88277	0.0:0.1227:0.8773:0.0	.	133	P18847	ATF3_HUMAN	K	133;133;133;76	ENSP00000355948:E133K;ENSP00000355954:E133K;ENSP00000344352:E133K;ENSP00000355952:E76K	ENSP00000344352:E133K	E	+	1	0	ATF3	210859371	1.000000	0.71417	0.959000	0.39883	0.954000	0.61252	6.532000	0.73825	1.611000	0.50210	0.655000	0.94253	GAG	.	.		0.517	ATF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089296.1	NM_001674	
DISP1	84976	hgsc.bcm.edu	37	1	223116176	223116176	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr1:223116176G>A	ENST00000284476.6	+	2	175	c.11G>A	c.(10-12)aGc>aAc	p.S4N	DISP1_ENST00000495684.1_Intron|DISP1_ENST00000360254.2_Missense_Mutation_p.S4N	NM_032890.3	NP_116279.2	Q96F81	DISP1_HUMAN	dispatched homolog 1 (Drosophila)	4					determination of left/right symmetry (GO:0007368)|diaphragm development (GO:0060539)|dorsal/ventral pattern formation (GO:0009953)|embryonic pattern specification (GO:0009880)|patched ligand maturation (GO:0007225)|peptide transport (GO:0015833)|protein homotrimerization (GO:0070207)|regulation of protein secretion (GO:0050708)|smoothened signaling pathway (GO:0007224)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	hedgehog receptor activity (GO:0008158)|peptide transporter activity (GO:0015197)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(20)|lung(25)|prostate(4)|skin(1)|stomach(1)|urinary_tract(5)	69				GBM - Glioblastoma multiforme(131;0.102)		ATGGCTATGAGCAATGGAAAC	0.458																																					p.S4N		Atlas-SNP	.											.	DISP1	145	.	0			c.G11A						.						94.0	88.0	90.0					1																	223116176		2203	4300	6503	SO:0001583	missense	84976	exon4			CTATGAGCAATGG	AK056569	CCDS1536.1	1q42.12	2008-02-05			ENSG00000154309	ENSG00000154309			19711	protein-coding gene	gene with protein product		607502				10619433	Standard	NM_032890		Approved	DISPA, MGC13130, DKFZP434I0428, MGC16796	uc001hnu.2	Q96F81	OTTHUMG00000037893	ENST00000284476.6:c.11G>A	chr1.hg19:g.223116176G>A	ENSP00000284476:p.Ser4Asn	111.0	0.0		153.0	7.0	NM_032890	Q8N7C2|Q96I92|Q9H698|Q9H8H9|Q9UFA2	Missense_Mutation	SNP	ENST00000284476.6	hg19	CCDS1536.1	.	.	.	.	.	.	.	.	.	.	G	14.54	2.567095	0.45694	.	.	ENSG00000154309	ENST00000360254;ENST00000284476	T;D	0.93426	0.63;-3.22	5.77	3.86	0.44501	.	0.152863	0.56097	D	0.000032	D	0.88897	0.6562	L	0.46157	1.445	0.27661	N	0.947087	B	0.11235	0.004	B	0.11329	0.006	T	0.80054	-0.1543	10	0.44086	T	0.13	-17.7172	7.1702	0.25715	0.1408:0.0:0.7165:0.1427	.	4	Q96F81	DISP1_HUMAN	N	4	ENSP00000355848:S4N;ENSP00000284476:S4N	ENSP00000284476:S4N	S	+	2	0	DISP1	221182799	0.995000	0.38212	0.994000	0.49952	0.997000	0.91878	2.180000	0.42537	0.743000	0.32719	0.650000	0.86243	AGC	.	.		0.458	DISP1-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092512.1	NM_032890	
OTOF	9381	hgsc.bcm.edu	37	2	26681020	26681020	+	3'UTR	SNP	C	C	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:26681020C>A	ENST00000272371.2	-	0	6206				OTOF_ENST00000339598.3_Missense_Mutation_p.R1194L|OTOF_ENST00000403946.3_Missense_Mutation_p.R1961L|OTOF_ENST00000338581.6_3'UTR|OTOF_ENST00000402415.3_3'UTR	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin						membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCACTTGTACCGGGTGCAGAT	0.582																																					p.R1194L	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G3581T						.						92.0	79.0	84.0					2																	26681020		2203	4300	6503	SO:0001624	3_prime_UTR_variant	9381	exon29			TTGTACCGGGTGC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.*86G>T	chr2.hg19:g.26681020C>A		135.0	0.0		163.0	67.0	NM_194323	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	hg19	CCDS1725.1	.	.	.	.	.	.	.	.	.	.	C	17.61	3.431724	0.62844	.	.	ENSG00000115155	ENST00000339598;ENST00000403946;ENST00000361394	T;T	0.81247	-1.2;-1.47	4.93	4.06	0.47325	.	.	.	.	.	T	0.73984	0.3657	.	.	.	0.31931	N	0.612168	B	0.26120	0.142	B	0.26310	0.068	T	0.74253	-0.3725	8	0.44086	T	0.13	.	13.0503	0.58950	0.0:0.9207:0.0:0.0793	.	1194	Q9HC10-2	.	L	1194;1961;44	ENSP00000344521:R1194L;ENSP00000385255:R1961L	ENSP00000344521:R1194L	R	-	2	0	OTOF	26534524	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.909000	0.63314	1.069000	0.40788	0.551000	0.68910	CGG	.	.		0.582	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
MRPL35	51318	hgsc.bcm.edu	37	2	86433255	86433255	+	Missense_Mutation	SNP	G	G	T	rs17851803		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:86433255G>T	ENST00000337109.4	+	2	104	c.70G>T	c.(70-72)Gca>Tca	p.A24S	MRPL35_ENST00000409180.1_Missense_Mutation_p.A24S|MRPL35_ENST00000605125.1_Missense_Mutation_p.A24S|MRPL35_ENST00000254644.8_Missense_Mutation_p.A24S	NM_016622.3	NP_057706.2	Q9NZE8	RM35_HUMAN	mitochondrial ribosomal protein L35	24			A -> T (in dbSNP:rs17851803). {ECO:0000269|PubMed:15489334}.		translation (GO:0006412)	mitochondrial ribosome (GO:0005761)	structural constituent of ribosome (GO:0003735)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|skin(1)|stomach(1)|urinary_tract(2)	14						GAATATTTTGGCATCTTCAAC	0.378																																					p.A24S		Atlas-SNP	.											.	MRPL35	23	.	0			c.G70T						.						158.0	155.0	156.0					2																	86433255		2203	4300	6503	SO:0001583	missense	51318	exon2			ATTTTGGCATCTT	AF208849	CCDS1987.1, CCDS1988.1	2p11.2	2012-09-13			ENSG00000132313	ENSG00000132313		"""Mitochondrial ribosomal proteins / large subunits"""	14489	protein-coding gene	gene with protein product		611841				11042152, 11551941	Standard	NM_016622		Approved		uc002srg.4	Q9NZE8	OTTHUMG00000037385	ENST00000337109.4:c.70G>T	chr2.hg19:g.86433255G>T	ENSP00000338389:p.Ala24Ser	352.0	1.0		426.0	167.0	NM_016622	A6NKV6|B2RB93|Q658U7|Q8WWA2	Missense_Mutation	SNP	ENST00000337109.4	hg19	CCDS1988.1	.	.	.	.	.	.	.	.	.	.	G	17.36	3.370309	0.61624	.	.	ENSG00000132313	ENST00000254644;ENST00000337109;ENST00000409180	T;T;T	0.15139	2.48;2.71;2.45	5.62	5.62	0.85841	.	0.594515	0.18878	N	0.128652	T	0.20088	0.0483	L	0.60455	1.87	0.29229	N	0.873397	B	0.31318	0.319	B	0.30105	0.111	T	0.05649	-1.0872	10	0.30078	T	0.28	-1.2034	15.5672	0.76303	0.0:0.0:1.0:0.0	.	24	Q9NZE8	RM35_HUMAN	S	24	ENSP00000254644:A24S;ENSP00000338389:A24S;ENSP00000386255:A24S	ENSP00000254644:A24S	A	+	1	0	MRPL35	86286766	0.998000	0.40836	0.581000	0.28614	0.971000	0.66376	3.301000	0.51842	2.820000	0.97059	0.650000	0.86243	GCA	.	G|1.000;|0.000		0.378	MRPL35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000091002.2	NM_016622	
DNAH7	56171	hgsc.bcm.edu	37	2	196799358	196799358	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:196799358C>A	ENST00000312428.6	-	21	3528	c.3428G>T	c.(3427-3429)tGg>tTg	p.W1143L		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	1143	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TTCAACCAACCACTTCTCCAC	0.373																																					p.W1143L		Atlas-SNP	.											.	DNAH7	512	.	0			c.G3428T						.						185.0	179.0	181.0					2																	196799358		1856	4112	5968	SO:0001583	missense	56171	exon21			ACCAACCACTTCT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.3428G>T	chr2.hg19:g.196799358C>A	ENSP00000311273:p.Trp1143Leu	193.0	0.0		201.0	77.0	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	hg19	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	C	32	5.116190	0.94339	.	.	ENSG00000118997	ENST00000312428	T	0.71341	-0.56	5.72	5.72	0.89469	Dynein heavy chain, domain-2 (1);	0.000000	0.85682	D	0.000000	D	0.91942	0.7448	H	0.99545	4.62	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95125	0.8250	10	0.87932	D	0	.	19.474	0.94979	0.0:1.0:0.0:0.0	.	1143	Q8WXX0	DYH7_HUMAN	L	1143	ENSP00000311273:W1143L	ENSP00000311273:W1143L	W	-	2	0	DNAH7	196507603	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.661000	0.83786	2.695000	0.91970	0.655000	0.94253	TGG	.	.		0.373	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
SF3B1	23451	hgsc.bcm.edu	37	2	198274569	198274569	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:198274569C>A	ENST00000335508.6	-	7	920	c.829G>T	c.(829-831)Gcg>Tcg	p.A277S		NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	277	Interaction with PPP1R8.|U2AF homology region; mediates interaction with RMB39.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			CCTGGTGTCGCATGGCCTGGT	0.547			Mis		myelodysplastic syndrome																																p.A277S		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	.	SF3B1	1038	.	0			c.G829T						.						222.0	220.0	221.0					2																	198274569		2203	4300	6503	SO:0001583	missense	23451	exon7			GTGTCGCATGGCC	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.829G>T	chr2.hg19:g.198274569C>A	ENSP00000335321:p.Ala277Ser	142.0	0.0		155.0	60.0	NM_012433	E9PCH3	Missense_Mutation	SNP	ENST00000335508.6	hg19	CCDS33356.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442572	0.43326	.	.	ENSG00000115524	ENST00000335508	.	.	.	5.36	5.36	0.76844	.	0.000000	0.85682	D	0.000000	T	0.57140	0.2033	N	0.22421	0.69	0.80722	D	1	P	0.44690	0.841	P	0.54210	0.745	T	0.48115	-0.9063	9	0.11485	T	0.65	.	19.0839	0.93194	0.0:1.0:0.0:0.0	.	277	O75533	SF3B1_HUMAN	S	277	.	ENSP00000335321:A277S	A	-	1	0	SF3B1	197982814	1.000000	0.71417	0.731000	0.30826	0.485000	0.33311	7.729000	0.84864	2.502000	0.84385	0.655000	0.94253	GCG	.	.		0.547	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
ABCA12	26154	hgsc.bcm.edu	37	2	215848388	215848388	+	Silent	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:215848388G>A	ENST00000272895.7	-	29	4584	c.4365C>T	c.(4363-4365)ctC>ctT	p.L1455L	ABCA12_ENST00000389661.4_Silent_p.L1137L	NM_173076.2	NP_775099.2	Q86UK0	ABCAC_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 12	1455	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cellular homeostasis (GO:0019725)|ceramide transport (GO:0035627)|establishment of skin barrier (GO:0061436)|keratinization (GO:0031424)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lung alveolus development (GO:0048286)|phospholipid efflux (GO:0033700)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of protein localization to cell surface (GO:2000010)|protein localization to plasma membrane (GO:0072659)|regulated secretory pathway (GO:0045055)|secretion by cell (GO:0032940)|surfactant homeostasis (GO:0043129)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|epidermal lamellar body (GO:0097209)|integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|plasma membrane (GO:0005886)	apolipoprotein A-I receptor binding (GO:0034191)|ATP binding (GO:0005524)|lipid transporter activity (GO:0005319)|lipid-transporting ATPase activity (GO:0034040)|receptor binding (GO:0005102)			NS(3)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(45)|lung(44)|ovary(8)|pancreas(2)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	139		Renal(323;0.127)		Epithelial(149;1.01e-05)|all cancers(144;0.00112)|LUSC - Lung squamous cell carcinoma(224;0.00829)|Lung(261;0.011)		CTTCCTCGTGGAGCTGCTTTT	0.433																																					p.L1455L	Ovarian(66;664 1488 5121 34295)	Atlas-SNP	.											.	ABCA12	368	.	0			c.C4365T						.						171.0	155.0	161.0					2																	215848388		2203	4300	6503	SO:0001819	synonymous_variant	26154	exon29			CTCGTGGAGCTGC	AF418105	CCDS33372.1, CCDS33373.1	2q34	2012-03-14			ENSG00000144452	ENSG00000144452		"""ATP binding cassette transporters / subfamily A"""	14637	protein-coding gene	gene with protein product		607800	"""ichthyosis congenita II, lamellar ichthyosis B"""	ICR2B		11435397, 12915478, 8845852, 10094194	Standard	NM_015657		Approved	DKFZP434G232, LI2	uc002vew.3	Q86UK0	OTTHUMG00000154801	ENST00000272895.7:c.4365C>T	chr2.hg19:g.215848388G>A		121.0	0.0		130.0	56.0	NM_173076	Q53QE2|Q53S55|Q8IZW6|Q96JT3|Q9Y4M5	Silent	SNP	ENST00000272895.7	hg19	CCDS33372.1																																																																																			.	.		0.433	ABCA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337111.1	NM_173076	
CTNNB1	1499	hgsc.bcm.edu	37	3	41266098	41266098	+	Missense_Mutation	SNP	A	A	G	rs121913396|rs121913416		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:41266098A>G	ENST00000349496.5	+	3	375	c.95A>G	c.(94-96)gAc>gGc	p.D32G	CTNNB1_ENST00000396185.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000405570.1_Missense_Mutation_p.D32G|CTNNB1_ENST00000396183.3_Missense_Mutation_p.D32G|CTNNB1_ENST00000453024.1_Missense_Mutation_p.D25G	NM_001904.3	NP_001895.1	P35222	CTNB1_HUMAN	catenin (cadherin-associated protein), beta 1, 88kDa	32			D -> A (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.|D -> G (in PTR and hepatocellular carcinoma). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629}.|D -> Y (in PTR, hepatoblastoma and hepatocellular carcinoma; dbSNP:rs28931588). {ECO:0000269|PubMed:10192393, ECO:0000269|PubMed:10435629, ECO:0000269|PubMed:11703283, ECO:0000269|PubMed:9927029}.|Missing (in hepatocellular carcinoma). {ECO:0000269|PubMed:10435629}.		