#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
PERM1	84808	hgsc.bcm.edu	37	1	915431	915431	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:915431delC	ENST00000341290.2	-	3	672	c.637delG	c.(637-639)gacfs	p.D213fs	C1orf170_ENST00000433179.2_Frame_Shift_Del_p.D233fs			Q5SV97	PERM1_HUMAN		327					regulation of transcription, DNA-templated (GO:0006355)|response to muscle activity (GO:0014850)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACAGCCATGTCCCTGTCAGAT	0.597																																					.		Atlas-Indel	.											.	C1orf170	5	.	0			.						PASS	.																																			SO:0001589	frameshift_variant	84808	.			.																												ENST00000341290.2:c.637delG	1.37:g.915431delC	ENSP00000343864:p.Asp213fs	196.0	0.0	0		190.0	13.0	0.0684211	.	Q6ZVZ7|Q9BRF2|S5G239	RNA	DEL	ENST00000341290.2	37																																																																																				.	.	none		0.597	C1orf170-001	PUTATIVE	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000097943.2		
TAP1	6890	hgsc.bcm.edu	37	6	32814856	32814859	+	Frame_Shift_Del	DEL	TGTT	TGTT	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TGTT	TGTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32814856_32814859delTGTT	ENST00000354258.4	-	10	2367_2370	c.2206_2209delAACA	c.(2206-2211)aacagcfs	p.NS736fs	PSMB8_ENST00000374881.2_5'Flank|TAPSAR1_ENST00000453426.1_lincRNA|TAP1_ENST00000425148.2_Frame_Shift_Del_p.NS475fs|PSMB9_ENST00000395330.1_Intron	NM_000593.5	NP_000584.2	Q03518	TAP1_HUMAN	transporter 1, ATP-binding cassette, sub-family B (MDR/TAP)	736	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|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 peptide antigen via MHC class I (GO:0002474)|cytosol to ER transport (GO:0046967)|defense response (GO:0006952)|intracellular transport of viral protein in host cell (GO:0019060)|peptide transport (GO:0015833)|transmembrane transport (GO:0055085)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|mitochondrion (GO:0005739)|TAP complex (GO:0042825)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|MHC class Ib protein binding (GO:0023029)|peptide antigen binding (GO:0042605)|peptide transporter activity (GO:0015197)|protein homodimerization activity (GO:0042803)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(4)|prostate(1)|skin(1)	21					Lapatinib(DB01259)	TGTAACTGGCTGTTTGCATCCAGG	0.475																																					p.736_737del		Atlas-Indel	.											.	TAP1	39	.	0			c.2207_2210del						PASS	.																																			SO:0001589	frameshift_variant	6890	exon10			.		CCDS4758.1	6p21.3	2014-09-17			ENSG00000168394	ENSG00000168394		"""ATP binding cassette transporters / subfamily B"""	43	protein-coding gene	gene with protein product		170260		ABCB2		1529427, 1946428	Standard	NM_000593		Approved	PSF1, RING4, D6S114E	uc003ocg.3	Q03518	OTTHUMG00000031067	ENST00000354258.4:c.2206_2209delAACA	6.37:g.32814856_32814859delTGTT	ENSP00000346206:p.Asn736fs	28.0	0.0	0		35.0	10.0	0.285714	NM_000593	Q16149|Q96CP4	Frame_Shift_Del	DEL	ENST00000354258.4	37	CCDS4758.1																																																																																			.	.	none		0.475	TAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076087.2	NM_000593	
PROSER1	80209	hgsc.bcm.edu	37	13	39588144	39588146	+	In_Frame_Del	DEL	AGC	AGC	-	rs568365521		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AGC	AGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:39588144_39588146delAGC	ENST00000352251.3	-	11	2076_2078	c.1243_1245delGCT	c.(1243-1245)gctdel	p.A415del	PROSER1_ENST00000484434.3_Intron|PROSER1_ENST00000350125.3_In_Frame_Del_p.A393del	NM_025138.4	NP_079414.3	Q86XN7	PRSR1_HUMAN	proline and serine rich 1	415	Ser-rich.																TGCTGGTAGAAGCAGCAGAAGAG	0.522																																					p.415_416del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1244_1246del						PASS	.																																			SO:0001651	inframe_deletion	80209	exon11			.	AK022723	CCDS9368.2	13q13.2	2011-08-09	2011-08-09	2011-08-09	ENSG00000120685	ENSG00000120685			20291	protein-coding gene	gene with protein product			"""chromosome 13 open reading frame 23"""	C13orf23			Standard	NM_025138		Approved	bA50D16.2, FLJ12661	uc001uwy.4	Q86XN7	OTTHUMG00000016764	ENST00000352251.3:c.1243_1245delGCT	13.37:g.39588147_39588149delAGC	ENSP00000332034:p.Ala415del	108.0	0.0	.		113.0	37.0	0.327	NM_025138	A6NJ97|Q6P2S2|Q7Z3X5|Q8N3D2|Q8N3P1|Q9H9M1	In_Frame_Del	DEL	ENST00000352251.3	37	CCDS9368.2																																																																																			.	.	none		0.522	PROSER1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044607.5	NM_025138	
APBB2	323	hgsc.bcm.edu	37	4	41016418	41016418	+	Intron	DEL	G	G	-	rs201401961		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:41016418delG	ENST00000295974.8	-	6	649				APBB2_ENST00000513140.1_Intron|APBB2_ENST00000508593.1_Intron|APBB2_ENST00000506352.1_Intron	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2						axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						TGAGTCAGCTGGGGAAAAAAA	0.418																																					.	Ovarian(3;20 75 16686 49997)	Atlas-Indel	.											.	APBB2	61	.	0			c.20-2C>-						PASS	.						42.0	41.0	41.0					4																	41016418		1897	4118	6015	SO:0001627	intron_variant	323	exon7			.	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.20-3C>-	4.37:g.41016418delG		136.0	0.0	0		121.0	12.0	0.0991736	NM_001166050	B4DSL4|E9PG87|Q8IUI6	Splice_Site	DEL	ENST00000295974.8	37	CCDS54761.1																																																																																			G|0.971;-|0.029	0.029	strong		0.418	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
SLAMF8	56833	hgsc.bcm.edu	37	1	159799824	159799825	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:159799824_159799825delCT	ENST00000289707.5	+	2	358_359	c.209_210delCT	c.(208-210)actfs	p.T70fs	SLAMF8_ENST00000368104.4_Intron|SLAMF8_ENST00000471286.1_3'UTR	NM_020125.2	NP_064510.1	Q9P0V8	SLAF8_HUMAN	SLAM family member 8	70					cellular response to drug (GO:0035690)|defense response to bacterium (GO:0042742)|phagosome acidification (GO:0090383)|regulation of kinase activity (GO:0043549)|regulation of NAD(P)H oxidase activity (GO:0033860)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			endometrium(2)|large_intestine(4)|lung(6)	12	all_hematologic(112;0.0597)					TCCCTGGAGACTCTGTACCATT	0.629																																					p.70_70del		Pindel,Atlas-Indel	.											.	SLAMF8	30	.	0			c.208_209del						PASS	.			0,4266		0,0,2133						4.4	1.0			106	3,8249		0,3,4123	no	frameshift	SLAMF8	NM_020125.2		0,3,6256	A1A1,A1R,RR		0.0364,0.0,0.024				3,12515				SO:0001589	frameshift_variant	56833	exon2			.	AF146761	CCDS1188.1	1q23.1	2013-01-11			ENSG00000158714	ENSG00000158714		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	21391	protein-coding gene	gene with protein product		606620				11313408	Standard	NM_020125		Approved	BLAME, SBBI42, CD353	uc001fue.4	Q9P0V8	OTTHUMG00000035433	ENST00000289707.5:c.209_210delCT	1.37:g.159799826_159799827delCT	ENSP00000289707:p.Thr70fs	69.0	0.0	.		96.0	42.0	0.438	NM_020125	Q32MC6|Q5VU15	Frame_Shift_Del	DEL	ENST00000289707.5	37	CCDS1188.1																																																																																			.	.	none		0.629	SLAMF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085983.1	NM_020125	
FAM193A	8603	hgsc.bcm.edu	37	4	2632799	2632800	+	Frame_Shift_Ins	INS	-	-	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:2632799_2632800insC	ENST00000324666.5	+	3	419_420	c.68_69insC	c.(67-72)ggcccgfs	p.GP23fs	FAM193A_ENST00000382839.3_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000502458.1_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000545951.1_Frame_Shift_Ins_p.GP23fs|FAM193A_ENST00000505311.1_Frame_Shift_Ins_p.GP23fs	NM_001256666.1	NP_001243595.1	P78312	F193A_HUMAN	family with sequence similarity 193, member A	23										NS(2)|breast(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(12)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	40						GGCCTGCAGGGCCCGCCGCAAG	0.639																																					p.G23fs		Atlas-Indel	.											.	FAM193A	103	.	0			c.68_69insC						PASS	.																																			SO:0001589	frameshift_variant	8603	exon3			.	AB000459	CCDS33943.1, CCDS58874.1, CCDS58875.1, CCDS58876.1	4p16.3	2009-09-04	2009-09-04	2009-09-04					16822	protein-coding gene	gene with protein product			"""chromosome 4 open reading frame 8"""	C4orf8		9734812	Standard	NR_046335		Approved	RES4-22	uc010ick.3	P78312		ENST00000324666.5:c.71dupC	4.37:g.2632802_2632802dupC	ENSP00000324587:p.Gly23fs	113.0	0.0	0		127.0	12.0	0.0944882	NM_001256666	B7ZM85|B9EGR0|E9PFA1|O43607|P78311|P78313|Q9UEG8	Frame_Shift_Ins	INS	ENST00000324666.5	37	CCDS58875.1																																																																																			.	.	none		0.639	FAM193A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360903.1	NM_003704	
PNPLA7	375775	hgsc.bcm.edu	37	9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T	rs372921391|rs372038516	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:140444627_140444628insT	ENST00000277531.4	-	1	208_209	c.22_23insA	c.(22-24)agcfs	p.S8fs	MRPL41_ENST00000371443.5_5'Flank|PNPLA7_ENST00000406427.1_Frame_Shift_Ins_p.S8fs	NM_152286.3	NP_689499.3	Q6ZV29	PLPL7_HUMAN	patatin-like phospholipase domain containing 7	8					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)		TACCTGTGGGCTGTCATCTTTC	0.559													C|T|TT|complex_insertion	13	0.00259585	0.0	0.0043	5008	,	,		18178	0.0		0.0099	False		,,,				2504	0.0				p.S8fs		Pindel,Atlas-Indel	.											.	PNPLA7	124	.	0			c.23_24insA						PASS	.		,	12,4252		0,12,2120					,	0.2	0.0			114	100,8154		0,100,4027	no	frameshift,frameshift	PNPLA7	NM_152286.3,NM_001098537.1	,	0,112,6147	A1A1,A1R,RR		1.2115,0.2814,0.8947	,	,		112,12406				SO:0001589	frameshift_variant	375775	exon1			.	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.23dupA	9.37:g.140444628_140444628dupT	ENSP00000277531:p.Ser8fs	42.0	0.0	.		36.0	19.0	0.528	NM_152286	B5MDD3|Q5T364|Q658X0|Q658Y3|Q6ZTS1|Q86YU8|Q8TAY5|Q96N75|Q9H7N5	Frame_Shift_Ins	INS	ENST00000277531.4	37	CCDS7045.1																																																																																			.	.	weak		0.559	PNPLA7-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254787.1	NM_152286	
APOB	338	hgsc.bcm.edu	37	2	21233099	21233101	+	In_Frame_Del	DEL	TCA	TCA	-	rs541497967	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TCA	TCA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:21233099_21233101delTCA	ENST00000233242.1	-	26	6766_6768	c.6639_6641delTGA	c.(6637-6642)gatgag>gag	p.D2213del		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	2213					artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)			NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					ATGATAGTGCTCATCAAGACTTT	0.246														9	0.00179712	0.0	0.0014	5008	,	,		19525	0.0		0.007	False		,,,				2504	0.001				p.2214_2214del		Pindel,Atlas-Indel	.											.	APOB	761	.	0			c.6640_6642del						PASS	.			1,4235		0,1,2117						0.7	0.9		dbSNP_130	33	39,8177		3,33,4072	no	coding	APOB	NM_000384.2		3,34,6189	A1A1,A1R,RR		0.4747,0.0236,0.3212				40,12412				SO:0001651	inframe_deletion	338	exon26			.	M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.6639_6641delTGA	2.37:g.21233102_21233104delTCA	ENSP00000233242:p.Asp2213del	41.0	0.0	.		46.0	17.0	0.370	NM_000384	O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	In_Frame_Del	DEL	ENST00000233242.1	37	CCDS1703.1																																																																																			.	.	none		0.246	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1		
ENO4	387712	hgsc.bcm.edu	37	10	118609160	118609160	+	Frame_Shift_Del	DEL	G	G	-	rs368456269	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:118609160delG	ENST00000409522.1	+	1	138	c.83delG	c.(82-84)cggfs	p.R28fs	ENO4_ENST00000341276.5_Frame_Shift_Del_p.R28fs|RP11-539I5.1_ENST00000434227.1_RNA|RP11-539I5.1_ENST00000453491.1_RNA			A6NNW6	ENO4_HUMAN	enolase family member 4	28					glycolytic process (GO:0006096)	phosphopyruvate hydratase complex (GO:0000015)	magnesium ion binding (GO:0000287)|phosphopyruvate hydratase activity (GO:0004634)			lung(1)	1						GAGTACTACCGGGAGAACGAC	0.612													GGG|GGG|GG|deletion	3	0.000599042	0.0	0.0	5008	,	,		14513	0.0		0.003	False		,,,				2504	0.0				p.R28fs		Pindel,Atlas-Indel	.											.	ENO4	1	.	0			c.82delC						PASS	.																																			SO:0001589	frameshift_variant	387712	exon1			.		CCDS73206.1	10q25.3	2012-04-19	2009-12-15	2009-12-15	ENSG00000188316	ENSG00000188316			31670	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 134"""	C10orf134			Standard	NM_001242699		Approved	AC023283.3	uc021pzj.1	A6NNW6	OTTHUMG00000019113	ENST00000409522.1:c.83delG	10.37:g.118609160delG	ENSP00000387194:p.Arg28fs	124.0	0.0	.		143.0	41.0	0.287	NM_001242699	B8ZZN9	Frame_Shift_Del	DEL	ENST00000409522.1	37																																																																																				.	.	none		0.612	ENO4-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331643.1	NM_001242699	
CRACR2B	283229	hgsc.bcm.edu	37	11	831552	831553	+	Frame_Shift_Ins	INS	-	-	GC			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:831552_831553insGC	ENST00000525077.1	+	9	1144_1145	c.1043_1044insGC	c.(1042-1047)ctgcggfs	p.LR348fs	CD151_ENST00000322008.4_5'Flank|EFCAB4A_ENST00000528542.2_Frame_Shift_Ins_p.A293fs|CD151_ENST00000397420.3_5'Flank|CD151_ENST00000397421.1_5'Flank|EFCAB4A_ENST00000450448.1_Frame_Shift_Ins_p.A293fs|AP006621.8_ENST00000532946.1_RNA			Q8N4Y2	EFC4A_HUMAN		348					cellular protein localization (GO:0034613)|regulation of store-operated calcium entry (GO:2001256)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(1)	3		all_cancers(49;2.31e-08)|all_epithelial(84;3.72e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.179)|all_lung(207;0.227)		all cancers(45;1.45e-25)|Epithelial(43;1.17e-24)|OV - Ovarian serous cystadenocarcinoma(40;6.76e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		AATACACGGCTGCGGGATGACA	0.673																																					p.A292fs		Pindel,Atlas-Indel	.											.	EFCAB4A	16	.	0			c.876_877insGC						PASS	.			0,3832		0,0,1916						4.1	0.5			34	2,7932		0,2,3965	no	frameshift	EFCAB4A	NM_173584.3		0,2,5881	A1A1,A1R,RR		0.0252,0.0,0.017				2,11764				SO:0001589	frameshift_variant	283229	exon9			.																												ENST00000525077.1:c.1044_1045dupGC	11.37:g.831553_831554dupGC	ENSP00000435299:p.Leu348fs	60.0	0.0	.		71.0	20.0	0.282	NM_173584	D5LPR2|Q8NBW8	Frame_Shift_Ins	INS	ENST00000525077.1	37																																																																																				.	.	none		0.673	EFCAB4A-007	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383097.1		
PI4KB	5298	hgsc.bcm.edu	37	1	151263677	151263678	+	IGR	INS	-	-	ACA	rs145032688	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		23.0	0.0	.		27.0	10.0	0.370	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	
DDX58	23586	hgsc.bcm.edu	37	9	32457307	32457308	+	Frame_Shift_Ins	INS	-	-	AGAA	rs573952640	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32457307_32457308insAGAA	ENST00000379883.2	-	18	2747_2748	c.2590_2591insTTCT	c.(2590-2592)tgtfs	p.C864fs	DDX58_ENST00000379882.1_Frame_Shift_Ins_p.C819fs|DDX58_ENST00000542096.1_Frame_Shift_Ins_p.C793fs|DDX58_ENST00000379868.1_Frame_Shift_Ins_p.C661fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	864	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		CTGTCGGGCACAGAATATCTTT	0.396														3	0.000599042	0.0	0.0014	5008	,	,		16937	0.0		0.0	False		,,,				2504	0.002				p.C864fs		Pindel,Atlas-Indel	.											.	DDX58	82	.	0			c.2591_2592insTTCT						PASS	.			0,4262		0,0,2131						5.8	1.0			112	13,8241		0,13,4114	no	frameshift	DDX58	NM_014314.3		0,13,6245	A1A1,A1R,RR		0.1575,0.0,0.1039				13,12503				SO:0001589	frameshift_variant	23586	exon18			.	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2587_2590dupTTCT	9.37:g.32457308_32457311dupAGAA	ENSP00000369213:p.Cys864fs	108.0	0.0	.		103.0	33.0	0.320	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Ins	INS	ENST00000379883.2	37	CCDS6526.1																																																																																			.	.	none		0.396	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	
CDAN1	146059	hgsc.bcm.edu	37	15	43020456	43020457	+	Frame_Shift_Ins	INS	-	-	TGAC			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:43020456_43020457insTGAC	ENST00000356231.3	-	21	2836_2837	c.2813_2814insGTCA	c.(2812-2814)caafs	p.-938fs		NM_138477.2	NP_612486.2	Q8IWY9	CDAN1_HUMAN	codanin 1						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)		GGCTCTTCCTTTGACAGAACCT	0.619																																					p.Q938fs		Pindel,Atlas-Indel	.											.	CDAN1	70	.	0			c.2814_2815insGTCA						PASS	.																																			SO:0001589	frameshift_variant	146059	exon21			.	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.2810_2813dupGTCA	15.37:g.43020457_43020460dupTGAC	ENSP00000348564:p.Gln938fs	63.0	0.0	.		60.0	19.0	0.317	NM_138477	Q6NYD0|Q7Z7L5|Q969N3	Frame_Shift_Ins	INS	ENST00000356231.3	37	CCDS32209.1																																																																																			.	.	none		0.619	CDAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000431103.1	XM_085300	
FCN3	8547	hgsc.bcm.edu	37	1	27699671	27699671	+	Frame_Shift_Del	DEL	G	G	-	rs28357092|rs532781899	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:27699671delG	ENST00000270879.4	-	5	354	c.349delC	c.(349-351)ctcfs	p.L117fs	FCN3_ENST00000354982.2_Frame_Shift_Del_p.L106fs	NM_003665.2	NP_003656.2	O75636	FCN3_HUMAN	ficolin (collagen/fibrinogen domain containing) 3	117	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				complement activation (GO:0006956)|complement activation, lectin pathway (GO:0001867)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|collagen trimer (GO:0005581)|extracellular region (GO:0005576)	carbohydrate binding (GO:0030246)			endometrium(2)|kidney(2)|large_intestine(1)|lung(1)|urinary_tract(1)	7		all_lung(284;1.6e-05)|Lung NSC(340;2.92e-05)|Colorectal(325;3.46e-05)|Renal(390;0.0007)|Breast(348;0.0021)|Ovarian(437;0.0175)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0381)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0415)|OV - Ovarian serous cystadenocarcinoma(117;1.42e-27)|Colorectal(126;1.24e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|BRCA - Breast invasive adenocarcinoma(304;0.00128)|KIRC - Kidney renal clear cell carcinoma(1967;0.00155)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0419)		AAGACTGGGAGGGCCCTGCCC	0.632													GGG|GGG|GG|deletion	94	0.01877	0.0242	0.013	5008	,	,		16176	0.0		0.0268	False		,,,				2504	0.0266				p.L117fs		Pindel,Atlas-Indel	.											.	FCN3	30	.	0			c.350delT	GRCh37	CD052457	FCN3	D		PASS	.		,	117,4149		4,109,2020	51.0	57.0	55.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	,	3.1	0.0	1	dbSNP_125	56	147,8107		6,135,3986	no	frameshift,frameshift	FCN3	NM_173452.1,NM_003665.2	,	10,244,6006	A1A1,A1R,RR		1.781,2.7426,2.1086	,	,	27699671	264,12256	2202	4300	6502	SO:0001589	frameshift_variant	8547	exon5			.	D88587	CCDS300.1, CCDS301.1	1p36.11	2014-09-17	2013-09-12		ENSG00000142748	ENSG00000142748		"""Fibrinogen C domain containing"""	3625	protein-coding gene	gene with protein product	"""Hakata antigen"""	604973	"""ficolin (collagen/fibrinogen domain-containing) 3 (Hakata antigen)"""			9694814, 10330454	Standard	NM_003665		Approved	FCNH, HAKA1	uc001boa.3	O75636	OTTHUMG00000005722	ENST00000270879.4:c.349delC	1.37:g.27699671delG	ENSP00000270879:p.Leu117fs	184.0	0.0	.		175.0	50.0	0.286	NM_003665	Q6IBJ5|Q8WW86	Frame_Shift_Del	DEL	ENST00000270879.4	37	CCDS300.1																																																																																			G|0.985;-|0.015	0.015	strong		0.632	FCN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000015667.1		
SMEK2	57223	hgsc.bcm.edu	37	2	55777083	55777085	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:55777083_55777085delTTC	ENST00000345102.5	-	17	2813_2815	c.2512_2514delGAA	c.(2512-2514)gaadel	p.E838del	SMEK2_ENST00000407823.3_In_Frame_Del_p.E806del|SMEK2_ENST00000272313.5_In_Frame_Del_p.E753del	NM_001122964.1	NP_001116436	Q5MIZ7	P4R3B_HUMAN	SMEK homolog 2, suppressor of mek1 (Dictyostelium)	838	Poly-Glu.				positive regulation of gluconeogenesis (GO:0045722)|protein dephosphorylation (GO:0006470)|regulation of lipid metabolic process (GO:0019216)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)|protein phosphatase 4 complex (GO:0030289)				kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16			LUSC - Lung squamous cell carcinoma(58;0.127)|Lung(47;0.132)			TGGGGGACGATTCTTCTTCTTCA	0.369																																					p.838_839del		Pindel,Atlas-Indel	.											SMEK2_ENST00000345102,colon,carcinoma,+1,4	SMEK2	86	4	0			c.2513_2515del						PASS	.		,	1,4265		0,1,2132					,	3.0	1.0			95	2,8252		0,2,4125	no	coding,coding	SMEK2	NM_020463.2,NM_001122964.1	,	0,3,6257	A1A1,A1R,RR		0.0242,0.0234,0.024	,	,		3,12517				SO:0001651	inframe_deletion	57223	exon17			.	AB037808	CCDS1855.1, CCDS46289.1, CCDS62913.1	2p16.1	2008-09-15			ENSG00000138041				29267	protein-coding gene	gene with protein product		610352				16085932, 18614045	Standard	NM_001122964		Approved	PSY2, FLFL2, KIAA1387, FLJ31474	uc002rzc.3	Q5MIZ7	OTTHUMG00000129336	ENST00000345102.5:c.2512_2514delGAA	2.37:g.55777092_55777094delTTC	ENSP00000339769:p.Glu838del	42.0	0.0	.		45.0	15.0	0.333	NM_001122964	Q6P9B0|Q86XB8|Q9BQJ0|Q9BRK2|Q9H913|Q9P2G0	In_Frame_Del	DEL	ENST00000345102.5	37	CCDS46289.1																																																																																			.	.	none		0.369	SMEK2-002	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251483.1	NM_020463	
DLX4	1748	hgsc.bcm.edu	37	17	48050500	48050501	+	Frame_Shift_Ins	INS	-	-	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:48050500_48050501insC	ENST00000240306.3	+	2	642_643	c.347_348insC	c.(346-351)aagctcfs	p.KL116fs	DLX4_ENST00000503410.1_3'UTR|DLX4_ENST00000411890.2_Frame_Shift_Ins_p.KL44fs	NM_138281.2	NP_612138.1	Q92988	DLX4_HUMAN	distal-less homeobox 4	116					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(3)	10						CCCGCCAAAAAGCTCCGCAAGC	0.678																																					p.K116fs		Atlas-Indel	.											.	DLX4	25	.	0			c.347_348insC						PASS	.																																			SO:0001589	frameshift_variant	1748	exon2			.		CCDS11555.1, CCDS45728.1	17q21.33	2011-06-20			ENSG00000108813	ENSG00000108813		"""Homeoboxes / ANTP class : NKL subclass"""	2917	protein-coding gene	gene with protein product		601911		DLX7, DLX9			Standard	NM_138281		Approved	DLX8, BP1	uc002ipv.3	Q92988	OTTHUMG00000161839	Exception_encountered	17.37:g.48050500_48050501insC	ENSP00000240306:p.Lys116fs	140.0	0.0	0		138.0	10.0	0.0724638	NM_138281	D3DTX2|D3DTX3|O60480|Q13265|Q6PJK0|Q9HBE0	Frame_Shift_Ins	INS	ENST00000240306.3	37	CCDS11555.1																																																																																			.	.	none		0.678	DLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366214.1		
Unknown	0	hgsc.bcm.edu	37	7	101988929	101988930	+	IGR	DEL	TG	TG	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:101988929_101988930delTG								Y_RNA (11547 upstream) : PRKRIP1 (15413 downstream)																							ACGGTATAACTGGAACCGACGC	0.569																																					p.315_315del		Atlas-Indel	.											.	SPDYE6	1	.	0			c.944_945del						PASS	.			2,1230		1,0,615							0.0			1	3,2919		1,1,1459	no	frameshift	SPDYE6	NM_001146210.1		2,1,2074	A1A1,A1R,RR		0.1027,0.1623,0.1204				5,4149				SO:0001628	intergenic_variant	729597	exon6			.																													7.37:g.101988929_101988930delTG		347.0	0.0	0		686.0	48.0	0.0699708	NM_001146210		Frame_Shift_Del	DEL		37																																																																																				.	.	none	0	0.569								
