#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
ACAP3	116983	hgsc.bcm.edu	37	1	1235981	1235981	+	Missense_Mutation	SNP	T	T	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:1235981T>C	ENST00000354700.5	-	6	632	c.430A>G	c.(430-432)Agg>Ggg	p.R144G	ACAP3_ENST00000379037.2_5'Flank|ACAP3_ENST00000353662.3_Missense_Mutation_p.R102G	NM_030649.2	NP_085152.2	Q96P50	ACAP3_HUMAN	ArfGAP with coiled-coil, ankyrin repeat and PH domains 3	144					regulation of ARF GTPase activity (GO:0032312)		ARF GTPase activator activity (GO:0008060)|zinc ion binding (GO:0008270)			endometrium(3)|lung(9)|skin(1)|upper_aerodigestive_tract(1)	14						GGCCGGTGCCTCGGGGCCTGG	0.652																																					p.R144G		Atlas-SNP	.											.	ACAP3	87	.	0			c.A430G						PASS	.						42.0	45.0	44.0					1																	1235981		2198	4296	6494	SO:0001583	missense	116983	exon6			GGTGCCTCGGGGC	AF411981	CCDS19.2	1p36	2013-01-10	2008-09-22	2008-09-22	ENSG00000131584	ENSG00000131584		"""ADP-ribosylation factor GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16754	protein-coding gene	gene with protein product			"""centaurin, beta 5"""	CENTB5			Standard	NM_030649		Approved	KIAA1716	uc001aeb.2	Q96P50	OTTHUMG00000002235	ENST00000354700.5:c.430A>G	chr1.hg19:g.1235981T>C	ENSP00000346733:p.Arg144Gly	162.0	0.0	.		156.0	53.0	.	NM_030649	B1AMF5|Q5TA42|Q5TA43|Q86UT3|Q9BSR9|Q9C0E7	Missense_Mutation	SNP	ENST00000354700.5	hg19	CCDS19.2	.	.	.	.	.	.	.	.	.	.	T	13.86	2.362995	0.41902	.	.	ENSG00000131584	ENST00000354700;ENST00000353662	T;T	0.04119	3.7;3.7	4.05	-0.178	0.13303	.	0.063063	0.64402	D	0.000010	T	0.21631	0.0521	M	0.87180	2.865	0.21355	N	0.999713	D;D;D	0.76494	0.999;0.997;0.996	D;P;D	0.77557	0.988;0.889;0.99	T	0.04373	-1.0956	10	0.87932	D	0	.	13.3526	0.60611	0.0:0.0:0.4193:0.5807	.	184;144;102	Q5TA40;Q96P50;Q96P50-1	.;ACAP3_HUMAN;.	G	144;102	ENSP00000346733:R144G;ENSP00000321139:R102G	ENSP00000321139:R102G	R	-	1	2	ACAP3	1225844	0.971000	0.33674	0.507000	0.27676	0.763000	0.43281	1.603000	0.36794	0.182000	0.20032	0.260000	0.18958	AGG	.	.	.	none		0.652	ACAP3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006366.2	NM_030649	
GJB3	2707	hgsc.bcm.edu	37	1	35250656	35250656	+	Missense_Mutation	SNP	G	G	A	rs201314683		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:35250656G>A	ENST00000373366.2	+	2	908	c.293G>A	c.(292-294)cGt>cAt	p.R98H	GJB3_ENST00000373362.3_Missense_Mutation_p.R98H|RP1-34M23.5_ENST00000542839.1_RNA	NM_024009.2	NP_076872.1	O75712	CXB3_HUMAN	gap junction protein, beta 3, 31kDa	98					cell communication (GO:0007154)|in utero embryonic development (GO:0001701)|placenta development (GO:0001890)|sensory perception of sound (GO:0007605)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	connexon complex (GO:0005922)|cytoplasm (GO:0005737)|gap junction (GO:0005921)|integral component of membrane (GO:0016021)	gap junction channel activity (GO:0005243)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(2)|prostate(3)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				GTGGCCTACCGTGAGGAGCGG	0.632																																					p.R98H		Atlas-SNP	.											GJB3,NS,carcinoma,0,1	GJB3	40	.	0			c.G293A						PASS	.						133.0	127.0	129.0					1																	35250656		2203	4300	6503	SO:0001583	missense	2707	exon2			CCTACCGTGAGGA	BC012918	CCDS384.1	1p34	2008-05-14	2007-01-16		ENSG00000188910	ENSG00000188910		"""Ion channels / Gap junction proteins (connexins)"""	4285	protein-coding gene	gene with protein product	"""connexin 31"""	603324	"""gap junction protein, beta 3, 31kD (connexin 31)"", ""gap junction protein, beta 3, 31kDa (connexin 31)"", ""erythrokeratodermia variabilis"""	DFNA2, EKV		9843210, 9704026	Standard	NM_024009		Approved	CX31	uc001bxy.3	O75712	OTTHUMG00000004051	ENST00000373366.2:c.293G>A	chr1.hg19:g.35250656G>A	ENSP00000362464:p.Arg98His	49.0	0.0	.		63.0	26.0	.	NM_001005752	B2R790|Q2TAZ8	Missense_Mutation	SNP	ENST00000373366.2	hg19	CCDS384.1	.	.	.	.	.	.	.	.	.	.	g	23.2	4.390343	0.82902	.	.	ENSG00000188910	ENST00000373366;ENST00000373362;ENST00000543647	D;D	0.99129	-5.46;-5.46	5.85	5.85	0.93711	Connexin, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98782	0.9590	M	0.76328	2.33	0.58432	D	0.99999	D	0.63880	0.993	P	0.53185	0.72	D	0.98959	1.0797	10	0.56958	D	0.05	.	15.6548	0.77124	0.0:0.0:0.8623:0.1377	.	98	O75712	CXB3_HUMAN	H	98	ENSP00000362464:R98H;ENSP00000362460:R98H	ENSP00000362460:R98H	R	+	2	0	GJB3	35023243	1.000000	0.71417	0.966000	0.40874	0.668000	0.39293	7.966000	0.87956	2.771000	0.95319	0.561000	0.74099	CGT	.	G|0.999;A|0.001	0.001	weak		0.632	GJB3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011559.1	NM_024009	
MUTYH	4595	hgsc.bcm.edu	37	1	45797447	45797447	+	Missense_Mutation	SNP	A	A	G	rs587781601		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:45797447A>G	ENST00000372098.3	-	12	1196	c.1063T>C	c.(1063-1065)Ttc>Ctc	p.F355L	MUTYH_ENST00000372100.5_Missense_Mutation_p.F341L|MUTYH_ENST00000456914.2_Missense_Mutation_p.F330L|MUTYH_ENST00000448481.1_Missense_Mutation_p.F341L|MUTYH_ENST00000372115.3_Missense_Mutation_p.F344L|MUTYH_ENST00000450313.1_Missense_Mutation_p.F358L|MUTYH_ENST00000488731.2_Intron|MUTYH_ENST00000355498.2_Missense_Mutation_p.F330L|MUTYH_ENST00000372110.3_Missense_Mutation_p.F345L|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000529984.1_Intron|MUTYH_ENST00000528013.2_Missense_Mutation_p.F344L|MUTYH_ENST00000354383.6_Missense_Mutation_p.F331L|MUTYH_ENST00000372104.1_Missense_Mutation_p.F330L|MUTYH_ENST00000528332.2_Intron			Q9UIF7	MUTYH_HUMAN	mutY homolog	355					base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TTTCTGGGGAAGTTGACCACT	0.647			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																												p.F358L		Atlas-SNP	.	yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	.	MUTYH	38	.	0			c.T1072C						PASS	.						20.0	24.0	23.0					1																	45797447		2202	4300	6502	SO:0001583	missense	4595	exon12	Familial Cancer Database	MAP, MYH-associated polyposis	TGGGGAAGTTGAC	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1063T>C	chr1.hg19:g.45797447A>G	ENSP00000361170:p.Phe355Leu	46.0	0.0	.		46.0	17.0	.	NM_001128425	D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	hg19	CCDS520.1	.	.	.	.	.	.	.	.	.	.	A	16.11	3.031555	0.54790	.	.	ENSG00000132781	ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000450313;ENST00000372100;ENST00000525481;ENST00000412971	T;T;T;T;T;T;T;T;T;T;T	0.26660	2.67;2.67;2.67;2.67;2.67;2.66;2.65;2.65;2.64;2.67;1.72	5.5	4.39	0.52855	.	0.047785	0.85682	D	0.000000	T	0.18299	0.0439	N	0.17312	0.475	0.46774	D	0.999199	B;B;B;B;B;B;B	0.27823	0.19;0.001;0.185;0.001;0.19;0.054;0.19	B;B;B;B;B;B;B	0.33799	0.118;0.02;0.17;0.02;0.118;0.046;0.082	T	0.07986	-1.0744	10	0.56958	D	0.05	-13.047	10.8161	0.46575	0.926:0.0:0.074:0.0	.	358;355;345;355;344;238;331	E5KP25;E5KP26;Q9UIF7-2;Q9UIF7;E5KP27;D3DPZ6;E5KP28	.;.;.;MUTYH_HUMAN;.;.;.	L	330;341;330;331;330;355;345;344;358;341;202;202	ENSP00000361176:F330L;ENSP00000409718:F341L;ENSP00000407590:F330L;ENSP00000346354:F331L;ENSP00000347685:F330L;ENSP00000361170:F355L;ENSP00000361182:F345L;ENSP00000361187:F344L;ENSP00000408176:F358L;ENSP00000361172:F341L;ENSP00000410263:F202L	ENSP00000346354:F331L	F	-	1	0	MUTYH	45570034	1.000000	0.71417	1.000000	0.80357	0.767000	0.43475	6.850000	0.75420	2.100000	0.63781	0.533000	0.62120	TTC	.	.	.	none		0.647	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1	NM_012222	
CCDC17	149483	hgsc.bcm.edu	37	1	46088725	46088725	+	Silent	SNP	C	C	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:46088725C>A	ENST00000528266.1	-	4	705	c.558G>T	c.(556-558)ctG>ctT	p.L186L	CCDC17_ENST00000343901.2_Silent_p.L154L|CCDC17_ENST00000464739.1_5'Flank|CCDC17_ENST00000421127.2_Silent_p.L177L|CCDC17_ENST00000445048.2_Intron			Q96LX7	CCD17_HUMAN	coiled-coil domain containing 17	186										kidney(1)|large_intestine(1)|lung(1)|ovary(2)	5	Acute lymphoblastic leukemia(166;0.155)					TCTCCTGCTCCAGGCCGAAGA	0.667																																					p.L186L		Atlas-SNP	.											.	CCDC17	54	.	0			c.G558T						PASS	.						22.0	26.0	25.0					1																	46088725		2203	4300	6503	SO:0001819	synonymous_variant	149483	exon4			CTGCTCCAGGCCG		CCDS44131.1, CCDS44131.2, CCDS53314.1	1p34.1	2014-02-12			ENSG00000159588	ENSG00000159588			26574	protein-coding gene	gene with protein product							Standard	NM_001190182		Approved	FLJ33084	uc010olt.2	Q96LX7	OTTHUMG00000007822	ENST00000528266.1:c.558G>T	chr1.hg19:g.46088725C>A		58.0	0.0	.		79.0	41.0	.	NM_001114938	A1A4Y7|B4DNX7|B4E1Q5|C9J8L2|Q0P683|Q5T629	Silent	SNP	ENST00000528266.1	hg19	CCDS44131.2																																																																																			.	.	.	none		0.667	CCDC17-008	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386833.1	NM_152500	
ABCD3	5825	hgsc.bcm.edu	37	1	94939389	94939389	+	Missense_Mutation	SNP	C	C	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:94939389C>A	ENST00000370214.4	+	5	427	c.403C>A	c.(403-405)Ctt>Att	p.L135I	ABCD3_ENST00000536817.1_Missense_Mutation_p.L62I|ABCD3_ENST00000315713.5_Missense_Mutation_p.L135I|ABCD3_ENST00000394233.2_Missense_Mutation_p.L135I|ABCD3_ENST00000454898.2_Missense_Mutation_p.L159I	NM_002858.3	NP_002849.1	P28288	ABCD3_HUMAN	ATP-binding cassette, sub-family D (ALD), member 3	135	ABC transmembrane type-1. {ECO:0000255|PROSITE-ProRule:PRU00441}.|Interaction with PEX19.				ATP catabolic process (GO:0006200)|fatty acid beta-oxidation (GO:0006635)|peroxisome organization (GO:0007031)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|liver(2)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26		all_lung(203;0.000434)|Lung NSC(277;0.0019)		all cancers(265;0.0261)|Epithelial(280;0.165)		TGCCATGCCTCTTGTAAGTTT	0.328																																					p.L135I		Atlas-SNP	.											.	ABCD3	62	.	0			c.C403A						PASS	.						110.0	105.0	107.0					1																	94939389		2203	4300	6503	SO:0001583	missense	5825	exon5			ATGCCTCTTGTAA	M81182	CCDS749.1, CCDS44175.1	1p21.3	2012-05-16			ENSG00000117528	ENSG00000117528		"""ATP binding cassette transporters / subfamily D"""	67	protein-coding gene	gene with protein product		170995		PXMP1		1301993, 8449508	Standard	NM_002858		Approved	PMP70, ZWS2	uc001dqn.4	P28288	OTTHUMG00000010717	ENST00000370214.4:c.403C>A	chr1.hg19:g.94939389C>A	ENSP00000359233:p.Leu135Ile	66.0	0.0	.		65.0	23.0	.	NM_002858	D3DT46|Q15271|Q6NUN5|Q96DA3|Q9H529	Missense_Mutation	SNP	ENST00000370214.4	hg19	CCDS749.1	.	.	.	.	.	.	.	.	.	.	C	10.59	1.392782	0.25118	.	.	ENSG00000117528	ENST00000394233;ENST00000454898;ENST00000536817;ENST00000370214;ENST00000315713	D;D;D;D;D	0.99652	-3.5;-3.5;-3.5;-3.5;-6.3	5.78	5.78	0.91487	ABC transporter, N-terminal (1);ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);	0.437369	0.25526	N	0.030069	D	0.96703	0.8924	L	0.31065	0.9	0.27177	N	0.960763	B;B;B;B	0.31680	0.005;0.335;0.001;0.004	B;B;B;B	0.31686	0.014;0.134;0.005;0.01	D	0.92520	0.6024	10	0.12766	T	0.61	-13.3859	14.7668	0.69646	0.0:0.7487:0.2513:0.0	.	159;135;135;135	E7EUE1;P28288-2;P28288;P28288-3	.;.;ABCD3_HUMAN;.	I	135;159;62;135;135	ENSP00000377780:L135I;ENSP00000403357:L159I;ENSP00000440692:L62I;ENSP00000359233:L135I;ENSP00000326880:L135I	ENSP00000326880:L135I	L	+	1	0	ABCD3	94711977	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.930000	0.40124	2.894000	0.99253	0.655000	0.94253	CTT	.	.	.	none		0.328	ABCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029597.1	NM_002858	
CSDE1	7812	hgsc.bcm.edu	37	1	115280171	115280171	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:115280171A>T	ENST00000358528.4	-	5	749	c.323T>A	c.(322-324)gTt>gAt	p.V108D	CSDE1_ENST00000438362.2_Missense_Mutation_p.V154D|CSDE1_ENST00000261443.5_Intron|CSDE1_ENST00000534699.1_Missense_Mutation_p.V108D|CSDE1_ENST00000369530.1_Intron|CSDE1_ENST00000530886.1_Intron|CSDE1_ENST00000339438.6_Intron	NM_001007553.2	NP_001007554.1	O75534	CSDE1_HUMAN	cold shock domain containing E1, RNA-binding	108					male gonad development (GO:0008584)|nuclear-transcribed mRNA catabolic process, no-go decay (GO:0070966)|regulation of transcription, DNA-templated (GO:0006355)	CRD-mediated mRNA stability complex (GO:0070937)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(4)|endometrium(11)|kidney(2)|large_intestine(12)|lung(17)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	51	all_epithelial(7;5.11e-05)|all_lung(7;0.000179)|Lung NSC(6;0.00195)|Lung SC(450;0.211)	all_cancers(81;2.21e-07)|all_epithelial(167;4.2e-07)|all_lung(203;9.97e-06)|Lung NSC(69;1.74e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|COAD - Colon adenocarcinoma(174;0.111)|all cancers(265;0.112)|Epithelial(280;0.124)|LUSC - Lung squamous cell carcinoma(189;0.133)		GTTGTGAGGAACAGCGCACAC	0.398																																					p.V154D		Atlas-SNP	.											.	CSDE1	145	.	0			c.T461A						PASS	.						64.0	55.0	58.0					1																	115280171		2203	4300	6503	SO:0001583	missense	7812	exon6			TGAGGAACAGCGC		CCDS30811.1, CCDS30812.1, CCDS44197.1, CCDS55626.1	1p13.2	2011-11-02			ENSG00000009307	ENSG00000009307			29905	protein-coding gene	gene with protein product	"""upstream of NRAS"""	191510				2204029, 10048485	Standard	NM_007158		Approved	D1S155E, UNR	uc001efi.3	O75534	OTTHUMG00000012060	ENST00000358528.4:c.323T>A	chr1.hg19:g.115280171A>T	ENSP00000351329:p.Val108Asp	351.0	1.0	.		368.0	148.0	.	NM_001242891	A8K281|E9PGZ0|G5E9Q2|O94961|Q5TF04|Q5TF05|Q68DF1|Q68DI9|Q9Y2S4	Missense_Mutation	SNP	ENST00000358528.4	hg19	CCDS30812.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.041985	0.75732	.	.	ENSG00000009307	ENST00000438362;ENST00000358528;ENST00000534699	.	.	.	5.87	5.87	0.94306	.	.	.	.	.	T	0.50752	0.1634	N	0.22421	0.69	0.80722	D	1	D;D	0.61697	0.971;0.99	P;P	0.58266	0.598;0.836	T	0.56715	-0.7933	8	0.49607	T	0.09	.	16.2631	0.82557	1.0:0.0:0.0:0.0	.	108;154	O75534;G5E9Q2	CSDE1_HUMAN;.	D	154;108;108	.	ENSP00000351329:V108D	V	-	2	0	CSDE1	115081694	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.676000	0.91199	2.239000	0.73571	0.528000	0.53228	GTT	.	.	.	none		0.398	CSDE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033397.1	NM_007158	
KPRP	448834	hgsc.bcm.edu	37	1	152732843	152732843	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:152732843G>A	ENST00000606109.1	+	1	807	c.779G>A	c.(778-780)cGg>cAg	p.R260Q	KPRP_ENST00000368773.1_Missense_Mutation_p.R260Q			Q5T749	KPRP_HUMAN	keratinocyte proline-rich protein	260	Pro-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				NS(1)|breast(1)|endometrium(9)|kidney(1)|large_intestine(10)|lung(21)|ovary(6)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			CCTCCTCCTCGGCGGCTGCAG	0.602																																					p.R260Q		Atlas-SNP	.											.	KPRP	152	.	0			c.G779A						PASS	.						38.0	44.0	42.0					1																	152732843		2203	4300	6503	SO:0001583	missense	448834	exon2			CTCCTCGGCGGCT	AY960854	CCDS30862.1	1q21.3	2008-02-05	2007-02-02	2006-12-07	ENSG00000203786	ENSG00000203786			31823	protein-coding gene	gene with protein product		613260	"""chromosome 1 open reading frame 45"""	C1orf45		16297201	Standard	NM_001025231		Approved		uc001fal.1	Q5T749	OTTHUMG00000012402	ENST00000606109.1:c.779G>A	chr1.hg19:g.152732843G>A	ENSP00000475216:p.Arg260Gln	62.0	0.0	.		80.0	4.0	.	NM_001025231		Missense_Mutation	SNP	ENST00000606109.1	hg19	CCDS30862.1	.	.	.	.	.	.	.	.	.	.	G	10.77	1.442856	0.25987	.	.	ENSG00000203786	ENST00000368773	T	0.16073	2.37	5.55	2.56	0.30785	.	0.833462	0.10411	N	0.677910	T	0.05731	0.0150	L	0.29908	0.895	0.09310	N	1	D	0.55385	0.971	P	0.45099	0.469	T	0.25467	-1.0131	10	0.72032	D	0.01	-9.8249	5.4492	0.16552	0.1811:0.1841:0.6347:0.0	.	260	Q5T749	KPRP_HUMAN	Q	260	ENSP00000357762:R260Q	ENSP00000357762:R260Q	R	+	2	0	KPRP	150999467	0.000000	0.05858	0.002000	0.10522	0.023000	0.10783	0.342000	0.19926	0.778000	0.33520	0.563000	0.77884	CGG	.	.	.	none		0.602	KPRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034522.2	NM_001025231	
FCRL4	83417	hgsc.bcm.edu	37	1	157548316	157548316	+	Silent	SNP	T	T	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:157548316T>A	ENST00000271532.1	-	10	1512	c.1377A>T	c.(1375-1377)ggA>ggT	p.G459G	FCRL4_ENST00000448509.2_5'UTR	NM_031282.2	NP_112572.1	Q96PJ5	FCRL4_HUMAN	Fc receptor-like 4	459					immune system process (GO:0002376)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(5)|lung(20)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	40	all_hematologic(112;0.0378)|Hepatocellular(266;0.178)	Prostate(1639;0.245)				ATACCAAATCTCCCTTTTTGG	0.423																																					p.G459G		Atlas-SNP	.											.	FCRL4	95	.	0			c.A1377T						PASS	.						102.0	101.0	102.0					1																	157548316		2203	4300	6503	SO:0001819	synonymous_variant	83417	exon10			CAAATCTCCCTTT	AF343661	CCDS1166.1	1q21	2013-01-14			ENSG00000163518	ENSG00000163518		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	18507	protein-coding gene	gene with protein product		605876				11290337, 11493702	Standard	NM_031282		Approved	FCRH4, IRTA1, IGFP2, CD307d	uc001fqw.3	Q96PJ5	OTTHUMG00000035488	ENST00000271532.1:c.1377A>T	chr1.hg19:g.157548316T>A		108.0	0.0	.		70.0	32.0	.	NM_031282	Q96PJ3|Q96RE0	Silent	SNP	ENST00000271532.1	hg19	CCDS1166.1																																																																																			.	.	.	none		0.423	FCRL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086180.1	NM_031282	
MYO7B	4648	hgsc.bcm.edu	37	2	128389949	128389949	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr2:128389949G>C	ENST00000409816.2	+	37	5332	c.5300G>C	c.(5299-5301)tGc>tCc	p.C1767S	MYO7B_ENST00000409090.1_Missense_Mutation_p.C620S|MYO7B_ENST00000389524.4_Missense_Mutation_p.C1768S|MYO7B_ENST00000428314.1_Missense_Mutation_p.C1767S			Q6PIF6	MYO7B_HUMAN	myosin VIIB	1767	MyTH4 2. {ECO:0000255|PROSITE- ProRule:PRU00359}.					extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(46)|ovary(3)|pancreas(1)|prostate(3)|urinary_tract(1)	75	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0753)		GCCCCCGACTGCAGCCGCCGA	0.682																																					p.C1767S		Atlas-SNP	.											.	MYO7B	359	.	0			c.G5300C						PASS	.						34.0	43.0	40.0					2																	128389949		1762	3946	5708	SO:0001583	missense	4648	exon38			CCGACTGCAGCCG		CCDS46405.1	2q21.1	2011-09-27			ENSG00000169994	ENSG00000169994		"""Myosins / Myosin superfamily : Class VII"""	7607	protein-coding gene	gene with protein product		606541				8022818, 8884266	Standard	NM_001080527		Approved		uc002top.3	Q6PIF6	OTTHUMG00000153419	ENST00000409816.2:c.5300G>C	chr2.hg19:g.128389949G>C	ENSP00000386461:p.Cys1767Ser	212.0	0.0	.		251.0	112.0	.	NM_001080527	Q14786|Q8TEE1	Missense_Mutation	SNP	ENST00000409816.2	hg19	CCDS46405.1	.	.	.	.	.	.	.	.	.	.	g	16.39	3.108746	0.56291	.	.	ENSG00000169994	ENST00000389524;ENST00000428314;ENST00000272666;ENST00000409816;ENST00000409090	D;D;D;D	0.92495	-3.05;-3.05;-3.05;-3.05	4.84	4.84	0.62591	MyTH4 domain (3);	0.000000	0.85682	D	0.000000	D	0.93746	0.8001	L	0.56396	1.775	0.54753	D	0.999982	D	0.55605	0.972	P	0.56216	0.794	D	0.93035	0.6452	10	0.36615	T	0.2	.	17.9396	0.89023	0.0:0.0:1.0:0.0	.	1767	Q6PIF6	MYO7B_HUMAN	S	1768;1767;863;1767;620	ENSP00000374175:C1768S;ENSP00000415090:C1767S;ENSP00000386461:C1767S;ENSP00000386850:C620S	ENSP00000272666:C863S	C	+	2	0	MYO7B	128106419	1.000000	0.71417	0.996000	0.52242	0.162000	0.22319	6.281000	0.72632	2.229000	0.72834	0.561000	0.74099	TGC	.	.	.	none		0.682	MYO7B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000331124.3	XM_291001	
