#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
PRAMEF12	390999	hgsc.bcm.edu	37	1	12835789	12835789	+	Nonsense_Mutation	SNP	C	C	T	rs201386508		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:12835789C>T	ENST00000357726.4	+	2	418	c.391C>T	c.(391-393)Cga>Tga	p.R131*		NM_001080830.1	NP_001074299.1	O95522	PRA12_HUMAN	PRAME family member 12	131					negative regulation of apoptotic process (GO:0043066)|negative regulation of cell differentiation (GO:0045596)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cell proliferation (GO:0008284)					NS(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(9)|ovary(3)|skin(1)|urinary_tract(1)	23	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00143)|all_lung(284;0.00181)|Colorectal(325;0.00215)|Breast(348;0.0042)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0623)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00818)|Colorectal(212;5.04e-06)|Kidney(185;4.99e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000198)|COAD - Colon adenocarcinoma(227;0.000245)|BRCA - Breast invasive adenocarcinoma(304;0.000295)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		GAGTAAGAGACGAACAGCAGG	0.542																																					p.R131X		Atlas-SNP	.											.	PRAMEF12	69	.	0			c.C391T						PASS	.	C	stop/ARG	1,4345		0,1,2172	109.0	123.0	118.0		391	-2.5	0.0	1		118	0,8588		0,0,4294	no	stop-gained	PRAMEF12	NM_001080830.1		0,1,6466	TT,TC,CC		0.0,0.023,0.0077		131/484	12835789	1,12933	2173	4294	6467	SO:0001587	stop_gained	390999	exon2			AAGAGACGAACAG		CCDS41254.1	1p36.21	2013-01-17			ENSG00000116726	ENSG00000116726		"""-"""	22125	protein-coding gene	gene with protein product							Standard	NM_001080830		Approved	OTTHUMG00000001927	uc001aui.3	O95522	OTTHUMG00000001927	ENST00000357726.4:c.391C>T	chr1.hg19:g.12835789C>T	ENSP00000350358:p.Arg131*	137.0	0.0	.		126.0	49.0	.	NM_001080830		Nonsense_Mutation	SNP	ENST00000357726.4	hg19	CCDS41254.1	.	.	.	.	.	.	.	.	.	.	.	14.34	2.507496	0.44558	2.3E-4	0.0	ENSG00000116726	ENST00000357726	.	.	.	2.8	-2.45	0.06481	.	6.292790	0.00896	N	0.002291	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.30078	T	0.28	.	5.4193	0.16392	0.3728:0.2852:0.3419:0.0	.	.	.	.	X	131	.	ENSP00000350358:R131X	R	+	1	2	PRAMEF12	12758376	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-2.908000	0.00700	-0.506000	0.06558	0.313000	0.20887	CGA	.	C|0.999;A|0.001	.	alt		0.542	PRAMEF12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005457.1	XM_372760	
MYCL	4610	hgsc.bcm.edu	37	1	40366677	40366677	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:40366677C>T	ENST00000372816.2	-	1	877	c.430G>A	c.(430-432)Gcc>Acc	p.A144T	MYCL_ENST00000372815.1_Missense_Mutation_p.A174T|MYCL_ENST00000397332.2_Missense_Mutation_p.A174T|MYCL_ENST00000429311.1_Missense_Mutation_p.A144T|RP1-118J21.5_ENST00000418255.1_RNA			P12524	MYCL_HUMAN	v-myc avian myelocytomatosis viral oncogene lung carcinoma derived homolog	144						nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										GGACAGGGGGCGGCGGGCGCC	0.761																																					p.A174T		Atlas-SNP	.											.	MYCL1	36	.	0			c.G520A						PASS	.																																			SO:0001583	missense	4610	exon2			AGGGGGCGGCGGG		CCDS30682.1, CCDS44117.1, CCDS44117.2, CCDS53300.1	1p34.3	2013-07-09	2013-07-09	2013-07-09	ENSG00000116990	ENSG00000116990		"""Basic helix-loop-helix proteins"""	7555	protein-coding gene	gene with protein product	"""l-myc protein"", ""myc-related gene from lung cancer"", ""oncogene lmyc"""	164850	"""v-myc avian myelocytomatosis viral oncogene homolog 1, lung carcinoma derived"""	MYCL1		8978772	Standard	NM_001033082		Approved	LMYC, bHLHe38	uc001cer.2	P12524	OTTHUMG00000009243	ENST00000372816.2:c.430G>A	chr1.hg19:g.40366677C>T	ENSP00000361903:p.Ala144Thr	1.0	0.0	.		7.0	4.0	.	NM_005376	A2A2C9|B4DJH2|Q14897|Q5QPL0|Q5QPL1|Q9NUE9	Missense_Mutation	SNP	ENST00000372816.2	hg19	CCDS30682.1	.	.	.	.	.	.	.	.	.	.	C	11.68	1.711171	0.30322	.	.	ENSG00000116990	ENST00000397332;ENST00000372816;ENST00000372815;ENST00000429311	T;T;T;T	0.78003	-0.93;-1.14;1.92;1.51	5.05	1.59	0.23543	.	0.621427	0.17026	N	0.189921	T	0.57814	0.2079	N	0.22421	0.69	0.22531	N	0.999018	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.003	T	0.44050	-0.9353	10	0.41790	T	0.15	-27.6027	2.4699	0.04561	0.233:0.4938:0.1472:0.126	.	144;144	P12524-2;P12524	.;MYCL1_HUMAN	T	174;144;174;144	ENSP00000380494:A174T;ENSP00000361903:A144T;ENSP00000361902:A174T;ENSP00000389358:A144T	ENSP00000361902:A174T	A	-	1	0	MYCL1	40139264	0.999000	0.42202	1.000000	0.80357	0.982000	0.71751	1.103000	0.31062	0.575000	0.29434	0.563000	0.77884	GCC	.	.	.	none		0.761	MYCL-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277004.1	NM_001033082	
FOXD2	2306	hgsc.bcm.edu	37	1	47905224	47905224	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:47905224G>A	ENST00000334793.5	+	1	3536	c.1417G>A	c.(1417-1419)Ggg>Agg	p.G473R		NM_004474.3	NP_004465.3	O60548	FOXD2_HUMAN	forkhead box D2	473					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			lung(4)	4				READ - Rectum adenocarcinoma(2;0.0908)		CTCGCATCCCGGGGACGCGCT	0.701																																					p.G473R		Atlas-SNP	.											FOXD2,caecum,carcinoma,0,1	FOXD2	16	.	0			c.G1417A						PASS	.						5.0	6.0	6.0					1																	47905224		2116	4208	6324	SO:0001583	missense	2306	exon1			CATCCCGGGGACG	AF042832	CCDS30708.1	1p34-p32	2008-02-05			ENSG00000186564	ENSG00000186564		"""Forkhead boxes"""	3803	protein-coding gene	gene with protein product		602211		FKHL17		9403061, 12621056	Standard	NM_004474		Approved	FREAC9	uc001crm.3	O60548	OTTHUMG00000007950	ENST00000334793.5:c.1417G>A	chr1.hg19:g.47905224G>A	ENSP00000335493:p.Gly473Arg	11.0	0.0	.		34.0	21.0	.	NM_004474	Q5SVZ3	Missense_Mutation	SNP	ENST00000334793.5	hg19	CCDS30708.1	.	.	.	.	.	.	.	.	.	.	G	15.97	2.990550	0.54041	.	.	ENSG00000186564	ENST00000334793	T	0.61627	0.09	4.99	4.06	0.47325	.	0.529712	0.18195	U	0.148720	T	0.32010	0.0815	N	0.14661	0.345	0.28578	N	0.910271	P	0.38992	0.653	B	0.19946	0.027	T	0.31052	-0.9957	10	0.51188	T	0.08	.	9.9291	0.41512	0.0969:0.0:0.9031:0.0	.	473	O60548	FOXD2_HUMAN	R	473	ENSP00000335493:G473R	ENSP00000335493:G473R	G	+	1	0	FOXD2	47677811	0.000000	0.05858	1.000000	0.80357	0.936000	0.57629	0.303000	0.19210	2.280000	0.76307	0.561000	0.74099	GGG	.	.	.	none		0.701	FOXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021831.1	NM_004474	
PRDX6	9588	hgsc.bcm.edu	37	1	173454563	173454563	+	Missense_Mutation	SNP	A	A	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:173454563A>G	ENST00000340385.5	+	3	448	c.316A>G	c.(316-318)Agg>Ggg	p.R106G	PRDX6_ENST00000470017.1_3'UTR	NM_004905.2	NP_004896.1	P30041	PRDX6_HUMAN	peroxiredoxin 6	106	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.				hydrogen peroxide catabolic process (GO:0042744)|phospholipid catabolic process (GO:0009395)|response to oxidative stress (GO:0006979)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|membrane (GO:0016020)	antioxidant activity (GO:0016209)|glutathione peroxidase activity (GO:0004602)|peroxiredoxin activity (GO:0051920)|phospholipase A2 activity (GO:0004623)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(5)|urinary_tract(1)	12						CATCGATGATAGGAATCGGGA	0.453																																					p.R106G		Atlas-SNP	.											.	PRDX6	20	.	0			c.A316G						PASS	.						141.0	133.0	136.0					1																	173454563		2203	4300	6503	SO:0001583	missense	9588	exon3			GATGATAGGAATC	D14662	CCDS1307.1	1q24.1	2008-02-05			ENSG00000117592	ENSG00000117592			16753	protein-coding gene	gene with protein product		602316				11233154	Standard	NM_004905		Approved	AOP2, KIAA0106, 1-Cys, NSGPx, PRX, aiPLA2, MGC46173, p29	uc001giy.1	P30041	OTTHUMG00000034804	ENST00000340385.5:c.316A>G	chr1.hg19:g.173454563A>G	ENSP00000342026:p.Arg106Gly	132.0	0.0	.		109.0	44.0	.	NM_004905	A8JZY7|P32077|Q5TAH4|Q5ZEZ8	Missense_Mutation	SNP	ENST00000340385.5	hg19	CCDS1307.1	.	.	.	.	.	.	.	.	.	.	A	5.323	0.244994	0.10077	.	.	ENSG00000117592	ENST00000340385	T	0.30182	1.54	5.27	1.5	0.22942	Alkyl hydroperoxide reductase subunit C/ Thiol specific antioxidant (1);Thioredoxin-like fold (3);	0.924235	0.09408	N	0.806253	T	0.05318	0.0141	N	0.13299	0.325	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35847	-0.9772	10	0.35671	T	0.21	-4.8805	2.931	0.05800	0.3634:0.413:0.086:0.1375	.	106	P30041	PRDX6_HUMAN	G	106	ENSP00000342026:R106G	ENSP00000342026:R106G	R	+	1	2	PRDX6	171721186	0.000000	0.05858	0.966000	0.40874	0.149000	0.21700	0.209000	0.17435	0.911000	0.36747	0.528000	0.53228	AGG	.	.	.	none		0.453	PRDX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084222.1	NM_004905	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232600607	232600607	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:232600607C>G	ENST00000366630.1	-	8	3157	c.2799G>C	c.(2797-2799)agG>agC	p.R933S	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.R933S|SIPA1L2_ENST00000308942.4_5'Flank			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	933					regulation of small GTPase mediated signal transduction (GO:0051056)		GTPase activator activity (GO:0005096)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(13)|lung(49)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	103		all_cancers(173;0.00605)|Prostate(94;0.128)|all_epithelial(177;0.186)				GAACAATTTCCCTGATGTCTT	0.408																																					p.R933S		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.G2799C						PASS	.						63.0	58.0	60.0					1																	232600607		1902	4124	6026	SO:0001583	missense	57568	exon7			AATTTCCCTGATG	AB037810	CCDS41474.1	1q42.2	2008-02-05			ENSG00000116991	ENSG00000116991			23800	protein-coding gene	gene with protein product		611609					Standard	NM_020808		Approved	KIAA1389	uc001hvg.3	Q9P2F8	OTTHUMG00000037820	ENST00000366630.1:c.2799G>C	chr1.hg19:g.232600607C>G	ENSP00000355589:p.Arg933Ser	110.0	0.0	.		95.0	37.0	.	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	hg19	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	C	12.18	1.859942	0.32884	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.79554	-1.28;-1.28	6.07	1.09	0.20402	.	0.000000	0.85682	D	0.000000	T	0.81163	0.4765	L	0.52759	1.655	0.51233	D	0.999913	P	0.51351	0.944	P	0.55455	0.776	T	0.77197	-0.2676	10	0.46703	T	0.11	-29.1302	10.0474	0.42195	0.0:0.3607:0.0:0.6393	.	933	Q9P2F8	SI1L2_HUMAN	S	933	ENSP00000355589:R933S;ENSP00000262861:R933S	ENSP00000262861:R933S	R	-	3	2	SIPA1L2	230667230	0.443000	0.25641	0.814000	0.32528	0.705000	0.40729	-0.151000	0.10175	-0.062000	0.13088	-0.136000	0.14681	AGG	.	.	.	none		0.408	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
SNTG2	54221	hgsc.bcm.edu	37	2	1241762	1241763	+	Missense_Mutation	DNP	CA	CA	AT			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C|A	C|A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:1241762_1241763CA>AT	ENST00000308624.5	+	10	951_952	c.822_823CA>AT	c.(820-825)gcCAac>gcATac	p.N275Y	SNTG2_ENST00000407292.1_Missense_Mutation_p.N148Y	NM_018968.3	NP_061841.2	Q9NY99	SNTG2_HUMAN	syntrophin, gamma 2	275					central nervous system development (GO:0007417)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|syntrophin complex (GO:0016013)	PDZ domain binding (GO:0030165)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(9)|lung(20)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.0797)	all_cancers(51;0.00469)		all cancers(51;0.0178)|OV - Ovarian serous cystadenocarcinoma(76;0.07)|Epithelial(75;0.0864)|GBM - Glioblastoma multiforme(21;0.173)		CGGTCTCAGCCAACATCAGGGA	0.55																																					p.A274A|p.N275Y		Atlas-SNP	.											.	SNTG2	125	.	0			c.C822A|c.A823T						PASS	.																																			SO:0001583	missense	54221	exon10			CTCAGCCAACATC|TCAGCCAACATCA	AJ003029	CCDS46220.1	2p25	2008-05-23			ENSG00000172554	ENSG00000172554			13741	protein-coding gene	gene with protein product		608715				10747910	Standard	NM_018968		Approved	SYN5, G2SYN	uc002qwq.3	Q9NY99	OTTHUMG00000151370	Exception_encountered	chr2.hg19:g.1241762_1241763delinsAT	ENSP00000311837:p.Asn275Tyr	33.0	0.0	.		48.0|47.0	32.0|31.0	.	NM_018968	Q05AH5	Silent|Missense_Mutation	SNP	ENST00000308624.5	hg19	CCDS46220.1																																																																																			.	.	.	none		0.550	SNTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322454.1	NM_018968	
AAK1	22848	hgsc.bcm.edu	37	2	69741762	69741762	+	Silent	SNP	T	T	C	rs77547121		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:69741762T>C	ENST00000409085.4	-	13	1993	c.1617A>G	c.(1615-1617)caA>caG	p.Q539Q	RN7SL604P_ENST00000492589.2_RNA|AAK1_ENST00000409068.1_Silent_p.Q539Q|AAK1_ENST00000406297.3_Silent_p.Q539Q	NM_014911.3	NP_055726	Q2M2I8	AAK1_HUMAN	AP2 associated kinase 1	539	Gln-rich.				endocytosis (GO:0006897)|positive regulation of Notch signaling pathway (GO:0045747)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)|regulation of clathrin-mediated endocytosis (GO:2000369)|regulation of protein localization (GO:0032880)	cell leading edge (GO:0031252)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|extrinsic component of plasma membrane (GO:0019897)|terminal bouton (GO:0043195)	AP-2 adaptor complex binding (GO:0035612)|ATP binding (GO:0005524)|Notch binding (GO:0005112)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|prostate(1)	17						gctgttgttgttgctgctgct	0.542																																					p.Q539Q		Atlas-SNP	.											AAK1_ENST00000409085,colon,carcinoma,0,2	AAK1	121	.	0			c.A1617G						PASS	.						32.0	34.0	34.0					2																	69741762		2195	4297	6492	SO:0001819	synonymous_variant	22848	exon13			TTGTTGTTGCTGC	AB028971	CCDS1893.2	2p13.3	2012-07-10			ENSG00000115977	ENSG00000115977			19679	protein-coding gene	gene with protein product						11877461, 12471243	Standard	NM_014911		Approved	KIAA1048, DKFZp686K16132	uc002sfp.2	Q2M2I8	OTTHUMG00000129648	ENST00000409085.4:c.1617A>G	chr2.hg19:g.69741762T>C		73.0	0.0	.		39.0	11.0	.	NM_014911	Q4ZFZ3|Q53RX6|Q9UPV4	Silent	SNP	ENST00000409085.4	hg19	CCDS1893.2																																																																																			.	C|1.000;|0.000	1.000	weak		0.542	AAK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251847.4	NM_014911	
IL1A	3552	hgsc.bcm.edu	37	2	113540317	113540317	+	Silent	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:113540317G>T	ENST00000263339.3	-	3	227	c.72C>A	c.(70-72)tcC>tcA	p.S24S		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	24					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|cytokine-mediated signaling pathway (GO:0019221)|ectopic germ cell programmed cell death (GO:0035234)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|fever generation (GO:0001660)|immune response (GO:0006955)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell division (GO:0051781)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of mitosis (GO:0045840)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation vascular endothelial growth factor production (GO:0010575)|response to copper ion (GO:0046688)	cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	copper ion binding (GO:0005507)|cytokine activity (GO:0005125)			breast(2)|large_intestine(1)|lung(9)	12					Rilonacept(DB06372)	GATGATCAATGGAGGAACTGT	0.373																																					p.S24S		Atlas-SNP	.											.	IL1A	19	.	0			c.C72A						PASS	.						243.0	215.0	224.0					2																	113540317		2203	4300	6503	SO:0001819	synonymous_variant	3552	exon3			ATCAATGGAGGAA	M28983	CCDS2101.1	2q14	2014-01-30			ENSG00000115008	ENSG00000115008		"""Interleukins and interleukin receptors"", ""Endogenous ligands"""	5991	protein-coding gene	gene with protein product	"""preinterleukin 1 alpha"", ""hematopoietin-1"", ""pro-interleukin-1-alpha"""	147760		IL1		8188271, 2989698	Standard	NM_000575		Approved	IL1F1, IL-1A, IL1-ALPHA	uc002tig.3	P01583	OTTHUMG00000131315	ENST00000263339.3:c.72C>A	chr2.hg19:g.113540317G>T		111.0	0.0	.		124.0	25.0	.	NM_000575	Q53QF9|Q7RU02	Silent	SNP	ENST00000263339.3	hg19	CCDS2101.1																																																																																			.	.	.	none		0.373	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575	
FAM168B	130074	hgsc.bcm.edu	37	2	131812937	131812937	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:131812937G>A	ENST00000409185.1	-	5	490	c.383C>T	c.(382-384)cCt>cTt	p.P128L	FAM168B_ENST00000389915.3_Missense_Mutation_p.P128L	NM_001009993.2	NP_001009993.2	A1KXE4	F168B_HUMAN	family with sequence similarity 168, member B	128						cell projection (GO:0042995)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|lung(2)	5						CACCGTTGCAGGCATGCCGTT	0.622																																					p.P128L		Atlas-SNP	.											.	FAM168B	15	.	0			c.C383T						PASS	.						153.0	170.0	164.0					2																	131812937		2164	4258	6422	SO:0001583	missense	130074	exon5			GTTGCAGGCATGC		CCDS42755.1	2q21.1	2008-08-08			ENSG00000152102	ENSG00000152102			27016	protein-coding gene	gene with protein product							Standard	NM_001009993		Approved	KIAA0280L	uc002tsd.3	A1KXE4	OTTHUMG00000153473	ENST00000409185.1:c.383C>T	chr2.hg19:g.131812937G>A	ENSP00000387051:p.Pro128Leu	196.0	1.0	.		241.0	154.0	.	NM_001009993	Q2TAZ6|Q6NZ40	Missense_Mutation	SNP	ENST00000409185.1	hg19	CCDS42755.1	.	.	.	.	.	.	.	.	.	.	G	27.6	4.849158	0.91277	.	.	ENSG00000152102	ENST00000409185;ENST00000389915	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.67524	0.2902	L	0.34521	1.04	0.80722	D	1	D	0.69078	0.997	D	0.78314	0.991	T	0.70364	-0.4892	9	0.87932	D	0	-5.3044	16.8479	0.85986	0.0:0.0:1.0:0.0	.	128	A1KXE4	F168B_HUMAN	L	128	.	ENSP00000374565:P128L	P	-	2	0	FAM168B	131529407	1.000000	0.71417	0.971000	0.41717	0.857000	0.48899	9.249000	0.95470	2.640000	0.89533	0.655000	0.94253	CCT	.	.	.	none		0.622	FAM168B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331299.2	NM_001009993	
RAPH1	65059	hgsc.bcm.edu	37	2	204304798	204304798	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:204304798C>G	ENST00000319170.5	-	14	3414	c.3115G>C	c.(3115-3117)Gga>Cga	p.G1039R	RAPH1_ENST00000457812.1_Intron|RAPH1_ENST00000374493.3_Missense_Mutation_p.G1091R|ABI2_ENST00000295851.5_3'UTR	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	1039					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						TGGAGAACTCCAGGAAGGTTG	0.552																																					p.G1039R		Atlas-SNP	.											.	RAPH1	118	.	0			c.G3115C						PASS	.						45.0	52.0	50.0					2																	204304798		2203	4300	6503	SO:0001583	missense	65059	exon14			GAACTCCAGGAAG	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.3115G>C	chr2.hg19:g.204304798C>G	ENSP00000316543:p.Gly1039Arg	56.0	0.0	.		92.0	27.0	.	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	hg19	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	C	14.09	2.432725	0.43224	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	T;T	0.43294	0.95;0.96	4.46	1.62	0.23740	.	.	.	.	.	T	0.19327	0.0464	N	0.08118	0	0.09310	N	0.999998	B	0.31125	0.309	B	0.25884	0.064	T	0.16541	-1.0399	9	0.26408	T	0.33	.	7.532	0.27689	0.0:0.4758:0.0:0.5242	.	1039	Q70E73	RAPH1_HUMAN	R	1039;1091	ENSP00000316543:G1039R;ENSP00000363617:G1091R	ENSP00000316543:G1039R	G	-	1	0	RAPH1	204013043	0.026000	0.19158	0.000000	0.03702	0.668000	0.39293	0.417000	0.21214	0.104000	0.17725	0.467000	0.42956	GGA	.	.	.	none		0.552	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
ZFAND2B	130617	hgsc.bcm.edu	37	2	220072714	220072714	+	Silent	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:220072714C>T	ENST00000289528.5	+	4	583	c.388C>T	c.(388-390)Ctg>Ttg	p.L130L	ZFAND2B_ENST00000444522.2_Silent_p.L130L|ZFAND2B_ENST00000409319.1_Silent_p.L130L|ZFAND2B_ENST00000468301.1_3'UTR|ZFAND2B_ENST00000409097.1_Silent_p.L130L|ZFAND2B_ENST00000409217.1_Silent_p.L130L|ZFAND2B_ENST00000409206.1_Silent_p.L130L|ZFAND2B_ENST00000409594.1_Silent_p.L130L|ZFAND2B_ENST00000409412.1_Silent_p.L130L|ZFAND2B_ENST00000409336.1_Silent_p.L130L	NM_001270998.1|NM_001270999.1|NM_138802.2	NP_001257927.1|NP_001257928.1|NP_620157.1	Q8WV99	ZFN2B_HUMAN	zinc finger, AN1-type domain 2B	130						endoplasmic reticulum (GO:0005783)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(4)|lung(4)|upper_aerodigestive_tract(1)	11		Renal(207;0.0915)		Epithelial(149;1.16e-06)|all cancers(144;0.000191)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCGGCATCCACTGGACCATGA	0.552																																					p.L130L		Atlas-SNP	.											.	ZFAND2B	28	.	0			c.C388T						PASS	.						80.0	86.0	84.0					2																	220072714		2203	4300	6503	SO:0001819	synonymous_variant	130617	exon4			CATCCACTGGACC	AK074571	CCDS2435.1, CCDS74656.1	2q35	2010-04-23	2005-08-22		ENSG00000158552	ENSG00000158552		"""Zinc fingers, AN1-type domain containing"""	25206	protein-coding gene	gene with protein product	"""arsenite inducible RNA associated protein-like"""	613474	"""zinc finger, AN1-type 2B"""			18467495	Standard	NM_138802		Approved	AIRAPL	uc002vka.4	Q8WV99	OTTHUMG00000133135	ENST00000289528.5:c.388C>T	chr2.hg19:g.220072714C>T		250.0	0.0	.		156.0	107.0	.	NM_138802	Q8NB98	Silent	SNP	ENST00000289528.5	hg19	CCDS2435.1																																																																																			.	.	.	none		0.552	ZFAND2B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256824.2	NM_138802	