CACNA1E	777	hgsc.bcm.edu	37	1	181732594	181732594	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:181732594delC	ENST00000367573.2	+	34	4742	c.4742delC	c.(4741-4743)gccfs	p.A1581fs	CACNA1E_ENST00000360108.3_Frame_Shift_Del_p.A1562fs|CACNA1E_ENST00000526775.1_Frame_Shift_Del_p.A1562fs|CACNA1E_ENST00000367570.1_Frame_Shift_Del_p.A1581fs|CACNA1E_ENST00000358338.5_Frame_Shift_Del_p.A1513fs|CACNA1E_ENST00000357570.5_Frame_Shift_Del_p.A1532fs|CACNA1E_ENST00000367567.4_Frame_Shift_Del_p.A1188fs	NM_001205293.1	NP_001192222.1	Q15878	CAC1E_HUMAN	calcium channel, voltage-dependent, R type, alpha 1E subunit	1581					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						TTCCGAGCTGCCCGCCTCATA	0.463																																					p.A1581fs		Pindel,Atlas-Indel	.											.	CACNA1E	778	.	0			c.4741delG						PASS	.						84.0	82.0	83.0					1																	181732594		1863	4100	5963	SO:0001589	frameshift_variant	777	exon34			.	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.4742delC	1.37:g.181732594delC	ENSP00000356545:p.Ala1581fs	80.0	0.0	.		109.0	34.0	0.312	NM_000721	B1AM12|B1AM13|B1AM14|Q14580|Q14581	Frame_Shift_Del	DEL	ENST00000367573.2	37	CCDS55664.1																																																																																			.	.	none		0.463	CACNA1E-003	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000090793.2	NM_000721	
NBEAL1	65065	hgsc.bcm.edu	37	2	204002925	204002926	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:204002925_204002926delAG	ENST00000449802.1	+	29	4852_4853	c.4519_4520delAG	c.(4519-4521)agafs	p.R1507fs		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	1507										NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						CTCAGAAAACAGAGAAGCAAAA	0.376																																					p.1506_1507del		Pindel,Atlas-Indel	.											.	NBEAL1	266	.	0			c.4518_4519del						PASS	.																																			SO:0001589	frameshift_variant	65065	exon29			.	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.4519_4520delAG	2.37:g.204002927_204002928delAG	ENSP00000399903:p.Arg1507fs	165.0	0.0	.		176.0	58.0	0.330	NM_001114132	A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Frame_Shift_Del	DEL	ENST00000449802.1	37	CCDS46495.1																																																																																			.	.	none		0.376	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
KDM4A	9682	hgsc.bcm.edu	37	1	44170034	44170035	+	Frame_Shift_Ins	INS	-	-	GGAGTAGGTGCTTCCA			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:44170034_44170035insGGAGTAGGTGCTTCCA	ENST00000372396.3	+	22	3322_3323	c.3188_3189insGGAGTAGGTGCTTCCA	c.(3187-3192)atggagfs	p.-1064fs	KDM4A-AS1_ENST00000418149.1_RNA|KDM4A-AS1_ENST00000453015.1_RNA|KDM4A-AS1_ENST00000434346.1_RNA|KDM4A-AS1_ENST00000398804.3_RNA|KDM4A-AS1_ENST00000439057.1_RNA	NM_014663.2	NP_055478.2	O75164	KDM4A_HUMAN	lysine (K)-specific demethylase 4A						cardiac muscle hypertrophy in response to stress (GO:0014898)|histone demethylation (GO:0016577)|histone H3-K36 demethylation (GO:0070544)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	histone demethylase activity (H3-K36 specific) (GO:0051864)|methylated histone binding (GO:0035064)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(13)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	37						CGGGCCATCATGGAGTAGGTGC	0.49																																					p.M1063_E1064delinsMEX		Pindel	.											.	KDM4A	74	.	0			c.3188_3189insGGAGTAGGTGCTTCCA						PASS	.																																			SO:0001589	frameshift_variant	9682	exon22			.	AB014577	CCDS491.1	1p34.1	2013-01-23	2009-04-06	2009-04-06	ENSG00000066135	ENSG00000066135		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	22978	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 3A"", ""tudor domain containing 14A"""	609764	"""jumonji domain containing 2"", ""jumonji domain containing 2A"""	JMJD2, JMJD2A		9734811, 15138608	Standard	XM_005271354		Approved	KIAA0677, JHDM3A, TDRD14A	uc001cjx.3	O75164	OTTHUMG00000007560	ENST00000372396.3:c.3189_3204dupGGAGTAGGTGCTTCCA	1.37:g.44170034_44170035insGGAGTAGGTGCTTCCA	ENSP00000361473:p.Glu1064fs	89.0	0.0	.		68.0	15.0	0.221	NM_014663	Q5VVB1	Frame_Shift_Ins	INS	ENST00000372396.3	37	CCDS491.1																																																																																			.	.	none		0.490	KDM4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019960.1	NM_014663	
OR4F4	26682	hgsc.bcm.edu	37	15	102462857	102462857	+	Missense_Mutation	SNP	C	C	T	rs200667206	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:102462857C>T	ENST00000326183.3	-	1	441	c.406G>A	c.(406-408)Ggc>Agc	p.G136S		NM_001004195.2	NP_001004195.2	Q96R69	OR4F4_HUMAN	olfactory receptor, family 4, subfamily F, member 4	136						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			ovary(1)	1	Lung NSC(78;0.000991)|all_lung(78;0.00128)|Melanoma(26;0.00505)		OV - Ovarian serous cystadenocarcinoma(32;0.00039)|Lung(145;0.17)|LUSC - Lung squamous cell carcinoma(107;0.187)			GCCATAATGCCGACACATGCG	0.493													c|||	154	0.0307508	0.0182	0.0187	5008	,	,		39921	0.006		0.0239	False		,,,				2504	0.089				p.G136S		Atlas-SNP	.											OR4F4,NS,carcinoma,0,1	OR4F4	6	1	0			c.G406A						scavenged	.						2.0	2.0	2.0					15																	102462857		514	1891	2405	SO:0001583	missense	26682	exon1			TAATGCCGACACA		CCDS32343.1	15q26.3	2012-08-09			ENSG00000177693	ENSG00000177693		"""GPCR / Class A : Olfactory receptors"""	8301	protein-coding gene	gene with protein product							Standard	NM_001004195		Approved	OR4F18	uc002cdf.1	Q96R69		ENST00000326183.3:c.406G>A	15.37:g.102462857C>T	ENSP00000317482:p.Gly136Ser	1380.0	2.0	0.00144928		1421.0	155.0	0.109078	NM_001004195	B2RNI5|Q6IFN9	Missense_Mutation	SNP	ENST00000326183.3	37	CCDS32343.1	.	.	.	.	.	.	.	.	.	.	.	0.556	-0.847333	0.02651	.	.	ENSG00000177693	ENST00000326183	T	0.00063	8.78	2.81	-0.391	0.12446	GPCR, rhodopsin-like superfamily (1);	0.377447	0.19878	N	0.104026	T	0.00073	0.0002	N	0.11341	0.13	0.09310	N	1	B	0.33198	0.401	B	0.25506	0.061	T	0.02721	-1.1119	9	.	.	.	.	4.6638	0.12655	0.3767:0.5061:0.0:0.1172	.	136	Q96R69	OR4F4_HUMAN	S	136	ENSP00000317482:G136S	.	G	-	1	0	OR4F4	100280380	0.000000	0.05858	0.000000	0.03702	0.076000	0.17211	-2.532000	0.00943	-0.069000	0.12931	0.298000	0.19748	GGC	C|0.972;T|0.028	0.028	strong		0.493	OR4F4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417599.1	NM_001004195	
PTCHD2	57540	hgsc.bcm.edu	37	1	11561577	11561577	+	Silent	SNP	C	C	T	rs181120200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:11561577C>T	ENST00000294484.6	+	2	666	c.528C>T	c.(526-528)ccC>ccT	p.P176P	PTCHD2_ENST00000389575.3_Silent_p.P176P	NM_020780.1	NP_065831.1	Q9P2K9	PTHD2_HUMAN	patched domain containing 2	176					cholesterol homeostasis (GO:0042632)|regulation of lipid transport (GO:0032368)|smoothened signaling pathway (GO:0007224)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)	hedgehog receptor activity (GO:0008158)			NS(3)|breast(2)|endometrium(9)|kidney(4)|large_intestine(5)|lung(34)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(3)	76	Ovarian(185;0.249)	Lung NSC(185;4.16e-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;3.13e-07)|COAD - Colon adenocarcinoma(227;4.83e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000325)|Kidney(185;0.000877)|KIRC - Kidney renal clear cell carcinoma(229;0.00273)|STAD - Stomach adenocarcinoma(313;0.00766)|READ - Rectum adenocarcinoma(331;0.0549)		GCGTCATCCCCGCGGCCTCAC	0.692													C|||	11	0.00219649	0.0015	0.0014	5008	,	,		14434	0.0		0.008	False		,,,				2504	0.0				p.P176P		Atlas-SNP	.											.	PTCHD2	193	.	0			c.C528T						PASS	.	C		2,3818		0,2,1908	12.0	15.0	14.0		528	-8.6	0.0	1		14	51,8167		0,51,4058	no	coding-synonymous	PTCHD2	NM_020780.1		0,53,5966	TT,TC,CC		0.6206,0.0524,0.4403		176/1393	11561577	53,11985	1910	4109	6019	SO:0001819	synonymous_variant	57540	exon2			CATCCCCGCGGCC	AB037758	CCDS41247.1	1p36.22	2010-02-17			ENSG00000204624	ENSG00000204624			29251	protein-coding gene	gene with protein product		611251				15738394	Standard	NM_020780		Approved	KIAA1337, DISP3	uc001ash.4	Q9P2K9	OTTHUMG00000002074	ENST00000294484.6:c.528C>T	1.37:g.11561577C>T		45.0	0.0	0		48.0	22.0	0.458333	NM_020780	Q5VTU9|Q9UJD6	Silent	SNP	ENST00000294484.6	37	CCDS41247.1																																																																																			C|0.997;T|0.003	0.003	strong		0.692	PTCHD2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000005770.2	XM_052561	
KIF27	55582	hgsc.bcm.edu	37	9	86518566	86518566	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:86518566T>C	ENST00000297814.2	-	4	1010	c.867A>G	c.(865-867)tcA>tcG	p.S289S	KIF27_ENST00000413982.1_Silent_p.S289S|KIF27_ENST00000334204.2_Silent_p.S289S	NM_017576.1	NP_060046.1	Q86VH2	KIF27_HUMAN	kinesin family member 27	289	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						ATGGAATATGTGAACTCTTCC	0.453																																					p.S289S		Atlas-SNP	.											.	KIF27	103	.	0			c.A867G						PASS	.						74.0	79.0	77.0					9																	86518566		2203	4300	6503	SO:0001819	synonymous_variant	55582	exon4			AATATGTGAACTC	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.867A>G	9.37:g.86518566T>C		196.0	0.0	0		219.0	96.0	0.438356	NM_017576	B2RTR8|Q5T6W0|Q86VH0|Q86VH1|Q9UF54	Silent	SNP	ENST00000297814.2	37	CCDS6665.1																																																																																			.	.	none		0.453	KIF27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052861.1	NM_017576	
PVRL2	5819	hgsc.bcm.edu	37	19	45381649	45381649	+	Intron	SNP	C	C	T	rs373022885		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45381649C>T	ENST00000252483.5	+	6	1042				PVRL2_ENST00000252485.4_Silent_p.D404D	NM_001042724.1	NP_001036189.1	Q92692	PVRL2_HUMAN	poliovirus receptor-related 2 (herpesvirus entry mediator B)						acrosome assembly (GO:0001675)|adherens junction organization (GO:0034332)|adhesion of symbiont to host (GO:0044406)|cell junction assembly (GO:0034329)|cell part morphogenesis (GO:0032990)|cell-cell junction organization (GO:0045216)|cilium organization (GO:0044782)|coreceptor-mediated virion attachment to host cell (GO:0046814)|cytoskeleton organization (GO:0007010)|establishment of mitochondrion localization (GO:0051654)|fertilization (GO:0009566)|fusion of virus membrane with host plasma membrane (GO:0019064)|homophilic cell adhesion (GO:0007156)|positive regulation of immunoglobulin mediated immune response (GO:0002891)|positive regulation of mast cell activation (GO:0033005)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated cytotoxicity directed against tumor cell target (GO:0002860)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)|sperm mitochondrion organization (GO:0030382)|spermatid development (GO:0007286)|spermatid nucleus differentiation (GO:0007289)|susceptibility to natural killer cell mediated cytotoxicity (GO:0042271)|susceptibility to T cell mediated cytotoxicity (GO:0060370)	cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|zonula adherens (GO:0005915)	cell adhesion molecule binding (GO:0050839)|coreceptor activity (GO:0015026)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|virus receptor activity (GO:0001618)			breast(1)|endometrium(1)|large_intestine(6)|lung(5)	13	Lung NSC(12;0.00195)|all_lung(12;0.00522)	Ovarian(192;0.0728)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0143)		CCAGTGGCGACGGGGGATTCT	0.612																																					p.D404D		Atlas-SNP	.											.	PVRL2	58	.	0			c.C1212T						PASS	.	C	,	0,4336		0,0,2168	60.0	42.0	48.0		,1212	-2.3	0.0	19		48	1,8497		0,1,4248	no	intron,coding-synonymous	PVRL2	NM_001042724.1,NM_002856.2	,	0,1,6416	TT,TC,CC		0.0118,0.0,0.0078	,	,404/480	45381649	1,12833	2168	4249	6417	SO:0001627	intron_variant	5819	exon6			TGGCGACGGGGGA	X80038	CCDS12645.1, CCDS42576.1	19q13.32	2013-01-29			ENSG00000130202	ENSG00000130202		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9707	protein-coding gene	gene with protein product		600798		HVEB		7622062, 10196354	Standard	NM_001042724		Approved	PVRR2, PRR2, CD112	uc002ozw.1	Q92692	OTTHUMG00000180839	ENST00000252483.5:c.1043-3819C>T	19.37:g.45381649C>T		75.0	0.0	0		69.0	36.0	0.521739	NM_002856	A8K5L5|O75455|Q6IBI6|Q96J29	Silent	SNP	ENST00000252483.5	37	CCDS42576.1																																																																																			.	.	weak		0.612	PVRL2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453231.1	NM_002856	
PLXND1	23129	hgsc.bcm.edu	37	3	129297255	129297255	+	Missense_Mutation	SNP	T	T	C	rs112755880	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	78.0	0.0	0		125.0	81.0	0.648	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	
PRDM1	639	hgsc.bcm.edu	37	6	106543533	106543533	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:106543533G>A	ENST00000369096.4	+	3	569	c.335G>A	c.(334-336)cGt>cAt	p.R112H	PRDM1_ENST00000369091.2_Missense_Mutation_p.R76H	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	112	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		AAGGGCACACGTTTTGGACCC	0.363			"""D, N, Mis, F, S"""		DLBCL																																p.R112H		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	PRDM1,colon,carcinoma,0,1	PRDM1	195	1	0			c.G335A						PASS	.						97.0	91.0	93.0					6																	106543533		2203	4300	6503	SO:0001583	missense	639	exon3			GCACACGTTTTGG		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.335G>A	6.37:g.106543533G>A	ENSP00000358092:p.Arg112His	63.0	0.0	0		68.0	6.0	0.0882353	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	G	35	5.532045	0.96446	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278	T;T	0.73363	-0.74;-0.74	6.06	6.06	0.98353	SET domain (3);	0.052943	0.85682	D	0.000000	D	0.83968	0.5369	M	0.63208	1.945	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.83781	0.0225	10	0.87932	D	0	-14.1659	20.6208	0.99490	0.0:0.0:1.0:0.0	.	112	O75626	PRDM1_HUMAN	H	76;112;76	ENSP00000358087:R76H;ENSP00000358092:R112H	ENSP00000358087:R76H	R	+	2	0	PRDM1	106650226	1.000000	0.71417	0.890000	0.34922	0.962000	0.63368	9.869000	0.99810	2.882000	0.98803	0.655000	0.94253	CGT	.	.	none		0.363	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
CHIC1	53344	hgsc.bcm.edu	37	X	72797296	72797296	+	Splice_Site	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:72797296A>T	ENST00000373502.5	+	2	427	c.350A>T	c.(349-351)aAg>aTg	p.K117M	CHIC1_ENST00000373504.6_Splice_Site_p.K117M	NM_001039840.2	NP_001034929.2	Q5VXU3	CHIC1_HUMAN	cysteine-rich hydrophobic domain 1	117						cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(1)|lung(2)	4	Renal(35;0.156)					CTAACAGGGAAGGTAAGTGAG	0.343																																					p.K117M		Atlas-SNP	.											.	CHIC1	13	.	0			c.A350T						PASS	.						225.0	188.0	201.0					X																	72797296		2203	4300	6503	SO:0001630	splice_region_variant	53344	exon2			CAGGGAAGGTAAG	Y11897	CCDS35335.2, CCDS75993.1	Xq13.2	2008-05-14			ENSG00000204116	ENSG00000204116			1934	protein-coding gene	gene with protein product		300922				9321471, 11257495	Standard	NM_001039840		Approved	BRX	uc004ebk.4	Q5VXU3	OTTHUMG00000021835	ENST00000373502.5:c.351+1A>T	X.37:g.72797296A>T		41.0	0.0	0		45.0	25.0	0.555556	NM_001039840	A0PJZ2|B0QZ87|B9EGS5|Q5CZ84	Missense_Mutation	SNP	ENST00000373502.5	37	CCDS35335.2	.	.	.	.	.	.	.	.	.	.	A	19.40	3.820831	0.71028	.	.	ENSG00000204116	ENST00000373502;ENST00000373504	.	.	.	4.4	4.4	0.53042	Golgin subfamily A member 7/ERF4 (1);	0.000000	0.85682	D	0.000000	T	0.76644	0.4016	M	0.76574	2.34	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.995;0.999;1.0	T	0.79132	-0.1929	9	0.72032	D	0.01	-22.424	11.0475	0.47867	1.0:0.0:0.0:0.0	.	117;117;117	B7Z3I1;Q5VXU3-2;Q5VXU3	.;.;CHIC1_HUMAN	M	117	.	ENSP00000362601:K117M	K	+	2	0	CHIC1	72714021	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.715000	0.91416	1.682000	0.51000	0.437000	0.28790	AAG	.	.	none		0.343	CHIC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057233.3		Missense_Mutation
RNF213	57674	hgsc.bcm.edu	37	17	78363033	78363033	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:78363033G>A	ENST00000582970.1	+	65	15204	c.15061G>A	c.(15061-15063)Gcc>Acc	p.A5021T	CTD-2047H16.4_ENST00000572151.1_RNA|CTD-2047H16.4_ENST00000575034.1_RNA|RNF213_ENST00000508628.2_Missense_Mutation_p.A5070T|RNF213_ENST00000427003.3_3'UTR|RNF213_ENST00000336301.6_Missense_Mutation_p.A3094T|CTD-2047H16.4_ENST00000573394.1_RNA	NM_001256071.1	NP_001243000.1	Q63HN8	RN213_HUMAN	ring finger protein 213	5021			A -> V (variant detected in cases of Moyamoya disease in East Asian populations; dbSNP:rs138130613). {ECO:0000269|PubMed:21799892}.		ATP catabolic process (GO:0006200)|protein autoubiquitination (GO:0051865)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|membrane (GO:0016020)	ATPase activity (GO:0016887)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(23)|lung(36)|ovary(11)|pancreas(2)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	130	all_neural(118;0.0538)		BRCA - Breast invasive adenocarcinoma(99;0.0252)|OV - Ovarian serous cystadenocarcinoma(97;0.057)			CTACAGCGATGCCTGTGAAGT	0.537																																					p.A5021T		Atlas-SNP	.											.	RNF213	766	.	0			c.G15061A						PASS	.						141.0	123.0	129.0					17																	78363033		2203	4300	6503	SO:0001583	missense	57674	exon65			AGCGATGCCTGTG	AK074030	CCDS58606.1	17q25.3	2013-01-09	2007-02-08	2007-02-08		ENSG00000173821		"""RING-type (C3HC4) zinc fingers"""	14539	protein-coding gene	gene with protein product		613768	"""chromosome 17 open reading frame 27"", ""KIAA1618"", ""moyamoya disease 2"", ""Moyamoya disease 2"""	C17orf27, KIAA1618, MYMY2		10997877, 21048783, 21799892	Standard	NM_020954		Approved	KIAA1554, NET57	uc021uen.2	Q63HN8		ENST00000582970.1:c.15061G>A	17.37:g.78363033G>A	ENSP00000464087:p.Ala5021Thr	151.0	0.0	0		179.0	89.0	0.497207	NM_001256071	C9JCP4|D6RI12|F8WKS1|Q658P6|Q69YK7|Q6MZR1|Q8IWF4|Q8IZX1|Q8IZX2|Q8N406|Q8TEU0|Q9H6C9|Q9H6H9|Q9H6P3|Q9H8A9|Q9HCF4|Q9HCL8	Missense_Mutation	SNP	ENST00000582970.1	37	CCDS58606.1	.	.	.	.	.	.	.	.	.	.	G	12.70	2.015431	0.35511	.	.	ENSG00000173821	ENST00000508628;ENST00000411702;ENST00000336301;ENST00000427003	T	0.23950	1.88	5.39	1.87	0.25490	.	0.435749	0.22236	N	0.062742	T	0.26340	0.0643	M	0.72479	2.2	0.25084	N	0.990904	B;B	0.22146	0.031;0.065	B;B	0.14578	0.011;0.01	T	0.19877	-1.0292	10	0.56958	D	0.05	.	9.3461	0.38109	0.3281:0.0:0.6719:0.0	.	5021;3094	D6RI12;Q63HN8	.;RN213_HUMAN	T	5021;5070;3094;371	ENSP00000338218:A3094T	ENSP00000338218:A3094T	A	+	1	0	RNF213	75977628	1.000000	0.71417	0.244000	0.24202	0.451000	0.32288	2.945000	0.49043	0.124000	0.18369	-0.345000	0.07892	GCC	.	.	none		0.537	RNF213-020	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443298.1	NM_020914	
DAPK1	1612	hgsc.bcm.edu	37	9	90321293	90321293	+	Missense_Mutation	SNP	G	G	A	rs200627640		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:90321293G>A	ENST00000408954.3	+	26	3642	c.3307G>A	c.(3307-3309)Gtc>Atc	p.V1103I	DAPK1_ENST00000358077.5_Missense_Mutation_p.V1103I|DAPK1_ENST00000469640.2_Missense_Mutation_p.V1128I|DAPK1_ENST00000472284.1_Missense_Mutation_p.V1103I|DAPK1_ENST00000491893.1_Missense_Mutation_p.V1037I	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1103					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CATGGTGGACGTCCCAGCCCT	0.647									Chronic Lymphocytic Leukemia, Familial Clustering of				G|||	1	0.000199681	0.0	0.0	5008	,	,		18449	0.0		0.001	False		,,,				2504	0.0				p.V1103I		Atlas-SNP	.											.	DAPK1	329	.	0			c.G3307A						PASS	.	G	ILE/VAL	0,4382		0,0,2191	76.0	87.0	84.0		3307	3.4	1.0	9		84	2,8538		0,2,4268	yes	missense	DAPK1	NM_004938.2	29	0,2,6459	AA,AG,GG		0.0234,0.0,0.0155	benign	1103/1431	90321293	2,12920	2191	4270	6461	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	GTGGACGTCCCAG	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.3307G>A	9.37:g.90321293G>A	ENSP00000386135:p.Val1103Ile	175.0	0.0	0		221.0	99.0	0.447964	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	37	CCDS43842.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	1.630	-0.519121	0.04171	0.0	2.34E-4	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04;-0.03	5.59	3.42	0.39159	.	0.243390	0.26366	N	0.024792	T	0.25717	0.0626	N	0.01267	-0.92	0.31840	N	0.623597	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.34900	-0.9810	10	0.02654	T	1	.	8.3592	0.32348	0.8799:0.0:0.1201:0.0	.	1037;1103;1103	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	I	1103;1103;1128;1103;1037	ENSP00000350785:V1103I;ENSP00000417076:V1103I;ENSP00000418885:V1128I;ENSP00000386135:V1103I;ENSP00000419026:V1037I	ENSP00000350785:V1103I	V	+	1	0	DAPK1	89511113	0.992000	0.36948	0.994000	0.49952	0.932000	0.56968	2.244000	0.43124	0.540000	0.28808	0.561000	0.74099	GTC	G|0.999;A|0.001	0.001	strong		0.647	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256920	140256920	+	Silent	SNP	G	G	C	rs115718636	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140256920G>C	ENST00000398631.2	+	1	1863	c.1863G>C	c.(1861-1863)ccG>ccC	p.P621P	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	621	Cadherin 6. {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(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGCACATCCCGTTCCACGTGG	0.672													.|||	111	0.0221645	0.0129	0.0303	5008	,	,		17234	0.0		0.0656	False		,,,				2504	0.0072				p.P621P	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											PCDHA12,colon,carcinoma,0,2	PCDHA12	196	2	0			c.G1863C						PASS	.	G	,,,,,,,,,,,,,,,	117,4289	87.8+/-126.4	0,117,2086	228.0	205.0	213.0		,,,1863,,,,,,,,,,,,1863	-0.7	0.9	5	dbSNP_132	213	437,8161	133.5+/-191.0	11,415,3873	no	intron,intron,intron,coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous	PCDHA9,PCDHA12,PCDHA11,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,NM_018902.3,NM_018903.2,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_031864.1	,,,,,,,,,,,,,,,	11,532,5959	CC,CG,GG		5.0826,2.6555,4.2602	,,,,,,,,,,,,,,,	,,,621/942,,,,,,,,,,,,621/793	140256920	554,12450	2203	4299	6502	SO:0001819	synonymous_variant	56137	exon1			CATCCCGTTCCAC	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1863G>C	5.37:g.140256920G>C		195.0	0.0	0		262.0	124.0	0.473282	NM_018903	O75278|Q2M1N8	Silent	SNP	ENST00000398631.2	37	CCDS47285.1																																																																																			G|0.959;C|0.041	0.041	strong		0.672	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
LRIT1	26103	hgsc.bcm.edu	37	10	85992255	85992255	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85992255C>T	ENST00000372105.3	-	4	1321	c.1300G>A	c.(1300-1302)Gtg>Atg	p.V434M		NM_015613.2	NP_056428.1	Q9P2V4	LRIT1_HUMAN	leucine-rich repeat, immunoglobulin-like and transmembrane domains 1	434	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|skin(1)	23						ACCACCTTCACAGACCTCACC	0.587																																					p.V434M		Atlas-SNP	.											.	LRIT1	73	.	0			c.G1300A						PASS	.						107.0	83.0	91.0					10																	85992255		2203	4300	6503	SO:0001583	missense	26103	exon4			CCTTCACAGACCT	AB031547	CCDS7373.1	10q23	2013-02-11	2007-06-19	2007-06-19	ENSG00000148602	ENSG00000148602		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	23404	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 9"""		"""leucine rich repeat containing 21"""	LRRC21		10777785	Standard	NM_015613		Approved	PAL, DKFZP434K091, FIGLER9	uc001kcz.1	Q9P2V4	OTTHUMG00000018632	ENST00000372105.3:c.1300G>A	10.37:g.85992255C>T	ENSP00000361177:p.Val434Met	100.0	0.0	0		82.0	19.0	0.231707	NM_015613	Q0QD41|Q9Y4N7	Missense_Mutation	SNP	ENST00000372105.3	37	CCDS7373.1	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303962	0.60305	.	.	ENSG00000148602	ENST00000372105	T	0.60797	0.16	5.58	3.68	0.42216	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.124327	0.53938	D	0.000047	T	0.52533	0.1740	L	0.43923	1.385	0.51012	D	0.999902	P	0.37276	0.589	B	0.39935	0.314	T	0.58668	-0.7596	10	0.62326	D	0.03	.	13.8294	0.63370	0.0:0.5725:0.4275:0.0	.	434	Q9P2V4	LRIT1_HUMAN	M	434	ENSP00000361177:V434M	ENSP00000361177:V434M	V	-	1	0	LRIT1	85982235	0.996000	0.38824	0.897000	0.35233	0.451000	0.32288	2.950000	0.49081	1.347000	0.45714	-0.165000	0.13383	GTG	.	.	none		0.587	LRIT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049109.1	NM_015613	