LRTM1	57408	hgsc.bcm.edu	37	3	54958819	54958819	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr3:54958819G>A	ENST00000273286.5	-	2	593	c.431C>T	c.(430-432)aCt>aTt	p.T144I	CACNA2D3_ENST00000474759.1_Intron|LRTM1_ENST00000493075.1_Missense_Mutation_p.T68I|CACNA2D3_ENST00000490478.1_Intron|CACNA2D3_ENST00000415676.2_Intron|CACNA2D3_ENST00000288197.5_Intron	NM_020678.2	NP_065729.1	Q9HBL6	LRTM1_HUMAN	leucine-rich repeats and transmembrane domains 1	144						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|large_intestine(7)|lung(6)|prostate(1)|skin(4)	21				KIRC - Kidney renal clear cell carcinoma(284;0.00975)|Kidney(284;0.0112)|OV - Ovarian serous cystadenocarcinoma(275;0.0502)		GTTCTCCCAAGTCTCTCCCAA	0.493																																					p.T144I		Atlas-SNP	.											.	LRTM1	52	.	0			c.C431T						PASS	.						95.0	91.0	93.0					3																	54958819		2203	4300	6503	SO:0001583	missense	57408	exon2			TCCCAAGTCTCTC	AF225421	CCDS2876.1	3p14.3	2006-01-02			ENSG00000144771	ENSG00000144771			25023	protein-coding gene	gene with protein product						12477932	Standard	NM_020678		Approved	HT017	uc003dhl.3	Q9HBL6	OTTHUMG00000158578	ENST00000273286.5:c.431C>T	chr3.hg19:g.54958819G>A	ENSP00000273286:p.Thr144Ile	107.0	0.0	.		88.0	42.0	.	NM_020678	Q8IUU2	Missense_Mutation	SNP	ENST00000273286.5	hg19	CCDS2876.1	.	.	.	.	.	.	.	.	.	.	G	3.291	-0.144996	0.06627	.	.	ENSG00000144771	ENST00000273286;ENST00000493075	T;D	0.90069	4.29;-2.61	5.96	2.13	0.27403	.	0.822907	0.11590	N	0.548818	T	0.78842	0.4347	L	0.32530	0.975	0.09310	N	1	B	0.28713	0.22	B	0.24848	0.056	T	0.65261	-0.6211	10	0.37606	T	0.19	.	1.0945	0.01670	0.1978:0.2377:0.3423:0.2222	.	144	Q9HBL6	LRTM1_HUMAN	I	144;68	ENSP00000273286:T144I;ENSP00000419772:T68I	ENSP00000273286:T144I	T	-	2	0	LRTM1	54933859	0.009000	0.17119	0.032000	0.17829	0.140000	0.21249	0.516000	0.22817	0.102000	0.17638	-0.126000	0.14955	ACT	.	.	.	none		0.493	LRTM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351399.1	NM_020678	
KALRN	8997	hgsc.bcm.edu	37	3	124210171	124210171	+	Splice_Site	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr3:124210171C>T	ENST00000240874.3	+	31	4740	c.4583C>T	c.(4582-4584)aCc>aTc	p.T1528I	KALRN_ENST00000460856.1_Splice_Site_p.T1519I|KALRN_ENST00000360013.3_Splice_Site_p.T1528I	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1528	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						TGTCTACAGACCTCAGAGCTG	0.577																																					p.T1528I		Atlas-SNP	.											.	KALRN	556	.	0			c.C4583T						PASS	.						55.0	51.0	52.0					3																	124210171		2203	4300	6503	SO:0001630	splice_region_variant	8997	exon31			TACAGACCTCAGA	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.4582-1C>T	chr3.hg19:g.124210171C>T		83.0	0.0	.		97.0	51.0	.	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	hg19	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	25.2|25.2	4.610758|4.610758	0.87258|0.87258	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000354186|ENST00000460856;ENST00000240874;ENST00000360013	.|T;T;T	.|0.10668	.|2.85;2.85;2.85	5.12|5.12	5.12|5.12	0.69794|0.69794	.|Pleckstrin homology-type (1);Pleckstrin homology domain (2);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.35158|0.35158	0.0922|0.0922	M|M	0.80422|0.80422	2.495|2.495	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.64830	.|0.986;0.994;0.992	.|P;D;P	.|0.67231	.|0.602;0.95;0.776	T|T	0.03354|0.03354	-1.1045|-1.1045	5|10	.|0.34782	.|T	.|0.22	.|.	18.7502|18.7502	0.91810|0.91810	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|1519;1528;1528	.|C9IZQ6;O60229;O60229-2	.|.;KALRN_HUMAN;.	S|I	1497|1519;1528;1528	.|ENSP00000418611:T1519I;ENSP00000240874:T1528I;ENSP00000353109:T1528I	.|ENSP00000240874:T1528I	P|T	+|+	1|2	0|0	KALRN|KALRN	125692861|125692861	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.651000|7.651000	0.83577|0.83577	2.664000|2.664000	0.90586|0.90586	0.655000|0.655000	0.94253|0.94253	CCT|ACC	.	.	.	none		0.577	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	Missense_Mutation
IFT122	55764	hgsc.bcm.edu	37	3	129185869	129185869	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr3:129185869G>A	ENST00000348417.2	+	8	777	c.700G>A	c.(700-702)Gaa>Aaa	p.E234K	IFT122_ENST00000440957.2_Intron|IFT122_ENST00000431818.2_Missense_Mutation_p.E84K|IFT122_ENST00000504021.1_Intron|IFT122_ENST00000347300.2_Intron|IFT122_ENST00000296266.3_Missense_Mutation_p.E285K|IFT122_ENST00000349441.2_Intron|IFT122_ENST00000507564.1_Intron	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	234					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						AGAGGAGGAAGAACCAGAGGA	0.532																																					p.E285K		Atlas-SNP	.											.	IFT122	117	.	0			c.G853A						PASS	.						149.0	155.0	153.0					3																	129185869		2203	4300	6503	SO:0001583	missense	55764	exon9			GAGGAAGAACCAG	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.700G>A	chr3.hg19:g.129185869G>A	ENSP00000324005:p.Glu234Lys	95.0	0.0	.		119.0	28.0	.	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	.	.	.	.	.	.	.	.	.	.	G	12.34	1.907475	0.33721	.	.	ENSG00000163913	ENST00000296266;ENST00000431818;ENST00000348417	T;T;T	0.60797	0.16;0.37;0.85	4.64	3.77	0.43336	WD40 repeat-like-containing domain (1);	1.002150	0.08040	N	0.995052	T	0.34193	0.0889	N	0.08118	0	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.001;0.004	T	0.10222	-1.0639	10	0.05959	T	0.93	-10.4607	10.2543	0.43388	0.094:0.0:0.906:0.0	.	234;285	Q9HBG6;G3XAB1	IF122_HUMAN;.	K	285;84;234	ENSP00000296266:E285K;ENSP00000410946:E84K;ENSP00000324005:E234K	ENSP00000296266:E285K	E	+	1	0	IFT122	130668559	1.000000	0.71417	0.999000	0.59377	0.943000	0.58893	2.087000	0.41653	1.190000	0.43042	-0.448000	0.05591	GAA	.	.	.	none		0.532	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
SEL1L3	23231	hgsc.bcm.edu	37	4	25759396	25759396	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr4:25759396T>A	ENST00000399878.3	-	22	3222	c.3100A>T	c.(3100-3102)Aac>Tac	p.N1034Y	SEL1L3_ENST00000502949.1_Missense_Mutation_p.N881Y|SEL1L3_ENST00000264868.5_Missense_Mutation_p.N999Y	NM_015187.3	NP_056002.2	Q68CR1	SE1L3_HUMAN	sel-1 suppressor of lin-12-like 3 (C. elegans)	1034						integral component of membrane (GO:0016021)				breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(2)	14						GACTCCTCGTTACTGTGGCTC	0.567																																					p.N1034Y		Atlas-SNP	.											.	SEL1L3	62	.	0			c.A3100T						PASS	.						45.0	56.0	52.0					4																	25759396		2095	4221	6316	SO:0001583	missense	23231	exon22			CCTCGTTACTGTG	BC009945	CCDS47037.1, CCDS75113.1	4p15.2	2009-09-24			ENSG00000091490	ENSG00000091490			29108	protein-coding gene	gene with protein product	"""KIAA0746 protein"""					9872452	Standard	XM_005248143		Approved	KIAA0746	uc003gru.4	Q68CR1	OTTHUMG00000160331	ENST00000399878.3:c.3100A>T	chr4.hg19:g.25759396T>A	ENSP00000382767:p.Asn1034Tyr	260.0	0.0	.		256.0	92.0	.	NM_015187	A0PJH6|A8K0X2|O94847|Q6P999|Q96G59	Missense_Mutation	SNP	ENST00000399878.3	hg19	CCDS47037.1	.	.	.	.	.	.	.	.	.	.	T	15.32	2.798546	0.50208	.	.	ENSG00000091490	ENST00000399878;ENST00000264868;ENST00000502949	T;T;T	0.16743	2.53;2.54;2.32	5.61	1.51	0.23008	.	0.645110	0.17263	N	0.180719	T	0.31167	0.0788	L	0.60455	1.87	0.09310	N	1	D;P	0.65815	0.995;0.918	P;P	0.59221	0.854;0.534	T	0.11867	-1.0570	10	0.72032	D	0.01	-0.8083	12.2959	0.54847	0.0:0.0:0.4122:0.5878	.	441;1034	B4DTH5;Q68CR1	.;SE1L3_HUMAN	Y	1034;999;881	ENSP00000382767:N1034Y;ENSP00000264868:N999Y;ENSP00000425438:N881Y	ENSP00000264868:N999Y	N	-	1	0	SEL1L3	25368494	0.040000	0.19996	0.000000	0.03702	0.644000	0.38419	2.343000	0.44001	0.092000	0.17331	0.533000	0.62120	AAC	.	.	.	none		0.567	SEL1L3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360261.1	NM_015187	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68934461	68934461	+	Missense_Mutation	SNP	C	C	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr4:68934461C>A	ENST00000356291.2	-	7	689	c.630G>T	c.(628-630)agG>agT	p.R210S	UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000511571.1_RNA|UBA6-AS1_ENST00000500538.2_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	210	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						TAGCTGTTTCCCTTCCTTGGA	0.498																																					p.R210S		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G630T						PASS	.						120.0	107.0	111.0					4																	68934461		2203	4300	6503	SO:0001583	missense	389208	exon7			TGTTTCCCTTCCT	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.630G>T	chr4.hg19:g.68934461C>A	ENSP00000348639:p.Arg210Ser	104.0	0.0	.		82.0	36.0	.	NM_207407	A8MXX2	Missense_Mutation	SNP	ENST00000356291.2	hg19	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	C	6.884	0.532541	0.13127	.	.	ENSG00000198092	ENST00000356291	D	0.88354	-2.37	5.43	-0.132	0.13489	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.197117	0.34932	N	0.003580	T	0.69351	0.3101	N	0.05574	-0.02	0.09310	N	1	B	0.10296	0.003	B	0.12837	0.008	T	0.54814	-0.8237	10	0.12103	T	0.63	.	3.808	0.08785	0.2927:0.4276:0.0:0.2797	.	210	Q6ZWK6	TM11F_HUMAN	S	210	ENSP00000348639:R210S	ENSP00000348639:R210S	R	-	3	2	TMPRSS11F	68617056	0.000000	0.05858	0.816000	0.32577	0.629000	0.37895	-0.086000	0.11233	0.008000	0.14787	-0.136000	0.14681	AGG	.	.	.	none		0.498	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	
FNIP2	57600	hgsc.bcm.edu	37	4	159812743	159812743	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr4:159812743C>G	ENST00000264433.6	+	15	3170	c.3095C>G	c.(3094-3096)tCc>tGc	p.S1032C	FNIP2_ENST00000379346.3_Missense_Mutation_p.S1055C|C4orf45_ENST00000508011.1_5'Flank	NM_020840.1	NP_065891.1	Q9P278	FNIP2_HUMAN	folliculin interacting protein 2	1032					intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein phosphorylation (GO:0006468)|regulation of protein phosphorylation (GO:0001932)	cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	9	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.00936)		AGTCAGGTGTCCAGTTTGCTT	0.428																																					p.S1032C		Atlas-SNP	.											.	FNIP2	90	.	0			c.C3095G						PASS	.						150.0	142.0	145.0					4																	159812743		1955	4149	6104	SO:0001583	missense	57600	exon15			AGGTGTCCAGTTT	AB040883	CCDS47155.1	4q32.1	2012-10-31			ENSG00000052795	ENSG00000052795			29280	protein-coding gene	gene with protein product	"""O6-methylguanine-induced apoptosis 1"""	612768				18403135	Standard	NM_020840		Approved	KIAA1450, FNIPL, MAPO1	uc003iqe.4	Q9P278	OTTHUMG00000161983	ENST00000264433.6:c.3095C>G	chr4.hg19:g.159812743C>G	ENSP00000264433:p.Ser1032Cys	80.0	0.0	.		61.0	27.0	.	NM_020840	Q05DC3|Q96I31|Q9H994	Missense_Mutation	SNP	ENST00000264433.6	hg19	CCDS47155.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.938238	0.52972	.	.	ENSG00000052795	ENST00000264433;ENST00000379346	T;T	0.30448	1.53;1.53	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	T	0.45418	0.1341	M	0.86740	2.835	0.50039	D	0.999849	B	0.22909	0.077	B	0.27170	0.077	T	0.43734	-0.9373	9	.	.	.	.	19.466	0.94939	0.0:1.0:0.0:0.0	.	1032	Q9P278	FNIP2_HUMAN	C	1032;1055	ENSP00000264433:S1032C;ENSP00000368651:S1055C	.	S	+	2	0	FNIP2	160032193	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	3.916000	0.56416	2.607000	0.88179	0.655000	0.94253	TCC	.	.	.	none		0.428	FNIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366602.1	NM_020840	
RAPGEF6	51735	hgsc.bcm.edu	37	5	130791652	130791652	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr5:130791652G>C	ENST00000509018.1	-	20	3123	c.2918C>G	c.(2917-2919)cCa>cGa	p.P973R	CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.P1023R|RAPGEF6_ENST00000512052.1_Missense_Mutation_p.P688R|RAPGEF6_ENST00000308008.6_Missense_Mutation_p.P973R|RAPGEF6_ENST00000307984.5_Missense_Mutation_p.P978R|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.P973R|RAPGEF6_ENST00000507093.1_Missense_Mutation_p.P973R	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	973	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		GTATTTGCTTGGTAACTTTTC	0.373																																					p.P978R	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											.	RAPGEF6	361	.	0			c.C2933G						PASS	.						120.0	113.0	116.0					5																	130791652		2203	4300	6503	SO:0001583	missense	51735	exon21			TTGCTTGGTAACT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.2918C>G	chr5.hg19:g.130791652G>C	ENSP00000421684:p.Pro973Arg	110.0	0.0	.		100.0	43.0	.	NM_001164387	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	hg19	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	G	25.4	4.634801	0.87760	.	.	ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000307984;ENST00000507093;ENST00000296859;ENST00000358714;ENST00000512052;ENST00000308008;ENST00000514667	T;T;T;T;T;T;T	0.33654	1.4;1.4;1.4;1.4;1.4;1.4;1.4	5.2	5.2	0.72013	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.000000	0.85682	D	0.000000	T	0.69771	0.3148	M	0.91717	3.235	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;0.999;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;0.991;1.0;1.0;1.0;1.0;0.999	T	0.77504	-0.2563	10	0.87932	D	0	.	19.0931	0.93235	0.0:0.0:1.0:0.0	.	973;973;973;688;1023;978;973	A3KN82;B7ZML2;Q8TEU7-2;D6RE77;E9PCH4;Q8TEU7-3;Q8TEU7	.;.;.;.;.;.;RPGF6_HUMAN	R	973;978;973;973;978;688;973;1023	ENSP00000421684:P973R;ENSP00000309298:P978R;ENSP00000426081:P973R;ENSP00000296859:P973R;ENSP00000426910:P688R;ENSP00000311419:P973R;ENSP00000426948:P1023R	ENSP00000426948:P1023R	P	-	2	0	RAPGEF6;FNIP1	130819551	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.809000	0.99208	2.591000	0.87537	0.591000	0.81541	CCA	.	.	.	none		0.373	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340	
PCDHB3	56132	hgsc.bcm.edu	37	5	140482079	140482079	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr5:140482079G>C	ENST00000231130.2	+	1	1846	c.1846G>C	c.(1846-1848)Ggc>Cgc	p.G616R	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	616	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGGCTGTTCGGCGTGTGGGC	0.687																																					p.G616R		Atlas-SNP	.											.	PCDHB3	208	.	0			c.G1846C						PASS	.						26.0	28.0	27.0					5																	140482079		2076	4062	6138	SO:0001583	missense	56132	exon1			CTGTTCGGCGTGT	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1846G>C	chr5.hg19:g.140482079G>C	ENSP00000231130:p.Gly616Arg	31.0	0.0	.		30.0	16.0	.	NM_018937	B2R8P2	Missense_Mutation	SNP	ENST00000231130.2	hg19	CCDS4245.1	.	.	.	.	.	.	.	.	.	.	G	17.04	3.286214	0.59867	.	.	ENSG00000113205	ENST00000231130	T	0.45276	0.9	4.38	-3.96	0.04106	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.23171	0.0560	N	0.00750	-1.22	0.25473	N	0.987806	P	0.51449	0.945	P	0.56916	0.809	T	0.35549	-0.9784	9	0.72032	D	0.01	.	8.1319	0.31033	0.6547:0.233:0.1123:0.0	.	616	Q9Y5E6	PCDB3_HUMAN	R	616	ENSP00000231130:G616R	ENSP00000231130:G616R	G	+	1	0	PCDHB3	140462263	0.000000	0.05858	0.994000	0.49952	0.984000	0.73092	-2.316000	0.01123	-0.517000	0.06461	-0.378000	0.06908	GGC	.	.	.	none		0.687	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937	
KIFC1	3833	hgsc.bcm.edu	37	6	33365934	33365934	+	Silent	SNP	G	G	A	rs368144446		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr6:33365934G>A	ENST00000428849.2	+	2	591	c.141G>A	c.(139-141)gaG>gaA	p.E47E		NM_002263.3	NP_002254.2	Q9BW19	KIFC1_HUMAN	kinesin family member C1	47					ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|spindle assembly (GO:0051225)	endosome (GO:0005768)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|minus-end-directed microtubule motor activity (GO:0008569)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(3)|skin(1)	13						ATGGCCTGGAGCCTGAGAAGG	0.537																																					p.E47E		Atlas-SNP	.											.	KIFC1	47	.	0			c.G141A						PASS	.	G		0,4406		0,0,2203	59.0	62.0	61.0		141	3.0	1.0	6		61	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIFC1	NM_002263.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		47/674	33365934	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	3833	exon2			CCTGGAGCCTGAG	D14678	CCDS34430.1	6p21.32	2014-05-15	2003-01-09	2003-01-10	ENSG00000237649	ENSG00000237649		"""Kinesins"""	6389	protein-coding gene	gene with protein product		603763	"""kinesin-like 2"""	KNSL2		8276466	Standard	NM_002263		Approved	HSET	uc003oef.4	Q9BW19	OTTHUMG00000031209	ENST00000428849.2:c.141G>A	chr6.hg19:g.33365934G>A		119.0	0.0	.		123.0	57.0	.	NM_002263	O60887|Q14834|Q4KMP0|Q5SU09|Q6GMS7|Q6P4A5|Q9UQP7	Silent	SNP	ENST00000428849.2	hg19	CCDS34430.1																																																																																			.	.	.	weak		0.537	KIFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076417.1	NM_002263	
POP7	10248	hgsc.bcm.edu	37	7	100304640	100304640	+	Nonsense_Mutation	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:100304640C>T	ENST00000303151.4	+	2	449	c.187C>T	c.(187-189)Cag>Tag	p.Q63*		NM_005837.2	NP_005828.2	O75817	POP7_HUMAN	processing of precursor 7, ribonuclease P/MRP subunit (S. cerevisiae)	63					RNA phosphodiester bond hydrolysis (GO:0090501)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|tRNA processing (GO:0008033)	cytoplasm (GO:0005737)|nucleolar ribonuclease P complex (GO:0005655)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|ribonuclease P activity (GO:0004526)			endometrium(2)|kidney(1)|ovary(1)	4	Lung NSC(181;0.041)|all_lung(186;0.0581)					GGCCCGGGGTCAGAACGCGTG	0.622																																					p.Q63X		Atlas-SNP	.											.	POP7	8	.	0			c.C187T						PASS	.						89.0	102.0	98.0					7																	100304640		2203	4300	6503	SO:0001587	stop_gained	10248	exon2			CGGGGTCAGAACG	U94316	CCDS5704.1	7q22	2012-05-21	2007-06-26		ENSG00000172336	ENSG00000172336			19949	protein-coding gene	gene with protein product	"""ribonuclease P protein subunit p20"""	606113	"""processing of precursor 7, ribonuclease P subunit (S. cerevisiae)"""			9630247	Standard	NM_005837		Approved	RPP20, RPP2	uc003uwh.4	O75817	OTTHUMG00000044311	ENST00000303151.4:c.187C>T	chr7.hg19:g.100304640C>T	ENSP00000304353:p.Gln63*	86.0	0.0	.		230.0	78.0	.	NM_005837	A4D2E0|Q9BV74	Nonsense_Mutation	SNP	ENST00000303151.4	hg19	CCDS5704.1	.	.	.	.	.	.	.	.	.	.	C	33	5.245502	0.95272	.	.	ENSG00000172336	ENST00000303151;ENST00000457480	.	.	.	5.47	4.54	0.55810	.	0.000000	0.45361	D	0.000366	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06236	T	0.91	-19.7764	11.4012	0.49871	0.0:0.8177:0.1823:0.0	.	.	.	.	X	63	.	ENSP00000304353:Q63X	Q	+	1	0	POP7	100142576	0.998000	0.40836	0.999000	0.59377	0.699000	0.40488	3.263000	0.51546	2.558000	0.86282	0.561000	0.74099	CAG	.	.	.	none		0.622	POP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103070.1	NM_005837	
RELN	5649	hgsc.bcm.edu	37	7	103474054	103474054	+	Missense_Mutation	SNP	G	G	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:103474054G>C	ENST00000428762.1	-	3	562	c.403C>G	c.(403-405)Cac>Gac	p.H135D	RELN_ENST00000424685.2_Missense_Mutation_p.H135D|RELN_ENST00000343529.5_Missense_Mutation_p.H135D	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	135	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		GTGGGCAGGTGACTCACGTGA	0.483																																					p.H135D	NSCLC(146;835 1944 15585 22231 52158)	Atlas-SNP	.											.	RELN	593	.	0			c.C403G						PASS	.						121.0	106.0	111.0					7																	103474054		2203	4300	6503	SO:0001583	missense	5649	exon3			GCAGGTGACTCAC		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.403C>G	chr7.hg19:g.103474054G>C	ENSP00000392423:p.His135Asp	140.0	0.0	.		228.0	39.0	.	NM_173054	A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Missense_Mutation	SNP	ENST00000428762.1	hg19	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	28.9	4.958642	0.92726	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	T;T;T	0.21543	2.0;2.0;2.0	5.33	5.33	0.75918	Reeler domain (2);	0.000000	0.85682	D	0.000000	T	0.31857	0.0810	N	0.14661	0.345	0.80722	D	1	D;D	0.62365	0.989;0.991	D;D	0.78314	0.985;0.991	T	0.17167	-1.0378	10	0.42905	T	0.14	.	19.3931	0.94592	0.0:0.0:1.0:0.0	.	135;135	P78509-2;P78509	.;RELN_HUMAN	D	135	ENSP00000392423:H135D;ENSP00000345694:H135D;ENSP00000388446:H135D	ENSP00000345694:H135D	H	-	1	0	RELN	103261290	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.788000	0.91834	2.634000	0.89283	0.650000	0.86243	CAC	.	.	.	none		0.483	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
SND1	27044	hgsc.bcm.edu	37	7	127725765	127725765	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:127725765A>G	ENST00000354725.3	+	20	2431	c.2237A>G	c.(2236-2238)tAc>tGc	p.Y746C		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	746	Tudor. {ECO:0000255|PROSITE- ProRule:PRU00211}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						CATTGCAGGTACCGTGCCCGA	0.572																																					p.Y746C		Atlas-SNP	.											.	SND1	104	.	0			c.A2237G						PASS	.						173.0	156.0	162.0					7																	127725765		2203	4300	6503	SO:0001583	missense	27044	exon20			GCAGGTACCGTGC		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.2237A>G	chr7.hg19:g.127725765A>G	ENSP00000346762:p.Tyr746Cys	53.0	0.0	.		83.0	10.0	.	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	hg19	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.305315	0.81247	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	T	0.14022	2.54	5.34	5.34	0.76211	Tudor subgroup (1);Staphylococcal nuclease (SNase-like) (1);Staphylococcal nuclease (SNase-like), OB-fold (1);Maternal tudor protein (1);Tudor domain (1);	0.118078	0.64402	D	0.000014	T	0.52370	0.1730	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68891	-0.5289	10	0.62326	D	0.03	-15.954	13.5717	0.61851	1.0:0.0:0.0:0.0	.	746	Q7KZF4	SND1_HUMAN	C	746;736	ENSP00000346762:Y746C	ENSP00000346762:Y746C	Y	+	2	0	SND1	127513001	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	8.540000	0.90641	2.144000	0.66660	0.533000	0.62120	TAC	.	.	.	none		0.572	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390	