CUL3	8452	hgsc.bcm.edu	37	2	225422463	225422463	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:225422463T>G	ENST00000264414.4	-	2	515	c.177A>C	c.(175-177)agA>agC	p.R59S	CUL3_ENST00000432260.2_5'UTR|CUL3_ENST00000409777.1_Missense_Mutation_p.R35S|CUL3_ENST00000409096.1_Missense_Mutation_p.R35S|CUL3_ENST00000344951.4_Intron	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	59					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		TATATGCATTTCTATAGAGCT	0.338																																					p.R65S		Atlas-SNP	.											.	CUL3	96	.	0			c.A195C						PASS	.						99.0	97.0	98.0					2																	225422463		2203	4298	6501	SO:0001583	missense	8452	exon2			TGCATTTCTATAG	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.177A>C	chr2.hg19:g.225422463T>G	ENSP00000264414:p.Arg59Ser	47.0	0.0	.		36.0	24.0	.	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Missense_Mutation	SNP	ENST00000264414.4	hg19	CCDS2462.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	16.79|16.79	3.221692|3.221692	0.58560|0.58560	.|.	.|.	ENSG00000036257|ENSG00000036257	ENST00000436172|ENST00000264414;ENST00000409096;ENST00000409777	.|T;T;T	.|0.29917	.|1.55;1.55;1.55	5.55|5.55	5.55|5.55	0.83447|0.83447	.|Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.55641|0.55641	0.1933|0.1933	M|M	0.86420|0.86420	2.815|2.815	0.80722|0.80722	D|D	1|1	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.67725	.|0.953;0.953	T|T	0.62511|0.62511	-0.6839|-0.6839	5|10	.|0.72032	.|D	.|0.01	.|.	8.148|8.148	0.31124|0.31124	0.0:0.1903:0.0:0.8097|0.0:0.1903:0.0:0.8097	.|.	.|37;59	.|Q53S54;Q13618	.|.;CUL3_HUMAN	Q|S	80|59;35;35	.|ENSP00000264414:R59S;ENSP00000387200:R35S;ENSP00000386525:R35S	.|ENSP00000264414:R59S	K|R	-|-	1|3	0|2	CUL3|CUL3	225130707|225130707	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.980000|1.980000	0.40618|0.40618	2.234000|2.234000	0.73211|0.73211	0.533000|0.533000	0.62120|0.62120	AAA|AGA	.	.	.	none		0.338	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		
CMTM7	112616	hgsc.bcm.edu	37	3	32433539	32433539	+	Silent	SNP	G	G	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr3:32433539G>C	ENST00000334983.5	+	1	377	c.141G>C	c.(139-141)ctG>ctC	p.L47L	CMTM7_ENST00000349718.4_Silent_p.L47L	NM_138410.2	NP_612419.1	Q96FZ5	CKLF7_HUMAN	CKLF-like MARVEL transmembrane domain containing 7	47	MARVEL. {ECO:0000255|PROSITE- ProRule:PRU00581}.				chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|large_intestine(1)|lung(2)	4						ACGCGGCCCTGCTGAAAGTGG	0.756																																					p.L47L		Atlas-SNP	.											.	CMTM7	14	.	0			c.G141C						PASS	.						2.0	2.0	2.0					3																	32433539		1638	3364	5002	SO:0001819	synonymous_variant	112616	exon1			GGCCCTGCTGAAA	AF479263	CCDS33730.1, CCDS33731.1	3p22.2	2005-11-08	2005-11-08	2005-11-08	ENSG00000153551	ENSG00000153551			19178	protein-coding gene	gene with protein product		607890	"""chemokine-like factor super family 7"", ""chemokine-like factor superfamily 7"""	CKLFSF7			Standard	NM_138410		Approved	FLJ30992	uc003cey.1	Q96FZ5	OTTHUMG00000155869	ENST00000334983.5:c.141G>C	chr3.hg19:g.32433539G>C		0.0	0.0	.		4.0	4.0	.	NM_138410	Q5VLK1	Silent	SNP	ENST00000334983.5	hg19	CCDS33730.1																																																																																			.	.	.	none		0.756	CMTM7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342084.1		
KIT	3815	hgsc.bcm.edu	37	4	55570036	55570036	+	Silent	SNP	C	C	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr4:55570036C>G	ENST00000288135.5	+	5	1000	c.903C>G	c.(901-903)gtC>gtG	p.V301V		NM_000222.2|NM_001093772.1	NP_000213.1|NP_001087241.1	P10721	KIT_HUMAN	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	301	Ig-like C2-type 3.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|cell chemotaxis (GO:0060326)|cellular response to thyroid hormone stimulus (GO:0097067)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell cytokine production (GO:0002371)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|digestive tract development (GO:0048565)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell proliferation (GO:0050673)|erythrocyte differentiation (GO:0030218)|erythropoietin-mediated signaling pathway (GO:0038162)|Fc receptor signaling pathway (GO:0038093)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|germ cell migration (GO:0008354)|glycosphingolipid metabolic process (GO:0006687)|hemopoiesis (GO:0030097)|immature B cell differentiation (GO:0002327)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|Kit signaling pathway (GO:0038109)|lamellipodium assembly (GO:0030032)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|mast cell chemotaxis (GO:0002551)|mast cell cytokine production (GO:0032762)|mast cell degranulation (GO:0043303)|mast cell differentiation (GO:0060374)|mast cell proliferation (GO:0070662)|megakaryocyte development (GO:0035855)|melanocyte adhesion (GO:0097326)|melanocyte differentiation (GO:0030318)|melanocyte migration (GO:0097324)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of programmed cell death (GO:0043069)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ovarian follicle development (GO:0001541)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|pigmentation (GO:0043473)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of pseudopodium assembly (GO:0031274)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of developmental pigmentation (GO:0048070)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|somatic stem cell division (GO:0048103)|somatic stem cell maintenance (GO:0035019)|spermatid development (GO:0007286)|spermatogenesis (GO:0007283)|stem cell differentiation (GO:0048863)|stem cell maintenance (GO:0019827)|T cell differentiation (GO:0030217)|visual learning (GO:0008542)	acrosomal vesicle (GO:0001669)|cell-cell junction (GO:0005911)|cytoplasmic side of plasma membrane (GO:0009898)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|mast cell granule (GO:0042629)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|stem cell factor receptor activity (GO:0005020)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(8)|autonomic_ganglia(1)|bone(21)|breast(2)|central_nervous_system(4)|endometrium(10)|eye(12)|genital_tract(18)|haematopoietic_and_lymphoid_tissue(1820)|kidney(17)|large_intestine(17)|lung(27)|ovary(23)|pancreas(4)|prostate(1)|salivary_gland(15)|skin(228)|soft_tissue(4117)|stomach(3)|testis(55)|thymus(7)|upper_aerodigestive_tract(1)	6411	all_cancers(7;0.00453)|all_lung(4;0.000565)|Lung NSC(11;0.00129)|all_epithelial(27;0.0104)|Glioma(25;0.08)|all_neural(26;0.101)		LUSC - Lung squamous cell carcinoma(32;0.000276)|Epithelial(7;0.209)	Colorectal(1;0.0276)|COAD - Colon adenocarcinoma(1;0.171)	Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	CAGCAAATGTCACAACAACCT	0.348		1	"""Mis, O"""		"""GIST, AML, TGCT, mastocytosis, mucosal melanoma"""	"""GIST, epithelioma"""	Piebald trait		Piebaldism;Mast Cell disease, Familial Clustering of;Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Gastrointestinal Stromal Tumors																												p.V301V		Atlas-SNP	.	yes	Dom	yes	Familial gastrointestinal stromal tumour	4	4q12	3815	v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog	yes	"""L, M, O, E"""	.	KIT	7396	.	0			c.C903G						PASS	.						168.0	163.0	165.0					4																	55570036		2203	4300	6503	SO:0001819	synonymous_variant	3815	exon5	Familial Cancer Database	Piebald trait;incl.: Familial Cutaneous Mastocytosis (Urticaria Pigmentosum);Sporadic Multiple GIST;Familial GIST, incl. Multiple Familial Gastrointestinal Autonomic Nerve Tumors (GANT)	AAATGTCACAACA	S67773	CCDS3496.1, CCDS47058.1	4q12	2014-09-17			ENSG00000157404	ENSG00000157404		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6342	protein-coding gene	gene with protein product		164920	"""piebald trait"""	PBT		9027509	Standard	NM_001093772		Approved	CD117, SCFR, C-Kit	uc010igr.3	P10721	OTTHUMG00000128713	ENST00000288135.5:c.903C>G	chr4.hg19:g.55570036C>G		162.0	0.0	.		164.0	58.0	.	NM_000222	B5A956|D5LXN2|D5M931|F5H8F8|Q6IQ28|Q99662|Q9UM99	Silent	SNP	ENST00000288135.5	hg19	CCDS3496.1																																																																																			.	.	.	none		0.348	KIT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250618.1		
ADAMTS3	9508	hgsc.bcm.edu	37	4	73148995	73148995	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr4:73148995C>T	ENST00000286657.4	-	22	3512	c.3476G>A	c.(3475-3477)aGt>aAt	p.S1159N		NM_014243.2	NP_055058.2	O15072	ATS3_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 3	1159					collagen biosynthetic process (GO:0032964)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular fibril organization (GO:0043206)|extracellular matrix organization (GO:0030198)|positive regulation of vascular endothelial growth factor signaling pathway (GO:1900748)|protein processing (GO:0016485)|vascular endothelial growth factor production (GO:0010573)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)	endopeptidase activity (GO:0004175)|heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(21)|lung(33)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	76			Epithelial(6;4.97e-05)|OV - Ovarian serous cystadenocarcinoma(6;5.66e-05)|all cancers(17;0.000486)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			TGAAGCTGAACTGAGGTGGAC	0.498																																					p.S1159N	NSCLC(168;1941 2048 2918 13048 43078)	Atlas-SNP	.											.	ADAMTS3	164	.	0			c.G3476A						PASS	.						195.0	172.0	180.0					4																	73148995		2203	4300	6503	SO:0001583	missense	9508	exon22			GCTGAACTGAGGT	AB002364	CCDS3553.1	4q21	2008-07-29	2005-08-19		ENSG00000156140	ENSG00000156140	3.4.24.-	"""ADAM metallopeptidases with thrombospondin type 1 motif"""	219	protein-coding gene	gene with protein product		605011	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 3"""			10094461	Standard	NM_014243		Approved	KIAA0366, ADAMTS-4	uc003hgk.2	O15072	OTTHUMG00000129912	ENST00000286657.4:c.3476G>A	chr4.hg19:g.73148995C>T	ENSP00000286657:p.Ser1159Asn	138.0	0.0	.		157.0	51.0	.	NM_014243	A1L3U9|Q9BXZ8	Missense_Mutation	SNP	ENST00000286657.4	hg19	CCDS3553.1	.	.	.	.	.	.	.	.	.	.	C	0	-2.777427	0.00080	.	.	ENSG00000156140	ENST00000286657	T	0.61040	0.14	5.23	-10.5	0.00291	.	1.555640	0.04150	N	0.321125	T	0.22282	0.0537	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27706	-1.0066	10	0.09084	T	0.74	.	11.9585	0.52995	0.0:0.5187:0.2677:0.2136	.	1159	O15072	ATS3_HUMAN	N	1159	ENSP00000286657:S1159N	ENSP00000286657:S1159N	S	-	2	0	ADAMTS3	73367859	0.000000	0.05858	0.000000	0.03702	0.014000	0.08584	-2.403000	0.01046	-2.504000	0.00508	-0.423000	0.05987	AGT	.	.	.	none		0.498	ADAMTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252164.2		
DMXL1	1657	hgsc.bcm.edu	37	5	118451949	118451949	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:118451949A>T	ENST00000311085.8	+	7	741	c.661A>T	c.(661-663)Att>Ttt	p.I221F	DMXL1_ENST00000539542.1_Missense_Mutation_p.I221F	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	221			I -> M (in dbSNP:rs7700801).							breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		CCAAGGAGAAATTGACTTTTC	0.403																																					p.I221F		Atlas-SNP	.											.	DMXL1	268	.	0			c.A661T						PASS	.						136.0	130.0	132.0					5																	118451949		2202	4300	6502	SO:0001583	missense	1657	exon7			GGAGAAATTGACT	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.661A>T	chr5.hg19:g.118451949A>T	ENSP00000309690:p.Ile221Phe	79.0	0.0	.		95.0	27.0	.	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	hg19	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	A	14.50	2.554283	0.45487	.	.	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.66815	1.93;-0.23;2.94	4.96	2.25	0.28309	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.551167	0.19764	N	0.106592	T	0.46328	0.1387	L	0.28400	0.85	0.25888	N	0.983509	B;B	0.22541	0.071;0.042	B;B	0.23018	0.043;0.019	T	0.17930	-1.0353	10	0.24483	T	0.36	-0.2952	3.3933	0.07297	0.3747:0.2296:0.3958:0.0	.	221;221	F5H269;Q9Y485	.;DMXL1_HUMAN	F	221	ENSP00000427692:I221F;ENSP00000309690:I221F;ENSP00000439479:I221F	ENSP00000309690:I221F	I	+	1	0	DMXL1	118479848	1.000000	0.71417	0.979000	0.43373	0.953000	0.61014	1.200000	0.32247	0.842000	0.35045	0.533000	0.62120	ATT	.	.	.	none		0.403	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
ARAP3	64411	hgsc.bcm.edu	37	5	141035313	141035313	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:141035313G>C	ENST00000239440.4	-	31	4050	c.3985C>G	c.(3985-3987)Cag>Gag	p.Q1329E	ARAP3_ENST00000512390.1_5'UTR|ARAP3_ENST00000513878.1_Missense_Mutation_p.Q991E|ARAP3_ENST00000508305.1_Missense_Mutation_p.Q1160E	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	1329					cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						ACCACTGGCTGCTGGTCATCG	0.617																																					p.Q1329E		Atlas-SNP	.											.	ARAP3	139	.	0			c.C3985G						PASS	.						84.0	79.0	81.0					5																	141035313		2203	4300	6503	SO:0001583	missense	64411	exon31			CTGGCTGCTGGTC	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.3985C>G	chr5.hg19:g.141035313G>C	ENSP00000239440:p.Gln1329Glu	135.0	0.0	.		195.0	58.0	.	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	hg19	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	11.92	1.782249	0.31502	.	.	ENSG00000120318	ENST00000508305;ENST00000239440;ENST00000513878	T;T;T	0.14893	2.47;3.19;3.04	5.66	5.66	0.87406	Pleckstrin homology-type (1);	0.184808	0.46442	D	0.000286	T	0.14960	0.0361	N	0.24115	0.695	0.36230	D	0.852566	P;P;P	0.46220	0.65;0.874;0.637	B;B;B	0.40375	0.306;0.327;0.087	T	0.06844	-1.0804	10	0.35671	T	0.21	.	19.3334	0.94303	0.0:0.0:1.0:0.0	.	991;1160;1329	B4DIT1;G5E9Y3;Q8WWN8	.;.;ARAP3_HUMAN	E	1160;1329;991	ENSP00000421826:Q1160E;ENSP00000239440:Q1329E;ENSP00000421468:Q991E	ENSP00000239440:Q1329E	Q	-	1	0	ARAP3	141015497	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	5.807000	0.69157	2.675000	0.91044	0.655000	0.94253	CAG	.	.	.	none		0.617	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
ADAMTS2	9509	hgsc.bcm.edu	37	5	178567002	178567002	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:178567002G>A	ENST00000251582.7	-	11	1765	c.1664C>T	c.(1663-1665)cCt>cTt	p.P555L		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	555	Disintegrin.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GAGGATGTCAGGTGTCAGCCA	0.607																																					p.P555L		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C1664T						PASS	.						162.0	170.0	167.0					5																	178567002		2203	4300	6503	SO:0001583	missense	9509	exon11			ATGTCAGGTGTCA	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.1664C>T	chr5.hg19:g.178567002G>A	ENSP00000251582:p.Pro555Leu	90.0	0.0	.		190.0	56.0	.	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	hg19	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	G	13.86	2.362637	0.41902	.	.	ENSG00000087116	ENST00000251582	T	0.61274	0.12	4.92	4.92	0.64577	.	0.000000	0.53938	D	0.000058	T	0.62841	0.2461	N	0.20685	0.6	0.80722	D	1	D	0.71674	0.998	D	0.68765	0.96	T	0.67201	-0.5730	10	0.52906	T	0.07	.	17.1242	0.86710	0.0:0.0:1.0:0.0	.	555	O95450	ATS2_HUMAN	L	555	ENSP00000251582:P555L	ENSP00000251582:P555L	P	-	2	0	ADAMTS2	178499608	1.000000	0.71417	0.117000	0.21633	0.227000	0.25037	9.282000	0.95840	2.281000	0.76405	0.561000	0.74099	CCT	.	.	.	none		0.607	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
ZNF451	26036	hgsc.bcm.edu	37	6	56966590	56966590	+	Intron	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:56966590C>T	ENST00000370706.4	+	3	430				ZNF451_ENST00000491832.2_Intron|ZNF451_ENST00000357489.3_Intron|ZNF451_ENST00000370702.1_Intron|ZNF451_ENST00000370708.4_Missense_Mutation_p.A459V	NM_001031623.2	NP_001026794.1	Q9Y4E5	ZN451_HUMAN	zinc finger protein 451						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32	Lung NSC(77;0.145)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			AGACGGCAGGCCTGGCTTCGA	0.468																																					p.A459V		Atlas-SNP	.											.	ZNF451	181	.	0			c.C1376T						PASS	.																																			SO:0001627	intron_variant	26036	exon4			GGCAGGCCTGGCT	AB011148	CCDS4960.1, CCDS43477.1, CCDS59026.1	6p12.1	2012-08-08			ENSG00000112200	ENSG00000112200		"""Zinc fingers, C2H2-type"""	21091	protein-coding gene	gene with protein product		615708				9628581	Standard	NM_001031623		Approved	KIAA0576, COASTER, dJ417I1.1, KIAA1702	uc003pdm.2	Q9Y4E5	OTTHUMG00000014916	ENST00000370706.4:c.186+2651C>T	chr6.hg19:g.56966590C>T		122.0	0.0	.		73.0	37.0	.	NM_001257273	Q5VVE9|Q5VVF1|Q86YE4|Q8N380|Q8TD15|Q9C0G1|Q9NQM1	Missense_Mutation	SNP	ENST00000370706.4	hg19	CCDS43477.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.541949	0.65198	.	.	ENSG00000112200	ENST00000370708	T	0.52526	0.66	4.58	4.58	0.56647	.	.	.	.	.	T	0.37046	0.0989	N	0.08118	0	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	T	0.37865	-0.9687	9	0.42905	T	0.14	.	13.1903	0.59706	0.0:1.0:0.0:0.0	.	459	Q9Y4E5-4	.	V	459	ENSP00000359742:A459V	ENSP00000359742:A459V	A	+	2	0	ZNF451	57074549	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.665000	0.37449	2.820000	0.97059	0.655000	0.94253	GCC	.	.	.	none		0.468	ZNF451-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041035.2	NM_015555	
LAMA2	3908	hgsc.bcm.edu	37	6	129766960	129766960	+	Silent	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:129766960C>T	ENST00000421865.2	+	45	6472	c.6423C>T	c.(6421-6423)gcC>gcT	p.A2141A		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	2141	Domain II and I.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|muscle organ development (GO:0007517)|myelination in peripheral nervous system (GO:0022011)|positive regulation of synaptic transmission, cholinergic (GO:0032224)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|sarcolemma (GO:0042383)	structural molecule activity (GO:0005198)			NS(2)|biliary_tract(2)|breast(10)|central_nervous_system(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(35)|lung(84)|ovary(10)|prostate(4)|skin(9)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(2)	194				OV - Ovarian serous cystadenocarcinoma(136;0.178)|all cancers(137;0.245)		GGAAACAAGCCAATTCTGTAA	0.368																																					p.A2141A		Atlas-SNP	.											.	LAMA2	481	.	0			c.C6423T						PASS	.						53.0	48.0	50.0					6																	129766960		2203	4300	6503	SO:0001819	synonymous_variant	3908	exon45			ACAAGCCAATTCT	Z26653	CCDS5138.1	6q22-q23	2014-09-17	2008-08-01		ENSG00000196569	ENSG00000196569		"""Laminins"""	6482	protein-coding gene	gene with protein product	"""merosin"", ""congenital muscular dystrophy"""	156225		LAMM		2185464, 8294519	Standard	NM_000426		Approved		uc003qbn.3	P24043	OTTHUMG00000015545	ENST00000421865.2:c.6423C>T	chr6.hg19:g.129766960C>T		54.0	0.0	.		45.0	19.0	.	NM_000426	Q14736|Q5VUM2|Q93022	Silent	SNP	ENST00000421865.2	hg19	CCDS5138.1																																																																																			.	.	.	none		0.368	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
REPS1	85021	hgsc.bcm.edu	37	6	139235873	139235873	+	Silent	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:139235873G>T	ENST00000450536.2	-	15	2320	c.1746C>A	c.(1744-1746)gcC>gcA	p.A582A	REPS1_ENST00000415951.2_Silent_p.A555A|REPS1_ENST00000258062.5_Silent_p.A581A|REPS1_ENST00000367663.4_Silent_p.A555A|REPS1_ENST00000409812.2_Silent_p.A491A			Q96D71	REPS1_HUMAN	RALBP1 associated Eps domain containing 1	582	Pro-rich.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|SH3 domain binding (GO:0017124)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(8)|upper_aerodigestive_tract(2)	19				GBM - Glioblastoma multiforme(68;0.000434)|OV - Ovarian serous cystadenocarcinoma(155;0.000548)		CAGGAGGATGGGCAACAACTC	0.398																																					p.A581A		Atlas-SNP	.											.	REPS1	58	.	0			c.C1743A						PASS	.						142.0	141.0	142.0					6																	139235873		2203	4300	6503	SO:0001819	synonymous_variant	85021	exon15			AGGATGGGCAACA		CCDS5193.2, CCDS47488.1, CCDS69212.1, CCDS69213.1	6q24.1	2013-01-10			ENSG00000135597	ENSG00000135597		"""EF-hand domain containing"""	15578	protein-coding gene	gene with protein product		614825					Standard	XM_005267177		Approved		uc011edr.2	Q96D71	OTTHUMG00000015685	ENST00000450536.2:c.1746C>A	chr6.hg19:g.139235873G>T		108.0	0.0	.		74.0	33.0	.	NM_031922	B7ZBZ8|B7ZBZ9|B7ZC00|J3KP76|Q5JWJ5|Q5JWJ6|Q5JWJ7|Q8NDR7|Q8WU62|Q9BXY9	Silent	SNP	ENST00000450536.2	hg19																																																																																				.	.	.	none		0.398	REPS1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000042447.3		
MEOX2	4223	hgsc.bcm.edu	37	7	15725867	15725867	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:15725867G>C	ENST00000262041.5	-	1	570	c.161C>G	c.(160-162)cCc>cGc	p.P54R	AC005550.5_ENST00000438923.1_lincRNA|AC005550.4_ENST00000442176.1_lincRNA	NM_005924.4	NP_005915.2	P50222	MEOX2_HUMAN	mesenchyme homeobox 2	54					angiogenesis (GO:0001525)|blood circulation (GO:0008015)|limb development (GO:0060173)|multicellular organismal development (GO:0007275)|neuron death (GO:0070997)|palate development (GO:0060021)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|skeletal muscle tissue development (GO:0007519)|somite specification (GO:0001757)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(11)|ovary(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	24				UCEC - Uterine corpus endometrioid carcinoma (126;0.0822)		CTCTTCGTTGGGGTATCCCGC	0.572																																					p.P54R	Esophageal Squamous(140;197 1769 16409 18257 29929)	Atlas-SNP	.											.	MEOX2	68	.	0			c.C161G						PASS	.						59.0	53.0	55.0					7																	15725867		2203	4300	6503	SO:0001583	missense	4223	exon1			TCGTTGGGGTATC		CCDS34605.1	7p22.1-p21.3	2014-07-15	2005-12-22		ENSG00000106511	ENSG00000106511		"""Homeoboxes / ANTP class : HOXL subclass"""	7014	protein-coding gene	gene with protein product	"""growth arrest-specific homeobox"""	600535	"""mesenchyme homeo box 2 (growth arrest-specific homeo box)"", ""mesenchyme homeobox 2 (growth arrest-specific homeo box)"""	GAX		7713505	Standard	NM_005924		Approved	MOX2	uc003stc.3	P50222	OTTHUMG00000152390	ENST00000262041.5:c.161C>G	chr7.hg19:g.15725867G>C	ENSP00000262041:p.Pro54Arg	91.0	0.0	.		161.0	43.0	.	NM_005924	B2R8I7|O75263|Q9UPL6	Missense_Mutation	SNP	ENST00000262041.5	hg19	CCDS34605.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877795	0.51801	.	.	ENSG00000106511	ENST00000262041	D	0.91068	-2.78	4.88	4.88	0.63580	.	0.233514	0.43919	D	0.000502	D	0.89269	0.6667	L	0.54323	1.7	0.54753	D	0.999981	B	0.23891	0.093	B	0.26517	0.07	D	0.86520	0.1815	10	0.44086	T	0.13	-23.5827	18.4725	0.90779	0.0:0.0:1.0:0.0	.	54	P50222	MEOX2_HUMAN	R	54	ENSP00000262041:P54R	ENSP00000262041:P54R	P	-	2	0	MEOX2	15692392	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.705000	0.91357	2.424000	0.82194	0.650000	0.86243	CCC	.	.	.	none		0.572	MEOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326058.2	NM_005924	