adherens junction assembly (GO:0034333)|androgen receptor signaling pathway (GO:0030521)|anterior/posterior axis specification (GO:0009948)|apoptotic process (GO:0006915)|bone resorption (GO:0045453)|branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of cardiac outflow tract cell proliferation (GO:0061324)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|cell adhesion (GO:0007155)|cell fate specification (GO:0001708)|cell maturation (GO:0048469)|cell-matrix adhesion (GO:0007160)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to growth factor stimulus (GO:0071363)|cellular response to indole-3-methanol (GO:0071681)|cellular response to mechanical stimulus (GO:0071260)|central nervous system vasculogenesis (GO:0022009)|cytoskeletal anchoring at plasma membrane (GO:0007016)|determination of dorsal/ventral asymmetry (GO:0048262)|dorsal/ventral axis specification (GO:0009950)|ectoderm development (GO:0007398)|embryonic axis specification (GO:0000578)|embryonic digit morphogenesis (GO:0042733)|embryonic foregut morphogenesis (GO:0048617)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal limb joint morphogenesis (GO:0036023)|endodermal cell fate commitment (GO:0001711)|endothelial tube morphogenesis (GO:0061154)|epithelial cell differentiation involved in prostate gland development (GO:0060742)|epithelial to mesenchymal transition (GO:0001837)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|fungiform papilla formation (GO:0061198)|gastrulation with mouth forming second (GO:0001702)|genitalia morphogenesis (GO:0035112)|glial cell fate determination (GO:0007403)|hair cell differentiation (GO:0035315)|hair follicle morphogenesis (GO:0031069)|hair follicle placode formation (GO:0060789)|hindbrain development (GO:0030902)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|layer formation in cerebral cortex (GO:0021819)|lens morphogenesis in camera-type eye (GO:0002089)|liver development (GO:0001889)|lung cell differentiation (GO:0060479)|lung induction (GO:0060492)|lung-associated mesenchyme development (GO:0060484)|male genitalia development (GO:0030539)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|midgut development (GO:0007494)|muscle cell differentiation (GO:0042692)|myoblast differentiation (GO:0045445)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of neuron death (GO:1901215)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein sumoylation (GO:0033234)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nephron tubule formation (GO:0072079)|neural plate development (GO:0001840)|neuron migration (GO:0001764)|odontogenesis of dentin-containing tooth (GO:0042475)|oocyte development (GO:0048599)|osteoclast differentiation (GO:0030316)|oviduct development (GO:0060066)|pancreas development (GO:0031016)|patterning of blood vessels (GO:0001569)|positive regulation of apoptotic process (GO:0043065)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of determination of dorsal identity (GO:2000017)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of epithelial cell proliferation involved in prostate gland development (GO:0060769)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein heterooligomerization (GO:0051291)|protein localization to cell surface (GO:0034394)|proximal/distal pattern formation (GO:0009954)|regulation of angiogenesis (GO:0045765)|regulation of calcium ion import (GO:0090279)|regulation of centriole-centriole cohesion (GO:0030997)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of fibroblast proliferation (GO:0048145)|regulation of myelination (GO:0031641)|regulation of nephron tubule epithelial cell differentiation (GO:0072182)|regulation of protein localization to cell surface (GO:2000008)|regulation of secondary heart field cardioblast proliferation (GO:0003266)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of T cell proliferation (GO:0042129)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|renal vesicle formation (GO:0072033)|response to cadmium ion (GO:0046686)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|Schwann cell proliferation (GO:0014010)|single organismal cell-cell adhesion (GO:0016337)|smooth muscle cell differentiation (GO:0051145)|synapse organization (GO:0050808)|synaptic vesicle transport (GO:0048489)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tongue morphogenesis (GO:0043587)|trachea formation (GO:0060440)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|basolateral plasma membrane (GO:0016323)|beta-catenin destruction complex (GO:0030877)|beta-catenin-TCF7L2 complex (GO:0070369)|catenin complex (GO:0016342)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cell periphery (GO:0071944)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microvillus membrane (GO:0031528)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Scrib-APC-beta-catenin complex (GO:0034750)|synapse (GO:0045202)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|androgen receptor binding (GO:0050681)|cadherin binding (GO:0045296)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|estrogen receptor binding (GO:0030331)|I-SMAD binding (GO:0070411)|ion channel binding (GO:0044325)|kinase binding (GO:0019900)|nuclear hormone receptor binding (GO:0035257)|protein C-terminus binding (GO:0008022)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|R-SMAD binding (GO:0070412)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|SMAD binding (GO:0046332)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.D32G(65)|p.A5_A80del(53)|p.D32V(33)|p.D32A(16)|p.A5_Q143del(7)|p.A5_A80>D(7)|p.Q28_H134del(5)|p.WQQQSYLD25?(5)|p.W25_D32del(4)|p.?(4)|p.V22_G38del(3)|p.W25_I140del(3)|p.T3_A126del(2)|p.S23_S33del(2)|p.V22_S33del(2)|p.A5fs*7(2)|p.D32_S47del(2)|p.M5_N141>D(2)|p.L10_N141del(2)|p.A5_Y142>D(2)|p.Y30_S33del(2)|p.A5_Q143>E(1)|p.A13_R151del(1)|p.S29_H36del(1)|p.D32del(1)|p.M14_S45del(1)|p.Q28_D32>H(1)|p.A20_N141del(1)|p.M1_A87del(1)|p.D11_Y142>H(1)|p.H24_G38del(1)|p.S23_I35del(1)|p.Y30_A97del(1)|p.W25_S33del(1)|p.V22_T102del(1)|p.A20_A80del(1)|p.V22_S71>A(1)|p.Q28_A43del(1)|p.A5_T59del(1)|p.D32fs*9(1)|p.A20_I35del(1)|p.M1_V173del(1)|p.E15_I140>V(1)|p.S23_A39del(1)|p.H24_M131del(1)|p.A21_A80del(1)|p.Y30_A80del(1)|p.A5_T40del(1)|p.A5_E54del(1)|p.W25_I35del(1)|p.M8_A80del(1)|p.P16_K133del(1)|p.V22_Y64del(1)|p.Q28_Q61del(1)|p.A20_S111del(1)|p.Y30_T40del(1)|p.A5_I35del(1)|p.D32_H36del(1)	CTNNB1/PLAG1(60)	NS(4)|adrenal_gland(103)|biliary_tract(43)|bone(21)|breast(7)|central_nervous_system(260)|cervix(9)|endometrium(293)|eye(1)|haematopoietic_and_lymphoid_tissue(60)|kidney(202)|large_intestine(269)|liver(1010)|lung(63)|oesophagus(6)|ovary(106)|pancreas(126)|parathyroid(11)|pituitary(111)|pleura(2)|prostate(31)|salivary_gland(13)|skin(103)|small_intestine(17)|soft_tissue(792)|stomach(165)|thyroid(55)|upper_aerodigestive_tract(2)|urinary_tract(8)	3893				KIRC - Kidney renal clear cell carcinoma(284;0.0028)|Kidney(284;0.00294)		TCTTACCTGGACTCTGGAATC	0.483	D32V(HEC265_ENDOMETRIUM)|D32V(HEC6_ENDOMETRIUM)	15	"""H, Mis, T"""	PLAG1	"""colorectal, cvarian,  hepatoblastoma, others, pleomorphic salivary adenoma"""				Pilomatrixoma, Familial Clustering of																												p.D32G	Colon(6;3 56 14213 18255)	Atlas-SNP	.		Dom	yes		3	3p22-p21.3	1499	"""catenin (cadherin-associated protein), beta 1"""		"""E, M, O"""	CTNNB1,gallbladder,other,+1,128	CTNNB1	4904	.	260	Deletion - In frame(120)|Substitution - Missense(114)|Complex - deletion inframe(16)|Unknown(7)|Deletion - Frameshift(3)	liver(154)|large_intestine(24)|pancreas(19)|central_nervous_system(16)|stomach(14)|endometrium(7)|skin(7)|ovary(4)|prostate(3)|pituitary(3)|small_intestine(2)|NS(2)|adrenal_gland(1)|soft_tissue(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|urinary_tract(1)	c.A95G						.						92.0	77.0	82.0					3																	41266098		2203	4300	6503	SO:0001583	missense	1499	exon3	Familial Cancer Database	Pilomatricoma, Familial Clustering of, Epithelioma Calcificans of Malherbe	ACCTGGACTCTGG	X87838	CCDS2694.1	3p21	2013-02-15	2002-08-29		ENSG00000168036	ENSG00000168036		"""Armadillo repeat containing"""	2514	protein-coding gene	gene with protein product		116806	"""catenin (cadherin-associated protein), beta 1 (88kD)"""	CTNNB		7829088	Standard	NM_001098210		Approved	beta-catenin, armadillo	uc003ckr.2	P35222	OTTHUMG00000131393	ENST00000349496.5:c.95A>G	chr3.hg19:g.41266098A>G	ENSP00000344456:p.Asp32Gly	161.0	0.0		258.0	84.0	NM_001098209	A8K1L7|Q8NEW9|Q8NI94|Q9H391	Missense_Mutation	SNP	ENST00000349496.5	hg19	CCDS2694.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.308122	0.81247	.	.	ENSG00000168036	ENST00000426215;ENST00000405570;ENST00000431914;ENST00000396183;ENST00000349496;ENST00000453024;ENST00000396185;ENST00000450969;ENST00000441708	T;T;T;T;T;T;T;T;T	0.50001	0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76;0.76	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.69788	0.3150	M	0.79614	2.46	0.80722	D	1	D	0.89917	1.0	D	0.74674	0.984	T	0.74137	-0.3762	10	0.87932	D	0	0.3843	16.0676	0.80897	1.0:0.0:0.0:0.0	.	32	P35222	CTNB1_HUMAN	G	25;32;32;32;32;25;32;32;32	ENSP00000400508:D25G;ENSP00000385604:D32G;ENSP00000412219:D32G;ENSP00000379486:D32G;ENSP00000344456:D32G;ENSP00000411226:D25G;ENSP00000379488:D32G;ENSP00000409302:D32G;ENSP00000401599:D32G	ENSP00000344456:D32G	D	+	2	0	CTNNB1	41241102	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.339000	0.96797	2.201000	0.70794	0.533000	0.62120	GAC	.	.		0.483	CTNNB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254182.2	NM_001098210	
CACNA2D2	9254	hgsc.bcm.edu	37	3	50404287	50404287	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:50404287C>T	ENST00000479441.1	-	30	2584	c.2585G>A	c.(2584-2586)cGt>cAt	p.R862H	CACNA2D2_ENST00000424201.2_Missense_Mutation_p.R855H|CACNA2D2_ENST00000266039.3_Missense_Mutation_p.R855H|XXcos-LUCA11.4_ENST00000606259.1_RNA|CACNA2D2_ENST00000423994.2_Missense_Mutation_p.R862H|CACNA2D2_ENST00000395083.1_Missense_Mutation_p.R855H|CACNA2D2_ENST00000429770.1_Missense_Mutation_p.R855H|CACNA2D2_ENST00000435965.1_Missense_Mutation_p.R862H|XXcos-LUCA11.4_ENST00000607583.1_RNA|CACNA2D2_ENST00000360963.3_Missense_Mutation_p.R786H|XXcos-LUCA11.4_ENST00000607088.1_RNA|XXcos-LUCA11.4_ENST00000607362.1_RNA|XXcos-LUCA11.5_ENST00000606589.1_Intron|XXcos-LUCA11.4_ENST00000606665.1_RNA|XXcos-LUCA11.4_ENST00000607121.1_RNA			Q9NY47	CA2D2_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 2	862					energy reserve metabolic process (GO:0006112)|muscle fiber development (GO:0048747)|neuromuscular junction development (GO:0007528)|positive regulation of organ growth (GO:0046622)|regulation of insulin secretion (GO:0050796)|regulation of multicellular organism growth (GO:0040014)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|cervix(1)|endometrium(4)|large_intestine(4)|lung(8)|ovary(2)|prostate(4)|skin(4)|urinary_tract(1)	31				BRCA - Breast invasive adenocarcinoma(193;0.000365)|KIRC - Kidney renal clear cell carcinoma(197;0.00862)|Kidney(197;0.01)	Amiodarone(DB01118)|Bepridil(DB01244)|Felodipine(DB01023)|Gabapentin(DB00996)|Isradipine(DB00270)|Nitrendipine(DB01054)|Spironolactone(DB00421)	TTGGTGGGTACGGTTGCTGGC	0.617																																					p.R862H		Atlas-SNP	.											.	CACNA2D2	82	.	0			c.G2585A						.						64.0	54.0	57.0					3																	50404287		2202	4299	6501	SO:0001583	missense	9254	exon30			TGGGTACGGTTGC	AF040709	CCDS33763.1, CCDS54588.1, CCDS63647.1	3p21.3	2004-02-27			ENSG00000007402	ENSG00000007402		"""Calcium channel subunits"""	1400	protein-coding gene	gene with protein product	"""gene 26"""	607082					Standard	XM_005265581		Approved	KIAA0558	uc003daq.3	Q9NY47	OTTHUMG00000156887	ENST00000479441.1:c.2585G>A	chr3.hg19:g.50404287C>T	ENSP00000418081:p.Arg862His	46.0	0.0		52.0	6.0	NM_001174051	A7MD15|Q9NY48|Q9UEW0|Q9Y268	Missense_Mutation	SNP	ENST00000479441.1	hg19	CCDS54588.1	.	.	.	.	.	.	.	.	.	.	C	11.61	1.689400	0.29962	.	.	ENSG00000007402	ENST00000423994;ENST00000429770;ENST00000266039;ENST00000360963;ENST00000435965;ENST00000395083;ENST00000424201;ENST00000479441	T;T;T;T;T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82;-0.82;-0.82;-0.82;-0.82	5.22	5.22	0.72569	.	0.946890	0.08901	N	0.877207	T	0.58793	0.2147	N	0.08118	0	0.35394	D	0.790977	B;B	0.15930	0.011;0.015	B;B	0.08055	0.002;0.003	T	0.50406	-0.8832	10	0.13853	T	0.58	-6.9204	17.359	0.87345	0.0:1.0:0.0:0.0	.	862;855	Q9NY47;Q9NY47-2	CA2D2_HUMAN;.	H	862;855;855;786;862;855;855;862	ENSP00000407393:R862H;ENSP00000404631:R855H;ENSP00000266039:R855H;ENSP00000354228:R786H;ENSP00000390526:R862H;ENSP00000378519:R855H;ENSP00000390329:R855H;ENSP00000418081:R862H	ENSP00000266039:R855H	R	-	2	0	CACNA2D2	50379291	0.995000	0.38212	1.000000	0.80357	0.995000	0.86356	3.024000	0.49674	2.436000	0.82500	0.655000	0.94253	CGT	.	.		0.617	CACNA2D2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346457.1	NM_006030	
CADPS	8618	hgsc.bcm.edu	37	3	62648033	62648033	+	Silent	SNP	G	G	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:62648033G>T	ENST00000383710.4	-	4	1274	c.925C>A	c.(925-927)Cga>Aga	p.R309R	CADPS_ENST00000283269.9_Silent_p.R309R|CADPS_ENST00000490353.2_Silent_p.R309R|CADPS_ENST00000357948.3_Silent_p.R309R	NM_003716.3	NP_003707.2	Q9ULU8	CAPS1_HUMAN	Ca++-dependent secretion activator	309					catecholamine secretion (GO:0050432)|exocytosis (GO:0006887)|protein transport (GO:0015031)|synaptic vesicle priming (GO:0016082)|vesicle organization (GO:0016050)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)|synapse (GO:0045202)	lipid binding (GO:0008289)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)			breast(3)|central_nervous_system(2)|endometrium(6)|kidney(6)|large_intestine(24)|lung(38)|ovary(4)|prostate(3)|skin(3)|stomach(1)|urinary_tract(2)	92		Lung SC(41;0.0452)		BRCA - Breast invasive adenocarcinoma(55;5.98e-05)|KIRC - Kidney renal clear cell carcinoma(15;0.0246)|Kidney(15;0.0334)		TCCAGCTCTCGTCTGATCTGG	0.493																																					p.R309R		Atlas-SNP	.											.	CADPS	387	.	0			c.C925A						.						165.0	136.0	146.0					3																	62648033		2203	4300	6503	SO:0001819	synonymous_variant	8618	exon4			GCTCTCGTCTGAT	U36448	CCDS2898.1, CCDS2899.1, CCDS46858.1	3p21.1	2013-01-10	2008-08-28		ENSG00000163618	ENSG00000163618		"""Pleckstrin homology (PH) domain containing"""	1426	protein-coding gene	gene with protein product		604667				1516133	Standard	NM_183393		Approved	CAPS, KIAA1121, CAPS1	uc003dll.2	Q9ULU8	OTTHUMG00000158651	ENST00000383710.4:c.925C>A	chr3.hg19:g.62648033G>T		67.0	0.0		42.0	24.0	NM_003716	A6NF60|Q13339|Q6GQQ6|Q8N2Z5|Q8N3M7|Q8NFR0|Q96BC2	Silent	SNP	ENST00000383710.4	hg19	CCDS46858.1																																																																																			.	.		0.493	CADPS-013	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351951.5	NM_003716, NM_183393, NM_183394	
LRIG1	26018	hgsc.bcm.edu	37	3	66430695	66430695	+	Missense_Mutation	SNP	T	T	G	rs199537042		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:66430695T>G	ENST00000273261.3	-	19	3798	c.3274A>C	c.(3274-3276)Aaa>Caa	p.K1092Q	LRIG1_ENST00000383703.3_Missense_Mutation_p.K1069Q|LRIG1_ENST00000496559.2_5'UTR|SLC25A26_ENST00000536651.1_3'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	1092					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		ACCTAGCTTTTTGGTGCCAAC	0.552																																					p.K1092Q		Atlas-SNP	.											.	LRIG1	138	.	0			c.A3274C						.						58.0	55.0	56.0					3																	66430695		2203	4300	6503	SO:0001583	missense	26018	exon19			AGCTTTTTGGTGC	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.3274A>C	chr3.hg19:g.66430695T>G	ENSP00000273261:p.Lys1092Gln	81.0	0.0		74.0	26.0	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	hg19	CCDS33783.1	.	.	.	.	.	.	.	.	.	.	T	10.68	1.418757	0.25552	.	.	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.64260	-0.09;-0.04	5.27	2.8	0.32819	.	0.480260	0.19445	N	0.114081	T	0.47783	0.1464	N	0.24115	0.695	0.21841	N	0.999518	B;B;B	0.14438	0.01;0.005;0.003	B;B;B	0.18561	0.022;0.003;0.007	T	0.40175	-0.9577	10	0.51188	T	0.08	.	12.1617	0.54107	0.0:0.0:0.2707:0.7292	.	1069;1092;1092	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	Q	1092;1069;995	ENSP00000273261:K1092Q;ENSP00000373208:K1069Q	ENSP00000273261:K1092Q	K	-	1	0	LRIG1	66513385	0.437000	0.25593	0.729000	0.30791	0.078000	0.17371	2.453000	0.44970	0.290000	0.22444	-0.313000	0.08912	AAA	.	.		0.552	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