SENP8	123228	hgsc.bcm.edu	37	15	72432140	72432140	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:72432140C>T	ENST00000542035.2	+	2	509	c.176C>T	c.(175-177)aCc>aTc	p.T59I	SENP8_ENST00000544411.1_Missense_Mutation_p.T59I|SENP8_ENST00000340912.4_Missense_Mutation_p.T59I|SENP8_ENST00000544171.1_Missense_Mutation_p.T59I|RP11-2I17.4_ENST00000568984.1_RNA	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	59	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						CCTGAAGTCACCCAGTTCATC	0.453																																					p.T59I		Atlas-SNP	.											.	SENP8	18	.	0			c.C176T						PASS	.						156.0	135.0	142.0					15																	72432140		2199	4297	6496	SO:0001583	missense	123228	exon2			AAGTCACCCAGTT	BC031411	CCDS10240.1	15q22.33	2005-08-17	2005-08-17	2004-01-30	ENSG00000166192	ENSG00000166192			22992	protein-coding gene	gene with protein product	"""NEDD8-specific protease 1"", ""sentrin/SUMO-specific protease SENP8"", ""deneddylase 1"""	608659	"""protease, cysteine, 2 (NEDD8 specific)"", ""SUMO/sentrin specific protease family member 8"""	PRSC2		12730221, 12759362	Standard	NM_145204		Approved	NEDP1, DEN1, HsT17512	uc021spt.1	Q96LD8	OTTHUMG00000133441	ENST00000542035.2:c.176C>T	15.37:g.72432140C>T	ENSP00000446057:p.Thr59Ile	106.0	0.0	0		125.0	5.0	0.04	NM_001166340	Q96QA4	Missense_Mutation	SNP	ENST00000542035.2	37	CCDS10240.1	.	.	.	.	.	.	.	.	.	.	C	19.03	3.747790	0.69533	.	.	ENSG00000166192	ENST00000542035;ENST00000544411;ENST00000340912;ENST00000544171	T;T;T;T	0.30448	1.53;1.53;1.53;1.53	5.62	4.71	0.59529	.	0.167236	0.52532	D	0.000072	T	0.40347	0.1113	M	0.70903	2.155	0.58432	D	0.999993	P	0.40332	0.713	P	0.45577	0.486	T	0.27606	-1.0069	10	0.42905	T	0.14	-21.7606	11.9463	0.52930	0.137:0.7313:0.1317:0.0	.	59	Q96LD8	SENP8_HUMAN	I	59	ENSP00000446057:T59I;ENSP00000441753:T59I;ENSP00000340505:T59I;ENSP00000439415:T59I	ENSP00000340505:T59I	T	+	2	0	SENP8	70219194	1.000000	0.71417	1.000000	0.80357	0.759000	0.43091	5.879000	0.69690	1.517000	0.48917	0.655000	0.94253	ACC	.	.	none		0.453	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204	
SYT15	83849	hgsc.bcm.edu	37	10	46965017	46965017	+	Missense_Mutation	SNP	C	C	T	rs200586361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:46965017C>T	ENST00000374321.4	-	6	994	c.928G>A	c.(928-930)Gac>Aac	p.D310N	SYT15_ENST00000374325.3_Missense_Mutation_p.D310N|RP11-38L15.3_ENST00000506914.1_RNA|SYT15_ENST00000374323.4_Missense_Mutation_p.D363N|SYT15_ENST00000503753.1_Missense_Mutation_p.D310N	NM_031912.4	NP_114118.2	Q9BQS2	SYT15_HUMAN	synaptotagmin XV	310	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				cervix(1)|endometrium(5)|kidney(2)|lung(5)	13						ATGCCTCTGTCCTCCTGGAGC	0.612													C|||	11	0.00219649	0.0	0.0043	5008	,	,		40565	0.0		0.008	False		,,,				2504	0.0				p.D310N	Ovarian(57;1152 1428 19651 37745)	Atlas-SNP	.											SYT15_ENST00000374328,NS,carcinoma,-1,1	SYT15	165	1	0			c.G928A						PASS	.	C	ASN/ASP,ASN/ASP	6,4270		0,6,2132	53.0	61.0	58.0		928,928	3.2	0.0	10		58	47,8463		0,47,4208	yes	missense,missense	SYT15	NM_031912.4,NM_181519.2	23,23	0,53,6340	TT,TC,CC		0.5523,0.1403,0.4145	benign,benign	310/422,310/391	46965017	53,12733	2138	4255	6393	SO:0001583	missense	83849	exon6			CTCTGTCCTCCTG	AJ303363	CCDS73103.1, CCDS73104.1	10q11.1	2013-01-21			ENSG00000204176	ENSG00000204176		"""Synaptotagmins"""	17167	protein-coding gene	gene with protein product		608081				11543631	Standard	NM_031912		Approved	CHR10SYT	uc001jea.3	Q9BQS2	OTTHUMG00000018103	ENST00000374321.4:c.928G>A	10.37:g.46965017C>T	ENSP00000363441:p.Asp310Asn	107.0	0.0	0		115.0	26.0	0.226087	NM_031912	A5D6W8|Q5VY53|Q5VY55|Q7Z439|Q7Z440	Missense_Mutation	SNP	ENST00000374321.4	37	CCDS44376.1	.	.	.	.	.	.	.	.	.	.	.	12.54	1.967239	0.34754	0.001403	0.005523	ENSG00000204176	ENST00000416127;ENST00000374328;ENST00000374325;ENST00000503753;ENST00000374330;ENST00000374323;ENST00000374321	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	5.06	3.16	0.36331	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.144113	0.64402	N	0.000009	T	0.45115	0.1326	L	0.35793	1.09	0.21290	N	0.999734	B;B	0.11235	0.004;0.004	B;B	0.13407	0.009;0.005	T	0.39563	-0.9608	10	0.38643	T	0.18	.	9.1541	0.36983	0.0:0.7682:0.1482:0.0836	.	310;310	Q9BQS2;Q9BQS2-2	SYT15_HUMAN;.	N	310;100;310;310;149;363;310	ENSP00000363448:D100N;ENSP00000363445:D310N;ENSP00000427607:D310N;ENSP00000363443:D363N;ENSP00000363441:D310N	ENSP00000363441:D310N	D	-	1	0	SYT15	46385023	0.254000	0.23992	0.011000	0.14972	0.936000	0.57629	1.068000	0.30629	0.763000	0.33175	0.561000	0.74099	GAC	C|0.998;T|0.002	0.002	weak		0.612	SYT15-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367008.1	NM_031912	
CCDC71	64925	hgsc.bcm.edu	37	3	49201140	49201140	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49201140C>T	ENST00000321895.6	-	2	608	c.502G>A	c.(502-504)Ggt>Agt	p.G168S		NM_022903.3	NP_075054.3	Q8IV32	CCD71_HUMAN	coiled-coil domain containing 71	168										endometrium(1)|large_intestine(4)|lung(3)|ovary(1)|prostate(1)	10				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00217)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGGTAGACACCTGGATAAAGG	0.587																																					p.G168S		Atlas-SNP	.											.	CCDC71	33	.	0			c.G502A						PASS	.						54.0	58.0	56.0					3																	49201140		2203	4300	6503	SO:0001583	missense	64925	exon2			AGACACCTGGATA	AK022862	CCDS2790.1	3p21.31	2014-02-12			ENSG00000177352	ENSG00000177352			25760	protein-coding gene	gene with protein product						12477932	Standard	NM_022903		Approved	FLJ12800	uc003cwg.4	Q8IV32	OTTHUMG00000156815	ENST00000321895.6:c.502G>A	3.37:g.49201140C>T	ENSP00000319006:p.Gly168Ser	56.0	0.0	0		76.0	16.0	0.210526	NM_022903	Q6IPE2|Q9H8H4|Q9H9F1	Missense_Mutation	SNP	ENST00000321895.6	37	CCDS2790.1	.	.	.	.	.	.	.	.	.	.	C	16.31	3.086570	0.55861	.	.	ENSG00000177352	ENST00000321895	T	0.36699	1.24	5.44	4.57	0.56435	.	0.068720	0.56097	D	0.000035	T	0.52533	0.1740	M	0.66939	2.045	0.36735	D	0.881929	D	0.60160	0.987	P	0.57425	0.82	T	0.65080	-0.6255	10	0.72032	D	0.01	-30.1272	14.1305	0.65250	0.0:0.9276:0.0:0.0724	.	168	Q8IV32	CCD71_HUMAN	S	168	ENSP00000319006:G168S	ENSP00000319006:G168S	G	-	1	0	CCDC71	49176144	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	3.531000	0.53546	1.313000	0.45069	0.585000	0.79938	GGT	.	.	none		0.587	CCDC71-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345980.1	NM_022903	
PGR	5241	hgsc.bcm.edu	37	11	100933407	100933407	+	Silent	SNP	G	G	A	rs139646398		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:100933407G>A	ENST00000325455.5	-	4	3436	c.1983C>T	c.(1981-1983)ggC>ggT	p.G661G	PGR_ENST00000263463.5_Intron|PGR_ENST00000534013.1_Silent_p.G67G	NM_000926.4|NM_001202474.1|NM_001271162.1	NP_000917.3|NP_001189403.1|NP_001258091.1	P06401	PRGR_HUMAN	progesterone receptor	661					cell-cell signaling (GO:0007267)|epithelial cell maturation (GO:0002070)|gene expression (GO:0010467)|negative regulation of gene expression (GO:0010629)|ovulation from ovarian follicle (GO:0001542)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|progesterone receptor signaling pathway (GO:0050847)|regulation of epithelial cell proliferation (GO:0050678)|signal transduction (GO:0007165)|tertiary branching involved in mammary gland duct morphogenesis (GO:0060748)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mitochondrial outer membrane (GO:0005741)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|receptor binding (GO:0005102)|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)|steroid binding (GO:0005496)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(4)|liver(1)|lung(18)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	36		Acute lymphoblastic leukemia(157;0.000885)|all_hematologic(158;0.014)		LUSC - Lung squamous cell carcinoma(1;0.0387)|BRCA - Breast invasive adenocarcinoma(274;0.124)|OV - Ovarian serous cystadenocarcinoma(223;0.148)|Lung(307;0.164)	Allylestrenol(DB01431)|Danazol(DB01406)|Desogestrel(DB00304)|Drospirenone(DB01395)|Dydrogesterone(DB00378)|Ethynodiol(DB00823)|Etonogestrel(DB00294)|Fluticasone Propionate(DB00588)|Levonorgestrel(DB00367)|Medroxyprogesterone Acetate(DB00603)|Megestrol acetate(DB00351)|Mifepristone(DB00834)|Norelgestromin(DB06713)|Norethindrone(DB00717)|Norgestimate(DB00957)|Progesterone(DB00396)|Spironolactone(DB00421)	CATTTGGAACGCCCACTGGCT	0.418													G|||	1	0.000199681	0.0008	0.0	5008	,	,		15046	0.0		0.0	False		,,,				2504	0.0				p.G661G	Pancreas(124;2271 2354 21954 22882)	Atlas-SNP	.											.	PGR	115	.	0			c.C1983T						PASS	.	G	,	2,4404	4.2+/-10.8	0,2,2201	129.0	112.0	118.0		1983,1491	4.5	0.9	11	dbSNP_134	118	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	PGR	NM_000926.4,NM_001202474.1	,	0,12,6491	AA,AG,GG		0.1163,0.0454,0.0923	,	661/934,497/770	100933407	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	5241	exon4			TGGAACGCCCACT	M15716	CCDS8310.1, CCDS59229.1	11q22-q23	2013-01-16			ENSG00000082175	ENSG00000082175		"""Nuclear hormone receptors"""	8910	protein-coding gene	gene with protein product		607311					Standard	NM_000926		Approved	PR, NR3C3	uc001pgh.2	P06401	OTTHUMG00000167531	ENST00000325455.5:c.1983C>T	11.37:g.100933407G>A		89.0	0.0	0		72.0	31.0	0.430556	NM_000926	A7LQ08|A7X8B0|B4E3T0|Q8TDS3|Q9UPF7	Silent	SNP	ENST00000325455.5	37	CCDS8310.1																																																																																			G|0.999;A|0.001	0.001	strong		0.418	PGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394934.1		
SYCP2L	221711	hgsc.bcm.edu	37	6	10964015	10964015	+	Splice_Site	SNP	G	G	A	rs115084361	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:10964015G>A	ENST00000283141.6	+	29	2711	c.2415G>A	c.(2413-2415)agG>agA	p.R805R	SYCP2L_ENST00000465872.1_3'UTR	NM_001040274.2	NP_001035364.2	Q5T4T6	SYC2L_HUMAN	synaptonemal complex protein 2-like	805						nucleus (GO:0005634)				breast(3)|central_nervous_system(1)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	36	Breast(50;0.0838)|Ovarian(93;0.107)	all_hematologic(90;0.135)	Epithelial(50;0.239)			TTTCTTCCAGGTTCAATTCAA	0.358													G|||	49	0.00978435	0.0015	0.0173	5008	,	,		18130	0.0		0.0239	False		,,,				2504	0.0112				p.R805R		Atlas-SNP	.											.	SYCP2L	101	.	0			c.G2415A						PASS	.	G		11,3687		0,11,1838	103.0	96.0	98.0		2415	2.3	0.9	6	dbSNP_132	98	175,8007		1,173,3917	yes	coding-synonymous-near-splice	SYCP2L	NM_001040274.2		1,184,5755	AA,AG,GG		2.1388,0.2975,1.5657		805/813	10964015	186,11694	1849	4091	5940	SO:0001630	splice_region_variant	221711	exon29			TTCCAGGTTCAAT	AK128130	CCDS43423.1	6p24.2	2008-11-06	2007-07-02	2007-07-02	ENSG00000153157	ENSG00000153157			21537	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 177"""	C6orf177			Standard	NM_001040274		Approved	dJ62D2.1, NO145	uc003mzo.3	Q5T4T6	OTTHUMG00000014250	ENST00000283141.6:c.2415-1G>A	6.37:g.10964015G>A		79.0	0.0	0		64.0	32.0	0.5	NM_001040274	A6NDS5|Q08GK5|Q6ZRM2|Q96EJ2	Silent	SNP	ENST00000283141.6	37	CCDS43423.1																																																																																			G|0.987;A|0.013	0.013	strong		0.358	SYCP2L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039845.3	NM_194299	Silent
TMEM89	440955	hgsc.bcm.edu	37	3	48658924	48658924	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:48658924C>T	ENST00000330862.3	-	1	364	c.266G>A	c.(265-267)cGg>cAg	p.R89Q		NM_001008269.1	NP_001008270.1	A2RUT3	TMM89_HUMAN	transmembrane protein 89	89						integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(1)|lung(1)|stomach(1)	3				BRCA - Breast invasive adenocarcinoma(193;0.000286)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TGAGCGCCGCCGCCCCTGCAG	0.622																																					p.R89Q		Atlas-SNP	.											TMEM89,NS,carcinoma,+1,1	TMEM89	10	1	0			c.G266A						PASS	.						31.0	30.0	30.0					3																	48658924		2203	4299	6502	SO:0001583	missense	440955	exon1			CGCCGCCGCCCCT	AX657016	CCDS33751.1	3p21.31	2005-11-02			ENSG00000183396	ENSG00000183396			32372	protein-coding gene	gene with protein product							Standard	NM_001008269		Approved		uc011bbo.2	A2RUT3	OTTHUMG00000156647	ENST00000330862.3:c.266G>A	3.37:g.48658924C>T	ENSP00000329557:p.Arg89Gln	144.0	0.0	0		194.0	108.0	0.556701	NM_001008269		Missense_Mutation	SNP	ENST00000330862.3	37	CCDS33751.1	.	.	.	.	.	.	.	.	.	.	C	15.01	2.705879	0.48412	.	.	ENSG00000183396	ENST00000330862	T	0.57107	0.42	4.79	4.79	0.61399	.	0.182364	0.26899	N	0.021928	T	0.51483	0.1677	L	0.36672	1.1	0.09310	N	1	D	0.64830	0.994	P	0.51229	0.663	T	0.47222	-0.9134	10	0.44086	T	0.13	-19.7761	13.2009	0.59767	0.0:1.0:0.0:0.0	.	89	A2RUT3	TMM89_HUMAN	Q	89	ENSP00000329557:R89Q	ENSP00000329557:R89Q	R	-	2	0	TMEM89	48633928	.	.	0.011000	0.14972	0.055000	0.15305	.	.	2.492000	0.84095	0.462000	0.41574	CGG	.	.	none		0.622	TMEM89-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345046.1	NM_001008269	
GABRG3	2567	hgsc.bcm.edu	37	15	27772697	27772697	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:27772697C>A	ENST00000333743.6	+	8	1238	c.984C>A	c.(982-984)ttC>ttA	p.F328L	RP11-100M12.3_ENST00000556642.1_RNA	NM_033223.4	NP_150092.2	Q99928	GBRG3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 3	328					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(23)|skin(1)|upper_aerodigestive_tract(4)	42		all_lung(180;4.58e-12)|Breast(32;0.000625)|Colorectal(260;0.235)		all cancers(64;3.15e-07)|Epithelial(43;1.17e-06)|BRCA - Breast invasive adenocarcinoma(123;0.0261)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	TGTTTGTCTTCGCCGCGCTGA	0.542																																					p.F328L	NSCLC(114;800 1656 7410 37729 45293)	Atlas-SNP	.											GABRG3,NS,carcinoma,0,2	GABRG3	115	2	0			c.C984A						PASS	.						124.0	112.0	116.0					15																	27772697		2161	4270	6431	SO:0001583	missense	2567	exon8			TGTCTTCGCCGCG		CCDS45195.1, CCDS59251.1	15q12	2012-06-22			ENSG00000182256	ENSG00000182256		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4088	protein-coding gene	gene with protein product	"""GABA(G) receptor, gamma 3"""	600233				7601451	Standard	NM_033223		Approved		uc001zbg.2	Q99928	OTTHUMG00000044462	ENST00000333743.6:c.984C>A	15.37:g.27772697C>A	ENSP00000331912:p.Phe328Leu	126.0	0.0	0		105.0	37.0	0.352381	NM_033223	G3V594|Q9HD46|Q9NYT2	Missense_Mutation	SNP	ENST00000333743.6	37	CCDS45195.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.45|18.45	3.626426|3.626426	0.66901|0.66901	.|.	.|.	ENSG00000182256|ENSG00000182256	ENST00000333743|ENST00000451330	D|.	0.87029|.	-2.2|.	5.48|5.48	-0.806|-0.806	0.10875|0.10875	Neurotransmitter-gated ion-channel transmembrane domain (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.71375|.	0.3332|.	M|M	0.82323|0.82323	2.585|2.585	0.80722|0.80722	D|D	1|1	D|.	0.67145|.	0.996|.	D|.	0.79108|.	0.992|.	T|.	0.71290|.	-0.4637|.	10|.	0.87932|.	D|.	0|.	.|.	10.0297|10.0297	0.42092|0.42092	0.0:0.3808:0.0:0.6192|0.0:0.3808:0.0:0.6192	.|.	328|.	Q99928|.	GBRG3_HUMAN|.	L|X	328|91	ENSP00000331912:F328L|.	ENSP00000331912:F328L|.	F|S	+|+	3|2	2|0	GABRG3|GABRG3	25446292|25446292	0.994000|0.994000	0.37717|0.37717	0.988000|0.988000	0.46212|0.46212	0.588000|0.588000	0.36517|0.36517	0.247000|0.247000	0.18179|0.18179	0.045000|0.045000	0.15804|0.15804	-0.251000|-0.251000	0.11542|0.11542	TTC|TCG	.	.	none		0.542	GABRG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103584.2		
NEIL1	79661	hgsc.bcm.edu	37	15	75646194	75646194	+	Missense_Mutation	SNP	C	C	T	rs142213781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75646194C>T	ENST00000564784.1	+	7	1462	c.833C>T	c.(832-834)aCc>aTc	p.T278I	NEIL1_ENST00000569035.1_Missense_Mutation_p.T278I|NEIL1_ENST00000355059.4_Missense_Mutation_p.T278I|RP11-817O13.6_ENST00000563660.1_lincRNA|MIR631_ENST00000384904.1_RNA			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)	278					base-excision repair (GO:0006284)|negative regulation of nuclease activity (GO:0032074)|nucleotide-excision repair (GO:0006289)|response to oxidative stress (GO:0006979)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|protein C-terminus binding (GO:0008022)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|large_intestine(4)|lung(4)|ovary(1)	13						CATGGCCGTACCATCTGGTTC	0.617								Base excision repair (BER), DNA glycosylases					C|||	3	0.000599042	0.0	0.0	5008	,	,		21794	0.0		0.001	False		,,,				2504	0.002				p.T364I		Atlas-SNP	.											.	NEIL1	36	.	0			c.C1091T						PASS	.	C	ILE/THR	0,4394		0,0,2197	79.0	83.0	81.0		833	5.1	1.0	15	dbSNP_134	81	6,8582	4.3+/-15.6	0,6,4288	yes	missense	NEIL1	NM_024608.2	89	0,6,6485	TT,TC,CC		0.0699,0.0,0.0462	probably-damaging	278/391	75646194	6,12976	2197	4294	6491	SO:0001583	missense	79661	exon6			GCCGTACCATCTG	AK026055	CCDS10278.1	15q33.33	2008-07-18			ENSG00000140398	ENSG00000140398			18448	protein-coding gene	gene with protein product		608844				11904416	Standard	NM_024608		Approved	FLJ22402, hFPG1, NEI1, FPG1	uc002bae.4	Q96FI4	OTTHUMG00000142821	ENST00000564784.1:c.833C>T	15.37:g.75646194C>T	ENSP00000457352:p.Thr278Ile	36.0	0.0	0		47.0	22.0	0.468085	NM_001256552	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Missense_Mutation	SNP	ENST00000564784.1	37	CCDS10278.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	26.0	4.695071	0.88830	0.0	6.99E-4	ENSG00000140398	ENST00000355059	T	0.65916	-0.18	5.09	5.09	0.68999	Endonuclease VIII-like 1, DNA binding (1);	0.000000	0.85682	D	0.000000	T	0.77525	0.4143	L	0.61218	1.895	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.79836	-0.1635	10	0.72032	D	0.01	-31.8003	17.4649	0.87629	0.0:1.0:0.0:0.0	.	278	Q96FI4	NEIL1_HUMAN	I	278	ENSP00000347170:T278I	ENSP00000347170:T278I	T	+	2	0	NEIL1	73433247	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	6.710000	0.74670	2.375000	0.81037	0.561000	0.74099	ACC	C|0.999;T|0.001	0.001	strong		0.617	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	
BTBD8	284697	hgsc.bcm.edu	37	1	92554283	92554283	+	Missense_Mutation	SNP	G	G	A	rs34856868	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:92554283G>A	ENST00000342818.3	+	2	414	c.178G>A	c.(178-180)Gtt>Att	p.V60I	BTBD8_ENST00000540648.1_Missense_Mutation_p.V60I|BTBD8_ENST00000370382.3_Missense_Mutation_p.V60I	NM_183242.3	NP_899065.2	Q5XKL5	BTBD8_HUMAN	BTB (POZ) domain containing 8	60	BTB 1. {ECO:0000255|PROSITE- ProRule:PRU00037}.		V -> I (in dbSNP:rs34856868).			nucleus (GO:0005634)				breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)	16		all_lung(203;0.0484)|Lung NSC(277;0.126)|Glioma(108;0.222)		all cancers(265;0.0153)|Epithelial(280;0.0982)		CCATACAGATGTTACCTTCTC	0.323													G|||	41	0.0081869	0.0	0.013	5008	,	,		15123	0.0		0.0298	False		,,,				2504	0.002				p.V60I		Atlas-SNP	.											.	BTBD8	32	.	0			c.G178A						PASS	.	G	ILE/VAL	26,4380	32.6+/-62.9	0,26,2177	96.0	96.0	96.0		178	3.4	0.9	1	dbSNP_126	96	260,8340	101.0+/-162.3	6,248,4046	yes	missense	BTBD8	NM_183242.3	29	6,274,6223	AA,AG,GG		3.0233,0.5901,2.199	benign	60/379	92554283	286,12720	2203	4300	6503	SO:0001583	missense	284697	exon2			ACAGATGTTACCT	AY346333	CCDS737.1	1p22.1	2013-01-08			ENSG00000189195	ENSG00000189195		"""BTB/POZ domain containing"""	21019	protein-coding gene	gene with protein product						14654994	Standard	NM_183242		Approved		uc001doo.3	Q5XKL5	OTTHUMG00000010289	ENST00000342818.3:c.178G>A	1.37:g.92554283G>A	ENSP00000343686:p.Val60Ile	75.0	0.0	0		89.0	40.0	0.449438	NM_183242	Q6V9S5	Missense_Mutation	SNP	ENST00000342818.3	37	CCDS737.1	28	0.01282051282051282	0	0.0	5	0.013812154696132596	0	0.0	23	0.030343007915567283	G	13.65	2.301359	0.40694	0.005901	0.030233	ENSG00000189195	ENST00000370382;ENST00000342818;ENST00000540648	T;T;T	0.76316	-1.01;-1.01;-1.01	5.31	3.42	0.39159	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.247350	0.28273	N	0.015951	T	0.54822	0.1882	L	0.59967	1.855	0.23003	N	0.99845	B	0.24963	0.115	B	0.27076	0.076	T	0.49031	-0.8981	10	0.33940	T	0.23	-10.1214	8.3882	0.32512	0.2616:0.0:0.7384:0.0	rs34856868	60	Q5XKL5	BTBD8_HUMAN	I	60	ENSP00000359408:V60I;ENSP00000343686:V60I;ENSP00000443397:V60I	ENSP00000343686:V60I	V	+	1	0	BTBD8	92326871	1.000000	0.71417	0.859000	0.33776	0.832000	0.47134	1.026000	0.30103	0.718000	0.32166	0.591000	0.81541	GTT	G|0.980;A|0.020	0.020	strong		0.323	BTBD8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028372.1	NM_183242	
RB1CC1	9821	hgsc.bcm.edu	37	8	53558307	53558307	+	Missense_Mutation	SNP	A	A	T	rs34701924	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:53558307A>T	ENST00000025008.5	-	16	4465	c.3942T>A	c.(3940-3942)aaT>aaA	p.N1314K	RB1CC1_ENST00000435644.2_Missense_Mutation_p.N1314K|RB1CC1_ENST00000539297.1_Missense_Mutation_p.N1314K|RB1CC1_ENST00000521611.1_Intron	NM_014781.4	NP_055596.3	Q8TDY2	RBCC1_HUMAN	RB1-inducible coiled-coil 1	1314			N -> K (in dbSNP:rs34701924).		autophagic vacuole assembly (GO:0000045)|cell cycle (GO:0007049)|heart development (GO:0007507)|JNK cascade (GO:0007254)|liver development (GO:0001889)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell size (GO:0045793)|positive regulation of protein phosphorylation (GO:0001934)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|pre-autophagosomal structure membrane (GO:0034045)|ULK1-ATG13-FIP200 complex (GO:0070969)				NS(2)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(9)|lung(19)|ovary(8)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	60		all_cancers(86;0.137)|all_epithelial(80;0.00494)|Lung NSC(129;0.011)|all_lung(136;0.023)				GCATTTCTTCATTCTTTCTTT	0.343													A|||	22	0.00439297	0.0015	0.0	5008	,	,		16444	0.002		0.0129	False		,,,				2504	0.0051				p.N1314K	GBM(180;1701 2102 13475 42023 52570)	Atlas-SNP	.											.	RB1CC1	163	.	0			c.T3942A						PASS	.	A	LYS/ASN,LYS/ASN	6,4400	12.9+/-30.5	0,6,2197	85.0	80.0	82.0		3942,3942	4.3	1.0	8	dbSNP_126	82	87,8513	49.8+/-109.6	1,85,4214	yes	missense,missense	RB1CC1	NM_001083617.1,NM_014781.4	94,94	1,91,6411	TT,TA,AA		1.0116,0.1362,0.7151	probably-damaging,probably-damaging	1314/1592,1314/1595	53558307	93,12913	2203	4300	6503	SO:0001583	missense	9821	exon16			TTCTTCATTCTTT	AB059622	CCDS34892.1, CCDS47856.1	8q11	2014-06-13				ENSG00000023287			15574	protein-coding gene	gene with protein product	"""200 kDa FAK family kinase-interacting protein"", ""phosphatase 1, regulatory subunit 131"""	606837				11850849, 7724523, 18443221	Standard	NM_014781		Approved	KIAA0203, Cc1, DRAGOU14, FIP200, ATG17, PPP1R131	uc003xre.4	Q8TDY2		ENST00000025008.5:c.3942T>A	8.37:g.53558307A>T	ENSP00000025008:p.Asn1314Lys	63.0	0.0	0		88.0	45.0	0.511364	NM_001083617	Q86YR4|Q8WVU9|Q92601	Missense_Mutation	SNP	ENST00000025008.5	37	CCDS34892.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	2	0.0034965034965034965	9	0.011873350923482849	A	16.47	3.132726	0.56828	0.001362	0.010116	ENSG00000023287	ENST00000025008;ENST00000435644;ENST00000539297	T;T;T	0.16743	2.32;2.32;2.32	5.43	4.26	0.50523	.	0.000000	0.85682	D	0.000000	T	0.18087	0.0434	L	0.36672	1.1	0.58432	D	0.999998	D;D	0.89917	1.0;0.999	D;D	0.85130	0.997;0.994	T	0.08493	-1.0719	10	0.06757	T	0.87	-23.2034	10.0886	0.42434	0.8596:0.0:0.1404:0.0	rs34701924;rs52802517	1314;1314	Q8TDY2-2;Q8TDY2	.;RBCC1_HUMAN	K	1314	ENSP00000025008:N1314K;ENSP00000396067:N1314K;ENSP00000445960:N1314K	ENSP00000025008:N1314K	N	-	3	2	RB1CC1	53720860	0.997000	0.39634	1.000000	0.80357	0.998000	0.95712	0.523000	0.22925	0.896000	0.36366	0.533000	0.62120	AAT	A|0.993;T|0.007	0.007	strong		0.343	RB1CC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378011.1	NM_014781	