HDAC9	9734	hgsc.bcm.edu	37	7	18975517	18975517	+	Silent	SNP	C	C	T	rs534633020		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:18975517C>T	ENST00000432645.2	+	22	2880	c.2880C>T	c.(2878-2880)gcC>gcT	p.A960A	HDAC9_ENST00000401921.1_Silent_p.A919A|HDAC9_ENST00000406451.4_Silent_p.A960A|HDAC9_ENST00000441542.2_Silent_p.A963A	NM_058176.2	NP_478056.1	Q9UKV0	HDAC9_HUMAN	histone deacetylase 9	960	Histone deacetylase.				B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cellular response to insulin stimulus (GO:0032869)|heart development (GO:0007507)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell migration involved in sprouting angiogenesis (GO:0090050)|regulation of skeletal muscle fiber development (GO:0048742)|regulation of striated muscle cell differentiation (GO:0051153)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|histone deacetylase complex (GO:0000118)|histone methyltransferase complex (GO:0035097)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|metal ion binding (GO:0046872)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|protein deacetylase activity (GO:0033558)|protein kinase C binding (GO:0005080)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(3)|central_nervous_system(4)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(18)|liver(2)|lung(37)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	82	all_lung(11;0.187)				Valproic Acid(DB00313)	ATCTCACAGCCATCTGTGATG	0.433																																					p.A963A		Atlas-SNP	.											.	HDAC9	560	.	0			c.C2889T						PASS	.						200.0	193.0	195.0					7																	18975517		1929	4145	6074	SO:0001819	synonymous_variant	9734	exon22			CACAGCCATCTGT	AF124924	CCDS47553.1, CCDS47554.1, CCDS47555.1, CCDS47557.1, CCDS56465.1, CCDS56466.1, CCDS56467.1, CCDS56468.1, CCDS75565.1	7p21.1	2008-05-15			ENSG00000048052	ENSG00000048052			14065	protein-coding gene	gene with protein product		606543				10523670, 10487760	Standard	NM_178425		Approved	KIAA0744, HDAC, MITR, HD7, HDAC7B	uc003sui.3	Q9UKV0	OTTHUMG00000152487	ENST00000432645.2:c.2880C>T	chr7.hg19:g.18975517C>T		105.0	0.0	.		203.0	48.0	.	NM_178425	A7E2F3|B7Z4I4|B7Z917|B7Z928|B7Z940|C9JS87|E7EX34|F8W9E0|O94845|O95028|Q2M2R6|Q86SL1|Q86US3	Silent	SNP	ENST00000432645.2	hg19	CCDS47555.1																																																																																			.	.	.	none		0.433	HDAC9-023	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376176.1		
FAM221A	340277	hgsc.bcm.edu	37	7	23728992	23728992	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:23728992C>G	ENST00000344962.4	+	3	433	c.344C>G	c.(343-345)cCc>cGc	p.P115R	FAM221A_ENST00000409192.3_Missense_Mutation_p.P115R|FAM221A_ENST00000409994.3_Missense_Mutation_p.P57R|FAM221A_ENST00000409653.1_Missense_Mutation_p.P57R	NM_199136.3	NP_954587.2	A4D161	F221A_HUMAN	family with sequence similarity 221, member A	115																	CTTTATGTCCCCTTGAATGGT	0.493																																					p.P115R		Atlas-SNP	.											.	.	.	.	0			c.C344G						PASS	.						86.0	78.0	81.0					7																	23728992		2203	4300	6503	SO:0001583	missense	340277	exon3			ATGTCCCCTTGAA		CCDS5385.1, CCDS47561.1, CCDS47562.1, CCDS75570.1	7p15.3	2012-04-02	2012-04-02	2012-04-02	ENSG00000188732	ENSG00000188732			27977	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 46"""	C7orf46		12477932	Standard	XR_242080		Approved	FLJ45875, MGC72075, DKFZp686F0810	uc003swo.4	A4D161	OTTHUMG00000128463	ENST00000344962.4:c.344C>G	chr7.hg19:g.23728992C>G	ENSP00000342576:p.Pro115Arg	84.0	0.0	.		124.0	34.0	.	NM_199136	Q05CG4|Q4G0Q7|Q6P519	Missense_Mutation	SNP	ENST00000344962.4	hg19	CCDS5385.1	.	.	.	.	.	.	.	.	.	.	C	19.81	3.896270	0.72639	.	.	ENSG00000188732	ENST00000409192;ENST00000344962;ENST00000409653;ENST00000409994	T;T;T;T	0.19394	2.15;2.15;2.15;2.15	5.58	5.58	0.84498	.	0.051181	0.85682	D	0.000000	T	0.57272	0.2042	M	0.90650	3.135	0.53005	D	0.999968	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.83275	0.94;0.996;0.996	T	0.65841	-0.6070	10	0.87932	D	0	-12.9907	19.5733	0.95430	0.0:1.0:0.0:0.0	.	57;115;115	A4D161-3;A4D161-2;A4D161	.;.;CG046_HUMAN	R	115;115;57;57	ENSP00000386927:P115R;ENSP00000342576:P115R;ENSP00000386900:P57R;ENSP00000386631:P57R	ENSP00000342576:P115R	P	+	2	0	C7orf46	23695517	1.000000	0.71417	0.971000	0.41717	0.755000	0.42902	5.491000	0.66887	2.622000	0.88805	0.585000	0.79938	CCC	.	.	.	none		0.493	FAM221A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250261.1	NM_199136	
NEUROD6	63974	hgsc.bcm.edu	37	7	31377935	31377935	+	Silent	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:31377935G>A	ENST00000297142.3	-	2	1270	c.948C>T	c.(946-948)taC>taT	p.Y316Y		NM_022728.2	NP_073565.2	Q96NK8	NDF6_HUMAN	neuronal differentiation 6	316					cell differentiation (GO:0030154)|dentate gyrus development (GO:0021542)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.Y316Y(1)		breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	32						GATGTAAGTCGTAAGGGAAGT	0.453																																					p.Y316Y		Atlas-SNP	.											NEUROD6,NS,carcinoma,0,1	NEUROD6	84	.	1	Substitution - coding silent(1)	endometrium(1)	c.C948T						PASS	.						82.0	81.0	81.0					7																	31377935		2203	4300	6503	SO:0001819	synonymous_variant	63974	exon2			TAAGTCGTAAGGG	AF248954	CCDS5434.1	7p15.1	2013-05-21	2012-02-22		ENSG00000164600	ENSG00000164600		"""Basic helix-loop-helix proteins"""	13804	protein-coding gene	gene with protein product		611513	"""neurogenic differentiation 6"""			12357074	Standard	NM_022728		Approved	Atoh2, NEX1M, Math-2, bHLHa2, Nex1	uc003tch.4	Q96NK8	OTTHUMG00000022865	ENST00000297142.3:c.948C>T	chr7.hg19:g.31377935G>A		72.0	0.0	.		107.0	53.0	.	NM_022728	Q548T9|Q9H3H6	Silent	SNP	ENST00000297142.3	hg19	CCDS5434.1																																																																																			.	.	.	none		0.453	NEUROD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215050.1	NM_022728	
SAMD9L	219285	hgsc.bcm.edu	37	7	92764048	92764048	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:92764048A>T	ENST00000318238.4	-	5	2453	c.1237T>A	c.(1237-1239)Tac>Aac	p.Y413N	SAMD9L_ENST00000437805.1_Missense_Mutation_p.Y413N|SAMD9L_ENST00000411955.1_Missense_Mutation_p.Y413N	NM_152703.2	NP_689916.2	Q8IVG5	SAM9L_HUMAN	sterile alpha motif domain containing 9-like	413					common myeloid progenitor cell proliferation (GO:0035726)|endosomal vesicle fusion (GO:0034058)|hematopoietic progenitor cell differentiation (GO:0002244)|regulation of protein catabolic process (GO:0042176)|spleen development (GO:0048536)|stem cell division (GO:0017145)	early endosome (GO:0005769)				central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(23)|liver(2)|lung(31)|ovary(5)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(4)	88	all_cancers(62;4.15e-11)|all_epithelial(64;2.29e-10)|Breast(17;0.000675)|Lung NSC(181;0.0755)|all_lung(186;0.0989)		STAD - Stomach adenocarcinoma(171;0.000302)			CAGTCATAGTATGAATTATCC	0.358																																					p.Y413N		Atlas-SNP	.											.	SAMD9L	227	.	0			c.T1237A						PASS	.						136.0	138.0	137.0					7																	92764048		2203	4299	6502	SO:0001583	missense	219285	exon5			CATAGTATGAATT	AB095926	CCDS34681.1	7q21.2	2013-01-10		2005-04-26	ENSG00000177409	ENSG00000177409		"""Sterile alpha motif (SAM) domain containing"""	1349	protein-coding gene	gene with protein product		611170	"""chromosome 7 open reading frame 6"""	C7orf6			Standard	NM_152703		Approved	KIAA2005, FLJ39885	uc003umh.1	Q8IVG5	OTTHUMG00000155807	ENST00000318238.4:c.1237T>A	chr7.hg19:g.92764048A>T	ENSP00000326247:p.Tyr413Asn	17.0	0.0	.		25.0	7.0	.	NM_152703	A0JP23|A0JP24|A0PJG8|A4D1G8|D6W5Q6|Q2TV71|Q2TV75|Q2UZV8|Q8IWI4|Q8N3L9|Q8N875	Missense_Mutation	SNP	ENST00000318238.4	hg19	CCDS34681.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892471	0.52121	.	.	ENSG00000177409	ENST00000318238;ENST00000411955;ENST00000437805	T;T;T	0.13538	2.58;2.58;2.58	4.74	4.74	0.60224	.	0.088161	0.46442	D	0.000299	T	0.31104	0.0786	L	0.51422	1.61	0.42354	D	0.992381	D	0.89917	1.0	D	0.77557	0.99	T	0.03514	-1.1029	10	0.72032	D	0.01	-9.3295	14.0508	0.64734	1.0:0.0:0.0:0.0	.	413	Q8IVG5	SAM9L_HUMAN	N	413	ENSP00000326247:Y413N;ENSP00000405760:Y413N;ENSP00000408796:Y413N	ENSP00000326247:Y413N	Y	-	1	0	SAMD9L	92601984	0.688000	0.27680	0.999000	0.59377	0.977000	0.68977	2.301000	0.43628	1.991000	0.58162	0.377000	0.23210	TAC	.	.	.	none		0.358	SAMD9L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341730.1	NM_152703	
CCDC132	55610	hgsc.bcm.edu	37	7	92953019	92953019	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:92953019A>T	ENST00000305866.5	+	21	2080	c.1952A>T	c.(1951-1953)tAt>tTt	p.Y651F	CCDC132_ENST00000544910.1_Missense_Mutation_p.Y621F|CCDC132_ENST00000535481.1_Missense_Mutation_p.Y371F|CCDC132_ENST00000541136.1_Missense_Mutation_p.Y462F	NM_017667.3	NP_060137.2	Q96JG6	CC132_HUMAN	coiled-coil domain containing 132	651						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				endometrium(1)|large_intestine(2)|lung(5)	8	all_cancers(62;2.64e-11)|all_epithelial(64;1.4e-10)|Breast(17;0.000675)|Lung NSC(181;0.0618)|all_lung(186;0.0837)		STAD - Stomach adenocarcinoma(171;0.000302)			TATGCAATATATACCTTTTTT	0.279																																					p.Y651F		Atlas-SNP	.											.	CCDC132	136	.	0			c.A1952T						PASS	.						77.0	71.0	73.0					7																	92953019		1800	4052	5852	SO:0001583	missense	55610	exon21			CAATATATACCTT	AL833112, AK055965, AL832393	CCDS5630.1, CCDS43617.1, CCDS59065.1	7q21.3	2007-07-23			ENSG00000004766	ENSG00000004766			25956	protein-coding gene	gene with protein product						11347906	Standard	NM_024553		Approved	KIAA1861, FLJ20097, DKFZp313I2429	uc003umo.4	Q96JG6	OTTHUMG00000131733	ENST00000305866.5:c.1952A>T	chr7.hg19:g.92953019A>T	ENSP00000307666:p.Tyr651Phe	28.0	0.0	.		36.0	7.0	.	NM_017667	B3KX22|D1MQ00|F5H5U7|Q75N07|Q8WVK3|Q9H5C6	Missense_Mutation	SNP	ENST00000305866.5	hg19	CCDS43617.1	.	.	.	.	.	.	.	.	.	.	A	20.9	4.071795	0.76301	.	.	ENSG00000004766	ENST00000305866;ENST00000544910;ENST00000541136;ENST00000535481	.	.	.	4.68	4.68	0.58851	.	0.061363	0.64402	D	0.000002	T	0.53158	0.1779	N	0.12853	0.265	0.80722	D	1	D;D;D	0.64830	0.993;0.994;0.993	D;D;D	0.68192	0.956;0.915;0.956	T	0.57768	-0.7754	9	0.41790	T	0.15	-9.4515	14.0796	0.64912	1.0:0.0:0.0:0.0	.	371;621;651	B4DS55;F5H5U7;Q96JG6	.;.;CC132_HUMAN	F	651;621;462;371	.	ENSP00000307666:Y651F	Y	+	2	0	CCDC132	92790955	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.058000	0.93896	1.877000	0.54381	0.402000	0.26972	TAT	.	.	.	none		0.279	CCDC132-019	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341687.1	NM_017667	
BHLHA15	168620	hgsc.bcm.edu	37	7	97842056	97842056	+	Silent	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:97842056G>A	ENST00000609256.1	+	2	561	c.435G>A	c.(433-435)ccG>ccA	p.P145P	BHLHA15_ENST00000314018.2_Silent_p.P145P			Q7RTS1	BHA15_HUMAN	basic helix-loop-helix family, member a15	145					calcium-mediated signaling (GO:0019722)|cell maturation (GO:0048469)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|Golgi organization (GO:0007030)|intracellular distribution of mitochondria (GO:0048312)|mitochondrial calcium ion transport (GO:0006851)	nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)										TGGAGGGGCCGGGCCCCAAGC	0.667																																					p.P145P		Atlas-SNP	.											.	BHLHA15	11	.	0			c.G435A						PASS	.						12.0	12.0	12.0					7																	97842056		2137	4189	6326	SO:0001819	synonymous_variant	168620	exon1			GGGGCCGGGCCCC	BK000276	CCDS5655.1	7q21.3	2009-01-12	2009-01-12	2009-01-12	ENSG00000180535	ENSG00000180535		"""Basic helix-loop-helix proteins"""	22265	protein-coding gene	gene with protein product		608606	"""basic helix-loop-helix domain containing, class B, 8"""	BHLHB8		14516699, 18557763	Standard	NM_177455		Approved	MIST1, bHLHa15	uc003upf.1	Q7RTS1	OTTHUMG00000154289	ENST00000609256.1:c.435G>A	chr7.hg19:g.97842056G>A		37.0	0.0	.		155.0	7.0	.	NM_177455	A4D271|Q14DE4	Silent	SNP	ENST00000609256.1	hg19	CCDS5655.1																																																																																			.	.	.	none		0.667	BHLHA15-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472733.1	NM_177455	
MUC17	140453	hgsc.bcm.edu	37	7	100676808	100676808	+	Missense_Mutation	SNP	A	A	G	rs71517134		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:100676808A>G	ENST00000306151.4	+	3	2175	c.2111A>G	c.(2110-2112)gAg>gGg	p.E704G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	704	59 X approximate tandem repeats.|Ser-rich.				cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					GCCAGTTCTGAGGCTAGCACC	0.502																																					p.E704G		Atlas-SNP	.											.	MUC17	804	.	0			c.A2111G						PASS	.						340.0	344.0	343.0					7																	100676808		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTCTGAGGCTAG	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.2111A>G	chr7.hg19:g.100676808A>G	ENSP00000302716:p.Glu704Gly	140.0	0.0	.		234.0	54.0	.	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	hg19	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	A	1.191	-0.635436	0.03584	.	.	ENSG00000169876	ENST00000306151	T	0.02737	4.18	1.07	-0.378	0.12497	.	.	.	.	.	T	0.01189	0.0039	N	0.11560	0.145	0.09310	N	1	P	0.47604	0.898	B	0.31686	0.134	T	0.51458	-0.8703	9	0.25751	T	0.34	.	5.6279	0.17492	0.4094:0.5906:0.0:0.0	.	704	Q685J3	MUC17_HUMAN	G	704	ENSP00000302716:E704G	ENSP00000302716:E704G	E	+	2	0	MUC17	100463528	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.400000	0.07241	-0.070000	0.12908	-0.949000	0.02662	GAG	.	.	.	none		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
TRPV5	56302	hgsc.bcm.edu	37	7	142606703	142606703	+	Silent	SNP	G	G	A	rs368151896	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr7:142606703G>A	ENST00000265310.1	-	14	2196	c.1848C>T	c.(1846-1848)tcC>tcT	p.S616S		NM_019841.4	NP_062815.2	Q9NQA5	TRPV5_HUMAN	transient receptor potential cation channel, subfamily V, member 5	616					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium ion transport into cytosol (GO:0060402)|ion transmembrane transport (GO:0034220)|protein tetramerization (GO:0051262)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)			NS(1)|breast(2)|central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(14)|lung(32)|ovary(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	67	Melanoma(164;0.059)					CACAGATCCCGGAGCGAGGCC	0.597													G|||	7	0.00139776	0.0	0.0	5008	,	,		20437	0.0		0.0	False		,,,				2504	0.0072				p.S616S		Atlas-SNP	.											.	TRPV5	164	.	0			c.C1848T						PASS	.						79.0	70.0	73.0					7																	142606703		2203	4300	6503	SO:0001819	synonymous_variant	56302	exon14			GATCCCGGAGCGA	AJ271207	CCDS5875.1	7q34	2013-01-10	2002-01-29	2002-02-01	ENSG00000127412	ENSG00000127412		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	3145	protein-coding gene	gene with protein product		606679	"""epithelial calcium channel 1"""	ECAC1		10944439, 10945469, 16382100	Standard	NM_019841		Approved	CaT2	uc003wby.1	Q9NQA5	OTTHUMG00000157157	ENST00000265310.1:c.1848C>T	chr7.hg19:g.142606703G>A		52.0	0.0	.		112.0	6.0	.	NM_019841	A4D2H7|E9PBZ6|Q8N4C1|Q8NDW5|Q8NDX7|Q8NDX8|Q96PM6	Silent	SNP	ENST00000265310.1	hg19	CCDS5875.1																																																																																			.	.	.	weak		0.597	TRPV5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347660.1	NM_019841	
COL22A1	169044	hgsc.bcm.edu	37	8	139707076	139707076	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr8:139707076C>T	ENST00000303045.6	-	33	3085	c.2639G>A	c.(2638-2640)gGg>gAg	p.G880E	COL22A1_ENST00000435777.1_Missense_Mutation_p.G880E|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	880	Collagen-like 7.|Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CACCGGTTCCCCAGGCAGGCC	0.602										HNSCC(7;0.00092)																											p.G880E		Atlas-SNP	.											.	COL22A1	390	.	0			c.G2639A						PASS	.						104.0	98.0	100.0					8																	139707076		2203	4300	6503	SO:0001583	missense	169044	exon33			GGTTCCCCAGGCA	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.2639G>A	chr8.hg19:g.139707076C>T	ENSP00000303153:p.Gly880Glu	108.0	0.0	.		90.0	38.0	.	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Missense_Mutation	SNP	ENST00000303045.6	hg19	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	C	9.130	1.011213	0.19277	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	D;D	0.99353	-5.77;-5.77	4.06	3.19	0.36642	.	0.000000	0.48286	U	0.000190	D	0.99489	0.9818	H	0.96518	3.835	0.43412	D	0.995558	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.99078	1.0836	10	0.87932	D	0	.	7.6856	0.28538	0.0:0.883:0.0:0.117	.	880;880	Q8NFW1-2;Q8NFW1	.;COMA1_HUMAN	E	880;880;593	ENSP00000303153:G880E;ENSP00000387655:G880E	ENSP00000303153:G880E	G	-	2	0	COL22A1	139776258	0.931000	0.31567	0.745000	0.31077	0.080000	0.17528	3.173000	0.50839	1.056000	0.40484	0.551000	0.68910	GGG	.	.	.	none		0.602	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
TOP1MT	116447	hgsc.bcm.edu	37	8	144397926	144397926	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr8:144397926G>C	ENST00000329245.4	-	12	1558	c.1524C>G	c.(1522-1524)caC>caG	p.H508Q	TOP1MT_ENST00000523676.1_Missense_Mutation_p.H410Q|TOP1MT_ENST00000519148.1_Missense_Mutation_p.H410Q|TOP1MT_ENST00000521193.1_Missense_Mutation_p.H410Q|AC087793.1_ENST00000585120.1_RNA	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	508					DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	CTTGGGCTTTGTGCTCAGCCC	0.662																																					p.H508Q		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1524G						PASS	.						131.0	84.0	100.0					8																	144397926		2203	4300	6503	SO:0001583	missense	116447	exon12			GGCTTTGTGCTCA	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1524C>G	chr8.hg19:g.144397926G>C	ENSP00000328835:p.His508Gln	54.0	0.0	.		75.0	35.0	.	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Missense_Mutation	SNP	ENST00000329245.4	hg19	CCDS6400.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	1.192|1.192	-0.634970|-0.634970	0.03584|0.03584	.|.	.|.	ENSG00000184428|ENSG00000184428	ENST00000329245;ENST00000521193;ENST00000519148;ENST00000523676|ENST00000519977	T;T;T;T|.	0.42131|.	0.98;0.98;0.98;0.98|.	3.56|3.56	-0.755|-0.755	0.11061|0.11061	DNA breaking-rejoining enzyme, catalytic core (1);DNA topoisomerase I, C-terminal, eukaryotic-type (1);DNA topoisomerase I, catalytic core, alpha/beta subdomain, eukaryotic-type (1);DNA topoisomerases I, dispensable insert, eukaryotic-type (1);|.	1.222760|.	0.06298|.	U|.	0.700351|.	T|T	0.41119|0.41119	0.1145|0.1145	M|M	0.64997|0.64997	1.995|1.995	0.09310|0.09310	N|N	1|1	P;B|.	0.43826|.	0.818;0.437|.	B;B|.	0.43194|.	0.411;0.131|.	T|T	0.38308|0.38308	-0.9667|-0.9667	10|5	0.18276|.	T|.	0.48|.	.|.	4.746|4.746	0.13038|0.13038	0.4744:0.1621:0.3634:0.0|0.4744:0.1621:0.3634:0.0	.|.	303;508|.	E7ESI1;Q969P6|.	.;TOP1M_HUMAN|.	Q|E	508;410;410;410|18	ENSP00000328835:H508Q;ENSP00000428369:H410Q;ENSP00000429169:H410Q;ENSP00000429181:H410Q|.	ENSP00000328835:H508Q|.	H|Q	-|-	3|1	2|0	TOP1MT|TOP1MT	144469301|144469301	0.018000|0.018000	0.18449|0.18449	0.000000|0.000000	0.03702|0.03702	0.002000|0.002000	0.02628|0.02628	0.132000|0.132000	0.15891|0.15891	-0.145000|-0.145000	0.11294|0.11294	-0.351000|-0.351000	0.07748|0.07748	CAC|CAA	.	.	.	none		0.662	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
KCNT1	57582	hgsc.bcm.edu	37	9	138649177	138649177	+	Missense_Mutation	SNP	C	C	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr9:138649177C>G	ENST00000263604.3	+	9	652	c.652C>G	c.(652-654)Ccc>Gcc	p.P218A	KCNT1_ENST00000487664.1_Missense_Mutation_p.P189A|KCNT1_ENST00000298480.5_Missense_Mutation_p.P237A|KCNT1_ENST00000371757.2_Missense_Mutation_p.P237A|KCNT1_ENST00000488444.2_Missense_Mutation_p.P218A|KCNT1_ENST00000486577.2_Missense_Mutation_p.P198A|KCNT1_ENST00000490355.2_Missense_Mutation_p.P218A|KCNT1_ENST00000491806.2_Missense_Mutation_p.P204A			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	218					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		CCTGTTCATCCCCGTCTTTCT	0.667																																					p.P237A		Atlas-SNP	.											.	KCNT1	139	.	0			c.C709G						PASS	.						51.0	58.0	55.0					9																	138649177		2203	4300	6503	SO:0001583	missense	57582	exon9			TTCATCCCCGTCT	AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.652C>G	chr9.hg19:g.138649177C>G	ENSP00000263604:p.Pro218Ala	34.0	0.0	.		55.0	18.0	.	NM_020822	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	ENST00000263604.3	hg19		.	.	.	.	.	.	.	.	.	.	.	23.4	4.416656	0.83449	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;D;T	0.97186	1.86;1.86;1.86;-4.28;1.86	4.63	4.63	0.57726	.	0.000000	0.85682	U	0.000000	D	0.98337	0.9448	M	0.79926	2.475	0.80722	D	1	D;D;D	0.89917	1.0;0.998;0.999	D;D;D	0.91635	0.999;0.989;0.992	D	0.99577	1.0972	10	0.72032	D	0.01	-28.7902	16.4704	0.84109	0.0:1.0:0.0:0.0	.	204;237;189	C9JYL2;B9EGP2;G5E9V0	.;.;.	A	189;237;237;184;198;204;218;218;218	ENSP00000417851:P189A;ENSP00000298480:P237A;ENSP00000360822:P237A;ENSP00000420764:P184A;ENSP00000263604:P218A	ENSP00000263604:P218A	P	+	1	0	KCNT1	137788998	1.000000	0.71417	0.995000	0.50966	0.866000	0.49608	7.427000	0.80284	2.124000	0.65301	0.460000	0.39030	CCC	.	.	.	none		0.667	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_020822	