PLXNA4	91584	hgsc.bcm.edu	37	7	131864511	131864511	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:131864511G>A	ENST00000359827.3	-	20	4771	c.3809C>T	c.(3808-3810)aCg>aTg	p.T1270M	PLXNA4_ENST00000321063.4_Missense_Mutation_p.T1270M			Q9HCM2	PLXA4_HUMAN	plexin A4	1270					anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CCGCTTCAGCGTGAGGTCACT	0.597																																					p.T1270M		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3809T						PASS	.						55.0	52.0	53.0					7																	131864511		2203	4300	6503	SO:0001583	missense	91584	exon20			TTCAGCGTGAGGT	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3809C>T	chr7.hg19:g.131864511G>A	ENSP00000352882:p.Thr1270Met	70.0	0.0	.		130.0	25.0	.	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	hg19	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.723727	0.89298	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.00986	5.47;5.47	4.82	4.82	0.62117	.	0.089584	0.85682	D	0.000000	T	0.05777	0.0151	M	0.73962	2.25	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.18587	-1.0332	10	0.59425	D	0.04	.	18.0686	0.89398	0.0:0.0:1.0:0.0	.	1270	Q9HCM2	PLXA4_HUMAN	M	1270	ENSP00000323194:T1270M;ENSP00000352882:T1270M	ENSP00000323194:T1270M	T	-	2	0	PLXNA4	131515051	1.000000	0.71417	0.924000	0.36721	0.952000	0.60782	9.618000	0.98365	2.524000	0.85096	0.484000	0.47621	ACG	.	.	.	none		0.597	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
ZNF425	155054	hgsc.bcm.edu	37	7	148801369	148801369	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:148801369C>T	ENST00000378061.2	-	4	1726	c.1594G>A	c.(1594-1596)Ggc>Agc	p.G532S		NM_001001661.2	NP_001001661.1	Q6IV72	ZN425_HUMAN	zinc finger protein 425	532					negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(6)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	50	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00463)			AAACTGCGGCCGCACTCGGCG	0.627																																					p.G532S		Atlas-SNP	.											ZNF425,colon,carcinoma,0,1	ZNF425	99	.	0			c.G1594A						PASS	.						38.0	34.0	35.0					7																	148801369		2203	4300	6503	SO:0001583	missense	155054	exon4			TGCGGCCGCACTC	AK056498	CCDS34773.1	7q36.1	2013-01-08			ENSG00000204947	ENSG00000204947		"""Zinc fingers, C2H2-type"", ""-"""	20690	protein-coding gene	gene with protein product							Standard	NM_001001661		Approved		uc003wfj.3	Q6IV72	OTTHUMG00000158971	ENST00000378061.2:c.1594G>A	chr7.hg19:g.148801369C>T	ENSP00000367300:p.Gly532Ser	51.0	0.0	.		145.0	31.0	.	NM_001001661	B3KPM1|Q08AG3	Missense_Mutation	SNP	ENST00000378061.2	hg19	CCDS34773.1	.	.	.	.	.	.	.	.	.	.	C	13.55	2.270839	0.40194	.	.	ENSG00000204947	ENST00000378061	T	0.20463	2.07	2.75	-4.16	0.03869	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.12135	0.0295	L	0.38175	1.15	0.23704	N	0.997065	P	0.44816	0.844	B	0.29942	0.109	T	0.10613	-1.0622	9	0.87932	D	0	.	11.3998	0.49864	0.0:0.7947:0.0:0.2053	.	532	Q6IV72	ZN425_HUMAN	S	532	ENSP00000367300:G532S	ENSP00000367300:G532S	G	-	1	0	ZNF425	148432302	0.000000	0.05858	0.015000	0.15790	0.114000	0.19823	-0.148000	0.10219	-1.040000	0.03271	-0.768000	0.03414	GGC	.	.	.	none		0.627	ZNF425-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352726.1	XM_088140	
SSPO	23145	hgsc.bcm.edu	37	7	149518600	149518600	+	RNA	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:149518600C>T	ENST00000378016.2	+	0	12669							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			GCTCCCGCACCCTGGGGGACA	0.721																																					p.T4223T		Atlas-SNP	.											.	.	.	.	0			c.C12669T						PASS	.						4.0	5.0	5.0					7																	149518600		1851	3972	5823			23145	exon88			CCGCACCCTGGGG	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		chr7.hg19:g.149518600C>T		55.0	0.0	.		76.0	31.0	.	NM_198455	Q76B61	Silent	SNP	ENST00000378016.2	hg19																																																																																				.	.	.	none		0.721	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
GPR124	25960	hgsc.bcm.edu	37	8	37693093	37693093	+	Missense_Mutation	SNP	A	A	G	rs377757244		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr8:37693093A>G	ENST00000412232.2	+	13	1868	c.1855A>G	c.(1855-1857)Atc>Gtc	p.I619V	GPR124_ENST00000315215.7_Intron	NM_032777.9	NP_116166.9	Q96PE1	GP124_HUMAN	G protein-coupled receptor 124	619					central nervous system development (GO:0007417)|endothelial cell migration (GO:0043542)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|neuropeptide signaling pathway (GO:0007218)|positive regulation of endothelial cell migration (GO:0010595)|regulation of angiogenesis (GO:0045765)|regulation of chemotaxis (GO:0050920)|regulation of establishment of blood-brain barrier (GO:0090210)|sprouting angiogenesis (GO:0002040)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(4)|lung(16)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	37			BRCA - Breast invasive adenocarcinoma(5;2.75e-24)|LUSC - Lung squamous cell carcinoma(8;3.5e-10)			CCTGGCCTCCATCCAGCTGCC	0.652																																					p.I619V		Atlas-SNP	.											.	GPR124	85	.	0			c.A1855G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	72.0	87.0	82.0		1855	5.2	1.0	8		82	1,8599	1.2+/-3.3	0,1,4299	no	missense	GPR124	NM_032777.9	29	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	619/1339	37693093	1,13005	2203	4300	6503	SO:0001583	missense	25960	exon13			GCCTCCATCCAGC	AB040964	CCDS6097.2	8p11.22	2014-08-08			ENSG00000020181	ENSG00000020181		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17849	protein-coding gene	gene with protein product	"""tumor endothelial marker 5"""	606823				11559528, 12565841	Standard	NM_032777		Approved	TEM5, DKFZp434C211, DKFZp434J0911, KIAA1531, FLJ14390	uc003xkj.3	Q96PE1	OTTHUMG00000156182	ENST00000412232.2:c.1855A>G	chr8.hg19:g.37693093A>G	ENSP00000406367:p.Ile619Val	56.0	0.0	.		40.0	15.0	.	NM_032777	A6H8W3|D3DSW4|Q8N3R1|Q8TEM3|Q96KB2|Q9P1Z7|Q9UFY4	Missense_Mutation	SNP	ENST00000412232.2	hg19	CCDS6097.2	.	.	.	.	.	.	.	.	.	.	A	12.56	1.973999	0.34848	0.0	1.16E-4	ENSG00000020181	ENST00000416514;ENST00000412232	T	0.57907	0.37	5.16	5.16	0.70880	.	0.073105	0.56097	D	0.000031	T	0.35508	0.0934	N	0.12961	0.28	0.45118	D	0.998131	B	0.24963	0.115	B	0.15870	0.014	T	0.14144	-1.0483	10	0.30854	T	0.27	-23.7224	14.9878	0.71362	1.0:0.0:0.0:0.0	.	619	Q96PE1	GP124_HUMAN	V	612;619	ENSP00000406367:I619V	ENSP00000406367:I619V	I	+	1	0	GPR124	37812251	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.170000	0.50816	1.965000	0.57142	0.459000	0.35465	ATC	.	.	.	weak		0.652	GPR124-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343331.2		
NOL6	65083	hgsc.bcm.edu	37	9	33467705	33467705	+	Missense_Mutation	SNP	C	C	T	rs546933819		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr9:33467705C>T	ENST00000379471.2	-	12	1673	c.1586G>A	c.(1585-1587)cGa>cAa	p.R529Q	NOL6_ENST00000455041.2_Missense_Mutation_p.R477Q|NOL6_ENST00000464829.1_Intron			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	529					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		GACTGGGGGTCGAGAGTGAGC	0.617																																					p.R529Q		Atlas-SNP	.											.	NOL6	85	.	0			c.G1586A						PASS	.						28.0	30.0	29.0					9																	33467705		2203	4300	6503	SO:0001583	missense	65083	exon12			GGGGGTCGAGAGT	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1586G>A	chr9.hg19:g.33467705C>T	ENSP00000368784:p.Arg529Gln	60.0	0.0	.		76.0	39.0	.	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.723	0.697590	0.15106	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.22	5.22	0.72569	.	0.374443	0.27298	N	0.020004	T	0.32041	0.0816	L	0.58101	1.795	0.34379	D	0.692933	P;P;P;P;P	0.39044	0.646;0.594;0.594;0.656;0.646	B;B;B;B;B	0.30943	0.087;0.052;0.052;0.122;0.087	T	0.39121	-0.9629	10	0.11794	T	0.64	.	11.3263	0.49450	0.2257:0.7743:0.0:0.0	.	477;526;529;529;529	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	Q	529;529;529;85;529;477	ENSP00000313978:R529Q;ENSP00000297990:R529Q;ENSP00000368784:R529Q;ENSP00000395915:R477Q	ENSP00000297990:R529Q	R	-	2	0	NOL6	33457705	1.000000	0.71417	1.000000	0.80357	0.249000	0.25844	1.842000	0.39250	2.720000	0.93068	0.655000	0.94253	CGA	.	.	.	none		0.617	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
PRKACG	5568	hgsc.bcm.edu	37	9	71628443	71628443	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr9:71628443G>A	ENST00000377276.2	-	1	596	c.566C>T	c.(565-567)gCc>gTc	p.A189V		NM_002732.3	NP_002723.2	P22612	KAPCG_HUMAN	protein kinase, cAMP-dependent, catalytic, gamma	189	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|blood coagulation (GO:0007596)|carbohydrate metabolic process (GO:0005975)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|male gonad development (GO:0008584)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|spermatogenesis (GO:0007283)|transmembrane transport (GO:0055085)|triglyceride catabolic process (GO:0019433)|water transport (GO:0006833)	cytosol (GO:0005829)	ATP binding (GO:0005524)|cAMP-dependent protein kinase activity (GO:0004691)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22						CACGCGCTTGGCGAAACCGAA	0.617																																					p.A189V	Esophageal Squamous(110;2236 2623 32146)	Atlas-SNP	.											.	PRKACG	65	.	0			c.C566T						PASS	.						45.0	45.0	45.0					9																	71628443		2203	4300	6503	SO:0001583	missense	5568	exon1			CGCTTGGCGAAAC	M34182	CCDS6625.1	9q13	2012-10-02			ENSG00000165059	ENSG00000165059	2.7.11.1		9382	protein-coding gene	gene with protein product		176893				2342480, 9598317	Standard	NM_002732		Approved	PKACg	uc004agy.3	P22612	OTTHUMG00000019974	ENST00000377276.2:c.566C>T	chr9.hg19:g.71628443G>A	ENSP00000366488:p.Ala189Val	67.0	0.0	.		79.0	30.0	.	NM_002732	O60850|Q5VZ02|Q86YI1	Missense_Mutation	SNP	ENST00000377276.2	hg19	CCDS6625.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.565223	0.65651	.	.	ENSG00000165059	ENST00000377276	T	0.75821	-0.97	1.03	1.03	0.20045	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.30859	U	0.008721	T	0.75925	0.3916	L	0.56124	1.755	0.33063	D	0.534337	D	0.61697	0.99	P	0.57776	0.827	T	0.79082	-0.1949	10	0.87932	D	0	.	7.4815	0.27408	0.0:0.0:1.0:0.0	.	189	P22612	KAPCG_HUMAN	V	189	ENSP00000366488:A189V	ENSP00000366488:A189V	A	-	2	0	PRKACG	70818263	1.000000	0.71417	0.025000	0.17156	0.026000	0.11368	2.854000	0.48325	0.458000	0.26988	0.467000	0.42956	GCC	.	.	.	none		0.617	PRKACG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052559.1		
RALGDS	5900	hgsc.bcm.edu	37	9	135975749	135975749	+	Silent	SNP	A	A	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr9:135975749A>C	ENST00000372050.3	-	17	2496	c.2475T>G	c.(2473-2475)gcT>gcG	p.A825A	RALGDS_ENST00000469972.1_5'UTR|RALGDS_ENST00000542690.1_Silent_p.A896A|RALGDS_ENST00000372047.3_Silent_p.A813A|RALGDS_ENST00000393160.3_Silent_p.A770A|RALGDS_ENST00000393157.3_Silent_p.A824A|RALGDS_ENST00000372062.3_Silent_p.A796A	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	825	Ras-associating. {ECO:0000255|PROSITE- ProRule:PRU00166}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		TTACAGCCGGAGCCTTATCTT	0.597			T	CIITA	"""PMBL, Hodgkin Lymphona, """																																p.A825A	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.T2475G						PASS	.						145.0	138.0	140.0					9																	135975749		2203	4300	6503	SO:0001819	synonymous_variant	5900	exon17			AGCCGGAGCCTTA	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.2475T>G	chr9.hg19:g.135975749A>C		62.0	0.0	.		76.0	29.0	.	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	hg19	CCDS6959.1																																																																																			.	.	.	none		0.597	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
OPTN	10133	hgsc.bcm.edu	37	10	13167963	13167963	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:13167963T>A	ENST00000378748.3	+	12	1528	c.1166T>A	c.(1165-1167)cTa>cAa	p.L389Q	OPTN_ENST00000378752.3_Missense_Mutation_p.L383Q|OPTN_ENST00000263036.5_Missense_Mutation_p.L389Q|OPTN_ENST00000378747.3_Missense_Mutation_p.L389Q|OPTN_ENST00000378757.2_Missense_Mutation_p.L389Q|OPTN_ENST00000378764.2_Missense_Mutation_p.L383Q	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	389					cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						TTAACTGTGCTACAGATGACA	0.323																																					p.L389Q		Atlas-SNP	.											.	OPTN	57	.	0			c.T1166A						PASS	.						74.0	72.0	73.0					10																	13167963		2203	4299	6502	SO:0001583	missense	10133	exon11			CTGTGCTACAGAT	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"""glaucoma 1, open angle, E (adult-onset)"""	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.1166T>A	chr10.hg19:g.13167963T>A	ENSP00000368022:p.Leu389Gln	157.0	0.0	.		139.0	47.0	.	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	hg19	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	T	12.79	2.042827	0.36085	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	D;D;D;D;D;D	0.93604	-3.25;-3.23;-3.25;-3.23;-3.25;-3.25	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	D	0.96340	0.8806	M	0.79123	2.44	0.36206	D	0.851028	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.99620	1.0983	10	0.87932	D	0	-7.3191	13.5457	0.61702	0.0:0.0:0.0:1.0	.	383;389	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	Q	389;383;389;383;389;389	ENSP00000263036:L389Q;ENSP00000368040:L383Q;ENSP00000368032:L389Q;ENSP00000368027:L383Q;ENSP00000368022:L389Q;ENSP00000368021:L389Q	ENSP00000263036:L389Q	L	+	2	0	OPTN	13207969	0.887000	0.30362	0.150000	0.22450	0.037000	0.13140	4.685000	0.61693	2.239000	0.73571	0.528000	0.53228	CTA	.	.	.	none		0.323	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980	
JMJD1C	221037	hgsc.bcm.edu	37	10	64957243	64957243	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:64957243A>G	ENST00000399262.2	-	13	5790	c.5572T>C	c.(5572-5574)Tgg>Cgg	p.W1858R	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000402544.1_Missense_Mutation_p.W1639R|JMJD1C_ENST00000542921.1_Missense_Mutation_p.W1676R	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	1858					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					TGGCAGACCCAGTGAATGTTA	0.388																																					p.W1858R		Atlas-SNP	.											.	JMJD1C	347	.	0			c.T5572C						PASS	.						134.0	125.0	128.0					10																	64957243		1918	4150	6068	SO:0001583	missense	221037	exon13			AGACCCAGTGAAT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.5572T>C	chr10.hg19:g.64957243A>G	ENSP00000382204:p.Trp1858Arg	110.0	0.0	.		90.0	35.0	.	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	hg19	CCDS41532.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.667939	0.88348	.	.	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	D;T;T	0.89050	-2.46;-0.49;-0.2	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.95465	0.8527	M	0.89534	3.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.96187	0.9135	10	0.72032	D	0.01	-4.2633	16.1819	0.81915	1.0:0.0:0.0:0.0	.	1399;1858;1676	A6PW35;Q15652;A0T124	.;JHD2C_HUMAN;.	R	1858;1639;1676	ENSP00000382204:W1858R;ENSP00000384990:W1639R;ENSP00000444682:W1676R	ENSP00000382204:W1858R	W	-	1	0	JMJD1C	64627249	1.000000	0.71417	0.995000	0.50966	0.991000	0.79684	9.255000	0.95524	2.279000	0.76181	0.533000	0.62120	TGG	.	.	.	none		0.388	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
CDH23	64072	hgsc.bcm.edu	37	10	73567274	73567274	+	Splice_Site	SNP	C	C	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:73567274C>G	ENST00000224721.6	+	58	8330	c.8325C>G	c.(8323-8325)gcC>gcG	p.A2775A	CDH23_ENST00000398788.3_Splice_Site_p.A530A|CDH23_ENST00000475158.1_3'UTR	NM_022124.5	NP_071407.4	Q9H251	CAD23_HUMAN	cadherin-related 23	2770	Cadherin 26. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cytosolic calcium ion homeostasis (GO:0051480)|equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)	calcium ion binding (GO:0005509)	p.A2775A(1)		NS(1)|breast(2)|central_nervous_system(6)|endometrium(15)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(27)|lung(49)|ovary(3)|pancreas(1)|prostate(7)|stomach(7)|upper_aerodigestive_tract(3)	133						CACCCTCAGCCGGCAACGAAG	0.607																																					p.A2770A		Atlas-SNP	.											CDH23,colon,carcinoma,0,1	CDH23	365	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C8310G						PASS	.						34.0	40.0	38.0					10																	73567274		2081	4204	6285	SO:0001630	splice_region_variant	64072	exon57			CTCAGCCGGCAAC	AY010111	CCDS53540.1, CCDS73146.1	10q22.1	2014-08-08	2010-01-25		ENSG00000107736	ENSG00000107736		"""Cadherins / Cadherin-related"""	13733	protein-coding gene	gene with protein product	"""cadherin-related family member 23"""	605516	"""cadherin related 23"", ""cadherin-like 23"""	DFNB12, USH1D		11090341	Standard	NM_022124		Approved	CDHR23	uc001jrx.4	Q9H251	OTTHUMG00000019347	ENST00000224721.6:c.8324-1C>G	chr10.hg19:g.73567274C>G		55.0	0.0	.		78.0	33.0	.	NM_022124	C4IXS9|F6U049|Q5QGS1|Q5QGS2|Q5QGS5|Q5QGS6|Q5XKN2|Q6UWW1|Q96JL3|Q9H4K9	Silent	SNP	ENST00000224721.6	hg19																																																																																				.	.	.	none		0.607	CDH23-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000051227.4	NM_052836	Silent
ECD	11319	hgsc.bcm.edu	37	10	74899240	74899240	+	Silent	SNP	T	T	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:74899240T>C	ENST00000372979.4	-	11	1454	c.1248A>G	c.(1246-1248)ttA>ttG	p.L416L	ECD_ENST00000454759.2_Silent_p.L373L|ECD_ENST00000430082.2_Silent_p.L449L	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	416					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					GTGAGAGATCTAACCACTGGT	0.443																																					p.L449L		Atlas-SNP	.											.	ECD	50	.	0			c.A1347G						PASS	.						83.0	86.0	85.0					10																	74899240		2203	4300	6503	SO:0001819	synonymous_variant	11319	exon12			GAGATCTAACCAC	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1248A>G	chr10.hg19:g.74899240T>C		58.0	0.0	.		47.0	20.0	.	NM_001135752	C9JX46|E9PAW8	Silent	SNP	ENST00000372979.4	hg19	CCDS7321.1																																																																																			.	.	.	none		0.443	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
MUC2	4583	hgsc.bcm.edu	37	11	1093437	1093437	+	Silent	SNP	G	G	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr11:1093437G>C	ENST00000441003.2	+	30	5283	c.5256G>C	c.(5254-5256)acG>acC	p.T1752T	MUC2_ENST00000333592.6_Silent_p.T40T|MUC2_ENST00000359061.5_Silent_p.T1719T|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0					cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)		p.T1752T(1)|p.T1719T(1)		NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccacggtgaccccaa	0.632																																					p.T1752T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	.	2	Substitution - coding silent(2)	kidney(2)	c.G5256C						PASS	.						180.0	207.0	198.0					11																	1093437		2046	4038	6084	SO:0001819	synonymous_variant	4583	exon30			CACCACGGTGACC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5256G>C	chr11.hg19:g.1093437G>C		25.0	0.0	.		25.0	3.0	.	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	hg19																																																																																				.	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