PAK4	10298	hgsc.bcm.edu	37	19	39668381	39668381	+	Missense_Mutation	SNP	G	G	A	rs372098486		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:39668381G>A	ENST00000593690.1	+	10	1979	c.1552G>A	c.(1552-1554)Gag>Aag	p.E518K	PAK4_ENST00000599470.1_Missense_Mutation_p.E365K|PAK4_ENST00000435673.2_Missense_Mutation_p.E518K|PAK4_ENST00000599386.1_Missense_Mutation_p.E365K|PAK4_ENST00000358301.3_Missense_Mutation_p.E518K|PAK4_ENST00000321944.4_Missense_Mutation_p.E428K|PAK4_ENST00000360442.3_Missense_Mutation_p.E518K	NM_001014831.2	NP_001014831.1	O96013	PAK4_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 4	518	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|cell cycle (GO:0007049)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cytoskeleton organization (GO:0007010)|signal transduction (GO:0007165)	focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|kidney(2)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)	13	all_cancers(60;1.03e-07)|all_epithelial(25;9.66e-08)|all_lung(34;1.58e-07)|Lung NSC(34;1.88e-07)|Ovarian(47;0.0454)		Epithelial(26;4.82e-25)|all cancers(26;2.94e-22)|Lung(45;0.000797)|LUSC - Lung squamous cell carcinoma(53;0.00113)			CTACTTCAACGAGCCACCCCT	0.602																																					p.E518K		Atlas-SNP	.											.	PAK4	40	.	0			c.G1552A						PASS	.	G	LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU,LYS/GLU	0,4406		0,0,2203	166.0	134.0	145.0		1552,1552,1093,1093,1552	5.1	1.0	19		145	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	PAK4	NM_001014831.2,NM_001014832.1,NM_001014834.2,NM_001014835.1,NM_005884.3	56,56,56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	518/592,518/592,365/439,365/439,518/592	39668381	1,13005	2203	4300	6503	SO:0001583	missense	10298	exon8			TTCAACGAGCCAC	AJ011855	CCDS12528.1, CCDS33019.1	19p11-q11	2008-06-17	2008-06-17						16059	protein-coding gene	gene with protein product		605451	"""p21(CDKN1A)-activated kinase 4"""			9822598, 10461188	Standard	NM_001014831		Approved		uc002okn.1	O96013		ENST00000593690.1:c.1552G>A	19.37:g.39668381G>A	ENSP00000469413:p.Glu518Lys	75.0	0.0	0		98.0	4.0	0.0408163	NM_001014832	B4DGG6|Q8N4E1|Q8NCH5|Q8NDE3|Q9BU33|Q9ULS8	Missense_Mutation	SNP	ENST00000593690.1	37	CCDS12528.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.248588	0.80024	0.0	1.16E-4	ENSG00000130669	ENST00000358301;ENST00000321944;ENST00000358801;ENST00000542377;ENST00000435673;ENST00000360442	T;T;T	0.65364	-0.15;-0.15;-0.15	5.07	5.07	0.68467	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.64204	0.2577	N	0.12471	0.22	0.80722	D	1	D;P;P	0.76494	0.999;0.782;0.817	D;B;B	0.70716	0.97;0.115;0.276	T	0.71083	-0.4695	10	0.87932	D	0	.	15.9831	0.80127	0.0:0.0:1.0:0.0	.	428;365;518	O96013-4;O96013-3;O96013	.;.;PAK4_HUMAN	K	518;365;322;274;518;518	ENSP00000351049:E518K;ENSP00000392753:E518K;ENSP00000353625:E518K	ENSP00000326864:E365K	E	+	1	0	PAK4	44360221	1.000000	0.71417	0.979000	0.43373	0.795000	0.44927	9.657000	0.98554	2.629000	0.89072	0.555000	0.69702	GAG	.	.	weak		0.602	PAK4-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463823.1		
COL22A1	169044	hgsc.bcm.edu	37	8	139609156	139609156	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:139609156G>A	ENST00000303045.6	-	62	4869	c.4423C>T	c.(4423-4425)Cag>Tag	p.Q1475*	COL22A1_ENST00000435777.1_Nonsense_Mutation_p.Q1455*|COL22A1_ENST00000341807.4_5'UTR	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	1475	Gly-rich.|Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)		p.Q1475K(1)		breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			CTTTCAAGCTGCTTCCCCAGC	0.507										HNSCC(7;0.00092)																											p.Q1475X		Atlas-SNP	.											COL22A1,NS,carcinoma,0,1	COL22A1	390	1	1	Substitution - Missense(1)	lung(1)	c.C4423T						PASS	.						182.0	182.0	182.0					8																	139609156		2203	4300	6503	SO:0001587	stop_gained	169044	exon62			CAAGCTGCTTCCC	AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.4423C>T	8.37:g.139609156G>A	ENSP00000303153:p.Gln1475*	113.0	0.0	0		92.0	20.0	0.217391	NM_152888	B7ZMH0|C9K0G4|Q8IVT9	Nonsense_Mutation	SNP	ENST00000303045.6	37	CCDS6376.1	.	.	.	.	.	.	.	.	.	.	G	47	13.734218	0.99760	.	.	ENSG00000169436	ENST00000303045;ENST00000435777;ENST00000545577	.	.	.	5.06	5.06	0.68205	.	0.000000	0.44688	U	0.000425	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	17.4049	0.87470	0.0:0.0:1.0:0.0	.	.	.	.	X	1475;1455;1168	.	ENSP00000303153:Q1475X	Q	-	1	0	COL22A1	139678338	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	8.323000	0.90002	2.349000	0.79799	0.563000	0.77884	CAG	.	.	none		0.507	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2	XM_291257	
CLK2	1196	hgsc.bcm.edu	37	1	155239302	155239302	+	Missense_Mutation	SNP	G	G	A	rs375441160		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:155239302G>A	ENST00000368361.4	-	3	691	c.376C>T	c.(376-378)Cgg>Tgg	p.R126W	CLK2_ENST00000497188.1_5'Flank|CLK2_ENST00000361168.5_Missense_Mutation_p.R126W|CLK2_ENST00000355560.4_Missense_Mutation_p.R125W|CLK2_ENST00000536801.1_Missense_Mutation_p.R126W			P49760	CLK2_HUMAN	CDC-like kinase 2	126					negative regulation of gluconeogenesis (GO:0045721)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of RNA splicing (GO:0043484)|response to ionizing radiation (GO:0010212)|response to retinoic acid (GO:0032526)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|lung(12)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	22	all_lung(78;2.32e-23)|Hepatocellular(266;0.0877)|all_hematologic(923;0.088)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			CTAAATGTCCGGCTGCGCCTC	0.597								Other conserved DNA damage response genes					G|||	1	0.000199681	0.0008	0.0	5008	,	,		18555	0.0		0.0	False		,,,				2504	0.0				p.R126W		Atlas-SNP	.											.	CLK2	55	.	0			c.C376T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	69.0	63.0	65.0		376	3.0	1.0	1		65	2,8598		0,2,4298	no	missense	CLK2	NM_003993.2	101	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	126/499	155239302	2,13004	2203	4300	6503	SO:0001583	missense	1196	exon3			ATGTCCGGCTGCG	L29218	CCDS1107.1, CCDS72939.1	1q21	2008-05-02			ENSG00000176444	ENSG00000176444		"""CDC-like kinases"""	2069	protein-coding gene	gene with protein product		602989				7990150, 9856501	Standard	XM_005244876		Approved	clk2	uc001fjw.3	P49760	OTTHUMG00000035873	ENST00000368361.4:c.376C>T	1.37:g.155239302G>A	ENSP00000357345:p.Arg126Trp	34.0	0.0	0		58.0	20.0	0.344828	NM_003993	B1AVS9|B5MBX6|Q96CQ0	Missense_Mutation	SNP	ENST00000368361.4	37		.	.	.	.	.	.	.	.	.	.	.	17.04	3.286501	0.59867	0.0	2.33E-4	ENSG00000176444	ENST00000361168;ENST00000368361;ENST00000355560;ENST00000536801	T;T;T;T	0.55760	0.51;0.51;0.5;0.51	4.96	3.05	0.35203	.	0.567586	0.20018	N	0.100976	T	0.47893	0.1470	L	0.59436	1.845	0.58432	D	0.999999	D;D	0.69078	0.995;0.997	P;P	0.53401	0.535;0.725	T	0.51980	-0.8636	10	0.56958	D	0.05	.	13.0486	0.58942	0.0:0.0:0.7088:0.2911	.	126;126	P49760;P49760-3	CLK2_HUMAN;.	W	126;126;125;126	ENSP00000354856:R126W;ENSP00000357345:R126W;ENSP00000347759:R125W;ENSP00000441023:R126W	ENSP00000347759:R125W	R	-	1	2	CLK2	153505926	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.717000	0.54911	0.671000	0.31185	0.650000	0.86243	CGG	.	.	none		0.597	CLK2-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000087391.1	NM_003993	
PTCD3	55037	hgsc.bcm.edu	37	2	86352925	86352925	+	Silent	SNP	A	A	G	rs139474497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:86352925A>G	ENST00000254630.7	+	12	939	c.873A>G	c.(871-873)gtA>gtG	p.V291V	PTCD3_ENST00000409277.3_3'UTR	NM_017952.5	NP_060422.4	Q96EY7	PTCD3_HUMAN	pentatricopeptide repeat domain 3	291					mitochondrial translation (GO:0032543)|regulation of translation (GO:0006417)	mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|ribosomal small subunit binding (GO:0043024)|rRNA binding (GO:0019843)			NS(1)|breast(2)|endometrium(3)|kidney(4)|large_intestine(4)|lung(6)|ovary(1)|prostate(1)	22						CAGCTGATGTATACACATTTA	0.338													A|||	28	0.00559105	0.0	0.0086	5008	,	,		20926	0.0		0.0219	False		,,,				2504	0.0				p.V291V		Atlas-SNP	.											.	PTCD3	51	.	0			c.A873G						PASS	.	A		6,4400	11.4+/-27.6	0,6,2197	44.0	49.0	47.0		873	-11.5	0.0	2	dbSNP_134	47	127,8473	64.6+/-126.8	1,125,4174	no	coding-synonymous	PTCD3	NM_017952.5		1,131,6371	GG,GA,AA		1.4767,0.1362,1.0226		291/690	86352925	133,12873	2203	4300	6503	SO:0001819	synonymous_variant	55037	exon12			TGATGTATACACA		CCDS33235.1	2p11.2	2014-02-12	2012-02-24		ENSG00000132300	ENSG00000132300			24717	protein-coding gene	gene with protein product		614918				8889548	Standard	NM_017952		Approved	FLJ20758, DKFZp666K071	uc002sqw.2	Q96EY7	OTTHUMG00000153168	ENST00000254630.7:c.873A>G	2.37:g.86352925A>G		113.0	0.0	0		86.0	38.0	0.44186	NM_017952	A6NHD2|D6W5M1|Q597H0|Q658Y9|Q9BUZ8|Q9NWL0	Silent	SNP	ENST00000254630.7	37	CCDS33235.1																																																																																			A|0.991;G|0.009	0.009	strong		0.338	PTCD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329854.1	NM_017952	
ABL1	25	hgsc.bcm.edu	37	9	133760029	133760029	+	Silent	SNP	C	C	G	rs2229070	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		21.0	0.0	0		27.0	14.0	0.518519	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	
LYST	1130	hgsc.bcm.edu	37	1	235955276	235955276	+	Silent	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:235955276G>T	ENST00000389794.3	-	12	4440	c.4266C>A	c.(4264-4266)gcC>gcA	p.A1422A	LYST_ENST00000536965.1_Intron|LYST_ENST00000389793.2_Silent_p.A1422A			Q99698	LYST_HUMAN	lysosomal trafficking regulator	1422					blood coagulation (GO:0007596)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|defense response to virus (GO:0051607)|endosome to lysosome transport via multivesicular body sorting pathway (GO:0032510)|leukocyte chemotaxis (GO:0030595)|lysosome organization (GO:0007040)|mast cell secretory granule organization (GO:0033364)|melanosome organization (GO:0032438)|microtubule-based process (GO:0007017)|natural killer cell mediated cytotoxicity (GO:0042267)|neutrophil mediated immunity (GO:0002446)|phospholipid homeostasis (GO:0055091)|phospholipid metabolic process (GO:0006644)|pigmentation (GO:0043473)|positive regulation of natural killer cell activation (GO:0032816)|response to drug (GO:0042493)|secretion of lysosomal enzymes (GO:0033299)|T cell mediated immunity (GO:0002456)	cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)				NS(1)|breast(13)|central_nervous_system(3)|cervix(3)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(27)|lung(66)|ovary(7)|pancreas(1)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	162	Ovarian(103;0.0634)|Breast(184;0.23)	all_cancers(173;0.00246)|Prostate(94;0.0771)|Acute lymphoblastic leukemia(190;0.228)	OV - Ovarian serous cystadenocarcinoma(106;0.000674)			ATAAACCCATGGCCTTACTGT	0.458																																					p.A1422A		Atlas-SNP	.											.	LYST	370	.	0			c.C4266A						PASS	.						152.0	155.0	154.0					1																	235955276		2203	4300	6503	SO:0001819	synonymous_variant	1130	exon12			ACCCATGGCCTTA	U70064	CCDS31062.1	1q42.1-q42.2	2014-09-17	2004-12-09	2004-12-10	ENSG00000143669	ENSG00000143669		"""WD repeat domain containing"""	1968	protein-coding gene	gene with protein product		606897	"""Chediak-Higashi syndrome 1"""	CHS1		8717042, 8896560	Standard	NM_000081		Approved	CHS	uc001hxj.3	Q99698	OTTHUMG00000040527	ENST00000389794.3:c.4266C>A	1.37:g.235955276G>T		85.0	0.0	0		85.0	42.0	0.494118	NM_000081	O43274|Q5T2U9|Q96TD7|Q96TD8|Q99709|Q9H133	Silent	SNP	ENST00000389794.3	37	CCDS31062.1																																																																																			.	.	none		0.458	LYST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097533.5		
MDH2	4191	hgsc.bcm.edu	37	7	75687382	75687382	+	Missense_Mutation	SNP	G	G	A	rs111879470	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:75687382G>A	ENST00000315758.5	+	4	509	c.415G>A	c.(415-417)Gtc>Atc	p.V139I	MDH2_ENST00000432020.2_Missense_Mutation_p.V139I|MDH2_ENST00000443006.1_Missense_Mutation_p.V32I	NM_005918.2	NP_005909.2	P40926	MDHM_HUMAN	malate dehydrogenase 2, NAD (mitochondrial)	139					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|internal protein amino acid acetylation (GO:0006475)|malate metabolic process (GO:0006108)|NADH metabolic process (GO:0006734)|oxaloacetate metabolic process (GO:0006107)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	L-malate dehydrogenase activity (GO:0030060)|malate dehydrogenase (NADP+) activity (GO:0046554)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(2)|skin(2)	14						CATGATCTGCGTCATTGCCAA	0.592													a|||	4	0.000798722	0.0	0.0	5008	,	,		19731	0.0		0.004	False		,,,				2504	0.0				p.V139I		Atlas-SNP	.											.	MDH2	35	.	0			c.G415A						PASS	.	A	ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	57.0	47.0	51.0		415	-4.4	0.9	7	dbSNP_132	51	31,8569	21.0+/-64.5	0,31,4269	yes	missense	MDH2	NM_005918.2	29	0,34,6469	AA,AG,GG		0.3605,0.0681,0.2614	benign	139/339	75687382	34,12972	2203	4300	6503	SO:0001583	missense	4191	exon4			ATCTGCGTCATTG		CCDS5581.1, CCDS64691.1, CCDS75622.1	7q11.23	2013-09-20			ENSG00000146701	ENSG00000146701	1.1.1.37		6971	protein-coding gene	gene with protein product		154100					Standard	NM_005918		Approved		uc003ueo.3	P40926	OTTHUMG00000023827	ENST00000315758.5:c.415G>A	7.37:g.75687382G>A	ENSP00000327070:p.Val139Ile	31.0	0.0	0		53.0	20.0	0.377358	NM_005918	A8K414|B2RE78|B4DE44|E9PDB2|O43682	Missense_Mutation	SNP	ENST00000315758.5	37	CCDS5581.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	g	1.743	-0.491096	0.04322	6.81E-4	0.003605	ENSG00000146701	ENST00000315758;ENST00000443006;ENST00000432020	D;D;D	0.90676	-2.71;-2.71;-2.71	5.56	-4.41	0.03590	Lactate/malate dehydrogenase, N-terminal (1);NAD(P)-binding domain (1);	0.347793	0.35903	N	0.002909	T	0.63058	0.2479	N	0.02876	-0.465	0.09310	N	0.999998	B;B	0.09022	0.002;0.0	B;B	0.11329	0.006;0.002	T	0.61456	-0.7059	10	0.02654	T	1	-12.2486	12.6346	0.56677	0.6019:0.0:0.3981:0.0	.	139;139	E9PDB2;P40926	.;MDHM_HUMAN	I	139;32;139	ENSP00000327070:V139I;ENSP00000416929:V32I;ENSP00000408649:V139I	ENSP00000327070:V139I	V	+	1	0	MDH2	75525318	0.934000	0.31675	0.889000	0.34880	0.512000	0.34134	0.266000	0.18534	-0.966000	0.03587	-2.037000	0.00419	GTC	G|0.998;A|0.002	0.002	strong		0.592	MDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252851.1		
IL34	146433	hgsc.bcm.edu	37	16	70693991	70693991	+	Silent	SNP	C	C	T	rs138439611		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:70693991C>T	ENST00000288098.2	+	6	1013	c.630C>T	c.(628-630)acC>acT	p.T210T	IL34_ENST00000429149.2_Silent_p.T210T|FLJ00418_ENST00000597002.1_5'Flank|IL34_ENST00000566361.1_Silent_p.T185T	NM_001172772.1	NP_001166243.1	Q6ZMJ4	IL34_HUMAN	interleukin 34	210					inflammatory response (GO:0006954)|innate immune response (GO:0045087)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein phosphorylation (GO:0001934)	extracellular space (GO:0005615)	macrophage colony-stimulating factor receptor binding (GO:0005157)			breast(1)|central_nervous_system(1)|kidney(9)|large_intestine(1)|lung(1)|skin(2)|urinary_tract(2)	17						ATGCGGCCACCCAGCTGTACC	0.652																																					p.T210T		Atlas-SNP	.											.	IL34	26	.	0			c.C630T						PASS	.	C	,,	0,4396		0,0,2198	84.0	94.0	91.0		627,630,630	-1.8	0.0	16	dbSNP_134	91	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous,coding-synonymous	IL34	NM_001172771.1,NM_001172772.1,NM_152456.2	,,	0,2,6496	TT,TC,CC		0.0233,0.0,0.0154	,,	209/242,210/243,210/243	70693991	2,12994	2198	4300	6498	SO:0001819	synonymous_variant	146433	exon7			GGCCACCCAGCTG	BC029804	CCDS10895.1	16q22.1	2008-08-01	2008-06-04	2008-06-04	ENSG00000157368	ENSG00000157368		"""Interleukins and interleukin receptors"""	28529	protein-coding gene	gene with protein product		612081	"""chromosome 16 open reading frame 77"""	C16orf77		18467591	Standard	NM_152456		Approved	MGC34647, IL-34	uc002ezh.2	Q6ZMJ4	OTTHUMG00000137581	ENST00000288098.2:c.630C>T	16.37:g.70693991C>T		153.0	0.0	0		189.0	65.0	0.343915	NM_152456	B2RC28|B2Z4A8|B2ZC70|Q8N6L2	Silent	SNP	ENST00000288098.2	37	CCDS10895.1																																																																																			C|1.000;T|0.000	0.000	weak		0.652	IL34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268971.3	NM_152456	
CDHR2	54825	hgsc.bcm.edu	37	5	176004680	176004680	+	Missense_Mutation	SNP	A	A	C	rs34767982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176004680A>C	ENST00000510636.1	+	14	1667	c.1393A>C	c.(1393-1395)Atg>Ctg	p.M465L	CDHR2_ENST00000506348.1_Missense_Mutation_p.M465L|CDHR2_ENST00000261944.5_Missense_Mutation_p.M465L	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	465	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CTCCGTCGCCATGGTGACCAT	0.632													A|||	98	0.0195687	0.0333	0.0072	5008	,	,		18027	0.0		0.0229	False		,,,				2504	0.0266				p.M465L		Atlas-SNP	.											.	CDHR2	152	.	0			c.A1393C						PASS	.	A	LEU/MET,LEU/MET	129,4277	95.3+/-134.0	0,129,2074	90.0	82.0	85.0		1393,1393	-5.5	0.0	5	dbSNP_126	85	150,8450	73.2+/-135.9	2,146,4152	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	15,15	2,275,6226	CC,CA,AA		1.7442,2.9278,2.1452	benign,benign	465/1311,465/1311	176004680	279,12727	2203	4300	6503	SO:0001583	missense	54825	exon14			GTCGCCATGGTGA	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.1393A>C	5.37:g.176004680A>C	ENSP00000424565:p.Met465Leu	44.0	0.0	0		67.0	33.0	0.492537	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	33	0.01510989010989011	18	0.036585365853658534	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	13.81	2.349616	0.41599	0.029278	0.017442	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.59772	0.24;0.24;0.24	4.8	-5.53	0.02552	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.06826	0.0174	N	0.05012	-0.13	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.06250	-1.0837	9	0.44086	T	0.13	0.0331	2.189	0.03894	0.446:0.2189:0.0691:0.266	rs34767982;rs62404700	465	Q9BYE9	CDHR2_HUMAN	L	465	ENSP00000424565:M465L;ENSP00000261944:M465L;ENSP00000421078:M465L	ENSP00000261944:M465L	M	+	1	0	CDHR2	175937286	0.063000	0.20901	0.000000	0.03702	0.408000	0.30992	0.800000	0.27042	-1.193000	0.02688	0.391000	0.25812	ATG	A|0.979;C|0.021	0.021	strong		0.632	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
TMEM240	339453	hgsc.bcm.edu	37	1	1471126	1471126	+	Silent	SNP	G	G	A	rs114114317	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1471126G>A	ENST00000378733.4	-	3	226	c.216C>T	c.(214-216)gaC>gaT	p.D72D	TMEM240_ENST00000425828.1_Silent_p.D72D	NM_001114748.1	NP_001108220.1	Q5SV17	TM240_HUMAN	transmembrane protein 240	72						integral component of membrane (GO:0016021)											TCTCGGAGGCGTCCACCACCG	0.647													G|||	20	0.00399361	0.0015	0.0043	5008	,	,		10251	0.0		0.0149	False		,,,				2504	0.0				p.D72D		Atlas-SNP	.											.	TMEM240	8	.	0			c.C216T						PASS	.	G		2,1382		0,2,690	66.0	69.0	68.0		216	2.5	1.0	1	dbSNP_132	68	37,3145		0,37,1554	no	coding-synonymous	C1orf70	NM_001114748.1		0,39,2244	AA,AG,GG		1.1628,0.1445,0.8541		72/174	1471126	39,4527	692	1591	2283	SO:0001819	synonymous_variant	339453	exon3			GGAGGCGTCCACC		CCDS44040.1	1p36.33	2011-11-25	2011-11-25	2011-11-25	ENSG00000205090	ENSG00000205090			25186	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 70"""	C1orf70			Standard	NM_001114748		Approved		uc009vkf.3	Q5SV17	OTTHUMG00000042193	ENST00000378733.4:c.216C>T	1.37:g.1471126G>A		85.0	0.0	0		78.0	30.0	0.384615	NM_001114748	B9EJG7	Silent	SNP	ENST00000378733.4	37	CCDS44040.1																																																																																			G|0.994;A|0.006	0.006	strong		0.647	TMEM240-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100391.2	NM_001114748	
MYO3A	53904	hgsc.bcm.edu	37	10	26455090	26455090	+	Missense_Mutation	SNP	G	G	A	rs34918608	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:26455090G>A	ENST00000265944.5	+	27	3260	c.3094G>A	c.(3094-3096)Gct>Act	p.A1032T	MYO3A_ENST00000543632.1_Intron	NM_017433.4	NP_059129.3	Q8NEV4	MYO3A_HUMAN	myosin IIIA	1032	Myosin motor.		A -> T (in dbSNP:rs34918608). {ECO:0000269|PubMed:17344846}.		ATP catabolic process (GO:0006200)|inner ear development (GO:0048839)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of filopodium assembly (GO:0051491)|protein autophosphorylation (GO:0046777)|response to stimulus (GO:0050896)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|filopodium (GO:0030175)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|photoreceptor inner segment (GO:0001917)|stereocilium bundle tip (GO:0032426)	actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|plus-end directed microfilament motor activity (GO:0060002)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(9)|central_nervous_system(3)|endometrium(9)|kidney(10)|large_intestine(28)|liver(1)|lung(46)|ovary(11)|pancreas(1)|prostate(6)|skin(11)|stomach(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	146						CGATAACTGGGCTCTTGGAAA	0.408													G|||	18	0.00359425	0.0008	0.0072	5008	,	,		18704	0.0		0.0119	False		,,,				2504	0.0				p.A1032T		Atlas-SNP	.											MYO3A,NS,carcinoma,-1,1	MYO3A	371	1	0			c.G3094A						PASS	.	G	THR/ALA	8,4398	12.9+/-30.5	0,8,2195	96.0	103.0	101.0		3094	5.2	1.0	10	dbSNP_126	101	73,8527	44.0+/-102.2	1,71,4228	yes	missense	MYO3A	NM_017433.4	58	1,79,6423	AA,AG,GG		0.8488,0.1816,0.6228	possibly-damaging	1032/1617	26455090	81,12925	2203	4300	6503	SO:0001583	missense	53904	exon27			AACTGGGCTCTTG	AF229172	CCDS7148.1	10p11.1	2011-09-27	2004-05-19		ENSG00000095777	ENSG00000095777		"""Myosins / Myosin superfamily : Class III"""	7601	protein-coding gene	gene with protein product		606808	"""deafness, autosomal recessive 30"""	DFNB30		10936054	Standard	NM_017433		Approved		uc001isn.2	Q8NEV4	OTTHUMG00000017837	ENST00000265944.5:c.3094G>A	10.37:g.26455090G>A	ENSP00000265944:p.Ala1032Thr	45.0	0.0	0		35.0	18.0	0.514286	NM_017433	Q4G0X2|Q5VZ28|Q8WX17|Q9NYS8	Missense_Mutation	SNP	ENST00000265944.5	37	CCDS7148.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	20.1	3.938089	0.73557	0.001816	0.008488	ENSG00000095777	ENST00000265944	D	0.87256	-2.23	6.07	5.17	0.71159	Myosin head, motor domain (2);	0.231325	0.47455	N	0.000222	D	0.84338	0.5450	M	0.63428	1.95	0.80722	D	1	P	0.43412	0.806	P	0.47705	0.555	D	0.84836	0.0805	10	0.39692	T	0.17	.	12.1062	0.53813	0.1365:0.0:0.8635:0.0	rs34918608;rs61729832	1032	Q8NEV4	MYO3A_HUMAN	T	1032	ENSP00000265944:A1032T	ENSP00000265944:A1032T	A	+	1	0	MYO3A	26495096	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.247000	0.65416	1.586000	0.49944	0.650000	0.86243	GCT	G|0.994;A|0.006	0.006	strong		0.408	MYO3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047259.1	NM_017433	
