#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_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
FAM154B	283726	hgsc.bcm.edu	37	15	82574734	82574735	+	Frame_Shift_Del	DEL	AC	AC	-	rs531481065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	AC	AC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:82574734_82574735delAC	ENST00000339465.5	+	3	597_598	c.528_529delAC	c.(526-531)caacgcfs	p.R177fs	FAM154B_ENST00000565501.1_3'UTR|FAM154B_ENST00000427381.2_Frame_Shift_Del_p.R162fs	NM_001008226.1	NP_001008227.1	Q658L1	F154B_HUMAN	family with sequence similarity 154, member B	177										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)	19						CAACTGACCAACGCTTTGAGGA	0.441														6	0.00119808	0.0	0.0	5008	,	,		20560	0.0		0.006	False		,,,				2504	0.0				p.176_176del		Pindel,Atlas-Indel	.											.	FAM154B	50	.	0			c.527_528del						PASS	.			11,4253		0,11,2121						1.4	0.0			67	78,8176		1,76,4050	no	frameshift	FAM154B	NM_001008226.1		1,87,6171	A1A1,A1R,RR		0.945,0.258,0.711				89,12429				SO:0001589	frameshift_variant	283726	exon3			.	AL833762	CCDS32310.1	15q25.2	2008-02-21				ENSG00000188659			33727	protein-coding gene	gene with protein product							Standard	XM_005254317		Approved	DKFZp666G057	uc002bgv.3	Q658L1		ENST00000339465.5:c.528_529delAC	15.37:g.82574734_82574735delAC	ENSP00000340445:p.Arg177fs	87.0	0.0	.		91.0	34.0	0.374	NM_001008226	B4E2M2	Frame_Shift_Del	DEL	ENST00000339465.5	37	CCDS32310.1																																																																																			.	.	none		0.441	FAM154B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419644.1	NM_001008226	
CA9	768	hgsc.bcm.edu	37	9	35674059	35674059	+	Frame_Shift_Del	DEL	G	G	-	rs565650695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35674059delG	ENST00000378357.4	+	1	207	c.103delG	c.(103-105)gtcfs	p.V35fs	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	35					bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	TCTGGTGCCTGTCCATCCCCA	0.652													G|G|-|deletion	3	0.000599042	0.0	0.0029	5008	,	,		18058	0.0		0.001	False		,,,				2504	0.0				p.P34fs		Pindel,Atlas-Indel	.											.	CA9	48	.	0			c.102delT						PASS	.						61.0	56.0	57.0					9																	35674059		2203	4300	6503	SO:0001589	frameshift_variant	768	exon1			.	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.103delG	9.37:g.35674059delG	ENSP00000367608:p.Val35fs	120.0	0.0	.		121.0	37.0	0.306	NM_001216	Q5T4R1	Frame_Shift_Del	DEL	ENST00000378357.4	37	CCDS6585.1																																																																																			.	.	none		0.652	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
NFKBIE	4794	hgsc.bcm.edu	37	6	44232842	44232845	+	Frame_Shift_Del	DEL	GTGT	GTGT	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GTGT	GTGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:44232842_44232845delGTGT	ENST00000275015.5	-	1	655_658	c.656_659delACAC	c.(655-660)tacaccfs	p.YT219fs		NM_004556.2	NP_004547.2	O00221	IKBE_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, epsilon	219					cytoplasmic sequestering of transcription factor (GO:0042994)|D-serine transport (GO:0042942)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)				breast(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(3)|urinary_tract(1)	10	all_cancers(18;2e-05)|all_lung(25;0.00747)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			CAAGGACAGGGTGTAGGTGAGCGA	0.681																																					p.219_220del		Pindel,Atlas-Indel	.											.	NFKBIE	31	.	0			c.657_660del						PASS	.																																			SO:0001589	frameshift_variant	4794	exon1			.	U91616	CCDS34463.1	6p21.1	2013-01-10			ENSG00000146232	ENSG00000146232		"""Ankyrin repeat domain containing"""	7799	protein-coding gene	gene with protein product		604548				9135156	Standard	NM_004556		Approved	IKBE	uc003oxe.1	O00221	OTTHUMG00000014762	ENST00000275015.5:c.656_659delACAC	6.37:g.44232842_44232845delGTGT	ENSP00000275015:p.Tyr219fs	112.0	0.0	.		146.0	22.0	0.151	NM_004556	Q5T9V9	Frame_Shift_Del	DEL	ENST00000275015.5	37	CCDS34463.1																																																																																			.	.	none		0.681	NFKBIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040733.2		
GLIPR1L2	144321	hgsc.bcm.edu	37	12	75804262	75804262	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:75804262delT	ENST00000550916.1	+	2	330	c.283delT	c.(283-285)tgtfs	p.C95fs	GLIPR1L2_ENST00000547164.1_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000441218.1_Frame_Shift_Del_p.C30fs|GLIPR1L2_ENST00000435775.1_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000320460.4_Frame_Shift_Del_p.C95fs|GLIPR1L2_ENST00000378692.3_5'UTR	NM_001270396.1	NP_001257325.1	Q4G1C9	GRPL2_HUMAN	GLI pathogenesis-related 1 like 2	95	SCP.					integral component of membrane (GO:0016021)				kidney(1)|large_intestine(3)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	16						GGGAAAAAAATGTTTGTTTAC	0.323																																					p.K94fs		Pindel,Atlas-Indel	.											.	GLIPR1L2	54	.	0			c.282delA						PASS	.			0,4264		0,0,2132	87.0	87.0	87.0			0.1	1.0	12		87	3,8247		0,3,4122	no	frameshift	GLIPR1L2	NM_152436.1		0,3,6254	A1A1,A1R,RR		0.0364,0.0,0.024			75804262	3,12511	2203	4299	6502	SO:0001589	frameshift_variant	144321	exon2			.	BC029557	CCDS9010.1, CCDS58258.1	12q21.1	2014-06-03				ENSG00000180481			28592	protein-coding gene	gene with protein product		610394				12477932	Standard	NM_001270396		Approved	MGC39497	uc001sxr.2	Q4G1C9	OTTHUMG00000169756	ENST00000550916.1:c.283delT	12.37:g.75804262delT	ENSP00000448248:p.Cys95fs	134.0	0.0	.		136.0	43.0	0.316	NM_152436	Q6MZS1|Q8N6N0|Q8NA43	Frame_Shift_Del	DEL	ENST00000550916.1	37	CCDS58258.1																																																																																			.	.	none		0.323	GLIPR1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405718.1	NM_152436	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230309	23230311	+	In_Frame_Del	DEL	CTG	CTG	-	rs551962377	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTG	CTG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:23230309_23230311delCTG	ENST00000526893.1	+	1	350_352	c.76_78delCTG	c.(76-78)ctgdel	p.L29del	IGLL5_ENST00000532223.2_In_Frame_Del_p.L29del|hsa-mir-5571_ENST00000577998.1_RNA|IGLL5_ENST00000531372.1_In_Frame_Del_p.L29del	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	29						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						GCGCTGGCCCCTGCTGCTGCTGG	0.665																																					p.25_26del		Atlas-Indel	.											.	IGLL5	26	.	0			c.75_77del						PASS	.																																			SO:0001651	inframe_deletion	100423062	exon1			.	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.76_78delCTG	22.37:g.23230318_23230320delCTG	ENSP00000431254:p.Leu29del	151.0	0.0	0		146.0	19.0	0.130137	NM_001178126		In_Frame_Del	DEL	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.665	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
TGM6	343641	hgsc.bcm.edu	37	20	2411657	2411658	+	In_Frame_Ins	INS	-	-	AAC	rs557817405		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2411657_2411658insAAC	ENST00000202625.2	+	12	2012_2013	c.1951_1952insAAC	c.(1951-1953)gaa>gAACaa	p.652_653insQ	TGM6_ENST00000381423.1_Intron	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	652					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	CCTTCTCCAGGAACAGCTCAGC	0.594																																					p.E651delinsEQ		Pindel,Atlas-Indel	.											.	TGM6	126	.	0			c.1951_1952insAAC						PASS	.			4,4260		0,4,2128						5.2	1.0			81	27,8227		0,27,4100	no	coding	TGM6	NM_198994.2		0,31,6228	A1A1,A1R,RR		0.3271,0.0938,0.2476				31,12487				SO:0001652	inframe_insertion	343641	exon12			.	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.1952_1954dupAAC	20.37:g.2411658_2411660dupAAC	ENSP00000202625:p.Gln652_Gln652dup	63.0	0.0	.		80.0	30.0	0.375	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	In_Frame_Ins	INS	ENST00000202625.2	37	CCDS13025.1																																																																																			.	.	none		0.594	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
MDFIC	29969	hgsc.bcm.edu	37	7	114562638	114562639	+	In_Frame_Ins	INS	-	-	GAG			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:114562638_114562639insGAG	ENST00000257724.3	+	1	430_431	c.167_168insGAG	c.(166-171)aagagg>aaGAGgagg	p.62_63insR	MDFIC_ENST00000423503.1_5'Flank|MDFIC_ENST00000393486.1_5'UTR|MDFIC_ENST00000448022.1_5'UTR					MyoD family inhibitor domain containing											breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	8						CCGGGGCggaagaggaggagga	0.703											OREG0003787	type=REGULATORY REGION|Gene=MDFIC|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.K56delinsKR		Pindel,Atlas-Indel	.											.	MDFIC	30	.	0			c.167_168insGAG						PASS	.																																			SO:0001652	inframe_insertion	29969	exon1			.	AF054589	CCDS34737.1, CCDS55155.1	7q31.1-q31.2	2006-01-11			ENSG00000135272	ENSG00000135272			28870	protein-coding gene	gene with protein product		614511				10671520	Standard	NM_199072		Approved	HIC	uc003vhf.3	Q9P1T7	OTTHUMG00000023647	ENST00000257724.3:c.183_185dupGAG	7.37:g.114562645_114562647dupGAG	ENSP00000257724:p.Arg62_Arg62dup	40.0	0.0	.	1459	42.0	13.0	0.310	NM_001166346		In_Frame_Ins	INS	ENST00000257724.3	37	CCDS34737.1																																																																																			.	.	none		0.703	MDFIC-007	KNOWN	non_ATG_start|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000366397.1	NM_199072	
GAL3ST3	89792	hgsc.bcm.edu	37	11	65811114	65811116	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	GAG	GAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65811114_65811116delGAG	ENST00000312006.4	-	3	439_441	c.158_160delCTC	c.(157-162)cctctg>ctg	p.P53del	GAL3ST3_ENST00000527878.1_In_Frame_Del_p.P53del	NM_033036.2	NP_149025.1	Q96A11	G3ST3_HUMAN	galactose-3-O-sulfotransferase 3	53					monosaccharide metabolic process (GO:0005996)|oligosaccharide metabolic process (GO:0009311)|poly-N-acetyllactosamine metabolic process (GO:0030309)|proteoglycan biosynthetic process (GO:0030166)|sulfur compound metabolic process (GO:0006790)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	3'-phosphoadenosine 5'-phosphosulfate binding (GO:0050656)|carbohydrate binding (GO:0030246)|galactose 3-O-sulfotransferase activity (GO:0050694)|galactosylceramide sulfotransferase activity (GO:0001733)|proteoglycan sulfotransferase activity (GO:0050698)			kidney(1)|lung(9)|ovary(2)|skin(2)	14						GAGTTCCGCAGAGGAGGGCAGCT	0.645																																					p.53_54del		Pindel,Atlas-Indel	.											.	GAL3ST3	40	.	0			c.159_161del						PASS	.																																			SO:0001651	inframe_deletion	89792	exon3			.	AY026481	CCDS8128.1	11q13.1	2014-08-12			ENSG00000175229	ENSG00000175229		"""Sulfotransferases, membrane-bound"""	24144	protein-coding gene	gene with protein product		608234				11323440, 11356829	Standard	NM_033036		Approved	GAL3ST2	uc001ogw.3	Q96A11	OTTHUMG00000166667	ENST00000312006.4:c.158_160delCTC	11.37:g.65811117_65811119delGAG	ENSP00000308591:p.Pro53del	185.0	0.0	.		161.0	55.0	0.342	NM_033036	Q14D05	In_Frame_Del	DEL	ENST00000312006.4	37	CCDS8128.1																																																																																			.	.	none		0.645	GAL3ST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391052.1	NM_033036	
RPGR	6103	hgsc.bcm.edu	37	X	38145632	38145646	+	Intron	DEL	CTTCCTCCCCTTCTT	CTTCCTCCCCTTCTT	-	rs201131185|rs200824587		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CTTCCTCCCCTTCTT	CTTCCTCCCCTTCTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:38145632_38145646delCTTCCTCCCCTTCTT	ENST00000339363.3	-	14	2688				RPGR_ENST00000318842.7_Intron|TM4SF2_ENST00000465127.1_Intron|RPGR_ENST00000309513.3_Intron|RPGR_ENST00000338898.3_Intron|RPGR_ENST00000378505.2_In_Frame_Del_p.EEGEE869del|RPGR_ENST00000342811.3_Intron			Q92834	RPGR_HUMAN	retinitis pigmentosa GTPase regulator						cilium assembly (GO:0042384)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|intraciliary transport (GO:0042073)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|Golgi apparatus (GO:0005794)|photoreceptor outer segment (GO:0001750)|sperm flagellum (GO:0036126)	guanyl-nucleotide exchange factor activity (GO:0005085)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	25						tccccttctccttcctccccttcttcctccccttc	0.6																																					p.869_874del		Atlas-Indel	.											.	RPGR	175	.	0			c.2607_2621del	GRCh37	CD033265|CD064604|CI013682|CM074396	orf15	D|I|M		PASS	.		,	43,2971		2,33,6,1315,308					,	-0.2	0.0			10	195,4756		24,97,50,1779,1101	no	coding,intron	RPGR	NM_001034853.1,NM_000328.2	,	26,130,56,3094,1409	A1A1,A1R,A1,RR,R		3.9386,1.4267,2.9881	,	,		238,7727				SO:0001627	intron_variant	6103	exon15			.	U57629	CCDS14246.1, CCDS35229.1	Xp11.4	2013-06-06	2004-02-13		ENSG00000156313	ENSG00000156313			10295	protein-coding gene	gene with protein product		312610	"""retinitis pigmentosa 15"", ""cone dystrophy 1 (X-linked)"""	CRD, RP3, RP15, COD1		8673101, 8817343	Standard	XM_005272633		Approved	CORDX1	uc004ded.1	Q92834	OTTHUMG00000021361	ENST00000339363.3:c.2520+700AAGAAGGGGAGGAAG>-	X.37:g.38145632_38145646delCTTCCTCCCCTTCTT		44.0	0.0	0		27.0	20.0	0.740741	NM_001034853	B1ARN3|E9PE28|O00702|O00737|Q3KN84|Q8N5T6|Q93039|Q9HD29|Q9UMR1	In_Frame_Del	DEL	ENST00000339363.3	37																																																																																				CTTCCTCCCCTTCTT|0.987;-|0.013	0.013	strong		0.600	RPGR-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_000328	
PI4KB	5298	hgsc.bcm.edu	37	1	151263677	151263678	+	IGR	INS	-	-	ACA	rs145032688	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151263677_151263678insACA	ENST00000368873.1	-	0	3340				ZNF687_ENST00000368879.2_3'UTR			Q9UBF8	PI4KB_HUMAN	phosphatidylinositol 4-kinase, catalytic, beta						phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi membrane (GO:0000139)|mitochondrial outer membrane (GO:0005741)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(5)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	27	Lung SC(34;0.00471)|Ovarian(49;0.0147)|Hepatocellular(266;0.0997)|all_hematologic(923;0.127)|Melanoma(130;0.185)		UCEC - Uterine corpus endometrioid carcinoma (35;0.112)|LUSC - Lung squamous cell carcinoma(543;0.181)			GGCTGTTGGGGACAACTAGTCT	0.584														82	0.0163738	0.0023	0.0144	5008	,	,		16222	0.0		0.0547	False		,,,				2504	0.0143				p.D1236delinsDN	Colon(154;765 1838 9854 28443 37492)	Pindel,Atlas-Indel	.											.	ZNF687	94	.	0			c.3706_3707insACA						PASS	.			59,4025		4,51,1987						4.7	1.0		dbSNP_134	30	528,7434		53,422,3506	no	coding	ZNF687	NM_020832.1		57,473,5493	A1A1,A1R,RR		6.6315,1.4447,4.873				587,11459				SO:0001628	intergenic_variant	57592	exon9			.	AB005910	CCDS993.1, CCDS55637.1, CCDS55638.1	1q21	2008-02-05	2007-08-14	2007-08-02	ENSG00000143393	ENSG00000143393			8984	protein-coding gene	gene with protein product		602758		PIK4CB		9020160, 9405938	Standard	NM_002651		Approved	PI4K-BETA, pi4K92	uc001exu.3	Q9UBF8	OTTHUMG00000012348		1.37:g.151263678_151263680dupACA		25.0	0.0	.		32.0	14.0	0.438	NM_020832	B4DGI2|O15096|P78405|Q5VWB9|Q5VWC0|Q5VWC1|Q9BWR6	In_Frame_Ins	INS	ENST00000368873.1	37																																																																																				-|0.977;ACA|0.023	0.023	strong		0.584	PI4KB-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000034400.3	NM_002651	
TNFAIP3	7128	hgsc.bcm.edu	37	6	138192494	138192501	+	Frame_Shift_Del	DEL	CACCGATA	CACCGATA	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	CACCGATA	CACCGATA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:138192494_138192501delCACCGATA	ENST00000237289.4	+	2	196_203	c.130_137delCACCGATA	c.(130-138)caccgatacfs	p.HRY44fs		NM_001270507.1|NM_001270508.1|NM_006290.3	NP_001257436.1|NP_001257437.1|NP_006281.1	P21580	TNAP3_HUMAN	tumor necrosis factor, alpha-induced protein 3	44					apoptotic process (GO:0006915)|B-1 B cell homeostasis (GO:0001922)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to lipopolysaccharide (GO:0071222)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|negative regulation of B cell activation (GO:0050869)|negative regulation of bone resorption (GO:0045779)|negative regulation of CD40 signaling pathway (GO:2000349)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of osteoclast proliferation (GO:0090291)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of smooth muscle cell proliferation (GO:0048662)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of toll-like receptor 3 signaling pathway (GO:0034140)|negative regulation of toll-like receptor 4 signaling pathway (GO:0034144)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of protein catabolic process (GO:0045732)|protein deubiquitination (GO:0016579)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K48-linked ubiquitination (GO:0070936)|protein K63-linked deubiquitination (GO:0070536)|protein oligomerization (GO:0051259)|regulation of defense response to virus by host (GO:0050691)|regulation of germinal center formation (GO:0002634)|regulation of vascular wound healing (GO:0061043)|response to molecule of bacterial origin (GO:0002237)|tolerance induction to lipopolysaccharide (GO:0072573)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|protease binding (GO:0002020)|protein self-association (GO:0043621)|ubiquitin binding (GO:0043130)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.0?(25)|p.M43fs*55(1)		breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(196)|kidney(1)|large_intestine(4)|lung(13)|ovary(4)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	225	Breast(32;0.135)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000849)|OV - Ovarian serous cystadenocarcinoma(155;0.00468)		TAAAACCATGCACCGATACACACTGGAA	0.438			"""D, N, F"""		"""marginal zone B-cell lymphomas, Hodgkin's lymphoma, primary mediastinal B cell lymphoma"""																																p.43_46del	GBM(130;153 1739 22295 28918 47987)	Atlas-Indel	.		Rec	yes		6	6q23	7128	"""tumor necrosis factor, alpha-induced protein 3"""		L	.	TNFAIP3	340	.	26	Whole gene deletion(25)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(26)	c.129_136del						PASS	.																																			SO:0001589	frameshift_variant	7128	exon2			.	M59465	CCDS5187.1	6q23-q25	2013-01-21			ENSG00000118503	ENSG00000118503		"""OTU domain containing"""	11896	protein-coding gene	gene with protein product		191163				2118515	Standard	NM_006290		Approved	A20, OTUD7C	uc031spw.1	P21580	OTTHUMG00000015664	ENST00000237289.4:c.130_137delCACCGATA	6.37:g.138192494_138192501delCACCGATA	ENSP00000237289:p.His44fs	148.0	0.0	0		114.0	12.0	0.105263	NM_006290	B2R767|E1P588|Q2HIX9|Q5VXQ7|Q9NSR6	Frame_Shift_Del	DEL	ENST00000237289.4	37	CCDS5187.1																																																																																			.	.	none		0.438	TNFAIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042414.1		
TET2	54790	hgsc.bcm.edu	37	4	106197061	106197061	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106197061delA	ENST00000540549.1	+	11	6254	c.5394delA	c.(5392-5394)tcafs	p.S1798fs	TET2_ENST00000513237.1_Frame_Shift_Del_p.S1819fs|TET2_ENST00000380013.4_Frame_Shift_Del_p.S1798fs|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1798					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ATGGGTTATCAAAGATGCTTC	0.463			"""Mis N, F"""		MDS																																p.S1798X		Atlas-Indel	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.5393delC						PASS	.						23.0	21.0	21.0					4																	106197061		692	1591	2283	SO:0001589	frameshift_variant	54790	exon11			.	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.5394delA	4.37:g.106197061delA	ENSP00000442788:p.Ser1798fs	140.0	0.0	0		130.0	22.0	0.169231	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Frame_Shift_Del	DEL	ENST00000540549.1	37	CCDS47120.1																																																																																			.	.	none		0.463	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
TAS2R8	50836	hgsc.bcm.edu	37	12	10958845	10958846	+	Frame_Shift_Ins	INS	-	-	A	rs200711805|rs149008514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10958845_10958846insA	ENST00000240615.2	-	1	1046_1047	c.734_735insT	c.(733-735)ttcfs	p.F245fs		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	245					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TATAGTATAGGAAAAAAAAGAA	0.366													AAAAAAAA|AAAAAAAA|AAAAAAAAA|insertion	40	0.00798722	0.0	0.0216	5008	,	,		15757	0.002		0.0119	False		,,,				2504	0.0112				p.F245fs		Pindel,Atlas-Indel	.											TAS2R8,NS,malignant_melanoma,0,1	TAS2R8	42	1	0			c.735_736insT						PASS	.																																			SO:0001589	frameshift_variant	50836	exon1			.	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.735dupT	12.37:g.10958853_10958853dupA	ENSP00000240615:p.Phe245fs	110.0	0.0	.		90.0	33.0	0.367	NM_023918	Q4KN29|Q645Y2	Frame_Shift_Ins	INS	ENST00000240615.2	37	CCDS8632.1																																																																																			-|0.994;A|0.006	0.006	strong		0.366	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
CCDC150	284992	hgsc.bcm.edu	37	2	197521469	197521470	+	Frame_Shift_Del	DEL	TG	TG	-	rs143904259		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:197521469_197521470delTG	ENST00000389175.4	+	3	424_425	c.289_290delTG	c.(289-291)tgtfs	p.C97fs	CCDC150_ENST00000272831.7_Intron|CCDC150_ENST00000472405.2_5'UTR|CCDC150_ENST00000423093.2_Intron	NM_001080539.1	NP_001074008.1	Q8NCX0	CC150_HUMAN	coiled-coil domain containing 150	97										breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(14)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	33						ATGGAAGAACTGTGAGTTTCTG	0.411																																					p.96_97del		Pindel,Atlas-Indel	.											.	CCDC150	96	.	0			c.288_289del						PASS	.			9,3541		2,5,1768						5.0	1.0		dbSNP_134	110	123,7711		1,121,3795	no	frameshift	CCDC150	NM_001080539.1		3,126,5563	A1A1,A1R,RR		1.5701,0.2535,1.1595				132,11252				SO:0001589	frameshift_variant	284992	exon3			.		CCDS46478.1	2q33.1	2008-04-10			ENSG00000144395	ENSG00000144395			26834	protein-coding gene	gene with protein product							Standard	NM_001080539		Approved	FLJ39660	uc002utp.1	Q8NCX0	OTTHUMG00000154475	ENST00000389175.4:c.289_290delTG	2.37:g.197521471_197521472delTG	ENSP00000373827:p.Cys97fs	142.0	0.0	.		151.0	50.0	0.331	NM_001080539	Q6P5U6|Q6P663|Q8N8V5	Frame_Shift_Del	DEL	ENST00000389175.4	37	CCDS46478.1																																																																																			TG|0.989;-|0.011	0.011	strong		0.411	CCDC150-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335377.2	NM_001080539	
TRPM7	54822	hgsc.bcm.edu	37	15	50884289	50884294	+	In_Frame_Del	DEL	ATTTTT	ATTTTT	-			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	ATTTTT	ATTTTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:50884289_50884294delATTTTT	ENST00000313478.7	-	26	4419_4424	c.4138_4143delAAAAAT	c.(4138-4143)aaaaatdel	p.KN1380del	TRPM7_ENST00000560955.1_In_Frame_Del_p.KN1380del	NM_017672.4	NP_060142.3	Q96QT4	TRPM7_HUMAN	transient receptor potential cation channel, subfamily M, member 7	1380					actomyosin structure organization (GO:0031032)|calcium ion transmembrane transport (GO:0070588)|calcium-dependent cell-matrix adhesion (GO:0016340)|cellular magnesium ion homeostasis (GO:0010961)|ion transmembrane transport (GO:0034220)|necroptotic process (GO:0070266)|protein autophosphorylation (GO:0046777)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(17)|lung(13)|ovary(4)|pancreas(1)|skin(4)|stomach(3)	52				all cancers(107;0.000819)|GBM - Glioblastoma multiforme(94;0.0045)		Ctaatttttgatttttattaaatatt	0.417																																					p.1380_1382del		Pindel,Atlas-Indel	.											.	TRPM7	145	.	0			c.4139_4144del						PASS	.			3,3465		1,1,1732						0.5	0.6			62	3,7803		0,3,3900	no	coding	TRPM7	NM_017672.4		1,4,5632	A1A1,A1R,RR		0.0384,0.0865,0.0532				6,11268				SO:0001651	inframe_deletion	54822	exon26			.	AF346629	CCDS42035.1, CCDS73725.1	15q21	2011-12-14				ENSG00000092439		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	17994	protein-coding gene	gene with protein product		605692				11161216, 11385574, 16382100	Standard	XM_005254486		Approved	CHAK1, LTRPC7, TRP-PLIK	uc001zyt.4	Q96QT4		ENST00000313478.7:c.4138_4143delAAAAAT	15.37:g.50884289_50884294delATTTTT	ENSP00000320239:p.Lys1380_Asn1381del	35.0	0.0	.		35.0	10.0	0.286	NM_017672	Q6ZMF5|Q86VJ4|Q8NBW2|Q9BXB2|Q9NXQ2	In_Frame_Del	DEL	ENST00000313478.7	37	CCDS42035.1																																																																																			.	.	none		0.417	TRPM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000418604.1	NM_017672	
RSU1	6251	hgsc.bcm.edu	37	10	16635400	16635402	+	In_Frame_Del	DEL	TTC	TTC	-	rs575845875		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:16635400_16635402delTTC	ENST00000377921.3	-	8	1126_1128	c.825_827delGAA	c.(823-828)aagaac>aac	p.K275del	RSU1_ENST00000602389.1_In_Frame_Del_p.K222del|RSU1_ENST00000345264.5_In_Frame_Del_p.K275del|RSU1_ENST00000464074.2_5'UTR			Q15404	RSU1_HUMAN	Ras suppressor protein 1	275					cell junction assembly (GO:0034329)|positive regulation of neural precursor cell proliferation (GO:2000179)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(7)|stomach(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(1;7.54e-08)		TCCTTATCTGTTCTTGGCTGCCA	0.507																																					p.276_276del		Pindel,Atlas-Indel	.											.	RSU1	31	.	0			c.826_828del						PASS	.																																			SO:0001651	inframe_deletion	6251	exon9			.	AK055596	CCDS7112.1, CCDS31157.1	10p13	2012-09-20			ENSG00000148484	ENSG00000148484			10464	protein-coding gene	gene with protein product		179555				8288261	Standard	NM_152724		Approved	RSP-1, FLJ31034	uc001iol.3	Q15404	OTTHUMG00000017740	ENST00000377921.3:c.825_827delGAA	10.37:g.16635400_16635402delTTC	ENSP00000367154:p.Lys275del	205.0	0.0	.		213.0	71.0	0.333	NM_012425	A8KA46|D3DRU3|Q6FI17	In_Frame_Del	DEL	ENST00000377921.3	37	CCDS7112.1																																																																																			.	.	none		0.507	RSU1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047006.1	NM_012425, NM_152724	
RIMBP3B	440804	hgsc.bcm.edu	37	22	21741340	21741341	+	In_Frame_Ins	INS	-	-	TGCAGG	rs555102406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21741340_21741341insTGCAGG	ENST00000434111.1	+	1	3678_3679	c.3193_3194insTGCAGG	c.(3193-3195)ctg>cTGCAGGtg	p.1067_1068insQV	SCARNA18_ENST00000516505.1_RNA|SCARNA17_ENST00000516211.1_RNA|RN7SKP63_ENST00000363187.1_RNA	NM_001128635.1	NP_001122107.1	A6NNM3	RIM3B_HUMAN	RIMS binding protein 3B	1067	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.																ATGGGACTTGCTGCAGGTGTAT	0.663																																					p.L1065delinsLQV		Pindel	.											.	RIMBP3C	6	.	0			c.3193_3194insTGCAGG						PASS	.			6,24		3,0,12						-2.0	0.0			1	7,131		3,1,65	no	coding	RIMBP3B	NM_001128635.1		6,1,77	A1A1,A1R,RR		5.0725,20.0,7.7381				13,155				SO:0001652	inframe_insertion	150221	exon1			.		CCDS46668.1	22q11.21	2008-10-23			ENSG00000196934	ENSG00000274600			33891	protein-coding gene	gene with protein product		612700				17855024	Standard	NM_001128635		Approved			A6NNM3	OTTHUMG00000150819	ENST00000434111.1:c.3194_3199dupTGCAGG	22.37:g.21741341_21741346dupTGCAGG	ENSP00000407925:p.Gln1066_Val1067dup	2.0	0.0	.		15.0	15.0	1.000	NM_001128633		In_Frame_Ins	INS	ENST00000434111.1	37	CCDS46668.1																																																																																			.	.	none		0.663	RIMBP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320196.2	XM_036936	
PELP1	27043	hgsc.bcm.edu	37	17	4576216	4576217	+	In_Frame_Ins	INS	-	-	GGCATGGGGCCTGCTGAA	rs147763003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576216_4576217insGGCATGGGGCCTGCTGAA	ENST00000574876.1	-	16	2086_2087	c.2069_2070insTTCAGCAGGCCCCATGCC	c.(2068-2070)ccc>ccTTCAGCAGGCCCCATGCCc	p.690_690P>PSAGPMP	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_In_Frame_Ins_p.600_600P>PSAGPMP|PELP1_ENST00000572293.1_In_Frame_Ins_p.740_740P>PSAGPMP|PELP1_ENST00000301396.4_In_Frame_Ins_p.834_834P>PSAGPMP|PELP1_ENST00000436683.2_In_Frame_Ins_p.543_543P>PSAGPMP			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	690	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GGCCTGCTGAGGGCATGGGGCC	0.688																																					p.P690delinsPSAGPMP		Pindel	.											.	PELP1	102	.	0			c.2070_2071insTTCAGCAGGCCCCATGCC						PASS	.																																			SO:0001652	inframe_insertion	27043	exon16			.		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2052_2069dupTTCAGCAGGCCCCATGCC	17.37:g.4576216_4576217insGGCATGGGGCCTGCTGAA	ENSP00000461625:p.SerAlaGlyProMetPro690dup	147.0	0.0	.		146.0	33.0	0.226	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	In_Frame_Ins	INS	ENST00000574876.1	37	CCDS58503.1																																																																																			.	.	none		0.688	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
EXOSC2	23404	hgsc.bcm.edu	37	9	133579152	133579152	+	Silent	SNP	G	G	A	rs34680820	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133579152G>A	ENST00000372358.5	+	9	944	c.873G>A	c.(871-873)caG>caA	p.Q291Q	EXOSC2_ENST00000546165.1_Silent_p.Q265Q|EXOSC2_ENST00000372352.3_Silent_p.Q283Q|EXOSC2_ENST00000372351.3_Silent_p.Q261Q|EXOSC2_ENST00000467138.1_3'UTR			Q13868	EXOS2_HUMAN	exosome component 2	291					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|positive regulation of cell growth (GO:0030307)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|rRNA processing (GO:0006364)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|exosome (RNase complex) (GO:0000178)|nucleus (GO:0005634)	3'-5'-exoribonuclease activity (GO:0000175)|7S RNA binding (GO:0008312)			breast(1)|endometrium(1)|large_intestine(3)|ovary(1)	6		Acute lymphoblastic leukemia(5;0.0508)|all_hematologic(13;0.0588)		OV - Ovarian serous cystadenocarcinoma(145;0.000324)		TTTTGGAACAGGAGGGATAAG	0.478													G|||	22	0.00439297	0.0023	0.0043	5008	,	,		20923	0.0		0.0109	False		,,,				2504	0.0051				p.Q291Q	Pancreas(134;1683 1824 10118 27928 31640)	Atlas-SNP	.											.	EXOSC2	15	.	0			c.G873A						PASS	.	G		24,4382	29.9+/-59.1	0,24,2179	119.0	128.0	125.0		873	4.1	1.0	9	dbSNP_126	125	230,8370	93.8+/-155.7	3,224,4073	no	coding-synonymous	EXOSC2	NM_014285.5		3,248,6252	AA,AG,GG		2.6744,0.5447,1.9529		291/294	133579152	254,12752	2203	4300	6503	SO:0001819	synonymous_variant	23404	exon9			GGAACAGGAGGGA	AK001916	CCDS6935.1, CCDS65160.1, CCDS65161.1	9q34	2008-02-05			ENSG00000130713	ENSG00000130713			17097	protein-coding gene	gene with protein product	"""homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4)"""	602238				8600032, 1538749	Standard	XM_005272176		Approved	hRrp4p, Rrp4p, RRP4, p7	uc004bzu.2	Q13868	OTTHUMG00000020811	ENST00000372358.5:c.873G>A	9.37:g.133579152G>A		70.0	0.0	0		36.0	13.0	0.361111	NM_014285	A3KFL3|B4DKK6|Q9NUY4	Silent	SNP	ENST00000372358.5	37	CCDS6935.1																																																																																			G|0.986;A|0.014	0.014	strong		0.478	EXOSC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054673.1	NM_014285	
MMS22L	253714	hgsc.bcm.edu	37	6	97599674	97599674	+	Missense_Mutation	SNP	G	G	A	rs138146580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:97599674G>A	ENST00000275053.4	-	23	3720	c.3455C>T	c.(3454-3456)cCt>cTt	p.P1152L	MMS22L_ENST00000369251.2_Missense_Mutation_p.P1112L	NM_198468.2	NP_940870.2	Q6ZRQ5	MMS22_HUMAN	MMS22-like, DNA repair protein	1152					double-strand break repair via homologous recombination (GO:0000724)|replication fork processing (GO:0031297)	nuclear replication fork (GO:0043596)				breast(1)|endometrium(9)|kidney(2)|large_intestine(12)|lung(20)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	50						CTGGGAGGAAGGTTCTTCTTC	0.433													G|||	37	0.00738818	0.0023	0.0058	5008	,	,		15425	0.0		0.0239	False		,,,				2504	0.0061				p.P1152L		Atlas-SNP	.											.	MMS22L	102	.	0			c.C3455T						PASS	.	G	LEU/PRO	17,4389	24.3+/-50.5	0,17,2186	204.0	203.0	203.0		3455	3.6	1.0	6	dbSNP_134	203	155,8445	73.5+/-136.2	2,151,4147	yes	missense	MMS22L	NM_198468.2	98	2,168,6333	AA,AG,GG		1.8023,0.3858,1.3225	benign	1152/1244	97599674	172,12834	2203	4300	6503	SO:0001583	missense	253714	exon23			GAGGAAGGTTCTT		CCDS5039.1	6q16.3	2010-11-11	2010-11-11	2010-11-11	ENSG00000146263	ENSG00000146263			21475	protein-coding gene	gene with protein product		615614	"""chromosome 6 open reading frame 167"""	C6orf167		21055983, 21055984	Standard	NM_198468		Approved	dJ39B17.2	uc003ppb.3	Q6ZRQ5	OTTHUMG00000015248	ENST00000275053.4:c.3455C>T	6.37:g.97599674G>A	ENSP00000275053:p.Pro1152Leu	189.0	0.0	0		184.0	109.0	0.592391	NM_198468	D6R9Y8|D6RBQ4|E1P529|Q5THT2|Q68CQ6|Q68D32	Missense_Mutation	SNP	ENST00000275053.4	37	CCDS5039.1	26	0.011904761904761904	3	0.006097560975609756	4	0.011049723756906077	0	0.0	19	0.025065963060686015	G	9.389	1.074903	0.20227	0.003858	0.018023	ENSG00000146263	ENST00000275053;ENST00000369251	T;T	0.29655	3.93;1.56	5.44	3.59	0.41128	.	0.290094	0.38492	N	0.001666	T	0.09202	0.0227	L	0.56769	1.78	0.44966	D	0.997984	B;B	0.31548	0.328;0.082	B;B	0.27380	0.079;0.036	T	0.13255	-1.0516	10	0.14252	T	0.57	.	3.4047	0.07336	0.1576:0.1261:0.5698:0.1465	.	1112;1152	E2QRD4;Q6ZRQ5	.;MMS22_HUMAN	L	1152;1112	ENSP00000275053:P1152L;ENSP00000358254:P1112L	ENSP00000275053:P1152L	P	-	2	0	MMS22L	97706395	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	1.175000	0.31944	0.606000	0.29965	0.650000	0.86243	CCT	G|0.987;A|0.013	0.013	strong		0.433	MMS22L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041573.3	NM_198468	
ABL1	25	hgsc.bcm.edu	37	9	133760029	133760029	+	Silent	SNP	C	C	G	rs2229070	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760029C>G	ENST00000318560.5	+	11	2733	c.2352C>G	c.(2350-2352)ccC>ccG	p.P784P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	784	Pro-rich.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CGCCTCCCCCCAGGCTGGTGA	0.592			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	534	0.106629	0.2821	0.0865	5008	,	,		18610	0.001		0.0696	False		,,,				2504	0.0307				p.P803P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2409G						PASS	.	C	,	985,3415		107,771,1322	26.0	30.0	28.0		2352,2409	1.6	0.2	9	dbSNP_98	28	622,7976		27,568,3704	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	134,1339,5026	GG,GC,CC		7.2342,22.3864,12.3634	,	784/1131,803/1150	133760029	1607,11391	2200	4299	6499	SO:0001819	synonymous_variant	25	exon11			TCCCCCCAGGCTG	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2352C>G	9.37:g.133760029C>G		36.0	0.0	0		33.0	16.0	0.484848	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			C|0.885;G|0.115	0.115	strong		0.592	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
ZFP41	286128	hgsc.bcm.edu	37	8	144332045	144332045	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144332045C>T	ENST00000330701.4	+	2	401	c.32C>T	c.(31-33)aCg>aTg	p.T11M	ZFP41_ENST00000522452.1_Missense_Mutation_p.T11M|ZFP41_ENST00000520584.1_Missense_Mutation_p.T11M	NM_173832.4	NP_776193.1	Q8N8Y5	ZFP41_HUMAN	ZFP41 zinc finger protein	11					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|lung(4)|ovary(1)	8	all_cancers(97;1.01e-10)|all_epithelial(106;4.6e-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)			AAAAAGAAGACGCCGACCCCA	0.592																																					p.T11M		Atlas-SNP	.											ZFP41,NS,carcinoma,0,1	ZFP41	25	1	0			c.C32T						PASS	.						26.0	29.0	28.0					8																	144332045		2200	4299	6499	SO:0001583	missense	286128	exon2			AGAAGACGCCGAC		CCDS6397.1	8q24.3	2013-01-08	2012-11-27		ENSG00000181638	ENSG00000181638		"""Zinc fingers, C2H2-type"""	26786	protein-coding gene	gene with protein product			"""zinc finger protein 41 homolog (mouse)"""			11214971	Standard	NM_173832		Approved	FLJ38705, FLJ00028, ZNF753	uc003yxw.4	Q8N8Y5	OTTHUMG00000164951	ENST00000330701.4:c.32C>T	8.37:g.144332045C>T	ENSP00000327427:p.Thr11Met	73.0	0.0	0		81.0	43.0	0.530864	NM_173832	D3DWJ5	Missense_Mutation	SNP	ENST00000330701.4	37	CCDS6397.1	.	.	.	.	.	.	.	.	.	.	C	9.340	1.062804	0.19987	.	.	ENSG00000181638	ENST00000520584;ENST00000330701;ENST00000522452	T;T;T	0.06371	3.31;3.31;3.31	2.64	-1.62	0.08372	.	.	.	.	.	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	1	B	0.27013	0.166	B	0.12837	0.008	T	0.42310	-0.9459	9	0.66056	D	0.02	-0.6933	0.4835	0.00552	0.1961:0.3496:0.1927:0.2616	.	11	Q8N8Y5	ZFP41_HUMAN	M	11	ENSP00000430465:T11M;ENSP00000327427:T11M;ENSP00000428966:T11M	ENSP00000327427:T11M	T	+	2	0	ZFP41	144403420	.	.	0.000000	0.03702	0.001000	0.01503	.	.	-0.428000	0.07339	-0.339000	0.08088	ACG	.	.	none		0.592	ZFP41-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381114.2	NM_173832	
NOD2	64127	hgsc.bcm.edu	37	16	50746228	50746228	+	Silent	SNP	G	G	T	rs104895495		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50746228G>T	ENST00000300589.2	+	4	2511	c.2406G>T	c.(2404-2406)gtG>gtT	p.V802V	RP11-327F22.6_ENST00000602304.1_RNA	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	802					activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				ACAACTCTGTGGGTGACATTG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		21477	0.0		0.001	False		,,,				2504	0.0				p.V802V		Atlas-SNP	.											.	NOD2	118	.	0			c.G2406T						PASS	.	G		2,4394	4.2+/-10.8	0,2,2196	113.0	115.0	114.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2406	3.3	1.0	16	dbSNP_132	114	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	NOD2	NM_022162.1		0,18,6480	TT,TG,GG		0.186,0.0455,0.1385		802/1041	50746228	18,12978	2198	4300	6498	SO:0001819	synonymous_variant	64127	exon4			CTCTGTGGGTGAC	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.2406G>T	16.37:g.50746228G>T		146.0	0.0	0		147.0	66.0	0.44898	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Silent	SNP	ENST00000300589.2	37	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	G	6.792	0.515223	0.12944	4.55E-4	0.00186	ENSG00000167207	ENST00000534057	.	.	.	5.29	3.28	0.37604	.	.	.	.	.	T	0.54983	0.1892	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47262	-0.9131	4	.	.	.	.	6.42	0.21738	0.0846:0.0:0.5875:0.3279	.	.	.	.	W	42	.	.	G	+	1	0	NOD2	49303729	0.786000	0.28738	0.995000	0.50966	0.966000	0.64601	-0.179000	0.09768	0.575000	0.29434	0.555000	0.69702	GGG	G|0.998;T|0.002	0.002	strong		0.602	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
CROCC	9696	hgsc.bcm.edu	37	1	17265601	17265601	+	Silent	SNP	C	C	T	rs146792981	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:17265601C>T	ENST00000375541.5	+	12	1641	c.1572C>T	c.(1570-1572)atC>atT	p.I524I	CROCC_ENST00000467938.1_3'UTR	NM_014675.3	NP_055490.3			ciliary rootlet coiled-coil, rootletin											breast(3)|central_nervous_system(2)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(1)|lung(20)|ovary(3)|prostate(9)|skin(3)|urinary_tract(1)	62		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000174)|all_lung(284;0.000234)|Renal(390;0.000518)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.63e-06)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(64;0.000163)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.181)		TCGCCCTGATCCACTCCGCCC	0.751													c|||	82	0.0163738	0.0038	0.0303	5008	,	,		10936	0.0		0.0447	False		,,,				2504	0.0112				p.I524I		Atlas-SNP	.											CROCC,NS,haematopoietic_neoplasm,0,1	CROCC	185	1	0			c.C1572T						PASS	.						6.0	6.0	6.0					1																	17265601		2025	3910	5935	SO:0001819	synonymous_variant	9696	exon12			CCTGATCCACTCC	AB007914	CCDS30616.1	1p36.13	2010-06-04	2009-03-04	2009-03-04	ENSG00000058453	ENSG00000058453			21299	protein-coding gene	gene with protein product	"""rootletin, ciliary rootlet protein"""	615776				12427867, 17971504	Standard	XM_006711056		Approved	rootletin, ROLT	uc001azt.2	Q5TZA2	OTTHUMG00000002200	ENST00000375541.5:c.1572C>T	1.37:g.17265601C>T		12.0	0.0	0		17.0	10.0	0.588235	NM_014675		Silent	SNP	ENST00000375541.5	37	CCDS30616.1																																																																																			C|0.984;T|0.016	0.016	strong		0.751	CROCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006249.2	NM_014675	
ZSWIM5	57643	hgsc.bcm.edu	37	1	45500064	45500064	+	Missense_Mutation	SNP	C	C	T	rs182892990	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:45500064C>T	ENST00000359600.5	-	11	2574	c.2369G>A	c.(2368-2370)cGt>cAt	p.R790H	AL359473.1_ENST00000583502.1_RNA	NM_020883.1	NP_065934.1	Q9P217	ZSWM5_HUMAN	zinc finger, SWIM-type containing 5	790						extracellular space (GO:0005615)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|liver(1)|lung(13)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	28	Acute lymphoblastic leukemia(166;0.155)					GCGAGGATAACGGCTGGGCAC	0.517													C|||	9	0.00179712	0.0	0.0101	5008	,	,		19192	0.0		0.002	False		,,,				2504	0.0				p.R790H		Atlas-SNP	.											.	ZSWIM5	72	.	0			c.G2369A						PASS	.	C	HIS/ARG	0,4164		0,0,2082	123.0	124.0	124.0		2369	4.6	1.0	1		124	6,8430		0,6,4212	yes	missense	ZSWIM5	NM_020883.1	29	0,6,6294	TT,TC,CC		0.0711,0.0,0.0476	possibly-damaging	790/1186	45500064	6,12594	2082	4218	6300	SO:0001583	missense	57643	exon11			GGATAACGGCTGG	AB040944	CCDS41319.1	1p34.1	2010-06-16			ENSG00000162415	ENSG00000162415		"""Zinc fingers, SWIM-type"""	29299	protein-coding gene	gene with protein product						10819331	Standard	NM_020883		Approved	KIAA1511	uc001cnd.2	Q9P217	OTTHUMG00000008950	ENST00000359600.5:c.2369G>A	1.37:g.45500064C>T	ENSP00000352614:p.Arg790His	100.0	0.0	0		82.0	23.0	0.280488	NM_020883	Q5SXQ9	Missense_Mutation	SNP	ENST00000359600.5	37	CCDS41319.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	c	35	5.453739	0.96223	0.0	7.11E-4	ENSG00000162415	ENST00000359600	T	0.49432	0.78	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.60766	0.2294	M	0.77103	2.36	0.80722	D	1	D	0.60160	0.987	P	0.50049	0.629	T	0.69281	-0.5186	10	0.66056	D	0.02	-8.8461	18.2179	0.89893	0.0:1.0:0.0:0.0	.	790	Q9P217	ZSWM5_HUMAN	H	790	ENSP00000352614:R790H	ENSP00000352614:R790H	R	-	2	0	ZSWIM5	45272651	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.561000	0.82288	2.479000	0.83701	0.563000	0.77884	CGT	C|0.999;T|0.001	0.001	strong		0.517	ZSWIM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000024823.2	XM_046581	
LIFR	3977	hgsc.bcm.edu	37	5	38510603	38510603	+	Silent	SNP	G	G	A	rs61748202	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:38510603G>A	ENST00000263409.4	-	7	1116	c.954C>T	c.(952-954)acC>acT	p.T318T	LIFR_ENST00000453190.2_Silent_p.T318T|LIFR_ENST00000503088.1_5'UTR	NM_002310.5	NP_002301.1	P42702	LIFR_HUMAN	leukemia inhibitory factor receptor alpha	318					cell surface receptor signaling pathway (GO:0007166)|ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|leukemia inhibitory factor signaling pathway (GO:0048861)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of cell proliferation (GO:0008284)|response to cytokine (GO:0034097)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|leukemia inhibitory factor receptor activity (GO:0004923)			NS(2)|breast(4)|endometrium(6)|kidney(2)|large_intestine(30)|liver(2)|lung(21)|ovary(3)|skin(5)|stomach(1)|urinary_tract(2)	78	all_lung(31;0.00021)					TGTTATCTTCGGTTGTAAAAA	0.348			T	PLAG1	salivary adenoma								G|||	10	0.00199681	0.0	0.0058	5008	,	,		18085	0.0		0.004	False		,,,				2504	0.002				p.T318T	Melanoma(13;4 730 6426 9861 34751)	Atlas-SNP	.		Dom	yes		5	5p13-p12	3977	leukemia inhibitory factor receptor		E	.	LIFR	348	.	0			c.C954T						PASS	.	G	,	6,4400	12.9+/-30.5	0,6,2197	77.0	75.0	75.0		954,954	1.6	0.0	5	dbSNP_129	75	41,8559	27.4+/-76.7	0,41,4259	no	coding-synonymous,coding-synonymous	LIFR	NM_001127671.1,NM_002310.5	,	0,47,6456	AA,AG,GG		0.4767,0.1362,0.3614	,	318/1098,318/1098	38510603	47,12959	2203	4300	6503	SO:0001819	synonymous_variant	3977	exon7			ATCTTCGGTTGTA	X61615	CCDS3927.1	5p13-p12	2013-02-11	2006-05-17		ENSG00000113594	ENSG00000113594		"""CD molecules"", ""Fibronectin type III domain containing"""	6597	protein-coding gene	gene with protein product		151443	"""leukemia inhibitory factor receptor"""			1915266	Standard	NM_001127671		Approved	CD118	uc003jli.2	P42702	OTTHUMG00000131138	ENST00000263409.4:c.954C>T	5.37:g.38510603G>A		112.0	0.0	0		135.0	52.0	0.385185	NM_002310	Q6LCD9	Silent	SNP	ENST00000263409.4	37	CCDS3927.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	LIFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253823.1	NM_002310	
CHCHD2	51142	hgsc.bcm.edu	37	7	56172086	56172086	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:56172086A>C	ENST00000395422.3	-	2	295	c.133T>G	c.(133-135)Tct>Gct	p.S45A		NM_016139.2	NP_057223.1	Q9Y6H1	CHCH2_HUMAN	coiled-coil-helix-coiled-coil-helix domain containing 2	45						mitochondrion (GO:0005739)				endometrium(1)|large_intestine(1)|lung(3)	5	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			GCAGCAGAAGAGCCAACTGCA	0.637																																					p.S45A		Atlas-SNP	.											.	CHCHD2	10	.	0			c.T133G						PASS	.						13.0	16.0	15.0					7																	56172086		2196	4288	6484	SO:0001583	missense	51142	exon2			CAGAAGAGCCAAC	AF078845	CCDS5526.1	7p11.2	2014-07-14	2004-01-19	2004-01-21	ENSG00000106153	ENSG00000106153		"""Coiled-coil-helix-coiled-coil-helix domain containing"""	21645	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 17"""	C7orf17		23303788	Standard	NM_016139		Approved		uc003tsa.3	Q9Y6H1	OTTHUMG00000129429	ENST00000395422.3:c.133T>G	7.37:g.56172086A>C	ENSP00000378812:p.Ser45Ala	204.0	0.0	0		200.0	94.0	0.47	NM_016139	Q498C3|Q6NZ50	Missense_Mutation	SNP	ENST00000395422.3	37	CCDS5526.1	.	.	.	.	.	.	.	.	.	.	A	10.83	1.459974	0.26248	.	.	ENSG00000106153	ENST00000395422	T	0.40225	1.04	5.09	2.66	0.31614	.	0.447785	0.23465	N	0.047899	T	0.20047	0.0482	N	0.21194	0.64	0.27295	N	0.957738	B	0.02656	0.0	B	0.01281	0.0	T	0.16988	-1.0384	10	0.07813	T	0.8	.	3.1841	0.06594	0.5928:0.2281:0.1791:0.0	.	45	Q9Y6H1	CHCH2_HUMAN	A	45	ENSP00000378812:S45A	ENSP00000378812:S45A	S	-	1	0	CHCHD2	56139580	0.246000	0.23909	0.544000	0.28141	0.931000	0.56810	0.333000	0.19768	0.936000	0.37367	0.533000	0.62120	TCT	.	.	none		0.637	CHCHD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251589.1	NM_016139	
TST	7263	hgsc.bcm.edu	37	22	37414321	37414321	+	Silent	SNP	G	G	A	rs61743068		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:37414321G>A	ENST00000403892.3	-	1	1187	c.453C>T	c.(451-453)gcC>gcT	p.A151A	MPST_ENST00000397129.1_5'Flank|MPST_ENST00000404393.1_5'Flank|MPST_ENST00000401419.3_5'Flank|MPST_ENST00000429360.2_5'Flank|MPST_ENST00000341116.3_5'Flank|MPST_ENST00000404802.3_5'Flank|TST_ENST00000249042.3_Silent_p.A151A	NM_001270483.1	NP_001257412.1	Q16762	THTR_HUMAN	thiosulfate sulfurtransferase (rhodanese)	151	Hinge.				cellular nitrogen compound metabolic process (GO:0034641)|cyanate catabolic process (GO:0009440)|epithelial cell differentiation (GO:0030855)|rRNA import into mitochondrion (GO:0035928)|rRNA transport (GO:0051029)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5S rRNA binding (GO:0008097)|thiosulfate sulfurtransferase activity (GO:0004792)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)|skin(1)|urinary_tract(1)	7						CTTTGAAGACGGCCGGTTCTG	0.592																																					p.A151A		Atlas-SNP	.											.	TST	22	.	0			c.C453T						PASS	.						76.0	67.0	70.0					22																	37414321		2202	4300	6502	SO:0001819	synonymous_variant	7263	exon2			GAAGACGGCCGGT	Z73420	CCDS13938.1	22q13.1	2002-02-05			ENSG00000128311	ENSG00000128311	2.8.1.1		12388	protein-coding gene	gene with protein product		180370				1953758	Standard	NM_003312		Approved	RDS	uc003aqh.4	Q16762	OTTHUMG00000150533	ENST00000403892.3:c.453C>T	22.37:g.37414321G>A		187.0	0.0	0		167.0	37.0	0.221557	NM_003312	B3KRM1|Q6IB06	Silent	SNP	ENST00000403892.3	37	CCDS13938.1																																																																																			G|0.985;T|0.015	.	alt		0.592	TST-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318790.1		
CUL7	9820	hgsc.bcm.edu	37	6	43006687	43006687	+	Nonsense_Mutation	SNP	G	G	A	rs121918228		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43006687G>A	ENST00000265348.3	-	23	4418	c.4333C>T	c.(4333-4335)Cga>Tga	p.R1445*	CUL7_ENST00000535468.1_Nonsense_Mutation_p.R1529*|RN7SL403P_ENST00000481783.2_RNA			Q14999	CUL7_HUMAN	cullin 7	1445					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CACTGCAGTCGCCTCTGTGAG	0.607													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19760	0.0		0.0	False		,,,				2504	0.0				p.R1529X		Atlas-SNP	.											.	CUL7	133	.	0			c.C4585T	GRCh37	CM053196	CUL7	M	rs121918228	PASS	.	G	stop/ARG,stop/ARG	0,4406		0,0,2203	61.0	54.0	56.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4585,4333	3.6	0.0	6	dbSNP_133	56	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained,stop-gained	CUL7	NM_001168370.1,NM_014780.4	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	1529/1783,1445/1699	43006687	1,13005	2203	4300	6503	SO:0001587	stop_gained	9820	exon23			GCAGTCGCCTCTG	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.4333C>T	6.37:g.43006687G>A	ENSP00000265348:p.Arg1445*	88.0	0.0	0		106.0	52.0	0.490566	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Nonsense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	45	11.398506	0.99556	0.0	1.16E-4	ENSG00000044090	ENST00000265348;ENST00000535468	.	.	.	4.52	3.63	0.41609	.	0.343472	0.30989	N	0.008461	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7945	13.7801	0.63077	0.0:0.0:0.8456:0.1544	.	.	.	.	X	1445;1529	.	ENSP00000265348:R1445X	R	-	1	2	CUL7	43114665	0.819000	0.29175	0.030000	0.17652	0.998000	0.95712	4.557000	0.60782	1.087000	0.41251	0.650000	0.86243	CGA	G|1.000;A|0.000	0.000	strong		0.607	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
GRIP1	23426	hgsc.bcm.edu	37	12	66773075	66773075	+	Missense_Mutation	SNP	C	C	T	rs145115262	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:66773075C>T	ENST00000398016.3	-	19	2518	c.2450G>A	c.(2449-2451)cGg>cAg	p.R817Q	GRIP1_ENST00000359742.4_Missense_Mutation_p.R869Q|GRIP1_ENST00000286445.7_Missense_Mutation_p.R869Q	NM_021150.3	NP_066973.2	Q96DT0	LEG12_HUMAN	glutamate receptor interacting protein 1	0					intrinsic apoptotic signaling pathway (GO:0097193)	nucleus (GO:0005634)	lactose binding (GO:0030395)			NS(3)|breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(10)|lung(19)|ovary(2)|prostate(2)|skin(1)	50			GBM - Glioblastoma multiforme(2;0.00069)	GBM - Glioblastoma multiforme(28;0.0933)		GGCTGTGGACCGGTCCCAGTC	0.517													C|||	15	0.00299521	0.0008	0.0058	5008	,	,		17397	0.003		0.007	False		,,,				2504	0.0				p.R817Q		Atlas-SNP	.											.	GRIP1	106	.	0			c.G2450A						PASS	.	C	GLN/ARG,GLN/ARG	9,3877		0,9,1934	169.0	165.0	166.0		2450,2450	2.0	1.0	12	dbSNP_134	166	69,8193		0,69,4062	yes	missense,missense	GRIP1	NM_001178074.1,NM_021150.3	43,43	0,78,5996	TT,TC,CC		0.8351,0.2316,0.6421	benign,benign	817/1062,817/1077	66773075	78,12070	1943	4131	6074	SO:0001583	missense	23426	exon19			GTGGACCGGTCCC	AJ133439	CCDS41807.1	12q13.13	2008-05-02			ENSG00000155974	ENSG00000155974			18708	protein-coding gene	gene with protein product		604597				10197531	Standard	NM_021150		Approved		uc001stk.3	Q9Y3R0	OTTHUMG00000169019	ENST00000398016.3:c.2450G>A	12.37:g.66773075C>T	ENSP00000381098:p.Arg817Gln	215.0	0.0	0		182.0	87.0	0.478022	NM_001178074	B2R9N2|G5E970|Q96DS9|Q96PR9|Q9H258|Q9H259|Q9NZ02	Missense_Mutation	SNP	ENST00000398016.3	37	CCDS41807.1	6|6	0.0027472527472527475|0.0027472527472527475	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	5|5	0.006596306068601583|0.006596306068601583	C|C	13.77|13.77	2.337222|2.337222	0.41398|0.41398	0.002316|0.002316	0.008351|0.008351	ENSG00000155974|ENSG00000155974	ENST00000538164|ENST00000398016;ENST00000359742;ENST00000286445;ENST00000538211;ENST00000540433;ENST00000536215	.|T;T;T;T;T;T	.|0.81415	.|-1.49;-1.49;-1.49;-1.49;-1.49;-1.49	4.8|4.8	1.95|1.95	0.26073|0.26073	.|.	.|0.233910	.|0.42294	.|N	.|0.000731	T|T	0.69178|0.69178	0.3082|0.3082	M|M	0.62723|0.62723	1.935|1.935	0.44129|0.44129	D|D	0.996911|0.996911	.|P;P;P;D	.|0.54397	.|0.911;0.88;0.956;0.966	.|B;B;B;B	.|0.43018	.|0.173;0.108;0.297;0.405	T|T	0.69124|0.69124	-0.5228|-0.5228	5|9	.|.	.|.	.|.	-5.1095|-5.1095	9.3305|9.3305	0.38018|0.38018	0.0:0.7035:0.0:0.2965|0.0:0.7035:0.0:0.2965	.|.	.|817;869;817;869	.|F5H4N6;Q9Y3R0;Q9Y3R0-3;Q9Y3R0-2	.|.;GRIP1_HUMAN;.;.	S|Q	684|817;869;869;817;761;709	.|ENSP00000381098:R817Q;ENSP00000352780:R869Q;ENSP00000286445:R869Q;ENSP00000446047:R817Q;ENSP00000446024:R761Q;ENSP00000446011:R709Q	.|.	G|R	-|-	1|2	0|0	GRIP1|GRIP1	65059342|65059342	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.988000|0.988000	0.76386|0.76386	2.867000|2.867000	0.48428|0.48428	0.317000|0.317000	0.23160|0.23160	-0.258000|-0.258000	0.10820|0.10820	GGT|CGG	C|0.997;T|0.003	0.003	strong		0.517	GRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401975.2		
BUB1	699	hgsc.bcm.edu	37	2	111413444	111413444	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:111413444C>G	ENST00000302759.6	-	16	1866	c.1748G>C	c.(1747-1749)gGt>gCt	p.G583A	BUB1_ENST00000535254.1_Missense_Mutation_p.G563A|BUB1_ENST00000409311.1_Missense_Mutation_p.G583A	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	583					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		GCAGCGAATACCCCATACAGT	0.468																																					p.G583A		Atlas-SNP	.											.	BUB1	91	.	0			c.G1748C						PASS	.						263.0	252.0	256.0					2																	111413444		2203	4300	6503	SO:0001583	missense	699	exon16			CGAATACCCCATA	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"""budding uninhibited by benzimidazoles 1 (yeast homolog)"", ""budding uninhibited by benzimidazoles 1 homolog (yeast)"""	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.1748G>C	2.37:g.111413444C>G	ENSP00000302530:p.Gly583Ala	219.0	1.0	0.00456621		247.0	119.0	0.481781	NM_004336	E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573710	0.65765	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	T;T;T	0.52057	1.41;0.68;1.71	5.73	5.73	0.89815	.	0.211524	0.48286	D	0.000188	T	0.58293	0.2112	L	0.49640	1.575	0.36843	D	0.887494	D;D;D	0.76494	0.999;0.997;0.993	D;P;P	0.71870	0.975;0.788;0.725	T	0.55848	-0.8076	10	0.14252	T	0.57	-20.8313	13.0477	0.58937	0.0:0.8385:0.1615:0.0	.	563;583;583	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	A	563;583;583;583	ENSP00000441013:G563A;ENSP00000386701:G583A;ENSP00000302530:G583A	ENSP00000302530:G583A	G	-	2	0	BUB1	111129917	0.928000	0.31464	0.986000	0.45419	0.975000	0.68041	1.580000	0.36547	2.687000	0.91594	0.655000	0.94253	GGT	.	.	none		0.468	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336	
OBSL1	23363	hgsc.bcm.edu	37	2	220422126	220422126	+	Silent	SNP	G	G	A	rs375716830	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220422126G>A	ENST00000404537.1	-	12	4061	c.4005C>T	c.(4003-4005)gaC>gaT	p.D1335D	OBSL1_ENST00000265317.5_Intron|OBSL1_ENST00000373876.1_Intron|OBSL1_ENST00000265318.4_Silent_p.D1243D|OBSL1_ENST00000603926.1_Silent_p.D1335D|RP11-256I23.2_ENST00000597192.1_RNA	NM_015311.2	NP_056126.1	O75147	OBSL1_HUMAN	obscurin-like 1	1335	Ig-like 11.				cardiac myofibril assembly (GO:0055003)|cytoskeleton organization (GO:0007010)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|positive regulation of dendrite morphogenesis (GO:0050775)|protein localization to Golgi apparatus (GO:0034067)|regulation of mitosis (GO:0007088)	3M complex (GO:1990393)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|M band (GO:0031430)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)						Renal(207;0.0376)		Epithelial(149;2.02e-07)|all cancers(144;1.68e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00834)		ACTCCCCAGCGTCCCCGCTCC	0.692													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14604	0.0		0.005	False		,,,				2504	0.0				p.D1335D		Atlas-SNP	.											.	OBSL1	120	.	0			c.C4005T						PASS	.	G	,	4,4268		0,4,2132	16.0	20.0	19.0		4005,4005	-1.8	1.0	2	dbSNP_134	19	33,8311		0,33,4139	no	coding-synonymous,coding-synonymous	OBSL1	NM_001173431.1,NM_015311.2	,	0,37,6271	AA,AG,GG		0.3955,0.0936,0.2933	,	1335/1544,1335/1897	220422126	37,12579	2136	4172	6308	SO:0001819	synonymous_variant	23363	exon12			CCCAGCGTCCCCG	BC007201	CCDS46520.1, CCDS54433.1, CCDS63134.1	2q35	2013-01-29			ENSG00000124006	ENSG00000124006		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	29092	protein-coding gene	gene with protein product		610991				9734811	Standard	NM_015311		Approved	KIAA0657	uc010fwk.3	O75147	OTTHUMG00000059157	ENST00000404537.1:c.4005C>T	2.37:g.220422126G>A		22.0	0.0	0		25.0	19.0	0.76	NM_001173431	A4KVA4|A4KVA5|Q96IW3|S4R3M6	Silent	SNP	ENST00000404537.1	37	CCDS46520.1																																																																																			.	.	weak		0.692	OBSL1-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322012.1		
NUMA1	4926	hgsc.bcm.edu	37	11	71720030	71720030	+	Missense_Mutation	SNP	G	G	A	rs74985106	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71720030G>A	ENST00000393695.3	-	19	5372	c.5041C>T	c.(5041-5043)Cgc>Tgc	p.R1681C	NUMA1_ENST00000351960.6_Missense_Mutation_p.R545C|NUMA1_ENST00000358965.6_Missense_Mutation_p.R1667C	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TCCAGGCTGCGCACCTGGGCA	0.612			T	RARA	APL								G|||	67	0.0133786	0.0008	0.0231	5008	,	,		13503	0.0188		0.0179	False		,,,				2504	0.0133				p.R1681C		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.C5041T						PASS	.	G	CYS/ARG	26,4374	31.7+/-61.6	0,26,2174	63.0	62.0	63.0		5041	5.6	1.0	11	dbSNP_131	63	203,8383	86.3+/-148.7	2,199,4092	yes	missense	NUMA1	NM_006185.2	180	2,225,6266	AA,AG,GG		2.3643,0.5909,1.7634	probably-damaging	1681/2116	71720030	229,12757	2200	4293	6493	SO:0001583	missense	4926	exon19			GGCTGCGCACCTG	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.5041C>T	11.37:g.71720030G>A	ENSP00000377298:p.Arg1681Cys	166.0	0.0	0		140.0	67.0	0.478571	NM_006185		Missense_Mutation	SNP	ENST00000393695.3	37	CCDS31633.1	36	0.016483516483516484	0	0.0	11	0.03038674033149171	14	0.024475524475524476	11	0.014511873350923483	G	21.4	4.145619	0.77888	0.005909	0.023643	ENSG00000137497	ENST00000351960;ENST00000358965;ENST00000393695;ENST00000359652;ENST00000536544	T;T;T	0.50001	2.07;0.76;2.52	5.56	5.56	0.83823	.	0.127189	0.36409	N	0.002604	T	0.31451	0.0797	L	0.32530	0.975	0.46586	D	0.999115	D;D;D;D;D	0.89917	0.998;0.998;0.996;0.998;1.0	P;P;P;P;D	0.65010	0.629;0.819;0.819;0.629;0.931	T	0.48103	-0.9064	10	0.72032	D	0.01	.	14.0441	0.64695	0.0:0.0:0.8489:0.1511	.	1687;1151;1667;1681;545	Q4LE64;Q59HB8;Q14980-2;Q14980;Q9BTE9	.;.;.;NUMA1_HUMAN;.	C	545;1667;1681;1230;636	ENSP00000260051:R545C;ENSP00000351851:R1667C;ENSP00000377298:R1681C	ENSP00000260051:R545C	R	-	1	0	NUMA1	71397678	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.624000	0.46444	2.618000	0.88619	0.561000	0.74099	CGC	G|0.982;A|0.018	0.018	strong		0.612	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
CD1D	912	hgsc.bcm.edu	37	1	158151892	158151892	+	Silent	SNP	T	T	C	rs140563679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158151892T>C	ENST00000368171.3	+	4	898	c.399T>C	c.(397-399)caT>caC	p.H133H		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	133					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					ACTTCTTCCATGTAGCATTTC	0.498													T|||	3	0.000599042	0.0	0.0	5008	,	,		19718	0.0		0.003	False		,,,				2504	0.0				p.H133H		Atlas-SNP	.											.	CD1D	60	.	0			c.T399C						PASS	.	T		0,4406		0,0,2203	130.0	143.0	138.0		399	-9.5	0.0	1	dbSNP_134	138	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	CD1D	NM_001766.3		0,17,6486	CC,CT,TT		0.1977,0.0,0.1307		133/336	158151892	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	912	exon4			CTTCCATGTAGCA	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1637	protein-coding gene	gene with protein product		188410	"""CD1D antigen, d polypeptide"", ""CD1d antigen"""			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.399T>C	1.37:g.158151892T>C		206.0	0.0	0		291.0	160.0	0.549828	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Silent	SNP	ENST00000368171.3	37	CCDS1173.1																																																																																			T|0.999;C|0.001	0.001	strong		0.498	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766	
ZNF780A	284323	hgsc.bcm.edu	37	19	40580545	40580545	+	Nonsense_Mutation	SNP	G	G	A	rs149702621	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40580545G>A	ENST00000595687.2	-	6	2013	c.1804C>T	c.(1804-1806)Cga>Tga	p.R602*	ZNF780A_ENST00000340963.5_Nonsense_Mutation_p.R602*|ZNF780A_ENST00000414720.2_Intron|ZNF780A_ENST00000455521.1_Nonsense_Mutation_p.R603*|AC005614.5_ENST00000595508.1_RNA|ZNF780A_ENST00000450241.2_Nonsense_Mutation_p.R568*|ZNF780A_ENST00000594395.1_Nonsense_Mutation_p.R603*	NM_001010880.2	NP_001010880.2	O75290	Z780A_HUMAN	zinc finger protein 780A	602					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(16)|upper_aerodigestive_tract(3)|urinary_tract(1)	31	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					TTCTGATGTCGAATAAGTTGC	0.398													g|||	2	0.000399361	0.0	0.0	5008	,	,		23667	0.0		0.002	False		,,,				2504	0.0				p.R603X		Atlas-SNP	.											ZNF780A_ENST00000455521,NS,carcinoma,0,2	ZNF780A	156	2	0			c.C1807T						PASS	.	G	stop/ARG,stop/ARG,stop/ARG,	1,4405	2.1+/-5.4	0,1,2202	140.0	138.0	139.0		1804,1807,1804,	-0.8	0.0	19	dbSNP_134	139	11,8589	7.7+/-29.5	0,11,4289	no	stop-gained,stop-gained,stop-gained,intron	ZNF780A	NM_001010880.2,NM_001142577.1,NM_001142578.1,NM_001142579.1	,,,	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,,,	602/642,603/643,602/642,	40580545	12,12994	2203	4300	6503	SO:0001587	stop_gained	284323	exon6			GATGTCGAATAAG	AK091274	CCDS33026.2, CCDS46078.1, CCDS46079.1	19q13.2	2014-02-12	2006-08-15		ENSG00000197782	ENSG00000197782		"""Zinc fingers, C2H2-type"", ""-"""	27603	protein-coding gene	gene with protein product							Standard	NM_001142577		Approved	ZNF780	uc010xvh.2	O75290	OTTHUMG00000155119	ENST00000595687.2:c.1804C>T	19.37:g.40580545G>A	ENSP00000472189:p.Arg602*	192.0	0.0	0		158.0	72.0	0.455696	NM_001142577	E9PB48|Q6ZN87	Nonsense_Mutation	SNP	ENST00000595687.2	37	CCDS33026.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	g	36	5.627543	0.96671	2.27E-4	0.001279	ENSG00000197782	ENST00000450241;ENST00000455521;ENST00000340963	.	.	.	1.93	-0.836	0.10770	.	.	.	.	.	.	.	.	.	.	.	0.51482	D	0.999922	.	.	.	.	.	.	.	.	.	.	0.14252	T	0.57	.	4.3525	0.11162	0.1631:0.4575:0.3794:0.0	.	.	.	.	X	602;603;602	.	ENSP00000341507:R602X	R	-	1	2	ZNF780A	45272385	0.000000	0.05858	0.000000	0.03702	0.504000	0.33889	-5.163000	0.00145	-0.286000	0.09076	0.313000	0.20887	CGA	G|0.999;A|0.001	0.001	strong		0.398	ZNF780A-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000470066.1	NM_001010880	
IL17RC	84818	hgsc.bcm.edu	37	3	9970062	9970062	+	Silent	SNP	C	C	T	rs151110374	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:9970062C>T	ENST00000295981.3	+	11	1382	c.1164C>T	c.(1162-1164)gaC>gaT	p.D388D	IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000455057.1_Silent_p.D302D|IL17RC_ENST00000413608.1_Silent_p.D317D|IL17RC_ENST00000403601.3_Silent_p.D317D|IL17RC_ENST00000416074.2_Silent_p.D173D|IL17RC_ENST00000383812.4_Silent_p.D302D	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	388					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GGCTGCTGGACGCACCGTGCT	0.682													C|||	30	0.00599042	0.0	0.0	5008	,	,		15079	0.0		0.0	False		,,,				2504	0.0307				p.D388D		Atlas-SNP	.											.	IL17RC	55	.	0			c.C1164T						PASS	.	C	,,,,,	3,4403	6.2+/-15.9	0,3,2200	30.0	36.0	34.0		951,951,906,906,951,1164	-7.9	0.0	3	dbSNP_134	34	6,8592	5.0+/-18.6	0,6,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	,,,,,	0,9,6493	TT,TC,CC		0.0698,0.0681,0.0692	,,,,,	317/708,317/691,302/689,302/706,317/721,388/792	9970062	9,12995	2203	4299	6502	SO:0001819	synonymous_variant	84818	exon11			GCTGGACGCACCG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.1164C>T	3.37:g.9970062C>T		42.0	0.0	0		30.0	10.0	0.333333	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			C|0.999;T|0.001	0.001	strong		0.682	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
SLC35F4	341880	hgsc.bcm.edu	37	14	58060707	58060707	+	Missense_Mutation	SNP	T	T	C	rs145246618	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58060707T>C	ENST00000339762.6	-	2	346	c.347A>G	c.(346-348)cAa>cGa	p.Q116R	SLC35F4_ENST00000557430.1_5'Flank|SLC35F4_ENST00000554729.1_5'UTR|SLC35F4_ENST00000556826.1_Missense_Mutation_p.Q80R			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	116					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						TGAGGATCCTTGGTTTTGAAG	0.478													C|||	9	0.00179712	0.0068	0.0	5008	,	,		18702	0.0		0.0	False		,,,				2504	0.0				p.Q80R		Atlas-SNP	.											SLC35F4_ENST00000339762,right_upper_lobe,carcinoma,0,2	SLC35F4	105	2	0			c.A239G						PASS	.	C	ARG/GLN	26,3862		0,26,1918	92.0	92.0	92.0		239	5.8	1.0	14	dbSNP_134	92	4,8274		0,4,4135	yes	missense	SLC35F4	NM_001206920.1	43	0,30,6053	CC,CT,TT		0.0483,0.6687,0.2466	benign	80/485	58060707	30,12136	1944	4139	6083	SO:0001583	missense	341880	exon2			GATCCTTGGTTTT			14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"""Solute carriers"""	19845	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 36"""	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.347A>G	14.37:g.58060707T>C	ENSP00000342518:p.Gln116Arg	231.0	0.0	0		186.0	94.0	0.505376	NM_001206920	A6NDQ3	Missense_Mutation	SNP	ENST00000339762.6	37		7	0.003205128205128205	7	0.014227642276422764	0	0.0	0	0.0	0	0.0	C	7.347	0.622089	0.14193	0.006687	4.83E-4	ENSG00000151812	ENST00000556826;ENST00000339762	T;T	0.38722	1.15;1.12	5.83	5.83	0.93111	.	0.207799	0.41500	N	0.000877	T	0.10337	0.0253	N	0.01048	-1.04	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.16453	-1.0402	10	0.02654	T	1	-3.5905	13.5376	0.61655	0.0:0.928:0.0:0.072	.	116	A4IF30	S35F4_HUMAN	R	80;116	ENSP00000452086:Q80R;ENSP00000342518:Q116R	ENSP00000342518:Q116R	Q	-	2	0	SLC35F4	57130460	1.000000	0.71417	1.000000	0.80357	0.859000	0.49053	3.174000	0.50847	1.489000	0.48450	-0.197000	0.12766	CAA	T|0.997;C|0.003	0.003	strong		0.478	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260	
KLC3	147700	hgsc.bcm.edu	37	19	45848869	45848869	+	Missense_Mutation	SNP	G	G	A	rs546355544		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:45848869G>A	ENST00000391946.2	+	2	172	c.70G>A	c.(70-72)Gtg>Atg	p.V24M	KLC3_ENST00000585434.1_Missense_Mutation_p.V24M|KLC3_ENST00000470402.1_Missense_Mutation_p.V38M	NM_177417.2	NP_803136.2	Q6P597	KLC3_HUMAN	kinesin light chain 3	24					axon cargo transport (GO:0008088)	ciliary rootlet (GO:0035253)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|motile cilium (GO:0031514)|neuron projection (GO:0043005)	microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(1)|lung(1)|ovary(1)	8		Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0226)		TGAGGAGCTGGTGCGGCAGAC	0.706													G|||	1	0.000199681	0.0	0.0014	5008	,	,		13844	0.0		0.0	False		,,,				2504	0.0				p.V24M		Atlas-SNP	.											.	KLC3	37	.	0			c.G70A						PASS	.						5.0	7.0	7.0					19																	45848869		1932	4073	6005	SO:0001583	missense	147700	exon2			GAGCTGGTGCGGC	AK092481	CCDS12660.2	19q13	2013-01-10			ENSG00000104892	ENSG00000104892		"""Tetratricopeptide (TTC) repeat domain containing"""	20717	protein-coding gene	gene with protein product		601334					Standard	XM_005258536		Approved	KLC2L, KNS2B, KLCt	uc002pbf.1	Q6P597	OTTHUMG00000143722	ENST00000391946.2:c.70G>A	19.37:g.45848869G>A	ENSP00000375810:p.Val24Met	141.0	0.0	0		133.0	59.0	0.443609	NM_177417	A0AVM3|A2RUT6|Q6GMU2|Q8NAL1|Q8WWJ9	Missense_Mutation	SNP	ENST00000391946.2	37	CCDS12660.2	.	.	.	.	.	.	.	.	.	.	G	12.08	1.830370	0.32329	.	.	ENSG00000104892	ENST00000391946;ENST00000470402	D;D	0.85171	-1.93;-1.95	3.4	3.4	0.38934	.	0.110159	0.38272	N	0.001756	T	0.77356	0.4118	N	0.25485	0.75	0.36902	D	0.890437	P;P;P	0.49635	0.926;0.926;0.879	P;P;B	0.46825	0.528;0.528;0.328	T	0.80141	-0.1506	10	0.56958	D	0.05	.	6.7358	0.23409	0.1316:0.0:0.8684:0.0	.	24;38;24	Q6P597-2;Q6P597-3;Q6P597	.;.;KLC3_HUMAN	M	24;38	ENSP00000375810:V24M;ENSP00000436019:V38M	ENSP00000375810:V24M	V	+	1	0	KLC3	50540709	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	2.415000	0.44635	1.918000	0.55548	0.313000	0.20887	GTG	.	.	none		0.706	KLC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289776.1	NM_145275	
OSTN	344901	hgsc.bcm.edu	37	3	190936577	190936577	+	Silent	SNP	A	A	G	rs34687554	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:190936577A>G	ENST00000339051.1	+	2	144	c.144A>G	c.(142-144)acA>acG	p.T48T	OSTN-AS1_ENST00000430375.1_RNA|OSTN_ENST00000445281.1_Silent_p.T48T	NM_198184.1	NP_937827.1	P61366	OSTN_HUMAN	osteocrin	48					cell differentiation (GO:0030154)|cell surface receptor signaling pathway (GO:0007166)|endochondral bone growth (GO:0003416)|negative regulation of glucose import (GO:0046325)|negative regulation of osteoblast differentiation (GO:0045668)|ossification (GO:0001503)|positive regulation of cGMP biosynthetic process (GO:0030828)	extracellular space (GO:0005615)				kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|skin(2)	13	all_cancers(143;6.79e-09)|Ovarian(172;0.103)		LUSC - Lung squamous cell carcinoma(58;2.42e-06)|Lung(62;2.86e-06)	GBM - Glioblastoma multiforme(46;0.000254)		CAACACCCACAGTCAGGGAAG	0.418													A|||	32	0.00638978	0.0	0.0072	5008	,	,		18556	0.0		0.0149	False		,,,				2504	0.0123				p.T48T		Atlas-SNP	.											.	OSTN	25	.	0			c.A144G						PASS	.	A		10,4396	16.8+/-37.8	0,10,2193	140.0	127.0	132.0		144	5.5	0.9	3	dbSNP_126	132	96,8504	54.0+/-114.7	2,92,4206	no	coding-synonymous	OSTN	NM_198184.1		2,102,6399	GG,GA,AA		1.1163,0.227,0.815		48/134	190936577	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	344901	exon2			ACCCACAGTCAGG	AY398681	CCDS3299.1	3q29	2004-01-22			ENSG00000188729	ENSG00000188729			29961	protein-coding gene	gene with protein product		610280				14523025	Standard	NM_198184		Approved		uc011bsn.2	P61366	OTTHUMG00000156190	ENST00000339051.1:c.144A>G	3.37:g.190936577A>G		78.0	0.0	0		68.0	29.0	0.426471	NM_198184	A1A4U3	Silent	SNP	ENST00000339051.1	37	CCDS3299.1																																																																																			A|0.992;G|0.008	0.008	strong		0.418	OSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343350.1	NM_198184	
KIF26B	55083	hgsc.bcm.edu	37	1	245772692	245772692	+	Silent	SNP	A	A	C	rs61755865	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:245772692A>C	ENST00000407071.2	+	8	2216	c.1776A>C	c.(1774-1776)tcA>tcC	p.S592S	KIF26B_ENST00000366518.4_Silent_p.S211S	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	592	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			CCCGTTTCTCAGTCCGGGTTT	0.612													A|||	142	0.0283546	0.0318	0.0648	5008	,	,		16776	0.0278		0.0149	False		,,,				2504	0.0123				p.S592S		Atlas-SNP	.											.	KIF26B	343	.	0			c.A1776C						PASS	.	A		107,3701		1,105,1798	26.0	29.0	28.0		1776	-10.4	0.9	1	dbSNP_129	28	150,8090		2,146,3972	no	coding-synonymous	KIF26B	NM_018012.3		3,251,5770	CC,CA,AA		1.8204,2.8099,2.1331		592/2109	245772692	257,11791	1904	4120	6024	SO:0001819	synonymous_variant	55083	exon8			TTTCTCAGTCCGG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1776A>C	1.37:g.245772692A>C		223.0	0.0	0		228.0	102.0	0.447368	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Silent	SNP	ENST00000407071.2	37	CCDS44342.1																																																																																			A|0.970;C|0.030	0.030	strong		0.612	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
PTPRJ	5795	hgsc.bcm.edu	37	11	48145397	48145397	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:48145397C>A	ENST00000418331.2	+	5	1201	c.849C>A	c.(847-849)gaC>gaA	p.D283E	PTPRJ_ENST00000440289.2_Missense_Mutation_p.D283E	NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	283	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.|Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						CAAAGGGAGACCCCTTGGGCA	0.433																																					p.D283E		Atlas-SNP	.											.	PTPRJ	225	.	0			c.C849A						PASS	.						67.0	64.0	65.0					11																	48145397		2201	4298	6499	SO:0001583	missense	5795	exon5			GGGAGACCCCTTG	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.849C>A	11.37:g.48145397C>A	ENSP00000400010:p.Asp283Glu	103.0	0.0	0		131.0	53.0	0.40458	NM_001098503	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	C	9.966	1.224237	0.22457	.	.	ENSG00000149177	ENST00000278456;ENST00000418331;ENST00000440289	T;T	0.35236	2.65;1.32	4.27	-1.19	0.09585	Fibronectin, type III (2);	.	.	.	.	T	0.14098	0.0341	N	0.17082	0.46	0.09310	N	1	B;P	0.36874	0.004;0.572	B;B	0.33454	0.003;0.164	T	0.16541	-1.0399	9	0.10902	T	0.67	.	1.6576	0.02785	0.1508:0.3485:0.3127:0.188	.	283;283	Q12913;Q6P4H4	PTPRJ_HUMAN;.	E	283	ENSP00000400010:D283E;ENSP00000409733:D283E	ENSP00000278456:D283E	D	+	3	2	PTPRJ	48101973	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.779000	0.04659	-0.334000	0.08463	0.557000	0.71058	GAC	.	.	none		0.433	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
PSORS1C1	170679	hgsc.bcm.edu	37	6	31085226	31085226	+	Intron	SNP	G	G	A	rs7742033	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31085226G>A	ENST00000259881.9	+	1	61				PSORS1C1_ENST00000467107.1_3'UTR|CDSN_ENST00000376288.2_Missense_Mutation_p.L56F	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1											kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TTCCCAGTGAGGCAGGGGTCG	0.582													G|||	115	0.0229633	0.0598	0.013	5008	,	,		18022	0.003		0.0099	False		,,,				2504	0.0143				p.L56F		Atlas-SNP	.											.	CDSN	48	.	0			c.C166T						PASS	.	G	PHE/LEU,	134,3408		2,130,1639	13.0	10.0	11.0		166,	2.0	0.7	6	dbSNP_116	11	54,6800		0,54,3373	yes	missense,intron	CDSN,PSORS1C1	NM_001264.4,NM_014068.2	22,	2,184,5012	AA,AG,GG		0.7879,3.7832,1.8084	probably-damaging,	56/530,	31085226	188,10208	1771	3427	5198	SO:0001627	intron_variant	1041	exon2			CAGTGAGGCAGGG	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.-229+2558G>A	6.37:g.31085226G>A		155.0	0.0	0		176.0	107.0	0.607955	NM_001264	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	31	0.014194139194139194	23	0.046747967479674794	3	0.008287292817679558	2	0.0034965034965034965	3	0.00395778364116095	G	9.818	1.185048	0.21870	0.037832	0.007879	ENSG00000204539	ENST00000376288	T	0.07444	3.19	4.93	1.98	0.26296	.	0.486240	0.16016	N	0.233557	T	0.02649	0.0080	L	0.55990	1.75	0.09310	N	1	B	0.21225	0.053	B	0.21917	0.037	T	0.36407	-0.9749	10	0.44086	T	0.13	-14.2507	3.4184	0.07384	0.2129:0.0:0.5839:0.2031	rs7742033;rs52820068;rs7742033	56	Q15517	CDSN_HUMAN	F	56	ENSP00000365465:L56F	ENSP00000365465:L56F	L	-	1	0	CDSN	31193205	0.039000	0.19947	0.665000	0.29768	0.069000	0.16628	0.060000	0.14342	1.222000	0.43521	0.549000	0.68633	CTC	G|0.979;A|0.021	0.021	strong		0.582	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
DGKI	9162	hgsc.bcm.edu	37	7	137150761	137150761	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:137150761C>T	ENST00000288490.5	-	27	2529	c.2529G>A	c.(2527-2529)atG>atA	p.M843I	DGKI_ENST00000424189.2_Missense_Mutation_p.M856I|DGKI_ENST00000453654.2_Missense_Mutation_p.M553I|DGKI_ENST00000446122.1_Missense_Mutation_p.M825I	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	843					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						GGGAAATCTCCATCACAAAGT	0.448																																					p.M843I		Atlas-SNP	.											.	DGKI	335	.	0			c.G2529A						PASS	.						70.0	74.0	72.0					7																	137150761		2203	4300	6503	SO:0001583	missense	9162	exon27			AATCTCCATCACA	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.2529G>A	7.37:g.137150761C>T	ENSP00000288490:p.Met843Ile	104.0	0.0	0		98.0	4.0	0.0408163	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	C	13.45	2.240246	0.39598	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.32023	2.02;1.47;1.67	5.82	5.82	0.92795	.	0.140824	0.64402	D	0.000004	T	0.17959	0.0431	N	0.08118	0	0.38820	D	0.955614	B;B	0.18968	0.004;0.032	B;B	0.17722	0.012;0.019	T	0.11012	-1.0605	10	0.27785	T	0.31	.	14.8811	0.70534	0.1434:0.8566:0.0:0.0	.	553;843	E9PFX6;O75912	.;DGKI_HUMAN	I	553;801;846;843;825	ENSP00000392161:M553I;ENSP00000288490:M843I;ENSP00000399131:M825I	ENSP00000288490:M843I	M	-	3	0	DGKI	136801301	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	0.836000	0.27545	2.767000	0.95098	0.655000	0.94253	ATG	.	.	none		0.448	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
MT-ND6	4541	hgsc.bcm.edu	37	M	14587	14587	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrM:14587A>G	ENST00000361681.2	-	1	86	c.87T>C	c.(85-87)ggT>ggC	p.G29G	MT-TS2_ENST00000387449.1_RNA|MT-TP_ENST00000387461.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	29					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain (GO:0070469)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(1)|endometrium(10)|kidney(17)|urinary_tract(1)	29						ATCAGTACTAAACCCCCATAA	0.388																																					p.G29G		Atlas-SNP	.											.	.	.	.	0			c.T87C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TACTAAACCCCCA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198695	ENSG00000198695	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7462	protein-coding gene	gene with protein product	"""complex I ND6 subunit"", ""NADH-ubiquinone oxidoreductase chain 6"""	516006	"""NADH dehydrogenase 6"""	MTND6			Standard			Approved	NAD6, ND6		P03923		ENST00000361681.2:c.87T>C	M.37:g.14587A>G		61.0	0.0	0		67.0	65.0	0.970149	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.388	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
GCLC	2729	hgsc.bcm.edu	37	6	53387230	53387230	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:53387230C>T	ENST00000229416.6	-	2	729	c.246G>A	c.(244-246)ggG>ggA	p.G82G	GCLC_ENST00000514004.1_Silent_p.G82G	NM_001197115.1|NM_001498.3	NP_001184044.1|NP_001489.1	P48506	GSH1_HUMAN	glutamate-cysteine ligase, catalytic subunit	82					apoptotic mitochondrial changes (GO:0008637)|cell redox homeostasis (GO:0045454)|cellular nitrogen compound metabolic process (GO:0034641)|cysteine metabolic process (GO:0006534)|glutamate metabolic process (GO:0006536)|glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|L-ascorbic acid metabolic process (GO:0019852)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|regulation of blood vessel size (GO:0050880)|regulation of mitochondrial depolarization (GO:0051900)|response to arsenic-containing substance (GO:0046685)|response to heat (GO:0009408)|response to hormone (GO:0009725)|response to nitrosative stress (GO:0051409)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|sulfur amino acid metabolic process (GO:0000096)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|glutamate-cysteine ligase complex (GO:0017109)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|coenzyme binding (GO:0050662)|glutamate binding (GO:0016595)|glutamate-cysteine ligase activity (GO:0004357)|magnesium ion binding (GO:0000287)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(4)|liver(1)|lung(11)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	22	Lung NSC(77;0.0137)				L-Cysteine(DB00151)|Vitamin E(DB00163)	TTGTCCTTTCCCCCTTCTCTT	0.378																																					p.G82G		Atlas-SNP	.											.	GCLC	58	.	0			c.G246A						PASS	.						115.0	112.0	113.0					6																	53387230		2203	4300	6503	SO:0001819	synonymous_variant	2729	exon2			CCTTTCCCCCTTC	M90656	CCDS4952.1, CCDS75471.1	6p12	2008-02-05				ENSG00000001084	6.3.2.2		4311	protein-coding gene	gene with protein product		606857		GLCLC, GLCL		1350904	Standard	NM_001498		Approved	GCS	uc003pbw.2	P48506		ENST00000229416.6:c.246G>A	6.37:g.53387230C>T		74.0	0.0	0		91.0	12.0	0.131868	NM_001197115	Q14399	Silent	SNP	ENST00000229416.6	37	CCDS4952.1	.	.	.	.	.	.	.	.	.	.	C	9.717	1.158655	0.21454	.	.	ENSG00000001084	ENST00000513939	T	0.72725	-0.68	5.67	1.4	0.22301	.	0.000000	0.85682	D	0.000000	T	0.19765	0.0475	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34925	-0.9809	7	0.02654	T	1	.	4.0727	0.09889	0.237:0.4463:0.0:0.3167	.	.	.	.	E	70	ENSP00000424211:G70E	ENSP00000424211:G70E	G	-	2	0	GCLC	53495189	0.003000	0.15002	1.000000	0.80357	0.995000	0.86356	-1.302000	0.02746	0.193000	0.20303	0.585000	0.79938	GGG	.	.	none		0.378	GCLC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359710.2		
KALRN	8997	hgsc.bcm.edu	37	3	123953756	123953756	+	Silent	SNP	C	C	A	rs144465315	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123953756C>A	ENST00000240874.3	+	3	380	c.223C>A	c.(223-225)Cgg>Agg	p.R75R	KALRN_ENST00000360013.3_Silent_p.R75R|KALRN_ENST00000460856.1_Silent_p.R75R	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	75	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.				apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GGAAGACCTGCGGAAACTCGT	0.582													C|||	4	0.000798722	0.0	0.0	5008	,	,		20662	0.0		0.002	False		,,,				2504	0.002				p.R75R		Atlas-SNP	.											.	KALRN	556	.	0			c.C223A						PASS	.		,	1,4405	2.1+/-5.4	0,1,2202	49.0	41.0	44.0		223,223	2.5	1.0	3	dbSNP_134	44	11,8587	7.1+/-27.0	0,11,4288	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	0,12,6490	AA,AC,CC		0.1279,0.0227,0.0923	,	75/2987,75/1664	123953756	12,12992	2203	4299	6502	SO:0001819	synonymous_variant	8997	exon3			GACCTGCGGAAAC	U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.223C>A	3.37:g.123953756C>A		75.0	0.0	0		81.0	30.0	0.37037	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	c	10.77	1.444443	0.25987	2.27E-4	0.001279	ENSG00000160145	ENST00000448253;ENST00000354186	.	.	.	5.49	2.54	0.30619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.0069	0.64470	0.52:0.48:0.0:0.0	.	.	.	.	X	102;52	.	.	C	+	3	2	KALRN	125436446	1.000000	0.71417	0.999000	0.59377	0.941000	0.58515	1.511000	0.35801	0.672000	0.31204	0.651000	0.88453	TGC	C|0.999;A|0.001	0.001	strong		0.582	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
PUM2	23369	hgsc.bcm.edu	37	2	20494189	20494189	+	Missense_Mutation	SNP	T	T	C	rs34032508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:20494189T>C	ENST00000361078.2	-	8	1122	c.1100A>G	c.(1099-1101)aAt>aGt	p.N367S	PUM2_ENST00000403432.1_Missense_Mutation_p.N367S|PUM2_ENST00000338086.5_Missense_Mutation_p.N367S|PUM2_ENST00000319801.5_Missense_Mutation_p.N367S|PUM2_ENST00000536417.1_Missense_Mutation_p.N311S			Q8TB72	PUM2_HUMAN	pumilio RNA-binding family member 2	367	Ala-rich.|Gln-rich.		N -> S (in dbSNP:rs34032508).		regulation of translation (GO:0006417)|stress granule assembly (GO:0034063)	cytoplasm (GO:0005737)|cytoplasmic stress granule (GO:0010494)|nuclear membrane (GO:0031965)|perinuclear region of cytoplasm (GO:0048471)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(7)|lung(13)|ovary(2)|prostate(4)|urinary_tract(3)	42	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGCTGTGTTATTTGCCGCAGC	0.488													T|||	11	0.00219649	0.0	0.0014	5008	,	,		16235	0.0		0.0099	False		,,,				2504	0.0				p.N367S		Atlas-SNP	.											.	PUM2	91	.	0			c.A1100G						PASS	.	T	SER/ASN	3,4403	6.2+/-15.9	0,3,2200	117.0	111.0	113.0		1100	3.3	1.0	2	dbSNP_126	113	28,8572	19.8+/-62.0	0,28,4272	yes	missense	PUM2	NM_015317.1	46	0,31,6472	CC,CT,TT		0.3256,0.0681,0.2384	benign	367/1065	20494189	31,12975	2203	4300	6503	SO:0001583	missense	23369	exon8			GTGTTATTTGCCG	AF315591	CCDS1698.1, CCDS74486.1, CCDS74487.1	2p22-p21	2013-09-02	2013-09-02		ENSG00000055917	ENSG00000055917			14958	protein-coding gene	gene with protein product		607205	"""pumilio (Drosphila) homolog 2"", ""pumilio homolog 2 (Drosophila)"""			9039502, 12459267, 12511597	Standard	XM_005262607		Approved	PUMH2, KIAA0235	uc002rds.1	Q8TB72	OTTHUMG00000122098	ENST00000361078.2:c.1100A>G	2.37:g.20494189T>C	ENSP00000354370:p.Asn367Ser	98.0	0.0	0		114.0	56.0	0.491228	NM_015317	B3KSL0|B4E2B6|D6W527|O00234|Q53TV7|Q8WY43|Q9HAN2	Missense_Mutation	SNP	ENST00000361078.2	37		7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	T	2.595	-0.294380	0.05568	6.81E-4	0.003256	ENSG00000055917	ENST00000338086;ENST00000361078;ENST00000319801;ENST00000440577;ENST00000403432;ENST00000536417	T;T;T;T;T;T	0.17528	2.3;2.54;2.55;2.27;2.3;2.3	5.81	3.32	0.38043	.	0.390535	0.33180	N	0.005192	T	0.03390	0.0098	N	0.01576	-0.805	0.24245	N	0.995342	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.38265	-0.9669	10	0.19147	T	0.46	-4.0477	6.8251	0.23878	0.0:0.1485:0.1398:0.7117	rs34032508	311;367;367	B4E2B6;B7ZL34;Q8TB72-3	.;.;.	S	367;367;367;258;367;311	ENSP00000338173:N367S;ENSP00000354370:N367S;ENSP00000326746:N367S;ENSP00000409905:N258S;ENSP00000385992:N367S;ENSP00000440093:N311S	ENSP00000326746:N367S	N	-	2	0	PUM2	20357670	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	1.260000	0.32968	1.044000	0.40200	0.455000	0.32223	AAT	T|0.996;C|0.004	0.004	strong		0.488	PUM2-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015317	
ENTPD3	956	hgsc.bcm.edu	37	3	40453432	40453432	+	Missense_Mutation	SNP	C	C	T	rs377644776		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:40453432C>T	ENST00000301825.3	+	5	534	c.416C>T	c.(415-417)aCg>aTg	p.T139M	ENTPD3-AS1_ENST00000425156.1_RNA|ENTPD3-AS1_ENST00000452768.1_RNA|ENTPD3-AS1_ENST00000439293.1_RNA|ENTPD3_ENST00000445129.1_Missense_Mutation_p.T139M|ENTPD3_ENST00000456402.1_Missense_Mutation_p.T139M	NM_001248.2	NP_001239.2	O75355	ENTP3_HUMAN	ectonucleoside triphosphate diphosphohydrolase 3	139					nucleoside diphosphate catabolic process (GO:0009134)|nucleoside triphosphate catabolic process (GO:0009143)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|nucleoside-diphosphatase activity (GO:0017110)|nucleoside-triphosphatase activity (GO:0017111)			endometrium(1)|kidney(3)|large_intestine(5)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				KIRC - Kidney renal clear cell carcinoma(284;0.0605)|Kidney(284;0.0758)		CTGGGAGCCACGGCTGGGATG	0.517													C|||	1	0.000199681	0.0	0.0	5008	,	,		15474	0.0		0.0	False		,,,				2504	0.001				p.T139M		Atlas-SNP	.											.	ENTPD3	48	.	0			c.C416T						PASS	.	C	MET/THR	1,4405	2.1+/-5.4	0,1,2202	60.0	49.0	52.0		416	5.6	1.0	3		52	1,8599	1.2+/-3.3	0,1,4299	no	missense	ENTPD3	NM_001248.2	81	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	probably-damaging	139/530	40453432	2,13004	2203	4300	6503	SO:0001583	missense	956	exon5			GAGCCACGGCTGG	AF039917	CCDS2691.1, CCDS74919.1	3p21.3	2004-02-26			ENSG00000168032	ENSG00000168032			3365	protein-coding gene	gene with protein product		603161		CD39L3		9676430	Standard	XM_005265605		Approved	NTPDase-3, HB6	uc003ckd.4	O75355	OTTHUMG00000131390	ENST00000301825.3:c.416C>T	3.37:g.40453432C>T	ENSP00000301825:p.Thr139Met	40.0	0.0	0		38.0	27.0	0.710526	NM_001248	B2R8D0|G5E9N0|O60495|Q8N6K2	Missense_Mutation	SNP	ENST00000301825.3	37	CCDS2691.1	.	.	.	.	.	.	.	.	.	.	C	25.6	4.653329	0.88056	2.27E-4	1.16E-4	ENSG00000168032	ENST00000301825;ENST00000456402;ENST00000445129	T;T;T	0.35421	1.31;1.31;1.31	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.72407	0.3456	H	0.95437	3.67	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.80542	-0.1336	10	0.87932	D	0	-14.6669	17.579	0.87960	0.0:1.0:0.0:0.0	.	139	O75355	ENTP3_HUMAN	M	139	ENSP00000301825:T139M;ENSP00000401565:T139M;ENSP00000404671:T139M	ENSP00000301825:T139M	T	+	2	0	ENTPD3	40428436	1.000000	0.71417	0.984000	0.44739	0.875000	0.50365	6.934000	0.75880	2.832000	0.97577	0.655000	0.94253	ACG	.	.	weak		0.517	ENTPD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254179.2	NM_001248	
KIAA0319	9856	hgsc.bcm.edu	37	6	24570151	24570151	+	Silent	SNP	G	G	A	rs41271797	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:24570151G>A	ENST00000378214.3	-	12	2495	c.1971C>T	c.(1969-1971)ttC>ttT	p.F657F	KIAA0319_ENST00000543707.1_Silent_p.F657F|KIAA0319_ENST00000430948.2_Silent_p.F612F|KIAA0319_ENST00000535378.1_Silent_p.F648F|KIAA0319_ENST00000537886.1_Silent_p.F657F	NM_001168375.1|NM_014809.3	NP_001161847.1|NP_055624.2	Q5VV43	K0319_HUMAN	KIAA0319	657	PKD 4. {ECO:0000255|PROSITE- ProRule:PRU00151}.				negative regulation of dendrite development (GO:2000171)|neuron migration (GO:0001764)	early endosome (GO:0005769)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(3)|endometrium(6)|kidney(3)|large_intestine(11)|lung(19)|ovary(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	53						CCCAGTGGTAGAAGACAATGC	0.537													G|||	2	0.000399361	0.0	0.0	5008	,	,		20249	0.0		0.002	False		,,,				2504	0.0				p.F657F		Atlas-SNP	.											KIAA0319,NS,carcinoma,0,1	KIAA0319	117	1	0			c.C1971T						PASS	.	G	,,,,	2,4404	4.2+/-10.8	0,2,2201	118.0	103.0	108.0		1944,1971,1836,1971,1971	2.1	0.8	6	dbSNP_127	108	15,8585	12.6+/-44.7	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KIAA0319	NM_001168374.1,NM_001168375.1,NM_001168376.1,NM_001168377.1,NM_014809.3	,,,,	0,17,6486	AA,AG,GG		0.1744,0.0454,0.1307	,,,,	648/1064,657/1073,612/1028,657/1012,657/1073	24570151	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	9856	exon12			GTGGTAGAAGACA	AB002317	CCDS34348.1, CCDS54969.1, CCDS54970.1, CCDS54971.1, CCDS75409.1	6p22.3	2013-12-13			ENSG00000137261	ENSG00000137261			21580	protein-coding gene	gene with protein product	"""neuronal migration"""	609269				9205841, 15514892	Standard	NM_014809		Approved	NMIG	uc003neh.1	Q5VV43	OTTHUMG00000014358	ENST00000378214.3:c.1971C>T	6.37:g.24570151G>A		209.0	0.0	0		250.0	126.0	0.504	NM_001168377	A7MD37|B2RTU7|B4DHA7|B4DK75|B7ZML3|F5H123|Q9UJC8|Q9Y4G7	Silent	SNP	ENST00000378214.3	37	CCDS34348.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	KIAA0319-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040009.1	NM_014809	
SCNN1A	6337	hgsc.bcm.edu	37	12	6472752	6472752	+	Missense_Mutation	SNP	G	G	A	rs55797039	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6472752G>A	ENST00000228916.2	-	3	639	c.541C>T	c.(541-543)Cgg>Tgg	p.R181W	SCNN1A_ENST00000540037.1_5'UTR|SCNN1A_ENST00000358945.3_Missense_Mutation_p.R181W|SCNN1A_ENST00000360168.3_Missense_Mutation_p.R240W|SCNN1A_ENST00000396966.2_Missense_Mutation_p.R181W|SCNN1A_ENST00000543768.1_Missense_Mutation_p.R204W|SCNN1A_ENST00000538979.1_Intron	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	181			R -> W (functional polymorphism; significant increase of amiloride- sensitive sodium currents; dbSNP:rs55797039). {ECO:0000269|PubMed:16207733, ECO:0000269|PubMed:19462466}.		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	AGAGTCCCCCGCAGGTCGCGA	0.682													G|||	36	0.0071885	0.0	0.0072	5008	,	,		10784	0.0		0.0209	False		,,,				2504	0.0102				p.R240W		Atlas-SNP	.											.	SCNN1A	54	.	0			c.C718T	GRCh37	CM055536	SCNN1A	M	rs55797039	PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	15,4385		0,15,2185	13.0	15.0	14.0		541,610,718	-3.5	0.0	12	dbSNP_129	14	141,8449		4,133,4158	no	missense,missense,missense	SCNN1A	NM_001038.5,NM_001159575.1,NM_001159576.1	101,101,101	4,148,6343	AA,AG,GG		1.6414,0.3409,1.2009	probably-damaging,probably-damaging,probably-damaging	181/670,204/693,240/729	6472752	156,12834	2200	4295	6495	SO:0001583	missense	6337	exon2			TCCCCCGCAGGTC	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.541C>T	12.37:g.6472752G>A	ENSP00000228916:p.Arg181Trp	26.0	0.0	0		17.0	11.0	0.647059	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Missense_Mutation	SNP	ENST00000228916.2	37	CCDS8543.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	14.54	2.565723	0.45694	0.003409	0.016414	ENSG00000111319	ENST00000360168;ENST00000358945;ENST00000228916;ENST00000396966;ENST00000543768	T;T;T;T;T	0.70986	-0.49;-0.53;-0.46;-0.13;-0.47	5.46	-3.48	0.04739	.	1.661160	0.03643	N	0.239873	T	0.62974	0.2472	L	0.32530	0.975	0.09310	N	1	D;D;D	0.76494	0.999;0.999;0.998	P;P;P	0.59703	0.862;0.809;0.827	T	0.69870	-0.5028	10	0.59425	D	0.04	-31.5772	17.9864	0.89157	0.0:0.7352:0.164:0.1009	rs55797039;rs61759925	204;181;240	B4E2Q5;P37088;P37088-2	.;SCNNA_HUMAN;.	W	240;181;181;181;204	ENSP00000353292:R240W;ENSP00000351825:R181W;ENSP00000228916:R181W;ENSP00000380166:R181W;ENSP00000438739:R204W	ENSP00000228916:R181W	R	-	1	2	SCNN1A	6343013	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.833000	0.01695	-0.647000	0.05444	0.561000	0.74099	CGG	G|0.986;A|0.014	0.014	strong		0.682	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
NCOR2	9612	hgsc.bcm.edu	37	12	124824869	124824869	+	Missense_Mutation	SNP	G	G	A	rs61755988	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124824869G>A	ENST00000405201.1	-	36	5459	c.5459C>T	c.(5458-5460)aCg>aTg	p.T1820M	NCOR2_ENST00000429285.2_Missense_Mutation_p.T1810M|NCOR2_ENST00000356219.3_Missense_Mutation_p.T1827M|NCOR2_ENST00000404121.2_Missense_Mutation_p.T1381M|NCOR2_ENST00000404621.1_Missense_Mutation_p.T1810M|NCOR2_ENST00000397355.1_Missense_Mutation_p.T1811M			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1828					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		GTGCTCCACCGTCGTGGTGGA	0.672													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		15239	0.0		0.004	False		,,,				2504	0.0				p.T1820M		Atlas-SNP	.											.	NCOR2	475	.	0			c.C5459T						PASS	.	G	MET/THR,MET/THR,MET/THR	7,4175		0,7,2084	54.0	65.0	61.0		5429,5429,5459	4.2	0.2	12	dbSNP_129	61	86,8354		0,86,4134	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	81,81,81	0,93,6218	AA,AG,GG		1.019,0.1674,0.7368	probably-damaging,probably-damaging,probably-damaging	1810/2459,1810/2505,1820/2515	124824869	93,12529	2091	4220	6311	SO:0001583	missense	9612	exon38			TCCACCGTCGTGG	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.5459C>T	12.37:g.124824869G>A	ENSP00000384018:p.Thr1820Met	45.0	0.0	0		48.0	26.0	0.541667	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	8.853	0.944957	0.18356	0.001674	0.01019	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285	T;T;T;T;T;T	0.19394	2.15;2.42;2.16;2.42;2.16;2.42	4.18	4.18	0.49190	.	0.204758	0.40554	N	0.001069	T	0.30293	0.0760	L	0.40543	1.245	0.28417	N	0.917932	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.991;0.996;0.994	T	0.14671	-1.0464	10	0.72032	D	0.01	-13.5861	16.4861	0.84184	0.0:0.0:1.0:0.0	rs61755988	1810;1811;1820	C9J0Q5;C9J239;C9JFD3	.;.;.	M	1820;1810;1827;1811;1819;1381;1810	ENSP00000384018:T1820M;ENSP00000384202:T1810M;ENSP00000348551:T1827M;ENSP00000380513:T1811M;ENSP00000385618:T1381M;ENSP00000400281:T1810M	ENSP00000348551:T1827M	T	-	2	0	NCOR2	123390822	1.000000	0.71417	0.195000	0.23364	0.015000	0.08874	6.455000	0.73497	1.858000	0.53909	0.491000	0.48974	ACG	G|0.997;A|0.003	0.003	strong		0.672	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
DHX37	57647	hgsc.bcm.edu	37	12	125438712	125438712	+	Silent	SNP	C	C	A	rs11829165	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:125438712C>A	ENST00000308736.2	-	19	2597	c.2499G>T	c.(2497-2499)cgG>cgT	p.R833R	DHX37_ENST00000544745.1_Silent_p.R620R	NM_032656.3	NP_116045.2	Q8IY37	DHX37_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 37	833							ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(5)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(11)|liver(1)|lung(27)|ovary(1)|prostate(2)|skin(3)	65	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;8.05e-05)|Epithelial(86;0.000486)|all cancers(50;0.00653)		CCACCCGGGCCCGCTTGCTCT	0.652													C|||	712	0.142173	0.4728	0.0605	5008	,	,		15886	0.0		0.0338	False		,,,				2504	0.0112				p.R833R		Atlas-SNP	.											DHX37,NS,carcinoma,0,1	DHX37	114	1	0			c.G2499T						PASS	.	C		1886,2520	527.8+/-372.2	401,1084,718	32.0	36.0	35.0		2499	2.4	1.0	12	dbSNP_120	35	342,8258	114.6+/-174.5	3,336,3961	no	coding-synonymous	DHX37	NM_032656.3		404,1420,4679	AA,AC,CC		3.9767,42.8053,17.1306		833/1158	125438712	2228,10778	2203	4300	6503	SO:0001819	synonymous_variant	57647	exon19			CCGGGCCCGCTTG	AB040950	CCDS9261.1	12q24.31	2004-03-25	2003-06-13	2003-06-20		ENSG00000150990		"""DEAH-boxes"""	17210	protein-coding gene	gene with protein product			"""DEAD/DEAH box helicase DDX37"""	DDX37		10819331	Standard	NM_032656		Approved	KIAA1517, MGC4322, MGC2695	uc001ugy.3	Q8IY37		ENST00000308736.2:c.2499G>T	12.37:g.125438712C>A		118.0	0.0	0		147.0	79.0	0.537415	NM_032656	Q9BUI7|Q9P211	Silent	SNP	ENST00000308736.2	37	CCDS9261.1																																																																																			C|0.852;A|0.148	0.148	strong		0.652	DHX37-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_032656	
MUC4	4585	hgsc.bcm.edu	37	3	195511268	195511268	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195511268T>A	ENST00000463781.3	-	2	7642	c.7183A>T	c.(7183-7185)Aca>Tca	p.T2395S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2395S	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GTGTCACCTGTGGATGCTGAG	0.592																																					p.T2395S		Atlas-SNP	.											.	MUC4	1505	.	0			c.A7183T						PASS	.						27.0	30.0	29.0					3																	195511268		688	1585	2273	SO:0001583	missense	4585	exon2			CACCTGTGGATGC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.7183A>T	3.37:g.195511268T>A	ENSP00000417498:p.Thr2395Ser	156.0	0.0	0		569.0	27.0	0.0474517	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	T	5.173	0.217483	0.09810	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.50277	0.75;0.79	.	.	.	.	.	.	.	.	T	0.25680	0.0625	N	0.19112	0.55	0.09310	N	1	P	0.37985	0.613	B	0.35899	0.213	T	0.09952	-1.0651	7	.	.	.	.	2.7352	0.05238	0.0:0.3911:0.0:0.6089	.	2395	E7ESK3	.	S	2395	ENSP00000417498:T2395S;ENSP00000420243:T2395S	.	T	-	1	0	MUC4	196995663	0.004000	0.15560	0.008000	0.14137	0.059000	0.15707	0.962000	0.29280	0.408000	0.25621	0.055000	0.15244	ACA	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LAMA3	3909	hgsc.bcm.edu	37	18	21492734	21492734	+	Silent	SNP	C	C	T	rs62093184		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21492734C>T	ENST00000313654.9	+	56	7459	c.7218C>T	c.(7216-7218)gaC>gaT	p.D2406D	LAMA3_ENST00000399516.3_Silent_p.D2350D|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.D797D|LAMA3_ENST00000587184.1_Silent_p.D741D	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2406	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					TGCCAAATGACCTGGAAGATT	0.448													C|||	1	0.000199681	0.0	0.0	5008	,	,		22166	0.0		0.001	False		,,,				2504	0.0				p.D2406D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7218T						PASS	.	C	,,,	3,4403	6.2+/-15.9	0,3,2200	114.0	113.0	114.0		2391,7050,2223,7218	4.8	1.0	18	dbSNP_129	114	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	0,20,6483	TT,TC,CC		0.1977,0.0681,0.1538	,,,	797/1725,2350/3278,741/1669,2406/3334	21492734	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon56			AAATGACCTGGAA	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7218C>T	18.37:g.21492734C>T		85.0	0.0	0		78.0	31.0	0.397436	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.999;T|0.001	0.001	strong		0.448	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
LYPD2	137797	hgsc.bcm.edu	37	8	143833840	143833840	+	Silent	SNP	C	C	G	rs78400087	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:143833840C>G	ENST00000359228.3	-	1	112	c.30G>C	c.(28-30)gcG>gcC	p.A10A		NM_205545.1	NP_991108.1	Q6UXB3	LYPD2_HUMAN	LY6/PLAUR domain containing 2	10						anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)				endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(2)	7	all_cancers(97;3.96e-12)|all_epithelial(106;1.19e-08)|Lung NSC(106;0.000413)|all_lung(105;0.00106)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)					CCAGCACCAGCGCCAGGAGCG	0.687													C|||	46	0.0091853	0.0015	0.0159	5008	,	,		12658	0.0		0.0328	False		,,,				2504	0.0				p.A10A		Atlas-SNP	.											LYPD2,NS,carcinoma,0,1	LYPD2	18	1	0			c.G30C						PASS	.	C		20,4384	24.3+/-50.5	0,20,2182	44.0	50.0	48.0		30	-3.3	0.0	8	dbSNP_133	48	186,8406	78.4+/-141.0	4,178,4114	no	coding-synonymous	LYPD2	NM_205545.1		4,198,6296	GG,GC,CC		2.1648,0.4541,1.5851		10/126	143833840	206,12790	2202	4296	6498	SO:0001819	synonymous_variant	137797	exon1			CACCAGCGCCAGG	AY358432	CCDS6388.1	8q24.3	2005-08-30		2005-08-30	ENSG00000197353	ENSG00000197353			25215	protein-coding gene	gene with protein product				LYPDC2		12975309	Standard	NM_205545		Approved	RGTR430, UNQ430	uc003ywz.3	Q6UXB3	OTTHUMG00000164686	ENST00000359228.3:c.30G>C	8.37:g.143833840C>G		303.0	0.0	0		162.0	82.0	0.506173	NM_205545	A8K2R6|Q0VD64|Q0VF31	Silent	SNP	ENST00000359228.3	37	CCDS6388.1																																																																																			C|0.985;G|0.015	0.015	strong		0.687	LYPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379742.1	NM_205545	
CEP120	153241	hgsc.bcm.edu	37	5	122720648	122720648	+	Missense_Mutation	SNP	T	T	A	rs147430819		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:122720648T>A	ENST00000306467.5	-	11	2064	c.1760A>T	c.(1759-1761)cAa>cTa	p.Q587L	CEP120_ENST00000306481.6_Missense_Mutation_p.Q561L|CEP120_ENST00000328236.5_Missense_Mutation_p.Q587L			Q8N960	CE120_HUMAN	centrosomal protein 120kDa	587					astral microtubule organization (GO:0030953)|cerebral cortex development (GO:0021987)|interkinetic nuclear migration (GO:0022027)|neurogenesis (GO:0022008)|regulation of microtubule-based process (GO:0032886)|regulation of protein localization (GO:0032880)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	29						GCATTACCCTTGTGCTGCTAT	0.373																																					p.Q587L		Atlas-SNP	.											.	CEP120	72	.	0			c.A1760T						PASS	.	T	LEU/GLN,LEU/GLN	1,4405	2.1+/-5.4	0,1,2202	103.0	95.0	97.0		1682,1760	5.5	1.0	5	dbSNP_134	97	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CEP120	NM_001166226.1,NM_153223.3	113,113	0,2,6501	AA,AT,TT		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	561/961,587/987	122720648	2,13004	2203	4300	6503	SO:0001583	missense	153241	exon12			TACCCTTGTGCTG	AK095646	CCDS4134.2, CCDS54890.1	5q23.2	2014-02-20	2008-08-14	2008-08-14	ENSG00000168944	ENSG00000168944			26690	protein-coding gene	gene with protein product		613446	"""coiled-coil domain containing 100"""	CCDC100		17920017	Standard	NM_153223		Approved	FLJ36090	uc003ktk.3	Q8N960	OTTHUMG00000128922	ENST00000306467.5:c.1760A>T	5.37:g.122720648T>A	ENSP00000303058:p.Gln587Leu	95.0	0.0	0		117.0	62.0	0.529915	NM_153223	Q6AI52|Q6AW89|Q8IWB5|Q8N9Y0|Q8NDE8	Missense_Mutation	SNP	ENST00000306467.5	37	CCDS4134.2	.	.	.	.	.	.	.	.	.	.	T	23.5	4.419777	0.83559	2.27E-4	1.16E-4	ENSG00000168944	ENST00000306467;ENST00000328236;ENST00000306481;ENST00000508442	T;T;T;T	0.51071	0.72;0.72;0.72;0.72	5.52	5.52	0.82312	.	0.126760	0.53938	D	0.000049	T	0.47838	0.1467	L	0.50333	1.59	0.80722	D	1	P	0.48640	0.913	P	0.44394	0.448	T	0.47100	-0.9143	10	0.41790	T	0.15	.	15.6517	0.77099	0.0:0.0:0.0:1.0	.	587	Q8N960	CE120_HUMAN	L	587;587;561;561	ENSP00000303058:Q587L;ENSP00000327504:Q587L;ENSP00000307419:Q561L;ENSP00000421620:Q561L	ENSP00000303058:Q587L	Q	-	2	0	CEP120	122748547	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.532000	0.81985	2.108000	0.64289	0.477000	0.44152	CAA	T|1.000;A|0.000	0.000	weak		0.373	CEP120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250899.2	NM_153223	
PDHX	8050	hgsc.bcm.edu	37	11	34937828	34937828	+	5'Flank	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:34937828A>G	ENST00000227868.4	+	0	0				APIP_ENST00000395787.3_Missense_Mutation_p.S2P|APIP_ENST00000278359.5_5'UTR|APIP_ENST00000527830.1_5'UTR|PDHX_ENST00000430469.2_5'Flank|PDHX_ENST00000448838.3_5'UTR			O00330	ODPX_HUMAN	pyruvate dehydrogenase complex, component X						cellular metabolic process (GO:0044237)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	transferase activity, transferring acyl groups (GO:0016746)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)	16	all_epithelial(35;0.115)|Lung NSC(22;0.218)|all_lung(20;0.242)	all_hematologic(20;0.124)	STAD - Stomach adenocarcinoma(6;0.00113)			TCACAGCCAGACATGGCCCAG	0.687																																					p.S2P		Atlas-SNP	.											.	APIP	21	.	0			c.T4C						PASS	.						16.0	18.0	17.0					11																	34937828		2197	4293	6490	SO:0001631	upstream_gene_variant	51074	exon1			AGCCAGACATGGC	U82328	CCDS7896.1, CCDS44569.1, CCDS53616.1	11p13	2008-02-05			ENSG00000110435	ENSG00000110435			21350	protein-coding gene	gene with protein product		608769				9467010, 12372595	Standard	NM_003477		Approved	E3BP, proX, PDX1, OPDX, DLDBP	uc001mvt.3	O00330	OTTHUMG00000166491		11.37:g.34937828A>G	Exception_encountered	62.0	0.0	0		83.0	25.0	0.301205	NM_015957	B4DW62|D3DR11|E9PB14|E9PBP7|O60221|Q96FV8|Q99783	Missense_Mutation	SNP	ENST00000227868.4	37	CCDS7896.1	.	.	.	.	.	.	.	.	.	.	A	16.07	3.018048	0.54576	.	.	ENSG00000149089	ENST00000395787	T	0.19394	2.15	4.68	-0.69	0.11309	.	0.808144	0.11278	N	0.580708	T	0.09024	0.0223	N	0.08118	0	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14117	-1.0484	10	0.54805	T	0.06	.	4.192	0.10426	0.4606:0.3478:0.1917:0.0	.	2	Q96GX9	MTNB_HUMAN	P	2	ENSP00000379133:S2P	ENSP00000379133:S2P	S	-	1	0	APIP	34894404	0.998000	0.40836	0.865000	0.33974	0.003000	0.03518	0.450000	0.21762	0.064000	0.16427	-0.441000	0.05720	TCT	.	.	none		0.687	PDHX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390017.1	NM_003477	
NUMA1	4926	hgsc.bcm.edu	37	11	71724784	71724784	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71724784C>T	ENST00000393695.3	-	15	4096	c.3765G>A	c.(3763-3765)gtG>gtA	p.V1255V	NUMA1_ENST00000351960.6_Intron|NUMA1_ENST00000358965.6_Silent_p.V1255V|RP11-849H4.4_ENST00000502284.1_RNA	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						ACTCGGCCATCACCAGCCGCT	0.597			T	RARA	APL																																p.V1255V		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.G3765A						PASS	.						51.0	52.0	52.0					11																	71724784		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			GGCCATCACCAGC	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.3765G>A	11.37:g.71724784C>T		64.0	0.0	0		58.0	29.0	0.5	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			.	.	none		0.597	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
FGD5	152273	hgsc.bcm.edu	37	3	14860968	14860968	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14860968G>A	ENST00000285046.5	+	1	500	c.390G>A	c.(388-390)gcG>gcA	p.A130A	FGD5_ENST00000543601.1_De_novo_Start_InFrame	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	130	Glu-rich.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						GTGCAGGAGCGCTGAGCAGGG	0.627																																					p.A130A		Atlas-SNP	.											FGD5_ENST00000285046,NS,carcinoma,+1,1	FGD5	248	1	0			c.G390A						PASS	.						19.0	22.0	22.0					3																	14860968		692	1591	2283	SO:0001819	synonymous_variant	152273	exon1			AGGAGCGCTGAGC	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.390G>A	3.37:g.14860968G>A		212.0	0.0	0		293.0	126.0	0.430034	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Silent	SNP	ENST00000285046.5	37	CCDS46767.1																																																																																			.	.	none		0.627	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
KIAA0226	9711	hgsc.bcm.edu	37	3	197427515	197427515	+	Silent	SNP	C	C	T	rs116791711	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:197427515C>T	ENST00000296343.5	-	7	1229	c.1230G>A	c.(1228-1230)tcG>tcA	p.S410S	KIAA0226_ENST00000273582.5_Silent_p.S350S|KIAA0226_ENST00000467303.1_5'Flank|KIAA0226_ENST00000389665.5_Silent_p.S410S|KIAA0226_ENST00000449205.1_Silent_p.S410S	NM_014687.1	NP_055502.1	Q92622	RUBIC_HUMAN	KIAA0226	410	Ser-rich.				autophagy (GO:0006914)|cell death (GO:0008219)|endocytosis (GO:0006897)|negative regulation of autophagy (GO:0010507)|negative regulation of endocytosis (GO:0045806)	early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)				NS(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	31	all_cancers(143;8.26e-10)|Ovarian(172;0.0418)|Breast(254;0.0976)		Epithelial(36;2.19e-23)|all cancers(36;1.39e-21)|OV - Ovarian serous cystadenocarcinoma(49;1.21e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(93;0.0446)		TGCTGGTATCCGAATGGGAGC	0.547													C|||	33	0.00658946	0.0	0.0058	5008	,	,		18378	0.0		0.0278	False		,,,				2504	0.001				p.S410S	Esophageal Squamous(3;167 355 3763 15924)	Atlas-SNP	.											Q96CK5_HUMAN,NS,carcinoma,-1,6	KIAA0226	136	6	0			c.G1230A						PASS	.	C	,	18,4026		0,18,2004	83.0	84.0	84.0		1050,1230	-10.9	0.1	3	dbSNP_132	84	155,8197		1,153,4022	no	coding-synonymous,coding-synonymous	KIAA0226	NM_001145642.2,NM_014687.1	,	1,171,6026	TT,TC,CC		1.8558,0.4451,1.3956	,	350/928,410/973	197427515	173,12223	2022	4176	6198	SO:0001819	synonymous_variant	9711	exon7			GGTATCCGAATGG	D86979	CCDS43195.1, CCDS46987.1	3q29	2011-08-09			ENSG00000145016	ENSG00000145016			28991	protein-coding gene	gene with protein product	"""RUN domain and cysteine-rich domain containing, Beclin 1-interacting protein"""	613516				9039502, 19270693, 20826435	Standard	XM_005269374		Approved	rubicon, rundataxin	uc003fyc.2	Q92622	OTTHUMG00000155452	ENST00000296343.5:c.1230G>A	3.37:g.197427515C>T		204.0	0.0	0		209.0	77.0	0.368421	NM_014687	Q96CK5	Silent	SNP	ENST00000296343.5	37	CCDS43195.1	23|23	0.010531135531135532|0.010531135531135532	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	22|22	0.029023746701846966|0.029023746701846966	C|C	5.052|5.052	0.195309|0.195309	0.09599|0.09599	0.004451|0.004451	0.018558|0.018558	ENSG00000145016|ENSG00000145016	ENST00000413360|ENST00000415452	.|.	.|.	.|.	5.46|5.46	-10.9|-10.9	0.00192|0.00192	.|.	.|.	.|.	.|.	.|.	T|T	0.21962|0.21962	0.0529|0.0529	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.59616|0.59616	-0.7421|-0.7421	4|4	.|.	.|.	.|.	.|.	8.7159|8.7159	0.34411|0.34411	0.1713:0.5525:0.0677:0.2085|0.1713:0.5525:0.0677:0.2085	.|.	.|.	.|.	.|.	R|Q	389|169	.|.	.|.	G|R	-|-	1|2	0|0	KIAA0226|KIAA0226	198911912|198911912	0.000000|0.000000	0.05858|0.05858	0.145000|0.145000	0.22337|0.22337	0.727000|0.727000	0.41649|0.41649	-3.954000|-3.954000	0.00326|0.00326	-3.421000|-3.421000	0.00166|0.00166	-1.099000|-1.099000	0.02127|0.02127	GGA|CGG	C|0.987;T|0.013	0.013	strong		0.547	KIAA0226-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000340184.1	XM_032901	
BEAN1	146227	hgsc.bcm.edu	37	16	66514549	66514549	+	Silent	SNP	A	A	G	rs141546513		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:66514549A>G	ENST00000536005.2	+	5	718	c.501A>G	c.(499-501)ccA>ccG	p.P167P	RP11-403P17.5_ENST00000561728.1_Intron|BEAN1_ENST00000563075.1_Intron|BEAN1_ENST00000564819.1_Intron|BEAN1_ENST00000561796.1_Intron|BEAN1_ENST00000299694.8_Silent_p.P58P|CTD-2258A20.5_ENST00000569125.1_RNA	NM_001178020.2	NP_001171491.1	Q3B7T3	BEAN1_HUMAN	brain expressed, associated with NEDD4, 1	167					cell death (GO:0008219)	integral component of membrane (GO:0016021)				kidney(1)	1						ACGCACCACCACCCTACTCGC	0.667																																					p.P167P		Atlas-SNP	.											.	BEAN1	6	.	0			c.A501G						PASS	.	A	,,,	0,1384		0,0,692	59.0	66.0	64.0		174,501,,	-9.5	0.1	16	dbSNP_134	64	5,3177		0,5,1586	no	coding-synonymous,coding-synonymous,intron,intron	BEAN1	NM_001136106.3,NM_001178020.1,NM_001197224.1,NM_001197225.1	,,,	0,5,2278	GG,GA,AA		0.1571,0.0,0.1095	,,,	58/151,167/260,,	66514549	5,4561	692	1591	2283	SO:0001819	synonymous_variant	146227	exon5			ACCACCACCCTAC	BC000818	CCDS54015.1, CCDS58469.1, CCDS58470.1	16q21	2014-07-30			ENSG00000166546	ENSG00000166546			24160	protein-coding gene	gene with protein product		612051	"""spinocerebellar ataxia 31"""	SCA31		11042109, 8619474, 23607545	Standard	NM_001178020		Approved		uc021tjl.1	Q3B7T3	OTTHUMG00000173370	ENST00000536005.2:c.501A>G	16.37:g.66514549A>G		153.0	0.0	0		140.0	59.0	0.421429	NM_001178020	B3KPC0|H3BP97	Silent	SNP	ENST00000536005.2	37	CCDS54015.1																																																																																			A|1.000;G|0.000	0.000	strong		0.667	BEAN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422908.1	NM_001136106	
PHLDB1	23187	hgsc.bcm.edu	37	11	118516274	118516274	+	Missense_Mutation	SNP	G	G	A	rs149914355	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118516274G>A	ENST00000361417.2	+	17	3733	c.3322G>A	c.(3322-3324)Gcc>Acc	p.A1108T	PHLDB1_ENST00000356063.5_Missense_Mutation_p.A1061T|PHLDB1_ENST00000524713.1_Missense_Mutation_p.A251T|PHLDB1_ENST00000534672.1_3'UTR|PHLDB1_ENST00000527898.1_Missense_Mutation_p.A159T	NM_015157.3	NP_055972.1	Q86UU1	PHLB1_HUMAN	pleckstrin homology-like domain, family B, member 1	1108										breast(3)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(10)|liver(3)|lung(14)|ovary(2)|pancreas(1)|prostate(3)|skin(1)	46	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_hematologic(192;0.0735)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;3.4e-05)		GGGTGAGCACGCCTATGATAC	0.647													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18185	0.0		0.005	False		,,,				2504	0.001				p.A1108T		Atlas-SNP	.											.	PHLDB1	103	.	0			c.G3322A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	3,4397	6.2+/-15.9	0,3,2197	95.0	92.0	93.0		3322,3181,3322	5.5	0.9	11	dbSNP_134	93	12,8578	9.1+/-34.3	0,12,4283	yes	missense,missense,missense	PHLDB1	NM_001144758.1,NM_001144759.1,NM_015157.2	58,58,58	0,15,6480	AA,AG,GG		0.1397,0.0682,0.1155	benign,benign,benign	1108/1378,1061/1320,1108/1378	118516274	15,12975	2200	4295	6495	SO:0001583	missense	23187	exon16			GAGCACGCCTATG		CCDS8401.1, CCDS44750.1	11q23.3	2013-01-10			ENSG00000019144	ENSG00000019144		"""Pleckstrin homology (PH) domain containing"""	23697	protein-coding gene	gene with protein product		612834				14532993	Standard	NM_015157		Approved	FLJ00141, LL5a, KIAA0638	uc001pts.3	Q86UU1	OTTHUMG00000166341	ENST00000361417.2:c.3322G>A	11.37:g.118516274G>A	ENSP00000354498:p.Ala1108Thr	91.0	0.0	0		126.0	61.0	0.484127	NM_001144758	B0YJ63|B0YJ64|O75133|Q4KMF8|Q8TEQ2	Missense_Mutation	SNP	ENST00000361417.2	37	CCDS8401.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	15.18	2.757205	0.49468	6.82E-4	0.001397	ENSG00000019144	ENST00000361417;ENST00000361465;ENST00000358191;ENST00000356063;ENST00000527898;ENST00000524713	T;T;T;T	0.61040	0.14;0.14;0.14;0.14	5.52	5.52	0.82312	.	0.223446	0.46758	D	0.000268	T	0.45498	0.1345	L	0.56280	1.765	0.29675	N	0.842181	P;P;P;P;P	0.48016	0.904;0.681;0.898;0.764;0.883	B;B;B;B;B	0.38296	0.23;0.216;0.27;0.151;0.27	T	0.56396	-0.7986	10	0.36615	T	0.2	-19.0047	18.4343	0.90638	0.0:0.0:1.0:0.0	.	251;472;867;1061;1108	B4DK17;B0YJ65;Q5W9G0;Q86UU1-2;Q86UU1	.;.;.;.;PHLB1_HUMAN	T	1108;882;472;1061;159;251	ENSP00000354498:A1108T;ENSP00000348359:A1061T;ENSP00000435388:A159T;ENSP00000434905:A251T	ENSP00000348359:A1061T	A	+	1	0	PHLDB1	118021484	0.998000	0.40836	0.928000	0.36995	0.654000	0.38779	2.954000	0.49113	2.596000	0.87737	0.655000	0.94253	GCC	G|0.998;A|0.002	0.002	strong		0.647	PHLDB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389279.1	NM_015157	
UGT2B4	7363	hgsc.bcm.edu	37	4	70361163	70361163	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70361163T>C	ENST00000305107.6	-	1	463	c.417A>G	c.(415-417)aaA>aaG	p.K139K	UGT2B4_ENST00000512583.1_Silent_p.K139K|UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000506580.1_5'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	139					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	ACTCCTGTAGTTTCTTCATAA	0.368																																					p.K139K		Atlas-SNP	.											.	UGT2B4	105	.	0			c.A417G						PASS	.						37.0	38.0	38.0					4																	70361163		2144	4283	6427	SO:0001819	synonymous_variant	7363	exon1			CTGTAGTTTCTTC	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.417A>G	4.37:g.70361163T>C		135.0	0.0	0		157.0	28.0	0.178344	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			.	.	none		0.368	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
KLKB1	3818	hgsc.bcm.edu	37	4	187178437	187178437	+	Missense_Mutation	SNP	G	G	A	rs121964951	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187178437G>A	ENST00000264690.6	+	14	1830	c.1643G>A	c.(1642-1644)tGc>tAc	p.C548Y	KLKB1_ENST00000513864.1_Intron	NM_000892.3	NP_000883.2	P03952	KLKB1_HUMAN	kallikrein B, plasma (Fletcher factor) 1	548	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		C -> Y (in PKK deficiency). {ECO:0000269|PubMed:14652634}.		blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|Factor XII activation (GO:0002542)|fibrinolysis (GO:0042730)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)|proteolysis (GO:0006508)|zymogen activation (GO:0031638)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)	p.C548Y(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	40		all_cancers(14;1.55e-52)|all_epithelial(14;7.69e-39)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00664)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.243)		OV - Ovarian serous cystadenocarcinoma(60;1.29e-10)|BRCA - Breast invasive adenocarcinoma(30;3.8e-05)|GBM - Glioblastoma multiforme(59;0.000131)|STAD - Stomach adenocarcinoma(60;0.000292)|LUSC - Lung squamous cell carcinoma(40;0.00241)|READ - Rectum adenocarcinoma(43;0.168)		AATGAAGAATGCCAGAAAAGA	0.338																																					p.C548Y		Atlas-SNP	.											KLKB1_ENST00000264690,colon,carcinoma,0,2	KLKB1	155	2	2	Substitution - Missense(2)	large_intestine(2)	c.G1643A	GRCh37	CM033394	KLKB1	M	rs121964951	scavenged	.	G	TYR/CYS	0,4402		0,0,2201	72.0	84.0	80.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1643	5.8	1.0	4	dbSNP_133	80	4,8590	3.7+/-12.6	0,4,4293	yes	missense	KLKB1	NM_000892.3	194	0,4,6494	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	548/639	187178437	4,12992	2201	4297	6498	SO:0001583	missense	3818	exon14			AAGAATGCCAGAA	M13143	CCDS34120.1	4q35	2008-02-05			ENSG00000164344	ENSG00000164344		"""Kallikreins"""	6371	protein-coding gene	gene with protein product		229000		KLK3		9535413, 3521732	Standard	XM_005262987		Approved		uc003iyy.3	P03952	OTTHUMG00000150347	ENST00000264690.6:c.1643G>A	4.37:g.187178437G>A	ENSP00000264690:p.Cys548Tyr	125.0	1.0	0.008		130.0	55.0	0.423077	NM_000892	A6NH96|B2R8H9|Q17RE8|Q17RE9|Q4W5C3	Missense_Mutation	SNP	ENST00000264690.6	37	CCDS34120.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.165611|4.165611	0.78339|0.78339	0.0|0.0	4.65E-4|4.65E-4	ENSG00000164344|ENSG00000164344	ENST00000511608|ENST00000264690	.|D	.|0.96992	.|-4.2	5.75|5.75	5.75|5.75	0.90469|0.90469	.|Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.99102|0.99102	0.9691|0.9691	H|H	0.99042|0.99042	4.41|4.41	0.80722|0.80722	A|A	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.997	D|D	0.98891|0.98891	1.0773|1.0773	4|9	.|0.87932	.|D	.|0	.|.	19.9525|19.9525	0.97208|0.97208	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|548;548	.|A8K9A9;P03952	.|.;KLKB1_HUMAN	T|Y	596|548	.|ENSP00000264690:C548Y	.|ENSP00000264690:C548Y	A|C	+|+	1|2	0|0	KLKB1|KLKB1	187415431|187415431	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.898000|0.898000	0.52572|0.52572	6.062000|6.062000	0.71155|0.71155	2.719000|2.719000	0.93026|0.93026	0.655000|0.655000	0.94253|0.94253	GCC|TGC	G|1.000;A|0.000	0.000	strong		0.338	KLKB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317732.1	NM_000892	
ARHGEF10	9639	hgsc.bcm.edu	37	8	1893773	1893773	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:1893773C>A	ENST00000398564.1	+	27	3424	c.3424C>A	c.(3424-3426)Cac>Aac	p.H1142N	ARHGEF10_ENST00000520359.1_Missense_Mutation_p.H1079N|ARHGEF10_ENST00000262112.6_Missense_Mutation_p.H1113N|ARHGEF10_ENST00000349830.3_Missense_Mutation_p.H1117N|ARHGEF10_ENST00000518288.1_Missense_Mutation_p.H1141N|ARHGEF10_ENST00000521927.1_3'UTR			O15013	ARHGA_HUMAN	Rho guanine nucleotide exchange factor (GEF) 10	1142					centrosome duplication (GO:0051298)|myelination in peripheral nervous system (GO:0022011)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of stress fiber assembly (GO:0051496)|spindle assembly involved in mitosis (GO:0090307)	centrosome (GO:0005813)|cytosol (GO:0005829)	kinesin binding (GO:0019894)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(3)|large_intestine(11)|lung(11)|prostate(3)|skin(3)|stomach(3)|urinary_tract(1)	35		Colorectal(14;3.46e-05)|Renal(68;0.000518)|Ovarian(12;0.00409)|Myeloproliferative disorder(644;0.0255)|Hepatocellular(245;0.0834)		COAD - Colon adenocarcinoma(149;1.62e-05)|BRCA - Breast invasive adenocarcinoma(11;1.68e-05)|KIRC - Kidney renal clear cell carcinoma(542;0.00361)|READ - Rectum adenocarcinoma(644;0.0718)		AACTCTCAAGCACCTGCAGGA	0.617																																					p.H1117N		Atlas-SNP	.											.	ARHGEF10	255	.	0			c.C3349A						PASS	.						134.0	106.0	115.0					8																	1893773		2203	4300	6503	SO:0001583	missense	9639	exon27			CTCAAGCACCTGC	AF009205	CCDS34794.1	8p23	2014-09-17			ENSG00000104728	ENSG00000104728		"""Rho guanine nucleotide exchange factors"""	14103	protein-coding gene	gene with protein product		608136				9205841, 16896804	Standard	XM_005266039		Approved	KIAA0294, Gef10	uc003wpr.3	O15013	OTTHUMG00000163626	ENST00000398564.1:c.3424C>A	8.37:g.1893773C>A	ENSP00000381571:p.His1142Asn	112.0	0.0	0		139.0	71.0	0.510791	NM_014629	O14665|Q2KHR8|Q68D55|Q8IWD9|Q8IY77	Missense_Mutation	SNP	ENST00000398564.1	37		.	.	.	.	.	.	.	.	.	.	c	14.10	2.433766	0.43224	.	.	ENSG00000104728	ENST00000349830;ENST00000520359;ENST00000518288;ENST00000398564;ENST00000262112;ENST00000522435	T;T;T;T;T;T	0.62639	1.55;1.55;1.55;1.55;0.01;0.01	5.01	5.01	0.66863	.	0.000000	0.85682	D	0.000000	T	0.68668	0.3026	M	0.82823	2.61	0.80722	D	1	B;P	0.34892	0.047;0.474	B;B	0.36335	0.059;0.222	T	0.72757	-0.4197	10	0.48119	T	0.1	-35.744	18.2931	0.90137	0.0:1.0:0.0:0.0	.	1079;1117	O15013-7;O15013-5	.;.	N	1117;1079;1141;1142;1113;761	ENSP00000340297:H1117N;ENSP00000427909:H1079N;ENSP00000431012:H1141N;ENSP00000381571:H1142N;ENSP00000262112:H1113N;ENSP00000427768:H761N	ENSP00000262112:H1113N	H	+	1	0	ARHGEF10	1881180	1.000000	0.71417	0.927000	0.36925	0.343000	0.28985	6.849000	0.75414	2.302000	0.77476	0.431000	0.28591	CAC	.	.	none		0.617	ARHGEF10-203	KNOWN	basic	protein_coding	protein_coding			
FHOD3	80206	hgsc.bcm.edu	37	18	34289118	34289118	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:34289118G>T	ENST00000359247.4	+	14	1721	c.1721G>T	c.(1720-1722)gGg>gTg	p.G574V	FHOD3_ENST00000257209.4_Missense_Mutation_p.G591V|FHOD3_ENST00000445677.1_Missense_Mutation_p.G553V|FHOD3_ENST00000590592.1_Missense_Mutation_p.G766V|FHOD3_ENST00000587493.1_3'UTR|FHOD3_ENST00000591635.1_Intron	NM_001281739.1	NP_001268668.1	Q2V2M9	FHOD3_HUMAN	formin homology 2 domain containing 3	574					actin filament network formation (GO:0051639)|cardiac myofibril assembly (GO:0055003)|negative regulation of actin filament polymerization (GO:0030837)|sarcomere organization (GO:0045214)	striated muscle thin filament (GO:0005865)				NS(1)|breast(5)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|liver(2)|lung(29)|ovary(3)|prostate(4)|skin(5)|upper_aerodigestive_tract(1)	90		all_epithelial(2;0.0181)|Colorectal(2;0.0195)				GCAGGGGCGGGGCAGGTTGCT	0.572																																					p.G591V		Atlas-SNP	.											FHOD3,NS,carcinoma,+1,1	FHOD3	210	1	0			c.G1772T						PASS	.						69.0	86.0	80.0					18																	34289118		2203	4300	6503	SO:0001583	missense	80206	exon15			GGGCGGGGCAGGT	AK091899	CCDS32816.1, CCDS62418.1, CCDS62419.1	18q12	2007-08-02				ENSG00000134775			26178	protein-coding gene	gene with protein product		609691				11214970	Standard	NM_025135		Approved	FHOS2, KIAA1695, FLJ22297, FLJ22717	uc021uiv.1	Q2V2M9		ENST00000359247.4:c.1721G>T	18.37:g.34289118G>T	ENSP00000352186:p.Gly574Val	248.0	0.0	0		225.0	89.0	0.395556	NM_025135	A8MQT4|E5F5Q0|Q642I2|Q6ZRQ7|Q86TF9|Q8N3A5|Q9C0G8|Q9H604|Q9H6G7	Missense_Mutation	SNP	ENST00000359247.4	37		.	.	.	.	.	.	.	.	.	.	G	14.69	2.609383	0.46527	.	.	ENSG00000134775	ENST00000257209;ENST00000359247;ENST00000445677	T;T;T	0.19105	2.2;2.17;2.17	5.84	-2.56	0.06268	.	0.594819	0.18286	N	0.145873	T	0.12860	0.0312	L	0.34521	1.04	0.20489	N	0.999893	B;B;B;B	0.23735	0.078;0.09;0.078;0.047	B;B;B;B	0.23419	0.036;0.046;0.022;0.036	T	0.17379	-1.0371	10	0.49607	T	0.09	.	7.3434	0.26650	0.5464:0.1225:0.3311:0.0	.	553;574;591;766	Q2V2M9-2;Q2V2M9;Q2V2M9-3;E5F5Q0	.;FHOD3_HUMAN;.;.	V	591;574;553	ENSP00000257209:G591V;ENSP00000352186:G574V;ENSP00000411430:G553V	ENSP00000257209:G591V	G	+	2	0	FHOD3	32543116	0.966000	0.33281	0.000000	0.03702	0.001000	0.01503	1.014000	0.29950	-0.327000	0.08551	-1.202000	0.01658	GGG	.	.	none		0.572	FHOD3-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460884.1	XM_371114	
HCAR1	27198	hgsc.bcm.edu	37	12	123214372	123214372	+	Missense_Mutation	SNP	G	G	A	rs61742326	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123214372G>A	ENST00000436083.2	-	1	1018	c.515C>T	c.(514-516)tCg>tTg	p.S172L	HCAR1_ENST00000432564.1_Missense_Mutation_p.S172L|HCAR1_ENST00000356987.2_Missense_Mutation_p.S172L			Q9BXC0	HCAR1_HUMAN	hydroxycarboxylic acid receptor 1	172					response to estradiol (GO:0032355)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|breast(3)|endometrium(1)|kidney(1)|lung(1)|ovary(1)|pancreas(1)|skin(1)	10						GCCATTGGCCGACTCCATGAT	0.532													G|||	12	0.00239617	0.0	0.0072	5008	,	,		20664	0.001		0.006	False		,,,				2504	0.0				p.S172L		Atlas-SNP	.											.	HCAR1	21	.	0			c.C515T						PASS	.	G	LEU/SER	5,4401	9.9+/-24.2	0,5,2198	56.0	57.0	57.0		515	5.5	1.0	12	dbSNP_129	57	31,8569	21.0+/-64.5	0,31,4269	yes	missense	HCAR1	NM_032554.3	145	0,36,6467	AA,AG,GG		0.3605,0.1135,0.2768	benign	172/347	123214372	36,12970	2203	4300	6503	SO:0001583	missense	27198	exon1			TTGGCCGACTCCA	AF411110	CCDS9236.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000196917	ENSG00000196917		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	4532	protein-coding gene	gene with protein product	"""lactate receptor 1"""	606923	"""G protein-coupled receptor 104"", ""G protein-coupled receptor 81"""	GPR104, GPR81		11574155, 19047060, 18952058, 21454438	Standard	NM_032554		Approved	HCA1, FKSG80, TA-GPCR, LACR1	uc001ucz.3	Q9BXC0		ENST00000436083.2:c.515C>T	12.37:g.123214372G>A	ENSP00000409980:p.Ser172Leu	22.0	0.0	0		27.0	14.0	0.518519	NM_032554	B2R9X4|Q3Y5J3|Q4VBN1|Q6NXU5	Missense_Mutation	SNP	ENST00000436083.2	37	CCDS9236.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	12.54	1.968654	0.34754	0.001135	0.003605	ENSG00000196917	ENST00000356987;ENST00000432564;ENST00000436083	T;T;T	0.28255	1.62;1.62;1.62	5.52	5.52	0.82312	GPCR, rhodopsin-like superfamily (1);	0.194005	0.34802	N	0.003663	T	0.14570	0.0352	L	0.33710	1.025	0.33582	D	0.599988	B	0.32829	0.386	B	0.25884	0.064	T	0.23762	-1.0179	10	0.28530	T	0.3	-8.6437	10.379	0.44099	0.089:0.0:0.911:0.0	.	172	Q9BXC0	HCAR1_HUMAN	L	172	ENSP00000349478:S172L;ENSP00000389255:S172L;ENSP00000409980:S172L	ENSP00000349478:S172L	S	-	2	0	HCAR1	121780325	0.143000	0.22626	0.952000	0.39060	0.774000	0.43823	1.785000	0.38684	2.577000	0.86979	0.655000	0.94253	TCG	G|0.996;A|0.004	0.004	strong		0.532	HCAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401415.1		
APOA4	337	hgsc.bcm.edu	37	11	116693871	116693871	+	Missense_Mutation	SNP	C	C	T	rs12721041	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:116693871C>T	ENST00000357780.3	-	1	151	c.37G>A	c.(37-39)Gtg>Atg	p.V13M		NM_000482.3	NP_000473.2	P06727	APOA4_HUMAN	apolipoprotein A-IV	13			V -> M (in allele APOA-IV*1D). {ECO:0000269|PubMed:1349197, ECO:0000269|PubMed:15108119}.		cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|chylomicron assembly (GO:0034378)|chylomicron remodeling (GO:0034371)|high-density lipoprotein particle remodeling (GO:0034375)|hydrogen peroxide catabolic process (GO:0042744)|innate immune response in mucosa (GO:0002227)|leukocyte cell-cell adhesion (GO:0007159)|lipid homeostasis (GO:0055088)|lipid transport (GO:0006869)|lipoprotein metabolic process (GO:0042157)|multicellular organismal lipid catabolic process (GO:0044240)|negative regulation of plasma lipoprotein particle oxidation (GO:0034445)|phosphatidylcholine metabolic process (GO:0046470)|phospholipid efflux (GO:0033700)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of lipoprotein lipase activity (GO:0051006)|positive regulation of triglyceride catabolic process (GO:0010898)|protein-lipid complex assembly (GO:0065005)|regulation of cholesterol transport (GO:0032374)|regulation of intestinal cholesterol absorption (GO:0030300)|removal of superoxide radicals (GO:0019430)|response to lipid hydroperoxide (GO:0006982)|response to stilbenoid (GO:0035634)|retinoid metabolic process (GO:0001523)|reverse cholesterol transport (GO:0043691)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle remodeling (GO:0034372)	blood microparticle (GO:0072562)|chylomicron (GO:0042627)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|very-low-density lipoprotein particle (GO:0034361)	antioxidant activity (GO:0016209)|cholesterol transporter activity (GO:0017127)|copper ion binding (GO:0005507)|lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|phosphatidylcholine binding (GO:0031210)|phosphatidylcholine-sterol O-acyltransferase activator activity (GO:0060228)|protein homodimerization activity (GO:0042803)			cervix(1)|endometrium(2)|lung(10)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Breast(348;0.0126)|Medulloblastoma(222;0.0425)|all_hematologic(158;0.0564)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;8.54e-06)|Epithelial(105;1.62e-05)|all cancers(92;0.000165)|OV - Ovarian serous cystadenocarcinoma(223;0.148)		GCGACAGCCACCAGGGCCAGG	0.582													C|||	15	0.00299521	0.0	0.0014	5008	,	,		19224	0.0		0.0129	False		,,,				2504	0.001				p.V13M		Atlas-SNP	.											.	APOA4	51	.	0			c.G37A						PASS	.	C	MET/VAL	12,4390	21.2+/-45.6	0,12,2189	138.0	133.0	135.0		37	3.4	1.0	11	dbSNP_126	135	144,8440	71.0+/-133.6	1,142,4149	yes	missense	APOA4	NM_000482.3	21	1,154,6338	TT,TC,CC		1.6775,0.2726,1.2013	benign	13/397	116693871	156,12830	2201	4292	6493	SO:0001583	missense	337	exon1			CAGCCACCAGGGC		CCDS31681.1	11q23.3	2013-01-24			ENSG00000110244	ENSG00000110244		"""Apolipoproteins"""	602	protein-coding gene	gene with protein product		107690					Standard	NM_000482		Approved		uc001pps.1	P06727	OTTHUMG00000046110	ENST00000357780.3:c.37G>A	11.37:g.116693871C>T	ENSP00000350425:p.Val13Met	121.0	0.0	0		143.0	77.0	0.538462	NM_000482	A8MSL6|Q14CW8|Q6Q787	Missense_Mutation	SNP	ENST00000357780.3	37	CCDS31681.1	12	0.005494505494505495	0	0.0	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	C	13.60	2.286795	0.40494	0.002726	0.016775	ENSG00000110244	ENST00000357780	T	0.77098	-1.07	4.33	3.39	0.38822	.	0.512987	0.17527	N	0.171020	T	0.69672	0.3137	M	0.83012	2.62	0.22489	N	0.999052	B	0.29301	0.241	B	0.38880	0.284	T	0.72043	-0.4409	10	0.72032	D	0.01	-28.2212	10.1918	0.43030	0.0:0.798:0.202:0.0	rs12721041;rs45558133	13	P06727	APOA4_HUMAN	M	13	ENSP00000350425:V13M	ENSP00000350425:V13M	V	-	1	0	APOA4	116199081	0.999000	0.42202	1.000000	0.80357	0.774000	0.43823	0.411000	0.21115	1.383000	0.46405	0.655000	0.94253	GTG	C|0.990;T|0.010	0.010	strong		0.582	APOA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106279.2	NM_000482	
FRMPD2	143162	hgsc.bcm.edu	37	10	49431171	49431171	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:49431171C>T	ENST00000374201.3	-	11	1613	c.1311G>A	c.(1309-1311)ctG>ctA	p.L437L	FRMPD2_ENST00000407470.4_Silent_p.L406L|FRMPD2_ENST00000305531.3_Silent_p.L413L	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	437	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CTCACTGGAGCAGCCCATAGT	0.473																																					p.L437L		Atlas-SNP	.											.	FRMPD2	157	.	0			c.G1311A						PASS	.						85.0	82.0	83.0					10																	49431171		2203	4300	6503	SO:0001819	synonymous_variant	143162	exon11			CTGGAGCAGCCCA	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.1311G>A	10.37:g.49431171C>T		83.0	0.0	0		84.0	51.0	0.607143	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Silent	SNP	ENST00000374201.3	37	CCDS31195.1																																																																																			.	.	none		0.473	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
MYH11	4629	hgsc.bcm.edu	37	16	15808876	15808876	+	Missense_Mutation	SNP	C	C	G	rs113964173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15808876C>G	ENST00000300036.5	-	40	5785	c.5676G>C	c.(5674-5676)gaG>gaC	p.E1892D	NDE1_ENST00000396355.1_Intron|NDE1_ENST00000396354.1_Intron|MYH11_ENST00000396324.3_Missense_Mutation_p.E1899D|MYH11_ENST00000576790.2_Missense_Mutation_p.E1892D|MYH11_ENST00000452625.2_Missense_Mutation_p.E1899D|NDE1_ENST00000342673.5_Intron	NM_002474.2	NP_002465.1	P35749	MYH11_HUMAN	myosin, heavy chain 11, smooth muscle	1892					axon guidance (GO:0007411)|cardiac muscle fiber development (GO:0048739)|elastic fiber assembly (GO:0048251)|muscle contraction (GO:0006936)|skeletal muscle myosin thick filament assembly (GO:0030241)|smooth muscle contraction (GO:0006939)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|muscle myosin complex (GO:0005859)|myosin filament (GO:0032982)|smooth muscle contractile fiber (GO:0030485)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|motor activity (GO:0003774)|structural constituent of muscle (GO:0008307)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(11)|kidney(5)|large_intestine(34)|liver(1)|lung(37)|ovary(9)|pancreas(1)|prostate(7)|skin(7)|upper_aerodigestive_tract(1)	123						TGCGCTGGGACTCCTCCTCTG	0.642			T	CBFB	AML								C|||	17	0.00339457	0.0015	0.0029	5008	,	,		13850	0.0		0.0109	False		,,,				2504	0.002				p.E1899D		Atlas-SNP	.		Dom	yes		16	16p13.13-p13.12	4629	"""myosin, heavy polypeptide 11, smooth muscle"""		L	.	MYH11	520	.	0			c.G5697C						PASS	.	C	ASP/GLU,ASP/GLU,,ASP/GLU,,ASP/GLU	7,4387	12.9+/-30.5	0,7,2190	128.0	121.0	123.0		5697,5697,,5676,,5676	1.1	1.0	16	dbSNP_132	123	61,8539	37.4+/-92.8	0,61,4239	yes	missense,missense,intron,missense,intron,missense	MYH11,NDE1	NM_001040113.1,NM_001040114.1,NM_001143979.1,NM_002474.2,NM_017668.2,NM_022844.2	45,45,,45,,45	0,68,6429	GG,GC,CC		0.7093,0.1593,0.5233	possibly-damaging,possibly-damaging,,possibly-damaging,,possibly-damaging	1899/1946,1899/1980,,1892/1973,,1892/1939	15808876	68,12926	2197	4300	6497	SO:0001583	missense	4629	exon41			CTGGGACTCCTCC	X69292	CCDS10565.1, CCDS10566.1, CCDS45423.1, CCDS45424.1	16p13.11	2011-09-27	2006-09-29		ENSG00000133392	ENSG00000133392		"""Myosins / Myosin superfamily : Class II"""	7569	protein-coding gene	gene with protein product		160745	"""myosin, heavy polypeptide 11, smooth muscle"""			7684189	Standard	NM_001040113		Approved	SMMHC, SMHC	uc002ddx.3	P35749	OTTHUMG00000129935	ENST00000300036.5:c.5676G>C	16.37:g.15808876C>G	ENSP00000300036:p.Glu1892Asp	127.0	0.0	0		152.0	76.0	0.5	NM_001040114	D2JYH7|O00396|O94944|P78422|Q3MIV8|Q3MNF0|Q3MNF1	Missense_Mutation	SNP	ENST00000300036.5	37	CCDS10565.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	19.31	3.802956	0.70682	0.001593	0.007093	ENSG00000133392	ENST00000300036;ENST00000338282;ENST00000396320;ENST00000396324;ENST00000452625	T;T;T;T	0.78816	-1.21;-1.21;-1.21;-1.21	4.76	1.09	0.20402	Myosin tail (1);	0.000000	0.85682	D	0.000000	T	0.81992	0.4940	M	0.91140	3.18	0.58432	D	0.999998	P;P;P;P;P	0.46784	0.884;0.884;0.884;0.884;0.884	P;P;P;P;P	0.55011	0.766;0.766;0.766;0.766;0.766	D	0.84056	0.0372	10	0.72032	D	0.01	.	9.1943	0.37217	0.0:0.6481:0.0:0.3519	.	1899;1892;1899;1892;1899	B1PS43;P35749;Q3MNF1;Q3MIV8;Q3MNF0	.;MYH11_HUMAN;.;.;.	D	1892;1892;1899;1899;1899	ENSP00000300036:E1892D;ENSP00000345136:E1892D;ENSP00000379616:E1899D;ENSP00000407821:E1899D	ENSP00000300036:E1892D	E	-	3	2	MYH11	15716377	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	2.567000	0.45956	0.401000	0.25424	0.455000	0.32223	GAG	C|0.993;G|0.007	0.007	strong		0.642	MYH11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252192.2	NM_001040113	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549584	32549584	+	Silent	SNP	C	C	T	rs200078051|rs35616319|rs200088269		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549584C>T	ENST00000360004.5	-	3	507	c.402G>A	c.(400-402)aaG>aaA	p.K134K		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	134	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						GGGGCTGGGTCTTTGAAGGAT	0.507										Multiple Myeloma(14;0.17)																											p.K134K		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.G402A						PASS	.						64.0	80.0	74.0					6																	32549584		1510	2709	4219	SO:0001819	synonymous_variant	3123	exon3			CTGGGTCTTTGAA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.402G>A	6.37:g.32549584C>T		183.0	0.0	0		368.0	36.0	0.0978261	NM_002124	P01914|Q9MYF5	Silent	SNP	ENST00000360004.5	37	CCDS47409.1																																																																																			.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
AP3B1	8546	hgsc.bcm.edu	37	5	77423965	77423965	+	Silent	SNP	A	A	C	rs115892142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:77423965A>C	ENST00000255194.6	-	17	2032	c.1857T>G	c.(1855-1857)ctT>ctG	p.L619L	AP3B1_ENST00000519295.1_Silent_p.L570L	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	619					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		ATAAGGTGCCAAGCTGGAAAT	0.373									Hermansky-Pudlak syndrome				A|||	5	0.000998403	0.0	0.0	5008	,	,		16956	0.0		0.005	False		,,,				2504	0.0				p.L619L		Atlas-SNP	.											.	AP3B1	94	.	0			c.T1857G						PASS	.	A		4,4402	4.2+/-10.8	0,4,2199	48.0	48.0	48.0		1857	3.5	1.0	5	dbSNP_132	48	22,8578	8.4+/-32.0	1,20,4279	no	coding-synonymous	AP3B1	NM_003664.3		1,24,6478	CC,CA,AA		0.2558,0.0908,0.1999		619/1095	77423965	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	8546	exon17	Familial Cancer Database	HPS, HPS1-8	GGTGCCAAGCTGG	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.1857T>G	5.37:g.77423965A>C		35.0	0.0	0		45.0	21.0	0.466667	NM_003664	E5RJ68|O00580|Q7Z393|Q9HD66	Silent	SNP	ENST00000255194.6	37	CCDS4041.1																																																																																			A|0.998;C|0.002	0.002	strong		0.373	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2		
EIF4G1	1981	hgsc.bcm.edu	37	3	184037523	184037523	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:184037523C>T	ENST00000346169.2	+	7	742	c.471C>T	c.(469-471)ggC>ggT	p.G157G	EIF4G1_ENST00000435046.2_5'Flank|EIF4G1_ENST00000342981.4_Silent_p.G157G|EIF4G1_ENST00000352767.3_Silent_p.G164G|EIF4G1_ENST00000319274.6_Silent_p.G157G|EIF2B5_ENST00000444495.1_Intron|EIF4G1_ENST00000441154.1_5'Flank|EIF4G1_ENST00000434061.2_5'Flank|EIF4G1_ENST00000392537.2_Silent_p.G70G|EIF4G1_ENST00000382330.3_Silent_p.G164G|EIF4G1_ENST00000411531.1_Silent_p.G117G|EIF4G1_ENST00000427845.1_Silent_p.G70G|EIF4G1_ENST00000350481.5_5'UTR|EIF4G1_ENST00000414031.1_Silent_p.G117G|EIF4G1_ENST00000424196.1_Silent_p.G164G	NM_198241.2	NP_937884	Q04637	IF4G1_HUMAN	eukaryotic translation initiation factor 4 gamma, 1	157					cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|lung development (GO:0030324)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|response to ethanol (GO:0045471)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)|viral process (GO:0016032)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)|translation initiation factor activity (GO:0003743)			central_nervous_system(1)|cervix(2)|endometrium(3)|kidney(5)|large_intestine(14)|lung(41)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	75	all_cancers(143;1.06e-10)|Ovarian(172;0.0339)		Epithelial(37;1.53e-33)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TTCCCACTGGCGTGGCCCCCA	0.622																																					p.G164G		Atlas-SNP	.											.	EIF4G1	151	.	0			c.C492T						PASS	.						28.0	24.0	26.0					3																	184037523		2203	4299	6502	SO:0001819	synonymous_variant	1981	exon8			CACTGGCGTGGCC	D12686	CCDS3259.1, CCDS3260.1, CCDS3261.1, CCDS46970.1, CCDS46970.2, CCDS54687.1, CCDS54688.1	3q27.1	2013-09-19			ENSG00000114867	ENSG00000114867		"""Parkinson disease"""	3296	protein-coding gene	gene with protein product		600495		EIF4G, EIF4F		1429670, 9372926, 21907011	Standard	NM_182917		Approved	p220, PARK18	uc010hxy.3	Q04637	OTTHUMG00000156784	ENST00000346169.2:c.471C>T	3.37:g.184037523C>T		315.0	0.0	0		392.0	230.0	0.586735	NM_001194946	D3DNT2|D3DNT4|D3DNT5|E9PFM1|G5E9S1|O43177|O95066|Q5HYG0|Q6ZN21|Q8N102	Silent	SNP	ENST00000346169.2	37	CCDS3259.1																																																																																			.	.	none		0.622	EIF4G1-007	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000345733.1	NM_182917	
GPATCH8	23131	hgsc.bcm.edu	37	17	42477385	42477385	+	Missense_Mutation	SNP	T	T	C	rs61744303	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42477385T>C	ENST00000591680.1	-	8	2090	c.2060A>G	c.(2059-2061)cAc>cGc	p.H687R	GPATCH8_ENST00000434000.1_Missense_Mutation_p.H609R	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	687	Lys-rich.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		TTTACGTTTGTGTTTGCTGGA	0.443													T|||	18	0.00359425	0.0	0.0058	5008	,	,		20906	0.0		0.0139	False		,,,				2504	0.0				p.H687R		Atlas-SNP	.											.	GPATCH8	114	.	0			c.A2060G						PASS	.	T	ARG/HIS	19,4387	26.2+/-53.5	0,19,2184	240.0	240.0	240.0		2060	5.1	1.0	17	dbSNP_129	240	130,8470	67.0+/-129.4	0,130,4170	yes	missense	GPATCH8	NM_001002909.2	29	0,149,6354	CC,CT,TT		1.5116,0.4312,1.1456	benign	687/1503	42477385	149,12857	2203	4300	6503	SO:0001583	missense	23131	exon8			CGTTTGTGTTTGC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.2060A>G	17.37:g.42477385T>C	ENSP00000467556:p.His687Arg	140.0	0.0	0		153.0	63.0	0.411765	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	T	6.634	0.485507	0.12641	0.004312	0.015116	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.02258	4.37	5.11	5.11	0.69529	.	0.096415	0.64402	D	0.000001	T	0.00845	0.0028	N	0.17082	0.46	0.39216	D	0.963406	B	0.24920	0.114	B	0.24974	0.057	T	0.60047	-0.7339	10	0.16420	T	0.52	-16.2378	9.5574	0.39348	0.0:0.0782:0.0:0.9218	.	687	Q9UKJ3	GPTC8_HUMAN	R	687;609	ENSP00000395016:H609R	ENSP00000335486:H687R	H	-	2	0	GPATCH8	39832911	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	2.849000	0.48286	2.156000	0.67533	0.402000	0.26972	CAC	T|0.989;C|0.011	0.011	strong		0.443	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
CCDC61	729440	hgsc.bcm.edu	37	19	46520069	46520069	+	Silent	SNP	C	C	T	rs144277506	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46520069C>T	ENST00000595358.1	+	10	1258	c.1209C>T	c.(1207-1209)cgC>cgT	p.R403R	CCDC61_ENST00000536603.1_Silent_p.R223R|MIR769_ENST00000390225.1_RNA|CCDC61_ENST00000594087.1_Silent_p.R223R|CCDC61_ENST00000263284.2_Silent_p.R422R	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	403						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		CCCCTAACCGCTCCCGAAACC	0.726													C|||	37	0.00738818	0.0	0.0101	5008	,	,		8715	0.0		0.0219	False		,,,				2504	0.0082				p.R403R		Atlas-SNP	.											.	CCDC61	32	.	0			c.C1209T						PASS	.			12,3400		0,12,1694	6.0	8.0	7.0		1266	1.8	1.0	19	dbSNP_134	7	132,7592		0,132,3730	no	coding-synonymous	CCDC61	NM_001080402.1		0,144,5424	TT,TC,CC		1.709,0.3517,1.2931		422/532	46520069	144,10992	1706	3862	5568	SO:0001819	synonymous_variant	729440	exon10			TAACCGCTCCCGA		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.1209C>T	19.37:g.46520069C>T		69.0	0.0	0		77.0	47.0	0.61039	NM_001267723	C8CAP4|Q9HDB6	Silent	SNP	ENST00000595358.1	37	CCDS46120.2																																																																																			C|0.989;T|0.011	0.011	strong		0.726	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	
LILRB4	11006	hgsc.bcm.edu	37	19	55179184	55179184	+	Silent	SNP	T	T	C	rs142100665	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55179184T>C	ENST00000391736.1	+	13	1455	c.1140T>C	c.(1138-1140)tcT>tcC	p.S380S	LILRB4_ENST00000391733.3_Silent_p.S381S|LILRB4_ENST00000430952.2_Silent_p.S379S|LILRB4_ENST00000270452.2_Silent_p.S380S|LILRB4_ENST00000391734.3_Intron	NM_001278426.2|NM_001278428.2|NM_001278429.2|NM_001278430.2	NP_001265355.1|NP_001265357.1|NP_001265358.1|NP_001265359.1	Q8NHJ6	LIRB4_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 4	380					immune system process (GO:0002376)|negative regulation of osteoclast differentiation (GO:0045671)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antigen binding (GO:0003823)|receptor activity (GO:0004872)			breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(20)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)	39				GBM - Glioblastoma multiforme(193;0.035)		CCCCACTGTCTGGGGAATTCC	0.587													T|||	47	0.00938498	0.025	0.0029	5008	,	,		18397	0.0		0.005	False		,,,				2504	0.0072				p.S380S		Atlas-SNP	.											.	LILRB4	86	.	0			c.T1140C						PASS	.						68.0	68.0	68.0					19																	55179184		2201	4297	6498	SO:0001819	synonymous_variant	11006	exon11			ACTGTCTGGGGAA	U82979	CCDS12902.1, CCDS42618.1	19q13.4	2013-01-11				ENSG00000186818		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6608	protein-coding gene	gene with protein product		604821				9151699, 9079806	Standard	XM_005277050		Approved	LIR-5, ILT3, HM18, LIR5, CD85k	uc002qgp.3	Q8NHJ6		ENST00000391736.1:c.1140T>C	19.37:g.55179184T>C		468.0	0.0	0		493.0	58.0	0.117647	NM_006847	A8MVL8|O15468|O75021|Q6FGQ9|Q8N1C7|Q8NHL5	Silent	SNP	ENST00000391736.1	37	CCDS12902.1																																																																																			T|0.633;C|0.367	0.367	strong		0.587	LILRB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141127.3		
SLCO1B1	10599	hgsc.bcm.edu	37	12	21331940	21331940	+	Missense_Mutation	SNP	G	G	A	rs374113543		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:21331940G>A	ENST00000256958.2	+	7	809	c.713G>A	c.(712-714)gGa>gAa	p.G238E		NM_006446.4	NP_006437.3	Q9Y6L6	SO1B1_HUMAN	solute carrier organic anion transporter family, member 1B1	238					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|organic anion transport (GO:0015711)|small molecule metabolic process (GO:0044281)|sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-independent organic anion transmembrane transporter activity (GO:0015347)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(14)|lung(33)|ovary(3)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	70					Acetylcysteine(DB06151)|Aminohippurate(DB00345)|Atorvastatin(DB01076)|Axitinib(DB06626)|Benzylpenicillin(DB01053)|Bezafibrate(DB01393)|Cabazitaxel(DB06772)|Caspofungin(DB00520)|Conjugated Estrogens(DB00286)|Cyclosporine(DB00091)|Dabrafenib(DB08912)|Dextrothyroxine(DB00509)|Digoxin(DB00390)|Dinoprostone(DB00917)|Eltrombopag(DB06210)|Estradiol(DB00783)|Estrone(DB00655)|Ezetimibe(DB00973)|Fexofenadine(DB00950)|Fluvastatin(DB01095)|Gadoxetate(DB08884)|Gemfibrozil(DB01241)|Indinavir(DB00224)|Irinotecan(DB00762)|L-Carnitine(DB00583)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Lovastatin(DB00227)|Methotrexate(DB00563)|Mycophenolate mofetil(DB00688)|Nelfinavir(DB00220)|Olmesartan(DB00275)|Ouabain(DB01092)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Penicillamine(DB00859)|Pioglitazone(DB01132)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Quinidine(DB00908)|Repaglinide(DB00912)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Saquinavir(DB01232)|SIMEPREVIR(DB06290)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sumatriptan(DB00669)|Valsartan(DB00177)|Verapamil(DB00661)	GTGGATATTGGATATGTAGAT	0.333																																					p.G238E		Atlas-SNP	.											.	SLCO1B1	151	.	0			c.G713A						PASS	.	G	GLU/GLY	0,4406		0,0,2203	105.0	105.0	105.0		713	3.8	1.0	12		105	1,8593	1.2+/-3.3	0,1,4296	no	missense	SLCO1B1	NM_006446.4	98	0,1,6499	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	238/692	21331940	1,12999	2203	4297	6500	SO:0001583	missense	10599	exon7			ATATTGGATATGT		CCDS8685.1	12p12	2013-05-22	2003-11-25	2003-11-26	ENSG00000134538	ENSG00000134538		"""Solute carriers"""	10959	protein-coding gene	gene with protein product		604843	"""solute carrier family 21 (organic anion transporter), member 6"""	SLC21A6		10358072	Standard	NM_006446		Approved	OATP-C, LST-1, OATP1B1	uc001req.4	Q9Y6L6	OTTHUMG00000169047	ENST00000256958.2:c.713G>A	12.37:g.21331940G>A	ENSP00000256958:p.Gly238Glu	74.0	0.0	0		56.0	20.0	0.357143	NM_006446	B2R7G2|Q29R64|Q9NQ37|Q9UBF3|Q9UH89	Missense_Mutation	SNP	ENST00000256958.2	37	CCDS8685.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.747048	0.49257	0.0	1.16E-4	ENSG00000134538	ENST00000256958	T	0.71579	-0.58	3.76	3.76	0.43208	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.83751	0.5322	M	0.80028	2.48	0.53005	D	0.999961	D	0.71674	0.998	D	0.75484	0.986	D	0.85519	0.1202	10	0.46703	T	0.11	.	16.1164	0.81306	0.0:0.0:1.0:0.0	.	238	Q9Y6L6	SO1B1_HUMAN	E	238	ENSP00000256958:G238E	ENSP00000256958:G238E	G	+	2	0	SLCO1B1	21223207	1.000000	0.71417	1.000000	0.80357	0.470000	0.32858	7.186000	0.77722	2.096000	0.63516	0.305000	0.20034	GGA	.	.	weak		0.333	SLCO1B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402070.1	NM_006446	
LMAN2L	81562	hgsc.bcm.edu	37	2	97368800	97368800	+	IGR	SNP	C	C	A	rs373937760		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:97368800C>A	ENST00000264963.4	-	0	2397				FER1L5_ENST00000457909.1_RNA	NM_030805.3	NP_110432.1	Q9H0V9	LMA2L_HUMAN	lectin, mannose-binding 2-like						ER to Golgi vesicle-mediated transport (GO:0006888)|protein folding (GO:0006457)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle (GO:0030134)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(1)|lung(2)|skin(1)|urinary_tract(1)	7						ATCTTCTCCCCCGACGACTTC	0.557																																					p.P1864H		Atlas-SNP	.											.	FER1L5	113	.	0			c.C5591A						PASS	.	C	HIS/PRO	0,4002		0,0,2001	70.0	66.0	68.0		5591	-2.4	0.0	2		68	1,8327		0,1,4163	no	missense	FER1L5	NM_001113382.1	77	0,1,6164	AA,AC,CC		0.012,0.0,0.0081	benign	1864/2094	97368800	1,12329	2001	4164	6165	SO:0001628	intergenic_variant	90342	exon48			TCTCCCCCGACGA	AL136617	CCDS2023.1, CCDS46365.1	2q11.1	2008-02-05			ENSG00000114988	ENSG00000114988			19263	protein-coding gene	gene with protein product		609552				12609988	Standard	NM_001142292		Approved	DKFZp564L2423, VIPL	uc002swv.3	Q9H0V9	OTTHUMG00000130453		2.37:g.97368800C>A		184.0	0.0	0		205.0	96.0	0.468293	NM_001113382	B4DSH3|D3DXH6|Q53GV3|Q53S67|Q63HN6|Q8NBQ6|Q9BQ14	Missense_Mutation	SNP	ENST00000264963.4	37	CCDS2023.1	.	.	.	.	.	.	.	.	.	.	C	10.53	1.376462	0.24857	0.0	1.2E-4	ENSG00000214272	ENST00000414152;ENST00000436930;ENST00000397978	.	.	.	5.67	-2.36	0.06663	C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.693696	0.11893	U	0.519455	T	0.61627	0.2362	L	0.52126	1.63	.	.	.	P;D;P	0.57571	0.954;0.98;0.944	P;P;B	0.54590	0.482;0.756;0.35	T	0.64960	-0.6284	8	0.15499	T	0.54	2.0843	18.405	0.90532	0.0:0.1727:0.7607:0.0667	.	572;1864;573	B7ZLI3;A0AVI2;A0AVI2-2	.;FR1L5_HUMAN;.	H	1864;1868;573	.	ENSP00000442027:P573H	P	+	2	0	FER1L5	96732527	0.000000	0.05858	0.000000	0.03702	0.987000	0.75469	-0.594000	0.05733	-0.882000	0.03987	0.655000	0.94253	CCC	.	.	weak		0.557	LMAN2L-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252844.1	NM_030805	
OR10P1	121130	hgsc.bcm.edu	37	12	56031318	56031318	+	Missense_Mutation	SNP	A	A	T	rs76940436	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56031318A>T	ENST00000309675.2	+	1	675	c.643A>T	c.(643-645)Att>Ttt	p.I215F	RP11-644F5.16_ENST00000556606.1_RNA	NM_206899.1	NP_996782.1	Q8NGE3	O10P1_HUMAN	olfactory receptor, family 10, subfamily P, member 1	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	26						CTTCTCTCTGATTGTCACCTC	0.567													A|||	53	0.0105831	0.0386	0.0029	5008	,	,		18931	0.0		0.0	False		,,,				2504	0.0				p.I215F		Atlas-SNP	.											.	OR10P1	48	.	0			c.A643T						PASS	.	A	PHE/ILE	209,4197	130.2+/-166.9	3,203,1997	133.0	112.0	119.0		643	4.4	0.2	12	dbSNP_131	119	3,8597	2.2+/-6.3	0,3,4297	yes	missense	OR10P1	NM_206899.1	21	3,206,6294	TT,TA,AA		0.0349,4.7435,1.63	probably-damaging	215/314	56031318	212,12794	2203	4300	6503	SO:0001583	missense	121130	exon1			TCTCTGATTGTCA	BK004259	CCDS31828.1	12q13.13	2012-08-09		2004-03-10		ENSG00000175398		"""GPCR / Class A : Olfactory receptors"""	15378	protein-coding gene	gene with protein product				OR10P1P, OR10P2P, OR10P3P			Standard	NM_206899		Approved	OST701	uc010spq.2	Q8NGE3	OTTHUMG00000169961	ENST00000309675.2:c.643A>T	12.37:g.56031318A>T	ENSP00000308082:p.Ile215Phe	91.0	0.0	0		103.0	52.0	0.504854	NM_206899	B9EGY4	Missense_Mutation	SNP	ENST00000309675.2	37	CCDS31828.1	19	0.0086996336996337	17	0.034552845528455285	2	0.0055248618784530384	0	0.0	0	0.0	A	12.41	1.929041	0.34002	0.047435	3.49E-4	ENSG00000175398	ENST00000309675	T	0.00333	8.07	4.44	4.44	0.53790	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48286	D	0.000194	T	0.00241	0.0007	H	0.97564	4.03	0.37082	D	0.899042	D	0.76494	0.999	D	0.75484	0.986	T	0.08452	-1.0721	10	0.87932	D	0	.	6.7619	0.23546	0.8955:0.0:0.1045:0.0	.	215	Q8NGE3	O10P1_HUMAN	F	215	ENSP00000308082:I215F	ENSP00000308082:I215F	I	+	1	0	OR10P1	54317585	0.728000	0.28080	0.178000	0.23040	0.033000	0.12548	2.073000	0.41519	1.999000	0.58509	0.459000	0.35465	ATT	A|0.985;T|0.015	0.015	strong		0.567	OR10P1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406680.1		
EML2	24139	hgsc.bcm.edu	37	19	46137712	46137712	+	Missense_Mutation	SNP	C	C	T	rs144104945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46137712C>T	ENST00000245925.3	-	4	247	c.197G>A	c.(196-198)cGa>cAa	p.R66Q	EML2_ENST00000589876.1_Missense_Mutation_p.R66Q|EML2_ENST00000536630.1_Missense_Mutation_p.R213Q|EML2_ENST00000587152.1_Missense_Mutation_p.R267Q|EML2_ENST00000586902.1_5'Flank	NM_012155.2	NP_036287.1	O95834	EMAL2_HUMAN	echinoderm microtubule associated protein like 2	66	Tandem atypical propeller in EMLs. {ECO:0000250}.				negative regulation of microtubule polymerization (GO:0031115)|regulation of microtubule nucleation (GO:0010968)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	microtubule binding (GO:0008017)|tubulin binding (GO:0015631)			NS(1)|breast(2)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(13)|ovary(1)|urinary_tract(1)	31		Ovarian(192;0.179)|all_neural(266;0.224)		OV - Ovarian serous cystadenocarcinoma(262;0.00553)|GBM - Glioblastoma multiforme(486;0.131)|Epithelial(262;0.197)		CCGGCAGTCTCGGCCACGGTA	0.488													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		14049	0.0		0.008	False		,,,				2504	0.001				p.R267Q		Atlas-SNP	.											.	EML2	64	.	0			c.G800A						PASS	.		GLN/ARG,GLN/ARG,GLN/ARG	9,4397	15.5+/-35.6	0,9,2194	35.0	27.0	30.0		800,638,197	4.7	1.0	19	dbSNP_134	30	50,8550	26.3+/-74.7	1,48,4251	yes	missense,missense,missense	EML2	NM_001193268.1,NM_001193269.1,NM_012155.2	43,43,43	1,57,6445	TT,TC,CC		0.5814,0.2043,0.4536	probably-damaging,probably-damaging,probably-damaging	267/851,213/797,66/650	46137712	59,12947	2203	4300	6503	SO:0001583	missense	24139	exon7			CAGTCTCGGCCAC	AF103939	CCDS12670.1, CCDS54280.1, CCDS59399.1	19q13.32	2013-01-10				ENSG00000125746		"""WD repeat domain containing"""	18035	protein-coding gene	gene with protein product	"""echinoderm MT-associated protein (EMAP)-like protein 70"", ""microtubule-associated protein like echinoderm EMAP"""					11694528, 10521658	Standard	NM_012155		Approved	EMAP2, ELP70, EMAP-2	uc010xxm.2	O95834		ENST00000245925.3:c.197G>A	19.37:g.46137712C>T	ENSP00000245925:p.Arg66Gln	68.0	0.0	0		81.0	44.0	0.54321	NM_001193268	B7Z3I2|B7Z3Q9|K7ERL7|Q59EN8|Q8N5A2|Q9UG50	Missense_Mutation	SNP	ENST00000245925.3	37	CCDS12670.1	9	0.004120879120879121	1	0.0020325203252032522	0	0.0	0	0.0	8	0.010554089709762533	C	26.6	4.755325	0.89843	0.002043	0.005814	ENSG00000125746	ENST00000536630;ENST00000245925;ENST00000448055;ENST00000399594	T;T;T	0.32515	1.45;1.45;5.06	4.74	4.74	0.60224	HELP (1);Quinonprotein alcohol dehydrogenase-like (1);	0.000000	0.85682	D	0.000000	T	0.45418	0.1341	M	0.66378	2.025	0.51012	D	0.999905	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.999;1.0;0.998;0.999;1.0	T	0.49969	-0.8882	10	0.51188	T	0.08	-8.2435	15.2541	0.73571	0.0:1.0:0.0:0.0	.	66;232;213;224;66	B7Z918;B7Z3Q9;B7Z3I2;B7Z872;O95834	.;.;.;.;EMAL2_HUMAN	Q	213;66;267;224	ENSP00000442365:R213Q;ENSP00000245925:R66Q;ENSP00000382503:R224Q	ENSP00000245925:R66Q	R	-	2	0	EML2	50829552	1.000000	0.71417	0.994000	0.49952	0.924000	0.55760	5.478000	0.66806	2.475000	0.83589	0.462000	0.41574	CGA	C|0.996;T|0.004	0.004	strong		0.488	EML2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459608.1	NM_012155	
MYH15	22989	hgsc.bcm.edu	37	3	108163559	108163559	+	Silent	SNP	C	C	T	rs148022324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108163559C>T	ENST00000273353.3	-	23	2699	c.2643G>A	c.(2641-2643)caG>caA	p.Q881Q		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	881						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						GTTCCTCCCTCTGAAACTCTG	0.428													C|||	8	0.00159744	0.0	0.0014	5008	,	,		17597	0.0		0.003	False		,,,				2504	0.0041				p.Q881Q		Atlas-SNP	.											.	MYH15	223	.	0			c.G2643A						PASS	.	C		1,3779		0,1,1889	122.0	114.0	117.0		2643	2.1	0.2	3	dbSNP_134	117	16,8238		0,16,4111	no	coding-synonymous	MYH15	NM_014981.1		0,17,6000	TT,TC,CC		0.1938,0.0265,0.1413		881/1947	108163559	17,12017	1890	4127	6017	SO:0001819	synonymous_variant	22989	exon23			CTCCCTCTGAAAC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.2643G>A	3.37:g.108163559C>T		277.0	1.0	0.00361011		247.0	106.0	0.42915	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			C|0.998;T|0.002	0.002	strong		0.428	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
LAMA2	3908	hgsc.bcm.edu	37	6	129635920	129635920	+	Missense_Mutation	SNP	G	G	A	rs34505698		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:129635920G>A	ENST00000421865.2	+	24	3581	c.3532G>A	c.(3532-3534)Gca>Aca	p.A1178T		NM_000426.3|NM_001079823.1	NP_000417|NP_001073291.1	P24043	LAMA2_HUMAN	laminin, alpha 2	1178	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				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)		GTGCTCTGAAGCAAAAGGACT	0.527													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18459	0.0		0.0	False		,,,				2504	0.0				p.A1178T		Atlas-SNP	.											.	LAMA2	481	.	0			c.G3532A						PASS	.	G	THR/ALA,THR/ALA	0,4406		0,0,2203	87.0	83.0	84.0		3532,3532	5.6	1.0	6	dbSNP_126	84	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	LAMA2	NM_000426.3,NM_001079823.1	58,58	0,13,6490	AA,AG,GG		0.1512,0.0,0.1	benign,benign	1178/3123,1178/3119	129635920	13,12993	2203	4300	6503	SO:0001583	missense	3908	exon24			TCTGAAGCAAAAG	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.3532G>A	6.37:g.129635920G>A	ENSP00000400365:p.Ala1178Thr	73.0	0.0	0		59.0	27.0	0.457627	NM_000426	Q14736|Q5VUM2|Q93022	Missense_Mutation	SNP	ENST00000421865.2	37	CCDS5138.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	18.81	3.703093	0.68501	0.0	0.001512	ENSG00000196569	ENST00000358023;ENST00000354729;ENST00000421865	T	0.36878	1.23	5.59	5.59	0.84812	.	0.000000	0.85682	D	0.000000	T	0.46151	0.1378	L	0.50333	1.59	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.997;0.997	T	0.09271	-1.0682	10	0.21540	T	0.41	.	19.5763	0.95446	0.0:0.0:1.0:0.0	rs34505698	1178;1178	A6NF00;P24043	.;LAMA2_HUMAN	T	1178	ENSP00000400365:A1178T	ENSP00000346769:A1178T	A	+	1	0	LAMA2	129677613	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.230000	0.95299	2.646000	0.89796	0.655000	0.94253	GCA	G|0.999;A|0.001	0.001	strong		0.527	LAMA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042180.1		
CTNND1	1500	hgsc.bcm.edu	37	11	57564451	57564451	+	Missense_Mutation	SNP	C	C	T	rs199813020		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57564451C>T	ENST00000399050.4	+	6	1479	c.943C>T	c.(943-945)Cgt>Tgt	p.R315C	CTNND1_ENST00000428599.2_Missense_Mutation_p.R315C|CTNND1_ENST00000415361.2_Missense_Mutation_p.R214C|CTNND1_ENST00000360682.6_Missense_Mutation_p.R315C|CTNND1_ENST00000532245.1_Missense_Mutation_p.R214C|CTNND1_ENST00000361391.6_Missense_Mutation_p.R315C|CTNND1_ENST00000530748.1_Missense_Mutation_p.R261C|CTNND1_ENST00000528621.1_Missense_Mutation_p.R261C|CTNND1_ENST00000361332.4_Missense_Mutation_p.R315C|CTNND1_ENST00000399039.4_Missense_Mutation_p.R315C|CTNND1_ENST00000533667.1_Intron|CTNND1_ENST00000528232.1_Missense_Mutation_p.R214C|CTNND1_ENST00000526772.1_Intron|CTNND1_ENST00000529873.1_Missense_Mutation_p.R261C|CTNND1_ENST00000525902.1_Intron|CTNND1_ENST00000426142.2_Missense_Mutation_p.R214C|CTNND1_ENST00000358694.6_Missense_Mutation_p.R315C|CTNND1_ENST00000532463.1_Missense_Mutation_p.R214C|CTNND1_ENST00000532787.1_Missense_Mutation_p.R214C|CTNND1_ENST00000361796.4_Missense_Mutation_p.R315C|CTNND1_ENST00000526357.1_Missense_Mutation_p.R261C|CTNND1_ENST00000530094.1_Missense_Mutation_p.R214C|CTNND1_ENST00000529986.1_Missense_Mutation_p.R214C|CTNND1_ENST00000524630.1_Missense_Mutation_p.R315C|CTNND1_ENST00000527467.1_Intron|CTNND1_ENST00000534579.1_Missense_Mutation_p.R261C|CTNND1_ENST00000529526.1_Missense_Mutation_p.R261C|CTNND1_ENST00000532844.1_Missense_Mutation_p.R261C|CTNND1_ENST00000531014.1_Intron|CTNND1_ENST00000529919.1_Missense_Mutation_p.R315C|CTNND1_ENST00000532649.1_Missense_Mutation_p.R261C|CTNND1_ENST00000526938.1_Missense_Mutation_p.R315C	NM_001085458.1	NP_001078927.1	O60716	CTND1_HUMAN	catenin (cadherin-associated protein), delta 1	315					adherens junction organization (GO:0034332)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|regulation of transcription, DNA-templated (GO:0006355)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)|zonula adherens (GO:0005915)	cadherin binding (GO:0045296)|receptor binding (GO:0005102)			breast(5)|endometrium(8)|kidney(4)|large_intestine(7)|liver(2)|lung(16)|ovary(1)|upper_aerodigestive_tract(2)	45		all_epithelial(135;0.155)				CTCTGACCCTCGTCGGCGCCT	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		13710	0.001		0.0	False		,,,				2504	0.0				p.R315C		Atlas-SNP	.											.	CTNND1	203	.	0			c.C943T						PASS	.	C	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	1,3955		0,1,1977	60.0	62.0	61.0		943,943,943,943,943,640,640,640,640,640,640,640,781,781,943,781,781,781,781,640,781,943	5.8	1.0	11		61	2,8326		0,2,4162	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	CTNND1	NM_001085458.1,NM_001085459.1,NM_001085460.1,NM_001085461.1,NM_001085462.1,NM_001085463.1,NM_001085464.1,NM_001085465.1,NM_001085466.1,NM_001085467.1,NM_001085468.1,NM_001085469.1,NM_001206883.1,NM_001206884.1,NM_001206885.1,NM_001206886.1,NM_001206887.1,NM_001206888.1,NM_001206889.1,NM_001206890.1,NM_001206891.1,NM_001331.2	180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180,180	0,3,6139	TT,TC,CC		0.024,0.0253,0.0244	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	315/969,315/963,315/934,315/934,315/934,214/868,214/862,214/841,214/839,214/833,214/833,214/833,261/915,261/886,315/940,261/909,261/888,261/880,261/880,214/833,261/880,315/942	57564451	3,12281	1978	4164	6142	SO:0001583	missense	1500	exon6			GACCCTCGTCGGC	AB002382	CCDS44604.1, CCDS44605.1, CCDS44606.1, CCDS44607.1, CCDS44608.1, CCDS44609.1, CCDS53632.1, CCDS53633.1, CCDS53634.1, CCDS55763.1, CCDS55764.1, CCDS55765.1, CCDS55766.1, CCDS55767.1, CCDS73290.1	11q12.1	2013-02-14				ENSG00000198561		"""Armadillo repeat containing"""	2515	protein-coding gene	gene with protein product		601045		CTNND		8808291	Standard	NM_001085460		Approved	KIAA0384, p120, p120cas, p120ctn	uc001nmc.4	O60716		ENST00000399050.4:c.943C>T	11.37:g.57564451C>T	ENSP00000382004:p.Arg315Cys	89.0	0.0	0		96.0	42.0	0.4375	NM_001085461	A8K939|O15088|O60713|O60714|O60715|O60935|Q6DHZ7|Q6RBX8|Q9UP71|Q9UP72|Q9UP73	Missense_Mutation	SNP	ENST00000399050.4	37	CCDS44604.1	.	.	.	.	.	.	.	.	.	.	C	18.67	3.674466	0.67928	2.53E-4	2.4E-4	ENSG00000198561	ENST00000524630;ENST00000529919;ENST00000399039;ENST00000360682;ENST00000361796;ENST00000529526;ENST00000426142;ENST00000399050;ENST00000361391;ENST00000361332;ENST00000532463;ENST00000529986;ENST00000358694;ENST00000532787;ENST00000532649;ENST00000528621;ENST00000530748;ENST00000428599;ENST00000528232;ENST00000529873;ENST00000532844;ENST00000526357;ENST00000530094;ENST00000415361;ENST00000532245;ENST00000534579;ENST00000526938;ENST00000534647	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.73258	-0.36;-0.36;-0.36;-0.73;-0.36;-0.36;-0.27;-0.37;-0.73;-0.37;-0.27;-0.27;-0.36;-0.62;-0.36;-0.36;-0.37;-0.36;-0.28;-0.73;-0.38;-0.37;-0.36;-0.37;-0.27;-0.36;-0.73;2.06	5.82	5.82	0.92795	Armadillo-like helical (1);	0.158729	0.64402	D	0.000018	T	0.79269	0.4417	L	0.43152	1.355	0.53005	D	0.999967	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;P;D;D;D;D;P	0.65010	0.917;0.917;0.828;0.917;0.917;0.931;0.917;0.828	T	0.76556	-0.2916	10	0.39692	T	0.17	-4.6961	19.6883	0.95987	0.0:1.0:0.0:0.0	.	315;315;315;261;261;315;315;315	O60716-3;O60716-2;O60716;O60716-14;O60716-10;O60716-5;F8WA43;C9JZR2	.;.;CTND1_HUMAN;.;.;.;.;.	C	315;315;315;315;315;261;214;315;315;315;214;214;315;214;261;261;261;315;214;261;261;261;214;214;214;261;315;237	ENSP00000436543:R315C;ENSP00000434808:R315C;ENSP00000381996:R315C;ENSP00000353902:R315C;ENSP00000354907:R315C;ENSP00000436323:R261C;ENSP00000409930:R214C;ENSP00000382004:R315C;ENSP00000354785:R315C;ENSP00000354823:R315C;ENSP00000432075:R214C;ENSP00000437156:R214C;ENSP00000351527:R315C;ENSP00000434949:R214C;ENSP00000435379:R261C;ENSP00000432243:R261C;ENSP00000436744:R261C;ENSP00000413586:R315C;ENSP00000435266:R214C;ENSP00000435494:R261C;ENSP00000433276:R261C;ENSP00000433334:R261C;ENSP00000437327:R214C;ENSP00000403518:R214C;ENSP00000434017:R214C;ENSP00000435789:R261C;ENSP00000432041:R315C;ENSP00000434202:R237C	ENSP00000351527:R315C	R	+	1	0	CTNND1	57321027	0.996000	0.38824	1.000000	0.80357	0.974000	0.67602	2.279000	0.43435	2.747000	0.94245	0.655000	0.94253	CGT	.	.	weak		0.527	CTNND1-006	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000393944.1	NM_001331	
ZNF763	284390	hgsc.bcm.edu	37	19	12087921	12087921	+	Silent	SNP	G	G	C	rs376310072	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12087921G>C	ENST00000358987.3	+	2	199	c.72G>C	c.(70-72)tcG>tcC	p.S24S	ZNF763_ENST00000591944.1_Silent_p.S93S|ZNF763_ENST00000545530.1_Intron|ZNF763_ENST00000343949.5_Silent_p.S27S|ZNF763_ENST00000590798.1_Silent_p.S44S|ZNF763_ENST00000592625.1_Silent_p.S24S|ZNF763_ENST00000538752.1_Silent_p.S44S			Q0D2J5	ZN763_HUMAN	zinc finger protein 763	24	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(9)	15						TGGATATTTCGCAGAGGAAAC	0.493													N|||	4	0.000798722	0.0023	0.0	5008	,	,		18630	0.0		0.001	False		,,,				2504	0.0				p.S27S		Atlas-SNP	.											ZNF763,NS,carcinoma,+1,2	ZNF763	31	2	0			c.G81C						scavenged	.						150.0	152.0	151.0					19																	12087921		2203	4300	6503	SO:0001819	synonymous_variant	284390	exon2			TATTTCGCAGAGG	AK092240	CCDS45982.1	19p13.2	2014-02-12	2006-08-14		ENSG00000197054	ENSG00000197054		"""Zinc fingers, C2H2-type"", ""-"""	27614	protein-coding gene	gene with protein product							Standard	NM_001012753		Approved	ZNF440L		Q0D2J5	OTTHUMG00000156430	ENST00000358987.3:c.72G>C	19.37:g.12087921G>C		216.0	0.0	0		256.0	12.0	0.046875	NM_001012753	B3KRU3|B4DRE7	Silent	SNP	ENST00000358987.3	37																																																																																				.	.	alt		0.493	ZNF763-002	KNOWN	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000344158.1	NM_001012753	
GAS2L2	246176	hgsc.bcm.edu	37	17	34072031	34072031	+	Missense_Mutation	SNP	G	G	A	rs56386706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34072031G>A	ENST00000254466.6	-	6	2512	c.2485C>T	c.(2485-2487)Cgg>Tgg	p.R829W	GAS2L2_ENST00000587565.1_Missense_Mutation_p.R813W	NM_139285.3	NP_644814.1	Q8NHY3	GA2L2_HUMAN	growth arrest-specific 2 like 2	829			R -> W (in dbSNP:rs56386706).		cell cycle arrest (GO:0007050)|microtubule bundle formation (GO:0001578)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	actin filament binding (GO:0051015)|cytoskeletal adaptor activity (GO:0008093)|microtubule binding (GO:0008017)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	35		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CCATCCACCCGGGATGCCTCC	0.642													G|||	130	0.0259585	0.0045	0.0375	5008	,	,		17817	0.0		0.0626	False		,,,				2504	0.0358				p.R829W		Atlas-SNP	.											.	GAS2L2	94	.	0			c.C2485T						PASS	.	G	TRP/ARG	56,4350	54.9+/-90.9	0,56,2147	56.0	60.0	59.0		2485	0.3	0.0	17	dbSNP_129	59	471,8129	138.3+/-195.1	9,453,3838	yes	missense	GAS2L2	NM_139285.3	101	9,509,5985	AA,AG,GG		5.4767,1.271,4.052	possibly-damaging	829/881	34072031	527,12479	2203	4300	6503	SO:0001583	missense	246176	exon6			CCACCCGGGATGC	AF508784	CCDS11298.1	17q21	2014-05-06			ENSG00000132139	ENSG00000270765			24846	protein-coding gene	gene with protein product		611398				12584248	Standard	NM_139285		Approved	GAR17	uc002hjv.2	Q8NHY3	OTTHUMG00000188386	ENST00000254466.6:c.2485C>T	17.37:g.34072031G>A	ENSP00000254466:p.Arg829Trp	96.0	0.0	0		104.0	51.0	0.490385	NM_139285	Q8NHY4	Missense_Mutation	SNP	ENST00000254466.6	37	CCDS11298.1	57	0.0260989010989011	5	0.01016260162601626	11	0.03038674033149171	0	0.0	41	0.05408970976253298	G	11.13	1.547655	0.27652	0.01271	0.054767	ENSG00000132139	ENST00000254466;ENST00000359507	T	0.18810	2.19	3.57	0.351	0.16042	.	3.764050	0.01567	N	0.020407	T	0.01287	0.0042	N	0.08118	0	0.09310	N	1	D	0.53885	0.963	B	0.34452	0.183	T	0.14200	-1.0481	10	0.66056	D	0.02	6.0647	4.358	0.11188	0.2131:0.3724:0.4144:0.0	rs56386706	829	Q8NHY3	GA2L2_HUMAN	W	829;243	ENSP00000254466:R829W	ENSP00000254466:R829W	R	-	1	2	GAS2L2	31096144	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.218000	0.17622	0.131000	0.18576	-0.304000	0.09214	CGG	G|0.964;A|0.036	0.036	strong		0.642	GAS2L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256497.1	NM_139285	
ZNF483	158399	hgsc.bcm.edu	37	9	114305075	114305075	+	Silent	SNP	G	G	A	rs142830150		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:114305075G>A	ENST00000309235.5	+	6	2018	c.1860G>A	c.(1858-1860)acG>acA	p.T620T	ZNF483_ENST00000358151.4_Intron	NM_133464.2	NP_597721.2	Q8TF39	ZN483_HUMAN	zinc finger protein 483	620					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(1)|large_intestine(11)|lung(11)|ovary(1)|skin(5)	31						GCCATTTTACGTCTGTGATTT	0.408																																					p.T620T		Atlas-SNP	.											ZNF483,NS,carcinoma,+1,1	ZNF483	78	1	0			c.G1860A						scavenged	.	G	,	1,4405	2.1+/-5.4	0,1,2202	65.0	67.0	66.0		,1860	-5.3	0.1	9	dbSNP_134	66	0,8600		0,0,4300	no	intron,coding-synonymous	ZNF483	NM_001007169.2,NM_133464.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	,620/745	114305075	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	158399	exon6			TTTTACGTCTGTG	AB075842	CCDS35105.1, CCDS35106.1	9q32	2013-01-09			ENSG00000173258	ENSG00000173258		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23384	protein-coding gene	gene with protein product							Standard	NM_001007169		Approved	ZKSCAN16, KIAA1962, ZSCAN48	uc004bff.2	Q8TF39	OTTHUMG00000020490	ENST00000309235.5:c.1860G>A	9.37:g.114305075G>A		103.0	1.0	0.00970874		84.0	5.0	0.0595238	NM_133464	Q5VZN2|Q8NAE1	Silent	SNP	ENST00000309235.5	37	CCDS35106.1																																																																																			G|1.000;A|0.000	0.000	weak		0.408	ZNF483-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053641.1	XM_088567	
LPAR3	23566	hgsc.bcm.edu	37	1	85331462	85331462	+	Silent	SNP	A	A	C	rs41289037	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:85331462A>C	ENST00000440886.1	-	1	380	c.342T>G	c.(340-342)acT>acG	p.T114T	LPAR3_ENST00000491034.1_5'UTR|LPAR3_ENST00000370611.3_Silent_p.T114T			Q9UBY5	LPAR3_HUMAN	lysophosphatidic acid receptor 3	114					activation of MAPK activity (GO:0000187)|bleb assembly (GO:0032060)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of collateral sprouting (GO:0048672)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|synaptic transmission (GO:0007268)	axon (GO:0030424)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|lipid binding (GO:0008289)|lysophosphatidic acid receptor activity (GO:0070915)|phospholipid binding (GO:0005543)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|urinary_tract(1)	24						TGAGGGAAGCAGTCAAGCTAC	0.502													A|||	24	0.00479233	0.0015	0.0086	5008	,	,		18401	0.0		0.0159	False		,,,				2504	0.0				p.T114T		Atlas-SNP	.											.	LPAR3	53	.	0			c.T342G						PASS	.	A		11,4395	19.1+/-41.9	0,11,2192	189.0	195.0	193.0		342	-11.3	0.2	1	dbSNP_127	193	118,8482	62.1+/-124.0	2,114,4184	no	coding-synonymous	LPAR3	NM_012152.2		2,125,6376	CC,CA,AA		1.3721,0.2497,0.9918		114/354	85331462	129,12877	2203	4300	6503	SO:0001819	synonymous_variant	23566	exon2			GGAAGCAGTCAAG	AF127138	CCDS700.1	1p22.3	2012-08-08	2008-04-11	2008-04-11	ENSG00000171517	ENSG00000171517		"""GPCR / Class A : Lysophospholipid receptors : Lysophosphatidic acid"""	14298	protein-coding gene	gene with protein product		605106	"""endothelial differentiation, lysophosphatidic acid G-protein-coupled receptor, 7"""	EDG7		10488122	Standard	NM_012152		Approved	LP-A3, Edg-7, RP4-678I3, HOFNH30, LPA3	uc009wcj.1	Q9UBY5	OTTHUMG00000009925	ENST00000440886.1:c.342T>G	1.37:g.85331462A>C		206.0	0.0	0		170.0	104.0	0.611765	NM_012152	A0AVA3	Silent	SNP	ENST00000440886.1	37	CCDS700.1																																																																																			A|0.991;C|0.009	0.009	strong		0.502	LPAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027467.1	NM_012152	
ATM	472	hgsc.bcm.edu	37	11	108175462	108175462	+	Missense_Mutation	SNP	G	G	A	rs1801516	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108175462G>A	ENST00000452508.2	+	38	5746	c.5557G>A	c.(5557-5559)Gat>Aat	p.D1853N	ATM_ENST00000278616.4_Missense_Mutation_p.D1853N			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1853			D -> N (common polymorphism; dbSNP:rs1801516). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10425038, ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9711876, ECO:0000269|PubMed:9887333}.|D -> V (might contribute to B-cell chronic lymphocytic leukemia; dbSNP:rs1801673). {ECO:0000269|PubMed:10397742, ECO:0000269|PubMed:10817650, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9872980, ECO:0000269|PubMed:9887333}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.D1853N(10)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TTTACTCCAAGATACAAATGA	0.388			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			G|||	335	0.066893	0.0083	0.0965	5008	,	,		16727	0.0159		0.162	False		,,,				2504	0.0798				p.D1853N		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM_ENST00000278616,colon,carcinoma,-1,17	ATM	1657	17	10	Substitution - Missense(10)	breast(9)|skin(1)	c.G5557A	GRCh37	CM077896	ATM	M	rs1801516	PASS	.	G	ASN/ASP	125,4277	92.5+/-131.2	3,119,2079	75.0	72.0	73.0	http://www.ncbi.nlm.nih.gov/pubmed?term	5557	5.5	1.0	11	dbSNP_89	73	1205,7391	241.8+/-272.0	99,1007,3192	yes	missense	ATM	NM_000051.3	23	102,1126,5271	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	14.0181,2.8396,10.2323	possibly-damaging	1853/3057	108175462	1330,11668	2201	4298	6499	SO:0001583	missense	472	exon37	Familial Cancer Database	AT, Louis-Bar syndrome	CTCCAAGATACAA	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.5557G>A	11.37:g.108175462G>A	ENSP00000388058:p.Asp1853Asn	120.0	0.0	0		111.0	54.0	0.486486	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	172	0.07875457875457875	5	0.01016260162601626	40	0.11049723756906077	7	0.012237762237762238	120	0.158311345646438	G	17.18	3.324076	0.60634	0.028396	0.140181	ENSG00000149311	ENST00000278616;ENST00000452508	T;T	0.73152	-0.72;-0.72	5.52	5.52	0.82312	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.00580	0.0019	L	0.61036	1.89	0.19945	P	0.9999491241	B	0.20368	0.044	B	0.16289	0.015	T	0.10730	-1.0617	9	0.33940	T	0.23	.	19.8041	0.96521	0.0:0.0:1.0:0.0	rs1801516;rs17503060;rs52821794;rs60879649;rs1801516	1853	Q13315	ATM_HUMAN	N	1853	ENSP00000278616:D1853N;ENSP00000388058:D1853N	ENSP00000278616:D1853N	D	+	1	0	ATM	107680672	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.342000	0.72982	2.748000	0.94277	0.591000	0.81541	GAT	G|0.910;A|0.090	0.090	strong		0.388	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
GPATCH2	55105	hgsc.bcm.edu	37	1	217793484	217793484	+	Silent	SNP	C	C	T	rs140815718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:217793484C>T	ENST00000366935.3	-	2	524	c.414G>A	c.(412-414)ggG>ggA	p.G138G	GPATCH2_ENST00000366934.3_Silent_p.G138G	NM_018040.2	NP_060510.1	Q9NW75	GPTC2_HUMAN	G patch domain containing 2	138					negative regulation of phosphatase activity (GO:0010923)		nucleic acid binding (GO:0003676)			NS(1)|breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)	35				OV - Ovarian serous cystadenocarcinoma(81;0.0397)|all cancers(67;0.0744)|GBM - Glioblastoma multiforme(131;0.0872)		GAGGTCTTTTCCCTCGAACAT	0.408													C|||	18	0.00359425	0.0008	0.0043	5008	,	,		20562	0.0		0.0139	False		,,,				2504	0.0				p.G138G		Atlas-SNP	.											.	GPATCH2	53	.	0			c.G414A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	131.0	120.0	124.0		414	-5.8	0.7	1	dbSNP_134	124	93,8507	51.1+/-111.2	0,93,4207	no	coding-synonymous	GPATCH2	NM_018040.2		0,98,6405	TT,TC,CC		1.0814,0.1135,0.7535		138/529	217793484	98,12908	2203	4300	6503	SO:0001819	synonymous_variant	55105	exon2			TCTTTTCCCTCGA	AK001114	CCDS1518.1, CCDS73031.1	1q41	2013-01-28		2006-12-13	ENSG00000092978	ENSG00000092978		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""G patch domain containing"""	25499	protein-coding gene	gene with protein product	"""cancer/testis antigen 110"", ""protein phosphatase 1, regulatory subunit 30"""			GPATC2		19432882, 15375528	Standard	XM_005273174		Approved	FLJ10252, CT110, PPP1R30	uc001hlf.1	Q9NW75	OTTHUMG00000000527	ENST00000366935.3:c.414G>A	1.37:g.217793484C>T		94.0	0.0	0		76.0	37.0	0.486842	NM_018040	Q5VYK7|Q5VYK8|Q86YE7	Silent	SNP	ENST00000366935.3	37	CCDS1518.1																																																																																			C|0.994;T|0.006	0.006	strong		0.408	GPATCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001272.1	NM_018040	
NCOA7	135112	hgsc.bcm.edu	37	6	126210797	126210797	+	Missense_Mutation	SNP	G	G	A	rs35223550	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:126210797G>A	ENST00000368357.3	+	10	1949	c.1597G>A	c.(1597-1599)Ggg>Agg	p.G533R	NCOA7_ENST00000392477.2_Missense_Mutation_p.G533R|NCOA7_ENST00000229634.9_Missense_Mutation_p.G418R	NM_001199619.1|NM_001199620.1	NP_001186548.1|NP_001186549.1	Q8NI08	NCOA7_HUMAN	nuclear receptor coactivator 7	533			G -> R (in dbSNP:rs35223550).		positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)			NS(1)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(1)|urinary_tract(2)	39				UCEC - Uterine corpus endometrioid carcinoma (4;0.0803)|GBM - Glioblastoma multiforme(226;0.0193)|all cancers(137;0.237)		GAACAAAGAAGGGCCACAGGT	0.373													G|||	6	0.00119808	0.0008	0.0043	5008	,	,		20188	0.0		0.0	False		,,,				2504	0.002				p.G533R		Atlas-SNP	.											.	NCOA7	92	.	0			c.G1597A						PASS	.	G	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3,4401		0,3,2199	39.0	43.0	42.0		1564,1597,1597,1252,1597	3.7	0.5	6	dbSNP_126	42	50,8540		0,50,4245	yes	missense,missense,missense,missense,missense	NCOA7	NM_001122842.2,NM_001199619.1,NM_001199620.1,NM_001199621.1,NM_181782.4	125,125,125,125,125	0,53,6444	AA,AG,GG		0.5821,0.0681,0.4079	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	522/932,533/943,533/943,418/828,533/943	126210797	53,12941	2202	4295	6497	SO:0001583	missense	135112	exon10			AAAGAAGGGCCAC	AJ420542	CCDS5132.1, CCDS56448.1	6q22.33	2013-03-14			ENSG00000111912	ENSG00000111912			21081	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 4"""	609752				11971969	Standard	NM_001199619		Approved	ERAP140, dJ187J11.3, TLDC4	uc003qai.3	Q8NI08	OTTHUMG00000015513	ENST00000368357.3:c.1597G>A	6.37:g.126210797G>A	ENSP00000357341:p.Gly533Arg	62.0	0.0	0		56.0	32.0	0.571429	NM_001199619	B2RNS2|B7Z2C4|B9EH71|G8JL91|Q3LID6|Q4G0V1|Q5TF95|Q6IPQ4|Q6NE83|Q86T89|Q8N1W4	Missense_Mutation	SNP	ENST00000368357.3	37	CCDS5132.1	4	0.0018315018315018315	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	0	0.0	G	14.31	2.497726	0.44455	6.81E-4	0.005821	ENSG00000111912	ENST00000368357;ENST00000392477;ENST00000229634;ENST00000413085	T;T;T;T	0.37235	1.21;1.21;1.21;1.21	5.52	3.73	0.42828	.	0.382752	0.30277	N	0.009999	T	0.25494	0.0620	N	0.24115	0.695	0.24605	N	0.993753	B;D;D	0.76494	0.002;0.999;0.999	B;D;D	0.69479	0.004;0.964;0.922	T	0.09400	-1.0676	10	0.51188	T	0.08	-0.0117	9.3566	0.38171	0.0756:0.1447:0.7796:0.0	rs35223550	522;522;533	B3KXK4;Q8NI08-2;Q8NI08	.;.;NCOA7_HUMAN	R	533;533;418;331	ENSP00000357341:G533R;ENSP00000376269:G533R;ENSP00000229634:G418R;ENSP00000389186:G331R	ENSP00000229634:G418R	G	+	1	0	NCOA7	126252490	1.000000	0.71417	0.535000	0.28026	0.811000	0.45836	2.682000	0.46934	0.670000	0.31165	0.655000	0.94253	GGG	G|0.996;A|0.004	0.004	strong		0.373	NCOA7-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042083.4	XM_059748	
TTC37	9652	hgsc.bcm.edu	37	5	94834122	94834122	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94834122T>C	ENST00000358746.2	-	33	3813	c.3515A>G	c.(3514-3516)cAa>cGa	p.Q1172R		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	1172						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						ACTGCGGCCTTGGAGTGCATA	0.393																																					p.Q1172R		Atlas-SNP	.											.	TTC37	128	.	0			c.A3515G						PASS	.						208.0	199.0	202.0					5																	94834122		2203	4300	6503	SO:0001583	missense	9652	exon33			CGGCCTTGGAGTG	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.3515A>G	5.37:g.94834122T>C	ENSP00000351596:p.Gln1172Arg	250.0	0.0	0		258.0	146.0	0.565891	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	T	17.09	3.299214	0.60195	.	.	ENSG00000198677	ENST00000358746	T	0.38401	1.14	5.72	5.72	0.89469	Tetratricopeptide-like helical (1);	0.054387	0.85682	D	0.000000	T	0.57140	0.2033	M	0.66939	2.045	0.50467	D	0.99987	D	0.89917	1.0	D	0.74023	0.982	T	0.53019	-0.8497	10	0.26408	T	0.33	.	16.0084	0.80380	0.0:0.0:0.0:1.0	.	1172	Q6PGP7	TTC37_HUMAN	R	1172	ENSP00000351596:Q1172R	ENSP00000351596:Q1172R	Q	-	2	0	TTC37	94859878	1.000000	0.71417	0.946000	0.38457	0.425000	0.31504	5.509000	0.67012	2.180000	0.69256	0.460000	0.39030	CAA	.	.	none		0.393	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
CDC27	996	hgsc.bcm.edu	37	17	45214661	45214661	+	Silent	SNP	G	G	A	rs111322439		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45214661G>A	ENST00000066544.3	-	14	1863	c.1770C>T	c.(1768-1770)ttC>ttT	p.F590F	CDC27_ENST00000446365.2_Silent_p.F529F|CDC27_ENST00000531206.1_Silent_p.F596F|CDC27_ENST00000527547.1_Silent_p.F589F	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	590					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)			NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAGCTCTCTGGAAGAATTTAA	0.383																																					p.F596F		Atlas-SNP	.											CDC27_ENST00000531206,rectum,carcinoma,0,4	CDC27	337	4	0			c.C1788T						scavenged	.						58.0	61.0	60.0					17																	45214661		2203	4300	6503	SO:0001819	synonymous_variant	996	exon14			TCTCTGGAAGAAT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1770C>T	17.37:g.45214661G>A		19.0	1.0	0.0526316		40.0	5.0	0.125	NM_001114091	G3V1C4|Q16349|Q96F35	Silent	SNP	ENST00000066544.3	37	CCDS11509.1																																																																																			G|0.500;A|0.500	0.500	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000458205.2_5'UTR	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.I219V(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TATTCGCTCCATCTTTGGAAA	0.368		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145.0	129.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1.0	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	2203	4300	6503	SO:0001583	missense	4292	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CGCTCCATCTTTG	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	99.0	0.0	0		93.0	55.0	0.591398	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
CD300LB	124599	hgsc.bcm.edu	37	17	72521967	72521967	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72521967T>C	ENST00000392621.1	-	2	405	c.401A>G	c.(400-402)gAt>gGt	p.D134G	CD300LB_ENST00000314401.3_Missense_Mutation_p.D134G	NM_174892.2	NP_777552	A8K4G0	CLM7_HUMAN	CD300 molecule-like family member b	97					cellular response to lipopolysaccharide (GO:0071222)|innate immune response (GO:0045087)|neutrophil mediated immunity (GO:0002446)|positive regulation of mast cell activation (GO:0033005)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|prostate(1)|skin(1)	21						ATCTGCGTCATCTCGCCTGAG	0.512																																					p.D134G		Atlas-SNP	.											.	CD300LB	38	.	0			c.A401G						PASS	.						247.0	222.0	231.0					17																	72521967		2203	4300	6503	SO:0001583	missense	124599	exon2			GCGTCATCTCGCC	AF427618	CCDS11700.1, CCDS11700.2	17q25.1	2013-01-11	2006-03-29		ENSG00000178789	ENSG00000178789		"""Immunoglobulin superfamily / V-set domain containing"""	30811	protein-coding gene	gene with protein product	"""triggering receptor expressed on myeloid cells 5"""	610705	"""CD300 antigen like family member B"""			12975309	Standard	NM_174892		Approved	TREM5, CLM7	uc002jkx.2	A8K4G0	OTTHUMG00000067606	ENST00000392621.1:c.401A>G	17.37:g.72521967T>C	ENSP00000376397:p.Asp134Gly	215.0	0.0	0		210.0	35.0	0.166667	NM_174892	Q1EG73|Q8IX40|Q8N6D1	Missense_Mutation	SNP	ENST00000392621.1	37	CCDS11700.1	.	.	.	.	.	.	.	.	.	.	T	8.070	0.770010	0.15983	.	.	ENSG00000178789	ENST00000392621;ENST00000314401	T	0.04454	3.62	5.17	2.93	0.34026	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	1.155110	0.06495	N	0.735307	T	0.08044	0.0201	L	0.58354	1.805	0.09310	N	1	B;B	0.19935	0.003;0.04	B;B	0.24006	0.015;0.05	T	0.35822	-0.9773	10	0.54805	T	0.06	-16.8791	7.7177	0.28715	0.0:0.1769:0.0:0.8231	.	134;97	B4DQ71;A8K4G0	.;CLM7_HUMAN	G	97;134	ENSP00000317337:D134G	ENSP00000317337:D134G	D	-	2	0	CD300LB	70033562	0.000000	0.05858	0.001000	0.08648	0.005000	0.04900	-0.348000	0.07740	0.900000	0.36469	0.460000	0.39030	GAT	.	.	none		0.512	CD300LB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145082.2	NM_174892	
MGA	23269	hgsc.bcm.edu	37	15	41989091	41989091	+	Missense_Mutation	SNP	C	C	A	rs61736074	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41989091C>A	ENST00000570161.1	+	2	1883	c.1883C>A	c.(1882-1884)cCa>cAa	p.P628Q	MGA_ENST00000566586.1_Missense_Mutation_p.P628Q|MGA_ENST00000389936.4_Missense_Mutation_p.P628Q|MGA_ENST00000545763.1_Missense_Mutation_p.P628Q|MGA_ENST00000219905.7_Missense_Mutation_p.P628Q			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0	Maltase.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GCAGGACGACCACCTAAGAAC	0.448													C|||	30	0.00599042	0.0008	0.0058	5008	,	,		19971	0.0		0.0209	False		,,,				2504	0.0041				p.P628Q		Atlas-SNP	.											.	MGA	264	.	0			c.C1883A						PASS	.	C	GLN/PRO,GLN/PRO	14,3724		0,14,1855	23.0	21.0	21.0		1883,1883	5.2	1.0	15	dbSNP_129	21	154,8048		2,150,3949	yes	missense,missense	MGA	NM_001080541.2,NM_001164273.1	76,76	2,164,5804	AA,AC,CC		1.8776,0.3745,1.407	probably-damaging,probably-damaging	628/2857,628/3066	41989091	168,11772	1869	4101	5970	SO:0001583	missense	23269	exon3			GACGACCACCTAA	AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.1883C>A	15.37:g.41989091C>A	ENSP00000457035:p.Pro628Gln	100.0	0.0	0		134.0	75.0	0.559702	NM_001080541	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000570161.1	37	CCDS55959.1	22	0.010073260073260074	0	0.0	4	0.011049723756906077	0	0.0	18	0.023746701846965697	C	18.09	3.545802	0.65198	0.003745	0.018776	ENSG00000174197	ENST00000219905;ENST00000389936;ENST00000545763	T;T;T	0.47528	0.84;0.84;0.84	5.21	5.21	0.72293	.	2.567660	0.01142	N	0.006237	T	0.44973	0.1319	N	0.24115	0.695	0.31046	N	0.715753	D;D	0.76494	0.999;0.999	D;D	0.77004	0.989;0.973	T	0.51513	-0.8696	10	0.87932	D	0	.	12.162	0.54109	0.0:0.9216:0.0:0.0784	rs61736074	628;628	F5H7K2;E7ENI0	.;.	Q	628	ENSP00000219905:P628Q;ENSP00000374586:P628Q;ENSP00000442467:P628Q	ENSP00000219905:P628Q	P	+	2	0	MGA	39776383	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.086000	0.57664	2.441000	0.82636	0.462000	0.41574	CCA	C|0.987;A|0.013	0.013	strong		0.448	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420229.1	NM_001164273.1	
MAGEC1	9947	hgsc.bcm.edu	37	X	140993885	140993885	+	Missense_Mutation	SNP	C	C	T	rs74847167	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:140993885C>T	ENST00000285879.4	+	4	981	c.695C>T	c.(694-696)cCt>cTt	p.P232L	MAGEC1_ENST00000406005.2_Intron	NM_005462.4	NP_005453.2	O60732	MAGC1_HUMAN	melanoma antigen family C, 1	232								p.P232L(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(22)|lung(60)|ovary(1)|pancreas(1)|prostate(1)|skin(7)|stomach(5)|upper_aerodigestive_tract(7)|urinary_tract(1)	127	Acute lymphoblastic leukemia(192;6.56e-05)					GCCCAGTCTCCTCTCCAGATT	0.488										HNSCC(15;0.026)																											p.P232L		Atlas-SNP	.											.	MAGEC1	317	.	1	Substitution - Missense(1)	skin(1)	c.C695T						PASS	.	C	LEU/PRO	12,3823		0,11,1,1621,570	100.0	96.0	98.0		695		0.1	X	dbSNP_131	98	74,6638		0,69,5,2359,1851	no	missense	MAGEC1	NM_005462.4	98	0,80,6,3980,2421	TT,TC,T,CC,C		1.1025,0.3129,0.8154	benign	232/1143	140993885	86,10461	2203	4284	6487	SO:0001583	missense	9947	exon4			AGTCTCCTCTCCA	AF064589	CCDS35417.1	Xq26	2009-03-18			ENSG00000155495	ENSG00000155495			6812	protein-coding gene	gene with protein product	"""cancer/testis antigen family 7, member 1"""	300223				9485030, 9618514	Standard	NM_005462		Approved	MAGE-C1, CT7, MGC39366, CT7.1	uc004fbt.3	O60732	OTTHUMG00000022569	ENST00000285879.4:c.695C>T	X.37:g.140993885C>T	ENSP00000285879:p.Pro232Leu	822.0	2.0	0.00243309		327.0	215.0	0.657492	NM_005462	A0PK03|O75451|Q8TCV4	Missense_Mutation	SNP	ENST00000285879.4	37	CCDS35417.1	17	0.010247136829415311	0	0.0	5	0.013812154696132596	0	0.0	13	0.017195767195767195	c	5.440	0.266208	0.10294	0.003129	0.011025	ENSG00000155495	ENST00000285879;ENST00000370510	T	0.02216	4.39	.	.	.	.	.	.	.	.	T	0.00637	0.0021	N	0.08118	0	0.23341	N	0.997875	B	0.06786	0.001	B	0.01281	0.0	T	0.47947	-0.9077	8	0.87932	D	0	.	2.6694	0.05063	0.0:0.5025:0.0:0.4974	.	232	O60732	MAGC1_HUMAN	L	232;33	ENSP00000285879:P232L	ENSP00000285879:P232L	P	+	2	0	MAGEC1	140821551	0.002000	0.14202	0.066000	0.19879	0.066000	0.16364	0.991000	0.29654	0.054000	0.16065	0.054000	0.15206	CCT	C|0.989;T|0.011	0.011	strong		0.488	MAGEC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058604.1	NM_005462	
ANO9	338440	hgsc.bcm.edu	37	11	421036	421036	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:421036C>T	ENST00000332826.6	-	17	1483	c.1399G>A	c.(1399-1401)Gcc>Acc	p.A467T		NM_001012302.2	NP_001012302	A1A5B4	ANO9_HUMAN	anoctamin 9	467					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|negative regulation of intracellular calcium activated chloride channel activity (GO:1902939)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(1)|lung(5)|ovary(1)|prostate(4)|skin(4)	21						CAGCCGCTGGCGTGGCACTGC	0.652																																					p.A467T		Atlas-SNP	.											.	ANO9	61	.	0			c.G1399A						PASS	.						24.0	26.0	26.0					11																	421036		2200	4297	6497	SO:0001583	missense	338440	exon17			CGCTGGCGTGGCA	U33271	CCDS31326.1	11p15.5	2014-04-09	2008-08-28	2008-08-28	ENSG00000185101	ENSG00000185101		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	20679	protein-coding gene	gene with protein product			"""tumor protein p53 inducible protein 5"", ""transmembrane protein 16J"""	TP53I5, TMEM16J		9305847, 24692353	Standard	NM_001012302		Approved	PIG5	uc001lpi.2	A1A5B4	OTTHUMG00000165446	ENST00000332826.6:c.1399G>A	11.37:g.421036C>T	ENSP00000332788:p.Ala467Thr	70.0	0.0	0		84.0	43.0	0.511905	NM_001012302	B3KUC4|B4E134|Q8TEN4	Missense_Mutation	SNP	ENST00000332826.6	37	CCDS31326.1	.	.	.	.	.	.	.	.	.	.	C	24.4	4.532417	0.85812	.	.	ENSG00000185101	ENST00000332826	T	0.63255	-0.03	3.99	3.06	0.35304	.	0.419080	0.22997	N	0.053128	T	0.56949	0.2020	L	0.46157	1.445	0.80722	D	1	P;P	0.49961	0.903;0.93	B;B	0.43194	0.215;0.411	T	0.61242	-0.7102	10	0.62326	D	0.03	.	13.5161	0.61541	0.0:0.1658:0.8342:0.0	.	168;467	A1A5B4-2;A1A5B4	.;ANO9_HUMAN	T	467	ENSP00000332788:A467T	ENSP00000332788:A467T	A	-	1	0	ANO9	411036	1.000000	0.71417	0.971000	0.41717	0.933000	0.57130	6.568000	0.73987	0.789000	0.33779	0.306000	0.20318	GCC	.	.	none		0.652	ANO9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384116.1	NM_001012302	
CYP2A6	1548	hgsc.bcm.edu	37	19	41351211	41351211	+	Silent	SNP	G	G	A	rs150586234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41351211G>A	ENST00000301141.5	-	7	1169	c.1149C>T	c.(1147-1149)ttC>ttT	p.F383F	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	383					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TAGGGAGGAAGAAATCCCGAA	0.552													.|||	8	0.00159744	0.0	0.0029	5008	,	,		16324	0.0		0.006	False		,,,				2504	0.0				p.F383F		Atlas-SNP	.											.	CYP2A6	69	.	0			c.C1149T						PASS	.						101.0	99.0	100.0					19																	41351211		2203	4300	6503	SO:0001819	synonymous_variant	1548	exon7			GAGGAAGAAATCC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1149C>T	19.37:g.41351211G>A		213.0	0.0	0		235.0	18.0	0.0765957	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Silent	SNP	ENST00000301141.5	37	CCDS12568.1																																																																																			G|0.998;A|0.002	0.002	strong		0.552	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
SHC1	6464	hgsc.bcm.edu	37	1	154938076	154938076	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154938076G>A	ENST00000368445.5	-	11	1780	c.1566C>T	c.(1564-1566)ctC>ctT	p.L522L	SHC1_ENST00000368450.1_Silent_p.L412L|SHC1_ENST00000606391.1_Silent_p.L323L|SHC1_ENST00000368453.4_Silent_p.L413L|SHC1_ENST00000448116.2_Silent_p.L523L|PYGO2_ENST00000483463.1_5'Flank|SHC1_ENST00000490667.1_Intron|SHC1_ENST00000368449.4_Silent_p.L293L|RP11-307C12.12_ENST00000605085.1_RNA	NM_183001.4	NP_892113.4	P29353	SHC1_HUMAN	SHC (Src homology 2 domain containing) transforming protein 1	522	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				actin cytoskeleton reorganization (GO:0031532)|activation of MAPK activity (GO:0000187)|activation of signaling protein activity involved in unfolded protein response (GO:0006987)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|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)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|Ras protein signal transduction (GO:0007265)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of growth (GO:0040008)|single organismal cell-cell adhesion (GO:0016337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|Shc-EGFR complex (GO:0070435)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|insulin receptor binding (GO:0005158)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phospholipid binding (GO:0005543)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)			breast(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	20	all_epithelial(22;4.9e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GCAAGCCAGTGAGCACATACT	0.607																																					p.L523L	NSCLC(4;32 234 1864 2492 3259 13747 17376)	Atlas-SNP	.											.	SHC1	91	.	0			c.C1569T						PASS	.						110.0	92.0	98.0					1																	154938076		2203	4300	6503	SO:0001819	synonymous_variant	6464	exon11			GCCAGTGAGCACA	U73377	CCDS1076.1, CCDS30881.1, CCDS44233.1, CCDS44234.1	1q21	2013-02-14	2002-01-14		ENSG00000160691	ENSG00000160691		"""SH2 domain containing"""	10840	protein-coding gene	gene with protein product		600560	"""SHC (Src homology 2 domain-containing) transforming protein 1"""	SHC		1623525	Standard	NM_003029		Approved	p66	uc001ffw.3	P29353	OTTHUMG00000037295	ENST00000368445.5:c.1566C>T	1.37:g.154938076G>A		239.0	0.0	0		288.0	37.0	0.128472	NM_001130040	B5BU19|D3DV78|O15290|Q5T180|Q5T183|Q5T184|Q5T185|Q5T186|Q8N4K5|Q96CL1	Silent	SNP	ENST00000368445.5	37	CCDS30881.1	.	.	.	.	.	.	.	.	.	.	G	8.211	0.800408	0.16397	.	.	ENSG00000160691	ENST00000444664	.	.	.	4.76	2.74	0.32292	.	.	.	.	.	T	0.38506	0.1043	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32455	-0.9906	4	.	.	.	.	5.1264	0.14886	0.2088:0.3259:0.4652:0.0	.	.	.	.	Y	186	.	.	H	-	1	0	SHC1	153204700	1.000000	0.71417	0.999000	0.59377	0.998000	0.95712	0.970000	0.29383	1.235000	0.43724	0.557000	0.71058	CAC	.	.	none		0.607	SHC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090781.2	NM_183001	
SLC24A1	9187	hgsc.bcm.edu	37	15	65917220	65917220	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:65917220G>T	ENST00000261892.6	+	2	1089	c.802G>T	c.(802-804)Gtc>Ttc	p.V268F	SLC24A1_ENST00000546330.1_Missense_Mutation_p.V268F|SLC24A1_ENST00000339868.6_Missense_Mutation_p.V268F|SLC24A1_ENST00000544319.2_Missense_Mutation_p.V268F|SLC24A1_ENST00000537259.1_Missense_Mutation_p.V268F|SLC24A1_ENST00000399033.4_Missense_Mutation_p.V268F	NM_001254740.1|NM_004727.2	NP_001241669.1|NP_004718.1	O60721	NCKX1_HUMAN	solute carrier family 24 (sodium/potassium/calcium exchanger), member 1	268					calcium ion transport (GO:0006816)|ion transport (GO:0006811)|phototransduction, visible light (GO:0007603)|response to light intensity (GO:0009642)|rhodopsin mediated signaling pathway (GO:0016056)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|outer membrane (GO:0019867)|plasma membrane (GO:0005886)	calcium, potassium:sodium antiporter activity (GO:0008273)|symporter activity (GO:0015293)			breast(2)|endometrium(7)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23						AGAAGCAAACGTCTTGACTTC	0.473																																					p.V268F		Atlas-SNP	.											.	SLC24A1	58	.	0			c.G802T						PASS	.						102.0	94.0	96.0					15																	65917220		1878	4106	5984	SO:0001583	missense	9187	exon2			GCAAACGTCTTGA	AF062922	CCDS45284.1, CCDS73742.1, CCDS73743.1, CCDS73744.1	15q22.31	2014-01-28			ENSG00000074621	ENSG00000074621		"""Solute carriers"""	10975	protein-coding gene	gene with protein product		603617				9856482	Standard	NM_004727		Approved	NCKX1, NCKX, RODX, KIAA0702, HsT17412, CSNB1D	uc010ujf.2	O60721	OTTHUMG00000167960	ENST00000261892.6:c.802G>T	15.37:g.65917220G>T	ENSP00000261892:p.Val268Phe	156.0	0.0	0		188.0	25.0	0.132979	NM_004727	O43485|O75184|Q17RM9	Missense_Mutation	SNP	ENST00000261892.6	37	CCDS45284.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.441223	0.83993	.	.	ENSG00000074621	ENST00000537259;ENST00000261892;ENST00000339868;ENST00000544319;ENST00000399033;ENST00000546330	T;T;T;T;T;T	0.66280	0.02;-0.2;-0.2;-0.2;-0.17;-0.2	5.19	-0.15	0.13416	.	1.232500	0.05722	N	0.597927	T	0.47893	0.1470	N	0.22421	0.69	0.09310	N	1	P;B;B;D;D	0.56746	0.454;0.325;0.325;0.977;0.961	B;B;B;P;B	0.46049	0.132;0.062;0.062;0.502;0.305	T	0.39143	-0.9628	10	0.66056	D	0.02	.	1.7943	0.03058	0.3931:0.3506:0.0977:0.1586	.	268;268;268;268;268	O60721-2;Q17RM9;O60721;F5H127;B4E1W0	.;.;NCKX1_HUMAN;.;.	F	268	ENSP00000439693:V268F;ENSP00000261892:V268F;ENSP00000341837:V268F;ENSP00000445163:V268F;ENSP00000381991:V268F;ENSP00000439190:V268F	ENSP00000261892:V268F	V	+	1	0	SLC24A1	63704273	0.000000	0.05858	0.001000	0.08648	0.977000	0.68977	0.279000	0.18771	-0.180000	0.10637	-0.302000	0.09304	GTC	.	.	none		0.473	SLC24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397304.1	NM_004727	
PLEKHG2	64857	hgsc.bcm.edu	37	19	39914225	39914225	+	Missense_Mutation	SNP	G	G	C	rs201914405	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39914225G>C	ENST00000409794.3	+	18	3381	c.2531G>C	c.(2530-2532)cGc>cCc	p.R844P	PLEKHG2_ENST00000458508.2_Missense_Mutation_p.R785P|PLEKHG2_ENST00000425673.1_Missense_Mutation_p.R815P|PLEKHG2_ENST00000409797.2_Intron|CTB-60E11.4_ENST00000601124.1_lincRNA|PLEKHG2_ENST00000378550.1_Intron	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	844					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			AATGCCCCGCGCCGCCGGCCT	0.697													G|||	3	0.000599042	0.0	0.0	5008	,	,		13101	0.0		0.001	False		,,,				2504	0.002				p.R844P		Atlas-SNP	.											PLEKHG2_ENST00000458508,colon,carcinoma,0,3	PLEKHG2	329	3	0			c.G2531C						PASS	.	G	PRO/ARG	0,4390		0,0,2195	12.0	13.0	13.0		2531	5.7	1.0	19		13	5,8565		0,5,4280	yes	missense	PLEKHG2	NM_022835.2	103	0,5,6475	CC,CG,GG		0.0583,0.0,0.0386	probably-damaging	844/1387	39914225	5,12955	2195	4285	6480	SO:0001583	missense	64857	exon18			CCCCGCGCCGCCG	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.2531G>C	19.37:g.39914225G>C	ENSP00000386733:p.Arg844Pro	78.0	0.0	0		43.0	23.0	0.534884	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Missense_Mutation	SNP	ENST00000409794.3	37	CCDS33022.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.2|22.2	4.264441|4.264441	0.80358|0.80358	0.0|0.0	5.83E-4|5.83E-4	ENSG00000090924|ENSG00000090924	ENST00000205135|ENST00000409794;ENST00000425673;ENST00000458508	.|T;T;T	.|0.73575	.|-0.62;-0.67;-0.76	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.000000	.|0.48767	.|D	.|0.000180	T|T	0.77864|0.77864	0.4194|0.4194	L|L	0.32530|0.32530	0.975|0.975	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.63880	.|0.993;0.988;0.988	.|P;P;P	.|0.62649	.|0.905;0.806;0.806	T|T	0.75428|0.75428	-0.3321|-0.3321	5|9	.|.	.|.	.|.	.|.	15.3419|15.3419	0.74303|0.74303	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|815;844;785	.|Q9H7P9-3;Q9H7P9;E7ESZ3	.|.;PKHG2_HUMAN;.	P|P	712|844;815;785	.|ENSP00000386733:R844P;ENSP00000392906:R815P;ENSP00000408857:R785P	.|.	A|R	+|+	1|2	0|0	PLEKHG2|PLEKHG2	44606065|44606065	0.911000|0.911000	0.30947|0.30947	1.000000|1.000000	0.80357|0.80357	0.765000|0.765000	0.43378|0.43378	1.287000|1.287000	0.33284|0.33284	2.694000|2.694000	0.91930|0.91930	0.655000|0.655000	0.94253|0.94253	GCC|CGC	.	.	weak		0.697	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
PPP1R14D	54866	hgsc.bcm.edu	37	15	41120675	41120675	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41120675G>C	ENST00000299174.5	-	1	232	c.165C>G	c.(163-165)agC>agG	p.S55R	PPP1R14D_ENST00000427255.2_Missense_Mutation_p.S55R	NM_017726.7	NP_060196.1	Q9NXH3	PP14D_HUMAN	protein phosphatase 1, regulatory (inhibitor) subunit 14D	55					regulation of phosphorylation (GO:0042325)	cytoplasm (GO:0005737)	protein phosphatase inhibitor activity (GO:0004864)			breast(1)|large_intestine(2)|lung(2)|skin(1)	6		all_cancers(109;6.29e-14)|all_epithelial(112;1.48e-11)|Lung NSC(122;5.77e-09)|all_lung(180;1.08e-07)|Melanoma(134;0.091)|Colorectal(260;0.175)|Ovarian(310;0.243)		GBM - Glioblastoma multiforme(113;2.88e-05)|COAD - Colon adenocarcinoma(120;0.153)|BRCA - Breast invasive adenocarcinoma(123;0.166)		CTGTCAGGCGGCTGGGTCTCC	0.597																																					p.S55R		Atlas-SNP	.											.	PPP1R14D	8	.	0			c.C165G						PASS	.						77.0	75.0	76.0					15																	41120675		2203	4300	6503	SO:0001583	missense	54866	exon1			CAGGCGGCTGGGT	AK000258	CCDS10066.1, CCDS45230.1	15q11.2-q14	2012-04-17			ENSG00000166143	ENSG00000166143		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14953	protein-coding gene	gene with protein product	"""gut and brain phosphatase inhibitor 1"", ""PKC-dependent PP1 inhibitory protein"""	613256				11948623	Standard	NM_017726		Approved	CPI17-like, FLJ20251, GBPI-1, MGC119014, MGC119016	uc001zmz.3	Q9NXH3	OTTHUMG00000130064	ENST00000299174.5:c.165C>G	15.37:g.41120675G>C	ENSP00000299174:p.Ser55Arg	143.0	0.0	0		149.0	69.0	0.463087	NM_017726	Q4V773	Missense_Mutation	SNP	ENST00000299174.5	37	CCDS10066.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.682021	0.68042	.	.	ENSG00000166143	ENST00000299174;ENST00000427255	.	.	.	5.82	4.91	0.64330	.	0.067227	0.64402	D	0.000004	T	0.50752	0.1634	N	0.24115	0.695	0.34284	D	0.682531	D;D	0.76494	0.999;0.983	D;P	0.69479	0.964;0.839	T	0.61845	-0.6979	9	0.38643	T	0.18	-11.6822	10.8969	0.47027	0.086:0.0:0.914:0.0	.	55;55	E9PAT1;Q9NXH3	.;PP14D_HUMAN	R	55	.	ENSP00000299174:S55R	S	-	3	2	PPP1R14D	38907967	1.000000	0.71417	1.000000	0.80357	0.910000	0.53928	2.421000	0.44688	1.490000	0.48466	-0.142000	0.14014	AGC	.	.	none		0.597	PPP1R14D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252355.2	NM_017726	
HKDC1	80201	hgsc.bcm.edu	37	10	71026433	71026433	+	Missense_Mutation	SNP	T	T	C	rs148418934	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:71026433T>C	ENST00000354624.5	+	18	2807	c.2674T>C	c.(2674-2676)Tca>Cca	p.S892P	RP11-227H15.5_ENST00000413220.1_RNA	NM_025130.3	NP_079406	Q2TB90	HKDC1_HUMAN	hexokinase domain containing 1	892	Hexokinase type-2 2.				carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)	cytosol (GO:0005829)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|mannokinase activity (GO:0019158)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(11)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	34						ATTCATGCTGTCAGAAGATGG	0.478													T|||	3	0.000599042	0.0	0.0029	5008	,	,		19517	0.0		0.001	False		,,,				2504	0.0				p.S892P		Atlas-SNP	.											.	HKDC1	98	.	0			c.T2674C						PASS	.	T	PRO/SER	2,4404	4.2+/-10.8	0,2,2201	163.0	145.0	151.0		2674	5.0	1.0	10	dbSNP_134	151	16,8584	11.9+/-42.8	0,16,4284	yes	missense	HKDC1	NM_025130.3	74	0,18,6485	CC,CT,TT		0.186,0.0454,0.1384	probably-damaging	892/918	71026433	18,12988	2203	4300	6503	SO:0001583	missense	80201	exon18			ATGCTGTCAGAAG		CCDS7288.1	10q22.1	2006-10-24			ENSG00000156510	ENSG00000156510			23302	protein-coding gene	gene with protein product						12477932	Standard	NM_025130		Approved	FLJ37767, FLJ22761	uc001jpf.4	Q2TB90	OTTHUMG00000018371	ENST00000354624.5:c.2674T>C	10.37:g.71026433T>C	ENSP00000346643:p.Ser892Pro	113.0	0.0	0		128.0	63.0	0.492188	NM_025130	B5MDN9|Q2TB91|Q5VTC7|Q7Z373|Q8WU37|Q96EH2|Q9H5Y9	Missense_Mutation	SNP	ENST00000354624.5	37	CCDS7288.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	T	20.7	4.030350	0.75504	4.54E-4	0.00186	ENSG00000156510	ENST00000354624	D	0.97279	-4.32	4.96	4.96	0.65561	Hexokinase, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98607	0.9534	H	0.97540	4.025	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.96137	0.9097	10	0.87932	D	0	-5.87	15.069	0.72021	0.0:0.0:0.0:1.0	.	892	Q2TB90	HKDC1_HUMAN	P	892	ENSP00000346643:S892P	ENSP00000346643:S892P	S	+	1	0	HKDC1	70696439	1.000000	0.71417	1.000000	0.80357	0.605000	0.37080	7.387000	0.79785	2.206000	0.71126	0.533000	0.62120	TCA	T|0.998;C|0.002	0.002	strong		0.478	HKDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048389.1	NM_025130	
GIGYF1	64599	hgsc.bcm.edu	37	7	100279988	100279988	+	Silent	SNP	G	G	A	rs117477530	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100279988G>A	ENST00000275732.5	-	21	3927	c.2718C>T	c.(2716-2718)tgC>tgT	p.C906C	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	906					insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					GCATCTGCTCGCACCACTGGG	0.672													G|||	6	0.00119808	0.0	0.0058	5008	,	,		15974	0.0		0.002	False		,,,				2504	0.0				p.C906C		Atlas-SNP	.											.	GIGYF1	113	.	0			c.C2718T						PASS	.	G		3,4401		0,3,2199	54.0	46.0	49.0		2718	-2.7	0.9	7	dbSNP_132	49	27,8573		0,27,4273	yes	coding-synonymous	GIGYF1	NM_022574.4		0,30,6472	AA,AG,GG		0.314,0.0681,0.2307		906/1036	100279988	30,12974	2202	4300	6502	SO:0001819	synonymous_variant	64599	exon21			CTGCTCGCACCAC	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.2718C>T	7.37:g.100279988G>A		65.0	0.0	0		64.0	28.0	0.4375	NM_022574	Q6Y7W7|Q8WZ38	Silent	SNP	ENST00000275732.5	37	CCDS34708.1																																																																																			G|0.998;A|0.002	0.002	strong		0.672	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347205.2	NM_022574	
MFSD12	126321	hgsc.bcm.edu	37	19	3546264	3546264	+	Missense_Mutation	SNP	C	C	T	rs34878396	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:3546264C>T	ENST00000355415.2	-	7	1352	c.1183G>A	c.(1183-1185)Ggt>Agt	p.G395S	AC005786.7_ENST00000589360.1_RNA|MFSD12_ENST00000398558.4_Missense_Mutation_p.G395S|MFSD12_ENST00000591878.1_5'Flank|MFSD12_ENST00000389395.3_Missense_Mutation_p.G395S	NM_174983.3	NP_778148.2	Q6NUT3	MFS12_HUMAN	major facilitator superfamily domain containing 12	395			G -> S (in dbSNP:rs34878396).		transport (GO:0006810)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)				cervix(1)|endometrium(2)|lung(4)|urinary_tract(2)	9						GTGTGGGGACCGATGAGGTCG	0.682													C|||	10	0.00199681	0.0	0.0029	5008	,	,		13963	0.0		0.007	False		,,,				2504	0.001				p.G395S		Atlas-SNP	.											.	MFSD12	22	.	0			c.G1183A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	6,4266		0,6,2130	17.0	22.0	20.0		1183,1183,1183	4.6	1.0	19	dbSNP_126	20	58,8420		0,58,4181	no	missense,missense,missense	C19orf28	NM_001042680.1,NM_021731.2,NM_174983.3	56,56,56	0,64,6311	TT,TC,CC		0.6841,0.1404,0.502	possibly-damaging,possibly-damaging,possibly-damaging	395/474,395/539,395/481	3546264	64,12686	2136	4239	6375	SO:0001583	missense	126321	exon7			GGGGACCGATGAG	AF218008	CCDS42465.1, CCDS74256.1	19p13.3	2012-03-09	2011-11-24	2011-11-24	ENSG00000161091	ENSG00000161091			28299	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 28"""	C19orf28		12477932	Standard	NM_174983		Approved	MGC20700, PP3501	uc002lxw.3	Q6NUT3		ENST00000355415.2:c.1183G>A	19.37:g.3546264C>T	ENSP00000347583:p.Gly395Ser	94.0	0.0	0		56.0	31.0	0.553571	NM_001042680	A8MXP7|D6W615|E9PAJ8|Q8N459	Missense_Mutation	SNP	ENST00000355415.2	37	CCDS42465.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	32	5.162522	0.94727	0.001404	0.006841	ENSG00000161091	ENST00000389395;ENST00000398558;ENST00000355415	D;D;D	0.87029	-2.2;-2.2;-2.2	4.63	4.63	0.57726	Major facilitator superfamily domain, general substrate transporter (1);	0.053348	0.64402	D	0.000001	D	0.90466	0.7014	M	0.77616	2.38	0.54753	D	0.999988	D;D;D	0.76494	0.992;0.997;0.999	P;P;D	0.65874	0.889;0.828;0.939	D	0.91435	0.5169	10	0.51188	T	0.08	-25.4799	16.4799	0.84155	0.0:1.0:0.0:0.0	rs34878396	395;386;395	Q6NUT3;Q6NUT3-2;A8MXP7	CS028_HUMAN;.;.	S	395	ENSP00000374046:G395S;ENSP00000381566:G395S;ENSP00000347583:G395S	ENSP00000347583:G395S	G	-	1	0	C19orf28	3497264	1.000000	0.71417	0.999000	0.59377	0.923000	0.55619	7.195000	0.77798	2.126000	0.65437	0.561000	0.74099	GGT	C|0.996;T|0.004	0.004	strong		0.682	MFSD12-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000452949.2	NM_174983	
KLF2	10365	hgsc.bcm.edu	37	19	16436775	16436775	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:16436775G>A	ENST00000248071.5	+	2	931	c.824G>A	c.(823-825)aGc>aAc	p.S275N	KLF2_ENST00000592003.1_Intron|CTD-2562J15.6_ENST00000588799.1_RNA	NM_016270.2	NP_057354.1	Q9Y5W3	KLF2_HUMAN	Kruppel-like factor 2	275					cell morphogenesis (GO:0000902)|cellular response to cycloheximide (GO:0071409)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interleukin-1 (GO:0071347)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to peptide (GO:1901653)|cellular response to tumor necrosis factor (GO:0071356)|erythrocyte maturation (GO:0043249)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|negative regulation of interleukin-6 production (GO:0032715)|positive regulation of protein metabolic process (GO:0051247)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|regulation of gene expression, epigenetic (GO:0040029)|transcription, DNA-templated (GO:0006351)|Type I pneumocyte differentiation (GO:0060509)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			haematopoietic_and_lymphoid_tissue(3)|lung(1)|skin(1)	5						CACACCTGCAGCTACGCGGGC	0.697																																					p.S275N		Atlas-SNP	.											.	KLF2	10	.	0			c.G824A						PASS	.						8.0	5.0	6.0					19																	16436775		2074	4072	6146	SO:0001583	missense	10365	exon2			CCTGCAGCTACGC	AF123344	CCDS12343.1	19p13.11	2013-10-15	2013-10-15		ENSG00000127528	ENSG00000127528		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	6347	protein-coding gene	gene with protein product		602016	"""Kruppel-like factor 2 (lung)"""			10217429, 10458913	Standard	NM_016270		Approved	LKLF	uc002ndw.3	Q9Y5W3	OTTHUMG00000182330	ENST00000248071.5:c.824G>A	19.37:g.16436775G>A	ENSP00000248071:p.Ser275Asn	50.0	0.0	0		39.0	5.0	0.128205	NM_016270	Q6IPC4|Q9UJS5|Q9UKR6	Missense_Mutation	SNP	ENST00000248071.5	37	CCDS12343.1	.	.	.	.	.	.	.	.	.	.	G	12.34	1.908073	0.33721	.	.	ENSG00000127528	ENST00000248071	T	0.08634	3.07	3.44	2.39	0.29439	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13072	0.0317	L	0.58810	1.83	0.80722	D	1	P	0.50943	0.94	P	0.52159	0.691	T	0.11867	-1.0570	9	0.25751	T	0.34	.	6.8756	0.24145	0.1023:0.3171:0.5806:0.0	.	275	Q9Y5W3	KLF2_HUMAN	N	275	ENSP00000248071:S275N	ENSP00000248071:S275N	S	+	2	0	KLF2	16297775	1.000000	0.71417	0.997000	0.53966	0.014000	0.08584	2.573000	0.46007	0.553000	0.29044	-0.384000	0.06662	AGC	.	.	none		0.697	KLF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460562.1		
RHBDL3	162494	hgsc.bcm.edu	37	17	30615883	30615883	+	Silent	SNP	C	C	T	rs150485822	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:30615883C>T	ENST00000269051.4	+	4	381	c.367C>T	c.(367-369)Ctg>Ttg	p.L123L	RHBDL3_ENST00000538145.1_Silent_p.L115L|RHBDL3_ENST00000536287.1_Silent_p.L25L	NM_138328.2	NP_612201.1	P58872	RHBL3_HUMAN	rhomboid, veinlet-like 3 (Drosophila)	123						integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)|skin(1)	16		Breast(31;0.116)|Ovarian(249;0.182)				CAGCAAGGCCCTGCTGGAGGA	0.597																																					p.L123L		Atlas-SNP	.											.	RHBDL3	49	.	0			c.C367T						PASS	.	C		0,4406		0,0,2203	50.0	46.0	47.0		367	4.9	1.0	17	dbSNP_134	47	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	RHBDL3	NM_138328.2		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		123/405	30615883	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	162494	exon4			AAGGCCCTGCTGG	AJ313480	CCDS32613.1	17q11.2	2013-01-10				ENSG00000141314		"""EF-hand domain containing"""	16502	protein-coding gene	gene with protein product			"""rhomboid, veinlet-like 4 (Drosophila)"""	RHBDL4		11900977	Standard	XM_006721733		Approved	VRHO	uc002hhe.1	P58872		ENST00000269051.4:c.367C>T	17.37:g.30615883C>T		210.0	0.0	0		232.0	110.0	0.474138	NM_138328	A6NMH1|Q495Y4|Q495Y5|Q495Y6	Silent	SNP	ENST00000269051.4	37	CCDS32613.1																																																																																			C|1.000;T|0.000	0.000	strong		0.597	RHBDL3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447120.1	NM_138328	
OR5H1	26341	hgsc.bcm.edu	37	3	97852291	97852291	+	Silent	SNP	A	A	G	rs112819024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:97852291A>G	ENST00000354565.2	+	1	750	c.750A>G	c.(748-750)ttA>ttG	p.L250L	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005338.1	NP_001005338.1	A6NKK0	OR5H1_HUMAN	olfactory receptor, family 5, subfamily H, member 1	250						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(7)|kidney(8)|large_intestine(3)|lung(13)|ovary(1)|skin(1)	34						CTGTCTCTTTATACTATGGAC	0.418													A|||	18	0.00359425	0.0008	0.0029	5008	,	,		17560	0.0		0.0099	False		,,,				2504	0.0051				p.L250L		Atlas-SNP	.											OR5H1,NS,carcinoma,+2,1	OR5H1	71	1	0			c.A750G						PASS	.	A		15,4391	22.3+/-47.3	0,15,2188	123.0	133.0	130.0		750	-0.3	0.8	3	dbSNP_132	130	115,8483	60.2+/-122.0	3,109,4187	no	coding-synonymous	OR5H1	NM_001005338.1		3,124,6375	GG,GA,AA		1.3375,0.3404,0.9997		250/314	97852291	130,12874	2203	4299	6502	SO:0001819	synonymous_variant	26341	exon1			CTCTTTATACTAT	X64988	CCDS33797.1	3q12.1	2012-08-09			ENSG00000231192	ENSG00000231192		"""GPCR / Class A : Olfactory receptors"""	8346	protein-coding gene	gene with protein product						1370859	Standard	NM_001005338		Approved	HTPCRX14, HSHTPCRX14	uc011bgt.2	A6NKK0	OTTHUMG00000160070	ENST00000354565.2:c.750A>G	3.37:g.97852291A>G		302.0	0.0	0		346.0	165.0	0.476879	NM_001005338		Silent	SNP	ENST00000354565.2	37	CCDS33797.1																																																																																			A|0.993;G|0.007	0.007	strong		0.418	OR5H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359100.2	NM_001005338	
SH3BP1	23616	hgsc.bcm.edu	37	22	38051493	38051493	+	Silent	SNP	G	G	T	rs117382629	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38051493G>T	ENST00000357436.4	+	18	2221	c.1908G>T	c.(1906-1908)cgG>cgT	p.R636R	Z83844.1_ENST00000456099.1_RNA|SH3BP1_ENST00000599616.1_Intron	NM_018957.3	NP_061830.3	Q9Y3L3	3BP1_HUMAN	SH3-domain binding protein 1	636					signal transduction (GO:0007165)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)			breast(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Melanoma(58;0.0574)					GCCAAAGCCGGCGTTCACCAG	0.711													G|||	40	0.00798722	0.0015	0.0101	5008	,	,		4118	0.0		0.0268	False		,,,				2504	0.0041				p.R636R		Atlas-SNP	.											.	SH3BP1	41	.	0			c.G1908T						PASS	.	G		23,3653		0,23,1815	3.0	4.0	4.0		1908	-1.4	0.5	22	dbSNP_132	4	149,7211		0,149,3531	no	coding-synonymous	SH3BP1	NM_018957.3		0,172,5346	TT,TG,GG		2.0245,0.6257,1.5585		636/702	38051493	172,10864	1838	3680	5518	SO:0001819	synonymous_variant	23616	exon18			AAGCCGGCGTTCA		CCDS13952.2	22q13.1	2011-07-04			ENSG00000100092	ENSG00000100092		"""Rho GTPase activating proteins"""	10824	protein-coding gene	gene with protein product						10591208, 12029088	Standard	NM_018957		Approved	ARHGAP43	uc003ati.3	Q9Y3L3	OTTHUMG00000030996	ENST00000357436.4:c.1908G>T	22.37:g.38051493G>T		58.0	0.0	0		58.0	33.0	0.568965	NM_018957	Q5R3N0|Q6IBZ2|Q6ZVL9|Q96HQ5|Q9NSQ9	Silent	SNP	ENST00000357436.4	37	CCDS13952.2																																																																																			G|0.987;T|0.013	0.013	strong		0.711	SH3BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075884.4	NM_018957	
GRHPR	9380	hgsc.bcm.edu	37	9	37436755	37436755	+	Silent	SNP	G	G	A	rs76299266	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37436755G>A	ENST00000318158.6	+	9	1048	c.963G>A	c.(961-963)ccG>ccA	p.P321P		NM_012203.1	NP_036335.1	Q9UBQ7	GRHPR_HUMAN	glyoxylate reductase/hydroxypyruvate reductase	321					cellular nitrogen compound metabolic process (GO:0034641)|dicarboxylic acid metabolic process (GO:0043648)|excretion (GO:0007588)|glyoxylate metabolic process (GO:0046487)|metabolic process (GO:0008152)|oxidation-reduction process (GO:0055114)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|peroxisomal matrix (GO:0005782)	carboxylic acid binding (GO:0031406)|glycerate dehydrogenase activity (GO:0008465)|glyoxylate reductase (NADP) activity (GO:0030267)|hydroxypyruvate reductase activity (GO:0016618)|NAD binding (GO:0051287)|NADPH binding (GO:0070402)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	12				GBM - Glioblastoma multiforme(29;0.00687)		GAGGGGAGCCGATGCCTAGTG	0.557													G|||	60	0.0119808	0.0272	0.0029	5008	,	,		18599	0.001		0.005	False		,,,				2504	0.0164				p.P321P		Atlas-SNP	.											.	GRHPR	35	.	0			c.G963A						PASS	.	G		103,4303	81.4+/-119.9	2,99,2102	162.0	154.0	157.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	963	-4.3	1.0	9	dbSNP_132	157	45,8555	30.1+/-81.4	0,45,4255	no	coding-synonymous	GRHPR	NM_012203.1		2,144,6357	AA,AG,GG		0.5233,2.3377,1.1379		321/329	37436755	148,12858	2203	4300	6503	SO:0001819	synonymous_variant	9380	exon9			GGAGCCGATGCCT	AF134895	CCDS6609.1	9q12	2012-07-13			ENSG00000137106	ENSG00000137106	1.1.1.79, 1.1.1.81		4570	protein-coding gene	gene with protein product	"""primary hyperoxaluria type 2"""	604296		GLXR		10524214, 10484776	Standard	XM_005251631		Approved	PH2	uc003zzu.1	Q9UBQ7	OTTHUMG00000019914	ENST00000318158.6:c.963G>A	9.37:g.37436755G>A		80.0	0.0	0		91.0	37.0	0.406593	NM_012203	Q5T945|Q9H3E9|Q9H636|Q9UKX1	Silent	SNP	ENST00000318158.6	37	CCDS6609.1																																																																																			G|0.992;A|0.008	0.008	strong		0.557	GRHPR-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052442.1	NM_012203	