NUP160	23279	hgsc.bcm.edu	37	11	47869930	47869930	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr11:47869930C>T	ENST00000378460.2	-	1	89	c.43G>A	c.(43-45)Gtg>Atg	p.V15M	NUP160_ENST00000526870.1_Missense_Mutation_p.V15M|NUP160_ENST00000530326.1_5'Flank|NUP160_ENST00000532747.1_5'Flank	NM_015231.1	NP_056046.1	Q12769	NU160_HUMAN	nucleoporin 160kDa	15					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)	nucleocytoplasmic transporter activity (GO:0005487)			NS(1)|biliary_tract(2)|breast(7)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(8)|lung(15)|ovary(6)|prostate(2)|skin(2)|urinary_tract(2)	53						GTCGCCGTCACTTCCGGGGGT	0.706																																					p.V15M		Atlas-SNP	.											.	NUP160	116	.	0			c.G43A						PASS	.						8.0	10.0	9.0					11																	47869930		2114	4175	6289	SO:0001583	missense	23279	exon1			CCGTCACTTCCGG	D83781	CCDS31484.1	11p11.12	2008-07-21	2002-08-29		ENSG00000030066	ENSG00000030066			18017	protein-coding gene	gene with protein product		607614	"""nucleoporin 160kD"""			11684705	Standard	NM_015231		Approved	KIAA0197, FLJ22583	uc001ngm.3	Q12769	OTTHUMG00000166534	ENST00000378460.2:c.43G>A	chr11.hg19:g.47869930C>T	ENSP00000367721:p.Val15Met	49.0	0.0	.		45.0	18.0	.	NM_015231	B4DYE8|B4E2J9|Q08AD3|Q7Z5X6|Q96GB3|Q9H660	Missense_Mutation	SNP	ENST00000378460.2	hg19	CCDS31484.1	.	.	.	.	.	.	.	.	.	.	C	16.97	3.269963	0.59540	.	.	ENSG00000030066	ENST00000378460;ENST00000526870	T;T	0.55930	1.37;0.49	4.85	4.85	0.62838	.	0.863746	0.09405	N	0.806618	T	0.55033	0.1895	N	0.08118	0	0.27571	N	0.949872	D;P	0.71674	0.998;0.94	D;P	0.68353	0.957;0.462	T	0.57648	-0.7775	10	0.48119	T	0.1	.	15.2321	0.73398	0.0:1.0:0.0:0.0	.	15;15	Q12769-2;Q12769	.;NU160_HUMAN	M	15	ENSP00000367721:V15M;ENSP00000431495:V15M	ENSP00000367721:V15M	V	-	1	0	NUP160	47826506	1.000000	0.71417	0.999000	0.59377	0.156000	0.22039	1.572000	0.36461	2.404000	0.81709	0.491000	0.48974	GTG	.	.	.	none		0.706	NUP160-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390239.2	NM_015231	
ZBTB3	79842	hgsc.bcm.edu	37	11	62520283	62520283	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr11:62520283A>T	ENST00000394807.3	-	2	1129	c.1004T>A	c.(1003-1005)gTc>gAc	p.V335D		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	335	Pro-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						tggagctgagacaggggctgg	0.577																																					p.V335D		Atlas-SNP	.											.	ZBTB3	47	.	0			c.T1004A						PASS	.						42.0	41.0	41.0					11																	62520283		2202	4296	6498	SO:0001583	missense	79842	exon2			GCTGAGACAGGGG	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.1004T>A	chr11.hg19:g.62520283A>T	ENSP00000378286:p.Val335Asp	56.0	0.0	.		65.0	24.0	.	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	hg19	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	A	0.331	-0.955916	0.02267	.	.	ENSG00000185670	ENST00000394807	T	0.11385	2.78	2.63	-3.45	0.04781	.	1.305960	0.05604	U	0.576827	T	0.05181	0.0138	N	0.14661	0.345	0.09310	N	0.999999	B	0.18968	0.032	B	0.20955	0.032	T	0.42275	-0.9461	10	0.12430	T	0.62	.	4.4604	0.11663	0.4401:0.1782:0.3817:0.0	.	335	Q9H5J0	ZBTB3_HUMAN	D	335	ENSP00000378286:V335D	ENSP00000378286:V335D	V	-	2	0	ZBTB3	62276859	0.000000	0.05858	0.027000	0.17364	0.061000	0.15899	-0.163000	0.09997	-0.972000	0.03559	0.459000	0.35465	GTC	.	.	.	none		0.577	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
FAM186A	121006	hgsc.bcm.edu	37	12	50744556	50744556	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:50744556G>A	ENST00000327337.5	-	4	6058	c.6059C>T	c.(6058-6060)aCc>aTc	p.T2020I	FAM186A_ENST00000543096.1_Missense_Mutation_p.T31I|FAM186A_ENST00000543111.1_Missense_Mutation_p.T2020I	NM_001145475.1	NP_001138947.1	A6NE01	F186A_HUMAN	family with sequence similarity 186, member A	2020																	CCTATATTTGGTGAAATGGGA	0.423																																					p.T2020I	NSCLC(138;1796 1887 12511 19463 37884)	Atlas-SNP	.											.	FAM186A	181	.	0			c.C6059T						PASS	.						333.0	300.0	310.0					12																	50744556		692	1591	2283	SO:0001583	missense	121006	exon4			TATTTGGTGAAAT		CCDS44878.1	12q13.13	2009-04-22			ENSG00000185958	ENSG00000185958			26980	protein-coding gene	gene with protein product							Standard	NM_001145475		Approved	LOC121006	uc001rwl.2	A6NE01	OTTHUMG00000167889	ENST00000327337.5:c.6059C>T	chr12.hg19:g.50744556G>A	ENSP00000329995:p.Thr2020Ile	111.0	0.0	.		151.0	78.0	.	NM_001145475		Missense_Mutation	SNP	ENST00000327337.5	hg19	CCDS44878.1	.	.	.	.	.	.	.	.	.	.	G	17.61	3.431776	0.62844	.	.	ENSG00000185958	ENST00000543111;ENST00000543096;ENST00000327337	T;T;T	0.24538	2.15;1.85;2.16	4.32	4.32	0.51571	.	.	.	.	.	T	0.30039	0.0752	N	0.08118	0	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.75020	0.985;0.985	T	0.21552	-1.0242	9	0.66056	D	0.02	.	12.5043	0.55972	0.0:0.0:1.0:0.0	.	2020;2020	F5GYN0;A6NE01	.;F186A_HUMAN	I	2020;31;2020	ENSP00000441337:T2020I;ENSP00000443703:T31I;ENSP00000329995:T2020I	ENSP00000329995:T2020I	T	-	2	0	FAM186A	49030823	0.488000	0.25996	0.061000	0.19648	0.343000	0.28985	2.925000	0.48884	2.408000	0.81797	0.561000	0.74099	ACC	.	.	.	none		0.423	FAM186A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000396838.1	XM_001718353	
SLC4A8	9498	hgsc.bcm.edu	37	12	51853759	51853759	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:51853759A>G	ENST00000453097.2	+	8	1097	c.880A>G	c.(880-882)Att>Gtt	p.I294V	SLC4A8_ENST00000514353.3_Missense_Mutation_p.I241V|SLC4A8_ENST00000358657.3_Missense_Mutation_p.I321V|SLC4A8_ENST00000535225.2_Missense_Mutation_p.I241V|SLC4A8_ENST00000394856.1_Missense_Mutation_p.I241V	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		CATGAAAAAAATTCCTACTGG	0.418																																					p.I294V		Atlas-SNP	.											.	SLC4A8	292	.	0			c.A880G						PASS	.						132.0	138.0	136.0					12																	51853759		2203	4300	6503	SO:0001583	missense	9498	exon8			AAAAAAATTCCTA	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.880A>G	chr12.hg19:g.51853759A>G	ENSP00000405812:p.Ile294Val	138.0	0.0	.		138.0	70.0	.	NM_001039960		Missense_Mutation	SNP	ENST00000453097.2	hg19	CCDS44890.1	.	.	.	.	.	.	.	.	.	.	A	17.71	3.456390	0.63401	.	.	ENSG00000050438	ENST00000535225;ENST00000358657;ENST00000453097;ENST00000394856;ENST00000319957;ENST00000514353;ENST00000547697;ENST00000551071	T;T;T;T;T	0.69806	-0.43;-0.43;-0.43;-0.43;-0.43	5.53	5.53	0.82687	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.83092	0.5179	M	0.85542	2.76	0.80722	D	1	D;B;B;B;B;B;B	0.53151	0.958;0.04;0.018;0.001;0.004;0.002;0.033	D;B;B;B;B;B;B	0.70716	0.97;0.073;0.028;0.077;0.072;0.073;0.036	D	0.85916	0.1443	10	0.87932	D	0	.	14.9425	0.71006	1.0:0.0:0.0:0.0	.	241;321;241;294;294;294;241	E7EML0;Q2Y0W8-2;F5GZ31;Q2Y0W8;Q2Y0W8-3;Q2Y0W8-6;F8VSA8	.;.;.;S4A8_HUMAN;.;.;.	V	241;321;294;241;294;241;241;241	ENSP00000441520:I241V;ENSP00000351483:I321V;ENSP00000405812:I294V;ENSP00000378325:I241V;ENSP00000442561:I241V	ENSP00000315789:I294V	I	+	1	0	SLC4A8	50140026	1.000000	0.71417	0.995000	0.50966	0.865000	0.49528	9.283000	0.95860	2.236000	0.73375	0.482000	0.46254	ATT	.	.	.	none		0.418	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
ANKS1B	56899	hgsc.bcm.edu	37	12	99837527	99837527	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:99837527G>A	ENST00000547776.2	-	11	1498	c.1499C>T	c.(1498-1500)aCa>aTa	p.T500I	ANKS1B_ENST00000329257.7_Missense_Mutation_p.T500I|ANKS1B_ENST00000547010.1_Missense_Mutation_p.T80I	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	500						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGTTGGGCCTGTTGAGCTGTT	0.433																																					p.T500I		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1499T						PASS	.						203.0	196.0	198.0					12																	99837527		1901	4130	6031	SO:0001583	missense	56899	exon11			GGGCCTGTTGAGC	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1499C>T	chr12.hg19:g.99837527G>A	ENSP00000449629:p.Thr500Ile	164.0	1.0	.		209.0	139.0	.	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.428944	0.83667	.	.	ENSG00000185046	ENST00000547776;ENST00000547010;ENST00000329257;ENST00000538702;ENST00000549866	T;T;T;T	0.69175	0.59;-0.38;0.59;0.42	6.04	6.04	0.98038	.	0.000000	0.85682	D	0.000000	T	0.76557	0.4004	L	0.40543	1.245	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.998	D;D;D	0.85130	0.997;0.996;0.987	T	0.72520	-0.4268	9	.	.	.	-11.037	18.7754	0.91910	0.0:0.0:1.0:0.0	.	466;80;500	F8VVQ4;Q7Z6G8-6;Q7Z6G8	.;.;ANS1B_HUMAN	I	500;80;500;79;466	ENSP00000449629:T500I;ENSP00000448512:T80I;ENSP00000331381:T500I;ENSP00000449894:T466I	.	T	-	2	0	ANKS1B	98361658	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	8.328000	0.90014	2.873000	0.98535	0.563000	0.77884	ACA	.	.	.	none		0.433	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
POLE	5426	hgsc.bcm.edu	37	12	133219525	133219525	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:133219525G>A	ENST00000320574.5	-	36	4652	c.4609C>T	c.(4609-4611)Ctc>Ttc	p.L1537F	POLE_ENST00000434528.3_5'Flank|POLE_ENST00000535270.1_Missense_Mutation_p.L1510F	NM_006231.2	NP_006222.2	Q07864	DPOE1_HUMAN	polymerase (DNA directed), epsilon, catalytic subunit	1537					base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA synthesis involved in DNA repair (GO:0000731)|G1/S transition of mitotic cell cycle (GO:0000082)|in utero embryonic development (GO:0001701)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	cytoplasm (GO:0005737)|epsilon DNA polymerase complex (GO:0008622)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|nucleotide binding (GO:0000166)|zinc ion binding (GO:0008270)			NS(2)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(16)|lung(41)|ovary(3)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	89	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0416)		OV - Ovarian serous cystadenocarcinoma(86;5.22e-08)|Epithelial(86;4.03e-07)|all cancers(50;1.18e-05)	Cladribine(DB00242)	TTCTCCAGGAGGAGGCCGTGC	0.642								DNA polymerases (catalytic subunits)																													p.L1537F		Atlas-SNP	.											.	POLE	416	.	0			c.C4609T						PASS	.						60.0	58.0	59.0					12																	133219525		2203	4300	6503	SO:0001583	missense	5426	exon36			CCAGGAGGAGGCC		CCDS9278.1	12q24.3	2014-09-17	2012-05-18		ENSG00000177084	ENSG00000177084		"""DNA polymerases"""	9177	protein-coding gene	gene with protein product	"""DNA polymerase epsilon catalytic subunit A"""	174762	"""polymerase (DNA directed), epsilon"""			8020968	Standard	NM_006231		Approved	POLE1	uc001uks.1	Q07864	OTTHUMG00000168045	ENST00000320574.5:c.4609C>T	chr12.hg19:g.133219525G>A	ENSP00000322570:p.Leu1537Phe	72.0	0.0	.		93.0	38.0	.	NM_006231	Q13533|Q86VH9	Missense_Mutation	SNP	ENST00000320574.5	hg19	CCDS9278.1	.	.	.	.	.	.	.	.	.	.	G	5.595	0.294522	0.10567	.	.	ENSG00000177084	ENST00000320574;ENST00000455752;ENST00000535270	T;T;T	0.24151	1.87;1.87;1.87	5.82	2.89	0.33648	DNA polymerase epsilon, catalytic subunit A, C-terminal (1);	0.063724	0.64402	D	0.000004	T	0.28234	0.0697	M	0.81112	2.525	0.49915	D	0.999831	B	0.30179	0.271	B	0.33121	0.158	T	0.03086	-1.1074	10	0.27785	T	0.31	.	5.8191	0.18518	0.1349:0.0:0.4872:0.3779	.	1537	Q07864	DPOE1_HUMAN	F	1537;1548;1510	ENSP00000322570:L1537F;ENSP00000406383:L1548F;ENSP00000445753:L1510F	ENSP00000322570:L1537F	L	-	1	0	POLE	131729598	0.997000	0.39634	0.986000	0.45419	0.071000	0.16799	2.540000	0.45727	0.322000	0.23283	-1.087000	0.02190	CTC	.	.	.	none		0.642	POLE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397689.2	NM_006231	
SACS	26278	hgsc.bcm.edu	37	13	23909168	23909168	+	Silent	SNP	A	A	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr13:23909168A>G	ENST00000382292.3	-	9	9120	c.8847T>C	c.(8845-8847)atT>atC	p.I2949I	SACS_ENST00000382298.3_Silent_p.I2949I|SACS_ENST00000402364.1_Silent_p.I2199I			Q9NZJ4	SACS_HUMAN	sacsin molecular chaperone	2949					cell death (GO:0008219)|negative regulation of inclusion body assembly (GO:0090084)|protein folding (GO:0006457)	axon (GO:0030424)|cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|proteasome binding (GO:0070628)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(22)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(54)|lung(49)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(11)	189		all_cancers(29;1.51e-22)|all_epithelial(30;7.82e-19)|all_lung(29;4.71e-18)|Lung SC(185;0.0225)|Breast(139;0.128)		all cancers(112;0.00197)|Epithelial(112;0.00854)|OV - Ovarian serous cystadenocarcinoma(117;0.0298)|Lung(94;0.189)		TTACAACATGAATAGGGGTGT	0.348																																					p.I2949I		Atlas-SNP	.											.	SACS	871	.	0			c.T8847C						PASS	.						100.0	101.0	101.0					13																	23909168		2203	4300	6503	SO:0001819	synonymous_variant	26278	exon10			AACATGAATAGGG	AF193556	CCDS9300.2	13q11	2014-06-13	2014-01-30		ENSG00000151835	ENSG00000151835		"""Heat shock proteins / DNAJ (HSP40)"""	10519	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 138"""	604490	"""spastic ataxia of Charlevoix-Saguenay (sacsin)"""			10610707, 15057823, 21726565	Standard	NM_001278055		Approved	ARSACS, KIAA0730, DKFZp686B15167, DNAJC29, SPAX6, PPP1R138	uc001uon.3	Q9NZJ4	OTTHUMG00000016562	ENST00000382292.3:c.8847T>C	chr13.hg19:g.23909168A>G		72.0	0.0	.		81.0	37.0	.	NM_014363	O94835|Q5T9J5|Q5T9J7|Q5T9J8|Q68DF5|Q6MZR4|Q8NBF9	Silent	SNP	ENST00000382292.3	hg19	CCDS9300.2																																																																																			.	.	.	none		0.348	SACS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044148.3	NM_014363	
CDK8	1024	hgsc.bcm.edu	37	13	26975672	26975672	+	Missense_Mutation	SNP	A	A	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr13:26975672A>T	ENST00000381527.3	+	12	1683	c.1180A>T	c.(1180-1182)Agt>Tgt	p.S394C	CDK8_ENST00000536792.1_3'UTR|CDK8_ENST00000480323.1_3'UTR	NM_001260.1	NP_001251.1	P49336	CDK8_HUMAN	cyclin-dependent kinase 8	394					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)			breast(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	25	Colorectal(5;0.000442)	Lung SC(185;0.0156)|Breast(139;0.147)		all cancers(112;0.0384)|Epithelial(112;0.142)|OV - Ovarian serous cystadenocarcinoma(117;0.188)		TCAAGACAGCAGTCACACACA	0.483																																					p.S394C		Atlas-SNP	.											.	CDK8	61	.	0			c.A1180T						PASS	.						100.0	93.0	96.0					13																	26975672		2203	4300	6503	SO:0001583	missense	1024	exon12			GACAGCAGTCACA	X85753	CCDS9317.1	13q12	2011-11-08			ENSG00000132964	ENSG00000132964		"""Cyclin-dependent kinases"""	1779	protein-coding gene	gene with protein product		603184				7568034	Standard	NM_001260		Approved	K35	uc001uqr.1	P49336	OTTHUMG00000016617	ENST00000381527.3:c.1180A>T	chr13.hg19:g.26975672A>T	ENSP00000370938:p.Ser394Cys	115.0	0.0	.		118.0	47.0	.	NM_001260	Q5VUF3|Q6ISB5	Missense_Mutation	SNP	ENST00000381527.3	hg19	CCDS9317.1	.	.	.	.	.	.	.	.	.	.	A	21.9	4.210803	0.79240	.	.	ENSG00000132964	ENST00000381527	T	0.69806	-0.43	5.58	1.92	0.25849	.	0.070976	0.85682	D	0.000000	T	0.68550	0.3013	L	0.51422	1.61	0.80722	D	1	D;D	0.56968	0.978;0.97	P;P	0.56514	0.8;0.711	T	0.66728	-0.5850	10	0.54805	T	0.06	-1.6909	8.8309	0.35082	0.7859:0.0:0.2141:0.0	.	393;394	P49336-2;P49336	.;CDK8_HUMAN	C	394	ENSP00000370938:S394C	ENSP00000370938:S394C	S	+	1	0	CDK8	25873672	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.426000	0.44731	0.418000	0.25898	0.533000	0.62120	AGT	.	.	.	none		0.483	CDK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044250.1		
ARHGEF40	55701	hgsc.bcm.edu	37	14	21543510	21543510	+	Silent	SNP	C	C	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr14:21543510C>G	ENST00000298694.4	+	4	1597	c.1470C>G	c.(1468-1470)ggC>ggG	p.G490G	ARHGEF40_ENST00000298693.3_Silent_p.G490G			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	490						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						GCCCAGAAGGCCCCCTGTCTG	0.557																																					p.G490G		Atlas-SNP	.											.	ARHGEF40	84	.	0			c.C1470G						PASS	.						119.0	122.0	121.0					14																	21543510		2203	4300	6503	SO:0001819	synonymous_variant	55701	exon4			AGAAGGCCCCCTG		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1470C>G	chr14.hg19:g.21543510C>G		116.0	0.0	.		129.0	51.0	.	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Silent	SNP	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.	.	none		0.557	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
PPP2R3C	55012	hgsc.bcm.edu	37	14	35579746	35579746	+	Silent	SNP	A	A	G	rs201403377		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr14:35579746A>G	ENST00000261475.5	-	3	629	c.276T>C	c.(274-276)gaT>gaC	p.D92D	PPP2R3C_ENST00000555644.1_Silent_p.D92D	NM_017917.2	NP_060387.2	Q969Q6	P2R3C_HUMAN	protein phosphatase 2, regulatory subunit B'', gamma	92					activation of protein kinase activity (GO:0032147)|B cell homeostasis (GO:0001782)|positive regulation of B cell differentiation (GO:0045579)|regulation of antimicrobial humoral response (GO:0002759)|regulation of mitochondrial depolarization (GO:0051900)|spleen development (GO:0048536)|T cell homeostasis (GO:0043029)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			central_nervous_system(1)|kidney(1)|large_intestine(8)|lung(4)|ovary(1)	15	Breast(36;0.0545)|Hepatocellular(127;0.158)|Prostate(35;0.184)		Lung(238;8.62e-06)|LUAD - Lung adenocarcinoma(48;1.42e-05)|Epithelial(34;0.0177)|all cancers(34;0.0491)	GBM - Glioblastoma multiforme(112;0.0803)		ATTCTTCATTATCTAACAGTT	0.348																																					p.D92D		Atlas-SNP	.											.	PPP2R3C	44	.	0			c.T276C						PASS	.						199.0	184.0	189.0					14																	35579746		2203	4299	6502	SO:0001819	synonymous_variant	55012	exon3			TTCATTATCTAAC	AK000651	CCDS9654.1	14q13.2	2010-06-18	2010-06-18	2007-01-22	ENSG00000092020	ENSG00000092020		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	17485	protein-coding gene	gene with protein product		615902	"""chromosome 14 open reading frame 10"", ""protein phosphatase 2 (formerly 2A), regulatory subunit B'', gamma"""	C14orf10		12167160, 16129705	Standard	NM_017917		Approved	FLJ20644, G4-1, G5PR	uc001wss.3	Q969Q6	OTTHUMG00000140224	ENST00000261475.5:c.276T>C	chr14.hg19:g.35579746A>G		38.0	0.0	.		43.0	14.0	.	NM_017917	B4DEN7|D3DS97|D3DS98|Q5GJ55|Q5GJ56|Q6P4G2|Q86TZ3|Q9NWR9	Silent	SNP	ENST00000261475.5	hg19	CCDS9654.1	.	.	.	.	.	.	.	.	.	.	A	8.279	0.815077	0.16607	.	.	ENSG00000092020	ENST00000555614	.	.	.	5.8	4.65	0.58169	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-11.4249	8.5736	0.33585	0.7983:0.0:0.2017:0.0	.	.	.	.	Q	31	.	.	X	-	1	0	PPP2R3C	34649497	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	1.457000	0.35212	2.207000	0.71202	0.528000	0.53228	TAA	.	.	.	alt		0.348	PPP2R3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276687.1	NM_017917	
DUT	1854	hgsc.bcm.edu	37	15	48623926	48623926	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:48623926A>G	ENST00000331200.3	+	1	307	c.214A>G	c.(214-216)Aca>Gca	p.T72A	DUT_ENST00000559540.1_5'Flank|RP11-154J22.1_ENST00000560323.1_RNA|RP11-154J22.1_ENST00000559134.1_RNA|DUT_ENST00000559935.1_Intron|DUT_ENST00000559416.1_Intron|DUT_ENST00000558813.1_Intron|DUT_ENST00000455976.2_5'Flank	NM_001025248.1|NM_001025249.1	NP_001020419.1|NP_001020420.1	P33316	DUT_HUMAN	deoxyuridine triphosphatase	72					DNA replication (GO:0006260)|dUMP biosynthetic process (GO:0006226)|dUTP catabolic process (GO:0046081)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|nucleobase-containing small molecule metabolic process (GO:0055086)|protein homotrimerization (GO:0070207)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of protein heterodimerization activity (GO:0043497)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dUTP diphosphatase activity (GO:0004170)|poly(A) RNA binding (GO:0044822)|pyrimidine deoxyribonucleotide binding (GO:0032556)|receptor inhibitor activity (GO:0030547)			kidney(2)	2		all_lung(180;0.00265)		all cancers(107;2.66e-09)|GBM - Glioblastoma multiforme(94;6.76e-07)		CGGAGCCAGTACAGTCGGGGC	0.781								Modulation of nucleotide pools																													p.T72A		Atlas-SNP	.											.	DUT	9	.	0			c.A214G						PASS	.						1.0	1.0	1.0					15																	48623926		592	1311	1903	SO:0001583	missense	1854	exon1			GCCAGTACAGTCG	M89913	CCDS32231.1, CCDS45255.1, CCDS45256.1	15q21.1	2010-06-24	2007-12-17		ENSG00000128951	ENSG00000128951	3.6.1.23		3078	protein-coding gene	gene with protein product		601266	"""dUTP pyrophosphatase"""			1325640, 9070952	Standard	XM_005254211		Approved	dUTPase	uc001zws.3	P33316		ENST00000331200.3:c.214A>G	chr15.hg19:g.48623926A>G	ENSP00000370376:p.Thr72Ala	27.0	0.0	.		29.0	6.0	.	NM_001025248	A8K650|B4DPR5|O14785|Q16708|Q16860|Q6FHN1|Q6NSA3|Q96Q81	Missense_Mutation	SNP	ENST00000331200.3	hg19	CCDS32231.1	.	.	.	.	.	.	.	.	.	.	A	13.01	2.109003	0.37242	.	.	ENSG00000128951	ENST00000331200;ENST00000249783	T	0.45668	0.89	3.42	2.3	0.28687	.	2.177750	0.02159	N	0.058606	T	0.29389	0.0732	N	0.19112	0.55	0.20074	N	0.999933	B	0.14012	0.009	B	0.08055	0.003	T	0.14337	-1.0476	10	0.30078	T	0.28	.	5.3774	0.16172	0.8697:0.0:0.1303:0.0	.	72	P33316	DUT_HUMAN	A	72;70	ENSP00000370376:T72A	ENSP00000249783:T70A	T	+	1	0	DUT	46411218	0.046000	0.20272	0.045000	0.18777	0.277000	0.26821	-0.093000	0.11111	0.686000	0.31488	0.455000	0.32223	ACA	.	.	.	none		0.781	DUT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000417142.2		