HMGCR	3156	hgsc.bcm.edu	37	5	74652199	74652199	+	Missense_Mutation	SNP	A	A	G	rs5908	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:74652199A>G	ENST00000287936.4	+	15	2068	c.1912A>G	c.(1912-1914)Ata>Gta	p.I638V	HMGCR_ENST00000343975.5_Missense_Mutation_p.I585V|HMGCR_ENST00000511206.1_Missense_Mutation_p.I638V	NM_000859.2	NP_000850.1	P04035	HMDH_HUMAN	3-hydroxy-3-methylglutaryl-CoA reductase	638	Catalytic.		I -> V (in dbSNP:rs5908). {ECO:0000269|PubMed:10391209}.		aging (GO:0007568)|cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|coenzyme A metabolic process (GO:0015936)|isoprenoid biosynthetic process (GO:0008299)|myoblast differentiation (GO:0045445)|negative regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061179)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of vasodilation (GO:0045908)|negative regulation of wound healing (GO:0061045)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of skeletal muscle tissue development (GO:0048643)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein tetramerization (GO:0051262)|response to ethanol (GO:0045471)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|ubiquinone metabolic process (GO:0006743)|visual learning (GO:0008542)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|peroxisomal membrane (GO:0005778)	coenzyme binding (GO:0050662)|hydroxymethylglutaryl-CoA reductase (NADPH) activity (GO:0004420)|hydroxymethylglutaryl-CoA reductase activity (GO:0042282)|NADPH binding (GO:0070402)			breast(1)|endometrium(5)|kidney(3)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)	20		all_lung(232;0.00101)|Lung NSC(167;0.00278)|Ovarian(174;0.0129)|Prostate(461;0.174)		OV - Ovarian serous cystadenocarcinoma(47;2.24e-54)	Atorvastatin(DB01076)|Fluvastatin(DB01095)|Lovastatin(DB00227)|Pitavastatin(DB08860)|Pravastatin(DB00175)|Rosuvastatin(DB01098)|Simvastatin(DB00641)	TCATACAAGTATAGCTGGACG	0.348													A|||	25	0.00499201	0.0	0.0043	5008	,	,		17301	0.0		0.0159	False		,,,				2504	0.0061				p.I638V		Atlas-SNP	.											.	HMGCR	53	.	0			c.A1912G						PASS	.	A	VAL/ILE,VAL/ILE	20,4386	27.2+/-55.0	0,20,2183	91.0	93.0	92.0		1912,1753	-2.0	0.1	5	dbSNP_52	92	163,8437	76.6+/-139.3	0,163,4137	yes	missense,missense	HMGCR	NM_000859.2,NM_001130996.1	29,29	0,183,6320	GG,GA,AA		1.8953,0.4539,1.407	benign,benign	638/889,585/836	74652199	183,12823	2203	4300	6503	SO:0001583	missense	3156	exon15			ACAAGTATAGCTG		CCDS4027.1, CCDS47234.1	5q13.3-q14	2012-10-02	2010-04-30		ENSG00000113161	ENSG00000113161	1.1.1.88, 1.1.1.34		5006	protein-coding gene	gene with protein product	"""hydroxymethylglutaryl-CoA reductase"", ""3-hydroxy-3-methylglutaryl CoA reductase (NADPH)"""	142910	"""3-hydroxy-3-methylglutaryl-Coenzyme A reductase"""				Standard	NM_000859		Approved		uc003kdp.3	P04035	OTTHUMG00000102069	ENST00000287936.4:c.1912A>G	5.37:g.74652199A>G	ENSP00000287936:p.Ile638Val	161.0	0.0	0		183.0	97.0	0.530055	NM_000859	B7Z3Y9|Q8N190	Missense_Mutation	SNP	ENST00000287936.4	37	CCDS4027.1	15	0.006868131868131868	0	0.0	1	0.0027624309392265192	0	0.0	14	0.018469656992084433	A	9.059	0.994103	0.19043	0.004539	0.018953	ENSG00000113161	ENST00000511206;ENST00000544469;ENST00000287936;ENST00000343975	T;T;T	0.43294	0.95;0.95;0.95	6.02	-2.05	0.07321	Hydroxymethylglutaryl-CoA reductase, class I/II, NAD/NADP-binding (2);Hydroxymethylglutaryl-CoA reductase, class I/II, substrate-binding (1);	0.522971	0.23585	N	0.046609	T	0.08403	0.0209	N	0.16743	0.435	0.26226	N	0.979089	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.002;0.001;0.002	T	0.05716	-1.0868	10	0.26408	T	0.33	-2.7341	0.1633	0.00105	0.3439:0.226:0.177:0.2532	rs5908;rs17648133;rs52793370;rs5908	638;585;638	B2R649;P04035-2;P04035	.;.;HMDH_HUMAN	V	638;569;638;585	ENSP00000426745:I638V;ENSP00000287936:I638V;ENSP00000340816:I585V	ENSP00000287936:I638V	I	+	1	0	HMGCR	74687955	0.014000	0.17966	0.142000	0.22268	0.982000	0.71751	-0.342000	0.07801	-0.440000	0.07211	0.529000	0.55759	ATA	A|0.990;G|0.010	0.010	strong		0.348	HMGCR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219877.2		
OR2B3	442184	hgsc.bcm.edu	37	6	29054923	29054923	+	Missense_Mutation	SNP	A	A	G	rs149723131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:29054923A>G	ENST00000377173.2	-	1	167	c.103T>C	c.(103-105)Tac>Cac	p.Y35H		NM_001005226.2	NP_001005226.1	O76000	OR2B3_HUMAN	olfactory receptor, family 2, subfamily B, member 3	35						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(1)|kidney(2)|lung(17)|prostate(1)|skin(2)	24						GTGATTGTGTATGATATTAAC	0.408													A|||	10	0.00199681	0.0	0.0	5008	,	,		19983	0.0		0.0099	False		,,,				2504	0.0				p.Y35H		Atlas-SNP	.											OR2B3,NS,carcinoma,+2,1	OR2B3	44	1	0			c.T103C						PASS	.	A	HIS/TYR	15,4391	21.2+/-45.6	0,15,2188	135.0	124.0	128.0		103	2.7	0.0	6	dbSNP_134	128	87,8513	49.8+/-109.6	0,87,4213	yes	missense	OR2B3	NM_001005226.2	83	0,102,6401	GG,GA,AA		1.0116,0.3404,0.7843	probably-damaging	35/314	29054923	102,12904	2203	4300	6503	SO:0001583	missense	442184	exon1			TTGTGTATGATAT		CCDS34358.1	6p22.2-p21.31	2012-08-09	2008-10-22	2008-10-22	ENSG00000204703	ENSG00000204703		"""GPCR / Class A : Olfactory receptors"""	8238	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily B, member 3 pseudogene"""	OR2B3P			Standard	NM_001005226		Approved	OR6-4	uc003nlx.3	O76000	OTTHUMG00000031226	ENST00000377173.2:c.103T>C	6.37:g.29054923A>G	ENSP00000366378:p.Tyr35His	85.0	0.0	0		54.0	25.0	0.462963	NM_001005226	B0UYQ1|Q5ST41|Q96R13	Missense_Mutation	SNP	ENST00000377173.2	37	CCDS34358.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	A	14.13	2.442681	0.43326	0.003404	0.010116	ENSG00000204703	ENST00000377173	T	0.04654	3.58	3.9	2.72	0.32119	.	0.000000	0.36854	U	0.002376	T	0.15825	0.0381	H	0.95043	3.615	0.09310	N	1	D	0.89917	1.0	D	0.87578	0.998	T	0.12041	-1.0563	10	0.87932	D	0	.	8.8277	0.35065	0.9058:0.0:0.0942:0.0	.	35	O76000	OR2B3_HUMAN	H	35	ENSP00000366378:Y35H	ENSP00000366378:Y35H	Y	-	1	0	OR2B3	29162902	0.799000	0.28903	0.011000	0.14972	0.799000	0.45148	4.031000	0.57267	0.370000	0.24538	-0.396000	0.06452	TAC	A|0.993;G|0.007	0.007	strong		0.408	OR2B3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076469.2		
TBX10	347853	hgsc.bcm.edu	37	11	67399173	67399173	+	Missense_Mutation	SNP	C	C	T	rs146672518	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:67399173C>T	ENST00000335385.3	-	8	1148	c.1061G>A	c.(1060-1062)cGg>cAg	p.R354Q	NUDT8_ENST00000376693.2_5'Flank|NUDT8_ENST00000301490.4_5'Flank	NM_005995.4	NP_005986.2	O75333	TBX10_HUMAN	T-box 10	354					anatomical structure morphogenesis (GO:0009653)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(2)|lung(4)|ovary(1)	7						CCTATCAGCCCGGATGTTGGG	0.652													C|||	18	0.00359425	0.0015	0.0058	5008	,	,		15763	0.0		0.0089	False		,,,				2504	0.0031				p.R354Q		Atlas-SNP	.											.	TBX10	25	.	0			c.G1061A	GRCh37	CM055547	TBX10	M	rs146672518	PASS	.	C	GLN/ARG	6,4394		0,6,2194	22.0	20.0	21.0		1061	-6.5	0.0	11	dbSNP_134	21	99,8487		1,97,4195	yes	missense	TBX10	NM_005995.4	43	1,103,6389	TT,TC,CC		1.153,0.1364,0.8086	benign	354/386	67399173	105,12881	2200	4293	6493	SO:0001583	missense	347853	exon8			TCAGCCCGGATGT	AH006177	CCDS31621.1	11q13.2	2005-10-11	2004-10-05		ENSG00000167800	ENSG00000167800		"""T-boxes"""	11593	protein-coding gene	gene with protein product		604648	"""T-box 7"""	TBX7		9545502	Standard	NM_005995		Approved	TBX13	uc001omp.3	O75333	OTTHUMG00000167291	ENST00000335385.3:c.1061G>A	11.37:g.67399173C>T	ENSP00000335191:p.Arg354Gln	43.0	0.0	0		46.0	26.0	0.565217	NM_005995	Q14D64|Q86XS3	Missense_Mutation	SNP	ENST00000335385.3	37	CCDS31621.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	4.834	0.155029	0.09236	0.001364	0.01153	ENSG00000167800	ENST00000335385	D	0.85955	-2.05	3.79	-6.47	0.01902	.	5.537720	0.00166	N	0.000011	T	0.55242	0.1908	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.53788	-0.8389	10	0.25106	T	0.35	.	2.5625	0.04775	0.1339:0.1628:0.1338:0.5696	.	354	O75333	TBX10_HUMAN	Q	354	ENSP00000335191:R354Q	ENSP00000335191:R354Q	R	-	2	0	TBX10	67155749	0.000000	0.05858	0.001000	0.08648	0.063000	0.16089	-0.708000	0.05035	-0.878000	0.04007	-0.258000	0.10820	CGG	C|0.994;T|0.006	0.006	strong		0.652	TBX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394034.1	NM_005995	
PSG8	440533	hgsc.bcm.edu	37	19	43268388	43268388	+	Missense_Mutation	SNP	G	G	A	rs142689447		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:43268388G>A	ENST00000306511.4	-	2	207	c.110C>T	c.(109-111)aCg>aTg	p.T37M	PSG8_ENST00000401467.2_Missense_Mutation_p.T37M|PSG8_ENST00000404209.4_Missense_Mutation_p.T37M|PSG8_ENST00000406636.3_Intron	NM_182707.2	NP_874366.1	Q9UQ74	PSG8_HUMAN	pregnancy specific beta-1-glycoprotein 8	37	Ig-like V-type.					extracellular region (GO:0005576)				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(19)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	40		Prostate(69;0.00899)				GGCTTCAATCGTGACTTGGGC	0.463													.|||	1	0.000199681	0.0	0.0	5008	,	,		21250	0.0		0.001	False		,,,				2504	0.0				p.T37M		Atlas-SNP	.											.	PSG8	101	.	0			c.C110T						PASS	.	G	MET/THR,,MET/THR	0,4406		0,0,2203	173.0	170.0	171.0		110,,110	1.4	0.0	19	dbSNP_134	171	8,8590	6.4+/-24.3	0,8,4291	no	missense,intron,missense	PSG8	NM_001130167.1,NM_001130168.1,NM_182707.2	81,,81	0,8,6494	AA,AG,GG		0.093,0.0,0.0615	benign,,benign	37/420,,37/427	43268388	8,12996	2203	4299	6502	SO:0001583	missense	440533	exon2			TCAATCGTGACTT	M74106	CCDS33037.1, CCDS46090.1, CCDS46091.1	19q13.2	2013-01-29			ENSG00000124467	ENSG00000124467		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	9525	protein-coding gene	gene with protein product		176397				1672663, 1572651	Standard	NM_182707		Approved		uc002ouo.2	Q9UQ74	OTTHUMG00000151118	ENST00000306511.4:c.110C>T	19.37:g.43268388G>A	ENSP00000305005:p.Thr37Met	135.0	0.0	0		105.0	50.0	0.47619	NM_001130167	A5PKV3|B2RPL4|B4DTI6|O60410|Q68CR6	Missense_Mutation	SNP	ENST00000306511.4	37	CCDS33037.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	5.019	0.189287	0.09547	0.0	9.3E-4	ENSG00000124467	ENST00000404209;ENST00000401467;ENST00000407488;ENST00000306511	T;T;T	0.68331	-0.32;-0.32;-0.32	1.35	1.35	0.21983	Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.72415	0.3457	M	0.77712	2.385	0.09310	N	1	P;B;P;B;B	0.44690	0.841;0.062;0.538;0.174;0.208	P;B;B;B;B	0.52646	0.705;0.063;0.204;0.066;0.109	T	0.60662	-0.7219	9	0.49607	T	0.09	.	6.1568	0.20342	0.0:0.0:1.0:0.0	.	37;37;37;37;37	B5MCQ0;Q9UQ74;E7ENH0;Q9UQ74-3;A5PKV3	.;PSG8_HUMAN;.;.;.	M	37	ENSP00000385869:T37M;ENSP00000386090:T37M;ENSP00000305005:T37M	ENSP00000305005:T37M	T	-	2	0	PSG8	47960228	0.007000	0.16637	0.011000	0.14972	0.031000	0.12232	2.204000	0.42761	1.063000	0.40649	0.184000	0.17185	ACG	G|1.000;A|0.000	0.000	strong		0.463	PSG8-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464526.1		
PKD2	5311	hgsc.bcm.edu	37	4	88996673	88996673	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:88996673G>A	ENST00000508588.1	+	10	1383	c.988G>A	c.(988-990)Gag>Aag	p.E330K	PKD2_ENST00000237596.2_Missense_Mutation_p.E912K|PKD2_ENST00000511337.1_3'UTR|PKD2_ENST00000502363.1_Missense_Mutation_p.E330K			Q9BZL6	KPCD2_HUMAN	polycystic kidney disease 2 (autosomal dominant)	0					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(2)|lung(15)|skin(4)|upper_aerodigestive_tract(1)	36		Hepatocellular(203;0.114)|Acute lymphoblastic leukemia(40;0.221)		OV - Ovarian serous cystadenocarcinoma(123;9.98e-10)|COAD - Colon adenocarcinoma(81;0.0237)		AGTACGTGAAGAGTTGGAACG	0.517																																					p.E912K		Atlas-SNP	.											.	PKD2	82	.	0			c.G2734A						PASS	.						157.0	155.0	155.0					4																	88996673		2203	4300	6503	SO:0001583	missense	5311	exon15			CGTGAAGAGTTGG	U50928	CCDS3627.1	4q22.1	2014-01-28			ENSG00000118762	ENSG00000118762		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""EF-hand domain containing"""	9009	protein-coding gene	gene with protein product	"""transient receptor potential cation channel, subfamily P, member 2"""	173910				8298643	Standard	NM_000297		Approved	PKD4, PC2, Pc-2, TRPP2	uc003hre.3	Q13563	OTTHUMG00000160982	ENST00000508588.1:c.988G>A	4.37:g.88996673G>A	ENSP00000427131:p.Glu330Lys	88.0	0.0	0		93.0	20.0	0.215054	NM_000297	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000508588.1	37		.	.	.	.	.	.	.	.	.	.	G	34	5.343226	0.95783	.	.	ENSG00000118762	ENST00000237596;ENST00000508588;ENST00000502363	T;D;D	0.94613	-0.82;-3.47;-3.47	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.96793	0.8953	M	0.68593	2.085	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	D	0.97032	0.9751	10	0.59425	D	0.04	-22.2119	18.7273	0.91718	0.0:0.0:1.0:0.0	.	912	Q13563	PKD2_HUMAN	K	912;330;330	ENSP00000237596:E912K;ENSP00000427131:E330K;ENSP00000425289:E330K	ENSP00000237596:E912K	E	+	1	0	PKD2	89215697	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.183000	0.94887	2.409000	0.81822	0.585000	0.79938	GAG	.	.	none		0.517	PKD2-002	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000363253.2	NM_000297	
LRRC40	55631	hgsc.bcm.edu	37	1	70616830	70616830	+	Missense_Mutation	SNP	T	T	C	rs3180401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:70616830T>C	ENST00000370952.3	-	13	1577	c.1498A>G	c.(1498-1500)Atc>Gtc	p.I500V		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	500			I -> V (in dbSNP:rs3180401).			membrane (GO:0016020)				breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						GAAAGATTGATCGTTTGCAGT	0.294													T|||	18	0.00359425	0.0015	0.0014	5008	,	,		14238	0.0		0.0149	False		,,,				2504	0.0				p.I500V		Atlas-SNP	.											.	LRRC40	66	.	0			c.A1498G						PASS	.	T	VAL/ILE	21,4377	27.2+/-55.0	0,21,2178	58.0	58.0	58.0		1498	5.7	0.9	1	dbSNP_105	58	141,8447	69.0+/-131.5	1,139,4154	yes	missense	LRRC40	NM_017768.4	29	1,160,6332	CC,CT,TT		1.6418,0.4775,1.2475	benign	500/603	70616830	162,12824	2199	4294	6493	SO:0001583	missense	55631	exon13			GATTGATCGTTTG		CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1498A>G	1.37:g.70616830T>C	ENSP00000359990:p.Ile500Val	204.0	0.0	0		199.0	94.0	0.472362	NM_017768	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	T	9.540	1.113220	0.20795	0.004775	0.016418	ENSG00000066557	ENST00000370952	T	0.53640	0.61	5.74	5.74	0.90152	.	0.097488	0.64402	D	0.000001	T	0.21590	0.0520	L	0.37561	1.115	0.38436	D	0.946563	B	0.29805	0.257	B	0.23018	0.043	T	0.14309	-1.0477	10	0.51188	T	0.08	.	10.3913	0.44171	0.0:0.0727:0.0:0.9273	rs3180401;rs3210316;rs17414609;rs52834337;rs3180401	500	Q9H9A6	LRC40_HUMAN	V	500	ENSP00000359990:I500V	ENSP00000359990:I500V	I	-	1	0	LRRC40	70389418	0.993000	0.37304	0.911000	0.35937	0.431000	0.31685	2.354000	0.44098	2.168000	0.68352	0.533000	0.62120	ATC	T|0.991;C|0.009	0.009	strong		0.294	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1	NM_017768	
TENM1	10178	hgsc.bcm.edu	37	X	123514900	123514900	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:123514900T>C	ENST00000371130.3	-	31	7727	c.7664A>G	c.(7663-7665)aAt>aGt	p.N2555S	STAG2_ENST00000469481.1_Intron|TENM1_ENST00000422452.2_Missense_Mutation_p.N2562S	NM_014253.3	NP_055068.2	Q9UKZ4	TEN1_HUMAN	teneurin transmembrane protein 1	2555					immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|nervous system development (GO:0007399)|neuropeptide signaling pathway (GO:0007218)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|regulation of transcription from RNA polymerase III promoter (GO:0006359)|response to stress (GO:0006950)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)										ATGGGCATTATTGAGAATGGC	0.443																																					p.N2562S		Atlas-SNP	.											.	.	.	.	0			c.A7685G						PASS	.						88.0	79.0	82.0					X																	123514900		2203	4300	6503	SO:0001583	missense	10178	exon32			GCATTATTGAGAA	AF100772	CCDS14609.1, CCDS55488.1	Xq25	2012-10-02	2012-10-02	2012-10-02	ENSG00000009694	ENSG00000009694			8117	protein-coding gene	gene with protein product		300588	"""tenascin M"", ""odz, odd Oz/ten-m homolog 1 (Drosophila)"""	ODZ3, TNM, ODZ1		10331952, 10341219	Standard	NM_001163278		Approved	TEN-M1	uc010nqy.3	Q9UKZ4	OTTHUMG00000022721	ENST00000371130.3:c.7664A>G	X.37:g.123514900T>C	ENSP00000360171:p.Asn2555Ser	52.0	0.0	0		55.0	55.0	1	NM_001163278	B2RTR5|Q5JZ17	Missense_Mutation	SNP	ENST00000371130.3	37	CCDS14609.1	.	.	.	.	.	.	.	.	.	.	T	18.76	3.692756	0.68271	.	.	ENSG00000009694	ENST00000371130;ENST00000422452	D;D	0.87491	-2.26;-2.23	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.91754	0.7392	M	0.63843	1.955	0.80722	D	1	D;D;D	0.89917	0.997;0.997;1.0	D;D;D	0.83275	0.97;0.985;0.996	D	0.90007	0.4118	10	0.24483	T	0.36	.	15.1686	0.72850	0.0:0.0:0.0:1.0	.	2561;2562;2555	B7ZMH4;B2RTR5;Q9UKZ4	.;.;TEN1_HUMAN	S	2555;2562	ENSP00000360171:N2555S;ENSP00000403954:N2562S	ENSP00000360171:N2555S	N	-	2	0	ODZ1	123342581	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	8.040000	0.89188	1.965000	0.57142	0.486000	0.48141	AAT	.	.	none		0.443	TENM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058985.1	NM_014253	
SCN7A	6332	hgsc.bcm.edu	37	2	167284444	167284444	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:167284444G>A	ENST00000409855.1	-	17	2833	c.2707C>T	c.(2707-2709)Cgc>Tgc	p.R903C		NM_002976.3	NP_002967.2	Q01118	SCN7A_HUMAN	sodium channel, voltage-gated, type VII, alpha subunit	903					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion homeostasis (GO:0055078)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	glial cell projection (GO:0097386)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(30)|prostate(4)|soft_tissue(1)|urinary_tract(1)	44					Valproic Acid(DB00313)	GAAGATCCGCGTCTGCAACCT	0.383																																					p.R903C		Atlas-SNP	.											SCN7A_ENST00000409855,NS,carcinoma,+1,6	SCN7A	410	6	0			c.C2707T						PASS	.						90.0	83.0	85.0					2																	167284444		1856	4093	5949	SO:0001583	missense	6332	exon17			ATCCGCGTCTGCA	M91556	CCDS46442.1	2q21-q23	2012-03-05	2012-02-28	2002-06-14	ENSG00000136546	ENSG00000136546		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10594	protein-coding gene	gene with protein product		182392	"""sodium channel, voltage-gated, type VI, alpha"", ""sodium channel, voltage-gated, type VII, alpha"""	SCN6A		10198179	Standard	NM_002976		Approved	Nav2.1, Nav2.2, NaG	uc002udu.2	Q01118	OTTHUMG00000154078	ENST00000409855.1:c.2707C>T	2.37:g.167284444G>A	ENSP00000386796:p.Arg903Cys	92.0	0.0	0		96.0	24.0	0.25	NM_002976		Missense_Mutation	SNP	ENST00000409855.1	37	CCDS46442.1	.	.	.	.	.	.	.	.	.	.	G	14.08	2.428994	0.43122	.	.	ENSG00000136546	ENST00000409855;ENST00000259060	D	0.84730	-1.89	5.2	3.32	0.38043	Sodium ion transport-associated (1);	1.098480	0.06996	N	0.822524	D	0.87700	0.6243	M	0.80616	2.505	0.09310	N	1	D	0.61697	0.99	P	0.51101	0.659	T	0.71537	-0.4563	10	0.33141	T	0.24	.	4.2946	0.10895	0.0858:0.1551:0.5991:0.16	.	903	Q01118	SCN7A_HUMAN	C	903	ENSP00000386796:R903C	ENSP00000259060:R903C	R	-	1	0	SCN7A	166992690	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.174000	0.09839	0.630000	0.30394	0.591000	0.81541	CGC	.	.	none		0.383	SCN7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333745.1		
ZP2	7783	hgsc.bcm.edu	37	16	21213101	21213101	+	Missense_Mutation	SNP	T	T	C	rs201054139		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21213101T>C	ENST00000574002.1	-	14	1912	c.1430A>G	c.(1429-1431)aAc>aGc	p.N477S	ZP2_ENST00000219593.4_Missense_Mutation_p.N477S|ZP2_ENST00000574091.1_Missense_Mutation_p.N468S|AF001550.7_ENST00000572747.1_RNA			Q05996	ZP2_HUMAN	zona pellucida glycoprotein 2 (sperm receptor)	477	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|intracellular protein transport (GO:0006886)|multicellular organism reproduction (GO:0032504)|prevention of polyspermy (GO:0060468)|signal transduction (GO:0007165)|single fertilization (GO:0007338)	endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|coreceptor activity (GO:0015026)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(16)|ovary(1)|prostate(1)|stomach(1)	41				GBM - Glioblastoma multiforme(48;0.0573)		GCTTTCAACGTTGATGTTTAG	0.418													T|||	1	0.000199681	0.0	0.0014	5008	,	,		20965	0.0		0.0	False		,,,				2504	0.0				p.N477S		Atlas-SNP	.											.	ZP2	92	.	0			c.A1430G						PASS	.						166.0	151.0	156.0					16																	21213101		2200	4300	6500	SO:0001583	missense	7783	exon13			TCAACGTTGATGT	M90366	CCDS10596.1, CCDS73843.1	16p12	2014-07-04			ENSG00000103310	ENSG00000103310		"""Zona pellucida glycoproteins"""	13188	protein-coding gene	gene with protein product		182888				8385033	Standard	XM_005255562		Approved	ZPA	uc002dii.2	Q05996	OTTHUMG00000090681	ENST00000574002.1:c.1430A>G	16.37:g.21213101T>C	ENSP00000460971:p.Asn477Ser	210.0	0.0	0		208.0	104.0	0.5	NM_003460	B2R7J2|Q4VAN9|Q4VAP0|Q4VAP1	Missense_Mutation	SNP	ENST00000574002.1	37	CCDS10596.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	4.765	0.142318	0.09083	.	.	ENSG00000103310	ENST00000219593	D	0.81499	-1.5	5.64	-0.5	0.12012	Zona pellucida sperm-binding protein (3);	0.414857	0.24343	N	0.039351	T	0.68970	0.3059	L	0.33245	0.995	0.09310	N	1	B;B	0.25105	0.118;0.1	B;B	0.32090	0.14;0.088	T	0.54768	-0.8244	10	0.21540	T	0.41	-4.7459	11.0072	0.47641	0.0:0.3295:0.0:0.6705	.	468;477	Q4VAP1;Q05996	.;ZP2_HUMAN	S	477	ENSP00000219593:N477S	ENSP00000219593:N477S	N	-	2	0	ZP2	21120602	0.000000	0.05858	0.000000	0.03702	0.125000	0.20455	0.162000	0.16501	-0.387000	0.07809	-0.326000	0.08463	AAC	T|1.000;C|0.000	0.000	strong		0.418	ZP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207365.2		
KCNU1	157855	hgsc.bcm.edu	37	8	36692303	36692303	+	Splice_Site	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:36692303G>T	ENST00000399881.3	+	12	1249		c.e12-1			NM_001031836.2	NP_001027006.2	A8MYU2	KCNU1_HUMAN	potassium channel, subfamily U, member 1						multicellular organism reproduction (GO:0032504)|potassium ion transmembrane transport (GO:0071805)|single fertilization (GO:0007338)|sperm-egg recognition (GO:0035036)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	large conductance calcium-activated potassium channel activity (GO:0060072)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(31)|ovary(1)|urinary_tract(1)	57				KIRC - Kidney renal clear cell carcinoma(67;0.0504)|Kidney(114;0.0634)		TTGAAGGGTAGGTGGAATCTG	0.408																																					.		Atlas-SNP	.											KCNU1_ENST00000399881,colon,carcinoma,0,2	KCNU1	359	2	0			c.1213-1G>T						PASS	.						103.0	100.0	101.0					8																	36692303		1871	4112	5983	SO:0001630	splice_region_variant	157855	exon12			AGGGTAGGTGGAA	BC028701	CCDS55220.1	8p11.2	2012-07-05				ENSG00000215262		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18867	protein-coding gene	gene with protein product		615215				16382103	Standard	NM_001031836		Approved	KCa5.1, Slo3, KCNMC1, Kcnma3	uc010lvw.3	A8MYU2		ENST00000399881.3:c.1213-1G>T	8.37:g.36692303G>T		141.0	0.0	0		116.0	61.0	0.525862	NM_001031836		Splice_Site	SNP	ENST00000399881.3	37	CCDS55220.1	.	.	.	.	.	.	.	.	.	.	G	12.20	1.865287	0.32977	.	.	ENSG00000215262	ENST00000399881	.	.	.	5.9	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.9023	0.63812	0.0733:0.0:0.9266:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	KCNU1	36811461	1.000000	0.71417	0.998000	0.56505	0.080000	0.17528	8.882000	0.92420	1.499000	0.48617	0.650000	0.86243	.	.	.	none		0.408	KCNU1-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376631.1	NM_001031836	Intron
GZF1	64412	hgsc.bcm.edu	37	20	23350290	23350290	+	Missense_Mutation	SNP	G	G	A	rs144872945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:23350290G>A	ENST00000338121.5	+	5	1774	c.1697G>A	c.(1696-1698)cGc>cAc	p.R566H	GZF1_ENST00000377051.2_Missense_Mutation_p.R566H|GZF1_ENST00000542987.1_Missense_Mutation_p.R75H|GZF1_ENST00000544236.1_Missense_Mutation_p.R90H			Q9H116	GZF1_HUMAN	GDNF-inducible zinc finger protein 1	566					branching involved in ureteric bud morphogenesis (GO:0001658)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|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 distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001206)|sequence-specific DNA binding (GO:0043565)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|urinary_tract(2)	24	Lung NSC(19;0.0605)|Colorectal(13;0.0993)|all_lung(19;0.135)					CAGCGCCACCGCCGCATCCAC	0.632													G|||	5	0.000998403	0.0	0.0014	5008	,	,		18962	0.0		0.004	False		,,,				2504	0.0				p.R566H		Atlas-SNP	.											GZF1,NS,adenocarcinoma,0,1	GZF1	61	1	0			c.G1697A						PASS	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	94.0	85.0	88.0		1697	3.7	1.0	20	dbSNP_134	88	12,8588	9.1+/-34.3	0,12,4288	yes	missense	GZF1	NM_022482.3	29	0,13,6490	AA,AG,GG		0.1395,0.0227,0.1	benign	566/712	23350290	13,12993	2203	4300	6503	SO:0001583	missense	64412	exon4			GCCACCGCCGCAT	AK025447	CCDS13151.1	20p11.21	2013-01-09	2006-09-19	2006-09-19	ENSG00000125812	ENSG00000125812		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	15808	protein-coding gene	gene with protein product		613842	"""zinc finger protein 336"""	ZNF336		14522971, 16049025	Standard	NM_022482		Approved	dJ322G13.2, ZBTB23	uc002wsz.3	Q9H116	OTTHUMG00000032069	ENST00000338121.5:c.1697G>A	20.37:g.23350290G>A	ENSP00000338290:p.Arg566His	80.0	0.0	0		78.0	33.0	0.423077	NM_022482	A8K199|B2RBC3|B3KPL4|B4DF58|D3DW39|Q54A22|Q96N08|Q9BQK9|Q9H117|Q9H6W6	Missense_Mutation	SNP	ENST00000338121.5	37	CCDS13151.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.792	1.178312	0.21787	2.27E-4	0.001395	ENSG00000125812	ENST00000544236;ENST00000338121;ENST00000542987;ENST00000377051	T;T;T;T	0.37584	3.17;1.19;3.17;1.19	5.95	3.74	0.42951	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.205916	0.32055	N	0.006644	T	0.15739	0.0379	N	0.26092	0.79	0.35685	D	0.814363	B	0.06786	0.001	B	0.06405	0.002	T	0.16129	-1.0413	10	0.16896	T	0.51	.	7.9996	0.30288	0.8298:0.0:0.1702:0.0	.	566	Q9H116	GZF1_HUMAN	H	90;566;75;566	ENSP00000445458:R90H;ENSP00000338290:R566H;ENSP00000445118:R75H;ENSP00000366250:R566H	ENSP00000338290:R566H	R	+	2	0	GZF1	23298290	1.000000	0.71417	0.993000	0.49108	0.987000	0.75469	6.157000	0.71846	0.545000	0.28902	0.655000	0.94253	CGC	G|0.999;A|0.001	0.001	strong		0.632	GZF1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078333.1	NM_022482	