GPRIN2	9721	hgsc.bcm.edu	37	10	46999193	46999193	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr10:46999193G>A	ENST00000374317.1	+	3	586	c.313G>A	c.(313-315)Gac>Aac	p.D105N	GPRIN2_ENST00000374314.4_Missense_Mutation_p.D105N	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	105										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GGGCGGCAGTGACCTGTGTCG	0.652																																					p.D105N		Atlas-SNP	.											.	GPRIN2	94	.	0			c.G313A						PASS	.						30.0	29.0	29.0					10																	46999193		2196	4288	6484	SO:0001583	missense	9721	exon3			GGCAGTGACCTGT	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.313G>A	chr10.hg19:g.46999193G>A	ENSP00000363436:p.Asp105Asn	8.0	0.0	.		23.0	8.0	.	NM_014696	Q5SVF0	Missense_Mutation	SNP	ENST00000374317.1	hg19	CCDS31192.1	.	.	.	.	.	.	.	.	.	.	G	17.75	3.467432	0.63625	.	.	ENSG00000204175	ENST00000374317;ENST00000374314	T;T	0.03982	3.74;3.74	5.11	5.11	0.69529	.	0.279617	0.25830	N	0.028026	T	0.11495	0.0280	L	0.54323	1.7	0.09310	N	1	D	0.56746	0.977	P	0.52957	0.714	T	0.04678	-1.0934	10	0.45353	T	0.12	-14.3008	14.245	0.65983	0.0:0.0:1.0:0.0	.	105	O60269	GRIN2_HUMAN	N	105	ENSP00000363436:D105N;ENSP00000363433:D105N	ENSP00000363433:D105N	D	+	1	0	GPRIN2	46419199	0.655000	0.27376	0.709000	0.30452	0.969000	0.65631	3.163000	0.50763	2.833000	0.97629	0.650000	0.86243	GAC	.	.	.	none		0.652	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
PNLIPRP1	5407	hgsc.bcm.edu	37	10	118357347	118357347	+	Silent	SNP	T	T	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr10:118357347T>C	ENST00000528052.1	+	7	653	c.582T>C	c.(580-582)gaT>gaC	p.D194D	PNLIPRP1_ENST00000534537.1_Silent_p.D194D|PNLIPRP1_ENST00000358834.4_Silent_p.D194D			P54315	LIPR1_HUMAN	pancreatic lipase-related protein 1	194					lipid metabolic process (GO:0006629)	extracellular region (GO:0005576)	calcium ion binding (GO:0005509)|triglyceride lipase activity (GO:0004806)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	38				all cancers(201;0.0161)		TAGGGTTGGATCCTGTAGAAG	0.507																																					p.D194D		Atlas-SNP	.											.	PNLIPRP1	82	.	0			c.T582C						PASS	.						149.0	129.0	136.0					10																	118357347		2203	4300	6503	SO:0001819	synonymous_variant	5407	exon7			GTTGGATCCTGTA	BC025784	CCDS7595.1	10q26.12	2006-07-04			ENSG00000187021	ENSG00000187021			9156	protein-coding gene	gene with protein product		604422				1379598	Standard	NM_006229		Approved	PLRP1	uc001lco.1	P54315	OTTHUMG00000019109	ENST00000528052.1:c.582T>C	chr10.hg19:g.118357347T>C		141.0	0.0	.		149.0	57.0	.	NM_006229	Q68D83|Q68DR6|Q8TAU2|Q9BS82	Silent	SNP	ENST00000528052.1	hg19	CCDS7595.1																																																																																			.	.	.	none		0.507	PNLIPRP1-011	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384633.1	NM_006229	
MUC2	4583	hgsc.bcm.edu	37	11	1094686	1094686	+	Missense_Mutation	SNP	C	C	T	rs375767205		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:1094686C>T	ENST00000441003.2	+	31	5801	c.5774C>T	c.(5773-5775)aCg>aTg	p.T1925M	MUC2_ENST00000361558.6_Missense_Mutation_p.T63M|MUC2_ENST00000333592.6_Missense_Mutation_p.T213M	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	4287					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)				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)	CGCGGTACCACGACCGGGTCA	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		16685	0.0		0.0	False		,,,				2504	0.001				p.T1921M		Atlas-SNP	.											.	MUC2	614	.	0			c.C5762T						PASS	.		MET/THR	3,4229		0,3,2113	70.0	87.0	82.0		5759	-0.2	0.0	11		82	1,8447		0,1,4223	no	missense	MUC2	NM_002457.2	81	0,4,6336	TT,TC,CC		0.0118,0.0709,0.0315	benign	1920/2813	1094686	4,12676	2116	4224	6340	SO:0001583	missense	4583	exon32			GTACCACGACCGG	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.5774C>T	chr11.hg19:g.1094686C>T	ENSP00000415183:p.Thr1925Met	80.0	0.0	.		165.0	64.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	7.600	0.672559	0.14776	7.09E-4	1.18E-4	ENSG00000198788	ENST00000441003;ENST00000361558;ENST00000333592	T;T;T	0.51071	2.55;0.72;3.15	2.06	-0.251	0.13003	.	.	.	.	.	T	0.40094	0.1103	M	0.65975	2.015	0.09310	N	1	B	0.18610	0.029	B	0.04013	0.001	T	0.40869	-0.9540	9	0.62326	D	0.03	.	3.434	0.07438	0.2454:0.5996:0.0:0.155	.	1925	E7EUV1	.	M	1925;63;213	ENSP00000415183:T1925M;ENSP00000354885:T63M;ENSP00000331373:T213M	ENSP00000331373:T213M	T	+	2	0	MUC2	1084686	0.000000	0.05858	0.000000	0.03702	0.017000	0.09413	0.419000	0.21247	-0.196000	0.10366	-0.354000	0.07668	ACG	.	.	.	weak		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
ABTB2	25841	hgsc.bcm.edu	37	11	34378951	34378951	+	Silent	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:34378951G>T	ENST00000435224.2	-	1	604	c.180C>A	c.(178-180)tcC>tcA	p.S60S	ABTB2_ENST00000298992.2_5'Flank	NM_145804.2	NP_665803.2	Q8N961	ABTB2_HUMAN	ankyrin repeat and BTB (POZ) domain containing 2	60					cellular response to toxic substance (GO:0097237)	nucleus (GO:0005634)				breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(1)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(20;0.0691)				GGCTGTTCATGGAGCCGGAGT	0.692																																					p.S60S		Atlas-SNP	.											.	ABTB2	101	.	0			c.C180A						PASS	.																																			SO:0001819	synonymous_variant	25841	exon1			GTTCATGGAGCCG	AK056863	CCDS7890.1, CCDS7890.2	11p13	2013-10-02			ENSG00000166016	ENSG00000166016		"""BTB/POZ domain containing"", ""Ankyrin repeat domain containing"""	23842	protein-coding gene	gene with protein product							Standard	NM_145804		Approved	DKFZP586C1619, BTBD22, ABTB2A	uc001mvl.2	Q8N961	OTTHUMG00000044382	ENST00000435224.2:c.180C>A	chr11.hg19:g.34378951G>T		13.0	0.0	.		62.0	22.0	.	NM_145804	A8K6S9|E9PRW7|Q52LD6|Q6MZW4|Q8NB44	Silent	SNP	ENST00000435224.2	hg19	CCDS7890.2																																																																																			.	.	.	none		0.692	ABTB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388703.3	NM_145804	
OR4C3	256144	hgsc.bcm.edu	37	11	48347236	48347236	+	Silent	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:48347236C>T	ENST00000319856.4	+	1	765	c.744C>T	c.(742-744)taC>taT	p.Y248Y		NM_001004702.1	NP_001004702.1	Q8NH37	OR4C3_HUMAN	olfactory receptor, family 4, subfamily C, member 3	221						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(18)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	32						TCATCCTGTACTCCTTGAGGT	0.493																																					p.Y248Y		Atlas-SNP	.											.	OR4C3	75	.	0			c.C744T						PASS	.						268.0	192.0	218.0					11																	48347236		2201	4298	6499	SO:0001819	synonymous_variant	256144	exon1			CCTGTACTCCTTG	AB065567	CCDS31489.1	11p11.2	2012-08-09				ENSG00000176547		"""GPCR / Class A : Olfactory receptors"""	14697	protein-coding gene	gene with protein product							Standard	NM_001004702		Approved		uc010rhv.2	Q8NH37	OTTHUMG00000166579	ENST00000319856.4:c.744C>T	chr11.hg19:g.48347236C>T		267.0	0.0	.		280.0	46.0	.	NM_001004702	B2RNF2|Q6IFB3	Silent	SNP	ENST00000319856.4	hg19	CCDS31489.1																																																																																			.	.	.	none		0.493	OR4C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390557.1	NM_001004702	
RPS6KA4	8986	hgsc.bcm.edu	37	11	64136019	64136019	+	Missense_Mutation	SNP	G	G	A	rs199674030		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:64136019G>A	ENST00000334205.4	+	11	1345	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	RPS6KA4_ENST00000294261.4_Intron|MIR1237_ENST00000408346.1_RNA|RPS6KA4_ENST00000528057.1_Missense_Mutation_p.R420H	NM_003942.2	NP_003933.1	O75676	KS6A4_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 4	427	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|negative regulation of cytokine production (GO:0001818)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|mitogen-activated protein kinase p38 binding (GO:0048273)|protein serine/threonine kinase activity (GO:0004674)|ribosomal protein S6 kinase activity (GO:0004711)			breast(1)|endometrium(3)|lung(7)|ovary(1)|prostate(1)	13						GTGTGTCGCCGCTGCCGCCAG	0.701													G|||	1	0.000199681	0.0	0.0	5008	,	,		9970	0.0		0.001	False		,,,				2504	0.0				p.R427H		Atlas-SNP	.											.	RPS6KA4	85	.	0			c.G1280A						PASS	.	G	HIS/ARG,HIS/ARG	1,4357		0,1,2178	9.0	11.0	11.0		1262,1280	4.5	1.0	11		11	12,8514		0,12,4251	yes	missense,missense	RPS6KA4	NM_001006944.1,NM_003942.2	29,29	0,13,6429	AA,AG,GG		0.1407,0.0229,0.1009	probably-damaging,probably-damaging	421/767,427/773	64136019	13,12871	2179	4263	6442	SO:0001583	missense	8986	exon11			GTCGCCGCTGCCG	AJ010119	CCDS8073.1, CCDS73313.1	11q11-q13	2011-04-05	2002-08-29		ENSG00000162302	ENSG00000162302			10433	protein-coding gene	gene with protein product		603606	"""ribosomal protein S6 kinase, 90kD, polypeptide 4"""			9792677, 9687510	Standard	XM_005274379		Approved	RSK-B, MSK2	uc001oae.3	O75676	OTTHUMG00000046094	ENST00000334205.4:c.1280G>A	chr11.hg19:g.64136019G>A	ENSP00000333896:p.Arg427His	1.0	0.0	.		13.0	10.0	.	NM_003942	A8K7Z8|O75585|Q53ES8	Missense_Mutation	SNP	ENST00000334205.4	hg19	CCDS8073.1	.	.	.	.	.	.	.	.	.	.	g	17.24	3.339473	0.60963	2.29E-4	0.001407	ENSG00000162302	ENST00000528057;ENST00000334205;ENST00000530504	T;T;T	0.42513	0.97;0.97;0.97	4.5	4.5	0.54988	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.221656	0.37530	N	0.002053	T	0.47451	0.1446	L	0.33339	1.005	0.09310	N	0.999995	D;D;D	0.69078	0.963;0.997;0.984	P;D;P	0.65323	0.616;0.934;0.843	T	0.32214	-0.9915	10	0.72032	D	0.01	.	8.538	0.33375	0.108:0.0:0.892:0.0	.	420;427;421	E9PJN1;O75676;O75676-2	.;KS6A4_HUMAN;.	H	420;427;405	ENSP00000435580:R420H;ENSP00000333896:R427H;ENSP00000432945:R405H	ENSP00000333896:R427H	R	+	2	0	RPS6KA4	63892595	0.333000	0.24731	0.997000	0.53966	0.668000	0.39293	2.159000	0.42339	2.059000	0.61396	0.462000	0.41574	CGC	.	.	.	weak		0.701	RPS6KA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106246.2	NM_003942	
FGF19	9965	hgsc.bcm.edu	37	11	69514314	69514314	+	Missense_Mutation	SNP	C	C	T	rs377419016		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:69514314C>T	ENST00000294312.3	-	3	1132	c.367G>A	c.(367-369)Gag>Aag	p.E123K		NM_005117.2	NP_005108.1	O95750	FGF19_HUMAN	fibroblast growth factor 19	123					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|heart development (GO:0007507)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|negative regulation of bile acid biosynthetic process (GO:0070858)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of glucose import (GO:0046326)|positive regulation of JNK cascade (GO:0046330)	extracellular region (GO:0005576)	fibroblast growth factor receptor binding (GO:0005104)			large_intestine(2)|lung(2)|skin(2)	6	all_cancers(3;5.53e-114)|all_epithelial(3;1.34e-121)|Breast(3;9.28e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;6.15e-15)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;3.05e-56)|all cancers(3;2.69e-50)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)			ATCTCCTCCTCGAAAGCACAG	0.562																																					p.E123K		Atlas-SNP	.											.	FGF19	11	.	0			c.G367A						PASS	.	C	LYS/GLU	0,4400		0,0,2200	51.0	47.0	48.0		367	2.8	1.0	11		48	1,8587	1.2+/-3.3	0,1,4293	no	missense	FGF19	NM_005117.2	56	0,1,6493	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	123/217	69514314	1,12987	2200	4294	6494	SO:0001583	missense	9965	exon3			CCTCCTCGAAAGC	AB018122	CCDS8193.1	11q13.1	2008-02-01			ENSG00000162344	ENSG00000162344			3675	protein-coding gene	gene with protein product		603891				9931477, 10525310	Standard	NM_005117		Approved		uc001opf.3	O95750	OTTHUMG00000167886	ENST00000294312.3:c.367G>A	chr11.hg19:g.69514314C>T	ENSP00000294312:p.Glu123Lys	106.0	0.0	.		110.0	5.0	.	NM_005117		Missense_Mutation	SNP	ENST00000294312.3	hg19	CCDS8193.1	.	.	.	.	.	.	.	.	.	.	C	10.10	1.258639	0.23051	0.0	1.16E-4	ENSG00000162344	ENST00000294312	T	0.80304	-1.36	4.9	2.82	0.32997	.	0.379197	0.28659	N	0.014570	T	0.49423	0.1556	N	0.11341	0.13	0.34812	D	0.737793	P	0.40376	0.715	B	0.25759	0.063	T	0.61955	-0.6956	10	0.02654	T	1	-19.2795	7.4934	0.27475	0.0:0.7302:0.166:0.1038	.	123	O95750	FGF19_HUMAN	K	123	ENSP00000294312:E123K	ENSP00000294312:E123K	E	-	1	0	FGF19	69223495	0.833000	0.29383	0.979000	0.43373	0.961000	0.63080	1.017000	0.29989	0.323000	0.23307	0.555000	0.69702	GAG	.	.	.	weak		0.562	FGF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396833.1	NM_005117	
EXPH5	23086	hgsc.bcm.edu	37	11	108384826	108384826	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:108384826C>T	ENST00000265843.4	-	6	1518	c.1408G>A	c.(1408-1410)Gga>Aga	p.G470R	EXPH5_ENST00000428840.1_Missense_Mutation_p.G394R|EXPH5_ENST00000524840.1_5'UTR|EXPH5_ENST00000443411.1_Missense_Mutation_p.G282R|EXPH5_ENST00000525344.1_Missense_Mutation_p.G463R	NM_015065.2	NP_055880	Q8NEV8	EXPH5_HUMAN	exophilin 5	470					intracellular protein transport (GO:0006886)|keratinocyte development (GO:0003334)|multivesicular body sorting pathway (GO:0071985)|positive regulation of exocytosis (GO:0045921)|positive regulation of protein secretion (GO:0050714)	endosome (GO:0005768)	Rab GTPase binding (GO:0017137)			breast(3)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(13)|liver(1)|lung(34)|ovary(3)|pancreas(2)|prostate(2)|skin(11)|stomach(3)|upper_aerodigestive_tract(1)	91		all_cancers(61;3.99e-08)|Acute lymphoblastic leukemia(157;3.97e-05)|Melanoma(852;4.04e-05)|all_epithelial(67;0.000116)|all_hematologic(158;0.000315)|Breast(348;0.104)|all_neural(303;0.16)		Epithelial(105;8.1e-06)|BRCA - Breast invasive adenocarcinoma(274;1.22e-05)|all cancers(92;0.000129)|OV - Ovarian serous cystadenocarcinoma(223;0.11)|Colorectal(284;0.184)		CTCTGTTCTCCGCTTCGTCCA	0.433																																					p.G470R		Atlas-SNP	.											.	EXPH5	193	.	0			c.G1408A						PASS	.						130.0	127.0	128.0					11																	108384826		2201	4298	6499	SO:0001583	missense	23086	exon6			GTTCTCCGCTTCG		CCDS8341.1	11q22.3	2008-02-05			ENSG00000110723	ENSG00000110723			30578	protein-coding gene	gene with protein product	"""synaptotagmin-like homologue lacking C2 domains b"""	612878				9734811, 11773082	Standard	NM_015065		Approved	SLAC2-B	uc001pkk.3	Q8NEV8	OTTHUMG00000166536	ENST00000265843.4:c.1408G>A	chr11.hg19:g.108384826C>T	ENSP00000265843:p.Gly470Arg	96.0	0.0	.		109.0	27.0	.	NM_015065	Q2KHM1|Q9Y4D6	Missense_Mutation	SNP	ENST00000265843.4	hg19	CCDS8341.1	.	.	.	.	.	.	.	.	.	.	C	1.713	-0.498555	0.04291	.	.	ENSG00000110723	ENST00000265843;ENST00000428840;ENST00000443411;ENST00000525344;ENST00000439956;ENST00000526312;ENST00000533052	T;T;T;T;T;T	0.03152	4.59;4.53;4.37;4.59;4.47;4.03	5.8	4.61	0.57282	.	0.279252	0.31461	N	0.007616	T	0.00815	0.0027	N	0.00104	-2.125	0.19945	N	0.999949	B	0.06786	0.001	B	0.06405	0.002	T	0.43877	-0.9364	10	0.02654	T	1	-6.2184	9.3795	0.38304	0.0:0.0824:0.0:0.9176	.	470	Q8NEV8	EXPH5_HUMAN	R	470;394;282;463;314;394;282	ENSP00000265843:G470R;ENSP00000391966:G394R;ENSP00000411390:G282R;ENSP00000432546:G463R;ENSP00000432683:G394R;ENSP00000446434:G282R	ENSP00000265843:G470R	G	-	1	0	EXPH5	107890036	0.012000	0.17670	0.950000	0.38849	0.930000	0.56654	0.504000	0.22626	1.011000	0.39340	-0.423000	0.05987	GGA	.	.	.	none		0.433	EXPH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390279.1	NM_015065	
ABCG4	64137	hgsc.bcm.edu	37	11	119027153	119027153	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:119027153G>T	ENST00000449422.2	+	7	989	c.801G>T	c.(799-801)atG>atT	p.M267I	ABCG4_ENST00000307417.3_Missense_Mutation_p.M267I|ABCG4_ENST00000531739.1_Missense_Mutation_p.M267I	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	267	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		TCTTTGAGATGTTTGACAAGG	0.577																																					p.M267I		Atlas-SNP	.											.	ABCG4	77	.	0			c.G801T						PASS	.						141.0	137.0	138.0					11																	119027153		2200	4295	6495	SO:0001583	missense	64137	exon7			TGAGATGTTTGAC	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.801G>T	chr11.hg19:g.119027153G>T	ENSP00000406874:p.Met267Ile	199.0	0.0	.		231.0	131.0	.	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	16.92	3.255972	0.59321	.	.	ENSG00000172350	ENST00000307417;ENST00000449422;ENST00000531739	T;T;T	0.34667	1.35;1.35;1.35	4.82	4.82	0.62117	ATPase, AAA+ type, core (1);ABC transporter-like (1);	0.037537	0.85682	D	0.000000	T	0.25382	0.0617	N	0.19112	0.55	0.80722	D	1	B	0.32245	0.361	B	0.25140	0.058	T	0.05971	-1.0853	10	0.38643	T	0.18	-32.7477	18.0972	0.89494	0.0:0.0:1.0:0.0	.	267	Q9H172	ABCG4_HUMAN	I	267	ENSP00000304111:M267I;ENSP00000406874:M267I;ENSP00000434318:M267I	ENSP00000304111:M267I	M	+	3	0	ABCG4	118532363	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.808000	0.86044	2.502000	0.84385	0.655000	0.94253	ATG	.	.	.	none		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
PIK3C2G	5288	hgsc.bcm.edu	37	12	18435382	18435382	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:18435382G>A	ENST00000266497.5	+	1	405	c.367G>A	c.(367-369)Gaa>Aaa	p.E123K	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.E123K|RERGL_ENST00000541632.1_Intron|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.E123K|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.E123K			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	123					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)			breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TACGAATAAAGAATGCTCCTG	0.398																																					p.E123K		Atlas-SNP	.											.	PIK3C2G	315	.	0			c.G367A						PASS	.						69.0	69.0	69.0					12																	18435382		1829	4080	5909	SO:0001583	missense	5288	exon2			AATAAAGAATGCT	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.367G>A	chr12.hg19:g.18435382G>A	ENSP00000266497:p.Glu123Lys	40.0	0.0	.		44.0	6.0	.	NM_004570	A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	hg19	CCDS44839.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.480900	0.44044	.	.	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.62788	1.35;-0.0;-0.0;-0.0	4.79	2.91	0.33838	.	.	.	.	.	T	0.44138	0.1279	N	0.24115	0.695	0.09310	N	1	B;B	0.31548	0.328;0.22	B;B	0.28011	0.085;0.039	T	0.15809	-1.0424	9	0.15952	T	0.53	-4.9931	11.4633	0.50223	0.0:0.3511:0.6488:0.0	.	123;123	F5H369;O75747	.;P3C2G_HUMAN	K	123	ENSP00000443850:E123K;ENSP00000404845:E123K;ENSP00000266497:E123K;ENSP00000445381:E123K	ENSP00000266497:E123K	E	+	1	0	PIK3C2G	18326649	0.022000	0.18835	0.006000	0.13384	0.083000	0.17756	0.866000	0.27954	0.897000	0.36392	0.655000	0.94253	GAA	.	.	.	none		0.398	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
PKP2	5318	hgsc.bcm.edu	37	12	33031889	33031889	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:33031889G>A	ENST00000070846.6	-	2	325	c.301C>T	c.(301-303)Cgt>Tgt	p.R101C	PKP2_ENST00000340811.4_Missense_Mutation_p.R101C	NM_004572.3	NP_004563.2	Q99959	PKP2_HUMAN	plakophilin 2	101					adherens junction maintenance (GO:0034334)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cardiac muscle cell action potential (GO:0086001)|cardiac muscle cell action potential involved in contraction (GO:0086002)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cell-cell signaling involved in cardiac conduction (GO:0086019)|desmosome assembly (GO:0002159)|gap junction assembly (GO:0016264)|heart development (GO:0007507)|intermediate filament bundle assembly (GO:0045110)|lipid homeostasis (GO:0055088)|maintenance of organ identity (GO:0048496)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of tight junction assembly (GO:2000810)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)	adherens junction (GO:0005912)|cell junction (GO:0030054)|cell-cell junction (GO:0005911)|desmosome (GO:0030057)|integral component of membrane (GO:0016021)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|protein kinase C binding (GO:0005080)|sodium channel regulator activity (GO:0017080)			NS(1)|breast(2)|endometrium(1)|kidney(9)|large_intestine(8)|lung(21)|ovary(1)|pancreas(2)|prostate(2)|skin(2)|urinary_tract(1)	50	Lung NSC(5;9.35e-07)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.239)					ACAGGGGAACGGCCTCCAACA	0.378																																					p.R101C		Atlas-SNP	.											.	PKP2	110	.	0			c.C301T						PASS	.						96.0	91.0	93.0					12																	33031889		2203	4300	6503	SO:0001583	missense	5318	exon2			GGGAACGGCCTCC	X97675	CCDS8731.1, CCDS31771.1	12p11	2014-09-17				ENSG00000057294		"""Armadillo repeat containing"""	9024	protein-coding gene	gene with protein product		602861				8922383	Standard	NM_001005242		Approved		uc001rlj.4	Q99959	OTTHUMG00000169500	ENST00000070846.6:c.301C>T	chr12.hg19:g.33031889G>A	ENSP00000070846:p.Arg101Cys	70.0	0.0	.		72.0	4.0	.	NM_004572	A0AV37|B8QFA1|B8QGS6|B8QGS7|D3DUW9|Q4VC01|Q99960	Missense_Mutation	SNP	ENST00000070846.6	hg19	CCDS8731.1	.	.	.	.	.	.	.	.	.	.	G	16.45	3.126134	0.56721	.	.	ENSG00000057294	ENST00000340811;ENST00000070846;ENST00000537278	T;T	0.81163	-1.46;-1.42	5.7	3.72	0.42706	.	1.351310	0.04721	N	0.419289	T	0.76076	0.3937	L	0.47716	1.5	0.09310	N	1	B;B;B	0.21381	0.055;0.033;0.033	B;B;B	0.10450	0.005;0.002;0.003	T	0.60835	-0.7184	10	0.52906	T	0.07	-0.1096	8.3857	0.32499	0.0822:0.0:0.7645:0.1533	.	101;101;101	Q99959-2;A0AV37;Q99959	.;.;PKP2_HUMAN	C	101	ENSP00000342800:R101C;ENSP00000070846:R101C	ENSP00000070846:R101C	R	-	1	0	PKP2	32923156	0.000000	0.05858	0.010000	0.14722	0.864000	0.49448	0.261000	0.18442	2.679000	0.91253	0.650000	0.86243	CGT	.	.	.	none		0.378	PKP2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404449.1	NM_004572	