EPHA3	2042	hgsc.bcm.edu	37	3	89259351	89259351	+	Silent	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:89259351C>T	ENST00000336596.2	+	3	720	c.495C>T	c.(493-495)aaC>aaT	p.N165N	EPHA3_ENST00000452448.2_Silent_p.N165N|EPHA3_ENST00000494014.1_Silent_p.N165N	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	165	Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		TGAAGCTCAACACTGAGATTA	0.418										TSP Lung(6;0.00050)																											p.N165N		Atlas-SNP	.											.	EPHA3	501	.	0			c.C495T						.						157.0	136.0	143.0					3																	89259351		2203	4300	6503	SO:0001819	synonymous_variant	2042	exon3			GCTCAACACTGAG	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.495C>T	chr3.hg19:g.89259351C>T		117.0	0.0		106.0	45.0	NM_005233	Q9H2V3|Q9H2V4	Silent	SNP	ENST00000336596.2	hg19	CCDS2922.1																																																																																			.	.		0.418	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
IFT122	55764	hgsc.bcm.edu	37	3	129239078	129239078	+	Missense_Mutation	SNP	C	C	G			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:129239078C>G	ENST00000348417.2	+	30	3773	c.3696C>G	c.(3694-3696)tgC>tgG	p.C1232W	IFT122_ENST00000504021.1_Missense_Mutation_p.C1109W|IFT122_ENST00000347300.2_Missense_Mutation_p.C1173W|IFT122_ENST00000507564.1_Missense_Mutation_p.C1225W|IFT122_ENST00000296266.3_Missense_Mutation_p.C1283W|IFT122_ENST00000440957.2_Missense_Mutation_p.C1023W|IFT122_ENST00000431818.2_Missense_Mutation_p.C1082W|IFT122_ENST00000349441.2_Missense_Mutation_p.C1122W	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1232					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						GCCCCTACTGCCGCAGGTGCA	0.587																																					p.C1283W		Atlas-SNP	.											.	IFT122	117	.	0			c.C3849G						.						78.0	64.0	68.0					3																	129239078		2203	4300	6503	SO:0001583	missense	55764	exon31			CTACTGCCGCAGG	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3696C>G	chr3.hg19:g.129239078C>G	ENSP00000324005:p.Cys1232Trp	24.0	0.0		31.0	5.0	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Missense_Mutation	SNP	ENST00000348417.2	hg19	CCDS3061.1	.	.	.	.	.	.	.	.	.	.	C	16.91	3.251713	0.59212	.	.	ENSG00000163913	ENST00000347300;ENST00000296266;ENST00000507564;ENST00000431818;ENST00000504021;ENST00000349441;ENST00000348417;ENST00000446384;ENST00000440957	T;T;T;T;T;T;T;T	0.74526	-0.18;-0.85;-0.69;-0.65;-0.01;-0.02;-0.22;-0.6	5.69	2.84	0.33178	.	0.000000	0.85682	D	0.000000	D	0.85261	0.5656	M	0.85777	2.775	0.80722	D	1	D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;0.998;1.0;1.0;1.0;1.0;1.0;0.999;1.0	D;D;D;D;D;D;D;D;D;D	0.97110	0.997;1.0;0.987;1.0;0.999;0.999;0.999;1.0;0.993;0.997	D	0.85357	0.1105	10	0.87932	D	0	-25.7075	9.606	0.39634	0.0:0.5836:0.0:0.4164	.	1023;558;1225;620;1109;1074;1122;1173;1232;1283	E9PDG2;B3KUD1;E7EQF4;B3KT43;B4DEY9;B4DPW7;Q9BTY4;Q9HBG6-3;Q9HBG6;G3XAB1	.;.;.;.;.;.;.;.;IF122_HUMAN;.	W	1173;1283;1225;1082;1109;1122;1232;1074;1023	ENSP00000323973:C1173W;ENSP00000296266:C1283W;ENSP00000425536:C1225W;ENSP00000410946:C1082W;ENSP00000422179:C1109W;ENSP00000324165:C1122W;ENSP00000324005:C1232W;ENSP00000401569:C1023W	ENSP00000296266:C1283W	C	+	3	2	IFT122	130721768	0.997000	0.39634	1.000000	0.80357	0.941000	0.58515	0.541000	0.23207	0.714000	0.32081	0.563000	0.77884	TGC	.	.		0.587	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
FAM157A	728262	hgsc.bcm.edu	37	3	197880167	197880167	+	lincRNA	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr3:197880167G>A	ENST00000437428.2	+	0	47							C9JC47	F157A_HUMAN	family with sequence similarity 157, member A											NS(1)|skin(1)	2						agcagcagcagcagcaACTGG	0.527																																					p.Q82Q		Atlas-SNP	.											.	FAM157A	4	.	0			c.G246A						.						2.0	6.0	5.0					3																	197880167		369	1057	1426			728262	exon2			GCAGCAGCAGCAA			3q29	2013-01-30			ENSG00000236438	ENSG00000236438			34079	other	unknown							Standard	NM_001145248		Approved		uc011bup.1	C9JC47			chr3.hg19:g.197880167G>A		276.0	0.0		315.0	21.0	NM_001145248		Silent	SNP	ENST00000437428.2	hg19																																																																																				.	.		0.527	FAM157A-001	KNOWN	not_best_in_genome_evidence|mRNA_end_NF|basic	lincRNA	lincRNA	OTTHUMT00000340078.2	NM_001145248	
TMEM175	84286	hgsc.bcm.edu	37	4	944244	944244	+	Silent	SNP	A	A	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:944244A>T	ENST00000264771.4	+	4	413	c.228A>T	c.(226-228)acA>acT	p.T76T	TMEM175_ENST00000504180.1_3'UTR|TMEM175_ENST00000508204.1_De_novo_Start_OutOfFrame|TMEM175_ENST00000515740.1_De_novo_Start_OutOfFrame	NM_032326.2	NP_115702.1	Q9BSA9	TM175_HUMAN	transmembrane protein 175	76						integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				NS(1)|endometrium(1)|large_intestine(2)|lung(6)|pancreas(1)|upper_aerodigestive_tract(3)	14			OV - Ovarian serous cystadenocarcinoma(23;0.0158)			TTCTGGCAACACGGATTGCCG	0.577																																					p.T76T		Atlas-SNP	.											.	TMEM175	44	.	0			c.A228T						.						131.0	114.0	120.0					4																	944244		2203	4300	6503	SO:0001819	synonymous_variant	84286	exon4			GGCAACACGGATT	BC005158	CCDS3341.1, CCDS75087.1, CCDS75088.1	4p16.3	2008-02-05			ENSG00000127419	ENSG00000127419			28709	protein-coding gene	gene with protein product						12477932	Standard	XM_005272301		Approved	MGC4618	uc003gbq.3	Q9BSA9	OTTHUMG00000118996	ENST00000264771.4:c.228A>T	chr4.hg19:g.944244A>T		149.0	0.0		177.0	83.0	NM_032326	D3DVN4|Q8ND13	Silent	SNP	ENST00000264771.4	hg19	CCDS3341.1																																																																																			.	.		0.577	TMEM175-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239193.2	NM_032326	
EVC2	132884	hgsc.bcm.edu	37	4	5620343	5620343	+	Missense_Mutation	SNP	A	A	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:5620343A>T	ENST00000344408.5	-	15	2621	c.2568T>A	c.(2566-2568)caT>caA	p.H856Q	EVC2_ENST00000344938.1_Missense_Mutation_p.H856Q|EVC2_ENST00000310917.2_Missense_Mutation_p.H776Q	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	856					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						CAAAGCAGCCATGGACCTCCT	0.567																																					p.H856Q		Atlas-SNP	.											.	EVC2	202	.	0			c.T2568A						.						36.0	33.0	34.0					4																	5620343		2203	4300	6503	SO:0001583	missense	132884	exon15			GCAGCCATGGACC	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.2568T>A	chr4.hg19:g.5620343A>T	ENSP00000342144:p.His856Gln	147.0	0.0		159.0	83.0	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	hg19	CCDS3382.2	.	.	.	.	.	.	.	.	.	.	A	3.921	-0.018201	0.07681	.	.	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.73363	-0.74;-0.72;-0.73	5.3	-7.38	0.01407	.	0.000000	0.85682	D	0.000000	T	0.48223	0.1488	N	0.20986	0.625	0.09310	N	0.999993	B	0.17465	0.022	B	0.14023	0.01	T	0.44922	-0.9296	10	0.11485	T	0.65	-10.0435	9.8688	0.41162	0.3791:0.4641:0.1568:0.0	.	856	Q86UK5	LBN_HUMAN	Q	856;776;856	ENSP00000339954:H856Q;ENSP00000311683:H776Q;ENSP00000342144:H856Q	ENSP00000311683:H776Q	H	-	3	2	EVC2	5671244	0.330000	0.24705	0.069000	0.20011	0.711000	0.40976	-0.495000	0.06443	-1.498000	0.01824	-1.148000	0.01847	CAT	.	.		0.567	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
PLRG1	5356	hgsc.bcm.edu	37	4	155457860	155457860	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:155457860T>G	ENST00000499023.2	-	15	1648	c.1522A>C	c.(1522-1524)Att>Ctt	p.I508L	PLRG1_ENST00000302078.5_Missense_Mutation_p.I499L|PLRG1_ENST00000393905.2_Missense_Mutation_p.I508L	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	508					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				CTCTTGATAATTTCTGGTTTC	0.289																																					p.I508L		Atlas-SNP	.											.	PLRG1	43	.	0			c.A1522C						.						49.0	53.0	52.0					4																	155457860		2198	4283	6481	SO:0001583	missense	5356	exon15			TGATAATTTCTGG	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1522A>C	chr4.hg19:g.155457860T>G	ENSP00000424417:p.Ile508Leu	201.0	0.0		215.0	94.0	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Missense_Mutation	SNP	ENST00000499023.2	hg19	CCDS34083.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	9.825|9.825	1.186766|1.186766	0.21870|0.21870	.|.	.|.	ENSG00000171566|ENSG00000171566	ENST00000499023;ENST00000393905;ENST00000302078|ENST00000503251	T;T;T|T	0.61158|0.63096	0.13;0.13;0.17|-0.02	5.4|5.4	4.2|4.2	0.49525|0.49525	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.48187|0.48187	0.1486|0.1486	L|L	0.31752|0.31752	0.955|0.955	0.58432|0.58432	D|D	0.999999|0.999999	B;B|.	0.09022|.	0.002;0.0|.	B;B|.	0.06405|.	0.002;0.001|.	T|T	0.40156|0.40156	-0.9578|-0.9578	10|7	0.11485|0.02654	T|T	0.65|1	-22.8578|-22.8578	11.226|11.226	0.48884|0.48884	0.0:0.0745:0.0:0.9255|0.0:0.0745:0.0:0.9255	.|.	499;508|.	O43660-2;O43660|.	.;PLRG1_HUMAN|.	L|T	508;508;499|86	ENSP00000424417:I508L;ENSP00000377483:I508L;ENSP00000303191:I499L|ENSP00000426497:N86T	ENSP00000303191:I499L|ENSP00000426497:N86T	I|N	-|-	1|2	0|0	PLRG1|PLRG1	155677310|155677310	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.696000|5.696000	0.68287|0.68287	2.046000|2.046000	0.60703|0.60703	0.482000|0.482000	0.46254|0.46254	ATT|AAT	.	.		0.289	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
PLRG1	5356	hgsc.bcm.edu	37	4	155460301	155460301	+	Silent	SNP	T	T	C			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr4:155460301T>C	ENST00000499023.2	-	12	1233	c.1107A>G	c.(1105-1107)acA>acG	p.T369T	PLRG1_ENST00000302078.5_Silent_p.T360T|PLRG1_ENST00000393905.2_Silent_p.T369T	NM_001201564.1|NM_002669.3	NP_001188493.1|NP_002660.1	O43660	PLRG1_HUMAN	pleiotropic regulator 1	369					mRNA splicing, via spliceosome (GO:0000398)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|protein localization to nucleus (GO:0034504)|regulation of RNA biosynthetic process (GO:2001141)|signal transduction (GO:0007165)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(11)|skin(1)|urinary_tract(1)	22	all_hematologic(180;0.215)	Renal(120;0.0854)				TTTTGTGATTTGTTAATGTCA	0.348																																					p.T369T		Atlas-SNP	.											.	PLRG1	43	.	0			c.A1107G						.						237.0	220.0	225.0					4																	155460301		2203	4300	6503	SO:0001819	synonymous_variant	5356	exon12			GTGATTTGTTAAT	AF044333	CCDS34083.1, CCDS56341.1	4q31.2-q32.1	2013-01-10	2011-05-19		ENSG00000171566	ENSG00000171566		"""WD repeat domain containing"""	9089	protein-coding gene	gene with protein product	"""transport and golgi organization 4 homolog (Drosophila)"""	605961	"""pleiotropic regulator 1 (PRL1, Arabidopsis homolog)"", ""pleiotropic regulator 1 (PRL1 homolog, Arabidopsis)"""				Standard	NM_002669		Approved	PRL1, Prp46, PRPF46, Cwc1, TANGO4	uc003iny.3	O43660	OTTHUMG00000161411	ENST00000499023.2:c.1107A>G	chr4.hg19:g.155460301T>C		126.0	0.0		135.0	65.0	NM_002669	B3KMK4|Q3KQY5|Q8WUD8	Silent	SNP	ENST00000499023.2	hg19	CCDS34083.1																																																																																			.	.		0.348	PLRG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364824.1	NM_002669	
KIAA0825	285600	hgsc.bcm.edu	37	5	93798152	93798152	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:93798152T>C	ENST00000513200.3	-	11	2258	c.2186A>G	c.(2185-2187)cAt>cGt	p.H729R	KIAA0825_ENST00000312498.7_Missense_Mutation_p.H729R|KIAA0825_ENST00000427991.2_Missense_Mutation_p.H729R	NM_001145678.1	NP_001139150.1	Q8IV33	K0825_HUMAN	KIAA0825	729										breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(1)|pancreas(1)|prostate(1)|skin(1)	13						ATTATTACAATGAGTGTGAAT	0.274																																					p.H729R		Atlas-SNP	.											.	KIAA0825	172	.	0			c.A2186G						.						81.0	73.0	76.0					5																	93798152		692	1585	2277	SO:0001583	missense	285600	exon12			TTACAATGAGTGT	BX648338	CCDS4070.1	5q15	2011-02-23	2011-02-23	2011-02-23	ENSG00000185261	ENSG00000185261			28532	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 36"""	C5orf36		12477932	Standard	NM_173665		Approved	DKFZp686F0372, MGC34713	uc011cuk.2	Q8IV33	OTTHUMG00000131331	ENST00000513200.3:c.2186A>G	chr5.hg19:g.93798152T>C	ENSP00000424618:p.His729Arg	314.0	0.0		558.0	332.0	NM_001145678	O94914|Q6ZNN2	Missense_Mutation	SNP	ENST00000513200.3	hg19		.	.	.	.	.	.	.	.	.	.	T	6.930	0.541368	0.13250	.	.	ENSG00000185261	ENST00000513200;ENST00000427991;ENST00000312498	T;T;T	0.46063	0.88;0.88;0.88	5.51	4.35	0.52113	.	0.193223	0.34025	N	0.004321	T	0.41581	0.1165	M	0.66939	2.045	0.31999	N	0.60364	B	0.18166	0.026	B	0.18561	0.022	T	0.50285	-0.8846	10	0.48119	T	0.1	.	11.3381	0.49516	0.0:0.0713:0.0:0.9287	.	729	Q8IV33	K0825_HUMAN	R	729	ENSP00000424618:H729R;ENSP00000400288:H729R;ENSP00000312205:H729R	ENSP00000312205:H729R	H	-	2	0	KIAA0825	93823908	1.000000	0.71417	0.974000	0.42286	0.632000	0.37999	5.433000	0.66520	1.032000	0.39892	0.533000	0.62120	CAT	.	.		0.274	KIAA0825-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000254102.5	NM_173665	
PCDH12	51294	hgsc.bcm.edu	37	5	141324975	141324976	+	Missense_Mutation	DNP	CT	CT	TG	rs13188049|rs3833449		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:141324975_141324976CT>TG	ENST00000231484.3	-	4	4735_4736	c.3525_3526AG>CA	c.(3523-3528)agAGgc>agCAgc	p.1175_1176RG>SS		NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	1175					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ctgctgctgcctctgctCTTGC	0.584																																					p.G1176S|p.R1175S		Atlas-SNP	.											.	PCDH12	133	.	0			c.G3526A|c.A3525C						.																																			SO:0001583	missense	51294	exon4			TGCTGCCTCTGCT|GCTGCCTCTGCTC	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.3525_3526delinsTG	chr5.hg19:g.141324975_141324976delinsTG	ENSP00000231484:p.R1175_G1176delinsSS	43.0|44.0	0.0		125.0	14.0|12.0	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.		0.584	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