TEKT4	150483	hgsc.bcm.edu	37	2	95539833	95539833	+	Silent	SNP	C	C	T	rs111469930	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:95539833C>T	ENST00000295201.4	+	3	830	c.693C>T	c.(691-693)taC>taT	p.Y231Y	AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	231					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						CTCATCCGTACTCCACCACCT	0.662													.|||	28	0.00559105	0.0015	0.0101	5008	,	,		14386	0.0		0.0149	False		,,,				2504	0.0041				p.Y231Y		Atlas-SNP	.											.	TEKT4	72	.	0			c.C693T						PASS	.	C		14,4392		0,14,2189	73.0	70.0	71.0		693	2.2	0.0	2	dbSNP_132	71	177,8423		1,175,4124	no	coding-synonymous	TEKT4	NM_144705.2		1,189,6313	TT,TC,CC		2.0581,0.3177,1.4686		231/436	95539833	191,12815	2203	4300	6503	SO:0001819	synonymous_variant	150483	exon3			TCCGTACTCCACC	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.693C>T	2.37:g.95539833C>T		94.0	0.0	0		65.0	28.0	0.430769	NM_144705		Silent	SNP	ENST00000295201.4	37	CCDS2005.1																																																																																			C|0.988;T|0.012	0.012	strong		0.662	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
C14orf159	80017	hgsc.bcm.edu	37	14	91666131	91666131	+	Silent	SNP	C	C	T	rs28481732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91666131C>T	ENST00000523771.1	+	11	1914	c.1311C>T	c.(1309-1311)gcC>gcT	p.A437A	C14orf159_ENST00000521077.2_Silent_p.A442A|C14orf159_ENST00000428926.2_Silent_p.A437A|C14orf159_ENST00000522322.1_Silent_p.A437A|C14orf159_ENST00000520328.1_Silent_p.A425A|C14orf159_ENST00000412671.2_Silent_p.A442A|C14orf159_ENST00000518868.1_Silent_p.A442A|C14orf159_ENST00000256324.10_Silent_p.A442A|C14orf159_ENST00000525393.2_Silent_p.A313A|C14orf159_ENST00000523816.1_Silent_p.A437A			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	437						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		TAGAGCGTGCCGGAAGAGCTG	0.512													C|||	121	0.0241613	0.0658	0.0303	5008	,	,		19104	0.0		0.0089	False		,,,				2504	0.0041				p.A442A		Atlas-SNP	.											.	C14orf159	57	.	0			c.C1326T						PASS	.	C	,,,,	223,4183	134.9+/-171.1	8,207,1988	125.0	119.0	121.0		1311,1311,1326,1275,1311	-9.8	0.0	14	dbSNP_125	121	112,8488	59.5+/-121.1	0,112,4188	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	8,319,6176	TT,TC,CC		1.3023,5.0613,2.5757	,,,,	437/617,437/617,442/622,425/565,437/617	91666131	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	80017	exon11			GCGTGCCGGAAGA	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1311C>T	14.37:g.91666131C>T		122.0	0.0	0		138.0	69.0	0.5	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	41	0.018772893772893772	24	0.04878048780487805	11	0.03038674033149171	0	0.0	6	0.0079155672823219	C	0.268	-0.994827	0.02145	0.050613	0.013023	ENSG00000133943	ENST00000522816	.	.	.	5.05	-9.84	0.00479	.	.	.	.	.	T	0.05686	0.0149	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33979	-0.9847	4	.	.	.	.	0.4736	0.00536	0.1844:0.1765:0.3025:0.3367	rs28481732	.	.	.	L	38	.	.	P	+	2	0	C14orf159	90735884	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.872000	0.01639	-2.087000	0.00862	-2.357000	0.00240	CCG	C|0.977;T|0.023	0.023	strong		0.512	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
FXR2	9513	hgsc.bcm.edu	37	17	7496411	7496411	+	Silent	SNP	G	G	A	rs61730843	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7496411G>A	ENST00000250113.7	-	13	1753	c.1419C>T	c.(1417-1419)ccC>ccT	p.P473P	SOX15_ENST00000250055.2_5'Flank|FXR2_ENST00000573057.1_5'Flank	NM_004860.3	NP_004851.2	P51116	FXR2_HUMAN	fragile X mental retardation, autosomal homolog 2	473						cytoplasm (GO:0005737)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(7)|lung(8)|prostate(1)	26				READ - Rectum adenocarcinoma(115;0.17)		CTCGGGTTGGGGGATCCCTGT	0.627													G|||	29	0.00579073	0.0	0.0101	5008	,	,		13144	0.0		0.0119	False		,,,				2504	0.0102				p.P473P		Atlas-SNP	.											.	FXR2	44	.	0			c.C1419T						PASS	.	G		6,3684		0,6,1839	19.0	19.0	19.0		1419	1.9	1.0	17	dbSNP_129	19	66,8118		0,66,4026	no	coding-synonymous	FXR2	NM_004860.3		0,72,5865	AA,AG,GG		0.8065,0.1626,0.6064		473/674	7496411	72,11802	1845	4092	5937	SO:0001819	synonymous_variant	9513	exon13			GGTTGGGGGATCC	U31501	CCDS45604.1	17p13.3	2014-09-17				ENSG00000129245			4024	protein-coding gene	gene with protein product		605339		FMR1L2		7489725, 9259278	Standard	NM_004860		Approved		uc002gia.2	P51116		ENST00000250113.7:c.1419C>T	17.37:g.7496411G>A		71.0	0.0	0		74.0	41.0	0.554054	NM_004860	B2R9M2|D3DTQ1|Q86V09|Q8WUM2	Silent	SNP	ENST00000250113.7	37	CCDS45604.1																																																																																			G|0.995;A|0.005	0.005	strong		0.627	FXR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441084.1		
IMMP1L	196294	hgsc.bcm.edu	37	11	31482246	31482246	+	Missense_Mutation	SNP	T	T	C	rs370083551		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:31482246T>C	ENST00000278200.1	-	4	316	c.121A>G	c.(121-123)Atg>Gtg	p.M41V	IMMP1L_ENST00000533642.1_Intron|IMMP1L_ENST00000532287.1_Missense_Mutation_p.M41V|IMMP1L_ENST00000534812.1_Intron|IMMP1L_ENST00000526776.1_Intron|IMMP1L_ENST00000528161.1_Intron	NM_144981.1	NP_659418.1	Q96LU5	IMP1L_HUMAN	IMP1 inner mitochondrial membrane peptidase-like (S. cerevisiae)	41					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	serine-type peptidase activity (GO:0008236)			breast(1)|cervix(1)|large_intestine(1)|lung(4)	7	Lung SC(675;0.225)					GTAGGCTCCATTGATGGTCCA	0.279																																					p.M41V		Atlas-SNP	.											.	IMMP1L	16	.	0			c.A121G						PASS	.	T	VAL/MET	0,4404		0,0,2202	69.0	72.0	71.0		121	5.6	1.0	11		71	1,8585	1.2+/-3.3	0,1,4292	no	missense	IMMP1L	NM_144981.1	21	0,1,6494	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging	41/167	31482246	1,12989	2202	4293	6495	SO:0001583	missense	196294	exon4			GCTCCATTGATGG		CCDS7874.1	11p13	2014-07-30			ENSG00000148950	ENSG00000148950			26317	protein-coding gene	gene with protein product		612323					Standard	NM_144981		Approved	FLJ25059	uc001msy.1	Q96LU5	OTTHUMG00000166226	ENST00000278200.1:c.121A>G	11.37:g.31482246T>C	ENSP00000278200:p.Met41Val	220.0	0.0	0		228.0	111.0	0.486842	NM_144981	D3DQZ7|Q96SH9	Missense_Mutation	SNP	ENST00000278200.1	37	CCDS7874.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.083575	0.76642	0.0	1.16E-4	ENSG00000148950	ENST00000532287;ENST00000278200;ENST00000529749;ENST00000530023	.	.	.	5.58	5.58	0.84498	Peptidase S24/S26A/S26B/S26C (1);Peptidase S24/S26A/S26B/S26C, beta-ribbon domain (1);Peptidase S24/S26A/S26B (1);	0.000000	0.85682	D	0.000000	D	0.86997	0.6068	H	0.95043	3.615	0.80722	D	1	D;P	0.53885	0.963;0.873	D;P	0.69824	0.966;0.687	D	0.90553	0.4510	9	0.66056	D	0.02	-8.7493	16.0334	0.80603	0.0:0.0:0.0:1.0	.	41;41	E9PIG6;Q96LU5	.;IMP1L_HUMAN	V	41	.	ENSP00000278200:M41V	M	-	1	0	IMMP1L	31438822	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.023000	0.76437	2.243000	0.73865	0.533000	0.62120	ATG	.	.	weak		0.279	IMMP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388496.1	NM_144981	
UTP20	27340	hgsc.bcm.edu	37	12	101767224	101767224	+	Silent	SNP	C	C	T	rs112278934	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:101767224C>T	ENST00000261637.4	+	53	7098	c.6924C>T	c.(6922-6924)gcC>gcT	p.A2308A		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2308					endonucleolytic cleavage in 5'-ETS of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000480)|endonucleolytic cleavage in ITS1 to separate SSU-rRNA from 5.8S rRNA and LSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000447)|endonucleolytic cleavage to generate mature 5'-end of SSU-rRNA from (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000472)|negative regulation of cell proliferation (GO:0008285)|rRNA processing (GO:0006364)	90S preribosome (GO:0030686)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|preribosome, small subunit precursor (GO:0030688)|small-subunit processome (GO:0032040)	poly(A) RNA binding (GO:0044822)			NS(3)|biliary_tract(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(26)|lung(30)|ovary(2)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	88						AAATGATCGCCTATCTCTTTG	0.463													C|||	4	0.000798722	0.0	0.0014	5008	,	,		17679	0.0		0.002	False		,,,				2504	0.001				p.A2308A		Atlas-SNP	.											.	UTP20	222	.	0			c.C6924T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	88.0	88.0	88.0		6924	-3.3	0.6	12	dbSNP_132	88	8,8592	5.7+/-21.5	0,8,4292	no	coding-synonymous	UTP20	NM_014503.2		0,9,6494	TT,TC,CC		0.093,0.0227,0.0692		2308/2786	101767224	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	27340	exon53			GATCGCCTATCTC	AJ006778	CCDS9081.1	12q23	2006-02-11				ENSG00000120800			17897	protein-coding gene	gene with protein product	"""down regulated in metastasis"""	612822				9673349, 15590835, 12837249	Standard	NM_014503		Approved	DRIM	uc001tia.1	O75691	OTTHUMG00000170270	ENST00000261637.4:c.6924C>T	12.37:g.101767224C>T		84.0	0.0	0		76.0	35.0	0.460526	NM_014503	Q9H3H4	Silent	SNP	ENST00000261637.4	37	CCDS9081.1																																																																																			C|0.998;T|0.002	0.002	strong		0.463	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	
KDM4C	23081	hgsc.bcm.edu	37	9	7011719	7011719	+	Missense_Mutation	SNP	T	T	C	rs34369202		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:7011719T>C	ENST00000381309.3	+	13	2373	c.1808T>C	c.(1807-1809)aTt>aCt	p.I603T	KDM4C_ENST00000428870.2_Missense_Mutation_p.I290T|KDM4C_ENST00000543771.1_Missense_Mutation_p.I603T|KDM4C_ENST00000442236.2_Missense_Mutation_p.I348T|KDM4C_ENST00000381306.3_Missense_Mutation_p.I603T|KDM4C_ENST00000536108.1_Missense_Mutation_p.I422T|KDM4C_ENST00000535193.1_Missense_Mutation_p.I625T	NM_015061.3	NP_055876.2	Q9H3R0	KDM4C_HUMAN	lysine (K)-specific demethylase 4C	603					histone H3-K9 demethylation (GO:0033169)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	androgen receptor binding (GO:0050681)|dioxygenase activity (GO:0051213)|enzyme binding (GO:0019899)|histone demethylase activity (H3-K9 specific) (GO:0032454)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	43						GTTCTGTCCATTGAGGAGGAA	0.463													T|||	1	0.000199681	0.0	0.0	5008	,	,		21962	0.0		0.0	False		,,,				2504	0.001				p.I625T		Atlas-SNP	.											.	KDM4C	186	.	0			c.T1874C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	0,4406		0,0,2203	99.0	97.0	98.0		1808,1808,1874,1808	0.8	0.0	9	dbSNP_126	98	10,8590	7.7+/-29.5	0,10,4290	yes	missense,missense,missense,missense	KDM4C	NM_001146694.1,NM_001146695.1,NM_001146696.1,NM_015061.3	89,89,89,89	0,10,6493	CC,CT,TT		0.1163,0.0,0.0769	benign,benign,benign,benign	603/1048,603/814,625/836,603/1057	7011719	10,12996	2203	4300	6503	SO:0001583	missense	23081	exon13			TGTCCATTGAGGA	AB018323	CCDS6471.1, CCDS55285.1, CCDS55286.1, CCDS55287.1	9p24-p23	2013-01-23	2009-04-06	2009-04-06	ENSG00000107077	ENSG00000107077		"""Chromatin-modifying enzymes / K-demethylases"", ""Tudor domain containing"""	17071	protein-coding gene	gene with protein product	"""tudor domain containing 14C"""	605469	"""jumonji domain containing 2C"""	JMJD2C		9872452, 15138608	Standard	NM_015061		Approved	GASC1, KIAA0780, TDRD14C	uc003zkh.3	Q9H3R0	OTTHUMG00000019536	ENST00000381309.3:c.1808T>C	9.37:g.7011719T>C	ENSP00000370710:p.Ile603Thr	109.0	0.0	0		101.0	39.0	0.386139	NM_001146696	B4E1Y4|B7ZL46|F5H347|F5H7P0|O94877|Q2M3M0|Q5JUC9|Q5VYJ2|Q5VYJ3	Missense_Mutation	SNP	ENST00000381309.3	37	CCDS6471.1	.	.	.	.	.	.	.	.	.	.	T	1.169	-0.641475	0.03531	0.0	0.001163	ENSG00000107077	ENST00000535193;ENST00000543771;ENST00000381309;ENST00000381306;ENST00000442236;ENST00000536108;ENST00000428870	T;T;T;T;T;T;T	0.54279	0.58;0.58;0.58;0.58;0.58;0.58;0.58	5.76	0.841	0.18918	.	0.988395	0.08268	N	0.971876	T	0.40791	0.1131	L	0.47716	1.5	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0	B;B;B;B;B	0.08055	0.001;0.003;0.002;0.001;0.001	T	0.27468	-1.0073	10	0.20046	T	0.44	.	5.1095	0.14802	0.1283:0.3276:0.0:0.544	rs34369202	348;603;625;603;603	E7EV17;F5H347;F5H7P0;Q9H3R0;Q9H3R0-2	.;.;.;KDM4C_HUMAN;.	T	625;603;603;603;348;422;290	ENSP00000442382:I625T;ENSP00000445427:I603T;ENSP00000370710:I603T;ENSP00000370707:I603T;ENSP00000409353:I348T;ENSP00000440656:I422T;ENSP00000405739:I290T	ENSP00000370707:I603T	I	+	2	0	KDM4C	7001719	0.000000	0.05858	0.027000	0.17364	0.458000	0.32498	0.834000	0.27518	-0.091000	0.12440	-0.333000	0.08304	ATT	T|0.999;C|0.001	0.001	strong		0.463	KDM4C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051692.1	NM_015061	
RP1	6101	hgsc.bcm.edu	37	8	55533805	55533805	+	Silent	SNP	G	G	T	rs144293929	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:55533805G>T	ENST00000220676.1	+	2	427	c.279G>T	c.(277-279)acG>acT	p.T93T		NM_006269.1	NP_006260.1	P56715	RP1_HUMAN	retinitis pigmentosa 1 (autosomal dominant)	93	Doublecortin 1. {ECO:0000255|PROSITE- ProRule:PRU00072}.				axoneme assembly (GO:0035082)|cellular response to light stimulus (GO:0071482)|intracellular signal transduction (GO:0035556)|photoreceptor cell development (GO:0042461)|photoreceptor cell maintenance (GO:0045494)|photoreceptor cell outer segment organization (GO:0035845)|phototransduction, visible light (GO:0007603)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|visual perception (GO:0007601)	axoneme (GO:0005930)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	microtubule binding (GO:0008017)			NS(4)|breast(6)|central_nervous_system(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(29)|lung(69)|ovary(6)|pancreas(1)|prostate(9)|skin(17)|upper_aerodigestive_tract(3)|urinary_tract(2)	169		all_lung(136;0.0831)|Lung NSC(129;0.109)|all_epithelial(80;0.123)	OV - Ovarian serous cystadenocarcinoma(7;4.4e-07)|Epithelial(17;3.37e-05)|all cancers(17;0.000285)			ACAGCATCACGCGCCTGGAGG	0.617													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		13894	0.0		0.001	False		,,,				2504	0.0041				p.T93T	Colon(91;1014 1389 7634 14542 40420)	Atlas-SNP	.											.	RP1	429	.	0			c.G279T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	83.0	71.0	75.0		279	-6.7	0.1	8	dbSNP_134	75	21,8579	15.3+/-51.7	0,21,4279	no	coding-synonymous	RP1	NM_006269.1		0,23,6480	TT,TG,GG		0.2442,0.0454,0.1768		93/2157	55533805	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	6101	exon2			CATCACGCGCCTG	AF146592	CCDS6160.1	8q12.1	2013-01-08				ENSG00000104237			10263	protein-coding gene	gene with protein product		603937				1783394	Standard	NM_006269		Approved	DCDC4A	uc003xsd.1	P56715		ENST00000220676.1:c.279G>T	8.37:g.55533805G>T		56.0	0.0	0		43.0	27.0	0.627907	NM_006269		Silent	SNP	ENST00000220676.1	37	CCDS6160.1																																																																																			G|0.998;T|0.002	0.002	strong		0.617	RP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378532.2	NM_006269	
OCA2	4948	hgsc.bcm.edu	37	15	28117060	28117060	+	Silent	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:28117060T>A	ENST00000354638.3	-	20	2243	c.2088A>T	c.(2086-2088)gcA>gcT	p.A696A	OCA2_ENST00000353809.5_Silent_p.A672A	NM_000275.2	NP_000266.2	Q04671	P_HUMAN	oculocutaneous albinism II	696					cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|spermatid development (GO:0007286)|tyrosine transport (GO:0015828)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|endosome membrane (GO:0010008)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|melanosome membrane (GO:0033162)	L-tyrosine transmembrane transporter activity (GO:0005302)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(3)|large_intestine(11)|lung(48)|ovary(4)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	85		all_lung(180;2.93e-12)|Breast(32;0.000315)|Colorectal(260;0.234)		all cancers(64;5.03e-07)|Epithelial(43;2.13e-06)|BRCA - Breast invasive adenocarcinoma(123;0.045)		AGTGGAGATGTGCCAATGCCT	0.338									Oculocutaneous Albinism																												p.A696A		Atlas-SNP	.											.	OCA2	173	.	0			c.A2088T						PASS	.						112.0	116.0	115.0					15																	28117060		2203	4300	6503	SO:0001819	synonymous_variant	4948	exon20	Familial Cancer Database		GAGATGTGCCAAT		CCDS10020.1, CCDS73701.1	15q12	2013-01-08	2008-01-30		ENSG00000104044	ENSG00000104044			8101	protein-coding gene	gene with protein product	"""melanocyte-specific transporter protein"""	611409	"""oculocutaneous albinism II (pink-eye dilution (murine) homolog)"", ""eye color 3 (brown)"", ""eye color 2 (central brown)"", ""oculocutaneous albinism II (pink-eye dilution homolog, mouse)"""	D15S12, P, EYCL3, EYCL2			Standard	NM_000275		Approved	BEY2, EYCL, BEY, BEY1	uc001zbh.4	Q04671	OTTHUMG00000128871	ENST00000354638.3:c.2088A>T	15.37:g.28117060T>A		52.0	0.0	0		36.0	6.0	0.166667	NM_000275	Q15211|Q15212|Q96EN1|Q9UMI5	Silent	SNP	ENST00000354638.3	37	CCDS10020.1																																																																																			.	.	none		0.338	OCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250823.1	NM_000275	
TRPM5	29850	hgsc.bcm.edu	37	11	2436464	2436464	+	Missense_Mutation	SNP	C	C	T	rs34551253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2436464C>T	ENST00000155858.6	-	9	1374	c.1366G>A	c.(1366-1368)Gcg>Acg	p.A456T	TRPM5_ENST00000528453.1_Missense_Mutation_p.A456T|TRPM5_ENST00000533060.1_Missense_Mutation_p.A456T|TRPM5_ENST00000452833.1_Missense_Mutation_p.A458T	NM_014555.3	NP_055370.1			transient receptor potential cation channel, subfamily M, member 5											breast(1)|central_nervous_system(1)|endometrium(4)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(2)|urinary_tract(2)	23		Medulloblastoma(188;0.0049)|Breast(177;0.00586)|all_epithelial(84;0.0075)|Ovarian(85;0.0256)|all_neural(188;0.0311)		BRCA - Breast invasive adenocarcinoma(625;0.00147)|LUSC - Lung squamous cell carcinoma(625;0.191)		GGTGGCCCCGCGGGTGGCTCC	0.716													C|||	54	0.0107827	0.0023	0.0245	5008	,	,		13476	0.001		0.0308	False		,,,				2504	0.002				p.A456T	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1366A						PASS	.	C	THR/ALA	35,4235		1,33,2101	7.0	9.0	9.0		1366	-6.4	0.0	11	dbSNP_126	9	273,8141		6,261,3940	yes	missense	TRPM5	NM_014555.3	58	7,294,6041	TT,TC,CC		3.2446,0.8197,2.4283	benign	456/1166	2436464	308,12376	2135	4207	6342	SO:0001583	missense	29850	exon9			GCCCCGCGGGTGG	AF177473	CCDS31340.1	11p15.5	2011-12-14			ENSG00000070985	ENSG00000070985		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	14323	protein-coding gene	gene with protein product		604600				10607831, 16382100	Standard	NM_014555		Approved	LTRPC5, MTR1	uc001lwm.4	Q9NZQ8	OTTHUMG00000009896	ENST00000155858.6:c.1366G>A	11.37:g.2436464C>T	ENSP00000155858:p.Ala456Thr	3.0	0.0	0		10.0	5.0	0.5	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	35	0.016025641025641024	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	22	0.029023746701846966	C	0.009	-1.820965	0.00595	0.008197	0.032446	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	T;T;T;T;T	0.68181	-0.31;-0.31;-0.31;-0.31;-0.31	3.19	-6.37	0.01963	.	1.134030	0.06672	N	0.766349	T	0.14227	0.0344	N	0.08118	0	0.09310	N	1	B;B;B	0.13594	0.005;0.005;0.008	B;B;B	0.09377	0.002;0.001;0.004	T	0.05517	-1.0880	10	0.14252	T	0.57	0.2166	1.5474	0.02568	0.2706:0.3676:0.1989:0.1629	rs34551253	456;458;456	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	T	450;456;458;456;456;456	ENSP00000434383:A450T;ENSP00000155858:A456T;ENSP00000387965:A458T;ENSP00000434121:A456T;ENSP00000436809:A456T	ENSP00000155858:A456T	A	-	1	0	TRPM5	2393040	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-2.025000	0.01435	-3.859000	0.00098	-1.579000	0.00862	GCG	C|0.983;T|0.017	0.017	strong		0.716	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
TXNDC5	81567	hgsc.bcm.edu	37	6	7910865	7910865	+	Missense_Mutation	SNP	G	G	A	rs183777097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:7910865G>A	ENST00000379757.4	-	1	182	c.145C>T	c.(145-147)Ccc>Tcc	p.P49S	BLOC1S5-TXNDC5_ENST00000439343.2_Intron|TXNDC5_ENST00000473453.1_5'Flank|TXNDC5_ENST00000539054.1_Intron	NM_030810.3	NP_110437.2	Q8NBS9	TXND5_HUMAN	thioredoxin domain containing 5 (endoplasmic reticulum)	49	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|membrane organization (GO:0061024)|negative regulation of apoptotic process (GO:0043066)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	protein disulfide isomerase activity (GO:0003756)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(2)	22	Ovarian(93;0.0398)					GCCGCGGGGGGCCCGTccgcc	0.771													g|||	70	0.0139776	0.0023	0.0187	5008	,	,		3218	0.001		0.0408	False		,,,				2504	0.0123				p.P49S	Ovarian(119;1430 1625 3928 26125 34589)	Atlas-SNP	.											.	TXNDC5	33	.	0			c.C145T						PASS	.		SER/PRO	31,3679		1,29,1825	11.0	11.0	11.0		145	-5.6	0.0	6		11	258,6904		3,252,3326	no	missense	TXNDC5	NM_030810.3	74	4,281,5151	AA,AG,GG		3.6023,0.8356,2.6582	benign	49/433	7910865	289,10583	1855	3581	5436	SO:0001583	missense	81567	exon1			CGGGGGGCCCGTC	AK025006	CCDS4505.1, CCDS47369.1	6p24.3	2011-10-19	2009-02-23		ENSG00000239264	ENSG00000239264		"""Protein disulfide isomerases"""	21073	protein-coding gene	gene with protein product	"""protein disulfide isomerase family A, member 15"""		"""thioredoxin domain containing 5"""				Standard	NM_001145549		Approved	MGC3178, FLJ21353, FLJ90810, EndoPDI, Hcc-2, ERp46, PDIA15	uc003mxv.3	Q8NBS9	OTTHUMG00000014216	ENST00000379757.4:c.145C>T	6.37:g.7910865G>A	ENSP00000369081:p.Pro49Ser	7.0	0.0	0		11.0	7.0	0.636364	NM_030810	B2RDM2|Q5TCQ0|Q8ND33|Q8TCT2|Q9BVH9	Missense_Mutation	SNP	ENST00000379757.4	37	CCDS4505.1	73	0.033424908424908424	19	0.03861788617886179	8	0.022099447513812154	2	0.0034965034965034965	44	0.05804749340369393	.	0.221	-1.028982	0.02045	0.008356	0.036023	ENSG00000239264	ENST00000379757	T	0.03441	3.93	2.8	-5.61	0.02489	Thioredoxin-like fold (1);	0.991997	0.08180	N	0.985621	T	0.00468	0.0015	N	0.11201	0.11	0.09310	N	0.999996	B	0.02656	0.0	B	0.01281	0.0	T	0.45527	-0.9255	10	0.22109	T	0.4	.	5.4918	0.16781	0.3092:0.4165:0.2743:0.0	.	49	Q8NBS9	TXND5_HUMAN	S	49	ENSP00000369081:P49S	ENSP00000369081:P49S	P	-	1	0	TXNDC5	7855864	0.000000	0.05858	0.000000	0.03702	0.043000	0.13939	-0.769000	0.04710	-3.133000	0.00235	-1.338000	0.01255	CCC	G|0.966;A|0.034	0.034	strong		0.771	TXNDC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039792.1	NM_030810	