KRT86	3892	hgsc.bcm.edu	37	12	52700004	52700004	+	Missense_Mutation	SNP	A	A	G	rs542735645		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:52700004A>G	ENST00000423955.2	+	9	1365	c.1187A>G	c.(1186-1188)aAg>aGg	p.K396R	KRT86_ENST00000544024.1_Missense_Mutation_p.K396R|KRT86_ENST00000293525.5_Missense_Mutation_p.K396R|RP11-845M18.6_ENST00000552441.1_RNA			O43790	KRT86_HUMAN	keratin 86	396	Coil 2.|Rod.					extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			breast(1)|cervix(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(357;0.189)		ATGAACTCCAAGCTGGGCCTG	0.637											OREG0021845	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	a|||	1	0.000199681	0.0	0.0014	5008	,	,		18796	0.0		0.0	False		,,,				2504	0.0				p.K396R		Atlas-SNP	.											.	KRT86	33	.	0			c.A1187G						PASS	.						78.0	77.0	77.0					12																	52700004		2203	4295	6498	SO:0001583	missense	3892	exon7			ACTCCAAGCTGGG	X99142	CCDS41785.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000170442		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6463	protein-coding gene	gene with protein product	"""hard keratin type II 6"""	601928	"""keratin, hair, basic, 6 (monilethrix)"""	KRTHB6		9241275, 16831889	Standard	NM_002284		Approved	MNX, Hb6	uc001sad.3	O43790		ENST00000423955.2:c.1187A>G	chr12.hg19:g.52700004A>G	ENSP00000444533:p.Lys396Arg	97.0	0.0	.	987	170.0	52.0	.	NM_002284	P78387	Missense_Mutation	SNP	ENST00000423955.2	hg19	CCDS41785.1	.	.	.	.	.	.	.	.	.	.	A	28.8	4.954205	0.92726	.	.	ENSG00000170442;ENSG00000170442;ENSG00000170442;ENSG00000258832	ENST00000544024;ENST00000423955;ENST00000293525;ENST00000553310	D;D;D	0.94376	-3.41;-3.41;-3.41	5.35	5.35	0.76521	Filament (1);	0.000000	0.43747	U	0.000525	D	0.97179	0.9078	M	0.91300	3.195	0.43399	D	0.99552	D	0.89917	1.0	D	0.80764	0.994	D	0.98008	1.0364	10	0.87932	D	0	.	13.9101	0.63862	1.0:0.0:0.0:0.0	.	396	O43790	KRT86_HUMAN	R	396	ENSP00000443169:K396R;ENSP00000444533:K396R;ENSP00000293525:K396R	ENSP00000293525:K396R	K	+	2	0	AC021066.1;KRT86	50986271	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.425000	0.80255	2.020000	0.59435	0.454000	0.30748	AAG	.	.	.	none		0.637	KRT86-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404911.1	NM_002284	
SRGAP1	57522	hgsc.bcm.edu	37	12	64491125	64491125	+	Missense_Mutation	SNP	G	G	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:64491125G>C	ENST00000355086.3	+	15	2307	c.1783G>C	c.(1783-1785)Gaa>Caa	p.E595Q	SRGAP1_ENST00000357825.3_Missense_Mutation_p.E572Q|SRGAP1_ENST00000543397.1_Missense_Mutation_p.E532Q|RP11-196H14.2_ENST00000535594.1_RNA	NM_020762.2	NP_065813.1	Q7Z6B7	SRGP1_HUMAN	SLIT-ROBO Rho GTPase activating protein 1	595	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				axon guidance (GO:0007411)|cell migration (GO:0016477)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(26)|ovary(2)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	65			GBM - Glioblastoma multiforme(3;0.000139)|BRCA - Breast invasive adenocarcinoma(9;0.225)	GBM - Glioblastoma multiforme(28;0.0608)		CTTTCCTAAGGAAAGATTTAA	0.398																																					p.E595Q		Atlas-SNP	.											SRGAP1,NS,carcinoma,0,1	SRGAP1	146	.	0			c.G1783C						PASS	.						89.0	86.0	87.0					12																	64491125		2203	4300	6503	SO:0001583	missense	57522	exon15			CCTAAGGAAAGAT	AB037725	CCDS8967.1	12q13.13	2011-07-04			ENSG00000196935	ENSG00000196935		"""Rho GTPase activating proteins"""	17382	protein-coding gene	gene with protein product		606523				11672528	Standard	NM_020762		Approved	KIAA1304, ARHGAP13	uc010ssp.1	Q7Z6B7	OTTHUMG00000168750	ENST00000355086.3:c.1783G>C	chr12.hg19:g.64491125G>C	ENSP00000347198:p.Glu595Gln	49.0	0.0	.		54.0	18.0	.	NM_020762	Q9H8A3|Q9P2P2	Missense_Mutation	SNP	ENST00000355086.3	hg19	CCDS8967.1	.	.	.	.	.	.	.	.	.	.	G	31	5.095528	0.94197	.	.	ENSG00000196935	ENST00000355086;ENST00000357825;ENST00000543397	T;T;T	0.48201	0.82;0.82;0.82	5.48	5.48	0.80851	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.000000	0.36002	U	0.002860	T	0.62636	0.2444	L	0.53561	1.675	0.80722	D	1	P;P	0.52463	0.953;0.946	P;P	0.59825	0.864;0.786	T	0.57266	-0.7841	9	.	.	.	.	19.7379	0.96215	0.0:0.0:1.0:0.0	.	595;532	Q7Z6B7;G5EA48	SRGP1_HUMAN;.	Q	595;572;532	ENSP00000347198:E595Q;ENSP00000350480:E572Q;ENSP00000437948:E532Q	.	E	+	1	0	SRGAP1	62777392	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.748000	0.98867	2.733000	0.93635	0.655000	0.94253	GAA	.	.	.	none		0.398	SRGAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400896.1		
CCER1	196477	hgsc.bcm.edu	37	12	91347593	91347593	+	Missense_Mutation	SNP	A	A	C	rs137989103		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:91347593A>C	ENST00000358859.2	-	1	1360	c.927T>G	c.(925-927)gaT>gaG	p.D309E	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	309	Glu-rich.																cttcctcctcatcttcgacct	0.527																																					p.D309E		Atlas-SNP	.											.	.	.	.	0			c.T927G						PASS	.						221.0	189.0	200.0					12																	91347593		2203	4300	6503	SO:0001583	missense	196477	exon1			CTCCTCATCTTCG	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 12"""	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.927T>G	chr12.hg19:g.91347593A>C	ENSP00000351727:p.Asp309Glu	97.0	0.0	.		101.0	9.0	.	NM_152638	Q8TC47	Missense_Mutation	SNP	ENST00000358859.2	hg19	CCDS9036.1	.	.	.	.	.	.	.	.	.	.	A	0.040	-1.288355	0.01387	.	.	ENSG00000197651	ENST00000358859	T	0.15139	2.45	4.85	-9.69	0.00524	.	1.727330	0.03768	N	0.259267	T	0.05686	0.0149	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.37934	-0.9684	10	0.02654	T	1	-2.4783	8.0014	0.30299	0.6481:0.1314:0.0:0.2205	.	309	Q8TC90	CL012_HUMAN	E	309	ENSP00000351727:D309E	ENSP00000351727:D309E	D	-	3	2	C12orf12	89871724	0.000000	0.05858	0.000000	0.03702	0.094000	0.18550	-0.544000	0.06077	-1.269000	0.02436	0.378000	0.23410	GAT	.	.	.	weak		0.527	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638	
TBX5	6910	hgsc.bcm.edu	37	12	114841566	114841566	+	Silent	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:114841566G>A	ENST00000310346.4	-	2	804	c.138C>T	c.(136-138)ttC>ttT	p.F46F	TBX5_ENST00000526441.1_Silent_p.F46F|TBX5_ENST00000349716.5_Intron|TBX5_ENST00000405440.2_Silent_p.F46F|TBX5_ENST00000552726.1_5'UTR	NM_000192.3	NP_000183.2	Q99593	TBX5_HUMAN	T-box 5	46				GFGLAHTPLEPDAKDLPCDSKPESALGAPSKSPSSPQAAFT QQ -> ALAGAHLWSLTQKTCLRFEPRARSGPPASPPGRPR SRLHPA (in Ref. 1; CAA70592). {ECO:0000305}.	apoptotic nuclear changes (GO:0030262)|atrial septum morphogenesis (GO:0060413)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His development (GO:0003166)|cardiac left ventricle formation (GO:0003218)|cardiac muscle cell differentiation (GO:0055007)|cell migration involved in coronary vasculogenesis (GO:0060980)|cell-cell signaling (GO:0007267)|embryonic forelimb morphogenesis (GO:0035115)|embryonic limb morphogenesis (GO:0030326)|endocardial cushion development (GO:0003197)|forelimb morphogenesis (GO:0035136)|gene expression (GO:0010467)|heart development (GO:0007507)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|negative regulation of cardiac muscle cell proliferation (GO:0060044)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|pattern specification process (GO:0007389)|pericardium development (GO:0060039)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of secondary heart field cardioblast proliferation (GO:0072513)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of execution phase of apoptosis (GO:1900117)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle tissue development (GO:0003229)|ventricular septum development (GO:0003281)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(29)|ovary(6)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	Medulloblastoma(191;0.163)|all_neural(191;0.178)			BRCA - Breast invasive adenocarcinoma(302;0.0893)		CCTGCTGGGTGAAGGCGGCCT	0.632																																					p.F46F	NSCLC(152;1358 1980 4050 23898 40356)	Atlas-SNP	.											.	TBX5	188	.	0			c.C138T						PASS	.						42.0	52.0	48.0					12																	114841566		2199	4299	6498	SO:0001819	synonymous_variant	6910	exon2			CTGGGTGAAGGCG	U89353	CCDS9173.1, CCDS9174.1	12q24.1	2014-09-17			ENSG00000089225	ENSG00000089225		"""T-boxes"""	11604	protein-coding gene	gene with protein product		601620		HOS		8988165, 8054982	Standard	NM_000192		Approved		uc001tvo.4	Q99593	OTTHUMG00000166191	ENST00000310346.4:c.138C>T	chr12.hg19:g.114841566G>A		8.0	0.0	.		29.0	10.0	.	NM_000192	A6ND77|O15301|Q96TB0|Q9Y4I2	Silent	SNP	ENST00000310346.4	hg19	CCDS9173.1																																																																																			.	.	.	none		0.632	TBX5-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388297.1	NM_080717	
LRRC43	254050	hgsc.bcm.edu	37	12	122669246	122669246	+	Silent	SNP	T	T	C	rs373684289		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:122669246T>C	ENST00000339777.4	+	2	359	c.331T>C	c.(331-333)Ttg>Ctg	p.L111L	LRRC43_ENST00000425921.1_5'UTR	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	111										NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CCTGAGAGAATTGGCCATCCG	0.592													T|||	1	0.000199681	0.0008	0.0	5008	,	,		20729	0.0		0.0	False		,,,				2504	0.0				p.L111L		Atlas-SNP	.											.	LRRC43	105	.	0			c.T331C						PASS	.	T	,	1,3991		0,1,1995	51.0	53.0	52.0		331,	4.2	0.8	12		52	0,8312		0,0,4156	no	coding-synonymous,utr-5	LRRC43	NM_001098519.1,NM_152759.4	,	0,1,6151	CC,CT,TT		0.0,0.0251,0.0081	,	111/657,	122669246	1,12303	1996	4156	6152	SO:0001819	synonymous_variant	254050	exon2			AGAGAATTGGCCA	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.331T>C	chr12.hg19:g.122669246T>C		181.0	0.0	.		213.0	92.0	.	NM_001098519	Q6ZVT9	Silent	SNP	ENST00000339777.4	hg19	CCDS45001.1																																																																																			.	.	.	weak		0.592	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
DNAH10	196385	hgsc.bcm.edu	37	12	124335495	124335495	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:124335495G>A	ENST00000409039.3	+	34	5834	c.5809G>A	c.(5809-5811)Ggc>Agc	p.G1937S		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1937	AAA 1. {ECO:0000250}.				microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(14)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	52	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000207)|Epithelial(86;0.000556)|all cancers(50;0.00346)		CATGAACCCCGGCTACGCAGG	0.582																																					p.G1937S		Atlas-SNP	.											.	DNAH10	888	.	0			c.G5809A						PASS	.						40.0	45.0	44.0					12																	124335495		2155	4286	6441	SO:0001583	missense	196385	exon34			AACCCCGGCTACG	AJ132089	CCDS9255.2	12q24	2008-02-05	2006-09-04		ENSG00000197653	ENSG00000197653		"""Axonemal dyneins"""	2941	protein-coding gene	gene with protein product		605884	"""dynein, axonemal, heavy polypeptide 10"""				Standard	NM_207437		Approved	FLJ43808	uc001uft.4	Q8IVF4	OTTHUMG00000154477	ENST00000409039.3:c.5809G>A	chr12.hg19:g.124335495G>A	ENSP00000386770:p.Gly1937Ser	28.0	0.0	.		94.0	51.0	.	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	hg19	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	35	5.476132	0.96291	.	.	ENSG00000197653	ENST00000409039	T	0.16743	2.32	5.48	5.48	0.80851	ATPase, AAA+ type, core (1);	0.000000	0.64402	U	0.000001	T	0.53546	0.1803	M	0.91510	3.215	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.64232	-0.6456	10	0.87932	D	0	.	19.3709	0.94484	0.0:0.0:1.0:0.0	.	1937	Q8IVF4	DYH10_HUMAN	S	1937	ENSP00000386770:G1937S	ENSP00000386770:G1937S	G	+	1	0	DNAH10	122901448	1.000000	0.71417	0.956000	0.39512	0.972000	0.66771	8.010000	0.88615	2.576000	0.86940	0.655000	0.94253	GGC	.	.	.	none		0.582	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
BRI3BP	140707	hgsc.bcm.edu	37	12	125509696	125509696	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:125509696G>T	ENST00000341446.8	+	3	567	c.476G>T	c.(475-477)tGg>tTg	p.W159L		NM_080626.5	NP_542193.3			BRI3 binding protein									p.W159S(1)		large_intestine(1)|lung(8)|ovary(1)	10	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.35e-05)|Epithelial(86;0.000426)|all cancers(50;0.00576)		CGCTTCTTCTGGATCGTGCGG	0.622																																					p.W159L		Atlas-SNP	.											BRI3BP,NS,carcinoma,0,1	BRI3BP	18	.	1	Substitution - Missense(1)	lung(1)	c.G476T						PASS	.						131.0	99.0	110.0					12																	125509696		2203	4300	6503	SO:0001583	missense	140707	exon3			TCTTCTGGATCGT	AF284094	CCDS9262.1	12q24.1	2008-08-04			ENSG00000184992	ENSG00000184992			14251	protein-coding gene	gene with protein product		615627				11860200, 17765869	Standard	NM_080626		Approved	BNAS1, KG19, HCCR-2	uc001uha.1	Q8WY22	OTTHUMG00000168548	ENST00000341446.8:c.476G>T	chr12.hg19:g.125509696G>T	ENSP00000340761:p.Trp159Leu	59.0	1.0	.		90.0	41.0	.	NM_080626		Missense_Mutation	SNP	ENST00000341446.8	hg19	CCDS9262.1	.	.	.	.	.	.	.	.	.	.	g	29.4	5.001126	0.93227	.	.	ENSG00000184992	ENST00000341446	.	.	.	5.09	5.09	0.68999	.	0.000000	0.85682	D	0.000000	T	0.77336	0.4115	L	0.57536	1.79	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.79841	-0.1633	9	0.87932	D	0	-1.2314	18.495	0.90861	0.0:0.0:1.0:0.0	.	159	Q8WY22	BRI3B_HUMAN	L	159	.	ENSP00000340761:W159L	W	+	2	0	BRI3BP	124075649	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	9.284000	0.95882	2.344000	0.79699	0.556000	0.70494	TGG	.	.	.	none		0.622	BRI3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400200.2	NM_080626	
TBC1D4	9882	hgsc.bcm.edu	37	13	75923415	75923415	+	Silent	SNP	C	C	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr13:75923415C>A	ENST00000377636.3	-	5	1645	c.1299G>T	c.(1297-1299)ctG>ctT	p.L433L	TBC1D4_ENST00000425511.1_5'UTR|TBC1D4_ENST00000377625.2_Silent_p.L433L|TBC1D4_ENST00000431480.2_Silent_p.L433L	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	433	PID 2. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		AGGCCTGTTTCAGAGTCAGCA	0.473																																					p.L433L		Atlas-SNP	.											.	TBC1D4	142	.	0			c.G1299T						PASS	.						57.0	58.0	58.0					13																	75923415		1948	4168	6116	SO:0001819	synonymous_variant	9882	exon5			CTGTTTCAGAGTC	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.1299G>T	chr13.hg19:g.75923415C>A		72.0	0.0	.		48.0	25.0	.	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Silent	SNP	ENST00000377636.3	hg19	CCDS41901.1																																																																																			.	.	.	none		0.473	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
TEP1	7011	hgsc.bcm.edu	37	14	20846267	20846267	+	Silent	SNP	G	G	C	rs201698574		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:20846267G>C	ENST00000262715.5	-	39	5677	c.5637C>G	c.(5635-5637)gcC>gcG	p.A1879A	TEP1_ENST00000545983.1_Silent_p.A217A|TEP1_ENST00000556935.1_Silent_p.A1771A	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1879					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GGGCAGGGAAGGCAGCCAGCC	0.632																																					p.A1879A		Atlas-SNP	.											.	TEP1	224	.	0			c.C5637G						PASS	.						87.0	85.0	86.0					14																	20846267		2203	4300	6503	SO:0001819	synonymous_variant	7011	exon39			AGGGAAGGCAGCC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5637C>G	chr14.hg19:g.20846267G>C		33.0	0.0	.		119.0	40.0	.	NM_007110	A0AUV9	Silent	SNP	ENST00000262715.5	hg19	CCDS9548.1																																																																																			.	G|1.000;A|0.000	.	alt		0.632	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
KCNH5	27133	hgsc.bcm.edu	37	14	63447729	63447729	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:63447729G>A	ENST00000322893.7	-	6	1071	c.803C>T	c.(802-804)aCg>aTg	p.T268M	KCNH5_ENST00000394968.1_Missense_Mutation_p.T210M|KCNH5_ENST00000420622.2_Missense_Mutation_p.T268M|KCNH5_ENST00000394964.2_Missense_Mutation_p.T210M	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	268					potassium ion transmembrane transport (GO:0071805)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(33)|ovary(5)|prostate(2)|skin(17)|upper_aerodigestive_tract(4)|urinary_tract(2)	99				OV - Ovarian serous cystadenocarcinoma(108;0.00958)|BRCA - Breast invasive adenocarcinoma(234;0.168)		CACGAAAGTCGTGTGAAAATT	0.423																																					p.T268M		Atlas-SNP	.											.	KCNH5	320	.	0			c.C803T						PASS	.						70.0	71.0	71.0					14																	63447729		2203	4300	6503	SO:0001583	missense	27133	exon6			AAAGTCGTGTGAA	U69185	CCDS9756.1, CCDS45122.1	14q23.1	2012-07-05			ENSG00000140015	ENSG00000140015		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6254	protein-coding gene	gene with protein product		605716				9738473, 16382104	Standard	NM_139318		Approved	Kv10.2, H-EAG2, eag2	uc001xfx.3	Q8NCM2	OTTHUMG00000029041	ENST00000322893.7:c.803C>T	chr14.hg19:g.63447729G>A	ENSP00000321427:p.Thr268Met	121.0	0.0	.		94.0	40.0	.	NM_172375	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	hg19	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	G	22.7	4.325830	0.81580	.	.	ENSG00000140015	ENST00000322893;ENST00000420622;ENST00000394968;ENST00000394964	D;D;D;D	0.95622	-3.76;-3.76;-3.76;-3.76	5.54	5.54	0.83059	Ion transport (1);	0.000000	0.85682	D	0.000000	D	0.98229	0.9414	M	0.90542	3.125	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.995;1.0;1.0;1.0	D	0.98956	1.0796	10	0.87932	D	0	.	19.4888	0.95042	0.0:0.0:1.0:0.0	.	210;210;268;268	Q86XI1;Q8NCM2-3;Q8NCM2-2;Q8NCM2	.;.;.;KCNH5_HUMAN	M	268;268;210;210	ENSP00000321427:T268M;ENSP00000395439:T268M;ENSP00000378419:T210M;ENSP00000378415:T210M	ENSP00000321427:T268M	T	-	2	0	KCNH5	62517482	1.000000	0.71417	0.992000	0.48379	0.740000	0.42216	9.799000	0.99117	2.607000	0.88179	0.585000	0.79938	ACG	.	.	.	none		0.423	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
PPP1R36	145376	hgsc.bcm.edu	37	14	65053588	65053588	+	Silent	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:65053588G>A	ENST00000298705.1	+	9	798	c.702G>A	c.(700-702)aaG>aaA	p.K234K	RP11-973N13.3_ENST00000554454.1_RNA|RP11-973N13.3_ENST00000556634.1_RNA	NM_172365.1	NP_758953.1	Q96LQ0	PPR36_HUMAN	protein phosphatase 1, regulatory subunit 36	234					negative regulation of phosphatase activity (GO:0010923)		phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)										AAGACTGGAAGTTCTTTGAGG	0.353																																					p.K234K		Atlas-SNP	.											.	.	.	.	0			c.G702A						PASS	.						134.0	126.0	128.0					14																	65053588		2203	4300	6503	SO:0001819	synonymous_variant	145376	exon9			CTGGAAGTTCTTT		CCDS9767.1	14q23.2	2012-04-17	2011-10-11	2011-10-11	ENSG00000165807	ENSG00000165807		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	20097	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 50"""	C14orf50			Standard	NM_172365		Approved		uc001xhl.1	Q96LQ0	OTTHUMG00000141316	ENST00000298705.1:c.702G>A	chr14.hg19:g.65053588G>A		71.0	0.0	.		51.0	11.0	.	NM_172365	Q6NTH6	Silent	SNP	ENST00000298705.1	hg19	CCDS9767.1																																																																																			.	.	.	none		0.353	PPP1R36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280667.1	NM_172365	
ARHGAP11A	9824	hgsc.bcm.edu	37	15	32929467	32929467	+	Silent	SNP	T	T	C	rs373558097		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:32929467T>C	ENST00000361627.3	+	12	3215	c.2493T>C	c.(2491-2493)ctT>ctC	p.L831L	ARHGAP11A_ENST00000565905.1_Silent_p.L642L|ARHGAP11A_ENST00000543522.1_Silent_p.L642L	NM_014783.3	NP_055598.1	Q6P4F7	RHGBA_HUMAN	Rho GTPase activating protein 11A	831					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	31		all_lung(180;1.3e-11)		all cancers(64;3.34e-21)|Epithelial(43;2.64e-15)|GBM - Glioblastoma multiforme(186;5.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.00112)|Lung(196;0.227)		AGTCACCTCTTAAGTTTCAGC	0.388																																					p.L831L	Colon(45;757 1134 30003 36652)	Atlas-SNP	.											.	ARHGAP11A	84	.	0			c.T2493C						PASS	.						99.0	103.0	101.0					15																	32929467		2201	4300	6501	SO:0001819	synonymous_variant	9824	exon12			ACCTCTTAAGTTT	D87717	CCDS10028.1, CCDS58349.1, CCDS66730.1	15q13.3	2006-09-19			ENSG00000198826	ENSG00000198826		"""Rho GTPase activating proteins"""	15783	protein-coding gene	gene with protein product	"""GAP (1-12)"""	610589				11829490	Standard	NM_199357		Approved	KIAA0013	uc001zgy.1	Q6P4F7	OTTHUMG00000129289	ENST00000361627.3:c.2493T>C	chr15.hg19:g.32929467T>C		125.0	0.0	.		117.0	52.0	.	NM_014783	B4DZN9|Q6PI96|Q9Y3S6	Silent	SNP	ENST00000361627.3	hg19	CCDS10028.1																																																																																			.	.	.	alt		0.388	ARHGAP11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251417.1	NM_014783	