GABRA1	2554	hgsc.bcm.edu	37	5	161317904	161317904	+	Splice_Site	SNP	G	G	C			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:161317904G>C	ENST00000428797.2	+	9	1059	c.704G>C	c.(703-705)gGa>gCa	p.G235A	GABRA1_ENST00000420560.1_Splice_Site_p.G235A|GABRA1_ENST00000444819.1_Splice_Site_p.G235A|GABRA1_ENST00000023897.6_Splice_Site_p.G235A|GABRA1_ENST00000393943.4_Splice_Site_p.G235A|GABRA1_ENST00000437025.2_Splice_Site_p.G235A	NM_001127643.1	NP_001121115.1	P14867	GBRA1_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 1	235					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|drug binding (GO:0008144)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|endometrium(2)|kidney(3)|large_intestine(4)|liver(1)|lung(22)|ovary(2)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(1)	42	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.228)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethanol(DB00898)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Ketazolam(DB01587)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methohexital(DB00474)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Prazepam(DB01588)|Primidone(DB00794)|Progabide(DB00837)|Propofol(DB00818)|Quazepam(DB01589)|Quinidine barbiturate(DB01346)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiamylal(DB01154)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zaleplon(DB00962)|Zolpidem(DB00425)|Zopiclone(DB01198)	TACTTCTCAGGAGAATATGTT	0.363																																					p.G235A		Atlas-SNP	.											.	GABRA1	132	.	0			c.G704C						.						121.0	115.0	117.0					5																	161317904		2203	4300	6503	SO:0001630	splice_region_variant	2554	exon9			TCTCAGGAGAATA		CCDS4357.1	5q34	2012-06-22			ENSG00000022355	ENSG00000022355		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4075	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 1"""	137160				1330891	Standard	NM_000806		Approved	EJM5	uc003lyx.4	P14867	OTTHUMG00000163586	ENST00000428797.2:c.704-1G>C	chr5.hg19:g.161317904G>C		69.0	0.0		110.0	67.0	NM_001127643	D3DQK6|Q8N629	Missense_Mutation	SNP	ENST00000428797.2	hg19	CCDS4357.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.424680	0.83667	.	.	ENSG00000022355	ENST00000023897;ENST00000428797;ENST00000393943;ENST00000437025;ENST00000420560;ENST00000444819	T;T;T;T;T;T	0.80738	-1.41;-1.41;-1.41;-1.41;-1.41;-1.41	5.52	5.52	0.82312	Neurotransmitter-gated ion-channel ligand-binding (3);	0.000000	0.85682	D	0.000000	D	0.92766	0.7700	M	0.93638	3.44	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.94197	0.7446	9	.	.	.	.	19.4464	0.94849	0.0:0.0:1.0:0.0	.	235	P14867	GBRA1_HUMAN	A	235	ENSP00000023897:G235A;ENSP00000393097:G235A;ENSP00000377517:G235A;ENSP00000415441:G235A;ENSP00000408041:G235A;ENSP00000414232:G235A	.	G	+	2	0	GABRA1	161250482	1.000000	0.71417	1.000000	0.80357	0.732000	0.41865	9.695000	0.98691	2.603000	0.88011	0.650000	0.86243	GGA	.	.		0.363	GABRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252702.2	NM_000806.5	Missense_Mutation
DRD1	1812	hgsc.bcm.edu	37	5	174869355	174869355	+	Missense_Mutation	SNP	G	G	A	rs200037245	byFrequency	TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr5:174869355G>A	ENST00000393752.2	-	2	1740	c.748C>T	c.(748-750)Cct>Tct	p.P250S		NM_000794.3	NP_000785.1	P21728	DRD1_HUMAN	dopamine receptor D1	250					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult walking behavior (GO:0007628)|astrocyte development (GO:0014002)|behavioral fear response (GO:0001662)|behavioral response to cocaine (GO:0048148)|cellular response to catecholamine stimulus (GO:0071870)|cerebral cortex GABAergic interneuron migration (GO:0021853)|conditioned taste aversion (GO:0001661)|dentate gyrus development (GO:0021542)|dopamine metabolic process (GO:0042417)|dopamine transport (GO:0015872)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose import (GO:0046323)|grooming behavior (GO:0007625)|habituation (GO:0046959)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|maternal behavior (GO:0042711)|mating behavior (GO:0007617)|memory (GO:0007613)|neuronal action potential (GO:0019228)|operant conditioning (GO:0035106)|peristalsis (GO:0030432)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of potassium ion transport (GO:0043268)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|prepulse inhibition (GO:0060134)|protein import into nucleus (GO:0006606)|regulation of dopamine metabolic process (GO:0042053)|regulation of dopamine uptake involved in synaptic transmission (GO:0051584)|response to amphetamine (GO:0001975)|response to drug (GO:0042493)|sensitization (GO:0046960)|striatum development (GO:0021756)|synapse assembly (GO:0007416)|synaptic transmission, dopaminergic (GO:0001963)|temperature homeostasis (GO:0001659)|transmission of nerve impulse (GO:0019226)|vasodilation (GO:0042311)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	23	all_cancers(89;0.00895)|Renal(175;0.000159)|Lung NSC(126;0.00625)|all_lung(126;0.0104)	Medulloblastoma(196;0.0208)|all_neural(177;0.0277)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)		Acepromazine(DB01614)|Acetophenazine(DB01063)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Chlorprothixene(DB01239)|Cinnarizine(DB00568)|Clozapine(DB00363)|Dopamine(DB00988)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Flupentixol(DB00875)|Fluphenazine(DB00623)|Haloperidol(DB00502)|Iloperidone(DB04946)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Methylergometrine(DB00353)|Mianserin(DB06148)|Minaprine(DB00805)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Paliperidone(DB01267)|Pergolide(DB01186)|Perphenazine(DB00850)|Phenylpropanolamine(DB00397)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Promazine(DB00420)|Propericiazine(DB01608)|Propiomazine(DB00777)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Thioproperazine(DB01622)|Thioridazine(DB00679)|Thiothixene(DB01623)|Triflupromazine(DB00508)|Trimipramine(DB00726)|Ziprasidone(DB00246)	CATTCGACAGGCTTTCCATTA	0.478													G|||	2	0.000399361	0.0	0.0	5008	,	,		20953	0.0		0.0	False		,,,				2504	0.002				p.P250S		Atlas-SNP	.											.	DRD1	56	.	0			c.C748T						.						101.0	105.0	103.0					5																	174869355		2203	4300	6503	SO:0001583	missense	1812	exon2			CGACAGGCTTTCC	X55760	CCDS4393.1	5q34-q35	2012-08-08			ENSG00000184845	ENSG00000184845		"""GPCR / Class A : Dopamine receptors"""	3020	protein-coding gene	gene with protein product		126449					Standard	NM_000794		Approved		uc003mcz.3	P21728	OTTHUMG00000130557	ENST00000393752.2:c.748C>T	chr5.hg19:g.174869355G>A	ENSP00000377353:p.Pro250Ser	65.0	0.0		122.0	31.0	NM_000794	B2RA44|Q4QRJ0	Missense_Mutation	SNP	ENST00000393752.2	hg19	CCDS4393.1	.	.	.	.	.	.	.	.	.	.	G	2.740	-0.262460	0.05791	.	.	ENSG00000184845	ENST00000393752;ENST00000329144	T	0.69435	-0.4	5.2	3.05	0.35203	GPCR, rhodopsin-like superfamily (1);	0.351936	0.34110	N	0.004243	T	0.27697	0.0681	N	0.01009	-1.055	0.22479	N	0.999064	B	0.02656	0.0	B	0.09377	0.004	T	0.34004	-0.9846	10	0.02654	T	1	.	7.3006	0.26418	0.0:0.1267:0.5002:0.3731	.	250	P21728	DRD1_HUMAN	S	250	ENSP00000377353:P250S	ENSP00000327652:P250S	P	-	1	0	DRD1	174801961	1.000000	0.71417	0.195000	0.23364	0.521000	0.34408	3.417000	0.52714	1.281000	0.44480	0.650000	0.86243	CCT	.	G|0.999;A|0.001		0.478	DRD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252982.2	NM_000794	
DPCR1	135656	hgsc.bcm.edu	37	6	30918818	30918818	+	Silent	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr6:30918818G>A	ENST00000462446.1	+	2	2605	c.2577G>A	c.(2575-2577)gaG>gaA	p.E859E	DPCR1_ENST00000304311.2_5'UTR|HCG21_ENST00000419481.1_RNA			Q3MIW9	DPCR1_HUMAN	diffuse panbronchiolitis critical region 1	303						integral component of membrane (GO:0016021)				endometrium(1)|kidney(2)|large_intestine(3)|lung(3)|pancreas(1)	10						TCCCAGCAGAGCCTACAGAAA	0.473																																					p.E859E		Atlas-SNP	.											.	DPCR1	99	.	0			c.G2577A						.						79.0	70.0	73.0					6																	30918818		692	1591	2283	SO:0001819	synonymous_variant	135656	exon2			AGCAGAGCCTACA	AB064272	CCDS4692.1, CCDS4692.2	6p21.32	2008-02-05			ENSG00000168631	ENSG00000168631			21666	protein-coding gene	gene with protein product		613928				12185533, 10677310	Standard	NM_080870		Approved	PBLT, bCX105N19.6	uc003nsg.2	Q3MIW9	OTTHUMG00000031104	ENST00000462446.1:c.2577G>A	chr6.hg19:g.30918818G>A		70.0	0.0		88.0	44.0	NM_080870	C9IZC0|Q658M7|Q8WYN2	Silent	SNP	ENST00000462446.1	hg19	CCDS4692.2																																																																																			.	.		0.473	DPCR1-001	NOVEL	not_organism_supported|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000076173.3	NM_080870	
DDX39B	7919	hgsc.bcm.edu	37	6	31500561	31500561	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr6:31500561T>C	ENST00000396172.1	-	7	1493	c.863A>G	c.(862-864)aAc>aGc	p.N288S	DDX39B_ENST00000376177.2_Missense_Mutation_p.N288S|DDX39B_ENST00000415382.2_Missense_Mutation_p.N210S|DDX39B_ENST00000462421.1_5'Flank|DDX39B_ENST00000458640.1_Missense_Mutation_p.N288S|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR|DDX39B_ENST00000417556.2_Missense_Mutation_p.N303S	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	288	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						ACTGACCTGGTTGAACTCAAG	0.473																																					p.N288S		Atlas-SNP	.											DDX39B,NS,carcinoma,0,1	DDX39B	38	.	0			c.A863G						.						129.0	105.0	114.0					6																	31500561		1511	2709	4220	SO:0001583	missense	7919	exon7			ACCTGGTTGAACT	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"""DEAD-boxes"""	13917	protein-coding gene	gene with protein product	"""U2AF65-associated protein 56"""	142560	"""HLA-B associated transcript 1"""	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.863A>G	chr6.hg19:g.31500561T>C	ENSP00000379475:p.Asn288Ser	101.0	0.0		142.0	65.0	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Missense_Mutation	SNP	ENST00000396172.1	hg19	CCDS4697.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.3|20.3	3.965361|3.965361	0.74131|0.74131	.|.	.|.	ENSG00000198563|ENSG00000198563	ENST00000376177;ENST00000458640;ENST00000396172;ENST00000417556;ENST00000415382;ENST00000431908;ENST00000427214|ENST00000417023	D;T;T;T;T;T;T|.	0.92099|.	-2.97;3.61;3.61;3.61;3.61;3.61;3.37|.	5.28|5.28	5.28|5.28	0.74379|0.74379	Helicase, C-terminal (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.45895|0.45895	0.1365|0.1365	L|L	0.41236|0.41236	1.265|1.265	0.80722|0.80722	D|D	1|1	D;D;D;P|.	0.89917|.	0.967;1.0;0.984;0.806|.	P;D;P;P|.	0.77004|.	0.561;0.989;0.703;0.796|.	T|T	0.44847|0.44847	-0.9301|-0.9301	10|5	0.72032|.	D|.	0.01|.	-18.6328|-18.6328	13.1727|13.1727	0.59609|0.59609	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	210;288;288;303|.	B4DP52;Q13838;Q5STU3;F8VQ10|.	.;DX39B_HUMAN;.;.|.	S|A	288;288;288;303;210;210;288|52	ENSP00000365347:N288S;ENSP00000416269:N288S;ENSP00000379475:N288S;ENSP00000412582:N303S;ENSP00000392669:N210S;ENSP00000408000:N210S;ENSP00000399371:N288S|.	ENSP00000365347:N288S|.	N|T	-|-	2|1	0|0	DDX39B|DDX39B	31608540|31608540	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.673000|7.673000	0.83973|0.83973	2.000000|2.000000	0.58554|0.58554	0.533000|0.533000	0.62120|0.62120	AAC|ACC	.	.		0.473	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640	
TAS2R39	259285	hgsc.bcm.edu	37	7	142880762	142880762	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr7:142880762T>C	ENST00000446620.1	+	1	251	c.251T>C	c.(250-252)aTa>aCa	p.I84T		NM_176881.2	NP_795362.2	P59534	T2R39_HUMAN	taste receptor, type 2, member 39	84					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	Melanoma(164;0.059)					GTATCCAGAATAGCTCTCCAA	0.393																																					p.I84T		Atlas-SNP	.											.	TAS2R39	42	.	0			c.T251C						.						115.0	109.0	111.0					7																	142880762		1871	4113	5984	SO:0001583	missense	259285	exon1			CCAGAATAGCTCT	AF494230	CCDS47729.1	7q34	2012-08-22			ENSG00000236398	ENSG00000236398		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	18886	protein-coding gene	gene with protein product						12379855	Standard	NM_176881		Approved		uc011ksw.2	P59534	OTTHUMG00000152636	ENST00000446620.1:c.251T>C	chr7.hg19:g.142880762T>C	ENSP00000405095:p.Ile84Thr	54.0	0.0		78.0	34.0	NM_176881	A4FUI7|Q3ZCN6|Q645W4	Missense_Mutation	SNP	ENST00000446620.1	hg19	CCDS47729.1	.	.	.	.	.	.	.	.	.	.	T	17.02	3.282503	0.59867	.	.	ENSG00000236398	ENST00000446620	T	0.01192	5.2	4.76	2.35	0.29111	.	.	.	.	.	T	0.05318	0.0141	M	0.86864	2.845	0.22317	N	0.999204	D	0.58970	0.984	P	0.57960	0.83	T	0.17289	-1.0374	9	0.87932	D	0	.	7.1654	0.25687	0.0:0.0776:0.147:0.7754	.	84	P59534	T2R39_HUMAN	T	84	ENSP00000405095:I84T	ENSP00000405095:I84T	I	+	2	0	TAS2R39	142590884	0.581000	0.26741	0.306000	0.25113	0.937000	0.57800	1.411000	0.34702	0.398000	0.25338	0.528000	0.53228	ATA	.	.		0.393	TAS2R39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327090.2	NM_176881	
SH2D4A	63898	hgsc.bcm.edu	37	8	19192209	19192209	+	Silent	SNP	T	T	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr8:19192209T>A	ENST00000265807.3	+	4	765	c.354T>A	c.(352-354)tcT>tcA	p.S118S	SH2D4A_ENST00000519207.1_Silent_p.S118S|SH2D4A_ENST00000518040.1_Silent_p.S73S	NM_001174160.1|NM_022071.3	NP_001167631.1|NP_071354.2	Q9H788	SH24A_HUMAN	SH2 domain containing 4A	118					negative regulation of phosphatase activity (GO:0010923)	cytoplasm (GO:0005737)	phosphatase binding (GO:0019902)			endometrium(2)|kidney(1)|large_intestine(5)|lung(7)|stomach(1)	16				Colorectal(111;0.0732)		AAACTCACTCTGAAGAATTCA	0.388																																					p.S118S		Atlas-SNP	.											.	SH2D4A	49	.	0			c.T354A						.						62.0	63.0	63.0					8																	19192209		2203	4300	6503	SO:0001819	synonymous_variant	63898	exon4			TCACTCTGAAGAA	AY190323	CCDS6009.1, CCDS55206.1	8p21	2013-02-14			ENSG00000104611	ENSG00000104611		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""SH2 domain containing"""	26102	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 38"""	614968					Standard	NM_022071		Approved	FLJ20967, SH2A, PPP1R38	uc003wzc.3	Q9H788	OTTHUMG00000097005	ENST00000265807.3:c.354T>A	chr8.hg19:g.19192209T>A		98.0	0.0		126.0	62.0	NM_022071	B4DDR1|Q5XKC1|Q6NXE9|Q86YM2|Q96C88|Q9H7F7	Silent	SNP	ENST00000265807.3	hg19	CCDS6009.1																																																																																			.	.		0.388	SH2D4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214094.1	NM_022071	
NRG1	3084	hgsc.bcm.edu	37	8	32505644	32505644	+	Intron	SNP	G	G	A	rs192228210		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr8:32505644G>A	ENST00000405005.3	+	5	502				NRG1_ENST00000520502.2_Silent_p.S136S|NRG1_ENST00000521670.1_Intron|NRG1_ENST00000523079.1_Intron|NRG1_ENST00000341377.5_Intron|NRG1_ENST00000338921.4_Intron|NRG1_ENST00000287842.3_Intron|NRG1_ENST00000287845.5_Intron|NRG1_ENST00000519301.1_Intron|NRG1_ENST00000356819.4_Intron|NRG1_ENST00000520407.1_Intron			Q02297	NRG1_HUMAN	neuregulin 1						activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		TGTGGGTGTCGTCTGAGGCAT	0.502																																					p.S136S		Atlas-SNP	.											.	NRG1	260	.	0			c.G408A						.						147.0	128.0	134.0					8																	32505644		2203	4300	6503	SO:0001627	intron_variant	3084	exon1			GGTGTCGTCTGAG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.502+31241G>A	chr8.hg19:g.32505644G>A		93.0	0.0		110.0	19.0	NM_013959	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Silent	SNP	ENST00000405005.3	hg19	CCDS6085.1																																																																																			.	G|1.000;T|0.000		0.502	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