ZNF280D	54816	hgsc.bcm.edu	37	15	56935189	56935189	+	Silent	SNP	T	T	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:56935189T>C	ENST00000267807.7	-	20	2436	c.2220A>G	c.(2218-2220)aaA>aaG	p.K740K	ZNF280D_ENST00000559237.1_Silent_p.K727K	NM_017661.2	NP_060131.2	Q6N043	Z280D_HUMAN	zinc finger protein 280D	740					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(5)|kidney(4)|large_intestine(7)|lung(12)|ovary(1)|skin(1)	30				all cancers(107;0.0399)|GBM - Glioblastoma multiforme(80;0.0787)		GAGCTTCTTTTTTTAATCTTG	0.274																																					p.K740K		Atlas-SNP	.											.	ZNF280D	82	.	0			c.A2220G						PASS	.						20.0	19.0	19.0					15																	56935189		2154	4168	6322	SO:0001819	synonymous_variant	54816	exon20			TTCTTTTTTTAAT	AB046804	CCDS32245.1, CCDS42041.1, CCDS58364.1	15q21.2	2008-05-02	2007-09-20	2007-09-20					25953	protein-coding gene	gene with protein product			"""suppressor of hairy wing homolog 4 (Drosophila)"""	SUHW4		10997877	Standard	XM_005254481		Approved	FLJ20086, ZNF634	uc002adu.3	Q6N043		ENST00000267807.7:c.2220A>G	chr15.hg19:g.56935189T>C		405.0	0.0	.		419.0	167.0	.	NM_017661	A1L495|B2RMT6|Q6MZM6|Q6N085|Q6P2R6|Q7Z6J5|Q9H0U5|Q9HCI8|Q9NXS0	Silent	SNP	ENST00000267807.7	hg19	CCDS32245.1																																																																																			.	.	.	none		0.274	ZNF280D-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418891.2	XM_370867	
MRPL46	26589	hgsc.bcm.edu	37	15	89010546	89010546	+	Silent	SNP	C	C	T	rs540944922		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:89010546C>T	ENST00000312475.4	-	1	104	c.63G>A	c.(61-63)agG>agA	p.R21R	MRPS11_ENST00000353598.6_5'Flank|MRPS11_ENST00000325844.4_5'Flank|MRPL46_ENST00000559538.1_5'Flank	NM_022163.3	NP_071446.2	Q9H2W6	RM46_HUMAN	mitochondrial ribosomal protein L46	21						mitochondrion (GO:0005739)|ribosome (GO:0005840)	hydrolase activity (GO:0016787)			central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)	5	Lung NSC(78;0.203)		BRCA - Breast invasive adenocarcinoma(143;0.188)			CGGCCCAGAGCCTCTCGAACC	0.672																																					p.R21R		Atlas-SNP	.											.	MRPL46	13	.	0			c.G63A						PASS	.						16.0	19.0	18.0					15																	89010546		2198	4295	6493	SO:0001819	synonymous_variant	26589	exon1			CCAGAGCCTCTCG	AF210056	CCDS10341.1	15q25.3	2012-10-08	2001-12-10	2001-12-14	ENSG00000259494	ENSG00000259494		"""Mitochondrial ribosomal proteins / large subunits"""	1192	protein-coding gene	gene with protein product		611851	"""chromosome 15 open reading frame 4"""	C15orf4		11761714, 11551941	Standard	NM_022163		Approved	LIECG2, P2ECSL	uc002bmj.2	Q9H2W6	OTTHUMG00000148683	ENST00000312475.4:c.63G>A	chr15.hg19:g.89010546C>T		114.0	0.0	.		107.0	50.0	.	NM_022163	B2RD75|Q9HBU8	Silent	SNP	ENST00000312475.4	hg19	CCDS10341.1																																																																																			.	.	.	none		0.672	MRPL46-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309073.1	NM_022163	
LRRK1	79705	hgsc.bcm.edu	37	15	101602839	101602839	+	Missense_Mutation	SNP	G	G	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:101602839G>T	ENST00000388948.3	+	31	5217	c.4858G>T	c.(4858-4860)Gcc>Tcc	p.A1620S	RP11-505E24.2_ENST00000559857.1_RNA|LRRK1_ENST00000284395.5_Missense_Mutation_p.A1617S	NM_024652.3	NP_078928.3			leucine-rich repeat kinase 1											breast(2)|central_nervous_system(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(25)|ovary(4)|prostate(1)|skin(1)	72	Melanoma(26;0.00505)|Lung NSC(78;0.00793)|all_lung(78;0.0094)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.187)|Lung(145;0.23)			ACCCCAACAGGCCTTGGATAC	0.542																																					p.A1620S		Atlas-SNP	.											.	LRRK1	310	.	0			c.G4858T						PASS	.						155.0	160.0	158.0					15																	101602839		1989	4164	6153	SO:0001583	missense	79705	exon31			CAACAGGCCTTGG	AB058693	CCDS42086.1	15q26.3	2007-01-29			ENSG00000154237	ENSG00000154237			18608	protein-coding gene	gene with protein product		610986				11347906, 14654223	Standard	XM_005254979		Approved	FLJ23119, KIAA1790, Roco1, RIPK6	uc002bwr.3	Q38SD2	OTTHUMG00000165514	ENST00000388948.3:c.4858G>T	chr15.hg19:g.101602839G>T	ENSP00000373600:p.Ala1620Ser	119.0	0.0	.		88.0	34.0	.	NM_024652		Missense_Mutation	SNP	ENST00000388948.3	hg19	CCDS42086.1	.	.	.	.	.	.	.	.	.	.	G	9.469	1.095041	0.20471	.	.	ENSG00000154237	ENST00000388948;ENST00000284395;ENST00000529762;ENST00000542170	T;T	0.69685	-0.42;-0.42	5.29	5.29	0.74685	WD40 repeat-like-containing domain (1);	0.562258	0.19004	N	0.125255	T	0.59770	0.2218	L	0.51422	1.61	0.25804	N	0.984476	B	0.29716	0.255	B	0.22152	0.038	T	0.49969	-0.8882	10	0.11485	T	0.65	.	18.9297	0.92560	0.0:0.0:1.0:0.0	.	1620	Q38SD2	LRRK1_HUMAN	S	1620;1617;311;174	ENSP00000373600:A1620S;ENSP00000284395:A1617S	ENSP00000284395:A1617S	A	+	1	0	LRRK1	99420362	0.998000	0.40836	0.975000	0.42487	0.027000	0.11550	3.003000	0.49505	2.484000	0.83849	0.491000	0.48974	GCC	.	.	.	none		0.542	LRRK1-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384567.2	NM_024652	
PPL	5493	hgsc.bcm.edu	37	16	4933991	4933991	+	Silent	SNP	G	G	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:4933991G>C	ENST00000345988.2	-	22	4754	c.4665C>G	c.(4663-4665)tcC>tcG	p.S1555S	PPL_ENST00000590782.2_Silent_p.S1553S	NM_002705.4	NP_002696	O60437	PEPL_HUMAN	periplakin	1555					keratinization (GO:0031424)	cell junction (GO:0030054)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(6)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(12)|lung(12)|ovary(4)|prostate(5)|skin(3)|stomach(1)|urinary_tract(2)	62						CTAGTTCCTTGGATGACTTGG	0.557																																					p.S1555S		Atlas-SNP	.											.	PPL	168	.	0			c.C4665G						PASS	.						102.0	102.0	102.0					16																	4933991		2197	4300	6497	SO:0001819	synonymous_variant	5493	exon22			TTCCTTGGATGAC	AF013717	CCDS10526.1	16p13.3	2008-02-05			ENSG00000118898	ENSG00000118898			9273	protein-coding gene	gene with protein product		602871				9570964, 9521878	Standard	NM_002705		Approved		uc002cyd.1	O60437	OTTHUMG00000129528	ENST00000345988.2:c.4665C>G	chr16.hg19:g.4933991G>C		51.0	0.0	.		33.0	16.0	.	NM_002705	O60314|O60454|Q14C98	Silent	SNP	ENST00000345988.2	hg19	CCDS10526.1																																																																																			.	.	.	none		0.557	PPL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251715.1	NM_002705	
C16orf72	29035	hgsc.bcm.edu	37	16	9186850	9186850	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:9186850T>A	ENST00000327827.7	+	2	696	c.299T>A	c.(298-300)cTc>cAc	p.L100H		NM_014117.2	NP_054836.2	Q14CZ0	CP072_HUMAN	chromosome 16 open reading frame 72	100										endometrium(4)|large_intestine(2)|lung(2)	8						GTCACCAATCTCTACAAAGGT	0.522																																					p.L100H		Atlas-SNP	.											.	C16orf72	26	.	0			c.T299A						PASS	.						44.0	40.0	41.0					16																	9186850		2197	4300	6497	SO:0001583	missense	29035	exon2			CCAATCTCTACAA	AK123266	CCDS10538.1	16p13.2	2012-11-19			ENSG00000182831	ENSG00000182831			30103	protein-coding gene	gene with protein product						8889548	Standard	NM_014117		Approved	FLJ41272, PRO0149	uc002czm.3	Q14CZ0	OTTHUMG00000178147	ENST00000327827.7:c.299T>A	chr16.hg19:g.9186850T>A	ENSP00000331720:p.Leu100His	131.0	0.0	.		124.0	48.0	.	NM_014117		Missense_Mutation	SNP	ENST00000327827.7	hg19	CCDS10538.1	.	.	.	.	.	.	.	.	.	.	T	26.0	4.692171	0.88735	.	.	ENSG00000182831	ENST00000327827	T	0.72167	-0.63	4.09	4.09	0.47781	.	0.065681	0.64402	D	0.000012	D	0.82375	0.5023	M	0.81341	2.54	0.80722	D	1	D	0.76494	0.999	D	0.63703	0.917	D	0.85423	0.1144	10	0.87932	D	0	-16.5797	13.2393	0.59987	0.0:0.0:0.0:1.0	.	100	Q14CZ0	CP072_HUMAN	H	100	ENSP00000331720:L100H	ENSP00000331720:L100H	L	+	2	0	C16orf72	9094351	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.699000	0.84547	1.693000	0.51124	0.533000	0.62120	CTC	.	.	.	none		0.522	C16orf72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440760.2	NM_014117	
SLC6A2	6530	hgsc.bcm.edu	37	16	55719085	55719085	+	Silent	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:55719085C>T	ENST00000379906.2	+	4	930	c.675C>T	c.(673-675)agC>agT	p.S225S	SLC6A2_ENST00000414754.3_Silent_p.S225S|SLC6A2_ENST00000566163.1_Silent_p.S225S|SLC6A2_ENST00000567238.1_Silent_p.S120S|SLC6A2_ENST00000561820.1_Silent_p.S225S|SLC6A2_ENST00000219833.8_Silent_p.S225S|SLC6A2_ENST00000568943.1_Silent_p.S225S	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	225					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	ACGAGAGCAGCGGGATTCATG	0.587																																					p.S225S		Atlas-SNP	.											.	SLC6A2	189	.	0			c.C675T						PASS	.						118.0	103.0	108.0					16																	55719085		2198	4300	6498	SO:0001819	synonymous_variant	6530	exon5			GAGCAGCGGGATT		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.675C>T	chr16.hg19:g.55719085C>T		46.0	0.0	.		60.0	26.0	.	NM_001172501	B2R707|B4DX48|Q96KH8	Silent	SNP	ENST00000379906.2	hg19	CCDS10754.1																																																																																			.	.	.	none		0.587	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
DPEP1	1800	hgsc.bcm.edu	37	16	89704613	89704613	+	Missense_Mutation	SNP	T	T	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:89704613T>C	ENST00000393092.3	+	11	1510	c.1219T>C	c.(1219-1221)Tgt>Cgt	p.C407R	DPEP1_ENST00000261615.4_Missense_Mutation_p.C407R|DPEP1_ENST00000421184.1_Missense_Mutation_p.C407R	NM_004413.3	NP_004404.1	P16444	DPEP1_HUMAN	dipeptidase 1 (renal)	407					antibiotic metabolic process (GO:0016999)|arachidonic acid metabolic process (GO:0019369)|cellular lactam catabolic process (GO:0072340)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|cellular response to nitric oxide (GO:0071732)|glutathione metabolic process (GO:0006749)|homocysteine metabolic process (GO:0050667)|leukotriene metabolic process (GO:0006691)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell migration (GO:0030336)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|small molecule metabolic process (GO:0044281)	anchored component of membrane (GO:0031225)|apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|dipeptidyl-peptidase activity (GO:0008239)|GPI anchor binding (GO:0034235)|metallodipeptidase activity (GO:0070573)|metalloexopeptidase activity (GO:0008235)|modified amino acid binding (GO:0072341)|zinc ion binding (GO:0008270)			large_intestine(2)|lung(10)|prostate(1)|urinary_tract(1)	14		all_lung(18;0.0054)|all_hematologic(23;0.094)		BRCA - Breast invasive adenocarcinoma(80;0.0258)	Cilastatin(DB01597)	CCTGGTCCTCTGTCTGTCTCT	0.657																																					p.C407R		Atlas-SNP	.											.	DPEP1	39	.	0			c.T1219C						PASS	.						30.0	36.0	34.0					16																	89704613		2188	4290	6478	SO:0001583	missense	1800	exon11			GTCCTCTGTCTGT		CCDS10982.1	16q24	2011-07-22			ENSG00000015413	ENSG00000015413	3.4.13.19		3002	protein-coding gene	gene with protein product		179780					Standard	NM_004413		Approved		uc002fnr.4	P16444	OTTHUMG00000138052	ENST00000393092.3:c.1219T>C	chr16.hg19:g.89704613T>C	ENSP00000376807:p.Cys407Arg	27.0	0.0	.		33.0	10.0	.	NM_001128141	D3DX80|Q96AK2	Missense_Mutation	SNP	ENST00000393092.3	hg19	CCDS10982.1	.	.	.	.	.	.	.	.	.	.	t	9.017	0.983958	0.18889	.	.	ENSG00000015413	ENST00000421184;ENST00000393092;ENST00000261615	T;T;T	0.20738	2.05;2.05;2.05	5.11	-10.2	0.00374	.	2.970350	0.01127	N	0.005905	T	0.09730	0.0239	N	0.16478	0.41	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.14531	-1.0469	10	0.36615	T	0.2	-6.3644	3.003	0.06019	0.135:0.0879:0.3417:0.4354	.	407	P16444	DPEP1_HUMAN	R	407	ENSP00000397313:C407R;ENSP00000376807:C407R;ENSP00000261615:C407R	ENSP00000261615:C407R	C	+	1	0	DPEP1	88232114	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-2.591000	0.00899	-2.931000	0.00300	-0.575000	0.04146	TGT	.	.	.	none		0.657	DPEP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000423058.1	NM_001128141	
SCARF1	8578	hgsc.bcm.edu	37	17	1540075	1540075	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:1540075C>T	ENST00000263071.4	-	10	1610	c.1561G>A	c.(1561-1563)Gac>Aac	p.D521N	SCARF1_ENST00000571272.1_Missense_Mutation_p.M508I|SCARF1_ENST00000348987.3_Missense_Mutation_p.D435N	NM_003693.2|NM_145350.1	NP_003684.2|NP_663325.1	Q14162	SREC_HUMAN	scavenger receptor class F, member 1	521	Pro/Ser-rich.				cell adhesion (GO:0007155)|cholesterol catabolic process (GO:0006707)|dendrite development (GO:0016358)|neuron remodeling (GO:0016322)|positive regulation of axon regeneration (GO:0048680)|positive regulation of neuron projection development (GO:0010976)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	low-density lipoprotein particle binding (GO:0030169)|scavenger receptor activity (GO:0005044)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(3)|kidney(2)|lung(9)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	20				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		GAGAAGGAGTCATCAGTGGCC	0.607																																					p.D521N		Atlas-SNP	.											.	SCARF1	46	.	0			c.G1561A						PASS	.						106.0	108.0	107.0					17																	1540075		2203	4300	6503	SO:0001583	missense	8578	exon10			AGGAGTCATCAGT	D63483	CCDS11007.1, CCDS45564.1	17p13.3	2008-07-18			ENSG00000074660	ENSG00000074660			16820	protein-coding gene	gene with protein product	"""scavenger receptor expressed by endothelial cells"", ""acetyl LDL receptor"""	607873				9395444, 8590280	Standard	NM_003693		Approved	SREC, KIAA0149	uc002fsz.2	Q14162	OTTHUMG00000090555	ENST00000263071.4:c.1561G>A	chr17.hg19:g.1540075C>T	ENSP00000263071:p.Asp521Asn	67.0	0.0	.		68.0	31.0	.	NM_003693	A8MQ05|O43701|Q8NHD2|Q8NHD3|Q8NHD4|Q8NHD5	Missense_Mutation	SNP	ENST00000263071.4	hg19	CCDS11007.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	15.34|15.34	2.805426|2.805426	0.50315|0.50315	.|.	.|.	ENSG00000074660|ENSG00000074660	ENST00000263071;ENST00000348987|ENST00000434376	T;T|.	0.33216|.	1.99;1.42|.	5.15|5.15	5.15|5.15	0.70609|0.70609	.|.	0.154024|.	0.31177|.	N|.	0.008101|.	T|T	0.31199|0.31199	0.0789|0.0789	.|.	.|.	.|.	0.31528|0.31528	N|N	0.661541|0.661541	P;B|B	0.45715|0.23249	0.865;0.349|0.082	B;B|B	0.42555|0.21917	0.391;0.122|0.037	T|T	0.23619|0.23619	-1.0183|-1.0183	9|7	0.08179|0.22706	T|T	0.78|0.39	-32.7609|-32.7609	7.8595|7.8595	0.29501|0.29501	0.0:0.8217:0.0:0.1783|0.0:0.8217:0.0:0.1783	.|.	435;521|508	Q14162-2;Q14162|Q14162-3	.;SREC_HUMAN|.	N|I	521;435|508	ENSP00000263071:D521N;ENSP00000323964:D435N|.	ENSP00000263071:D521N|ENSP00000411167:M508I	D|M	-|-	1|3	0|0	SCARF1|SCARF1	1486825|1486825	0.987000|0.987000	0.35691|0.35691	0.959000|0.959000	0.39883|0.39883	0.817000|0.817000	0.46193|0.46193	2.387000|2.387000	0.44389|0.44389	2.580000|2.580000	0.87095|0.87095	0.556000|0.556000	0.70494|0.70494	GAC|ATG	.	.	.	none		0.607	SCARF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207081.4	NM_003693	
ALOX15B	247	hgsc.bcm.edu	37	17	7948885	7948885	+	Missense_Mutation	SNP	C	C	T	rs370434436		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:7948885C>T	ENST00000380183.4	+	8	1220	c.1081C>T	c.(1081-1083)Cgc>Tgc	p.R361C	ALOX15B_ENST00000380173.2_Missense_Mutation_p.R361C|ALOX15B_ENST00000573359.1_Missense_Mutation_p.R361C|ALOX15B_ENST00000572022.1_Missense_Mutation_p.R361C	NM_001141.2	NP_001132.2	O15296	LX15B_HUMAN	arachidonate 15-lipoxygenase, type B	361	Lipoxygenase. {ECO:0000255|PROSITE- ProRule:PRU00726}.				apoptotic process (GO:0006915)|arachidonic acid metabolic process (GO:0019369)|hepoxilin biosynthetic process (GO:0051122)|linoleic acid metabolic process (GO:0043651)|lipid metabolic process (GO:0006629)|lipoxygenase pathway (GO:0019372)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of growth (GO:0045926)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|prostate gland development (GO:0030850)|regulation of epithelial cell differentiation (GO:0030856)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	arachidonate 15-lipoxygenase activity (GO:0050473)|arachidonate 8(S)-lipoxygenase activity (GO:0036403)|calcium ion binding (GO:0005509)|iron ion binding (GO:0005506)|linoleate 13S-lipoxygenase activity (GO:0016165)|lipid binding (GO:0008289)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(3)|ovary(1)|prostate(2)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	24						GACCTGGGTGCGCAATGCCGA	0.637													C|||	1	0.000199681	0.0008	0.0	5008	,	,		17957	0.0		0.0	False		,,,				2504	0.0				p.R361C		Atlas-SNP	.											ALOX15B,NS,carcinoma,0,1	ALOX15B	66	.	0			c.C1081T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG	4,4402	9.9+/-24.2	0,4,2199	108.0	80.0	90.0		1081,1081,1081	1.4	0.8	17		90	0,8600		0,0,4300	no	missense,missense,missense	ALOX15B	NM_001039130.1,NM_001039131.1,NM_001141.2	180,180,180	0,4,6499	TT,TC,CC		0.0,0.0908,0.0308	probably-damaging,probably-damaging,probably-damaging	361/648,361/603,361/677	7948885	4,13002	2203	4300	6503	SO:0001583	missense	247	exon8			TGGGTGCGCAATG	U78294	CCDS11128.1, CCDS32558.1, CCDS32559.1	17p13.1	2013-03-20	2006-01-16		ENSG00000179593	ENSG00000179593	1.13.11.33	"""Arachidonate lipoxygenases"""	434	protein-coding gene	gene with protein product		603697	"""arachidonate 15-lipoxygenase, second type"""			9177185	Standard	NM_001039130		Approved	15-LOX-2	uc002gju.3	O15296	OTTHUMG00000108181	ENST00000380183.4:c.1081C>T	chr17.hg19:g.7948885C>T	ENSP00000369530:p.Arg361Cys	50.0	0.0	.		41.0	3.0	.	NM_001141	D3DTR2|Q8IYQ2|Q8TEV3|Q8TEV4|Q8TEV5|Q8TEV6|Q9UKM4	Missense_Mutation	SNP	ENST00000380183.4	hg19	CCDS11128.1	.	.	.	.	.	.	.	.	.	.	C	15.48	2.846791	0.51164	9.08E-4	0.0	ENSG00000179593	ENST00000380173;ENST00000339694;ENST00000380183	D;D	0.90444	-2.67;-2.67	4.53	1.38	0.22167	Lipoxygenase, C-terminal (4);	0.054757	0.64402	D	0.000001	D	0.92509	0.7621	L	0.55103	1.725	0.49299	D	0.999772	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.97110	0.97;1.0;0.999;1.0	D	0.91190	0.4983	10	0.87932	D	0	-29.9769	9.8306	0.40939	0.0:0.7463:0.0:0.2537	.	361;361;361;361	B4DNW8;O15296-2;O15296-4;O15296	.;.;.;LX15B_HUMAN	C	361	ENSP00000369520:R361C;ENSP00000369530:R361C	ENSP00000344337:R361C	R	+	1	0	ALOX15B	7889610	0.511000	0.26179	0.776000	0.31678	0.679000	0.39708	0.972000	0.29409	0.466000	0.27193	-0.244000	0.11960	CGC	.	.	.	weak		0.637	ALOX15B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226985.2		
MYH10	4628	hgsc.bcm.edu	37	17	8448780	8448780	+	Missense_Mutation	SNP	A	A	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:8448780A>G	ENST00000269243.4	-	12	1525	c.1387T>C	c.(1387-1389)Ttt>Ctt	p.F463L	MYH10_ENST00000360416.3_Missense_Mutation_p.F473L|RN7SL129P_ENST00000479993.2_RNA|MYH10_ENST00000396239.1_Missense_Mutation_p.F463L|MYH10_ENST00000379980.4_Missense_Mutation_p.F479L	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	463	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						AAAATTTCAAATCCAGCAATA	0.433																																					p.F473L		Atlas-SNP	.											.	MYH10	148	.	0			c.T1417C						PASS	.						106.0	99.0	102.0					17																	8448780		2203	4300	6503	SO:0001583	missense	4628	exon13			TTTCAAATCCAGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.1387T>C	chr17.hg19:g.8448780A>G	ENSP00000269243:p.Phe463Leu	74.0	0.0	.		69.0	27.0	.	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Missense_Mutation	SNP	ENST00000269243.4	hg19	CCDS11144.1	.	.	.	.	.	.	.	.	.	.	A	32	5.108528	0.94292	.	.	ENSG00000133026	ENST00000269243;ENST00000360416;ENST00000396239;ENST00000379980	D;D;D;D	0.98701	-2.12;-2.12;-5.08;-2.12	5.0	5.0	0.66597	Myosin head, motor domain (3);	0.049358	0.85682	N	0.000000	D	0.99545	0.9837	H	0.99143	4.445	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.97669	1.0165	10	0.87932	D	0	.	15.1595	0.72771	1.0:0.0:0.0:0.0	.	472;473;463	B2RWP9;F8VTL3;P35580	.;.;MYH10_HUMAN	L	463;473;463;479	ENSP00000269243:F463L;ENSP00000353590:F473L;ENSP00000379539:F463L;ENSP00000369315:F479L	ENSP00000269243:F463L	F	-	1	0	MYH10	8389505	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.032000	0.93736	2.216000	0.71823	0.533000	0.62120	TTT	.	.	.	none		0.433	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