PLEK	5341	hgsc.bcm.edu	37	2	68607984	68607984	+	Missense_Mutation	SNP	G	G	T	rs147263237		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:68607984G>T	ENST00000234313.7	+	3	507	c.328G>T	c.(328-330)Gcc>Tcc	p.A110S		NM_002664.2	NP_002655.2	P08567	PLEK_HUMAN	pleckstrin	110					actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cell projection organization (GO:0030030)|cortical actin cytoskeleton organization (GO:0030866)|hematopoietic progenitor cell differentiation (GO:0002244)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of calcium-mediated signaling (GO:0050849)|negative regulation of G-protein coupled receptor protein signaling pathway (GO:0045744)|negative regulation of inositol phosphate biosynthetic process (GO:0010920)|phosphatidylinositol metabolic process (GO:0046488)|phospholipase C-inhibiting G-protein coupled receptor signaling pathway (GO:0030845)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of actin filament bundle assembly (GO:0032233)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of inositol-polyphosphate 5-phosphatase activity (GO:0010925)|positive regulation of integrin activation (GO:0033625)|positive regulation of platelet activation (GO:0010572)|protein kinase C signaling (GO:0070528)|protein secretion by platelet (GO:0070560)|regulation of cell diameter (GO:0060305)|ruffle organization (GO:0031529)|thrombin receptor signaling pathway (GO:0070493)|vesicle docking involved in exocytosis (GO:0006904)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|membrane (GO:0016020)|ruffle membrane (GO:0032587)	phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)	p.A110T(1)		autonomic_ganglia(1)|endometrium(3)|large_intestine(6)|lung(12)|ovary(1)|skin(1)	24		Ovarian(717;0.0129)		STAD - Stomach adenocarcinoma(1183;0.00159)|READ - Rectum adenocarcinoma(193;0.0419)		CCAGAAATTTGCCAGGAAATC	0.478																																					p.A110S		Atlas-SNP	.											PLEK,NS,carcinoma,0,2	PLEK	64	2	1	Substitution - Missense(1)	endometrium(1)	c.G328T						PASS	.	G	SER/ALA	0,4406		0,0,2203	143.0	137.0	139.0		328	2.9	0.9	2	dbSNP_134	139	2,8598	2.2+/-6.3	0,2,4298	yes	missense	PLEK	NM_002664.2	99	0,2,6501	TT,TG,GG		0.0233,0.0,0.0154	benign	110/351	68607984	2,13004	2203	4300	6503	SO:0001583	missense	5341	exon3			AAATTTGCCAGGA	X07743	CCDS1887.1	2p13.3	2013-01-10			ENSG00000115956	ENSG00000115956		"""Pleckstrin homology (PH) domain containing"""	9070	protein-coding gene	gene with protein product		173570				2897630, 12054651	Standard	NM_002664		Approved	P47	uc002sen.4	P08567	OTTHUMG00000129562	ENST00000234313.7:c.328G>T	2.37:g.68607984G>T	ENSP00000234313:p.Ala110Ser	94.0	0.0	0		77.0	24.0	0.311688	NM_002664	B2R9E8|Q53SU8|Q6FGM8|Q6FGQ1|Q8WV81	Missense_Mutation	SNP	ENST00000234313.7	37	CCDS1887.1	.	.	.	.	.	.	.	.	.	.	G	13.27	2.187751	0.38609	0.0	2.33E-4	ENSG00000115956	ENST00000234313	T	0.19806	2.12	5.8	2.87	0.33458	.	0.192484	0.56097	N	0.000035	T	0.16599	0.0399	L	0.31065	0.9	0.53005	D	0.999968	B;B	0.13145	0.007;0.003	B;B	0.12156	0.007;0.004	T	0.03212	-1.1060	10	0.28530	T	0.3	.	15.4457	0.75228	0.0:0.0:0.3642:0.6358	.	128;110	Q59GZ2;P08567	.;PLEK_HUMAN	S	110	ENSP00000234313:A110S	ENSP00000234313:A110S	A	+	1	0	PLEK	68461488	1.000000	0.71417	0.941000	0.38009	0.953000	0.61014	3.637000	0.54324	0.295000	0.22570	-0.274000	0.10170	GCC	G|1.000;T|0.000	0.000	weak		0.478	PLEK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251755.1	NM_002664	
TTN	7273	hgsc.bcm.edu	37	2	179582738	179582738	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179582738C>T	ENST00000591111.1	-	84	24268	c.24044G>A	c.(24043-24045)gGa>gAa	p.G8015E	TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.G8332E|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Missense_Mutation_p.G7088E			Q8WZ42	TITIN_HUMAN	titin	12207	Ig-like 62.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			TGAATACTCTCCCACATCACT	0.418																																					p.G8332E		Atlas-SNP	.											.	TTN	18412	.	0			c.G24995A						PASS	.						209.0	199.0	202.0					2																	179582738		2017	4178	6195	SO:0001583	missense	7273	exon86			TACTCTCCCACAT	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.24044G>A	2.37:g.179582738C>T	ENSP00000465570:p.Gly8015Glu	120.0	0.0	0		152.0	80.0	0.526316	NM_001267550	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	C	12.42	1.934003	0.34096	.	.	ENSG00000155657	ENST00000342992	D	0.86956	-2.19	6.03	6.03	0.97812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.97012	0.9024	H	0.99545	4.62	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	D	0.98008	1.0364	9	0.87932	D	0	.	20.5753	0.99366	0.0:1.0:0.0:0.0	.	8015	Q8WZ42	TITIN_HUMAN	E	7088	ENSP00000343764:G7088E	ENSP00000343764:G7088E	G	-	2	0	TTN	179290983	1.000000	0.71417	1.000000	0.80357	0.866000	0.49608	6.027000	0.70881	2.868000	0.98415	0.557000	0.71058	GGA	.	.	none		0.418	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
AGO1	26523	hgsc.bcm.edu	37	1	36367665	36367665	+	Silent	SNP	C	C	T	rs61751003	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36367665C>T	ENST00000373204.4	+	10	1470	c.1257C>T	c.(1255-1257)ggC>ggT	p.G419G	AGO1_ENST00000373206.1_Silent_p.G344G	NM_012199.2	NP_036331.1	Q9UL18	AGO1_HUMAN	argonaute RISC catalytic component 1	419					epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|gene expression (GO:0010467)|innate immune response (GO:0045087)|negative regulation of translation involved in gene silencing by miRNA (GO:0035278)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|nuclear-transcribed mRNA catabolic process (GO:0000956)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|micro-ribonucleoprotein complex (GO:0035068)|polysome (GO:0005844)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)										TGCAGTACGGCGGCCGGGTGA	0.582													C|||	3	0.000599042	0.0	0.0	5008	,	,		17254	0.0		0.002	False		,,,				2504	0.001				p.G419G		Atlas-SNP	.											.	.	.	.	0			c.C1257T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	50.0	56.0	54.0		1257	2.7	1.0	1	dbSNP_129	54	30,8570	21.6+/-65.8	0,30,4270	no	coding-synonymous	EIF2C1	NM_012199.2		0,32,6471	TT,TC,CC		0.3488,0.0454,0.246		419/858	36367665	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	26523	exon10			GTACGGCGGCCGG	AF093097	CCDS398.1	1p34.3	2013-02-15	2013-02-15	2013-02-15	ENSG00000092847	ENSG00000092847		"""Argonaute/PIWI family"""	3262	protein-coding gene	gene with protein product	"""argonaute 1"""	606228	"""eukaryotic translation initiation factor 2C, 1"""	EIF2C1		10534406, 12906857	Standard	NM_012199		Approved	hAGO1	uc001bzl.3	Q9UL18	OTTHUMG00000007381	ENST00000373204.4:c.1257C>T	1.37:g.36367665C>T		110.0	0.0	0		118.0	75.0	0.635593	NM_012199	Q5TA57|Q6P4S0	Silent	SNP	ENST00000373204.4	37	CCDS398.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	AGO1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019337.3		
ZNF529	57711	hgsc.bcm.edu	37	19	37038584	37038584	+	Silent	SNP	T	T	C	rs183728423	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:37038584T>C	ENST00000591340.1	-	5	1034	c.876A>G	c.(874-876)agA>agG	p.R292R	ZNF529_ENST00000334116.7_Silent_p.R187R	NM_020951.4	NP_066002.3	Q6P280	ZN529_HUMAN	zinc finger protein 529	292					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	Esophageal squamous(110;0.198)					GTGCATGCACTCTAAAGGATT	0.383													T|||	10	0.00199681	0.0	0.0	5008	,	,		20320	0.0		0.007	False		,,,				2504	0.0031				p.R292R		Atlas-SNP	.											.	ZNF529	82	.	0			c.A876G						PASS	.	T	,,	3,4007		0,3,2002	144.0	144.0	144.0		876,822,876	-0.1	0.5	19		144	44,8372		0,44,4164	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF529	NM_001145649.1,NM_001145650.1,NM_020951.4	,,	0,47,6166	CC,CT,TT		0.5228,0.0748,0.3782	,,	292/564,274/546,292/564	37038584	47,12379	2005	4208	6213	SO:0001819	synonymous_variant	57711	exon6			ATGCACTCTAAAG	AK025110	CCDS54256.1	19q13.13	2014-08-22			ENSG00000186020	ENSG00000186020		"""Zinc fingers, C2H2-type"", ""-"""	29328	protein-coding gene	gene with protein product						10997877	Standard	NM_020951		Approved	KIAA1615	uc002oeh.4	Q6P280	OTTHUMG00000180714	ENST00000591340.1:c.876A>G	19.37:g.37038584T>C		162.0	0.0	0		182.0	86.0	0.472527	NM_001145649	K7EKE1|Q9H731|Q9HCF7	Silent	SNP	ENST00000591340.1	37	CCDS54256.1																																																																																			T|0.998;C|0.002	0.002	strong		0.383	ZNF529-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452730.1	NM_020951	
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	3'UTR	SNP	G	G	A	rs1047057	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000369060.4_3'UTR|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000357555.5_Silent_p.L703L|FGFR2_ENST00000356226.4_3'UTR	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.L703L(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86.0	84.0	85.0		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.*259C>T	10.37:g.123239112G>A		86.0	0.0	0		90.0	47.0	0.522222	NM_001144915	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
UBE2O	63893	hgsc.bcm.edu	37	17	74387455	74387455	+	Missense_Mutation	SNP	C	C	T	rs34070229	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74387455C>T	ENST00000319380.7	-	18	3512	c.3448G>A	c.(3448-3450)Gcc>Acc	p.A1150T		NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	1150				A -> T (in Ref. 6; BAB14320). {ECO:0000305}.	positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						TCCAGCAGGGCATGGGTTTCC	0.657													c|||	21	0.00419329	0.0008	0.0043	5008	,	,		14338	0.0		0.0099	False		,,,				2504	0.0072				p.A1150T		Atlas-SNP	.											.	UBE2O	207	.	0			c.G3448A						PASS	.		THR/ALA	9,4395		0,9,2193	32.0	31.0	31.0		3448	3.6	0.6	17	dbSNP_126	31	125,8473		0,125,4174	yes	missense	UBE2O	NM_022066.3	58	0,134,6367	TT,TC,CC		1.4538,0.2044,1.0306	benign	1150/1293	74387455	134,12868	2202	4299	6501	SO:0001583	missense	63893	exon18			GCAGGGCATGGGT	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.3448G>A	17.37:g.74387455C>T	ENSP00000323687:p.Ala1150Thr	69.0	0.0	0		107.0	48.0	0.448598	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Missense_Mutation	SNP	ENST00000319380.7	37	CCDS32742.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	c	11.30	1.597943	0.28445	0.002044	0.014538	ENSG00000175931	ENST00000319380	T	0.72615	-0.67	4.58	3.62	0.41486	Ubiquitin-conjugating enzyme/RWD-like (1);	0.271361	0.30085	N	0.010460	T	0.42381	0.1200	N	0.22421	0.69	0.25600	N	0.986606	B	0.06786	0.001	B	0.04013	0.001	T	0.19614	-1.0300	10	0.14656	T	0.56	-14.1712	7.7518	0.28901	0.161:0.7564:0.0:0.0826	rs34070229	1150	Q9C0C9	UBE2O_HUMAN	T	1150	ENSP00000323687:A1150T	ENSP00000323687:A1150T	A	-	1	0	UBE2O	71899050	0.997000	0.39634	0.648000	0.29521	0.911000	0.54048	2.190000	0.42630	1.146000	0.42352	0.556000	0.70494	GCC	C|0.991;T|0.009	0.009	strong		0.657	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066	
ITM2C	81618	hgsc.bcm.edu	37	2	231742138	231742138	+	Silent	SNP	G	G	A	rs34910213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:231742138G>A	ENST00000326427.6	+	5	711	c.585G>A	c.(583-585)acG>acA	p.T195T	ITM2C_ENST00000326407.6_Silent_p.T158T|ITM2C_ENST00000409704.2_Silent_p.T133T|ITM2C_ENST00000335005.6_Silent_p.T148T	NM_030926.4	NP_112188.1	Q9NQX7	ITM2C_HUMAN	integral membrane protein 2C	195	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				negative regulation of neuron projection development (GO:0010977)|neuron differentiation (GO:0030182)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|beta-amyloid binding (GO:0001540)			cervix(2)|lung(1)|ovary(1)|skin(1)	5		Renal(207;0.0112)|all_lung(227;0.0741)|all_hematologic(139;0.0748)|Acute lymphoblastic leukemia(138;0.167)|Lung NSC(271;0.204)		Epithelial(121;8.47e-12)|all cancers(144;3.44e-09)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		TGCCGCAGACGTACATCATCC	0.607													G|||	23	0.00459265	0.0	0.0072	5008	,	,		18458	0.0		0.0179	False		,,,				2504	0.0				p.T195T		Atlas-SNP	.											.	ITM2C	17	.	0			c.G585A						PASS	.	G	,,	24,4382	29.9+/-59.1	0,24,2179	86.0	79.0	81.0		444,474,585	0.3	1.0	2	dbSNP_126	81	140,8460	69.7+/-132.2	1,138,4161	no	coding-synonymous,coding-synonymous,coding-synonymous	ITM2C	NM_001012514.1,NM_001012516.1,NM_030926.4	,,	1,162,6340	AA,AG,GG		1.6279,0.5447,1.261	,,	148/221,158/231,195/268	231742138	164,12842	2203	4300	6503	SO:0001819	synonymous_variant	81618	exon5			GCAGACGTACATC	AF038953	CCDS2479.1, CCDS33395.1, CCDS33396.1, CCDS74665.1	2q37	2012-10-10			ENSG00000135916	ENSG00000135916		"""BRICHOS domain containing"""	6175	protein-coding gene	gene with protein product	"""BRICHOS domain containing 2C"""	609554				9653160	Standard	NM_030926		Approved	BRI3, E25, hRPC.1050_D_4, ITM3, BRICD2C	uc002vqz.3	Q9NQX7	OTTHUMG00000133219	ENST00000326427.6:c.585G>A	2.37:g.231742138G>A		164.0	0.0	0		181.0	84.0	0.464088	NM_030926	B3KPG4|Q4G0A8|Q53H84|Q6IAE7|Q86VK5|Q8N288|Q8TAW0|Q9BUP8	Silent	SNP	ENST00000326427.6	37	CCDS2479.1																																																																																			G|0.988;A|0.012	0.012	strong		0.607	ITM2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256954.2	NM_030926	
CYLD	1540	hgsc.bcm.edu	37	16	50810149	50810149	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50810149G>A	ENST00000427738.3	+	6	1187	c.982G>A	c.(982-984)Gac>Aac	p.D328N	CYLD_ENST00000566206.1_Missense_Mutation_p.D325N|CYLD_ENST00000569418.1_Missense_Mutation_p.D325N|CYLD_ENST00000311559.9_Missense_Mutation_p.D328N|CYLD_ENST00000398568.2_Missense_Mutation_p.D325N|CYLD_ENST00000540145.1_Missense_Mutation_p.D328N|CYLD_ENST00000568704.2_Missense_Mutation_p.D325N|CYLD_ENST00000564326.1_Missense_Mutation_p.D325N			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	328	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				AGGTGTTGGGGACAAAGGTTC	0.388			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.D328N		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.G982A						PASS	.						102.0	102.0	102.0					16																	50810149		1861	4094	5955	SO:0001583	missense	1540	exon8	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	GTTGGGGACAAAG	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.982G>A	16.37:g.50810149G>A	ENSP00000392025:p.Asp328Asn	97.0	0.0	0		104.0	13.0	0.125	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	22.5	4.299579	0.81136	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.19669	2.13;2.13;2.13	6.17	6.17	0.99709	.	0.151321	0.64402	D	0.000010	T	0.17365	0.0417	N	0.14661	0.345	0.49582	D	0.999803	B;B;B;B	0.12013	0.003;0.005;0.005;0.003	B;B;B;B	0.11329	0.003;0.006;0.006;0.003	T	0.05937	-1.0855	10	0.48119	T	0.1	-20.1557	20.8794	0.99867	0.0:0.0:1.0:0.0	.	325;328;325;328	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	N	328;328;325;325	ENSP00000445447:D328N;ENSP00000308928:D328N;ENSP00000381574:D325N	ENSP00000308928:D328N	D	+	1	0	CYLD	49367650	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.760000	0.74939	2.941000	0.99782	0.655000	0.94253	GAC	.	.	none		0.388	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
PCDHGA8	9708	hgsc.bcm.edu	37	5	140774505	140774505	+	Missense_Mutation	SNP	G	G	T	rs367656720		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140774505G>T	ENST00000398604.2	+	1	2125	c.2125G>T	c.(2125-2127)Gct>Tct	p.A709S	PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	709					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCCTTTGTCGCTGTGCTTCT	0.602																																					p.A709S		Atlas-SNP	.											.	PCDHGA8	146	.	0			c.G2125T						PASS	.	G	,SER/ALA,,,,,,,,,,,SER/ALA	0,4378		0,0,2189	35.0	40.0	38.0		,2125,,,,,,,,,,,2125	0.6	0.0	5		38	1,8587		0,1,4293	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense	PCDHGB4,PCDHGA8,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_014004.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_032088.1	,99,,,,,,,,,,,99	0,1,6482	TT,TG,GG		0.0116,0.0,0.0077	,,,,,,,,,,,,	,709/821,,,,,,,,,,,709/933	140774505	1,12965	2189	4294	6483	SO:0001583	missense	9708	exon1			TTTGTCGCTGTGC	AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.2125G>T	5.37:g.140774505G>T	ENSP00000381605:p.Ala709Ser	141.0	0.0	0		130.0	89.0	0.684615	NM_014004	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	6.375	0.437282	0.12104	0.0	1.16E-4	ENSG00000253767	ENST00000398604	T	0.14266	2.52	4.5	0.627	0.17675	.	0.671943	0.11133	U	0.596072	T	0.07908	0.0198	N	0.14661	0.345	0.09310	N	1	B;B	0.22851	0.024;0.076	B;B	0.26310	0.032;0.068	T	0.36383	-0.9750	10	0.87932	D	0	.	4.7807	0.13201	0.4634:0.3303:0.2063:0.0	.	709;709	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	S	709	ENSP00000381605:A709S	ENSP00000381605:A709S	A	+	1	0	PCDHGA8	140754689	0.000000	0.05858	0.008000	0.14137	0.021000	0.10359	-0.022000	0.12480	-0.041000	0.13558	-0.910000	0.02820	GCT	.	.	weak		0.602	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1	NM_032088	
RAI1	10743	hgsc.bcm.edu	37	17	17698023	17698023	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17698023C>T	ENST00000353383.1	+	3	2230	c.1761C>T	c.(1759-1761)ttC>ttT	p.F587F	RAI1_ENST00000261641.6_Silent_p.F587F	NM_030665.3	NP_109590.3	Q7Z5J4	RAI1_HUMAN	retinoic acid induced 1	587					circadian regulation of gene expression (GO:0032922)|negative regulation of multicellular organism growth (GO:0040015)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enhancer binding (GO:0035326)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(14)|ovary(1)|prostate(1)|skin(5)|urinary_tract(7)	48				READ - Rectum adenocarcinoma(1115;0.0276)		TCTCCAAGTTCGTGGCGGGTG	0.632																																					p.F587F		Atlas-SNP	.											.	RAI1	121	.	0			c.C1761T						PASS	.						68.0	70.0	69.0					17																	17698023		2201	4293	6494	SO:0001819	synonymous_variant	10743	exon3			CAAGTTCGTGGCG	AJ230819	CCDS11188.1	17p11.2	2011-02-08			ENSG00000108557	ENSG00000108557			9834	protein-coding gene	gene with protein product		607642	"""Smith-Magenis syndrome chromosome region"""	SMCR		10036180	Standard	NM_030665		Approved	DKFZP434A139, SMS, KIAA1820, MGC12824	uc002grm.3	Q7Z5J4	OTTHUMG00000059314	ENST00000353383.1:c.1761C>T	17.37:g.17698023C>T		70.0	0.0	0		50.0	25.0	0.5	NM_030665	Q8N3B4|Q8ND08|Q8WU64|Q96JK5|Q9H1C1|Q9H1C2|Q9UF69	Silent	SNP	ENST00000353383.1	37	CCDS11188.1																																																																																			.	.	none		0.632	RAI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131775.1	NM_030665	
CLCNKB	1188	hgsc.bcm.edu	37	1	16382243	16382243	+	Missense_Mutation	SNP	C	C	A	rs375375144		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:16382243C>A	ENST00000375679.4	+	18	2030	c.1919C>A	c.(1918-1920)tCc>tAc	p.S640Y	CLCNKB_ENST00000375667.3_Missense_Mutation_p.S470Y|FAM131C_ENST00000494078.1_5'Flank	NM_000085.4	NP_000076.2	P51801	CLCKB_HUMAN	chloride channel, voltage-sensitive Kb	640	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(2)|prostate(1)|skin(6)|stomach(2)|urinary_tract(1)	21		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)		CCAGAGACTTCCCTGCATGAG	0.617											OREG0013133	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.S640Y		Atlas-SNP	.											.	CLCNKB	50	.	0			c.C1919A						PASS	.	C	TYR/SER,TYR/SER	0,4406		0,0,2203	70.0	68.0	68.0		1919,1412	4.7	1.0	1		68	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	CLCNKB	NM_000085.3,NM_001165945.1	144,144	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	640/688,471/519	16382243	1,13005	2203	4300	6503	SO:0001583	missense	1188	exon18			AGACTTCCCTGCA	AK098217	CCDS168.1, CCDS57974.1	1p36	2012-09-26	2012-02-23		ENSG00000184908	ENSG00000184908		"""Ion channels / Chloride channels : Voltage-sensitive"""	2027	protein-coding gene	gene with protein product		602023	"""chloride channel Kb"""				Standard	NM_000085		Approved	hClC-Kb		P51801	OTTHUMG00000009530	ENST00000375679.4:c.1919C>A	1.37:g.16382243C>A	ENSP00000364831:p.Ser640Tyr	170.0	0.0	0	709	135.0	54.0	0.4	NM_000085	B3KUY3|Q5T5Q7|Q5T5Q8	Missense_Mutation	SNP	ENST00000375679.4	37	CCDS168.1	.	.	.	.	.	.	.	.	.	.	c	19.03	3.747160	0.69418	0.0	1.16E-4	ENSG00000184908	ENST00000375668;ENST00000375679;ENST00000375667;ENST00000431772	D;D;D	0.95035	-3.59;-3.59;-2.62	4.7	4.7	0.59300	Cystathionine beta-synthase, core (3);	0.067228	0.64402	D	0.000011	D	0.96191	0.8758	M	0.90198	3.095	0.80722	D	1	B;B	0.27380	0.177;0.078	B;B	0.39503	0.301;0.135	D	0.96375	0.9277	10	0.72032	D	0.01	.	15.1589	0.72764	0.0:1.0:0.0:0.0	.	470;640	Q5T5Q7;P51801	.;CLCKB_HUMAN	Y	137;640;470;128	ENSP00000364831:S640Y;ENSP00000364819:S470Y;ENSP00000389344:S128Y	ENSP00000364819:S470Y	S	+	2	0	CLCNKB	16254830	0.957000	0.32711	0.995000	0.50966	0.702000	0.40608	4.220000	0.58567	2.322000	0.78497	0.555000	0.69702	TCC	.	.	none		0.617	CLCNKB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026331.1	NM_000085	
SFTPB	6439	hgsc.bcm.edu	37	2	85893842	85893842	+	Silent	SNP	C	C	T	rs34682912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85893842C>T	ENST00000519937.2	-	4	310	c.291G>A	c.(289-291)gaG>gaA	p.E97E	SFTPB_ENST00000342375.3_Silent_p.E97E|SFTPB_ENST00000409383.1_Silent_p.E109E|SFTPB_ENST00000393822.3_Silent_p.E109E			P07988	PSPB_HUMAN	surfactant protein B	97	Saposin B-type 1. {ECO:0000255|PROSITE- ProRule:PRU00415}.				organ morphogenesis (GO:0009887)|respiratory gaseous exchange (GO:0007585)|sphingolipid metabolic process (GO:0006665)	extracellular region (GO:0005576)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)	16						TGCACTCCTGCTCCAGGAACT	0.612													C|||	14	0.00279553	0.0	0.0014	5008	,	,		18379	0.0		0.001	False		,,,				2504	0.0123				p.E109E		Atlas-SNP	.											.	SFTPB	49	.	0			c.G327A						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	163.0	144.0	151.0		327,327	-2.2	0.2	2	dbSNP_126	151	26,8574	19.2+/-60.6	0,26,4274	no	coding-synonymous,coding-synonymous	SFTPB	NM_000542.3,NM_198843.2	,	0,27,6476	TT,TC,CC		0.3023,0.0227,0.2076	,	109/394,109/394	85893842	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	6439	exon5			CTCCTGCTCCAGG	J02761	CCDS1983.1, CCDS1983.2	2p12-p11.2	2008-08-26	2008-08-26		ENSG00000168878	ENSG00000168878			10801	protein-coding gene	gene with protein product		178640	"""surfactant, pulmonary-associated protein B"""	SFTP3		2924687, 1346779	Standard	NM_198843		Approved	SP-B	uc002sqh.3	P07988	OTTHUMG00000130181	ENST00000519937.2:c.291G>A	2.37:g.85893842C>T		77.0	0.0	0		83.0	38.0	0.457831	NM_198843	Q96R04	Silent	SNP	ENST00000519937.2	37		.	.	.	.	.	.	.	.	.	.	C	0.073	-1.197902	0.01594	2.27E-4	0.003023	ENSG00000168878	ENST00000428225	.	.	.	4.47	-2.19	0.07015	.	.	.	.	.	T	0.47930	0.1472	.	.	.	0.35445	D	0.795177	.	.	.	.	.	.	T	0.52003	-0.8633	4	.	.	.	-12.307	9.1563	0.36994	0.0:0.3994:0.0:0.6006	rs34682912	.	.	.	T	94	.	.	A	-	1	0	SFTPB	85747353	0.023000	0.18921	0.170000	0.22879	0.066000	0.16364	-0.258000	0.08733	-0.589000	0.05874	-0.291000	0.09656	GCA	C|0.997;T|0.003	0.003	strong		0.612	SFTPB-001	KNOWN	alternative_3_UTR|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000252499.3	NM_198843	
AGTPBP1	23287	hgsc.bcm.edu	37	9	88248239	88248239	+	Silent	SNP	T	T	C	rs144890878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:88248239T>C	ENST00000357081.3	-	14	1497	c.1353A>G	c.(1351-1353)aaA>aaG	p.K451K	AGTPBP1_ENST00000337006.4_3'UTR|AGTPBP1_ENST00000432218.1_Silent_p.K289K|AGTPBP1_ENST00000376083.3_Silent_p.K411K|AGTPBP1_ENST00000376109.3_Silent_p.K463K			Q9UPW5	CBPC1_HUMAN	ATP/GTP binding protein 1	451					adult walking behavior (GO:0007628)|C-terminal protein deglutamylation (GO:0035609)|cerebellar Purkinje cell differentiation (GO:0021702)|eye photoreceptor cell differentiation (GO:0001754)|mitochondrion organization (GO:0007005)|neuromuscular process (GO:0050905)|neurotransmitter metabolic process (GO:0042133)|olfactory bulb development (GO:0021772)|protein side chain deglutamylation (GO:0035610)|retina development in camera-type eye (GO:0060041)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	metallocarboxypeptidase activity (GO:0004181)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(12)|lung(12)|ovary(5)|skin(2)|urinary_tract(3)	44						GACCACGTACTTTTCCCTCAA	0.328													T|||	31	0.0061901	0.0015	0.0043	5008	,	,		17053	0.0		0.008	False		,,,				2504	0.0184				p.K411K		Atlas-SNP	.											.	AGTPBP1	128	.	0			c.A1233G						PASS	.	T		5,4387		0,5,2191	56.0	60.0	58.0		1233	-3.0	0.0	9	dbSNP_134	58	42,8514		0,42,4236	no	coding-synonymous	AGTPBP1	NM_015239.2		0,47,6427	CC,CT,TT		0.4909,0.1138,0.363		411/1187	88248239	47,12901	2196	4278	6474	SO:0001819	synonymous_variant	23287	exon14			ACGTACTTTTCCC	AB028958	CCDS6672.1, CCDS75854.1	9q21.33	2014-06-23			ENSG00000135049	ENSG00000135049			17258	protein-coding gene	gene with protein product	"""cytosolic carboxypeptidase 1"", ""tubulinyl-Tyr carboxypeptidase"", ""carboxypeptidase-tubulin"", ""tyrosine carboxypeptidase"", ""soluble carboxypeptidase"""	606830				11083920	Standard	NM_015239		Approved	KIAA1035, Nna1, CCP1	uc010mqc.3	Q9UPW5	OTTHUMG00000020124	ENST00000357081.3:c.1353A>G	9.37:g.88248239T>C		154.0	0.0	0		133.0	57.0	0.428571	NM_015239	B4DIT6|B4DRZ8|Q5VV80|Q63HM7|Q658P5|Q6P9D6|Q9H8U6|Q9H9W8|Q9NVK1	Silent	SNP	ENST00000357081.3	37																																																																																				T|0.994;C|0.006	0.006	strong		0.328	AGTPBP1-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000052893.1	NM_015239	
SLITRK4	139065	hgsc.bcm.edu	37	X	142718181	142718181	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:142718181T>C	ENST00000381779.4	-	2	969	c.744A>G	c.(742-744)ttA>ttG	p.L248L	SLITRK4_ENST00000356928.1_Silent_p.L248L|SLITRK4_ENST00000338017.4_Silent_p.L248L	NM_001184749.2|NM_001184750.1|NM_173078.4	NP_001171678.1|NP_001171679.1|NP_775101.1	Q8IW52	SLIK4_HUMAN	SLIT and NTRK-like family, member 4	248	LRRCT 1.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(6)|kidney(2)|large_intestine(11)|lung(27)|ovary(2)|pancreas(2)|prostate(4)|skin(2)|upper_aerodigestive_tract(2)	60	Acute lymphoblastic leukemia(192;6.56e-05)					GCCTTCCATATAAGTCACTGG	0.443																																					p.L248L		Atlas-SNP	.											.	SLITRK4	162	.	0			c.A744G						PASS	.						66.0	61.0	63.0					X																	142718181		2203	4300	6503	SO:0001819	synonymous_variant	139065	exon2			TCCATATAAGTCA	BC040986	CCDS14679.1	Xq27.3	2004-06-23			ENSG00000179542	ENSG00000179542			23502	protein-coding gene	gene with protein product		300562				14557068	Standard	NM_001184749		Approved	DKFZp547M2010	uc004fby.3	Q8IW52	OTTHUMG00000022580	ENST00000381779.4:c.744A>G	X.37:g.142718181T>C		214.0	0.0	0		94.0	93.0	0.989362	NM_001184750	Q5JXG3|Q8TCM8|Q96DL3	Silent	SNP	ENST00000381779.4	37	CCDS14679.1																																																																																			.	.	none		0.443	SLITRK4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058617.1	NM_173078	
NLGN2	57555	hgsc.bcm.edu	37	17	7319124	7319124	+	Silent	SNP	C	C	T	rs145633225		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7319124C>T	ENST00000302926.2	+	6	1405	c.1332C>T	c.(1330-1332)ggC>ggT	p.G444G	NLGN2_ENST00000575301.1_Silent_p.G444G	NM_020795.2	NP_065846.1	Q8NFZ4	NLGN2_HUMAN	neuroligin 2	444					cell-cell junction maintenance (GO:0045217)|gephyrin clustering (GO:0097116)|locomotory exploration behavior (GO:0035641)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synaptic transmission, GABAergic (GO:0032230)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|protein localization to synapse (GO:0035418)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of respiratory gaseous exchange by neurological system process (GO:0002087)|regulation of synaptic transmission (GO:0050804)|sensory perception of pain (GO:0019233)|single organismal cell-cell adhesion (GO:0016337)|synapse assembly (GO:0007416)|synapse organization (GO:0050808)|terminal button organization (GO:0072553)	cell junction (GO:0030054)|cell surface (GO:0009986)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|neurexin family protein binding (GO:0042043)|receptor activity (GO:0004872)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(7)|prostate(2)|skin(3)	22		Prostate(122;0.157)				GGGACAATGGCGAAATGCGCC	0.582													C|||	1	0.000199681	0.0	0.0	5008	,	,		18788	0.0		0.001	False		,,,				2504	0.0				p.G444G		Atlas-SNP	.											.	NLGN2	61	.	0			c.C1332T						PASS	.	C		0,4406		0,0,2203	85.0	82.0	83.0		1332	-0.8	1.0	17	dbSNP_134	83	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	NLGN2	NM_020795.2		0,14,6489	TT,TC,CC		0.1628,0.0,0.1076		444/836	7319124	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	57555	exon6			CAATGGCGAAATG	AB037787	CCDS11103.1	17p13.2	2008-07-18			ENSG00000169992	ENSG00000169992			14290	protein-coding gene	gene with protein product		606479				10767552, 10819331	Standard	NM_020795		Approved	KIAA1366	uc002ggt.1	Q8NFZ4	OTTHUMG00000108138	ENST00000302926.2:c.1332C>T	17.37:g.7319124C>T		60.0	0.0	0		85.0	49.0	0.576471	NM_020795	Q9P2I1	Silent	SNP	ENST00000302926.2	37	CCDS11103.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	NLGN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226941.2	NM_020795	
SOS2	6655	hgsc.bcm.edu	37	14	50626657	50626657	+	Silent	SNP	C	C	T	rs35530861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:50626657C>T	ENST00000216373.5	-	10	1618	c.1344G>A	c.(1342-1344)ttG>ttA	p.L448L	SOS2_ENST00000543680.1_Silent_p.L415L|SOS2_ENST00000555794.1_5'UTR	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	448	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					CGATTCTTGTCAATGGTCCCT	0.383													C|||	6	0.00119808	0.0	0.0014	5008	,	,		19647	0.0		0.005	False		,,,				2504	0.0				p.L448L		Atlas-SNP	.											.	SOS2	195	.	0			c.G1344A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	197.0	185.0	189.0		1344	3.7	1.0	14	dbSNP_126	189	41,8559	27.9+/-77.7	0,41,4259	no	coding-synonymous	SOS2	NM_006939.2		0,43,6460	TT,TC,CC		0.4767,0.0454,0.3306		448/1333	50626657	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	6655	exon10			TCTTGTCAATGGT	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.1344G>A	14.37:g.50626657C>T		272.0	0.0	0		281.0	140.0	0.498221	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Silent	SNP	ENST00000216373.5	37	CCDS9697.1																																																																																			C|0.997;T|0.003	0.003	strong		0.383	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
C2orf78	388960	hgsc.bcm.edu	37	2	74043857	74043857	+	Missense_Mutation	SNP	G	G	A	rs539780072		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74043857G>A	ENST00000409561.1	+	3	2628	c.2507G>A	c.(2506-2508)cGg>cAg	p.R836Q		NM_001080474.1	NP_001073943.1	A6NCI8	CB078_HUMAN	chromosome 2 open reading frame 78	836								p.R806Q(1)		cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(21)|ovary(2)|prostate(2)|soft_tissue(1)|urinary_tract(1)	34						ACCAGTCTCCGGTCACTGCCC	0.512													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19547	0.0		0.0	False		,,,				2504	0.0				p.R836Q		Atlas-SNP	.											C2orf78,striated_muscle,rhabdoid_tumour,0,1	C2orf78	150	1	1	Substitution - Missense(1)	soft_tissue(1)	c.G2507A						scavenged	.						95.0	91.0	93.0					2																	74043857		1940	4145	6085	SO:0001583	missense	388960	exon3			GTCTCCGGTCACT	AC092653, AC136006, AK125975	CCDS46338.1	2p13.2	2008-07-18			ENSG00000187833	ENSG00000187833			34349	protein-coding gene	gene with protein product							Standard	NM_001080474		Approved	FLJ43987, hCG1989538, COG5373	uc002sjr.1	A6NCI8	OTTHUMG00000152819	ENST00000409561.1:c.2507G>A	2.37:g.74043857G>A	ENSP00000387124:p.Arg836Gln	124.0	1.0	0.00806452		127.0	16.0	0.125984	NM_001080474		Missense_Mutation	SNP	ENST00000409561.1	37	CCDS46338.1	.	.	.	.	.	.	.	.	.	.	G	1.645	-0.515425	0.04200	.	.	ENSG00000187833	ENST00000409561;ENST00000342345	T	0.40225	1.04	5.35	-3.06	0.05379	.	1.732830	0.04010	N	0.297965	T	0.08670	0.0215	N	0.00119	-2.075	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15867	-1.0422	10	0.14252	T	0.57	-2.5945	3.6028	0.08031	0.3735:0.0:0.3371:0.2893	.	836	A6NCI8	CB078_HUMAN	Q	836;806	ENSP00000387124:R836Q	ENSP00000340692:R806Q	R	+	2	0	C2orf78	73897365	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.105000	0.15333	-0.429000	0.07329	-1.440000	0.01072	CGG	.	.	none		0.512	C2orf78-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000328083.1	NM_001080474	
AXIN2	8313	hgsc.bcm.edu	37	17	63532528	63532528	+	Missense_Mutation	SNP	G	G	A	rs138287857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:63532528G>A	ENST00000375702.5	-	6	1964	c.1856C>T	c.(1855-1857)gCg>gTg	p.A619V	AXIN2_ENST00000307078.5_Missense_Mutation_p.A684V			Q9Y2T1	AXIN2_HUMAN	axin 2	668				Missing (in Ref. 2; AAF22799). {ECO:0000305}.	bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to organic cyclic compound (GO:0071407)|chondrocyte differentiation involved in endochondral bone morphogenesis (GO:0003413)|dorsal/ventral axis specification (GO:0009950)|intramembranous ossification (GO:0001957)|maintenance of DNA repeat elements (GO:0043570)|mRNA stabilization (GO:0048255)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of cell proliferation (GO:0008285)|negative regulation of osteoblast differentiation (GO:0045668)|odontogenesis (GO:0042476)|positive regulation of cell death (GO:0010942)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein phosphorylation (GO:0001934)|regulation of centromeric sister chromatid cohesion (GO:0070602)|regulation of chondrocyte development (GO:0061181)|regulation of mismatch repair (GO:0032423)|secondary heart field specification (GO:0003139)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|Wnt signaling pathway involved in somitogenesis (GO:0090244)	beta-catenin destruction complex (GO:0030877)|cell cortex (GO:0005938)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytoplasmic microtubule (GO:0005881)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|enzyme binding (GO:0019899)|GTPase activator activity (GO:0005096)|protein kinase binding (GO:0019901)|ubiquitin protein ligase binding (GO:0031625)			NS(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	34						GGGAGGCATCGCAGGGTCCTG	0.687									Oligodontia, Ectodermal Dysplasia and Colorectal Polyp syndrome				G|||	2	0.000399361	0.0	0.0	5008	,	,		15448	0.0		0.002	False		,,,				2504	0.0				p.A684V		Atlas-SNP	.											.	AXIN2	92	.	0			c.C2051T						PASS	.	G	VAL/ALA	3,4399	6.2+/-15.9	0,3,2198	24.0	26.0	25.0		2051	4.4	0.8	17	dbSNP_134	25	15,8585	10.5+/-38.8	0,15,4285	yes	missense	AXIN2	NM_004655.3	64	0,18,6483	AA,AG,GG		0.1744,0.0682,0.1384	possibly-damaging	684/844	63532528	18,12984	2201	4300	6501	SO:0001583	missense	8313	exon8	Familial Cancer Database	Oligodontia-Colorectal Cancer syndrome, Tooth Agenesis-Colorectal Cancer Syndrome	GGCATCGCAGGGT	AF078165	CCDS11662.1	17q24.1	2014-09-17	2008-08-01		ENSG00000168646				904	protein-coding gene	gene with protein product	"""conductin"", ""axil"""	604025				10049590	Standard	NM_004655		Approved	MGC126582, DKFZp781B0869	uc002jfi.3	Q9Y2T1	OTTHUMG00000179353	ENST00000375702.5:c.1856C>T	17.37:g.63532528G>A	ENSP00000364854:p.Ala619Val	146.0	0.0	0		124.0	68.0	0.548387	NM_004655	Q3MJ88|Q9H3M6|Q9UH84	Missense_Mutation	SNP	ENST00000375702.5	37		.	.	.	.	.	.	.	.	.	.	G	22.6	4.307951	0.81247	6.82E-4	0.001744	ENSG00000168646	ENST00000307078;ENST00000375702	T;T	0.66280	-0.2;-0.18	5.41	4.37	0.52481	.	0.262657	0.43579	D	0.000560	T	0.57388	0.2050	L	0.48642	1.525	0.46260	D	0.998951	P;P	0.52061	0.95;0.923	B;B	0.40782	0.298;0.34	T	0.66818	-0.5827	10	0.66056	D	0.02	-11.6392	17.7442	0.88415	0.0:0.1327:0.8673:0.0	.	684;619	Q9Y2T1;E7ES00	AXIN2_HUMAN;.	V	684;619	ENSP00000302625:A684V;ENSP00000364854:A619V	ENSP00000302625:A684V	A	-	2	0	AXIN2	60962990	1.000000	0.71417	0.795000	0.32087	0.951000	0.60555	7.302000	0.78861	2.516000	0.84829	0.650000	0.86243	GCG	G|0.998;A|0.002	0.002	strong		0.687	AXIN2-004	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000445901.1	NM_004655	
UNC13D	201294	hgsc.bcm.edu	37	17	73838639	73838639	+	Silent	SNP	C	C	T	rs373551579		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73838639C>T	ENST00000207549.4	-	6	823	c.444G>A	c.(442-444)ggG>ggA	p.G148G	UNC13D_ENST00000412096.2_Silent_p.G148G|UNC13D_ENST00000587504.1_5'UTR	NM_199242.2	NP_954712.1	Q70J99	UN13D_HUMAN	unc-13 homolog D (C. elegans)	148	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				defense response to virus (GO:0051607)|germinal center formation (GO:0002467)|granuloma formation (GO:0002432)|natural killer cell degranulation (GO:0043320)|phagocytosis (GO:0006909)|positive regulation of exocytosis (GO:0045921)|regulation of mast cell degranulation (GO:0043304)	endosome (GO:0005768)|exocytic vesicle (GO:0070382)|lysosome (GO:0005764)|membrane (GO:0016020)				central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29			all cancers(21;2.11e-06)|Epithelial(20;2.32e-06)|BRCA - Breast invasive adenocarcinoma(9;0.000618)|LUSC - Lung squamous cell carcinoma(166;0.154)			CGGGGCTGCCCCCTGGCACAC	0.677									Familial Hemophagocytic Lymphohistiocytosis				C|||	1	0.000199681	0.0	0.0014	5008	,	,		16781	0.0		0.0	False		,,,				2504	0.0				p.G148G		Atlas-SNP	.											.	UNC13D	68	.	0			c.G444A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	55.0	56.0	55.0		444	-0.2	0.6	17		55	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	UNC13D	NM_199242.2		0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231		148/1091	73838639	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	201294	exon6	Familial Cancer Database	FHLH, FHL, Familial Hemophagocytic Reticulosis, FHR	GCTGCCCCCTGGC	AK024474	CCDS11730.1	17q25.3	2014-09-17				ENSG00000092929			23147	protein-coding gene	gene with protein product		608897					Standard	NM_199242		Approved	Munc13-4	uc002jpp.3	Q70J99		ENST00000207549.4:c.444G>A	17.37:g.73838639C>T		84.0	0.0	0		95.0	43.0	0.452632	NM_199242	B4DWG9|Q9H7K5	Silent	SNP	ENST00000207549.4	37	CCDS11730.1																																																																																			.	.	weak		0.677	UNC13D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448847.2	XM_113950	
LAMA3	3909	hgsc.bcm.edu	37	18	21496533	21496533	+	Silent	SNP	C	C	T	rs61751706	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:21496533C>T	ENST00000313654.9	+	60	8038	c.7797C>T	c.(7795-7797)gaC>gaT	p.D2599D	LAMA3_ENST00000399516.3_Silent_p.D2543D|LAMA3_ENST00000588770.1_3'UTR|LAMA3_ENST00000269217.6_Silent_p.D990D|LAMA3_ENST00000587184.1_Silent_p.D934D	NM_198129.1	NP_937762.1	Q16787	LAMA3_HUMAN	laminin, alpha 3	2599	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|endodermal cell differentiation (GO:0035987)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)	basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-5 complex (GO:0005610)	structural molecule activity (GO:0005198)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(24)|lung(54)|ovary(8)|prostate(6)|skin(7)|urinary_tract(4)	128	all_cancers(21;7.81e-05)|all_epithelial(16;4.45e-07)|Lung NSC(20;0.00156)|all_lung(20;0.00508)|Colorectal(14;0.0202)|Ovarian(20;0.17)					AAGAGTCAGACAAAAATTATT	0.423													C|||	5	0.000998403	0.0	0.0014	5008	,	,		18308	0.0		0.004	False		,,,				2504	0.0				p.D2599D		Atlas-SNP	.											.	LAMA3	397	.	0			c.C7797T						PASS	.	C	,,,	5,4401	9.9+/-24.2	0,5,2198	161.0	149.0	153.0		2970,7629,2802,7797	5.2	1.0	18	dbSNP_129	153	60,8540	37.8+/-93.5	1,58,4241	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LAMA3	NM_000227.3,NM_001127717.1,NM_001127718.1,NM_198129.1	,,,	1,63,6439	TT,TC,CC		0.6977,0.1135,0.4998	,,,	990/1725,2543/3278,934/1669,2599/3334	21496533	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	3909	exon60			GTCAGACAAAAAT	L34155	CCDS11880.1, CCDS42419.1, CCDS45838.1, CCDS59307.1	18q11.2	2013-03-01	2002-08-29		ENSG00000053747	ENSG00000053747		"""Laminins"""	6483	protein-coding gene	gene with protein product		600805	"""laminin, alpha 3 (nicein (150kD), kalinin (165kD), BM600 (150kD), epilegrin)"""	LAMNA		8077230	Standard	NM_000227		Approved	nicein-150kDa, kalinin-165kDa, BM600-150kDa, epiligrin	uc002kuq.3	Q16787	OTTHUMG00000131874	ENST00000313654.9:c.7797C>T	18.37:g.21496533C>T		103.0	0.0	0		66.0	33.0	0.5	NM_198129	B0YJ33|Q13679|Q13680|Q6VU67|Q6VU68|Q6VU69|Q76E14|Q96TG0	Silent	SNP	ENST00000313654.9	37	CCDS42419.1																																																																																			C|0.995;T|0.005	0.005	strong		0.423	LAMA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254824.3	NM_000227, NM_198129	
PDE4C	5143	hgsc.bcm.edu	37	19	18333062	18333062	+	Missense_Mutation	SNP	C	C	T	rs146818532	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18333062C>T	ENST00000355502.3	-	6	1185	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	AC068499.10_ENST00000594805.3_RNA|PDE4C_ENST00000594465.3_Missense_Mutation_p.R105Q|PDE4C_ENST00000539010.1_5'Flank|PDE4C_ENST00000447275.3_5'UTR|PDE4C_ENST00000262805.12_Missense_Mutation_p.R73Q|PDE4C_ENST00000598111.2_5'Flank|PDE4C_ENST00000597297.1_5'Flank|PDE4C_ENST00000594617.3_Missense_Mutation_p.R105Q			Q08493	PDE4C_HUMAN	phosphodiesterase 4C, cAMP-specific	105					cAMP catabolic process (GO:0006198)|signal transduction (GO:0007165)	cytosol (GO:0005829)|extracellular space (GO:0005615)|primary cilium (GO:0072372)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(2)|lung(9)|ovary(2)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	33					Caffeine(DB00201)|Dyphylline(DB00651)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Roflumilast(DB01656)	CTGCATAATCCGGCCCAGGCC	0.617													C|||	4	0.000798722	0.0008	0.0	5008	,	,		18538	0.0		0.0	False		,,,				2504	0.0031				p.R105Q		Atlas-SNP	.											.	PDE4C	80	.	0			c.G314A						PASS	.	C	GLN/ARG,GLN/ARG,	4,4402	8.1+/-20.4	0,4,2199	49.0	49.0	49.0		314,218,	-1.8	0.0	19	dbSNP_134	49	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,utr-5	PDE4C	NM_000923.4,NM_001098818.2,NM_001098819.2	43,43,	0,7,6496	TT,TC,CC		0.0349,0.0908,0.0538	benign,benign,	105/713,73/681,	18333062	7,12999	2203	4300	6503	SO:0001583	missense	5143	exon3			ATAATCCGGCCCA		CCDS12373.1, CCDS42523.1, CCDS46016.1	19p13.11	2010-06-24	2010-06-24			ENSG00000105650	3.1.4.17	"""Phosphodiesterases"""	8782	protein-coding gene	gene with protein product	"""phosphodiesterase E1 dunce homolog (Drosophila)"""	600128	"""phosphodiesterase 4C, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E1)"""	DPDE1			Standard	NM_001098818		Approved		uc002nik.4	Q08493		ENST00000355502.3:c.314G>A	19.37:g.18333062C>T	ENSP00000347689:p.Arg105Gln	79.0	0.0	0		93.0	46.0	0.494624	NM_000923	B3KTC4|Q9UN44|Q9UN45|Q9UN46|Q9UPJ6	Missense_Mutation	SNP	ENST00000355502.3	37	CCDS12373.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	11.09	1.537093	0.27475	9.08E-4	3.49E-4	ENSG00000105650	ENST00000536045;ENST00000355502;ENST00000536507;ENST00000262805;ENST00000543547	T;T	0.69926	0.96;-0.44	4.13	-1.8	0.07907	.	0.902683	0.09345	N	0.814920	T	0.48714	0.1515	L	0.33485	1.01	0.80722	D	1	B;B;B	0.21905	0.054;0.062;0.003	B;B;B	0.13407	0.006;0.007;0.009	T	0.41787	-0.9489	10	0.62326	D	0.03	.	3.6337	0.08141	0.3236:0.2868:0.0:0.3896	.	214;105;73	B7Z2S3;Q08493;Q08493-3	.;PDE4C_HUMAN;.	Q	184;105;93;73;214	ENSP00000347689:R105Q;ENSP00000262805:R73Q	ENSP00000262805:R73Q	R	-	2	0	PDE4C	18194062	0.995000	0.38212	0.032000	0.17829	0.140000	0.21249	3.332000	0.52083	-0.112000	0.11979	0.306000	0.20318	CGG	C|0.999;T|0.001	0.001	strong		0.617	PDE4C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466295.1		
ZNF737	100129842	hgsc.bcm.edu	37	19	20736639	20736639	+	Silent	SNP	C	C	T	rs111988999	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20736639C>T	ENST00000427401.4	-	2	100	c.6G>A	c.(4-6)ggG>ggA	p.G2G	ZNF737_ENST00000596797.1_Silent_p.G2G|CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001159293.1	NP_001152765.1	O75373	ZN737_HUMAN	zinc finger protein 737	2					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|kidney(1)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	13						ATTGCAATGGCCCCTGAAACA	0.408													t|||	295	0.0589058	0.2118	0.0216	5008	,	,		14230	0.0		0.0	False		,,,				2504	0.0				p.G2G		Atlas-SNP	.											.	ZNF737	50	.	0			c.G6A						PASS	.	T		248,1136		23,202,467	30.0	27.0	28.0		6	-1.6	0.0	19	dbSNP_132	28	3,3179		0,3,1588	no	coding-synonymous	ZNF737	NM_001159293.1		23,205,2055	TT,TC,CC		0.0943,17.9191,5.4972		2/537	20736639	251,4315	692	1591	2283	SO:0001819	synonymous_variant	100129842	exon2			CAATGGCCCCTGA	BC015765	CCDS54238.1	19p12	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	32468	protein-coding gene	gene with protein product		603984					Standard	NM_001159293		Approved	ZNF102	uc002npa.3	O75373		ENST00000427401.4:c.6G>A	19.37:g.20736639C>T		65.0	0.0	0		71.0	40.0	0.56338	NM_001159293	C9JHM3	Silent	SNP	ENST00000427401.4	37	CCDS54238.1																																																																																			C|0.940;T|0.060	0.060	strong		0.408	ZNF737-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447844.2	NM_145289	
TRIM65	201292	hgsc.bcm.edu	37	17	73887089	73887089	+	Missense_Mutation	SNP	C	C	T	rs61754864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73887089C>T	ENST00000269383.3	-	6	1390	c.1325G>A	c.(1324-1326)cGc>cAc	p.R442H		NM_001256124.1|NM_173547.3	NP_001243053.1|NP_775818.2	Q6PJ69	TRI65_HUMAN	tripartite motif containing 65	442	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					intracellular (GO:0005622)	zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|lung(5)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	12			Epithelial(20;7.53e-06)|all cancers(21;9.11e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00092)|LUSC - Lung squamous cell carcinoma(166;0.154)			CCCTGGGAGGCGCTGGGCTTC	0.687													C|||	4	0.000798722	0.0	0.0	5008	,	,		15760	0.0		0.004	False		,,,				2504	0.0				p.R442H		Atlas-SNP	.											.	TRIM65	23	.	0			c.G1325A						PASS	.	C	HIS/ARG	11,4369		0,11,2179	17.0	20.0	19.0		1325	3.4	1.0	17	dbSNP_129	19	97,8473		1,95,4189	yes	missense	TRIM65	NM_173547.2	29	1,106,6368	TT,TC,CC		1.1319,0.2511,0.834	benign	442/518	73887089	108,12842	2190	4285	6475	SO:0001583	missense	201292	exon6			GGGAGGCGCTGGG	BC006138	CCDS11732.1	17q25.1	2013-01-09	2011-01-25		ENSG00000141569	ENSG00000141569		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	27316	protein-coding gene	gene with protein product			"""tripartite motif-containing 65"""			12477932	Standard	NM_173547		Approved		uc002jpx.4	Q6PJ69	OTTHUMG00000132127	ENST00000269383.3:c.1325G>A	17.37:g.73887089C>T	ENSP00000269383:p.Arg442His	56.0	0.0	0		55.0	28.0	0.509091	NM_173547	Q4G0F0|Q6DKJ6|Q9BRP6	Missense_Mutation	SNP	ENST00000269383.3	37	CCDS11732.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	14.58	2.578467	0.46006	0.002511	0.011319	ENSG00000141569	ENST00000269383	T	0.69175	-0.38	5.35	3.36	0.38483	Concanavalin A-like lectin/glucanase (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.248458	0.29113	N	0.013101	T	0.36054	0.0953	N	0.20483	0.58	0.21020	N	0.999809	B	0.18461	0.028	B	0.17098	0.017	T	0.11299	-1.0593	10	0.21014	T	0.42	.	5.3044	0.15795	0.0:0.6089:0.0:0.3911	.	442	Q6PJ69	TRI65_HUMAN	H	442	ENSP00000269383:R442H	ENSP00000269383:R442H	R	-	2	0	TRIM65	71398684	0.014000	0.17966	0.998000	0.56505	0.957000	0.61999	0.102000	0.15272	1.267000	0.44247	0.561000	0.74099	CGC	C|0.997;T|0.003	0.003	strong		0.687	TRIM65-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255170.2	NM_173547	
DNAH10	196385	hgsc.bcm.edu	37	12	124298380	124298380	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124298380G>A	ENST00000409039.3	+	20	3372	c.3347G>A	c.(3346-3348)aGa>aAa	p.R1116K		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1116	Stem. {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)		GCAGAAATTAGAAGTAAATCT	0.398																																					p.R1116K		Atlas-SNP	.											.	DNAH10	888	.	0			c.G3347A						PASS	.						73.0	72.0	72.0					12																	124298380		2044	4232	6276	SO:0001583	missense	196385	exon20			AAATTAGAAGTAA	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.3347G>A	12.37:g.124298380G>A	ENSP00000386770:p.Arg1116Lys	80.0	0.0	0		89.0	41.0	0.460674	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	14.43	2.531934	0.45073	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.72	2.94	0.34122	.	.	.	.	.	T	0.18882	0.0453	L	0.54323	1.7	0.36729	D	0.881622	B	0.14805	0.011	B	0.16722	0.016	T	0.11324	-1.0592	9	0.17832	T	0.49	.	9.9842	0.41832	0.2701:0.0:0.7299:0.0	.	1116	Q8IVF4	DYH10_HUMAN	K	1116	ENSP00000386770:R1116K	ENSP00000386770:R1116K	R	+	2	0	DNAH10	122864333	0.988000	0.35896	0.047000	0.18901	0.982000	0.71751	1.629000	0.37071	0.364000	0.24374	-0.136000	0.14681	AGA	.	.	none		0.398	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
SH3BP2	6452	hgsc.bcm.edu	37	4	2828969	2828969	+	Silent	SNP	G	G	A	rs145235325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:2828969G>A	ENST00000356331.5	+	6	702	c.441G>A	c.(439-441)tcG>tcA	p.S147S	SH3BP2_ENST00000515183.1_3'UTR|SH3BP2_ENST00000435136.2_Silent_p.S147S|SH3BP2_ENST00000442312.2_Silent_p.S175S|SH3BP2_ENST00000511747.1_Silent_p.S147S|SH3BP2_ENST00000452765.2_Silent_p.S147S|SH3BP2_ENST00000503393.2_Silent_p.S204S	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	147					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		ACTCCAGCTCGGACACAGACA	0.602									Cherubism				g|||	3	0.000599042	0.0008	0.0	5008	,	,		22783	0.0		0.002	False		,,,				2504	0.0				p.S204S		Atlas-SNP	.											.	SH3BP2	43	.	0			c.G612A						PASS	.		,,,	1,4405	2.1+/-5.4	0,1,2202	133.0	107.0	116.0		441,525,612,441	-9.9	0.9	4	dbSNP_134	116	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SH3BP2	NM_001122681.1,NM_001145855.1,NM_001145856.1,NM_003023.4	,,,	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	,,,	147/562,175/590,204/619,147/562	2828969	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	6452	exon6	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	CAGCTCGGACACA	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	10825	protein-coding gene	gene with protein product		602104	"""Cherubism"""			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.441G>A	4.37:g.2828969G>A		55.0	0.0	0		58.0	30.0	0.517241	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Silent	SNP	ENST00000356331.5	37	CCDS33944.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
SHISA9	729993	hgsc.bcm.edu	37	16	13297348	13297348	+	Silent	SNP	C	C	T	rs12444395	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:13297348C>T	ENST00000424107.3	+	3	1234	c.789C>T	c.(787-789)ccC>ccT	p.P263P	AC009134.1_ENST00000571939.1_RNA|SHISA9_ENST00000558583.1_Silent_p.P304P			B4DS77	SHSA9_HUMAN	shisa family member 9	263					regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|dendritic spine membrane (GO:0032591)|ionotropic glutamate receptor complex (GO:0008328)|synapse (GO:0045202)				breast(1)|endometrium(2)|kidney(1)|lung(2)|prostate(1)|skin(2)	9						TCTCCAACCCCTATGAACAGC	0.542													C|||	80	0.0159744	0.0015	0.0173	5008	,	,		18542	0.001		0.0318	False		,,,				2504	0.0337				p.P263P		Atlas-SNP	.											.	SHISA9	33	.	0			c.C789T						PASS	.	C		5,1379		0,5,687	176.0	163.0	167.0		789	1.1	1.0	16	dbSNP_120	167	104,3078		2,100,1489	no	coding-synonymous	SHISA9	NM_001145204.2		2,105,2176	TT,TC,CC		3.2684,0.3613,2.3872		263/425	13297348	109,4457	692	1591	2283	SO:0001819	synonymous_variant	729993	exon3			CAACCCCTATGAA		CCDS45417.1, CCDS45418.1, CCDS45417.2, CCDS45418.2	16p13.12	2013-07-31	2013-07-31		ENSG00000237515	ENSG00000237515		"""Shisa homologs"""	37231	protein-coding gene	gene with protein product		613346	"""shisa homolog 9 (Xenopus laevis)"""				Standard	NM_001145205		Approved		uc010uyy.2	B4DS77	OTTHUMG00000154258	ENST00000424107.3:c.789C>T	16.37:g.13297348C>T		63.0	0.0	0		70.0	31.0	0.442857	NM_001145204	C9J314|C9JCE9	Silent	SNP	ENST00000424107.3	37	CCDS45417.2																																																																																			C|0.980;T|0.020	0.020	strong		0.542	SHISA9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334564.5	NM_001145204	
PCDHAC1	56135	hgsc.bcm.edu	37	5	140307485	140307485	+	Silent	SNP	T	T	C	rs147219331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140307485T>C	ENST00000253807.2	+	1	1008	c.1008T>C	c.(1006-1008)caT>caC	p.H336H	PCDHA4_ENST00000512229.2_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA12_ENST00000398631.2_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA13_ENST00000289272.2_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHAC1_ENST00000409700.3_Silent_p.H336H|PCDHA13_ENST00000409494.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018898.3	NP_061721.2	Q9H158	PCDC1_HUMAN	protocadherin alpha subfamily C, 1	336	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|liver(2)|lung(13)|ovary(3)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	65			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGAACGATCATGCCCCCGAAC	0.532													t|||	2	0.000399361	0.0	0.0	5008	,	,		21222	0.0		0.002	False		,,,				2504	0.0				p.H336H		Atlas-SNP	.											.	PCDHAC1	141	.	0			c.T1008C						PASS	.	T	,,,,,,,,,,,,,,,,,	5,4401	9.9+/-24.2	0,5,2198	174.0	160.0	164.0		1008,,,,,,,,,,,,,,,,,1008	-0.5	0.3	5	dbSNP_134	164	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHAC1,PCDHA13,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018898.3,NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,NM_018904.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_018909.2,NM_018910.2,NM_018911.2,NM_031411.1,NM_031849.1,NM_031857.1,NM_031860.1,NM_031882.2	,,,,,,,,,,,,,,,,,	0,16,6487	CC,CT,TT		0.1279,0.1135,0.123	,,,,,,,,,,,,,,,,,	336/964,,,,,,,,,,,,,,,,,336/819	140307485	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	56135	exon1			CGATCATGCCCCC	AF152473	CCDS4241.1	5q31	2010-11-26			ENSG00000248383	ENSG00000248383		"""Cadherins / Protocadherins : Clustered"""	8676	other	complex locus constituent	"""PCDH-ALPHA-C1"""	606320				10380929	Standard	NM_018898		Approved			Q9H158	OTTHUMG00000129603	ENST00000253807.2:c.1008T>C	5.37:g.140307485T>C		185.0	0.0	0		194.0	61.0	0.314433	NM_031882	Q9Y5F5|Q9Y5I5	Silent	SNP	ENST00000253807.2	37	CCDS4241.1																																																																																			T|0.999;C|0.001	0.001	strong		0.532	PCDHAC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000251798.1	NM_018898	
OR2V1	26693	hgsc.bcm.edu	37	5	180551660	180551660	+	Silent	SNP	G	G	T	rs141508488	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180551660G>T	ENST00000329365.2	-	1	644	c.645C>A	c.(643-645)atC>atA	p.I215I		NM_001258283.1	NP_001245212.1	Q8NHB1	OR2V1_HUMAN	olfactory receptor, family 2, subfamily V, member 1	215						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			lung(4)	4						AGGAGGCCATGATGATGGAGA	0.532													g|||	24	0.00479233	0.0	0.0072	5008	,	,		21397	0.0		0.0099	False		,,,				2504	0.0092				p.I215I		Atlas-SNP	.											.	OR2V1	20	.	0			c.C645A						PASS	.																																			SO:0001819	synonymous_variant	26693	exon1			GGCCATGATGATG	AB065465	CCDS58992.1	5q35.3	2012-08-09		2004-03-10	ENSG00000185372	ENSG00000185372		"""GPCR / Class A : Olfactory receptors"""	8280	protein-coding gene	gene with protein product				OR2V1P			Standard	NM_001258283		Approved	OST265	uc031smg.1	Q8NHB1	OTTHUMG00000162118	ENST00000329365.2:c.645C>A	5.37:g.180551660G>T		105.0	0.0	0		98.0	59.0	0.602041	NM_001258283		Silent	SNP	ENST00000329365.2	37	CCDS58992.1																																																																																			G|0.994;T|0.006	0.006	strong		0.532	OR2V1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367367.1		
MAP7D1	55700	hgsc.bcm.edu	37	1	36636774	36636774	+	Silent	SNP	G	G	A	rs139650826	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:36636774G>A	ENST00000373151.2	+	2	465	c.249G>A	c.(247-249)caG>caA	p.Q83Q	MAP7D1_ENST00000316156.4_Silent_p.Q83Q|MAP7D1_ENST00000373150.4_Silent_p.Q83Q	NM_018067.3	NP_060537.3	Q3KQU3	MA7D1_HUMAN	MAP7 domain containing 1	83	Pro-rich.				microtubule cytoskeleton organization (GO:0000226)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)				breast(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(3)|prostate(3)|skin(1)|urinary_tract(1)	19		Myeloproliferative disorder(586;0.0393)				CCCCCCCGCAGGAAGAGTCCC	0.642													G|||	23	0.00459265	0.0008	0.0043	5008	,	,		13296	0.0		0.0179	False		,,,				2504	0.001				p.Q83Q		Atlas-SNP	.											.	MAP7D1	62	.	0			c.G249A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	39.0	43.0	41.0		249	2.2	1.0	1	dbSNP_134	41	125,8475	62.4+/-124.4	1,123,4176	no	coding-synonymous	MAP7D1	NM_018067.3		1,135,6367	AA,AG,GG		1.4535,0.2724,1.0534		83/842	36636774	137,12869	2203	4300	6503	SO:0001819	synonymous_variant	55700	exon2			CCCGCAGGAAGAG	AK096341	CCDS30673.1, CCDS65492.1, CCDS65493.1	1p34.3	2008-02-05	2007-02-08	2007-02-08	ENSG00000116871	ENSG00000116871			25514	protein-coding gene	gene with protein product			"""proline arginine rich coiled coil 1"", ""arginine/proline rich coiled-coil 1"""	PARCC1, RPRC1		10574461	Standard	XM_005271024		Approved	FLJ10350, FLJ39022	uc001bzz.3	Q3KQU3	OTTHUMG00000007714	ENST00000373151.2:c.249G>A	1.37:g.36636774G>A		112.0	0.0	0		100.0	74.0	0.74	NM_018067	D3DPS4|Q7L8J5|Q8N905|Q8TAK0|Q9HBQ2|Q9NW29|Q9ULN3	Silent	SNP	ENST00000373151.2	37	CCDS30673.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	MAP7D1-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000382095.1	NM_018067	
SMARCC2	6601	hgsc.bcm.edu	37	12	56558483	56558483	+	Missense_Mutation	SNP	G	G	A	rs76701112	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56558483G>A	ENST00000267064.4	-	27	3258	c.3172C>T	c.(3172-3174)Ccc>Tcc	p.P1058S	SMARCC2_ENST00000347471.4_Missense_Mutation_p.P1089S|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550164.1_Missense_Mutation_p.P1089S|SMARCC2_ENST00000394023.3_Missense_Mutation_p.P1089S	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	1058	Pro-rich.				ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			ATCATTGAGGGAGGAGTTTGT	0.522													G|||	26	0.00519169	0.0159	0.0072	5008	,	,		17586	0.0		0.0	False		,,,				2504	0.0				p.P1089S		Atlas-SNP	.											SMARCC2_ENST00000267064,NS,carcinoma,+1,2	SMARCC2	212	2	0			c.C3265T						PASS	.	G	SER/PRO,SER/PRO,SER/PRO	33,4373	36.8+/-68.6	1,31,2171	30.0	29.0	30.0		3265,3172,3265	4.7	1.0	12	dbSNP_131	30	6,8594	3.0+/-9.4	0,6,4294	yes	missense,missense,missense	SMARCC2	NM_139067.2,NM_003075.3,NM_001130420.1	74,74,74	1,37,6465	AA,AG,GG		0.0698,0.749,0.2999	benign,benign,benign	1089/1131,1058/1215,1089/1153	56558483	39,12967	2203	4300	6503	SO:0001583	missense	6601	exon28			TTGAGGGAGGAGT	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.3172C>T	12.37:g.56558483G>A	ENSP00000267064:p.Pro1058Ser	101.0	0.0	0		102.0	42.0	0.411765	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Missense_Mutation	SNP	ENST00000267064.4	37	CCDS8907.1	11	0.005036630036630037	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	0	0.0	G	10.44	1.350723	0.24512	0.00749	6.98E-4	ENSG00000139613	ENST00000394023;ENST00000550164;ENST00000347471;ENST00000267064	T;T;T;T	0.55760	1.08;0.57;0.5;0.61	4.67	4.67	0.58626	.	0.000000	0.45126	D	0.000388	T	0.14787	0.0357	N	0.08118	0	0.41798	D	0.989902	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.001;0.001	B;B;B;B;B	0.04013	0.001;0.001;0.001;0.001;0.001	T	0.08973	-1.0696	10	0.27082	T	0.32	-10.7152	6.6581	0.22998	0.0933:0.0:0.7261:0.1806	.	978;1089;1093;1058;1089	B4DF22;F8VTJ5;Q59G16;Q8TAQ2;Q8TAQ2-2	.;.;.;SMRC2_HUMAN;.	S	1089;1089;1089;1058	ENSP00000377591:P1089S;ENSP00000449396:P1089S;ENSP00000302919:P1089S;ENSP00000267064:P1058S	ENSP00000267064:P1058S	P	-	1	0	SMARCC2	54844750	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.937000	0.40193	2.528000	0.85240	0.557000	0.71058	CCC	G|0.995;A|0.005	0.005	strong		0.522	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
SYTL2	54843	hgsc.bcm.edu	37	11	85435805	85435805	+	Intron	SNP	T	T	C	rs532374094		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:85435805T>C	ENST00000528231.1	-	7	1737				SYTL2_ENST00000524452.1_Intron|SYTL2_ENST00000527523.1_Intron|SYTL2_ENST00000316356.4_Intron|SYTL2_ENST00000389960.4_Intron|SYTL2_ENST00000354566.3_Silent_p.T565T|SYTL2_ENST00000525423.1_Silent_p.T565T|SYTL2_ENST00000359152.5_Silent_p.T1089T	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2						exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TGGGCTCCTCTGTACTACCTA	0.423													T|||	1	0.000199681	0.0	0.0	5008	,	,		16092	0.0		0.001	False		,,,				2504	0.0				p.T565T		Atlas-SNP	.											.	SYTL2	231	.	0			c.A1695G						PASS	.						66.0	67.0	67.0					11																	85435805		2203	4299	6502	SO:0001627	intron_variant	54843	exon1			CTCCTCTGTACTA	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.1459+3133A>G	11.37:g.85435805T>C		131.0	0.0	0		155.0	74.0	0.477419	NM_206927	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Silent	SNP	ENST00000528231.1	37	CCDS53688.1																																																																																			.	.	none		0.423	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
GOLGB1	2804	hgsc.bcm.edu	37	3	121413239	121413239	+	Missense_Mutation	SNP	T	T	G	rs75383249	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:121413239T>G	ENST00000340645.5	-	13	6241	c.6116A>C	c.(6115-6117)gAg>gCg	p.E2039A	GOLGB1_ENST00000393667.3_Missense_Mutation_p.E2044A	NM_001256487.1|NM_001256488.1|NM_004487.4	NP_001243416.1|NP_001243417.1|NP_004478.3	Q14789	GOGB1_HUMAN	golgin B1	2039					Golgi organization (GO:0007030)	cis-Golgi network (GO:0005801)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(7)|central_nervous_system(2)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(26)|liver(2)|lung(36)|ovary(7)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(13)	119				GBM - Glioblastoma multiforme(114;0.0989)		AACAGTTCTCTCCAGAGCACT	0.368													T|||	9	0.00179712	0.0	0.0	5008	,	,		19970	0.0		0.0089	False		,,,				2504	0.0				p.E2044A		Atlas-SNP	.											.	GOLGB1	319	.	0			c.A6131C						PASS	.	T	ALA/GLU	6,4400	9.9+/-24.2	0,6,2197	109.0	110.0	110.0		6116	5.5	1.0	3	dbSNP_132	110	38,8560	25.1+/-72.6	0,38,4261	yes	missense	GOLGB1	NM_004487.3	107	0,44,6458	GG,GT,TT		0.442,0.1362,0.3384	probably-damaging	2039/3260	121413239	44,12960	2203	4299	6502	SO:0001583	missense	2804	exon13			GTTCTCTCCAGAG	X75304	CCDS3004.1, CCDS58847.1, CCDS74989.1	3q13	2010-02-12	2010-02-12	2007-07-27	ENSG00000173230	ENSG00000173230			4429	protein-coding gene	gene with protein product	"""macrogolgin"", ""golgi integral membrane protein 1"""	602500	"""golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1"", ""golgin B1, golgi integral membrane protein"""			7691276, 15004235	Standard	NM_001256486		Approved	GCP, GCP372, giantin, GOLIM1	uc010hrc.4	Q14789	OTTHUMG00000159411	ENST00000340645.5:c.6116A>C	3.37:g.121413239T>G	ENSP00000341848:p.Glu2039Ala	130.0	0.0	0		105.0	54.0	0.514286	NM_001256486	B2ZZ91|D3DN92|E7EP74|Q14398	Missense_Mutation	SNP	ENST00000340645.5	37	CCDS3004.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	T	9.851	1.193741	0.22037	0.001362	0.00442	ENSG00000173230	ENST00000340645;ENST00000393667	T;T	0.20069	2.1;2.1	5.46	5.46	0.80206	.	0.000000	0.53938	D	0.000051	T	0.30885	0.0779	L	0.49640	1.575	0.34058	D	0.656894	D;D;P;D	0.71674	0.998;0.998;0.607;0.977	D;D;B;P	0.81914	0.995;0.995;0.255;0.69	T	0.45381	-0.9265	10	0.37606	T	0.19	.	13.5212	0.61569	0.0:0.0:0.0:1.0	.	1964;2044;2044;2039	F1T0J2;E7EP74;B2ZZ91;Q14789	.;.;.;GOGB1_HUMAN	A	2039;2044	ENSP00000341848:E2039A;ENSP00000377275:E2044A	ENSP00000341848:E2039A	E	-	2	0	GOLGB1	122895929	1.000000	0.71417	1.000000	0.80357	0.953000	0.61014	2.911000	0.48774	2.289000	0.77006	0.482000	0.46254	GAG	T|0.997;G|0.003	0.003	strong		0.368	GOLGB1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000355159.1	NM_004487	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549582	32549582	+	Missense_Mutation	SNP	G	G	T	rs200516145		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549582G>T	ENST00000360004.5	-	3	509	c.404C>A	c.(403-405)aCc>aAc	p.T135N		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						CAGGGGCTGGGTCTTTGAAGG	0.507										Multiple Myeloma(14;0.17)																											p.T135N		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.C404A						PASS	.						67.0	84.0	78.0					6																	32549582		1510	2709	4219	SO:0001583	missense	3123	exon3			GGCTGGGTCTTTG	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.404C>A	6.37:g.32549582G>T	ENSP00000353099:p.Thr135Asn	188.0	0.0	0		375.0	37.0	0.0986667	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	11.78	1.740603	0.30865	.	.	ENSG00000196126	ENST00000360004	T	0.02863	4.13	3.87	2.92	0.33932	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.06781	0.0173	M	0.76574	2.34	0.26397	N	0.97649	D	0.76494	0.999	D	0.87578	0.998	T	0.02632	-1.1131	10	0.87932	D	0	.	10.9743	0.47456	0.0:0.0:0.8139:0.1861	.	135	P01911	2B1F_HUMAN	N	135	ENSP00000353099:T135N	ENSP00000353099:T135N	T	-	2	0	HLA-DRB1	32657560	0.030000	0.19436	0.762000	0.31397	0.139000	0.21198	1.809000	0.38922	1.883000	0.54544	0.453000	0.30009	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
ALK	238	hgsc.bcm.edu	37	2	29543663	29543663	+	Silent	SNP	T	T	C	rs2293564	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29543663T>C	ENST00000389048.3	-	7	2406	c.1500A>G	c.(1498-1500)caA>caG	p.Q500Q	ALK_ENST00000498037.1_5'Flank|ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	500	MAM 2. {ECO:0000255|PROSITE- ProRule:PRU00128}.				activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	TGACCTGCCATTGAGGAGTGT	0.547			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				t|||	3889	0.776558	0.4334	0.8847	5008	,	,		17652	0.9206		0.9235	False		,,,				2504	0.864				p.Q500Q		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.A1500G						PASS	.	T		2356,2050	609.3+/-391.3	618,1120,465	184.0	157.0	166.0		1500	1.0	0.1	2	dbSNP_100	166	7931,669	789.2+/-407.6	3657,617,26	no	coding-synonymous	ALK	NM_004304.4		4275,1737,491	CC,CT,TT		7.7791,46.5275,20.9057		500/1621	29543663	10287,2719	2203	4300	6503	SO:0001819	synonymous_variant	238	exon7	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CTGCCATTGAGGA	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.1500A>G	2.37:g.29543663T>C		210.0	1.0	0.0047619		187.0	187.0	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			T|0.203;C|0.797	0.797	strong		0.547	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
ERBB2	2064	hgsc.bcm.edu	37	17	37879588	37879588	+	Missense_Mutation	SNP	A	A	G	rs1136201	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:37879588A>G	ENST00000269571.5	+	17	2122	c.1963A>G	c.(1963-1965)Atc>Gtc	p.I655V	ERBB2_ENST00000406381.2_Missense_Mutation_p.I625V|ERBB2_ENST00000540147.1_Missense_Mutation_p.I625V|ERBB2_ENST00000445658.2_Missense_Mutation_p.I379V|ERBB2_ENST00000584601.1_Missense_Mutation_p.I625V|ERBB2_ENST00000541774.1_Missense_Mutation_p.I640V|ERBB2_ENST00000584450.1_Missense_Mutation_p.I655V			P04626	ERBB2_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2	655			I -> V (in allele B2 and allele B3; dbSNP:rs1136201). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:8095488, ECO:0000269|Ref.3}.		axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|enzyme linked receptor protein signaling pathway (GO:0007167)|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)|motor neuron axon guidance (GO:0008045)|myelination (GO:0042552)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription from RNA polymerase I promoter (GO:0045943)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of translation (GO:0045727)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of angiogenesis (GO:0045765)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of microtubule-based process (GO:0032886)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|ErbB-3 class receptor binding (GO:0043125)|identical protein binding (GO:0042802)|protein C-terminus binding (GO:0008022)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|RNA polymerase I core binding (GO:0001042)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(16)|central_nervous_system(17)|endometrium(6)|haematopoietic_and_lymphoid_tissue(8)|kidney(4)|large_intestine(16)|liver(3)|lung(125)|ovary(18)|pancreas(1)|prostate(4)|skin(1)|stomach(14)|upper_aerodigestive_tract(9)|urinary_tract(4)	247	all_cancers(6;1.06e-93)|all_epithelial(6;2.33e-113)|Breast(7;9.37e-100)|Lung NSC(9;9.76e-10)|all_lung(9;5.34e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)	Ovarian(249;0.0547)|Colorectal(1115;0.234)	UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|Epithelial(3;9.42e-64)|all cancers(3;5.61e-57)|BRCA - Breast invasive adenocarcinoma(8;2.5e-45)|STAD - Stomach adenocarcinoma(3;9.03e-13)|Colorectal(5;6.23e-08)|COAD - Colon adenocarcinoma(5;8.58e-06)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|OV - Ovarian serous cystadenocarcinoma(8;0.0917)|LUSC - Lung squamous cell carcinoma(15;0.171)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0767)	ado-trastuzumab emtansine(DB05773)|Afatinib(DB08916)|Lapatinib(DB01259)|Pertuzumab(DB06366)|Trastuzumab(DB00072)	GACGTCCATCATCTCTGCGGT	0.612		1	"""A, Mis, O"""		"""breast, ovarian, other tumour types, NSCLC, gastric"""					TCGA GBM(5;<1E-08)			A|||	608	0.121406	0.0098	0.1369	5008	,	,		13960	0.124		0.2455	False		,,,				2504	0.1309				p.I655V		Atlas-SNP	.		Dom	yes		17	17q21.1	2064	"""v-erb-b2 erythroblastic leukemia viral oncogene homolog 2, neuro/glioblastoma derived oncogene homolog (avian)"""		E	.	ERBB2	429	.	0			c.A1963G	GRCh37	CM004332	ERBB2	M	rs1136201	PASS	.	A	VAL/ILE,VAL/ILE	212,4194	132.1+/-168.6	5,202,1996	113.0	103.0	106.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1873,1963	5.0	1.0	17	dbSNP_86	106	1980,6620	346.8+/-326.3	223,1534,2543	yes	missense,missense	ERBB2	NM_001005862.1,NM_004448.2	29,29	228,1736,4539	GG,GA,AA		23.0233,4.8116,16.8538	benign,benign	625/1226,655/1256	37879588	2192,10814	2203	4300	6503	SO:0001583	missense	2064	exon17			TCCATCATCTCTG	X03363	CCDS32642.1, CCDS45667.1, CCDS74052.1	17q11.2-q12	2014-09-17	2013-07-09			ENSG00000141736		"""CD molecules"""	3430	protein-coding gene	gene with protein product	"""neuro/glioblastoma derived oncogene homolog"""	164870	"""v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 2 (neuro/glioblastoma derived oncogene homolog)"""	NGL			Standard	XM_005257140		Approved	NEU, HER-2, CD340, HER2	uc002hso.3	P04626		ENST00000269571.5:c.1963A>G	17.37:g.37879588A>G	ENSP00000269571:p.Ile655Val	249.0	0.0	0		238.0	93.0	0.390756	NM_004448	B2RZG3|B4DHN3|Q14256|Q6LDV1|Q9UMK4|X5D2V5	Missense_Mutation	SNP	ENST00000269571.5	37	CCDS32642.1	339	0.15521978021978022	5	0.01016260162601626	58	0.16022099447513813	83	0.1451048951048951	193	0.2546174142480211	A	13.67	2.306999	0.40795	0.048116	0.230233	ENSG00000141736	ENST00000406381;ENST00000541774;ENST00000445658;ENST00000269571;ENST00000540147	T;T;T;T;T	0.76316	-1.01;-1.01;-0.99;-1.01;-1.01	4.97	4.97	0.65823	Cytochrome c1, transmembrane anchor, C-terminal (1);	.	.	.	.	T	0.00039	0.0001	N	0.25485	0.75	0.09310	P	1.0	B;P;B	0.39576	0.406;0.679;0.406	B;B;B	0.37650	0.108;0.255;0.108	T	0.05920	-1.0856	8	0.22706	T	0.39	.	8.987	0.35999	0.9164:0.0:0.0836:0.0	rs1136201;rs1801200;rs2006406;rs2230699;rs17606815;rs59955961;rs1801200	379;640;655	B4DTR1;P04626-4;P04626	.;.;ERBB2_HUMAN	V	625;640;379;655;625	ENSP00000385185:I625V;ENSP00000446466:I640V;ENSP00000404047:I379V;ENSP00000269571:I655V;ENSP00000443562:I625V	ENSP00000269571:I655V	I	+	1	0	ERBB2	35133114	1.000000	0.71417	0.995000	0.50966	0.892000	0.51952	4.008000	0.57103	1.880000	0.54463	0.459000	0.35465	ATC	A|0.845;G|0.155;N|0.000;T|0.000	0.155	strong		0.612	ERBB2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445621.2		
ITGA9	3680	hgsc.bcm.edu	37	3	37860417	37860417	+	Silent	SNP	C	C	T	rs142961075		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37860417C>T	ENST00000264741.5	+	28	3301	c.3045C>T	c.(3043-3045)atC>atT	p.I1015I	AC093415.2_ENST00000420870.1_RNA|AC093415.2_ENST00000594579.1_RNA|AC093415.2_ENST00000430620.1_RNA|AC093415.2_ENST00000429532.1_RNA|AC093415.2_ENST00000366441.2_RNA|AC093415.2_ENST00000457661.1_RNA|AC093415.2_ENST00000608505.1_RNA|AC093415.2_ENST00000445429.1_RNA|AC093415.2_ENST00000438136.1_RNA|AC093415.2_ENST00000450990.1_RNA	NM_002207.2	NP_002198.2	Q13797	ITA9_HUMAN	integrin, alpha 9	1015					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|neutrophil chemotaxis (GO:0030593)|wound healing (GO:0042060)	basal plasma membrane (GO:0009925)|integrin alpha9-beta1 complex (GO:0034679)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(9)|lung(17)|pancreas(1)|prostate(2)|skin(6)|stomach(1)|urinary_tract(1)	44				KIRC - Kidney renal clear cell carcinoma(284;0.165)|Kidney(284;0.197)		AAGAAATTATCGAAGCTGAGA	0.473													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18335	0.0		0.0	False		,,,				2504	0.0				p.I1015I		Atlas-SNP	.											.	ITGA9	98	.	0			c.C3045T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	67.0	68.0	68.0		3045	-8.5	0.7	3	dbSNP_134	68	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	ITGA9	NM_002207.2		0,16,6487	TT,TC,CC		0.1628,0.0454,0.123		1015/1036	37860417	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	3680	exon28			AATTATCGAAGCT	L24158	CCDS2669.1	3p21.3	2010-03-23			ENSG00000144668	ENSG00000144668		"""Integrins"""	6145	protein-coding gene	gene with protein product	"""integrin, alpha 4-like"""	603963				8245132, 8290272	Standard	NM_002207		Approved	RLC, ITGA4L, ALPHA-RLC	uc003chd.3	Q13797	OTTHUMG00000130815	ENST00000264741.5:c.3045C>T	3.37:g.37860417C>T		148.0	0.0	0		144.0	82.0	0.569444	NM_002207	Q14638	Silent	SNP	ENST00000264741.5	37	CCDS2669.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	8.284	0.816181	0.16607	4.54E-4	0.001628	ENSG00000144668	ENST00000411817	.	.	.	6.17	-8.54	0.00912	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	21.0516	0.99944	0.0:0.7126:0.0:0.2874	.	.	.	.	X	49	.	.	R	+	1	2	ITGA9	37835421	0.027000	0.19231	0.654000	0.29608	0.922000	0.55478	-0.950000	0.03889	-1.656000	0.01495	-0.794000	0.03295	CGA	C|0.999;T|0.001	0.001	strong		0.473	ITGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253361.1	NM_002207	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58564863	58564863	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58564863C>T	ENST00000282326.1	+	6	918	c.671C>T	c.(670-672)cCc>cTc	p.P224L		NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	224					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)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		CTCGCAGGGCCCTCCTCAGAC	0.622																																					p.P224L		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.C671T						PASS	.						48.0	51.0	50.0					19																	58564863		2203	4300	6503	SO:0001583	missense	284312	exon6			CAGGGCCCTCCTC	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.671C>T	19.37:g.58564863C>T	ENSP00000282326:p.Pro224Leu	71.0	0.0	0		63.0	10.0	0.15873	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	C	6.071	0.381441	0.11524	.	.	ENSG00000152467	ENST00000282326	T	0.04862	3.54	1.04	-2.09	0.07232	.	.	.	.	.	T	0.03178	0.0093	N	0.19112	0.55	0.09310	N	0.999993	B	0.09022	0.002	B	0.06405	0.002	T	0.45934	-0.9227	9	0.23302	T	0.38	.	2.0317	0.03530	0.2546:0.35:0.0:0.3953	.	224	Q8NBB4	ZSCA1_HUMAN	L	224	ENSP00000282326:P224L	ENSP00000282326:P224L	P	+	2	0	ZSCAN1	63256675	0.004000	0.15560	0.005000	0.12908	0.357000	0.29423	0.275000	0.18698	-0.640000	0.05495	0.491000	0.48974	CCC	.	.	none		0.622	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
FCAMR	83953	hgsc.bcm.edu	37	1	207140447	207140447	+	Missense_Mutation	SNP	C	C	T	rs199884709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:207140447C>T	ENST00000324852.4	-	3	593	c.119G>A	c.(118-120)aGg>aAg	p.R40K	FCAMR_ENST00000400962.3_Missense_Mutation_p.R40K|FCAMR_ENST00000450945.2_Missense_Mutation_p.R40K	NM_001170631.1	NP_001164102.1	Q8WWV6	FCAMR_HUMAN	Fc receptor, IgA, IgM, high affinity	339					immune system process (GO:0002376)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(1)	11						TCCCGCCCTCCTGCTGGTGAC	0.527													C|||	3	0.000599042	0.0	0.0014	5008	,	,		20112	0.0		0.001	False		,,,				2504	0.001				p.R40K	Ovarian(199;1883 2142 16966 44409 45154)	Atlas-SNP	.											.	FCAMR	125	.	0			c.G119A						PASS	.	C	LYS/ARG,LYS/ARG,LYS/ARG	2,3134		0,2,1566	61.0	55.0	57.0		119,119,119	-5.3	0.0	1		57	22,7142		0,22,3560	yes	missense,missense,missense	FCAMR	NM_001122979.2,NM_001170631.1,NM_032029.4	26,26,26	0,24,5126	TT,TC,CC		0.3071,0.0638,0.233	,,	40/266,40/578,40/266	207140447	24,10276	1568	3582	5150	SO:0001583	missense	83953	exon3			GCCCTCCTGCTGG	AF354295	CCDS41460.1, CCDS53468.1	1q32.1	2013-01-14			ENSG00000162897	ENSG00000162897		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	24692	protein-coding gene	gene with protein product		605484				11779189	Standard	NM_001122979		Approved	FKSG87, FCA/MR, CD351	uc001hfa.4	Q8WWV6	OTTHUMG00000036579	ENST00000324852.4:c.119G>A	1.37:g.207140447C>T	ENSP00000316491:p.Arg40Lys	91.0	0.0	0		119.0	42.0	0.352941	NM_001170631	Q32M82|Q8WWV5|Q96SA2	Missense_Mutation	SNP	ENST00000324852.4	37	CCDS53468.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	9.612	1.131495	0.21041	6.38E-4	0.003071	ENSG00000162897	ENST00000400962;ENST00000324852;ENST00000450945	T;T;T	0.06768	3.26;3.55;3.26	5.35	-5.32	0.02722	.	.	.	.	.	T	0.03011	0.0089	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.47861	-0.9084	6	0.11182	T	0.66	2.788	5.9013	0.18967	0.2988:0.471:0.0:0.2302	.	.	.	.	K	40	ENSP00000383746:R40K;ENSP00000316491:R40K;ENSP00000392707:R40K	ENSP00000316491:R40K	R	-	2	0	FCAMR	205207070	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.129000	0.03244	-0.509000	0.06532	-0.302000	0.09304	AGG	C|0.999;T|0.001	0.001	strong		0.527	FCAMR-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088969.2	NM_032029	
MS4A4A	51338	hgsc.bcm.edu	37	11	60073626	60073626	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:60073626G>A	ENST00000337908.4	+	6	690	c.600G>A	c.(598-600)gtG>gtA	p.V200V	MS4A4A_ENST00000395016.3_Silent_p.V181V|MS4A4A_ENST00000355131.3_Silent_p.V181V|MS4A4A_ENST00000532114.1_Silent_p.V147V	NM_148975.2	NP_683876.1	Q96JQ5	M4A4A_HUMAN	membrane-spanning 4-domains, subfamily A, member 4A	200				V -> C (in Ref. 4; AAL56220). {ECO:0000305}.		integral component of membrane (GO:0016021)				autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(12)|prostate(1)|skin(4)	23						GCATTGCTGTGTCCCTCTCTG	0.453																																					p.V200V		Atlas-SNP	.											.	MS4A4A	76	.	0			c.G600A						PASS	.						335.0	284.0	301.0					11																	60073626		2203	4300	6503	SO:0001819	synonymous_variant	51338	exon6			TGCTGTGTCCCTC	AB013102	CCDS7982.1, CCDS58135.1	11q12	2012-02-28	2012-02-28		ENSG00000110079	ENSG00000110079			13371	protein-coding gene	gene with protein product		606547	"""membrane-spanning 4-domains, subfamily A, member 4"""	MS4A4		11245982, 11401424	Standard	NM_148975		Approved	CD20L1, MS4A7	uc001noz.3	Q96JQ5	OTTHUMG00000154949	ENST00000337908.4:c.600G>A	11.37:g.60073626G>A		408.0	1.0	0.00245098		377.0	179.0	0.474801	NM_148975	Q8TEZ6|Q96PG7|Q9BY18|Q9H3V3|Q9P1S3	Silent	SNP	ENST00000337908.4	37	CCDS7982.1																																																																																			.	.	none		0.453	MS4A4A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000337774.2		
FAM209B	388799	hgsc.bcm.edu	37	20	55108507	55108507	+	Missense_Mutation	SNP	C	C	A	rs200150839|rs386815438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108507C>A	ENST00000371325.1	+	1	206	c.110C>A	c.(109-111)cCg>cAg	p.P37Q		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	37				PC -> QY (in Ref. 2; AAI05793). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)											GGGAAGGTGCCGTGTGGAGAG	0.537													C|||	49	0.00978435	0.0023	0.0086	5008	,	,		20353	0.003		0.0089	False		,,,				2504	0.0286				p.P37Q		Atlas-SNP	.											.	.	.	.	0			c.C110A						PASS	.						167.0	140.0	149.0					20																	55108507		2203	4290	6493	SO:0001583	missense	388799	exon1			AGGTGCCGTGTGG	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.110C>A	20.37:g.55108507C>A	ENSP00000360376:p.Pro37Gln	293.0	0.0	0		181.0	26.0	0.143646	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	C	3.871	-0.027889	0.07589	.	.	ENSG00000213714	ENST00000371325	T	0.08720	3.06	2.8	2.8	0.32819	.	0.000000	0.49305	D	0.000143	T	0.15522	0.0374	L	0.36672	1.1	0.33241	D	0.557293	D	0.89917	1.0	D	0.91635	0.999	T	0.10200	-1.0640	10	0.30854	T	0.27	-19.843	9.141	0.36903	0.0:1.0:0.0:0.0	.	37	Q5JX69	CT107_HUMAN	Q	37	ENSP00000360376:P37Q	ENSP00000360376:P37Q	P	+	2	0	C20orf107	54541914	0.973000	0.33851	0.988000	0.46212	0.019000	0.09904	1.612000	0.36889	1.556000	0.49512	0.393000	0.25936	CCG	.	.	weak		0.537	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
ATG2B	55102	hgsc.bcm.edu	37	14	96800027	96800027	+	Missense_Mutation	SNP	C	C	T	rs183527316	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:96800027C>T	ENST00000359933.4	-	8	2098	c.1205G>A	c.(1204-1206)cGt>cAt	p.R402H		NM_018036.5	NP_060506	Q96BY7	ATG2B_HUMAN	autophagy related 2B	402					autophagic vacuole assembly (GO:0000045)|cellular response to nitrogen starvation (GO:0006995)|mitochondrion degradation (GO:0000422)|nucleophagy (GO:0044804)	extrinsic component of membrane (GO:0019898)|lipid particle (GO:0005811)|pre-autophagosomal structure (GO:0000407)				breast(3)|cervix(2)|endometrium(7)|kidney(4)|large_intestine(11)|liver(1)|lung(26)|ovary(1)|prostate(1)|skin(1)|urinary_tract(7)	64		all_cancers(154;0.0462)|all_epithelial(191;0.123)|Melanoma(154;0.155)		Epithelial(152;0.21)|COAD - Colon adenocarcinoma(157;0.244)		TTGCTTACCACGGCTAGAAGG	0.363													C|||	2	0.000399361	0.0	0.0	5008	,	,		16337	0.0		0.002	False		,,,				2504	0.0				p.R402H		Atlas-SNP	.											.	ATG2B	169	.	0			c.G1205A						PASS	.	C	HIS/ARG	4,3650		0,4,1823	77.0	70.0	72.0		1205	5.6	1.0	14		72	59,8131		0,59,4036	yes	missense	ATG2B	NM_018036.5	29	0,63,5859	TT,TC,CC		0.7204,0.1095,0.5319	benign	402/2079	96800027	63,11781	1827	4095	5922	SO:0001583	missense	55102	exon8			TTACCACGGCTAG	AK001104	CCDS9944.2	14q32.31	2014-02-12	2012-06-06	2007-07-31	ENSG00000066739	ENSG00000066739			20187	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 103"", ""ATG2 autophagy related 2 homolog B (S. cerevisiae)"""	C14orf103		22350415	Standard	NM_018036		Approved	FLJ10242	uc001yfi.3	Q96BY7	OTTHUMG00000149933	ENST00000359933.4:c.1205G>A	14.37:g.96800027C>T	ENSP00000353010:p.Arg402His	106.0	0.0	0		95.0	46.0	0.484211	NM_018036	Q6ZRE7|Q96DQ3|Q9NW80	Missense_Mutation	SNP	ENST00000359933.4	37	CCDS9944.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.68	3.189548	0.57909	0.001095	0.007204	ENSG00000066739	ENST00000359933	T	0.10382	2.88	5.6	5.6	0.85130	.	0.423584	0.20315	U	0.094755	T	0.05640	0.0148	N	0.19112	0.55	0.47341	D	0.999394	B	0.22211	0.066	B	0.14023	0.01	T	0.24657	-1.0154	10	0.41790	T	0.15	.	13.2187	0.59875	0.0:0.9272:0.0:0.0728	.	402	Q96BY7	ATG2B_HUMAN	H	402	ENSP00000353010:R402H	ENSP00000353010:R402H	R	-	2	0	ATG2B	95869780	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.238000	0.65366	2.793000	0.96121	0.591000	0.81541	CGT	C|0.998;T|0.002	0.002	strong		0.363	ATG2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314037.1	NM_018036	
PRRC2A	7916	hgsc.bcm.edu	37	6	31605016	31605016	+	Missense_Mutation	SNP	T	T	C	rs35595439	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31605016T>C	ENST00000376033.2	+	30	6482	c.6248T>C	c.(6247-6249)tTc>tCc	p.F2083S	PRRC2A_ENST00000376007.4_Missense_Mutation_p.F2083S	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	2083	3 X 50 AA type C repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						CTTAGGTCCTTCTCTGGCCTC	0.552													T|||	42	0.00838658	0.0068	0.0072	5008	,	,		17444	0.003		0.0099	False		,,,				2504	0.0153				p.F2083S		Atlas-SNP	.											.	PRRC2A	152	.	0			c.T6248C						PASS	.	T	SER/PHE,SER/PHE	10,3010		0,10,1500	86.0	81.0	83.0		6248,6248	5.6	1.0	6	dbSNP_126	83	41,5375		0,41,2667	yes	missense,missense	PRRC2A	NM_004638.3,NM_080686.2	155,155	0,51,4167	CC,CT,TT		0.757,0.3311,0.6046	probably-damaging,probably-damaging	2083/2158,2083/2158	31605016	51,8385	1510	2708	4218	SO:0001583	missense	7916	exon30			GGTCCTTCTCTGG	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.6248T>C	6.37:g.31605016T>C	ENSP00000365201:p.Phe2083Ser	104.0	0.0	0		100.0	52.0	0.52	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	T	11.20	1.569725	0.28003	0.003311	0.00757	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.01871	4.59;4.59	5.63	5.63	0.86233	.	0.374635	0.24516	N	0.037848	T	0.01800	0.0057	N	0.19112	0.55	0.42923	D	0.994293	D	0.61697	0.99	P	0.51657	0.676	T	0.64193	-0.6465	10	0.87932	D	0	-0.0191	13.6537	0.62325	0.0:0.0:0.0:1.0	rs35595439	2083	P48634	PRC2A_HUMAN	S	2075;2064;2083;2083;1308	ENSP00000365175:F2083S;ENSP00000365201:F2083S	ENSP00000365175:F2083S	F	+	2	0	PRRC2A	31712995	1.000000	0.71417	0.999000	0.59377	0.774000	0.43823	2.456000	0.44997	2.271000	0.75665	0.533000	0.62120	TTC	T|0.993;C|0.007	0.007	strong		0.552	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
NDRG1	10397	hgsc.bcm.edu	37	8	134296524	134296524	+	Missense_Mutation	SNP	C	C	T	rs145871479	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:134296524C>T	ENST00000414097.2	-	2	898	c.31G>A	c.(31-33)Gct>Act	p.A11T	NDRG1_ENST00000537882.1_5'UTR|NDRG1_ENST00000518066.1_Missense_Mutation_p.A11T|NDRG1_ENST00000354944.5_Missense_Mutation_p.A11T|NDRG1_ENST00000522476.1_Intron|NDRG1_ENST00000323851.7_Missense_Mutation_p.A11T|NDRG1_ENST00000518176.1_Missense_Mutation_p.A11T	NM_001135242.1	NP_001128714.1	Q92597	NDRG1_HUMAN	N-myc downstream regulated 1	11					cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|mast cell activation (GO:0045576)|peripheral nervous system myelin maintenance (GO:0032287)|positive regulation of spindle checkpoint (GO:0090232)|response to metal ion (GO:0010038)	cell-cell adherens junction (GO:0005913)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)	cadherin binding (GO:0045296)|gamma-tubulin binding (GO:0043015)|microtubule binding (GO:0008017)|Rab GTPase binding (GO:0017137)		NDRG1/ERG(5)	endometrium(2)|kidney(2)|large_intestine(2)|lung(5)|ovary(4)|prostate(1)|skin(1)	17	all_epithelial(106;4.26e-24)|Lung NSC(106;7.26e-07)|all_lung(105;2.77e-06)|Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0107)			TTCACCTCAGCGAGGTCTACA	0.552			T	ERG	prostate								C|||	3	0.000599042	0.0	0.0014	5008	,	,		20508	0.0		0.002	False		,,,				2504	0.0				p.A11T		Atlas-SNP	.		Dom	yes		8	8q24.3	10397	N-myc downstream regulated 1		E	.	NDRG1	40	.	0			c.G31A						PASS	.	C	THR/ALA,THR/ALA	3,4403	6.2+/-15.9	0,3,2200	234.0	169.0	191.0		31,31	5.0	0.4	8	dbSNP_134	191	15,8585	11.2+/-40.8	0,15,4285	yes	missense,missense	NDRG1	NM_001135242.1,NM_006096.3	58,58	0,18,6485	TT,TC,CC		0.1744,0.0681,0.1384	probably-damaging,probably-damaging	11/395,11/395	134296524	18,12988	2203	4300	6503	SO:0001583	missense	10397	exon2			CCTCAGCGAGGTC	X92845	CCDS34945.1, CCDS59112.1, CCDS59113.1	8q24	2014-09-17	2008-09-12		ENSG00000104419	ENSG00000104419			7679	protein-coding gene	gene with protein product		605262		CAP43		9251681, 8939898, 18455888	Standard	NM_006096		Approved	DRG1, RTP, TDD5, NDR1	uc003yue.2	Q92597	OTTHUMG00000164441	ENST00000414097.2:c.31G>A	8.37:g.134296524C>T	ENSP00000404854:p.Ala11Thr	201.0	0.0	0		213.0	117.0	0.549296	NM_006096	B3KR80|B7Z446|O15207|Q6IBG2|Q9NYR6|Q9UK29	Missense_Mutation	SNP	ENST00000414097.2	37	CCDS34945.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	6.861	0.528153	0.13127	6.81E-4	0.001744	ENSG00000104419	ENST00000323851;ENST00000537144;ENST00000354944;ENST00000414097;ENST00000518176;ENST00000518066;ENST00000520230;ENST00000519228;ENST00000519580;ENST00000522890;ENST00000520943;ENST00000521544;ENST00000522738	T;T;T;T;T;T;T;T;T;T	0.17854	2.44;2.51;2.44;2.35;2.41;2.39;2.39;2.35;2.39;2.25	5.03	5.03	0.67393	.	0.055881	0.64402	D	0.000001	T	0.21387	0.0515	N	0.17800	0.525	0.80722	D	1	D;B	0.76494	0.999;0.027	D;B	0.77004	0.989;0.011	T	0.01791	-1.1273	10	0.02654	T	1	-24.0443	13.7228	0.62737	0.0:1.0:0.0:0.0	.	11;11	E7ESM1;Q92597	.;NDRG1_HUMAN	T	11;11;11;11;11;11;28;11;11;11;22;11;65	ENSP00000319977:A11T;ENSP00000347028:A11T;ENSP00000404854:A11T;ENSP00000428345:A28T;ENSP00000429994:A11T;ENSP00000429272:A11T;ENSP00000428384:A11T;ENSP00000429840:A22T;ENSP00000429524:A11T;ENSP00000428991:A65T	ENSP00000319977:A11T	A	-	1	0	NDRG1	134365706	0.868000	0.29978	0.417000	0.26559	0.896000	0.52359	3.701000	0.54793	2.609000	0.88269	0.650000	0.86243	GCT	C|0.999;T|0.001	0.001	strong		0.552	NDRG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378805.1		
MUC4	4585	hgsc.bcm.edu	37	3	195508060	195508060	+	Missense_Mutation	SNP	G	G	A	rs200799263		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508060G>A	ENST00000463781.3	-	2	10850	c.10391C>T	c.(10390-10392)tCa>tTa	p.S3464L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S3464L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTGGATGCTGAGGAAGTGTC	0.582																																					p.S3464L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C10391T						PASS	.						27.0	23.0	24.0					3																	195508060		680	1581	2261	SO:0001583	missense	4585	exon2			GATGCTGAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10391C>T	3.37:g.195508060G>A	ENSP00000417498:p.Ser3464Leu	101.0	0.0	0		296.0	21.0	0.0709459	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	g	6.692	0.496377	0.12762	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28069	1.63;1.64	0.743	-1.49	0.08718	.	.	.	.	.	T	0.29389	0.0732	N	0.19112	0.55	0.09310	N	1	D	0.56968	0.978	D	0.65443	0.935	T	0.19712	-1.0297	8	.	.	.	.	3.8921	0.09123	0.0:0.0:0.3778:0.6221	.	3336	E7ESK3	.	L	3464	ENSP00000417498:S3464L;ENSP00000420243:S3464L	.	S	-	2	0	MUC4	196992839	0.001000	0.12720	0.130000	0.21974	0.131000	0.20780	0.570000	0.23653	0.088000	0.17205	0.089000	0.15464	TCA	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CYP2C9	1559	hgsc.bcm.edu	37	10	96740981	96740981	+	Missense_Mutation	SNP	C	C	T	rs28371685	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:96740981C>T	ENST00000260682.6	+	7	1015	c.1003C>T	c.(1003-1005)Cgg>Tgg	p.R335W		NM_000771.3	NP_000762.2	P11712	CP2C9_HUMAN	cytochrome P450, family 2, subfamily C, polypeptide 9	335			R -> W (in allele CYP2C9*11; dbSNP:rs28371685). {ECO:0000269|PubMed:11926893, ECO:0000269|PubMed:15469410}.		arachidonic acid metabolic process (GO:0019369)|cellular amide metabolic process (GO:0043603)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|urea metabolic process (GO:0019627)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	(R)-limonene 6-monooxygenase activity (GO:0052741)|(S)-limonene 6-monooxygenase activity (GO:0018675)|(S)-limonene 7-monooxygenase activity (GO:0018676)|caffeine oxidase activity (GO:0034875)|drug binding (GO:0008144)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|steroid hydroxylase activity (GO:0008395)			breast(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(9)|ovary(2)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	34		Colorectal(252;0.0902)		all cancers(201;6.93e-05)	Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Acetylsalicylic acid(DB00945)|Agomelatine(DB06594)|Alosetron(DB00969)|Alprazolam(DB00404)|Aminophenazone(DB01424)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amodiaquine(DB00613)|Amprenavir(DB00701)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Arformoterol(DB01274)|Artemether(DB06697)|Atazanavir(DB01072)|Atorvastatin(DB01076)|Atovaquone(DB01117)|Azelastine(DB00972)|Bexarotene(DB00307)|Bicalutamide(DB01128)|Bortezomib(DB00188)|Bosentan(DB00559)|Brompheniramine(DB00835)|Buprenorphine(DB00921)|Bupropion(DB01156)|Cabozantinib(DB08875)|Caffeine(DB00201)|Candesartan(DB00796)|Capecitabine(DB01101)|Carbamazepine(DB00564)|Carbinoxamine(DB00748)|Carvedilol(DB01136)|Celecoxib(DB00482)|Chloramphenicol(DB00446)|Chlorpropamide(DB00672)|Cholecalciferol(DB00169)|Cimetidine(DB00501)|Cinnarizine(DB00568)|Cisapride(DB00604)|Cisplatin(DB00515)|Clevidipine(DB04920)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cocaine(DB00907)|Colchicine(DB01394)|Cyclizine(DB01176)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapagliflozin(DB06292)|Dapsone(DB00250)|Delavirdine(DB00705)|Desloratadine(DB00967)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Dextromethorphan(DB00514)|Dextropropoxyphene(DB00647)|Diazepam(DB00829)|Diclofenac(DB00586)|Diclofenamide(DB01144)|Dicoumarol(DB00266)|Diethylstilbestrol(DB00255)|Diltiazem(DB00343)|Diphenhydramine(DB01075)|Disulfiram(DB00822)|Dolasetron(DB00757)|Donepezil(DB00843)|Dopamine(DB00988)|Dorzolamide(DB00869)|Doxepin(DB01142)|Dronabinol(DB00470)|Efavirenz(DB00625)|Eletriptan(DB00216)|Enzalutamide(DB08899)|Epinephrine(DB00668)|Epoprostenol(DB01240)|Eprosartan(DB00876)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Eszopiclone(DB00402)|Ethanol(DB00898)|Etodolac(DB00749)|Etoricoxib(DB01628)|Etravirine(DB06414)|Felodipine(DB01023)|Fenofibrate(DB01039)|Flecainide(DB01195)|Fluconazole(DB00196)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Flurbiprofen(DB00712)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Formoterol(DB00983)|Fosphenytoin(DB01320)|Gefitinib(DB00317)|Gemfibrozil(DB01241)|Ginkgo biloba(DB01381)|Gliclazide(DB01120)|Glimepiride(DB00222)|Glipizide(DB01067)|Glyburide(DB01016)|Guanfacine(DB01018)|Haloperidol(DB00502)|Halothane(DB01159)|Hexobarbital(DB01355)|Histamine Phosphate(DB00667)|Human Serum Albumin(DB00062)|Hydromorphone(DB00327)|Ibuprofen(DB01050)|Idarubicin(DB01177)|Ifosfamide(DB01181)|Imatinib(DB00619)|Indinavir(DB00224)|Indomethacin(DB00328)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketamine(DB01221)|Ketobemidone(DB06738)|Ketoconazole(DB01026)|Ketoprofen(DB01009)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Lidocaine(DB00281)|Lopinavir(DB01601)|Loratadine(DB00455)|Lornoxicam(DB06725)|Losartan(DB00678)|Lovastatin(DB00227)|Lumiracoxib(DB01283)|Medroxyprogesterone Acetate(DB00603)|Mefenamic acid(DB00784)|Melatonin(DB01065)|Meloxicam(DB00814)|Mestranol(DB01357)|Methadone(DB00333)|Methazolamide(DB00703)|Methimazole(DB00763)|Methoxyflurane(DB01028)|Metronidazole(DB00916)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Montelukast(DB00471)|Naproxen(DB00788)|Nateglinide(DB00731)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilotinib(DB04868)|Nilutamide(DB00665)|Nilvadipine(DB06712)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Ospemifene(DB04938)|Oxaprozin(DB00991)|Paclitaxel(DB01229)|Pantoprazole(DB00213)|Paramethadione(DB00617)|Paroxetine(DB00715)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phenprocoumon(DB00946)|Phentermine(DB00191)|Phenylbutazone(DB00812)|Phenytoin(DB00252)|Pioglitazone(DB01132)|Piroxicam(DB00554)|Pitavastatin(DB08860)|Pranlukast(DB01411)|Prasugrel(DB06209)|Pravastatin(DB00175)|Primidone(DB00794)|Probenecid(DB01032)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Promethazine(DB01069)|Propafenone(DB01182)|Propofol(DB00818)|Pyrimethamine(DB00205)|Quazepam(DB01589)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Regorafenib(DB08896)|Rifampicin(DB01045)|Rifapentine(DB01201)|Ritonavir(DB00503)|Rosiglitazone(DB00412)|Rosuvastatin(DB01098)|Salicylic acid(DB00936)|Saquinavir(DB01232)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sitaxentan(DB06268)|Sorafenib(DB00398)|Sulfadiazine(DB00359)|Sulfadimethoxine(DB06150)|Sulfamethizole(DB00576)|Sulfamethoxazole(DB01015)|Sulfamoxole(DB08798)|Sulfanilamide(DB00259)|Sulfaphenazole(DB06729)|Sulfapyridine(DB00891)|Sulfinpyrazone(DB01138)|Sulfisoxazole(DB00263)|Suprofen(DB00870)|Tamoxifen(DB00675)|Tapentadol(DB06204)|Temazepam(DB00231)|Teniposide(DB00444)|Tenoxicam(DB00469)|Terbinafine(DB00857)|Testosterone(DB00624)|Thalidomide(DB01041)|Theophylline(DB00277)|Thiamylal(DB01154)|Thioridazine(DB00679)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tolbutamide(DB01124)|Tolcapone(DB00323)|Tolterodine(DB01036)|Torasemide(DB00214)|Trabectedin(DB05109)|Tranylcypromine(DB00752)|Treprostinil(DB00374)|Tretinoin(DB00755)|Triazolam(DB00897)|Trimethadione(DB00347)|Trimethoprim(DB00440)|Trimipramine(DB00726)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Valsartan(DB00177)|Venlafaxine(DB00285)|Verapamil(DB00661)|Vismodegib(DB08828)|Voriconazole(DB00582)|Warfarin(DB00682)|Ximelagatran(DB04898)|Zafirlukast(DB00549)|Zalcitabine(DB00943)|Zidovudine(DB00495)|Zileuton(DB00744)|Zolpidem(DB00425)|Zopiclone(DB01198)	TGGCAGAAACCGGAGCCCCTG	0.498													C|||	36	0.0071885	0.0242	0.0014	5008	,	,		17934	0.0		0.002	False		,,,				2504	0.001				p.R335W	Ovarian(54;1266 1406 16072 35076)	Atlas-SNP	.											CYP2C9,NS,carcinoma,-1,1	CYP2C9	82	1	0			c.C1003T	GRCh37	CM056574	CYP2C9	M	rs28371685	scavenged	.	C	TRP/ARG	84,4322		0,84,2119	164.0	146.0	152.0		1003	2.8	0.9	10	dbSNP_125	152	16,8584		0,16,4284	no	missense	CYP2C9	NM_000771.3	101	0,100,6403	TT,TC,CC		0.186,1.9065,0.7689	probably-damaging	335/491	96740981	100,12906	2203	4300	6503	SO:0001583	missense	1559	exon7			AGAAACCGGAGCC	M61855	CCDS7437.1	10q24.1	2007-12-14	2003-01-14		ENSG00000138109	ENSG00000138109		"""Cytochrome P450s"""	2623	protein-coding gene	gene with protein product		601130	"""cytochrome P450, subfamily IIC (mephenytoin 4-hydroxylase), polypeptide 9"""	CYP2C10		2009263, 7841444	Standard	NM_000771		Approved	P450IIC9	uc001kka.4	P11712	OTTHUMG00000018805	ENST00000260682.6:c.1003C>T	10.37:g.96740981C>T	ENSP00000260682:p.Arg335Trp	158.0	1.0	0.00632911		199.0	107.0	0.537688	NM_000771	P11713|Q16756|Q16872|Q5VX92|Q6IRV8|Q8WW80	Missense_Mutation	SNP	ENST00000260682.6	37	CCDS7437.1	14	0.00641025641025641	14	0.028455284552845527	0	0.0	0	0.0	0	0.0	.	12.02	1.813765	0.32053	0.019065	0.00186	ENSG00000138109	ENST00000545448;ENST00000260682	T	0.71698	-0.59	3.78	2.85	0.33270	.	0.293574	0.27035	U	0.021241	T	0.74772	0.3760	H	0.97186	3.955	0.18873	N	0.999988	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.73905	-0.3835	10	0.87932	D	0	.	10.7287	0.46083	0.191:0.809:0.0:0.0	rs28371685;rs60219528	335;335	Q5VX92;P11712	.;CP2C9_HUMAN	W	335	ENSP00000260682:R335W	ENSP00000260682:R335W	R	+	1	2	CYP2C9	96730971	0.615000	0.27026	0.866000	0.34008	0.172000	0.22775	1.328000	0.33758	0.910000	0.36722	0.305000	0.20034	CGG	C|0.986;T|0.014	0.014	strong		0.498	CYP2C9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049501.1	NM_000771	
WNT10A	80326	hgsc.bcm.edu	37	2	219754822	219754822	+	Missense_Mutation	SNP	G	G	A	rs77583146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:219754822G>A	ENST00000258411.3	+	3	1126	c.493G>A	c.(493-495)Ggg>Agg	p.G165R		NM_025216.2	NP_079492.2	Q9GZT5	WN10A_HUMAN	wingless-type MMTV integration site family, member 10A	165					cell fate commitment (GO:0045165)|cellular response to transforming growth factor beta stimulus (GO:0071560)|epidermis morphogenesis (GO:0048730)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|neural crest cell differentiation (GO:0014033)|neuron differentiation (GO:0030182)|odontogenesis (GO:0042476)|positive regulation of gene expression (GO:0010628)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|sebaceous gland development (GO:0048733)|skin development (GO:0043588)|tongue development (GO:0043586)|Wnt signaling pathway (GO:0016055)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|cervix(1)|endometrium(2)|lung(6)|skin(2)	12		Renal(207;0.0474)		Epithelial(149;4.26e-07)|all cancers(144;8.8e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GTCCCGGCGAGGGGACGAGGA	0.642													G|||	11	0.00219649	0.0015	0.0014	5008	,	,		18771	0.0		0.007	False		,,,				2504	0.001				p.G165R		Atlas-SNP	.											.	WNT10A	35	.	0			c.G493A						PASS	.	G	ARG/GLY	10,4396	16.8+/-37.8	0,10,2193	68.0	56.0	60.0		493	4.5	1.0	2	dbSNP_131	60	92,8508	51.1+/-111.2	0,92,4208	yes	missense	WNT10A	NM_025216.2	125	0,102,6401	AA,AG,GG		1.0698,0.227,0.7843	probably-damaging	165/418	219754822	102,12904	2203	4300	6503	SO:0001583	missense	80326	exon3			CGGCGAGGGGACG	AB059569	CCDS2426.1	2q35	2008-05-23			ENSG00000135925	ENSG00000135925		"""Wingless-type MMTV integration sites"""	13829	protein-coding gene	gene with protein product		606268				11350055, 17847007	Standard	NM_025216		Approved		uc002vjd.1	Q9GZT5	OTTHUMG00000133085	ENST00000258411.3:c.493G>A	2.37:g.219754822G>A	ENSP00000258411:p.Gly165Arg	64.0	0.0	0		83.0	44.0	0.53012	NM_025216	Q53S44|Q96TA7|Q9H7S8	Missense_Mutation	SNP	ENST00000258411.3	37	CCDS2426.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	16.51	3.143104	0.57044	0.00227	0.010698	ENSG00000135925	ENST00000258411	T	0.76060	-0.99	4.46	4.46	0.54185	.	0.457875	0.21825	N	0.068570	T	0.69296	0.3095	M	0.66297	2.02	0.80722	D	1	B	0.24576	0.106	B	0.31751	0.135	T	0.74444	-0.3663	10	0.59425	D	0.04	.	16.2054	0.82126	0.0:0.0:1.0:0.0	.	165	Q9GZT5	WN10A_HUMAN	R	165	ENSP00000258411:G165R	ENSP00000258411:G165R	G	+	1	0	WNT10A	219463066	1.000000	0.71417	0.989000	0.46669	0.487000	0.33371	7.398000	0.79919	2.478000	0.83669	0.655000	0.94253	GGG	G|0.993;A|0.007	0.007	strong		0.642	WNT10A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256730.2	NM_025216	
MUC5B	727897	hgsc.bcm.edu	37	11	1258387	1258387	+	Missense_Mutation	SNP	G	G	A	rs202160055		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1258387G>A	ENST00000529681.1	+	25	3348	c.3290G>A	c.(3289-3291)cGc>cAc	p.R1097H	MUC5B_ENST00000447027.1_Missense_Mutation_p.R1100H	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1097	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCCGCCTGCCGCTCCCAGGTG	0.682																																					p.R1097H		Atlas-SNP	.											MUC5B,NS,carcinoma,+1,4	MUC5B	473	4	0			c.G3290A						scavenged	.						10.0	16.0	14.0					11																	1258387		1900	4086	5986	SO:0001583	missense	727897	exon25			CCTGCCGCTCCCA	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.3290G>A	11.37:g.1258387G>A	ENSP00000436812:p.Arg1097His	39.0	0.0	0		24.0	3.0	0.125	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	6.941	0.543406	0.13250	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.72505	-0.66;-0.66	4.38	-0.728	0.11162	von Willebrand factor, type D domain (1);Uncharacterised domain, cysteine-rich (2);	.	.	.	.	T	0.30198	0.0757	N	0.00135	-2.02	0.26154	N	0.980103	B;B;B	0.24132	0.004;0.098;0.098	B;B;B	0.12837	0.001;0.008;0.008	T	0.37934	-0.9684	9	0.87932	D	0	.	8.5449	0.33415	0.6733:0.0:0.3267:0.0	rs35573593	1097;1790;1100	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	H	1097;1100;1098;1167	ENSP00000436812:R1097H;ENSP00000415793:R1100H	ENSP00000343037:R1098H	R	+	2	0	MUC5B	1214963	0.002000	0.14202	0.101000	0.21167	0.007000	0.05969	0.139000	0.16036	-0.476000	0.06842	-0.379000	0.06801	CGC	.	.	weak		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
SYNE1	23345	hgsc.bcm.edu	37	6	152730807	152730807	+	Missense_Mutation	SNP	C	C	G	rs374482089		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:152730807C>G	ENST00000367255.5	-	43	6869	c.6268G>C	c.(6268-6270)Gaa>Caa	p.E2090Q	SYNE1_ENST00000423061.1_Missense_Mutation_p.E2097Q|SYNE1_ENST00000265368.4_Missense_Mutation_p.E2090Q|SYNE1_ENST00000448038.1_Missense_Mutation_p.E2097Q|RNA5SP223_ENST00000365174.1_RNA|SYNE1_ENST00000341594.5_Missense_Mutation_p.E2127Q	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2090					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		TTCTGATATTCTCTCATTAAG	0.368										HNSCC(10;0.0054)																											p.E2097Q		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G6289C						PASS	.	C	GLN/GLU,GLN/GLU	0,4406		0,0,2203	98.0	96.0	96.0		6268,6289	5.9	1.0	6		96	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	SYNE1	NM_182961.3,NM_033071.3	29,29	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	benign,benign	2090/8798,2097/8750	152730807	1,13005	2203	4300	6503	SO:0001583	missense	23345	exon43			GATATTCTCTCAT	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.6268G>C	6.37:g.152730807C>G	ENSP00000356224:p.Glu2090Gln	83.0	0.0	0		85.0	43.0	0.505882	NM_033071	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658164	0.47467	0.0	1.16E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.31510	1.49;1.49;1.49;1.49;1.49	5.92	5.92	0.95590	.	0.192526	0.36134	N	0.002765	T	0.18841	0.0452	L	0.59436	1.845	0.80722	D	1	P;B;B;B	0.38250	0.624;0.011;0.023;0.019	B;B;B;B	0.39706	0.307;0.005;0.008;0.011	T	0.02244	-1.1189	10	0.12430	T	0.62	.	14.4744	0.67537	0.0:0.9305:0.0:0.0695	.	2073;2090;2090;2097	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	Q	2090;2097;2090;2097;2127	ENSP00000356224:E2090Q;ENSP00000396024:E2097Q;ENSP00000265368:E2090Q;ENSP00000390975:E2097Q;ENSP00000341887:E2127Q	ENSP00000265368:E2090Q	E	-	1	0	SYNE1	152772500	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.922000	0.63404	2.822000	0.97130	0.650000	0.86243	GAA	.	.	weak		0.368	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
FST	10468	hgsc.bcm.edu	37	5	52781029	52781029	+	Silent	SNP	G	G	A	rs11746136	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:52781029G>A	ENST00000256759.3	+	5	1307	c.924G>A	c.(922-924)ctG>ctA	p.L308L	FST_ENST00000396947.3_Silent_p.L308L	NM_013409.2	NP_037541.1	P19883	FST_HUMAN	follistatin	308	Kazal-like 3. {ECO:0000255|PROSITE- ProRule:PRU00798}.				BMP signaling pathway (GO:0030509)|female gonad development (GO:0008585)|gamete generation (GO:0007276)|hair follicle morphogenesis (GO:0031069)|hematopoietic progenitor cell differentiation (GO:0002244)|keratinocyte proliferation (GO:0043616)|negative regulation of activin receptor signaling pathway (GO:0032926)|negative regulation of cell differentiation (GO:0045596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|odontogenesis of dentin-containing tooth (GO:0042475)|pattern specification process (GO:0007389)|positive regulation of hair follicle development (GO:0051798)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nucleus (GO:0005634)	activin binding (GO:0048185)|signal transducer activity (GO:0004871)			breast(1)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|urinary_tract(1)	15		Ovarian(174;1.78e-06)|Lung NSC(810;3.55e-06)|Breast(144;4.08e-05)				GTGTGCTACTGGAAGTAAAGC	0.502													G|||	45	0.00898562	0.0144	0.013	5008	,	,		17704	0.0		0.0169	False		,,,				2504	0.0				p.L308L		Atlas-SNP	.											.	FST	42	.	0			c.G924A						PASS	.	G	,	81,4325	70.9+/-108.8	1,79,2123	120.0	105.0	110.0		924,924	3.5	1.0	5	dbSNP_120	110	140,8460	69.4+/-131.9	2,136,4162	no	coding-synonymous,coding-synonymous	FST	NM_006350.3,NM_013409.2	,	3,215,6285	AA,AG,GG		1.6279,1.8384,1.6992	,	308/318,308/345	52781029	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	10468	exon5			GCTACTGGAAGTA	M19481	CCDS3959.1, CCDS43315.1	5q11.2	2008-02-05			ENSG00000134363	ENSG00000134363			3971	protein-coding gene	gene with protein product		136470				10411917, 3380788	Standard	NM_006350		Approved	FS	uc003jpd.3	P19883	OTTHUMG00000131183	ENST00000256759.3:c.924G>A	5.37:g.52781029G>A		52.0	0.0	0		57.0	27.0	0.473684	NM_013409	B5BU94|Q9BTH0	Silent	SNP	ENST00000256759.3	37	CCDS3959.1	31	0.014194139194139194	11	0.022357723577235773	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	3.057	-0.193992	0.06259	0.018384	0.016279	ENSG00000134363	ENST00000497789	.	.	.	5.35	3.52	0.40303	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-12.3382	7.2089	0.25923	0.1577:0.0:0.6997:0.1425	rs11746136	.	.	.	X	93	.	.	W	+	2	0	FST	52816786	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.792000	0.47837	0.705000	0.31890	0.655000	0.94253	TGG	G|0.983;A|0.017	0.017	strong		0.502	FST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253906.1	NM_013409	
TRAF6	7189	hgsc.bcm.edu	37	11	36518764	36518764	+	Missense_Mutation	SNP	C	C	T	rs577802750		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:36518764C>T	ENST00000526995.1	-	4	746	c.500G>A	c.(499-501)cGt>cAt	p.R167H	TRAF6_ENST00000348124.5_Missense_Mutation_p.R167H|TRAF6_ENST00000529150.1_5'Flank	NM_004620.3	NP_004611.1	Q9Y4K3	TRAF6_HUMAN	TNF receptor-associated factor 6, E3 ubiquitin protein ligase	167	Interaction with TAX1BP1.				activation of MAPK activity (GO:0000187)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of protein kinase activity (GO:0032147)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|apoptotic signaling pathway (GO:0097190)|bone resorption (GO:0045453)|cell development (GO:0048468)|cellular response to lipopolysaccharide (GO:0071222)|Fc-epsilon receptor signaling pathway (GO:0038095)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|JNK cascade (GO:0007254)|membrane protein intracellular domain proteolysis (GO:0031293)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of apoptotic process (GO:0043066)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of lipopolysaccharide-mediated signaling pathway (GO:0031666)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of T cell activation (GO:0050870)|positive regulation of T cell cytokine production (GO:0002726)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription regulatory region DNA binding (GO:2000679)|protein autoubiquitination (GO:0051865)|protein complex assembly (GO:0006461)|protein K63-linked ubiquitination (GO:0070534)|protein polyubiquitination (GO:0000209)|regulation of immunoglobulin secretion (GO:0051023)|response to interleukin-1 (GO:0070555)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|lipid particle (GO:0005811)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	histone deacetylase binding (GO:0042826)|ligase activity (GO:0016874)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thioesterase binding (GO:0031996)|tumor necrosis factor receptor binding (GO:0005164)|ubiquitin conjugating enzyme binding (GO:0031624)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(13)|ovary(2)|pancreas(1)	27	all_lung(20;0.211)	all_hematologic(20;0.107)				TTGGAAGGGACGCTGGCATTG	0.378																																					p.R167H		Atlas-SNP	.											.	TRAF6	56	.	0			c.G500A						PASS	.						72.0	75.0	74.0					11																	36518764		2202	4298	6500	SO:0001583	missense	7189	exon4			AAGGGACGCTGGC		CCDS7901.1	11p12	2013-01-09	2012-02-23		ENSG00000175104	ENSG00000175104		"""RING-type (C3HC4) zinc fingers"""	12036	protein-coding gene	gene with protein product		602355	"""TNF receptor-associated factor 6"""			8837778	Standard	NM_004620		Approved	RNF85	uc001mws.2	Q9Y4K3	OTTHUMG00000166391	ENST00000526995.1:c.500G>A	11.37:g.36518764C>T	ENSP00000433623:p.Arg167His	68.0	0.0	0		42.0	19.0	0.452381	NM_004620	A6NKI7|A8KAB3|D3DR16|Q8NEH5	Missense_Mutation	SNP	ENST00000526995.1	37	CCDS7901.1	.	.	.	.	.	.	.	.	.	.	C	6.898	0.535263	0.13188	.	.	ENSG00000175104	ENST00000526995;ENST00000348124	T;T	0.25579	1.79;1.79	5.49	-1.99	0.07457	Zinc finger, TRAF-type (1);	0.684611	0.15781	N	0.244901	T	0.13586	0.0329	N	0.22421	0.69	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.16928	-1.0386	10	0.42905	T	0.14	-4.1496	7.0542	0.25089	0.1248:0.5163:0.0:0.3588	.	167	Q9Y4K3	TRAF6_HUMAN	H	167	ENSP00000433623:R167H;ENSP00000337853:R167H	ENSP00000337853:R167H	R	-	2	0	TRAF6	36475340	0.055000	0.20627	0.000000	0.03702	0.226000	0.24999	1.129000	0.31381	-0.206000	0.10203	0.650000	0.86243	CGT	.	.	none		0.378	TRAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389530.1	NM_145803	
MARCH7	64844	hgsc.bcm.edu	37	2	160604781	160604781	+	Missense_Mutation	SNP	G	G	A	rs142330597		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160604781G>A	ENST00000259050.4	+	5	1102	c.980G>A	c.(979-981)cGt>cAt	p.R327H	MARCH7_ENST00000409591.1_Missense_Mutation_p.R289H|MARCH7_ENST00000539065.1_Missense_Mutation_p.R271H|MARCH7_ENST00000409175.1_Missense_Mutation_p.R327H	NM_001282805.1|NM_001282807.1|NM_022826.2	NP_001269734.1|NP_001269736.1|NP_073737.1	Q9H992	MARH7_HUMAN	membrane-associated ring finger (C3HC4) 7, E3 ubiquitin protein ligase	327	Ser-rich.				protein ubiquitination (GO:0016567)		ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(3)|prostate(1)|skin(1)|stomach(2)	18						TCACAGTCCCGTAGTAATGTA	0.398													G|||	1	0.000199681	0.0	0.0	5008	,	,		19489	0.0		0.001	False		,,,				2504	0.0				p.R327H		Atlas-SNP	.											MARCH7,NS,carcinoma,+1,1	MARCH7	48	1	0			c.G980A						PASS	.	G	HIS/ARG	0,4404		0,0,2202	52.0	56.0	54.0		980	5.7	1.0	2	dbSNP_134	54	11,8589	8.4+/-32.0	0,11,4289	yes	missense	MARCH7	NM_022826.2	29	0,11,6491	AA,AG,GG		0.1279,0.0,0.0846	possibly-damaging	327/705	160604781	11,12993	2202	4300	6502	SO:0001583	missense	64844	exon5			AGTCCCGTAGTAA	AK022973	CCDS2210.1, CCDS63038.1, CCDS63039.1	2q24.2	2013-01-09	2012-02-23	2005-01-27	ENSG00000136536	ENSG00000136536		"""MARCH membrane-associated ring fingers"", ""RING-type (C3HC4) zinc fingers"""	17393	protein-coding gene	gene with protein product		613334	"""axotrophin"", ""membrane-associated ring finger (C3HC4) 7"""	AXOT		14722266	Standard	XM_005246773		Approved	MARCH-VII, RNF177	uc002uax.3	Q9H992	OTTHUMG00000132029	ENST00000259050.4:c.980G>A	2.37:g.160604781G>A	ENSP00000259050:p.Arg327His	77.0	0.0	0		97.0	41.0	0.42268	NM_022826	A8K9X1|B7Z7P5|D3DPB0|Q53GQ1|Q9BTR9	Missense_Mutation	SNP	ENST00000259050.4	37	CCDS2210.1	.	.	.	.	.	.	.	.	.	.	G	19.19	3.780091	0.70222	0.0	0.001279	ENSG00000136536	ENST00000409175;ENST00000539065;ENST00000259050;ENST00000409591	T;T;T;T	0.36520	1.25;1.25;1.25;1.25	5.72	5.72	0.89469	.	0.363453	0.33382	N	0.004966	T	0.45637	0.1352	L	0.29908	0.895	0.30173	N	0.801097	D;D;D	0.69078	0.997;0.99;0.99	P;P;B	0.57548	0.823;0.469;0.374	T	0.36432	-0.9748	10	0.41790	T	0.15	-7.7841	19.8788	0.96888	0.0:0.0:1.0:0.0	.	271;289;327	F5H6W4;B7Z7P5;Q9H992	.;.;MARH7_HUMAN	H	327;271;327;289	ENSP00000386830:R327H;ENSP00000442992:R271H;ENSP00000259050:R327H;ENSP00000387238:R289H	ENSP00000259050:R327H	R	+	2	0	MARCH7	160313027	1.000000	0.71417	1.000000	0.80357	0.850000	0.48378	6.983000	0.76180	2.683000	0.91414	0.655000	0.94253	CGT	G|0.999;A|0.001	0.001	strong		0.398	MARCH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255040.3	NM_022826	
EDEM1	9695	hgsc.bcm.edu	37	3	5229643	5229643	+	Silent	SNP	C	C	T	rs144177905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:5229643C>T	ENST00000256497.4	+	1	286	c.153C>T	c.(151-153)ggC>ggT	p.G51G	AC026202.1_ENST00000600805.1_Missense_Mutation_p.A114T|AC026202.3_ENST00000439325.1_RNA|EDEM1_ENST00000445686.1_5'Flank	NM_014674.2	NP_055489.1	Q92611	EDEM1_HUMAN	ER degradation enhancer, mannosidase alpha-like 1	51					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	calcium ion binding (GO:0005509)|misfolded protein binding (GO:0051787)			NS(1)|breast(1)|endometrium(1)|large_intestine(5)|liver(2)|lung(4)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	22				Epithelial(13;0.0588)|OV - Ovarian serous cystadenocarcinoma(96;0.0682)		GCCCCGACGGCCCCGCGTCGC	0.736													c|||	84	0.0167732	0.0008	0.013	5008	,	,		8316	0.001		0.0408	False		,,,				2504	0.0327				p.G51G		Atlas-SNP	.											.	EDEM1	45	.	0			c.C153T						PASS	.			18,3802		0,18,1892	4.0	5.0	5.0		153	3.5	0.3	3	dbSNP_134	5	227,7631		2,223,3704	no	coding-synonymous	EDEM1	NM_014674.2		2,241,5596	TT,TC,CC		2.8888,0.4712,2.098		51/658	5229643	245,11433	1910	3929	5839	SO:0001819	synonymous_variant	9695	exon1			CGACGGCCCCGCG	D86967	CCDS33686.1	3p26.1	2008-02-05			ENSG00000134109	ENSG00000134109			18967	protein-coding gene	gene with protein product		607673				12610306	Standard	NM_014674		Approved	KIAA0212, EDEM	uc003bqi.3	Q92611	OTTHUMG00000154896	ENST00000256497.4:c.153C>T	3.37:g.5229643C>T		39.0	0.0	0		21.0	15.0	0.714286	NM_014674	A8K9C8|B4DXP3	Silent	SNP	ENST00000256497.4	37	CCDS33686.1																																																																																			C|0.985;T|0.015	0.015	strong		0.736	EDEM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337566.2	NM_014674	
CCDC174	51244	hgsc.bcm.edu	37	3	14712433	14712433	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14712433A>G	ENST00000383794.3	+	11	1209	c.1136A>G	c.(1135-1137)cAg>cGg	p.Q379R	CCDC174_ENST00000303688.7_Missense_Mutation_p.Q303R|CCDC174_ENST00000476763.1_3'UTR	NM_016474.4	NP_057558.3	Q6PII3	CC174_HUMAN	coiled-coil domain containing 174	379						cytoplasm (GO:0005737)|nucleus (GO:0005634)											TCGAAGAGGCAGTCAGATCTC	0.423																																					p.Q379R		Atlas-SNP	.											.	.	.	.	0			c.A1136G						PASS	.						44.0	42.0	42.0					3																	14712433		2203	4300	6503	SO:0001583	missense	51244	exon11			AGAGGCAGTCAGA	AF151046	CCDS2620.2	3p25.1	2012-09-20	2012-09-20	2012-09-20	ENSG00000154781	ENSG00000154781			28033	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 19"""	C3orf19		11042152	Standard	NM_016474		Approved	FLJ33839	uc003byw.3	Q6PII3	OTTHUMG00000129837	ENST00000383794.3:c.1136A>G	3.37:g.14712433A>G	ENSP00000373304:p.Gln379Arg	165.0	0.0	0		206.0	91.0	0.441748	NM_016474	Q96CS5	Missense_Mutation	SNP	ENST00000383794.3	37	CCDS2620.2	.	.	.	.	.	.	.	.	.	.	A	10.78	1.447406	0.25987	.	.	ENSG00000154781	ENST00000383794;ENST00000303688;ENST00000285042	T;T	0.41065	1.01;1.07	5.38	5.38	0.77491	.	0.056905	0.64402	D	0.000002	T	0.28499	0.0705	L	0.43923	1.385	0.24589	N	0.993836	B	0.06786	0.001	B	0.06405	0.002	T	0.22173	-1.0224	10	0.11794	T	0.64	-35.5946	4.9429	0.13975	0.751:0.0:0.0857:0.1633	.	379	Q6PII3	CC019_HUMAN	R	379;303;206	ENSP00000373304:Q379R;ENSP00000302344:Q303R	ENSP00000285042:Q206R	Q	+	2	0	C3orf19	14687437	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.611000	0.54132	2.042000	0.60477	0.482000	0.46254	CAG	.	.	none		0.423	CCDC174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252077.2	NM_016474	
CDAN1	146059	hgsc.bcm.edu	37	15	43022868	43022868	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43022868G>A	ENST00000356231.3	-	14	2125	c.2102C>T	c.(2101-2103)tCc>tTc	p.S701F		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1	701					chromatin assembly (GO:0031497)|chromatin organization (GO:0006325)|negative regulation of DNA replication (GO:0008156)|protein localization (GO:0008104)	cytoplasm (GO:0005737)|endomembrane system (GO:0012505)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(3)	24		all_cancers(109;5.4e-16)|all_epithelial(112;2.97e-14)|Lung NSC(122;1.75e-08)|all_lung(180;5.99e-08)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;2.49e-07)		GTCAGCAAAGGAGAGAAACTC	0.622																																					p.S701F		Atlas-SNP	.											.	CDAN1	70	.	0			c.C2102T						PASS	.						38.0	41.0	40.0					15																	43022868		2203	4299	6502	SO:0001583	missense	146059	exon14			GCAAAGGAGAGAA	AF525398	CCDS32209.1	15q15.2	2012-04-25	2012-04-25			ENSG00000140326			1713	protein-coding gene	gene with protein product		607465	"""congenital dyserythropoietic anemia, type I"""			8634422, 12434312	Standard	XM_005254177		Approved	CDA-I, CDAI	uc001zql.3	Q8IWY9		ENST00000356231.3:c.2102C>T	15.37:g.43022868G>A	ENSP00000348564:p.Ser701Phe	179.0	0.0	0		186.0	10.0	0.0537634	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Missense_Mutation	SNP	ENST00000356231.3	37	CCDS32209.1	.	.	.	.	.	.	.	.	.	.	G	31	5.097079	0.94197	.	.	ENSG00000140326	ENST00000356231;ENST00000267892	D	0.86432	-2.12	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	D	0.93887	0.8044	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.93948	0.7229	10	0.87932	D	0	-20.6001	19.9915	0.97366	0.0:0.0:1.0:0.0	.	701	Q8IWY9	CDAN1_HUMAN	F	701;699	ENSP00000348564:S701F	ENSP00000267892:S699F	S	-	2	0	CDAN1	40810160	1.000000	0.71417	0.705000	0.30386	0.941000	0.58515	9.420000	0.97426	2.723000	0.93209	0.655000	0.94253	TCC	.	.	none		0.622	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
SALL3	27164	hgsc.bcm.edu	37	18	76757145	76757145	+	Silent	SNP	C	C	T	rs148335210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:76757145C>T	ENST00000537592.2	+	3	3726	c.3726C>T	c.(3724-3726)ccC>ccT	p.P1242P	SALL3_ENST00000575389.2_Silent_p.P1170P|SALL3_ENST00000536229.3_Silent_p.P1037P	NM_171999.3	NP_741996.2	Q9BXA9	SALL3_HUMAN	spalt-like transcription factor 3	1242					forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|negative regulation of smoothened signaling pathway (GO:0045879)|olfactory bulb interneuron development (GO:0021891)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.P1242P(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(8)|lung(40)|ovary(4)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	74		Esophageal squamous(42;0.129)|Melanoma(33;0.16)|Prostate(75;0.167)		OV - Ovarian serous cystadenocarcinoma(15;4.69e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0256)		CCCAGCTCCCCGTGAGTCTTG	0.612													C|||	6	0.00119808	0.0	0.0029	5008	,	,		17088	0.0		0.003	False		,,,				2504	0.001				p.P1242P		Atlas-SNP	.											SALL3,NS,malignant_melanoma,+2,1	SALL3	162	1	1	Substitution - coding silent(1)	lung(1)	c.C3726T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	94.0	90.0	92.0		3726	-10.8	0.0	18	dbSNP_134	92	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous	SALL3	NM_171999.2		0,14,6489	TT,TC,CC		0.1163,0.0908,0.1076		1242/1301	76757145	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	27164	exon3			GCTCCCCGTGAGT	AJ007421	CCDS12013.1	18q23	2013-10-17	2013-10-17		ENSG00000256463	ENSG00000256463		"""Zinc fingers, C2H2-type"""	10527	protein-coding gene	gene with protein product		605079	"""sal (Drosophila)-like 3"", ""sal-like 3 (Drosophila)"""			10610715	Standard	NM_171999		Approved	ZNF796	uc002lmt.3	Q9BXA9	OTTHUMG00000132896	ENST00000537592.2:c.3726C>T	18.37:g.76757145C>T		76.0	0.0	0		86.0	4.0	0.0465116	NM_171999	Q9UGH1	Silent	SNP	ENST00000537592.2	37	CCDS12013.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	SALL3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256397.1	NM_171999	
SCNN1A	6337	hgsc.bcm.edu	37	12	6472753	6472753	+	Silent	SNP	C	C	A	rs55859427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6472753C>A	ENST00000228916.2	-	3	638	c.540G>T	c.(538-540)ctG>ctT	p.L180L	SCNN1A_ENST00000540037.1_5'UTR|SCNN1A_ENST00000358945.3_Silent_p.L180L|SCNN1A_ENST00000360168.3_Silent_p.L239L|SCNN1A_ENST00000396966.2_Silent_p.L180L|SCNN1A_ENST00000543768.1_Silent_p.L203L|SCNN1A_ENST00000538979.1_Intron	NM_001038.5	NP_001029.1	P37088	SCNNA_HUMAN	sodium channel, non-voltage-gated 1 alpha subunit	180					excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|multicellular organismal water homeostasis (GO:0050891)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ciliary membrane (GO:0060170)|cortical actin cytoskeleton (GO:0030864)|cytosol (GO:0005829)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)|sodium channel complex (GO:0034706)	ligand-gated sodium channel activity (GO:0015280)|WW domain binding (GO:0050699)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|liver(2)|lung(6)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	27					Amiloride(DB00594)|Triamterene(DB00384)	GAGTCCCCCGCAGGTCGCGAC	0.682													C|||	36	0.0071885	0.0	0.0072	5008	,	,		10426	0.0		0.0209	False		,,,				2504	0.0102				p.L239L		Atlas-SNP	.											.	SCNN1A	54	.	0			c.G717T						PASS	.	C	,,	17,4383		0,17,2183	13.0	15.0	14.0		540,609,717	-0.9	0.0	12	dbSNP_129	14	150,8444		5,140,4152	no	coding-synonymous,coding-synonymous,coding-synonymous	SCNN1A	NM_001038.5,NM_001159575.1,NM_001159576.1	,,	5,157,6335	AA,AC,CC		1.7454,0.3864,1.2852	,,	180/670,203/693,239/729	6472753	167,12827	2200	4297	6497	SO:0001819	synonymous_variant	6337	exon2			CCCCCGCAGGTCG	Z92978	CCDS8543.1, CCDS53738.1, CCDS53739.1	12p13	2012-02-28	2012-02-28		ENSG00000111319	ENSG00000111319		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10599	protein-coding gene	gene with protein product		600228	"""sodium channel, nonvoltage-gated 1 alpha"", ""sodium channel, non-voltage-gated 1 alpha"""	SCNN1		7896277	Standard	NM_001038		Approved	ENaCalpha	uc001qnw.3	P37088	OTTHUMG00000168268	ENST00000228916.2:c.540G>T	12.37:g.6472753C>A		26.0	0.0	0		17.0	11.0	0.647059	NM_001159576	A5X2U9|B4E2Q5|C5HTZ0|O43271|Q6GSQ6|Q9UM64	Silent	SNP	ENST00000228916.2	37	CCDS8543.1																																																																																			C|0.985;A|0.015	0.015	strong		0.682	SCNN1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399055.1		
ADAMTS2	9509	hgsc.bcm.edu	37	5	178564906	178564906	+	Silent	SNP	G	G	A	rs369654932		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178564906G>A	ENST00000251582.7	-	12	1916	c.1815C>T	c.(1813-1815)taC>taT	p.Y605Y		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	605	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				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)		GCTGGAAGTCGTAGGCAAGGC	0.682																																					p.Y605Y		Atlas-SNP	.											ADAMTS2,colon,carcinoma,0,1	ADAMTS2	190	1	0			c.C1815T						PASS	.	G		0,4264		0,0,2132	14.0	14.0	14.0		1815	-0.5	1.0	5		14	2,8428		0,2,4213	no	coding-synonymous	ADAMTS2	NM_014244.4		0,2,6345	AA,AG,GG		0.0237,0.0,0.0158		605/1212	178564906	2,12692	2132	4215	6347	SO:0001819	synonymous_variant	9509	exon12			GAAGTCGTAGGCA	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.1815C>T	5.37:g.178564906G>A		132.0	0.0	0		77.0	24.0	0.311688	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.	.	weak		0.682	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
CHN2	1124	hgsc.bcm.edu	37	7	29539639	29539639	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:29539639G>A	ENST00000222792.6	+	9	1426	c.896G>A	c.(895-897)cGg>cAg	p.R299Q	CHN2_ENST00000539406.1_Missense_Mutation_p.R374Q|CHN2_ENST00000424025.2_Missense_Mutation_p.R118Q|CHN2_ENST00000421775.2_Intron|CHN2_ENST00000410098.1_3'UTR|CHN2_ENST00000439711.2_Missense_Mutation_p.R163Q|CHN2_ENST00000539389.1_Missense_Mutation_p.R155Q|CHN2_ENST00000409041.4_Missense_Mutation_p.R163Q|CHN2_ENST00000435288.2_Intron|CHN2_ENST00000546235.1_Missense_Mutation_p.R284Q|CHN2_ENST00000495789.2_Missense_Mutation_p.R312Q	NM_004067.2	NP_004058.1	P52757	CHIO_HUMAN	chimerin 2	299	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of GTPase activity (GO:0043547)|positive regulation of signal transduction (GO:0009967)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|endometrium(3)|large_intestine(2)|lung(12)|ovary(2)|urinary_tract(2)	23						ATATGCATTCGGGAAATTGAA	0.378																																					p.R299Q	Ovarian(1;44 48 13232 18918 31480)	Atlas-SNP	.											.	CHN2	98	.	0			c.G896A						PASS	.						69.0	63.0	65.0					7																	29539639		2203	4300	6503	SO:0001583	missense	1124	exon9			GCATTCGGGAAAT	L29126	CCDS5420.1	7p15.3	2013-02-14	2012-10-17		ENSG00000106069	ENSG00000106069		"""Rho GTPase activating proteins"", ""SH2 domain containing"""	1944	protein-coding gene	gene with protein product	"""beta chimerin"", ""chimaerin 2"""	602857	"""chimerin (chimaerin) 2"""			8175705	Standard	XM_005249602		Approved	ARHGAP3, RhoGAP3	uc003szz.3	P52757	OTTHUMG00000023063	ENST00000222792.6:c.896G>A	7.37:g.29539639G>A	ENSP00000222792:p.Arg299Gln	110.0	0.0	0		67.0	9.0	0.134328	NM_004067	A4D1A2|B3VCF1|B3VCF2|B3VCF3|B3VCF7|B3VCG1|C9J7B0|E9PGE0|F8QPL9|Q2M203|Q75MM2	Missense_Mutation	SNP	ENST00000222792.6	37	CCDS5420.1	.	.	.	.	.	.	.	.	.	.	G	13.24	2.177801	0.38413	.	.	ENSG00000106069	ENST00000539406;ENST00000222792;ENST00000495789;ENST00000539389;ENST00000546235;ENST00000446446;ENST00000409041;ENST00000424025;ENST00000439711	T;T;T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23;2.23;2.23	5.6	5.6	0.85130	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.109458	0.64402	D	0.000006	T	0.07458	0.0188	N	0.10945	0.07	0.80722	D	1	B;B;B;B;B;B;P;B;B;B;B;B;B;B	0.39665	0.031;0.006;0.046;0.206;0.051;0.104;0.682;0.051;0.224;0.055;0.014;0.083;0.224;0.014	B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.24006	0.002;0.004;0.002;0.015;0.01;0.037;0.05;0.015;0.016;0.006;0.002;0.016;0.01;0.002	T	0.36915	-0.9728	10	0.28530	T	0.3	.	12.8884	0.58057	0.0753:0.0:0.9247:0.0	.	92;284;312;374;118;118;163;163;163;155;299;69;163;299	B7Z215;B7Z1W9;B7Z1V0;F5H003;B3VCF1;B3VCF2;B3VCF5;B3VCF7;B3VCF6;B3VCG1;A4D1A2;B3VCF8;E9PGE0;P52757	.;.;.;.;.;.;.;.;.;.;.;.;.;CHIO_HUMAN	Q	374;299;312;155;284;124;163;118;163	ENSP00000444063:R374Q;ENSP00000222792:R299Q;ENSP00000438587:R312Q;ENSP00000440526:R155Q;ENSP00000442812:R284Q;ENSP00000396867:R124Q;ENSP00000386849:R163Q;ENSP00000406337:R118Q;ENSP00000387425:R163Q	ENSP00000222792:R299Q	R	+	2	0	CHN2	29506164	1.000000	0.71417	1.000000	0.80357	0.961000	0.63080	4.894000	0.63206	2.800000	0.96347	0.455000	0.32223	CGG	.	.	none		0.378	CHN2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214228.2	NM_004067	
NT5C	30833	hgsc.bcm.edu	37	17	73127348	73127348	+	Missense_Mutation	SNP	G	G	A	rs11541956	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:73127348G>A	ENST00000245552.2	-	2	290	c.203C>T	c.(202-204)cCg>cTg	p.P68L	NT5C_ENST00000582170.1_Missense_Mutation_p.P68L|NT5C_ENST00000579082.1_5'UTR|NT5C_ENST00000578337.1_5'UTR|NT5C_ENST00000582160.1_5'UTR	NM_014595.2	NP_055410.1	Q8TCD5	NT5C_HUMAN	5', 3'-nucleotidase, cytosolic	68			P -> L (in dbSNP:rs11541956). {ECO:0000269|PubMed:15489334}.		dephosphorylation (GO:0016311)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|pyrimidine deoxyribonucleotide catabolic process (GO:0009223)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	5'-nucleotidase activity (GO:0008253)|metal ion binding (GO:0046872)|nucleotidase activity (GO:0008252)|pyrimidine nucleotide binding (GO:0019103)					all_lung(278;0.14)|Lung NSC(278;0.168)		LUSC - Lung squamous cell carcinoma(166;0.162)|Lung(188;0.235)		Lamivudine(DB00709)	GAAAAAGCCCGGGGCTTCGTA	0.652													G|||	40	0.00798722	0.0008	0.0159	5008	,	,		12233	0.0		0.0249	False		,,,				2504	0.0031				p.P68L		Atlas-SNP	.											.	NT5C	3	.	0			c.C203T						PASS	.	G	LEU/PRO	23,4383	25.3+/-52.1	0,23,2180	36.0	43.0	41.0		203	3.4	0.2	17	dbSNP_120	41	242,8358	94.7+/-156.6	4,234,4062	yes	missense	NT5C	NM_014595.1	98	4,257,6242	AA,AG,GG		2.814,0.522,2.0375	probably-damaging	68/202	73127348	265,12741	2203	4300	6503	SO:0001583	missense	30833	exon2			AAGCCCGGGGCTT	AF154829	CCDS11715.1	17q25	2011-03-29	2002-05-23		ENSG00000125458	ENSG00000125458	3.1.3.5		17144	protein-coding gene	gene with protein product		191720	"""5' nucleotidase, deoxy (pyrimidine), cytosolic type C"", ""uridine 5-prime monophosphate hydrolase 2"""	UMPH2		10899995	Standard	NM_014595		Approved	DNT1, DNT-1, PN-I, cdN, dNT-1	uc002jmx.3	Q8TCD5		ENST00000245552.2:c.203C>T	17.37:g.73127348G>A	ENSP00000245552:p.Pro68Leu	264.0	0.0	0		231.0	113.0	0.489177	NM_001252377	Q96HS6|Q9NP82	Missense_Mutation	SNP	ENST00000245552.2	37	CCDS11715.1	27	0.012362637362637362	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	21	0.027704485488126648	G	12.25	1.882990	0.33255	0.00522	0.02814	ENSG00000125458	ENST00000245552	T	0.48836	0.8	4.35	3.36	0.38483	HAD-like domain (2);	0.372569	0.27581	N	0.018735	T	0.34774	0.0909	M	0.68317	2.08	0.80722	D	1	D	0.71674	0.998	P	0.61070	0.883	T	0.51293	-0.8724	10	0.56958	D	0.05	-1.2806	9.557	0.39346	0.0:0.0:0.6178:0.3822	rs11541956;rs17851989	68	Q8TCD5	NT5C_HUMAN	L	68	ENSP00000245552:P68L	ENSP00000245552:P68L	P	-	2	0	NT5C	70638943	0.998000	0.40836	0.217000	0.23759	0.737000	0.42083	3.393000	0.52544	1.154000	0.42482	0.555000	0.69702	CCG	G|0.983;A|0.017	0.017	strong		0.652	NT5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445853.1		
DXO	1797	hgsc.bcm.edu	37	6	31939319	31939319	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31939319C>T	ENST00000375349.3	-	2	545	c.134G>A	c.(133-135)cGc>cAc	p.R45H	DXO_ENST00000478221.1_Intron|STK19_ENST00000375333.2_5'Flank|DXO_ENST00000375356.3_Missense_Mutation_p.R45H|DXO_ENST00000337523.5_Missense_Mutation_p.R45H|STK19_ENST00000375331.2_5'Flank			O77932	DXO_HUMAN	decapping exoribonuclease	45					metabolic process (GO:0008152)|mRNA catabolic process (GO:0006402)|nuclear mRNA surveillance (GO:0071028)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|RNA destabilization (GO:0050779)	nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)|magnesium ion binding (GO:0000287)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|RNA pyrophosphohydrolase activity (GO:0034353)										TTCCGAAGGGCGCCGGTAGAA	0.602																																					p.R45H		Atlas-SNP	.											.	DOM3Z	20	.	0			c.G134A						PASS	.						88.0	95.0	93.0					6																	31939319		2203	4300	6503	SO:0001583	missense	1797	exon2			GAAGGGCGCCGGT	AF059252	CCDS4732.1	6p21.3	2013-09-11	2013-09-11	2013-09-11	ENSG00000204348	ENSG00000204348			2992	protein-coding gene	gene with protein product		605996	"""DOM-3 (C. elegans) homolog Z"", ""dom-3 homolog Z (C. elegans)"""	DOM3Z		9799600, 23523372	Standard	NM_005510		Approved		uc003nyp.1	O77932	OTTHUMG00000031272	ENST00000375349.3:c.134G>A	6.37:g.31939319C>T	ENSP00000364498:p.Arg45His	90.0	0.0	0		118.0	35.0	0.29661	NM_005510	A2CER3|B0UZ80|O15004|O78127|O78128|Q5ST60|Q6IPZ2|Q9NPK4	Missense_Mutation	SNP	ENST00000375349.3	37	CCDS4732.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.356161	0.82243	.	.	ENSG00000204348	ENST00000337523;ENST00000375349;ENST00000375356	T;T;T	0.21031	2.03;2.03;2.03	4.92	4.03	0.46877	.	0.198410	0.46442	D	0.000300	T	0.23806	0.0576	M	0.75884	2.315	0.80722	D	1	D;D	0.67145	0.996;0.994	P;P	0.52554	0.702;0.512	T	0.05484	-1.0882	10	0.66056	D	0.02	0.0351	11.4467	0.50127	0.3265:0.6735:0.0:0.0	.	45;45	F8WC68;O77932	.;DOM3Z_HUMAN	H	45	ENSP00000337759:R45H;ENSP00000364498:R45H;ENSP00000364505:R45H	ENSP00000337759:R45H	R	-	2	0	DOM3Z	32047298	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	2.796000	0.47869	1.234000	0.43709	0.561000	0.74099	CGC	.	.	none		0.602	DXO-006	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076592.3		
SREBF1	6720	hgsc.bcm.edu	37	17	17723595	17723595	+	Missense_Mutation	SNP	G	G	A	rs115855236	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:17723595G>A	ENST00000261646.5	-	2	516	c.332C>T	c.(331-333)cCg>cTg	p.P111L	SREBF1_ENST00000435530.2_Missense_Mutation_p.P111L|SREBF1_ENST00000395757.1_5'Flank|SREBF1_ENST00000355815.4_Missense_Mutation_p.P141L|SREBF1_ENST00000583732.1_Intron|SREBF1_ENST00000338854.5_Missense_Mutation_p.P111L	NM_004176.4	NP_004167.3	P36956	SRBP1_HUMAN	sterol regulatory element binding transcription factor 1	111	Pro/Ser-rich.				aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|cholesterol metabolic process (GO:0008203)|circadian rhythm (GO:0007623)|insulin receptor signaling pathway (GO:0008286)|lipid biosynthetic process (GO:0008610)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|negative regulation of insulin secretion (GO:0046676)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cholesterol biosynthetic process (GO:0045542)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|regulation of fatty acid metabolic process (GO:0019217)|regulation of heart rate by chemical signal (GO:0003062)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to drug (GO:0042493)|response to food (GO:0032094)|response to glucagon (GO:0033762)|response to glucose (GO:0009749)|response to progesterone (GO:0032570)|response to retinoic acid (GO:0032526)|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)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|sterol response element binding (GO:0032810)			cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)|urinary_tract(1)	14						GGGCATGGACGGGTACATCTT	0.647													G|||	3	0.000599042	0.0	0.0	5008	,	,		17350	0.0		0.003	False		,,,				2504	0.0				p.P141L		Atlas-SNP	.											.	SREBF1	47	.	0			c.C422T						PASS	.	G	LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	65.0	72.0	69.0		422,332	2.2	0.9	17	dbSNP_132	69	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	SREBF1	NM_001005291.2,NM_004176.4	98,98	0,9,6494	AA,AG,GG		0.093,0.0227,0.0692	probably-damaging,probably-damaging	141/1178,111/1148	17723595	9,12997	2203	4300	6503	SO:0001583	missense	6720	exon3			ATGGACGGGTACA	BC057388	CCDS11189.1, CCDS32583.1	17p11.2	2013-05-21			ENSG00000072310	ENSG00000072310		"""Basic helix-loop-helix proteins"""	11289	protein-coding gene	gene with protein product		184756				8402897, 7759101	Standard	NM_001005291		Approved	SREBP1, bHLHd1, SREBP-1c	uc002grt.2	P36956	OTTHUMG00000059313	ENST00000261646.5:c.332C>T	17.37:g.17723595G>A	ENSP00000261646:p.Pro111Leu	81.0	0.0	0		96.0	50.0	0.520833	NM_001005291	B0I4X3|B0I4X4|D3DXC4|Q16062|Q59F52|Q6P4R7|Q6PFW7|Q6PJ36|Q8TAK9	Missense_Mutation	SNP	ENST00000261646.5	37	CCDS11189.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	6.553	0.470364	0.12461	2.27E-4	9.3E-4	ENSG00000072310	ENST00000338854;ENST00000355815;ENST00000261646;ENST00000418712;ENST00000423161;ENST00000435530	T;T;T;T;T	0.79454	0.49;0.53;0.54;-0.11;-1.27	4.52	2.2	0.27929	.	0.352176	0.24580	N	0.037309	T	0.67449	0.2894	L	0.54323	1.7	0.09310	N	1	P;P;P;P	0.47545	0.897;0.897;0.725;0.82	B;B;B;B	0.41135	0.256;0.186;0.134;0.348	T	0.59037	-0.7529	10	0.31617	T	0.26	-8.4746	6.4826	0.22071	0.1164:0.1911:0.6925:0.0	.	111;87;111;141	B0I4X3;B0I4X4;P36956;P36956-4	.;.;SRBP1_HUMAN;.	L	111;141;111;87;37;111	ENSP00000345822:P111L;ENSP00000348069:P141L;ENSP00000261646:P111L;ENSP00000411516:P37L;ENSP00000413389:P111L	ENSP00000261646:P111L	P	-	2	0	SREBF1	17664320	0.781000	0.28676	0.877000	0.34402	0.264000	0.26372	2.529000	0.45632	2.081000	0.62600	0.555000	0.69702	CCG	G|0.999;A|0.001	0.001	strong		0.647	SREBF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131771.1	NM_004176	
RAD51B	5890	hgsc.bcm.edu	37	14	68353893	68353893	+	Missense_Mutation	SNP	A	A	G	rs34594234	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:68353893A>G	ENST00000487270.1	+	7	776	c.728A>G	c.(727-729)aAg>aGg	p.K243R	RAD51B_ENST00000471583.1_Missense_Mutation_p.K243R|RAD51B_ENST00000488612.1_Missense_Mutation_p.K243R|RAD51B_ENST00000487861.1_Missense_Mutation_p.K243R|RAD51B_ENST00000469165.2_3'UTR|RAD51B_ENST00000390683.3_Missense_Mutation_p.K243R	NM_133509.3	NP_598193.2	O15315	RA51B_HUMAN	RAD51 paralog B	243			K -> R (in dbSNP:rs34594234). {ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair via homologous recombination (GO:0000724)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|reciprocal meiotic recombination (GO:0007131)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Rad51B-Rad51C-Rad51D-XRCC2 complex (GO:0033063)|replication fork (GO:0005657)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)		HMGA2/RAD51B(11)	breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	11						TCCTCCTTGAAGTATTTGGCT	0.358								Direct reversal of damage					A|||	15	0.00299521	0.0	0.0043	5008	,	,		14243	0.0		0.0089	False		,,,				2504	0.0031				p.K243R		Atlas-SNP	.											.	RAD51B	80	.	0			c.A728G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	17,4389	22.3+/-47.3	0,17,2186	74.0	76.0	76.0		728,728,728	5.9	1.0	14	dbSNP_126	76	97,8503	51.1+/-111.2	2,93,4205	yes	missense,missense,missense	RAD51B	NM_002877.5,NM_133509.3,NM_133510.3	26,26,26	2,110,6391	GG,GA,AA		1.1279,0.3858,0.8765	probably-damaging,probably-damaging,probably-damaging	243/351,243/385,243/351	68353893	114,12892	2203	4300	6503	SO:0001583	missense	5890	exon7			CCTTGAAGTATTT	U84138	CCDS9789.1, CCDS9790.1	14q23-q24.2	2013-07-02	2013-07-02	2011-07-01	ENSG00000182185	ENSG00000182185			9822	protein-coding gene	gene with protein product		602948	"""RAD51 (S. cerevisiae)-like 1"", ""RAD51-like 1 (S. cerevisiae)"", ""RAD51 homolog B (S. cerevisiae)"""	RAD51L1		6261043, 9207106	Standard	NM_002877		Approved	REC2, hREC2, R51H2	uc001xkf.2	O15315	OTTHUMG00000157530	ENST00000487270.1:c.728A>G	14.37:g.68353893A>G	ENSP00000419471:p.Lys243Arg	110.0	0.0	0		152.0	67.0	0.440789	NM_133509	O60914|O75210|Q3Y4F8|Q6FHX8|Q86SY3|Q86SY4|Q86TR0|Q86U92|Q86U93|Q86U94|Q8N6H4|Q9UPL5	Missense_Mutation	SNP	ENST00000487270.1	37	CCDS9789.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	A	25.4	4.630716	0.87660	0.003858	0.011279	ENSG00000182185	ENST00000487861;ENST00000471583;ENST00000487270;ENST00000488612;ENST00000390683;ENST00000402498;ENST00000342389	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.9	5.9	0.94986	DNA recombination/repair protein RecA/RadB, ATP-binding domain (1);ATPase, AAA+ type, core (1);DNA recombination and repair protein Rad51, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.66819	0.2828	L	0.33293	1	0.44485	D	0.997423	D;D;D;D;D;P	0.89917	1.0;1.0;1.0;1.0;1.0;0.746	D;D;D;D;D;P	0.97110	1.0;1.0;1.0;1.0;1.0;0.8	T	0.69595	-0.5103	10	0.34782	T	0.22	-21.1874	14.8985	0.70661	1.0:0.0:0.0:0.0	rs34594234	243;243;243;243;243;243	C9JYJ0;C9JSP9;O15315-4;O15315;O15315-1;O15315-2	.;.;.;RA51B_HUMAN;.;.	R	243	ENSP00000419881:K243R;ENSP00000418859:K243R;ENSP00000419471:K243R;ENSP00000420061:K243R;ENSP00000375101:K243R	ENSP00000343531:K243R	K	+	2	0	RAD51B	67423646	1.000000	0.71417	1.000000	0.80357	0.938000	0.57974	6.799000	0.75160	2.266000	0.75297	0.528000	0.53228	AAG	A|0.992;G|0.008	0.008	strong		0.358	RAD51B-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349063.1		
MPPED2	744	hgsc.bcm.edu	37	11	30433028	30433028	+	Missense_Mutation	SNP	G	G	A	rs146268212		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:30433028G>A	ENST00000358117.5	-	6	994	c.872C>T	c.(871-873)cCa>cTa	p.P291L	MPPED2_ENST00000524667.1_5'UTR|MPPED2_ENST00000448418.2_Intron	NM_001584.2	NP_001575.1	Q15777	MPPD2_HUMAN	metallophosphoesterase domain containing 2	291					nervous system development (GO:0007399)		hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(15)|skin(2)|upper_aerodigestive_tract(2)	33						GGAACCCTGTGGGTTTGGAAG	0.418																																					p.P291L		Atlas-SNP	.											.	MPPED2	106	.	0			c.C872T						PASS	.	G	,LEU/PRO	0,4404		0,0,2202	112.0	97.0	102.0		,872	5.6	1.0	11	dbSNP_134	102	1,8597	1.2+/-3.3	0,1,4298	no	intron,missense	MPPED2	NM_001145399.1,NM_001584.2	,98	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	,probably-damaging	,291/295	30433028	1,13001	2202	4299	6501	SO:0001583	missense	744	exon6			CCCTGTGGGTTTG	U57911	CCDS7870.1, CCDS44560.1	11p13	2008-07-18	2005-10-10	2005-10-10	ENSG00000066382	ENSG00000066382			1180	protein-coding gene	gene with protein product		600911	"""chromosome 11 open reading frame 8"""	C11orf8		8666403, 9266672	Standard	NM_001584		Approved	239FB, D11S302E, Hs.46638, FAM1B, dJ873F21.1, dJ1024C24.1	uc001msr.3	Q15777	OTTHUMG00000166159	ENST00000358117.5:c.872C>T	11.37:g.30433028G>A	ENSP00000350833:p.Pro291Leu	121.0	0.0	0		101.0	46.0	0.455446	NM_001584	D3DQZ5|E9PB10|Q59GE6	Missense_Mutation	SNP	ENST00000358117.5	37	CCDS7870.1	.	.	.	.	.	.	.	.	.	.	G	23.1	4.376204	0.82682	0.0	1.16E-4	ENSG00000066382	ENST00000358117	T	0.51325	0.71	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.82716	2.605	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.74352	-0.3693	10	0.52906	T	0.07	-7.0431	19.8808	0.96899	0.0:0.0:1.0:0.0	.	291	Q15777	MPPD2_HUMAN	L	291	ENSP00000350833:P291L	ENSP00000350833:P291L	P	-	2	0	MPPED2	30389604	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.771000	0.95319	0.561000	0.74099	CCA	G|1.000;A|0.000	0.000	weak		0.418	MPPED2-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388155.2	NM_001584	
ACOX2	8309	hgsc.bcm.edu	37	3	58517520	58517520	+	Silent	SNP	A	A	G	rs57216393	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:58517520A>G	ENST00000302819.5	-	6	894	c.603T>C	c.(601-603)caT>caC	p.H201H	ACOX2_ENST00000459701.2_Silent_p.H201H	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	201					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		GGACCAGGGCATGGGTGGCTG	0.627													G|||	355	0.0708866	0.2262	0.0375	5008	,	,		18088	0.0		0.0189	False		,,,				2504	0.0112				p.H201H		Atlas-SNP	.											.	ACOX2	53	.	0			c.T603C						PASS	.	G		884,3522	741.6+/-411.3	92,700,1411	59.0	53.0	55.0		603	-9.4	0.1	3	dbSNP_129	55	184,8416	810.9+/-407.1	3,178,4119	no	coding-synonymous	ACOX2	NM_003500.3		95,878,5530	GG,GA,AA		2.1395,20.0635,8.2116		201/682	58517520	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			CAGGGCATGGGTG	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.603T>C	3.37:g.58517520A>G		70.0	0.0	0		64.0	29.0	0.453125	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.923;G|0.077	0.077	strong		0.627	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
DERA	51071	hgsc.bcm.edu	37	12	16189279	16189279	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:16189279A>G	ENST00000428559.2	+	8	1076	c.864A>G	c.(862-864)atA>atG	p.I288M	DERA_ENST00000526530.1_Missense_Mutation_p.I200M|DERA_ENST00000532964.1_Missense_Mutation_p.I245M	NM_015954.2	NP_057038.2	Q9Y315	DEOC_HUMAN	deoxyribose-phosphate aldolase (putative)	288					deoxyribonucleoside catabolic process (GO:0046121)|deoxyribonucleotide catabolic process (GO:0009264)|deoxyribose phosphate catabolic process (GO:0046386)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	deoxyribose-phosphate aldolase activity (GO:0004139)			endometrium(1)|large_intestine(2)|lung(3)|skin(1)	7		Hepatocellular(102;0.121)				TCTTTCGAATAGGTGCCAGTA	0.458																																					p.I288M		Atlas-SNP	.											.	DERA	20	.	0			c.A864G						PASS	.						101.0	99.0	99.0					12																	16189279		1867	4110	5977	SO:0001583	missense	51071	exon8			TCGAATAGGTGCC	AF132960	CCDS44838.1, CCDS73451.1	12p12.3	2010-06-24	2010-06-24		ENSG00000023697	ENSG00000023697	4.1.2.4		24269	protein-coding gene	gene with protein product			"""2-deoxyribose-5-phosphate aldolase homolog (C. elegans)"""			12546782	Standard	XM_006719083		Approved	CGI-26, DEOC	uc001rde.3	Q9Y315	OTTHUMG00000165537	ENST00000428559.2:c.864A>G	12.37:g.16189279A>G	ENSP00000416583:p.Ile288Met	88.0	0.0	0		77.0	33.0	0.428571	NM_015954	Q53HN9|Q6PHW2	Missense_Mutation	SNP	ENST00000428559.2	37	CCDS44838.1	.	.	.	.	.	.	.	.	.	.	A	16.36	3.102495	0.56183	.	.	ENSG00000023697	ENST00000428559;ENST00000532964;ENST00000526530	.	.	.	5.57	-0.0832	0.13695	Aldolase-type TIM barrel (1);	0.155772	0.56097	D	0.000032	T	0.67040	0.2851	M	0.91249	3.19	0.47407	D	0.99941	P	0.52577	0.954	P	0.52957	0.714	T	0.64685	-0.6349	9	0.72032	D	0.01	-25.8467	3.2921	0.06953	0.2024:0.4745:0.0912:0.2318	.	288	Q9Y315	DEOC_HUMAN	M	288;245;200	.	ENSP00000416583:I288M	I	+	3	3	DERA	16080546	0.982000	0.34865	0.979000	0.43373	0.913000	0.54294	0.125000	0.15749	0.039000	0.15632	-0.327000	0.08410	ATA	.	.	none		0.458	DERA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384731.1	NM_015954	
ARHGAP42	143872	hgsc.bcm.edu	37	11	100803982	100803982	+	Silent	SNP	C	C	T	rs79213484	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:100803982C>T	ENST00000298815.8	+	7	696	c.693C>T	c.(691-693)aaC>aaT	p.N231N	ARHGAP42_ENST00000524892.2_Silent_p.N197N|snoU13_ENST00000459511.1_RNA	NM_152432.2	NP_689645.2	A6NI28	RHG42_HUMAN	Rho GTPase activating protein 42	231	BAR.				signal transduction (GO:0007165)	intracellular (GO:0005622)	GTPase activator activity (GO:0005096)			endometrium(3)|skin(2)	5						TGCAGTTCAACTTGCAGAATG	0.388													C|||	41	0.0081869	0.0015	0.0115	5008	,	,		15042	0.0		0.0268	False		,,,				2504	0.0041				p.N231N		Atlas-SNP	.											.	ARHGAP42	32	.	0			c.C693T						PASS	.	C		6,1378		0,6,686	132.0	102.0	111.0		693	4.6	1.0	11	dbSNP_132	111	99,3083		1,97,1493	no	coding-synonymous	ARHGAP42	NM_152432.2		1,103,2179	TT,TC,CC		3.1113,0.4335,2.2996		231/875	100803982	105,4461	692	1591	2283	SO:0001819	synonymous_variant	143872	exon7			GTTCAACTTGCAG			11q22.1	2012-04-19			ENSG00000165895	ENSG00000165895		"""Rho GTPase activating proteins"""	26545	protein-coding gene	gene with protein product		615936				18954304	Standard	NM_152432		Approved	FLJ32810, GRAF3	uc001pge.2	A6NI28	OTTHUMG00000167530	ENST00000298815.8:c.693C>T	11.37:g.100803982C>T		109.0	0.0	0		132.0	75.0	0.568182	NM_152432	Q96M56	Silent	SNP	ENST00000298815.8	37																																																																																				C|0.983;T|0.017	0.017	strong		0.388	ARHGAP42-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_152432	
MAP1A	4130	hgsc.bcm.edu	37	15	43818959	43818959	+	Missense_Mutation	SNP	C	C	G	rs375898111		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43818959C>G	ENST00000300231.5	+	4	5738	c.5288C>G	c.(5287-5289)cCa>cGa	p.P1763R	MAP1A_ENST00000399453.1_Missense_Mutation_p.P1763R|MAP1A_ENST00000382031.1_Missense_Mutation_p.P2001R			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	1763					microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GAATCCTCACCACAGAAGGGG	0.572																																					p.P1763R		Atlas-SNP	.											.	MAP1A	189	.	0			c.C5288G						PASS	.	C	ARG/PRO	0,3894		0,0,1947	74.0	76.0	76.0		5288	4.5	0.5	15		76	1,8265		0,1,4132	no	missense	MAP1A	NM_002373.5	103	0,1,6079	GG,GC,CC		0.0121,0.0,0.0082	benign	1763/2804	43818959	1,12159	1947	4133	6080	SO:0001583	missense	4130	exon4			CCTCACCACAGAA	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.5288C>G	15.37:g.43818959C>G	ENSP00000300231:p.Pro1763Arg	87.0	0.0	0		106.0	46.0	0.433962	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	37	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	C	2.185	-0.386740	0.04966	0.0	1.21E-4	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231	T;T;T	0.01854	4.6;4.61;4.61	4.46	4.46	0.54185	.	0.268702	0.20049	N	0.100342	T	0.03390	0.0098	L	0.32530	0.975	0.20563	N	0.999883	B	0.32467	0.372	B	0.36989	0.238	T	0.38672	-0.9650	10	0.66056	D	0.02	0.9333	15.0779	0.72090	0.0:1.0:0.0:0.0	.	1763	P78559	MAP1A_HUMAN	R	2001;1763;1763	ENSP00000371462:P2001R;ENSP00000382380:P1763R;ENSP00000300231:P1763R	ENSP00000300231:P1763R	P	+	2	0	MAP1A	41606251	0.953000	0.32496	0.451000	0.26982	0.145000	0.21501	2.451000	0.44952	2.321000	0.78463	0.455000	0.32223	CCA	.	.	weak		0.572	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
NOL6	65083	hgsc.bcm.edu	37	9	33467397	33467397	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:33467397G>A	ENST00000379471.2	-	13	1807	c.1720C>T	c.(1720-1722)Cct>Tct	p.P574S	NOL6_ENST00000464829.1_Intron|NOL6_ENST00000455041.2_Missense_Mutation_p.P522S			Q9H6R4	NOL6_HUMAN	nucleolar protein 6 (RNA-associated)	574					rRNA processing (GO:0006364)	condensed nuclear chromosome (GO:0000794)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			endometrium(4)|kidney(4)|large_intestine(5)|lung(8)|ovary(2)|prostate(2)|skin(2)	27			LUSC - Lung squamous cell carcinoma(29;0.00788)	GBM - Glioblastoma multiforme(74;0.152)		CCCACCTCAGGCTGGTCTGCC	0.617											OREG0019137	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P574S		Atlas-SNP	.											.	NOL6	85	.	0			c.C1720T						PASS	.						56.0	54.0	54.0					9																	33467397		2203	4300	6503	SO:0001583	missense	65083	exon13			CCTCAGGCTGGTC	AF361079	CCDS6543.1, CCDS6544.1	9p12	2013-02-22	2013-02-22		ENSG00000165271	ENSG00000165271			19910	protein-coding gene	gene with protein product		611532	"""nucleolar protein family 6 (RNA-associated)"""			11895476, 15590835	Standard	NM_022917		Approved	bA311H10.1, Nrap, FLJ21959, MGC14896, MGC14921, MGC20838, UTP22	uc003zsz.3	Q9H6R4	OTTHUMG00000000394	ENST00000379471.2:c.1720C>T	9.37:g.33467397G>A	ENSP00000368784:p.Pro574Ser	153.0	0.0	0	840	165.0	30.0	0.181818	NM_022917	Q5T5M3|Q5T5M4|Q7L4G6|Q8N6I0|Q8TEY9|Q8TEZ0|Q8TEZ1|Q9H675	Missense_Mutation	SNP	ENST00000379471.2	37		.	.	.	.	.	.	.	.	.	.	G	16.58	3.162530	0.57368	.	.	ENSG00000165271	ENST00000353159;ENST00000297990;ENST00000379471;ENST00000541373;ENST00000325914;ENST00000455041	T;T;T;T	0.39997	1.05;1.05;1.05;1.05	5.06	4.12	0.48240	.	0.154190	0.64402	D	0.000013	T	0.37156	0.0993	L	0.45422	1.42	0.58432	D	0.999999	P;P;P;P;P	0.40398	0.716;0.499;0.499;0.708;0.555	B;B;B;B;B	0.42245	0.381;0.161;0.161;0.331;0.248	T	0.06006	-1.0851	10	0.19147	T	0.46	.	14.0961	0.65023	0.0:0.1492:0.8508:0.0	.	522;571;574;574;574	B4DF80;Q9H6R4-4;Q9H6R4-2;Q9H6R4-3;Q9H6R4	.;.;.;.;NOL6_HUMAN	S	574;574;574;130;574;522	ENSP00000313978:P574S;ENSP00000297990:P574S;ENSP00000368784:P574S;ENSP00000395915:P522S	ENSP00000297990:P574S	P	-	1	0	NOL6	33457397	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.752000	0.55172	2.638000	0.89438	0.655000	0.94253	CCT	.	.	none		0.617	NOL6-005	NOVEL	non_canonical_TEC|basic	protein_coding	protein_coding	OTTHUMT00000001019.2	NM_022917	
SPAG5	10615	hgsc.bcm.edu	37	17	26919344	26919344	+	Silent	SNP	T	T	C	rs113667723	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:26919344T>C	ENST00000321765.5	-	3	1250	c.918A>G	c.(916-918)acA>acG	p.T306T		NM_006461.3	NP_006452.3	Q96R06	SPAG5_HUMAN	sperm associated antigen 5	306					chromosome segregation (GO:0007059)|mitotic sister chromatid segregation (GO:0000070)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|kinetochore (GO:0000776)|microtubule plus-end (GO:0035371)|mitotic spindle (GO:0072686)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43	Lung NSC(42;0.00431)					GTGTCAGGCATGTGGACAGAA	0.453													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		22177	0.0		0.0099	False		,,,				2504	0.0				p.T306T		Atlas-SNP	.											.	SPAG5	92	.	0			c.A918G						PASS	.	T		11,4395	15.5+/-35.6	0,11,2192	135.0	121.0	126.0		918	-1.2	0.0	17	dbSNP_132	126	111,8489	59.8+/-121.6	1,109,4190	no	coding-synonymous	SPAG5	NM_006461.3		1,120,6382	CC,CT,TT		1.2907,0.2497,0.938		306/1194	26919344	122,12884	2203	4300	6503	SO:0001819	synonymous_variant	10615	exon3			CAGGCATGTGGAC	AF063308	CCDS32594.1	17q11.2	2008-07-18			ENSG00000076382	ENSG00000076382			13452	protein-coding gene	gene with protein product	"""mitotic spindle coiled-coil related protein"", ""astrin"", ""mitotic spindle associated protein p126"""	615562				11549262	Standard	NM_006461		Approved	DEEPEST, MAP126, hMAP126	uc002hbq.3	Q96R06	OTTHUMG00000166586	ENST00000321765.5:c.918A>G	17.37:g.26919344T>C		103.0	0.0	0		124.0	64.0	0.516129	NM_006461	O95213|Q9BWE8|Q9NT17|Q9UFE6	Silent	SNP	ENST00000321765.5	37	CCDS32594.1																																																																																			T|0.992;C|0.008	0.008	strong		0.453	SPAG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390564.2	NM_006461	
DYRK2	8445	hgsc.bcm.edu	37	12	68043643	68043643	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:68043643G>A	ENST00000344096.3	+	2	529	c.116G>A	c.(115-117)cGg>cAg	p.R39Q	DYRK2_ENST00000537632.1_3'UTR|DYRK2_ENST00000393555.3_Intron	NM_006482.2	NP_006473.2	Q92630	DYRK2_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 2	39					cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|negative regulation of NFAT protein import into nucleus (GO:0051534)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of glycogen biosynthetic process (GO:0045725)|protein phosphorylation (GO:0006468)|smoothened signaling pathway (GO:0007224)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|ubiquitin ligase complex (GO:0000151)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|ubiquitin binding (GO:0043130)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	30			Lung(24;6.81e-05)|LUAD - Lung adenocarcinoma(15;0.00107)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(7;0.000573)		GGGGCCACCCGGAGCGGAGTG	0.741																																					p.R39Q		Atlas-SNP	.											.	DYRK2	63	.	0			c.G116A						PASS	.						12.0	14.0	13.0					12																	68043643		2187	4283	6470	SO:0001583	missense	8445	exon2			CCACCCGGAGCGG	Y09216	CCDS8978.1, CCDS8979.1	12q15	2008-07-03				ENSG00000127334			3093	protein-coding gene	gene with protein product		603496				9748265	Standard	NM_003583		Approved		uc001str.4	Q92630		ENST00000344096.3:c.116G>A	12.37:g.68043643G>A	ENSP00000342105:p.Arg39Gln	65.0	0.0	0		52.0	34.0	0.653846	NM_006482	B2R9V9|Q9BRB5	Missense_Mutation	SNP	ENST00000344096.3	37	CCDS8978.1	.	.	.	.	.	.	.	.	.	.	G	10.88	1.475230	0.26511	.	.	ENSG00000127334	ENST00000344096	T	0.66638	-0.22	3.91	3.01	0.34805	.	0.416053	0.21001	N	0.081872	T	0.47322	0.1439	N	0.19112	0.55	0.80722	D	1	B	0.11235	0.004	B	0.01281	0.0	T	0.28839	-1.0031	9	.	.	.	.	10.5729	0.45211	0.0975:0.0:0.9025:0.0	.	39	Q92630	DYRK2_HUMAN	Q	39	ENSP00000342105:R39Q	.	R	+	2	0	DYRK2	66329910	1.000000	0.71417	0.998000	0.56505	0.278000	0.26855	4.423000	0.59861	0.997000	0.38969	-0.258000	0.10820	CGG	.	.	none		0.741	DYRK2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402218.1		
SPATC1L	84221	hgsc.bcm.edu	37	21	47581869	47581869	+	Silent	SNP	G	G	A	rs139199473	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47581869G>A	ENST00000291672.5	-	4	1718	c.657C>T	c.(655-657)taC>taT	p.Y219Y	SPATC1L_ENST00000330205.6_Silent_p.Y65Y	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	219																	CCGTGAAGCCGTAGAGCCGCG	0.731																																					p.Y219Y		Atlas-SNP	.											.	.	.	.	0			c.C657T						PASS	.	G	,	2,4390		0,2,2194	32.0	28.0	29.0		657,195	-8.4	0.7	21	dbSNP_134	29	10,8576		0,10,4283	no	coding-synonymous,coding-synonymous	C21orf56	NM_001142854.1,NM_032261.4	,	0,12,6477	AA,AG,GG		0.1165,0.0455,0.0925	,	219/341,65/187	47581869	12,12966	2196	4293	6489	SO:0001819	synonymous_variant	84221	exon4			GAAGCCGTAGAGC	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"""speriolin-like protein"""	612412	"""chromosome 21 open reading frame 56"""	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.657C>T	21.37:g.47581869G>A		62.0	0.0	0		30.0	16.0	0.533333	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Silent	SNP	ENST00000291672.5	37	CCDS46653.1																																																																																			G|1.000;A|0.000	0.000	strong		0.731	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
ZCCHC7	84186	hgsc.bcm.edu	37	9	37304232	37304232	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:37304232C>T	ENST00000336755.5	+	4	808	c.702C>T	c.(700-702)taC>taT	p.Y234Y	ZCCHC7_ENST00000461038.1_3'UTR|ZCCHC7_ENST00000534928.1_5'UTR	NM_032226.2	NP_115602.2	Q8N3Z6	ZCHC7_HUMAN	zinc finger, CCHC domain containing 7	234						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	30				GBM - Glioblastoma multiforme(29;0.0137)		CCCAGCGGTACTATTCAGCCA	0.363																																					p.Y234Y		Atlas-SNP	.											.	ZCCHC7	56	.	0			c.C702T						PASS	.						99.0	95.0	96.0					9																	37304232		2203	4300	6503	SO:0001819	synonymous_variant	84186	exon4			GCGGTACTATTCA	AK026264	CCDS6608.2	9p13.1	2008-05-02			ENSG00000147905	ENSG00000147905		"""Zinc fingers, CCHC domain containing"""	26209	protein-coding gene	gene with protein product							Standard	NM_032226		Approved	FLJ22611, AIR1	uc003zzq.3	Q8N3Z6	OTTHUMG00000019915	ENST00000336755.5:c.702C>T	9.37:g.37304232C>T		128.0	0.0	0		107.0	25.0	0.233645	NM_032226	B2RCI4|D3DRQ0|Q5T0Q8|Q5T0Q9|Q5T0R0|Q8N2M1|Q8N4J2|Q8TBK8|Q9H648|Q9P0F0	Silent	SNP	ENST00000336755.5	37	CCDS6608.2																																																																																			.	.	none		0.363	ZCCHC7-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052453.2	NM_032226	
OR5B12	390191	hgsc.bcm.edu	37	11	58207494	58207494	+	Missense_Mutation	SNP	A	A	G	rs140525146	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:58207494A>G	ENST00000302572.2	-	1	152	c.131T>C	c.(130-132)aTt>aCt	p.I44T		NM_001004733.2	NP_001004733.1	Q96R08	OR5BC_HUMAN	olfactory receptor, family 5, subfamily B, member 12	44						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(6)|liver(1)|lung(28)|ovary(1)|prostate(3)|skin(1)	40	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				AATCAATTCAATCATCCCCAG	0.488													A|||	11	0.00219649	0.0076	0.0014	5008	,	,		18591	0.0		0.0	False		,,,				2504	0.0				p.I44T		Atlas-SNP	.											.	OR5B12	80	.	0			c.T131C						PASS	.	A	THR/ILE	53,4349	52.9+/-88.7	2,49,2150	76.0	85.0	82.0		131	1.1	0.0	11	dbSNP_134	82	4,8586	3.7+/-12.6	0,4,4291	yes	missense	OR5B12	NM_001004733.2	89	2,53,6441	GG,GA,AA		0.0466,1.204,0.4387	benign	44/315	58207494	57,12935	2201	4295	6496	SO:0001583	missense	390191	exon1			AATTCAATCATCC	AB065851	CCDS31551.1	11q12.1	2012-08-09		2004-03-10	ENSG00000172362	ENSG00000172362		"""GPCR / Class A : Olfactory receptors"""	15432	protein-coding gene	gene with protein product				OR5B12P, OR5B16		12213199	Standard	NM_001004733		Approved	OST743	uc010rkh.2	Q96R08	OTTHUMG00000167543	ENST00000302572.2:c.131T>C	11.37:g.58207494A>G	ENSP00000306657:p.Ile44Thr	108.0	0.0	0		109.0	60.0	0.550459	NM_001004733	B2RNL2|Q6IEV5	Missense_Mutation	SNP	ENST00000302572.2	37	CCDS31551.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	A	5.557	0.287633	0.10513	0.01204	4.66E-4	ENSG00000172362	ENST00000302572	T	0.00640	6.03	4.74	1.11	0.20524	GPCR, rhodopsin-like superfamily (1);	1.336050	0.05196	N	0.503944	T	0.00815	0.0027	M	0.85777	2.775	0.09310	N	1	B	0.18741	0.03	B	0.24394	0.053	T	0.47328	-0.9126	10	0.62326	D	0.03	-6.3258	7.7035	0.28636	0.7459:0.0:0.254:0.0	.	44	Q96R08	OR5BC_HUMAN	T	44	ENSP00000306657:I44T	ENSP00000306657:I44T	I	-	2	0	OR5B12	57964070	0.014000	0.17966	0.049000	0.19019	0.222000	0.24845	2.799000	0.47892	0.087000	0.17167	0.459000	0.35465	ATT	A|0.995;G|0.005	0.005	strong		0.488	OR5B12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394987.1	NM_001004733	
PLXND1	23129	hgsc.bcm.edu	37	3	129297255	129297255	+	Missense_Mutation	SNP	T	T	C	rs112755880	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:129297255T>C	ENST00000324093.4	-	9	2441	c.2263A>G	c.(2263-2265)Acc>Gcc	p.T755A	PLXND1_ENST00000393239.1_Missense_Mutation_p.T755A	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	755					angiogenesis (GO:0001525)|axon guidance (GO:0007411)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell migration (GO:0043542)|outflow tract morphogenesis (GO:0003151)|patterning of blood vessels (GO:0001569)|positive regulation of protein binding (GO:0032092)|regulation of angiogenesis (GO:0045765)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|synapse assembly (GO:0007416)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)	protein domain specific binding (GO:0019904)|semaphorin receptor activity (GO:0017154)		PLXND1/TMCC1(4)	NS(1)|breast(1)|endometrium(4)|kidney(5)|large_intestine(17)|lung(28)|prostate(10)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	72						GAGAGCAGGGTCCGGGGGCAG	0.617																																					p.T755A	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.A2263G						PASS	.	T	ALA/THR	5,4399		0,5,2197	32.0	36.0	35.0		2263	4.6	1.0	3	dbSNP_132	35	30,8566		0,30,4268	yes	missense	PLXND1	NM_015103.2	58	0,35,6465	CC,CT,TT		0.349,0.1135,0.2692	benign	755/1926	129297255	35,12965	2202	4298	6500	SO:0001583	missense	23129	exon9			GCAGGGTCCGGGG	AY116661	CCDS33854.1	3q21.3	2007-05-16			ENSG00000004399	ENSG00000004399		"""Plexins"""	9107	protein-coding gene	gene with protein product		604282				12412018	Standard	NM_015103		Approved	KIAA0620	uc003emx.2	Q9Y4D7	OTTHUMG00000159547	ENST00000324093.4:c.2263A>G	3.37:g.129297255T>C	ENSP00000317128:p.Thr755Ala	125.0	0.0	0		133.0	64.0	0.481203	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	T	10.99	1.505945	0.26949	0.001135	0.00349	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.33654	1.45;1.4	4.62	4.62	0.57501	.	0.643158	0.13899	N	0.355056	T	0.23572	0.0570	N	0.14661	0.345	0.23581	N	0.997361	B	0.12630	0.006	B	0.06405	0.002	T	0.16600	-1.0397	10	0.87932	D	0	.	10.4209	0.44350	0.0:0.0:0.0:1.0	.	755	Q9Y4D7	PLXD1_HUMAN	A	755	ENSP00000317128:T755A;ENSP00000376931:T755A	ENSP00000317128:T755A	T	-	1	0	PLXND1	130779945	1.000000	0.71417	1.000000	0.80357	0.483000	0.33249	2.729000	0.47327	1.708000	0.51301	0.459000	0.35465	ACC	T|0.997;C|0.003	0.003	strong		0.617	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
SERPING1	710	hgsc.bcm.edu	37	11	57373646	57373646	+	Silent	SNP	C	C	T	rs143760635	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:57373646C>T	ENST00000278407.4	+	5	1076	c.849C>T	c.(847-849)tcC>tcT	p.S283S	SERPING1_ENST00000403558.1_Silent_p.S317S|SERPING1_ENST00000340687.6_Silent_p.S283S|SERPING1_ENST00000378323.4_Silent_p.S288S|SERPING1_ENST00000378324.2_Silent_p.S231S	NM_000062.2	NP_000053.2	P05155	IC1_HUMAN	serpin peptidase inhibitor, clade G (C1 inhibitor), member 1	283					blood circulation (GO:0008015)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|complement activation, classical pathway (GO:0006958)|fibrinolysis (GO:0042730)|innate immune response (GO:0045087)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	serine-type endopeptidase inhibitor activity (GO:0004867)	p.S283S(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(11)|pancreas(2)|prostate(1)|urinary_tract(1)	27						GTCTGCCCTCCGATACCCGCC	0.542													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20271	0.0		0.001	False		,,,				2504	0.0				p.S283S		Atlas-SNP	.											SERPING1,NS,carcinoma,0,1	SERPING1	57	1	1	Substitution - coding silent(1)	lung(1)	c.C849T						PASS	.	C	,	1,4401	2.1+/-5.4	0,1,2200	190.0	178.0	183.0		849,849	-10.3	0.0	11	dbSNP_134	183	22,8570	16.0+/-53.3	0,22,4274	no	coding-synonymous,coding-synonymous	SERPING1	NM_000062.2,NM_001032295.1	,	0,23,6474	TT,TC,CC		0.2561,0.0227,0.177	,	283/501,283/501	57373646	23,12971	2201	4296	6497	SO:0001819	synonymous_variant	710	exon4			GCCCTCCGATACC	X54486	CCDS7962.1	11q12.1	2014-09-17	2008-07-31		ENSG00000149131	ENSG00000149131		"""Serine (or cysteine) peptidase inhibitors"""	1228	protein-coding gene	gene with protein product	"""plasma protease C1 inhibitor"", ""angioedema, hereditary"""	606860	"""serine (or cysteine) proteinase inhibitor, clade G (C1 inhibitor), member 1, (angioedema, hereditary)"""	C1NH		2026152, 24172014	Standard	NM_000062		Approved	C1IN, C1-INH, HAE1, HAE2	uc001nkp.1	P05155	OTTHUMG00000150304	ENST00000278407.4:c.849C>T	11.37:g.57373646C>T		219.0	1.0	0.00456621		239.0	124.0	0.518828	NM_001032295	A6NMU0|A8KAI9|B2R6L5|B4E1F0|B4E1H2|Q16304|Q547W3|Q59EI5|Q7Z455|Q96FE0|Q9UC49|Q9UCF9	Silent	SNP	ENST00000278407.4	37	CCDS7962.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	SERPING1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317465.1	NM_000062	
TDP2	51567	hgsc.bcm.edu	37	6	24653283	24653283	+	Silent	SNP	T	T	C	rs11559067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:24653283T>C	ENST00000378198.4	-	6	905	c.735A>G	c.(733-735)ttA>ttG	p.L245L	TDP2_ENST00000341060.3_Silent_p.L187L|TDP2_ENST00000545995.1_Silent_p.L275L|TDP2_ENST00000478285.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	245					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						GCATTTTCTTTAAAACCATTT	0.428								Direct reversal of damage					T|||	60	0.0119808	0.003	0.0202	5008	,	,		17943	0.001		0.0318	False		,,,				2504	0.0092				p.L245L		Atlas-SNP	.											.	TDP2	29	.	0			c.A735G						PASS	.	T		39,4367	43.1+/-76.7	0,39,2164	212.0	222.0	219.0		735	-1.5	0.0	6	dbSNP_120	219	322,8278	113.5+/-173.5	7,308,3985	no	coding-synonymous	TDP2	NM_016614.2		7,347,6149	CC,CT,TT		3.7442,0.8852,2.7756		245/363	24653283	361,12645	2203	4300	6503	SO:0001819	synonymous_variant	51567	exon6			TTTCTTTAAAACC	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"""TRAF and TNF receptor associated protein"""	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.735A>G	6.37:g.24653283T>C		80.0	0.0	0		120.0	61.0	0.508333	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Silent	SNP	ENST00000378198.4	37	CCDS4557.1																																																																																			T|0.977;C|0.023	0.023	strong		0.428	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1		
NOP56	10528	hgsc.bcm.edu	37	20	2636059	2636059	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2636059C>T	ENST00000329276.5	+	6	1174	c.658C>T	c.(658-660)Cga>Tga	p.R220*	SNORD110_ENST00000408189.1_RNA|SNORA51_ENST00000606420.1_RNA|MIR1292_ENST00000408135.1_RNA|SNORD86_ENST00000391196.1_RNA|SNORD57_ENST00000448188.1_RNA|SNORD56_ENST00000413522.1_RNA|IDH3B_ENST00000488299.1_5'Flank	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	220					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						TATTGGAAACCGAAGGGAACT	0.537																																					p.R220X		Atlas-SNP	.											NOP56,NS,carcinoma,-2,1	NOP56	73	1	0			c.C658T						PASS	.						127.0	122.0	124.0					20																	2636059		2203	4300	6503	SO:0001587	stop_gained	10528	exon6			GGAAACCGAAGGG	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.658C>T	20.37:g.2636059C>T	ENSP00000370589:p.Arg220*	141.0	0.0	0		131.0	19.0	0.145038	NM_006392	Q2M3T6|Q9NQ05	Nonsense_Mutation	SNP	ENST00000329276.5	37	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.905811	0.92107	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	.	.	.	5.69	5.69	0.88448	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.0976	12.2785	0.54751	0.1695:0.8305:0.0:0.0	.	.	.	.	X	220;249	.	ENSP00000370589:R220X	R	+	1	2	NOP56	2584059	1.000000	0.71417	0.997000	0.53966	0.994000	0.84299	2.769000	0.47654	2.672000	0.90937	0.561000	0.74099	CGA	.	.	none		0.537	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
KLHL2	11275	hgsc.bcm.edu	37	4	166239083	166239083	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:166239083T>G	ENST00000226725.6	+	14	1974	c.1715T>G	c.(1714-1716)gTt>gGt	p.V572G	KLHL2_ENST00000509028.1_3'UTR|KLHL2_ENST00000421009.2_Missense_Mutation_p.V475G|KLHL2_ENST00000514860.1_Missense_Mutation_p.V576G|KLHL2_ENST00000506761.1_Missense_Mutation_p.V406G|KLHL2_ENST00000538127.1_Missense_Mutation_p.V484G	NM_007246.3	NP_009177.3	O95198	KLHL2_HUMAN	kelch-like family member 2	572					protein ubiquitination (GO:0016567)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)	actin binding (GO:0003779)			endometrium(3)|large_intestine(5)|lung(4)|prostate(1)|urinary_tract(1)	14	all_hematologic(180;0.221)			GBM - Glioblastoma multiforme(119;2.94e-27)|COAD - Colon adenocarcinoma(41;1.4e-05)|Kidney(143;4.95e-05)|KIRC - Kidney renal clear cell carcinoma(143;0.000927)		AAATGGACAGTTGTGTCATCG	0.388																																					p.V576G		Atlas-SNP	.											.	KLHL2	42	.	0			c.T1727G						PASS	.						159.0	154.0	156.0					4																	166239083		2203	4300	6503	SO:0001583	missense	11275	exon14			GGACAGTTGTGTC	AF059569	CCDS34094.1, CCDS54815.1, CCDS54816.1	4q21.2	2013-01-30	2013-01-30		ENSG00000109466	ENSG00000109466		"""Kelch-like"", ""BTB/POZ domain containing"""	6353	protein-coding gene	gene with protein product	"""mayven"""	605774	"""kelch (Drosophila)-like 2 (Mayven)"", ""kelch-like 2, Mayven (Drosophila)"""			10397770, 16035103	Standard	NM_007246		Approved	MAV	uc011cjm.2	O95198	OTTHUMG00000161294	ENST00000226725.6:c.1715T>G	4.37:g.166239083T>G	ENSP00000226725:p.Val572Gly	155.0	0.0	0		154.0	19.0	0.123377	NM_001161521	A6NCM7|B2RD18|B4DFH7|F5H6M3|Q8N484|Q8TBH5	Missense_Mutation	SNP	ENST00000226725.6	37	CCDS34094.1	.	.	.	.	.	.	.	.	.	.	T	19.82	3.897708	0.72639	.	.	ENSG00000109466	ENST00000226725;ENST00000514860;ENST00000538127;ENST00000421009;ENST00000506761	T;T;T;T;T	0.78126	-1.15;-1.15;-1.15;-1.15;-1.15	6.17	6.17	0.99709	Galactose oxidase, beta-propeller (1);	0.125811	0.56097	D	0.000040	T	0.73651	0.3614	L	0.28192	0.835	0.80722	D	1	P;B;P	0.37015	0.578;0.361;0.578	B;B;B	0.42625	0.393;0.298;0.393	T	0.76503	-0.2935	10	0.87932	D	0	.	16.8222	0.85835	0.0:0.0:0.0:1.0	.	576;572;572	B4DFH7;B2RD18;O95198	.;.;KLHL2_HUMAN	G	572;576;484;475;406	ENSP00000226725:V572G;ENSP00000424198:V576G;ENSP00000437526:V484G;ENSP00000408974:V475G;ENSP00000424108:V406G	ENSP00000226725:V572G	V	+	2	0	KLHL2	166458533	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	7.655000	0.83696	2.371000	0.80710	0.533000	0.62120	GTT	.	.	none		0.388	KLHL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000364439.1		
SOX30	11063	hgsc.bcm.edu	37	5	157078632	157078632	+	Missense_Mutation	SNP	G	G	A	rs13181859	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:157078632G>A	ENST00000265007.6	-	1	796	c.455C>T	c.(454-456)cCt>cTt	p.P152L	SOX30_ENST00000519442.1_Intron|SOX30_ENST00000311371.5_Missense_Mutation_p.P152L	NM_178424.1	NP_848511.1	O94993	SOX30_HUMAN	SRY (sex determining region Y)-box 30	152					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to corticosteroid (GO:0031960)|spermatogenesis (GO:0007283)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	23	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.138)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			GGCCCCTCGAGGCCCCACTGA	0.682													.|||	16	0.00319489	0.0	0.0072	5008	,	,		14330	0.0		0.002	False		,,,				2504	0.0092				p.P152L	Esophageal Squamous(31;525 799 19355 21125 41744)	Atlas-SNP	.											.	SOX30	67	.	0			c.C455T						PASS	.	G	LEU/PRO,LEU/PRO	1,4355		0,1,2177	15.0	18.0	17.0		455,455	2.2	0.0	5	dbSNP_121	17	28,8462		0,28,4217	yes	missense,missense	SOX30	NM_007017.2,NM_178424.1	98,98	0,29,6394	AA,AG,GG		0.3298,0.023,0.2258	benign,benign	152/502,152/754	157078632	29,12817	2178	4245	6423	SO:0001583	missense	11063	exon1			CCTCGAGGCCCCA	AB022083	CCDS4339.1, CCDS4340.1	5q33	2010-10-21			ENSG00000039600	ENSG00000039600		"""SRY (sex determining region Y)-boxes"""	30635	protein-coding gene	gene with protein product		606698				15019997, 11678506	Standard	NM_178424		Approved		uc003lxb.1	O94993	OTTHUMG00000130247	ENST00000265007.6:c.455C>T	5.37:g.157078632G>A	ENSP00000265007:p.Pro152Leu	100.0	0.0	0		128.0	89.0	0.695312	NM_178424	O94995|Q8IYX6	Missense_Mutation	SNP	ENST00000265007.6	37	CCDS4339.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	G	3.133	-0.178037	0.06380	2.3E-4	0.003298	ENSG00000039600	ENST00000311371;ENST00000265007	D;D	0.97665	-4.48;-4.13	4.09	2.25	0.28309	.	1.098170	0.07137	N	0.846598	D	0.89220	0.6653	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.32829	0.386;0.0	B;B	0.28232	0.087;0.0	D	0.84664	0.0708	10	0.72032	D	0.01	.	2.6853	0.05106	0.094:0.1461:0.3488:0.4112	rs13181859	152;152	O94993-2;O94993	.;SOX30_HUMAN	L	152	ENSP00000309343:P152L;ENSP00000265007:P152L	ENSP00000265007:P152L	P	-	2	0	SOX30	157011210	0.001000	0.12720	0.000000	0.03702	0.006000	0.05464	0.788000	0.26872	0.351000	0.24027	0.305000	0.20034	CCT	G|0.998;A|0.002	0.002	strong		0.682	SOX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252571.2	NM_007017	
HS6ST1	9394	hgsc.bcm.edu	37	2	129026358	129026358	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:129026358T>C	ENST00000259241.6	-	2	627	c.614A>G	c.(613-615)aAg>aGg	p.K205R		NM_004807.2	NP_004798.3	O60243	H6ST1_HUMAN	heparan sulfate 6-O-sulfotransferase 1	205					angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process, enzymatic modification (GO:0015015)|labyrinthine layer blood vessel development (GO:0060716)|lung alveolus development (GO:0048286)|neuron development (GO:0048666)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)	heparan sulfate 6-O-sulfotransferase activity (GO:0017095)|sulfotransferase activity (GO:0008146)			endometrium(3)|liver(1)|lung(7)|pancreas(1)|prostate(2)|skin(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.117)		CAACGACGTCTTCCACGTGGC	0.637																																					p.K205R		Atlas-SNP	.											.	HS6ST1	31	.	0			c.A614G						PASS	.						37.0	41.0	40.0					2																	129026358		2136	4244	6380	SO:0001583	missense	9394	exon2			GACGTCTTCCACG	AB006179	CCDS42748.1	2q21	2010-03-19		2002-08-23	ENSG00000136720	ENSG00000136720		"""Sulfotransferases, membrane-bound"""	5201	protein-coding gene	gene with protein product		604846		HS6ST		9535912	Standard	NM_004807		Approved		uc002tpt.4	O60243	OTTHUMG00000153542	ENST00000259241.6:c.614A>G	2.37:g.129026358T>C	ENSP00000259241:p.Lys205Arg	239.0	0.0	0		265.0	30.0	0.113208	NM_004807	B4DEP2|B4DJ29|Q53SL2|Q9BVI1	Missense_Mutation	SNP	ENST00000259241.6	37	CCDS42748.1	.	.	.	.	.	.	.	.	.	.	T	19.05	3.752695	0.69533	.	.	ENSG00000136720	ENST00000259241	T	0.75050	-0.9	4.85	4.85	0.62838	.	0.000000	0.85682	D	0.000000	D	0.84410	0.5466	M	0.72576	2.205	0.80722	D	1	D	0.69078	0.997	D	0.79108	0.992	D	0.85075	0.0942	9	.	.	.	.	14.4384	0.67298	0.0:0.0:0.0:1.0	.	205	O60243	H6ST1_HUMAN	R	205	ENSP00000259241:K205R	.	K	-	2	0	HS6ST1	128742828	1.000000	0.71417	1.000000	0.80357	0.511000	0.34104	5.971000	0.70440	1.813000	0.52934	0.379000	0.24179	AAG	.	.	none		0.637	HS6ST1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331572.1	NM_004807	
ADAM15	8751	hgsc.bcm.edu	37	1	155023917	155023917	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:155023917C>T	ENST00000356955.2	+	1	156	c.55C>T	c.(55-57)Cct>Tct	p.P19S	ADAM15_ENST00000368413.1_Missense_Mutation_p.P19S|ADAM15_ENST00000447332.3_Missense_Mutation_p.P19S|ADAM15_ENST00000472434.1_3'UTR|ADAM15_ENST00000355956.2_Missense_Mutation_p.P19S|ADAM15_ENST00000271836.6_Missense_Mutation_p.P19S|ADAM15_ENST00000368410.2_Missense_Mutation_p.P19S|ADAM15_ENST00000359280.4_Missense_Mutation_p.P19S|ADAM15_ENST00000368412.3_Missense_Mutation_p.P19S|ADAM15_ENST00000360674.4_Missense_Mutation_p.P19S|ADAM15_ENST00000531455.1_Missense_Mutation_p.P19S|ADAM15_ENST00000449910.2_Missense_Mutation_p.P19S	NM_207197.2	NP_997080.1	Q13444	ADA15_HUMAN	ADAM metallopeptidase domain 15	19					angiogenesis (GO:0001525)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of receptor binding (GO:1900121)|protein kinase C signaling (GO:0070528)|tissue regeneration (GO:0042246)	cell junction (GO:0030054)|cell projection (GO:0042995)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|cervix(1)|endometrium(9)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(5)|urinary_tract(1)	39	all_epithelial(22;1.43e-30)|all_lung(78;6.64e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.000434)			CAGCCCTCTGCCTTCCTGGCC	0.701																																					p.P19S		Atlas-SNP	.											.	ADAM15	92	.	0			c.C55T						PASS	.																																			SO:0001583	missense	8751	exon1			CCTCTGCCTTCCT	U46005	CCDS1084.1, CCDS1085.1, CCDS1086.1, CCDS1087.1, CCDS1088.1, CCDS44236.1, CCDS58031.1, CCDS58032.1, CCDS60282.1	1q21.3	2008-02-05	2007-06-04		ENSG00000143537	ENSG00000143537		"""ADAM metallopeptidase domain containing"""	193	protein-coding gene	gene with protein product	"""metargidin"""	605548	"""a disintegrin and metalloproteinase domain 15 (metargidin)"""			9516430	Standard	NM_003815		Approved	MDC15	uc001fgr.2	Q13444	OTTHUMG00000013898	ENST00000356955.2:c.55C>T	1.37:g.155023917C>T	ENSP00000349436:p.Pro19Ser	25.0	0.0	0		21.0	11.0	0.52381	NM_003815	B3KQU5|B4DLB5|B4DMH8|E9PN65|Q13493|Q53XQ0|Q5SR68|Q5SR69|Q6R267|Q71S61|Q71S62|Q71S63|Q71S64|Q71S65|Q71S66|Q71S67|Q71S68|Q71S69|Q96C78|U3KQL5	Missense_Mutation	SNP	ENST00000356955.2	37	CCDS1087.1	.	.	.	.	.	.	.	.	.	.	C	15.15	2.747467	0.49257	.	.	ENSG00000143537	ENST00000356955;ENST00000449910;ENST00000359280;ENST00000360674;ENST00000368412;ENST00000355956;ENST00000368410;ENST00000271836;ENST00000368413;ENST00000531455	T;T;T;T;T;T;T;T;T;T	0.03889	5.77;5.76;5.77;5.67;5.56;5.77;3.77;5.75;3.78;5.73	4.56	1.58	0.23477	.	0.195638	0.25189	N	0.032473	T	0.00998	0.0033	L	0.27053	0.805	0.21020	N	0.999802	B;B;B;B;B;B;B;B;B;B	0.27765	0.118;0.118;0.118;0.188;0.188;0.188;0.188;0.188;0.188;0.118	B;B;B;B;B;B;B;B;B;B	0.25759	0.029;0.029;0.029;0.063;0.063;0.063;0.063;0.063;0.063;0.029	T	0.47661	-0.9100	10	0.41790	T	0.15	.	3.3412	0.07119	0.2058:0.5753:0.0:0.2189	.	19;19;19;19;19;19;19;19;19;19	E9PN65;B7Z390;B4DMH8;Q13444-10;Q13444-2;Q13444-4;Q13444-5;Q13444-3;Q13444-9;Q13444	.;.;.;.;.;.;.;.;.;ADA15_HUMAN	S	19	ENSP00000349436:P19S;ENSP00000403843:P19S;ENSP00000352226:P19S;ENSP00000353892:P19S;ENSP00000357397:P19S;ENSP00000348227:P19S;ENSP00000357395:P19S;ENSP00000271836:P19S;ENSP00000357398:P19S;ENSP00000432927:P19S	ENSP00000271836:P19S	P	+	1	0	ADAM15	153290541	0.990000	0.36364	0.995000	0.50966	0.543000	0.35085	0.603000	0.24149	0.354000	0.24105	0.313000	0.20887	CCT	.	.	none		0.701	ADAM15-019	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387168.1	NM_003815	
SNAPC3	6619	hgsc.bcm.edu	37	9	15459821	15459821	+	Missense_Mutation	SNP	A	A	C	rs3087653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15459821A>C	ENST00000380821.3	+	9	1369	c.1193A>C	c.(1192-1194)gAa>gCa	p.E398A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	398			E -> A (in dbSNP:rs3087653).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		AAACTGGGGGAATTCCTTGCT	0.413													A|||	193	0.0385383	0.0416	0.0231	5008	,	,		16799	0.0		0.0596	False		,,,				2504	0.0634				p.E398A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.A1193C						PASS	.	A	ALA/GLU	145,4261	101.2+/-139.8	0,145,2058	134.0	122.0	126.0		1193	5.9	1.0	9	dbSNP_102	126	425,8175	131.8+/-189.6	13,399,3888	yes	missense	SNAPC3	NM_001039697.1	107	13,544,5946	CC,CA,AA		4.9419,3.291,4.3826	probably-damaging	398/412	15459821	570,12436	2203	4300	6503	SO:0001583	missense	6619	exon9			TGGGGGAATTCCT	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.1193A>C	9.37:g.15459821A>C	ENSP00000370200:p.Glu398Ala	145.0	0.0	0		138.0	44.0	0.318841	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	78	0.03571428571428571	26	0.052845528455284556	11	0.03038674033149171	0	0.0	41	0.05408970976253298	A	31	5.081553	0.94050	0.03291	0.049419	ENSG00000164975	ENST00000380821	T	0.44083	0.93	5.86	5.86	0.93980	.	0.138414	0.64402	D	0.000005	T	0.17450	0.0419	M	0.65498	2.005	0.80722	D	1	D	0.57571	0.98	P	0.53224	0.721	T	0.31447	-0.9943	10	0.56958	D	0.05	-42.6534	16.5602	0.84551	1.0:0.0:0.0:0.0	rs3087653;rs3198208;rs52828246;rs3087653	398	Q92966	SNPC3_HUMAN	A	398	ENSP00000370200:E398A	ENSP00000370200:E398A	E	+	2	0	SNAPC3	15449821	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.283000	0.78640	2.367000	0.80283	0.528000	0.53228	GAA	A|0.956;C|0.044	0.044	strong		0.413	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549583	32549583	+	Missense_Mutation	SNP	T	T	C	rs17433947		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32549583T>C	ENST00000360004.5	-	3	508	c.403A>G	c.(403-405)Acc>Gcc	p.T135A		NM_002124.3	NP_002115.2	Q30167	2B1A_HUMAN	major histocompatibility complex, class II, DR beta 1	135	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)				large_intestine(3)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	10						AGGGGCTGGGTCTTTGAAGGA	0.507										Multiple Myeloma(14;0.17)																											p.T135A		Atlas-SNP	.											.	HLA-DRB1	41	.	0			c.A403G						PASS	.						66.0	82.0	76.0					6																	32549583		1510	2709	4219	SO:0001583	missense	3123	exon3			GCTGGGTCTTTGA	AJ297583	CCDS47409.1	6p21.3	2013-01-11			ENSG00000196126	ENSG00000196126		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4948	protein-coding gene	gene with protein product		142857		HLA-DR1B			Standard	NM_001243965		Approved		uc011eri.2	P01911	OTTHUMG00000031196	ENST00000360004.5:c.403A>G	6.37:g.32549583T>C	ENSP00000353099:p.Thr135Ala	185.0	0.0	0		372.0	37.0	0.0994624	NM_002124	P01914|Q9MYF5	Missense_Mutation	SNP	ENST00000360004.5	37	CCDS47409.1	.	.	.	.	.	.	.	.	.	.	.	10.80	1.451590	0.26074	.	.	ENSG00000196126	ENST00000360004	T	0.02787	4.16	3.87	1.14	0.20703	Immunoglobulin-like (1);Immunoglobulin C1-set (1);Immunoglobulin-like fold (1);	0.480425	0.24686	N	0.036424	T	0.03959	0.0111	M	0.62088	1.915	0.25150	N	0.990439	D	0.54964	0.969	D	0.73708	0.981	T	0.28170	-1.0052	10	0.72032	D	0.01	.	5.5797	0.17243	0.0:0.1048:0.1704:0.7249	.	135	P01911	2B1F_HUMAN	A	135	ENSP00000353099:T135A	ENSP00000353099:T135A	T	-	1	0	HLA-DRB1	32657561	0.000000	0.05858	0.754000	0.31244	0.116000	0.19942	-1.406000	0.02490	0.483000	0.27608	-0.639000	0.03973	ACC	.	.	weak		0.507	HLA-DRB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076393.3	NM_002124	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859906	144859906	+	Missense_Mutation	SNP	G	G	T	rs182136884		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859906G>T	ENST00000369354.3	-	38	6367	c.6178C>A	c.(6178-6180)Cag>Aag	p.Q2060K	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.Q2145K|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.Q2196K|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.Q1954K|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.Q2060K			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2060					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGAATGCTCTGCTCCAGCTGC	0.577			T	PDGFRB	MPD																																p.Q2060K		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6178A						PASS	.						82.0	77.0	79.0					1																	144859906		2203	4298	6501	SO:0001583	missense	9659	exon38			TGCTCTGCTCCAG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6178C>A	1.37:g.144859906G>T	ENSP00000358360:p.Gln2060Lys	251.0	0.0	0		306.0	17.0	0.0555556	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	1.396	-0.579398	0.03854	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01505	4.82;4.91;4.91;4.92;4.91	5.1	0.961	0.19638	.	.	.	.	.	T	0.00608	0.0020	L	0.43152	1.355	0.80722	D	1	B;B	0.10296	0.003;0.0	B;B	0.09377	0.004;0.0	T	0.45731	-0.9241	9	0.34782	T	0.22	.	2.6421	0.04974	0.1614:0.2665:0.4356:0.1366	.	1954;2060	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	K	1954;2060;2060;2145;2196	ENSP00000327209:Q1954K;ENSP00000358360:Q2060K;ENSP00000358363:Q2060K;ENSP00000435654:Q2145K;ENSP00000358366:Q2196K	ENSP00000327209:Q1954K	Q	-	1	0	PDE4DIP	143571263	0.990000	0.36364	0.996000	0.52242	0.001000	0.01503	0.798000	0.27014	0.255000	0.21593	-0.894000	0.02916	CAG	G|1.000;T|0.000	0.000	strong		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
COL4A5	1287	hgsc.bcm.edu	37	X	107867476	107867476	+	Silent	SNP	A	A	T	rs104886373		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:107867476A>T	ENST00000361603.2	+	34	3172	c.2928A>T	c.(2926-2928)ggA>ggT	p.G976G	COL4A5_ENST00000328300.6_Silent_p.G976G	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	976	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						GTATACCTGGAGTTTCAGGGC	0.448									Alport syndrome with Diffuse Leiomyomatosis																												p.G976G		Atlas-SNP	.											.	COL4A5	262	.	0			c.A2928T						PASS	.						103.0	82.0	89.0					X																	107867476		2203	4300	6503	SO:0001819	synonymous_variant	1287	exon34	Familial Cancer Database		ACCTGGAGTTTCA	M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.2928A>T	X.37:g.107867476A>T		110.0	0.0	0		44.0	16.0	0.363636	NM_000495	Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Silent	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	A	3.794	-0.043138	0.07452	.	.	ENSG00000188153	ENST00000505728	.	.	.	5.5	2.99	0.34606	.	.	.	.	.	T	0.45716	0.1356	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.34354	-0.9832	4	.	.	.	.	2.442	0.04497	0.5622:0.1178:0.0786:0.2414	.	.	.	.	V	54	.	.	E	+	2	0	COL4A5	107754132	0.702000	0.27816	0.732000	0.30844	0.498000	0.33706	1.305000	0.33493	0.715000	0.32103	0.441000	0.28932	GAG	.	.	none		0.448	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2		
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859817	144859817	+	Silent	SNP	G	G	A	rs587702923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859817G>A	ENST00000369354.3	-	38	6456	c.6267C>T	c.(6265-6267)tcC>tcT	p.S2089S	PDE4DIP_ENST00000530740.1_Silent_p.S2174S|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Silent_p.S2225S|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Silent_p.S1983S|PDE4DIP_ENST00000369356.4_Silent_p.S2089S			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2089					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCTGGTTAATGGAGGAGGGGC	0.582			T	PDGFRB	MPD																																p.S2089S		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6267T						PASS	.						65.0	62.0	63.0					1																	144859817		2203	4300	6503	SO:0001819	synonymous_variant	9659	exon38			GTTAATGGAGGAG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6267C>T	1.37:g.144859817G>A		307.0	0.0	0		402.0	26.0	0.0646766	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Silent	SNP	ENST00000369354.3	37	CCDS30824.1																																																																																			.	.	none		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
ACTR3C	653857	hgsc.bcm.edu	37	7	149981856	149981856	+	Missense_Mutation	SNP	G	G	A	rs117425825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:149981856G>A	ENST00000539352.1	-	6	801	c.550C>T	c.(550-552)Cgt>Tgt	p.R184C	ACTR3C_ENST00000252071.4_Missense_Mutation_p.R184C	NM_001164458.1	NP_001157930.1	Q9C0K3	ARP3C_HUMAN	ARP3 actin-related protein 3 homolog C (yeast)	184						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)										TACAGCGGACGCCGCACATCG	0.403													G|||	105	0.0209665	0.003	0.0187	5008	,	,		13887	0.0		0.0457	False		,,,				2504	0.0429				p.R184C		Atlas-SNP	.											.	.	.	.	0			c.C550T						PASS	.	G	CYS/ARG,CYS/ARG	13,1371		0,13,679	85.0	73.0	77.0		550,550	2.2	0.9	7	dbSNP_132	77	125,3057		1,123,1467	yes	missense,missense	ACTR3C	NM_001164458.1,NM_001164459.1	180,180	1,136,2146	AA,AG,GG		3.9283,0.9393,3.0223	probably-damaging,probably-damaging	184/211,184/211	149981856	138,4428	692	1591	2283	SO:0001583	missense	653857	exon6			GCGGACGCCGCAC		CCDS47744.1	7q36.1	2009-09-23			ENSG00000106526	ENSG00000106526			37282	protein-coding gene	gene with protein product						11162478, 14651955	Standard	NM_001164458		Approved	ARP11	uc022aps.1	Q9C0K3	OTTHUMG00000158323	ENST00000539352.1:c.550C>T	7.37:g.149981856G>A	ENSP00000440990:p.Arg184Cys	84.0	0.0	0		95.0	40.0	0.421053	NM_001164459	Q5CZI4	Missense_Mutation	SNP	ENST00000539352.1	37	CCDS47744.1	43	0.019688644688644688	0	0.0	10	0.027624309392265192	1	0.0017482517482517483	32	0.04221635883905013	G	13.83	2.352944	0.41700	0.009393	0.039283	ENSG00000106526	ENST00000478393;ENST00000252071;ENST00000539352	T;T;T	0.09350	2.99;2.99;2.99	2.16	2.16	0.27623	.	0.221425	0.28151	N	0.016416	T	0.14141	0.0342	H	0.97587	4.035	0.39214	D	0.963377	D	0.89917	1.0	D	0.68943	0.961	T	0.52961	-0.8505	9	.	.	.	.	10.4552	0.44546	0.0:0.0:1.0:0.0	.	184	Q9C0K3	ARP3C_HUMAN	C	182;184;184	ENSP00000417426:R182C;ENSP00000252071:R184C;ENSP00000440990:R184C	.	R	-	1	0	ACTR3C	149612789	1.000000	0.71417	0.896000	0.35187	0.654000	0.38779	4.696000	0.61774	1.511000	0.48818	0.398000	0.26397	CGT	G|0.976;A|0.024	0.024	strong		0.403	ACTR3C-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350676.2		
MUC2	4583	hgsc.bcm.edu	37	11	1092971	1092971	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:1092971C>T	ENST00000441003.2	+	30	4817	c.4790C>T	c.(4789-4791)aCa>aTa	p.T1597I	MUC2_ENST00000359061.5_Intron|MUC2_ENST00000361558.6_Intron|MUC2_ENST00000333592.6_5'Flank	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				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)	ccaaccccaacacccaccggc	0.632																																					p.T1597I		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,1	MUC2	614	1	0			c.C4790T						scavenged	.						47.0	82.0	70.0					11																	1092971		1782	3233	5015	SO:0001583	missense	4583	exon30			CCCCAACACCCAC	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.4790C>T	11.37:g.1092971C>T	ENSP00000415183:p.Thr1597Ile	114.0	1.0	0.00877193		121.0	6.0	0.0495868	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	2.395	-0.338980	0.05243	.	.	ENSG00000198788	ENST00000441003	T	0.14640	2.49	1.75	0.762	0.18454	.	.	.	.	.	T	0.07143	0.0181	.	.	.	0.09310	N	1	B	0.13145	0.007	B	0.04013	0.001	T	0.41520	-0.9504	8	0.22109	T	0.4	.	4.3366	0.11089	0.0:0.6142:0.0:0.3858	.	1597	E7EUV1	.	I	1597	ENSP00000415183:T1597I	ENSP00000415183:T1597I	T	+	2	0	MUC2	1082971	0.029000	0.19370	0.001000	0.08648	0.134000	0.20937	1.107000	0.31110	0.104000	0.17725	0.121000	0.15741	ACA	.	.	none		0.632	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SPP2	6694	hgsc.bcm.edu	37	2	234959642	234959642	+	Missense_Mutation	SNP	C	C	T	rs34347825	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234959642C>T	ENST00000168148.3	+	2	201	c.113C>T	c.(112-114)tCc>tTc	p.S38F	SPP2_ENST00000373368.1_Missense_Mutation_p.S38F|SPP2_ENST00000492481.1_3'UTR	NM_006944.2	NP_008875.1	Q13103	SPP24_HUMAN	secreted phosphoprotein 2, 24kDa	38			S -> F (in dbSNP:rs34347825). {ECO:0000269|PubMed:15062857}.		bone remodeling (GO:0046849)|negative regulation of endopeptidase activity (GO:0010951)|protein complex assembly (GO:0006461)|skeletal system development (GO:0001501)	extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)	endopeptidase inhibitor activity (GO:0004866)			breast(1)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)|skin(1)	12		Breast(86;0.0109)|Renal(207;0.019)|all_lung(227;0.13)|all_hematologic(139;0.182)		Epithelial(121;5.73e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000166)|Lung(119;0.00539)|LUSC - Lung squamous cell carcinoma(224;0.00846)		TACGATCCATCCTCCTTAAGG	0.512													C|||	17	0.00339457	0.0	0.0144	5008	,	,		19633	0.0		0.007	False		,,,				2504	0.0				p.S38F		Atlas-SNP	.											.	SPP2	35	.	0			c.C113T						PASS	.	C	PHE/SER	7,4399	12.9+/-30.5	0,7,2196	141.0	118.0	126.0		113	4.4	0.1	2	dbSNP_126	126	64,8536	38.8+/-94.9	0,64,4236	yes	missense	SPP2	NM_006944.2	155	0,71,6432	TT,TC,CC		0.7442,0.1589,0.5459	possibly-damaging	38/212	234959642	71,12935	2203	4300	6503	SO:0001583	missense	6694	exon2			ATCCATCCTCCTT		CCDS2511.1	2q37.1	2012-08-14	2002-08-29		ENSG00000072080	ENSG00000072080			11256	protein-coding gene	gene with protein product		602637	"""secreted phosphoprotein 2, 24kD"""			9533032	Standard	XM_005246102		Approved	SPP24	uc002vvk.1	Q13103	OTTHUMG00000059208	ENST00000168148.3:c.113C>T	2.37:g.234959642C>T	ENSP00000168148:p.Ser38Phe	176.0	0.0	0		184.0	91.0	0.494565	NM_006944	A4QMV3|Q3B892|Q546M5	Missense_Mutation	SNP	ENST00000168148.3	37	CCDS2511.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	12.60	1.987057	0.35036	0.001589	0.007442	ENSG00000072080	ENST00000373368;ENST00000168148	T;T	0.50001	0.76;0.76	5.38	4.45	0.53987	.	1.384140	0.04525	N	0.385354	T	0.51568	0.1682	L	0.51422	1.61	0.09310	N	1	D	0.62365	0.991	P	0.55161	0.77	T	0.48163	-0.9059	10	0.66056	D	0.02	-4.2781	11.2458	0.48996	0.0:0.8155:0.1844:0.0	rs34347825;rs34347825	38	Q13103	SPP24_HUMAN	F	38	ENSP00000362466:S38F;ENSP00000168148:S38F	ENSP00000168148:S38F	S	+	2	0	SPP2	234624381	0.002000	0.14202	0.140000	0.22221	0.020000	0.10135	1.445000	0.35079	2.528000	0.85240	0.650000	0.86243	TCC	C|0.995;T|0.005	0.005	strong		0.512	SPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131313.3	NM_006944	
ZNF207	7756	hgsc.bcm.edu	37	17	30689985	30689985	+	Missense_Mutation	SNP	A	A	G	rs140641814		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:30689985A>G	ENST00000321233.6	+	6	758	c.604A>G	c.(604-606)Atg>Gtg	p.M202V	ZNF207_ENST00000341711.6_Missense_Mutation_p.M119V|ZNF207_ENST00000577908.1_Missense_Mutation_p.M218V|ZNF207_ENST00000394670.4_Missense_Mutation_p.M218V|ZNF207_ENST00000342555.6_Missense_Mutation_p.M221V|RP11-227G15.3_ENST00000581915.1_RNA|ZNF207_ENST00000394673.2_Missense_Mutation_p.M218V	NM_003457.3	NP_003448.1	O43670	ZN207_HUMAN	zinc finger protein 207	202					attachment of spindle microtubules to kinetochore (GO:0008608)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|protein stabilization (GO:0050821)|regulation of chromosome segregation (GO:0051983)|regulation of transcription, DNA-templated (GO:0006355)	kinetochore (GO:0000776)|microtubule (GO:0005874)|nucleus (GO:0005634)	DNA binding (GO:0003677)|heparin binding (GO:0008201)|microtubule binding (GO:0008017)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(2)|lung(3)|urinary_tract(2)	10		Breast(31;0.116)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.239)			ACCACCTCTGATGCCTGGAAT	0.363																																					p.M218V		Atlas-SNP	.											.	ZNF207	32	.	0			c.A652G						PASS	.	A	VAL/MET,VAL/MET,VAL/MET	0,4406		0,0,2203	111.0	108.0	109.0		652,652,604	5.7	1.0	17	dbSNP_134	109	1,8599		0,1,4299	no	missense,missense,missense	ZNF207	NM_001032293.2,NM_001098507.1,NM_003457.3	21,21,21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign,benign,benign	218/464,218/495,202/479	30689985	1,13005	2203	4300	6503	SO:0001583	missense	7756	exon7			CCTCTGATGCCTG	AF046001	CCDS11271.1, CCDS32614.1, CCDS42294.1	17q11.2	2008-07-10			ENSG00000010244	ENSG00000010244		"""Zinc fingers, C2H2-type"""	12998	protein-coding gene	gene with protein product		603428				9799612	Standard	NM_001098507		Approved		uc002hhj.4	O43670	OTTHUMG00000132810	ENST00000321233.6:c.604A>G	17.37:g.30689985A>G	ENSP00000322777:p.Met202Val	74.0	0.0	0		56.0	31.0	0.553571	NM_001098507	A8K6Y6|E1P660|E1P661|E1P662|Q53XS9|Q96HW5|Q9BUQ7	Missense_Mutation	SNP	ENST00000321233.6	37	CCDS11271.1	.	.	.	.	.	.	.	.	.	.	A	3.923	-0.017677	0.07681	0.0	1.16E-4	ENSG00000010244	ENST00000394670;ENST00000394673;ENST00000394679;ENST00000321233;ENST00000341711;ENST00000342555	T;T;T	0.54279	0.95;0.88;0.58	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	T	0.46464	0.1394	L	0.50333	1.59	0.80722	D	1	B;B;B;B;B	0.24576	0.106;0.106;0.106;0.039;0.106	B;B;B;B;B	0.15484	0.013;0.013;0.013;0.013;0.013	T	0.38286	-0.9668	10	0.17369	T	0.5	.	16.0101	0.80396	1.0:0.0:0.0:0.0	.	202;221;218;218;202	A8MTG3;Q59G94;E1P660;O43670-2;O43670	.;.;.;.;ZN207_HUMAN	V	218;202;221;218;119;202	ENSP00000378165:M218V;ENSP00000378168:M202V;ENSP00000344913:M119V	ENSP00000322777:M218V	M	+	1	0	ZNF207	27714098	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.267000	0.78462	2.171000	0.68590	0.533000	0.62120	ATG	A|1.000;G|0.000	0.000	weak		0.363	ZNF207-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256251.2		
C16orf71	146562	hgsc.bcm.edu	37	16	4790446	4790446	+	Missense_Mutation	SNP	C	C	T	rs35599524	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:4790446C>T	ENST00000299320.5	+	4	1047	c.569C>T	c.(568-570)tCa>tTa	p.S190L	RP11-127I20.7_ENST00000588099.1_RNA|C16orf71_ENST00000590191.1_Missense_Mutation_p.S204L	NM_139170.2	NP_631909.2	Q8IYS4	CP071_HUMAN	chromosome 16 open reading frame 71	190			S -> L (in dbSNP:rs35599524).							breast(1)|central_nervous_system(1)|large_intestine(4)|lung(4)|ovary(1)	11						AGCACTGCCTCACAAGAATCT	0.612													C|||	73	0.0145767	0.0061	0.0245	5008	,	,		17919	0.0069		0.0239	False		,,,				2504	0.0174				p.S190L		Atlas-SNP	.											.	C16orf71	46	.	0			c.C569T						PASS	.	C	LEU/SER	53,4341	53.6+/-89.4	1,51,2145	41.0	44.0	43.0		569	-0.2	0.0	16	dbSNP_126	43	218,8382	89.7+/-151.9	2,214,4084	yes	missense	C16orf71	NM_139170.2	145	3,265,6229	TT,TC,CC		2.5349,1.2062,2.0856	benign	190/521	4790446	271,12723	2197	4300	6497	SO:0001583	missense	146562	exon4			CTGCCTCACAAGA	AF447587	CCDS10521.1	16p13.3	2008-02-05			ENSG00000166246	ENSG00000166246			25081	protein-coding gene	gene with protein product						12477932	Standard	XM_005255144		Approved	FLJ43261, DKFZp686H2240	uc002cxn.3	Q8IYS4	OTTHUMG00000129480	ENST00000299320.5:c.569C>T	16.37:g.4790446C>T	ENSP00000299320:p.Ser190Leu	82.0	0.0	0		112.0	55.0	0.491071	NM_139170	Q8NCV0	Missense_Mutation	SNP	ENST00000299320.5	37	CCDS10521.1	32	0.014652014652014652	2	0.0040650406504065045	3	0.008287292817679558	6	0.01048951048951049	21	0.027704485488126648	C	10.63	1.404118	0.25291	0.012062	0.025349	ENSG00000166246	ENST00000299320	T	0.12147	2.71	4.18	-0.182	0.13287	.	1.917540	0.03379	N	0.200152	T	0.03390	0.0098	L	0.50333	1.59	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.28554	-1.0040	10	0.02654	T	1	0.8564	4.4743	0.11727	0.0:0.4558:0.2178:0.3264	rs35599524	190	Q8IYS4	CP071_HUMAN	L	190	ENSP00000299320:S190L	ENSP00000299320:S190L	S	+	2	0	C16orf71	4730447	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	-0.499000	0.06413	-0.065000	0.13021	-0.232000	0.12228	TCA	C|0.981;T|0.019	0.019	strong		0.612	C16orf71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251644.1	NM_139170	
RAB39A	54734	hgsc.bcm.edu	37	11	107833065	107833065	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:107833065A>C	ENST00000320578.2	+	2	687	c.621A>C	c.(619-621)gaA>gaC	p.E207D		NM_017516.1	NP_059986.1	Q14964	RB39A_HUMAN	RAB39A, member RAS oncogene family	207					phagosome acidification (GO:0090383)|phagosome-lysosome fusion (GO:0090385)|protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)										CTTCTGAGGAAGCAGTAAAGC	0.383																																					p.E207D		Atlas-SNP	.											.	.	.	.	0			c.A621C						PASS	.						49.0	55.0	53.0					11																	107833065		2200	4298	6498	SO:0001583	missense	54734	exon2			TGAGGAAGCAGTA	X99962	CCDS8338.1	11q22.3	2011-11-22	2011-11-22	2011-11-22	ENSG00000179331	ENSG00000179331		"""RAB, member RAS oncogene"""	16521	protein-coding gene	gene with protein product	"""rab-related GTP-binding protein"""		"""RAB39, member RAS oncogene family"""	RAB39		9119394	Standard	NM_017516		Approved		uc001pjt.3	Q14964	OTTHUMG00000166367	ENST00000320578.2:c.621A>C	11.37:g.107833065A>C	ENSP00000322594:p.Glu207Asp	116.0	0.0	0		135.0	66.0	0.488889	NM_017516	A8KAA4|Q8N6W2	Missense_Mutation	SNP	ENST00000320578.2	37	CCDS8338.1	.	.	.	.	.	.	.	.	.	.	A	10.34	1.323277	0.24080	.	.	ENSG00000179331	ENST00000320578	T	0.66995	-0.24	5.55	3.27	0.37495	.	0.000000	0.64402	D	0.000010	T	0.45034	0.1322	N	0.19112	0.55	0.32971	D	0.52234	B	0.16166	0.016	B	0.12156	0.007	T	0.43766	-0.9371	10	0.13108	T	0.6	.	8.0299	0.30459	0.7816:0.0:0.2184:0.0	.	207	Q14964	RB39A_HUMAN	D	207	ENSP00000322594:E207D	ENSP00000322594:E207D	E	+	3	2	RAB39	107338275	0.984000	0.35163	1.000000	0.80357	0.984000	0.73092	0.350000	0.20079	0.553000	0.29044	0.482000	0.46254	GAA	.	.	none		0.383	RAB39A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389423.1	NM_017516	
MLH1	4292	hgsc.bcm.edu	37	3	37089131	37089131	+	Missense_Mutation	SNP	A	A	C	rs587778949|rs63749986|rs35502531|rs63750449	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37089131A>C	ENST00000231790.2	+	16	2069	c.1853A>C	c.(1852-1854)aAg>aCg	p.K618T	MLH1_ENST00000539477.1_Missense_Mutation_p.K377T|MLH1_ENST00000536378.1_Missense_Mutation_p.K377T|MLH1_ENST00000435176.1_Missense_Mutation_p.K520T|MLH1_ENST00000455445.2_Missense_Mutation_p.K377T|MLH1_ENST00000458205.2_Missense_Mutation_p.K377T	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	618	Interaction with EXO1.		K -> A (common polymorphism; requires 2 nucleotide substitutions; dbSNP:rs35502531). {ECO:0000269|PubMed:10598809, ECO:0000269|PubMed:10713887, ECO:0000269|PubMed:11726306, ECO:0000269|PubMed:11870161, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12373605, ECO:0000269|PubMed:16083711, ECO:0000269|PubMed:18033691, ECO:0000269|PubMed:9311737}.|K -> R (in colorectal cancer; dbSNP:rs63750449). {ECO:0000269|PubMed:14504054}.|K -> T (in HNPCC2; type II). {ECO:0000269|PubMed:10573010, ECO:0000269|PubMed:11839723, ECO:0000269|PubMed:12095971, ECO:0000269|PubMed:7757073, ECO:0000269|PubMed:8872463}.|Missing (in HNPCC2). {ECO:0000269|PubMed:16451135}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.K618del(1)|p.0?(1)|p.K618T(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						CTGAAGAAGAAGGCTGAGATG	0.428		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	16	0.00319489	0.0008	0.0072	5008	,	,		20491	0.0		0.0099	False		,,,				2504	0.0				p.K618T		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,colon,carcinoma,0,5	MLH1	226	5	3	Substitution - Missense(1)|Whole gene deletion(1)|Deletion - In frame(1)	large_intestine(2)|ovary(1)	c.A1853C	GRCh37	CM950808	MLH1	M	rs63750449	PASS	.	A	THR/LYS,THR/LYS,THR/LYS,THR/LYS	9,4397	15.5+/-35.6	0,9,2194	158.0	161.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1853,1559,1130,1130	5.3	1.0	3	dbSNP_130	160	40,8560	22.2+/-67.0	0,40,4260	yes	missense,missense,missense,missense	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	78,78,78,78	0,49,6454	CC,CA,AA		0.4651,0.2043,0.3767	probably-damaging,probably-damaging,probably-damaging,probably-damaging	618/757,520/659,377/516,377/516	37089131	49,12957	2203	4300	6503	SO:0001583	missense	4292	exon16	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AGAAGAAGGCTGA	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1853A>C	3.37:g.37089131A>C	ENSP00000231790:p.Lys618Thr	130.0	0.0	0		134.0	80.0	0.597015	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	9	0.004120879120879121	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	23.0	4.366099	0.82463	0.002043	0.004651	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.94650	-3.48;-3.48;-3.48;-3.48;-3.48;-3.48	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96430	0.8835	M	0.87097	2.86	0.80722	D	1	D;D;D;D	0.76494	0.999;0.997;0.999;0.997	D;D;D;D	0.73708	0.981;0.968;0.981;0.975	D	0.95622	0.8682	10	0.66056	D	0.02	-23.9591	15.372	0.74573	1.0:0.0:0.0:0.0	rs63750449	520;618;618;618	E9PCU2;B2R6K0;Q53GX1;P40692	.;.;.;MLH1_HUMAN	T	618;482;377;377;377;520;377	ENSP00000231790:K618T;ENSP00000402667:K377T;ENSP00000443665:K377T;ENSP00000398272:K377T;ENSP00000402564:K520T;ENSP00000444286:K377T	ENSP00000231790:K618T	K	+	2	0	MLH1	37064135	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.339000	0.79282	2.044000	0.60594	0.477000	0.44152	AAG	A|0.995;C|0.005	0.005	strong		0.428	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
FBXO44	93611	hgsc.bcm.edu	37	1	11718859	11718859	+	Silent	SNP	C	C	T	rs150816569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11718859C>T	ENST00000251547.5	+	5	637	c.555C>T	c.(553-555)caC>caT	p.H185H	FBXO44_ENST00000251546.4_Missense_Mutation_p.R144C|FBXO44_ENST00000376768.1_Missense_Mutation_p.R176C|FBXO44_ENST00000376760.1_Missense_Mutation_p.R144C|FBXO44_ENST00000376762.4_Missense_Mutation_p.R144C|FBXO44_ENST00000376770.1_Silent_p.H185H	NM_033182.5	NP_149438.2	Q9H4M3	FBX44_HUMAN	F-box protein 44	185	FBA. {ECO:0000255|PROSITE- ProRule:PRU00482}.					SCF ubiquitin ligase complex (GO:0019005)				kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|prostate(1)	8	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.41e-06)|COAD - Colon adenocarcinoma(227;0.000255)|BRCA - Breast invasive adenocarcinoma(304;0.0003)|Kidney(185;0.000758)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		CGTCCGCGCACGCGCCTCTGG	0.692													C|||	24	0.00479233	0.0008	0.0159	5008	,	,		14300	0.0		0.0119	False		,,,				2504	0.0				p.R144C		Atlas-SNP	.											.	FBXO44	20	.	0			c.C430T						PASS	.	C	,,CYS/ARG,CYS/ARG	16,4390	23.3+/-48.9	0,16,2187	61.0	61.0	61.0		555,555,430,430	-3.8	0.1	1	dbSNP_134	61	83,8517	48.9+/-108.6	2,79,4219	yes	coding-synonymous,coding-synonymous,missense,missense	FBXO44	NM_001014765.1,NM_033182.5,NM_183412.2,NM_183413.2	,,180,180	2,95,6406	TT,TC,CC		0.9651,0.3631,0.7612	,,,	185/256,185/256,144/225,144/225	11718859	99,12907	2203	4300	6503	SO:0001819	synonymous_variant	93611	exon4			CGCGCACGCGCCT	AY040878	CCDS131.1, CCDS132.1	1p36.21	2008-03-26			ENSG00000132879	ENSG00000132879		"""F-boxes /  ""other"""""	24847	protein-coding gene	gene with protein product		609111				12383498	Standard	XM_005263535		Approved	FBX30, FBG3, MGC14140, Fbxo6a, Fbx44	uc001asm.3	Q9H4M3	OTTHUMG00000002071	ENST00000251547.5:c.555C>T	1.37:g.11718859C>T		67.0	0.0	0		77.0	54.0	0.701299	NM_183412	B3KNZ2|B7Z743|Q5TGX2|Q5TGX4|Q5TGX5|Q68DJ9|Q8WWY2	Missense_Mutation	SNP	ENST00000251547.5	37	CCDS132.1	17	0.007783882783882784	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	8	0.010554089709762533	C	5.363	0.252260	0.10185	0.003631	0.009651	ENSG00000132879	ENST00000251546;ENST00000425796;ENST00000376768;ENST00000376762;ENST00000376760	T;T;T;T;T	0.40225	1.3;1.12;1.04;1.3;1.3	5.01	-3.78	0.04333	.	0.423822	0.29737	N	0.011321	T	0.14700	0.0355	.	.	.	0.09310	N	0.999995	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.10965	-1.0607	9	0.41790	T	0.15	-28.3452	13.2172	0.59867	0.0:0.7229:0.0:0.2771	.	176;144	B7Z1P2;Q9H4M3-2	.;.	C	144;144;176;144;144	ENSP00000251546:R144C;ENSP00000389820:R144C;ENSP00000365959:R176C;ENSP00000365953:R144C;ENSP00000365951:R144C	ENSP00000251546:R144C	R	+	1	0	FBXO44	11641446	0.000000	0.05858	0.059000	0.19551	0.034000	0.12701	-1.363000	0.02592	-0.722000	0.04922	-0.409000	0.06214	CGC	C|0.992;T|0.008	0.008	strong		0.692	FBXO44-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005761.1	NM_183412	
EGF	1950	hgsc.bcm.edu	37	4	110884396	110884396	+	Silent	SNP	A	A	G	rs11568953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110884396A>G	ENST00000265171.5	+	9	1825	c.1380A>G	c.(1378-1380)gaA>gaG	p.E460E	EGF_ENST00000503392.1_Silent_p.E460E|EGF_ENST00000509793.1_Silent_p.E418E	NM_001178130.1|NM_001963.4	NP_001171601.1|NP_001954.2	P01133	EGF_HUMAN	epidermal growth factor	460	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				activation of MAPKK activity (GO:0000186)|activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|branching morphogenesis of an epithelial tube (GO:0048754)|DNA replication (GO:0006260)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERK1 and ERK2 cascade (GO:0070371)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|mammary gland alveolus development (GO:0060749)|negative regulation of cholesterol efflux (GO:0090370)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of secretion (GO:0051048)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cerebellar granule cell precursor proliferation (GO:0021940)|positive regulation of DNA binding (GO:0043388)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of calcium ion import (GO:0090279)|regulation of protein localization to cell surface (GO:2000008)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	calcium ion binding (GO:0005509)|epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			breast(1)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(19)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Hepatocellular(203;0.0893)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-06)	Sucralfate(DB00364)	TATCCTGGGAATGTGATTGCT	0.453													A|||	22	0.00439297	0.0015	0.0043	5008	,	,		15769	0.0		0.0169	False		,,,				2504	0.0				p.E460E		Atlas-SNP	.											.	EGF	113	.	0			c.A1380G						PASS	.	A	,,	9,4397	15.5+/-35.6	0,9,2194	223.0	208.0	213.0		1380,1254,1380	0.7	1.0	4	dbSNP_120	213	123,8477	64.2+/-126.4	2,119,4179	no	coding-synonymous,coding-synonymous,coding-synonymous	EGF	NM_001178130.1,NM_001178131.1,NM_001963.4	,,	2,128,6373	GG,GA,AA		1.4302,0.2043,1.0149	,,	460/1167,418/1166,460/1208	110884396	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	1950	exon9			CTGGGAATGTGAT	X04571	CCDS3689.1, CCDS54794.1, CCDS54795.1	4q25	2012-10-02	2010-05-11		ENSG00000138798	ENSG00000138798			3229	protein-coding gene	gene with protein product		131530	"""epidermal growth factor (beta-urogastrone)"""				Standard	NM_001963		Approved		uc003hzy.4	P01133	OTTHUMG00000132044	ENST00000265171.5:c.1380A>G	4.37:g.110884396A>G		148.0	0.0	0		132.0	66.0	0.5	NM_001963	B4DRK7|E7EVD2|E9PBF0|Q52LZ6	Silent	SNP	ENST00000265171.5	37	CCDS3689.1																																																																																			A|0.990;G|0.010	0.010	strong		0.453	EGF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255065.1		
SNAPC4	6621	hgsc.bcm.edu	37	9	139272045	139272045	+	Missense_Mutation	SNP	C	C	A	rs79283598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139272045C>A	ENST00000298532.2	-	21	4602	c.4234G>T	c.(4234-4236)Gca>Tca	p.A1412S		NM_003086.2	NP_003077.2			small nuclear RNA activating complex, polypeptide 4, 190kDa											biliary_tract(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|prostate(3)|skin(2)|urinary_tract(1)	33		Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.31e-06)|Epithelial(140;7.13e-06)		TCCCTGTCTGCAAGTTCCAGC	0.677													C|||	68	0.0135783	0.0023	0.0187	5008	,	,		15784	0.001		0.0477	False		,,,				2504	0.0031				p.A1412S		Atlas-SNP	.											.	SNAPC4	82	.	0			c.G4234T						PASS	.		SER/ALA	26,4380	29.0+/-57.7	0,26,2177	38.0	37.0	37.0		4234	-7.5	0.0	9	dbSNP_131	37	273,8317	100.3+/-161.8	4,265,4026	yes	missense	SNAPC4	NM_003086.2	99	4,291,6203	AA,AC,CC		3.1781,0.5901,2.3007	benign	1412/1470	139272045	299,12697	2203	4295	6498	SO:0001583	missense	6621	exon21			TGTCTGCAAGTTC	AF032387	CCDS6998.1	9q34.3	2008-07-21	2002-08-29		ENSG00000165684	ENSG00000165684			11137	protein-coding gene	gene with protein product		602777	"""small nuclear RNA activating complex, polypeptide 4, 190kD"""			9418884	Standard	XM_005266096		Approved	SNAP190, PTFalpha, FLJ13451	uc004chh.3	Q5SXM2	OTTHUMG00000020929	ENST00000298532.2:c.4234G>T	9.37:g.139272045C>A	ENSP00000298532:p.Ala1412Ser	59.0	0.0	0		71.0	37.0	0.521127	NM_003086		Missense_Mutation	SNP	ENST00000298532.2	37	CCDS6998.1	45	0.020604395604395604	2	0.0040650406504065045	6	0.016574585635359115	1	0.0017482517482517483	36	0.047493403693931395	c	0.796	-0.757231	0.03019	0.005901	0.031781	ENSG00000165684	ENST00000298532	T	0.21191	2.02	3.74	-7.47	0.01365	.	7.836560	0.00531	N	0.000204	T	0.01320	0.0043	N	0.12182	0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.13255	-1.0516	10	0.40728	T	0.16	1.8076	1.6888	0.02847	0.3671:0.1135:0.0831:0.4363	.	1412	Q5SXM2	SNPC4_HUMAN	S	1412	ENSP00000298532:A1412S	ENSP00000298532:A1412S	A	-	1	0	SNAPC4	138391866	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.362000	0.01082	-3.382000	0.00175	-0.387000	0.06579	GCA	C|0.976;A|0.024	0.024	strong		0.677	SNAPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055071.1	NM_003086	
STAMBP	10617	hgsc.bcm.edu	37	2	74077556	74077556	+	Silent	SNP	G	G	T	rs77000353	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74077556G>T	ENST00000394070.2	+	7	1424	c.921G>T	c.(919-921)ggG>ggT	p.G307G	STAMBP_ENST00000409707.1_Silent_p.G307G|STAMBP_ENST00000339566.3_Silent_p.G307G|STAMBP_ENST00000394073.1_Silent_p.G307G|STAMBP_ENST00000486458.1_3'UTR	NM_213622.2	NP_998787.1	O95630	STABP_HUMAN	STAM binding protein	307	MPN.				JAK-STAT cascade (GO:0007259)|mitotic cytokinesis (GO:0000281)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of cell proliferation (GO:0008284)|protein deubiquitination (GO:0016579)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	18						AAAGTGCTGGGTCTGATTACT	0.468													G|||	56	0.0111821	0.0015	0.0086	5008	,	,		19685	0.006		0.0169	False		,,,				2504	0.0256				p.G307G		Atlas-SNP	.											.	STAMBP	37	.	0			c.G921T						PASS	.	G	,,	18,4388	23.3+/-48.9	0,18,2185	149.0	131.0	137.0		921,921,921	-4.0	0.9	2	dbSNP_133	137	132,8468	66.3+/-128.7	0,132,4168	yes	coding-synonymous,coding-synonymous,coding-synonymous	STAMBP	NM_006463.4,NM_201647.2,NM_213622.2	,,	0,150,6353	TT,TG,GG		1.5349,0.4085,1.1533	,,	307/425,307/425,307/425	74077556	150,12856	2203	4300	6503	SO:0001819	synonymous_variant	10617	exon8			TGCTGGGTCTGAT	BC007682	CCDS1929.1	2p24.3-p24.1	2008-02-05			ENSG00000124356	ENSG00000124356			16950	protein-coding gene	gene with protein product		606247				10383417	Standard	NM_006463		Approved	AMSH	uc002sjs.3	O95630	OTTHUMG00000129817	ENST00000394070.2:c.921G>T	2.37:g.74077556G>T		204.0	0.0	0		187.0	185.0	0.989305	NM_006463	B5M0B6|D6W5H7|Q3MJE7	Silent	SNP	ENST00000394070.2	37	CCDS1929.1																																																																																			G|0.988;T|0.012	0.012	strong		0.468	STAMBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252048.2	NM_006463	
UBE3B	89910	hgsc.bcm.edu	37	12	109972462	109972462	+	Missense_Mutation	SNP	G	G	A	rs374046452		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109972462G>A	ENST00000342494.3	+	28	3677	c.3082G>A	c.(3082-3084)Ggc>Agc	p.G1028S	UBE3B_ENST00000434735.2_Missense_Mutation_p.G1028S	NM_130466.3	NP_569733.2	Q7Z3V4	UBE3B_HUMAN	ubiquitin protein ligase E3B	1028	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(3)|endometrium(6)|kidney(4)|large_intestine(7)|lung(20)|ovary(2)|urinary_tract(2)	45						GGAGCCAGGCGGCCGCCTGCC	0.632																																					p.G1028S		Atlas-SNP	.											.	UBE3B	116	.	0			c.G3082A						PASS	.	G	SER/GLY,SER/GLY	1,4405	2.1+/-5.4	0,1,2202	64.0	59.0	60.0		3082,3082	5.3	1.0	12		60	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	UBE3B	NM_130466.2,NM_183415.1	56,56	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	benign,benign	1028/1069,1028/1069	109972462	2,13004	2203	4300	6503	SO:0001583	missense	89910	exon28			CCAGGCGGCCGCC	BC032301	CCDS9129.1, CCDS58277.1	12q24.12	2004-03-02			ENSG00000151148	ENSG00000151148			13478	protein-coding gene	gene with protein product		608047					Standard	NM_130466		Approved		uc001toq.4	Q7Z3V4	OTTHUMG00000169254	ENST00000342494.3:c.3082G>A	12.37:g.109972462G>A	ENSP00000340596:p.Gly1028Ser	147.0	0.0	0		174.0	37.0	0.212644	NM_130466	A5D8Z3|Q05BX9|Q659F7|Q7Z7Q1|Q9BXZ4	Missense_Mutation	SNP	ENST00000342494.3	37	CCDS9129.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.924638	0.52653	2.27E-4	1.16E-4	ENSG00000151148	ENST00000434735;ENST00000342494	T;T	0.41065	1.01;1.01	5.3	5.3	0.74995	HECT (4);	0.000000	0.85682	D	0.000000	T	0.21801	0.0525	N	0.02539	-0.55	0.80722	D	1	B	0.25105	0.118	B	0.22386	0.039	T	0.10086	-1.0645	10	0.25106	T	0.35	-23.3915	17.9631	0.89092	0.0:0.0:1.0:0.0	.	1028	Q7Z3V4	UBE3B_HUMAN	S	1028	ENSP00000391529:G1028S;ENSP00000340596:G1028S	ENSP00000340596:G1028S	G	+	1	0	UBE3B	108456845	1.000000	0.71417	0.956000	0.39512	0.961000	0.63080	9.385000	0.97223	2.474000	0.83562	0.563000	0.77884	GGC	.	.	weak		0.632	UBE3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403119.1	NM_183415	
RALGAPB	57148	hgsc.bcm.edu	37	20	37199443	37199443	+	Silent	SNP	G	G	A	rs139543103	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37199443G>A	ENST00000262879.6	+	28	4379	c.4095G>A	c.(4093-4095)gaG>gaA	p.E1365E	RALGAPB_ENST00000397038.1_Silent_p.E1144E|RALGAPB_ENST00000397040.1_Silent_p.E1365E|RALGAPB_ENST00000397042.3_Silent_p.E1362E			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1365	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						TGATGACAGAGATCAGTACTG	0.358													G|||	14	0.00279553	0.0	0.0043	5008	,	,		17277	0.0		0.0109	False		,,,				2504	0.0				p.E1365E		Atlas-SNP	.											.	RALGAPB	134	.	0			c.G4095A						PASS	.	G		18,4388	24.3+/-50.5	0,18,2185	82.0	83.0	83.0		4095	1.1	1.0	20	dbSNP_134	83	118,8482	62.4+/-124.4	1,116,4183	no	coding-synonymous	RALGAPB	NM_020336.2		1,134,6368	AA,AG,GG		1.3721,0.4085,1.0457		1365/1495	37199443	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	57148	exon28			GACAGAGATCAGT	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.4095G>A	20.37:g.37199443G>A		60.0	0.0	0		85.0	49.0	0.576471	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Silent	SNP	ENST00000262879.6	37	CCDS13305.1																																																																																			G|0.991;A|0.009	0.009	strong		0.358	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
SLC4A1	6521	hgsc.bcm.edu	37	17	42327847	42327847	+	Missense_Mutation	SNP	G	G	C	rs377326869		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:42327847G>C	ENST00000262418.6	-	20	2870	c.2715C>G	c.(2713-2715)gaC>gaG	p.D905E	AC003102.1_ENST00000399246.2_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	905	Membrane (anion exchange).				anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		TGGCCACTTCGTCGTATTCAT	0.592																																					p.D905E		Atlas-SNP	.											.	SLC4A1	104	.	0			c.C2715G						PASS	.						109.0	75.0	86.0					17																	42327847		2203	4300	6503	SO:0001583	missense	6521	exon20			CACTTCGTCGTAT		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.2715C>G	17.37:g.42327847G>C	ENSP00000262418:p.Asp905Glu	45.0	0.0	0		51.0	26.0	0.509804	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	G	1.789	-0.479900	0.04383	.	.	ENSG00000004939	ENST00000262418	T	0.73363	-0.74	4.91	-5.15	0.02866	.	0.251137	0.30649	N	0.009173	T	0.58352	0.2116	L	0.40543	1.245	0.30038	N	0.81285	B	0.10296	0.003	B	0.08055	0.003	T	0.46076	-0.9217	10	0.20046	T	0.44	.	13.9273	0.63970	0.7677:0.0:0.2323:0.0	.	905	P02730	B3AT_HUMAN	E	905	ENSP00000262418:D905E	ENSP00000262418:D905E	D	-	3	2	SLC4A1	39683373	0.000000	0.05858	0.009000	0.14445	0.005000	0.04900	-1.941000	0.01542	-0.728000	0.04882	-0.224000	0.12420	GAC	.	.	alt		0.592	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