ZNF770	54989	hgsc.bcm.edu	37	15	35275620	35275620	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:35275620T>A	ENST00000356321.4	-	3	360	c.16A>T	c.(16-18)Aat>Tat	p.N6Y		NM_014106.3	NP_054825.2	Q6IQ21	ZN770_HUMAN	zinc finger protein 770	6					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)	29		Lung NSC(122;4.59e-10)|all_lung(180;8.78e-09)		all cancers(64;1.97e-18)|GBM - Glioblastoma multiforme(113;2.11e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0643)		ATTTTTAAATTGTTTTCAGCC	0.313																																					p.N6Y		Atlas-SNP	.											.	ZNF770	64	.	0			c.A16T						PASS	.						68.0	62.0	64.0					15																	35275620		2201	4298	6499	SO:0001583	missense	54989	exon3			TTAAATTGTTTTC	BC071603	CCDS10042.1	15q14	2013-01-08			ENSG00000198146	ENSG00000198146		"""Zinc fingers, C2H2-type"""	26061	protein-coding gene	gene with protein product							Standard	NM_014106		Approved	FLJ20582, PRO1914	uc001ziw.3	Q6IQ21	OTTHUMG00000129689	ENST00000356321.4:c.16A>T	chr15.hg19:g.35275620T>A	ENSP00000348673:p.Asn6Tyr	79.0	0.0	.		74.0	27.0	.	NM_014106	Q6ZMZ6|Q9NWV2	Missense_Mutation	SNP	ENST00000356321.4	hg19	CCDS10042.1	.	.	.	.	.	.	.	.	.	.	T	4.657	0.122204	0.08931	.	.	ENSG00000198146	ENST00000356321	T	0.09538	2.97	4.27	3.14	0.36123	.	0.420309	0.21769	N	0.069391	T	0.05227	0.0139	N	0.14661	0.345	0.09310	N	1	B	0.15473	0.013	B	0.11329	0.006	T	0.32481	-0.9905	10	0.66056	D	0.02	-8.2947	0.8062	0.01084	0.1598:0.1796:0.1664:0.4942	.	6	Q6IQ21	ZN770_HUMAN	Y	6	ENSP00000348673:N6Y	ENSP00000348673:N6Y	N	-	1	0	ZNF770	33062912	1.000000	0.71417	0.962000	0.40283	0.306000	0.27790	1.749000	0.38319	0.959000	0.37980	-0.297000	0.09499	AAT	.	.	.	none		0.313	ZNF770-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251896.2	NM_014106	
ARMC5	79798	hgsc.bcm.edu	37	16	31473812	31473812	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:31473812G>A	ENST00000563544.1	+	4	1490	c.944G>A	c.(943-945)cGg>cAg	p.R315Q	ARMC5_ENST00000268314.4_Missense_Mutation_p.R315Q|ARMC5_ENST00000457010.2_Missense_Mutation_p.R315Q|ARMC5_ENST00000412665.2_Intron|ARMC5_ENST00000538189.1_Missense_Mutation_p.R347Q|ARMC5_ENST00000408912.3_Missense_Mutation_p.R410Q|RP11-452L6.5_ENST00000564629.1_RNA			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	315										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GGCCTGATTCGGCCTGCACTG	0.652																																					p.R315Q		Atlas-SNP	.											.	ARMC5	94	.	0			c.G944A						PASS	.						33.0	37.0	36.0					16																	31473812		2058	4214	6272	SO:0001583	missense	79798	exon3			TGATTCGGCCTGC	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.944G>A	chr16.hg19:g.31473812G>A	ENSP00000456877:p.Arg315Gln	11.0	0.0	.		73.0	34.0	.	NM_024742	Q86WM9|Q9H7P8|Q9H925	Missense_Mutation	SNP	ENST00000563544.1	hg19	CCDS45472.1	.	.	.	.	.	.	.	.	.	.	g	19.23	3.787652	0.70337	.	.	ENSG00000140691	ENST00000408912;ENST00000538189;ENST00000268314;ENST00000457010	T;T;T;T	0.21932	1.98;1.98;1.98;1.98	4.51	4.51	0.55191	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43411	0.1246	M	0.62723	1.935	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.998;0.998;0.996;0.996	T	0.35968	-0.9767	10	0.54805	T	0.06	-20.0021	14.7442	0.69477	0.0:0.0:1.0:0.0	.	347;410;315;315	F5H156;B4DIU9;Q96C12;Q96C12-4	.;.;ARMC5_HUMAN;.	Q	410;347;315;315	ENSP00000386125:R410Q;ENSP00000443995:R347Q;ENSP00000268314:R315Q;ENSP00000399561:R315Q	ENSP00000268314:R315Q	R	+	2	0	ARMC5	31381313	1.000000	0.71417	0.970000	0.41538	0.216000	0.24613	5.851000	0.69481	2.060000	0.61445	0.450000	0.29827	CGG	.	.	.	none		0.652	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
TANGO6	79613	hgsc.bcm.edu	37	16	68941414	68941414	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:68941414G>T	ENST00000261778.1	+	10	1748	c.1736G>T	c.(1735-1737)gGg>gTg	p.G579V		NM_024562.1	NP_078838.1	Q9C0B7	TNG6_HUMAN	transport and golgi organization 6 homolog (Drosophila)	579						integral component of membrane (GO:0016021)											GAGCATCTCGGGGACTTGCTG	0.488																																					p.G579V		Atlas-SNP	.											.	.	.	.	0			c.G1736T						PASS	.						93.0	92.0	92.0					16																	68941414		1892	4105	5997	SO:0001583	missense	79613	exon10			ATCTCGGGGACTT		CCDS45516.1	16q22.1	2012-12-13	2012-12-13	2012-12-13	ENSG00000103047	ENSG00000103047			25749	protein-coding gene	gene with protein product			"""transmembrane and coiled-coil domains 7"""	TMCO7		11214970	Standard	NM_024562		Approved	FLJ12688, KIAA1746	uc002ewi.4	Q9C0B7	OTTHUMG00000176743	ENST00000261778.1:c.1736G>T	chr16.hg19:g.68941414G>T	ENSP00000261778:p.Gly579Val	86.0	0.0	.		147.0	46.0	.	NM_024562	Q569F9|Q9H9K1	Missense_Mutation	SNP	ENST00000261778.1	hg19	CCDS45516.1	.	.	.	.	.	.	.	.	.	.	G	12.59	1.982626	0.34942	.	.	ENSG00000103047	ENST00000261778	.	.	.	5.95	3.84	0.44239	Armadillo-type fold (1);	0.334836	0.36444	N	0.002597	T	0.30541	0.0768	N	0.11724	0.165	0.51012	D	0.999904	B	0.19706	0.038	B	0.17433	0.018	T	0.08391	-1.0724	9	0.12766	T	0.61	-9.4786	11.0925	0.48123	0.0:0.0:0.5339:0.4661	.	579	Q9C0B7	TMCO7_HUMAN	V	579	.	ENSP00000261778:G579V	G	+	2	0	TMCO7	67498915	1.000000	0.71417	0.996000	0.52242	0.835000	0.47333	2.559000	0.45888	1.483000	0.48342	0.655000	0.94253	GGG	.	.	.	none		0.488	TANGO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433471.2	XM_928235.2	
AP1G1	164	hgsc.bcm.edu	37	16	71779166	71779166	+	Missense_Mutation	SNP	T	T	G			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr16:71779166T>G	ENST00000299980.4	-	19	2321	c.1880A>C	c.(1879-1881)gAt>gCt	p.D627A	AP1G1_ENST00000569748.1_Missense_Mutation_p.D627A|AP1G1_ENST00000433195.2_Missense_Mutation_p.D650A|AP1G1_ENST00000393512.3_Missense_Mutation_p.D630A|AP1G1_ENST00000423132.2_Missense_Mutation_p.D630A|AP1G1_ENST00000564155.1_Missense_Mutation_p.D52A	NM_001128.5	NP_001119.3	O43747	AP1G1_HUMAN	adaptor-related protein complex 1, gamma 1 subunit	627					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|Golgi to lysosome transport (GO:0090160)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|positive regulation of natural killer cell degranulation (GO:0043323)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)|trans-Golgi network membrane (GO:0032588)	GTP-dependent protein binding (GO:0030742)|kinesin binding (GO:0019894)|protein transporter activity (GO:0008565)|Rab GTPase binding (GO:0017137)|transporter activity (GO:0005215)			breast(1)|endometrium(8)|large_intestine(6)|lung(7)|ovary(4)|pancreas(1)|urinary_tract(1)	28		Ovarian(137;0.125)				ATCCAATAAATCATTGGCCTA	0.358																																					p.D630A		Atlas-SNP	.											.	AP1G1	83	.	0			c.A1889C						PASS	.						87.0	81.0	83.0					16																	71779166		2198	4300	6498	SO:0001583	missense	164	exon20			AATAAATCATTGG	Y12226	CCDS32480.1, CCDS45522.1	16q23	2009-08-03				ENSG00000166747			555	protein-coding gene	gene with protein product	"""gamma1-adaptin"""	603533		CLAPG1, ADTG		9653655, 9733768	Standard	NM_001128		Approved		uc010cgg.3	O43747		ENST00000299980.4:c.1880A>C	chr16.hg19:g.71779166T>G	ENSP00000299980:p.Asp627Ala	78.0	0.0	.		112.0	74.0	.	NM_001030007	O75709|O75842|Q9UG09|Q9Y3U4	Missense_Mutation	SNP	ENST00000299980.4	hg19	CCDS32480.1	.	.	.	.	.	.	.	.	.	.	T	11.24	1.579662	0.28180	.	.	ENSG00000166747	ENST00000299980;ENST00000393512;ENST00000423132;ENST00000433195	T;T;T;T	0.15718	2.41;2.41;2.42;2.4	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.10551	0.0258	N	0.13198	0.31	0.80722	D	1	B;B;B	0.14012	0.001;0.002;0.009	B;B;B	0.17098	0.001;0.004;0.017	T	0.11542	-1.0583	10	0.08599	T	0.76	-12.6522	15.3832	0.74676	0.0:0.0:0.0:1.0	.	627;650;630	O43747;B3KXW5;O43747-2	AP1G1_HUMAN;.;.	A	627;630;630;650	ENSP00000299980:D627A;ENSP00000377148:D630A;ENSP00000409153:D630A;ENSP00000403259:D650A	ENSP00000299980:D627A	D	-	2	0	AP1G1	70336667	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.054000	0.61138	0.459000	0.35465	GAT	.	.	.	none		0.358	AP1G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434147.1		
WDR81	124997	hgsc.bcm.edu	37	17	1630298	1630298	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:1630298C>T	ENST00000409644.1	+	1	2045	c.2045C>T	c.(2044-2046)tCc>tTc	p.S682F	WDR81_ENST00000437219.2_Intron|WDR81_ENST00000309182.5_Intron|WDR81_ENST00000419248.1_Intron|RP11-961A15.1_ENST00000576540.1_RNA|WDR81_ENST00000446363.1_Intron	NM_001163809.1	NP_001157281.1	Q562E7	WDR81_HUMAN	WD repeat domain 81	682					negative regulation of phosphatase activity (GO:0010923)		transferase activity, transferring phosphorus-containing groups (GO:0016772)			cervix(1)|endometrium(1)|kidney(3)|lung(6)|ovary(2)|prostate(2)|skin(1)	16				UCEC - Uterine corpus endometrioid carcinoma (25;0.0822)		CTGGGCTCCTCCAGTCAAGCG	0.607																																					p.S682F		Atlas-SNP	.											.	WDR81	180	.	0			c.C2045T						PASS	.						12.0	14.0	14.0					17																	1630298		691	1588	2279	SO:0001583	missense	124997	exon1			GCTCCTCCAGTCA	AK074111	CCDS54061.1, CCDS54062.1, CCDS54063.1	17p13.3	2014-06-13			ENSG00000167716	ENSG00000167716		"""WD repeat domain containing"""	26600	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 166"""	614218					Standard	NM_001163673		Approved	FLJ33817, PPP1R166	uc002ftj.2	Q562E7	OTTHUMG00000153941	ENST00000409644.1:c.2045C>T	chr17.hg19:g.1630298C>T	ENSP00000386609:p.Ser682Phe	87.0	0.0	.		45.0	31.0	.	NM_001163809	B3KW16|B3KXU1|B7Z579|E9PHG7|Q24JP6|Q8N277|Q8N3F3|Q8TEL1	Missense_Mutation	SNP	ENST00000409644.1	hg19	CCDS54062.1	.	.	.	.	.	.	.	.	.	.	C	2.791	-0.251404	0.05867	.	.	ENSG00000167716	ENST00000409644	T	0.56444	0.46	5.5	4.5	0.54988	.	.	.	.	.	T	0.52158	0.1717	.	.	.	0.29534	N	0.85255	.	.	.	.	.	.	T	0.50180	-0.8858	6	0.37606	T	0.19	.	11.6034	0.51017	0.0:0.8056:0.1247:0.0697	.	.	.	.	F	682	ENSP00000386609:S682F	ENSP00000386609:S682F	S	+	2	0	WDR81	1577048	0.044000	0.20184	0.251000	0.24312	0.026000	0.11368	0.643000	0.24750	2.580000	0.87095	0.561000	0.74099	TCC	.	.	.	none		0.607	WDR81-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000333118.2	NM_152348	
TP53	7157	hgsc.bcm.edu	37	17	7577559	7577559	+	Missense_Mutation	SNP	G	G	C	rs397516437|rs28934573		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:7577559G>C	ENST00000269305.4	-	7	911	c.722C>G	c.(721-723)tCc>tGc	p.S241C	TP53_ENST00000413465.2_Missense_Mutation_p.S241C|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Missense_Mutation_p.S241C|TP53_ENST00000420246.2_Missense_Mutation_p.S241C|TP53_ENST00000455263.2_Missense_Mutation_p.S241C|TP53_ENST00000359597.4_Missense_Mutation_p.S241C	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	241	Interaction with AXIN1. {ECO:0000250}.|Interaction with HIPK1. {ECO:0000250}.|Interacts with the 53BP2 SH3 domain.|Required for interaction with ZNF385A.		S -> A (in sporadic cancers; somatic mutation). {ECO:0000269|PubMed:17224074}.|S -> C (in sporadic cancers; somatic mutation).|S -> F (in LFS; germline mutation and in sporadic cancers; somatic mutation; dbSNP:rs28934573). {ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:1699228}.|S -> P (in sporadic cancers; somatic mutation).|S -> T (in LFS; germline mutation and in sporadic cancers; somatic mutation).|S -> Y (in sporadic cancers; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.S241F(85)|p.S241C(26)|p.0?(8)|p.S241Y(8)|p.C242fs*5(6)|p.?(5)|p.S241del(5)|p.S148F(4)|p.N239_C242delNSSC(3)|p.N239_C242>S(1)|p.C238fs*21(1)|p.S241fs*22(1)|p.N239_C242del(1)|p.Y236_M243delYMCNSSCM(1)|p.S241_G245delSCMGG(1)|p.S148C(1)|p.N239fs*4(1)|p.C238_M246delCNSSCMGGM(1)|p.H233_C242del10(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	GCCCATGCAGGAACTGTTACA	0.572		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.S241C	Pancreas(47;798 1329 9957 10801)	Atlas-SNP	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	TP53_ENST00000545858,NS,carcinoma,0,4	TP53	33396	.	160	Substitution - Missense(124)|Deletion - In frame(13)|Deletion - Frameshift(9)|Whole gene deletion(8)|Unknown(5)|Complex - deletion inframe(1)	urinary_tract(19)|large_intestine(18)|breast(17)|endometrium(15)|ovary(15)|lung(12)|skin(9)|biliary_tract(8)|central_nervous_system(8)|haematopoietic_and_lymphoid_tissue(7)|upper_aerodigestive_tract(6)|stomach(6)|oesophagus(5)|bone(5)|liver(3)|pancreas(3)|eye(2)|thyroid(1)|kidney(1)	c.C722G	GRCh37	CM920673	TP53	M	rs28934573	PASS	.						139.0	108.0	118.0					17																	7577559		2203	4300	6503	SO:0001583	missense	7157	exon7	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	ATGCAGGAACTGT	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.722C>G	chr17.hg19:g.7577559G>C	ENSP00000269305:p.Ser241Cys	203.0	0.0	.		98.0	72.0	.	NM_000546	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Missense_Mutation	SNP	ENST00000269305.4	hg19	CCDS11118.1	.	.	.	.	.	.	.	.	.	.	G	17.00	3.276619	0.59758	.	.	ENSG00000141510	ENST00000413465;ENST00000359597;ENST00000269305;ENST00000455263;ENST00000420246;ENST00000445888;ENST00000396473;ENST00000545858;ENST00000509690;ENST00000514944	D;D;D;D;D;D;D;D	0.99857	-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22;-7.22	4.62	3.64	0.41730	p53, DNA-binding domain (1);p53-like transcription factor, DNA-binding (1);p53/RUNT-type transcription factor, DNA-binding domain (1);	0.120078	0.56097	D	0.000022	D	0.99871	0.9939	M	0.92784	3.345	0.51233	D	0.999916	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.999;1.0;1.0;1.0;0.999	D	0.96551	0.9408	10	0.87932	D	0	-35.4617	12.8645	0.57932	0.0:0.1651:0.8349:0.0	.	241;241;148;241;241;241	P04637-2;P04637-3;E9PFT5;P04637;Q1MSW8;E7EQX7	.;.;.;P53_HUMAN;.;.	C	241;241;241;241;241;241;230;148;109;148	ENSP00000410739:S241C;ENSP00000352610:S241C;ENSP00000269305:S241C;ENSP00000398846:S241C;ENSP00000391127:S241C;ENSP00000391478:S241C;ENSP00000425104:S109C;ENSP00000423862:S148C	ENSP00000269305:S241C	S	-	2	0	TP53	7518284	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.346000	0.44027	1.295000	0.44724	0.462000	0.41574	TCC	.	.	.	alt		0.572	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
SSH2	85464	hgsc.bcm.edu	37	17	27958146	27958146	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:27958146T>C	ENST00000269033.3	-	15	4136	c.3985A>G	c.(3985-3987)Aca>Gca	p.T1329A	RP11-68I3.2_ENST00000581474.1_RNA|SSH2_ENST00000540801.1_Missense_Mutation_p.T1356A	NM_001282129.1|NM_033389.2	NP_001269058.1|NP_203747.2	Q76I76	SSH2_HUMAN	slingshot protein phosphatase 2	1329					actin cytoskeleton organization (GO:0030036)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of lamellipodium assembly (GO:0010591)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)	actin binding (GO:0003779)|DNA binding (GO:0003677)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)		SSH2/SUZ12(2)	breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(16)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	39						CACTCTGTTGTTGTGAGTTGT	0.532																																					p.T1329A		Atlas-SNP	.											.	SSH2	107	.	0			c.A3985G						PASS	.						57.0	50.0	52.0					17																	27958146		2203	4300	6503	SO:0001583	missense	85464	exon15			CTGTTGTTGTGAG	AB072359	CCDS11253.1, CCDS74024.1	17q11.2	2013-03-05	2013-03-05		ENSG00000141298	ENSG00000141298		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30580	protein-coding gene	gene with protein product		606779	"""slingshot homolog 2 (Drosophila)"""			11832213, 11214970	Standard	XM_005258059		Approved	KIAA1725	uc002heo.1	Q76I76	OTTHUMG00000132752	ENST00000269033.3:c.3985A>G	chr17.hg19:g.27958146T>C	ENSP00000269033:p.Thr1329Ala	72.0	0.0	.		133.0	33.0	.	NM_033389	Q8TDB5|Q8WYL1|Q8WYL2|Q96F40|Q96H36|Q9C0D8	Missense_Mutation	SNP	ENST00000269033.3	hg19	CCDS11253.1	.	.	.	.	.	.	.	.	.	.	T	14.58	2.576881	0.45902	.	.	ENSG00000141298	ENST00000269033;ENST00000540801	T;T	0.58506	0.33;0.33	6.17	6.17	0.99709	.	0.593826	0.17897	N	0.158323	T	0.58509	0.2127	M	0.64997	1.995	0.80722	D	1	P;P	0.41131	0.739;0.622	B;B	0.40782	0.34;0.183	T	0.62234	-0.6897	10	0.59425	D	0.04	-13.774	13.2295	0.59933	0.0:0.0:0.1323:0.8677	.	1356;1329	F5H527;Q76I76	.;SSH2_HUMAN	A	1329;1356	ENSP00000269033:T1329A;ENSP00000444743:T1356A	ENSP00000269033:T1329A	T	-	1	0	SSH2	24982272	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	2.987000	0.49378	2.371000	0.80710	0.533000	0.62120	ACA	.	.	.	none		0.532	SSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256116.1	NM_033389	
NSRP1	84081	hgsc.bcm.edu	37	17	28512533	28512533	+	Silent	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:28512533G>T	ENST00000247026.5	+	7	1581	c.1518G>T	c.(1516-1518)ggG>ggT	p.G506G	NSRP1_ENST00000540900.3_3'UTR	NM_001261467.1|NM_032141.3	NP_001248396.1|NP_115517.1	Q9H0G5	NSRP1_HUMAN	nuclear speckle splicing regulatory protein 1	506					developmental process (GO:0032502)|mRNA processing (GO:0006397)|nucleocytoplasmic transport (GO:0006913)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)	14						CAGAGGAAGGGCAAGAGAAGG	0.433																																					p.G506G		Atlas-SNP	.											.	NSRP1	49	.	0			c.G1518T						PASS	.						103.0	101.0	102.0					17																	28512533		2203	4300	6503	SO:0001819	synonymous_variant	84081	exon7			GGAAGGGCAAGAG	AL136806	CCDS11255.1, CCDS74025.1	17q11.2	2011-05-24	2011-05-24	2011-05-24	ENSG00000126653	ENSG00000126653			25305	protein-coding gene	gene with protein product			"""coiled-coil domain containing 55"""	CCDC55		11230166	Standard	NM_032141		Approved	DKFZP434K1421, NSrp70	uc002heu.4	Q9H0G5	OTTHUMG00000132754	ENST00000247026.5:c.1518G>T	chr17.hg19:g.28512533G>T		125.0	0.0	.		170.0	95.0	.	NM_032141	Q6FI71	Silent	SNP	ENST00000247026.5	hg19	CCDS11255.1																																																																																			.	.	.	none		0.433	NSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256121.2	NM_032141	
YJEFN3	374887	hgsc.bcm.edu	37	19	19640278	19640278	+	Missense_Mutation	SNP	G	G	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:19640278G>T	ENST00000514277.4	+	2	203	c.165G>T	c.(163-165)caG>caT	p.Q55H	CTC-260F20.3_ENST00000586674.1_3'UTR|YJEFN3_ENST00000436027.5_Intron|YJEFN3_ENST00000608404.1_Intron|CTC-260F20.3_ENST00000555938.1_Intron|NDUFA13_ENST00000512771.3_Missense_Mutation_p.Q177H	NM_198537.3	NP_940939.2	A6XGL0	YJEN3_HUMAN	YjeF N-terminal domain containing 3	55										NS(1)|breast(1)|lung(3)	5						GGGGAAGGCAGTCATGGCTAG	0.577																																					p.Q55H		Atlas-SNP	.											.	YJEFN3	10	.	0			c.G165T						PASS	.						53.0	58.0	56.0					19																	19640278		2035	4179	6214	SO:0001583	missense	374887	exon2			AAGGCAGTCATGG		CCDS42530.1, CCDS54236.1	19p13.11	2014-09-11			ENSG00000250067	ENSG00000250067			24785	protein-coding gene	gene with protein product						17533573	Standard	NM_198537		Approved	hYjeF_N3-19p13.11, FLJ44968	uc002nmt.2	A6XGL0	OTTHUMG00000162251	ENST00000514277.4:c.165G>T	chr19.hg19:g.19640278G>T	ENSP00000426964:p.Gln55His	188.0	0.0	.		172.0	39.0	.	NM_198537	A6XGK9|Q4G1C0	Missense_Mutation	SNP	ENST00000514277.4	hg19	CCDS42530.1	.	.	.	.	.	.	.	.	.	.	G	9.605	1.129720	0.21041	.	.	ENSG00000250067	ENST00000397179;ENST00000514277	T	0.48201	0.82	2.12	2.12	0.27331	.	.	.	.	.	T	0.20981	0.0505	N	0.08118	0	0.58432	D	0.999999	P;B	0.39831	0.69;0.191	B;B	0.35353	0.201;0.008	T	0.02991	-1.1085	9	0.15952	T	0.53	.	7.8598	0.29504	0.0:0.0:1.0:0.0	.	177;55	B4DF76;A6XGL0	.;YJEN3_HUMAN	H	55	ENSP00000426964:Q55H	ENSP00000380364:Q55H	Q	+	3	2	YJEFN3	19501278	0.071000	0.21146	0.059000	0.19551	0.062000	0.15995	1.327000	0.33746	1.530000	0.49136	0.555000	0.69702	CAG	.	.	.	none		0.577	YJEFN3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368157.5	NM_198537	
TSHZ3	57616	hgsc.bcm.edu	37	19	31769063	31769063	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:31769063C>T	ENST00000240587.4	-	2	1963	c.1636G>A	c.(1636-1638)Ggc>Agc	p.G546S		NM_020856.2	NP_065907.2	Q63HK5	TSH3_HUMAN	teashirt zinc finger homeobox 3	546					in utero embryonic development (GO:0001701)|kidney morphogenesis (GO:0060993)|kidney smooth muscle cell differentiation (GO:0072195)|lung development (GO:0030324)|metanephros development (GO:0001656)|musculoskeletal movement (GO:0050881)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of smooth muscle cell differentiation (GO:0051152)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|sensory perception of touch (GO:0050975)|transcription, DNA-templated (GO:0006351)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)|ureteric peristalsis (GO:0072105)	growth cone (GO:0030426)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(15)|kidney(9)|large_intestine(20)|lung(60)|ovary(4)|pancreas(2)|prostate(4)|skin(5)	123	Esophageal squamous(110;0.226)					CTGGGATAGCCCCCCCAGCTA	0.557																																					p.G546S		Atlas-SNP	.											.	TSHZ3	549	.	0			c.G1636A						PASS	.						120.0	120.0	120.0					19																	31769063		2203	4300	6503	SO:0001583	missense	57616	exon2			GATAGCCCCCCCA	AL136805	CCDS12421.2	19q13.11	2013-11-20	2007-07-16	2006-03-14	ENSG00000121297	ENSG00000121297		"""Teashirt zinc fingers"", ""Homeoboxes / ZF class"", ""Zinc fingers, C2H2-type"""	30700	protein-coding gene	gene with protein product	"""teashirt 3"""	614119	"""zinc finger protein 537"", ""teashirt family zinc finger 3"""	ZNF537			Standard	NM_020856		Approved	KIAA1474, TSH3	uc002nsy.4	Q63HK5	OTTHUMG00000150184	ENST00000240587.4:c.1636G>A	chr19.hg19:g.31769063C>T	ENSP00000240587:p.Gly546Ser	135.0	0.0	.		171.0	83.0	.	NM_020856	Q9H0G6|Q9P254	Missense_Mutation	SNP	ENST00000240587.4	hg19	CCDS12421.2	.	.	.	.	.	.	.	.	.	.	C	25.9	4.689081	0.88735	.	.	ENSG00000121297	ENST00000240587	T	0.59502	0.26	5.4	5.4	0.78164	.	0.000000	0.85682	D	0.000000	T	0.75221	0.3820	M	0.64404	1.975	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.77054	-0.2730	10	0.72032	D	0.01	-41.0424	19.1896	0.93660	0.0:1.0:0.0:0.0	.	546	Q63HK5	TSH3_HUMAN	S	546	ENSP00000240587:G546S	ENSP00000240587:G546S	G	-	1	0	TSHZ3	36460903	1.000000	0.71417	0.999000	0.59377	0.995000	0.86356	7.461000	0.80834	2.519000	0.84933	0.655000	0.94253	GGC	.	.	.	none		0.557	TSHZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316743.2	NM_020856	