KRT10	3858	hgsc.bcm.edu	37	17	38975316	38975316	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:38975316G>A	ENST00000269576.5	-	7	1480	c.1471C>T	c.(1471-1473)Cac>Tac	p.H491Y	TMEM99_ENST00000301665.3_5'Flank	NM_000421.3	NP_000412	P13645	K1C10_HUMAN	keratin 10	491	Gly-rich.|Ser-rich.|Tail.			Missing (in Ref. 1; AAA60544). {ECO:0000305}.	cellular response to calcium ion (GO:0071277)|keratinocyte differentiation (GO:0030216)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of epidermis (GO:0030280)			NS(2)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	11		Breast(137;0.000301)				ctgccgccgtggccgccgccg	0.801																																					p.H491Y		Atlas-SNP	.											.	KRT10	56	.	0			c.C1471T						PASS	.						1.0	1.0	1.0					17																	38975316		219	517	736	SO:0001583	missense	3858	exon7			CGCCGTGGCCGCC	J04029	CCDS11377.1	17q21.2	2013-06-20	2008-08-01		ENSG00000186395	ENSG00000186395		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6413	protein-coding gene	gene with protein product	"""cytokeratin 10"", ""epidermolytic hyperkeratosis"""	148080	"""keratosis palmaris et plantaris"""	KPP		2461420, 16831889	Standard	NM_000421		Approved	K10, CK10	uc002hvi.3	P13645	OTTHUMG00000133368	ENST00000269576.5:c.1471C>T	chr17.hg19:g.38975316G>A	ENSP00000269576:p.His491Tyr	44.0	0.0	.		125.0	8.0	.	NM_000421	Q14664|Q8N175	Missense_Mutation	SNP	ENST00000269576.5	hg19	CCDS11377.1	.	.	.	.	.	.	.	.	.	.	g	15.09	2.731363	0.48939	.	.	ENSG00000186395	ENST00000269576	D	0.83591	-1.74	5.21	-9.23	0.00672	.	2.489830	0.01848	N	0.035767	T	0.64724	0.2624	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.59397	-0.7462	10	0.45353	T	0.12	.	9.3977	0.38412	0.3538:0.2897:0.3564:0.0	.	491	P13645	K1C10_HUMAN	Y	491	ENSP00000269576:H491Y	ENSP00000269576:H491Y	H	-	1	0	KRT10	36228842	0.000000	0.05858	0.000000	0.03702	0.034000	0.12701	-4.792000	0.00185	-2.762000	0.00369	-2.316000	0.00254	CAC	.	.	.	none		0.801	KRT10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257875.1	NM_000421	
PLEKHH3	79990	hgsc.bcm.edu	37	17	40823573	40823573	+	Silent	SNP	G	G	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:40823573G>T	ENST00000591022.1	-	8	1467	c.1080C>A	c.(1078-1080)acC>acA	p.T360T	PLEKHH3_ENST00000456950.2_5'UTR|PLEKHH3_ENST00000293349.6_Silent_p.T360T|PLEKHH3_ENST00000412503.1_Silent_p.T360T	NM_024927.4	NP_079203	Q7Z736	PKHH3_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 3	360	MyTH4. {ECO:0000255|PROSITE- ProRule:PRU00359}.				signal transduction (GO:0007165)	cytoskeleton (GO:0005856)|extracellular space (GO:0005615)				endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(2)|skin(2)	13		Breast(137;0.00116)		BRCA - Breast invasive adenocarcinoma(366;0.14)		GTGCCTGCTCGGTCCTGGGTT	0.592																																					p.T360T		Atlas-SNP	.											.	PLEKHH3	49	.	0			c.C1080A						PASS	.						12.0	14.0	13.0					17																	40823573		2200	4298	6498	SO:0001819	synonymous_variant	79990	exon8			CTGCTCGGTCCTG	BC052978	CCDS11434.1	17q21.2	2013-01-11				ENSG00000068137		"""Pleckstrin homology (PH) domain containing"""	26105	protein-coding gene	gene with protein product						12477932	Standard	NM_024927		Approved	FLJ21019	uc002iau.3	Q7Z736		ENST00000591022.1:c.1080C>A	chr17.hg19:g.40823573G>T		112.0	0.0	.		152.0	40.0	.	NM_024927	C9JQ76|Q59H20|Q96B28|Q9H7D6|Q9NT18	Silent	SNP	ENST00000591022.1	hg19	CCDS11434.1																																																																																			.	.	.	none		0.592	PLEKHH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452332.1	NM_024927	
DHX8	1659	hgsc.bcm.edu	37	17	41597598	41597598	+	Missense_Mutation	SNP	T	T	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr17:41597598T>A	ENST00000262415.3	+	19	2972	c.2900T>A	c.(2899-2901)cTg>cAg	p.L967Q	DHX8_ENST00000540306.1_Missense_Mutation_p.L967Q	NM_004941.1	NP_004932.1	Q14562	DHX8_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 8	967					ATP catabolic process (GO:0006200)|mRNA splicing, via spliceosome (GO:0000398)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(17)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	42		Breast(137;0.00908)		BRCA - Breast invasive adenocarcinoma(366;0.08)		CTGGGGGCCCTGGATGACGAG	0.547											OREG0024435	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L967Q	NSCLC(56;1548 1661 49258 49987)	Atlas-SNP	.											.	DHX8	98	.	0			c.T2900A						PASS	.						89.0	85.0	86.0					17																	41597598		2203	4300	6503	SO:0001583	missense	1659	exon19			GGGCCCTGGATGA	D50487	CCDS11464.1	17q21.31	2005-08-19	2003-06-13	2003-06-20		ENSG00000067596		"""DEAH-boxes"""	2749	protein-coding gene	gene with protein product		600396	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 8 (RNA helicase)"""	DDX8		7935475	Standard	NM_004941		Approved	HRH1, PRP22, PRPF22	uc002idu.1	Q14562		ENST00000262415.3:c.2900T>A	chr17.hg19:g.41597598T>A	ENSP00000262415:p.Leu967Gln	77.0	0.0	.	902	84.0	22.0	.	NM_004941		Missense_Mutation	SNP	ENST00000262415.3	hg19	CCDS11464.1	.	.	.	.	.	.	.	.	.	.	T	28.3	4.905425	0.92107	.	.	ENSG00000067596	ENST00000540306;ENST00000262415	T;T	0.10382	2.88;2.88	5.8	5.8	0.92144	Helicase-associated domain (2);	0.000000	0.64402	D	0.000004	T	0.51517	0.1679	H	0.98664	4.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	T	0.71573	-0.4552	10	0.87932	D	0	.	15.3296	0.74196	0.0:0.0:0.0:1.0	.	967;967	F5H658;Q14562	.;DHX8_HUMAN	Q	967	ENSP00000437886:L967Q;ENSP00000262415:L967Q	ENSP00000262415:L967Q	L	+	2	0	DHX8	38953124	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.876000	0.87215	2.226000	0.72624	0.459000	0.35465	CTG	.	.	.	none		0.547	DHX8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453485.1		
DSG4	147409	hgsc.bcm.edu	37	18	28968923	28968923	+	Silent	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr18:28968923C>T	ENST00000308128.4	+	5	594	c.459C>T	c.(457-459)aaC>aaT	p.N153N	RP11-534N16.1_ENST00000581856.1_RNA|RP11-534N16.1_ENST00000578477.1_RNA|DSG4_ENST00000359747.4_Silent_p.N153N|RP11-534N16.1_ENST00000581452.1_RNA	NM_177986.3	NP_817123.1	Q86SJ6	DSG4_HUMAN	desmoglein 4	153	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Missing (in HYPT6). {ECO:0000269|PubMed:12705872, ECO:0000269|PubMed:15191570}.		anagen (GO:0042640)|BMP signaling pathway (GO:0030509)|homophilic cell adhesion (GO:0007156)|keratinocyte differentiation (GO:0030216)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|central_nervous_system(6)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(11)|liver(2)|lung(35)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	70			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TAAATGATAACGCTCCAGTCT	0.413																																					p.N153N		Atlas-SNP	.											.	DSG4	343	.	0			c.C459T						PASS	.						108.0	104.0	106.0					18																	28968923		2203	4299	6502	SO:0001819	synonymous_variant	147409	exon5			TGATAACGCTCCA	AY177664, AY168788	CCDS11897.1, CCDS45845.1	18q12.1	2010-01-26			ENSG00000175065	ENSG00000175065		"""Cadherins / Major cadherins"""	21307	protein-coding gene	gene with protein product		607892				12648213	Standard	NM_001134453		Approved	CDHF13, LAH	uc002kwq.2	Q86SJ6	OTTHUMG00000131979	ENST00000308128.4:c.459C>T	chr18.hg19:g.28968923C>T		77.0	0.0	.		100.0	46.0	.	NM_001134453	A2RUI1|Q6Y9L9|Q8IXV4	Silent	SNP	ENST00000308128.4	hg19	CCDS11897.1																																																																																			.	.	.	none		0.413	DSG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254941.1	NM_177986	
FZR1	51343	hgsc.bcm.edu	37	19	3527661	3527661	+	Missense_Mutation	SNP	C	C	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:3527661C>G	ENST00000395095.3	+	6	503	c.503C>G	c.(502-504)aCc>aGc	p.T168S	FZR1_ENST00000441788.2_Missense_Mutation_p.T168S|FZR1_ENST00000313639.8_Intron	NM_001136198.1	NP_001129670.1	Q9UM11	FZR_HUMAN	fizzy/cell division cycle 20 related 1 (Drosophila)	168					activation of anaphase-promoting complex activity (GO:0051488)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|DNA repair (GO:0006281)|G2 DNA damage checkpoint (GO:0031572)|lens fiber cell differentiation (GO:0070306)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of cell aging (GO:0090344)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of meiosis (GO:0040020)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				endometrium(1)|kidney(4)|liver(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)	13				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.00253)|STAD - Stomach adenocarcinoma(1328;0.18)		CGGAAACCCACCCGCAAGATC	0.622																																					p.T168S		Atlas-SNP	.											.	FZR1	42	.	0			c.C503G						PASS	.						68.0	57.0	61.0					19																	3527661		2199	4296	6495	SO:0001583	missense	51343	exon6			AACCCACCCGCAA	AF083810	CCDS12109.1, CCDS45916.1, CCDS45917.1	19p13.3	2013-01-10				ENSG00000105325		"""WD repeat domain containing"""	24824	protein-coding gene	gene with protein product		603619				9734353, 11003657	Standard	NM_016263		Approved	HCDH1, CDH1, HCDH, FZR, FZR2, KIAA1242, CDC20C	uc010dtk.2	Q9UM11		ENST00000395095.3:c.503C>G	chr19.hg19:g.3527661C>G	ENSP00000378529:p.Thr168Ser	41.0	0.0	.		40.0	15.0	.	NM_001136198	O75869|Q86U66|Q96NW8|Q9UI96|Q9ULH8|Q9UM10|Q9UNQ1|Q9Y2T8	Missense_Mutation	SNP	ENST00000395095.3	hg19	CCDS45916.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.675167	0.67928	.	.	ENSG00000105325	ENST00000441788;ENST00000395095	T;T	0.07327	3.2;3.2	5.14	5.14	0.70334	WD40 repeat-like-containing domain (1);	0.095599	0.64402	D	0.000001	T	0.10809	0.0264	L	0.53249	1.67	0.80722	D	1	B;B	0.09022	0.0;0.002	B;B	0.08055	0.001;0.003	T	0.12708	-1.0537	10	0.18276	T	0.48	-27.132	17.2027	0.86910	0.0:1.0:0.0:0.0	.	168;168	Q9UM11;Q9UM11-2	FZR_HUMAN;.	S	168	ENSP00000410369:T168S;ENSP00000378529:T168S	ENSP00000378529:T168S	T	+	2	0	FZR1	3478661	1.000000	0.71417	0.972000	0.41901	0.989000	0.77384	5.865000	0.69583	2.399000	0.81585	0.655000	0.94253	ACC	.	.	.	none		0.622	FZR1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452869.2	NM_016263	
PLIN4	729359	hgsc.bcm.edu	37	19	4512405	4512405	+	Missense_Mutation	SNP	T	T	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:4512405T>G	ENST00000301286.3	-	3	1524	c.1525A>C	c.(1525-1527)Acc>Ccc	p.T509P		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	509	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						GTCTTGGTGGTGTCTACGCCG	0.612																																					p.T509P		Atlas-SNP	.											.	PLIN4	191	.	0			c.A1525C						PASS	.						105.0	111.0	109.0					19																	4512405		2036	4180	6216	SO:0001583	missense	729359	exon3			TGGTGGTGTCTAC	AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1525A>C	chr19.hg19:g.4512405T>G	ENSP00000301286:p.Thr509Pro	81.0	0.0	.		92.0	32.0	.	NM_001080400	A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	hg19	CCDS45927.1	.	.	.	.	.	.	.	.	.	.	T	14.90	2.674559	0.47781	.	.	ENSG00000167676	ENST00000301286	T	0.06608	3.28	5.43	4.4	0.53042	.	0.131117	0.35040	N	0.003484	T	0.25082	0.0609	M	0.85859	2.78	0.36524	D	0.870345	D	0.89917	1.0	D	0.74348	0.983	T	0.15665	-1.0429	10	0.51188	T	0.08	-21.1732	9.9845	0.41832	0.1518:0.0:0.0:0.8482	.	509	Q96Q06	PLIN4_HUMAN	P	509	ENSP00000301286:T509P	ENSP00000301286:T509P	T	-	1	0	PLIN4	4463405	0.125000	0.22332	0.993000	0.49108	0.030000	0.12068	1.598000	0.36740	0.866000	0.35629	0.459000	0.35465	ACC	.	.	.	none		0.612	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1	XM_170901	
CLEC4M	10332	hgsc.bcm.edu	37	19	7830731	7830731	+	Missense_Mutation	SNP	G	G	A	rs76899402		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:7830731G>A	ENST00000327325.5	+	4	540	c.422G>A	c.(421-423)cGg>cAg	p.R141Q	CLEC4M_ENST00000596363.1_Missense_Mutation_p.R113Q|CLEC4M_ENST00000394122.2_Missense_Mutation_p.R129Q|CLEC4M_ENST00000596707.1_Missense_Mutation_p.R120Q|CLEC4M_ENST00000357361.2_Missense_Mutation_p.R141Q|CLEC4M_ENST00000334806.5_Intron|CLEC4M_ENST00000595496.1_Missense_Mutation_p.R120Q|CLEC4M_ENST00000248228.4_Intron|CLEC4M_ENST00000359059.5_Intron|CLEC4M_ENST00000597522.1_Missense_Mutation_p.R141Q	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M	141	7 X approximate tandem repeats.				antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)	p.R141Q(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						GAGCTGACCCGGCTGAAGGCT	0.582																																					p.R141Q		Atlas-SNP	.											CLEC4M,colon,carcinoma,0,1	CLEC4M	58	.	1	Substitution - Missense(1)	large_intestine(1)	c.G422A						PASS	.						13.0	13.0	13.0					19																	7830731		1642	3266	4908	SO:0001583	missense	10332	exon4			TGACCCGGCTGAA	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.422G>A	chr19.hg19:g.7830731G>A	ENSP00000316228:p.Arg141Gln	28.0	0.0	.		30.0	2.0	.	NM_001144908	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Missense_Mutation	SNP	ENST00000327325.5	hg19	CCDS12187.1	.	.	.	.	.	.	.	.	.	.	A	0.008	-1.920834	0.00498	.	.	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000357361;ENST00000358690	T;T;T	0.22336	1.97;1.96;1.97	0.905	-1.81	0.07882	.	.	.	.	.	T	0.07188	0.0182	N	0.04636	-0.2	0.09310	N	1	B;B;B;B;B;B;B	0.17268	0.004;0.001;0.001;0.0;0.007;0.021;0.001	B;B;B;B;B;B;B	0.10450	0.003;0.005;0.001;0.0;0.002;0.003;0.005	T	0.33059	-0.9883	9	0.07482	T	0.82	.	6.6496	0.22955	0.409:0.0:0.591:0.0	.	120;113;141;113;120;141;85	Q9H2X3-5;B4DNV9;Q9H2X3;Q9H2X3-9;Q9H2X3-7;Q9H2X3-4;Q9H2X3-10	.;.;CLC4M_HUMAN;.;.;.;.	Q	141;129;141;85	ENSP00000316228:R141Q;ENSP00000377680:R129Q;ENSP00000349924:R141Q	ENSP00000316228:R141Q	R	+	2	0	CLEC4M	7736731	0.001000	0.12720	0.004000	0.12327	0.024000	0.10985	-1.792000	0.01756	-2.527000	0.00494	-2.768000	0.00120	CGG	.	G|0.250;A|0.750	0.750	weak		0.582	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	
TNPO2	30000	hgsc.bcm.edu	37	19	12816127	12816127	+	Missense_Mutation	SNP	T	T	C			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:12816127T>C	ENST00000592287.1	-	17	2057	c.1949A>G	c.(1948-1950)gAg>gGg	p.E650G	TNPO2_ENST00000450764.2_Missense_Mutation_p.E650G|TNPO2_ENST00000588216.1_Missense_Mutation_p.E650G|TNPO2_ENST00000425528.1_Missense_Mutation_p.E650G|SNORD41_ENST00000386967.1_RNA|TNPO2_ENST00000441499.1_Missense_Mutation_p.E650G|TNPO2_ENST00000356861.5_Missense_Mutation_p.E650G	NM_001136196.1	NP_001129668.1	O14787	TNPO2_HUMAN	transportin 2	650					intracellular protein transport (GO:0006886)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	nuclear localization sequence binding (GO:0008139)			autonomic_ganglia(1)|breast(2)|endometrium(5)|kidney(2)|large_intestine(2)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						ACCCAGGCCCTCGGCCAGGCC	0.597																																					p.E650G		Atlas-SNP	.											.	TNPO2	108	.	0			c.A1949G						PASS	.						27.0	29.0	28.0					19																	12816127		2152	4253	6405	SO:0001583	missense	30000	exon17			AGGCCCTCGGCCA	AF019039	CCDS45991.1, CCDS45992.1	19p13.13	2009-01-12	2009-01-12			ENSG00000105576		"""Importins"""	19998	protein-coding gene	gene with protein product	"""importin 3"", ""karyopherin beta 2b"""	603002				9298975, 12384575	Standard	NM_013433		Approved	IPO3, KPNB2B, FLJ12155, TRN2	uc002muo.3	O14787		ENST00000592287.1:c.1949A>G	chr19.hg19:g.12816127T>C	ENSP00000468434:p.Glu650Gly	58.0	0.0	.		58.0	23.0	.	NM_013433	O14655|Q6IN77	Missense_Mutation	SNP	ENST00000592287.1	hg19	CCDS45991.1	.	.	.	.	.	.	.	.	.	.	T	16.63	3.175437	0.57692	.	.	ENSG00000105576	ENST00000536114;ENST00000425528;ENST00000441499;ENST00000450764;ENST00000356861;ENST00000420511;ENST00000546320	T;T;T;T	0.61158	0.13;0.13;0.13;0.13	5.64	5.64	0.86602	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69504	0.3118	M	0.89353	3.025	0.80722	D	1	P;P	0.49862	0.756;0.929	P;P	0.46339	0.495;0.513	T	0.77702	-0.2489	10	0.87932	D	0	-20.3413	14.8368	0.70190	0.0:0.0:0.0:1.0	.	814;650	Q4LE60;O14787	.;TNPO2_HUMAN	G	814;650;650;650;650;650;650	ENSP00000407182:E650G;ENSP00000389648:E650G;ENSP00000397379:E650G;ENSP00000349321:E650G	ENSP00000349321:E650G	E	-	2	0	TNPO2	12677127	1.000000	0.71417	1.000000	0.80357	0.112000	0.19704	7.671000	0.83941	2.144000	0.66660	0.460000	0.39030	GAG	.	.	.	none		0.597	TNPO2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450785.1	NM_013433	
ZNF536	9745	hgsc.bcm.edu	37	19	30934626	30934626	+	Missense_Mutation	SNP	C	C	T			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:30934626C>T	ENST00000355537.3	+	2	304	c.157C>T	c.(157-159)Cgg>Tgg	p.R53W		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	53					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GCTCCATCCCCGGCCCAACCC	0.667																																					p.R53W		Atlas-SNP	.											.	ZNF536	424	.	0			c.C157T						PASS	.						57.0	59.0	58.0					19																	30934626		2203	4300	6503	SO:0001583	missense	9745	exon2			CATCCCCGGCCCA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.157C>T	chr19.hg19:g.30934626C>T	ENSP00000347730:p.Arg53Trp	89.0	0.0	.		80.0	42.0	.	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	hg19	CCDS32984.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.824161	0.32237	.	.	ENSG00000198597	ENST00000355537	T	0.09163	3.01	5.37	0.305	0.15801	.	0.059306	0.64402	D	0.000002	T	0.15046	0.0363	L	0.27053	0.805	0.40413	D	0.979763	B;D	0.89917	0.014;1.0	B;P	0.61874	0.003;0.895	T	0.02275	-1.1184	10	0.87932	D	0	-26.6384	10.0943	0.42466	0.4232:0.5051:0.0:0.0716	.	53;53	A7E228;O15090	.;ZN536_HUMAN	W	53	ENSP00000347730:R53W	ENSP00000347730:R53W	R	+	1	2	ZNF536	35626466	0.637000	0.27216	0.761000	0.31378	0.804000	0.45430	1.329000	0.33770	0.302000	0.22762	0.462000	0.41574	CGG	.	.	.	none		0.667	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
MKKS	8195	hgsc.bcm.edu	37	20	10393727	10393727	+	Missense_Mutation	SNP	T	T	G	rs113994195		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr20:10393727T>G	ENST00000347364.3	-	3	1198	c.436A>C	c.(436-438)Agt>Cgt	p.S146R	MKKS_ENST00000399054.2_Missense_Mutation_p.S146R	NM_170784.2	NP_740754.1	Q9NPJ1	MKKS_HUMAN	McKusick-Kaufman syndrome	146					artery smooth muscle contraction (GO:0014824)|brain morphogenesis (GO:0048854)|cartilage development (GO:0051216)|cerebral cortex development (GO:0021987)|chaperone-mediated protein complex assembly (GO:0051131)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|determination of left/right symmetry (GO:0007368)|fat cell differentiation (GO:0045444)|gonad development (GO:0008406)|heart development (GO:0007507)|heart looping (GO:0001947)|hippocampus development (GO:0021766)|intracellular transport (GO:0046907)|melanosome transport (GO:0032402)|negative regulation of appetite by leptin-mediated signaling pathway (GO:0038108)|negative regulation of blood pressure (GO:0045776)|negative regulation of gene expression (GO:0010629)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|pigment granule aggregation in cell center (GO:0051877)|positive regulation of multicellular organism growth (GO:0040018)|protein folding (GO:0006457)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|sensory perception of smell (GO:0007608)|social behavior (GO:0035176)|spermatid development (GO:0007286)|striatum development (GO:0021756)|vasodilation (GO:0042311)|visual perception (GO:0007601)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intracellular (GO:0005622)|motile cilium (GO:0031514)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)|unfolded protein binding (GO:0051082)			kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)|stomach(2)	16						ATCTGAGTACTACTAAAGTCC	0.413																																					p.S146R	Melanoma(79;1979 2212 6640)	Atlas-SNP	.											.	MKKS	35	.	0			c.A436C						PASS	.						93.0	88.0	90.0					20																	10393727		2203	4300	6503	SO:0001583	missense	8195	exon3			GAGTACTACTAAA	AF221993	CCDS13111.1	20p12	2013-01-08			ENSG00000125863	ENSG00000125863		"""Heat Shock Proteins / Chaperonins"""	7108	protein-coding gene	gene with protein product		604896		BBS6		9467007	Standard	NR_072977		Approved		uc002wnu.2	Q9NPJ1	OTTHUMG00000031868	ENST00000347364.3:c.436A>C	chr20.hg19:g.10393727T>G	ENSP00000246062:p.Ser146Arg	62.0	0.0	.		53.0	24.0	.	NM_170784	A8K7B0|D3DW18	Missense_Mutation	SNP	ENST00000347364.3	hg19	CCDS13111.1	.	.	.	.	.	.	.	.	.	.	T	7.604	0.673385	0.14776	.	.	ENSG00000125863	ENST00000347364;ENST00000399054	D;D	0.87650	-2.28;-2.28	5.63	3.29	0.37713	.	0.254278	0.51477	N	0.000093	T	0.80924	0.4717	L	0.41824	1.3	0.44603	D	0.99757	P	0.35011	0.48	B	0.35413	0.202	T	0.76767	-0.2838	10	0.62326	D	0.03	-36.1867	9.1713	0.37083	0.1233:0.0:0.1295:0.7473	.	146	Q9NPJ1	MKKS_HUMAN	R	146	ENSP00000246062:S146R;ENSP00000382008:S146R	ENSP00000246062:S146R	S	-	1	0	MKKS	10341727	0.997000	0.39634	0.001000	0.08648	0.008000	0.06430	4.565000	0.60836	0.449000	0.26747	0.477000	0.44152	AGT	.	.	.	none		0.413	MKKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077991.3		