TRIM21	6737	hgsc.bcm.edu	37	11	4411471	4411471	+	Missense_Mutation	SNP	G	G	A	rs200488796		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4411471G>A	ENST00000254436.7	-	2	281	c.169C>T	c.(169-171)Cgc>Tgc	p.R57C	TRIM21_ENST00000543625.1_Missense_Mutation_p.R57C	NM_003141.3	NP_003132.2	P19474	RO52_HUMAN	tripartite motif containing 21	57					cell cycle (GO:0007049)|innate immune response (GO:0045087)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein deubiquitination (GO:0090086)|negative regulation of viral release from host cell (GO:1902187)|negative regulation of viral transcription (GO:0032897)|positive regulation of cell cycle (GO:0045787)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of type I interferon production (GO:0032481)|positive regulation of viral entry into host cell (GO:0046598)|protein autoubiquitination (GO:0051865)|protein destabilization (GO:0031648)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of type I interferon production (GO:0032479)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)	16		Medulloblastoma(188;0.0025)|Breast(177;0.0101)|all_neural(188;0.0227)		Epithelial(150;2.08e-11)|BRCA - Breast invasive adenocarcinoma(625;0.0851)|LUSC - Lung squamous cell carcinoma(625;0.194)		AGCAGAAAGCGCTGCCGGCAC	0.582													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19735	0.0		0.0	False		,,,				2504	0.0				p.R57C		Atlas-SNP	.											.	TRIM21	45	.	0			c.C169T						PASS	.	G	CYS/ARG	0,4246		0,0,2123	90.0	94.0	93.0		169	-1.4	0.0	11		93	17,8461		0,17,4222	yes	missense	TRIM21	NM_003141.3	180	0,17,6345	AA,AG,GG		0.2005,0.0,0.1336	possibly-damaging	57/476	4411471	17,12707	2123	4239	6362	SO:0001583	missense	6737	exon2			GAAAGCGCTGCCG	AF391283	CCDS44525.1	11p15.5-p15.3	2014-02-14	2011-01-25	2004-11-26		ENSG00000132109		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	11312	protein-coding gene	gene with protein product		109092	"""Sjogren syndrome antigen A1 (52kDa, ribonucleoprotein autoantigen SS-A/Ro)"", ""tripartite motif-containing 21"""	SSA1		8094596	Standard	NM_003141		Approved	RNF81, RO52, Ro/SSA	uc001lyy.1	P19474		ENST00000254436.7:c.169C>T	11.37:g.4411471G>A	ENSP00000254436:p.Arg57Cys	99.0	0.0	0		123.0	69.0	0.560976	NM_003141	Q5XPV5|Q96RF8	Missense_Mutation	SNP	ENST00000254436.7	37	CCDS44525.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	5.894	0.349073	0.11182	0.0	0.002005	ENSG00000132109	ENST00000254436;ENST00000543625	D;D	0.84223	-1.82;-1.82	4.46	-1.39	0.08997	Zinc finger, RING/FYVE/PHD-type (1);	4.312490	0.00166	N	0.000018	T	0.72228	0.3434	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.62224	-0.6899	10	0.62326	D	0.03	.	7.6016	0.28079	0.1865:0.0:0.6493:0.1642	.	57	P19474	RO52_HUMAN	C	57	ENSP00000254436:R57C;ENSP00000444045:R57C	ENSP00000254436:R57C	R	-	1	0	TRIM21	4368047	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.155000	0.03163	-0.237000	0.09739	0.655000	0.94253	CGC	G|1.000;A|0.000	0.000	strong		0.582	TRIM21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000385842.1	NM_003141	
ADAT1	23536	hgsc.bcm.edu	37	16	75642801	75642801	+	Missense_Mutation	SNP	G	G	A	rs77029992	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75642801G>A	ENST00000307921.3	-	8	1274	c.1129C>T	c.(1129-1131)Cgc>Tgc	p.R377C	RP11-77K12.8_ENST00000564489.1_RNA	NM_012091.3	NP_036223.2	Q9BUB4	ADAT1_HUMAN	adenosine deaminase, tRNA-specific 1	377	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|RNA binding (GO:0003723)|tRNA-specific adenosine deaminase activity (GO:0008251)			breast(1)|endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(1)|stomach(1)	19						ACCGCACTGCGGCTCTGTTCA	0.473													G|||	27	0.00539137	0.0008	0.0086	5008	,	,		21246	0.0		0.0189	False		,,,				2504	0.001				p.R377C		Atlas-SNP	.											.	ADAT1	45	.	0			c.C1129T						PASS	.	G	CYS/ARG	20,4376	27.2+/-55.0	0,20,2178	80.0	74.0	76.0		1129	5.1	1.0	16	dbSNP_131	76	240,8360	97.2+/-158.9	3,234,4063	yes	missense	ADAT1	NM_012091.3	180	3,254,6241	AA,AG,GG		2.7907,0.455,2.0006	probably-damaging	377/503	75642801	260,12736	2198	4300	6498	SO:0001583	missense	23536	exon8			CACTGCGGCTCTG	AF125188	CCDS10922.1	16q23	2008-02-05			ENSG00000065457	ENSG00000065457			228	protein-coding gene	gene with protein product		604230				10430867	Standard	NM_012091		Approved		uc002feo.2	Q9BUB4	OTTHUMG00000137611	ENST00000307921.3:c.1129C>T	16.37:g.75642801G>A	ENSP00000310015:p.Arg377Cys	89.0	0.0	0		91.0	48.0	0.527473	NM_012091	Q9NVB7|Q9UNG3	Missense_Mutation	SNP	ENST00000307921.3	37	CCDS10922.1	22	0.010073260073260074	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	16	0.021108179419525065	G	14.21	2.467031	0.43839	0.00455	0.027907	ENSG00000065457	ENST00000307921;ENST00000542252	D	0.94184	-3.37	6.03	5.09	0.68999	Adenosine deaminase/editase (3);	0.476723	0.23298	N	0.049703	D	0.85124	0.5625	M	0.90542	3.125	0.58432	D	0.999999	B	0.27140	0.169	B	0.20767	0.031	D	0.87066	0.2156	10	0.56958	D	0.05	1.6221	8.8692	0.35305	0.0749:0.0:0.7765:0.1486	.	377	Q9BUB4	ADAT1_HUMAN	C	377;348	ENSP00000310015:R377C	ENSP00000310015:R377C	R	-	1	0	ADAT1	74200302	1.000000	0.71417	1.000000	0.80357	0.691000	0.40173	3.454000	0.52986	1.568000	0.49683	0.557000	0.71058	CGC	G|0.983;A|0.017	0.017	strong		0.473	ADAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269027.1	NM_012091	
SOX12	6666	hgsc.bcm.edu	37	20	306733	306733	+	Silent	SNP	G	G	A	rs73071018	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:306733G>A	ENST00000342665.2	+	1	495	c.165G>A	c.(163-165)cgG>cgA	p.R55R	RP5-1103G7.4_ENST00000442637.1_RNA|RP5-1103G7.4_ENST00000414676.1_RNA|SOX12_ENST00000544632.1_Silent_p.R55R	NM_006943.2	NP_008874.2	O15370	SOX12_HUMAN	SRY (sex determining region Y)-box 12	55					cell fate commitment (GO:0045165)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein-DNA complex assembly (GO:0065004)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord development (GO:0021510)	nucleus (GO:0005634)|protein-DNA complex (GO:0032993)	DNA binding (GO:0003677)|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 transcription coactivator activity (GO:0001105)|transcription regulatory region sequence-specific DNA binding (GO:0000976)	p.R55R(1)		haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)	2		all_cancers(10;0.000331)|Lung NSC(37;0.0496)|all_lung(30;0.0831)|all_epithelial(17;0.0868)|Breast(17;0.231)	OV - Ovarian serous cystadenocarcinoma(29;0.149)			AGCACGAACGGCGGAAGATCA	0.672													G|||	29	0.00579073	0.0015	0.0115	5008	,	,		7149	0.0		0.0179	False		,,,				2504	0.001				p.R55R		Atlas-SNP	.											SOX12,NS,lymphoid_neoplasm,0,1	SOX12	8	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G165A						PASS	.	G		15,4391		0,15,2188	35.0	29.0	31.0		165	3.6	1.0	20	dbSNP_130	31	188,8408		1,186,4111	no	coding-synonymous	SOX12	NM_006943.2		1,201,6299	AA,AG,GG		2.1871,0.3404,1.5613		55/316	306733	203,12799	2203	4298	6501	SO:0001819	synonymous_variant	6666	exon1			CGAACGGCGGAAG	U35612	CCDS12995.1	20p13	2008-07-28	2002-07-22	2002-07-26	ENSG00000177732	ENSG00000177732		"""SRY (sex determining region Y)-boxes"""	11198	protein-coding gene	gene with protein product		601947	"""SRY (sex determining region Y)-box 22"""	SOX22		9215677	Standard	NM_006943		Approved		uc002wdh.4	O15370	OTTHUMG00000031623	ENST00000342665.2:c.165G>A	20.37:g.306733G>A		147.0	0.0	0		157.0	89.0	0.566879	NM_006943	Q5D038|Q9NUD4	Silent	SNP	ENST00000342665.2	37	CCDS12995.1																																																																																			G|0.985;A|0.015	0.015	strong		0.672	SOX12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077435.2	NM_006943	
PARP14	54625	hgsc.bcm.edu	37	3	122419210	122419210	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:122419210T>C	ENST00000474629.2	+	6	2075	c.1809T>C	c.(1807-1809)gtT>gtC	p.V603V		NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	603					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		GCATTGAAGTTGAGAACAAAG	0.393																																					p.V603V		Atlas-SNP	.											.	PARP14	242	.	0			c.T1809C						PASS	.						37.0	35.0	36.0					3																	122419210		1870	4093	5963	SO:0001819	synonymous_variant	54625	exon6			TGAAGTTGAGAAC	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.1809T>C	3.37:g.122419210T>C		74.0	0.0	0		72.0	16.0	0.222222	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	37	CCDS46894.1																																																																																			.	.	none		0.393	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
ZBBX	79740	hgsc.bcm.edu	37	3	167035332	167035332	+	Missense_Mutation	SNP	T	T	C	rs34465133	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167035332T>C	ENST00000392766.2	-	13	1377	c.1037A>G	c.(1036-1038)cAt>cGt	p.H346R	ZBBX_ENST00000307529.5_Missense_Mutation_p.H346R|ZBBX_ENST00000469220.1_Intron|ZBBX_ENST00000392764.1_Missense_Mutation_p.H317R|ZBBX_ENST00000392767.2_Missense_Mutation_p.H346R|ZBBX_ENST00000455345.2_Missense_Mutation_p.H346R	NM_001199201.1|NM_024687.3	NP_001186130.1|NP_078963.2	A8MT70	ZBBX_HUMAN	zinc finger, B-box domain containing	346			H -> R (in dbSNP:rs34465133).			intracellular (GO:0005622)	zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(5)|kidney(5)|large_intestine(9)|liver(1)|lung(38)|ovary(2)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)	70						AGTGGTTTCATGTGGATGTGG	0.333													C|||	28	0.00559105	0.0008	0.0058	5008	,	,		17626	0.0		0.0229	False		,,,				2504	0.0				p.H346R		Atlas-SNP	.											.	ZBBX	299	.	0			c.A1037G						PASS	.	C	ARG/HIS,ARG/HIS,ARG/HIS	8,3698		0,8,1845	191.0	174.0	179.0		1037,950,1037	0.3	0.0	3	dbSNP_126	179	179,8009		1,177,3916	yes	missense,missense,missense	ZBBX	NM_001199201.1,NM_001199202.1,NM_024687.3	29,29,29	1,185,5761	CC,CT,TT		2.1861,0.2159,1.5722	benign,benign,benign	346/840,317/772,346/801	167035332	187,11707	1853	4094	5947	SO:0001583	missense	79740	exon13			GTTTCATGTGGAT	AK026702	CCDS3199.2, CCDS56295.1, CCDS56296.1	3q26.1	2010-03-23			ENSG00000169064	ENSG00000169064			26245	protein-coding gene	gene with protein product						12477932	Standard	NM_024687		Approved	FLJ23049	uc011bpc.2	A8MT70	OTTHUMG00000133560	ENST00000392766.2:c.1037A>G	3.37:g.167035332T>C	ENSP00000376519:p.His346Arg	189.0	0.0	0		219.0	78.0	0.356164	NM_024687	A8MV69|B3KSC1|B5MDJ6|F2Z370|Q9H5T8	Missense_Mutation	SNP	ENST00000392766.2	37	CCDS3199.2	26	0.011904761904761904	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	22	0.029023746701846966	C	7.094	0.572764	0.13623	0.002159	0.021861	ENSG00000169064	ENST00000392766;ENST00000392767;ENST00000455345;ENST00000307529;ENST00000392764	T;T;T;T;T	0.08896	3.21;3.21;3.21;3.21;3.04	5.34	0.327	0.15913	.	0.965568	0.08617	N	0.919032	T	0.01287	0.0042	N	0.14661	0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.47636	-0.9102	10	0.11182	T	0.66	3.6647	5.0072	0.14293	0.0:0.4377:0.1458:0.4165	rs34465133	346;346	A8MT70-2;A8MT70	.;ZBBX_HUMAN	R	346;346;346;346;317	ENSP00000376519:H346R;ENSP00000376520:H346R;ENSP00000390232:H346R;ENSP00000305065:H346R;ENSP00000376517:H317R	ENSP00000305065:H346R	H	-	2	0	ZBBX	168518026	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.546000	0.02188	-0.059000	0.13154	-0.128000	0.14901	CAT	T|0.987;C|0.013	0.013	strong		0.333	ZBBX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257657.3	NM_024687	
ATXN1L	342371	hgsc.bcm.edu	37	16	71884430	71884430	+	Missense_Mutation	SNP	C	C	G	rs199599582		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:71884430C>G	ENST00000427980.2	+	3	1080	c.787C>G	c.(787-789)Ctg>Gtg	p.L263V	ATXN1L_ENST00000569119.1_Intron	NM_001137675.3	NP_001131147.1	P0C7T5	ATX1L_HUMAN	ataxin 1-like	263					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell projection (GO:0042995)|nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			central_nervous_system(1)|endometrium(3)	4						CCAGTCTGCTCTGGAAGCAGC	0.532																																					p.L263V		Atlas-SNP	.											.	ATXN1L	18	.	0			c.C787G						PASS	.	C	VAL/LEU	0,1384		0,0,692	35.0	36.0	36.0		787	5.2	1.0	16		36	2,3180		0,2,1589	yes	missense	ATXN1L	NM_001137675.2	32	0,2,2281	GG,GC,CC		0.0629,0.0,0.0438	benign	263/690	71884430	2,4564	692	1591	2283	SO:0001583	missense	342371	exon3			TCTGCTCTGGAAG		CCDS45523.1	16q22.2	2014-09-04			ENSG00000224470	ENSG00000224470			33279	protein-coding gene	gene with protein product	"""brother of ataxin 1"""	614301				16121196, 17322884, 21475249	Standard	NM_001137675		Approved	BOAT1	uc002fbd.3	P0C7T5	OTTHUMG00000176872	ENST00000427980.2:c.787C>G	16.37:g.71884430C>G	ENSP00000415822:p.Leu263Val	99.0	0.0	0		107.0	43.0	0.401869	NM_001137675		Missense_Mutation	SNP	ENST00000427980.2	37	CCDS45523.1	.	.	.	.	.	.	.	.	.	.	C	7.589	0.670309	0.14776	0.0	6.29E-4	ENSG00000224470	ENST00000427980	T	0.32023	1.47	5.25	5.25	0.73442	.	.	.	.	.	T	0.17109	0.0411	N	0.14661	0.345	0.28195	N	0.927604	B	0.30914	0.3	B	0.19666	0.026	T	0.06698	-1.0812	9	0.27082	T	0.32	.	11.2832	0.49208	0.0:0.9077:0.0:0.0923	.	263	P0C7T5	ATX1L_HUMAN	V	263	ENSP00000415822:L263V	ENSP00000415822:L263V	L	+	1	2	ATXN1L	70441931	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	0.900000	0.28431	2.631000	0.89168	0.555000	0.69702	CTG	.	.	weak		0.532	ATXN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434171.1	NM_001137675.2	
KLF3	51274	hgsc.bcm.edu	37	4	38696385	38696385	+	Silent	SNP	C	C	T	rs142916199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38696385C>T	ENST00000261438.5	+	5	1019	c.714C>T	c.(712-714)atC>atT	p.I238I		NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	238	Pro-rich.				cellular response to peptide (GO:1901653)|multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18						CTTCGGTCATCGTGCAGCCTG	0.458													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19533	0.0		0.001	False		,,,				2504	0.0				p.I238I		Atlas-SNP	.											.	KLF3	40	.	0			c.C714T						PASS	.	C		0,4406		0,0,2203	137.0	135.0	136.0		714	-12.3	0.3	4	dbSNP_134	136	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	KLF3	NM_016531.5		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		238/346	38696385	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	51274	exon5			GGTCATCGTGCAG	AF285837	CCDS3444.1	4p16.1-p15.2	2013-01-08			ENSG00000109787	ENSG00000109787		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	16516	protein-coding gene	gene with protein product	"""basic Kruppel-like factor"""	609392				18391014	Standard	NM_016531		Approved	BKLF	uc003gth.4	P57682	OTTHUMG00000097821	ENST00000261438.5:c.714C>T	4.37:g.38696385C>T		109.0	0.0	0		126.0	67.0	0.531746	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Silent	SNP	ENST00000261438.5	37	CCDS3444.1																																																																																			C|0.999;T|0.001	0.001	strong		0.458	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2		
MED13	9969	hgsc.bcm.edu	37	17	60038404	60038404	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60038404T>C	ENST00000397786.2	-	23	5380	c.5304A>G	c.(5302-5304)ccA>ccG	p.P1768P		NM_005121.2	NP_005112.2	Q9UHV7	MED13_HUMAN	mediator complex subunit 13	1768					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			breast(4)|central_nervous_system(1)|endometrium(10)|kidney(24)|large_intestine(15)|liver(1)|lung(20)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGTCCTTCACTGGAGCCAGAA	0.338																																					p.P1768P		Atlas-SNP	.											MED13,NS,carcinoma,-1,1	MED13	181	1	0			c.A5304G						PASS	.						112.0	97.0	102.0					17																	60038404		1828	4074	5902	SO:0001819	synonymous_variant	9969	exon23			CTTCACTGGAGCC	AB011165	CCDS42366.1	17q22-q23	2007-07-30	2007-07-30	2007-07-30		ENSG00000108510			22474	protein-coding gene	gene with protein product		603808	"""thyroid hormone receptor associated protein 1"""	THRAP1		1019863	Standard	NM_005121		Approved	KIAA0593, TRAP240	uc002izo.3	Q9UHV7		ENST00000397786.2:c.5304A>G	17.37:g.60038404T>C		102.0	0.0	0		102.0	52.0	0.509804	NM_005121	B2RU05|O60334	Silent	SNP	ENST00000397786.2	37	CCDS42366.1																																																																																			.	.	none		0.338	MED13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445461.1	NM_005121	
SGSM1	129049	hgsc.bcm.edu	37	22	25251027	25251027	+	Silent	SNP	T	T	C	rs201064977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:25251027T>C	ENST00000400359.4	+	6	527	c.520T>C	c.(520-522)Ttg>Ctg	p.L174L	SGSM1_ENST00000400358.4_Silent_p.L174L	NM_001039948.2|NM_133454.2	NP_001035037.1|NP_597711.1	Q2NKQ1	SGSM1_HUMAN	small G protein signaling modulator 1	174	RUN. {ECO:0000255|PROSITE- ProRule:PRU00178}.					Golgi apparatus (GO:0005794)	Rab GTPase activator activity (GO:0005097)			NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(14)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	41						TGCATCTTTGTTGGGTAAGTT	0.532													T|||	4	0.000798722	0.0	0.0029	5008	,	,		19277	0.0		0.002	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	SGSM1	150	.	0			c.T520C						PASS	.	T	,,,	1,3963		0,1,1981	95.0	95.0	95.0		520,520,520,520	-0.5	0.9	22		95	41,8295		0,41,4127	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SGSM1	NM_001039948.2,NM_001098497.1,NM_001098498.1,NM_133454.2	,,,	0,42,6108	CC,CT,TT		0.4918,0.0252,0.3415	,,,	174/1149,174/1094,174/1033,174/1088	25251027	42,12258	1982	4168	6150	SO:0001819	synonymous_variant	129049	exon6			TCTTTGTTGGGTA	AB075821	CCDS46674.1, CCDS46675.1, CCDS74834.1	22q11.23	2013-07-09	2007-08-14	2007-08-14	ENSG00000167037	ENSG00000167037		"""Small G protein signaling modulators"""	29410	protein-coding gene	gene with protein product		611417	"""RUN and TBC1 domain containing 2"""	RUTBC2		11853319, 17509819, 22637480	Standard	NM_133454		Approved	KIAA1941	uc003abg.2	Q2NKQ1	OTTHUMG00000150837	ENST00000400359.4:c.520T>C	22.37:g.25251027T>C		249.0	0.0	0		271.0	115.0	0.424354	NM_001098497	A5LGW1|A8MUT4|B0QYW0|B0QYW1|B5MEG1|B9A6J4|Q5TFL3|Q8TF60	Silent	SNP	ENST00000400359.4	37	CCDS46674.1																																																																																			T|0.998;C|0.002	0.002	strong		0.532	SGSM1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320282.1	XM_059318	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4458515	4458515	+	Missense_Mutation	SNP	G	G	T	rs117128211	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4458515G>T	ENST00000254718.4	-	1	411	c.105C>A	c.(103-105)ttC>ttA	p.F35L	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.F35L			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	35	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						AGAAGTCCAAGAACTCGCGAC	0.637													G|||	74	0.0147764	0.0008	0.0086	5008	,	,		16072	0.0		0.0348	False		,,,				2504	0.0327				p.F35L		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C105A						PASS	.	G	LEU/PHE,LEU/PHE	19,4383	20.2+/-43.8	0,19,2182	27.0	27.0	27.0		105,105	2.9	1.0	17	dbSNP_132	27	241,8351	93.1+/-155.1	5,231,4060	yes	missense,missense	MYBBP1A	NM_001105538.1,NM_014520.3	22,22	5,250,6242	TT,TG,GG		2.8049,0.4316,2.0009	probably-damaging,probably-damaging	35/1333,35/1329	4458515	260,12734	2201	4296	6497	SO:0001583	missense	10514	exon1			GTCCAAGAACTCG	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.105C>A	17.37:g.4458515G>T	ENSP00000254718:p.Phe35Leu	80.0	0.0	0		61.0	34.0	0.557377	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	29	0.013278388278388278	0	0.0	3	0.008287292817679558	0	0.0	26	0.03430079155672823	G	19.15	3.772199	0.69992	0.004316	0.028049	ENSG00000132382	ENST00000381556;ENST00000254718;ENST00000426435	T;T	0.56103	0.48;0.48	4.94	2.93	0.34026	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	L	0.34521	1.04	0.35719	D	0.817008	D;D	0.71674	0.997;0.998	D;D	0.72982	0.954;0.979	T	0.49457	-0.8938	10	0.11794	T	0.64	-29.3099	7.6026	0.28085	0.2721:0.0:0.7279:0.0	.	35;35	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	L	35	ENSP00000370968:F35L;ENSP00000254718:F35L	ENSP00000254718:F35L	F	-	3	2	MYBBP1A	4405264	1.000000	0.71417	0.998000	0.56505	0.252000	0.25951	1.905000	0.39878	0.662000	0.31006	-0.191000	0.12829	TTC	G|0.983;T|0.017	0.017	strong		0.637	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
PIEZO1	9780	hgsc.bcm.edu	37	16	88793155	88793155	+	Missense_Mutation	SNP	C	C	T	rs185326407	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88793155C>T	ENST00000301015.9	-	25	3913	c.3667G>A	c.(3667-3669)Gtc>Atc	p.V1223I		NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1223					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|detection of mechanical stimulus (GO:0050982)|positive regulation of cell-cell adhesion mediated by integrin (GO:0033634)|positive regulation of integrin activation (GO:0033625)|regulation of membrane potential (GO:0042391)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation channel activity (GO:0005261)|mechanically-gated ion channel activity (GO:0008381)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(2)|prostate(2)|skin(1)	10						ATGACGGTGACGTTGTACAGA	0.687													C|||	6	0.00119808	0.0	0.0014	5008	,	,		13508	0.0		0.005	False		,,,				2504	0.0				p.V1223I		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G3667A						PASS	.	C	ILE/VAL	1,1383		0,1,691	46.0	43.0	44.0		3667	4.5	1.0	16		44	10,3168		0,10,1579	yes	missense	PIEZO1	NM_001142864.2	29	0,11,2270	TT,TC,CC		0.3147,0.0723,0.2411	possibly-damaging	1223/2522	88793155	11,4551	692	1589	2281	SO:0001583	missense	9780	exon25			CGGTGACGTTGTA	D87071	CCDS54058.1	16q24.3	2011-08-31	2011-08-31	2011-08-31	ENSG00000103335	ENSG00000103335			28993	protein-coding gene	gene with protein product		611184	"""family with sequence similarity 38, member A"""	FAM38A		20813920, 21056836, 21299953, 21696149	Standard	NM_001142864		Approved	KIAA0233	uc010vpb.2	Q92508	OTTHUMG00000156776	ENST00000301015.9:c.3667G>A	16.37:g.88793155C>T	ENSP00000301015:p.Val1223Ile	42.0	0.0	0		41.0	18.0	0.439024	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	7|7	0.003205128205128205|0.003205128205128205	1|1	0.0020325203252032522|0.0020325203252032522	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	C|C	16.91|16.91	3.252370|3.252370	0.59212|0.59212	7.23E-4|7.23E-4	0.003147|0.003147	ENSG00000103335|ENSG00000103335	ENST00000451779|ENST00000301015	.|T	.|0.15952	.|2.38	4.51|4.51	4.51|4.51	0.55191|0.55191	.|.	.|0.283471	.|0.34291	.|N	.|0.004099	T|T	0.07999|0.07999	0.0200|0.0200	L|L	0.46947|0.46947	1.48|1.48	0.80722|0.80722	D|D	1|1	.|P	.|0.41748	.|0.761	.|B	.|0.29176	.|0.099	T|T	0.09818|0.09818	-1.0657|-1.0657	5|10	.|0.25106	.|T	.|0.35	-59.6841|-59.6841	9.855|9.855	0.41079|0.41079	0.0:0.9038:0.0:0.0962|0.0:0.9038:0.0:0.0962	.|.	.|1223	.|Q92508	.|PIEZ1_HUMAN	H|I	1168|1223	.|ENSP00000301015:V1223I	.|ENSP00000301015:V1223I	R|V	-|-	2|1	0|0	FAM38A|FAM38A	87320656|87320656	0.969000|0.969000	0.33509|0.33509	0.991000|0.991000	0.47740|0.47740	0.962000|0.962000	0.63368|0.63368	2.164000|2.164000	0.42387|0.42387	2.354000|2.354000	0.79902|0.79902	0.491000|0.491000	0.48974|0.48974	CGT|GTC	C|0.997;T|0.003	0.003	strong		0.687	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
WNT16	51384	hgsc.bcm.edu	37	7	120972016	120972016	+	Missense_Mutation	SNP	C	C	A	rs74389152	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:120972016C>A	ENST00000222462.2	+	3	921	c.631C>A	c.(631-633)Cag>Aag	p.Q211K	WNT16_ENST00000361301.2_Missense_Mutation_p.Q201K	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	211					bone remodeling (GO:0046849)|cardiac epithelial to mesenchymal transition (GO:0060317)|cell fate commitment (GO:0045165)|keratinocyte differentiation (GO:0030216)|keratinocyte proliferation (GO:0043616)|negative regulation of cell death (GO:0060548)|neuron differentiation (GO:0030182)|optic cup formation involved in camera-type eye development (GO:0003408)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|replicative senescence (GO:0090399)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			breast(1)|large_intestine(4)|lung(9)|ovary(3)|prostate(1)	18	all_neural(327;0.117)					AGCTGGAAGGCAGGTATGTAT	0.378													C|||	4	0.000798722	0.0	0.0	5008	,	,		19182	0.0		0.003	False		,,,				2504	0.001				p.Q211K		Atlas-SNP	.											.	WNT16	97	.	0			c.C631A						PASS	.	C	LYS/GLN,LYS/GLN	3,4403	6.2+/-15.9	0,3,2200	51.0	52.0	51.0		601,631	6.0	1.0	7	dbSNP_131	51	20,8580	14.6+/-50.1	0,20,4280	yes	missense,missense	WNT16	NM_016087.2,NM_057168.1	53,53	0,23,6480	AA,AC,CC		0.2326,0.0681,0.1768	benign,benign	201/356,211/366	120972016	23,12983	2203	4300	6503	SO:0001583	missense	51384	exon3			GGAAGGCAGGTAT	AF152584	CCDS5780.1, CCDS5781.1	7q31	2008-07-18			ENSG00000002745	ENSG00000002745		"""Wingless-type MMTV integration sites"""	16267	protein-coding gene	gene with protein product		606267				10500199	Standard	NM_016087		Approved		uc003vjw.3	Q9UBV4	OTTHUMG00000156963	ENST00000222462.2:c.631C>A	7.37:g.120972016C>A	ENSP00000222462:p.Gln211Lys	93.0	0.0	0		80.0	40.0	0.5	NM_057168	Q2M3G1|Q9Y5C0	Missense_Mutation	SNP	ENST00000222462.2	37	CCDS5781.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	7.287	0.610367	0.14066	6.81E-4	0.002326	ENSG00000002745	ENST00000361301;ENST00000222462	T;T	0.74632	-0.86;-0.86	6.02	6.02	0.97574	.	0.000000	0.85682	D	0.000000	T	0.60856	0.2301	N	0.13098	0.295	0.58432	D	0.999997	B;B	0.21688	0.059;0.059	B;B	0.29353	0.101;0.101	T	0.57723	-0.7762	10	0.05436	T	0.98	.	20.547	0.99278	0.0:1.0:0.0:0.0	.	211;201	Q9UBV4;E9PH60	WNT16_HUMAN;.	K	201;211	ENSP00000355065:Q201K;ENSP00000222462:Q211K	ENSP00000222462:Q211K	Q	+	1	0	WNT16	120759252	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.875000	0.56108	2.850000	0.98022	0.650000	0.86243	CAG	C|0.998;A|0.002	0.002	strong		0.378	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168	
IQCK	124152	hgsc.bcm.edu	37	16	19775403	19775403	+	Missense_Mutation	SNP	A	A	C	rs149444739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19775403A>C	ENST00000320394.6	+	7	1273	c.574A>C	c.(574-576)Att>Ctt	p.I192L	IQCK_ENST00000433597.2_Missense_Mutation_p.I104L|CTD-2380F24.1_ENST00000564490.1_RNA|CTD-2380F24.1_ENST00000568843.1_RNA|CTD-2380F24.1_ENST00000565817.1_RNA|IQCK_ENST00000541926.1_Missense_Mutation_p.I192L|IQCK_ENST00000564186.1_Missense_Mutation_p.I192L|IQCK_ENST00000562762.1_3'UTR	NM_153208.1	NP_694940.1	Q8N0W5	IQCK_HUMAN	IQ motif containing K	192										kidney(1)|large_intestine(2)|lung(2)|skin(1)	6						ATTTTTCTCCATTCCATTTGT	0.368																																					p.I192L		Atlas-SNP	.											.	IQCK	35	.	0			c.A574C						PASS	.	A	LEU/ILE	5,4389	8.1+/-20.4	0,5,2192	79.0	76.0	77.0		574	5.1	1.0	16	dbSNP_134	77	40,8560	26.8+/-75.7	0,40,4260	yes	missense	IQCK	NM_153208.1	5	0,45,6452	CC,CA,AA		0.4651,0.1138,0.3463	probably-damaging	192/288	19775403	45,12949	2197	4300	6497	SO:0001583	missense	124152	exon7			TTCTCCATTCCAT	AF520569	CCDS10580.1	16p12.3	2008-02-05			ENSG00000174628	ENSG00000174628			28556	protein-coding gene	gene with protein product						10493829	Standard	NM_153208		Approved	MGC35048, FLJ36575	uc002dgr.3	Q8N0W5	OTTHUMG00000131453	ENST00000320394.6:c.574A>C	16.37:g.19775403A>C	ENSP00000324901:p.Ile192Leu	157.0	0.0	0		124.0	66.0	0.532258	NM_153208	B2RDU0|O43327|Q8NFF4	Missense_Mutation	SNP	ENST00000320394.6	37	CCDS10580.1	.	.	.	.	.	.	.	.	.	.	A	22.6	4.314559	0.81358	0.001138	0.004651	ENSG00000174628	ENST00000320394;ENST00000541926;ENST00000433597	T;T;T	0.23348	1.91;1.91;1.91	5.11	5.11	0.69529	.	0.000000	0.51477	D	0.000092	T	0.49932	0.1586	M	0.74881	2.28	0.38431	D	0.94645	D;D	0.67145	0.996;0.996	D;D	0.80764	0.994;0.994	T	0.55186	-0.8180	9	.	.	.	-15.7553	13.6471	0.62288	1.0:0.0:0.0:0.0	.	192;192	B4DXE1;Q8N0W5	.;IQCK_HUMAN	L	192;192;104	ENSP00000324901:I192L;ENSP00000439344:I192L;ENSP00000406013:I104L	.	I	+	1	0	IQCK	19682904	1.000000	0.71417	1.000000	0.80357	0.932000	0.56968	5.500000	0.66943	2.152000	0.67230	0.528000	0.53228	ATT	A|0.996;C|0.004	0.004	strong		0.368	IQCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254273.2	NM_153208	
HYDIN	54768	hgsc.bcm.edu	37	16	71054116	71054116	+	Missense_Mutation	SNP	T	T	C	rs183427172	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:71054116T>C	ENST00000393567.2	-	22	3441	c.3291A>G	c.(3289-3291)atA>atG	p.I1097M	HYDIN_ENST00000448089.2_Missense_Mutation_p.I1049M	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1097					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				CAGTCTCACATATAAAGAAGG	0.502													T|||	8	0.00159744	0.0	0.0014	5008	,	,		16126	0.0		0.005	False		,,,				2504	0.002				p.I1097M		Atlas-SNP	.											.	HYDIN	788	.	0			c.A3291G						PASS	.	T	MET/ILE	2,3636		0,2,1817	35.0	37.0	37.0		3291	-9.2	0.0	16		37	23,8143		0,23,4060	yes	missense	HYDIN	NM_032821.2	10	0,25,5877	CC,CT,TT		0.2817,0.055,0.2118	possibly-damaging	1097/5121	71054116	25,11779	1819	4083	5902	SO:0001583	missense	54768	exon22			CTCACATATAAAG	AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.3291A>G	16.37:g.71054116T>C	ENSP00000377197:p.Ile1097Met	69.0	0.0	0		63.0	36.0	0.571429	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	14.02	2.410733	0.42817	5.5E-4	0.002817	ENSG00000157423	ENST00000393567;ENST00000316490;ENST00000448089	T;T	0.11063	2.81;2.81	4.61	-9.21	0.00678	.	0.254648	0.19540	U	0.111835	T	0.04363	0.0120	L	0.43923	1.385	0.51482	D	0.999923	P	0.40107	0.703	B	0.34385	0.181	T	0.38200	-0.9672	10	0.28530	T	0.3	.	1.6982	0.02866	0.2194:0.232:0.3592:0.1895	.	1097	F8WD23	.	M	1097;1097;1049	ENSP00000377197:I1097M;ENSP00000398544:I1049M	ENSP00000313052:I1097M	I	-	3	3	HYDIN	69611617	0.357000	0.24938	0.045000	0.18777	0.300000	0.27592	-0.549000	0.06041	-1.172000	0.02762	-0.394000	0.06481	ATA	T|0.998;C|0.002	0.002	strong		0.502	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
ADAM21	8747	hgsc.bcm.edu	37	14	70924432	70924432	+	Silent	SNP	C	C	T	rs553149454		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:70924432C>T	ENST00000603540.1	+	2	474	c.216C>T	c.(214-216)caC>caT	p.H72H	ADAM21_ENST00000267499.3_Silent_p.H72H|RP11-486O13.4_ENST00000556646.1_lincRNA	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	72					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.H72H(2)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GCCAGAAACACGTTGTTCATA	0.537													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20886	0.0		0.0	False		,,,				2504	0.0				p.H72H		Atlas-SNP	.											ADAM21_ENST00000267499,colon,carcinoma,0,2	ADAM21	181	2	2	Substitution - coding silent(2)	large_intestine(2)	c.C216T						scavenged	.						122.0	128.0	126.0					14																	70924432		2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			GAAACACGTTGTT	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.216C>T	14.37:g.70924432C>T		315.0	0.0	0		265.0	14.0	0.0528302	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			.	.	none		0.537	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
TMC5	79838	hgsc.bcm.edu	37	16	19481020	19481020	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:19481020G>A	ENST00000396229.2	+	10	2404	c.1655G>A	c.(1654-1656)cGg>cAg	p.R552Q	TMC5_ENST00000381414.4_Missense_Mutation_p.R552Q|TMC5_ENST00000541464.1_Missense_Mutation_p.R552Q|TMC5_ENST00000561503.1_Missense_Mutation_p.R193Q|TMC5_ENST00000219821.5_Missense_Mutation_p.R306Q|TMC5_ENST00000564959.1_Missense_Mutation_p.R235Q|TMC5_ENST00000542583.2_Missense_Mutation_p.R552Q	NM_001105248.1	NP_001098718.1	Q6UXY8	TMC5_HUMAN	transmembrane channel-like 5	552					ion transport (GO:0006811)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(12)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	31						AAGTATTTCCGGAACAACTTC	0.473																																					p.R552Q		Atlas-SNP	.											TMC5_ENST00000396229,NS,malignant_melanoma,0,2	TMC5	169	2	0			c.G1655A						PASS	.						117.0	107.0	111.0					16																	19481020		2197	4300	6497	SO:0001583	missense	79838	exon10			ATTTCCGGAACAA	AY263164	CCDS10577.1, CCDS42126.1, CCDS45431.1	16p13.11	2008-02-05			ENSG00000103534	ENSG00000103534			22999	protein-coding gene	gene with protein product						12812529, 12906855	Standard	NM_024780		Approved	FLJ13593	uc010var.2	Q6UXY8	OTTHUMG00000131458	ENST00000396229.2:c.1655G>A	16.37:g.19481020G>A	ENSP00000379531:p.Arg552Gln	104.0	0.0	0		145.0	28.0	0.193103	NM_001105249	Q68DK8|Q8IY20|Q8NHV6|Q9H8I7	Missense_Mutation	SNP	ENST00000396229.2	37	CCDS45431.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.990463	0.35131	.	.	ENSG00000103534	ENST00000541464;ENST00000381414;ENST00000396229;ENST00000542583;ENST00000219821;ENST00000440743	T;T;T;T;T	0.55930	0.49;0.49;0.49;0.49;0.49	5.65	5.65	0.86999	.	0.249267	0.41605	D	0.000859	T	0.47154	0.1430	M	0.64260	1.97	0.29006	N	0.887155	P;P;P;P;P;P	0.45902	0.868;0.81;0.74;0.622;0.676;0.782	B;B;B;B;B;B	0.42386	0.386;0.372;0.218;0.109;0.216;0.386	T	0.52238	-0.8602	10	0.27082	T	0.32	-25.7205	6.6578	0.22996	0.0715:0.1292:0.6653:0.134	.	552;235;306;306;552;552	F5GYU8;E7EU57;Q6UXY8-3;B3KUQ8;Q6UXY8;Q6UXY8-2	.;.;.;.;TMC5_HUMAN;.	Q	552;552;552;552;306;235	ENSP00000441227:R552Q;ENSP00000370822:R552Q;ENSP00000379531:R552Q;ENSP00000446274:R552Q;ENSP00000219821:R306Q	ENSP00000219821:R306Q	R	+	2	0	TMC5	19388521	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	2.204000	0.42761	2.663000	0.90544	0.655000	0.94253	CGG	.	.	none		0.473	TMC5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435888.1	NM_024780	
GSTZ1	2954	hgsc.bcm.edu	37	14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	rs7972	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:77793237G>A	ENST00000556627.1	+	3	255	c.124G>A	c.(124-126)Ggg>Agg	p.G42R	GSTZ1_ENST00000554279.1_Missense_Mutation_p.G42R|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R|GSTZ1_ENST00000557053.1_5'UTR|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000361389.4_5'UTR|GSTZ1_ENST00000393734.1_5'UTR			O43708	MAAI_HUMAN	glutathione S-transferase zeta 1	42	GST N-terminal.		R -> G (in allele GSTZ1*B and allele GSTZ1*C; dbSNP:rs7972). {ECO:0000269|PubMed:10373324, ECO:0000269|PubMed:10739172, ECO:0000269|PubMed:12508121, ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:9417084, ECO:0000269|PubMed:9925947, ECO:0000269|Ref.6, ECO:0000269|Ref.7, ECO:0000269|Ref.9}.		cellular nitrogen compound metabolic process (GO:0034641)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|L-phenylalanine catabolic process (GO:0006559)|oxidation-reduction process (GO:0055114)|small molecule metabolic process (GO:0044281)|tyrosine catabolic process (GO:0006572)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|maleylacetoacetate isomerase activity (GO:0016034)|protein homodimerization activity (GO:0042803)			lung(2)|prostate(1)	3			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	Glutathione(DB00143)	CATAAAGGATGGGGGCCAACA	0.567													G|||	153	0.0305511	0.0038	0.0274	5008	,	,		21279	0.0		0.1113	False		,,,				2504	0.0174				p.G42R		Atlas-SNP	.											.	GSTZ1	35	.	0			c.G124A						PASS	.	G	,ARG/GLY,ARG/GLY	78,4326	62.9+/-100.1	0,78,2124	43.0	35.0	37.0		,124,124	5.6	1.0	14	dbSNP_52	37	707,7893	164.3+/-216.7	41,625,3634	yes	utr-5,missense,missense	GSTZ1	NM_001513.3,NM_145870.2,NM_145871.2	,125,125	41,703,5758	AA,AG,GG		8.2209,1.7711,6.0366	,benign,benign	,42/217,42/175	77793237	785,12219	2202	4300	6502	SO:0001583	missense	2954	exon3			AAGGATGGGGGCC	U86529	CCDS9858.1, CCDS9859.1, CCDS9860.1	14q24.3	2012-06-22	2012-06-22		ENSG00000100577	ENSG00000100577	5.2.1.2, 2.5.1.18	"""Glutathione S-transferases / Soluble"""	4643	protein-coding gene	gene with protein product	"""maleylacetoacetate isomerase"""	603758	"""glutathione transferase zeta 1"""			9396740, 9417084	Standard	NM_001513		Approved	GSTZ1-1, MAAI, MAI	uc001xtj.3	O43708	OTTHUMG00000171551	ENST00000556627.1:c.124G>A	14.37:g.77793237G>A	ENSP00000450487:p.Gly42Arg	64.0	0.0	0		66.0	27.0	0.409091	NM_145871	A6NED0|A6NNB8|A8MWD7|B2RCK3|O15308|O75430|Q6IB17|Q7Z610|Q9BV63	Missense_Mutation	SNP	ENST00000556627.1	37		109	0.04990842490842491	2	0.0040650406504065045	11	0.03038674033149171	0	0.0	96	0.1266490765171504	G	28.3	4.909294	0.92107	0.017711	0.082209	ENSG00000100577	ENST00000216465;ENST00000554279;ENST00000349555;ENST00000556627;ENST00000553586	T;T;T;T;T	0.18810	4.45;3.14;2.19;2.36;4.44	5.57	5.57	0.84162	.	0.000000	0.85682	D	0.000000	T	0.00637	0.0021	.	.	.	0.09310	P	1.0	D	0.89917	1.0	D	0.83275	0.996	T	0.00335	-1.1808	8	0.72032	D	0.01	-6.8373	16.4581	0.84029	0.0:0.0:1.0:0.0	rs7972;rs1128968;rs2266617;rs3177429;rs3186383;rs11551317;rs17353483;rs17750846;rs52835763;rs58270987;rs7972	42	A6NED0	.	R	42;42;42;42;43	ENSP00000216465:G42R;ENSP00000452498:G42R;ENSP00000314404:G42R;ENSP00000450487:G42R;ENSP00000451976:G43R	ENSP00000216465:G42R	G	+	1	0	GSTZ1	76862990	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	5.705000	0.68355	2.614000	0.88457	0.655000	0.94253	GGG	G|0.949;A|0.051	0.051	strong		0.567	GSTZ1-012	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000414090.1	NM_145870	
APPL1	26060	hgsc.bcm.edu	37	3	57293908	57293908	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:57293908C>A	ENST00000288266.3	+	17	1666	c.1519C>A	c.(1519-1521)Ctt>Att	p.L507I		NM_012096.2	NP_036228.1	Q9UKG1	DP13A_HUMAN	adaptor protein, phosphotyrosine interaction, PH domain and leucine zipper containing 1	507	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell proliferation (GO:0008283)|insulin receptor signaling pathway (GO:0008286)|positive regulation of apoptotic process (GO:0043065)|regulation of apoptotic process (GO:0042981)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of glucose import (GO:0046324)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|vesicle membrane (GO:0012506)	identical protein binding (GO:0042802)|protein kinase B binding (GO:0043422)			breast(3)|endometrium(3)|kidney(3)|large_intestine(10)|liver(2)|lung(4)|prostate(2)	27				KIRC - Kidney renal clear cell carcinoma(284;0.0124)|Kidney(284;0.0144)		TGTCCGATTCCTTGGTTCAAT	0.318																																					p.L507I		Atlas-SNP	.											.	APPL1	59	.	0			c.C1519A						PASS	.						76.0	75.0	76.0					3																	57293908		2203	4300	6503	SO:0001583	missense	26060	exon17			CGATTCCTTGGTT	AB037849	CCDS2882.1	3p21.1-p14.3	2013-01-11			ENSG00000157500	ENSG00000157500		"""Pleckstrin homology (PH) domain containing"""	24035	protein-coding gene	gene with protein product		604299				10490823, 17030088	Standard	NM_012096		Approved	APPL	uc003dio.3	Q9UKG1	OTTHUMG00000133756	ENST00000288266.3:c.1519C>A	3.37:g.57293908C>A	ENSP00000288266:p.Leu507Ile	184.0	0.0	0		137.0	23.0	0.167883	NM_012096	Q9P2B9	Missense_Mutation	SNP	ENST00000288266.3	37	CCDS2882.1	.	.	.	.	.	.	.	.	.	.	C	32	5.114466	0.94339	.	.	ENSG00000157500	ENST00000288266	T	0.33216	1.42	5.43	5.43	0.79202	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.60077	0.2241	M	0.77313	2.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.63287	-0.6671	10	0.87932	D	0	.	19.6173	0.95639	0.0:1.0:0.0:0.0	.	490;507	B4DQX8;Q9UKG1	.;DP13A_HUMAN	I	507	ENSP00000288266:L507I	ENSP00000288266:L507I	L	+	1	0	APPL1	57268948	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.729000	0.84864	2.712000	0.92718	0.557000	0.71058	CTT	.	.	none		0.318	APPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258196.2	NM_012096	
DBF4	10926	hgsc.bcm.edu	37	7	87537188	87537188	+	Missense_Mutation	SNP	A	A	G	rs61747462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87537188A>G	ENST00000265728.1	+	12	2239	c.1735A>G	c.(1735-1737)Aaa>Gaa	p.K579E		NM_006716.3	NP_006707.1	Q9UBU7	DBF4A_HUMAN	DBF4 zinc finger	579					DNA replication (GO:0006260)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|positive regulation of catalytic activity (GO:0043085)	nucleoplasm (GO:0005654)	enzyme activator activity (GO:0008047)|nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(1)|large_intestine(6)|lung(13)|ovary(1)|skin(3)	28	Esophageal squamous(14;0.00202)	Breast(660;0.0334)				TCGAAAAGTGAAAATAATATT	0.333													A|||	29	0.00579073	0.0008	0.013	5008	,	,		19546	0.0		0.0169	False		,,,				2504	0.002				p.K579E		Atlas-SNP	.											.	DBF4	67	.	0			c.A1735G						PASS	.	A	GLU/LYS	16,4388		0,16,2186	46.0	53.0	51.0		1735	4.0	1.0	7	dbSNP_129	51	99,8435		1,97,4169	no	missense	DBF4	NM_006716.3	56	1,113,6355	GG,GA,AA		1.1601,0.3633,0.8889	possibly-damaging	579/675	87537188	115,12823	2202	4267	6469	SO:0001583	missense	10926	exon12			AAAGTGAAAATAA	AF160876	CCDS5611.1	7q21.3	2014-02-17	2014-02-17		ENSG00000006634	ENSG00000006634		"""Zinc fingers, DBF-type"""	17364	protein-coding gene	gene with protein product	"""activator of S phase kinase"", ""chiffon homolog (Drosophila)"", ""zinc finger, DBF-type containing 1"", ""DBF4 zinc finger A"""	604281	"""DBF4 homolog (S. cerevisiae)"""			10373557, 10517317	Standard	NM_006716		Approved	ASK, chif, ZDBF1, DBF4A	uc003ujf.1	Q9UBU7	OTTHUMG00000131034	ENST00000265728.1:c.1735A>G	7.37:g.87537188A>G	ENSP00000265728:p.Lys579Glu	250.0	0.0	0		269.0	130.0	0.483271	NM_006716	A4D1D8|A8K954|O75226|Q75MS6|Q75N01|Q9Y2M6	Missense_Mutation	SNP	ENST00000265728.1	37	CCDS5611.1	14	0.00641025641025641	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	10	0.013192612137203167	A	13.61	2.289011	0.40494	0.003633	0.011601	ENSG00000006634	ENST00000265728	T	0.37235	1.21	5.13	3.98	0.46160	.	0.088141	0.47852	D	0.000204	T	0.25005	0.0607	L	0.56769	1.78	0.30535	N	0.767027	B;B	0.26195	0.144;0.068	B;B	0.21708	0.036;0.036	T	0.35674	-0.9779	10	0.66056	D	0.02	-9.6101	8.964	0.35865	0.9161:0.0:0.0839:0.0	rs61747462	355;579	B7Z8C6;Q9UBU7	.;DBF4A_HUMAN	E	579	ENSP00000265728:K579E	ENSP00000265728:K579E	K	+	1	0	DBF4	87375124	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	4.387000	0.59626	1.934000	0.56057	0.528000	0.53228	AAA	A|0.992;G|0.008	0.008	strong		0.333	DBF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253678.1	NM_006716	
OR6N1	128372	hgsc.bcm.edu	37	1	158736217	158736217	+	Missense_Mutation	SNP	G	G	A	rs857828	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:158736217G>A	ENST00000335094.2	-	1	275	c.256C>T	c.(256-258)Ctc>Ttc	p.L86F		NM_001005185.1	NP_001005185.1	Q8NGY5	OR6N1_HUMAN	olfactory receptor, family 6, subfamily N, member 1	86				L -> F (in Ref. 3; AAK95093). {ECO:0000305}.		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(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(22)|ovary(1)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	54	all_hematologic(112;0.0378)					TTCTCACTGAGCAAGTTTGCC	0.498													G|||	18	0.00359425	0.0	0.0	5008	,	,		20366	0.0		0.0099	False		,,,				2504	0.0082				p.L86F		Atlas-SNP	.											.	OR6N1	96	.	0			c.C256T						PASS	.	G	PHE/LEU	10,4396	17.9+/-39.9	0,10,2193	82.0	76.0	78.0		256	5.1	1.0	1	dbSNP_86	78	79,8521	46.7+/-105.8	1,77,4222	yes	missense	OR6N1	NM_001005185.1	22	1,87,6415	AA,AG,GG		0.9186,0.227,0.6843	probably-damaging	86/313	158736217	89,12917	2203	4300	6503	SO:0001583	missense	128372	exon1			CACTGAGCAAGTT	BK004199	CCDS30905.1	1q23.1	2012-08-09			ENSG00000197403	ENSG00000197403		"""GPCR / Class A : Olfactory receptors"""	15034	protein-coding gene	gene with protein product							Standard	NM_001005185		Approved		uc010piq.2	Q8NGY5	OTTHUMG00000022774	ENST00000335094.2:c.256C>T	1.37:g.158736217G>A	ENSP00000335535:p.Leu86Phe	84.0	0.0	0		118.0	76.0	0.644068	NM_001005185	Q5VUU8|Q96R35	Missense_Mutation	SNP	ENST00000335094.2	37	CCDS30905.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	15.99	2.995570	0.54147	0.00227	0.009186	ENSG00000197403	ENST00000335094	T	0.10668	2.85	5.1	5.1	0.69264	GPCR, rhodopsin-like superfamily (1);	0.000000	0.41605	D	0.000856	T	0.11707	0.0285	L	0.46157	1.445	0.30949	N	0.725006	D	0.61080	0.989	P	0.60949	0.881	T	0.06162	-1.0842	10	0.23302	T	0.38	-21.3514	13.7262	0.62759	0.0:0.1556:0.8444:0.0	rs857828;rs1633200	86	Q8NGY5	OR6N1_HUMAN	F	86	ENSP00000335535:L86F	ENSP00000335535:L86F	L	-	1	0	OR6N1	157002841	0.011000	0.17503	1.000000	0.80357	0.995000	0.86356	0.349000	0.20055	2.623000	0.88846	0.655000	0.94253	CTC	G|0.994;A|0.006	0.006	strong		0.498	OR6N1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059067.1	NM_001005185	
CD44	960	hgsc.bcm.edu	37	11	35211471	35211471	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:35211471G>A	ENST00000428726.2	+	5	649	c.526G>A	c.(526-528)Gat>Aat	p.D176N	CD44_ENST00000360158.4_Missense_Mutation_p.D176N|CD44_ENST00000434472.2_Missense_Mutation_p.D176N|CD44_ENST00000278386.6_Intron|CD44_ENST00000526669.2_Intron|CD44_ENST00000263398.6_Missense_Mutation_p.D176N|CD44_ENST00000352818.4_Missense_Mutation_p.D176N|CD44_ENST00000433892.2_Missense_Mutation_p.D176N|CD44_ENST00000433354.2_Missense_Mutation_p.D176N|CD44_ENST00000415148.2_Missense_Mutation_p.D176N|CD44_ENST00000449691.2_Missense_Mutation_p.D176N|CD44_ENST00000437706.2_Missense_Mutation_p.D176N	NM_000610.3	NP_000601.3	P16070	CD44_HUMAN	CD44 molecule (Indian blood group)	176					blood coagulation (GO:0007596)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|carbohydrate metabolic process (GO:0005975)|cartilage development (GO:0051216)|cell-matrix adhesion (GO:0007160)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cytokine-mediated signaling pathway (GO:0019221)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|hyaluronan catabolic process (GO:0030214)|hyaluronan metabolic process (GO:0030212)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|monocyte aggregation (GO:0070487)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|single organismal cell-cell adhesion (GO:0016337)|small molecule metabolic process (GO:0044281)|Wnt signaling pathway (GO:0016055)|wound healing involved in inflammatory response (GO:0002246)	basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|pancreas(1)|skin(1)	23	all_cancers(35;0.212)|all_lung(20;0.0874)|all_epithelial(35;0.112)	all_hematologic(20;0.107)	STAD - Stomach adenocarcinoma(6;0.00731)		Hyaluronan(DB08818)	CCCTACTGATGATGACGTGAG	0.502																																					p.D176N		Atlas-SNP	.											.	CD44	48	.	0			c.G526A						PASS	.						123.0	98.0	106.0					11																	35211471		2202	4298	6500	SO:0001583	missense	960	exon5			ACTGATGATGACG	M59040	CCDS7897.1, CCDS31455.1, CCDS31456.1, CCDS31457.1, CCDS31458.1, CCDS55754.1, CCDS55755.1	11p13	2014-07-18	2006-03-28		ENSG00000026508	ENSG00000026508		"""CD molecules"", ""Blood group antigens"", ""Proteoglycans / Cell surface : Other"""	1681	protein-coding gene	gene with protein product	"""hematopoietic cell E- and L-selectin ligand"", ""chondroitin sulfate proteoglycan 8"""	107269	"""CD44 antigen (homing function and Indian blood group system)"""	MIC4, MDU2, MDU3		2454887	Standard	NM_001202555		Approved	IN, MC56, Pgp1, CD44R, HCELL, CSPG8	uc001mvu.3	P16070	OTTHUMG00000044388	ENST00000428726.2:c.526G>A	11.37:g.35211471G>A	ENSP00000398632:p.Asp176Asn	198.0	0.0	0		239.0	120.0	0.502092	NM_001001391	A5YRN9|B6EAT9|D3DR12|D3DR13|O95370|P22511|Q04858|Q13419|Q13957|Q13958|Q13959|Q13960|Q13961|Q13967|Q13968|Q13980|Q15861|Q16064|Q16065|Q16066|Q16208|Q16522|Q86T72|Q86Z27|Q8N694|Q92493|Q96J24|Q9H5A5|Q9UC28|Q9UC29|Q9UC30|Q9UCB0|Q9UJ36	Missense_Mutation	SNP	ENST00000428726.2	37	CCDS7897.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.4|21.4	4.140023|4.140023	0.77775|0.77775	.|.	.|.	ENSG00000026508|ENSG00000026508	ENST00000263398;ENST00000415148;ENST00000433354;ENST00000449691;ENST00000437706;ENST00000360158;ENST00000428726;ENST00000433892;ENST00000434472;ENST00000352818;ENST00000525211;ENST00000526000;ENST00000279452;ENST00000531110;ENST00000525688;ENST00000278385;ENST00000533222|ENST00000527889;ENST00000531873;ENST00000525685	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T|.	0.36699|.	1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24;1.24|.	5.82|5.82	5.82|5.82	0.92795|0.92795	.|.	0.411612|.	0.26136|.	N|.	0.026133|.	T|T	0.59702|0.59702	0.2213|0.2213	M|M	0.65975|0.65975	2.015|2.015	0.26051|0.26051	N|N	0.981485|0.981485	P;P;P;D;P;D|.	0.71674|.	0.453;0.614;0.798;0.998;0.867;0.993|.	B;P;P;D;P;D|.	0.76575|.	0.42;0.49;0.815;0.988;0.803;0.946|.	T|T	0.55366|0.55366	-0.8152|-0.8152	10|5	0.35671|.	T|.	0.21|.	-24.8201|-24.8201	15.6093|15.6093	0.76704|0.76704	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	176;176;176;176;176;176|.	B6EAT9;P16070-11;P16070-12;P16070-10;P16070-4;P16070|.	.;.;.;.;.;CD44_HUMAN|.	N|I	176;176;176;176;176;176;176;176;176;176;155;154;136;50;15;12;9|131;96;43	ENSP00000263398:D176N;ENSP00000389830:D176N;ENSP00000414567:D176N;ENSP00000391008:D176N;ENSP00000403990:D176N;ENSP00000353280:D176N;ENSP00000398632:D176N;ENSP00000392331:D176N;ENSP00000404447:D176N;ENSP00000309732:D176N;ENSP00000432405:D155N;ENSP00000434465:D154N;ENSP00000279452:D136N;ENSP00000436549:D50N;ENSP00000436980:D15N;ENSP00000278385:D12N;ENSP00000435321:D9N|.	ENSP00000263398:D176N|.	D|M	+|+	1|3	0|0	CD44|CD44	35168047|35168047	0.417000|0.417000	0.25432|0.25432	0.083000|0.083000	0.20561|0.20561	0.003000|0.003000	0.03518|0.03518	2.101000|2.101000	0.41787|0.41787	2.745000|2.745000	0.94114|0.94114	0.655000|0.655000	0.94253|0.94253	GAT|ATG	.	.	none		0.502	CD44-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000388927.1	NM_000610	
SF3B1	23451	hgsc.bcm.edu	37	2	198270017	198270017	+	Silent	SNP	T	T	C	rs35493573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:198270017T>C	ENST00000335508.6	-	10	1510	c.1419A>G	c.(1417-1419)caA>caG	p.Q473Q	SNORA4_ENST00000365564.1_RNA|SF3B1_ENST00000462613.1_5'Flank	NM_012433.2	NP_036565.2	O75533	SF3B1_HUMAN	splicing factor 3b, subunit 1, 155kDa	473	Interaction with PPP1R8.				anterior/posterior pattern specification (GO:0009952)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	catalytic step 2 spliceosome (GO:0071013)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|U12-type spliceosomal complex (GO:0005689)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)			NS(35)|breast(10)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(524)|kidney(4)|large_intestine(10)|lung(19)|ovary(1)|pancreas(4)|prostate(6)|salivary_gland(1)|skin(4)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	633			OV - Ovarian serous cystadenocarcinoma(117;0.246)			TATCAAAGTATTGAATATCAT	0.303			Mis		myelodysplastic syndrome								T|||	68	0.0135783	0.0091	0.0014	5008	,	,		16834	0.0		0.002	False		,,,				2504	0.0542				p.Q473Q		Atlas-SNP	.		Dom	yes		2	2q33.1	23451	"""splicing factor 3b, subunit 1, 155kDa"""		L	SF3B1,NS,carcinoma,-2,1	SF3B1	1038	1	0			c.A1419G						PASS	.	T		9,4397	15.5+/-35.6	0,9,2194	43.0	46.0	45.0		1419	0.5	1.0	2	dbSNP_126	45	23,8573	16.6+/-54.9	0,23,4275	no	coding-synonymous	SF3B1	NM_012433.2		0,32,6469	CC,CT,TT		0.2676,0.2043,0.2461		473/1305	198270017	32,12970	2203	4298	6501	SO:0001819	synonymous_variant	23451	exon10			AAAGTATTGAATA	AF054284	CCDS33356.1, CCDS46479.1	2q33.1	2014-09-17	2002-08-29		ENSG00000115524	ENSG00000115524			10768	protein-coding gene	gene with protein product		605590	"""splicing factor 3b, subunit 1, 155kD"""			9585501	Standard	XM_005246428		Approved	SAP155, SF3b155, PRPF10, Prp10, Hsh155	uc002uue.3	O75533	OTTHUMG00000154447	ENST00000335508.6:c.1419A>G	2.37:g.198270017T>C		134.0	0.0	0		133.0	77.0	0.578947	NM_012433	E9PCH3	Silent	SNP	ENST00000335508.6	37	CCDS33356.1																																																																																			T|0.994;C|0.006	0.006	strong		0.303	SF3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335245.2		
SV2B	9899	hgsc.bcm.edu	37	15	91827271	91827271	+	Missense_Mutation	SNP	A	A	G	rs117361551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:91827271A>G	ENST00000394232.1	+	11	1998	c.1528A>G	c.(1528-1530)Atc>Gtc	p.I510V	SV2B_ENST00000330276.4_Missense_Mutation_p.I510V|SV2B_ENST00000545111.2_Missense_Mutation_p.I359V	NM_014848.4	NP_055663.1	Q7L1I2	SV2B_HUMAN	synaptic vesicle glycoprotein 2B	510					neurotransmitter transport (GO:0006836)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle (GO:0008021)	transmembrane transporter activity (GO:0022857)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(17)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	42	Lung NSC(78;0.0987)|all_lung(78;0.172)		BRCA - Breast invasive adenocarcinoma(143;0.0895)			GCACAAGTTCATCAACTGTCG	0.507													A|||	56	0.0111821	0.0008	0.013	5008	,	,		19869	0.0		0.0169	False		,,,				2504	0.0297				p.I510V		Atlas-SNP	.											.	SV2B	98	.	0			c.A1528G						PASS	.	A	VAL/ILE,VAL/ILE	12,4384	19.1+/-41.9	0,12,2186	192.0	184.0	187.0		1075,1528	5.6	1.0	15	dbSNP_132	187	127,8469	64.9+/-127.2	2,123,4173	yes	missense,missense	SV2B	NM_001167580.1,NM_014848.4	29,29	2,135,6359	GG,GA,AA		1.4774,0.273,1.0699	benign,benign	359/533,510/684	91827271	139,12853	2198	4298	6496	SO:0001583	missense	9899	exon12			AAGTTCATCAACT	AB018278	CCDS10370.1, CCDS53972.1	15q26.1	2005-01-10			ENSG00000185518	ENSG00000185518			16874	protein-coding gene	gene with protein product		185861				9872452, 7681585	Standard	NM_014848		Approved	KIAA0735, HsT19680	uc002bqv.3	Q7L1I2	OTTHUMG00000149833	ENST00000394232.1:c.1528A>G	15.37:g.91827271A>G	ENSP00000377779:p.Ile510Val	104.0	0.0	0		160.0	81.0	0.50625	NM_014848	B4DH30|C6G489|O94840|Q6IAR8	Missense_Mutation	SNP	ENST00000394232.1	37	CCDS10370.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	10.16	1.274723	0.23307	0.00273	0.014774	ENSG00000185518	ENST00000545111;ENST00000394232;ENST00000330276	T;T;T	0.41400	1.0;1.0;1.0	5.61	5.61	0.85477	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.099589	0.64402	D	0.000004	T	0.21145	0.0509	L	0.39245	1.2	0.47584	D	0.999462	B	0.23937	0.094	B	0.31016	0.123	T	0.08911	-1.0699	10	0.12766	T	0.61	-31.4023	14.6867	0.69055	1.0:0.0:0.0:0.0	.	510	Q7L1I2	SV2B_HUMAN	V	359;510;510	ENSP00000443243:I359V;ENSP00000377779:I510V;ENSP00000332818:I510V	ENSP00000332818:I510V	I	+	1	0	SV2B	89628275	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	2.317000	0.43770	2.152000	0.67230	0.477000	0.44152	ATC	A|0.990;G|0.010	0.010	strong		0.507	SV2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313494.3	NM_014848	
FAM161A	84140	hgsc.bcm.edu	37	2	62066986	62066986	+	Missense_Mutation	SNP	G	G	C	rs139266382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:62066986G>C	ENST00000405894.3	-	3	1254	c.1153C>G	c.(1153-1155)Cag>Gag	p.Q385E	FAM161A_ENST00000404929.1_Missense_Mutation_p.Q385E	NM_032180.2	NP_115556.2	Q3B820	F161A_HUMAN	family with sequence similarity 161, member A	385					cilium assembly (GO:0042384)|response to stimulus (GO:0050896)|visual perception (GO:0007601)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)				breast(1)|endometrium(5)|large_intestine(8)|lung(4)|ovary(3)|pancreas(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	25						GCTCTCAGCTGTGTCCTAAGG	0.453													G|||	4	0.000798722	0.0015	0.0	5008	,	,		19117	0.0		0.002	False		,,,				2504	0.0				p.Q385E		Atlas-SNP	.											.	FAM161A	200	.	0			c.C1153G						PASS	.	G	GLU/GLN,GLU/GLN	4,3922		0,4,1959	100.0	101.0	101.0		1153,1153	3.8	0.0	2	dbSNP_134	101	39,8259		0,39,4110	yes	missense,missense	FAM161A	NM_001201543.1,NM_032180.2	29,29	0,43,6069	CC,CG,GG		0.47,0.1019,0.3518	possibly-damaging,possibly-damaging	385/717,385/661	62066986	43,12181	1963	4149	6112	SO:0001583	missense	84140	exon3			TCAGCTGTGTCCT		CCDS42687.2, CCDS56120.1	2p15	2011-03-15			ENSG00000170264	ENSG00000170264			25808	protein-coding gene	gene with protein product		613596	"""retinitis pigmentosa 28 (autosomal recessive)"""	RP28		10507729, 20705278, 20705279	Standard	NM_032180		Approved	FLJ13305	uc002sbm.4	Q3B820	OTTHUMG00000152165	ENST00000405894.3:c.1153C>G	2.37:g.62066986G>C	ENSP00000385893:p.Gln385Glu	276.0	0.0	0		257.0	114.0	0.44358	NM_032180	B4DJV7|Q9H8R2	Missense_Mutation	SNP	ENST00000405894.3	37	CCDS42687.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.89	2.967701	0.53507	0.001019	0.0047	ENSG00000170264	ENST00000404929;ENST00000405894	T;T	0.21191	2.02;2.02	5.67	3.83	0.44106	.	0.603842	0.18460	N	0.140544	T	0.34716	0.0907	M	0.72894	2.215	0.09310	N	1	D;D	0.58620	0.982;0.983	P;P	0.56434	0.764;0.798	T	0.12630	-1.0540	10	0.27785	T	0.31	-12.0385	9.065	0.36458	0.0702:0.0:0.6683:0.2615	.	385;385	Q3B820;Q3B820-3	F161A_HUMAN;.	E	385	ENSP00000385158:Q385E;ENSP00000385893:Q385E	ENSP00000385158:Q385E	Q	-	1	0	FAM161A	61920490	0.918000	0.31147	0.000000	0.03702	0.014000	0.08584	3.936000	0.56568	0.700000	0.31782	-0.140000	0.14226	CAG	G|0.998;C|0.002	0.002	strong		0.453	FAM161A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000325537.2	NM_032180	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156910020	156910020	+	Missense_Mutation	SNP	C	C	T	rs144803270		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156910020C>T	ENST00000361409.2	-	35	4334	c.3592G>A	c.(3592-3594)Gct>Act	p.A1198T	ARHGEF11_ENST00000487682.1_5'UTR|ARHGEF11_ENST00000368194.3_Missense_Mutation_p.A1238T|ARHGEF11_ENST00000315174.8_Missense_Mutation_p.A614T	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11	1198					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|cellular component movement (GO:0006928)|cytokinesis (GO:0000910)|establishment of cell polarity (GO:0030010)|G-protein coupled receptor signaling pathway (GO:0007186)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cell growth (GO:0001558)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)|striated muscle contraction (GO:0006941)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)	G-protein coupled receptor binding (GO:0001664)|GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(27)|ovary(4)|pancreas(2)|pleura(1)|prostate(4)|skin(7)|stomach(1)|urinary_tract(2)	81	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					GCGGAGTCAGCGAGCCCTTCC	0.627																																					p.A1238T		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G3712A						PASS	.	C	THR/ALA,THR/ALA	0,4406		0,0,2203	77.0	69.0	72.0		3592,3712	4.2	0.8	1	dbSNP_134	72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ARHGEF11	NM_014784.2,NM_198236.1	58,58	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging	1198/1523,1238/1563	156910020	1,13005	2203	4300	6503	SO:0001583	missense	9826	exon36			AGTCAGCGAGCCC	AB002378	CCDS1162.1, CCDS1163.1	1q21	2011-11-16			ENSG00000132694	ENSG00000132694		"""Rho guanine nucleotide exchange factors"""	14580	protein-coding gene	gene with protein product		605708				10526156, 9205841	Standard	NM_014784		Approved	KIAA0380, GTRAP48, PDZ-RHOGEF	uc001fqn.3	O15085	OTTHUMG00000041292	ENST00000361409.2:c.3592G>A	1.37:g.156910020C>T	ENSP00000354644:p.Ala1198Thr	135.0	0.0	0		168.0	85.0	0.505952	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	24.8	4.569825	0.86439	0.0	1.16E-4	ENSG00000132694	ENST00000368194;ENST00000361409;ENST00000315174	T;T;T	0.76709	-1.0;-0.99;-1.04	4.16	4.16	0.48862	.	0.000000	0.48286	D	0.000200	T	0.77738	0.4175	L	0.34521	1.04	0.40759	D	0.982985	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.85130	0.997;0.993;0.997	T	0.79708	-0.1690	10	0.48119	T	0.1	-10.0453	15.3955	0.74790	0.0:1.0:0.0:0.0	.	614;1198;1238	F8W8P9;O15085;O15085-2	.;ARHGB_HUMAN;.	T	1238;1198;614	ENSP00000357177:A1238T;ENSP00000354644:A1198T;ENSP00000313470:A614T	ENSP00000313470:A614T	A	-	1	0	ARHGEF11	155176644	0.999000	0.42202	0.770000	0.31555	0.925000	0.55904	5.158000	0.64917	2.135000	0.66039	0.561000	0.74099	GCT	C|1.000;T|0.000	0.000	weak		0.627	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
ABL1	25	hgsc.bcm.edu	37	9	133760380	133760380	+	Silent	SNP	C	C	G	rs56017837	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760380C>G	ENST00000318560.5	+	11	3084	c.2703C>G	c.(2701-2703)ccC>ccG	p.P901P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	901	DNA-binding. {ECO:0000250}.|Poly-Pro.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	CCCCGCCGCCCCCACCAGCAG	0.672			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	4	0.000798722	0.0	0.0014	5008	,	,		15690	0.0		0.002	False		,,,				2504	0.001				p.P920P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2760G						PASS	.	C	,	0,4338		0,0,2169	8.0	11.0	10.0		2703,2760	-2.0	0.8	9	dbSNP_129	10	14,8502		0,14,4244	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	0,14,6413	GG,GC,CC		0.1644,0.0,0.1089	,	901/1131,920/1150	133760380	14,12840	2169	4258	6427	SO:0001819	synonymous_variant	25	exon11			GCCGCCCCCACCA	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2703C>G	9.37:g.133760380C>G		80.0	0.0	0		80.0	39.0	0.4875	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			.	.	weak		0.672	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
DENND6B	414918	hgsc.bcm.edu	37	22	50753263	50753263	+	Silent	SNP	G	G	A	rs113856947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50753263G>A	ENST00000413817.3	-	10	917	c.846C>T	c.(844-846)ccC>ccT	p.P282P	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	282					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										AGGACACGTCGGGCGAGGGTG	0.682													G|||	23	0.00459265	0.0008	0.0072	5008	,	,		17171	0.0		0.0089	False		,,,				2504	0.0082				p.P282P		Atlas-SNP	.											.	.	.	.	0			c.C846T						PASS	.	G		11,4179		0,11,2084	26.0	35.0	32.0		846	-7.3	0.3	22	dbSNP_132	32	70,8310		0,70,4120	no	coding-synonymous	FAM116B	NM_001001794.3		0,81,6204	AA,AG,GG		0.8353,0.2625,0.6444		282/586	50753263	81,12489	2095	4190	6285	SO:0001819	synonymous_variant	414918	exon10			CACGTCGGGCGAG	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.846C>T	22.37:g.50753263G>A		227.0	0.0	0		186.0	76.0	0.408602	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	G	11.25	1.583626	0.28268	0.002625	0.008353	ENSG00000205593	ENST00000433760	.	.	.	5.01	-7.27	0.01461	.	0.000000	0.85682	D	0.000000	T	0.34106	0.0886	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.49214	-0.8963	6	0.87932	D	0	-21.3129	0.6044	0.00750	0.3433:0.203:0.2759:0.1779	.	.	.	.	L	303	.	ENSP00000414072:P303L	P	-	2	0	FAM116B	49095835	0.000000	0.05858	0.317000	0.25265	0.735000	0.41995	-3.056000	0.00625	-0.646000	0.05452	0.305000	0.20034	CCG	G|0.994;A|0.006	0.006	strong		0.682	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
TSC2	7249	hgsc.bcm.edu	37	16	2136842	2136842	+	Silent	SNP	C	C	T	rs45517384|rs137854272	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2136842C>T	ENST00000219476.3	+	38	5589	c.4959C>T	c.(4957-4959)tcC>tcT	p.S1653S	TSC2_ENST00000350773.4_Silent_p.S1630S|TSC2_ENST00000568454.1_Silent_p.S1597S|TSC2_ENST00000353929.4_Silent_p.S1610S|TSC2_ENST00000382538.6_Silent_p.S1538S|TSC2_ENST00000439673.2_Silent_p.S1550S|TSC2_ENST00000401874.2_Silent_p.S1586S	NM_000548.3	NP_000539.2	P49815	TSC2_HUMAN	tuberous sclerosis 2	1653	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.		S -> F (in TSC2). {ECO:0000269|PubMed:15024740}.		acute-phase response (GO:0006953)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|endocytosis (GO:0006897)|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)|insulin-like growth factor receptor signaling pathway (GO:0048009)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of TOR signaling (GO:0032007)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol-mediated signaling (GO:0048015)|positive chemotaxis (GO:0050918)|positive regulation of Ras GTPase activity (GO:0032320)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|protein import into nucleus (GO:0006606)|protein kinase B signaling (GO:0043491)|protein localization (GO:0008104)|regulation of cell cycle (GO:0051726)|regulation of endocytosis (GO:0030100)|regulation of insulin receptor signaling pathway (GO:0046626)|response to hypoxia (GO:0001666)|vesicle-mediated transport (GO:0016192)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|TSC1-TSC2 complex (GO:0033596)	GTPase activator activity (GO:0005096)|phosphatase binding (GO:0019902)|protein homodimerization activity (GO:0042803)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(3)|lung(19)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|soft_tissue(1)	56		Hepatocellular(780;0.0202)				ACAATGACTCCGGTGAGGACT	0.612			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				c|||	17	0.00339457	0.0023	0.0086	5008	,	,		20855	0.0		0.008	False		,,,				2504	0.0				p.S1653S		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 2	16	16p13.3	7249	tuberous sclerosis 2 gene		"""E, O"""	.	TSC2	364	.	0			c.C4959T						PASS	.	T	,,	11,4377	16.8+/-37.8	0,11,2183	71.0	52.0	59.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4959,4758,4890	-9.4	0.2	16	dbSNP_127	59	127,8453	60.6+/-122.4	0,127,4163	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC2	NM_000548.3,NM_001077183.1,NM_001114382.1	,,	0,138,6346	TT,TC,CC		1.4802,0.2507,1.0642	,,	1653/1808,1586/1741,1630/1785	2136842	138,12830	2194	4290	6484	SO:0001819	synonymous_variant	7249	exon38	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	TGACTCCGGTGAG	AB014460	CCDS10458.1, CCDS45384.1, CCDS58408.1	16p13.3	2014-09-17			ENSG00000103197	ENSG00000103197			12363	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 160"""	191092		TSC4		1303246, 7558029	Standard	NM_001077183		Approved	tuberin, LAM, PPP1R160	uc002con.3	P49815	OTTHUMG00000128745	ENST00000219476.3:c.4959C>T	16.37:g.2136842C>T		84.0	0.0	0		85.0	43.0	0.505882	NM_000548	A7E2E2|B4DIL8|B4DIQ7|B4DRN2|B7Z2B8|C9J378|O75275|Q4LE71|Q8TAZ1	Silent	SNP	ENST00000219476.3	37	CCDS10458.1																																																																																			C|0.992;T|0.008	0.008	strong		0.612	TSC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250657.2	NM_000548	
MAP3K11	4296	hgsc.bcm.edu	37	11	65367223	65367223	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65367223A>G	ENST00000530153.1	-	9	1598	c.1077T>C	c.(1075-1077)ccT>ccC	p.P359P	MAP3K11_ENST00000534432.1_5'UTR|MAP3K11_ENST00000532507.1_Silent_p.P32P|MAP3K11_ENST00000309100.3_Silent_p.P616P					mitogen-activated protein kinase kinase kinase 11											breast(3)|central_nervous_system(1)|kidney(1)|large_intestine(4)|lung(14)|skin(1)	24						GCTCCAGGCTAGGCCGCGGGG	0.697																																					p.P616P		Atlas-SNP	.											.	MAP3K11	67	.	0			c.T1848C						PASS	.						7.0	8.0	8.0					11																	65367223		2068	4080	6148	SO:0001819	synonymous_variant	4296	exon9			CAGGCTAGGCCGC		CCDS8107.1	11q13.1-q13.3	2011-06-09			ENSG00000173327	ENSG00000173327	2.7.10.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6850	protein-coding gene	gene with protein product		600050		MLK3, PTK1		9267807, 8183572	Standard	NM_002419		Approved	SPRK, MEKK11	uc001oew.3	Q16584	OTTHUMG00000166529	ENST00000530153.1:c.1077T>C	11.37:g.65367223A>G		28.0	0.0	0		30.0	4.0	0.133333	NM_002419		Silent	SNP	ENST00000530153.1	37																																																																																				.	.	none		0.697	MAP3K11-004	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000390233.2		
KRT74	121391	hgsc.bcm.edu	37	12	52966368	52966368	+	Silent	SNP	C	C	T	rs78832381	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:52966368C>T	ENST00000305620.2	-	2	602	c.555G>A	c.(553-555)aaG>aaA	p.K185K	KRT74_ENST00000549343.1_Silent_p.K185K	NM_175053.3	NP_778223.2	Q7RTS7	K2C74_HUMAN	keratin 74	185	Linker 1.|Rod.				intermediate filament cytoskeleton organization (GO:0045104)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	keratin filament binding (GO:1990254)|structural molecule activity (GO:0005198)			kidney(2)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	28				BRCA - Breast invasive adenocarcinoma(357;0.191)		GCTCCAGGTTCTTCTTGCAGT	0.562													C|||	79	0.0157748	0.003	0.0389	5008	,	,		20869	0.0		0.0398	False		,,,				2504	0.0082				p.K185K		Atlas-SNP	.											.	KRT74	67	.	0			c.G555A						PASS	.	C		42,4364	46.0+/-80.4	1,40,2162	151.0	139.0	143.0		555	-3.5	0.8	12	dbSNP_132	143	310,8290	111.4+/-171.7	7,296,3997	no	coding-synonymous	KRT74	NM_175053.3		8,336,6159	TT,TC,CC		3.6047,0.9532,2.7064		185/530	52966368	352,12654	2203	4300	6503	SO:0001819	synonymous_variant	121391	exon2			CAGGTTCTTCTTG	BK000977	CCDS8832.1	12q13.13	2013-06-25			ENSG00000170484	ENSG00000170484		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28929	protein-coding gene	gene with protein product		608248				12648212, 16831889	Standard	NM_175053		Approved	K6IRS4, KRT5C, KRT6IRS4	uc001sap.1	Q7RTS7	OTTHUMG00000169658	ENST00000305620.2:c.555G>A	12.37:g.52966368C>T		224.0	0.0	0		270.0	116.0	0.42963	NM_175053	B5MD61|Q86Y45	Silent	SNP	ENST00000305620.2	37	CCDS8832.1																																																																																			C|0.974;T|0.026	0.026	strong		0.562	KRT74-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405324.1	NM_175053	
HTRA1	5654	hgsc.bcm.edu	37	10	124268261	124268261	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124268261G>A	ENST00000368984.3	+	6	1223	c.1095G>A	c.(1093-1095)acG>acA	p.T365T		NM_002775.4	NP_002766.1	Q92743	HTRA1_HUMAN	HtrA serine peptidase 1	365	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			endometrium(1)|kidney(1)|large_intestine(8)|lung(7)	17		all_neural(114;0.0765)|Lung NSC(174;0.133)|all_lung(145;0.163)|Breast(234;0.238)				AGTTCCTCACGGAGTCCCATG	0.517																																					p.T365T		Atlas-SNP	.											HTRA1,colon,carcinoma,+2,2	HTRA1	40	2	0			c.G1095A						PASS	.						98.0	102.0	100.0					10																	124268261		2203	4300	6503	SO:0001819	synonymous_variant	5654	exon6			CCTCACGGAGTCC	AF097709	CCDS7630.1	10q26.3	2014-01-28	2005-08-18	2005-08-18	ENSG00000166033	ENSG00000166033		"""Serine peptidases / Serine peptidases"""	9476	protein-coding gene	gene with protein product		602194	"""protease, serine, 11 (IGF binding)"""	PRSS11		8977104	Standard	NM_002775		Approved	HtrA, IGFBP5-protease, ARMD7	uc001lgj.2	Q92743	OTTHUMG00000019186	ENST00000368984.3:c.1095G>A	10.37:g.124268261G>A		52.0	0.0	0		64.0	11.0	0.171875	NM_002775	D3DRE4|Q9UNS5	Silent	SNP	ENST00000368984.3	37	CCDS7630.1																																																																																			.	.	none		0.517	HTRA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128327.1	NM_002775	
HSDL2	84263	hgsc.bcm.edu	37	9	115167994	115167994	+	Missense_Mutation	SNP	A	A	T	rs41280175	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:115167994A>T	ENST00000398805.3	+	3	499	c.272A>T	c.(271-273)aAa>aTa	p.K91I	HSDL2_ENST00000539114.1_5'UTR|HSDL2_ENST00000488101.1_3'UTR|HSDL2_ENST00000262542.7_5'UTR|HSDL2_ENST00000398803.1_Missense_Mutation_p.K91I	NM_032303.4	NP_115679.2	Q6YN16	HSDL2_HUMAN	hydroxysteroid dehydrogenase like 2	91						membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)			NS(1)|breast(2)|cervix(2)|endometrium(1)|large_intestine(2)|lung(2)|prostate(1)|upper_aerodigestive_tract(2)	13						GCCATCAAGAAATTTGGAGGT	0.318													A|||	10	0.00199681	0.0008	0.0058	5008	,	,		16111	0.0		0.005	False		,,,				2504	0.0				p.K91I		Atlas-SNP	.											.	HSDL2	24	.	0			c.A272T						PASS	.	A	ILE/LYS,ILE/LYS	7,3743		0,7,1868	128.0	126.0	126.0		272,272	3.2	1.0	9	dbSNP_127	126	107,8109		1,105,4002	yes	missense,missense	HSDL2	NM_001195822.1,NM_032303.4	102,102	1,112,5870	TT,TA,AA		1.3023,0.1867,0.9527	benign,benign	91/346,91/419	115167994	114,11852	1875	4108	5983	SO:0001583	missense	84263	exon3			TCAAGAAATTTGG	AY093428	CCDS43864.1, CCDS56582.1	9q32	2011-09-14			ENSG00000119471	ENSG00000119471		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	18572	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 13C, member 1"""		"""chromosome 9 open reading frame 99"""	C9orf99		12834046, 19027726	Standard	NM_032303		Approved	SDR13C1	uc004bga.2	Q6YN16	OTTHUMG00000020504	ENST00000398805.3:c.272A>T	9.37:g.115167994A>T	ENSP00000381785:p.Lys91Ile	65.0	0.0	0		46.0	32.0	0.695652	NM_032303	A8K1L4|A8K8X1|A8MSV3|Q658M8|Q9BT58	Missense_Mutation	SNP	ENST00000398805.3	37	CCDS43864.1	8	0.003663003663003663	0	0.0	3	0.008287292817679558	0	0.0	5	0.006596306068601583	A	12.14	1.848888	0.32699	0.001867	0.013023	ENSG00000119471	ENST00000398805;ENST00000398803	D;D	0.88431	-2.38;-2.38	5.57	3.15	0.36227	NAD(P)-binding domain (1);	0.456598	0.25677	N	0.029030	D	0.82296	0.5006	M	0.69823	2.125	0.80722	D	1	P;B	0.45902	0.868;0.064	B;B	0.42138	0.377;0.159	T	0.79027	-0.1971	10	0.39692	T	0.17	.	6.4508	0.21902	0.6281:0.2284:0.1434:0.0	rs41280175	91;91	Q6YN16-2;Q6YN16	.;HSDL2_HUMAN	I	91	ENSP00000381785:K91I;ENSP00000381783:K91I	ENSP00000381783:K91I	K	+	2	0	HSDL2	114207815	0.922000	0.31269	0.991000	0.47740	0.021000	0.10359	0.964000	0.29306	0.369000	0.24510	0.260000	0.18958	AAA	A|0.995;T|0.005	0.005	strong		0.318	HSDL2-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053681.1	NM_032303	
FGF21	26291	hgsc.bcm.edu	37	19	49261218	49261218	+	Missense_Mutation	SNP	G	G	A	rs142980324		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49261218G>A	ENST00000593756.1	+	4	943	c.371G>A	c.(370-372)cGg>cAg	p.R124Q	FUT1_ENST00000310160.3_5'Flank|FGF21_ENST00000222157.3_Missense_Mutation_p.R124Q			Q9NSA1	FGF21_HUMAN	fibroblast growth factor 21	124					cell-cell signaling (GO:0007267)|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 low-density lipoprotein particle receptor biosynthetic process (GO:0045716)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|regulation of low-density lipoprotein particle clearance (GO:0010988)|signal transduction (GO:0007165)	extracellular region (GO:0005576)				breast(1)|cervix(2)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	8		all_lung(116;1.7e-06)|all_epithelial(76;3.52e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TGCAGCTTCCGGGAGCTGCTT	0.582																																					p.R124Q		Atlas-SNP	.											.	FGF21	21	.	0			c.G371A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	158.0	173.0	168.0		371	3.4	1.0	19	dbSNP_134	168	4,8592	3.7+/-12.6	0,4,4294	yes	missense	FGF21	NM_019113.2	43	0,4,6495	AA,AG,GG		0.0465,0.0,0.0308	probably-damaging	124/210	49261218	4,12994	2201	4298	6499	SO:0001583	missense	26291	exon3			GCTTCCGGGAGCT	AB021975	CCDS12734.1	19q13.33	2012-09-20			ENSG00000105550	ENSG00000105550			3678	protein-coding gene	gene with protein product		609436				10858549	Standard	XM_005258731		Approved		uc002pko.1	Q9NSA1		ENST00000593756.1:c.371G>A	19.37:g.49261218G>A	ENSP00000471477:p.Arg124Gln	153.0	0.0	0		132.0	57.0	0.431818	NM_019113	Q8N683	Missense_Mutation	SNP	ENST00000593756.1	37	CCDS12734.1	.	.	.	.	.	.	.	.	.	.	G	19.37	3.814192	0.70912	0.0	4.65E-4	ENSG00000105550	ENST00000222157	D	0.81579	-1.51	4.44	3.4	0.38934	.	0.076506	0.49916	D	0.000128	T	0.80969	0.4726	M	0.74258	2.255	0.37112	D	0.900381	D	0.53745	0.962	P	0.48270	0.572	T	0.82814	-0.0271	10	0.46703	T	0.11	-15.5157	8.3528	0.32312	0.1087:0.0:0.8913:0.0	.	124	Q9NSA1	FGF21_HUMAN	Q	124	ENSP00000222157:R124Q	ENSP00000222157:R124Q	R	+	2	0	FGF21	53953030	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	1.173000	0.31920	1.220000	0.43490	0.511000	0.50034	CGG	G|1.000;A|0.000	0.000	weak		0.582	FGF21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466200.1		
COQ10B	80219	hgsc.bcm.edu	37	2	198334871	198334871	+	Silent	SNP	A	A	C	rs140640160		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:198334871A>C	ENST00000263960.2	+	4	663	c.525A>C	c.(523-525)ccA>ccC	p.P175P	COQ10B_ENST00000409010.1_Silent_p.P147P|COQ10B_ENST00000409398.1_Silent_p.P125P|COQ10B_ENST00000545340.1_Silent_p.P132P	NM_025147.3	NP_079423.1	Q9H8M1	CQ10B_HUMAN	coenzyme Q10 homolog B (S. cerevisiae)	175						mitochondrial inner membrane (GO:0005743)				endometrium(1)|large_intestine(2)|lung(3)	6			Epithelial(96;0.231)|OV - Ovarian serous cystadenocarcinoma(117;0.246)			CTGGCTACCCAAGAACTTGTA	0.353													A|||	1	0.000199681	0.0008	0.0	5008	,	,		16923	0.0		0.0	False		,,,				2504	0.0				p.P175P		Atlas-SNP	.											.	COQ10B	18	.	0			c.A525C						PASS	.	A		3,4403	4.2+/-10.8	0,3,2200	126.0	111.0	116.0		525	-0.2	1.0	2	dbSNP_134	116	14,8586	8.4+/-32.0	0,14,4286	no	coding-synonymous	COQ10B	NM_025147.3		0,17,6486	CC,CA,AA		0.1628,0.0681,0.1307		175/239	198334871	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	80219	exon4			CTACCCAAGAACT	AK023510	CCDS2319.1	2q33.1	2008-02-05	2006-04-04		ENSG00000115520	ENSG00000115520			25819	protein-coding gene	gene with protein product			"""coenzyme Q10 homolog B (yeast)"""				Standard	NM_025147		Approved	FLJ13448	uc002uuh.1	Q9H8M1	OTTHUMG00000132745	ENST00000263960.2:c.525A>C	2.37:g.198334871A>C		308.0	0.0	0		329.0	165.0	0.50152	NM_025147	B7Z1Y4	Silent	SNP	ENST00000263960.2	37	CCDS2319.1																																																																																			A|0.998;C|0.002	0.002	strong		0.353	COQ10B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256105.2	NM_025147	
SCYL1	57410	hgsc.bcm.edu	37	11	65293819	65293819	+	Silent	SNP	G	G	A	rs75169347	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:65293819G>A	ENST00000270176.5	+	4	677	c.600G>A	c.(598-600)aaG>aaA	p.K200K	SCYL1_ENST00000279270.6_Silent_p.K200K|SCYL1_ENST00000525364.1_Silent_p.K200K|SCYL1_ENST00000420247.2_Silent_p.K200K|SCYL1_ENST00000533862.1_Silent_p.K200K|SCYL1_ENST00000527009.1_Silent_p.K57K|SCYL1_ENST00000524944.1_Silent_p.K200K	NM_020680.3	NP_065731.3	Q96KG9	NTKL_HUMAN	SCY1-like 1 (S. cerevisiae)	200	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|transcription, DNA-templated (GO:0006351)	cis-Golgi network (GO:0005801)|COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|protein tyrosine kinase activity (GO:0004713)			ovary(1)|skin(1)	2						TCAGAGAGAAGTGGTGGGTGA	0.657													G|||	91	0.0181709	0.0015	0.0303	5008	,	,		16563	0.0		0.0616	False		,,,				2504	0.0061				p.K200K		Atlas-SNP	.											.	SCYL1	76	.	0			c.G600A						PASS	.	G	,	34,4166		0,34,2066	16.0	19.0	18.0		600,600	-1.8	0.8	11	dbSNP_131	18	504,7942		14,476,3733	no	coding-synonymous,coding-synonymous	SCYL1	NM_001048218.1,NM_020680.3	,	14,510,5799	AA,AG,GG		5.9673,0.8095,4.2543	,	200/792,200/809	65293819	538,12108	2100	4223	6323	SO:0001819	synonymous_variant	57410	exon4			AGAGAAGTGGTGG	AF225424	CCDS41672.1, CCDS44646.1	11q11-q12	2008-07-21	2002-11-26	2002-11-29	ENSG00000142186	ENSG00000142186			14372	protein-coding gene	gene with protein product	"""teratoma-associated tyrosine kinase"", ""telomerase transcriptional elements-interacting factor"", ""telomerase regulation-associated protein"""	607982	"""N-terminal kinase-like"""	NTKL		11118629	Standard	NM_020680		Approved	HT019, P105, GKLP, NKTL, TAPK, TRAP, TEIF, MGC78454	uc001oea.1	Q96KG9	OTTHUMG00000166325	ENST00000270176.5:c.600G>A	11.37:g.65293819G>A		119.0	0.0	0		110.0	44.0	0.4	NM_020680	A6NJF1|Q96G50|Q96KG8|Q96KH1|Q9HAW5|Q9HBL3|Q9NR53	Silent	SNP	ENST00000270176.5	37	CCDS41672.1																																																																																			G|0.968;A|0.032	0.032	strong		0.657	SCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389159.2	NM_020680	
CYB5R3	1727	hgsc.bcm.edu	37	22	43032811	43032811	+	Missense_Mutation	SNP	A	A	T	rs370253340		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43032811A>T	ENST00000352397.5	-	2	315	c.63T>A	c.(61-63)agT>agA	p.S21R	CYB5R3_ENST00000407332.1_5'UTR|CYB5R3_ENST00000402438.1_5'UTR|CYB5R3_ENST00000407623.3_5'UTR|CYB5R3_ENST00000361740.4_Missense_Mutation_p.S54R|CYB5R3_ENST00000396303.3_5'UTR	NM_000398.6	NP_000389.1	P00387	NB5R3_HUMAN	cytochrome b5 reductase 3	21					blood circulation (GO:0008015)|cholesterol biosynthetic process (GO:0006695)|L-ascorbic acid metabolic process (GO:0019852)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|hemoglobin complex (GO:0005833)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ADP binding (GO:0043531)|AMP binding (GO:0016208)|cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|FAD binding (GO:0071949)|flavin adenine dinucleotide binding (GO:0050660)|NAD binding (GO:0051287)			kidney(2)|large_intestine(1)|lung(2)|skin(1)	6					Flavin adenine dinucleotide(DB03147)	TCATGAGCAGACTGTACAGGA	0.622																																					p.S54R		Atlas-SNP	.											.	CYB5R3	31	.	0			c.T162A						PASS	.	A	,,,ARG/SER,ARG/SER	0,4406		0,0,2203	78.0	67.0	71.0		,,,162,63	0.2	0.9	22		71	1,8599	1.2+/-3.3	0,1,4299	no	utr-5,utr-5,utr-5,missense,missense	CYB5R3	NM_001129819.2,NM_001171661.1,NM_007326.4,NM_001171660.1,NM_000398.6	,,,110,110	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	,,,benign,benign	,,,54/335,21/302	43032811	1,13005	2203	4300	6503	SO:0001583	missense	1727	exon2			GAGCAGACTGTAC	M16461	CCDS14040.1, CCDS33658.1, CCDS54535.1	22q13.2	2012-10-02		2005-07-13	ENSG00000100243	ENSG00000100243	1.6.2.2		2873	protein-coding gene	gene with protein product		613213	"""diaphorase (NADH) (cytochrome b-5 reductase)"""	DIA1		2479590, 3268037	Standard	NM_001129819		Approved		uc011aps.2	P00387	OTTHUMG00000150745	ENST00000352397.5:c.63T>A	22.37:g.43032811A>T	ENSP00000338461:p.Ser21Arg	51.0	0.0	0		49.0	14.0	0.285714	NM_001171660	B1AHF2|B7Z7L3|O75675|Q8TDL8|Q8WTS8|Q9UEN4|Q9UEN5|Q9UL55|Q9UL56	Missense_Mutation	SNP	ENST00000352397.5	37	CCDS33658.1	.	.	.	.	.	.	.	.	.	.	A	12.25	1.881744	0.33255	0.0	1.16E-4	ENSG00000100243	ENST00000361740;ENST00000352397	D;D	0.87256	-2.23;-2.2	4.82	0.217	0.15264	.	0.474289	0.25037	N	0.033621	T	0.75982	0.3924	L	0.44542	1.39	0.80722	D	1	P;B	0.37864	0.61;0.007	B;B	0.29942	0.109;0.025	T	0.65191	-0.6228	10	0.25751	T	0.34	-14.0956	8.2667	0.31819	0.3607:0.0:0.6393:0.0	.	54;21	B7Z7L3;P00387	.;NB5R3_HUMAN	R	54;21	ENSP00000354468:S54R;ENSP00000338461:S21R	ENSP00000338461:S21R	S	-	3	2	CYB5R3	41362755	0.801000	0.28930	0.938000	0.37757	0.799000	0.45148	0.491000	0.22419	-0.057000	0.13199	0.260000	0.18958	AGT	.	.	weak		0.622	CYB5R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320439.1		
CDH6	1004	hgsc.bcm.edu	37	5	31294254	31294254	+	Silent	SNP	C	C	T	rs147617483	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:31294254C>T	ENST00000265071.2	+	3	679	c.414C>T	c.(412-414)ccC>ccT	p.P138P	CDH6_ENST00000514738.1_Silent_p.P83P	NM_004932.3	NP_004923.1	P55285	CADH6_HUMAN	cadherin 6, type 2, K-cadherin (fetal kidney)	138	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P138P(1)		NS(3)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(42)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						CAGGGAGACCCGTGGAGCCCG	0.473													C|||	6	0.00119808	0.0	0.0043	5008	,	,		18421	0.0		0.003	False		,,,				2504	0.0				p.P138P		Atlas-SNP	.											.	CDH6	175	.	1	Substitution - coding silent(1)	lung(1)	c.C414T						PASS	.	C		8,4398	12.9+/-30.5	0,8,2195	134.0	135.0	134.0		414	-11.5	0.2	5	dbSNP_134	134	55,8545	35.3+/-89.8	0,55,4245	no	coding-synonymous	CDH6	NM_004932.3		0,63,6440	TT,TC,CC		0.6395,0.1816,0.4844		138/791	31294254	63,12943	2203	4300	6503	SO:0001819	synonymous_variant	1004	exon3			GAGACCCGTGGAG	D31784	CCDS3894.1	5p13.3	2010-01-26			ENSG00000113361	ENSG00000113361		"""Cadherins / Major cadherins"""	1765	protein-coding gene	gene with protein product	"""K-Cadherin"""	603007				7743525, 10191097	Standard	NM_004932		Approved		uc003jhe.2	P55285	OTTHUMG00000090673	ENST00000265071.2:c.414C>T	5.37:g.31294254C>T		88.0	0.0	0		107.0	55.0	0.514019	NM_004932	A8K5H5|Q9BWS0	Silent	SNP	ENST00000265071.2	37	CCDS3894.1																																																																																			C|0.995;T|0.005	0.005	strong		0.473	CDH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207355.2	NM_004932	
UGT2B4	7363	hgsc.bcm.edu	37	4	70361334	70361334	+	Silent	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:70361334A>C	ENST00000305107.6	-	1	292	c.246T>G	c.(244-246)acT>acG	p.T82T	UGT2B4_ENST00000512583.1_Silent_p.T82T|UGT2B4_ENST00000381096.3_Intron|UGT2B4_ENST00000506580.1_5'UTR	NM_021139.2	NP_066962.2	P06133	UD2B4_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B4	82					cellular glucuronidation (GO:0052695)|estrogen catabolic process (GO:0006711)|metabolic process (GO:0008152)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	glucuronosyltransferase activity (GO:0015020)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(29)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	47					Canagliflozin(DB08907)|Codeine(DB00318)|Dapagliflozin(DB06292)|Flurbiprofen(DB00712)|Ibuprofen(DB01050)|Morphine(DB00295)	ACTCAGTTTTAGTTAAAGATA	0.373																																					p.T82T		Atlas-SNP	.											.	UGT2B4	105	.	0			c.T246G						PASS	.						53.0	54.0	54.0					4																	70361334		2133	4279	6412	SO:0001819	synonymous_variant	7363	exon1			AGTTTTAGTTAAA	BC026264	CCDS43234.1, CCDS75137.1	4q13	2008-02-05	2005-07-20			ENSG00000156096		"""UDP glucuronosyltransferases"""	12553	protein-coding gene	gene with protein product		600067	"""UDP glycosyltransferase 2 family, polypeptide B4"""			3109396, 7835904	Standard	NM_021139		Approved	UGT2B11	uc003hek.4	P06133		ENST00000305107.6:c.246T>G	4.37:g.70361334A>C		136.0	0.0	0		143.0	24.0	0.167832	NM_021139	A6NCP7|B4DT75|G5E9X8|O60731|O60867|O75614|P36538|Q1HBF9|Q6QQX7	Silent	SNP	ENST00000305107.6	37	CCDS43234.1																																																																																			.	.	none		0.373	UGT2B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365526.1	NM_021139	
MED12	9968	hgsc.bcm.edu	37	X	70354254	70354254	+	Silent	SNP	G	G	A	rs375001801		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:70354254G>A	ENST00000374080.3	+	34	4697	c.4665G>A	c.(4663-4665)acG>acA	p.T1555T	MED12_ENST00000374102.1_Silent_p.T1555T|MED12_ENST00000333646.6_Silent_p.T1555T			Q93074	MED12_HUMAN	mediator complex subunit 12	1555					androgen receptor signaling pathway (GO:0030521)|axis elongation involved in somitogenesis (GO:0090245)|canonical Wnt signaling pathway (GO:0060070)|gene expression (GO:0010467)|heart development (GO:0007507)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|negative regulation of Wnt signaling pathway (GO:0030178)|neural tube closure (GO:0001843)|oligodendrocyte development (GO:0014003)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|Schwann cell development (GO:0014044)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)|Wnt signaling pathway, planar cell polarity pathway (GO:0060071)	mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|receptor activity (GO:0004872)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II transcription cofactor activity (GO:0001104)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)	p.T1555T(2)		breast(6)|central_nervous_system(2)|endometrium(22)|kidney(5)|large_intestine(8)|lung(31)|ovary(2)|pancreas(1)|prostate(11)|skin(5)|soft_tissue(323)|upper_aerodigestive_tract(1)|urinary_tract(3)	420	Renal(35;0.156)					AGCAGACCACGGAGTGGGCCA	0.592			"""M, S"""		uterine leiomyoma		Opitz-Kaveggia Syndrome																														p.T1555T		Atlas-SNP	.		Dom	yes		X	Xq13	9968	mediator complex subunit 12	Yes	M	.	MED12	984	.	2	Substitution - coding silent(2)	endometrium(2)	c.G4665A						PASS	.			0,3706		0,0,1571,564	40.0	38.0	39.0		4665	-8.9	0.5	X		39	1,6607		0,1,2401,1804	no	coding-synonymous	MED12	NM_005120.2		0,1,3972,2368	AA,AG,GG,G		0.0151,0.0,0.0097		1555/2178	70354254	1,10313	2135	4206	6341	SO:0001819	synonymous_variant	9968	exon34			GACCACGGAGTGG	U80742	CCDS43970.1	Xq13	2011-02-14	2007-07-30	2004-11-26	ENSG00000184634	ENSG00000184634			11957	protein-coding gene	gene with protein product		300188	"""trinucleotide repeat containing 11 (THR-associated protein, 230kDa subunit)"", ""mediator of RNA polymerase II transcription, subunit 12 homolog (S. cerevisiae)"", ""FG syndrome 1"""	TNRC11, FGS1		9225980, 10198638, 17334363, 20507344	Standard	NM_005120		Approved	CAGH45, HOPA, OPA1, TRAP230, KIAA0192, OKS	uc004dyy.3	Q93074	OTTHUMG00000021788	ENST00000374080.3:c.4665G>A	X.37:g.70354254G>A		166.0	0.0	0		92.0	92.0	1	NM_005120	O15410|O75557|Q9UHV6|Q9UND7	Silent	SNP	ENST00000374080.3	37	CCDS43970.1																																																																																			.	.	weak		0.592	MED12-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000057105.1	NM_005120	
ABCA7	10347	hgsc.bcm.edu	37	19	1062285	1062285	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1062285C>T	ENST00000263094.6	+	42	5916	c.5685C>T	c.(5683-5685)cgC>cgT	p.R1895R	ABCA7_ENST00000433129.1_Silent_p.R1895R|ABCA7_ENST00000435683.2_Silent_p.R1757R	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1895	ABC transporter 2. {ECO:0000255|PROSITE- ProRule:PRU00434}.				apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CGCGCCTGCGCGGTGTCCCGG	0.677																																					p.R1895R		Atlas-SNP	.											.	ABCA7	174	.	0			c.C5685T						PASS	.						84.0	91.0	89.0					19																	1062285		2203	4296	6499	SO:0001819	synonymous_variant	10347	exon42			CCTGCGCGGTGTC	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.5685C>T	19.37:g.1062285C>T		60.0	0.0	0		52.0	10.0	0.192308	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Silent	SNP	ENST00000263094.6	37	CCDS12055.1																																																																																			.	.	none		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
ADAR	103	hgsc.bcm.edu	37	1	154560614	154560614	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:154560614G>A	ENST00000368474.4	-	11	3205	c.3006C>T	c.(3004-3006)acC>acT	p.T1002T	ADAR_ENST00000292205.5_Silent_p.T1045T|ADAR_ENST00000368471.3_Silent_p.T707T	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	1002	A to I editase. {ECO:0000255|PROSITE- ProRule:PRU00240}.				adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		TCTCCACCTTGGTGCGGAGCT	0.552																																					p.T1002T		Atlas-SNP	.											.	ADAR	113	.	0			c.C3006T						PASS	.						256.0	231.0	239.0					1																	154560614		2203	4300	6503	SO:0001819	synonymous_variant	103	exon11			CACCTTGGTGCGG	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.3006C>T	1.37:g.154560614G>A		72.0	0.0	0		90.0	39.0	0.433333	NM_001111	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Silent	SNP	ENST00000368474.4	37	CCDS1071.1																																																																																			.	.	none		0.552	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
IZUMO1	284359	hgsc.bcm.edu	37	19	49244260	49244260	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:49244260C>T	ENST00000332955.2	-	10	1505	c.958G>A	c.(958-960)Gat>Aat	p.D320N	RASIP1_ENST00000222145.4_5'Flank|RASIP1_ENST00000594232.1_5'Flank	NM_182575.2	NP_872381.2	Q8IYV9	IZUM1_HUMAN	izumo sperm-egg fusion 1	320					cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	acrosomal membrane (GO:0002080)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			endometrium(4)|kidney(3)|large_intestine(4)|lung(2)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	17		all_lung(116;0.000156)|Lung NSC(112;0.000251)|all_epithelial(76;0.000761)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000134)|all cancers(93;0.000348)|Epithelial(262;0.019)|GBM - Glioblastoma multiforme(486;0.022)		TTGATGAAATCGATCACCTTC	0.517																																					p.D320N		Atlas-SNP	.											.	IZUMO1	30	.	0			c.G958A						PASS	.						118.0	104.0	109.0					19																	49244260		2203	4300	6503	SO:0001583	missense	284359	exon10			TGAAATCGATCAC	BC034769	CCDS12732.1	19q13.33	2014-07-23			ENSG00000182264	ENSG00000182264		"""-"""	28539	protein-coding gene	gene with protein product	"""oocyte binding/fusion factor"""	609278				15759005, 18952059, 19658160, 22957301	Standard	NM_182575		Approved	IZUMO, MGC34799, OBF	uc002pkj.3	Q8IYV9	OTTHUMG00000183324	ENST00000332955.2:c.958G>A	19.37:g.49244260C>T	ENSP00000327786:p.Asp320Asn	79.0	0.0	0		94.0	4.0	0.0425532	NM_182575	Q6Q8P6|Q6Q8P7	Missense_Mutation	SNP	ENST00000332955.2	37	CCDS12732.1	.	.	.	.	.	.	.	.	.	.	C	9.996	1.232155	0.22626	.	.	ENSG00000182264	ENST00000332955	T	0.26660	1.72	3.11	-1.93	0.07594	.	3.286190	0.01067	N	0.004759	T	0.12860	0.0312	N	0.19112	0.55	0.09310	N	1	B	0.28470	0.213	B	0.15870	0.014	T	0.08351	-1.0726	10	0.12430	T	0.62	0.0495	3.5485	0.07837	0.0:0.4402:0.1948:0.365	.	320	Q8IYV9	IZUM1_HUMAN	N	320	ENSP00000327786:D320N	ENSP00000327786:D320N	D	-	1	0	IZUMO1	53936072	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	-0.629000	0.05508	-0.218000	0.10018	-0.150000	0.13652	GAT	.	.	none		0.517	IZUMO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466189.1	NM_182575	
FAM209B	388799	hgsc.bcm.edu	37	20	55108508	55108508	+	Silent	SNP	G	G	A	rs150517677|rs386815438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:55108508G>A	ENST00000371325.1	+	1	207	c.111G>A	c.(109-111)ccG>ccA	p.P37P		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	37				PC -> QY (in Ref. 2; AAI05793). {ECO:0000305}.		integral component of membrane (GO:0016021)|nucleus (GO:0005634)											GGAAGGTGCCGTGTGGAGAGC	0.537													G|||	51	0.0101837	0.003	0.0086	5008	,	,		20351	0.003		0.0099	False		,,,				2504	0.0286				p.P37P		Atlas-SNP	.											.	.	.	.	0			c.G111A						PASS	.						169.0	142.0	151.0					20																	55108508		2203	4286	6489	SO:0001819	synonymous_variant	388799	exon1			GGTGCCGTGTGGA	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.111G>A	20.37:g.55108508G>A		294.0	0.0	0		181.0	26.0	0.143646	NM_001013646	Q3KRB5	Silent	SNP	ENST00000371325.1	37	CCDS33494.1																																																																																			G|0.985;A|0.015	0.015	strong		0.537	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
TTC37	9652	hgsc.bcm.edu	37	5	94882781	94882781	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:94882781G>A	ENST00000358746.2	-	4	372	c.74C>T	c.(73-75)gCt>gTt	p.A25V		NM_014639.3	NP_055454.1	Q6PGP7	TTC37_HUMAN	tetratricopeptide repeat domain 37	25						cytoplasm (GO:0005737)|nucleus (GO:0005634)|Ski complex (GO:0055087)|transcriptionally active chromatin (GO:0035327)				breast(2)|endometrium(6)|kidney(3)|large_intestine(13)|liver(1)|lung(15)|ovary(4)|pancreas(1)|prostate(1)|skin(1)	47						GTGTTTCAAAGCTTCTTTGTA	0.338																																					p.A25V		Atlas-SNP	.											.	TTC37	128	.	0			c.C74T						PASS	.						178.0	180.0	179.0					5																	94882781		2203	4300	6503	SO:0001583	missense	9652	exon4			TTCAAAGCTTCTT	AB002370	CCDS4072.1	5q15	2014-09-17	2008-06-11	2008-06-11	ENSG00000198677	ENSG00000198677		"""Tetratricopeptide (TTC) repeat domain containing"""	23639	protein-coding gene	gene with protein product		614589	"""KIAA0372"""	KIAA0372		9205841	Standard	NM_014639		Approved		uc003klb.3	Q6PGP7	OTTHUMG00000121165	ENST00000358746.2:c.74C>T	5.37:g.94882781G>A	ENSP00000351596:p.Ala25Val	103.0	0.0	0		84.0	35.0	0.416667	NM_014639	O15077|Q6PJI3	Missense_Mutation	SNP	ENST00000358746.2	37	CCDS4072.1	.	.	.	.	.	.	.	.	.	.	G	16.59	3.165839	0.57476	.	.	ENSG00000198677	ENST00000358746;ENST00000514952;ENST00000513823	D;T;D	0.83591	-1.74;-0.69;-1.74	5.38	4.5	0.54988	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.064313	0.64402	N	0.000008	T	0.81983	0.4938	M	0.67953	2.075	0.51767	D	0.999938	B;B	0.20887	0.032;0.049	B;B	0.31390	0.016;0.129	T	0.78758	-0.2079	10	0.49607	T	0.09	.	10.6469	0.45626	0.1497:0.0:0.8503:0.0	.	25;25	D6RCE2;Q6PGP7	.;TTC37_HUMAN	V	25	ENSP00000351596:A25V;ENSP00000423742:A25V;ENSP00000425403:A25V	ENSP00000351596:A25V	A	-	2	0	TTC37	94908537	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	5.086000	0.64474	1.235000	0.43724	0.591000	0.81541	GCT	.	.	none		0.338	TTC37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241651.1	NM_014639	
OR2AK2	391191	hgsc.bcm.edu	37	1	248129304	248129304	+	Missense_Mutation	SNP	T	T	C	rs143777155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248129304T>C	ENST00000366480.3	+	1	770	c.671T>C	c.(670-672)cTa>cCa	p.L224P	OR2L13_ENST00000366478.2_Intron	NM_001004491.1	NP_001004491.1	Q8NG84	O2AK2_HUMAN	olfactory receptor, family 2, subfamily AK, member 2	224						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	36	all_cancers(71;0.000139)|all_epithelial(71;1.58e-05)|Breast(184;0.0117)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0152)			ATCTTGCTACTACCATTCCTA	0.453													.|||	8	0.00159744	0.0	0.0029	5008	,	,		20749	0.0		0.003	False		,,,				2504	0.0031				p.L224P	Melanoma(45;390 1181 23848 28461 41504)	Atlas-SNP	.											.	OR2AK2	90	.	0			c.T671C						PASS	.	T	PRO/LEU,	2,4404		0,2,2201	92.0	80.0	84.0		671,	1.3	0.0	1	dbSNP_134	84	11,8589		0,11,4289	yes	missense,intron	OR2L13,OR2AK2	NM_001004491.1,NM_175911.2	98,	0,13,6490	CC,CT,TT		0.1279,0.0454,0.1	probably-damaging,	224/336,	248129304	13,12993	2203	4300	6503	SO:0001583	missense	391191	exon1			TGCTACTACCATT	BK004457	CCDS31102.1	1q44	2012-08-09			ENSG00000187080	ENSG00000187080		"""GPCR / Class A : Olfactory receptors"""	19569	protein-coding gene	gene with protein product				OR2AK1P			Standard	NM_001004491		Approved		uc010pzd.2	Q8NG84	OTTHUMG00000040201	ENST00000366480.3:c.671T>C	1.37:g.248129304T>C	ENSP00000355436:p.Leu224Pro	179.0	0.0	0		150.0	77.0	0.513333	NM_001004491	B2RND1|Q6IF05	Missense_Mutation	SNP	ENST00000366480.3	37	CCDS31102.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	.	10.89	1.477945	0.26511	4.54E-4	0.001279	ENSG00000187080	ENST00000366480	T	0.45668	0.89	2.48	1.33	0.21861	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.52041	0.1710	L	0.50847	1.595	0.09310	N	0.999995	D	0.89917	1.0	D	0.79108	0.992	T	0.31724	-0.9933	9	0.56958	D	0.05	.	5.7206	0.17985	0.0:0.1483:0.0:0.8517	.	224	Q8NG84	O2AK2_HUMAN	P	224	ENSP00000355436:L224P	ENSP00000355436:L224P	L	+	2	0	OR2AK2	246195927	0.000000	0.05858	0.005000	0.12908	0.130000	0.20726	-0.642000	0.05427	0.372000	0.24591	0.379000	0.24179	CTA	T|0.998;C|0.002	0.002	strong		0.453	OR2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096858.2	NM_001004491	
BICD1	636	hgsc.bcm.edu	37	12	32458756	32458756	+	Silent	SNP	C	C	T	rs11051922	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32458756C>T	ENST00000281474.5	+	4	808	c.705C>T	c.(703-705)ctC>ctT	p.L235L	BICD1_ENST00000548411.1_Silent_p.L235L	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	235					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AAGAAGCCCTCGAGACTTTAA	0.458													C|||	28	0.00559105	0.0008	0.0058	5008	,	,		16322	0.0		0.0189	False		,,,				2504	0.0041				p.L235L		Atlas-SNP	.											.	BICD1	89	.	0			c.C705T						PASS	.	C	,	19,4387	26.2+/-53.5	0,19,2184	63.0	60.0	61.0		705,705	-8.6	0.0	12	dbSNP_120	61	204,8396	87.9+/-150.2	5,194,4101	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	5,213,6285	TT,TC,CC		2.3721,0.4312,1.7146	,	235/836,235/976	32458756	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	636	exon4			AGCCCTCGAGACT	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.705C>T	12.37:g.32458756C>T		69.0	0.0	0		52.0	28.0	0.538462	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			C|0.988;T|0.012	0.012	strong		0.458	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
GPR152	390212	hgsc.bcm.edu	37	11	67218787	67218787	+	Missense_Mutation	SNP	G	G	A	rs137906019		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:67218787G>A	ENST00000312457.2	-	1	1413	c.1409C>T	c.(1408-1410)aCg>aTg	p.T470M	CABP4_ENST00000438189.2_5'Flank	NM_206997.1	NP_996880.1	Q8TDT2	GP152_HUMAN	G protein-coupled receptor 152	470						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	16			BRCA - Breast invasive adenocarcinoma(15;8.18e-06)			GGACCCTCACGTGGGGCCTGC	0.687													G|||	1	0.000199681	0.0008	0.0	5008	,	,		13832	0.0		0.0	False		,,,				2504	0.0				p.T470M	Pancreas(102;800 1581 2723 7382 33622)	Atlas-SNP	.											.	GPR152	41	.	0			c.C1409T						PASS	.	G	MET/THR	0,4364		0,0,2182	28.0	38.0	35.0		1409	2.4	0.5	11	dbSNP_134	35	18,8506		0,18,4244	yes	missense	GPR152	NM_206997.1	81	0,18,6426	AA,AG,GG		0.2112,0.0,0.1397	benign	470/471	67218787	18,12870	2182	4262	6444	SO:0001583	missense	390212	exon1			CCTCACGTGGGGC	AY255600	CCDS8165.1	11q13.2	2013-09-20			ENSG00000175514	ENSG00000175514		"""GPCR / Class A : Orphans"""	23622	protein-coding gene	gene with protein product						12679517	Standard	NM_206997		Approved	PGR5	uc001olm.3	Q8TDT2	OTTHUMG00000168032	ENST00000312457.2:c.1409C>T	11.37:g.67218787G>A	ENSP00000310255:p.Thr470Met	45.0	0.0	0		52.0	30.0	0.576923	NM_206997	Q0VD88|Q86SM0	Missense_Mutation	SNP	ENST00000312457.2	37	CCDS8165.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	12.15	1.853057	0.32699	0.0	0.002112	ENSG00000175514	ENST00000312457	T	0.19938	2.11	4.28	2.37	0.29283	.	0.439888	0.16902	N	0.194879	T	0.13756	0.0333	L	0.29908	0.895	0.20489	N	0.999897	B	0.17038	0.02	B	0.12156	0.007	T	0.21827	-1.0234	10	0.87932	D	0	.	5.1949	0.15232	0.1064:0.0:0.6923:0.2012	.	470	Q8TDT2	GP152_HUMAN	M	470	ENSP00000310255:T470M	ENSP00000310255:T470M	T	-	2	0	GPR152	66975363	0.706000	0.27856	0.469000	0.27204	0.026000	0.11368	0.692000	0.25482	0.423000	0.26033	-0.226000	0.12346	ACG	G|0.998;A|0.002	0.002	strong		0.687	GPR152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397623.1		
MEST	4232	hgsc.bcm.edu	37	7	130140729	130140729	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:130140729C>T	ENST00000223215.4	+	9	968	c.747C>T	c.(745-747)gaC>gaT	p.D249D	MEST_ENST00000341441.5_Silent_p.D240D|MEST_ENST00000378576.4_Intron|MEST_ENST00000393187.1_Silent_p.D240D|MEST_ENST00000416162.2_Intron|MEST_ENST00000462132.1_3'UTR|MEST_ENST00000437945.1_Silent_p.D249D|hsa-mir-335_ENST00000604666.1_RNA	NM_001253900.1|NM_002402.3	NP_001240829.1|NP_002393.2	Q5EB52	MEST_HUMAN	mesoderm specific transcript	249					mesoderm development (GO:0007498)|regulation of lipid storage (GO:0010883)|response to retinoic acid (GO:0032526)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			breast(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(2)	12	Melanoma(18;0.0435)					TAGTCATTGACAGGTAAGAAG	0.512																																					p.D249D	Colon(126;2182 2305 6517 35181)	Atlas-SNP	.											.	MEST	28	.	0			c.C747T						PASS	.						98.0	78.0	85.0					7																	130140729		2203	4300	6503	SO:0001819	synonymous_variant	4232	exon9			CATTGACAGGTAA		CCDS5822.1, CCDS5823.1, CCDS59081.1	7q32	2014-08-22	2012-12-07		ENSG00000106484	ENSG00000106484			7028	protein-coding gene	gene with protein product	"""Paternally-expressed gene 1"""	601029	"""mesoderm specific transcript (mouse) homolog"", ""mesoderm specific transcript homolog (mouse)"""			8884280	Standard	NM_002402		Approved	PEG1	uc003vqg.3	Q5EB52	OTTHUMG00000156661	ENST00000223215.4:c.747C>T	7.37:g.130140729C>T		79.0	0.0	0		95.0	46.0	0.484211	NM_002402	B2R6S1|O14973|O15007|Q6AI49|Q92571	Silent	SNP	ENST00000223215.4	37	CCDS5822.1																																																																																			.	.	none		0.512	MEST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345183.2	NM_002402	
TPO	7173	hgsc.bcm.edu	37	2	1418210	1418210	+	Silent	SNP	G	G	A	rs28909989	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:1418210G>A	ENST00000345913.4	+	2	121	c.30G>A	c.(28-30)acG>acA	p.T10T	TPO_ENST00000337415.3_Silent_p.T10T|TPO_ENST00000382198.1_Silent_p.T10T|TPO_ENST00000346956.3_Silent_p.T10T|TPO_ENST00000329066.4_Silent_p.T10T|TPO_ENST00000539820.1_Silent_p.T10T|TPO_ENST00000382269.3_Silent_p.T10T|TPO_ENST00000497517.2_Intron|TPO_ENST00000349624.3_Silent_p.T10T|TPO_ENST00000382201.3_Silent_p.T10T	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	10					cellular nitrogen compound metabolic process (GO:0034641)|embryonic hemopoiesis (GO:0035162)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|small molecule metabolic process (GO:0044281)|thyroid hormone generation (GO:0006590)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|iodide peroxidase activity (GO:0004447)|peroxidase activity (GO:0004601)			breast(1)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(14)|liver(2)|lung(33)|ovary(8)|pancreas(6)|prostate(4)|skin(7)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	95	all_hematologic(175;0.0487)|Acute lymphoblastic leukemia(172;0.0627)	all_cancers(51;0.0338)		all cancers(51;0.0356)|OV - Ovarian serous cystadenocarcinoma(76;0.0748)|Epithelial(75;0.12)	Carbimazole(DB00389)|Dextrothyroxine(DB00509)|Methimazole(DB00763)|Propylthiouracil(DB00550)	TGTCTGTCACGCTGGTTATGG	0.498													G|||	9	0.00179712	0.0008	0.0	5008	,	,		17467	0.0		0.007	False		,,,				2504	0.001				p.T10T		Atlas-SNP	.											TPO,NS,carcinoma,+1,1	TPO	224	1	0			c.G30A						scavenged	.	G	,,,,,	6,4400	11.4+/-27.6	0,6,2197	87.0	81.0	83.0		30,30,30,30,30,30	-9.9	0.0	2	dbSNP_125	83	50,8550	32.3+/-84.9	0,50,4250	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TPO	NM_000547.5,NM_001206744.1,NM_001206745.1,NM_175719.3,NM_175721.3,NM_175722.3	,,,,,	0,56,6447	AA,AG,GG		0.5814,0.1362,0.4306	,,,,,	10/934,10/934,10/877,10/877,10/890,10/761	1418210	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	7173	exon2			TGTCACGCTGGTT		CCDS1643.1, CCDS1644.1, CCDS1646.1	2p25	2008-02-05			ENSG00000115705	ENSG00000115705	1.11.1.7		12015	protein-coding gene	gene with protein product		606765					Standard	NM_175722		Approved	TPX	uc002qww.3	P07202	OTTHUMG00000090271	ENST00000345913.4:c.30G>A	2.37:g.1418210G>A		184.0	1.0	0.00543478		141.0	53.0	0.375887	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Silent	SNP	ENST00000345913.4	37	CCDS1643.1																																																																																			G|0.996;A|0.004	0.004	strong		0.498	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
FAM222A	84915	hgsc.bcm.edu	37	12	110206760	110206760	+	Silent	SNP	C	C	A	rs79456911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:110206760C>A	ENST00000538780.1	+	3	1742	c.1026C>A	c.(1024-1026)ggC>ggA	p.G342G	FAM222A-AS1_ENST00000541723.1_RNA|FAM222A-AS1_ENST00000541460.1_RNA|FAM222A_ENST00000358906.3_Silent_p.G342G	NM_032829.2	NP_116218.2	Q5U5X8	F222A_HUMAN	family with sequence similarity 222, member A	342																	TCACCGTAGGCCAGTACTTTG	0.701													C|||	29	0.00579073	0.0015	0.0043	5008	,	,		14090	0.0		0.0149	False		,,,				2504	0.0092				p.G342G		Atlas-SNP	.											.	.	.	.	0			c.C1026A						PASS	.	C		12,4352		0,12,2170	14.0	13.0	13.0		1026	0.1	1.0	12	dbSNP_131	13	56,8518		0,56,4231	no	coding-synonymous	C12orf34	NM_032829.2		0,68,6401	AA,AC,CC		0.6531,0.275,0.5256		342/453	110206760	68,12870	2182	4287	6469	SO:0001819	synonymous_variant	84915	exon3			CGTAGGCCAGTAC	AK027627	CCDS9133.1	12q24.11	2012-04-27	2012-04-27	2012-04-27	ENSG00000139438	ENSG00000139438			25915	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 34"""	C12orf34		12477932	Standard	NM_032829		Approved	FLJ14721	uc001tpd.2	Q5U5X8	OTTHUMG00000169260	ENST00000538780.1:c.1026C>A	12.37:g.110206760C>A		20.0	0.0	0		21.0	10.0	0.47619	NM_032829	Q8NCD5|Q96SP6	Silent	SNP	ENST00000538780.1	37	CCDS9133.1																																																																																			C|0.994;A|0.006	0.006	strong		0.701	FAM222A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403175.1	NM_032829	
ATP12A	479	hgsc.bcm.edu	37	13	25267017	25267017	+	Missense_Mutation	SNP	A	A	C	rs56291145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25267017A>C	ENST00000381946.3	+	10	1527	c.1360A>C	c.(1360-1362)Aat>Cat	p.N454H	ATP12A_ENST00000218548.6_Missense_Mutation_p.N460H			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	454					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		AGGACAGGAAAATGTCCCCAT	0.453													A|||	74	0.0147764	0.0023	0.0187	5008	,	,		21024	0.001		0.0388	False		,,,				2504	0.0184				p.N460H	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.A1378C						PASS	.	A	HIS/ASN,HIS/ASN	25,4381	33.5+/-64.1	0,25,2178	157.0	145.0	149.0		1378,1360	5.7	0.1	13	dbSNP_129	149	332,8268	116.6+/-176.3	5,322,3973	yes	missense,missense	ATP12A	NM_001185085.1,NM_001676.5	68,68	5,347,6151	CC,CA,AA		3.8605,0.5674,2.7449	benign,benign	460/1046,454/1040	25267017	357,12649	2203	4300	6503	SO:0001583	missense	479	exon10			CAGGAAAATGTCC	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.1360A>C	13.37:g.25267017A>C	ENSP00000371372:p.Asn454His	84.0	0.0	0		69.0	28.0	0.405797	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Missense_Mutation	SNP	ENST00000381946.3	37	CCDS31948.1	42	0.019230769230769232	3	0.006097560975609756	6	0.016574585635359115	1	0.0017482517482517483	32	0.04221635883905013	A	10.05	1.245297	0.22796	0.005674	0.038605	ENSG00000075673	ENST00000218548;ENST00000381946	T;T	0.80123	-1.34;-1.34	5.65	5.65	0.86999	ATPase, cation-transporting, domain N (1);Haloacid dehalogenase-like hydrolase (1);HAD-like domain (1);ATPase, P-type, cytoplasmic domain N (1);	0.486738	0.23874	N	0.043705	T	0.36963	0.0986	N	0.13198	0.31	0.09310	N	1	B;B	0.30889	0.242;0.299	B;B	0.38156	0.197;0.266	T	0.52472	-0.8571	10	0.40728	T	0.16	.	8.3857	0.32499	0.9132:0.0:0.0868:0.0	rs56291145;rs61729900	460;454	P54707-2;P54707	.;AT12A_HUMAN	H	460;454	ENSP00000218548:N460H;ENSP00000371372:N454H	ENSP00000218548:N460H	N	+	1	0	ATP12A	24165017	0.002000	0.14202	0.133000	0.22050	0.757000	0.42996	1.843000	0.39259	2.154000	0.67381	0.533000	0.62120	AAT	A|0.975;C|0.025	0.025	strong		0.453	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
KIF26B	55083	hgsc.bcm.edu	37	1	245772651	245772651	+	Missense_Mutation	SNP	C	C	G	rs61754955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:245772651C>G	ENST00000407071.2	+	8	2175	c.1735C>G	c.(1735-1737)Ctc>Gtc	p.L579V	KIF26B_ENST00000366518.4_Missense_Mutation_p.L198V	NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	579	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCTCTTCAAGCTCATAAACGA	0.552													C|||	107	0.0213658	0.0053	0.0648	5008	,	,		17935	0.0278		0.0149	False		,,,				2504	0.0123				p.L579V		Atlas-SNP	.											.	KIF26B	343	.	0			c.C1735G						PASS	.	C	VAL/LEU	28,3818		0,28,1895	38.0	38.0	38.0		1735	5.2	1.0	1	dbSNP_129	38	154,8102		2,150,3976	yes	missense	KIF26B	NM_018012.3	32	2,178,5871	GG,GC,CC		1.8653,0.728,1.5039	probably-damaging	579/2109	245772651	182,11920	1923	4128	6051	SO:0001583	missense	55083	exon8			TTCAAGCTCATAA	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.1735C>G	1.37:g.245772651C>G	ENSP00000385545:p.Leu579Val	203.0	0.0	0		225.0	105.0	0.466667	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	37	CCDS44342.1	54	0.024725274725274724	5	0.01016260162601626	20	0.055248618784530384	14	0.024475524475524476	15	0.01978891820580475	C	16.22	3.060277	0.55432	0.00728	0.018653	ENSG00000162849	ENST00000407071;ENST00000366518;ENST00000413001	T;T	0.74947	-0.89;-0.89	5.22	5.22	0.72569	Kinesin, motor domain (4);	.	.	.	.	T	0.37073	0.0990	L	0.52759	1.655	0.58432	D	0.999999	P;P	0.47191	0.891;0.877	P;P	0.59948	0.866;0.809	T	0.65751	-0.6092	9	0.56958	D	0.05	.	12.9655	0.58481	0.0:0.915:0.0:0.085	rs61754955	198;579	B7WPD9;Q2KJY2	.;KI26B_HUMAN	V	579;198;195	ENSP00000385545:L579V;ENSP00000355475:L198V	ENSP00000355475:L198V	L	+	1	0	KIF26B	243839274	1.000000	0.71417	0.991000	0.47740	0.947000	0.59692	2.028000	0.41088	2.590000	0.87494	0.650000	0.86243	CTC	C|0.976;G|0.024	0.024	strong		0.552	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
BRIP1	83990	hgsc.bcm.edu	37	17	59761336	59761336	+	Missense_Mutation	SNP	C	C	A	rs587781744		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:59761336C>A	ENST00000259008.2	-	20	3338	c.3071G>T	c.(3070-3072)gGg>gTg	p.G1024V		NM_032043.2	NP_114432.2	Q9BX63	FANCJ_HUMAN	BRCA1 interacting protein C-terminal helicase 1	1024	Interaction with BRCA1.				DNA damage checkpoint (GO:0000077)|DNA duplex unwinding (GO:0032508)|double-strand break repair (GO:0006302)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(9)|kidney(5)|large_intestine(9)|liver(2)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	55						CTCTGATGACCCGAGCTCAGG	0.403			"""F, N, Mis"""			"""AML, leukemia, breast"""		Involved in tolerance or repair of DNA crosslinks																													p.G1024V		Atlas-SNP	.	yes	Rec		"""Fanconi anaemia J, breast cancer susceptiblity"""	17	17q22	83990	BRCA1 interacting protein C-terminal helicase 1		"""L, E"""	BRIP1_ENST00000259008,NS,carcinoma,-1,4	BRIP1	237	4	0			c.G3071T						scavenged	.						114.0	109.0	110.0					17																	59761336		2203	4300	6503	SO:0001583	missense	83990	exon20			GATGACCCGAGCT	AF360549	CCDS11631.1	17q22.2	2014-09-17				ENSG00000136492		"""Fanconi anemia, complementation groups"""	20473	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-associated helicase 1"""	605882				11595410, 11301010	Standard	NM_032043		Approved	OF, BACH1, FANCJ	uc002izk.2	Q9BX63		ENST00000259008.2:c.3071G>T	17.37:g.59761336C>A	ENSP00000259008:p.Gly1024Val	111.0	1.0	0.00900901		128.0	58.0	0.453125	NM_032043	Q3MJE2|Q8NCI5	Missense_Mutation	SNP	ENST00000259008.2	37	CCDS11631.1	.	.	.	.	.	.	.	.	.	.	C	2.733	-0.263935	0.05754	.	.	ENSG00000136492	ENST00000259008	T	0.73681	-0.77	5.33	2.23	0.28157	.	1.080930	0.06971	N	0.818190	T	0.56673	0.2001	N	0.14661	0.345	0.09310	N	1	B	0.14438	0.01	B	0.17722	0.019	T	0.40720	-0.9548	9	.	.	.	-0.8307	7.1819	0.25778	0.0:0.7123:0.0:0.2877	.	1024	Q9BX63	FANCJ_HUMAN	V	1024	ENSP00000259008:G1024V	.	G	-	2	0	BRIP1	57116118	0.000000	0.05858	0.016000	0.15963	0.065000	0.16274	-0.987000	0.03743	0.316000	0.23135	-0.145000	0.13849	GGG	.	.	none		0.403	BRIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445362.1	NM_032043	
MAP3K1	4214	hgsc.bcm.edu	37	5	56155672	56155672	+	Missense_Mutation	SNP	A	A	G	rs56069227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:56155672A>G	ENST00000399503.3	+	3	764	c.764A>G	c.(763-765)aAc>aGc	p.N255S	snoU13_ENST00000459264.1_RNA|AC008937.2_ENST00000415589.1_RNA	NM_005921.1	NP_005912.1	Q13233	M3K1_HUMAN	mitogen-activated protein kinase kinase kinase 1, E3 ubiquitin protein ligase	255					activation of MAPKK activity (GO:0000186)|apoptotic mitochondrial changes (GO:0008637)|cellular response to mechanical stimulus (GO:0071260)|epithelial cell morphogenesis (GO:0003382)|eyelid development in camera-type eye (GO:0061029)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of actin filament polymerization (GO:0030838)|protein phosphorylation (GO:0006468)|regulation of cell migration (GO:0030334)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	cytosol (GO:0005829)	ATP binding (GO:0005524)|JUN kinase kinase activity (GO:0008545)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			NS(1)|breast(19)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(11)|ovary(1)|skin(3)|urinary_tract(1)	57		Lung NSC(810;4.65e-05)|Prostate(74;0.0132)|Breast(144;0.0321)|Ovarian(174;0.223)		OV - Ovarian serous cystadenocarcinoma(10;6.08e-40)		TCTCCTGGCAACTCCCCATCA	0.488													A|||	83	0.0165735	0.025	0.0216	5008	,	,		15055	0.0		0.0338	False		,,,				2504	0.001				p.N255S		Atlas-SNP	.											.	MAP3K1	355	.	0			c.A764G						PASS	.	A	SER/ASN	79,3755		1,77,1839	42.0	42.0	42.0		764	3.9	0.9	5	dbSNP_129	42	229,8029		5,219,3905	yes	missense	MAP3K1	NM_005921.1	46	6,296,5744	GG,GA,AA		2.7731,2.0605,2.5471	benign	255/1513	56155672	308,11784	1917	4129	6046	SO:0001583	missense	4214	exon3			CTGGCAACTCCCC	U29671, AF042838	CCDS43318.1	5q11.2	2012-02-23	2012-02-23		ENSG00000095015	ENSG00000095015		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6848	protein-coding gene	gene with protein product		600982	"""mitogen-activated protein kinase kinase kinase 1"""	MEKK1		8597633	Standard	NM_005921		Approved	MEKK, MAPKKK1	uc003jqw.4	Q13233	OTTHUMG00000059486	ENST00000399503.3:c.764A>G	5.37:g.56155672A>G	ENSP00000382423:p.Asn255Ser	217.0	0.0	0		229.0	116.0	0.50655	NM_005921		Missense_Mutation	SNP	ENST00000399503.3	37	CCDS43318.1	40	0.018315018315018316	6	0.012195121951219513	9	0.024861878453038673	0	0.0	25	0.032981530343007916	A	13.57	2.277282	0.40294	0.020605	0.027731	ENSG00000095015	ENST00000399503	T	0.63255	-0.03	5.72	3.93	0.45458	.	0.316826	0.39544	N	0.001335	T	0.10465	0.0256	N	0.01352	-0.895	0.26121	N	0.98055	B	0.02656	0.0	B	0.01281	0.0	T	0.14448	-1.0472	10	0.02654	T	1	.	11.7667	0.51935	0.1441:0.0:0.8559:0.0	rs56069227;rs61736548	255	Q13233	M3K1_HUMAN	S	255	ENSP00000382423:N255S	ENSP00000382423:N255S	N	+	2	0	MAP3K1	56191429	1.000000	0.71417	0.938000	0.37757	0.734000	0.41952	3.001000	0.49488	0.871000	0.35750	-0.242000	0.12053	AAC	A|0.976;G|0.024	0.024	strong		0.488	MAP3K1-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000132309.2	XM_042066	
C1QB	713	hgsc.bcm.edu	37	1	22987744	22987744	+	Silent	SNP	C	C	T	rs149718049	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:22987744C>T	ENST00000314933.6	+	3	759	c.627C>T	c.(625-627)acC>acT	p.T209T	C1QB_ENST00000509305.1_Silent_p.T207T	NM_000491.3	NP_000482.3	P02746	C1QB_HUMAN	complement component 1, q subcomponent, B chain	209	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|inner ear development (GO:0048839)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|complement component C1 complex (GO:0005602)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(2)|large_intestine(1)|lung(9)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;6.55e-05)|all_lung(284;9.87e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0227)|OV - Ovarian serous cystadenocarcinoma(117;7.06e-27)|Colorectal(126;1.58e-07)|GBM - Glioblastoma multiforme(114;6.72e-06)|COAD - Colon adenocarcinoma(152;1.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000551)|KIRC - Kidney renal clear cell carcinoma(1967;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.198)	Abciximab(DB00054)|Adalimumab(DB00051)|Alefacept(DB00092)|Alemtuzumab(DB00087)|Basiliximab(DB00074)|Bevacizumab(DB00112)|Cetuximab(DB00002)|Daclizumab(DB00111)|Efalizumab(DB00095)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Natalizumab(DB00108)|Palivizumab(DB00110)|Rituximab(DB00073)|Tositumomab(DB00081)|Trastuzumab(DB00072)	AGGTCACCACCGGTGGCATGG	0.587																																					p.T209T		Atlas-SNP	.											.	C1QB	40	.	0			c.C627T						PASS	.	C		0,4406		0,0,2203	60.0	55.0	57.0		627	-6.8	0.0	1	dbSNP_134	57	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	C1QB	NM_000491.3		0,8,6495	TT,TC,CC		0.093,0.0,0.0615		209/254	22987744	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	713	exon3			CACCACCGGTGGC	X03084	CCDS228.1	1p36.3-p34.1	2014-09-17	2006-02-09		ENSG00000173369	ENSG00000173369		"""Complement system"""	1242	protein-coding gene	gene with protein product		120570	"""complement component 1, q subcomponent, beta polypeptide"""			1537612	Standard	XM_005245982		Approved		uc001bgd.3	P02746	OTTHUMG00000002896	ENST00000314933.6:c.627C>T	1.37:g.22987744C>T		122.0	0.0	0		91.0	54.0	0.593407	NM_000491	Q5T959|Q96H17	Silent	SNP	ENST00000314933.6	37	CCDS228.1																																																																																			C|0.999;T|0.001	0.001	strong		0.587	C1QB-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_000491	
EYS	346007	hgsc.bcm.edu	37	6	64488001	64488001	+	Missense_Mutation	SNP	T	T	C	rs74636274	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:64488001T>C	ENST00000370621.3	-	40	8322	c.7796A>G	c.(7795-7797)cAc>cGc	p.H2599R	PHF3_ENST00000420043.1_3'UTR|EYS_ENST00000370616.2_Missense_Mutation_p.H2599R|EYS_ENST00000503581.1_Missense_Mutation_p.H2599R			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	2599	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.		H -> R (in dbSNP:rs74636274). {ECO:0000269|PubMed:20333770}.		detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						AGCATTTGGGTGGCCCTCAGG	0.473													T|||	23	0.00459265	0.0	0.0043	5008	,	,		17905	0.0		0.0109	False		,,,				2504	0.0092				p.H2599R		Atlas-SNP	.											.	EYS	527	.	0			c.A7796G						PASS	.	T	ARG/HIS	1,1383		0,1,691	100.0	82.0	88.0		7796	1.5	0.5	6	dbSNP_131	88	35,3147		0,35,1556	yes	missense	EYS	NM_001142800.1	29	0,36,2247	CC,CT,TT		1.0999,0.0723,0.7884	benign	2599/3145	64488001	36,4530	692	1591	2283	SO:0001583	missense	346007	exon40			TTTGGGTGGCCCT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.7796A>G	6.37:g.64488001T>C	ENSP00000359655:p.His2599Arg	270.0	0.0	0		250.0	114.0	0.456	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Missense_Mutation	SNP	ENST00000370621.3	37		9|9|9	0.004120879120879121|0.004120879120879121|0.004120879120879121	0|0|0	0.0|0.0|0.0	2|2|2	0.0055248618784530384|0.0055248618784530384|0.0055248618784530384	0|0|0	0.0|0.0|0.0	7|7|7	0.009234828496042216|0.009234828496042216|0.009234828496042216	T|T|T	9.321|9.321|9.321	1.057987|1.057987|1.057987	0.19987|0.19987|0.19987	7.23E-4|7.23E-4|7.23E-4	0.010999|0.010999|0.010999	ENSG00000188107|ENSG00000188107|ENSG00000118482	ENST00000503581;ENST00000370621;ENST00000370616|ENST00000398580|ENST00000505138	D;T;T|.|.	0.81659|.|.	-1.52;-1.49;-1.49|.|.	4.02|4.02|4.02	1.47|1.47|1.47	0.22746|0.22746|0.22746	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);|.|.	0.285145|.|.	0.21597|.|.	N|.|.	0.072010|.|.	T|T|T	0.14874|0.14874|0.14874	0.0359|0.0359|0.0359	N|N|N	0.11201|0.11201|0.11201	0.11|0.11|0.11	0.80722|0.80722|0.80722	D|D|D	1|1|1	B;B|.|.	0.23540|.|.	0.087;0.053|.|.	B;B|.|.	0.20384|.|.	0.029;0.013|.|.	T|T|T	0.05937|0.05937|0.05937	-1.0855|-1.0855|-1.0855	10|5|5	0.25106|.|.	T|.|.	0.35|.|.	.|.|.	7.1543|7.1543|7.1543	0.25628|0.25628|0.25628	0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133|0.0:0.1867:0.0:0.8133	.|.|.	2599;2599|.|.	Q5T1H1-1;Q5T1H1|.|.	.;EYS_HUMAN|.|.	R|A|R	2599|371|136	ENSP00000424243:H2599R;ENSP00000359655:H2599R;ENSP00000359650:H2599R|.|.	ENSP00000359650:H2599R|.|.	H|T|W	-|-|+	2|1|1	0|0|0	EYS|EYS|PHF3	64545960|64545960|64545960	1.000000|1.000000|1.000000	0.71417|0.71417|0.71417	0.475000|0.475000|0.475000	0.27278|0.27278|0.27278	0.032000|0.032000|0.032000	0.12392|0.12392|0.12392	1.000000|1.000000|1.000000	0.29770|0.29770|0.29770	0.020000|0.020000|0.020000	0.15106|0.15106|0.15106	0.533000|0.533000|0.533000	0.62120|0.62120|0.62120	CAC|ACC|TGG	T|0.996;C|0.004	0.004	strong		0.473	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
HECW1	23072	hgsc.bcm.edu	37	7	43506113	43506113	+	Silent	SNP	A	A	C	rs138489968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:43506113A>C	ENST00000395891.2	+	15	3464	c.2859A>C	c.(2857-2859)ccA>ccC	p.P953P	HECW1_ENST00000453890.1_Silent_p.P919P	NM_015052.3	NP_055867.3	Q76N89	HECW1_HUMAN	HECT, C2 and WW domain containing E3 ubiquitin protein ligase 1	953					protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(10)|central_nervous_system(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(57)|ovary(8)|pancreas(2)|prostate(2)|skin(6)|urinary_tract(3)	125						TGCAGTCCCCAGCGGTCAAGT	0.498													A|||	29	0.00579073	0.0023	0.0058	5008	,	,		15535	0.001		0.0169	False		,,,				2504	0.0041				p.P953P		Atlas-SNP	.											.	HECW1	540	.	0			c.A2859C						PASS	.	A		12,3884		0,12,1936	113.0	107.0	109.0		2859	-4.4	0.8	7	dbSNP_134	109	186,8096		2,182,3957	no	coding-synonymous	HECW1	NM_015052.3		2,194,5893	CC,CA,AA		2.2458,0.308,1.6259		953/1607	43506113	198,11980	1948	4141	6089	SO:0001819	synonymous_variant	23072	exon15			GTCCCCAGCGGTC	AB048365	CCDS5469.2, CCDS69286.1	7p13	2004-12-13			ENSG00000002746	ENSG00000002746			22195	protein-coding gene	gene with protein product		610384				12690205, 14684739	Standard	XM_005249665		Approved	KIAA0322, NEDL1	uc003tid.1	Q76N89	OTTHUMG00000128917	ENST00000395891.2:c.2859A>C	7.37:g.43506113A>C		57.0	0.0	0		72.0	36.0	0.5	NM_015052	A7E2X0|A8MYS3|B4DH42|O15036|Q9HCC7	Silent	SNP	ENST00000395891.2	37	CCDS5469.2																																																																																			A|0.990;C|0.010	0.010	strong		0.498	HECW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250893.2	NM_015052	
C19orf57	79173	hgsc.bcm.edu	37	19	14001206	14001206	+	Missense_Mutation	SNP	G	G	A	rs144502446	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:14001206G>A	ENST00000586783.1	-	5	462	c.463C>T	c.(463-465)Ctc>Ttc	p.L155F	C19orf57_ENST00000454313.1_Missense_Mutation_p.L155F|C19orf57_ENST00000346736.2_Missense_Mutation_p.L155F|C19orf57_ENST00000591586.1_Intron			Q0VDD7	CS057_HUMAN	chromosome 19 open reading frame 57	155					multicellular organismal development (GO:0007275)					breast(2)|kidney(1)|lung(3)|ovary(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;2e-21)			GCCTCCTGGAGGGGGACCCCC	0.677													G|||	14	0.00279553	0.0023	0.0014	5008	,	,		13636	0.0		0.0089	False		,,,				2504	0.001				p.L155F		Atlas-SNP	.											.	C19orf57	34	.	0			c.C463T						PASS	.	G	PHE/LEU	5,4397		0,5,2196	28.0	34.0	32.0		463	-5.3	0.0	19	dbSNP_134	32	55,8527		0,55,4236	yes	missense	C19orf57	NM_024323.3	22	0,60,6432	AA,AG,GG		0.6409,0.1136,0.4621	benign	155/638	14001206	60,12924	2201	4291	6492	SO:0001583	missense	79173	exon6			CCTGGAGGGGGAC	BC012945	CCDS12299.1	19p13.12	2012-10-26			ENSG00000132016	ENSG00000132016			28153	protein-coding gene	gene with protein product						8228263	Standard	NM_024323		Approved	MGC11271	uc002mxl.1	Q0VDD7	OTTHUMG00000181851	ENST00000586783.1:c.463C>T	19.37:g.14001206G>A	ENSP00000465822:p.Leu155Phe	45.0	0.0	0		38.0	28.0	0.736842	NM_024323	Q13411|Q8N825|Q96D63|Q9BU49	Missense_Mutation	SNP	ENST00000586783.1	37		10	0.004578754578754579	2	0.0040650406504065045	0	0.0	0	0.0	8	0.010554089709762533	G	0.447	-0.895879	0.02472	0.001136	0.006409	ENSG00000132016	ENST00000454313;ENST00000346736	T;T	0.27402	1.67;1.67	2.65	-5.29	0.02747	.	.	.	.	.	T	0.07818	0.0196	N	0.11560	0.145	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.09796	-1.0658	9	0.32370	T	0.25	5.6759	0.5749	0.00702	0.256:0.2127:0.323:0.2083	.	155;155	Q0VDD7-2;Q0VDD7	.;CS057_HUMAN	F	155	ENSP00000404382:L155F;ENSP00000254336:L155F	ENSP00000254336:L155F	L	-	1	0	C19orf57	13862206	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-4.466000	0.00229	-3.561000	0.00141	-1.672000	0.00744	CTC	G|0.994;A|0.006	0.006	strong		0.677	C19orf57-003	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000457947.1	NM_024323	
DYNC2H1	79659	hgsc.bcm.edu	37	11	103153765	103153765	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:103153765T>G	ENST00000375735.2	+	73	10985	c.10841T>G	c.(10840-10842)cTt>cGt	p.L3614R	DYNC2H1_ENST00000398093.3_Missense_Mutation_p.L3621R|DYNC2H1_ENST00000334267.7_Intron	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	3614					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CGTGATCAGCTTCCGTCTTGG	0.328																																					p.L3621R		Atlas-SNP	.											.	DYNC2H1	246	.	0			c.T10862G						PASS	.						69.0	68.0	68.0					11																	103153765		1829	4067	5896	SO:0001583	missense	79659	exon74			ATCAGCTTCCGTC	AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.10841T>G	11.37:g.103153765T>G	ENSP00000364887:p.Leu3614Arg	100.0	0.0	0		136.0	29.0	0.213235	NM_001080463	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	T	15.93	2.978729	0.53720	.	.	ENSG00000187240	ENST00000375735;ENST00000398093	T;T	0.08634	3.07;3.07	5.44	5.44	0.79542	Dynein heavy chain (1);	2.073920	0.01925	N	0.040832	T	0.18173	0.0436	M	0.66297	2.02	0.37386	D	0.912237	B;B	0.24043	0.096;0.078	B;B	0.31442	0.13;0.116	T	0.44205	-0.9343	10	0.20046	T	0.44	.	14.4816	0.67587	0.0:0.0:0.0:1.0	.	3614;3621	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	R	3614;3621	ENSP00000364887:L3614R;ENSP00000381167:L3621R	ENSP00000364887:L3614R	L	+	2	0	DYNC2H1	102658975	1.000000	0.71417	0.989000	0.46669	0.970000	0.65996	3.813000	0.55636	2.062000	0.61559	0.377000	0.23210	CTT	.	.	none		0.328	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1	XM_370652	
CHRNA3	1136	hgsc.bcm.edu	37	15	78894420	78894420	+	Silent	SNP	A	A	G	rs8192480|rs74315118	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78894420A>G	ENST00000326828.5	-	5	948	c.564T>C	c.(562-564)gaT>gaC	p.D188D	CHRNA3_ENST00000348639.3_Silent_p.D188D	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	188					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	TCAGGACCAGATCGATTTTCG	0.488													A|||	14	0.00279553	0.0008	0.0	5008	,	,		18118	0.0		0.0099	False		,,,				2504	0.0031				p.D188D		Atlas-SNP	.											.	CHRNA3	56	.	0			c.T564C						PASS	.	A	,	3,4389	6.2+/-15.9	0,3,2193	180.0	160.0	167.0		564,564	0.9	1.0	15	dbSNP_117	167	39,8547	26.3+/-74.7	1,37,4255	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	1,40,6448	GG,GA,AA		0.4542,0.0683,0.3236	,	188/506,188/490	78894420	42,12936	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			GACCAGATCGATT		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.564T>C	15.37:g.78894420A>G		223.0	0.0	0		189.0	93.0	0.492063	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			A|0.995;G|0.005	0.005	strong		0.488	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
KIAA0754	643314	hgsc.bcm.edu	37	1	39876573	39876573	+	Missense_Mutation	SNP	A	A	C	rs74607331	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39876573A>C	ENST00000530275.1	+	1	423	c.228A>C	c.(226-228)ttA>ttC	p.L76F	MACF1_ENST00000289893.4_Intron|MACF1_ENST00000317713.7_Intron|MACF1_ENST00000539005.1_Intron|MACF1_ENST00000567887.1_Intron|MACF1_ENST00000564288.1_Intron|MACF1_ENST00000372915.3_Intron|MACF1_ENST00000361689.2_Intron|MACF1_ENST00000545844.1_Intron	NM_015038.1	NP_055853.1	O94854	K0754_HUMAN	KIAA0754	76	13 X 13 AA approximate tandem repeat of P-T-S-P-A-A-A-V-P-T-P-E-E.									central_nervous_system(1)|large_intestine(6)|skin(1)	8	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0393)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TTAAAAACTTAAGTGGAGACT	0.448											OREG0013393	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	A|||	22	0.00439297	0.0	0.0086	5008	,	,		21714	0.0		0.0159	False		,,,				2504	0.0				p.L212F		Atlas-SNP	.											KIAA0754_ENST00000530275,NS,carcinoma,+2,2	KIAA0754	93	2	0			c.A636C						PASS	.	A	,,PHE/LEU	11,3737		0,11,1863	72.0	73.0	72.0		,,636	-0.7	0.6	1	dbSNP_132	72	110,8098		2,106,3996	yes	intron,intron,missense	MACF1,KIAA0754	NM_012090.4,NM_033044.3,NM_015038.1	,,22	2,117,5859	CC,CA,AA		1.3402,0.2935,1.012	,,benign	,,212/1428	39876573	121,11835	1874	4104	5978	SO:0001583	missense	643314	exon1			AAACTTAAGTGGA			1p34.2	2009-07-09				ENSG00000255103			29111	protein-coding gene	gene with protein product						9872452	Standard	NM_015038		Approved		uc009vvt.1	O94854		ENST00000530275.1:c.228A>C	1.37:g.39876573A>C	ENSP00000431179:p.Leu76Phe	206.0	0.0	0	889	176.0	51.0	0.289773	NM_015038	E9PMC2|Q6ZSB2	Missense_Mutation	SNP	ENST00000530275.1	37		16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	A	11.25	1.583420	0.28268	0.002935	0.013402	ENSG00000255103	ENST00000530275	T	0.31247	1.5	4.78	-0.745	0.11098	.	.	.	.	.	T	0.08714	0.0216	L	0.27053	0.805	0.09310	N	1	B	0.27932	0.194	B	0.26094	0.066	T	0.24977	-1.0145	9	0.87932	D	0	.	2.8467	0.05546	0.1825:0.4305:0.2676:0.1194	.	76	O94854	K0754_HUMAN	F	76	ENSP00000431179:L76F	ENSP00000431179:L76F	L	+	3	2	RP4-562N20.1	39649160	0.000000	0.05858	0.643000	0.29450	0.853000	0.48598	0.209000	0.17435	0.196000	0.20367	0.454000	0.30748	TTA	A|0.988;C|0.012	0.012	strong		0.448	KIAA0754-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000392100.1	NM_015038	
SPTAN1	6709	hgsc.bcm.edu	37	9	131371241	131371241	+	Missense_Mutation	SNP	A	A	G	rs145038571		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131371241A>G	ENST00000372731.4	+	35	4690	c.4580A>G	c.(4579-4581)aAt>aGt	p.N1527S	SPTAN1_ENST00000358161.5_Missense_Mutation_p.N1527S|SPTAN1_ENST00000372739.3_Missense_Mutation_p.N1527S	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1527					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						AGCCGGCGCAATGAGGTCTTG	0.572													A|||	1	0.000199681	0.0	0.0014	5008	,	,		20265	0.0		0.0	False		,,,				2504	0.0				p.N1527S	NSCLC(120;833 1744 2558 35612 37579)	Atlas-SNP	.											.	SPTAN1	266	.	0			c.A4580G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN	0,4406		0,0,2203	118.0	121.0	120.0		4580,4520,4580	5.8	1.0	9	dbSNP_134	120	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense,missense	SPTAN1	NM_001130438.2,NM_001195532.1,NM_003127.3	46,46,46	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	benign,benign,benign	1527/2478,1507/2453,1527/2473	131371241	14,12992	2203	4300	6503	SO:0001583	missense	6709	exon35			GGCGCAATGAGGT	M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4580A>G	9.37:g.131371241A>G	ENSP00000361816:p.Asn1527Ser	140.0	0.0	0		160.0	75.0	0.46875	NM_003127	Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Missense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	A	13.35	2.209863	0.39003	0.0	0.001628	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	T;T;T	0.46063	0.88;1.39;0.88	5.77	5.77	0.91146	.	0.141471	0.64402	D	0.000005	T	0.27900	0.0687	N	0.16266	0.395	0.54753	D	0.999983	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.11227	-1.0596	10	0.11485	T	0.65	.	16.383	0.83481	1.0:0.0:0.0:0.0	.	1507;1527;1527	Q13813-3;Q13813-2;Q13813	.;.;SPTA2_HUMAN	S	1527;1527;1527;1507	ENSP00000350882:N1527S;ENSP00000361816:N1527S;ENSP00000361824:N1527S	ENSP00000350882:N1527S	N	+	2	0	SPTAN1	130411062	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	4.013000	0.57138	2.326000	0.78906	0.533000	0.62120	AAT	A|0.999;G|0.001	0.001	strong		0.572	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1	NM_003127	
PNPLA8	50640	hgsc.bcm.edu	37	7	108155377	108155377	+	Missense_Mutation	SNP	G	G	A	rs139626312	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:108155377G>A	ENST00000422087.1	-	4	965	c.559C>T	c.(559-561)Cgc>Tgc	p.R187C	PNPLA8_ENST00000257694.8_Missense_Mutation_p.R187C|PNPLA8_ENST00000483879.1_Intron|PNPLA8_ENST00000436062.1_Missense_Mutation_p.R187C|PNPLA8_ENST00000453144.1_Missense_Mutation_p.R87C|PNPLA8_ENST00000426128.2_Missense_Mutation_p.R187C|PNPLA8_ENST00000388728.5_Missense_Mutation_p.R187C	NM_015723.3	NP_056538.1	Q9NP80	PLPL8_HUMAN	patatin-like phospholipase domain containing 8	187					arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|cell death (GO:0008219)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|linoleic acid metabolic process (GO:0043651)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylcholine catabolic process (GO:0034638)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylethanolamine catabolic process (GO:0046338)|phospholipid metabolic process (GO:0006644)|prostaglandin biosynthetic process (GO:0001516)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|calcium-independent phospholipase A2 activity (GO:0047499)|lysophospholipase activity (GO:0004622)			breast(5)|endometrium(1)|kidney(3)|large_intestine(5)|lung(12)|upper_aerodigestive_tract(3)	29						AAAAGACTGCGTTTACCTATA	0.294													G|||	7	0.00139776	0.0	0.0014	5008	,	,		18615	0.0		0.004	False		,,,				2504	0.002				p.R187C		Atlas-SNP	.											PNPLA8,caecum,carcinoma,+1,2	PNPLA8	82	2	0			c.C559T						PASS	.	G	CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	52.0	55.0	54.0		559	3.8	0.1	7	dbSNP_134	54	43,8557	27.9+/-77.7	0,43,4257	yes	missense	PNPLA8	NM_015723.2	180	0,49,6454	AA,AG,GG		0.5,0.1362,0.3767	possibly-damaging	187/783	108155377	49,12957	2203	4300	6503	SO:0001583	missense	50640	exon2			GACTGCGTTTACC	AF217519	CCDS34733.1, CCDS59075.1, CCDS59508.1	7q31	2012-07-31			ENSG00000135241	ENSG00000135241		"""Patatin-like phospholipase domain containing"""	28900	protein-coding gene	gene with protein product		612123				10744668, 10833412, 16799181, 19029121	Standard	NM_015723		Approved	IPLA2G, IPLA2-2, iPLA2gamma	uc003vfj.2	Q9NP80	OTTHUMG00000154870	ENST00000422087.1:c.559C>T	7.37:g.108155377G>A	ENSP00000410804:p.Arg187Cys	35.0	0.0	0		42.0	23.0	0.547619	NM_001256008	A4D0S1|C9JZI4|O95035|Q8N3I3|Q9H7T5|Q9NR17|Q9NUN2|Q9NZ79	Missense_Mutation	SNP	ENST00000422087.1	37	CCDS34733.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	10.38	1.334998	0.24253	0.001362	0.005	ENSG00000135241	ENST00000426128;ENST00000257694;ENST00000388728;ENST00000422087;ENST00000453144;ENST00000436062;ENST00000453085;ENST00000427008	D;D;D;D;D;D;D	0.97959	-3.43;-4.63;-3.43;-4.63;-4.62;-4.63;-4.62	5.78	3.83	0.44106	.	0.974744	0.08470	N	0.941087	D	0.90445	0.7008	N	0.08118	0	0.09310	N	1	P	0.47762	0.9	B	0.40009	0.316	D	0.86221	0.1631	10	0.66056	D	0.02	.	8.1982	0.31409	0.0:0.2353:0.4795:0.2852	.	187	Q9NP80	PLPL8_HUMAN	C	187;187;187;187;87;187;87;187	ENSP00000394988:R187C;ENSP00000257694:R187C;ENSP00000373380:R187C;ENSP00000410804:R187C;ENSP00000387789:R87C;ENSP00000406779:R187C;ENSP00000402274:R87C	ENSP00000257694:R187C	R	-	1	0	PNPLA8	107942613	0.537000	0.26386	0.086000	0.20670	0.523000	0.34469	0.688000	0.25422	1.406000	0.46857	0.591000	0.81541	CGC	G|0.997;A|0.003	0.003	strong		0.294	PNPLA8-002	NOVEL	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337475.1	NM_015723	
FAAH	2166	hgsc.bcm.edu	37	1	46871746	46871746	+	Silent	SNP	G	G	A	rs41305628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:46871746G>A	ENST00000243167.8	+	6	906	c.822G>A	c.(820-822)gaG>gaA	p.E274E	FAAH_ENST00000493735.1_3'UTR	NM_001441.2	NP_001432.2	O00519	FAAH1_HUMAN	fatty acid amide hydrolase	274					fatty acid catabolic process (GO:0009062)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|organelle membrane (GO:0031090)	acylglycerol lipase activity (GO:0047372)|carbon-nitrogen ligase activity, with glutamine as amido-N-donor (GO:0016884)|fatty acid amide hydrolase activity (GO:0017064)			breast(3)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(2)|skin(1)	22	Acute lymphoblastic leukemia(166;0.155)				Propofol(DB00818)|Thiopental(DB00599)	ATGGACAGGAGGCAGGTGAGG	0.632											OREG0013458	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	71	0.0141773	0.0008	0.0231	5008	,	,		16684	0.0		0.0427	False		,,,				2504	0.0112				p.E274E		Atlas-SNP	.											.	FAAH	36	.	0			c.G822A						PASS	.	G		44,4362	47.5+/-82.1	0,44,2159	77.0	77.0	77.0		822	-1.5	0.2	1	dbSNP_127	77	390,8210	125.0+/-183.6	10,370,3920	no	coding-synonymous	FAAH	NM_001441.2		10,414,6079	AA,AG,GG		4.5349,0.9986,3.3369		274/580	46871746	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	2166	exon6			ACAGGAGGCAGGT	U82535	CCDS535.1	1p35-p34	2008-02-05			ENSG00000117480	ENSG00000117480			3553	protein-coding gene	gene with protein product		602935				9122178	Standard	NM_001441		Approved	FAAH-1	uc001cpu.2	O00519	OTTHUMG00000007811	ENST00000243167.8:c.822G>A	1.37:g.46871746G>A		87.0	0.0	0	942	104.0	66.0	0.634615	NM_001441	D3DQ19|Q52M86|Q5TDF8	Silent	SNP	ENST00000243167.8	37	CCDS535.1																																																																																			G|0.970;A|0.030	0.030	strong		0.632	FAAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021443.1	NM_001441	
MYLK	4638	hgsc.bcm.edu	37	3	123332995	123332995	+	Missense_Mutation	SNP	G	G	A	rs200490629		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:123332995G>A	ENST00000475616.1	-	31	5701	c.5702C>T	c.(5701-5703)aCg>aTg	p.T1901M	MYLK_ENST00000354792.5_Missense_Mutation_p.T701M|MYLK-AS1_ENST00000470449.1_RNA|MYLK_ENST00000578202.1_Missense_Mutation_p.T140M|MYLK_ENST00000583087.1_Missense_Mutation_p.T141M|MYLK_ENST00000418370.2_Missense_Mutation_p.T141M|MYLK_ENST00000360772.3_Missense_Mutation_p.T1850M|MYLK_ENST00000346322.5_Missense_Mutation_p.T1832M|MYLK_ENST00000360304.3_Missense_Mutation_p.T1901M|MYLK-AS1_ENST00000485162.1_RNA|MYLK-AS1_ENST00000463408.1_RNA|MYLK_ENST00000359169.1_Missense_Mutation_p.T1850M			Q15746	MYLK_HUMAN	myosin light chain kinase	1901					actin filament organization (GO:0007015)|aorta smooth muscle tissue morphogenesis (GO:0060414)|bleb assembly (GO:0032060)|cellular hypotonic response (GO:0071476)|muscle contraction (GO:0006936)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cell migration (GO:0030335)|positive regulation of wound healing (GO:0090303)|protein phosphorylation (GO:0006468)|smooth muscle contraction (GO:0006939)|tonic smooth muscle contraction (GO:0014820)	cell-cell junction (GO:0005911)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	ATP binding (GO:0005524)|calmodulin-dependent protein kinase activity (GO:0004683)|metal ion binding (GO:0046872)|myosin light chain kinase activity (GO:0004687)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(37)|ovary(7)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	113		Lung NSC(201;0.0496)		GBM - Glioblastoma multiforme(114;0.0736)		TTCCTCCATCGTTTCCACAAT	0.448													G|||	1	0.000199681	0.0	0.0	5008	,	,		19431	0.0		0.001	False		,,,				2504	0.0				p.T1901M		Atlas-SNP	.											.	MYLK	224	.	0			c.C5702T						PASS	.	G	MET/THR,MET/THR,MET/THR,MET/THR,MET/THR,MET/THR	0,4406		0,0,2203	171.0	177.0	175.0		5702,5495,5549,5342,419,422	5.3	1.0	3		175	1,8599		0,1,4299	yes	missense,missense,missense,missense,missense,missense	MYLK	NM_053025.3,NM_053026.3,NM_053027.3,NM_053028.3,NM_053031.2,NM_053032.2	81,81,81,81,81,81	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	1901/1915,1832/1846,1850/1864,1781/1795,140/154,141/155	123332995	1,13005	2203	4300	6503	SO:0001583	missense	4638	exon34			TCCATCGTTTCCA	X85337	CCDS3023.1, CCDS43141.1, CCDS46896.1, CCDS46897.1, CCDS58849.1	3q21	2013-02-11	2008-01-23		ENSG00000065534	ENSG00000065534	2.7.11.18	"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7590	protein-coding gene	gene with protein product	"""smooth muscle myosin light chain kinase"""	600922	"""myosin, light polypeptide kinase"""			8575746	Standard	NM_053026		Approved	MLCK, smMLCK, MYLK1, MLCK1	uc003ego.3	Q15746	OTTHUMG00000141304	ENST00000475616.1:c.5702C>T	3.37:g.123332995G>A	ENSP00000418335:p.Thr1901Met	112.0	0.0	0		142.0	78.0	0.549296	NM_053025	B4DUE3|D3DN97|O95796|O95797|O95798|O95799|Q14844|Q16794|Q17S15|Q3ZCP9|Q5MY99|Q5MYA0|Q6P2N0|Q7Z4J0|Q9C0L5|Q9UBG5|Q9UBY6|Q9UIT9	Missense_Mutation	SNP	ENST00000475616.1	37	CCDS46896.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	17.77	3.471882	0.63737	0.0	1.16E-4	ENSG00000065534	ENST00000360772;ENST00000360304;ENST00000359169;ENST00000418370;ENST00000346322;ENST00000354792;ENST00000475616	T;T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99;0.99	5.27	5.27	0.74061	.	.	.	.	.	T	0.42698	0.1214	N	0.08118	0	0.36368	D	0.86111	D;D;D;D;D;P	0.89917	1.0;0.999;1.0;1.0;1.0;0.889	D;D;D;D;D;B	0.74674	0.984;0.928;0.96;0.97;0.964;0.03	T	0.54227	-0.8325	9	0.52906	T	0.07	.	12.4119	0.55471	0.0761:0.0:0.9239:0.0	.	1900;1781;1850;1832;1901;213	Q15746-6;Q15746-4;Q15746-3;Q15746-2;Q15746;Q05D81	.;.;.;.;MYLK_HUMAN;.	M	1850;1901;1850;141;1832;701;1901	ENSP00000354004:T1850M;ENSP00000353452:T1901M;ENSP00000352088:T1850M;ENSP00000428967:T141M;ENSP00000320622:T1832M;ENSP00000346846:T701M;ENSP00000418335:T1901M	ENSP00000320622:T1832M	T	-	2	0	MYLK	124815685	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	5.648000	0.67930	2.732000	0.93576	0.650000	0.86243	ACG	G|1.000;A|0.000	0.000	strong		0.448	MYLK-004	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356464.1	NM_053025	
APRT	353	hgsc.bcm.edu	37	16	88873824	88873824	+	IGR	SNP	C	C	G	rs141663679	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88873824C>G	ENST00000378364.3	-	0	947				CDT1_ENST00000301019.4_Missense_Mutation_p.P471A	NM_000485.2	NP_000476.1	P07741	APT_HUMAN	adenine phosphoribosyltransferase						adenine salvage (GO:0006168)|AMP salvage (GO:0044209)|cellular response to insulin stimulus (GO:0032869)|grooming behavior (GO:0007625)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	adenine binding (GO:0002055)|adenine phosphoribosyltransferase activity (GO:0003999)|AMP binding (GO:0016208)			cervix(1)|endometrium(1)|liver(1)	3				BRCA - Breast invasive adenocarcinoma(80;0.0477)	Adenine(DB00173)|Adenosine monophosphate(DB00131)	CGAACGCAAGCCTGCGCTCAG	0.667													C|||	5	0.000998403	0.0	0.0014	5008	,	,		17483	0.0		0.002	False		,,,				2504	0.002				p.P471A		Atlas-SNP	.											.	CDT1	30	.	0			c.C1411G						PASS	.	C	ALA/PRO	3,4391	6.2+/-15.9	0,3,2194	60.0	49.0	53.0		1411	3.5	0.8	16	dbSNP_134	53	44,8556	29.0+/-79.6	0,44,4256	yes	missense	CDT1	NM_030928.3	27	0,47,6450	GG,GC,CC		0.5116,0.0683,0.3617	benign	471/547	88873824	47,12947	2197	4300	6497	SO:0001628	intergenic_variant	81620	exon9			CGCAAGCCTGCGC		CCDS32511.1, CCDS45546.1	16q24	2012-10-02				ENSG00000198931	2.4.2.7		626	protein-coding gene	gene with protein product		102600					Standard	NM_000485		Approved		uc002flv.3	P07741			16.37:g.88873824C>G		121.0	0.0	0		147.0	87.0	0.591837	NM_030928	G5E9J2|Q3KP55|Q68DF9	Missense_Mutation	SNP	ENST00000378364.3	37	CCDS32511.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	9.456	1.091956	0.20471	6.83E-4	0.005116	ENSG00000167513	ENST00000301019	T	0.77098	-1.07	5.43	3.49	0.39957	.	0.056769	0.64402	D	0.000001	T	0.63838	0.2545	M	0.61703	1.905	0.53688	D	0.999975	B	0.26744	0.158	B	0.23419	0.046	T	0.60722	-0.7207	10	0.27785	T	0.31	-16.1815	8.6516	0.34038	0.0:0.7221:0.1338:0.144	.	471	Q9H211	CDT1_HUMAN	A	471	ENSP00000301019:P471A	ENSP00000301019:P471A	P	+	1	0	CDT1	87401325	1.000000	0.71417	0.843000	0.33291	0.003000	0.03518	2.711000	0.47177	0.667000	0.31107	-0.251000	0.11542	CCT	C|0.998;G|0.002	0.002	strong		0.667	APRT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430000.2	NM_000485	
LCNL1	401562	hgsc.bcm.edu	37	9	139879196	139879196	+	Silent	SNP	C	C	T	rs201494183		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139879196C>T	ENST00000408973.2	+	3	822	c.228C>T	c.(226-228)ttC>ttT	p.F76F	LCNL1_ENST00000432827.1_Intron	NM_207510.3	NP_997393.3	Q6ZST4	LCNL1_HUMAN	lipocalin-like 1	76																	GAGTGGCCTTCTCCGACTACC	0.687													c|||	1	0.000199681	0.0	0.0	5008	,	,		13386	0.0		0.001	False		,,,				2504	0.0				p.F76F		Atlas-SNP	.											.	LCNL1	4	.	0			c.C228T						PASS	.			3,4273		0,3,2135	30.0	33.0	32.0		228	2.0	0.0	9		32	38,8454		0,38,4208	no	coding-synonymous	LCNL1	NM_207510.3		0,41,6343	TT,TC,CC		0.4475,0.0702,0.3211		76/165	139879196	41,12727	2138	4246	6384	SO:0001819	synonymous_variant	401562	exon3			GGCCTTCTCCGAC		CCDS43908.1	9q34.3	2014-01-22			ENSG00000214402	ENSG00000214402		"""Lipocalins"""	34436	protein-coding gene	gene with protein product							Standard	NM_207510		Approved	FLJ45224	uc004ckh.1	Q6ZST4	OTTHUMG00000159546	ENST00000408973.2:c.228C>T	9.37:g.139879196C>T		62.0	0.0	0		70.0	35.0	0.5	NM_207510		Silent	SNP	ENST00000408973.2	37	CCDS43908.1																																																																																			C|0.996;T|0.004	0.004	strong		0.687	LCNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356128.1	NM_207510	
KRTAP5-9	3846	hgsc.bcm.edu	37	11	71259841	71259841	+	Silent	SNP	C	C	T	rs189729045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:71259841C>T	ENST00000528743.2	+	1	376	c.138C>T	c.(136-138)tgC>tgT	p.C46C		NM_005553.3	NP_005544.4	P26371	KRA59_HUMAN	keratin associated protein 5-9	46	8 X 4 AA repeats of C-C-X-P.				epidermis development (GO:0008544)	keratin filament (GO:0045095)				kidney(1)|large_intestine(1)|lung(6)|prostate(3)	11						AGCCCGTGTGCTGCTGTGTTC	0.652													c|||	16	0.00319489	0.0	0.0086	5008	,	,		18955	0.0		0.007	False		,,,				2504	0.0031				p.C46C		Atlas-SNP	.											.	KRTAP5-9	19	.	0			c.C138T						PASS	.	C		7,4393		0,7,2193	95.0	107.0	103.0		138	1.6	1.0	11		103	85,8503		0,85,4209	no	coding-synonymous	KRTAP5-9	NM_005553.3		0,92,6402	TT,TC,CC		0.9898,0.1591,0.7083		46/170	71259841	92,12896	2200	4294	6494	SO:0001819	synonymous_variant	3846	exon1			CGTGTGCTGCTGT	AB126078	CCDS53677.1	11q13.4	2008-02-05				ENSG00000254997		"""Keratin associated proteins"""	23604	protein-coding gene	gene with protein product		148021		KRN1		15144888	Standard	NM_005553		Approved	KRTAP5.9, KRTAP5-1	uc001oqs.1	P26371		ENST00000528743.2:c.138C>T	11.37:g.71259841C>T		290.0	0.0	0		355.0	159.0	0.447887	NM_005553	Q14564|Q3MIP8	Silent	SNP	ENST00000528743.2	37	CCDS53677.1																																																																																			C|0.996;T|0.004	0.004	strong		0.652	KRTAP5-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393901.2		
VPS13D	55187	hgsc.bcm.edu	37	1	12429611	12429611	+	Silent	SNP	C	C	T	rs2295338	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12429611C>T	ENST00000358136.3	+	54	10792	c.10662C>T	c.(10660-10662)gaC>gaT	p.D3554D	VPS13D_ENST00000496628.1_3'UTR|VPS13D_ENST00000356315.4_Silent_p.D3529D	NM_015378.2	NP_056193.2			vacuolar protein sorting 13 homolog D (S. cerevisiae)											NS(1)|breast(6)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(28)|lung(44)|ovary(5)|pancreas(1)|prostate(8)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(4)	130	Ovarian(185;0.249)	Lung NSC(185;4.08e-05)|all_lung(284;4.55e-05)|Renal(390;0.000147)|Colorectal(325;0.00058)|Breast(348;0.00093)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0327)|Colorectal(212;4.63e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000289)|COAD - Colon adenocarcinoma(227;0.000801)|Kidney(185;0.00216)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(313;0.012)|READ - Rectum adenocarcinoma(331;0.0476)|Lung(427;0.209)		ATGCCTGGGACGAACCCACCT	0.502													C|||	324	0.0646965	0.1142	0.0634	5008	,	,		17469	0.0179		0.0427	False		,,,				2504	0.0695				p.D3554D		Atlas-SNP	.											.	VPS13D	316	.	0			c.C10662T						PASS	.	C	,	457,3949	216.1+/-234.9	24,409,1770	143.0	144.0	144.0		10662,10587	-6.5	0.7	1	dbSNP_100	144	313,8287	111.8+/-172.0	8,297,3995	no	coding-synonymous,coding-synonymous	VPS13D	NM_015378.2,NM_018156.2	,	32,706,5765	TT,TC,CC		3.6395,10.3722,5.9203	,	3554/4389,3529/4364	12429611	770,12236	2203	4300	6503	SO:0001819	synonymous_variant	55187	exon54			CTGGGACGAACCC	AJ608774	CCDS30588.1, CCDS30589.1	1p36.21	2008-02-05	2006-04-04		ENSG00000048707	ENSG00000048707			23595	protein-coding gene	gene with protein product		608877	"""vacuolar protein sorting 13D (yeast)"""				Standard	NM_015378		Approved	FLJ10619, KIAA0453	uc001atv.3	Q5THJ4	OTTHUMG00000013155	ENST00000358136.3:c.10662C>T	1.37:g.12429611C>T		138.0	0.0	0		157.0	69.0	0.43949	NM_015378		Silent	SNP	ENST00000358136.3	37	CCDS30588.1	139	0.06364468864468864	56	0.11382113821138211	33	0.09116022099447514	14	0.024475524475524476	36	0.047493403693931395	C	9.101	1.004065	0.19199	0.103722	0.036395	ENSG00000048707	ENST00000011700	.	.	.	5.93	-6.53	0.01866	.	.	.	.	.	T	0.02083	0.0065	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.51371	-0.8714	3	.	.	.	.	18.7169	0.91679	0.0:0.1617:0.0:0.8383	rs2295338;rs56588517;rs2295338	.	.	.	M	2376	.	.	T	+	2	0	VPS13D	12352198	0.771000	0.28555	0.748000	0.31131	0.959000	0.62525	-0.140000	0.10342	-1.561000	0.01684	-0.806000	0.03193	ACG	C|0.940;T|0.060	0.060	strong		0.502	VPS13D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000036897.2	NM_015378	
WDR62	284403	hgsc.bcm.edu	37	19	36594676	36594676	+	Missense_Mutation	SNP	C	C	G	rs35811023	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36594676C>G	ENST00000270301.7	+	30	3931	c.3931C>G	c.(3931-3933)Cag>Gag	p.Q1311E	WDR62_ENST00000401500.2_Missense_Mutation_p.Q1316E			O43379	WDR62_HUMAN	WD repeat domain 62	1311			Q -> E (in dbSNP:rs35811023).		cerebral cortex development (GO:0021987)|neurogenesis (GO:0022008)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle pole (GO:0000922)				cervix(1)|endometrium(8)|kidney(2)|large_intestine(8)|lung(15)|prostate(4)|stomach(2)|urinary_tract(3)	43	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			CGTGGATACCCAGCCTGGCGT	0.677													C|||	7	0.00139776	0.0008	0.0	5008	,	,		19234	0.0		0.006	False		,,,				2504	0.0				p.Q1316E		Atlas-SNP	.											.	WDR62	102	.	0			c.C3946G						PASS	.	C	GLU/GLN,GLU/GLN	9,4397	15.5+/-35.6	0,9,2194	71.0	62.0	65.0		3946,3931	1.5	0.0	19	dbSNP_126	65	54,8546	34.8+/-89.0	0,54,4246	yes	missense,missense	WDR62	NM_001083961.1,NM_173636.4	29,29	0,63,6440	GG,GC,CC		0.6279,0.2043,0.4844	benign,benign	1316/1524,1311/1519	36594676	63,12943	2203	4300	6503	SO:0001583	missense	284403	exon30			GATACCCAGCCTG	BX647726	CCDS33001.1, CCDS46059.1	19q13.12	2013-01-09	2005-05-09	2005-05-09	ENSG00000075702	ENSG00000075702		"""WD repeat domain containing"""	24502	protein-coding gene	gene with protein product		613583	"""chromosome 19 open reading frame 14"", ""microcephaly, primary autosomal recessive 2"""	C19orf14, MCPH2		19910486, 20729831, 20890278, 21496009	Standard	NM_001083961		Approved	DKFZP434J046, FLJ33298	uc002odd.2	O43379	OTTHUMG00000048139	ENST00000270301.7:c.3931C>G	19.37:g.36594676C>G	ENSP00000270301:p.Gln1311Glu	57.0	0.0	0		52.0	27.0	0.519231	NM_001083961	Q63HP9|Q659D7|Q8NBF7|Q96AD9	Missense_Mutation	SNP	ENST00000270301.7	37	CCDS33001.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	C	6.239	0.412249	0.11812	0.002043	0.006279	ENSG00000075702	ENST00000401500;ENST00000270301	T;T	0.46451	0.96;0.87	5.06	1.47	0.22746	.	0.568333	0.16576	N	0.208382	T	0.13970	0.0338	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.001	T	0.25882	-1.0119	10	0.02654	T	1	-5.5063	7.7082	0.28663	0.3295:0.5109:0.1597:0.0	rs35811023;rs62636634	1316;1311	O43379-4;O43379	.;WDR62_HUMAN	E	1316;1311	ENSP00000384792:Q1316E;ENSP00000270301:Q1311E	ENSP00000270301:Q1311E	Q	+	1	0	WDR62	41286516	0.003000	0.15002	0.007000	0.13788	0.008000	0.06430	0.484000	0.22308	0.689000	0.31550	0.555000	0.69702	CAG	C|0.995;G|0.005	0.005	strong		0.677	WDR62-006	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457436.1	NM_015671	
IRX2	153572	hgsc.bcm.edu	37	5	2749539	2749539	+	Silent	SNP	G	G	C	rs61748183	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:2749539G>C	ENST00000382611.6	-	2	860	c.612C>G	c.(610-612)ccC>ccG	p.P204P	C5orf38_ENST00000457752.2_5'Flank|C5orf38_ENST00000334000.3_5'Flank|C5orf38_ENST00000397835.4_5'Flank|C5orf38_ENST00000515640.1_5'Flank|IRX2_ENST00000302057.5_Silent_p.P204P|IRX2_ENST00000502957.1_5'UTR|C5orf38_ENST00000505778.1_5'Flank	NM_001134222.1	NP_001127694.1	Q9BZI1	IRX2_HUMAN	iroquois homeobox 2	204					proximal/distal pattern formation involved in metanephric nephron development (GO:0072272)|regulation of transcription, DNA-templated (GO:0006355)|specification of loop of Henle identity (GO:0072086)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			breast(1)|central_nervous_system(3)|endometrium(4)|kidney(1)|large_intestine(2)|lung(12)|prostate(1)|skin(2)	26				GBM - Glioblastoma multiforme(108;0.204)		GCGCCTTGTCGGGACTCTCGT	0.652													G|||	5	0.000998403	0.0	0.0	5008	,	,		14303	0.0		0.004	False		,,,				2504	0.001				p.P204P		Atlas-SNP	.											.	IRX2	60	.	0			c.C612G						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	94.0	86.0	89.0		612,612	-6.5	0.0	5	dbSNP_129	89	47,8553	30.1+/-81.4	0,47,4253	no	coding-synonymous,coding-synonymous	IRX2	NM_001134222.1,NM_033267.4	,	0,50,6453	CC,CG,GG		0.5465,0.0681,0.3844	,	204/472,204/472	2749539	50,12956	2203	4300	6503	SO:0001819	synonymous_variant	153572	exon2			CTTGTCGGGACTC	AF319967	CCDS3868.1	5p15.33	2011-06-20	2007-07-13		ENSG00000170561	ENSG00000170561		"""Homeoboxes / TALE class"""	14359	protein-coding gene	gene with protein product		606198				11435706	Standard	NM_033267		Approved		uc003jdb.3	Q9BZI1	OTTHUMG00000090377	ENST00000382611.6:c.612C>G	5.37:g.2749539G>C		232.0	0.0	0		266.0	155.0	0.582707	NM_001134222	Q68A19|Q7Z2I7	Silent	SNP	ENST00000382611.6	37	CCDS3868.1																																																																																			G|0.997;C|0.003	0.003	strong		0.652	IRX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206749.2		
ZNF449	203523	hgsc.bcm.edu	37	X	134494878	134494878	+	Silent	SNP	C	C	T	rs141878135	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:134494878C>T	ENST00000339249.4	+	5	1574	c.1434C>T	c.(1432-1434)ctC>ctT	p.L478L		NM_152695.5	NP_689908.3	Q6P9G9	ZN449_HUMAN	zinc finger protein 449	478					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|ovary(2)|prostate(1)|skin(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					GACCAAGCCTCGTTATTCATT	0.423																																					p.L478L		Atlas-SNP	.											.	ZNF449	68	.	0			c.C1434T						PASS	.	C		2,3833		0,2,0,1630,571	121.0	120.0	121.0		1434	0.2	1.0	X	dbSNP_134	121	10,6716		0,7,3,2420,1869	no	coding-synonymous	ZNF449	NM_152695.5		0,9,3,4050,2440	TT,TC,T,CC,C		0.1487,0.0522,0.1136		478/519	134494878	12,10549	2203	4299	6502	SO:0001819	synonymous_variant	203523	exon5			AAGCCTCGTTATT	AY280801	CCDS14649.1	Xq26.3	2013-01-09			ENSG00000173275	ENSG00000173275		"""-"", ""Zinc fingers, C2H2-type"""	21039	protein-coding gene	gene with protein product		300627					Standard	NM_152695		Approved	ZSCAN19, FLJ23614	uc004eys.3	Q6P9G9	OTTHUMG00000022478	ENST00000339249.4:c.1434C>T	X.37:g.134494878C>T		127.0	0.0	0		70.0	69.0	0.985714	NM_152695	Q5JRZ7|Q5JRZ8|Q6NZX2|Q8N3Q1|Q8TED7	Silent	SNP	ENST00000339249.4	37	CCDS14649.1																																																																																			C|0.999;T|0.001	0.001	strong		0.423	ZNF449-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058411.1	NM_152695	
SETD8	387893	hgsc.bcm.edu	37	12	123892235	123892235	+	Silent	SNP	G	G	A	rs61955128	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:123892235G>A	ENST00000402868.3	+	8	1470	c.1044G>A	c.(1042-1044)ccG>ccA	p.P348P	SETD8_ENST00000330479.4_Silent_p.P348P			Q9NQR1	SETD8_HUMAN	SET domain containing (lysine methyltransferase) 8	389	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				histone lysine methylation (GO:0034968)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|transcription corepressor activity (GO:0003714)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(3)|urinary_tract(1)	13	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.00101)|Epithelial(86;0.00425)		AAGCCCACCCGTGGCTGAAGC	0.562													G|||	26	0.00519169	0.0083	0.0014	5008	,	,		14479	0.003		0.003	False		,,,				2504	0.0082				p.P348P		Atlas-SNP	.											SETD8,NS,neuroblastoma,0,1	SETD8	35	1	0			c.G1044A						scavenged	.						15.0	15.0	15.0					12																	123892235		2194	4279	6473	SO:0001819	synonymous_variant	387893	exon8			CCACCCGTGGCTG	AY102937	CCDS9247.1	12q24.31	2011-07-01			ENSG00000183955	ENSG00000183955		"""Chromatin-modifying enzymes / K-methyltransferases"""	29489	protein-coding gene	gene with protein product		607240				15933070, 12086618, 12121615	Standard	NM_020382		Approved	SET8, SET07, PR-Set7, KMT5A	uc001uew.3	Q9NQR1	OTTHUMG00000150477	ENST00000402868.3:c.1044G>A	12.37:g.123892235G>A		73.0	1.0	0.0136986		75.0	3.0	0.04	NM_020382	A8K9D0|Q86W83|Q8TD09	Silent	SNP	ENST00000402868.3	37	CCDS9247.1																																																																																			G|0.999;A|0.001	0.001	strong		0.562	SETD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318263.1	NM_020382	
RNF133	168433	hgsc.bcm.edu	37	7	122338071	122338071	+	Missense_Mutation	SNP	A	A	G	rs113127267	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:122338071A>G	ENST00000340112.2	-	1	1139	c.902T>C	c.(901-903)cTt>cCt	p.L301P	CADPS2_ENST00000449022.2_Intron|CADPS2_ENST00000412584.2_Intron|CADPS2_ENST00000313070.7_Intron|CADPS2_ENST00000334010.7_Intron	NM_139175.1	NP_631914.1	Q8WVZ7	RN133_HUMAN	ring finger protein 133	301					protein autoubiquitination (GO:0051865)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|urinary_tract(1)	21						CAAAACTTTAAGAATATCACA	0.383													A|||	9	0.00179712	0.0	0.0014	5008	,	,		20051	0.0		0.006	False		,,,				2504	0.002				p.L301P	Colon(198;1778 2057 7449 19869 45985)	Atlas-SNP	.											.	RNF133	41	.	0			c.T902C						PASS	.	A	,,,PRO/LEU	4,4402	8.1+/-20.4	0,4,2199	80.0	81.0	80.0		,,,902	5.5	1.0	7	dbSNP_132	80	55,8543	33.8+/-87.4	0,55,4244	yes	intron,intron,intron,missense	CADPS2,RNF133	NM_001009571.3,NM_001167940.1,NM_017954.10,NM_139175.1	,,,98	0,59,6443	GG,GA,AA		0.6397,0.0908,0.4537	,,,probably-damaging	,,,301/377	122338071	59,12945	2203	4299	6502	SO:0001583	missense	168433	exon1			ACTTTAAGAATAT	AF447589	CCDS5784.1	7q31.33	2013-01-09			ENSG00000188050	ENSG00000188050		"""RING-type (C3HC4) zinc fingers"""	21154	protein-coding gene	gene with protein product							Standard	NM_139175		Approved		uc003vkj.1	Q8WVZ7	OTTHUMG00000157092	ENST00000340112.2:c.902T>C	7.37:g.122338071A>G	ENSP00000344489:p.Leu301Pro	120.0	0.0	0		134.0	69.0	0.514925	NM_139175	A4D0W2|Q8N7G7	Missense_Mutation	SNP	ENST00000340112.2	37	CCDS5784.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	14.28	2.489317	0.44249	9.08E-4	0.006397	ENSG00000188050	ENST00000340112	T	0.68479	-0.33	5.53	5.53	0.82687	.	0.000000	0.56097	U	0.000021	T	0.65709	0.2717	L	0.36672	1.1	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	T	0.72377	-0.4312	10	0.66056	D	0.02	.	10.0982	0.42488	0.8506:0.0:0.0:0.1494	.	301	Q8WVZ7	RN133_HUMAN	P	301	ENSP00000344489:L301P	ENSP00000344489:L301P	L	-	2	0	RNF133	122125307	1.000000	0.71417	0.995000	0.50966	0.527000	0.34593	4.633000	0.61318	2.099000	0.63709	0.402000	0.26972	CTT	A|0.997;G|0.003	0.003	strong		0.383	RNF133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347413.1	NM_139175	
NRXN2	9379	hgsc.bcm.edu	37	11	64457892	64457892	+	Missense_Mutation	SNP	G	G	A	rs141807338		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64457892G>A	ENST00000377551.1	-	4	1046	c.835C>T	c.(835-837)Cac>Tac	p.H279Y	NRXN2_ENST00000377559.3_Intron|NRXN2_ENST00000409571.1_Missense_Mutation_p.H279Y|NRXN2_ENST00000265459.6_Missense_Mutation_p.H279Y			Q9P2S2	NRX2A_HUMAN	neurexin 2	279					adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GTTGGCTGGTGCACATCGCCG	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		15787	0.0		0.001	False		,,,				2504	0.0				p.H279Y		Atlas-SNP	.											.	NRXN2	247	.	0			c.C835T						PASS	.	G	TYR/HIS,	0,4402		0,0,2201	58.0	53.0	54.0		835,	4.5	1.0	11	dbSNP_134	54	2,8592	2.2+/-6.3	0,2,4295	no	missense,intron	NRXN2	NM_015080.3,NM_138732.2	83,	0,2,6496	AA,AG,GG		0.0233,0.0,0.0154	benign,	279/1713,	64457892	2,12994	2201	4297	6498	SO:0001583	missense	9379	exon5			GCTGGTGCACATC		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.835C>T	11.37:g.64457892G>A	ENSP00000366774:p.His279Tyr	109.0	0.0	0		89.0	48.0	0.539326	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	37	CCDS8077.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	3.483|3.483	-0.105541|-0.105541	0.06967|0.06967	0.0|0.0	2.33E-4|2.33E-4	ENSG00000110076|ENSG00000110076	ENST00000437746|ENST00000377551;ENST00000265459;ENST00000409571;ENST00000442300	.|T;T;T;T	.|0.59772	.|0.24;0.24;0.32;1.31	4.47|4.47	4.47|4.47	0.54385|0.54385	.|.	.|.	.|.	.|.	.|.	T|T	0.31040|0.31040	0.0784|0.0784	N|N	0.08118|0.08118	0|0	0.35143|0.35143	D|D	0.769073|0.769073	.|P	.|0.43909	.|0.821	.|B	.|0.38225	.|0.268	T|T	0.43343|0.43343	-0.9397|-0.9397	5|9	.|0.02654	.|T	.|1	.|.	12.9884|12.9884	0.58604|0.58604	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|279	.|Q9P2S2	.|NRX2A_HUMAN	V|Y	68|279;279;279;50	.|ENSP00000366774:H279Y;ENSP00000265459:H279Y;ENSP00000386416:H279Y;ENSP00000388971:H50Y	.|ENSP00000265459:H279Y	A|H	-|-	2|1	0|0	NRXN2|NRXN2	64214468|64214468	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.991000|0.991000	0.79684|0.79684	3.226000|3.226000	0.51254|0.51254	2.216000|2.216000	0.71823|0.71823	0.442000|0.442000	0.29010|0.29010	GCA|CAC	G|1.000;A|0.000	0.000	strong		0.627	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
ADCY4	196883	hgsc.bcm.edu	37	14	24803710	24803710	+	Missense_Mutation	SNP	G	G	A	rs77202343	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24803710G>A	ENST00000310677.4	-	2	262	c.149C>T	c.(148-150)gCc>gTc	p.A50V	ADCY4_ENST00000558563.1_5'UTR|ADCY4_ENST00000554068.2_Missense_Mutation_p.A50V|ADCY4_ENST00000418030.2_Missense_Mutation_p.A50V|RP11-934B9.3_ENST00000555591.1_Intron|ADCY4_ENST00000396747.3_5'UTR	NM_001198568.1|NM_001198592.1|NM_139247.3	NP_001185497.1|NP_001185521.1|NP_640340.2	Q8NFM4	ADCY4_HUMAN	adenylate cyclase 4	50					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cAMP biosynthetic process (GO:0006171)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenylate cyclase activity (GO:0004016)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(13)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				GBM - Glioblastoma multiforme(265;0.0192)		CCTGCCGCTGGCCCAGGCCAC	0.637													G|||	42	0.00838658	0.0023	0.0101	5008	,	,		11094	0.0		0.0229	False		,,,				2504	0.0092				p.A50V		Atlas-SNP	.											.	ADCY4	86	.	0			c.C149T						PASS	.	G	VAL/ALA,VAL/ALA,VAL/ALA	21,4081		0,21,2030	5.0	5.0	5.0		149,149,149	5.4	1.0	14	dbSNP_131	5	159,7961		2,155,3903	no	missense,missense,missense	ADCY4	NM_001198568.1,NM_001198592.1,NM_139247.3	64,64,64	2,176,5933	AA,AG,GG		1.9581,0.5119,1.4728	benign,benign,benign	50/1078,50/1078,50/1078	24803710	180,12042	2051	4060	6111	SO:0001583	missense	196883	exon2			CCGCTGGCCCAGG	AF497516	CCDS9627.1	14q11.2	2013-02-04			ENSG00000129467	ENSG00000129467	4.6.1.1	"""Adenylate cyclases"""	235	protein-coding gene	gene with protein product		600292				7766992	Standard	NM_001198592		Approved	AC4	uc001woy.3	Q8NFM4	OTTHUMG00000029347	ENST00000310677.4:c.149C>T	14.37:g.24803710G>A	ENSP00000312126:p.Ala50Val	26.0	0.0	0		14.0	9.0	0.642857	NM_001198592	B3KV74|D3DS75|Q17R40|Q6ZTM6|Q96ML7	Missense_Mutation	SNP	ENST00000310677.4	37	CCDS9627.1	26	0.011904761904761904	3	0.006097560975609756	3	0.008287292817679558	0	0.0	20	0.026385224274406333	G	35	5.421899	0.96111	0.005119	0.019581	ENSG00000129467	ENST00000310677;ENST00000554068;ENST00000418030	T;T;T	0.76316	-1.01;-1.01;-1.01	5.45	5.45	0.79879	.	0.000000	0.46145	D	0.000314	T	0.66066	0.2752	L	0.50333	1.59	0.80722	D	1	D;D	0.63046	0.992;0.985	D;P	0.66602	0.945;0.771	T	0.71174	-0.4670	10	0.15499	T	0.54	.	16.8265	0.85933	0.0:0.0:1.0:0.0	.	50;50	G3V258;Q8NFM4	.;ADCY4_HUMAN	V	50	ENSP00000312126:A50V;ENSP00000452250:A50V;ENSP00000393177:A50V	ENSP00000312126:A50V	A	-	2	0	ADCY4	23873550	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.145000	0.71769	2.838000	0.97847	0.655000	0.94253	GCC	G|0.987;A|0.013	0.013	strong		0.637	ADCY4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073200.4		
NLRP1	22861	hgsc.bcm.edu	37	17	5442790	5442790	+	Missense_Mutation	SNP	C	C	T	rs61754791	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:5442790C>T	ENST00000572272.1	-	7	2814	c.2815G>A	c.(2815-2817)Gtg>Atg	p.V939M	NLRP1_ENST00000262467.5_Missense_Mutation_p.V939M|NLRP1_ENST00000354411.3_Missense_Mutation_p.V939M|NLRP1_ENST00000269280.4_Missense_Mutation_p.V939M|NLRP1_ENST00000577119.1_Missense_Mutation_p.V939M|NLRP1_ENST00000345221.3_Missense_Mutation_p.V939M|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	939					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				AGCAGTCGCACGCCAACGTCA	0.622													C|||	58	0.0115815	0.0318	0.0058	5008	,	,		18777	0.0		0.0109	False		,,,				2504	0.001				p.V939M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G2815A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	105,4301	82.9+/-121.4	3,99,2101	79.0	62.0	67.0		2815,2815,2815,2815,2815	0.5	0.0	17	dbSNP_129	67	134,8466	67.7+/-130.1	2,130,4168	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	5,229,6269	TT,TC,CC		1.5581,2.3831,1.8376	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	939/1376,939/1430,939/1474,939/1444,939/1400	5442790	239,12767	2203	4300	6503	SO:0001583	missense	22861	exon7			GTCGCACGCCAAC	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2815G>A	17.37:g.5442790C>T	ENSP00000460475:p.Val939Met	83.0	0.0	0		77.0	34.0	0.441558	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	26	0.011904761904761904	14	0.028455284552845527	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.12	2.440438	0.43326	0.023831	0.015581	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	3.7	0.477	0.16784	.	0.224064	0.22878	N	0.054551	T	0.10680	0.0261	M	0.74546	2.27	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.997;1.0	D;D;D;D;P;D	0.91635	0.912;0.999;0.997;0.982;0.896;0.982	T	0.03641	-1.1017	10	0.87932	D	0	.	2.8517	0.05560	0.2212:0.5366:0.0:0.2423	rs61754791	205;939;939;939;939;939	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	939;939;939;939;939;205	ENSP00000442029:V939M;ENSP00000262467:V939M;ENSP00000269280:V939M;ENSP00000346390:V939M;ENSP00000324366:V939M	ENSP00000262467:V939M	V	-	1	0	NLRP1	5383514	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	0.004000	0.13106	0.155000	0.19261	0.650000	0.86243	GTG	A|0.000;C|0.986;T|0.014	0.014	strong		0.622	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
NAT14	57106	hgsc.bcm.edu	37	19	55998317	55998317	+	Missense_Mutation	SNP	C	C	A	rs118182626	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55998317C>A	ENST00000205194.4	+	3	918	c.615C>A	c.(613-615)gaC>gaA	p.D205E	NAT14_ENST00000592719.1_Intron|SSC5D_ENST00000587166.1_5'Flank|SSC5D_ENST00000389623.6_5'Flank|NAT14_ENST00000587400.1_Intron	NM_020378.3	NP_065111.1	Q8WUY8	NAT14_HUMAN	N-acetyltransferase 14 (GCN5-related, putative)	205	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				DNA-templated transcription, initiation (GO:0006352)|positive regulation of transcription, DNA-templated (GO:0045893)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|N-acetyltransferase activity (GO:0008080)			central_nervous_system(1)|large_intestine(1)|ovary(1)|pancreas(1)	4	Breast(117;0.155)		BRCA - Breast invasive adenocarcinoma(297;0.18)|LUSC - Lung squamous cell carcinoma(43;0.193)	GBM - Glioblastoma multiforme(193;0.0527)		TCAGCAAAGACCTGTGAAGCT	0.652													c|||	78	0.0155751	0.0008	0.036	5008	,	,		12211	0.0		0.0328	False		,,,				2504	0.0194				p.D205E		Atlas-SNP	.											.	NAT14	11	.	0			c.C615A						PASS	.	C	GLU/ASP	22,4034		0,22,2006	9.0	10.0	9.0		615	0.6	1.0	19	dbSNP_132	9	279,7729		2,275,3727	yes	missense	NAT14	NM_020378.3	45	2,297,5733	AA,AC,CC		3.484,0.5424,2.495	benign	205/207	55998317	301,11763	2028	4004	6032	SO:0001583	missense	57106	exon3			CAAAGACCTGTGA	AB055059	CCDS12926.1	19q13.42	2011-11-25	2008-09-24		ENSG00000090971	ENSG00000090971			28918	protein-coding gene	gene with protein product	"""K562 cells-derived leucine zipper-like protein 1"""		"""N-acetyltransferase 14"""			10873651	Standard	NM_020378		Approved	KLP1	uc002qle.2	Q8WUY8		ENST00000205194.4:c.615C>A	19.37:g.55998317C>A	ENSP00000205194:p.Asp205Glu	4.0	0.0	0		8.0	7.0	0.875	NM_020378	Q8TDY7|Q9NS72	Missense_Mutation	SNP	ENST00000205194.4	37	CCDS12926.1	46	0.021062271062271064	1	0.0020325203252032522	16	0.04419889502762431	0	0.0	29	0.03825857519788918	.	16.91	3.253386	0.59212	0.005424	0.03484	ENSG00000090971	ENST00000205194	.	.	.	4.44	0.636	0.17729	GCN5-related N-acetyltransferase (GNAT) domain (1);	0.238192	0.30809	N	0.008836	T	0.14527	0.0351	L	0.34521	1.04	0.35928	D	0.8323	B	0.14012	0.009	B	0.12837	0.008	T	0.36016	-0.9765	9	0.48119	T	0.1	-29.4319	11.7987	0.52114	0.455:0.5449:0.0:0.0	.	205	Q8WUY8	NAT14_HUMAN	E	205	.	ENSP00000205194:D205E	D	+	3	2	NAT14	60690129	0.982000	0.34865	1.000000	0.80357	0.839000	0.47603	0.051000	0.14141	0.394000	0.25230	0.455000	0.32223	GAC	C|0.978;A|0.022	0.022	strong		0.652	NAT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453339.1	NM_020378	
CCNB3	85417	hgsc.bcm.edu	37	X	50085217	50085217	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:50085217C>T	ENST00000376042.1	+	9	3831	c.3533C>T	c.(3532-3534)aCc>aTc	p.T1178I	CCNB3_ENST00000276014.7_Missense_Mutation_p.T1178I|CCNB3_ENST00000348603.2_Missense_Mutation_p.T74I|CCNB3_ENST00000376038.1_Missense_Mutation_p.T74I			Q8WWL7	CCNB3_HUMAN	cyclin B3	1178					meiotic nuclear division (GO:0007126)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)	nucleus (GO:0005634)				breast(3)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	75	Ovarian(276;0.236)					TTTGAGATGACCCATGAGACC	0.493																																					p.T1178I		Atlas-SNP	.											.	CCNB3	367	.	0			c.C3533T						PASS	.						221.0	179.0	194.0					X																	50085217		2203	4300	6503	SO:0001583	missense	85417	exon8			AGATGACCCATGA	AJ314764	CCDS14331.1, CCDS14332.1	Xp11	2008-07-03			ENSG00000147082	ENSG00000147082			18709	protein-coding gene	gene with protein product		300456				11846420, 12185076	Standard	XM_006724610		Approved		uc004doy.3	Q8WWL7	OTTHUMG00000021519	ENST00000376042.1:c.3533C>T	X.37:g.50085217C>T	ENSP00000365210:p.Thr1178Ile	166.0	0.0	0		87.0	26.0	0.298851	NM_033031	B1AQI5|B1AQI6|Q96SB5|Q96SB6|Q96SB7|Q9NT38	Missense_Mutation	SNP	ENST00000376042.1	37	CCDS14331.1	.	.	.	.	.	.	.	.	.	.	C	4.077	0.012091	0.07912	.	.	ENSG00000147082	ENST00000376042;ENST00000376038;ENST00000348603;ENST00000276014	T;T;T;T	0.12465	2.68;2.75;2.75;2.68	5.11	-1.37	0.09056	Cyclin, N-terminal (1);Cyclin-like (3);	0.889284	0.09724	N	0.764028	T	0.14614	0.0353	L	0.41710	1.295	0.23820	N	0.996759	P;B;P	0.37688	0.605;0.411;0.605	P;B;B	0.45946	0.498;0.176;0.37	T	0.37502	-0.9703	9	.	.	.	.	7.004	0.24826	0.328:0.4757:0.1963:0.0	.	1178;74;1178	A8K8T9;Q8WWL7-2;Q8WWL7	.;.;CCNB3_HUMAN	I	1178;74;74;1178	ENSP00000365210:T1178I;ENSP00000365206:T74I;ENSP00000338682:T74I;ENSP00000276014:T1178I	.	T	+	2	0	CCNB3	50101957	0.933000	0.31639	0.312000	0.25196	0.443000	0.32047	-0.013000	0.12678	-0.093000	0.12396	-0.568000	0.04159	ACC	.	.	none		0.493	CCNB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056558.1		
HPS4	89781	hgsc.bcm.edu	37	22	26864577	26864577	+	Silent	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26864577G>C	ENST00000398145.2	-	8	1225	c.609C>G	c.(607-609)acC>acG	p.T203T	HPS4_ENST00000336873.5_Silent_p.T203T|HPS4_ENST00000402105.3_Silent_p.T198T|HPS4_ENST00000398141.1_Silent_p.T198T	NM_022081.5	NP_071364.4	Q9NQG7	HPS4_HUMAN	Hermansky-Pudlak syndrome 4	203					blood coagulation (GO:0007596)|hemostasis (GO:0007599)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of eye pigmentation (GO:0048075)|protein stabilization (GO:0050821)|protein targeting (GO:0006605)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|lysosome (GO:0005764)|melanosome (GO:0042470)|membrane (GO:0016020)|platelet dense granule (GO:0042827)	protein dimerization activity (GO:0046983)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(3)|kidney(5)|large_intestine(4)|lung(12)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	32						GCGGGAGTTGGGTGCTGACAA	0.532									Hermansky-Pudlak syndrome																												p.T203T		Atlas-SNP	.											.	HPS4	123	.	0			c.C609G						PASS	.						96.0	77.0	83.0					22																	26864577		2203	4300	6503	SO:0001819	synonymous_variant	89781	exon8	Familial Cancer Database	HPS, HPS1-8	GAGTTGGGTGCTG		CCDS13835.1, CCDS46677.1	22q12.1	2014-09-17			ENSG00000100099	ENSG00000100099			15844	protein-coding gene	gene with protein product		606682				11836498, 12663659	Standard	NM_022081		Approved	KIAA1667, LE	uc003aci.4	Q9NQG7	OTTHUMG00000030459	ENST00000398145.2:c.609C>G	22.37:g.26864577G>C		142.0	0.0	0		174.0	88.0	0.505747	NM_022081	B1AHQ4|Q5H8V6|Q96LX6|Q9BY93|Q9UH37|Q9UH38	Silent	SNP	ENST00000398145.2	37	CCDS13835.1																																																																																			.	.	none		0.532	HPS4-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320778.1	NM_022081	
C6orf165	154313	hgsc.bcm.edu	37	6	88173748	88173748	+	Missense_Mutation	SNP	G	G	A	rs139574881	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:88173748G>A	ENST00000507897.1	+	13	1732	c.1649G>A	c.(1648-1650)cGc>cAc	p.R550H	C6orf165_ENST00000506888.1_3'UTR|C6ORF165_ENST00000369562.4_Missense_Mutation_p.R550H			Q8IYR0	CF165_HUMAN	chromosome 6 open reading frame 165	550										NS(1)|central_nervous_system(1)|large_intestine(5)|lung(8)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19		all_cancers(76;3.93e-06)|Acute lymphoblastic leukemia(125;3.55e-10)|Prostate(29;3.51e-09)|all_hematologic(105;3.29e-06)|all_epithelial(107;0.00575)		BRCA - Breast invasive adenocarcinoma(108;0.0419)		GCTAATTTGCGCCAGAAAGTT	0.358													.|||	4	0.000798722	0.0008	0.0	5008	,	,		18450	0.003		0.0	False		,,,				2504	0.0				p.R550H		Atlas-SNP	.											.	C6orf165	116	.	0			c.G1649A						PASS	.	G	HIS/ARG	3,4403	6.2+/-15.9	0,3,2200	39.0	40.0	40.0		1649	2.1	0.6	6	dbSNP_134	40	13,8587	9.8+/-36.6	0,13,4287	yes	missense	C6orf165	NM_001031743.2	29	0,16,6487	AA,AG,GG		0.1512,0.0681,0.123	possibly-damaging	550/623	88173748	16,12990	2203	4300	6503	SO:0001583	missense	154313	exon13			ATTTGCGCCAGAA	BC035083	CCDS34498.1	6q15	2012-02-07			ENSG00000213204	ENSG00000213204			21405	protein-coding gene	gene with protein product							Standard	NM_001031743		Approved	FLJ25974, dJ382I10.1	uc003plv.3	Q8IYR0	OTTHUMG00000015173	ENST00000507897.1:c.1649G>A	6.37:g.88173748G>A	ENSP00000426769:p.Arg550His	45.0	0.0	0		31.0	13.0	0.419355	NM_001031743	A8K969|E1P507|Q8N9U4	Missense_Mutation	SNP	ENST00000507897.1	37	CCDS34498.1	4	0.0018315018315018315	0	0.0	0	0.0	4	0.006993006993006993	0	0.0	G	9.169	1.020606	0.19433	6.81E-4	0.001512	ENSG00000213204	ENST00000369562	T	0.38560	1.13	5.78	2.06	0.26882	.	0.152890	0.64402	N	0.000017	T	0.26448	0.0646	M	0.70842	2.15	0.36551	D	0.871855	D	0.57257	0.979	B	0.41666	0.363	T	0.13683	-1.0500	10	0.33940	T	0.23	.	14.1357	0.65287	0.1855:0.0:0.8145:0.0	.	550	Q8IYR0	CF165_HUMAN	H	550	ENSP00000358575:R550H	ENSP00000358575:R550H	R	+	2	0	C6orf165	88230467	0.998000	0.40836	0.619000	0.29118	0.204000	0.24138	2.447000	0.44917	0.089000	0.17243	-1.332000	0.01269	CGC	G|0.999;A|0.001	0.001	strong		0.358	C6orf165-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	nonsense_mediated_decay	protein_coding	OTTHUMT00000470406.1	NM_178823	
PABPN1L	390748	hgsc.bcm.edu	37	16	88932857	88932857	+	Missense_Mutation	SNP	T	T	C	rs139390142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:88932857T>C	ENST00000419291.2	-	1	169	c.158A>G	c.(157-159)gAg>gGg	p.E53G	PABPN1L_ENST00000378358.4_Missense_Mutation_p.E53G|PABPN1L_ENST00000427766.1_Missense_Mutation_p.E53G|PABPN1L_ENST00000411789.2_Missense_Mutation_p.E53G	NM_001080487.2	NP_001073956.2	A6NDY0	EPAB2_HUMAN	poly(A) binding protein, nuclear 1-like (cytoplasmic)	53						cytoplasm (GO:0005737)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			kidney(1)	1						atcctcttcctcctctttctc	0.607													t|||	11	0.00219649	0.0	0.0043	5008	,	,		19104	0.0		0.006	False		,,,				2504	0.002				p.E53G		Atlas-SNP	.											.	PABPN1L	25	.	0			c.A158G						PASS	.	T	GLY/GLU	3,3929		0,3,1963	51.0	57.0	55.0		158	-4.2	0.0	16	dbSNP_134	55	42,7942		0,42,3950	yes	missense	PABPN1L	NM_001080487.2	98	0,45,5913	CC,CT,TT		0.5261,0.0763,0.3776	benign	53/279	88932857	45,11871	1966	3992	5958	SO:0001583	missense	390748	exon1			TCTTCCTCCTCTT		CCDS45547.1, CCDS45547.2, CCDS73925.1	16q24.3	2013-02-12	2009-12-17		ENSG00000205022	ENSG00000205022		"""RNA binding motif (RRM) containing"""	37237	protein-coding gene	gene with protein product	"""embryonic poly(A) binding protein 2"""					18483763	Standard	NM_001080487		Approved	ePABP2	uc010vpe.2	A6NDY0		ENST00000419291.2:c.158A>G	16.37:g.88932857T>C	ENSP00000408598:p.Glu53Gly	98.0	0.0	0		106.0	52.0	0.490566	NM_001080487	A1L3B3|A2VDI2	Missense_Mutation	SNP	ENST00000419291.2	37	CCDS45547.2	9	0.004120879120879121	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	5	0.006596306068601583	T	7.862	0.726328	0.15439	7.63E-4	0.005261	ENSG00000205022	ENST00000378358;ENST00000419291;ENST00000427766;ENST00000411789;ENST00000547152	T;T	0.19250	2.16;2.42	3.52	-4.19	0.03835	.	2.185190	0.02057	N	0.050477	T	0.11324	0.0276	N	0.24115	0.695	0.09310	N	1	B;B;B;P	0.46512	0.0;0.0;0.0;0.879	B;B;B;P	0.45998	0.0;0.001;0.0;0.5	T	0.18935	-1.0321	10	0.44086	T	0.13	.	4.3382	0.11097	0.1664:0.4546:0.0:0.379	.	53;53;53;53	A6NDY0;A6NDY0-4;C9JEK9;A6NDY0-2	EPAB2_HUMAN;.;.;.	G	53	ENSP00000367609:E53G;ENSP00000408598:E53G	ENSP00000367609:E53G	E	-	2	0	PABPN1L	87460358	0.314000	0.24563	0.000000	0.03702	0.026000	0.11368	0.515000	0.22801	-0.355000	0.08199	0.172000	0.16884	GAG	T|0.996;C|0.004	0.004	strong		0.607	PABPN1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407502.1	NM_001080487	
PELP1	27043	hgsc.bcm.edu	37	17	4576195	4576195	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576195C>T	ENST00000574876.1	-	16	2108	c.2091G>A	c.(2089-2091)tcG>tcA	p.S697S	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Silent_p.S607S|PELP1_ENST00000572293.1_Silent_p.S747S|PELP1_ENST00000301396.4_Silent_p.S841S|PELP1_ENST00000436683.2_Silent_p.S550S			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	697	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						CAGGGCGTGCCGAGGGCACAG	0.677																																					p.S697S		Atlas-SNP	.											PELP1_ENST00000301396,NS,carcinoma,-1,3	PELP1	102	3	0			c.G2091A						PASS	.						32.0	38.0	36.0					17																	4576195		1989	4144	6133	SO:0001819	synonymous_variant	27043	exon16			GCGTGCCGAGGGC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2091G>A	17.37:g.4576195C>T		141.0	0.0	0		129.0	19.0	0.147287	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Silent	SNP	ENST00000574876.1	37	CCDS58503.1																																																																																			.	.	none		0.677	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
TUBA8	51807	hgsc.bcm.edu	37	22	18609703	18609703	+	Missense_Mutation	SNP	C	C	T	rs140202346		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:18609703C>T	ENST00000330423.3	+	4	1031	c.958C>T	c.(958-960)Cgg>Tgg	p.R320W	TUBA8_ENST00000316027.6_Missense_Mutation_p.R254W	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	320					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						CATGCTCTACCGGGGCGACGT	0.562													c|||	1	0.000199681	0.0	0.0	5008	,	,		20392	0.0		0.001	False		,,,				2504	0.0				p.R320W		Atlas-SNP	.											.	TUBA8	36	.	0			c.C958T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404		0,2,2201	99.0	83.0	89.0		760,958	3.5	1.0	22	dbSNP_134	89	3,8597		0,3,4297	yes	missense,missense	TUBA8	NM_001193414.1,NM_018943.2	101,101	0,5,6498	TT,TC,CC		0.0349,0.0454,0.0384	probably-damaging,probably-damaging	254/384,320/450	18609703	5,13001	2203	4300	6503	SO:0001583	missense	51807	exon4			CTCTACCGGGGCG	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"""Tubulins"""	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.958C>T	22.37:g.18609703C>T	ENSP00000333326:p.Arg320Trp	142.0	0.0	0		174.0	96.0	0.551724	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	16.41	3.115564	0.56505	4.54E-4	3.49E-4	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	D;D;D	0.84589	-1.87;-1.87;-1.87	5.67	3.48	0.39840	Tubulin/FtsZ, 2-layer sandwich domain (3);Tubulin/FtsZ, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.95853	0.8650	H	0.99815	4.805	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95830	0.8857	10	0.87932	D	0	.	11.9598	0.53001	0.1374:0.7305:0.1321:0.0	.	254;344;320	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	W	254;320;344	ENSP00000318575:R254W;ENSP00000333326:R320W;ENSP00000412646:R344W	ENSP00000318575:R254W	R	+	1	2	TUBA8	16989703	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.755000	0.62198	0.782000	0.33613	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.562	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943	
CTNNA2	1496	hgsc.bcm.edu	37	2	80646660	80646660	+	Silent	SNP	C	C	T	rs148134866	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:80646660C>T	ENST00000402739.4	+	8	1229	c.1224C>T	c.(1222-1224)agC>agT	p.S408S	CTNNA2_ENST00000343114.3_Silent_p.S87S|CTNNA2_ENST00000540488.1_Silent_p.S408S|CTNNA2_ENST00000496558.1_Silent_p.S408S|CTNNA2_ENST00000361291.4_Silent_p.S442S|CTNNA2_ENST00000541047.1_Silent_p.S408S|CTNNA2_ENST00000466387.1_Silent_p.S408S	NM_001282597.1	NP_001269526.1	P26232	CTNA2_HUMAN	catenin (cadherin-associated protein), alpha 2	408					axonogenesis (GO:0007409)|brain morphogenesis (GO:0048854)|dendrite morphogenesis (GO:0048813)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|prepulse inhibition (GO:0060134)|radial glia guided migration of Purkinje cell (GO:0021942)|regulation of synapse structural plasticity (GO:0051823)|single organismal cell-cell adhesion (GO:0016337)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|axon (GO:0030424)|basolateral plasma membrane (GO:0016323)|cell-cell adherens junction (GO:0005913)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lamellipodium (GO:0030027)	structural constituent of cytoskeleton (GO:0005200)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(49)|pancreas(4)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	78						CTGCAAAGAGCGGAAATGAAA	0.443													C|||	5	0.000998403	0.0023	0.0014	5008	,	,		15925	0.0		0.001	False		,,,				2504	0.0				p.S408S		Atlas-SNP	.											.	CTNNA2	462	.	0			c.C1224T						PASS	.	C	,	27,4035		0,27,2004	117.0	116.0	116.0		1224,1224	-3.1	0.9	2	dbSNP_134	116	4,8432		0,4,4214	no	coding-synonymous,coding-synonymous	CTNNA2	NM_001164883.1,NM_004389.3	,	0,31,6218	TT,TC,CC		0.0474,0.6647,0.248	,	408/861,408/906	80646660	31,12467	2031	4218	6249	SO:0001819	synonymous_variant	1496	exon9			AAAGAGCGGAAAT		CCDS42703.2, CCDS62944.1, CCDS62945.1, CCDS74531.1	2p12-p11.1	2010-05-04			ENSG00000066032	ENSG00000066032			2510	protein-coding gene	gene with protein product	"""cadherin-associated protein, related"", ""cancer/testis antigen 114"""	114025				8432524	Standard	NM_004389		Approved	CAP-R, CT114	uc010ysf.2	P26232	OTTHUMG00000152903	ENST00000402739.4:c.1224C>T	2.37:g.80646660C>T		67.0	0.0	0		60.0	29.0	0.483333	NM_001164883	B3KXE5|B7Z2W7|B7Z352|B7Z898|Q4ZFW1|Q53R26|Q53R33|Q53T67|Q53T71|Q53TM8|Q7Z3L1|Q7Z3Y0	Silent	SNP	ENST00000402739.4	37																																																																																				C|0.998;T|0.002	0.002	strong		0.443	CTNNA2-003	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000328511.4	NM_004389	
SMARCC2	6601	hgsc.bcm.edu	37	12	56559415	56559415	+	Silent	SNP	C	C	T	rs116595430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56559415C>T	ENST00000267064.4	-	26	2912	c.2826G>A	c.(2824-2826)gcG>gcA	p.A942A	SMARCC2_ENST00000347471.4_Silent_p.A973A|RP11-977G19.5_ENST00000553176.1_RNA|SMARCC2_ENST00000550164.1_Silent_p.A973A|SMARCC2_ENST00000394023.3_Silent_p.A973A	NM_003075.3	NP_003066.2	Q8TAQ2	SMRC2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily c, member 2	942				A -> P (in Ref. 1; AAC50694). {ECO:0000305}.	ATP-dependent chromatin remodeling (GO:0043044)|chromatin remodeling (GO:0006338)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome disassembly (GO:0006337)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription from RNA polymerase II promoter involved in forebrain neuron fate commitment (GO:0021882)|transcription, DNA-templated (GO:0006351)	nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(3)|endometrium(6)|kidney(3)|large_intestine(3)|lung(20)|ovary(1)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)	41			OV - Ovarian serous cystadenocarcinoma(18;0.123)			CCCTCATCTCCGCATACTTCA	0.587													C|||	26	0.00519169	0.0159	0.0072	5008	,	,		17950	0.0		0.0	False		,,,				2504	0.0				p.A973A		Atlas-SNP	.											.	SMARCC2	212	.	0			c.G2919A						PASS	.	C	,,	36,4370	40.8+/-73.8	1,34,2168	53.0	56.0	55.0		2919,2826,2919	-8.5	0.1	12	dbSNP_132	55	7,8593	6.4+/-24.3	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous	SMARCC2	NM_001130420.1,NM_003075.3,NM_139067.2	,,	1,41,6461	TT,TC,CC		0.0814,0.8171,0.3306	,,	973/1153,942/1215,973/1131	56559415	43,12963	2203	4300	6503	SO:0001819	synonymous_variant	6601	exon27			CATCTCCGCATAC	U66616	CCDS8907.1, CCDS8908.1, CCDS55835.1	12q13.2	2008-05-14				ENSG00000139613			11105	protein-coding gene	gene with protein product		601734				8804307, 9693044	Standard	NM_001130420		Approved	BAF170, Rsc8, CRACC2	uc001skb.3	Q8TAQ2	OTTHUMG00000170288	ENST00000267064.4:c.2826G>A	12.37:g.56559415C>T		142.0	0.0	0		149.0	78.0	0.52349	NM_139067	F8VTJ5|Q59GV3|Q92923|Q96E12|Q96GY4	Silent	SNP	ENST00000267064.4	37	CCDS8907.1																																																																																			C|0.996;T|0.004	0.004	strong		0.587	SMARCC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408370.1		
PRRC2A	7916	hgsc.bcm.edu	37	6	31599556	31599556	+	Silent	SNP	A	A	C	rs78503551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31599556A>C	ENST00000376033.2	+	16	3340	c.3106A>C	c.(3106-3108)Agg>Cgg	p.R1036R	PRRC2A_ENST00000376007.4_Silent_p.R1036R	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1036	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						TGCCAGAGGGAGGGGTTTTCG	0.622													A|||	42	0.00838658	0.0068	0.0072	5008	,	,		12527	0.003		0.0099	False		,,,				2504	0.0153				p.R1036R		Atlas-SNP	.											.	PRRC2A	152	.	0			c.A3106C						PASS	.	A	,	10,3000		0,10,1495	13.0	17.0	15.0		3106,3106	5.0	1.0	6	dbSNP_131	15	37,5373		0,37,2668	no	coding-synonymous,coding-synonymous	PRRC2A	NM_004638.3,NM_080686.2	,	0,47,4163	CC,CA,AA		0.6839,0.3322,0.5582	,	1036/2158,1036/2158	31599556	47,8373	1505	2705	4210	SO:0001819	synonymous_variant	7916	exon16			AGAGGGAGGGGTT	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3106A>C	6.37:g.31599556A>C		43.0	0.0	0		55.0	33.0	0.6	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Silent	SNP	ENST00000376033.2	37	CCDS4708.1																																																																																			A|0.995;C|0.005	0.005	strong		0.622	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
OTOL1	131149	hgsc.bcm.edu	37	3	161220819	161220819	+	Missense_Mutation	SNP	C	C	A	rs149127996	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:161220819C>A	ENST00000327928.4	+	4	523	c.523C>A	c.(523-525)Cct>Act	p.P175T		NM_001080440.1	NP_001073909.1	A6NHN0	OTOL1_HUMAN	otolin 1	175	Collagen-like 1.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				central_nervous_system(2)|kidney(2)|large_intestine(8)|lung(11)|ovary(1)|prostate(2)|skin(1)	27						TTCAGGTGAACCTGGCCCTAA	0.398													C|||	14	0.00279553	0.0015	0.0043	5008	,	,		14597	0.0		0.0089	False		,,,				2504	0.0				p.P175T		Atlas-SNP	.											.	OTOL1	63	.	0			c.C523A						PASS	.	C	THR/PRO	4,3334		0,4,1665	7.0	6.0	6.0		523	1.9	1.0	3	dbSNP_134	6	28,7420		0,28,3696	yes	missense	OTOL1	NM_001080440.1	38	0,32,5361	AA,AC,CC		0.3759,0.1198,0.2967	benign	175/478	161220819	32,10754	1669	3724	5393	SO:0001583	missense	131149	exon4			GGTGAACCTGGCC		CCDS46948.1	3q26.1	2011-05-19	2011-05-19			ENSG00000182447			34071	protein-coding gene	gene with protein product	"""C1q and tumor necrosis factor related protein 15"""		"""otolin 1 homolog (zebrafish)"""			17544811, 15905077	Standard	NM_001080440		Approved	C1QTNF15	uc011bpb.2	A6NHN0		ENST00000327928.4:c.523C>A	3.37:g.161220819C>A	ENSP00000330808:p.Pro175Thr	170.0	0.0	0		184.0	77.0	0.418478	NM_001080440		Missense_Mutation	SNP	ENST00000327928.4	37	CCDS46948.1	11	0.005036630036630037	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	5.563	0.288736	0.10513	0.001198	0.003759	ENSG00000182447	ENST00000327928	D	0.96651	-4.08	4.94	1.94	0.25998	.	1.313780	0.05051	N	0.478274	D	0.90741	0.7094	L	0.41906	1.305	0.09310	N	1	B	0.20887	0.049	B	0.26693	0.072	T	0.81556	-0.0879	10	0.37606	T	0.19	.	2.6803	0.05091	0.2842:0.3954:0.2304:0.09	.	175	A6NHN0	OTOL1_HUMAN	T	175	ENSP00000330808:P175T	ENSP00000330808:P175T	P	+	1	0	OTOL1	162703513	0.004000	0.15560	0.987000	0.45799	0.976000	0.68499	0.410000	0.21098	0.462000	0.27095	0.557000	0.71058	CCT	C|0.995;A|0.005	0.005	strong		0.398	OTOL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353184.1	NM_001080440	
THEM4	117145	hgsc.bcm.edu	37	1	151867528	151867528	+	Missense_Mutation	SNP	C	C	T	rs114800758	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151867528C>T	ENST00000368814.3	-	2	591	c.242G>A	c.(241-243)cGt>cAt	p.R81H	THEM4_ENST00000489410.1_Missense_Mutation_p.R81H	NM_053055.4	NP_444283.2	Q5T1C6	THEM4_HUMAN	thioesterase superfamily member 4	81					epidermal growth factor receptor signaling pathway (GO:0007173)|fatty acid metabolic process (GO:0006631)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|protein kinase B signaling (GO:0043491)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)	cell projection (GO:0042995)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	palmitoyl-CoA hydrolase activity (GO:0016290)			endometrium(1)|large_intestine(4)|lung(3)|urinary_tract(1)	9	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			AGTAGGTGTACGTTTATATGA	0.408													C|||	10	0.00199681	0.0	0.0	5008	,	,		18187	0.0		0.0099	False		,,,				2504	0.0				p.R81H		Atlas-SNP	.											.	THEM4	19	.	0			c.G242A						PASS	.	C	HIS/ARG	14,4392	21.2+/-45.6	0,14,2189	121.0	120.0	121.0		242	-6.8	0.0	1	dbSNP_132	121	82,8518	47.6+/-106.9	0,82,4218	yes	missense	THEM4	NM_053055.4	29	0,96,6407	TT,TC,CC		0.9535,0.3177,0.7381	benign	81/241	151867528	96,12910	2203	4300	6503	SO:0001583	missense	117145	exon2			GGTGTACGTTTAT	AJ313515	CCDS1006.1	1q21.3	2008-02-05			ENSG00000159445	ENSG00000159445			17947	protein-coding gene	gene with protein product	"""C-terminal modulator protein"""	606388				11598301	Standard	NM_053055		Approved	CTMP	uc001ezj.2	Q5T1C6	OTTHUMG00000013049	ENST00000368814.3:c.242G>A	1.37:g.151867528C>T	ENSP00000357804:p.Arg81His	141.0	0.0	0		149.0	100.0	0.671141	NM_053055	B2RBX2|Q96KR2	Missense_Mutation	SNP	ENST00000368814.3	37	CCDS1006.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	7.135	0.580580	0.13686	0.003177	0.009535	ENSG00000159445	ENST00000368814;ENST00000489410	T;T	0.24538	1.86;1.85	3.39	-6.77	0.01727	.	1.373530	0.04534	N	0.386920	T	0.04588	0.0125	L	0.50333	1.59	0.09310	N	1	B	0.31968	0.349	B	0.28916	0.096	T	0.20042	-1.0287	10	0.15952	T	0.53	6.1133	1.5837	0.02639	0.2296:0.1696:0.1141:0.4867	.	81	Q5T1C6	THEM4_HUMAN	H	81	ENSP00000357804:R81H;ENSP00000433304:R81H	ENSP00000357804:R81H	R	-	2	0	THEM4	150134152	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	-3.893000	0.00340	-2.045000	0.00910	-0.157000	0.13467	CGT	C|0.994;T|0.006	0.006	strong		0.408	THEM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036615.1	NM_053055	
AKAP13	11214	hgsc.bcm.edu	37	15	86124861	86124861	+	Missense_Mutation	SNP	C	C	A	rs371702364		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:86124861C>A	ENST00000394518.2	+	7	3657	c.3562C>A	c.(3562-3564)Ctg>Atg	p.L1188M	RP11-815J21.2_ENST00000561409.1_RNA|AKAP13_ENST00000361243.2_Missense_Mutation_p.L1188M	NM_001270546.1|NM_007200.4	NP_001257475.1|NP_009131.2	Q12802	AKP13_HUMAN	A kinase (PRKA) anchor protein 13	1188					apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nuclear export (GO:0051168)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|regulation of cardiac muscle hypertrophy (GO:0010611)|regulation of glucocorticoid mediated signaling pathway (GO:1900169)|regulation of protein kinase activity (GO:0045859)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cAMP-dependent protein kinase activity (GO:0004691)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|signal transducer activity (GO:0004871)			NS(1)|breast(2)|central_nervous_system(4)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(13)|liver(1)|lung(43)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	98						TCCTGTCCTACTGCAGCCTGT	0.582																																					p.L1188M	Melanoma(94;603 1453 3280 32295 32951)	Atlas-SNP	.											.	AKAP13	394	.	0			c.C3562A						PASS	.	C	MET/LEU,MET/LEU	0,4404		0,0,2202	71.0	69.0	69.0		3562,3562	2.5	0.0	15		69	1,8597	1.2+/-3.3	0,1,4298	no	missense,missense	AKAP13	NM_006738.4,NM_007200.3	15,15	0,1,6500	AA,AC,CC		0.0116,0.0,0.0077	benign,benign	1188/2818,1188/2814	86124861	1,13001	2202	4299	6501	SO:0001583	missense	11214	exon7			GTCCTACTGCAGC	M90360	CCDS32319.1, CCDS32320.1, CCDS73778.1	15q24-q25	2013-01-10	2002-06-13			ENSG00000170776		"""A-kinase anchor proteins"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	371	protein-coding gene	gene with protein product		604686	"""lymphoid blast crisis oncogene"""	LBC		9627117, 1860836	Standard	NM_007200		Approved	Ht31, BRX, AKAP-Lbc, c-lbc, PROTO-LB, HA-3, ARHGEF13	uc002blu.2	Q12802		ENST00000394518.2:c.3562C>A	15.37:g.86124861C>A	ENSP00000378026:p.Leu1188Met	124.0	0.0	0		101.0	55.0	0.544554	NM_007200	Q14572|Q59FP6|Q86W90|Q8WXQ6|Q96JP6|Q96P79|Q9Y5T0|Q9Y5T6	Missense_Mutation	SNP	ENST00000394518.2	37	CCDS32319.1	.	.	.	.	.	.	.	.	.	.	C	9.556	1.117178	0.20795	0.0	1.16E-4	ENSG00000170776	ENST00000361243;ENST00000394518;ENST00000394516;ENST00000458540	T;T	0.16196	2.36;2.36	5.49	2.49	0.30216	.	.	.	.	.	T	0.09024	0.0223	N	0.14661	0.345	0.09310	N	0.999999	B;B	0.28291	0.028;0.206	B;B	0.27170	0.014;0.077	T	0.31916	-0.9926	9	0.45353	T	0.12	.	4.1054	0.10035	0.1653:0.5884:0.1595:0.0867	.	1188;1188	Q12802;Q12802-2	AKP13_HUMAN;.	M	1188;1188;1187;1187	ENSP00000354718:L1188M;ENSP00000378026:L1188M	ENSP00000354718:L1188M	L	+	1	2	AKAP13	83925865	0.001000	0.12720	0.000000	0.03702	0.217000	0.24651	1.161000	0.31773	0.236000	0.21180	0.650000	0.86243	CTG	.	.	weak		0.582	AKAP13-004	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417318.1	NM_007200	
ALG14	199857	hgsc.bcm.edu	37	1	95538424	95538424	+	Missense_Mutation	SNP	C	C	T	rs34364382	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:95538424C>T	ENST00000370205.5	-	1	77	c.31G>A	c.(31-33)Gca>Aca	p.A11T	ALG14_ENST00000495856.1_5'UTR	NM_144988.3	NP_659425.1	Q96F25	ALG14_HUMAN	ALG14, UDP-N-acetylglucosaminyltransferase subunit	11					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				endometrium(2)|large_intestine(1)|lung(2)|pancreas(1)	6		all_lung(203;0.0232)|Lung NSC(277;0.0739)		all cancers(265;0.0615)|Epithelial(280;0.139)		ACAGCTCCTGCGGCCGCAGCT	0.582													C|||	9	0.00179712	0.0008	0.0029	5008	,	,		18389	0.0		0.005	False		,,,				2504	0.001				p.A11T		Atlas-SNP	.											.	ALG14	13	.	0			c.G31A						PASS	.	C	THR/ALA	6,4400	11.4+/-27.6	0,6,2197	79.0	77.0	78.0		31	3.3	0.0	1	dbSNP_126	78	101,8499	56.0+/-117.1	0,101,4199	yes	missense	ALG14	NM_144988.3	58	0,107,6396	TT,TC,CC		1.1744,0.1362,0.8227	possibly-damaging	11/217	95538424	107,12899	2203	4300	6503	SO:0001583	missense	199857	exon1			CTCCTGCGGCCGC		CCDS752.1	1p21.3	2013-02-21	2013-02-21		ENSG00000172339	ENSG00000172339			28287	protein-coding gene	gene with protein product		612866	"""asparagine-linked glycosylation 14 homolog (yeast)"", ""asparagine-linked glycosylation 14 homolog (S. cerevisiae)"""			15615718	Standard	NM_144988		Approved	MGC19780	uc001dra.2	Q96F25	OTTHUMG00000010781	ENST00000370205.5:c.31G>A	1.37:g.95538424C>T	ENSP00000359224:p.Ala11Thr	53.0	0.0	0		38.0	16.0	0.421053	NM_144988	A8K030	Missense_Mutation	SNP	ENST00000370205.5	37	CCDS752.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	14.66	2.600442	0.46423	0.001362	0.011744	ENSG00000172339	ENST00000370205	T	0.44083	0.93	5.21	3.34	0.38264	.	1.316220	0.04936	N	0.457681	T	0.09247	0.0228	N	0.08118	0	0.09310	N	1	B	0.16166	0.016	B	0.06405	0.002	T	0.25502	-1.0130	10	0.22109	T	0.4	0.4063	9.4756	0.38869	0.0:0.8285:0.0:0.1715	rs34364382	11	Q96F25	ALG14_HUMAN	T	11	ENSP00000359224:A11T	ENSP00000359224:A11T	A	-	1	0	ALG14	95311012	0.000000	0.05858	0.001000	0.08648	0.009000	0.06853	0.652000	0.24888	0.772000	0.33382	0.591000	0.81541	GCA	C|0.994;T|0.006	0.006	strong		0.582	ALG14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029699.2	NM_144988	
SEMA4F	10505	hgsc.bcm.edu	37	2	74883750	74883750	+	Missense_Mutation	SNP	G	G	A	rs139676653	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74883750G>A	ENST00000357877.2	+	2	384	c.235G>A	c.(235-237)Gtt>Att	p.V79I	SEMA4F_ENST00000339773.5_Missense_Mutation_p.V79I	NM_004263.3	NP_004254.2	O95754	SEM4F_HUMAN	sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4F	79	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|cell-cell signaling (GO:0007267)|negative regulation of axon extension (GO:0030517)|nervous system development (GO:0007399)|retinal ganglion cell axon guidance (GO:0031290)	endoplasmic reticulum (GO:0005783)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)			biliary_tract(1)|breast(2)|endometrium(8)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(2)	45						CACACTTTATGTTGGCGCCCG	0.577													G|||	14	0.00279553	0.0	0.0043	5008	,	,		18054	0.0		0.0109	False		,,,				2504	0.0				p.V79I		Atlas-SNP	.											.	SEMA4F	89	.	0			c.G235A						PASS	.	G	ILE/VAL	4,4402	11.4+/-27.6	0,4,2199	121.0	108.0	112.0		235	3.1	1.0	2	dbSNP_134	112	66,8534	39.8+/-96.3	0,66,4234	yes	missense	SEMA4F	NM_004263.3	29	0,70,6433	AA,AG,GG		0.7674,0.0908,0.5382	probably-damaging	79/771	74883750	70,12936	2203	4300	6503	SO:0001583	missense	10505	exon2			CTTTATGTTGGCG	AF038652	CCDS1955.1, CCDS62942.1, CCDS74529.1	2p13.1	2008-05-21			ENSG00000135622	ENSG00000135622		"""Semaphorins"""	10734	protein-coding gene	gene with protein product	"""m-Sema M"""	603706		SEMAM		10051670	Standard	NM_004263		Approved	SEMAW	uc002sna.2	O95754	OTTHUMG00000129952	ENST00000357877.2:c.235G>A	2.37:g.74883750G>A	ENSP00000350547:p.Val79Ile	176.0	0.0	0		153.0	72.0	0.470588	NM_001271662	Q542Y7|Q9NS35	Missense_Mutation	SNP	ENST00000357877.2	37	CCDS1955.1	20	0.009157509157509158	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	15	0.01978891820580475	G	12.16	1.855717	0.32791	9.08E-4	0.007674	ENSG00000135622	ENST00000357877;ENST00000339773;ENST00000434486;ENST00000453930	T;T;T;T	0.23147	1.92;1.92;1.92;1.92	4.9	3.12	0.35913	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.176655	0.38164	N	0.001800	T	0.18509	0.0444	L	0.37697	1.125	0.21579	N	0.999638	B;B;B;D	0.55605	0.005;0.003;0.002;0.972	B;B;B;D	0.66716	0.015;0.01;0.007;0.946	T	0.03403	-1.1040	10	0.29301	T	0.29	.	7.4621	0.27302	0.1937:0.0:0.8063:0.0	.	79;79;79;79	B7Z931;C9K0A1;O95754-2;O95754	.;.;.;SEM4F_HUMAN	I	79	ENSP00000350547:V79I;ENSP00000342675:V79I;ENSP00000407698:V79I;ENSP00000409141:V79I	ENSP00000342675:V79I	V	+	1	0	SEMA4F	74737258	1.000000	0.71417	0.996000	0.52242	0.966000	0.64601	2.773000	0.47686	0.688000	0.31529	-0.143000	0.13931	GTT	G|0.993;A|0.007	0.007	strong		0.577	SEMA4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252214.2	NM_004263	
TRABD2A	129293	hgsc.bcm.edu	37	2	85059204	85059204	+	Missense_Mutation	SNP	C	C	T	rs201984217		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:85059204C>T	ENST00000409520.2	-	5	1099	c.1057G>A	c.(1057-1059)Gcc>Acc	p.A353T	TRABD2A_ENST00000479944.1_5'UTR|TRABD2A_ENST00000335459.5_Missense_Mutation_p.A304T	NM_001277053.1	NP_001263982.1	Q86V40	TIKI1_HUMAN	TraB domain containing 2A	353					head development (GO:0060322)|metabolic process (GO:0008152)|negative regulation of Wnt signaling pathway (GO:0030178)|protein oxidation (GO:0018158)|Wnt signaling pathway (GO:0016055)	integral component of organelle membrane (GO:0031301)|integral component of plasma membrane (GO:0005887)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)|Wnt-protein binding (GO:0017147)										CCAGCAGGGGCGTGTTCTACC	0.562													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19756	0.0		0.0	False		,,,				2504	0.0				p.V304I		Atlas-SNP	.											.	.	.	.	0			c.G910A						PASS	.						135.0	134.0	134.0					2																	85059204		2027	4201	6228	SO:0001583	missense	129293	exon4			CAGGGGCGTGTTC	BC049209	CCDS46349.1, CCDS62946.1	2p11.2	2012-07-04	2012-07-04	2012-07-04	ENSG00000186854	ENSG00000186854			27013	protein-coding gene	gene with protein product		614912	"""chromosome 2 open reading frame 89"""	C2orf89		12477932	Standard	NM_001080824		Approved		uc010ysl.3	Q86V40	OTTHUMG00000152922	ENST00000409520.2:c.1057G>A	2.37:g.85059204C>T	ENSP00000387075:p.Ala353Thr	113.0	0.0	0		145.0	66.0	0.455172	NM_001080824	B4DKK8|I6UMB9	Missense_Mutation	SNP	ENST00000409520.2	37		.	.	.	.	.	.	.	.	.	.	C	0.676	-0.799962	0.02841	.	.	ENSG00000186854	ENST00000335459;ENST00000409520	T;T	0.19532	2.25;2.14	2.76	0.829	0.18847	.	0.419056	0.20863	N	0.084306	T	0.07503	0.0189	.	.	.	0.23492	N	0.997562	B;B	0.06786	0.0;0.001	B;B	0.04013	0.001;0.001	T	0.30534	-0.9975	9	0.10636	T	0.68	.	2.0163	0.03499	0.277:0.4522:0.0:0.2708	.	353;304	Q86V40;Q86V40-2	CB089_HUMAN;.	T	304;353	ENSP00000335004:A304T;ENSP00000387075:A353T	ENSP00000335004:A304T	A	-	1	0	C2orf89	84912715	1.000000	0.71417	0.990000	0.47175	0.749000	0.42624	0.750000	0.26334	0.465000	0.27167	0.462000	0.41574	GCC	C|0.998;T|0.002	0.002	weak		0.562	TRABD2A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001080824	
FOXO3	2309	hgsc.bcm.edu	37	6	108882915	108882915	+	Silent	SNP	C	C	T	rs150320900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:108882915C>T	ENST00000343882.6	+	2	808	c.504C>T	c.(502-504)cgC>cgT	p.R168R	FOXO3_ENST00000406360.1_Silent_p.R168R	NM_201559.2	NP_963853.1	O43524	FOXO3_HUMAN	forkhead box O3	168					antral ovarian follicle growth (GO:0001547)|cellular response to oxidative stress (GO:0034599)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose homeostasis (GO:0042593)|initiation of primordial ovarian follicle growth (GO:0001544)|innate immune response (GO:0045087)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|oocyte maturation (GO:0001556)|ovulation from ovarian follicle (GO:0001542)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of erythrocyte differentiation (GO:0045648)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of translation (GO:0006417)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|protein kinase binding (GO:0019901)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(5)|endometrium(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(4)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	26		all_cancers(87;1.78e-07)|Acute lymphoblastic leukemia(125;2.66e-08)|all_hematologic(75;1.13e-06)|all_epithelial(87;3.88e-05)|Colorectal(196;0.0294)|all_lung(197;0.0487)|Lung SC(18;0.152)		Epithelial(106;0.000759)|all cancers(137;0.00121)|BRCA - Breast invasive adenocarcinoma(108;0.00163)|OV - Ovarian serous cystadenocarcinoma(136;0.00718)		TGATCACCCGCGCCATCGAGA	0.657													C|||	12	0.00239617	0.0	0.0029	5008	,	,		13235	0.0		0.008	False		,,,				2504	0.002				p.R168R		Atlas-SNP	.											.	FOXO3	67	.	0			c.C504T						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	28.0	24.0	25.0		504,504	0.4	1.0	6	dbSNP_134	25	70,8530	42.2+/-99.7	0,70,4230	no	coding-synonymous,coding-synonymous	FOXO3	NM_001455.3,NM_201559.2	,	0,73,6430	TT,TC,CC		0.814,0.0681,0.5613	,	168/674,168/674	108882915	73,12933	2203	4300	6503	SO:0001819	synonymous_variant	2309	exon1			CACCCGCGCCATC	AF032886	CCDS5068.1	6q21	2008-09-08	2007-05-02	2007-05-02	ENSG00000118689	ENSG00000118689		"""Forkhead boxes"""	3821	protein-coding gene	gene with protein product		602681		FKHRL1, FOXO3A		9479491	Standard	NM_001455		Approved	AF6q21, FOXO2	uc003psm.2	O43524	OTTHUMG00000015327	ENST00000343882.6:c.504C>T	6.37:g.108882915C>T		125.0	0.0	0		127.0	65.0	0.511811	NM_001455	B4DVZ6|E1P5E6|O15171|Q5T2I7|Q9BZ04	Silent	SNP	ENST00000343882.6	37	CCDS5068.1																																																																																			C|0.995;T|0.005	0.005	strong		0.657	FOXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041722.2		
DSPP	1834	hgsc.bcm.edu	37	4	88536321	88536321	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:88536321G>A	ENST00000282478.7	+	4	2540	c.2507G>A	c.(2506-2508)aGc>aAc	p.S836N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.S836N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	836	Asp/Ser-rich.			S -> C (in Ref. 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		agcgatagcagcaacagcagt	0.498																																					p.S836N		Atlas-SNP	.											.	DSPP	174	.	0			c.G2507A						PASS	.						87.0	109.0	101.0					4																	88536321		1645	2951	4596	SO:0001583	missense	1834	exon5			ATAGCAGCAACAG	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.2507G>A	4.37:g.88536321G>A	ENSP00000282478:p.Ser836Asn	415.0	0.0	0		389.0	18.0	0.0462725	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	2.602	-0.292775	0.05568	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.87412	-2.25;-2.25	0.918	0.918	0.19386	.	.	.	.	.	T	0.80623	0.4658	L	0.46157	1.445	0.09310	N	1	B	0.19817	0.039	B	0.20384	0.029	T	0.70281	-0.4915	9	0.54805	T	0.06	.	5.1892	0.15201	0.0:0.0:1.0:0.0	.	836	Q9NZW4	DSPP_HUMAN	N	836	ENSP00000382213:S836N;ENSP00000282478:S836N	ENSP00000282478:S836N	S	+	2	0	DSPP	88755345	0.550000	0.26489	0.027000	0.17364	0.003000	0.03518	0.902000	0.28459	0.792000	0.33850	0.165000	0.16767	AGC	.	.	none		0.498	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
SNCAIP	9627	hgsc.bcm.edu	37	5	121780312	121780312	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:121780312C>A	ENST00000261368.8	+	8	1739	c.1477C>A	c.(1477-1479)Ccc>Acc	p.P493T	SNCAIP_ENST00000542191.1_Missense_Mutation_p.P51T|SNCAIP_ENST00000379538.3_Missense_Mutation_p.P127T|SNCAIP_ENST00000379533.2_Missense_Mutation_p.P540T|CTC-210G5.1_ENST00000510972.1_RNA|SNCAIP_ENST00000504884.2_3'UTR|SNCAIP_ENST00000414317.2_Missense_Mutation_p.P95T|SNCAIP_ENST00000261367.7_Missense_Mutation_p.P540T|CTC-210G5.1_ENST00000503529.1_RNA|SNCAIP_ENST00000503116.2_3'UTR|CTC-210G5.1_ENST00000509993.1_RNA|SNCAIP_ENST00000379536.2_Missense_Mutation_p.P433T|CTC-210G5.1_ENST00000506053.1_RNA|CTC-210G5.1_ENST00000505546.1_RNA	NM_005460.2	NP_005451.2	Q9Y6H5	SNCAP_HUMAN	synuclein, alpha interacting protein	493					cell death (GO:0008219)|dopamine metabolic process (GO:0042417)|regulation of inclusion body assembly (GO:0090083)|regulation of neurotransmitter secretion (GO:0046928)	cytoplasm (GO:0005737)|neuronal cell body (GO:0043025)|presynaptic membrane (GO:0042734)|synaptic vesicle (GO:0008021)	identical protein binding (GO:0042802)|ubiquitin protein ligase binding (GO:0031625)			NS(3)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(9)|ovary(2)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	39		all_cancers(142;0.00787)|Prostate(80;0.0327)	KIRC - Kidney renal clear cell carcinoma(527;0.206)	OV - Ovarian serous cystadenocarcinoma(64;0.000625)|Epithelial(69;0.00216)|all cancers(49;0.0232)		TGGGGAAAAGCCCTCCCAGAG	0.547																																					p.P493T		Atlas-SNP	.											.	SNCAIP	308	.	0			c.C1477A						PASS	.						105.0	100.0	102.0					5																	121780312		2203	4300	6503	SO:0001583	missense	9627	exon8			GAAAAGCCCTCCC	AF167306	CCDS4131.1, CCDS58964.1	5q23.2	2013-01-10	2008-07-31		ENSG00000064692	ENSG00000064692		"""Ankyrin repeat domain containing"""	11139	protein-coding gene	gene with protein product	"""synphilin"""	603779				10319874	Standard	NM_001242935		Approved	SYPH1	uc003ksw.1	Q9Y6H5	OTTHUMG00000128915	ENST00000261368.8:c.1477C>A	5.37:g.121780312C>A	ENSP00000261368:p.Pro493Thr	125.0	0.0	0		115.0	55.0	0.478261	NM_005460	D3DSZ1|Q05BS1|Q1PSC2|Q49AC6|Q504U9|Q6L984|Q6L985|Q6L986|Q9HC59	Missense_Mutation	SNP	ENST00000261368.8	37	CCDS4131.1	.	.	.	.	.	.	.	.	.	.	C	24.2	4.501545	0.85176	.	.	ENSG00000064692	ENST00000542191;ENST00000509154;ENST00000261368;ENST00000379533;ENST00000379536;ENST00000379538;ENST00000261367;ENST00000414317;ENST00000447854	T;T;T;T;T;T;T;T	0.70869	0.99;0.14;0.14;0.14;0.14;0.99;0.14;-0.52	5.66	5.66	0.87406	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	D	0.91126	0.7206	H	0.98276	4.19	0.53688	D	0.999971	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.91635	0.998;0.999;0.997;0.988;0.999;0.988;0.996;0.993	D	0.94040	0.7308	10	0.72032	D	0.01	-20.578	19.7543	0.96284	0.0:1.0:0.0:0.0	.	433;121;95;433;127;127;540;493	D6R9G8;Q9NVG1;B7Z995;Q9Y6H5-4;Q9Y6H5-5;Q9Y6H5-2;Q9Y6H5-3;Q9Y6H5	.;.;.;.;.;.;.;SNCAP_HUMAN	T	51;433;493;540;433;127;540;95;133	ENSP00000441681:P51T;ENSP00000422106:P433T;ENSP00000261368:P493T;ENSP00000368848:P540T;ENSP00000368851:P433T;ENSP00000368854:P127T;ENSP00000261367:P540T;ENSP00000394392:P95T	ENSP00000261367:P540T	P	+	1	0	SNCAIP	121808211	1.000000	0.71417	1.000000	0.80357	0.872000	0.50106	5.903000	0.69877	2.680000	0.91292	0.561000	0.74099	CCC	.	.	none		0.547	SNCAIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250888.1		
C17orf77	146723	hgsc.bcm.edu	37	17	72588438	72588438	+	Nonsense_Mutation	SNP	G	G	T	rs79556281	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:72588438G>T	ENST00000392620.1	+	3	615	c.253G>T	c.(253-255)Gaa>Taa	p.E85*	C17orf77_ENST00000328023.2_Nonsense_Mutation_p.E85*|CD300LD_ENST00000375352.1_5'Flank	NM_152460.2	NP_689673.2	Q96MU5	CQ077_HUMAN	chromosome 17 open reading frame 77	85						extracellular region (GO:0005576)				breast(2)|large_intestine(2)|lung(5)|prostate(1)|stomach(1)	11						AAACCTACTCGAATCTCCTTC	0.453													g|||	23	0.00459265	0.0	0.0043	5008	,	,		22359	0.0		0.0179	False		,,,				2504	0.002				p.E85X		Atlas-SNP	.											.	C17orf77	31	.	0			c.G253T						PASS	.	A	stop/GLU	10,4396	16.8+/-37.8	0,10,2193	90.0	86.0	87.0		253	-8.1	0.0	17	dbSNP_131	87	85,8515	49.4+/-109.1	1,83,4216	yes	stop-gained	C17orf77	NM_152460.2		1,93,6409	TT,TG,GG		0.9884,0.227,0.7304		85/244	72588438	95,12911	2203	4300	6503	SO:0001587	stop_gained	146723	exon3			CTACTCGAATCTC		CCDS32721.1	17q25.1	2006-01-16			ENSG00000182352	ENSG00000182352			26480	protein-coding gene	gene with protein product							Standard	NM_152460		Approved	FLJ31882	uc002jla.1	Q96MU5	OTTHUMG00000067611	ENST00000392620.1:c.253G>T	17.37:g.72588438G>T	ENSP00000376396:p.Glu85*	46.0	0.0	0		62.0	38.0	0.612903	NM_152460		Nonsense_Mutation	SNP	ENST00000392620.1	37	CCDS32721.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	g	20.2	3.948429	0.73787	0.00227	0.009884	ENSG00000182352	ENST00000392620;ENST00000328023	.	.	.	4.07	-8.14	0.01069	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	2.7694	0.05329	0.489:0.2388:0.1618:0.1105	.	.	.	.	X	85	.	.	E	+	1	0	C17orf77	70100033	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.219000	0.02973	-1.873000	0.01135	-1.316000	0.01300	GAA	G|0.994;T|0.006	0.006	strong		0.453	C17orf77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000145090.2	NM_152460	
ADAM28	10863	hgsc.bcm.edu	37	8	24167700	24167700	+	Silent	SNP	G	G	A	rs150620720	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:24167700G>A	ENST00000265769.4	+	4	362	c.252G>A	c.(250-252)acG>acA	p.T84T	RP11-624C23.1_ENST00000523578.1_RNA|ADAM28_ENST00000540823.1_5'UTR|RP11-624C23.1_ENST00000518988.1_RNA|ADAM28_ENST00000397649.3_5'UTR|RP11-624C23.1_ENST00000519689.1_RNA|RP11-624C23.1_ENST00000523700.1_RNA|ADAM28_ENST00000437154.2_Silent_p.T84T	NM_014265.4	NP_055080.2	Q9UKQ2	ADA28_HUMAN	ADAM metallopeptidase domain 28	84					spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(7)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	42		Prostate(55;0.0959)		Colorectal(74;0.0129)|COAD - Colon adenocarcinoma(73;0.0434)|BRCA - Breast invasive adenocarcinoma(99;0.175)		CAGGCTACACGGAAACATATT	0.398													A|||	2	0.000399361	0.0	0.0	5008	,	,		18307	0.0		0.002	False		,,,				2504	0.0				p.T84T	NSCLC(193;488 2149 22258 34798 40734)	Atlas-SNP	.											ADAM28,NS,carcinoma,0,1	ADAM28	100	1	0			c.G252A						PASS	.	A	,	1,4405	825.4+/-416.5	0,1,2202	92.0	79.0	83.0		252,252	-9.1	0.0	8	dbSNP_134	83	1,8599	818.4+/-406.9	0,1,4299	no	coding-synonymous,coding-synonymous	ADAM28	NM_014265.4,NM_021777.3	,	0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154	,	84/776,84/541	24167700	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	10863	exon4			CTACACGGAAACA	AJ242015	CCDS34865.1, CCDS47830.1	8p21.2	2005-11-29	2005-08-18		ENSG00000042980	ENSG00000042980		"""ADAM metallopeptidase domain containing"""	206	protein-coding gene	gene with protein product		606188	"""a disintegrin and metalloproteinase domain 28"""				Standard	XM_005273378		Approved	eMDCII, MDC-Lm, MDC-Ls, ADAM23	uc003xdy.3	Q9UKQ2	OTTHUMG00000163780	ENST00000265769.4:c.252G>A	8.37:g.24167700G>A		72.0	0.0	0		93.0	37.0	0.397849	NM_014265	B2RMV5|Q9Y339|Q9Y3S0	Silent	SNP	ENST00000265769.4	37	CCDS34865.1																																																																																			G|1.000;A|0.000	0.000	strong		0.398	ADAM28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375441.2	NM_021778	
PTPRN	5798	hgsc.bcm.edu	37	2	220162129	220162129	+	Silent	SNP	C	C	T	rs144452294	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220162129C>T	ENST00000295718.2	-	14	2154	c.1914G>A	c.(1912-1914)acG>acA	p.T638T	PTPRN_ENST00000423636.2_Silent_p.T548T|PTPRN_ENST00000409251.3_Silent_p.T609T|AC114803.3_ENST00000417355.1_RNA|PTPRN_ENST00000497977.1_5'Flank	NM_002846.3	NP_002837.1	Q16849	PTPRN_HUMAN	protein tyrosine phosphatase, receptor type, N	638					cytokine-mediated signaling pathway (GO:0019221)|peptidyl-tyrosine dephosphorylation (GO:0035335)|response to cAMP (GO:0051591)|response to estrogen (GO:0043627)|response to glucose (GO:0009749)|response to insulin (GO:0032868)|response to reactive oxygen species (GO:0000302)	integral component of plasma membrane (GO:0005887)	spectrin binding (GO:0030507)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(3)|prostate(4)|skin(11)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Renal(207;0.0474)		Epithelial(149;4.22e-07)|all cancers(144;8.82e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)|STAD - Stomach adenocarcinoma(1183;0.0875)		ACAAGGACTTCGTGGCCATGT	0.622													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		17782	0.0		0.007	False		,,,				2504	0.001				p.T638T		Atlas-SNP	.											PTPRN,colon,carcinoma,-1,1	PTPRN	138	1	0			c.G1914A						PASS	.	C	,,	9,4397	15.5+/-35.6	0,9,2194	53.0	56.0	55.0		1827,1644,1914	-4.2	1.0	2	dbSNP_134	55	78,8522	45.4+/-104.0	0,78,4222	no	coding-synonymous,coding-synonymous,coding-synonymous	PTPRN	NM_001199763.1,NM_001199764.1,NM_002846.3	,,	0,87,6416	TT,TC,CC		0.907,0.2043,0.6689	,,	609/951,548/890,638/980	220162129	87,12919	2203	4300	6503	SO:0001819	synonymous_variant	5798	exon14			GGACTTCGTGGCC		CCDS2440.1, CCDS56167.1, CCDS56168.1	2q35-q36.1	2011-06-09			ENSG00000054356	ENSG00000054356		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9676	protein-coding gene	gene with protein product		601773				8024693	Standard	NM_001199763		Approved	IA-2	uc002vkz.3	Q16849	OTTHUMG00000133129	ENST00000295718.2:c.1914G>A	2.37:g.220162129C>T		91.0	0.0	0		86.0	41.0	0.476744	NM_002846	B4DK12|F5GZS3|Q08319|Q53QD6|Q6NSL1	Silent	SNP	ENST00000295718.2	37	CCDS2440.1																																																																																			C|0.996;T|0.004	0.004	strong		0.622	PTPRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256819.2		
LDLRAD1	388633	hgsc.bcm.edu	37	1	54480033	54480033	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:54480033G>A	ENST00000371360.1	-	3	95	c.78C>T	c.(76-78)ggC>ggT	p.G26G	LDLRAD1_ENST00000420619.1_Intron|LDLRAD1_ENST00000545928.1_Intron|LDLRAD1_ENST00000371362.3_Intron	NM_001010978.2	NP_001010978.2	Q5T700	LRAD1_HUMAN	low density lipoprotein receptor class A domain containing 1	26						integral component of membrane (GO:0016021)				large_intestine(3)|prostate(1)|skin(3)	7						GGTGGCCGCCGCCTGCTGTGT	0.692																																					p.G26G		Atlas-SNP	.											.	LDLRAD1	22	.	0			c.C78T						PASS	.						12.0	13.0	12.0					1																	54480033		1980	3842	5822	SO:0001819	synonymous_variant	388633	exon3			GCCGCCGCCTGCT		CCDS30725.1, CCDS60145.1, CCDS60146.1, CCDS60147.1	1p32.3	2008-02-05	2005-10-07		ENSG00000203985	ENSG00000203985			32069	protein-coding gene	gene with protein product			"""low density lipoprotein receptor A domain containing 1"""				Standard	NM_001010978		Approved		uc001cwm.2	Q5T700	OTTHUMG00000008433	ENST00000371360.1:c.78C>T	1.37:g.54480033G>A		90.0	0.0	0		61.0	34.0	0.557377	NM_001010978	A0PJY0|B7ZME3|Q5T6Z9	Silent	SNP	ENST00000371360.1	37	CCDS30725.1																																																																																			.	.	none		0.692	LDLRAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023243.1	NM_001010978	