PIK3C2A	5286	hgsc.bcm.edu	37	11	17118730	17118730	+	Silent	SNP	A	A	G	rs113662142	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:17118730A>G	ENST00000265970.7	-	26	4199	c.4200T>C	c.(4198-4200)ggT>ggC	p.G1400G	PIK3C2A_ENST00000531428.1_5'UTR|PIK3C2A_ENST00000540361.1_Silent_p.G1020G	NM_002645.2	NP_002636.2	O00443	P3C2A_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 alpha	1400					clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|exocytosis (GO:0006887)|insulin receptor signaling pathway (GO:0008286)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|small molecule metabolic process (GO:0044281)|vascular smooth muscle contraction (GO:0014829)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol binding (GO:0035091)			central_nervous_system(4)|endometrium(5)|kidney(5)|large_intestine(7)|lung(24)|ovary(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	58						TAGAAGGAAGACCAGAAAAAC	0.358													A|||	27	0.00539137	0.0023	0.0	5008	,	,		19765	0.0		0.0089	False		,,,				2504	0.0153				p.G1400G		Atlas-SNP	.											.	PIK3C2A	148	.	0			c.T4200C						PASS	.	A		12,4388	19.1+/-41.9	0,12,2188	116.0	111.0	113.0		4200	0.9	1.0	11	dbSNP_132	113	80,8506	45.8+/-104.6	1,78,4214	no	coding-synonymous	PIK3C2A	NM_002645.2		1,90,6402	GG,GA,AA		0.9317,0.2727,0.7085		1400/1687	17118730	92,12894	2200	4293	6493	SO:0001819	synonymous_variant	5286	exon26			AGGAAGACCAGAA	Y13367	CCDS7824.1	11p15.5-p14	2012-07-13	2012-07-13			ENSG00000011405	2.7.1.154		8971	protein-coding gene	gene with protein product		603601	"""phosphoinositide-3-kinase, class 2, alpha polypeptide"""			9337861	Standard	NM_002645		Approved	PI3K-C2alpha	uc001mmq.4	O00443		ENST00000265970.7:c.4200T>C	11.37:g.17118730A>G		58.0	0.0	0		55.0	19.0	0.345455	NM_002645	B0LPH2|B4E2G4|Q14CQ9	Silent	SNP	ENST00000265970.7	37	CCDS7824.1																																																																																			A|0.992;G|0.008	0.008	strong		0.358	PIK3C2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387553.1	NM_002645	
DSCAM	1826	hgsc.bcm.edu	37	21	42064785	42064785	+	Silent	SNP	C	C	T	rs79669041	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:42064785C>T	ENST00000400454.1	-	3	936	c.459G>A	c.(457-459)gcG>gcA	p.A153A		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	153	Ig-like C2-type 2.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CAGTGATGTACGCCTCCACCG	0.527													c|||	23	0.00459265	0.0	0.0072	5008	,	,		20320	0.0		0.0159	False		,,,				2504	0.002				p.A153A	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.G459A						PASS	.	T		9,4065		0,9,2028	136.0	134.0	134.0		459	-1.4	1.0	21	dbSNP_132	134	88,8274		0,88,4093	no	coding-synonymous	DSCAM	NM_001389.3		0,97,6121	TT,TC,CC		1.0524,0.2209,0.78		153/2013	42064785	97,12339	2037	4181	6218	SO:0001819	synonymous_variant	1826	exon3			GATGTACGCCTCC	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.459G>A	21.37:g.42064785C>T		49.0	0.0	0		62.0	33.0	0.532258	NM_001271534	O60468	Silent	SNP	ENST00000400454.1	37	CCDS42929.1																																																																																			C|0.993;T|0.007	0.007	strong		0.527	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
ZBP1	81030	hgsc.bcm.edu	37	20	56191475	56191475	+	Silent	SNP	C	C	T	rs16981188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:56191475C>T	ENST00000371173.3	-	2	261	c.84G>A	c.(82-84)ccG>ccA	p.P28P	ZBP1_ENST00000538947.1_5'UTR|ZBP1_ENST00000395822.3_Intron|ZBP1_ENST00000541799.1_Silent_p.P28P|ZBP1_ENST00000340462.4_Silent_p.P28P|ZBP1_ENST00000343535.4_Silent_p.P28P	NM_001160417.1|NM_030776.2	NP_001153889.1|NP_110403.2	Q9H171	ZBP1_HUMAN	Z-DNA binding protein 1	28					innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|positive regulation of type I interferon-mediated signaling pathway (GO:0060340)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|left-handed Z-DNA binding (GO:0003692)|RNA binding (GO:0003723)			large_intestine(11)|lung(8)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	27	Lung NSC(12;0.000545)|all_lung(29;0.00195)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(13;7.87e-13)|Epithelial(14;3.26e-09)|all cancers(14;3.62e-08)			CAAGTTTCACCGGGGAGCCAG	0.577													C|||	98	0.0195687	0.028	0.0317	5008	,	,		18817	0.0		0.0308	False		,,,				2504	0.0082				p.P28P		Atlas-SNP	.											.	ZBP1	65	.	0			c.G84A						PASS	.	C	,,,	158,4248	108.2+/-146.6	0,158,2045	95.0	94.0	94.0		84,,84,84	-7.3	0.0	20	dbSNP_123	94	318,8282	112.9+/-173.0	5,308,3987	no	coding-synonymous,intron,coding-synonymous,coding-synonymous	ZBP1	NM_001160417.1,NM_001160418.1,NM_001160419.1,NM_030776.2	,,,	5,466,6032	TT,TC,CC		3.6977,3.586,3.6598	,,,	28/429,,28/249,28/430	56191475	476,12530	2203	4300	6503	SO:0001819	synonymous_variant	81030	exon2			TTTCACCGGGGAG	AJ300575	CCDS13461.1, CCDS54477.1, CCDS54478.1	20q13.31	2009-08-21	2002-07-25	2002-07-26	ENSG00000124256	ENSG00000124256			16176	protein-coding gene	gene with protein product	"""DNA-dependent activator of IRFs"""	606750	"""chromosome 20 open reading frame 183"""	C20orf183		11842111	Standard	NM_030776		Approved	dJ718J7.3, DLM1, DLM-1, DAI	uc002xyo.3	Q9H171	OTTHUMG00000032824	ENST00000371173.3:c.84G>A	20.37:g.56191475C>T		82.0	0.0	0		118.0	54.0	0.457627	NM_001160419	A2A2F7|B3KVA1|F5GYT1|Q5JY39|Q9BYW4	Silent	SNP	ENST00000371173.3	37	CCDS13461.1																																																																																			C|0.967;T|0.033	0.033	strong		0.577	ZBP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079849.1	NM_030776	
PIGS	94005	hgsc.bcm.edu	37	17	26888506	26888506	+	Missense_Mutation	SNP	G	G	C	rs140545278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26888506G>C	ENST00000308360.7	-	6	985	c.610C>G	c.(610-612)Ctg>Gtg	p.L204V	PIGS_ENST00000395346.2_Missense_Mutation_p.L196V|PIGS_ENST00000543734.1_Missense_Mutation_p.L143V|PIGS_ENST00000465444.1_5'UTR	NM_033198.3	NP_149975.1	Q96S52	PIGS_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class S	204					attachment of GPI anchor to protein (GO:0016255)|C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)	endoplasmic reticulum membrane (GO:0005789)|GPI-anchor transamidase complex (GO:0042765)|membrane (GO:0016020)	GPI-anchor transamidase activity (GO:0003923)			breast(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(42;0.00431)					TGGTCAGCCAGAGCAGCAGCA	0.602																																					p.L204V		Atlas-SNP	.											.	PIGS	42	.	0			c.C610G						PASS	.	G	VAL/LEU	0,4406		0,0,2203	83.0	66.0	72.0		610	2.2	0.9	17	dbSNP_134	72	4,8596	3.7+/-12.6	0,4,4296	yes	missense	PIGS	NM_033198.3	32	0,4,6499	CC,CG,GG		0.0465,0.0,0.0308	probably-damaging	204/556	26888506	4,13002	2203	4300	6503	SO:0001583	missense	94005	exon6			CAGCCAGAGCAGC		CCDS11235.1	17p13.2	2013-02-26	2006-06-28		ENSG00000087111	ENSG00000087111		"""Phosphatidylinositol glycan anchor biosynthesis"""	14937	protein-coding gene	gene with protein product	"""GPI transamidase subunit"""	610271	"""phosphatidylinositol glycan, class S"""				Standard	NM_033198		Approved		uc002hbo.2	Q96S52	OTTHUMG00000132604	ENST00000308360.7:c.610C>G	17.37:g.26888506G>C	ENSP00000309430:p.Leu204Val	106.0	0.0	0		111.0	55.0	0.495495	NM_033198	Q6UVX6	Missense_Mutation	SNP	ENST00000308360.7	37	CCDS11235.1	.	.	.	.	.	.	.	.	.	.	G	17.70	3.454766	0.63290	0.0	4.65E-4	ENSG00000087111	ENST00000395346;ENST00000308360;ENST00000543734	T;T;T	0.49139	0.86;0.86;0.79	5.68	2.21	0.28008	.	0.000000	0.85682	D	0.000000	T	0.59390	0.2190	M	0.72479	2.2	0.52099	D	0.99994	D;D	0.63880	0.993;0.991	D;P	0.66084	0.941;0.862	T	0.55218	-0.8175	10	0.17832	T	0.49	-12.9026	10.0958	0.42475	0.2491:0.0:0.7509:0.0	.	204;196	Q96S52;Q96S52-2	PIGS_HUMAN;.	V	196;204;143	ENSP00000378755:L196V;ENSP00000309430:L204V;ENSP00000438447:L143V	ENSP00000309430:L204V	L	-	1	2	PIGS	23912633	1.000000	0.71417	0.939000	0.37840	0.997000	0.91878	2.033000	0.41136	0.191000	0.20236	0.655000	0.94253	CTG	G|0.999;C|0.001	0.001	strong		0.602	PIGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255833.3	NM_033198	
TJP3	27134	hgsc.bcm.edu	37	19	3747891	3747891	+	Missense_Mutation	SNP	G	G	A	rs144472063	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:3747891G>A	ENST00000541714.2	+	19	2884	c.2422G>A	c.(2422-2424)Gag>Aag	p.E808K	TJP3_ENST00000587686.1_Missense_Mutation_p.E827K|TJP3_ENST00000589378.1_Missense_Mutation_p.E817K|TJP3_ENST00000382008.3_Missense_Mutation_p.E822K|TJP3_ENST00000539908.2_Missense_Mutation_p.E772K|TJP3_ENST00000262968.9_Missense_Mutation_p.E841K	NM_001267560.1	NP_001254489.1	O95049	ZO3_HUMAN	tight junction protein 3	808					regulation of G1/S transition of mitotic cell cycle (GO:2000045)	apical plasma membrane (GO:0016324)|nucleus (GO:0005634)|tight junction (GO:0005923)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	26				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0118)|STAD - Stomach adenocarcinoma(1328;0.18)		CAGCGACTACGAGACGGACGG	0.677													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		16795	0.0		0.0	False		,,,				2504	0.0				p.E817K		Atlas-SNP	.											.	TJP3	79	.	0			c.G2449A						PASS	.	G	LYS/GLU	1,4403	2.1+/-5.4	0,1,2201	35.0	30.0	32.0		2521	4.5	0.8	19	dbSNP_134	32	0,8596		0,0,4298	no	missense	TJP3	NM_014428.1	56	0,1,6499	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	841/953	3747891	1,12999	2202	4298	6500	SO:0001583	missense	27134	exon19			GACTACGAGACGG	AC005954	CCDS32873.1, CCDS32873.2, CCDS59332.1	19p13.3	2012-07-12	2012-07-12			ENSG00000105289			11829	protein-coding gene	gene with protein product	"""zona occludens 3"""	612689					Standard	NM_001267560		Approved	ZO-3	uc010xhu.3	O95049		ENST00000541714.2:c.2422G>A	19.37:g.3747891G>A	ENSP00000439278:p.Glu808Lys	72.0	0.0	0		92.0	50.0	0.543478	NM_001267561	A6NFP3|B3KR73|B3KXZ0|B4E2W6|F5H2X0|F5H4S9|K7EK22|Q32N01	Missense_Mutation	SNP	ENST00000541714.2	37	CCDS32873.2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	21.2	4.114574	0.77210	2.27E-4	0.0	ENSG00000105289	ENST00000541714;ENST00000539908;ENST00000382008;ENST00000262968	T;T;T;T	0.11821	2.76;2.93;2.74;2.81	4.54	4.54	0.55810	.	0.112463	0.64402	D	0.000016	T	0.39410	0.1077	M	0.77820	2.39	0.51482	D	0.999924	D;D;D;D	0.89917	1.0;1.0;0.998;1.0	D;D;P;D	0.76575	0.946;0.988;0.771;0.946	T	0.40850	-0.9541	10	0.87932	D	0	.	16.2624	0.82553	0.0:0.0:1.0:0.0	.	827;841;822;808	O95049-3;O95049-2;O95049;F5H2X0	.;.;ZO3_HUMAN;.	K	808;772;822;841	ENSP00000439278:E808K;ENSP00000439991:E772K;ENSP00000371438:E822K;ENSP00000262968:E841K	ENSP00000262968:E841K	E	+	1	0	TJP3	3698891	1.000000	0.71417	0.841000	0.33234	0.048000	0.14542	7.375000	0.79646	2.062000	0.61559	0.561000	0.74099	GAG	G|1.000;A|0.000	0.000	strong		0.677	TJP3-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000453434.1		
CDKN1A	1026	hgsc.bcm.edu	37	6	36652228	36652228	+	Missense_Mutation	SNP	G	G	A	rs148679597		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:36652228G>A	ENST00000405375.1	+	2	585	c.350G>A	c.(349-351)tGt>tAt	p.C117Y	CDKN1A_ENST00000244741.5_Missense_Mutation_p.C117Y|CDKN1A_ENST00000478800.1_3'UTR|CDKN1A_ENST00000373711.2_Missense_Mutation_p.C117Y|CDKN1A_ENST00000448526.2_Missense_Mutation_p.C151Y	NM_001220778.1	NP_001207707.1	P38936	CDN1A_HUMAN	cyclin-dependent kinase inhibitor 1A (p21, Cip1)	117					cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to extracellular stimulus (GO:0031668)|cellular response to ionizing radiation (GO:0071479)|cellular senescence (GO:0090398)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle (GO:0000278)|mitotic cell cycle arrest (GO:0071850)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of gene expression (GO:0010629)|negative regulation of phosphorylation (GO:0042326)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ regeneration (GO:0031100)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of programmed cell death (GO:0043068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein phosphorylation (GO:0006468)|Ras protein signal transduction (GO:0007265)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of DNA biosynthetic process (GO:2000278)|regulation of protein import into nucleus, translocation (GO:0033158)|response to arsenic-containing substance (GO:0046685)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to organonitrogen compound (GO:0010243)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|stress-induced premature senescence (GO:0090400)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCNA-p21 complex (GO:0070557)	cyclin-dependent protein kinase activating kinase activity (GO:0019912)|cyclin-dependent protein serine/threonine kinase inhibitor activity (GO:0004861)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(1)|lung(3)|ovary(1)|urinary_tract(5)	15						TCACTGTCTTGTACCCTTGTG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		19561	0.0		0.001	False		,,,				2504	0.0				p.C117Y		Atlas-SNP	.											.	CDKN1A	27	.	0			c.G350A						PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS	3,4403	6.2+/-15.9	0,3,2200	45.0	44.0	44.0		350,350,350,350	5.2	1.0	6	dbSNP_134	44	30,8570	19.8+/-62.0	0,30,4270	yes	missense,missense,missense,missense	CDKN1A	NM_000389.4,NM_001220777.1,NM_001220778.1,NM_078467.2	194,194,194,194	0,33,6470	AA,AG,GG		0.3488,0.0681,0.2537	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	117/165,117/165,117/165,117/165	36652228	33,12973	2203	4300	6503	SO:0001583	missense	1026	exon2			TGTCTTGTACCCT	U03106	CCDS4824.1	6p21.1	2009-01-21			ENSG00000124762	ENSG00000124762			1784	protein-coding gene	gene with protein product		116899		CDKN1			Standard	NM_000389		Approved	P21, CIP1, WAF1, SDI1, CAP20, p21CIP1, p21Cip1/Waf1	uc021yzb.1	P38936	OTTHUMG00000014603	ENST00000405375.1:c.350G>A	6.37:g.36652228G>A	ENSP00000384849:p.Cys117Tyr	33.0	0.0	0		45.0	17.0	0.377778	NM_001220778	Q14010|Q6FI05|Q9BUT4	Missense_Mutation	SNP	ENST00000405375.1	37	CCDS4824.1	.	.	.	.	.	.	.	.	.	.	G	14.12	2.441009	0.43326	6.81E-4	0.003488	ENSG00000124762	ENST00000448526;ENST00000244741;ENST00000405375;ENST00000373711	T;T;T;T	0.78003	-1.14;-1.14;-1.14;-1.14	5.23	5.23	0.72850	.	0.000000	0.64402	D	0.000010	T	0.81240	0.4781	L	0.49126	1.545	0.48040	D	0.999578	D;D;D	0.69078	0.997;0.995;0.997	D;D;D	0.73380	0.98;0.916;0.956	T	0.81911	-0.0716	10	0.56958	D	0.05	-36.2508	14.1752	0.65537	0.0:0.0:1.0:0.0	.	151;117;117	B4DQP9;P38936;Q96LE1	.;CDN1A_HUMAN;.	Y	151;117;117;117	ENSP00000409259:C151Y;ENSP00000244741:C117Y;ENSP00000384849:C117Y;ENSP00000362815:C117Y	ENSP00000244741:C117Y	C	+	2	0	CDKN1A	36760206	0.127000	0.22367	0.981000	0.43875	0.040000	0.13550	1.857000	0.39399	2.724000	0.93272	0.561000	0.74099	TGT	G|0.998;A|0.002	0.002	strong		0.642	CDKN1A-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040354.1	NM_078467	
CNTNAP3B	728577	hgsc.bcm.edu	37	9	43861012	43861012	+	Missense_Mutation	SNP	C	C	T	rs530378867	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:43861012C>T	ENST00000377564.3	+	13	2279	c.1886C>T	c.(1885-1887)gCg>gTg	p.A629V		NM_001201380.1	NP_001188309.1	Q96NU0	CNT3B_HUMAN	contactin associated protein-like 3B	629	Fibrinogen C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00739}.				cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|lung(3)|pancreas(1)|prostate(3)	10						GCAGACTCCGCGTGGACGGTG	0.647													C|||	19	0.00379393	0.0	0.0	5008	,	,		17105	0.0		0.0119	False		,,,				2504	0.0072				p.A629V		Atlas-SNP	.											.	CNTNAP3B	37	.	0			c.C1886T						PASS	.																																			SO:0001583	missense	728577	exon13			ACTCCGCGTGGAC	BX538190	CCDS75836.1	9p12	2007-12-14			ENSG00000154529	ENSG00000154529			32035	protein-coding gene	gene with protein product						15820314	Standard	XM_006716853		Approved		uc004abr.1	Q96NU0	OTTHUMG00000013174	ENST00000377564.3:c.1886C>T	9.37:g.43861012C>T	ENSP00000366787:p.Ala629Val	30.0	0.0	0		52.0	21.0	0.403846	NM_001201380	B1B0V7|B1B0V8|B1B0V9|B1B0W0|B1B0X8|B1B162|Q4VXF0|Q9H7W3	Missense_Mutation	SNP	ENST00000377564.3	37	CCDS55312.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	5.700|5.700	0.313777|0.313777	0.10789|0.10789	.|.	.|.	ENSG00000154529|ENSG00000154529	ENST00000377564;ENST00000341990;ENST00000403166|ENST00000377561	T|.	0.21361|.	2.01|.	1.94|1.94	1.94|1.94	0.25998|0.25998	.|.	.|.	.|.	.|.	.|.	T|T	0.31949|0.31949	0.0813|0.0813	L|L	0.27975|0.27975	0.815|0.815	0.09310|0.09310	N|N	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|T	0.21143|0.21143	-1.0254|-1.0254	7|5	0.02654|.	T|.	1|.	.|.	9.4766|9.4766	0.38875|0.38875	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|.	.|.	.|.	V|C	629;629;535|678	ENSP00000366787:A629V|.	ENSP00000340890:A629V|.	A|R	+|+	2|1	0|0	CNTNAP3B|CNTNAP3B	43801008|43801008	0.004000|0.004000	0.15560|0.15560	0.008000|0.008000	0.14137|0.14137	0.015000|0.015000	0.08874|0.08874	1.729000|1.729000	0.38115|0.38115	1.408000|1.408000	0.46895|0.46895	0.423000|0.423000	0.28283|0.28283	GCG|CGT	.	.	none		0.647	CNTNAP3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036930.3		
FTO	79068	hgsc.bcm.edu	37	16	53860253	53860253	+	Missense_Mutation	SNP	G	G	A	rs150450891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:53860253G>A	ENST00000471389.1	+	3	823	c.601G>A	c.(601-603)Gta>Ata	p.V201I	FTO_ENST00000394647.3_Intron	NM_001080432.2	NP_001073901.1	Q9C0B1	FTO_HUMAN	fat mass and obesity associated	201	Fe2OG dioxygenase domain.				adipose tissue development (GO:0060612)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA demethylation (GO:0080111)|oxidative demethylation (GO:0070989)|oxidative single-stranded DNA demethylation (GO:0035552)|oxidative single-stranded RNA demethylation (GO:0035553)|regulation of lipid storage (GO:0010883)|regulation of multicellular organism growth (GO:0040014)|regulation of respiratory system process (GO:0044065)|regulation of white fat cell proliferation (GO:0070350)|RNA repair (GO:0042245)|temperature homeostasis (GO:0001659)	nuclear speck (GO:0016607)|nucleus (GO:0005634)	DNA-N1-methyladenine dioxygenase activity (GO:0043734)|ferrous iron binding (GO:0008198)|oxidative DNA demethylase activity (GO:0035516)|oxidative RNA demethylase activity (GO:0035515)			endometrium(1)|kidney(2)|large_intestine(7)|lung(13)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						AGCATACAACGTAACTTTGCT	0.453																																					p.V201I		Atlas-SNP	.											.	FTO	51	.	0			c.G601A						PASS	.	G	ILE/VAL	0,4396		0,0,2198	158.0	139.0	145.0		601	3.1	0.9	16	dbSNP_134	145	7,8593	5.7+/-21.5	0,7,4293	yes	missense	FTO	NM_001080432.2	29	0,7,6491	AA,AG,GG		0.0814,0.0,0.0539	benign	201/506	53860253	7,12989	2198	4300	6498	SO:0001583	missense	79068	exon3			TACAACGTAACTT	BC003583	CCDS32448.1	16q12.2	2013-11-15			ENSG00000140718	ENSG00000140718		"""Alkylation repair homologs"""	24678	protein-coding gene	gene with protein product	"""AlkB homolog 9"", ""alpha-ketoglutarate-dependent dioxygenase"""	610966				17434869, 17991826, 22002720	Standard	NM_001080432		Approved	KIAA1752, MGC5149, ALKBH9	uc002ehr.3	Q9C0B1	OTTHUMG00000158780	ENST00000471389.1:c.601G>A	16.37:g.53860253G>A	ENSP00000418823:p.Val201Ile	115.0	0.0	0		103.0	56.0	0.543689	NM_001080432	A2RUH1|B2RNS0|Q0P676|Q7Z785	Missense_Mutation	SNP	ENST00000471389.1	37	CCDS32448.1	.	.	.	.	.	.	.	.	.	.	G	15.53	2.861372	0.51482	0.0	8.14E-4	ENSG00000140718	ENST00000471389	T	0.80994	-1.44	5.32	3.09	0.35607	Alpha-ketoglutarate-dependent dioxygenase FTO, catalytic domain (1);	0.170382	0.49916	D	0.000131	T	0.74981	0.3788	M	0.64404	1.975	0.80722	D	1	P	0.39576	0.679	B	0.35114	0.196	T	0.76868	-0.2800	10	0.62326	D	0.03	-8.3027	10.9439	0.47289	0.0:0.1016:0.6004:0.298	.	201	Q9C0B1	FTO_HUMAN	I	201	ENSP00000418823:V201I	ENSP00000418823:V201I	V	+	1	0	FTO	52417754	0.751000	0.28327	0.911000	0.35937	0.981000	0.71138	0.893000	0.28336	1.196000	0.43129	0.655000	0.94253	GTA	G|0.999;A|0.001	0.001	strong		0.453	FTO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352196.1	NM_001080432	
PSORS1C1	170679	hgsc.bcm.edu	37	6	31106489	31106489	+	Missense_Mutation	SNP	G	G	A	rs1265096	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:31106489G>A	ENST00000259881.9	+	5	389	c.100G>A	c.(100-102)Gag>Aag	p.E34K	PSORS1C2_ENST00000259845.4_Intron|PSORS1C1_ENST00000481450.2_Intron|PSORS1C1_ENST00000547221.1_5'UTR	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	34			E -> K (in dbSNP:rs1265096). {ECO:0000269|PubMed:10545595, ECO:0000269|PubMed:12930300}.|E -> Q. {ECO:0000269|PubMed:12930300}.							kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TCCCAGCTCCGAGGAAACTCG	0.567													G|||	85	0.0169728	0.0053	0.0115	5008	,	,		16762	0.0		0.0656	False		,,,				2504	0.0041				p.E34K		Atlas-SNP	.											.	PSORS1C1	11	.	0			c.G100A						PASS	.	G	LYS/GLU,	50,2972		0,50,1461	141.0	142.0	142.0		100,	0.3	0.0	6	dbSNP_87	142	361,5057		14,333,2362	yes	missense,intron	PSORS1C1,PSORS1C2	NM_014068.2,NM_014069.2	56,	14,383,3823	AA,AG,GG		6.663,1.6545,4.8697	benign,	34/153,	31106489	411,8029	1511	2709	4220	SO:0001583	missense	170679	exon5			AGCTCCGAGGAAA	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.100G>A	6.37:g.31106489G>A	ENSP00000259881:p.Glu34Lys	103.0	0.0	0		103.0	45.0	0.436893	NM_014068	B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	CCDS34390.1	64	0.029304029304029304	3	0.006097560975609756	4	0.011049723756906077	0	0.0	57	0.07519788918205805	G	10.18	1.278140	0.23307	0.016545	0.06663	ENSG00000204540	ENST00000259881	T	0.14266	2.52	2.33	0.351	0.16042	.	.	.	.	.	T	0.01189	0.0039	N	0.08118	0	0.09310	N	1	P	0.44578	0.838	B	0.29353	0.101	T	0.44375	-0.9332	9	0.26408	T	0.33	.	4.9377	0.13948	0.3537:0.0:0.6463:0.0	rs1265096;rs3912054;rs1265096	34	Q9UIG5	PS1C1_HUMAN	K	34	ENSP00000259881:E34K	ENSP00000259881:E34K	E	+	1	0	PSORS1C1	31214468	0.000000	0.05858	0.000000	0.03702	0.020000	0.10135	-2.035000	0.01423	-0.095000	0.12351	0.297000	0.19635	GAG	G|0.960;A|0.040	0.040	strong		0.567	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
CCDC66	285331	hgsc.bcm.edu	37	3	56650054	56650054	+	Missense_Mutation	SNP	T	T	C	rs112267342|rs111934125	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:56650054T>C	ENST00000394672.3	+	13	1886	c.1816T>C	c.(1816-1818)Tct>Cct	p.S606P	CCDC66_ENST00000436465.2_Missense_Mutation_p.S606P|CCDC66_ENST00000326595.7_Missense_Mutation_p.S572P	NM_001012506.4|NM_001141947.1	NP_001012524.4|NP_001135419.1	A2RUB6	CCD66_HUMAN	coiled-coil domain containing 66	606					post-embryonic retina morphogenesis in camera-type eye (GO:0060060)|retinal rod cell development (GO:0046548)					breast(1)|kidney(1)|large_intestine(2)|liver(1)|lung(4)|skin(2)|urinary_tract(1)	12				KIRC - Kidney renal clear cell carcinoma(284;0.0478)|Kidney(284;0.0597)|OV - Ovarian serous cystadenocarcinoma(275;0.233)		TTCTACGACTTCTAAGAAGGA	0.289																																					p.S606P		Atlas-SNP	.											CCDC66_ENST00000394672,caecum,carcinoma,0,2	CCDC66	145	2	0			c.T1816C						PASS	.						86.0	99.0	94.0					3																	56650054		2203	4291	6494	SO:0001583	missense	285331	exon13			ACGACTTCTAAGA	AL832692	CCDS33770.2, CCDS46852.1	3p14.3	2006-03-27			ENSG00000180376	ENSG00000180376			27709	protein-coding gene	gene with protein product						14702039	Standard	NR_024460		Approved	DKFZp686C0433	uc003dhz.3	A2RUB6	OTTHUMG00000155748	ENST00000394672.3:c.1816T>C	3.37:g.56650054T>C	ENSP00000378167:p.Ser606Pro	87.0	0.0	0		116.0	8.0	0.0689655	NM_001141947	B3KWL8|Q4VC34|Q8N949	Missense_Mutation	SNP	ENST00000394672.3	37	CCDS46852.1	.	.	.	.	.	.	.	.	.	.	T	11.57	1.676847	0.29783	.	.	ENSG00000180376	ENST00000422222;ENST00000394672;ENST00000326595;ENST00000436465	T;T;T;T	0.19105	2.17;2.28;2.28;2.28	5.5	4.32	0.51571	.	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	M	0.72894	2.215	0.80722	D	1	D	0.58268	0.982	P	0.57911	0.829	T	0.40924	-0.9537	10	0.02654	T	1	-4.7355	10.7191	0.46030	0.0:0.0:0.1601:0.8399	.	606	A2RUB6	CCD66_HUMAN	P	562;606;572;606	ENSP00000401451:S562P;ENSP00000378167:S606P;ENSP00000326050:S572P;ENSP00000404320:S606P	ENSP00000326050:S572P	S	+	1	0	CCDC66	56625094	0.993000	0.37304	0.582000	0.28627	0.363000	0.29612	2.520000	0.45554	1.007000	0.39238	0.482000	0.46254	TCT	C|1.000;|0.000	1.000	weak		0.289	CCDC66-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341473.1	NM_001012506	