CCDC171	203238	hgsc.bcm.edu	37	9	15778979	15778980	+	Missense_Mutation	DNP	CG	CG	AC	rs375214888		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C|G	C|G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr9:15778979_15778980CG>AC	ENST00000380701.3	+	20	3240_3241	c.2912_2913CG>AC	c.(2911-2913)tCG>tAC	p.S971Y	RNU6-14P_ENST00000384630.1_RNA|CCDC171_ENST00000297641.3_Missense_Mutation_p.S971Y	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	971																	AGCACAGCATCGTTGCAGAAGC	0.366																																					p.S971X|p.S971S		Atlas-SNP	.											.	.	.	.	0			c.C2912A|c.G2913C						.																																			SO:0001583	missense	203238	exon20			CAGCATCGTTGCA|AGCATCGTTGCAG	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	Exception_encountered	chr9.hg19:g.15778979_15778980delinsAC	ENSP00000370077:p.Ser971Tyr	111.0|110.0	0.0		41.0	24.0	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Nonsense_Mutation|Silent	SNP	ENST00000380701.3	hg19	CCDS6481.1																																																																																			.	.		0.366	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
ANKRD18B	441459	hgsc.bcm.edu	37	9	33558114	33558114	+	Missense_Mutation	SNP	T	T	C			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr9:33558114T>C	ENST00000290943.6	+	12	2299	c.2203T>C	c.(2203-2205)Ttc>Ctc	p.F735L		NM_001244752.1	NP_001231681.1	A2A2Z9	AN18B_HUMAN	ankyrin repeat domain 18B	735										NS(1)|breast(1)|endometrium(2)|lung(1)|prostate(1)|stomach(1)	7						AAATGAAGACTTCAGTTGCCA	0.279																																					p.F734L		Atlas-SNP	.											.	ANKRD18B	46	.	0			c.T2200C						.																																			SO:0001583	missense	441459	exon12			GAAGACTTCAGTT			9p13.3	2013-01-10			ENSG00000230453	ENSG00000230453		"""Ankyrin repeat domain containing"""	23644	protein-coding gene	gene with protein product							Standard	NM_001244752		Approved	bA255A11.3	uc010mjw.2	A2A2Z9	OTTHUMG00000019776	ENST00000290943.6:c.2203T>C	chr9.hg19:g.33558114T>C	ENSP00000290943:p.Phe735Leu	696.0	1.0		1103.0	733.0	NM_001244752		Missense_Mutation	SNP	ENST00000290943.6	hg19		.	.	.	.	.	.	.	.	.	.	t	1.323	-0.599027	0.03744	.	.	ENSG00000230453	ENST00000290943;ENST00000357927	T;T	0.25579	1.79;3.27	1.72	0.431	0.16523	.	.	.	.	.	T	0.08492	0.0211	.	.	.	0.22896	N	0.998591	.	.	.	.	.	.	T	0.37314	-0.9711	5	0.07175	T	0.84	.	3.187	0.06604	0.0:0.4348:0.0:0.5652	.	.	.	.	L	735;116	ENSP00000290943:F735L;ENSP00000350607:F116L	ENSP00000290943:F735L	F	+	1	0	ANKRD18B	33548114	0.000000	0.05858	0.009000	0.14445	0.241000	0.25554	-0.102000	0.10956	0.106000	0.17784	0.240000	0.17902	TTC	.	.		0.279	ANKRD18B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000313729.2	XM_001718334	
FRMPD1	22844	hgsc.bcm.edu	37	9	37707441	37707441	+	Missense_Mutation	SNP	G	G	T	rs2296556	byFrequency	TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr9:37707441G>T	ENST00000539465.1	+	3	723	c.130G>T	c.(130-132)Gcc>Tcc	p.A44S	FRMPD1_ENST00000377765.3_Missense_Mutation_p.A44S|RP11-613M10.9_ENST00000540557.1_Intron			Q5SYB0	FRPD1_HUMAN	FERM and PDZ domain containing 1	44			A -> T (in dbSNP:rs2296556).			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				NS(3)|breast(2)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(22)|lung(34)|ovary(5)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	93				GBM - Glioblastoma multiforme(29;0.00655)		TGATGGGCCCGCCAGGAACCC	0.498																																					p.A44S		Atlas-SNP	.											.	FRMPD1	237	.	0			c.G130T						.						91.0	94.0	93.0					9																	37707441		2203	4300	6503	SO:0001583	missense	22844	exon3			GGGCCCGCCAGGA	AB023184	CCDS6612.1	9p13.1	2008-02-05			ENSG00000070601	ENSG00000070601			29159	protein-coding gene	gene with protein product						10231032	Standard	NM_014907		Approved	KIAA0967, FRMD2	uc004aag.1	Q5SYB0	OTTHUMG00000019927	ENST00000539465.1:c.130G>T	chr9.hg19:g.37707441G>T	ENSP00000444411:p.Ala44Ser	93.0	0.0		104.0	23.0	NM_014907	B4DZC8|B7Z807|D3DRQ3|Q14C73|Q5HY96|Q9Y2H3	Missense_Mutation	SNP	ENST00000539465.1	hg19	CCDS6612.1	.	.	.	.	.	.	.	.	.	.	G	6.373	0.437009	0.12104	.	.	ENSG00000070601	ENST00000377765;ENST00000539465;ENST00000359927	T;T;T	0.37752	1.18;1.18;1.84	5.66	-3.77	0.04346	PDZ/DHR/GLGF (1);	0.757438	0.12731	N	0.443880	T	0.14356	0.0347	N	0.14661	0.345	0.54753	P	1.0999999999983245E-5	B	0.06786	0.001	B	0.04013	0.001	T	0.27088	-1.0084	9	0.16896	T	0.51	-2.5959	3.8898	0.09114	0.1038:0.285:0.4164:0.1948	.	44	Q5SYB0	FRPD1_HUMAN	S	44	ENSP00000366995:A44S;ENSP00000444411:A44S;ENSP00000439868:A44S	ENSP00000439868:A44S	A	+	1	0	FRMPD1	37697441	0.000000	0.05858	0.006000	0.13384	0.922000	0.55478	-0.656000	0.05342	-0.631000	0.05560	-0.798000	0.03219	GCC	.	G|0.935;A|0.065		0.498	FRMPD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402969.1	NM_014907	
FANCC	2176	hgsc.bcm.edu	37	9	98011462	98011462	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr9:98011462C>A	ENST00000289081.3	-	2	366	c.112G>T	c.(112-114)Gtg>Ttg	p.V38L	FANCC_ENST00000375305.1_Missense_Mutation_p.V38L	NM_000136.2	NP_000127.2	Q00597	FANCC_HUMAN	Fanconi anemia, complementation group C	38					DNA repair (GO:0006281)|germ cell development (GO:0007281)|myeloid cell homeostasis (GO:0002262)|nucleotide-excision repair (GO:0006289)|protein complex assembly (GO:0006461)|removal of superoxide radicals (GO:0019430)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				kidney(1)|skin(1)|upper_aerodigestive_tract(1)	3		Acute lymphoblastic leukemia(62;0.138)				AACTGAGCCACGTGAAGACAG	0.423			"""D, Mis, N, F, S"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.V38L		Atlas-SNP	.	yes	Rec		Fanconi anaemia C	9	9q22.3	2176	"""Fanconi anemia, complementation group C"""		L	FANCC_ENST00000289081,caecum,carcinoma,0,1	FANCC	53	.	0			c.G112T						.						117.0	109.0	112.0					9																	98011462		2203	4300	6503	SO:0001583	missense	2176	exon2	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	GAGCCACGTGAAG	BC006303	CCDS35071.1, CCDS75861.1	9q22.3	2014-09-17			ENSG00000158169	ENSG00000158169		"""Fanconi anemia, complementation groups"""	3584	protein-coding gene	gene with protein product		613899		FACC		1303234	Standard	NM_001243743		Approved	FAC, FA3	uc004avh.3	Q00597	OTTHUMG00000020279	ENST00000289081.3:c.112G>T	chr9.hg19:g.98011462C>A	ENSP00000289081:p.Val38Leu	82.0	0.0		83.0	44.0	NM_001243743	B1ALR8	Missense_Mutation	SNP	ENST00000289081.3	hg19	CCDS35071.1	.	.	.	.	.	.	.	.	.	.	G	0.005	-2.128330	0.00342	.	.	ENSG00000158169	ENST00000289081;ENST00000375305;ENST00000433829	T;T;T	0.35421	1.31;1.31;1.31	5.13	3.27	0.37495	.	0.000000	0.64402	N	0.000001	T	0.05960	0.0155	N	0.00142	-2.005	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.37314	-0.9711	10	0.02654	T	1	-3.5558	3.8829	0.09086	0.3822:0.1751:0.4427:0.0	.	38;38	B1ALR7;Q00597	.;FANCC_HUMAN	L	38	ENSP00000289081:V38L;ENSP00000364454:V38L;ENSP00000406908:V38L	ENSP00000289081:V38L	V	-	1	0	FANCC	97051283	0.992000	0.36948	0.709000	0.30452	0.913000	0.54294	0.145000	0.16157	0.421000	0.25980	-0.127000	0.14921	GTG	.	.		0.423	FANCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053219.1	NM_000136	
TMEM26	219623	hgsc.bcm.edu	37	10	63170436	63170436	+	Missense_Mutation	SNP	T	T	G			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr10:63170436T>G	ENST00000399298.3	-	6	1119	c.751A>C	c.(751-753)Agt>Cgt	p.S251R	TMEM26_ENST00000507507.1_5'UTR	NM_178505.6	NP_848600.2	Q6ZUK4	TMM26_HUMAN	transmembrane protein 26	251						integral component of membrane (GO:0016021)				kidney(1)|large_intestine(2)|lung(11)|prostate(1)|skin(2)|urinary_tract(1)	18	Prostate(12;0.0112)					AGATCGGCACTGTACTGGCAA	0.473																																					p.S251R		Atlas-SNP	.											.	TMEM26	47	.	0			c.A751C						.						55.0	59.0	57.0					10																	63170436		2073	4225	6298	SO:0001583	missense	219623	exon6			CGGCACTGTACTG	BC042872	CCDS41530.1	10q21.3	2008-10-20			ENSG00000196932	ENSG00000196932			28550	protein-coding gene	gene with protein product						12477932	Standard	NM_178505		Approved	MGC35010, Em:AC068892.1	uc001jlo.2	Q6ZUK4	OTTHUMG00000018293	ENST00000399298.3:c.751A>C	chr10.hg19:g.63170436T>G	ENSP00000382237:p.Ser251Arg	203.0	0.0		264.0	126.0	NM_178505	Q6ZVM0|Q8IVN9	Missense_Mutation	SNP	ENST00000399298.3	hg19	CCDS41530.1	.	.	.	.	.	.	.	.	.	.	T	18.72	3.683708	0.68157	.	.	ENSG00000196932	ENST00000399298	.	.	.	6.17	6.17	0.99709	.	0.079457	0.85682	D	0.000000	T	0.78830	0.4345	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.78959	-0.1998	9	0.49607	T	0.09	0.0227	16.8222	0.85835	0.0:0.0:0.0:1.0	.	251	Q6ZUK4	TMM26_HUMAN	R	251	.	ENSP00000382237:S251R	S	-	1	0	TMEM26	62840442	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	5.974000	0.70465	2.371000	0.80710	0.533000	0.62120	AGT	.	.		0.473	TMEM26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359121.1	NM_178505	
GRID1	2894	hgsc.bcm.edu	37	10	87489367	87489367	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr10:87489367G>A	ENST00000327946.7	-	9	1323	c.1238C>T	c.(1237-1239)gCg>gTg	p.A413V	GRID1_ENST00000536331.1_5'UTR	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	413					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						GTCCCATGTCGCCAACTGTGA	0.527										Multiple Myeloma(13;0.14)																											p.A413V		Atlas-SNP	.											.	GRID1	204	.	0			c.C1238T						.						64.0	58.0	60.0					10																	87489367		2203	4300	6503	SO:0001583	missense	2894	exon9			CATGTCGCCAACT	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.1238C>T	chr10.hg19:g.87489367G>A	ENSP00000330148:p.Ala413Val	89.0	0.0		101.0	6.0	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	hg19	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	G	26.0	4.691298	0.88735	.	.	ENSG00000182771	ENST00000327946	D	0.87491	-2.26	5.54	5.54	0.83059	.	0.051892	0.85682	D	0.000000	D	0.90338	0.6977	L	0.32530	0.975	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	D	0.91409	0.5149	10	0.87932	D	0	.	18.4481	0.90693	0.0:0.0:1.0:0.0	.	413	Q9ULK0	GRID1_HUMAN	V	413	ENSP00000330148:A413V	ENSP00000330148:A413V	A	-	2	0	GRID1	87479347	1.000000	0.71417	0.954000	0.39281	0.599000	0.36880	9.476000	0.97823	2.593000	0.87608	0.655000	0.94253	GCG	.	.		0.527	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	
MUC5B	727897	hgsc.bcm.edu	37	11	1279381	1279381	+	Silent	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:1279381G>A	ENST00000529681.1	+	42	16561	c.16503G>A	c.(16501-16503)caG>caA	p.Q5501Q	MUC5B_ENST00000447027.1_Silent_p.Q5504Q	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5501					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CGCCAGGGCAGGAGTCCATCT	0.697																																					p.Q5501Q		Atlas-SNP	.											.	MUC5B	473	.	0			c.G16503A						.						9.0	12.0	11.0					11																	1279381		1956	4096	6052	SO:0001819	synonymous_variant	727897	exon42			AGGGCAGGAGTCC	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16503G>A	chr11.hg19:g.1279381G>A		160.0	0.0		117.0	47.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.697	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
APLNR	187	hgsc.bcm.edu	37	11	57004140	57004140	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:57004140C>T	ENST00000606794.1	-	1	535	c.339G>A	c.(337-339)atG>atA	p.M113I		NM_005161.4	NP_005152.1	P35414	APJ_HUMAN	apelin receptor	113					G-protein coupled receptor signaling pathway (GO:0007186)|gastrulation (GO:0007369)|heart development (GO:0007507)|regulation of body fluid levels (GO:0050878)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32						CGCTGGCGTACATGTTGACGA	0.622																																					p.M113I		Atlas-SNP	.											.	APLNR	62	.	0			c.G339A						.						62.0	45.0	51.0					11																	57004140		2201	4296	6497	SO:0001583	missense	187	exon1			GGCGTACATGTTG	U03642	CCDS7950.1	11q12.1	2012-08-08	2008-05-12	2008-05-12	ENSG00000134817	ENSG00000134817			339	protein-coding gene	gene with protein product	"""APJ (apelin) receptor"""	600052	"""angiotensin II receptor-like 1"""	AGTRL1		8294032, 14622440	Standard	NM_005161		Approved	FLJ90771, APJ, APJR	uc001njo.3	P35414	OTTHUMG00000167021	ENST00000606794.1:c.339G>A	chr11.hg19:g.57004140C>T	ENSP00000475344:p.Met113Ile	40.0	0.0		49.0	20.0	NM_005161		Missense_Mutation	SNP	ENST00000606794.1	hg19	CCDS7950.1	.	.	.	.	.	.	.	.	.	.	C	24.9	4.584923	0.86748	.	.	ENSG00000134817	ENST00000257254;ENST00000444275	T	0.71934	-0.61	5.46	5.46	0.80206	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	D	0.85066	0.5612	M	0.76938	2.355	0.58432	D	0.999997	D	0.89917	1.0	D	0.87578	0.998	D	0.86448	0.1771	10	0.72032	D	0.01	-35.4311	18.9023	0.92448	0.0:1.0:0.0:0.0	.	113	P35414	APJ_HUMAN	I	113;78	ENSP00000257254:M113I	ENSP00000257254:M113I	M	-	3	0	APLNR	56760716	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.923000	0.63412	2.558000	0.86282	0.555000	0.69702	ATG	.	.		0.622	APLNR-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470575.1	NM_005161	
GUCY1A2	2977	hgsc.bcm.edu	37	11	106888708	106888708	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:106888708T>A	ENST00000526355.2	-	1	542	c.74A>T	c.(73-75)gAg>gTg	p.E25V	GUCY1A2_ENST00000347596.2_Missense_Mutation_p.E25V|GUCY1A2_ENST00000282249.2_Missense_Mutation_p.E25V	NM_000855.2	NP_000846.1	P33402	GCYA2_HUMAN	guanylate cyclase 1, soluble, alpha 2	25					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|positive regulation of cGMP biosynthetic process (GO:0030828)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|heme binding (GO:0020037)			breast(5)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(18)|liver(1)|lung(32)|ovary(1)|pancreas(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	74		all_epithelial(67;3.66e-05)|Melanoma(852;0.000382)|Acute lymphoblastic leukemia(157;0.001)|all_hematologic(158;0.0017)|Breast(348;0.026)|all_neural(303;0.068)		BRCA - Breast invasive adenocarcinoma(274;8.04e-05)|Epithelial(105;0.0036)|all cancers(92;0.0476)	Isosorbide Mononitrate(DB01020)|Nitric Oxide(DB00435)	CTCCCCCTCCTCCTCCGGGCT	0.721																																					p.E25V		Atlas-SNP	.											.	GUCY1A2	180	.	0			c.A74T						.						12.0	14.0	13.0					11																	106888708		2162	4244	6406	SO:0001583	missense	2977	exon1			CCCTCCTCCTCCG	X63282	CCDS8335.1, CCDS58170.1	11q21-q22	2008-03-18			ENSG00000152402	ENSG00000152402	4.6.1.2		4684	protein-coding gene	gene with protein product		601244		GUC1A2		1683630	Standard	NM_000855		Approved	GC-SA2	uc001pjg.2	P33402	OTTHUMG00000166296	ENST00000526355.2:c.74A>T	chr11.hg19:g.106888708T>A	ENSP00000431245:p.Glu25Val	52.0	0.0		74.0	18.0	NM_000855	A1L4C4|B7ZLT5	Missense_Mutation	SNP	ENST00000526355.2	hg19	CCDS8335.1	.	.	.	.	.	.	.	.	.	.	T	17.47	3.397752	0.62177	.	.	ENSG00000152402	ENST00000526355;ENST00000282249;ENST00000347596	D;D;D	0.87571	-1.95;-2.27;-1.95	3.34	3.34	0.38264	.	.	.	.	.	T	0.80639	0.4661	L	0.36672	1.1	0.42502	D	0.992939	B;P;B	0.35656	0.145;0.514;0.38	B;B;B	0.34242	0.086;0.178;0.086	T	0.81411	-0.0945	9	0.72032	D	0.01	.	11.0229	0.47728	0.0:0.0:0.0:1.0	.	25;25;25	B7ZLT5;P33402-2;P33402	.;.;GCYA2_HUMAN	V	25	ENSP00000431245:E25V;ENSP00000282249:E25V;ENSP00000344874:E25V	ENSP00000282249:E25V	E	-	2	0	GUCY1A2	106393918	1.000000	0.71417	0.961000	0.40146	0.662000	0.39071	2.441000	0.44864	1.370000	0.46153	0.334000	0.21626	GAG	.	.		0.721	GUCY1A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389003.2		