RP1L1	94137	hgsc.bcm.edu	37	8	10469292	10469292	+	Silent	SNP	C	C	T	rs62490857	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:10469292C>T	ENST00000382483.3	-	4	2539	c.2316G>A	c.(2314-2316)tcG>tcA	p.S772S		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	772					cell projection organization (GO:0030030)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|visual perception (GO:0007601)	axoneme (GO:0005930)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)|photoreceptor connecting cilium (GO:0032391)|photoreceptor outer segment (GO:0001750)				breast(5)|central_nervous_system(2)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(16)|lung(82)|ovary(8)|prostate(5)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	148				COAD - Colon adenocarcinoma(149;0.0811)		TGGGGGCCGGCGAGCATGTCC	0.662													C|||	152	0.0303514	0.0023	0.0288	5008	,	,		16095	0.001		0.1083	False		,,,				2504	0.0194				p.S772S		Atlas-SNP	.											.	RP1L1	453	.	0			c.G2316A						PASS	.	C		64,3840		0,64,1888	50.0	57.0	55.0		2316	-10.2	0.0	8	dbSNP_129	55	681,7581		25,631,3475	no	coding-synonymous	RP1L1	NM_178857.5		25,695,5363	TT,TC,CC		8.2426,1.6393,6.1236		772/2401	10469292	745,11421	1952	4131	6083	SO:0001819	synonymous_variant	94137	exon4			GGCCGGCGAGCAT	AY168346	CCDS43708.1	8p23.1	2011-12-06			ENSG00000183638	ENSG00000183638			15946	protein-coding gene	gene with protein product		608581				12634863	Standard	NM_178857		Approved	DCDC4B	uc003wtc.3	Q8IWN7	OTTHUMG00000163806	ENST00000382483.3:c.2316G>A	8.37:g.10469292C>T		141.0	0.0	0		123.0	65.0	0.528455	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Silent	SNP	ENST00000382483.3	37	CCDS43708.1																																																																																			C|0.945;T|0.055	0.055	strong		0.662	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
EBF4	57593	hgsc.bcm.edu	37	20	2686317	2686317	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:2686317C>T	ENST00000609451.1	+	2	304	c.232C>T	c.(232-234)Cgg>Tgg	p.R78W	EBF4_ENST00000380648.4_Missense_Mutation_p.R74W			Q9BQW3	COE4_HUMAN	early B-cell factor 4	78					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)										CATGTACGACCGGCAGGGGCA	0.617																																					p.R74W		Atlas-SNP	.											.	.	.	.	0			c.C220T						PASS	.						75.0	77.0	76.0					20																	2686317		692	1591	2283	SO:0001583	missense	57593	exon3			TACGACCGGCAGG	BC019106	CCDS46573.1	20p13	2008-10-23			ENSG00000088881	ENSG00000088881			29278	protein-coding gene	gene with protein product		609935				10718198	Standard	NM_001110514		Approved	KIAA1442, COE4, RP5-860F19.3, O/E-4	uc002wgt.4	Q9BQW3	OTTHUMG00000031709	ENST00000609451.1:c.232C>T	20.37:g.2686317C>T	ENSP00000477023:p.Arg78Trp	113.0	0.0	0		112.0	53.0	0.473214	NM_001110514	Q1MTP7|Q5JY53|Q9NUB6|Q9P2A6	Missense_Mutation	SNP	ENST00000609451.1	37		.	.	.	.	.	.	.	.	.	.	C	19.44	3.827666	0.71143	.	.	ENSG00000088881	ENST00000380648;ENST00000342725	T;T	0.54071	0.59;0.59	4.64	4.64	0.57946	.	0.149754	0.31051	N	0.008358	T	0.70718	0.3256	M	0.70595	2.14	0.44798	D	0.997804	D	0.89917	1.0	D	0.73380	0.98	T	0.75077	-0.3445	10	0.87932	D	0	-8.4514	15.4209	0.75009	0.0:1.0:0.0:0.0	.	74	E9PEI2	.	W	74;78	ENSP00000370022:R74W;ENSP00000345030:R78W	ENSP00000345030:R78W	R	+	1	2	EBF4	2634317	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.065000	0.30592	2.301000	0.77427	0.485000	0.47835	CGG	.	.	none		0.617	EBF4-011	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471930.1	XM_938882	
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760533	186760533	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760533C>T	ENST00000169298.3	+	4	716	c.42C>T	c.(40-42)gtC>gtT	p.V14V	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Silent_p.V14V	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	14					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		GCTGCTGCGTCCTGGTCTTTC	0.403																																					p.V14V		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.C42T						PASS	.						165.0	161.0	162.0					3																	186760533		2203	4300	6503	SO:0001819	synonymous_variant	6480	exon3			CTGCGTCCTGGTC	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.42C>T	3.37:g.186760533C>T		193.0	0.0	0		207.0	22.0	0.10628	NM_003032	A8KA14|B2R513|D3DNV3	Silent	SNP	ENST00000169298.3	37	CCDS3285.1																																																																																			.	.	none		0.403	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
RNF41	10193	hgsc.bcm.edu	37	12	56601998	56601998	+	Silent	SNP	G	G	A	rs17118378	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56601998G>A	ENST00000345093.4	-	5	816	c.447C>T	c.(445-447)atC>atT	p.I149I	RNF41_ENST00000552244.1_Silent_p.I149I|RNF41_ENST00000394013.2_Silent_p.I78I|RNF41_ENST00000552656.1_Silent_p.I149I	NM_005785.3|NM_194359.2	NP_005776.1|NP_919340.1	Q9H4P4	RNF41_HUMAN	ring finger protein 41, E3 ubiquitin protein ligase	149					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|proteasomal protein catabolic process (GO:0010498)|protein autoubiquitination (GO:0051865)|protein polyubiquitination (GO:0000209)|regulation of establishment of cell polarity (GO:2000114)|regulation of lymphocyte differentiation (GO:0045619)|regulation of MAPK cascade (GO:0043408)|regulation of myeloid cell differentiation (GO:0045637)|regulation of protein kinase B signaling (GO:0051896)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytosol (GO:0005829)	acid-amino acid ligase activity (GO:0016881)|protein tag (GO:0031386)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|large_intestine(2)|lung(1)|skin(2)|urinary_tract(1)	11						CCAGCTCTGCGATGCGTGTCT	0.562													G|||	77	0.0153754	0.0424	0.0072	5008	,	,		19990	0.0		0.0	False		,,,				2504	0.0164				p.I149I		Atlas-SNP	.											.	RNF41	31	.	0			c.C447T						PASS	.	G	,,,	142,4264	101.6+/-140.2	6,130,2067	132.0	104.0	114.0		447,447,234,447	-4.0	0.9	12	dbSNP_123	114	9,8591	7.7+/-29.5	0,9,4291	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	RNF41	NM_001242826.1,NM_005785.3,NM_194358.2,NM_194359.2	,,,	6,139,6358	AA,AG,GG		0.1047,3.2229,1.161	,,,	149/318,149/318,78/247,149/318	56601998	151,12855	2203	4300	6503	SO:0001819	synonymous_variant	10193	exon5			CTCTGCGATGCGT	AF077599	CCDS8909.1, CCDS8910.1	12q13.13	2014-03-24	2014-03-24		ENSG00000181852	ENSG00000181852		"""RING-type (C3HC4) zinc fingers"""	18401	protein-coding gene	gene with protein product			"""ring finger protein 41"""				Standard	NM_005785		Approved	SBBI03, NRDP1	uc001skg.2	Q9H4P4	OTTHUMG00000170328	ENST00000345093.4:c.447C>T	12.37:g.56601998G>A		160.0	0.0	0		214.0	96.0	0.448598	NM_005785	A6NFW0|B2RBT8|O75598	Silent	SNP	ENST00000345093.4	37	CCDS8909.1																																																																																			G|0.986;A|0.014	0.014	strong		0.562	RNF41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408525.1	NM_005785	
MICA	100507436	hgsc.bcm.edu	37	6	31378928	31378928	+	Silent	SNP	C	C	T	rs41553614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31378928C>T	ENST00000449934.2	+	3	459	c.405C>T	c.(403-405)taC>taT	p.Y135Y	HCP5_ENST00000414046.2_RNA	NM_001177519.1	NP_001170990.1			MHC class I polypeptide-related sequence A											breast(1)|endometrium(3)|kidney(1)	5		Ovarian(999;0.0253)				ATTTCTACTACGATGGGGAGC	0.552													c|||	77	0.0153754	0.0212	0.0245	5008	,	,		20471	0.003		0.0159	False		,,,				2504	0.0133				p.Y135Y		Atlas-SNP	.											.	MICA	21	.	0			c.C405T						PASS	.	C		38,1346		1,36,655	45.0	42.0	43.0		405	-3.0	0.0	6	dbSNP_127	43	49,3133		1,47,1543	no	coding-synonymous	MICA	NM_001177519.1		2,83,2198	TT,TC,CC		1.5399,2.7457,1.9054		135/333	31378928	87,4479	692	1591	2283	SO:0001819	synonymous_variant	100507436	exon3			CTACTACGATGGG	L14848	CCDS56412.1, CCDS75421.1	6p21.3	2013-01-11			ENSG00000204520	ENSG00000204520		"""Immunoglobulin superfamily / C1-set domain containing"""	7090	protein-coding gene	gene with protein product		600169				8022771	Standard	NM_000247		Approved	PERB11.1	uc003ntk.1	Q29983	OTTHUMG00000031073	ENST00000449934.2:c.405C>T	6.37:g.31378928C>T		161.0	0.0	0		221.0	113.0	0.511312	NM_001177519		Silent	SNP	ENST00000449934.2	37	CCDS56412.1																																																																																			C|0.987;T|0.013	0.013	strong		0.552	MICA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076101.7	NM_001177519	
FBXW5	54461	hgsc.bcm.edu	37	9	139838414	139838414	+	Missense_Mutation	SNP	C	C	T	rs200423543		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139838414C>T	ENST00000325285.3	-	2	201	c.122G>A	c.(121-123)cGg>cAg	p.R41Q	FBXW5_ENST00000483559.1_5'UTR|C8G_ENST00000224181.3_5'Flank	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	41	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				centrosome duplication (GO:0051298)|mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	protein kinase binding (GO:0019901)			breast(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	12	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.19)	OV - Ovarian serous cystadenocarcinoma(145;7.8e-06)|Epithelial(140;0.000106)		GAACTCGTCCCGCGACACGGC	0.701																																					p.R41Q		Atlas-SNP	.											.	FBXW5	36	.	0			c.G122A						PASS	.		GLN/ARG	4,4272		0,4,2134	12.0	14.0	13.0		122	2.1	0.9	9		13	30,8458		0,30,4214	yes	missense	FBXW5	NM_018998.2	43	0,34,6348	TT,TC,CC		0.3534,0.0935,0.2664	probably-damaging	41/567	139838414	34,12730	2138	4244	6382	SO:0001583	missense	54461	exon2			TCGTCCCGCGACA	BC014130	CCDS7014.1	9q34.3	2013-01-09	2007-02-08		ENSG00000159069	ENSG00000159069		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13613	protein-coding gene	gene with protein product		609072	"""F-box and WD-40 domain protein 5"""				Standard	NM_018998		Approved	DKFZP434B205, MGC20962, Fbw5	uc004cjx.3	Q969U6	OTTHUMG00000020967	ENST00000325285.3:c.122G>A	9.37:g.139838414C>T	ENSP00000313034:p.Arg41Gln	98.0	0.0	0		30.0	21.0	0.7	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	.	.	.	.	.	.	.	.	.	.	c	19.18	3.777882	0.70107	9.35E-4	0.003534	ENSG00000159069	ENST00000325285;ENST00000428398;ENST00000443788	T;T;T	0.66460	-0.21;-0.21;-0.21	4.02	2.08	0.27032	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.139015	0.47852	D	0.000201	T	0.67078	0.2855	L	0.35414	1.06	0.40830	D	0.983582	D	0.89917	1.0	D	0.68765	0.96	T	0.62334	-0.6876	10	0.33940	T	0.23	-1.4432	7.9151	0.29814	0.1841:0.6384:0.1775:0.0	.	41	Q969U6	FBXW5_HUMAN	Q	41	ENSP00000313034:R41Q;ENSP00000404829:R41Q;ENSP00000394011:R41Q	ENSP00000313034:R41Q	R	-	2	0	FBXW5	138958235	1.000000	0.71417	0.898000	0.35279	0.387000	0.30353	5.101000	0.64566	0.321000	0.23259	-0.529000	0.04317	CGG	.	.	weak		0.701	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
KLHL32	114792	hgsc.bcm.edu	37	6	97562207	97562207	+	Silent	SNP	G	G	T	rs74787311	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:97562207G>T	ENST00000369261.4	+	7	1539	c.1176G>T	c.(1174-1176)gtG>gtT	p.V392V	KLHL32_ENST00000539200.1_Silent_p.V323V|KLHL32_ENST00000536676.1_Silent_p.V356V|KLHL32_ENST00000544166.1_Intron	NM_052904.3	NP_443136.2	Q96NJ5	KLH32_HUMAN	kelch-like family member 32	392										breast(2)|endometrium(3)|kidney(4)|large_intestine(9)|lung(13)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		all_cancers(76;1.19e-06)|Acute lymphoblastic leukemia(125;5.83e-10)|all_hematologic(75;3.67e-07)|all_epithelial(107;0.00778)|Colorectal(196;0.122)		BRCA - Breast invasive adenocarcinoma(108;0.0558)		AGCATTTTGTGCTGGGTGCCA	0.542													G|||	92	0.0183706	0.0023	0.0375	5008	,	,		19608	0.001		0.0517	False		,,,				2504	0.0102				p.V392V		Atlas-SNP	.											.	KLHL32	85	.	0			c.G1176T						PASS	.	G		55,4349	52.3+/-87.9	1,53,2148	44.0	42.0	43.0		1176	2.5	1.0	6	dbSNP_132	43	590,8010	157.0+/-210.8	23,544,3733	no	coding-synonymous	KLHL32	NM_052904.3		24,597,5881	TT,TG,GG		6.8605,1.2489,4.96		392/621	97562207	645,12359	2202	4300	6502	SO:0001819	synonymous_variant	114792	exon7			TTTTGTGCTGGGT	AB067487	CCDS5038.1, CCDS69154.1, CCDS69155.1, CCDS75495.1	6q16.3	2013-02-22	2013-02-22	2007-01-09	ENSG00000186231	ENSG00000186231		"""Kelch-like"", ""BTB/POZ domain containing"""	21221	protein-coding gene	gene with protein product			"""BTB and kelch domain containing 5"", ""KIAA1900"", ""kelch-like 32 (Drosophila)"""	BKLHD5, KIAA1900			Standard	NM_052904		Approved		uc010kcm.1	Q96NJ5	OTTHUMG00000015247	ENST00000369261.4:c.1176G>T	6.37:g.97562207G>T		70.0	0.0	0		82.0	32.0	0.390244	NM_052904	B7Z346|B7Z4E2|E1P528|Q5THT0|Q96PY7	Silent	SNP	ENST00000369261.4	37	CCDS5038.1																																																																																			G|0.960;T|0.040	0.040	strong		0.542	KLHL32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041570.1	NM_052904	
HPR	3250	hgsc.bcm.edu	37	16	72110872	72110872	+	Silent	SNP	G	G	A	rs147707949	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:72110872G>A	ENST00000540303.2	+	5	971	c.939G>A	c.(937-939)gcG>gcA	p.A313A	HPR_ENST00000228226.8_Silent_p.A350A|HPR_ENST00000356967.5_Silent_p.A313A|HPR_ENST00000561690.1_Missense_Mutation_p.G112S	NM_020995.3	NP_066275.3	P00739	HPTR_HUMAN	haptoglobin-related protein	313	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|spherical high-density lipoprotein particle (GO:0034366)	hemoglobin binding (GO:0030492)|serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|stomach(1)|urinary_tract(2)	20		Ovarian(137;0.125)				CCTGGTACGCGGCTGGGATCC	0.547													G|||	8	0.00159744	0.0	0.0014	5008	,	,		25381	0.0		0.005	False		,,,				2504	0.002				p.A313A		Atlas-SNP	.											HPR,NS,carcinoma,+2,1	HPR	43	1	0			c.G939A						PASS	.	G		2,4190		0,2,2094	270.0	180.0	210.0		939	-0.2	1.0	16	dbSNP_134	210	21,8425		0,21,4202	no	coding-synonymous	HPR	NM_020995.3		0,23,6296	AA,AG,GG		0.2486,0.0477,0.182		313/349	72110872	23,12615	2096	4223	6319	SO:0001819	synonymous_variant	3250	exon5			GTACGCGGCTGGG	BC160066	CCDS42193.1	16q22.2	2012-10-03			ENSG00000261701	ENSG00000261701			5156	protein-coding gene	gene with protein product		140210				2987228, 16778136	Standard	NM_020995		Approved		uc002fby.3	P00739	OTTHUMG00000173010	ENST00000540303.2:c.939G>A	16.37:g.72110872G>A		206.0	0.0	0		251.0	106.0	0.422311	NM_020995	Q7LE20|Q92658|Q92659|Q9ULB0	Silent	SNP	ENST00000540303.2	37	CCDS42193.1																																																																																			G|0.997;A|0.003	0.003	strong		0.547	HPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421696.1	NM_020995	
HNF1A	6927	hgsc.bcm.edu	37	12	121437114	121437114	+	Silent	SNP	G	G	A	rs55834942	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121437114G>A	ENST00000257555.6	+	8	1771	c.1545G>A	c.(1543-1545)acG>acA	p.T515T	HNF1A_ENST00000541395.1_Silent_p.T515T|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.T515T			P20823	HNF1A_HUMAN	HNF1 homeobox A	515					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					ACACCCACACGGGCCTGCTCC	0.677									Hepatic Adenoma, Familial Clustering of				.|||	315	0.0628994	0.0121	0.1095	5008	,	,		16172	0.001		0.1988	False		,,,				2504	0.0225				p.T515T		Atlas-SNP	.											HNF1A,brain,glioma,0,4	HNF1A	302	4	0			c.G1545A						PASS	.	G		175,4231	113.3+/-151.4	4,167,2032	68.0	70.0	70.0		1545	-7.7	0.9	12	dbSNP_129	70	1654,6944	303.3+/-306.4	156,1342,2801	yes	coding-synonymous	HNF1A	NM_000545.5		160,1509,4833	AA,AG,GG		19.237,3.9719,14.0649		515/632	121437114	1829,11175	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon8	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCACACGGGCCTG	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.1545G>A	12.37:g.121437114G>A		189.0	0.0	0		207.0	112.0	0.541063	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.860;A|0.140	0.140	strong		0.677	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
MYO7A	4647	hgsc.bcm.edu	37	11	76895787	76895787	+	Intron	SNP	G	G	A	rs111033223|rs143953991	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76895787G>A	ENST00000409709.3	+	27	3775				MYO7A_ENST00000458637.2_Intron|MYO7A_ENST00000409893.1_Missense_Mutation_p.R1177K|MYO7A_ENST00000409619.2_Intron	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA						actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						GGGGACACCAGGGCCTGAAAG	0.602																																					p.R1177K		Atlas-SNP	.											.	MYO7A	164	.	0			c.G3530A						PASS	.						13.0	15.0	14.0					11																	76895787		1872	3718	5590	SO:0001627	intron_variant	4647	exon27			ACACCAGGGCCTG	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.3503+27G>A	11.37:g.76895787G>A		0.0	0.0	.		71.0	71.0	1	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	.	1.085	-0.665772	0.03428	.	.	ENSG00000137474	ENST00000409893	D	0.87729	-2.29	4.38	0.879	0.19155	.	.	.	.	.	T	0.68705	0.3030	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.53851	-0.8380	8	.	.	.	.	3.7783	0.08669	0.2584:0.0:0.5575:0.1841	.	1177	B9A012	.	K	1177	ENSP00000386689:R1177K	.	R	+	2	0	MYO7A	76573435	0.001000	0.12720	0.009000	0.14445	0.011000	0.07611	0.416000	0.21198	0.304000	0.22809	-0.452000	0.05504	AGG	.	.	none		0.602	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
BTG2	7832	hgsc.bcm.edu	37	1	203274867	203274867	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:203274867G>T	ENST00000290551.4	+	1	204	c.133G>T	c.(133-135)Gca>Tca	p.A45S	RP11-134P9.1_ENST00000457348.1_lincRNA	NM_006763.2	NP_006754.1	P78543	BTG2_HUMAN	BTG family, member 2	45					anterior/posterior pattern specification (GO:0009952)|associative learning (GO:0008306)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system neuron development (GO:0021954)|dentate gyrus development (GO:0021542)|DNA repair (GO:0006281)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of translation (GO:0017148)|neuron projection development (GO:0031175)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|protein methylation (GO:0006479)|response to electrical stimulus (GO:0051602)|response to mechanical stimulus (GO:0009612)|response to organic cyclic compound (GO:0014070)|response to peptide hormone (GO:0043434)|skeletal muscle cell differentiation (GO:0035914)	extracellular vesicular exosome (GO:0070062)	RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)	p.A45T(1)		haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	9			BRCA - Breast invasive adenocarcinoma(75;0.203)			GCTCCAGGAGGCACTCACAGG	0.706																																					p.A45S		Atlas-SNP	.											BTG2,lymph_node,lymphoid_neoplasm,-1,2	BTG2	16	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G133T						PASS	.						11.0	13.0	13.0					1																	203274867		2020	3950	5970	SO:0001583	missense	7832	exon1			CAGGAGGCACTCA		CCDS1437.1	1q32	2008-07-18			ENSG00000159388	ENSG00000159388			1131	protein-coding gene	gene with protein product	"""B-cell translocation gene 2"", ""pheochromacytoma cell-3"", ""NGF-inducible anti-proliferative protein PC3"", ""nerve growth factor-inducible anti-proliferative"""	601597				8944033	Standard	NM_006763		Approved	PC3, TIS21, MGC126063, MGC126064	uc001gzq.3	P78543	OTTHUMG00000035834	ENST00000290551.4:c.133G>T	1.37:g.203274867G>T	ENSP00000290551:p.Ala45Ser	95.0	0.0	0		87.0	11.0	0.126437	NM_006763	A0A024R986|Q3KR25|Q5VUT0	Missense_Mutation	SNP	ENST00000290551.4	37	CCDS1437.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.877798	0.51801	.	.	ENSG00000159388	ENST00000290551	T	0.23754	1.89	4.4	4.4	0.53042	Anti-proliferative protein (3);	0.078518	0.49916	D	0.000121	T	0.28928	0.0718	L	0.43152	1.355	0.43417	D	0.995564	B	0.15930	0.015	B	0.33521	0.165	T	0.09907	-1.0653	10	0.40728	T	0.16	-33.413	15.7078	0.77598	0.0:0.0:1.0:0.0	.	45	P78543	BTG2_HUMAN	S	45	ENSP00000290551:A45S	ENSP00000290551:A45S	A	+	1	0	BTG2	201541490	1.000000	0.71417	0.991000	0.47740	0.943000	0.58893	4.326000	0.59241	2.282000	0.76494	0.471000	0.43371	GCA	.	.	none		0.706	BTG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087168.1	NM_006763	
DCHS2	54798	hgsc.bcm.edu	37	4	155219540	155219540	+	Missense_Mutation	SNP	C	C	A	rs141467714	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155219540C>A	ENST00000357232.4	-	18	4560	c.4561G>T	c.(4561-4563)Gct>Tct	p.A1521S		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1521	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		GCACCAGAAGCCTCATCAGTC	0.483																																					p.A1521S		Atlas-SNP	.											.	DCHS2	594	.	0			c.G4561T						PASS	.	C	SER/ALA	2,4404	4.2+/-10.8	0,2,2201	133.0	126.0	128.0		4561	0.8	0.0	4	dbSNP_134	128	33,8567	22.8+/-68.1	0,33,4267	yes	missense	DCHS2	NM_017639.3	99	0,35,6468	AA,AC,CC		0.3837,0.0454,0.2691	benign	1521/2917	155219540	35,12971	2203	4300	6503	SO:0001583	missense	54798	exon18			CAGAAGCCTCATC	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.4561G>T	4.37:g.155219540C>A	ENSP00000349768:p.Ala1521Ser	160.0	0.0	0		159.0	79.0	0.496855	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.010	-1.763380	0.00651	4.54E-4	0.003837	ENSG00000197410	ENST00000357232	T	0.49432	0.78	5.76	0.801	0.18679	Cadherin (4);Cadherin-like (1);	0.619653	0.16206	N	0.224698	T	0.19685	0.0473	N	0.11724	0.165	0.09310	N	1	B	0.14438	0.01	B	0.17433	0.018	T	0.15925	-1.0420	10	0.09084	T	0.74	.	0.908	0.01288	0.3676:0.2927:0.1326:0.2071	.	1521	Q6V1P9	PCD23_HUMAN	S	1521	ENSP00000349768:A1521S	ENSP00000349768:A1521S	A	-	1	0	DCHS2	155438990	0.000000	0.05858	0.000000	0.03702	0.135000	0.20990	0.074000	0.14662	-0.106000	0.12110	0.650000	0.86243	GCT	C|0.998;A|0.002	0.002	strong		0.483	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
OR7G1	125962	hgsc.bcm.edu	37	19	9225662	9225662	+	Missense_Mutation	SNP	T	T	C	rs138190811		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:9225662T>C	ENST00000541538.1	-	1	777	c.778A>G	c.(778-780)Att>Gtt	p.I260V	OR7G1_ENST00000293614.1_Missense_Mutation_p.I260V	NM_001005192.2	NP_001005192.2	Q8NGA0	OR7G1_HUMAN	olfactory receptor, family 7, subfamily G, member 1	260						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|skin(2)	20						GCAGAACTAATGTACACCCCA	0.468													T|||	1	0.000199681	0.0	0.0	5008	,	,		18140	0.001		0.0	False		,,,				2504	0.0				p.I260V		Atlas-SNP	.											.	OR7G1	53	.	0			c.A778G						PASS	.	T	VAL/ILE	0,4406		0,0,2203	109.0	102.0	104.0		778	-7.6	0.0	19	dbSNP_134	104	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OR7G1	NM_001005192.2	29	0,4,6499	CC,CT,TT		0.0465,0.0,0.0308	benign	260/312	9225662	4,13002	2203	4300	6503	SO:0001583	missense	125962	exon1			AACTAATGTACAC		CCDS32898.1, CCDS32898.2	19p13.2	2013-09-24			ENSG00000161807	ENSG00000161807		"""GPCR / Class A : Olfactory receptors"""	8465	protein-coding gene	gene with protein product				OR7G1P			Standard	NM_001005192		Approved	OR19-15	uc021uoi.1	Q8NGA0	OTTHUMG00000168067	ENST00000541538.1:c.778A>G	19.37:g.9225662T>C	ENSP00000444134:p.Ile260Val	77.0	0.0	0		95.0	51.0	0.536842	NM_001005192	Q6IFJ5|Q96RA1	Missense_Mutation	SNP	ENST00000541538.1	37	CCDS32898.2	.	.	.	.	.	.	.	.	.	.	t	9.233	1.036306	0.19669	0.0	4.65E-4	ENSG00000161807	ENST00000293614;ENST00000541538	T;T	0.37058	1.22;1.22	3.78	-7.55	0.01327	GPCR, rhodopsin-like superfamily (1);	0.478549	0.15276	U	0.270958	T	0.18509	0.0444	N	0.25825	0.765	0.09310	N	1	B	0.16603	0.018	B	0.30943	0.122	T	0.22277	-1.0221	10	0.72032	D	0.01	.	2.0374	0.03542	0.2085:0.2559:0.3872:0.1484	.	260	Q8NGA0	OR7G1_HUMAN	V	260	ENSP00000293614:I260V;ENSP00000444134:I260V	ENSP00000293614:I260V	I	-	1	0	OR7G1	9086662	0.000000	0.05858	0.012000	0.15200	0.016000	0.09150	-2.649000	0.00858	-1.542000	0.01725	-0.539000	0.04255	ATT	T|0.999;C|0.001	0.001	strong		0.468	OR7G1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397912.1		
DNAJC13	23317	hgsc.bcm.edu	37	3	132221139	132221139	+	Missense_Mutation	SNP	C	C	T	rs55825559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:132221139C>T	ENST00000260818.6	+	40	4791	c.4543C>T	c.(4543-4545)Ccc>Tcc	p.P1515S		NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	1515			P -> S (in dbSNP:rs55825559).		osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						TCAGAGTATTCCCCGCGTAGC	0.413													C|||	60	0.0119808	0.0	0.0245	5008	,	,		15388	0.0		0.0368	False		,,,				2504	0.0061				p.P1515S		Atlas-SNP	.											.	DNAJC13	253	.	0			c.C4543T						PASS	.	C	SER/PRO	26,4380	32.6+/-62.9	0,26,2177	117.0	113.0	115.0		4543	5.8	1.0	3	dbSNP_129	115	239,8361	94.5+/-156.4	5,229,4066	yes	missense	DNAJC13	NM_015268.3	74	5,255,6243	TT,TC,CC		2.7791,0.5901,2.0375	benign	1515/2244	132221139	265,12741	2203	4300	6503	SO:0001583	missense	23317	exon40			AGTATTCCCCGCG	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.4543C>T	3.37:g.132221139C>T	ENSP00000260818:p.Pro1515Ser	135.0	0.0	0		144.0	50.0	0.347222	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Missense_Mutation	SNP	ENST00000260818.6	37	CCDS33857.1	34	0.015567765567765568	0	0.0	9	0.024861878453038673	0	0.0	25	0.032981530343007916	C	14.92	2.678748	0.47886	0.005901	0.027791	ENSG00000138246	ENST00000260818;ENST00000538066	T	0.52057	0.68	5.81	5.81	0.92471	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.24812	0.0602	M	0.69185	2.1	0.54753	D	0.999985	B	0.20368	0.044	B	0.15870	0.014	T	0.17653	-1.0362	10	0.40728	T	0.16	.	16.3288	0.82997	0.0:0.868:0.132:0.0	rs55825559;rs61748104	1515	O75165	DJC13_HUMAN	S	1515;162	ENSP00000260818:P1515S	ENSP00000260818:P1515S	P	+	1	0	DNAJC13	133703829	1.000000	0.71417	0.998000	0.56505	0.614000	0.37383	4.644000	0.61397	2.734000	0.93682	0.650000	0.86243	CCC	C|0.981;T|0.019	0.019	strong		0.413	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318826	21318826	+	Missense_Mutation	SNP	G	G	A	rs142399667	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:21318826G>A	ENST00000583088.1	+	3	1067	c.172G>A	c.(172-174)Gcc>Acc	p.A58T	KCNJ12_ENST00000331718.5_Missense_Mutation_p.A58T	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	58					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	CATTGAGTTCGCCAACATGGA	0.597										Prostate(3;0.18)																											p.A58T		Atlas-SNP	.											KCNJ12,NS,carcinoma,0,1	.	.	1	0			c.G172A						scavenged	.	G	THR/ALA	69,4337	52.3+/-87.9	0,69,2134	197.0	131.0	153.0		172	5.3	1.0	17	dbSNP_134	153	62,8538	26.8+/-75.7	0,62,4238	yes	missense	KCNJ12	NM_021012.4	58	0,131,6372	AA,AG,GG		0.7209,1.566,1.0072	benign	58/434	21318826	131,12875	2203	4300	6503	SO:0001583	missense	100134444	exon3			GAGTTCGCCAACA	L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.172G>A	17.37:g.21318826G>A	ENSP00000463778:p.Ala58Thr	246.0	1.0	0.00406504		259.0	45.0	0.173745	NM_001194958	O43401|Q15756|Q8NG63	Missense_Mutation	SNP	ENST00000583088.1	37	CCDS11219.1	.	.	.	.	.	.	.	.	.	.	G	11.62	1.692589	0.30052	0.01566	0.007209	ENSG00000184185	ENST00000331718	D	0.93859	-3.3	5.33	5.33	0.75918	Potassium channel, inwardly rectifying, Kir, conserved region 2 (1);	0.248894	0.40908	D	0.000997	T	0.77631	0.4159	N	0.16233	0.39	0.36661	D	0.877951	B	0.12630	0.006	B	0.18263	0.021	T	0.80009	-0.1562	10	0.32370	T	0.25	.	10.2342	0.43273	0.1224:0.0:0.8776:0.0	.	58	Q14500	IRK12_HUMAN	T	58	ENSP00000328150:A58T	ENSP00000328150:A58T	A	+	1	0	KCNJ12	21259419	0.993000	0.37304	1.000000	0.80357	0.988000	0.76386	2.230000	0.42999	2.506000	0.84524	0.591000	0.81541	GCC	G|0.993;A|0.007	0.007	strong		0.597	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2	NM_021012	
IRF5	3663	hgsc.bcm.edu	37	7	128588712	128588712	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128588712C>T	ENST00000402030.2	+	9	1409	c.1337C>T	c.(1336-1338)tCa>tTa	p.S446L	IRF5_ENST00000473745.1_Missense_Mutation_p.S446L|IRF5_ENST00000249375.4_Missense_Mutation_p.S446L|IRF5_ENST00000477535.1_Missense_Mutation_p.S360L|IRF5_ENST00000357234.5_Missense_Mutation_p.S462L	NM_001098629.1|NM_001098630.1	NP_001092099.1|NP_001092100.1	Q13568	IRF5_HUMAN	interferon regulatory factor 5	446					cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of apoptotic process (GO:0043065)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to muramyl dipeptide (GO:0032495)|response to peptidoglycan (GO:0032494)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(1)|prostate(1)	15						CTACAGATCTCAAACCCAGAC	0.577																																					p.S462L		Atlas-SNP	.											.	IRF5	40	.	0			c.C1385T						PASS	.						123.0	128.0	126.0					7																	128588712		2203	4300	6503	SO:0001583	missense	3663	exon9			AGATCTCAAACCC		CCDS5808.1, CCDS43645.1, CCDS56512.1	7q32	2008-07-18			ENSG00000128604	ENSG00000128604			6120	protein-coding gene	gene with protein product		607218					Standard	XM_005250317		Approved		uc003vog.3	Q13568	OTTHUMG00000158410	ENST00000402030.2:c.1337C>T	7.37:g.128588712C>T	ENSP00000385352:p.Ser446Leu	93.0	0.0	0		99.0	16.0	0.161616	NM_001098629	A4D1J8|A8DUA8|A8DUA9|E7EQ16|E7EW54|Q1A7B4|Q64GA9|Q64GB1|Q64GB2|Q6RCM8|Q9BQF0	Missense_Mutation	SNP	ENST00000402030.2	37	CCDS5808.1	.	.	.	.	.	.	.	.	.	.	C	33	5.274132	0.95459	.	.	ENSG00000128604	ENST00000357234;ENST00000477535;ENST00000402030;ENST00000249375;ENST00000473745;ENST00000412326	D;D;D;D;D	0.96136	-3.92;-3.92;-3.92;-3.92;-3.92	5.88	5.88	0.94601	SMAD domain-like (1);SMAD/FHA domain (1);	0.000000	0.49916	D	0.000135	D	0.97445	0.9164	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.993;0.993;0.999	D	0.97569	1.0103	10	0.62326	D	0.03	-6.6903	17.7218	0.88353	0.0:1.0:0.0:0.0	.	360;446;462	E7EW54;Q13568;Q13568-2	.;IRF5_HUMAN;.	L	462;360;446;446;446;436	ENSP00000349770:S462L;ENSP00000419950:S360L;ENSP00000385352:S446L;ENSP00000249375:S446L;ENSP00000419149:S446L	ENSP00000249375:S446L	S	+	2	0	IRF5	128375948	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.487000	0.81328	2.778000	0.95560	0.655000	0.94253	TCA	.	.	none		0.577	IRF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350934.1	NM_001098627	
DCTN1	1639	hgsc.bcm.edu	37	2	74589828	74589828	+	Missense_Mutation	SNP	C	C	T	rs200834352		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74589828C>T	ENST00000361874.3	-	30	3875	c.3558G>A	c.(3556-3558)atG>atA	p.M1186I	DCTN1_ENST00000409868.1_Missense_Mutation_p.M1164I|DCTN1_ENST00000394003.3_Missense_Mutation_p.M1179I|DCTN1_ENST00000409567.3_Missense_Mutation_p.M1161I|DCTN1_ENST00000409438.1_Missense_Mutation_p.M1047I|DCTN1_ENST00000407639.2_Missense_Mutation_p.M1052I|DCTN1_ENST00000409240.1_Missense_Mutation_p.M1144I|RP11-287D1.3_ENST00000451608.2_Missense_Mutation_p.M99I	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	1186					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|G2/M transition of mitotic cell cycle (GO:0000086)|melanosome transport (GO:0032402)|microtubule-based transport (GO:0010970)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|nervous system development (GO:0007399)	cell leading edge (GO:0031252)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|dynein complex (GO:0030286)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	motor activity (GO:0003774)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(20)|ovary(4)|prostate(1)|skin(3)	45						CCACTTGCTCCATAAGTTGGG	0.572																																					p.M1186I		Atlas-SNP	.											.	DCTN1	110	.	0			c.G3558A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET,ILE/MET	0,4406		0,0,2203	62.0	49.0	53.0		3483,3141,3432,3537,3558,3156	4.7	1.0	2		53	3,8597	2.2+/-6.3	0,3,4297	no	missense,missense,missense,missense,missense,missense	DCTN1	NM_001135040.2,NM_001135041.2,NM_001190836.1,NM_001190837.1,NM_004082.4,NM_023019.3	10,10,10,10,10,10	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign,benign,benign,benign,benign,benign	1161/1254,1047/1140,1144/1237,1179/1272,1186/1279,1052/1145	74589828	3,13003	2203	4300	6503	SO:0001583	missense	1639	exon30			TTGCTCCATAAGT		CCDS1939.1, CCDS46341.1, CCDS46342.1, CCDS54368.1, CCDS54369.1	2p13	2014-09-17	2010-06-24		ENSG00000204843	ENSG00000204843			2711	protein-coding gene	gene with protein product	"""p150 glued homolog (Drosophila)"""	601143	"""dynactin 1 (p150, Glued (Drosophila) homolog)"""			1828535	Standard	NM_001190836		Approved		uc002skx.3	Q14203	OTTHUMG00000129963	ENST00000361874.3:c.3558G>A	2.37:g.74589828C>T	ENSP00000354791:p.Met1186Ile	84.0	0.0	0		86.0	50.0	0.581395	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	.	.	.	.	.	.	.	.	.	.	C	10.15	1.269980	0.23221	0.0	3.49E-4	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76186	-1.0;-1.0;-1.0;-1.0;-1.0;-1.0;-1.0	5.53	4.65	0.58169	.	0.185557	0.25978	N	0.027082	T	0.59702	0.2213	N	0.19112	0.55	0.34587	D	0.715042	B;B;B;B;B;B;B	0.09022	0.0;0.0;0.001;0.0;0.002;0.0;0.0	B;B;B;B;B;B;B	0.10450	0.0;0.0;0.0;0.0;0.005;0.001;0.001	T	0.61964	-0.6954	10	0.25751	T	0.34	-3.2341	13.1932	0.59723	0.0:0.9221:0.0:0.0779	.	1161;1144;1186;1179;1052;1047;1169	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4;A8MWX9	.;.;DCTN1_HUMAN;.;.;.;.	I	1186;1179;1169;1052;1047;1144;1164;1161	ENSP00000354791:M1186I;ENSP00000377571:M1179I;ENSP00000384844:M1052I;ENSP00000387270:M1047I;ENSP00000386406:M1144I;ENSP00000387327:M1164I;ENSP00000386843:M1161I	ENSP00000354791:M1186I	M	-	3	0	DCTN1	74443336	1.000000	0.71417	1.000000	0.80357	0.213000	0.24496	1.852000	0.39348	1.332000	0.45431	-0.218000	0.12543	ATG	C|0.999;T|0.001	0.001	weak		0.572	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
KAT6A	7994	hgsc.bcm.edu	37	8	41790866	41790866	+	Silent	SNP	G	G	C	rs2980901	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:41790866G>C	ENST00000396930.3	-	18	5415	c.4872C>G	c.(4870-4872)gtC>gtG	p.V1624V	KAT6A_ENST00000265713.2_Silent_p.V1624V|KAT6A_ENST00000406337.1_Silent_p.V1624V	NM_001099412.1	NP_001092882.1	Q92794	KAT6A_HUMAN	K(lysine) acetyltransferase 6A	1624	Interaction with PML.|Interaction with RUNX1-2.				aorta morphogenesis (GO:0035909)|cellular senescence (GO:0090398)|chromatin organization (GO:0006325)|DNA packaging (GO:0006323)|embryonic hemopoiesis (GO:0035162)|face morphogenesis (GO:0060325)|heart morphogenesis (GO:0003007)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|myeloid cell differentiation (GO:0030099)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|protein acetylation (GO:0006473)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|PML body (GO:0016605)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										CAGCAGGCTGGACGCTGCTCT	0.642													G|||	182	0.0363419	0.1074	0.0159	5008	,	,		16184	0.0089		0.0089	False		,,,				2504	0.0112				p.V1624V		Atlas-SNP	.											.	.	.	.	0			c.C4872G						PASS	.	G	,,	386,4016		16,354,1831	29.0	26.0	27.0		4872,4872,4872	1.7	1.0	8	dbSNP_101	27	123,8469		0,123,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	KAT6A	NM_001099412.1,NM_001099413.1,NM_006766.3	,,	16,477,6004	CC,CG,GG		1.4316,8.7687,3.9172	,,	1624/2005,1624/2005,1624/2005	41790866	509,12485	2201	4296	6497	SO:0001819	synonymous_variant	7994	exon18			AGGCTGGACGCTG	U47742	CCDS6124.1	8p11	2013-01-28	2011-07-21	2011-07-21	ENSG00000083168	ENSG00000083168		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	13013	protein-coding gene	gene with protein product	"""Monocytic leukemia zinc finger protein"""	601408	"""runt-related transcription factor binding protein 2"", ""MYST histone acetyltransferase (monocytic leukemia) 3"""	ZNF220, RUNXBP2, MYST3		8849440, 8782817	Standard	NM_001099412		Approved	MOZ, ZC2HC6A	uc003xon.4	Q92794	OTTHUMG00000150453	ENST00000396930.3:c.4872C>G	8.37:g.41790866G>C		50.0	0.0	0		46.0	25.0	0.543478	NM_001099412	Q76L81	Silent	SNP	ENST00000396930.3	37	CCDS6124.1																																																																																			G|0.964;C|0.036	0.036	strong		0.642	KAT6A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318163.1	NM_006766	
VWA2	340706	hgsc.bcm.edu	37	10	116050058	116050058	+	Missense_Mutation	SNP	G	G	C	rs45560935	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:116050058G>C	ENST00000392982.3	+	13	2432	c.2182G>C	c.(2182-2184)Gtc>Ctc	p.V728L				Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	728	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		GGGCAGCTGCGTCCTGCAGAA	0.602													G|||	6	0.00119808	0.0	0.0	5008	,	,		18275	0.0		0.006	False		,,,				2504	0.0				p.V728L		Atlas-SNP	.											.	VWA2	64	.	0			c.G2182C						PASS	.																																			SO:0001583	missense	340706	exon13			AGCTGCGTCCTGC	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.2182G>C	10.37:g.116050058G>C	ENSP00000376708:p.Val728Leu	113.0	0.0	0		151.0	74.0	0.490066	NM_001272046	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	10.73	1.433111	0.25813	.	.	ENSG00000165816	ENST00000392982	D	0.92249	-3.0	5.65	-1.47	0.08772	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.461364	0.22065	N	0.065105	T	0.78591	0.4307	.	.	.	0.40475	D	0.980387	P	0.43857	0.819	B	0.38378	0.272	T	0.74553	-0.3627	9	0.16896	T	0.51	.	10.3483	0.43920	0.5818:0.0:0.4182:0.0	rs45560935	728	Q5GFL6	VWA2_HUMAN	L	728	ENSP00000376708:V728L	ENSP00000376708:V728L	V	+	1	0	VWA2	116040048	0.021000	0.18746	0.176000	0.23000	0.151000	0.21798	0.312000	0.19397	-0.137000	0.11455	-0.759000	0.03464	GTC	G|0.998;C|0.002	0.002	strong		0.602	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050456.3	NM_198496	
ARHGEF5	7984	hgsc.bcm.edu	37	7	144069807	144069807	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:144069807C>T	ENST00000056217.5	+	9	4181	c.4007C>T	c.(4006-4008)tCg>tTg	p.S1336L	ARHGEF5_ENST00000471847.2_Missense_Mutation_p.S258L	NM_005435.3	NP_005426.2	Q12774	ARHG5_HUMAN	Rho guanine nucleotide exchange factor (GEF) 5	1336	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				actin cytoskeleton organization (GO:0030036)|intracellular signal transduction (GO:0035556)|myeloid dendritic cell chemotaxis (GO:0002408)|positive regulation of podosome assembly (GO:0071803)|regulation of Rho GTPase activity (GO:0032319)		GTP binding (GO:0005525)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|endometrium(6)|kidney(8)|large_intestine(9)|liver(1)|lung(8)|ovary(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	Melanoma(164;0.14)					CCTGGCTCCTCGGAGGAGGCA	0.542																																					p.S1336L		Atlas-SNP	.											ARHGEF5,NS,carcinoma,-1,1	ARHGEF5	73	1	0			c.C4007T						scavenged	.						12.0	12.0	12.0					7																	144069807		2148	4221	6369	SO:0001583	missense	7984	exon9			GCTCCTCGGAGGA	U02082	CCDS34771.1	7q35	2012-09-20			ENSG00000050327	ENSG00000050327		"""Rho guanine nucleotide exchange factors"""	13209	protein-coding gene	gene with protein product	"""transforming immortalized mammary oncogene"", ""guanine nucleotide regulatory protein TIM"""	600888				8134109, 7656213	Standard	NM_005435		Approved	TIM, TIM1, GEF5, P60	uc003wel.3	Q12774	OTTHUMG00000158004	ENST00000056217.5:c.4007C>T	7.37:g.144069807C>T	ENSP00000056217:p.Ser1336Leu	881.0	2.0	0.00227015		587.0	114.0	0.194208	NM_005435	A6NNJ2|Q6ZML7	Missense_Mutation	SNP	ENST00000056217.5	37	CCDS34771.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	11.58|11.58	1.682337|1.682337	0.29872|0.29872	.|.	.|.	ENSG00000050327|ENSG00000050327	ENST00000474817|ENST00000056217;ENST00000344879;ENST00000471847	.|T;T	.|0.63913	.|-0.07;-0.07	5.1|5.1	5.1|5.1	0.69264|0.69264	.|Dbl homology (DH) domain (5);	.|0.925322	.|0.09085	.|N	.|0.850706	T|T	0.40448|0.40448	0.1117|0.1117	N|N	0.11255|0.11255	0.115|0.115	0.09310|0.09310	N|N	0.999996|0.999996	.|B;P	.|0.49307	.|0.0;0.922	.|B;B	.|0.36534	.|0.005;0.227	T|T	0.10451|0.10451	-1.0629|-1.0629	5|10	.|0.40728	.|T	.|0.16	0.254|0.254	9.6027|9.6027	0.39615|0.39615	0.0:0.9043:0.0:0.0957|0.0:0.9043:0.0:0.0957	.|.	.|191;1336	.|B3KQX6;Q12774	.|.;ARHG5_HUMAN	W|L	590|1336;191;258	.|ENSP00000056217:S1336L;ENSP00000418227:S258L	.|ENSP00000056217:S1336L	R|S	+|+	1|2	2|0	ARHGEF5|ARHGEF5	143700740|143700740	0.001000|0.001000	0.12720|0.12720	0.974000|0.974000	0.42286|0.42286	0.355000|0.355000	0.29361|0.29361	1.151000|1.151000	0.31651|0.31651	2.369000|2.369000	0.80426|0.80426	0.655000|0.655000	0.94253|0.94253	CGG|TCG	.	.	none		0.542	ARHGEF5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349981.1	NM_005435	
ARSF	416	hgsc.bcm.edu	37	X	2990197	2990197	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:2990197T>C	ENST00000381127.1	+	3	363	c.142T>C	c.(142-144)Tac>Cac	p.Y48H	ARSF_ENST00000359361.2_Missense_Mutation_p.Y48H|ARSF_ENST00000537104.1_Missense_Mutation_p.Y48H	NM_001201538.1|NM_001201539.1	NP_001188467.1|NP_001188468.1	P54793	ARSF_HUMAN	arylsulfatase F	48					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(15)|ovary(2)|prostate(3)|skin(3)|urinary_tract(2)	38		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				TCTGGGCTGCTACGGCAATGA	0.517																																					p.Y48H		Atlas-SNP	.											.	ARSF	97	.	0			c.T142C						PASS	.						207.0	172.0	184.0					X																	2990197		2203	4300	6503	SO:0001583	missense	416	exon3			GGCTGCTACGGCA	X97868	CCDS14123.1	Xp22.3	2013-02-14			ENSG00000062096	ENSG00000062096		"""Arylsulfatase family"""	721	protein-coding gene	gene with protein product		300003				7720070	Standard	NM_004042		Approved		uc022brz.1	P54793	OTTHUMG00000021081	ENST00000381127.1:c.142T>C	X.37:g.2990197T>C	ENSP00000370519:p.Tyr48His	174.0	0.0	0		83.0	4.0	0.0481928	NM_004042	Q8TCC5	Missense_Mutation	SNP	ENST00000381127.1	37	CCDS14123.1	.	.	.	.	.	.	.	.	.	.	t	12.11	1.838448	0.32513	.	.	ENSG00000062096	ENST00000381127;ENST00000537104;ENST00000359361	D;D;D	0.95069	-3.6;-3.6;-3.6	2.46	2.46	0.29980	Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	0.155495	0.44285	U	0.000472	D	0.96185	0.8756	M	0.89785	3.06	0.44862	D	0.997877	P	0.40000	0.698	P	0.50490	0.642	D	0.95657	0.8712	10	0.72032	D	0.01	.	9.9827	0.41824	0.0:0.0:0.0:1.0	.	48	P54793	ARSF_HUMAN	H	48	ENSP00000370519:Y48H;ENSP00000445594:Y48H;ENSP00000352319:Y48H	ENSP00000352319:Y48H	Y	+	1	0	ARSF	3000197	1.000000	0.71417	0.023000	0.16930	0.074000	0.17049	5.704000	0.68347	0.805000	0.34159	0.339000	0.21740	TAC	.	.	none		0.517	ARSF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055652.1		
MFSD9	84804	hgsc.bcm.edu	37	2	103343356	103343356	+	Silent	SNP	A	A	C	rs34997861	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:103343356A>C	ENST00000258436.5	-	4	418	c.375T>G	c.(373-375)ctT>ctG	p.L125L		NM_032718.3	NP_116107.3	Q8NBP5	MFSD9_HUMAN	major facilitator superfamily domain containing 9	125					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			breast(3)|large_intestine(7)|liver(1)|lung(6)|ovary(2)|skin(1)	20						CTGCTCCGAGAAGGAGATAGC	0.493																																					p.L125L		Atlas-SNP	.											.	MFSD9	56	.	0			c.T375G						PASS	.	A		0,4406		0,0,2203	79.0	77.0	78.0		375	-4.7	0.1	2	dbSNP_126	78	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	MFSD9	NM_032718.3		0,8,6495	CC,CA,AA		0.093,0.0,0.0615		125/475	103343356	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	84804	exon4			TCCGAGAAGGAGA		CCDS2063.1	2q12.1	2007-01-12			ENSG00000135953	ENSG00000135953			28158	protein-coding gene	gene with protein product							Standard	NM_032718		Approved	MGC11332	uc002tcb.2	Q8NBP5	OTTHUMG00000130781	ENST00000258436.5:c.375T>G	2.37:g.103343356A>C		207.0	0.0	0		181.0	91.0	0.502762	NM_032718	Q4ZG89|Q53TU0|Q96GQ4|Q9BRI8	Silent	SNP	ENST00000258436.5	37	CCDS2063.1																																																																																			A|0.999;C|0.001	0.001	strong		0.493	MFSD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253295.2	NM_032718	
XIRP2	129446	hgsc.bcm.edu	37	2	168106803	168106803	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:168106803G>C	ENST00000409195.1	+	9	8990	c.8901G>C	c.(8899-8901)gaG>gaC	p.E2967D	XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.E2967D|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Missense_Mutation_p.E2745D	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2792				S -> A (in Ref. 8; CAD91141). {ECO:0000305}.	actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						TTGAAGCAGAGCCAAATAAAA	0.383																																					p.E2967D		Atlas-SNP	.											.	XIRP2	914	.	0			c.G8901C						PASS	.						90.0	88.0	88.0					2																	168106803		1822	4088	5910	SO:0001583	missense	129446	exon9			AGCAGAGCCAAAT	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8901G>C	2.37:g.168106803G>C	ENSP00000386840:p.Glu2967Asp	182.0	0.0	0		194.0	29.0	0.149485	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	37	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	G	9.715	1.158030	0.21454	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.03212	4.01;4.01;4.01	6.02	-1.98	0.07480	.	0.623038	0.17625	N	0.167595	T	0.02848	0.0085	L	0.40543	1.245	0.09310	N	0.999996	B;B;B	0.17667	0.013;0.023;0.023	B;B;B	0.18871	0.01;0.023;0.023	T	0.38134	-0.9675	10	0.40728	T	0.16	-11.4362	3.8151	0.08812	0.394:0.0974:0.4094:0.0991	.	2792;2792;2745	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	D	2967;2967;2745;381	ENSP00000386840:E2967D;ENSP00000295237:E2967D;ENSP00000387255:E2745D	ENSP00000295237:E2967D	E	+	3	2	XIRP2	167815049	0.595000	0.26857	0.958000	0.39756	0.978000	0.69477	-0.106000	0.10890	-0.277000	0.09193	-0.150000	0.13652	GAG	.	.	none		0.383	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
PNMA3	29944	hgsc.bcm.edu	37	X	152226189	152226189	+	Silent	SNP	G	G	A	rs141778950	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:152226189G>A	ENST00000370264.4	+	1	803	c.777G>A	c.(775-777)gaG>gaA	p.E259E	PNMA3_ENST00000370265.4_Silent_p.E259E|PNMA3_ENST00000447306.1_Silent_p.E259E			Q9UL41	PNMA3_HUMAN	paraneoplastic Ma antigen 3	259					positive regulation of apoptotic process (GO:0043065)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(2)	16	Acute lymphoblastic leukemia(192;6.56e-05)					cctatcaggaggcaggagaga	0.488													G|||	4	0.0010596	0.0	0.0	3775	,	,		15718	0.0		0.004	False		,,,				2504	0.0				p.E259E		Atlas-SNP	.											.	PNMA3	81	.	0			c.G777A						PASS	.	G		3,3832		0,3,0,1629,571	166.0	157.0	160.0		777	-0.1	0.0	X	dbSNP_134	160	12,6716		0,10,2,2418,1870	no	coding-synonymous	PNMA3	NM_013364.4		0,13,2,4047,2441	AA,AG,A,GG,G		0.1784,0.0782,0.142		259/464	152226189	15,10548	2203	4300	6503	SO:0001819	synonymous_variant	29944	exon2			TCAGGAGGCAGGA	AF083116	CCDS35435.2, CCDS65344.1	Xq28	2012-02-09	2012-02-09		ENSG00000183837	ENSG00000183837		"""Paraneoplastic Ma antigens"""	18742	protein-coding gene	gene with protein product	"""paraneoplastic cancer-testis-brain antigen"""	300675	"""paraneoplastic antigen MA3"""			11558790	Standard	NM_013364		Approved	MA5, MA3, MGC132756, MGC132758	uc004fhc.2	Q9UL41	OTTHUMG00000024195	ENST00000370264.4:c.777G>A	X.37:g.152226189G>A		245.0	0.0	0		110.0	108.0	0.981818	NM_013364	D3DWT7|Q9H0A4	Silent	SNP	ENST00000370264.4	37	CCDS35435.2																																																																																			G|0.999;A|0.001	0.001	strong		0.488	PNMA3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060946.2	NM_013364	
TYRO3	7301	hgsc.bcm.edu	37	15	41862436	41862436	+	Splice_Site	SNP	A	A	G	rs201371674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41862436A>G	ENST00000263798.3	+	11	1606		c.e11-1		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GTTTTCCTTTAGGCAAGCCTT	0.587																																					.		Atlas-SNP	.											.	TYRO3	169	.	0			c.1383-2A>G						PASS	.																																			SO:0001630	splice_region_variant	7301	exon11			TCCTTTAGGCAAG	D50479	CCDS10080.1	15q15.1-q21.1	2013-02-11			ENSG00000092445	ENSG00000092445	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12446	protein-coding gene	gene with protein product		600341		RSE		7851890	Standard	NM_006293		Approved	Dtk, Brt, Tif, Sky	uc001zof.2	Q06418	OTTHUMG00000130341	ENST00000263798.3:c.1383-1A>G	15.37:g.41862436A>G		79.0	0.0	0		86.0	8.0	0.0930233	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	A	19.62	3.862477	0.71949	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.0491	0.58944	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39649728	1.000000	0.71417	0.998000	0.56505	0.942000	0.58702	7.007000	0.76335	2.208000	0.71279	0.533000	0.62120	.	A|0.986;G|0.014	0.014	strong		0.587	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron
CACNA1E	777	hgsc.bcm.edu	37	1	181724381	181724381	+	Silent	SNP	C	C	T	rs41315709	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:181724381C>T	ENST00000367573.2	+	28	3837	c.3837C>T	c.(3835-3837)ttC>ttT	p.F1279F	CACNA1E_ENST00000360108.3_Silent_p.F1260F|CACNA1E_ENST00000526775.1_Silent_p.F1260F|CACNA1E_ENST00000367567.4_Silent_p.F886F|CACNA1E_ENST00000357570.5_Silent_p.F1230F|CACNA1E_ENST00000358338.5_Silent_p.F1211F|CACNA1E_ENST00000367570.1_Silent_p.F1279F	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1279					calcium ion import (GO:0070509)|energy reserve metabolic process (GO:0006112)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|voltage-gated calcium channel activity (GO:0005245)			NS(2)|breast(9)|central_nervous_system(3)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(6)|kidney(4)|large_intestine(34)|lung(99)|ovary(6)|pancreas(1)|prostate(9)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	204						AGGCCGTCTTCGACTGCGTAG	0.512													C|||	4	0.000798722	0.0008	0.0	5008	,	,		21515	0.001		0.002	False		,,,				2504	0.0				p.F1279F		Atlas-SNP	.											CACNA1E_ENST00000367573,caecum,carcinoma,0,2	CACNA1E	778	2	0			c.C3837T						PASS	.	C	,,	0,4012		0,0,2006	120.0	116.0	118.0		3837,3837,3780	-5.9	0.9	1	dbSNP_127	118	7,8373		0,7,4183	no	coding-synonymous,coding-synonymous,coding-synonymous	CACNA1E	NM_000721.3,NM_001205293.1,NM_001205294.1	,,	0,7,6189	TT,TC,CC		0.0835,0.0,0.0565	,,	1279/2271,1279/2314,1260/2252	181724381	7,12385	2006	4190	6196	SO:0001819	synonymous_variant	777	exon28			CGTCTTCGACTGC	AK096563	CCDS53443.1, CCDS55664.1, CCDS55665.1	1q25.3	2013-01-10	2007-02-16		ENSG00000198216	ENSG00000198216		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1392	protein-coding gene	gene with protein product		601013		CACNL1A6		8388125, 16382099	Standard	NM_001205293		Approved	Cav2.3, BII, CACH6	uc009wxt.3	Q15878	OTTHUMG00000037301	ENST00000367573.2:c.3837C>T	1.37:g.181724381C>T		54.0	0.0	0		86.0	41.0	0.476744	NM_001205293	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Silent	SNP	ENST00000367573.2	37	CCDS55664.1																																																																																			C|0.999;T|0.001	0.001	strong		0.512	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
BBS10	79738	hgsc.bcm.edu	37	12	76741341	76741341	+	Missense_Mutation	SNP	C	C	T	rs142863601	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:76741341C>T	ENST00000393262.3	-	2	507	c.424G>A	c.(424-426)Gac>Aac	p.D142N		NM_024685.3	NP_078961.3	Q8TAM1	BBS10_HUMAN	Bardet-Biedl syndrome 10	142			D -> N (in dbSNP:rs142863601). {ECO:0000269|PubMed:20120035}.		cellular protein metabolic process (GO:0044267)|chaperone-mediated protein complex assembly (GO:0051131)|nonmotile primary cilium assembly (GO:0035058)|photoreceptor cell maintenance (GO:0045494)|regulation of protein complex assembly (GO:0043254)|response to stimulus (GO:0050896)|retina homeostasis (GO:0001895)|visual perception (GO:0007601)	cell projection (GO:0042995)	ATP binding (GO:0005524)|RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)	19						ATAATACCGTCTAATATTTGT	0.388									Bardet-Biedl syndrome				C|||	14	0.00279553	0.0008	0.0029	5008	,	,		19235	0.0		0.0109	False		,,,				2504	0.0				p.D142N		Atlas-SNP	.											.	BBS10	46	.	0			c.G424A						PASS	.	C	ASN/ASP	11,4395	17.9+/-39.9	0,11,2192	72.0	68.0	70.0		424	5.3	0.9	12	dbSNP_134	70	92,8508	51.9+/-112.3	1,90,4209	yes	missense	BBS10	NM_024685.3	23	1,101,6401	TT,TC,CC		1.0698,0.2497,0.7919	possibly-damaging	142/724	76741341	103,12903	2203	4300	6503	SO:0001583	missense	79738	exon2	Familial Cancer Database	BBS, Bardet-Biedl syndrome, type 1-12: BBS1-12,Laurence-Moon-Biedl syndrome	TACCGTCTAATAT	BC026355	CCDS9014.2	12q21.2	2014-06-17	2006-04-28	2006-04-28	ENSG00000179941	ENSG00000179941		"""Heat Shock Proteins / Chaperonins"""	26291	protein-coding gene	gene with protein product		610148	"""chromosome 12 open reading frame 58"""	C12orf58		16582908	Standard	NM_024685		Approved	FLJ23560	uc001syd.1	Q8TAM1	OTTHUMG00000147352	ENST00000393262.3:c.424G>A	12.37:g.76741341C>T	ENSP00000376946:p.Asp142Asn	115.0	0.0	0		104.0	56.0	0.538462	NM_024685	Q96CW2|Q9H5D2	Missense_Mutation	SNP	ENST00000393262.3	37	CCDS9014.2	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	C	25.9	4.683655	0.88639	0.002497	0.010698	ENSG00000179941	ENST00000393262;ENST00000547830	D	0.89050	-2.46	5.34	5.34	0.76211	.	0.128969	0.49916	D	0.000131	D	0.88948	0.6576	L	0.60455	1.87	0.40719	D	0.982642	D	0.58970	0.984	P	0.55303	0.773	D	0.89985	0.4103	10	0.56958	D	0.05	-8.0958	16.9217	0.86166	0.0:1.0:0.0:0.0	.	142	Q8TAM1	BBS10_HUMAN	N	142;76	ENSP00000376946:D142N	ENSP00000376946:D142N	D	-	1	0	BBS10	75265472	1.000000	0.71417	0.950000	0.38849	0.971000	0.66376	5.183000	0.65065	2.937000	0.99478	0.650000	0.86243	GAC	C|0.994;T|0.006	0.006	strong		0.388	BBS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303983.2	NM_024685	
LSS	4047	hgsc.bcm.edu	37	21	47626602	47626602	+	Silent	SNP	G	G	A	rs111779817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:47626602G>A	ENST00000397728.3	-	16	1626	c.1548C>T	c.(1546-1548)aaC>aaT	p.N516N	LSS_ENST00000356396.4_Silent_p.N516N|LSS_ENST00000457828.2_Silent_p.N436N|LSS_ENST00000522411.1_Silent_p.N505N	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	516					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	endoplasmic reticulum membrane (GO:0005789)|lipid particle (GO:0005811)|membrane (GO:0016020)	lanosterol synthase activity (GO:0000250)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(3)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	21	Breast(49;0.214)					CCTCCGAGGGGTTCAGCAGCT	0.612													G|||	30	0.00599042	0.0	0.0072	5008	,	,		17554	0.0		0.007	False		,,,				2504	0.0184				p.N516N	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C1548T						PASS	.	G	,,,	3,4403	6.2+/-15.9	0,3,2200	78.0	72.0	74.0		1548,1515,1308,1548	2.6	1.0	21	dbSNP_132	74	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	,,,	0,32,6471	AA,AG,GG		0.3372,0.0681,0.246	,,,	516/733,505/722,436/653,516/733	47626602	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	4047	exon16			CGAGGGGTTCAGC	U22526	CCDS13733.1, CCDS46654.1, CCDS54489.1	21q22.3	1998-05-07			ENSG00000160285	ENSG00000160285	5.4.99.7		6708	protein-coding gene	gene with protein product		600909				7639730, 8655142	Standard	NM_001001438		Approved	OSC	uc002zij.3	P48449	OTTHUMG00000090633	ENST00000397728.3:c.1548C>T	21.37:g.47626602G>A		53.0	0.0	0		52.0	28.0	0.538462	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Silent	SNP	ENST00000397728.3	37	CCDS13733.1																																																																																			G|0.997;A|0.003	0.003	strong		0.612	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
MED15	51586	hgsc.bcm.edu	37	22	20922809	20922809	+	Splice_Site	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:20922809T>C	ENST00000263205.7	+	8	1112	c.1043T>C	c.(1042-1044)gTc>gCc	p.V348A	MED15_ENST00000541476.1_Splice_Site_p.V322A|MED15_ENST00000382974.2_Splice_Site_p.V277A|MED15_ENST00000478831.1_3'UTR|MED15_ENST00000542773.1_Splice_Site_p.V153A|MED15_ENST00000292733.7_Splice_Site_p.V348A|MED15_ENST00000425759.2_Splice_Site_p.V237A|MED15_ENST00000406969.1_Splice_Site_p.V322A	NM_001003891.1	NP_001003891.1	Q96RN5	MED15_HUMAN	mediator complex subunit 15	348	Pro-rich.				gene expression (GO:0010467)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	RNA polymerase II transcription cofactor activity (GO:0001104)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	25	all_cancers(11;2.07e-24)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0221)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.00102)|Lung(15;0.0173)|Epithelial(17;0.209)			TCCCTCAAGGTCCGAGCTCCG	0.582																																					p.V348A		Atlas-SNP	.											.	MED15	68	.	0			c.T1043C						PASS	.						29.0	29.0	29.0					22																	20922809		2199	4297	6496	SO:0001630	splice_region_variant	51586	exon8			TCAAGGTCCGAGC	AF056191	CCDS13781.1, CCDS33602.1, CCDS74824.1	22q11.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000099917	ENSG00000099917			14248	protein-coding gene	gene with protein product		607372	"""trinucleotide repeat containing 7"", ""PC2 (positive cofactor 2, multiprotein complex) glutamine/Q-rich-associated protein"""	TNRC7, PCQAP		11024300, 11414760, 15175163	Standard	XM_005261632		Approved	TIG-1, CAG7A, Arc105	uc002zsp.3	Q96RN5	OTTHUMG00000150810	ENST00000263205.7:c.1042-1T>C	22.37:g.20922809T>C		90.0	0.0	0		94.0	52.0	0.553191	NM_015889	D3DX31|D3DX32|O15413|Q6IC31|Q8NF16|Q96CT0|Q96IH7|Q9P1T3	Missense_Mutation	SNP	ENST00000263205.7	37	CCDS33602.1	.	.	.	.	.	.	.	.	.	.	T	13.54	2.268558	0.40095	.	.	ENSG00000099917	ENST00000425759;ENST00000292733;ENST00000542773;ENST00000263205;ENST00000406969;ENST00000382974;ENST00000541476;ENST00000542312	T	0.41400	1.0	5.4	5.4	0.78164	Mediator complex, subunit Med15, metazoa (1);	0.481828	0.21991	N	0.066154	T	0.47116	0.1428	L	0.36672	1.1	0.42239	D	0.991925	D;D;P;P;D	0.53885	0.963;0.963;0.954;0.954;0.963	D;D;D;D;D	0.71414	0.973;0.973;0.954;0.954;0.973	T	0.40251	-0.9573	10	0.02654	T	1	.	11.7332	0.51750	0.0:0.0:0.0:1.0	.	294;367;322;348;348	B4DGD6;Q6PKB8;G3V1P5;Q96RN5-2;Q96RN5	.;.;.;.;MED15_HUMAN	A	237;348;153;348;322;277;322;294	ENSP00000263205:V348A	ENSP00000263205:V348A	V	+	2	0	MED15	19252809	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	3.611000	0.54132	2.274000	0.75844	0.533000	0.62120	GTC	.	.	none		0.582	MED15-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000320177.2	NM_015889	Missense_Mutation
ZNF354C	30832	hgsc.bcm.edu	37	5	178503472	178503472	+	Silent	SNP	C	C	T	rs116407910	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178503472C>T	ENST00000315475.6	+	3	360	c.54C>T	c.(52-54)gcC>gcT	p.A18A		NM_014594.1	NP_055409.1	Q86Y25	Z354C_HUMAN	zinc finger protein 354C	18	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|kidney(1)|large_intestine(10)|lung(13)|ovary(1)|urinary_tract(3)	30	all_cancers(89;0.00065)|all_epithelial(37;0.000153)|Renal(175;0.000159)|Lung NSC(126;0.00175)|all_lung(126;0.00309)	all_cancers(40;0.19)|all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.247)		GGGATGTGGCCGTGTTCTTCA	0.552													C|||	11	0.00219649	0.0	0.0072	5008	,	,		17713	0.0		0.006	False		,,,				2504	0.0				p.A18A		Atlas-SNP	.											ZNF354C,NS,carcinoma,+2,1	ZNF354C	77	1	0			c.C54T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	173.0	153.0	160.0		54	-5.6	0.3	5	dbSNP_132	160	40,8560	26.8+/-75.7	0,40,4260	no	coding-synonymous	ZNF354C	NM_014594.1		0,44,6459	TT,TC,CC		0.4651,0.0908,0.3383		18/555	178503472	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	30832	exon3			TGTGGCCGTGTTC		CCDS4443.1	5q35	2013-01-08			ENSG00000177932	ENSG00000177932		"""Zinc fingers, C2H2-type"", ""-"""	16736	protein-coding gene	gene with protein product						10786630	Standard	NM_014594		Approved	KID3	uc003mju.3	Q86Y25	OTTHUMG00000130888	ENST00000315475.6:c.54C>T	5.37:g.178503472C>T		290.0	0.0	0		287.0	164.0	0.571429	NM_014594	Q6P4P9|Q8NFX1	Silent	SNP	ENST00000315475.6	37	CCDS4443.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	ZNF354C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253473.2		
MYO18B	84700	hgsc.bcm.edu	37	22	26164408	26164408	+	Silent	SNP	C	C	G	rs575271363		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26164408C>G	ENST00000407587.2	+	4	694	c.525C>G	c.(523-525)gcC>gcG	p.A175A	MYO18B_ENST00000335473.7_Silent_p.A175A|MYO18B_ENST00000536101.1_Silent_p.A175A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	175						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CCCATGACGCCCCCCCTTGCA	0.597													c|||	1	0.000199681	0.0	0.0	5008	,	,		13166	0.0		0.0	False		,,,				2504	0.001				p.A175A		Atlas-SNP	.											.	MYO18B	322	.	0			c.C525G						PASS	.						21.0	25.0	24.0					22																	26164408		1966	4142	6108	SO:0001819	synonymous_variant	84700	exon4			TGACGCCCCCCCT	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.525C>G	22.37:g.26164408C>G		85.0	0.0	0		83.0	38.0	0.457831	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37																																																																																				.	.	none		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
SLC18A2	6571	hgsc.bcm.edu	37	10	119003546	119003546	+	Silent	SNP	G	G	A	rs11568722		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:119003546G>A	ENST00000298472.5	+	3	329	c.186G>A	c.(184-186)acG>acA	p.T62T	RP11-501J20.5_ENST00000425264.1_RNA|SLC18A2_ENST00000497497.1_3'UTR	NM_003054.4	NP_003045.2	Q05940	VMAT2_HUMAN	solute carrier family 18 (vesicular monoamine transporter), member 2	62					aging (GO:0007568)|cellular response to ammonium ion (GO:0071242)|cellular response to drug (GO:0035690)|death (GO:0016265)|dopamine transport (GO:0015872)|endocytic recycling (GO:0032456)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|locomotory behavior (GO:0007626)|monoamine transport (GO:0015844)|negative regulation of neurotransmitter transport (GO:0051589)|neurotransmitter loading into synaptic vesicle (GO:0098700)|neurotransmitter secretion (GO:0007269)|post-embryonic development (GO:0009791)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|response to corticosterone (GO:0051412)|response to herbicide (GO:0009635)|response to starvation (GO:0042594)|response to zinc ion (GO:0010043)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	clathrin-sculpted monoamine transport vesicle membrane (GO:0070083)|dense core granule (GO:0031045)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)|synaptic vesicle membrane (GO:0030672)|terminal bouton (GO:0043195)	amine transmembrane transporter activity (GO:0005275)|drug binding (GO:0008144)|monoamine transmembrane transporter activity (GO:0008504)|serotonin transmembrane transporter activity (GO:0015222)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(16)	29		Colorectal(252;0.19)		all cancers(201;0.029)	Amphetamine(DB00182)|Benzphetamine(DB00865)|Deserpidine(DB01089)|Dextroamphetamine(DB01576)|Ephedra(DB01363)|Ephedrine(DB01364)|Isometheptene(DB06706)|Methamphetamine(DB01577)|Norepinephrine(DB00368)|Propylhexedrine(DB06714)|Reserpine(DB00206)|Tetrabenazine(DB04844)	AAATCCAGACGGCCAGGCCAG	0.498																																					p.T62T		Atlas-SNP	.											SLC18A2,NS,carcinoma,+1,1	SLC18A2	58	1	0			c.G186A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	88.0	76.0	80.0		186	-11.6	0.0	10	dbSNP_126	80	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	SLC18A2	NM_003054.4		0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538		62/515	119003546	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	6571	exon3			CCAGACGGCCAGG	L14269	CCDS7599.1	10q25	2013-07-18	2013-07-18		ENSG00000165646	ENSG00000165646		"""Solute carriers"""	10935	protein-coding gene	gene with protein product		193001		VMAT2			Standard	NM_003054		Approved	SVMT, SVAT	uc001ldd.2	Q05940	OTTHUMG00000019121	ENST00000298472.5:c.186G>A	10.37:g.119003546G>A		121.0	0.0	0		99.0	55.0	0.555556	NM_003054	B2RC96|D3DRC4|Q15876|Q4G147|Q5VW49|Q9H3P6	Silent	SNP	ENST00000298472.5	37	CCDS7599.1																																																																																			G|1.000;A|0.000	0.000	weak		0.498	SLC18A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050563.1	NM_003054	
MTUS1	57509	hgsc.bcm.edu	37	8	17503612	17503612	+	Silent	SNP	C	C	G	rs61733704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17503612C>G	ENST00000262102.6	-	15	3860	c.3636G>C	c.(3634-3636)tcG>tcC	p.S1212S	MTUS1_ENST00000544260.1_Silent_p.S357S|MTUS1_ENST00000381861.3_Silent_p.S459S|MTUS1_ENST00000297488.6_Silent_p.S378S|MTUS1_ENST00000519263.1_Silent_p.S1158S|MTUS1_ENST00000400046.1_Silent_p.S284S|MTUS1_ENST00000381869.3_Silent_p.S1158S	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	1212					cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		CCTTCTCCAGCGACTCTTGCA	0.448													C|||	77	0.0153754	0.0015	0.0115	5008	,	,		14078	0.0		0.0388	False		,,,				2504	0.0286				p.S1212S		Atlas-SNP	.											.	MTUS1	144	.	0			c.G3636C						PASS	.	C	,,,,	21,3729		0,21,1854	38.0	39.0	39.0		3636,3474,1377,1071,1134	-8.9	0.0	8	dbSNP_129	39	329,7903		2,325,3789	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	,,,,	2,346,5643	GG,GC,CC		3.9966,0.56,2.921	,,,,	1212/1271,1158/1217,459/518,357/416,378/437	17503612	350,11632	1875	4116	5991	SO:0001819	synonymous_variant	57509	exon15			CTCCAGCGACTCT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.3636G>C	8.37:g.17503612C>G		68.0	0.0	0		76.0	41.0	0.539474	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Silent	SNP	ENST00000262102.6	37	CCDS43717.1																																																																																			C|0.956;G|0.044	0.044	strong		0.448	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
ALK	238	hgsc.bcm.edu	37	2	29940529	29940529	+	Silent	SNP	A	A	T	rs2246745	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29940529A>T	ENST00000389048.3	-	2	1608	c.702T>A	c.(700-702)ccT>ccA	p.P234P	ALK_ENST00000431873.1_Silent_p.P234P	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	234					activation of MAPK activity (GO:0000187)|cell proliferation (GO:0008283)|neuron development (GO:0048666)|NIK/NF-kappaB signaling (GO:0038061)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|protein complex (GO:0043234)	ATP binding (GO:0005524)|NF-kappaB-inducing kinase activity (GO:0004704)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		ATIC/ALK(24)|FN1/ALK(2)|C2orf44/ALK(2)|TPM3/ALK(33)|KLC1/ALK(2)|VCL/ALK(4)|TPM4/ALK(12)|KIF5B/ALK(8)|RANBP2/ALK(34)|SQSTM1/ALK(2)|EML4/ALK(543)|PPFIBP1/ALK(3)|SEC31A/ALK(3)|NPM1/ALK(632)|CLTC/ALK(44)|CARS/ALK(5)|MSN/ALK(6)|TFG/ALK(9)	NS(2)|autonomic_ganglia(198)|breast(8)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(7)|kidney(4)|large_intestine(25)|lung(61)|ovary(6)|pancreas(1)|prostate(2)|skin(5)|soft_tissue(3)|stomach(2)|thyroid(2)	340	Acute lymphoblastic leukemia(172;0.155)				Adenosine triphosphate(DB00171)|Crizotinib(DB08865)	GAGAAGGAGAAGGCATGTTTG	0.408			"""T, Mis, A"""	"""NPM1, TPM3, TFG, TPM4, ATIC, CLTC, MSN, ALO17, CARS, EML4, KIF5B, C2orf22"""	"""ALCL, NSCLC, Neuroblastoma"""	neuroblastoma			Neuroblastoma, Familial Clustering of;Congenital Central Hypoventilation Syndrome				A|||	2951	0.589257	0.1513	0.6902	5008	,	,		20442	0.7827		0.7913	False		,,,				2504	0.7025				p.P234P		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,-1,1	ALK	533	1	0			c.T702A						PASS	.	A		1172,3234	409.7+/-335.1	157,858,1188	165.0	142.0	150.0		702	1.8	0.9	2	dbSNP_100	150	6983,1617	742.8+/-407.2	2840,1303,157	no	coding-synonymous	ALK	NM_004304.4		2997,2161,1345	TT,TA,AA		18.8023,26.6001,37.2982		234/1621	29940529	8155,4851	2203	4300	6503	SO:0001819	synonymous_variant	238	exon2	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	AGGAGAAGGCATG	D45915	CCDS33172.1	2p23	2014-09-17	2008-01-23		ENSG00000171094	ENSG00000171094		"""CD molecules"""	427	protein-coding gene	gene with protein product		105590	"""anaplastic lymphoma kinase (Ki-1)"""			8122112	Standard	NM_004304		Approved	CD246	uc002rmy.3	Q9UM73	OTTHUMG00000152034	ENST00000389048.3:c.702T>A	2.37:g.29940529A>T		264.0	0.0	0		247.0	247.0	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			A|0.355;T|0.645	0.645	strong		0.408	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
ZNRF1	84937	hgsc.bcm.edu	37	16	75146357	75146357	+	IGR	SNP	T	T	G	rs372986804		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:75146357T>G	ENST00000335325.4	+	0	4620				RP11-252E2.1_ENST00000499110.1_RNA|LDHD_ENST00000300051.4_Missense_Mutation_p.Q474P|LDHD_ENST00000450168.2_Missense_Mutation_p.Q451P	NM_032268.4	NP_115644.1	Q8ND25	ZNRF1_HUMAN	zinc and ring finger 1, E3 ubiquitin protein ligase						proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|lysosome (GO:0005764)|membrane (GO:0016020)|synapse (GO:0045202)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(1)	1						CTGCAGCAGCTGCCGCTTGCC	0.667																																					p.Q474P		Atlas-SNP	.											.	LDHD	34	.	0			c.A1421C						PASS	.	T	PRO/GLN,PRO/GLN	0,4396		0,0,2198	27.0	28.0	28.0		1421,1352	4.2	1.0	16		28	2,8598		0,2,4298	no	missense,missense	LDHD	NM_153486.3,NM_194436.2	76,76	0,2,6496	GG,GT,TT		0.0233,0.0,0.0154	benign,benign	474/508,451/485	75146357	2,12994	2198	4300	6498	SO:0001628	intergenic_variant	197257	exon11			AGCAGCTGCCGCT	AF378524	CCDS10912.1	16q22.3	2013-01-09	2012-02-23		ENSG00000186187	ENSG00000186187		"""RING-type (C3HC4) zinc fingers"""	18452	protein-coding gene	gene with protein product		612060	"""zinc and ring finger 1"""				Standard	NM_032268		Approved	nin283, FLJ14846, DKFZp434E229	uc002fdl.1	Q8ND25	OTTHUMG00000137606		16.37:g.75146357T>G		84.0	0.0	0		70.0	31.0	0.442857	NM_153486	D3DUJ9|Q9H083	Missense_Mutation	SNP	ENST00000335325.4	37	CCDS10912.1	.	.	.	.	.	.	.	.	.	.	T	14.78	2.636542	0.47049	0.0	2.33E-4	ENSG00000166816	ENST00000450168;ENST00000300051	D;D	0.87179	-2.22;-2.22	5.27	4.16	0.48862	Vanillyl-alcohol oxidase, C-terminal subdomain 2 (1);FAD-linked oxidase-like, C-terminal (1);FAD-linked oxidase, C-terminal (1);	0.450708	0.22902	N	0.054258	T	0.79741	0.4498	N	0.13003	0.285	0.30172	N	0.801213	P;P	0.41546	0.579;0.754	B;P	0.48089	0.43;0.566	T	0.74275	-0.3718	10	0.33141	T	0.24	-16.5283	6.5485	0.22420	0.2656:0.0:0.138:0.5963	.	451;474	Q86WU2-2;Q86WU2	.;LDHD_HUMAN	P	451;474	ENSP00000417011:Q451P;ENSP00000300051:Q474P	ENSP00000300051:Q474P	Q	-	2	0	LDHD	73703858	0.800000	0.28916	1.000000	0.80357	0.974000	0.67602	1.415000	0.34748	0.821000	0.34540	0.460000	0.39030	CAG	.	.	weak		0.667	ZNRF1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269020.2		
CBX2	84733	hgsc.bcm.edu	37	17	77758653	77758653	+	Missense_Mutation	SNP	C	C	G	rs141957173	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:77758653C>G	ENST00000310942.4	+	5	1515	c.1411C>G	c.(1411-1413)Ccc>Gcc	p.P471A		NM_005189.2	NP_005180.1	Q14781	CBX2_HUMAN	chromobox homolog 2	471					cell differentiation (GO:0030154)|chromatin modification (GO:0016568)|development of primary sexual characteristics (GO:0045137)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	euchromatin (GO:0000791)|heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|upper_aerodigestive_tract(1)	16			OV - Ovarian serous cystadenocarcinoma(97;0.0102)|BRCA - Breast invasive adenocarcinoma(99;0.0224)			GGACTCCGACCCCGACTCCGC	0.667													C|||	6	0.00119808	0.0	0.0	5008	,	,		15360	0.0		0.006	False		,,,				2504	0.0				p.P471A		Atlas-SNP	.											.	CBX2	50	.	0			c.C1411G						PASS	.	C	ALA/PRO	3,4403	6.2+/-15.9	0,3,2200	38.0	36.0	37.0		1411	5.4	1.0	17	dbSNP_134	37	87,8513	47.6+/-106.9	0,87,4213	yes	missense	CBX2	NM_005189.2	27	0,90,6413	GG,GC,CC		1.0116,0.0681,0.692	possibly-damaging	471/533	77758653	90,12916	2203	4300	6503	SO:0001583	missense	84733	exon5			TCCGACCCCGACT	BC004252, BG354579	CCDS11764.1, CCDS32757.1	17q25.3	2010-07-06	2010-06-24		ENSG00000173894	ENSG00000173894			1552	protein-coding gene	gene with protein product	"""Pc class homolog (Drosophila)"""	602770	"""chromobox homolog 2 (Drosophila Pc class)"", ""cell division cycle associated 6"""	CDCA6		7782071, 2477932	Standard	NM_005189		Approved	MGC10561	uc002jxc.3	Q14781		ENST00000310942.4:c.1411C>G	17.37:g.77758653C>G	ENSP00000308750:p.Pro471Ala	70.0	0.0	0		51.0	20.0	0.392157	NM_005189	Q0VDA5|Q9BTB1	Missense_Mutation	SNP	ENST00000310942.4	37	CCDS32757.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	9.419	1.082569	0.20309	6.81E-4	0.010116	ENSG00000173894	ENST00000310942	.	.	.	5.45	5.45	0.79879	.	1.949320	0.02055	N	0.050337	T	0.46347	0.1388	L	0.36672	1.1	0.80722	D	1	B	0.34015	0.435	B	0.27262	0.078	T	0.30208	-0.9986	9	0.54805	T	0.06	13.4368	14.9645	0.71182	0.1433:0.8567:0.0:0.0	.	471	Q14781	CBX2_HUMAN	A	471	.	ENSP00000308750:P471A	P	+	1	0	CBX2	75373248	1.000000	0.71417	0.987000	0.45799	0.018000	0.09664	5.777000	0.68931	2.568000	0.86640	0.650000	0.86243	CCC	C|0.996;G|0.004	0.004	strong		0.667	CBX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437040.1	NM_032647	
HJURP	55355	hgsc.bcm.edu	37	2	234752863	234752863	+	Missense_Mutation	SNP	C	C	T	rs140874442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:234752863C>T	ENST00000411486.2	-	7	627	c.562G>A	c.(562-564)Gtg>Atg	p.V188M	HJURP_ENST00000434039.1_Intron|HJURP_ENST00000432087.1_Missense_Mutation_p.V134M|HJURP_ENST00000441687.1_Missense_Mutation_p.V103M	NM_018410.3	NP_060880.3	Q8NCD3	HJURP_HUMAN	Holliday junction recognition protein	188					cell cycle (GO:0007049)|CENP-A containing nucleosome assembly (GO:0034080)|chromosome segregation (GO:0007059)|nucleosome assembly (GO:0006334)|regulation of DNA binding (GO:0051101)|regulation of protein complex assembly (GO:0043254)	chromosome, centromeric region (GO:0000775)|condensed chromosome kinetochore (GO:0000777)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone binding (GO:0042393)|identical protein binding (GO:0042802)			NS(2)|breast(2)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(3)|lung(11)|ovary(2)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Breast(86;0.00204)|all_lung(227;0.00433)|Renal(207;0.00685)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0326)|Lung NSC(271;0.0719)|Lung SC(224;0.128)		Epithelial(121;2.01e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000186)|Lung(119;0.00521)|LUSC - Lung squamous cell carcinoma(224;0.00829)		GGGGCAGGCACGGCAGGTGAG	0.532													C|||	4	0.000798722	0.0008	0.0014	5008	,	,		21900	0.0		0.002	False		,,,				2504	0.0				p.V188M		Atlas-SNP	.											.	HJURP	72	.	0			c.G562A						PASS	.	C	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	101.0	98.0	99.0		562	-4.4	0.0	2	dbSNP_134	99	36,8564	24.0+/-70.4	0,36,4264	yes	missense	HJURP	NM_018410.3	21	0,37,6466	TT,TC,CC		0.4186,0.0227,0.2845	benign	188/749	234752863	37,12969	2203	4300	6503	SO:0001583	missense	55355	exon7			CAGGCACGGCAGG		CCDS33406.1, CCDS63166.1, CCDS63167.1	2q37.1	2007-12-06			ENSG00000123485	ENSG00000123485			25444	protein-coding gene	gene with protein product		612667				17823411	Standard	NM_001282962		Approved	DKFZp762E1312, URLC9, hFLEG1, FAKTS	uc002vvg.3	Q8NCD3	OTTHUMG00000059125	ENST00000411486.2:c.562G>A	2.37:g.234752863C>T	ENSP00000414109:p.Val188Met	84.0	0.0	0		110.0	54.0	0.490909	NM_018410	A8IRH5|B4DWR0|B4DZV4|Q9BUT2|Q9NSL8	Missense_Mutation	SNP	ENST00000411486.2	37	CCDS33406.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	7.453	0.642993	0.14451	2.27E-4	0.004186	ENSG00000123485	ENST00000411486;ENST00000432087;ENST00000441687;ENST00000414924;ENST00000454020	T;T;T;T;T	0.32023	3.25;3.24;3.22;2.91;1.47	4.09	-4.38	0.03622	.	2.541040	0.01846	N	0.035607	T	0.09291	0.0229	N	0.00538	-1.39	0.09310	N	1	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.06405	0.002;0.002;0.001	T	0.27020	-1.0086	10	0.44086	T	0.13	0.4745	6.3534	0.21389	0.0:0.4492:0.1535:0.3973	.	103;134;188	Q8NCD3-3;Q8NCD3-2;Q8NCD3	.;.;HJURP_HUMAN	M	188;134;103;103;147	ENSP00000414109:V188M;ENSP00000407208:V134M;ENSP00000401944:V103M;ENSP00000393253:V103M;ENSP00000414051:V147M	ENSP00000414109:V188M	V	-	1	0	HJURP	234417602	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.680000	0.05197	-0.832000	0.04251	-1.085000	0.02201	GTG	C|0.998;T|0.002	0.002	strong		0.532	HJURP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000130996.6	NM_018410	
ELOVL2	54898	hgsc.bcm.edu	37	6	11005776	11005776	+	Silent	SNP	C	C	T	rs559223553		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:11005776C>T	ENST00000354666.3	-	3	167	c.84G>A	c.(82-84)ggG>ggA	p.G28G		NM_017770.3	NP_060240.3	Q9NXB9	ELOV2_HUMAN	ELOVL fatty acid elongase 2	28					alpha-linolenic acid metabolic process (GO:0036109)|cellular lipid metabolic process (GO:0044255)|fatty acid elongation, polyunsaturated fatty acid (GO:0034626)|linoleic acid metabolic process (GO:0043651)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|unsaturated fatty acid biosynthetic process (GO:0006636)|unsaturated fatty acid metabolic process (GO:0033559)|very long-chain fatty acid biosynthetic process (GO:0042761)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	fatty acid elongase activity (GO:0009922)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|stomach(1)|upper_aerodigestive_tract(2)	14	Breast(50;0.0418)|Ovarian(93;0.0919)	all_hematologic(90;0.117)	Epithelial(50;0.176)			ACATGAACCACCCTCTGACTC	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		23355	0.0		0.0	False		,,,				2504	0.001				p.G28G		Atlas-SNP	.											.	ELOVL2	40	.	0			c.G84A						PASS	.						107.0	82.0	90.0					6																	11005776		2203	4300	6503	SO:0001819	synonymous_variant	54898	exon3			GAACCACCCTCTG	AK000341	CCDS4518.1	6p24.1	2011-05-25	2011-05-25		ENSG00000197977	ENSG00000197977			14416	protein-coding gene	gene with protein product		611814	"""elongation of very long chain fatty acids (FEN1/Elo2, SUR4/Elo3, yeast)-like 2"""			12371743, 16564093	Standard	NM_017770		Approved	Ssc2	uc003mzp.4	Q9NXB9	OTTHUMG00000014252	ENST00000354666.3:c.84G>A	6.37:g.11005776C>T		72.0	0.0	0		101.0	51.0	0.504951	NM_017770	Q6P9E1|Q86W94	Silent	SNP	ENST00000354666.3	37	CCDS4518.1																																																																																			.	.	none		0.408	ELOVL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039849.1		
LY6G6F	259215	hgsc.bcm.edu	37	6	31677953	31677953	+	Missense_Mutation	SNP	G	G	A	rs61740977	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31677953G>A	ENST00000375832.4	+	4	819	c.797G>A	c.(796-798)gGc>gAc	p.G266D	MEGT1_ENST00000503322.1_Missense_Mutation_p.G266D|LY6G6F_ENST00000556581.1_Missense_Mutation_p.G266D|XXbac-BPG32J3.20_ENST00000461287.1_Intron	NM_001003693.1	NP_001003693.1	Q5SQ64	LY66F_HUMAN	lymphocyte antigen 6 complex, locus G6F	266						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(4)	12						GGGGCTCCAGGCAGAGGTGAG	0.632													G|||	42	0.00838658	0.0068	0.0072	5008	,	,		19569	0.003		0.0099	False		,,,				2504	0.0153				p.G266D		Atlas-SNP	.											LY6G6F,colon,carcinoma,+1,1	LY6G6F	23	1	0			c.G797A						scavenged	.	G	ASP/GLY	10,3012		0,10,1501	60.0	62.0	61.0		797	-0.1	0.0	6	dbSNP_129	61	41,5373		0,41,2666	yes	missense	LY6G6F	NM_001003693.1	94	0,51,4167	AA,AG,GG		0.7573,0.3309,0.6046	probably-damaging	266/298	31677953	51,8385	1511	2707	4218	SO:0001583	missense	259215	exon4			CTCCAGGCAGAGG		CCDS34403.1	6p21	2013-01-11	2008-05-21	2008-05-21		ENSG00000204424		"""Immunoglobulin superfamily / V-set domain containing"""	13933	protein-coding gene	gene with protein product		611404	"""chromosome 6 open reading frame 21"""	LY6G6D, C6orf21		12852788	Standard	NM_001003693		Approved	G6f, NG32	uc003nwa.1	Q5SQ64	OTTHUMG00000031252	ENST00000375832.4:c.797G>A	6.37:g.31677953G>A	ENSP00000364992:p.Gly266Asp	117.0	1.0	0.00854701		112.0	53.0	0.473214	NM_001003693	B0UXB7|O95869|Q7Z5H2|Q96QC7|Q9NZJ1	Missense_Mutation	SNP	ENST00000375832.4	37	CCDS34403.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	G	8.620	0.891217	0.17613	0.003309	0.007573	ENSG00000204424;ENSG00000204424;ENSG00000250641	ENST00000556581;ENST00000375832;ENST00000503322	T;T;T	0.16196	2.52;2.36;2.52	5.25	-0.08	0.13708	.	0.971401	0.08471	N	0.940953	T	0.01627	0.0052	N	0.02539	-0.55	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.47560	-0.9108	10	0.27785	T	0.31	0.4188	5.858	0.18730	0.353:0.0:0.5128:0.1342	rs61740977	266;266	Q9NZJ1;Q5SQ64	.;LY66F_HUMAN	D	266	ENSP00000452432:G266D;ENSP00000364992:G266D;ENSP00000421232:G266D	ENSP00000364992:G266D	G	+	2	0	XXbac-BPG32J3.19;LY6G6F	31785932	0.007000	0.16637	0.020000	0.16555	0.036000	0.12997	0.191000	0.17076	-0.177000	0.10690	-1.491000	0.00971	GGC	G|0.994;A|0.006	0.006	strong		0.632	LY6G6F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076532.2	NM_001003693	
TGM5	9333	hgsc.bcm.edu	37	15	43527819	43527819	+	Missense_Mutation	SNP	T	T	C	rs35985214	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43527819T>C	ENST00000220420.5	-	10	1569	c.1562A>G	c.(1561-1563)cAg>cGg	p.Q521R	TGM5_ENST00000349114.4_Missense_Mutation_p.Q439R	NM_201631.3	NP_963925.2	O43548	TGM5_HUMAN	transglutaminase 5	521			Q -> R (in dbSNP:rs35985214).		cellular protein modification process (GO:0006464)|epidermis development (GO:0008544)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(11)|lung(15)|skin(6)|urinary_tract(1)	44		all_cancers(109;1.37e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;2.46e-08)|all_lung(180;2.75e-07)|Melanoma(134;0.0476)|Colorectal(260;0.216)		GBM - Glioblastoma multiforme(94;4e-07)	L-Glutamine(DB00130)	GCATATATCCTGGCCCATGTT	0.577													T|||	28	0.00559105	0.0008	0.0086	5008	,	,		21464	0.0		0.0179	False		,,,				2504	0.0031				p.Q521R		Atlas-SNP	.											TGM5,rectum,carcinoma,-1,1	TGM5	88	1	0			c.A1562G						PASS	.	T	ARG/GLN,ARG/GLN	17,4389	23.3+/-48.9	0,17,2186	99.0	81.0	87.0		1316,1562	1.7	1.0	15	dbSNP_126	87	146,8452	70.7+/-133.2	1,144,4154	yes	missense,missense	TGM5	NM_004245.3,NM_201631.3	43,43	1,161,6340	CC,CT,TT		1.6981,0.3858,1.2535	benign,benign	439/639,521/721	43527819	163,12841	2203	4299	6502	SO:0001583	missense	9333	exon10			ATATCCTGGCCCA	AF035960	CCDS32211.1, CCDS32212.1	15q15	2004-07-07				ENSG00000104055		"""Transglutaminases"""	11781	protein-coding gene	gene with protein product		603805				9452468, 11390390	Standard	NM_201631		Approved	TGX	uc001zrd.2	O43548		ENST00000220420.5:c.1562A>G	15.37:g.43527819T>C	ENSP00000220420:p.Gln521Arg	186.0	0.0	0		160.0	59.0	0.36875	NM_201631	O43549|Q0VF40|Q9UEZ4	Missense_Mutation	SNP	ENST00000220420.5	37	CCDS32212.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	T	7.086	0.571152	0.13623	0.003858	0.016981	ENSG00000104055	ENST00000220420;ENST00000349114;ENST00000396996	T;T	0.69561	-0.41;-0.41	5.58	1.73	0.24493	Transglutaminase, C-terminal (2);Immunoglobulin-like fold (1);	0.134279	0.47852	D	0.000201	T	0.37919	0.1021	L	0.50333	1.59	0.27114	N	0.962306	B;B	0.12630	0.004;0.006	B;B	0.19666	0.013;0.026	T	0.39502	-0.9611	10	0.42905	T	0.14	-8.616	4.8757	0.13655	0.1649:0.1715:0.0:0.6635	rs35985214	439;521	O43548-2;O43548	.;TGM5_HUMAN	R	521;439;520	ENSP00000220420:Q521R;ENSP00000220419:Q439R	ENSP00000220420:Q521R	Q	-	2	0	TGM5	41315111	1.000000	0.71417	0.997000	0.53966	0.029000	0.11900	1.138000	0.31491	0.387000	0.25024	-0.274000	0.10170	CAG	T|0.988;C|0.012	0.012	strong		0.577	TGM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432257.1	NM_004245	
C9orf40	55071	hgsc.bcm.edu	37	9	77567335	77567335	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:77567335C>T	ENST00000376854.5	-	1	467	c.193G>A	c.(193-195)Gag>Aag	p.E65K	RP11-197P3.4_ENST00000455609.1_RNA	NM_017998.2	NP_060468.2	Q8IXQ3	CI040_HUMAN	chromosome 9 open reading frame 40	65										lung(2)|stomach(1)	3						GCCGAGGGCTCTGCCATGGTC	0.706																																					p.E65K		Atlas-SNP	.											.	C9orf40	5	.	0			c.G193A						PASS	.						11.0	11.0	11.0					9																	77567335		2086	4155	6241	SO:0001583	missense	55071	exon1			AGGGCTCTGCCAT	AK000972	CCDS6648.1	9q21.31	2012-03-15			ENSG00000135045	ENSG00000135045			23433	protein-coding gene	gene with protein product							Standard	NM_017998		Approved	FLJ10110	uc004ajo.4	Q8IXQ3	OTTHUMG00000020031	ENST00000376854.5:c.193G>A	9.37:g.77567335C>T	ENSP00000366050:p.Glu65Lys	89.0	0.0	0		60.0	24.0	0.4	NM_017998	Q9NWD3	Missense_Mutation	SNP	ENST00000376854.5	37	CCDS6648.1	.	.	.	.	.	.	.	.	.	.	C	20.0	3.930235	0.73327	.	.	ENSG00000135045	ENST00000376854	.	.	.	5.21	4.25	0.50352	.	0.327978	0.21929	N	0.067058	T	0.50769	0.1635	M	0.61703	1.905	0.23620	N	0.997277	P	0.50156	0.932	P	0.53450	0.726	T	0.44034	-0.9354	9	0.56958	D	0.05	-11.2091	10.2293	0.43245	0.1977:0.8023:0.0:0.0	.	65	Q8IXQ3	CI040_HUMAN	K	65	.	ENSP00000366050:E65K	E	-	1	0	C9orf40	76757155	0.160000	0.22878	0.496000	0.27539	0.498000	0.33706	1.673000	0.37534	2.447000	0.82792	0.305000	0.20034	GAG	.	.	none		0.706	C9orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052702.1	NM_017998	
CHRNA3	1136	hgsc.bcm.edu	37	15	78893787	78893787	+	Silent	SNP	G	G	A	rs56403513	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78893787G>A	ENST00000326828.5	-	5	1581	c.1197C>T	c.(1195-1197)gaC>gaT	p.D399D	CHRNA3_ENST00000348639.3_Silent_p.D399D	NM_000743.4	NP_000734.2	P32297	ACHA3_HUMAN	cholinergic receptor, nicotinic, alpha 3 (neuronal)	399					activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|behavioral response to nicotine (GO:0035095)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transmembrane transport (GO:0034220)|ion transport (GO:0006811)|locomotory behavior (GO:0007626)|nervous system development (GO:0007399)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of dendrite morphogenesis (GO:0048814)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane potential (GO:0042391)|regulation of smooth muscle contraction (GO:0006940)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|synaptic transmission involved in micturition (GO:0060084)|synaptic transmission, cholinergic (GO:0007271)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|ligand-gated ion channel activity (GO:0015276)			central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	18					Bupropion(DB01156)|Dextromethorphan(DB00514)|Galantamine(DB00674)|Levomethadyl Acetate(DB01227)|Nicotine(DB00184)|Pentolinium(DB01090)|Varenicline(DB01273)	CACACATCCCGTCCTGGCAGG	0.542													G|||	5	0.000998403	0.0008	0.0	5008	,	,		19435	0.001		0.003	False		,,,				2504	0.0				p.D399D		Atlas-SNP	.											.	CHRNA3	56	.	0			c.C1197T						PASS	.	G	,	2,4390	4.2+/-10.8	0,2,2194	104.0	93.0	97.0		1197,1197	-12.0	0.0	15	dbSNP_129	97	33,8553	22.8+/-68.1	0,33,4260	no	coding-synonymous,coding-synonymous	CHRNA3	NM_000743.4,NM_001166694.1	,	0,35,6454	AA,AG,GG		0.3843,0.0455,0.2697	,	399/506,399/490	78893787	35,12943	2196	4293	6489	SO:0001819	synonymous_variant	1136	exon5			CATCCCGTCCTGG		CCDS10305.1, CCDS53964.1	15q24	2012-02-11	2012-02-07		ENSG00000080644	ENSG00000080644		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1957	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 3 (neuronal)"""	118503	"""cholinergic receptor, nicotinic, alpha polypeptide 3"""			2004777	Standard	NM_000743		Approved		uc002bec.3	P32297	OTTHUMG00000143863	ENST00000326828.5:c.1197C>T	15.37:g.78893787G>A		239.0	0.0	0		243.0	115.0	0.473251	NM_000743	Q15823|Q4KMN8|Q86U77|Q96RH3|Q99553|Q9BQ93|Q9BRR4	Silent	SNP	ENST00000326828.5	37	CCDS10305.1																																																																																			G|0.996;A|0.004	0.004	strong		0.542	CHRNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290111.3		
FHDC1	85462	hgsc.bcm.edu	37	4	153886104	153886104	+	Silent	SNP	G	G	A	rs2018007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:153886104G>A	ENST00000511601.1	+	9	1265	c.1077G>A	c.(1075-1077)ttG>ttA	p.L359L	FHDC1_ENST00000260008.3_Silent_p.L359L			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	359	FH2. {ECO:0000255|PROSITE- ProRule:PRU00774}.								ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					CAGAAAAATTGCATCATGTTC	0.303													G|||	113	0.0225639	0.0749	0.0086	5008	,	,		18165	0.0		0.005	False		,,,				2504	0.0031				p.L359L		Atlas-SNP	.											.	FHDC1	102	.	0			c.G1077A						PASS	.	G		277,4129	152.2+/-185.9	13,251,1939	75.0	81.0	79.0		1077	0.9	0.0	4	dbSNP_92	79	37,8557	24.6+/-71.5	1,35,4261	no	coding-synonymous	FHDC1	NM_033393.2		14,286,6200	AA,AG,GG		0.4305,6.2869,2.4154		359/1144	153886104	314,12686	2203	4297	6500	SO:0001819	synonymous_variant	85462	exon8			AAAATTGCATCAT	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.1077G>A	4.37:g.153886104G>A		359.0	0.0	0		401.0	183.0	0.456359	NM_033393		Silent	SNP	ENST00000511601.1	37	CCDS34081.1																																																																																			G|0.973;A|0.027	0.027	strong		0.303	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393	
BTN2A1	11120	hgsc.bcm.edu	37	6	26468637	26468637	+	Missense_Mutation	SNP	G	G	A	rs142664900	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26468637G>A	ENST00000312541.5	+	8	1692	c.1444G>A	c.(1444-1446)Gtg>Atg	p.V482M	BTN2A1_ENST00000469185.1_Intron|BTN2A1_ENST00000429381.1_3'UTR|BTN2A1_ENST00000541522.1_Missense_Mutation_p.V421M	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	482	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						AGCCTTTTCCGTGCCTGTGAG	0.577																																					p.V482M		Atlas-SNP	.											.	BTN2A1	118	.	0			c.G1444A						PASS	.	G	MET/VAL,,MET/VAL,	2,4404	4.2+/-10.8	0,2,2201	173.0	135.0	148.0		1261,,1444,	1.8	0.1	6	dbSNP_134	148	1,8599	1.2+/-3.3	0,1,4299	yes	missense,intron,missense,utr-3	BTN2A1	NM_001197233.1,NM_001197234.1,NM_007049.3,NM_078476.2	21,,21,	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	possibly-damaging,,possibly-damaging,	421/467,,482/528,	26468637	3,13003	2203	4300	6503	SO:0001583	missense	11120	exon8			TTTTCCGTGCCTG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.1444G>A	6.37:g.26468637G>A	ENSP00000312158:p.Val482Met	347.0	1.0	0.00288184		515.0	263.0	0.51068	NM_007049	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.773|7.773	0.707775|0.707775	0.15239|0.15239	4.54E-4|4.54E-4	1.16E-4|1.16E-4	ENSG00000112763|ENSG00000112763	ENST00000265424|ENST00000312541;ENST00000541522	.|T;T	.|0.60920	.|0.15;0.15	2.72|2.72	1.84|1.84	0.25277|0.25277	.|Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.|.	.|.	.|.	.|.	.|T	.|0.45617	.|0.1351	L|L	0.61218|0.61218	1.895|1.895	0.09310|0.09310	N|N	1|1	.|D	.|0.58620	.|0.983	.|P	.|0.51055	.|0.657	.|T	.|0.23655	.|-1.0182	.|9	.|0.59425	.|D	.|0.04	.|.	8.0041|8.0041	0.30315|0.30315	0.1317:0.0:0.8683:0.0|0.1317:0.0:0.8683:0.0	.|.	.|482	.|Q7KYR7	.|BT2A1_HUMAN	.|M	-1|482;421	.|ENSP00000312158:V482M;ENSP00000443909:V421M	.|ENSP00000312158:V482M	.|V	+|+	.|1	.|0	BTN2A1|BTN2A1	26576616|26576616	0.006000|0.006000	0.16342|0.16342	0.051000|0.051000	0.19133|0.19133	0.003000|0.003000	0.03518|0.03518	1.564000|1.564000	0.36375|0.36375	0.712000|0.712000	0.32039|0.32039	-0.424000|-0.424000	0.05967|0.05967	.|GTG	G|0.999;A|0.001	0.001	strong		0.577	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
NEUROD4	58158	hgsc.bcm.edu	37	12	55420785	55420785	+	Missense_Mutation	SNP	G	G	A	rs151143558	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:55420785G>A	ENST00000242994.3	+	2	940	c.562G>A	c.(562-564)Gat>Aat	p.D188N		NM_021191.2	NP_067014.2	Q9HD90	NDF4_HUMAN	neuronal differentiation 4	188					amacrine cell differentiation (GO:0035881)|cell fate commitment (GO:0045165)|glial cell differentiation (GO:0010001)|neuroblast proliferation (GO:0007405)|neuron development (GO:0048666)|neuron migration (GO:0001764)|Notch signaling pathway (GO:0007219)|positive regulation of cell differentiation (GO:0045597)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|ovary(3)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	41						GAAGCACGAGGATAAATCTCC	0.517													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18905	0.0		0.003	False		,,,				2504	0.0				p.D188N		Atlas-SNP	.											.	NEUROD4	87	.	0			c.G562A						PASS	.	G	ASN/ASP	0,4406		0,0,2203	77.0	81.0	80.0		562	5.6	1.0	12	dbSNP_134	80	39,8561	24.6+/-71.5	0,39,4261	yes	missense	NEUROD4	NM_021191.2	23	0,39,6464	AA,AG,GG		0.4535,0.0,0.2999	benign	188/332	55420785	39,12967	2203	4300	6503	SO:0001583	missense	58158	exon2			CACGAGGATAAAT	AF203901	CCDS8886.1	12q13.13	2013-05-21	2012-02-22			ENSG00000123307		"""Basic helix-loop-helix proteins"""	13802	protein-coding gene	gene with protein product		611635	"""neurogenic differentiation 4"""				Standard	NM_021191		Approved	Atoh3, ATH-3, MATH-3, bHLHa4	uc001sgp.4	Q9HD90		ENST00000242994.3:c.562G>A	12.37:g.55420785G>A	ENSP00000242994:p.Asp188Asn	51.0	0.0	0		56.0	30.0	0.535714	NM_021191	B2RAC9	Missense_Mutation	SNP	ENST00000242994.3	37	CCDS8886.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	20.4	3.977793	0.74360	0.0	0.004535	ENSG00000123307	ENST00000242994	T	0.65178	-0.14	5.56	5.56	0.83823	Neurogenic differentiation factor, domain of unknown function (1);	0.214698	0.47455	D	0.000236	T	0.67739	0.2925	L	0.41492	1.28	0.37808	D	0.927932	B	0.24317	0.101	B	0.43809	0.432	T	0.70414	-0.4878	10	0.72032	D	0.01	-37.9711	17.4011	0.87459	0.0:0.0:1.0:0.0	.	188	Q9HD90	NDF4_HUMAN	N	188	ENSP00000242994:D188N	ENSP00000242994:D188N	D	+	1	0	NEUROD4	53707052	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	6.774000	0.75012	2.774000	0.95407	0.655000	0.94253	GAT	G|0.997;A|0.003	0.003	strong		0.517	NEUROD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406104.1		
ZNF526	116115	hgsc.bcm.edu	37	19	42729121	42729121	+	Missense_Mutation	SNP	C	C	T	rs150807158	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42729121C>T	ENST00000301215.3	+	3	791	c.566C>T	c.(565-567)cCa>cTa	p.P189L		NM_133444.1	NP_597701.1	Q8TF50	ZN526_HUMAN	zinc finger protein 526	189					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|cervix(1)|endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(3)	22		Prostate(69;0.0704)				CCTTCTCCCCCATCCGAAGTC	0.597													C|||	13	0.00259585	0.0008	0.0	5008	,	,		19799	0.0		0.006	False		,,,				2504	0.0061				p.P189L		Atlas-SNP	.											.	ZNF526	51	.	0			c.C566T						PASS	.	C	LEU/PRO	9,4397	15.5+/-35.6	0,9,2194	135.0	127.0	130.0		566	4.4	0.1	19	dbSNP_134	130	124,8476	64.9+/-127.2	2,120,4178	yes	missense	ZNF526	NM_133444.1	98	2,129,6372	TT,TC,CC		1.4419,0.2043,1.0226	possibly-damaging	189/671	42729121	133,12873	2203	4300	6503	SO:0001583	missense	116115	exon3			CTCCCCCATCCGA	AB075831	CCDS12598.1	19q13.31	2013-01-08				ENSG00000167625		"""Zinc fingers, C2H2-type"""	29415	protein-coding gene	gene with protein product		614387				11853319	Standard	NM_133444		Approved	KIAA1951, MGC4267	uc002osz.1	Q8TF50		ENST00000301215.3:c.566C>T	19.37:g.42729121C>T	ENSP00000301215:p.Pro189Leu	149.0	0.0	0		139.0	72.0	0.517986	NM_133444	B3KV29|Q69YI2|Q96E24	Missense_Mutation	SNP	ENST00000301215.3	37	CCDS12598.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	6.077	0.382572	0.11524	0.002043	0.014419	ENSG00000167625	ENST00000437878;ENST00000301215	T	0.08634	3.07	4.4	4.4	0.53042	.	0.555420	0.16362	N	0.217738	T	0.06096	0.0158	L	0.44542	1.39	0.33667	D	0.61049	B	0.12013	0.005	B	0.10450	0.005	T	0.02683	-1.1124	10	0.72032	D	0.01	-4.7579	9.9765	0.41786	0.0:0.9038:0.0:0.0962	.	189	Q8TF50	ZN526_HUMAN	L	45;189	ENSP00000301215:P189L	ENSP00000301215:P189L	P	+	2	0	ZNF526	47420961	0.022000	0.18835	0.057000	0.19452	0.395000	0.30598	2.169000	0.42434	2.449000	0.82847	0.467000	0.42956	CCA	C|0.991;T|0.009	0.009	strong		0.597	ZNF526-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463681.2	XM_057401	
CFHR5	81494	hgsc.bcm.edu	37	1	196953220	196953220	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:196953220C>T	ENST00000256785.4	+	3	492	c.383C>T	c.(382-384)tCg>tTg	p.S128L	CFHR5_ENST00000367414.5_Missense_Mutation_p.S152L			Q9BXR6	FHR5_HUMAN	complement factor H-related 5	128	Sushi 2. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation, alternative pathway (GO:0006957)	extracellular region (GO:0005576)				NS(2)|breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|liver(2)|lung(23)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)	49						AAAAACATTTCGTGTGTAGAA	0.378																																					p.S128L		Atlas-SNP	.											CFHR5_ENST00000367414,NS,malignant_melanoma,0,6	CFHR5	150	6	0			c.C383T						PASS	.						96.0	86.0	89.0					1																	196953220		2203	4300	6503	SO:0001583	missense	81494	exon3			ACATTTCGTGTGT	AF295327	CCDS1387.1	1q31.3	2014-09-17		2006-02-28	ENSG00000134389	ENSG00000134389		"""Complement system"""	24668	protein-coding gene	gene with protein product	"""factor H related protein 5"""	608593		CFHL5		11058592, 12041828	Standard	NM_030787		Approved	FHR5, FHR-5	uc001gts.4	Q9BXR6	OTTHUMG00000036517	ENST00000256785.4:c.383C>T	1.37:g.196953220C>T	ENSP00000256785:p.Ser128Leu	87.0	0.0	0		95.0	11.0	0.115789	NM_030787	Q2NKK2	Missense_Mutation	SNP	ENST00000256785.4	37	CCDS1387.1	.	.	.	.	.	.	.	.	.	.	C	12.35	1.912751	0.33721	.	.	ENSG00000134389	ENST00000367414;ENST00000256785	T;T	0.63580	-0.05;-0.05	3.89	0.396	0.16309	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.44767	0.1309	L	0.36672	1.1	0.09310	N	1	B	0.26363	0.147	B	0.26202	0.067	T	0.26155	-1.0111	9	0.19590	T	0.45	.	4.7535	0.13071	0.3661:0.5179:0.0:0.116	.	128	Q9BXR6	FHR5_HUMAN	L	152;128	ENSP00000356384:S152L;ENSP00000256785:S128L	ENSP00000256785:S128L	S	+	2	0	CFHR5	195219843	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.282000	0.08445	0.212000	0.20703	0.467000	0.42956	TCG	.	.	none		0.378	CFHR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088814.2	NM_030787	
SLC34A3	142680	hgsc.bcm.edu	37	9	140127725	140127725	+	Silent	SNP	C	C	T	rs34796681	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140127725C>T	ENST00000538474.1	+	7	849	c.625C>T	c.(625-627)Ctg>Ttg	p.L209L	SLC34A3_ENST00000361134.2_Silent_p.L209L	NM_001177316.1|NM_001177317.1	NP_001170787|NP_001170788	Q8N130	NPT2C_HUMAN	solute carrier family 34 (type II sodium/phosphate contransporter), member 3	209					cellular phosphate ion homeostasis (GO:0030643)|ion transport (GO:0006811)|phosphate ion transmembrane transport (GO:0035435)|phosphate ion transport (GO:0006817)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|brush border (GO:0005903)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|sodium:phosphate symporter activity (GO:0005436)			kidney(3)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(76;0.0926)		STAD - Stomach adenocarcinoma(284;0.0698)	OV - Ovarian serous cystadenocarcinoma(145;6.37e-05)|Epithelial(140;0.00057)		CCTGCTGCCACTGGAGAGCGC	0.682													c|||	2	0.000399361	0.0	0.0014	5008	,	,		11300	0.0		0.001	False		,,,				2504	0.0				p.L209L		Atlas-SNP	.											.	SLC34A3	32	.	0			c.C625T						PASS	.		,,	8,4304		0,8,2148	14.0	15.0	15.0		625,625,625	2.7	0.6	9	dbSNP_126	15	59,8433		0,59,4187	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC34A3	NM_001177316.1,NM_001177317.1,NM_080877.2	,,	0,67,6335	TT,TC,CC		0.6948,0.1855,0.5233	,,	209/600,209/600,209/600	140127725	67,12737	2156	4246	6402	SO:0001819	synonymous_variant	142680	exon7			CTGCCACTGGAGA	AB055000	CCDS7038.1	9q34.3	2013-07-17	2013-07-17		ENSG00000198569	ENSG00000198569		"""Solute carriers"""	20305	protein-coding gene	gene with protein product		609826	"""solute carrier family 34 (sodium phosphate), member 3"""			11880379, 16358215, 16358214	Standard	NM_080877		Approved	NPTIIc, FLJ38680	uc004cmf.1	Q8N130	OTTHUMG00000131780	ENST00000538474.1:c.625C>T	9.37:g.140127725C>T		46.0	0.0	0		58.0	31.0	0.534483	NM_001177317	A2BFA1	Silent	SNP	ENST00000538474.1	37	CCDS7038.1																																																																																			C|0.993;T|0.007	0.007	strong		0.682	SLC34A3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254712.1	NM_080877	
ZNF528	84436	hgsc.bcm.edu	37	19	52909200	52909200	+	Missense_Mutation	SNP	A	A	G	rs370656674		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:52909200A>G	ENST00000360465.3	+	5	482	c.56A>G	c.(55-57)cAg>cGg	p.Q19R	ZNF528_ENST00000391788.2_Missense_Mutation_p.Q9R|ZNF528_ENST00000594530.1_Missense_Mutation_p.Q19R|ZNF528_ENST00000598192.1_Missense_Mutation_p.Q19R	NM_032423.2	NP_115799.2	Q3MIS6	ZN528_HUMAN	zinc finger protein 528	19	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(6)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	39				GBM - Glioblastoma multiforme(134;0.00249)|OV - Ovarian serous cystadenocarcinoma(262;0.00817)		GAGTTCTCTCAGGAAGAGTGG	0.468																																					p.Q19R		Atlas-SNP	.											.	ZNF528	95	.	0			c.A56G						PASS	.	A	ARG/GLN	0,4406		0,0,2203	182.0	179.0	180.0		56	-0.7	0.0	19		180	1,8599	1.2+/-3.3	0,1,4299	no	missense	ZNF528	NM_032423.2	43	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	19/629	52909200	1,13005	2203	4300	6503	SO:0001583	missense	84436	exon5			TCTCTCAGGAAGA	AB058730	CCDS33091.1	19q13	2013-01-08			ENSG00000167555	ENSG00000167555		"""Zinc fingers, C2H2-type"", ""-"""	29384	protein-coding gene	gene with protein product		615580				11347906	Standard	NM_032423		Approved	KIAA1827	uc002pzh.3	Q3MIS6	OTTHUMG00000156494	ENST00000360465.3:c.56A>G	19.37:g.52909200A>G	ENSP00000353652:p.Gln19Arg	197.0	0.0	0		200.0	96.0	0.48	NM_032423	B3KPN4|Q86T88|Q96JK0	Missense_Mutation	SNP	ENST00000360465.3	37	CCDS33091.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.438395	0.25900	0.0	1.16E-4	ENSG00000167555	ENST00000391788;ENST00000391787;ENST00000360465	T;T;T	0.01963	4.53;4.53;4.53	1.93	-0.733	0.11144	Krueppel-associated box (4);	.	.	.	.	T	0.05777	0.0151	L	0.53729	1.69	0.19775	N	0.999957	D	0.76494	0.999	D	0.72338	0.977	T	0.35151	-0.9800	9	0.45353	T	0.12	.	0.995	0.01465	0.2762:0.3854:0.1474:0.1911	.	19	Q3MIS6	ZN528_HUMAN	R	9;19;19	ENSP00000375665:Q9R;ENSP00000375664:Q19R;ENSP00000353652:Q19R	ENSP00000353652:Q19R	Q	+	2	0	ZNF528	57601012	0.001000	0.12720	0.015000	0.15790	0.517000	0.34286	-0.590000	0.05760	-0.452000	0.07087	0.402000	0.26972	CAG	.	.	weak		0.468	ZNF528-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344336.1	NM_032423	
UPF3A	65110	hgsc.bcm.edu	37	13	115067419	115067419	+	Silent	SNP	G	G	A	rs146464930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:115067419G>A	ENST00000375299.3	+	9	1277	c.1221G>A	c.(1219-1221)ccG>ccA	p.P407P	UPF3A_ENST00000351487.5_Silent_p.P374P|UPF3A_ENST00000475218.2_3'UTR	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	407					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		GCGGGGCTCCGGGGGAGGCCA	0.567													G|||	14	0.00279553	0.0008	0.0043	5008	,	,		19212	0.0		0.0099	False		,,,				2504	0.0				p.P407P		Atlas-SNP	.											.	UPF3A	47	.	0			c.G1221A						PASS	.	G	,	13,4359		0,13,2173	14.0	19.0	17.0		1221,1122	-9.9	0.0	13	dbSNP_134	17	156,8366		2,152,4107	no	coding-synonymous,coding-synonymous	UPF3A	NM_023011.3,NM_080687.2	,	2,165,6280	AA,AG,GG		1.8306,0.2973,1.3107	,	407/477,374/444	115067419	169,12725	2186	4261	6447	SO:0001819	synonymous_variant	65110	exon9			GGCTCCGGGGGAG	AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.1221G>A	13.37:g.115067419G>A		140.0	0.0	0		115.0	60.0	0.521739	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	37	CCDS9543.1																																																																																			G|0.991;A|0.009	0.009	strong		0.567	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
ACACB	32	hgsc.bcm.edu	37	12	109665242	109665242	+	Missense_Mutation	SNP	G	G	A	rs60293430	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109665242G>A	ENST00000338432.7	+	28	4068	c.3949G>A	c.(3949-3951)Ggc>Agc	p.G1317S	ACACB_ENST00000377854.5_Missense_Mutation_p.G1247S|ACACB_ENST00000377848.3_Missense_Mutation_p.G1317S			O00763	ACACB_HUMAN	acetyl-CoA carboxylase beta	1317					acetyl-CoA metabolic process (GO:0006084)|biotin metabolic process (GO:0006768)|carnitine shuttle (GO:0006853)|cellular lipid metabolic process (GO:0044255)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|malonyl-CoA biosynthetic process (GO:2001295)|positive regulation of cellular metabolic process (GO:0031325)|protein homotetramerization (GO:0051289)|response to drug (GO:0042493)|response to organic cyclic compound (GO:0014070)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	acetyl-CoA carboxylase activity (GO:0003989)|ATP binding (GO:0005524)|biotin binding (GO:0009374)|biotin carboxylase activity (GO:0004075)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(9)|kidney(5)|large_intestine(20)|lung(40)|ovary(6)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95					Adenine(DB00173)|Biotin(DB00121)	GCTCCCGGACGGCACCTGCGT	0.577													G|||	259	0.0517173	0.1074	0.0548	5008	,	,		17197	0.002		0.0586	False		,,,				2504	0.0184				p.G1317S		Atlas-SNP	.											.	ACACB	330	.	0			c.G3949A						PASS	.	G	SER/GLY	456,3950	214.8+/-234.0	23,410,1770	53.0	45.0	47.0		3949	5.4	1.0	12	dbSNP_129	47	522,8078	144.3+/-200.2	19,484,3797	yes	missense	ACACB	NM_001093.3	56	42,894,5567	AA,AG,GG		6.0698,10.3495,7.5196	benign	1317/2459	109665242	978,12028	2203	4300	6503	SO:0001583	missense	32	exon27			CCGGACGGCACCT	U89344	CCDS31898.1	12q24.1	2010-05-07	2010-04-30		ENSG00000076555	ENSG00000076555	6.4.1.2		85	protein-coding gene	gene with protein product	"""acetyl-CoA carboxylase 2"""	601557	"""acetyl-Coenzyme A carboxylase beta"""			8670171	Standard	NM_001093		Approved	HACC275, ACC2, ACCB	uc001toc.3	O00763	OTTHUMG00000169250	ENST00000338432.7:c.3949G>A	12.37:g.109665242G>A	ENSP00000341044:p.Gly1317Ser	91.0	0.0	0		120.0	64.0	0.533333	NM_001093	A6NK36|Q16852|Q1HEC1|Q6KE87|Q6KE89|Q6TY48	Missense_Mutation	SNP	ENST00000338432.7	37	CCDS31898.1	105	0.04807692307692308	45	0.09146341463414634	22	0.06077348066298342	0	0.0	38	0.05013192612137203	G	16.13	3.034855	0.54896	0.103495	0.060698	ENSG00000076555	ENST00000338432;ENST00000377848;ENST00000377854;ENST00000390027	T;T;T	0.44881	0.91;0.91;0.91	5.38	5.38	0.77491	Acetyl-CoA carboxylase, central domain (1);	0.053759	0.85682	D	0.000000	T	0.02342	0.0072	L	0.55213	1.73	0.09310	P	1.0	D	0.65815	0.995	P	0.62813	0.907	T	0.04128	-1.0975	9	0.17832	T	0.49	.	14.364	0.66792	0.0:0.0:0.852:0.148	rs60293430;rs61752506	1317	O00763	ACACB_HUMAN	S	1317;1317;1247;548	ENSP00000341044:G1317S;ENSP00000367079:G1317S;ENSP00000367085:G1247S	ENSP00000341044:G1317S	G	+	1	0	ACACB	108149625	1.000000	0.71417	0.985000	0.45067	0.984000	0.73092	4.727000	0.61993	2.679000	0.91253	0.655000	0.94253	GGC	G|0.932;A|0.068	0.068	strong		0.577	ACACB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403077.1	NM_001093	
MTBP	27085	hgsc.bcm.edu	37	8	121463425	121463425	+	Silent	SNP	T	T	C	rs61753755	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:121463425T>C	ENST00000305949.1	+	4	333	c.288T>C	c.(286-288)gaT>gaC	p.D96D		NM_022045.4	NP_071328.2	Q96DY7	MTBP_HUMAN	MDM2 binding protein	96					cell cycle arrest (GO:0007050)|mitotic spindle checkpoint (GO:0071174)|negative regulation of cell proliferation (GO:0008285)|protein localization to kinetochore (GO:0034501)|traversing start control point of mitotic cell cycle (GO:0007089)	chromatin (GO:0000785)|kinetochore (GO:0000776)				NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	Lung NSC(37;5.68e-08)|Ovarian(258;0.00769)|all_neural(195;0.0804)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00503)			GTAGTTCTGATTGGCAAGAGA	0.269													T|||	189	0.0377396	0.0847	0.0144	5008	,	,		15992	0.0		0.0288	False		,,,				2504	0.0389				p.D96D		Atlas-SNP	.											.	MTBP	77	.	0			c.T288C						PASS	.	T		360,4046	178.0+/-206.8	12,336,1855	60.0	61.0	61.0		288	-0.1	1.0	8	dbSNP_129	61	181,8409	80.9+/-143.5	2,177,4116	no	coding-synonymous	MTBP	NM_022045.3		14,513,5971	CC,CT,TT		2.1071,8.1707,4.1628		96/905	121463425	541,12455	2203	4295	6498	SO:0001819	synonymous_variant	27085	exon4			TTCTGATTGGCAA		CCDS6333.1	8q24.1-q24.2	2014-03-03	2014-03-03		ENSG00000172167	ENSG00000172167			7417	protein-coding gene	gene with protein product		605927	"""MDM2 (mouse double minute 2)-binding protein, 104kD"", ""Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) binding protein, 104kDa"""			10906133, 11060448	Standard	NM_022045		Approved		uc003ypc.2	Q96DY7	OTTHUMG00000165040	ENST00000305949.1:c.288T>C	8.37:g.121463425T>C		86.0	0.0	0		54.0	24.0	0.444444	NM_022045	B4DUR5|Q9HA89	Silent	SNP	ENST00000305949.1	37	CCDS6333.1																																																																																			T|0.966;C|0.034	0.034	strong		0.269	MTBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381530.1	NM_022045	
NYAP1	222950	hgsc.bcm.edu	37	7	100086246	100086246	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100086246G>A	ENST00000300179.2	+	4	1061	c.902G>A	c.(901-903)cGc>cAc	p.R301H	NYAP1_ENST00000454988.1_Missense_Mutation_p.R244H|NYAP1_ENST00000423930.1_Missense_Mutation_p.R301H	NM_173564.2	NP_775835.2	Q6ZVC0	NYAP1_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 1	301	Pro-rich.				neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												CATGCCCACCGCCGCCCAGCT	0.692																																					p.R301H		Atlas-SNP	.											.	.	.	.	0			c.G902A						PASS	.						46.0	49.0	48.0					7																	100086246		2203	4296	6499	SO:0001583	missense	222950	exon4			CCCACCGCCGCCC	AK094857	CCDS5696.1	7q22.1	2011-11-30	2011-11-30	2011-11-30	ENSG00000166924	ENSG00000166924			22009	protein-coding gene	gene with protein product		615477	"""chromosome 7 open reading frame 51"", ""KIAA1486-like"""	C7orf51, KIAA1486L		21946561	Standard	NM_173564		Approved	FLJ37538	uc003uvd.2	Q6ZVC0	OTTHUMG00000155290	ENST00000300179.2:c.902G>A	7.37:g.100086246G>A	ENSP00000300179:p.Arg301His	150.0	0.0	0		91.0	13.0	0.142857	NM_173564	Q6U9Y3|Q8N1V0	Missense_Mutation	SNP	ENST00000300179.2	37	CCDS5696.1	.	.	.	.	.	.	.	.	.	.	G	7.182	0.589872	0.13812	.	.	ENSG00000166924	ENST00000300179;ENST00000423930;ENST00000454988	T;T;T	0.32988	1.43;1.43;1.45	4.9	4.02	0.46733	.	0.133388	0.34802	N	0.003671	T	0.21921	0.0528	L	0.34521	1.04	0.43719	D	0.996195	P;P	0.40834	0.68;0.73	B;B	0.38500	0.214;0.275	T	0.02371	-1.1169	10	0.33940	T	0.23	-13.797	9.197	0.37235	0.1022:0.0:0.8978:0.0	.	244;301	C9JS30;Q6ZVC0	.;CG051_HUMAN	H	301;301;244	ENSP00000300179:R301H;ENSP00000411861:R301H;ENSP00000394424:R244H	ENSP00000300179:R301H	R	+	2	0	C7orf51	99924182	0.929000	0.31497	0.990000	0.47175	0.190000	0.23558	1.581000	0.36558	1.055000	0.40461	0.407000	0.27541	CGC	.	.	none		0.692	NYAP1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339335.2	NM_173564	
DSCR4	10281	hgsc.bcm.edu	37	21	39493232	39493232	+	Missense_Mutation	SNP	G	G	A	rs61731605	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:39493232G>A	ENST00000328264.3	-	1	222	c.118C>T	c.(118-120)Cct>Tct	p.P40S	DSCR4_ENST00000398948.1_Missense_Mutation_p.P40S|DSCR8_ENST00000400477.3_5'Flank|DSCR8_ENST00000357704.4_5'Flank	NM_005867.2	NP_005858.1	P56555	DSCR4_HUMAN	Down syndrome critical region gene 4	40										large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)	6						ctgtggagaggagaagctgag	0.512													G|||	51	0.0101837	0.0	0.0245	5008	,	,		17151	0.002		0.0278	False		,,,				2504	0.0041				p.P40S		Atlas-SNP	.											.	DSCR4	20	.	0			c.C118T						PASS	.	G		30,4376	35.2+/-66.4	0,30,2173	75.0	69.0	71.0			1.3	0.0	21	dbSNP_129	71	256,8344	98.8+/-160.4	3,250,4047	yes	intergenic				3,280,6220	AA,AG,GG		2.9767,0.6809,2.199			39493232	286,12720	2203	4300	6503	SO:0001583	missense	10281	exon1			GGAGAGGAGAAGC	AB000099	CCDS33554.1	21q22.2	2012-04-19			ENSG00000184029	ENSG00000184029			3045	protein-coding gene	gene with protein product		604829				9455479	Standard	NM_005867		Approved	DCRB	uc002ywp.3	P56555	OTTHUMG00000086673	ENST00000328264.3:c.118C>T	21.37:g.39493232G>A	ENSP00000328676:p.Pro40Ser	67.0	0.0	0		55.0	25.0	0.454545	NM_005867	Q4VB31	Missense_Mutation	SNP	ENST00000328264.3	37	CCDS33554.1	37	0.01694139194139194	0	0.0	12	0.03314917127071823	2	0.0034965034965034965	23	0.030343007915567283	G	9.758	1.169279	0.21621	0.006809	0.029767	ENSG00000184029	ENST00000398948;ENST00000328264	.	.	.	1.33	1.33	0.21861	.	.	.	.	.	T	0.30355	0.0762	.	.	.	0.09310	N	1	D	0.65815	0.995	D	0.65323	0.934	T	0.13098	-1.0522	7	0.87932	D	0	.	6.0593	0.19828	0.0:0.0:1.0:0.0	rs61731605	40	P56555	DSCR4_HUMAN	S	40	.	ENSP00000328676:P40S	P	-	1	0	DSCR4	38415102	0.006000	0.16342	0.011000	0.14972	0.058000	0.15608	0.196000	0.17176	1.058000	0.40530	0.313000	0.20887	CCT	G|0.980;A|0.020	0.020	strong		0.512	DSCR4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000194834.1	NM_005867	
HORMAD2	150280	hgsc.bcm.edu	37	22	30489945	30489945	+	Missense_Mutation	SNP	G	G	A	rs34150968	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30489945G>A	ENST00000336726.6	+	2	359	c.4G>A	c.(4-6)Gcc>Acc	p.A2T	HORMAD2_ENST00000403975.1_Missense_Mutation_p.A2T	NM_152510.2	NP_689723.1	Q8N7B1	HORM2_HUMAN	HORMA domain containing 2	2			A -> T (in dbSNP:rs34150968).		meiotic nuclear division (GO:0007126)|meiotic sister chromatid cohesion (GO:0051177)	chromosome (GO:0005694)|nucleus (GO:0005634)				large_intestine(1)|lung(1)	2			Epithelial(10;0.125)			TCCTACAATGGCCACTGCTCA	0.328													G|||	16	0.00319489	0.0	0.0043	5008	,	,		15203	0.0		0.0129	False		,,,				2504	0.0				p.A2T		Atlas-SNP	.											.	HORMAD2	12	.	0			c.G4A						PASS	.	G	THR/ALA	7,3711		0,7,1852	74.0	66.0	69.0		4	1.6	1.0	22	dbSNP_126	69	94,8134		0,94,4020	yes	missense	HORMAD2	NM_152510.2	58	0,101,5872	AA,AG,GG		1.1424,0.1883,0.8455	possibly-damaging	2/308	30489945	101,11845	1859	4114	5973	SO:0001583	missense	150280	exon2			ACAATGGCCACTG	AK098703	CCDS46683.1	22q12.2	2014-01-21			ENSG00000176635	ENSG00000176635			28383	protein-coding gene	gene with protein product						12477932	Standard	NM_152510		Approved	MGC26710, CT46.2	uc003agy.3	Q8N7B1	OTTHUMG00000150881	ENST00000336726.6:c.4G>A	22.37:g.30489945G>A	ENSP00000336984:p.Ala2Thr	243.0	1.0	0.00411523		249.0	110.0	0.441767	NM_152510	B5MEB2|Q8NHR2	Missense_Mutation	SNP	ENST00000336726.6	37	CCDS46683.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	11.81	1.748595	0.30955	0.001883	0.011424	ENSG00000176635	ENST00000336726;ENST00000403975	T;T	0.35973	1.28;1.28	5.02	1.62	0.23740	.	0.497968	0.20580	N	0.089551	T	0.25827	0.0629	M	0.74881	2.28	0.31316	N	0.686633	B	0.23540	0.087	B	0.17433	0.018	T	0.28933	-1.0028	10	0.56958	D	0.05	-7.1149	5.765	0.18221	0.0917:0.0:0.577:0.3313	rs34150968	2	Q8N7B1	HORM2_HUMAN	T	2	ENSP00000336984:A2T;ENSP00000385055:A2T	ENSP00000336984:A2T	A	+	1	0	HORMAD2	28819945	1.000000	0.71417	1.000000	0.80357	0.379000	0.30106	1.781000	0.38644	0.340000	0.23745	0.491000	0.48974	GCC	G|0.993;A|0.007	0.007	strong		0.328	HORMAD2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320416.2	NM_152510	
SPAG17	200162	hgsc.bcm.edu	37	1	118535211	118535211	+	Missense_Mutation	SNP	T	T	C	rs35290515	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:118535211T>C	ENST00000336338.5	-	36	5304	c.5239A>G	c.(5239-5241)Aaa>Gaa	p.K1747E		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1747						cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)|sperm flagellum (GO:0036126)				NS(1)|biliary_tract(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(30)|liver(2)|lung(56)|ovary(3)|prostate(5)|skin(5)|upper_aerodigestive_tract(6)|urinary_tract(1)	123	Esophageal squamous(2;0.0106)	all_cancers(81;0.0204)|all_lung(203;9.46e-05)|Lung NSC(69;0.000675)|all_epithelial(167;0.01)		Lung(183;0.0858)		ACTAGCTGTTTGGACTCAATG	0.448													T|||	65	0.0129792	0.0008	0.0288	5008	,	,		15614	0.0		0.0318	False		,,,				2504	0.0123				p.K1747E		Atlas-SNP	.											.	SPAG17	263	.	0			c.A5239G						PASS	.	T	GLU/LYS	26,4380	32.6+/-62.9	0,26,2177	92.0	90.0	91.0		5239	-1.9	0.0	1	dbSNP_126	91	285,8315	105.4+/-166.3	4,277,4019	yes	missense	SPAG17	NM_206996.2	56	4,303,6196	CC,CT,TT		3.314,0.5901,2.3912	probably-damaging	1747/2224	118535211	311,12695	2203	4300	6503	SO:0001583	missense	200162	exon36			GCTGTTTGGACTC		CCDS899.1	1p12	2014-01-21			ENSG00000155761	ENSG00000155761			26620	protein-coding gene	gene with protein product							Standard	NM_206996		Approved	FLJ34497, PF6, RP4-776P7.2, CT143	uc001ehk.2	Q6Q759	OTTHUMG00000012198	ENST00000336338.5:c.5239A>G	1.37:g.118535211T>C	ENSP00000337804:p.Lys1747Glu	185.0	0.0	0		181.0	75.0	0.414365	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	35	0.016025641025641024	0	0.0	13	0.03591160220994475	0	0.0	22	0.029023746701846966	T	12.87	2.068360	0.36470	0.005901	0.03314	ENSG00000155761	ENST00000336338;ENST00000437255	T	0.21734	1.99	5.6	-1.87	0.07737	.	0.536654	0.20400	N	0.093080	T	0.10465	0.0256	M	0.61703	1.905	0.09310	N	1	P	0.38078	0.617	B	0.37144	0.242	T	0.25328	-1.0135	10	0.49607	T	0.09	.	15.5645	0.76281	0.0:0.0:0.5819:0.4181	rs35290515	1747	Q6Q759	SPG17_HUMAN	E	1747;227	ENSP00000337804:K1747E	ENSP00000337804:K1747E	K	-	1	0	SPAG17	118336734	0.176000	0.23096	0.004000	0.12327	0.059000	0.15707	0.839000	0.27586	0.049000	0.15920	-0.313000	0.08912	AAA	T|0.979;C|0.021	0.021	strong		0.448	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
AKR1C3	8644	hgsc.bcm.edu	37	10	5138747	5138747	+	Missense_Mutation	SNP	A	A	G	rs11551177	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5138747A>G	ENST00000380554.3	+	2	882	c.230A>G	c.(229-231)gAa>gGa	p.E77G	AKR1C3_ENST00000470862.2_3'UTR|AKR1C3_ENST00000439082.2_5'UTR|AKR1C3_ENST00000605149.1_Missense_Mutation_p.E54G	NM_001253908.1|NM_003739.5	NP_001240837.1|NP_003730.4	P42330	AK1C3_HUMAN	aldo-keto reductase family 1, member C3	77			E -> G (in dbSNP:rs41306308).		arachidonic acid metabolic process (GO:0019369)|cellular response to cadmium ion (GO:0071276)|cellular response to calcium ion (GO:0071277)|cellular response to corticosteroid stimulus (GO:0071384)|cellular response to jasmonic acid stimulus (GO:0071395)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to reactive oxygen species (GO:0034614)|cellular response to starvation (GO:0009267)|cyclooxygenase pathway (GO:0019371)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|farnesol catabolic process (GO:0016488)|G-protein coupled receptor signaling pathway (GO:0007186)|keratinocyte differentiation (GO:0030216)|male gonad development (GO:0008584)|multicellular organismal macromolecule metabolic process (GO:0044259)|negative regulation of retinoic acid biosynthetic process (GO:1900053)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|positive regulation of cell death (GO:0010942)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|progesterone metabolic process (GO:0042448)|prostaglandin metabolic process (GO:0006693)|protein import into nucleus, translocation (GO:0000060)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of testosterone biosynthetic process (GO:2000224)|renal absorption (GO:0070293)|response to nutrient (GO:0007584)|response to prostaglandin (GO:0034694)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|nucleus (GO:0005634)	15-hydroxyprostaglandin-D dehydrogenase (NADP+) activity (GO:0047020)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|delta4-3-oxosteroid 5beta-reductase activity (GO:0047787)|dihydrotestosterone 17-beta-dehydrogenase activity (GO:0035410)|geranylgeranyl reductase activity (GO:0045550)|indanol dehydrogenase activity (GO:0047718)|ketoreductase activity (GO:0045703)|ketosteroid monooxygenase activity (GO:0047086)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|phenanthrene 9,10-monooxygenase activity (GO:0018636)|prostaglandin D2 11-ketoreductase activity (GO:0036131)|prostaglandin F receptor activity (GO:0004958)|prostaglandin-F synthase activity (GO:0047017)|retinal dehydrogenase activity (GO:0001758)|retinol dehydrogenase activity (GO:0004745)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)|testosterone dehydrogenase (NAD+) activity (GO:0047035)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(6)|skin(1)	14					Bimatoprost(DB00905)|Doxorubicin(DB00997)	GTGAAGAGAGAAGACATATTC	0.423													A|||	184	0.0367412	0.028	0.0663	5008	,	,		22113	0.001		0.0825	False		,,,				2504	0.0174				p.E77G		Atlas-SNP	.											.	AKR1C3	21	.	0			c.A230G						PASS	.	A	GLY/GLU	111,4295	86.8+/-125.4	0,111,2092	175.0	138.0	151.0		230	2.0	0.5	10	dbSNP_120	151	543,8053	149.5+/-204.6	13,517,3768	no	missense	AKR1C3	NM_003739.4	98	13,628,5860	GG,GA,AA		6.3169,2.5193,5.03	benign	77/324	5138747	654,12348	2203	4298	6501	SO:0001583	missense	8644	exon2			AGAGAGAAGACAT	L43839	CCDS7063.1, CCDS73062.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000196139	ENSG00000196139	1.1.1.213, 1.1.1.188	"""Aldo-keto reductases"""	386	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase X"", ""prostaglandin F synthase"", ""3-alpha hydroxysteroid dehydrogenase, type II"""	603966	"""hydroxysteroid (17-beta) dehydrogenase 5"", ""aldo-keto reductase family 1, member C3 (3-alpha hydroxysteroid dehydrogenase, type II)"""	HSD17B5		7650035, 9792917	Standard	NM_003739		Approved	KIAA0119, DDX, HAKRB, PGFS	uc021pml.1	P42330	OTTHUMG00000017585	ENST00000380554.3:c.230A>G	10.37:g.5138747A>G	ENSP00000369927:p.Glu77Gly	285.0	1.0	0.00350877		328.0	157.0	0.478659	NM_001253908	A8K2V0|B4DL37|Q5T2L1|Q96DJ1|Q96KI8|Q99530|Q9UCX1|Q9UII3|Q9UKL9	Missense_Mutation	SNP	ENST00000380554.3	37	CCDS7063.1	103	0.04716117216117216	14	0.028455284552845527	25	0.06906077348066299	1	0.0017482517482517483	63	0.08311345646437995	A	17.28	3.349582	0.61183	0.025193	0.063169	ENSG00000196139	ENST00000380554	T	0.56611	0.45	2.0	2.0	0.26442	NADP-dependent oxidoreductase domain (3);	0.103283	0.39544	N	0.001339	T	0.04861	0.0131	M	0.78637	2.42	0.80722	D	1	B;B	0.20780	0.029;0.048	B;B	0.29598	0.096;0.104	T	0.36138	-0.9760	10	0.87932	D	0	.	7.9207	0.29843	1.0:0.0:0.0:0.0	rs41306308	77;77	B4DKT3;P42330	.;AK1C3_HUMAN	G	77	ENSP00000369927:E77G	ENSP00000369927:E77G	E	+	2	0	AKR1C3	5128747	1.000000	0.71417	0.478000	0.27316	0.756000	0.42949	6.896000	0.75665	1.168000	0.42723	0.260000	0.18958	GAA	A|0.950;G|0.050	0.050	strong		0.423	AKR1C3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046533.2	NM_003739	
MAPK11	5600	hgsc.bcm.edu	37	22	50704028	50704028	+	Missense_Mutation	SNP	C	C	T	rs33932986	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50704028C>T	ENST00000330651.6	-	10	924	c.824G>A	c.(823-825)cGt>cAt	p.R275H	MAPK11_ENST00000495277.1_5'Flank	NM_002751.5	NP_002742.3	Q15759	MK11_HUMAN	mitogen-activated protein kinase 11	275	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		R -> H (in dbSNP:rs33932986). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.9}.		activation of MAPK activity (GO:0000187)|gene expression (GO:0010467)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|mRNA metabolic process (GO:0016071)|muscle cell differentiation (GO:0042692)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of muscle cell differentiation (GO:0051149)|Ras protein signal transduction (GO:0007265)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|lung(4)	6		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.205)|LUAD - Lung adenocarcinoma(64;0.247)	Regorafenib(DB08896)	GTTGGCTCCACGGAAGATGCT	0.642													C|||	83	0.0165735	0.0151	0.0331	5008	,	,		16651	0.0		0.0219	False		,,,				2504	0.0184				p.R275H	GBM(9;634 739 50668)	Atlas-SNP	.											.	MAPK11	23	.	0			c.G824A						PASS	.	C	HIS/ARG	44,4362	45.3+/-79.5	0,44,2159	46.0	46.0	46.0		824	-5.0	0.1	22	dbSNP_126	46	167,8433	75.4+/-138.0	0,167,4133	yes	missense	MAPK11	NM_002751.5	29	0,211,6292	TT,TC,CC		1.9419,0.9986,1.6223	benign	275/365	50704028	211,12795	2203	4300	6503	SO:0001583	missense	5600	exon10			GCTCCACGGAAGA	Y14440	CCDS14090.1	22q13.33	2011-06-09			ENSG00000185386	ENSG00000185386	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6873	protein-coding gene	gene with protein product		602898		PRKM11		9218798	Standard	NM_002751		Approved	p38-2, p38Beta, SAPK2	uc003bkr.3	Q15759	OTTHUMG00000150226	ENST00000330651.6:c.824G>A	22.37:g.50704028C>T	ENSP00000333685:p.Arg275His	74.0	0.0	0		102.0	29.0	0.284314	NM_002751	A8K730|B0LPG1|B7Z630|E7ETQ1|L7RT27|O00284|O15472|Q2XNF2	Missense_Mutation	SNP	ENST00000330651.6	37	CCDS14090.1	37	0.01694139194139194	7	0.014227642276422764	16	0.04419889502762431	0	0.0	14	0.018469656992084433	C	11.81	1.750982	0.31046	0.009986	0.019419	ENSG00000185386	ENST00000330651	T	0.14022	2.54	4.29	-4.97	0.03029	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.391142	0.24262	N	0.040077	T	0.01765	0.0056	L	0.28504	0.86	0.36446	D	0.865812	B	0.09022	0.002	B	0.11329	0.006	T	0.13361	-1.0512	10	0.33141	T	0.24	.	14.0629	0.64810	0.0:0.8033:0.0:0.1967	rs33932986	275	Q15759	MK11_HUMAN	H	275	ENSP00000333685:R275H	ENSP00000333685:R275H	R	-	2	0	MAPK11	49046155	0.000000	0.05858	0.122000	0.21767	0.970000	0.65996	-1.513000	0.02256	-0.973000	0.03555	-0.458000	0.05436	CGT	C|0.985;T|0.015	0.015	strong		0.642	MAPK11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316900.1		
FABP9	646480	hgsc.bcm.edu	37	8	82370894	82370894	+	Silent	SNP	T	T	C	rs139486050	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:82370894T>C	ENST00000379071.2	-	3	346	c.291A>G	c.(289-291)aaA>aaG	p.K97K	RP11-157I4.4_ENST00000524085.2_RNA	NM_001080526.1	NP_001073995.1	Q0Z7S8	FABP9_HUMAN	fatty acid binding protein 9, testis	97					acrosome assembly (GO:0001675)	acrosomal vesicle (GO:0001669)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)|prostate(1)	6			Epithelial(68;0.186)			TGCCAAGCCATTTTTGGACGT	0.328													T|||	2	0.000399361	0.0	0.0014	5008	,	,		18485	0.0		0.001	False		,,,				2504	0.0				p.K97K		Atlas-SNP	.											.	FABP9	15	.	0			c.A291G						PASS	.	T		5,4397	9.9+/-24.2	0,5,2196	103.0	95.0	98.0		291	2.7	1.0	8	dbSNP_134	98	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	FABP9	NM_001080526.1		0,25,6476	CC,CT,TT		0.2326,0.1136,0.1923		97/133	82370894	25,12977	2201	4300	6501	SO:0001819	synonymous_variant	646480	exon3			AAGCCATTTTTGG			8q21.13	2013-03-01			ENSG00000205186	ENSG00000205186		"""Fatty acid binding protein family"""	3563	protein-coding gene	gene with protein product						7958448	Standard	NM_001080526		Approved	PERF, T-FABP, PERF15	uc011lfo.2	Q0Z7S8	OTTHUMG00000164601	ENST00000379071.2:c.291A>G	8.37:g.82370894T>C		224.0	0.0	0		254.0	127.0	0.5	NM_001080526		Silent	SNP	ENST00000379071.2	37																																																																																				T|0.999;C|0.001	0.001	strong		0.328	FABP9-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000379367.2	NM_001080526	
ADCY1	107	hgsc.bcm.edu	37	7	45701762	45701762	+	Silent	SNP	C	C	T	rs61729596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:45701762C>T	ENST00000297323.7	+	8	1576	c.1554C>T	c.(1552-1554)ttC>ttT	p.F518F	ADCY1_ENST00000432715.1_Silent_p.F293F	NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	518	Interaction with calmodulin. {ECO:0000250}.				activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GGAAAATGTTCAAGGCCGAGA	0.542													C|||	50	0.00998403	0.0	0.0101	5008	,	,		19969	0.0		0.0239	False		,,,				2504	0.0194				p.F518F		Atlas-SNP	.											.	ADCY1	187	.	0			c.C1554T						PASS	.	C		20,4386	27.2+/-55.0	0,20,2183	84.0	70.0	75.0		1554	3.9	1.0	7	dbSNP_129	75	175,8425	79.2+/-141.9	3,169,4128	no	coding-synonymous	ADCY1	NM_021116.2		3,189,6311	TT,TC,CC		2.0349,0.4539,1.4993		518/1120	45701762	195,12811	2203	4300	6503	SO:0001819	synonymous_variant	107	exon8			AATGTTCAAGGCC	L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"""Adenylate cyclases"""	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.1554C>T	7.37:g.45701762C>T		106.0	0.0	0		94.0	43.0	0.457447	NM_021116	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																			C|0.986;T|0.014	0.014	strong		0.542	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2	NM_021116	
CMYA5	202333	hgsc.bcm.edu	37	5	79025592	79025592	+	Missense_Mutation	SNP	C	C	T	rs114648445	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:79025592C>T	ENST00000446378.2	+	2	1035	c.1004C>T	c.(1003-1005)aCa>aTa	p.T335I		NM_153610.3	NP_705838.3	Q8N3K9	CMYA5_HUMAN	cardiomyopathy associated 5	335					negative regulation of calcineurin-NFAT signaling cascade (GO:0070885)|negative regulation of protein phosphatase type 2B activity (GO:0032513)|regulation of skeletal muscle adaptation (GO:0014733)	costamere (GO:0043034)				NS(2)|breast(4)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(37)|lung(34)|ovary(6)|pancreas(2)|prostate(5)|skin(5)|stomach(11)|upper_aerodigestive_tract(3)|urinary_tract(1)	128		Lung NSC(167;0.00296)|all_lung(232;0.00327)|Ovarian(174;0.0262)		OV - Ovarian serous cystadenocarcinoma(54;9.85e-46)|Epithelial(54;3.38e-40)|all cancers(79;3.43e-35)		CTAAATGCCACATCTGCATTG	0.463													C|||	13	0.00259585	0.0008	0.0029	5008	,	,		21455	0.0		0.0099	False		,,,				2504	0.0				p.T335I		Atlas-SNP	.											.	CMYA5	643	.	0			c.C1004T						PASS	.	C	ILE/THR	3,3987		0,3,1992	68.0	65.0	66.0		1004	3.4	0.0	5	dbSNP_132	66	56,8284		0,56,4114	yes	missense	CMYA5	NM_153610.3	89	0,59,6106	TT,TC,CC		0.6715,0.0752,0.4785	possibly-damaging	335/4070	79025592	59,12271	1995	4170	6165	SO:0001583	missense	202333	exon2			ATGCCACATCTGC	AW755254, AL831986	CCDS47238.1	5q14.1	2013-02-11			ENSG00000164309	ENSG00000164309		"""Tripartite motif containing / Tripartite motif containing"", ""A-kinase anchor proteins"", ""Fibronectin type III domain containing"""	14305	protein-coding gene	gene with protein product	"""genethonin-3"", ""tripartite motif-containing 76"""	612193	"""chromosome 5 open reading frame 10"""	C5orf10		14688250	Standard	NM_153610		Approved	myospryn, SPRYD2, DKFZp451G223, TRIM76	uc003kgc.3	Q8N3K9	OTTHUMG00000162548	ENST00000446378.2:c.1004C>T	5.37:g.79025592C>T	ENSP00000394770:p.Thr335Ile	131.0	0.0	0		171.0	76.0	0.444444	NM_153610	A0PJB7|Q05CT4|Q2NKX1|Q2T9G9|Q69YQ8|Q69YQ9|Q6P517|Q6P5U3|Q7Z4I1|Q86T34|Q86T49|Q8N3S4|Q8N3S7|Q8NAG8|Q9UK88	Missense_Mutation	SNP	ENST00000446378.2	37	CCDS47238.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	10.74	1.435181	0.25813	7.52E-4	0.006715	ENSG00000164309	ENST00000446378	T	0.43688	0.94	5.15	3.36	0.38483	.	1.320480	0.05114	N	0.489480	T	0.19406	0.0466	N	0.14661	0.345	0.09310	N	1	B	0.30763	0.294	B	0.27887	0.084	T	0.25813	-1.0121	10	0.87932	D	0	.	3.333	0.07091	0.2023:0.565:0.0:0.2327	.	335	Q8N3K9	CMYA5_HUMAN	I	335	ENSP00000394770:T335I	ENSP00000394770:T335I	T	+	2	0	CMYA5	79061348	0.000000	0.05858	0.012000	0.15200	0.079000	0.17450	0.580000	0.23803	0.729000	0.32403	-0.181000	0.13052	ACA	C|0.997;T|0.003	0.003	strong		0.463	CMYA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369497.1	NM_153610	
MEGF6	1953	hgsc.bcm.edu	37	1	3411235	3411235	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:3411235G>A	ENST00000356575.4	-	31	4168	c.3942C>T	c.(3940-3942)caC>caT	p.H1314H	MEGF6_ENST00000294599.4_Silent_p.H1079H	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	1314	EGF-like 24. {ECO:0000255|PROSITE- ProRule:PRU00076}.					extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			cervix(2)|endometrium(3)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_cancers(77;0.00681)|all_epithelial(69;0.00301)|Ovarian(185;0.0634)|Lung NSC(156;0.0969)|all_lung(157;0.105)	all_epithelial(116;7.41e-22)|all_lung(118;8.3e-09)|Lung NSC(185;3.55e-06)|Breast(487;0.000659)|Renal(390;0.00121)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Lung SC(97;0.0262)|Ovarian(437;0.0308)|Medulloblastoma(700;0.211)		Epithelial(90;3.78e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.86e-22)|GBM - Glioblastoma multiforme(42;1.96e-12)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.000448)|BRCA - Breast invasive adenocarcinoma(365;0.000779)|KIRC - Kidney renal clear cell carcinoma(229;0.00645)|STAD - Stomach adenocarcinoma(132;0.00669)|Lung(427;0.213)		CGTTGCTGGCGTGGCACAGGC	0.701																																					p.H1314H	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.C3942T						PASS	.						9.0	13.0	12.0					1																	3411235		2003	4143	6146	SO:0001819	synonymous_variant	1953	exon31			GCTGGCGTGGCAC	AB011539	CCDS41237.1	1p36.3	2008-02-05	2006-03-31	2006-03-31	ENSG00000162591	ENSG00000162591			3232	protein-coding gene	gene with protein product		604266	"""EGF-like-domain, multiple 3"""	EGFL3		9693030	Standard	NM_001409		Approved		uc001akl.3	O75095	OTTHUMG00000000611	ENST00000356575.4:c.3942C>T	1.37:g.3411235G>A		51.0	0.0	0		28.0	17.0	0.607143	NM_001409	Q4AC86|Q5VV39	Silent	SNP	ENST00000356575.4	37	CCDS41237.1	.	.	.	.	.	.	.	.	.	.	g	0.020	-1.445500	0.01089	.	.	ENSG00000162591	ENST00000491842	.	.	.	3.72	-0.402	0.12404	.	.	.	.	.	T	0.57519	0.2059	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.51841	-0.8654	4	.	.	.	-25.4103	10.398	0.44211	0.3477:0.0:0.6523:0.0	.	.	.	.	M	88	.	.	T	-	2	0	MEGF6	3401095	0.001000	0.12720	0.046000	0.18839	0.039000	0.13416	0.019000	0.13444	-0.178000	0.10672	-1.295000	0.01343	ACG	.	.	none		0.701	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
ST5	6764	hgsc.bcm.edu	37	11	8724191	8724191	+	Missense_Mutation	SNP	A	A	G	rs113126215	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:8724191A>G	ENST00000534127.1	-	17	3033	c.2648T>C	c.(2647-2649)gTg>gCg	p.V883A	ST5_ENST00000534278.1_Missense_Mutation_p.V74A|ST5_ENST00000526099.1_Missense_Mutation_p.V396A|ST5_ENST00000530438.1_Missense_Mutation_p.V463A|ST5_ENST00000357665.1_Missense_Mutation_p.V883A|ST5_ENST00000313726.6_Missense_Mutation_p.V883A|ST5_ENST00000526757.1_Missense_Mutation_p.V463A|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000530991.1_Missense_Mutation_p.V355A	NM_005418.3	NP_005409.3	P78524	ST5_HUMAN	suppression of tumorigenicity 5	883	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rab GTPase activity (GO:0032851)		Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(1)|breast(2)|endometrium(5)|kidney(3)|large_intestine(13)|liver(1)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	39				Epithelial(150;2.63e-07)|BRCA - Breast invasive adenocarcinoma(625;0.0352)		GAGCTGGCGCACACTGAGGCA	0.582													a|||	8	0.00159744	0.0008	0.0014	5008	,	,		19188	0.0		0.005	False		,,,				2504	0.001				p.V883A		Atlas-SNP	.											.	ST5	85	.	0			c.T2648C						PASS	.	A	ALA/VAL,ALA/VAL,ALA/VAL	9,4393	15.5+/-35.6	0,9,2192	86.0	79.0	81.0		2648,1388,2648	4.7	1.0	11	dbSNP_132	81	48,8544	31.2+/-83.2	0,48,4248	yes	missense,missense,missense	ST5	NM_005418.3,NM_139157.2,NM_213618.1	64,64,64	0,57,6440	GG,GA,AA		0.5587,0.2045,0.4387	benign,benign,benign	883/1138,463/718,883/1138	8724191	57,12937	2201	4296	6497	SO:0001583	missense	6764	exon17			TGGCGCACACTGA	U15131	CCDS7791.1, CCDS7792.1	11p15	2012-10-04				ENSG00000166444		"""DENN/MADD domain containing"""	11350	protein-coding gene	gene with protein product	"""DENN/MADD domain containing 2B"""	140750				1390339	Standard	NM_005418		Approved	HTS1, DENND2B, p126	uc001mgt.3	P78524		ENST00000534127.1:c.2648T>C	11.37:g.8724191A>G	ENSP00000433528:p.Val883Ala	50.0	0.0	0		43.0	19.0	0.44186	NM_005418	B2R6X7|B3KXQ6|P78523|Q16492|Q7KYY2|Q7KZ12|Q8NE12|Q9BQQ6	Missense_Mutation	SNP	ENST00000534127.1	37	CCDS7791.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	a	16.30	3.083512	0.55861	0.002045	0.005587	ENSG00000166444	ENST00000526757;ENST00000534127;ENST00000313726;ENST00000530991;ENST00000357665;ENST00000526099;ENST00000534278;ENST00000530438;ENST00000533081	T;T;T;T;T;T;T;T;T	0.12147	2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71;2.71	4.72	4.72	0.59763	DENN (3);	0.000000	0.85682	D	0.000000	T	0.19406	0.0466	M	0.78801	2.425	0.53005	D	0.999961	B;B;B	0.28026	0.023;0.012;0.198	B;B;B	0.38755	0.202;0.038;0.281	T	0.05699	-1.0869	10	0.87932	D	0	-10.884	14.2346	0.65916	1.0:0.0:0.0:0.0	.	396;463;883	B4DDL8;P78524-2;P78524	.;.;ST5_HUMAN	A	463;883;883;355;883;396;74;463;73	ENSP00000435097:V463A;ENSP00000433528:V883A;ENSP00000319678:V883A;ENSP00000432887:V355A;ENSP00000350294:V883A;ENSP00000436808:V396A;ENSP00000433349:V74A;ENSP00000436802:V463A;ENSP00000436067:V73A	ENSP00000319678:V883A	V	-	2	0	ST5	8680767	0.990000	0.36364	1.000000	0.80357	0.992000	0.81027	7.573000	0.82421	1.760000	0.52011	0.398000	0.26397	GTG	A|0.996;G|0.004	0.004	strong		0.582	ST5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000386518.1	NM_005418	
ZC3H4	23211	hgsc.bcm.edu	37	19	47572395	47572395	+	Silent	SNP	C	C	T	rs202116030	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:47572395C>T	ENST00000253048.5	-	14	2389	c.2352G>A	c.(2350-2352)gcG>gcA	p.A784A	ZC3H4_ENST00000594019.1_Intron	NM_015168.1	NP_055983.1	Q9UPT8	ZC3H4_HUMAN	zinc finger CCCH-type containing 4	784							metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(13)|ovary(4)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)	41		all_cancers(25;3.3e-08)|all_epithelial(76;2.28e-06)|all_lung(116;7.86e-06)|Lung NSC(112;2.31e-05)|all_neural(266;0.026)|Ovarian(192;0.0392)|Breast(70;0.0889)		OV - Ovarian serous cystadenocarcinoma(262;5.76e-05)|all cancers(93;7.69e-05)|Epithelial(262;0.00354)|GBM - Glioblastoma multiforme(486;0.0372)		CCAGCCTCCTCGCTCTCTCCT	0.692													C|||	3	0.000599042	0.0015	0.0014	5008	,	,		17200	0.0		0.0	False		,,,				2504	0.0				p.A784A		Atlas-SNP	.											.	ZC3H4	96	.	0			c.G2352A						PASS	.	C		3,4171		0,3,2084	68.0	80.0	76.0		2352	-2.5	1.0	19		76	4,8412		0,4,4204	no	coding-synonymous	ZC3H4	NM_015168.1		0,7,6288	TT,TC,CC		0.0475,0.0719,0.0556		784/1304	47572395	7,12583	2087	4208	6295	SO:0001819	synonymous_variant	23211	exon14			CCTCCTCGCTCTC	AB028987	CCDS42582.1	19q13.33	2012-07-05	2007-10-18	2007-10-18		ENSG00000130749		"""Zinc fingers, CCCH-type domain containing"""	17808	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 7"""	C19orf7			Standard	NM_015168		Approved	KIAA1064	uc002pga.4	Q9UPT8		ENST00000253048.5:c.2352G>A	19.37:g.47572395C>T		54.0	0.0	0		45.0	17.0	0.377778	NM_015168	Q9Y420	Silent	SNP	ENST00000253048.5	37	CCDS42582.1																																																																																			C|1.000;T|0.000	0.000	strong		0.692	ZC3H4-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466667.1		
NOTCH2	4853	hgsc.bcm.edu	37	1	120458122	120458122	+	Missense_Mutation	SNP	A	A	T	rs35586704	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120458122A>T	ENST00000256646.2	-	34	7442	c.7223T>A	c.(7222-7224)cTc>cAc	p.L2408H		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2408					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		CTCACCCTGGAGGTGACCACT	0.567			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome				A|||	4	0.000798722	0.0	0.0	5008	,	,		21639	0.0		0.004	False		,,,				2504	0.0				p.L2408H		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.T7223A						PASS	.	A	HIS/LEU	5,4401	9.9+/-24.2	0,5,2198	123.0	108.0	113.0		7223	5.3	1.0	1	dbSNP_126	113	22,8578	16.6+/-54.9	0,22,4278	yes	missense	NOTCH2	NM_024408.3	99	0,27,6476	TT,TA,AA		0.2558,0.1135,0.2076	probably-damaging	2408/2472	120458122	27,12979	2203	4300	6503	SO:0001583	missense	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	CCCTGGAGGTGAC	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.7223T>A	1.37:g.120458122A>T	ENSP00000256646:p.Leu2408His	129.0	0.0	0		124.0	73.0	0.58871	NM_024408	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	15.05	2.717318	0.48622	0.001135	0.002558	ENSG00000134250	ENST00000256646	T	0.77489	-1.1	5.35	5.35	0.76521	Domain of unknown function DUF3454, notch (1);	0.000000	0.32769	U	0.005675	T	0.79375	0.4435	L	0.43923	1.385	0.34826	D	0.739179	D	0.76494	0.999	D	0.70487	0.969	D	0.83604	0.0130	10	0.87932	D	0	.	14.5066	0.67758	1.0:0.0:0.0:0.0	rs35586704	2408	Q04721	NOTC2_HUMAN	H	2408	ENSP00000256646:L2408H	ENSP00000256646:L2408H	L	-	2	0	NOTCH2	120259645	0.946000	0.32159	1.000000	0.80357	0.958000	0.62258	2.431000	0.44775	2.027000	0.59764	0.482000	0.46254	CTC	A|0.998;T|0.002	0.002	strong		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
XIRP1	165904	hgsc.bcm.edu	37	3	39228774	39228774	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:39228774G>A	ENST00000340369.3	-	2	2391	c.2163C>T	c.(2161-2163)ccC>ccT	p.P721P	XIRP1_ENST00000396251.1_Silent_p.P721P|XIRP1_ENST00000421646.1_Intron	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	721					cardiac muscle cell development (GO:0055013)|negative regulation of cell proliferation (GO:0008285)|regulation of membrane potential (GO:0042391)|sarcomere organization (GO:0045214)	fascia adherens (GO:0005916)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(14)|lung(22)|ovary(4)|pancreas(1)|prostate(2)|skin(6)	71				KIRC - Kidney renal clear cell carcinoma(284;0.0517)|Kidney(284;0.065)		CAGAACCCGCGGGGATGGACC	0.582																																					p.P721P		Atlas-SNP	.											.	XIRP1	173	.	0			c.C2163T						PASS	.						52.0	55.0	54.0					3																	39228774		2203	4300	6503	SO:0001819	synonymous_variant	165904	exon2			ACCCGCGGGGATG	AW755250	CCDS2683.1, CCDS56245.1	3p21.33	2008-02-05	2007-06-27	2007-06-27	ENSG00000168334	ENSG00000168334			14301	protein-coding gene	gene with protein product		609777	"""cardiomyopathy associated 1"""	CMYA1		12203715, 15454575	Standard	NM_001198621		Approved	DKFZp451D042, Xin	uc003cjk.2	Q702N8	OTTHUMG00000131297	ENST00000340369.3:c.2163C>T	3.37:g.39228774G>A		115.0	0.0	0		105.0	39.0	0.371429	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Silent	SNP	ENST00000340369.3	37	CCDS2683.1																																																																																			.	.	none		0.582	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
PRRC2A	7916	hgsc.bcm.edu	37	6	31600430	31600430	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31600430G>A	ENST00000376033.2	+	16	4214	c.3980G>A	c.(3979-3981)aGc>aAc	p.S1327N	PRRC2A_ENST00000376007.4_Missense_Mutation_p.S1327N	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	1327	4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GCATCAGAGAGCAGTGACTTC	0.602																																					p.S1327N		Atlas-SNP	.											.	PRRC2A	152	.	0			c.G3980A						PASS	.						76.0	79.0	78.0					6																	31600430		1509	2709	4218	SO:0001583	missense	7916	exon16			CAGAGAGCAGTGA	M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.3980G>A	6.37:g.31600430G>A	ENSP00000365201:p.Ser1327Asn	132.0	0.0	0		156.0	91.0	0.583333	NM_004638	B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	G	11.25	1.584062	0.28268	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033;ENST00000376010	T;T	0.04234	3.67;3.67	5.22	5.22	0.72569	.	0.084158	0.52532	D	0.000067	T	0.11537	0.0281	L	0.60067	1.865	0.45747	D	0.99864	D	0.67145	0.996	P	0.62740	0.906	T	0.00717	-1.1596	10	0.87932	D	0	-14.4073	17.7172	0.88341	0.0:0.0:1.0:0.0	.	1327	P48634	PRC2A_HUMAN	N	1321;1310;1327;1327;552	ENSP00000365175:S1327N;ENSP00000365201:S1327N	ENSP00000365175:S1327N	S	+	2	0	PRRC2A	31708409	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.369000	0.79578	2.714000	0.92807	0.561000	0.74099	AGC	.	.	none		0.602	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1	NM_080686	
ASB2	51676	hgsc.bcm.edu	37	14	94405616	94405616	+	Silent	SNP	G	G	A	rs140791740		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94405616G>A	ENST00000315988.4	-	6	1799	c.1311C>T	c.(1309-1311)gcC>gcT	p.A437A	ASB2_ENST00000555019.1_Silent_p.A485A|ASB2_ENST00000556337.1_5'Flank|RP11-131H24.4_ENST00000557646.1_5'Flank	NM_016150.4	NP_057234.2	Q96Q27	ASB2_HUMAN	ankyrin repeat and SOCS box containing 2	437					intracellular signal transduction (GO:0035556)|myoblast differentiation (GO:0045445)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)	Cul5-RING ubiquitin ligase complex (GO:0031466)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|soft_tissue(1)|urinary_tract(1)	27		all_cancers(154;0.13)		COAD - Colon adenocarcinoma(157;0.217)|Epithelial(152;0.232)		GGCACTTCATGGCGAACATGA	0.667													G|||	1	0.000199681	0.0	0.0014	5008	,	,		15940	0.0		0.0	False		,,,				2504	0.0				p.A485A		Atlas-SNP	.											.	ASB2	71	.	0			c.C1455T						PASS	.	G	,	0,4406		0,0,2203	55.0	56.0	56.0		1455,1311	5.1	1.0	14	dbSNP_134	56	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous	ASB2	NM_001202429.1,NM_016150.4	,	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,	485/636,437/588	94405616	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	51676	exon8			CTTCATGGCGAAC	AF159164	CCDS9915.1, CCDS55940.1	14q31-q32	2013-01-10	2011-01-25					"""Ankyrin repeat domain containing"""	16012	protein-coding gene	gene with protein product		605759	"""ankyrin repeat and SOCS box-containing 2"""				Standard	NM_016150		Approved	ASB-2	uc001ycd.3	Q96Q27		ENST00000315988.4:c.1311C>T	14.37:g.94405616G>A		105.0	0.0	0		97.0	44.0	0.453608	NM_001202429	B2RDP9|B4E166|Q9NSU5|Q9Y567	Silent	SNP	ENST00000315988.4	37	CCDS9915.1																																																																																			G|1.000;A|0.000	0.000	strong		0.667	ASB2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000412845.1		
ZNF20	7568	hgsc.bcm.edu	37	19	12244656	12244656	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:12244656C>T	ENST00000334213.5	-	4	569	c.345G>A	c.(343-345)acG>acA	p.T115T	ZNF20_ENST00000600335.1_Intron|ZNF20_ENST00000485451.1_5'UTR|ZNF625-ZNF20_ENST00000430024.1_3'UTR	NM_001203250.1|NM_021143.3	NP_001190179.1|NP_066966.2	P17024	ZNF20_HUMAN	zinc finger protein 20	115					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|lung(6)	8						ATGAATGACCCGTGCCAACTT	0.423																																					p.T115T		Atlas-SNP	.											.	ZNF20	86	.	0			c.G345A						PASS	.						259.0	260.0	259.0					19																	12244656		2117	4252	6369	SO:0001819	synonymous_variant	7568	exon4			ATGACCCGTGCCA	X52344	CCDS45986.1	19p13.2	2013-01-08	2006-05-10		ENSG00000132010	ENSG00000132010		"""Zinc fingers, C2H2-type"", ""-"""	12992	protein-coding gene	gene with protein product		194557	"""zinc finger protein 20 (KOX 13)"""				Standard	NM_021143		Approved	KOX13	uc002mtf.2	P17024	OTTHUMG00000156409	ENST00000334213.5:c.345G>A	19.37:g.12244656C>T		171.0	0.0	0		210.0	112.0	0.533333	NM_021143	Q8N457|Q9UG41	Silent	SNP	ENST00000334213.5	37	CCDS45986.1																																																																																			.	.	none		0.423	ZNF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344101.1	NM_021143	
MUC4	4585	hgsc.bcm.edu	37	3	195513772	195513772	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195513772G>A	ENST00000463781.3	-	2	5138	c.4679C>T	c.(4678-4680)tCa>tTa	p.S1560L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.S1560L	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGTGGATACTGAGGAAGCGTC	0.577																																					p.S1560L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C4679T						PASS	.						16.0	12.0	13.0					3																	195513772		686	1568	2254	SO:0001583	missense	4585	exon2			GATACTGAGGAAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.4679C>T	3.37:g.195513772G>A	ENSP00000417498:p.Ser1560Leu	243.0	0.0	0		267.0	18.0	0.0674157	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	-	4.658	0.122338	0.08931	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.29655	1.57;1.56	.	.	.	.	.	.	.	.	T	0.15305	0.0369	N	0.19112	0.55	0.09310	N	1	B	0.22480	0.07	B	0.14023	0.01	T	0.28004	-1.0057	7	.	.	.	.	4.7275	0.12948	1.0E-4:0.0:0.6493:0.3506	.	1560	E7ESK3	.	L	1560	ENSP00000417498:S1560L;ENSP00000420243:S1560L	.	S	-	2	0	MUC4	196998167	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	0.230000	0.17852	0.064000	0.16427	0.064000	0.15345	TCA	.	.	none		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TUBGCP6	85378	hgsc.bcm.edu	37	22	50660064	50660064	+	Silent	SNP	C	C	T	rs140491142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50660064C>T	ENST00000248846.5	-	16	2828	c.2724G>A	c.(2722-2724)ccG>ccA	p.P908P	TUBGCP6_ENST00000439308.2_Silent_p.P908P|TUBGCP6_ENST00000491449.1_5'UTR			Q96RT7	GCP6_HUMAN	tubulin, gamma complex associated protein 6	908					G2/M transition of mitotic cell cycle (GO:0000086)|microtubule nucleation (GO:0007020)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|gamma-tubulin ring complex (GO:0008274)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle pole (GO:0000922)	microtubule binding (GO:0008017)			breast(4)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(13)|ovary(3)|prostate(2)|skin(2)	45		all_cancers(38;5.79e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		LUAD - Lung adenocarcinoma(64;0.109)|BRCA - Breast invasive adenocarcinoma(115;0.21)		TCTGCACGGACGGCTCAGCCC	0.677																																					p.P908P		Atlas-SNP	.											TUBGCP6,NS,carcinoma,0,1	TUBGCP6	132	1	0			c.G2724A						scavenged	.	C		0,4406		0,0,2203	42.0	38.0	39.0		2724	-2.5	0.0	22	dbSNP_134	39	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	TUBGCP6	NM_020461.3		0,6,6497	TT,TC,CC		0.0698,0.0,0.0461		908/1820	50660064	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	85378	exon16			CACGGACGGCTCA	AB051456	CCDS14087.1	22q13.31-q13.33	2008-07-01			ENSG00000128159	ENSG00000128159			18127	protein-coding gene	gene with protein product	"""gamma-tubulin complex component 6"""	610053				11694571, 11258795	Standard	XR_244458		Approved	GCP6, KIAA1669, DJ402G11.6	uc003bkb.1	Q96RT7	OTTHUMG00000030150	ENST00000248846.5:c.2724G>A	22.37:g.50660064C>T		226.0	1.0	0.00442478		220.0	89.0	0.404545	NM_020461	Q5JZ80|Q6PJ40|Q86YE9|Q9BY91|Q9UGX3|Q9UGX4	Silent	SNP	ENST00000248846.5	37	CCDS14087.1																																																																																			C|0.999;T|0.001	0.001	strong		0.677	TUBGCP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075004.3	NM_020461	
CATSPER3	347732	hgsc.bcm.edu	37	5	134345062	134345062	+	Splice_Site	SNP	A	A	G	rs72800379	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:134345062A>G	ENST00000282611.6	+	6	904	c.818A>G	c.(817-819)gAc>gGc	p.D273G		NM_178019.2	NP_821138.1	Q86XQ3	CTSR3_HUMAN	cation channel, sperm associated 3	273					calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|single fertilization (GO:0007338)|sodium ion transport (GO:0006814)|sperm capacitation (GO:0048240)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|CatSper complex (GO:0036128)|endoplasmic reticulum (GO:0005783)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			NS(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)|urinary_tract(1)	18			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACTCTCTAGGACTCCATCAGA	0.562													A|||	2	0.000399361	0.0	0.0	5008	,	,		21912	0.0		0.002	False		,,,				2504	0.0				p.D273G		Atlas-SNP	.											.	CATSPER3	38	.	0			c.A818G						PASS	.	A	GLY/ASP	3,4403	8.1+/-20.4	0,3,2200	131.0	121.0	125.0		818	2.6	1.0	5	dbSNP_130	125	26,8574	19.2+/-60.6	0,26,4274	yes	missense-near-splice	CATSPER3	NM_178019.2	94	0,29,6474	GG,GA,AA		0.3023,0.0681,0.223	probably-damaging	273/399	134345062	29,12977	2203	4300	6503	SO:0001630	splice_region_variant	347732	exon6			TCTAGGACTCCAT	AF432876	CCDS4181.1	5q31.2	2011-07-05			ENSG00000152705	ENSG00000152705		"""Voltage-gated ion channels / Cation channels, sperm associated"""	20819	protein-coding gene	gene with protein product		609120				12646162, 12932298, 17227845, 16382101	Standard	NM_178019		Approved	CACRC	uc003lag.3	Q86XQ3	OTTHUMG00000129137	ENST00000282611.6:c.817-1A>G	5.37:g.134345062A>G		74.0	0.0	0		96.0	61.0	0.635417	NM_178019	Q86XS6	Missense_Mutation	SNP	ENST00000282611.6	37	CCDS4181.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	8.757	0.922728	0.18056	6.81E-4	0.003023	ENSG00000152705	ENST00000282611	D	0.97256	-4.31	5.18	2.63	0.31362	.	0.441063	0.21510	N	0.073389	D	0.94440	0.8211	L	0.59436	1.845	0.32616	N	0.523999	P	0.46987	0.888	B	0.42062	0.374	D	0.92979	0.6404	10	0.59425	D	0.04	-12.8622	5.9345	0.19158	0.6619:0.1727:0.0:0.1654	.	273	Q86XQ3	CTSR3_HUMAN	G	273	ENSP00000282611:D273G	ENSP00000282611:D273G	D	+	2	0	CATSPER3	134372961	0.982000	0.34865	0.995000	0.50966	0.200000	0.23975	1.330000	0.33781	0.430000	0.26230	0.533000	0.62120	GAC	A|0.998;G|0.002	0.002	strong		0.562	CATSPER3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251191.2	NM_178019	Missense_Mutation
QRFPR	84109	hgsc.bcm.edu	37	4	122301595	122301595	+	Missense_Mutation	SNP	C	C	A	rs55693553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:122301595C>A	ENST00000394427.2	-	1	619	c.208G>T	c.(208-210)Gtg>Ttg	p.V70L	QRFPR_ENST00000334383.5_Missense_Mutation_p.V70L	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	70					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						CTGCGGGTCACCACGTAGAAC	0.612													C|||	38	0.00758786	0.0008	0.0187	5008	,	,		15467	0.0		0.0239	False		,,,				2504	0.0				p.V70L		Atlas-SNP	.											.	QRFPR	65	.	0			c.G208T						PASS	.						93.0	74.0	81.0					4																	122301595		2203	4300	6503	SO:0001583	missense	84109	exon1			GGGTCACCACGTA	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.208G>T	4.37:g.122301595C>A	ENSP00000377948:p.Val70Leu	159.0	0.0	0		180.0	94.0	0.522222	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	26.5	4.740826	0.89573	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.35048	1.33;1.33	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.054824	0.64402	D	0.000001	T	0.24236	0.0587	L	0.46947	1.48	0.58432	D	0.999997	P;P;P	0.47841	0.626;0.901;0.88	B;P;P	0.45610	0.233;0.487;0.47	T	0.04078	-1.0979	10	0.34782	T	0.22	.	18.2778	0.90088	0.0:1.0:0.0:0.0	rs55693553;rs61741355	70;70;70	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	L	70	ENSP00000377948:V70L;ENSP00000335610:V70L	ENSP00000335610:V70L	V	-	1	0	QRFPR	122521045	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	2.614000	0.46359	2.383000	0.81215	0.467000	0.42956	GTG	C|0.987;A|0.013	0.013	strong		0.612	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
GOLIM4	27333	hgsc.bcm.edu	37	3	167747707	167747707	+	Missense_Mutation	SNP	C	C	T	rs140974195	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:167747707C>T	ENST00000470487.1	-	10	1983	c.1294G>A	c.(1294-1296)Gaa>Aaa	p.E432K	GOLIM4_ENST00000309027.4_Missense_Mutation_p.E404K	NM_014498.3	NP_055313.1	O00461	GOLI4_HUMAN	golgi integral membrane protein 4	432	Gln-rich.|Glu-rich.				transport (GO:0006810)	cis-Golgi network (GO:0005801)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(5)|endometrium(2)|large_intestine(8)|lung(26)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						tgcaaagcttcctggtgttcc	0.587													C|||	6	0.00119808	0.0	0.0043	5008	,	,		15802	0.0		0.003	False		,,,				2504	0.0				p.E432K		Atlas-SNP	.											.	GOLIM4	71	.	0			c.G1294A						PASS	.	C	LYS/GLU	0,4406		0,0,2203	71.0	65.0	67.0		1294	4.7	0.9	3	dbSNP_134	67	19,8581	14.0+/-48.4	0,19,4281	yes	missense	GOLIM4	NM_014498.3	56	0,19,6484	TT,TC,CC		0.2209,0.0,0.1461	possibly-damaging	432/697	167747707	19,12987	2203	4300	6503	SO:0001583	missense	27333	exon10			AAGCTTCCTGGTG	U55853	CCDS3204.1	3q26	2007-07-30	2007-07-30	2007-07-30	ENSG00000173905	ENSG00000173905			15448	protein-coding gene	gene with protein product		606805	"""golgi phosphoprotein 4"""	GOLPH4		9201717, 15004235	Standard	NM_014498		Approved	GPP130, GIMPC, P138	uc003ffe.2	O00461	OTTHUMG00000158554	ENST00000470487.1:c.1294G>A	3.37:g.167747707C>T	ENSP00000417354:p.Glu432Lys	116.0	0.0	0		118.0	40.0	0.338983	NM_014498		Missense_Mutation	SNP	ENST00000470487.1	37	CCDS3204.1	6	0.0027472527472527475	0	0.0	3	0.008287292817679558	0	0.0	3	0.00395778364116095	C	28.6	4.935733	0.92458	0.0	0.002209	ENSG00000173905	ENST00000470487;ENST00000309027	.	.	.	5.65	4.74	0.60224	.	0.188818	0.56097	D	0.000034	T	0.62768	0.2455	M	0.71581	2.175	0.33996	D	0.64974	D;P	0.54397	0.966;0.941	P;P	0.56216	0.794;0.731	T	0.76069	-0.3094	9	0.45353	T	0.12	-10.4908	16.3164	0.82930	0.0:0.868:0.132:0.0	.	404;432	F8W785;O00461	.;GOLI4_HUMAN	K	432;404	.	ENSP00000309893:E404K	E	-	1	0	GOLIM4	169230401	1.000000	0.71417	0.950000	0.38849	0.833000	0.47200	4.851000	0.62896	2.694000	0.91930	0.555000	0.69702	GAA	C|0.998;T|0.002	0.002	strong		0.587	GOLIM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351278.2		
DDX39B	7919	hgsc.bcm.edu	37	6	31503219	31503219	+	Silent	SNP	G	G	A	rs55799418	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31503219G>A	ENST00000396172.1	-	6	1290	c.660C>T	c.(658-660)caC>caT	p.H220H	DDX39B_ENST00000415382.2_Silent_p.H142H|DDX39B_ENST00000453105.2_Silent_p.H173H|DDX39B_ENST00000417556.2_Silent_p.H235H|DDX39B_ENST00000458640.1_Silent_p.H220H|SNORD117_ENST00000364915.1_RNA|DDX39B_ENST00000376177.2_Silent_p.H220H|ATP6V1G2-DDX39B_ENST00000376185.1_3'UTR	NM_004640.6	NP_004631.1	Q13838	DX39B_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B	220	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				ATP catabolic process (GO:0006200)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA damage checkpoint (GO:2000002)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|RNA secondary structure unwinding (GO:0010501)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)|transcription export complex (GO:0000346)	ATP binding (GO:0005524)|ATP-dependent protein binding (GO:0043008)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)|RNA-dependent ATPase activity (GO:0008186)|U4 snRNA binding (GO:0030621)|U6 snRNA binding (GO:0017070)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	19						CCTGCTTCTCGTGGGGGGTCA	0.443													G|||	46	0.0091853	0.0098	0.0086	5008	,	,		19144	0.003		0.0089	False		,,,				2504	0.0153				p.H220H		Atlas-SNP	.											.	DDX39B	38	.	0			c.C660T						PASS	.	G	,	18,3004		0,18,1493	190.0	151.0	165.0		660,660	-3.5	1.0	6	dbSNP_129	165	45,5373		0,45,2664	no	coding-synonymous,coding-synonymous	DDX39B	NM_004640.6,NM_080598.5	,	0,63,4157	AA,AG,GG		0.8306,0.5956,0.7464	,	220/429,220/429	31503219	63,8377	1511	2709	4220	SO:0001819	synonymous_variant	7919	exon6			CTTCTCGTGGGGG	Z37166	CCDS4697.1	6p21.33	2011-02-09	2011-02-08	2011-02-08	ENSG00000198563	ENSG00000198563		"""DEAD-boxes"""	13917	protein-coding gene	gene with protein product	"""U2AF65-associated protein 56"""	142560	"""HLA-B associated transcript 1"""	BAT1		7601445, 2813433	Standard	NM_004640		Approved	D6S81E, UAP56	uc003ntu.3	Q13838	OTTHUMG00000031165	ENST00000396172.1:c.660C>T	6.37:g.31503219G>A		94.0	0.0	0		104.0	53.0	0.509615	NM_004640	B0S8C0|O43496|Q0EFA1|Q2L6F9|Q53GL9|Q5RJ64|Q5RJ66|Q5ST94|Q5STB4|Q5STB5|Q5STB7|Q5STB8|Q5STU4|Q5STU5|Q5STU6|Q5STU8|Q71V76	Silent	SNP	ENST00000396172.1	37	CCDS4697.1																																																																																			G|0.993;A|0.007	0.007	strong		0.443	DDX39B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259083.1	NM_004640	
ZNF626	199777	hgsc.bcm.edu	37	19	20808414	20808414	+	Missense_Mutation	SNP	C	C	T	rs8110802	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20808414C>T	ENST00000601440.1	-	4	415	c.269G>A	c.(268-270)aGc>aAc	p.S90N	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	90			S -> N (in dbSNP:rs8110802).		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)|endometrium(1)|lung(3)|skin(1)	6						ATCTTTCATGCTCTGCTCTGG	0.323													N|||	363	0.072484	0.2436	0.0259	5008	,	,		17039	0.0		0.0139	False		,,,				2504	0.0092				p.S90N		Atlas-SNP	.											.	ZNF626	121	.	0			c.G269A						PASS	.	C	ASN/SER	774,3566		90,594,1486	51.0	57.0	55.0		269	1.1	0.0	19	dbSNP_116	55	84,8476		3,78,4199	no	missense	ZNF626	NM_001076675.2	46	93,672,5685	TT,TC,CC		0.9813,17.8341,6.6512	benign	90/529	20808414	858,12042	2170	4280	6450	SO:0001583	missense	199777	exon4			TTCATGCTCTGCT	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.269G>A	19.37:g.20808414C>T	ENSP00000469958:p.Ser90Asn	86.0	0.0	0		122.0	50.0	0.409836	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	140	0.0641025641025641	119	0.241869918699187	10	0.027624309392265192	0	0.0	11	0.014511873350923483	N	2.780	-0.253612	0.05829	0.178341	0.009813	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	T	0.00012	0.0000	N	0.20574	0.59	0.80722	P	0.0	B	0.06786	0.001	B	0.06405	0.002	T	0.33752	-0.9856	7	0.14656	T	0.56	.	3.4203	0.07391	0.0:0.703:0.0:0.297	rs8110802;rs16996433;rs8110802	90	Q68DY1	ZN626_HUMAN	N	90;14;90	.	ENSP00000445201:S90N	S	-	2	0	ZNF626	20600254	0.000000	0.05858	0.012000	0.15200	0.263000	0.26337	-0.331000	0.07914	0.503000	0.28060	0.289000	0.19496	AGC	C|0.961;T|0.039	0.039	strong		0.323	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
ZNF519	162655	hgsc.bcm.edu	37	18	14105770	14105770	+	Missense_Mutation	SNP	T	T	C	rs61730995	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:14105770T>C	ENST00000590202.1	-	3	921	c.769A>G	c.(769-771)Ata>Gta	p.I257V	ZNF519_ENST00000589203.1_Intron|ZNF519_ENST00000589498.1_Intron|RP11-411B10.3_ENST00000592926.1_RNA	NM_145287.3	NP_660330.2	Q8TB69	ZN519_HUMAN	zinc finger protein 519	257					negative regulation of transcription during meiosis (GO:0051038)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|urinary_tract(1)	18						GTGTTAATTATCTTATGTCCC	0.328													T|||	7	0.00139776	0.0008	0.0014	5008	,	,		18546	0.0		0.004	False		,,,				2504	0.001				p.I257V		Atlas-SNP	.											.	ZNF519	53	.	0			c.A769G						PASS	.	T	VAL/ILE	5,4399	9.9+/-24.2	0,5,2197	43.0	48.0	46.0		769	0.6	0.0	18	dbSNP_129	46	72,8524	41.7+/-99.0	1,70,4227	no	missense	ZNF519	NM_145287.3	29	1,75,6424	CC,CT,TT		0.8376,0.1135,0.5923	benign	257/541	14105770	77,12923	2202	4298	6500	SO:0001583	missense	162655	exon3			TAATTATCTTATG	BC024227	CCDS32797.1	18p11.21	2014-06-18			ENSG00000175322	ENSG00000175322		"""Zinc fingers, C2H2-type"", ""-"""	30574	protein-coding gene	gene with protein product	"""similar to Zinc finger protein 85 (Zinc finger protein HPF4) (HTF1)"""					12477932	Standard	NM_145287		Approved	HsT2362, FLJ36809	uc002kst.2	Q8TB69	OTTHUMG00000182055	ENST00000590202.1:c.769A>G	18.37:g.14105770T>C	ENSP00000464872:p.Ile257Val	94.0	0.0	0		66.0	31.0	0.469697	NM_145287		Missense_Mutation	SNP	ENST00000590202.1	37	CCDS32797.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	0.378	-0.930146	0.02359	0.001135	0.008376	ENSG00000175322	ENST00000309305	.	.	.	0.646	0.646	0.17789	.	.	.	.	.	T	0.19087	0.0458	N	0.25890	0.77	0.09310	N	0.999993	B	0.13594	0.008	B	0.08055	0.003	T	0.16041	-1.0416	8	0.39692	T	0.17	.	5.6281	0.17495	0.0:1.0E-4:0.0:0.9999	.	257	Q8TB69	ZN519_HUMAN	V	257	.	ENSP00000307908:I257V	I	-	1	0	ZNF519	14095770	0.000000	0.05858	0.005000	0.12908	0.342000	0.28953	-0.164000	0.09983	0.552000	0.29026	0.076000	0.15429	ATA	T|0.996;C|0.004	0.004	strong		0.328	ZNF519-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459037.1	NM_145287	
LGR5	8549	hgsc.bcm.edu	37	12	71977427	71977427	+	Splice_Site	SNP	G	G	A	rs200272164		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:71977427G>A	ENST00000266674.5	+	18	1948	c.1637G>A	c.(1636-1638)gGc>gAc	p.G546D	LGR5_ENST00000536515.1_Splice_Site_p.G474D|RP11-186F10.2_ENST00000546601.1_RNA|LGR5_ENST00000540815.2_Splice_Site_p.G522D			O75473	LGR5_HUMAN	leucine-rich repeat containing G protein-coupled receptor 5	546					G-protein coupled receptor signaling pathway (GO:0007186)|inner ear development (GO:0048839)|positive regulation of canonical Wnt signaling pathway (GO:0090263)	integral component of plasma membrane (GO:0005887)|trans-Golgi network membrane (GO:0032588)	G-protein coupled receptor activity (GO:0004930)|transmembrane signaling receptor activity (GO:0004888)		NUP107/LGR5(2)	endometrium(2)|kidney(3)|large_intestine(2)|lung(24)|ovary(1)|pancreas(2)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	48						GGACTTCTAGGCCCCTTCAAA	0.423													G|||	1	0.000199681	0.0	0.0	5008	,	,		22325	0.0		0.001	False		,,,				2504	0.0				p.G546D		Atlas-SNP	.											.	LGR5	103	.	0			c.G1637A						PASS	.						180.0	173.0	176.0					12																	71977427		2203	4300	6503	SO:0001630	splice_region_variant	8549	exon18			TTCTAGGCCCCTT	AF062006	CCDS9000.1, CCDS61194.1, CCDS61195.1	12q22-q23	2012-08-21	2011-01-25	2004-11-12				"""GPCR / Class A : Orphans"""	4504	protein-coding gene	gene with protein product		606667	"""G protein-coupled receptor 49"", ""leucine-rich repeat-containing G protein-coupled receptor 5"""	GPR67, GPR49		9642114	Standard	NM_003667		Approved	HG38, FEX	uc001swl.4	O75473	OTTHUMG00000169543	ENST00000266674.5:c.1637-1G>A	12.37:g.71977427G>A		281.0	0.0	0		268.0	123.0	0.458955	NM_003667	D8MCT0|Q4VAM0|Q4VAM2|Q9UP75	Missense_Mutation	SNP	ENST00000266674.5	37	CCDS9000.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	25.7	4.663054	0.88251	.	.	ENSG00000139292	ENST00000266674;ENST00000451585;ENST00000536515;ENST00000540815	D;D;D	0.90563	-2.69;-2.69;-2.69	5.69	5.69	0.88448	.	0.000000	0.64402	D	0.000005	D	0.92570	0.7640	L	0.31065	0.9	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.87578	0.99;0.998	D	0.91262	0.5037	9	.	.	.	.	19.812	0.96551	0.0:0.0:1.0:0.0	.	522;546	O75473-2;O75473	.;LGR5_HUMAN	D	546;546;474;522	ENSP00000266674:G546D;ENSP00000443033:G474D;ENSP00000441035:G522D	.	G	+	2	0	LGR5	70263694	1.000000	0.71417	0.991000	0.47740	0.940000	0.58332	9.807000	0.99171	2.685000	0.91497	0.655000	0.94253	GGC	G|1.000;A|0.000	0.000	strong		0.423	LGR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404744.1	NM_003667	Missense_Mutation
UBE2O	63893	hgsc.bcm.edu	37	17	74392249	74392249	+	Silent	SNP	G	G	A	rs76110889	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:74392249G>A	ENST00000319380.7	-	14	2833	c.2769C>T	c.(2767-2769)agC>agT	p.S923S	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	923					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						CGCCCTTGGCGCTGGTGAAGG	0.642													G|||	16	0.00319489	0.0	0.0058	5008	,	,		17280	0.0		0.0119	False		,,,				2504	0.0				p.S923S		Atlas-SNP	.											.	UBE2O	207	.	0			c.C2769T						PASS	.	G		12,4394	17.9+/-39.9	0,12,2191	40.0	43.0	42.0		2769	-0.5	1.0	17	dbSNP_132	42	106,8494	59.1+/-120.7	0,106,4194	no	coding-synonymous	UBE2O	NM_022066.3		0,118,6385	AA,AG,GG		1.2326,0.2724,0.9073		923/1293	74392249	118,12888	2203	4300	6503	SO:0001819	synonymous_variant	63893	exon14			CTTGGCGCTGGTG	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.2769C>T	17.37:g.74392249G>A		78.0	0.0	0		80.0	38.0	0.475	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	37	CCDS32742.1																																																																																			G|0.992;A|0.008	0.008	strong		0.642	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066	
ADAM29	11086	hgsc.bcm.edu	37	4	175898913	175898913	+	Missense_Mutation	SNP	C	C	T	rs142711835		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:175898913C>T	ENST00000359240.3	+	5	2907	c.2237C>T	c.(2236-2238)aCg>aTg	p.T746M	ADAM29_ENST00000445694.1_Missense_Mutation_p.T746M|ADAM29_ENST00000404450.4_Missense_Mutation_p.T746M|ADAM29_ENST00000514159.1_Missense_Mutation_p.T746M|RP13-577H12.2_ENST00000507525.1_RNA	NM_001278125.1|NM_014269.4	NP_001265054.1|NP_055084.3	Q9UKF5	ADA29_HUMAN	ADAM metallopeptidase domain 29	746	9 X 9 AA approximate repeats.				spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)	p.T746M(2)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(25)|ovary(3)|pancreas(1)|prostate(7)|skin(24)|urinary_tract(2)	93		Breast(14;0.00908)|Melanoma(52;0.00951)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;3.08e-19)|Epithelial(43;6.24e-18)|OV - Ovarian serous cystadenocarcinoma(60;1.78e-09)|STAD - Stomach adenocarcinoma(60;0.00303)|GBM - Glioblastoma multiforme(59;0.0106)|LUSC - Lung squamous cell carcinoma(193;0.0286)		CCTCCTGTGACGCCTTCCCAG	0.537																																					p.T746M	Ovarian(140;1727 1835 21805 25838 41440)	Atlas-SNP	.											ADAM29,rectum,carcinoma,0,22	ADAM29	262	22	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(1)|central_nervous_system(1)	c.C2237T						scavenged	.						149.0	132.0	138.0					4																	175898913		2203	4300	6503	SO:0001583	missense	11086	exon4			CTGTGACGCCTTC	AF171929	CCDS3823.1	4q34.1	2012-05-16	2005-08-18		ENSG00000168594	ENSG00000168594		"""ADAM metallopeptidase domain containing"""	207	protein-coding gene	gene with protein product	"""cancer/testis antigen 73"""	604778	"""a disintegrin and metalloproteinase domain 29"""			10644455	Standard	NM_014269		Approved	svph1, CT73	uc031shw.1	Q9UKF5	OTTHUMG00000160764	ENST00000359240.3:c.2237C>T	4.37:g.175898913C>T	ENSP00000352177:p.Thr746Met	145.0	0.0	0		202.0	21.0	0.10396	NM_001130703	Q4W5F3|Q9UHP1|Q9UKF3|Q9UKF4	Missense_Mutation	SNP	ENST00000359240.3	37	CCDS3823.1	.	.	.	.	.	.	.	.	.	.	C	8.511	0.866447	0.17250	.	.	ENSG00000168594	ENST00000359240;ENST00000445694;ENST00000404450;ENST00000514159	T;T;T;T	0.02015	4.5;4.5;4.5;4.5	1.54	0.582	0.17412	.	.	.	.	.	T	0.01558	0.0050	N	0.08118	0	0.09310	N	1	D	0.62365	0.991	P	0.45998	0.5	T	0.53005	-0.8499	8	.	.	.	.	6.1783	0.20457	0.0:0.802:0.0:0.198	.	746	Q9UKF5	ADA29_HUMAN	M	746	ENSP00000352177:T746M;ENSP00000414544:T746M;ENSP00000384229:T746M;ENSP00000423517:T746M	.	T	+	2	0	ADAM29	176135488	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.798000	0.04565	-0.059000	0.13154	0.478000	0.44815	ACG	.	.	weak		0.537	ADAM29-201	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding			
FOLH1	2346	hgsc.bcm.edu	37	11	49207398	49207398	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:49207398C>T	ENST00000256999.2	-	6	909	c.649G>A	c.(649-651)Gcc>Acc	p.A217T	FOLH1_ENST00000340334.7_Missense_Mutation_p.A202T|FOLH1_ENST00000343844.4_Intron|FOLH1_ENST00000533034.1_Missense_Mutation_p.A202T|FOLH1_ENST00000356696.3_Missense_Mutation_p.A217T	NM_004476.1	NP_004467.1	Q04609	FOLH1_HUMAN	folate hydrolase (prostate-specific membrane antigen) 1	217					folic acid-containing compound metabolic process (GO:0006760)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|peptidase activity (GO:0008233)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(34)|ovary(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	60					Capromab(DB00089)	GCCAGCTGGGCATTTTTAACC	0.418																																					p.A217T		Atlas-SNP	.											.	FOLH1	141	.	0			c.G649A						PASS	.						37.0	44.0	42.0					11																	49207398		2201	4296	6497	SO:0001583	missense	2346	exon6			GCTGGGCATTTTT	M99487	CCDS7946.1, CCDS31493.1, CCDS53626.1, CCDS53627.1, CCDS53628.1	11p11.2	2011-07-22			ENSG00000086205	ENSG00000086205	3.4.17.21		3788	protein-coding gene	gene with protein product	"""glutamate carboxylase II"", ""glutamate carboxypeptidase II"""	600934		FOLH		9838072	Standard	NM_001193472		Approved	PSM, PSMA, NAALAD1, NAALAdase, GCP2, GCPII	uc001ngy.3	Q04609	OTTHUMG00000166625	ENST00000256999.2:c.649G>A	11.37:g.49207398C>T	ENSP00000256999:p.Ala217Thr	195.0	0.0	0		206.0	31.0	0.150485	NM_004476	A4UU12|A9CB79|B7Z312|B7Z343|D3DQS5|E9PDX8|O43748|Q16305|Q541A4|Q8TAY3|Q9NP15|Q9NYE2|Q9P1P8	Missense_Mutation	SNP	ENST00000256999.2	37	CCDS7946.1	.	.	.	.	.	.	.	.	.	.	C	18.98	3.737168	0.69304	.	.	ENSG00000086205	ENST00000256999;ENST00000356696;ENST00000340334;ENST00000533034;ENST00000389724	T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63	3.01	2.06	0.26882	Protease-associated domain, PA (1);	0.126165	0.35407	N	0.003233	D	0.87822	0.6274	H	0.97516	4.02	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.993;0.999	D	0.88363	0.2989	10	0.87932	D	0	.	9.7982	0.40748	0.0:0.7869:0.2131:0.0	.	202;202;217;217	Q04609-9;Q04609-7;Q04609-8;Q04609	.;.;.;FOLH1_HUMAN	T	217;217;202;202;217	ENSP00000256999:A217T;ENSP00000349129:A217T;ENSP00000344131:A202T;ENSP00000431463:A202T	ENSP00000256999:A217T	A	-	1	0	FOLH1	49163974	1.000000	0.71417	0.992000	0.48379	0.974000	0.67602	5.974000	0.70465	0.593000	0.29745	0.400000	0.26472	GCC	.	.	none		0.418	FOLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390896.1	NM_004476	
GSE1	23199	hgsc.bcm.edu	37	16	85702028	85702028	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:85702028A>G	ENST00000253458.7	+	14	3589	c.3413A>G	c.(3412-3414)gAa>gGa	p.E1138G	GSE1_ENST00000405402.2_Missense_Mutation_p.E1034G|GSE1_ENST00000393243.1_Missense_Mutation_p.E1065G	NM_014615.2	NP_055430.1	Q14687	GSE1_HUMAN	Gse1 coiled-coil protein	1138																	GAACACATAGAAGGTAAGGGG	0.547																																					p.E1138G		Atlas-SNP	.											KIAA0182,NS,carcinoma,+1,1	.	.	1	0			c.A3413G						scavenged	.						27.0	31.0	29.0					16																	85702028		2196	4300	6496	SO:0001583	missense	23199	exon14			ACATAGAAGGTAA	D80004	CCDS10952.1, CCDS45539.1, CCDS62007.1	16q24.1	2012-12-07	2012-12-07	2012-10-02	ENSG00000131149	ENSG00000131149			28979	protein-coding gene	gene with protein product	"""genetic suppressor element 1"""		"""KIAA0182"", ""Gse1 coiled-coil protein homolog (mouse)"""	KIAA0182		8724849, 8786132	Standard	NM_014615		Approved		uc002fix.4	Q14687	OTTHUMG00000137650	ENST00000253458.7:c.3413A>G	16.37:g.85702028A>G	ENSP00000253458:p.Glu1138Gly	23.0	0.0	0		25.0	7.0	0.28	NM_014615	D3DUM4|Q8IY61|Q96GA4|Q9BW09	Missense_Mutation	SNP	ENST00000253458.7	37	CCDS10952.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	21.4|21.4	4.142274|4.142274	0.77775|0.77775	.|.	.|.	ENSG00000131149|ENSG00000131149	ENST00000405402;ENST00000253458;ENST00000393243|ENST00000412692;ENST00000438180	T;T;T|.	0.34472|.	1.36;1.36;1.36|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71091|0.71091	0.3299|0.3299	M|M	0.64997|0.64997	1.995|1.995	0.58432|0.58432	D|D	0.999999|0.999999	D;D;D;D|.	0.89917|.	0.999;1.0;1.0;1.0|.	D;D;D;D|.	0.91635|.	0.995;0.999;0.999;0.998|.	T|T	0.70930|0.70930	-0.4738|-0.4738	10|5	0.72032|.	D|.	0.01|.	-11.1152|-11.1152	14.9832|14.9832	0.71327|0.71327	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	901;1034;1065;1138|.	Q59GZ0;Q14687-2;Q14687-3;Q14687|.	.;.;.;GSE1_HUMAN|.	G|E	1034;1138;1065|907;340	ENSP00000384839:E1034G;ENSP00000253458:E1138G;ENSP00000376934:E1065G|.	ENSP00000253458:E1138G|.	E|K	+|+	2|1	0|0	KIAA0182|KIAA0182	84259529|84259529	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.603000|0.603000	0.37013|0.37013	8.832000|8.832000	0.92079|0.92079	1.951000|1.951000	0.56629|0.56629	0.459000|0.459000	0.35465|0.35465	GAA|AAG	.	.	none		0.547	GSE1-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325527.1	NM_014615	
ADRA2B	151	hgsc.bcm.edu	37	2	96780863	96780863	+	Silent	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:96780863C>G	ENST00000409345.3	-	1	1121	c.1026G>C	c.(1024-1026)ctG>ctC	p.L342L		NM_000682.5	NP_000673	P18089	ADA2B_HUMAN	adrenoceptor alpha 2B	342					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|MAPK cascade (GO:0000165)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|platelet activation (GO:0030168)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of uterine smooth muscle contraction (GO:0070474)|regulation of vascular smooth muscle contraction (GO:0003056)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)			endometrium(2)|large_intestine(2)|lung(9)|ovary(3)	16					Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Apraclonidine(DB00964)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Etomidate(DB00292)|Fenoldopam(DB00800)|Guanabenz(DB00629)|Guanfacine(DB01018)|Lisuride(DB00589)|Loxapine(DB00408)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Prazosin(DB00457)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Tizanidine(DB00697)|Tolazoline(DB00797)|Trimipramine(DB00726)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	CGCCCCTGCCCAGGAGCACCT	0.701																																					p.L342L		Atlas-SNP	.											.	ADRA2B	115	.	0			c.G1026C						PASS	.																																			SO:0001819	synonymous_variant	151	exon1			CCTGCCCAGGAGC	M34041	CCDS56129.1	2q11.1	2014-05-06	2012-05-09		ENSG00000222040	ENSG00000274286		"""GPCR / Class A : Adrenoceptors : alpha"""	282	protein-coding gene	gene with protein product		104260	"""adrenergic, alpha-2B-, receptor"""	ADRA2L1, ADRA2RL1		2164221	Standard	NM_000682		Approved	ADRARL1	uc021vlh.1	P18089	OTTHUMG00000188276	ENST00000409345.3:c.1026G>C	2.37:g.96780863C>G		106.0	0.0	0		71.0	34.0	0.478873	NM_000682	Q4TUH9|Q53RF2|Q9BZK0	Silent	SNP	ENST00000409345.3	37	CCDS56129.1																																																																																			.	.	none		0.701	ADRA2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334990.1		
METTL3	56339	hgsc.bcm.edu	37	14	21971694	21971694	+	Silent	SNP	C	C	G	rs11540964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:21971694C>G	ENST00000298717.4	-	3	496	c.345G>C	c.(343-345)ggG>ggC	p.G115G	METTL3_ENST00000538267.1_Silent_p.G115G	NM_019852.3	NP_062826.2	Q86U44	MTA70_HUMAN	methyltransferase like 3	115					circadian rhythm (GO:0007623)|gene expression (GO:0010467)|mRNA destabilization (GO:0061157)|mRNA methylation (GO:0080009)|mRNA processing (GO:0006397)|RNA methylation (GO:0001510)|stem cell maintenance (GO:0019827)	MIS complex (GO:0036396)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity (GO:0016422)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(1)	20	all_cancers(95;0.000628)		Epithelial(56;6.61e-06)	GBM - Glioblastoma multiforme(265;0.0146)		GGCTTTCTACCCCATCTTGAG	0.478													C|||	2	0.000399361	0.0	0.0	5008	,	,		23416	0.0		0.002	False		,,,				2504	0.0				p.G115G		Atlas-SNP	.											.	METTL3	48	.	0			c.G345C						PASS	.	C		0,4406		0,0,2203	60.0	56.0	57.0		345	-4.0	0.9	14	dbSNP_120	57	25,8575	16.6+/-54.9	0,25,4275	no	coding-synonymous	METTL3	NM_019852.3		0,25,6478	GG,GC,CC		0.2907,0.0,0.1922		115/581	21971694	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	56339	exon3			TTCTACCCCATCT	AF014837	CCDS32044.1	14q11.1	2012-06-12			ENSG00000165819	ENSG00000165819	2.1.1.62		17563	protein-coding gene	gene with protein product	"""N6-adenosine-methyltransferase 70 kDa subunit"""	612472					Standard	XM_006720206		Approved	Spo8, M6A, MT-A70	uc001wbc.3	Q86U44	OTTHUMG00000168825	ENST00000298717.4:c.345G>C	14.37:g.21971694C>G		54.0	0.0	0		59.0	27.0	0.457627	NM_019852	O14736|Q86V05|Q9HB32	Silent	SNP	ENST00000298717.4	37	CCDS32044.1																																																																																			C|0.998;G|0.002	0.002	strong		0.478	METTL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401227.1	NM_019852	
RFXANK	8625	hgsc.bcm.edu	37	19	19307817	19307817	+	Missense_Mutation	SNP	G	G	A	rs375541634		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:19307817G>A	ENST00000303088.4	+	4	707	c.233G>A	c.(232-234)cGa>cAa	p.R78Q	RFXANK_ENST00000456252.3_Missense_Mutation_p.R78Q|RFXANK_ENST00000392324.4_Missense_Mutation_p.R77Q|RFXANK_ENST00000407360.3_Missense_Mutation_p.R78Q|RFXANK_ENST00000353145.1_Missense_Mutation_p.R77Q	NM_003721.2	NP_003712.1	O14593	RFXK_HUMAN	regulatory factor X-associated ankyrin-containing protein	78					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Ras protein signal transduction (GO:0007265)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription cofactor activity (GO:0003712)			NS(1)|breast(1)|endometrium(1)|lung(8)|ovary(2)|prostate(1)	14			Epithelial(12;0.00228)			AACCGGCAGCGAGGGAACGAG	0.617																																					p.R78Q		Atlas-SNP	.											.	RFXANK	31	.	0			c.G233A						PASS	.	G	GLN/ARG,GLN/ARG	0,4406		0,0,2203	81.0	76.0	77.0		233,230	4.1	1.0	19		77	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	RFXANK	NM_003721.2,NM_134440.1	43,43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	78/261,77/238	19307817	1,13005	2203	4300	6503	SO:0001583	missense	8625	exon4			GGCAGCGAGGGAA	AF094760	CCDS12395.1, CCDS12396.1, CCDS62611.1	19p12	2014-09-17			ENSG00000064490	ENSG00000064490		"""Ankyrin repeat domain containing"""	9987	protein-coding gene	gene with protein product	"""ankyrin repeat-containing regulatory factor X-associated protein"", ""regulatory factor X subunit B"", ""RFX-Bdelta4"", ""DNA-binding protein RFXANK"""	603200				9806546, 10072068	Standard	NM_003721		Approved	BLS, RFX-B, ANKRA1, F14150_1, MGC138628	uc002nls.3	O14593	OTTHUMG00000169224	ENST00000303088.4:c.233G>A	19.37:g.19307817G>A	ENSP00000305071:p.Arg78Gln	40.0	0.0	0		47.0	18.0	0.382979	NM_003721	O95839|Q24JQ1|Q6FGA8	Missense_Mutation	SNP	ENST00000303088.4	37	CCDS12395.1	.	.	.	.	.	.	.	.	.	.	G	24.1	4.492551	0.84962	0.0	1.16E-4	ENSG00000064490	ENST00000353145;ENST00000456252;ENST00000303088;ENST00000407360;ENST00000543652;ENST00000540981;ENST00000541873;ENST00000392324;ENST00000535017	T;T;T;T;T;T;T;T	0.70869	-0.52;1.01;1.1;1.03;1.7;-0.28;-0.52;-0.28	5.16	4.13	0.48395	.	0.054459	0.85682	N	0.000000	T	0.80391	0.4614	M	0.78049	2.395	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;1.0;0.996	T	0.78275	-0.2267	10	0.09338	T	0.73	-18.4611	11.3832	0.49770	0.0888:0.0:0.9112:0.0	.	78;78;77;78	Q6IB23;Q24JQ1;O14593-2;O14593	.;.;.;RFXK_HUMAN	Q	77;78;78;77;78;78;77;77;43	ENSP00000262804:R77Q;ENSP00000409138:R78Q;ENSP00000305071:R78Q;ENSP00000384572:R77Q;ENSP00000439581:R78Q;ENSP00000440325:R78Q;ENSP00000376138:R77Q;ENSP00000444280:R43Q	ENSP00000305071:R78Q	R	+	2	0	RFXANK	19168817	1.000000	0.71417	0.968000	0.41197	0.456000	0.32438	9.574000	0.98184	1.184000	0.42957	0.561000	0.74099	CGA	.	.	weak		0.617	RFXANK-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402923.2	NM_003721	
TRDN	10345	hgsc.bcm.edu	37	6	123703291	123703291	+	Splice_Site	SNP	A	A	C	rs200706450		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:123703291A>C	ENST00000398178.3	-	15	1158	c.1137T>G	c.(1135-1137)gaT>gaG	p.D379E	TRDN_ENST00000334268.4_Splice_Site_p.D379E	NM_006073.3	NP_006064.2	Q13061	TRDN_HUMAN	triadin	379					cellular calcium ion homeostasis (GO:0006874)|cytoplasmic microtubule organization (GO:0031122)|endoplasmic reticulum membrane organization (GO:0090158)|heart contraction (GO:0060047)|ion transmembrane transport (GO:0034220)|muscle contraction (GO:0006936)|myotube differentiation (GO:0014902)|negative regulation of ryanodine-sensitive calcium-release channel activity (GO:0060315)|positive regulation of cell communication by electrical coupling involved in cardiac conduction (GO:1901846)|positive regulation of ryanodine-sensitive calcium-release channel activity (GO:0060316)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cell communication by electrical coupling (GO:0010649)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0010880)|release of sequestered calcium ion into cytosol by sarcoplasmic reticulum (GO:0014808)|response to organic cyclic compound (GO:0014070)|transmembrane transport (GO:0055085)	calcium channel complex (GO:0034704)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)	ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(1)|kidney(1)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	41				GBM - Glioblastoma multiforme(226;0.184)		TTTTCTTGGAATCTGAAAACA	0.284																																					p.D380E		Atlas-SNP	.											.	TRDN	88	.	0			c.T1140G						PASS	.						21.0	19.0	20.0					6																	123703291		1645	3752	5397	SO:0001630	splice_region_variant	10345	exon15			CTTGGAATCTGAA	U18985	CCDS59035.1, CCDS75511.1	6q22.31	2008-05-15			ENSG00000186439	ENSG00000186439			12261	protein-coding gene	gene with protein product		603283				7588753	Standard	NM_001251987		Approved		uc003pzj.2	Q13061	OTTHUMG00000015497	ENST00000398178.3:c.1136-1T>G	6.37:g.123703291A>C		180.0	0.0	0		132.0	55.0	0.416667	NM_001251987	A5D6W5|F5H2W7|Q6NSB8	Missense_Mutation	SNP	ENST00000398178.3	37	CCDS55053.1	.	.	.	.	.	.	.	.	.	.	A	12.01	1.809011	0.31961	.	.	ENSG00000186439	ENST00000398178;ENST00000398161;ENST00000334268	T;T	0.21361	2.02;2.01	4.42	1.95	0.26073	.	0.317399	0.28420	N	0.015417	T	0.02230	0.0069	N	0.14661	0.345	0.80722	D	1	B;B;B	0.17667	0.023;0.023;0.023	B;B;B	0.12837	0.008;0.008;0.008	T	0.43669	-0.9377	10	0.02654	T	1	.	3.799	0.08751	0.7097:0.0:0.1035:0.1868	.	379;380;379	Q5SWK9;Q8IVK2;Q13061	.;.;TRDN_HUMAN	E	379;381;379	ENSP00000381240:D379E;ENSP00000333984:D379E	ENSP00000333984:D379E	D	-	3	2	TRDN	123744990	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	1.025000	0.30090	0.297000	0.22615	0.377000	0.23210	GAT	.	.	weak		0.284	TRDN-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			Missense_Mutation
STRAP	11171	hgsc.bcm.edu	37	12	16042908	16042908	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:16042908C>T	ENST00000419869.2	+	3	608	c.295C>T	c.(295-297)Cat>Tat	p.H99Y	STRAP_ENST00000538352.1_Missense_Mutation_p.H5Y|STRAP_ENST00000025399.6_Missense_Mutation_p.H112Y	NM_007178.3	NP_009109.3	Q9Y3F4	STRAP_HUMAN	serine/threonine kinase receptor associated protein	99					maintenance of gastrointestinal epithelium (GO:0030277)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of epithelial to mesenchymal transition (GO:0010719)|negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|spliceosomal snRNP assembly (GO:0000387)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)	poly(A) RNA binding (GO:0044822)			cervix(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|skin(1)	15		Hepatocellular(102;0.121)				GACCCTGGCTCATAAACACAT	0.338																																					p.H99Y		Atlas-SNP	.											.	STRAP	33	.	0			c.C295T						PASS	.						112.0	105.0	107.0					12																	16042908		2203	4300	6503	SO:0001583	missense	11171	exon3			CTGGCTCATAAAC	AB024327	CCDS8676.1	12p13.1	2013-01-10			ENSG00000023734	ENSG00000023734		"""WD repeat domain containing"""	30796	protein-coding gene	gene with protein product	"""Unr-interacting protein"""	605986					Standard	NM_007178		Approved	UNRIP, pt-wd, MAWD	uc001rdc.4	Q9Y3F4	OTTHUMG00000168791	ENST00000419869.2:c.295C>T	12.37:g.16042908C>T	ENSP00000392270:p.His99Tyr	309.0	0.0	0		325.0	45.0	0.138462	NM_007178	B2R5S5|B4DNJ6|Q5TZT4|Q9NTK0|Q9UQC8	Missense_Mutation	SNP	ENST00000419869.2	37	CCDS8676.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.221170	0.79464	.	.	ENSG00000023734	ENST00000538352;ENST00000025399;ENST00000419869	T;T;T	0.81415	-1.49;-1.49;-1.49	4.69	3.78	0.43462	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.047356	0.85682	D	0.000000	D	0.91429	0.7295	M	0.92649	3.33	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.93213	0.6602	10	0.87932	D	0	-16.9887	14.0735	0.64874	0.1519:0.8481:0.0:0.0	.	112;99	B4DNJ6;Q9Y3F4	.;STRAP_HUMAN	Y	5;112;99	ENSP00000439761:H5Y;ENSP00000025399:H112Y;ENSP00000392270:H99Y	ENSP00000025399:H112Y	H	+	1	0	STRAP	15934175	1.000000	0.71417	0.965000	0.40720	0.996000	0.88848	5.453000	0.66645	1.143000	0.42306	0.655000	0.94253	CAT	.	.	none		0.338	STRAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401114.1	NM_007178	
CNTN1	1272	hgsc.bcm.edu	37	12	41312471	41312471	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:41312471T>C	ENST00000551295.2	+	4	242	c.125T>C	c.(124-126)aTt>aCt	p.I42T	CNTN1_ENST00000547702.1_Missense_Mutation_p.I42T|CNTN1_ENST00000360099.3_Missense_Mutation_p.I42T|CNTN1_ENST00000547849.1_Missense_Mutation_p.I42T|CNTN1_ENST00000348761.2_Missense_Mutation_p.I31T|CNTN1_ENST00000347616.1_Missense_Mutation_p.I42T	NM_001843.3	NP_001834.2	Q12860	CNTN1_HUMAN	contactin 1	42	Ig-like C2-type 1.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cerebellum development (GO:0021549)|Notch signaling pathway (GO:0007219)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|positive regulation of sodium ion transport (GO:0010765)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(21)|lung(49)|ovary(3)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(2)	90	all_cancers(12;2.07e-06)|all_epithelial(1;4.26e-06)|Breast(8;0.0716)	Lung NSC(34;0.0211)|all_lung(34;0.0294)				TTTGGACCAATTTTTGAAGAG	0.378																																					p.I42T		Atlas-SNP	.											.	CNTN1	207	.	0			c.T125C						PASS	.						73.0	79.0	77.0					12																	41312471		2203	4300	6503	SO:0001583	missense	1272	exon4			GACCAATTTTTGA	Z21488	CCDS8737.1, CCDS8738.1, CCDS58225.1	12q11-q12	2014-01-30				ENSG00000018236		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"", ""Endogenous ligands"""	2171	protein-coding gene	gene with protein product	"""glycoprotein gP135"""	600016				7959734, 8586965	Standard	NM_001843		Approved	F3, GP135	uc031qgz.1	Q12860		ENST00000551295.2:c.125T>C	12.37:g.41312471T>C	ENSP00000447006:p.Ile42Thr	184.0	0.0	0		205.0	34.0	0.165854	NM_001256063	A8K0H9|A8K0Y3|Q12861|Q14030|Q7M4P0|Q8N466	Missense_Mutation	SNP	ENST00000551295.2	37	CCDS8737.1	.	.	.	.	.	.	.	.	.	.	T	26.1	4.707931	0.89018	.	.	ENSG00000018236	ENST00000547702;ENST00000551424;ENST00000551295;ENST00000548005;ENST00000552248;ENST00000547849;ENST00000552913;ENST00000347616;ENST00000360099;ENST00000348761	T;T;T;T;T;T;T;T	0.65178	-0.14;0.25;1.05;1.05;-0.14;0.25;-0.14;0.18	5.36	5.36	0.76844	Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.059649	0.64402	D	0.000003	T	0.63331	0.2502	N	0.25957	0.775	0.41091	D	0.985594	P;P;P	0.50156	0.9;0.917;0.932	B;P;P	0.57009	0.39;0.637;0.811	T	0.60576	-0.7236	10	0.25106	T	0.35	.	15.6713	0.77279	0.0:0.0:0.0:1.0	.	42;31;42	Q12860-3;Q12860-2;Q12860	.;.;CNTN1_HUMAN	T	42;42;42;42;42;42;42;42;42;31	ENSP00000448004:I42T;ENSP00000447006:I42T;ENSP00000447862:I42T;ENSP00000447860:I42T;ENSP00000448653:I42T;ENSP00000325660:I42T;ENSP00000353213:I42T;ENSP00000261160:I31T	ENSP00000325660:I42T	I	+	2	0	CNTN1	39598738	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.314000	0.78988	2.167000	0.68274	0.477000	0.44152	ATT	.	.	none		0.378	CNTN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403692.2	NM_001843	
SLC4A8	9498	hgsc.bcm.edu	37	12	51856159	51856159	+	Silent	SNP	C	C	T	rs71449805	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:51856159C>T	ENST00000453097.2	+	10	1384	c.1167C>T	c.(1165-1167)ttC>ttT	p.F389F	SLC4A8_ENST00000514353.3_Silent_p.F336F|SLC4A8_ENST00000535225.2_Silent_p.F336F|SLC4A8_ENST00000394856.1_Silent_p.F336F|SLC4A8_ENST00000358657.3_Silent_p.F416F	NM_001039960.2|NM_001258401.2	NP_001035049.1|NP_001245330.1			solute carrier family 4, sodium bicarbonate cotransporter, member 8											NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(18)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|stomach(2)|urinary_tract(5)	55				BRCA - Breast invasive adenocarcinoma(357;0.15)		TTGATGAGTTCCTAGACCAGG	0.473													C|||	48	0.00958466	0.0015	0.0187	5008	,	,		18122	0.0		0.0278	False		,,,				2504	0.0051				p.F389F		Atlas-SNP	.											.	SLC4A8	292	.	0			c.C1167T						PASS	.	C	,	36,4370	41.6+/-74.8	0,36,2167	123.0	118.0	120.0		1167,1167	4.3	1.0	12	dbSNP_130	120	351,8249	118.5+/-177.9	5,341,3954	no	coding-synonymous,coding-synonymous	SLC4A8	NM_001039960.1,NM_004858.2	,	5,377,6121	TT,TC,CC		4.0814,0.8171,2.9755	,	389/1094,389/1045	51856159	387,12619	2203	4300	6503	SO:0001819	synonymous_variant	9498	exon10			TGAGTTCCTAGAC	AB018282	CCDS44890.1, CCDS58232.1, CCDS58233.1, CCDS73470.1	12q13.13	2013-05-22			ENSG00000050438	ENSG00000050438		"""Solute carriers"""	11034	protein-coding gene	gene with protein product		605024				11133997	Standard	NM_001039960		Approved	NBC3	uc001rys.2	Q2Y0W8	OTTHUMG00000169489	ENST00000453097.2:c.1167C>T	12.37:g.51856159C>T		104.0	0.0	0		130.0	61.0	0.469231	NM_001039960		Silent	SNP	ENST00000453097.2	37	CCDS44890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.473	SLC4A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404356.1	NM_004858	
GEMIN4	50628	hgsc.bcm.edu	37	17	649984	649984	+	Silent	SNP	G	G	A	rs147516197	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:649984G>A	ENST00000319004.5	-	2	1417	c.1299C>T	c.(1297-1299)ttC>ttT	p.F433F	GEMIN4_ENST00000437269.1_3'UTR|GEMIN4_ENST00000576778.1_Silent_p.F422F	NM_015721.2	NP_056536.2	P57678	GEMI4_HUMAN	gem (nuclear organelle) associated protein 4	433					gene expression (GO:0010467)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|rRNA processing (GO:0006364)|spliceosomal snRNP assembly (GO:0000387)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN complex (GO:0032797)|SMN-Sm protein complex (GO:0034719)				breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(4)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22		Myeloproliferative disorder(207;0.204)		UCEC - Uterine corpus endometrioid carcinoma (25;0.022)		ACTCGTCCGAGAAGGCCCACT	0.547													G|||	46	0.0091853	0.0	0.0043	5008	,	,		19907	0.0149		0.0089	False		,,,				2504	0.0194				p.F433F		Atlas-SNP	.											.	GEMIN4	116	.	0			c.C1299T						PASS	.	G		1,3955		0,1,1977	53.0	55.0	55.0		1299	5.1	1.0	17	dbSNP_134	55	86,8214		1,84,4065	no	coding-synonymous	GEMIN4	NM_015721.2		1,85,6042	AA,AG,GG		1.0361,0.0253,0.7099		433/1059	649984	87,12169	1978	4150	6128	SO:0001819	synonymous_variant	50628	exon2			GTCCGAGAAGGCC	AF177341	CCDS45559.1	17p13.3	2008-07-18				ENSG00000179409			15717	protein-coding gene	gene with protein product	"""HCC-associated protein 1"", ""component of gems 4"""	606969				10725331	Standard	NM_015721		Approved	HHRF-1, DKFZP434B131, p97, DKFZP434D174, HC56, HCAP1	uc002frs.1	P57678		ENST00000319004.5:c.1299C>T	17.37:g.649984G>A		89.0	0.0	0		99.0	52.0	0.525253	NM_015721	Q9NZS7|Q9UG32|Q9Y4Q2	Silent	SNP	ENST00000319004.5	37	CCDS45559.1																																																																																			G|0.991;A|0.009	0.009	strong		0.547	GEMIN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437181.1	NM_015721	
SAMD9	54809	hgsc.bcm.edu	37	7	92735154	92735154	+	Missense_Mutation	SNP	G	G	A	rs147157740	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:92735154G>A	ENST00000379958.2	-	3	526	c.257C>T	c.(256-258)tCt>tTt	p.S86F		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	86						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			TCCCATCTTAGATGTCTGAAT	0.383													G|||	15	0.00299521	0.0	0.0072	5008	,	,		18338	0.0		0.0099	False		,,,				2504	0.0				p.S86F		Atlas-SNP	.											.	SAMD9	239	.	0			c.C257T						PASS	.	G	PHE/SER,PHE/SER	7,4399	12.9+/-30.5	0,7,2196	171.0	169.0	170.0		257,257	-2.1	0.0	7	dbSNP_134	170	58,8542	36.4+/-91.3	0,58,4242	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	155,155	0,65,6438	AA,AG,GG		0.6744,0.1589,0.4998	benign,benign	86/1590,86/1590	92735154	65,12941	2203	4300	6503	SO:0001583	missense	54809	exon2			ATCTTAGATGTCT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.257C>T	7.37:g.92735154G>A	ENSP00000369292:p.Ser86Phe	161.0	0.0	0		217.0	105.0	0.483871	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	9.731	1.162254	0.21538	0.001589	0.006744	ENSG00000205413	ENST00000379958;ENST00000446617	T;T	0.25250	1.81;2.63	4.6	-2.08	0.07254	.	1.711930	0.03721	N	0.251921	T	0.11922	0.0290	L	0.27053	0.805	0.09310	N	1	B	0.32653	0.379	B	0.30782	0.12	T	0.20605	-1.0270	10	0.62326	D	0.03	.	4.2849	0.10850	0.0861:0.4566:0.2508:0.2066	.	86	Q5K651	SAMD9_HUMAN	F	86	ENSP00000369292:S86F;ENSP00000414529:S86F	ENSP00000369292:S86F	S	-	2	0	SAMD9	92573090	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.011000	0.12721	-0.530000	0.06349	-1.368000	0.01194	TCT	G|0.995;A|0.005	0.005	strong		0.383	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
FAM13A	10144	hgsc.bcm.edu	37	4	89950630	89950630	+	Silent	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:89950630C>G	ENST00000264344.5	-	2	405	c.198G>C	c.(196-198)gtG>gtC	p.V66V	FAM13A_ENST00000515600.1_Silent_p.V66V|FAM13A_ENST00000502459.1_5'UTR|FAM13A_ENST00000509094.1_Silent_p.V66V|FAM13A_ENST00000511976.1_5'UTR	NM_014883.3	NP_055698.2	O94988	FA13A_HUMAN	family with sequence similarity 13, member A	66	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|liver(1)|lung(22)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	55						TCAAATATTCCACTATATTCC	0.393																																					p.V66V		Atlas-SNP	.											.	FAM13A	181	.	0			c.G198C						PASS	.						158.0	152.0	154.0					4																	89950630		2203	4300	6503	SO:0001819	synonymous_variant	10144	exon2			ATATTCCACTATA	AB020721	CCDS34029.1, CCDS43251.1, CCDS58911.1, CCDS58912.1, CCDS58913.1	4q22.1	2011-09-07	2009-01-20	2009-01-20	ENSG00000138640	ENSG00000138640		"""Rho GTPase activating proteins"""	19367	protein-coding gene	gene with protein product		613299	"""family with sequence similarity 13, member A1"""	FAM13A1			Standard	NM_014883		Approved	KIAA0914, ARHGAP48	uc003hse.2	O94988	OTTHUMG00000161006	ENST00000264344.5:c.198G>C	4.37:g.89950630C>G		124.0	0.0	0		137.0	17.0	0.124088	NM_014883	B4DLC1|Q24JP0|Q5PR21|Q8NBA3	Silent	SNP	ENST00000264344.5	37	CCDS34029.1																																																																																			.	.	none		0.393	FAM13A-022	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363371.1		
RLN1	6013	hgsc.bcm.edu	37	9	5335590	5335590	+	Silent	SNP	T	T	G	rs35426888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:5335590T>G	ENST00000223862.1	-	2	345	c.219A>C	c.(217-219)gtA>gtC	p.V73V	RLN1_ENST00000487557.2_5'UTR|RLN1_ENST00000223858.4_Missense_Mutation_p.Y107S	NM_006911.2	NP_008842.1	P04808	REL1_HUMAN	relaxin 1	73					female pregnancy (GO:0007565)|signal transduction (GO:0007165)	extracellular region (GO:0005576)	hormone activity (GO:0005179)			large_intestine(1)|lung(4)	5	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.02)|Lung(218;0.0984)		TGAAGGATGGTACAATTTCTG	0.363													T|||	37	0.00738818	0.0	0.0173	5008	,	,		20846	0.0		0.0109	False		,,,				2504	0.0143				p.V73V		Atlas-SNP	.											.	RLN1	16	.	0			c.A219C						PASS	.						46.0	48.0	47.0					9																	5335590		2202	4300	6502	SO:0001819	synonymous_variant	6013	exon2			GGATGGTACAATT		CCDS6462.1	9p24.1	2013-02-26	2004-11-15		ENSG00000107018	ENSG00000107018		"""Endogenous ligands"""	10026	protein-coding gene	gene with protein product	"""prorelaxin H1"""	179730	"""relaxin 1 (H1)"""				Standard	NM_006911		Approved	H1	uc003zjb.2	P04808	OTTHUMG00000019495	ENST00000223862.1:c.219A>C	9.37:g.5335590T>G		64.0	0.0	0		40.0	15.0	0.375	NM_006911	Q99936|Q9UQJ1	Silent	SNP	ENST00000223862.1	37	CCDS6462.1	.	.	.	.	.	.	.	.	.	.	T	2.574	-0.298894	0.05532	.	.	ENSG00000107018	ENST00000223858	T	0.23348	1.91	2.21	0.163	0.14986	.	.	.	.	.	T	0.10035	0.0246	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.34527	-0.9825	6	0.12430	T	0.62	.	3.1868	0.06603	0.2517:0.5914:0.0:0.1569	rs35426888;rs61758132	.	.	.	S	107	ENSP00000223858:Y107S	ENSP00000223858:Y107S	Y	-	2	0	RLN1	5325590	0.000000	0.05858	0.009000	0.14445	0.005000	0.04900	-0.303000	0.08210	0.053000	0.16036	-1.550000	0.00899	TAC	C|0.005;G|0.002;T|0.993	0.002	strong		0.363	RLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051617.1		
PLEKHG2	64857	hgsc.bcm.edu	37	19	39909394	39909394	+	Silent	SNP	C	C	T	rs146672674	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:39909394C>T	ENST00000409794.3	+	10	1954	c.1104C>T	c.(1102-1104)agC>agT	p.S368S	PLEKHG2_ENST00000458508.2_Silent_p.S309S|PLEKHG2_ENST00000425673.1_Silent_p.S368S|PLEKHG2_ENST00000409797.2_Silent_p.S368S|PLEKHG2_ENST00000378550.1_Silent_p.S368S	NM_022835.2	NP_073746.2	Q9H7P9	PKHG2_HUMAN	pleckstrin homology domain containing, family G (with RhoGef domain) member 2	368	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(2)|liver(1)|lung(13)|pancreas(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	40	all_cancers(60;3.08e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;6.57e-07)|Ovarian(47;0.0569)		Epithelial(26;2.92e-26)|all cancers(26;2.01e-23)|Lung(45;0.000499)|LUSC - Lung squamous cell carcinoma(53;0.000657)			TGAGCGTGAGCGAGAGTCCCC	0.577													C|||	2	0.000399361	0.0015	0.0	5008	,	,		18474	0.0		0.0	False		,,,				2504	0.0				p.S368S		Atlas-SNP	.											.	PLEKHG2	329	.	0			c.C1104T						PASS	.	C		6,4400	11.4+/-27.6	0,6,2197	230.0	231.0	231.0		1104	-3.3	1.0	19	dbSNP_134	231	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	PLEKHG2	NM_022835.2		0,12,6491	TT,TC,CC		0.0698,0.1362,0.0923		368/1387	39909394	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	64857	exon10			CGTGAGCGAGAGT	AK024429	CCDS33022.2	19q13.2	2013-01-11			ENSG00000090924	ENSG00000090924		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	29515	protein-coding gene	gene with protein product		611893				11839748, 18045877	Standard	NM_022835		Approved	CLG, FLJ00018, ARHGEF42	uc010xuz.2	Q9H7P9	OTTHUMG00000152570	ENST00000409794.3:c.1104C>T	19.37:g.39909394C>T		81.0	0.0	0		85.0	39.0	0.458824	NM_022835	B8ZZK6|C9J0Y4|Q6DHV6|Q96BU2|Q96D18|Q9H699	Silent	SNP	ENST00000409794.3	37	CCDS33022.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	9.421	1.082999	0.20309	0.001362	6.98E-4	ENSG00000090924	ENST00000205135	.	.	.	4.4	-3.26	0.05064	.	.	.	.	.	T	0.48537	0.1505	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44406	-0.9330	4	.	.	.	.	6.3348	0.21291	0.1262:0.3477:0.0:0.5261	.	.	.	.	V	265	.	.	A	+	2	0	PLEKHG2	44601234	0.000000	0.05858	0.990000	0.47175	0.799000	0.45148	-4.066000	0.00302	-0.329000	0.08527	0.462000	0.41574	GCG	C|0.999;T|0.001	0.001	strong		0.577	PLEKHG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326802.1	NM_022835	
NEFH	4744	hgsc.bcm.edu	37	22	29886354	29886354	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:29886354G>A	ENST00000310624.6	+	4	2758	c.2725G>A	c.(2725-2727)Gag>Aag	p.E909K		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	915	Tail.				axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						CCCAGAGAAGGAGGCTCCTGC	0.502																																					p.E909K		Atlas-SNP	.											.	NEFH	178	.	0			c.G2725A						PASS	.						57.0	62.0	60.0					22																	29886354		2203	4300	6503	SO:0001583	missense	4744	exon4			GAGAAGGAGGCTC		CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.2725G>A	22.37:g.29886354G>A	ENSP00000311997:p.Glu909Lys	114.0	0.0	0		145.0	77.0	0.531034	NM_021076	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	Missense_Mutation	SNP	ENST00000310624.6	37	CCDS13858.1	.	.	.	.	.	.	.	.	.	.	G	10.76	1.442446	0.25987	.	.	ENSG00000100285	ENST00000328842;ENST00000310624	D	0.84223	-1.82	5.48	4.4	0.53042	.	0.270105	0.26719	N	0.022846	T	0.79633	0.4479	L	0.59436	1.845	0.41319	D	0.98716	P	0.38020	0.615	B	0.33121	0.158	T	0.79137	-0.1927	10	0.40728	T	0.16	.	10.1869	0.43002	0.0756:0.1391:0.7853:0.0	.	915	P12036	NFH_HUMAN	K	860;909	ENSP00000311997:E909K	ENSP00000311997:E909K	E	+	1	0	NEFH	28216354	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	3.431000	0.52814	2.739000	0.93911	0.655000	0.94253	GAG	.	.	none		0.502	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2	NM_021076	
CLIC3	9022	hgsc.bcm.edu	37	9	139890105	139890105	+	Silent	SNP	C	C	G	rs141765089	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139890105C>G	ENST00000494426.1	-	2	397	c.138G>C	c.(136-138)acG>acC	p.T46T	CLIC3_ENST00000480181.1_5'UTR	NM_004669.2	NP_004660.2	O95833	CLIC3_HUMAN	chloride intracellular channel 3	46	GST N-terminal.|Required for insertion into the membrane. {ECO:0000250}.				chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|signal transduction (GO:0007165)	chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	chloride channel activity (GO:0005254)|voltage-gated chloride channel activity (GO:0005247)			lung(1)|skin(1)	2	all_cancers(76;0.11)	Myeloproliferative disorder(178;0.0511)	STAD - Stomach adenocarcinoma(284;0.123)	OV - Ovarian serous cystadenocarcinoma(145;2.94e-05)|Epithelial(140;0.00048)		CTCACCTGCGCGTGTCCACCG	0.706													C|||	21	0.00419329	0.0015	0.0058	5008	,	,		10979	0.0		0.0149	False		,,,				2504	0.0				p.T46T		Atlas-SNP	.											.	CLIC3	13	.	0			c.G138C						PASS	.	C		19,4383	25.3+/-52.1	0,19,2182	40.0	37.0	38.0		138	-7.4	0.0	9	dbSNP_134	38	162,8434	69.4+/-131.9	2,158,4138	no	coding-synonymous	CLIC3	NM_004669.2		2,177,6320	GG,GC,CC		1.8846,0.4316,1.3925		46/237	139890105	181,12817	2201	4298	6499	SO:0001819	synonymous_variant	9022	exon2			CCTGCGCGTGTCC	AF102166	CCDS7021.1	9q34.3	2012-09-26			ENSG00000169583	ENSG00000169583		"""Ion channels / Chloride channels : Intracellular"""	2064	protein-coding gene	gene with protein product		606533				9880541	Standard	NM_004669		Approved		uc004ckj.1	O95833	OTTHUMG00000020954	ENST00000494426.1:c.138G>C	9.37:g.139890105C>G		75.0	0.0	0		68.0	44.0	0.647059	NM_004669	Q5SPZ7	Silent	SNP	ENST00000494426.1	37	CCDS7021.1																																																																																			C|0.991;G|0.009	0.009	strong		0.706	CLIC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055173.2	NM_004669	
CCDC88A	55704	hgsc.bcm.edu	37	2	55615950	55615950	+	Silent	SNP	T	T	C	rs147639776	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:55615950T>C	ENST00000436346.1	-	3	1078	c.237A>G	c.(235-237)ctA>ctG	p.L79L	CCDC88A_ENST00000413716.2_Silent_p.L79L|CCDC88A_ENST00000336838.6_Silent_p.L79L|CCDC88A_ENST00000263630.8_Silent_p.L79L	NM_001135597.1|NM_001254943.1	NP_001129069.1|NP_001241872.1	Q3V6T2	GRDN_HUMAN	coiled-coil domain containing 88A	79					activation of protein kinase B activity (GO:0032148)|cell migration (GO:0016477)|DNA replication (GO:0006260)|lamellipodium assembly (GO:0030032)|membrane organization (GO:0061024)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cell proliferation (GO:0042127)|regulation of DNA replication (GO:0006275)|regulation of neuron projection development (GO:0010975)|regulation of protein phosphorylation (GO:0001932)|TOR signaling (GO:0031929)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|membrane (GO:0016020)|plasma membrane (GO:0005886)	actin binding (GO:0003779)|microtubule binding (GO:0008017)|phosphatidylinositol binding (GO:0035091)|protein homodimerization activity (GO:0042803)|protein kinase B binding (GO:0043422)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(22)|lung(23)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	69						CCAAAATGGATAGATTGTGCA	0.269													T|||	3	0.000599042	0.0	0.0029	5008	,	,		12742	0.0		0.001	False		,,,				2504	0.0				p.L79L		Atlas-SNP	.											.	CCDC88A	336	.	0			c.A237G						PASS	.	T	,	2,4400	4.2+/-10.8	0,2,2199	69.0	74.0	72.0		237,237	-11.9	0.1	2	dbSNP_134	72	23,8531	17.3+/-56.4	0,23,4254	no	coding-synonymous,coding-synonymous	CCDC88A	NM_001135597.1,NM_018084.4	,	0,25,6453	CC,CT,TT		0.2689,0.0454,0.193	,	79/1871,79/1844	55615950	25,12931	2201	4277	6478	SO:0001819	synonymous_variant	55704	exon3			AATGGATAGATTG	AB033038, AF112218	CCDS33203.1, CCDS46288.1, CCDS58710.1	2p16.3	2013-03-13	2007-05-31	2007-05-31	ENSG00000115355	ENSG00000115355			25523	protein-coding gene	gene with protein product	"""Galpha-interacting vesicle-associated protein"", ""Akt-phosphorylation enhancer"", ""girdin"", ""girders of actin filaments"""	609736	"""KIAA1212"""	KIAA1212		15749703, 15753085	Standard	NM_001135597		Approved	FLJ10392, APE, GIV, HkRP1, GRDN	uc002ryv.2	Q3V6T2	OTTHUMG00000151915	ENST00000436346.1:c.237A>G	2.37:g.55615950T>C		262.0	0.0	0		304.0	141.0	0.463816	NM_018084	A1IGE7|B7ZM78|C9JG83|Q53SF1|Q581G3|Q5HYD0|Q7Z339|Q7Z3C5	Silent	SNP	ENST00000436346.1	37																																																																																				T|0.998;C|0.002	0.002	strong		0.269	CCDC88A-203	KNOWN	basic	protein_coding	protein_coding		NM_017571	
TAS2R8	50836	hgsc.bcm.edu	37	12	10958896	10958896	+	Missense_Mutation	SNP	T	T	G	rs143804727	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:10958896T>G	ENST00000240615.2	-	1	996	c.684A>C	c.(682-684)gaA>gaC	p.E228D		NM_023918.1	NP_076407.1	Q9NYW2	TA2R8_HUMAN	taste receptor, type 2, member 8	228					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	bitter taste receptor activity (GO:0033038)|taste receptor activity (GO:0008527)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						TCACATGAACTTCTGTGCTGG	0.333													T|||	42	0.00838658	0.0	0.0231	5008	,	,		18097	0.002		0.0129	False		,,,				2504	0.0112				p.E228D		Atlas-SNP	.											TAS2R8,colon,carcinoma,0,1	TAS2R8	42	1	0			c.A684C						PASS	.	T	ASP/GLU	14,4392	21.2+/-45.6	0,14,2189	82.0	86.0	84.0		684	-1.8	0.0	12	dbSNP_134	84	197,8401	84.8+/-147.2	2,193,4104	yes	missense	TAS2R8	NM_023918.1	45	2,207,6293	GG,GT,TT		2.2912,0.3177,1.6226	possibly-damaging	228/310	10958896	211,12793	2203	4299	6502	SO:0001583	missense	50836	exon1			ATGAACTTCTGTG	AF227134	CCDS8632.1	12p13	2012-08-22			ENSG00000121314	ENSG00000121314		"""Taste receptors / Type 2"", ""GPCR / Unclassified : Taste receptors"""	14915	protein-coding gene	gene with protein product		604794				10761934, 10766242	Standard	NM_023918		Approved	T2R8, TRB5	uc010shh.2	Q9NYW2	OTTHUMG00000168506	ENST00000240615.2:c.684A>C	12.37:g.10958896T>G	ENSP00000240615:p.Glu228Asp	80.0	0.0	0		78.0	44.0	0.564103	NM_023918	Q4KN29|Q645Y2	Missense_Mutation	SNP	ENST00000240615.2	37	CCDS8632.1	14	0.00641025641025641	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	5	0.006596306068601583	T	11.29	1.595797	0.28445	0.003177	0.022912	ENSG00000121314	ENST00000240615	T	0.37752	1.18	5.38	-1.83	0.07833	GPCR, rhodopsin-like superfamily (1);	0.488214	0.16827	U	0.197913	T	0.35098	0.0920	M	0.80332	2.49	0.09310	N	1	D	0.63046	0.992	D	0.65573	0.936	T	0.36089	-0.9762	10	0.72032	D	0.01	.	5.7484	0.18132	0.1379:0.3212:0.0:0.5409	.	228	Q9NYW2	TA2R8_HUMAN	D	228	ENSP00000240615:E228D	ENSP00000240615:E228D	E	-	3	2	TAS2R8	10850163	0.000000	0.05858	0.032000	0.17829	0.008000	0.06430	-3.643000	0.00405	-0.700000	0.05070	-0.904000	0.02843	GAA	T|0.987;G|0.013	0.013	strong		0.333	TAS2R8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399932.1		
TET2	54790	hgsc.bcm.edu	37	4	106183003	106183003	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:106183003C>A	ENST00000540549.1	+	8	4902	c.4042C>A	c.(4042-4044)Cag>Aag	p.Q1348K	TET2_ENST00000513237.1_Missense_Mutation_p.Q1369K|TET2_ENST00000380013.4_Missense_Mutation_p.Q1348K|TET2_ENST00000545826.1_3'UTR			Q6N021	TET2_HUMAN	tet methylcytosine dioxygenase 2	1348					5-methylcytosine catabolic process (GO:0006211)|cell cycle (GO:0007049)|DNA demethylation (GO:0080111)|histone H3-K4 trimethylation (GO:0080182)|kidney development (GO:0001822)|myeloid cell differentiation (GO:0030099)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein O-linked glycosylation (GO:0006493)		DNA binding (GO:0003677)|ferrous iron binding (GO:0008198)|methylcytosine dioxygenase activity (GO:0070579)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1272)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	1314		Myeloproliferative disorder(5;0.0393)		OV - Ovarian serous cystadenocarcinoma(123;7.18e-08)		ATATAATAATCAGGTAAGTTT	0.308			"""Mis N, F"""		MDS																																p.Q1348K		Atlas-SNP	.		Rec	yes		4	4q24	54790	tet oncogene family member 2		L	.	TET2	1762	.	0			c.C4042A						PASS	.						66.0	58.0	60.0					4																	106183003		692	1587	2279	SO:0001583	missense	54790	exon8			AATAATCAGGTAA	AB046766	CCDS3666.1, CCDS47120.1	4q24	2014-09-17	2011-09-30	2008-03-12	ENSG00000168769	ENSG00000168769			25941	protein-coding gene	gene with protein product		612839	"""KIAA1546"", ""tet oncogene family member 2"""	KIAA1546		10997877, 12646957	Standard	NM_017628		Approved	FLJ20032	uc003hxk.3	Q6N021	OTTHUMG00000131213	ENST00000540549.1:c.4042C>A	4.37:g.106183003C>A	ENSP00000442788:p.Gln1348Lys	269.0	0.0	0		253.0	28.0	0.110672	NM_001127208	B5MDU0|Q2TB88|Q3LIB8|Q96JX5|Q9HCM6|Q9NXW0	Missense_Mutation	SNP	ENST00000540549.1	37	CCDS47120.1	.	.	.	.	.	.	.	.	.	.	C	32	5.148220	0.94603	.	.	ENSG00000168769	ENST00000540549;ENST00000513237;ENST00000380013	T;T;T	0.14266	2.52;2.52;2.52	5.36	5.36	0.76844	TET cysteine-rich domain (1);	.	.	.	.	T	0.45034	0.1322	M	0.86268	2.805	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.91635	0.999;0.999	T	0.50566	-0.8813	9	0.87932	D	0	-11.679	19.0905	0.93225	0.0:1.0:0.0:0.0	.	1369;1348	E7EQS8;Q6N021	.;TET2_HUMAN	K	1348;1369;1348	ENSP00000442788:Q1348K;ENSP00000425443:Q1369K;ENSP00000369351:Q1348K	ENSP00000369351:Q1348K	Q	+	1	0	TET2	106402452	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.585000	0.82584	2.526000	0.85167	0.555000	0.69702	CAG	.	.	none		0.308	TET2-202	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253952.2	NM_017628	
MTMR3	8897	hgsc.bcm.edu	37	22	30415983	30415983	+	Missense_Mutation	SNP	C	C	T	rs61737780	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:30415983C>T	ENST00000401950.2	+	17	2677	c.2335C>T	c.(2335-2337)Ctc>Ttc	p.L779F	MTMR3_ENST00000323630.5_Missense_Mutation_p.L643F|MTMR3_ENST00000406629.1_Missense_Mutation_p.L779F|CTA-85E5.10_ENST00000429350.1_RNA|MTMR3_ENST00000351488.3_Missense_Mutation_p.L779F|CTA-85E5.10_ENST00000453743.2_RNA|MTMR3_ENST00000333027.3_Missense_Mutation_p.L779F	NM_021090.3	NP_066576.1	Q13615	MTMR3_HUMAN	myotubularin related protein 3	779					peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|membrane (GO:0016020)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3,5-bisphosphate 3-phosphatase activity (GO:0052629)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|large_intestine(3)|ovary(2)|skin(8)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(5;0.00204)|Epithelial(10;0.06)|all cancers(5;0.107)			CCTCAGTTCTCTCCAGGTCCC	0.552													C|||	17	0.00339457	0.0	0.0043	5008	,	,		18968	0.0		0.0139	False		,,,				2504	0.0				p.L779F		Atlas-SNP	.											.	MTMR3	106	.	0			c.C2335T						PASS	.	C	PHE/LEU,PHE/LEU,PHE/LEU	7,4399	12.9+/-30.5	0,7,2196	73.0	77.0	76.0		2335,2335,2335	3.7	0.9	22	dbSNP_129	76	99,8501	55.2+/-116.2	0,99,4201	yes	missense,missense,missense	MTMR3	NM_021090.3,NM_153050.2,NM_153051.2	22,22,22	0,106,6397	TT,TC,CC		1.1512,0.1589,0.815	possibly-damaging,possibly-damaging,possibly-damaging	779/1199,779/1171,779/1162	30415983	106,12900	2203	4300	6503	SO:0001583	missense	8897	exon17			AGTTCTCTCCAGG	U58034	CCDS13870.1, CCDS13871.1, CCDS46682.1	22q12.2	2011-06-09			ENSG00000100330	ENSG00000100330		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7451	protein-coding gene	gene with protein product		603558				8640223, 9736772	Standard	NM_153050		Approved	KIAA0371, ZFYVE10, FYVE-DSP1	uc003agv.4	Q13615	OTTHUMG00000151278	ENST00000401950.2:c.2335C>T	22.37:g.30415983C>T	ENSP00000384651:p.Leu779Phe	148.0	0.0	0		161.0	70.0	0.434783	NM_021090	A5PL26|A7MD32|Q9NYN5|Q9NYN6|Q9UDX6|Q9UEG3	Missense_Mutation	SNP	ENST00000401950.2	37	CCDS13870.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	2.316	-0.356778	0.05138	0.001589	0.011512	ENSG00000100330	ENST00000401950;ENST00000333027;ENST00000323630;ENST00000351488;ENST00000406629	D;D;D;D;D	0.93763	-3.08;-3.05;-3.28;-3.1;-3.05	4.73	3.66	0.41972	.	1.991870	0.01826	N	0.034355	D	0.84826	0.5558	N	0.19112	0.55	0.09310	N	1	P;B;P	0.37636	0.603;0.257;0.603	B;B;B	0.36186	0.219;0.109;0.219	T	0.76208	-0.3043	10	0.10111	T	0.7	.	12.5279	0.56098	0.3353:0.6647:0.0:0.0	rs61737780	779;779;779	Q13615-3;Q13615;Q13615-2	.;MTMR3_HUMAN;.	F	779;779;643;779;779	ENSP00000384651:L779F;ENSP00000331649:L779F;ENSP00000318070:L643F;ENSP00000307271:L779F;ENSP00000384077:L779F	ENSP00000318070:L643F	L	+	1	0	MTMR3	28745983	0.000000	0.05858	0.924000	0.36721	0.812000	0.45895	-0.164000	0.09983	2.448000	0.82819	0.462000	0.41574	CTC	C|0.992;T|0.008	0.008	strong		0.552	MTMR3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000322066.1	NM_021090	
HBS1L	10767	hgsc.bcm.edu	37	6	135287597	135287597	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:135287597C>T	ENST00000367837.5	-	17	2119	c.1913G>A	c.(1912-1914)gGc>gAc	p.G638D	HBS1L_ENST00000445176.2_Missense_Mutation_p.G362D|HBS1L_ENST00000415177.2_Missense_Mutation_p.G573D|HBS1L_ENST00000367826.2_Missense_Mutation_p.G596D|HBS1L_ENST00000367824.4_Missense_Mutation_p.G474D|HBS1L_ENST00000527578.1_Missense_Mutation_p.G474D	NM_001145158.1|NM_006620.3	NP_001138630.1|NP_006611.1	Q9Y450	HBS1L_HUMAN	HBS1-like translational GTPase	638					signal transduction (GO:0007165)|translation (GO:0006412)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|translation elongation factor activity (GO:0003746)			NS(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	20	Colorectal(23;0.221)			OV - Ovarian serous cystadenocarcinoma(155;0.0046)|GBM - Glioblastoma multiforme(68;0.00702)		TGCATTCTGGCCTTTAGTCAA	0.328																																					p.G638D		Atlas-SNP	.											.	HBS1L	75	.	0			c.G1913A						PASS	.						106.0	105.0	106.0					6																	135287597		2203	4300	6503	SO:0001583	missense	10767	exon17			TTCTGGCCTTTAG	U87791	CCDS5173.1, CCDS47479.1, CCDS47480.1	6q23.3	2014-04-30	2014-04-30		ENSG00000112339	ENSG00000112339			4834	protein-coding gene	gene with protein product	"""eRF3 family member"""	612450	"""HBS1 (S. cerevisiae)-like"", ""HBS1-like (S. cerevisiae)"""			9872408, 23667253	Standard	NM_006620		Approved	ERFS, HBS1, HSPC276, KIAA1038, DKFZp434g247, EF-1a, eRF3c	uc003qez.2	Q9Y450	OTTHUMG00000015626	ENST00000367837.5:c.1913G>A	6.37:g.135287597C>T	ENSP00000356811:p.Gly638Asp	70.0	0.0	0		54.0	20.0	0.37037	NM_006620	B7Z365|Q4VX89|Q4VX90|Q5T7G3|Q8NDW9|Q9UPW3	Missense_Mutation	SNP	ENST00000367837.5	37	CCDS5173.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.145634	0.77888	.	.	ENSG00000112339	ENST00000367837;ENST00000527578;ENST00000415177;ENST00000367826;ENST00000367824;ENST00000533274;ENST00000445176	T;T;T;T;T;T;T	0.69561	-0.38;-0.38;-0.34;-0.4;-0.38;-0.41;0.71	5.96	5.96	0.96718	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (1);Translation elongation factor EFTu/EF1A, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80008	0.4545	M	0.73319	2.225	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.79108	0.967;0.992	T	0.80279	-0.1449	10	0.87932	D	0	-8.0087	20.4008	0.98991	0.0:1.0:0.0:0.0	.	596;638	Q9Y450-4;Q9Y450	.;HBS1L_HUMAN	D	638;474;573;596;474;508;362	ENSP00000356811:G638D;ENSP00000436256:G474D;ENSP00000389826:G573D;ENSP00000356800:G596D;ENSP00000356798:G474D;ENSP00000434533:G508D;ENSP00000415305:G362D	ENSP00000356798:G474D	G	-	2	0	HBS1L	135329290	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.265000	0.78442	2.826000	0.97356	0.655000	0.94253	GGC	.	.	none		0.328	HBS1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042339.2		
LIG1	3978	hgsc.bcm.edu	37	19	48626236	48626236	+	Silent	SNP	A	A	G	rs116999747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:48626236A>G	ENST00000263274.7	-	23	2606	c.2187T>C	c.(2185-2187)gtT>gtC	p.V729V	CTC-453G23.5_ENST00000596839.1_RNA|LIG1_ENST00000536218.1_Silent_p.V661V|LIG1_ENST00000427526.2_Silent_p.V698V|CTC-453G23.5_ENST00000596563.1_RNA	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	729					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|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)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	AGGTGGCATCAACATCCAGGG	0.617								Nucleotide excision repair (NER)					A|||	6	0.00119808	0.0	0.0029	5008	,	,		18483	0.0		0.004	False		,,,				2504	0.0				p.V729V		Atlas-SNP	.											.	LIG1	151	.	0			c.T2187C						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	166.0	149.0	155.0		2187	-9.9	0.1	19	dbSNP_132	155	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	LIG1	NM_000234.1		0,37,6466	GG,GA,AA		0.407,0.0454,0.2845		729/920	48626236	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	3978	exon23			GGCATCAACATCC		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.2187T>C	19.37:g.48626236A>G		136.0	0.0	0		119.0	57.0	0.478992	NM_000234	B2RAI8|Q2TB12|Q32P23	Silent	SNP	ENST00000263274.7	37	CCDS12711.1																																																																																			A|0.997;G|0.003	0.003	strong		0.617	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
KATNAL1	84056	hgsc.bcm.edu	37	13	30784566	30784566	+	Silent	SNP	A	A	G	rs11617724	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:30784566A>G	ENST00000380615.3	-	10	1328	c.1161T>C	c.(1159-1161)gcT>gcC	p.A387A	KATNAL1_ENST00000380617.3_Silent_p.A387A	NM_032116.4	NP_115492.1			katanin p60 subunit A-like 1											autonomic_ganglia(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|skin(1)|urinary_tract(3)	19		Lung SC(185;0.0257)		all cancers(112;0.114)|OV - Ovarian serous cystadenocarcinoma(117;0.213)		TCAGAAGCTCAGCTCTTCCTT	0.378													a|||	224	0.0447284	0.1233	0.036	5008	,	,		18073	0.0		0.0328	False		,,,				2504	0.0031				p.A387A		Atlas-SNP	.											.	KATNAL1	53	.	0			c.T1161C						PASS	.	A	,	483,3923	226.9+/-242.2	30,423,1750	181.0	170.0	174.0		1161,1161	-11.5	0.3	13	dbSNP_120	174	319,8281	113.3+/-173.4	3,313,3984	no	coding-synonymous,coding-synonymous	KATNAL1	NM_001014380.1,NM_032116.3	,	33,736,5734	GG,GA,AA		3.7093,10.9623,6.1664	,	387/491,387/491	30784566	802,12204	2203	4300	6503	SO:0001819	synonymous_variant	84056	exon10			AAGCTCAGCTCTT	AK097423	CCDS31956.1	13q12.3	2010-04-21			ENSG00000102781	ENSG00000102781		"""ATPases / AAA-type"""	28361	protein-coding gene	gene with protein product		614764				12477932	Standard	NM_001014380		Approved	MGC2599	uc001uss.4	Q9BW62	OTTHUMG00000016665	ENST00000380615.3:c.1161T>C	13.37:g.30784566A>G		261.0	0.0	0		209.0	206.0	0.985646	NM_001014380		Silent	SNP	ENST00000380615.3	37	CCDS31956.1																																																																																			A|0.940;G|0.060	0.060	strong		0.378	KATNAL1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044346.2	NM_032116	
HK2	3099	hgsc.bcm.edu	37	2	75107651	75107651	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:75107651G>A	ENST00000290573.2	+	10	2125	c.1525G>A	c.(1525-1527)Gtc>Atc	p.V509I	HK2_ENST00000409174.1_Missense_Mutation_p.V481I	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	509	Catalytic.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.V509I(2)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						CAGTGCCCCCGTCAAGATGCT	0.597																																					p.V509I		Atlas-SNP	.											HK2,NS,carcinoma,0,1	HK2	85	1	2	Substitution - Missense(2)	lung(2)	c.G1525A						PASS	.						74.0	73.0	73.0					2																	75107651		2203	4300	6503	SO:0001583	missense	3099	exon10			GCCCCCGTCAAGA		CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1525G>A	2.37:g.75107651G>A	ENSP00000290573:p.Val509Ile	135.0	0.0	0		203.0	22.0	0.108374	NM_000189	D6W5J2|Q8WU87|Q9UN82	Missense_Mutation	SNP	ENST00000290573.2	37	CCDS1956.1	.	.	.	.	.	.	.	.	.	.	G	17.31	3.358474	0.61403	.	.	ENSG00000159399	ENST00000290573;ENST00000535740;ENST00000409174	D;D	0.98345	-4.88;-4.88	4.99	4.99	0.66335	Hexokinase, N-terminal (1);	0.000000	0.85682	D	0.000000	D	0.98270	0.9427	L	0.51853	1.615	0.80722	D	1	D	0.61697	0.99	D	0.73380	0.98	D	0.97702	1.0185	10	0.35671	T	0.21	-40.4869	16.1435	0.81544	0.0:0.0:1.0:0.0	.	509	P52789	HXK2_HUMAN	I	509;509;481	ENSP00000290573:V509I;ENSP00000387140:V481I	ENSP00000290573:V509I	V	+	1	0	HK2	74961159	1.000000	0.71417	0.963000	0.40424	0.607000	0.37147	7.613000	0.82986	2.756000	0.94617	0.655000	0.94253	GTC	.	.	none		0.597	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2	NM_000189	