RYR1	6261	hgsc.bcm.edu	37	19	39019255	39019255	+	Missense_Mutation	SNP	A	A	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:39019255A>T	ENST00000359596.3	+	75	10954	c.10954A>T	c.(10954-10956)Atg>Ttg	p.M3652L	RYR1_ENST00000355481.4_Missense_Mutation_p.M3647L|RYR1_ENST00000360985.3_Missense_Mutation_p.M3652L|AC067969.1_ENST00000597015.1_RNA			P21817	RYR1_HUMAN	ryanodine receptor 1 (skeletal)	3652					calcium ion transport (GO:0006816)|cellular response to caffeine (GO:0071313)|cytosolic calcium ion homeostasis (GO:0051480)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|ossification involved in bone maturation (GO:0043931)|outflow tract morphogenesis (GO:0003151)|release of sequestered calcium ion into cytosol (GO:0051209)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to caffeine (GO:0031000)|response to hypoxia (GO:0001666)|skeletal muscle fiber development (GO:0048741)|skin development (GO:0043588)|transmembrane transport (GO:0055085)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|I band (GO:0031674)|integral component of plasma membrane (GO:0005887)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna (GO:0014802)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)|calcium-release channel activity (GO:0015278)|calmodulin binding (GO:0005516)|ryanodine-sensitive calcium-release channel activity (GO:0005219)|voltage-gated calcium channel activity (GO:0005245)			NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(5)|endometrium(26)|haematopoietic_and_lymphoid_tissue(3)|kidney(34)|large_intestine(42)|liver(1)|lung(106)|ovary(11)|pancreas(5)|prostate(9)|skin(12)|stomach(11)|upper_aerodigestive_tract(4)|urinary_tract(7)	285	all_cancers(60;7.91e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)		Caffeine(DB00201)|Dantrolene(DB01219)|Suramin(DB04786)	GGCATGTAACATGTTCCTGGA	0.612																																					p.M3652L		Atlas-SNP	.											.	RYR1	708	.	0			c.A10954T						PASS	.						106.0	87.0	93.0					19																	39019255		2203	4300	6503	SO:0001583	missense	6261	exon75			TGTAACATGTTCC	J05200	CCDS33011.1, CCDS42563.1	19q13.1	2014-09-17				ENSG00000196218		"""Ion channels / Ryanodine receptors"""	10483	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 137"""	180901	"""central core disease of muscle"""	MHS, MHS1, CCO		1862346, 16621918	Standard	NM_000540		Approved	RYR, PPP1R137	uc002oit.3	P21817		ENST00000359596.3:c.10954A>T	chr19.hg19:g.39019255A>T	ENSP00000352608:p.Met3652Leu	129.0	0.0	.		219.0	76.0	.	NM_000540	Q16314|Q16368|Q9NPK1|Q9P1U4	Missense_Mutation	SNP	ENST00000359596.3	hg19	CCDS33011.1	.	.	.	.	.	.	.	.	.	.	A	13.52	2.262183	0.39995	.	.	ENSG00000196218	ENST00000359596;ENST00000355481;ENST00000360985;ENST00000538206	D;D;D	0.95518	-3.73;-3.73;-3.73	5.43	5.43	0.79202	.	0.000000	0.85682	U	0.000000	D	0.88901	0.6563	N	0.16307	0.4	0.36251	D	0.853928	B;B;B	0.11235	0.004;0.002;0.001	B;B;B	0.10450	0.005;0.001;0.001	D	0.84199	0.0449	10	0.02654	T	1	.	14.4595	0.67440	1.0:0.0:0.0:0.0	.	3652;3647;3652	P21817-3;P21817-2;P21817	.;.;RYR1_HUMAN	L	3652;3647;3652;572	ENSP00000352608:M3652L;ENSP00000347667:M3647L;ENSP00000354254:M3652L	ENSP00000347667:M3647L	M	+	1	0	RYR1	43711095	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	2.641000	0.46587	2.074000	0.62210	0.459000	0.35465	ATG	.	.	.	none		0.612	RYR1-010	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000462137.1		
POLD1	5424	hgsc.bcm.edu	37	19	50918079	50918079	+	Missense_Mutation	SNP	T	T	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:50918079T>A	ENST00000440232.2	+	20	2449	c.2396T>A	c.(2395-2397)tTc>tAc	p.F799Y	POLD1_ENST00000595904.1_Missense_Mutation_p.F825Y|POLD1_ENST00000599857.1_Missense_Mutation_p.F799Y|CTD-2545M3.6_ENST00000599632.1_5'Flank	NM_001256849.1|NM_002691.3	NP_001243778.1|NP_002682.2	P28340	DPOD1_HUMAN	polymerase (DNA directed), delta 1, catalytic subunit	799					base-excision repair (GO:0006284)|base-excision repair, gap-filling (GO:0006287)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA replication proofreading (GO:0045004)|DNA replication, removal of RNA primer (GO:0043137)|DNA strand elongation involved in DNA replication (GO:0006271)|DNA synthesis involved in DNA repair (GO:0000731)|fatty acid homeostasis (GO:0055089)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|regulation of mitotic cell cycle (GO:0007346)|response to UV (GO:0009411)|small molecule metabolic process (GO:0044281)|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)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|delta DNA polymerase complex (GO:0043625)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(6)|lung(8)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	39		all_neural(266;0.0571)		OV - Ovarian serous cystadenocarcinoma(262;0.00794)|GBM - Glioblastoma multiforme(134;0.0195)		CAGGTCTACTTCCCATACCTG	0.642								DNA polymerases (catalytic subunits)			OREG0025635	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.F799Y		Atlas-SNP	.											.	POLD1	174	.	0			c.T2396A						PASS	.						55.0	54.0	54.0					19																	50918079		2203	4300	6503	SO:0001583	missense	5424	exon20			TCTACTTCCCATA		CCDS12795.1	19q13.3	2014-09-17	2012-05-18		ENSG00000062822	ENSG00000062822		"""DNA polymerases"""	9175	protein-coding gene	gene with protein product	"""CDC2 homolog (S. cerevisiae)"""	174761	"""polymerase (DNA directed), delta 1, catalytic subunit (125kD)"""	POLD		1722322	Standard	NM_001256849		Approved	CDC2	uc002psc.5	P28340		ENST00000440232.2:c.2396T>A	chr19.hg19:g.50918079T>A	ENSP00000406046:p.Phe799Tyr	75.0	0.0	.	973	96.0	34.0	.	NM_002691	Q8NER3|Q96H98	Missense_Mutation	SNP	ENST00000440232.2	hg19	CCDS12795.1	.	.	.	.	.	.	.	.	.	.	T	14.85	2.657494	0.47467	.	.	ENSG00000062822	ENST00000440232;ENST00000376930	T	0.16597	2.33	4.84	4.84	0.62591	DNA polymerase, palm domain (1);DNA-directed DNA polymerase, family B, multifunctional domain (1);	0.060647	0.64402	D	0.000003	T	0.12305	0.0299	N	0.17764	0.52	0.46521	D	0.999085	B;B	0.12013	0.005;0.002	B;B	0.20384	0.029;0.013	T	0.10636	-1.0621	10	0.27785	T	0.31	-24.2344	13.7358	0.62817	0.0:0.0:0.0:1.0	.	825;799	E7EVW0;P28340	.;DPOD1_HUMAN	Y	799;800	ENSP00000406046:F799Y	ENSP00000366129:F800Y	F	+	2	0	POLD1	55609891	1.000000	0.71417	1.000000	0.80357	0.917000	0.54804	2.937000	0.48979	1.970000	0.57323	0.449000	0.29647	TTC	.	.	.	none		0.642	POLD1-002	KNOWN	alternative_5_UTR|NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464732.1		
ZNF548	147694	hgsc.bcm.edu	37	19	57908473	57908473	+	Missense_Mutation	SNP	C	C	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:57908473C>T	ENST00000366197.5	+	2	323	c.73C>T	c.(73-75)Ctt>Ttt	p.L25F	ZNF548_ENST00000336128.7_Missense_Mutation_p.L37F|AC003002.6_ENST00000596400.1_Intron|AC003002.4_ENST00000597658.1_Intron|AC003002.6_ENST00000600421.1_3'UTR|ZNF548_ENST00000597400.1_Missense_Mutation_p.L37F|ZNF548_ENST00000598895.1_Missense_Mutation_p.L37F|AC004076.7_ENST00000597410.1_Intron	NM_152909.3	NP_690873.2	Q8NEK5	ZN548_HUMAN	zinc finger protein 548	25	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				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(1)	1		Colorectal(82;0.000256)|all_neural(62;0.0577)|Ovarian(87;0.221)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.026)		GTGGGGGCACCTTGATGAGGC	0.512																																					p.L37F		Atlas-SNP	.											.	ZNF548	64	.	0			c.C109T						PASS	.						377.0	349.0	358.0					19																	57908473		2203	4300	6503	SO:0001583	missense	147694	exon3			GGGCACCTTGATG	AK057494	CCDS46209.1, CCDS54324.1	19q13.43	2013-01-08				ENSG00000188785		"""Zinc fingers, C2H2-type"", ""-"""	26561	protein-coding gene	gene with protein product						12477932	Standard	NM_152909		Approved	FLJ32932	uc002qon.3	Q8NEK5		ENST00000366197.5:c.73C>T	chr19.hg19:g.57908473C>T	ENSP00000379482:p.Leu25Phe	331.0	0.0	.		321.0	126.0	.	NM_001172773	Q96M05	Missense_Mutation	SNP	ENST00000366197.5	hg19	CCDS46209.1	.	.	.	.	.	.	.	.	.	.	C	16.79	3.220274	0.58560	.	.	ENSG00000188785	ENST00000336128;ENST00000366197	T;T	0.18960	2.18;2.18	2.55	2.55	0.30701	Krueppel-associated box (4);	.	.	.	.	T	0.61640	0.2363	H	0.99286	4.5	0.21782	N	0.999543	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	T	0.55933	-0.8062	9	0.66056	D	0.02	.	8.7465	0.34589	0.0:1.0:0.0:0.0	.	37;25	Q8NEK5-2;Q8NEK5	.;ZN548_HUMAN	F	37;25	ENSP00000337555:L37F;ENSP00000379482:L25F	ENSP00000337555:L37F	L	+	1	0	ZNF548	62600285	0.277000	0.24220	0.716000	0.30569	0.995000	0.86356	1.271000	0.33098	1.763000	0.52060	0.563000	0.77884	CTT	.	.	.	none		0.512	ZNF548-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465937.1	NM_152909	
PAK7	57144	hgsc.bcm.edu	37	20	9525075	9525075	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:9525075C>A	ENST00000378429.3	-	9	2356	c.1810G>T	c.(1810-1812)Gtt>Ttt	p.V604F	PAK7_ENST00000378423.1_Missense_Mutation_p.V604F|PAK7_ENST00000353224.5_Missense_Mutation_p.V604F	NM_020341.3	NP_065074.1	Q9P286	PAK7_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 7	604	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in a metastatic melanoma sample; somatic mutation). {ECO:0000269|PubMed:17344846}.		apoptotic process (GO:0006915)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|learning (GO:0007612)|locomotory behavior (GO:0007626)|memory (GO:0007613)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|signal transduction (GO:0007165)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)	p.V604I(1)		NS(1)|central_nervous_system(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(44)|ovary(2)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)	81			COAD - Colon adenocarcinoma(9;0.194)			GGAGTGCCAACCAATGATTTC	0.478																																					p.V604F		Atlas-SNP	.											PAK7,rectum,carcinoma,+2,1	PAK7	194	.	1	Substitution - Missense(1)	skin(1)	c.G1810T						PASS	.						121.0	111.0	114.0					20																	9525075		2203	4300	6503	SO:0001583	missense	57144	exon8			TGCCAACCAATGA	AB033090	CCDS13107.1	20p12	2008-06-17	2008-06-17		ENSG00000101349	ENSG00000101349			15916	protein-coding gene	gene with protein product		608038	"""p21(CDKN1A)-activated kinase 7"""			11756552, 10574462	Standard	NM_020341		Approved	KIAA1264, PAK5	uc002wnk.2	Q9P286	OTTHUMG00000031857	ENST00000378429.3:c.1810G>T	chr20.hg19:g.9525075C>A	ENSP00000367686:p.Val604Phe	141.0	0.0	.		99.0	32.0	.	NM_177990	A8K5T6|D3DW14|Q5W115|Q9BX09|Q9ULF6	Missense_Mutation	SNP	ENST00000378429.3	hg19	CCDS13107.1	.	.	.	.	.	.	.	.	.	.	C	35	5.415885	0.96092	.	.	ENSG00000101349	ENST00000378429;ENST00000353224;ENST00000378423	T;T;T	0.70282	-0.47;-0.47;-0.47	5.97	5.97	0.96955	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.86736	0.6004	M	0.84585	2.705	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.86251	0.1649	9	.	.	.	.	20.4388	0.99107	0.0:1.0:0.0:0.0	.	604	Q9P286	PAK7_HUMAN	F	604	ENSP00000367686:V604F;ENSP00000322957:V604F;ENSP00000367679:V604F	.	V	-	1	0	PAK7	9473075	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.768000	0.85345	2.836000	0.97738	0.655000	0.94253	GTT	.	.	.	none		0.478	PAK7-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077962.1		
KIAA1755	85449	hgsc.bcm.edu	37	20	36869309	36869309	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:36869309C>A	ENST00000279024.4	-	3	1495	c.1224G>T	c.(1222-1224)gaG>gaT	p.E408D		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	408										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				GCACCATATTCTCTGGGTTTC	0.577																																					p.E408D		Atlas-SNP	.											.	KIAA1755	145	.	0			c.G1224T						PASS	.						67.0	67.0	67.0					20																	36869309		2203	4300	6503	SO:0001583	missense	85449	exon3			CATATTCTCTGGG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.1224G>T	chr20.hg19:g.36869309C>A	ENSP00000279024:p.Glu408Asp	70.0	0.0	.		53.0	23.0	.	NM_001029864	Q9C0A8	Missense_Mutation	SNP	ENST00000279024.4	hg19	CCDS33467.1	.	.	.	.	.	.	.	.	.	.	C	11.25	1.582898	0.28268	.	.	ENSG00000149633	ENST00000279024	T	0.61040	0.14	4.64	0.4	0.16331	.	0.300502	0.24046	N	0.042048	T	0.62221	0.2410	M	0.67953	2.075	0.09310	N	1	D	0.67145	0.996	P	0.58266	0.836	T	0.53823	-0.8384	10	0.30078	T	0.28	.	7.1114	0.25392	0.0:0.5955:0.0:0.4045	.	408	Q5JYT7	K1755_HUMAN	D	408	ENSP00000279024:E408D	ENSP00000279024:E408D	E	-	3	2	KIAA1755	36302723	0.001000	0.12720	0.026000	0.17262	0.036000	0.12997	-0.298000	0.08265	-0.072000	0.12864	0.655000	0.94253	GAG	.	.	.	none		0.577	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
SGK2	10110	hgsc.bcm.edu	37	20	42199308	42199308	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:42199308T>C	ENST00000341458.4	+	6	811	c.592T>C	c.(592-594)Ttc>Ctc	p.F198L	SGK2_ENST00000485914.1_3'UTR|SGK2_ENST00000373092.3_Missense_Mutation_p.F138L|SGK2_ENST00000426287.1_Missense_Mutation_p.F164L|SGK2_ENST00000423407.3_Missense_Mutation_p.F138L|SGK2_ENST00000373077.1_Missense_Mutation_p.F137L|SGK2_ENST00000373100.1_Missense_Mutation_p.F138L	NM_016276.3	NP_057360.2	Q9HBY8	SGK2_HUMAN	serum/glucocorticoid regulated kinase 2	198	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transmembrane transport (GO:0034220)|positive regulation of transporter activity (GO:0032411)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|response to oxidative stress (GO:0006979)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|potassium channel regulator activity (GO:0015459)|protein serine/threonine kinase activity (GO:0004674)|sodium channel regulator activity (GO:0017080)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.0031)			CCGGGCCAGGTTCTACGCTGC	0.627																																					p.F198L		Atlas-SNP	.											.	SGK2	50	.	0			c.T592C						PASS	.						57.0	60.0	59.0					20																	42199308		2203	4300	6503	SO:0001583	missense	10110	exon6			GCCAGGTTCTACG	AF169034	CCDS13320.1, CCDS13321.1	20q13.2	2008-07-04			ENSG00000101049	ENSG00000101049			13900	protein-coding gene	gene with protein product		607589				10548550	Standard	NM_016276		Approved		uc002xkv.3	Q9HBY8	OTTHUMG00000033054	ENST00000341458.4:c.592T>C	chr20.hg19:g.42199308T>C	ENSP00000340608:p.Phe198Leu	45.0	0.0	.		67.0	15.0	.	NM_016276	Q52PK5|Q5H8Y6|Q5H8Z1|Q5TZR3|Q9UKG6	Missense_Mutation	SNP	ENST00000341458.4	hg19	CCDS13320.1	.	.	.	.	.	.	.	.	.	.	T	34	5.328708	0.95733	.	.	ENSG00000101049	ENST00000373100;ENST00000373092;ENST00000373077;ENST00000412111;ENST00000423407;ENST00000341458;ENST00000426287	T;T;T;T;T;T;T	0.64991	-0.13;-0.13;-0.13;-0.13;-0.13;-0.13;-0.13	4.92	4.92	0.64577	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.75243	0.3823	L	0.59912	1.85	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	T	0.77448	-0.2584	10	0.62326	D	0.03	.	14.235	0.65919	0.0:0.0:0.0:1.0	.	164;198;138	Q9HBY8-3;Q9HBY8;Q9HBY8-2	.;SGK2_HUMAN;.	L	138;138;137;137;138;198;164	ENSP00000362192:F138L;ENSP00000362184:F138L;ENSP00000362168:F137L;ENSP00000396222:F137L;ENSP00000392795:F138L;ENSP00000340608:F198L;ENSP00000412214:F164L	ENSP00000340608:F198L	F	+	1	0	SGK2	41632722	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.860000	0.86993	2.148000	0.66965	0.533000	0.62120	TTC	.	.	.	none		0.627	SGK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080383.1		
SEMG1	6406	hgsc.bcm.edu	37	20	43836817	43836817	+	Silent	SNP	A	A	G	rs17850164		TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr20:43836817A>G	ENST00000372781.3	+	2	936	c.879A>G	c.(877-879)acA>acG	p.T293T	SEMG1_ENST00000244069.6_Intron	NM_003007.3	NP_002998.1	P04279	SEMG1_HUMAN	semenogelin I	293	2 X 60 AA tandem repeats, type 1.|Repeat-rich region. {ECO:0000250}.				insemination (GO:0007320)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.T293T(2)		cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|liver(1)|lung(12)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.0122)				CTTCAAGTACAGAAGAAAGAC	0.383																																					p.T293T		Atlas-SNP	.											SEMG1,NS,carcinoma,0,2	SEMG1	71	.	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.A879G						PASS	.						67.0	64.0	65.0					20																	43836817		2203	4300	6503	SO:0001819	synonymous_variant	6406	exon2			AAGTACAGAAGAA		CCDS13345.1	20q12-q13.2	2009-08-06			ENSG00000124233	ENSG00000124233			10742	protein-coding gene	gene with protein product	"""semen coagulating protein"", ""cancer/testis antigen 103"""	182140		SEMG		2912989, 15563730	Standard	NM_003007		Approved	CT103		P04279	OTTHUMG00000032565	ENST00000372781.3:c.879A>G	chr20.hg19:g.43836817A>G		154.0	1.0	.		148.0	7.0	.	NM_003007	Q53ZV0|Q53ZV1|Q53ZV2|Q6X4I9|Q6Y809|Q6Y822|Q6Y823|Q86U64|Q96QM3	Silent	SNP	ENST00000372781.3	hg19	CCDS13345.1																																																																																			.	.	.	weak		0.383	SEMG1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079416.3	NM_003007	
SREBF2	6721	hgsc.bcm.edu	37	22	42289163	42289163	+	Missense_Mutation	SNP	C	C	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr22:42289163C>A	ENST00000361204.4	+	12	2417	c.2251C>A	c.(2251-2253)Cac>Aac	p.H751N	SREBF2_ENST00000491541.1_3'UTR	NM_004599.2	NP_004590.2	Q12772	SRBP2_HUMAN	sterol regulatory element binding transcription factor 2	751					cellular lipid metabolic process (GO:0044255)|cellular response to laminar fluid shear stress (GO:0071499)|cholesterol metabolic process (GO:0008203)|lipid metabolic process (GO:0006629)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cholesterol homeostasis (GO:2000188)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|response to low-density lipoprotein particle (GO:0055098)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SREBP-SCAP-Insig complex (GO:0032937)	E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(2)|breast(6)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	38						TGGCCCCGAGCACAGTGCTGT	0.612																																					p.H751N		Atlas-SNP	.											.	SREBF2	99	.	0			c.C2251A						PASS	.						77.0	77.0	77.0					22																	42289163		2203	4300	6503	SO:0001583	missense	6721	exon12			CCCGAGCACAGTG	U02031	CCDS14023.1	22q13.2	2013-05-21			ENSG00000198911	ENSG00000198911		"""Basic helix-loop-helix proteins"""	11290	protein-coding gene	gene with protein product		600481				7903453	Standard	NM_004599		Approved	SREBP2, bHLHd2	uc003bbi.3	Q12772	OTTHUMG00000151261	ENST00000361204.4:c.2251C>A	chr22.hg19:g.42289163C>A	ENSP00000354476:p.His751Asn	72.0	0.0	.		78.0	41.0	.	NM_004599	Q05BD5|Q6GTH7|Q86V36|Q9UH04	Missense_Mutation	SNP	ENST00000361204.4	hg19	CCDS14023.1	.	.	.	.	.	.	.	.	.	.	C	5.682	0.310364	0.10733	.	.	ENSG00000198911	ENST00000361204;ENST00000457567	T	0.07216	3.21	5.42	4.36	0.52297	.	0.494236	0.23861	N	0.043856	T	0.03959	0.0111	N	0.03608	-0.345	0.26458	N	0.975491	B	0.14438	0.01	B	0.11329	0.006	T	0.39440	-0.9614	10	0.14252	T	0.57	-3.4319	13.8968	0.63778	0.1516:0.8484:0.0:0.0	.	751	Q12772	SRBP2_HUMAN	N	751	ENSP00000354476:H751N	ENSP00000354476:H751N	H	+	1	0	SREBF2	40619109	0.993000	0.37304	0.234000	0.24042	0.412000	0.31113	2.219000	0.42899	2.543000	0.85770	0.650000	0.86243	CAC	.	.	.	none		0.612	SREBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321956.1	NM_004599	
MT-ND1	4535	hgsc.bcm.edu	37	M	3850	3850	+	Missense_Mutation	SNP	G	G	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chrM:3850G>A	ENST00000361390.2	+	1	544	c.544G>A	c.(544-546)Gcc>Acc	p.A182T	MT-TV_ENST00000387342.1_RNA|MT-TN_ENST00000387400.1_RNA|MT-RNR1_ENST00000389680.2_RNA|MT-TY_ENST00000387409.1_RNA|MT-TQ_ENST00000387372.1_RNA|MT-TC_ENST00000387405.1_RNA|MT-TL1_ENST00000386347.1_RNA|MT-TM_ENST00000387377.1_RNA|MT-CO1_ENST00000361624.2_5'Flank|MT-ND2_ENST00000361453.3_5'Flank|MT-TI_ENST00000387365.1_RNA|MT-RNR2_ENST00000387347.2_RNA|MT-TW_ENST00000387382.1_RNA|MT-TA_ENST00000387392.1_RNA			P03886	NU1M_HUMAN	mitochondrially encoded NADH dehydrogenase 1	182					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial membrane (GO:0031966)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(13)|kidney(17)|lung(2)|prostate(1)	34					Desflurane(DB01189)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	CATGACCCTTGGCCATAATAT	0.458																																					p.A182T		Atlas-SNP	.											.	.	.	.	0			c.G544A						PASS	.																																			SO:0001583	missense	10625	exon1			CCCTTGGCCATAA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198888	ENSG00000198888	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7455	protein-coding gene	gene with protein product	"""complex I ND1 subunit"", ""NADH-ubiquinone oxidoreductase chain 1"""	516000	"""NADH dehydrogenase 1"""	MTND1			Standard			Approved	ND1, NAD1		P03886		ENST00000361390.2:c.544G>A	chrM.hg19:g.3850G>A	ENSP00000354687:p.Ala182Thr	10.0	0.0	.		22.0	4.0	.	ENST00000361390	C0JKH6|Q37523	Missense_Mutation	SNP	ENST00000361390.2	hg19																																																																																				.	.	.	none		0.458	MT-ND1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024026	