EXPH5	23086	hgsc.bcm.edu	37	11	108382004	108382004	+	Silent	SNP	A	A	C	rs369244769		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:108382004A>C	ENST00000265843.4	-	6	4340	c.4230T>G	c.(4228-4230)tcT>tcG	p.S1410S	EXPH5_ENST00000443411.1_Silent_p.S1222S|EXPH5_ENST00000428840.1_Silent_p.S1334S|EXPH5_ENST00000525344.1_Silent_p.S1403S|EXPH5_ENST00000524840.1_5'Flank	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	1410					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		GACAATTTTCAGATTTTTCTT	0.353																																					p.S1410S		Atlas-SNP	.											.	EXPH5	193	.	0			c.T4230G						.						95.0	97.0	96.0					11																	108382004		2200	4298	6498	SO:0001819	synonymous_variant	23086	exon6			ATTTTCAGATTTT		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.4230T>G	chr11.hg19:g.108382004A>C		142.0	0.0		108.0	50.0	NM_015065	Q2KHM1|Q9Y4D6	Silent	SNP	ENST00000265843.4	hg19	CCDS8341.1																																																																																			.	.		0.353	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
MEDAG	84935	hgsc.bcm.edu	37	13	31495898	31495898	+	Silent	SNP	G	G	A	rs375543579		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr13:31495898G>A	ENST00000380482.4	+	4	1027	c.702G>A	c.(700-702)acG>acA	p.T234T	TEX26-AS1_ENST00000588425.1_RNA|TEX26-AS1_ENST00000590344.1_RNA|TEX26-AS1_ENST00000586464.1_RNA|TEX26-AS1_ENST00000588726.1_RNA|TEX26-AS1_ENST00000451495.2_RNA|TEX26-AS1_ENST00000585870.1_RNA|TEX26-AS1_ENST00000590721.1_RNA|TEX26-AS1_ENST00000593246.1_RNA|TEX26-AS1_ENST00000586973.1_RNA|TEX26-AS1_ENST00000592950.1_RNA	NM_032849.3	NP_116238	Q5VYS4	MEDAG_HUMAN	mesenteric estrogen-dependent adipogenesis	234					positive regulation of fat cell differentiation (GO:0045600)	cytoplasm (GO:0005737)											AGAAGGAGACGATTAAGTTAT	0.353																																					p.T234T		Atlas-SNP	.											C13orf33,caecum,carcinoma,0,1	.	.	.	0			c.G702A						.						59.0	60.0	60.0					13																	31495898		2203	4300	6503	SO:0001819	synonymous_variant	84935	exon4			GGAGACGATTAAG	AB055407	CCDS9338.1	13q12.3	2013-10-11	2012-09-26	2012-09-26	ENSG00000102802	ENSG00000102802			25926	protein-coding gene	gene with protein product	"""mesenteric estrogen-dependent adipose 4"", ""activated in W/Wv mouse stomach 3 homolog"""		"""chromosome 13 open reading frame 33"""	C13orf33		22510272	Standard	NM_032849		Approved	FLJ14834, AWMS3, MEDA-4	uc001uth.4	Q5VYS4	OTTHUMG00000016679	ENST00000380482.4:c.702G>A	chr13.hg19:g.31495898G>A		181.0	0.0		200.0	76.0	NM_032849	Q8IXF1|Q96K26|Q96NC8	Silent	SNP	ENST00000380482.4	hg19	CCDS9338.1																																																																																			.	.		0.353	MEDAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044375.1	NM_032849	
REM2	161253	hgsc.bcm.edu	37	14	23355255	23355255	+	Missense_Mutation	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr14:23355255G>A	ENST00000267396.4	+	4	665	c.542G>A	c.(541-543)cGg>cAg	p.R181Q	REM2_ENST00000536884.1_Silent_p.A156A	NM_173527.2	NP_775798.2	Q8IYK8	REM2_HUMAN	RAS (RAD and GEM)-like GTP binding 2	181					small GTPase mediated signal transduction (GO:0007264)	plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|central_nervous_system(1)|large_intestine(2)|ovary(1)	5	all_cancers(95;4.69e-05)			GBM - Glioblastoma multiforme(265;0.012)		GGGTGGCTGCGGGACCACTGC	0.597																																					p.R181Q		Atlas-SNP	.											.	REM2	21	.	0			c.G542A						.						53.0	59.0	57.0					14																	23355255		2039	4173	6212	SO:0001583	missense	161253	exon4			GGCTGCGGGACCA		CCDS45082.1	14q11.2	2014-05-09	2006-12-14		ENSG00000139890	ENSG00000139890			20248	protein-coding gene	gene with protein product			"""RAS (RAD and GEM) like GTP binding 2"""			10727423	Standard	NM_173527		Approved	FLJ38964	uc001whf.1	Q8IYK8	OTTHUMG00000170277	ENST00000267396.4:c.542G>A	chr14.hg19:g.23355255G>A	ENSP00000267396:p.Arg181Gln	58.0	0.0		108.0	48.0	NM_173527	B7Z5P1|Q8N8R8	Missense_Mutation	SNP	ENST00000267396.4	hg19	CCDS45082.1	.	.	.	.	.	.	.	.	.	.	G	8.539	0.872759	0.17322	.	.	ENSG00000139890	ENST00000267396	T	0.80994	-1.44	5.48	-2.23	0.06930	.	0.644098	0.16252	N	0.222680	T	0.61248	0.2332	N	0.25201	0.72	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.32771	-0.9894	10	0.16896	T	0.51	.	8.0204	0.30406	0.5986:0.1207:0.2807:0.0	.	181	Q8IYK8	REM2_HUMAN	Q	181	ENSP00000267396:R181Q	ENSP00000267396:R181Q	R	+	2	0	REM2	22425095	1.000000	0.71417	0.970000	0.41538	0.993000	0.82548	1.149000	0.31626	-0.624000	0.05611	0.563000	0.77884	CGG	.	.		0.597	REM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408290.1	NM_173527	
NOVA1	4857	hgsc.bcm.edu	37	14	26949340	26949340	+	Missense_Mutation	SNP	T	T	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr14:26949340T>A	ENST00000344429.5	-	3	293	c.290A>T	c.(289-291)gAg>gTg	p.E97V	NOVA1_ENST00000547619.1_Missense_Mutation_p.E97V|NOVA1_ENST00000267422.7_5'UTR|NOVA1_ENST00000539517.2_Missense_Mutation_p.E97V|NOVA1_ENST00000465357.2_Missense_Mutation_p.E97V|NOVA1_ENST00000574031.1_Missense_Mutation_p.E97V	NM_006491.2	NP_006482.1	P51513	NOVA1_HUMAN	neuro-oncological ventral antigen 1	100	KH 1. {ECO:0000255|PROSITE- ProRule:PRU00117}.				locomotory behavior (GO:0007626)|mRNA splicing, via spliceosome (GO:0000398)|regulation of RNA metabolic process (GO:0051252)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)	intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)|nucleus (GO:0005634)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(265;0.0135)		GCACACTCGCTCAGTAGTACC	0.368																																					p.E97V		Atlas-SNP	.											.	NOVA1	146	.	0			c.A290T						.						78.0	68.0	72.0					14																	26949340		2203	4300	6503	SO:0001583	missense	4857	exon3			ACTCGCTCAGTAG	U04840	CCDS9635.1, CCDS32060.1, CCDS32061.1	14q12	2006-06-09			ENSG00000139910	ENSG00000139910			7886	protein-coding gene	gene with protein product		602157				8558240	Standard	NM_006489		Approved		uc001wpy.3	P51513	OTTHUMG00000029385	ENST00000344429.5:c.290A>T	chr14.hg19:g.26949340T>A	ENSP00000342387:p.Glu97Val	54.0	0.0		77.0	26.0	NM_006489	A8K0S4|A8K4Q7|D3DS81|D3DS82|Q6B004	Missense_Mutation	SNP	ENST00000344429.5	hg19	CCDS9635.1	.	.	.	.	.	.	.	.	.	.	T	18.94	3.730730	0.69074	.	.	ENSG00000139910	ENST00000465357;ENST00000539517;ENST00000449198;ENST00000549571;ENST00000344429;ENST00000547619	T;T;T;T;T;T	0.35973	1.28;1.28;1.28;1.28;1.28;1.28	5.26	5.26	0.73747	.	0.839868	0.10332	N	0.687495	T	0.67711	0.2922	M	0.86953	2.85	0.80722	D	1	D;D;D	0.89917	1.0;0.991;0.989	D;D;D	0.85130	0.997;0.987;0.978	T	0.67448	-0.5668	10	0.87932	D	0	-6.5518	15.1667	0.72833	0.0:0.0:0.0:1.0	.	97;97;97	P51513-2;D3DS81;P51513-4	.;.;.	V	97;97;56;60;97;97	ENSP00000447391:E97V;ENSP00000438875:E97V;ENSP00000408914:E56V;ENSP00000449185:E60V;ENSP00000342387:E97V;ENSP00000448157:E97V	ENSP00000342387:E97V	E	-	2	0	NOVA1	26019180	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.013000	0.88655	2.002000	0.58637	0.477000	0.44152	GAG	.	.		0.368	NOVA1-001	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276557.1	NM_006491	
GABRA5	2558	hgsc.bcm.edu	37	15	27126102	27126102	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr15:27126102C>A	ENST00000335625.5	+	4	1084	c.196C>A	c.(196-198)Ccc>Acc	p.P66T	GABRB3_ENST00000541819.2_Intron|GABRA5_ENST00000557449.1_3'UTR|GABRA5_ENST00000355395.5_Missense_Mutation_p.P66T|GABRA5_ENST00000400081.3_Missense_Mutation_p.P66T	NM_000810.3	NP_000801.1	P31644	GBRA5_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 5	66					associative learning (GO:0008306)|behavioral fear response (GO:0001662)|brain development (GO:0007420)|cochlea development (GO:0090102)|gamma-aminobutyric acid signaling pathway (GO:0007214)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|sensory perception of sound (GO:0007605)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuronal cell body membrane (GO:0032809)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.P66T(1)		NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(1)|upper_aerodigestive_tract(1)	49		all_lung(180;4.59e-13)|Breast(32;0.000563)|Colorectal(260;0.227)		all cancers(64;1.45e-08)|Epithelial(43;4.96e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0232)|Lung(196;0.182)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zopiclone(DB01198)	CAGACTTCGGCCCGGGCTGGG	0.517																																					p.P66T		Atlas-SNP	.											GABRA5,rectum,carcinoma,-1,1	GABRA5	127	.	1	Substitution - Missense(1)	kidney(1)	c.C196A						.						70.0	71.0	70.0					15																	27126102		2003	4172	6175	SO:0001583	missense	2558	exon4			CTTCGGCCCGGGC		CCDS45194.1	15q12	2012-06-22			ENSG00000186297	ENSG00000186297		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4079	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 5"""	137142				1321750	Standard	NM_000810		Approved		uc021sgi.1	P31644	OTTHUMG00000171824	ENST00000335625.5:c.196C>A	chr15.hg19:g.27126102C>A	ENSP00000335592:p.Pro66Thr	108.0	0.0		82.0	37.0	NM_001165037	A8K338|Q14DC2|Q53XL6|Q9NYT3|Q9NYT4|Q9NYT5	Missense_Mutation	SNP	ENST00000335625.5	hg19	CCDS45194.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.530918	0.85706	.	.	ENSG00000186297	ENST00000335625;ENST00000355395;ENST00000555182;ENST00000400081;ENST00000554038;ENST00000554596;ENST00000554599;ENST00000554083	D;D;D;D;D;D;D;D	0.94966	-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57;-3.57	5.22	5.22	0.72569	Neurotransmitter-gated ion-channel ligand-binding (3);	0.105687	0.64402	D	0.000003	D	0.98153	0.9390	H	0.95079	3.62	0.80722	D	1	D	0.76494	0.999	D	0.77004	0.989	D	0.99501	1.0953	10	0.87932	D	0	.	17.756	0.88449	0.0:1.0:0.0:0.0	.	66	P31644	GBRA5_HUMAN	T	66;66;34;66;66;66;66;34	ENSP00000335592:P66T;ENSP00000347557:P66T;ENSP00000450653:P34T;ENSP00000382953:P66T;ENSP00000451527:P66T;ENSP00000450806:P66T;ENSP00000450717:P66T;ENSP00000450529:P34T	ENSP00000335592:P66T	P	+	1	0	GABRA5	24677195	1.000000	0.71417	0.991000	0.47740	0.856000	0.48823	7.617000	0.83032	2.441000	0.82636	0.561000	0.74099	CCC	.	.		0.517	GABRA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415234.1		
CHRNA7	1139	hgsc.bcm.edu	37	15	32455518	32455518	+	Silent	SNP	G	G	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr15:32455518G>A	ENST00000306901.3	+	9	1069	c.972G>A	c.(970-972)ggG>ggA	p.G324G	CHRNA7_ENST00000454250.3_Silent_p.G353G|CHRNA7_ENST00000455693.2_Silent_p.G143G	NM_000746.5	NP_000737.1	P36544	ACHA7_HUMAN	cholinergic receptor, nicotinic, alpha 7 (neuronal)	324					activation of MAPK activity (GO:0000187)|associative learning (GO:0008306)|B cell activation (GO:0042113)|behavioral response to ethanol (GO:0048149)|behavioral response to nicotine (GO:0035095)|calcium ion transport (GO:0006816)|cation transmembrane transport (GO:0098655)|cellular calcium ion homeostasis (GO:0006874)|cognition (GO:0050890)|dopamine biosynthetic process (GO:0042416)|endocytosis (GO:0006897)|generation of ovulation cycle rhythm (GO:0060112)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|memory (GO:0007613)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-1 beta production (GO:0032691)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of tumor necrosis factor production (GO:0032720)|neuronal action potential (GO:0019228)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell proliferation (GO:0008284)|positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure (GO:0001988)|regulation of norepinephrine secretion (GO:0014061)|regulation of synaptic transmission, dopaminergic (GO:0032225)|response to food (GO:0032094)|response to hypoxia (GO:0001666)|response to nicotine (GO:0035094)|signal transduction (GO:0007165)|sperm motility (GO:0030317)|synaptic transmission (GO:0007268)|synaptic transmission, cholinergic (GO:0007271)|T cell activation (GO:0042110)	acetylcholine-gated channel complex (GO:0005892)|apical plasma membrane (GO:0016324)|asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|external side of plasma membrane (GO:0009897)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|acetylcholine-gated cation channel activity (GO:0022848)|beta-amyloid binding (GO:0001540)|chloride channel regulator activity (GO:0017081)|drug binding (GO:0008144)|protein homodimerization activity (GO:0042803)|toxic substance binding (GO:0015643)			endometrium(3)|large_intestine(1)|lung(6)|ovary(2)	12		all_lung(180;6.35e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Nicotine(DB00184)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)|Varenicline(DB01273)	ACCCCGACGGGGGCAAGATGC	0.582																																					p.G353G	Esophageal Squamous(193;529 2900 40232 43193)	Atlas-SNP	.											.	CHRNA7	57	.	0			c.G1059A						.						16.0	17.0	16.0					15																	32455518		1244	2181	3425	SO:0001819	synonymous_variant	1139	exon9			CGACGGGGGCAAG	Z23141	CCDS10027.1, CCDS53924.1	15q13.3	2012-02-11	2012-02-07		ENSG00000175344	ENSG00000175344		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1960	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 7 (neuronal)"""	118511	"""cholinergic receptor, nicotinic, alpha polypeptide 7"""			8188270	Standard	NM_001190455		Approved		uc021sic.2	P36544	OTTHUMG00000129285	ENST00000306901.3:c.972G>A	chr15.hg19:g.32455518G>A		411.0	0.0		428.0	220.0	NM_001190455	A8K7Q4|B4DFS0|Q15826|Q8IUZ4|Q96RH2|Q99555|Q9BXH0	Silent	SNP	ENST00000306901.3	hg19	CCDS10027.1																																																																																			.	.		0.582	CHRNA7-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251410.2		