LARP1	23367	hgsc.bcm.edu	37	5	154092616	154092616	+	Missense_Mutation	SNP	C	C	T	rs148235669	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:154092616C>T	ENST00000336314.4	+	1	155	c.131C>T	c.(130-132)gCc>gTc	p.A44V		NM_015315.3	NP_056130.2	Q6PKG0	LARP1_HUMAN	La ribonucleoprotein domain family, member 1	62					cell proliferation (GO:0008283)|positive regulation of macroautophagy (GO:0016239)|positive regulation of translation (GO:0045727)|TOR signaling (GO:0031929)|translational initiation (GO:0006413)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	eukaryotic initiation factor 4E binding (GO:0008190)|mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|poly(A) RNA binding (GO:0044822)|RNA cap binding (GO:0000339)|translation activator activity (GO:0008494)|translation initiation factor binding (GO:0031369)			breast(1)|endometrium(3)|kidney(2)|large_intestine(10)|lung(9)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33	Renal(175;0.00488)	Medulloblastoma(196;0.0354)|all_neural(177;0.147)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)			TTGGCAGCTGCCCCGAGGAAG	0.602													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		17738	0.0		0.0	False		,,,				2504	0.001				p.A44V		Atlas-SNP	.											.	LARP1	187	.	0			c.C131T						PASS	.	C	VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	53.0	53.0	53.0		131	2.9	0.8	5	dbSNP_134	53	22,8578	16.0+/-53.3	0,22,4278	yes	missense	LARP1	NM_015315.3	64	0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		44/1020	154092616	24,12982	2203	4300	6503	SO:0001583	missense	23367	exon1			CAGCTGCCCCGAG	AB018274	CCDS4328.1	5q33.2	2014-02-12			ENSG00000155506	ENSG00000155506		"""La ribonucleoprotein domain containing"""	29531	protein-coding gene	gene with protein product		612059				9872452, 10878606	Standard	NM_015315		Approved	LARP, KIAA0731, MGC19556	uc003lvo.4	Q6PKG0	OTTHUMG00000130191	ENST00000336314.4:c.131C>T	5.37:g.154092616C>T	ENSP00000336721:p.Ala44Val	285.0	0.0	0		269.0	90.0	0.334572	NM_015315	O94836|Q8N4M2|Q8NB73|Q9UFD7	Missense_Mutation	SNP	ENST00000336314.4	37	CCDS4328.1	.	.	.	.	.	.	.	.	.	.	C	6.440	0.449233	0.12223	4.54E-4	0.002558	ENSG00000155506	ENST00000336314	T	0.25085	1.82	3.81	2.94	0.34122	.	.	.	.	.	T	0.17577	0.0422	.	.	.	0.19300	N	0.999973	B	0.27997	0.197	B	0.29176	0.099	T	0.19484	-1.0304	8	0.30078	T	0.28	.	8.8895	0.35425	0.2222:0.7778:0.0:0.0	.	44	Q6PKG0-3	.	V	44	ENSP00000336721:A44V	ENSP00000336721:A44V	A	+	2	0	LARP1	154072809	0.960000	0.32886	0.823000	0.32752	0.013000	0.08279	2.833000	0.48159	1.182000	0.42928	-0.310000	0.09108	GCC	C|0.998;T|0.002	0.002	strong		0.602	LARP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252509.1	NM_033551	
ERBB4	2066	hgsc.bcm.edu	37	2	212251864	212251864	+	Silent	SNP	T	T	C	rs3748962	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:212251864T>C	ENST00000342788.4	-	27	3505	c.3195A>G	c.(3193-3195)gtA>gtG	p.V1065V	ERBB4_ENST00000402597.1_Silent_p.V1055V|ERBB4_ENST00000436443.1_Silent_p.V1049V	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	1065					cardiac muscle tissue regeneration (GO:0061026)|cell fate commitment (GO:0045165)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system morphogenesis (GO:0021551)|embryonic pattern specification (GO:0009880)|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)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell differentiation (GO:0060644)|mitochondrial fragmentation involved in apoptotic process (GO:0043653)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|olfactory bulb interneuron differentiation (GO:0021889)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of STAT protein import into nucleus (GO:2000366)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|regulation of cell migration (GO:0030334)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	basolateral plasma membrane (GO:0016323)|cytosol (GO:0005829)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|epidermal growth factor receptor binding (GO:0005154)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transcription regulatory region DNA binding (GO:0044212)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|breast(7)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(31)|lung(71)|pancreas(1)|prostate(3)|skin(39)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	179		Renal(323;0.06)|Lung NSC(271;0.197)		UCEC - Uterine corpus endometrioid carcinoma (47;0.214)|Epithelial(149;5.86e-06)|all cancers(144;2.95e-05)|Lung(261;0.00244)|LUSC - Lung squamous cell carcinoma(224;0.00266)	Afatinib(DB08916)	CATCTCGGTATACAAACTGGT	0.433										TSP Lung(8;0.080)			T|||	1117	0.223043	0.0756	0.2983	5008	,	,		18765	0.2887		0.2992	False		,,,				2504	0.2229				p.V1065V		Atlas-SNP	.											.	ERBB4	480	.	0			c.A3195G						PASS	.	T	,	444,3962	214.5+/-233.7	29,386,1788	110.0	113.0	112.0		3147,3195	-8.9	0.3	2	dbSNP_107	112	2843,5757	447.9+/-361.7	499,1845,1956	no	coding-synonymous,coding-synonymous	ERBB4	NM_001042599.1,NM_005235.2	,	528,2231,3744	CC,CT,TT		33.0581,10.0772,25.273	,	1049/1293,1065/1309	212251864	3287,9719	2203	4300	6503	SO:0001819	synonymous_variant	2066	exon27			TCGGTATACAAAC	L07868	CCDS2394.1, CCDS42811.1	2q33.3-q34	2013-10-11	2013-07-09		ENSG00000178568	ENSG00000178568			3432	protein-coding gene	gene with protein product		600543	"""v-erb-a avian erythroblastic leukemia viral oncogene homolog-like 4"""			7700649, 17018285	Standard	NM_001042599		Approved	ALS19	uc002veg.1	Q15303	OTTHUMG00000133012	ENST00000342788.4:c.3195A>G	2.37:g.212251864T>C		245.0	0.0	0		266.0	137.0	0.515038	NM_005235	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1																																																																																			T|0.756;C|0.244	0.244	strong		0.433	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	
TNK1	8711	hgsc.bcm.edu	37	17	7287992	7287992	+	Silent	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7287992C>A	ENST00000576812.1	+	7	1425	c.1056C>A	c.(1054-1056)ctC>ctA	p.L352L	TNK1_ENST00000570896.1_Silent_p.L352L|TNK1_ENST00000311668.2_Silent_p.L352L	NM_001251902.1	NP_001238831.1			tyrosine kinase, non-receptor, 1											central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(2)|pancreas(1)	16		Prostate(122;0.157)				CCAGGGCCCTCTACTCCCTCG	0.711																																					p.L352L		Atlas-SNP	.											.	TNK1	31	.	0			c.C1056A						PASS	.						16.0	20.0	19.0					17																	7287992		1951	4129	6080	SO:0001819	synonymous_variant	8711	exon7			GGCCCTCTACTCC	U43408	CCDS45602.1, CCDS58510.1	17p13.1	2005-09-22				ENSG00000174292			11940	protein-coding gene	gene with protein product		608076				8632913	Standard	NM_003985		Approved		uc002ggi.4	Q13470		ENST00000576812.1:c.1056C>A	17.37:g.7287992C>A		68.0	0.0	0		48.0	25.0	0.520833	NM_003985		Silent	SNP	ENST00000576812.1	37	CCDS58510.1																																																																																			.	.	none		0.711	TNK1-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000440832.2	NM_003985	
MTMR4	9110	hgsc.bcm.edu	37	17	56585593	56585593	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:56585593C>T	ENST00000323456.5	-	8	718	c.594G>A	c.(592-594)tgG>tgA	p.W198*	MTMR4_ENST00000579925.1_Nonsense_Mutation_p.W198*	NM_004687.4	NP_004678.3	Q9NYA4	MTMR4_HUMAN	myotubularin related protein 4	198	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|small molecule metabolic process (GO:0044281)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytosol (GO:0005829)|early endosome membrane (GO:0031901)|extracellular space (GO:0005615)	metal ion binding (GO:0046872)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)			breast(10)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|skin(5)	36	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TGTCAGTGATCCACACAGGAA	0.557																																					p.W198X		Atlas-SNP	.											.	MTMR4	91	.	0			c.G594A						PASS	.						79.0	74.0	75.0					17																	56585593		2203	4300	6503	SO:0001587	stop_gained	9110	exon8			AGTGATCCACACA	AB014547	CCDS11608.1	17q22-q23	2011-06-09				ENSG00000108389		"""Zinc fingers, FYVE domain containing"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7452	protein-coding gene	gene with protein product		603559				9736772	Standard	NM_004687		Approved	KIAA0647, ZFYVE11	uc002iwj.2	Q9NYA4		ENST00000323456.5:c.594G>A	17.37:g.56585593C>T	ENSP00000325285:p.Trp198*	35.0	0.0	0		42.0	4.0	0.0952381	NM_004687	D3DTZ6|Q8IV27|Q9Y4D5	Nonsense_Mutation	SNP	ENST00000323456.5	37	CCDS11608.1	.	.	.	.	.	.	.	.	.	.	C	36	5.881577	0.97062	.	.	ENSG00000108389	ENST00000323456	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	18.8095	0.92053	0.0:1.0:0.0:0.0	.	.	.	.	X	198	.	ENSP00000325285:W198X	W	-	3	0	MTMR4	53940592	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.942000	0.70203	2.775000	0.95449	0.650000	0.86243	TGG	.	.	none		0.557	MTMR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444721.1	NM_004687	
FAF2	23197	hgsc.bcm.edu	37	5	175919324	175919324	+	Silent	SNP	G	G	A	rs78597771	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:175919324G>A	ENST00000261942.6	+	5	527	c.474G>A	c.(472-474)acG>acA	p.T158T		NM_014613.2	NP_055428.1	Q96CS3	FAF2_HUMAN	Fas associated factor family member 2	158					lipid particle organization (GO:0034389)|negative regulation of catalytic activity (GO:0043086)|response to unfolded protein (GO:0006986)	Cdc48p-Npl4p-Ufd1p AAA ATPase complex (GO:0034098)|endoplasmic reticulum (GO:0005783)|intracellular membrane-bounded organelle (GO:0043231)|lipid particle (GO:0005811)	lipase binding (GO:0035473)|lipase inhibitor activity (GO:0055102)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|large_intestine(3)|lung(4)|ovary(1)|skin(1)	10						ACCAGGGAACGTACAGCCAGG	0.493													G|||	42	0.00838658	0.0015	0.0144	5008	,	,		20504	0.0		0.0288	False		,,,				2504	0.001				p.T158T		Atlas-SNP	.											.	FAF2	38	.	0			c.G474A						PASS	.	G		27,4379	32.6+/-62.9	0,27,2176	62.0	57.0	59.0		474	0.4	1.0	5	dbSNP_132	59	286,8314	107.0+/-167.8	4,278,4018	no	coding-synonymous	FAF2	NM_014613.2		4,305,6194	AA,AG,GG		3.3256,0.6128,2.4066		158/446	175919324	313,12693	2203	4300	6503	SO:0001819	synonymous_variant	23197	exon5			GGGAACGTACAGC	BC015791	CCDS34296.1	5q35.2	2011-06-28	2008-07-25	2008-07-25	ENSG00000113194	ENSG00000113194		"""UBX domain containing"""	24666	protein-coding gene	gene with protein product	"""expressed in T cells and eosinophils in atopic dermatitis"", ""UBX domain protein 3B"""		"""UBX domain containing 8"""	UBXD8		10048485, 12372427	Standard	NM_014613		Approved	ETEA, KIAA0887, UBXN3B	uc003mej.4	Q96CS3	OTTHUMG00000163228	ENST00000261942.6:c.474G>A	5.37:g.175919324G>A		80.0	0.0	0		76.0	27.0	0.355263	NM_014613	O94963|Q8IUF2|Q9BRP2|Q9BVM7	Silent	SNP	ENST00000261942.6	37	CCDS34296.1																																																																																			G|0.978;A|0.022	0.022	strong		0.493	FAF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372194.1	NM_014613	
EXD1	161829	hgsc.bcm.edu	37	15	41488231	41488231	+	Missense_Mutation	SNP	G	G	C	rs139947718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:41488231G>C	ENST00000314992.5	-	6	555	c.365C>G	c.(364-366)gCc>gGc	p.A122G	EXD1_ENST00000458580.2_Missense_Mutation_p.A180G	NM_152596.2	NP_689809.2	Q8NHP7	EXD1_HUMAN	exonuclease 3'-5' domain containing 1	122	3'-5' exonuclease.						3'-5' exonuclease activity (GO:0008408)|nucleic acid binding (GO:0003676)			large_intestine(5)|liver(1)|lung(4)|ovary(2)|prostate(2)|skin(2)	16						GCAATTTGTGGCCACCTACAA	0.383													G|||	8	0.00159744	0.0	0.0043	5008	,	,		19008	0.0		0.004	False		,,,				2504	0.001				p.A122G		Atlas-SNP	.											.	EXD1	52	.	0			c.C365G						PASS	.	G	GLY/ALA	5,4401	4.2+/-10.8	0,5,2198	46.0	47.0	47.0		365	5.7	1.0	15	dbSNP_134	47	48,8552	26.3+/-74.7	0,48,4252	yes	missense	EXD1	NM_152596.2	60	0,53,6450	CC,CG,GG		0.5581,0.1135,0.4075	probably-damaging	122/515	41488231	53,12953	2203	4300	6503	SO:0001583	missense	161829	exon6			TTTGTGGCCACCT	BC030628	CCDS10072.1, CCDS66738.1	15q15.1	2009-02-24	2009-02-24	2009-02-24	ENSG00000178997	ENSG00000178997			28507	protein-coding gene	gene with protein product			"""exonuclease 3'-5' domain-like 1"""	EXDL1		12477932	Standard	NM_001286441		Approved	MGC33637	uc001znk.3	Q8NHP7	OTTHUMG00000130232	ENST00000314992.5:c.365C>G	15.37:g.41488231G>C	ENSP00000321029:p.Ala122Gly	52.0	0.0	0		70.0	32.0	0.457143	NM_152596	A8K909|B7Z839|Q6ZW94	Missense_Mutation	SNP	ENST00000314992.5	37	CCDS10072.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	21.6	4.173271	0.78452	0.001135	0.005581	ENSG00000178997	ENST00000314992;ENST00000458580	T;T	0.61742	0.08;0.08	5.65	5.65	0.86999	-5&apos (2);Ribonuclease H-like (1); exonuclease (2);3&apos (2);	0.062205	0.64402	D	0.000008	T	0.63885	0.2549	L	0.46885	1.475	0.50813	D	0.999899	D;D	0.71674	0.998;0.998	D;D	0.74023	0.982;0.982	T	0.67887	-0.5554	10	0.52906	T	0.07	-8.9912	17.4865	0.87689	0.0:0.0:1.0:0.0	.	180;122	B7Z839;Q8NHP7	.;EXD1_HUMAN	G	122;180	ENSP00000321029:A122G;ENSP00000415056:A180G	ENSP00000321029:A122G	A	-	2	0	EXD1	39275523	1.000000	0.71417	1.000000	0.80357	0.882000	0.50991	5.633000	0.67825	2.665000	0.90641	0.462000	0.41574	GCC	G|0.996;C|0.004	0.004	strong		0.383	EXD1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252553.2	NM_152596	
TCP10	6953	hgsc.bcm.edu	37	6	167786686	167786686	+	Missense_Mutation	SNP	C	C	T	rs140649985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167786686C>T	ENST00000397829.4	-	8	1119	c.952G>A	c.(952-954)Gct>Act	p.A318T	TCP10_ENST00000366827.2_Intron	NM_004610.3	NP_004601.3	Q12799	TCP10_HUMAN	t-complex 10	345						cytosol (GO:0005829)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(6)	18		Breast(66;1.53e-05)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;4.05e-20)|BRCA - Breast invasive adenocarcinoma(81;1.1e-06)|GBM - Glioblastoma multiforme(31;0.0386)		CTGGAGGGAGCGGCGTGCAGA	0.532																																					p.A318T		Atlas-SNP	.											.	TCP10	35	.	0			c.G952A						PASS	.	C	THR/ALA	5,3699		0,5,1847	86.0	91.0	89.0		952	-3.3	0.0	6	dbSNP_134	89	45,8151		0,45,4053	no	missense	TCP10	NM_004610.3	58	0,50,5900	TT,TC,CC		0.549,0.135,0.4202	probably-damaging	318/327	167786686	50,11850	1852	4098	5950	SO:0001583	missense	6953	exon8			AGGGAGCGGCGTG	U03399	CCDS43527.1	6q27	2012-09-20	2012-09-20		ENSG00000203690	ENSG00000203690			11656	protein-coding gene	gene with protein product		187020	"""t-complex 10 (a murine tcp homolog)"", ""t-complex 10 (mouse)"", ""t-complex 10 homolog (mouse)"""			8111376	Standard	NM_004610		Approved		uc003qvv.1	Q12799	OTTHUMG00000016026	ENST00000397829.4:c.952G>A	6.37:g.167786686C>T	ENSP00000380929:p.Ala318Thr	173.0	0.0	0		188.0	49.0	0.260638	NM_004610	Q5JR60|Q6P4F4	Missense_Mutation	SNP	ENST00000397829.4	37	CCDS43527.1	18	0.008241758241758242	2	0.0040650406504065045	1	0.0027624309392265192	5	0.008741258741258742	10	0.013192612137203167	c	13.11	2.137893	0.37728	0.00135	0.00549	ENSG00000203690	ENST00000397829	T	0.27890	1.64	1.64	-3.29	0.05017	.	.	.	.	.	T	0.03178	0.0093	N	0.14661	0.345	0.09310	N	0.999998	P	0.45126	0.851	B	0.24848	0.056	T	0.23547	-1.0185	9	0.87932	D	0	.	4.2044	0.10481	0.3777:0.3043:0.3179:0.0	.	345	Q12799	TCP10_HUMAN	T	318	ENSP00000380929:A318T	ENSP00000380929:A318T	A	-	1	0	TCP10	167706676	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.523000	0.06230	-1.547000	0.01715	0.467000	0.42956	GCT	C|0.994;T|0.006	0.006	strong		0.532	TCP10-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000365570.1	NM_004610	
SLC23A3	151295	hgsc.bcm.edu	37	2	220034377	220034377	+	Silent	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:220034377C>A	ENST00000409878.3	-	2	218	c.186G>T	c.(184-186)ctG>ctT	p.L62L	SLC23A3_ENST00000295738.7_Silent_p.L62L|SLC23A3_ENST00000455516.2_Silent_p.L62L|SLC23A3_ENST00000396775.3_Silent_p.L4L	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	62					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGACACAGAGCAGAGAAGCCA	0.532																																					p.L62L		Atlas-SNP	.											.	SLC23A3	60	.	0			c.G186T						PASS	.						57.0	76.0	69.0					2																	220034377		2091	4226	6317	SO:0001819	synonymous_variant	151295	exon2			ACAGAGCAGAGAA	BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901		"""Solute carriers"""	20601	protein-coding gene	gene with protein product							Standard	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.186G>T	2.37:g.220034377C>A		107.0	0.0	0		105.0	5.0	0.047619	NM_001144890	B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	37	CCDS46518.1																																																																																			.	.	none		0.532	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712	
NUAK2	81788	hgsc.bcm.edu	37	1	205273040	205273040	+	Silent	SNP	G	G	A	rs56069742	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:205273040G>A	ENST00000367157.3	-	7	1551	c.1425C>T	c.(1423-1425)ggC>ggT	p.G475G		NM_030952.1	NP_112214.1			NUAK family, SNF1-like kinase, 2											breast(3)|kidney(3)|large_intestine(4)|lung(4)|ovary(3)|prostate(3)|skin(1)|stomach(1)|urinary_tract(1)	23	Breast(84;0.186)		BRCA - Breast invasive adenocarcinoma(75;0.117)			CAAACACGTCGCCTGCGTCCA	0.582													G|||	11	0.00219649	0.0	0.0072	5008	,	,		16957	0.001		0.005	False		,,,				2504	0.0				p.G475G		Atlas-SNP	.											.	NUAK2	107	.	0			c.C1425T						PASS	.	G		12,4394	16.8+/-37.8	0,12,2191	35.0	34.0	34.0		1425	-9.7	0.0	1	dbSNP_129	34	132,8468	66.7+/-129.0	0,132,4168	no	coding-synonymous	NUAK2	NM_030952.1		0,144,6359	AA,AG,GG		1.5349,0.2724,1.1072		475/629	205273040	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	81788	exon7			CACGTCGCCTGCG	AK074830	CCDS1453.1	1q32.1	2008-02-05			ENSG00000163545	ENSG00000163545			29558	protein-coding gene	gene with protein product	"""SNF1/AMP activated protein kinase"""	608131				11230166	Standard	NM_030952		Approved	SNARK, FLJ90349	uc001hce.3	Q9H093	OTTHUMG00000037196	ENST00000367157.3:c.1425C>T	1.37:g.205273040G>A		134.0	0.0	0		116.0	59.0	0.508621	NM_030952		Silent	SNP	ENST00000367157.3	37	CCDS1453.1																																																																																			G|0.992;A|0.008	0.008	strong		0.582	NUAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090390.1	NM_030952	
SMIM3	85027	hgsc.bcm.edu	37	5	150175109	150175109	+	Missense_Mutation	SNP	C	C	T	rs61736140	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:150175109C>T	ENST00000526627.1	+	2	1145	c.107C>T	c.(106-108)tCg>tTg	p.S36L	AC010441.1_ENST00000600109.1_3'UTR	NM_032947.4	NP_116565.3	Q9BZL3	SMIM3_HUMAN	small integral membrane protein 3	36						integral component of membrane (GO:0016021)											ATCATGACCTCGTTGTTGCTG	0.547													C|||	10	0.00199681	0.0	0.0029	5008	,	,		22069	0.0		0.008	False		,,,				2504	0.0				p.S36L		Atlas-SNP	.											.	.	.	.	0			c.C107T						PASS	.																																			SO:0001583	missense	85027	exon2			TGACCTCGTTGTT	AF313413	CCDS47312.1, CCDS47312.2	5q33.1	2012-10-01	2012-10-01	2012-10-01	ENSG00000256235	ENSG00000256235			30248	protein-coding gene	gene with protein product		608324	"""chromosome 5 open reading frame 62"""	C5orf62		11288140	Standard	NM_032947		Approved	MSTP150, NID67	uc003lsw.3	Q9BZL3	OTTHUMG00000163646	ENST00000526627.1:c.107C>T	5.37:g.150175109C>T	ENSP00000436897:p.Ser36Leu	59.0	0.0	0		58.0	40.0	0.689655	NM_032947	Q3MIG3|Q6ZUV4	Missense_Mutation	SNP	ENST00000526627.1	37	CCDS47312.2	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	18.98	3.737622	0.69304	.	.	ENSG00000256235	ENST00000526627	.	.	.	5.11	5.11	0.69529	.	.	.	.	.	T	0.65554	0.2702	.	.	.	0.38915	D	0.957602	.	.	.	.	.	.	T	0.69514	-0.5125	4	.	.	.	.	16.8482	0.85986	0.0:1.0:0.0:0.0	rs61736140	.	.	.	L	36	.	.	S	+	2	0	C5orf62	150155302	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.723000	0.54955	2.768000	0.95171	0.491000	0.48974	TCG	C|0.996;T|0.004	0.004	strong		0.547	SMIM3-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374647.2	NM_032947	
CCDC146	57639	hgsc.bcm.edu	37	7	76891535	76891535	+	Nonsense_Mutation	SNP	C	C	T	rs371350411		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:76891535C>T	ENST00000285871.4	+	9	1211	c.1084C>T	c.(1084-1086)Cga>Tga	p.R362*	CCDC146_ENST00000431197.1_Nonsense_Mutation_p.R108*|CCDC146_ENST00000415740.2_3'UTR	NM_020879.2	NP_065930.2	Q8IYE0	CC146_HUMAN	coiled-coil domain containing 146	362										breast(3)|central_nervous_system(3)|endometrium(1)|kidney(4)|large_intestine(7)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(2)	34		all_cancers(73;0.128)|all_lung(88;0.0986)|all_epithelial(88;0.163)|Myeloproliferative disorder(862;0.205)				ACGAGATTTTCGAAATTTAAG	0.423																																					p.R362X		Atlas-SNP	.											CCDC146,NS,carcinoma,0,2	CCDC146	87	2	0			c.C1084T						PASS	.	C	stop/ARG	0,4406		0,0,2203	99.0	98.0	98.0		1084	4.8	1.0	7		98	1,8599	1.2+/-3.3	0,1,4299	no	stop-gained	CCDC146	NM_020879.2		0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		362/956	76891535	1,13005	2203	4300	6503	SO:0001587	stop_gained	57639	exon9			GATTTTCGAAATT	BC029458	CCDS34671.1	7q11.23	2011-09-07			ENSG00000135205	ENSG00000135205			29296	protein-coding gene	gene with protein product						10819331	Standard	NM_020879		Approved	KIAA1505	uc003uga.3	Q8IYE0	OTTHUMG00000162595	ENST00000285871.4:c.1084C>T	7.37:g.76891535C>T	ENSP00000285871:p.Arg362*	74.0	0.0	0		102.0	13.0	0.127451	NM_020879	A8K8X6|Q9P223	Nonsense_Mutation	SNP	ENST00000285871.4	37	CCDS34671.1	.	.	.	.	.	.	.	.	.	.	C	38	6.998870	0.97990	0.0	1.16E-4	ENSG00000135205	ENST00000285871;ENST00000431197	.	.	.	5.78	4.82	0.62117	.	0.207319	0.41823	D	0.000813	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.9971	13.1907	0.59709	0.2483:0.7517:0.0:0.0	.	.	.	.	X	362;108	.	ENSP00000285871:R362X	R	+	1	2	AC007000.1	76729471	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	1.811000	0.38942	2.744000	0.94065	0.563000	0.77884	CGA	.	.	weak		0.423	CCDC146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341449.1	NM_020879	
NLRP5	126206	hgsc.bcm.edu	37	19	56538723	56538723	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56538723C>T	ENST00000390649.3	+	7	1124	c.1124C>T	c.(1123-1125)aCa>aTa	p.T375I		NM_153447.4	NP_703148.4	P59047	NALP5_HUMAN	NLR family, pyrin domain containing 5	375	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cellular protein complex assembly (GO:0043623)|cellular protein localization (GO:0034613)|embryo implantation (GO:0007566)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|neuron death (GO:0070997)|organ morphogenesis (GO:0009887)|regulation of protein stability (GO:0031647)|regulation of RNA stability (GO:0043487)	apical cortex (GO:0045179)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|protein complex (GO:0043234)	ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|ovary(5)|skin(2)|stomach(4)|upper_aerodigestive_tract(2)	25		Colorectal(82;3.46e-05)|Ovarian(87;0.0481)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0326)		AACAATGACACAAAGCTCTGC	0.557																																					p.T375I		Atlas-SNP	.											.	NLRP5	217	.	0			c.C1124T						PASS	.						45.0	46.0	46.0					19																	56538723		2075	4215	6290	SO:0001583	missense	126206	exon7			ATGACACAAAGCT	AY154460	CCDS12938.1	19q13.43	2008-10-30	2006-12-08	2006-12-08	ENSG00000171487	ENSG00000171487		"""Nucleotide-binding domain and leucine rich repeat containing"""	21269	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 5"""	609658	"""NACHT, leucine rich repeat and PYD containing 5"""	NALP5		12563287, 11925379	Standard	NM_153447		Approved	PYPAF8, MATER, PAN11, CLR19.8	uc002qmj.3	P59047	OTTHUMG00000149887	ENST00000390649.3:c.1124C>T	19.37:g.56538723C>T	ENSP00000375063:p.Thr375Ile	57.0	0.0	0		48.0	11.0	0.229167	NM_153447	A8MTY4|Q86W29	Missense_Mutation	SNP	ENST00000390649.3	37	CCDS12938.1	.	.	.	.	.	.	.	.	.	.	C	3.198	-0.164275	0.06502	.	.	ENSG00000171487	ENST00000390649	T	0.73897	-0.79	3.35	-6.71	0.01760	NACHT nucleoside triphosphatase (1);	5.357820	0.00397	N	0.000045	T	0.50973	0.1647	N	0.17082	0.46	0.09310	N	1	B	0.15719	0.014	B	0.21708	0.036	T	0.44375	-0.9332	10	0.17832	T	0.49	.	0.8494	0.01169	0.2606:0.2256:0.11:0.4037	.	375	P59047	NALP5_HUMAN	I	375	ENSP00000375063:T375I	ENSP00000375063:T375I	T	+	2	0	NLRP5	61230535	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.527000	0.00441	-2.083000	0.00867	0.655000	0.94253	ACA	.	.	none		0.557	NLRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313735.1	NM_153447	
MUC17	140453	hgsc.bcm.edu	37	7	100696348	100696348	+	Silent	SNP	G	G	T	rs200413820		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:100696348G>T	ENST00000306151.4	+	10	13249	c.13185G>T	c.(13183-13185)gtG>gtT	p.V4395V		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	4395					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)					ACGGCCTCGTGGGGGCAGGGG	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		17902	0.0		0.001	False		,,,				2504	0.0				p.V4395V		Atlas-SNP	.											MUC17,right_lower_lobe,carcinoma,0,1	MUC17	804	1	0			c.G13185T						PASS	.						91.0	77.0	82.0					7																	100696348		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon10			CCTCGTGGGGGCA	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.13185G>T	7.37:g.100696348G>T		97.0	0.0	0		112.0	43.0	0.383929	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|1.000;T|0.000	0.000	strong		0.597	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
WWTR1	25937	hgsc.bcm.edu	37	3	149290781	149290781	+	Silent	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:149290781T>G	ENST00000465804.1	-	4	694	c.438A>C	c.(436-438)atA>atC	p.I146I	WWTR1_ENST00000360632.3_Silent_p.I146I|WWTR1_ENST00000467467.1_Silent_p.I146I	NM_001168278.1	NP_001161750.1	Q9GZV5	WWTR1_HUMAN	WW domain containing transcription regulator 1	146	WW. {ECO:0000255|PROSITE- ProRule:PRU00224}.				cilium morphogenesis (GO:0060271)|gene expression (GO:0010467)|glomerulus development (GO:0032835)|hippo signaling (GO:0035329)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catenin import into nucleus (GO:0035414)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|osteoblast differentiation (GO:0001649)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of metanephric nephron tubule epithelial cell differentiation (GO:0072307)|regulation of SMAD protein import into nucleus (GO:0060390)|regulation of transcription, DNA-templated (GO:0006355)|stem cell division (GO:0017145)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			breast(5)|cervix(1)|endometrium(2)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)	23			LUSC - Lung squamous cell carcinoma(72;0.0378)|Lung(72;0.048)			TGATTTTTTCTATGTGACTAA	0.388			T	CAMTA1	epitheliod hemangioendothelioma																																p.I146I		Atlas-SNP	.		Dom	yes		3	3q23-q24	607392	WW domain containing transcription regulator 1		M	.	WWTR1	42	.	0			c.A438C						PASS	.						125.0	118.0	120.0					3																	149290781		2203	4300	6503	SO:0001819	synonymous_variant	25937	exon4			TTTTTCTATGTGA	AK022036	CCDS3144.1	3q23-q24	2004-12-03			ENSG00000018408	ENSG00000018408			24042	protein-coding gene	gene with protein product		607392				11118213, 15096513	Standard	NM_015472		Approved	TAZ, DKFZp586I1419	uc021xfm.1	Q9GZV5	OTTHUMG00000159614	ENST00000465804.1:c.438A>C	3.37:g.149290781T>G		92.0	0.0	0		95.0	15.0	0.157895	NM_001168278	D3DNH7|Q8N3P2|Q9Y3W6	Silent	SNP	ENST00000465804.1	37	CCDS3144.1																																																																																			.	.	none		0.388	WWTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356498.1	NM_015472	
JMJD1C	221037	hgsc.bcm.edu	37	10	64927837	64927837	+	Missense_Mutation	SNP	C	C	T	rs71508957	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:64927837C>T	ENST00000399262.2	-	26	7809	c.7591G>A	c.(7591-7593)Gag>Aag	p.E2531K	JMJD1C_ENST00000399251.1_3'UTR|JMJD1C_ENST00000542921.1_Missense_Mutation_p.E2349K|JMJD1C_ENST00000402544.1_Missense_Mutation_p.E2294K	NM_032776.1	NP_116165.1	Q15652	JHD2C_HUMAN	jumonji domain containing 1C	2531					blood coagulation (GO:0007596)|chromatin modification (GO:0016568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleoplasm (GO:0005654)	dioxygenase activity (GO:0051213)|metal ion binding (GO:0046872)|thyroid hormone receptor binding (GO:0046966)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(8)|large_intestine(9)|lung(27)|ovary(6)|prostate(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(3)	77	Prostate(12;0.0119)|all_hematologic(501;0.191)					ACTTCATCCTCGTGTATCTTC	0.333													C|||	10	0.00199681	0.0008	0.0	5008	,	,		18116	0.0		0.004	False		,,,				2504	0.0051				p.E2531K		Atlas-SNP	.											.	JMJD1C	347	.	0			c.G7591A						PASS	.	C	LYS/GLU,LYS/GLU	6,3716		0,6,1855	181.0	163.0	169.0		6880,7591	5.4	1.0	10	dbSNP_130	169	82,8102		1,80,4011	yes	missense,missense	JMJD1C	NM_004241.2,NM_032776.1	56,56	1,86,5866	TT,TC,CC		1.002,0.1612,0.7391	probably-damaging,probably-damaging	2294/2304,2531/2541	64927837	88,11818	1861	4092	5953	SO:0001583	missense	221037	exon26			CATCCTCGTGTAT	L40411	CCDS41532.1, CCDS60538.1	10q22.1	2011-05-25	2004-03-31	2004-04-01	ENSG00000171988	ENSG00000171988			12313	protein-coding gene	gene with protein product		604503	"""thyroid hormone receptor interactor 8"""	TRIP8		7776974	Standard	XM_005269624		Approved	DKFZp761F0118, KIAA1380, FLJ14374	uc001jmn.3	Q15652	OTTHUMG00000018311	ENST00000399262.2:c.7591G>A	10.37:g.64927837C>T	ENSP00000382204:p.Glu2531Lys	102.0	0.0	0		112.0	45.0	0.401786	NM_032776	A0T124|Q5SQZ8|Q5SQZ9|Q5SR00|Q7Z3E7|Q8N3U0|Q96KB9|Q9P2G7	Missense_Mutation	SNP	ENST00000399262.2	37	CCDS41532.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.89	3.499039	0.64298	0.001612	0.01002	ENSG00000171988	ENST00000399262;ENST00000402544;ENST00000542921	T;T;T	0.67698	-0.28;-0.28;-0.28	5.42	5.42	0.78866	.	0.128349	0.53938	D	0.000055	T	0.62502	0.2433	L	0.34521	1.04	0.80722	D	1	D;B	0.69078	0.997;0.403	P;B	0.53450	0.726;0.17	T	0.70306	-0.4908	10	0.62326	D	0.03	-21.4168	19.2123	0.93760	0.0:1.0:0.0:0.0	.	2531;2349	Q15652;A0T124	JHD2C_HUMAN;.	K	2531;2294;2349	ENSP00000382204:E2531K;ENSP00000384990:E2294K;ENSP00000444682:E2349K	ENSP00000382204:E2531K	E	-	1	0	JMJD1C	64597843	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.593000	0.46180	2.528000	0.85240	0.591000	0.81541	GAG	C|0.998;T|0.002	0.002	strong		0.333	JMJD1C-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048249.2	NM_004241	
CEP250	11190	hgsc.bcm.edu	37	20	34092076	34092076	+	Missense_Mutation	SNP	G	G	A	rs56259282	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:34092076G>A	ENST00000397527.1	+	30	6599	c.5879G>A	c.(5878-5880)cGg>cAg	p.R1960Q	CEP250_ENST00000342580.4_Missense_Mutation_p.R1904Q	NM_007186.3	NP_009117.2	Q9BV73	CP250_HUMAN	centrosomal protein 250kDa	1960	Gln/Glu-rich.				centriole-centriole cohesion (GO:0010457)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|protein localization (GO:0008104)|protein localization to organelle (GO:0033365)|regulation of centriole-centriole cohesion (GO:0030997)	centriole (GO:0005814)|centrosome (GO:0005813)|cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)|spindle pole centrosome (GO:0031616)	protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(13)|lung(13)|ovary(4)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	45	Lung NSC(9;0.00156)|all_lung(11;0.00243)		BRCA - Breast invasive adenocarcinoma(18;0.0106)			GAGGCTGCCCGGGCCCGGGCT	0.657													G|||	24	0.00479233	0.0008	0.0115	5008	,	,		18767	0.0		0.0119	False		,,,				2504	0.0031				p.R1960Q		Atlas-SNP	.											.	CEP250	141	.	0			c.G5879A						PASS	.	G	GLN/ARG	9,4369		0,9,2180	9.0	11.0	10.0		5879	-4.0	0.0	20	dbSNP_129	10	103,8479		2,99,4190	yes	missense	CEP250	NM_007186.3	43	2,108,6370	AA,AG,GG		1.2002,0.2056,0.8642	benign	1960/2443	34092076	112,12848	2189	4291	6480	SO:0001583	missense	11190	exon30			CTGCCCGGGCCCG	AF022655	CCDS13255.1	20q11.22	2014-02-20	2006-01-11	2006-01-11	ENSG00000126001	ENSG00000126001			1859	protein-coding gene	gene with protein product		609689	"""centrosomal protein 2"""	CEP2		9506584, 9647649	Standard	NM_007186		Approved	C-NAP1	uc021wco.1	Q9BV73	OTTHUMG00000032343	ENST00000397527.1:c.5879G>A	20.37:g.34092076G>A	ENSP00000380661:p.Arg1960Gln	48.0	0.0	0		54.0	21.0	0.388889	NM_007186	E1P5Q3|O14812|O60588|Q9H450	Missense_Mutation	SNP	ENST00000397527.1	37	CCDS13255.1	15	0.006868131868131868	0	0.0	8	0.022099447513812154	0	0.0	7	0.009234828496042216	G	2.257	-0.370208	0.05069	0.002056	0.012002	ENSG00000126001	ENST00000397527;ENST00000342580;ENST00000422671	T;T;T	0.41065	3.05;3.04;1.01	4.95	-4.04	0.04010	.	1.940040	0.02640	N	0.105311	T	0.11836	0.0288	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.05550	-1.0878	10	0.12430	T	0.62	.	0.1713	0.00113	0.3233:0.1493:0.21:0.3175	rs56259282	1960	Q9BV73	CP250_HUMAN	Q	1960;1904;448	ENSP00000380661:R1960Q;ENSP00000341541:R1904Q;ENSP00000395992:R448Q	ENSP00000341541:R1904Q	R	+	2	0	CEP250	33555490	0.000000	0.05858	0.000000	0.03702	0.025000	0.11179	-0.281000	0.08456	-0.484000	0.06763	-0.733000	0.03571	CGG	G|0.993;A|0.007	0.007	strong		0.657	CEP250-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078877.7	NM_007186	
CYP2A13	1553	hgsc.bcm.edu	37	19	41600311	41600311	+	Missense_Mutation	SNP	A	A	C	rs115698903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41600311A>C	ENST00000330436.3	+	7	1135	c.1135A>C	c.(1135-1137)Aag>Cag	p.K379Q		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	379					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	CAAGGACACCAAGTTTCGGGA	0.567													a|||	83	0.0165735	0.0061	0.0	5008	,	,		19775	0.0069		0.008	False		,,,				2504	0.0613				p.K379Q		Atlas-SNP	.											CYP2A13,NS,carcinoma,-1,1	CYP2A13	90	1	0			c.A1135C						PASS	.	A	GLN/LYS	19,4387		0,19,2184	116.0	106.0	110.0		1135	2.2	1.0	19	dbSNP_132	110	46,8554		0,46,4254	yes	missense	CYP2A13	NM_000766.3	53	0,65,6438	CC,CA,AA		0.5349,0.4312,0.4998	benign	379/495	41600311	65,12941	2203	4300	6503	SO:0001583	missense	1553	exon7			GACACCAAGTTTC	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"""Cytochrome P450s"""	2608	protein-coding gene	gene with protein product		608055	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"""			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.1135A>C	19.37:g.41600311A>C	ENSP00000332679:p.Lys379Gln	229.0	0.0	0		213.0	108.0	0.507042	NM_000766	Q53YR8|Q6R569|Q6R570|Q9H2X2	Missense_Mutation	SNP	ENST00000330436.3	37	CCDS12571.1	12	0.005494505494505495	6	0.012195121951219513	0	0.0	1	0.0017482517482517483	5	0.006596306068601583	.	7.352	0.623028	0.14193	0.004312	0.005349	ENSG00000197838	ENST00000330436	T	0.70164	-0.46	4.36	2.18	0.27775	.	0.237828	0.34652	N	0.003790	T	0.35537	0.0935	N	0.17764	0.52	0.21652	N	0.99961	B	0.12630	0.006	B	0.12837	0.008	T	0.14476	-1.0471	10	0.30078	T	0.28	.	4.1933	0.10431	0.6726:0.0:0.1762:0.1512	.	379	Q16696	CP2AD_HUMAN	Q	379	ENSP00000332679:K379Q	ENSP00000332679:K379Q	K	+	1	0	CYP2A13	46292151	0.000000	0.05858	0.974000	0.42286	0.188000	0.23474	-0.232000	0.09055	0.193000	0.20303	0.397000	0.26171	AAG	A|0.995;C|0.005	0.005	strong		0.567	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766	
TPST2	8459	hgsc.bcm.edu	37	22	26937198	26937198	+	Silent	SNP	C	C	G	rs140525210	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:26937198C>G	ENST00000338754.4	-	3	669	c.399G>C	c.(397-399)ctG>ctC	p.L133L	TPST2_ENST00000403880.1_Silent_p.L133L|TPST2_ENST00000398110.2_Silent_p.L133L	NM_003595.3	NP_003586.3	O60704	TPST2_HUMAN	tyrosylprotein sulfotransferase 2	133					fusion of sperm to egg plasma membrane (GO:0007342)|peptidyl-tyrosine sulfation (GO:0006478)|prevention of polyspermy (GO:0060468)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	protein-tyrosine sulfotransferase activity (GO:0008476)			central_nervous_system(1)|large_intestine(1)|lung(5)	7						TGGCGGCGTCCAGCACCTCAT	0.662													C|||	32	0.00638978	0.0	0.0029	5008	,	,		14224	0.0		0.0189	False		,,,				2504	0.0112				p.L133L		Atlas-SNP	.											.	TPST2	23	.	0			c.G399C						PASS	.	C	,	20,4386	25.3+/-52.1	0,20,2183	43.0	34.0	37.0		399,399	3.2	1.0	22	dbSNP_134	37	182,8416	80.6+/-143.3	1,180,4118	no	coding-synonymous,coding-synonymous	TPST2	NM_001008566.1,NM_003595.3	,	1,200,6301	GG,GC,CC		2.1168,0.4539,1.5534	,	133/378,133/378	26937198	202,12802	2203	4299	6502	SO:0001819	synonymous_variant	8459	exon3			GGCGTCCAGCACC	AF049891	CCDS13839.1	22q12.1	2012-12-13			ENSG00000128294	ENSG00000128294	2.8.2.20	"""Sulfotransferases, membrane-bound"""	12021	protein-coding gene	gene with protein product	"""transport and golgi organization 13 homolog B (Drosophila)"""	603126				9736702, 9733778	Standard	NM_003595		Approved	TANGO13B	uc003acx.3	O60704	OTTHUMG00000150987	ENST00000338754.4:c.399G>C	22.37:g.26937198C>G		38.0	0.0	0		49.0	23.0	0.469388	NM_001008566	B3KQA7|Q6FI98|Q9H0V4	Silent	SNP	ENST00000338754.4	37	CCDS13839.1																																																																																			C|0.985;G|0.015	0.015	strong		0.662	TPST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320820.3	NM_003595	
LTA	4049	hgsc.bcm.edu	37	6	31541086	31541086	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31541086C>T	ENST00000454783.1	+	4	492	c.234C>T	c.(232-234)ctC>ctT	p.L78L	LTA_ENST00000418386.2_Silent_p.L78L|TNF_ENST00000449264.2_5'Flank	NM_001159740.2	NP_001153212.1	P01374	TNFB_HUMAN	lymphotoxin alpha	78					apoptotic process (GO:0006915)|cell-cell signaling (GO:0007267)|defense response to Gram-positive bacterium (GO:0050830)|humoral immune response (GO:0006959)|lymph node development (GO:0048535)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of growth of symbiont in host (GO:0044130)|positive regulation of apoptotic process (GO:0043065)|positive regulation of chronic inflammatory response to antigenic stimulus (GO:0002876)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of interferon-gamma production (GO:0032729)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|membrane (GO:0016020)	receptor binding (GO:0005102)			endometrium(2)|kidney(2)|lung(4)|upper_aerodigestive_tract(1)	9					Etanercept(DB00005)	ACTCACTGCTCTGGAGAGCAA	0.562																																					p.L78L		Atlas-SNP	.											.	LTA	18	.	0			c.C234T						PASS	.						73.0	63.0	67.0					6																	31541086		2203	4300	6503	SO:0001819	synonymous_variant	4049	exon4			ACTGCTCTGGAGA	X01393	CCDS4701.1	6p21.3	2013-05-22	2013-05-22		ENSG00000226979	ENSG00000226979		"""Tumor necrosis factor (ligand) superfamily"""	6709	protein-coding gene	gene with protein product	"""TNF superfamily member 1"""	153440	"""lymphotoxin alpha (TNF superfamily, member 1)"""	TNFB		2995927, 3001529	Standard	NM_001159740		Approved	TNFSF1, LT	uc011dnu.2	P01374	OTTHUMG00000031135	ENST00000454783.1:c.234C>T	6.37:g.31541086C>T		175.0	0.0	0		157.0	50.0	0.318471	NM_001159740	Q8N4C3|Q9UKS8	Silent	SNP	ENST00000454783.1	37	CCDS4701.1																																																																																			.	.	none		0.562	LTA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259097.1		
USP24	23358	hgsc.bcm.edu	37	1	55589175	55589175	+	Silent	SNP	C	C	T	rs145599916		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55589175C>T	ENST00000294383.6	-	36	4220	c.4221G>A	c.(4219-4221)gcG>gcA	p.A1407A	USP24_ENST00000407756.1_Silent_p.A1247A	NM_015306.2	NP_056121.2	Q9UPU5	UBP24_HUMAN	ubiquitin specific peptidase 24	1407					ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(4)|cervix(1)|endometrium(8)|kidney(13)|large_intestine(7)|lung(16)|ovary(6)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	60						AAGCCTCTCCCGCAATCAGCG	0.507													C|||	1	0.000199681	0.0	0.0	5008	,	,		17947	0.0		0.001	False		,,,				2504	0.0				p.A1407A		Atlas-SNP	.											.	USP24	323	.	0			c.G4221A						PASS	.	C		1,3863		0,1,1931	64.0	63.0	63.0		4221	-10.2	0.3	1	dbSNP_134	63	11,8251		0,11,4120	no	coding-synonymous	USP24	NM_015306.2		0,12,6051	TT,TC,CC		0.1331,0.0259,0.099		1407/2621	55589175	12,12114	1932	4131	6063	SO:0001819	synonymous_variant	23358	exon36			CTCTCCCGCAATC	AB028980	CCDS44154.1, CCDS44154.2	1p32.3	2008-04-11	2005-08-08		ENSG00000162402	ENSG00000162402		"""Ubiquitin-specific peptidases"""	12623	protein-coding gene	gene with protein product		610569	"""ubiquitin specific protease 24"""			12838346	Standard	NM_015306		Approved	KIAA1057	uc021onw.1	Q9UPU5	OTTHUMG00000008135	ENST00000294383.6:c.4221G>A	1.37:g.55589175C>T		124.0	0.0	0		124.0	50.0	0.403226	NM_015306	Q6ZSY2|Q8N2Y4|Q9NXD1	Silent	SNP	ENST00000294383.6	37	CCDS44154.2																																																																																			C|1.000;T|0.000	0.000	strong		0.507	USP24-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022275.2		
EHMT1	79813	hgsc.bcm.edu	37	9	140638534	140638534	+	Missense_Mutation	SNP	G	G	A	rs11137198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140638534G>A	ENST00000460843.1	+	6	1189	c.1162G>A	c.(1162-1164)Gcc>Acc	p.A388T	EHMT1_ENST00000334856.6_Missense_Mutation_p.A357T|EHMT1_ENST00000371394.2_3'UTR|EHMT1_ENST00000462484.1_Missense_Mutation_p.A388T	NM_024757.4	NP_079033.4	Q9H9B1	EHMT1_HUMAN	euchromatic histone-lysine N-methyltransferase 1	388			A -> T (in dbSNP:rs11137198).		chromatin modification (GO:0016568)|DNA methylation (GO:0006306)|embryo development (GO:0009790)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone methyltransferase activity (H3-K27 specific) (GO:0046976)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|histone-lysine N-methyltransferase activity (GO:0018024)|methyltransferase activity (GO:0008168)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	41	all_cancers(76;0.164)			OV - Ovarian serous cystadenocarcinoma(145;0.000183)|Epithelial(140;0.000728)		GGCTGATCGCGCCCAGAAGGT	0.567													G|||	34	0.00678914	0.0008	0.0058	5008	,	,		16838	0.0		0.0199	False		,,,				2504	0.0092				p.A388T		Atlas-SNP	.											.	EHMT1	196	.	0			c.G1162A						PASS	.	G	THR/ALA,THR/ALA	16,4390	23.3+/-48.9	0,16,2187	60.0	63.0	62.0		1162,1162	-0.3	0.0	9	dbSNP_120	62	187,8413	84.2+/-146.7	3,181,4116	yes	missense,missense	EHMT1	NM_001145527.1,NM_024757.4	58,58	3,197,6303	AA,AG,GG		2.1744,0.3631,1.5608	benign,benign	388/809,388/1299	140638534	203,12803	2203	4300	6503	SO:0001583	missense	79813	exon6			GATCGCGCCCAGA	AY083210	CCDS7050.1, CCDS7050.2, CCDS56595.1	9q34.3	2013-09-20			ENSG00000181090	ENSG00000181090	2.1.1.43	"""Chromatin-modifying enzymes / K-methyltransferases"", ""Ankyrin repeat domain containing"""	24650	protein-coding gene	gene with protein product		607001	"""euchromatic histone methyltransferase 1"""			11347906, 12004135	Standard	NM_024757		Approved	Eu-HMTase1, FLJ12879, KIAA1876, bA188C12.1, KMT1D	uc011mfc.2	Q9H9B1	OTTHUMG00000020995	ENST00000460843.1:c.1162G>A	9.37:g.140638534G>A	ENSP00000417980:p.Ala388Thr	40.0	0.0	0		50.0	31.0	0.62	NM_001145527	B1AQ58|B1AQ59|Q86X08|Q8TCN7|Q96F53|Q96JF1|Q96KH4	Missense_Mutation	SNP	ENST00000460843.1	37	CCDS7050.2	19	0.0086996336996337	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	17	0.022427440633245383	G	4.068	0.010439	0.07912	0.003631	0.021744	ENSG00000181090	ENST00000334856;ENST00000371400;ENST00000462484;ENST00000460843	T;T;T	0.69685	1.67;0.91;-0.42	5.25	-0.306	0.12780	.	0.794414	0.11854	N	0.523050	T	0.26304	0.0642	N	0.22421	0.69	0.09310	N	0.999992	B;B;B	0.14012	0.002;0.009;0.009	B;B;B	0.13407	0.001;0.009;0.009	T	0.14952	-1.0454	10	0.09084	T	0.74	.	4.0512	0.09796	0.3854:0.0:0.3682:0.2464	rs11137198;rs11137198	388;357;388	Q9H9B1;Q9H9B1-2;Q9H9B1-4	EHMT1_HUMAN;.;.	T	357;357;388;388	ENSP00000334476:A357T;ENSP00000417328:A388T;ENSP00000417980:A388T	ENSP00000334476:A357T	A	+	1	0	EHMT1	139758355	0.022000	0.18835	0.021000	0.16686	0.026000	0.11368	0.074000	0.14662	-0.417000	0.07461	-1.036000	0.02392	GCC	G|0.986;A|0.014	0.014	strong		0.567	EHMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055371.2	NM_024757	
C11orf40	143501	hgsc.bcm.edu	37	11	4594648	4594648	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:4594648C>G	ENST00000307616.1	-	2	195	c.196G>C	c.(196-198)Gat>Cat	p.D66H		NM_144663.1	NP_653264.1	Q8WZ69	CK040_HUMAN	chromosome 11 open reading frame 40	66										large_intestine(3)|lung(1)|ovary(2)|stomach(1)	7		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;4.28e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0288)|LUSC - Lung squamous cell carcinoma(625;0.192)		ATGAACACATCCTTATCTAAG	0.433																																					p.D66H		Atlas-SNP	.											C11orf40,NS,carcinoma,0,1	C11orf40	37	1	0			c.G196C						PASS	.						164.0	146.0	152.0					11																	4594648		2201	4298	6499	SO:0001583	missense	143501	exon2			ACACATCCTTATC		CCDS31354.1	11p15.5	2005-10-03			ENSG00000171987	ENSG00000171987			23986	protein-coding gene	gene with protein product							Standard	NM_144663		Approved	NOV1	uc010qyg.2	Q8WZ69	OTTHUMG00000165345	ENST00000307616.1:c.196G>C	11.37:g.4594648C>G	ENSP00000302918:p.Asp66His	154.0	0.0	0		150.0	78.0	0.52	NM_144663		Missense_Mutation	SNP	ENST00000307616.1	37	CCDS31354.1	.	.	.	.	.	.	.	.	.	.	C	5.540	0.284501	0.10513	.	.	ENSG00000171987	ENST00000307616	T	0.57107	0.42	1.49	-1.98	0.07480	.	.	.	.	.	T	0.30634	0.0771	N	0.08118	0	0.09310	N	1	D	0.58268	0.982	P	0.47603	0.551	T	0.17592	-1.0364	9	0.87932	D	0	.	1.9732	0.03410	0.2617:0.3567:0.0:0.3816	.	66	Q8WZ69	CK040_HUMAN	H	66	ENSP00000302918:D66H	ENSP00000302918:D66H	D	-	1	0	C11orf40	4551224	0.000000	0.05858	0.000000	0.03702	0.098000	0.18820	-1.399000	0.02506	-0.671000	0.05274	0.563000	0.77884	GAT	.	.	none		0.433	C11orf40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383529.1	NM_144663	
CECR6	27439	hgsc.bcm.edu	37	22	17600420	17600420	+	Missense_Mutation	SNP	C	C	A	rs184892903	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:17600420C>A	ENST00000331437.3	-	1	1723	c.1598G>T	c.(1597-1599)gGc>gTc	p.G533V	AC006946.15_ENST00000441544.1_5'Flank|CECR6_ENST00000399875.1_Missense_Mutation_p.G178V	NM_031890.3	NP_114096.1	Q9BXQ6	CECR6_HUMAN	cat eye syndrome chromosome region, candidate 6	533										haematopoietic_and_lymphoid_tissue(1)	1		all_epithelial(15;0.0181)|Lung NSC(13;0.109)|all_lung(157;0.132)		Colorectal(9;0.221)		AGCACCGTAGCCCCCTCTGGC	0.706													C|||	3	0.000599042	0.0008	0.0014	5008	,	,		11413	0.0		0.001	False		,,,				2504	0.0				p.G533V		Atlas-SNP	.											.	CECR6	11	.	0			c.G1598T						PASS	.	C	VAL/GLY,VAL/GLY	2,4254		0,2,2126	9.0	9.0	9.0		533,1598	3.2	0.3	22		9	20,8360		0,20,4170	no	missense,missense	CECR6	NM_001163079.1,NM_031890.3	109,109	0,22,6296	AA,AC,CC		0.2387,0.047,0.1741	probably-damaging,probably-damaging	178/224,533/579	17600420	22,12614	2128	4190	6318	SO:0001583	missense	27439	exon1			CCGTAGCCCCCTC	AF307451	CCDS13740.1, CCDS54494.1	22q11.2	2008-06-12			ENSG00000183307	ENSG00000183307			1844	protein-coding gene	gene with protein product						11381032	Standard	NM_031890		Approved		uc002zmb.2	Q9BXQ6	OTTHUMG00000030471	ENST00000331437.3:c.1598G>T	22.37:g.17600420C>A	ENSP00000329318:p.Gly533Val	26.0	0.0	0		15.0	11.0	0.733333	NM_031890	A8MYY1	Missense_Mutation	SNP	ENST00000331437.3	37	CCDS13740.1	.	.	.	.	.	.	.	.	.	.	C	10.37	1.331834	0.24167	4.7E-4	0.002387	ENSG00000183307	ENST00000399875;ENST00000331437	.	.	.	4.26	3.22	0.36961	.	0.421699	0.17930	U	0.157200	T	0.33059	0.0850	N	0.19112	0.55	0.34394	D	0.6945	P	0.37207	0.587	B	0.37989	0.262	T	0.50189	-0.8857	9	0.59425	D	0.04	.	10.2222	0.43203	0.0:0.7984:0.2016:0.0	.	533	Q9BXQ6	CECR6_HUMAN	V	178;533	.	ENSP00000329318:G533V	G	-	2	0	CECR6	15980420	0.943000	0.32029	0.307000	0.25127	0.185000	0.23345	2.249000	0.43169	1.119000	0.41883	0.561000	0.74099	GGC	.	.	weak		0.706	CECR6-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000075359.4	NM_031890	
USP26	83844	hgsc.bcm.edu	37	X	132161159	132161159	+	Missense_Mutation	SNP	G	G	A	rs35397110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:132161159G>A	ENST00000511190.1	-	6	1559	c.1090C>T	c.(1090-1092)Ctt>Ttt	p.L364F	USP26_ENST00000406273.1_Missense_Mutation_p.L364F|USP26_ENST00000370832.1_Missense_Mutation_p.L364F	NM_031907.1	NP_114113.1	Q9BXU7	UBP26_HUMAN	ubiquitin specific peptidase 26	364	USP.		L -> F (in dbSNP:rs35397110). {ECO:0000269|PubMed:15970005, ECO:0000269|PubMed:18377898, ECO:0000269|PubMed:18927127}.		protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)	nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)			breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(11)|liver(2)|lung(18)|ovary(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(3)	60	Acute lymphoblastic leukemia(192;0.000127)					GCCTTTTTAAGATTCAAGAGT	0.373													g|||	61	0.0161589	0.0038	0.0101	3775	,	,		13219	0.0		0.0457	False		,,,				2504	0.0031				p.L364F	NSCLC(104;342 1621 36940 47097 52632)	Atlas-SNP	.											.	USP26	135	.	0			c.C1090T	GRCh37	CM056721	USP26	M	rs35397110	PASS	.		PHE/LEU	34,3801		0,29,5,1603,566	64.0	63.0	63.0		1090	-4.0	0.0	X	dbSNP_126	63	421,6305		8,297,108,2122,1764	yes	missense	USP26	NM_031907.1	22	8,326,113,3725,2330	AA,AG,A,GG,G		6.2593,0.8866,4.3083	benign	364/914	132161159	455,10106	2203	4299	6502	SO:0001583	missense	83844	exon1			TTTTAAGATTCAA	AF285593	CCDS14635.1	Xq26.2	2012-07-13	2005-08-08		ENSG00000134588	ENSG00000134588	3.4.19.12	"""Ubiquitin-specific peptidases"""	13485	protein-coding gene	gene with protein product		300309	"""ubiquitin specific protease 26"""			12838346	Standard	NM_031907		Approved		uc011mvf.2	Q9BXU7	OTTHUMG00000022429	ENST00000511190.1:c.1090C>T	X.37:g.132161159G>A	ENSP00000423390:p.Leu364Phe	265.0	0.0	0		136.0	133.0	0.977941	NM_031907	B9WRT6|Q5H9H4	Missense_Mutation	SNP	ENST00000511190.1	37	CCDS14635.1	47	0.028330319469559977	1	0.0020325203252032522	4	0.0111731843575419	0	0.0	28	0.03814713896457766	g	9.121	1.009071	0.19199	0.008866	0.062593	ENSG00000134588	ENST00000370832;ENST00000511190;ENST00000406273	T;T;T	0.74526	-0.85;-0.85;-0.85	3.78	-4.02	0.04034	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.458295	0.16597	N	0.207518	T	0.05914	0.0154	N	0.05124	-0.11	0.80722	P	0.0	B	0.10296	0.003	B	0.12156	0.007	T	0.15122	-1.0448	9	0.11794	T	0.64	-4.0857	2.0978	0.03672	0.1422:0.1889:0.4345:0.2344	rs35397110;rs61751330	364	Q9BXU7	UBP26_HUMAN	F	364	ENSP00000359869:L364F;ENSP00000423390:L364F;ENSP00000384360:L364F	ENSP00000359869:L364F	L	-	1	0	USP26	131988825	0.086000	0.21541	0.001000	0.08648	0.015000	0.08874	0.254000	0.18314	-0.932000	0.03742	-0.432000	0.05891	CTT	G|0.963;A|0.037	0.037	strong		0.373	USP26-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359441.1	NM_031907	
CAPN15	6650	hgsc.bcm.edu	37	16	602430	602430	+	Silent	SNP	C	C	T	rs148358614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:602430C>T	ENST00000219611.2	+	11	3000	c.2637C>T	c.(2635-2637)ttC>ttT	p.F879F	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	879					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCAAGAAGTTCGTCAGCTGCG	0.701													t|||	29	0.00579073	0.0008	0.0014	5008	,	,		12936	0.005		0.002	False		,,,				2504	0.0204				p.F879F		Atlas-SNP	.											SOLH,NS,carcinoma,0,1	SOLH	47	1	0			c.C2637T						PASS	.	T		5,4343		0,5,2169	21.0	26.0	24.0		2637	-8.4	0.4	16	dbSNP_134	24	68,8490		0,68,4211	no	coding-synonymous	SOLH	NM_005632.2		0,73,6380	TT,TC,CC		0.7946,0.115,0.5656		879/1087	602430	73,12833	2174	4279	6453	SO:0001819	synonymous_variant	6650	exon11			GAAGTTCGTCAGC	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2637C>T	16.37:g.602430C>T		34.0	0.0	0		16.0	10.0	0.625	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Silent	SNP	ENST00000219611.2	37	CCDS10410.1																																																																																			C|0.995;T|0.005	0.005	strong		0.701	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
ZBTB3	79842	hgsc.bcm.edu	37	11	62519806	62519806	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62519806T>C	ENST00000394807.3	-	2	1606	c.1481A>G	c.(1480-1482)cAc>cGc	p.H494R		NM_024784.3	NP_079060.1	Q9H5J0	ZBTB3_HUMAN	zinc finger and BTB domain containing 3	494					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|liver(1)|lung(9)|ovary(2)|prostate(2)	24						CTCACGTGTGTGCACCGTGGC	0.572																																					p.H494R		Atlas-SNP	.											.	ZBTB3	47	.	0			c.A1481G						PASS	.						92.0	81.0	85.0					11																	62519806		2202	4299	6501	SO:0001583	missense	79842	exon2			CGTGTGTGCACCG	AK027045	CCDS8034.1	11q12.3	2013-01-09				ENSG00000185670		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	22918	protein-coding gene	gene with protein product							Standard	NM_024784		Approved	FLJ23392	uc001nuz.3	Q9H5J0		ENST00000394807.3:c.1481A>G	11.37:g.62519806T>C	ENSP00000378286:p.His494Arg	80.0	0.0	0		101.0	54.0	0.534653	NM_024784		Missense_Mutation	SNP	ENST00000394807.3	37	CCDS8034.1	.	.	.	.	.	.	.	.	.	.	T	18.58	3.654116	0.67472	.	.	ENSG00000185670	ENST00000394807	T	0.67523	-0.27	4.61	4.61	0.57282	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	M	0.89095	3.005	0.43777	D	0.996307	D	0.89917	1.0	D	0.91635	0.999	D	0.86175	0.1602	10	0.87932	D	0	.	11.9849	0.53142	0.0:0.0:0.0:1.0	.	494	Q9H5J0	ZBTB3_HUMAN	R	494	ENSP00000378286:H494R	ENSP00000378286:H494R	H	-	2	0	ZBTB3	62276382	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	7.698000	0.84413	1.724000	0.51502	0.459000	0.35465	CAC	.	.	none		0.572	ZBTB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395342.1	NM_024784	
SEMA3E	9723	hgsc.bcm.edu	37	7	82996931	82996931	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:82996931G>A	ENST00000307792.3	-	17	2766	c.2299C>T	c.(2299-2301)Cgc>Tgc	p.R767C	SEMA3E_ENST00000427262.1_Missense_Mutation_p.R707C	NM_012431.2	NP_036563.1	O15041	SEM3E_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3E	767	Arg/Lys-rich (basic).				axon guidance (GO:0007411)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell-matrix adhesion (GO:0001953)|patterning of blood vessels (GO:0001569)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of cell shape (GO:0008360)|semaphorin-plexin signaling pathway (GO:0071526)|sprouting angiogenesis (GO:0002040)|synapse organization (GO:0050808)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane (GO:0016020)	receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(19)|ovary(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)	51		Medulloblastoma(109;0.109)				CTGGGCAGGCGGTAATGCTCA	0.418																																					p.R767C		Atlas-SNP	.											.	SEMA3E	125	.	0			c.C2299T						PASS	.						172.0	172.0	172.0					7																	82996931		2203	4300	6503	SO:0001583	missense	9723	exon17			GCAGGCGGTAATG	AB002329	CCDS34674.1, CCDS55121.1	7q21.11	2013-01-11			ENSG00000170381	ENSG00000170381		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10727	protein-coding gene	gene with protein product	"""M-sema H"""	608166		SEMAH		9205841, 9515811	Standard	NM_012431		Approved	M-SemaK, KIAA0331, coll-5	uc003uhy.2	O15041	OTTHUMG00000154693	ENST00000307792.3:c.2299C>T	7.37:g.82996931G>A	ENSP00000303212:p.Arg767Cys	249.0	0.0	0		233.0	112.0	0.480687	NM_012431	B4E1P1|Q75M94|Q75M97	Missense_Mutation	SNP	ENST00000307792.3	37	CCDS34674.1	.	.	.	.	.	.	.	.	.	.	G	22.4	4.281561	0.80692	.	.	ENSG00000170381	ENST00000307792;ENST00000427262;ENST00000541514	T;T	0.36157	1.31;1.27	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.65396	0.2687	M	0.81802	2.56	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.68727	-0.5332	10	0.87932	D	0	.	19.7061	0.96072	0.0:0.0:1.0:0.0	.	767	O15041	SEM3E_HUMAN	C	767;707;758	ENSP00000303212:R767C;ENSP00000405052:R707C	ENSP00000303212:R767C	R	-	1	0	SEMA3E	82834867	1.000000	0.71417	0.986000	0.45419	0.664000	0.39144	4.641000	0.61375	2.660000	0.90430	0.585000	0.79938	CGC	.	.	none		0.418	SEMA3E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336606.1	NM_012431	
CAPN15	6650	hgsc.bcm.edu	37	16	602647	602647	+	Missense_Mutation	SNP	C	C	T	rs200960455	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:602647C>T	ENST00000219611.2	+	12	3143	c.2780C>T	c.(2779-2781)cCg>cTg	p.P927L	LA16c-366D1.3_ENST00000565879.1_RNA	NM_005632.2	NP_005623.1	O75808	CAN15_HUMAN	calpain 15	927					proteolysis (GO:0006508)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|peptidase activity (GO:0008233)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										TCCCCAGAGCCGCCGGGCCAC	0.711													c|||	4	0.000798722	0.0008	0.0	5008	,	,		10136	0.001		0.002	False		,,,				2504	0.0				p.P927L		Atlas-SNP	.											.	SOLH	47	.	0			c.C2780T						PASS	.	C	LEU/PRO	2,3806		0,2,1902	4.0	6.0	5.0		2780	4.7	0.6	16		5	19,7667		0,19,3824	yes	missense	SOLH	NM_005632.2	98	0,21,5726	TT,TC,CC		0.2472,0.0525,0.1827	benign	927/1087	602647	21,11473	1904	3843	5747	SO:0001583	missense	6650	exon12			CAGAGCCGCCGGG	U85647	CCDS10410.1	16p13.3	2013-06-27	2013-06-27	2013-06-27	ENSG00000103326	ENSG00000103326			11182	protein-coding gene	gene with protein product		603267	"""small optic lobes (Drosophila) homolog"", ""small optic lobes homolog (Drosophila)"""	SOLH		9722942	Standard	NM_005632		Approved		uc002chi.3	O75808	OTTHUMG00000119059	ENST00000219611.2:c.2780C>T	16.37:g.602647C>T	ENSP00000219611:p.Pro927Leu	37.0	0.0	0		20.0	9.0	0.45	NM_005632	B1B1M4|Q2KHS2|Q8WTY9|Q9BUW0	Missense_Mutation	SNP	ENST00000219611.2	37	CCDS10410.1	.	.	.	.	.	.	.	.	.	.	c	3.563	-0.089241	0.07097	5.25E-4	0.002472	ENSG00000103326	ENST00000219611	D	0.87887	-2.31	4.71	4.71	0.59529	.	0.247201	0.41938	D	0.000781	T	0.76800	0.4038	N	0.22421	0.69	0.44012	D	0.99672	B	0.30179	0.271	B	0.15870	0.014	T	0.73672	-0.3909	10	0.14656	T	0.56	.	16.7447	0.85469	0.0:1.0:0.0:0.0	.	927	O75808	CAN15_HUMAN	L	927	ENSP00000219611:P927L	ENSP00000219611:P927L	P	+	2	0	SOLH	542648	0.953000	0.32496	0.593000	0.28771	0.069000	0.16628	1.901000	0.39838	2.607000	0.88179	0.556000	0.70494	CCG	.	.	weak		0.711	CAPN15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239271.1	NM_005632	
CACNA1H	8912	hgsc.bcm.edu	37	16	1258033	1258033	+	Missense_Mutation	SNP	G	G	T	rs41292285	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1258033G>T	ENST00000348261.5	+	16	3423	c.3175G>T	c.(3175-3177)Gcc>Tcc	p.A1059S	CACNA1H_ENST00000358590.4_Missense_Mutation_p.A1059S|RP11-616M22.3_ENST00000564700.1_RNA|CACNA1H_ENST00000565831.1_Missense_Mutation_p.A1059S	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	1059					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	GTGTTCCCTGGCCGTGACCCC	0.647													G|||	17	0.00339457	0.0008	0.0086	5008	,	,		15928	0.0		0.007	False		,,,				2504	0.0031				p.A1059S		Atlas-SNP	.											.	CACNA1H	317	.	0			c.G3175T	GRCh37	CM076048	CACNA1H	M	rs41292285	PASS	.	G	SER/ALA,SER/ALA	10,4036		0,10,2013	24.0	31.0	29.0		3175,3175	3.0	0.7	16	dbSNP_127	29	83,8211		0,83,4064	yes	missense,missense	CACNA1H	NM_001005407.1,NM_021098.2	99,99	0,93,6077	TT,TG,GG		1.0007,0.2472,0.7536	probably-damaging,probably-damaging	1059/2348,1059/2354	1258033	93,12247	2023	4147	6170	SO:0001583	missense	8912	exon16			TCCCTGGCCGTGA	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.3175G>T	16.37:g.1258033G>T	ENSP00000334198:p.Ala1059Ser	121.0	0.0	0		125.0	64.0	0.512	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	14	0.00641025641025641	0	0.0	7	0.019337016574585635	0	0.0	7	0.009234828496042216	G	4.225	0.040710	0.08196	0.002472	0.010007	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.96491	-4.03;-3.98	4.01	3.02	0.34903	.	1.003600	0.08028	N	0.992969	D	0.88865	0.6553	L	0.44542	1.39	0.29001	N	0.887463	P;P	0.48089	0.675;0.905	B;B	0.40825	0.311;0.341	T	0.82293	-0.0529	10	0.20046	T	0.44	.	11.9499	0.52948	0.0:0.0:0.8251:0.1749	rs41292285;rs61406959	1059;1059	O95180-2;O95180	.;CAC1H_HUMAN	S	1059	ENSP00000334198:A1059S;ENSP00000351401:A1059S	ENSP00000334198:A1059S	A	+	1	0	CACNA1H	1198034	1.000000	0.71417	0.742000	0.31022	0.188000	0.23474	5.661000	0.68025	0.876000	0.35872	0.650000	0.86243	GCC	G|0.992;T|0.008	0.008	strong		0.647	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
OTUD7A	161725	hgsc.bcm.edu	37	15	31776837	31776837	+	Missense_Mutation	SNP	C	C	G	rs76704217	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:31776837C>G	ENST00000307050.4	-	11	1533	c.1441G>C	c.(1441-1443)Gtg>Ctg	p.V481L	OTUD7A_ENST00000382902.1_Missense_Mutation_p.V488L	NM_130901.1	NP_570971.1	Q8TE49	OTU7A_HUMAN	OTU deubiquitinase 7A	481					protein K11-linked deubiquitination (GO:0035871)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			endometrium(7)|large_intestine(4)|lung(11)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	30		all_lung(180;1.6e-09)		all cancers(64;2.44e-19)|Epithelial(43;6.82e-14)|GBM - Glioblastoma multiforme(186;1.49e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00189)|Lung(196;0.208)		TTGCTGCACACCGAATCGCGG	0.642													C|||	57	0.0113818	0.0015	0.0173	5008	,	,		19876	0.001		0.0378	False		,,,				2504	0.0041				p.V481L		Atlas-SNP	.											.	OTUD7A	89	.	0			c.G1441C						PASS	.	C	LEU/VAL	30,4354		0,30,2162	80.0	57.0	64.0		1441	2.4	1.0	15	dbSNP_131	64	415,8183		14,387,3898	yes	missense	OTUD7A	NM_130901.1	32	14,417,6060	GG,GC,CC		4.8267,0.6843,3.4278	benign	481/927	31776837	445,12537	2192	4299	6491	SO:0001583	missense	161725	exon11			TGCACACCGAATC	AJ430383	CCDS10026.1	15q13.1	2014-02-24	2014-02-24	2006-07-07	ENSG00000169918	ENSG00000169918		"""OTU domain containing"""	20718	protein-coding gene	gene with protein product		612024	"""chromosome 15 open reading frame 16"", ""OTU domain containing 7"", ""OTU domain containing 7A"""	C15orf16, OTUD7		23827681	Standard	NM_130901		Approved	CEZANNE2	uc001zfq.3	Q8TE49	OTTHUMG00000129275	ENST00000307050.4:c.1441G>C	15.37:g.31776837C>G	ENSP00000305926:p.Val481Leu	126.0	0.0	0		137.0	59.0	0.430657	NM_130901	Q8IWK5	Missense_Mutation	SNP	ENST00000307050.4	37	CCDS10026.1	45	0.020604395604395604	2	0.0040650406504065045	7	0.019337016574585635	1	0.0017482517482517483	35	0.04617414248021108	C	14.83	2.652700	0.47362	0.006843	0.048267	ENSG00000169918	ENST00000307050;ENST00000382902	T;T	0.34472	1.37;1.36	4.35	2.4	0.29515	.	0.175056	0.50627	D	0.000102	T	0.06005	0.0156	M	0.69823	2.125	0.28750	N	0.90147	B;B	0.12013	0.005;0.003	B;B	0.13407	0.009;0.004	T	0.12656	-1.0539	10	0.51188	T	0.08	-32.5726	3.9645	0.09424	0.0:0.5203:0.2199:0.2599	.	488;481	Q8TE49-2;Q8TE49	.;OTU7A_HUMAN	L	481;488	ENSP00000305926:V481L;ENSP00000372358:V488L	ENSP00000305926:V481L	V	-	1	0	OTUD7A	29564129	1.000000	0.71417	0.994000	0.49952	0.995000	0.86356	2.060000	0.41394	0.936000	0.37367	0.655000	0.94253	GTG	C|0.970;G|0.030	0.030	strong		0.642	OTUD7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251393.2	NM_130901	
SUOX	6821	hgsc.bcm.edu	37	12	56397802	56397802	+	Missense_Mutation	SNP	C	C	T	rs141735896	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:56397802C>T	ENST00000394109.3	+	3	1353	c.629C>T	c.(628-630)cCc>cTc	p.P210L	SUOX_ENST00000551841.2_Intron|SUOX_ENST00000356124.4_Missense_Mutation_p.P210L|SUOX_ENST00000266971.3_Missense_Mutation_p.P210L|SUOX_ENST00000394115.2_Missense_Mutation_p.P210L|SUOX_ENST00000548274.1_Missense_Mutation_p.P210L			P51687	SUOX_HUMAN	sulfite oxidase	210	Moco domain. {ECO:0000250}.				cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)|sulfide oxidation, using sulfide:quinone oxidoreductase (GO:0070221)|sulfur amino acid catabolic process (GO:0000098)|sulfur amino acid metabolic process (GO:0000096)	mitochondrial matrix (GO:0005759)	electron carrier activity (GO:0009055)|heme binding (GO:0020037)|molybdenum ion binding (GO:0030151)|molybdopterin cofactor binding (GO:0043546)|sulfite oxidase activity (GO:0008482)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(6)	15			UCEC - Uterine corpus endometrioid carcinoma (6;0.0471)|OV - Ovarian serous cystadenocarcinoma(18;0.119)			TACATCACACCCAACCCTATC	0.552													C|||	9	0.00179712	0.0	0.0101	5008	,	,		20235	0.0		0.002	False		,,,				2504	0.0				p.P210L		Atlas-SNP	.											.	SUOX	33	.	0			c.C629T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO	5,4401	9.9+/-24.2	0,5,2198	114.0	106.0	109.0		629,629,629	5.1	1.0	12	dbSNP_134	109	31,8569	21.6+/-65.8	0,31,4269	yes	missense,missense,missense	SUOX	NM_000456.2,NM_001032386.1,NM_001032387.1	98,98,98	0,36,6467	TT,TC,CC		0.3605,0.1135,0.2768	probably-damaging,probably-damaging,probably-damaging	210/546,210/546,210/546	56397802	36,12970	2203	4300	6503	SO:0001583	missense	6821	exon6			TCACACCCAACCC	BC065193	CCDS8901.2	12q13.13	2011-02-10			ENSG00000139531	ENSG00000139531	1.8.3.1		11460	protein-coding gene	gene with protein product		606887				7599189	Standard	XM_005269112		Approved		uc001siz.3	P51687	OTTHUMG00000128503	ENST00000394109.3:c.629C>T	12.37:g.56397802C>T	ENSP00000377668:p.Pro210Leu	263.0	0.0	0		270.0	131.0	0.485185	NM_000456		Missense_Mutation	SNP	ENST00000394109.3	37	CCDS8901.2	9	0.004120879120879121	0	0.0	6	0.016574585635359115	0	0.0	3	0.00395778364116095	C	23.2	4.384135	0.82792	0.001135	0.003605	ENSG00000139531	ENST00000356124;ENST00000266971;ENST00000394115;ENST00000548274;ENST00000394109	D;D;D;D;D	0.96041	-3.89;-3.89;-3.89;-3.89;-3.89	5.12	5.12	0.69794	Oxidoreductase, molybdopterin-binding domain (2);	0.000000	0.85682	D	0.000000	D	0.96185	0.8756	M	0.92317	3.295	0.80722	D	1	D	0.63880	0.993	P	0.60117	0.869	D	0.94083	0.7346	10	0.72032	D	0.01	-26.2213	17.8714	0.88812	0.0:1.0:0.0:0.0	.	210	P51687	SUOX_HUMAN	L	210	ENSP00000348440:P210L;ENSP00000266971:P210L;ENSP00000377674:P210L;ENSP00000450245:P210L;ENSP00000377668:P210L	ENSP00000266971:P210L	P	+	2	0	SUOX	54684069	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	6.994000	0.76251	2.837000	0.97791	0.591000	0.81541	CCC	C|0.997;T|0.003	0.003	strong		0.552	SUOX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250309.1	NM_000456	
PTPN1	5770	hgsc.bcm.edu	37	20	49195749	49195749	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:49195749G>A	ENST00000371621.3	+	7	921	c.747G>A	c.(745-747)gtG>gtA	p.V249V	RP4-530I15.9_ENST00000431019.1_RNA|PTPN1_ENST00000541713.1_Silent_p.V176V	NM_001278618.1|NM_002827.2	NP_001265547.1|NP_002818.1	P18031	PTN1_HUMAN	protein tyrosine phosphatase, non-receptor type 1	249	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				actin cytoskeleton reorganization (GO:0031532)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|endoplasmic reticulum unfolded protein response (GO:0030968)|insulin receptor signaling pathway (GO:0008286)|interferon-gamma-mediated signaling pathway (GO:0060333)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|peptidyl-tyrosine dephosphorylation (GO:0035335)|peptidyl-tyrosine dephosphorylation involved in inactivation of protein kinase activity (GO:1990264)|platelet activation (GO:0030168)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)|regulation of endocytosis (GO:0030100)|regulation of hepatocyte growth factor receptor signaling pathway (GO:1902202)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of signal transduction (GO:0009966)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|sorting endosome (GO:0097443)	enzyme binding (GO:0019899)|ephrin receptor binding (GO:0046875)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)|receptor tyrosine kinase binding (GO:0030971)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|skin(2)	16		Lung NSC(126;0.163)			Tiludronate(DB01133)	TCAAGAAAGTGCTGTTAGAAA	0.493																																					p.V249V		Atlas-SNP	.											.	PTPN1	36	.	0			c.G747A						PASS	.						148.0	149.0	148.0					20																	49195749		2203	4300	6503	SO:0001819	synonymous_variant	5770	exon7			GAAAGTGCTGTTA		CCDS13430.1, CCDS63309.1	20q13.1-q13.2	2011-06-09			ENSG00000196396	ENSG00000196396		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9642	protein-coding gene	gene with protein product		176885		PTP1B		2164224	Standard	NM_002827		Approved		uc002xvl.3	P18031	OTTHUMG00000032729	ENST00000371621.3:c.747G>A	20.37:g.49195749G>A		58.0	0.0	0		72.0	24.0	0.333333	NM_002827	Q5TGD8|Q9BQV9|Q9NQQ4	Silent	SNP	ENST00000371621.3	37	CCDS13430.1																																																																																			.	.	none		0.493	PTPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079694.2		
TMTC2	160335	hgsc.bcm.edu	37	12	83290083	83290083	+	Missense_Mutation	SNP	G	G	A	rs35725509	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:83290083G>A	ENST00000321196.3	+	3	1848	c.1141G>A	c.(1141-1143)Gta>Ata	p.V381I	TMTC2_ENST00000549919.1_Missense_Mutation_p.V375I|TMTC2_ENST00000548305.1_Missense_Mutation_p.V381I	NM_152588.1	NP_689801.1	Q8N394	TMTC2_HUMAN	transmembrane and tetratricopeptide repeat containing 2	381					calcium ion homeostasis (GO:0055074)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(7)|lung(13)|ovary(2)|skin(1)|urinary_tract(1)	39						TAAAAACGATGTATCACAGAG	0.408													G|||	58	0.0115815	0.0	0.0072	5008	,	,		20195	0.0		0.0089	False		,,,				2504	0.045				p.V381I		Atlas-SNP	.											.	TMTC2	100	.	0			c.G1141A						PASS	.	G	ILE/VAL	5,4401	11.4+/-27.6	0,5,2198	172.0	167.0	169.0		1141	5.0	0.0	12	dbSNP_126	169	66,8534	40.3+/-97.0	0,66,4234	yes	missense	TMTC2	NM_152588.1	29	0,71,6432	AA,AG,GG		0.7674,0.1135,0.5459	benign	381/837	83290083	71,12935	2203	4300	6503	SO:0001583	missense	160335	exon3			AACGATGTATCAC	AK074634	CCDS9025.1	12q21.31	2014-06-09			ENSG00000179104	ENSG00000179104		"""Tetratricopeptide (TTC) repeat domain containing"""	25440	protein-coding gene	gene with protein product		615856				24764305	Standard	NM_152588		Approved	DKFZp762A217	uc001szt.3	Q8N394	OTTHUMG00000169736	ENST00000321196.3:c.1141G>A	12.37:g.83290083G>A	ENSP00000322300:p.Val381Ile	121.0	0.0	0		107.0	43.0	0.401869	NM_152588	B2RCU7|Q8N2K8	Missense_Mutation	SNP	ENST00000321196.3	37	CCDS9025.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	0.548	-0.850759	0.02651	0.001135	0.007674	ENSG00000179104	ENST00000321196;ENST00000548305;ENST00000549919;ENST00000546590	T;T;T	0.61274	0.77;0.12;0.67	5.86	4.98	0.66077	.	1.043000	0.07418	N	0.893502	T	0.27419	0.0673	N	0.08118	0	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.26538	-1.0100	10	0.12766	T	0.61	-0.0418	6.9111	0.24335	0.1418:0.0:0.7159:0.1423	rs35725509	381;136;381	Q8N394;F8VRQ2;F8VSH2	TMTC2_HUMAN;.;.	I	381;381;375;136	ENSP00000322300:V381I;ENSP00000448292:V381I;ENSP00000447609:V375I	ENSP00000322300:V381I	V	+	1	0	TMTC2	81814214	0.028000	0.19301	0.014000	0.15608	0.171000	0.22731	1.832000	0.39151	1.494000	0.48533	-0.142000	0.14014	GTA	G|0.994;A|0.006	0.006	strong		0.408	TMTC2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405663.1	NM_152588	
CAPN5	726	hgsc.bcm.edu	37	11	76796082	76796082	+	Silent	SNP	G	G	A	rs368891933		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:76796082G>A	ENST00000278559.3	+	2	339	c.150G>A	c.(148-150)agG>agA	p.R50R	CAPN5_ENST00000456580.2_Silent_p.R50R|CAPN5_ENST00000531028.1_Splice_Site|CAPN5_ENST00000529629.1_Silent_p.R50R	NM_004055.4	NP_004046.2	O15484	CAN5_HUMAN	calpain 5	50	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				proteolysis (GO:0006508)|signal transduction (GO:0007165)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			NS(1)|breast(2)|endometrium(2)|large_intestine(7)|lung(17)|urinary_tract(1)	30						CCGCCGTCAGGTGGAAGCGAC	0.692																																					p.R50R		Atlas-SNP	.											.	CAPN5	67	.	0			c.G150A						PASS	.	G		0,4396		0,0,2198	21.0	24.0	23.0		150	3.0	0.9	11		23	1,8583		0,1,4291	no	coding-synonymous	CAPN5	NM_004055.4		0,1,6489	AA,AG,GG		0.0116,0.0,0.0077		50/641	76796082	1,12979	2198	4292	6490	SO:0001819	synonymous_variant	726	exon2			CGTCAGGTGGAAG		CCDS8248.1	11q14	2014-01-29				ENSG00000149260			1482	protein-coding gene	gene with protein product		602537	"""vitreoretinopathy, neovascular inflammatory"""	VRNI		9503024, 9367857, 23055945	Standard	NM_004055		Approved	nCL-3, HTRA3, ADNIV	uc001oxx.3	O15484		ENST00000278559.3:c.150G>A	11.37:g.76796082G>A		69.0	0.0	0		63.0	40.0	0.634921	NM_004055	O00263	Silent	SNP	ENST00000278559.3	37	CCDS8248.1																																																																																			.	.	weak		0.692	CAPN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382564.2	NM_004055	
PTPRZ1	5803	hgsc.bcm.edu	37	7	121698871	121698871	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:121698871A>C	ENST00000393386.2	+	28	6957	c.6546A>C	c.(6544-6546)gaA>gaC	p.E2182D	PTPRZ1_ENST00000449182.1_Missense_Mutation_p.E1315D	NM_001206838.1|NM_002851.2	NP_001193767.1|NP_002842.2	P23471	PTPRZ_HUMAN	protein tyrosine phosphatase, receptor-type, Z polypeptide 1	2182	Tyrosine-protein phosphatase 2. {ECO:0000255|PROSITE-ProRule:PRU00160}.				axonogenesis (GO:0007409)|central nervous system development (GO:0007417)|hematopoietic progenitor cell differentiation (GO:0002244)|learning or memory (GO:0007611)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of oligodendrocyte progenitor proliferation (GO:0070445)	integral component of plasma membrane (GO:0005887)|perineuronal net (GO:0072534)|proteinaceous extracellular matrix (GO:0005578)	protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(3)|central_nervous_system(4)|cervix(1)|endometrium(4)|kidney(12)|large_intestine(17)|liver(1)|lung(42)|ovary(4)|prostate(5)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	106						ATGTACTTGAAGTGAGGCACT	0.358																																					p.E2182D		Atlas-SNP	.											PTPRZ1_ENST00000393386,NS,carcinoma,0,2	PTPRZ1	605	2	0			c.A6546C						PASS	.						104.0	103.0	103.0					7																	121698871		2203	4300	6503	SO:0001583	missense	5803	exon28			ACTTGAAGTGAGG	M93426	CCDS34740.1, CCDS56505.1	7q31.3	2013-02-11			ENSG00000106278	ENSG00000106278		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9685	protein-coding gene	gene with protein product		176891		PTPZ, PTPRZ		7736789, 8387522	Standard	NM_001206838		Approved	PTP18, RPTPB, phosphacan	uc003vjy.3	P23471	OTTHUMG00000157057	ENST00000393386.2:c.6546A>C	7.37:g.121698871A>C	ENSP00000377047:p.Glu2182Asp	80.0	0.0	0		87.0	8.0	0.091954	NM_002851	A4D0W5|C9JFM0|O76043|Q9UDR6	Missense_Mutation	SNP	ENST00000393386.2	37	CCDS34740.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.758217	0.69763	.	.	ENSG00000106278	ENST00000393386;ENST00000449182	D;D	0.84146	-1.81;-1.81	6.07	6.07	0.98685	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	D	0.90960	0.7158	M	0.76938	2.355	0.52501	D	0.999957	B;B;P	0.47191	0.38;0.236;0.891	B;B;P	0.55667	0.229;0.173;0.781	D	0.91729	0.5395	10	0.72032	D	0.01	.	16.6406	0.85098	1.0:0.0:0.0:0.0	.	1321;1315;2182	P23471-2;C9JFM0;P23471	.;.;PTPRZ_HUMAN	D	2182;1315	ENSP00000377047:E2182D;ENSP00000410000:E1315D	ENSP00000377047:E2182D	E	+	3	2	PTPRZ1	121486107	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.621000	0.54210	2.326000	0.78906	0.533000	0.62120	GAA	.	.	none		0.358	PTPRZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347288.1	NM_002851	
DNAH8	1769	hgsc.bcm.edu	37	6	38903421	38903421	+	Silent	SNP	G	G	A	rs61748646	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38903421G>A	ENST00000359357.3	+	75	11114	c.10860G>A	c.(10858-10860)cgG>cgA	p.R3620R	RP1-207H1.3_ENST00000416948.1_RNA|DNAH8_ENST00000449981.2_Silent_p.R3837R|RP1-207H1.3_ENST00000453417.1_RNA|DNAH8_ENST00000441566.1_Silent_p.R3584R			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	3620	AAA 5. {ECO:0000250}.				cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						TTAATAAGCGGAAGATGAAAG	0.308													G|||	59	0.0117812	0.003	0.0144	5008	,	,		17584	0.006		0.0328	False		,,,				2504	0.0061				p.R3837R		Atlas-SNP	.											.	DNAH8	1239	.	0			c.G11511A						PASS	.	G		23,4383	29.9+/-59.1	0,23,2180	159.0	178.0	172.0		11511	5.1	1.0	6	dbSNP_129	172	286,8310	104.6+/-165.6	4,278,4016	no	coding-synonymous	DNAH8	NM_001206927.1		4,301,6196	AA,AG,GG		3.3271,0.522,2.3766		3837/4708	38903421	309,12693	2203	4298	6501	SO:0001819	synonymous_variant	1769	exon77			TAAGCGGAAGATG	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.10860G>A	6.37:g.38903421G>A		40.0	0.0	0		44.0	23.0	0.522727	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				G|0.980;A|0.020	0.020	strong		0.308	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
HIPK4	147746	hgsc.bcm.edu	37	19	40886987	40886987	+	Missense_Mutation	SNP	G	G	T	rs79330270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:40886987G>T	ENST00000291823.2	-	3	1195	c.911C>A	c.(910-912)aCc>aAc	p.T304N		NM_144685.3	NP_653286.2	Q8NE63	HIPK4_HUMAN	homeodomain interacting protein kinase 4	304	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				histone phosphorylation (GO:0016572)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|regulation of signal transduction by p53 class mediator (GO:1901796)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(5)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	20			Lung(22;4.95e-05)|LUSC - Lung squamous cell carcinoma(20;0.000292)			GTCAGGGAAGGTTAGCCGACT	0.612													G|||	10	0.00199681	0.0	0.0043	5008	,	,		19961	0.0		0.006	False		,,,				2504	0.001				p.T304N		Atlas-SNP	.											.	HIPK4	100	.	0			c.C911A						PASS	.	G	ASN/THR	13,4391		0,13,2189	44.0	40.0	41.0		911	-2.1	1.0	19	dbSNP_131	41	76,8522		0,76,4223	yes	missense	HIPK4	NM_144685.3	65	0,89,6412	TT,TG,GG		0.8839,0.2952,0.6845	benign	304/617	40886987	89,12913	2202	4299	6501	SO:0001583	missense	147746	exon3			GGGAAGGTTAGCC	BC034501	CCDS12555.1	19q13.2	2008-02-05				ENSG00000160396			19007	protein-coding gene	gene with protein product		611712					Standard	NM_144685		Approved	FLJ32818	uc002onp.3	Q8NE63		ENST00000291823.2:c.911C>A	19.37:g.40886987G>T	ENSP00000291823:p.Thr304Asn	67.0	0.0	0		58.0	33.0	0.568965	NM_144685	A8K863|Q96M54	Missense_Mutation	SNP	ENST00000291823.2	37	CCDS12555.1	.	.	.	.	.	.	.	.	.	.	G	2.504	-0.314455	0.05422	0.002952	0.008839	ENSG00000160396	ENST00000291823;ENST00000452139	T	0.20200	2.09	5.67	-2.14	0.07123	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.892967	0.09630	N	0.776416	T	0.03564	0.0102	N	0.01140	-0.99	0.25057	N	0.9911	B	0.06786	0.001	B	0.09377	0.004	T	0.41770	-0.9490	10	0.10902	T	0.67	.	5.9158	0.19053	0.0701:0.4725:0.2585:0.1989	.	304	Q8NE63	HIPK4_HUMAN	N	304;269	ENSP00000291823:T304N	ENSP00000291823:T304N	T	-	2	0	HIPK4	45578827	0.005000	0.15991	0.958000	0.39756	0.028000	0.11728	0.266000	0.18534	-0.454000	0.07066	-1.140000	0.01884	ACC	A|0.001;G|0.993;T|0.006	0.006	strong		0.612	HIPK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462593.1	NM_144685	
KRTAP1-1	81851	hgsc.bcm.edu	37	17	39197485	39197485	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:39197485A>G	ENST00000306271.4	-	1	228	c.165T>C	c.(163-165)tgT>tgC	p.C55C		NM_030967.2	NP_112229.1	Q07627	KRA11_HUMAN	keratin associated protein 1-1	55			Missing (in allele KAP1.7). {ECO:0000269|PubMed:11841537}.|PSCSTSGTCGSSCCQPSCCETSSCQPRCCETSCCQPSCCQT SFCGFP -> R (in allele KAP1.6).			keratin filament (GO:0045095)				NS(2)|endometrium(2)|kidney(5)|lung(4)|prostate(1)	14		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TAGGAAATCCACAGAAGCTGG	0.602																																					p.C55C		Atlas-SNP	.											.	KRTAP1-1	23	.	0			c.T165C						PASS	.						83.0	92.0	89.0					17																	39197485		2026	4210	6236	SO:0001819	synonymous_variant	81851	exon1			AAATCCACAGAAG	AJ406926	CCDS42324.1	17q21.2	2014-06-05			ENSG00000188581	ENSG00000188581		"""Keratin associated proteins"""	16772	protein-coding gene	gene with protein product		608819				11279113	Standard	NM_030967		Approved	KAP1.1B, HB2A, KAP1.1, KAP1.1A	uc002hvw.1	Q07627	OTTHUMG00000133592	ENST00000306271.4:c.165T>C	17.37:g.39197485A>G		180.0	0.0	0		196.0	24.0	0.122449	NM_030967	A6NC32|Q96S60|Q96S67	Silent	SNP	ENST00000306271.4	37	CCDS42324.1																																																																																			.	.	none		0.602	KRTAP1-1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257696.1	NM_030967	
C15orf27	123591	hgsc.bcm.edu	37	15	76494569	76494569	+	Missense_Mutation	SNP	A	A	G	rs62030189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:76494569A>G	ENST00000388942.3	+	10	1261	c.985A>G	c.(985-987)Agc>Ggc	p.S329G		NM_152335.2	NP_689548.2	Q2M3C6	CO027_HUMAN	chromosome 15 open reading frame 27	329					calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|membrane depolarization during action potential (GO:0086010)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	voltage-gated calcium channel activity (GO:0005245)			endometrium(1)|large_intestine(1)|lung(10)|pancreas(1)	13						CGACATGAACAGCTACATCAG	0.522													A|||	3	0.000599042	0.0	0.0	5008	,	,		21160	0.0		0.003	False		,,,				2504	0.0				p.S329G		Atlas-SNP	.											.	C15orf27	32	.	0			c.A985G						PASS	.	A	GLY/SER	4,4390	9.9+/-24.2	0,4,2193	191.0	141.0	158.0		985	3.3	1.0	15	dbSNP_129	158	47,8541	30.1+/-81.4	0,47,4247	yes	missense	C15orf27	NM_152335.2	56	0,51,6440	GG,GA,AA		0.5473,0.091,0.3929	benign	329/532	76494569	51,12931	2197	4294	6491	SO:0001583	missense	123591	exon10			ATGAACAGCTACA	AK095509	CCDS10289.2	15q23-q24.1	2012-09-27			ENSG00000169758	ENSG00000169758			26763	protein-coding gene	gene with protein product						14702039, 22020278	Standard	NM_152335		Approved	FLJ38190	uc002bbq.3	Q2M3C6	OTTHUMG00000142918	ENST00000388942.3:c.985A>G	15.37:g.76494569A>G	ENSP00000373594:p.Ser329Gly	140.0	0.0	0		151.0	80.0	0.529801	NM_152335	Q8N993|Q96LL5	Missense_Mutation	SNP	ENST00000388942.3	37	CCDS10289.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	A	14.79	2.640347	0.47153	9.1E-4	0.005473	ENSG00000169758	ENST00000388942	T	0.33865	1.39	4.48	3.31	0.37934	.	0.148543	0.64402	D	0.000016	T	0.19846	0.0477	L	0.40543	1.245	0.32431	N	0.548089	B;B	0.33171	0.4;0.03	B;B	0.30855	0.121;0.037	T	0.26087	-1.0113	10	0.44086	T	0.13	-11.903	9.2607	0.37610	0.8177:0.1823:0.0:0.0	rs62030189	293;329	Q2M3C6-2;Q2M3C6	.;CO027_HUMAN	G	329	ENSP00000373594:S329G	ENSP00000373594:S329G	S	+	1	0	C15orf27	74281624	1.000000	0.71417	1.000000	0.80357	0.915000	0.54546	6.533000	0.73829	0.630000	0.30394	0.379000	0.24179	AGC	A|0.996;G|0.004	0.004	strong		0.522	C15orf27-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000286637.2	NM_152335	
CEBPZ	10153	hgsc.bcm.edu	37	2	37455232	37455232	+	Silent	SNP	C	C	A	rs35414551	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:37455232C>A	ENST00000234170.5	-	2	1249	c.1104G>T	c.(1102-1104)gtG>gtT	p.V368V		NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	368					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|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)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				GCTCATGAGCCACGGTAAGGG	0.423													C|||	19	0.00379393	0.0023	0.0029	5008	,	,		20686	0.0		0.0139	False		,,,				2504	0.0				p.V368V		Atlas-SNP	.											.	CEBPZ	68	.	0			c.G1104T						PASS	.	C		23,4383	29.9+/-59.1	0,23,2180	91.0	98.0	95.0		1104	-1.6	0.1	2	dbSNP_126	95	164,8436	77.5+/-140.1	1,162,4137	no	coding-synonymous	CEBPZ	NM_005760.2		1,185,6317	AA,AC,CC		1.907,0.522,1.4378		368/1055	37455232	187,12819	2203	4300	6503	SO:0001819	synonymous_variant	10153	exon2			ATGAGCCACGGTA	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.1104G>T	2.37:g.37455232C>A		135.0	0.0	0		158.0	78.0	0.493671	NM_005760	Q8NE75	Silent	SNP	ENST00000234170.5	37	CCDS1787.1																																																																																			C|0.989;A|0.011	0.011	strong		0.423	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
MAPKAPK2	9261	hgsc.bcm.edu	37	1	206905040	206905040	+	Silent	SNP	C	C	T	rs34526867	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:206905040C>T	ENST00000367103.3	+	8	1141	c.948C>T	c.(946-948)atC>atT	p.I316I	MAPKAPK2_ENST00000479009.1_3'UTR|MAPKAPK2_ENST00000294981.4_Silent_p.I316I	NM_004759.4|NM_032960.3	NP_004750.1|NP_116584.2	P49137	MAPK2_HUMAN	mitogen-activated protein kinase-activated protein kinase 2	316	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				3'-UTR-mediated mRNA stabilization (GO:0070935)|activation of MAPK activity (GO:0000187)|arachidonic acid metabolic process (GO:0019369)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|G2 DNA damage checkpoint (GO:0031572)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|leukotriene metabolic process (GO:0006691)|macropinocytosis (GO:0044351)|MAPK cascade (GO:0000165)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-serine phosphorylation (GO:0018105)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of interleukin-6 production (GO:0032675)|regulation of tumor necrosis factor production (GO:0032680)|response to cytokine (GO:0034097)|response to lipopolysaccharide (GO:0032496)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	19	Breast(84;0.183)		BRCA - Breast invasive adenocarcinoma(75;0.211)			GAATGACCATCACCGAGTTTA	0.562													C|||	204	0.0407348	0.1248	0.0288	5008	,	,		18568	0.0		0.0149	False		,,,				2504	0.0041				p.I316I		Atlas-SNP	.											.	MAPKAPK2	45	.	0			c.C948T						PASS	.	C	,	516,3890	237.7+/-249.4	28,460,1715	135.0	133.0	134.0		948,948	5.1	1.0	1	dbSNP_126	134	111,8489	59.1+/-120.7	0,111,4189	no	coding-synonymous,coding-synonymous	MAPKAPK2	NM_004759.4,NM_032960.3	,	28,571,5904	TT,TC,CC		1.2907,11.7113,4.8209	,	316/371,316/401	206905040	627,12379	2203	4300	6503	SO:0001819	synonymous_variant	9261	exon8			GACCATCACCGAG	U12779	CCDS1466.1, CCDS31001.1	1q32	2008-02-05			ENSG00000162889	ENSG00000162889			6887	protein-coding gene	gene with protein product		602006				8179591, 8280084	Standard	NM_004759		Approved		uc001hem.2	P49137	OTTHUMG00000036342	ENST00000367103.3:c.948C>T	1.37:g.206905040C>T		182.0	0.0	0		212.0	107.0	0.504717	NM_004759	Q5SY30|Q5SY41|Q8IYD6	Silent	SNP	ENST00000367103.3	37	CCDS31001.1																																																																																			C|0.956;T|0.044	0.044	strong		0.562	MAPKAPK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088465.1	NM_004759	
DNAH8	1769	hgsc.bcm.edu	37	6	38805753	38805753	+	Silent	SNP	G	G	A	rs45622336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:38805753G>A	ENST00000359357.3	+	31	4004	c.3750G>A	c.(3748-3750)acG>acA	p.T1250T	DNAH8_ENST00000449981.2_Silent_p.T1467T|DNAH8_ENST00000441566.1_Silent_p.T1250T			Q96JB1	DYH8_HUMAN	dynein, axonemal, heavy chain 8	1250					cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	axonemal dynein complex (GO:0005858)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(7)|breast(9)|central_nervous_system(4)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(3)|kidney(16)|large_intestine(44)|liver(4)|lung(101)|ovary(7)|pancreas(2)|prostate(8)|skin(28)|stomach(4)|upper_aerodigestive_tract(6)|urinary_tract(4)	260						AATTTGTTACGTATTCATCTG	0.313													A|||	11	0.00219649	0.0023	0.0	5008	,	,		17985	0.0		0.007	False		,,,				2504	0.001				p.T1467T		Atlas-SNP	.											DNAH8_ENST00000359357,head_neck,malignant_melanoma,+1,2	DNAH8	1239	2	0			c.G4401A						PASS	.	A		10,4396	824.8+/-416.5	0,10,2193	169.0	154.0	159.0		4401	-9.2	0.6	6	dbSNP_127	159	76,8524	815.6+/-407.0	1,74,4225	no	coding-synonymous	DNAH8	NM_001206927.1		1,84,6418	AA,AG,GG		0.8837,0.227,0.6612		1467/4708	38805753	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	1769	exon33			TGTTACGTATTCA	Z83806	CCDS75447.1	6p21.2	2012-04-19	2006-09-04		ENSG00000124721	ENSG00000124721		"""Axonemal dyneins"""	2952	protein-coding gene	gene with protein product		603337	"""dynein, axonemal, heavy polypeptide 8"""			9373155	Standard	NM_001206927		Approved	hdhc9	uc021yzh.1	Q96JB1	OTTHUMG00000016253	ENST00000359357.3:c.3750G>A	6.37:g.38805753G>A		123.0	0.0	0		173.0	95.0	0.549133	NM_001206927	O00438|Q5JYI2|Q5T2M3|Q5T2M4|Q5TG00|Q9UEM4	Silent	SNP	ENST00000359357.3	37																																																																																				G|0.995;A|0.005	0.005	strong		0.313	DNAH8-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000043574.1	NM_001206927	
NARS2	79731	hgsc.bcm.edu	37	11	78189653	78189653	+	Missense_Mutation	SNP	T	T	C	rs116930926	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:78189653T>C	ENST00000281038.5	-	8	1274	c.899A>G	c.(898-900)aAa>aGa	p.K300R	NARS2_ENST00000528850.1_Missense_Mutation_p.K73R	NM_001243251.1|NM_024678.5	NP_001230180.1|NP_078954.4	Q96I59	SYNM_HUMAN	asparaginyl-tRNA synthetase 2, mitochondrial (putative)	300					asparaginyl-tRNA aminoacylation (GO:0006421)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	mitochondrion (GO:0005739)	asparagine-tRNA ligase activity (GO:0004816)|ATP binding (GO:0005524)|nucleic acid binding (GO:0003676)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(9)|ovary(2)|prostate(2)|skin(1)	27	all_cancers(14;2.63e-17)|all_epithelial(13;1.85e-19)				L-Asparagine(DB00174)	TGCTATGAATTTGTGACAGAG	0.313													T|||	29	0.00579073	0.0038	0.0043	5008	,	,		15374	0.0		0.0199	False		,,,				2504	0.001				p.K300R		Atlas-SNP	.											.	NARS2	62	.	0			c.A899G						PASS	.	T	ARG/LYS	26,4374	31.7+/-61.6	0,26,2174	118.0	112.0	114.0		899	0.6	0.8	11	dbSNP_132	114	240,8344	96.1+/-157.9	2,236,4054	yes	missense	NARS2	NM_024678.5	26	2,262,6228	CC,CT,TT		2.7959,0.5909,2.0487	benign	300/478	78189653	266,12718	2200	4292	6492	SO:0001583	missense	79731	exon8			ATGAATTTGTGAC	BC007800	CCDS8261.1, CCDS58164.1	11q14.1	2011-07-01	2007-02-23		ENSG00000137513	ENSG00000137513	6.1.1.22	"""Aminoacyl tRNA synthetases / Class II"""	26274	protein-coding gene	gene with protein product	"""asparagine tRNA ligase 2, mitochondrial (putative)"""	612803				15779907	Standard	NM_024678		Approved	FLJ23441, SLM5	uc001ozi.3	Q96I59	OTTHUMG00000166702	ENST00000281038.5:c.899A>G	11.37:g.78189653T>C	ENSP00000281038:p.Lys300Arg	150.0	0.0	0		166.0	71.0	0.427711	NM_024678	G3V178	Missense_Mutation	SNP	ENST00000281038.5	37	CCDS8261.1	20	0.009157509157509158	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	T	13.75	2.329174	0.41197	0.005909	0.027959	ENSG00000137513	ENST00000281038;ENST00000528850	T;T	0.77489	-1.1;0.92	5.38	0.559	0.17272	Aminoacyl-tRNA synthetase, class II (1);Aminoacyl-tRNA synthetase, class II (D/K/N) (1);	0.174888	0.64402	N	0.000011	T	0.41166	0.1147	L	0.37630	1.12	0.38330	D	0.943783	B	0.20459	0.045	B	0.23716	0.048	T	0.50996	-0.8761	10	0.62326	D	0.03	-6.9707	7.4242	0.27090	0.0:0.3544:0.0:0.6456	.	300	Q96I59	SYNM_HUMAN	R	300;73	ENSP00000281038:K300R;ENSP00000432635:K73R	ENSP00000281038:K300R	K	-	2	0	NARS2	77867301	0.997000	0.39634	0.798000	0.32154	0.997000	0.91878	1.180000	0.32005	-0.058000	0.13177	0.528000	0.53228	AAA	T|0.984;C|0.016	0.016	strong		0.313	NARS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391138.2	NM_024678	
DISP2	85455	hgsc.bcm.edu	37	15	40660043	40660043	+	Missense_Mutation	SNP	G	G	T	rs76331864	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:40660043G>T	ENST00000267889.3	+	8	1817	c.1730G>T	c.(1729-1731)gGg>gTg	p.G577V	RP11-64K12.4_ENST00000558421.1_RNA	NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	577	SSD. {ECO:0000255|PROSITE- ProRule:PRU00199}.				smoothened signaling pathway (GO:0007224)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(12)|ovary(4)	30		all_cancers(109;9.35e-19)|all_epithelial(112;1.18e-15)|Lung NSC(122;2.45e-11)|all_lung(180;6.47e-10)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;3.39e-06)|Colorectal(105;0.0114)|READ - Rectum adenocarcinoma(2;0.0649)|BRCA - Breast invasive adenocarcinoma(123;0.0798)|Lung(196;0.15)|LUAD - Lung adenocarcinoma(183;0.247)		CCGTCGGGGGGGCTGGCGCAG	0.667													G|||	93	0.0185703	0.0469	0.0144	5008	,	,		13554	0.002		0.0159	False		,,,				2504	0.0031				p.G577V		Atlas-SNP	.											.	DISP2	86	.	0			c.G1730T						PASS	.	G	VAL/GLY	178,4228	105.2+/-143.6	4,170,2029	23.0	23.0	23.0		1730	4.7	1.0	15	dbSNP_131	23	113,8487	52.7+/-113.3	1,111,4188	yes	missense	DISP2	NM_033510.1	109	5,281,6217	TT,TG,GG		1.314,4.0399,2.2374	benign	577/1402	40660043	291,12715	2203	4300	6503	SO:0001583	missense	85455	exon8			CGGGGGGGCTGGC	AB051529	CCDS10056.1	15q14	2004-01-15			ENSG00000140323	ENSG00000140323			19712	protein-coding gene	gene with protein product		607503				11214970, 10619433	Standard	NM_033510		Approved	DISPB, KIAA1742, HsT16908	uc001zlk.1	A7MBM2	OTTHUMG00000129983	ENST00000267889.3:c.1730G>T	15.37:g.40660043G>T	ENSP00000267889:p.Gly577Val	22.0	0.0	0		22.0	10.0	0.454545	NM_033510	Q6AHW3|Q9C0C1	Missense_Mutation	SNP	ENST00000267889.3	37	CCDS10056.1	46	0.021062271062271064	27	0.054878048780487805	10	0.027624309392265192	0	0.0	9	0.011873350923482849	G	13.16	2.155343	0.38021	0.040399	0.01314	ENSG00000140323	ENST00000267889	D	0.95377	-3.69	5.58	4.66	0.58398	Sterol-sensing domain (1);	0.166012	0.53938	D	0.000060	T	0.75882	0.3910	L	0.48362	1.52	0.80722	D	1	P	0.45715	0.865	B	0.42555	0.391	T	0.81671	-0.0827	10	0.31617	T	0.26	-15.0114	14.6339	0.68676	0.0703:0.0:0.9297:0.0	.	577	A7MBM2	DISP2_HUMAN	V	577	ENSP00000267889:G577V	ENSP00000267889:G577V	G	+	2	0	DISP2	38447335	1.000000	0.71417	0.998000	0.56505	0.741000	0.42261	5.783000	0.68982	1.357000	0.45904	0.561000	0.74099	GGG	G|0.977;T|0.023	0.023	strong		0.667	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
COBLL1	22837	hgsc.bcm.edu	37	2	165578602	165578602	+	Missense_Mutation	SNP	C	C	T	rs74459242	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:165578602C>T	ENST00000392717.2	-	7	1097	c.1093G>A	c.(1093-1095)Gtg>Atg	p.V365M	COBLL1_ENST00000342193.4_Missense_Mutation_p.V327M|COBLL1_ENST00000375458.2_Missense_Mutation_p.V327M|COBLL1_ENST00000409184.3_Missense_Mutation_p.V365M|COBLL1_ENST00000194871.6_Missense_Mutation_p.V393M|COBLL1_ENST00000491126.2_Intron			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	365						extracellular vesicular exosome (GO:0070062)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(12)|liver(1)|lung(12)|ovary(3)|pancreas(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	47						GTCTCATCCACGCTCATGGAT	0.458													C|||	63	0.0125799	0.0023	0.0202	5008	,	,		16844	0.0		0.0368	False		,,,				2504	0.0092				p.V327M		Atlas-SNP	.											.	COBLL1	122	.	0			c.G979A						PASS	.	C	MET/VAL	34,4372	40.0+/-72.8	0,34,2169	77.0	83.0	81.0		979	1.4	0.5	2	dbSNP_132	81	421,8179	130.5+/-188.4	13,395,3892	yes	missense	COBLL1	NM_014900.3	21	13,429,6061	TT,TC,CC		4.8953,0.7717,3.4984	probably-damaging	327/1167	165578602	455,12551	2203	4300	6503	SO:0001583	missense	22837	exon6			CATCCACGCTCAT	AB023194	CCDS2223.2, CCDS63045.1	2q24.3	2012-12-07	2012-12-07		ENSG00000082438	ENSG00000082438			23571	protein-coding gene	gene with protein product		610318	"""COBL-like 1"""				Standard	NM_001278458		Approved	KIAA0977	uc002ucp.3	Q53SF7	OTTHUMG00000074019	ENST00000392717.2:c.1093G>A	2.37:g.165578602C>T	ENSP00000376478:p.Val365Met	130.0	0.0	0		130.0	71.0	0.546154	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Missense_Mutation	SNP	ENST00000392717.2	37		41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.89	2.073757	0.36566	0.007717	0.048953	ENSG00000082438	ENST00000375458;ENST00000342193;ENST00000409184;ENST00000392717;ENST00000194871	D	0.93076	-3.16	6.17	1.37	0.22104	Cordon-bleu domain (1);	0.602245	0.17823	N	0.160815	T	0.75428	0.3848	L	0.47716	1.5	0.21553	N	0.999649	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.74023	0.982;0.982;0.968	T	0.76080	-0.3090	10	0.52906	T	0.07	-0.5122	2.5206	0.04679	0.1029:0.3543:0.2961:0.2466	.	365;393;365	Q53SF7;B7Z2P5;Q53SF7-2	COBL1_HUMAN;.;.	M	327;327;365;365;393	ENSP00000194871:V393M	ENSP00000194871:V393M	V	-	1	0	COBLL1	165286848	0.099000	0.21834	0.503000	0.27626	0.406000	0.30931	0.134000	0.15932	0.180000	0.19960	0.655000	0.94253	GTG	C|0.971;T|0.029	0.029	strong		0.458	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
EDNRA	1909	hgsc.bcm.edu	37	4	148461071	148461071	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:148461071G>A	ENST00000324300.5	+	6	1518	c.1003G>A	c.(1003-1005)Gag>Aag	p.E335K	EDNRA_ENST00000339690.5_3'UTR|EDNRA_ENST00000358556.4_Missense_Mutation_p.E226K|EDNRA_ENST00000503721.1_3'UTR|EDNRA_ENST00000506066.1_Missense_Mutation_p.E226K|EDNRA_ENST00000511804.1_Missense_Mutation_p.E110K	NM_001957.3	NP_001948.1	P25101	EDNRA_HUMAN	endothelin receptor type A	335					activation of adenylate cyclase activity (GO:0007190)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|artery smooth muscle contraction (GO:0014824)|cell proliferation (GO:0008283)|cellular response to mechanical stimulus (GO:0071260)|endothelin receptor signaling pathway (GO:0086100)|enteric nervous system development (GO:0048484)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|glomerular filtration (GO:0003094)|glucose transport (GO:0015758)|head development (GO:0060322)|heart development (GO:0007507)|histamine secretion (GO:0001821)|in utero embryonic development (GO:0001701)|maternal process involved in parturition (GO:0060137)|metabolic process (GO:0008152)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP biosynthetic process (GO:0030818)|neural crest cell development (GO:0014032)|patterning of blood vessels (GO:0001569)|penile erection (GO:0043084)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of inflammatory response (GO:0050729)|positive regulation of kidney development (GO:0090184)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of odontogenesis (GO:0042482)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of blood pressure (GO:0008217)|regulation of epithelial cell proliferation (GO:0050678)|respiratory gaseous exchange (GO:0007585)|response to hypoxia (GO:0001666)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|Rho protein signal transduction (GO:0007266)|sensory perception of pain (GO:0019233)|signal transduction (GO:0007165)|smooth muscle cell proliferation (GO:0048659)|smooth muscle contraction (GO:0006939)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|nuclear membrane (GO:0031965)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)	endothelin receptor activity (GO:0004962)|phosphatidylinositol phospholipase C activity (GO:0004435)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(4)|large_intestine(4)|lung(3)|ovary(1)	17	all_hematologic(180;0.151)			GBM - Glioblastoma multiforme(119;0.154)	Acetylsalicylic acid(DB00945)|Bosentan(DB00559)|MACITENTAN(DB08932)|Sitaxentan(DB06268)	TGTGTATAACGAGATGGACAA	0.348																																					p.E335K		Atlas-SNP	.											EDNRA,NS,carcinoma,-1,2	EDNRA	48	2	0			c.G1003A						PASS	.						183.0	182.0	182.0					4																	148461071		2203	4300	6503	SO:0001583	missense	1909	exon6			TATAACGAGATGG	D90348	CCDS3769.1, CCDS54810.1, CCDS58927.1	4q31.22	2013-09-20			ENSG00000151617	ENSG00000151617		"""GPCR / Class A : Endothelin receptors"""	3179	protein-coding gene	gene with protein product		131243				1659806	Standard	NM_001957		Approved		uc003iky.3	P25101	OTTHUMG00000161354	ENST00000324300.5:c.1003G>A	4.37:g.148461071G>A	ENSP00000315011:p.Glu335Lys	155.0	0.0	0		174.0	30.0	0.172414	NM_001957	B2R723|B4E2V6|B7Z9G6|D3DP03|E7ER36|O43441|Q16432|Q16433|Q8TBH2	Missense_Mutation	SNP	ENST00000324300.5	37	CCDS3769.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333880	0.81801	.	.	ENSG00000151617	ENST00000358556;ENST00000324300;ENST00000511804;ENST00000506066	T;T;T;T	0.71817	-0.6;-0.6;-0.6;-0.6	5.44	4.59	0.56863	GPCR, rhodopsin-like superfamily (1);	0.197416	0.53938	D	0.000053	T	0.78246	0.4253	M	0.74258	2.255	0.80722	D	1	P;D	0.57899	0.951;0.981	B;P	0.51055	0.24;0.657	T	0.81680	-0.0823	10	0.59425	D	0.04	-18.8044	16.5127	0.84290	0.0:0.131:0.869:0.0	.	226;335	P25101-4;P25101	.;EDNRA_HUMAN	K	226;335;110;226	ENSP00000351359:E226K;ENSP00000315011:E335K;ENSP00000425354:E110K;ENSP00000425281:E226K	ENSP00000315011:E335K	E	+	1	0	EDNRA	148680521	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	3.186000	0.50942	1.409000	0.46915	0.650000	0.86243	GAG	.	.	none		0.348	EDNRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364635.1		
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497986	32497986	+	Missense_Mutation	SNP	G	G	A	rs200744795		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:32497986G>A	ENST00000374975.3	-	1	78	c.16C>T	c.(16-18)Ctc>Ttc	p.L6F		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CCTCCAGGGAGCTTCAGACAC	0.577																																					p.L6F		Atlas-SNP	.											HLA-DRB5,rectum,carcinoma,0,1	HLA-DRB5	31	1	0			c.C16T						scavenged	.						55.0	61.0	59.0					6																	32497986		2203	4296	6499	SO:0001583	missense	3127	exon1			CAGGGAGCTTCAG		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.16C>T	6.37:g.32497986G>A	ENSP00000364114:p.Leu6Phe	62.0	2.0	0.0322581		209.0	13.0	0.062201	NM_002125		Missense_Mutation	SNP	ENST00000374975.3	37	CCDS4751.1	.	.	.	.	.	.	.	.	.	.	.	4.629	0.117010	0.08881	.	.	ENSG00000198502	ENST00000374975	T	0.00281	8.32	4.42	-2.83	0.05769	MHC classes I/II-like antigen recognition protein (1);	.	.	.	.	T	0.00039	0.0001	L	0.27975	0.815	0.09310	N	1	B	0.06786	0.001	B	0.12156	0.007	T	0.28808	-1.0032	9	0.06891	T	0.86	.	5.2478	0.15506	0.2872:0.0:0.5657:0.1472	rs1059548;rs2308658;rs3200252;rs16822997	6	Q30154	DRB5_HUMAN	F	6	ENSP00000364114:L6F	ENSP00000364114:L6F	L	-	1	0	HLA-DRB5	32605964	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.163000	0.09997	-0.229000	0.09854	-0.350000	0.07774	CTC	.	.	weak		0.577	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
MFN2	9927	hgsc.bcm.edu	37	1	12061598	12061598	+	Silent	SNP	C	C	T	rs41278632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:12061598C>T	ENST00000235329.5	+	9	1279	c.957C>T	c.(955-957)ggC>ggT	p.G319G	MFN2_ENST00000444836.1_Silent_p.G319G	NM_014874.3	NP_055689.1	O95140	MFN2_HUMAN	mitofusin 2	319	Dynamin-type G.				apoptotic process (GO:0006915)|autophagy (GO:0006914)|blastocyst formation (GO:0001825)|blood coagulation (GO:0007596)|camera-type eye morphogenesis (GO:0048593)|mitochondrial fusion (GO:0008053)|mitochondrial membrane organization (GO:0007006)|mitochondrion localization (GO:0051646)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of smooth muscle cell proliferation (GO:0048662)|protein localization to pre-autophagosomal structure (GO:0034497)|protein targeting to mitochondrion (GO:0006626)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intrinsic component of mitochondrial outer membrane (GO:0031306)|microtubule cytoskeleton (GO:0015630)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|ubiquitin protein ligase binding (GO:0031625)			endometrium(4)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|ovary(1)|pancreas(1)|prostate(2)|skin(2)	20	Ovarian(185;0.249)	Lung NSC(185;8.69e-05)|all_lung(284;9.87e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Ovarian(437;0.00965)|Hepatocellular(190;0.0202)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;7.25e-06)|COAD - Colon adenocarcinoma(227;0.000302)|BRCA - Breast invasive adenocarcinoma(304;0.000329)|Kidney(185;0.000896)|KIRC - Kidney renal clear cell carcinoma(229;0.00274)|STAD - Stomach adenocarcinoma(313;0.00773)|READ - Rectum adenocarcinoma(331;0.0656)		AAGCCCAGGGCATGCCTGAAG	0.517											OREG0013107	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	22	0.00439297	0.0015	0.0072	5008	,	,		19027	0.0		0.0099	False		,,,				2504	0.0051				p.G319G		Atlas-SNP	.											.	MFN2	83	.	0			c.C957T						PASS	.	C	,	11,4395	19.1+/-41.9	0,11,2192	80.0	75.0	77.0		957,957	3.3	1.0	1	dbSNP_127	77	95,8505	53.6+/-114.3	0,95,4205	no	coding-synonymous,coding-synonymous	MFN2	NM_001127660.1,NM_014874.3	,	0,106,6397	TT,TC,CC		1.1047,0.2497,0.815	,	319/758,319/758	12061598	106,12900	2203	4300	6503	SO:0001819	synonymous_variant	9927	exon9			CCAGGGCATGCCT	AF036536	CCDS30587.1	1p36.22	2014-09-17			ENSG00000116688	ENSG00000116688			16877	protein-coding gene	gene with protein product		608507				12499352, 11181170	Standard	NM_014874		Approved	CPRP1, KIAA0214, MARF, CMT2A2	uc009vni.3	O95140	OTTHUMG00000002392	ENST00000235329.5:c.957C>T	1.37:g.12061598C>T		107.0	0.0	0	677	135.0	79.0	0.585185	NM_014874	A8K1B3|O95572|Q5JXC3|Q5JXC4|Q9H131|Q9NSX8	Silent	SNP	ENST00000235329.5	37	CCDS30587.1																																																																																			C|0.991;T|0.009	0.009	strong		0.517	MFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006859.2	NM_014874	
ANKS1B	56899	hgsc.bcm.edu	37	12	99139559	99139559	+	Intron	SNP	G	G	T	rs61932058	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:99139559G>T	ENST00000547776.2	-	25	3672				ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron|ANKS1B_ENST00000549025.2_Silent_p.A344A|ANKS1B_ENST00000549493.2_Silent_p.A497A|ANKS1B_ENST00000550693.2_Silent_p.A437A|ANKS1B_ENST00000546568.1_Silent_p.A413A|ANKS1B_ENST00000333732.7_Silent_p.A276A|ANKS1B_ENST00000547446.1_Silent_p.A381A|ANKS1B_ENST00000332712.7_Silent_p.A437A|ANKS1B_ENST00000341752.7_Intron|ANKS1B_ENST00000549558.2_Intron	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B							cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGCCCCTCTTGGCTTCTTGGC	0.537													G|||	57	0.0113818	0.0113	0.0101	5008	,	,		16338	0.001		0.0189	False		,,,				2504	0.0153				p.A497A		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1491A						PASS	.	G	,,,,,,,,,,,	63,3759		1,61,1849	104.0	108.0	107.0		831,1032,1143,,1311,1239,831,759,,,,1491	2.7	1.0	12	dbSNP_129	107	181,8087		1,179,3954	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,intron,intron,intron,coding-synonymous	ANKS1B	NM_001204065.1,NM_001204066.1,NM_001204067.1,NM_001204068.1,NM_001204069.1,NM_001204070.1,NM_001204079.1,NM_001204080.1,NM_001204081.1,NM_020140.3,NM_152788.4,NM_181670.3	,,,,,,,,,,,	2,240,5803	TT,TG,GG		2.1892,1.6484,2.0182	,,,,,,,,,,,	277/291,344/358,381/395,,437/451,413/427,277/291,253/267,,,,497/511	99139559	244,11846	1911	4134	6045	SO:0001627	intron_variant	56899	exon13			CCTCTTGGCTTCT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.3672+5573C>A	12.37:g.99139559G>T		106.0	0.0	0		114.0	59.0	0.517544	NM_181670	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	37	CCDS55872.1	32	0.014652014652014652	10	0.02032520325203252	4	0.011049723756906077	0	0.0	18	0.023746701846965697	G	5.366	0.252738	0.10185	0.016484	0.021892	ENSG00000185046	ENST00000550778	.	.	.	4.66	2.65	0.31530	.	.	.	.	.	T	0.42585	0.1209	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.47761	-0.9092	4	.	.	.	.	9.5531	0.39321	0.0:0.1547:0.685:0.1604	rs61932058	.	.	.	Q	519	.	.	P	-	2	0	ANKS1B	97663690	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	2.200000	0.42724	1.048000	0.40298	-0.326000	0.08463	CCA	G|0.984;T|0.016	0.016	strong		0.537	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
TECTA	7007	hgsc.bcm.edu	37	11	121028666	121028666	+	Silent	SNP	C	C	T	rs33981325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:121028666C>T	ENST00000392793.1	+	14	4693	c.4422C>T	c.(4420-4422)aaC>aaT	p.N1474N	TECTA_ENST00000264037.2_Silent_p.N1474N			O75443	TECTA_HUMAN	tectorin alpha	1474					cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		CGCTGCGCAACGGGGTGCGCG	0.682													C|||	58	0.0115815	0.0015	0.0187	5008	,	,		10842	0.0		0.0348	False		,,,				2504	0.0082				p.N1474N		Atlas-SNP	.											TECTA,NS,carcinoma,+1,1	TECTA	329	1	0			c.C4422T						PASS	.	C		26,4380	32.6+/-62.9	1,24,2178	41.0	39.0	39.0		4422	-1.3	0.8	11	dbSNP_126	39	288,8308	105.2+/-166.2	4,280,4014	no	coding-synonymous	TECTA	NM_005422.2		5,304,6192	TT,TC,CC		3.3504,0.5901,2.415		1474/2156	121028666	314,12688	2203	4298	6501	SO:0001819	synonymous_variant	7007	exon13			GCGCAACGGGGTG	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.4422C>T	11.37:g.121028666C>T		64.0	0.0	0		53.0	35.0	0.660377	NM_005422		Silent	SNP	ENST00000392793.1	37	CCDS8434.1																																																																																			C|0.978;T|0.022	0.022	strong		0.682	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
GPNMB	10457	hgsc.bcm.edu	37	7	23313745	23313745	+	Silent	SNP	C	C	T	rs78340800	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:23313745C>T	ENST00000381990.2	+	11	1782	c.1621C>T	c.(1621-1623)Ctg>Ttg	p.L541L	GPNMB_ENST00000478451.1_3'UTR|GPNMB_ENST00000258733.4_Silent_p.L529L|GPNMB_ENST00000539136.1_Silent_p.L430L|GPNMB_ENST00000453162.2_Silent_p.L483L	NM_001005340.1|NM_002510.2	NP_001005340.1|NP_002501.1	Q14956	GPNMB_HUMAN	glycoprotein (transmembrane) nmb	541					bone mineralization (GO:0030282)|cell adhesion (GO:0007155)|negative regulation of cell proliferation (GO:0008285)|osteoblast differentiation (GO:0001649)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	heparin binding (GO:0008201)			breast(5)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(2)|lung(17)|ovary(3)|stomach(2)	41			GBM - Glioblastoma multiforme(13;0.154)			AAGCAAAGGCCTGAGTGTCTT	0.388													C|||	10	0.00199681	0.0	0.0	5008	,	,		17461	0.0		0.0099	False		,,,				2504	0.0				p.L541L		Atlas-SNP	.											.	GPNMB	88	.	0			c.C1621T						PASS	.	C	,	7,4399	12.9+/-30.5	0,7,2196	84.0	85.0	85.0		1621,1585	4.2	0.2	7	dbSNP_132	85	59,8541	35.9+/-90.5	0,59,4241	no	coding-synonymous,coding-synonymous	GPNMB	NM_001005340.1,NM_002510.2	,	0,66,6437	TT,TC,CC		0.686,0.1589,0.5075	,	541/573,529/561	23313745	66,12940	2203	4300	6503	SO:0001819	synonymous_variant	10457	exon11			AAAGGCCTGAGTG	X76534	CCDS5380.1, CCDS34610.1	7p	2008-07-18			ENSG00000136235	ENSG00000136235			4462	protein-coding gene	gene with protein product	"""transmembrane glycoprotein"", ""glycoprotein NMB"", ""glycoprotein nmb-like protein"", ""osteoactivin"""	604368				7814155	Standard	NM_002510		Approved	NMB, HGFIN	uc003swc.3	Q14956	OTTHUMG00000022811	ENST00000381990.2:c.1621C>T	7.37:g.23313745C>T		106.0	0.0	0		122.0	55.0	0.45082	NM_001005340	A4D155|Q6UVX1|Q8N1A1	Silent	SNP	ENST00000381990.2	37	CCDS34610.1																																																																																			C|0.995;T|0.005	0.005	strong		0.388	GPNMB-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327152.1	NM_001005340	
CYP3A5	1577	hgsc.bcm.edu	37	7	99261643	99261643	+	Nonsense_Mutation	SNP	A	A	T	rs201260783		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:99261643A>T	ENST00000222982.4	-	8	845	c.746T>A	c.(745-747)tTa>tAa	p.L249*	CYP3A5_ENST00000343703.5_Nonsense_Mutation_p.L239*|CYP3A5_ENST00000339843.2_3'UTR|CYP3A5_ENST00000480723.1_5'Flank	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	249					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	AGATTTACTTAAAAAATTTAT	0.318													A|||	1	0.000199681	0.0	0.0	5008	,	,		18056	0.001		0.0	False		,,,				2504	0.0				p.L249X		Atlas-SNP	.											.	CYP3A5	46	.	0			c.T746A						PASS	.						101.0	97.0	99.0					7																	99261643		2203	4300	6503	SO:0001587	stop_gained	1577	exon8			TTACTTAAAAAAT	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.746T>A	7.37:g.99261643A>T	ENSP00000222982:p.Leu249*	141.0	0.0	0		166.0	78.0	0.46988	NM_000777	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Nonsense_Mutation	SNP	ENST00000222982.4	37	CCDS5672.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.424707	0.83667	.	.	ENSG00000106258	ENST00000222982;ENST00000343703	.	.	.	4.61	4.61	0.57282	.	0.204155	0.50627	D	0.000105	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	11.9716	0.53067	1.0:0.0:0.0:0.0	.	.	.	.	X	249;239	.	ENSP00000222982:L249X	L	-	2	0	CYP3A5	99099579	1.000000	0.71417	0.708000	0.30435	0.010000	0.07245	6.921000	0.75805	1.708000	0.51301	0.533000	0.62120	TTA	.	.	weak		0.318	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
SUV39H2	79723	hgsc.bcm.edu	37	10	14939485	14939485	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:14939485G>A	ENST00000354919.6	+	3	818	c.818G>A	c.(817-819)aGa>aAa	p.R273K	SUV39H2_ENST00000313519.5_Missense_Mutation_p.R213K|SUV39H2_ENST00000378325.3_Intron|DCLRE1C_ENST00000378289.4_3'UTR	NM_001193424.1	NP_001180353.1	Q9H5I1	SUV92_HUMAN	suppressor of variegation 3-9 homolog 2 (Drosophila)	273	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell differentiation (GO:0030154)|chromatin assembly or disassembly (GO:0006333)|chromatin remodeling (GO:0006338)|histone H3-K9 dimethylation (GO:0036123)|histone H3-K9 trimethylation (GO:0036124)|male meiosis (GO:0007140)|negative regulation of circadian rhythm (GO:0042754)|negative regulation of transcription, DNA-templated (GO:0045892)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	chromatin (GO:0000785)|chromosome, centromeric region (GO:0000775)|nuclear heterochromatin (GO:0005720)	chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|transcription regulatory region sequence-specific DNA binding (GO:0000976)|zinc ion binding (GO:0008270)	p.R213I(1)		breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)	19						AAGATTAAAAGAATGAGTTTT	0.383																																					p.R273K		Atlas-SNP	.											SUV39H2,colon,carcinoma,0,1	SUV39H2	72	1	1	Substitution - Missense(1)	large_intestine(1)	c.G818A						PASS	.						73.0	69.0	71.0					10																	14939485		2203	4300	6503	SO:0001583	missense	79723	exon3			TTAAAAGAATGAG	AK027067	CCDS7104.1, CCDS53493.1, CCDS53494.1	10p13	2011-07-01			ENSG00000152455	ENSG00000152455		"""Chromatin-modifying enzymes / K-methyltransferases"""	17287	protein-coding gene	gene with protein product		606503				11094092	Standard	NM_001193424		Approved	FLJ23414, KMT1B	uc021png.1	Q9H5I1	OTTHUMG00000017718	ENST00000354919.6:c.818G>A	10.37:g.14939485G>A	ENSP00000346997:p.Arg273Lys	64.0	0.0	0		59.0	23.0	0.38983	NM_001193424	D3DRT4|Q5JSS4|Q5JSS5|Q6I9Y3|Q8ND06	Missense_Mutation	SNP	ENST00000354919.6	37	CCDS53494.1	.	.	.	.	.	.	.	.	.	.	G	4.956	0.177547	0.09443	.	.	ENSG00000152455	ENST00000354919;ENST00000313519;ENST00000420416	T;T;D	0.87103	-1.19;-1.19;-2.21	5.86	4.96	0.65561	SET domain (3);	0.200646	0.44688	N	0.000427	T	0.52885	0.1762	N	0.00226	-1.805	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.60682	-0.7215	10	0.02654	T	1	.	6.9776	0.24686	0.1531:0.1541:0.6928:0.0	.	273	Q9H5I1	SUV92_HUMAN	K	273;213;213	ENSP00000346997:R273K;ENSP00000319208:R213K;ENSP00000392201:R213K	ENSP00000319208:R213K	R	+	2	0	SUV39H2	14979491	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.691000	0.47010	1.631000	0.50456	0.650000	0.86243	AGA	.	.	none		0.383	SUV39H2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046947.2	NM_024670	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:167592571G>A	ENST00000366832.2	+	6	861	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	244										endometrium(1)|kidney(2)|lung(3)	6						TTCCCAGGCCGCCACGCTGCA	0.592																																					p.A244T		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G730A						PASS	.						23.0	28.0	27.0					6																	167592571		692	1591	2283	SO:0001583	missense	401285	exon6			CAGGCCGCCACGC		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.730G>A	6.37:g.167592571G>A	ENSP00000355797:p.Ala244Thr	98.0	0.0	0		135.0	16.0	0.118519	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	87	0.03983516483516483	17	0.034552845528455285	12	0.03314917127071823	14	0.024475524475524476	44	0.05804749340369393	c	8.486	0.860926	0.17178	.	.	ENSG00000166984	ENST00000366832	T	0.13901	2.55	1.87	-1.19	0.09585	.	.	.	.	.	T	0.00906	0.0030	N	0.11560	0.145	0.09310	N	1	B	0.32968	0.392	B	0.17433	0.018	T	0.43718	-0.9374	9	0.02654	T	1	.	2.6095	0.04887	0.3443:0.2689:0.3868:0.0	rs28690444	244	B9ZVM9	TCP2L_HUMAN	T	244	ENSP00000355797:A244T	ENSP00000283507:A244T	A	+	1	0	TCP10L2	167512561	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.863000	0.04259	-0.321000	0.08627	-1.962000	0.00476	GCC	G|0.965;A|0.035	0.035	strong		0.592	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
OTOF	9381	hgsc.bcm.edu	37	2	26696374	26696374	+	Missense_Mutation	SNP	C	C	T	rs56054534	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:26696374C>T	ENST00000272371.2	-	28	3596	c.3470G>A	c.(3469-3471)cGg>cAg	p.R1157Q	OTOF_ENST00000402415.3_Missense_Mutation_p.R467Q|OTOF_ENST00000403946.3_Missense_Mutation_p.R1157Q|OTOF_ENST00000338581.6_Missense_Mutation_p.R410Q|OTOF_ENST00000339598.3_Missense_Mutation_p.R410Q	NM_194248.2	NP_919224.1	Q9HC10	OTOF_HUMAN	otoferlin	1157			R -> Q (in dbSNP:rs56054534). {ECO:0000269|PubMed:16371502}.		membrane fusion (GO:0061025)|sensory perception of sound (GO:0007605)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic vesicle membrane (GO:0030672)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(9)|central_nervous_system(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(35)|ovary(8)|pancreas(1)|prostate(5)|skin(5)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	106	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GATGTCCACCCGTGGCCGGTC	0.592													C|||	23	0.00459265	0.0	0.013	5008	,	,		16468	0.0		0.0139	False		,,,				2504	0.0				p.R1157Q	GBM(102;732 1451 20652 24062 31372)	Atlas-SNP	.											.	OTOF	524	.	0			c.G3470A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	14,4392	20.2+/-43.8	0,14,2189	63.0	63.0	63.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1229,3470,1400,1229	5.2	1.0	2	dbSNP_129	63	129,8471	66.0+/-128.3	1,127,4172	yes	missense,missense,missense,missense	OTOF	NM_004802.3,NM_194248.2,NM_194322.2,NM_194323.2	43,43,43,43	1,141,6361	TT,TC,CC		1.5,0.3177,1.0995	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	410/1231,1157/1998,467/1308,410/1231	26696374	143,12863	2203	4300	6503	SO:0001583	missense	9381	exon28			TCCACCCGTGGCC	AF107403	CCDS1724.1, CCDS1725.1, CCDS1726.1, CCDS46241.1, CCDS74497.1	2p23.1	2014-06-27			ENSG00000115155	ENSG00000115155			8515	protein-coding gene	gene with protein product	"""fer-1-like family member 2"""	603681		DFNB9		10192385, 18381613	Standard	NM_194248		Approved	FER1L2, DFNB6	uc002rhk.3	Q9HC10	OTTHUMG00000096977	ENST00000272371.2:c.3470G>A	2.37:g.26696374C>T	ENSP00000272371:p.Arg1157Gln	79.0	0.0	0		91.0	42.0	0.461538	NM_194248	B4DJX0|B5MCC1|B9A0H6|Q53R90|Q9HC08|Q9HC09|Q9Y650	Missense_Mutation	SNP	ENST00000272371.2	37	CCDS1725.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	15.19	2.761009	0.49468	0.003177	0.015	ENSG00000115155	ENST00000338581;ENST00000339598;ENST00000402415;ENST00000272371;ENST00000403946	D;D;D;T;T	0.84516	-1.86;-1.86;-1.86;-0.22;-0.22	5.21	5.21	0.72293	C2 calcium-dependent membrane targeting (1);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.76807	0.4039	N	0.03281	-0.365	0.80722	D	1	D;P;D;B	0.89917	1.0;0.477;0.99;0.304	D;B;P;B	0.87578	0.998;0.08;0.596;0.08	T	0.76650	-0.2881	10	0.07813	T	0.8	-22.4695	18.3421	0.90309	0.0:1.0:0.0:0.0	rs56054534	1157;410;467;410	Q9HC10;Q9HC10-2;Q9HC10-3;Q9HC10-4	OTOF_HUMAN;.;.;.	Q	410;410;467;1157;1157	ENSP00000345137:R410Q;ENSP00000344521:R410Q;ENSP00000383906:R467Q;ENSP00000272371:R1157Q;ENSP00000385255:R1157Q	ENSP00000272371:R1157Q	R	-	2	0	OTOF	26549878	0.995000	0.38212	0.997000	0.53966	0.870000	0.49936	3.321000	0.51999	2.436000	0.82500	0.484000	0.47621	CGG	C|0.991;T|0.009	0.009	strong		0.592	OTOF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214047.3		
ZNF516	9658	hgsc.bcm.edu	37	18	74090864	74090864	+	Missense_Mutation	SNP	A	A	G	rs140499406	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74090864A>G	ENST00000443185.2	-	5	3522	c.3205T>C	c.(3205-3207)Ttt>Ctt	p.F1069L	ZNF516_ENST00000524431.2_5'UTR|RP11-504I13.3_ENST00000583287.1_RNA	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	1069					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(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		AGGGTCGCAAAGTCCTTTGGA	0.602													A|||	14	0.00279553	0.0015	0.0043	5008	,	,		17438	0.0		0.008	False		,,,				2504	0.001				p.F1069L		Atlas-SNP	.											.	ZNF516	102	.	0			c.T3205C						PASS	.	A	LEU/PHE	5,4081		0,5,2038	41.0	48.0	46.0		3206	-0.6	1.0	18	dbSNP_134	46	77,8287		2,73,4107	yes	missense	ZNF516	NM_014643.3	22	2,78,6145	GG,GA,AA		0.9206,0.1224,0.6586	benign	1069/1164	74090864	82,12368	2043	4182	6225	SO:0001583	missense	9658	exon5			TCGCAAAGTCCTT	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.3205T>C	18.37:g.74090864A>G	ENSP00000394757:p.Phe1069Leu	104.0	0.0	0		77.0	26.0	0.337662	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	2|2	0.0055248618784530384|0.0055248618784530384	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	a|a	3.367|3.367	-0.129188|-0.129188	0.06753|0.06753	0.001224|0.001224	0.009206|0.009206	ENSG00000101493|ENSG00000101493	ENST00000443185|ENST00000542818	T|.	0.05786|.	3.39|.	3.8|3.8	-0.563|-0.563	0.11778|0.11778	.|.	0.482470|.	0.19919|.	N|.	0.103134|.	T|T	0.14614|0.14614	0.0353|0.0353	N|N	0.08118|0.08118	0|0	0.31674|0.31674	N|N	0.643972|0.643972	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.34750|0.34750	-0.9816|-0.9816	10|5	0.02654|.	T|.	1|.	-0.2046|-0.2046	7.7942|7.7942	0.29138|0.29138	0.34:0.0:0.66:0.0|0.34:0.0:0.66:0.0	.|.	1069|.	Q92618|.	ZN516_HUMAN|.	L|P	1069|2	ENSP00000394757:F1069L|.	ENSP00000394757:F1069L|.	F|L	-|-	1|2	0|0	ZNF516|ZNF516	72219852|72219852	1.000000|1.000000	0.71417|0.71417	0.961000|0.961000	0.40146|0.40146	0.841000|0.841000	0.47740|0.47740	3.490000|3.490000	0.53245|0.53245	-0.197000|-0.197000	0.10350|0.10350	0.478000|0.478000	0.44815|0.44815	TTT|CTT	A|0.994;G|0.006	0.006	strong		0.602	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
CERS4	79603	hgsc.bcm.edu	37	19	8326672	8326672	+	Missense_Mutation	SNP	G	G	A	rs141592194		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:8326672G>A	ENST00000251363.5	+	11	1249	c.949G>A	c.(949-951)Gtg>Atg	p.V317M	CERS4_ENST00000595722.1_3'UTR|CERS4_ENST00000559450.1_Missense_Mutation_p.V317M|CERS4_ENST00000558331.1_Missense_Mutation_p.V266M|CERS4_ENST00000559336.1_Intron	NM_024552.2	NP_078828.2	Q9HA82	CERS4_HUMAN	ceramide synthase 4	317	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										GCTGCTGCACGTGTTCTGGTC	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		16989	0.0		0.0	False		,,,				2504	0.001				p.V317M		Atlas-SNP	.											.	.	.	.	0			c.G949A						PASS	.	G	MET/VAL	1,4405	2.1+/-5.4	0,1,2202	105.0	88.0	94.0		949	0.6	0.7	19	dbSNP_134	94	6,8594	5.0+/-18.6	0,6,4294	yes	missense	CERS4	NM_024552.2	21	0,7,6496	AA,AG,GG		0.0698,0.0227,0.0538	probably-damaging	317/395	8326672	7,12999	2203	4300	6503	SO:0001583	missense	79603	exon11			CTGCACGTGTTCT		CCDS12197.1	19p13.2	2014-09-11	2011-07-08	2011-07-08	ENSG00000090661	ENSG00000090661		"""Homeoboxes / CERS class"""	23747	protein-coding gene	gene with protein product		615334	"""LAG1 longevity assurance homolog 4 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 4"""	LASS4			Standard	NM_024552		Approved	FLJ12089, Trh1	uc002mjg.3	Q9HA82	OTTHUMG00000172570	ENST00000251363.5:c.949G>A	19.37:g.8326672G>A	ENSP00000251363:p.Val317Met	304.0	0.0	0		269.0	110.0	0.408922	NM_024552	D6W665	Missense_Mutation	SNP	ENST00000251363.5	37	CCDS12197.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454447	0.63290	2.27E-4	6.98E-4	ENSG00000090661	ENST00000251363	D	0.86164	-2.08	5.13	0.644	0.17776	TRAM/LAG1/CLN8 homology domain (3);	0.257428	0.39985	N	0.001212	D	0.90363	0.6984	M	0.71296	2.17	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.87521	0.2446	10	0.62326	D	0.03	-22.7678	6.9208	0.24387	0.4709:0.0:0.5291:0.0	.	317	Q9HA82	CERS4_HUMAN	M	317	ENSP00000251363:V317M	ENSP00000251363:V317M	V	+	1	0	CERS4	8232672	0.711000	0.27906	0.672000	0.29872	0.694000	0.40290	1.129000	0.31381	0.194000	0.20326	0.561000	0.74099	GTG	G|0.999;A|0.001	0.001	strong		0.567	CERS4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419200.1	NM_024552	
GALNT11	63917	hgsc.bcm.edu	37	7	151791435	151791435	+	Silent	SNP	C	C	T	rs138436495	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:151791435C>T	ENST00000434507.1	+	4	560	c.123C>T	c.(121-123)ccC>ccT	p.P41P	GALNT11_ENST00000422997.2_Silent_p.P41P|GALNT11_ENST00000320311.2_Silent_p.P41P|GALNT11_ENST00000415421.1_Silent_p.P41P|GALNT11_ENST00000452146.2_Intron|GALNT11_ENST00000482812.1_3'UTR|GALNT11_ENST00000430044.2_Silent_p.P41P			Q8NCW6	GLT11_HUMAN	polypeptide N-acetylgalactosaminyltransferase 11	41					cellular protein metabolic process (GO:0044267)|cilium morphogenesis (GO:0060271)|determination of left/right symmetry (GO:0007368)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via threonine (GO:0018243)|regulation of Notch signaling pathway (GO:0008593)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|Notch binding (GO:0005112)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|prostate(5)|skin(2)	27	all_neural(206;0.187)	all_hematologic(28;0.0592)|Prostate(32;0.214)	OV - Ovarian serous cystadenocarcinoma(82;0.00168)	UCEC - Uterine corpus endometrioid carcinoma (81;0.177)|BRCA - Breast invasive adenocarcinoma(188;0.0932)		AGAATGTGCCCGTCAAGGGGT	0.473													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16967	0.0		0.002	False		,,,				2504	0.0				p.P41P		Atlas-SNP	.											GALNT11,NS,carcinoma,+1,1	GALNT11	59	1	0			c.C123T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	138.0	141.0	140.0		123	5.7	1.0	7	dbSNP_134	140	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous	GALNT11	NM_022087.2		0,27,6476	TT,TC,CC		0.2674,0.0908,0.2076		41/609	151791435	27,12979	2203	4300	6503	SO:0001819	synonymous_variant	63917	exon2			TGTGCCCGTCAAG	AC006017	CCDS5930.1	7q36.1	2014-05-09	2014-05-09		ENSG00000178234	ENSG00000178234	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	19875	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 11"""	615130	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 11 (GalNAc-T11)"""			11925450	Standard	NM_022087		Approved	GalNAc-T11	uc010lqg.1	Q8NCW6	OTTHUMG00000157251	ENST00000434507.1:c.123C>T	7.37:g.151791435C>T		93.0	0.0	0		122.0	72.0	0.590164	NM_022087	B3KWF4|Q6PCD1|Q9H6C2|Q9H6Z5|Q9UDR8	Silent	SNP	ENST00000434507.1	37	CCDS5930.1																																																																																			C|0.998;T|0.002	0.002	strong		0.473	GALNT11-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348184.1	NM_022087	
ANKS1B	56899	hgsc.bcm.edu	37	12	100048924	100048924	+	Missense_Mutation	SNP	G	G	A	rs377459874		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:100048924G>A	ENST00000547776.2	-	9	1192	c.1193C>T	c.(1192-1194)aCg>aTg	p.T398M	ANKS1B_ENST00000329257.7_Missense_Mutation_p.T398M|ANKS1B_ENST00000547010.1_De_novo_Start_InFrame	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	398						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TGGCCCACACGTATTTTCATC	0.378													G|||	1	0.000199681	0.0	0.0	5008	,	,		16060	0.0		0.001	False		,,,				2504	0.0				p.T398M		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C1193T						PASS	.	G	MET/THR	1,3821		0,1,1910	119.0	117.0	118.0		1193	3.5	0.2	12		118	1,8241		0,1,4120	no	missense	ANKS1B	NM_152788.4	81	0,2,6030	AA,AG,GG		0.0121,0.0262,0.0166	possibly-damaging	398/1249	100048924	2,12062	1911	4121	6032	SO:0001583	missense	56899	exon9			CCACACGTATTTT	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.1193C>T	12.37:g.100048924G>A	ENSP00000449629:p.Thr398Met	224.0	0.0	0		250.0	114.0	0.456	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Missense_Mutation	SNP	ENST00000547776.2	37	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	9.507	1.104632	0.20632	2.62E-4	1.21E-4	ENSG00000185046	ENST00000547776;ENST00000329257;ENST00000549866	T;T;T	0.51071	0.85;0.85;0.72	5.47	3.51	0.40186	.	0.251827	0.30959	N	0.008522	T	0.31104	0.0786	N	0.22421	0.69	0.46078	D	0.998858	P;P	0.51791	0.948;0.913	B;B	0.39876	0.312;0.165	T	0.05971	-1.0853	9	.	.	.	-4.2304	12.7356	0.57222	0.0:0.4365:0.5635:0.0	.	364;398	F8VVQ4;Q7Z6G8	.;ANS1B_HUMAN	M	398;398;364	ENSP00000449629:T398M;ENSP00000331381:T398M;ENSP00000449894:T364M	.	T	-	2	0	ANKS1B	98573055	1.000000	0.71417	0.180000	0.23079	0.246000	0.25737	2.677000	0.46892	1.292000	0.44672	-0.283000	0.09986	ACG	.	.	weak		0.378	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
CSMD2	114784	hgsc.bcm.edu	37	1	34052137	34052137	+	Silent	SNP	G	G	A	rs371199413		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:34052137G>A	ENST00000373381.4	-	46	7194	c.7018C>T	c.(7018-7020)Ctg>Ttg	p.L2340L		NM_001281956.1|NM_052896.3	NP_001268885.1|NP_443128.2	Q7Z408	CSMD2_HUMAN	CUB and Sushi multiple domains 2	2342	Sushi 13. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(5)|breast(5)|central_nervous_system(3)|cervix(2)|endometrium(20)|haematopoietic_and_lymphoid_tissue(4)|kidney(9)|large_intestine(43)|lung(114)|ovary(8)|pancreas(1)|prostate(6)|skin(20)|upper_aerodigestive_tract(5)|urinary_tract(1)	246		Myeloproliferative disorder(586;0.0294)|all_neural(195;0.249)				TCAAACTGCAGGTAGGTTCCA	0.483																																					p.L2342L		Atlas-SNP	.											.	CSMD2	946	.	0			c.C7024T						PASS	.	G		0,4406		0,0,2203	109.0	99.0	102.0		7024	4.0	1.0	1		102	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CSMD2	NM_052896.3		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		2342/3488	34052137	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	114784	exon47			ACTGCAGGTAGGT	AY210418	CCDS380.1, CCDS60082.1	1p34.3	2014-01-28			ENSG00000121904	ENSG00000121904			19290	protein-coding gene	gene with protein product		608398				11472063, 11572484	Standard	NM_001281956		Approved	KIAA1884	uc001bxn.1	Q7Z408	OTTHUMG00000011135	ENST00000373381.4:c.7018C>T	1.37:g.34052137G>A		146.0	0.0	0		92.0	36.0	0.391304	NM_052896	B1AM50|E7EUA6|Q53TY4|Q5VT59|Q8N963|Q96Q03|Q9H4V7|Q9H4V8|Q9H4V9|Q9H4W0|Q9H4W1|Q9H4W2|Q9H4W3|Q9H4W4|Q9HCY5|Q9HCY6|Q9HCY7	Silent	SNP	ENST00000373381.4	37																																																																																				.	.	none		0.483	CSMD2-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_052896	
DCHS2	54798	hgsc.bcm.edu	37	4	155158284	155158284	+	Nonsense_Mutation	SNP	A	A	C	rs146298768	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:155158284A>C	ENST00000357232.4	-	25	6154	c.6155T>G	c.(6154-6156)tTa>tGa	p.L2052*		NM_017639.3	NP_060109.2	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	2052	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|cervix(3)|endometrium(8)|kidney(5)|large_intestine(54)|lung(63)|ovary(4)|pancreas(1)|prostate(14)|skin(12)|stomach(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	176	all_hematologic(180;0.208)	Renal(120;0.0854)		LUSC - Lung squamous cell carcinoma(193;0.107)		ATCCAGAAGTAATACGGGACT	0.378																																					p.L2052X		Atlas-SNP	.											.	DCHS2	594	.	0			c.T6155G						PASS	.	A	stop/LEU	2,4402	4.2+/-10.8	0,2,2200	69.0	71.0	70.0		6155	2.0	0.0	4	dbSNP_134	70	34,8566	22.2+/-67.0	0,34,4266	yes	stop-gained	DCHS2	NM_017639.3		0,36,6466	CC,CA,AA		0.3953,0.0454,0.2768		2052/2917	155158284	36,12968	2202	4300	6502	SO:0001587	stop_gained	54798	exon25			AGAAGTAATACGG	BC140919	CCDS3785.1, CCDS47150.1	4q32.1	2014-06-04	2013-10-04	2004-09-03		ENSG00000197410		"""Cadherins / Cadherin-related"""	23111	protein-coding gene	gene with protein product	"""cadherin-related family member 7"""	612486	"""cadherin-like 27"", ""dachsous 2 (Drosophila)"""	CDH27, PCDH23		15003449	Standard	NM_017639		Approved	CDHJ, FLJ20047, PCDHJ, CDHR7	uc003inw.2	Q6V1P9		ENST00000357232.4:c.6155T>G	4.37:g.155158284A>C	ENSP00000349768:p.Leu2052*	102.0	0.0	0		102.0	52.0	0.509804	NM_017639	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Nonsense_Mutation	SNP	ENST00000357232.4	37	CCDS3785.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	42	9.636087	0.99226	4.54E-4	0.003953	ENSG00000197410	ENST00000357232	.	.	.	5.67	2.04	0.26737	.	1.456590	0.04346	N	0.354832	.	.	.	.	.	.	0.09310	N	1	.	.	.	.	.	.	.	.	.	.	0.17369	T	0.5	.	5.7442	0.18110	0.5901:0.1313:0.2786:0.0	.	.	.	.	X	2052	.	ENSP00000349768:L2052X	L	-	2	0	DCHS2	155377734	0.000000	0.05858	0.007000	0.13788	0.558000	0.35554	0.244000	0.18124	0.130000	0.18549	0.455000	0.32223	TTA	A|0.998;C|0.002	0.002	strong		0.378	DCHS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365281.2	NM_001142552	
POTEF	728378	hgsc.bcm.edu	37	2	130832364	130832364	+	Missense_Mutation	SNP	G	G	A	rs185469611	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:130832364G>A	ENST00000409914.2	-	17	3080	c.2681C>T	c.(2680-2682)aCc>aTc	p.T894I	POTEF_ENST00000357462.5_Missense_Mutation_p.T894I	NM_001099771.2	NP_001093241.1	A5A3E0	POTEF_HUMAN	POTE ankyrin domain family, member F	894	Actin-like.				retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(4)|lung(28)|ovary(3)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	53						GCCATGCTCGGTGAGGATCTT	0.582													.|||	89	0.0177716	0.0424	0.013	5008	,	,		11371	0.0		0.0229	False		,,,				2504	0.001				p.T894I		Atlas-SNP	.											.	POTEF	140	.	0			c.C2681T						PASS	.	G	ILE/THR	58,3640		3,52,1794	20.0	28.0	25.0		2681		0.1	2		25	120,7650		23,74,3788	no	missense	POTEF	NM_001099771.2	89	26,126,5582	AA,AG,GG		1.5444,1.5684,1.5521	probably-damaging	894/1076	130832364	178,11290	1849	3885	5734	SO:0001583	missense	728378	exon17			TGCTCGGTGAGGA	EF523384	CCDS46409.1	2q21.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000196604	ENSG00000196604		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33905	protein-coding gene	gene with protein product			"""ANKRD26-like family C, member 1B"""	A26C1B		17101985	Standard	NM_001099771		Approved	POTEACTIN, POTE2alpha	uc010fmh.2	A5A3E0	OTTHUMG00000153628	ENST00000409914.2:c.2681C>T	2.37:g.130832364G>A	ENSP00000386786:p.Thr894Ile	250.0	0.0	0		409.0	362.0	0.885086	NM_001099771	A6NC34	Missense_Mutation	SNP	ENST00000409914.2	37	CCDS46409.1	25	0.011446886446886446	11	0.022357723577235773	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	.	14.01	2.406630	0.42715	0.015684	0.015444	ENSG00000196604	ENST00000357462;ENST00000409914	D;D	0.94613	-3.47;-3.47	.	.	.	.	.	.	.	.	D	0.89371	0.6696	M	0.90650	3.135	0.80722	D	1	B	0.18863	0.031	B	0.22152	0.038	D	0.86999	0.2115	8	0.87932	D	0	.	5.9051	0.18992	8.0E-4:0.0:0.9992:0.0	.	894	A5A3E0	POTEF_HUMAN	I	894	ENSP00000350052:T894I;ENSP00000386786:T894I	ENSP00000350052:T894I	T	-	2	0	POTEF	130548834	1.000000	0.71417	0.105000	0.21289	0.105000	0.19272	4.869000	0.63028	0.119000	0.18210	0.121000	0.15741	ACC	G|0.988;A|0.012	0.012	strong		0.582	POTEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331889.2	NM_001099771	
LRRTM3	347731	hgsc.bcm.edu	37	10	68687942	68687942	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:68687942G>C	ENST00000361320.4	+	2	1846	c.1268G>C	c.(1267-1269)gGc>gCc	p.G423A	CTNNA3_ENST00000433211.2_Intron|CTNNA3_ENST00000373744.4_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	423					positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						ATCATCGCGGGCAGCGTGGCG	0.612																																					p.G423A		Atlas-SNP	.											.	LRRTM3	241	.	0			c.G1268C						PASS	.						70.0	68.0	69.0					10																	68687942		2203	4300	6503	SO:0001583	missense	347731	exon2			TCGCGGGCAGCGT	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.1268G>C	10.37:g.68687942G>C	ENSP00000355187:p.Gly423Ala	71.0	0.0	0		56.0	21.0	0.375	NM_178011	A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	37	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	G	18.76	3.692071	0.68271	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.75367	-0.93	5.94	5.94	0.96194	.	0.000000	0.64402	D	0.000001	D	0.87525	0.6199	M	0.82056	2.57	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.87653	0.2529	10	0.62326	D	0.03	.	19.1373	0.93433	0.0:0.0:1.0:0.0	.	423;423	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	A	423	ENSP00000355187:G423A	ENSP00000355187:G423A	G	+	2	0	LRRTM3	68357948	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	9.869000	0.99810	2.820000	0.97059	0.650000	0.86243	GGC	.	.	none		0.612	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011	
NCOR2	9612	hgsc.bcm.edu	37	12	124831388	124831388	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124831388G>A	ENST00000405201.1	-	31	4081	c.4081C>T	c.(4081-4083)Cgg>Tgg	p.R1361W	NCOR2_ENST00000429285.2_Missense_Mutation_p.R1351W|NCOR2_ENST00000356219.3_Missense_Mutation_p.R1368W|NCOR2_ENST00000404121.2_Missense_Mutation_p.R922W|NCOR2_ENST00000404621.1_Missense_Mutation_p.R1351W|NCOR2_ENST00000397355.1_Missense_Mutation_p.R1352W			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	1369					cellular lipid metabolic process (GO:0044255)|gene expression (GO:0010467)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|regulation of cellular ketone metabolic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072365)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	membrane (GO:0016020)|nuclear body (GO:0016604)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|histone deacetylase binding (GO:0042826)|Notch binding (GO:0005112)|protein N-terminus binding (GO:0047485)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(2)|endometrium(7)|kidney(5)|large_intestine(7)|lung(28)|ovary(3)|pancreas(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_neural(191;0.0804)|Medulloblastoma(191;0.163)			Epithelial(86;3.99e-05)|OV - Ovarian serous cystadenocarcinoma(86;9.14e-05)|all cancers(50;0.000402)|BRCA - Breast invasive adenocarcinoma(302;0.0764)		ACGTAGGACCGAGGGATCCCT	0.687																																					p.R1361W		Atlas-SNP	.											.	NCOR2	475	.	0			c.C4081T						PASS	.						7.0	10.0	9.0					12																	124831388		2025	4146	6171	SO:0001583	missense	9612	exon33			AGGACCGAGGGAT	U37146	CCDS41857.1, CCDS41858.1, CCDS41857.2, CCDS41858.2, CCDS55892.1	12q24	2010-06-10	2010-06-10		ENSG00000196498	ENSG00000196498			7673	protein-coding gene	gene with protein product		600848	"""nuclear receptor co-repressor 2"""			7566127, 8813722	Standard	NM_001077261		Approved	SMRT, SMRTE, TRAC-1, CTG26, TNRC14	uc010tbb.2	Q9Y618	OTTHUMG00000150455	ENST00000405201.1:c.4081C>T	12.37:g.124831388G>A	ENSP00000384018:p.Arg1361Trp	44.0	0.0	0		46.0	24.0	0.521739	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	.	.	.	.	.	.	.	.	.	.	G	12.13	1.846645	0.32606	.	.	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.15;0.15;0.15	5.2	2.19	0.27852	.	0.000000	0.85682	D	0.000000	T	0.73087	0.3542	M	0.71036	2.16	0.54753	D	0.999988	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.993;0.997	T	0.74544	-0.3630	10	0.87932	D	0	-29.7811	13.8264	0.63352	0.0:0.0:0.5877:0.4123	.	1351;1352;1361	C9J0Q5;C9J239;C9JFD3	.;.;.	W	1361;1351;1368;1352;1360;922;1351;1369	ENSP00000384018:R1361W;ENSP00000384202:R1351W;ENSP00000348551:R1368W;ENSP00000380513:R1352W;ENSP00000385618:R922W;ENSP00000400281:R1351W;ENSP00000402808:R1369W	ENSP00000348551:R1368W	R	-	1	2	NCOR2	123397341	1.000000	0.71417	0.020000	0.16555	0.346000	0.29079	3.614000	0.54160	0.144000	0.18951	-0.448000	0.05591	CGG	.	.	none		0.687	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
CASZ1	54897	hgsc.bcm.edu	37	1	10725469	10725469	+	Missense_Mutation	SNP	G	G	A	rs149479567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:10725469G>A	ENST00000377022.3	-	5	493	c.176C>T	c.(175-177)tCg>tTg	p.S59L	CASZ1_ENST00000344008.5_Missense_Mutation_p.S59L|CASZ1_ENST00000478728.2_5'UTR	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	59					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CCGGGGCTGCGATGGGCTGCC	0.687													G|||	24	0.00479233	0.0008	0.0086	5008	,	,		15263	0.001		0.0149	False		,,,				2504	0.001				p.S59L		Atlas-SNP	.											.	CASZ1	150	.	0			c.C176T						PASS	.	G	LEU/SER,LEU/SER	7,4247		0,7,2120	28.0	34.0	32.0		176,176	2.1	0.0	1	dbSNP_134	32	95,8333		1,93,4120	yes	missense,missense	CASZ1	NM_001079843.1,NM_017766.3	145,145	1,100,6240	AA,AG,GG		1.1272,0.1646,0.8043	benign,benign	59/1760,59/1167	10725469	102,12580	2127	4214	6341	SO:0001583	missense	54897	exon5			GGCTGCGATGGGC	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.176C>T	1.37:g.10725469G>A	ENSP00000366221:p.Ser59Leu	65.0	0.0	0		32.0	24.0	0.75	NM_001079843	Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Missense_Mutation	SNP	ENST00000377022.3	37	CCDS41246.1	17	0.007783882783882784	0	0.0	5	0.013812154696132596	1	0.0017482517482517483	11	0.014511873350923483	G	3.148	-0.174917	0.06421	0.001646	0.011272	ENSG00000130940	ENST00000377022;ENST00000344008	.	.	.	4.42	2.11	0.27256	.	0.674203	0.13380	N	0.392225	T	0.08670	0.0215	N	0.03608	-0.345	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.31641	-0.9936	9	0.06891	T	0.86	-2.4618	4.9221	0.13874	0.6052:0.0:0.3948:0.0	.	83;59;59	B7Z1S3;Q86V15-2;Q86V15	.;.;CASZ1_HUMAN	L	59	.	ENSP00000339445:S59L	S	-	2	0	CASZ1	10648056	0.004000	0.15560	0.008000	0.14137	0.008000	0.06430	1.763000	0.38461	0.692000	0.31613	-0.424000	0.05967	TCG	G|0.993;A|0.007	0.007	strong		0.687	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
ATM	472	hgsc.bcm.edu	37	11	108124761	108124761	+	Missense_Mutation	SNP	T	T	C	rs4986761	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:108124761T>C	ENST00000452508.2	+	14	2308	c.2119T>C	c.(2119-2121)Tct>Cct	p.S707P	ATM_ENST00000278616.4_Missense_Mutation_p.S707P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	707			S -> P (in dbSNP:rs4986761). {ECO:0000269|PubMed:10534763, ECO:0000269|PubMed:17344846}.|YSS -> FIP (in AT; might be associated with susceptibility to cancer).		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to gamma radiation (GO:0071480)|DNA damage induced protein phosphorylation (GO:0006975)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|heart development (GO:0007507)|histone mRNA catabolic process (GO:0071044)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|lipoprotein catabolic process (GO:0042159)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of B cell proliferation (GO:0030889)|neuron apoptotic process (GO:0051402)|oocyte development (GO:0048599)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of neuron apoptotic process (GO:0043525)|pre-B cell allelic exclusion (GO:0002331)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|reciprocal meiotic recombination (GO:0007131)|replicative senescence (GO:0090399)|response to hypoxia (GO:0001666)|response to ionizing radiation (GO:0010212)|signal transduction (GO:0007165)|signal transduction involved in mitotic G2 DNA damage checkpoint (GO:0072434)|somitogenesis (GO:0001756)|telomere maintenance (GO:0000723)	cytoplasmic vesicle (GO:0031410)|nucleoplasm (GO:0005654)|spindle (GO:0005819)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA-dependent protein kinase activity (GO:0004677)|histone serine kinase activity (GO:0035174)|protein complex binding (GO:0032403)|protein dimerization activity (GO:0046983)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)	p.S707P(2)|p.S707fs*29(1)		NS(4)|breast(23)|central_nervous_system(11)|endometrium(10)|haematopoietic_and_lymphoid_tissue(227)|kidney(19)|large_intestine(53)|liver(5)|lung(62)|ovary(6)|pancreas(4)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	448		all_cancers(61;9.64e-12)|all_epithelial(67;9.97e-08)|Melanoma(852;2.55e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		Epithelial(105;9.05e-06)|BRCA - Breast invasive adenocarcinoma(274;1.06e-05)|all cancers(92;0.000208)|Colorectal(284;0.116)|OV - Ovarian serous cystadenocarcinoma(223;0.147)	Caffeine(DB00201)	TAATTACTCATCTGAGGTGAG	0.393			"""D, Mis, N, F, S"""		T-PLL	"""leukemia, lymphoma, medulloblastoma, glioma"""		Genes defective in diseases associated with sensitivity to DNA damaging agents	Ataxia Telangiectasia	TSP Lung(14;0.12)			T|||	22	0.00439297	0.0	0.0101	5008	,	,		16199	0.0		0.0129	False		,,,				2504	0.002				p.S707P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	ATM,NS,carcinoma,0,2	ATM	1657	2	3	Substitution - Missense(2)|Deletion - Frameshift(1)	breast(2)|haematopoietic_and_lymphoid_tissue(1)	c.T2119C	GRCh37	CM013692	ATM	M	rs4986761	PASS	.	T	PRO/SER	17,4383	21.2+/-45.6	0,17,2183	55.0	55.0	55.0		2119	3.8	1.0	11	dbSNP_111	55	94,8502	50.6+/-110.7	1,92,4205	yes	missense	ATM	NM_000051.3	74	1,109,6388	CC,CT,TT		1.0935,0.3864,0.8541	benign	707/3057	108124761	111,12885	2200	4298	6498	SO:0001583	missense	472	exon13	Familial Cancer Database	AT, Louis-Bar syndrome	TACTCATCTGAGG	AB209133	CCDS31669.1	11q22-q23	2014-09-17	2014-06-17		ENSG00000149311	ENSG00000149311			795	protein-coding gene	gene with protein product	"""TEL1, telomere maintenance 1, homolog (S. cerevisiae)"""	607585	"""ataxia telangiectasia mutated (includes complementation groups A, C and D)"", ""ataxia telangiectasia mutated"""	ATA, ATDC, ATC, ATD			Standard	XM_005271561		Approved	TEL1, TELO1	uc001pkb.1	Q13315	OTTHUMG00000166480	ENST00000452508.2:c.2119T>C	11.37:g.108124761T>C	ENSP00000388058:p.Ser707Pro	63.0	0.0	0		67.0	35.0	0.522388	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Missense_Mutation	SNP	ENST00000452508.2	37	CCDS31669.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	T	11.63	1.694897	0.30052	0.003864	0.010935	ENSG00000149311	ENST00000527805;ENST00000278616;ENST00000452508	T;T;T	0.78364	-1.17;-1.17;-1.17	6.11	3.81	0.43845	Armadillo-type fold (1);	0.179298	0.50627	N	0.000119	T	0.52141	0.1716	N	0.17872	0.535	0.23076	N	0.998335	B	0.02656	0.0	B	0.01281	0.0	T	0.42565	-0.9444	10	0.31617	T	0.26	.	7.5463	0.27768	0.0:0.2362:0.0:0.7638	rs4986761;rs52832782;rs4986761	707	Q13315	ATM_HUMAN	P	707	ENSP00000435747:S707P;ENSP00000278616:S707P;ENSP00000388058:S707P	ENSP00000278616:S707P	S	+	1	0	ATM	107629971	0.015000	0.18098	0.999000	0.59377	0.911000	0.54048	-0.127000	0.10547	0.553000	0.29044	0.533000	0.62120	TCT	T|0.993;C|0.007	0.007	strong		0.393	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
KLF3	51274	hgsc.bcm.edu	37	4	38690515	38690515	+	Missense_Mutation	SNP	A	A	G	rs199559194		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38690515A>G	ENST00000261438.5	+	3	672	c.367A>G	c.(367-369)Atg>Gtg	p.M123V	KLF3_ENST00000514033.1_Missense_Mutation_p.M123V	NM_016531.5	NP_057615.3	P57682	KLF3_HUMAN	Kruppel-like factor 3 (basic)	123	Pro-rich.				cellular response to peptide (GO:1901653)|multicellular organismal development (GO:0007275)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|skin(2)	18						GCCGCTGTCCATGCCACCAGT	0.632																																					p.M123V		Atlas-SNP	.											.	KLF3	40	.	0			c.A367G						PASS	.	A	VAL/MET	0,4406		0,0,2203	51.0	54.0	53.0		367	5.5	1.0	4		53	1,8599	1.2+/-3.3	0,1,4299	no	missense	KLF3	NM_016531.5	21	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	benign	123/346	38690515	1,13005	2203	4300	6503	SO:0001583	missense	51274	exon3			CTGTCCATGCCAC	AF285837	CCDS3444.1	4p16.1-p15.2	2013-01-08			ENSG00000109787	ENSG00000109787		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	16516	protein-coding gene	gene with protein product	"""basic Kruppel-like factor"""	609392				18391014	Standard	NM_016531		Approved	BKLF	uc003gth.4	P57682	OTTHUMG00000097821	ENST00000261438.5:c.367A>G	4.37:g.38690515A>G	ENSP00000261438:p.Met123Val	141.0	0.0	0		161.0	73.0	0.453416	NM_016531	Q6PIR1|Q86TN0|Q9P2X6	Missense_Mutation	SNP	ENST00000261438.5	37	CCDS3444.1	.	.	.	.	.	.	.	.	.	.	A	14.68	2.607253	0.46527	0.0	1.16E-4	ENSG00000109787	ENST00000261438;ENST00000514033	T;T	0.42900	0.96;0.96	5.53	5.53	0.82687	.	0.059640	0.64402	D	0.000002	T	0.24160	0.0585	N	0.08118	0	0.28589	N	0.909727	B	0.02656	0.0	B	0.01281	0.0	T	0.06917	-1.0800	10	0.14656	T	0.56	.	15.827	0.78718	1.0:0.0:0.0:0.0	.	123	P57682	KLF3_HUMAN	V	123	ENSP00000261438:M123V;ENSP00000421252:M123V	ENSP00000261438:M123V	M	+	1	0	KLF3	38366910	1.000000	0.71417	1.000000	0.80357	0.838000	0.47535	4.350000	0.59392	2.324000	0.78689	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	weak		0.632	KLF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215093.2		
EML5	161436	hgsc.bcm.edu	37	14	89220874	89220874	+	Silent	SNP	C	C	T	rs201072176		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:89220874C>T	ENST00000380664.5	-	2	338	c.339G>A	c.(337-339)gcG>gcA	p.A113A	EML5_ENST00000554922.1_Silent_p.A113A|EML5_ENST00000352093.5_Silent_p.A113A			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	113						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CTAAGTCAAACGCCAAGCAAG	0.299													C|||	1	0.000199681	0.0	0.0	5008	,	,		15572	0.0		0.0	False		,,,				2504	0.001				p.A113A		Atlas-SNP	.											.	EML5	141	.	0			c.G339A						PASS	.	C		1,3729		0,1,1864	105.0	92.0	96.0		339	1.0	1.0	14		96	8,8200		0,8,4096	no	coding-synonymous	EML5	NM_183387.2		0,9,5960	TT,TC,CC		0.0975,0.0268,0.0754		113/1978	89220874	9,11929	1865	4104	5969	SO:0001819	synonymous_variant	161436	exon2			GTCAAACGCCAAG	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.339G>A	14.37:g.89220874C>T		93.0	0.0	0		95.0	53.0	0.557895	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	37	CCDS45148.1																																																																																			C|0.999;T|0.001	0.001	weak		0.299	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
PHC3	80012	hgsc.bcm.edu	37	3	169846937	169846937	+	Silent	SNP	A	A	G	rs373112767		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:169846937A>G	ENST00000494943.1	-	8	1355	c.1287T>C	c.(1285-1287)gcT>gcC	p.A429A	PHC3_ENST00000495893.2_Silent_p.A441A|PHC3_ENST00000467570.1_Silent_p.A388A			Q8NDX5	PHC3_HUMAN	polyhomeotic homolog 3 (Drosophila)	429	Gln-rich.|Pro-rich.				multicellular organismal development (GO:0007275)	actin cytoskeleton (GO:0015629)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(12)|ovary(1)|upper_aerodigestive_tract(2)	26	all_cancers(22;2.67e-22)|all_epithelial(15;4.73e-27)|all_lung(20;6.31e-17)|Lung NSC(18;2.61e-16)|Ovarian(172;0.000337)|Breast(254;0.169)		Lung(28;2.71e-13)|STAD - Stomach adenocarcinoma(35;0.0655)			CTGGCTGGAGAGCTGATGACA	0.493													A|||	1	0.000199681	0.0	0.0	5008	,	,		22525	0.0		0.001	False		,,,				2504	0.0				p.A441A		Atlas-SNP	.											.	PHC3	113	.	0			c.T1323C						PASS	.	A		0,4170		0,0,2085	61.0	64.0	63.0		1323	2.4	1.0	3		63	1,8431		0,1,4215	no	coding-synonymous	PHC3	NM_024947.3		0,1,6300	GG,GA,AA		0.0119,0.0,0.0079		441/996	169846937	1,12601	2085	4216	6301	SO:0001819	synonymous_variant	80012	exon8			CTGGAGAGCTGAT		CCDS46952.1	3q26.32	2014-01-28	2006-09-12		ENSG00000173889	ENSG00000173889		"""Sterile alpha motif (SAM) domain containing"""	15682	protein-coding gene	gene with protein product	"""early development regulator 3"", ""polyhomeotic like 3"""		"""polyhomeotic like 3 (Drosophila)"""			12167701, 12384788	Standard	NM_024947		Approved	EDR3, FLJ12967, FLJ12729, HPH3	uc003fgl.2	Q8NDX5	OTTHUMG00000158777	ENST00000494943.1:c.1287T>C	3.37:g.169846937A>G		128.0	0.0	0		131.0	58.0	0.442748	NM_024947	A2RRP9|Q5HYF0|Q6NSG2|Q8NFT7|Q8NFZ1|Q8TBM2|Q9H971|Q9H9I4	Silent	SNP	ENST00000494943.1	37																																																																																				.	.	weak		0.493	PHC3-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000352182.3	NM_024947	
AK2	204	hgsc.bcm.edu	37	1	33502376	33502376	+	Silent	SNP	G	G	A	rs76061645	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33502376G>A	ENST00000487289.1	-	1	69	c.54C>T	c.(52-54)gcC>gcT	p.A18A	AK2_ENST00000480134.1_Silent_p.A18A|AK2_ENST00000548033.1_Silent_p.A18A|AK2_ENST00000467905.1_Silent_p.A18A|AK2_ENST00000373449.2_Silent_p.A18A|AK2_ENST00000354858.6_Silent_p.A18A					adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				CCAGCAGCACGGCCCGGATGC	0.682																																					p.A18A		Atlas-SNP	.											.	AK2	27	.	0			c.C54T						PASS	.						14.0	13.0	14.0					1																	33502376		2202	4296	6498	SO:0001819	synonymous_variant	204	exon1			CAGCACGGCCCGG	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"""Adenylate kinases"""	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000487289.1:c.54C>T	1.37:g.33502376G>A		333.0	0.0	0		244.0	26.0	0.106557	NM_001199199		Silent	SNP	ENST00000487289.1	37																																																																																				G|0.955;A|0.045	0.045	strong		0.682	AK2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000011889.4	NM_001625	
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:41351321C>T	ENST00000301141.5	-	7	1059	c.1039G>A	c.(1039-1041)Gcc>Acc	p.A347T	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	347					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	GGCATCTTGGCCCGGTCCTCA	0.537																																					p.A347T		Atlas-SNP	.											.	CYP2A6	69	.	0			c.G1039A						PASS	.						115.0	104.0	108.0					19																	41351321		2203	4300	6503	SO:0001583	missense	1548	exon7			TCTTGGCCCGGTC	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.1039G>A	19.37:g.41351321C>T	ENSP00000301141:p.Ala347Thr	406.0	0.0	0		368.0	44.0	0.119565	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Missense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	.	.	.	.	.	.	.	.	.	.	-	4.025	0.002161	0.07819	.	.	ENSG00000255974	ENST00000301141	T	0.69306	-0.39	2.76	-2.87	0.05700	.	0.614141	0.16066	U	0.231229	T	0.43853	0.1266	L	0.31120	0.905	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.002;0.004	T	0.17319	-1.0373	10	0.22706	T	0.39	.	4.9051	0.13795	0.0:0.2915:0.1649:0.5436	.	347;347	Q13120;P11509	.;CP2A6_HUMAN	T	347	ENSP00000301141:A347T	ENSP00000301141:A347T	A	-	1	0	CYP2A6	46043161	0.000000	0.05858	0.011000	0.14972	0.659000	0.38960	-1.191000	0.03055	-0.603000	0.05767	-0.912000	0.02778	GCC	C|0.500;T|0.500	0.500	strong		0.537	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
DNAH9	1770	hgsc.bcm.edu	37	17	11511480	11511480	+	Missense_Mutation	SNP	G	G	A	rs17599639	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:11511480G>A	ENST00000262442.4	+	2	520	c.452G>A	c.(451-453)cGc>cAc	p.R151H	DNAH9_ENST00000454412.2_Missense_Mutation_p.R151H|DNAH9_ENST00000579828.1_Missense_Mutation_p.R151H	NM_001372.3	NP_001363.2	Q9NYC9	DYH9_HUMAN	dynein, axonemal, heavy chain 9	151	Stem. {ECO:0000250}.		R -> H (in dbSNP:rs17599639).		cell projection organization (GO:0030030)|cellular component movement (GO:0006928)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|cytoskeleton (GO:0005856)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)			NS(2)|autonomic_ganglia(1)|breast(15)|central_nervous_system(5)|endometrium(17)|haematopoietic_and_lymphoid_tissue(6)|kidney(17)|large_intestine(49)|liver(2)|lung(123)|ovary(6)|pancreas(1)|prostate(6)|skin(21)|stomach(2)|upper_aerodigestive_tract(13)|urinary_tract(4)	290		Breast(5;0.0122)|all_epithelial(5;0.131)		Colorectal(4;6.88e-05)|COAD - Colon adenocarcinoma(4;0.000813)|READ - Rectum adenocarcinoma(10;0.157)		GAGAAGAATCGCCTAAACTGG	0.488													G|||	117	0.0233626	0.0159	0.0216	5008	,	,		19075	0.0		0.0417	False		,,,				2504	0.0399				p.R151H		Atlas-SNP	.											DNAH9,NS,malignant_melanoma,+1,1	DNAH9	695	1	0			c.G452A						PASS	.	G	HIS/ARG	82,4324	69.8+/-107.6	0,82,2121	150.0	146.0	147.0		452	0.9	0.0	17	dbSNP_123	147	353,8247	119.9+/-179.2	8,337,3955	yes	missense	DNAH9	NM_001372.3	29	8,419,6076	AA,AG,GG		4.1047,1.8611,3.3446	benign	151/4487	11511480	435,12571	2203	4300	6503	SO:0001583	missense	1770	exon2			AGAATCGCCTAAA	U61740	CCDS11160.1, CCDS11161.1	17p12	2009-05-07	2006-09-04		ENSG00000007174	ENSG00000007174		"""Axonemal dyneins"""	2953	protein-coding gene	gene with protein product		603330	"""dynein, axonemal, heavy polypeptide 17-like"", ""dynein, axonemal, heavy polypeptide 9"""	DNAH17L		8812413, 11247663	Standard	NM_001372		Approved	Dnahc9, KIAA0357, HL20, HL-20, DNAL1, DYH9	uc002gne.3	Q9NYC9	OTTHUMG00000130383	ENST00000262442.4:c.452G>A	17.37:g.11511480G>A	ENSP00000262442:p.Arg151His	84.0	0.0	0		92.0	45.0	0.48913	NM_001372	A2VCQ8|O15064|O95494|Q9NQ28	Missense_Mutation	SNP	ENST00000262442.4	37	CCDS11160.1	54	0.024725274725274724	11	0.022357723577235773	9	0.024861878453038673	0	0.0	34	0.044854881266490766	G	0.021	-1.427313	0.01117	0.018611	0.041047	ENSG00000007174	ENST00000262442;ENST00000454412	T;T	0.25749	1.82;1.78	5.7	0.937	0.19494	.	0.633514	0.15787	N	0.244627	T	0.01124	0.0037	N	0.00321	-1.65	0.80722	D	1	B;B	0.06786	0.0;0.001	B;B	0.01281	0.0;0.0	T	0.45366	-0.9266	10	0.02654	T	1	.	11.4204	0.49978	0.8892:0.0:0.1108:0.0	rs17599639;rs52801139;rs17599639	151;151	Q9NYC9;E7EP17	DYH9_HUMAN;.	H	151	ENSP00000262442:R151H;ENSP00000414874:R151H	ENSP00000262442:R151H	R	+	2	0	DNAH9	11452205	0.998000	0.40836	0.000000	0.03702	0.104000	0.19210	4.213000	0.58520	-0.114000	0.11936	-0.812000	0.03155	CGC	G|0.971;A|0.029	0.029	strong		0.488	DNAH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252756.2	NM_001372	
PUM1	9698	hgsc.bcm.edu	37	1	31441316	31441316	+	Silent	SNP	T	T	C	rs202191174	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:31441316T>C	ENST00000257075.5	-	11	1623	c.1530A>G	c.(1528-1530)caA>caG	p.Q510Q	PUM1_ENST00000424085.2_Silent_p.Q268Q|PUM1_ENST00000423018.2_Silent_p.Q414Q|PUM1_ENST00000373742.2_Silent_p.Q451Q|PUM1_ENST00000373741.4_Silent_p.Q546Q|PUM1_ENST00000490546.1_5'UTR|SNORD85_ENST00000363311.1_RNA|PUM1_ENST00000426105.2_Silent_p.Q510Q|PUM1_ENST00000373747.3_Silent_p.Q511Q|PUM1_ENST00000440538.2_Silent_p.Q511Q	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	510	Ala-rich.|Gln-rich.				membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		TCAAAGGACGTTGGCTGGCTC	0.522													T|||	2	0.000399361	0.0	0.0014	5008	,	,		18651	0.0		0.0	False		,,,				2504	0.001				p.Q510Q		Atlas-SNP	.											.	PUM1	107	.	0			c.A1530G						PASS	.	T	,	0,4406		0,0,2203	105.0	96.0	99.0		1530,1530	0.6	1.0	1		99	7,8593	5.7+/-21.5	0,7,4293	yes	coding-synonymous,coding-synonymous	PUM1	NM_001020658.1,NM_014676.2	,	0,7,6496	CC,CT,TT		0.0814,0.0,0.0538	,	510/1189,510/1187	31441316	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	9698	exon11			AGGACGTTGGCTG	AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.1530A>G	1.37:g.31441316T>C		139.0	0.0	0		100.0	29.0	0.29	NM_014676	A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Silent	SNP	ENST00000257075.5	37	CCDS338.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	9.593	1.126645	0.20959	0.0	8.14E-4	ENSG00000134644	ENST00000525843;ENST00000498419;ENST00000532678	.	.	.	5.77	0.558	0.17266	.	.	.	.	.	T	0.58836	0.2150	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53940	-0.8367	4	.	.	.	-4.9988	11.0358	0.47799	0.0:0.6746:0.0:0.3254	.	.	.	.	A	528;222;198	.	.	T	-	1	0	PUM1	31213903	1.000000	0.71417	0.999000	0.59377	0.955000	0.61496	0.888000	0.28268	0.136000	0.18733	-0.912000	0.02778	ACG	T|1.000;C|0.000	0.000	strong		0.522	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1		
F13B	2165	hgsc.bcm.edu	37	1	197029592	197029592	+	Missense_Mutation	SNP	C	C	T	rs145637157		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:197029592C>T	ENST00000367412.1	-	5	752	c.709G>A	c.(709-711)Gtt>Att	p.V237I		NM_001994.2	NP_001985.2	P05160	F13B_HUMAN	coagulation factor XIII, B polypeptide	237	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.				blood coagulation (GO:0007596)	extracellular region (GO:0005576)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(5)|liver(1)|lung(40)|prostate(2)|skin(4)|upper_aerodigestive_tract(3)	66						AAAAACTGAACGACATCTCCT	0.313																																					p.V237I		Atlas-SNP	.											.	F13B	137	.	0			c.G709A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	66.0	73.0	71.0		709	3.9	0.8	1	dbSNP_134	71	6,8588	5.0+/-18.6	0,6,4291	yes	missense	F13B	NM_001994.2	29	0,7,6493	TT,TC,CC		0.0698,0.0227,0.0538	probably-damaging	237/662	197029592	7,12993	2203	4297	6500	SO:0001583	missense	2165	exon5			ACTGAACGACATC	M14057	CCDS1388.1	1q31-q32.1	2012-10-02			ENSG00000143278	ENSG00000143278			3534	protein-coding gene	gene with protein product		134580				2339067, 2271707	Standard	NM_001994		Approved	FXIIIB	uc001gtt.1	P05160	OTTHUMG00000036519	ENST00000367412.1:c.709G>A	1.37:g.197029592C>T	ENSP00000356382:p.Val237Ile	184.0	0.0	0		203.0	105.0	0.517241	NM_001994	A8K3E5|Q5VYL5	Missense_Mutation	SNP	ENST00000367412.1	37	CCDS1388.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.908059	0.52333	2.27E-4	6.98E-4	ENSG00000143278	ENST00000367412	T	0.68331	-0.32	5.76	3.86	0.44501	Complement control module (2);Sushi/SCR/CCP (3);	0.296520	0.18406	N	0.142199	T	0.68220	0.2977	L	0.50847	1.595	0.34229	D	0.676347	D	0.54772	0.968	P	0.49085	0.6	T	0.73707	-0.3898	10	0.35671	T	0.21	.	15.9628	0.79945	0.0:0.8763:0.0:0.1237	.	237	P05160	F13B_HUMAN	I	237	ENSP00000356382:V237I	ENSP00000356382:V237I	V	-	1	0	F13B	195296215	0.828000	0.29307	0.781000	0.31783	0.963000	0.63663	1.393000	0.34497	0.448000	0.26722	-0.813000	0.03139	GTT	C|1.000;T|0.000	0.000	weak		0.313	F13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088821.2	NM_001994	
KIAA1217	56243	hgsc.bcm.edu	37	10	24834980	24834980	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:24834980C>T	ENST00000376454.3	+	21	5589	c.5559C>T	c.(5557-5559)ctC>ctT	p.L1853L	KIAA1217_ENST00000458595.1_Silent_p.L1259L|KIAA1217_ENST00000376452.3_Silent_p.L1284L|KIAA1217_ENST00000396445.1_3'UTR|KIAA1217_ENST00000376462.1_Silent_p.L1174L|KIAA1217_ENST00000376451.2_3'UTR	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1853	Ser-rich. {ECO:0000255}.				embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)		p.L1853L(1)		breast(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(19)|lung(19)|ovary(5)|prostate(3)|skin(3)|urinary_tract(1)	70						CTGCCTCCCTCATCCCTTCTG	0.502																																					p.L1853L		Atlas-SNP	.											KIAA1217,NS,carcinoma,0,1	KIAA1217	235	1	1	Substitution - coding silent(1)	kidney(1)	c.C5559T						PASS	.						173.0	177.0	176.0					10																	24834980		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon21			CTCCCTCATCCCT	BX640796	CCDS31165.1, CCDS41496.1, CCDS60501.1, CCDS60502.1, CCDS60504.1, CCDS60505.1	10p12.31	2009-09-16			ENSG00000120549	ENSG00000120549			25428	protein-coding gene	gene with protein product	"""sickle tail"""					10574462	Standard	XM_005252500		Approved	DKFZP761L0424, SKT	uc001iru.4	Q5T5P2	OTTHUMG00000017824	ENST00000376454.3:c.5559C>T	10.37:g.24834980C>T		255.0	0.0	0		271.0	129.0	0.476015	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			.	.	none		0.502	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
TEKT4	150483	hgsc.bcm.edu	37	2	95537568	95537568	+	Missense_Mutation	SNP	C	C	T	rs80243548	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:95537568C>T	ENST00000295201.4	+	1	381	c.244C>T	c.(244-246)Cgc>Tgc	p.R82C	TEKT4_ENST00000427593.2_Missense_Mutation_p.R82C|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	82					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCTGGCGCAGCGCACGCAGCA	0.692													.|||	53	0.0105831	0.0	0.0072	5008	,	,		16615	0.001		0.0169	False		,,,				2504	0.0307				p.R82C		Atlas-SNP	.											TEKT4,bladder,carcinoma,-2,2	TEKT4	72	2	0			c.C244T						PASS	.	C	CYS/ARG	12,4370		0,12,2179	16.0	17.0	17.0		244	2.0	0.7	2	dbSNP_131	17	182,8356		2,178,4089	no	missense	TEKT4	NM_144705.2	180	2,190,6268	TT,TC,CC		2.1316,0.2738,1.5015	benign	82/436	95537568	194,12726	2191	4269	6460	SO:0001583	missense	150483	exon1			GCGCAGCGCACGC	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.244C>T	2.37:g.95537568C>T	ENSP00000295201:p.Arg82Cys	36.0	0.0	0		16.0	10.0	0.625	NM_144705		Missense_Mutation	SNP	ENST00000295201.4	37	CCDS2005.1	14	0.00641025641025641	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	12	0.0158311345646438	.	13.71	2.317321	0.40996	0.002738	0.021316	ENSG00000163060	ENST00000295201;ENST00000427593	T;T	0.02863	4.13;4.13	1.97	1.97	0.26223	.	0.121716	0.56097	N	0.000027	T	0.01592	0.0051	L	0.55990	1.75	0.80722	D	1	B	0.27997	0.197	B	0.25405	0.06	T	0.49808	-0.8900	10	0.37606	T	0.19	-10.6904	9.5816	0.39490	0.0:1.0:0.0:0.0	.	82	Q8WW24	TEKT4_HUMAN	C	82	ENSP00000295201:R82C;ENSP00000407596:R82C	ENSP00000295201:R82C	R	+	1	0	TEKT4	94901295	0.174000	0.23070	0.741000	0.31004	0.479000	0.33129	-0.002000	0.12924	1.094000	0.41399	0.558000	0.71614	CGC	C|0.978;G|0.007;T|0.015	0.015	strong		0.692	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
FRMPD2	143162	hgsc.bcm.edu	37	10	49400730	49400730	+	Missense_Mutation	SNP	C	C	T	rs116034788	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:49400730C>T	ENST00000374201.3	-	16	2464	c.2162G>A	c.(2161-2163)cGc>cAc	p.R721H	FRMPD2_ENST00000407470.4_Missense_Mutation_p.R689H|FRMPD2_ENST00000305531.3_Missense_Mutation_p.R696H	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	721					tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		CACCCACCTGCGCCCGATGCC	0.493													C|||	14	0.00279553	0.0	0.0029	5008	,	,		20123	0.0089		0.003	False		,,,				2504	0.0				p.R721H		Atlas-SNP	.											FRMPD2,NS,carcinoma,-1,1	FRMPD2	157	1	0			c.G2162A						PASS	.	C	HIS/ARG	6,4400	11.4+/-27.6	0,6,2197	75.0	54.0	61.0		2162	0.9	0.7	10	dbSNP_132	61	19,8581	14.0+/-48.4	0,19,4281	yes	missense	FRMPD2	NM_001018071.3	29	0,25,6478	TT,TC,CC		0.2209,0.1362,0.1922	possibly-damaging	721/1310	49400730	25,12981	2203	4300	6503	SO:0001583	missense	143162	exon16			CACCTGCGCCCGA	AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.2162G>A	10.37:g.49400730C>T	ENSP00000363317:p.Arg721His	121.0	0.0	0		131.0	60.0	0.458015	NM_001018071	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	ENST00000374201.3	37	CCDS31195.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	4	0.006993006993006993	1	0.0013192612137203166	C	9.151	1.016217	0.19355	0.001362	0.002209	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.64803	-0.08;-0.12;-0.11	5.01	0.934	0.19477	.	.	.	.	.	T	0.29882	0.0747	N	0.14661	0.345	0.21184	N	0.999768	B;D;B	0.54207	0.024;0.965;0.024	B;B;B	0.38156	0.003;0.266;0.003	T	0.13818	-1.0495	9	0.45353	T	0.12	.	6.935	0.24461	0.0:0.5514:0.2905:0.1581	.	696;721;689	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	H	721;696;689	ENSP00000363317:R721H;ENSP00000307079:R696H;ENSP00000384339:R689H	ENSP00000307079:R696H	R	-	2	0	FRMPD2	49070736	0.170000	0.23016	0.681000	0.30009	0.090000	0.18270	0.379000	0.20585	0.234000	0.21139	-0.211000	0.12701	CGC	C|0.998;T|0.002	0.002	strong		0.493	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047923.3	NM_152428	
SDC4	6385	hgsc.bcm.edu	37	20	43956017	43956017	+	Missense_Mutation	SNP	C	C	T	rs202142981		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:43956017C>T	ENST00000372733.3	-	5	523	c.484G>A	c.(484-486)Gtc>Atc	p.V162I	SDC4_ENST00000537976.1_Missense_Mutation_p.V90I	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	162					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				ATCAGGAAGACGGCAAAGAGG	0.532			T	ROS1	NSCLC								C|||	1	0.000199681	0.0	0.0	5008	,	,		17406	0.0		0.001	False		,,,				2504	0.0				p.V162I		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.G484A						PASS	.	C	ILE/VAL	1,4405	2.1+/-5.4	0,1,2202	95.0	85.0	89.0		484	-3.4	0.0	20		89	0,8600		0,0,4300	yes	missense	SDC4	NM_002999.3	29	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	benign	162/199	43956017	1,13005	2203	4300	6503	SO:0001583	missense	6385	exon5			GGAAGACGGCAAA	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"""Proteoglycans / Cell Surface : Syndecans"""	10661	protein-coding gene	gene with protein product	"""syndecan proteoglycan 4"""	600017	"""syndecan 4 (amphiglycan, ryudocan)"""			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.484G>A	20.37:g.43956017C>T	ENSP00000361818:p.Val162Ile	103.0	0.0	0		116.0	55.0	0.474138	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.725885	0.00694	2.27E-4	0.0	ENSG00000124145	ENST00000372733;ENST00000537976	T	0.24350	1.86	5.24	-3.38	0.04883	.	0.925625	0.09152	N	0.841349	T	0.13372	0.0324	N	0.21194	0.64	0.19300	N	0.999978	B	0.29766	0.256	B	0.23150	0.044	T	0.31888	-0.9927	10	0.07482	T	0.82	-1.8487	13.6197	0.62130	0.0:0.4611:0.0:0.5389	.	162	P31431	SDC4_HUMAN	I	162;90	ENSP00000361818:V162I	ENSP00000361818:V162I	V	-	1	0	SDC4	43389431	0.000000	0.05858	0.004000	0.12327	0.064000	0.16182	-0.645000	0.05409	-0.505000	0.06568	-0.253000	0.11424	GTC	.	.	weak		0.532	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999	
MYOM1	8736	hgsc.bcm.edu	37	18	3141939	3141939	+	Missense_Mutation	SNP	T	T	C	rs200179081	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:3141939T>C	ENST00000356443.4	-	14	2356	c.2023A>G	c.(2023-2025)Aag>Gag	p.K675E	MYOM1_ENST00000400569.3_Missense_Mutation_p.K675E|MYOM1_ENST00000261606.7_Missense_Mutation_p.K675E	NM_003803.3|NM_019856.1	NP_003794.3|NP_062830.1	P52179	MYOM1_HUMAN	myomesin 1	675	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				muscle contraction (GO:0006936)	M band (GO:0031430)|striated muscle myosin thick filament (GO:0005863)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|structural constituent of muscle (GO:0008307)			NS(2)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(20)|ovary(4)|pancreas(1)|prostate(4)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	77						AGTCTTACCTTTTCCACAAAG	0.507													T|||	2	0.000399361	0.0	0.0	5008	,	,		19010	0.0		0.002	False		,,,				2504	0.0				p.K675E		Atlas-SNP	.											.	MYOM1	192	.	0			c.A2023G						PASS	.	T	GLU/LYS,GLU/LYS	0,3942		0,0,1971	91.0	93.0	93.0		2023,2023	5.8	1.0	18		93	4,8312		0,4,4154	yes	missense,missense	MYOM1	NM_003803.3,NM_019856.1	56,56	0,4,6125	CC,CT,TT		0.0481,0.0,0.0326	probably-damaging,probably-damaging	675/1686,675/1590	3141939	4,12254	1971	4158	6129	SO:0001583	missense	8736	exon14			TTACCTTTTCCAC	AF185573	CCDS45823.1, CCDS45824.1	18p11.31	2014-09-17	2012-10-17		ENSG00000101605	ENSG00000101605		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	7613	protein-coding gene	gene with protein product	"""skelemin"""	603508	"""myomesin 1 (skelemin) (185kD)"", ""myomesin 1 (skelemin) 185kDa"", ""myomesin 1, 185kDa"""			9806852	Standard	NM_019856		Approved		uc002klp.3	P52179	OTTHUMG00000178209	ENST00000356443.4:c.2023A>G	18.37:g.3141939T>C	ENSP00000348821:p.Lys675Glu	83.0	0.0	0		89.0	29.0	0.325843	NM_003803	Q14BD6|Q6H969|Q6ZUU0	Missense_Mutation	SNP	ENST00000356443.4	37	CCDS45824.1	.	.	.	.	.	.	.	.	.	.	T	22.8	4.336470	0.81801	0.0	4.81E-4	ENSG00000101605	ENST00000356443;ENST00000400569;ENST00000261606	T;T;T	0.57752	0.38;0.38;0.38	5.8	5.8	0.92144	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.75824	0.3902	M	0.87758	2.905	0.58432	D	0.999995	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.76942	-0.2772	10	0.34782	T	0.22	.	16.1611	0.81712	0.0:0.0:0.0:1.0	.	675;675	P52179-2;P52179	.;MYOM1_HUMAN	E	675	ENSP00000348821:K675E;ENSP00000383413:K675E;ENSP00000261606:K675E	ENSP00000261606:K675E	K	-	1	0	MYOM1	3131939	1.000000	0.71417	1.000000	0.80357	0.956000	0.61745	8.040000	0.89188	2.213000	0.71641	0.477000	0.44152	AAG	.	.	weak		0.507	MYOM1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441037.2	NM_003803	
PHRF1	57661	hgsc.bcm.edu	37	11	582056	582056	+	Silent	SNP	G	G	A	rs117660271	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:582056G>A	ENST00000264555.5	+	3	317	c.189G>A	c.(187-189)gaG>gaA	p.E63E	PHRF1_ENST00000533464.1_Silent_p.E59E|PHRF1_ENST00000416188.2_Silent_p.E63E|PHRF1_ENST00000413872.2_Silent_p.E62E	NM_020901.2	NP_065952.2	Q9P1Y6	PHRF1_HUMAN	PHD and ring finger domains 1	63					mRNA processing (GO:0006397)|transcription from RNA polymerase II promoter (GO:0006366)	membrane (GO:0016020)	RNA polymerase binding (GO:0070063)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(13)|urinary_tract(2)	28						GGGCGTCTGAGGAGGAAGACC	0.572													G|||	7	0.00139776	0.0	0.0014	5008	,	,		17686	0.0		0.005	False		,,,				2504	0.001				p.E63E		Atlas-SNP	.											.	PHRF1	188	.	0			c.G189A						PASS	.	G		4,4256		0,4,2126	50.0	67.0	62.0		189	-5.6	0.0	11	dbSNP_132	62	35,8479		0,35,4222	no	coding-synonymous	PHRF1	NM_020901.2		0,39,6348	AA,AG,GG		0.4111,0.0939,0.3053		63/1649	582056	39,12735	2130	4257	6387	SO:0001819	synonymous_variant	57661	exon3			GTCTGAGGAGGAA	BC004950	CCDS44507.1, CCDS65987.1, CCDS65988.1, CCDS65989.1	11p15.5	2014-06-13			ENSG00000070047	ENSG00000070047		"""RING-type (C3HC4) zinc fingers"", ""Zinc fingers, PHD-type"""	24351	protein-coding gene	gene with protein product	"""CTD binding SR like protein rA9"", ""protein phosphatase 1, regulatory subunit 125"""	611780		RNF221			Standard	XM_005253027		Approved	KIAA1542, PPP1R125	uc010qwc.2	Q9P1Y6	OTTHUMG00000165141	ENST00000264555.5:c.189G>A	11.37:g.582056G>A		67.0	0.0	0		77.0	34.0	0.441558	NM_020901	A6H8W1|B7ZM64|B9EGP0|C9JS82|Q6PJP2|Q8IVY2|Q8N2Y7|Q9BSM2	Silent	SNP	ENST00000264555.5	37																																																																																				G|0.997;A|0.003	0.003	strong		0.572	PHRF1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382133.1	NM_020901	
IREB2	3658	hgsc.bcm.edu	37	15	78789534	78789534	+	Missense_Mutation	SNP	A	A	G	rs140959198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78789534A>G	ENST00000258886.8	+	21	2811	c.2662A>G	c.(2662-2664)Ata>Gta	p.I888V		NM_004136.2	NP_004127	P48200	IREB2_HUMAN	iron-responsive element binding protein 2	888					aging (GO:0007568)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|erythrocyte homeostasis (GO:0034101)|intestinal absorption (GO:0050892)|iron ion transport (GO:0006826)|osteoclast differentiation (GO:0030316)|post-embryonic development (GO:0009791)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to iron(II) ion (GO:0010040)|response to retinoic acid (GO:0032526)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|translation repressor activity (GO:0030371)			central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	41				UCEC - Uterine corpus endometrioid carcinoma (272;0.232)		TGGAATTGGCATAGCTCCACT	0.393													A|||	8	0.00159744	0.0	0.0058	5008	,	,		16922	0.0		0.004	False		,,,				2504	0.0				p.I888V	NSCLC(200;764 2208 35157 49871 50830)	Atlas-SNP	.											.	IREB2	106	.	0			c.A2662G						PASS	.	A	VAL/ILE	2,4390	4.2+/-10.8	0,2,2194	114.0	106.0	109.0		2662	4.8	1.0	15	dbSNP_134	109	41,8545	27.4+/-76.7	0,41,4252	yes	missense	IREB2	NM_004136.2	29	0,43,6446	GG,GA,AA		0.4775,0.0455,0.3313	benign	888/964	78789534	43,12935	2196	4293	6489	SO:0001583	missense	3658	exon21			ATTGGCATAGCTC	M58511	CCDS10302.1	15q25.1	2013-09-20			ENSG00000136381	ENSG00000136381			6115	protein-coding gene	gene with protein product		147582				2172968	Standard	NM_004136		Approved	IRP2	uc002bdr.2	P48200	OTTHUMG00000143861	ENST00000258886.8:c.2662A>G	15.37:g.78789534A>G	ENSP00000258886:p.Ile888Val	167.0	0.0	0		170.0	83.0	0.488235	NM_004136	A8KAC7|E1CJT9|H0YKU0|Q13095|Q1HE21|Q59FQ7|Q8WVK6|Q9UF17	Missense_Mutation	SNP	ENST00000258886.8	37	CCDS10302.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	12.03	1.814651	0.32053	4.55E-4	0.004775	ENSG00000136381	ENST00000258886	T	0.13657	2.57	5.87	4.75	0.60458	Aconitase/3-isopropylmalate dehydratase, swivel (2);Aconitase A/isopropylmalate dehydratase small subunit, swivel (1);	0.084546	0.85682	D	0.000000	T	0.06962	0.0177	L	0.28458	0.855	0.80722	D	1	B	0.12630	0.006	B	0.20184	0.028	T	0.10636	-1.0621	10	0.09843	T	0.71	.	12.1948	0.54290	0.9334:0.0:0.0666:0.0	.	888	P48200	IREB2_HUMAN	V	888	ENSP00000258886:I888V	ENSP00000258886:I888V	I	+	1	0	IREB2	76576589	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.693000	0.74582	1.148000	0.42385	0.533000	0.62120	ATA	A|0.998;G|0.002	0.002	strong		0.393	IREB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000290109.3	NM_004136	
NBPF10	100132406	hgsc.bcm.edu	37	1	145299838	145299838	+	Missense_Mutation	SNP	G	G	A	rs200473325	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:145299838G>A	ENST00000369338.1	+	2	264	c.74G>A	c.(73-75)cGc>cAc	p.R25H	NBPF10_ENST00000369339.3_Intron|RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000342960.5_Missense_Mutation_p.R296H			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	296						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.R296H(3)|p.R25H(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAGAAATTGCGCCCCCAGCTG	0.488																																					p.R296H		Atlas-SNP	.											NBPF10_ENST00000369338,NS,carcinoma,0,10	NBPF10	221	10	6	Substitution - Missense(6)	endometrium(4)|urinary_tract(2)	c.G887A						scavenged	.						15.0	13.0	13.0					1																	145299838		690	1577	2267	SO:0001583	missense	100132406	exon6			AATTGCGCCCCCA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.74G>A	1.37:g.145299838G>A	ENSP00000358344:p.Arg25His	208.0	1.0	0.00480769		98.0	7.0	0.0714286	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	2.633	-0.285860	0.05605	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.03301	4.04;3.98	1.05	-2.1	0.07210	.	.	.	.	.	T	0.01905	0.0060	.	.	.	0.09310	N	1	D	0.59767	0.986	P	0.53006	0.715	T	0.27088	-1.0084	8	0.31617	T	0.26	.	5.8606	0.18745	0.445:0.0:0.555:0.0	.	25	Q86T75-2	.	H	221;25;25;296	ENSP00000358344:R25H;ENSP00000345684:R296H	ENSP00000345684:R296H	R	+	2	0	NBPF10	144011195	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.156000	0.03160	-1.371000	0.02141	-1.477000	0.00996	CGC	G|0.733;A|0.266	0.266	strong		0.488	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
VPRBP	9730	hgsc.bcm.edu	37	3	51475454	51475454	+	Intron	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:51475454T>C	ENST00000335891.5	-	6	682							Q9Y4B6	VPRBP_HUMAN	Vpr (HIV-1) binding protein						B cell differentiation (GO:0030183)|cell competition in a multicellular organism (GO:0035212)|histone H2A-T120 phosphorylation (GO:1990245)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)|V(D)J recombination (GO:0033151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|histone kinase activity (H2A-T120 specific) (GO:1990244)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(193;0.000272)|Kidney(197;0.000729)|KIRC - Kidney renal clear cell carcinoma(197;0.000875)		CGCTGCTCGATAGCAGGAGTC	0.433																																					p.I325V		Atlas-SNP	.											.	VPRBP	107	.	0			c.A973G						PASS	.						68.0	60.0	63.0					3																	51475454		1873	4112	5985	SO:0001627	intron_variant	9730	exon8			GCTCGATAGCAGG	AB018343	CCDS74943.1, CCDS74944.1	3p21.2	2011-06-17			ENSG00000145041	ENSG00000145041		"""DDB1 and CUL4 associated factors"""	30911	protein-coding gene	gene with protein product	"""DDB1 and CUL4 associated factor 1"""					8195203, 11223251	Standard	NM_014703		Approved	KIAA0800, MGC102804, DCAF1	uc003dbe.2	Q9Y4B6	OTTHUMG00000156895	ENST00000335891.5:c.672+300A>G	3.37:g.51475454T>C		123.0	0.0	0		145.0	68.0	0.468966	NM_014703	Q2YD74|Q8TBD9|Q9HCA1|Q9UG37	Missense_Mutation	SNP	ENST00000335891.5	37		.	.	.	.	.	.	.	.	.	.	T	9.759	1.169677	0.21621	.	.	ENSG00000145041	ENST00000504652	D	0.98684	-5.07	5.5	4.27	0.50696	Armadillo-type fold (1);	0.050174	0.85682	D	0.000000	D	0.97185	0.9080	N	0.19112	0.55	0.80722	D	1	P	0.38863	0.65	P	0.54140	0.743	D	0.95430	0.8515	10	0.19147	T	0.46	-17.7053	12.3368	0.55071	0.1262:0.0:0.0:0.8738	.	325	Q9Y4B6	VPRBP_HUMAN	V	325	ENSP00000421724:I325V	ENSP00000421724:I325V	I	-	1	0	VPRBP	51450494	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.890000	0.69774	2.209000	0.71365	0.533000	0.62120	ATC	.	.	none		0.433	VPRBP-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_014703	
EVC	2121	hgsc.bcm.edu	37	4	5806512	5806512	+	Silent	SNP	G	G	A	rs115976359	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:5806512G>A	ENST00000264956.6	+	17	2689	c.2505G>A	c.(2503-2505)tcG>tcA	p.S835S	EVC_ENST00000382674.2_Silent_p.S835S	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	835					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				GCAACCCTTCGTCGGGCAGCA	0.552													G|||	66	0.0131789	0.0008	0.0043	5008	,	,		20795	0.0		0.0109	False		,,,				2504	0.0521				p.S835S		Atlas-SNP	.											EVC,colon,carcinoma,0,3	EVC	90	3	0			c.G2505A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	113.0	110.0	111.0		2505	-5.0	0.0	4	dbSNP_132	111	123,8477	64.2+/-126.4	1,121,4178	no	coding-synonymous	EVC	NM_153717.2		1,131,6371	AA,AG,GG		1.4302,0.227,1.0226		835/993	5806512	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	2121	exon17			CCCTTCGTCGGGC	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.2505G>A	4.37:g.5806512G>A		54.0	0.0	0		96.0	40.0	0.416667	NM_153717		Silent	SNP	ENST00000264956.6	37	CCDS3383.1																																																																																			G|0.991;A|0.009	0.009	strong		0.552	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
BTBD7	55727	hgsc.bcm.edu	37	14	93712290	93712290	+	Missense_Mutation	SNP	C	C	A	rs61991737	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:93712290C>A	ENST00000334746.5	-	10	2771	c.2464G>T	c.(2464-2466)Gct>Tct	p.A822S	BTBD7_ENST00000393170.2_Missense_Mutation_p.A396S|BTBD7_ENST00000554565.1_Missense_Mutation_p.A471S	NM_001002860.2	NP_001002860.2	Q9P203	BTBD7_HUMAN	BTB (POZ) domain containing 7	822	Pro-rich.				multicellular organismal development (GO:0007275)|regulation of branching involved in salivary gland morphogenesis (GO:0060693)	nucleus (GO:0005634)				breast(1)|endometrium(3)|kidney(3)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(8)|upper_aerodigestive_tract(1)	35		all_cancers(154;0.08)		Epithelial(152;0.196)|COAD - Colon adenocarcinoma(157;0.212)|all cancers(159;0.223)		GGCGGTGCAGCTTTCACACTC	0.572													C|||	3	0.000599042	0.0	0.0	5008	,	,		17134	0.0		0.001	False		,,,				2504	0.002				p.A822S		Atlas-SNP	.											.	BTBD7	112	.	0			c.G2464T						PASS	.	C	SER/ALA	2,4404	4.2+/-10.8	0,2,2201	55.0	56.0	55.0		2464	5.9	0.3	14	dbSNP_129	55	10,8590	7.7+/-29.5	0,10,4290	yes	missense	BTBD7	NM_001002860.2	99	0,12,6491	AA,AC,CC		0.1163,0.0454,0.0923	possibly-damaging	822/1133	93712290	12,12994	2203	4300	6503	SO:0001583	missense	55727	exon10			GTGCAGCTTTCAC	AB040958	CCDS32146.1, CCDS32147.1, CCDS73684.1	14q32.13	2013-01-08			ENSG00000011114	ENSG00000011114		"""BTB/POZ domain containing"""	18269	protein-coding gene	gene with protein product		610386				10819331, 11527404	Standard	NM_001289133		Approved	FLJ10648, FUP1	uc001ybo.3	Q9P203	OTTHUMG00000171269	ENST00000334746.5:c.2464G>T	14.37:g.93712290C>A	ENSP00000335615:p.Ala822Ser	71.0	0.0	0		77.0	34.0	0.441558	NM_001002860	A8K5V7|Q69Z05|Q7Z308|Q86TS0|Q9HAA4|Q9NVM0	Missense_Mutation	SNP	ENST00000334746.5	37	CCDS32146.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	15.21	2.766791	0.49574	4.54E-4	0.001163	ENSG00000011114	ENST00000334746;ENST00000554565;ENST00000553975;ENST00000393170	T;T	0.49139	1.14;0.79	5.94	5.94	0.96194	.	0.141339	0.64402	D	0.000004	T	0.41627	0.1167	N	0.19112	0.55	0.37849	D	0.929331	P;B;B	0.39480	0.675;0.449;0.058	B;B;B	0.41813	0.367;0.26;0.042	T	0.32241	-0.9914	10	0.34782	T	0.22	.	20.3517	0.98814	0.0:1.0:0.0:0.0	rs61991737	396;471;822	E7ERI4;Q9P203-5;Q9P203	.;.;BTBD7_HUMAN	S	822;471;437;396	ENSP00000335615:A822S;ENSP00000451010:A471S	ENSP00000335615:A822S	A	-	1	0	BTBD7	92782043	1.000000	0.71417	0.295000	0.24960	0.026000	0.11368	3.688000	0.54699	2.818000	0.97014	0.650000	0.86243	GCT	C|0.999;A|0.001	0.001	strong		0.572	BTBD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412701.1	NM_001002860	
HMGCS2	3158	hgsc.bcm.edu	37	1	120293454	120293454	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:120293454G>A	ENST00000369406.3	-	9	1547	c.1498C>T	c.(1498-1500)Cgc>Tgc	p.R500C	HMGCS2_ENST00000544913.2_Missense_Mutation_p.R458C	NM_005518.3	NP_005509.1	P54868	HMCS2_HUMAN	3-hydroxy-3-methylglutaryl-CoA synthase 2 (mitochondrial)	500			R -> H (in HMGCS deficiency). {ECO:0000269|PubMed:11479731}.		cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|ketone body biosynthetic process (GO:0046951)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	hydroxymethylglutaryl-CoA synthase activity (GO:0004421)			NS(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28	all_cancers(5;6.38e-10)|all_epithelial(5;1.1e-10)|Melanoma(3;1.93e-05)|Breast(55;0.218)|all_neural(166;0.219)	all_lung(203;1.29e-06)|Lung NSC(69;9.35e-06)|all_epithelial(167;0.00124)		Lung(183;0.0112)|LUSC - Lung squamous cell carcinoma(189;0.0595)		TACTTTCGGCGATGCTGCTCG	0.517																																					p.R500C		Atlas-SNP	.											.	HMGCS2	58	.	0			c.C1498T						PASS	.						78.0	68.0	72.0					1																	120293454		2203	4300	6503	SO:0001583	missense	3158	exon9			TTCGGCGATGCTG	BC044217	CCDS905.1, CCDS53353.1	1p13-p12	2014-09-17	2010-04-30		ENSG00000134240	ENSG00000134240			5008	protein-coding gene	gene with protein product		600234	"""3-hydroxy-3-methylglutaryl-Coenzyme A synthase 2 (mitochondrial)"""			7851882, 7893153	Standard	NM_005518		Approved		uc001eid.3	P54868	OTTHUMG00000012101	ENST00000369406.3:c.1498C>T	1.37:g.120293454G>A	ENSP00000358414:p.Arg500Cys	113.0	0.0	0		114.0	60.0	0.526316	NM_005518	B7Z8R3|D3Y5K6|Q5SZU2|Q6IBF4	Missense_Mutation	SNP	ENST00000369406.3	37	CCDS905.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.499155	0.64298	.	.	ENSG00000134240	ENST00000369406;ENST00000544913	D;D	0.90324	-2.65;-2.65	5.3	5.3	0.74995	Hydroxymethylglutaryl-coenzyme A synthase C-terminal (1);Thiolase-like (1);	0.000000	0.64402	D	0.000002	D	0.95928	0.8674	M	0.93638	3.44	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.96419	0.9310	10	0.87932	D	0	-2.0E-4	12.9248	0.58254	0.0:0.0:0.8377:0.1623	.	458;500	B7Z8R3;P54868	.;HMCS2_HUMAN	C	500;458	ENSP00000358414:R500C;ENSP00000439495:R458C	ENSP00000358414:R500C	R	-	1	0	HMGCS2	120094977	1.000000	0.71417	0.511000	0.27724	0.425000	0.31504	5.604000	0.67626	2.633000	0.89246	0.561000	0.74099	CGC	.	.	none		0.517	HMGCS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033469.2	NM_005518	
GUCA1B	2979	hgsc.bcm.edu	37	6	42152583	42152583	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:42152583A>G	ENST00000230361.3	-	4	668	c.573T>C	c.(571-573)gcT>gcC	p.A191A		NM_002098.5	NP_002089.4	Q9UMX6	GUC1B_HUMAN	guanylate cyclase activator 1B (retina)	191					body fluid secretion (GO:0007589)|cell-cell signaling (GO:0007267)|phototransduction, visible light (GO:0007603)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)	calcium ion binding (GO:0005509)|calcium sensitive guanylate cyclase activator activity (GO:0008048)			large_intestine(3)|lung(3)|skin(2)	8	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00154)|STAD - Stomach adenocarcinoma(11;0.00177)			GTCTCTGCTGAGCGAGCCAGC	0.587																																					p.A191A		Atlas-SNP	.											.	GUCA1B	19	.	0			c.T573C						PASS	.						117.0	99.0	105.0					6																	42152583		2203	4300	6503	SO:0001819	synonymous_variant	2979	exon4			CTGCTGAGCGAGC	AF173227	CCDS4865.1	6p21.1	2013-02-14			ENSG00000112599	ENSG00000112599		"""EF-hand domain containing"""	4679	protein-coding gene	gene with protein product		602275				9119368	Standard	NM_002098		Approved	GCAP2, RP48	uc003orz.3	Q9UMX6	OTTHUMG00000014697	ENST00000230361.3:c.573T>C	6.37:g.42152583A>G		74.0	0.0	0		98.0	4.0	0.0408163	NM_002098	Q9NU15	Silent	SNP	ENST00000230361.3	37	CCDS4865.1																																																																																			.	.	none		0.587	GUCA1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040550.1	NM_002098	
GUF1	60558	hgsc.bcm.edu	37	4	44680660	44680660	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:44680660G>A	ENST00000281543.5	+	1	215	c.21G>A	c.(19-21)cgG>cgA	p.R7R	GUF1_ENST00000506793.1_Intron	NM_021927.2	NP_068746.2			GUF1 GTPase homolog (S. cerevisiae)											breast(1)|cervix(1)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	19						TCGTGGGTCGGGGCTGGGGGT	0.721																																					p.R7R		Atlas-SNP	.											.	GUF1	72	.	0			c.G21A						PASS	.						5.0	6.0	5.0					4																	44680660		1813	3768	5581	SO:0001819	synonymous_variant	60558	exon1			GGGTCGGGGCTGG		CCDS3468.1	4p13	2006-02-16			ENSG00000151806	ENSG00000151806			25799	protein-coding gene	gene with protein product						8553703	Standard	NM_021927		Approved	FLJ13220	uc003gww.4	Q8N442	OTTHUMG00000128608	ENST00000281543.5:c.21G>A	4.37:g.44680660G>A		44.0	0.0	0		34.0	16.0	0.470588	NM_021927		Silent	SNP	ENST00000281543.5	37	CCDS3468.1																																																																																			.	.	none		0.721	GUF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250469.3	NM_021927	
SIPA1L1	26037	hgsc.bcm.edu	37	14	72090809	72090809	+	Silent	SNP	G	G	A	rs113082664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:72090809G>A	ENST00000555818.1	+	4	2022	c.1674G>A	c.(1672-1674)tcG>tcA	p.S558S	SIPA1L1_ENST00000358550.2_Silent_p.S558S|SIPA1L1_ENST00000537413.1_Silent_p.S33S|SIPA1L1_ENST00000381232.3_Silent_p.S558S	NM_001284247.1|NM_015556.1	NP_001271176.1|NP_056371.1	O43166	SI1L1_HUMAN	signal-induced proliferation-associated 1 like 1	558					actin cytoskeleton reorganization (GO:0031532)|activation of Rap GTPase activity (GO:0032861)|ephrin receptor signaling pathway (GO:0048013)|regulation of axonogenesis (GO:0050770)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of Rap GTPase activity (GO:0032317)|regulation of synaptic plasticity (GO:0048167)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(1)|large_intestine(22)|liver(2)|lung(25)|ovary(3)|prostate(3)|skin(3)|stomach(1)	78				all cancers(60;0.00169)|BRCA - Breast invasive adenocarcinoma(234;0.00912)|OV - Ovarian serous cystadenocarcinoma(108;0.0109)		CCATTCCGTCGACAGCCAAGC	0.577													G|||	26	0.00519169	0.0151	0.0029	5008	,	,		19331	0.0		0.004	False		,,,				2504	0.0				p.S558S		Atlas-SNP	.											.	SIPA1L1	219	.	0			c.G1674A						PASS	.	G		78,4328	69.2+/-107.0	1,76,2126	170.0	154.0	159.0		1674	-4.7	0.9	14	dbSNP_132	159	14,8586	11.2+/-40.8	0,14,4286	no	coding-synonymous	SIPA1L1	NM_015556.1		1,90,6412	AA,AG,GG		0.1628,1.7703,0.7074		558/1805	72090809	92,12914	2203	4300	6503	SO:0001819	synonymous_variant	26037	exon4			TCCGTCGACAGCC	AB007900	CCDS9807.1, CCDS61490.1, CCDS61491.1	14q24.1	2003-12-11				ENSG00000197555			20284	protein-coding gene	gene with protein product						9858596	Standard	XM_005267514		Approved	KIAA0440, E6TP1	uc001xmr.1	O43166		ENST00000555818.1:c.1674G>A	14.37:g.72090809G>A		80.0	0.0	0		85.0	35.0	0.411765	NM_015556	J3KP19|O95321|Q9UDU4|Q9UNU4	Silent	SNP	ENST00000555818.1	37	CCDS9807.1																																																																																			G|0.994;A|0.006	0.006	strong		0.577	SIPA1L1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412806.1	NM_015556	
SLIT2	9353	hgsc.bcm.edu	37	4	20533613	20533613	+	Silent	SNP	C	C	G	rs150677598	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:20533613C>G	ENST00000504154.1	+	17	1872	c.1620C>G	c.(1618-1620)ctC>ctG	p.L540L	SLIT2_ENST00000503837.1_Silent_p.L536L|SLIT2_ENST00000273739.5_Silent_p.L544L|SLIT2_ENST00000503823.1_Silent_p.L532L	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	540					apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						TCAGGCGTCTCAATAATAATG	0.279													C|||	8	0.00159744	0.0015	0.0029	5008	,	,		15813	0.0		0.002	False		,,,				2504	0.002				p.L540L		Atlas-SNP	.											SLIT2,NS,carcinoma,+2,1	SLIT2	290	1	0			c.C1620G						PASS	.	C		3,4403	4.2+/-10.8	0,3,2200	45.0	44.0	45.0		1620	3.0	1.0	4	dbSNP_134	45	30,8560	21.0+/-64.5	0,30,4265	no	coding-synonymous	SLIT2	NM_004787.1		0,33,6465	GG,GC,CC		0.3492,0.0681,0.2539		540/1530	20533613	33,12963	2203	4295	6498	SO:0001819	synonymous_variant	9353	exon17			GCGTCTCAATAAT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.1620C>G	4.37:g.20533613C>G		286.0	0.0	0		265.0	128.0	0.483019	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Silent	SNP	ENST00000504154.1	37	CCDS3426.1																																																																																			C|0.998;G|0.002	0.002	strong		0.279	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
CLASP1	23332	hgsc.bcm.edu	37	2	122104692	122104692	+	Silent	SNP	G	G	A	rs374603441		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:122104692G>A	ENST00000263710.4	-	39	4841	c.4452C>T	c.(4450-4452)agC>agT	p.S1484S	CLASP1_ENST00000455322.2_Silent_p.S1440S|CLASP1_ENST00000541859.1_Silent_p.S1201S|CLASP1_ENST00000545861.1_Silent_p.S1191S|CLASP1_ENST00000397587.3_Silent_p.S1424S|CLASP1_ENST00000409078.3_Silent_p.S1417S|CLASP1_ENST00000541377.1_Silent_p.S1423S	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1484	Interaction with CLIP2. {ECO:0000250}.|Interaction with PHLDB2 and RSN.|Localization to kinetochores.				axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					AGCAAAACACGCTGGCCTTAC	0.468																																					p.S1484S		Atlas-SNP	.											.	CLASP1	135	.	0			c.C4452T						PASS	.	G	,,,	0,4100		0,0,2050	93.0	89.0	90.0		4275,4251,4269,4452	-5.2	0.9	2		90	1,8377		0,1,4188	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CLASP1	NM_001142273.1,NM_001142274.1,NM_001207051.1,NM_015282.2	,,,	0,1,6238	AA,AG,GG		0.0119,0.0,0.0080	,,,	1425/1480,1417/1472,1423/1478,1484/1539	122104692	1,12477	2050	4189	6239	SO:0001819	synonymous_variant	23332	exon38			AAACACGCTGGCC	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.4452C>T	2.37:g.122104692G>A		148.0	0.0	0		137.0	59.0	0.430657	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Silent	SNP	ENST00000263710.4	37																																																																																				.	.	weak		0.468	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
POU4F2	5458	hgsc.bcm.edu	37	4	147561147	147561147	+	Missense_Mutation	SNP	C	C	A	rs147517729	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:147561147C>A	ENST00000281321.3	+	2	665	c.417C>A	c.(415-417)gaC>gaA	p.D139E	AC093887.1_ENST00000584185.1_RNA	NM_004575.2	NP_004566.2	Q12837	PO4F2_HUMAN	POU class 4 homeobox 2	139					axon extension (GO:0048675)|axon guidance (GO:0007411)|intracellular estrogen receptor signaling pathway (GO:0030520)|MAPK cascade (GO:0000165)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retina development in camera-type eye (GO:0060041)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			NS(1)|breast(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(8)|skin(1)|upper_aerodigestive_tract(1)	33	all_hematologic(180;0.151)					TCAAACCGGACGCCACCTACC	0.657													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		13029	0.0		0.007	False		,,,				2504	0.001				p.D139E		Atlas-SNP	.											.	POU4F2	83	.	0			c.C417A						PASS	.	C	GLU/ASP	16,4390	23.3+/-48.9	0,16,2187	118.0	143.0	135.0		417	5.8	1.0	4	dbSNP_134	135	111,8489	59.8+/-121.6	2,107,4191	yes	missense	POU4F2	NM_004575.2	45	2,123,6378	AA,AC,CC		1.2907,0.3631,0.9765	probably-damaging	139/410	147561147	127,12879	2203	4300	6503	SO:0001583	missense	5458	exon2			ACCGGACGCCACC	U06233	CCDS34074.1	4q31.22	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9219	protein-coding gene	gene with protein product		113725	"""POU domain, class 4, transcription factor 2"", ""POU domain class 4, transcription factor 2"""	BRN3B		8332509	Standard	NM_004575		Approved	Brn-3b	uc003ikv.3	Q12837		ENST00000281321.3:c.417C>A	4.37:g.147561147C>A	ENSP00000281321:p.Asp139Glu	82.0	0.0	0		78.0	36.0	0.461538	NM_004575	B1PJR6|B2RC84|Q13883|Q14987	Missense_Mutation	SNP	ENST00000281321.3	37	CCDS34074.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	19.43	3.826606	0.71143	0.003631	0.012907	ENSG00000151615	ENST00000281321	T	0.25912	1.77	5.77	5.77	0.91146	.	0.000000	0.43110	D	0.000613	T	0.39064	0.1064	L	0.58510	1.815	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.04976	-1.0914	10	0.23891	T	0.37	.	18.7641	0.91865	0.0:1.0:0.0:0.0	.	139	Q12837	PO4F2_HUMAN	E	139	ENSP00000281321:D139E	ENSP00000281321:D139E	D	+	3	2	POU4F2	147780597	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.140000	0.50585	2.729000	0.93468	0.467000	0.42956	GAC	C|0.992;A|0.008	0.008	strong		0.657	POU4F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367020.1	NM_004575	
COL15A1	1306	hgsc.bcm.edu	37	9	101797679	101797679	+	Silent	SNP	C	C	G	rs35494947	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:101797679C>G	ENST00000375001.3	+	19	2691	c.2268C>G	c.(2266-2268)ctC>ctG	p.L756L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	756	Nonhelical region 3 (NC3).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				AACCCAAACTCTCCAGACCAA	0.512													C|||	21	0.00419329	0.0	0.0058	5008	,	,		19093	0.001		0.0129	False		,,,				2504	0.0031				p.L756L		Atlas-SNP	.											.	COL15A1	211	.	0			c.C2268G						PASS	.	C		13,4393	20.2+/-43.8	0,13,2190	100.0	95.0	97.0		2268	4.2	0.1	9	dbSNP_126	97	107,8493	58.3+/-119.8	0,107,4193	no	coding-synonymous	COL15A1	NM_001855.3		0,120,6383	GG,GC,CC		1.2442,0.2951,0.9227		756/1389	101797679	120,12886	2203	4300	6503	SO:0001819	synonymous_variant	1306	exon19			CAAACTCTCCAGA	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2268C>G	9.37:g.101797679C>G		76.0	0.0	0		85.0	85.0	1	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Silent	SNP	ENST00000375001.3	37	CCDS35081.1																																																																																			C|0.992;G|0.008	0.008	strong		0.512	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
METTL2A	339175	hgsc.bcm.edu	37	17	60525113	60525113	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:60525113A>C	ENST00000311506.5	+	8	1004	c.968A>C	c.(967-969)tAc>tCc	p.Y323S		NM_181725.3	NP_859076.3	Q96IZ6	MET2A_HUMAN	methyltransferase like 2A	323					tRNA methylation (GO:0030488)		tRNA (cytosine) methyltransferase activity (GO:0016427)			breast(2)|central_nervous_system(1)|endometrium(1)|upper_aerodigestive_tract(2)	6			BRCA - Breast invasive adenocarcinoma(2;1.08e-10)			ACCAGAGTTTACTTCTTCACA	0.408																																					p.Y323S		Atlas-SNP	.											.	METTL2A	31	.	0			c.A968C						PASS	.						268.0	272.0	271.0					17																	60525113		2203	4300	6503	SO:0001583	missense	339175	exon8			GAGTTTACTTCTT	AK000991	CCDS45752.1	17q23.3	2012-12-20		2006-02-10	ENSG00000087995	ENSG00000087995			25755	protein-coding gene	gene with protein product						12477932	Standard	NM_181725		Approved	FLJ12760, METTL2	uc002izv.2	Q96IZ6	OTTHUMG00000164527	ENST00000311506.5:c.968A>C	17.37:g.60525113A>C	ENSP00000309610:p.Tyr323Ser	268.0	1.0	0.00373134		274.0	134.0	0.489051	NM_181725	A6NNC4|Q9H9G9|Q9NUI8|Q9P0B5	Missense_Mutation	SNP	ENST00000311506.5	37	CCDS45752.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.102365	0.76983	.	.	ENSG00000087995	ENST00000311506	T	0.11821	2.74	4.26	4.26	0.50523	.	0.056321	0.64402	D	0.000001	T	0.50137	0.1598	H	0.97415	4	0.80722	D	1	D	0.69078	0.997	D	0.74348	0.983	T	0.66590	-0.5885	10	0.87932	D	0	-0.4554	11.69	0.51510	1.0:0.0:0.0:0.0	.	323	Q96IZ6	MTL2A_HUMAN	S	323	ENSP00000309610:Y323S	ENSP00000309610:Y323S	Y	+	2	0	METTL2A	57878845	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	8.901000	0.92560	1.712000	0.51347	0.397000	0.26171	TAC	.	.	none		0.408	METTL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445130.1	NM_181725	
CASQ1	844	hgsc.bcm.edu	37	1	160162591	160162591	+	Splice_Site	SNP	G	G	C	rs145486953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:160162591G>C	ENST00000368078.3	+	2	475		c.e2-1		CASQ1_ENST00000368079.3_Splice_Site			P31415	CASQ1_HUMAN	calsequestrin 1 (fast-twitch, skeletal muscle)						endoplasmic reticulum organization (GO:0007029)|ion transmembrane transport (GO:0034220)|protein polymerization (GO:0051258)|regulation of sequestering of calcium ion (GO:0051282)|regulation of skeletal muscle contraction by regulation of release of sequestered calcium ion (GO:0014809)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to heat (GO:0009408)|response to organic substance (GO:0010033)|sarcomere organization (GO:0045214)|skeletal muscle tissue development (GO:0007519)|transmembrane transport (GO:0055085)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum lumen (GO:0033018)|sarcoplasmic reticulum membrane (GO:0033017)|smooth endoplasmic reticulum (GO:0005790)|T-tubule (GO:0030315)|terminal cisterna lumen (GO:0014804)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(9)|ovary(1)|skin(1)	21	all_cancers(52;2.56e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			CTTCCCTCCAGTTAGCAGCCC	0.488											OREG0013927	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	3	0.000599042	0.0	0.0	5008	,	,		16886	0.0		0.003	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CASQ1	55	.	0			c.280-1G>C						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	115.0	123.0	121.0			4.5	1.0	1	dbSNP_134	121	19,8581	14.0+/-48.4	0,19,4281	yes	splice-3	CASQ1	NM_001231.4		0,20,6483	CC,CG,GG		0.2209,0.0227,0.1538			160162591	20,12986	2203	4300	6503	SO:0001630	splice_region_variant	844	exon2			CCTCCAGTTAGCA	S73775	CCDS1198.1, CCDS1198.2	1q21	2011-10-19			ENSG00000143318	ENSG00000143318		"""Protein disulfide isomerases"""	1512	protein-coding gene	gene with protein product	"""calsequestrin 1, fast-twitch, skeletal muscle"", ""calmitine"""	114250		CASQ		8406504, 2321095	Standard	NM_001231		Approved	PDIB1	uc010pja.2	P31415	OTTHUMG00000031607	ENST00000368078.3:c.280-1G>C	1.37:g.160162591G>C		117.0	0.0	0	1806	144.0	51.0	0.354167	NM_001231	B1AKZ2|B2R863|Q8TBW7	Splice_Site	SNP	ENST00000368078.3	37	CCDS1198.2	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.18	3.566858	0.65651	2.27E-4	0.002209	ENSG00000143318	ENST00000368079;ENST00000368078	.	.	.	4.54	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.2739	0.82634	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CASQ1	158429215	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	8.990000	0.93510	2.358000	0.79984	0.449000	0.29647	.	G|0.998;C|0.002	0.002	strong		0.488	CASQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077412.1	NM_001231	Intron
LRRC4C	57689	hgsc.bcm.edu	37	11	40136049	40136049	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:40136049A>G	ENST00000278198.2	-	2	3757	c.1794T>C	c.(1792-1794)taT>taC	p.Y598Y	LRRC4C_ENST00000527150.1_Silent_p.Y598Y|LRRC4C_ENST00000528697.1_Silent_p.Y598Y|LRRC4C_ENST00000530763.1_Silent_p.Y598Y			Q9HCJ2	LRC4C_HUMAN	leucine rich repeat containing 4C	598					regulation of axonogenesis (GO:0050770)	cell junction (GO:0030054)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|postsynaptic membrane (GO:0045211)				NS(2)|central_nervous_system(3)|endometrium(1)|large_intestine(14)|lung(43)|ovary(5)|prostate(2)|skin(9)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	86		all_lung(304;0.0575)|Lung NSC(402;0.138)				TGTATGAGTTATAGTGATTTA	0.408																																					p.Y598Y		Atlas-SNP	.											LRRC4C,NS,carcinoma,0,1	LRRC4C	190	1	0			c.T1794C						PASS	.						230.0	222.0	225.0					11																	40136049		2203	4300	6503	SO:0001819	synonymous_variant	57689	exon7			TGAGTTATAGTGA	AB046800	CCDS31464.1	11p12	2013-01-14				ENSG00000148948		"""Immunoglobulin superfamily / I-set domain containing"""	29317	protein-coding gene	gene with protein product		608817				14595443	Standard	NM_020929		Approved	KIAA1580, NGL-1	uc031pzu.1	Q9HCJ2		ENST00000278198.2:c.1794T>C	11.37:g.40136049A>G		265.0	0.0	0		295.0	133.0	0.450847	NM_001258419	A8K0T1|Q7L0N3	Silent	SNP	ENST00000278198.2	37	CCDS31464.1																																																																																			.	.	none		0.408	LRRC4C-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389499.1	NM_020929	
RNF144B	255488	hgsc.bcm.edu	37	6	18457574	18457574	+	Silent	SNP	C	C	T	rs75403847		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:18457574C>T	ENST00000259939.3	+	5	837	c.520C>T	c.(520-522)Ctg>Ttg	p.L174L	RNF144B_ENST00000429054.2_Silent_p.L85L	NM_182757.3	NP_877434.2	Q7Z419	R144B_HUMAN	ring finger protein 144B	174					apoptotic process (GO:0006915)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|mitochondrial membrane (GO:0031966)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(1)|lung(7)	11	Ovarian(93;0.00365)|Breast(50;0.0145)	all_hematologic(90;0.0536)	OV - Ovarian serous cystadenocarcinoma(7;0.00165)|all cancers(50;0.0102)|Epithelial(50;0.0105)			GCCTATTGTCCTGCCAACAGA	0.453													C|||	1	0.000199681	0.0	0.0	5008	,	,		20281	0.0		0.001	False		,,,				2504	0.0				p.L174L		Atlas-SNP	.											.	RNF144B	18	.	0			c.C520T						PASS	.	C		0,4406		0,0,2203	184.0	170.0	175.0		520	3.3	1.0	6	dbSNP_132	175	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	RNF144B	NM_182757.3		0,11,6492	TT,TC,CC		0.1279,0.0,0.0846		174/304	18457574	11,12995	2203	4300	6503	SO:0001819	synonymous_variant	255488	exon5			ATTGTCCTGCCAA	AK096832	CCDS34345.1	6p22.3	2011-05-23	2009-01-05	2007-08-20	ENSG00000137393	ENSG00000137393		"""RING-type (C3HC4) zinc fingers"""	21578	protein-coding gene	gene with protein product			"""IBR domain containing 2"""	IBRDC2			Standard	NM_182757		Approved	bA528A10.3	uc003ncs.3	Q7Z419	OTTHUMG00000014322	ENST00000259939.3:c.520C>T	6.37:g.18457574C>T		109.0	0.0	0		156.0	72.0	0.461538	NM_182757	B3KUA8|B4DZI2|Q5TB85|Q6P4Q0|Q8N3R7|Q9BX38	Silent	SNP	ENST00000259939.3	37	CCDS34345.1																																																																																			C|0.999;T|0.001	0.001	strong		0.453	RNF144B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039965.2	XM_172581	
PYGO1	26108	hgsc.bcm.edu	37	15	55838976	55838976	+	Missense_Mutation	SNP	C	C	G	rs144876912	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:55838976C>G	ENST00000302000.6	-	3	599	c.505G>C	c.(505-507)Gtc>Ctc	p.V169L	PYGO1_ENST00000563719.1_Missense_Mutation_p.V169L	NM_015617.1	NP_056432.1	Q9Y3Y4	PYGO1_HUMAN	pygopus family PHD finger 1	169	Asn-rich.				hematopoietic progenitor cell differentiation (GO:0002244)|kidney development (GO:0001822)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|spermatid nucleus differentiation (GO:0007289)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(6)|lung(6)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	27				all cancers(107;0.0131)|GBM - Glioblastoma multiforme(80;0.18)		GGCATGTTGACATTCTGACTT	0.383																																					p.V169L		Atlas-SNP	.											PYGO1,NS,carcinoma,+2,1	PYGO1	56	1	0			c.G505C						PASS	.	C	LEU/VAL	2,4384	4.2+/-10.8	0,2,2191	114.0	116.0	115.0		505	3.3	1.0	15	dbSNP_134	115	16,8568	11.9+/-42.8	0,16,4276	yes	missense	PYGO1	NM_015617.1	32	0,18,6467	GG,GC,CC		0.1864,0.0456,0.1388	benign	169/420	55838976	18,12952	2193	4292	6485	SO:0001583	missense	26108	exon3			TGTTGACATTCTG	AF457207	CCDS10155.1	15q21.1	2013-10-09	2013-10-09		ENSG00000171016	ENSG00000171016		"""Zinc fingers, PHD-type"""	30256	protein-coding gene	gene with protein product		606902	"""pygopus homolog 1 (Drosophila)"""			11988739	Standard	NM_015617		Approved		uc002adf.1	Q9Y3Y4	OTTHUMG00000132009	ENST00000302000.6:c.505G>C	15.37:g.55838976C>G	ENSP00000302327:p.Val169Leu	180.0	0.0	0		187.0	99.0	0.529412	NM_015617	A7Y2D6	Missense_Mutation	SNP	ENST00000302000.6	37	CCDS10155.1	.	.	.	.	.	.	.	.	.	.	C	9.561	1.118537	0.20877	4.56E-4	0.001864	ENSG00000171016	ENST00000302000;ENST00000401688	T	0.45668	0.89	5.23	3.33	0.38152	.	0.395337	0.23849	N	0.043976	T	0.23532	0.0569	N	0.19112	0.55	0.27105	N	0.962529	B;B	0.15473	0.013;0.013	B;B	0.17979	0.011;0.02	T	0.21484	-1.0244	10	0.11794	T	0.64	-7.226	8.1499	0.31134	0.0:0.7585:0.0:0.2415	.	169;169	A7Y2D6;Q9Y3Y4	.;PYGO1_HUMAN	L	169	ENSP00000302327:V169L	ENSP00000302327:V169L	V	-	1	0	PYGO1	53626268	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.943000	0.29030	0.685000	0.31468	0.585000	0.79938	GTC	C|0.998;G|0.002	0.002	strong		0.383	PYGO1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254977.2	NM_015617	
ZNF831	128611	hgsc.bcm.edu	37	20	57766113	57766113	+	Silent	SNP	G	G	A	rs148289392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:57766113G>A	ENST00000371030.2	+	1	39	c.39G>A	c.(37-39)gcG>gcA	p.A13A		NM_178457.1	NP_848552.1	Q5JPB2	ZN831_HUMAN	zinc finger protein 831	13	Pro-rich.						metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(15)|lung(71)|ovary(2)|pancreas(1)|prostate(4)|skin(16)|upper_aerodigestive_tract(2)|urinary_tract(3)	125	all_lung(29;0.0085)					CCCCTCCTGCGAGGGACCAGC	0.637													.|||	3	0.000599042	0.0	0.0014	5008	,	,		17085	0.0		0.002	False		,,,				2504	0.0				p.A13A		Atlas-SNP	.											.	ZNF831	287	.	0			c.G39A						PASS	.	G		0,3912		0,0,1956	27.0	32.0	30.0		39	2.5	1.0	20	dbSNP_134	30	6,8286		0,6,4140	no	coding-synonymous	ZNF831	NM_178457.1		0,6,6096	AA,AG,GG		0.0724,0.0,0.0492		13/1678	57766113	6,12198	1956	4146	6102	SO:0001819	synonymous_variant	128611	exon1			TCCTGCGAGGGAC	AL121919	CCDS42894.1	20q13.32	2008-10-20	2008-03-25	2008-03-25	ENSG00000124203	ENSG00000124203			16167	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 174"""	C20orf174			Standard	NM_178457		Approved	dJ492J12.1	uc002yan.3	Q5JPB2	OTTHUMG00000032864	ENST00000371030.2:c.39G>A	20.37:g.57766113G>A		49.0	0.0	0		27.0	14.0	0.518519	NM_178457	Q5TDR4|Q8TCP0	Silent	SNP	ENST00000371030.2	37	CCDS42894.1																																																																																			G|0.999;A|0.001	0.001	strong		0.637	ZNF831-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079916.2	NM_178457	
TSTD2	158427	hgsc.bcm.edu	37	9	100364900	100364900	+	Missense_Mutation	SNP	A	A	C	rs145024955	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:100364900A>C	ENST00000341170.4	-	10	1784	c.1402T>G	c.(1402-1404)Tca>Gca	p.S468A		NM_139246.4	NP_640339.4	Q5T7W7	TSTD2_HUMAN	thiosulfate sulfurtransferase (rhodanese)-like domain containing 2	468										large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	15						ATAGGGCCTGAAACTTTCCTG	0.557													A|||	2	0.000399361	0.0	0.0	5008	,	,		20972	0.0		0.002	False		,,,				2504	0.0				p.S468A		Atlas-SNP	.											.	TSTD2	42	.	0			c.T1402G						PASS	.	A	ALA/SER	1,4405	2.1+/-5.4	0,1,2202	264.0	222.0	236.0		1402	1.8	0.2	9	dbSNP_134	236	14,8586	10.5+/-38.8	0,14,4286	yes	missense	TSTD2	NM_139246.4	99	0,15,6488	CC,CA,AA		0.1628,0.0227,0.1153	benign	468/517	100364900	15,12991	2203	4300	6503	SO:0001583	missense	158427	exon10			GGCCTGAAACTTT	AF258575	CCDS6727.2	9q22.33	2013-09-20	2009-08-12	2009-08-12	ENSG00000136925	ENSG00000136925			30087	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 97"""	C9orf97		12477932	Standard	NM_139246		Approved	PP4189	uc004axn.3	Q5T7W7	OTTHUMG00000020328	ENST00000341170.4:c.1402T>G	9.37:g.100364900A>C	ENSP00000342499:p.Ser468Ala	252.0	0.0	0		228.0	111.0	0.486842	NM_139246	A6NMJ4|A8K584|Q6ZQZ6|Q8IYM3|Q8WY73|Q96ML6|Q96MU1	Missense_Mutation	SNP	ENST00000341170.4	37	CCDS6727.2	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	5.124	0.208479	0.09757	2.27E-4	0.001628	ENSG00000136925	ENST00000375173;ENST00000341170	T;T	0.28895	1.59;1.59	5.5	1.77	0.24775	.	0.830019	0.10733	N	0.640447	T	0.15478	0.0373	N	0.17872	0.535	0.26488	N	0.974986	B	0.06786	0.001	B	0.04013	0.001	T	0.29912	-0.9996	10	0.25106	T	0.35	-2.0967	1.4504	0.02373	0.4114:0.2983:0.1611:0.1292	.	468	Q5T7W7	TSTD2_HUMAN	A	64;468	ENSP00000364316:S64A;ENSP00000342499:S468A	ENSP00000342499:S468A	S	-	1	0	TSTD2	99404721	0.016000	0.18221	0.206000	0.23566	0.267000	0.26476	0.794000	0.26958	0.117000	0.18138	0.460000	0.39030	TCA	A|0.999;C|0.001	0.001	strong		0.557	TSTD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053325.4	NM_139246	
TMEM61	199964	hgsc.bcm.edu	37	1	55451850	55451850	+	Silent	SNP	G	G	A	rs148773188		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:55451850G>A	ENST00000371268.3	+	2	370	c.96G>A	c.(94-96)acG>acA	p.T32T	RP11-12C17.2_ENST00000436960.1_RNA	NM_182532.1	NP_872338.1	Q8N0U2	TMM61_HUMAN	transmembrane protein 61	32						integral component of membrane (GO:0016021)				endometrium(1)|lung(1)|prostate(1)|upper_aerodigestive_tract(1)	4						TGGCCGGGACGCTCTGCTTCG	0.667																																					p.T32T		Atlas-SNP	.											.	TMEM61	22	.	0			c.G96A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	51.0	52.0	51.0		96	-7.4	0.2	1	dbSNP_134	51	0,8600		0,0,4300	no	coding-synonymous	TMEM61	NM_182532.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		32/211	55451850	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	199964	exon2			CGGGACGCTCTGC	BC029775	CCDS601.1	1p32.3	2008-02-05			ENSG00000143001	ENSG00000143001			27296	protein-coding gene	gene with protein product						12477932	Standard	NM_182532		Approved		uc001cyd.3	Q8N0U2	OTTHUMG00000009991	ENST00000371268.3:c.96G>A	1.37:g.55451850G>A		111.0	0.0	0		61.0	25.0	0.409836	NM_182532		Silent	SNP	ENST00000371268.3	37	CCDS601.1																																																																																			G|1.000;A|0.000	0.000	weak		0.667	TMEM61-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027683.1	NM_182532	
TEX40	25858	hgsc.bcm.edu	37	11	64071272	64071272	+	Missense_Mutation	SNP	G	G	C	rs117629442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:64071272G>C	ENST00000328404.6	+	4	480	c.460G>C	c.(460-462)Gag>Cag	p.E154Q	RP11-783K16.10_ENST00000539086.1_RNA|ESRRA_ENST00000405666.1_5'Flank|ESRRA_ENST00000406310.1_5'Flank|ESRRA_ENST00000000442.6_5'Flank|TEX40_ENST00000539943.1_Missense_Mutation_p.E112Q	NM_001039496.1	NP_001034585.1	Q9NTU4	TEX40_HUMAN	testis expressed 40	154					cell differentiation (GO:0030154)|male meiosis (GO:0007140)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)											GGAACTCATGGAGAATGAAGC	0.567													G|||	27	0.00539137	0.0008	0.0101	5008	,	,		13275	0.0		0.0169	False		,,,				2504	0.002				p.E154Q		Atlas-SNP	.											.	.	.	.	0			c.G460C						PASS	.	G	GLN/GLU	13,3981		0,13,1984	33.0	36.0	35.0		460	2.3	1.0	11	dbSNP_132	35	123,8191		0,123,4034	yes	missense	C11orf20	NM_001039496.1	29	0,136,6018	CC,CG,GG		1.4794,0.3255,1.105	possibly-damaging	154/201	64071272	136,12172	1997	4157	6154	SO:0001583	missense	25858	exon4			CTCATGGAGAATG			11q13.1	2013-01-11	2013-01-11	2013-01-11	ENSG00000219435	ENSG00000219435			19231	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 20"""	C11orf20			Standard	NM_001039496		Approved	DKFZP566E164	uc009ypm.3	Q9NTU4	OTTHUMG00000167820	ENST00000328404.6:c.460G>C	11.37:g.64071272G>C	ENSP00000330877:p.Glu154Gln	97.0	0.0	0		126.0	66.0	0.52381	NM_001039496		Missense_Mutation	SNP	ENST00000328404.6	37		18	0.008241758241758242	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	13	0.017150395778364115	G	13.31	2.198647	0.38806	0.003255	0.014794	ENSG00000219435	ENST00000328404;ENST00000539943	T;T	0.58210	0.35;0.37	4.22	2.3	0.28687	.	.	.	.	.	T	0.39572	0.1083	L	0.32530	0.975	0.25789	N	0.984643	D	0.76494	0.999	D	0.70487	0.969	T	0.28870	-1.0030	9	0.62326	D	0.03	-18.7303	5.3022	0.15783	0.1056:0.0:0.6949:0.1995	.	154	Q9NTU4	CK020_HUMAN	Q	154;112	ENSP00000330877:E154Q;ENSP00000443917:E112Q	ENSP00000330877:E154Q	E	+	1	0	C11orf20	63827848	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	2.823000	0.48081	0.528000	0.28580	-0.300000	0.09419	GAG	G|0.991;C|0.009	0.009	strong		0.567	TEX40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039496	
GALR1	2587	hgsc.bcm.edu	37	18	74980553	74980553	+	Missense_Mutation	SNP	G	G	A	rs142216832	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:74980553G>A	ENST00000299727.3	+	3	745	c.745G>A	c.(745-747)Gtt>Att	p.V249I		NM_001480.3	NP_001471.2	P47211	GALR1_HUMAN	galanin receptor 1	249					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|digestion (GO:0007586)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cortisol secretion (GO:0051464)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|neuropeptide binding (GO:0042923)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	24		Prostate(75;0.0865)|Esophageal squamous(42;0.129)|Melanoma(33;0.211)		OV - Ovarian serous cystadenocarcinoma(15;1.03e-06)|BRCA - Breast invasive adenocarcinoma(31;0.104)		TGCACAGACAGTTCTGGTGGT	0.517													G|||	19	0.00379393	0.0136	0.0014	5008	,	,		13369	0.0		0.0	False		,,,				2504	0.0				p.V249I		Atlas-SNP	.											.	GALR1	53	.	0			c.G745A						PASS	.	G	ILE/VAL	89,4317	74.7+/-112.8	0,89,2114	100.0	107.0	104.0		745	3.0	0.1	18	dbSNP_134	104	0,8600		0,0,4300	yes	missense	GALR1	NM_001480.3	29	0,89,6414	AA,AG,GG		0.0,2.02,0.6843	probably-damaging	249/350	74980553	89,12917	2203	4300	6503	SO:0001583	missense	2587	exon3			CAGACAGTTCTGG	U90658	CCDS12012.1	18q23	2012-08-08			ENSG00000166573	ENSG00000166573		"""GPCR / Class A : Galanin receptors"""	4132	protein-coding gene	gene with protein product		600377		GALNR1, GALNR		7524088	Standard	NM_001480		Approved		uc002lms.4	P47211	OTTHUMG00000132875	ENST00000299727.3:c.745G>A	18.37:g.74980553G>A	ENSP00000299727:p.Val249Ile	77.0	0.0	0		52.0	31.0	0.596154	NM_001480	Q4VBL7	Missense_Mutation	SNP	ENST00000299727.3	37	CCDS12012.1	10	0.004578754578754579	10	0.02032520325203252	0	0.0	0	0.0	0	0.0	G	7.358	0.624331	0.14193	0.0202	0.0	ENSG00000166573	ENST00000299727	T	0.36878	1.23	4.74	2.96	0.34315	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.32704	0.0838	L	0.58101	1.795	0.80722	D	1	D	0.76494	0.999	D	0.71656	0.974	T	0.21415	-1.0246	10	0.17369	T	0.5	.	10.7925	0.46440	0.152:0.0:0.848:0.0	.	249	P47211	GALR1_HUMAN	I	249	ENSP00000299727:V249I	ENSP00000299727:V249I	V	+	1	0	GALR1	73109541	1.000000	0.71417	0.071000	0.20095	0.026000	0.11368	4.647000	0.61418	0.446000	0.26666	-1.012000	0.02466	GTT	G|0.993;A|0.007	0.007	strong		0.517	GALR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256362.1		
EPHA3	2042	hgsc.bcm.edu	37	3	89448610	89448610	+	Missense_Mutation	SNP	A	A	T	rs150469112		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:89448610A>T	ENST00000336596.2	+	7	1799	c.1574A>T	c.(1573-1575)gAg>gTg	p.E525V	EPHA3_ENST00000452448.2_Missense_Mutation_p.E525V|EPHA3_ENST00000494014.1_Missense_Mutation_p.E525V	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	525	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CGCAAGTTTGAGTTTGAAACT	0.448										TSP Lung(6;0.00050)																											p.E525V		Atlas-SNP	.											.	EPHA3	501	.	0			c.A1574T						PASS	.	A	VAL/GLU,VAL/GLU	0,4406		0,0,2203	106.0	98.0	101.0		1574,1574	5.5	1.0	3	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	EPHA3	NM_005233.5,NM_182644.2	121,121	0,1,6502	TT,TA,AA		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	525/984,525/540	89448610	1,13005	2203	4300	6503	SO:0001583	missense	2042	exon7			AGTTTGAGTTTGA	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1574A>T	3.37:g.89448610A>T	ENSP00000337451:p.Glu525Val	93.0	0.0	0		58.0	33.0	0.568965	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	.	.	.	.	.	.	.	.	.	.	A	24.9	4.578556	0.86645	0.0	1.16E-4	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.53423	0.62;0.62;0.62	5.53	5.53	0.82687	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.051723	0.85682	D	0.000000	T	0.61502	0.2352	M	0.67700	2.07	0.80722	D	1	B;D	0.53312	0.181;0.959	B;P	0.56088	0.134;0.791	T	0.62191	-0.6906	9	.	.	.	.	15.6643	0.77213	1.0:0.0:0.0:0.0	.	525;525	P29320;P29320-2	EPHA3_HUMAN;.	V	525	ENSP00000337451:E525V;ENSP00000399926:E525V;ENSP00000419190:E525V	.	E	+	2	0	EPHA3	89531300	1.000000	0.71417	1.000000	0.80357	0.617000	0.37484	9.339000	0.96797	2.107000	0.64212	0.460000	0.39030	GAG	A|1.000;T|0.000	0.000	weak		0.448	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