ISM1	140862	hgsc.bcm.edu	37	20	13273028	13273028	+	Silent	SNP	A	A	G			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr20:13273028A>G	ENST00000262487.4	+	5	801	c.795A>G	c.(793-795)gaA>gaG	p.E265E	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	265						extracellular region (GO:0005576)				NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						TAGGAATTGAAGACACTTTTA	0.388																																					p.E265E		Atlas-SNP	.											.	ISM1	41	.	0			c.A795G						PASS	.						85.0	84.0	84.0					20																	13273028		1893	4122	6015	SO:0001819	synonymous_variant	140862	exon5			AATTGAAGACACT	AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"""chromosome 20 open reading frame 82"", ""isthmin 1 homolog (zebrafish)"""	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.795A>G	chr20.hg19:g.13273028A>G		91.0	0.0	.		67.0	27.0	.	NM_080826	Q8WVH9	Silent	SNP	ENST00000262487.4	hg19	CCDS46579.1																																																																																			.	.	.	none		0.388	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2		
PLXNB2	23654	hgsc.bcm.edu	37	22	50721158	50721158	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr22:50721158G>A	ENST00000449103.1	-	18	3109	c.2969C>T	c.(2968-2970)cCg>cTg	p.P990L	PLXNB2_ENST00000496720.1_5'Flank|PLXNB2_ENST00000359337.4_Missense_Mutation_p.P990L			O15031	PLXB2_HUMAN	plexin B2	990	IPT/TIG 3.				brain development (GO:0007420)|neural tube closure (GO:0001843)|neuroblast proliferation (GO:0007405)|positive regulation of axonogenesis (GO:0050772)|regulation of cell shape (GO:0008360)|regulation of neuron migration (GO:2001222)|regulation of protein phosphorylation (GO:0001932)|regulation of Rho GTPase activity (GO:0032319)|semaphorin-plexin signaling pathway (GO:0071526)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)	GTPase activator activity (GO:0005096)|semaphorin receptor activity (GO:0017154)	p.P1033R(1)		breast(2)|central_nervous_system(4)|cervix(2)|endometrium(11)|kidney(4)|large_intestine(3)|liver(1)|lung(20)|ovary(5)|prostate(6)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	66		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)		GCTTCGTAGCGGCTCGAAGGC	0.657																																					p.P990L		Atlas-SNP	.											PLXNB2,NS,carcinoma,0,1	PLXNB2	172	.	1	Substitution - Missense(1)	ovary(1)	c.C2969T						PASS	.						15.0	22.0	20.0					22																	50721158		1975	4135	6110	SO:0001583	missense	23654	exon18			CGTAGCGGCTCGA		CCDS43035.1	22q13.33	2008-06-12			ENSG00000196576	ENSG00000196576		"""Plexins"""	9104	protein-coding gene	gene with protein product		604293				10520995, 12183458	Standard	NM_012401		Approved	MM1, KIAA0315, PLEXB2	uc003bkv.4	O15031	OTTHUMG00000150219	ENST00000449103.1:c.2969C>T	chr22.hg19:g.50721158G>A	ENSP00000409171:p.Pro990Leu	111.0	0.0	.		121.0	57.0	.	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Missense_Mutation	SNP	ENST00000449103.1	hg19	CCDS43035.1	.	.	.	.	.	.	.	.	.	.	G	16.89	3.246268	0.59103	.	.	ENSG00000196576	ENST00000449103;ENST00000359337;ENST00000427829	D;D	0.89196	-2.48;-2.48	3.66	3.66	0.41972	Cell surface receptor IPT/TIG (2);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.51477	D	0.000082	D	0.93605	0.7958	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.94236	0.7481	10	0.87932	D	0	.	12.8931	0.58082	0.0:0.0:1.0:0.0	.	990	O15031	PLXB2_HUMAN	L	990;990;51	ENSP00000409171:P990L;ENSP00000352288:P990L	ENSP00000352288:P990L	P	-	2	0	PLXNB2	49063285	1.000000	0.71417	0.513000	0.27749	0.186000	0.23388	4.090000	0.57693	1.898000	0.54952	0.313000	0.20887	CCG	.	.	.	none		0.657	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
MAGIX	79917	hgsc.bcm.edu	37	X	49022721	49022721	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chrX:49022721G>A	ENST00000412696.2	+	6	988	c.988G>A	c.(988-990)Gga>Aga	p.G330R	MAGIX_ENST00000498742.1_3'UTR|MAGIX_ENST00000425661.2_Missense_Mutation_p.G254R|MAGIX_ENST00000376339.1_Missense_Mutation_p.G266R|MAGIX_ENST00000376338.3_Missense_Mutation_p.G271R	NM_024859.2	NP_079135.3	Q9H6Y5	MAGIX_HUMAN	MAGI family member, X-linked	330																	GATGGCAGCCGGAAGGCGGAG	0.711																																					p.G330R		Atlas-SNP	.											.	MAGIX	25	.	0			c.G988A						PASS	.						3.0	4.0	4.0					X																	49022721		1782	3702	5484	SO:0001583	missense	79917	exon6			GCAGCCGGAAGGC	AK025340	CCDS48106.1, CCDS48107.1, CCDS75976.1	Xp11.23	2014-05-06			ENSG00000017621	ENSG00000269313			30006	protein-coding gene	gene with protein product							Standard	XM_005278065		Approved	PDZX, JM10, FLJ21687	uc010nin.1	Q9H6Y5	OTTHUMG00000188218	ENST00000412696.2:c.988G>A	chrX.hg19:g.49022721G>A	ENSP00000387928:p.Gly330Arg	77.0	0.0	.		57.0	10.0	.	NM_024859	A6XND4|A8MSX9|B7WP26|Q14C81	Missense_Mutation	SNP	ENST00000412696.2	hg19	CCDS48106.1	.	.	.	.	.	.	.	.	.	.	.	17.51	3.406473	0.62399	.	.	ENSG00000017621	ENST00000376339;ENST00000425661;ENST00000412696;ENST00000376338	T;T;T;T	0.52754	0.8;1.11;0.66;0.65	4.06	1.19	0.21007	.	.	.	.	.	T	0.50684	0.1630	L	0.32530	0.975	0.24950	N	0.991796	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79784	0.989;0.983;0.993;0.993	T	0.35895	-0.9770	9	0.87932	D	0	1.7998	3.7223	0.08462	0.2326:0.0:0.5753:0.1921	.	254;330;266;271	F8WCY7;Q9H6Y5;Q9H6Y5-3;Q9H6Y5-2	.;MAGIX_HUMAN;.;.	R	266;254;330;271	ENSP00000365517:G266R;ENSP00000403515:G254R;ENSP00000387928:G330R;ENSP00000365516:G271R	ENSP00000365516:G271R	G	+	1	0	MAGIX	48909665	0.509000	0.26163	0.376000	0.26042	0.719000	0.41307	1.763000	0.38461	-0.009000	0.14296	0.538000	0.68166	GGA	.	.	.	none		0.711	MAGIX-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378832.1	NM_024859	
GABRQ	55879	hgsc.bcm.edu	37	X	151821371	151821371	+	Missense_Mutation	SNP	G	G	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chrX:151821371G>A	ENST00000370306.2	+	9	1546	c.1526G>A	c.(1525-1527)cGc>cAc	p.R509H		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	509					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|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)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.R509H(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TCGGATGAGCGCCATGGCCAT	0.542																																					p.R509H		Atlas-SNP	.											.	GABRQ	131	.	1	Substitution - Missense(1)	large_intestine(1)	c.G1526A						PASS	.						79.0	68.0	71.0					X																	151821371		2203	4300	6503	SO:0001583	missense	55879	exon9			ATGAGCGCCATGG	U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.1526G>A	chrX.hg19:g.151821371G>A	ENSP00000359329:p.Arg509His	90.0	0.0	.		97.0	81.0	.	NM_018558	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	hg19	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	9.142	1.013975	0.19277	.	.	ENSG00000147402	ENST00000370306	T	0.78707	-1.2	4.4	-0.308	0.12773	Neurotransmitter-gated ion-channel transmembrane domain (2);	4.416530	0.00424	N	0.000073	T	0.61173	0.2326	N	0.08118	0	0.09310	N	1	B	0.17038	0.02	B	0.09377	0.004	T	0.51585	-0.8687	10	0.44086	T	0.13	.	8.3332	0.32200	0.4021:0.0:0.5979:0.0	.	509	Q9UN88	GBRT_HUMAN	H	509	ENSP00000359329:R509H	ENSP00000359329:R509H	R	+	2	0	GABRQ	151572027	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-1.804000	0.01738	-0.229000	0.09854	-1.016000	0.02456	CGC	.	.	.	none		0.542	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2	NM_018558	
USP15	9958	hgsc.bcm.edu	37	12	62777661	62777667	+	Frame_Shift_Del	DEL	AGCAGCA	AGCAGCA	-	rs112510834		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	AGCAGCA	AGCAGCA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr12:62777661_62777667delAGCAGCA	ENST00000280377.5	+	10	1188_1194	c.1130_1136delAGCAGCA	c.(1129-1137)cagcagcaafs	p.QQQ377fs	USP15_ENST00000393654.3_Frame_Shift_Del_p.QQQ352fs|USP15_ENST00000353364.3_Frame_Shift_Del_p.QQQ348fs	NM_001252078.1	NP_001239007.1	Q9Y4E8	UBP15_HUMAN	ubiquitin specific peptidase 15	377	USP.				BMP signaling pathway (GO:0030509)|monoubiquitinated protein deubiquitination (GO:0035520)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|protein deubiquitination (GO:0016579)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|identical protein binding (GO:0042802)|SMAD binding (GO:0046332)|transforming growth factor beta receptor binding (GO:0005160)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(8)|lung(15)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	37			GBM - Glioblastoma multiforme(1;0.000276)	GBM - Glioblastoma multiforme(28;0.0622)		TCTGGATATCAGCAGCAAGACTGTCAA	0.353																																					p.377_379del	Melanoma(181;615 2041 39364 49691 50001)	Atlas-Indel,Pindel	.											.	USP15	105	.	0			c.1129_1135del						PASS	.																																			SO:0001589	frameshift_variant	9958	exon10			.	AB011101	CCDS8963.1, CCDS58250.1, CCDS58251.1	12q14	2006-07-18	2005-08-08					"""Ubiquitin-specific peptidases"""	12613	protein-coding gene	gene with protein product		604731	"""ubiquitin specific protease 15"""			12838346	Standard	NM_001252078		Approved	KIAA0529, UNPH4	uc001src.2	Q9Y4E8	OTTHUMG00000170186	ENST00000280377.5:c.1130_1136delAGCAGCA	chr12.hg19:g.62777661_62777667delAGCAGCA	ENSP00000280377:p.Gln377fs	88.0	0.0	0		89.0	28.0	0.314607	NM_001252078	Q08AL5|Q9H8G9|Q9HCA6|Q9UNP0|Q9Y5B5	Frame_Shift_Del	DEL	ENST00000280377.5	hg19	CCDS58251.1																																																																																			.	.	.	none		0.353	USP15-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407831.2	NM_006313	
ACN9	57001	hgsc.bcm.edu	37	7	96810419	96810420	+	Frame_Shift_Ins	INS	-	-	A	rs150372148		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:96810419_96810420insA	ENST00000432641.2	+	2	1404_1405	c.270_271insA	c.(271-273)aatfs	p.N91fs	ACN9_ENST00000360382.4_3'UTR|ACN9_ENST00000479853.1_3'UTR	NM_020186.2	NP_064571.1			ACN9 homolog (S. cerevisiae)											large_intestine(1)|lung(4)|ovary(1)|skin(1)|urinary_tract(3)	10	all_cancers(62;2.54e-08)|all_epithelial(64;2.24e-08)|Esophageal squamous(72;0.00507)|all_lung(186;0.154)|Lung NSC(181;0.159)					AAGAAAAACTTAATGACTTTCG	0.391																																					p.L90fs		Atlas-Indel,Pindel	.											.	ACN9	19	.	0			c.270_271insA						PASS	.																																			SO:0001589	frameshift_variant	57001	exon2			.	BC028409	CCDS5648.1	7q22.1	2006-02-09			ENSG00000196636	ENSG00000196636			21752	protein-coding gene	gene with protein product		615773					Standard	NM_020186		Approved	DC11	uc003uoo.4	Q9NRP4	OTTHUMG00000154064	ENST00000432641.2:c.272dupA	chr7.hg19:g.96810421_96810421dupA	ENSP00000414066:p.Asn91fs	410.0	0.0	0		924.0	671.0	0.72619	NM_020186		Frame_Shift_Ins	INS	ENST00000432641.2	hg19	CCDS5648.1																																																																																			.	.	.	none		0.391	ACN9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333685.3	NM_020186	
GABRB3	2562	hgsc.bcm.edu	37	15	26793258	26793258	+	Frame_Shift_Del	DEL	C	C	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:26793258delC	ENST00000311550.5	-	9	1215	c.1104delG	c.(1102-1104)ctgfs	p.L369fs	GABRB3_ENST00000400188.3_Frame_Shift_Del_p.L298fs|GABRB3_ENST00000299267.4_Frame_Shift_Del_p.L369fs|GABRB3_ENST00000545868.1_Frame_Shift_Del_p.L284fs|GABRB3_ENST00000541819.2_Frame_Shift_Del_p.L425fs	NM_000814.5|NM_001278631.1	NP_000805.1|NP_001265560.1	P28472	GBRB3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, beta 3	369					cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|cochlea development (GO:0090102)|inner ear receptor cell development (GO:0060119)|innervation (GO:0060384)|ion transmembrane transport (GO:0034220)|negative regulation of neuron apoptotic process (GO:0043524)|palate development (GO:0060021)|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)|GABA-A receptor complex (GO:1902711)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|GABA-gated chloride ion channel activity (GO:0022851)			NS(2)|breast(1)|central_nervous_system(1)|cervix(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|liver(1)|lung(41)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	68		all_cancers(20;1.89e-22)|all_lung(180;6.35e-15)|Breast(32;0.000279)|Colorectal(260;0.232)		all cancers(64;1.46e-07)|Epithelial(43;2.89e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0251)|COAD - Colon adenocarcinoma(236;0.235)|Lung(196;0.243)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Fospropofol(DB06716)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Ivermectin(DB00602)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Piperazine(DB00592)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GCGATGTCAACAGAATATTTC	0.448																																					p.L369X		Atlas-Indel,Pindel	.											.	GABRB3	338	.	0			c.1105delT						PASS	.						115.0	111.0	112.0					15																	26793258		2203	4300	6503	SO:0001589	frameshift_variant	2562	exon9			.		CCDS10018.1, CCDS10019.1, CCDS53920.1, CCDS53921.1	15q12	2012-06-22			ENSG00000166206	ENSG00000166206		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4083	protein-coding gene	gene with protein product	"""GABA(A) receptor, beta 3"""	137192					Standard	NM_000814		Approved		uc001zaz.3	P28472	OTTHUMG00000129231	ENST00000311550.5:c.1104delG	chr15.hg19:g.26793258delC	ENSP00000308725:p.Leu369fs	65.0	0.0	0		55.0	29.0	0.527273	NM_021912	B7Z2W1|B7Z825|F5H3D2|H7BYV8|Q14352|Q96FM5	Frame_Shift_Del	DEL	ENST00000311550.5	hg19	CCDS10019.1																																																																																			.	.	.	none		0.448	GABRB3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251352.2		
CYP2J2	1573	hgsc.bcm.edu	37	1	60370654	60370654	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:60370654delG	ENST00000371204.3	-	7	1123	c.1080delC	c.(1078-1080)cccfs	p.P360fs	CYP2J2_ENST00000492633.1_5'UTR	NM_000775.2	NP_000766.2	P51589	CP2J2_HUMAN	cytochrome P450, family 2, subfamily J, polypeptide 2	360					arachidonic acid metabolic process (GO:0019369)|epoxygenase P450 pathway (GO:0019373)|icosanoid metabolic process (GO:0006690)|linoleic acid metabolic process (GO:0043651)|regulation of heart contraction (GO:0008016)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	arachidonic acid 11,12-epoxygenase activity (GO:0008405)|arachidonic acid 14,15-epoxygenase activity (GO:0008404)|arachidonic acid epoxygenase activity (GO:0008392)|aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|linoleic acid epoxygenase activity (GO:0071614)			NS(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(15)|ovary(1)|skin(1)	26	all_cancers(7;0.000396)				Apixaban(DB06605)|Astemizole(DB00637)|Cholecalciferol(DB00169)|Levomilnacipran(DB08918)|Masoprocol(DB00179)|Rivaroxaban(DB06228)	CATTGGTGTAGGGCATGGACT	0.542																																					p.Y361fs		Atlas-Indel,Pindel	.											.	CYP2J2	34	.	0			c.1081delT						PASS	.						157.0	129.0	139.0					1																	60370654		2203	4300	6503	SO:0001589	frameshift_variant	1573	exon7			.	BC032594	CCDS613.1	1p31.3-p31.2	2008-02-05	2003-01-14		ENSG00000134716	ENSG00000134716		"""Cytochrome P450s"""	2634	protein-coding gene	gene with protein product		601258	"""cytochrome P450, subfamily IIJ (arachidonic acid epoxygenase) polypeptide 2"""			9570962	Standard	NM_000775		Approved		uc001czq.3	P51589	OTTHUMG00000008991	ENST00000371204.3:c.1080delC	chr1.hg19:g.60370654delG	ENSP00000360247:p.Pro360fs	89.0	0.0	0		76.0	26.0	0.342105	NM_000775	B2RD33|Q8TF13	Frame_Shift_Del	DEL	ENST00000371204.3	hg19	CCDS613.1																																																																																			.	.	.	none		0.542	CYP2J2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024940.1	NM_000775	
IL12RB2	3595	hgsc.bcm.edu	37	1	67816591	67816592	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr1:67816591_67816592insTA	ENST00000262345.1	+	9	1717_1718	c.1077_1078insTA	c.(1078-1080)tatfs	p.Y360fs	IL12RB2_ENST00000541374.1_Frame_Shift_Ins_p.Y360fs|IL12RB2_ENST00000544434.1_Frame_Shift_Ins_p.Y360fs|IL12RB2_ENST00000371000.1_Frame_Shift_Ins_p.Y360fs	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	360	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)	p.Y360H(1)		breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						AAATTCTCCACTATCAGGTGAC	0.47																																					p.H359fs		Atlas-Indel,Pindel	.											.	IL12RB2	94	.	1	Substitution - Missense(1)	lung(1)	c.1077_1078insTA						PASS	.																																			SO:0001589	frameshift_variant	3595	exon9			.	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1078_1079dupTA	chr1.hg19:g.67816592_67816593dupTA	ENSP00000262345:p.Tyr360fs	395.0	0.0	0		381.0	144.0	0.377953	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Frame_Shift_Ins	INS	ENST00000262345.1	hg19	CCDS638.1																																																																																			.	.	.	none		0.470	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
CHP1	11261	hgsc.bcm.edu	37	15	41555021	41555022	+	Frame_Shift_Ins	INS	-	-	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr15:41555021_41555022insA	ENST00000334660.5	+	4	529_530	c.289_290insA	c.(289-291)gaafs	p.E97fs	CHP1_ENST00000558351.1_3'UTR|CHP1_ENST00000560397.1_Frame_Shift_Ins_p.E97fs	NM_007236.4	NP_009167.1	Q99653	CHP1_HUMAN	calcineurin-like EF-hand protein 1	97	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion-dependent exocytosis (GO:0017156)|cellular response to acidic pH (GO:0071468)|cytoplasmic microtubule organization (GO:0031122)|membrane docking (GO:0022406)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|microtubule bundle formation (GO:0001578)|negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of phosphatase activity (GO:0010923)|negative regulation of protein autophosphorylation (GO:0031953)|negative regulation of protein import into nucleus (GO:0042308)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of protein ubiquitination (GO:0031397)|positive regulation of protein glycosylation (GO:0060050)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of protein transport (GO:0051222)|positive regulation of sodium:proton antiporter activity (GO:0032417)|potassium ion transport (GO:0006813)|protein export from nucleus (GO:0006611)|protein oligomerization (GO:0051259)|protein stabilization (GO:0050821)|regulation of intracellular pH (GO:0051453)|small GTPase mediated signal transduction (GO:0007264)|transcytosis (GO:0045056)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi membrane (GO:0000139)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|kinase binding (GO:0019900)|microtubule binding (GO:0008017)|potassium channel regulator activity (GO:0015459)|protein kinase inhibitor activity (GO:0004860)|transporter activity (GO:0005215)										TGAGGATAATGAAAAGAGCAAA	0.431																																					p.E97fs		Atlas-Indel,Pindel	.											.	.	.	.	0			c.289_290insA						PASS	.																																			SO:0001589	frameshift_variant	11261	exon4			.		CCDS10073.1	15q13.3	2013-01-11	2013-01-11		ENSG00000187446	ENSG00000187446		"""EF-hand domain containing"""	17433	protein-coding gene	gene with protein product	"""calcineurin homologous protein"""	606988				15987692, 20720019	Standard	NM_007236		Approved	Sid470p, CHP, SLC9A1BP, p22, p24	uc001znl.3	Q99653	OTTHUMG00000130233	ENST00000334660.5:c.293dupA	chr15.hg19:g.41555025_41555025dupA	ENSP00000335632:p.Glu97fs	190.0	0.0	0		236.0	84.0	0.355932	NM_007236	B2R6H9|Q6FHZ9	Frame_Shift_Ins	INS	ENST00000334660.5	hg19	CCDS10073.1																																																																																			.	.	.	none		0.431	CHP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252554.2	NM_007236	