HERC1	8925	hgsc.bcm.edu	37	15	63922816	63922816	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr15:63922816G>T	ENST00000443617.2	-	69	12902	c.12815C>A	c.(12814-12816)cCa>cAa	p.P4272Q		NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	4272					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						ACGCCCCTCTGGCAAGCCTAT	0.438																																					p.P4272Q		Atlas-SNP	.											.	HERC1	624	.	0			c.C12815A						.						87.0	87.0	87.0					15																	63922816		1929	4132	6061	SO:0001583	missense	8925	exon69			CCCTCTGGCAAGC	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.12815C>A	chr15.hg19:g.63922816G>T	ENSP00000390158:p.Pro4272Gln	91.0	0.0		110.0	5.0	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	hg19	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	G	30	5.050103	0.93740	.	.	ENSG00000103657	ENST00000443617	D	0.84730	-1.89	5.77	5.77	0.91146	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.85682	D	0.000000	D	0.92051	0.7481	M	0.67953	2.075	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.91129	0.4936	10	0.52906	T	0.07	.	20.3473	0.98799	0.0:0.0:1.0:0.0	.	4272	Q15751	HERC1_HUMAN	Q	4272	ENSP00000390158:P4272Q	ENSP00000390158:P4272Q	P	-	2	0	HERC1	61709869	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.813000	0.99286	2.884000	0.98904	0.655000	0.94253	CCA	.	.		0.438	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
INTS2	57508	hgsc.bcm.edu	37	17	59958425	59958425	+	Missense_Mutation	SNP	G	G	A	rs201173583		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr17:59958425G>A	ENST00000444766.3	-	17	2296	c.2221C>T	c.(2221-2223)Cgg>Tgg	p.R741W	INTS2_ENST00000251334.6_Missense_Mutation_p.R733W	NM_020748.2	NP_065799	Q9H0H0	INT2_HUMAN	integrator complex subunit 2	741					snRNA processing (GO:0016180)	integral component of membrane (GO:0016021)|integrator complex (GO:0032039)|intracellular (GO:0005622)|membrane (GO:0016020)				NS(1)|breast(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	38						AGCATTCGCCGTAGCAGGGCA	0.393																																					p.R741W		Atlas-SNP	.											.	INTS2	89	.	0			c.C2221T						.						118.0	111.0	113.0					17																	59958425		1897	4111	6008	SO:0001583	missense	57508	exon17			TTCGCCGTAGCAG	AB033113	CCDS45750.1	17q23.2	2006-04-26	2006-03-15	2006-03-15		ENSG00000108506			29241	protein-coding gene	gene with protein product		611346	"""KIAA1287"""	KIAA1287		16239144	Standard	NR_026641		Approved	INT2	uc002izn.3	Q9H0H0		ENST00000444766.3:c.2221C>T	chr17.hg19:g.59958425G>A	ENSP00000414237:p.Arg741Trp	81.0	0.0		192.0	59.0	NM_020748	Q9ULD3	Missense_Mutation	SNP	ENST00000444766.3	hg19	CCDS45750.1	.	.	.	.	.	.	.	.	.	.	G	19.00	3.741282	0.69304	.	.	ENSG00000108506	ENST00000444766;ENST00000251334	T	0.48201	0.82	5.74	0.689	0.18033	.	0.000000	0.85682	D	0.000000	T	0.58764	0.2145	L	0.47716	1.5	0.58432	D	0.999998	D	0.89917	1.0	D	0.79108	0.992	T	0.55711	-0.8098	9	.	.	.	-12.666	15.4887	0.75587	0.0:0.0:0.5122:0.4878	.	741	Q9H0H0	INT2_HUMAN	W	741;740	ENSP00000414237:R741W	.	R	-	1	2	INTS2	57313207	0.976000	0.34144	0.997000	0.53966	0.980000	0.70556	0.245000	0.18142	0.086000	0.17137	-0.474000	0.04947	CGG	.	.		0.393	INTS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000445368.1	NM_020748	
MYOM1	8736	hgsc.bcm.edu	37	18	3100192	3100192	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr18:3100192C>T	ENST00000356443.4	-	25	4025	c.3692G>A	c.(3691-3693)cGt>cAt	p.R1231H	MYOM1_ENST00000261606.7_Missense_Mutation_p.R1135H|MYOM1_ENST00000400569.3_Missense_Mutation_p.R1231H	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	1231					muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGCAAGTAAACGTTTCAATTC	0.363																																					p.R1231H		Atlas-SNP	.											.	MYOM1	192	.	0			c.G3692A						.						117.0	112.0	114.0					18																	3100192		1851	4094	5945	SO:0001583	missense	8736	exon25			AGTAAACGTTTCA	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.3692G>A	chr18.hg19:g.3100192C>T	ENSP00000348821:p.Arg1231His	144.0	0.0		184.0	49.0	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	hg19	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	C	17.54	3.415621	0.62511	.	.	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.50277	0.89;0.9;0.75	5.38	5.38	0.77491	.	0.145720	0.53938	D	0.000060	T	0.70945	0.3282	M	0.77103	2.36	0.58432	D	0.999997	D;D	0.89917	1.0;1.0	D;D	0.72338	0.977;0.963	T	0.73388	-0.3998	10	0.72032	D	0.01	.	19.317	0.94218	0.0:1.0:0.0:0.0	.	1135;1231	P52179-2;P52179	.;MYOM1_HUMAN	H	1231;1231;1135	ENSP00000348821:R1231H;ENSP00000383413:R1231H;ENSP00000261606:R1135H	ENSP00000261606:R1135H	R	-	2	0	MYOM1	3090192	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.565000	0.60836	2.806000	0.96561	0.655000	0.94253	CGT	.	.		0.363	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
CHAF1A	10036	hgsc.bcm.edu	37	19	4428721	4428721	+	Missense_Mutation	SNP	G	G	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:4428721G>T	ENST00000301280.5	+	8	1539	c.1438G>T	c.(1438-1440)Gcc>Tcc	p.A480S	CTB-50L17.5_ENST00000590159.1_RNA	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	480					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CATGGTCCTGGCCCCTCGGCG	0.572								Chromatin Structure																													p.A480S		Atlas-SNP	.											.	CHAF1A	69	.	0			c.G1438T						.						62.0	67.0	65.0					19																	4428721		2203	4300	6503	SO:0001583	missense	10036	exon8			GTCCTGGCCCCTC	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.1438G>T	chr19.hg19:g.4428721G>T	ENSP00000301280:p.Ala480Ser	73.0	0.0		69.0	38.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	hg19	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.555584	0.86231	.	.	ENSG00000167670	ENST00000344143;ENST00000535117;ENST00000301280	T	0.25912	1.77	5.4	5.4	0.78164	.	.	.	.	.	T	0.51686	0.1689	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.53337	-0.8453	9	0.87932	D	0	-38.3682	18.1396	0.89634	0.0:0.0:1.0:0.0	.	480	Q13111	CAF1A_HUMAN	S	480	ENSP00000301280:A480S	ENSP00000301280:A480S	A	+	1	0	CHAF1A	4379721	1.000000	0.71417	0.888000	0.34837	0.399000	0.30720	9.622000	0.98378	2.518000	0.84900	0.455000	0.32223	GCC	.	.		0.572	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	
CHAF1A	10036	hgsc.bcm.edu	37	19	4428728	4428728	+	Missense_Mutation	SNP	G	G	T	rs373148905		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:4428728G>T	ENST00000301280.5	+	8	1546	c.1445G>T	c.(1444-1446)cGg>cTg	p.R482L	CTB-50L17.5_ENST00000590159.1_RNA	NM_005483.2	NP_005474	Q13111	CAF1A_HUMAN	chromatin assembly factor 1, subunit A (p150)	482					cell cycle (GO:0007049)|chromatin assembly (GO:0031497)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication-dependent nucleosome assembly (GO:0006335)|protein complex assembly (GO:0006461)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	CAF-1 complex (GO:0033186)|nuclear chromatin (GO:0000790)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|identical protein binding (GO:0042802)|unfolded protein binding (GO:0051082)			breast(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|urinary_tract(1)	27		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0148)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGGCCCCTCGGCGTCGGACC	0.587								Chromatin Structure																													p.R482L		Atlas-SNP	.											CHAF1A,NS,carcinoma,0,1	CHAF1A	69	.	0			c.G1445T						.						62.0	66.0	64.0					19																	4428728		2203	4300	6503	SO:0001583	missense	10036	exon8			CCCCTCGGCGTCG	U20979	CCDS32875.1	19p13.3	2008-07-16				ENSG00000167670			1910	protein-coding gene	gene with protein product	"""chromatin assembly factor I (150 kDa)"""	601246				7600578	Standard	NM_005483		Approved	CAF1P150, CAF1B, CAF-1, CAF1, P150, MGC71229	uc002mal.3	Q13111		ENST00000301280.5:c.1445G>T	chr19.hg19:g.4428728G>T	ENSP00000301280:p.Arg482Leu	69.0	0.0		66.0	39.0	NM_005483	Q6NXG5|Q7Z7K3|Q9UJY8	Missense_Mutation	SNP	ENST00000301280.5	hg19	CCDS32875.1	.	.	.	.	.	.	.	.	.	.	G	3.511	-0.099825	0.07010	.	.	ENSG00000167670	ENST00000344143;ENST00000535117;ENST00000301280	T	0.11821	2.74	5.52	-1.97	0.07503	.	.	.	.	.	T	0.05593	0.0147	N	0.04636	-0.2	0.09310	N	1	B	0.21753	0.06	B	0.09377	0.004	T	0.34625	-0.9821	9	0.87932	D	0	-8.6972	6.6881	0.23156	0.2506:0.0:0.1606:0.5888	.	482	Q13111	CAF1A_HUMAN	L	482	ENSP00000301280:R482L	ENSP00000301280:R482L	R	+	2	0	CHAF1A	4379728	0.738000	0.28186	0.000000	0.03702	0.197000	0.23852	2.058000	0.41374	-0.587000	0.05890	-0.263000	0.10527	CGG	.	.		0.587	CHAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458310.2	NM_005483	
C19orf80	55908	hgsc.bcm.edu	37	19	11350522	11350522	+	Missense_Mutation	SNP	A	A	G			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:11350522A>G	ENST00000252453.8	+	1	228	c.209A>G	c.(208-210)tAt>tGt	p.Y70C	DOCK6_ENST00000294618.7_Intron|DOCK6_ENST00000319867.7_5'Flank|C19orf80_ENST00000591200.1_Intron	NM_018687.6	NP_061157.3	Q6UXH0	BETAT_HUMAN	chromosome 19 open reading frame 80	70					cellular lipid metabolic process (GO:0044255)|glucose metabolic process (GO:0006006)|positive regulation of protein processing (GO:0010954)|regulation of lipoprotein metabolic process (GO:0050746)|triglyceride homeostasis (GO:0070328)|type B pancreatic cell proliferation (GO:0044342)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			NS(1)|breast(1)|endometrium(2)	4						CTGGGTCTCTATGGCCGCACA	0.642																																					p.Y70C		Atlas-SNP	.											.	C19orf80	8	.	0			c.A209G						.						20.0	24.0	23.0					19																	11350522		1967	4138	6105	SO:0001583	missense	55908	exon1			GTCTCTATGGCCG		CCDS54220.1	19p13.2	2014-02-13			ENSG00000130173	ENSG00000130173			24933	protein-coding gene	gene with protein product	"""lipasin"", ""betatrophin"""					22809513, 23150577, 24262987	Standard	NM_018687		Approved	TD26, RIFL, ANGPTL8	uc021upg.1	Q6UXH0		ENST00000252453.8:c.209A>G	chr19.hg19:g.11350522A>G	ENSP00000252453:p.Tyr70Cys	144.0	0.0		134.0	71.0	NM_018687	Q9NQZ1	Missense_Mutation	SNP	ENST00000252453.8	hg19	CCDS54220.1	.	.	.	.	.	.	.	.	.	.	A	12.59	1.982465	0.34942	.	.	ENSG00000130173	ENST00000252453	T	0.53857	0.6	4.62	2.29	0.28610	.	0.153884	0.30347	N	0.009822	T	0.60444	0.2269	L	0.52573	1.65	0.28431	N	0.917275	D	0.76494	0.999	D	0.66351	0.943	T	0.55780	-0.8087	10	0.87932	D	0	-14.8018	8.0808	0.30744	0.7517:0.0:0.0:0.2483	.	70	Q6UXH0	TD26_HUMAN	C	70	ENSP00000252453:Y70C	ENSP00000252453:Y70C	Y	+	2	0	C19orf80	11211522	0.035000	0.19736	0.192000	0.23308	0.134000	0.20937	0.351000	0.20096	0.032000	0.15435	0.379000	0.24179	TAT	.	.		0.642	C19orf80-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453175.1	NM_018687	
GIPC1	10755	hgsc.bcm.edu	37	19	14591536	14591536	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr19:14591536C>T	ENST00000393033.4	-	5	612	c.343G>A	c.(343-345)Ggc>Agc	p.G115S	GIPC1_ENST00000591349.1_Missense_Mutation_p.G18S|GIPC1_ENST00000586027.1_Missense_Mutation_p.G115S|GIPC1_ENST00000393029.3_Missense_Mutation_p.G18S|GIPC1_ENST00000345425.2_Missense_Mutation_p.G115S|GIPC1_ENST00000393028.1_Missense_Mutation_p.G18S	NM_005716.3	NP_005707.1	O14908	GIPC1_HUMAN	GIPC PDZ domain containing family, member 1	115					endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|glutamate secretion (GO:0014047)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of cytokinesis (GO:0032467)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|protein targeting (GO:0006605)|regulation of protein stability (GO:0031647)|regulation of synaptic plasticity (GO:0048167)|synaptic transmission (GO:0007268)	brush border (GO:0005903)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)|vesicle membrane (GO:0012506)	actin binding (GO:0003779)|myosin binding (GO:0017022)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(1)|lung(4)|upper_aerodigestive_tract(1)	6						CCGATCTGGCCCCCCAGGAGC	0.617											OREG0025316	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.G115S	Pancreas(33;78 923 2910 41023 52850)	Atlas-SNP	.											.	GIPC1	21	.	0			c.G343A						.						126.0	106.0	113.0					19																	14591536		2203	4300	6503	SO:0001583	missense	10755	exon4			TCTGGCCCCCCAG	AF089816	CCDS12310.1, CCDS12311.1	19p13.1	2009-09-22	2005-06-28	2005-06-28					1226	protein-coding gene	gene with protein product		605072	"""chromosome 19 open reading frame 3"", ""regulator of G-protein signalling 19 interacting protein 1"""	C19orf3, RGS19IP1		9770488, 9482110	Standard	NM_005716		Approved	TIP-2, Hs.6454, GIPC, SEMCAP, GLUT1CBP, SYNECTIN, NIP	uc002myx.4	O14908		ENST00000393033.4:c.343G>A	chr19.hg19:g.14591536C>T	ENSP00000376753:p.Gly115Ser	80.0	0.0	696	98.0	31.0	NM_202468	A8K4I3|A8MZG3|Q9BTC9	Missense_Mutation	SNP	ENST00000393033.4	hg19	CCDS12310.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303551	0.60195	.	.	ENSG00000123159	ENST00000393033;ENST00000345425;ENST00000393029;ENST00000393028;ENST00000351277	T;T;T;T	0.37915	1.17;1.17;1.17;1.17	4.22	4.22	0.49857	PDZ/DHR/GLGF (1);	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	M	0.64567	1.98	0.80722	D	1	P	0.37864	0.61	B	0.37267	0.245	T	0.32322	-0.9911	10	0.40728	T	0.16	-9.9044	14.4052	0.67079	0.0:1.0:0.0:0.0	.	115	O14908	GIPC1_HUMAN	S	115;115;18;18;115	ENSP00000376753:G115S;ENSP00000340698:G115S;ENSP00000376749:G18S;ENSP00000376748:G18S	ENSP00000340698:G115S	G	-	1	0	GIPC1	14452536	0.996000	0.38824	0.995000	0.50966	0.737000	0.42083	7.195000	0.77798	2.079000	0.62486	0.561000	0.74099	GGC	.	.		0.617	GIPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460239.2		
TUBB1	81027	hgsc.bcm.edu	37	20	57594619	57594619	+	Missense_Mutation	SNP	C	C	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr20:57594619C>A	ENST00000217133.1	+	1	311	c.42C>A	c.(40-42)aaC>aaA	p.N14K		NM_030773.3	NP_110400.1	Q9H4B7	TBB1_HUMAN	tubulin, beta 1 class VI	14					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)|protein polymerization (GO:0051258)|spindle assembly (GO:0051225)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|skin(2)	16	all_lung(29;0.00711)		Colorectal(105;0.109)		Cabazitaxel(DB06772)|Colchicine(DB01394)|Docetaxel(DB01248)|Paclitaxel(DB01229)|Vindesine(DB00309)	AGTGTGGCAACCAGATCGGAG	0.463																																					p.N14K		Atlas-SNP	.											.	TUBB1	42	.	0			c.C42A						.						156.0	137.0	144.0					20																	57594619		2203	4300	6503	SO:0001583	missense	81027	exon1			TGGCAACCAGATC	AJ292757	CCDS13475.1	20q13.32	2014-09-17	2011-10-10		ENSG00000101162	ENSG00000101162		"""Tubulins"""	16257	protein-coding gene	gene with protein product	"""class VI beta-tubulin"""	612901	"""tubulin, beta 1"""				Standard	NM_030773		Approved	dJ543J19.4	uc002yak.3	Q9H4B7	OTTHUMG00000032860	ENST00000217133.1:c.42C>A	chr20.hg19:g.57594619C>A	ENSP00000217133:p.Asn14Lys	74.0	0.0		105.0	35.0	NM_030773		Missense_Mutation	SNP	ENST00000217133.1	hg19	CCDS13475.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.220782	0.79464	.	.	ENSG00000101162	ENST00000217133	T	0.74947	-0.89	5.51	3.55	0.40652	Tubulin/FtsZ, GTPase domain (3);	0.091425	0.64402	D	0.000001	D	0.89389	0.6701	H	0.98370	4.215	0.53688	D	0.999974	D	0.71674	0.998	P	0.61070	0.883	D	0.92012	0.5619	10	0.87932	D	0	.	11.8023	0.52135	0.0:0.8713:0.0:0.1287	.	14	Q9H4B7	TBB1_HUMAN	K	14	ENSP00000217133:N14K	ENSP00000217133:N14K	N	+	3	2	TUBB1	57028014	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.639000	0.37176	2.592000	0.87571	0.563000	0.77884	AAC	.	.		0.463	TUBB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079903.1	NM_030773	