TBP	6908	hgsc.bcm.edu	37	6	170871103	170871103	+	Silent	SNP	G	G	A	rs149441883	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:170871103G>A	ENST00000392092.2	+	3	558	c.279G>A	c.(277-279)caG>caA	p.Q93Q	TBP_ENST00000230354.6_Silent_p.Q93Q|TBP_ENST00000540980.1_Silent_p.Q73Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	93	Poly-Gln.		Missing. {ECO:0000269|PubMed:2374612}.		cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcagcaacaggcag	0.612													G|||	7	0.00139776	0.0015	0.0029	5008	,	,		13775	0.0		0.002	False		,,,				2504	0.001				p.Q93Q		Atlas-SNP	.											TBP,NS,carcinoma,0,2	TBP	58	2	0			c.G279A						scavenged	.						28.0	33.0	31.0					6																	170871103		1986	3826	5812	SO:0001819	synonymous_variant	6908	exon3			GCAGCAGCAACAG	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.279G>A	6.37:g.170871103G>A		106.0	1.0	0.00943396		113.0	6.0	0.0530973	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			G|0.998;A|0.002	0.002	strong		0.612	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760520	186760520	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760520T>G	ENST00000169298.3	+	4	703	c.29T>G	c.(28-30)tTc>tGc	p.F10C	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Missense_Mutation_p.F10C	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	10					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		AAGAAAAAGTTCAGCTGCTGC	0.403																																					p.F10C		Atlas-SNP	.											ST6GAL1,NS,carcinoma,+1,1	ST6GAL1	36	1	0			c.T29G						PASS	.						165.0	161.0	163.0					3																	186760520		2203	4300	6503	SO:0001583	missense	6480	exon3			AAAAGTTCAGCTG	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.29T>G	3.37:g.186760520T>G	ENSP00000169298:p.Phe10Cys	184.0	0.0	0		196.0	23.0	0.117347	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	T	18.32	3.599029	0.66332	.	.	ENSG00000073849	ENST00000169298;ENST00000458216;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.23950	1.88;1.88	5.44	5.44	0.79542	.	0.415059	0.26804	N	0.022416	T	0.24586	0.0596	L	0.52364	1.645	0.80722	D	1	B	0.06786	0.001	B	0.06405	0.002	T	0.03103	-1.1072	10	0.33940	T	0.23	-27.897	12.2097	0.54373	0.0:0.0:0.0:1.0	.	10	P15907	SIAT1_HUMAN	C	10	ENSP00000169298:F10C;ENSP00000389337:F10C	ENSP00000169298:F10C	F	+	2	0	ST6GAL1	188243214	0.614000	0.27017	0.996000	0.52242	0.933000	0.57130	1.719000	0.38011	2.200000	0.70718	0.459000	0.35465	TTC	.	.	none		0.403	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
SIPA1L2	57568	hgsc.bcm.edu	37	1	232650163	232650163	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:232650163G>A	ENST00000366630.1	-	2	1281	c.923C>T	c.(922-924)aCg>aTg	p.T308M	SIPA1L2_ENST00000262861.4_Missense_Mutation_p.T308M			Q9P2F8	SI1L2_HUMAN	signal-induced proliferation-associated 1 like 2	308					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)				CAGCTCAGACGTGAACTTGAA	0.458																																					p.T308M		Atlas-SNP	.											.	SIPA1L2	218	.	0			c.C923T						PASS	.						57.0	59.0	58.0					1																	232650163		1921	4141	6062	SO:0001583	missense	57568	exon1			TCAGACGTGAACT	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.923C>T	1.37:g.232650163G>A	ENSP00000355589:p.Thr308Met	60.0	0.0	0		66.0	26.0	0.393939	NM_020808	Q2TV88|Q5VXR7|Q5VXR8|Q641Q4|Q8NA38|Q96DZ3|Q9H9F6	Missense_Mutation	SNP	ENST00000366630.1	37	CCDS41474.1	.	.	.	.	.	.	.	.	.	.	G	12.56	1.974684	0.34848	.	.	ENSG00000116991	ENST00000366630;ENST00000262861	T;T	0.78924	-1.22;-1.22	5.39	4.48	0.54585	.	0.295098	0.33144	N	0.005238	T	0.58452	0.2123	N	0.08118	0	0.34703	D	0.726925	P	0.35493	0.505	B	0.32465	0.146	T	0.68123	-0.5492	10	0.33141	T	0.24	-5.5177	14.1111	0.65121	0.0719:0.0:0.9281:0.0	.	308	Q9P2F8	SI1L2_HUMAN	M	308	ENSP00000355589:T308M;ENSP00000262861:T308M	ENSP00000262861:T308M	T	-	2	0	SIPA1L2	230716786	1.000000	0.71417	0.818000	0.32626	0.930000	0.56654	4.769000	0.62300	1.503000	0.48686	0.650000	0.86243	ACG	.	.	none		0.458	SIPA1L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092318.1	XM_045839	
SCN1A	6323	hgsc.bcm.edu	37	2	166850872	166850872	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:166850872T>G	ENST00000303395.4	-	25	4635	c.4636A>C	c.(4636-4638)Agc>Cgc	p.S1546R	SCN1A_ENST00000375405.3_Missense_Mutation_p.S1535R|SCN1A_ENST00000409050.1_Missense_Mutation_p.S1518R|AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000423058.2_Missense_Mutation_p.S1546R|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1546					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATCATGATGCTTATGTCAAAA	0.363																																					p.S1546R		Atlas-SNP	.											.	SCN1A	641	.	0			c.A4636C						PASS	.						129.0	113.0	118.0					2																	166850872		2203	4300	6503	SO:0001583	missense	6323	exon25			TGATGCTTATGTC	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.4636A>C	2.37:g.166850872T>G	ENSP00000303540:p.Ser1546Arg	182.0	0.0	0		160.0	21.0	0.13125	NM_001165963	E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Missense_Mutation	SNP	ENST00000303395.4	37	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	18.59	3.657766	0.67586	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	D;D;D;D	0.97404	-4.37;-4.37;-4.37;-4.37	5.9	5.9	0.94986	.	0.118890	0.64402	D	0.000011	D	0.97278	0.9110	M	0.61703	1.905	0.32543	N	0.533434	D	0.59357	0.985	P	0.59012	0.85	D	0.99104	1.0844	10	0.62326	D	0.03	.	10.6319	0.45541	0.0:0.0709:0.0:0.9291	.	1535	P35498-2	.	R	1546;1546;1535;1518	ENSP00000407030:S1546R;ENSP00000303540:S1546R;ENSP00000364554:S1535R;ENSP00000386312:S1518R	ENSP00000303540:S1546R	S	-	1	0	SCN1A	166559118	0.452000	0.25713	0.998000	0.56505	0.995000	0.86356	0.724000	0.25954	2.251000	0.74343	0.528000	0.53228	AGC	.	.	none		0.363	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000436117.2_Silent_p.Q648Q|MET_ENST00000397752.3_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GGACAACACAATACAGTACAT	0.318			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93.0	92.0	92.0		1944,1944	-6.5	0.0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1944A>G	7.37:g.116397572A>G		88.0	0.0	0		71.0	25.0	0.352113	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
PELP1	27043	hgsc.bcm.edu	37	17	4576203	4576203	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4576203C>T	ENST00000574876.1	-	16	2100	c.2083G>A	c.(2083-2085)Gtg>Atg	p.V695M	AC091153.4_ENST00000441700.2_RNA|PELP1_ENST00000269230.7_Missense_Mutation_p.V605M|PELP1_ENST00000572293.1_Missense_Mutation_p.V745M|PELP1_ENST00000301396.4_Missense_Mutation_p.V839M|PELP1_ENST00000436683.2_Missense_Mutation_p.V548M			Q8IZL8	PELP1_HUMAN	proline, glutamate and leucine rich protein 1	695	Pro-rich.				cellular response to estrogen stimulus (GO:0071391)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|transcriptionally active chromatin (GO:0035327)	chromatin binding (GO:0003682)|poly(A) RNA binding (GO:0044822)|transcription factor binding (GO:0008134)			breast(2)|central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	15						GCCGAGGGCACAGGGCCTGCT	0.687																																					p.V695M		Atlas-SNP	.											.	PELP1	102	.	0			c.G2083A						PASS	.						33.0	39.0	37.0					17																	4576203		1990	4145	6135	SO:0001583	missense	27043	exon16			AGGGCACAGGGCC		CCDS58503.1, CCDS58503.2, CCDS62038.1	17p13.2	2012-05-02	2008-02-21			ENSG00000141456			30134	protein-coding gene	gene with protein product		609455	"""proline, glutamic acid and leucine rich protein 1"""			11481323, 12682072	Standard	NM_014389		Approved	MNAR	uc002fyi.4	Q8IZL8		ENST00000574876.1:c.2083G>A	17.37:g.4576203C>T	ENSP00000461625:p.Val695Met	141.0	0.0	0		136.0	26.0	0.191176	NM_014389	O15450|Q5EGN3|Q6NTE6|Q96FT1|Q9BU60	Missense_Mutation	SNP	ENST00000574876.1	37	CCDS58503.1	.	.	.	.	.	.	.	.	.	.	C	1.457	-0.563579	0.03939	.	.	ENSG00000141456	ENST00000301396;ENST00000269230;ENST00000436683	T;T;T	0.48201	0.82;0.88;1.48	4.54	-7.16	0.01516	.	0.654618	0.14932	N	0.290033	T	0.21468	0.0517	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.001;0.002	T	0.06303	-1.0834	10	0.37606	T	0.19	-2.13	6.9569	0.24576	0.0:0.2953:0.3218:0.3829	.	548;695	E7EV54;Q8IZL8	.;PELP1_HUMAN	M	839;605;548	ENSP00000301396:V839M;ENSP00000269230:V605M;ENSP00000416231:V548M	ENSP00000269230:V605M	V	-	1	0	AC091153.1	4522952	0.000000	0.05858	0.001000	0.08648	0.155000	0.21991	-1.525000	0.02231	-1.363000	0.02164	-0.136000	0.14681	GTG	.	.	none		0.687	PELP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000439140.2	NM_014389	
SEMA6B	10501	hgsc.bcm.edu	37	19	4555079	4555079	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:4555079G>A	ENST00000586582.1	-	8	901	c.591C>T	c.(589-591)acC>acT	p.T197T	SEMA6B_ENST00000301293.3_Silent_p.T197T|SEMA6B_ENST00000586965.1_Silent_p.T197T	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	197	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(2)|large_intestine(4)|lung(11)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0149)|STAD - Stomach adenocarcinoma(1328;0.18)		CTAGGAAGTCGGTAACAGTAG	0.592																																					p.T197T		Atlas-SNP	.											.	SEMA6B	51	.	0			c.C591T						PASS	.						111.0	89.0	96.0					19																	4555079		2202	4300	6502	SO:0001819	synonymous_variant	10501	exon8			GAAGTCGGTAACA	AB022433	CCDS12131.1	19p13.3	2008-07-22				ENSG00000167680		"""Semaphorins"""	10739	protein-coding gene	gene with protein product	"""Sema VIb"", ""semaphorin Z"", ""semaphorin VIB"""	608873		SEMAN		9361278	Standard	NM_032108		Approved	semaZ, SEMA-VIB, SEM-SEMA-Y	uc010dud.2	Q9H3T3		ENST00000586582.1:c.591C>T	19.37:g.4555079G>A		63.0	0.0	0		75.0	9.0	0.12	NM_032108	A5PKU4|F6IB19|Q9NRK9	Silent	SNP	ENST00000586582.1	37	CCDS12131.1																																																																																			.	.	none		0.592	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
UBE2U	148581	hgsc.bcm.edu	37	1	64672478	64672478	+	Silent	SNP	A	A	G	rs35112334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:64672478A>G	ENST00000371076.3	+	3	424	c.180A>G	c.(178-180)acA>acG	p.T60T		NM_152489.1	NP_689702.1	Q5VVX9	UBE2U_HUMAN	ubiquitin-conjugating enzyme E2U (putative)	60					protein ubiquitination (GO:0016567)		acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)			large_intestine(3)|lung(2)|skin(1)	6						TACATTTTACATCGGAGTACA	0.299													A|||	51	0.0101837	0.0	0.0159	5008	,	,		16516	0.004		0.0288	False		,,,				2504	0.0072				p.T60T		Atlas-SNP	.											.	UBE2U	16	.	0			c.A180G						PASS	.	A		22,4380	29.9+/-59.1	0,22,2179	56.0	58.0	57.0		180	-2.9	0.0	1	dbSNP_126	57	265,8319	99.5+/-161.0	7,251,4034	no	coding-synonymous	UBE2U	NM_152489.1		7,273,6213	GG,GA,AA		3.0871,0.4998,2.2101		60/227	64672478	287,12699	2201	4292	6493	SO:0001819	synonymous_variant	148581	exon3			TTTTACATCGGAG	BC029895	CCDS627.1	1p31.3	2008-02-05			ENSG00000177414	ENSG00000177414		"""Ubiquitin-conjugating enzymes E2"""	28559	protein-coding gene	gene with protein product						12477932	Standard	NM_152489		Approved	MGC35130	uc001dbn.1	Q5VVX9	OTTHUMG00000009023	ENST00000371076.3:c.180A>G	1.37:g.64672478A>G		265.0	0.0	0		225.0	87.0	0.386667	NM_152489	Q8N1D4	Silent	SNP	ENST00000371076.3	37	CCDS627.1																																																																																			A|0.982;G|0.018	0.018	strong		0.299	UBE2U-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025005.1	NM_152489	
USP42	84132	hgsc.bcm.edu	37	7	6175526	6175526	+	Missense_Mutation	SNP	C	C	T	rs61757573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:6175526C>T	ENST00000306177.5	+	4	655	c.497C>T	c.(496-498)gCa>gTa	p.A166V		NM_032172.2	NP_115548.1	Q9H9J4	UBP42_HUMAN	ubiquitin specific peptidase 42	166	USP.				cell differentiation (GO:0030154)|protein deubiquitination (GO:0016579)|spermatogenesis (GO:0007283)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(2)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|urinary_tract(1)	35		Ovarian(82;0.0423)		UCEC - Uterine corpus endometrioid carcinoma (126;0.108)|OV - Ovarian serous cystadenocarcinoma(56;5.77e-14)		ATTACCCAGGCACTCAGTAAT	0.348													C|||	8	0.00159744	0.0	0.0058	5008	,	,		16238	0.0		0.001	False		,,,				2504	0.0031				p.A166V		Atlas-SNP	.											.	USP42	138	.	0			c.C497T						PASS	.	C	VAL/ALA	2,3760		0,2,1879	119.0	110.0	113.0		497	5.2	1.0	7	dbSNP_129	113	42,8208		0,42,4083	yes	missense	USP42	NM_032172.2	64	0,44,5962	TT,TC,CC		0.5091,0.0532,0.3663	benign	166/1317	6175526	44,11968	1881	4125	6006	SO:0001583	missense	84132	exon4			CCCAGGCACTCAG	AK022759	CCDS47535.1	7p22.2	2005-08-08	2005-08-08		ENSG00000106346	ENSG00000106346		"""Ubiquitin-specific peptidases"""	20068	protein-coding gene	gene with protein product			"""ubiquitin specific protease 42"""			12838346	Standard	NM_032172		Approved	FLJ12697	uc011jwp.2	Q9H9J4	OTTHUMG00000151888	ENST00000306177.5:c.497C>T	7.37:g.6175526C>T	ENSP00000301962:p.Ala166Val	176.0	0.0	0		170.0	69.0	0.405882	NM_032172	A2RUE3|B5MDA5|Q0VIN8|Q3C166|Q6P9B4	Missense_Mutation	SNP	ENST00000306177.5	37	CCDS47535.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	19.15	3.771386	0.69992	5.32E-4	0.005091	ENSG00000106346	ENST00000306177;ENST00000465073;ENST00000426246	T;T;T	0.02709	4.19;4.19;4.19	5.19	5.19	0.71726	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.091899	0.47455	D	0.000230	T	0.03178	0.0093	N	0.21373	0.66	0.35910	D	0.831063	P;P;P	0.41597	0.712;0.756;0.756	P;P;P	0.49953	0.493;0.627;0.627	T	0.54330	-0.8310	10	0.40728	T	0.16	.	13.4431	0.61125	0.0:0.9214:0.0:0.0786	rs61757573	166;166;166	Q9H9J4-2;Q9H9J4;A4D2N6	.;UBP42_HUMAN;.	V	166;99;12	ENSP00000301962:A166V;ENSP00000430568:A99V;ENSP00000408217:A12V	ENSP00000301962:A166V	A	+	2	0	USP42	6142052	0.755000	0.28372	1.000000	0.80357	0.997000	0.91878	1.296000	0.33389	2.578000	0.87016	0.467000	0.42956	GCA	C|0.999;T|0.001	0.001	strong		0.348	USP42-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324262.3	XM_166526	
DECR2	26063	hgsc.bcm.edu	37	16	461443	461443	+	Silent	SNP	C	C	T	rs138044046	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:461443C>T	ENST00000219481.5	+	8	882	c.744C>T	c.(742-744)agC>agT	p.S248S	DECR2_ENST00000461947.1_Intron|DECR2_ENST00000424398.2_Silent_p.S236S	NM_020664.3	NP_065715.1	Q9NUI1	DECR2_HUMAN	2,4-dienoyl CoA reductase 2, peroxisomal	248					unsaturated fatty acid biosynthetic process (GO:0006636)	peroxisomal membrane (GO:0005778)	2,4-dienoyl-CoA reductase (NADPH) activity (GO:0008670)|receptor binding (GO:0005102)|trans-2-enoyl-CoA reductase (NADPH) activity (GO:0019166)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)	9		Hepatocellular(16;0.00015)				TCGCCCACAGCGTGCTCTACC	0.667													C|||	4	0.000798722	0.0	0.0	5008	,	,		17246	0.0		0.004	False		,,,				2504	0.0				p.S248S		Atlas-SNP	.											.	DECR2	47	.	0			c.C744T						PASS	.	C		4,4400	8.1+/-20.4	0,4,2198	80.0	75.0	77.0		744	-5.8	0.0	16	dbSNP_134	77	51,8549	32.3+/-84.9	0,51,4249	no	coding-synonymous	DECR2	NM_020664.3		0,55,6447	TT,TC,CC		0.593,0.0908,0.4229		248/293	461443	55,12949	2202	4300	6502	SO:0001819	synonymous_variant	26063	exon8			CCACAGCGTGCTC	AJ293009	CCDS10409.1	16p13.3	2011-09-14			ENSG00000242612	ENSG00000242612	1.3.1.34	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	2754	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 17C, member 1"""	615839				11514237, 19027726	Standard	NM_020664		Approved	PDCR, SDR17C1	uc002chb.3	Q9NUI1	OTTHUMG00000047846	ENST00000219481.5:c.744C>T	16.37:g.461443C>T		94.0	0.0	0		106.0	60.0	0.566038	NM_020664	Q6ZRS7|Q96ET0	Silent	SNP	ENST00000219481.5	37	CCDS10409.1																																																																																			C|0.997;T|0.003	0.003	strong		0.667	DECR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109069.4	NM_020664	
EEA1	8411	hgsc.bcm.edu	37	12	93172994	93172994	+	Missense_Mutation	SNP	G	G	A	rs138526188	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:93172994G>A	ENST00000322349.8	-	25	3815	c.3551C>T	c.(3550-3552)gCa>gTa	p.A1184V		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1184	Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TTCAACAGCTGCCTTCAGGGA	0.388																																					p.A1184V		Atlas-SNP	.											.	EEA1	104	.	0			c.C3551T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	132.0	128.0	129.0		3551	3.7	0.0	12	dbSNP_134	129	3,8597	3.0+/-9.4	0,3,4297	yes	missense	EEA1	NM_003566.3	64	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	1184/1412	93172994	3,13003	2203	4300	6503	SO:0001583	missense	8411	exon25			ACAGCTGCCTTCA	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.3551C>T	12.37:g.93172994G>A	ENSP00000317955:p.Ala1184Val	260.0	0.0	0		258.0	139.0	0.53876	NM_003566	Q14221	Missense_Mutation	SNP	ENST00000322349.8	37	CCDS31874.1	.	.	.	.	.	.	.	.	.	.	G	7.333	0.619287	0.14129	0.0	3.49E-4	ENSG00000102189	ENST00000322349	T	0.65549	-0.16	5.63	3.74	0.42951	.	0.607873	0.14539	N	0.313361	T	0.46171	0.1379	N	0.19112	0.55	0.09310	N	1	B	0.24258	0.1	B	0.19148	0.024	T	0.24657	-1.0154	10	0.30078	T	0.28	.	12.553	0.56238	0.0:0.1276:0.7395:0.1329	.	1184	Q15075	EEA1_HUMAN	V	1184	ENSP00000317955:A1184V	ENSP00000317955:A1184V	A	-	2	0	EEA1	91697125	0.159000	0.22864	0.032000	0.17829	0.164000	0.22412	1.860000	0.39428	0.672000	0.31204	0.557000	0.71058	GCA	G|1.000;A|0.000	0.000	strong		0.388	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
FBXO18	84893	hgsc.bcm.edu	37	10	5948352	5948352	+	Silent	SNP	G	G	A	rs138692839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:5948352G>A	ENST00000362091.4	+	3	625	c.510G>A	c.(508-510)acG>acA	p.T170T	FBXO18_ENST00000397269.3_5'UTR|FBXO18_ENST00000379999.5_Silent_p.T221T|FBXO18_ENST00000470089.1_3'UTR	NM_001258453.1|NM_178150.2	NP_001245382.1|NP_835363.1	Q8NFZ0	FBX18_HUMAN	F-box protein, helicase, 18	170	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				DNA catabolic process, endonucleolytic (GO:0000737)|positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage (GO:1902231)|positive regulation of protein phosphorylation (GO:0001934)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)			NS(2)|breast(2)|kidney(2)|large_intestine(16)|lung(9)|ovary(2)|prostate(3)|skin(3)|stomach(1)	40						AGGACAGTACGTCTCGGCTCT	0.572													G|||	6	0.00119808	0.0	0.0	5008	,	,		22855	0.0		0.006	False		,,,				2504	0.0				p.T221T		Atlas-SNP	.											.	FBXO18	108	.	0			c.G663A						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	60.0	52.0	55.0		663,510	0.3	0.0	10	dbSNP_134	55	42,8558	27.4+/-76.7	0,42,4258	no	coding-synonymous,coding-synonymous	FBXO18	NM_032807.3,NM_178150.1	,	0,46,6457	AA,AG,GG		0.4884,0.0908,0.3537	,	221/1095,170/1044	5948352	46,12960	2203	4300	6503	SO:0001819	synonymous_variant	84893	exon4			CAGTACGTCTCGG	AK095343	CCDS7072.1, CCDS7073.1, CCDS73064.1	10p15.1	2004-08-24	2004-06-15		ENSG00000134452	ENSG00000134452		"""F-boxes /  ""other"""""	13620	protein-coding gene	gene with protein product		607222	"""F-box only protein 18"""			10531037, 11956208	Standard	NM_032807		Approved	FBH1, FLJ14590, Fbx18	uc001iit.4	Q8NFZ0	OTTHUMG00000017609	ENST00000362091.4:c.510G>A	10.37:g.5948352G>A		157.0	0.0	0		140.0	78.0	0.557143	NM_032807	Q5JVB0|Q5JVB1|Q7Z4Q6|Q7Z4R0|Q8N1P5|Q8N586|Q96E82|Q96K67|Q96SW7|Q9UFB2	Silent	SNP	ENST00000362091.4	37	CCDS7072.1																																																																																			G|0.998;A|0.002	0.002	strong		0.572	FBXO18-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046596.1	NM_032807	
DDN	23109	hgsc.bcm.edu	37	12	49391682	49391682	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49391682T>C	ENST00000421952.2	-	2	998	c.977A>G	c.(976-978)aAc>aGc	p.N326S	RP11-386G11.5_ENST00000552284.1_RNA|RP11-386G11.5_ENST00000547395.1_RNA|RP11-386G11.5_ENST00000552933.1_RNA|RP11-386G11.3_ENST00000549516.1_RNA|RP11-386G11.5_ENST00000547866.1_RNA	NM_015086.1	NP_055901.2	O94850	DEND_HUMAN	dendrin	326						cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|kidney(1)|large_intestine(1)|lung(3)|prostate(1)|stomach(1)	8						GCTACCACTGTTCAGGTCAGC	0.662																																					p.N326S		Atlas-SNP	.											.	DDN	54	.	0			c.A977G						PASS	.						45.0	53.0	50.0					12																	49391682		2203	4298	6501	SO:0001583	missense	23109	exon2			CCACTGTTCAGGT	AB018292	CCDS31791.2	12q13	2008-02-05			ENSG00000181418	ENSG00000181418			24458	protein-coding gene	gene with protein product		610588					Standard	NM_015086		Approved	KIAA0749	uc001rsv.1	O94850	OTTHUMG00000156183	ENST00000421952.2:c.977A>G	12.37:g.49391682T>C	ENSP00000390590:p.Asn326Ser	72.0	0.0	0		72.0	36.0	0.5	NM_015086		Missense_Mutation	SNP	ENST00000421952.2	37	CCDS31791.2	.	.	.	.	.	.	.	.	.	.	T	9.110	1.006312	0.19199	.	.	ENSG00000181418	ENST00000421952	T	0.47528	0.84	3.88	0.238	0.15480	.	0.712920	0.12723	N	0.444514	T	0.24044	0.0582	N	0.12182	0.205	0.09310	N	1	B	0.16396	0.017	B	0.10450	0.005	T	0.21415	-1.0246	10	0.18710	T	0.47	-24.1145	6.6688	0.23056	0.0:0.3358:0.0:0.6642	.	326	O94850	DEND_HUMAN	S	326	ENSP00000390590:N326S	ENSP00000390590:N326S	N	-	2	0	DDN	47677949	0.000000	0.05858	0.001000	0.08648	0.629000	0.37895	0.452000	0.21795	0.039000	0.15632	0.459000	0.35465	AAC	.	.	none		0.662	DDN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343335.1		
USP17L10	100287144	hgsc.bcm.edu	37	4	9212676	9212676	+	Silent	SNP	G	G	A	rs528291442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:9212676G>A	ENST00000417945.1	+	1	294	c.294G>A	c.(292-294)ctG>ctA	p.L98L	USP17L13_ENST00000421288.2_Intron	NM_001256852.1	NP_001243781.1	C9JJH3	U17LA_HUMAN	ubiquitin specific peptidase 17-like family member 10	98	USP.				ubiquitin-dependent protein catabolic process (GO:0006511)	endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|ubiquitinyl hydrolase activity (GO:0036459)										TGCAGTGCCTGACATACAAAC	0.557													g|||	4	0.000798722	0.0	0.0	5008	,	,		2145	0.0		0.0	False		,,,				2504	0.0041				p.L98L		Atlas-SNP	.											.	.	.	.	0			c.G294A						PASS	.																																			SO:0001819	synonymous_variant	100287144	exon1			GTGCCTGACATAC		CCDS59454.1	4p16.1	2014-02-12	2012-10-09		ENSG00000231396	ENSG00000231396			44438	protein-coding gene	gene with protein product							Standard	NM_001256852		Approved		uc031sdg.1	C9JJH3	OTTHUMG00000160160	ENST00000417945.1:c.294G>A	4.37:g.9212676G>A		0.0	0.0	.		38.0	38.0	1	NM_001256852		Silent	SNP	ENST00000417945.1	37	CCDS59454.1																																																																																			.	.	none		0.557	USP17L10-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359428.1	NM_001256852	
B3GNT1	11041	hgsc.bcm.edu	37	11	66113995	66113995	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:66113995C>T	ENST00000311181.4	-	1	1168	c.1022G>A	c.(1021-1023)cGc>cAc	p.R341H	RP11-867G23.8_ENST00000531602.1_5'Flank|BRMS1_ENST00000425825.2_5'Flank|BRMS1_ENST00000359957.3_5'Flank	NM_006876.2	NP_006867.1	O43505	B3GN1_HUMAN	UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 1	341					axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|poly-N-acetyllactosamine biosynthetic process (GO:0030311)|protein glycosylation (GO:0006486)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase activity (GO:0008532)			breast(2)|kidney(1)|large_intestine(2)|lung(6)|urinary_tract(1)	12						CTGCCGAAAGCGCTCGTCGAA	0.627																																					p.R341H		Atlas-SNP	.											.	B3GNT1	28	.	0			c.G1022A						PASS	.						77.0	82.0	80.0					11																	66113995		2200	4291	6491	SO:0001583	missense	11041	exon1			CGAAAGCGCTCGT	AF029893	CCDS8136.1	11q13.2	2014-07-08	2006-04-12	2006-04-12	ENSG00000174684	ENSG00000174684	2.4.1.149	"""Beta 3-glycosyltransferases"""	15685	protein-coding gene	gene with protein product	"""N-acetyllactosaminide beta-1,3-N-acetylglucosaminyltransferase"""	605517	"""UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 6"""	B3GNT6		9405606	Standard	NM_006876		Approved	iGNT, iGAT, iGnT, BETA3GNTI, B3GN-T1	uc001ohr.3	O43505	OTTHUMG00000167082	ENST00000311181.4:c.1022G>A	11.37:g.66113995C>T	ENSP00000309096:p.Arg341His	87.0	0.0	0		86.0	34.0	0.395349	NM_006876	Q4TTN0	Missense_Mutation	SNP	ENST00000311181.4	37	CCDS8136.1	.	.	.	.	.	.	.	.	.	.	C	18.51	3.640477	0.67244	.	.	ENSG00000174684	ENST00000311181;ENST00000538757	T	0.32272	1.46	5.83	5.83	0.93111	.	0.165306	0.51477	D	0.000098	T	0.61627	0.2362	M	0.84846	2.72	0.46203	D	0.998928	D	0.89917	1.0	D	0.79784	0.993	T	0.65450	-0.6165	10	0.66056	D	0.02	-24.2929	17.6063	0.88039	0.0:1.0:0.0:0.0	.	341	O43505	B3GN1_HUMAN	H	341;112	ENSP00000309096:R341H	ENSP00000309096:R341H	R	-	2	0	B3GNT1	65870571	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	2.911000	0.48774	2.761000	0.94854	0.563000	0.77884	CGC	.	.	none		0.627	B3GNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392959.1	NM_006876	
MROH6	642475	hgsc.bcm.edu	37	8	144654730	144654730	+	Missense_Mutation	SNP	G	G	T	rs185255597	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:144654730G>T	ENST00000398882.3	-	1	411	c.155C>A	c.(154-156)cCt>cAt	p.P52H	NAPRT1_ENST00000460623.1_5'Flank|MROH6_ENST00000533679.1_5'Flank|RP11-661A12.9_ENST00000531730.1_RNA	NM_001100878.1	NP_001094348.1	A6NGR9	MROH6_HUMAN	maestro heat-like repeat family member 6	52																	CTCAGCCTCAGGTTTGACCTC	0.682													g|||	4	0.000798722	0.0	0.0	5008	,	,		13956	0.0		0.004	False		,,,				2504	0.0				p.P52H		Atlas-SNP	.											.	.	.	.	0			c.C155A						PASS	.		HIS/PRO	6,3902		0,6,1948	16.0	20.0	19.0		155	0.3	0.0	8		19	28,8238		0,28,4105	yes	missense	C8orf73	NM_001100878.1	77	0,34,6053	TT,TG,GG		0.3387,0.1535,0.2793	probably-damaging	52/720	144654730	34,12140	1954	4133	6087	SO:0001583	missense	642475	exon1			GCCTCAGGTTTGA	AF289596	CCDS47928.1	8q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000204839	ENSG00000204839		"""maestro heat-like repeat containing"""	27814	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 73"""	C8orf73		12477932	Standard	NM_001100878		Approved		uc010mff.3	A6NGR9	OTTHUMG00000165164	ENST00000398882.3:c.155C>A	8.37:g.144654730G>T	ENSP00000381857:p.Pro52His	79.0	0.0	0		67.0	42.0	0.626866	NM_001100878	A8MWB1	Missense_Mutation	SNP	ENST00000398882.3	37	CCDS47928.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	16.46	3.129400	0.56721	0.001535	0.003387	ENSG00000204839	ENST00000398882;ENST00000529971	T;T	0.30981	3.71;1.51	4.54	0.342	0.15996	.	.	.	.	.	T	0.15262	0.0368	N	0.14661	0.345	0.09310	N	0.999998	D;P	0.54207	0.965;0.681	P;B	0.50378	0.639;0.371	T	0.09796	-1.0658	9	0.87932	D	0	-1.6263	2.8407	0.05528	0.1024:0.334:0.3925:0.1711	.	52;52	E9PPP7;A6NGR9	.;CH073_HUMAN	H	52	ENSP00000381857:P52H;ENSP00000436959:P52H	ENSP00000381857:P52H	P	-	2	0	C8orf73	144725873	0.000000	0.05858	0.000000	0.03702	0.131000	0.20780	0.024000	0.13555	0.449000	0.26747	0.461000	0.40582	CCT	G|0.998;T|0.002	0.002	strong		0.682	MROH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382330.3	NM_001100878	
TLR1	7096	hgsc.bcm.edu	37	4	38799493	38799493	+	Silent	SNP	A	A	G	rs200631178		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:38799493A>G	ENST00000502213.2	-	3	1189	c.960T>C	c.(958-960)taT>taC	p.Y320Y	TLR1_ENST00000308979.2_Silent_p.Y320Y			Q15399	TLR1_HUMAN	toll-like receptor 1	320					cellular response to triacyl bacterial lipopeptide (GO:0071727)|detection of triacyl bacterial lipopeptide (GO:0042495)|immune response (GO:0006955)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|positive regulation of interleukin-6 biosynthetic process (GO:0045410)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|regulation of cytokine secretion (GO:0050707)|signal transduction (GO:0007165)|toll-like receptor 1 signaling pathway (GO:0034130)	cytoplasmic vesicle (GO:0031410)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)|Toll-like receptor 1-Toll-like receptor 2 protein complex (GO:0035354)	protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(11)|ovary(1)|prostate(1)|skin(4)|stomach(2)	28						AAAAGATTTCATAGATATAAC	0.413																																					p.Y320Y	GBM(5;216 373 40795 46382)	Atlas-SNP	.											.	TLR1	70	.	0			c.T960C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	58.0	61.0	60.0		960	-4.8	0.0	4		60	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	TLR1	NM_003263.3		0,2,6501	GG,GA,AA		0.0116,0.0227,0.0154		320/787	38799493	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	7096	exon4			GATTTCATAGATA	U88540	CCDS33973.1	4p14	2008-02-05				ENSG00000174125		"""CD molecules"""	11847	protein-coding gene	gene with protein product		601194				9435236, 7584026	Standard	NM_003263		Approved	rsc786, KIAA0012, CD281	uc003gtl.3	Q15399		ENST00000502213.2:c.960T>C	4.37:g.38799493A>G		55.0	0.0	0		46.0	26.0	0.565217	NM_003263	D1CS39|D1CS41|O15452|Q32MK3|Q32MK4|Q9UG90	Silent	SNP	ENST00000502213.2	37	CCDS33973.1																																																																																			A|0.999;G|0.001	0.001	weak		0.413	TLR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360510.3		
ZNF496	84838	hgsc.bcm.edu	37	1	247473018	247473018	+	Missense_Mutation	SNP	G	G	A	rs149858668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:247473018G>A	ENST00000294753.4	-	7	1339	c.875C>T	c.(874-876)cCc>cTc	p.P292L	ZNF496_ENST00000462139.1_5'UTR|ZNF496_ENST00000366498.2_Missense_Mutation_p.P328L	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	292					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			GGAGACCTGGGGCACTTCTTT	0.572													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		17285	0.0		0.0	False		,,,				2504	0.0				p.P292L		Atlas-SNP	.											.	ZNF496	80	.	0			c.C875T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	86.0	76.0	80.0		875	4.7	0.9	1	dbSNP_134	80	6,8594	5.0+/-18.6	0,6,4294	yes	missense	ZNF496	NM_032752.1	98	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	benign	292/588	247473018	6,13000	2203	4300	6503	SO:0001583	missense	84838	exon7			ACCTGGGGCACTT	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.875C>T	1.37:g.247473018G>A	ENSP00000294753:p.Pro292Leu	94.0	0.0	0		95.0	48.0	0.505263	NM_032752	Q8TBS2	Missense_Mutation	SNP	ENST00000294753.4	37	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	G	13.26	2.184918	0.38609	0.0	6.98E-4	ENSG00000162714	ENST00000294753;ENST00000366498	T;T	0.07800	3.18;3.16	4.7	4.7	0.59300	.	0.508746	0.16561	N	0.209034	T	0.07098	0.0180	N	0.24115	0.695	0.46260	D	0.998956	B;B	0.09022	0.002;0.001	B;B	0.08055	0.003;0.001	T	0.30707	-0.9969	10	0.33940	T	0.23	-9.6614	13.5458	0.61702	0.0:0.0:1.0:0.0	.	328;292	Q96IT1-2;Q96IT1	.;ZN496_HUMAN	L	292;328	ENSP00000294753:P292L;ENSP00000355454:P328L	ENSP00000294753:P292L	P	-	2	0	ZNF496	245539641	0.976000	0.34144	0.911000	0.35937	0.925000	0.55904	1.892000	0.39748	2.341000	0.79615	0.561000	0.74099	CCC	G|0.999;A|0.001	0.001	strong		0.572	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
STRA6	64220	hgsc.bcm.edu	37	15	74472525	74472525	+	Missense_Mutation	SNP	G	G	A	rs200178616		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:74472525G>A	ENST00000323940.5	-	19	2145	c.1900C>T	c.(1900-1902)Cgc>Tgc	p.R634C	STRA6_ENST00000574278.1_Missense_Mutation_p.R649C|STRA6_ENST00000535552.1_Missense_Mutation_p.R671C|STRA6_ENST00000395105.4_Missense_Mutation_p.R634C|STRA6_ENST00000574439.1_5'UTR|STRA6_ENST00000563965.1_Missense_Mutation_p.R673C|STRA6_ENST00000449139.2_Missense_Mutation_p.R634C|STRA6_ENST00000416286.3_Missense_Mutation_p.R626C|RP11-665J16.1_ENST00000561647.1_RNA|STRA6_ENST00000423167.2_Missense_Mutation_p.R625C	NM_001142617.1|NM_001142618.1|NM_001142619.1	NP_001136089.1|NP_001136090.1|NP_001136091.1	Q9BX79	STRA6_HUMAN	stimulated by retinoic acid 6	634					adrenal gland development (GO:0030325)|alveolar primary septum development (GO:0061143)|artery morphogenesis (GO:0048844)|blood vessel development (GO:0001568)|cognition (GO:0050890)|developmental growth (GO:0048589)|diaphragm development (GO:0060539)|digestive tract morphogenesis (GO:0048546)|ductus arteriosus closure (GO:0097070)|ear development (GO:0043583)|embryonic camera-type eye formation (GO:0060900)|embryonic digestive tract development (GO:0048566)|eyelid development in camera-type eye (GO:0061029)|face morphogenesis (GO:0060325)|feeding behavior (GO:0007631)|female genitalia development (GO:0030540)|head development (GO:0060322)|head morphogenesis (GO:0060323)|heart development (GO:0007507)|kidney development (GO:0001822)|learning (GO:0007612)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung vasculature development (GO:0060426)|neuromuscular process (GO:0050905)|nose morphogenesis (GO:0043585)|paramesonephric duct development (GO:0061205)|phototransduction, visible light (GO:0007603)|positive regulation of behavior (GO:0048520)|positive regulation of JAK-STAT cascade (GO:0046427)|pulmonary artery morphogenesis (GO:0061156)|pulmonary valve morphogenesis (GO:0003184)|retinoic acid metabolic process (GO:0042573)|retinoid metabolic process (GO:0001523)|retinol transport (GO:0034633)|smooth muscle tissue development (GO:0048745)|uterus morphogenesis (GO:0061038)|ventricular septum development (GO:0003281)|vitamin A import (GO:0071939)|vocal learning (GO:0042297)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	receptor activity (GO:0004872)|vitamin transporter activity (GO:0051183)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(4)|lung(5)|skin(1)|stomach(2)	26						GCCCTGCCGCGGCTGGCCCCG	0.637													G|||	1	0.000199681	0.0008	0.0	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.R673C		Atlas-SNP	.											STRA6,NS,carcinoma,+1,1	STRA6	66	1	0			c.C2017T						scavenged	.						91.0	104.0	100.0					15																	74472525		2198	4297	6495	SO:0001583	missense	64220	exon19			TGCCGCGGCTGGC	AF352728	CCDS10261.1, CCDS45301.1, CCDS45302.1, CCDS55973.1, CCDS55974.1, CCDS58387.1	15q24.1	2014-07-14	2012-12-07		ENSG00000137868	ENSG00000137868			30650	protein-coding gene	gene with protein product	"""retinol binding protein 4 receptor"""	610745	"""stimulated by retinoic acid gene 6 homolog (mouse)"", ""stimulated by retinoic acid 6 homolog (mouse)"""			17255476, 17273977	Standard	NM_022369		Approved	FLJ12541	uc002axj.3	Q9BX79	OTTHUMG00000138998	ENST00000323940.5:c.1900C>T	15.37:g.74472525G>A	ENSP00000326085:p.Arg634Cys	147.0	1.0	0.00680272		158.0	77.0	0.487342	NM_001199042	A8K7F1|B7Z5M9|B7Z862|D3DW54|F5GYI8|I3L1G8|Q6PJF8|Q71RB9|Q7L9G1|Q7Z3U9|Q8TB21|Q9BX78|Q9H9U8	Missense_Mutation	SNP	ENST00000323940.5	37	CCDS10261.1	.	.	.	.	.	.	.	.	.	.	G	11.53	1.666348	0.29604	.	.	ENSG00000137868	ENST00000395105;ENST00000323940;ENST00000416286;ENST00000545137;ENST00000449139;ENST00000423167;ENST00000535552;ENST00000536129	D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99	4.5	2.61	0.31194	.	0.757532	0.12544	N	0.459624	D	0.86205	0.5877	L	0.48642	1.525	0.21473	N	0.999671	D;D;D;D;D;D	0.76494	0.999;0.999;0.999;0.999;0.999;0.999	P;P;P;P;P;P	0.56916	0.804;0.804;0.736;0.736;0.804;0.809	T	0.75286	-0.3371	10	0.66056	D	0.02	-2.8476	8.8353	0.35109	0.1759:0.0:0.8241:0.0	.	671;672;625;634;673;443	F5GYI8;B7Z5G7;Q9BX79-3;Q9BX79;Q9BX79-4;B3KRT6	.;.;.;STRA6_HUMAN;.;.	C	634;634;566;443;673;625;671;524	ENSP00000378537:R634C;ENSP00000326085:R634C;ENSP00000413012:R625C;ENSP00000440238:R671C	ENSP00000326085:R634C	R	-	1	0	STRA6	72259578	0.075000	0.21258	0.004000	0.12327	0.013000	0.08279	2.732000	0.47352	0.351000	0.24027	-0.379000	0.06801	CGC	G|0.999;A|0.001	0.001	weak		0.637	STRA6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272891.1		
C6orf15	29113	hgsc.bcm.edu	37	6	31079310	31079310	+	Missense_Mutation	SNP	T	T	G	rs560168888	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31079310T>G	ENST00000259870.3	-	2	829	c.826A>C	c.(826-828)Aat>Cat	p.N276H		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	276	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GGATACCGATTAATATTCCCC	0.502													T|||	2	0.000399361	0.0008	0.0	5008	,	,		16631	0.0		0.0	False		,,,				2504	0.001				p.N276H		Atlas-SNP	.											.	C6orf15	29	.	0			c.A826C						PASS	.						67.0	76.0	73.0					6																	31079310		1743	3414	5157	SO:0001583	missense	29113	exon2			ACCGATTAATATT	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.826A>C	6.37:g.31079310T>G	ENSP00000259870:p.Asn276His	123.0	0.0	0		137.0	9.0	0.0656934	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Missense_Mutation	SNP	ENST00000259870.3	37	CCDS4693.1	.	.	.	.	.	.	.	.	.	.	T	13.91	2.378711	0.42207	.	.	ENSG00000204542	ENST00000259870	T	0.06687	3.27	4.19	1.66	0.24008	.	0.372474	0.19119	U	0.122222	T	0.07143	0.0181	L	0.54323	1.7	0.09310	N	1	D	0.76494	0.999	D	0.65684	0.937	T	0.15954	-1.0419	10	0.45353	T	0.12	-12.0482	3.1014	0.06327	0.3753:0.1067:0.0:0.518	.	276	Q6UXA7	CF015_HUMAN	H	276	ENSP00000259870:N276H	ENSP00000259870:N276H	N	-	1	0	C6orf15	31187289	0.000000	0.05858	0.012000	0.15200	0.265000	0.26407	-0.001000	0.12947	0.149000	0.19098	0.372000	0.22366	AAT	.	.	none		0.502	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
RET	5979	hgsc.bcm.edu	37	10	43610119	43610119	+	Missense_Mutation	SNP	G	G	A	rs1799939	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:43610119G>A	ENST00000355710.3	+	11	2303	c.2071G>A	c.(2071-2073)Ggt>Agt	p.G691S	RET_ENST00000340058.5_Missense_Mutation_p.G691S	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	691			G -> S (in dbSNP:rs1799939). {ECO:0000269|PubMed:14566559, ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9223675, ECO:0000269|PubMed:9497256}.		activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	CTCCTCTTCCGGTGCCCGCCG	0.647		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma				G|||	847	0.169129	0.0923	0.2565	5008	,	,		18422	0.121		0.1889	False		,,,				2504	0.2403				p.G691S	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	RET_ENST00000340058,adrenal_gland,pheochromocytoma,0,2	RET	916	2	0			c.G2071A	GRCh37	CM023821	RET	M	rs1799939	PASS	.	G	SER/GLY,SER/GLY	455,3951	216.4+/-235.1	19,417,1767	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2071,2071	-1.1	0.0	10	dbSNP_89	57	1587,7013	295.7+/-302.5	155,1277,2868	yes	missense,missense	RET	NM_020630.4,NM_020975.4	56,56	174,1694,4635	AA,AG,GG		18.4535,10.3268,15.7004	possibly-damaging,possibly-damaging	691/1073,691/1115	43610119	2042,10964	2203	4300	6503	SO:0001583	missense	5979	exon11	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	TCTTCCGGTGCCC	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.2071G>A	10.37:g.43610119G>A	ENSP00000347942:p.Gly691Ser	58.0	0.0	0		79.0	37.0	0.468354	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Missense_Mutation	SNP	ENST00000355710.3	37	CCDS7200.1	338	0.15476190476190477	45	0.09146341463414634	82	0.2265193370165746	60	0.1048951048951049	151	0.19920844327176782	G	8.525	0.869582	0.17322	0.103268	0.184535	ENSG00000165731	ENST00000355710;ENST00000340058	T;T	0.78246	-1.05;-1.16	4.75	-1.08	0.09936	.	0.349618	0.34603	N	0.003826	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	B;B;B	0.24426	0.062;0.062;0.103	B;B;B	0.16722	0.004;0.007;0.016	T	0.04128	-1.0975	9	0.07990	T	0.79	.	9.2584	0.37597	0.7374:0.0:0.2626:0.0	rs1799939;rs3781260;rs17362555;rs17845010;rs17857772;rs1799939	437;691;691	B4DGX8;P07949;P07949-2	.;RET_HUMAN;.	S	691	ENSP00000347942:G691S;ENSP00000344798:G691S	ENSP00000344798:G691S	G	+	1	0	RET	42930125	1.000000	0.71417	0.000000	0.03702	0.411000	0.31082	4.395000	0.59678	-0.060000	0.13132	0.462000	0.41574	GGT	G|0.839;A|0.161	0.161	strong		0.647	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
CRB2	286204	hgsc.bcm.edu	37	9	126125327	126125327	+	Missense_Mutation	SNP	G	G	A	rs138381817	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126125327G>A	ENST00000373631.3	+	2	279	c.278G>A	c.(277-279)cGc>cAc	p.R93H	CRB2_ENST00000359999.3_Missense_Mutation_p.R93H	NM_173689.5	NP_775960.4	Q5IJ48	CRUM2_HUMAN	crumbs family member 2	93	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cardiovascular system development (GO:0072358)|maintenance of epithelial cell apical/basal polarity (GO:0045199)|mesoderm formation (GO:0001707)|negative regulation of endopeptidase activity (GO:0010951)|notochord formation (GO:0014028)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|somitogenesis (GO:0001756)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)			NS(2)|breast(1)|cervix(1)|endometrium(2)|lung(11)|ovary(1)|prostate(2)|skin(3)	23						ACCGGCTTCCGCTGCTACTGC	0.692													G|||	15	0.00299521	0.0	0.0101	5008	,	,		14806	0.0		0.008	False		,,,				2504	0.0				p.R93H		Atlas-SNP	.											.	CRB2	86	.	0			c.G278A						PASS	.	G	HIS/ARG	8,4398		0,8,2195	40.0	39.0	39.0		278	2.7	1.0	9	dbSNP_134	39	102,8494		2,98,4198	yes	missense	CRB2	NM_173689.5	29	2,106,6393	AA,AG,GG		1.1866,0.1816,0.846	probably-damaging	93/1286	126125327	110,12892	2203	4298	6501	SO:0001583	missense	286204	exon2			GCTTCCGCTGCTA	AK095783	CCDS6852.2	9q33.2	2014-02-06	2014-02-06		ENSG00000148204	ENSG00000148204			18688	protein-coding gene	gene with protein product		609720	"""crumbs homolog 2 (Drosophila)"""			14767562	Standard	XM_005251934		Approved	FLJ38464, FLJ16786	uc004bnx.1	Q5IJ48	OTTHUMG00000020638	ENST00000373631.3:c.278G>A	9.37:g.126125327G>A	ENSP00000362734:p.Arg93His	126.0	0.0	0		89.0	52.0	0.58427	NM_173689	A2A3N4|Q0QD46|Q5JS41|Q5JS43|Q6ZTA9|Q6ZWI6	Missense_Mutation	SNP	ENST00000373631.3	37	CCDS6852.2	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	14.66	2.601296	0.46423	0.001816	0.011866	ENSG00000148204	ENST00000359999;ENST00000373631	T;T	0.61274	0.12;0.12	4.7	2.69	0.31865	Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.172979	0.27841	N	0.017634	T	0.28366	0.0701	L	0.31664	0.95	0.80722	D	1	B;B	0.28971	0.013;0.229	B;B	0.21360	0.004;0.034	T	0.24440	-1.0160	10	0.51188	T	0.08	.	2.6651	0.05041	0.104:0.1689:0.5289:0.1981	.	93;93	Q5IJ48;Q5IJ48-2	CRUM2_HUMAN;.	H	93	ENSP00000353092:R93H;ENSP00000362734:R93H	ENSP00000353092:R93H	R	+	2	0	CRB2	125165148	0.035000	0.19736	1.000000	0.80357	0.834000	0.47266	0.452000	0.21795	1.214000	0.43395	0.448000	0.29417	CGC	G|0.993;A|0.007	0.007	strong		0.692	CRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053990.3	NM_173689	
TOPAZ1	375337	hgsc.bcm.edu	37	3	44329245	44329245	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:44329245C>T	ENST00000309765.4	+	11	3763	c.3595C>T	c.(3595-3597)Ctg>Ttg	p.L1199L		NM_001145030.1	NP_001138502.1	Q8N9V7	TOPZ1_HUMAN	testis and ovary specific PAZ domain containing 1	1199						cytoplasm (GO:0005737)	metal ion binding (GO:0046872)										CCAGCCTTCTCTGAAAATATT	0.284																																					p.L1199L		Atlas-SNP	.											.	.	.	.	0			c.C3595T						PASS	.						190.0	167.0	174.0					3																	44329245		692	1591	2283	SO:0001819	synonymous_variant	375337	exon11			CCTTCTCTGAAAA	AK093476	CCDS46809.1	3p21.33	2012-10-08	2012-10-08	2012-10-08	ENSG00000173769	ENSG00000173769			24746	protein-coding gene	gene with protein product		614412	"""chromosome 3 open reading frame 77"""	C3orf77		22069478	Standard	NM_001145030		Approved	FLJ36157	uc003cna.4	Q8N9V7	OTTHUMG00000156172	ENST00000309765.4:c.3595C>T	3.37:g.44329245C>T		70.0	0.0	0		59.0	14.0	0.237288	NM_001145030		Silent	SNP	ENST00000309765.4	37	CCDS46809.1																																																																																			.	.	none		0.284	TOPAZ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343247.1	NM_001145030	
CCDC61	729440	hgsc.bcm.edu	37	19	46520506	46520506	+	Splice_Site	SNP	G	G	C	rs61742389	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:46520506G>C	ENST00000595358.1	+	12	1361	c.1312G>C	c.(1312-1314)Ggt>Cgt	p.G438R	CCDC61_ENST00000536603.1_Splice_Site_p.G258R|MIR769_ENST00000390225.1_RNA|CCDC61_ENST00000594087.1_Splice_Site_p.G258R|CCDC61_ENST00000263284.2_Splice_Site_p.G457R	NM_001267723.1	NP_001254652.1	Q9Y6R9	CCD61_HUMAN	coiled-coil domain containing 61	438						centrosome (GO:0005813)				endometrium(3)|kidney(3)|large_intestine(1)|lung(5)|ovary(1)	13		all_neural(266;0.113)|Ovarian(192;0.127)		OV - Ovarian serous cystadenocarcinoma(262;0.00221)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.164)		TTTTCTCAGGGGTCACCGCCG	0.607											OREG0025565	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	40	0.00798722	0.0015	0.0101	5008	,	,		10932	0.0		0.0219	False		,,,				2504	0.0092				p.G438R		Atlas-SNP	.											.	CCDC61	32	.	0			c.G1312C						PASS	.		ARG/GLY	20,3958		0,20,1969	21.0	26.0	25.0		1369	-1.7	0.0	19	dbSNP_129	25	131,8161		0,131,4015	yes	missense-near-splice	CCDC61	NM_001080402.1	125	0,151,5984	CC,CG,GG		1.5798,0.5028,1.2306	benign	457/532	46520506	151,12119	1989	4146	6135	SO:0001630	splice_region_variant	729440	exon12			CTCAGGGGTCACC		CCDS46120.1, CCDS46120.2	19q13.32	2014-09-04			ENSG00000104983	ENSG00000104983			33629	protein-coding gene	gene with protein product							Standard	NM_001267723		Approved		uc031rlj.1	Q9Y6R9	OTTHUMG00000182488	ENST00000595358.1:c.1311-1G>C	19.37:g.46520506G>C		53.0	0.0	0	939	39.0	14.0	0.358974	NM_001267723	C8CAP4|Q9HDB6	Missense_Mutation	SNP	ENST00000595358.1	37	CCDS46120.2	24	0.01098901098901099	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	8.859	0.946358	0.18356	0.005028	0.015798	ENSG00000104983	ENST00000263284;ENST00000536603	.	.	.	3.77	-1.73	0.08081	.	1.284800	0.05551	N	0.567480	T	0.04227	0.0117	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.24048	-1.0171	9	0.10636	T	0.68	5.2453	2.635	0.04955	0.1288:0.4667:0.2536:0.1509	rs61742389	400	Q9Y6R9	CCD61_HUMAN	R	457;258	.	ENSP00000263284:G457R	G	+	1	0	CCDC61	51212346	0.000000	0.05858	0.002000	0.10522	0.022000	0.10575	-0.122000	0.10627	-0.025000	0.13918	0.450000	0.29827	GGT	A|0.000;C|0.012;G|0.987	0.012	strong		0.607	CCDC61-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461689.1	NM_001080402	Missense_Mutation
MYH15	22989	hgsc.bcm.edu	37	3	108147510	108147510	+	Silent	SNP	A	A	G	rs201473403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:108147510A>G	ENST00000273353.3	-	28	3647	c.3591T>C	c.(3589-3591)ttT>ttC	p.F1197F		NM_014981.1	NP_055796.1	Q9Y2K3	MYH15_HUMAN	myosin, heavy chain 15	1197						cytoplasm (GO:0005737)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(1)|breast(3)|central_nervous_system(2)|cervix(4)|endometrium(10)|kidney(4)|large_intestine(14)|lung(47)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	105						AAGTTGTCTCAAAGTGCAGAG	0.483													A|||	5	0.000998403	0.0	0.0014	5008	,	,		19235	0.0		0.004	False		,,,				2504	0.0				p.F1197F		Atlas-SNP	.											.	MYH15	223	.	0			c.T3591C						PASS	.	A		2,3922		0,2,1960	130.0	125.0	126.0		3591	-3.7	0.3	3		126	19,8307		0,19,4144	no	coding-synonymous	MYH15	NM_014981.1		0,21,6104	GG,GA,AA		0.2282,0.051,0.1714		1197/1947	108147510	21,12229	1962	4163	6125	SO:0001819	synonymous_variant	22989	exon28			TGTCTCAAAGTGC	AB023217	CCDS43127.1	3q13	2011-09-27	2006-09-29		ENSG00000144821	ENSG00000144821		"""Myosins / Myosin superfamily : Class II"""	31073	protein-coding gene	gene with protein product		609929	"""myosin, heavy polypeptide 15"""			15014174, 15042088	Standard	NM_014981		Approved	KIAA1000	uc003dxa.1	Q9Y2K3	OTTHUMG00000159226	ENST00000273353.3:c.3591T>C	3.37:g.108147510A>G		234.0	0.0	0		261.0	139.0	0.532567	NM_014981		Silent	SNP	ENST00000273353.3	37	CCDS43127.1																																																																																			A|0.999;G|0.001	0.001	strong		0.483	MYH15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353935.1	XM_036988	
P2RY11	5032	hgsc.bcm.edu	37	19	10226686	10226686	+	IGR	SNP	G	G	A	rs200490441	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:10226686G>A	ENST00000321826.4	+	0	1943				EIF3G_ENST00000253108.4_Silent_p.D220D|EIF3G_ENST00000587168.1_5'Flank	NM_002566.4	NP_002557.2	Q96G91	P2Y11_HUMAN	purinergic receptor P2Y, G-protein coupled, 11						activation of adenylate cyclase activity (GO:0007190)|adenosine receptor signaling pathway (GO:0001973)|calcium-mediated signaling (GO:0019722)|cellular response to ATP (GO:0071318)|defense response (GO:0006952)|G-protein coupled receptor signaling pathway (GO:0007186)|neuronal signal transduction (GO:0023041)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ATP-activated nucleotide receptor activity (GO:0045031)|G-protein coupled purinergic nucleotide receptor activity (GO:0045028)|neurotransmitter receptor activity (GO:0030594)|receptor activity (GO:0004872)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(2)|ovary(2)	16			OV - Ovarian serous cystadenocarcinoma(20;3.53e-09)|Epithelial(33;4.91e-06)|all cancers(31;1.1e-05)			GGCTGGCCCCGTCGCGCAGGC	0.662													G|||	2	0.000399361	0.0	0.0	5008	,	,		15153	0.002		0.0	False		,,,				2504	0.0				p.D220D		Atlas-SNP	.											.	EIF3G	16	.	0			c.C660T						PASS	.	G		0,4402		0,0,2201	26.0	27.0	27.0		660	-5.3	0.9	19		27	1,8593		0,1,4296	no	coding-synonymous	EIF3G	NM_003755.3		0,1,6497	AA,AG,GG		0.0116,0.0,0.0077		220/321	10226686	1,12995	2201	4297	6498	SO:0001628	intergenic_variant	8666	exon8			GGCCCCGTCGCGC	AF030335	CCDS12226.1	19p13.2	2012-08-08			ENSG00000244165	ENSG00000244165		"""Purinergic receptors"", ""GPCR / Class A : Purinergic receptors, P2Y"""	8540	protein-coding gene	gene with protein product		602697				9405388	Standard	NM_002566		Approved	P2Y11		Q96G91	OTTHUMG00000150166		19.37:g.10226686G>A		68.0	0.0	0		61.0	34.0	0.557377	NM_003755	B2R8X9|O43190|Q9BYU4|Q9H170	Silent	SNP	ENST00000321826.4	37	CCDS12226.1																																																																																			G|0.999;A|0.001	0.001	strong		0.662	P2RY11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316664.2	NM_002566	
PLXNA2	5362	hgsc.bcm.edu	37	1	208227814	208227814	+	Silent	SNP	C	C	T	rs2274447	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:208227814C>T	ENST00000367033.3	-	14	3565	c.2808G>A	c.(2806-2808)gaG>gaA	p.E936E		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	936	IPT/TIG 1.				axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		CTGGCTTACACTCGCCAATAC	0.582													C|||	52	0.0103834	0.0	0.0029	5008	,	,		21260	0.0129		0.004	False		,,,				2504	0.0337				p.E936E		Atlas-SNP	.											PLXNA2,caecum,carcinoma,-2,1	PLXNA2	178	1	0			c.G2808A						scavenged	.	C		6,4400	11.4+/-27.6	0,6,2197	105.0	83.0	90.0		2808	3.5	1.0	1	dbSNP_100	90	35,8565	24.0+/-70.4	0,35,4265	no	coding-synonymous	PLXNA2	NM_025179.3		0,41,6462	TT,TC,CC		0.407,0.1362,0.3152		936/1895	208227814	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	5362	exon14			CTTACACTCGCCA	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.2808G>A	1.37:g.208227814C>T		87.0	1.0	0.0114943		127.0	52.0	0.409449	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Silent	SNP	ENST00000367033.3	37	CCDS31013.1																																																																																			C|0.995;T|0.005	0.005	strong		0.582	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
AKAP5	9495	hgsc.bcm.edu	37	14	64935726	64935726	+	Missense_Mutation	SNP	C	C	T	rs2230492	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:64935726C>T	ENST00000394718.4	+	2	992	c.614C>T	c.(613-615)tCt>tTt	p.S205F	ZBTB25_ENST00000555424.1_Intron|AKAP5_ENST00000320636.5_Missense_Mutation_p.S205F|ZBTB25_ENST00000555220.1_Intron	NM_004857.3	NP_004848.3	P24588	AKAP5_HUMAN	A kinase (PRKA) anchor protein 5	205					energy reserve metabolic process (GO:0006112)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of protein kinase A signaling (GO:0010739)|protein targeting (GO:0006605)|regulation of insulin secretion (GO:0050796)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	adenylate cyclase binding (GO:0008179)|protein kinase A binding (GO:0051018)			endometrium(2)|kidney(1)|large_intestine(5)|lung(4)|stomach(1)	13				all cancers(60;0.00749)|OV - Ovarian serous cystadenocarcinoma(108;0.0095)|BRCA - Breast invasive adenocarcinoma(234;0.0449)		AGCACAACTTCTGGAGAGAAA	0.413													C|||	7	0.00139776	0.0	0.0	5008	,	,		21422	0.0		0.006	False		,,,				2504	0.001				p.S205F		Atlas-SNP	.											.	AKAP5	23	.	0			c.C614T						PASS	.	C	PHE/SER	7,4399	12.9+/-30.5	0,7,2196	97.0	101.0	100.0		614	6.0	1.0	14	dbSNP_98	100	56,8544	35.9+/-90.5	0,56,4244	yes	missense	AKAP5	NM_004857.3	155	0,63,6440	TT,TC,CC		0.6512,0.1589,0.4844	benign	205/428	64935726	63,12943	2203	4300	6503	SO:0001583	missense	9495	exon2			CAACTTCTGGAGA	M90359	CCDS9764.1	14q23.3	2012-05-16			ENSG00000179841	ENSG00000179841		"""A-kinase anchor proteins"""	375	protein-coding gene	gene with protein product		604688				1512224, 1618839	Standard	NM_004857		Approved	AKAP75, AKAP79	uc001xhd.4	P24588	OTTHUMG00000029634	ENST00000394718.4:c.614C>T	14.37:g.64935726C>T	ENSP00000378207:p.Ser205Phe	86.0	0.0	0		94.0	39.0	0.414894	NM_004857	A2RRB8	Missense_Mutation	SNP	ENST00000394718.4	37	CCDS9764.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	15.66	2.899719	0.52227	0.001589	0.006512	ENSG00000179841	ENST00000394718;ENST00000320636	T;T	0.32272	1.46;1.46	6.02	6.02	0.97574	.	0.341615	0.25383	N	0.031074	T	0.39860	0.1094	L	0.55481	1.735	0.37227	D	0.905491	D	0.65815	0.995	P	0.57371	0.819	T	0.46652	-0.9176	10	0.87932	D	0	-9.0253	17.454	0.87602	0.0:1.0:0.0:0.0	rs2230492;rs2230492	205	P24588	AKAP5_HUMAN	F	205	ENSP00000378207:S205F;ENSP00000315615:S205F	ENSP00000315615:S205F	S	+	2	0	AKAP5	64005479	0.035000	0.19736	0.957000	0.39632	0.717000	0.41224	1.428000	0.34892	2.857000	0.98124	0.650000	0.86243	TCT	C|0.996;T|0.004	0.004	strong		0.413	AKAP5-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268070.3		
MYO15A	51168	hgsc.bcm.edu	37	17	18058468	18058468	+	Missense_Mutation	SNP	G	G	A	rs140140417	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18058468G>A	ENST00000205890.5	+	46	8607	c.8269G>A	c.(8269-8271)Gtg>Atg	p.V2757M	MYO15A_ENST00000585180.1_Missense_Mutation_p.V21M|MYO15A_ENST00000418233.3_Missense_Mutation_p.V21M	NM_016239.3	NP_057323.3	Q9UKN7	MYO15_HUMAN	myosin XVA	2757	Tail.				inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|stereocilium (GO:0032420)	ATP binding (GO:0005524)|motor activity (GO:0003774)			breast(5)|central_nervous_system(2)|endometrium(17)|kidney(3)|large_intestine(16)|lung(27)|ovary(3)|pancreas(1)|prostate(6)|skin(13)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	99	all_neural(463;0.228)					AACGGAAAGCGTGAAGCGGGC	0.642													G|||	11	0.00219649	0.0015	0.0058	5008	,	,		18941	0.0		0.002	False		,,,				2504	0.0031				p.V2757M		Atlas-SNP	.											.	MYO15A	268	.	0			c.G8269A						PASS	.	G	MET/VAL	0,4188		0,0,2094	41.0	51.0	47.0		8269	-0.2	0.3	17	dbSNP_134	47	18,8416		0,18,4199	yes	missense	MYO15A	NM_016239.3	21	0,18,6293	AA,AG,GG		0.2134,0.0,0.1426	probably-damaging	2757/3531	18058468	18,12604	2094	4217	6311	SO:0001583	missense	51168	exon45			GAAAGCGTGAAGC	AF144094	CCDS42271.1	17p11.2	2011-09-27			ENSG00000091536	ENSG00000091536		"""Myosins / Myosin superfamily : Class XV"""	7594	protein-coding gene	gene with protein product		602666		DFNB3, MYO15		9603736	Standard	NM_016239		Approved		uc021trl.1	Q9UKN7	OTTHUMG00000059390	ENST00000205890.5:c.8269G>A	17.37:g.18058468G>A	ENSP00000205890:p.Val2757Met	96.0	0.0	0		93.0	35.0	0.376344	NM_016239	B4DFC7	Missense_Mutation	SNP	ENST00000205890.5	37	CCDS42271.1	6	0.0027472527472527475	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	4.445	0.082431	0.08533	0.0	0.002134	ENSG00000091536	ENST00000205890	D	0.90788	-2.73	5.2	-0.241	0.13043	.	.	.	.	.	D	0.83709	0.5313	M	0.71206	2.165	0.39248	D	0.963971	B;B	0.29341	0.242;0.149	B;B	0.29663	0.105;0.01	T	0.80765	-0.1236	9	0.87932	D	0	.	6.7414	0.23439	0.2809:0.0:0.5946:0.1245	.	21;2757	B4DFC7;Q9UKN7	.;MYO15_HUMAN	M	2757	ENSP00000205890:V2757M	ENSP00000205890:V2757M	V	+	1	0	MYO15A	17999193	0.906000	0.30813	0.279000	0.24732	0.136000	0.21042	1.276000	0.33156	0.104000	0.17725	0.561000	0.74099	GTG	G|0.998;A|0.002	0.002	strong		0.642	MYO15A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132048.1	NM_016239	
WDFY2	115825	hgsc.bcm.edu	37	13	52313253	52313253	+	Missense_Mutation	SNP	G	G	A	rs77486739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:52313253G>A	ENST00000298125.5	+	7	847	c.667G>A	c.(667-669)Gtc>Atc	p.V223I		NM_052950.3	NP_443182.1	Q96P53	WDFY2_HUMAN	WD repeat and FYVE domain containing 2	223							metal ion binding (GO:0046872)			breast(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(4)|skin(2)|upper_aerodigestive_tract(1)	16		Breast(56;0.000208)|Lung NSC(96;0.000517)|Prostate(109;0.0041)|Hepatocellular(98;0.0652)|Myeloproliferative disorder(33;0.164)|all_neural(104;0.191)		GBM - Glioblastoma multiforme(99;9e-08)		AGATCACTCTGTCATCATGTG	0.512													G|||	18	0.00359425	0.0106	0.0058	5008	,	,		18017	0.0		0.0	False		,,,				2504	0.0				p.V223I		Atlas-SNP	.											.	WDFY2	36	.	0			c.G667A						PASS	.	G	ILE/VAL	63,4343	59.3+/-96.0	0,63,2140	160.0	140.0	147.0		667	5.3	1.0	13	dbSNP_131	147	4,8596	3.7+/-12.6	0,4,4296	yes	missense	WDFY2	NM_052950.3	29	0,67,6436	AA,AG,GG		0.0465,1.4299,0.5151	benign	223/401	52313253	67,12939	2203	4300	6503	SO:0001583	missense	115825	exon7			CACTCTGTCATCA	AF411978	CCDS9429.1	13q14.12	2013-01-09	2003-03-13		ENSG00000139668	ENSG00000139668		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20482	protein-coding gene	gene with protein product		610418	"""WD40 and FYVE domain containing 2"""				Standard	NM_052950		Approved	ZFYVE22	uc001vfp.3	Q96P53	OTTHUMG00000017407	ENST00000298125.5:c.667G>A	13.37:g.52313253G>A	ENSP00000298125:p.Val223Ile	142.0	0.0	0		149.0	75.0	0.503356	NM_052950	B1AL86|Q96CS1	Missense_Mutation	SNP	ENST00000298125.5	37	CCDS9429.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	G	9.675	1.147653	0.21288	0.014299	4.65E-4	ENSG00000139668	ENST00000298125	T	0.57107	0.42	6.17	5.32	0.75619	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.049499	0.85682	D	0.000000	T	0.25680	0.0625	L	0.35542	1.07	0.49798	D	0.999829	B;B	0.14805	0.011;0.001	B;B	0.14023	0.01;0.003	T	0.16482	-1.0401	10	0.02654	T	1	-25.4701	7.2469	0.26127	0.2059:0.0:0.7941:0.0	.	120;223	Q96LK4;Q96P53	.;WDFY2_HUMAN	I	223	ENSP00000298125:V223I	ENSP00000298125:V223I	V	+	1	0	WDFY2	51211254	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.740000	0.68629	2.941000	0.99782	0.655000	0.94253	GTC	G|0.996;A|0.004	0.004	strong		0.512	WDFY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045985.3	NM_052950	
CACNA2D1	781	hgsc.bcm.edu	37	7	81593541	81593541	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:81593541T>C	ENST00000356253.5	-	33	3000	c.2745A>G	c.(2743-2745)ggA>ggG	p.G915G	CACNA2D1_ENST00000535308.1_Silent_p.G115G|CACNA2D1_ENST00000356860.3_Silent_p.G903G			P54289	CA2D1_HUMAN	calcium channel, voltage-dependent, alpha 2/delta subunit 1	915					calcium ion transport (GO:0006816)|regulation of calcium ion transport (GO:0051924)	extracellular vesicular exosome (GO:0070062)|sarcoplasmic reticulum (GO:0016529)|T-tubule (GO:0030315)|voltage-gated calcium channel complex (GO:0005891)	metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(15)|liver(1)|lung(42)|ovary(6)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	81					Amlodipine(DB00381)|Cyclandelate(DB04838)|Felodipine(DB01023)|Gabapentin(DB00996)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)	CTGAGCGATGTCCTGCTCCTT	0.408																																					p.G903G		Atlas-SNP	.											.	CACNA2D1	191	.	0			c.A2709G						PASS	.						128.0	128.0	128.0					7																	81593541		2203	4300	6503	SO:0001819	synonymous_variant	781	exon33			GCGATGTCCTGCT	M76559	CCDS5598.1	7q21-q22	2014-09-17			ENSG00000153956	ENSG00000153956		"""Calcium channel subunits"""	1399	protein-coding gene	gene with protein product		114204	"""long intergenic non-protein coding RNA 1112"""	CACNL2A, CACNA2, MHS3, LINC01112		8188232	Standard	XM_005250570		Approved	lncRNA-N3	uc003uhr.1	P54289	OTTHUMG00000023622	ENST00000356253.5:c.2745A>G	7.37:g.81593541T>C		97.0	0.0	0		121.0	8.0	0.0661157	NM_000722	Q17R45|Q9UD80|Q9UD81|Q9UD82	Silent	SNP	ENST00000356253.5	37																																																																																				.	.	none		0.408	CACNA2D1-201	KNOWN	basic	protein_coding	protein_coding			
PGAM5	192111	hgsc.bcm.edu	37	12	133294371	133294371	+	Missense_Mutation	SNP	A	A	G	rs117147264	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:133294371A>G	ENST00000498926.2	+	4	630	c.572A>G	c.(571-573)aAg>aGg	p.K191R	PXMP2_ENST00000545677.1_3'UTR|PGAM5_ENST00000543955.1_Missense_Mutation_p.K42R|PGAM5_ENST00000454808.2_Missense_Mutation_p.K42R|PGAM5_ENST00000317555.2_Missense_Mutation_p.K191R	NM_001170543.1|NM_001170544.1	NP_001164014.1|NP_001164015.1	Q96HS1	PGAM5_HUMAN	phosphoglycerate mutase family member 5	191					dephosphorylation (GO:0016311)|necroptotic process (GO:0070266)|positive regulation of GTPase activity (GO:0043547)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	GTPase activator activity (GO:0005096)|phosphatase activity (GO:0016791)|phosphoprotein phosphatase activity (GO:0004721)|protein complex binding (GO:0032403)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)	5	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.89e-08)|Epithelial(86;1.14e-07)|all cancers(50;3.57e-06)		TCTCATTGGAAGCCGGAAGCT	0.652													A|||	163	0.0325479	0.003	0.1671	5008	,	,		12769	0.0		0.0358	False		,,,				2504	0.0072				p.K191R		Atlas-SNP	.											PGAM5,NS,carcinoma,0,1	PGAM5	18	1	0			c.A572G						PASS	.	A	ARG/LYS,ARG/LYS,ARG/LYS	38,4320		0,38,2141	22.0	28.0	26.0		572,572,572	5.5	1.0	12	dbSNP_132	26	321,8239		3,315,3962	yes	missense,missense,missense	PGAM5	NM_001170543.1,NM_001170544.1,NM_138575.3	26,26,26	3,353,6103	GG,GA,AA		3.75,0.872,2.7791	benign,benign,benign	191/290,191/289,191/256	133294371	359,12559	2179	4280	6459	SO:0001583	missense	192111	exon4			ATTGGAAGCCGGA	BC008196	CCDS9280.1, CCDS53845.1	12q24.33	2011-07-28			ENSG00000247077	ENSG00000247077			28763	protein-coding gene	gene with protein product		614939				11283018	Standard	NM_001170543		Approved	MGC5352, BXLBv68	uc009zyv.3	Q96HS1	OTTHUMG00000168021	ENST00000498926.2:c.572A>G	12.37:g.133294371A>G	ENSP00000438465:p.Lys191Arg	56.0	0.0	0		52.0	15.0	0.288462	NM_138575	A9LN06|C9IZY7|Q96JB0	Missense_Mutation	SNP	ENST00000498926.2	37	CCDS53845.1	74	0.03388278388278388	2	0.0040650406504065045	48	0.13259668508287292	0	0.0	24	0.0316622691292876	A	11.76	1.734893	0.30774	0.00872	0.0375	ENSG00000247077	ENST00000317555;ENST00000498926;ENST00000543955;ENST00000454808	T;T	0.71817	-0.6;-0.6	5.5	5.5	0.81552	Histidine phosphatase superfamily, clade-1 (2);	0.000000	0.85682	D	0.000000	T	0.00724	0.0024	N	0.10760	0.04	0.09310	P	0.99999969864	B;B	0.22683	0.035;0.073	B;B	0.19148	0.024;0.019	T	0.10245	-1.0638	9	0.34782	T	0.22	-20.1292	15.6131	0.76744	1.0:0.0:0.0:0.0	.	191;191	Q96HS1;Q96HS1-2	PGAM5_HUMAN;.	R	191;191;42;42	ENSP00000321503:K191R;ENSP00000438465:K191R	ENSP00000321503:K191R	K	+	2	0	PGAM5	131804444	1.000000	0.71417	1.000000	0.80357	0.183000	0.23260	8.497000	0.90488	2.084000	0.62774	0.533000	0.62120	AAG	A|0.971;G|0.029	0.029	strong		0.652	PGAM5-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397562.1	NM_138575	
NPHS1	4868	hgsc.bcm.edu	37	19	36339247	36339247	+	Missense_Mutation	SNP	C	C	T	rs33950747	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36339247C>T	ENST00000378910.5	-	10	1222	c.1223G>A	c.(1222-1224)cGg>cAg	p.R408Q	NPHS1_ENST00000353632.6_Missense_Mutation_p.R408Q	NM_004646.3	NP_004637.1	O60500	NPHN_HUMAN	nephrosis 1, congenital, Finnish type (nephrin)	408	Ig-like C2-type 4.		R -> Q (in NPHS1; uncertain pathological significance; does not affect protein expression on the cell surface; dbSNP:rs33950747). {ECO:0000269|PubMed:11317351, ECO:0000269|PubMed:20172850, ECO:0000269|PubMed:9915943}.		cell adhesion (GO:0007155)|excretion (GO:0007588)|glomerular basement membrane development (GO:0032836)|glomerular visceral epithelial cell development (GO:0072015)|JNK cascade (GO:0007254)|myoblast fusion (GO:0007520)|positive regulation of actin filament polymerization (GO:0030838)|regulation of excretion (GO:0044062)|skeletal muscle tissue development (GO:0007519)	cell projection (GO:0042995)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|slit diaphragm (GO:0036057)	myosin binding (GO:0017022)			NS(2)|breast(1)|cervix(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(16)|liver(1)|lung(26)|ovary(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	74	all_lung(56;7.14e-07)|Lung NSC(56;1.12e-06)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GTTGTCCTCCCGCCGCGCCAG	0.577													C|||	103	0.0205671	0.0023	0.0403	5008	,	,		17854	0.0		0.0557	False		,,,				2504	0.0164				p.R408Q		Atlas-SNP	.											.	NPHS1	165	.	0			c.G1223A	GRCh37	CM990958	NPHS1	M	rs33950747	PASS	.	C	GLN/ARG	56,4350	53.6+/-89.4	0,56,2147	99.0	87.0	91.0		1223	5.5	0.9	19	dbSNP_126	91	545,8055	151.0+/-205.8	27,491,3782	yes	missense	NPHS1	NM_004646.3	43	27,547,5929	TT,TC,CC		6.3372,1.271,4.6209	probably-damaging	408/1242	36339247	601,12405	2203	4300	6503	SO:0001583	missense	4868	exon10			TCCTCCCGCCGCG		CCDS32996.1	19q12-q13.1	2014-09-17				ENSG00000161270		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7908	protein-coding gene	gene with protein product		602716				9915943, 9660941	Standard	NM_004646		Approved	CNF, NPHN	uc002oby.3	O60500		ENST00000378910.5:c.1223G>A	19.37:g.36339247C>T	ENSP00000368190:p.Arg408Gln	81.0	0.0	0		98.0	38.0	0.387755	NM_004646	A6NDH2|C3RX61	Missense_Mutation	SNP	ENST00000378910.5	37	CCDS32996.1	64	0.029304029304029304	2	0.0040650406504065045	15	0.04143646408839779	0	0.0	47	0.06200527704485488	C	20.4	3.982368	0.74474	0.01271	0.063372	ENSG00000161270	ENST00000378910;ENST00000353632	T;T	0.78003	-1.14;-1.14	5.53	5.53	0.82687	CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.135150	0.49305	D	0.000144	T	0.51024	0.1650	M	0.72894	2.215	0.48901	D	0.999722	D	0.89917	1.0	D	0.85130	0.997	T	0.72297	-0.4335	10	0.35671	T	0.21	-25.372	16.9674	0.86290	0.0:1.0:0.0:0.0	rs33950747	408	O60500	NPHN_HUMAN	Q	408	ENSP00000368190:R408Q;ENSP00000343634:R408Q	ENSP00000343634:R408Q	R	-	2	0	NPHS1	41031087	0.795000	0.28851	0.933000	0.37362	0.485000	0.33311	5.506000	0.66993	2.596000	0.87737	0.591000	0.81541	CGG	C|0.958;T|0.042	0.042	strong		0.577	NPHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452553.1		
ARHGEF26	26084	hgsc.bcm.edu	37	3	153943770	153943770	+	Missense_Mutation	SNP	C	C	G	rs74965475	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:153943770C>G	ENST00000356448.4	+	11	2345	c.2061C>G	c.(2059-2061)aaC>aaG	p.N687K	ARHGEF26_ENST00000483068.1_3'UTR|ARHGEF26_ENST00000465817.1_Intron|ARHGEF26_ENST00000465093.1_Missense_Mutation_p.N687K	NM_001251962.1	NP_001238891.1	Q96DR7	ARHGQ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 26	687	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.			N -> K (in Ref. 6; AAH16628). {ECO:0000305}.	endothelial cell morphogenesis (GO:0001886)|ruffle assembly (GO:0097178)	cell projection (GO:0042995)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			endometrium(4)|kidney(1)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|urinary_tract(1)	23						TTCTCTTTAACGATGTGCTCA	0.398													C|||	37	0.00738818	0.003	0.0101	5008	,	,		18598	0.0		0.0189	False		,,,				2504	0.0072				p.N687K	GBM(163;191 2003 24758 29593 48540)|Ovarian(152;631 1885 20165 22910 51013)	Atlas-SNP	.											.	ARHGEF26	158	.	0			c.C2061G						PASS	.	C	LYS/ASN	15,3767		0,15,1876	104.0	91.0	95.0		2061	-6.0	0.7	3	dbSNP_131	95	158,8064		1,156,3954	yes	missense	ARHGEF26	NM_015595.3	94	1,171,5830	GG,GC,CC		1.9217,0.3966,1.4412	probably-damaging	687/872	153943770	173,11831	1891	4111	6002	SO:0001583	missense	26084	exon11			CTTTAACGATGTG	BC016628	CCDS46938.1, CCDS58858.1	3q25.2	2013-01-10			ENSG00000114790	ENSG00000114790		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	24490	protein-coding gene	gene with protein product	"""Src homology 3 domain-containing guanine nucleotide exchange factor"""					15133129, 12697679	Standard	NM_015595		Approved	DKFZP434D146, SGEF	uc021xgc.1	Q96DR7	OTTHUMG00000159098	ENST00000356448.4:c.2061C>G	3.37:g.153943770C>G	ENSP00000348828:p.Asn687Lys	187.0	0.0	0		221.0	105.0	0.475113	NM_001251962	B3KVP8|E9PBD0|Q68CL1|Q6AZ96|Q6Q8Q8|Q96AW8|Q96DR6|Q9H9D7|Q9H9R2|Q9UFW5	Missense_Mutation	SNP	ENST00000356448.4	37	CCDS46938.1	17	0.007783882783882784	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	C	17.13	3.310099	0.60414	0.003966	0.019217	ENSG00000114790	ENST00000356448;ENST00000465093	T;T	0.68331	-0.32;-0.32	5.65	-5.96	0.02234	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.66616	0.2807	M	0.84219	2.685	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.81914	0.991;0.995	T	0.80441	-0.1381	10	0.87932	D	0	-33.6174	16.1896	0.81977	0.0:0.3521:0.0:0.6479	.	687;687	E9PBD0;Q96DR7	.;ARHGQ_HUMAN	K	687	ENSP00000348828:N687K;ENSP00000423418:N687K	ENSP00000348828:N687K	N	+	3	2	ARHGEF26	155426460	0.000000	0.05858	0.726000	0.30738	0.884000	0.51177	-3.244000	0.00542	-0.995000	0.03459	-1.193000	0.01689	AAC	C|0.990;G|0.010	0.010	strong		0.398	ARHGEF26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353287.3	NM_015595	
ZMYND8	23613	hgsc.bcm.edu	37	20	45878118	45878118	+	Missense_Mutation	SNP	C	C	G	rs77137073	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:45878118C>G	ENST00000311275.7	-	13	1880	c.1627G>C	c.(1627-1629)Gtt>Ctt	p.V543L	ZMYND8_ENST00000471951.2_Missense_Mutation_p.V563L|ZMYND8_ENST00000355972.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000352431.2_Missense_Mutation_p.V563L|ZMYND8_ENST00000468376.2_5'UTR|ZMYND8_ENST00000446994.2_Missense_Mutation_p.V480L|ZMYND8_ENST00000372023.3_Missense_Mutation_p.V538L|ZMYND8_ENST00000458360.2_Missense_Mutation_p.V538L|ZMYND8_ENST00000540497.1_Missense_Mutation_p.V491L|ZMYND8_ENST00000360911.3_Missense_Mutation_p.V538L|ZMYND8_ENST00000262975.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000396281.4_Missense_Mutation_p.V543L|ZMYND8_ENST00000536340.1_Missense_Mutation_p.V570L|ZMYND8_ENST00000461685.1_Missense_Mutation_p.V563L	NM_001281772.1|NM_001281778.1|NM_001281783.1	NP_001268701.1|NP_001268707.1|NP_001268712.1	Q9ULU4	PKCB1_HUMAN	zinc finger, MYND-type containing 8	543					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	repressing transcription factor binding (GO:0070491)|RNA polymerase II transcription corepressor activity (GO:0001106)|zinc ion binding (GO:0008270)	p.V563L(1)		NS(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|prostate(3)|skin(2)|urinary_tract(8)	62			Epithelial(1;0.0289)|all cancers(1;0.0962)|OV - Ovarian serous cystadenocarcinoma(1;0.154)			ATGAGAGGAACAGGGGTGGAC	0.493													C|||	19	0.00379393	0.0	0.0043	5008	,	,		21570	0.0		0.0149	False		,,,				2504	0.001				p.V563L		Atlas-SNP	.											ZMYND8,NS,lymphoid_neoplasm,0,1	ZMYND8	166	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G1687C						PASS	.	C	LEU/VAL,LEU/VAL,LEU/VAL	15,4391	22.3+/-47.3	0,15,2188	148.0	129.0	136.0		1687,1687,1612	5.7	0.1	20	dbSNP_132	136	114,8486	61.0+/-122.8	3,108,4189	yes	missense,missense,missense	ZMYND8	NM_012408.3,NM_183047.1,NM_183048.1	32,32,32	3,123,6377	GG,GC,CC		1.3256,0.3404,0.9918	benign,benign,benign	563/1161,563/1189,538/1136	45878118	129,12877	2203	4300	6503	SO:0001583	missense	23613	exon13			GAGGAACAGGGGT	U48251	CCDS13404.1, CCDS13405.1, CCDS46613.1, CCDS63300.1, CCDS63301.1, CCDS63304.1, CCDS63306.1, CCDS74738.1	20q13.12	2013-01-28	2007-01-29	2007-01-29	ENSG00000101040	ENSG00000101040		"""Zinc fingers, MYND-type"", ""Zinc fingers, PHD-type"""	9397	protein-coding gene	gene with protein product		615713	"""protein kinase C binding protein 1"""	PRKCBP1			Standard	NM_001281769		Approved	RACK7	uc002xtb.1	Q9ULU4	OTTHUMG00000032667	ENST00000311275.7:c.1627G>C	20.37:g.45878118C>G	ENSP00000312237:p.Val543Leu	124.0	0.0	0		135.0	62.0	0.459259	NM_183047	B3KVL2|B7Z2A8|B7Z3E0|B7Z680|B7ZM62|E1P5U5|F5H0X3|H7C0U2|J3KPU3|Q13517|Q2HXV1|Q2HXV2|Q2HXV3|Q2HXV4|Q2HXV7|Q2HXV8|Q2HXV9|Q2HXW0|Q2HXW1|Q2HXW2|Q4JJ94|Q4JJ95|Q5TH09|Q5TH11|Q6MZM1|Q8WXC5|Q9H1F3|Q9H1F4|Q9H1F5|Q9H1L8|Q9H1L9|Q9H2G5|Q9NYN3|Q9UIX6	Missense_Mutation	SNP	ENST00000311275.7	37		14|14	0.00641025641025641|0.00641025641025641	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	C|C	8.782|8.782	0.928382|0.928382	0.18131|0.18131	0.003404|0.003404	0.013256|0.013256	ENSG00000101040|ENSG00000101040	ENST00000467200|ENST00000360911;ENST00000311275;ENST00000458360;ENST00000262975;ENST00000471951;ENST00000352431;ENST00000396281;ENST00000536340;ENST00000355972;ENST00000446994;ENST00000461685;ENST00000372023;ENST00000540497	.|D;D;D;D;D;D;D;D;D;D;D	.|0.90563	.|-1.84;-1.74;-1.87;-1.74;-1.85;-1.75;-1.74;-2.69;-1.73;-1.84;-1.8	5.7|5.7	5.7|5.7	0.88788|0.88788	.|.	.|0.203494	.|0.42294	.|D	.|0.000725	D|D	0.82953|0.82953	0.5149|0.5149	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999992|0.999992	.|P;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	.|0.46621	.|0.881;0.243;0.078;0.078;0.0;0.277;0.112;0.0;0.0;0.0;0.0;0.078;0.0;0.0;0.078;0.073;0.0;0.078	.|B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	.|0.40702	.|0.338;0.138;0.217;0.217;0.009;0.314;0.138;0.005;0.005;0.005;0.005;0.217;0.012;0.012;0.217;0.053;0.006;0.217	T|T	0.79969|0.79969	-0.1579|-0.1579	5|10	.|0.42905	.|T	.|0.14	-17.669|-17.669	13.0828|13.0828	0.59123|0.59123	0.0:0.927:0.0:0.073|0.0:0.927:0.0:0.073	.|.	.|538;570;538;538;518;537;563;543;538;563;563;543;480;538;491;563;491;543	.|B7ZM62;F5H0X3;Q2HXV7;Q2HXV3;Q5TH11;Q5JV90;Q9ULU4-7;Q9ULU4-9;Q9ULU4-14;Q9ULU4-12;Q9ULU4-13;Q9ULU4;B3KVL2;Q2HXV9;Q2HXV1;Q9ULU4-8;Q2HXV4;B7Z2A8	.|.;.;.;.;.;.;.;.;.;.;.;PKCB1_HUMAN;.;.;.;.;.;.	S|L	470|538;543;538;544;564;563;543;570;543;480;563;538;491	.|ENSP00000354166:V538L;ENSP00000312237:V543L;ENSP00000392964:V538L;ENSP00000335537:V563L;ENSP00000379577:V543L;ENSP00000439800:V570L;ENSP00000348246:V543L;ENSP00000396725:V480L;ENSP00000418210:V563L;ENSP00000361093:V538L;ENSP00000443086:V491L	.|ENSP00000262975:V544L	C|V	-|-	2|1	0|0	ZMYND8|ZMYND8	45311525|45311525	0.952000|0.952000	0.32445|0.32445	0.053000|0.053000	0.19242|0.19242	0.055000|0.055000	0.15305|0.15305	3.209000|3.209000	0.51122|0.51122	2.683000|2.683000	0.91414|0.91414	0.650000|0.650000	0.86243|0.86243	TGT|GTT	C|0.991;G|0.009	0.009	strong		0.493	ZMYND8-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000079596.2	NM_183047	
RHD	6007	hgsc.bcm.edu	37	1	25629896	25629896	+	Missense_Mutation	SNP	G	G	T	rs371803235		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:25629896G>T	ENST00000328664.4	+	6	1040	c.885G>T	c.(883-885)atG>atT	p.M295I	RHD_ENST00000423253.1_3'UTR|RHD_ENST00000568195.1_Missense_Mutation_p.M295I|RHD_ENST00000423810.2_Missense_Mutation_p.M295I|RHD_ENST00000454452.2_Missense_Mutation_p.M295I|RHD_ENST00000342055.5_Missense_Mutation_p.M295I|RHD_ENST00000417538.2_Missense_Mutation_p.M295I|RHD_ENST00000357542.4_Missense_Mutation_p.M295I	NM_001282867.1|NM_016124.3	NP_001269796.1|NP_057208	Q02161	RHD_HUMAN	Rh blood group, D antigen	295						integral component of plasma membrane (GO:0005887)	ammonium transmembrane transporter activity (GO:0008519)			breast(2)|large_intestine(4)|lung(7)|prostate(1)	14		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0101)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;7.39e-27)|Colorectal(126;8.83e-09)|COAD - Colon adenocarcinoma(152;6.43e-07)|STAD - Stomach adenocarcinoma(196;0.000332)|BRCA - Breast invasive adenocarcinoma(304;0.000438)|KIRC - Kidney renal clear cell carcinoma(1967;0.000716)|GBM - Glioblastoma multiforme(114;0.000908)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GGCTTGCCATGGTGCTGGGTC	0.572																																					p.M295I		Atlas-SNP	.											.	RHD	38	.	0			c.G885T	GRCh37	CM994723	RHD	M		PASS	.	G	ILE/MET,ILE/MET	0,4226		0,0,2113	85.0	59.0	68.0		885,885	3.2	1.0	1		68	1,7421		0,1,3710	no	missense,missense	RHD	NM_001127691.1,NM_016124.3	10,10	0,1,5823	TT,TG,GG		0.0135,0.0,0.0086	probably-damaging,probably-damaging	295/322,295/418	25629896	1,11647	2113	3711	5824	SO:0001583	missense	6007	exon6			TGCCATGGTGCTG	AB012623	CCDS262.1, CCDS53285.1, CCDS60027.1, CCDS60028.1, CCDS60029.1, CCDS60030.1, CCDS60031.1	1p36.11	2014-07-19	2013-10-02		ENSG00000187010	ENSG00000187010		"""CD molecules"", ""Blood group antigens"""	10009	protein-coding gene	gene with protein product		111680	"""Rhesus blood group, D antigen"", ""Rh blood group, D antigen"""	RH		8220426	Standard	NM_016124		Approved	Rh30a, Rh4, RhPI, RhII, DIIIc, CD240D	uc001bjz.3	Q02161	OTTHUMG00000003476	ENST00000328664.4:c.885G>T	1.37:g.25629896G>T	ENSP00000331871:p.Met295Ile	154.0	0.0	0		247.0	101.0	0.408907	NM_001127691	Q02162|Q07618|Q16147|Q16235|Q16355|Q5VSK0|Q5XLS9|Q5XLT1|Q5XLT2|Q9NPK0|Q9UQ20|Q9UQ21|Q9UQ22|Q9UQ23	Missense_Mutation	SNP	ENST00000328664.4	37	CCDS262.1	.	.	.	.	.	.	.	.	.	.	.	7.093	0.572463	0.13623	0.0	1.35E-4	ENSG00000187010	ENST00000328664;ENST00000419831;ENST00000454452;ENST00000342055;ENST00000357542;ENST00000417538;ENST00000423810	T;T;T;T;T;T	0.20738	2.05;2.05;2.05;2.05;2.05;2.05	3.19	3.19	0.36642	Ammonium transporter AmtB-like (3);	0.000000	0.85682	D	0.000000	T	0.38852	0.1056	M	0.61703	1.905	0.58432	D	0.999998	D;D;P;D;D;P;D;D	0.89917	1.0;1.0;0.86;1.0;1.0;0.947;1.0;1.0	D;D;P;D;D;D;D;D	0.97110	1.0;0.999;0.844;1.0;1.0;0.932;0.999;1.0	T	0.11131	-1.0600	10	0.42905	T	0.14	-40.782	9.7501	0.40470	0.0:0.0:1.0:0.0	.	295;295;295;295;295;295;295;295	B4DLT8;Q5XLT1;Q5XLS9;Q5XLT2;Q5XLT3;E7EVW1;Q5XLT0;Q02161	.;.;.;.;.;.;.;RHD_HUMAN	I	295	ENSP00000331871:M295I;ENSP00000413849:M295I;ENSP00000339577:M295I;ENSP00000350150:M295I;ENSP00000396420:M295I;ENSP00000399640:M295I	ENSP00000331871:M295I	M	+	3	0	RHD	25502483	1.000000	0.71417	0.994000	0.49952	0.027000	0.11550	5.868000	0.69605	1.623000	0.50342	0.393000	0.25936	ATG	.	.	none		0.572	RHD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000009660.5	NM_016124	
VIPR1	7433	hgsc.bcm.edu	37	3	42568935	42568935	+	Silent	SNP	C	C	T	rs201579976		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:42568935C>T	ENST00000325123.4	+	5	563	c.450C>T	c.(448-450)taC>taT	p.Y150Y	VIPR1_ENST00000433647.1_Silent_p.Y109Y|VIPR1_ENST00000543411.1_Silent_p.Y102Y|VIPR1-AS1_ENST00000593621.1_RNA|VIPR1-AS1_ENST00000602176.1_RNA|VIPR1_ENST00000473575.1_3'UTR|VIPR1-AS1_ENST00000593611.1_RNA|VIPR1_ENST00000438259.2_Intron|VIPR1-AS1_ENST00000601312.1_RNA|VIPR1-AS1_ENST00000600342.1_RNA|VIPR1-AS1_ENST00000596630.1_RNA|VIPR1-AS1_ENST00000598837.1_RNA|VIPR1-AS1_ENST00000452639.3_RNA	NM_001251885.1|NM_004624.3	NP_001238814.1|NP_004615.2	P32241	VIPR1_HUMAN	vasoactive intestinal peptide receptor 1	150					digestion (GO:0007586)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|immune response (GO:0006955)|muscle contraction (GO:0006936)|positive regulation of cell proliferation (GO:0008284)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	vasoactive intestinal polypeptide receptor activity (GO:0004999)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(6)|ovary(2)|skin(1)|urinary_tract(3)	18				KIRC - Kidney renal clear cell carcinoma(284;0.241)		CCATTGGCTACGGCCTGTCCC	0.602																																					p.Y150Y		Atlas-SNP	.											VIPR1,NS,carcinoma,0,1	VIPR1	45	1	0			c.C450T						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	118.0	105.0	110.0		450	4.1	1.0	3		110	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	VIPR1	NM_004624.3		0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231		150/458	42568935	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	7433	exon5			TGGCTACGGCCTG	AH005329	CCDS2698.1, CCDS58827.1, CCDS58828.1, CCDS58829.1	3p22	2012-08-10			ENSG00000114812	ENSG00000114812		"""GPCR / Class B : VIP and PACAP (ADCYAP1) receptors"""	12694	protein-coding gene	gene with protein product	"""VIP and PACAP receptor 1"""	192321				7708752	Standard	NM_004624		Approved	VPAC1, RDC1, HVR1, VPAC1R	uc003clf.2	P32241	OTTHUMG00000131792	ENST00000325123.4:c.450C>T	3.37:g.42568935C>T		74.0	0.0	0		53.0	35.0	0.660377	NM_004624	A5JUT9|B3KPV1|B4DEB5|B4DGI4|F5H1F5|G3V0I1|Q15871|Q6P2M6	Silent	SNP	ENST00000325123.4	37	CCDS2698.1																																																																																			C|0.999;T|0.001	0.001	strong		0.602	VIPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254728.4	NM_004624	
TANC1	85461	hgsc.bcm.edu	37	2	160074132	160074132	+	Silent	SNP	G	G	T	rs373000954	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:160074132G>T	ENST00000263635.6	+	20	3606	c.3369G>T	c.(3367-3369)ggG>ggT	p.G1123G	TANC1_ENST00000454300.1_Silent_p.G1017G	NM_001145909.1|NM_033394.2	NP_001139381.1|NP_203752.2	Q9C0D5	TANC1_HUMAN	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 1	1123					dendritic spine maintenance (GO:0097062)|myoblast fusion (GO:0007520)|visual learning (GO:0008542)	axon terminus (GO:0043679)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)				breast(3)|central_nervous_system(4)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(25)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	77						CACGCCAGGGGCATTGGCAGG	0.592													G|||	3	0.000599042	0.0	0.0	5008	,	,		20076	0.0		0.003	False		,,,				2504	0.0				p.G1123G		Atlas-SNP	.											TANC1,NS,NS,+2,1	TANC1	157	1	0			c.G3369T						PASS	.	G	,	0,3934		0,0,1967	61.0	68.0	66.0		3345,3369	-5.3	1.0	2		66	7,8347		0,7,4170	no	coding-synonymous,coding-synonymous	TANC1	NM_001145909.1,NM_033394.2	,	0,7,6137	TT,TG,GG		0.0838,0.0,0.057	,	1115/1391,1123/1862	160074132	7,12281	1967	4177	6144	SO:0001819	synonymous_variant	85461	exon20			CCAGGGGCATTGG	AB051515	CCDS42766.1	2q24.2	2013-01-11			ENSG00000115183	ENSG00000115183		"""Ankyrin repeat domain containing"", ""Tetratricopeptide (TTC) repeat domain containing"""	29364	protein-coding gene	gene with protein product	"""rolling pebbles homolog B (Drosophila)"""	611397				15673434	Standard	NM_033394		Approved	KIAA1728, ROLSB	uc002uag.3	Q9C0D5	OTTHUMG00000153945	ENST00000263635.6:c.3369G>T	2.37:g.160074132G>T		106.0	0.0	0		150.0	82.0	0.546667	NM_033394	C9JD88|Q49AI8	Silent	SNP	ENST00000263635.6	37	CCDS42766.1																																																																																			.	.	weak		0.592	TANC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333135.1		
BMP8A	353500	hgsc.bcm.edu	37	1	39988708	39988708	+	Silent	SNP	A	A	G	rs2889739	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:39988708A>G	ENST00000331593.5	+	6	1324	c.978A>G	c.(976-978)tcA>tcG	p.S326S	RP11-69E11.4_ENST00000458207.1_RNA|RP11-69E11.4_ENST00000440190.1_RNA|RP11-69E11.4_ENST00000441741.1_RNA|RP11-69E11.4_ENST00000331856.2_RNA|RP11-69E11.4_ENST00000431553.1_RNA|RP11-69E11.4_ENST00000417869.1_RNA|RP11-69E11.4_ENST00000450157.1_RNA	NM_181809.3	NP_861525.2	Q7Z5Y6	BMP8A_HUMAN	bone morphogenetic protein 8a	326					cartilage development (GO:0051216)|cell differentiation (GO:0030154)|diet induced thermogenesis (GO:0002024)|growth (GO:0040007)|negative regulation of insulin secretion (GO:0046676)|ossification (GO:0001503)|regulation of energy homeostasis (GO:2000505)	extracellular space (GO:0005615)				kidney(1)|large_intestine(2)|lung(1)|skin(1)	5	Lung NSC(20;2.08e-06)|Ovarian(52;0.00769)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;9.69e-19)|Epithelial(16;9.34e-17)|all cancers(16;1.73e-15)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			AAGGCTACTCAGCCTATTACT	0.627													A|||	130	0.0259585	0.0045	0.0303	5008	,	,		17612	0.0		0.0905	False		,,,				2504	0.0123				p.S326S		Atlas-SNP	.											.	BMP8A	24	.	0			c.A978G						PASS	.	A		70,4336	64.1+/-101.4	1,68,2134	184.0	161.0	169.0		978	-8.4	0.3	1	dbSNP_101	169	664,7936	167.8+/-219.5	21,622,3657	no	coding-synonymous	BMP8A	NM_181809.3		22,690,5791	GG,GA,AA		7.7209,1.5887,5.6435		326/403	39988708	734,12272	2203	4300	6503	SO:0001819	synonymous_variant	353500	exon6			CTACTCAGCCTAT	AY303954	CCDS437.1	1p35-p32	2014-01-30			ENSG00000183682	ENSG00000183682		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	21650	protein-coding gene	gene with protein product							Standard	NM_181809		Approved		uc001cdi.3	Q7Z5Y6	OTTHUMG00000008394	ENST00000331593.5:c.978A>G	1.37:g.39988708A>G		153.0	0.0	0		150.0	59.0	0.393333	NM_181809	Q5T3A5	Silent	SNP	ENST00000331593.5	37	CCDS437.1																																																																																			A|0.945;G|0.055	0.055	strong		0.627	BMP8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023079.1	NM_181809	
LILRA6	79168	hgsc.bcm.edu	37	19	54744919	54744919	+	Missense_Mutation	SNP	T	T	A	rs61734504	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54744919T>A	ENST00000396365.2	-	5	782	c.743A>T	c.(742-744)gAt>gTt	p.D248V	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_3'UTR|LILRA6_ENST00000419410.2_Missense_Mutation_p.D248V|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.D248V|LILRA6_ENST00000245621.5_Missense_Mutation_p.D248V	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	248	Ig-like C2-type 1.				immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		GTAGCCGACATCAGAGCCACA	0.637																																					p.D248V		Atlas-SNP	.											LILRA6,NS,carcinoma,-1,1	LILRA6	75	1	0			c.A743T						PASS	.	T	VAL/ASP	22,4384	23.3+/-48.9	0,22,2181	98.0	107.0	104.0		743	1.3	0.0	19	dbSNP_129	104	253,8347	85.0+/-147.5	0,253,4047	no	missense	LILRA6	NM_024318.2	152	0,275,6228	AA,AT,TT		2.9419,0.4993,2.1144		248/482	54744919	275,12731	2203	4300	6503	SO:0001583	missense	79168	exon5			CCGACATCAGAGC	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.743A>T	19.37:g.54744919T>A	ENSP00000379651:p.Asp248Val	655.0	1.0	0.00152672		666.0	171.0	0.256757	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	31	0.014194139194139194	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	28	0.036939313984168866	T	12.50	1.957220	0.34565	0.004993	0.029419	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	2.39	1.27	0.21489	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.862360	0.09874	N	0.744562	T	0.11367	0.0277	M	0.87547	2.89	0.09310	N	1	D;D;D;D	0.89917	0.999;0.999;0.994;1.0	D;D;D;D	0.87578	0.992;0.989;0.925;0.998	T	0.02821	-1.1106	10	0.87932	D	0	.	5.2029	0.15275	0.0:0.0:0.3054:0.6946	rs61734504	248;248;248;248	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	V	248	ENSP00000390120:D248V;ENSP00000411227:D248V;ENSP00000379651:D248V;ENSP00000245621:D248V	ENSP00000245621:D248V	D	-	2	0	LILRA6	59436731	0.003000	0.15002	0.006000	0.13384	0.043000	0.13939	0.447000	0.21710	0.312000	0.23038	0.155000	0.16302	GAT	T|0.968;A|0.032	0.032	strong		0.637	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
WBP4	11193	hgsc.bcm.edu	37	13	41646958	41646958	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:41646958A>G	ENST00000379487.3	+	7	927	c.527A>G	c.(526-528)gAt>gGt	p.D176G	WBP4_ENST00000542082.1_Missense_Mutation_p.D155G	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	176	WW 2. {ECO:0000255|PROSITE- ProRule:PRU00224}.				mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		TTAAGTGAAGATGGTTTTACC	0.343																																					p.D176G		Atlas-SNP	.											.	WBP4	40	.	0			c.A527G						PASS	.						136.0	137.0	137.0					13																	41646958		2203	4300	6503	SO:0001583	missense	11193	exon7			GTGAAGATGGTTT	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.527A>G	13.37:g.41646958A>G	ENSP00000368801:p.Asp176Gly	117.0	0.0	0		105.0	47.0	0.447619	NM_007187	B7Z4M2|Q32P29	Missense_Mutation	SNP	ENST00000379487.3	37	CCDS9375.1	.	.	.	.	.	.	.	.	.	.	A	26.1	4.704428	0.88924	.	.	ENSG00000120688	ENST00000379487;ENST00000542082	D;D	0.84223	-1.82;-1.82	5.6	5.6	0.85130	WW/Rsp5/WWP (6);	0.156971	0.56097	D	0.000034	D	0.90741	0.7094	M	0.72624	2.21	0.58432	D	0.999994	P;D	0.64830	0.865;0.994	P;D	0.64595	0.57;0.927	D	0.89758	0.3945	10	0.33940	T	0.23	-16.308	15.7909	0.78364	1.0:0.0:0.0:0.0	.	155;176	B7Z4M2;O75554	.;WBP4_HUMAN	G	176;155	ENSP00000368801:D176G;ENSP00000439301:D155G	ENSP00000368801:D176G	D	+	2	0	WBP4	40544958	1.000000	0.71417	1.000000	0.80357	0.931000	0.56810	7.627000	0.83176	2.121000	0.65114	0.460000	0.39030	GAT	.	.	none		0.343	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
TRIM41	90933	hgsc.bcm.edu	37	5	180661468	180661468	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:180661468G>A	ENST00000315073.5	+	6	2296	c.1586G>A	c.(1585-1587)cGc>cAc	p.R529H	TRIM41_ENST00000351937.5_Intron|TRIM41_ENST00000510072.1_3'UTR	NM_033549.4	NP_291027.3	Q8WV44	TRI41_HUMAN	tripartite motif containing 41	529	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(3)|prostate(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	26	all_cancers(89;9.17e-06)|all_epithelial(37;1.19e-06)|Renal(175;0.000159)|Lung NSC(126;0.00354)|all_lung(126;0.00609)|Breast(19;0.0684)	all_cancers(40;0.000209)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_lung(500;0.0221)|all_hematologic(541;0.0433)|Lung NSC(249;0.132)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGCTCCTCGCGCCATCACCAT	0.692																																					p.R529H		Atlas-SNP	.											.	TRIM41	96	.	0			c.G1586A						PASS	.						21.0	23.0	22.0					5																	180661468		2200	4296	6496	SO:0001583	missense	90933	exon6			CCTCGCGCCATCA	AF258579	CCDS4465.1, CCDS4466.1	5q35.3	2013-01-09	2011-01-25		ENSG00000146063	ENSG00000146063		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19013	protein-coding gene	gene with protein product	"""RING-finger protein that interacts with C kinase"""	610530	"""tripartite motif-containing 41"""			16022281	Standard	NM_033549		Approved	MGC1127, RINCK	uc003mne.2	Q8WV44	OTTHUMG00000130965	ENST00000315073.5:c.1586G>A	5.37:g.180661468G>A	ENSP00000320869:p.Arg529His	122.0	0.0	0		80.0	34.0	0.425	NM_033549	B3KNJ6|D3DWR9|Q5BKT0|Q7L484|Q96Q10|Q9BSL8	Missense_Mutation	SNP	ENST00000315073.5	37	CCDS4466.1	.	.	.	.	.	.	.	.	.	.	G	12.61	1.989186	0.35131	.	.	ENSG00000146063	ENST00000315073;ENST00000438174	T	0.55413	0.52	5.32	4.45	0.53987	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	0.000000	0.52532	D	0.000063	T	0.33731	0.0873	N	0.14661	0.345	0.27302	N	0.957547	B	0.15141	0.012	B	0.10450	0.005	T	0.19128	-1.0315	10	0.37606	T	0.19	.	9.9313	0.41523	0.0946:0.0:0.9054:0.0	.	529	Q8WV44	TRI41_HUMAN	H	529;214	ENSP00000320869:R529H	ENSP00000320869:R529H	R	+	2	0	TRIM41	180594074	0.998000	0.40836	0.955000	0.39395	0.211000	0.24417	4.196000	0.58407	1.255000	0.44051	0.449000	0.29647	CGC	.	.	none		0.692	TRIM41-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253574.3	NM_201627	
AGTR2	186	hgsc.bcm.edu	37	X	115303837	115303837	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:115303837A>C	ENST00000371906.4	+	3	494	c.304A>C	c.(304-306)Acc>Ccc	p.T102P		NM_000686.4	NP_000677.2	P50052	AGTR2_HUMAN	angiotensin II receptor, type 2	102					aldosterone secretion (GO:0035932)|angiotensin-activated signaling pathway (GO:0038166)|blood vessel remodeling (GO:0001974)|brain development (GO:0007420)|brain renin-angiotensin system (GO:0002035)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell surface receptor signaling pathway (GO:0007166)|cellular response to dexamethasone stimulus (GO:0071549)|cellular sodium ion homeostasis (GO:0006883)|cerebellar cortex development (GO:0021695)|dopamine biosynthetic process (GO:0042416)|exploration behavior (GO:0035640)|extracellular negative regulation of signal transduction (GO:1900116)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|inflammatory response (GO:0006954)|intracellular signal transduction (GO:0035556)|negative regulation of blood vessel endothelial cell migration (GO:0043537)|negative regulation of cell growth (GO:0030308)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of heart rate (GO:0010459)|negative regulation of icosanoid secretion (GO:0032304)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of norepinephrine secretion (GO:0010700)|nitric oxide mediated signal transduction (GO:0007263)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokine secretion (GO:0050715)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of vasodilation (GO:0045909)|regulation of blood pressure (GO:0008217)|regulation of metanephros size (GO:0035566)|regulation of systemic arterial blood pressure by circulatory renin-angiotensin (GO:0001991)|regulation of transcription factor import into nucleus (GO:0042990)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to organonitrogen compound (GO:0010243)|vasodilation by angiotensin involved in regulation of systemic arterial blood pressure (GO:0002033)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	angiotensin type II receptor activity (GO:0004945)|peptide hormone binding (GO:0017046)|receptor antagonist activity (GO:0048019)			breast(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|skin(1)	24					Tasosartan(DB01349)	TCTATGGGCAACCTATTATTC	0.378																																					p.T102P		Atlas-SNP	.											.	AGTR2	62	.	0			c.A304C						PASS	.						177.0	172.0	174.0					X																	115303837		2203	4300	6503	SO:0001583	missense	186	exon3			TGGGCAACCTATT	AY324607	CCDS14569.1	Xq22-q23	2012-08-08			ENSG00000180772	ENSG00000180772		"""GPCR / Class A : Angiotensin receptors"""	338	protein-coding gene	gene with protein product		300034	"""angiotensin receptor 2"""			1550596	Standard	NM_000686		Approved	AT2, MRX88	uc004eqh.4	P50052	OTTHUMG00000022243	ENST00000371906.4:c.304A>C	X.37:g.115303837A>C	ENSP00000360973:p.Thr102Pro	343.0	0.0	0		181.0	52.0	0.287293	NM_000686	B2R9V1|Q13016|Q6FGY7	Missense_Mutation	SNP	ENST00000371906.4	37	CCDS14569.1	.	.	.	.	.	.	.	.	.	.	A	13.43	2.235143	0.39498	.	.	ENSG00000180772	ENST00000371906	T	0.37584	1.19	4.48	2.01	0.26516	GPCR, rhodopsin-like superfamily (1);	0.327695	0.32459	N	0.006071	T	0.47838	0.1467	M	0.82630	2.6	0.29718	N	0.8389	B	0.33777	0.425	P	0.48227	0.571	T	0.48525	-0.9028	10	0.37606	T	0.19	-0.9265	4.2699	0.10782	0.7194:0.0:0.1019:0.1787	.	102	P50052	AGTR2_HUMAN	P	102	ENSP00000360973:T102P	ENSP00000360973:T102P	T	+	1	0	AGTR2	115217865	0.000000	0.05858	0.995000	0.50966	0.995000	0.86356	0.792000	0.26929	0.122000	0.18314	0.412000	0.27726	ACC	.	.	none		0.378	AGTR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057984.1	NM_000686	
ARHGAP8	23779	hgsc.bcm.edu	37	22	45255688	45255688	+	Missense_Mutation	SNP	C	C	T	rs73176189	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45255688C>T	ENST00000389774.2	+	12	1189	c.1048C>T	c.(1048-1050)Cgc>Tgc	p.R350C	ARHGAP8_ENST00000389773.5_Missense_Mutation_p.R441C|PRR5-ARHGAP8_ENST00000361473.5_Missense_Mutation_p.R450C|ARHGAP8_ENST00000336963.4_Intron|PRR5-ARHGAP8_ENST00000352766.7_Missense_Mutation_p.R529C|ARHGAP8_ENST00000517296.3_Missense_Mutation_p.R529C|ARHGAP8_ENST00000356099.6_Missense_Mutation_p.R319C	NM_001017526.1	NP_001017526.1	P85298	RHG08_HUMAN	Rho GTPase activating protein 8	350	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	Rho GTPase activator activity (GO:0005100)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(7)|lung(9)|prostate(1)|skin(7)	29		all_neural(38;0.00409)|Ovarian(80;0.00976)|Glioma(61;0.0649)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0204)		CGTCGTCCTCCGCTACCTCAT	0.652													c|||	16	0.00319489	0.0008	0.0014	5008	,	,		19710	0.001		0.0099	False		,,,				2504	0.0031				p.R441C		Atlas-SNP	.											PRR5-ARHGAP8,caecum,carcinoma,0,2	PRR5-ARHGAP8	53	2	0			c.C1321T						PASS	.	T	CYS/ARG,,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	80.0	67.0	71.0		1048,,1321,955	-5.2	0.5	22	dbSNP_130	71	18,8582	11.9+/-42.8	0,18,4282	yes	missense,intron,missense,missense	ARHGAP8,PRR5-ARHGAP8	NM_001017526.1,NM_001198726.1,NM_181334.4,NM_181335.2	180,,180,180	0,23,6480	TT,TC,CC		0.2093,0.1135,0.1768	benign,,benign,benign	350/465,,441/556,319/434	45255688	23,12983	2203	4300	6503	SO:0001583	missense	553158	exon14			GTCCTCCGCTACC	AF177331	CCDS14060.2, CCDS33664.1, CCDS56233.1	22q13.3	2010-05-11			ENSG00000241484	ENSG00000241484		"""Rho GTPase activating proteins"""	677	protein-coding gene	gene with protein product		609405				10591208	Standard	NM_001198726		Approved	FLJ20185, BPGAP1		P85298	OTTHUMG00000030234	ENST00000389774.2:c.1048C>T	22.37:g.45255688C>T	ENSP00000374424:p.Arg350Cys	85.0	0.0	0		78.0	43.0	0.551282	NM_181334	A6ZJ79|A6ZJ80|O75983|O95695|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000389774.2	37	CCDS33664.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	c	5.988	0.366197	0.11352	0.001135	0.002093	ENSG00000248405;ENSG00000248405;ENSG00000241484;ENSG00000241484;ENSG00000241484;ENSG00000241484	ENST00000361473;ENST00000352766;ENST00000517296;ENST00000389773;ENST00000389774;ENST00000356099	T;T;T;T;T;T	0.21361	2.01;2.01;2.01;2.01;2.01;2.01	4.14	-5.19	0.02832	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	1.659120	0.04129	N	0.317650	T	0.13200	0.0320	L	0.28014	0.82	0.29807	N	0.831972	B;D;B;D;P	0.76494	0.03;0.999;0.033;0.989;0.56	B;P;B;B;B	0.50617	0.008;0.646;0.013;0.337;0.032	T	0.27088	-1.0084	10	0.52906	T	0.07	.	5.1071	0.14790	0.4424:0.3917:0.0766:0.0893	.	372;355;350;529;450	B7ZMA4;A2RU51;P85298;B1AHC4;B1AHC3	.;.;RHG08_HUMAN;.;.	C	450;529;529;441;350;319	ENSP00000354732:R450C;ENSP00000262731:R529C;ENSP00000429240:R529C;ENSP00000374423:R441C;ENSP00000374424:R350C;ENSP00000348407:R319C	ENSP00000348407:R319C	R	+	1	0	PRR5-ARHGAP8;ARHGAP8	43634352	0.427000	0.25514	0.455000	0.27031	0.005000	0.04900	0.560000	0.23500	-1.150000	0.02840	-1.499000	0.00960	CGC	C|0.998;T|0.002	0.002	strong		0.652	ARHGAP8-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000075088.4	NM_017701	
AK2	204	hgsc.bcm.edu	37	1	33502357	33502357	+	Missense_Mutation	SNP	C	C	T	rs199641857		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:33502357C>T	ENST00000487289.1	-	1	88	c.73G>A	c.(73-75)Ggg>Agg	p.G25R	AK2_ENST00000480134.1_Missense_Mutation_p.G25R|AK2_ENST00000548033.1_Missense_Mutation_p.G25R|AK2_ENST00000467905.1_Missense_Mutation_p.G25R|AK2_ENST00000373449.2_Missense_Mutation_p.G25R|AK2_ENST00000354858.6_Missense_Mutation_p.G25R					adenylate kinase 2											kidney(1)|large_intestine(2)|lung(4)|skin(1)	8		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)				TTACCGGCCCCGGGAGGCCCC	0.672																																					p.G25R		Atlas-SNP	.											.	AK2	27	.	0			c.G73A						PASS	.						10.0	11.0	11.0					1																	33502357		2201	4289	6490	SO:0001583	missense	204	exon1			CGGCCCCGGGAGG	U84371	CCDS373.1, CCDS374.1	1p35.1	2014-09-17			ENSG00000004455	ENSG00000004455	2.7.4.3	"""Adenylate kinases"""	362	protein-coding gene	gene with protein product		103020				8843353, 6961883	Standard	NM_013411		Approved		uc001bwp.2	P54819	OTTHUMG00000004131	ENST00000487289.1:c.73G>A	1.37:g.33502357C>T	ENSP00000446849:p.Gly25Arg	339.0	0.0	0		229.0	14.0	0.0611354	NM_001199199		Missense_Mutation	SNP	ENST00000487289.1	37		.	.	.	.	.	.	.	.	.	.	C	27.9	4.874354	0.91664	.	.	ENSG00000004455	ENST00000373449;ENST00000548033;ENST00000467905;ENST00000480134;ENST00000354858;ENST00000398192;ENST00000487289	D;D;D;D;D;D	0.91686	-2.89;-2.89;-2.89;-2.89;-2.89;-2.89	4.92	4.92	0.64577	.	0.000000	0.85682	D	0.000000	D	0.97470	0.9172	H	0.99958	5.055	0.80722	D	1	P;P;D;P	0.54207	0.895;0.826;0.965;0.895	P;B;P;P	0.52710	0.459;0.142;0.707;0.459	D	0.98100	1.0414	10	0.72032	D	0.01	-23.3449	13.8506	0.63494	0.0:1.0:0.0:0.0	.	25;25;25;25	P54819-5;F8VY04;P54819;P54819-2	.;.;KAD2_HUMAN;.	R	25	ENSP00000362548:G25R;ENSP00000449003:G25R;ENSP00000447082:G25R;ENSP00000450109:G25R;ENSP00000346921:G25R;ENSP00000446849:G25R	ENSP00000346921:G25R	G	-	1	0	AK2	33274944	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.868000	0.56055	2.724000	0.93272	0.563000	0.77884	GGG	.	.	weak		0.672	AK2-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000011889.4	NM_001625	
DENND1A	57706	hgsc.bcm.edu	37	9	126144390	126144390	+	Missense_Mutation	SNP	G	G	T	rs189947178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:126144390G>T	ENST00000373624.2	-	22	2552	c.2351C>A	c.(2350-2352)gCc>gAc	p.A784D	DENND1A_ENST00000542603.1_Missense_Mutation_p.A569D|DENND1A_ENST00000394219.3_Missense_Mutation_p.A795D|DENND1A_ENST00000473039.1_5'UTR	NM_020946.1	NP_065997.1	Q8TEH3	DEN1A_HUMAN	DENN/MADD domain containing 1A	784	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|protein transport (GO:0015031)|regulation of Rab protein signal transduction (GO:0032483)|synaptic vesicle endocytosis (GO:0048488)	cell junction (GO:0030054)|clathrin-coated vesicle (GO:0030136)|clathrin-coated vesicle membrane (GO:0030665)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|synapse (GO:0045202)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|liver(2)|lung(18)|ovary(2)|prostate(1)|skin(1)|stomach(1)	43						GTCCAGGAGGGCGAGCAGGGC	0.697													G|||	16	0.00319489	0.0	0.0101	5008	,	,		10971	0.0		0.0089	False		,,,				2504	0.0				p.A784D		Atlas-SNP	.											.	DENND1A	112	.	0			c.C2351A						PASS	.	G	ASP/ALA	8,4368		0,8,2180	10.0	14.0	13.0		2351	3.5	1.0	9		13	81,8467		1,79,4194	no	missense	DENND1A	NM_020946.1	126	1,87,6374	TT,TG,GG		0.9476,0.1828,0.6886	possibly-damaging	784/1010	126144390	89,12835	2188	4274	6462	SO:0001583	missense	57706	exon22			AGGAGGGCGAGCA	AB046828	CCDS35133.1, CCDS35134.1	9q34.11	2012-10-03	2005-08-17	2005-08-17	ENSG00000119522	ENSG00000119522		"""DENN/MADD domain containing"""	29324	protein-coding gene	gene with protein product		613633	"""KIAA1608"""	KIAA1608		10997877	Standard	XM_005252109		Approved	FLJ21129, FAM31A	uc004bnz.1	Q8TEH3	OTTHUMG00000020643	ENST00000373624.2:c.2351C>A	9.37:g.126144390G>T	ENSP00000362727:p.Ala784Asp	54.0	0.0	0		46.0	30.0	0.652174	NM_020946	A8MZA3|B1AM80|B7Z3C8|B7Z669|D3PFD3|Q05C88|Q5VWF0|Q6PJZ5|Q8IVD6|Q9H796	Missense_Mutation	SNP	ENST00000373624.2	37	CCDS35133.1	15	0.006868131868131868	5	0.01016260162601626	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	11.10	1.538370	0.27475	0.001828	0.009476	ENSG00000119522	ENST00000373624;ENST00000542603;ENST00000394219	T;T;T	0.23754	3.34;1.89;3.21	4.47	3.5	0.40072	.	0.251626	0.36101	N	0.002785	T	0.20210	0.0486	L	0.27053	0.805	0.80722	D	1	D;D;P;P	0.58970	0.984;0.984;0.926;0.483	P;P;P;B	0.55161	0.77;0.77;0.454;0.084	T	0.01405	-1.1363	10	0.56958	D	0.05	-15.6303	9.6391	0.39828	0.0:0.3391:0.5308:0.1301	.	795;785;784;647	Q8TEH3-6;Q8TEH3-7;Q8TEH3;Q9HCG4	.;.;DEN1A_HUMAN;.	D	784;569;795	ENSP00000362727:A784D;ENSP00000437457:A569D;ENSP00000377766:A795D	ENSP00000362727:A784D	A	-	2	0	DENND1A	125184211	1.000000	0.71417	0.982000	0.44146	0.008000	0.06430	2.369000	0.44231	2.029000	0.59856	0.557000	0.71058	GCC	G|0.993;T|0.007	0.007	strong		0.697	DENND1A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000053997.1	NM_024820	
PLS3	5358	hgsc.bcm.edu	37	X	114863593	114863593	+	Silent	SNP	T	T	A	rs140121121	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:114863593T>A	ENST00000420625.2	+	4	455	c.321T>A	c.(319-321)ggT>ggA	p.G107G	PLS3_ENST00000537301.1_Silent_p.G85G|PLS3_ENST00000355899.3_Silent_p.G107G|PLS3_ENST00000539310.1_Silent_p.G62G|PLS3_ENST00000289290.3_Silent_p.G62G	NM_001136025.3|NM_001172335.1|NM_001282338.1	NP_001129497.1|NP_001165806.1|NP_001269267.1	P13797	PLST_HUMAN	plastin 3	107					bone development (GO:0060348)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			NS(2)|breast(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(11)	26						GTGCTCTGGGTGGAACTTCAG	0.378													T|||	23	0.00609272	0.0	0.0029	3775	,	,		12691	0.0		0.0169	False		,,,				2504	0.0041				p.G107G	Colon(160;1047 1864 8490 12969 29601)	Atlas-SNP	.											.	PLS3	60	.	0			c.T321A						PASS	.	T	,,	10,3825		0,9,1,1623,570	130.0	115.0	120.0		321,240,321	-0.8	1.0	X	dbSNP_134	120	99,6629		2,75,20,2351,1852	no	coding-synonymous,coding-synonymous,coding-synonymous	PLS3	NM_001136025.3,NM_001172335.1,NM_005032.5	,,	2,84,21,3974,2422	AA,AT,A,TT,T		1.4715,0.2608,1.0319	,,	107/631,80/604,107/631	114863593	109,10454	2203	4300	6503	SO:0001819	synonymous_variant	5358	exon4			TCTGGGTGGAACT	L05491	CCDS14568.1, CCDS65312.1	Xq23	2013-01-10	2010-02-10		ENSG00000102024	ENSG00000102024		"""EF-hand domain containing"""	9091	protein-coding gene	gene with protein product		300131	"""plastin 3 (T isoform)"""			8428952	Standard	NM_005032		Approved	T-plastin	uc004eqe.3	P13797	OTTHUMG00000022237	ENST00000420625.2:c.321T>A	X.37:g.114863593T>A		265.0	1.0	0.00377358		128.0	128.0	1	NM_005032	A8K579|B1AQ09|B4DGB4|B7Z6M1|Q86YI6	Silent	SNP	ENST00000420625.2	37	CCDS14568.1																																																																																			T|0.990;A|0.010	0.010	strong		0.378	PLS3-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057976.2		
ZBTB21	49854	hgsc.bcm.edu	37	21	43413158	43413158	+	Silent	SNP	C	C	T	rs147318145	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:43413158C>T	ENST00000310826.5	-	3	1230	c.1047G>A	c.(1045-1047)caG>caA	p.Q349Q	ZBTB21_ENST00000398499.1_Silent_p.Q349Q|ZBTB21_ENST00000398511.3_Silent_p.Q349Q|ZBTB21_ENST00000398505.3_Silent_p.Q349Q|ZBTB21_ENST00000465968.1_Intron	NM_001098402.1	NP_001091872.1	Q9ULJ3	ZBT21_HUMAN	zinc finger and BTB domain containing 21	349					negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyl-CpG binding (GO:0008327)										AGACAGGAACCTGGCTATCCA	0.478													C|||	38	0.00758786	0.0008	0.0144	5008	,	,		19466	0.0		0.0229	False		,,,				2504	0.0041				p.Q349Q		Atlas-SNP	.											.	.	.	.	0			c.G1047A						PASS	.	C	,,	27,4379	33.5+/-64.1	0,27,2176	99.0	98.0	99.0		1047,1047,1047	5.1	1.0	21	dbSNP_134	99	232,8368	94.2+/-156.2	3,226,4071	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF295	NM_001098402.1,NM_001098403.1,NM_020727.4	,,	3,253,6247	TT,TC,CC		2.6977,0.6128,1.9914	,,	349/1067,349/866,349/1067	43413158	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	49854	exon3			AGGAACCTGGCTA	AB033053	CCDS13678.1, CCDS42934.1	21q22.3	2013-01-09	2013-01-09	2013-01-09	ENSG00000173276	ENSG00000173276		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13083	protein-coding gene	gene with protein product			"""zinc finger protein 295"""	ZNF295			Standard	NM_020727		Approved	KIAA1227	uc002yzy.4	Q9ULJ3	OTTHUMG00000086789	ENST00000310826.5:c.1047G>A	21.37:g.43413158C>T		119.0	0.0	0		107.0	53.0	0.495327	NM_001098402	Q5R2W1|Q5R2W2|Q6P4R0	Silent	SNP	ENST00000310826.5	37	CCDS13678.1																																																																																			C|0.983;T|0.017	0.017	strong		0.478	ZBTB21-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195308.1	NM_020727	
KRT1	3848	hgsc.bcm.edu	37	12	53070174	53070174	+	Missense_Mutation	SNP	C	C	A	rs17678945	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:53070174C>A	ENST00000252244.3	-	7	1418	c.1360G>T	c.(1360-1362)Gcc>Tcc	p.A454S		NM_006121.3	NP_006112.3	P04264	K2C1_HUMAN	keratin 1	454	Coil 2.|Rod.		A -> S (in dbSNP:rs17678945).		complement activation, lectin pathway (GO:0001867)|establishment of skin barrier (GO:0061436)|fibrinolysis (GO:0042730)|negative regulation of inflammatory response (GO:0050728)|regulation of angiogenesis (GO:0045765)|response to oxidative stress (GO:0006979)|retina homeostasis (GO:0001895)	blood microparticle (GO:0072562)|cytoskeleton (GO:0005856)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(7)|skin(3)	39						TCTTCCTTGGCCTGCTGCAGG	0.587													c|||	27	0.00539137	0.0	0.0101	5008	,	,		19137	0.0		0.0169	False		,,,				2504	0.0031				p.A454S		Atlas-SNP	.											.	KRT1	110	.	0			c.G1360T						PASS	.	C	SER/ALA	26,4380	31.7+/-61.6	0,26,2177	80.0	71.0	74.0		1360	3.2	1.0	12	dbSNP_123	74	231,8369	94.5+/-156.4	3,225,4072	no	missense	KRT1	NM_006121.3	99	3,251,6249	AA,AC,CC		2.686,0.5901,1.976	benign	454/645	53070174	257,12749	2203	4300	6503	SO:0001583	missense	3848	exon7			CCTTGGCCTGCTG	X69725	CCDS8836.1	12q13.13	2014-06-05	2008-08-01		ENSG00000167768	ENSG00000167768		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6412	protein-coding gene	gene with protein product		139350	"""epidermolytic hyperkeratosis 1"""	EHK1		2461420, 2470667, 16831889	Standard	NM_006121		Approved	KRT1A	uc001sau.1	P04264	OTTHUMG00000169749	ENST00000252244.3:c.1360G>T	12.37:g.53070174C>A	ENSP00000252244:p.Ala454Ser	251.0	0.0	0		238.0	121.0	0.508403	NM_006121	B2RA01|P85925|P86104|Q14720|Q6GSJ0|Q9H298	Missense_Mutation	SNP	ENST00000252244.3	37	CCDS8836.1	20	0.009157509157509158	0	0.0	4	0.011049723756906077	0	0.0	16	0.021108179419525065	c	17.21	3.332241	0.60853	0.005901	0.02686	ENSG00000167768	ENST00000252244	T	0.75589	-0.95	5.03	3.15	0.36227	Prefoldin (1);Filament (1);	.	.	.	.	T	0.62085	0.2399	M	0.73217	2.22	0.25099	N	0.990795	P	0.47350	0.894	D	0.63033	0.91	T	0.62895	-0.6757	9	0.59425	D	0.04	.	3.3536	0.07162	0.1474:0.5686:0.143:0.141	rs17678945;rs17678945	454	P04264	K2C1_HUMAN	S	454	ENSP00000252244:A454S	ENSP00000252244:A454S	A	-	1	0	KRT1	51356441	0.595000	0.26857	0.965000	0.40720	0.684000	0.39900	1.225000	0.32551	1.226000	0.43582	0.462000	0.41574	GCC	C|0.981;A|0.019	0.019	strong		0.587	KRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405706.1	NM_006121	
ITGA6	3655	hgsc.bcm.edu	37	2	173362720	173362720	+	Silent	SNP	T	T	C	rs139596061	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:173362720T>C	ENST00000264106.6	+	25	3326	c.3123T>C	c.(3121-3123)ttT>ttC	p.F1041F	ITGA6_ENST00000409532.1_Silent_p.F883F|ITGA6_ENST00000343713.4_Silent_p.F997F|ITGA6_ENST00000375221.2_Silent_p.F1041F|ITGA6_ENST00000409080.1_Silent_p.F1002F|AC093818.1_ENST00000442417.1_RNA|ITGA6_ENST00000264107.7_Silent_p.F1002F			P23229	ITA6_HUMAN	integrin, alpha 6	1041					amelogenesis (GO:0097186)|blood coagulation (GO:0007596)|brown fat cell differentiation (GO:0050873)|cell adhesion mediated by integrin (GO:0033627)|cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|cellular response to extracellular stimulus (GO:0031668)|cellular response to organic cyclic compound (GO:0071407)|digestive tract development (GO:0048565)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|nail development (GO:0035878)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell-cell adhesion (GO:0022409)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|renal system development (GO:0072001)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell surface (GO:0009986)|cell-cell adherens junction (GO:0005913)|external side of plasma membrane (GO:0009897)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integrin alpha6-beta4 complex (GO:0034676)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	44			OV - Ovarian serous cystadenocarcinoma(117;0.0979)			TGACTGTGTTTCCCTCAAAGA	0.438													T|||	4	0.000798722	0.0008	0.0	5008	,	,		18824	0.0		0.003	False		,,,				2504	0.0				p.F1002F		Atlas-SNP	.											.	ITGA6	171	.	0			c.T3006C						PASS	.	T	,	2,4404	4.2+/-10.8	0,2,2201	248.0	214.0	225.0		3006,3006	3.8	1.0	2	dbSNP_134	225	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	ITGA6	NM_000210.2,NM_001079818.1	,	0,14,6489	CC,CT,TT		0.1395,0.0454,0.1076	,	1002/1074,1002/1092	173362720	14,12992	2203	4300	6503	SO:0001819	synonymous_variant	3655	exon24			TGTGTTTCCCTCA		CCDS2249.1, CCDS46451.1	2q31.1	2010-09-20			ENSG00000091409	ENSG00000091409		"""CD molecules"", ""Integrins"""	6142	protein-coding gene	gene with protein product		147556					Standard	NM_001079818		Approved	CD49f	uc002uhp.1	P23229	OTTHUMG00000132277	ENST00000264106.6:c.3123T>C	2.37:g.173362720T>C		243.0	0.0	0		252.0	107.0	0.424603	NM_001079818	B2RMU9|B4DG69|B4DKB8|C4AM96|G5E9H1|Q08443|Q0MRC7|Q14646|Q16508|Q53RX7|Q59HB7|Q86VL6|Q9UCT1|Q9UN03	Silent	SNP	ENST00000264106.6	37																																																																																				T|0.999;C|0.001	0.001	strong		0.438	ITGA6-201	KNOWN	basic	protein_coding	protein_coding			
KIFC2	90990	hgsc.bcm.edu	37	8	145698758	145698758	+	Silent	SNP	G	G	A	rs201074786	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:145698758G>A	ENST00000301332.2	+	17	2819	c.2442G>A	c.(2440-2442)agG>agA	p.R814R	FOXH1_ENST00000525197.1_5'Flank|KIFC2_ENST00000301331.5_3'UTR	NM_145754.2	NP_665697.1	Q96AC6	KIFC2_HUMAN	kinesin family member C2	814	Pro-rich.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(7)|ovary(3)|prostate(3)|skin(2)|urinary_tract(1)	19	all_cancers(97;4.61e-11)|all_epithelial(106;2.89e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.08e-41)|Epithelial(56;8.67e-41)|all cancers(56;1.1e-35)|BRCA - Breast invasive adenocarcinoma(115;0.035)|Colorectal(110;0.055)			GCCCGCAGAGGGCCTGCCCCT	0.706													G|||	11	0.00219649	0.0	0.0072	5008	,	,		9786	0.0		0.006	False		,,,				2504	0.0				p.R814R		Atlas-SNP	.											.	KIFC2	53	.	0			c.G2442A						PASS	.	G		2,3926		0,2,1962	7.0	6.0	6.0		2442	1.7	0.0	8		6	61,7875		0,61,3907	no	coding-synonymous	KIFC2	NM_145754.2		0,63,5869	AA,AG,GG		0.7686,0.0509,0.531		814/839	145698758	63,11801	1964	3968	5932	SO:0001819	synonymous_variant	90990	exon17			GCAGAGGGCCTGC	AY007121	CCDS6427.1	8q24.3	2007-02-13			ENSG00000167702	ENSG00000167702		"""Kinesins"""	29530	protein-coding gene	gene with protein product						9115737	Standard	NM_145754		Approved		uc003zcz.3	Q96AC6	OTTHUMG00000165133	ENST00000301332.2:c.2442G>A	8.37:g.145698758G>A		37.0	0.0	0		22.0	10.0	0.454545	NM_145754	E9PHB2|Q96NN6	Silent	SNP	ENST00000301332.2	37	CCDS6427.1	6	0.0027472527472527475	4	0.008130081300813009	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	8.900	0.956047	0.18507	5.09E-4	0.007686	ENSG00000167702	ENST00000528415	.	.	.	3.48	1.66	0.24008	.	.	.	.	.	T	0.26738	0.0654	.	.	.	0.28321	N	0.922249	.	.	.	.	.	.	T	0.22103	-1.0226	4	.	.	.	-4.4999	7.859	0.29499	0.2172:0.0:0.7828:0.0	.	.	.	.	E	539	.	.	G	+	2	0	KIFC2	145669566	0.001000	0.12720	0.037000	0.18230	0.019000	0.09904	0.281000	0.18810	0.474000	0.27392	0.484000	0.47621	GGG	G|0.997;A|0.003	0.003	strong		0.706	KIFC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382052.2	NM_145754	
DAXX	1616	hgsc.bcm.edu	37	6	33287810	33287810	+	Silent	SNP	G	G	A	rs370615019		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:33287810G>A	ENST00000374542.5	-	5	1647	c.1443C>T	c.(1441-1443)gaC>gaT	p.D481D	DAXX_ENST00000414083.2_Silent_p.D406D|ZBTB22_ENST00000418724.1_5'Flank|DAXX_ENST00000477162.1_5'UTR|DAXX_ENST00000266000.6_Silent_p.D481D|ZBTB22_ENST00000431845.2_5'Flank	NM_001141969.1|NM_001141970.1|NM_001350.4	NP_001135441.1|NP_001135442.1|NP_001341.1	Q9UER7	DAXX_HUMAN	death-domain associated protein	481	Asp/Glu-rich (acidic).|Necessary for interaction with USP7.				activation of JUN kinase activity (GO:0007257)|androgen receptor signaling pathway (GO:0030521)|apoptotic process (GO:0006915)|chromatin remodeling (GO:0006338)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|mitotic cytokinesis (GO:0000281)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of neuron death (GO:1901216)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein phosphorylation (GO:0001934)|regulation of protein ubiquitination (GO:0031396)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|PML body (GO:0016605)|SWI/SNF superfamily-type complex (GO:0070603)	androgen receptor binding (GO:0050681)|enzyme binding (GO:0019899)|heat shock protein binding (GO:0031072)|histone binding (GO:0042393)|p53 binding (GO:0002039)|protein homodimerization activity (GO:0042803)|protein kinase activator activity (GO:0030295)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|receptor signaling protein activity (GO:0005057)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(5)|large_intestine(2)|lung(7)|ovary(3)|pancreas(18)|prostate(3)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(1)	55						cttcctcttcgtcctcctctt	0.502			"""Mis, F, N"""		Pancreatic neuroendocrine tumors. Paediatric GBM								G|||	1	0.000199681	0.0	0.0	5008	,	,		20984	0.001		0.0	False		,,,				2504	0.0				p.D493D		Atlas-SNP	.		Rec	yes		6	6p21.3	1616	death-domain associated protein		E	.	DAXX	111	.	0			c.C1479T						PASS	.	G	,,	0,4406		0,0,2203	238.0	162.0	188.0		1443,1479,1443	-2.5	0.2	6		188	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	DAXX	NM_001141969.1,NM_001141970.1,NM_001350.4	,,	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	,,	481/741,493/753,481/741	33287810	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	1616	exon5			CTCTTCGTCCTCC	AF006041	CCDS4776.1, CCDS59008.1	6p21.3	2008-08-29	2008-08-29			ENSG00000204209			2681	protein-coding gene	gene with protein product		603186	"""death-associated protein 6"""			9407001, 9215629	Standard	NM_001141970		Approved	DAP6	uc011dre.2	Q9UER7		ENST00000374542.5:c.1443C>T	6.37:g.33287810G>A		244.0	0.0	0		303.0	170.0	0.561056	NM_001141970	B4E1I3|F5H082|O14747|O15141|O15208|Q5STK9|Q9BWI3	Silent	SNP	ENST00000374542.5	37	CCDS4776.1																																																																																			.	.	weak		0.502	DAXX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076403.1		
ICE1	23379	hgsc.bcm.edu	37	5	5461976	5461976	+	Silent	SNP	T	T	C	rs72646682	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:5461976T>C	ENST00000296564.7	+	13	2751	c.2529T>C	c.(2527-2529)aaT>aaC	p.N843N		NM_015325.2	NP_056140.1	Q9Y2F5	ICE1_HUMAN		843					positive regulation of intracellular protein transport (GO:0090316)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|upper_aerodigestive_tract(1)	35						AAAATAACAATCCTGTAGAAT	0.403													t|||	4	0.000798722	0.0	0.0029	5008	,	,		19727	0.0		0.002	False		,,,				2504	0.0				p.N843N		Atlas-SNP	.											.	KIAA0947	301	.	0			c.T2529C						PASS	.			2,3766		0,2,1882	86.0	80.0	82.0		2529	-5.2	0.0	5	dbSNP_130	82	21,8215		0,21,4097	no	coding-synonymous	KIAA0947	NM_015325.1		0,23,5979	CC,CT,TT		0.255,0.0531,0.1916		843/2267	5461976	23,11981	1884	4118	6002	SO:0001819	synonymous_variant	23379	exon13			TAACAATCCTGTA																												ENST00000296564.7:c.2529T>C	5.37:g.5461976T>C		132.0	0.0	0		147.0	58.0	0.394558	NM_015325	Q68DE1|Q6ZT40|Q7L587|Q7Z3A9|Q9NTH9	Silent	SNP	ENST00000296564.7	37	CCDS47187.1																																																																																			T|0.998;C|0.002	0.002	strong		0.403	KIAA0947-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365575.1		
CNTNAP3	79937	hgsc.bcm.edu	37	9	39103796	39103796	+	Silent	SNP	G	G	A	rs145100345	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:39103796G>A	ENST00000297668.6	-	16	2554	c.2481C>T	c.(2479-2481)tcC>tcT	p.S827S	CNTNAP3_ENST00000358144.2_Silent_p.S739S|CNTNAP3_ENST00000377656.2_Silent_p.S826S	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	827	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.S827S(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		TAAACACCCCGGAGGAAACTG	0.483													G|||	11	0.00219649	0.0015	0.0	5008	,	,		15781	0.002		0.002	False		,,,				2504	0.0051				p.S827S		Atlas-SNP	.											CNTNAP3,NS,carcinoma,0,1	CNTNAP3	82	1	1	Substitution - coding silent(1)	endometrium(1)	c.C2481T						PASS	.	G		4,4402	6.2+/-15.9	0,4,2199	34.0	39.0	38.0		2481	-5.6	0.8	9	dbSNP_134	38	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	CNTNAP3	NM_033655.3		0,10,6493	AA,AG,GG		0.0698,0.0908,0.0769		827/1289	39103796	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	79937	exon16			CACCCCGGAGGAA	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.2481C>T	9.37:g.39103796G>A		597.0	0.0	0		633.0	256.0	0.404423	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			G|0.999;A|0.001	0.001	strong		0.483	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
SLC35E4	339665	hgsc.bcm.edu	37	22	31042606	31042606	+	Missense_Mutation	SNP	G	G	A	rs148304964	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:31042606G>A	ENST00000343605.4	+	2	1440	c.641G>A	c.(640-642)aGg>aAg	p.R214K	SLC35E4_ENST00000406566.1_Intron|SLC35E4_ENST00000300385.8_Intron	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	214	Leu-rich.					integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						CAGGAGGAGAGGCTGGACGCG	0.672													G|||	7	0.00139776	0.0	0.0029	5008	,	,		15892	0.0		0.005	False		,,,				2504	0.0				p.R214K		Atlas-SNP	.											.	SLC35E4	22	.	0			c.G641A						PASS	.	C	LYS/ARG	4,4374		0,4,2185	47.0	44.0	45.0		641	0.6	0.9	22	dbSNP_134	45	44,8528		0,44,4242	yes	missense	SLC35E4	NM_001001479.2	26	0,48,6427	AA,AG,GG		0.5133,0.0914,0.3707	benign	214/351	31042606	48,12902	2189	4286	6475	SO:0001583	missense	339665	exon2			AGGAGAGGCTGGA		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"""Solute carriers"""	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.641G>A	22.37:g.31042606G>A	ENSP00000339626:p.Arg214Lys	60.0	0.0	0		40.0	15.0	0.375	NM_001001479	Q567P0	Missense_Mutation	SNP	ENST00000343605.4	37	CCDS13882.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	g	0.181	-1.061767	0.01950	9.14E-4	0.005133	ENSG00000100036	ENST00000343605	T	0.60672	0.17	5.02	0.588	0.17445	Domain of unknown function DUF250 (1);	0.168007	0.51477	D	0.000083	T	0.15089	0.0364	N	0.02357	-0.585	0.80722	D	1	B	0.10296	0.003	B	0.10450	0.005	T	0.26121	-1.0112	10	0.02654	T	1	-15.9629	4.9658	0.14089	0.3219:0.148:0.53:0.0	.	214	Q6ICL7	S35E4_HUMAN	K	214	ENSP00000339626:R214K	ENSP00000339626:R214K	R	+	2	0	SLC35E4	29372606	0.994000	0.37717	0.915000	0.36163	0.067000	0.16453	0.739000	0.26173	0.267000	0.21916	-0.217000	0.12591	AGG	G|0.997;A|0.003	0.003	strong		0.672	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973	
PRMT9	90826	hgsc.bcm.edu	37	4	148589711	148589711	+	Missense_Mutation	SNP	G	G	A	rs146854725	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:148589711G>A	ENST00000322396.6	-	6	1174	c.932C>T	c.(931-933)gCa>gTa	p.A311V	TMEM184C_ENST00000508208.1_Intron|PRMT10_ENST00000541232.1_Missense_Mutation_p.A198V	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		311	SAM-dependent MTase PRMT-type 1. {ECO:0000255|PROSITE-ProRule:PRU01015}.					cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TCTTATCTCTGCACATTCTAC	0.348													G|||	4	0.000798722	0.0	0.0	5008	,	,		19299	0.0		0.004	False		,,,				2504	0.0				p.A311V		Atlas-SNP	.											.	PRMT10	68	.	0			c.C932T						PASS	.	G	VAL/ALA	5,4399	9.9+/-24.2	0,5,2197	133.0	123.0	126.0		932	4.2	1.0	4	dbSNP_134	126	50,8550	31.2+/-83.2	0,50,4250	yes	missense	PRMT10	NM_138364.2	64	0,55,6447	AA,AG,GG		0.5814,0.1135,0.4229	benign	311/846	148589711	55,12949	2202	4300	6502	SO:0001583	missense	90826	exon6			ATCTCTGCACATT																												ENST00000322396.6:c.932C>T	4.37:g.148589711G>A	ENSP00000314396:p.Ala311Val	113.0	0.0	0		110.0	51.0	0.463636	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	13.63	2.295916	0.40594	0.001135	0.005814	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.43294	0.95;0.95	5.9	4.17	0.49024	.	0.605454	0.18477	N	0.140055	T	0.21022	0.0506	N	0.25647	0.755	0.29735	N	0.837584	B	0.02656	0.0	B	0.04013	0.001	T	0.13469	-1.0508	10	0.28530	T	0.3	-30.4136	9.1674	0.37060	0.0703:0.0:0.617:0.3127	.	311	Q6P2P2	ANM10_HUMAN	V	311;198	ENSP00000314396:A311V;ENSP00000439508:A198V	ENSP00000314396:A311V	A	-	2	0	PRMT10	148809161	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	1.665000	0.37449	0.836000	0.34901	0.453000	0.30009	GCA	G|0.996;A|0.004	0.004	strong		0.348	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
IQGAP3	128239	hgsc.bcm.edu	37	1	156508792	156508792	+	Silent	SNP	T	T	C	rs79402045	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:156508792T>C	ENST00000361170.2	-	26	3100	c.3090A>G	c.(3088-3090)acA>acG	p.T1030T	IQGAP3_ENST00000498755.1_5'UTR	NM_178229.4	NP_839943.2	Q86VI3	IQGA3_HUMAN	IQ motif containing GTPase activating protein 3	1030	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				activation of MAPK activity (GO:0000187)|cellular response to organic substance (GO:0071310)|ERK1 and ERK2 cascade (GO:0070371)|G1/S transition of mitotic cell cycle (GO:0000082)|negative regulation of gene expression (GO:0010629)|positive regulation of gene expression (GO:0010628)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|Ras protein signal transduction (GO:0007265)|regulation of cell size (GO:0008361)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)	Ras GTPase activator activity (GO:0005099)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(14)|lung(29)|ovary(5)|prostate(5)|skin(5)|urinary_tract(3)	75	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTGGGTTGCCTGTCACCACGT	0.542													T|||	21	0.00419329	0.0015	0.0	5008	,	,		21851	0.001		0.0139	False		,,,				2504	0.0041				p.T1030T		Atlas-SNP	.											.	IQGAP3	146	.	0			c.A3090G						PASS	.	T		13,4393	17.9+/-39.9	0,13,2190	72.0	64.0	67.0		3090	-2.6	1.0	1	dbSNP_132	67	117,8483	61.7+/-123.6	0,117,4183	no	coding-synonymous	IQGAP3	NM_178229.4		0,130,6373	CC,CT,TT		1.3605,0.2951,0.9995		1030/1632	156508792	130,12876	2203	4300	6503	SO:0001819	synonymous_variant	128239	exon26			GTTGCCTGTCACC	AY253300	CCDS1144.1	1q21.3	2008-02-05			ENSG00000183856	ENSG00000183856			20669	protein-coding gene	gene with protein product							Standard	NM_178229		Approved		uc001fpf.3	Q86VI3	OTTHUMG00000033114	ENST00000361170.2:c.3090A>G	1.37:g.156508792T>C		167.0	0.0	0		209.0	114.0	0.545455	NM_178229	Q5T3H8	Silent	SNP	ENST00000361170.2	37	CCDS1144.1																																																																																			T|0.992;C|0.008	0.008	strong		0.542	IQGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080657.1	NM_178229	
NBAS	51594	hgsc.bcm.edu	37	2	15679410	15679410	+	Silent	SNP	G	G	A	rs147692911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:15679410G>A	ENST00000281513.5	-	7	475	c.450C>T	c.(448-450)gcC>gcT	p.A150A	NBAS_ENST00000441750.1_Silent_p.A150A	NM_015909.3	NP_056993.2	A2RRP1	NBAS_HUMAN	neuroblastoma amplified sequence	150					negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:2000623)|nuclear-transcribed mRNA catabolic process (GO:0000956)	cytoplasm (GO:0005737)|membrane (GO:0016020)				NS(4)|breast(4)|central_nervous_system(3)|endometrium(6)|kidney(5)|large_intestine(12)|liver(1)|lung(54)|ovary(2)|pancreas(3)|prostate(9)|skin(6)|stomach(3)	112						CTGTGCTTTCGGCATAGGCCA	0.443													G|||	2	0.000399361	0.0	0.0	5008	,	,		18414	0.0		0.002	False		,,,				2504	0.0				p.A150A		Atlas-SNP	.											.	NBAS	246	.	0			c.C450T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	116.0	104.0	108.0		450	-11.6	0.0	2	dbSNP_134	108	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	NBAS	NM_015909.2		0,5,6498	AA,AG,GG		0.0465,0.0227,0.0384		150/2372	15679410	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	51594	exon7			GCTTTCGGCATAG	BC051792	CCDS1685.1	2p24.3	2009-02-23			ENSG00000151779	ENSG00000151779			15625	protein-coding gene	gene with protein product		608025				9926938, 12706883	Standard	NM_015909		Approved	NAG	uc002rcc.2	A2RRP1	OTTHUMG00000121153	ENST00000281513.5:c.450C>T	2.37:g.15679410G>A		185.0	0.0	0		186.0	77.0	0.413978	NM_015909	O95790|Q2VPJ7|Q53TK6|Q86V39|Q8NFY8|Q9Y3W5	Silent	SNP	ENST00000281513.5	37	CCDS1685.1																																																																																			G|0.999;A|0.001	0.001	strong		0.443	NBAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241638.1	NM_015909	
ZNF621	285268	hgsc.bcm.edu	37	3	40574395	40574395	+	Silent	SNP	C	C	T	rs151057224		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:40574395C>T	ENST00000339296.5	+	5	1586	c.1134C>T	c.(1132-1134)gcC>gcT	p.A378A	ZNF621_ENST00000403205.2_Silent_p.A378A|ZNF621_ENST00000310898.1_Intron|ZNF621_ENST00000490457.1_Intron|ZNF621_ENST00000431278.1_Silent_p.A267A	NM_198484.3	NP_940886.1	Q6ZSS3	ZN621_HUMAN	zinc finger protein 621	378					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0515)|Kidney(284;0.0648)		ctgcttcagccgtagctgtgc	0.527													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19238	0.0		0.0	False		,,,				2504	0.0				p.A378A		Atlas-SNP	.											.	ZNF621	42	.	0			c.C1134T						PASS	.	C	,	3,4397		0,3,2197	102.0	72.0	82.0		1134,1134	-6.8	0.0	3	dbSNP_134	82	1,8595		0,1,4297	no	coding-synonymous,coding-synonymous	ZNF621	NM_001098414.1,NM_198484.3	,	0,4,6494	TT,TC,CC		0.0116,0.0682,0.0308	,	378/440,378/440	40574395	4,12992	2200	4298	6498	SO:0001819	synonymous_variant	285268	exon5			TTCAGCCGTAGCT	AK127181	CCDS2693.1, CCDS74920.1	3p21.33	2013-01-08			ENSG00000172888	ENSG00000172888		"""Zinc fingers, C2H2-type"", ""-"""	24787	protein-coding gene	gene with protein product							Standard	XM_005265079		Approved	FLJ45246	uc003ckm.2	Q6ZSS3	OTTHUMG00000131389	ENST00000339296.5:c.1134C>T	3.37:g.40574395C>T		216.0	0.0	0		162.0	55.0	0.339506	NM_001098414	Q14DC7|Q8TE91	Silent	SNP	ENST00000339296.5	37	CCDS2693.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	ZNF621-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254178.2	NM_198484	
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246956	47246956	+	Missense_Mutation	SNP	C	C	T	rs61743617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:47246956C>T	ENST00000300404.2	+	11	1626	c.1567C>T	c.(1567-1569)Cgg>Tgg	p.R523W	B4GALNT2_ENST00000504681.1_Missense_Mutation_p.R437W|B4GALNT2_ENST00000393354.2_Missense_Mutation_p.R463W|RP11-708H21.4_ENST00000575159.1_lincRNA	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	523					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			TCACCAGTCTCGGTCTCCAGT	0.542													C|||	24	0.00479233	0.0008	0.0101	5008	,	,		20911	0.0		0.0129	False		,,,				2504	0.0031				p.R523W	GBM(124;244 1635 8663 18097 33175)	Atlas-SNP	.											.	B4GALNT2	67	.	0			c.C1567T						PASS	.	C	TRP/ARG,TRP/ARG,TRP/ARG	12,4394	19.1+/-41.9	0,12,2191	96.0	93.0	94.0		1387,1309,1567	2.5	0.0	17	dbSNP_129	94	130,8470	67.3+/-129.8	0,130,4170	yes	missense,missense,missense	B4GALNT2	NM_001159387.1,NM_001159388.1,NM_153446.2	101,101,101	0,142,6361	TT,TC,CC		1.5116,0.2724,1.0918	probably-damaging,probably-damaging,probably-damaging	463/507,437/481,523/567	47246956	142,12864	2203	4300	6503	SO:0001583	missense	124872	exon11			CAGTCTCGGTCTC	AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1567C>T	17.37:g.47246956C>T	ENSP00000300404:p.Arg523Trp	44.0	0.0	0		29.0	19.0	0.655172	NM_153446	B4DZE4|Q14CP1|Q86Y40	Missense_Mutation	SNP	ENST00000300404.2	37	CCDS11544.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	C	17.61	3.432031	0.62844	0.002724	0.015116	ENSG00000167080	ENST00000504681;ENST00000393354;ENST00000300404	T;T;T	0.22743	1.94;1.94;1.94	5.79	2.47	0.30058	.	0.829068	0.10702	N	0.643916	T	0.14141	0.0342	L	0.50333	1.59	0.09310	N	1	D;D	0.69078	0.996;0.997	P;P	0.50231	0.635;0.543	T	0.07481	-1.0770	10	0.66056	D	0.02	-1.4776	7.8032	0.29187	0.3935:0.5316:0.0:0.0749	rs61743617	463;523	Q8NHY0-2;Q8NHY0	.;B4GN2_HUMAN	W	437;463;523	ENSP00000425510:R437W;ENSP00000377022:R463W;ENSP00000300404:R523W	ENSP00000300404:R523W	R	+	1	2	B4GALNT2	44601955	0.000000	0.05858	0.000000	0.03702	0.178000	0.23041	0.599000	0.24089	0.757000	0.33036	0.561000	0.74099	CGG	C|0.989;T|0.011	0.011	strong		0.542	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1	NM_153446	
LTBP1	4052	hgsc.bcm.edu	37	2	33567990	33567990	+	Silent	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33567990T>C	ENST00000404816.2	+	25	4169	c.3816T>C	c.(3814-3816)taT>taC	p.Y1272Y	LTBP1_ENST00000390003.4_Silent_p.Y947Y|LTBP1_ENST00000404525.1_Silent_p.Y893Y|LTBP1_ENST00000418533.2_Intron|LTBP1_ENST00000402934.1_Silent_p.Y893Y|LTBP1_ENST00000407925.1_Silent_p.Y946Y|LTBP1_ENST00000272273.5_Intron|LTBP1_ENST00000354476.3_Silent_p.Y1273Y			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1272	EGF-like 13; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				GCCTCTGTTATCAGGGCTTTC	0.448																																					p.Y1272Y		Atlas-SNP	.											.	LTBP1	317	.	0			c.T3816C						PASS	.						101.0	85.0	90.0					2																	33567990		2203	4300	6503	SO:0001819	synonymous_variant	4052	exon25			CTGTTATCAGGGC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3816T>C	2.37:g.33567990T>C		137.0	0.0	0		138.0	83.0	0.601449	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Silent	SNP	ENST00000404816.2	37	CCDS33177.2	.	.	.	.	.	.	.	.	.	.	T	9.629	1.135806	0.21123	.	.	ENSG00000049323	ENST00000415140	.	.	.	5.91	3.39	0.38822	.	.	.	.	.	T	0.55924	0.1951	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50792	-0.8786	4	.	.	.	.	7.2434	0.26109	0.0:0.3609:0.0:0.6391	.	.	.	.	T	234	.	.	I	+	2	0	LTBP1	33421494	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.377000	0.44300	0.932000	0.37266	0.455000	0.32223	ATC	.	.	none		0.448	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
PDZRN4	29951	hgsc.bcm.edu	37	12	41966771	41966771	+	Silent	SNP	G	G	A	rs113916113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:41966771G>A	ENST00000402685.2	+	10	2198	c.2190G>A	c.(2188-2190)aaG>aaA	p.K730K	PDZRN4_ENST00000298919.7_Silent_p.K470K|PDZRN4_ENST00000539469.2_Silent_p.K472K	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	730							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				ATCCAGAAAAGTCTGACAAGG	0.478													G|||	14	0.00279553	0.0008	0.0029	5008	,	,		22463	0.0		0.008	False		,,,				2504	0.0031				p.K730K		Atlas-SNP	.											.	PDZRN4	346	.	0			c.G2190A						PASS	.	G	,	11,4395	17.9+/-39.9	0,11,2192	114.0	116.0	115.0		2190,1416	3.1	1.0	12	dbSNP_132	115	98,8502	54.4+/-115.2	1,96,4203	no	coding-synonymous,coding-synonymous	PDZRN4	NM_001164595.1,NM_013377.3	,	1,107,6395	AA,AG,GG		1.1395,0.2497,0.8381	,	730/1037,472/779	41966771	109,12897	2203	4300	6503	SO:0001819	synonymous_variant	29951	exon10			AGAAAAGTCTGAC	AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.2190G>A	12.37:g.41966771G>A		49.0	0.0	0		68.0	41.0	0.602941	NM_001164595	Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Silent	SNP	ENST00000402685.2	37	CCDS53777.1																																																																																			G|0.992;A|0.008	0.008	strong		0.478	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1	NM_013377	
SLC16A8	23539	hgsc.bcm.edu	37	22	38477275	38477275	+	Missense_Mutation	SNP	G	G	A	rs75640043	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38477275G>A	ENST00000320521.5	-	4	878	c.770C>T	c.(769-771)gCc>gTc	p.A257V	SLC16A8_ENST00000469516.1_Intron	NM_013356.2	NP_037488.2	O95907	MOT3_HUMAN	solute carrier family 16 (monocarboxylate transporter), member 8	257					blood coagulation (GO:0007596)|cellular metabolic process (GO:0044237)|lactate transmembrane transport (GO:0035873)|lactate transport (GO:0015727)|leukocyte migration (GO:0050900)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	lactate transmembrane transporter activity (GO:0015129)|secondary active monocarboxylate transmembrane transporter activity (GO:0015355)|symporter activity (GO:0015293)			kidney(1)|large_intestine(1)|prostate(1)	3	Melanoma(58;0.045)				Pyruvic acid(DB00119)	CTTGGTGACGGCGTACACGGC	0.721													G|||	140	0.0279553	0.0053	0.0533	5008	,	,		11403	0.003		0.0785	False		,,,				2504	0.0143				p.A257V		Atlas-SNP	.											SLC16A8,NS,carcinoma,0,1	SLC16A8	13	1	0			c.C770T						PASS	.	G	VAL/ALA	70,4292		2,66,2113	18.0	17.0	17.0		770	-0.7	0.9	22	dbSNP_131	17	783,7775		28,727,3524	yes	missense	SLC16A8	NM_013356.2	64	30,793,5637	AA,AG,GG		9.1493,1.6048,6.6022	benign	257/505	38477275	853,12067	2181	4279	6460	SO:0001583	missense	23539	exon4			GTGACGGCGTACA	AF132610	CCDS13966.1	22q12.3-q13.2	2013-07-18	2013-07-18		ENSG00000100156	ENSG00000100156		"""Solute carriers"""	16270	protein-coding gene	gene with protein product	"""monocarboxylate transporter 3"""	610409	"""solute carrier 16 (monocarboxylic acid transporters), member 8"""			10493836	Standard	NM_013356		Approved	MCT3, REMP	uc003auu.3	O95907	OTTHUMG00000151196	ENST00000320521.5:c.770C>T	22.37:g.38477275G>A	ENSP00000321735:p.Ala257Val	46.0	0.0	0		38.0	28.0	0.736842	NM_013356	Q9UBE2	Missense_Mutation	SNP	ENST00000320521.5	37	CCDS13966.1	82	0.037545787545787544	5	0.01016260162601626	13	0.03591160220994475	2	0.0034965034965034965	62	0.08179419525065963	G	13.23	2.173754	0.38413	0.016048	0.091493	ENSG00000100156	ENST00000320521	T	0.55930	0.49	3.34	-0.715	0.11215	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	1.106640	0.06977	N	0.819091	T	0.01870	0.0059	L	0.41124	1.26	0.22975	N	0.998482	B	0.19583	0.037	B	0.24974	0.057	T	0.10428	-1.0630	10	0.20046	T	0.44	.	7.5375	0.27719	0.4057:0.0:0.5943:0.0	.	257	O95907	MOT3_HUMAN	V	257	ENSP00000321735:A257V	ENSP00000321735:A257V	A	-	2	0	SLC16A8	36807221	0.995000	0.38212	0.948000	0.38648	0.931000	0.56810	2.753000	0.47524	-0.042000	0.13535	0.313000	0.20887	GCC	G|0.951;A|0.049	0.049	strong		0.721	SLC16A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321724.1	NM_013356	
GARS	2617	hgsc.bcm.edu	37	7	30634548	30634548	+	Missense_Mutation	SNP	C	C	T	rs62636572	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:30634548C>T	ENST00000389266.3	+	1	252	c.11C>T	c.(10-12)cCg>cTg	p.P4L	AC005154.6_ENST00000579174.1_RNA|AC005154.6_ENST00000580440.1_RNA|AC005154.6_ENST00000583664.1_RNA|AC005154.6_ENST00000584372.1_RNA|AC005154.6_ENST00000578994.1_RNA|AC005154.6_ENST00000584199.1_RNA|AC005154.6_ENST00000582549.1_RNA|AC005154.6_ENST00000581665.1_RNA	NM_002047.2	NP_002038.2	P41250	SYG_HUMAN	glycyl-tRNA synthetase	4					cell death (GO:0008219)|diadenosine tetraphosphate biosynthetic process (GO:0015966)|gene expression (GO:0010467)|glycyl-tRNA aminoacylation (GO:0006426)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)|secretory granule (GO:0030141)	ATP binding (GO:0005524)|glycine-tRNA ligase activity (GO:0004820)|protein dimerization activity (GO:0046983)			breast(3)|endometrium(2)|kidney(1)|large_intestine(4)|lung(9)|ovary(1)|skin(3)|urinary_tract(1)	24					Glycine(DB00145)	ATGCCCTCTCCGCGTCCAGTG	0.711													C|||	42	0.00838658	0.0	0.0245	5008	,	,		14101	0.0		0.0239	False		,,,				2504	0.001				p.P4L		Atlas-SNP	.											.	GARS	52	.	0			c.C11T						PASS	.	C	LEU/PRO	10,3978		0,10,1984	7.0	8.0	8.0		11	-1.4	0.0	7	dbSNP_129	8	113,8037		0,113,3962	yes	missense	GARS	NM_002047.2	98	0,123,5946	TT,TC,CC		1.3865,0.2508,1.0133	benign	4/740	30634548	123,12015	1994	4075	6069	SO:0001583	missense	2617	exon1			CCTCTCCGCGTCC	AK074524	CCDS43564.1	7p15	2014-09-17	2004-02-13		ENSG00000106105	ENSG00000106105	6.1.1.14	"""Aminoacyl tRNA synthetases / Class II"""	4162	protein-coding gene	gene with protein product	"""glycine tRNA ligase"""	600287	"""Charcot-Marie-Tooth neuropathy 2D"""	CMT2D		8595897, 8872480	Standard	NM_002047		Approved	GlyRS, DSMAV, SMAD1	uc003tbm.3	P41250	OTTHUMG00000152769	ENST00000389266.3:c.11C>T	7.37:g.30634548C>T	ENSP00000373918:p.Pro4Leu	23.0	0.0	0		9.0	7.0	0.777778	NM_002047	B3KQA2|B4DIA0|Q969Y1	Missense_Mutation	SNP	ENST00000389266.3	37	CCDS43564.1	29	0.013278388278388278	0	0.0	11	0.03038674033149171	0	0.0	18	0.023746701846965697	C	0.026	-1.372300	0.01214	0.002508	0.013865	ENSG00000106105	ENST00000389266	T	0.80566	-1.39	3.33	-1.39	0.08997	.	0.647368	0.15500	N	0.259091	T	0.29817	0.0745	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.25641	-1.0126	10	0.10377	T	0.69	0.9595	7.0049	0.24830	0.0:0.4002:0.0:0.5998	rs62636572	4	P41250	SYG_HUMAN	L	4	ENSP00000373918:P4L	ENSP00000373918:P4L	P	+	2	0	GARS	30601073	0.000000	0.05858	0.011000	0.14972	0.317000	0.28152	-0.624000	0.05540	-0.325000	0.08577	-0.133000	0.14855	CCG	C|0.986;T|0.014	0.014	strong		0.711	GARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327735.1	NM_002047	
FAT1	2195	hgsc.bcm.edu	37	4	187549443	187549443	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:187549443C>T	ENST00000441802.2	-	9	4884	c.4675G>A	c.(4675-4677)Gcc>Acc	p.A1559T		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	1559	Cadherin 13. {ECO:0000255|PROSITE- ProRule:PRU00043}.				actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						AACCACGGGGCGTGGTCATTC	0.498										HNSCC(5;0.00058)																											p.A1559T	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G4675A						PASS	.						56.0	58.0	57.0					4																	187549443		2103	4226	6329	SO:0001583	missense	2195	exon9			ACGGGGCGTGGTC	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.4675G>A	4.37:g.187549443C>T	ENSP00000406229:p.Ala1559Thr	167.0	0.0	0		192.0	85.0	0.442708	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	.	.	.	.	.	.	.	.	.	.	C	16.42	3.117363	0.56505	.	.	ENSG00000083857	ENST00000441802;ENST00000260147	T	0.03181	4.02	5.36	4.52	0.55395	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.100704	0.64402	D	0.000002	T	0.06600	0.0169	M	0.72894	2.215	0.80722	D	1	B	0.24920	0.114	B	0.17722	0.019	T	0.20605	-1.0270	10	0.19590	T	0.45	.	15.7693	0.78152	0.1368:0.8631:0.0:0.0	.	1559	Q14517	FAT1_HUMAN	T	1559;1558	ENSP00000406229:A1559T	ENSP00000260147:A1558T	A	-	1	0	FAT1	187786437	0.945000	0.32115	0.915000	0.36163	0.916000	0.54674	2.092000	0.41700	1.477000	0.48234	0.563000	0.77884	GCC	.	.	none		0.498	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
ZNF574	64763	hgsc.bcm.edu	37	19	42583743	42583743	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:42583743C>T	ENST00000600245.1	+	2	1640	c.985C>T	c.(985-987)Cgg>Tgg	p.R329W	CTB-59C6.3_ENST00000594531.1_RNA|ZNF574_ENST00000222339.7_Missense_Mutation_p.R419W|ZNF574_ENST00000359044.4_Missense_Mutation_p.R329W			Q6ZN55	ZN574_HUMAN	zinc finger protein 574	329					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	20		Prostate(69;0.059)				GCAGCACCTGCGGAGTCACCG	0.607																																					p.R329W		Atlas-SNP	.											.	ZNF574	57	.	0			c.C985T						PASS	.						99.0	108.0	105.0					19																	42583743		2203	4300	6503	SO:0001583	missense	64763	exon2			CACCTGCGGAGTC	AK074788	CCDS12596.1	19q13.2	2013-09-20			ENSG00000105732	ENSG00000105732		"""Zinc fingers, C2H2-type"""	26166	protein-coding gene	gene with protein product						12477932	Standard	NM_022752		Approved	FLJ22059	uc002osm.4	Q6ZN55	OTTHUMG00000182751	ENST00000600245.1:c.985C>T	19.37:g.42583743C>T	ENSP00000469029:p.Arg329Trp	149.0	0.0	0		159.0	69.0	0.433962	NM_022752	Q6IPE0|Q6ZN10|Q7L5Z5|Q8NCE3|Q9H6N0	Missense_Mutation	SNP	ENST00000600245.1	37	CCDS12596.1	.	.	.	.	.	.	.	.	.	.	c	15.18	2.756649	0.49362	.	.	ENSG00000105732	ENST00000222339;ENST00000359044	T;T	0.26223	1.75;1.75	4.63	3.58	0.41010	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);	0.141481	0.45361	D	0.000364	T	0.53190	0.1781	M	0.86502	2.82	0.26272	N	0.978409	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.992	T	0.50800	-0.8785	10	0.87932	D	0	-19.0607	11.469	0.50257	0.3259:0.6741:0.0:0.0	.	329;418	Q6ZN55;Q6ZN55-2	ZN574_HUMAN;.	W	419;329	ENSP00000222339:R419W;ENSP00000351939:R329W	ENSP00000222339:R419W	R	+	1	2	ZNF574	47275583	0.563000	0.26594	1.000000	0.80357	0.762000	0.43233	2.030000	0.41108	1.287000	0.44583	-0.174000	0.13273	CGG	.	.	none		0.607	ZNF574-002	KNOWN	upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463458.1	NM_022752	
TYW3	127253	hgsc.bcm.edu	37	1	75199023	75199023	+	Missense_Mutation	SNP	A	A	C	rs143670067	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:75199023A>C	ENST00000370867.3	+	1	184	c.95A>C	c.(94-96)gAg>gCg	p.E32A	CRYZ_ENST00000370872.3_5'Flank|TYW3_ENST00000479111.1_5'UTR|TYW3_ENST00000457880.2_Missense_Mutation_p.E32A|TYW3_ENST00000421739.2_Missense_Mutation_p.E32A|CRYZ_ENST00000417775.1_5'UTR|CRYZ_ENST00000370871.3_5'Flank|CRYZ_ENST00000340866.5_5'Flank	NM_138467.2	NP_612476.1	Q6IPR3	TYW3_HUMAN	tRNA-yW synthesizing protein 3 homolog (S. cerevisiae)	32					tRNA processing (GO:0008033)		methyltransferase activity (GO:0008168)			central_nervous_system(1)|endometrium(2)|kidney(1)|lung(7)|ovary(2)|prostate(1)|skin(1)	15						GATGTGGTAGAGCTTGTGCAG	0.572													A|||	10	0.00199681	0.0	0.0029	5008	,	,		19178	0.0		0.008	False		,,,				2504	0.0				p.E32A		Atlas-SNP	.											.	TYW3	36	.	0			c.A95C						PASS	.	A	,,,ALA/GLU,,ALA/GLU	6,4400	11.4+/-27.6	0,6,2197	142.0	114.0	123.0		,,,95,,95	3.5	0.4	1	dbSNP_134	123	35,8565	24.6+/-71.5	0,35,4265	yes	utr-5,utr-5,utr-5,missense,utr-5,missense	CRYZ,TYW3	NM_001130042.1,NM_001130043.1,NM_001134759.1,NM_001162916.1,NM_001889.3,NM_138467.2	,,,107,,107	0,41,6462	CC,CA,AA		0.407,0.1362,0.3152	,,,possibly-damaging,,possibly-damaging	,,,32/227,,32/260	75199023	41,12965	2203	4300	6503	SO:0001583	missense	127253	exon1			TGGTAGAGCTTGT	BX647591	CCDS666.1, CCDS53334.1	1p31.1	2008-02-05	2006-05-25	2006-05-25	ENSG00000162623	ENSG00000162623			24757	protein-coding gene	gene with protein product		611245	"""chromosome 1 open reading frame 171"""	C1orf171		17150819	Standard	NM_138467		Approved	FLJ40918	uc001dgn.3	Q6IPR3	OTTHUMG00000009641	ENST00000370867.3:c.95A>C	1.37:g.75199023A>C	ENSP00000359904:p.Glu32Ala	99.0	0.0	0		84.0	32.0	0.380952	NM_001162916	B4DSP9|E9PGR7|Q5HYJ0|Q8N7L1	Missense_Mutation	SNP	ENST00000370867.3	37	CCDS666.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	12.16	1.854352	0.32791	0.001362	0.00407	ENSG00000162623	ENST00000457880;ENST00000370867;ENST00000421739	T;T;T	0.31247	1.5;1.5;1.5	4.61	3.49	0.39957	tRNA wybutosine-synthesizing protein (2);	0.257365	0.39615	N	0.001304	T	0.10981	0.0268	M	0.66378	2.025	0.09310	N	1	B;P;B	0.40970	0.153;0.734;0.056	B;B;B	0.34452	0.076;0.183;0.053	T	0.12116	-1.0560	10	0.24483	T	0.36	-7.0777	7.3561	0.26719	0.8192:0.0:0.1808:0.0	.	32;32;32	B4DFU6;E9PGR7;Q6IPR3	.;.;TYW3_HUMAN	A	32	ENSP00000407025:E32A;ENSP00000359904:E32A;ENSP00000409336:E32A	ENSP00000359904:E32A	E	+	2	0	TYW3	74971611	0.089000	0.21612	0.445000	0.26908	0.987000	0.75469	1.673000	0.37534	0.797000	0.33971	0.459000	0.35465	GAG	A|0.997;C|0.003	0.003	strong		0.572	TYW3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026573.1	NM_138467	
MPHOSPH10	10199	hgsc.bcm.edu	37	2	71360055	71360055	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:71360055C>T	ENST00000244230.2	+	2	469	c.117C>T	c.(115-117)ttC>ttT	p.F39F	MPHOSPH10_ENST00000498451.2_Silent_p.F39F|MPHOSPH10_ENST00000468427.1_3'UTR|MCEE_ENST00000244217.5_5'Flank	NM_005791.2	NP_005782.1	O00566	MPP10_HUMAN	M-phase phosphoprotein 10 (U3 small nucleolar ribonucleoprotein)	39					negative regulation of phosphatase activity (GO:0010923)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)|rRNA processing (GO:0006364)	chromosome (GO:0005694)|nucleolus (GO:0005730)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(2)|pancreas(2)|skin(2)|stomach(1)	26						CATCAAAGTTCACTTCTTTAA	0.308																																					p.F39F		Atlas-SNP	.											.	MPHOSPH10	81	.	0			c.C117T						PASS	.						34.0	40.0	38.0					2																	71360055		2151	4271	6422	SO:0001819	synonymous_variant	10199	exon2			AAAGTTCACTTCT	X98494	CCDS1916.1	2p13.3	2014-06-12			ENSG00000124383	ENSG00000124383			7213	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 106"""	605503				8885239, 9450966	Standard	NM_005791		Approved	MPP10, MPP10P, CT90, PPP1R106	uc002sht.2	O00566	OTTHUMG00000129715	ENST00000244230.2:c.117C>T	2.37:g.71360055C>T		161.0	0.0	0		155.0	76.0	0.490323	NM_005791	A0AVJ8	Silent	SNP	ENST00000244230.2	37	CCDS1916.1																																																																																			.	.	none		0.308	MPHOSPH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251924.2	NM_005791	
WDR6	11180	hgsc.bcm.edu	37	3	49044932	49044932	+	Missense_Mutation	SNP	G	G	T	rs62262472	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:49044932G>T	ENST00000608424.1	+	1	107	c.68G>T	c.(67-69)gGt>gTt	p.G23V	WDR6_ENST00000395474.3_Missense_Mutation_p.G53V|WDR6_ENST00000489684.1_3'UTR|WDR6_ENST00000448293.1_5'Flank|WDR6_ENST00000415265.2_Missense_Mutation_p.G23V			Q9NNW5	WDR6_HUMAN	WD repeat domain 6	23					cell cycle arrest (GO:0007050)|negative regulation of autophagy (GO:0010507)|negative regulation of cell proliferation (GO:0008285)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|large_intestine(1)|liver(1)|lung(9)|ovary(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	26				Kidney(197;9.12e-07)|KIRC - Kidney renal clear cell carcinoma(197;1.32e-05)|BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|OV - Ovarian serous cystadenocarcinoma(275;0.000155)		CCAGTGACGGGTCTGGAGTGC	0.657													g|||	3	0.000599042	0.0	0.0	5008	,	,		15634	0.0		0.003	False		,,,				2504	0.0				p.G53V		Atlas-SNP	.											.	WDR6	79	.	0			c.G158T						PASS	.		VAL/GLY	9,4397	15.5+/-35.6	0,9,2194	48.0	43.0	45.0		158	4.1	1.0	3	dbSNP_129	45	42,8558	26.8+/-75.7	0,42,4258	yes	missense	WDR6	NM_018031.3	109	0,51,6452	TT,TG,GG		0.4884,0.2043,0.3921	probably-damaging	53/1152	49044932	51,12955	2203	4300	6503	SO:0001583	missense	11180	exon1			TGACGGGTCTGGA	AF099100	CCDS2782.2	3p21.31	2013-01-09			ENSG00000178252	ENSG00000178252		"""WD repeat domain containing"""	12758	protein-coding gene	gene with protein product		606031					Standard	NM_018031		Approved		uc003cvj.2	Q9NNW5	OTTHUMG00000133546	ENST00000608424.1:c.68G>T	3.37:g.49044932G>T	ENSP00000477389:p.Gly23Val	169.0	0.0	0		162.0	80.0	0.493827	NM_018031	B4DHK2|Q3MIT1|Q9UF63	Missense_Mutation	SNP	ENST00000608424.1	37		1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	14.52	2.560336	0.45590	0.002043	0.004884	ENSG00000178252	ENST00000395474;ENST00000438660;ENST00000354294;ENST00000415265	T;T	0.69685	-0.34;-0.42	5.02	4.08	0.47627	.	0.245193	0.30930	N	0.008587	T	0.62889	0.2465	N	0.19112	0.55	0.80722	D	1	B;D	0.64830	0.002;0.994	B;P	0.56865	0.003;0.808	T	0.65619	-0.6124	10	0.59425	D	0.04	-10.7481	10.8606	0.46825	0.0:0.2887:0.7113:0.0	rs62262472	23;23	E9PBK6;B4DK45	.;.	V	53;23;23;23	ENSP00000378857:G53V;ENSP00000387692:G23V	ENSP00000346247:G23V	G	+	2	0	WDR6	49019936	1.000000	0.71417	0.998000	0.56505	0.988000	0.76386	1.989000	0.40707	2.505000	0.84491	0.645000	0.84053	GGT	G|0.997;T|0.003	0.003	strong		0.657	WDR6-024	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471652.1		
ATP12A	479	hgsc.bcm.edu	37	13	25255705	25255705	+	Silent	SNP	C	C	A	rs41288276	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:25255705C>A	ENST00000381946.3	+	2	182	c.15C>A	c.(13-15)acC>acA	p.T5T	ATP12A_ENST00000218548.6_Silent_p.T5T			P54707	AT12A_HUMAN	ATPase, H+/K+ transporting, nongastric, alpha polypeptide	5					ATP biosynthetic process (GO:0006754)|ion transmembrane transport (GO:0034220)|potassium ion homeostasis (GO:0055075)|regulation of pH (GO:0006885)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|hydrogen:potassium-exchanging ATPase complex (GO:0005889)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|hydrogen:potassium-exchanging ATPase activity (GO:0008900)|metal ion binding (GO:0046872)			breast(6)|central_nervous_system(4)|endometrium(3)|kidney(5)|large_intestine(23)|lung(23)|ovary(2)|pancreas(1)|prostate(2)|skin(5)	74		Lung SC(185;0.0225)|Breast(139;0.077)		all cancers(112;0.0307)|Epithelial(112;0.086)|OV - Ovarian serous cystadenocarcinoma(117;0.228)		TTCAGAAAACCCCAGAAATTT	0.542													C|||	256	0.0511182	0.1044	0.0303	5008	,	,		17355	0.001		0.0477	False		,,,				2504	0.0491				p.T5T	Pancreas(156;1582 1935 18898 22665 26498)	Atlas-SNP	.											.	ATP12A	172	.	0			c.C15A						PASS	.	C	,	401,4005	199.8+/-223.2	18,365,1820	51.0	54.0	53.0		15,15	-6.3	0.0	13	dbSNP_127	53	391,8209	125.5+/-184.1	5,381,3914	no	coding-synonymous,coding-synonymous	ATP12A	NM_001185085.1,NM_001676.5	,	23,746,5734	AA,AC,CC		4.5465,9.1012,6.0895	,	5/1046,5/1040	25255705	792,12214	2203	4300	6503	SO:0001819	synonymous_variant	479	exon2			GAAAACCCCAGAA	L42558	CCDS31948.1, CCDS53858.1	13q11-q12.1	2010-04-20	2002-02-25		ENSG00000075673	ENSG00000075673	3.6.3.10	"""ATPases / P-type"""	13816	protein-coding gene	gene with protein product	"""ATPase, Na+K+ transporting, alpha-1 polypeptide-like"", ""potassium-transporting ATPase alpha chain 2"", ""proton pump"", ""non-gastric H(+)/K(+) ATPase alpha subunit"", ""sodium/potassium ATPase, alpha polypeptide-like"""	182360	"""ATPase, Na+/K+ transporting, alpha polypeptide-like 1"""	ATP1AL1		8838794, 2842249	Standard	NM_001676		Approved		uc010aaa.3	P54707	OTTHUMG00000016588	ENST00000381946.3:c.15C>A	13.37:g.25255705C>A		77.0	0.0	0		56.0	25.0	0.446429	NM_001185085	Q13816|Q13817|Q16734|Q5W035|Q8N5U2	Silent	SNP	ENST00000381946.3	37	CCDS31948.1																																																																																			C|0.942;A|0.058	0.058	strong		0.542	ATP12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044199.1	NM_001676	
CPT1C	126129	hgsc.bcm.edu	37	19	50216050	50216050	+	Missense_Mutation	SNP	C	C	A	rs79488403	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:50216050C>A	ENST00000392518.4	+	18	2449	c.2077C>A	c.(2077-2079)Ctg>Atg	p.L693M	CPT1C_ENST00000405931.2_Missense_Mutation_p.L682M|CPT1C_ENST00000598293.1_Missense_Mutation_p.L693M|CPT1C_ENST00000354199.5_Intron|CPT1C_ENST00000323446.5_Missense_Mutation_p.L693M	NM_001199752.1	NP_001186681.1	Q8TCG5	CPT1C_HUMAN	carnitine palmitoyltransferase 1C	693					carnitine metabolic process (GO:0009437)|fatty acid beta-oxidation (GO:0006635)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|endoplasmic reticulum membrane (GO:0005789)|mitochondrial outer membrane (GO:0005741)|synapse (GO:0045202)	carnitine O-palmitoyltransferase activity (GO:0004095)			breast(1)|central_nervous_system(3)|endometrium(3)|kidney(1)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	27		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.0011)|GBM - Glioblastoma multiforme(134;0.00786)		GCAAATGCATCTGTTTGACGT	0.592													c|||	4	0.000798722	0.0	0.0	5008	,	,		15329	0.0		0.004	False		,,,				2504	0.0				p.L693M		Atlas-SNP	.											.	CPT1C	93	.	0			c.C2077A						PASS	.	C	MET/LEU,MET/LEU,MET/LEU,MET/LEU	4,4402	8.1+/-20.4	0,4,2199	103.0	80.0	88.0		2044,2077,2077,2077	3.5	1.0	19	dbSNP_131	88	63,8537	37.4+/-92.8	0,63,4237	yes	missense,missense,missense,missense	CPT1C	NM_001136052.2,NM_001199752.1,NM_001199753.1,NM_152359.2	15,15,15,15	0,67,6436	AA,AC,CC		0.7326,0.0908,0.5151	probably-damaging,probably-damaging,probably-damaging,probably-damaging	682/793,693/804,693/804,693/804	50216050	67,12939	2203	4300	6503	SO:0001583	missense	126129	exon18			ATGCATCTGTTTG	AF357970	CCDS12779.1, CCDS46147.1	19q13.33	2014-03-14				ENSG00000169169			18540	protein-coding gene	gene with protein product		608846				12376098, 11001805	Standard	NM_001136052		Approved	FLJ23809, CPTIC, CPT1P	uc010eng.3	Q8TCG5		ENST00000392518.4:c.2077C>A	19.37:g.50216050C>A	ENSP00000376303:p.Leu693Met	252.0	0.0	0		218.0	90.0	0.412844	NM_001199752	A8K0Z8|Q5K6N5|Q8N6Q9|Q8NDS6|Q8TE84	Missense_Mutation	SNP	ENST00000392518.4	37	CCDS12779.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	16.60	3.167352	0.57476	9.08E-4	0.007326	ENSG00000169169	ENST00000392518;ENST00000405931;ENST00000323446	D;D;D	0.86366	-2.11;-2.09;-2.11	4.59	3.55	0.40652	.	0.000000	0.35207	N	0.003375	D	0.84804	0.5553	L	0.45698	1.435	0.80722	D	1	P;P	0.42649	0.746;0.786	P;P	0.55222	0.561;0.771	D	0.84213	0.0457	10	0.34782	T	0.22	-14.6614	11.8375	0.52333	0.0:0.9125:0.0:0.0875	.	682;693	Q8TCG5-2;Q8TCG5	.;CPT1C_HUMAN	M	693;682;693	ENSP00000376303:L693M;ENSP00000384465:L682M;ENSP00000319343:L693M	ENSP00000319343:L693M	L	+	1	2	CPT1C	54907862	0.882000	0.30256	0.987000	0.45799	0.996000	0.88848	0.767000	0.26575	1.305000	0.44909	0.650000	0.86243	CTG	C|0.996;A|0.004	0.004	strong		0.592	CPT1C-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465873.1	NM_152359	
PDXDC1	23042	hgsc.bcm.edu	37	16	15100301	15100301	+	Missense_Mutation	SNP	C	C	T	rs141901522	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:15100301C>T	ENST00000396410.4	+	6	537	c.440C>T	c.(439-441)gCa>gTa	p.A147V	PDXDC1_ENST00000447912.2_Missense_Mutation_p.A56V|PDXDC1_ENST00000325823.7_Missense_Mutation_p.A132V|PDXDC1_ENST00000569715.1_Missense_Mutation_p.A120V|PDXDC1_ENST00000455313.2_Missense_Mutation_p.A147V|PDXDC1_ENST00000563679.1_Missense_Mutation_p.A165V|PDXDC1_ENST00000535621.2_Missense_Mutation_p.A147V|PDXDC1_ENST00000450288.2_Missense_Mutation_p.A119V	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	147					carboxylic acid metabolic process (GO:0019752)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)	carboxy-lyase activity (GO:0016831)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(10)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						GAAGGACTTGCAAAGATATGT	0.353													.|||	3	0.000599042	0.0	0.0	5008	,	,		33956	0.0		0.003	False		,,,				2504	0.0				p.A147V		Atlas-SNP	.											.	PDXDC1	59	.	0			c.C440T						PASS	.	C	VAL/ALA	2,4392	4.2+/-10.8	0,2,2195	149.0	150.0	150.0		440	4.8	1.0	16	dbSNP_134	150	21,8579	14.0+/-48.4	0,21,4279	no	missense	PDXDC1	NM_015027.2	64	0,23,6474	TT,TC,CC		0.2442,0.0455,0.177	benign	147/789	15100301	23,12971	2197	4300	6497	SO:0001583	missense	23042	exon6			GACTTGCAAAGAT	AK025504, BX647809	CCDS32393.1, CCDS66954.1, CCDS66957.1, CCDS73830.1, CCDS73831.1	16p13.11	2008-02-05							28995	protein-coding gene	gene with protein product		614244					Standard	XM_005255173		Approved	KIAA0251	uc002dda.4	Q6P996	OTTHUMG00000166304	ENST00000396410.4:c.440C>T	16.37:g.15100301C>T	ENSP00000379691:p.Ala147Val	381.0	0.0	0		372.0	103.0	0.276882	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	C	12.02	1.813847	0.32053	4.55E-4	0.002442	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000535621;ENST00000396410;ENST00000450288;ENST00000455313	T;T;T;T;T;T	0.36157	1.27;2.41;1.27;1.27;1.27;1.27	5.82	4.79	0.61399	Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.260219	0.37178	N	0.002204	T	0.11153	0.0272	N	0.02539	-0.55	0.33168	D	0.547894	B;B;B;B;B;B;B	0.13145	0.005;0.002;0.005;0.007;0.005;0.005;0.003	B;B;B;B;B;B;B	0.15052	0.008;0.004;0.008;0.007;0.012;0.008;0.006	T	0.32428	-0.9907	10	0.06891	T	0.86	-0.0283	4.3523	0.11162	0.0:0.7219:0.0:0.2781	.	119;56;132;147;119;147;147	E7EPL4;E7EMH5;B4DHL7;Q86XE2;B4DR55;Q6P996;Q6P996-2	.;.;.;.;.;PDXD1_HUMAN;.	V	132;56;147;147;119;147	ENSP00000322807:A132V;ENSP00000400310:A56V;ENSP00000437835:A147V;ENSP00000379691:A147V;ENSP00000391147:A119V;ENSP00000406703:A147V	ENSP00000322807:A132V	A	+	2	0	PDXDC1	15007802	0.932000	0.31603	1.000000	0.80357	0.901000	0.52897	3.426000	0.52778	2.765000	0.95021	0.650000	0.86243	GCA	C|0.998;T|0.002	0.002	strong		0.353	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
RASA2	5922	hgsc.bcm.edu	37	3	141295907	141295907	+	Missense_Mutation	SNP	G	G	A	rs201190266		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:141295907G>A	ENST00000452898.1	+	15	1584	c.1549G>A	c.(1549-1551)Gta>Ata	p.V517I	RASA2_ENST00000286364.3_Missense_Mutation_p.V517I	NM_006506.2	NP_006497.2	Q15283	RASA2_HUMAN	RAS p21 protein activator 2	517	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.V517I(2)		NS(1)|breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	34						TGCTGTAGCCGTAGTATCACC	0.353																																					p.V517I		Atlas-SNP	.											RASA2_ENST00000286364,NS,carcinoma,0,2	RASA2	169	2	2	Substitution - Missense(2)	kidney(2)	c.G1549A						PASS	.						228.0	215.0	219.0					3																	141295907		2203	4300	6503	SO:0001583	missense	5922	exon15			GTAGCCGTAGTAT	AF115573	CCDS3117.1	3q22-q23	2013-01-10			ENSG00000155903	ENSG00000155903		"""Pleckstrin homology (PH) domain containing"""	9872	protein-coding gene	gene with protein product		601589				8699317	Standard	NM_006506		Approved	GAP1M	uc003etz.1	Q15283	OTTHUMG00000160221	ENST00000452898.1:c.1549G>A	3.37:g.141295907G>A	ENSP00000391677:p.Val517Ile	156.0	0.0	0		170.0	98.0	0.576471	NM_006506	A8K7K1|G3V0F9|O00695|Q15284|Q92594|Q99577|Q9UEQ2	Missense_Mutation	SNP	ENST00000452898.1	37		.	.	.	.	.	.	.	.	.	.	G	7.080	0.570046	0.13560	.	.	ENSG00000155903	ENST00000286364;ENST00000452898;ENST00000423660	T;T	0.71934	-0.61;-0.61	6.03	4.24	0.50183	Ras GTPase-activating protein, conserved site (1);Rho GTPase activation protein (1);Ras GTPase-activating protein (4);	0.059991	0.64402	N	0.000004	T	0.35653	0.0939	N	0.00808	-1.17	0.49213	D	0.999769	B;B;B;B	0.21147	0.052;0.005;0.004;0.005	B;B;B;B	0.21917	0.037;0.012;0.007;0.012	T	0.43376	-0.9395	10	0.02654	T	1	.	12.1791	0.54202	0.1391:0.0:0.8609:0.0	.	109;517;517;517	E7EU60;A8K7K1;G3V0F9;Q15283	.;.;.;RASA2_HUMAN	I	517;517;109	ENSP00000286364:V517I;ENSP00000391677:V517I	ENSP00000286364:V517I	V	+	1	0	RASA2	142778597	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.269000	0.72558	0.870000	0.35726	0.557000	0.71058	GTA	G|0.999;T|0.001	.	alt		0.353	RASA2-201	KNOWN	basic	protein_coding	protein_coding		NM_006506	
WDR43	23160	hgsc.bcm.edu	37	2	29164387	29164387	+	Missense_Mutation	SNP	A	A	G	rs200896154		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:29164387A>G	ENST00000407426.3	+	15	1737	c.1681A>G	c.(1681-1683)Act>Gct	p.T561A		NM_015131.1	NP_055946.1	Q15061	WDR43_HUMAN	WD repeat domain 43	561						nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|kidney(1)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)	20	Acute lymphoblastic leukemia(172;0.155)					CAGAGTCAAAACTTTTCAGAA	0.383																																					p.T561A		Atlas-SNP	.											.	WDR43	38	.	0			c.A1681G						PASS	.	A	ALA/THR	1,3707		0,1,1853	96.0	89.0	91.0		1681	5.5	1.0	2		91	6,8144		0,6,4069	yes	missense	WDR43	NM_015131.1	58	0,7,5922	GG,GA,AA		0.0736,0.027,0.059	possibly-damaging	561/678	29164387	7,11851	1854	4075	5929	SO:0001583	missense	23160	exon15			GTCAAAACTTTTC	D87716	CCDS46251.1	2p23.3	2013-01-09			ENSG00000163811	ENSG00000163811		"""WD repeat domain containing"""	28945	protein-coding gene	gene with protein product	"""UTP5, small subunit (SSU) processome component, homolog (yeast)"""					7584026, 7584028, 17699751	Standard	NM_015131		Approved	KIAA0007, NET12, UTP5	uc002rmo.2	Q15061	OTTHUMG00000152015	ENST00000407426.3:c.1681A>G	2.37:g.29164387A>G	ENSP00000384302:p.Thr561Ala	95.0	0.0	0		102.0	55.0	0.539216	NM_015131	Q15395|Q92577	Missense_Mutation	SNP	ENST00000407426.3	37	CCDS46251.1	.	.	.	.	.	.	.	.	.	.	A	16.06	3.016175	0.54468	2.7E-4	7.36E-4	ENSG00000163811	ENST00000407426	T	0.66460	-0.21	5.51	5.51	0.81932	.	0.171968	0.56097	D	0.000034	T	0.73094	0.3543	L	0.50333	1.59	0.34623	D	0.71884	D	0.63880	0.993	P	0.58928	0.848	T	0.76049	-0.3101	10	0.21014	T	0.42	-17.4972	15.9198	0.79552	1.0:0.0:0.0:0.0	.	561	Q15061	WDR43_HUMAN	A	561	ENSP00000384302:T561A	ENSP00000384302:T561A	T	+	1	0	WDR43	29017891	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	4.032000	0.57274	2.222000	0.72286	0.454000	0.30748	ACT	.	.	weak		0.383	WDR43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324865.1	XM_087089	
RPL3L	6123	hgsc.bcm.edu	37	16	2002960	2002960	+	Missense_Mutation	SNP	C	C	T	rs118144581	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:2002960C>T	ENST00000268661.7	-	3	374	c.280G>A	c.(280-282)Gcc>Acc	p.A94T	RPL3L_ENST00000566484.1_5'Flank	NM_005061.2	NP_005052.1	Q92901	RL3L_HUMAN	ribosomal protein L3-like	94					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|membrane (GO:0016020)|ribosome (GO:0005840)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			NS(1)|endometrium(5)|kidney(2)|large_intestine(2)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	17						CGAGGGGTGGCCACGTAGCCC	0.592													C|||	19	0.00379393	0.0015	0.0058	5008	,	,		17359	0.0		0.0129	False		,,,				2504	0.0				p.A94T		Atlas-SNP	.											.	RPL3L	42	.	0			c.G280A						PASS	.	C	THR/ALA	3,4395	6.2+/-15.9	0,3,2196	72.0	66.0	68.0		280	4.3	1.0	16	dbSNP_132	68	59,8541	37.8+/-93.5	0,59,4241	yes	missense	RPL3L	NM_005061.2	58	0,62,6437	TT,TC,CC		0.686,0.0682,0.477	benign	94/408	2002960	62,12936	2199	4300	6499	SO:0001583	missense	6123	exon3			GGGTGGCCACGTA	U65581	CCDS10450.1	16p13.3	2008-02-05			ENSG00000140986	ENSG00000140986		"""L ribosomal proteins"""	10351	protein-coding gene	gene with protein product						8921388	Standard	NM_005061		Approved		uc002cnh.3	Q92901	OTTHUMG00000128685	ENST00000268661.7:c.280G>A	16.37:g.2002960C>T	ENSP00000268661:p.Ala94Thr	80.0	0.0	0		81.0	50.0	0.617284	NM_005061		Missense_Mutation	SNP	ENST00000268661.7	37	CCDS10450.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	11.69	1.713498	0.30413	6.82E-4	0.00686	ENSG00000140986	ENST00000268661	T	0.21932	1.98	5.28	4.33	0.51752	Translation elongation/initiation factor/Ribosomal, beta-barrel (1);	0.519934	0.20912	N	0.083458	T	0.14485	0.0350	L	0.44542	1.39	0.30156	N	0.802631	B	0.06786	0.001	B	0.06405	0.002	T	0.08086	-1.0739	10	0.72032	D	0.01	-24.4315	12.7616	0.57367	0.0:0.9211:0.0:0.0789	.	94	Q92901	RL3L_HUMAN	T	94	ENSP00000268661:A94T	ENSP00000268661:A94T	A	-	1	0	RPL3L	1942961	1.000000	0.71417	1.000000	0.80357	0.115000	0.19883	1.833000	0.39161	1.238000	0.43771	0.609000	0.83330	GCC	C|0.996;T|0.004	0.004	strong		0.592	RPL3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250582.2	NM_005061	
AKAP9	10142	hgsc.bcm.edu	37	7	91632286	91632286	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:91632286T>G	ENST00000359028.2	+	9	3316	c.3091T>G	c.(3091-3093)Tta>Gta	p.L1031V	AKAP9_ENST00000356239.3_Missense_Mutation_p.L1019V|AKAP9_ENST00000358100.2_Missense_Mutation_p.L1031V			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	1031					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGTAAGCTCTTTATTAGATGG	0.358			T	BRAF	papillary thyroid																																p.L1019V		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.T3055G						PASS	.						84.0	85.0	85.0					7																	91632286		2203	4300	6503	SO:0001583	missense	10142	exon8			AGCTCTTTATTAG	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.3091T>G	7.37:g.91632286T>G	ENSP00000351922:p.Leu1031Val	151.0	0.0	0		134.0	65.0	0.485075	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	T	12.35	1.911886	0.33721	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565	T;T;T	0.03358	3.96;3.96;3.96	5.72	3.2	0.36748	.	0.556233	0.13630	N	0.373796	T	0.05364	0.0142	L	0.54323	1.7	0.09310	N	1	B;P;B;P	0.46220	0.094;0.874;0.152;0.493	B;B;B;B	0.41723	0.039;0.365;0.085;0.085	T	0.32348	-0.9910	10	0.56958	D	0.05	.	8.3792	0.32461	0.0:0.0687:0.1325:0.7988	.	1031;1019;1019;1031	Q99996;Q99996-2;Q99996-3;A4D1E4	AKAP9_HUMAN;.;.;.	V	1019;1031;1031;1031;1031	ENSP00000348573:L1019V;ENSP00000351922:L1031V;ENSP00000350813:L1031V	ENSP00000348573:L1019V	L	+	1	2	AKAP9	91470222	0.000000	0.05858	0.002000	0.10522	0.005000	0.04900	0.085000	0.14912	1.091000	0.41335	0.528000	0.53228	TTA	.	.	none		0.358	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
COG2	22796	hgsc.bcm.edu	37	1	230810858	230810858	+	Silent	SNP	T	T	C	rs113173809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:230810858T>C	ENST00000366669.4	+	9	1129	c.1014T>C	c.(1012-1014)gaT>gaC	p.D338D	COG2_ENST00000535166.1_Silent_p.D222D|COG2_ENST00000366668.3_Silent_p.D338D|COG2_ENST00000534989.1_Silent_p.D279D	NM_001145036.1|NM_007357.2	NP_001138508.1|NP_031383.1	Q14746	COG2_HUMAN	component of oligomeric golgi complex 2	338					Golgi organization (GO:0007030)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	cytosol (GO:0005829)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|Golgi transport complex (GO:0017119)	protein transporter activity (GO:0008565)			NS(1)|cervix(1)|endometrium(1)|large_intestine(6)|lung(11)|prostate(2)|skin(2)|urinary_tract(3)	27	Breast(184;0.0871)|Ovarian(103;0.183)	Prostate(94;0.178)				GGAATCCCGATGCATTTCATG	0.418													T|||	6	0.00119808	0.0	0.0014	5008	,	,		14495	0.0		0.002	False		,,,				2504	0.0031				p.D338D		Atlas-SNP	.											.	COG2	61	.	0			c.T1014C						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	103.0	104.0	103.0		1014,1014	-0.5	0.2	1	dbSNP_132	103	48,8552	31.2+/-83.2	0,48,4252	no	coding-synonymous,coding-synonymous	COG2	NM_001145036.1,NM_007357.2	,	0,52,6451	CC,CT,TT		0.5581,0.0908,0.3998	,	338/738,338/739	230810858	52,12954	2203	4300	6503	SO:0001819	synonymous_variant	22796	exon9			TCCCGATGCATTT	Z34975	CCDS1584.1, CCDS44329.1	1q42.2	2008-02-05	2002-05-28	2002-05-31	ENSG00000135775	ENSG00000135775		"""Components of oligomeric golgi complex"""	6546	protein-coding gene	gene with protein product		606974	"""low density lipoprotein receptor defect C complementing"""	LDLC		7962052	Standard	NM_007357		Approved		uc001htw.3	Q14746	OTTHUMG00000037753	ENST00000366669.4:c.1014T>C	1.37:g.230810858T>C		183.0	0.0	0		184.0	95.0	0.516304	NM_007357	Q86U99	Silent	SNP	ENST00000366669.4	37	CCDS1584.1																																																																																			T|0.997;C|0.003	0.003	strong		0.418	COG2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000092087.1	NM_007357	
ARFGEF1	10565	hgsc.bcm.edu	37	8	68130265	68130265	+	Missense_Mutation	SNP	C	C	A	rs142342517	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:68130265C>A	ENST00000262215.3	-	31	4836	c.4447G>T	c.(4447-4449)Gct>Tct	p.A1483S	ARFGEF1_ENST00000520381.1_Missense_Mutation_p.A937S|ARFGEF1_ENST00000518230.1_Missense_Mutation_p.A321S	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1483					endomembrane system organization (GO:0010256)|exocytosis (GO:0006887)|Golgi organization (GO:0007030)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of Rho GTPase activity (GO:0034259)|positive regulation of GTPase activity (GO:0043547)|positive regulation of protein glycosylation in Golgi (GO:0090284)|positive regulation of wound healing (GO:0090303)|protein transport (GO:0015031)|regulation of ARF protein signal transduction (GO:0032012)|regulation of establishment of cell polarity (GO:2000114)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|small nuclear ribonucleoprotein complex (GO:0030532)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|guanyl-nucleotide exchange factor activity (GO:0005085)|myosin binding (GO:0017022)|protein kinase A regulatory subunit binding (GO:0034237)			breast(1)|endometrium(14)|kidney(4)|large_intestine(17)|lung(20)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Breast(64;0.214)	Lung NSC(129;0.0908)|all_lung(136;0.152)	Epithelial(68;0.0043)|OV - Ovarian serous cystadenocarcinoma(28;0.00578)|all cancers(69;0.0173)|BRCA - Breast invasive adenocarcinoma(89;0.206)			TAGAGCTGAGCAAAAATGTCA	0.373													C|||	8	0.00159744	0.0	0.0014	5008	,	,		11866	0.0		0.007	False		,,,				2504	0.0				p.A1483S		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.G4447T						PASS	.	C	SER/ALA	8,4398	12.9+/-30.5	0,8,2195	108.0	96.0	100.0		4447	4.6	1.0	8	dbSNP_134	100	79,8521	46.3+/-105.2	0,79,4221	yes	missense	ARFGEF1	NM_006421.4	99	0,87,6416	AA,AC,CC		0.9186,0.1816,0.6689	benign	1483/1850	68130265	87,12919	2203	4300	6503	SO:0001583	missense	10565	exon31			GCTGAGCAAAAAT	AF084520	CCDS6199.1	8q13	2011-08-18	2011-08-18		ENSG00000066777	ENSG00000066777			15772	protein-coding gene	gene with protein product		604141				10212200, 8917509	Standard	NM_006421		Approved	DKFZP434L057, BIG1, ARFGEP1, p200	uc003xxo.2	Q9Y6D6	OTTHUMG00000164626	ENST00000262215.3:c.4447G>T	8.37:g.68130265C>A	ENSP00000262215:p.Ala1483Ser	112.0	0.0	0		128.0	62.0	0.484375	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	10.81	1.455699	0.26161	0.001816	0.009186	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518230	T;T;T	0.63913	0.07;-0.07;-0.03	5.48	4.59	0.56863	Armadillo-like helical (1);Armadillo-type fold (1);	0.052243	0.85682	D	0.000000	T	0.39784	0.1091	N	0.25890	0.77	0.44254	D	0.997101	B;B;B	0.12013	0.005;0.0;0.0	B;B;B	0.10450	0.005;0.001;0.002	T	0.34700	-0.9818	10	0.11182	T	0.66	.	15.9776	0.80083	0.136:0.864:0.0:0.0	.	1483;961;937	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	S	937;1483;321	ENSP00000428429:A937S;ENSP00000262215:A1483S;ENSP00000430891:A321S	ENSP00000262215:A1483S	A	-	1	0	ARFGEF1	68292819	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.366000	0.44204	1.427000	0.47276	0.655000	0.94253	GCT	C|0.995;A|0.005	0.005	strong		0.373	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
TTC3	7267	hgsc.bcm.edu	37	21	38538736	38538736	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:38538736T>G	ENST00000399017.2	+	33	6967	c.4220T>G	c.(4219-4221)cTt>cGt	p.L1407R	TTC3_ENST00000479930.1_3'UTR|TTC3_ENST00000355666.1_Missense_Mutation_p.L1407R|TTC3_ENST00000354749.2_Missense_Mutation_p.L1407R	NM_003316.3	NP_003307.3	P53804	TTC3_HUMAN	tetratricopeptide repeat domain 3	1407					negative regulation of cell morphogenesis involved in differentiation (GO:0010771)|negative regulation of neuron differentiation (GO:0045665)|protein K48-linked ubiquitination (GO:0070936)|ubiquitin-dependent protein catabolic process (GO:0006511)	mitochondrion (GO:0005739)|nucleus (GO:0005634)|vacuole (GO:0005773)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(5)|endometrium(7)|kidney(5)|large_intestine(17)|liver(1)|lung(18)|ovary(4)|prostate(2)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(5)	75		Myeloproliferative disorder(46;0.0412)				ACACAGATCCTTGAGGGCTCT	0.438																																					p.L1407R	Ovarian(38;194 1649 35661)	Atlas-SNP	.											.	TTC3	182	.	0			c.T4220G						PASS	.						121.0	114.0	117.0					21																	38538736		2203	4300	6503	SO:0001583	missense	7267	exon33			AGATCCTTGAGGG	D84296	CCDS13651.1	21q22.2	2013-01-11			ENSG00000182670	ENSG00000182670		"""RING-type (C3HC4) zinc fingers"", ""Tetratricopeptide (TTC) repeat domain containing"""	12393	protein-coding gene	gene with protein product		602259				8947847	Standard	NM_003316		Approved	TPRD, TPRDI, DCRR1, TPRDII, TPRDIII, RNF105	uc002yvz.3	P53804	OTTHUMG00000086654	ENST00000399017.2:c.4220T>G	21.37:g.38538736T>G	ENSP00000381981:p.Leu1407Arg	192.0	0.0	0		193.0	90.0	0.466321	NM_001001894	A8K7H7|B2RPA7|D3DSG9|D3DSH2|D3DSH3|O60767|P78476|P78477|Q569I2|Q6P578|Q9UEK4	Missense_Mutation	SNP	ENST00000399017.2	37	CCDS13651.1	.	.	.	.	.	.	.	.	.	.	T	9.860	1.196029	0.22037	.	.	ENSG00000182670	ENST00000355666;ENST00000399017;ENST00000354749	T;T;T	0.08807	3.05;3.05;3.05	4.85	-5.58	0.02512	.	1.732930	0.03051	N	0.154594	T	0.06690	0.0171	L	0.51422	1.61	0.09310	N	1	B;B	0.13145	0.001;0.007	B;B	0.09377	0.004;0.003	T	0.37454	-0.9705	9	.	.	.	0.1757	0.2964	0.00266	0.2464:0.163:0.2518:0.3389	.	465;1407	Q5GIT6;P53804	.;TTC3_HUMAN	R	1407	ENSP00000347889:L1407R;ENSP00000381981:L1407R;ENSP00000346791:L1407R	.	L	+	2	0	TTC3	37460606	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.249000	0.02888	-0.672000	0.05266	-0.290000	0.09829	CTT	.	.	none		0.438	TTC3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194776.1		
PRR5	55615	hgsc.bcm.edu	37	22	45132853	45132853	+	Missense_Mutation	SNP	C	C	T	rs187629442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:45132853C>T	ENST00000336985.6	+	8	1170	c.893C>T	c.(892-894)cCg>cTg	p.P298L	ARHGAP8_ENST00000389773.5_Intron|PRR5-ARHGAP8_ENST00000361473.5_Intron|PRR5_ENST00000403581.1_Missense_Mutation_p.P321L|PRR5_ENST00000006251.7_Missense_Mutation_p.P289L|PRR5-ARHGAP8_ENST00000352766.7_Intron|PRR5_ENST00000477331.1_3'UTR|ARHGAP8_ENST00000517296.3_Intron	NM_181333.3	NP_851850.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	298					cell cycle (GO:0007049)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)	TORC2 complex (GO:0031932)				central_nervous_system(1)|endometrium(2)|lung(6)|prostate(1)|skin(1)	11		all_neural(38;0.00409)|Ovarian(80;0.024)|Glioma(61;0.0647)		UCEC - Uterine corpus endometrioid carcinoma (28;0.168)		TTCTCCGACCCGCCCGGCCAG	0.741													C|||	19	0.00379393	0.0008	0.0086	5008	,	,		12627	0.0		0.0099	False		,,,				2504	0.002				p.P321L		Atlas-SNP	.											.	PRR5	75	.	0			c.C962T						PASS	.	C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO,	7,4311		0,7,2152	10.0	12.0	11.0		866,608,608,962,866,893,	0.9	0.0	22		11	91,8381		0,91,4145	yes	missense,missense,missense,missense,missense,missense,intron	PRR5,PRR5-ARHGAP8	NM_001017528.2,NM_001017529.2,NM_001017530.1,NM_001198721.1,NM_015366.3,NM_181333.3,NM_181334.4	98,98,98,98,98,98,	0,98,6297	TT,TC,CC		1.0741,0.1621,0.7662	,,,,,,	289/380,203/294,203/294,321/412,289/380,298/389,	45132853	98,12692	2159	4236	6395	SO:0001583	missense	55615	exon10			CCGACCCGCCCGG	AF177331	CCDS14058.1, CCDS14059.1, CCDS56232.1, CCDS74875.1	22q13.3	2011-02-10			ENSG00000186654	ENSG00000186654			31682	protein-coding gene	gene with protein product	"""protein observed with Rictor-1"""	609406				15718101, 17599906	Standard	NM_001017528		Approved	PP610, FLJ20185k, Protor-1		P85299	OTTHUMG00000150460	ENST00000336985.6:c.893C>T	22.37:g.45132853C>T	ENSP00000337464:p.Pro298Leu	17.0	0.0	0		9.0	6.0	0.666667	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000336985.6	37	CCDS14058.1	9|9	0.004120879120879121|0.004120879120879121	0|0	0.0|0.0	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	5|5	0.006596306068601583|0.006596306068601583	C|C	4.489|4.489	0.090760|0.090760	0.08632|0.08632	0.001621|0.001621	0.010741|0.010741	ENSG00000186654|ENSG00000186654	ENST00000006251;ENST00000404016;ENST00000403581;ENST00000336985|ENST00000455389	T;T;T|.	0.27557|.	1.68;1.66;1.68|.	4.27|4.27	0.846|0.846	0.18955|0.18955	.|.	.|.	.|.	.|.	.|.	T|T	0.03095|0.03095	0.0091|0.0091	N|N	0.00368|0.00368	-1.59|-1.59	0.09310|0.09310	N|N	1|1	B;B;B;B;B|.	0.02656|.	0.0;0.0;0.0;0.0;0.0|.	B;B;B;B;B|.	0.01281|.	0.0;0.0;0.0;0.0;0.0|.	T|T	0.38045|0.38045	-0.9679|-0.9679	8|5	.|.	.|.	.|.	.|.	1.0823|1.0823	0.01645|0.01645	0.1926:0.4208:0.128:0.2586|0.1926:0.4208:0.128:0.2586	.|.	262;321;197;298;298|.	B1AHF5;B1AHF6;P85299-2;P85299;A8K699|.	.;.;.;PRR5_HUMAN;.|.	L|C	289;262;321;298|258	ENSP00000006251:P289L;ENSP00000384848:P321L;ENSP00000337464:P298L|.	.|.	P|R	+|+	2|1	0|0	PRR5|PRR5	43511517|43511517	0.000000|0.000000	0.05858|0.05858	0.001000|0.001000	0.08648|0.08648	0.040000|0.040000	0.13550|0.13550	0.061000|0.061000	0.14366|0.14366	0.270000|0.270000	0.21984|0.21984	-0.680000|-0.680000	0.03767|0.03767	CCG|CGC	C|0.996;T|0.004	0.004	strong		0.741	PRR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318200.2	NM_001017528	
TTI2	80185	hgsc.bcm.edu	37	8	33361280	33361280	+	Silent	SNP	C	C	T	rs17850186	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:33361280C>T	ENST00000431156.2	-	5	1719	c.1101G>A	c.(1099-1101)ccG>ccA	p.P367P	TTI2_ENST00000519356.1_5'UTR|TTI2_ENST00000360742.5_Silent_p.P367P|TTI2_ENST00000520636.1_Silent_p.P336P	NM_001102401.2	NP_001095871.1	Q6NXR4	TTI2_HUMAN	TELO2 interacting protein 2	367																	TCACGAAAGCCGGCAGGTTTC	0.527													C|||	43	0.00858626	0.0023	0.0058	5008	,	,		17510	0.002		0.0229	False		,,,				2504	0.0112				p.P367P		Atlas-SNP	.											C8orf41,rectum,carcinoma,0,2	.	.	2	0			c.G1101A						PASS	.	C	,	17,4389	24.3+/-50.5	0,17,2186	33.0	31.0	32.0		1101,1101	-8.6	0.2	8	dbSNP_123	32	172,8428	78.4+/-141.0	3,166,4131	no	coding-synonymous,coding-synonymous	TTI2	NM_001102401.1,NM_025115.2	,	3,183,6317	TT,TC,CC		2.0,0.3858,1.4532	,	367/509,367/509	33361280	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	80185	exon5			GAAAGCCGGCAGG	AK026916	CCDS6090.1	8p12	2011-11-10	2011-11-10	2011-09-22		ENSG00000129696			26262	protein-coding gene	gene with protein product		614426	"""chromosome 8 open reading frame 41"", ""Tel2 interacting protein 2 homolog (S. pombe)"""	C8orf41		20801936, 20810650	Standard	NM_025115		Approved	FLJ23263	uc003xjm.5	Q6NXR4		ENST00000431156.2:c.1101G>A	8.37:g.33361280C>T		96.0	0.0	0		51.0	23.0	0.45098	NM_001265581	D3DSV7|Q96IM2|Q9H5N4	Silent	SNP	ENST00000431156.2	37	CCDS6090.1																																																																																			C|0.986;T|0.014	0.014	strong		0.527	TTI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376555.1	NM_025115	
FAM172A	83989	hgsc.bcm.edu	37	5	93410379	93410379	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:93410379A>T	ENST00000395965.3	-	2	220	c.78T>A	c.(76-78)gaT>gaA	p.D26E	FAM172A_ENST00000505869.1_Intron|FAM172A_ENST00000509163.1_Intron|FAM172A_ENST00000504768.2_5'UTR|FAM172A_ENST00000509739.1_5'UTR	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	26						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						TTTCTTTTTCATCTGGACCTC	0.368																																					p.D26E		Atlas-SNP	.											.	FAM172A	38	.	0			c.T78A						PASS	.						145.0	131.0	136.0					5																	93410379		2203	4300	6503	SO:0001583	missense	83989	exon2			TTTTTCATCTGGA		CCDS4069.1, CCDS54879.1, CCDS54880.1	5q15	2008-06-16	2008-06-16	2008-06-16	ENSG00000113391	ENSG00000113391			25365	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 21"""	C5orf21		11230166	Standard	NM_032042		Approved	DKFZP564D172	uc010jbd.3	Q8WUF8	OTTHUMG00000131329	ENST00000395965.3:c.78T>A	5.37:g.93410379A>T	ENSP00000379294:p.Asp26Glu	154.0	0.0	0		143.0	16.0	0.111888	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Missense_Mutation	SNP	ENST00000395965.3	37	CCDS4069.1	.	.	.	.	.	.	.	.	.	.	A	14.71	2.617897	0.46736	.	.	ENSG00000113391	ENST00000395965	T	0.41400	1.0	5.88	5.88	0.94601	.	0.370321	0.31495	N	0.007554	T	0.22666	0.0547	N	0.20685	0.6	0.80722	D	1	B;P	0.43094	0.01;0.799	B;B	0.35278	0.013;0.199	T	0.17107	-1.0380	10	0.02654	T	1	-0.91	13.8025	0.63208	1.0:0.0:0.0:0.0	.	26;26	Q8WUF8;Q8WUF8-2	F172A_HUMAN;.	E	26	ENSP00000379294:D26E	ENSP00000379294:D26E	D	-	3	2	FAM172A	93436135	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.859000	0.55987	2.243000	0.73865	0.533000	0.62120	GAT	.	.	none		0.368	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042	
KIF27	55582	hgsc.bcm.edu	37	9	86518433	86518433	+	Missense_Mutation	SNP	A	A	G	rs144003628		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:86518433A>G	ENST00000297814.2	-	4	1143	c.1000T>C	c.(1000-1002)Tat>Cat	p.Y334H	KIF27_ENST00000334204.2_Missense_Mutation_p.Y334H|KIF27_ENST00000413982.1_Missense_Mutation_p.Y334H	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	334	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|cilium assembly (GO:0042384)|epithelial cilium movement (GO:0003351)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|smoothened signaling pathway (GO:0007224)|ventricular system development (GO:0021591)	cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(7)|lung(17)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	43						CTGTTGGCATATTTGAGAGAA	0.433																																					p.Y334H		Atlas-SNP	.											.	KIF27	103	.	0			c.T1000C						PASS	.						95.0	95.0	95.0					9																	86518433		2203	4300	6503	SO:0001583	missense	55582	exon4			TGGCATATTTGAG	AY237536	CCDS6665.1, CCDS65071.1, CCDS65072.1	9q21.32	2008-03-03			ENSG00000165115	ENSG00000165115		"""Kinesins"""	18632	protein-coding gene	gene with protein product		611253					Standard	NM_017576		Approved	DKFZp434D0917	uc004ana.4	Q86VH2	OTTHUMG00000020109	ENST00000297814.2:c.1000T>C	9.37:g.86518433A>G	ENSP00000297814:p.Tyr334His	149.0	0.0	0		108.0	48.0	0.444444	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Missense_Mutation	SNP	ENST00000297814.2	37	CCDS6665.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.979561	0.74360	.	.	ENSG00000165115	ENST00000297814;ENST00000413982;ENST00000334204	T;T;T	0.81415	-1.49;-1.49;-1.49	5.56	4.44	0.53790	Kinesin, motor domain (3);	0.000000	0.52532	D	0.000072	D	0.93475	0.7918	H	0.99156	4.45	0.40294	D	0.978531	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.91635	0.987;0.998;0.999	D	0.95040	0.8177	10	0.87932	D	0	.	10.909	0.47097	0.9271:0.0:0.0729:0.0	.	334;334;334	Q86VH2-3;Q86VH2-2;Q86VH2	.;.;KIF27_HUMAN	H	334	ENSP00000297814:Y334H;ENSP00000401688:Y334H;ENSP00000333928:Y334H	ENSP00000297814:Y334H	Y	-	1	0	KIF27	85708253	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.531000	0.81973	2.125000	0.65367	0.533000	0.62120	TAT	A|1.000;T|0.000	.	alt		0.433	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
ZMYM4	9202	hgsc.bcm.edu	37	1	35853073	35853073	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:35853073T>A	ENST00000314607.6	+	13	2211	c.2131T>A	c.(2131-2133)Tgt>Agt	p.C711S	ZMYM4_ENST00000373297.2_Missense_Mutation_p.C622S	NM_005095.2	NP_005086.2	Q5VZL5	ZMYM4_HUMAN	zinc finger, MYM-type 4	711					cytoskeleton organization (GO:0007010)|multicellular organismal development (GO:0007275)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(13)|lung(16)|ovary(2)|prostate(3)|skin(2)	54		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GTTTCAGTTCTGTGGCAAGAA	0.299																																					p.C711S		Atlas-SNP	.											.	ZMYM4	143	.	0			c.T2131A						PASS	.						55.0	61.0	59.0					1																	35853073		2203	4300	6503	SO:0001583	missense	9202	exon13			CAGTTCTGTGGCA	AB007885	CCDS389.1	1p34-p32	2013-01-08	2005-12-19	2005-12-19	ENSG00000146463	ENSG00000146463		"""Zinc fingers, MYM type"""	13055	protein-coding gene	gene with protein product		613568	"""zinc finger protein 262"""	ZNF262		10449923	Standard	NM_005095		Approved	KIAA0425, ZNF198L3, MYM	uc001byt.3	Q5VZL5	OTTHUMG00000004241	ENST00000314607.6:c.2131T>A	1.37:g.35853073T>A	ENSP00000322915:p.Cys711Ser	110.0	0.0	0		82.0	4.0	0.0487805	NM_005095	A0JP19|A0JP20|O43308|Q5T5E1|Q5T5E2|Q7L3Q4	Missense_Mutation	SNP	ENST00000314607.6	37	CCDS389.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.9|20.9	4.064116|4.064116	0.76187|0.76187	.|.	.|.	ENSG00000146463|ENSG00000146463	ENST00000314607;ENST00000373297|ENST00000457946	T;T|.	0.39787|.	1.16;1.06|.	5.36|5.36	5.36|5.36	0.76844|0.76844	TRASH (1);Zinc finger, MYM-type (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.75324|0.75324	0.3834|0.3834	M|M	0.79258|0.79258	2.445|2.445	0.54753|0.54753	D|D	0.999988|0.999988	D|.	0.71674|.	0.998|.	D|.	0.79784|.	0.993|.	T|T	0.76955|0.76955	-0.2767|-0.2767	10|5	0.66056|.	D|.	0.02|.	-8.763|-8.763	14.5294|14.5294	0.67915|0.67915	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	711|.	Q5VZL5|.	ZMYM4_HUMAN|.	S|Q	711;622|370	ENSP00000322915:C711S;ENSP00000362394:C622S|.	ENSP00000322915:C711S|.	C|L	+|+	1|2	0|0	ZMYM4|ZMYM4	35625660|35625660	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	5.706000|5.706000	0.68362|0.68362	2.021000|2.021000	0.59480|0.59480	0.533000|0.533000	0.62120|0.62120	TGT|CTG	.	.	none		0.299	ZMYM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012207.3	NM_005095	
WDR90	197335	hgsc.bcm.edu	37	16	711429	711429	+	Missense_Mutation	SNP	C	C	T	rs199527716	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:711429C>T	ENST00000293879.4	+	30	3601	c.3601C>T	c.(3601-3603)Ctc>Ttc	p.L1201F	WDR90_ENST00000549091.1_Missense_Mutation_p.L1201F			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1201										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CTGCCAGCATCTCATTTTCCC	0.642													C|||	4	0.000798722	0.0	0.0	5008	,	,		15642	0.0		0.003	False		,,,				2504	0.001				p.L1201F		Atlas-SNP	.											.	WDR90	107	.	0			c.C3601T						PASS	.	C	PHE/LEU	2,4106		0,2,2052	44.0	51.0	48.0		3601	2.3	0.0	16		48	33,8345		0,33,4156	yes	missense	WDR90	NM_145294.4	22	0,35,6208	TT,TC,CC		0.3939,0.0487,0.2803	probably-damaging	1201/1749	711429	35,12451	2054	4189	6243	SO:0001583	missense	197335	exon30			CAGCATCTCATTT	AB067511	CCDS42092.1	16p13.3	2013-01-09			ENSG00000161996	ENSG00000161996		"""WD repeat domain containing"""	26960	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 17"", ""chromosome 16 open reading frame 15"", ""chromosome 16 open reading frame 16"", ""chromosome 16 open reading frame 19"", ""chromosome 16 open reading frame 18"""	C16orf17, C16orf15, C16orf16, C16orf19, C16orf18		11572484, 11157797	Standard	XM_005255160		Approved	FLJ36483, KIAA1924	uc002cii.1	Q96KV7	OTTHUMG00000048040	ENST00000293879.4:c.3601C>T	16.37:g.711429C>T	ENSP00000293879:p.Leu1201Phe	82.0	0.0	0		70.0	38.0	0.542857	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	12.40	1.927260	0.34002	4.87E-4	0.003939	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.29917	1.55;3.54	5.51	2.27	0.28462	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.521846	0.19207	N	0.120035	T	0.33702	0.0872	M	0.67953	2.075	0.09310	N	0.999991	D;D	0.56035	0.974;0.964	P;P	0.49140	0.601;0.504	T	0.20042	-1.0287	10	0.56958	D	0.05	.	3.7409	0.08530	0.1417:0.3854:0.3779:0.0949	.	1201;1201	F8VUX9;Q96KV7	.;WDR90_HUMAN	F	1201	ENSP00000448122:L1201F;ENSP00000293879:L1201F	ENSP00000293879:L1201F	L	+	1	0	WDR90	651430	0.002000	0.14202	0.002000	0.10522	0.026000	0.11368	1.451000	0.35145	0.647000	0.30713	0.555000	0.69702	CTC	C|0.998;T|0.002	0.002	strong		0.642	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
GGA2	23062	hgsc.bcm.edu	37	16	23504719	23504719	+	Missense_Mutation	SNP	G	G	C	rs143003037		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:23504719G>C	ENST00000309859.4	-	4	395	c.313C>G	c.(313-315)Cgt>Ggt	p.R105G	GGA2_ENST00000567468.1_Missense_Mutation_p.R105G	NM_015044.4	NP_055859.1	Q9UJY4	GGA2_HUMAN	golgi-associated, gamma adaptin ear containing, ARF binding protein 2	105	VHS. {ECO:0000255|PROSITE- ProRule:PRU00218}.				intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	clathrin adaptor complex (GO:0030131)|clathrin-coated vesicle (GO:0030136)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)	21				GBM - Glioblastoma multiforme(48;0.0386)		TTCAGGAAACGAAATTTGGCC	0.552																																					p.R105G		Atlas-SNP	.											GGA2,mucosal,malignant_melanoma,0,3	GGA2	49	3	0			c.C313G						PASS	.	G	GLY/ARG	0,4394		0,0,2197	183.0	135.0	151.0		313	5.6	1.0	16	dbSNP_134	151	4,8596	3.7+/-12.6	0,4,4296	no	missense	GGA2	NM_015044.4	125	0,4,6493	CC,CG,GG		0.0465,0.0,0.0308	probably-damaging	105/614	23504719	4,12990	2197	4300	6497	SO:0001583	missense	23062	exon4			GGAAACGAAATTT	AF190863	CCDS10611.1	16p12	2010-02-12	2010-02-12		ENSG00000103365	ENSG00000103365			16064	protein-coding gene	gene with protein product		606005				10747088, 10749927	Standard	NM_015044		Approved	VEAR, KIAA1080	uc002dlq.3	Q9UJY4	OTTHUMG00000096957	ENST00000309859.4:c.313C>G	16.37:g.23504719G>C	ENSP00000311962:p.Arg105Gly	76.0	0.0	0		85.0	34.0	0.4	NM_015044	D3DWF0|O14564|Q9NYN2|Q9UPS2	Missense_Mutation	SNP	ENST00000309859.4	37	CCDS10611.1	.	.	.	.	.	.	.	.	.	.	G	24.7	4.556060	0.86231	0.0	4.65E-4	ENSG00000103365	ENST00000309859	T	0.23348	1.91	5.58	5.58	0.84498	VHS subgroup (1);ENTH/VHS (2);VHS (2);	0.000000	0.85682	D	0.000000	T	0.56124	0.1964	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.60657	-0.7220	10	0.72032	D	0.01	-16.2173	17.0743	0.86582	0.0:0.0:1.0:0.0	.	105	Q9UJY4	GGA2_HUMAN	G	105	ENSP00000311962:R105G	ENSP00000311962:R105G	R	-	1	0	GGA2	23412220	1.000000	0.71417	1.000000	0.80357	0.572000	0.35998	6.105000	0.71505	2.638000	0.89438	0.448000	0.29417	CGT	G|1.000;C|0.000	0.000	weak		0.552	GGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214019.1		
VPS13B	157680	hgsc.bcm.edu	37	8	100454804	100454804	+	Missense_Mutation	SNP	A	A	G	rs61759485	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:100454804A>G	ENST00000358544.2	+	23	3497	c.3386A>G	c.(3385-3387)aAg>aGg	p.K1129R	VPS13B_ENST00000357162.2_Missense_Mutation_p.K1129R|VPS13B_ENST00000395996.1_Missense_Mutation_p.K1129R	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1129					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			GCTGGGCACAAGTATATGGAA	0.398													A|||	7	0.00139776	0.0	0.0058	5008	,	,		17905	0.0		0.003	False		,,,				2504	0.0				p.K1129R	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.A3386G						PASS	.	A	ARG/LYS,ARG/LYS	16,4390	24.3+/-50.5	0,16,2187	100.0	96.0	97.0		3386,3386	3.3	0.9	8	dbSNP_129	97	35,8565	22.8+/-68.1	0,35,4265	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	26,26	0,51,6452	GG,GA,AA		0.407,0.3631,0.3921	probably-damaging,probably-damaging	1129/4023,1129/3998	100454804	51,12955	2203	4300	6503	SO:0001583	missense	157680	exon23			GGCACAAGTATAT	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3386A>G	8.37:g.100454804A>G	ENSP00000351346:p.Lys1129Arg	134.0	0.0	0		150.0	75.0	0.5	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	7	0.003205128205128205	0	0.0	4	0.011049723756906077	0	0.0	3	0.00395778364116095	A	19.74	3.883056	0.72410	0.003631	0.00407	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.25912	1.77;1.77;1.77	5.71	3.34	0.38264	.	0.105634	0.64402	N	0.000012	T	0.32852	0.0843	L	0.49350	1.555	0.41967	D	0.990735	D;D;B;D	0.76494	0.999;0.998;0.125;0.989	D;D;B;D	0.78314	0.991;0.937;0.028;0.967	T	0.05321	-1.0892	10	0.51188	T	0.08	.	10.0017	0.41933	0.8633:0.0:0.1367:0.0	rs61759485	1128;1129;1129;1129	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	R	1129	ENSP00000349685:K1129R;ENSP00000351346:K1129R;ENSP00000379318:K1129R	ENSP00000349685:K1129R	K	+	2	0	VPS13B	100523980	1.000000	0.71417	0.933000	0.37362	0.815000	0.46073	4.769000	0.62300	0.447000	0.26695	-0.326000	0.08463	AAG	A|0.996;G|0.004	0.004	strong		0.398	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
OXCT1	5019	hgsc.bcm.edu	37	5	41862819	41862819	+	Missense_Mutation	SNP	G	G	A	rs76956231	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:41862819G>A	ENST00000196371.5	-	2	272	c.112C>T	c.(112-114)Cgc>Tgc	p.R38C		NM_000436.3	NP_000427.1	P55809	SCOT1_HUMAN	3-oxoacid CoA transferase 1	38					adipose tissue development (GO:0060612)|brain development (GO:0007420)|cellular ketone body metabolic process (GO:0046950)|cellular lipid metabolic process (GO:0044255)|cellular response to acid chemical (GO:0071229)|cellular response to glucose stimulus (GO:0071333)|heart development (GO:0007507)|ketone body catabolic process (GO:0046952)|ketone catabolic process (GO:0042182)|positive regulation of insulin secretion (GO:0032024)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hormone (GO:0009725)|response to nutrient (GO:0007584)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-oxoacid CoA-transferase activity (GO:0008260)|protein homodimerization activity (GO:0042803)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(1)|skin(2)	28					Succinic acid(DB00139)	TTGGTATGGCGATGAGCACTG	0.378													G|||	15	0.00299521	0.0008	0.0029	5008	,	,		14176	0.0		0.0099	False		,,,				2504	0.002				p.R38C		Atlas-SNP	.											OXCT1,NS,carcinoma,+1,1	OXCT1	54	1	0			c.C112T						PASS	.	G	CYS/ARG	4,4402	8.1+/-20.4	0,4,2199	120.0	107.0	112.0		112	3.8	0.0	5	dbSNP_132	112	83,8517	47.6+/-106.9	0,83,4217	yes	missense	OXCT1	NM_000436.3	180	0,87,6416	AA,AG,GG		0.9651,0.0908,0.6689	possibly-damaging	38/521	41862819	87,12919	2203	4300	6503	SO:0001583	missense	5019	exon2			TATGGCGATGAGC	U62961	CCDS3937.1	5p13	2008-02-05		2004-05-12	ENSG00000083720	ENSG00000083720			8527	protein-coding gene	gene with protein product		601424	"""3-oxoacid CoA transferase"""	OXCT		8751852	Standard	NM_000436		Approved	SCOT	uc003jmn.3	P55809	OTTHUMG00000094783	ENST00000196371.5:c.112C>T	5.37:g.41862819G>A	ENSP00000196371:p.Arg38Cys	160.0	0.0	0		125.0	61.0	0.488	NM_000436	B2R5V2|B7Z528	Missense_Mutation	SNP	ENST00000196371.5	37	CCDS3937.1	10	0.004578754578754579	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	11.72	1.723995	0.30593	9.08E-4	0.009651	ENSG00000083720	ENST00000196371	D	0.86164	-2.08	5.56	3.8	0.43715	.	0.298519	0.35495	N	0.003180	T	0.67411	0.2890	N	0.08118	0	0.21473	N	0.999674	B	0.09022	0.002	B	0.08055	0.003	T	0.60949	-0.7161	10	0.44086	T	0.13	0.7598	11.4381	0.50081	0.1494:0.0:0.8506:0.0	.	38	P55809	SCOT1_HUMAN	C	38	ENSP00000196371:R38C	ENSP00000196371:R38C	R	-	1	0	OXCT1	41898576	0.439000	0.25610	0.027000	0.17364	0.805000	0.45488	3.805000	0.55575	0.725000	0.32318	-0.216000	0.12614	CGC	G|0.994;A|0.006	0.006	strong		0.378	OXCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211594.2	NM_000436	
APOL3	80833	hgsc.bcm.edu	37	22	36537871	36537871	+	Missense_Mutation	SNP	C	C	T	rs140252051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:36537871C>T	ENST00000349314.2	-	3	623	c.586G>A	c.(586-588)Gct>Act	p.A196T	APOL3_ENST00000487423.1_5'UTR|APOL3_ENST00000361710.2_5'UTR|APOL3_ENST00000397293.2_Missense_Mutation_p.A125T|APOL3_ENST00000397287.2_5'UTR|APOL3_ENST00000424878.2_5'UTR	NM_145640.2	NP_663615.1	O95236	APOL3_HUMAN	apolipoprotein L, 3	196					inflammatory response (GO:0006954)|lipoprotein metabolic process (GO:0042157)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	lipid binding (GO:0008289)|lipid transporter activity (GO:0005319)|signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(1)|lung(1)|stomach(1)	5						CCAGAGGCAGCGCCAGTGGAG	0.562													C|||	5	0.000998403	0.0015	0.0014	5008	,	,		21116	0.0		0.002	False		,,,				2504	0.0				p.A196T		Atlas-SNP	.											APOL3_ENST00000349314,caecum,carcinoma,0,4	APOL3	60	4	0			c.G586A						PASS	.	C	THR/ALA,,	8,4398	14.3+/-33.2	0,8,2195	93.0	85.0	88.0		586,,	-0.3	0.0	22	dbSNP_134	88	44,8556	29.0+/-79.6	0,44,4256	yes	missense,utr-5,utr-5	APOL3	NM_145640.2,NM_145641.2,NM_145642.2	58,,	0,52,6451	TT,TC,CC		0.5116,0.1816,0.3998	benign,,	196/403,,	36537871	52,12954	2203	4300	6503	SO:0001583	missense	80833	exon3			AGGCAGCGCCAGT	AF305227	CCDS13922.1, CCDS13924.1	22q13.1	2013-01-24			ENSG00000128284	ENSG00000128284		"""Apolipoproteins"""	14868	protein-coding gene	gene with protein product		607253				11374903	Standard	NM_145640		Approved	CG12-1, APOLIII	uc003aot.3	O95236	OTTHUMG00000150632	ENST00000349314.2:c.586G>A	22.37:g.36537871C>T	ENSP00000344577:p.Ala196Thr	119.0	0.0	0		121.0	64.0	0.528926	NM_145640	B1AHI4|B1AHI5|Q5U5N4|Q9BQ82|Q9BQA3	Missense_Mutation	SNP	ENST00000349314.2	37	CCDS13922.1	5	0.0022893772893772895	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	9.409	1.080032	0.20309	0.001816	0.005116	ENSG00000128284	ENST00000397293;ENST00000349314	T;T	0.04156	3.69;3.69	4.3	-0.295	0.12828	.	0.919146	0.09404	N	0.806779	T	0.01558	0.0050	N	0.02708	-0.52	0.09310	N	0.999997	D;D	0.57571	0.98;0.975	P;B	0.44897	0.463;0.236	T	0.46275	-0.9203	10	0.16420	T	0.52	.	7.5658	0.27879	0.0:0.5334:0.0:0.4666	.	196;125	O95236;O95236-2	APOL3_HUMAN;.	T	125;196	ENSP00000380461:A125T;ENSP00000344577:A196T	ENSP00000344577:A196T	A	-	1	0	APOL3	34867817	0.000000	0.05858	0.000000	0.03702	0.050000	0.14768	-2.685000	0.00834	-0.030000	0.13804	-0.556000	0.04195	GCT	C|0.997;T|0.003	0.003	strong		0.562	APOL3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319268.1	NM_145641	
SLC38A8	146167	hgsc.bcm.edu	37	16	84063130	84063130	+	Missense_Mutation	SNP	C	C	G	rs11862366	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:84063130C>G	ENST00000299709.3	-	5	658	c.659G>C	c.(658-660)aGt>aCt	p.S220T		NM_001080442.1	NP_001073911.1	A6NNN8	S38A8_HUMAN	solute carrier family 38, member 8	220			S -> T (in dbSNP:rs11862366).		amino acid transport (GO:0006865)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(12)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	26						GGGGAAGACACTGAACACAGA	0.522													C|||	279	0.0557109	0.171	0.0144	5008	,	,		18537	0.0		0.0189	False		,,,				2504	0.0245				p.S220T		Atlas-SNP	.											.	SLC38A8	60	.	0			c.G659C						PASS	.	C	THR/SER	624,3776	270.7+/-269.8	34,556,1610	93.0	89.0	91.0		659	4.1	0.7	16	dbSNP_120	91	174,8426	78.4+/-141.0	4,166,4130	yes	missense	SLC38A8	NM_001080442.1	58	38,722,5740	GG,GC,CC		2.0233,14.1818,6.1385	benign	220/436	84063130	798,12202	2200	4300	6500	SO:0001583	missense	146167	exon5			AAGACACTGAACA		CCDS32495.1	16q23.3	2013-05-22				ENSG00000166558		"""Solute carriers"""	32434	protein-coding gene	gene with protein product		615585					Standard	XM_006721135		Approved		uc002fhg.1	A6NNN8		ENST00000299709.3:c.659G>C	16.37:g.84063130C>G	ENSP00000299709:p.Ser220Thr	74.0	0.0	0		84.0	45.0	0.535714	NM_001080442		Missense_Mutation	SNP	ENST00000299709.3	37	CCDS32495.1	113	0.051739926739926737	92	0.18699186991869918	4	0.011049723756906077	0	0.0	17	0.022427440633245383	C	13.96	2.394329	0.42410	0.141818	0.020233	ENSG00000166558	ENST00000299709	T	0.02177	4.41	5.25	4.07	0.47477	.	0.087359	0.85682	D	0.000000	T	0.00012	0.0000	M	0.76002	2.32	0.20975	P	0.999818287	P	0.42620	0.785	B	0.43508	0.422	T	0.53251	-0.8465	9	0.28530	T	0.3	.	12.3155	0.54953	0.0:0.8818:0.0:0.1182	rs11862366	220	A6NNN8	S38A8_HUMAN	T	220	ENSP00000299709:S220T	ENSP00000299709:S220T	S	-	2	0	SLC38A8	82620631	0.263000	0.24083	0.730000	0.30809	0.806000	0.45545	0.840000	0.27600	2.621000	0.88768	0.643000	0.83706	AGT	C|0.939;G|0.061	0.061	strong		0.522	SLC38A8-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432623.1	NM_001080442	
RIMS1	22999	hgsc.bcm.edu	37	6	72892796	72892796	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:72892796C>T	ENST00000521978.1	+	6	1622	c.1622C>T	c.(1621-1623)cCc>cTc	p.P541L	RIMS1_ENST00000522291.1_Missense_Mutation_p.P541L|RIMS1_ENST00000264839.7_Missense_Mutation_p.P541L|RIMS1_ENST00000348717.5_Missense_Mutation_p.P541L|RIMS1_ENST00000520567.1_Missense_Mutation_p.P541L|RIMS1_ENST00000517960.1_Missense_Mutation_p.P541L|RIMS1_ENST00000518273.1_Missense_Mutation_p.P541L|RIMS1_ENST00000491071.2_Missense_Mutation_p.P541L	NM_014989.5	NP_055804.2	Q86UR5	RIMS1_HUMAN	regulating synaptic membrane exocytosis 1	541					calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|glutamate secretion (GO:0014047)|intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|neurotransmitter secretion (GO:0007269)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)|protein complex assembly (GO:0006461)|regulated secretory pathway (GO:0045055)|regulation of catalytic activity (GO:0050790)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neurotransmitter secretion (GO:0046928)|response to stimulus (GO:0050896)|secretion (GO:0046903)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)|visual perception (GO:0007601)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)|small GTPase regulator activity (GO:0005083)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(25)|liver(4)|lung(35)|ovary(9)|pancreas(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	102		all_epithelial(107;0.179)|all_hematologic(105;0.212)				GTGTCGACGCCCGAGTACACC	0.682																																					p.P541L		Atlas-SNP	.											RIMS1,caecum,carcinoma,0,1	RIMS1	278	1	0			c.C1622T						scavenged	.						9.0	10.0	10.0					6																	72892796		1995	4142	6137	SO:0001583	missense	22999	exon6			CGACGCCCGAGTA	AB002338	CCDS47449.1, CCDS55029.1, CCDS55030.1, CCDS55031.1, CCDS55032.1, CCDS55033.1	6q12-q13	2008-10-16	2002-06-12	2002-06-14	ENSG00000079841	ENSG00000079841			17282	protein-coding gene	gene with protein product	"""Rab3-interacting molecule"""	606629	"""RAB3 interacting protein 2"""	RAB3IP2, CORD7		9205841, 11438518	Standard	NM_001168407		Approved	RIM, KIAA0340, RIM1	uc003pga.4	Q86UR5	OTTHUMG00000015009	ENST00000521978.1:c.1622C>T	6.37:g.72892796C>T	ENSP00000428417:p.Pro541Leu	73.0	0.0	0		56.0	3.0	0.0535714	NM_014989	A7MBN6|B7Z2M0|B7Z2Q9|B7Z3S3|B7Z6S2|E7EX08|E9PCB7|E9PCZ1|E9PF48|E9PHF5|E9PHR1|O15048|Q5JY21|Q5JY25|Q5SZK1|Q8TDY9|Q8TDZ5|Q9HBA1|Q9HBA2|Q9HBA3|Q9HBA4|Q9HBA5|Q9HBA6	Missense_Mutation	SNP	ENST00000521978.1	37	CCDS47449.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.088952	0.76756	.	.	ENSG00000079841	ENST00000491071;ENST00000350827;ENST00000352008;ENST00000348717;ENST00000349908;ENST00000346609;ENST00000264839;ENST00000517960;ENST00000518273;ENST00000520567;ENST00000522291;ENST00000521978	T;T;T;T;T;T;T;T	0.30714	1.57;1.72;1.63;1.73;1.65;1.67;1.74;1.52	4.05	3.16	0.36331	.	0.200172	0.34110	N	0.004245	T	0.43166	0.1235	M	0.72894	2.215	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.91635	0.94;0.966;0.999	T	0.49978	-0.8881	10	0.87932	D	0	-4.1408	13.4986	0.61440	0.0:0.8416:0.1584:0.0	.	541;541;541	E9PHR1;C9JNW6;Q86UR5	.;.;RIMS1_HUMAN	L	541	ENSP00000430101:P541L;ENSP00000275037:P541L;ENSP00000264839:P541L;ENSP00000429959:P541L;ENSP00000430408:P541L;ENSP00000430502:P541L;ENSP00000430932:P541L;ENSP00000428417:P541L	ENSP00000264839:P541L	P	+	2	0	RIMS1	72949517	1.000000	0.71417	0.681000	0.30009	0.907000	0.53573	7.468000	0.80943	0.657000	0.30906	-0.519000	0.04390	CCC	.	.	none		0.682	RIMS1-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374968.1		
UROC1	131669	hgsc.bcm.edu	37	3	126207049	126207049	+	Silent	SNP	G	G	A	rs139120643	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:126207049G>A	ENST00000290868.2	-	18	1835	c.1782C>T	c.(1780-1782)ggC>ggT	p.G594G	UROC1_ENST00000383579.3_Silent_p.G654G	NM_144639.2	NP_653240.1	Q96N76	HUTU_HUMAN	urocanate hydratase 1	594					cellular nitrogen compound metabolic process (GO:0034641)|histidine catabolic process (GO:0006548)|histidine catabolic process to glutamate and formamide (GO:0019556)|histidine catabolic process to glutamate and formate (GO:0019557)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	urocanate hydratase activity (GO:0016153)	p.G594G(1)		endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(27)|ovary(1)|skin(1)	39				GBM - Glioblastoma multiforme(114;0.17)		ACCAGCCCACGCCCCCTCCGT	0.602													G|||	3	0.000599042	0.0	0.0014	5008	,	,		19645	0.0		0.001	False		,,,				2504	0.001				p.G654G		Atlas-SNP	.											UROC1,NS,carcinoma,0,1	UROC1	150	1	1	Substitution - coding silent(1)	lung(1)	c.C1962T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	166.0	159.0	161.0		1962,1782	-3.2	1.0	3	dbSNP_134	161	19,8581	14.0+/-48.4	0,19,4281	no	coding-synonymous,coding-synonymous	UROC1	NM_001165974.1,NM_144639.2	,	0,24,6479	AA,AG,GG		0.2209,0.1135,0.1845	,	654/737,594/677	126207049	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	131669	exon19			GCCCACGCCCCCT	AK055862	CCDS3038.1, CCDS54636.1	3q21.2	2012-08-21	2012-08-21		ENSG00000159650	ENSG00000159650	4.2.1.49		26444	protein-coding gene	gene with protein product	"""urocanase 1"""	613012	"""urocanase domain containing 1"""			19304569	Standard	NM_144639		Approved	FLJ31300, HMFN0320	uc010hsi.2	Q96N76	OTTHUMG00000162753	ENST00000290868.2:c.1782C>T	3.37:g.126207049G>A		114.0	0.0	0		136.0	71.0	0.522059	NM_001165974	E9PE13|Q14C64|Q68CJ7	Silent	SNP	ENST00000290868.2	37	CCDS3038.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	UROC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370325.2	NM_144639	
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139397707G>A	ENST00000277541.6	-	27	5169	c.5094C>T	c.(5092-5094)gaC>gaT	p.D1698D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1698					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1699D(11)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATGCGGCCACGTCGGTGGCAC	0.632			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2772	0.553514	0.5552	0.5115	5008	,	,		17626	0.9018		0.4046	False		,,,				2504	0.3753				p.D1698D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	11	Substitution - coding silent(11)	haematopoietic_and_lymphoid_tissue(11)	c.C5094T						PASS	.	G		2208,2062		587,1034,514	57.0	67.0	64.0		5094	-4.9	0.8	9	dbSNP_52	64	3010,5508		545,1920,1794	no	coding-synonymous	NOTCH1	NM_017617.3		1132,2954,2308	AA,AG,GG		35.3369,48.2904,40.8039		1698/2556	139397707	5218,7570	2135	4259	6394	SO:0001819	synonymous_variant	4851	exon27			GGCCACGTCGGTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5094C>T	9.37:g.139397707G>A		82.0	0.0	0		87.0	35.0	0.402299	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.466;A|0.534	0.534	strong		0.632	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
CFAP46	54777	hgsc.bcm.edu	37	10	134649709	134649709	+	Missense_Mutation	SNP	C	C	T	rs76581191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:134649709C>T	ENST00000368586.5	-	46	6650	c.6550G>A	c.(6550-6552)Ggc>Agc	p.G2184S	TTC40_ENST00000263170.5_Missense_Mutation_p.G345S	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TAGGCAGCGCCGTACAGACGG	0.647													c|||	33	0.00658946	0.0015	0.0043	5008	,	,		11914	0.0		0.0129	False		,,,				2504	0.0153				p.G2184S		Atlas-SNP	.											TTC40,NS,carcinoma,0,2	TTC40	100	2	0			c.G6550A						PASS	.		SER/GLY	11,4391	16.8+/-37.8	0,11,2190	76.0	58.0	64.0		1486	0.1	0.0	10	dbSNP_131	64	145,8453	70.7+/-133.2	0,145,4154	yes	missense	C10orf92	NM_001200049.1	56	0,156,6344	TT,TC,CC		1.6864,0.2499,1.2	benign	496/1028	134649709	156,12844	2201	4299	6500	SO:0001583	missense	54777	exon46			CAGCGCCGTACAG																												ENST00000368586.5:c.6550G>A	10.37:g.134649709C>T	ENSP00000357575:p.Gly2184Ser	64.0	0.0	0		85.0	55.0	0.647059	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	c	4.026	0.002278	0.07819	0.002499	0.016864	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.25912	2.01;1.77	4.17	0.0804	0.14420	.	0.210433	0.27535	N	0.018933	T	0.06005	0.0156	N	0.25647	0.755	0.09310	N	0.999999	B	0.24132	0.098	B	0.15870	0.014	T	0.11966	-1.0566	10	0.40728	T	0.16	.	3.0641	0.06209	0.1917:0.4861:0.0:0.3222	.	345	Q8IYW2	CJ092_HUMAN	S	2184;345	ENSP00000357575:G2184S;ENSP00000263170:G345S	ENSP00000263170:G345S	G	-	1	0	C10orf93	134499699	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-0.167000	0.09940	0.040000	0.15660	-0.251000	0.11542	GGC	C|0.990;T|0.010	0.010	strong		0.647	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
LILRA6	79168	hgsc.bcm.edu	37	19	54745682	54745682	+	Missense_Mutation	SNP	C	C	T	rs111666280	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:54745682C>T	ENST00000396365.2	-	4	467	c.428G>A	c.(427-429)cGa>cAa	p.R143Q	LILRB3_ENST00000407860.2_Intron|LILRA6_ENST00000391735.3_Missense_Mutation_p.R143Q|LILRA6_ENST00000419410.2_Missense_Mutation_p.R143Q|LILRA6_ENST00000270464.5_Missense_Mutation_p.R143Q|LILRA6_ENST00000440558.2_Missense_Mutation_p.R143Q|LILRA6_ENST00000245621.5_Missense_Mutation_p.R143Q	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	143					immune system process (GO:0002376)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(20)|ovary(3)|skin(2)|urinary_tract(2)	38	all_cancers(19;0.00723)|all_epithelial(19;0.00389)|all_lung(19;0.0175)|Lung NSC(19;0.0325)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		TGAGCCACATCGGAGGGTCAT	0.567																																					p.R143Q		Atlas-SNP	.											.	LILRA6	75	.	0			c.G428A						PASS	.						29.0	50.0	43.0					19																	54745682		2122	4289	6411	SO:0001583	missense	79168	exon4			CCACATCGGAGGG	AF041262	CCDS42610.1	19q13.4	2013-01-11	2005-05-17	2005-05-17	ENSG00000244482	ENSG00000244482		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15495	protein-coding gene	gene with protein product			"""leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 6"""	LILRB6		10941842	Standard	NM_024318		Approved	ILT8, CD85b		Q6PI73	OTTHUMG00000066635	ENST00000396365.2:c.428G>A	19.37:g.54745682C>T	ENSP00000379651:p.Arg143Gln	719.0	0.0	0		768.0	101.0	0.13151	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	.	.	.	.	.	.	.	.	.	.	C	0.554	-0.848058	0.02651	.	.	ENSG00000244482	ENST00000440558;ENST00000270464;ENST00000419410;ENST00000391735;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T;T;T	0.12774	2.65;2.65;2.65;4.09;2.65;2.65	3.38	-6.77	0.01727	Immunoglobulin-like fold (1);	0.513077	0.18054	N	0.153187	T	0.02047	0.0064	N	0.01640	-0.785	0.09310	N	1	B;B;B;B;B;B	0.33000	0.046;0.003;0.332;0.049;0.046;0.393	B;B;B;B;B;B	0.32342	0.008;0.002;0.144;0.015;0.015;0.014	T	0.37454	-0.9705	10	0.02654	T	1	.	0.493	0.00567	0.2783:0.2174:0.3072:0.1971	.	143;143;143;143;143;143	C9JFH3;Q6PI73-2;Q6PI73;F8WCY4;D3YTC4;F8W6G6	.;.;LIRA6_HUMAN;.;.;.	Q	143	ENSP00000390120:R143Q;ENSP00000270464:R143Q;ENSP00000411227:R143Q;ENSP00000375615:R143Q;ENSP00000379651:R143Q;ENSP00000245621:R143Q	ENSP00000245621:R143Q	R	-	2	0	LILRA6	59437494	0.000000	0.05858	0.001000	0.08648	0.096000	0.18686	-1.554000	0.02172	-1.307000	0.02321	0.162000	0.16502	CGA	C|0.904;T|0.096	0.096	strong		0.567	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
CDC27	996	hgsc.bcm.edu	37	17	45216115	45216115	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:45216115T>A	ENST00000066544.3	-	13	1787	c.1694A>T	c.(1693-1695)aAt>aTt	p.N565I	CDC27_ENST00000446365.2_Missense_Mutation_p.N504I|CDC27_ENST00000531206.1_Missense_Mutation_p.N571I|CDC27_ENST00000527547.1_Missense_Mutation_p.N564I	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	565					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.N565I(1)|p.N571I(1)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						CTCTGGCGAATTTTTATCCAT	0.353																																					p.N571I		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	2	Substitution - Missense(2)	ovary(2)	c.A1712T						scavenged	.						50.0	55.0	54.0					17																	45216115		2201	4299	6500	SO:0001583	missense	996	exon13			GGCGAATTTTTAT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.1694A>T	17.37:g.45216115T>A	ENSP00000066544:p.Asn565Ile	45.0	1.0	0.0222222		33.0	2.0	0.0606061	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.271461	0.80469	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.40225	1.04;1.04;1.04;1.04	5.62	5.62	0.85841	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.041764	0.85682	D	0.000000	T	0.53997	0.1831	L	0.58810	1.83	0.58432	D	0.999999	D;P;D;P	0.57257	0.979;0.952;0.978;0.914	P;P;P;B	0.56788	0.806;0.546;0.645;0.36	T	0.52019	-0.8631	10	0.37606	T	0.19	-4.6177	13.77	0.63019	0.0:0.0:0.0:1.0	.	504;564;571;565	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	I	565;571;504;564	ENSP00000066544:N565I;ENSP00000434614:N571I;ENSP00000392802:N504I;ENSP00000437339:N564I	ENSP00000066544:N565I	N	-	2	0	CDC27	42571114	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	3.893000	0.56243	2.141000	0.66446	0.528000	0.53228	AAT	.	.	none		0.353	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
LTBP1	4052	hgsc.bcm.edu	37	2	33540307	33540307	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:33540307C>T	ENST00000404816.2	+	24	4054	c.3701C>T	c.(3700-3702)tCa>tTa	p.S1234L	LTBP1_ENST00000390003.4_Missense_Mutation_p.S909L|LTBP1_ENST00000404525.1_Missense_Mutation_p.S855L|LTBP1_ENST00000418533.2_Missense_Mutation_p.S908L|LTBP1_ENST00000402934.1_Missense_Mutation_p.S855L|LTBP1_ENST00000407925.1_Missense_Mutation_p.S908L|LTBP1_ENST00000272273.5_Missense_Mutation_p.S174L|LTBP1_ENST00000354476.3_Missense_Mutation_p.S1235L			Q14766	LTBP1_HUMAN	latent transforming growth factor beta binding protein 1	1234	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				extracellular matrix organization (GO:0030198)|sequestering of TGFbeta in extracellular matrix (GO:0035583)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|transforming growth factor beta binding (GO:0050431)|transforming growth factor beta-activated receptor activity (GO:0005024)			breast(2)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(13)|lung(60)|ovary(4)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(3)	108	all_hematologic(175;0.115)	Medulloblastoma(90;0.215)				CAGGGTTTCTCAATCTCTGCA	0.433																																					p.S1234L		Atlas-SNP	.											.	LTBP1	317	.	0			c.C3701T						PASS	.						115.0	102.0	107.0					2																	33540307		2203	4300	6503	SO:0001583	missense	4052	exon24			GTTTCTCAATCTC		CCDS33177.1, CCDS33178.1, CCDS33177.2, CCDS33178.2, CCDS54344.1, CCDS54345.1	2p22-p21	2008-05-23			ENSG00000049323	ENSG00000049323		"""Latent transforming growth factor, beta binding proteins"""	6714	protein-coding gene	gene with protein product	"""TGF-beta1-BP-1"""	150390				2350783, 11104663	Standard	NM_206943		Approved		uc021vft.1	Q14766	OTTHUMG00000152118	ENST00000404816.2:c.3701C>T	2.37:g.33540307C>T	ENSP00000386043:p.Ser1234Leu	118.0	0.0	0		129.0	21.0	0.162791	NM_206943	A1L3V1|P22064|Q53SD8|Q53SF3|Q53SG1|Q59HF7|Q8TD95	Missense_Mutation	SNP	ENST00000404816.2	37	CCDS33177.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	20.2|20.2	3.943601|3.943601	0.73672|0.73672	.|.	.|.	ENSG00000049323|ENSG00000049323	ENST00000415140|ENST00000404816;ENST00000354476;ENST00000390003;ENST00000418533;ENST00000402934;ENST00000404525;ENST00000407925;ENST00000272273;ENST00000422669	.|D;D;D;D;D;D;D;D;D	.|0.86865	.|-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18;-2.18	4.98|4.98	4.98|4.98	0.66077|0.66077	.|EGF-like region, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	.|.	.|.	.|.	.|.	.|D	.|0.85885	.|0.5801	L|L	0.38531|0.38531	1.155|1.155	0.40185|0.40185	D|D	0.977332|0.977332	.|B;B;P;B;P;P;P	.|0.41624	.|0.005;0.343;0.757;0.078;0.746;0.58;0.47	.|B;B;B;B;P;B;B	.|0.45610	.|0.027;0.392;0.293;0.087;0.487;0.407;0.341	.|D	.|0.86865	.|0.2032	.|9	.|0.46703	.|T	.|0.11	.|.	18.2782|18.2782	0.90089|0.90089	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|174;1234;908;855;908;909;1235	.|E7EUU6;Q14766;E7EV71;Q14766-3;Q14766-2;Q14766-5;Q14766-4	.|.;LTBP1_HUMAN;.;.;.;.;.	X|L	196|1234;1235;909;908;855;855;908;174;112	.|ENSP00000386043:S1234L;ENSP00000346467:S1235L;ENSP00000374653:S909L;ENSP00000393057:S908L;ENSP00000384373:S855L;ENSP00000385359:S855L;ENSP00000384091:S908L;ENSP00000272273:S174L;ENSP00000395211:S112L	.|ENSP00000272273:S174L	Q|S	+|+	1|2	0|0	LTBP1|LTBP1	33393811|33393811	1.000000|1.000000	0.71417|0.71417	0.984000|0.984000	0.44739|0.44739	0.886000|0.886000	0.51366|0.51366	5.677000|5.677000	0.68142|0.68142	2.295000|2.295000	0.77249|0.77249	0.655000|0.655000	0.94253|0.94253	CAA|TCA	.	.	none		0.433	LTBP1-014	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326227.2	NM_206943	
C14orf37	145407	hgsc.bcm.edu	37	14	58604730	58604730	+	Silent	SNP	T	T	C	rs137871178	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:58604730T>C	ENST00000267485.7	-	2	1541	c.1347A>G	c.(1345-1347)caA>caG	p.Q449Q	C14orf37_ENST00000334342.5_5'UTR	NM_001001872.2	NP_001001872.2	Q86TY3	CN037_HUMAN	chromosome 14 open reading frame 37	449						integral component of membrane (GO:0016021)		p.Q449Q(1)		breast(7)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(16)|pancreas(1)|skin(1)	33						TTCCCAACAGTTGGTCTGCCT	0.343													T|||	22	0.00439297	0.0	0.0043	5008	,	,		18899	0.001		0.0109	False		,,,				2504	0.0072				p.Q449Q		Atlas-SNP	.											C14orf37,NS,carcinoma,0,1	C14orf37	87	1	1	Substitution - coding silent(1)	pancreas(1)	c.A1347G						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	71.0	73.0	73.0		1347	-7.0	0.0	14	dbSNP_134	73	101,8499	54.8+/-115.7	1,99,4200	no	coding-synonymous	C14orf37	NM_001001872.2		1,102,6400	CC,CT,TT		1.1744,0.0681,0.7996		449/775	58604730	104,12902	2203	4300	6503	SO:0001819	synonymous_variant	145407	exon2			CAACAGTTGGTCT		CCDS32089.1	14q23.1	2012-09-03			ENSG00000139971	ENSG00000139971			19846	protein-coding gene	gene with protein product							Standard	NM_001001872		Approved		uc001xdc.3	Q86TY3	OTTHUMG00000171173	ENST00000267485.7:c.1347A>G	14.37:g.58604730T>C		64.0	0.0	0		68.0	36.0	0.529412	NM_001001872	A8K8Z8|Q6P5Q1|Q86TY1	Silent	SNP	ENST00000267485.7	37	CCDS32089.1																																																																																			T|0.992;C|0.008	0.008	strong		0.343	C14orf37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412059.1	NM_001001872	
TMC8	147138	hgsc.bcm.edu	37	17	76130576	76130576	+	Silent	SNP	C	C	T	rs149203228		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:76130576C>T	ENST00000318430.5	+	8	1292	c.918C>T	c.(916-918)aaC>aaT	p.N306N	TMC8_ENST00000589691.1_Silent_p.N83N|TMC6_ENST00000322914.3_5'Flank	NM_152468.4	NP_689681.2	Q8IU68	TMC8_HUMAN	transmembrane channel-like 8	306			N -> I (in dbSNP:rs7208422). {ECO:0000269|Ref.3}.		ion transport (GO:0006811)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|regulation of cell growth (GO:0001558)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|zinc ion homeostasis (GO:0055069)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	receptor binding (GO:0005102)	p.N306N(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	12			BRCA - Breast invasive adenocarcinoma(99;0.00269)|Lung(188;0.0973)|OV - Ovarian serous cystadenocarcinoma(97;0.192)			ACGTACTCAACGGGCTCCTGG	0.612													C|||	1	0.000199681	0.0	0.0	5008	,	,		17681	0.0		0.001	False		,,,				2504	0.0				p.N306N		Atlas-SNP	.											TMC8,NS,carcinoma,0,1	TMC8	44	1	1	Substitution - coding silent(1)	lung(1)	c.C918T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	51.0	56.0	54.0		918	-6.5	0.5	17	dbSNP_134	54	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	TMC8	NM_152468.4		0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153		306/727	76130576	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	147138	exon8			ACTCAACGGGCTC	AY057380	CCDS32749.1	17q25.3	2014-09-17	2005-11-10	2005-11-10	ENSG00000167895	ENSG00000167895			20474	protein-coding gene	gene with protein product		605829	"""epidermodysplasia verruciformis 2"""	EVER2		12426567	Standard	NM_152468		Approved	EVIN2	uc002jup.2	Q8IU68		ENST00000318430.5:c.918C>T	17.37:g.76130576C>T		82.0	0.0	0		87.0	42.0	0.482759	NM_152468	Q2YDC0|Q8IWU7|Q8N358|Q8NF04	Silent	SNP	ENST00000318430.5	37	CCDS32749.1																																																																																			C|0.998;T|0.002	0.002	strong		0.612	TMC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436900.3		