MT-ND4	4538	hgsc.bcm.edu	37	M	11556	11556	+	Missense_Mutation	SNP	T	T	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chrM:11556T>C	ENST00000361381.2	+	1	797	c.797T>C	c.(796-798)cTa>cCa	p.L266P	MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA			P03905	NU4M_HUMAN	mitochondrially encoded NADH dehydrogenase 4	266					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|prostate(1)	13						TGTACTATCCCTATGAGGCAT	0.448																																					p.L266P		Atlas-SNP	.											.	.	.	.	0			c.T797C						PASS	.																																			SO:0001583	missense	0	exon1			TATCCCTATGAGG			mitochondria	2014-02-03	2005-02-15	2005-02-16	ENSG00000198886	ENSG00000198886	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7459	protein-coding gene	gene with protein product	"""complex I ND4 subunit"", ""NADH-ubiquinone oxidoreductase chain 4"""	516003	"""NADH dehydrogenase 4"", ""Leber optic neuropathy"""	MTND4, LHON		8103501	Standard			Approved	ND4, NAD4		P03905		ENST00000361381.2:c.797T>C	chrM.hg19:g.11556T>C	ENSP00000354961:p.Leu266Pro	8.0	0.0	.		14.0	10.0	.	ENST00000361381	Q6RL39|Q6RQN9|Q8HNR8	Missense_Mutation	SNP	ENST00000361381.2	hg19																																																																																				.	.	.	none		0.448	MT-ND4-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024035	
SAMD14	201191	hgsc.bcm.edu	37	17	48191564	48191565	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr17:48191564_48191565delTG	ENST00000330175.4	-	8	1245_1246	c.928_929delCA	c.(928-930)cagfs	p.Q310fs	SAMD14_ENST00000503734.1_5'Flank|SAMD14_ENST00000503131.1_Frame_Shift_Del_p.Q338fs	NM_001257359.1	NP_001244288.1	Q8IZD0	SAM14_HUMAN	sterile alpha motif domain containing 14	310								p.Q338P(1)		breast(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(3)|prostate(1)|urinary_tract(1)	15						ATCTGAAGACTGAGACAGCGTG	0.624																																					p.338_338del		Atlas-Indel,Pindel	.											.	SAMD14	36	.	1	Substitution - Missense(1)	large_intestine(1)	c.1013_1014del						PASS	.																																			SO:0001589	frameshift_variant	201191	exon9			.		CCDS11560.1, CCDS58562.1	17q21.33	2013-01-10				ENSG00000167100		"""Sterile alpha motif (SAM) domain containing"""	27312	protein-coding gene	gene with protein product						8619474	Standard	NM_174920		Approved	FLJ36890	uc002iqg.4	Q8IZD0		ENST00000330175.4:c.928_929delCA	chr17.hg19:g.48191564_48191565delTG	ENSP00000329144:p.Gln310fs	147.0	0.0	0		219.0	58.0	0.26484	NM_174920	A5D8V1|Q8N2X0	Frame_Shift_Del	DEL	ENST00000330175.4	hg19	CCDS58562.1																																																																																			.	.	.	none		0.624	SAMD14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366661.1	NM_174920	
PRTG	283659	hgsc.bcm.edu	37	15	55931988	55931989	+	In_Frame_Ins	INS	-	-	GGTGGT			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931988_55931989insGGTGGT	ENST00000389286.4	-	13	2222_2223	c.2175_2176insACCACC	c.(2173-2178)ccccac>cccACCACCcac	p.725_726PH>PTTH		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		TAGAGATGGTGGGGTGGTGGTG	0.455																																					p.H726delinsTTH		Atlas-INDEL	.											.	PRTG	110	.	0			c.2176_2177insACCACC						PASS	.																																			SO:0001652	inframe_insertion	283659	exon13			.	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2175_2176insACCACC	chr15.hg19:g.55931988_55931989insGGTGGT	ENSP00000373937:p.Pro725_His726insThrThr	170.0	0.0	0		138.0	18.0	0.130435	NM_173814		In_Frame_Ins	INS	ENST00000389286.4	hg19	CCDS42040.1																																																																																			.	.	.	none		0.455	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
RTL1	388015	hgsc.bcm.edu	37	14	101350131	101350136	+	In_Frame_Del	DEL	TCGTTG	TCGTTG	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	TCGTTG	TCGTTG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:101350131_101350136delTCGTTG	ENST00000534062.1	-	1	1048_1053	c.990_995delCAACGA	c.(988-996)ctcaacgag>ctg	p.NE331del	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	331					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CCTGATCTCCTCGTTGAGCCCCTGGC	0.563																																					p.331_332del		Atlas-INDEL	.											.	RTL1	120	.	0			c.991_996del						PASS	.																																			SO:0001651	inframe_deletion	388015	exon1			.		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.990_995delCAACGA	chr14.hg19:g.101350131_101350136delTCGTTG	ENSP00000435342:p.Asn331_Glu332del	51.0	0.0	0		46.0	14.0	0.304348	NM_001134888	E9PKS8	In_Frame_Del	DEL	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.563	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
MRGPRX3	117195	hgsc.bcm.edu	37	11	18159591	18159591	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr11:18159591delG	ENST00000396275.2	+	3	1203	c.842delG	c.(841-843)cgtfs	p.R281fs		NM_054031.3	NP_473372.3	Q96LB0	MRGX3_HUMAN	MAS-related GPR, member X3	281				R -> L (in Ref. 2; AAL86879). {ECO:0000305}.		integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	27						TTTAGGCAGCGTCAAAATAGG	0.517																																					p.R281fs		Atlas-Indel,Pindel	.											MRGPRX3,mouth,carcinoma,0,1	MRGPRX3	59	.	0			c.841delC						PASS	.						56.0	60.0	58.0					11																	18159591		2200	4290	6490	SO:0001589	frameshift_variant	117195	exon3			.		CCDS7830.1	11p15.1	2013-10-10			ENSG00000179826	ENSG00000179826		"""GPCR / Class A : Orphans"""	17980	protein-coding gene	gene with protein product		607229				11551509	Standard	NM_054031		Approved	MRGX3	uc001mnu.3	Q96LB0	OTTHUMG00000166435	ENST00000396275.2:c.842delG	chr11.hg19:g.18159591delG	ENSP00000379571:p.Arg281fs	82.0	0.0	0		65.0	26.0	0.4	NM_054031	B0M0L1|Q8TDE0|Q8TDE1	Frame_Shift_Del	DEL	ENST00000396275.2	hg19	CCDS7830.1																																																																																			.	.	.	none		0.517	MRGPRX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389767.1	NM_054031	
PRTG	283659	hgsc.bcm.edu	37	15	55931987	55931988	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931987_55931988insC	ENST00000389286.4	-	13	2223_2224	c.2176_2177insG	c.(2176-2178)cacfs	p.H726fs		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		ATAGAGATGGTGGGGTGGTGGT	0.455																																					p.H726fs		Atlas-INDEL	.											.	PRTG	110	.	0			c.2177_2178insG						PASS	.																																			SO:0001589	frameshift_variant	283659	exon13			.	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2176_2177insG	chr15.hg19:g.55931987_55931988insC	ENSP00000373937:p.His726fs	170.0	0.0	0		138.0	18.0	0.130435	NM_173814		Frame_Shift_Ins	INS	ENST00000389286.4	hg19	CCDS42040.1																																																																																			.	.	.	none		0.455	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
TPM4	7171	hgsc.bcm.edu	37	19	16199862	16199862	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr19:16199862delG	ENST00000300933.4	+	5	723	c.463delG	c.(463-465)ggtfs	p.G155fs	TPM4_ENST00000538887.1_Frame_Shift_Del_p.G191fs|TPM4_ENST00000344824.6_Frame_Shift_Del_p.G191fs	NM_003290.2	NP_003281.1	P67936	TPM4_HUMAN	tropomyosin 4	155					cellular component movement (GO:0006928)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|osteoblast differentiation (GO:0001649)	cortical cytoskeleton (GO:0030863)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|focal adhesion (GO:0005925)|membrane (GO:0016020)|muscle thin filament tropomyosin (GO:0005862)|podosome (GO:0002102)|stress fiber (GO:0001725)	calcium ion binding (GO:0005509)|structural constituent of muscle (GO:0008307)		TPM4/ALK(12)	breast(1)|large_intestine(3)	4						CAGAAAATGTGGTGACCTGGA	0.428			T	ALK	ALCL						OREG0025329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.C190fs		Atlas-Indel,Pindel	.		Dom	yes		19	19p13.1	7171	tropomyosin 4		L	.	TPM4	28	.	0			c.570delT						PASS	.						125.0	113.0	117.0					19																	16199862		2203	4300	6503	SO:0001589	frameshift_variant	7171	exon6			.		CCDS12338.1, CCDS46007.1	19p13.1	2013-03-11			ENSG00000167460	ENSG00000167460		"""Tropomyosins"""	12013	protein-coding gene	gene with protein product		600317				8641132	Standard	NM_003290		Approved		uc002ndi.2	P67936	OTTHUMG00000182134	ENST00000300933.4:c.463delG	chr19.hg19:g.16199862delG	ENSP00000300933:p.Gly155fs	101.0	0.0	0	708	80.0	32.0	0.4	NM_001145160	P07226|Q15659|Q5U0D9|Q9BU85|Q9H8Q3|Q9UCS1|Q9UCS2|Q9UCS3|Q9UCS4	Frame_Shift_Del	DEL	ENST00000300933.4	hg19	CCDS12338.1																																																																																			.	.	.	none		0.428	TPM4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459673.2	NM_003290	
CIART	148523	hgsc.bcm.edu	37	1	150256865	150256882	+	In_Frame_Del	DEL	ATGGACAGGATCCAGCGT	ATGGACAGGATCCAGCGT	-	rs137955605	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	ATGGACAGGATCCAGCGT	ATGGACAGGATCCAGCGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:150256865_150256882delATGGACAGGATCCAGCGT	ENST00000290363.5	+	3	921_938	c.472_489delATGGACAGGATCCAGCGT	c.(472-489)atggacaggatccagcgtdel	p.MDRIQR158del	C1orf51_ENST00000469255.1_3'UTR|C1orf51_ENST00000369094.1_In_Frame_Del_p.MDRIQR70del|C1orf51_ENST00000369095.1_In_Frame_Del_p.MDRIQR158del	NM_144697.2	NP_653298.1	Q8N365	CIART_HUMAN		158					circadian regulation of gene expression (GO:0032922)|locomotor rhythm (GO:0045475)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|E-box binding (GO:0070888)	p.R163H(1)		endometrium(3)|large_intestine(2)|lung(3)|urinary_tract(2)	10	Lung NSC(24;7.29e-29)|Breast(34;0.00211)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)			GAGTGTGGCAATGGACAGGATCCAGCGTATTGTAGGTG	0.459																																					p.157_163del		Atlas-Indel,Pindel	.											.	C1orf51	35	.	1	Substitution - Missense(1)	urinary_tract(1)	c.471_488del						PASS	.																																			SO:0001651	inframe_deletion	148523	exon3			.																												ENST00000290363.5:c.472_489delATGGACAGGATCCAGCGT	chr1.hg19:g.150256865_150256882delATGGACAGGATCCAGCGT	ENSP00000290363:p.Met158_Arg163del	262.0	0.0	0		171.0	27.0	0.157895	NM_144697	B2RD43|D3DV01|Q8N795|Q96MG6	In_Frame_Del	DEL	ENST00000290363.5	hg19	CCDS949.1																																																																																			.	.	.	none		0.459	C1orf51-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000035058.1		
COL21A1	81578	hgsc.bcm.edu	37	6	55925556	55925557	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr6:55925556_55925557insA	ENST00000244728.5	-	27	2786_2787	c.2389_2390insT	c.(2389-2391)tgcfs	p.C797fs	COL21A1_ENST00000370808.2_Frame_Shift_Ins_p.C197fs|COL21A1_ENST00000535941.1_Frame_Shift_Ins_p.C797fs|COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370819.1_Frame_Shift_Ins_p.C794fs	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	797					extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TACATCTGTGCAAACTTGTCGA	0.297																																					p.C797fs		Atlas-Indel,Pindel	.											.	COL21A1	201	.	0			c.2390_2391insT						PASS	.																																			SO:0001589	frameshift_variant	81578	exon27			.	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2390dupT	chr6.hg19:g.55925559_55925559dupA	ENSP00000244728:p.Cys797fs	69.0	0.0	0		47.0	14.0	0.297872	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Frame_Shift_Ins	INS	ENST00000244728.5	hg19	CCDS55025.1																																																																																			.	.	.	none		0.297	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
RTL1	388015	hgsc.bcm.edu	37	14	101350138	101350138	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:101350138delG	ENST00000534062.1	-	1	1046	c.988delC	c.(988-990)ctcfs	p.L330fs	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	330					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						TCCTCGTTGAGCCCCTGGCAC	0.572																																					p.L330fs		Atlas-INDEL	.											.	RTL1	120	.	0			c.989delT						PASS	.						70.0	67.0	68.0					14																	101350138		692	1591	2283	SO:0001589	frameshift_variant	388015	exon1			.		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.988delC	chr14.hg19:g.101350138delG	ENSP00000435342:p.Leu330fs	48.0	0.0	0		45.0	14.0	0.311111	NM_001134888	E9PKS8	Frame_Shift_Del	DEL	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.572	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
PRUNE	58497	hgsc.bcm.edu	37	1	151001408	151001408	+	Frame_Shift_Del	DEL	A	A	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr1:151001408delA	ENST00000271620.3	+	7	1077	c.921delA	c.(919-921)gcafs	p.A307fs	PRUNE_ENST00000368935.1_Intron|PRUNE_ENST00000368934.1_Intron|PRUNE_ENST00000368936.1_Frame_Shift_Del_p.A125fs|PRUNE_ENST00000271619.8_Intron|PRUNE_ENST00000467771.1_3'UTR|PRUNE_ENST00000368937.1_Intron	NM_021222.1	NP_067045.1	Q86TP1	PRUNE_HUMAN	prune exopolyphosphatase	307						cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	inorganic diphosphatase activity (GO:0004427)|metal ion binding (GO:0046872)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14	all_lung(15;1.09e-34)|Lung NSC(24;1.1e-30)|Lung SC(34;0.00202)|Ovarian(49;0.0167)|all_hematologic(923;0.0597)|Hepatocellular(266;0.0997)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0486)|LUSC - Lung squamous cell carcinoma(543;0.211)			CCCATGTGGCACTCCAAACAA	0.502																																					p.A307fs		Atlas-Indel,Pindel	.											.	PRUNE	40	.	0			c.920delC						PASS	.						129.0	94.0	106.0					1																	151001408		2203	4300	6503	SO:0001589	frameshift_variant	58497	exon7			.	U67085	CCDS977.1	1q21.2	2013-04-29	2013-04-29		ENSG00000143363	ENSG00000143363	3.6.1.11		13420	protein-coding gene	gene with protein product			"""prune homolog (Drosophila)"""			10602478, 11687967, 18700747	Standard	NM_021222		Approved	DRES-17, HTCD37	uc001ewh.1	Q86TP1	OTTHUMG00000035062	ENST00000271620.3:c.921delA	chr1.hg19:g.151001408delA	ENSP00000271620:p.Ala307fs	143.0	0.0	0		114.0	43.0	0.377193	NM_021222	B2RCH8|B4DFL7|Q5SZF9|Q659E5|Q6P4E0|Q8N654|Q96JU5|Q9C071|Q9C072|Q9UIV0	Frame_Shift_Del	DEL	ENST00000271620.3	hg19	CCDS977.1																																																																																			.	.	.	none		0.502	PRUNE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084885.1	NM_021222	
CCER1	196477	hgsc.bcm.edu	37	12	91347581	91347582	+	In_Frame_Ins	INS	-	-	TCT	rs374196591|rs558083520|rs376547014	byFrequency	TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr12:91347581_91347582insTCT	ENST00000358859.2	-	1	1371_1372	c.938_939insAGA	c.(937-939)gag>gaAGAg	p.313_313E>EE	CCER1_ENST00000548187.1_Intron	NM_152638.2	NP_689851.1	Q8TC90	CCER1_HUMAN	coiled-coil glutamate-rich protein 1	313	Glu-rich.																catcttcgacctcttcctcctc	0.535																																					p.E313delinsEE		Atlas-INDEL	.											.	.	.	.	0			c.939_940insAGA						PASS	.			20,4244		0,20,2112						1.8	0.0		dbSNP_107	204	107,8147		2,103,4022	no	coding	C12orf12	NM_152638.2		2,123,6134	A1A1,A1R,RR		1.2963,0.469,1.0145				127,12391				SO:0001652	inframe_insertion	196477	exon1			.	BC024183	CCDS9036.1	12q21.33	2012-05-30	2012-05-30	2012-05-30	ENSG00000197651	ENSG00000197651			28373	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 12"""	C12orf12		17967063	Standard	NM_152638		Approved	MGC26598	uc001tbj.3	Q8TC90	OTTHUMG00000170070	ENST00000358859.2:c.936_938dupAGA	chr12.hg19:g.91347582_91347584dupTCT	ENSP00000351727:p.Glu313dup	84.0	0.0	0		83.0	12.0	0.144578	NM_152638	Q8TC47	In_Frame_Ins	INS	ENST00000358859.2	hg19	CCDS9036.1																																																																																			.	.	.	weak		0.535	CCER1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407142.2	NM_152638	
RIN3	79890	hgsc.bcm.edu	37	14	93117951	93117952	+	Frame_Shift_Ins	INS	-	-	T			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:93117951_93117952insT	ENST00000216487.7	+	6	716_717	c.557_558insT	c.(556-561)cctccafs	p.P187fs	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	187					endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				TCGCTGAATCCTCCACAAGAAA	0.629																																					p.P186fs		Atlas-Indel,Pindel	.											.	RIN3	81	.	0			c.557_558insT						PASS	.																																			SO:0001589	frameshift_variant	79890	exon6			.	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.558dupT	chr14.hg19:g.93117952_93117952dupT	ENSP00000216487:p.Pro187fs	47.0	0.0	0		39.0	24.0	0.615385	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Frame_Shift_Ins	INS	ENST00000216487.7	hg19	CCDS32144.1																																																																																			.	.	.	none		0.629	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
PCDH12	51294	hgsc.bcm.edu	37	5	141334867	141334868	+	Frame_Shift_Ins	INS	-	-	A			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr5:141334867_141334868insA	ENST00000231484.3	-	1	3759_3760	c.2549_2550insT	c.(2548-2550)ttcfs	p.F850fs	PCDH12_ENST00000512221.1_5'Flank|AC005740.6_ENST00000607378.1_RNA	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	850					calcium-dependent cell-cell adhesion (GO:0016339)|glycogen metabolic process (GO:0005977)|homophilic cell adhesion (GO:0007156)|labyrinthine layer development (GO:0060711)|neuron recognition (GO:0008038)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(3)|prostate(2)|skin(1)	38		all_hematologic(541;0.0999)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGGGATGGTTGAAAAGGAGGTT	0.629																																					p.F850fs		Pindel	.											PCDH12,bladder,carcinoma,0,1	PCDH12	133	.	0			c.2550_2551insT						PASS	.																																			SO:0001589	frameshift_variant	51294	exon1			.	AF231025	CCDS4269.1	5q31.3	2010-01-26			ENSG00000113555	ENSG00000113555		"""Cadherins / Protocadherins : Non-clustered"""	8657	protein-coding gene	gene with protein product		605622				10716726, 10380929	Standard	NM_016580		Approved	VE-cadherin-2	uc003llx.3	Q9NPG4	OTTHUMG00000129658	ENST00000231484.3:c.2550dupT	chr5.hg19:g.141334871_141334871dupA	ENSP00000231484:p.Phe850fs	68.0	0.0	.		158.0	47.0	0.297	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Frame_Shift_Ins	INS	ENST00000231484.3	hg19	CCDS4269.1																																																																																			.	.	.	none		0.629	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
RTL1	388015	hgsc.bcm.edu	37	14	101350131	101350138	+	Frame_Shift_Del	DEL	TCGTTGAG	TCGTTGAG	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	TCGTTGAG	TCGTTGAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr14:101350131_101350138delTCGTTGAG	ENST00000534062.1	-	1	1046_1053	c.988_995delCTCAACGA	c.(988-996)ctcaacgagfs	p.LNE330fs	MIR136_ENST00000385207.1_RNA|MIR127_ENST00000384876.1_RNA|MIR431_ENST00000385266.1_RNA|MIR433_ENST00000384837.1_RNA|MIR432_ENST00000606207.1_RNA	NM_001134888.2	NP_001128360.1	A6NKG5	RTL1_HUMAN	retrotransposon-like 1	330					multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)				breast(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(5)|pancreas(1)|prostate(2)|skin(2)	21						CCTGATCTCCTCGTTGAGCCCCTGGCAC	0.567																																					p.330_332del		Pindel	.											.	RTL1	120	.	0			c.989_996del						PASS	.																																			SO:0001589	frameshift_variant	388015	exon1			.		CCDS53910.1	14q32.2	2012-04-18			ENSG00000254656	ENSG00000254656			14665	protein-coding gene	gene with protein product		611896				16155747, 15854907, 12796779	Standard	NM_001134888		Approved	PEG11, MART1, Mar1	uc010txj.1	A6NKG5	OTTHUMG00000167573	ENST00000534062.1:c.988_995delCTCAACGA	chr14.hg19:g.101350131_101350138delTCGTTGAG	ENSP00000435342:p.Leu330fs	50.0	0.0	.		49.0	14.0	0.286	NM_001134888	E9PKS8	Frame_Shift_Del	DEL	ENST00000534062.1	hg19	CCDS53910.1																																																																																			.	.	.	none		0.567	RTL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395127.1	NM_001134888	
PRTG	283659	hgsc.bcm.edu	37	15	55931991	55931992	+	Frame_Shift_Ins	INS	-	-	TGGTGGG			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr15:55931991_55931992insTGGTGGG	ENST00000389286.4	-	13	2219_2220	c.2172_2173insCCCACCA	c.(2170-2175)ccacccfs	p.-725fs		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		AGATGGTGGGGTGGTGGTGGAG	0.45																																					p.P725fs		Pindel	.											.	PRTG	110	.	0			c.2173_2174insCCCACCA						PASS	.																																			SO:0001589	frameshift_variant	283659	exon13			.	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.2172_2173insCCCACCA	chr15.hg19:g.55931991_55931992insTGGTGGG	ENSP00000373937:p.Pro725fs	168.0	0.0	.		132.0	20.0	0.152	NM_173814		Frame_Shift_Ins	INS	ENST00000389286.4	hg19	CCDS42040.1																																																																																			.	.	.	none		0.450	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
KIF1A	547	hgsc.bcm.edu	37	2	241658528	241658528	+	Frame_Shift_Del	DEL	G	G	-			TCGA-A4-A57E-01A-11D-A26P-10	TCGA-A4-A57E-10A-01D-A26P-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	2deb8f9a-9e0a-46d1-bcb5-902db3b5c8ac	c57ad711-a7d0-472f-adf1-7ab186da971b	g.chr2:241658528delG	ENST00000320389.7	-	45	4964	c.4806delC	c.(4804-4806)cccfs	p.P1602fs	KIF1A_ENST00000498729.2_Frame_Shift_Del_p.P1703fs	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1602	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TGTAGGCATAGGGGCGCCGCA	0.622																																					p.Y1704fs		Pindel	.											.	KIF1A	152	.	0			c.5110delT						PASS	.						87.0	100.0	96.0					2																	241658528		2166	4274	6440	SO:0001589	frameshift_variant	547	exon47			.	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.4806delC	chr2.hg19:g.241658528delG	ENSP00000322791:p.Pro1602fs	79.0	0.0	.		289.0	95.0	0.329	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Frame_Shift_Del	DEL	ENST00000320389.7	hg19	CCDS46561.1																																																																																			.	.	.	none		0.622	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