ZNF831	128611	hgsc.bcm.edu	37	20	57767039	57767039	+	Missense_Mutation	SNP	C	C	T			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr20:57767039C>T	ENST00000371030.2	+	1	965	c.965C>T	c.(964-966)gCa>gTa	p.A322V		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	322							metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CAGGCGACGGCAGCGGAGAAG	0.716																																					p.A322V		Atlas-SNP	.											.	ZNF831	287	.	0			c.C965T						.						11.0	14.0	14.0					20																	57767039		1640	3881	5521	SO:0001583	missense	128611	exon1			CGACGGCAGCGGA	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.965C>T	chr20.hg19:g.57767039C>T	ENSP00000360069:p.Ala322Val	130.0	0.0		266.0	141.0	NM_178457	Q5TDR4|Q8TCP0	Missense_Mutation	SNP	ENST00000371030.2	hg19	CCDS42894.1	.	.	.	.	.	.	.	.	.	.	C	1.145	-0.648369	0.03506	.	.	ENSG00000124203	ENST00000371030	T	0.04275	3.66	5.29	1.93	0.25924	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.29716	0.255	B	0.19148	0.024	T	0.45877	-0.9231	9	0.18710	T	0.47	-1.8223	3.0916	0.06296	0.1565:0.5426:0.1428:0.1581	.	322	Q5JPB2	ZN831_HUMAN	V	322	ENSP00000360069:A322V	ENSP00000360069:A322V	A	+	2	0	ZNF831	57200434	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	0.639000	0.24690	1.192000	0.43071	0.655000	0.94253	GCA	.	.		0.716	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
KCNQ2	3785	hgsc.bcm.edu	37	20	62045484	62045484	+	Nonsense_Mutation	SNP	C	C	A			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr20:62045484C>A	ENST00000359125.2	-	14	1762	c.1588G>T	c.(1588-1590)Gag>Tag	p.E530*	KCNQ2_ENST00000344462.4_Nonsense_Mutation_p.E499*|KCNQ2_ENST00000357249.2_Nonsense_Mutation_p.E512*|KCNQ2_ENST00000360480.3_Nonsense_Mutation_p.E502*|KCNQ2_ENST00000359689.1_Nonsense_Mutation_p.E530*|KCNQ2_ENST00000354587.3_Nonsense_Mutation_p.E502*|KCNQ2_ENST00000370224.1_Nonsense_Mutation_p.E502*	NM_172107.2	NP_742105.1	O43526	KCNQ2_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 2	530					axon guidance (GO:0007411)|nervous system development (GO:0007399)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	ankyrin binding (GO:0030506)|delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(4)|liver(1)|lung(30)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65	all_cancers(38;1.24e-11)		BRCA - Breast invasive adenocarcinoma(10;1.04e-05)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	GTCAGGTCCTCGGTCACAAAC	0.682																																					p.E530X		Atlas-SNP	.											.	KCNQ2	201	.	0			c.G1588T						.						55.0	60.0	58.0					20																	62045484		2203	4300	6503	SO:0001587	stop_gained	3785	exon14			GGTCCTCGGTCAC	AF033348	CCDS13518.1, CCDS13519.1, CCDS13520.1, CCDS13521.1, CCDS46629.1	20q13.33	2012-07-05			ENSG00000075043	ENSG00000075043		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6296	protein-coding gene	gene with protein product		602235		EBN, EBN1		9425895, 16382104	Standard	NM_172107		Approved	Kv7.2, ENB1, BFNC, KCNA11, HNSPC	uc002yex.3	O43526	OTTHUMG00000033049	ENST00000359125.2:c.1588G>T	chr20.hg19:g.62045484C>A	ENSP00000352035:p.Glu530*	140.0	0.0		210.0	97.0	NM_172107	O43796|O75580|O95845|Q4VXP4|Q4VXR6|Q5VYT8|Q96J59|Q99454	Nonsense_Mutation	SNP	ENST00000359125.2	hg19	CCDS13520.1	.	.	.	.	.	.	.	.	.	.	C	38	7.049044	0.98029	.	.	ENSG00000075043	ENST00000357249;ENST00000359125;ENST00000370226;ENST00000354587;ENST00000359689;ENST00000430658;ENST00000360480;ENST00000344462;ENST00000370224;ENST00000370222	.	.	.	5.37	5.37	0.77165	.	0.064931	0.64402	D	0.000008	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	-3.0508	19.1082	0.93305	0.0:1.0:0.0:0.0	.	.	.	.	X	512;530;500;502;530;499;502;490;502;502	.	ENSP00000339611:E490X	E	-	1	0	KCNQ2	61515928	1.000000	0.71417	0.938000	0.37757	0.666000	0.39218	5.745000	0.68672	2.519000	0.84933	0.563000	0.77884	GAG	.	.		0.682	KCNQ2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080353.1	NM_172109	
IL36B	27177	hgsc.bcm.edu	37	2	113785625	113785635	+	Intron	DEL	TTATTGTGGAA	TTATTGTGGAA	-			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	TTATTGTGGAA	TTATTGTGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr2:113785625_113785635delTTATTGTGGAA	ENST00000259213.4	-	4	369				IL36B_ENST00000327407.2_Frame_Shift_Del_p.FHNK107fs	NM_014438.3	NP_055253.2	Q9NZH7	IL36B_HUMAN	interleukin 36, beta						immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of T cell differentiation (GO:0045582)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	interleukin-1 receptor binding (GO:0005149)	p.N109N(1)		kidney(1)|ovary(1)|pancreas(1)	3						GGAGCCTTCTTTATTGTGGAAAAAGAGAAAG	0.474																																					p.107_110del		Atlas-INDEL	.											.	IL36B	69	.	1	Substitution - coding silent(1)	lung(1)	c.320_330del						.																																			SO:0001627	intron_variant	27177	exon5			.	AF201833	CCDS2109.1, CCDS2110.1	2q14	2011-07-14	2011-06-06	2011-06-06	ENSG00000136696	ENSG00000136696		"""Interleukins and interleukin receptors"""	15564	protein-coding gene	gene with protein product		605508	"""interleukin 1 family, member 8 (eta)"""	IL1F8		10625660, 10512743, 16646978	Standard	NM_173178		Approved	FIL1, IL-1H2, IL-1F8, FILI-(ETA), IL1-ETA, IL1H2, MGC126880, MGC126882	uc002tiq.1	Q9NZH7	OTTHUMG00000131338	ENST00000259213.4:c.261+880TTCCACAATAA>-	chr2.hg19:g.113785625_113785635delTTATTGTGGAA		73.0	0.0		104.0	26.0	NM_173178	Q3MIH0|Q53SR6|Q7RTZ7|Q9UHA5	Frame_Shift_Del	DEL	ENST00000259213.4	hg19	CCDS2109.1																																																																																			.	.		0.474	IL36B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254110.1	NM_014438	
FZD4	8322	hgsc.bcm.edu	37	11	86665880	86665881	+	Frame_Shift_Ins	INS	-	-	T	rs80358283		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:86665880_86665881insT	ENST00000531380.1	-	1	552_553	c.247_248insA	c.(247-249)acafs	p.T83fs	RP11-736K20.6_ENST00000499504.3_lincRNA	NM_012193.3	NP_036325.2	Q9ULV1	FZD4_HUMAN	frizzled class receptor 4	83	FZ. {ECO:0000255|PROSITE- ProRule:PRU00090}.				brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|cellular response to retinoic acid (GO:0071300)|cerebellum vasculature morphogenesis (GO:0061301)|extracellular matrix-cell signaling (GO:0035426)|locomotion involved in locomotory behavior (GO:0031987)|negative regulation of cell-substrate adhesion (GO:0010812)|neuron differentiation (GO:0030182)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|progesterone secretion (GO:0042701)|regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030947)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal blood vessel morphogenesis (GO:0061304)|sensory perception of sound (GO:0007605)|substrate adhesion-dependent cell spreading (GO:0034446)|vasculogenesis (GO:0001570)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway, calcium modulating pathway (GO:0007223)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|G-protein coupled receptor activity (GO:0004930)|PDZ domain binding (GO:0030165)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			breast(1)|kidney(1)|large_intestine(3)|lung(9)|prostate(6)|skin(1)	21		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				GATGAGCGGTGTGAAAGTTGTC	0.634																																					p.T83fs		Atlas-INDEL	.											.	FZD4	52	.	0			c.248_249insA						.																																			SO:0001589	frameshift_variant	8322	exon1			.	AB032417	CCDS8279.1	11q14-q21	2014-01-29	2014-01-29			ENSG00000174804		"""GPCR / Class F : Frizzled receptors"", ""CD molecules"""	4042	protein-coding gene	gene with protein product		604579	"""frizzled (Drosophila) homolog 4"", ""exudative vitreoretinopathy 1"", ""frizzled homolog 4 (Drosophila)"", ""frizzled 4, seven transmembrane spanning receptor"", ""frizzled family receptor 4"""	EVR1		10544037, 15024691	Standard	NM_012193		Approved	CD344	uc001pce.3	Q9ULV1		ENST00000531380.1:c.248dupA	chr11.hg19:g.86665881_86665881dupT	ENSP00000434034:p.Thr83fs	140.0	0.0		124.0	29.0	NM_012193	A8K9Q3|Q14C97|Q6S9E4	Frame_Shift_Ins	INS	ENST00000531380.1	hg19	CCDS8279.1																																																																																			.	.		0.634	FZD4-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393818.2	NM_012193	
MUC5B	727897	hgsc.bcm.edu	37	11	1279360	1279376	+	Frame_Shift_Del	DEL	GCCTGTGTGCCCGCCAG	GCCTGTGTGCCCGCCAG	-			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	GCCTGTGTGCCCGCCAG	GCCTGTGTGCCCGCCAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr11:1279360_1279376delGCCTGTGTGCCCGCCAG	ENST00000529681.1	+	42	16540_16556	c.16482_16498delGCCTGTGTGCCCGCCAG	c.(16480-16500)ctgcctgtgtgcccgccagggfs	p.PVCPPG5495fs	MUC5B_ENST00000447027.1_Frame_Shift_Del_p.PVCPPG5498fs	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5495					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CCCAGAGCCTGCCTGTGTGCCCGCCAGGGCAGGAGTC	0.677																																					p.5494_5499del		Atlas-INDEL	.											.	MUC5B	473	.	0			c.16481_16497del						.																																			SO:0001589	frameshift_variant	727897	exon42			.	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.16482_16498delGCCTGTGTGCCCGCCAG	chr11.hg19:g.1279360_1279376delGCCTGTGTGCCCGCCAG	ENSP00000436812:p.Pro5495fs	187.0	0.0		124.0	41.0	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Frame_Shift_Del	DEL	ENST00000529681.1	hg19	CCDS44515.2																																																																																			.	.		0.677	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
MCF2L	23263	hgsc.bcm.edu	37	13	113731386	113731386	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr13:113731386delC	ENST00000375608.3	+	14	1669	c.1611delC	c.(1609-1611)ttcfs	p.F537fs	MCF2L_ENST00000421756.1_Frame_Shift_Del_p.F511fs|MCF2L_ENST00000375597.4_Frame_Shift_Del_p.F505fs|MCF2L_ENST00000375601.3_Frame_Shift_Del_p.F511fs|MCF2L_ENST00000423482.2_Frame_Shift_Del_p.F505fs|MCF2L_ENST00000535094.2_Frame_Shift_Del_p.F507fs|MCF2L_ENST00000375604.2_Frame_Shift_Del_p.F564fs|MCF2L_ENST00000397030.1_Frame_Shift_Del_p.F540fs|MCF2L_ENST00000442652.2_Frame_Shift_Del_p.F537fs|MCF2L_ENST00000434480.2_Frame_Shift_Del_p.F513fs			O15068	MCF2L_HUMAN	MCF.2 cell line derived transforming sequence-like	537					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular space (GO:0005615)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	1-phosphatidylinositol binding (GO:0005545)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			kidney(1)|large_intestine(5)|ovary(1)|stomach(1)	8	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_cancers(25;0.118)|all_lung(25;0.0368)|all_epithelial(44;0.0396)|Lung NSC(25;0.129)|Breast(118;0.188)				GAAAGGTCTTCCAGAAGCAGG	0.607																																					p.F507fs		Atlas-INDEL	.											.	MCF2L	182	.	0			c.1520delT						.						75.0	60.0	65.0					13																	113731386		2203	4300	6503	SO:0001589	frameshift_variant	23263	exon13			.	AB002360	CCDS9527.2, CCDS45070.1, CCDS9527.3, CCDS45070.2	13q34	2013-01-10			ENSG00000126217	ENSG00000126217		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	14576	protein-coding gene	gene with protein product		609499				9205841	Standard	NM_001112732		Approved	KIAA0362, DBS, OST, ARHGEF14	uc010tjr.2	O15068	OTTHUMG00000017377	ENST00000375608.3:c.1611delC	chr13.hg19:g.113731386delC	ENSP00000364758:p.Phe537fs	312.0	0.0		411.0	165.0	NM_001112732	A2A2X1|A2A2X2|A2A3G6|A2A3G8|B4DHD6|B4DIL6|E9PDN8|Q5JU56|Q5VXT1|Q6ZWD4|Q765G8|Q765G9|Q8N679	Frame_Shift_Del	DEL	ENST00000375608.3	hg19																																																																																				.	.		0.607	MCF2L-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000045849.4		
BPHL	670	hgsc.bcm.edu	37	6	3140642	3140660	+	Frame_Shift_Del	DEL	GCCCCGGGTCCAGTGCCCC	GCCCCGGGTCCAGTGCCCC	-	rs200713081		TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	GCCCCGGGTCCAGTGCCCC	GCCCCGGGTCCAGTGCCCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr6:3140642_3140660delGCCCCGGGTCCAGTGCCCC	ENST00000380379.5	+	6	736_754	c.687_705delGCCCCGGGTCCAGTGCCCC	c.(685-705)ctgccccgggtccagtgccccfs	p.LPRVQCP229fs	RP1-40E16.11_ENST00000447644.1_RNA|BPHL_ENST00000380368.2_3'UTR|BPHL_ENST00000380375.3_Frame_Shift_Del_p.LPRVQCP212fs|BPHL_ENST00000434640.1_Frame_Shift_Del_p.LPRVQCP212fs	NM_004332.2	NP_004323.2	Q86WA6	BPHL_HUMAN	biphenyl hydrolase-like (serine hydrolase)	229					cellular amino acid metabolic process (GO:0006520)|response to toxic substance (GO:0009636)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	hydrolase activity (GO:0016787)	p.R214L(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(6)	13	Ovarian(93;0.0386)	all_hematologic(90;0.108)				GGCACCTGCTGCCCCGGGTCCAGTGCCCCGCCTTGATTG	0.58																																					p.229_235del		Atlas-INDEL	.											.	BPHL	32	.	1	Substitution - Missense(1)	lung(1)	c.686_704del						.																																			SO:0001589	frameshift_variant	670	exon6			.	X81372	CCDS4483.2	6p25	2008-08-29	2008-08-29		ENSG00000137274	ENSG00000137274			1094	protein-coding gene	gene with protein product	"""breast epithelial mucin-associated antigen"""	603156		MCNAA		7759552, 9721218, 15832508	Standard	NM_004332		Approved	Bph-rp	uc003mva.3	Q86WA6	OTTHUMG00000014140	ENST00000380379.5:c.687_705delGCCCCGGGTCCAGTGCCCC	chr6.hg19:g.3140642_3140660delGCCCCGGGTCCAGTGCCCC	ENSP00000369739:p.Leu229fs	99.0	0.0		91.0	20.0	NM_004332	Q00306|Q13855|Q3KP51	Frame_Shift_Del	DEL	ENST00000380379.5	hg19	CCDS4483.2																																																																																			.	.		0.580	BPHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039670.5		
LMTK2	22853	hgsc.bcm.edu	37	7	97822810	97822814	+	Frame_Shift_Del	DEL	CTCTT	CTCTT	-			TCGA-G3-AAV1-01A-11D-A382-10	TCGA-G3-AAV1-10A-01D-A385-10	CTCTT	CTCTT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	0085fc07-88e4-460a-b85a-aa45fb9b1c59	9c5db754-20da-47ad-be09-78f6e300e818	g.chr7:97822810_97822814delCTCTT	ENST00000297293.5	+	11	3326_3330	c.3033_3037delCTCTT	c.(3031-3039)gactctttafs	p.SL1012fs		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1012					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					CGCTACTGGACTCTTTAGGATCTCA	0.58																																					p.1011_1012del		Atlas-INDEL	.											.	LMTK2	228	.	0			c.3032_3036del						.																																			SO:0001589	frameshift_variant	22853	exon11			.	AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3033_3037delCTCTT	chr7.hg19:g.97822810_97822814delCTCTT	ENSP00000297293:p.Ser1012fs	57.0	0.0		73.0	27.0	NM_014916	A4D272|Q75MG7|Q9UPS3	Frame_Shift_Del	DEL	ENST00000297293.5	hg19	CCDS5654.1																																																																																			.	.		0.580	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1	NM_014916	