MELK	9833	hgsc.bcm.edu	37	9	36597284	36597284	+	Silent	SNP	C	C	G	rs139481227	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:36597284C>G	ENST00000298048.2	+	6	655	c.471C>G	c.(469-471)ccC>ccG	p.P157P	MELK_ENST00000487398.1_3'UTR|MELK_ENST00000541717.1_Silent_p.P157P|MELK_ENST00000545008.1_Intron|MELK_ENST00000536860.1_Silent_p.P109P|MELK_ENST00000538311.1_5'UTR|MELK_ENST00000536329.1_Silent_p.P86P|MELK_ENST00000536987.1_Silent_p.P26P|MELK_ENST00000543751.1_Silent_p.P125P	NM_014791.3	NP_055606.1	Q14680	MELK_HUMAN	maternal embryonic leucine zipper kinase	157	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|G2/M transition of mitotic cell cycle (GO:0000086)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|neural precursor cell proliferation (GO:0061351)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)	cell cortex (GO:0005938)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|lipid binding (GO:0008289)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(6)|ovary(4)|skin(2)|upper_aerodigestive_tract(2)	29		Acute lymphoblastic leukemia(2;1.09e-08)|all_hematologic(2;8.15e-06)	STAD - Stomach adenocarcinoma(86;0.228)			GTGCAAAACCCAAGGTAAGTG	0.318																																					p.P157P	Ovarian(82;980 1317 7225 14391 18624)	Atlas-SNP	.											.	MELK	74	.	0			c.C471G						PASS	.	C		0,4406		0,0,2203	105.0	109.0	108.0		471	1.4	1.0	9	dbSNP_134	108	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	MELK	NM_014791.2		0,6,6497	GG,GC,CC		0.0698,0.0,0.0461		157/652	36597284	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	9833	exon6			AAAACCCAAGGTA	D79997	CCDS6606.1, CCDS59123.1, CCDS59124.1, CCDS59125.1, CCDS59126.1, CCDS59127.1, CCDS59128.1	9p13.1	2008-02-05			ENSG00000165304	ENSG00000165304			16870	protein-coding gene	gene with protein product		607025				8724849, 9136115	Standard	NM_001256689		Approved	KIAA0175	uc003zzn.4	Q14680	OTTHUMG00000019906	ENST00000298048.2:c.471C>G	9.37:g.36597284C>G		69.0	0.0	0		69.0	35.0	0.507246	NM_014791	A6P3A7|A6P3A8|B1AMQ6|B7Z1E6|B7Z5M5|B7Z6Q7|B7Z6R8|B7Z6Y0|B7Z7Q1|D3DRP8|F5H0Y0|F5H2R4|F5H689|Q7L3C3	Silent	SNP	ENST00000298048.2	37	CCDS6606.1																																																																																			C|0.999;G|0.001	0.001	strong		0.318	MELK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052428.3	NM_014791	
CEMIP	57214	hgsc.bcm.edu	37	15	81173354	81173354	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:81173354A>G	ENST00000394685.3	+	6	913	c.494A>G	c.(493-495)aAc>aGc	p.N165S	KIAA1199_ENST00000356249.5_Missense_Mutation_p.N165S|KIAA1199_ENST00000220244.3_Missense_Mutation_p.N165S			Q8WUJ3	CEMIP_HUMAN		165	G8. {ECO:0000255|PROSITE- ProRule:PRU00817}.				hyaluronan catabolic process (GO:0030214)|positive regulation of cell migration (GO:0030335)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of protein kinase C activity (GO:1900020)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|sensory perception of sound (GO:0007605)	clathrin-coated vesicle membrane (GO:0030665)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	clathrin heavy chain binding (GO:0032050)|ER retention sequence binding (GO:0046923)|hyaluronic acid binding (GO:0005540)|hyalurononglucosaminidase activity (GO:0004415)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(14)|ovary(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	49						ACATTTCTGAACAAGACCCTT	0.488																																					p.N165S		Atlas-SNP	.											.	KIAA1199	118	.	0			c.A494G						PASS	.						131.0	126.0	128.0					15																	81173354		2203	4300	6503	SO:0001583	missense	57214	exon5			TTCTGAACAAGAC																												ENST00000394685.3:c.494A>G	15.37:g.81173354A>G	ENSP00000378177:p.Asn165Ser	195.0	0.0	0		187.0	78.0	0.417112	NM_018689	Q6L9J5|Q9H1K5|Q9NPN9|Q9ULM1	Missense_Mutation	SNP	ENST00000394685.3	37	CCDS10315.1	.	.	.	.	.	.	.	.	.	.	A	7.211	0.595402	0.13875	.	.	ENSG00000103888	ENST00000220244;ENST00000394685;ENST00000356249;ENST00000394683	D;D;D	0.88509	-2.39;-2.39;-2.39	5.95	-0.988	0.10245	G8 domain (2);	0.111999	0.56097	N	0.000025	T	0.79191	0.4404	L	0.46157	1.445	0.41440	D	0.987918	B	0.02656	0.0	B	0.12156	0.007	T	0.61705	-0.7008	10	0.07813	T	0.8	-42.3377	6.5765	0.22569	0.6185:0.1162:0.2653:0.0	.	165	Q8WUJ3	K1199_HUMAN	S	165	ENSP00000220244:N165S;ENSP00000378177:N165S;ENSP00000348583:N165S	ENSP00000220244:N165S	N	+	2	0	KIAA1199	78960409	1.000000	0.71417	0.778000	0.31720	0.594000	0.36715	3.502000	0.53332	-0.411000	0.07530	0.533000	0.62120	AAC	.	.	none		0.488	KIAA1199-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291389.1		
USP25	29761	hgsc.bcm.edu	37	21	17236674	17236674	+	Missense_Mutation	SNP	G	G	C	rs142929561	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:17236674G>C	ENST00000285679.6	+	19	2794	c.2425G>C	c.(2425-2427)Gtc>Ctc	p.V809L	USP25_ENST00000351097.5_Intron|USP25_ENST00000400183.2_Missense_Mutation_p.V879L|USP25_ENST00000285681.2_Missense_Mutation_p.V841L	NM_013396.3	NP_037528.3	Q9UHP3	UBP25_HUMAN	ubiquitin specific peptidase 25	809					cellular protein modification process (GO:0006464)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|proteolysis (GO:0006508)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	peptidase activity (GO:0008233)|SUMO binding (GO:0032183)|ubiquitin-specific protease activity (GO:0004843)			breast(4)|endometrium(6)|kidney(2)|large_intestine(13)|liver(5)|lung(14)|ovary(4)|prostate(1)|skin(1)|urinary_tract(2)	52				Epithelial(23;7.55e-05)|all cancers(11;0.000429)|COAD - Colon adenocarcinoma(22;0.00543)|OV - Ovarian serous cystadenocarcinoma(11;0.00743)|Colorectal(24;0.0116)|Lung(58;0.0853)|LUSC - Lung squamous cell carcinoma(23;0.0889)		TCATGTAGTGGTCTACTTTAT	0.363													G|||	6	0.00119808	0.0	0.0029	5008	,	,		13115	0.0		0.004	False		,,,				2504	0.0				p.V809L		Atlas-SNP	.											USP25,NS,carcinoma,-1,1	USP25	156	1	0			c.G2425C						PASS	.	G	LEU/VAL	3,4403	6.2+/-15.9	0,3,2200	82.0	78.0	80.0		2425	5.6	1.0	21	dbSNP_134	80	6,8594	5.0+/-18.6	0,6,4294	yes	missense	USP25	NM_013396.3	32	0,9,6494	CC,CG,GG		0.0698,0.0681,0.0692	benign	809/1056	17236674	9,12997	2203	4300	6503	SO:0001583	missense	29761	exon19			GTAGTGGTCTACT	AF170562	CCDS33515.1, CCDS63336.1, CCDS63337.1	21q11.2	2011-02-24	2005-08-08		ENSG00000155313	ENSG00000155313		"""Ubiquitin-specific peptidases"""	12624	protein-coding gene	gene with protein product		604736	"""ubiquitin specific protease 25"""			12838346, 10612803	Standard	NM_013396		Approved	USP21	uc002yjy.1	Q9UHP3	OTTHUMG00000074343	ENST00000285679.6:c.2425G>C	21.37:g.17236674G>C	ENSP00000285679:p.Val809Leu	42.0	0.0	0		73.0	26.0	0.356164	NM_013396	C0LSZ0|Q6DHZ9|Q9H9W1	Missense_Mutation	SNP	ENST00000285679.6	37	CCDS33515.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	G|G	21.6|21.6	4.175610|4.175610	0.78564|0.78564	6.81E-4|6.81E-4	6.98E-4|6.98E-4	ENSG00000155313|ENSG00000155313	ENST00000285681;ENST00000285679;ENST00000400183|ENST00000449491	T;T;T|.	0.33438|.	1.54;1.7;1.41|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.053961|.	0.64402|.	D|.	0.000001|.	T|T	0.68183|0.68183	0.2973|0.2973	M|M	0.62723|0.62723	1.935|1.935	0.50813|0.50813	D|D	0.999893|0.999893	D;P;B|.	0.55172|.	0.97;0.83;0.214|.	P;B;B|.	0.53224|.	0.721;0.202;0.055|.	T|T	0.68394|0.68394	-0.5420|-0.5420	10|5	0.72032|.	D|.	0.01|.	.|.	20.0114|20.0114	0.97452|0.97452	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	879;841;809|.	Q9UHP3-3;Q9UHP3-1;Q9UHP3|.	.;.;UBP25_HUMAN|.	L|C	841;809;879|107	ENSP00000285681:V841L;ENSP00000285679:V809L;ENSP00000383044:V879L|.	ENSP00000285679:V809L|.	V|W	+|+	1|3	0|0	USP25|USP25	16158545|16158545	1.000000|1.000000	0.71417|0.71417	0.995000|0.995000	0.50966|0.50966	0.987000|0.987000	0.75469|0.75469	6.352000|6.352000	0.73027|0.73027	2.795000|2.795000	0.96236|0.96236	0.655000|0.655000	0.94253|0.94253	GTC|TGG	G|0.999;C|0.001	0.001	strong		0.363	USP25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157964.1		
SPAG16	79582	hgsc.bcm.edu	37	2	214354811	214354811	+	Missense_Mutation	SNP	G	G	A	rs61752199	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:214354811G>A	ENST00000331683.5	+	10	1162	c.1067G>A	c.(1066-1068)aGc>aAc	p.S356N	SPAG16_ENST00000374309.3_Missense_Mutation_p.S262N	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	356					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		CTTCCAGTGAGCTGGTAGGAT	0.318													G|||	62	0.0123802	0.0053	0.0058	5008	,	,		16436	0.004		0.0159	False		,,,				2504	0.0317				p.S356N		Atlas-SNP	.											.	SPAG16	134	.	0			c.G1067A						PASS	.	G	ASN/SER	33,4369	38.4+/-70.7	0,33,2168	51.0	55.0	54.0		1067	5.0	1.0	2	dbSNP_129	54	154,8440	72.9+/-135.5	2,150,4145	yes	missense	SPAG16	NM_024532.3	46	2,183,6313	AA,AG,GG		1.7919,0.7497,1.4389	probably-damaging	356/632	214354811	187,12809	2201	4297	6498	SO:0001583	missense	79582	exon10			CAGTGAGCTGGTA	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.1067G>A	2.37:g.214354811G>A	ENSP00000332592:p.Ser356Asn	279.0	0.0	0		251.0	119.0	0.474104	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	24	0.01098901098901099	6	0.012195121951219513	3	0.008287292817679558	2	0.0034965034965034965	13	0.017150395778364115	G	17.80	3.477248	0.63849	0.007497	0.017919	ENSG00000144451	ENST00000331683;ENST00000374309;ENST00000451561	T;T;T	0.59364	0.27;0.27;0.27	5.93	5.03	0.67393	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.106321	0.64402	D	0.000016	T	0.57695	0.2071	M	0.72894	2.215	0.34970	D	0.753049	P;D;P;P	0.89917	0.951;1.0;0.599;0.872	P;D;P;P	0.87578	0.636;0.998;0.574;0.636	T	0.73145	-0.4075	10	0.22109	T	0.4	.	12.9132	0.58190	0.0:0.1628:0.8372:0.0	rs61752199	262;207;296;356	B4DYB5;Q8N0X2-2;Q4G1A2;Q8N0X2	.;.;.;SPG16_HUMAN	N	356;262;42	ENSP00000332592:S356N;ENSP00000363428:S262N;ENSP00000416600:S42N	ENSP00000332592:S356N	S	+	2	0	SPAG16	214063056	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	2.442000	0.44873	1.454000	0.47793	0.555000	0.69702	AGC	G|0.984;A|0.016	0.016	strong		0.318	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
IGIP	492311	hgsc.bcm.edu	37	5	139508064	139508064	+	Start_Codon_SNP	SNP	G	G	A	rs141663065	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:139508064G>A	ENST00000333305.3	+	1	2544	c.3G>A	c.(1-3)atG>atA	p.M1I		NM_001007189.1	NP_001007190.1	A6NJ69	IGIP_HUMAN	IgA-inducing protein	1						extracellular region (GO:0005576)											TATTAAATATGTGCAGTTATT	0.378													G|||	2	0.000399361	0.0	0.0	5008	,	,		18171	0.0		0.002	False		,,,				2504	0.0				p.M1I		Atlas-SNP	.											.	.	.	.	0			c.G3A						PASS	.	G	ILE/MET	4,4402	8.1+/-20.4	0,4,2199	114.0	105.0	108.0		3	4.2	1.0	5	dbSNP_134	108	16,8584	11.9+/-42.8	0,16,4284	yes	missense	IGIP	NM_001007189.1	10	0,20,6483	AA,AG,GG		0.186,0.0908,0.1538	benign	1/54	139508064	20,12986	2203	4300	6503	SO:0001582	initiator_codon_variant	492311	exon1			AAATATGTGCAGT	AB073888, BC017422, BC041380	CCDS34244.1	5q31	2013-08-06	2013-08-06	2011-09-22	ENSG00000182700	ENSG00000182700			33847	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 53"", ""IgA-inducing protein homolog (Bos taurus)"""	C5orf53		19201837, 12874223, 21074276	Standard	NM_001007189		Approved	LOC492311	uc003lfb.1	A6NJ69	OTTHUMG00000163359	ENST00000333305.3:c.3G>A	5.37:g.139508064G>A	ENSP00000327344:p.Met1Ile	104.0	0.0	0		78.0	31.0	0.397436	NM_001007189		Missense_Mutation	SNP	ENST00000333305.3	37	CCDS34244.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	5.979	0.364590	0.11296	9.08E-4	0.00186	ENSG00000182700	ENST00000333305	.	.	.	5.28	4.18	0.49190	.	0.136380	0.33875	N	0.004466	T	0.44808	0.1311	.	.	.	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48937	-0.8990	8	0.87932	D	0	-1.909	6.7874	0.23682	0.1523:0.0:0.8477:0.0	.	1	A6NJ69	IGIP_HUMAN	I	1	.	ENSP00000327344:M1I	M	+	3	0	C5orf53	139488248	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.200000	0.51051	2.648000	0.89879	0.650000	0.86243	ATG	G|0.999;A|0.001	0.001	strong		0.378	IGIP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372850.1	NM_001007189	Missense_Mutation
ANK2	287	hgsc.bcm.edu	37	4	114274519	114274519	+	Missense_Mutation	SNP	G	G	A	rs138842207	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:114274519G>A	ENST00000357077.4	+	38	4798	c.4745G>A	c.(4744-4746)cGg>cAg	p.R1582Q	ANK2_ENST00000510275.2_Intron|ANK2_ENST00000394537.3_Intron|ANK2_ENST00000264366.6_Missense_Mutation_p.R1549Q|ANK2_ENST00000509550.1_Intron|ANK2_ENST00000506722.1_Intron	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	1582					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CAGAGCTCTCGGTCTGAGAGA	0.408													G|||	2	0.000399361	0.0	0.0	5008	,	,		21338	0.0		0.002	False		,,,				2504	0.0				p.R1582Q		Atlas-SNP	.											ANK2,rectum,carcinoma,+1,1	ANK2	576	1	0			c.G4745A						PASS	.	G	,GLN/ARG,	0,4406		0,0,2203	82.0	88.0	86.0		,4745,	0.9	0.0	4	dbSNP_134	86	11,8589	9.1+/-34.3	0,11,4289	yes	intron,missense,intron	ANK2	NM_001127493.1,NM_001148.4,NM_020977.3	,43,	0,11,6492	AA,AG,GG		0.1279,0.0,0.0846	,benign,	,1582/3958,	114274519	11,12995	2203	4300	6503	SO:0001583	missense	287	exon38			GCTCTCGGTCTGA	M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.4745G>A	4.37:g.114274519G>A	ENSP00000349588:p.Arg1582Gln	195.0	0.0	0		211.0	101.0	0.478673	NM_001148	Q01485|Q08AC7|Q08AC8|Q7Z3L5	Missense_Mutation	SNP	ENST00000357077.4	37	CCDS3702.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	0	-2.736183	0.00088	0.0	0.001279	ENSG00000145362	ENST00000503423;ENST00000504454;ENST00000357077;ENST00000264366	T;T;T;T	0.65364	0.08;-0.02;-0.11;-0.15	4.9	0.954	0.19595	.	1.073890	0.07232	N	0.862650	T	0.28732	0.0712	N	0.02539	-0.55	0.19575	N	0.999967	B;B	0.10296	0.001;0.003	B;B	0.06405	0.001;0.002	T	0.22661	-1.0210	10	0.11182	T	0.66	.	1.566	0.02605	0.549:0.1302:0.1777:0.143	.	1549;1582	Q01484;Q01484-4	ANK2_HUMAN;.	Q	1495;1597;1582;1549	ENSP00000421011:R1495Q;ENSP00000424722:R1597Q;ENSP00000349588:R1582Q;ENSP00000264366:R1549Q	ENSP00000264366:R1549Q	R	+	2	0	ANK2	114493968	0.622000	0.27085	0.017000	0.16124	0.013000	0.08279	0.864000	0.27926	0.340000	0.23745	0.557000	0.71058	CGG	G|0.999;A|0.001	0.001	strong		0.408	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2	NM_001148	
SLC12A3	6559	hgsc.bcm.edu	37	16	56928555	56928555	+	Splice_Site	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:56928555G>A	ENST00000563236.1	+	22	2658		c.e22+1		SLC12A3_ENST00000438926.2_Splice_Site|SLC12A3_ENST00000566786.1_Splice_Site|SLC12A3_ENST00000262502.5_Splice_Site			P55017	S12A3_HUMAN	solute carrier family 12 (sodium/chloride transporter), member 3						chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium:chloride symporter activity (GO:0015378)|transporter activity (GO:0005215)			breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(28)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	50					Bendroflumethiazide(DB00436)|Benzthiazide(DB00562)|Chlorothiazide(DB00880)|Diazoxide(DB01119)|Hydrochlorothiazide(DB00999)|Metolazone(DB00524)|Polythiazide(DB01324)|Quinethazone(DB01325)	AGAGAAAGGCGTAAGTGTGGA	0.577																																					.		Atlas-SNP	.											.	SLC12A3	99	.	0			c.2633+1G>A	GRCh37	CD077781|CS066650|CS076679	SLC12A3	D|S		PASS	.						111.0	82.0	92.0					16																	56928555		2198	4300	6498	SO:0001630	splice_region_variant	6559	exon22			AAAGGCGTAAGTG		CCDS10770.1, CCDS45491.1, CCDS58464.1	16q13	2013-07-18	2013-07-18		ENSG00000070915	ENSG00000070915		"""Solute carriers"""	10912	protein-coding gene	gene with protein product		600968				8812482	Standard	NM_000339		Approved	NCCT	uc002ekd.4	P55017	OTTHUMG00000133284	ENST00000563236.1:c.2633+1G>A	16.37:g.56928555G>A		108.0	0.0	0		110.0	56.0	0.509091	NM_001126108	A8MSJ2|C9JNN9	Splice_Site	SNP	ENST00000563236.1	37	CCDS58464.1	.	.	.	.	.	.	.	.	.	.	G	13.07	2.126969	0.37533	.	.	ENSG00000070915	ENST00000438926;ENST00000262502	.	.	.	4.76	4.76	0.60689	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.6949	0.85333	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SLC12A3	55486056	1.000000	0.71417	1.000000	0.80357	0.110000	0.19582	7.659000	0.83766	2.350000	0.79820	0.561000	0.74099	.	.	.	none		0.577	SLC12A3-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432337.1		Intron
HUWE1	10075	hgsc.bcm.edu	37	X	53654402	53654402	+	Missense_Mutation	SNP	T	T	C	rs41307640	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:53654402T>C	ENST00000342160.3	-	16	1905	c.1448A>G	c.(1447-1449)aAt>aGt	p.N483S	HUWE1_ENST00000218328.8_Missense_Mutation_p.N483S|HUWE1_ENST00000262854.6_Missense_Mutation_p.N483S			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	483			N -> S (in dbSNP:rs41307640).		base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						TTGTGTAGTATTGGGTCTCTG	0.368													t|||	34	0.00900662	0.003	0.0173	3775	,	,		10299	0.0		0.0179	False		,,,				2504	0.0				p.N483S		Atlas-SNP	.											.	HUWE1	724	.	0			c.A1448G						PASS	.		SER/ASN	15,3820		0,12,3,1620,568	191.0	160.0	171.0		1448	3.1	1.0	X	dbSNP_127	171	185,6543		4,127,50,2297,1822	yes	missense	HUWE1	NM_031407.4	46	4,139,53,3917,2390	CC,CT,C,TT,T		2.7497,0.3911,1.8934	benign	483/4375	53654402	200,10363	2203	4300	6503	SO:0001583	missense	10075	exon17			GTAGTATTGGGTC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.1448A>G	X.37:g.53654402T>C	ENSP00000340648:p.Asn483Ser	252.0	0.0	0		136.0	136.0	1	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Missense_Mutation	SNP	ENST00000342160.3	37	CCDS35301.1	22	0.013261000602772756	2	0.0040650406504065045	4	0.0111731843575419	0	0.0	11	0.014627659574468085	t	0.090	-1.169288	0.01660	0.003911	0.027497	ENSG00000086758	ENST00000342160;ENST00000262854;ENST00000218328;ENST00000396323	T;T;T	0.42900	0.96;0.96;0.96	4.89	3.09	0.35607	E3 ubiquitin ligase, domain of unknown function DUF913 (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.291697	0.30979	N	0.008486	T	0.04724	0.0128	N	0.02960	-0.455	0.21697	N	0.999585	B	0.06786	0.001	B	0.06405	0.002	T	0.29579	-1.0007	10	0.02654	T	1	.	7.9684	0.30113	0.0:0.4667:0.4405:0.0928	rs41307640;rs61752441	483	Q7Z6Z7	HUWE1_HUMAN	S	483;483;483;109	ENSP00000340648:N483S;ENSP00000262854:N483S;ENSP00000218328:N483S	ENSP00000218328:N483S	N	-	2	0	HUWE1	53671127	1.000000	0.71417	0.999000	0.59377	0.739000	0.42172	0.945000	0.29056	0.327000	0.23409	-1.244000	0.01528	AAT	T|0.984;C|0.016	0.016	strong		0.368	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
MET	4233	hgsc.bcm.edu	37	7	116339282	116339282	+	Silent	SNP	G	G	A	rs11762213	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:116339282G>A	ENST00000318493.6	+	2	331	c.144G>A	c.(142-144)gcG>gcA	p.A48A	MET_ENST00000436117.2_Silent_p.A48A|MET_ENST00000397752.3_Silent_p.A48A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	SAP. {ECO:0000255|PROSITE- ProRule:PRU00186}.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			ACTTCACCGCGGAAACACCCA	0.433			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	77	0.0153754	0.0023	0.0346	5008	,	,		21839	0.0		0.0398	False		,,,				2504	0.0102				p.A48A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,adenocarcinoma,+1,2	MET	412	2	0			c.G144A						PASS	.	G	,	42,3886		0,42,1922	100.0	99.0	99.0		144,144	-11.8	0.0	7	dbSNP_120	99	391,7915		6,379,3768	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	6,421,5690	AA,AG,GG		4.7074,1.0692,3.5393	,	48/1391,48/1409	116339282	433,11801	1964	4153	6117	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CACCGCGGAAACA	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.144G>A	7.37:g.116339282G>A		159.0	0.0	0		174.0	98.0	0.563218	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.974;A|0.026	0.026	strong		0.433	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
ACTN1	87	hgsc.bcm.edu	37	14	69341653	69341653	+	Missense_Mutation	SNP	T	T	A	rs11557769	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:69341653T>A	ENST00000193403.6	-	21	2985	c.2602A>T	c.(2602-2604)Acc>Tcc	p.T868S	ACTN1_ENST00000438964.2_Missense_Mutation_p.T863S|ACTN1_ENST00000376839.3_Missense_Mutation_p.T798S|ACTN1_ENST00000538545.2_Missense_Mutation_p.T906S|ACTN1_ENST00000394419.4_Missense_Mutation_p.T890S	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	868			T -> S (in dbSNP:rs11557769).		actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		TCGGGGCCGGTGTAGGGGGCC	0.662													t|||	31	0.0061901	0.0	0.0159	5008	,	,		14509	0.0		0.0189	False		,,,				2504	0.001				p.T890S		Atlas-SNP	.											ACTN1,NS,carcinoma,+2,1	ACTN1	77	1	0			c.A2668T						scavenged	.	T	SER/THR,SER/THR,SER/THR	16,4390	25.3+/-52.1	0,16,2187	42.0	41.0	41.0		2602,2668,2587	-2.7	0.9	14	dbSNP_120	41	142,8458	70.3+/-132.9	0,142,4158	yes	missense,missense,missense	ACTN1	NM_001102.3,NM_001130004.1,NM_001130005.1	58,58,58	0,158,6345	AA,AT,TT		1.6512,0.3631,1.2148	benign,benign,benign	868/893,890/915,863/888	69341653	158,12848	2203	4300	6503	SO:0001583	missense	87	exon22			GGCCGGTGTAGGG	M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.2602A>T	14.37:g.69341653T>A	ENSP00000193403:p.Thr868Ser	66.0	1.0	0.0151515		80.0	32.0	0.4	NM_001130004	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	18	0.008241758241758242	0	0.0	8	0.022099447513812154	0	0.0	10	0.013192612137203167	T	9.571	1.121108	0.20877	0.003631	0.016512	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.39229	1.6;1.09;1.09;1.09;1.09	4.68	-2.72	0.05968	EF-hand, Ca insensitive (1);EF-hand-like domain (1);	0.656003	0.15664	N	0.250756	T	0.09642	0.0237	L	0.28556	0.865	0.22185	N	0.999308	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.001	T	0.21690	-1.0238	10	0.08381	T	0.77	.	2.1866	0.03888	0.1289:0.3501:0.1331:0.3879	rs11557769	863;890;868;510	P12814-2;Q1HE25;P12814;B4DFY0	.;.;ACTN1_HUMAN;.	S	868;890;863;798;906	ENSP00000193403:T868S;ENSP00000377941:T890S;ENSP00000414272:T863S;ENSP00000366035:T798S;ENSP00000439828:T906S	ENSP00000193403:T868S	T	-	1	0	ACTN1	68411406	0.003000	0.15002	0.930000	0.37139	0.998000	0.95712	-0.007000	0.12810	-0.578000	0.05959	0.528000	0.53228	ACC	T|0.988;A|0.012	0.012	strong		0.662	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3	NM_001102	
TCN1	6947	hgsc.bcm.edu	37	11	59623479	59623479	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:59623479T>G	ENST00000257264.3	-	6	904	c.800A>C	c.(799-801)cAa>cCa	p.Q267P	TCN1_ENST00000532419.1_Intron	NM_001062.3	NP_001053.2	P20061	TCO1_HUMAN	transcobalamin I (vitamin B12 binding protein, R binder family)	267	Globular N-terminal alpha domain.				cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|cobalt ion transport (GO:0006824)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	cobalamin binding (GO:0031419)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	29		all_epithelial(135;0.198)			Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	ATTCAGAGTTTGTTGGCAATT	0.473																																					p.Q267P		Atlas-SNP	.											.	TCN1	64	.	0			c.A800C						PASS	.						122.0	124.0	124.0					11																	59623479		2201	4295	6496	SO:0001583	missense	6947	exon6			AGAGTTTGTTGGC	J05068	CCDS7978.1	11q11-q12	2008-07-21			ENSG00000134827	ENSG00000134827			11652	protein-coding gene	gene with protein product	"""haptocorin"", ""haptocorrin"""	189905					Standard	NM_001062		Approved	TCI, TC1	uc001noj.2	P20061	OTTHUMG00000167400	ENST00000257264.3:c.800A>C	11.37:g.59623479T>G	ENSP00000257264:p.Gln267Pro	144.0	0.0	0		194.0	34.0	0.175258	NM_001062	A8KAC5|Q8WV77	Missense_Mutation	SNP	ENST00000257264.3	37	CCDS7978.1	.	.	.	.	.	.	.	.	.	.	t	11.77	1.737860	0.30774	.	.	ENSG00000134827	ENST00000257264	T	0.35973	1.28	4.44	3.21	0.36854	.	0.874076	0.09641	N	0.775035	T	0.29423	0.0733	L	0.29908	0.895	0.09310	N	1	B	0.33919	0.432	B	0.39119	0.291	T	0.23511	-1.0186	10	0.45353	T	0.12	.	6.5473	0.22412	0.2145:0.0:0.0:0.7855	.	267	P20061	TCO1_HUMAN	P	267	ENSP00000257264:Q267P	ENSP00000257264:Q267P	Q	-	2	0	TCN1	59380055	0.622000	0.27085	0.497000	0.27552	0.055000	0.15305	1.583000	0.36579	1.638000	0.50547	0.473000	0.43528	CAA	.	.	none		0.473	TCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394503.1	NM_001062	
GAK	2580	hgsc.bcm.edu	37	4	877187	877187	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:877187C>A	ENST00000314167.4	-	13	1430	c.1320G>T	c.(1318-1320)ttG>ttT	p.L440F	GAK_ENST00000511163.1_Missense_Mutation_p.L361F	NM_005255.2	NP_005246.2	O14976	GAK_HUMAN	cyclin G associated kinase	440	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				cell cycle (GO:0007049)|cell development (GO:0048468)|clathrin coat disassembly (GO:0072318)|clathrin-mediated endocytosis (GO:0072583)|endoplasmic reticulum organization (GO:0007029)|epidermal cell differentiation (GO:0009913)|establishment of skin barrier (GO:0061436)|forebrain morphogenesis (GO:0048853)|Golgi organization (GO:0007030)|intrahepatic bile duct development (GO:0035622)|positive regulation of neural precursor cell proliferation (GO:2000179)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(16)|skin(7)|urinary_tract(2)	39				Colorectal(103;0.219)		AGTCCAGGAACAACCGCACAT	0.577																																					p.L440F		Atlas-SNP	.											.	GAK	104	.	0			c.G1320T						PASS	.						208.0	174.0	185.0					4																	877187		2203	4300	6503	SO:0001583	missense	2580	exon13			CAGGAACAACCGC	D88435	CCDS3340.1	4p16	2011-09-07			ENSG00000178950	ENSG00000178950		"""Heat shock proteins / DNAJ (HSP40)"""	4113	protein-coding gene	gene with protein product	"""auxilin-2"""	602052				9299234	Standard	NM_005255		Approved	DNAJC26	uc003gbm.4	O14976	OTTHUMG00000088301	ENST00000314167.4:c.1320G>T	4.37:g.877187C>A	ENSP00000314499:p.Leu440Phe	72.0	0.0	0		118.0	18.0	0.152542	NM_005255	Q5U4P5|Q9BVY6	Missense_Mutation	SNP	ENST00000314167.4	37	CCDS3340.1	.	.	.	.	.	.	.	.	.	.	C	12.34	1.910103	0.33721	.	.	ENSG00000178950	ENST00000314167;ENST00000511163	D;D	0.98602	-5.02;-5.02	5.34	1.53	0.23141	Phosphatase tensin type (1);	0.171640	0.38663	N	0.001620	D	0.95965	0.8686	L	0.48642	1.525	0.58432	D	0.999996	P;P;P;P	0.48640	0.913;0.848;0.849;0.849	P;P;B;B	0.47891	0.56;0.56;0.379;0.288	D	0.91526	0.5238	10	0.30854	T	0.27	-4.0961	5.1519	0.15015	0.139:0.515:0.2693:0.0766	.	361;361;440;336	Q5U4P5;E9PGR2;O14976;Q59HA5	.;.;GAK_HUMAN;.	F	440;361	ENSP00000314499:L440F;ENSP00000421361:L361F	ENSP00000314499:L440F	L	-	3	2	GAK	867187	0.927000	0.31430	0.089000	0.20774	0.004000	0.04260	0.128000	0.15810	-0.028000	0.13850	-1.047000	0.02352	TTG	.	.	none		0.577	GAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239188.1	NM_005255	
CAPZA3	93661	hgsc.bcm.edu	37	12	18891318	18891318	+	Missense_Mutation	SNP	G	G	A	rs117330813	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:18891318G>A	ENST00000317658.3	+	1	274	c.116G>A	c.(115-117)cGt>cAt	p.R39H	PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000447925.2_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000539875.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	39					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|spermatid development (GO:0007286)	acrosomal vesicle (GO:0001669)|cortical cytoskeleton (GO:0030863)|F-actin capping protein complex (GO:0008290)|membrane (GO:0016020)|nucleus (GO:0005634)|WASH complex (GO:0071203)		p.R39H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(6)|ovary(1)|prostate(1)	19	Acute lymphoblastic leukemia(4;0.000455)|all_hematologic(4;0.0241)	Hepatocellular(102;0.194)				CTGCTTATCCGTGATGAAAAA	0.458													G|||	11	0.00219649	0.0	0.0029	5008	,	,		19990	0.001		0.007	False		,,,				2504	0.001				p.R39H		Atlas-SNP	.											CAPZA3,NS,carcinoma,0,1	CAPZA3	51	1	1	Substitution - Missense(1)	breast(1)	c.G116A						scavenged	.	G	HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	121.0	111.0	115.0		116	3.8	1.0	12	dbSNP_132	115	67,8531	41.2+/-98.3	0,67,4232	yes	missense	CAPZA3	NM_033328.2	29	0,79,6423	AA,AG,GG		0.7793,0.2724,0.6075	possibly-damaging	39/300	18891318	79,12925	2203	4299	6502	SO:0001583	missense	93661	exon1			TTATCCGTGATGA	AB053259	CCDS8681.1	12p12.3	2008-02-05			ENSG00000177938	ENSG00000177938			24205	protein-coding gene	gene with protein product		608722				12029070	Standard	NM_033328		Approved	Gsg3, CAPPA3	uc001rdy.3	Q96KX2	OTTHUMG00000169001	ENST00000317658.3:c.116G>A	12.37:g.18891318G>A	ENSP00000326238:p.Arg39His	171.0	1.0	0.00584795		181.0	77.0	0.425414	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	5	0.006596306068601583	G	13.90	2.375049	0.42105	0.002724	0.007793	ENSG00000177938	ENST00000317658	.	.	.	4.8	3.83	0.44106	.	0.346611	0.27415	N	0.019461	T	0.38506	0.1043	L	0.36672	1.1	0.34727	D	0.72938	D	0.60575	0.988	P	0.56916	0.809	T	0.55108	-0.8192	9	0.51188	T	0.08	-1.6784	5.836	0.18607	0.1725:0.0:0.8275:0.0	.	39	Q96KX2	CAZA3_HUMAN	H	39	.	ENSP00000326238:R39H	R	+	2	0	CAPZA3	18782585	0.150000	0.22732	1.000000	0.80357	0.998000	0.95712	1.795000	0.38784	2.498000	0.84270	0.563000	0.77884	CGT	G|0.995;A|0.005	0.005	strong		0.458	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328	
MTHFSD	64779	hgsc.bcm.edu	37	16	86585743	86585743	+	Missense_Mutation	SNP	G	G	C	rs34005514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:86585743G>C	ENST00000360900.6	-	3	158	c.133C>G	c.(133-135)Ctg>Gtg	p.L45V	MTHFSD_ENST00000546093.1_Intron|MTHFSD_ENST00000568037.1_Intron|MTHFSD_ENST00000322911.6_Missense_Mutation_p.L44V|MTHFSD_ENST00000381214.5_Intron|MTHFSD_ENST00000543303.2_Intron	NM_001159380.1	NP_001152852.1	Q2M296	MTHSD_HUMAN	methenyltetrahydrofolate synthetase domain containing	45			L -> V (in dbSNP:rs34005514).				nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(1)|large_intestine(3)|lung(6)|skin(1)	11						TGGCAAGCCAGATAAGACCCC	0.473													G|||	95	0.0189696	0.0053	0.0274	5008	,	,		19532	0.004		0.0517	False		,,,				2504	0.0133				p.L45V		Atlas-SNP	.											.	MTHFSD	52	.	0			c.C133G						PASS	.	G	VAL/LEU,,,VAL/LEU,VAL/LEU	43,3753		0,43,1855	151.0	153.0	152.0		133,,,73,130	-0.4	0.6	16	dbSNP_126	152	398,7840		14,370,3735	yes	missense,intron,intron,missense,missense	MTHFSD	NM_001159377.1,NM_001159378.1,NM_001159379.1,NM_001159380.1,NM_022764.2	32,,,32,32	14,413,5590	CC,CG,GG		4.8313,1.1328,3.6646	,,,,	45/384,,,25/364,44/383	86585743	441,11593	1898	4119	6017	SO:0001583	missense	64779	exon3			AAGCCAGATAAGA	AK023060	CCDS54047.1, CCDS54048.1, CCDS58490.1	16q24.1	2013-02-12				ENSG00000103248		"""RNA binding motif (RRM) containing"""	25778	protein-coding gene	gene with protein product						12477932	Standard	NM_022764		Approved	FLJ12998	uc010vor.2	Q2M296		ENST00000360900.6:c.133C>G	16.37:g.86585743G>C	ENSP00000354152:p.Leu45Val	115.0	0.0	0		121.0	61.0	0.504132	NM_001159377	A8MQ77|B7ZLC0|B7ZLC2|D3DUM9|E9PAM1|Q9H878|Q9H954	Missense_Mutation	SNP	ENST00000360900.6	37	CCDS54047.1	55	0.025183150183150184	2	0.0040650406504065045	8	0.022099447513812154	4	0.006993006993006993	41	0.05408970976253298	G	10.80	1.453214	0.26161	0.011328	0.048313	ENSG00000103248	ENST00000543303;ENST00000360900;ENST00000322911	T;T	0.41400	1.0;1.0	5.93	-0.438	0.12268	5-formyltetrahydrofolate cyclo-ligase-like domain (1);	1.474430	0.04126	N	0.317098	T	0.04724	0.0128	N	0.04297	-0.235	0.09310	N	1	B;B	0.17465	0.022;0.017	B;B	0.23852	0.049;0.029	T	0.23726	-1.0180	10	0.35671	T	0.21	-11.0693	14.9226	0.70851	0.0:0.419:0.4829:0.0981	rs34005514	45;44	Q2M296;Q2M296-2	MTHSD_HUMAN;.	V	43;45;44	ENSP00000354152:L45V;ENSP00000326777:L44V	ENSP00000326777:L44V	L	-	1	2	MTHFSD	85143244	0.057000	0.20700	0.564000	0.28396	0.964000	0.63967	0.453000	0.21811	0.070000	0.16634	0.655000	0.94253	CTG	G|0.968;C|0.032	0.032	strong		0.473	MTHFSD-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000432182.1	NM_022764	
ZNF606	80095	hgsc.bcm.edu	37	19	58491382	58491382	+	Silent	SNP	G	G	A	rs142503772	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:58491382G>A	ENST00000341164.4	-	7	1286	c.666C>T	c.(664-666)aaC>aaT	p.N222N	ZNF606_ENST00000536132.1_Silent_p.N132N	NM_025027.3	NP_079303.2	Q8WXB4	ZN606_HUMAN	zinc finger protein 606	222					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	26		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0168)		CAAAGTTTAAGTTCTGGCTAA	0.423													G|||	17	0.00339457	0.0	0.0115	5008	,	,		19562	0.0		0.0089	False		,,,				2504	0.0				p.N222N		Atlas-SNP	.											.	ZNF606	155	.	0			c.C666T						PASS	.	G		12,4394	20.2+/-43.8	0,12,2191	103.0	101.0	101.0		666	-0.5	0.4	19	dbSNP_134	101	95,8505	52.7+/-113.3	1,93,4206	no	coding-synonymous	ZNF606	NM_025027.3		1,105,6397	AA,AG,GG		1.1047,0.2724,0.8227		222/793	58491382	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	80095	exon7			GTTTAAGTTCTGG	AB058755	CCDS12968.1	19q13.43	2013-01-08			ENSG00000166704	ENSG00000166704		"""Zinc fingers, C2H2-type"", ""-"""	25879	protein-coding gene	gene with protein product		613905		ZNF328		11347906	Standard	XM_005259276		Approved	FLJ14260, KIAA1852	uc002qqw.3	Q8WXB4	OTTHUMG00000169804	ENST00000341164.4:c.666C>T	19.37:g.58491382G>A		73.0	0.0	0		81.0	33.0	0.407407	NM_025027	A8KAN2|Q8NE04|Q96JH5	Silent	SNP	ENST00000341164.4	37	CCDS12968.1																																																																																			G|0.991;A|0.009	0.009	strong		0.423	ZNF606-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405961.1	NM_025027	
HIST1H1D	3007	hgsc.bcm.edu	37	6	26234923	26234923	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:26234923C>A	ENST00000244534.5	-	1	293	c.239G>T	c.(238-240)cGt>cTt	p.R80L		NM_005320.2	NP_005311.1	P16402	H13_HUMAN	histone cluster 1, H1d	80	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				nucleosome assembly (GO:0006334)|nucleosome positioning (GO:0016584)	nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|poly(A) RNA binding (GO:0044822)	p.R80H(1)		breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AAGCTTGATACGGCTGTTGTT	0.537																																					p.R80L		Atlas-SNP	.											HIST1H1D,NS,lymphoid_neoplasm,0,1	HIST1H1D	40	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.G239T						PASS	.						88.0	96.0	93.0					6																	26234923		2203	4300	6503	SO:0001583	missense	3007	exon1			TTGATACGGCTGT	M60747	CCDS4597.1	6p21.3	2012-10-02	2006-10-11	2003-02-21	ENSG00000124575	ENSG00000124575		"""Histones / Replication-dependent"""	4717	protein-coding gene	gene with protein product		142210	"""H1 histone family, member 3"", ""histone 1, H1d"""	H1F3		1916825, 12408966	Standard	NM_005320		Approved	H1.3, H1d, H1s-2	uc003nhd.3	P16402	OTTHUMG00000014432	ENST00000244534.5:c.239G>T	6.37:g.26234923C>A	ENSP00000244534:p.Arg80Leu	211.0	0.0	0		289.0	57.0	0.197232	NM_005320	B2R751|Q2M2I2	Missense_Mutation	SNP	ENST00000244534.5	37	CCDS4597.1	.	.	.	.	.	.	.	.	.	.	.	22.8	4.340881	0.81911	.	.	ENSG00000124575	ENST00000244534	T	0.09445	2.98	5.23	5.23	0.72850	Histone H1/H5 (3);Winged helix-turn-helix transcription repressor DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.18002	0.0432	L	0.56199	1.76	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04509	-1.0946	10	0.15499	T	0.54	-17.6271	18.1633	0.89717	0.0:1.0:0.0:0.0	.	80	P16402	H13_HUMAN	L	80	ENSP00000244534:R80L	ENSP00000244534:R80L	R	-	2	0	HIST1H1D	26342902	1.000000	0.71417	1.000000	0.80357	0.221000	0.24807	4.921000	0.63397	2.623000	0.88846	0.655000	0.94253	CGT	.	.	none		0.537	HIST1H1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040095.1	NM_005320	
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR|HRAS_ENST00000417302.1_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000397596.2_Silent_p.H27H	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"""E, L, M"""	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135.0	123.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1.0	1.0	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		144.0	0.0	0		102.0	59.0	0.578431	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795	
ETV1	2115	hgsc.bcm.edu	37	7	13950864	13950864	+	Splice_Site	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:13950864C>T	ENST00000430479.1	-	10	1538	c.871G>A	c.(871-873)Ggc>Agc	p.G291S	ETV1_ENST00000399357.3_Splice_Site_p.G188S|ETV1_ENST00000420159.2_Splice_Site_p.G233S|ETV1_ENST00000343495.5_Splice_Site_p.G273S|ETV1_ENST00000405192.2_Intron|ETV1_ENST00000403685.1_Splice_Site_p.G273S|ETV1_ENST00000403527.1_Splice_Site_p.G251S|ETV1_ENST00000242066.5_Splice_Site_p.G273S|ETV1_ENST00000476720.2_5'Flank|ETV1_ENST00000405358.4_Splice_Site_p.G305S|ETV1_ENST00000405218.2_Splice_Site_p.G291S	NM_004956.4	NP_004947.2	P50549	ETV1_HUMAN	ets variant 1	291					axon guidance (GO:0007411)|cell differentiation (GO:0030154)|mechanosensory behavior (GO:0007638)|muscle organ development (GO:0007517)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)		TMPRSS2/ETV1(34)|ACSL3_ENST00000357430/ETV1(2)|EWSR1/ETV1(7)|KLK2/ETV1(3)|SLC45A3/ETV1(3)|HNRNPA2B1/ETV1(8)	breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(9)|lung(15)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	31						GACAACTTAACTTCTGTTCTG	0.383			T	"""EWSR1, TMPRSS2, SLC45A3, C15orf21, HNRNPA2B1. ACSL3"""	"""Ewing sarcoma, prostate"""																																p.G291S		Atlas-SNP	.		Dom	yes		7	7p22	2115	ets variant gene 1		"""M, E"""	.	ETV1	138	.	0			c.G871A						PASS	.						81.0	80.0	81.0					7																	13950864		1904	4108	6012	SO:0001630	splice_region_variant	2115	exon10			ACTTAACTTCTGT		CCDS55083.1, CCDS55084.1, CCDS55085.1, CCDS55086.1, CCDS55087.1, CCDS55088.1	7p22	2008-09-12	2008-09-12		ENSG00000006468	ENSG00000006468			3490	protein-coding gene	gene with protein product		600541	"""ets variant gene 1"""			1340465	Standard	NM_004956		Approved	ER81	uc003ssw.4	P50549	OTTHUMG00000152403	ENST00000430479.1:c.871+1G>A	7.37:g.13950864C>T		134.0	0.0	0		115.0	14.0	0.121739	NM_004956	A4D118|B2R768|B7Z2I4|B7Z618|B7Z9P2|C9JT37|E9PHB1|F5GXR2|O75849|Q4KMQ6|Q59GA7|Q6AI30|Q9UQ71|Q9Y636	Missense_Mutation	SNP	ENST00000430479.1	37	CCDS55088.1	.	.	.	.	.	.	.	.	.	.	C	36	5.733116	0.96856	.	.	ENSG00000006468	ENST00000430479;ENST00000242066;ENST00000343495;ENST00000420159;ENST00000399357;ENST00000405358;ENST00000403527;ENST00000405218;ENST00000403685;ENST00000438956	T;T;T;T;T;T;T;T;T;T	0.30182	1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54;1.54	5.26	5.26	0.73747	.	2.792530	0.00481	N	0.000121	T	0.54464	0.1860	L	0.60067	1.865	0.80722	D	1	.	.	.	.	.	.	T	0.39820	-0.9595	7	.	.	.	.	19.7471	0.96257	0.0:1.0:0.0:0.0	.	.	.	.	S	291;273;273;233;188;305;251;291;273;233	ENSP00000405327:G291S;ENSP00000242066:G273S;ENSP00000340853:G273S;ENSP00000411626:G233S;ENSP00000382293:G188S;ENSP00000384085:G305S;ENSP00000384138:G251S;ENSP00000385551:G291S;ENSP00000385686:G273S;ENSP00000393078:G233S	.	G	-	1	0	ETV1	13917389	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.776000	0.85560	2.838000	0.97847	0.591000	0.81541	GGC	.	.	none		0.383	ETV1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326111.1	NM_004956	Missense_Mutation
KCNH2	3757	hgsc.bcm.edu	37	7	150644428	150644428	+	Missense_Mutation	SNP	C	C	A	rs36210421	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:150644428C>A	ENST00000262186.5	-	13	3541	c.3140G>T	c.(3139-3141)cGc>cTc	p.R1047L	KCNH2_ENST00000330883.4_Missense_Mutation_p.R707L|KCNH2_ENST00000392968.2_Missense_Mutation_p.R951L	NM_000238.3	NP_000229.1	Q12809	KCNH2_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 2	1047					cardiac muscle contraction (GO:0060048)|cellular response to drug (GO:0035690)|membrane depolarization during action potential (GO:0086010)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of potassium ion export (GO:1902303)|negative regulation of potassium ion transmembrane transport (GO:1901380)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transmembrane transport (GO:0071805)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of heart rate by hormone (GO:0003064)|regulation of membrane potential (GO:0042391)|regulation of membrane repolarization (GO:0060306)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|identical protein binding (GO:0042802)|inward rectifier potassium channel activity (GO:0005242)|phosphorelay sensor kinase activity (GO:0000155)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			NS(1)|cervix(1)|endometrium(10)|kidney(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	42	all_neural(206;0.219)		OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	Alfuzosin(DB00346)|Amiodarone(DB01118)|Amsacrine(DB00276)|Astemizole(DB00637)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Cisapride(DB00604)|Dofetilide(DB00204)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Halofantrine(DB01218)|Ibutilide(DB00308)|Imipramine(DB00458)|Miconazole(DB01110)|Pimozide(DB01100)|Prazosin(DB00457)|Propafenone(DB01182)|Quinidine(DB00908)|Sertindole(DB06144)|Sotalol(DB00489)|Terazosin(DB01162)|Thioridazine(DB00679)|Verapamil(DB00661)	GTTGAGCTGGCGCTGGAGGGC	0.716													C|||	45	0.00898562	0.0	0.0043	5008	,	,		8790	0.001		0.0378	False		,,,				2504	0.0031				p.R1047L	GBM(137;110 1844 13671 20123 45161)	Atlas-SNP	.											.	KCNH2	157	.	0			c.G3140T	GRCh37	CM045797	KCNH2	M	rs36210421	PASS	.	C	LEU/ARG,LEU/ARG	16,3806		0,16,1895	5.0	7.0	6.0		3140,2120	4.1	1.0	7	dbSNP_126	6	139,7661		0,139,3761	no	missense,missense	KCNH2	NM_000238.3,NM_172057.2	102,102	0,155,5656	AA,AC,CC		1.7821,0.4186,1.3337	possibly-damaging,possibly-damaging	1047/1160,707/820	150644428	155,11467	1911	3900	5811	SO:0001583	missense	3757	exon13			AGCTGGCGCTGGA	U04270	CCDS5910.1, CCDS5911.1	7q36.1	2014-09-17			ENSG00000055118	ENSG00000055118		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6251	protein-coding gene	gene with protein product		152427		LQT2		18616963, 7842012, 8159766, 16382104	Standard	NM_000238		Approved	Kv11.1, HERG, erg1	uc003wic.3	Q12809	OTTHUMG00000158341	ENST00000262186.5:c.3140G>T	7.37:g.150644428C>A	ENSP00000262186:p.Arg1047Leu	7.0	0.0	0		15.0	10.0	0.666667	NM_000238	A5H1P7|C4PFH9|D3DX04|O75418|O75680|Q708S9|Q9BT72|Q9BUT7|Q9H3P0	Missense_Mutation	SNP	ENST00000262186.5	37	CCDS5910.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	C	19.00	3.741960	0.69418	0.004186	0.017821	ENSG00000055118	ENST00000330883;ENST00000392968;ENST00000262186	D;D;D	0.87256	-2.23;-2.23;-2.23	4.97	4.09	0.47781	.	0.140191	0.45867	D	0.000324	T	0.52500	0.1738	L	0.40543	1.245	0.80722	D	1	B;B;B	0.22146	0.039;0.039;0.065	B;B;B	0.23275	0.028;0.02;0.045	T	0.64922	-0.6293	10	0.36615	T	0.2	.	7.6627	0.28413	0.0:0.8092:0.0:0.1908	rs36210421;rs41313758	951;1047;707	C4PFH9;Q12809;Q12809-2	.;KCNH2_HUMAN;.	L	707;951;1047	ENSP00000328531:R707L;ENSP00000376695:R951L;ENSP00000262186:R1047L	ENSP00000262186:R1047L	R	-	2	0	KCNH2	150275361	0.000000	0.05858	0.998000	0.56505	0.966000	0.64601	-0.090000	0.11163	1.094000	0.41399	0.555000	0.69702	CGC	C|0.983;A|0.017	0.017	strong		0.716	KCNH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350741.2	NM_000238	
NUBPL	80224	hgsc.bcm.edu	37	14	32319354	32319354	+	Nonsense_Mutation	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:32319354G>T	ENST00000281081.7	+	10	889	c.844G>T	c.(844-846)Gaa>Taa	p.E282*	NUBPL_ENST00000536705.1_Nonsense_Mutation_p.E186*|NUBPL_ENST00000418681.2_3'UTR	NM_001201573.1|NM_001201574.1|NM_025152.2	NP_001188502.1|NP_001188503.1|NP_079428.2	Q8TB37	NUBPL_HUMAN	nucleotide binding protein-like	282					mitochondrial respiratory chain complex I assembly (GO:0032981)|mitochondrion morphogenesis (GO:0070584)	mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)			endometrium(1)|lung(2)|prostate(1)|skin(1)	5	Hepatocellular(127;0.0604)|Prostate(35;0.15)|Breast(36;0.214)		LUAD - Lung adenocarcinoma(48;0.00192)|Lung(238;0.00714)|BRCA - Breast invasive adenocarcinoma(188;0.0677)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0102)		TAATATAAGGGAAGCTTCAGA	0.358																																					p.E282X		Atlas-SNP	.											.	NUBPL	21	.	0			c.G844T						PASS	.						95.0	89.0	91.0					14																	32319354		1811	4084	5895	SO:0001587	stop_gained	80224	exon10			ATAAGGGAAGCTT	AK022722	CCDS41940.1	14q12	2012-10-12	2005-01-07	2005-01-07	ENSG00000151413	ENSG00000151413		"""Mitochondrial respiratory chain complex assembly factors"""	20278	protein-coding gene	gene with protein product	"""iron-sulfur protein required for NADH dehydrogenase"""	613621	"""chromosome 14 open reading frame 127"""	C14orf127			Standard	NM_025152		Approved	FLJ12660, IND1, huInd1	uc001wrk.4	Q8TB37	OTTHUMG00000170521	ENST00000281081.7:c.844G>T	14.37:g.32319354G>T	ENSP00000281081:p.Glu282*	137.0	0.0	0		138.0	10.0	0.0724638	NM_025152	B4DHZ1|Q86TZ4|Q9H9M2	Nonsense_Mutation	SNP	ENST00000281081.7	37	CCDS41940.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524580	0.85600	.	.	ENSG00000151413	ENST00000550649;ENST00000281081;ENST00000536705	.	.	.	6.07	6.07	0.98685	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.66056	D	0.02	-10.7882	18.1531	0.89682	0.0:0.0:1.0:0.0	.	.	.	.	X	148;282;186	.	ENSP00000281081:E282X	E	+	1	0	NUBPL	31389105	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	4.773000	0.62331	2.885000	0.99019	0.655000	0.94253	GAA	.	.	none		0.358	NUBPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409519.1	NM_025152	
OSGIN1	29948	hgsc.bcm.edu	37	16	83999548	83999548	+	Missense_Mutation	SNP	T	T	C	rs62640905	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:83999548T>C	ENST00000343939.2	+	7	2002	c.1619T>C	c.(1618-1620)gTg>gCg	p.V540A	OSGIN1_ENST00000393306.1_Missense_Mutation_p.V457A|OSGIN1_ENST00000361711.3_Missense_Mutation_p.V457A|NECAB2_ENST00000305202.4_5'Flank			Q9UJX0	OSGI1_HUMAN	oxidative stress induced growth inhibitor 1	540					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|negative regulation of cell growth (GO:0030308)|positive regulation of apoptotic process (GO:0043065)		growth factor activity (GO:0008083)			autonomic_ganglia(1)|large_intestine(1)|lung(7)|prostate(2)|upper_aerodigestive_tract(1)	12						GTGAGGTTTGTGCAGGGGGGC	0.662													T|||	40	0.00798722	0.0	0.013	5008	,	,		17559	0.0		0.0278	False		,,,				2504	0.0031				p.V457A		Atlas-SNP	.											.	OSGIN1	33	.	0			c.T1370C						PASS	.	T	ALA/VAL,ALA/VAL,ALA/VAL	14,4370		0,14,2178	14.0	15.0	15.0		1619,1370,1370	4.4	1.0	16	dbSNP_129	15	218,8354		5,208,4073	yes	missense,missense,missense	OSGIN1	NM_013370.3,NM_182980.2,NM_182981.2	64,64,64	5,222,6251	CC,CT,TT		2.5432,0.3193,1.7907	possibly-damaging,possibly-damaging,possibly-damaging	540/561,457/478,457/478	83999548	232,12724	2192	4286	6478	SO:0001583	missense	29948	exon6			GGTTTGTGCAGGG	AY258066	CCDS10939.1	16q23.3	2010-11-23			ENSG00000140961	ENSG00000140961			30093	protein-coding gene	gene with protein product	"""bone marrow stromal cell-derived growth inhibitor"", ""pregnancy induced growth inhibitor"""	607975				11459809, 14570898	Standard	NM_182981		Approved	BDGI, OKL38	uc002fhc.3	Q9UJX0	OTTHUMG00000137640	ENST00000343939.2:c.1619T>C	16.37:g.83999548T>C	ENSP00000343376:p.Val540Ala	69.0	0.0	0		57.0	20.0	0.350877	NM_182981	Q52M33|Q86UQ1|Q96S88|Q9BZ70	Missense_Mutation	SNP	ENST00000343939.2	37		27	0.012362637362637362	0	0.0	6	0.016574585635359115	0	0.0	21	0.027704485488126648	T	16.86	3.238732	0.58995	0.003193	0.025432	ENSG00000140961	ENST00000343939;ENST00000361711;ENST00000393306	T;T;T	0.37411	1.2;1.2;1.2	4.37	4.37	0.52481	.	0.065516	0.64402	D	0.000009	T	0.15739	0.0379	M	0.63428	1.95	0.80722	D	1	D	0.58268	0.982	B	0.44315	0.446	T	0.04811	-1.0925	10	0.24483	T	0.36	-26.2537	12.7349	0.57218	0.0:0.0:0.0:1.0	rs62640905	540	Q9UJX0	OSGI1_HUMAN	A	540;457;457	ENSP00000343376:V540A;ENSP00000355374:V457A;ENSP00000376983:V457A	ENSP00000343376:V540A	V	+	2	0	OSGIN1	82557049	1.000000	0.71417	0.954000	0.39281	0.681000	0.39784	7.645000	0.83430	1.606000	0.50161	0.260000	0.18958	GTG	T|0.985;C|0.015	0.015	strong		0.662	OSGIN1-001	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000269081.1	NM_013370	
CLEC4M	10332	hgsc.bcm.edu	37	19	7828277	7828277	+	Splice_Site	SNP	A	A	G	rs62623420	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:7828277A>G	ENST00000327325.5	+	2	164		c.e2-1		CLEC4M_ENST00000334806.5_Intron|CLEC4M_ENST00000597522.1_Splice_Site|CLEC4M_ENST00000595496.1_Splice_Site|CLEC4M_ENST00000596707.1_Splice_Site|CLEC4M_ENST00000357361.2_Splice_Site|CLEC4M_ENST00000359059.5_Splice_Site|CLEC4M_ENST00000394122.2_Splice_Site|CLEC4M_ENST00000596363.1_Intron|CLEC4M_ENST00000248228.4_Splice_Site	NM_001144909.1|NM_014257.4	NP_001138381.1|NP_055072.3	Q9H2X3	CLC4M_HUMAN	C-type lectin domain family 4, member M						antigen processing and presentation (GO:0019882)|cell-cell recognition (GO:0009988)|endocytosis (GO:0006897)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|intracellular transport of virus (GO:0075733)|leukocyte cell-cell adhesion (GO:0007159)|modulation by virus of host morphology or physiology (GO:0019048)|peptide antigen transport (GO:0046968)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)|viral genome replication (GO:0019079)|virion attachment to host cell (GO:0019062)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)|ICAM-3 receptor activity (GO:0030369)|mannose binding (GO:0005537)|metal ion binding (GO:0046872)|peptide antigen binding (GO:0042605)|receptor activity (GO:0004872)|virion binding (GO:0046790)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(10)|pancreas(1)|prostate(1)|skin(1)	26						CTGTCAATTCAGAAGAAGATC	0.522													A|||	5	0.000998403	0.0	0.0	5008	,	,		18184	0.0		0.005	False		,,,				2504	0.0				.		Atlas-SNP	.											.	CLEC4M	58	.	0			c.47-2A>G						PASS	.	A	,,,,,,,,	6,4400	11.4+/-27.6	0,6,2197	129.0	124.0	126.0		,,,,,,,,	2.5	0.1	19	dbSNP_129	126	50,8550	31.7+/-84.0	0,50,4250	yes	intron,intron,splice-3,splice-3,splice-3,splice-3,splice-3,intron,splice-3	CLEC4M	NM_001144904.1,NM_001144905.1,NM_001144906.1,NM_001144907.1,NM_001144908.1,NM_001144909.1,NM_001144910.1,NM_001144911.1,NM_014257.4	,,,,,,,,	0,56,6447	GG,GA,AA		0.5814,0.1362,0.4306	,,,,,,,,	,,,,,,,,	7828277	56,12950	2203	4300	6503	SO:0001630	splice_region_variant	10332	exon2			CAATTCAGAAGAA	AB015629	CCDS12187.1, CCDS59346.1, CCDS59347.1, CCDS59348.1	19p13	2008-02-05	2005-02-04	2005-02-11		ENSG00000104938		"""C-type lectin domain containing"", ""CD molecules"""	13523	protein-coding gene	gene with protein product		605872	"""CD299 antigen"""	CD209L, CD299		10072769	Standard	NM_001144904		Approved	HP10347, DC-SIGNR, LSIGN, DCSIGNR, DC-SIGN2	uc010dvt.3	Q9H2X3		ENST00000327325.5:c.47-1A>G	19.37:g.7828277A>G		124.0	0.0	0		134.0	69.0	0.514925	NM_001144907	A6NKI4|A8K8B3|Q69F40|Q969M4|Q96QP3|Q96QP4|Q96QP5|Q96QP6|Q9BXS3|Q9H2Q9|Q9H8F0|Q9Y2A8	Splice_Site	SNP	ENST00000327325.5	37	CCDS12187.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	7.317	0.616157	0.14129	0.001362	0.005814	ENSG00000104938	ENST00000327325;ENST00000394122;ENST00000248228;ENST00000359059;ENST00000357361	.	.	.	2.5	2.5	0.30297	.	.	.	.	.	.	.	.	.	.	.	0.53688	D	0.99997	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.3238	0.26542	1.0:0.0:0.0:0.0	rs62623420	.	.	.	.	-1	.	.	.	+	.	.	CLEC4M	7734277	0.022000	0.18835	0.128000	0.21923	0.082000	0.17680	1.015000	0.29963	1.134000	0.42165	0.344000	0.21773	.	A|0.997;G|0.003	0.003	strong		0.522	CLEC4M-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000461161.1	NM_014257	Intron
CYB5R4	51167	hgsc.bcm.edu	37	6	84618792	84618792	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:84618792A>G	ENST00000369681.5	+	4	535	c.395A>G	c.(394-396)aAa>aGa	p.K132R	CYB5R4_ENST00000369679.4_Missense_Mutation_p.K98R	NM_016230.3	NP_057314.2	Q7L1T6	NB5R4_HUMAN	cytochrome b5 reductase 4	132					cell development (GO:0048468)|detection of oxygen (GO:0003032)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|insulin secretion (GO:0030073)|NADP metabolic process (GO:0006739)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|superoxide metabolic process (GO:0006801)	endoplasmic reticulum (GO:0005783)|perinuclear region of cytoplasm (GO:0048471)	cytochrome-b5 reductase activity, acting on NAD(P)H (GO:0004128)|flavin adenine dinucleotide binding (GO:0050660)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NAD(P)H oxidase activity (GO:0016174)|NADPH-hemoprotein reductase activity (GO:0003958)|oxidoreductase activity, acting on NAD(P)H, heme protein as acceptor (GO:0016653)			breast(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|prostate(1)|upper_aerodigestive_tract(1)	23		all_cancers(76;7e-07)|Acute lymphoblastic leukemia(125;2.69e-07)|all_hematologic(105;0.000151)|all_epithelial(107;0.00128)		BRCA - Breast invasive adenocarcinoma(397;0.0871)		ATGGCCATTAAACCTGCTGTT	0.398																																					p.K132R	Esophageal Squamous(86;1289 1332 25971 40349 52675)	Atlas-SNP	.											.	CYB5R4	72	.	0			c.A395G						PASS	.						133.0	118.0	123.0					6																	84618792		2203	4300	6503	SO:0001583	missense	51167	exon4			CCATTAAACCTGC	AF169803	CCDS5000.2	6q14.2	2012-09-19		2005-07-13	ENSG00000065615	ENSG00000065615	1.6.2.2		20147	protein-coding gene	gene with protein product		608343	"""NADPH cytochrome B5 oxidoreductase"""	NCB5OR		10611283	Standard	NM_016230		Approved	b5+b5R, dJ676J13.1	uc003pkf.3	Q7L1T6	OTTHUMG00000015118	ENST00000369681.5:c.395A>G	6.37:g.84618792A>G	ENSP00000358695:p.Lys132Arg	67.0	0.0	0		62.0	29.0	0.467742	NM_016230	B1AEM2|Q5TGI9|Q9NUE4|Q9UHI9	Missense_Mutation	SNP	ENST00000369681.5	37	CCDS5000.2	.	.	.	.	.	.	.	.	.	.	A	18.22	3.576672	0.65878	.	.	ENSG00000065615	ENST00000369681;ENST00000369679	D;D	0.84944	-1.92;-1.68	5.74	5.74	0.90152	Cytochrome b5 (1);	0.206931	0.48767	D	0.000169	T	0.62720	0.2451	N	0.19112	0.55	0.44862	D	0.99787	B	0.27910	0.193	B	0.22386	0.039	T	0.64689	-0.6348	10	0.31617	T	0.26	.	12.4249	0.55540	1.0:0.0:0.0:0.0	.	132	Q7L1T6	NB5R4_HUMAN	R	132;98	ENSP00000358695:K132R;ENSP00000358693:K98R	ENSP00000358693:K98R	K	+	2	0	CYB5R4	84675511	1.000000	0.71417	0.173000	0.22940	0.007000	0.05969	5.761000	0.68801	2.182000	0.69389	0.482000	0.46254	AAA	.	.	none		0.398	CYB5R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041362.4	NM_016230	
CENPM	79019	hgsc.bcm.edu	37	22	42342462	42342462	+	Silent	SNP	C	C	T	rs34730141	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:42342462C>T	ENST00000215980.5	-	2	183	c.96G>A	c.(94-96)gcG>gcA	p.A32A	CENPM_ENST00000404067.1_5'UTR|CENPM_ENST00000407253.3_Silent_p.A32A|CENPM_ENST00000402420.1_5'UTR|CENPM_ENST00000402338.1_5'UTR	NM_024053.3	NP_076958.1	Q9NSP4	CENPM_HUMAN	centromere protein M	32					mitotic cell cycle (GO:0000278)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nucleus (GO:0005634)				kidney(1)|large_intestine(1)|prostate(1)	3						GCATCGAGTCCGCCAGCTGCT	0.657											OREG0026600	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	73	0.0145767	0.0514	0.0072	5008	,	,		17483	0.0		0.0	False		,,,				2504	0.0				p.A32A		Atlas-SNP	.											.	CENPM	8	.	0			c.G96A						PASS	.	C	,	203,4203	121.7+/-159.2	7,189,2007	35.0	31.0	32.0		96,96	-1.8	1.0	22	dbSNP_126	32	2,8596	4.3+/-15.6	0,2,4297	no	coding-synonymous,coding-synonymous	CENPM	NM_001002876.1,NM_024053.3	,	7,191,6304	TT,TC,CC		0.0233,4.6074,1.5764	,	32/108,32/181	42342462	205,12799	2203	4299	6502	SO:0001819	synonymous_variant	79019	exon2			CGAGTCCGCCAGC	BC000705	CCDS14025.1, CCDS46719.1, CCDS46720.1	22q13.2	2013-11-05	2006-06-15	2006-06-15	ENSG00000100162	ENSG00000100162			18352	protein-coding gene	gene with protein product		610152	"""chromosome 22 open reading frame 18"""	C22orf18		16622420, 16622419	Standard	NM_001110215		Approved	Pane1, CENP-M, MGC861	uc003bbn.3	Q9NSP4	OTTHUMG00000151277	ENST00000215980.5:c.96G>A	22.37:g.42342462C>T		230.0	0.0	0	908	288.0	152.0	0.527778	NM_024053	A7LM22|B1AHQ9|Q6I9W3	Silent	SNP	ENST00000215980.5	37	CCDS14025.1																																																																																			C|0.983;T|0.017	0.017	strong		0.657	CENPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322058.1	NM_024053	
DNAH10	196385	hgsc.bcm.edu	37	12	124298030	124298030	+	Missense_Mutation	SNP	G	G	A	rs143713799	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:124298030G>A	ENST00000409039.3	+	19	3135	c.3110G>A	c.(3109-3111)cGc>cAc	p.R1037H		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	1037	Stem. {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)		GAGGTTATGCGCCACCCTCTA	0.438													G|||	65	0.0129792	0.0151	0.0058	5008	,	,		20812	0.0		0.008	False		,,,				2504	0.0337				p.R1037H		Atlas-SNP	.											DNAH10_ENST00000409039,colon,carcinoma,+1,7	DNAH10	888	7	0			c.G3110A						PASS	.	G	HIS/ARG	73,4333	64.7+/-102.0	1,71,2131	90.0	84.0	86.0		3110	0.7	0.0	12	dbSNP_134	86	125,8475	64.6+/-126.8	1,123,4176	yes	missense	DNAH10	NM_207437.3	29	2,194,6307	AA,AG,GG		1.4535,1.6568,1.5224	benign	1037/4472	124298030	198,12808	2203	4300	6503	SO:0001583	missense	196385	exon19			TTATGCGCCACCC	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.3110G>A	12.37:g.124298030G>A	ENSP00000386770:p.Arg1037His	103.0	0.0	0		134.0	65.0	0.485075	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	18	0.008241758241758242	10	0.02032520325203252	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	5.489	0.275238	0.10403	0.016568	0.014535	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.83	0.742	0.18341	.	0.186131	0.36200	N	0.002740	T	0.04137	0.0115	N	0.04959	-0.14	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.001	T	0.25572	-1.0128	10	0.44086	T	0.13	.	8.8463	0.35172	0.5998:0.0:0.4002:0.0	.	1037;912;1037	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	H	1037	ENSP00000386770:R1037H	ENSP00000386770:R1037H	R	+	2	0	DNAH10	122863983	0.001000	0.12720	0.035000	0.18076	0.004000	0.04260	0.637000	0.24659	0.067000	0.16545	-0.244000	0.11960	CGC	G|0.987;A|0.013	0.013	strong		0.438	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
TEX13A	56157	hgsc.bcm.edu	37	X	104464360	104464360	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:104464360G>A	ENST00000413579.1	-	3	629	c.518C>T	c.(517-519)gCa>gTa	p.A173V	TEX13A_ENST00000372575.1_Missense_Mutation_p.A173V|TEX13A_ENST00000372578.3_Missense_Mutation_p.A173V|IL1RAPL2_ENST00000344799.4_Intron|IL1RAPL2_ENST00000372582.1_Intron			Q9BXU3	TX13A_HUMAN	testis expressed 13A	173							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						CTCCTCAGCTGCTCCTTCTGT	0.642																																					p.A173V		Atlas-SNP	.											.	TEX13A	55	.	0			c.C518T						PASS	.						28.0	33.0	32.0					X																	104464360		2123	4174	6297	SO:0001583	missense	56157	exon3			TCAGCTGCTCCTT	AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.518C>T	X.37:g.104464360G>A	ENSP00000399753:p.Ala173Val	60.0	0.0	0		38.0	8.0	0.210526	NM_031274	B1B1G8|Q32NB6	Missense_Mutation	SNP	ENST00000413579.1	37		.	.	.	.	.	.	.	.	.	.	G	14.16	2.452266	0.43531	.	.	ENSG00000133149	ENST00000372578;ENST00000372575;ENST00000413579	.	.	.	3.02	-0.0125	0.13988	.	2.067560	0.02469	N	0.087303	T	0.29256	0.0728	.	.	.	0.09310	N	1	B;B	0.17852	0.024;0.024	B;B	0.15052	0.012;0.012	T	0.16897	-1.0387	8	0.49607	T	0.09	.	2.3339	0.04242	0.3036:0.0:0.4237:0.2727	.	173;173	C9JWK0;Q9BXU3	.;TX13A_HUMAN	V	173	.	ENSP00000361656:A173V	A	-	2	0	TEX13A	104351016	0.011000	0.17503	0.000000	0.03702	0.009000	0.06853	1.241000	0.32743	-0.119000	0.11830	-0.312000	0.09012	GCA	.	.	none		0.642	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_031274	
PRKG1	5592	hgsc.bcm.edu	37	10	52751177	52751177	+	Missense_Mutation	SNP	G	G	A	rs202017913		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:52751177G>A	ENST00000401604.2	+	1	233	c.39G>A	c.(37-39)atG>atA	p.M13I	PRKG1_ENST00000373985.1_Start_Codon_SNP_p.M1I			Q13976	KGP1_HUMAN	protein kinase, cGMP-dependent, type I	13	Leucine-zipper.|Required for dimerization.				actin cytoskeleton organization (GO:0030036)|blood coagulation (GO:0007596)|cGMP-mediated signaling (GO:0019934)|dendrite development (GO:0016358)|forebrain development (GO:0030900)|negative regulation of platelet aggregation (GO:0090331)|neuron migration (GO:0001764)|protein phosphorylation (GO:0006468)|regulation of GTPase activity (GO:0043087)|relaxation of vascular smooth muscle (GO:0060087)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(23)|ovary(1)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	53		all_cancers(4;2.13e-08)|all_epithelial(4;2.44e-08)|all_lung(4;0.000173)		all cancers(4;1.18e-05)|GBM - Glioblastoma multiforme(4;0.000359)|Epithelial(53;0.00532)|Lung(62;0.0606)		AGATTCTCATGCTCAAGGAGG	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		10226	0.0		0.001	False		,,,				2504	0.0				p.M13I		Atlas-SNP	.											.	PRKG1	167	.	0			c.G39A						PASS	.	G	ILE/MET	1,3781		0,1,1890	22.0	28.0	26.0		39	4.8	1.0	10		26	8,8204		0,8,4098	yes	missense	PRKG1	NM_001098512.2	10	0,9,5988	AA,AG,GG		0.0974,0.0264,0.075	benign	13/672	52751177	9,11985	1891	4106	5997	SO:0001583	missense	5592	exon1			TCTCATGCTCAAG		CCDS7244.1	10q11.2	2009-07-10			ENSG00000185532	ENSG00000185532	2.7.11.1		9414	protein-coding gene	gene with protein product		176894		PRKGR1B, PRKG1B		2792381, 1544322	Standard	NM_001098512		Approved	PGK, PKG	uc001jjo.3	Q13976	OTTHUMG00000018248	ENST00000401604.2:c.39G>A	10.37:g.52751177G>A	ENSP00000384200:p.Met13Ile	115.0	0.0	0		106.0	43.0	0.40566	NM_001098512	A5YM56|B3KSF3|E2PU10|P14619|Q5JP05|Q5JSJ6|Q6P5T7	Missense_Mutation	SNP	ENST00000401604.2	37	CCDS44399.1	.	.	.	.	.	.	.	.	.	.	G	12.50	1.956344	0.34565	2.64E-4	9.74E-4	ENSG00000185532	ENST00000401604;ENST00000373985	T;T	0.66638	-0.22;-0.13	4.76	4.76	0.60689	.	.	.	.	.	T	0.48466	0.1501	N	0.08118	0	0.27645	N	0.947607	B;B	0.06786	0.001;0.0	B;B	0.08055	0.003;0.001	T	0.33369	-0.9871	9	0.30854	T	0.27	.	15.5982	0.76602	0.0:0.0:1.0:0.0	.	13;13	B4DT93;Q13976	.;KGP1_HUMAN	I	13;1	ENSP00000384200:M13I;ENSP00000363097:M1I	ENSP00000363097:M1I	M	+	3	0	PRKG1	52421183	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.962000	0.63687	2.349000	0.79799	0.462000	0.41574	ATG	.	.	weak		0.567	PRKG1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
C6orf195	154386	hgsc.bcm.edu	37	6	2623960	2623960	+	Missense_Mutation	SNP	T	T	C	rs201134793	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:2623960T>C	ENST00000296847.3	-	3	620	c.97A>G	c.(97-99)Atg>Gtg	p.M33V		NM_152554.2	NP_689767.2	Q96MT4	CF195_HUMAN	chromosome 6 open reading frame 195	33										cervix(1)|endometrium(1)|lung(2)|skin(1)	5	Ovarian(93;0.0412)	all_hematologic(90;0.0895)				AGTGGCTCCATGCCATCAAAT	0.592													T|||	5	0.000998403	0.0	0.0043	5008	,	,		17886	0.0		0.002	False		,,,				2504	0.0				p.M33V		Atlas-SNP	.											.	C6orf195	10	.	0			c.A97G						PASS	.	T	VAL/MET	0,4034		0,0,2017	38.0	45.0	42.0		97	-0.6	0.0	6		42	25,8323		0,25,4149	yes	missense	C6orf195	NM_152554.2	21	0,25,6166	CC,CT,TT		0.2995,0.0,0.2019	benign	33/128	2623960	25,12357	2017	4174	6191	SO:0001583	missense	154386	exon3			GCTCCATGCCATC	AK056496	CCDS43416.1	6p25.2	2008-10-21			ENSG00000164385	ENSG00000164385			21600	protein-coding gene	gene with protein product							Standard	NM_152554		Approved	FLJ31934, bA145H9.2	uc003mtw.2	Q96MT4	OTTHUMG00000014122	ENST00000296847.3:c.97A>G	6.37:g.2623960T>C	ENSP00000296847:p.Met33Val	77.0	0.0	0		72.0	29.0	0.402778	NM_152554	Q3SY08|Q3SY09|Q3SY10|Q5TAW4	Missense_Mutation	SNP	ENST00000296847.3	37	CCDS43416.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	T	5.297	0.240255	0.10023	0.0	0.002995	ENSG00000164385	ENST00000296847	T	0.33438	1.41	3.3	-0.649	0.11461	.	.	.	.	.	T	0.04318	0.0119	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.38222	-0.9671	9	0.87932	D	0	.	2.698	0.05140	0.2349:0.433:0.0:0.3322	.	33	Q96MT4	CF195_HUMAN	V	33	ENSP00000296847:M33V	ENSP00000296847:M33V	M	-	1	0	C6orf195	2568959	0.001000	0.12720	0.000000	0.03702	0.129000	0.20672	-0.866000	0.04245	-0.105000	0.12132	0.482000	0.46254	ATG	T|0.999;C|0.001	0.001	strong		0.592	C6orf195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039633.1	NM_152554	
EZH2	2146	hgsc.bcm.edu	37	7	148525904	148525904	+	Missense_Mutation	SNP	C	C	G	rs2302427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:148525904C>G	ENST00000460911.1	-	6	641	c.553G>C	c.(553-555)Gac>Cac	p.D185H	EZH2_ENST00000476773.1_Missense_Mutation_p.D176H|EZH2_ENST00000541220.1_Missense_Mutation_p.D176H|EZH2_ENST00000350995.2_Missense_Mutation_p.D146H|EZH2_ENST00000536783.1_Missense_Mutation_p.D76H|EZH2_ENST00000320356.2_Missense_Mutation_p.D185H|EZH2_ENST00000478654.1_Missense_Mutation_p.D176H|EZH2_ENST00000483967.1_Missense_Mutation_p.D176H			Q15910	EZH2_HUMAN	enhancer of zeste 2 polycomb repressive complex 2 subunit	185	Interaction with DNMT1, DNMT3A and DNMT3B.		D -> H (in dbSNP:rs2302427).		cellular response to hydrogen peroxide (GO:0070301)|cerebellar cortex development (GO:0021695)|chromatin organization (GO:0006325)|DNA methylation (GO:0006306)|G1 to G0 transition (GO:0070314)|histone H3-K27 methylation (GO:0070734)|negative regulation of epidermal cell differentiation (GO:0045605)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of gene expression, epigenetic (GO:0045814)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of Ras GTPase activity (GO:0032320)|protein localization to chromatin (GO:0071168)|regulation of cell proliferation (GO:0042127)|regulation of circadian rhythm (GO:0042752)|regulation of gliogenesis (GO:0014013)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|ESC/E(Z) complex (GO:0035098)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)	chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone methyltransferase activity (GO:0042054)|histone methyltransferase activity (H3-K27 specific) (GO:0046976)|RNA binding (GO:0003723)|sequence-specific DNA binding (GO:0043565)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(313)|kidney(3)|large_intestine(8)|liver(1)|lung(23)|parathyroid(2)|skin(3)|upper_aerodigestive_tract(3)	359	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00239)			tcatcatcgtcatcatcatta	0.393			Mis		DLBCL								C|||	400	0.0798722	0.0038	0.0461	5008	,	,		19098	0.2063		0.0696	False		,,,				2504	0.0869				p.D185H		Atlas-SNP	.		Rec?	yes		7	7q35-q36	2146	enhancer of zeste homolog 2		L	EZH2_ENST00000350995,NS,carcinoma,+2,2	EZH2	823	2	0			c.G553C						PASS	.	C	HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP,HIS/ASP	66,4340	60.5+/-97.4	0,66,2137	178.0	146.0	157.0		553,526,526,553,436	5.7	0.9	7	dbSNP_100	157	719,7881	175.3+/-225.4	30,659,3611	yes	missense,missense,missense,missense,missense	EZH2	NM_001203247.1,NM_001203248.1,NM_001203249.1,NM_004456.4,NM_152998.2	81,81,81,81,81	30,725,5748	GG,GC,CC		8.3605,1.498,6.0357	benign,benign,benign,benign,benign	185/747,176/738,176/696,185/752,146/708	148525904	785,12221	2203	4300	6503	SO:0001583	missense	2146	exon6			CATCGTCATCATC		CCDS5891.1, CCDS5892.1, CCDS56516.1, CCDS56517.1, CCDS56518.1	7q35-q36	2014-09-17	2014-05-28		ENSG00000106462	ENSG00000106462		"""Chromatin-modifying enzymes / K-methyltransferases"""	3527	protein-coding gene	gene with protein product		601573	"""enhancer of zeste (Drosophila) homolog 2"", ""enhancer of zeste homolog 2 (Drosophila)"""			8954776, 17172412	Standard	NM_152998		Approved	EZH1, ENX-1, KMT6, KMT6A	uc003wfb.2	Q15910	OTTHUMG00000158973	ENST00000460911.1:c.553G>C	7.37:g.148525904C>G	ENSP00000419711:p.Asp185His	204.0	0.0	0		141.0	83.0	0.588652	NM_001203247	B2RAQ1|B3KS30|B7Z1D6|B7Z7L6|Q15755|Q75MG3|Q92857|Q96FI6	Missense_Mutation	SNP	ENST00000460911.1	37	CCDS56516.1	161	0.07371794871794872	3	0.006097560975609756	21	0.058011049723756904	83	0.1451048951048951	54	0.0712401055408971	C	19.43	3.826662	0.71143	0.01498	0.083605	ENSG00000106462	ENST00000478654;ENST00000320356;ENST00000460911;ENST00000350995;ENST00000541220;ENST00000476773;ENST00000483967;ENST00000536783	D;D;D;D;D;D;D;T	0.94828	-3.46;-3.5;-3.46;-3.5;-3.46;-3.46;-3.53;0.81	5.69	5.69	0.88448	SANT domain, DNA binding (1);	0.168733	0.49916	D	0.000127	T	0.08980	0.0222	L	0.34521	1.04	0.09310	P	0.99999641944	P;B;B;B;P;P	0.47604	0.898;0.348;0.348;0.41;0.659;0.676	P;B;B;B;B;P	0.49226	0.553;0.393;0.393;0.299;0.393;0.603	T	0.59161	-0.7506	9	0.72032	D	0.01	.	19.4235	0.94732	0.0:1.0:0.0:0.0	rs2302427;rs52833659	185;176;176;185;146;185	B7Z8K5;Q15910-4;Q15910-5;Q15910;Q15910-3;Q15910-2	.;.;.;EZH2_HUMAN;.;.	H	176;185;185;146;176;176;176;76	ENSP00000417062:D176H;ENSP00000320147:D185H;ENSP00000419711:D185H;ENSP00000223193:D146H;ENSP00000443219:D176H;ENSP00000419050:D176H;ENSP00000419856:D176H;ENSP00000439305:D76H	ENSP00000320147:D185H	D	-	1	0	EZH2	148156837	1.000000	0.71417	0.919000	0.36401	0.821000	0.46438	7.538000	0.82048	2.682000	0.91365	0.585000	0.79938	GAC	C|0.926;G|0.074	0.074	strong		0.393	EZH2-008	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352744.1	NM_004456	
LRIG1	26018	hgsc.bcm.edu	37	3	66434674	66434674	+	Silent	SNP	C	C	T	rs140903952	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:66434674C>T	ENST00000273261.3	-	14	2336	c.1812G>A	c.(1810-1812)acG>acA	p.T604T	LRIG1_ENST00000383703.3_Silent_p.T628T|SLC25A26_ENST00000536651.1_Intron|LRIG1_ENST00000496559.2_5'UTR	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	604	Ig-like C2-type 2.				innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)		p.T604T(1)		NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		TGTCGTGGGGCGTTTTGGTGA	0.547													c|||	7	0.00139776	0.0	0.0029	5008	,	,		18000	0.0		0.001	False		,,,				2504	0.0041				p.T604T		Atlas-SNP	.											LRIG1,colon,carcinoma,0,1	LRIG1	138	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1812A						PASS	.	T		2,4404	4.2+/-10.8	0,2,2201	233.0	225.0	228.0		1812	-1.0	0.8	3	dbSNP_134	228	22,8578	16.0+/-53.3	0,22,4278	no	coding-synonymous	LRIG1	NM_015541.2		0,24,6479	TT,TC,CC		0.2558,0.0454,0.1845		604/1094	66434674	24,12982	2203	4300	6503	SO:0001819	synonymous_variant	26018	exon14			GTGGGGCGTTTTG	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.1812G>A	3.37:g.66434674C>T		296.0	0.0	0		341.0	147.0	0.431085	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Silent	SNP	ENST00000273261.3	37	CCDS33783.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
DENND4C	55667	hgsc.bcm.edu	37	9	19290732	19290732	+	5'Flank	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:19290732A>G	ENST00000380432.2	+	0	0				DENND4C_ENST00000602925.1_Missense_Mutation_p.Y220C|DENND4C_ENST00000434457.2_Missense_Mutation_p.Y220C|RP11-146N23.4_ENST00000417577.2_RNA			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C						cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GAAGAGGACTATGAGTCATTT	0.343																																					p.Y220C		Atlas-SNP	.											.	DENND4C	120	.	0			c.A659G						PASS	.						96.0	85.0	88.0					9																	19290732		1829	4075	5904	SO:0001631	upstream_gene_variant	55667	exon5			AGGACTATGAGTC	AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627		9.37:g.19290732A>G	Exception_encountered	44.0	0.0	0		45.0	31.0	0.688889	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37																																																																																				.	.	none		0.343	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
OR52W1	120787	hgsc.bcm.edu	37	11	6221305	6221305	+	Missense_Mutation	SNP	C	C	G	rs374054864		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:6221305C>G	ENST00000311352.2	+	1	930	c.852C>G	c.(850-852)aaC>aaG	p.N284K	RP11-290F24.6_ENST00000600308.1_lincRNA	NM_001005178.1	NP_001005178.1	Q6IF63	O52W1_HUMAN	olfactory receptor, family 52, subfamily W, member 1	284						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)	11		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.114)		Epithelial(150;2.13e-08)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TTCTCTCCAACATCTACTTGC	0.527																																					p.N284K		Atlas-SNP	.											.	OR52W1	33	.	0			c.C852G						PASS	.	C	LYS/ASN	0,4402		0,0,2201	338.0	328.0	332.0		852	-0.5	1.0	11		332	1,8591	1.2+/-3.3	0,1,4295	no	missense	OR52W1	NM_001005178.1	94	0,1,6496	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	284/321	6221305	1,12993	2201	4296	6497	SO:0001583	missense	120787	exon1			CTCCAACATCTAC	AB065511	CCDS31407.1	11p15.4	2012-08-09		2004-03-10	ENSG00000175485	ENSG00000175485		"""GPCR / Class A : Olfactory receptors"""	15239	protein-coding gene	gene with protein product				OR52W1P			Standard	NM_001005178		Approved		uc010qzz.2	Q6IF63	OTTHUMG00000165378	ENST00000311352.2:c.852C>G	11.37:g.6221305C>G	ENSP00000309673:p.Asn284Lys	97.0	0.0	0		105.0	46.0	0.438095	NM_001005178	Q8NH78	Missense_Mutation	SNP	ENST00000311352.2	37	CCDS31407.1	.	.	.	.	.	.	.	.	.	.	C	15.85	2.954305	0.53293	0.0	1.16E-4	ENSG00000175485	ENST00000311352	T	0.00115	8.71	5.11	-0.514	0.11958	GPCR, rhodopsin-like superfamily (1);	0.173838	0.27245	N	0.020242	T	0.00241	0.0007	M	0.87971	2.92	0.22226	N	0.999278	P	0.47191	0.891	P	0.45377	0.478	T	0.42632	-0.9440	10	0.87932	D	0	.	6.437	0.21829	0.0:0.5957:0.1217:0.2826	.	284	Q6IF63	O52W1_HUMAN	K	284	ENSP00000309673:N284K	ENSP00000309673:N284K	N	+	3	2	OR52W1	6177881	0.000000	0.05858	0.995000	0.50966	0.975000	0.68041	-0.511000	0.06321	0.003000	0.14656	-0.253000	0.11424	AAC	.	.	weak		0.527	OR52W1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383758.1	NM_001005178	
PLXNA3	55558	hgsc.bcm.edu	37	X	153689643	153689643	+	Missense_Mutation	SNP	G	G	A	rs145244142	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrX:153689643G>A	ENST00000369682.3	+	3	974	c.799G>A	c.(799-801)Gcg>Acg	p.A267T		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	267	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					GCGCATGTGCGCGGGAGACTC	0.607																																					p.A267T		Atlas-SNP	.											.	PLXNA3	156	.	0			c.G799A						PASS	.	G	THR/ALA	3,3832		0,3,1629,571	95.0	88.0	90.0		799	3.5	0.0	X	dbSNP_134	90	2,6726		0,2,2426,1872	yes	missense	PLXNA3	NM_017514.3	58	0,5,4055,2443	AA,AG,GG,G		0.0297,0.0782,0.0473	benign	267/1872	153689643	5,10558	2203	4300	6503	SO:0001583	missense	55558	exon3			ATGTGCGCGGGAG	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.799G>A	X.37:g.153689643G>A	ENSP00000358696:p.Ala267Thr	121.0	0.0	0		49.0	49.0	1	NM_017514	Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	G	8.118	0.780273	0.16120	7.82E-4	2.97E-4	ENSG00000130827	ENST00000369682	T	0.10960	2.82	5.29	3.5	0.40072	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.124679	0.56097	D	0.000036	T	0.08133	0.0203	L	0.43152	1.355	0.23816	N	0.996762	B	0.24258	0.1	B	0.26202	0.067	T	0.40534	-0.9558	10	0.09338	T	0.73	.	6.5277	0.22310	0.087:0.0:0.5809:0.3321	.	267	P51805	PLXA3_HUMAN	T	267	ENSP00000358696:A267T	ENSP00000358696:A267T	A	+	1	0	PLXNA3	153342837	0.000000	0.05858	0.019000	0.16419	0.256000	0.26092	0.639000	0.24690	0.584000	0.29591	0.594000	0.82650	GCG	G|0.999;A|0.001	0.001	strong		0.607	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
TRUB2	26995	hgsc.bcm.edu	37	9	131073842	131073842	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131073842C>T	ENST00000372890.4	-	6	832	c.499G>A	c.(499-501)Gtt>Att	p.V167I	TRUB2_ENST00000460320.1_5'UTR|TRUB2_ENST00000546104.1_Missense_Mutation_p.V111I	NM_015679.1	NP_056494.1	O95900	TRUB2_HUMAN	TruB pseudouridine (psi) synthase family member 2	167					pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		poly(A) RNA binding (GO:0044822)|pseudouridine synthase activity (GO:0009982)			kidney(2)|large_intestine(2)|lung(3)|ovary(1)	8						CCTTGGATAACGGCCAGAATG	0.577																																					p.V167I		Atlas-SNP	.											.	TRUB2	26	.	0			c.G499A						PASS	.						121.0	102.0	108.0					9																	131073842		2203	4300	6503	SO:0001583	missense	26995	exon6			GGATAACGGCCAG	AK001956	CCDS6897.1	9q34.11	2014-01-28	2013-09-02		ENSG00000167112	ENSG00000167112			17170	protein-coding gene	gene with protein product		610727	"""TruB pseudouridine (psi) synthase homolog 2 (E. coli)"""			12736709	Standard	NM_015679		Approved	CLONE24922	uc004buq.1	O95900	OTTHUMG00000020741	ENST00000372890.4:c.499G>A	9.37:g.131073842C>T	ENSP00000361982:p.Val167Ile	126.0	0.0	0		137.0	20.0	0.145985	NM_015679	B7Z7G5	Missense_Mutation	SNP	ENST00000372890.4	37	CCDS6897.1	.	.	.	.	.	.	.	.	.	.	C	5.380	0.255372	0.10185	.	.	ENSG00000167112	ENST00000372890;ENST00000546104	T;T	0.51071	0.72;0.72	5.58	-2.46	0.06461	Pseudouridine synthase, catalytic domain (1);	0.527930	0.21014	N	0.081636	T	0.40398	0.1115	L	0.54323	1.7	0.21020	N	0.999806	B	0.10296	0.003	B	0.09377	0.004	T	0.25433	-1.0132	10	0.38643	T	0.18	-1.9214	15.1301	0.72517	0.0:0.7555:0.0944:0.1501	.	167	O95900	TRUB2_HUMAN	I	167;111	ENSP00000361982:V167I;ENSP00000438084:V111I	ENSP00000361982:V167I	V	-	1	0	TRUB2	130113663	0.001000	0.12720	0.009000	0.14445	0.593000	0.36681	-0.332000	0.07904	-0.900000	0.03896	-1.317000	0.01298	GTT	.	.	none		0.577	TRUB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054419.1	NM_015679	
FN3KRP	79672	hgsc.bcm.edu	37	17	80684843	80684843	+	Silent	SNP	G	G	A	rs146293327	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:80684843G>A	ENST00000269373.6	+	6	799	c.726G>A	c.(724-726)tcG>tcA	p.S242S	RP11-388C12.5_ENST00000570919.1_lincRNA|FN3KRP_ENST00000535965.1_Silent_p.S192S	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	242							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			ACGGCCACTCGGAATATGAGC	0.557													G|||	2	0.000399361	0.0008	0.0	5008	,	,		16728	0.0		0.001	False		,,,				2504	0.0				p.S242S		Atlas-SNP	.											FN3KRP,right_upper_lobe,carcinoma,+1,2	FN3KRP	31	2	0			c.G726A						PASS	.	G		0,4406		0,0,2203	61.0	64.0	63.0		726	-8.8	0.9	17	dbSNP_134	63	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	FN3KRP	NM_024619.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		242/310	80684843	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	79672	exon6			CCACTCGGAATAT	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.726G>A	17.37:g.80684843G>A		89.0	0.0	0		128.0	65.0	0.507812	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	37	CCDS11817.1																																																																																			G|0.999;A|0.001	0.001	strong		0.557	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
CHDH	55349	hgsc.bcm.edu	37	3	53855738	53855738	+	Silent	SNP	G	G	C	rs35064726	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:53855738G>C	ENST00000315251.6	-	5	1358	c.921C>G	c.(919-921)ctC>ctG	p.L307L		NM_018397.4	NP_060867.2	Q8NE62	CHDH_HUMAN	choline dehydrogenase	307					glycine betaine biosynthetic process from choline (GO:0019285)	mitochondrial inner membrane (GO:0005743)	choline dehydrogenase activity (GO:0008812)|flavin adenine dinucleotide binding (GO:0050660)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)	17		Hepatocellular(537;0.152)		BRCA - Breast invasive adenocarcinoma(193;0.000158)|KIRC - Kidney renal clear cell carcinoma(284;0.00588)|Kidney(284;0.00673)|OV - Ovarian serous cystadenocarcinoma(275;0.118)	Choline(DB00122)	CGATGCCAGAGAGCATGAGCA	0.562													G|||	123	0.0245607	0.0023	0.0216	5008	,	,		19271	0.0		0.0527	False		,,,				2504	0.0532				p.L307L		Atlas-SNP	.											.	CHDH	34	.	0			c.C921G						PASS	.	G		50,4356	50.9+/-86.3	0,50,2153	142.0	126.0	131.0		921	-2.7	0.6	3	dbSNP_126	131	472,8128	138.7+/-195.5	17,438,3845	no	coding-synonymous	CHDH	NM_018397.4		17,488,5998	CC,CG,GG		5.4884,1.1348,4.0135		307/595	53855738	522,12484	2203	4300	6503	SO:0001819	synonymous_variant	55349	exon5			GCCAGAGAGCATG	AJ272267	CCDS2873.1	3p21	2004-11-24			ENSG00000016391	ENSG00000016391	1.1.99.1		24288	protein-coding gene	gene with protein product							Standard	NM_018397		Approved		uc003dgz.3	Q8NE62	OTTHUMG00000158281	ENST00000315251.6:c.921C>G	3.37:g.53855738G>C		77.0	0.0	0		98.0	42.0	0.428571	NM_018397	Q9NY17	Silent	SNP	ENST00000315251.6	37	CCDS2873.1																																																																																			G|0.958;C|0.042	0.042	strong		0.562	CHDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350567.2	NM_018397	
OR2T5	401993	hgsc.bcm.edu	37	1	248652049	248652049	+	Missense_Mutation	SNP	C	C	T	rs554643879		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:248652049C>T	ENST00000366473.2	+	1	165	c.160C>T	c.(160-162)Cac>Tac	p.H54Y		NM_001004697.1	NP_001004697.1	Q6IEZ7	OR2T5_HUMAN	olfactory receptor, family 2, subfamily T, member 5	54						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)|ovary(2)|pancreas(1)|skin(2)	9	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)		OV - Ovarian serous cystadenocarcinoma(106;0.0265)			CCTTCTGATACACTGTGACGC	0.478													.|||	1	0.000199681	0.0	0.0	5008	,	,		22734	0.0		0.001	False		,,,				2504	0.0				p.H54Y		Atlas-SNP	.											.	OR2T5	17	.	0			c.C160T						PASS	.						26.0	58.0	47.0					1																	248652049		2151	4276	6427	SO:0001583	missense	401993	exon1			CTGATACACTGTG	BK004465	CCDS31118.1	1q44	2012-08-09			ENSG00000203661	ENSG00000203661		"""GPCR / Class A : Olfactory receptors"""	15017	protein-coding gene	gene with protein product							Standard	NM_001004697		Approved		uc001iem.1	Q6IEZ7	OTTHUMG00000040481	ENST00000366473.2:c.160C>T	1.37:g.248652049C>T	ENSP00000355429:p.His54Tyr	702.0	0.0	0		1045.0	302.0	0.288995	NM_001004697		Missense_Mutation	SNP	ENST00000366473.2	37	CCDS31118.1	.	.	.	.	.	.	.	.	.	.	c	0.003	-2.443662	0.00178	.	.	ENSG00000203661	ENST00000366473	T	0.02863	4.13	2.64	-5.28	0.02755	GPCR, rhodopsin-like superfamily (1);	0.834465	0.10259	N	0.696179	T	0.01353	0.0044	N	0.26092	0.79	0.09310	N	1	B	0.09022	0.002	B	0.10450	0.005	T	0.49579	-0.8925	10	0.02654	T	1	.	0.9068	0.01286	0.1456:0.2245:0.233:0.3969	.	54	Q6IEZ7	OR2T5_HUMAN	Y	54	ENSP00000355429:H54Y	ENSP00000355429:H54Y	H	+	1	0	OR2T5	246718672	0.000000	0.05858	0.093000	0.20910	0.019000	0.09904	-3.180000	0.00569	-0.589000	0.05874	-0.506000	0.04501	CAC	.	.	none		0.478	OR2T5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097422.1	NM_001004697	
DYRK1A	1859	hgsc.bcm.edu	37	21	38884589	38884589	+	Missense_Mutation	SNP	C	C	T	rs201554841		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:38884589C>T	ENST00000398960.2	+	11	2122	c.2047C>T	c.(2047-2049)Cgc>Tgc	p.R683C	DYRK1A_ENST00000338785.3_3'UTR|DYRK1A_ENST00000455387.2_Missense_Mutation_p.R455C|DYRK1A_ENST00000339659.4_Missense_Mutation_p.R674C	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	683					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CTACCAGAATCGCCCAGTGGC	0.517																																					p.R683C	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											DYRK1A,NS,malignant_melanoma,0,1	DYRK1A	85	1	0			c.C2047T						PASS	.						142.0	128.0	133.0					21																	38884589		2203	4300	6503	SO:0001583	missense	1859	exon11			CAGAATCGCCCAG	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.2047C>T	21.37:g.38884589C>T	ENSP00000381932:p.Arg683Cys	148.0	0.0	0		177.0	81.0	0.457627	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.272816	0.59649	.	.	ENSG00000157540	ENST00000339659;ENST00000398960;ENST00000455387	T;T;T	0.58652	0.32;0.35;0.88	5.73	4.85	0.62838	.	0.000000	0.85682	D	0.000000	T	0.45597	0.1350	N	0.24115	0.695	0.80722	D	1	B;B	0.17465	0.013;0.022	B;B	0.08055	0.001;0.003	T	0.40869	-0.9540	10	0.87932	D	0	.	14.9122	0.70767	0.0:0.9311:0.0:0.0689	.	683;674	Q13627;Q13627-2	DYR1A_HUMAN;.	C	674;683;455	ENSP00000340373:R674C;ENSP00000381932:R683C;ENSP00000407854:R455C	ENSP00000340373:R674C	R	+	1	0	DYRK1A	37806459	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.398000	0.79919	1.433000	0.47394	-0.150000	0.13652	CGC	C|0.999;T|0.001	0.001	weak		0.517	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
ZNF354A	6940	hgsc.bcm.edu	37	5	178139379	178139379	+	Silent	SNP	C	C	G	rs201342253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178139379C>G	ENST00000335815.2	-	5	1697	c.1500G>C	c.(1498-1500)ggG>ggC	p.G500G		NM_005649.2	NP_005640.2	O60765	Z354A_HUMAN	zinc finger protein 354A	500					regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|sensory perception of sound (GO:0007605)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|large_intestine(7)|lung(3)|ovary(2)|skin(2)|stomach(2)	19	all_cancers(89;0.000536)|Renal(175;0.000159)|all_epithelial(37;0.000221)|Lung NSC(126;0.00308)|all_lung(126;0.00536)	all_cancers(40;0.0452)|all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.185)		TGAATGTTTTCCCACACTCGT	0.393													C|||	14	0.00279553	0.0008	0.0029	5008	,	,		20195	0.0		0.0089	False		,,,				2504	0.002				p.G500G		Atlas-SNP	.											.	ZNF354A	74	.	0			c.G1500C						PASS	.						122.0	119.0	120.0					5																	178139379		2203	4300	6503	SO:0001819	synonymous_variant	6940	exon5			TGTTTTCCCACAC	AF116030	CCDS4438.1	5q35.3	2013-01-08		2001-11-23	ENSG00000169131	ENSG00000169131		"""Zinc fingers, C2H2-type"", ""-"""	11628	protein-coding gene	gene with protein product		602444		TCF17		9465904	Standard	NM_005649		Approved	KID-1, EZNF, HKL1, KID1	uc003mjj.3	O60765	OTTHUMG00000130895	ENST00000335815.2:c.1500G>C	5.37:g.178139379C>G		188.0	0.0	0		126.0	7.0	0.0555556	NM_005649	Q9UNJ8	Silent	SNP	ENST00000335815.2	37	CCDS4438.1																																																																																			C|0.999;G|0.001	0.001	weak		0.393	ZNF354A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253481.1	NM_005649	
KCNH5	27133	hgsc.bcm.edu	37	14	63175013	63175013	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63175013C>T	ENST00000322893.7	-	11	2448	c.2180G>A	c.(2179-2181)gGt>gAt	p.G727D	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	727					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)		CTCAGGGTCACCCTGTGTTGA	0.557																																					p.G727D		Atlas-SNP	.											KCNH5,NS,carcinoma,0,1	KCNH5	320	1	0			c.G2180A						PASS	.						115.0	107.0	110.0					14																	63175013		2203	4300	6503	SO:0001583	missense	27133	exon11			GGGTCACCCTGTG	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.2180G>A	14.37:g.63175013C>T	ENSP00000321427:p.Gly727Asp	159.0	0.0	0		161.0	68.0	0.42236	NM_139318	C9JP98	Missense_Mutation	SNP	ENST00000322893.7	37	CCDS9756.1	.	.	.	.	.	.	.	.	.	.	C	0.402	-0.917791	0.02396	.	.	ENSG00000140015	ENST00000322893	D	0.98849	-5.18	5.52	2.7	0.31948	.	0.410001	0.25494	N	0.030283	D	0.95191	0.8441	L	0.34521	1.04	0.34981	D	0.754079	B	0.10296	0.003	B	0.17098	0.017	D	0.91085	0.4902	10	0.19147	T	0.46	.	6.6545	0.22981	0.3021:0.5555:0.0:0.1423	.	727	Q8NCM2	KCNH5_HUMAN	D	727	ENSP00000321427:G727D	ENSP00000321427:G727D	G	-	2	0	KCNH5	62244766	0.000000	0.05858	0.065000	0.19835	0.001000	0.01503	0.059000	0.14322	0.297000	0.22615	-0.181000	0.13052	GGT	.	.	none		0.557	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
SMARCA4	6597	hgsc.bcm.edu	37	19	11145752	11145752	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11145752C>T	ENST00000429416.3	+	30	4395	c.4114C>T	c.(4114-4116)Cgc>Tgc	p.R1372C	SMARCA4_ENST00000590574.1_Missense_Mutation_p.R1339C|SMARCA4_ENST00000413806.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000358026.2_Missense_Mutation_p.R1372C|SMARCA4_ENST00000589677.1_Missense_Mutation_p.R1339C|SMARCA4_ENST00000541122.2_Missense_Mutation_p.R1339C|SMARCA4_ENST00000538456.3_3'UTR|SMARCA4_ENST00000444061.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000450717.3_Missense_Mutation_p.R1339C|SMARCA4_ENST00000344626.4_Missense_Mutation_p.R1372C	NM_001128844.1	NP_001122316.1	P51532	SMCA4_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4	1372					aortic smooth muscle cell differentiation (GO:0035887)|ATP catabolic process (GO:0006200)|ATP-dependent chromatin remodeling (GO:0043044)|blastocyst growth (GO:0001832)|blastocyst hatching (GO:0001835)|cell morphogenesis (GO:0000902)|chromatin remodeling (GO:0006338)|definitive erythrocyte differentiation (GO:0060318)|DNA methylation on cytosine within a CG sequence (GO:0010424)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic organ morphogenesis (GO:0048562)|epidermis morphogenesis (GO:0048730)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|glial cell fate determination (GO:0007403)|heart trabecula formation (GO:0060347)|hindbrain development (GO:0030902)|histone H3 acetylation (GO:0043966)|keratinocyte differentiation (GO:0030216)|lens fiber cell development (GO:0070307)|liver development (GO:0001889)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription, DNA-templated (GO:0045892)|neural retina development (GO:0003407)|nucleosome disassembly (GO:0006337)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of DNA binding (GO:0043388)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|vasculogenesis (GO:0001570)	extracellular space (GO:0005615)|heterochromatin (GO:0000792)|membrane (GO:0016020)|nBAF complex (GO:0071565)|npBAF complex (GO:0071564)|nuclear chromatin (GO:0000790)|nuclear euchromatin (GO:0005719)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perichromatin fibrils (GO:0005726)|protein complex (GO:0043234)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein N-terminus binding (GO:0047485)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription coactivator activity (GO:0001105)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)	p.?(1)		adrenal_gland(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(23)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|liver(4)|lung(60)|ovary(10)|pancreas(7)|prostate(3)|skin(8)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	163		all_lung(6;0.0512)|Lung NSC(9;0.0568)				CCGTGGCTCCCGCCACCGCAA	0.652			"""F, N, Mis"""		NSCLC																																p.R1372C		Atlas-SNP	.		Rec	yes		19	19p13.2	6597	"""SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4"""		E	.	SMARCA4	502	.	1	Unknown(1)	lung(1)	c.C4114T						PASS	.						44.0	36.0	39.0					19																	11145752		2203	4299	6502	SO:0001583	missense	6597	exon29			GGCTCCCGCCACC	D26156	CCDS12253.1, CCDS45972.1, CCDS45973.1, CCDS54217.1, CCDS54218.1	19p13.3	2014-09-17	2006-11-09		ENSG00000127616	ENSG00000127616			11100	protein-coding gene	gene with protein product	"""SNF2-like 4"", ""global transcription activator homologous sequence"", ""sucrose nonfermenting-like 4"", ""mitotic growth and transcription activator"", ""BRM/SWI2-related gene 1"", ""homeotic gene regulator"", ""nuclear protein GRB1"", ""brahma protein-like 1"", ""ATP-dependent helicase SMARCA4"""	603254		SNF2L4		8208605	Standard	NM_003072		Approved	hSNF2b, BRG1, BAF190, SNF2, SWI2, SNF2-BETA, SNF2LB, FLJ39786	uc010dxo.3	P51532	OTTHUMG00000169272	ENST00000429416.3:c.4114C>T	19.37:g.11145752C>T	ENSP00000395654:p.Arg1372Cys	174.0	0.0	0		163.0	28.0	0.171779	NM_003072	B1A8Z4|B1A8Z5|B1A8Z6|B1A8Z7|E9PBR8|O95052|Q9HBD3	Missense_Mutation	SNP	ENST00000429416.3	37	CCDS12253.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	25.0|25.0	4.593820|4.593820	0.86953|0.86953	.|.	.|.	ENSG00000127616|ENSG00000127616	ENST00000538456|ENST00000429416;ENST00000358026;ENST00000421844;ENST00000344626;ENST00000541122;ENST00000444061;ENST00000450717;ENST00000413806	.|D;D;D;D;D;D;D	.|0.95724	.|-3.77;-3.79;-3.77;-3.03;-3.0;-3.07;-3.03	4.59|4.59	3.56|3.56	0.40772|0.40772	.|.	.|0.065843	.|0.64402	.|D	.|0.000006	D|D	0.98239|0.98239	0.9417|0.9417	H|H	0.96239|0.96239	3.79|3.79	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D;D	.|0.97110	.|1.0;1.0;1.0;1.0;0.999;1.0;1.0	D|D	0.98554|0.98554	1.0638|1.0638	5|10	.|0.87932	.|D	.|0	-29.8756|-29.8756	11.6252|11.6252	0.51139|0.51139	0.0:0.9121:0.0:0.0879|0.0:0.9121:0.0:0.0879	.|.	.|1339;1339;1339;1372;1339;559;1372	.|B1A8Z6;B1A8Z4;B1A8Z7;Q9HBD4;B1A8Z5;B4E0F1;P51532	.|.;.;.;.;.;.;SMCA4_HUMAN	L|C	108|1372;1372;1403;1372;1339;1339;1339;1339	.|ENSP00000395654:R1372C;ENSP00000350720:R1372C;ENSP00000343896:R1372C;ENSP00000445036:R1339C;ENSP00000392837:R1339C;ENSP00000397783:R1339C;ENSP00000414727:R1339C	.|ENSP00000343896:R1372C	P|R	+|+	2|1	0|0	SMARCA4|SMARCA4	11006752|11006752	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.993000|0.993000	0.82548|0.82548	7.546000|7.546000	0.82137|0.82137	1.164000|1.164000	0.42652|0.42652	0.558000|0.558000	0.71614|0.71614	CCG|CGC	.	.	none		0.652	SMARCA4-007	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452638.2	NM_003072	
ZNF174	7727	hgsc.bcm.edu	37	16	3454480	3454480	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:3454480C>T	ENST00000268655.4	+	2	1042	c.457C>T	c.(457-459)Ctt>Ttt	p.L153F	ZNF174_ENST00000344823.5_Missense_Mutation_p.L153F|ZNF174_ENST00000572544.1_Missense_Mutation_p.L153F|ZNF174_ENST00000575752.1_Missense_Mutation_p.L153F|ZNF174_ENST00000571936.1_Missense_Mutation_p.L153F	NM_003450.2	NP_003441.1	Q15697	ZN174_HUMAN	zinc finger protein 174	153					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase II promoter (GO:0006366)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			endometrium(2)|large_intestine(3)|lung(3)|prostate(2)|urinary_tract(2)	12						TGGATCTCAGCTTGGAGAACA	0.537																																					p.L153F		Atlas-SNP	.											.	ZNF174	32	.	0			c.C457T						PASS	.						115.0	126.0	122.0					16																	3454480		2197	4300	6497	SO:0001583	missense	7727	exon2			TCTCAGCTTGGAG	U31248	CCDS10504.1, CCDS32380.1	16p13	2013-01-09			ENSG00000103343	ENSG00000103343		"""-"", ""Zinc fingers, C2H2-type"""	12963	protein-coding gene	gene with protein product		603900					Standard	NM_003450		Approved	ZSCAN8	uc002cvc.3	Q15697	OTTHUMG00000129358	ENST00000268655.4:c.457C>T	16.37:g.3454480C>T	ENSP00000268655:p.Leu153Phe	142.0	0.0	0		121.0	52.0	0.429752	NM_001032292	Q53Y68|Q9BQ34	Missense_Mutation	SNP	ENST00000268655.4	37	CCDS10504.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.508223	0.44660	.	.	ENSG00000103343	ENST00000344823;ENST00000268655	T;T	0.07444	4.06;3.19	5.32	3.34	0.38264	Transcription regulator SCAN (1);	0.161847	0.29631	N	0.011620	T	0.11153	0.0272	L	0.29908	0.895	0.29888	N	0.825478	P;D;P	0.53619	0.761;0.961;0.935	B;P;P	0.56700	0.36;0.804;0.642	T	0.02345	-1.1173	10	0.56958	D	0.05	.	5.9089	0.19016	0.1921:0.7141:0.0:0.0937	.	153;153;153	Q15697;Q15697-2;Q8IZN5	ZN174_HUMAN;.;.	F	153	ENSP00000339781:L153F;ENSP00000268655:L153F	ENSP00000268655:L153F	L	+	1	0	ZNF174	3394481	0.994000	0.37717	1.000000	0.80357	0.984000	0.73092	0.526000	0.22971	1.542000	0.49330	0.563000	0.77884	CTT	.	.	none		0.537	ZNF174-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251510.1	NM_003450	
FAM184B	27146	hgsc.bcm.edu	37	4	17636638	17636638	+	Silent	SNP	G	G	C	rs61745212	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:17636638G>C	ENST00000265018.3	-	16	3095	c.2883C>G	c.(2881-2883)tcC>tcG	p.S961S		NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	961										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						TTACCTTCATGGAAGGGGTCA	0.428													G|||	65	0.0129792	0.0295	0.0115	5008	,	,		18359	0.0		0.0149	False		,,,				2504	0.0031				p.S961S		Atlas-SNP	.											.	FAM184B	38	.	0			c.C2883G						PASS	.	G		29,1355		0,29,663	102.0	92.0	95.0		2883	5.3	1.0	4	dbSNP_129	95	48,3134		1,46,1544	no	coding-synonymous	FAM184B	NM_015688.1		1,75,2207	CC,CG,GG		1.5085,2.0954,1.6864		961/1061	17636638	77,4489	692	1591	2283	SO:0001819	synonymous_variant	27146	exon16			CTTCATGGAAGGG		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.2883C>G	4.37:g.17636638G>C		66.0	0.0	0		63.0	36.0	0.571429	NM_015688		Silent	SNP	ENST00000265018.3	37	CCDS47033.1																																																																																			G|0.960;C|0.040	0.040	strong		0.428	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
SPEF2	79925	hgsc.bcm.edu	37	5	35759812	35759812	+	Missense_Mutation	SNP	G	G	T	rs201517270	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:35759812G>T	ENST00000356031.3	+	25	3765	c.3611G>T	c.(3610-3612)aGc>aTc	p.S1204I	CTD-2113L7.1_ENST00000510433.1_RNA|SPEF2_ENST00000440995.2_Missense_Mutation_p.S1199I	NM_024867.3	NP_079143.3	Q9C093	SPEF2_HUMAN	sperm flagellar 2	1204					axoneme assembly (GO:0035082)|brain morphogenesis (GO:0048854)|embryonic neurocranium morphogenesis (GO:0048702)|fertilization (GO:0009566)|immune system development (GO:0002520)|multicellular organismal aging (GO:0010259)|respiratory system development (GO:0060541)|spermatogenesis (GO:0007283)	Golgi apparatus (GO:0005794)|manchette (GO:0002177)|sperm midpiece (GO:0097225)				breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(15)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	37	all_lung(31;7.56e-05)		Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			AATTCTGAAAGCCAGCTTAGG	0.348													G|||	3	0.000599042	0.0	0.0	5008	,	,		16893	0.0		0.003	False		,,,				2504	0.0				p.S1204I		Atlas-SNP	.											.	SPEF2	324	.	0			c.G3611T						PASS	.	G	ILE/SER	2,3688		0,2,1843	90.0	87.0	88.0		3611	-10.7	0.0	5		88	10,8146		0,10,4068	yes	missense	SPEF2	NM_024867.3	142	0,12,5911	TT,TG,GG		0.1226,0.0542,0.1013	benign	1204/1823	35759812	12,11834	1845	4078	5923	SO:0001583	missense	79925	exon25			CTGAAAGCCAGCT	AB051557	CCDS3910.1, CCDS43309.1	5p13.2	2010-05-04			ENSG00000152582	ENSG00000152582			26293	protein-coding gene	gene with protein product	"""cancer/testis antigen 122"""	610172				11214970, 16549801, 17610085	Standard	NM_024867		Approved	KPL2, FLJ23577, CT122	uc003jjo.3	Q9C093	OTTHUMG00000131111	ENST00000356031.3:c.3611G>T	5.37:g.35759812G>T	ENSP00000348314:p.Ser1204Ile	129.0	0.0	0		149.0	76.0	0.510067	NM_024867	Q2TAC9|Q96LL6|Q9H5C7|Q9H5Q7	Missense_Mutation	SNP	ENST00000356031.3	37	CCDS43309.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	3.572	-0.087472	0.07097	5.42E-4	0.001226	ENSG00000152582	ENST00000356031;ENST00000440995	T;T	0.36520	1.25;1.25	5.33	-10.7	0.00240	.	1.448510	0.03545	N	0.224510	T	0.27278	0.0669	L	0.50333	1.59	0.24410	N	0.994669	B;B	0.20261	0.043;0.014	B;B	0.20955	0.032;0.005	T	0.04870	-1.0921	10	0.19147	T	0.46	.	10.1477	0.42774	0.5976:0.0:0.229:0.1733	.	1199;1204	Q9C093-2;Q9C093	.;SPEF2_HUMAN	I	1204;1199	ENSP00000348314:S1204I;ENSP00000412125:S1199I	ENSP00000348314:S1204I	S	+	2	0	SPEF2	35795569	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-1.033000	0.03571	-2.982000	0.00282	-0.793000	0.03317	AGC	G|0.999;T|0.001	0.001	strong		0.348	SPEF2-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367199.1	NM_144722	
ZNF91	7644	hgsc.bcm.edu	37	19	23543078	23543078	+	Silent	SNP	C	C	T	rs117657695	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:23543078C>T	ENST00000300619.7	-	4	2908	c.2703G>A	c.(2701-2703)aaG>aaA	p.K901K	ZNF91_ENST00000397082.2_Silent_p.K869K|ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	901					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				TATGAATTCTCTTATGTTCAG	0.388													C|||	12	0.00239617	0.0023	0.0029	5008	,	,		21504	0.0		0.007	False		,,,				2504	0.0				p.K901K		Atlas-SNP	.											.	ZNF91	349	.	0			c.G2703A						PASS	.	C		6,4362	9.9+/-24.2	0,6,2178	59.0	65.0	63.0		2703	-1.5	0.0	19	dbSNP_132	63	70,8512	41.7+/-99.0	1,68,4222	no	coding-synonymous	ZNF91	NM_003430.2		1,74,6400	TT,TC,CC		0.8157,0.1374,0.5869		901/1192	23543078	76,12874	2184	4291	6475	SO:0001819	synonymous_variant	7644	exon4			AATTCTCTTATGT	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.2703G>A	19.37:g.23543078C>T		36.0	0.0	0		62.0	27.0	0.435484	NM_003430	A8K5E1|B7Z6G6	Silent	SNP	ENST00000300619.7	37	CCDS42541.1																																																																																			C|0.995;T|0.005	0.005	strong		0.388	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
TNFRSF18	8784	hgsc.bcm.edu	37	1	1140871	1140871	+	Splice_Site	SNP	G	G	A	rs142770542	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:1140871G>A	ENST00000379268.2	-	2	308	c.189C>T	c.(187-189)ggC>ggT	p.G63G	TNFRSF18_ENST00000328596.6_Splice_Site_p.G63G|TNFRSF18_ENST00000486728.1_5'UTR|TNFRSF18_ENST00000379265.5_Splice_Site_p.G63G	NM_004195.2|NM_148902.1	NP_004186.1|NP_683700.1	Q9Y5U5	TNR18_HUMAN	tumor necrosis factor receptor superfamily, member 18	63					apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|signal transduction (GO:0007165)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	tumor necrosis factor-activated receptor activity (GO:0005031)			lung(1)	1	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.73e-36)|OV - Ovarian serous cystadenocarcinoma(86;1.01e-21)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;4.22e-05)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.0025)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		AGCACTCCTCGCCTGGGCAGG	0.682													g|||	4	0.000798722	0.0015	0.0014	5008	,	,		16517	0.0		0.001	False		,,,				2504	0.0				p.G63G	GBM(157;472 1934 13810 14591 35952)	Atlas-SNP	.											.	TNFRSF18	13	.	0			c.C189T						PASS	.	G	,,	0,4394		0,0,2197	42.0	37.0	39.0		189,189,189	-4.2	0.0	1	dbSNP_134	39	21,8573	16.0+/-53.3	0,21,4276	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	TNFRSF18	NM_004195.2,NM_148901.1,NM_148902.1	,,	0,21,6473	AA,AG,GG		0.2444,0.0,0.1617	,,	63/242,63/256,63/235	1140871	21,12967	2197	4297	6494	SO:0001630	splice_region_variant	8784	exon2			CTCCTCGCCTGGG	AF125304	CCDS9.1, CCDS10.1, CCDS30552.1	1p36.3	2011-08-11			ENSG00000186891	ENSG00000186891		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11914	protein-coding gene	gene with protein product		603905				9177197, 10037686	Standard	NM_004195		Approved	AITR, GITR, CD357	uc001add.3	Q9Y5U5	OTTHUMG00000001414	ENST00000379268.2:c.188-1C>T	1.37:g.1140871G>A		139.0	0.0	0		132.0	71.0	0.537879	NM_148902	B1AME1|O95851|Q5U0I4|Q9NYJ9	Silent	SNP	ENST00000379268.2	37	CCDS10.1																																																																																			G|0.998;A|0.002	0.002	strong		0.682	TNFRSF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000004083.2	NM_004195	Silent
TTN	7273	hgsc.bcm.edu	37	2	179613651	179613651	+	Intron	SNP	G	G	A	rs72648904	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:179613651G>A	ENST00000591111.1	-	45	10585				TTN-AS1_ENST00000590773.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000589042.1_Intron|TTN_ENST00000360870.5_Silent_p.D4492D|TTN_ENST00000342175.6_Intron|TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron			Q8WZ42	TITIN_HUMAN	titin						adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			AAAAGGCTTTGTCATCAATCT	0.313													G|||	55	0.0109824	0.0015	0.0231	5008	,	,		19218	0.0		0.0239	False		,,,				2504	0.0133				p.D4492D		Atlas-SNP	.											.	TTN	18412	.	0			c.C13476T						PASS	.	G	,,,,	32,4374	37.6+/-69.7	0,32,2171	96.0	95.0	96.0		,,13476,,	0.9	0.0	2	dbSNP_130	96	306,8290	110.2+/-170.6	13,280,4005	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	13,312,6176	AA,AG,GG		3.5598,0.7263,2.5996	,,,,	,,4492/5605,,	179613651	338,12664	2203	4298	6501	SO:0001627	intron_variant	7273	exon46			GGCTTTGTCATCA	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.10360+4199C>T	2.37:g.179613651G>A		83.0	0.0	0		100.0	47.0	0.47	NM_133379	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.977;A|0.023	0.023	strong		0.313	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
IL22RA2	116379	hgsc.bcm.edu	37	6	137482840	137482840	+	Missense_Mutation	SNP	A	A	G	rs28385692	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:137482840A>G	ENST00000296980.2	-	2	347	c.47T>C	c.(46-48)cTt>cCt	p.L16P	IL22RA2_ENST00000339602.3_Missense_Mutation_p.L16P|IL22RA2_ENST00000349184.4_Missense_Mutation_p.L16P	NM_052962.2	NP_443194.1	Q969J5	I22R2_HUMAN	interleukin 22 receptor, alpha 2	16			L -> P (in dbSNP:rs28385692). {ECO:0000269|Ref.6}.		cytokine-mediated signaling pathway (GO:0019221)|negative regulation of inflammatory response (GO:0050728)|regulation of tyrosine phosphorylation of Stat3 protein (GO:0042516)	cytosol (GO:0005829)|extracellular space (GO:0005615)	interleukin-22 binding (GO:0042017)|interleukin-22 receptor activity (GO:0042018)			endometrium(1)|large_intestine(1)|lung(3)	5	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000313)|OV - Ovarian serous cystadenocarcinoma(155;0.00407)		TACACCAGTAAGGAAGAAACT	0.428													A|||	89	0.0177716	0.0023	0.0159	5008	,	,		17508	0.001		0.0318	False		,,,				2504	0.0429				p.L16P		Atlas-SNP	.											IL22RA2,NS,malignant_melanoma,-1,1	IL22RA2	17	1	0			c.T47C						PASS	.	A	PRO/LEU,PRO/LEU,PRO/LEU	30,4376	36.0+/-67.5	0,30,2173	119.0	92.0	101.0		47,47,47	3.3	0.7	6	dbSNP_125	101	295,8305	106.0+/-166.9	8,279,4013	yes	missense,missense,missense	IL22RA2	NM_052962.2,NM_181309.1,NM_181310.1	98,98,98	8,309,6186	GG,GA,AA		3.4302,0.6809,2.4988	benign,benign,benign	16/264,16/232,16/131	137482840	325,12681	2203	4300	6503	SO:0001583	missense	116379	exon2			CCAGTAAGGAAGA	AY044429	CCDS5182.1, CCDS5183.1, CCDS5184.1	6q24.1-q24.2	2008-02-05			ENSG00000164485	ENSG00000164485		"""Interleukins and interleukin receptors"""	14901	protein-coding gene	gene with protein product		606648				11481447, 11390454	Standard	NM_181309		Approved	CRF2-S1, IL-22BP	uc003qhl.3	Q969J5	OTTHUMG00000015655	ENST00000296980.2:c.47T>C	6.37:g.137482840A>G	ENSP00000296980:p.Leu16Pro	133.0	0.0	0		104.0	36.0	0.346154	NM_181309	Q08AH7|Q6UWM1|Q96A41|Q96QR0	Missense_Mutation	SNP	ENST00000296980.2	37	CCDS5182.1	29	0.013278388278388278	0	0.0	4	0.011049723756906077	0	0.0	25	0.032981530343007916	A	11.51	1.659956	0.29515	0.006809	0.034302	ENSG00000164485	ENST00000349184;ENST00000296980;ENST00000339602	T;T;T	0.79653	-1.29;-1.29;-1.29	4.55	3.3	0.37823	.	.	.	.	.	T	0.71879	0.3392	M	0.83384	2.64	0.38674	D	0.952373	B;B;P	0.45634	0.125;0.224;0.863	B;B;B	0.42112	0.037;0.097;0.376	T	0.72593	-0.4246	9	0.33141	T	0.24	.	7.7806	0.29062	0.7873:0.2127:0.0:0.0	rs28385692;rs35818500;rs28385692	16;16;16	Q969J5-3;Q969J5-2;Q969J5	.;.;I22R2_HUMAN	P	16	ENSP00000296979:L16P;ENSP00000296980:L16P;ENSP00000340920:L16P	ENSP00000296980:L16P	L	-	2	0	IL22RA2	137524533	0.004000	0.15560	0.734000	0.30879	0.386000	0.30323	0.318000	0.19504	2.060000	0.61445	0.524000	0.50904	CTT	A|0.974;G|0.026	0.026	strong		0.428	IL22RA2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042399.1		
BACE2	25825	hgsc.bcm.edu	37	21	42551270	42551270	+	Intron	SNP	A	A	G	rs199893430		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:42551270A>G	ENST00000330333.6	+	1	775				BACE2_ENST00000328735.6_Intron|PLAC4_ENST00000440221.2_RNA|BACE2_ENST00000347667.5_Intron|PLAC4_ENST00000430327.2_RNA|PLAC4_ENST00000414699.1_RNA|PLAC4_ENST00000536486.1_RNA|BACE2-IT1_ENST00000433378.1_RNA	NM_012105.3	NP_036237.2	Q9Y5Z0	BACE2_HUMAN	beta-site APP-cleaving enzyme 2						membrane protein ectodomain proteolysis (GO:0006509)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|peptide hormone processing (GO:0016486)|proteolysis (GO:0006508)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(2)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14		Prostate(19;1.57e-07)|all_epithelial(19;0.0251)				gagtgagggtatccagggtga	0.607																																					p.Y96H		Atlas-SNP	.											.	.	.	.	0			c.T286C						PASS	.						147.0	128.0	134.0					21																	42551270		2184	4258	6442	SO:0001627	intron_variant	191585	exon1			GAGGGTATCCAGG	AF117892	CCDS13668.1, CCDS13669.1, CCDS13670.1	21q22.3	2011-08-11			ENSG00000182240	ENSG00000182240			934	protein-coding gene	gene with protein product		605668		AEPLC		10965118, 10830953	Standard	NM_138991		Approved	CEAP1, DRAP, ALP56	uc002yyw.3	Q9Y5Z0	OTTHUMG00000086742	ENST00000330333.6:c.312+10768A>G	21.37:g.42551270A>G		244.0	0.0	0		283.0	21.0	0.0742049	NM_182832	A8K7P1|Q5DIH8|Q8N2D4|Q9H2V8|Q9NZL1|Q9NZL2|Q9UJT6	Missense_Mutation	SNP	ENST00000330333.6	37	CCDS13668.1																																																																																			.	.	weak		0.607	BACE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195056.1		
HSD17B1	3292	hgsc.bcm.edu	37	17	40706596	40706596	+	Missense_Mutation	SNP	C	C	T	rs147402365	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:40706596C>T	ENST00000585807.1	+	5	4433	c.713C>T	c.(712-714)gCg>gTg	p.A238V	RP11-400F19.8_ENST00000585572.1_RNA|HSD17B1_ENST00000225929.5_Missense_Mutation_p.A239V|RP11-400F19.6_ENST00000590513.1_RNA	NM_000413.2	NP_000404.2	P14061	DHB1_HUMAN	hydroxysteroid (17-beta) dehydrogenase 1	238			A -> V. {ECO:0000269|PubMed:8389226}.		bone development (GO:0060348)|cellular response to metal ion (GO:0071248)|estrogen biosynthetic process (GO:0006703)|estrogen metabolic process (GO:0008210)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)|steroid metabolic process (GO:0008202)|testosterone biosynthetic process (GO:0061370)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	catalytic activity (GO:0003824)|estradiol 17-beta-dehydrogenase activity (GO:0004303)			NS(1)|endometrium(1)|kidney(1)|lung(2)	5		all_cancers(22;5.59e-08)|all_epithelial(22;7e-07)|Ovarian(249;0.0261)		BRCA - Breast invasive adenocarcinoma(366;0.129)	Equilin(DB02187)	GAGGAGGTGGCGGAGGTGAGC	0.687													C|||	14	0.00279553	0.0008	0.0	5008	,	,		12600	0.0		0.0129	False		,,,				2504	0.0				p.A238V		Atlas-SNP	.											.	HSD17B1	24	.	0			c.C713T						PASS	.	C	VAL/ALA	9,4395	15.5+/-35.6	0,9,2193	39.0	31.0	34.0		713	-0.4	0.0	17	dbSNP_134	34	70,8530	42.2+/-99.7	0,70,4230	yes	missense	HSD17B1	NM_000413.2	64	0,79,6423	TT,TC,CC		0.814,0.2044,0.6075	benign	238/329	40706596	79,12925	2202	4300	6502	SO:0001583	missense	3292	exon5			AGGTGGCGGAGGT		CCDS11428.1	17q11-q21	2011-09-14					1.1.1.62	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	5210	protein-coding gene	gene with protein product	"""Estradiol 17-beta-dehydrogenase-1"", ""short chain dehydrogenase/reductase family 28CE, member 1"""	109684		EDHB17, EDH17B2		2330005, 19027726	Standard	NM_000413		Approved	HSD17, MGC138140, SDR28C1	uc002hzw.3	P14061		ENST00000585807.1:c.713C>T	17.37:g.40706596C>T	ENSP00000466799:p.Ala238Val	29.0	0.0	0		36.0	16.0	0.444444	NM_000413	B3KXS1|Q2M2L8	Missense_Mutation	SNP	ENST00000585807.1	37	CCDS11428.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	8.655	0.899159	0.17686	0.002044	0.00814	ENSG00000108786	ENST00000225929	.	.	.	4.16	-0.383	0.12477	NAD(P)-binding domain (1);	1.163550	0.06218	N	0.686122	T	0.07503	0.0189	N	0.04636	-0.2	0.09310	N	1	B;P	0.41102	0.002;0.738	B;B	0.28553	0.002;0.091	T	0.15065	-1.0450	9	0.30854	T	0.27	.	6.1916	0.20528	0.0:0.5144:0.0:0.4856	.	269;238	B3RFR9;P14061	.;DHB1_HUMAN	V	238	.	ENSP00000225929:A238V	A	+	2	0	HSD17B1	37960122	0.000000	0.05858	0.002000	0.10522	0.001000	0.01503	0.067000	0.14510	0.095000	0.17434	-0.658000	0.03865	GCG	C|0.996;T|0.004	0.004	strong		0.687	HSD17B1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000450392.1	NM_000413	
C7orf57	136288	hgsc.bcm.edu	37	7	48086151	48086151	+	Missense_Mutation	SNP	G	G	A	rs111480809	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:48086151G>A	ENST00000348904.3	+	5	657	c.445G>A	c.(445-447)Gac>Aac	p.D149N	C7orf57_ENST00000430738.1_Missense_Mutation_p.D194N|C7orf57_ENST00000420324.1_Missense_Mutation_p.D194N|C7orf57_ENST00000539619.1_Missense_Mutation_p.D149N|C7orf57_ENST00000435376.1_Missense_Mutation_p.D27N	NM_001100159.2	NP_001093629.1	Q8NEG2	CG057_HUMAN	chromosome 7 open reading frame 57	149										breast(1)|endometrium(2)|large_intestine(1)|lung(4)|ovary(1)	9						AGGGCCCTTCGACTTCGACAT	0.493													G|||	26	0.00519169	0.0	0.0101	5008	,	,		19923	0.0		0.0169	False		,,,				2504	0.002				p.D149N		Atlas-SNP	.											C7orf57_ENST00000348904,colon,carcinoma,0,2	C7orf57	59	2	0			c.G445A						PASS	.	G	ASN/ASP	5,3889		0,5,1942	61.0	57.0	59.0		445	4.6	1.0	7	dbSNP_132	59	103,8171		0,103,4034	yes	missense	C7orf57	NM_001100159.1	23	0,108,5976	AA,AG,GG		1.2449,0.1284,0.8876	probably-damaging	149/296	48086151	108,12060	1947	4137	6084	SO:0001583	missense	136288	exon5			CCCTTCGACTTCG	BC031107	CCDS47583.1, CCDS59054.1, CCDS75594.1	7p12.3	2011-11-25			ENSG00000164746	ENSG00000164746			22247	protein-coding gene	gene with protein product							Standard	NM_001100159		Approved		uc003toh.5	Q8NEG2	OTTHUMG00000155808	ENST00000348904.3:c.445G>A	7.37:g.48086151G>A	ENSP00000335500:p.Asp149Asn	75.0	0.0	0		91.0	43.0	0.472527	NM_001100159	C9JBJ8	Missense_Mutation	SNP	ENST00000348904.3	37	CCDS47583.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	G	17.67	3.447949	0.63178	0.001284	0.012449	ENSG00000164746	ENST00000420324;ENST00000435376;ENST00000430738;ENST00000348904;ENST00000539619	T;T;T;T;T	0.58060	0.36;0.36;0.36;0.36;0.36	5.44	4.56	0.56223	.	0.056720	0.64402	D	0.000001	T	0.55016	0.1894	M	0.76574	2.34	0.40682	D	0.982317	D;P	0.89917	1.0;0.638	D;B	0.73380	0.98;0.167	T	0.69022	-0.5255	10	0.59425	D	0.04	-23.6274	12.28	0.54759	0.0829:0.0:0.9171:0.0	.	27;149	C9JBJ8;Q8NEG2	.;CG057_HUMAN	N	194;27;194;149;149	ENSP00000394648:D194N;ENSP00000391652:D27N;ENSP00000410944:D194N;ENSP00000335500:D149N;ENSP00000442474:D149N	ENSP00000335500:D149N	D	+	1	0	C7orf57	48052676	1.000000	0.71417	0.965000	0.40720	0.991000	0.79684	4.434000	0.59935	1.425000	0.47237	0.655000	0.94253	GAC	G|0.989;A|0.011	0.011	strong		0.493	C7orf57-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341745.1	NM_001100159	
LAMB1	3912	hgsc.bcm.edu	37	7	107591763	107591763	+	Missense_Mutation	SNP	G	G	A	rs145485632	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:107591763G>A	ENST00000222399.6	-	24	3529	c.3299C>T	c.(3298-3300)aCg>aTg	p.T1100M	LAMB1_ENST00000393561.1_Missense_Mutation_p.T1124M	NM_002291.2	NP_002282.2	P07942	LAMB1_HUMAN	laminin, beta 1	1100	Laminin EGF-like 12. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|embryo implantation (GO:0007566)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell adhesion (GO:0007162)|neuron projection development (GO:0031175)|neuronal-glial interaction involved in cerebral cortex radial glia guided migration (GO:0021812)|odontogenesis (GO:0042476)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell proliferation (GO:0050679)|substrate adhesion-dependent cell spreading (GO:0034446)	basement membrane (GO:0005604)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|laminin-1 complex (GO:0005606)|laminin-10 complex (GO:0043259)|laminin-2 complex (GO:0005607)|laminin-8 complex (GO:0043257)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)|structural molecule activity (GO:0005198)			NS(3)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(37)|ovary(6)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)	82						GCACTGCCCCGTGAACTGCGG	0.572													G|||	5	0.000998403	0.0	0.0029	5008	,	,		16910	0.0		0.003	False		,,,				2504	0.0				p.T1100M		Atlas-SNP	.											.	LAMB1	185	.	0			c.C3299T						PASS	.	G	MET/THR	3,4403	6.2+/-15.9	0,3,2200	42.0	38.0	39.0		3299	5.0	1.0	7	dbSNP_134	39	1,8599	1.2+/-3.3	0,1,4299	yes	missense	LAMB1	NM_002291.2	81	0,4,6499	AA,AG,GG		0.0116,0.0681,0.0308	possibly-damaging	1100/1787	107591763	4,13002	2203	4300	6503	SO:0001583	missense	3912	exon24			TGCCCCGTGAACT	M61916	CCDS5750.1	7q22	2013-03-01			ENSG00000091136	ENSG00000091136		"""Laminins"""	6486	protein-coding gene	gene with protein product		150240	"""cutis laxa with marfanoid phenotype"""	CLM		2563160, 2704655, 1864606	Standard	NM_002291		Approved		uc003vew.2	P07942	OTTHUMG00000149966	ENST00000222399.6:c.3299C>T	7.37:g.107591763G>A	ENSP00000222399:p.Thr1100Met	104.0	0.0	0		116.0	54.0	0.465517	NM_002291	Q14D91	Missense_Mutation	SNP	ENST00000222399.6	37	CCDS5750.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	17.85	3.489271	0.64074	6.81E-4	1.16E-4	ENSG00000091136	ENST00000393561;ENST00000222399	T;T	0.66099	-0.19;-0.19	5.0	5.0	0.66597	EGF-like, laminin (3);	.	.	.	.	T	0.77532	0.4144	M	0.92507	3.315	0.80722	D	1	D;D	0.65815	0.995;0.991	P;B	0.59115	0.852;0.424	D	0.84831	0.0802	9	0.66056	D	0.02	.	18.8361	0.92164	0.0:0.0:1.0:0.0	.	1100;1124	P07942;G3XAI2	LAMB1_HUMAN;.	M	1124;1100	ENSP00000377191:T1124M;ENSP00000222399:T1100M	ENSP00000222399:T1100M	T	-	2	0	LAMB1	107378999	0.986000	0.35501	0.976000	0.42696	0.899000	0.52679	2.037000	0.41174	2.748000	0.94277	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.572	LAMB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000314584.1	NM_002291	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859816	144859816	+	Missense_Mutation	SNP	T	T	C	rs587702923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859816T>C	ENST00000369354.3	-	38	6457	c.6268A>G	c.(6268-6270)Att>Gtt	p.I2090V	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.I2175V|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.I2226V|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.I1984V|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.I2090V			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2090					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TTCTGGTTAATGGAGGAGGGG	0.577			T	PDGFRB	MPD																																p.I2090V		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.A6268G						PASS	.						65.0	63.0	63.0					1																	144859816		2203	4300	6503	SO:0001583	missense	9659	exon38			GGTTAATGGAGGA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6268A>G	1.37:g.144859816T>C	ENSP00000358360:p.Ile2090Val	309.0	0.0	0		409.0	26.0	0.0635697	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	T	0.010	-1.760839	0.00657	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01685	4.69;4.78;4.78;4.8;4.79	4.63	-9.26	0.00662	.	.	.	.	.	T	0.00178	0.0005	N	0.03608	-0.345	0.09310	N	0.999999	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.47058	-0.9146	9	0.02654	T	1	.	5.9795	0.19399	0.0819:0.4615:0.1653:0.2913	.	1984;2090	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	V	1984;2090;2090;2175;2226	ENSP00000327209:I1984V;ENSP00000358360:I2090V;ENSP00000358363:I2090V;ENSP00000435654:I2175V;ENSP00000358366:I2226V	ENSP00000327209:I1984V	I	-	1	0	PDE4DIP	143571173	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.249000	0.00266	-3.114000	0.00240	-1.162000	0.01777	ATT	.	.	none		0.577	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
HLA-C	3107	hgsc.bcm.edu	37	6	31239622	31239622	+	Missense_Mutation	SNP	C	C	G	rs9264668	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31239622C>G	ENST00000376228.5	-	2	111	c.97G>C	c.(97-99)Gac>Cac	p.D33H	HLA-C_ENST00000383329.3_Missense_Mutation_p.D33H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	33	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGGCGGTGTCGAAATACCTC	0.726													a|||	20	0.00399361	0.0113	0.0	5008	,	,		11654	0.001		0.003	False		,,,				2504	0.001				p.D33H		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	0			c.G97C						scavenged	.						16.0	17.0	17.0					6																	31239622		1477	2676	4153	SO:0001583	missense	3107	exon2			CGGTGTCGAAATA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.97G>C	6.37:g.31239622C>G	ENSP00000365402:p.Asp33His	79.0	0.0	0		76.0	12.0	0.157895	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.003|0.003	-2.468672|-2.468672	0.00169|0.00169	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.5;9.5|.	2.16|2.16	-4.32|-4.32	0.03688|0.03688	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	10.311600|.	0.00879|.	N|.	0.002109|.	T|T	0.03390|0.03390	0.0098|0.0098	L|L	0.31578|0.31578	0.945|0.945	0.09310|0.09310	N|N	1|1	P;P;P;P|.	0.51351|.	0.944;0.822;0.822;0.888|.	P;P;P;D|.	0.68483|.	0.904;0.904;0.829;0.958|.	T|T	0.58504|0.58504	-0.7625|-0.7625	10|5	0.42905|.	T|.	0.14|.	.|.	0.4543|0.4543	0.00506|0.00506	0.2454:0.267:0.2544:0.2332|0.2454:0.267:0.2544:0.2332	.|.	33;33;33;33|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	H|P	33;33;33;70|32	ENSP00000365402:D33H;ENSP00000372819:D33H|.	ENSP00000365402:D33H|.	D|R	-|-	1|2	0|0	HLA-C|HLA-C	31347601|31347601	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-13.217000|-13.217000	0.00001|0.00001	-7.736000|-7.736000	0.00000|0.00000	-4.008000|-4.008000	0.00013|0.00013	GAC|CGA	A|0.575;C|0.423;G|0.002	0.002	strong		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
BICD1	636	hgsc.bcm.edu	37	12	32480886	32480886	+	Silent	SNP	T	T	C	rs12369637	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:32480886T>C	ENST00000281474.5	+	5	1600	c.1497T>C	c.(1495-1497)agT>agC	p.S499S	BICD1_ENST00000548411.1_Silent_p.S499S	NM_001714.2	NP_001705.2	Q96G01	BICD1_HUMAN	bicaudal D homolog 1 (Drosophila)	499					anatomical structure morphogenesis (GO:0009653)|intracellular mRNA localization (GO:0008298)|microtubule anchoring at microtubule organizing center (GO:0072393)|minus-end-directed organelle transport along microtubule (GO:0072385)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of phospholipase C-activating G-protein coupled receptor signaling pathway (GO:1900737)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein localization to organelle (GO:0033365)|regulation of proteinase activated receptor activity (GO:1900276)|RNA processing (GO:0006396)|stress granule assembly (GO:0034063)|viral process (GO:0016032)	cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|host cell viral assembly compartment (GO:0072517)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	cytoskeletal adaptor activity (GO:0008093)|dynactin binding (GO:0034452)|dynein binding (GO:0045502)|proteinase activated receptor binding (GO:0031871)|Rab GTPase binding (GO:0017137)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(14)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	46	all_cancers(9;5.13e-11)|all_epithelial(9;2.71e-11)|all_lung(12;6.66e-10)|Acute lymphoblastic leukemia(23;0.0122)|Lung SC(12;0.0213)|all_hematologic(23;0.0429)|Esophageal squamous(101;0.204)		OV - Ovarian serous cystadenocarcinoma(6;0.0201)			AAAATCACAGTACCCTTAATA	0.468													T|||	27	0.00539137	0.0008	0.0058	5008	,	,		20862	0.0		0.0189	False		,,,				2504	0.0031				p.S499S		Atlas-SNP	.											.	BICD1	89	.	0			c.T1497C						PASS	.	T	,	21,4385	28.1+/-56.4	0,21,2182	143.0	119.0	127.0		1497,1497	-1.3	1.0	12	dbSNP_120	127	208,8392	89.2+/-151.4	5,198,4097	no	coding-synonymous,coding-synonymous	BICD1	NM_001003398.1,NM_001714.2	,	5,219,6279	CC,CT,TT		2.4186,0.4766,1.7607	,	499/836,499/976	32480886	229,12777	2203	4300	6503	SO:0001819	synonymous_variant	636	exon5			TCACAGTACCCTT	U90028	CCDS8726.1, CCDS44859.1	12p11.2-p11.1	2005-01-13	2001-11-28			ENSG00000151746			1049	protein-coding gene	gene with protein product		602204	"""Bicaudal D (Drosophila) homolog 1"""			9367685	Standard	NM_001714		Approved		uc001rku.3	Q96G01	OTTHUMG00000169307	ENST00000281474.5:c.1497T>C	12.37:g.32480886T>C		165.0	0.0	0		174.0	69.0	0.396552	NM_001714	A8K2C3|F8W113|O43892|O43893	Silent	SNP	ENST00000281474.5	37	CCDS8726.1																																																																																			T|0.987;C|0.013	0.013	strong		0.468	BICD1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403380.1	NM_001714	
PAH	5053	hgsc.bcm.edu	37	12	103288554	103288554	+	Missense_Mutation	SNP	G	G	T	rs398123291|rs62642929|rs199475570		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:103288554G>T	ENST00000553106.1	-	3	783	c.311C>A	c.(310-312)gCc>gAc	p.A104D	PAH_ENST00000307000.2_Missense_Mutation_p.A99D|PAH_ENST00000551988.1_5'UTR	NM_000277.1	NP_000268.1	P00439	PH4H_HUMAN	phenylalanine hydroxylase	104	ACT. {ECO:0000255|PROSITE- ProRule:PRU01007}.		A -> D (in PKU; mild; haplotype 1).		catecholamine biosynthetic process (GO:0042423)|cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-phenylalanine catabolic process (GO:0006559)|neurotransmitter biosynthetic process (GO:0042136)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|phenylalanine 4-monooxygenase activity (GO:0004505)			endometrium(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(5)|skin(2)|urinary_tract(1)	27					Droxidopa(DB06262)|Epinephrine(DB00668)|L-Phenylalanine(DB00120)|Norepinephrine(DB00368)|Tetrahydrobiopterin(DB00360)	ATGGACAGTGGCACCAATGTC	0.383																																					p.A104D		Atlas-SNP	.											.	PAH	77	.	0			c.C311A	GRCh37	CM920543	PAH	M	rs62642929	PASS	.						150.0	143.0	146.0					12																	103288554		2203	4300	6503	SO:0001583	missense	5053	exon3			ACAGTGGCACCAA	U49897	CCDS9092.1	12q22-q24.2	2010-04-27				ENSG00000171759	1.14.16.1		8582	protein-coding gene	gene with protein product	"""phenylalanine 4-monooxygenase"""	612349				2063869	Standard	NM_000277		Approved	PH	uc001tjq.1	P00439		ENST00000553106.1:c.311C>A	12.37:g.103288554G>T	ENSP00000448059:p.Ala104Asp	96.0	0.0	0		123.0	49.0	0.398374	NM_000277	Q16717|Q8TC14	Missense_Mutation	SNP	ENST00000553106.1	37	CCDS9092.1	.	.	.	.	.	.	.	.	.	.	G	14.05	2.418471	0.42918	.	.	ENSG00000171759	ENST00000553106;ENST00000307000;ENST00000551337;ENST00000546844	D;D;D;D	0.98280	-4.84;-4.84;-4.84;-4.84	6.17	5.29	0.74685	.	0.098719	0.64402	D	0.000002	D	0.95153	0.8429	L	0.29908	0.895	0.49299	D	0.999774	B;B	0.15930	0.015;0.002	B;B	0.11329	0.006;0.002	D	0.92907	0.6344	10	0.19147	T	0.46	-15.3988	13.5379	0.61657	0.1288:0.0:0.8712:0.0	rs62642929	104;104	B4DPN2;P00439	.;PH4H_HUMAN	D	104;99;104;104	ENSP00000448059:A104D;ENSP00000303500:A99D;ENSP00000447620:A104D;ENSP00000446658:A104D	ENSP00000303500:A99D	A	-	2	0	PAH	101812684	1.000000	0.71417	0.996000	0.52242	0.829000	0.46940	2.755000	0.47540	1.625000	0.50366	0.655000	0.94253	GCC	.	.	weak		0.383	PAH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406692.1		
C6orf15	29113	hgsc.bcm.edu	37	6	31079350	31079350	+	Silent	SNP	T	T	C	rs146335336	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:31079350T>C	ENST00000259870.3	-	2	789	c.786A>G	c.(784-786)ggA>ggG	p.G262G		NM_014070.2	NP_054789.2	Q6UXA7	CF015_HUMAN	chromosome 6 open reading frame 15	262	Gly-rich.				extracellular matrix organization (GO:0030198)	interstitial matrix (GO:0005614)	heparin binding (GO:0008201)|hyaluronic acid binding (GO:0005540)			endometrium(3)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|stomach(1)	17						GATTAATATTTCCCCAGCTGC	0.502																																					p.G262G		Atlas-SNP	.											.	C6orf15	29	.	0			c.A786G						PASS	.						64.0	75.0	71.0					6																	31079350		1739	3348	5087	SO:0001819	synonymous_variant	29113	exon2			AATATTTCCCCAG	AB031481	CCDS4693.1	6p21	2011-12-12			ENSG00000204542	ENSG00000204542			13927	protein-coding gene	gene with protein product		611401					Standard	NM_014070		Approved	STG	uc003nsk.1	Q6UXA7	OTTHUMG00000031111	ENST00000259870.3:c.786A>G	6.37:g.31079350T>C		147.0	0.0	0		184.0	63.0	0.342391	NM_014070	B0S7V8|Q0EFA6|Q2L6G7|Q5SQ81|Q86Z05|Q9UIG3	Silent	SNP	ENST00000259870.3	37	CCDS4693.1																																																																																			T|0.998;C|0.002	0.002	strong		0.502	C6orf15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076184.2	NM_014070	
CUL9	23113	hgsc.bcm.edu	37	6	43154017	43154017	+	Missense_Mutation	SNP	C	C	G	rs150188923	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:43154017C>G	ENST00000252050.4	+	4	1159	c.1075C>G	c.(1075-1077)Caa>Gaa	p.Q359E	CUL9_ENST00000372647.2_Missense_Mutation_p.Q359E|CUL9_ENST00000354495.3_Missense_Mutation_p.Q359E	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9	359					microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CCCCAGAAGACAAGGGTGGGT	0.587													C|||	15	0.00299521	0.0008	0.0029	5008	,	,		17488	0.0		0.0119	False		,,,				2504	0.0				p.Q359E		Atlas-SNP	.											.	CUL9	248	.	0			c.C1075G						PASS	.	C	GLU/GLN	8,4398	14.3+/-33.2	0,8,2195	78.0	82.0	81.0		1075	4.6	0.3	6	dbSNP_134	81	75,8525	44.5+/-102.8	1,73,4226	yes	missense	CUL9	NM_015089.2	29	1,81,6421	GG,GC,CC		0.8721,0.1816,0.6382	benign	359/2518	43154017	83,12923	2203	4300	6503	SO:0001583	missense	23113	exon4			AGAAGACAAGGGT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723	ENST00000252050.4:c.1075C>G	6.37:g.43154017C>G	ENSP00000252050:p.Gln359Glu	97.0	0.0	0		122.0	56.0	0.459016	NM_015089	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Missense_Mutation	SNP	ENST00000252050.4	37	CCDS4890.1	12	0.005494505494505495	0	0.0	0	0.0	0	0.0	12	0.0158311345646438	C	12.56	1.974769	0.34848	0.001816	0.008721	ENSG00000112659	ENST00000252050;ENST00000354495;ENST00000372647	T;T;T	0.72942	-0.7;-0.69;-0.6	5.5	4.63	0.57726	.	1.075350	0.07089	N	0.838384	T	0.49457	0.1558	L	0.42245	1.32	0.22001	N	0.999429	B;B;B	0.23937	0.094;0.094;0.044	B;B;B	0.21360	0.034;0.034;0.019	T	0.52601	-0.8554	10	0.45353	T	0.12	0.0071	14.0214	0.64558	0.0:0.9271:0.0:0.0729	.	359;359;359	E9PEZ1;Q8IWT3;Q05C85	.;CUL9_HUMAN;.	E	359	ENSP00000252050:Q359E;ENSP00000346490:Q359E;ENSP00000361730:Q359E	ENSP00000252050:Q359E	Q	+	1	0	CUL9	43261995	1.000000	0.71417	0.272000	0.24630	0.923000	0.55619	2.022000	0.41030	1.317000	0.45149	0.467000	0.42956	CAA	C|0.995;G|0.005	0.005	strong		0.587	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
CIDEB	27141	hgsc.bcm.edu	37	14	24775287	24775287	+	Silent	SNP	G	G	A	rs139893717	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:24775287G>A	ENST00000336557.5	-	7	1695	c.393C>T	c.(391-393)atC>atT	p.I131I	CIDEB_ENST00000258807.5_Silent_p.I131I|CIDEB_ENST00000554411.1_Silent_p.I131I|NOP9_ENST00000267425.3_3'UTR|LTB4R2_ENST00000528054.1_5'Flank			Q9UHD4	CIDEB_HUMAN	cell death-inducing DFFA-like effector b	131					apoptotic process (GO:0006915)|execution phase of apoptosis (GO:0097194)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|regulation of apoptotic process (GO:0042981)	cytosol (GO:0005829)|lipid particle (GO:0005811)	identical protein binding (GO:0042802)			NS(1)|endometrium(1)|kidney(1)|large_intestine(3)|urinary_tract(1)	7				GBM - Glioblastoma multiforme(265;0.0181)		TGAATCGGGCGATGTCCTTGC	0.527													G|||	8	0.00159744	0.0	0.0072	5008	,	,		21522	0.0		0.002	False		,,,				2504	0.001				p.I131I		Atlas-SNP	.											.	CIDEB	17	.	0			c.C393T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	196.0	166.0	176.0		393	0.1	1.0	14	dbSNP_134	176	72,8528	43.1+/-100.9	1,70,4229	no	coding-synonymous	CIDEB	NM_014430.2		1,79,6423	AA,AG,GG		0.8372,0.2043,0.6228		131/220	24775287	81,12925	2203	4300	6503	SO:0001819	synonymous_variant	27141	exon6			TCGGGCGATGTCC	AF190901	CCDS32056.1	14q12	2012-09-20			ENSG00000136305	ENSG00000136305			1977	protein-coding gene	gene with protein product		604441				10619428, 10837461	Standard	XM_005267540		Approved		uc001woo.3	Q9UHD4	OTTHUMG00000171555	ENST00000336557.5:c.393C>T	14.37:g.24775287G>A		70.0	0.0	0		62.0	28.0	0.451613	NM_014430	D3DS73|Q546V8|Q9NNW9	Silent	SNP	ENST00000336557.5	37	CCDS32056.1																																																																																			G|0.995;A|0.005	0.005	strong		0.527	CIDEB-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414120.1		
TSHR	7253	hgsc.bcm.edu	37	14	81558919	81558919	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:81558919C>G	ENST00000541158.2	+	7	834	c.512C>G	c.(511-513)gCt>gGt	p.A171G	TSHR_ENST00000298171.2_Missense_Mutation_p.A171G|TSHR_ENST00000554435.1_Missense_Mutation_p.A171G|TSHR_ENST00000554263.1_Missense_Mutation_p.A171G|TSHR_ENST00000342443.6_Missense_Mutation_p.A171G			P16473	TSHR_HUMAN	thyroid stimulating hormone receptor	171					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adult locomotory behavior (GO:0008344)|B cell differentiation (GO:0030183)|cell-cell signaling (GO:0007267)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|positive regulation of cell proliferation (GO:0008284)|positive regulation of multicellular organism growth (GO:0040018)|regulation of locomotion (GO:0040012)|thyroid-stimulating hormone signaling pathway (GO:0038194)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	thyroid-stimulating hormone receptor activity (GO:0004996)			breast(2)|endometrium(2)|kidney(1)|large_intestine(10)|lung(18)|ovary(6)|prostate(3)|skin(2)|stomach(1)|thyroid(291)|upper_aerodigestive_tract(1)	337				BRCA - Breast invasive adenocarcinoma(234;0.0402)	Thyrotropin Alfa(DB00024)	CCTGTGAATGCTTTTCAGGGA	0.388			Mis		toxic thyroid adenoma	thyroid  adenoma	Hereditary nonautoimmune hyperthyroidism; subclinical hypothyroidism																														p.A171G		Atlas-SNP	.	yes	Dom	yes		14	14q31	7253	thyroid stimulating hormone receptor	yes	E	TSHR_ENST00000554435,NS,carcinoma,+1,2	TSHR	462	2	0			c.C512G						PASS	.						204.0	181.0	189.0					14																	81558919		2203	4300	6503	SO:0001583	missense	7253	exon6			TGAATGCTTTTCA	AY429111	CCDS9872.1, CCDS32131.1, CCDS55935.1	14q24-q31	2014-09-17			ENSG00000165409	ENSG00000165409		"""GPCR / Class A : Gonadotropin and TSH receptors"""	12373	protein-coding gene	gene with protein product		603372				2558651, 2610690	Standard	NM_001018036		Approved	LGR3	uc001xvd.1	P16473		ENST00000541158.2:c.512C>G	14.37:g.81558919C>G	ENSP00000441235:p.Ala171Gly	152.0	0.0	0		201.0	26.0	0.129353	NM_000369	A0PJU7|F5GYU5|G3V2A9|Q16503|Q8TB90|Q96GT6|Q9P1V4|Q9ULA3|Q9UPH3	Missense_Mutation	SNP	ENST00000541158.2	37	CCDS9872.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.074553	0.76415	.	.	ENSG00000165409	ENST00000541158;ENST00000342443;ENST00000298171;ENST00000554263;ENST00000554435	D;D;D;D;D	0.93659	-3.26;-3.26;-3.26;-3.26;-3.26	5.28	5.28	0.74379	.	0.104905	0.64402	D	0.000003	D	0.97235	0.9096	H	0.94264	3.515	0.58432	D	0.999992	P;D;P;P	0.54207	0.918;0.965;0.953;0.852	P;P;P;P	0.61533	0.88;0.789;0.89;0.502	D	0.98083	1.0405	10	0.87932	D	0	.	14.4086	0.67101	0.0:1.0:0.0:0.0	.	171;171;171;171	G3V2A9;F5GYU5;P16473-2;P16473	.;.;.;TSHR_HUMAN	G	171	ENSP00000441235:A171G;ENSP00000340113:A171G;ENSP00000298171:A171G;ENSP00000451202:A171G;ENSP00000450549:A171G	ENSP00000298171:A171G	A	+	2	0	TSHR	80628672	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.359000	0.52292	2.483000	0.83821	0.655000	0.94253	GCT	.	.	none		0.388	TSHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413364.1	NM_000369	
TRIM54	57159	hgsc.bcm.edu	37	2	27521506	27521506	+	Silent	SNP	G	G	A	rs540676343		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:27521506G>A	ENST00000380075.2	+	2	580	c.240G>A	c.(238-240)tcG>tcA	p.S80S	TRIM54_ENST00000296098.4_Silent_p.S80S	NM_187841.2	NP_912730.2	Q9BYV2	TRI54_HUMAN	tripartite motif containing 54	80					cell differentiation (GO:0030154)|microtubule-based process (GO:0007017)|multicellular organismal development (GO:0007275)|negative regulation of microtubule depolymerization (GO:0007026)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	signal transducer activity (GO:0004871)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GCTGCCCATCGTGCAGGCATG	0.567													G|||	1	0.000199681	0.0	0.0	5008	,	,		19839	0.0		0.0	False		,,,				2504	0.001				p.S80S		Atlas-SNP	.											.	TRIM54	35	.	0			c.G240A						PASS	.						85.0	70.0	75.0					2																	27521506		2203	4300	6503	SO:0001819	synonymous_variant	57159	exon2			CCCATCGTGCAGG	AJ291714	CCDS1745.2, CCDS1746.2	2p23.3	2013-01-09	2011-01-25	2004-11-17	ENSG00000138100	ENSG00000138100		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16008	protein-coding gene	gene with protein product		606474	"""ring finger protein 30"", ""tripartite motif-containing 54"""	RNF30		11243782	Standard	NM_032546		Approved	MURF, MURF-3	uc002rjn.3	Q9BYV2	OTTHUMG00000097078	ENST00000380075.2:c.240G>A	2.37:g.27521506G>A		137.0	0.0	0		190.0	25.0	0.131579	NM_187841	A5D8T7|Q53SY4|Q9BYV3	Silent	SNP	ENST00000380075.2	37	CCDS1746.2																																																																																			.	.	none		0.567	TRIM54-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214199.2	NM_187841	
PKD1L2	114780	hgsc.bcm.edu	37	16	81232294	81232294	+	RNA	SNP	T	T	C	rs61734110	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81232294T>C	ENST00000525539.1	-	0	1515				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						AGGCGGCAAATCCCAAATGGC	0.582													T|||	154	0.0307508	0.0325	0.0317	5008	,	,		20196	0.004		0.0716	False		,,,				2504	0.0133				p.I506V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.A1516G						PASS	.	T	VAL/ILE,VAL/ILE	168,3844		1,166,1839	51.0	52.0	51.0		1516,1516	2.8	0.5	16	dbSNP_129	51	526,7782		17,492,3645	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	29,29	18,658,5484	CC,CT,TT		6.3312,4.1874,5.6331	benign,benign	506/992,506/2460	81232294	694,11626	2006	4154	6160			114780	exon7			GGCAAATCCCAAA	AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81232294T>C		102.0	0.0	0		101.0	60.0	0.594059	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000525539.1	37		85|85	0.03891941391941392|0.03891941391941392	17|17	0.034552845528455285|0.034552845528455285	16|16	0.04419889502762431|0.04419889502762431	1|1	0.0017482517482517483|0.0017482517482517483	51|51	0.06728232189973615|0.06728232189973615	T|T	0.006|0.006	-2.058861|-2.058861	0.00390|0.00390	0.041874|0.041874	0.063312|0.063312	ENSG00000166473|ENSG00000166473	ENST00000526632|ENST00000337114	.|T	.|0.01279	.|5.06	5.08|5.08	2.75|2.75	0.32379|0.32379	.|Egg jelly receptor, REJ-like (1);	.|1.001100	.|0.08058	.|N	.|0.997623	T|T	0.00144|0.00144	0.0004|0.0004	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B	.|0.16603	.|0.018;0.006	.|B;B	.|0.17722	.|0.019;0.004	T|T	0.50127|0.50127	-0.8864|-0.8864	4|9	.|0.22706	.|T	.|0.39	-3.0E-4|-3.0E-4	8.8296|8.8296	0.35076|0.35076	0.0:0.2087:0.0:0.7913|0.0:0.2087:0.0:0.7913	.|.	.|506;506	.|Q7Z442-3;Q7Z442	.|.;PK1L2_HUMAN	G|V	33|506	.|ENSP00000337397:I506V	.|ENSP00000337397:I506V	D|I	-|-	2|1	0|0	PKD1L2|PKD1L2	79789795|79789795	0.000000|0.000000	0.05858|0.05858	0.487000|0.487000	0.27428|0.27428	0.041000|0.041000	0.13682|0.13682	0.422000|0.422000	0.21296|0.21296	0.790000|0.790000	0.33803|0.33803	-0.398000|-0.398000	0.06409|0.06409	GAT|ATT	T|0.956;C|0.044	0.044	strong		0.582	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2		
ZNF462	58499	hgsc.bcm.edu	37	9	109692820	109692820	+	Silent	SNP	A	A	G	rs139184113	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:109692820A>G	ENST00000277225.5	+	4	6151	c.5862A>G	c.(5860-5862)ttA>ttG	p.L1954L	ZNF462_ENST00000457913.1_Silent_p.L1954L|ZNF462_ENST00000497489.1_3'UTR|ZNF462_ENST00000441147.2_Silent_p.L799L|ZNF462_ENST00000542028.1_5'Flank			Q96JM2	ZN462_HUMAN	zinc finger protein 462	1954					chromatin organization (GO:0006325)|negative regulation of DNA binding (GO:0043392)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|autonomic_ganglia(2)|breast(5)|central_nervous_system(4)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(20)|lung(32)|ovary(5)|prostate(6)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						TTGGTCACTTAGAAGAGGTGC	0.453																																					p.L1954L		Atlas-SNP	.											.	ZNF462	322	.	0			c.A5862G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	102.0	95.0	97.0		5862	5.4	1.0	9	dbSNP_134	97	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	ZNF462	NM_021224.4		0,29,6474	GG,GA,AA		0.314,0.0454,0.223		1954/2507	109692820	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	58499	exon4			TCACTTAGAAGAG	AB058706	CCDS35096.1	9q31.3	2008-02-05			ENSG00000148143	ENSG00000148143		"""Zinc fingers, C2H2-type"""	21684	protein-coding gene	gene with protein product							Standard	NM_021224		Approved	DKFZP762N2316, KIAA1803, Zfp462	uc004bcz.3	Q96JM2	OTTHUMG00000020438	ENST00000277225.5:c.5862A>G	9.37:g.109692820A>G		100.0	0.0	0		149.0	67.0	0.449664	NM_021224	Q5T0T4|Q8N408	Silent	SNP	ENST00000277225.5	37	CCDS35096.1																																																																																			A|0.999;G|0.001	0.001	strong		0.453	ZNF462-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053532.2	NM_021224	
MRPL9	65005	hgsc.bcm.edu	37	1	151735913	151735913	+	Missense_Mutation	SNP	G	G	A	rs199630729		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:151735913G>A	ENST00000368830.3	-	1	127	c.43C>T	c.(43-45)Cgg>Tgg	p.R15W	RP11-98D18.2_ENST00000420382.1_RNA|MRPL9_ENST00000467306.1_5'UTR|OAZ3_ENST00000321531.5_Intron|OAZ3_ENST00000315067.8_Intron|MRPL9_ENST00000368829.3_Missense_Mutation_p.R15W|OAZ3_ENST00000453029.2_5'Flank|RP11-98D18.3_ENST00000512280.1_RNA|OAZ3_ENST00000479764.1_5'Flank	NM_031420.2	NP_113608.1	Q9BYD2	RM09_HUMAN	mitochondrial ribosomal protein L9	15					translation (GO:0006412)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(2)|large_intestine(2)|lung(4)|ovary(1)|upper_aerodigestive_tract(1)	12	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.14)		LUSC - Lung squamous cell carcinoma(543;0.181)			GCGCCCGCCCGCAGCAGAGCT	0.692													G|||	1	0.000199681	0.0	0.0	5008	,	,		10868	0.0		0.001	False		,,,				2504	0.0				p.R15W		Atlas-SNP	.											.	MRPL9	21	.	0			c.C43T						PASS	.	G	,TRP/ARG	0,4330		0,0,2165	8.0	10.0	9.0		,43	0.8	0.0	1		9	13,8467		0,13,4227	yes	intron,missense	OAZ3,MRPL9	NM_001134939.1,NM_031420.2	,101	0,13,6392	AA,AG,GG		0.1533,0.0,0.1015	,probably-damaging	,15/268	151735913	13,12797	2165	4240	6405	SO:0001583	missense	65005	exon1			CCGCCCGCAGCAG	AK026363	CCDS1003.1, CCDS72916.1	1q21	2012-09-13			ENSG00000143436	ENSG00000143436		"""Mitochondrial ribosomal proteins / large subunits"""	14277	protein-coding gene	gene with protein product		611824					Standard	XM_005245455		Approved		uc001eyv.3	Q9BYD2	OTTHUMG00000013063	ENST00000368830.3:c.43C>T	1.37:g.151735913G>A	ENSP00000357823:p.Arg15Trp	52.0	0.0	0		46.0	31.0	0.673913	NM_031420	B2RD99|Q5SZR2|Q9BSW8	Missense_Mutation	SNP	ENST00000368830.3	37	CCDS1003.1	.	.	.	.	.	.	.	.	.	.	G	17.03	3.285275	0.59867	0.0	0.001533	ENSG00000143436	ENST00000368830;ENST00000368829	T;T	0.31510	1.5;1.49	4.93	0.779	0.18550	.	0.716541	0.14023	N	0.346675	T	0.04588	0.0125	N	0.12746	0.255	0.09310	N	1	B;B;B	0.19331	0.013;0.035;0.001	B;B;B	0.10450	0.002;0.005;0.001	T	0.37033	-0.9723	10	0.42905	T	0.14	-0.4378	3.2367	0.06767	0.3201:0.0:0.4969:0.183	.	15;15;15	B4DDZ7;B4DUJ1;Q9BYD2	.;.;RM09_HUMAN	W	15	ENSP00000357823:R15W;ENSP00000357822:R15W	ENSP00000357822:R15W	R	-	1	2	MRPL9	150002537	0.005000	0.15991	0.002000	0.10522	0.008000	0.06430	0.245000	0.18142	-0.015000	0.14150	-0.140000	0.14226	CGG	.	.	weak		0.692	MRPL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036653.2	NM_031420	
KIAA0141	9812	hgsc.bcm.edu	37	5	141309152	141309152	+	Nonsense_Mutation	SNP	C	C	T	rs114623503	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141309152C>T	ENST00000432126.2	+	5	552	c.418C>T	c.(418-420)Cga>Tga	p.R140*	KIAA0141_ENST00000194118.4_Nonsense_Mutation_p.R140*	NM_001142603.1|NM_014773.3	NP_001136075.1|NP_055588.3	Q14154	DELE_HUMAN	KIAA0141	140					extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)	mitochondrion (GO:0005739)				endometrium(3)|large_intestine(4)|lung(5)|skin(1)|urinary_tract(3)	16		all_hematologic(541;0.118)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TCCAGCACTGCGACAACACAT	0.632													C|||	2	0.000399361	0.0	0.0	5008	,	,		17987	0.0		0.002	False		,,,				2504	0.0				p.R140X		Atlas-SNP	.											.	KIAA0141	44	.	0			c.C418T						PASS	.	C	stop/ARG,stop/ARG	2,4404	4.2+/-10.8	0,2,2201	68.0	71.0	70.0		418,418	1.9	0.7	5	dbSNP_132	70	16,8584	11.2+/-40.8	0,16,4284	yes	stop-gained,stop-gained	KIAA0141	NM_001142603.1,NM_014773.3	,	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	,	140/516,140/516	141309152	18,12988	2203	4300	6503	SO:0001587	stop_gained	9812	exon5			GCACTGCGACAAC	BC011269	CCDS4268.1	5q31	2011-05-05			ENSG00000081791	ENSG00000081791			28969	protein-coding gene	gene with protein product	"""death ligand signal enhancer"""	615741				20563667	Standard	XM_005268549		Approved	DELE	uc003llt.3	Q14154	OTTHUMG00000129662	ENST00000432126.2:c.418C>T	5.37:g.141309152C>T	ENSP00000396225:p.Arg140*	109.0	0.0	0		109.0	40.0	0.366972	NM_001142603	Q969R4|Q96EU9	Nonsense_Mutation	SNP	ENST00000432126.2	37	CCDS4268.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	14.47	2.543632	0.45280	4.54E-4	0.00186	ENSG00000081791	ENST00000432126;ENST00000194118;ENST00000508751	.	.	.	3.95	1.87	0.25490	.	0.181406	0.33040	N	0.005360	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.4383	8.0362	0.30493	0.4754:0.5246:0.0:0.0	.	.	.	.	X	140	.	ENSP00000194118:R140X	R	+	1	2	KIAA0141	141289336	0.059000	0.20769	0.661000	0.29709	0.048000	0.14542	0.121000	0.15667	0.827000	0.34685	0.305000	0.20034	CGA	C|0.999;T|0.001	0.001	strong		0.632	KIAA0141-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251863.2	NM_014773	
DOPEY2	9980	hgsc.bcm.edu	37	21	37584331	37584331	+	Silent	SNP	C	C	T	rs147659226	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr21:37584331C>T	ENST00000399151.3	+	7	925	c.840C>T	c.(838-840)gcC>gcT	p.A280A	DOPEY2_ENST00000492760.1_3'UTR|RN7SL73P_ENST00000585239.1_RNA	NM_005128.2	NP_005119.2	Q9Y3R5	DOP2_HUMAN	dopey family member 2	280					cognition (GO:0050890)|endoplasmic reticulum organization (GO:0007029)|Golgi to endosome transport (GO:0006895)|multicellular organismal development (GO:0007275)|protein transport (GO:0015031)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)				autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(6)|lung(25)|ovary(2)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58						TTCTCTCAGCCGCCACCCAGA	0.468													c|||	8	0.00159744	0.0045	0.0029	5008	,	,		20397	0.0		0.0	False		,,,				2504	0.0				p.A280A		Atlas-SNP	.											DOPEY2,NS,carcinoma,+2,1	DOPEY2	184	1	0			c.C840T						scavenged	.	T		14,4392	21.2+/-45.6	0,14,2189	101.0	89.0	93.0		840	-10.2	0.0	21	dbSNP_134	93	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	DOPEY2	NM_005128.2		0,15,6488	TT,TC,CC		0.0116,0.3177,0.1153		280/2299	37584331	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	9980	exon7			CTCAGCCGCCACC	AJ237839	CCDS13643.1	21q22.2	2013-03-05	2006-02-02	2006-02-02	ENSG00000142197	ENSG00000142197			1291	protein-coding gene	gene with protein product		604803	"""chromosome 21 open reading frame 5"""	C21orf5		16301316, 16303751, 10931277	Standard	NM_005128		Approved	KIAA0933	uc002yvg.3	Q9Y3R5	OTTHUMG00000086619	ENST00000399151.3:c.840C>T	21.37:g.37584331C>T		93.0	1.0	0.0107527		100.0	49.0	0.49	NM_005128	D3DSG5|Q6PJQ7|Q9UEZ3	Silent	SNP	ENST00000399151.3	37	CCDS13643.1																																																																																			C|0.999;T|0.001	0.001	strong		0.468	DOPEY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194636.1	NM_005128	
SMYD4	114826	hgsc.bcm.edu	37	17	1686737	1686737	+	Missense_Mutation	SNP	C	C	T	rs374639152		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:1686737C>T	ENST00000305513.7	-	9	2221	c.2054G>A	c.(2053-2055)cGt>cAt	p.R685H		NM_052928.2	NP_443160.2	Q8IYR2	SMYD4_HUMAN	SET and MYND domain containing 4	685							metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			breast(4)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(5)|stomach(1)	21						CTCGGCGTCACGCTGGCACCC	0.607																																					p.R685H		Atlas-SNP	.											.	SMYD4	50	.	0			c.G2054A						PASS	.	C	HIS/ARG	0,4406		0,0,2203	24.0	24.0	24.0		2054	-10.0	0.0	17		24	1,8599		0,1,4299	no	missense	SMYD4	NM_052928.2	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	685/805	1686737	1,13005	2203	4300	6503	SO:0001583	missense	114826	exon9			GCGTCACGCTGGC	AB067523	CCDS11013.1	17p13.3	2004-04-21			ENSG00000186532	ENSG00000186532		"""Zinc fingers, MYND-type"""	21067	protein-coding gene	gene with protein product						11572484	Standard	NM_052928		Approved	KIAA1936, ZMYND21	uc002ftm.4	Q8IYR2	OTTHUMG00000090570	ENST00000305513.7:c.2054G>A	17.37:g.1686737C>T	ENSP00000304360:p.Arg685His	172.0	0.0	0		185.0	102.0	0.551351	NM_052928	Q8N1P2|Q8NAT0|Q96LV4|Q96PV2	Missense_Mutation	SNP	ENST00000305513.7	37	CCDS11013.1	.	.	.	.	.	.	.	.	.	.	C	9.257	1.042180	0.19748	0.0	1.16E-4	ENSG00000186532	ENST00000305513	T	0.64260	-0.09	5.75	-10.0	0.00425	Tetratricopeptide-like helical (1);	1.666840	0.02239	N	0.065610	T	0.29850	0.0746	N	0.01352	-0.895	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.34229	-0.9837	10	0.14252	T	0.57	1.9281	14.6337	0.68673	0.1008:0.6859:0.0:0.2133	.	685	Q8IYR2	SMYD4_HUMAN	H	685	ENSP00000304360:R685H	ENSP00000304360:R685H	R	-	2	0	SMYD4	1633487	0.000000	0.05858	0.000000	0.03702	0.078000	0.17371	-1.683000	0.01934	-2.027000	0.00932	-0.474000	0.04947	CGT	.	.	weak		0.607	SMYD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207108.4	XM_056082	
LPHN3	23284	hgsc.bcm.edu	37	4	62845326	62845326	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:62845326G>A	ENST00000514591.1	+	17	2976	c.2647G>A	c.(2647-2649)Gtt>Att	p.V883I	LPHN3_ENST00000514157.1_Missense_Mutation_p.V883I|LPHN3_ENST00000506746.1_Missense_Mutation_p.V951I|LPHN3_ENST00000512091.2_Missense_Mutation_p.V883I|LPHN3_ENST00000509896.1_Missense_Mutation_p.V951I|LPHN3_ENST00000507164.1_Missense_Mutation_p.V951I|LPHN3_ENST00000506700.1_Missense_Mutation_p.V883I|LPHN3_ENST00000508693.1_Missense_Mutation_p.V951I|LPHN3_ENST00000506720.1_Missense_Mutation_p.V951I|LPHN3_ENST00000545650.1_Missense_Mutation_p.V883I|LPHN3_ENST00000514996.1_Missense_Mutation_p.V883I|LPHN3_ENST00000504896.1_Missense_Mutation_p.V883I|LPHN3_ENST00000507625.1_Missense_Mutation_p.V951I|LPHN3_ENST00000508946.1_Missense_Mutation_p.V883I|LPHN3_ENST00000511324.1_Missense_Mutation_p.V951I			Q9HAR2	LPHN3_HUMAN	latrophilin 3	870					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)|G-protein coupled receptor activity (GO:0004930)			breast(5)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(5)|kidney(4)|large_intestine(21)|lung(73)|ovary(1)|pancreas(1)|prostate(6)|upper_aerodigestive_tract(1)	125						GATCACGTGGGTTGGAATTTT	0.458																																					p.V883I		Atlas-SNP	.											.	LPHN3	800	.	0			c.G2647A						PASS	.						321.0	314.0	316.0					4																	62845326		1998	4191	6189	SO:0001583	missense	23284	exon15			ACGTGGGTTGGAA	AB018311	CCDS54768.1	4q13.1	2014-08-08				ENSG00000150471		"""-"", ""GPCR / Class B : Orphans"""	20974	protein-coding gene	gene with protein product						10994649	Standard	NM_015236		Approved	KIAA0768, LEC3	uc010ihh.3	Q9HAR2		ENST00000514591.1:c.2647G>A	4.37:g.62845326G>A	ENSP00000422533:p.Val883Ile	417.0	0.0	0		435.0	66.0	0.151724	NM_015236	E9PE04|O94867|Q9NWK5	Missense_Mutation	SNP	ENST00000514591.1	37	CCDS54768.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	25.8|25.8	4.679692|4.679692	0.88542|0.88542	.|.	.|.	ENSG00000150471|ENSG00000150471	ENST00000502815|ENST00000512091;ENST00000514591;ENST00000509896;ENST00000511324;ENST00000506700;ENST00000545650;ENST00000295349;ENST00000280009;ENST00000507164;ENST00000508693;ENST00000507625;ENST00000514157;ENST00000504896;ENST00000508946;ENST00000506720;ENST00000506746;ENST00000514996	.|T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	.|0.54279	.|0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.5|5.5	5.5|5.5	0.81552|0.81552	.|GPCR, family 2-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.64789|0.64789	0.2630|0.2630	L|L	0.37800|0.37800	1.135|1.135	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.69078	.|0.997;0.997;0.996	.|D;D;D	.|0.79108	.|0.992;0.992;0.987	T|T	0.61207|0.61207	-0.7109|-0.7109	5|10	.|0.35671	.|T	.|0.21	.|.	19.0068|19.0068	0.92854|0.92854	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|883;870;883	.|E9PE04;Q9HAR2;Q9HAR2-2	.|.;LPHN3_HUMAN;.	D|I	340|883;883;951;951;883;883;870;883;951;951;951;883;883;883;951;951;883	.|ENSP00000423388:V883I;ENSP00000422533:V883I;ENSP00000423787:V951I;ENSP00000425033:V951I;ENSP00000424120:V883I;ENSP00000439831:V883I;ENSP00000421476:V951I;ENSP00000424030:V951I;ENSP00000421372:V951I;ENSP00000425201:V883I;ENSP00000423434:V883I;ENSP00000421627:V883I;ENSP00000420931:V951I;ENSP00000425884:V951I;ENSP00000424258:V883I	.|ENSP00000280009:V883I	G|V	+|+	2|1	0|0	LPHN3|LPHN3	62527921|62527921	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.992000|0.992000	0.81027|0.81027	9.808000|9.808000	0.99193|0.99193	2.580000|2.580000	0.87095|0.87095	0.467000|0.467000	0.42956|0.42956	GGT|GTT	.	.	none		0.458	LPHN3-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000361765.1		
SERPINA9	327657	hgsc.bcm.edu	37	14	94936062	94936062	+	Missense_Mutation	SNP	G	G	A	rs45438596	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:94936062G>A	ENST00000380365.3	-	2	194	c.116C>T	c.(115-117)aCc>aTc	p.T39I	SERPINA9_ENST00000424550.2_Intron|SERPINA9_ENST00000539349.1_5'Flank|SERPINA9_ENST00000546329.1_Intron|SERPINA9_ENST00000298845.7_Missense_Mutation_p.T57I|SERPINA9_ENST00000337425.5_Missense_Mutation_p.T57I|SERPINA9_ENST00000448305.2_Intron			Q86WD7	SPA9_HUMAN	serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9	39					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(17)	21		all_cancers(154;0.0691)|all_epithelial(191;0.233)		Epithelial(152;0.144)|COAD - Colon adenocarcinoma(157;0.224)|all cancers(159;0.24)		TGAGGCAGGGGTGCTCTTTGT	0.567													G|||	93	0.0185703	0.0393	0.0144	5008	,	,		17740	0.0		0.0278	False		,,,				2504	0.0031				p.T57I		Atlas-SNP	.											.	SERPINA9	105	.	0			c.C170T						PASS	.	G	ILE/THR,ILE/THR	176,3872		7,162,1855	86.0	89.0	88.0		170,170	-8.0	0.0	14	dbSNP_127	88	245,8115		2,241,3937	yes	missense,missense	SERPINA9	NM_001042518.1,NM_175739.3	89,89	9,403,5792	AA,AG,GG		2.9306,4.3478,3.393	possibly-damaging,possibly-damaging	57/336,57/436	94936062	421,11987	2024	4180	6204	SO:0001583	missense	327657	exon2			GCAGGGGTGCTCT	AY185497	CCDS41982.1, CCDS41983.1, CCDS61542.1	14q32.1	2014-02-18	2005-08-18		ENSG00000170054	ENSG00000170054		"""Serine (or cysteine) peptidase inhibitors"""	15995	protein-coding gene	gene with protein product		615677	"""serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 9"""			24172014	Standard	NM_175739		Approved	CENTERIN, SERPINA11b, GCET1	uc001ydf.3	Q86WD7	OTTHUMG00000167710	ENST00000380365.3:c.116C>T	14.37:g.94936062G>A	ENSP00000369723:p.Thr39Ile	97.0	0.0	0		92.0	51.0	0.554348	NM_175739	B4DVH4|B9ZVX3|Q2T9J2|Q6UWP9|Q86WD4|Q86WD5|Q86WD6|Q86YP6|Q86YP7	Missense_Mutation	SNP	ENST00000380365.3	37		40	0.018315018315018316	16	0.032520325203252036	4	0.011049723756906077	0	0.0	20	0.026385224274406333	G	11.98	1.800787	0.31869	0.043478	0.029306	ENSG00000170054	ENST00000298845;ENST00000337425;ENST00000380365	D;D;D	0.87571	-2.27;-2.27;-2.27	3.99	-7.98	0.01135	Serpin domain (1);	1.422810	0.05300	U	0.522890	T	0.41558	0.1164	N	0.08118	0	0.09310	N	1	B;B;B	0.18968	0.007;0.032;0.021	B;B;B	0.22386	0.01;0.039;0.025	T	0.57825	-0.7744	10	0.54805	T	0.06	.	9.7894	0.40697	0.0:0.3432:0.454:0.2028	rs45438596;rs61743375	39;57;57	Q86WD7;Q86WD7-7;Q86WD7-2	SPA9_HUMAN;.;.	I	57;57;39	ENSP00000298845:T57I;ENSP00000337133:T57I;ENSP00000369723:T39I	ENSP00000298845:T57I	T	-	2	0	SERPINA9	94005815	0.000000	0.05858	0.000000	0.03702	0.438000	0.31896	-1.284000	0.02793	-1.491000	0.01840	0.313000	0.20887	ACC	G|0.979;A|0.021	0.021	strong		0.567	SERPINA9-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395803.2	NM_175739	
MTMR7	9108	hgsc.bcm.edu	37	8	17169039	17169039	+	Missense_Mutation	SNP	C	C	T	rs147637471		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:17169039C>T	ENST00000180173.5	-	9	1116	c.1082G>A	c.(1081-1083)cGg>cAg	p.R361Q	MTMR7_ENST00000398099.3_5'UTR|MTMR7_ENST00000521857.1_Missense_Mutation_p.R361Q	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	361	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		CTTCAGAGTCCGGTAGTGAGG	0.582																																					p.R361Q		Atlas-SNP	.											.	MTMR7	75	.	0			c.G1082A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	214.0	209.0	211.0		1082	4.9	1.0	8	dbSNP_134	211	3,8597	3.0+/-9.4	0,3,4297	no	missense	MTMR7	NM_004686.4	43	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	probably-damaging	361/661	17169039	3,13003	2203	4300	6503	SO:0001583	missense	9108	exon9			AGAGTCCGGTAGT	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1082G>A	8.37:g.17169039C>T	ENSP00000180173:p.Arg361Gln	73.0	0.0	0		84.0	38.0	0.452381	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	37	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	C	34	5.299020	0.95574	0.0	3.49E-4	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.98135	-4.74;-4.74	4.86	4.86	0.63082	Myotubularin phosphatase domain (1);	0.047533	0.85682	D	0.000000	D	0.99405	0.9790	H	0.99516	4.605	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.997;1.0	D	0.98030	1.0376	10	0.87932	D	0	.	18.5539	0.91075	0.0:1.0:0.0:0.0	.	361;361	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	Q	361	ENSP00000180173:R361Q;ENSP00000429733:R361Q	ENSP00000180173:R361Q	R	-	2	0	MTMR7	17213410	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.651000	0.83577	2.697000	0.92050	0.655000	0.94253	CGG	C|1.000;T|0.000	0.000	weak		0.582	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
CA13	377677	hgsc.bcm.edu	37	8	86180719	86180719	+	Missense_Mutation	SNP	A	A	G	rs75353219	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:86180719A>G	ENST00000321764.3	+	6	834	c.532A>G	c.(532-534)Aca>Gca	p.T178A	CA13_ENST00000517298.1_3'UTR	NM_198584.2	NP_940986.1	Q8N1Q1	CAH13_HUMAN	carbonic anhydrase XIII	178					bicarbonate transport (GO:0015701)|one-carbon metabolic process (GO:0006730)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|myelin sheath (GO:0043209)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)			large_intestine(1)|lung(6)	7					Zonisamide(DB00909)	AACTCGATTCACAAATTTTGA	0.413													A|||	24	0.00479233	0.0015	0.0058	5008	,	,		17595	0.0		0.0139	False		,,,				2504	0.0041				p.T178A		Atlas-SNP	.											.	CA13	26	.	0			c.A532G						PASS	.	A	ALA/THR	8,4398	12.9+/-30.5	0,8,2195	171.0	159.0	163.0		532	5.5	1.0	8	dbSNP_131	163	132,8468	68.0+/-130.5	1,130,4169	yes	missense	CA13	NM_198584.2	58	1,138,6364	GG,GA,AA		1.5349,0.1816,1.0764	benign	178/263	86180719	140,12866	2203	4300	6503	SO:0001583	missense	377677	exon6			CGATTCACAAATT	BC052602	CCDS6236.1	8q21	2004-05-10				ENSG00000185015		"""Carbonic anhydrases"""	14914	protein-coding gene	gene with protein product		611436				14600151	Standard	NM_198584		Approved	CAXIII, FLJ37995, MGC59868	uc003ydg.2	Q8N1Q1		ENST00000321764.3:c.532A>G	8.37:g.86180719A>G	ENSP00000318912:p.Thr178Ala	185.0	0.0	0		187.0	98.0	0.524064	NM_198584		Missense_Mutation	SNP	ENST00000321764.3	37	CCDS6236.1	13	0.005952380952380952	0	0.0	0	0.0	0	0.0	13	0.017150395778364115	A	14.11	2.436542	0.43224	0.001816	0.015349	ENSG00000185015	ENST00000321764	T	0.63580	-0.05	5.5	5.5	0.81552	Carbonic anhydrase, alpha-class, catalytic domain (4);	0.144213	0.64402	D	0.000006	T	0.35885	0.0947	L	0.38953	1.18	0.46849	D	0.999224	B	0.21381	0.055	B	0.21917	0.037	T	0.38001	-0.9681	10	0.21540	T	0.41	-11.4932	14.5856	0.68322	1.0:0.0:0.0:0.0	.	178	Q8N1Q1	CAH13_HUMAN	A	178	ENSP00000318912:T178A	ENSP00000318912:T178A	T	+	1	0	CA13	86367971	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	2.135000	0.42112	2.104000	0.64026	0.383000	0.25322	ACA	A|0.992;G|0.008	0.008	strong		0.413	CA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381066.1	NM_198584	
TLR4	7099	hgsc.bcm.edu	37	9	120474891	120474891	+	Missense_Mutation	SNP	T	T	C	rs200168998		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:120474891T>C	ENST00000355622.6	+	3	586	c.485T>C	c.(484-486)aTc>aCc	p.I162T	TLR4_ENST00000394487.4_Missense_Mutation_p.I122T|TLR4_ENST00000472304.1_3'UTR	NM_138554.4|NM_138557.2	NP_612564.1|NP_612567.1	O00206	TLR4_HUMAN	toll-like receptor 4	162					activation of MAPK activity (GO:0000187)|B cell proliferation involved in immune response (GO:0002322)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|cellular response to mechanical stimulus (GO:0071260)|defense response to bacterium (GO:0042742)|defense response to Gram-negative bacterium (GO:0050829)|detection of fungus (GO:0016046)|detection of lipopolysaccharide (GO:0032497)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|I-kappaB phosphorylation (GO:0007252)|immune response (GO:0006955)|innate immune response (GO:0045087)|interferon-gamma production (GO:0032609)|intestinal epithelial structure maintenance (GO:0060729)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation (GO:0042116)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-17 production (GO:0032700)|negative regulation of interleukin-23 production (GO:0032707)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of tumor necrosis factor production (GO:0032720)|nitric oxide production involved in inflammatory response (GO:0002537)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of chemokine production (GO:0032722)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta biosynthetic process (GO:0045359)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 production (GO:0032732)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 biosynthetic process (GO:0045084)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of JNK cascade (GO:0046330)|positive regulation of macrophage cytokine production (GO:0060907)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of NF-kappaB import into nucleus (GO:0042346)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway (GO:0070430)|positive regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070434)|positive regulation of platelet activation (GO:0010572)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cytokine secretion (GO:0050707)|response to lipopolysaccharide (GO:0032496)|T-helper 1 type immune response (GO:0042088)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|endosome membrane (GO:0010008)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|lipopolysaccharide receptor complex (GO:0046696)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	lipopolysaccharide binding (GO:0001530)|lipopolysaccharide receptor activity (GO:0001875)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(12)|lung(66)|ovary(4)|pancreas(1)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	103					Naloxone(DB01183)	CACAATCTTATCCAATCTTTC	0.388																																					p.I162T		Atlas-SNP	.											.	TLR4	220	.	0			c.T485C						PASS	.	T	THR/ILE	0,4406		0,0,2203	94.0	98.0	97.0		485	5.1	0.3	9		97	1,8599	1.2+/-3.3	0,1,4299	yes	missense	TLR4	NM_138554.3	89	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging	162/840	120474891	1,13005	2203	4300	6503	SO:0001583	missense	7099	exon3			ATCTTATCCAATC	U88880	CCDS6818.1	9q33.1	2013-01-23			ENSG00000136869	ENSG00000136869		"""CD molecules"""	11850	protein-coding gene	gene with protein product		603030				9435236, 9237759	Standard	NM_138554		Approved	hToll, CD284, TLR-4, ARMD10	uc004bjz.4	O00206	OTTHUMG00000021046	ENST00000355622.6:c.485T>C	9.37:g.120474891T>C	ENSP00000363089:p.Ile162Thr	146.0	0.0	0		154.0	83.0	0.538961	NM_138554	A8K1Y8|A9XLP9|A9XLQ0|A9XLQ1|B4E194|D1CS52|D1CS53|Q5VZI8|Q5VZI9|Q9UK78|Q9UM57	Missense_Mutation	SNP	ENST00000355622.6	37	CCDS6818.1	.	.	.	.	.	.	.	.	.	.	T	14.73	2.622678	0.46840	0.0	1.16E-4	ENSG00000136869	ENST00000394487;ENST00000355622	T;T	0.21734	1.99;1.99	5.08	5.08	0.68730	.	0.000000	0.64402	D	0.000005	T	0.49236	0.1545	M	0.83012	2.62	0.40068	D	0.975989	D	0.76494	0.999	D	0.91635	0.999	T	0.53767	-0.8392	10	0.39692	T	0.17	.	14.8663	0.70419	0.0:0.0:0.0:1.0	.	162	O00206	TLR4_HUMAN	T	122;162	ENSP00000377997:I122T;ENSP00000363089:I162T	ENSP00000363089:I162T	I	+	2	0	TLR4	119514712	0.955000	0.32602	0.282000	0.24776	0.322000	0.28314	3.253000	0.51469	1.913000	0.55393	0.533000	0.62120	ATC	.	.	weak		0.388	TLR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055549.3	NM_138554	
KMT2D	8085	hgsc.bcm.edu	37	12	49439900	49439900	+	Silent	SNP	G	G	A	rs377048725		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:49439900G>A	ENST00000301067.7	-	17	4640	c.4641C>T	c.(4639-4641)gcC>gcT	p.A1547A		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1547				EQAA -> DHAP (in Ref. 1; AAC51734/ AAC51735). {ECO:0000305}.	chromatin silencing (GO:0006342)|histone H3-K4 methylation (GO:0051568)|oocyte growth (GO:0001555)|oogenesis (GO:0048477)|positive regulation of cell proliferation (GO:0008284)|positive regulation of intracellular estrogen receptor signaling pathway (GO:0033148)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone-lysine N-methyltransferase activity (GO:0018024)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)										AGCCTTCATCGGCTGCCTGCT	0.577																																					p.A1547A		Atlas-SNP	.											.	MLL2	1173	.	0			c.C4641T						PASS	.	G		1,4203		0,1,2101	39.0	47.0	44.0		4641	-10.7	0.2	12		44	1,8433		0,1,4216	no	coding-synonymous	MLL2	NM_003482.3		0,2,6317	AA,AG,GG		0.0119,0.0238,0.0158		1547/5538	49439900	2,12636	2102	4217	6319	SO:0001819	synonymous_variant	8085	exon17			TTCATCGGCTGCC	AF010403	CCDS44873.1	12q13.12	2013-05-09	2013-05-09	2013-05-09	ENSG00000167548	ENSG00000167548		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7133	protein-coding gene	gene with protein product		602113	"""trinucleotide repeat containing 21"", ""myeloid/lymphoid or mixed-lineage leukemia 2"""	TNRC21, MLL2		9247308	Standard	NM_003482		Approved	ALR, MLL4, CAGL114		O14686	OTTHUMG00000166524	ENST00000301067.7:c.4641C>T	12.37:g.49439900G>A		151.0	0.0	0		175.0	83.0	0.474286	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	weak		0.577	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
ELL2	22936	hgsc.bcm.edu	37	5	95234091	95234091	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:95234091T>C	ENST00000237853.4	-	8	1727	c.1378A>G	c.(1378-1380)Aaa>Gaa	p.K460E	ELL2_ENST00000431061.2_Missense_Mutation_p.K210E	NM_012081.5	NP_036213.2	O00472	ELL2_HUMAN	elongation factor, RNA polymerase II, 2	460					regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|transcription elongation from RNA polymerase II promoter (GO:0006368)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)	24		all_cancers(142;2.04e-06)|all_epithelial(76;3.1e-09)|all_lung(232;0.00309)|Lung NSC(167;0.00454)|Ovarian(225;0.0165)|Colorectal(57;0.0343)|Breast(839;0.198)		all cancers(79;2.16e-15)		TTGGACTTTTTGTGAGACATT	0.378																																					p.K460E		Atlas-SNP	.											.	ELL2	63	.	0			c.A1378G						PASS	.						130.0	134.0	132.0					5																	95234091		2203	4300	6503	SO:0001583	missense	22936	exon8			ACTTTTTGTGAGA	U88629	CCDS4080.1	5q15	2010-11-29			ENSG00000118985	ENSG00000118985			17064	protein-coding gene	gene with protein product		601874				9108030	Standard	NM_012081		Approved		uc003klr.4	O00472	OTTHUMG00000122085	ENST00000237853.4:c.1378A>G	5.37:g.95234091T>C	ENSP00000237853:p.Lys460Glu	311.0	0.0	0		330.0	165.0	0.5	NM_012081	B4DNK7	Missense_Mutation	SNP	ENST00000237853.4	37	CCDS4080.1	.	.	.	.	.	.	.	.	.	.	T	17.41	3.381477	0.61845	.	.	ENSG00000118985	ENST00000237853;ENST00000431061	T;T	0.30981	1.83;1.51	5.5	5.5	0.81552	.	0.235233	0.50627	N	0.000120	T	0.43299	0.1241	M	0.64997	1.995	0.58432	D	0.999996	D	0.60575	0.988	P	0.52343	0.696	T	0.26052	-1.0114	10	0.32370	T	0.25	2.215	15.2489	0.73529	0.0:0.0:0.0:1.0	.	460	O00472	ELL2_HUMAN	E	460;210	ENSP00000237853:K460E;ENSP00000399704:K210E	ENSP00000237853:K460E	K	-	1	0	ELL2	95259847	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	3.564000	0.53791	2.073000	0.62155	0.482000	0.46254	AAA	.	.	none		0.378	ELL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000242846.1	NM_012081	
HNF1A	6927	hgsc.bcm.edu	37	12	121432117	121432117	+	Silent	SNP	G	G	C	rs56348580	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:121432117G>C	ENST00000257555.6	+	4	1090	c.864G>C	c.(862-864)ggG>ggC	p.G288G	HNF1A_ENST00000400024.2_Silent_p.G288G|HNF1A_ENST00000541395.1_Silent_p.G288G|HNF1A_ENST00000543427.1_Silent_p.G171G|HNF1A_ENST00000544413.1_Silent_p.G288G|HNF1A_ENST00000402929.1_Silent_p.G288G|HNF1A_ENST00000538626.1_Intron			P20823	HNF1A_HUMAN	HNF1 homeobox A	288					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CGTACAGCGGGCCCCCCCCAG	0.667									Hepatic Adenoma, Familial Clustering of				g|||	907	0.18111	0.1778	0.415	5008	,	,		17094	0.005		0.3032	False		,,,				2504	0.0757				p.G288G		Atlas-SNP	.											HNF1A,brain,glioma,0,1	HNF1A	302	1	0			c.G864C	GRCh37	CI064741|CM067044	HNF1A	I|M	rs56348580	PASS	.	G		802,3604		95,612,1496	24.0	24.0	24.0		864	2.3	1.0	12	dbSNP_129	24	2264,6334		374,1516,2409	no	coding-synonymous	HNF1A	NM_000545.5		469,2128,3905	CC,CG,GG		26.3317,18.2025,23.5774		288/632	121432117	3066,9938	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon4	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CAGCGGGCCCCCC	M57732	CCDS9209.1	12q24.31	2014-09-17	2007-08-24	2007-08-24	ENSG00000135100	ENSG00000135100		"""Homeoboxes / HNF class"""	11621	protein-coding gene	gene with protein product		142410	"""transcription factor 1, hepatic; LF-B1, hepatic nuclear factor (HNF1), albumin proximal factor"""	MODY3, TCF1		1535333, 7795649	Standard	NM_000545		Approved	HNF1, LFB1	uc001tzg.3	P20823	OTTHUMG00000151015	ENST00000257555.6:c.864G>C	12.37:g.121432117G>C		55.0	0.0	0		31.0	17.0	0.548387	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.754;C|0.246	0.246	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
UBR1	197131	hgsc.bcm.edu	37	15	43256191	43256191	+	Missense_Mutation	SNP	T	T	C	rs3917223	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:43256191T>C	ENST00000290650.4	-	42	4720	c.4642A>G	c.(4642-4644)Aca>Gca	p.T1548A	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1548			T -> A (in dbSNP:rs3917223).		cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		AACAAATTTGTAGGTAAAGAT	0.373													T|||	166	0.033147	0.0023	0.0259	5008	,	,		18240	0.001		0.0736	False		,,,				2504	0.0716				p.T1548A		Atlas-SNP	.											.	UBR1	124	.	0			c.A4642G						PASS	.	T	ALA/THR	73,4333	65.3+/-102.7	1,71,2131	76.0	73.0	74.0		4642	4.7	1.0	15	dbSNP_108	74	632,7966	162.2+/-214.9	26,580,3693	yes	missense	UBR1	NM_174916.2	58	27,651,5824	CC,CT,TT		7.3505,1.6568,5.4214	benign	1548/1750	43256191	705,12299	2203	4299	6502	SO:0001583	missense	197131	exon42			AATTTGTAGGTAA		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.4642A>G	15.37:g.43256191T>C	ENSP00000290650:p.Thr1548Ala	85.0	0.0	0		116.0	71.0	0.612069	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	71	0.03250915750915751	0	0.0	11	0.03038674033149171	1	0.0017482517482517483	59	0.07783641160949868	T	14.23	2.472063	0.43942	0.016568	0.073505	ENSG00000159459	ENST00000290650	T	0.48836	0.8	4.65	4.65	0.58169	.	0.113840	0.64402	D	0.000011	T	0.02012	0.0063	L	0.33245	0.995	0.80722	D	1	P	0.40083	0.702	B	0.36092	0.217	T	0.00878	-1.1530	10	0.28530	T	0.3	-28.0639	12.4581	0.55716	0.0:0.0:0.0:1.0	rs3917223;rs17719808;rs52813857;rs61722037;rs17719808	1548	Q8IWV7	UBR1_HUMAN	A	1548	ENSP00000290650:T1548A	ENSP00000290650:T1548A	T	-	1	0	UBR1	41043483	1.000000	0.71417	1.000000	0.80357	0.948000	0.59901	3.860000	0.55995	1.969000	0.57287	0.528000	0.53228	ACA	T|0.847;G|0.006;C|0.046;A|0.102	0.046	strong		0.373	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
POLG	5428	hgsc.bcm.edu	37	15	89864987	89864987	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:89864987G>A	ENST00000268124.5	-	16	2911	c.2578C>T	c.(2578-2580)Ctc>Ttc	p.L860F	POLG_ENST00000442287.2_Missense_Mutation_p.L860F	NM_001126131.1|NM_002693.2	NP_001119603.1|NP_002684.1	P54098	DPOG1_HUMAN	polymerase (DNA directed), gamma	860					aging (GO:0007568)|base-excision repair, gap-filling (GO:0006287)|cell death (GO:0008219)|DNA metabolic process (GO:0006259)|DNA-dependent DNA replication (GO:0006261)|mitochondrial DNA replication (GO:0006264)	extracellular vesicular exosome (GO:0070062)|gamma DNA polymerase complex (GO:0005760)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|exonuclease activity (GO:0004527)|protease binding (GO:0002020)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(3)|urinary_tract(2)	33	Lung NSC(78;0.0472)|all_lung(78;0.089)		STAD - Stomach adenocarcinoma(125;0.165)			CTGGCGGTGAGCCATGTGGGC	0.617								DNA polymerases (catalytic subunits)																													p.L860F	Colon(73;648 1203 11348 18386 27782)	Atlas-SNP	.											.	POLG	75	.	0			c.C2578T						PASS	.						68.0	69.0	69.0					15																	89864987		2200	4299	6499	SO:0001583	missense	5428	exon16			CGGTGAGCCATGT	X98093	CCDS10350.1	15q24	2014-09-17			ENSG00000140521	ENSG00000140521		"""DNA polymerases"""	9179	protein-coding gene	gene with protein product		174763				9465903	Standard	NM_002693		Approved	POLG1, POLGA	uc002bnr.4	P54098	OTTHUMG00000149646	ENST00000268124.5:c.2578C>T	15.37:g.89864987G>A	ENSP00000268124:p.Leu860Phe	79.0	0.0	0		111.0	20.0	0.18018	NM_002693	Q8NFM2|Q92515	Missense_Mutation	SNP	ENST00000268124.5	37	CCDS10350.1	.	.	.	.	.	.	.	.	.	.	G	33	5.233367	0.95207	.	.	ENSG00000140521	ENST00000268124;ENST00000442287	D;D	0.99089	-5.41;-5.41	5.24	5.24	0.73138	DNA-directed DNA polymerase, family A, palm domain (1);	0.000000	0.85682	D	0.000000	D	0.99429	0.9798	M	0.90198	3.095	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.98735	1.0714	10	0.72032	D	0.01	-22.7577	18.8187	0.92088	0.0:0.0:1.0:0.0	.	860	P54098	DPOG1_HUMAN	F	860	ENSP00000268124:L860F;ENSP00000399851:L860F	ENSP00000268124:L860F	L	-	1	0	POLG	87665991	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	7.553000	0.82203	2.448000	0.82819	0.655000	0.94253	CTC	.	.	none		0.617	POLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000312854.2	NM_002693	
TDO2	6999	hgsc.bcm.edu	37	4	156830085	156830085	+	Missense_Mutation	SNP	G	G	A	rs375801975		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:156830085G>A	ENST00000536354.2	+	5	414	c.350G>A	c.(349-351)cGa>cAa	p.R117Q		NM_005651.3	NP_005642.1			tryptophan 2,3-dioxygenase											breast(3)|endometrium(1)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	18	all_hematologic(180;0.24)	Renal(120;0.0854)		KIRC - Kidney renal clear cell carcinoma(143;0.0455)|Kidney(143;0.0568)|COAD - Colon adenocarcinoma(41;0.141)		CGGATGCACCGAGTGTCAGTG	0.443																																					p.R117Q	Colon(57;928 1036 2595 6946 26094)	Atlas-SNP	.											.	TDO2	51	.	0			c.G350A						PASS	.	G	GLN/ARG	0,4406		0,0,2203	112.0	100.0	104.0		350	5.3	0.9	4		104	1,8599	1.2+/-3.3	0,1,4299	no	missense	TDO2	NM_005651.2	43	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	117/407	156830085	1,13005	2203	4300	6503	SO:0001583	missense	6999	exon5			TGCACCGAGTGTC		CCDS34086.1	4q31-q32	2008-02-05				ENSG00000151790	1.13.11.11		11708	protein-coding gene	gene with protein product		191070					Standard	NM_005651		Approved	TDO, TPH2	uc003ipf.2	P48775		ENST00000536354.2:c.350G>A	4.37:g.156830085G>A	ENSP00000444788:p.Arg117Gln	96.0	0.0	0		75.0	38.0	0.506667	NM_005651		Missense_Mutation	SNP	ENST00000536354.2	37	CCDS34086.1	.	.	.	.	.	.	.	.	.	.	G	35	5.453794	0.96223	0.0	1.16E-4	ENSG00000151790	ENST00000506072;ENST00000507590;ENST00000536354	.	.	.	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.89791	0.6817	H	0.95917	3.74	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92677	0.6155	9	0.87932	D	0	-12.6575	19.4005	0.94627	0.0:0.0:1.0:0.0	.	117	P48775	T23O_HUMAN	Q	10;10;117	.	ENSP00000281525:R117Q	R	+	2	0	TDO2	157049535	1.000000	0.71417	0.852000	0.33557	0.908000	0.53690	9.388000	0.97237	2.663000	0.90544	0.650000	0.86243	CGA	.	.	weak		0.443	TDO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366209.3	NM_005651	
SNAPC3	6619	hgsc.bcm.edu	37	9	15422888	15422888	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:15422888G>C	ENST00000380821.3	+	1	187	c.11G>C	c.(10-12)gGa>gCa	p.G4A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	4					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		ATGGCTGAAGGAAGCCGAGGT	0.632																																					p.G4A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.G11C						PASS	.						27.0	24.0	25.0					9																	15422888		2093	4148	6241	SO:0001583	missense	6619	exon1			CTGAAGGAAGCCG	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.11G>C	9.37:g.15422888G>C	ENSP00000370200:p.Gly4Ala	53.0	0.0	0		36.0	12.0	0.333333	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	.	.	.	.	.	.	.	.	.	.	G	12.57	1.977930	0.34942	.	.	ENSG00000164975	ENST00000380821;ENST00000380807;ENST00000447670;ENST00000421710	T	0.41400	1.0	5.13	1.96	0.26148	.	0.722427	0.13995	N	0.348553	T	0.29620	0.0739	L	0.36672	1.1	0.18873	N	0.999989	B;B	0.19583	0.013;0.037	B;B	0.18561	0.022;0.02	T	0.22417	-1.0217	10	0.54805	T	0.06	-21.5863	5.523	0.16943	0.5091:0.0:0.4909:0.0	.	4;4	B4DDR9;Q92966	.;SNPC3_HUMAN	A	4	ENSP00000370200:G4A	ENSP00000370185:G4A	G	+	2	0	SNAPC3	15412888	0.013000	0.17824	0.128000	0.21923	0.010000	0.07245	1.978000	0.40598	0.594000	0.29761	0.462000	0.41574	GGA	.	.	none		0.632	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
ARHGAP40	343578	hgsc.bcm.edu	37	20	37272551	37272551	+	Missense_Mutation	SNP	A	A	C	rs369137106		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37272551A>C	ENST00000373345.4	+	11	1576	c.1408A>C	c.(1408-1410)Acg>Ccg	p.T470P		NM_001164431.1	NP_001157903.1	Q5TG30	RHG40_HUMAN	Rho GTPase activating protein 40	470					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(1)	1						TCTGCTGTGGACGGTGAGTGC	0.637																																					p.T522P		Atlas-SNP	.											.	ARHGAP40	50	.	0			c.A1564C						PASS	.	A	PRO/THR	0,1384		0,0,692	87.0	88.0	88.0		1564	2.0	1.0	20		88	2,3180		0,2,1589	no	missense	ARHGAP40	NM_001164431.1	38	0,2,2281	CC,CA,AA		0.0629,0.0,0.0438		522/675	37272551	2,4564	692	1591	2283	SO:0001583	missense	343578	exon11			CTGTGGACGGTGA	AL035419		20q11.23	2011-06-29	2010-04-14	2010-04-14	ENSG00000124143	ENSG00000124143		"""Rho GTPase activating proteins"""	16226	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 95"""	C20orf95			Standard	NM_001164431		Approved	dJ1100H13.4	uc021wdn.1	Q5TG30	OTTHUMG00000032453	ENST00000373345.4:c.1408A>C	20.37:g.37272551A>C	ENSP00000362442:p.Thr470Pro	74.0	0.0	0		87.0	41.0	0.471264	NM_001164431		Missense_Mutation	SNP	ENST00000373345.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	18.61|18.61	3.661798|3.661798	0.67700|0.67700	0.0|0.0	6.29E-4|6.29E-4	ENSG00000124143|ENSG00000124143	ENST00000243967;ENST00000373346|ENST00000373345	.|T	.|0.09350	.|2.99	4.36|4.36	1.97|1.97	0.26223|0.26223	.|.	.|0.231755	.|0.42964	.|D	.|0.000638	T|T	0.17577|0.17577	0.0422|0.0422	M|M	0.70595|0.70595	2.14|2.14	0.38013|0.38013	D|D	0.934613|0.934613	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.03112|0.03112	-1.1071|-1.1071	5|8	.|0.41790	.|T	.|0.15	.|.	5.382|5.382	0.16196|0.16196	0.7236:0.1768:0.0996:0.0|0.7236:0.1768:0.0996:0.0	.|.	.|.	.|.	.|.	A|P	410;1|470	.|ENSP00000362442:T470P	.|ENSP00000362442:T470P	D|T	+|+	2|1	0|0	ARHGAP40|ARHGAP40	36705965|36705965	1.000000|1.000000	0.71417|0.71417	0.978000|0.978000	0.43139|0.43139	0.858000|0.858000	0.48976|0.48976	5.511000|5.511000	0.67024|0.67024	0.082000|0.082000	0.17018|0.17018	0.397000|0.397000	0.26171|0.26171	GAC|ACG	.	.	weak		0.637	ARHGAP40-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		XM_293123	
SBSN	374897	hgsc.bcm.edu	37	19	36018272	36018272	+	Silent	SNP	C	C	T	rs12461911	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:36018272C>T	ENST00000452271.2	-	1	940	c.912G>A	c.(910-912)gcG>gcA	p.A304A	SBSN_ENST00000518157.1_Intron	NM_001166034.1	NP_001159506.1	Q6UWP8	SBSN_HUMAN	suprabasin	304	Ala/Gly/His-rich.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)				large_intestine(5)|lung(6)|ovary(1)|prostate(2)	14	all_lung(56;1.62e-08)|Lung NSC(56;2.47e-08)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0724)			CGGCCTGCCCCGCAGCATGGT	0.652													c|||	1051	0.209864	0.0371	0.3401	5008	,	,		21069	0.3631		0.1392	False		,,,				2504	0.2658				p.A304A		Atlas-SNP	.											.	SBSN	58	.	0			c.G912A						PASS	.	A	,,	86,1298		3,80,609	29.0	37.0	34.0		912,,	-8.9	0.0	19	dbSNP_120	34	440,2742		33,374,1184	no	coding-synonymous,intron,intron	SBSN	NM_001166034.1,NM_001166035.1,NM_198538.3	,,	36,454,1793	TT,TC,CC		13.8278,6.2139,11.5199	,,	304/591,,	36018272	526,4040	692	1591	2283	SO:0001819	synonymous_variant	374897	exon1			CTGCCCCGCAGCA	AY358701	CCDS12464.1, CCDS54253.1	19q13.13	2008-02-05							24950	protein-coding gene	gene with protein product		609969				12228223	Standard	NM_198538		Approved	UNQ698, HLAR698	uc002oad.2	Q6UWP8		ENST00000452271.2:c.912G>A	19.37:g.36018272C>T		1.0	0.0	0		4.0	4.0	1	NM_001166034	A8K5J0|E9PBV3	Silent	SNP	ENST00000452271.2	37	CCDS54253.1																																																																																			C|0.795;T|0.205	0.205	strong		0.652	SBSN-002	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000109463.3	NM_198538	
FAM208A	23272	hgsc.bcm.edu	37	3	56680943	56680943	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:56680943G>A	ENST00000493960.2	-	14	1832	c.1822C>T	c.(1822-1824)Cgg>Tgg	p.R608W	FAM208A_ENST00000431842.2_Missense_Mutation_p.R212W|FAM208A_ENST00000355628.5_Missense_Mutation_p.R608W	NM_001112736.1	NP_001106207.1	Q9UK61	F208A_HUMAN	family with sequence similarity 208, member A	608							poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(11)|prostate(3)|skin(1)	32						ACTTCAGGCCGAAAAATATAG	0.308																																					p.R608W		Atlas-SNP	.											.	FAM208A	113	.	0			c.C1822T						PASS	.						33.0	34.0	34.0					3																	56680943		2199	4297	6496	SO:0001583	missense	23272	exon14			CAGGCCGAAAAAT	AF180425	CCDS2877.1, CCDS46853.1	3p14.3	2011-09-14	2011-09-14	2011-09-14	ENSG00000163946	ENSG00000163946			30314	protein-coding gene	gene with protein product			"""chromosome 3 open reading frame 63"""	C3orf63		10470851, 11149944	Standard	NM_015224		Approved	se89-1, RAP140, KIAA1105	uc003die.4	Q9UK61	OTTHUMG00000158827	ENST00000493960.2:c.1822C>T	3.37:g.56680943G>A	ENSP00000417509:p.Arg608Trp	109.0	0.0	0		119.0	27.0	0.226891	NM_001112736	A1L3A4|B5ME28|Q9H2F7|Q9UPP7	Missense_Mutation	SNP	ENST00000493960.2	37	CCDS46853.1	.	.	.	.	.	.	.	.	.	.	G	15.81	2.944599	0.53079	.	.	ENSG00000163946	ENST00000431842;ENST00000493960;ENST00000355628	T;T;T	0.12255	2.7;2.88;2.88	5.38	4.51	0.55191	.	1.076610	0.07180	N	0.853813	T	0.12433	0.0302	N	0.08118	0	0.26200	N	0.979465	D;D;D	0.71674	0.998;0.997;0.997	P;P;P	0.52856	0.711;0.533;0.648	T	0.21177	-1.0253	10	0.66056	D	0.02	1.8924	4.9438	0.13978	0.0785:0.2888:0.5061:0.1265	.	608;608;212	Q9UK61-3;Q9UK61-4;Q9UK61-2	.;.;.	W	212;608;608	ENSP00000399410:R212W;ENSP00000417509:R608W;ENSP00000347845:R608W	ENSP00000347845:R608W	R	-	1	2	C3orf63	56655983	0.528000	0.26314	0.955000	0.39395	0.975000	0.68041	1.045000	0.30341	1.505000	0.48720	-0.140000	0.14226	CGG	.	.	none		0.308	FAM208A-004	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352352.2	NM_015224	
FLII	2314	hgsc.bcm.edu	37	17	18156957	18156957	+	Silent	SNP	G	G	A	rs147128917		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:18156957G>A	ENST00000327031.4	-	8	981	c.756C>T	c.(754-756)aaC>aaT	p.N252N	FLII_ENST00000584444.1_Intron|FLII_ENST00000379450.4_Silent_p.N167N|FLII_ENST00000579294.1_Silent_p.N241N|FLII_ENST00000578558.1_Silent_p.N252N|FLII_ENST00000545457.2_Silent_p.N198N	NM_002018.3	NP_002009.1	Q13045	FLII_HUMAN	flightless I homolog (Drosophila)	252	Interaction with LRRFIP1 and LRRFIP2.				multicellular organismal development (GO:0007275)|muscle contraction (GO:0006936)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|nucleus (GO:0005634)	actin binding (GO:0003779)			central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(6)|lung(11)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	32	all_neural(463;0.228)					TGCTGCTGAGGTTGAGGCGGC	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		19548	0.0		0.001	False		,,,				2504	0.0				p.N252N		Atlas-SNP	.											.	FLII	79	.	0			c.C756T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	87.0	77.0	80.0		756	5.4	1.0	17	dbSNP_134	80	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FLII	NM_002018.2		0,4,6499	AA,AG,GG		0.0233,0.0454,0.0308		252/1270	18156957	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	2314	exon8			GCTGAGGTTGAGG	U01184	CCDS11192.1, CCDS58521.1, CCDS58522.1	17p11.2	2008-07-18	2001-11-28		ENSG00000177731	ENSG00000177731			3750	protein-coding gene	gene with protein product		600362	"""flightless I (Drosophila) homolog"""			7825574	Standard	NM_002018		Approved	FLI, FLIL, Fli1, MGC39265	uc002gsr.2	Q13045	OTTHUMG00000059389	ENST00000327031.4:c.756C>T	17.37:g.18156957G>A		128.0	0.0	0		171.0	75.0	0.438596	NM_002018	B4DIL0|F5H407|J3QLG3	Silent	SNP	ENST00000327031.4	37	CCDS11192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	FLII-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132032.2	NM_002018	
FBXO33	254170	hgsc.bcm.edu	37	14	39870594	39870594	+	Silent	SNP	T	T	C	rs61754302		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:39870594T>C	ENST00000298097.7	-	3	1519	c.1182A>G	c.(1180-1182)ctA>ctG	p.L394L	FBXO33_ENST00000554190.1_Intron	NM_203301.3	NP_976046.1	Q7Z6M2	FBX33_HUMAN	F-box protein 33	394					protein ubiquitination (GO:0016567)					endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(4)|urinary_tract(1)	9	Hepatocellular(127;0.213)		LUAD - Lung adenocarcinoma(48;0.00107)|Lung(238;0.00121)|Epithelial(34;0.169)	GBM - Glioblastoma multiforme(112;0.0425)		GAATCCTCTCTAGTGGTATAC	0.368																																					p.L394L		Atlas-SNP	.											.	FBXO33	21	.	0			c.A1182G						PASS	.	T		0,4406		0,0,2203	100.0	96.0	97.0		1182	0.4	1.0	14	dbSNP_129	97	3,8597	3.7+/-12.6	0,3,4297	no	coding-synonymous	FBXO33	NM_203301.3		0,3,6500	CC,CT,TT		0.0349,0.0,0.0231		394/556	39870594	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	254170	exon3			CCTCTCTAGTGGT	BI460761	CCDS9677.1	14q13.3	2004-08-24	2004-06-15		ENSG00000165355	ENSG00000165355		"""F-boxes /  ""other"""""	19833	protein-coding gene	gene with protein product		609103	"""F-box only protein 33"""				Standard	NM_203301		Approved	Fbx33	uc001wvk.3	Q7Z6M2	OTTHUMG00000140257	ENST00000298097.7:c.1182A>G	14.37:g.39870594T>C		125.0	0.0	0		143.0	70.0	0.48951	NM_203301	Q6PIR2|Q86TR2|Q86YE0	Silent	SNP	ENST00000298097.7	37	CCDS9677.1																																																																																			T|1.000;C|0.000	0.000	weak		0.368	FBXO33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276769.2		
BTBD16	118663	hgsc.bcm.edu	37	10	124036305	124036305	+	Splice_Site	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:124036305G>T	ENST00000260723.4	+	3	269		c.e3-1		BTBD16_ENST00000368994.2_Missense_Mutation_p.Q7H	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16											breast(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(3)|skin(2)|stomach(1)|urinary_tract(1)	15		all_neural(114;0.107)|Lung NSC(174;0.175)|all_lung(145;0.222)|Breast(234;0.238)				TTACCAAGCAGCACAAAGCTC	0.448																																					.		Atlas-SNP	.											BTBD16,bladder,carcinoma,0,1	BTBD16	44	1	0			c.19-1G>T						PASS	.						84.0	87.0	86.0					10																	124036305		2203	4300	6503	SO:0001630	splice_region_variant	118663	exon3			CAAGCAGCACAAA	AK058088	CCDS31301.1	10q26.13	2013-01-24	2006-07-04	2006-07-04	ENSG00000138152	ENSG00000138152		"""BTB/POZ domain containing"""	26340	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 87"""	C10orf87			Standard	NM_144587		Approved	FLJ25359, Em:AC061711.1	uc001lgc.1	Q32M84	OTTHUMG00000019182	ENST00000260723.4:c.19-1G>T	10.37:g.124036305G>T		125.0	0.0	0		134.0	18.0	0.134328	NM_144587	A6NM63|Q4VXL1|Q96LN0	Splice_Site	SNP	ENST00000260723.4	37	CCDS31301.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	9.139|9.139	1.013409|1.013409	0.19277|0.19277	.|.	.|.	ENSG00000138152|ENSG00000138152	ENST00000260723|ENST00000368994	.|T	.|0.19250	.|2.16	4.66|4.66	3.76|3.76	0.43208|0.43208	.|.	.|.	.|.	.|.	.|.	.|T	.|0.34571	.|0.0902	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|D	.|0.61697	.|0.99	.|P	.|0.58873	.|0.847	.|T	.|0.07139	.|-1.0788	.|8	.|0.44086	.|T	.|0.13	.|-0.0759	8.8669|8.8669	0.35291|0.35291	0.1013:0.0:0.8987:0.0|0.1013:0.0:0.8987:0.0	.|.	.|7	.|Q32M84-2	.|.	.|H	-1|7	.|ENSP00000357990:Q7H	.|ENSP00000357990:Q7H	.|Q	+|+	.|3	.|2	BTBD16|BTBD16	124026295|124026295	0.605000|0.605000	0.26941|0.26941	0.007000|0.007000	0.13788|0.13788	0.006000|0.006000	0.05464|0.05464	2.406000|2.406000	0.44557|0.44557	1.332000|1.332000	0.45431|0.45431	0.650000|0.650000	0.86243|0.86243	.|CAG	.	.	none		0.448	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	Intron
KCNA5	3741	hgsc.bcm.edu	37	12	5154064	5154064	+	Missense_Mutation	SNP	G	G	A	rs12720442	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:5154064G>A	ENST00000252321.3	+	1	980	c.751G>A	c.(751-753)Gcc>Acc	p.A251T		NM_002234.3	NP_002225.2	P22460	KCNA5_HUMAN	potassium voltage-gated channel, shaker-related subfamily, member 5	251					atrial cardiac muscle cell action potential (GO:0086014)|membrane hyperpolarization (GO:0060081)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|positive regulation of myoblast proliferation (GO:2000288)|potassium ion export (GO:0071435)|potassium ion homeostasis (GO:0055075)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of membrane potential (GO:0042391)|regulation of potassium ion transport (GO:0043266)|regulation of vasoconstriction (GO:0019229)|response to hypoxia (GO:0001666)|synaptic transmission (GO:0007268)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|intracellular canaliculus (GO:0046691)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|delayed rectifier potassium channel activity (GO:0005251)|outward rectifier potassium channel activity (GO:0015271)|potassium channel inhibitor activity (GO:0019870)|protein kinase binding (GO:0019901)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)			NS(1)|breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(21)|ovary(5)|prostate(2)|upper_aerodigestive_tract(2)	52					Dalfampridine(DB06637)	GTCCGCGCGGGCCATCGCCAT	0.587													G|||	41	0.0081869	0.0015	0.0274	5008	,	,		15304	0.0		0.0169	False		,,,				2504	0.0031				p.A251T		Atlas-SNP	.											KCNA5,brain,glioma,0,1	KCNA5	138	1	0			c.G751A						PASS	.	G	THR/ALA	14,4392	22.3+/-47.3	1,12,2190	109.0	118.0	115.0		751	4.8	0.9	12	dbSNP_126	115	109,8491	58.3+/-119.8	1,107,4192	yes	missense	KCNA5	NM_002234.2	58	2,119,6382	AA,AG,GG		1.2674,0.3177,0.9457	benign	251/614	5154064	123,12883	2203	4300	6503	SO:0001583	missense	3741	exon1			GCGCGGGCCATCG	M83254	CCDS8536.1	12p13	2012-07-05				ENSG00000130037		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6224	protein-coding gene	gene with protein product		176267				16382104	Standard	NM_002234		Approved	Kv1.5, HK2, HPCN1	uc001qni.4	P22460		ENST00000252321.3:c.751G>A	12.37:g.5154064G>A	ENSP00000252321:p.Ala251Thr	91.0	0.0	0		103.0	47.0	0.456311	NM_002234	Q4KKT8|Q4VAJ1|Q4VAJ2|Q9UDA4	Missense_Mutation	SNP	ENST00000252321.3	37	CCDS8536.1	22	0.010073260073260074	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	13	0.017150395778364115	G	10.28	1.305403	0.23736	0.003177	0.012674	ENSG00000130037	ENST00000252321	T	0.65178	-0.14	4.77	4.77	0.60923	.	0.227351	0.34484	U	0.003922	T	0.38480	0.1042	L	0.38175	1.15	0.28718	N	0.90318	B	0.13145	0.007	B	0.17722	0.019	T	0.48603	-0.9021	10	0.48119	T	0.1	.	16.9696	0.86295	0.0:0.0:1.0:0.0	rs12720442;rs45573135	251	P22460	KCNA5_HUMAN	T	251	ENSP00000252321:A251T	ENSP00000252321:A251T	A	+	1	0	KCNA5	5024325	0.948000	0.32251	0.932000	0.37286	0.982000	0.71751	5.267000	0.65530	2.478000	0.83669	0.561000	0.74099	GCC	G|0.990;A|0.010	0.010	strong		0.587	KCNA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398925.2	NM_002234	
ST14	6768	hgsc.bcm.edu	37	11	130060453	130060453	+	Missense_Mutation	SNP	G	G	A	rs35230546|rs144266633	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:130060453G>A	ENST00000278742.5	+	7	1157	c.739G>A	c.(739-741)Gcc>Acc	p.A247T		NM_021978.3	NP_068813.1	Q9Y5Y6	ST14_HUMAN	suppression of tumorigenicity 14 (colon carcinoma)	247	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				keratinocyte differentiation (GO:0030216)|proteolysis (GO:0006508)	basolateral plasma membrane (GO:0016323)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(12)|ovary(3)|pancreas(2)|prostate(1)|skin(3)	32	all_hematologic(175;0.0429)	Lung NSC(97;0.000602)|Breast(109;0.000962)|all_lung(97;0.00126)|Medulloblastoma(222;0.0425)|all_neural(223;0.0837)		OV - Ovarian serous cystadenocarcinoma(99;0.0183)|Lung(977;0.228)	Urokinase(DB00013)	CTGCCAGTGGGCCCTGCGGGG	0.687																																					p.A247T		Atlas-SNP	.											.	ST14	82	.	0			c.G739A						PASS	.	G	THR/ALA	0,4400		0,0,2200	27.0	25.0	26.0		739	1.3	1.0	11	dbSNP_134	26	7,8583		0,7,4288	yes	missense	ST14	NM_021978.3	58	0,7,6488	AA,AG,GG		0.0815,0.0,0.0539	benign	247/856	130060453	7,12983	2200	4295	6495	SO:0001583	missense	6768	exon7			CAGTGGGCCCTGC	AF118224	CCDS8487.1	11q24-q25	2011-08-31	2005-11-19		ENSG00000149418	ENSG00000149418		"""Serine peptidases / Transmembrane"""	11344	protein-coding gene	gene with protein product	"""epithin"", ""matriptase"""	606797		PRSS14		9925927, 10373424	Standard	NM_021978		Approved	SNC19, HAI, MT-SP1, TMPRSS14	uc001qfw.3	Q9Y5Y6	OTTHUMG00000165768	ENST00000278742.5:c.739G>A	11.37:g.130060453G>A	ENSP00000278742:p.Ala247Thr	106.0	0.0	0		45.0	29.0	0.644444	NM_021978	Q9BS01|Q9H3S0|Q9HB36|Q9HCA3	Missense_Mutation	SNP	ENST00000278742.5	37	CCDS8487.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.510543	0.27036	0.0	8.15E-4	ENSG00000149418	ENST00000278742;ENST00000525779	T	0.30714	1.52	5.45	1.26	0.21427	CUB (5);	1.014350	0.07937	N	0.978525	T	0.10035	0.0246	N	0.01188	-0.97	0.23271	N	0.998006	B;B	0.10296	0.003;0.002	B;B	0.12837	0.008;0.005	T	0.34625	-0.9821	10	0.08837	T	0.75	.	7.5637	0.27866	0.5136:0.0:0.4864:0.0	.	57;247	B4DYI7;Q9Y5Y6	.;ST14_HUMAN	T	247;149	ENSP00000278742:A247T	ENSP00000278742:A247T	A	+	1	0	ST14	129565663	0.025000	0.19082	0.997000	0.53966	0.915000	0.54546	0.259000	0.18405	-0.033000	0.13736	0.650000	0.86243	GCC	G|1.000;A|0.000	0.000	strong		0.687	ST14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386119.1		
KCNH5	27133	hgsc.bcm.edu	37	14	63175012	63175012	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63175012A>G	ENST00000322893.7	-	11	2449	c.2181T>C	c.(2179-2181)ggT>ggC	p.G727G	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	727					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)		TCTCAGGGTCACCCTGTGTTG	0.557																																					p.G727G		Atlas-SNP	.											KCNH5,NS,carcinoma,-1,1	KCNH5	320	1	0			c.T2181C						PASS	.						114.0	106.0	109.0					14																	63175012		2203	4300	6503	SO:0001819	synonymous_variant	27133	exon11			AGGGTCACCCTGT	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.2181T>C	14.37:g.63175012A>G		156.0	0.0	0		160.0	67.0	0.41875	NM_139318	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																			.	.	none		0.557	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
SEC11A	23478	hgsc.bcm.edu	37	15	85234858	85234858	+	Silent	SNP	T	T	C	rs369852123		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:85234858T>C	ENST00000268220.7	-	2	709	c.69A>G	c.(67-69)ctA>ctG	p.L23L	SEC11A_ENST00000560266.1_Silent_p.L23L|SEC11A_ENST00000558134.1_Silent_p.L23L|SEC11A_ENST00000455959.3_5'UTR	NM_014300.2	NP_055115.1	P67812	SC11A_HUMAN	SEC11 homolog A (S. cerevisiae)	23					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|regulation of insulin secretion (GO:0050796)|signal peptide processing (GO:0006465)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	serine-type peptidase activity (GO:0008236)			ovary(1)	1			BRCA - Breast invasive adenocarcinoma(143;0.199)			TTCCAAAATTTAGGACTTGAT	0.398																																					p.L23L		Atlas-SNP	.											.	SEC11A	8	.	0			c.A69G						PASS	.	T		0,3756		0,0,1878	75.0	69.0	71.0		69	-1.8	1.0	15		71	1,8227		0,1,4113	no	coding-synonymous	SEC11A	NM_014300.2		0,1,5991	CC,CT,TT		0.0122,0.0,0.0083		23/180	85234858	1,11983	1878	4114	5992	SO:0001819	synonymous_variant	23478	exon2			AAAATTTAGGACT	AF061737	CCDS45340.1, CCDS61742.1, CCDS61743.1, CCDS61744.1, CCDS73776.1	15q25.2	2006-11-07	2006-11-07	2006-11-07		ENSG00000140612			17718	protein-coding gene	gene with protein product			"""SEC11-like 1 (S. cerevisiae)"""	SEC11L1			Standard	NM_001271919		Approved	SPC18, sid2895, SPCS4A	uc031qtg.1	P67812		ENST00000268220.7:c.69A>G	15.37:g.85234858T>C		77.0	0.0	0		77.0	45.0	0.584416	NM_014300	B2RAD7|B4DUL4|H0YK72|H0YK83|O75957|P21378|Q53FQ8	Silent	SNP	ENST00000268220.7	37	CCDS45340.1																																																																																			.	.	weak		0.398	SEC11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418777.1	NM_014300	
HK3	3101	hgsc.bcm.edu	37	5	176309082	176309082	+	Silent	SNP	C	C	T	rs34127573	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:176309082C>T	ENST00000292432.5	-	16	2191	c.2100G>A	c.(2098-2100)gcG>gcA	p.A700A		NM_002115.2	NP_002106.2	P52790	HXK3_HUMAN	hexokinase 3 (white cell)	700	Catalytic.|Hexokinase type-2 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose metabolic process (GO:0019318)|hexose transport (GO:0008645)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|protein complex (GO:0043234)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|hormone binding (GO:0042562)|mannokinase activity (GO:0019158)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(21)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	47	all_cancers(89;0.000104)|Renal(175;0.000269)|Lung NSC(126;0.00696)|all_lung(126;0.0115)	Medulloblastoma(196;0.00498)|all_neural(177;0.0138)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CAGGCACGCCCGCCACATTCC	0.597													C|||	20	0.00399361	0.003	0.0014	5008	,	,		18484	0.0		0.0139	False		,,,				2504	0.001				p.A700A		Atlas-SNP	.											.	HK3	210	.	0			c.G2100A						PASS	.	C		10,4396	12.9+/-30.5	0,10,2193	52.0	50.0	51.0		2100	-10.1	0.0	5	dbSNP_126	51	119,8479	55.6+/-116.7	1,117,4181	no	coding-synonymous	HK3	NM_002115.2		1,127,6374	TT,TC,CC		1.384,0.227,0.992		700/924	176309082	129,12875	2203	4299	6502	SO:0001819	synonymous_variant	3101	exon16			CACGCCCGCCACA		CCDS4407.1	5q35.2	2008-02-05			ENSG00000160883	ENSG00000160883	2.7.1.1		4925	protein-coding gene	gene with protein product		142570				8812439	Standard	NM_002115		Approved		uc003mfa.3	P52790	OTTHUMG00000130855	ENST00000292432.5:c.2100G>A	5.37:g.176309082C>T		121.0	0.0	0		130.0	82.0	0.630769	NM_002115	Q8N1E7	Silent	SNP	ENST00000292432.5	37	CCDS4407.1																																																																																			C|0.992;T|0.008	0.008	strong		0.597	HK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253428.1		
CCDC107	203260	hgsc.bcm.edu	37	9	35660872	35660872	+	Silent	SNP	C	C	T	rs141349284	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:35660872C>T	ENST00000426546.2	+	5	606	c.540C>T	c.(538-540)ggC>ggT	p.G180G	ARHGEF39_ENST00000378395.2_3'UTR|CCDC107_ENST00000378406.1_3'UTR|RMRP_ENST00000602361.1_lincRNA|CCDC107_ENST00000327351.2_Intron|CCDC107_ENST00000378409.3_Intron|ARHGEF39_ENST00000490970.1_5'Flank|ARHGEF39_ENST00000378387.3_3'UTR|ARHGEF39_ENST00000343259.3_3'UTR|CCDC107_ENST00000378407.3_3'UTR|CCDC107_ENST00000421582.2_3'UTR	NM_001195200.1|NM_001195201.1|NM_001195217.1|NM_174923.2	NP_001182129.1|NP_001182130.1|NP_001182146.1|NP_777583.2	Q8WV48	CC107_HUMAN	coiled-coil domain containing 107	180						integral component of membrane (GO:0016021)				endometrium(1)|lung(3)|skin(1)	5	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)			GCTCGGGAGGCGAGTCTGCTG	0.527													C|||	4	0.000798722	0.0	0.0029	5008	,	,		19570	0.001		0.001	False		,,,				2504	0.0				p.G180G		Atlas-SNP	.											.	CCDC107	12	.	0			c.C540T						PASS	.	C	,,,,	0,4406		0,0,2203	123.0	134.0	130.0		,,,,540	-4.9	0.0	9	dbSNP_134	130	2,8598	2.2+/-6.3	0,2,4298	no	intron,intron,utr-3,utr-3,coding-synonymous	C9orf100,CCDC107	NM_001195200.1,NM_001195201.1,NM_001195217.1,NM_032818.2,NM_174923.2	,,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,,	,,,,180/284	35660872	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	203260	exon5			GGGAGGCGAGTCT	AK075523	CCDS6583.1, CCDS56573.1, CCDS56574.1, CCDS56575.1	9q13.3	2008-02-05			ENSG00000159884	ENSG00000159884			28465	protein-coding gene	gene with protein product						12477932	Standard	NM_174923		Approved	MGC31967	uc011lox.2	Q8WV48	OTTHUMG00000019868	ENST00000426546.2:c.540C>T	9.37:g.35660872C>T		64.0	0.0	0		80.0	36.0	0.45	NM_174923	A6XND6|Q5T4R5|Q5T4R8|Q5T4R9|Q86VB6|Q8N2E4	Silent	SNP	ENST00000426546.2	37	CCDS6583.1																																																																																			C|1.000;T|0.000	0.000	strong		0.527	CCDC107-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000052325.1	NM_174923	
CGNL1	84952	hgsc.bcm.edu	37	15	57731384	57731384	+	Missense_Mutation	SNP	G	G	T	rs148544821	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:57731384G>T	ENST00000281282.5	+	2	1265	c.1187G>T	c.(1186-1188)gGc>gTc	p.G396V		NM_001252335.1|NM_032866.4	NP_001239264.1|NP_116255.2	Q0VF96	CGNL1_HUMAN	cingulin-like 1	396	Head.					myosin complex (GO:0016459)|tight junction (GO:0005923)	motor activity (GO:0003774)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(4)|large_intestine(12)|lung(14)|ovary(4)|prostate(4)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)	60				all cancers(107;0.121)|GBM - Glioblastoma multiforme(80;0.186)		TTTCCTTTTGGCCTCCAAGGG	0.527													G|||	4	0.000798722	0.0008	0.0014	5008	,	,		18234	0.0		0.002	False		,,,				2504	0.0				p.G396V		Atlas-SNP	.											.	CGNL1	125	.	0			c.G1187T						PASS	.	G	VAL/GLY	2,4382	4.2+/-10.8	0,2,2190	94.0	96.0	95.0		1187	5.8	0.3	15	dbSNP_134	95	14,8570	9.8+/-36.6	0,14,4278	yes	missense	CGNL1	NM_032866.3	109	0,16,6468	TT,TG,GG		0.1631,0.0456,0.1234	probably-damaging	396/1303	57731384	16,12952	2192	4292	6484	SO:0001583	missense	84952	exon2			CTTTTGGCCTCCA	AY274808	CCDS10161.1	15q21.3	2011-06-10			ENSG00000128849	ENSG00000128849			25931	protein-coding gene	gene with protein product		607856				11214970	Standard	NM_001252335		Approved	FLJ14957, JACOP, KIAA1749, paracingulin	uc002aeg.3	Q0VF96	OTTHUMG00000166485	ENST00000281282.5:c.1187G>T	15.37:g.57731384G>T	ENSP00000281282:p.Gly396Val	128.0	0.0	0		115.0	46.0	0.4	NM_032866	Q05BZ4|Q52LR0|Q695C7|Q7Z2L3|Q96JV2|Q96MN6|Q9C0B4	Missense_Mutation	SNP	ENST00000281282.5	37	CCDS10161.1	4	0.0018315018315018315	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	17.89	3.498940	0.64298	4.56E-4	0.001631	ENSG00000128849	ENST00000281282	T	0.58940	0.3	5.79	5.79	0.91817	.	0.000000	0.52532	D	0.000073	T	0.68723	0.3032	L	0.54323	1.7	0.58432	D	0.999999	D	0.65815	0.995	P	0.59357	0.856	T	0.70733	-0.4791	10	0.87932	D	0	-28.2427	15.212	0.73230	0.0689:0.0:0.9311:0.0	.	396	Q0VF96	CGNL1_HUMAN	V	396	ENSP00000281282:G396V	ENSP00000281282:G396V	G	+	2	0	CGNL1	55518676	1.000000	0.71417	0.255000	0.24374	0.477000	0.33069	6.194000	0.72082	2.722000	0.93159	0.655000	0.94253	GGC	G|0.998;T|0.002	0.002	strong		0.527	CGNL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255482.2	NM_032866	
ECD	11319	hgsc.bcm.edu	37	10	74894526	74894526	+	Missense_Mutation	SNP	A	A	C	rs35331959	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:74894526A>C	ENST00000372979.4	-	14	1956	c.1750T>G	c.(1750-1752)Tct>Gct	p.S584A	ECD_ENST00000430082.2_Missense_Mutation_p.S617A|ECD_ENST00000454759.2_Missense_Mutation_p.S541A	NM_007265.2	NP_009196.1	O95905	SGT1_HUMAN	ecdysoneless homolog (Drosophila)	584					cell proliferation (GO:0008283)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of glycolytic process (GO:0006110)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|pancreas(1)|prostate(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	21	Prostate(51;0.0119)					CCCGTACCAGAATCTTCCTCA	0.428													A|||	14	0.00279553	0.0015	0.0029	5008	,	,		17074	0.0		0.0099	False		,,,				2504	0.0				p.S617A		Atlas-SNP	.											.	ECD	50	.	0			c.T1849G						PASS	.	A	ALA/SER,ALA/SER,ALA/SER	13,4393	20.2+/-43.8	0,13,2190	114.0	111.0	112.0		1849,1621,1750	4.3	1.0	10	dbSNP_126	112	136,8464	68.7+/-131.2	2,132,4166	yes	missense,missense,missense	ECD	NM_001135752.1,NM_001135753.1,NM_007265.2	99,99,99	2,145,6356	CC,CA,AA		1.5814,0.2951,1.1456	benign,benign,benign	617/678,541/602,584/645	74894526	149,12857	2203	4300	6503	SO:0001583	missense	11319	exon15			TACCAGAATCTTC	BC000721	CCDS7321.1, CCDS44433.1, CCDS44434.1	10q22.3	2006-02-07				ENSG00000122882			17029	protein-coding gene	gene with protein product						9928932, 15128659	Standard	NM_007265		Approved	hSGT1, GCR2	uc001jtn.3	O95905		ENST00000372979.4:c.1750T>G	10.37:g.74894526A>C	ENSP00000362070:p.Ser584Ala	169.0	0.0	0		160.0	67.0	0.41875	NM_001135752	C9JX46|E9PAW8	Missense_Mutation	SNP	ENST00000372979.4	37	CCDS7321.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	4.002	-0.002418	0.07819	0.002951	0.015814	ENSG00000122882	ENST00000372979;ENST00000430082;ENST00000454759	T;T;T	0.19394	2.15;2.15;2.15	5.48	4.29	0.51040	.	0.570097	0.19982	N	0.101760	T	0.04861	0.0131	N	0.12746	0.255	0.26648	N	0.972169	B;B;B	0.09022	0.002;0.002;0.001	B;B;B	0.15484	0.01;0.003;0.013	T	0.24297	-1.0164	10	0.09590	T	0.72	-0.8007	10.5006	0.44804	0.7883:0.2116:0.0:0.0	rs35331959	541;617;584	E9PAW8;C9JX46;O95905	.;.;SGT1_HUMAN	A	584;617;541	ENSP00000362070:S584A;ENSP00000401566:S617A;ENSP00000395786:S541A	ENSP00000362070:S584A	S	-	1	0	ECD	74564532	1.000000	0.71417	1.000000	0.80357	0.242000	0.25591	2.625000	0.46452	2.063000	0.61619	0.460000	0.39030	TCT	A|0.991;C|0.009	0.009	strong		0.428	ECD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048606.1	NM_007265	
C11orf48	79081	hgsc.bcm.edu	37	11	62437422	62437422	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:62437422G>A	ENST00000431002.2	-	1	1815	c.82C>T	c.(82-84)Ccc>Tcc	p.P28S	C11orf48_ENST00000532208.1_Missense_Mutation_p.P28S|C11orf83_ENST00000531323.1_5'Flank|C11orf48_ENST00000354588.3_Missense_Mutation_p.P28S|C11orf83_ENST00000377953.3_5'Flank			Q9BQE6	CK048_HUMAN	chromosome 11 open reading frame 48	28										endometrium(1)|lung(5)|urinary_tract(1)	7						GGCAGCCTGGGACTTTCTGGA	0.542																																					p.P28S		Atlas-SNP	.											.	C11orf48	18	.	0			c.C82T						PASS	.						101.0	94.0	96.0					11																	62437422		2202	4299	6501	SO:0001583	missense	79081	exon2			GCCTGGGACTTTC	BC001434	CCDS8028.1	11q12.3	2014-02-12			ENSG00000162194	ENSG00000162194			28351	protein-coding gene	gene with protein product						12477932	Standard	NM_024099		Approved	MGC2477	uc001nuf.3	Q9BQE6	OTTHUMG00000167588	ENST00000431002.2:c.82C>T	11.37:g.62437422G>A	ENSP00000416856:p.Pro28Ser	182.0	0.0	0		197.0	94.0	0.477157	NM_024099	Q96NA4	Missense_Mutation	SNP	ENST00000431002.2	37		.	.	.	.	.	.	.	.	.	.	G	13.80	2.346432	0.41599	.	.	ENSG00000162194	ENST00000354588;ENST00000431002;ENST00000532208;ENST00000377954;ENST00000526490	.	.	.	4.49	2.59	0.31030	.	0.201361	0.24988	N	0.034002	T	0.29288	0.0729	N	0.19112	0.55	0.32145	N	0.585027	P;B	0.46912	0.886;0.301	P;B	0.46275	0.51;0.184	T	0.37753	-0.9692	9	0.87932	D	0	-0.7818	5.6644	0.17687	0.1061:0.2021:0.6918:0.0	.	28;28	B4DYP8;Q9BQE6-2	.;.	S	28;28;28;53;28	.	ENSP00000346600:P28S	P	-	1	0	C11orf48	62193998	0.087000	0.21565	0.765000	0.31456	0.811000	0.45836	1.056000	0.30480	1.216000	0.43427	0.563000	0.77884	CCC	.	.	none		0.542	C11orf48-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000395233.1	NM_024099	
PNPLA7	375775	hgsc.bcm.edu	37	9	140438216	140438216	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:140438216G>A	ENST00000277531.4	-	4	436	c.250C>T	c.(250-252)Cgg>Tgg	p.R84W	PNPLA7_ENST00000406427.1_Missense_Mutation_p.R109W|AL365502.1_ENST00000580317.1_RNA	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	84					lipid metabolic process (GO:0006629)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(9)|lung(13)|ovary(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_cancers(76;0.126)			OV - Ovarian serous cystadenocarcinoma(145;0.000268)|Epithelial(140;0.000839)		TTCCTGGCCCGCTGCCGGGGC	0.637																																					p.R109W		Atlas-SNP	.											.	PNPLA7	124	.	0			c.C325T						PASS	.						85.0	77.0	80.0					9																	140438216		2203	4300	6503	SO:0001583	missense	375775	exon5			TGGCCCGCTGCCG	AK126267	CCDS7045.1, CCDS48070.1	9q34.3	2009-01-12	2006-06-12	2006-06-12	ENSG00000130653	ENSG00000130653		"""Patatin-like phospholipase domain containing"""	24768	protein-coding gene	gene with protein product		612122	"""chromosome 9 open reading frame 111"""	C9orf111		16799181, 12640454, 19029121	Standard	XM_005266082		Approved	FLJ43070, FLJ31318, FLJ44279, RP11-48C7.2, NTEL1, NTE-R1	uc010ncj.1	Q6ZV29	OTTHUMG00000020990	ENST00000277531.4:c.250C>T	9.37:g.140438216G>A	ENSP00000277531:p.Arg84Trp	150.0	0.0	0		171.0	74.0	0.432749	NM_001098537	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Missense_Mutation	SNP	ENST00000277531.4	37	CCDS7045.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.306502	0.60305	.	.	ENSG00000130653	ENST00000277531;ENST00000406427;ENST00000371451;ENST00000434090;ENST00000371450	T;T;T	0.62364	0.05;0.03;0.06	3.41	2.4	0.29515	.	0.066594	0.56097	D	0.000027	T	0.74966	0.3786	M	0.77103	2.36	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.997	T	0.76767	-0.2838	10	0.87932	D	0	-14.0749	8.3027	0.32023	0.0:0.0:0.5617:0.4382	.	109;84	Q6ZV29-5;Q6ZV29	.;PLPL7_HUMAN	W	84;109;84;75;109	ENSP00000277531:R84W;ENSP00000384610:R109W;ENSP00000400582:R75W	ENSP00000277531:R84W	R	-	1	2	PNPLA7	139558037	1.000000	0.71417	0.954000	0.39281	0.848000	0.48234	1.656000	0.37355	1.907000	0.55213	0.462000	0.41574	CGG	.	.	none		0.637	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
TPGS1	91978	hgsc.bcm.edu	37	19	507731	507731	+	Silent	SNP	C	C	T	rs16990489	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:507731C>T	ENST00000359315.5	+	1	433	c.225C>T	c.(223-225)ggC>ggT	p.G75G	AC005775.2_ENST00000592413.1_RNA	NM_033513.2	NP_277048.2	Q6ZTW0	TPGS1_HUMAN	tubulin polyglutamylase complex subunit 1	75					adult behavior (GO:0030534)|multicellular organismal development (GO:0007275)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|synaptic transmission (GO:0007268)|vesicle localization (GO:0051648)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)	tubulin-glutamic acid ligase activity (GO:0070740)										AGAACATGGGCCTGCGCTCGC	0.711													C|||	93	0.0185703	0.0545	0.0173	5008	,	,		12412	0.0		0.0089	False		,,,				2504	0.0				p.G75G		Atlas-SNP	.											.	.	.	.	0			c.C225T						PASS	.	C		140,3414		1,138,1638	7.0	10.0	9.0		225	2.2	1.0	19	dbSNP_123	9	51,7895		0,51,3922	no	coding-synonymous	C19orf20	NM_033513.2		1,189,5560	TT,TC,CC		0.6418,3.9392,1.6609		75/291	507731	191,11309	1777	3973	5750	SO:0001819	synonymous_variant	91978	exon1			CATGGGCCTGCGC	BC009520	CCDS42454.1	19p13.3	2011-11-23	2011-11-23	2011-11-23	ENSG00000141933	ENSG00000141933			25058	protein-coding gene	gene with protein product			"""chromosome 19 open reading frame 20"""	C19orf20		11441184, 12972506	Standard	NM_033513		Approved	GTRGEO22, PGs1	uc002lou.3	Q6ZTW0		ENST00000359315.5:c.225C>T	19.37:g.507731C>T		43.0	0.0	0		24.0	14.0	0.583333	NM_033513	Q96GE2	Silent	SNP	ENST00000359315.5	37	CCDS42454.1																																																																																			C|0.974;T|0.026	0.026	strong		0.711	TPGS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451887.2	NM_033513	
CXCR5	643	hgsc.bcm.edu	37	11	118764448	118764448	+	Silent	SNP	C	C	T	rs537787473		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:118764448C>T	ENST00000292174.4	+	2	371	c.195C>T	c.(193-195)ggC>ggT	p.G65G		NM_001716.4|NM_032966.2	NP_001707.1|NP_116743.1	P32302	CXCR5_HUMAN	chemokine (C-X-C motif) receptor 5	65					B cell activation (GO:0042113)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|lymph node development (GO:0048535)|positive regulation of cytokinesis (GO:0032467)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	C-X-C chemokine receptor activity (GO:0016494)|G-protein coupled receptor activity (GO:0004930)			breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(5)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.103)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.62e-05)		TCCTCCTGGGCGTGATCGGCA	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		19111	0.0		0.0	False		,,,				2504	0.0				p.G65G		Atlas-SNP	.											.	CXCR5	34	.	0			c.C195T						PASS	.						117.0	105.0	109.0					11																	118764448		2200	4295	6495	SO:0001819	synonymous_variant	643	exon2			CCTGGGCGTGATC	X68829	CCDS8402.1	11q23.3	2012-08-08	2008-01-22	2008-01-22	ENSG00000160683	ENSG00000160683		"""CD molecules"", ""GPCR / Class A : Chemokine receptors : C-X-C motif"""	1060	protein-coding gene	gene with protein product		601613	"""Burkitt lymphoma receptor 1, GTP-binding protein"", ""Burkitt lymphoma receptor 1, GTP binding protein (chemokine (C-X-C motif) receptor 5)"""	BLR1		1425907	Standard	NM_001716		Approved	MDR15, CD185	uc001pue.4	P32302	OTTHUMG00000166345	ENST00000292174.4:c.195C>T	11.37:g.118764448C>T		147.0	0.0	0		151.0	70.0	0.463576	NM_001716	Q14811	Silent	SNP	ENST00000292174.4	37	CCDS8402.1																																																																																			.	.	none		0.642	CXCR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389309.1	NM_001716	
ZSCAN9	7746	hgsc.bcm.edu	37	6	28195521	28195521	+	Silent	SNP	A	A	G	rs12197427	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:28195521A>G	ENST00000252207.5	+	3	622	c.474A>G	c.(472-474)ctA>ctG	p.L158L	ZSCAN9_ENST00000425468.2_Silent_p.L158L|ZSCAN9_ENST00000527436.1_Silent_p.L158L|ZSCAN9_ENST00000531979.1_Silent_p.L158L|ZSCAN9_ENST00000531981.1_3'UTR	NM_006299.4	NP_006290.1	O15535	ZSC9_HUMAN	zinc finger and SCAN domain containing 9	158					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TGGTGCCTCTAGCAGAGCAGA	0.488													A|||	78	0.0155751	0.0	0.0274	5008	,	,		18815	0.0129		0.0278	False		,,,				2504	0.0184				p.L158L		Atlas-SNP	.											ZNF193,NS,carcinoma,+2,1	.	.	1	0			c.A474G						PASS	.	A	,,	26,4380	32.6+/-62.9	0,26,2177	70.0	64.0	66.0		474,474,474	-3.5	0.0	6	dbSNP_120	66	313,8287	112.0+/-172.2	8,297,3995	no	coding-synonymous,coding-synonymous,coding-synonymous	ZNF193	NM_001199479.1,NM_001199480.1,NM_006299.4	,,	8,323,6172	GG,GA,AA		3.6395,0.5901,2.6065	,,	158/446,158/395,158/395	28195521	339,12667	2203	4300	6503	SO:0001819	synonymous_variant	7746	exon3			GCCTCTAGCAGAG	U62392	CCDS4646.1, CCDS56407.1	6p21	2013-01-09	2013-01-09	2013-01-09	ENSG00000137185	ENSG00000137185		"""-"", ""Zinc fingers, C2H2-type"""	12984	protein-coding gene	gene with protein product		602246	"""zinc finger protein 193"""	ZNF193			Standard	NM_001199479		Approved	PRD51	uc003nkq.2	O15535	OTTHUMG00000014515	ENST00000252207.5:c.474A>G	6.37:g.28195521A>G		205.0	0.0	0		213.0	125.0	0.586854	NM_006299	B4E1W6|E7EVQ2|Q2TTR1	Silent	SNP	ENST00000252207.5	37	CCDS4646.1																																																																																			A|0.971;G|0.029	0.029	strong		0.488	ZSCAN9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040183.2	NM_006299	
PTPN7	5778	hgsc.bcm.edu	37	1	202124690	202124690	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:202124690C>T	ENST00000308986.5	-	5	569	c.439G>A	c.(439-441)Gga>Aga	p.G147R	PTPN7_ENST00000492977.1_5'UTR|PTPN7_ENST00000543735.1_5'UTR|PTPN7_ENST00000309017.3_Missense_Mutation_p.G252R|PTPN7_ENST00000544762.1_Intron|PTPN7_ENST00000367279.4_Missense_Mutation_p.G186R			P35236	PTN7_HUMAN	protein tyrosine phosphatase, non-receptor type 7	147	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	protein tyrosine phosphatase activity (GO:0004725)	p.G186*(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(2)|skin(1)|soft_tissue(1)|urinary_tract(1)	13						ATGTAATCTCCGTCCTCCTGG	0.542																																					p.G252R		Atlas-SNP	.											PTPN7,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	PTPN7	31	1	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.G754A						PASS	.						93.0	77.0	83.0					1																	202124690		2203	4300	6503	SO:0001583	missense	5778	exon5			AATCTCCGTCCTC	BC001746	CCDS1422.1, CCDS1423.1, CCDS1423.2	1q32.1	2011-06-09			ENSG00000143851	ENSG00000143851		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9659	protein-coding gene	gene with protein product		176889				1510684	Standard	NM_002832		Approved	HEPTP, LC-PTP	uc010ppx.2	P35236	OTTHUMG00000035931	ENST00000308986.5:c.439G>A	1.37:g.202124690C>T	ENSP00000311133:p.Gly147Arg	109.0	0.0	0		111.0	50.0	0.45045	NM_002832	B3KXE1|Q53XK4|Q5SXQ0|Q5SXQ1|Q9BV05	Missense_Mutation	SNP	ENST00000308986.5	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.66|12.66	2.005836|2.005836	0.35415|0.35415	.|.	.|.	ENSG00000143851|ENSG00000143851	ENST00000367279;ENST00000309017;ENST00000308986;ENST00000477554;ENST00000476061;ENST00000467283;ENST00000464870|ENST00000477625;ENST00000435759	T;T;T;T;T;T;T|.	0.14022|.	2.54;2.54;2.54;2.54;2.75;2.75;2.75|.	5.26|5.26	4.33|4.33	0.51752|0.51752	Protein-tyrosine phosphatase, receptor/non-receptor type (3);|.	0.239923|.	0.29459|.	N|.	0.012088|.	T|T	0.49270|0.49270	0.1547|0.1547	M|M	0.62088|0.62088	1.915|1.915	0.19775|0.19775	N|N	0.999951|0.999951	P;B;B;B;P|.	0.43578|.	0.811;0.076;0.229;0.123;0.508|.	P;B;B;B;B|.	0.49561|.	0.615;0.223;0.256;0.223;0.314|.	T|T	0.44862|0.44862	-0.9300|-0.9300	10|6	0.87932|0.87932	D|D	0|0	-12.8237|-12.8237	9.366|9.366	0.38226|0.38226	0.0:0.8348:0.0:0.1652|0.0:0.8348:0.0:0.1652	.|.	221;95;99;147;186|.	B4DZD9;B4DVF0;Q8NFX3;P35236;P35236-2|.	.;.;.;PTN7_HUMAN;.|.	R|Q	186;252;147;228;146;146;147|78;153	ENSP00000356248:G186R;ENSP00000309116:G252R;ENSP00000311133:G147R;ENSP00000418416:G228R;ENSP00000419993:G146R;ENSP00000418837:G146R;ENSP00000420434:G147R|.	ENSP00000311133:G147R|ENSP00000406042:R153Q	G|R	-|-	1|2	0|0	PTPN7|PTPN7	200391313|200391313	0.005000|0.005000	0.15991|0.15991	0.011000|0.011000	0.14972|0.14972	0.665000|0.665000	0.39181|0.39181	1.125000|1.125000	0.31332|0.31332	1.180000|1.180000	0.42898|0.42898	0.655000|0.655000	0.94253|0.94253	GGA|CGG	.	.	none		0.542	PTPN7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_002832	
PIM3	415116	hgsc.bcm.edu	37	22	50354773	50354773	+	Splice_Site	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:50354773C>T	ENST00000360612.4	+	2	521	c.86C>T	c.(85-87)gCc>gTc	p.A29V		NM_001001852.3	NP_001001852.2	Q86V86	PIM3_HUMAN	Pim-3 proto-oncogene, serine/threonine kinase	29					apoptotic process (GO:0006915)|cell cycle (GO:0007049)|histone phosphorylation (GO:0016572)|negative regulation of apoptotic process (GO:0043066)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)						all_cancers(38;5.53e-07)|all_epithelial(38;3.84e-06)|all_lung(38;0.00208)|Breast(42;0.0104)|Lung NSC(38;0.0199)|Ovarian(80;0.0907)|Lung SC(80;0.236)		BRCA - Breast invasive adenocarcinoma(115;0.196)|LUAD - Lung adenocarcinoma(64;0.247)		CTCCCTGCAGCCAAGGCGGAC	0.786																																					p.A29V		Atlas-SNP	.											.	PIM3	15	.	0			c.C86T						PASS	.						5.0	5.0	5.0					22																	50354773		1996	4027	6023	SO:0001630	splice_region_variant	415116	exon2			CTGCAGCCAAGGC	BC052239	CCDS33678.1	22q13	2014-06-25	2014-06-25		ENSG00000198355	ENSG00000198355			19310	protein-coding gene	gene with protein product		610580	"""pim-3 oncogene"""			12477932	Standard	NM_001001852		Approved		uc003bjb.3	Q86V86	OTTHUMG00000150290	ENST00000360612.4:c.86-1C>T	22.37:g.50354773C>T		24.0	0.0	0		16.0	7.0	0.4375	NM_001001852	A5D8X8|A8K7J0|B1B0P0|Q68BM2	Missense_Mutation	SNP	ENST00000360612.4	37	CCDS33678.1	.	.	.	.	.	.	.	.	.	.	c	7.065	0.567090	0.13560	.	.	ENSG00000198355	ENST00000360612	T	0.56611	0.45	2.28	-0.308	0.12773	Protein kinase-like domain (1);	0.177323	0.37393	U	0.002107	T	0.19485	0.0468	N	0.02802	-0.49	0.36106	D	0.844454	B	0.06786	0.001	B	0.09377	0.004	T	0.03910	-1.0993	10	0.21540	T	0.41	.	3.0393	0.06133	0.0:0.3221:0.2312:0.4467	.	29	Q86V86	PIM3_HUMAN	V	29	ENSP00000353824:A29V	ENSP00000353824:A29V	A	+	2	0	PIM3	48740777	1.000000	0.71417	0.559000	0.28332	0.795000	0.44927	1.317000	0.33631	-0.287000	0.09064	0.291000	0.19559	GCC	.	.	none		0.786	PIM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317406.1	NM_001001852	Missense_Mutation