PSG9	5678	hgsc.bcm.edu	37	19	43762353	43762353	+	Splice_Site	DEL	C	C	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:43762353delC	ENST00000270077.3	-	5	1340		c.e5+1		PSG9_ENST00000443718.3_Splice_Site|PSG9_ENST00000244293.7_Frame_Shift_Del_p.G322fs|PSG9_ENST00000593948.1_Splice_Site|PSG9_ENST00000291752.5_Splice_Site|PSG9_ENST00000418820.2_Splice_Site|PSG9_ENST00000596730.1_Frame_Shift_Del_p.G229fs	NM_002784.3	NP_002775.3	Q00887	PSG9_HUMAN	pregnancy specific beta-1-glycoprotein 9						female pregnancy (GO:0007565)	extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	41		Prostate(69;0.00682)				GATCCACTTACCAGAGACTTT	0.458																																					.		Atlas-Indel,Pindel	.											.	PSG9	77	.	0			c.1243+2G>-						PASS	.						134.0	157.0	149.0					19																	43762353		2139	4280	6419	SO:0001630	splice_region_variant	5678	exon6			.	M34481	CCDS12618.1	19q13.2	2013-01-29			ENSG00000183668	ENSG00000183668		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9526	protein-coding gene	gene with protein product		176398		PSG11		7806221	Standard	XM_005259076		Approved	PSGII	uc002owd.4	Q00887	OTTHUMG00000182826	ENST00000270077.3:c.1243+1G>-	chr19.hg19:g.43762353delC		73.0	0.0	0		110.0	48.0	0.436364	NM_002784	B2R869|Q15227|Q15236|Q15237|Q8WW78|Q9UQ73	Splice_Site	DEL	ENST00000270077.3	hg19	CCDS12618.1																																																																																			.	.	.	none		0.458	PSG9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323065.1	NM_002784	Intron
MIRLET7BHG	400931	hgsc.bcm.edu	37	22	46501743	46501744	+	3'UTR	DEL	CA	CA	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr22:46501743_46501744delCA	ENST00000381051.2	+	0	715_716				FLJ27365_ENST00000360737.3_Intron																							GTGGGGTGACCACAGGGCGGGG	0.644																																					.		Atlas-Indel,Pindel	.											.	.	.	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	400931	.			.																												ENST00000381051.2:c.*3CA>-	chr22.hg19:g.46501745_46501746delCA		19.0	0.0	0		39.0	16.0	0.410256	.		RNA	DEL	ENST00000381051.2	hg19																																																																																				.	.	.	none		0.644	FLJ27365-003	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316783.1		
TULP4	56995	hgsc.bcm.edu	37	6	158882608	158882629	+	Frame_Shift_Del	DEL	GTGGTGCACACAGGGGGACTTG	GTGGTGCACACAGGGGGACTTG	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GTGGTGCACACAGGGGGACTTG	GTGGTGCACACAGGGGGACTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr6:158882608_158882629delGTGGTGCACACAGGGGGACTTG	ENST00000367097.3	+	6	2230_2251	c.873_894delGTGGTGCACACAGGGGGACTTG	c.(871-894)cagtggtgcacacagggggacttgfs	p.QWCTQGDL291fs	TULP4_ENST00000367094.2_Frame_Shift_Del_p.QWCTQGDL291fs	NM_020245.4	NP_064630.2	Q9NRJ4	TULP4_HUMAN	tubby like protein 4	291					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to nutrient (GO:0007584)	cytoplasm (GO:0005737)	sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(7)|kidney(2)|large_intestine(15)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	49		Breast(66;0.000781)|Ovarian(120;0.0308)|Lung SC(201;0.164)|Prostate(117;0.171)		OV - Ovarian serous cystadenocarcinoma(65;1.64e-18)|BRCA - Breast invasive adenocarcinoma(81;2.67e-05)		TGGTAGCCCAGTGGTGCACACAGGGGGACTTGCTGGCAGTCG	0.55																																					p.291_298del		Atlas-Indel,Pindel	.											.	TULP4	137	.	0			c.872_893del						PASS	.																																			SO:0001589	frameshift_variant	56995	exon6			.		CCDS34561.1, CCDS34562.1	6q25-q26	2013-01-10			ENSG00000130338	ENSG00000130338		"""WD repeat domain containing"""	15530	protein-coding gene	gene with protein product						11595174	Standard	NM_020245		Approved	TUSP, KIAA1397	uc003qrf.3	Q9NRJ4	OTTHUMG00000015910	ENST00000367097.3:c.873_894delGTGGTGCACACAGGGGGACTTG	chr6.hg19:g.158882608_158882629delGTGGTGCACACAGGGGGACTTG	ENSP00000356064:p.Gln291fs	46.0	0.0	0		41.0	15.0	0.365854	NM_001007466	Q5T3M2|Q5T3M3|Q9HD22|Q9P2F0	Frame_Shift_Del	DEL	ENST00000367097.3	hg19	CCDS34561.1																																																																																			.	.	.	none		0.550	TULP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042869.1	NM_020245	
ARHGEF40	55701	hgsc.bcm.edu	37	14	21543506	21543506	+	Frame_Shift_Del	DEL	A	A	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr14:21543506delA	ENST00000298694.4	+	4	1593	c.1466delA	c.(1465-1467)gaafs	p.E489fs	ARHGEF40_ENST00000298693.3_Frame_Shift_Del_p.E489fs			Q8TER5	ARH40_HUMAN	Rho guanine nucleotide exchange factor (GEF) 40	489						cytoplasm (GO:0005737)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			large_intestine(4)|ovary(3)|upper_aerodigestive_tract(2)	9						ACAGGCCCAGAAGGCCCCCTG	0.552																																					p.E489fs		Atlas-Indel,Pindel	.											.	ARHGEF40	84	.	0			c.1465delG						PASS	.						117.0	121.0	120.0					14																	21543506		2203	4300	6503	SO:0001589	frameshift_variant	55701	exon4			.		CCDS32041.1	14q11.2	2012-07-24			ENSG00000165801	ENSG00000165801		"""Rho guanine nucleotide exchange factors"""	25516	protein-coding gene	gene with protein product		610018				16143467	Standard	NM_001278529		Approved	solo, FLJ10357	uc001vzp.3	Q8TER5		ENST00000298694.4:c.1466delA	chr14.hg19:g.21543506delA	ENSP00000298694:p.Glu489fs	120.0	0.0	0		128.0	52.0	0.40625	NM_018071	A5PL07|Q9BWP5|Q9H7L6|Q9NTF9|Q9NW24	Frame_Shift_Del	DEL	ENST00000298694.4	hg19	CCDS32041.1																																																																																			.	.	.	none		0.552	ARHGEF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413122.1		
CUBN	8029	hgsc.bcm.edu	37	10	17113553	17113554	+	Frame_Shift_Ins	INS	-	-	A			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr10:17113553_17113554insA	ENST00000377833.4	-	19	2561_2562	c.2496_2497insT	c.(2494-2499)tttcctfs	p.P833fs		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	833	CUB 4. {ECO:0000255|PROSITE- ProRule:PRU00059}.				cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)	p.P833S(1)		breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	TACACGTTAGGAAAAAAAGGCG	0.416																																					p.P833fs		Atlas-Indel,Pindel	.											CUBN,NS,carcinoma,0,1	CUBN	515	.	1	Substitution - Missense(1)	lung(1)	c.2497_2498insT						PASS	.																																			SO:0001589	frameshift_variant	8029	exon19			.	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.2497dupT	chr10.hg19:g.17113560_17113560dupA	ENSP00000367064:p.Pro833fs	62.0	0.0	0		42.0	11.0	0.261905	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Frame_Shift_Ins	INS	ENST00000377833.4	hg19	CCDS7113.1																																																																																			.	.	.	none		0.416	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
CALCR	799	hgsc.bcm.edu	37	7	93090259	93090259	+	Splice_Site	DEL	C	C	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:93090259delC	ENST00000394441.1	-	7	837	c.522delG	c.(520-522)agg>ag	p.R174fs	CALCR_ENST00000421592.1_Splice_Site_p.L190fs|CALCR_ENST00000426151.1_Splice_Site_p.R174fs|CALCR_ENST00000360249.4_Splice_Site_p.L190fs|CALCR_ENST00000359558.2_Splice_Site_p.L208fs	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor	192					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	AGCCAAGGCTCCTGGAAGAAA	0.348																																					p.S209fs		Atlas-INDEL	.											.	CALCR	200	.	0			c.625delA						PASS	.						100.0	100.0	100.0					7																	93090259		2203	4300	6503	SO:0001630	splice_region_variant	799	exon10			.	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.522-1G>-	chr7.hg19:g.93090259delC		108.0	0.0	0		168.0	26.0	0.154762	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Frame_Shift_Del	DEL	ENST00000394441.1	hg19	CCDS5631.1																																																																																			.	.	.	none		0.348	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	Frame_Shift_Del
ZNF423	23090	hgsc.bcm.edu	37	16	49672690	49672690	+	Frame_Shift_Del	DEL	G	G	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:49672690delG	ENST00000561648.1	-	4	426	c.373delC	c.(373-375)ctcfs	p.L125fs	ZNF423_ENST00000562871.1_Frame_Shift_Del_p.L65fs|ZNF423_ENST00000535559.1_Frame_Shift_Del_p.L8fs|ZNF423_ENST00000563137.2_Frame_Shift_Del_p.L65fs|ZNF423_ENST00000562520.1_Frame_Shift_Del_p.L65fs|ZNF423_ENST00000567169.1_Frame_Shift_Del_p.L8fs|ZNF423_ENST00000262383.2_Frame_Shift_Del_p.L125fs	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	125					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				CCGAGGCCGAGGTCACAACCA	0.602																																					p.L125fs		Atlas-INDEL	.											.	ZNF423	463	.	0			c.374delT						PASS	.						64.0	60.0	61.0					16																	49672690		2198	4300	6498	SO:0001589	frameshift_variant	23090	exon4			.	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.373delC	chr16.hg19:g.49672690delG	ENSP00000455426:p.Leu125fs	59.0	0.0	0		60.0	22.0	0.366667	NM_015069	O94860|Q76N04|Q9NZ13	Frame_Shift_Del	DEL	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.	.	none		0.602	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
ZNF423	23090	hgsc.bcm.edu	37	16	49672693	49672695	+	In_Frame_Del	DEL	CAC	CAC	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CAC	CAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:49672693_49672695delCAC	ENST00000561648.1	-	4	421_423	c.368_370delGTG	c.(367-372)tgtgac>tac	p.123_124CD>Y	ZNF423_ENST00000562871.1_In_Frame_Del_p.63_64CD>Y|ZNF423_ENST00000535559.1_In_Frame_Del_p.6_7CD>Y|ZNF423_ENST00000563137.2_In_Frame_Del_p.63_64CD>Y|ZNF423_ENST00000562520.1_In_Frame_Del_p.63_64CD>Y|ZNF423_ENST00000567169.1_In_Frame_Del_p.6_7CD>Y|ZNF423_ENST00000262383.2_In_Frame_Del_p.123_124CD>Y	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	123					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				AGGCCGAGGTCACAACCATCTCC	0.596																																					p.123_124del		Atlas-INDEL	.											.	ZNF423	463	.	0			c.369_371del						PASS	.																																			SO:0001651	inframe_deletion	23090	exon4			.	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.368_370delGTG	chr16.hg19:g.49672693_49672695delCAC	ENSP00000455426:p.Cys123_Asp124delinsTyr	56.0	0.0	0		58.0	22.0	0.37931	NM_015069	O94860|Q76N04|Q9NZ13	In_Frame_Del	DEL	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.	.	none		0.596	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
CALCR	799	hgsc.bcm.edu	37	7	93090262	93090267	+	Intron	DEL	GGAAGA	GGAAGA	-	rs375917807		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GGAAGA	GGAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:93090262_93090267delGGAAGA	ENST00000394441.1	-	7	837				CALCR_ENST00000421592.1_Intron|CALCR_ENST00000426151.1_Intron|CALCR_ENST00000360249.4_Intron|CALCR_ENST00000359558.2_Intron	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor						adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	CAAGGCTCCTGGAAGAAAAAGTAACA	0.34																																					.		Atlas-INDEL	.											.	CALCR	200	.	0			.						PASS	.																																			SO:0001627	intron_variant	799	.			.	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.522-3TCTTCC>-	chr7.hg19:g.93090262_93090267delGGAAGA		108.0	0.0	0		161.0	25.0	0.15528	.	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Splice_Site	DEL	ENST00000394441.1	hg19	CCDS5631.1																																																																																			.	.	.	none		0.340	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	
TRIM13	10206	hgsc.bcm.edu	37	13	50588476	50588477	+	3'UTR	INS	-	-	T	rs367601390		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr13:50588476_50588477insT	ENST00000378182.3	+	0	3138_3139				KCNRG_ENST00000360473.4_5'Flank|KCNRG_ENST00000312942.1_5'Flank|TRIM13_ENST00000478111.1_Intron	NM_001007278.1|NM_005798.3|NM_052811.2|NM_213590.1	NP_001007279.1|NP_005789.2|NP_434698.1|NP_998755.1	O60858	TRI13_HUMAN	tripartite motif containing 13						anatomical structure morphogenesis (GO:0009653)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|innate immune response (GO:0045087)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell death (GO:0010942)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of macroautophagy (GO:0016239)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein autoubiquitination (GO:0051865)|response to gamma radiation (GO:0010332)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|perinuclear endoplasmic reticulum (GO:0097038)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(2)|ovary(2)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(7;3.41e-06)|Lung NSC(96;3.08e-05)|Breast(56;9.7e-05)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)		GBM - Glioblastoma multiforme(99;1.53e-10)|COAD - Colon adenocarcinoma(199;0.205)		aaaaaaaaaaaaaaaatatata	0.297																																					.		Atlas-INDEL	.											.	TRIM13	30	.	0			.						PASS	.																																			SO:0001624	3_prime_UTR_variant	10206	.			.	AF220127	CCDS9423.1, CCDS41888.1	13q14	2013-01-09	2011-01-25	2006-09-26	ENSG00000204977	ENSG00000204977		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	9976	protein-coding gene	gene with protein product		605661	"""ret finger protein 2"", ""tripartite motif-containing 13"""	RFP2		9599022	Standard	NM_213590		Approved	Leu5, RNF77, DLEU5	uc001vdp.1	O60858	OTTHUMG00000016926	ENST00000378182.3:c.*1177->T	chr13.hg19:g.50588476_50588477insT		26.0	0.0	0		28.0	13.0	0.464286	.	B2RB49|Q5UBW0|Q5W0U8|Q5W0U9|Q9BQ47|Q9C021	RNA	INS	ENST00000378182.3	hg19	CCDS9423.1																																																																																			.	.	.	none		0.297	TRIM13-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354875.1	NM_001007278	
TNRC18	84629	hgsc.bcm.edu	37	7	5352473	5352476	+	Frame_Shift_Del	DEL	ATCG	ATCG	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	ATCG	ATCG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:5352473_5352476delATCG	ENST00000430969.1	-	27	8394_8397	c.8046_8049delCGAT	c.(8044-8049)gacgatfs	p.DD2682fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.DD2682fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2682							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		GGGCTGCCTCATCGTCCGAGCTGC	0.691																																					p.2683_2684del		Atlas-Indel,Pindel	.											.	TNRC18	311	.	0			c.8047_8050del						PASS	.																																			SO:0001589	frameshift_variant	84629	exon27			.	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8046_8049delCGAT	chr7.hg19:g.5352473_5352476delATCG	ENSP00000395538:p.Asp2682fs	83.0	0.0	0		101.0	47.0	0.465347	NM_001080495	A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	hg19	CCDS47534.1																																																																																			.	.	.	none		0.691	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
CALCR	799	hgsc.bcm.edu	37	7	93090260	93090267	+	Splice_Site	DEL	CTGGAAGA	CTGGAAGA	-	rs375917807		TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	CTGGAAGA	CTGGAAGA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr7:93090260_93090267delCTGGAAGA	ENST00000394441.1	-	7	837		c.e7-1		CALCR_ENST00000421592.1_Splice_Site|CALCR_ENST00000426151.1_Splice_Site|CALCR_ENST00000360249.4_Splice_Site|CALCR_ENST00000359558.2_Splice_Site	NM_001164738.1	NP_001158210.1	P30988	CALCR_HUMAN	calcitonin receptor						adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|response to glucocorticoid (GO:0051384)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcitonin binding (GO:0032841)|calcitonin receptor activity (GO:0004948)|protein transporter activity (GO:0008565)|receptor activity (GO:0004872)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(3)	45	all_cancers(62;3.18e-12)|all_epithelial(64;1.34e-11)|Breast(17;0.000675)|Lung NSC(181;0.207)		STAD - Stomach adenocarcinoma(171;0.000244)		Pramlintide(DB01278)|Salmon Calcitonin(DB00017)	GCCAAGGCTCCTGGAAGAAAAAGTAACA	0.346																																					p.208_208del		Pindel	.											.,2	CALCR	200	.	0			c.624_624del						PASS	.																																			SO:0001630	splice_region_variant	799	exon10			.	L00587	CCDS5631.1, CCDS55125.1	7q21.3	2012-08-10			ENSG00000004948	ENSG00000004948		"""GPCR / Class B : Calcitonin receptors"""	1440	protein-coding gene	gene with protein product		114131				1331173	Standard	NM_001742		Approved	CTR	uc003umw.2	P30988	OTTHUMG00000023599	ENST00000394441.1:c.522-1TCTTCCAG>-	chr7.hg19:g.93090260_93090267delCTGGAAGA		107.0	0.0	.		163.0	23.0	0.141	NM_001164737	A4D1G6|F5H605|O14585|Q13941|Q5ZGL8|Q659U6|Q6DJU8|Q6T712	Frame_Shift_Del	DEL	ENST00000394441.1	hg19	CCDS5631.1																																																																																			.	.	.	none		0.346	CALCR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254661.2	NM_001742	Intron
NOTCH3	4854	hgsc.bcm.edu	37	19	15288556	15288567	+	In_Frame_Del	DEL	TGGCCTGGCAGG	TGGCCTGGCAGG	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	TGGCCTGGCAGG	TGGCCTGGCAGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr19:15288556_15288567delTGGCCTGGCAGG	ENST00000263388.2	-	24	4247_4258	c.4172_4183delCCTGCCAGGCCA	c.(4171-4185)gcctgccaggccaag>gag	p.1391_1395ACQAK>E		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	1391					forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			TCCCCGCGCTTGGCCTGGCAGGCGGCGCGCGG	0.778																																					p.1391_1395del		Pindel	.											.	NOTCH3	340	.	0			c.4173_4184del						PASS	.																																			SO:0001651	inframe_deletion	4854	exon24			.	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.4172_4183delCCTGCCAGGCCA	chr19.hg19:g.15288556_15288567delTGGCCTGGCAGG	ENSP00000263388:p.Ala1391_Lys1395delinsGlu	97.0	0.0	.		94.0	21.0	0.223	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	In_Frame_Del	DEL	ENST00000263388.2	hg19	CCDS12326.1																																																																																			.	.	.	none		0.778	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
ZNF423	23090	hgsc.bcm.edu	37	16	49672691	49672695	+	Frame_Shift_Del	DEL	GTCAC	GTCAC	-			TCGA-P4-AAVL-01A-11D-A42J-10	TCGA-P4-AAVL-11A-11D-A42M-10	GTCAC	GTCAC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	8b18e7e6-d0a7-4c8a-bfb9-9506aa7053e4	fb226698-844d-4a24-86c2-29571549b9bb	g.chr16:49672691_49672695delGTCAC	ENST00000561648.1	-	4	421_425	c.368_372delGTGAC	c.(367-372)tgtgacfs	p.CD123fs	ZNF423_ENST00000562871.1_Frame_Shift_Del_p.CD63fs|ZNF423_ENST00000535559.1_Frame_Shift_Del_p.CD6fs|ZNF423_ENST00000563137.2_Frame_Shift_Del_p.CD63fs|ZNF423_ENST00000562520.1_Frame_Shift_Del_p.CD63fs|ZNF423_ENST00000567169.1_Frame_Shift_Del_p.CD6fs|ZNF423_ENST00000262383.2_Frame_Shift_Del_p.CD123fs	NM_001271620.1	NP_001258549.1	Q2M1K9	ZN423_HUMAN	zinc finger protein 423	123					cell differentiation (GO:0030154)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(6)|large_intestine(16)|lung(47)|ovary(1)|pancreas(2)|prostate(4)|skin(1)|urinary_tract(2)	89		all_cancers(37;0.0155)				CGAGGCCGAGGTCACAACCATCTCC	0.6																																					p.123_125del		Pindel	.											.	ZNF423	463	.	0			c.369_373del						PASS	.																																			SO:0001589	frameshift_variant	23090	exon4			.	AB018303	CCDS32445.1, CCDS61930.1	16q12	2014-01-28				ENSG00000102935		"""Zinc fingers, C2H2-type"""	16762	protein-coding gene	gene with protein product	"""OLF-1/EBF associated zinc finger gene"", "" Smad- and Olf-interacting zinc finger protein"", ""early B-cell factor associated zinc finger protein"""	604557				9872452, 10660046	Standard	NM_001271620		Approved	KIAA0760, OAZ, Roaz, Ebfaz, Zfp104, NPHP14, JBTS19	uc031qwd.1	Q2M1K9		ENST00000561648.1:c.368_372delGTGAC	chr16.hg19:g.49672691_49672695delGTCAC	ENSP00000455426:p.Cys123fs	58.0	0.0	.		60.0	20.0	0.333	NM_015069	O94860|Q76N04|Q9NZ13	Frame_Shift_Del	DEL	ENST00000561648.1	hg19	CCDS32445.1																																																																																			.	.	.	none		0.600	ZNF423-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000423258.1	NM_015069	