TPM1	7168	hgsc.bcm.edu	37	15	63363291	63363291	+	Missense_Mutation	SNP	A	A	G	rs144045691	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:63363291A>G	ENST00000357980.4	+	10	980	c.901A>G	c.(901-903)Aaa>Gaa	p.K301E	TPM1_ENST00000358278.3_Missense_Mutation_p.K259E|TPM1_ENST00000559397.1_Missense_Mutation_p.K259E|RP11-244F12.2_ENST00000558905.1_RNA|TPM1_ENST00000559556.1_Missense_Mutation_p.K259E|TPM1_ENST00000404484.4_Missense_Mutation_p.K223E|TPM1_ENST00000267996.7_Missense_Mutation_p.K259E			P09493	TPM1_HUMAN	tropomyosin 1 (alpha)	259					cardiac muscle contraction (GO:0060048)|cellular component movement (GO:0006928)|cellular response to reactive oxygen species (GO:0034614)|cytoskeleton organization (GO:0007010)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|negative regulation of cell migration (GO:0030336)|positive regulation of ATPase activity (GO:0032781)|positive regulation of cell adhesion (GO:0045785)|positive regulation of heart rate by epinephrine (GO:0003065)|positive regulation of stress fiber assembly (GO:0051496)|regulation of heart contraction (GO:0008016)|regulation of muscle contraction (GO:0006937)|ruffle organization (GO:0031529)|sarcomere organization (GO:0045214)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|wound healing (GO:0042060)	bleb (GO:0032059)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|muscle thin filament tropomyosin (GO:0005862)|ruffle membrane (GO:0032587)|sarcomere (GO:0030017)|stress fiber (GO:0001725)	actin binding (GO:0003779)|cytoskeletal protein binding (GO:0008092)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(1)|large_intestine(1)|lung(2)	4						CACCACAGAGAAAGTGGCTCA	0.413													A|||	3	0.000599042	0.0	0.0	5008	,	,		23023	0.0		0.003	False		,,,				2504	0.0				p.K259E		Atlas-SNP	.											.	TPM1	59	.	0			c.A775G						PASS	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	0,4406		0,0,2203	122.0	113.0	116.0		775,775,775,775	6.0	1.0	15	dbSNP_134	116	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense,missense	TPM1	NM_001018004.1,NM_001018006.1,NM_001018007.1,NM_001018020.1	56,56,56,56	0,4,6499	GG,GA,AA		0.0465,0.0,0.0308	benign,benign,benign,benign	259/285,259/285,259/285,259/285	63363291	4,13002	2203	4300	6503	SO:0001583	missense	7168	exon9			ACAGAGAAAGTGG	AB209041	CCDS10181.1, CCDS32262.1, CCDS32263.1, CCDS32264.1, CCDS45273.1, CCDS58368.1, CCDS58369.1	15q22.1	2014-09-17			ENSG00000140416	ENSG00000140416		"""Tropomyosins"""	12010	protein-coding gene	gene with protein product		191010	"""chromosome 15 open reading frame 13"", ""cardiomyopathy, hypertrophic 3"""	C15orf13, CMH3		10343096, 8205619	Standard	XM_005254637		Approved		uc002all.3	P09493	OTTHUMG00000132803	ENST00000357980.4:c.901A>G	15.37:g.63363291A>G	ENSP00000350667:p.Lys301Glu	110.0	0.0	0		128.0	66.0	0.515625	NM_001018007	B7Z5T7|D9YZV2|D9YZV3|D9YZV8|P09494|P10469|Q6DV89|Q6DV90|Q7Z6L8|Q86W64|Q96IK2|Q9UCI1|Q9UCI2|Q9UCY9|Q9Y427	Missense_Mutation	SNP	ENST00000357980.4	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	10.44	1.350695	0.24512	0.0	4.65E-4	ENSG00000140416	ENST00000267996;ENST00000358278;ENST00000357980	T;T;T	0.73897	-0.79;-0.79;-0.79	6.02	6.02	0.97574	.	0.000000	0.56097	D	0.000039	T	0.52869	0.1761	N	0.05467	-0.045	0.80722	D	1	B;B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.0;0.0	B;B;B;B;B;B	0.15052	0.012;0.006;0.002;0.001;0.001;0.001	T	0.53858	-0.8379	10	0.02654	T	1	-4.6565	15.7258	0.77756	1.0:0.0:0.0:0.0	.	223;301;259;259;259;259	B7Z722;Q6ZN40;D9YZV8;D9YZV5;Q9Y427;D9YZV3	.;.;.;.;.;.	E	259;259;301	ENSP00000267996:K259E;ENSP00000351022:K259E;ENSP00000350667:K301E	ENSP00000267996:K259E	K	+	1	0	TPM1	61150344	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.122000	0.94380	2.311000	0.77944	0.533000	0.62120	AAA	A|0.999;G|0.001	0.001	strong		0.413	TPM1-008	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000417087.2	NM_001018004	
INO80D	54891	hgsc.bcm.edu	37	2	206872126	206872126	+	Silent	SNP	C	C	T	rs116331438	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:206872126C>T	ENST00000403263.1	-	10	2204	c.1800G>A	c.(1798-1800)ccG>ccA	p.P600P	Vault_ENST00000516676.1_RNA	NM_017759.4	NP_060229.3	Q53TQ3	IN80D_HUMAN	INO80 complex subunit D	600					DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)		p.P600P(1)|p.P495P(1)		NS(1)|cervix(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|urinary_tract(2)	26						CAATGTCATCCGGCAACTCAT	0.498													C|||	2	0.000399361	0.0	0.0	5008	,	,		19913	0.0		0.001	False		,,,				2504	0.001				p.P600P		Atlas-SNP	.											INO80D_ENST00000403263,NS,carcinoma,0,2	INO80D	134	2	2	Substitution - coding silent(2)	kidney(2)	c.G1800A						PASS	.	C		3,4115		0,3,2056	130.0	130.0	130.0		1800	2.8	1.0	2	dbSNP_132	130	22,8406		0,22,4192	no	coding-synonymous	INO80D	NM_017759.4		0,25,6248	TT,TC,CC		0.261,0.0729,0.1993		600/1028	206872126	25,12521	2059	4214	6273	SO:0001819	synonymous_variant	54891	exon10			GTCATCCGGCAAC		CCDS46500.1	2q33.3	2011-07-06			ENSG00000114933	ENSG00000114933		"""INO80 complex subunits"""	25997	protein-coding gene	gene with protein product						16230350	Standard	NM_017759		Approved	FLJ20309	uc002vaz.4	Q53TQ3	OTTHUMG00000154649	ENST00000403263.1:c.1800G>A	2.37:g.206872126C>T		266.0	0.0	0		309.0	145.0	0.469256	NM_017759	B3KU68|B9EG77|Q6PJC6|Q6PJU1|Q6PKA1|Q9NXD5	Silent	SNP	ENST00000403263.1	37	CCDS46500.1																																																																																			C|0.999;T|0.001	0.001	strong		0.498	INO80D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336459.1	NM_017759	
PTPRT	11122	hgsc.bcm.edu	37	20	40743945	40743945	+	Missense_Mutation	SNP	A	A	G	rs41310016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:40743945A>G	ENST00000373187.1	-	22	2992	c.2993T>C	c.(2992-2994)gTg>gCg	p.V998A	PTPRT_ENST00000373184.1_Missense_Mutation_p.V1008A|PTPRT_ENST00000373193.3_Missense_Mutation_p.V1001A|PTPRT_ENST00000373201.1_Missense_Mutation_p.V988A|PTPRT_ENST00000356100.2_Missense_Mutation_p.V1007A|PTPRT_ENST00000373190.1_Missense_Mutation_p.V997A|PTPRT_ENST00000373198.4_Missense_Mutation_p.V1017A			O14522	PTPRT_HUMAN	protein tyrosine phosphatase, receptor type, T	998	Tyrosine-protein phosphatase 1. {ECO:0000255|PROSITE-ProRule:PRU00160}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-catenin binding (GO:0045294)|beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|protein tyrosine phosphatase activity (GO:0004725)			NS(2)|breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(12)|large_intestine(26)|liver(1)|lung(63)|ovary(8)|pancreas(2)|prostate(5)|skin(35)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	176		Myeloproliferative disorder(115;0.00452)|Lung NSC(126;0.0573)|all_lung(126;0.0783)				CCAGTATCGCACACATTTCAC	0.507													A|||	7	0.00139776	0.0	0.0	5008	,	,		21027	0.0		0.006	False		,,,				2504	0.001				p.V1017A		Atlas-SNP	.											.	PTPRT	372	.	0			c.T3050C						PASS	.	A	ALA/VAL,ALA/VAL	3,4193		0,3,2095	120.0	126.0	124.0		3050,2993	5.8	1.0	20	dbSNP_127	124	39,8425		0,39,4193	yes	missense,missense	PTPRT	NM_133170.3,NM_007050.5	64,64	0,42,6288	GG,GA,AA		0.4608,0.0715,0.3318	benign,benign	1017/1461,998/1442	40743945	42,12618	2098	4232	6330	SO:0001583	missense	11122	exon23			TATCGCACACATT	AF043644	CCDS42874.1, CCDS68127.1	20q12-q13	2013-02-11			ENSG00000196090	ENSG00000196090		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9682	protein-coding gene	gene with protein product		608712				9486824, 9602027	Standard	NM_133170		Approved	RPTPrho, KIAA0283	uc010ggj.3	O14522	OTTHUMG00000033040	ENST00000373187.1:c.2993T>C	20.37:g.40743945A>G	ENSP00000362283:p.Val998Ala	109.0	0.0	0		134.0	68.0	0.507463	NM_133170	A8E4R6|O43655|O75664|Q5W0X9|Q5W0Y1|Q9BR24|Q9BR28|Q9H0Y8|Q9NTL1|Q9NU72|Q9UBD2|Q9UJL7	Missense_Mutation	SNP	ENST00000373187.1	37	CCDS42874.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	A	14.50	2.553285	0.45487	7.15E-4	0.004608	ENSG00000196090	ENST00000373190;ENST00000373187;ENST00000373193;ENST00000356100;ENST00000373198;ENST00000373184;ENST00000373201	D;D;D;D;D;D;D	0.81739	-1.53;-1.53;-1.53;-1.53;-1.53;-1.53;-1.53	5.85	5.85	0.93711	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.000000	0.85682	D	0.000000	T	0.66277	0.2773	N	0.04636	-0.2	0.58432	D	0.999998	P;B	0.39782	0.688;0.349	P;P	0.50378	0.639;0.516	T	0.71699	-0.4514	10	0.23302	T	0.38	.	16.2303	0.82332	1.0:0.0:0.0:0.0	rs41310016	1020;998	O14522-1;O14522	.;PTPRT_HUMAN	A	997;998;1001;1007;1020;1008;988	ENSP00000362286:V997A;ENSP00000362283:V998A;ENSP00000362289:V1001A;ENSP00000348408:V1007A;ENSP00000362294:V1020A;ENSP00000362280:V1008A;ENSP00000362297:V988A	ENSP00000348408:V1007A	V	-	2	0	PTPRT	40177359	1.000000	0.71417	0.994000	0.49952	0.972000	0.66771	4.153000	0.58118	2.233000	0.73108	0.533000	0.62120	GTG	A|0.997;G|0.003	0.003	strong		0.507	PTPRT-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000080315.1		
DOK1	1796	hgsc.bcm.edu	37	2	74783100	74783100	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:74783100G>A	ENST00000233668.5	+	4	1203	c.534G>A	c.(532-534)gtG>gtA	p.V178V	DOK1_ENST00000409429.1_Silent_p.V39V|M1AP_ENST00000464686.1_5'Flank|LOXL3_ENST00000409549.1_5'Flank|LOXL3_ENST00000264094.3_5'Flank|DOK1_ENST00000480318.1_3'UTR|DOK1_ENST00000340004.6_Intron|LOXL3_ENST00000393937.2_5'Flank|LOXL3_ENST00000409986.1_5'Flank	NM_001381.3	NP_001372.1	Q99704	DOK1_HUMAN	docking protein 1, 62kDa (downstream of tyrosine kinase 1)	178	IRS-type PTB. {ECO:0000255|PROSITE- ProRule:PRU00389}.				cell surface receptor signaling pathway (GO:0007166)|insulin receptor signaling pathway (GO:0008286)|Ras protein signal transduction (GO:0007265)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor signaling protein activity (GO:0005057)			endometrium(3)|large_intestine(2)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGCTGAGGGTGGAGGCTGAAA	0.617																																					p.V178V	Esophageal Squamous(36;520 860 12502 33616 51270)	Atlas-SNP	.											.	DOK1	39	.	0			c.G534A						PASS	.						55.0	57.0	56.0					2																	74783100		2203	4300	6503	SO:0001819	synonymous_variant	1796	exon4			GAGGGTGGAGGCT	U70987	CCDS1954.1, CCDS56125.1	2p13	2008-05-21	2002-08-29		ENSG00000115325	ENSG00000115325			2990	protein-coding gene	gene with protein product		602919	"""docking protein 1, 62kD (downstream of tyrosine kinase 1)"""			9008160, 9790776, 15546884	Standard	NM_001381		Approved	p62dok	uc002sms.3	Q99704	OTTHUMG00000129956	ENST00000233668.5:c.534G>A	2.37:g.74783100G>A		127.0	0.0	0		127.0	22.0	0.173228	NM_001381	O43204|Q53TY2|Q9UHG6	Silent	SNP	ENST00000233668.5	37	CCDS1954.1																																																																																			.	.	none		0.617	DOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252218.3	NM_001381	
CRKL	1399	hgsc.bcm.edu	37	22	21272249	21272249	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21272249G>A	ENST00000354336.3	+	1	536	c.27G>A	c.(25-27)tcG>tcA	p.S9S		NM_005207.3	NP_005198.1	P46109	CRKL_HUMAN	v-crk avian sarcoma virus CT10 oncogene homolog-like	9					activation of MAPKK activity (GO:0000186)|anterior/posterior pattern specification (GO:0009952)|blood vessel development (GO:0001568)|heart development (GO:0007507)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|parathyroid gland development (GO:0060017)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|thymus development (GO:0048538)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)	poly(A) RNA binding (GO:0044822)|SH3/SH2 adaptor activity (GO:0005070)|signal transducer activity (GO:0004871)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)	14	all_cancers(11;1.16e-25)|all_epithelial(7;3.37e-24)|Lung NSC(8;7.25e-16)|all_lung(8;1.37e-14)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.176)			TCGACTCCTCGGACCGCTCCG	0.692																																					p.S9S	Pancreas(85;3 1441 23889 42519 42763)	Atlas-SNP	.											.	CRKL	28	.	0			c.G27A						PASS	.						27.0	27.0	27.0					22																	21272249		2202	4299	6501	SO:0001819	synonymous_variant	1399	exon1			CTCCTCGGACCGC		CCDS13785.1	22q11.21	2013-07-09	2013-07-09		ENSG00000099942	ENSG00000099942		"""SH2 domain containing"""	2363	protein-coding gene	gene with protein product		602007				8361759, 8798523	Standard	NM_005207		Approved		uc002ztf.2	P46109	OTTHUMG00000150807	ENST00000354336.3:c.27G>A	22.37:g.21272249G>A		44.0	0.0	0		42.0	22.0	0.52381	NM_005207	A8KA44|D3DX35	Silent	SNP	ENST00000354336.3	37	CCDS13785.1																																																																																			.	.	none		0.692	CRKL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320158.1	NM_005207	
GPR146	115330	hgsc.bcm.edu	37	7	1097430	1097430	+	Silent	SNP	G	G	A	rs61742514	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:1097430G>A	ENST00000397095.1	+	2	502	c.279G>A	c.(277-279)gcG>gcA	p.A93A	C7orf50_ENST00000397098.3_Intron|GPR146_ENST00000297468.3_Silent_p.A93A|C7orf50_ENST00000397100.2_Intron|C7orf50_ENST00000488073.1_Intron|RP11-449P15.1_ENST00000549241.1_RNA|C7orf50_ENST00000357429.6_Intron			Q96CH1	GP146_HUMAN	G protein-coupled receptor 146	93						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(1)|ovary(1)|skin(1)	8		Ovarian(82;0.0779)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0178)|OV - Ovarian serous cystadenocarcinoma(56;1.74e-15)		CCCGGTGGGCGCTGTGGAGTG	0.667													g|||	45	0.00898562	0.0	0.0029	5008	,	,		18213	0.0		0.0318	False		,,,				2504	0.0112				p.A93A		Atlas-SNP	.											.	GPR146	20	.	0			c.G279A						PASS	.		,,,	30,4376	34.3+/-65.2	0,30,2173	35.0	37.0	36.0		,,,279	-10.2	0.0	7	dbSNP_129	36	313,8285	110.2+/-170.6	9,295,3995	no	intron,intron,intron,coding-synonymous	C7orf50,GPR146	NM_001134395.1,NM_001134396.1,NM_032350.5,NM_138445.2	,,,	9,325,6168	AA,AG,GG		3.6404,0.6809,2.6376	,,,	,,,93/334	1097430	343,12661	2203	4299	6502	SO:0001819	synonymous_variant	115330	exon1			GTGGGCGCTGTGG	BC014241	CCDS5321.1	7p22.3	2012-08-21			ENSG00000164849	ENSG00000164849		"""GPCR / Class A : Orphans"""	21718	protein-coding gene	gene with protein product							Standard	NM_138445		Approved	PGR8	uc003sjy.1	Q96CH1	OTTHUMG00000023934	ENST00000397095.1:c.279G>A	7.37:g.1097430G>A		78.0	0.0	0		67.0	36.0	0.537313	NM_138445	Q86SP5	Silent	SNP	ENST00000397095.1	37	CCDS5321.1																																																																																			G|0.978;A|0.022	0.022	strong		0.667	GPR146-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206855.1	NM_138445	
SH3RF3	344558	hgsc.bcm.edu	37	2	110065649	110065649	+	Missense_Mutation	SNP	C	C	G	rs201796718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:110065649C>G	ENST00000309415.6	+	8	1852	c.1852C>G	c.(1852-1854)Cag>Gag	p.Q618E		NM_001099289.1	NP_001092759.1	Q8TEJ3	SH3R3_HUMAN	SH3 domain containing ring finger 3	618							zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(6)|liver(2)|lung(5)|ovary(2)	18						AGCCCAGGCTCAGGACCGGCC	0.647													C|||	4	0.000798722	0.0	0.0029	5008	,	,		16125	0.0		0.002	False		,,,				2504	0.0				p.Q618E		Atlas-SNP	.											.	SH3RF3	62	.	0			c.C1852G						PASS	.	C	GLU/GLN	7,4313		0,7,2153	18.0	24.0	22.0		1852	5.2	0.4	2		22	31,8479		0,31,4224	yes	missense	SH3RF3	NM_001099289.1	29	0,38,6377	GG,GC,CC		0.3643,0.162,0.2962	benign	618/883	110065649	38,12792	2160	4255	6415	SO:0001583	missense	344558	exon8			CAGGCTCAGGACC	AK074131	CCDS74557.1	2q13	2013-01-11	2008-05-14	2008-05-14	ENSG00000172985	ENSG00000172985		"""RING-type (C3HC4) zinc fingers"""	24699	protein-coding gene	gene with protein product			"""SH3 multiple domains 4"""	SH3MD4		16374509	Standard	XM_006712493		Approved	FLJ00204, POSH2	uc010ywt.1	Q8TEJ3	OTTHUMG00000153439	ENST00000309415.6:c.1852C>G	2.37:g.110065649C>G	ENSP00000309186:p.Gln618Glu	237.0	0.0	0		216.0	120.0	0.555556	NM_001099289	A0SDZ7|A8MPR1|Q8NDU1	Missense_Mutation	SNP	ENST00000309415.6	37		.	.	.	.	.	.	.	.	.	.	C	10.24	1.295937	0.23564	0.00162	0.003643	ENSG00000172985	ENST00000418513;ENST00000309415	T;T	0.58210	0.35;2.12	5.15	5.15	0.70609	.	0.409870	0.27294	N	0.020036	T	0.48732	0.1516	.	.	.	0.28576	N	0.910391	P	0.45428	0.858	P	0.46389	0.515	T	0.40384	-0.9566	9	0.13108	T	0.6	-22.3701	18.8174	0.92081	0.0:1.0:0.0:0.0	.	618	Q8TEJ3	SH3R3_HUMAN	E	618	ENSP00000414997:Q618E;ENSP00000309186:Q618E	ENSP00000309186:Q618E	Q	+	1	0	SH3RF3	109432081	0.996000	0.38824	0.421000	0.26609	0.136000	0.21042	3.743000	0.55104	2.680000	0.91292	0.655000	0.94253	CAG	C|0.999;G|0.001	0.001	weak		0.647	SH3RF3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001099289	
PPHLN1	51535	hgsc.bcm.edu	37	12	42840082	42840082	+	Missense_Mutation	SNP	A	A	C	rs149559306	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:42840082A>C	ENST00000395568.2	+	12	1424	c.1340A>C	c.(1339-1341)aAc>aCc	p.N447T	PPHLN1_ENST00000317560.9_Intron|PPHLN1_ENST00000256678.8_Missense_Mutation_p.N352T|PPHLN1_ENST00000432191.2_Missense_Mutation_p.N423T	NM_016488.6	NP_057572.5	Q8NEY8	PPHLN_HUMAN	periphilin 1	447					keratinization (GO:0031424)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(5)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	16	all_cancers(12;0.00049)|Breast(8;0.165)	Lung NSC(34;0.123)		GBM - Glioblastoma multiforme(48;0.0875)		gtacattgcaactcacgcaag	0.433													A|||	11	0.00219649	0.0	0.0043	5008	,	,		17538	0.0		0.008	False		,,,				2504	0.0				p.N447T		Atlas-SNP	.											.	PPHLN1	101	.	0			c.A1340C						PASS	.	A	THR/ASN,THR/ASN	9,4163		0,9,2077	32.0	34.0	33.0		1268,1340	0.2	0.1	12	dbSNP_134	33	69,8029		0,69,3980	yes	missense,missense	PPHLN1	NM_001143787.1,NM_016488.6	65,65	0,78,6057	CC,CA,AA		0.8521,0.2157,0.6357	possibly-damaging,possibly-damaging	423/435,447/459	42840082	78,12192	2086	4049	6135	SO:0001583	missense	51535	exon12			ATTGCAACTCACG	AY157850	CCDS8741.1, CCDS31777.1, CCDS41773.1, CCDS44860.1, CCDS44861.1, CCDS55817.1	12q12	2006-10-24				ENSG00000134283			19369	protein-coding gene	gene with protein product		608150					Standard	NM_016488		Approved		uc001rng.1	Q8NEY8		ENST00000395568.2:c.1340A>C	12.37:g.42840082A>C	ENSP00000378935:p.Asn447Thr	14.0	0.0	0		18.0	6.0	0.333333	NM_016488	E9PAX8|Q86YT2|Q8IXN3|Q8TB09|Q96NB9|Q9NXL4|Q9P0P6|Q9P0R9	Missense_Mutation	SNP	ENST00000395568.2	37	CCDS31777.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	A	7.021	0.558783	0.13436	0.002157	0.008521	ENSG00000134283	ENST00000395568;ENST00000256678;ENST00000432191	.	.	.	0.158	0.158	0.14942	.	.	.	.	.	T	0.23492	0.0568	N	0.22421	0.69	0.09310	N	1	P;P;P;P	0.42039	0.769;0.659;0.769;0.659	P;B;P;B	0.49332	0.607;0.403;0.607;0.403	T	0.18398	-1.0338	7	0.87932	D	0	.	.	.	.	.	352;398;423;447	F8W6A0;B7Z695;Q8NEY8-3;Q8NEY8	.;.;.;PPHLN_HUMAN	T	447;352;423	.	ENSP00000256678:N352T	N	+	2	0	PPHLN1	41126349	0.169000	0.23002	0.075000	0.20258	0.076000	0.17211	0.241000	0.18065	0.175000	0.19841	0.172000	0.16884	AAC	A|0.992;C|0.008	0.008	strong		0.433	PPHLN1-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000404047.1	NM_201515	
ACTR5	79913	hgsc.bcm.edu	37	20	37394988	37394988	+	Silent	SNP	G	G	A	rs151070334	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:37394988G>A	ENST00000243903.4	+	7	1438	c.1401G>A	c.(1399-1401)ggG>ggA	p.G467G		NM_024855.3	NP_079131.3	Q9H9F9	ARP5_HUMAN	ARP5 actin-related protein 5 homolog (yeast)	467					DNA recombination (GO:0006310)|double-strand break repair (GO:0006302)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|UV-damage excision repair (GO:0070914)	cytoplasm (GO:0005737)|Ino80 complex (GO:0031011)|nucleus (GO:0005634)				kidney(2)|large_intestine(2)|liver(1)|lung(5)|skin(2)	12		Myeloproliferative disorder(115;0.00878)				AACAGGCTGGGATTGCAGAGA	0.428													G|||	7	0.00139776	0.0	0.0029	5008	,	,		19343	0.0		0.005	False		,,,				2504	0.0				p.G467G		Atlas-SNP	.											.	ACTR5	44	.	0			c.G1401A						PASS	.	G		10,4396	16.8+/-37.8	0,10,2193	109.0	111.0	110.0		1401	-0.5	0.0	20	dbSNP_134	110	43,8557	28.5+/-78.6	0,43,4257	no	coding-synonymous	ACTR5	NM_024855.3		0,53,6450	AA,AG,GG		0.5,0.227,0.4075		467/608	37394988	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	79913	exon7			GGCTGGGATTGCA	AK022847	CCDS13308.1	20q12	2011-07-06	2001-11-28		ENSG00000101442	ENSG00000101442		"""INO80 complex subunits"""	14671	protein-coding gene	gene with protein product	"""INO80 complex subunit M"""		"""ARP5 (actin-related protein 5, yeast) homolog"""			16230350	Standard	NM_024855		Approved	FLJ12785, Arp5, INO80M	uc002xjd.2	Q9H9F9	OTTHUMG00000032456	ENST00000243903.4:c.1401G>A	20.37:g.37394988G>A		171.0	0.0	0		173.0	79.0	0.456647	NM_024855	Q86WF7|Q8IUY5|Q8N724|Q9BRN0|Q9BVB7	Silent	SNP	ENST00000243903.4	37	CCDS13308.1																																																																																			G|0.996;A|0.004	0.004	strong		0.428	ACTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079205.2	NM_024855	
FMO1	2326	hgsc.bcm.edu	37	1	171249933	171249933	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:171249933C>T	ENST00000354841.4	+	5	767	c.636C>T	c.(634-636)ctC>ctT	p.L212L	FMO1_ENST00000402921.2_Silent_p.L149L|FMO1_ENST00000367750.3_Silent_p.L212L|FMO1_ENST00000469112.1_3'UTR	NM_001282692.1	NP_001269621.1	Q01740	FMO1_HUMAN	flavin containing monooxygenase 1	212					NADPH oxidation (GO:0070995)|organic acid metabolic process (GO:0006082)|small molecule metabolic process (GO:0044281)|toxin metabolic process (GO:0009404)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	flavin adenine dinucleotide binding (GO:0050660)|monooxygenase activity (GO:0004497)|N,N-dimethylaniline monooxygenase activity (GO:0004499)|NADP binding (GO:0050661)			NS(1)|breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(2)|skin(2)	27	all_hematologic(923;0.0922)|Acute lymphoblastic leukemia(37;0.181)				Cevimeline(DB00185)|Cimetidine(DB00501)|Lorcaserin(DB04871)|Tamoxifen(DB00675)|Vandetanib(DB05294)|Voriconazole(DB00582)	AGGTGTTCCTCAGCACCACCG	0.498																																					p.L212L		Atlas-SNP	.											.	FMO1	79	.	0			c.C636T						PASS	.						82.0	70.0	74.0					1																	171249933		2203	4300	6503	SO:0001819	synonymous_variant	2326	exon6			GTTCCTCAGCACC	M64082	CCDS1294.1, CCDS60351.1	1q24.3	2011-08-04			ENSG00000010932	ENSG00000010932	1.14.13.8		3769	protein-coding gene	gene with protein product		136130					Standard	XM_005245037		Approved		uc001ghl.3	Q01740	OTTHUMG00000035502	ENST00000354841.4:c.636C>T	1.37:g.171249933C>T		136.0	0.0	0		160.0	24.0	0.15	NM_002021	A8K248|B7Z3P4|Q5QPT2|Q9UJC2	Silent	SNP	ENST00000354841.4	37	CCDS1294.1																																																																																			.	.	none		0.498	FMO1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086212.1	NM_002021	
ZNF653	115950	hgsc.bcm.edu	37	19	11594928	11594928	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11594928G>A	ENST00000293771.5	-	8	1735	c.1599C>T	c.(1597-1599)tgC>tgT	p.C533C	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	533					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(2)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	17						AGGACTTGCCGCAGGTCTCGC	0.647																																					p.C533C	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.C1599T						PASS	.						42.0	34.0	37.0					19																	11594928		2189	4255	6444	SO:0001819	synonymous_variant	115950	exon8			CTTGCCGCAGGTC	AY072704	CCDS12261.1	19p13.2	2013-01-08						"""Zinc fingers, C2H2-type"""	25196	protein-coding gene	gene with protein product		611371				12477932	Standard	NM_138783		Approved	Zip67	uc002mrz.2	Q96CK0		ENST00000293771.5:c.1599C>T	19.37:g.11594928G>A		99.0	0.0	0		100.0	16.0	0.16	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			.	.	none		0.647	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
VNN2	8875	hgsc.bcm.edu	37	6	133073844	133073844	+	Silent	SNP	C	C	T	rs33980664	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:133073844C>T	ENST00000326499.6	-	4	706	c.582G>A	c.(580-582)ccG>ccA	p.P194P	VNN2_ENST00000526192.1_5'Flank|VNN2_ENST00000525289.1_Intron|RP1-55C23.7_ENST00000430895.1_RNA|VNN2_ENST00000525270.1_Silent_p.P141P	NM_004665.2	NP_004656	O95498	VNN2_HUMAN	vanin 2	194	CN hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00054}.				cellular component movement (GO:0006928)|pantothenate metabolic process (GO:0015939)	anchored component of membrane (GO:0031225)|plasma membrane (GO:0005886)	pantetheine hydrolase activity (GO:0017159)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(7)|lung(14)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(155;0.00237)|GBM - Glioblastoma multiforme(226;0.0267)		TCACCAACTCCGGCTTTTCAG	0.408													C|||	85	0.0169728	0.0023	0.049	5008	,	,		19553	0.004		0.0278	False		,,,				2504	0.0164				p.P194P		Atlas-SNP	.											.	VNN2	83	.	0			c.G582A						PASS	.	C	,,	24,4382	29.0+/-57.7	0,24,2179	119.0	115.0	116.0		,582,423	-10.8	0.0	6	dbSNP_126	116	294,8306	108.0+/-168.7	6,282,4012	no	intron,coding-synonymous,coding-synonymous	VNN2	NM_001242350.1,NM_004665.2,NM_078488.1	,,	6,306,6191	TT,TC,CC		3.4186,0.5447,2.445	,,	,194/521,141/468	133073844	318,12688	2203	4300	6503	SO:0001819	synonymous_variant	8875	exon4			CAACTCCGGCTTT	AB026705	CCDS5161.1, CCDS5162.1, CCDS56451.1	6q23-q24	2013-02-13			ENSG00000112303	ENSG00000112303	3.5.1.92	"""Vanins"""	12706	protein-coding gene	gene with protein product	"""pantetheinase"""	603571				9790769, 11491533	Standard	NM_078488		Approved	FOAP-4, GPI-80	uc003qdt.3	O95498	OTTHUMG00000015588	ENST00000326499.6:c.582G>A	6.37:g.133073844C>T		89.0	0.0	0		81.0	37.0	0.45679	NM_004665	A0AUZ3|A6NDY1|A8K4E3|A8K7W0|B2DFZ0|B2DFZ1|B2DFZ2|B2DFZ3|F6XL73|Q2XUN1|Q9UJF3|Q9UMW2	Silent	SNP	ENST00000326499.6	37	CCDS5161.1																																																																																			C|0.976;T|0.024	0.024	strong		0.408	VNN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042264.2		
DHRS11	79154	hgsc.bcm.edu	37	17	34951481	34951481	+	Silent	SNP	C	C	T	rs73993036	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:34951481C>T	ENST00000251312.5	+	2	440	c.228C>T	c.(226-228)gaC>gaT	p.D76D	DHRS11_ENST00000590554.1_5'UTR|DHRS11_ENST00000394445.1_3'UTR	NM_024308.3	NP_077284.2	Q6UWP2	DHR11_HUMAN	dehydrogenase/reductase (SDR family) member 11	76						extracellular region (GO:0005576)	oxidoreductase activity (GO:0016491)			endometrium(1)|lung(4)	5						ATGAAGAGGACATCCTCTCCA	0.537													C|||	104	0.0207668	0.0734	0.0101	5008	,	,		20188	0.0		0.0	False		,,,				2504	0.0				p.D76D		Atlas-SNP	.											.	DHRS11	10	.	0			c.C228T						PASS	.	C		278,4128	154.4+/-187.8	10,258,1935	146.0	126.0	133.0		228	3.7	1.0	17	dbSNP_130	133	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	DHRS11	NM_024308.3		10,261,6232	TT,TC,CC		0.0349,6.3096,2.1605		76/261	34951481	281,12725	2203	4300	6503	SO:0001819	synonymous_variant	79154	exon2			AGAGGACATCCTC		CCDS11315.2	17q12	2014-05-06			ENSG00000108272	ENSG00000278535		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	28639	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 24C, member 1"""					12975309, 19027726	Standard	NM_024308		Approved	MGC4172, SDR24C1	uc002hnd.3	Q6UWP2	OTTHUMG00000188442	ENST00000251312.5:c.228C>T	17.37:g.34951481C>T		138.0	0.0	0		123.0	65.0	0.528455	NM_024308	B2RDZ3|Q9BUC7|Q9H674	Silent	SNP	ENST00000251312.5	37	CCDS11315.2																																																																																			C|0.977;T|0.023	0.023	strong		0.537	DHRS11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256681.2	NM_024308	
RHBDL1	9028	hgsc.bcm.edu	37	16	726301	726301	+	Missense_Mutation	SNP	G	G	A	rs139776304	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:726301G>A	ENST00000219551.2	+	1	227	c.200G>A	c.(199-201)cGc>cAc	p.R67H	LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Intron|LA16c-313D11.9_ENST00000571933.1_RNA			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	67					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				GGTCGGGCCCGCACTCAGGCC	0.667													G|||	3	0.000599042	0.0	0.0	5008	,	,		12129	0.0		0.003	False		,,,				2504	0.0				p.R67H		Atlas-SNP	.											.	RHBDL1	14	.	0			c.G200A						PASS	.	G	HIS/ARG	3,4303		0,3,2150	10.0	11.0	10.0		200	-5.9	0.0	16	dbSNP_134	10	33,8439		0,33,4203	yes	missense	RHBDL1	NM_003961.1	29	0,36,6353	AA,AG,GG		0.3895,0.0697,0.2817	benign	67/439	726301	36,12742	2153	4236	6389	SO:0001583	missense	9028	exon1			GGGCCCGCACTCA	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"""rhomboid (veinlet, Drosophila)-like"""	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.200G>A	16.37:g.726301G>A	ENSP00000219551:p.Arg67His	168.0	0.0	0		160.0	86.0	0.5375	NM_003961	A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	37	CCDS10418.1	.	.	.	.	.	.	.	.	.	.	G	10.83	1.462076	0.26248	6.97E-4	0.003895	ENSG00000103269	ENST00000219551	T	0.33216	1.42	3.75	-5.92	0.02261	.	3.088160	0.01236	N	0.008493	T	0.12944	0.0314	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.14952	-1.0454	10	0.37606	T	0.19	-10.5783	1.9892	0.03442	0.1944:0.2915:0.3706:0.1436	.	67	O75783	RHBL1_HUMAN	H	67	ENSP00000219551:R67H	ENSP00000219551:R67H	R	+	2	0	RHBDL1	666302	0.000000	0.05858	0.001000	0.08648	0.011000	0.07611	-0.123000	0.10611	-0.437000	0.07243	-0.672000	0.03802	CGC	G|0.999;A|0.001	0.001	strong		0.667	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961	
CDKN2AIPNL	91368	hgsc.bcm.edu	37	5	133747354	133747354	+	Silent	SNP	C	C	G	rs141449831	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:133747354C>G	ENST00000458198.2	-	1	235	c.192G>C	c.(190-192)ctG>ctC	p.L64L	CDKN2AIPNL_ENST00000395009.3_Silent_p.L64L	NM_080656.2	NP_542387.1	Q96HQ2	C2AIL_HUMAN	CDKN2A interacting protein N-terminal like	64										central_nervous_system(1)|kidney(2)|prostate(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGGGAGAGCAGCTGGTCCA	0.657											OREG0016789	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	76	0.0151757	0.0008	0.0144	5008	,	,		14144	0.0		0.0398	False		,,,				2504	0.0256				p.L64L		Atlas-SNP	.											.	CDKN2AIPNL	5	.	0			c.G192C						PASS	.	C		22,4380		0,22,2179	18.0	22.0	20.0		192	3.6	1.0	5	dbSNP_134	20	241,8349		3,235,4057	no	coding-synonymous	CDKN2AIPNL	NM_080656.2		3,257,6236	GG,GC,CC		2.8056,0.4998,2.0243		64/117	133747354	263,12729	2201	4295	6496	SO:0001819	synonymous_variant	91368	exon1			GGAGAGCAGCTGG	BC008293	CCDS4175.1	5q31.1	2008-02-05			ENSG00000237190	ENSG00000237190			30545	protein-coding gene	gene with protein product						12477932	Standard	NM_080656		Approved	MGC13017	uc011cxs.2	Q96HQ2	OTTHUMG00000129123	ENST00000458198.2:c.192G>C	5.37:g.133747354C>G		421.0	0.0	0	1605	476.0	161.0	0.338235	NM_080656	Q8WVE3	Silent	SNP	ENST00000458198.2	37	CCDS4175.1																																																																																			C|0.982;G|0.018	0.018	strong		0.657	CDKN2AIPNL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251171.2	NM_080656	
MRPL12	6182	hgsc.bcm.edu	37	17	79671298	79671298	+	Silent	SNP	C	C	T	rs148659191	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:79671298C>T	ENST00000333676.3	+	2	244	c.99C>T	c.(97-99)gcC>gcT	p.A33A	SLC25A10_ENST00000571730.1_Silent_p.A33A|RP13-1032I1.7_ENST00000575312.1_RNA|SLC25A10_ENST00000541223.1_Silent_p.A33A	NM_002949.3	NP_002940.2	P52815	RM12_HUMAN	mitochondrial ribosomal protein L12	33				A -> T (in Ref. 1; CAA56249). {ECO:0000305}.	positive regulation of transcription, DNA-templated (GO:0045893)|transcription from mitochondrial promoter (GO:0006390)|translation (GO:0006412)	mitochondrial large ribosomal subunit (GO:0005762)|mitochondrion (GO:0005739)	RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|lung(2)|urinary_tract(1)	4	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			GTGTCTGTGCCGTGCGACATA	0.607													C|||	10	0.00199681	0.0	0.0029	5008	,	,		17178	0.0		0.005	False		,,,				2504	0.0031				p.A33A		Atlas-SNP	.											.	MRPL12	12	.	0			c.C99T						PASS	.	C		4,4400	6.2+/-15.9	0,4,2198	55.0	51.0	52.0		99	-9.1	0.0	17	dbSNP_134	52	63,8537	38.8+/-94.9	0,63,4237	no	coding-synonymous	MRPL12	NM_002949.3		0,67,6435	TT,TC,CC		0.7326,0.0908,0.5152		33/199	79671298	67,12937	2202	4300	6502	SO:0001819	synonymous_variant	6182	exon2			CTGTGCCGTGCGA	X79865	CCDS11785.1	17q25	2012-11-14			ENSG00000262814	ENSG00000262814		"""Mitochondrial ribosomal proteins / large subunits"""	10378	protein-coding gene	gene with protein product		602375		RPML12		8626705, 9169145	Standard	NM_002949		Approved	MRPL7/L12, MRPL7		P52815	OTTHUMG00000178171	ENST00000333676.3:c.99C>T	17.37:g.79671298C>T		91.0	0.0	0		100.0	60.0	0.6	NM_002949	Q969U0|Q9HCA2|Q9UQJ3	Silent	SNP	ENST00000333676.3	37	CCDS11785.1																																																																																			C|0.996;T|0.004	0.004	strong		0.607	MRPL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440812.1	NM_002949	
IFI30	10437	hgsc.bcm.edu	37	19	18286008	18286008	+	Silent	SNP	G	G	C	rs200372	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18286008G>C	ENST00000407280.3	+	2	466	c.291G>C	c.(289-291)acG>acC	p.T97T	PIK3R2_ENST00000593731.1_3'UTR	NM_006332.3	NP_006323.2	P13284	GILT_HUMAN	interferon, gamma-inducible protein 30	97					antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of fibroblast proliferation (GO:0048147)|protein stabilization (GO:0050821)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	oxidoreductase activity, acting on a sulfur group of donors (GO:0016667)			endometrium(1)|kidney(2)|large_intestine(1)|stomach(1)	5						TCAATGTCACGCTGGTGCCCT	0.617													G|||	37	0.00738818	0.0265	0.0029	5008	,	,		19002	0.0		0.0	False		,,,				2504	0.0				p.T97T		Atlas-SNP	.											IFI30,NS,carcinoma,+1,1	IFI30	12	1	0			c.G291C						PASS	.	G		103,4063		2,99,1982	38.0	38.0	38.0		291	-9.9	0.0	19	dbSNP_79	38	5,8409		0,5,4202	no	coding-synonymous	IFI30	NM_006332.3		2,104,6184	CC,CG,GG		0.0594,2.4724,0.8585		97/251	18286008	108,12472	2083	4207	6290	SO:0001819	synonymous_variant	10437	exon2			TGTCACGCTGGTG	J03909	CCDS46015.1	19p13.1	2008-07-16				ENSG00000216490			5398	protein-coding gene	gene with protein product	"""gamma-interferon-inducible lysosomal thiol reductase"", ""interferon gamma-inducible protein 30 preproprotein"""	604664				3136170, 10639150	Standard	NM_006332		Approved	IFI-30, GILT, IP30, MGC32056	uc002nic.1	P13284		ENST00000407280.3:c.291G>C	19.37:g.18286008G>C		93.0	0.0	0		115.0	50.0	0.434783	NM_006332	Q76MF9|Q8NEI4|Q8WU77|Q9UL08	Silent	SNP	ENST00000407280.3	37	CCDS46015.1																																																																																			G|0.994;C|0.006	0.006	strong		0.617	IFI30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466396.3	NM_006332	
TBC1D2B	23102	hgsc.bcm.edu	37	15	78290635	78290635	+	Missense_Mutation	SNP	C	C	T	rs200408968		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:78290635C>T	ENST00000300584.3	-	13	2758	c.2759G>A	c.(2758-2760)cGa>cAa	p.R920Q	TBC1D2B_ENST00000409931.3_Missense_Mutation_p.D903N|TBC1D2B_ENST00000492078.1_5'UTR	NM_015079.5|NM_144572.1	NP_055894.6|NP_653173.1	Q9UPU7	TBD2B_HUMAN	TBC1 domain family, member 2B	920							Rab GTPase activator activity (GO:0005097)	p.D903N(3)|p.R920Q(1)		breast(3)|cervix(2)|endometrium(4)|kidney(1)|large_intestine(7)|lung(2)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	26						GTAGGCGCGTCGGTTCCGGAT	0.617																																					p.R920Q		Atlas-SNP	.											TBC1D2B_ENST00000300584,bladder,carcinoma,0,17	TBC1D2B	104	17	4	Substitution - Missense(4)	cervix(2)|upper_aerodigestive_tract(1)|ovary(1)	c.G2759A						scavenged	.						39.0	33.0	35.0					15																	78290635		2196	4291	6487	SO:0001583	missense	23102	exon13			GCGCGTCGGTTCC	AB028978	CCDS32301.2, CCDS45314.1	15q24.3-q25.1	2005-11-29			ENSG00000167202	ENSG00000167202			29183	protein-coding gene	gene with protein product						10470851	Standard	NM_015079		Approved	KIAA1055	uc002bcy.4	Q9UPU7	OTTHUMG00000152885	ENST00000300584.3:c.2759G>A	15.37:g.78290635C>T	ENSP00000300584:p.Arg920Gln	120.0	0.0	0		158.0	11.0	0.0696203	NM_144572	A7MD42|Q8N1F9|Q9NXM0	Missense_Mutation	SNP	ENST00000300584.3	37	CCDS45314.1	88|88	0.040293040293040296|0.040293040293040296	2|2	0.0040650406504065045|0.0040650406504065045	10|10	0.027624309392265192|0.027624309392265192	8|8	0.013986013986013986|0.013986013986013986	68|68	0.08970976253298153|0.08970976253298153	c|c	22.6|22.6	4.311579|4.311579	0.81358|0.81358	.|.	.|.	ENSG00000167202|ENSG00000167202	ENST00000418039;ENST00000409931|ENST00000300584	T|T	0.11712|0.09445	2.75|2.98	4.48|4.48	4.48|4.48	0.54585|0.54585	.|.	0.787190|.	0.11177|.	N|.	0.591392|.	T|T	0.00608|0.00608	0.0020|0.0020	.|.	.|.	.|.	0.26703|0.26703	N|N	0.971136|0.971136	B|D	0.30193|0.57257	0.272|0.979	B|P	0.18561|0.51833	0.022|0.681	T|T	0.06807|0.06807	-1.0806|-1.0806	9|8	0.02654|0.23891	T|T	1|0.37	.|.	16.1645|16.1645	0.81745|0.81745	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	903|920	Q9UPU7-2|Q9UPU7	.|TBD2B_HUMAN	N|Q	802;903|920	ENSP00000387165:D903N|ENSP00000300584:R920Q	ENSP00000387165:D903N|ENSP00000300584:R920Q	D|R	-|-	1|2	0|0	TBC1D2B|TBC1D2B	76077690|76077690	1.000000|1.000000	0.71417|0.71417	0.990000|0.990000	0.47175|0.47175	0.855000|0.855000	0.48748|0.48748	6.002000|6.002000	0.70693|0.70693	2.033000|2.033000	0.60031|0.60031	0.479000|0.479000	0.44913|0.44913	GAC|CGA	C|0.960;T|0.040	0.040	strong		0.617	TBC1D2B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000328369.3	NM_015079	
KCNN1	3780	hgsc.bcm.edu	37	19	18104350	18104350	+	Silent	SNP	G	G	A	rs376852061		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:18104350G>A	ENST00000222249.9	+	10	1678	c.1359G>A	c.(1357-1359)acG>acA	p.T453T		NM_002248.3	NP_002239.2	Q92952	KCNN1_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 1	453	Calmodulin-binding. {ECO:0000250}.				potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			endometrium(1)|kidney(1)|lung(5)|urinary_tract(1)	8					Miconazole(DB01110)|Procaine(DB00721)	AGGCTAACACGCTTACCGACC	0.662																																					p.T453T		Atlas-SNP	.											.	KCNN1	74	.	0			c.G1359A						PASS	.	G		0,4080		0,0,2040	46.0	51.0	49.0		1359	-9.0	0.1	19		49	1,8349		0,1,4174	no	coding-synonymous	KCNN1	NM_002248.3		0,1,6214	AA,AG,GG		0.012,0.0,0.0080		453/544	18104350	1,12429	2040	4175	6215	SO:0001819	synonymous_variant	3780	exon10			TAACACGCTTACC	U69883	CCDS67611.1	19p13.1	2012-07-05				ENSG00000105642		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6290	protein-coding gene	gene with protein product		602982				8781233, 10516439, 16382103	Standard	NM_002248		Approved	KCa2.1, hSK1	uc002nht.3	Q92952		ENST00000222249.9:c.1359G>A	19.37:g.18104350G>A		242.0	0.0	0		221.0	101.0	0.457014	NM_002248	Q5KR10|Q6DJU4	Silent	SNP	ENST00000222249.9	37																																																																																				.	.	weak		0.662	KCNN1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000471896.2	NM_002248	
TNKS	8658	hgsc.bcm.edu	37	8	9605648	9605648	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:9605648G>A	ENST00000310430.6	+	18	2784	c.2758G>A	c.(2758-2760)Gcc>Acc	p.A920T	TNKS_ENST00000518281.1_Missense_Mutation_p.A683T	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	920					mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|mRNA transport (GO:0051028)|negative regulation of DNA binding (GO:0043392)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of telomere maintenance via telomerase (GO:0032212)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein ADP-ribosylation (GO:0006471)|protein auto-ADP-ribosylation (GO:0070213)|protein localization to chromosome, telomeric region (GO:0070198)|protein poly-ADP-ribosylation (GO:0070212)|protein polyubiquitination (GO:0000209)|protein transport (GO:0015031)|regulation of telomere maintenance via telomerase (GO:0032210)|spindle assembly (GO:0051225)|Wnt signaling pathway (GO:0016055)	chromosome, centromeric region (GO:0000775)|chromosome, telomeric region (GO:0000781)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nuclear chromosome, telomeric region (GO:0000784)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	NAD+ ADP-ribosyltransferase activity (GO:0003950)|zinc ion binding (GO:0008270)	p.A920T(1)		NS(1)|endometrium(10)|kidney(6)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)	49				COAD - Colon adenocarcinoma(149;0.0467)		GCAGCTGTGCGCCCTCCTCCT	0.507																																					p.A920T		Atlas-SNP	.											TNKS_ENST00000310430,NS,carcinoma,0,3	TNKS	198	3	1	Substitution - Missense(1)	kidney(1)	c.G2758A						PASS	.						93.0	88.0	90.0					8																	9605648		2203	4300	6503	SO:0001583	missense	8658	exon18			CTGTGCGCCCTCC	AF082556	CCDS5974.1	8p23.1	2013-01-10			ENSG00000173273	ENSG00000173273		"""Poly (ADP-ribose) polymerases"", ""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	11941	protein-coding gene	gene with protein product		603303				9822378, 10198177	Standard	XM_006716263		Approved	TIN1, TINF1, TNKS1, PARP-5a, PARP5A, pART5	uc003wss.3	O95271	OTTHUMG00000090481	ENST00000310430.6:c.2758G>A	8.37:g.9605648G>A	ENSP00000311579:p.Ala920Thr	112.0	0.0	0		113.0	16.0	0.141593	NM_003747	O95272|Q4G0F2	Missense_Mutation	SNP	ENST00000310430.6	37	CCDS5974.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.288784	0.59976	.	.	ENSG00000173273	ENST00000310430;ENST00000518281	T;T	0.65549	-0.16;-0.16	5.88	5.88	0.94601	Ankyrin repeat-containing domain (3);	0.000000	0.85682	D	0.000000	T	0.53948	0.1828	N	0.21194	0.64	0.80722	D	1	B	0.27791	0.189	B	0.29716	0.106	T	0.49123	-0.8972	10	0.41790	T	0.15	.	20.2381	0.98363	0.0:0.0:1.0:0.0	.	920	O95271	TNKS1_HUMAN	T	920;683	ENSP00000311579:A920T;ENSP00000429890:A683T	ENSP00000311579:A920T	A	+	1	0	TNKS	9643058	1.000000	0.71417	1.000000	0.80357	0.041000	0.13682	9.623000	0.98386	2.779000	0.95612	0.650000	0.86243	GCC	.	.	none		0.507	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
REV3L	5980	hgsc.bcm.edu	37	6	111694124	111694124	+	Missense_Mutation	SNP	C	C	G	rs3218599	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:111694124C>G	ENST00000358835.3	-	14	5888	c.5434G>C	c.(5434-5436)Gac>Cac	p.D1812H	REV3L_ENST00000368805.1_Missense_Mutation_p.D1812H|REV3L_ENST00000435970.1_Missense_Mutation_p.D1734H|REV3L_ENST00000368802.3_Missense_Mutation_p.D1812H			O60673	DPOLZ_HUMAN	REV3-like, polymerase (DNA directed), zeta, catalytic subunit	1812			D -> H (in dbSNP:rs3218599). {ECO:0000269|Ref.5}.		DNA-dependent DNA replication (GO:0006261)|translesion synthesis (GO:0019985)	chromosome (GO:0005694)|nucleus (GO:0005634)|zeta DNA polymerase complex (GO:0016035)	4 iron, 4 sulfur cluster binding (GO:0051539)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			NS(2)|breast(1)|endometrium(6)|kidney(7)|large_intestine(30)|lung(25)|ovary(3)|prostate(5)|skin(8)|upper_aerodigestive_tract(1)	88		all_cancers(87;7.57e-06)|Acute lymphoblastic leukemia(125;2.46e-08)|all_hematologic(75;1.08e-06)|all_epithelial(87;0.00138)|Colorectal(196;0.021)		OV - Ovarian serous cystadenocarcinoma(136;0.0314)|Epithelial(106;0.057)|all cancers(137;0.0663)		TTGGCTGAGTCAAGAGACTGT	0.428								DNA polymerases (catalytic subunits)					C|||	46	0.0091853	0.0008	0.0245	5008	,	,		19961	0.0		0.0278	False		,,,				2504	0.0				p.D1812H		Atlas-SNP	.											.	REV3L	386	.	0			c.G5434C	GRCh37	CM065439	REV3L	M	rs3218599	PASS	.	C	HIS/ASP	23,4383	30.8+/-60.4	0,23,2180	149.0	136.0	140.0		5434	5.1	1.0	6	dbSNP_106	140	187,8413	84.2+/-146.7	6,175,4119	yes	missense	REV3L	NM_002912.3	81	6,198,6299	GG,GC,CC		2.1744,0.522,1.6146	benign	1812/3131	111694124	210,12796	2203	4300	6503	SO:0001583	missense	5980	exon13			CTGAGTCAAGAGA	AF058701	CCDS5091.2, CCDS69177.1	6q22	2012-05-18	2012-05-18		ENSG00000009413	ENSG00000009413		"""DNA polymerases"""	9968	protein-coding gene	gene with protein product	"""polymerase, DNA, zeta"""	602776	"""REV3 (yeast homolog)-like, catalytic subunit of DNA polymerase zeta"", ""REV3-like, catalytic subunit of DNA polymerase zeta (yeast)"""			9618506, 9925914	Standard	NM_001286431		Approved	POLZ, REV3	uc003puy.4	O60673	OTTHUMG00000016318	ENST00000358835.3:c.5434G>C	6.37:g.111694124C>G	ENSP00000351697:p.Asp1812His	79.0	0.0	0		87.0	54.0	0.62069	NM_002912	O43214|Q5TC33	Missense_Mutation	SNP	ENST00000358835.3	37	CCDS5091.2	31	0.014194139194139194	0	0.0	7	0.019337016574585635	0	0.0	24	0.0316622691292876	C	10.13	1.266893	0.23136	0.00522	0.021744	ENSG00000009413	ENST00000368802;ENST00000368805;ENST00000358835;ENST00000435970	T;T;T;T	0.01685	4.79;4.79;4.79;4.69	5.93	5.06	0.68205	Ribonuclease H-like (1);	0.336140	0.29383	N	0.012319	T	0.00967	0.0032	L	0.56769	1.78	0.35663	D	0.812702	B	0.23735	0.09	B	0.20184	0.028	T	0.50039	-0.8874	10	0.21540	T	0.41	-0.47	10.7403	0.46149	0.0:0.7996:0.1321:0.0684	rs3218599;rs17539658;rs17686344;rs52831072;rs3218599	1812	O60673	DPOLZ_HUMAN	H	1812;1812;1812;1734	ENSP00000357792:D1812H;ENSP00000357795:D1812H;ENSP00000351697:D1812H;ENSP00000402003:D1734H	ENSP00000351697:D1812H	D	-	1	0	REV3L	111800817	1.000000	0.71417	1.000000	0.80357	0.706000	0.40770	3.495000	0.53280	1.484000	0.48361	0.655000	0.94253	GAC	C|0.985;G|0.015	0.015	strong		0.428	REV3L-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043695.1	NM_002912	
PLCG2	5336	hgsc.bcm.edu	37	16	81942134	81942134	+	Silent	SNP	G	G	A	rs372347274		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:81942134G>A	ENST00000359376.3	+	17	1885	c.1671G>A	c.(1669-1671)aaG>aaA	p.K557K		NM_002661.3	NP_002652.2	P16885	PLCG2_HUMAN	phospholipase C, gamma 2 (phosphatidylinositol-specific)	557	SH2 1. {ECO:0000255|PROSITE- ProRule:PRU00191}.				B cell differentiation (GO:0030183)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium-mediated signaling (GO:0019722)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|inositol phosphate metabolic process (GO:0043647)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid catabolic process (GO:0009395)|platelet activation (GO:0030168)|release of sequestered calcium ion into cytosol (GO:0051209)|small molecule metabolic process (GO:0044281)|T cell receptor signaling pathway (GO:0050852)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(18)|lung(21)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	58						CGGGGGGCAAGGATGGCACCT	0.557																																					p.K557K		Atlas-SNP	.											.	PLCG2	276	.	0			c.G1671A						PASS	.	G		1,4091		0,1,2045	73.0	80.0	78.0		1671	2.9	1.0	16		78	13,8357		0,13,4172	no	coding-synonymous	PLCG2	NM_002661.3		0,14,6217	AA,AG,GG		0.1553,0.0244,0.1123		557/1266	81942134	14,12448	2046	4185	6231	SO:0001819	synonymous_variant	5336	exon17			GGGCAAGGATGGC		CCDS42204.1	16q24.1	2014-09-17				ENSG00000197943	3.1.4.11	"""SH2 domain containing"""	9066	protein-coding gene	gene with protein product		600220				7835906	Standard	XR_248240		Approved		uc002fgt.3	P16885		ENST00000359376.3:c.1671G>A	16.37:g.81942134G>A		143.0	0.0	0		136.0	76.0	0.558824	NM_002661	D3DUL3|Q3ZTS2|Q59H45|Q969T5	Silent	SNP	ENST00000359376.3	37	CCDS42204.1																																																																																			.	.	weak		0.557	PLCG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432429.1		
HERC2	8924	hgsc.bcm.edu	37	15	28419566	28419566	+	Silent	SNP	T	T	C	rs201182375	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:28419566T>C	ENST00000261609.7	-	65	10140	c.10032A>G	c.(10030-10032)agA>agG	p.R3344R		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CTAAAGGGTCTCTTGCAGTCT	0.488																																					p.R3344R		Atlas-SNP	.											.	HERC2	501	.	0			c.A10032G						PASS	.						30.0	28.0	29.0					15																	28419566		2203	4297	6500	SO:0001819	synonymous_variant	8924	exon65			AGGGTCTCTTGCA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.10032A>G	15.37:g.28419566T>C		368.0	0.0	0		310.0	22.0	0.0709677	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			T|0.988;C|0.013	0.013	strong		0.488	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
ABL1	25	hgsc.bcm.edu	37	9	133755528	133755528	+	Silent	SNP	A	A	G	rs2227985	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133755528A>G	ENST00000318560.5	+	9	1878	c.1497A>G	c.(1495-1497)gaA>gaG	p.E499E		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	499					actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	TGTTCCAGGAATCCAGTATCT	0.542			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								A|||	429	0.0856629	0.2057	0.0836	5008	,	,		18557	0.001		0.0696	False		,,,				2504	0.0286				p.E518E		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.A1554G						PASS	.	A	,	757,3649	309.7+/-291.2	52,653,1498	106.0	106.0	106.0		1497,1554	-2.8	1.0	9	dbSNP_98	106	641,7959	164.3+/-216.7	27,587,3686	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	79,1240,5184	GG,GA,AA		7.4535,17.1811,10.7489	,	499/1131,518/1150	133755528	1398,11608	2203	4300	6503	SO:0001819	synonymous_variant	25	exon9			CCAGGAATCCAGT	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.1497A>G	9.37:g.133755528A>G		100.0	0.0	0		89.0	39.0	0.438202	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.898;G|0.102	0.102	strong		0.542	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
PIK3C2B	5287	hgsc.bcm.edu	37	1	204433627	204433627	+	Silent	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:204433627C>T	ENST00000367187.3	-	5	1696	c.1140G>A	c.(1138-1140)gtG>gtA	p.V380V	PIK3C2B_ENST00000424712.2_Silent_p.V380V	NM_002646.3	NP_002637.3	O00750	P3C2B_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 beta	380	PI3K-RBD. {ECO:0000255|PROSITE- ProRule:PRU00879}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|protein kinase B signaling (GO:0043491)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|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)|lipid kinase activity (GO:0001727)|phosphatidylinositol binding (GO:0035091)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(4)|large_intestine(11)|lung(24)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	52	all_cancers(21;0.00347)|all_neural(3;0.0218)|Glioma(3;0.0382)|all_epithelial(62;0.171)|Breast(84;0.179)|Prostate(682;0.227)		GBM - Glioblastoma multiforme(2;2.69e-45)|all cancers(3;1.66e-30)|KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.143)|Epithelial(59;0.193)			ACAACACAGTCACCTTCAGGT	0.547																																					p.V380V		Atlas-SNP	.											.	PIK3C2B	142	.	0			c.G1140A						PASS	.						149.0	127.0	134.0					1																	204433627		2203	4300	6503	SO:0001819	synonymous_variant	5287	exon5			CACAGTCACCTTC	Y11312	CCDS1446.1	1q32	2012-07-13	2012-07-13		ENSG00000133056	ENSG00000133056	2.7.1.154		8972	protein-coding gene	gene with protein product		602838	"""phosphoinositide-3-kinase, class 2, beta polypeptide"""			9144573, 9830063	Standard	NM_002646		Approved	C2-PI3K, PI3K-C2beta	uc001haw.3	O00750	OTTHUMG00000036101	ENST00000367187.3:c.1140G>A	1.37:g.204433627C>T		148.0	0.0	0		197.0	21.0	0.106599	NM_002646	O95666|Q5SW99	Silent	SNP	ENST00000367187.3	37	CCDS1446.1																																																																																			.	.	none		0.547	PIK3C2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087965.1	NM_002646	
TTLL1	25809	hgsc.bcm.edu	37	22	43447891	43447891	+	Silent	SNP	C	C	T	rs9607998	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:43447891C>T	ENST00000266254.7	-	9	1134	c.894G>A	c.(892-894)ccG>ccA	p.P298P	TTLL1_ENST00000331018.7_Intron|AL022476.2_ENST00000443063.1_RNA	NM_012263.4	NP_036395.1	O95922	TTLL1_HUMAN	tubulin tyrosine ligase-like family, member 1	298	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				axoneme assembly (GO:0035082)|epithelial cilium movement (GO:0003351)|protein polyglutamylation (GO:0018095)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	tubulin-glutamic acid ligase activity (GO:0070740)			breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|skin(2)|stomach(1)	23		Ovarian(80;0.0694)		BRCA - Breast invasive adenocarcinoma(115;0.00461)		TGTTCATCACCGGCTGGAGAG	0.577													C|||	78	0.0155751	0.0068	0.0216	5008	,	,		21914	0.0		0.0497	False		,,,				2504	0.0041				p.P298P		Atlas-SNP	.											TTLL1,NS,carcinoma,-2,1	TTLL1	41	1	0			c.G894A						PASS	.	C		46,4360	48.2+/-83.0	3,40,2160	263.0	185.0	212.0		894	-3.7	1.0	22	dbSNP_119	212	419,8181	130.0+/-188.0	10,399,3891	no	coding-synonymous	TTLL1	NM_012263.4		13,439,6051	TT,TC,CC		4.8721,1.044,3.5753		298/424	43447891	465,12541	2203	4300	6503	SO:0001819	synonymous_variant	25809	exon9			CATCACCGGCTGG	AL096886	CCDS14043.1	22q13.1	2013-02-14			ENSG00000100271	ENSG00000100271		"""Tubulin tyrosine ligase-like family"""	1312	protein-coding gene	gene with protein product		608955	"""tubulin tyrosine ligase-like 1"""	C22orf7		10591208, 11054573	Standard	NM_012263		Approved		uc003bdi.3	O95922	OTTHUMG00000150699	ENST00000266254.7:c.894G>A	22.37:g.43447891C>T		101.0	0.0	0		123.0	82.0	0.666667	NM_012263	B2RDS7|Q9BR27|Q9NRS9|Q9UMU0	Silent	SNP	ENST00000266254.7	37	CCDS14043.1	52	0.023809523809523808	6	0.012195121951219513	10	0.027624309392265192	0	0.0	36	0.047493403693931395	C	9.531	1.110796	0.20714	0.01044	0.048721	ENSG00000100271	ENST00000495814	.	.	.	5.97	-3.65	0.04502	.	.	.	.	.	T	0.07503	0.0189	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29941	-0.9995	4	.	.	.	.	0.9386	0.01351	0.3008:0.1773:0.3147:0.2072	rs9607998;rs52827145;rs9607998	.	.	.	Q	224	.	.	R	-	2	0	TTLL1	41777835	0.001000	0.12720	0.987000	0.45799	0.774000	0.43823	-1.617000	0.02051	-0.307000	0.08804	-0.126000	0.14955	CGG	C|0.971;T|0.029	0.029	strong		0.577	TTLL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319659.1	NM_012263	
NOTCH1	4851	hgsc.bcm.edu	37	9	139407932	139407932	+	Silent	SNP	A	A	G	rs2229971|rs587778559	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:139407932A>G	ENST00000277541.6	-	14	2340	c.2265T>C	c.(2263-2265)aaT>aaC	p.N755N		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	755	EGF-like 20. {ECO:0000255|PROSITE- ProRule:PRU00076}.				anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATTCACACTCATTGTTGTTGA	0.602			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2643	0.527756	0.6997	0.4784	5008	,	,		19531	0.7768		0.335	False		,,,				2504	0.272				p.N755N		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	0			c.T2265C						PASS	.	G		2695,1683		864,967,358	109.0	123.0	118.0		2265	-2.3	0.0	9	dbSNP_98	118	2445,6109		358,1729,2190	no	coding-synonymous	NOTCH1	NM_017617.3		1222,2696,2548	GG,GA,AA		28.5831,38.4422,39.7464		755/2556	139407932	5140,7792	2189	4277	6466	SO:0001819	synonymous_variant	4851	exon14			ACACTCATTGTTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.2265T>C	9.37:g.139407932A>G		102.0	0.0	0		138.0	138.0	1	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			A|0.484;G|0.516	0.516	strong		0.602	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
MMEL1	79258	hgsc.bcm.edu	37	1	2535672	2535672	+	Missense_Mutation	SNP	G	G	A	rs143132254	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:2535672G>A	ENST00000378412.3	-	10	1026	c.865C>T	c.(865-867)Cgg>Tgg	p.R289W	MMEL1_ENST00000288709.6_Missense_Mutation_p.R280W|MMEL1_ENST00000502556.1_Intron			Q495T6	MMEL1_HUMAN	membrane metallo-endopeptidase-like 1	289						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(13)|ovary(2)|prostate(1)|urinary_tract(1)	27	all_cancers(77;0.000233)|all_epithelial(69;8.55e-05)|all_lung(157;0.0228)|Lung NSC(156;0.0402)|Ovarian(185;0.0634)	all_epithelial(116;1.03e-20)|all_lung(118;5.15e-09)|Lung NSC(185;9.02e-07)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;8.52e-23)|GBM - Glioblastoma multiforme(42;1.49e-08)|Colorectal(212;4.79e-05)|COAD - Colon adenocarcinoma(227;0.000213)|Kidney(185;0.000371)|BRCA - Breast invasive adenocarcinoma(365;0.00219)|KIRC - Kidney renal clear cell carcinoma(229;0.00571)|STAD - Stomach adenocarcinoma(132;0.00645)|Lung(427;0.131)		GCATCCTCCCGCAGCAACGTG	0.667																																					p.R289W		Atlas-SNP	.											.	MMEL1	64	.	0			c.C865T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	60.0	61.0	61.0		865	1.2	0.1	1	dbSNP_134	61	2,8598	2.2+/-6.3	0,2,4298	no	missense	MMEL1	NM_033467.3	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	289/780	2535672	2,13004	2203	4300	6503	SO:0001583	missense	79258	exon10			CCTCCCGCAGCAA	AF336981	CCDS30569.1, CCDS30569.2	1p36	2008-02-05			ENSG00000142606	ENSG00000142606			14668	protein-coding gene	gene with protein product			"""membrane metallo-endopeptidase-like 2"""	MMEL2			Standard	NM_033467		Approved	SEP, NL1, NL2, NEPII	uc001ajy.2	Q495T6	OTTHUMG00000000846	ENST00000378412.3:c.865C>T	1.37:g.2535672G>A	ENSP00000367668:p.Arg289Trp	223.0	0.0	0		193.0	99.0	0.512953	NM_033467	B9DI79|Q495T7|Q495T8|Q5SZS6|Q96PH9	Missense_Mutation	SNP	ENST00000378412.3	37	CCDS30569.2	.	.	.	.	.	.	.	.	.	.	G	14.08	2.429289	0.43122	0.0	2.33E-4	ENSG00000142606	ENST00000288709;ENST00000378412	T;T	0.73897	-0.79;-0.79	4.43	1.16	0.20824	Peptidase M13 (1);	0.058612	0.64402	D	0.000002	D	0.84511	0.5488	M	0.80847	2.515	0.41175	D	0.986192	D	0.89917	1.0	D	0.97110	1.0	D	0.84034	0.0361	10	0.59425	D	0.04	-37.0008	12.2645	0.54670	0.0:0.0:0.5439:0.4561	.	289	Q495T6	MMEL1_HUMAN	W	280;289	ENSP00000288709:R280W;ENSP00000367668:R289W	ENSP00000288709:R280W	R	-	1	2	MMEL1	2525532	0.933000	0.31639	0.080000	0.20451	0.522000	0.34438	1.210000	0.32370	0.006000	0.14734	0.485000	0.47835	CGG	G|1.000;A|0.000	0.000	strong		0.667	MMEL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002395.2	NM_033467	
C6	729	hgsc.bcm.edu	37	5	41160293	41160293	+	Silent	SNP	A	A	G	rs62361567	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:41160293A>G	ENST00000263413.3	-	11	1899	c.1635T>C	c.(1633-1635)agT>agC	p.S545S	C6_ENST00000337836.5_Silent_p.S545S|C6_ENST00000475349.1_5'Flank	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	545	EGF-like.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				CATAGGTGCCACTCTGACACA	0.468													A|||	56	0.0111821	0.0038	0.0187	5008	,	,		20151	0.0		0.0358	False		,,,				2504	0.002				p.S545S		Atlas-SNP	.											.	C6	197	.	0			c.T1635C						PASS	.	A	,	23,4383	31.7+/-61.6	0,23,2180	160.0	152.0	154.0		1635,1635	-12.1	0.0	5	dbSNP_129	154	299,8301	109.2+/-169.8	5,289,4006	no	coding-synonymous,coding-synonymous	C6	NM_000065.2,NM_001115131.1	,	5,312,6186	GG,GA,AA		3.4767,0.522,2.4758	,	545/935,545/935	41160293	322,12684	2203	4300	6503	SO:0001819	synonymous_variant	729	exon11			GGTGCCACTCTGA	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1635T>C	5.37:g.41160293A>G		162.0	0.0	0		204.0	78.0	0.382353	NM_001115131		Silent	SNP	ENST00000263413.3	37	CCDS3936.1																																																																																			A|0.978;G|0.022	0.022	strong		0.468	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
SH3BP5	9467	hgsc.bcm.edu	37	3	15298590	15298590	+	Missense_Mutation	SNP	C	C	T	rs149397155	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:15298590C>T	ENST00000383791.3	-	8	1140	c.920G>A	c.(919-921)tGt>tAt	p.C307Y	SH3BP5-AS1_ENST00000420195.1_RNA|SH3BP5-AS1_ENST00000413977.1_RNA|SH3BP5_ENST00000426925.1_Missense_Mutation_p.C150Y|SH3BP5_ENST00000408919.3_Missense_Mutation_p.C150Y|SH3BP5_ENST00000253688.5_Missense_Mutation_p.C150Y|SH3BP5-AS1_ENST00000436602.1_RNA	NM_004844.4	NP_004835.2	O60239	3BP5_HUMAN	SH3-domain binding protein 5 (BTK-associated)	307	Ser-rich.				intracellular signal transduction (GO:0035556)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	protein kinase inhibitor activity (GO:0004860)			NS(1)|endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	12						AAAGTTGCTACAGCTGTCATC	0.527													C|||	2	0.000399361	0.0	0.0	5008	,	,		21362	0.0		0.002	False		,,,				2504	0.0				p.C307Y		Atlas-SNP	.											.	SH3BP5	32	.	0			c.G920A						PASS	.	C	TYR/CYS,TYR/CYS	1,4405	2.1+/-5.4	0,1,2202	92.0	83.0	86.0		449,920	5.7	1.0	3	dbSNP_134	86	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	SH3BP5	NM_001018009.2,NM_004844.3	194,194	0,14,6489	TT,TC,CC		0.1512,0.0227,0.1076	possibly-damaging,possibly-damaging	150/299,307/456	15298590	14,12992	2203	4300	6503	SO:0001583	missense	9467	exon8			TTGCTACAGCTGT	AB005047	CCDS2625.2, CCDS43055.1	3p24.3	2008-07-10			ENSG00000131370	ENSG00000131370			10827	protein-coding gene	gene with protein product	"""SH3 binding protein"""	605612				9571151, 10339589	Standard	NM_004844		Approved	Sab	uc003bzp.2	O60239	OTTHUMG00000129859	ENST00000383791.3:c.920G>A	3.37:g.15298590C>T	ENSP00000373301:p.Cys307Tyr	91.0	0.0	0		107.0	54.0	0.504673	NM_004844	B3KQW6|Q5JWV9	Missense_Mutation	SNP	ENST00000383791.3	37	CCDS2625.2	.	.	.	.	.	.	.	.	.	.	C	20.7	4.041622	0.75732	2.27E-4	0.001512	ENSG00000131370	ENST00000383791;ENST00000426925;ENST00000253688;ENST00000408919	.	.	.	5.65	5.65	0.86999	.	0.307183	0.40554	N	0.001077	T	0.47544	0.1451	L	0.58101	1.795	0.53005	D	0.999962	P	0.48640	0.913	B	0.37601	0.254	T	0.53215	-0.8470	9	0.48119	T	0.1	-27.3345	14.2486	0.66004	0.1492:0.8508:0.0:0.0	.	307	O60239	3BP5_HUMAN	Y	307;150;150;150	.	ENSP00000253688:C150Y	C	-	2	0	SH3BP5	15273594	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	5.359000	0.66074	2.683000	0.91414	0.456000	0.33151	TGT	C|0.999;T|0.001	0.001	strong		0.527	SH3BP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340740.2	NM_004844	
QRFPR	84109	hgsc.bcm.edu	37	4	122301597	122301597	+	Missense_Mutation	SNP	A	A	C	rs34270076	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:122301597A>C	ENST00000394427.2	-	1	617	c.206T>G	c.(205-207)gTg>gGg	p.V69G	QRFPR_ENST00000334383.5_Missense_Mutation_p.V69G	NM_198179.2	NP_937822.2	Q96P65	QRFPR_HUMAN	pyroglutamylated RFamide peptide receptor	69					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|neuropeptide Y receptor activity (GO:0004983)			endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(2)|skin(3)|stomach(1)	28						GCGGGTCACCACGTAGAACAC	0.612													A|||	38	0.00758786	0.0008	0.0187	5008	,	,		15547	0.0		0.0239	False		,,,				2504	0.0				p.V69G		Atlas-SNP	.											.	QRFPR	65	.	0			c.T206G						PASS	.						92.0	74.0	80.0					4																	122301597		2203	4300	6503	SO:0001583	missense	84109	exon1			GTCACCACGTAGA	AF411117	CCDS3719.1	4q27	2012-08-10	2008-12-18	2008-12-18	ENSG00000186867	ENSG00000186867		"""GPCR / Class A : RF amide peptide receptors"""	15565	protein-coding gene	gene with protein product		606925	"""G protein-coupled receptor 103"""	GPR103		11574155	Standard	NM_198179		Approved		uc010inj.1	Q96P65	OTTHUMG00000133036	ENST00000394427.2:c.206T>G	4.37:g.122301597A>C	ENSP00000377948:p.Val69Gly	156.0	0.0	0		180.0	93.0	0.516667	NM_198179		Missense_Mutation	SNP	ENST00000394427.2	37	CCDS3719.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	A	24.8	4.575947	0.86645	.	.	ENSG00000186867	ENST00000394427;ENST00000334383	T;T	0.46451	0.87;0.87	5.18	5.18	0.71444	GPCR, rhodopsin-like superfamily (1);	0.053895	0.64402	D	0.000001	T	0.60143	0.2246	H	0.95679	3.705	0.80722	D	1	D;D;D	0.76494	0.986;0.999;0.999	P;D;D	0.74674	0.907;0.984;0.963	T	0.79184	-0.1908	10	0.87932	D	0	.	14.6829	0.69031	1.0:0.0:0.0:0.0	rs34270076	69;69;69	F2Z3L3;Q96P65;G4XH69	.;QRFPR_HUMAN;.	G	69	ENSP00000377948:V69G;ENSP00000335610:V69G	ENSP00000335610:V69G	V	-	2	0	QRFPR	122521047	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.979000	0.93455	1.930000	0.55929	0.383000	0.25322	GTG	A|0.987;C|0.013	0.013	strong		0.612	QRFPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256641.2	NM_198179	
TRMT1	55621	hgsc.bcm.edu	37	19	13220734	13220734	+	Silent	SNP	G	G	A	rs142446751		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:13220734G>A	ENST00000592062.1	-	10	1671	c.1101C>T	c.(1099-1101)agC>agT	p.S367S	TRMT1_ENST00000437766.1_Silent_p.S367S|TRMT1_ENST00000221504.8_Intron|TRMT1_ENST00000357720.4_Silent_p.S367S			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	367	Trm1 methyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00958}.						metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|tRNA (guanine-N2-)-methyltransferase activity (GO:0004809)|tRNA binding (GO:0000049)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(19;6.08e-22)	GBM - Glioblastoma multiforme(1328;0.0356)		CTCACCGGCCGCTGGGGACTC	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		16571	0.0		0.0	False		,,,				2504	0.001				p.S367S		Atlas-SNP	.											.	TRMT1	31	.	0			c.C1101T						PASS	.	G	,,	0,4406		0,0,2203	58.0	66.0	64.0		1101,,1101	-8.5	0.0	19	dbSNP_134	64	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,intron,coding-synonymous	TRMT1	NM_001136035.2,NM_001142554.1,NM_017722.3	,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,	367/660,,367/660	13220734	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	55621	exon9			CCGGCCGCTGGGG	AF196479	CCDS12293.1, CCDS45997.1	19p13.13	2012-06-12	2012-06-12						25980	protein-coding gene	gene with protein product		611669				10982862	Standard	NM_001142554		Approved	FLJ20244, TRM1	uc002mwl.3	Q9NXH9		ENST00000592062.1:c.1101C>T	19.37:g.13220734G>A		65.0	0.0	0		60.0	21.0	0.35	NM_001136035	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	CCDS12293.1																																																																																			G|1.000;A|0.000	0.000	weak		0.642	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722	
USP6NL	9712	hgsc.bcm.edu	37	10	11504687	11504687	+	Missense_Mutation	SNP	G	G	A	rs41291253	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:11504687G>A	ENST00000609104.1	-	15	2634	c.2240C>T	c.(2239-2241)aCg>aTg	p.T747M	USP6NL_ENST00000379237.2_Missense_Mutation_p.T770M|USP6NL_ENST00000277575.5_Missense_Mutation_p.T764M	NM_014688.2	NP_055503.1	Q92738	US6NL_HUMAN	USP6 N-terminal like	747					Golgi organization (GO:0007030)|plasma membrane to endosome transport (GO:0048227)|positive regulation of GTP catabolic process (GO:0033126)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of Golgi organization (GO:1903358)|retrograde transport, plasma membrane to Golgi (GO:0035526)|virion assembly (GO:0019068)	cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)			endometrium(3)|kidney(2)|large_intestine(6)|lung(18)|prostate(1)|skin(1)|urinary_tract(1)	32						TTGTCCCTGCGTCTCAGGTCT	0.468													G|||	6	0.00119808	0.0008	0.0014	5008	,	,		20911	0.0		0.004	False		,,,				2504	0.0				p.T764M		Atlas-SNP	.											.	USP6NL	57	.	0			c.C2291T						PASS	.	G	MET/THR,MET/THR	5,3907		0,5,1951	137.0	142.0	140.0		2291,2240	-1.2	0.0	10	dbSNP_127	140	35,8269		0,35,4117	yes	missense,missense	USP6NL	NM_001080491.2,NM_014688.2	81,81	0,40,6068	AA,AG,GG		0.4215,0.1278,0.3274	benign,benign	764/846,747/829	11504687	40,12176	1956	4152	6108	SO:0001583	missense	9712	exon14			CCCTGCGTCTCAG	BC010351	CCDS44357.1, CCDS53492.1	10p13	2013-07-09			ENSG00000148429	ENSG00000148429			16858	protein-coding gene	gene with protein product	"""related to the N terminus of tre"""	605405	"""USP6NL intronic transcript 1 (non-protein coding)"""	USP6NL-IT1		8700515, 8700527, 12399475	Standard	XR_247492		Approved	RNTRE, KIAA0019, TRE2NL, RN-tre	uc001iks.1	Q92738	OTTHUMG00000017672	ENST00000609104.1:c.2240C>T	10.37:g.11504687G>A	ENSP00000476462:p.Thr747Met	75.0	0.0	0		84.0	42.0	0.5	NM_001080491	A8KA79|Q15400|Q5VV10|Q7L0K9	Missense_Mutation	SNP	ENST00000609104.1	37	CCDS53492.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.027	-0.200380	0.06219	0.001278	0.004215	ENSG00000148429	ENST00000535316;ENST00000277575;ENST00000379237	T;T	0.03889	3.77;3.77	6.17	-1.16	0.09678	.	1.547390	0.03119	N	0.163470	T	0.02888	0.0086	N	0.02802	-0.49	0.09310	N	1	B;B	0.18968	0.019;0.032	B;B	0.11329	0.002;0.006	T	0.44360	-0.9333	10	0.31617	T	0.26	.	11.551	0.50721	0.5617:0.0:0.4383:0.0	rs41291253	747;764	Q92738;Q92738-2	US6NL_HUMAN;.	M	747;764;747	ENSP00000277575:T764M;ENSP00000368539:T747M	ENSP00000277575:T764M	T	-	2	0	USP6NL	11544693	0.000000	0.05858	0.003000	0.11579	0.002000	0.02628	-0.006000	0.12833	-0.047000	0.13423	-0.290000	0.09829	ACG	G|0.997;A|0.003	0.003	strong		0.468	USP6NL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000046764.3	NM_014688	
PINK1	65018	hgsc.bcm.edu	37	1	20971158	20971158	+	Missense_Mutation	SNP	A	A	T	rs139226733		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:20971158A>T	ENST00000321556.4	+	4	1046	c.952A>T	c.(952-954)Atg>Ttg	p.M318L	PINK1-AS_ENST00000451424.1_RNA|PINK1_ENST00000492302.1_3'UTR	NM_032409.2	NP_115785.1	Q9BXM7	PINK1_HUMAN	PTEN induced putative kinase 1	318	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.		M -> L. {ECO:0000269|PubMed:15596610}.		activation of protein kinase B activity (GO:0032148)|cell death (GO:0008219)|cellular response to hypoxia (GO:0071456)|cellular response to toxic substance (GO:0097237)|intracellular signal transduction (GO:0035556)|mitochondrion degradation (GO:0000422)|mitochondrion organization (GO:0007005)|negative regulation of gene expression (GO:0010629)|negative regulation of hydrogen peroxide-induced neuron intrinsic apoptotic signaling pathway (GO:1903384)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of oxidative stress-induced cell death (GO:1903202)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|peptidyl-serine autophosphorylation (GO:0036289)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of dopamine secretion (GO:0033603)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of mitochondrial electron transport, NADH to ubiquinone (GO:1902958)|positive regulation of peptidase activity (GO:0010952)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of synaptic transmission, dopaminergic (GO:0032226)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of mitochondrion degradation (GO:1903146)|regulation of protein complex assembly (GO:0043254)|regulation of protein ubiquitination (GO:0031396)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of synaptic vesicle transport (GO:1902803)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|TORC2 signaling (GO:0038203)|ubiquitin-dependent protein catabolic process (GO:0006511)	astrocyte projection (GO:0097449)|axon (GO:0030424)|cell body (GO:0044297)|chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of mitochondrial outer membrane (GO:0031307)|Lewy body (GO:0097413)|membrane (GO:0016020)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	ATP binding (GO:0005524)|C3HC4-type RING finger domain binding (GO:0055131)|calcium-dependent protein kinase activity (GO:0010857)|kinase activity (GO:0016301)|magnesium ion binding (GO:0000287)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)|protein kinase B binding (GO:0043422)|protein serine/threonine kinase activity (GO:0004674)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(4)|ovary(2)	14		all_lung(284;2.72e-05)|Lung NSC(340;2.94e-05)|Colorectal(325;3.46e-05)|Renal(390;0.000147)|Breast(348;0.00179)|Ovarian(437;0.00327)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.21e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000146)|Kidney(64;0.000182)|GBM - Glioblastoma multiforme(114;0.000497)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00308)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		GTTCCTCGTTATGAAGAAGTA	0.632													A|||	1	0.000199681	0.0	0.0	5008	,	,		18148	0.0		0.001	False		,,,				2504	0.0				p.M318L	Esophageal Squamous(145;853 1803 8146 34412 35011)	Atlas-SNP	.											.	PINK1	37	.	0			c.A952T	GRCh37	CM053378	PINK1	M	rs139226733	PASS	.	A	LEU/MET	2,4404	4.2+/-10.8	0,2,2201	47.0	44.0	45.0		952	6.1	0.9	1	dbSNP_134	45	7,8593	4.3+/-15.6	0,7,4293	yes	missense	PINK1	NM_032409.2	15	0,9,6494	TT,TA,AA		0.0814,0.0454,0.0692	probably-damaging	318/582	20971158	9,12997	2203	4300	6503	SO:0001583	missense	65018	exon4			CTCGTTATGAAGA	AB053323	CCDS211.1	1p36.12	2011-07-21			ENSG00000158828	ENSG00000158828		"""Parkinson disease"""	14581	protein-coding gene	gene with protein product		608309	"""Parkinson disease (autosomal recessive) 6"""	PARK6		11494141, 15349860	Standard	NM_032409		Approved		uc001bdm.3	Q9BXM7	OTTHUMG00000002841	ENST00000321556.4:c.952A>T	1.37:g.20971158A>T	ENSP00000364204:p.Met318Leu	56.0	0.0	0		51.0	24.0	0.470588	NM_032409	Q8N6T9|Q8NBU3|Q96DE4	Missense_Mutation	SNP	ENST00000321556.4	37	CCDS211.1	.	.	.	.	.	.	.	.	.	.	A	19.96	3.923054	0.73213	4.54E-4	8.14E-4	ENSG00000158828	ENST00000321556	T	0.75589	-0.95	6.07	6.07	0.98685	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.72120	0.3421	L	0.60845	1.875	0.80722	D	1	B	0.23650	0.089	B	0.26517	0.07	T	0.70749	-0.4787	10	0.72032	D	0.01	-15.4264	13.0206	0.58784	1.0:0.0:0.0:0.0	.	318	Q9BXM7	PINK1_HUMAN	L	318	ENSP00000364204:M318L	ENSP00000364204:M318L	M	+	1	0	PINK1	20843745	1.000000	0.71417	0.946000	0.38457	0.934000	0.57294	7.964000	0.87933	2.326000	0.78906	0.533000	0.62120	ATG	A|0.999;T|0.001	0.001	strong		0.632	PINK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007954.1	NM_032409	
NRG1	3084	hgsc.bcm.edu	37	8	32611970	32611970	+	Missense_Mutation	SNP	G	G	T	rs74942016	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr8:32611970G>T	ENST00000405005.3	+	8	781	c.781G>T	c.(781-783)Gtg>Ttg	p.V261L	NRG1_ENST00000287845.5_Missense_Mutation_p.V232L|NRG1_ENST00000539990.1_Missense_Mutation_p.V104L|NRG1_ENST00000356819.4_Missense_Mutation_p.V266L|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000519301.1_Missense_Mutation_p.V211L|NRG1_ENST00000338921.4_Missense_Mutation_p.V269L|NRG1_ENST00000521670.1_Missense_Mutation_p.V261L|NRG1_ENST00000523079.1_Missense_Mutation_p.V258L|NRG1_ENST00000287842.3_Missense_Mutation_p.V258L			Q02297	NRG1_HUMAN	neuregulin 1	261				V -> L (in Ref. 10; ABQ53540). {ECO:0000305}.	activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CATCATGTGTGTGGTGGCCTA	0.527													G|||	72	0.014377	0.0008	0.0259	5008	,	,		17487	0.0		0.0467	False		,,,				2504	0.0061				p.V266L		Atlas-SNP	.											.	NRG1	260	.	0			c.G796T	GRCh37	CM066934	NRG1	M	rs74942016	PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	47,4359	48.9+/-83.8	0,47,2156	226.0	165.0	186.0		682,319,733,631,772,772,796,772,781,781	5.6	1.0	8	dbSNP_131	186	405,8195	127.5+/-185.8	12,381,3907	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159996.1,NM_001159999.1,NM_001160001.1,NM_001160004.1,NM_001160008.1,NM_013956.3,NM_013957.3,NM_013960.3,NM_013964.3	32,32,32,32,32,32,32,32,32,32	12,428,6063	TT,TG,GG		4.7093,1.0667,3.4753	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	228/608,107/309,245/625,211/591,258/460,258/421,266/646,258/638,261/463,261/641	32611970	452,12554	2203	4300	6503	SO:0001583	missense	3084	exon9			ATGTGTGTGGTGG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.781G>T	8.37:g.32611970G>T	ENSP00000384620:p.Val261Leu	172.0	0.0	0		188.0	69.0	0.367021	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	35	5.558867	0.96514	0.010667	0.047093	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000522402;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;2.63;0.14	5.62	5.62	0.85841	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;P;D;P;D;D	0.71674	0.979;0.998;0.995;0.979;0.983;0.995;0.599;0.962;0.946;0.979;0.994	D;D;D;P;D;D;B;P;P;P;D	0.85130	0.986;0.997;0.972;0.879;0.926;0.972;0.283;0.879;0.893;0.879;0.914	T	0.67722	-0.5597	10	0.72032	D	0.01	-36.9375	19.6569	0.95845	0.0:0.0:1.0:0.0	.	104;107;258;232;266;257;269;258;261;266;261	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	L	228;211;334;258;269;266;261;232;258;261;261;107;104;104	ENSP00000430053:V228L;ENSP00000429582:V211L;ENSP00000429067:V334L;ENSP00000430120:V258L;ENSP00000343395:V269L;ENSP00000349275:V266L;ENSP00000287840:V261L;ENSP00000287845:V232L;ENSP00000287842:V258L;ENSP00000384620:V261L;ENSP00000428828:V261L;ENSP00000430862:V107L;ENSP00000428411:V104L;ENSP00000439276:V104L	ENSP00000287840:V261L	V	+	1	0	NRG1	32731512	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.639000	0.89480	0.650000	0.86243	GTG	G|0.968;T|0.032	0.032	strong		0.527	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
SSH1	54434	hgsc.bcm.edu	37	12	109194652	109194652	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:109194652C>G	ENST00000326495.5	-	12	1145	c.1052G>C	c.(1051-1053)gGc>gCc	p.G351A	SSH1_ENST00000326470.5_Missense_Mutation_p.G362A|SSH1_ENST00000551165.1_Missense_Mutation_p.G351A|SSH1_ENST00000360239.3_Missense_Mutation_p.G39A	NM_018984.3	NP_061857.3	Q8WYL5	SSH1_HUMAN	slingshot protein phosphatase 1	351	Tyrosine-protein phosphatase.				actin cytoskeleton organization (GO:0030036)|cell morphogenesis (GO:0000902)|cellular response to ATP (GO:0071318)|protein dephosphorylation (GO:0006470)|regulation of actin polymerization or depolymerization (GO:0008064)|regulation of axonogenesis (GO:0050770)|regulation of cellular protein metabolic process (GO:0032268)|regulation of lamellipodium assembly (GO:0010591)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	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)			breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(8)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TGCAAATAAGCCAGGAAAAAA	0.348																																					p.G362A		Atlas-SNP	.											SSH1_ENST00000326470,NS,carcinoma,0,2	SSH1	144	2	0			c.G1085C						PASS	.						93.0	101.0	98.0					12																	109194652		2203	4300	6503	SO:0001583	missense	54434	exon11			AATAAGCCAGGAA	BC062341	CCDS9121.1, CCDS53825.1, CCDS55882.1	12q24.12	2013-03-05	2013-03-05			ENSG00000084112		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Slingshots"""	30579	protein-coding gene	gene with protein product		606778	"""slingshot homolog 1 (Drosophila)"""			10718198, 11832213	Standard	NM_018984		Approved	KIAA1298	uc001tnm.3	Q8WYL5	OTTHUMG00000169371	ENST00000326495.5:c.1052G>C	12.37:g.109194652C>G	ENSP00000315713:p.Gly351Ala	97.0	0.0	0		130.0	74.0	0.569231	NM_001161331	Q6P6C0|Q8N9A7|Q8WYL3|Q8WYL4|Q9P2P8	Missense_Mutation	SNP	ENST00000326495.5	37	CCDS9121.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.811838	0.90707	.	.	ENSG00000084112	ENST00000360239;ENST00000326495;ENST00000551165;ENST00000326470	D;T;T;T	0.85556	-2.0;0.09;0.09;0.09	5.72	5.72	0.89469	Dual specificity phosphatase, catalytic domain (1);Dual specificity phosphatase, subgroup, catalytic domain (2);	0.000000	0.85682	D	0.000000	D	0.90800	0.7111	L	0.50919	1.6	0.80722	D	1	B;P;B;D	0.76494	0.068;0.562;0.084;0.999	B;B;B;D	0.80764	0.077;0.239;0.125;0.994	D	0.89849	0.4008	10	0.51188	T	0.08	-49.7361	20.2626	0.98452	0.0:1.0:0.0:0.0	.	362;351;351;39	Q8WYL5-5;Q8WYL5-2;Q8WYL5;Q8WYL5-4	.;.;SSH1_HUMAN;.	A	39;351;351;362	ENSP00000353374:G39A;ENSP00000315713:G351A;ENSP00000448824:G351A;ENSP00000326107:G362A	ENSP00000326107:G362A	G	-	2	0	SSH1	107718781	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	7.818000	0.86416	2.873000	0.98535	0.563000	0.77884	GGC	.	.	none		0.348	SSH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403724.1	NM_018984	
PCDHGB6	56100	hgsc.bcm.edu	37	5	140788107	140788107	+	Missense_Mutation	SNP	C	C	T	rs201370009		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:140788107C>T	ENST00000520790.1	+	1	338	c.338C>T	c.(337-339)cCt>cTt	p.P113L	PCDHGB3_ENST00000576222.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGB4_ENST00000519479.1_Intron	NM_018926.2|NM_032100.1	NP_061749.1|NP_115271.1	Q9Y5F9	PCDGI_HUMAN	protocadherin gamma subfamily B, 6	113	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|endometrium(9)|kidney(1)|large_intestine(10)|lung(16)|ovary(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(2)	48			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GTGGAAAATCCTTTAAATATT	0.383													.|||	1	0.000199681	0.0	0.0	5008	,	,		17773	0.0		0.001	False		,,,				2504	0.0				p.P113L		Atlas-SNP	.											PCDHGB6,right_lower_lobe,carcinoma,0,1	PCDHGB6	120	1	0			c.C338T						PASS	.	C	,,,,,,,,,,,,,LEU/PRO,,LEU/PRO	1,3661		0,1,1830	156.0	162.0	160.0		,,,,,,,,,,,,,338,,338	5.4	1.0	5		160	14,8126		0,14,4056	no	intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,intron,missense	PCDHGB4,PCDHGA8,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_003736.2,NM_018912.2,NM_018915.2,NM_018916.3,NM_018917.2,NM_018918.2,NM_018919.2,NM_018920.2,NM_018921.2,NM_018922.2,NM_018923.2,NM_018924.2,NM_018925.2,NM_018926.2,NM_032088.1,NM_032100.1	,,,,,,,,,,,,,98,,98	0,15,5886	TT,TC,CC		0.172,0.0273,0.1271	,,,,,,,,,,,,,,,	,,,,,,,,,,,,,113/931,,113/821	140788107	15,11787	1831	4070	5901	SO:0001583	missense	56100	exon1			AAAATCCTTTAAA	AF152522	CCDS54929.1, CCDS75342.1	5q31	2010-01-26				ENSG00000253305		"""Cadherins / Protocadherins : Clustered"""	8713	other	protocadherin		606303				10380929	Standard	NM_018926		Approved	PCDH-GAMMA-B6		Q9Y5F9		ENST00000520790.1:c.338C>T	5.37:g.140788107C>T	ENSP00000428603:p.Pro113Leu	186.0	1.0	0.00537634		206.0	115.0	0.558252	NM_032100	Q9Y5C5	Missense_Mutation	SNP	ENST00000520790.1	37	CCDS54929.1	.	.	.	.	.	.	.	.	.	.	c	18.01	3.528330	0.64860	2.73E-4	0.00172	ENSG00000253305	ENST00000520790	T	0.37235	1.21	5.38	5.38	0.77491	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.72391	0.3454	H	0.95574	3.69	0.58432	D	0.999998	D;D	0.71674	0.998;0.998	D;D	0.71414	0.973;0.969	T	0.81824	-0.0755	9	0.87932	D	0	.	19.1331	0.93415	0.0:1.0:0.0:0.0	.	113;113	Q9Y5F9;Q9Y5F9-2	PCDGI_HUMAN;.	L	113	ENSP00000428603:P113L	ENSP00000428603:P113L	P	+	2	0	PCDHGB6	140768291	1.000000	0.71417	0.995000	0.50966	0.378000	0.30076	7.779000	0.85648	2.517000	0.84864	0.467000	0.42956	CCT	C|0.994;T|0.006	0.006	strong		0.383	PCDHGB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374746.1	NM_018926	
CCNJL	79616	hgsc.bcm.edu	37	5	159682580	159682580	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:159682580C>T	ENST00000393977.3	-	6	1148	c.863G>A	c.(862-864)aGc>aAc	p.S288N	CCNJL_ENST00000541762.1_Missense_Mutation_p.S239N|CCNJL_ENST00000257536.7_Missense_Mutation_p.S240N|CCNJL_ENST00000519673.1_Missense_Mutation_p.S240N|CCNJL_ENST00000377503.2_5'UTR	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	288						nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			AATACACGTGCTGAGGTGCTC	0.552																																					p.S288N		Atlas-SNP	.											.	CCNJL	36	.	0			c.G863A						PASS	.						174.0	175.0	174.0					5																	159682580		1905	4140	6045	SO:0001583	missense	79616	exon6			CACGTGCTGAGGT	BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.863G>A	5.37:g.159682580C>T	ENSP00000377547:p.Ser288Asn	159.0	0.0	0		199.0	67.0	0.336683	NM_024565	Q6ZN43|Q9H7W8	Missense_Mutation	SNP	ENST00000393977.3	37	CCDS4350.2	.	.	.	.	.	.	.	.	.	.	C	8.336	0.827560	0.16749	.	.	ENSG00000135083	ENST00000393977;ENST00000257536;ENST00000519673;ENST00000541762	T;T;T;T	0.21543	2.0;2.0;2.0;2.0	5.61	3.79	0.43588	Cyclin, C-terminal (1);Cyclin-like (3);	0.173358	0.51477	D	0.000099	T	0.09818	0.0241	N	0.20685	0.6	0.31077	N	0.712353	B;B;P	0.34724	0.014;0.099;0.465	B;B;B	0.30401	0.036;0.036;0.115	T	0.10965	-1.0607	10	0.19590	T	0.45	-12.2999	4.6847	0.12752	0.1373:0.4338:0.3483:0.0806	.	240;240;288	E7EN43;B4DZA8;Q8IV13	.;.;CCNJL_HUMAN	N	288;240;240;239	ENSP00000377547:S288N;ENSP00000257536:S240N;ENSP00000427960:S240N;ENSP00000446367:S239N	ENSP00000257536:S240N	S	-	2	0	CCNJL	159615158	1.000000	0.71417	0.976000	0.42696	0.446000	0.32137	2.239000	0.43079	1.334000	0.45468	0.655000	0.94253	AGC	.	.	none		0.552	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565	
CLEC16A	23274	hgsc.bcm.edu	37	16	11097155	11097155	+	Silent	SNP	G	G	A	rs45464291	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:11097155G>A	ENST00000409790.1	+	11	1526	c.1296G>A	c.(1294-1296)gaG>gaA	p.E432E	CLEC16A_ENST00000409552.3_Intron	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A											breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CGAGTGGGGAGAGTGAAGGTG	0.617													G|||	4	0.000798722	0.0	0.0	5008	,	,		17429	0.0		0.004	False		,,,				2504	0.0				p.E432E		Atlas-SNP	.											.	CLEC16A	101	.	0			c.G1296A						PASS	.	G		5,4135		0,5,2065	76.0	87.0	83.0		1296	3.6	1.0	16	dbSNP_127	83	25,8389		0,25,4182	no	coding-synonymous	CLEC16A	NM_015226.2		0,30,6247	AA,AG,GG		0.2971,0.1208,0.239		432/1054	11097155	30,12524	2070	4207	6277	SO:0001819	synonymous_variant	23274	exon10			TGGGGAGAGTGAA	AB002348	CCDS45409.1, CCDS58423.1	16p13.13	2010-04-27	2007-07-17	2007-07-17	ENSG00000038532	ENSG00000038532		"""C-type lectin domain containing"""	29013	protein-coding gene	gene with protein product		611303	"""KIAA0350"""	KIAA0350		9205841, 17632545	Standard	NM_015226		Approved	Gop-1	uc002dao.3	Q2KHT3	OTTHUMG00000152915	ENST00000409790.1:c.1296G>A	16.37:g.11097155G>A		154.0	0.0	0		136.0	57.0	0.419118	NM_015226		Silent	SNP	ENST00000409790.1	37	CCDS45409.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
IL1A	3552	hgsc.bcm.edu	37	2	113539246	113539246	+	Missense_Mutation	SNP	C	C	T	rs3783531	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:113539246C>T	ENST00000263339.3	-	4	409	c.254G>A	c.(253-255)cGg>cAg	p.R85Q		NM_000575.3	NP_000566.3	P01583	IL1A_HUMAN	interleukin 1, alpha	85			R -> Q (in dbSNP:rs3783531). {ECO:0000269|Ref.10}.		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)	TAAACTCAACCGTCTCTTCTT	0.453													C|||	3	0.000599042	0.0	0.0014	5008	,	,		23078	0.0		0.002	False		,,,				2504	0.0				p.R85Q		Atlas-SNP	.											.	IL1A	19	.	0			c.G254A						PASS	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	230.0	211.0	217.0		254	4.9	0.1	2	dbSNP_107	217	23,8577	16.6+/-54.9	0,23,4277	yes	missense	IL1A	NM_000575.3	43	0,25,6478	TT,TC,CC		0.2674,0.0454,0.1922	probably-damaging	85/272	113539246	25,12981	2203	4300	6503	SO:0001583	missense	3552	exon4			CTCAACCGTCTCT	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.254G>A	2.37:g.113539246C>T	ENSP00000263339:p.Arg85Gln	268.0	0.0	0		306.0	124.0	0.405229	NM_000575	Q53QF9|Q7RU02	Missense_Mutation	SNP	ENST00000263339.3	37	CCDS2101.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	19.02	3.745767	0.69418	4.54E-4	0.002674	ENSG00000115008	ENST00000263339	T	0.47177	0.85	5.78	4.88	0.63580	Interleukin-1 propeptide (1);	0.000000	0.52532	D	0.000061	T	0.66742	0.2820	M	0.80847	2.515	0.09310	N	1	D	0.89917	1.0	D	0.74348	0.983	T	0.60672	-0.7217	10	0.27082	T	0.32	-17.4428	12.36	0.55197	0.1687:0.8313:0.0:0.0	rs3783531;rs3783531	85	P01583	IL1A_HUMAN	Q	85	ENSP00000263339:R85Q	ENSP00000263339:R85Q	R	-	2	0	IL1A	113255717	0.053000	0.20554	0.081000	0.20488	0.602000	0.36980	3.439000	0.52878	1.543000	0.49345	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.453	IL1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254084.1	NM_000575	
FGD5	152273	hgsc.bcm.edu	37	3	14861665	14861665	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:14861665T>C	ENST00000285046.5	+	1	1197	c.1087T>C	c.(1087-1089)Tct>Cct	p.S363P	FGD5_ENST00000543601.1_Missense_Mutation_p.S122P	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	363					actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						CGAGAGCTGTTCTCCTCTTTC	0.532																																					p.S363P		Atlas-SNP	.											.	FGD5	248	.	0			c.T1087C						PASS	.						59.0	60.0	59.0					3																	14861665		1909	4138	6047	SO:0001583	missense	152273	exon1			AGCTGTTCTCCTC	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.1087T>C	3.37:g.14861665T>C	ENSP00000285046:p.Ser363Pro	115.0	0.0	0		149.0	6.0	0.0402685	NM_152536	B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	T	10.62	1.401385	0.25291	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.76316	-1.01;-0.85	5.34	-3.2	0.05156	.	0.543869	0.16888	N	0.195436	T	0.53883	0.1824	N	0.20986	0.625	0.09310	N	1	B;B	0.10296	0.003;0.001	B;B	0.08055	0.003;0.002	T	0.30475	-0.9977	10	0.38643	T	0.18	-0.7487	1.4964	0.02467	0.1367:0.2613:0.302:0.3	.	122;363	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	P	363;122	ENSP00000285046:S363P;ENSP00000445949:S122P	ENSP00000285046:S363P	S	+	1	0	FGD5	14836669	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.262000	0.08682	-0.905000	0.03871	-0.250000	0.11733	TCT	.	.	none		0.532	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
ZNF532	55205	hgsc.bcm.edu	37	18	56620910	56620910	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr18:56620910C>T	ENST00000336078.4	+	8	3805	c.3029C>T	c.(3028-3030)cCt>cTt	p.P1010L	ZNF532_ENST00000591230.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000591083.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000591808.1_Missense_Mutation_p.P1010L|ZNF532_ENST00000589288.1_Missense_Mutation_p.P1010L	NM_018181.4	NP_060651.2	Q9HCE3	ZN532_HUMAN	zinc finger protein 532	1010					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(5)|central_nervous_system(1)|cervix(2)|endometrium(14)|kidney(1)|large_intestine(9)|lung(14)|prostate(1)|skin(4)|urinary_tract(1)	52						TCTCCATCTCCTGTGAAAAAA	0.433																																					p.P1010L		Atlas-SNP	.											.	ZNF532	108	.	0			c.C3029T						PASS	.						77.0	77.0	77.0					18																	56620910		2203	4300	6503	SO:0001583	missense	55205	exon8			CATCTCCTGTGAA	AB046849	CCDS11969.1	18q21.32	2005-08-22			ENSG00000074657	ENSG00000074657		"""Zinc fingers, C2H2-type"""	30940	protein-coding gene	gene with protein product						10997877	Standard	XM_005266723		Approved	FLJ10697	uc002lho.3	Q9HCE3	OTTHUMG00000132759	ENST00000336078.4:c.3029C>T	18.37:g.56620910C>T	ENSP00000338217:p.Pro1010Leu	292.0	0.0	0		253.0	139.0	0.549407	NM_018181	Q4G0V6|Q7L7Z7|Q96QR7|Q9NVJ6	Missense_Mutation	SNP	ENST00000336078.4	37	CCDS11969.1	.	.	.	.	.	.	.	.	.	.	C	16.36	3.102745	0.56183	.	.	ENSG00000074657	ENST00000336078	T	0.01705	4.68	5.23	5.23	0.72850	.	0.109437	0.64402	D	0.000006	T	0.03520	0.0101	M	0.63843	1.955	0.80722	D	1	B;B	0.17852	0.024;0.012	B;B	0.15052	0.012;0.009	T	0.51779	-0.8662	10	0.22706	T	0.39	-0.2311	18.7617	0.91855	0.0:1.0:0.0:0.0	.	1010;1010	B3KXW2;Q9HCE3	.;ZN532_HUMAN	L	1010	ENSP00000338217:P1010L	ENSP00000338217:P1010L	P	+	2	0	ZNF532	54771890	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.384000	0.66225	2.599000	0.87857	0.637000	0.83480	CCT	.	.	none		0.433	ZNF532-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256130.1	NM_018181	
SPAG16	79582	hgsc.bcm.edu	37	2	214160817	214160817	+	Missense_Mutation	SNP	G	G	A	rs61752198	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:214160817G>A	ENST00000331683.5	+	2	261	c.166G>A	c.(166-168)Gac>Aac	p.D56N	SPAG16_ENST00000272898.7_Missense_Mutation_p.D56N|SPAG16_ENST00000447990.1_Missense_Mutation_p.D56N|SPAG16_ENST00000374309.3_Start_Codon_SNP_p.M1I|SPAG16_ENST00000414961.2_3'UTR|SPAG16_ENST00000413312.1_Intron|SPAG16_ENST00000432529.2_Missense_Mutation_p.D56N	NM_024532.4	NP_078808.3	Q8N0X2	SPG16_HUMAN	sperm associated antigen 16	56					cilium assembly (GO:0042384)|spermatogenesis (GO:0007283)	axoneme (GO:0005930)|microtubule cytoskeleton (GO:0015630)|motile cilium (GO:0031514)|nucleus (GO:0005634)				endometrium(4)|kidney(1)|large_intestine(15)|lung(27)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	56		Renal(323;0.00461)		UCEC - Uterine corpus endometrioid carcinoma (47;0.0525)|Epithelial(149;7.07e-07)|all cancers(144;7.96e-05)|Lung(261;0.00255)|LUSC - Lung squamous cell carcinoma(224;0.00599)		ATCTGAAGATGACTATGAATA	0.279													G|||	61	0.0121805	0.0053	0.0043	5008	,	,		15997	0.004		0.0159	False		,,,				2504	0.0317				p.D56N		Atlas-SNP	.											.	SPAG16	134	.	0			c.G166A						PASS	.	G	ASN/ASP,ASN/ASP	32,4372	37.6+/-69.7	0,32,2170	91.0	100.0	97.0		166,166	5.3	1.0	2	dbSNP_129	97	153,8431	72.9+/-135.5	2,149,4141	yes	missense,missense	SPAG16	NM_001025436.1,NM_024532.3	23,23	2,181,6311	AA,AG,GG		1.7824,0.7266,1.4244	benign,benign	56/184,56/632	214160817	185,12803	2202	4292	6494	SO:0001583	missense	79582	exon2			GAAGATGACTATG	AF310672	CCDS2396.1, CCDS46508.1	2q34	2013-05-21			ENSG00000144451	ENSG00000144451		"""WD repeat domain containing"""	23225	protein-coding gene	gene with protein product		612173				12391165, 11867345	Standard	NM_024532		Approved	PF20, FLJ22724, DKFZp666P1710, WDR29	uc002veq.4	Q8N0X2	OTTHUMG00000133015	ENST00000331683.5:c.166G>A	2.37:g.214160817G>A	ENSP00000332592:p.Asp56Asn	158.0	0.0	0		161.0	87.0	0.540373	NM_024532	Q498B7|Q658W1|Q68DB3|Q6I9Z6|Q8N9C7|Q9H601	Missense_Mutation	SNP	ENST00000331683.5	37	CCDS2396.1	23|23	0.010531135531135532|0.010531135531135532	6|6	0.012195121951219513|0.012195121951219513	2|2	0.0055248618784530384|0.0055248618784530384	2|2	0.0034965034965034965|0.0034965034965034965	13|13	0.017150395778364115|0.017150395778364115	G|G	11.78|11.78	1.742080|1.742080	0.30865|0.30865	0.007266|0.007266	0.017824|0.017824	ENSG00000144451|ENSG00000144451	ENST00000331683;ENST00000432529;ENST00000272898;ENST00000447990|ENST00000374309	T|T	0.60299|0.55588	0.2|0.51	5.27|5.27	5.27|5.27	0.74061|0.74061	.|.	0.175804|.	0.33419|.	N|.	0.004932|.	T|T	0.31670|0.31670	0.0804|0.0804	L|L	0.43152|0.43152	1.355|1.355	0.09310|0.09310	N|N	0.999998|0.999998	D;D;D|B	0.76494|0.25667	0.964;0.999;0.979|0.131	P;D;P|B	0.66979|0.22386	0.637;0.948;0.801|0.039	T|T	0.39396|0.39396	-0.9616|-0.9616	10|9	0.46703|0.87932	T|D	0.11|0	.|.	14.7325|14.7325	0.69393|0.69393	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	rs61752198|rs61752198	56;56;56|1	Q8N0X2;E7EWV3;Q8N0X2-4|B4DYB5	SPG16_HUMAN;.;.|.	N|I	56|1	ENSP00000332592:D56N|ENSP00000363428:M1I	ENSP00000272898:D56N|ENSP00000363428:M1I	D|M	+|+	1|3	0|0	SPAG16|SPAG16	213869062|213869062	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.795000|0.795000	0.44927|0.44927	5.541000|5.541000	0.67212|0.67212	2.597000|2.597000	0.87782|0.87782	0.585000|0.585000	0.79938|0.79938	GAC|ATG	G|0.985;A|0.015	0.015	strong		0.279	SPAG16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256601.2	NM_024532	
PCSK4	54760	hgsc.bcm.edu	37	19	1487981	1487981	+	Silent	SNP	C	C	T	rs151115553	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:1487981C>T	ENST00000300954.5	-	4	559	c.498G>A	c.(496-498)ccG>ccA	p.P166P	PCSK4_ENST00000587784.1_5'UTR|CTB-25B13.6_ENST00000585643.1_RNA	NM_017573.3	NP_060043.2			proprotein convertase subtilisin/kexin type 4											cervix(2)|endometrium(2)|kidney(1)|lung(6)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	15		Acute lymphoblastic leukemia(61;3.02e-13)|all_hematologic(61;4.32e-09)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CCCAGAGGTCCGGGTGGTCCT	0.692													C|||	3	0.000599042	0.0	0.0014	5008	,	,		14584	0.0		0.002	False		,,,				2504	0.0				p.P166P		Atlas-SNP	.											.	PCSK4	44	.	0			c.G498A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	71.0	71.0	71.0		498	-5.3	1.0	19	dbSNP_134	71	68,8532	40.3+/-97.0	0,68,4232	no	coding-synonymous	PCSK4	NM_017573.3		0,72,6431	TT,TC,CC		0.7907,0.0908,0.5536		166/756	1487981	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	54760	exon4			GAGGTCCGGGTGG	AK057235	CCDS12069.2	19p13.3	2008-02-05			ENSG00000115257	ENSG00000115257			8746	protein-coding gene	gene with protein product		600487				7782070	Standard	XM_005259586		Approved	PC4, SPC5, DKFZp434B217, MGC34749	uc002ltb.1	Q6UW60	OTTHUMG00000128541	ENST00000300954.5:c.498G>A	19.37:g.1487981C>T		72.0	0.0	0		54.0	26.0	0.481481	NM_017573		Silent	SNP	ENST00000300954.5	37	CCDS12069.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	2.497	-0.316156	0.05422	9.08E-4	0.007907	ENSG00000115257	ENST00000441747	.	.	.	2.67	-5.34	0.02705	.	.	.	.	.	T	0.29491	0.0735	.	.	.	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.04373	-1.0956	7	0.54805	T	0.06	.	3.7736	0.08652	0.2281:0.3213:0.0:0.4506	.	8	B3KQ28	.	Q	8	.	ENSP00000402772:R8Q	R	-	2	0	PCSK4	1438981	0.000000	0.05858	0.987000	0.45799	0.937000	0.57800	-7.956000	0.00027	-0.883000	0.03982	-0.658000	0.03865	CGG	C|0.996;T|0.004	0.004	strong		0.692	PCSK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449703.1	NM_017573	
MUC4	4585	hgsc.bcm.edu	37	3	195506555	195506555	+	Missense_Mutation	SNP	C	C	T	rs368695884	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195506555C>T	ENST00000463781.3	-	2	12355	c.11896G>A	c.(11896-11898)Gcc>Acc	p.A3966T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3966T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.A3966T(2)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGAGGTGGCGTGACCTGTG	0.592													.|||	176	0.0351438	0.0083	0.0677	5008	,	,		7977	0.0119		0.0915	False		,,,				2504	0.0143				p.A3966T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(1)|kidney(1)	c.G11896A						scavenged	.						15.0	10.0	11.0					3																	195506555		666	1488	2154	SO:0001583	missense	4585	exon2			AGGTGGCGTGACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11896G>A	3.37:g.195506555C>T	ENSP00000417498:p.Ala3966Thr	61.0	0.0	0		57.0	12.0	0.210526	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.905	-0.721125	0.03182	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.48522	1.23;0.81	.	.	.	.	.	.	.	.	T	0.22551	0.0544	N	0.19112	0.55	0.09310	N	1	B	0.18741	0.03	B	0.06405	0.002	T	0.12915	-1.0529	7	.	.	.	-3.1782	2.1866	0.03888	0.0:0.3341:0.3337:0.3322	.	3838	E7ESK3	.	T	3966	ENSP00000417498:A3966T;ENSP00000420243:A3966T	.	A	-	1	0	MUC4	196991334	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.202000	0.09451	-2.037000	0.00920	-2.088000	0.00374	GCC	.	.	weak		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SMO	6608	hgsc.bcm.edu	37	7	128846328	128846328	+	Silent	SNP	G	G	C	rs2228617	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:128846328G>C	ENST00000249373.3	+	6	1444	c.1164G>C	c.(1162-1164)ggG>ggC	p.G388G		NM_005631.4	NP_005622.1	Q99835	SMO_HUMAN	smoothened, frizzled class receptor	388					adenohypophysis development (GO:0021984)|anterior/posterior pattern specification (GO:0009952)|atrial septum morphogenesis (GO:0060413)|axon extension involved in axon guidance (GO:0048846)|canonical Wnt signaling pathway (GO:0060070)|cardioblast differentiation (GO:0010002)|cell fate specification (GO:0001708)|cellular response to cholesterol (GO:0071397)|central nervous system neuron differentiation (GO:0021953)|cerebellar cortex morphogenesis (GO:0021696)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|detection of cell density by contact stimulus involved in contact inhibition (GO:0060248)|determination of left/right asymmetry in lateral mesoderm (GO:0003140)|determination of left/right symmetry (GO:0007368)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic neurocranium morphogenesis (GO:0048702)|embryonic viscerocranium morphogenesis (GO:0048703)|epithelial-mesenchymal cell signaling (GO:0060684)|exocrine pancreas development (GO:0031017)|facial nerve development (GO:0021561)|floor plate formation (GO:0021508)|forebrain morphogenesis (GO:0048853)|gonad development (GO:0008406)|hair follicle morphogenesis (GO:0031069)|heart looping (GO:0001947)|heart morphogenesis (GO:0003007)|in utero embryonic development (GO:0001701)|mammary gland epithelial cell differentiation (GO:0060644)|mesenchymal to epithelial transition involved in metanephric renal vesicle formation (GO:0072285)|midgut development (GO:0007494)|multicellular organism growth (GO:0035264)|muscle cell fate commitment (GO:0042693)|myoblast migration (GO:0051451)|negative regulation of apoptotic process (GO:0043066)|negative regulation of DNA binding (GO:0043392)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of gene expression (GO:0010629)|negative regulation of hair follicle development (GO:0051799)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural crest cell migration (GO:0001755)|neuron fate commitment (GO:0048663)|neuron projection regeneration (GO:0031102)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|otolith morphogenesis (GO:0032474)|pancreas morphogenesis (GO:0061113)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gene expression (GO:0010628)|positive regulation of hh target transcription factor activity (GO:0007228)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of neuroblast proliferation (GO:0002052)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of heart morphogenesis (GO:2000826)|regulation of stem cell maintenance (GO:2000036)|renal system development (GO:0072001)|semicircular canal morphogenesis (GO:0048752)|skeletal muscle fiber development (GO:0048741)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021910)|somite development (GO:0061053)|spermatogenesis (GO:0007283)|thalamus development (GO:0021794)|type B pancreatic cell development (GO:0003323)|vasculogenesis (GO:0001570)|ventral midline determination (GO:0007371)	ciliary membrane (GO:0060170)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	drug binding (GO:0008144)|G-protein coupled receptor activity (GO:0004930)|patched binding (GO:0005113)|PDZ domain binding (GO:0030165)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			biliary_tract(1)|central_nervous_system(5)|endometrium(1)|kidney(4)|large_intestine(14)|liver(1)|lung(11)|pancreas(2)|prostate(1)|skin(20)|upper_aerodigestive_tract(3)|urinary_tract(1)	64					Fluocinonide(DB01047)|Vismodegib(DB08828)	CTGTGAGTGGGATTTGTTTTG	0.597			Mis		skin basal cell								C|||	3787	0.75619	0.6687	0.7896	5008	,	,		19589	0.7718		0.8231	False		,,,				2504	0.7658				p.G388G		Atlas-SNP	.		Dom	yes		7	7q31-q32	6608	smoothened homolog (Drosophila)		E	.	SMO	145	.	0			c.G1164C						PASS	.	C		3054,1352	451.8+/-349.8	1066,922,215	231.0	190.0	204.0		1164	5.3	1.0	7	dbSNP_98	204	7216,1384	269.4+/-288.4	3025,1166,109	no	coding-synonymous	SMO	NM_005631.4		4091,2088,324	CC,CG,GG		16.093,30.6854,21.0364		388/788	128846328	10270,2736	2203	4300	6503	SO:0001819	synonymous_variant	6608	exon6			GAGTGGGATTTGT	U84401	CCDS5811.1	7q32.1	2014-01-29	2014-01-29	2003-01-17	ENSG00000128602	ENSG00000128602		"""GPCR / Class F : Frizzled receptors"""	11119	protein-coding gene	gene with protein product	"""frizzled family member 11"""	601500	"""smoothened (Drosophila) homolog"", ""smoothened homolog (Drosophila)"", ""smoothened, seven transmembrane spanning receptor"", ""smoothened, frizzled family receptor"""	SMOH		9628830	Standard	NM_005631		Approved	FZD11	uc003vor.3	Q99835	OTTHUMG00000158421	ENST00000249373.3:c.1164G>C	7.37:g.128846328G>C		133.0	0.0	0		147.0	146.0	0.993197	NM_005631	A4D1K5	Silent	SNP	ENST00000249373.3	37	CCDS5811.1																																																																																			G|0.216;C|0.784	0.784	strong		0.597	SMO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350986.1	NM_005631	
GALR3	8484	hgsc.bcm.edu	37	22	38219570	38219570	+	Missense_Mutation	SNP	C	C	G	rs78650836	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:38219570C>G	ENST00000249041.2	+	1	182	c.157C>G	c.(157-159)Cct>Gct	p.P53A		NM_003614.1	NP_003605.1	O60755	GALR3_HUMAN	galanin receptor 3	53					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|feeding behavior (GO:0007631)|learning or memory (GO:0007611)|negative regulation of adenylate cyclase activity (GO:0007194)|neuropeptide signaling pathway (GO:0007218)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	galanin receptor activity (GO:0004966)|peptide hormone binding (GO:0017046)			endometrium(1)|liver(2)|lung(1)	4	Melanoma(58;0.045)					CTGGCAGGAGCCTGGCAGCAC	0.632													C|||	5	0.000998403	0.0008	0.0029	5008	,	,		11722	0.0		0.001	False		,,,				2504	0.001				p.P53A		Atlas-SNP	.											.	GALR3	12	.	0			c.C157G						PASS	.	C	ALA/PRO	5,4401	9.9+/-24.2	0,5,2198	72.0	53.0	59.0		157	4.2	1.0	22	dbSNP_131	59	52,8548	33.3+/-86.6	0,52,4248	yes	missense	GALR3	NM_003614.1	27	0,57,6446	GG,GC,CC		0.6047,0.1135,0.4383	possibly-damaging	53/369	38219570	57,12949	2203	4300	6503	SO:0001583	missense	8484	exon1			CAGGAGCCTGGCA	AF073799	CCDS13958.1	22q113.1	2012-08-08			ENSG00000128310	ENSG00000128310		"""GPCR / Class A : Galanin receptors"""	4134	protein-coding gene	gene with protein product		603692				9722565, 9832121	Standard	NM_003614		Approved		uc003aub.1	O60755	OTTHUMG00000150658	ENST00000249041.2:c.157C>G	22.37:g.38219570C>G	ENSP00000249041:p.Pro53Ala	162.0	0.0	0		154.0	73.0	0.474026	NM_003614	Q53YJ4	Missense_Mutation	SNP	ENST00000249041.2	37	CCDS13958.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	C	11.45	1.643789	0.29246	0.001135	0.006047	ENSG00000128310	ENST00000249041	T	0.36878	1.23	5.25	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.253805	0.39274	N	0.001413	T	0.12860	0.0312	N	0.20610	0.595	0.25697	N	0.985627	B	0.25206	0.12	B	0.18871	0.023	T	0.12993	-1.0526	10	0.12766	T	0.61	.	6.6972	0.23205	0.2991:0.6141:0.0:0.0869	.	53	O60755	GALR3_HUMAN	A	53	ENSP00000249041:P53A	ENSP00000249041:P53A	P	+	1	0	GALR3	36549516	0.992000	0.36948	1.000000	0.80357	0.921000	0.55340	2.077000	0.41557	2.885000	0.99019	0.655000	0.94253	CCT	C|0.996;G|0.004	0.004	strong		0.632	GALR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319452.1		
CEL	1056	hgsc.bcm.edu	37	9	135946483	135946483	+	Missense_Mutation	SNP	C	C	T	rs200231984		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:135946483C>T	ENST00000372080.4	+	11	1619	c.1603C>T	c.(1603-1605)Cgg>Tgg	p.R535W	CEL_ENST00000351304.7_Missense_Mutation_p.R466W	NM_001807.3	NP_001798.2	P19835	CEL_HUMAN	carboxyl ester lipase	532					cholesterol catabolic process (GO:0006707)|fatty acid catabolic process (GO:0009062)|intestinal cholesterol absorption (GO:0030299)|intestinal lipid catabolic process (GO:0044258)|lipid digestion (GO:0044241)|lipid metabolic process (GO:0006629)|pancreatic juice secretion (GO:0030157)|protein esterification (GO:0018350)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	acylglycerol lipase activity (GO:0047372)|catalytic activity (GO:0003824)|heparin binding (GO:0008201)|hydrolase activity (GO:0016787)|sterol esterase activity (GO:0004771)|triglyceride lipase activity (GO:0004806)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(9)|pancreas(2)|skin(1)	20				OV - Ovarian serous cystadenocarcinoma(145;1.03e-40)|Epithelial(140;3.58e-37)|GBM - Glioblastoma multiforme(294;0.00164)|READ - Rectum adenocarcinoma(205;0.196)		CTCCATGAAGCGGAGCCTGAG	0.622																																					p.R535W		Atlas-SNP	.											.	CEL	71	.	0			c.C1603T						PASS	.	C	TRP/ARG	2,3834		0,2,1916	30.0	35.0	33.0		1603	3.2	0.0	9		33	9,8191		0,9,4091	no	missense	CEL	NM_001807.3	101	0,11,6007	TT,TC,CC		0.1098,0.0521,0.0914	probably-damaging	535/757	135946483	11,12025	1918	4100	6018	SO:0001583	missense	1056	exon11			ATGAAGCGGAGCC	M54994	CCDS43896.1	9q34.3	2013-03-13	2013-03-13		ENSG00000170835	ENSG00000170835	3.1.1.3, 3.1.1.13		1848	protein-coding gene	gene with protein product	"""bile salt-stimulated lipase"""	114840				1676983	Standard	NM_001807		Approved	BSSL, MODY8	uc010naa.2	P19835	OTTHUMG00000020855	ENST00000372080.4:c.1603C>T	9.37:g.135946483C>T	ENSP00000361151:p.Arg535Trp	73.0	0.0	0		103.0	49.0	0.475728	NM_001807	Q16398|Q5T7U7|Q9UCH1|Q9UP41	Missense_Mutation	SNP	ENST00000372080.4	37	CCDS43896.1	.	.	.	.	.	.	.	.	.	.	C	12.66	2.003200	0.35320	5.21E-4	0.001098	ENSG00000170835	ENST00000372080;ENST00000351304;ENST00000303626	T;T	0.71341	-0.39;-0.56	5.2	3.23	0.37069	Carboxylesterase, type B (1);	0.713375	0.14331	N	0.326364	T	0.75568	0.3867	L	0.56769	1.78	0.09310	N	1	D	0.71674	0.998	P	0.56563	0.801	T	0.64740	-0.6336	10	0.72032	D	0.01	.	9.357	0.38173	0.0:0.7253:0.1927:0.082	.	532	P19835	CEL_HUMAN	W	535;466;534	ENSP00000361151:R535W;ENSP00000342217:R466W	ENSP00000304021:R534W	R	+	1	2	CEL	134936304	0.941000	0.31946	0.013000	0.15412	0.045000	0.14185	0.437000	0.21543	0.461000	0.27071	0.478000	0.44815	CGG	C|0.999;T|0.001	0.001	weak		0.622	CEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054823.1		
PKD1L1	168507	hgsc.bcm.edu	37	7	47851578	47851578	+	Missense_Mutation	SNP	G	G	A	rs140456142		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:47851578G>A	ENST00000289672.2	-	50	7468	c.7418C>T	c.(7417-7419)tCt>tTt	p.S2473F	PKD1L1_ENST00000462350.1_5'Flank|C7orf69_ENST00000258776.4_Intron|C7orf69_ENST00000418326.2_Intron	NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	2473					detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						GAAGTGCACAGACACAGCCCT	0.592													G|||	1	0.000199681	0.0	0.0	5008	,	,		19929	0.0		0.0	False		,,,				2504	0.001				p.S2473F		Atlas-SNP	.											.	PKD1L1	328	.	0			c.C7418T						PASS	.	G	,PHE/SER	2,4404		0,2,2201	79.0	64.0	69.0		,7418	4.6	0.8	7	dbSNP_134	69	10,8588		0,10,4289	yes	intron,missense	C7orf69,PKD1L1	NM_025031.2,NM_138295.3	,155	0,12,6490	AA,AG,GG		0.1163,0.0454,0.0923	,probably-damaging	,2473/2850	47851578	12,12992	2203	4299	6502	SO:0001583	missense	168507	exon50			TGCACAGACACAG	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.7418C>T	7.37:g.47851578G>A	ENSP00000289672:p.Ser2473Phe	133.0	0.0	0		118.0	56.0	0.474576	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	.	.	.	.	.	.	.	.	.	.	G	8.910	0.958416	0.18507	4.54E-4	0.001163	ENSG00000158683	ENST00000289672	T	0.61742	0.08	5.49	4.55	0.56014	Polycystin cation channel, PKD1/PKD2 (1);	0.725348	0.12568	N	0.457613	T	0.34629	0.0904	N	0.10874	0.06	0.18873	N	0.999984	P	0.38922	0.651	B	0.39068	0.289	T	0.09357	-1.0678	10	0.09843	T	0.71	-19.6503	8.5081	0.33199	0.0:0.166:0.6623:0.1717	.	2473	Q8TDX9	PK1L1_HUMAN	F	2473	ENSP00000289672:S2473F	ENSP00000289672:S2473F	S	-	2	0	PKD1L1	47818103	0.001000	0.12720	0.800000	0.32199	0.787000	0.44495	0.791000	0.26915	2.573000	0.86826	0.453000	0.30009	TCT	G|0.999;A|0.001	0.001	strong		0.592	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
CEP89	84902	hgsc.bcm.edu	37	19	33414392	33414392	+	Silent	SNP	T	T	C	rs17599843	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:33414392T>C	ENST00000305768.5	-	12	1309	c.1221A>G	c.(1219-1221)gaA>gaG	p.E407E		NM_032816.3	NP_116205.3	Q96ST8	CEP89_HUMAN	centrosomal protein 89kDa	407					cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary transition fiber (GO:0097539)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(2)|cervix(1)|endometrium(4)|large_intestine(4)|lung(15)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	35						CTTGGTGCAATTCTTCATTTT	0.373													T|||	38	0.00758786	0.0	0.0058	5008	,	,		18272	0.001		0.008	False		,,,				2504	0.0256				p.E407E		Atlas-SNP	.											.	CEP89	82	.	0			c.A1221G						PASS	.	T		12,4392	19.1+/-41.9	0,12,2190	250.0	221.0	231.0		1221	-2.9	0.0	19	dbSNP_123	231	70,8528	42.6+/-100.3	0,70,4229	no	coding-synonymous	CEP89	NM_032816.3		0,82,6419	CC,CT,TT		0.8141,0.2725,0.6307		407/784	33414392	82,12920	2202	4299	6501	SO:0001819	synonymous_variant	84902	exon12			GTGCAATTCTTCA	AL832158	CCDS32987.1	19q13.11	2014-02-20	2011-05-06	2011-05-06		ENSG00000121289			25907	protein-coding gene	gene with protein product		615470	"""coiled-coil domain containing 123"""	CCDC123		16395595	Standard	NM_032816		Approved	FLJ14640	uc002nty.3	Q96ST8		ENST00000305768.5:c.1221A>G	19.37:g.33414392T>C		213.0	0.0	0		216.0	97.0	0.449074	NM_032816	B9EGA6|Q8N5J8	Silent	SNP	ENST00000305768.5	37	CCDS32987.1																																																																																			T|0.995;C|0.005	0.005	strong		0.373	CEP89-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451300.2	NM_032816	
FAM98C	147965	hgsc.bcm.edu	37	19	38896204	38896204	+	Missense_Mutation	SNP	T	T	G	rs117354953	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:38896204T>G	ENST00000252530.5	+	6	698	c.679T>G	c.(679-681)Tgc>Ggc	p.C227G	FAM98C_ENST00000343358.7_Missense_Mutation_p.C201G|FAM98C_ENST00000588262.1_Intron	NM_174905.3	NP_777565.3	Q17RN3	FA98C_HUMAN	family with sequence similarity 98, member C	227										endometrium(2)|large_intestine(3)|lung(6)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	15	all_cancers(60;3.95e-06)		Lung(45;0.00172)|LUSC - Lung squamous cell carcinoma(53;0.00272)			TCAGTACCGCTGCCGCCGCTG	0.592													T|||	24	0.00479233	0.0008	0.0058	5008	,	,		16729	0.0		0.0169	False		,,,				2504	0.002				p.C227G		Atlas-SNP	.											FAM98C,NS,carcinoma,-1,1	FAM98C	39	1	0			c.T679G						PASS	.	T	GLY/CYS	12,4366		0,12,2177	52.0	59.0	57.0		679	4.0	1.0	19	dbSNP_132	57	127,8463		0,127,4168	yes	missense	FAM98C	NM_174905.3	159	0,139,6345	GG,GT,TT		1.4785,0.2741,1.0719	benign	227/350	38896204	139,12829	2189	4295	6484	SO:0001583	missense	147965	exon6			TACCGCTGCCGCC		CCDS42562.1	19q13.2	2008-02-05				ENSG00000130244			27119	protein-coding gene	gene with protein product						12477932	Standard	NM_174905		Approved	FLJ44669	uc002oin.1	Q17RN3		ENST00000252530.5:c.679T>G	19.37:g.38896204T>G	ENSP00000252530:p.Cys227Gly	66.0	0.0	0		85.0	42.0	0.494118	NM_174905	A6NMW3|Q66K45	Missense_Mutation	SNP	ENST00000252530.5	37	CCDS42562.1	19	0.0086996336996337	2	0.0040650406504065045	3	0.008287292817679558	1	0.0017482517482517483	13	0.017150395778364115	T	13.51	2.259355	0.39995	0.002741	0.014785	ENSG00000130244	ENST00000252530;ENST00000343358	T;T	0.45668	0.89;0.89	5.02	3.99	0.46301	.	0.548059	0.15348	N	0.267098	T	0.25457	0.0619	M	0.79926	2.475	0.44295	D	0.997163	P;B	0.47910	0.902;0.086	B;B	0.38225	0.268;0.056	T	0.13602	-1.0503	10	0.30854	T	0.27	-0.3593	8.8557	0.35227	0.0:0.0:0.1896:0.8104	.	201;227	Q17RN3-2;Q17RN3	.;FA98C_HUMAN	G	227;201	ENSP00000252530:C227G;ENSP00000340348:C201G	ENSP00000252530:C227G	C	+	1	0	FAM98C	43588044	0.998000	0.40836	0.969000	0.41365	0.832000	0.47134	2.019000	0.41001	0.738000	0.32606	0.456000	0.33151	TGC	T|0.989;G|0.011	0.011	strong		0.592	FAM98C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459222.1	NM_174905	
TTC28	23331	hgsc.bcm.edu	37	22	28501580	28501580	+	Silent	SNP	G	G	A	rs189318371	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:28501580G>A	ENST00000397906.2	-	8	3135	c.2994C>T	c.(2992-2994)gaC>gaT	p.D998D		NM_001145418.1	NP_001138890.1	Q96AY4	TTC28_HUMAN	tetratricopeptide repeat domain 28	998					mitotic nuclear division (GO:0007067)|regulation of mitotic cell cycle (GO:0007346)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)				endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)	12						CACAGGCTGCGTCACTCTCCA	0.532													G|||	15	0.00299521	0.0	0.0029	5008	,	,		18507	0.0		0.002	False		,,,				2504	0.0112				p.D998D		Atlas-SNP	.											.	TTC28	84	.	0			c.C2994T						PASS	.	G		2,1382		0,2,690	94.0	85.0	88.0		2994	-11.6	0.0	22		88	31,3151		1,29,1561	no	coding-synonymous	TTC28	NM_001145418.1		1,31,2251	AA,AG,GG		0.9742,0.1445,0.7227		998/2482	28501580	33,4533	692	1591	2283	SO:0001819	synonymous_variant	23331	exon8			GGCTGCGTCACTC	AB028966	CCDS46678.1	22q12.1	2013-01-10			ENSG00000100154	ENSG00000100154		"""Tetratricopeptide (TTC) repeat domain containing"""	29179	protein-coding gene	gene with protein product		615098				10470851	Standard	NM_001145418		Approved	KIAA1043	uc003adp.4	Q96AY4	OTTHUMG00000151006	ENST00000397906.2:c.2994C>T	22.37:g.28501580G>A		201.0	0.0	0		232.0	129.0	0.556035	NM_001145418	K7ZRV2|O95928|O95929|Q5W189|Q9NTE4|Q9UG31|Q9UGG5|Q9UPV8|Q9Y3S5	Silent	SNP	ENST00000397906.2	37	CCDS46678.1																																																																																			G|0.997;A|0.003	0.003	strong		0.532	TTC28-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000320930.2	XM_929318	
KRT25	147183	hgsc.bcm.edu	37	17	38910676	38910676	+	Missense_Mutation	SNP	G	G	C	rs146092638	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:38910676G>C	ENST00000312150.4	-	2	534	c.474C>G	c.(472-474)atC>atG	p.I158M		NM_181534.3	NP_853512.1			keratin 25											endometrium(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(4)	16		Breast(137;0.00526)				TGGCATTATCGATCTGCAGAA	0.388																																					p.I158M		Atlas-SNP	.											.	KRT25	63	.	0			c.C474G						PASS	.	G	MET/ILE	0,4406		0,0,2203	137.0	130.0	133.0		474	-1.5	1.0	17	dbSNP_134	133	2,8598	2.2+/-6.3	0,2,4298	no	missense	KRT25	NM_181534.3	10	0,2,6501	CC,CG,GG		0.0233,0.0,0.0154	possibly-damaging	158/451	38910676	2,13004	2203	4300	6503	SO:0001583	missense	147183	exon2			ATTATCGATCTGC	AK129503	CCDS11373.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000204897	ENSG00000204897		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30839	protein-coding gene	gene with protein product			"""keratin 25A"""	KRT25A		16831889	Standard	NM_181534		Approved		uc002hve.3	Q7Z3Z0	OTTHUMG00000133373	ENST00000312150.4:c.474C>G	17.37:g.38910676G>C	ENSP00000310573:p.Ile158Met	141.0	0.0	0		145.0	56.0	0.386207	NM_181534		Missense_Mutation	SNP	ENST00000312150.4	37	CCDS11373.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305005	0.60305	0.0	2.33E-4	ENSG00000204897	ENST00000394042;ENST00000312150	D	0.89810	-2.57	5.73	-1.51	0.08664	Filament (1);	0.088817	0.49305	D	0.000153	D	0.92760	0.7698	M	0.84156	2.68	0.39210	D	0.963294	D	0.67145	0.996	D	0.66196	0.942	D	0.91638	0.5324	10	0.72032	D	0.01	.	11.8009	0.52126	0.6185:0.0:0.3815:0.0	.	158	Q7Z3Z0	K1C25_HUMAN	M	158	ENSP00000310573:I158M	ENSP00000310573:I158M	I	-	3	3	KRT25	36164202	0.036000	0.19791	0.972000	0.41901	0.900000	0.52787	-0.494000	0.06451	-0.516000	0.06470	-0.136000	0.14681	ATC	A|0.000;C|0.000;G|1.000	0.000	strong		0.388	KRT25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257218.1	NM_181534	
GNAT1	2779	hgsc.bcm.edu	37	3	50232262	50232262	+	Silent	SNP	G	G	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:50232262G>T	ENST00000433068.1	+	8	983	c.927G>T	c.(925-927)cgG>cgT	p.R309R	GNAT1_ENST00000232461.3_Silent_p.R309R	NM_000172.3	NP_000163.2	P11488	GNAT1_HUMAN	guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1	309					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cell proliferation (GO:0008283)|cellular response to electrical stimulus (GO:0071257)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|detection of light stimulus involved in visual perception (GO:0050908)|eye photoreceptor cell development (GO:0042462)|negative regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051344)|phototransduction, visible light (GO:0007603)|positive regulation of cyclic-nucleotide phosphodiesterase activity (GO:0051343)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|response to light intensity (GO:0009642)|response to light stimulus (GO:0009416)|retina development in camera-type eye (GO:0060041)|rhodopsin mediated signaling pathway (GO:0016056)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)	acyl binding (GO:0000035)|G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GDP binding (GO:0019003)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(4)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TCAACATGCGGCGCGACGTGA	0.577											OREG0015580	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R309R		Atlas-SNP	.											.	GNAT1	39	.	0			c.G927T						PASS	.						91.0	73.0	79.0					3																	50232262		2203	4300	6503	SO:0001819	synonymous_variant	2779	exon8			CATGCGGCGCGAC		CCDS2812.1	3p21	2014-01-28			ENSG00000114349	ENSG00000114349			4393	protein-coding gene	gene with protein product		139330					Standard	NM_000172		Approved	CSNBAD3	uc003cyl.2	P11488	OTTHUMG00000156808	ENST00000433068.1:c.927G>T	3.37:g.50232262G>T		95.0	0.0	0	968	87.0	31.0	0.356322	NM_144499	Q4VBN2	Silent	SNP	ENST00000433068.1	37	CCDS2812.1																																																																																			.	.	none		0.577	GNAT1-002	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345957.1	NM_000172	
CIT	11113	hgsc.bcm.edu	37	12	120166407	120166407	+	Missense_Mutation	SNP	T	T	C	rs145731510	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:120166407T>C	ENST00000261833.7	-	27	3417	c.3365A>G	c.(3364-3366)aAt>aGt	p.N1122S	CIT_ENST00000392521.2_Missense_Mutation_p.N1164S|CIT_ENST00000537607.1_5'UTR	NM_007174.2	NP_009105.1	O14578	CTRO_HUMAN	citron rho-interacting serine/threonine kinase	1122	Interaction with Rho/Rac.				cytokinesis (GO:0000910)|dendrite development (GO:0016358)|G2/M transition of mitotic cell cycle (GO:0000086)|generation of neurons (GO:0048699)|Golgi organization (GO:0007030)|intracellular signal transduction (GO:0035556)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of dendrite morphogenesis (GO:0050774)|regulation of actin polymerization or depolymerization (GO:0008064)|spermatogenesis (GO:0007283)	actin cytoskeleton (GO:0015629)|Golgi cisterna (GO:0031985)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|ruffle (GO:0001726)|vacuole (GO:0005773)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(6)|endometrium(9)|kidney(4)|large_intestine(15)|liver(1)|lung(29)|ovary(7)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	86	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)	Myeloproliferative disorder(1001;0.0255)		BRCA - Breast invasive adenocarcinoma(302;0.211)		CTCCAGGTCATTGAGCTAGAC	0.443																																					p.N1164S		Atlas-SNP	.											.	CIT	535	.	0			c.A3491G						PASS	.	T	SER/ASN,SER/ASN	0,4406		0,0,2203	170.0	159.0	163.0		3491,3365	4.1	1.0	12	dbSNP_134	163	14,8586	10.5+/-38.8	0,14,4286	yes	missense,missense	CIT	NM_001206999.1,NM_007174.2	46,46	0,14,6489	CC,CT,TT		0.1628,0.0,0.1076	probably-damaging,probably-damaging	1164/2070,1122/2028	120166407	14,12992	2203	4300	6503	SO:0001583	missense	11113	exon28			AGGTCATTGAGCT	AB023166	CCDS9192.1, CCDS55891.1	12q24.23	2014-04-23	2014-04-23		ENSG00000122966	ENSG00000122966			1985	protein-coding gene	gene with protein product	"""serine/threonine kinase 21"""	605629	"""citron (rho-interacting, serine/threonine kinase 21)"""			9792683	Standard	NM_001206999		Approved	KIAA0949, STK21, CRIK	uc001txj.2	O14578	OTTHUMG00000134325	ENST00000261833.7:c.3365A>G	12.37:g.120166407T>C	ENSP00000261833:p.Asn1122Ser	59.0	0.0	0		73.0	41.0	0.561644	NM_001206999	Q2M5E1|Q6XUH8|Q86UQ9|Q9UPZ7	Missense_Mutation	SNP	ENST00000261833.7	37	CCDS9192.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	13.39|13.39	2.222469|2.222469	0.39300|0.39300	0.0|0.0	0.001628|0.001628	ENSG00000122966|ENSG00000122966	ENST00000392520|ENST00000392521;ENST00000261833	.|T;T	.|0.63913	.|-0.03;-0.07	5.29|5.29	4.14|4.14	0.48551|0.48551	.|.	.|0.052340	.|0.85682	.|N	.|0.000000	T|T	0.53769|0.53769	0.1817|0.1817	N|N	0.17082|0.17082	0.46|0.46	0.45791|0.45791	D|D	0.998671|0.998671	.|D;B;B	.|0.62365	.|0.991;0.0;0.023	.|P;B;B	.|0.52343	.|0.696;0.002;0.032	T|T	0.50792|0.50792	-0.8786|-0.8786	5|10	.|0.32370	.|T	.|0.25	.|.	11.2234|11.2234	0.48869|0.48869	0.0:0.0724:0.0:0.9276|0.0:0.0724:0.0:0.9276	.|.	.|1164;1122;655	.|Q2M5E1;O14578;O14578-3	.|.;CTRO_HUMAN;.	V|S	750|1164;1122	.|ENSP00000376306:N1164S;ENSP00000261833:N1122S	.|ENSP00000261833:N1122S	M|N	-|-	1|2	0|0	CIT|CIT	118650790|118650790	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.996000|0.996000	0.88848|0.88848	3.105000|3.105000	0.50314|0.50314	0.959000|0.959000	0.37980|0.37980	0.533000|0.533000	0.62120|0.62120	ATG|AAT	T|0.999;C|0.001	0.001	strong		0.443	CIT-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000259410.4	NM_007174	
C1orf192	257177	hgsc.bcm.edu	37	1	161335414	161335414	+	Missense_Mutation	SNP	G	G	A	rs141881555	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:161335414G>A	ENST00000367974.1	-	4	255	c.250C>T	c.(250-252)Cgt>Tgt	p.R84C	RP11-122G18.5_ENST00000437833.2_lincRNA	NM_001013625.2	NP_001013647.2	Q5VTH2	CA192_HUMAN	chromosome 1 open reading frame 192	84										endometrium(1)|large_intestine(3)|lung(5)|prostate(1)	10	all_cancers(52;4.64e-17)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00376)			GCAGTTGTACGGGAGGTCAGG	0.507													g|||	3	0.000599042	0.0	0.0	5008	,	,		16556	0.0		0.002	False		,,,				2504	0.001				p.R84C		Atlas-SNP	.											.	C1orf192	20	.	0			c.C250T						PASS	.	G	CYS/ARG	0,4406		0,0,2203	142.0	150.0	148.0		250	3.5	0.9	1	dbSNP_134	148	15,8585	11.2+/-40.8	0,15,4285	yes	missense	C1orf192	NM_001013625.2	180	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	probably-damaging	84/178	161335414	15,12991	2203	4300	6503	SO:0001583	missense	257177	exon4			TTGTACGGGAGGT		CCDS30921.1	1q23.3	2014-02-21			ENSG00000188931	ENSG00000188931			32325	protein-coding gene	gene with protein product							Standard	NM_001013625		Approved	Flattop, Fltp	uc001gal.4	Q5VTH2	OTTHUMG00000034462	ENST00000367974.1:c.250C>T	1.37:g.161335414G>A	ENSP00000356951:p.Arg84Cys	186.0	0.0	0		276.0	175.0	0.634058	NM_001013625		Missense_Mutation	SNP	ENST00000367974.1	37	CCDS30921.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	19.41	3.821832	0.71028	0.0	0.001744	ENSG00000188931	ENST00000367974	.	.	.	5.49	3.5	0.40072	.	0.074082	0.53938	N	0.000057	T	0.56877	0.2015	M	0.66939	2.045	0.36982	D	0.894331	D	0.89917	1.0	D	0.97110	1.0	T	0.62955	-0.6744	8	0.72032	D	0.01	-12.236	8.235	0.31620	0.0838:0.0:0.7599:0.1564	.	84	Q5VTH2	CA192_HUMAN	C	84	.	ENSP00000356951:R84C	R	-	1	0	C1orf192	159602038	1.000000	0.71417	0.902000	0.35471	0.983000	0.72400	3.636000	0.54317	1.456000	0.47831	0.655000	0.94253	CGT	G|0.999;A|0.001	0.001	strong		0.507	C1orf192-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083309.1	NM_001013625	
FBXO6	26270	hgsc.bcm.edu	37	1	11733846	11733846	+	Missense_Mutation	SNP	C	C	A	rs148957324	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:11733846C>A	ENST00000376753.4	+	6	955	c.820C>A	c.(820-822)Cag>Aag	p.Q274K		NM_018438.5	NP_060908.1	Q9NRD1	FBX6_HUMAN	F-box protein 6	274					DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|glycoprotein catabolic process (GO:0006516)|proteolysis (GO:0006508)|response to unfolded protein (GO:0006986)|SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)	cytoplasm (GO:0005737)|SCF ubiquitin ligase complex (GO:0019005)	carbohydrate binding (GO:0030246)|glycoprotein binding (GO:0001948)|ubiquitin-protein transferase activity (GO:0004842)			breast(1)|large_intestine(1)|lung(1)|ovary(1)|upper_aerodigestive_tract(2)	6	Ovarian(185;0.249)	Lung NSC(185;4.15e-05)|all_lung(284;4.76e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.00965)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.25e-06)|COAD - Colon adenocarcinoma(227;0.000251)|BRCA - Breast invasive adenocarcinoma(304;0.000297)|Kidney(185;0.000747)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.00727)|READ - Rectum adenocarcinoma(331;0.0649)		TCAGCCTGGGCAGAAGCATGG	0.607													C|||	10	0.00199681	0.0	0.0	5008	,	,		18989	0.0		0.0089	False		,,,				2504	0.001				p.Q274K	NSCLC(54;506 1562 46490 51389)	Atlas-SNP	.											.	FBXO6	17	.	0			c.C820A						PASS	.	C	LYS/GLN	11,4395	17.9+/-39.9	0,11,2192	79.0	77.0	78.0		820	-9.2	0.0	1	dbSNP_134	78	85,8515	48.9+/-108.6	1,83,4216	yes	missense	FBXO6	NM_018438.5	53	1,94,6408	AA,AC,CC		0.9884,0.2497,0.7381	benign	274/294	11733846	96,12910	2203	4300	6503	SO:0001583	missense	26270	exon6			CCTGGGCAGAAGC	AF129536	CCDS133.1	1p36.22	2008-05-14	2004-06-15		ENSG00000116663	ENSG00000116663		"""F-boxes /  ""other"""""	13585	protein-coding gene	gene with protein product		605647	"""F-box only protein 6"""			10531035, 10945468	Standard	NM_018438		Approved	FBX6, FBG2, FBS2, Fbx6b	uc001aso.3	Q9NRD1	OTTHUMG00000002229	ENST00000376753.4:c.820C>A	1.37:g.11733846C>A	ENSP00000365944:p.Gln274Lys	264.0	0.0	0		243.0	95.0	0.390947	NM_018438	B1AK42|B2RC88|Q9UKT3	Missense_Mutation	SNP	ENST00000376753.4	37	CCDS133.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	0.015	-1.552659	0.00918	0.002497	0.009884	ENSG00000116663	ENST00000376753	T	0.21734	1.99	4.63	-9.25	0.00666	.	6.681920	0.00166	N	0.000000	T	0.05868	0.0153	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.15206	-1.0445	10	0.22109	T	0.4	.	11.0102	0.47659	0.1177:0.5049:0.3774:0.0	.	274	Q9NRD1	FBX6_HUMAN	K	274	ENSP00000365944:Q274K	ENSP00000365944:Q274K	Q	+	1	0	FBXO6	11656433	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.870000	0.04228	-2.568000	0.00469	-3.108000	0.00062	CAG	C|0.994;A|0.006	0.006	strong		0.607	FBXO6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006332.1	NM_018438	
BRINP2	57795	hgsc.bcm.edu	37	1	177245369	177245369	+	Missense_Mutation	SNP	C	C	T	rs145109858	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:177245369C>T	ENST00000361539.4	+	6	1123	c.811C>T	c.(811-813)Cgc>Tgc	p.R271C	BRINP2_ENST00000478325.1_3'UTR	NM_021165.2	NP_066988.1	Q9C0B6	BRNP2_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 2	271	MACPF.				cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	extracellular region (GO:0005576)											TCTGCGTGAGCGCTTTGTAGC	0.562																																					p.R271C		Atlas-SNP	.											FAM5B,NS,carcinoma,0,3	FAM5B	191	3	0			c.C811T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	68.0	61.0	64.0		811	6.1	1.0	1	dbSNP_134	64	7,8593	5.7+/-21.5	0,7,4293	yes	missense	FAM5B	NM_021165.2	180	0,8,6495	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging	271/784	177245369	8,12998	2203	4300	6503	SO:0001583	missense	57795	exon6			CGTGAGCGCTTTG		CCDS1320.1	1q24	2013-08-06	2013-08-06	2013-07-31	ENSG00000198797	ENSG00000198797			13746	protein-coding gene	gene with protein product			"""family with sequence similarity 5, member B"""	FAM5B		15193423	Standard	NM_021165		Approved	DBCCR1L2	uc001glf.3	Q9C0B6	OTTHUMG00000034953	ENST00000361539.4:c.811C>T	1.37:g.177245369C>T	ENSP00000354481:p.Arg271Cys	193.0	0.0	0		224.0	126.0	0.5625	NM_021165	O95560|Q6ZWC1|Q7LCZ9|Q8N360	Missense_Mutation	SNP	ENST00000361539.4	37	CCDS1320.1	.	.	.	.	.	.	.	.	.	.	C	20.1	3.939863	0.73557	2.27E-4	8.14E-4	ENSG00000198797	ENST00000536589;ENST00000361539	T	0.15834	2.39	6.07	6.07	0.98685	Membrane attack complex component/perforin (MACPF) domain (1);	0.000000	0.85682	D	0.000000	T	0.38719	0.1051	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	1.0;0.999;0.993	D;P;P	0.67725	0.953;0.899;0.548	T	0.03453	-1.1035	10	0.87932	D	0	-25.4339	15.0142	0.71570	0.1424:0.8576:0.0:0.0	.	21;166;271	F5H8E0;Q9C0B6-2;Q9C0B6	.;.;FAM5B_HUMAN	C	21;271	ENSP00000354481:R271C	ENSP00000354481:R271C	R	+	1	0	FAM5B	175511992	0.998000	0.40836	1.000000	0.80357	0.989000	0.77384	0.813000	0.27225	2.884000	0.98904	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	strong		0.562	BRINP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084599.1	NM_021165	
ASGR2	433	hgsc.bcm.edu	37	17	7004927	7004927	+	Silent	SNP	C	C	T	rs11653054	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:7004927C>T	ENST00000380952.2	-	9	1167	c.903G>A	c.(901-903)gaG>gaA	p.E301E	ASGR2_ENST00000355035.5_Silent_p.E301E|ASGR2_ENST00000254850.7_Silent_p.E277E|ASGR2_ENST00000446679.2_Silent_p.E282E	NM_001181.4|NM_001201352.1|NM_080912.3	NP_001172|NP_001188281.1|NP_550434	P07307	ASGR2_HUMAN	asialoglycoprotein receptor 2	301	C-type lectin. {ECO:0000255|PROSITE- ProRule:PRU00040}.				bone mineralization (GO:0030282)|cell surface receptor signaling pathway (GO:0007166)|glycoprotein metabolic process (GO:0009100)|lipid homeostasis (GO:0055088)|receptor-mediated endocytosis (GO:0006898)|regulation of protein stability (GO:0031647)	integral component of membrane (GO:0016021)	asialoglycoprotein receptor activity (GO:0004873)|carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|skin(3)|stomach(4)	18					Antihemophilic Factor(DB00025)	TCCGCCTTTTCTCACACACCC	0.602													C|||	44	0.00878594	0.0008	0.0101	5008	,	,		18902	0.001		0.0328	False		,,,				2504	0.002				p.E301E		Atlas-SNP	.											.	ASGR2	38	.	0			c.G903A						PASS	.	C	,,,,	28,4378	34.3+/-65.2	0,28,2175	89.0	76.0	81.0		903,888,903,831,846	3.8	1.0	17	dbSNP_120	81	266,8334	102.7+/-163.9	6,254,4040	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ASGR2	NM_001181.4,NM_001201352.1,NM_080912.3,NM_080913.3,NM_080914.2	,,,,	6,282,6215	TT,TC,CC		3.093,0.6355,2.2605	,,,,	301/312,296/307,301/312,277/288,282/293	7004927	294,12712	2203	4300	6503	SO:0001819	synonymous_variant	433	exon9			CCTTTTCTCACAC	M11025	CCDS11088.1, CCDS32544.1, CCDS45598.1	17p	2011-08-30			ENSG00000161944	ENSG00000161944		"""C-type lectin domain containing"""	743	protein-coding gene	gene with protein product		108361				3863106	Standard	NM_080912		Approved	CLEC4H2	uc002ger.3	P07307	OTTHUMG00000102158	ENST00000380952.2:c.903G>A	17.37:g.7004927C>T		95.0	0.0	0		71.0	39.0	0.549296	NM_080912	A6NLV8|A8MT12|D3DTM9|D3DTN0|O00448|Q03969	Silent	SNP	ENST00000380952.2	37	CCDS32544.1																																																																																			C|0.980;T|0.020	0.020	strong		0.602	ASGR2-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000220003.1	NM_080914	
PCDH12	51294	hgsc.bcm.edu	37	5	141337177	141337177	+	Missense_Mutation	SNP	G	G	C	rs138689340	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:141337177G>C	ENST00000231484.3	-	1	1450	c.240C>G	c.(238-240)gaC>gaG	p.D80E	PCDH12_ENST00000512221.1_5'Flank	NM_016580.2	NP_057664.1	Q9NPG4	PCD12_HUMAN	protocadherin 12	80	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)			CTTCCTCAGAGTCCACCTGAA	0.637													G|||	28	0.00559105	0.0008	0.013	5008	,	,		17451	0.0		0.0149	False		,,,				2504	0.0031				p.D80E		Atlas-SNP	.											.	PCDH12	133	.	0			c.C240G						PASS	.	G	GLU/ASP	15,4391	22.3+/-47.3	0,15,2188	52.0	53.0	53.0		240	-1.3	0.0	5	dbSNP_134	53	145,8455	70.0+/-132.6	1,143,4156	yes	missense	PCDH12	NM_016580.2	45	1,158,6344	CC,CG,GG		1.686,0.3404,1.2302	benign	80/1185	141337177	160,12846	2203	4300	6503	SO:0001583	missense	51294	exon1			CTCAGAGTCCACC	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.240C>G	5.37:g.141337177G>C	ENSP00000231484:p.Asp80Glu	195.0	0.0	0		198.0	125.0	0.631313	NM_016580	Q6UXB6|Q96KB8|Q9H7Y6|Q9H8E0	Missense_Mutation	SNP	ENST00000231484.3	37	CCDS4269.1	21	0.009615384615384616	3	0.006097560975609756	6	0.016574585635359115	0	0.0	12	0.0158311345646438	G	5.339	0.247807	0.10130	0.003404	0.01686	ENSG00000113555	ENST00000231484	T	0.27890	1.64	4.81	-1.34	0.09143	Cadherin, N-terminal (1);Cadherin (4);	0.577641	0.19689	N	0.108338	T	0.13841	0.0335	L	0.57130	1.785	0.09310	N	1	B	0.12013	0.005	B	0.13407	0.009	T	0.20874	-1.0262	10	0.49607	T	0.09	.	9.9206	0.41462	0.5973:0.0:0.4027:0.0	.	80	Q9NPG4	PCD12_HUMAN	E	80	ENSP00000231484:D80E	ENSP00000231484:D80E	D	-	3	2	PCDH12	141317361	0.000000	0.05858	0.007000	0.13788	0.138000	0.21146	-1.159000	0.03150	-0.212000	0.10109	0.563000	0.77884	GAC	G|0.986;C|0.014	0.014	strong		0.637	PCDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251858.1	NM_016580	
TGFBRAP1	9392	hgsc.bcm.edu	37	2	105924731	105924731	+	Missense_Mutation	SNP	C	C	G	rs201941079		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:105924731C>G	ENST00000393359.2	-	2	454	c.28G>C	c.(28-30)Gtc>Ctc	p.V10L	TGFBRAP1_ENST00000258449.1_Missense_Mutation_p.V10L			Q8WUH2	TGFA1_HUMAN	transforming growth factor, beta receptor associated protein 1	10					intracellular protein transport (GO:0006886)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|membrane (GO:0016020)	SMAD binding (GO:0046332)|small GTPase regulator activity (GO:0005083)|transforming growth factor beta receptor binding (GO:0005160)			central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(11)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	31						ACAGCAGAGACAAGCGTAAAG	0.522																																					p.V10L	Esophageal Squamous(183;794 2019 9730 21801 48859)	Atlas-SNP	.											.	TGFBRAP1	70	.	0			c.G28C						PASS	.	C	LEU/VAL,LEU/VAL	0,4406		0,0,2203	36.0	36.0	36.0		28,28	4.8	1.0	2		36	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	TGFBRAP1	NM_001142621.1,NM_004257.4	32,32	0,3,6500	GG,GC,CC		0.0349,0.0,0.0231	probably-damaging,probably-damaging	10/861,10/861	105924731	3,13003	2203	4300	6503	SO:0001583	missense	9392	exon2			CAGAGACAAGCGT	AF022795	CCDS2067.1	2q12.1	2008-02-05			ENSG00000135966	ENSG00000135966			16836	protein-coding gene	gene with protein product		606237				9545258, 11278302	Standard	NM_001142621		Approved	TRAP-1, TRAP1	uc002tcr.4	Q8WUH2	OTTHUMG00000130809	ENST00000393359.2:c.28G>C	2.37:g.105924731C>G	ENSP00000377027:p.Val10Leu	58.0	0.0	0		56.0	23.0	0.410714	NM_004257	A8K5R7|D3DVJ8|O60466	Missense_Mutation	SNP	ENST00000393359.2	37	CCDS2067.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	20.4	3.979858	0.74360	0.0	3.49E-4	ENSG00000135966	ENST00000393359;ENST00000258449	T;T	0.49139	0.79;0.79	4.82	4.82	0.62117	.	0.000000	0.85682	D	0.000000	T	0.44265	0.1285	M	0.67953	2.075	0.80722	D	1	B	0.31968	0.349	B	0.24848	0.056	T	0.42949	-0.9421	10	0.10377	T	0.69	-44.8777	18.4493	0.90697	0.0:1.0:0.0:0.0	.	10	Q8WUH2	TGFA1_HUMAN	L	10	ENSP00000377027:V10L;ENSP00000258449:V10L	ENSP00000258449:V10L	V	-	1	0	TGFBRAP1	105291163	1.000000	0.71417	0.981000	0.43875	0.983000	0.72400	5.892000	0.69790	2.654000	0.90174	0.655000	0.94253	GTC	C|0.999;G|0.001	0.001	strong		0.522	TGFBRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253354.2	NM_004257	
SERPIND1	3053	hgsc.bcm.edu	37	22	21134023	21134023	+	Silent	SNP	G	G	A	rs35646566	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr22:21134023G>A	ENST00000215727.5	+	2	706	c.423G>A	c.(421-423)ctG>ctA	p.L141L	PI4KA_ENST00000572273.1_Intron|SERPIND1_ENST00000406799.1_Silent_p.L141L|PI4KA_ENST00000466162.1_Intron|PI4KA_ENST00000255882.6_Intron	NM_000185.3	NP_000176.2	P05546	HEP2_HUMAN	serpin peptidase inhibitor, clade D (heparin cofactor), member 1	141					blood coagulation (GO:0007596)|chemotaxis (GO:0006935)|negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|heparin binding (GO:0008201)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(11;6.16e-25)|all_epithelial(7;1.02e-22)|Melanoma(16;0.000465)|Ovarian(15;0.00167)|Colorectal(54;0.0332)|all_neural(72;0.142)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000536)|Lung(15;0.0108)|Epithelial(17;0.196)		Ardeparin(DB00407)|Sulodexide(DB06271)	ACCGAGTGCTGAAAGACCAGG	0.493													G|||	52	0.0103834	0.0	0.013	5008	,	,		20876	0.0		0.0268	False		,,,				2504	0.0164				p.L141L		Atlas-SNP	.											.	SERPIND1	92	.	0			c.G423A						PASS	.	G	,	25,4381	31.7+/-61.6	0,25,2178	96.0	81.0	86.0		423,	-0.4	0.2	22	dbSNP_126	86	242,8358	96.6+/-158.3	5,232,4063	no	coding-synonymous,intron	SERPIND1,PI4KA	NM_000185.3,NM_058004.3	,	5,257,6241	AA,AG,GG		2.814,0.5674,2.0529	,	141/500,	21134023	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	3053	exon2			AGTGCTGAAAGAC	M12849	CCDS13783.1	22q11.21	2014-02-18	2005-08-18		ENSG00000099937	ENSG00000099937		"""Serine (or cysteine) peptidase inhibitors"""	4838	protein-coding gene	gene with protein product	"""heparin cofactor II"""	142360	"""serine (or cysteine) proteinase inhibitor, clade D (heparin cofactor), member 1"""	HCF2		1671335, 24172014	Standard	XM_005261597		Approved	HC-II, HLS2, HC2, D22S673	uc002ztb.1	P05546	OTTHUMG00000150755	ENST00000215727.5:c.423G>A	22.37:g.21134023G>A		168.0	0.0	0		185.0	92.0	0.497297	NM_000185	B2RAI1|D3DX34|Q6IBZ5	Silent	SNP	ENST00000215727.5	37	CCDS13783.1																																																																																			G|0.984;A|0.016	0.016	strong		0.493	SERPIND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319961.1	NM_000185	
NAB2	4665	hgsc.bcm.edu	37	12	57485291	57485291	+	Missense_Mutation	SNP	G	G	A	rs140433833	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:57485291G>A	ENST00000300131.3	+	2	845	c.467G>A	c.(466-468)cGc>cAc	p.R156H	NAB2_ENST00000554718.1_3'UTR|NAB2_ENST00000357680.4_Missense_Mutation_p.R156H|NAB2_ENST00000342556.6_Missense_Mutation_p.R156H	NM_005967.3	NP_005958.1	Q15742	NAB2_HUMAN	NGFI-A binding protein 2 (EGR1 binding protein 2)	156					cell proliferation (GO:0008283)|endochondral ossification (GO:0001958)|myelination (GO:0042552)|negative regulation of transcription from RNA polymerase III promoter (GO:0016480)|nervous system development (GO:0007399)|regulation of epidermis development (GO:0045682)|Schwann cell differentiation (GO:0014037)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(5)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	20						GGCAGTGCCCGCAGTTTTAGC	0.632													G|||	12	0.00239617	0.0076	0.0029	5008	,	,		16784	0.0		0.0	False		,,,				2504	0.0				p.R156H		Atlas-SNP	.											NAB2,NS,carcinoma,-1,1	NAB2	47	1	0			c.G467A						PASS	.	G	HIS/ARG	13,4393	21.2+/-45.6	0,13,2190	55.0	56.0	56.0		467	4.2	1.0	12	dbSNP_134	56	5,8595	5.0+/-18.6	0,5,4295	yes	missense	NAB2	NM_005967.3	29	0,18,6485	AA,AG,GG		0.0581,0.2951,0.1384	probably-damaging	156/526	57485291	18,12988	2203	4300	6503	SO:0001583	missense	4665	exon2			GTGCCCGCAGTTT	BC065931	CCDS8930.1	12q13.3	2008-05-14				ENSG00000166886			7627	protein-coding gene	gene with protein product		602381				8668170, 8649813	Standard	XM_005268894		Approved	MADER	uc001smz.3	Q15742		ENST00000300131.3:c.467G>A	12.37:g.57485291G>A	ENSP00000300131:p.Arg156His	51.0	0.0	0		41.0	23.0	0.560976	NM_005967	B2RAK3|O76006|Q14797	Missense_Mutation	SNP	ENST00000300131.3	37	CCDS8930.1	9	0.004120879120879121	7	0.014227642276422764	2	0.0055248618784530384	0	0.0	0	0.0	G	16.63	3.176780	0.57692	0.002951	5.81E-4	ENSG00000166886	ENST00000300131;ENST00000342556;ENST00000357680	.	.	.	4.18	4.18	0.49190	.	0.433911	0.21867	N	0.067954	T	0.32315	0.0825	N	0.14661	0.345	0.49051	D	0.999745	D	0.59767	0.986	P	0.46299	0.511	T	0.35325	-0.9793	9	0.46703	T	0.11	-8.9058	14.0515	0.64739	0.0:0.0:1.0:0.0	.	156	Q15742	NAB2_HUMAN	H	156	.	ENSP00000300131:R156H	R	+	2	0	NAB2	55771558	0.991000	0.36638	0.997000	0.53966	0.957000	0.61999	1.829000	0.39121	2.156000	0.67533	0.462000	0.41574	CGC	G|0.997;A|0.003	0.003	strong		0.632	NAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412222.1	NM_005967	
ZNF626	199777	hgsc.bcm.edu	37	19	20808418	20808418	+	Missense_Mutation	SNP	G	G	C	rs8111015	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:20808418G>C	ENST00000601440.1	-	4	411	c.265C>G	c.(265-267)Cag>Gag	p.Q89E	CTC-513N18.7_ENST00000595094.1_lincRNA	NM_001076675.2	NP_001070143.1	Q68DY1	ZN626_HUMAN	zinc finger protein 626	89			Q -> E (in dbSNP:rs8111015).		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)|endometrium(1)|lung(3)|skin(1)	6						TTCATGCTCTGCTCTGGCCAA	0.313													N|||	363	0.072484	0.2436	0.0259	5008	,	,		17032	0.0		0.0139	False		,,,				2504	0.0092				p.Q89E		Atlas-SNP	.											.	ZNF626	121	.	0			c.C265G						PASS	.	G	GLU/GLN	758,3578		90,578,1500	50.0	56.0	54.0		265	1.1	0.0	19	dbSNP_116	54	82,8474		3,76,4199	no	missense	ZNF626	NM_001076675.2	29	93,654,5699	CC,CG,GG		0.9584,17.4815,6.5157	benign	89/529	20808418	840,12052	2168	4278	6446	SO:0001583	missense	199777	exon4			TGCTCTGCTCTGG	BC007116	CCDS32976.1, CCDS42535.1	19p13.11	2013-01-08				ENSG00000188171		"""Zinc fingers, C2H2-type"", ""-"""	30461	protein-coding gene	gene with protein product						12477932	Standard	NM_145297		Approved		uc002npb.1	Q68DY1		ENST00000601440.1:c.265C>G	19.37:g.20808418G>C	ENSP00000469958:p.Gln89Glu	85.0	0.0	0		118.0	48.0	0.40678	NM_001076675	Q8N8T4|Q96QM1	Missense_Mutation	SNP	ENST00000601440.1	37	CCDS42535.1	140	0.0641025641025641	119	0.241869918699187	10	0.027624309392265192	0	0.0	11	0.014511873350923483	N	7.931	0.740652	0.15642	0.174815	0.009584	ENSG00000188171	ENST00000392298;ENST00000453075;ENST00000305570	.	.	.	1.08	1.08	0.20341	.	.	.	.	.	T	0.00039	0.0001	M	0.91818	3.245	0.58432	P	1.999999999946489E-6	B	0.20780	0.048	B	0.29524	0.103	T	0.10474	-1.0628	7	0.37606	T	0.19	.	7.5639	0.27868	0.0:0.0:1.0:0.0	rs8111015;rs8111015	89	Q68DY1	ZN626_HUMAN	E	89;13;89	.	ENSP00000445201:Q89E	Q	-	1	0	ZNF626	20600258	0.000000	0.05858	0.014000	0.15608	0.369000	0.29798	-0.692000	0.05127	0.503000	0.28060	0.289000	0.19496	CAG	G|0.944;C|0.056	0.056	strong		0.313	ZNF626-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447845.2	NM_145297	
SVEP1	79987	hgsc.bcm.edu	37	9	113169619	113169619	+	Missense_Mutation	SNP	A	A	G	rs199899670	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:113169619A>G	ENST00000401783.2	-	38	8597	c.8261T>C	c.(8260-8262)tTa>tCa	p.L2754S	SVEP1_ENST00000297826.5_Missense_Mutation_p.L680S|SVEP1_ENST00000374469.1_Missense_Mutation_p.L2731S	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	2754	Sushi 22. {ECO:0000255|PROSITE- ProRule:PRU00302}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						ACAAAGCCTTAAGTCAGAGCC	0.453													A|||	8	0.00159744	0.0	0.0	5008	,	,		22575	0.0		0.002	False		,,,				2504	0.0061				p.L2754S		Atlas-SNP	.											.	SVEP1	326	.	0			c.T8261C						PASS	.	A	SER/LEU	0,3978		0,0,1989	76.0	80.0	79.0		8261	1.0	0.0	9	dbSNP_132	79	12,8300		0,12,4144	yes	missense	SVEP1	NM_153366.3	145	0,12,6133	GG,GA,AA		0.1444,0.0,0.0976	benign	2754/3572	113169619	12,12278	1989	4156	6145	SO:0001583	missense	79987	exon38			AGCCTTAAGTCAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.8261T>C	9.37:g.113169619A>G	ENSP00000384917:p.Leu2754Ser	264.0	0.0	0		260.0	121.0	0.465385	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	37	CCDS48004.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0.008	-1.912475	0.00508	0.0	0.001444	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000297826;ENST00000374463	T;T;T	0.63255	-0.03;-0.03;-0.03	5.87	0.967	0.19674	Complement control module (2);Sushi/SCR/CCP (3);	0.805314	0.12128	N	0.497090	T	0.28134	0.0694	N	0.04387	-0.21	0.09310	N	1	B	0.20164	0.042	B	0.25506	0.061	T	0.30679	-0.9970	10	0.06494	T	0.89	.	0.0954	0.00043	0.2867:0.1649:0.2327:0.3157	.	2754	Q4LDE5	SVEP1_HUMAN	S	2754;2731;680;426	ENSP00000384917:L2754S;ENSP00000363593:L2731S;ENSP00000297826:L680S	ENSP00000297826:L680S	L	-	2	0	SVEP1	112209440	0.073000	0.21202	0.001000	0.08648	0.119000	0.20118	2.094000	0.41719	1.062000	0.40625	0.477000	0.44152	TTA	A|0.998;G|0.002	0.002	strong		0.453	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
ARHGAP21	57584	hgsc.bcm.edu	37	10	24908668	24908668	+	Missense_Mutation	SNP	T	T	C	rs142573508	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:24908668T>C	ENST00000396432.2	-	9	2642	c.2156A>G	c.(2155-2157)cAa>cGa	p.Q719R	ARHGAP21_ENST00000320481.6_Missense_Mutation_p.Q506R	NM_020824.3	NP_065875.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 21	718					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(17)|lung(21)|ovary(7)|pancreas(1)|prostate(5)|skin(2)|stomach(2)|urinary_tract(1)	78						TTCAGCCTCTTGTAAACTTAA	0.453													T|||	11	0.00219649	0.0	0.0	5008	,	,		19618	0.0		0.0	False		,,,				2504	0.0112				p.Q719R		Atlas-SNP	.											.	ARHGAP21	185	.	0			c.A2156G						PASS	.	T	ARG/GLN	0,4406		0,0,2203	61.0	58.0	59.0		2156	-2.6	0.0	10	dbSNP_134	59	2,8598	2.2+/-6.3	0,2,4298	no	missense	ARHGAP21	NM_020824.3	43	0,2,6501	CC,CT,TT		0.0233,0.0,0.0154	benign	719/1959	24908668	2,13004	2203	4300	6503	SO:0001583	missense	57584	exon9			GCCTCTTGTAAAC	AF480466	CCDS7144.2	10p12.31	2013-01-10			ENSG00000107863	ENSG00000107863		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	23725	protein-coding gene	gene with protein product		609870				12056806	Standard	NM_020824		Approved	KIAA1424, ARHGAP10	uc001isb.2	Q5T5U3	OTTHUMG00000017825	ENST00000396432.2:c.2156A>G	10.37:g.24908668T>C	ENSP00000379709:p.Gln719Arg	154.0	0.0	0		143.0	65.0	0.454545	NM_020824	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000396432.2	37	CCDS7144.2	.	.	.	.	.	.	.	.	.	.	T	4.856	0.159203	0.09236	0.0	2.33E-4	ENSG00000107863	ENST00000396432;ENST00000320481;ENST00000376410;ENST00000446003;ENST00000445703	T;T;T;T	0.41065	1.01;1.01;1.01;1.01	5.1	-2.62	0.06152	.	1.071100	0.07121	N	0.843866	T	0.24774	0.0601	L	0.31294	0.92	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.24190	-1.0167	10	0.16420	T	0.52	.	5.0428	0.14467	0.1188:0.0718:0.4868:0.3226	.	709;718	F8W9U9;Q5T5U3	.;RHG21_HUMAN	R	719;506;709;719;554	ENSP00000379709:Q719R;ENSP00000365604:Q506R;ENSP00000365592:Q709R;ENSP00000405018:Q719R	ENSP00000365604:Q506R	Q	-	2	0	ARHGAP21	24948674	0.004000	0.15560	0.043000	0.18650	0.866000	0.49608	0.189000	0.17037	-0.256000	0.09473	0.533000	0.62120	CAA	T|1.000;C|0.000	0.000	strong		0.453	ARHGAP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047229.4	NM_020824	
MKI67	4288	hgsc.bcm.edu	37	10	129904286	129904286	+	Missense_Mutation	SNP	G	G	A	rs146273614	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr10:129904286G>A	ENST00000368654.3	-	13	6193	c.5818C>T	c.(5818-5820)Cgg>Tgg	p.R1940W	MKI67_ENST00000368653.3_Missense_Mutation_p.R1580W	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	1940	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GTTTGTGGCCGTCTCTTGCTG	0.493													G|||	15	0.00299521	0.0	0.0072	5008	,	,		18668	0.0		0.0089	False		,,,				2504	0.001				p.R1940W		Atlas-SNP	.											.	MKI67	363	.	0			c.C5818T						PASS	.	G	TRP/ARG,TRP/ARG	7,4399	14.3+/-33.2	0,7,2196	173.0	179.0	177.0		4738,5818	-8.8	0.0	10	dbSNP_134	177	78,8522	46.7+/-105.8	0,78,4222	no	missense,missense	MKI67	NM_001145966.1,NM_002417.4	101,101	0,85,6418	AA,AG,GG		0.907,0.1589,0.6535	benign,benign	1580/2897,1940/3257	129904286	85,12921	2203	4300	6503	SO:0001583	missense	4288	exon13			GTGGCCGTCTCTT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.5818C>T	10.37:g.129904286G>A	ENSP00000357643:p.Arg1940Trp	348.0	0.0	0		403.0	163.0	0.404467	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	9.208	1.030151	0.19512	0.001589	0.00907	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02446	4.29;4.29	4.42	-8.82	0.00810	.	.	.	.	.	T	0.01320	0.0043	L	0.35854	1.095	0.09310	N	1	B;B;B	0.30104	0.006;0.268;0.012	B;B;B	0.21360	0.005;0.034;0.005	T	0.26950	-1.0088	9	0.59425	D	0.04	.	4.3783	0.11281	0.1014:0.0852:0.3233:0.4901	.	1939;1580;1940	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	W	1940;1580;1939	ENSP00000357643:R1940W;ENSP00000357642:R1580W	ENSP00000357642:R1580W	R	-	1	2	MKI67	129794276	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.725000	0.01863	-2.749000	0.00375	-2.677000	0.00143	CGG	G|0.994;A|0.006	0.006	strong		0.493	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
LRCH1	23143	hgsc.bcm.edu	37	13	47279258	47279258	+	Missense_Mutation	SNP	G	G	T	rs11617392	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr13:47279258G>T	ENST00000389798.3	+	12	1653	c.1456G>T	c.(1456-1458)Gca>Tca	p.A486S	LRCH1_ENST00000311191.6_Missense_Mutation_p.A486S|LRCH1_ENST00000389797.3_Missense_Mutation_p.A486S	NM_015116.2	NP_055931	Q9Y2L9	LRCH1_HUMAN	leucine-rich repeats and calponin homology (CH) domain containing 1	486			A -> S (in dbSNP:rs11617392).							breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		all_lung(13;5.61e-07)|Lung NSC(96;0.000117)|Breast(56;0.000141)|Prostate(109;0.0029)|Lung SC(185;0.0367)|Myeloproliferative disorder(33;0.0505)|Hepatocellular(98;0.0556)	KIRC - Kidney renal clear cell carcinoma(16;0.234)	GBM - Glioblastoma multiforme(144;0.000123)		TATGGGATCAGCAGAAGCCTT	0.294													G|||	39	0.00778754	0.0008	0.0072	5008	,	,		17206	0.0		0.0288	False		,,,				2504	0.0041				p.A486S		Atlas-SNP	.											.	LRCH1	104	.	0			c.G1456T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	26,4380	32.6+/-62.9	0,26,2177	112.0	124.0	120.0		1456,1456,1456	5.1	0.9	13	dbSNP_120	120	273,8327	102.5+/-163.7	4,265,4031	yes	missense,missense,missense	LRCH1	NM_001164211.1,NM_001164213.1,NM_015116.2	99,99,99	4,291,6208	TT,TG,GG		3.1744,0.5901,2.2989	benign,benign,benign	486/764,486/697,486/729	47279258	299,12707	2203	4300	6503	SO:0001583	missense	23143	exon12			GGATCAGCAGAAG	AB023233	CCDS31972.1, CCDS53865.1, CCDS53866.1	13q14.11	2008-02-05	2004-05-27	2004-05-28	ENSG00000136141	ENSG00000136141			20309	protein-coding gene	gene with protein product		610368	"""calponin homology (CH) domain containing 1"""	CHDC1		10231032	Standard	NM_015116		Approved	KIAA1016	uc001vbk.3	Q9Y2L9	OTTHUMG00000016877	ENST00000389798.3:c.1456G>T	13.37:g.47279258G>T	ENSP00000374448:p.Ala486Ser	239.0	0.0	0		214.0	93.0	0.434579	NM_015116	B7ZLL5|F8W6F0|Q17R43|Q2KHR1|Q5TBU9|Q7Z5F6|Q7Z5F7	Missense_Mutation	SNP	ENST00000389798.3	37	CCDS31972.1	30	0.013736263736263736	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	25	0.032981530343007916	G	7.774	0.708144	0.15239	0.005901	0.031744	ENSG00000136141	ENST00000311191;ENST00000389798;ENST00000389797	T;T;T	0.55052	0.54;0.59;0.59	5.95	5.1	0.69264	.	0.509560	0.21773	N	0.069329	T	0.24812	0.0602	M	0.67953	2.075	0.23186	N	0.998159	B;B;B;B	0.14805	0.0;0.011;0.001;0.011	B;B;B;B	0.17098	0.004;0.017;0.009;0.005	T	0.31806	-0.9930	10	0.09338	T	0.73	-1.0147	13.4916	0.61399	0.0:0.0:0.8433:0.1566	rs11617392;rs17281816;rs52819157;rs61459892;rs11617392	486;486;486;486	Q17R43;Q9Y2L9-2;F8W6F0;Q9Y2L9	.;.;.;LRCH1_HUMAN	S	486	ENSP00000308493:A486S;ENSP00000374448:A486S;ENSP00000374447:A486S	ENSP00000308493:A486S	A	+	1	0	LRCH1	46177259	0.993000	0.37304	0.907000	0.35723	0.457000	0.32468	1.831000	0.39141	1.490000	0.48466	0.655000	0.94253	GCA	G|0.982;T|0.018	0.018	strong		0.294	LRCH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000044824.2	NM_015116	
PCSK5	5125	hgsc.bcm.edu	37	9	78638797	78638797	+	Splice_Site	SNP	C	C	T	rs34417623	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:78638797C>T	ENST00000545128.1	+	4	1093	c.555C>T	c.(553-555)taC>taT	p.Y185Y	PCSK5_ENST00000376752.4_Splice_Site_p.Y185Y|PCSK5_ENST00000376767.3_Splice_Site_p.Y185Y	NM_001190482.1	NP_001177411.1	Q92824	PCSK5_HUMAN	proprotein convertase subtilisin/kexin type 5	185	Peptidase S8.				anterior/posterior pattern specification (GO:0009952)|cell-cell signaling (GO:0007267)|cytokine biosynthetic process (GO:0042089)|embryo implantation (GO:0007566)|embryonic digestive tract development (GO:0048566)|embryonic skeletal system development (GO:0048706)|heart development (GO:0007507)|kidney development (GO:0001822)|limb morphogenesis (GO:0035108)|nerve growth factor processing (GO:0032455)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|protein processing (GO:0016485)|renin secretion into blood stream (GO:0002001)|respiratory tube development (GO:0030323)|signal peptide processing (GO:0006465)|viral life cycle (GO:0019058)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|secretory granule (GO:0030141)	peptidase activity (GO:0008233)|peptide binding (GO:0042277)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(7)|liver(2)|lung(25)|ovary(2)|pancreas(1)|prostate(2)|skin(3)	55						TGCAAAACTACGTGAGTGTAT	0.438													C|||	43	0.00858626	0.0174	0.0029	5008	,	,		19983	0.0		0.0129	False		,,,				2504	0.0051				p.Y185Y		Atlas-SNP	.											.	PCSK5	329	.	0			c.C555T						PASS	.	C	,	42,4364	46.0+/-80.4	1,40,2162	173.0	150.0	158.0		555,555	-11.3	0.3	9	dbSNP_126	158	110,8490	58.7+/-120.3	3,104,4193	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	PCSK5	NM_001190482.1,NM_006200.3	,	4,144,6355	TT,TC,CC		1.2791,0.9532,1.1687	,	185/1861,185/914	78638797	152,12854	2203	4300	6503	SO:0001630	splice_region_variant	5125	exon4			AAACTACGTGAGT		CCDS6652.1, CCDS55320.1	9q21.13	2013-09-24			ENSG00000099139	ENSG00000099139			8747	protein-coding gene	gene with protein product		600488				7782070	Standard	NM_001190482		Approved	PC5, PC6, SPC6	uc004akc.2	Q92824	OTTHUMG00000020039	ENST00000545128.1:c.555+1C>T	9.37:g.78638797C>T		147.0	0.0	0		148.0	71.0	0.47973	NM_006200	F5H2G7|Q13527|Q96EP4	Silent	SNP	ENST00000545128.1	37	CCDS55320.1																																																																																			C|0.989;T|0.011	0.011	strong		0.438	PCSK5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			Silent
LAG3	3902	hgsc.bcm.edu	37	12	6884585	6884585	+	Missense_Mutation	SNP	A	A	T	rs149434241	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:6884585A>T	ENST00000203629.2	+	5	1261	c.928A>T	c.(928-930)Act>Tct	p.T310S	LAG3_ENST00000441671.2_Missense_Mutation_p.T310S	NM_002286.5	NP_002277.4	P18627	LAG3_HUMAN	lymphocyte-activation gene 3	310	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell activation (GO:0050868)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	antigen binding (GO:0003823)|MHC class II protein binding (GO:0042289)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17						CCTCCTGGTGACTGGAGACAA	0.627													A|||	10	0.00199681	0.0	0.0043	5008	,	,		17324	0.0		0.007	False		,,,				2504	0.0				p.T310S		Atlas-SNP	.											.	LAG3	35	.	0			c.A928T						PASS	.	A	SER/THR	5,4401	11.4+/-27.6	0,5,2198	96.0	88.0	91.0		928	-2.2	1.0	12	dbSNP_134	91	74,8526	44.5+/-102.8	1,72,4227	yes	missense	LAG3	NM_002286.5	58	1,77,6425	TT,TA,AA		0.8605,0.1135,0.6074	benign	310/526	6884585	79,12927	2203	4300	6503	SO:0001583	missense	3902	exon5			CTGGTGACTGGAG		CCDS8561.1	12p13.3	2013-01-11			ENSG00000089692	ENSG00000089692		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6476	protein-coding gene	gene with protein product		153337					Standard	NM_002286		Approved	CD223	uc001qqt.4	P18627	OTTHUMG00000169197	ENST00000203629.2:c.928A>T	12.37:g.6884585A>T	ENSP00000203629:p.Thr310Ser	184.0	0.0	0		216.0	102.0	0.472222	NM_002286	A8K7T9|Q7Z643	Missense_Mutation	SNP	ENST00000203629.2	37	CCDS8561.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	A	6.623	0.483348	0.12581	0.001135	0.008605	ENSG00000089692	ENST00000441671;ENST00000203629	T;T	0.11169	2.8;2.8	5.55	-2.19	0.07015	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.731904	0.12659	N	0.449835	T	0.03390	0.0098	L	0.34521	1.04	0.09310	N	0.999994	B;B	0.06786	0.0;0.001	B;B	0.09377	0.001;0.004	T	0.43782	-0.9370	10	0.08599	T	0.76	-1.8946	2.0189	0.03505	0.235:0.2239:0.4154:0.1257	.	310;310	P18627;Q7Z643	LAG3_HUMAN;.	S	310	ENSP00000413825:T310S;ENSP00000203629:T310S	ENSP00000203629:T310S	T	+	1	0	LAG3	6754846	0.105000	0.21958	0.992000	0.48379	0.722000	0.41435	-0.198000	0.09505	-0.199000	0.10317	-1.741000	0.00685	ACT	A|0.994;T|0.006	0.006	strong		0.627	LAG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402846.1		
HES4	57801	hgsc.bcm.edu	37	1	934951	934951	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:934951T>C	ENST00000304952.6	-	3	384	c.247A>G	c.(247-249)Atg>Gtg	p.M83V	RP11-54O7.17_ENST00000606034.1_lincRNA|HES4_ENST00000484667.2_Missense_Mutation_p.M51V|HES4_ENST00000428771.2_Missense_Mutation_p.M109V			Q9HCC6	HES4_HUMAN	hes family bHLH transcription factor 4	83	bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cell differentiation (GO:0030154)|nervous system development (GO:0007399)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription factor binding (GO:0008134)			lung(2)	2	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;9.36e-38)|OV - Ovarian serous cystadenocarcinoma(86;4.41e-23)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00237)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		CTCACGGTCATCTCCAGGATG	0.736																																					p.M109V		Atlas-SNP	.											.	HES4	9	.	0			c.A325G						PASS	.						13.0	17.0	15.0					1																	934951		2167	4263	6430	SO:0001583	missense	57801	exon2			CGGTCATCTCCAG	BC012351	CCDS5.1, CCDS44034.1	1p36	2013-10-17	2013-10-17		ENSG00000188290	ENSG00000188290		"""Basic helix-loop-helix proteins"""	24149	protein-coding gene	gene with protein product		608060	"""hairy and enhancer of split 4 (Drosophila)"""			11260262, 15254753	Standard	NM_021170		Approved	bHLHb42	uc001aci.2	Q9HCC6	OTTHUMG00000040758	ENST00000304952.6:c.247A>G	1.37:g.934951T>C	ENSP00000304595:p.Met83Val	29.0	0.0	0		50.0	32.0	0.64	NM_001142467	Q5SVA5	Missense_Mutation	SNP	ENST00000304952.6	37	CCDS5.1	.	.	.	.	.	.	.	.	.	.	T	11.83	1.756340	0.31137	.	.	ENSG00000188290	ENST00000428771;ENST00000304952;ENST00000484667	D;D;T	0.98090	-4.71;-4.71;1.1	3.29	2.15	0.27550	Helix-loop-helix DNA-binding (5);	0.176901	0.26820	U	0.022332	D	0.97932	0.9320	M	0.86178	2.8	0.43868	D	0.996478	P;P	0.46859	0.883;0.885	P;P	0.55222	0.771;0.688	D	0.96838	0.9616	10	0.56958	D	0.05	.	9.0774	0.36531	0.0:0.0:0.1982:0.8018	.	109;83	E9PB28;Q9HCC6	.;HES4_HUMAN	V	109;83;51	ENSP00000393198:M109V;ENSP00000304595:M83V;ENSP00000425085:M51V	ENSP00000304595:M83V	M	-	1	0	HES4	924814	1.000000	0.71417	0.980000	0.43619	0.960000	0.62799	2.653000	0.46691	0.366000	0.24427	0.334000	0.21626	ATG	.	.	none		0.736	HES4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097944.1	NM_021170	
BRAT1	221927	hgsc.bcm.edu	37	7	2582878	2582878	+	Missense_Mutation	SNP	T	T	C	rs151317339	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:2582878T>C	ENST00000340611.4	-	6	1139	c.883A>G	c.(883-885)Atg>Gtg	p.M295V	BRAT1_ENST00000473879.1_5'Flank	NM_152743.3	NP_689956.2	Q6PJG6	BRAT1_HUMAN	BRCA1-associated ATM activator 1	295					response to ionizing radiation (GO:0010212)	membrane (GO:0016020)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(1)	23						AGGGGTCCCATGTGGGTGGGA	0.647													T|||	3	0.000599042	0.0023	0.0	5008	,	,		14712	0.0		0.0	False		,,,				2504	0.0				p.M295V		Atlas-SNP	.											.	BRAT1	57	.	0			c.A883G						PASS	.	T	VAL/MET	1,4405	2.1+/-5.4	0,1,2202	58.0	61.0	60.0		883	4.0	0.0	7	dbSNP_134	60	5,8595	3.7+/-12.6	0,5,4295	yes	missense	BRAT1	NM_152743.3	21	0,6,6497	CC,CT,TT		0.0581,0.0227,0.0461	benign	295/822	2582878	6,13000	2203	4300	6503	SO:0001583	missense	221927	exon6			GTCCCATGTGGGT	BC015632	CCDS5334.1	7p22.3	2011-03-22	2011-02-28	2011-03-22	ENSG00000106009	ENSG00000106009			21701	protein-coding gene	gene with protein product	"""BRCA1-associated protein required for ATM activation protein 1"""	614506	"""chromosome 7 open reading frame 27"""	C7orf27, BAAT1		16452482	Standard	NM_152743		Approved	MGC22916	uc003smi.3	Q6PJG6	OTTHUMG00000119091	ENST00000340611.4:c.883A>G	7.37:g.2582878T>C	ENSP00000339637:p.Met295Val	82.0	0.0	0		94.0	47.0	0.5	NM_152743	A4D200|C9JY24|Q8IW85|Q8IZ43|Q8WVR8|Q96IV9|Q9H7J8|Q9UFA3	Missense_Mutation	SNP	ENST00000340611.4	37	CCDS5334.1	.	.	.	.	.	.	.	.	.	.	T	0.409	-0.914401	0.02415	2.27E-4	5.81E-4	ENSG00000106009	ENST00000340611	T	0.67698	-0.28	5.85	4.02	0.46733	Armadillo-type fold (1);	0.985177	0.08314	N	0.964822	T	0.43166	0.1235	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31916	-0.9926	10	0.19590	T	0.45	-0.4835	5.0952	0.14729	0.1497:0.6269:0.1447:0.0787	.	295	Q6PJG6	BRAT1_HUMAN	V	295	ENSP00000339637:M295V	ENSP00000339637:M295V	M	-	1	0	BRAT1	2549404	0.006000	0.16342	0.001000	0.08648	0.031000	0.12232	0.555000	0.23422	0.788000	0.33755	-0.146000	0.13790	ATG	T|1.000;C|0.000	0.000	strong		0.647	BRAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239305.2	NM_152743	
FKBP5	2289	hgsc.bcm.edu	37	6	35544942	35544942	+	Silent	SNP	G	G	A	rs34866878	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:35544942G>A	ENST00000539068.1	-	10	1297	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	FKBP5_ENST00000540787.1_Silent_p.N186N|FKBP5_ENST00000536438.1_Silent_p.N365N|FKBP5_ENST00000357266.4_Silent_p.N365N	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	365					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						ACTCAAACTCGTTCATGAGCA	0.483													G|||	334	0.0666933	0.2239	0.0245	5008	,	,		18453	0.001		0.0179	False		,,,				2504	0.002				p.N365N		Atlas-SNP	.											.	FKBP5	64	.	0			c.C1095T						PASS	.	G	,,	815,3591	326.1+/-299.4	68,679,1456	161.0	154.0	156.0		1095,1095,1095	-3.6	0.8	6	dbSNP_126	156	225,8375	92.8+/-154.8	5,215,4080	no	coding-synonymous,coding-synonymous,coding-synonymous	FKBP5	NM_001145775.1,NM_001145776.1,NM_004117.3	,,	73,894,5536	AA,AG,GG		2.6163,18.4975,7.9963	,,	365/458,365/458,365/458	35544942	1040,11966	2203	4300	6503	SO:0001819	synonymous_variant	2289	exon11			AAACTCGTTCATG	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"""Tetratricopeptide (TTC) repeat domain containing"""	3721	protein-coding gene	gene with protein product		602623	"""FK506-binding protein 5"""			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.1095C>T	6.37:g.35544942G>A		198.0	0.0	0		206.0	82.0	0.398058	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	37	CCDS4808.1																																																																																			G|0.928;A|0.072	0.072	strong		0.483	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2		
GP6	51206	hgsc.bcm.edu	37	19	55539094	55539094	+	Silent	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:55539094G>A	ENST00000417454.1	-	4	489	c.462C>T	c.(460-462)taC>taT	p.Y154Y	CTC-550B14.7_ENST00000593060.1_RNA|GP6_ENST00000333884.2_Silent_p.Y154Y|CTC-550B14.7_ENST00000586961.1_RNA|GP6_ENST00000310373.3_Silent_p.Y154Y|CTC-550B14.7_ENST00000586845.1_RNA|CTC-550B14.6_ENST00000585492.1_RNA	NM_016363.4	NP_057447	Q9HCN6	GPVI_HUMAN	glycoprotein VI (platelet)	154	Ig-like C2-type 2.				blood coagulation (GO:0007596)|enzyme linked receptor protein signaling pathway (GO:0007167)|leukocyte migration (GO:0050900)|platelet activation (GO:0030168)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|tetraspanin-enriched microdomain (GO:0097197)	collagen binding (GO:0005518)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(2)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19			BRCA - Breast invasive adenocarcinoma(297;0.156)	GBM - Glioblastoma multiforme(193;0.0515)		CGGGATTCTTGTAGGGCGCAG	0.587																																					p.Y154Y		Atlas-SNP	.											.	GP6	55	.	0			c.C462T						PASS	.						77.0	86.0	83.0					19																	55539094		1985	4171	6156	SO:0001819	synonymous_variant	51206	exon4			ATTCTTGTAGGGC	AB035073	CCDS42626.1, CCDS46184.1, CCDS58678.1	19q13.4	2013-01-29			ENSG00000088053	ENSG00000088053		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14388	protein-coding gene	gene with protein product		605546				11027634	Standard	NM_001083899		Approved	GPVI	uc002qil.3	Q9HCN6	OTTHUMG00000159709	ENST00000417454.1:c.462C>T	19.37:g.55539094G>A		98.0	0.0	0		92.0	50.0	0.543478	NM_016363	Q9HCN7|Q9UIF2	Silent	SNP	ENST00000417454.1	37	CCDS46184.1																																																																																			.	.	none		0.587	GP6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000357006.1		
GNPTG	84572	hgsc.bcm.edu	37	16	1411894	1411894	+	Silent	SNP	G	G	A	rs76594024	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:1411894G>A	ENST00000204679.4	+	5	298	c.255G>A	c.(253-255)ccG>ccA	p.P85P	LA16c-316G12.2_ENST00000569831.1_RNA	NM_032520.4	NP_115909.1	Q9UJJ9	GNPTG_HUMAN	N-acetylglucosamine-1-phosphate transferase, gamma subunit	85	PRKCSH.				carbohydrate phosphorylation (GO:0046835)|N-glycan processing to lysosome (GO:0016256)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)	protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(2)	7		Hepatocellular(780;0.0893)				AGTTCTGCCCGTTCCACAACG	0.657													G|||	11	0.00219649	0.0015	0.0029	5008	,	,		15450	0.0		0.007	False		,,,				2504	0.0				p.P85P		Atlas-SNP	.											.	GNPTG	18	.	0			c.G255A						PASS	.	G		23,4375	29.9+/-59.1	0,23,2176	58.0	53.0	54.0		255	-10.0	0.0	16	dbSNP_131	54	71,8529	42.6+/-100.3	0,71,4229	no	coding-synonymous	GNPTG	NM_032520.4		0,94,6405	AA,AG,GG		0.8256,0.523,0.7232		85/306	1411894	94,12904	2199	4300	6499	SO:0001819	synonymous_variant	84572	exon5			CTGCCCGTTCCAC	BC014592	CCDS10436.1	16p13.3	2009-04-17		2004-10-01	ENSG00000090581	ENSG00000090581			23026	protein-coding gene	gene with protein product	"""GlcNAc-phosphotransferase gamma-subunit"""	607838	"""N-acetylglucosamine-1-phosphotransferase, gamma subunit"", ""chromosome 16 open reading frame 27"""	GNPTAG, C16orf27		10712439	Standard	NM_032520		Approved	CAB56184, c316G12.3	uc002clm.3	Q9UJJ9	OTTHUMG00000047835	ENST00000204679.4:c.255G>A	16.37:g.1411894G>A		64.0	0.0	0		76.0	42.0	0.552632	NM_032520	B2R556|Q6XYD7|Q96L13	Silent	SNP	ENST00000204679.4	37	CCDS10436.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	0.346	-0.947731	0.02304	0.00523	0.008256	ENSG00000090581	ENST00000529110	.	.	.	5.0	-10.0	0.00425	.	.	.	.	.	T	0.31231	0.0790	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.56288	-0.8004	4	.	.	.	-13.0868	2.9834	0.05961	0.31:0.094:0.4001:0.1959	.	.	.	.	I	108	.	.	V	+	1	0	GNPTG	1351895	0.000000	0.05858	0.027000	0.17364	0.670000	0.39368	-3.271000	0.00532	-4.717000	0.00035	-1.021000	0.02439	GTT	G|0.994;A|0.006	0.006	strong		0.657	GNPTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109058.2	NM_032520	
MYH7B	57644	hgsc.bcm.edu	37	20	33586674	33586674	+	Silent	SNP	C	C	T	rs377482062		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr20:33586674C>T	ENST00000262873.7	+	33	4364	c.4272C>T	c.(4270-4272)taC>taT	p.Y1424Y		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	1382						membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			GGAGCAAGTACGAAGCAGATG	0.632																																					p.Y1424Y		Atlas-SNP	.											.	MYH7B	145	.	0			c.C4272T						PASS	.	C		3,4401	4.2+/-10.8	0,3,2199	26.0	30.0	28.0		4272	-6.0	0.8	20		28	0,8596		0,0,4298	no	coding-synonymous	MYH7B	NM_020884.3		0,3,6497	TT,TC,CC		0.0,0.0681,0.0231		1424/1984	33586674	3,12997	2202	4298	6500	SO:0001819	synonymous_variant	57644	exon35			CAAGTACGAAGCA	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.4272C>T	20.37:g.33586674C>T		131.0	0.0	0		121.0	50.0	0.413223	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Silent	SNP	ENST00000262873.7	37	CCDS42869.1																																																																																			.	.	weak		0.632	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
ST6GAL1	6480	hgsc.bcm.edu	37	3	186760591	186760591	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:186760591T>A	ENST00000169298.3	+	4	774	c.100T>A	c.(100-102)Tac>Aac	p.Y34N	ST6GAL1_ENST00000457772.2_Intron|ST6GAL1_ENST00000448044.1_Missense_Mutation_p.Y34N	NM_173216.2	NP_775323.1	P15907	SIAT1_HUMAN	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	34					cellular protein metabolic process (GO:0044267)|humoral immune response (GO:0006959)|N-acetylneuraminate metabolic process (GO:0006054)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|sialylation (GO:0097503)	extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	beta-galactoside alpha-2,6-sialyltransferase activity (GO:0003835)|sialyltransferase activity (GO:0008373)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	7	all_cancers(143;2.33e-12)|Ovarian(172;0.0339)		OV - Ovarian serous cystadenocarcinoma(80;8.53e-19)	GBM - Glioblastoma multiforme(93;0.0939)		GAAAGGGAGTTACTATGATTC	0.438																																					p.Y34N		Atlas-SNP	.											.	ST6GAL1	36	.	0			c.T100A						PASS	.						132.0	134.0	134.0					3																	186760591		2203	4300	6503	SO:0001583	missense	6480	exon3			GGGAGTTACTATG	X62822	CCDS3285.1, CCDS46973.1	3q27-q28	2013-02-26	2003-01-14	2005-02-07	ENSG00000073849	ENSG00000073849	2.4.99.1		10860	protein-coding gene	gene with protein product	"""ST6Gal I"""	109675	"""sialyltransferase 1 (beta-galactoside alpha-2,6-sialytransferase)"""	SIAT1		2408023	Standard	NM_003032		Approved		uc003frd.3	P15907	OTTHUMG00000156500	ENST00000169298.3:c.100T>A	3.37:g.186760591T>A	ENSP00000169298:p.Tyr34Asn	174.0	0.0	0		189.0	20.0	0.10582	NM_003032	A8KA14|B2R513|D3DNV3	Missense_Mutation	SNP	ENST00000169298.3	37	CCDS3285.1	.	.	.	.	.	.	.	.	.	.	T	10.93	1.489702	0.26686	.	.	ENSG00000073849	ENST00000169298;ENST00000430309;ENST00000417392;ENST00000438590;ENST00000448408;ENST00000440338;ENST00000448044;ENST00000416235;ENST00000423451;ENST00000446170	T;T	0.24350	1.86;1.86	5.44	2.95	0.34219	.	0.288497	0.39020	N	0.001500	T	0.21347	0.0514	M	0.61703	1.905	0.80722	D	1	P	0.38582	0.638	B	0.34242	0.178	T	0.04440	-1.0951	10	0.15066	T	0.55	-39.6557	9.6725	0.40021	0.0:0.0:0.3568:0.6432	.	34	P15907	SIAT1_HUMAN	N	34	ENSP00000169298:Y34N;ENSP00000389337:Y34N	ENSP00000169298:Y34N	Y	+	1	0	ST6GAL1	188243285	1.000000	0.71417	0.826000	0.32828	0.613000	0.37349	1.659000	0.37387	0.410000	0.25675	0.459000	0.35465	TAC	.	.	none		0.438	ST6GAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344399.1	NM_173216	
CCDC151	115948	hgsc.bcm.edu	37	19	11545690	11545690	+	Missense_Mutation	SNP	G	G	A	rs143295007	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:11545690G>A	ENST00000356392.4	-	1	235	c.148C>T	c.(148-150)Cca>Tca	p.P50S	PRKCSH_ENST00000252455.2_5'Flank|PRKCSH_ENST00000592741.1_5'Flank|PRKCSH_ENST00000591462.1_5'Flank|PRKCSH_ENST00000589838.1_5'Flank|CCDC151_ENST00000586836.1_Intron|CCDC151_ENST00000591179.1_Missense_Mutation_p.P50S|PRKCSH_ENST00000412601.1_5'Flank|CCDC151_ENST00000545100.1_Intron|PRKCSH_ENST00000587327.1_5'Flank	NM_145045.4	NP_659482.3	A5D8V7	CC151_HUMAN	coiled-coil domain containing 151	50										endometrium(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	12						GAACGGCCTGGGGTCCACGCC	0.597											OREG0025257	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	13	0.00259585	0.0008	0.0058	5008	,	,		18177	0.0		0.008	False		,,,				2504	0.0				p.P50S		Atlas-SNP	.											.	CCDC151	44	.	0			c.C148T						PASS	.	G	SER/PRO	3,3943		0,3,1970	68.0	73.0	72.0		148	-2.5	0.0	19	dbSNP_134	72	34,8254		1,32,4111	yes	missense	CCDC151	NM_145045.4	74	1,35,6081	AA,AG,GG		0.4102,0.076,0.3024	benign	50/596	11545690	37,12197	1973	4144	6117	SO:0001583	missense	115948	exon1			GGCCTGGGGTCCA		CCDS42501.1	19p13.2	2014-02-20				ENSG00000198003			28303	protein-coding gene	gene with protein product		615956				24067530	Standard	NM_145045		Approved	MGC20983	uc002mrs.3	A5D8V7		ENST00000356392.4:c.148C>T	19.37:g.11545690G>A	ENSP00000348757:p.Pro50Ser	88.0	0.0	0	673	86.0	39.0	0.453488	NM_145045	B4DXT0|Q96CG5	Missense_Mutation	SNP	ENST00000356392.4	37	CCDS42501.1	10	0.004578754578754579	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	6	0.0079155672823219	G	10.12	1.263504	0.23136	7.6E-4	0.004102	ENSG00000198003	ENST00000356392;ENST00000543934	T	0.10192	2.9	4.54	-2.55	0.06288	.	0.428688	0.17419	N	0.174920	T	0.02727	0.0082	N	0.11560	0.145	0.18873	N	0.999989	B;B	0.12013	0.002;0.005	B;B	0.12837	0.008;0.003	T	0.45396	-0.9264	10	0.09338	T	0.73	-5.9352	9.2378	0.37477	0.1027:0.6325:0.2648:0.0	.	50;50	B3KPH7;A5D8V7	.;CC151_HUMAN	S	50;29	ENSP00000348757:P50S	ENSP00000348757:P50S	P	-	1	0	CCDC151	11406690	0.001000	0.12720	0.000000	0.03702	0.001000	0.01503	-0.152000	0.10159	-0.084000	0.12595	0.655000	0.94253	CCA	G|0.997;A|0.003	0.003	strong		0.597	CCDC151-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458800.1	NM_145045	
SPTBN5	51332	hgsc.bcm.edu	37	15	42162467	42162467	+	Nonsense_Mutation	SNP	G	G	A	rs61750839	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:42162467G>A	ENST00000320955.6	-	31	5874	c.5647C>T	c.(5647-5649)Cga>Tga	p.R1883*		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1883					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		ACGAGTTCTCGCTCCAGCCCC	0.662													G|||	54	0.0107827	0.0	0.0101	5008	,	,		17221	0.0		0.0358	False		,,,				2504	0.0112				p.R1848X		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C5542T						PASS	.	G	stop/ARG	20,3888		0,20,1934	10.0	12.0	12.0		5542	0.3	0.1	15	dbSNP_129	12	277,7857		7,263,3797	yes	stop-gained	SPTBN5	NM_016642.2		7,283,5731	AA,AG,GG		3.4055,0.5118,2.4664		1848/3640	42162467	297,11745	1954	4067	6021	SO:0001587	stop_gained	51332	exon31			GTTCTCGCTCCAG	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.5647C>T	15.37:g.42162467G>A	ENSP00000317790:p.Arg1883*	93.0	0.0	0		110.0	70.0	0.636364	NM_016642		Nonsense_Mutation	SNP	ENST00000320955.6	37		38	0.0173992673992674	0	0.0	6	0.016574585635359115	0	0.0	32	0.04221635883905013	.	44	10.798073	0.99469	0.005118	0.034055	ENSG00000137877	ENST00000320955	.	.	.	4.63	0.285	0.15705	.	0.608014	0.15586	N	0.254650	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	4.4729	0.11720	0.2652:0.0:0.5822:0.1526	.	.	.	.	X	1883	.	ENSP00000317790:R1883X	R	-	1	2	SPTBN5	39949759	0.002000	0.14202	0.057000	0.19452	0.159000	0.22180	0.862000	0.27899	0.057000	0.16193	0.655000	0.94253	CGA	G|0.982;A|0.018	0.018	strong		0.662	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
LRRC8A	56262	hgsc.bcm.edu	37	9	131670217	131670217	+	Silent	SNP	C	C	T	rs41275930	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:131670217C>T	ENST00000259324.5	+	3	1297	c.774C>T	c.(772-774)gaC>gaT	p.D258D	LRRC8A_ENST00000372600.4_Silent_p.D258D|LRRC8A_ENST00000372599.3_Silent_p.D258D	NM_001127244.1	NP_001120716.1	Q8IWT6	LRC8A_HUMAN	leucine rich repeat containing 8 family, member A	258					anion transport (GO:0006820)|cell volume homeostasis (GO:0006884)|pre-B cell differentiation (GO:0002329)|response to osmotic stress (GO:0006970)	cell surface (GO:0009986)|ion channel complex (GO:0034702)|membrane (GO:0016020)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(8)|ovary(1)|pancreas(1)|skin(3)	28						AGGAGGGGGACATTGTGTACC	0.547													C|||	76	0.0151757	0.0008	0.0115	5008	,	,		21421	0.0		0.0099	False		,,,				2504	0.0583				p.D258D		Atlas-SNP	.											.	LRRC8A	69	.	0			c.C774T						PASS	.	C	,,	9,4397	14.3+/-33.2	0,9,2194	200.0	172.0	182.0		774,774,774	2.3	1.0	9	dbSNP_127	182	127,8473	65.3+/-127.6	0,127,4173	no	coding-synonymous,coding-synonymous,coding-synonymous	LRRC8A	NM_001127244.1,NM_001127245.1,NM_019594.3	,,	0,136,6367	TT,TC,CC		1.4767,0.2043,1.0457	,,	258/811,258/811,258/811	131670217	136,12870	2203	4300	6503	SO:0001819	synonymous_variant	56262	exon3			GGGGGACATTGTG	AB037858	CCDS35155.1	9q34.2	2014-09-17	2005-06-29	2005-06-29	ENSG00000136802	ENSG00000136802			19027	protein-coding gene	gene with protein product		608360	"""leucine rich repeat containing 8"""	LRRC8			Standard	NM_001127244		Approved	KIAA1437, FLJ10337	uc010myp.3	Q8IWT6	OTTHUMG00000020766	ENST00000259324.5:c.774C>T	9.37:g.131670217C>T		134.0	0.0	0		147.0	67.0	0.455782	NM_001127244	Q6UXM2|Q8NCI0|Q9P2B1	Silent	SNP	ENST00000259324.5	37	CCDS35155.1																																																																																			C|0.991;T|0.009	0.009	strong		0.547	LRRC8A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054516.2	NM_019594	
ABL1	25	hgsc.bcm.edu	37	9	133760106	133760106	+	Missense_Mutation	SNP	C	C	T	rs2229071	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr9:133760106C>T	ENST00000318560.5	+	11	2810	c.2429C>T	c.(2428-2430)cCg>cTg	p.P810L		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	810	Pro-rich.		P -> L (in dbSNP:rs2229071). {ECO:0000269|PubMed:17344846}.		actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GGCTCCAGCCCGCCCAACCTG	0.627			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								C|||	11	0.00219649	0.0	0.0072	5008	,	,		17189	0.0		0.004	False		,,,				2504	0.002				p.P829L		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	.	ABL1	1632	.	0			c.C2486T						PASS	.	C	LEU/PRO,LEU/PRO	6,4394		0,6,2194	16.0	20.0	18.0		2429,2486	4.8	0.9	9	dbSNP_98	18	80,8518		0,80,4219	yes	missense,missense	ABL1	NM_005157.4,NM_007313.2	98,98	0,86,6413	TT,TC,CC		0.9304,0.1364,0.6616	probably-damaging,probably-damaging	810/1131,829/1150	133760106	86,12912	2200	4299	6499	SO:0001583	missense	25	exon11			CCAGCCCGCCCAA	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2429C>T	9.37:g.133760106C>T	ENSP00000323315:p.Pro810Leu	74.0	0.0	0		74.0	42.0	0.567568	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	CCDS35166.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	14.83	2.651718	0.47362	0.001364	0.009304	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.23950	1.88;1.88	5.69	4.79	0.61399	.	0.000000	0.85682	D	0.000000	T	0.25606	0.0623	L	0.27053	0.805	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.04128	-1.0975	10	0.08837	T	0.75	.	13.6197	0.62130	0.0:0.9257:0.0:0.0743	rs2229071	810;847	P00519;Q59FK4	ABL1_HUMAN;.	L	625;829;810	ENSP00000361423:P829L;ENSP00000323315:P810L	ENSP00000323315:P810L	P	+	2	0	ABL1	132749927	1.000000	0.71417	0.922000	0.36590	0.138000	0.21146	7.563000	0.82314	1.410000	0.46936	0.561000	0.74099	CCG	C|0.995;T|0.005	0.005	strong		0.627	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
OR1I1	126370	hgsc.bcm.edu	37	19	15198666	15198666	+	Missense_Mutation	SNP	T	T	A	rs144766527	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:15198666T>A	ENST00000209540.2	+	1	876	c.790T>A	c.(790-792)Tcc>Acc	p.S264T		NM_001004713.1	NP_001004713.1	O60431	OR1I1_HUMAN	olfactory receptor, family 1, subfamily I, member 1	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(3)|ovary(2)|stomach(2)	20						ACAGCCCACATCCCCCAGCTC	0.537													T|||	28	0.00559105	0.0008	0.0101	5008	,	,		22065	0.0		0.0189	False		,,,				2504	0.001				p.S264T		Atlas-SNP	.											OR1I1,NS,malignant_melanoma,-1,1	OR1I1	58	1	0			c.T790A						PASS	.	T	THR/SER	10,4396	17.9+/-39.9	0,10,2193	112.0	91.0	98.0		790	-0.9	0.0	19	dbSNP_134	98	132,8468	67.3+/-129.8	3,126,4171	yes	missense	OR1I1	NM_001004713.1	58	3,136,6364	AA,AT,TT		1.5349,0.227,1.0918	possibly-damaging	264/356	15198666	142,12864	2203	4300	6503	SO:0001583	missense	126370	exon1			CCCACATCCCCCA	AC004794	CCDS32937.1	19p13.1	2012-08-09				ENSG00000094661		"""GPCR / Class A : Olfactory receptors"""	8207	protein-coding gene	gene with protein product							Standard	NM_001004713		Approved	OR1I1P, OR19-20, OR1I1Q	uc010xoe.2	O60431		ENST00000209540.2:c.790T>A	19.37:g.15198666T>A	ENSP00000209540:p.Ser264Thr	112.0	0.0	0		132.0	54.0	0.409091	NM_001004713	Q96R92	Missense_Mutation	SNP	ENST00000209540.2	37	CCDS32937.1	19	0.0086996336996337	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	15	0.01978891820580475	T	6.410	0.443810	0.12164	0.00227	0.015349	ENSG00000094661	ENST00000209540	T	0.00258	8.41	4.33	-0.906	0.10524	GPCR, rhodopsin-like superfamily (1);	0.721661	0.10719	U	0.641993	T	0.00073	0.0002	L	0.46567	1.45	0.09310	N	1	B	0.30914	0.3	B	0.28916	0.096	T	0.09796	-1.0658	10	0.30854	T	0.27	.	1.0468	0.01571	0.2892:0.0999:0.3283:0.2825	.	264	O60431	OR1I1_HUMAN	T	264	ENSP00000209540:S264T	ENSP00000209540:S264T	S	+	1	0	OR1I1	15059666	0.000000	0.05858	0.006000	0.13384	0.236000	0.25371	-0.466000	0.06672	-0.070000	0.12908	0.449000	0.29647	TCC	T|0.989;A|0.011	0.011	strong		0.537	OR1I1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465665.1		
TFAP2B	7021	hgsc.bcm.edu	37	6	50791444	50791444	+	Missense_Mutation	SNP	G	G	C	rs139904414		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:50791444G>C	ENST00000393655.3	+	2	575	c.406G>C	c.(406-408)Gac>Cac	p.D136H	TFAP2B_ENST00000263046.4_Missense_Mutation_p.D145H|TFAP2B_ENST00000489228.1_3'UTR	NM_003221.3	NP_003212.2	Q92481	AP2B_HUMAN	transcription factor AP-2 beta (activating enhancer binding protein 2 beta)	136					aorta morphogenesis (GO:0035909)|calcium ion homeostasis (GO:0055074)|cellular ammonia homeostasis (GO:0097275)|cellular creatinine homeostasis (GO:0097276)|cellular urea homeostasis (GO:0097277)|collecting duct development (GO:0072044)|distal tubule development (GO:0072017)|ductus arteriosus closure (GO:0097070)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|hindlimb morphogenesis (GO:0035137)|kidney development (GO:0001822)|magnesium ion homeostasis (GO:0010960)|metanephric nephron development (GO:0072210)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|phosphate ion homeostasis (GO:0055062)|positive regulation of cell proliferation (GO:0008284)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of urine volume (GO:0035810)|potassium ion homeostasis (GO:0055075)|regulation of BMP signaling pathway (GO:0030510)|regulation of cell differentiation (GO:0045595)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|renal water homeostasis (GO:0003091)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|retina layer formation (GO:0010842)|skin development (GO:0043588)|sodium ion homeostasis (GO:0055078)|sympathetic nervous system development (GO:0048485)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|cysteine-type endopeptidase inhibitor activity involved in apoptotic process (GO:0043027)|DNA binding (GO:0003677)|enhancer sequence-specific DNA binding (GO:0001158)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|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 core promoter sequence-specific DNA binding transcription factor activity (GO:0000983)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription corepressor activity (GO:0001106)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(11)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)	40	Lung NSC(77;0.156)					CTCGGGCCTTGACCCCCGGAG	0.711																																					p.D136H	Pancreas(116;1373 2332 5475 10752)	Atlas-SNP	.											.	TFAP2B	91	.	0			c.G406C						PASS	.	G	HIS/ASP	0,4398		0,0,2199	13.0	16.0	15.0		406	5.6	0.9	6	dbSNP_134	15	1,8595		0,1,4297	no	missense	TFAP2B	NM_003221.3	81	0,1,6496	CC,CG,GG		0.0116,0.0,0.0077	possibly-damaging	136/461	50791444	1,12993	2199	4298	6497	SO:0001583	missense	7021	exon2			GGCCTTGACCCCC	X95694	CCDS4934.2	6p12	2008-02-05	2001-11-28		ENSG00000008196	ENSG00000008196			11743	protein-coding gene	gene with protein product		601601	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)"""			7555706, 8661133	Standard	NM_003221		Approved	AP2-B	uc003pag.3	Q92481	OTTHUMG00000014836	ENST00000393655.3:c.406G>C	6.37:g.50791444G>C	ENSP00000377265:p.Asp136His	52.0	0.0	0		34.0	21.0	0.617647	NM_003221	Q5JYX6|Q9NQ63|Q9NU99|Q9UJI7|Q9Y214|Q9Y3K3	Missense_Mutation	SNP	ENST00000393655.3	37	CCDS4934.2	.	.	.	.	.	.	.	.	.	.	G	30	5.057098	0.93846	0.0	1.16E-4	ENSG00000008196	ENST00000393655;ENST00000344788;ENST00000263046	D;D;D	0.88201	-2.35;-2.35;-2.35	5.58	5.58	0.84498	.	0.145200	0.64402	D	0.000012	D	0.86264	0.5891	L	0.58428	1.81	0.80722	D	1	P	0.41041	0.736	B	0.41036	0.346	D	0.87780	0.2611	10	0.59425	D	0.04	-16.9265	19.5711	0.95419	0.0:0.0:1.0:0.0	.	136	Q92481	AP2B_HUMAN	H	136;134;145	ENSP00000377265:D136H;ENSP00000342252:D134H;ENSP00000263046:D145H	ENSP00000263046:D145H	D	+	1	0	TFAP2B	50899403	1.000000	0.71417	0.926000	0.36857	0.956000	0.61745	7.875000	0.87205	2.638000	0.89438	0.563000	0.77884	GAC	G|1.000;C|0.000	0.000	weak		0.711	TFAP2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040886.3	NM_003221	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144859879	144859879	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr1:144859879G>A	ENST00000369354.3	-	38	6394	c.6205C>T	c.(6205-6207)Cga>Tga	p.R2069*	PDE4DIP_ENST00000530740.1_Nonsense_Mutation_p.R2154*|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000369359.4_Nonsense_Mutation_p.R2205*|PDE4DIP_ENST00000524974.1_5'UTR|PDE4DIP_ENST00000313382.9_Nonsense_Mutation_p.R1963*|PDE4DIP_ENST00000369356.4_Nonsense_Mutation_p.R2069*			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2069					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		AGCTGCAGTCGCAGACAATTG	0.582			T	PDGFRB	MPD																																p.R2069X		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.C6205T						PASS	.						70.0	67.0	68.0					1																	144859879		2203	4298	6501	SO:0001587	stop_gained	9659	exon38			GCAGTCGCAGACA	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.6205C>T	1.37:g.144859879G>A	ENSP00000358360:p.Arg2069*	242.0	0.0	0		307.0	27.0	0.0879479	NM_014644	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Nonsense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	.	.	.	.	.	.	.	.	.	.	G	44	11.091583	0.99515	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	.	.	.	4.95	1.8	0.24995	.	.	.	.	.	.	.	.	.	.	.	0.39652	D	0.97048	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.6096	0.28122	0.0839:0.0:0.6302:0.2859	.	.	.	.	X	1963;2069;2069;2154;2205	.	ENSP00000327209:R1963X	R	-	1	2	PDE4DIP	143571236	0.995000	0.38212	0.113000	0.21522	0.000000	0.00434	0.225000	0.17757	0.604000	0.29930	-0.911000	0.02809	CGA	.	.	none		0.582	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
MLH1	4292	hgsc.bcm.edu	37	3	37089130	37089130	+	Missense_Mutation	SNP	A	A	G	rs587778949|rs35502531|rs35001569	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:37089130A>G	ENST00000231790.2	+	16	2068	c.1852A>G	c.(1852-1854)Aag>Gag	p.K618E	MLH1_ENST00000539477.1_Missense_Mutation_p.K377E|MLH1_ENST00000536378.1_Missense_Mutation_p.K377E|MLH1_ENST00000435176.1_Missense_Mutation_p.K520E|MLH1_ENST00000455445.2_Missense_Mutation_p.K377E|MLH1_ENST00000458205.2_Missense_Mutation_p.K377E	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	618	Interaction with EXO1.		K -> A (common polymorphism; requires 2 nucleotide substitutions; dbSNP:rs35502531). {ECO:0000269|PubMed:10598809, ECO:0000269|PubMed:10713887, ECO:0000269|PubMed:11726306, ECO:0000269|PubMed:11870161, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12373605, ECO:0000269|PubMed:16083711, ECO:0000269|PubMed:18033691, ECO:0000269|PubMed:9311737}.|K -> R (in colorectal cancer; dbSNP:rs63750449). {ECO:0000269|PubMed:14504054}.|K -> T (in HNPCC2; type II). {ECO:0000269|PubMed:10573010, ECO:0000269|PubMed:11839723, ECO:0000269|PubMed:12095971, ECO:0000269|PubMed:7757073, ECO:0000269|PubMed:8872463}.|Missing (in HNPCC2). {ECO:0000269|PubMed:16451135}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.K618del(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TCTGAAGAAGAAGGCTGAGAT	0.428		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	16	0.00319489	0.0008	0.0072	5008	,	,		20450	0.0		0.0099	False		,,,				2504	0.0				p.K618E		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,colon,carcinoma,-1,5	MLH1	226	5	2	Whole gene deletion(1)|Deletion - In frame(1)	ovary(1)|large_intestine(1)	c.A1852G	GRCh37	CD951778|CM973729|CM981294|CP035449|CX973308	MLH1	D|M|X	rs35001569	scavenged	.	A	GLU/LYS,GLU/LYS,GLU/LYS,GLU/LYS	9,4397	15.5+/-35.6	0,9,2194	158.0	161.0	160.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1852,1558,1129,1129	5.3	1.0	3	dbSNP_126	160	39,8561	16.6+/-54.9	0,39,4261	yes	missense,missense,missense,missense	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	56,56,56,56	0,48,6455	GG,GA,AA		0.4535,0.2043,0.3691	probably-damaging,probably-damaging,probably-damaging,probably-damaging	618/757,520/659,377/516,377/516	37089130	48,12958	2203	4300	6503	SO:0001583	missense	4292	exon16	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AAGAAGAAGGCTG	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.1852A>G	3.37:g.37089130A>G	ENSP00000231790:p.Lys618Glu	131.0	1.0	0.00763359		134.0	80.0	0.597015	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	9	0.004120879120879121	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	4	0.005277044854881266	A	24.4	4.530975	0.85706	0.002043	0.004535	ENSG00000076242	ENST00000231790;ENST00000383761;ENST00000458205;ENST00000539477;ENST00000455445;ENST00000435176;ENST00000536378	D;D;D;D;D;D	0.94613	-3.47;-3.47;-3.47;-3.47;-3.47;-3.47	5.35	5.35	0.76521	.	0.000000	0.85682	D	0.000000	D	0.96583	0.8885	M	0.91406	3.205	0.58432	D	0.999999	D;D;D;D	0.76494	0.999;0.993;0.999;0.993	D;P;D;P	0.64042	0.921;0.779;0.921;0.868	D	0.95740	0.8782	10	0.66056	D	0.02	-23.9591	15.372	0.74573	1.0:0.0:0.0:0.0	rs35001569	520;618;618;618	E9PCU2;B2R6K0;Q53GX1;P40692	.;.;.;MLH1_HUMAN	E	618;482;377;377;377;520;377	ENSP00000231790:K618E;ENSP00000402667:K377E;ENSP00000443665:K377E;ENSP00000398272:K377E;ENSP00000402564:K520E;ENSP00000444286:K377E	ENSP00000231790:K618E	K	+	1	0	MLH1	37064134	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.070000	0.76763	2.044000	0.60594	0.477000	0.44152	AAG	.	.	alt		0.428	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4446217	4446217	+	Silent	SNP	C	C	T	rs138864176	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:4446217C>T	ENST00000254718.4	-	20	3189	c.2883G>A	c.(2881-2883)acG>acA	p.T961T	MYBBP1A_ENST00000381556.2_Silent_p.T961T			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	961					cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						CCTGCGGGCCCGTGGGCATGT	0.657													C|||	11	0.00219649	0.0	0.0029	5008	,	,		16836	0.0		0.0089	False		,,,				2504	0.0				p.T961T		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.G2883A						PASS	.	C	,	4,4402	8.1+/-20.4	0,4,2199	38.0	43.0	42.0		2883,2883	-0.6	0.0	17	dbSNP_134	42	37,8563	24.6+/-71.5	0,37,4263	no	coding-synonymous,coding-synonymous	MYBBP1A	NM_001105538.1,NM_014520.3	,	0,41,6462	TT,TC,CC		0.4302,0.0908,0.3152	,	961/1333,961/1329	4446217	41,12965	2203	4300	6503	SO:0001819	synonymous_variant	10514	exon20			CGGGCCCGTGGGC	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.2883G>A	17.37:g.4446217C>T		116.0	0.0	0		96.0	49.0	0.510417	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Silent	SNP	ENST00000254718.4	37	CCDS11046.1																																																																																			C|0.997;T|0.003	0.003	strong		0.657	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
MT-ATP8	4509	hgsc.bcm.edu	37	M	8448	8448	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chrM:8448T>C	ENST00000361851.1	+	1	83	c.83T>C	c.(82-84)aTa>aCa	p.I28T	MT-TN_ENST00000387400.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TK_ENST00000387421.1_RNA|MT-TW_ENST00000387382.1_RNA|MT-CO3_ENST00000362079.2_5'Flank|MT-TA_ENST00000387392.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-ATP6_ENST00000361899.2_5'Flank|MT-TC_ENST00000387405.1_RNA|MT-TY_ENST00000387409.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-ND3_ENST00000361227.2_5'Flank|MT-ND4_ENST00000361381.2_5'Flank|MT-TS1_ENST00000387416.2_RNA			P03928	ATP8_HUMAN	mitochondrially encoded ATP synthase 8	28			M -> T. {ECO:0000269|PubMed:9461455}.		ATP catabolic process (GO:0006200)|cellular metabolic process (GO:0044237)|mitochondrial ATP synthesis coupled proton transport (GO:0042776)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) (GO:0000276)	hydrogen ion transmembrane transporter activity (GO:0015078)|transmembrane transporter activity (GO:0022857)										CCAACTAAAAATATTAAACAC	0.383																																					p.M28T		Atlas-SNP	.											.	.	.	.	0			c.T83C						PASS	.																																			SO:0001583	missense	0	exon1			TAAAAATATTAAA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000228253	ENSG00000228253		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	7415	protein-coding gene	gene with protein product		516070	"""ATP synthase 8"""	MTATP8			Standard			Approved	ATP8, A6L		P03928		ENST00000361851.1:c.83T>C	M.37:g.8448T>C	ENSP00000355265:p.Ile28Thr	2.0	0.0	0		7.0	7.0	1	ENST00000361851	Q34771	Missense_Mutation	SNP	ENST00000361851.1	37																																																																																				.	.	none		0.383	MT-ATP8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024030	
MAD2L1	4085	hgsc.bcm.edu	37	4	120981323	120981323	+	Missense_Mutation	SNP	T	T	C	rs61752608	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:120981323T>C	ENST00000296509.6	-	5	907	c.568A>G	c.(568-570)Atc>Gtc	p.I190V		NM_002358.3	NP_002349.1	Q13257	MD2L1_HUMAN	MAD2 mitotic arrest deficient-like 1 (yeast)	190	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.			I -> V (in Ref. 11; AAH70283). {ECO:0000305}.	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mitotic anaphase-promoting complex activity (GO:0060564)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	cytosol (GO:0005829)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|spindle pole (GO:0000922)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)			breast(2)|kidney(2)|large_intestine(2)|lung(3)	9						ACTTTGTGGATTGTAGTAGTA	0.378													T|||	15	0.00299521	0.0015	0.0058	5008	,	,		17896	0.0		0.006	False		,,,				2504	0.0031				p.I190V		Atlas-SNP	.											.	MAD2L1	17	.	0			c.A568G						PASS	.	T	VAL/ILE	8,4398	14.3+/-33.2	0,8,2195	119.0	116.0	117.0		568	3.9	1.0	4	dbSNP_129	117	49,8551	31.2+/-83.2	1,47,4252	no	missense	MAD2L1	NM_002358.3	29	1,55,6447	CC,CT,TT		0.5698,0.1816,0.4383	benign	190/206	120981323	57,12949	2203	4300	6503	SO:0001583	missense	4085	exon5			TGTGGATTGTAGT	U65410	CCDS3715.1	4q27	2013-01-17	2001-11-28		ENSG00000164109	ENSG00000164109			6763	protein-coding gene	gene with protein product		601467	"""MAD2 (mitotic arrest deficient, yeast, homolog)-like 1"""			8824189, 9345911	Standard	NM_002358		Approved	MAD2, HSMAD2	uc003idl.2	Q13257	OTTHUMG00000132967	ENST00000296509.6:c.568A>G	4.37:g.120981323T>C	ENSP00000296509:p.Ile190Val	107.0	0.0	0		111.0	58.0	0.522523	NM_002358	Q53F56|Q548X9|Q6IRW7|Q8IZX3	Missense_Mutation	SNP	ENST00000296509.6	37	CCDS3715.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	12.85	2.062016	0.36373	0.001816	0.005698	ENSG00000164109	ENST00000296509	.	.	.	5.13	3.94	0.45596	DNA-binding HORMA (4);	0.000000	0.85682	D	0.000000	T	0.37210	0.0995	L	0.33753	1.03	0.80722	D	1	B	0.31274	0.317	B	0.34824	0.19	T	0.16453	-1.0402	9	0.21540	T	0.41	-14.1793	11.0557	0.47915	0.0:0.0739:0.0:0.9261	rs61752608	190	Q13257	MD2L1_HUMAN	V	190	.	ENSP00000296509:I190V	I	-	1	0	MAD2L1	121200771	1.000000	0.71417	0.974000	0.42286	0.993000	0.82548	5.799000	0.69101	0.888000	0.36160	0.482000	0.46254	ATC	T|0.997;C|0.003	0.003	strong		0.378	MAD2L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256525.2		
CKAP5	9793	hgsc.bcm.edu	37	11	46789135	46789135	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:46789135G>C	ENST00000529230.1	-	27	3447	c.3401C>G	c.(3400-3402)tCt>tGt	p.S1134C	CKAP5_ENST00000312055.5_Missense_Mutation_p.S1134C|CKAP5_ENST00000415402.1_Missense_Mutation_p.S1134C|CKAP5_ENST00000354558.3_Missense_Mutation_p.S1134C			Q14008	CKAP5_HUMAN	cytoskeleton associated protein 5	1134					centrosome organization (GO:0051297)|establishment or maintenance of microtubule cytoskeleton polarity (GO:0030951)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|RNA transport (GO:0050658)|spindle organization (GO:0007051)	centrosome (GO:0005813)|cytosol (GO:0005829)|membrane (GO:0016020)|protein complex (GO:0043234)|spindle pole (GO:0000922)				breast(1)|cervix(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(13)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	43						CTTTGCTTTAGAGGATAATCC	0.328																																					p.S1134C	Ovarian(4;85 273 2202 4844 13323)	Atlas-SNP	.											.	CKAP5	134	.	0			c.C3401G						PASS	.						128.0	131.0	130.0					11																	46789135		2201	4299	6500	SO:0001583	missense	9793	exon27			GCTTTAGAGGATA		CCDS7924.1, CCDS31477.1	11p11.2	2006-09-20			ENSG00000175216	ENSG00000175216			28959	protein-coding gene	gene with protein product		611142				7788527, 8536682	Standard	NM_014756		Approved	ch-TOG, KIAA0097, TOG, TOGp	uc001ndi.2	Q14008	OTTHUMG00000166599	ENST00000529230.1:c.3401C>G	11.37:g.46789135G>C	ENSP00000432768:p.Ser1134Cys	39.0	0.0	0		48.0	23.0	0.479167	NM_001008938	Q05D70|Q0VAX7|Q0VAX8|Q14668|Q2TA89|Q6NSH4	Missense_Mutation	SNP	ENST00000529230.1	37	CCDS31477.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.568689	0.86439	.	.	ENSG00000175216	ENST00000529230;ENST00000415402;ENST00000312055;ENST00000354558	T;T;T;T	0.52754	0.66;0.65;0.65;0.65	5.7	5.7	0.88788	Armadillo-type fold (1);	0.272597	0.42964	D	0.000632	T	0.68393	0.2996	M	0.63843	1.955	0.51767	D	0.999933	D;D;D	0.71674	0.996;0.998;0.98	D;D;P	0.79108	0.947;0.992;0.706	T	0.68887	-0.5290	10	0.66056	D	0.02	-10.0808	19.8276	0.96624	0.0:0.0:1.0:0.0	.	1134;1134;1134	Q14008-3;Q14008-2;Q14008	.;.;CKAP5_HUMAN	C	1134	ENSP00000432768:S1134C;ENSP00000395302:S1134C;ENSP00000310227:S1134C;ENSP00000346566:S1134C	ENSP00000310227:S1134C	S	-	2	0	CKAP5	46745711	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	7.176000	0.77643	2.697000	0.92050	0.585000	0.79938	TCT	.	.	none		0.328	CKAP5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390679.1	NM_014756	
SLC25A40	55972	hgsc.bcm.edu	37	7	87476292	87476292	+	Silent	SNP	A	A	G			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr7:87476292A>G	ENST00000341119.5	-	8	949	c.603T>C	c.(601-603)ccT>ccC	p.P201P		NM_018843.3	NP_061331.2	Q8TBP6	S2540_HUMAN	solute carrier family 25, member 40	201					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(6)|prostate(1)|skin(1)	17	Esophageal squamous(14;0.00202)					TAAGAACAGTAGGAGCCCAGC	0.393																																					p.P201P		Atlas-SNP	.											.	SLC25A40	32	.	0			c.T603C						PASS	.						99.0	106.0	104.0					7																	87476292		2203	4300	6503	SO:0001819	synonymous_variant	55972	exon8			AACAGTAGGAGCC	AF125531	CCDS5610.1	7q21.12	2013-05-22			ENSG00000075303	ENSG00000075303		"""Solute carriers"""	29680	protein-coding gene	gene with protein product		610821				16949250	Standard	NM_018843		Approved	MCFP	uc003uje.3	Q8TBP6	OTTHUMG00000131033	ENST00000341119.5:c.603T>C	7.37:g.87476292A>G		52.0	0.0	0		74.0	4.0	0.0540541	NM_018843	A8K483|D6W5P6|Q53GB1|Q9UHR1	Silent	SNP	ENST00000341119.5	37	CCDS5610.1																																																																																			.	.	none		0.393	SLC25A40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253677.5	NM_018843	
B4GALNT4	338707	hgsc.bcm.edu	37	11	380395	380395	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr11:380395C>T	ENST00000329962.6	+	18	2819	c.2819C>T	c.(2818-2820)gCg>gTg	p.A940V		NM_178537.4	NP_848632.2	Q76KP1	B4GN4_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 4	940					metabolic process (GO:0008152)	Golgi cisterna membrane (GO:0032580)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)|N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842)			endometrium(2)|kidney(4)|large_intestine(1)|liver(2)|lung(7)|ovary(2)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(1)	24		all_cancers(49;1.59e-06)|all_epithelial(84;0.000256)|Breast(177;0.00122)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;1.56e-27)|Epithelial(43;9.31e-27)|OV - Ovarian serous cystadenocarcinoma(40;1.11e-20)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0182)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGGCCTTCGCGCCCGTGGTC	0.687																																					p.A940V		Atlas-SNP	.											B4GALNT4,NS,carcinoma,+1,1	B4GALNT4	83	1	0			c.C2819T						scavenged	.						55.0	40.0	45.0					11																	380395		2202	4299	6501	SO:0001583	missense	338707	exon18			CCTTCGCGCCCGT	AB089939	CCDS7694.1	11p15.5	2013-02-19			ENSG00000182272	ENSG00000182272	2.4.1.-	"""Beta 4-glycosyltransferases"""	26315	protein-coding gene	gene with protein product						15044014	Standard	NM_178537		Approved	FLJ25045, NGalNAc-T1	uc001lpb.3	Q76KP1	OTTHUMG00000119075	ENST00000329962.6:c.2819C>T	11.37:g.380395C>T	ENSP00000328277:p.Ala940Val	87.0	0.0	0		52.0	3.0	0.0576923	NM_178537	Q96LV2	Missense_Mutation	SNP	ENST00000329962.6	37	CCDS7694.1	.	.	.	.	.	.	.	.	.	.	c	25.9	4.682412	0.88542	.	.	ENSG00000182272	ENST00000329962	T	0.35236	1.32	3.81	3.81	0.43845	.	0.000000	0.85682	D	0.000000	T	0.41858	0.1177	M	0.67517	2.055	0.58432	D	0.99999	P	0.46512	0.879	P	0.45856	0.495	T	0.36432	-0.9748	10	0.20519	T	0.43	-32.7173	16.2551	0.82510	0.0:1.0:0.0:0.0	.	940	Q76KP1	B4GN4_HUMAN	V	940	ENSP00000328277:A940V	ENSP00000328277:A940V	A	+	2	0	B4GALNT4	370395	1.000000	0.71417	0.977000	0.42913	0.811000	0.45836	7.456000	0.80751	2.118000	0.64928	0.561000	0.74099	GCG	.	.	none		0.687	B4GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239289.2	NM_178537	
KCNH5	27133	hgsc.bcm.edu	37	14	63174700	63174700	+	Silent	SNP	G	G	A	rs142813655		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr14:63174700G>A	ENST00000322893.7	-	11	2761	c.2493C>T	c.(2491-2493)gtC>gtT	p.V831V	KCNH5_ENST00000420622.2_3'UTR	NM_139318.3	NP_647479.2	Q8NCM2	KCNH5_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 5	831					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)		CAGCTTTAGTGACATTATTCC	0.433																																					p.V831V		Atlas-SNP	.											.	KCNH5	320	.	0			c.C2493T						PASS	.	G	,	0,4406		0,0,2203	158.0	148.0	151.0		2493,	5.0	1.0	14	dbSNP_134	151	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,utr-3	KCNH5	NM_139318.3,NM_172375.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	831/989,	63174700	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	27133	exon11			TTTAGTGACATTA	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.2493C>T	14.37:g.63174700G>A		359.0	0.0	0		425.0	210.0	0.494118	NM_139318	C9JP98	Silent	SNP	ENST00000322893.7	37	CCDS9756.1																																																																																			G|1.000;A|0.000	0.000	weak		0.433	KCNH5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411747.1	NM_139318	
MUC4	4585	hgsc.bcm.edu	37	3	195508235	195508235	+	Missense_Mutation	SNP	T	T	C	rs201826718	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr3:195508235T>C	ENST00000463781.3	-	2	10675	c.10216A>G	c.(10216-10218)Acc>Gcc	p.T3406A	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3406A	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		AGAGGCATGGTGTCACCTGTG	0.587																																					p.T3406A		Atlas-SNP	.											.	MUC4	1505	.	0			c.A10216G						PASS	.						29.0	22.0	24.0					3																	195508235		686	1575	2261	SO:0001583	missense	4585	exon2			GCATGGTGTCACC	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.10216A>G	3.37:g.195508235T>C	ENSP00000417498:p.Thr3406Ala	280.0	0.0	0		364.0	28.0	0.0769231	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	t	4.225	0.040596	0.08196	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.32023	1.47;1.53	0.743	0.743	0.18347	.	.	.	.	.	T	0.10078	0.0247	N	0.08118	0	0.09310	N	1	P	0.37985	0.613	B	0.25140	0.058	T	0.17410	-1.0370	8	.	.	.	.	3.5009	0.07673	0.0:0.0:0.4186:0.5813	.	3278	E7ESK3	.	A	3406	ENSP00000417498:T3406A;ENSP00000420243:T3406A	.	T	-	1	0	MUC4	196993014	0.000000	0.05858	0.010000	0.14722	0.010000	0.07245	-1.539000	0.02202	0.077000	0.16863	0.076000	0.15429	ACC	T|0.006;C|0.994	0.994	strong		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LIMA1	51474	hgsc.bcm.edu	37	12	50571221	50571221	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr12:50571221C>T	ENST00000341247.4	-	11	2055	c.1906G>A	c.(1906-1908)Gtg>Atg	p.V636M	LIMA1_ENST00000552823.1_Missense_Mutation_p.V476M|LIMA1_ENST00000547825.1_Missense_Mutation_p.V334M|LIMA1_ENST00000394943.3_Missense_Mutation_p.V637M|LIMA1_ENST00000552491.1_Missense_Mutation_p.V333M|LIMA1_ENST00000552909.1_Missense_Mutation_p.V475M|LIMA1_ENST00000552783.1_Missense_Mutation_p.V477M	NM_001113546.1|NM_016357.4	NP_001107018.1|NP_057441.1	Q9UHB6	LIMA1_HUMAN	LIM domain and actin binding 1	636					actin filament bundle assembly (GO:0051017)|negative regulation of actin filament depolymerization (GO:0030835)|ruffle organization (GO:0031529)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)|actin monomer binding (GO:0003785)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(2)	44						GCATTTTCCACTTGTTTCCTT	0.463																																					p.V637M		Atlas-SNP	.											.	LIMA1	67	.	0			c.G1909A						PASS	.						284.0	292.0	289.0					12																	50571221		2203	4300	6503	SO:0001583	missense	51474	exon11			TTTCCACTTGTTT	AF198454	CCDS8802.1, CCDS44877.1, CCDS55826.1, CCDS58230.1	12q13.12	2006-04-12				ENSG00000050405			24636	protein-coding gene	gene with protein product	"""epithelial protein lost in neoplasm beta"""	608364				10806352, 10618726, 12566430	Standard	NM_016357		Approved	EPLIN	uc001rwk.4	Q9UHB6		ENST00000341247.4:c.1906G>A	12.37:g.50571221C>T	ENSP00000340184:p.Val636Met	269.0	0.0	0		277.0	125.0	0.451264	NM_001113546	B2RB09|Q2TAN7|Q59FE8|Q9BVF2|Q9H8J1|Q9HBN5|Q9NX96|Q9NXC3|Q9NXU6|Q9P0H8|Q9UHB5	Missense_Mutation	SNP	ENST00000341247.4	37	CCDS8802.1	.	.	.	.	.	.	.	.	.	.	C	6.055	0.378474	0.11466	.	.	ENSG00000050405	ENST00000552491;ENST00000547825;ENST00000552823;ENST00000394943;ENST00000341247;ENST00000552783;ENST00000552909;ENST00000420992	T;T;T;D;T;T;T	0.84146	-1.07;-1.07;-1.39;-1.81;-1.07;-1.39;-1.39	5.31	1.23	0.21249	.	0.834586	0.11054	N	0.604718	T	0.65312	0.2679	N	0.03115	-0.41	0.09310	N	1	B;B;B	0.14438	0.01;0.01;0.007	B;B;B	0.15052	0.002;0.002;0.012	T	0.52305	-0.8593	10	0.22109	T	0.4	.	7.9273	0.29883	0.0:0.4745:0.0:0.5255	.	646;636;475	Q59FE8;Q9UHB6;F8VQE1	.;LIMA1_HUMAN;.	M	333;334;476;637;636;477;475;555	ENSP00000448463:V333M;ENSP00000448706:V334M;ENSP00000450266:V476M;ENSP00000378400:V637M;ENSP00000340184:V636M;ENSP00000448779:V477M;ENSP00000450087:V475M	ENSP00000340184:V636M	V	-	1	0	LIMA1	48857488	0.000000	0.05858	0.036000	0.18154	0.640000	0.38277	0.484000	0.22308	0.399000	0.25367	0.650000	0.86243	GTG	.	.	none		0.463	LIMA1-003	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406235.2	NM_016357	
CFI	3426	hgsc.bcm.edu	37	4	110682723	110682723	+	Missense_Mutation	SNP	G	G	A	rs138346388	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr4:110682723G>A	ENST00000394634.2	-	4	815	c.608C>T	c.(607-609)aCt>aTt	p.T203I	CFI_ENST00000512148.1_Missense_Mutation_p.T203I|CFI_ENST00000394635.3_Missense_Mutation_p.T203I	NM_000204.3	NP_000195	P05156	CFAI_HUMAN	complement factor I	203	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	metal ion binding (GO:0046872)|scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|skin(2)|stomach(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000331)		GTAACCCATAGTTCTTCTCTT	0.393													G|||	2	0.000399361	0.0	0.0029	5008	,	,		20003	0.0		0.0	False		,,,				2504	0.0				p.T203I		Atlas-SNP	.											.	CFI	59	.	0			c.C608T						PASS	.	G	ILE/THR	0,4406		0,0,2203	166.0	155.0	159.0		608	0.1	0.0	4	dbSNP_134	159	7,8593	5.7+/-21.5	0,7,4293	yes	missense	CFI	NM_000204.3	89	0,7,6496	AA,AG,GG		0.0814,0.0,0.0538	benign	203/584	110682723	7,12999	2203	4300	6503	SO:0001583	missense	3426	exon4			CCCATAGTTCTTC	J02770	CCDS34049.1	4q25	2014-09-17	2006-02-10	2006-02-10		ENSG00000205403	3.4.21.45	"""Complement system"""	5394	protein-coding gene	gene with protein product	"""Konglutinogen-activating factor"", ""C3b-inactivator"""	217030	"""I factor (complement)"""	IF		2956252	Standard	NM_000204		Approved	FI, C3b-INA, KAF	uc003hzr.4	P05156		ENST00000394634.2:c.608C>T	4.37:g.110682723G>A	ENSP00000378130:p.Thr203Ile	134.0	0.0	0		132.0	59.0	0.44697	NM_000204	O60442	Missense_Mutation	SNP	ENST00000394634.2	37	CCDS34049.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	8.946	0.967013	0.18659	0.0	8.14E-4	ENSG00000205403	ENST00000394635;ENST00000394634;ENST00000540104;ENST00000512148;ENST00000536228	T;T;T	0.36878	1.23;1.23;1.23	5.36	0.101	0.14517	Speract/scavenger receptor (2);Speract/scavenger receptor-related (2);	1.803530	0.01919	N	0.040391	T	0.27489	0.0675	L	0.41236	1.265	0.09310	N	1	B;B;B	0.24721	0.03;0.11;0.063	B;B;B	0.19946	0.01;0.025;0.027	T	0.10405	-1.0631	10	0.37606	T	0.19	-0.3525	1.2864	0.02052	0.1647:0.3065:0.2732:0.2555	.	203;203;203	E7ETH0;G3XAM2;P05156	.;.;CFAI_HUMAN	I	203;203;203;203;185	ENSP00000378131:T203I;ENSP00000378130:T203I;ENSP00000427438:T203I	ENSP00000378130:T203I	T	-	2	0	CFI	110902172	0.000000	0.05858	0.000000	0.03702	0.086000	0.17979	0.324000	0.19610	-0.031000	0.13781	-0.274000	0.10170	ACT	G|0.999;A|0.001	0.001	strong		0.393	CFI-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_000204	
ZNF354B	117608	hgsc.bcm.edu	37	5	178309735	178309735	+	Silent	SNP	A	A	C	rs148284462	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr5:178309735A>C	ENST00000322434.3	+	5	508	c.282A>C	c.(280-282)acA>acC	p.T94T	RNU1-39P_ENST00000383897.1_RNA	NM_058230.2	NP_478137.1	Q96LW1	Z354B_HUMAN	zinc finger protein 354B	94					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|kidney(2)|large_intestine(7)|liver(2)|lung(2)|ovary(2)|stomach(3)|urinary_tract(1)	21	all_cancers(89;0.000639)|all_epithelial(37;0.000109)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)	all_neural(177;0.00802)|Medulloblastoma(196;0.0145)|all_hematologic(541;0.248)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			CTAAAATGACAAAGTCAACTC	0.373																																					p.T94T		Atlas-SNP	.											.	ZNF354B	67	.	0			c.A282C						PASS	.	A		0,4388		0,0,2194	60.0	61.0	61.0		282	2.3	1.0	5	dbSNP_134	61	3,8587		0,3,4292	no	coding-synonymous	ZNF354B	NM_058230.2		0,3,6486	CC,CA,AA		0.0349,0.0,0.0231		94/613	178309735	3,12975	2194	4295	6489	SO:0001819	synonymous_variant	117608	exon5			AATGACAAAGTCA	AK057737	CCDS4439.1	5q35.3	2013-01-08			ENSG00000178338	ENSG00000178338		"""Zinc fingers, C2H2-type"", ""-"""	17197	protein-coding gene	gene with protein product							Standard	NM_058230		Approved	KID2, FLJ25008	uc003mjl.3	Q96LW1	OTTHUMG00000130896	ENST00000322434.3:c.282A>C	5.37:g.178309735A>C		149.0	0.0	0		160.0	70.0	0.4375	NM_058230	A8K0V2|Q5U5Z4	Silent	SNP	ENST00000322434.3	37	CCDS4439.1																																																																																			A|0.999;C|0.001	0.001	strong		0.373	ZNF354B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253482.1	NM_058230	
CPSF4L	642843	hgsc.bcm.edu	37	17	71248777	71248777	+	Silent	SNP	T	T	C	rs74909356	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr17:71248777T>C	ENST00000344935.4	-	5	550	c.489A>G	c.(487-489)caA>caG	p.Q163Q	CPSF4L_ENST00000397671.1_Silent_p.Q100Q	NM_001129885.1	NP_001123357.1	A6NMK7	CPS4L_HUMAN	cleavage and polyadenylation specific factor 4-like	163							metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|prostate(1)	2						ACTGAGCAAATTGGCACTTGG	0.493													T|||	8	0.00159744	0.0	0.0014	5008	,	,		21870	0.0		0.007	False		,,,				2504	0.0				p.Q163Q		Atlas-SNP	.											.	CPSF4L	8	.	0			c.A489G						PASS	.	T		0,1384		0,0,692	137.0	110.0	118.0		489	-3.6	0.2	17	dbSNP_132	118	10,3172		0,10,1581	no	coding-synonymous	CPSF4L	NM_001129885.1		0,10,2273	CC,CT,TT		0.3143,0.0,0.219		163/180	71248777	10,4556	692	1591	2283	SO:0001819	synonymous_variant	642843	exon5			AGCAAATTGGCAC		CCDS45768.1	17q25.1	2010-07-06			ENSG00000187959	ENSG00000187959			33632	protein-coding gene	gene with protein product							Standard	NM_001129885		Approved		uc010dfk.1	A6NMK7	OTTHUMG00000132640	ENST00000344935.4:c.489A>G	17.37:g.71248777T>C		206.0	0.0	0		164.0	79.0	0.481707	NM_001129885	A8MU95|B2RXI9	Silent	SNP	ENST00000344935.4	37	CCDS45768.1																																																																																			T|0.998;C|0.002	0.002	strong		0.493	CPSF4L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441896.1	NM_001129885	
MTHFS	10588	hgsc.bcm.edu	37	15	80189277	80189277	+	Silent	SNP	C	C	T	rs375170671	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr15:80189277C>T	ENST00000258874.3	-	1	114	c.54G>A	c.(52-54)aaG>aaA	p.K18K	ST20-MTHFS_ENST00000494999.1_Intron|ST20-MTHFS_ENST00000479961.1_Intron|MTHFS_ENST00000559722.1_Intron	NM_006441.3	NP_006432.1	P49914	MTHFS_HUMAN	5,10-methenyltetrahydrofolate synthetase (5-formyltetrahydrofolate cyclo-ligase)	18					formate metabolic process (GO:0015942)|tetrahydrofolate metabolic process (GO:0046653)	cytoplasm (GO:0005737)	5-formyltetrahydrofolate cyclo-ligase activity (GO:0030272)|ATP binding (GO:0005524)|folic acid binding (GO:0005542)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|liver(1)	5				all cancers(203;0.00467)		GCAGACGCTGCTTCAGCTCTC	0.736													C|||	8	0.00159744	0.0	0.0029	5008	,	,		11491	0.0		0.004	False		,,,				2504	0.002				p.K18K		Atlas-SNP	.											.	MTHFS	11	.	0			c.G54A						PASS	.	C	,,	3,3811		0,3,1904	6.0	6.0	6.0		,,54	4.0	1.0	15		6	24,7530		0,24,3753	no	intron,intron,coding-synonymous	MTHFS,ST20-MTHFS	NM_001199758.1,NM_001199760.1,NM_006441.3	,,	0,27,5657	TT,TC,CC		0.3177,0.0787,0.2375	,,	,,18/204	80189277	27,11341	1907	3777	5684	SO:0001819	synonymous_variant	10588	exon1			ACGCTGCTTCAGC	L38928	CCDS10311.1	15q24.3	2014-05-15			ENSG00000136371	ENSG00000136371	6.3.3.2		7437	protein-coding gene	gene with protein product		604197				8522195	Standard	NM_006441		Approved	HsT19268	uc002bex.4	P49914	OTTHUMG00000144174	ENST00000258874.3:c.54G>A	15.37:g.80189277C>T		46.0	0.0	0		19.0	15.0	0.789474	NM_006441	H3BQ75	Silent	SNP	ENST00000258874.3	37	CCDS10311.1																																																																																			.	.	weak		0.736	MTHFS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291374.2	NM_006441	
NKD1	85407	hgsc.bcm.edu	37	16	50667299	50667299	+	Silent	SNP	C	C	T	rs34100051	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr16:50667299C>T	ENST00000268459.3	+	10	1244	c.1020C>T	c.(1018-1020)gaC>gaT	p.D340D		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	340					eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GCACCCAGGACGGGAGCAAGC	0.657													C|||	55	0.0109824	0.0015	0.0245	5008	,	,		13464	0.0		0.0278	False		,,,				2504	0.0082				p.D340D		Atlas-SNP	.											.	NKD1	43	.	0			c.C1020T						PASS	.	C		18,4378	24.3+/-50.5	0,18,2180	64.0	74.0	71.0		1020	-2.4	1.0	16	dbSNP_126	71	258,8342	100.8+/-162.1	2,254,4044	no	coding-synonymous	NKD1	NM_033119.4		2,272,6224	TT,TC,CC		3.0,0.4095,2.1237		340/471	50667299	276,12720	2198	4300	6498	SO:0001819	synonymous_variant	85407	exon10			CCAGGACGGGAGC	AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"""EF-hand domain containing"""	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.1020C>T	16.37:g.50667299C>T		276.0	1.0	0.00362319		285.0	133.0	0.466667	NM_033119	B2RC39|Q8WZ08	Silent	SNP	ENST00000268459.3	37	CCDS10743.1																																																																																			C|0.981;T|0.019	0.019	strong		0.657	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1		
COL4A4	1286	hgsc.bcm.edu	37	2	228004877	228004877	+	Splice_Site	SNP	C	C	T			TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr2:228004877C>T	ENST00000396625.3	-	4	399	c.192G>A	c.(190-192)cgG>cgA	p.R64R	COL4A4_ENST00000329662.7_Splice_Site_p.R64R	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	64	7S domain.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		CATCACTTACCCGAGACCCCT	0.393																																					p.R64R		Atlas-SNP	.											COL4A4,NS,lymphoid_neoplasm,-1,2	COL4A4	215	2	0			c.G192A						PASS	.						117.0	112.0	114.0					2																	228004877		1885	4096	5981	SO:0001630	splice_region_variant	1286	exon4			ACTTACCCGAGAC		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.192+1G>A	2.37:g.228004877C>T		172.0	0.0	0		142.0	81.0	0.570423	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Silent	SNP	ENST00000396625.3	37	CCDS42828.1																																																																																			.	.	none		0.393	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	Silent
U2AF2	11338	hgsc.bcm.edu	37	19	56181019	56181019	+	Silent	SNP	C	C	T	rs147666260	byFrequency	TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr19:56181019C>T	ENST00000308924.4	+	11	1294	c.1254C>T	c.(1252-1254)ccC>ccT	p.P418P	CTD-2537I9.13_ENST00000592252.1_RNA|U2AF2_ENST00000450554.2_Silent_p.P414P|CTD-2537I9.12_ENST00000589456.1_RNA|U2AF2_ENST00000590551.1_Silent_p.P250P|CTD-2537I9.12_ENST00000585940.1_RNA			P26368	U2AF2_HUMAN	U2 small nuclear RNA auxiliary factor 2	418	RRM 3. {ECO:0000255|PROSITE- ProRule:PRU00176}.				gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	enzyme binding (GO:0019899)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|urinary_tract(2)	21		Colorectal(82;0.00244)|Ovarian(87;0.133)	BRCA - Breast invasive adenocarcinoma(297;0.18)	GBM - Glioblastoma multiforme(193;0.107)		TCGAGATCCCCCGGCCTGTGG	0.657													C|||	15	0.00299521	0.0	0.0101	5008	,	,		16186	0.0		0.008	False		,,,				2504	0.0				p.P418P		Atlas-SNP	.											.	U2AF2	62	.	0			c.C1254T						PASS	.	C	,	9,4397	15.5+/-35.6	0,9,2194	123.0	111.0	115.0		1242,1254	-0.6	1.0	19	dbSNP_134	115	87,8513	48.5+/-108.0	1,85,4214	no	coding-synonymous,coding-synonymous	U2AF2	NM_001012478.1,NM_007279.2	,	1,94,6408	TT,TC,CC		1.0116,0.2043,0.7381	,	414/472,418/476	56181019	96,12910	2203	4300	6503	SO:0001819	synonymous_variant	11338	exon11			GATCCCCCGGCCT	BC008740	CCDS12933.1, CCDS46197.1	19q13.43	2014-09-17	2006-04-11			ENSG00000063244		"""RNA binding motif (RRM) containing"""	23156	protein-coding gene	gene with protein product	"""U2 small nuclear ribonucleoprotein auxiliary factor (65kD)"", ""splicing factor U2AF 65 kD subunit"", ""U2 snRNP auxiliary factor large subunit"""	191318	"""U2 (RNU2) small nuclear RNA auxiliary factor 2"""			1538748	Standard	XM_006722994		Approved	U2AF65	uc002qlu.3	P26368		ENST00000308924.4:c.1254C>T	19.37:g.56181019C>T		125.0	0.0	0		156.0	76.0	0.487179	NM_007279	Q96HC5	Silent	SNP	ENST00000308924.4	37	CCDS12933.1																																																																																			C|0.994;T|0.006	0.006	strong		0.657	U2AF2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453599.1	NM_007279	
BCLAF1	9774	hgsc.bcm.edu	37	6	136599912	136599912	+	Missense_Mutation	SNP	G	G	T	rs200334350		TCGA-G8-6325-01A-11D-2210-10	TCGA-G8-6325-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	05e026f4-b51f-45b2-97a0-1ac81c953a07	3cfafc88-7fc2-4fe8-8f68-4787a2a933c6	g.chr6:136599912G>T	ENST00000531224.1	-	4	359	c.107C>A	c.(106-108)tCt>tAt	p.S36Y	BCLAF1_ENST00000392348.2_Intron|BCLAF1_ENST00000527536.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000530767.1_Missense_Mutation_p.S36Y|BCLAF1_ENST00000353331.4_Intron|BCLAF1_ENST00000527759.1_Intron	NM_001077441.1|NM_014739.2	NP_001070909.1|NP_055554.1	Q9NYF8	BCLF1_HUMAN	BCL2-associated transcription factor 1	36					apoptotic process (GO:0006915)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of DNA-templated transcription, initiation (GO:2000144)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of response to DNA damage stimulus (GO:2001022)|regulation of DNA-templated transcription in response to stress (GO:0043620)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|ovary(1)|skin(1)	9	Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.00226)|OV - Ovarian serous cystadenocarcinoma(155;0.00331)		ACGAGACCTAGAACTAAAAAT	0.318																																					p.S36Y	Colon(142;1534 1789 5427 7063 28491)	Atlas-SNP	.											BCLAF1_ENST00000531224,head_neck,carcinoma,-1,1	BCLAF1	203	1	0			c.C107A						scavenged	.						23.0	24.0	24.0					6																	136599912		2199	4289	6488	SO:0001583	missense	9774	exon4			GACCTAGAACTAA	AF249273	CCDS5177.1, CCDS47485.1, CCDS47486.1, CCDS75525.1	6q22-q23	2007-03-02			ENSG00000029363	ENSG00000029363			16863	protein-coding gene	gene with protein product		612588				8724849, 10330179	Standard	NM_001077440		Approved	KIAA0164, BTF	uc003qgx.1	Q9NYF8	OTTHUMG00000033323	ENST00000531224.1:c.107C>A	6.37:g.136599912G>T	ENSP00000435210:p.Ser36Tyr	29.0	1.0	0.0344828		20.0	2.0	0.1	NM_014739	A2RU75|B7ZM58|E1P586|Q14673|Q86WU6|Q86WY0	Missense_Mutation	SNP	ENST00000531224.1	37	CCDS5177.1	.	.	.	.	.	.	.	.	.	.	G	5.506	0.278344	0.10403	.	.	ENSG00000029363	ENST00000531224;ENST00000527536;ENST00000530767;ENST00000529826	T;T;T;T	0.46819	1.23;1.07;0.86;0.93	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000004	T	0.63295	0.2499	M	0.61703	1.905	0.80722	D	1	D;D	0.64830	0.994;0.994	D;D	0.74348	0.983;0.983	T	0.64245	-0.6453	10	0.87932	D	0	-6.9024	20.1392	0.98050	0.0:0.0:1.0:0.0	.	36;36	Q9NYF8;Q9NYF8-4	BCLF1_HUMAN;.	Y	36	ENSP00000435210:S36Y;ENSP00000435441:S36Y;ENSP00000436501:S36Y;ENSP00000431734:S36Y	ENSP00000435441:S36Y	S	-	2	0	BCLAF1	136641605	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.159000	0.77483	2.765000	0.95021	0.557000	0.71058	TCT	.	.	weak		0.318	BCLAF1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042375.2	NM_014739	