SEMA6A	57556	hgsc.bcm.edu	37	5	115782493	115782493	+	Missense_Mutation	SNP	T	T	G	rs200578077	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:115782493T>G	ENST00000343348.6	-	19	3696	c.2909A>C	c.(2908-2910)cAg>cCg	p.Q970P	CTB-118N6.3_ENST00000508640.1_RNA|CTB-118N6.3_ENST00000512128.1_RNA|SEMA6A_ENST00000282394.6_Missense_Mutation_p.Q447P|SEMA6A_ENST00000503865.1_Missense_Mutation_p.Q349P|CTB-118N6.3_ENST00000508424.1_RNA|SEMA6A_ENST00000513137.1_Missense_Mutation_p.Q397P|CTB-118N6.3_ENST00000510682.1_RNA|CTB-118N6.3_ENST00000514214.1_RNA|SEMA6A_ENST00000510263.1_Missense_Mutation_p.Q970P|SEMA6A_ENST00000257414.8_Missense_Mutation_p.Q987P	NM_020796.3	NP_065847	Q9H2E6	SEM6A_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6A	970					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cell surface receptor signaling pathway (GO:0007166)|centrosome localization (GO:0051642)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|positive regulation of neuron migration (GO:2001224)|semaphorin-plexin signaling pathway (GO:0071526)	axon (GO:0030424)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(15)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		all_cancers(142;0.00316)|all_epithelial(76;5.71e-05)|Prostate(80;0.00845)|Ovarian(225;0.0796)|Lung NSC(810;0.171)|all_lung(232;0.203)		OV - Ovarian serous cystadenocarcinoma(64;1.59e-08)|Epithelial(69;2e-08)|all cancers(49;5.7e-08)|COAD - Colon adenocarcinoma(49;0.151)		GCTGTGCACCTGGATGGAGTC	0.617																																					p.Q970P		Atlas-SNP	.											.	SEMA6A	93	.	0			c.A2909C						PASS	.	T	PRO/GLN	5,4167		0,5,2081	24.0	27.0	26.0		2909	4.3	1.0	5		26	62,8402		0,62,4170	yes	missense	SEMA6A	NM_020796.3	76	0,67,6251	GG,GT,TT		0.7325,0.1198,0.5302	probably-damaging	970/1031	115782493	67,12569	2086	4232	6318	SO:0001583	missense	57556	exon19			TGCACCTGGATGG	AB037789	CCDS47256.1, CCDS75288.1	5q23.1	2014-07-29			ENSG00000092421			"""Semaphorins"""	10738	protein-coding gene	gene with protein product	"""sema VIa"""	605885		SEMAQ		9204478, 10993894	Standard	XM_006714663		Approved	KIAA1368, SEMA6A1, SEMA, HT018	uc010jck.3	Q9H2E6	OTTHUMG00000162987	ENST00000343348.6:c.2909A>C	5.37:g.115782493T>G	ENSP00000345512:p.Gln970Pro	65.0	0.0	0		75.0	34.0	0.453333	NM_020796	Q9P2H9	Missense_Mutation	SNP	ENST00000343348.6	37	CCDS47256.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	T	15.45	2.836504	0.50951	0.001198	0.007325	ENSG00000092421	ENST00000343348;ENST00000257414;ENST00000513137;ENST00000282394;ENST00000503865;ENST00000510263	T;T;T;T;T;T	0.50001	2.11;2.1;0.76;2.59;0.79;2.11	4.27	4.27	0.50696	.	1.559450	0.04430	N	0.369061	T	0.51109	0.1655	L	0.46157	1.445	0.58432	D	0.999996	P;P;D;D;D;D	0.62365	0.936;0.874;0.991;0.974;0.965;0.965	P;B;P;P;P;P	0.55161	0.571;0.439;0.77;0.663;0.567;0.663	T	0.40739	-0.9547	10	0.59425	D	0.04	.	11.7765	0.51989	0.0:0.0:0.0:1.0	.	349;970;514;987;447;397	E9PDV9;Q9H2E6;Q96SM8;Q9H2E6-2;E7ERF3;B3KU01	.;SEM6A_HUMAN;.;.;.;.	P	970;987;397;447;349;970	ENSP00000345512:Q970P;ENSP00000257414:Q987P;ENSP00000422997:Q397P;ENSP00000282394:Q447P;ENSP00000425364:Q349P;ENSP00000424388:Q970P	ENSP00000257414:Q987P	Q	-	2	0	SEMA6A	115810392	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.512000	0.81728	1.793000	0.52555	0.379000	0.24179	CAG	T|0.997;G|0.003	0.003	strong		0.617	SEMA6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371270.1	NM_020796	
KIAA1549	57670	hgsc.bcm.edu	37	7	138602865	138602865	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:138602865T>G	ENST00000422774.1	-	2	1555	c.1507A>C	c.(1507-1509)Acg>Ccg	p.T503P	KIAA1549_ENST00000242365.4_Missense_Mutation_p.T453P|KIAA1549_ENST00000440172.1_Missense_Mutation_p.T503P			Q9HCM3	K1549_HUMAN	KIAA1549	503	Ser-rich.					integral component of membrane (GO:0016021)			KIAA1549/BRAF(703)	large_intestine(4)|pancreas(1)|upper_aerodigestive_tract(2)	7						CCAACACTCGTCTCTGAGATT	0.502			O	BRAF	pilocytic astrocytoma																																p.T503P	NSCLC(119;1534 1718 44213 46230 50068)	Atlas-SNP	.		Dom	yes		7	7q34	57670	KIAA1549		O	.	KIAA1549	314	.	0			c.A1507C						PASS	.						34.0	34.0	34.0					7																	138602865		1944	4154	6098	SO:0001583	missense	57670	exon2			CACTCGTCTCTGA		CCDS47723.1, CCDS47723.2, CCDS56513.1	7q34	2009-10-09			ENSG00000122778	ENSG00000122778			22219	protein-coding gene	gene with protein product		613344					Standard	NM_020910		Approved		uc011kql.2	Q9HCM3	OTTHUMG00000157214	ENST00000422774.1:c.1507A>C	7.37:g.138602865T>G	ENSP00000416040:p.Thr503Pro	31.0	0.0	0		58.0	32.0	0.551724	NM_020910	B6HY55|B6HY56|B6HY58|B6HY60|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q5BJD6|Q8IY15|Q9H0M3	Missense_Mutation	SNP	ENST00000422774.1	37	CCDS56513.1	.	.	.	.	.	.	.	.	.	.	T	10.13	1.264426	0.23136	.	.	ENSG00000122778	ENST00000440172;ENST00000242365;ENST00000422774	T;T;T	0.25912	1.77;1.77;1.77	4.24	-8.13	0.01073	.	2.614330	0.01241	N	0.008611	T	0.11110	0.0271	N	0.12182	0.205	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14587	-1.0467	10	0.18276	T	0.48	.	5.0234	0.14372	0.2255:0.5515:0.1044:0.1186	.	503;503	Q9HCM3;Q9HCM3-2	K1549_HUMAN;.	P	503;453;503	ENSP00000406661:T503P;ENSP00000242365:T453P;ENSP00000416040:T503P	ENSP00000242365:T453P	T	-	1	0	KIAA1549	138253405	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.452000	0.06787	-1.529000	0.01754	-0.290000	0.09829	ACG	.	.	none		0.502	KIAA1549-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348092.1		
KANK1	23189	hgsc.bcm.edu	37	9	712052	712052	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:712052C>T	ENST00000382303.1	+	7	1938	c.1286C>T	c.(1285-1287)aCa>aTa	p.T429I	KANK1_ENST00000489369.1_3'UTR|KANK1_ENST00000382297.2_Missense_Mutation_p.T429I|KANK1_ENST00000382293.3_Missense_Mutation_p.T271I	NM_001256876.1	NP_001243805.1	Q14678	KANK1_HUMAN	KN motif and ankyrin repeat domains 1	429	Interaction with KIF21A.				negative regulation of actin filament polymerization (GO:0030837)|negative regulation of cell migration (GO:0030336)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of lamellipodium morphogenesis (GO:2000393)|negative regulation of neuron projection development (GO:0010977)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of ruffle assembly (GO:1900028)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of Wnt signaling pathway (GO:0030177)|positive regulation of wound healing (GO:0090303)|regulation of establishment of cell polarity (GO:2000114)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|ruffle membrane (GO:0032587)	beta-catenin binding (GO:0008013)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(3)|large_intestine(9)|lung(8)|ovary(3)|pancreas(1)|prostate(3)|stomach(4)|upper_aerodigestive_tract(1)	43		Lung NSC(10;9.84e-12)|all_lung(10;1.02e-11)|Breast(48;0.128)		Epithelial(6;0.000153)|OV - Ovarian serous cystadenocarcinoma(1;0.000358)|Lung(218;0.0222)		GCTGTAGGGACACTTGTTGAG	0.532																																					p.T429I		Atlas-SNP	.											.	KANK1	231	.	0			c.C1286T						PASS	.						118.0	101.0	107.0					9																	712052		2203	4300	6503	SO:0001583	missense	23189	exon7			TAGGGACACTTGT	AL833161	CCDS6441.1, CCDS34976.1	9p24.3	2013-01-10	2008-01-29	2008-01-29	ENSG00000107104	ENSG00000107104		"""KN motif and ankyrin repeat domain containing"", ""Ankyrin repeat domain containing"""	19309	protein-coding gene	gene with protein product		607704	"""ankyrin repeat domain 15"""	ANKRD15		12133830, 17996375, 19554261	Standard	NM_015158		Approved	KIAA0172, KANK	uc003zgn.2	Q14678	OTTHUMG00000019434	ENST00000382303.1:c.1286C>T	9.37:g.712052C>T	ENSP00000371740:p.Thr429Ile	105.0	0.0	0		92.0	44.0	0.478261	NM_001256876	A2A2W8|D3DRH3|Q5W0W0|Q8IY65|Q8WX74	Missense_Mutation	SNP	ENST00000382303.1	37	CCDS34976.1	.	.	.	.	.	.	.	.	.	.	C	12.68	2.010448	0.35511	.	.	ENSG00000107104	ENST00000382303;ENST00000354485;ENST00000382297;ENST00000382293	T;T;T	0.43294	0.95;0.95;0.96	5.73	3.89	0.44902	.	0.112785	0.40728	N	0.001035	T	0.56277	0.1974	M	0.74258	2.255	0.80722	D	1	P;P	0.51147	0.942;0.865	P;P	0.56563	0.801;0.71	T	0.55976	-0.8055	10	0.44086	T	0.13	-15.3443	11.3529	0.49598	0.0:0.8043:0.127:0.0687	.	429;429	Q5W0W1;Q14678	.;KANK1_HUMAN	I	429;429;429;271	ENSP00000371740:T429I;ENSP00000371734:T429I;ENSP00000371730:T271I	ENSP00000346479:T429I	T	+	2	0	KANK1	702052	0.995000	0.38212	0.133000	0.22050	0.124000	0.20399	3.732000	0.55021	0.781000	0.33589	0.655000	0.94253	ACA	.	.	none		0.532	KANK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051484.2	NM_015158	
TMEM230	29058	hgsc.bcm.edu	37	20	5086918	5086918	+	Silent	SNP	G	G	A	rs147693982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:5086918G>A	ENST00000379286.2	-	4	558	c.138C>T	c.(136-138)atC>atT	p.I46I	TMEM230_ENST00000202834.7_Silent_p.I46I|TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379279.2_Silent_p.I46I|TMEM230_ENST00000379277.2_Silent_p.I46I|TMEM230_ENST00000342308.5_Silent_p.I109I|TMEM230_ENST00000379283.2_Silent_p.I46I	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	46						integral component of membrane (GO:0016021)											TGGCAAGTGCGATGGCCTTAT	0.443													G|||	21	0.00419329	0.0	0.0058	5008	,	,		15312	0.0		0.0169	False		,,,				2504	0.0				p.I109I		Atlas-SNP	.											.	.	.	.	0			c.C327T						PASS	.	G	,,,	26,4380	32.6+/-62.9	0,26,2177	63.0	62.0	62.0		327,138,138,138	-5.4	0.7	20	dbSNP_134	62	156,8444	74.5+/-137.1	2,152,4146	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	C20orf30	NM_001009923.1,NM_001009924.1,NM_001009925.1,NM_014145.4	,,,	2,178,6323	AA,AG,GG		1.814,0.5901,1.3994	,,,	109/184,46/121,46/121,46/121	5086918	182,12824	2203	4300	6503	SO:0001819	synonymous_variant	29058	exon4			AAGTGCGATGGCC	AF161392	CCDS13086.1, CCDS33438.1	20p13	2012-03-16	2012-03-16	2012-03-16	ENSG00000089063	ENSG00000089063			15876	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 30"""	C20orf30			Standard	XM_005260713		Approved	HSPC274	uc002wlk.3	Q96A57	OTTHUMG00000031796	ENST00000379286.2:c.138C>T	20.37:g.5086918G>A		88.0	0.0	0		81.0	43.0	0.530864	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Silent	SNP	ENST00000379286.2	37	CCDS13086.1																																																																																			G|0.990;A|0.010	0.010	strong		0.443	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1		
ITIH2	3698	hgsc.bcm.edu	37	10	7774397	7774397	+	Missense_Mutation	SNP	A	A	G	rs141156651		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:7774397A>G	ENST00000358415.4	+	14	1910	c.1744A>G	c.(1744-1746)Aaa>Gaa	p.K582E	ITIH2_ENST00000379587.4_Missense_Mutation_p.K571E	NM_002216.2	NP_002207.2	P19823	ITIH2_HUMAN	inter-alpha-trypsin inhibitor heavy chain 2	582					hyaluronan metabolic process (GO:0030212)|negative regulation of endopeptidase activity (GO:0010951)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	endopeptidase inhibitor activity (GO:0004866)|serine-type endopeptidase inhibitor activity (GO:0004867)			NS(2)|breast(1)|endometrium(8)|kidney(1)|large_intestine(17)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	64						TTTCACCAGGAAACTGTGGGC	0.493																																					p.K582E		Atlas-SNP	.											.	ITIH2	144	.	0			c.A1744G						PASS	.	A	GLU/LYS	0,4406		0,0,2203	101.0	91.0	95.0		1744	5.3	0.8	10	dbSNP_134	95	6,8594	5.7+/-21.5	0,6,4294	yes	missense	ITIH2	NM_002216.2	56	0,6,6497	GG,GA,AA		0.0698,0.0,0.0461	possibly-damaging	582/947	7774397	6,13000	2203	4300	6503	SO:0001583	missense	3698	exon14			ACCAGGAAACTGT	X07173	CCDS31141.1	10p14	2011-10-26	2011-10-26		ENSG00000151655	ENSG00000151655			6167	protein-coding gene	gene with protein product		146640	"""inter-alpha (globulin) inhibitor, H2 polypeptide"""			1385302, 10100603	Standard	NM_002216		Approved	H2P	uc001ijs.3	P19823	OTTHUMG00000017633	ENST00000358415.4:c.1744A>G	10.37:g.7774397A>G	ENSP00000351190:p.Lys582Glu	84.0	0.0	0		76.0	39.0	0.513158	NM_002216	Q14659|Q15484|Q5T986	Missense_Mutation	SNP	ENST00000358415.4	37	CCDS31141.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.202257	0.79127	0.0	6.98E-4	ENSG00000151655	ENST00000358415;ENST00000379587	T;T	0.30714	1.52;1.52	5.32	5.32	0.75619	.	0.054094	0.85682	D	0.000000	T	0.40619	0.1124	M	0.76838	2.35	0.41456	D	0.988014	P	0.45902	0.868	P	0.45167	0.472	T	0.47724	-0.9095	10	0.87932	D	0	-28.5342	11.323	0.49433	0.848:0.152:0.0:0.0	.	582	P19823	ITIH2_HUMAN	E	582;571	ENSP00000351190:K582E;ENSP00000368906:K571E	ENSP00000351190:K582E	K	+	1	0	ITIH2	7814403	1.000000	0.71417	0.827000	0.32855	0.967000	0.64934	6.049000	0.71053	2.022000	0.59522	0.523000	0.50628	AAA	A|1.000;G|0.000	0.000	weak		0.493	ITIH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046678.2	NM_002216	
CAPZA3	93661	hgsc.bcm.edu	37	12	18891966	18891966	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:18891966T>C	ENST00000317658.3	+	1	922	c.764T>C	c.(763-765)aTt>aCt	p.I255T	PLCZ1_ENST00000447925.2_5'Flank|RP11-361I14.2_ENST00000536931.1_RNA|PLCZ1_ENST00000435379.1_5'Flank|PLCZ1_ENST00000266505.7_5'Flank|PLCZ1_ENST00000539875.1_5'Flank	NM_033328.2	NP_201585.1	Q96KX2	CAZA3_HUMAN	capping protein (actin filament) muscle Z-line, alpha 3	255					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)				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)				CTGAGAAAAATTCTACGAAGG	0.418																																					p.I255T		Atlas-SNP	.											.	CAPZA3	51	.	0			c.T764C						PASS	.						48.0	51.0	50.0					12																	18891966		2203	4299	6502	SO:0001583	missense	93661	exon1			GAAAAATTCTACG	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.764T>C	12.37:g.18891966T>C	ENSP00000326238:p.Ile255Thr	23.0	0.0	0		31.0	9.0	0.290323	NM_033328	Q969J0	Missense_Mutation	SNP	ENST00000317658.3	37	CCDS8681.1	.	.	.	.	.	.	.	.	.	.	T	8.214	0.801016	0.16397	.	.	ENSG00000177938	ENST00000317658	.	.	.	4.63	2.16	0.27623	F-actin capping protein, alpha subunit, conserved site (1);	0.428352	0.23132	N	0.051565	T	0.21841	0.0526	N	0.16478	0.41	0.31847	N	0.622758	B	0.10296	0.003	B	0.11329	0.006	T	0.08722	-1.0708	9	0.39692	T	0.17	-16.7227	3.7138	0.08430	0.3352:0.0947:0.0:0.5702	.	255	Q96KX2	CAZA3_HUMAN	T	255	.	ENSP00000326238:I255T	I	+	2	0	CAPZA3	18783233	0.896000	0.30565	0.969000	0.41365	0.943000	0.58893	0.619000	0.24388	0.781000	0.33589	0.379000	0.24179	ATT	.	.	none		0.418	CAPZA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401902.1	NM_033328	
TM4SF19	116211	hgsc.bcm.edu	37	3	196050862	196050862	+	Silent	SNP	A	A	G	rs36016914	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196050862A>G	ENST00000273695.3	-	5	581	c.456T>C	c.(454-456)taT>taC	p.Y152Y	TM4SF19-AS1_ENST00000452051.1_RNA|TM4SF19_ENST00000446879.1_Missense_Mutation_p.I151T|TM4SF19_ENST00000442633.1_Silent_p.Y152Y|TM4SF19_ENST00000454715.1_Silent_p.Y126Y|TM4SF19-AS1_ENST00000444939.1_RNA|TM4SF19-AS1_ENST00000420226.1_RNA	NM_001204897.1|NM_138461.3	NP_001191826.1|NP_612470.2	Q96DZ7	T4S19_HUMAN	transmembrane 4 L six family member 19	152						integral component of membrane (GO:0016021)				endometrium(2)|kidney(2)|large_intestine(3)|lung(5)	12	all_cancers(143;1.19e-08)|Ovarian(172;0.0634)|Breast(254;0.206)		Epithelial(36;3.94e-24)|all cancers(36;4.34e-22)|OV - Ovarian serous cystadenocarcinoma(49;8.53e-19)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		GGTCATACAGATAATTCCTAT	0.552													A|||	32	0.00638978	0.0008	0.0259	5008	,	,		20131	0.0		0.0129	False		,,,				2504	0.0				p.I151T		Atlas-SNP	.											.	TM4SF19	21	.	0			c.T452C						PASS	.	A	THR/ILE,,	14,4392	20.2+/-43.8	0,14,2189	54.0	52.0	53.0		452,378,456	-0.1	0.6	3	dbSNP_126	53	114,8486	61.3+/-123.2	2,110,4188	yes	missense,coding-synonymous,coding-synonymous	TM4SF19	NM_001204897.1,NM_001204898.1,NM_138461.3	89,,	2,124,6377	GG,GA,AA		1.3256,0.3177,0.9842	,,	151/243,126/184,152/210	196050862	128,12878	2203	4300	6503	SO:0001819	synonymous_variant	116211	exon5			ATACAGATAATTC	BC013113	CCDS3316.1, CCDS56299.1	3q29	2005-08-09			ENSG00000145107	ENSG00000145107			25167	protein-coding gene	gene with protein product						12477932	Standard	NM_138461		Approved		uc021xjs.1	Q96DZ7	OTTHUMG00000155675	ENST00000273695.3:c.456T>C	3.37:g.196050862A>G		52.0	0.0	0		76.0	22.0	0.289474	NM_001204897	B2RV20|E9PH22|Q336K7	Missense_Mutation	SNP	ENST00000273695.3	37	CCDS3316.1	20|20	0.009157509157509158|0.009157509157509158	0|0	0.0|0.0	10|10	0.027624309392265192|0.027624309392265192	0|0	0.0|0.0	10|10	0.013192612137203167|0.013192612137203167	A|A	6.649|6.649	0.488243|0.488243	0.12641|0.12641	0.003177|0.003177	0.013256|0.013256	ENSG00000145107|ENSG00000145107	ENST00000446879|ENST00000440822	T|.	0.27402|.	1.67|.	5.13|5.13	-0.105|-0.105	0.13601|0.13601	.|.	.|.	.|.	.|.	.|.	T|T	0.29945|0.29945	0.0749|0.0749	.|.	.|.	.|.	0.54753|0.54753	D|D	0.99998|0.99998	B|.	0.24132|.	0.098|.	B|.	0.26094|.	0.066|.	T|T	0.27365|0.27365	-1.0076|-1.0076	8|4	0.27082|.	T|.	0.32|.	-5.5124|-5.5124	7.8335|7.8335	0.29358|0.29358	0.5849:0.0:0.415:0.0|0.5849:0.0:0.415:0.0	rs36016914;rs62409180|rs36016914;rs62409180	151|.	C9JCD5|.	.|.	T|P	151|19	ENSP00000395280:I151T|.	ENSP00000395280:I151T|.	I|S	-|-	2|1	0|0	TM4SF19|TM4SF19	197535259|197535259	0.355000|0.355000	0.24921|0.24921	0.565000|0.565000	0.28409|0.28409	0.176000|0.176000	0.22953|0.22953	0.361000|0.361000	0.20267|0.20267	0.002000|0.002000	0.14630|0.14630	0.460000|0.460000	0.39030|0.39030	ATC|TCT	A|0.989;G|0.011	0.011	strong		0.552	TM4SF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341174.1	NM_138461	
PTH2R	5746	hgsc.bcm.edu	37	2	209358262	209358262	+	Missense_Mutation	SNP	G	G	A	rs140566891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209358262G>A	ENST00000272847.2	+	13	1744	c.1531G>A	c.(1531-1533)Gag>Aag	p.E511K	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	511					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	CTCTTTCCACGAGGAGACCAA	0.527													G|||	2	0.000399361	0.0	0.0	5008	,	,		20843	0.0		0.001	False		,,,				2504	0.001				p.E511K		Atlas-SNP	.											.	PTH2R	92	.	0			c.G1531A						PASS	.	G	LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	84.0	77.0	80.0		1531	4.4	0.3	2	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	yes	missense	PTH2R	NM_005048.2	56	0,12,6491	AA,AG,GG		0.1279,0.0227,0.0923	probably-damaging	511/551	209358262	12,12994	2203	4300	6503	SO:0001583	missense	5746	exon13			TTCCACGAGGAGA	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"""GPCR / Class B : Parathyroid hormone receptors"""	9609	protein-coding gene	gene with protein product		601469	"""parathyroid hormone receptor 2"""	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1531G>A	2.37:g.209358262G>A	ENSP00000272847:p.Glu511Lys	136.0	0.0	0		179.0	96.0	0.536313	NM_005048	Q8N429	Missense_Mutation	SNP	ENST00000272847.2	37	CCDS2383.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	20.8	4.050399	0.75960	2.27E-4	0.001279	ENSG00000144407	ENST00000272847	T	0.58060	0.36	5.31	4.43	0.53597	.	0.000000	0.36740	U	0.002436	T	0.48750	0.1517	M	0.73962	2.25	0.31256	N	0.693435	P;P	0.51240	0.892;0.943	B;B	0.37144	0.178;0.242	T	0.62358	-0.6871	9	.	.	.	.	11.6752	0.51425	0.0868:0.0:0.9132:0.0	.	400;511	B4DFN8;P49190	.;PTH2R_HUMAN	K	511	ENSP00000272847:E511K	.	E	+	1	0	PTH2R	209066507	1.000000	0.71417	0.276000	0.24689	0.027000	0.11550	4.221000	0.58574	1.236000	0.43740	0.591000	0.81541	GAG	G|0.999;A|0.001	0.001	strong		0.527	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048	
TTK	7272	hgsc.bcm.edu	37	6	80718167	80718167	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:80718167G>A	ENST00000369798.2	+	4	538	c.427G>A	c.(427-429)Gct>Act	p.A143T	TTK_ENST00000230510.3_Missense_Mutation_p.A143T|TTK_ENST00000509894.1_Missense_Mutation_p.A143T	NM_001166691.1|NM_003318.4	NP_001160163.1|NP_003309.2	P33981	TTK_HUMAN	TTK protein kinase	143					chromosome separation (GO:0051304)|mitotic spindle assembly checkpoint (GO:0007094)|mitotic spindle organization (GO:0007052)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|spindle organization (GO:0007051)	membrane (GO:0016020)|spindle (GO:0005819)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)			endometrium(4)|kidney(2)|large_intestine(12)|lung(22)|ovary(7)|pancreas(1)|prostate(1)|stomach(3)|urinary_tract(1)	53		all_cancers(76;0.00177)|Acute lymphoblastic leukemia(125;1.24e-05)|all_hematologic(105;0.00223)|all_epithelial(107;0.2)		BRCA - Breast invasive adenocarcinoma(397;0.0321)		CAAGAAATTTGCTTTTGTTCA	0.299																																					p.A143T		Atlas-SNP	.											.	TTK	199	.	0			c.G427A						PASS	.						77.0	70.0	73.0					6																	80718167		2203	4299	6502	SO:0001583	missense	7272	exon4			AAATTTGCTTTTG		CCDS4993.1, CCDS55040.1	6q14.1	2014-04-07			ENSG00000112742	ENSG00000112742			12401	protein-coding gene	gene with protein product	"""cancer/testis antigen 96"", ""monopolar spindle 1 kinase"""	604092				1639825	Standard	NM_003318		Approved	MPS1, MPS1L1, CT96, MPH1	uc003pjc.3	P33981	OTTHUMG00000015088	ENST00000369798.2:c.427G>A	6.37:g.80718167G>A	ENSP00000358813:p.Ala143Thr	50.0	0.0	0		47.0	10.0	0.212766	NM_003318	A8K8U5|B2RDW2|E1P543|Q15272|Q5TCS0|Q9BW51|Q9NTM0	Missense_Mutation	SNP	ENST00000369798.2	37	CCDS4993.1	.	.	.	.	.	.	.	.	.	.	G	32	5.165323	0.94768	.	.	ENSG00000112742	ENST00000509894;ENST00000230510;ENST00000369798;ENST00000511260;ENST00000504040	D;D;D;D;D	0.89485	-2.52;-2.52;-2.52;-2.52;-2.52	6.16	5.27	0.74061	Tetratricopeptide-like helical (1);	0.000000	0.85682	D	0.000000	D	0.92328	0.7566	M	0.66939	2.045	0.49213	D	0.999764	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	D	0.93231	0.6617	10	0.62326	D	0.03	.	15.8123	0.78573	0.0:0.0:0.8632:0.1368	.	143;143	P33981;A8K8U5	TTK_HUMAN;.	T	143	ENSP00000422936:A143T;ENSP00000230510:A143T;ENSP00000358813:A143T;ENSP00000421636:A143T;ENSP00000427483:A143T	ENSP00000230510:A143T	A	+	1	0	TTK	80774886	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.619000	0.67729	1.557000	0.49525	0.650000	0.86243	GCT	.	.	none		0.299	TTK-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041316.2		
LILRB4	11006	hgsc.bcm.edu	37	19	55179184	55179184	+	Silent	SNP	T	T	C	rs142100665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55179184T>C	ENST00000391736.1	+	13	1455	c.1140T>C	c.(1138-1140)tcT>tcC	p.S380S	LILRB4_ENST00000430952.2_Silent_p.S379S|LILRB4_ENST00000391734.3_Intron|LILRB4_ENST00000270452.2_Silent_p.S380S|LILRB4_ENST00000391733.3_Silent_p.S381S	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		238.0	0.0	0		214.0	22.0	0.102804	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		
POLQ	10721	hgsc.bcm.edu	37	3	121207449	121207449	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:121207449A>C	ENST00000264233.5	-	16	4457	c.4329T>G	c.(4327-4329)aaT>aaG	p.N1443K		NM_199420.3	NP_955452.3	O75417	DPOLQ_HUMAN	polymerase (DNA directed), theta	1443					ATP catabolic process (GO:0006200)|DNA repair (GO:0006281)	nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|damaged DNA binding (GO:0003684)|DNA-directed DNA polymerase activity (GO:0003887)|single-stranded DNA-dependent ATPase activity (GO:0043142)			NS(2)|breast(7)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(16)|lung(55)|ovary(5)|prostate(3)|skin(4)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(2)	120				GBM - Glioblastoma multiforme(114;0.0915)		GAAGAAAACTATTTAATTGTG	0.348								DNA polymerases (catalytic subunits)																													p.N1443K	Pancreas(152;907 1925 26081 31236 36904)	Atlas-SNP	.											.	POLQ	273	.	0			c.T4329G						PASS	.						44.0	46.0	45.0					3																	121207449		2201	4296	6497	SO:0001583	missense	10721	exon16			AAAACTATTTAAT	AF052573	CCDS33833.1	3q13.3	2012-05-18			ENSG00000051341	ENSG00000051341	2.7.7.7	"""DNA polymerases"""	9186	protein-coding gene	gene with protein product		604419				10395804	Standard	NM_199420		Approved	POLH	uc003eee.4	O75417	OTTHUMG00000159396	ENST00000264233.5:c.4329T>G	3.37:g.121207449A>C	ENSP00000264233:p.Asn1443Lys	87.0	0.0	0		107.0	19.0	0.17757	NM_199420	O95160|Q6VMB5	Missense_Mutation	SNP	ENST00000264233.5	37	CCDS33833.1	.	.	.	.	.	.	.	.	.	.	A	16.42	3.118039	0.56505	.	.	ENSG00000051341	ENST00000543272;ENST00000264233;ENST00000393672	T	0.50548	0.74	6.11	3.38	0.38709	.	0.230437	0.44688	D	0.000425	T	0.48804	0.1520	L	0.34521	1.04	0.28458	N	0.916	D;D	0.67145	0.996;0.975	P;P	0.62740	0.906;0.781	T	0.40608	-0.9554	10	0.54805	T	0.06	.	5.3884	0.16229	0.5847:0.1381:0.2772:0.0	.	1443;615	O75417;O75417-2	DPOLQ_HUMAN;.	K	1066;1443;1579	ENSP00000264233:N1443K	ENSP00000264233:N1443K	N	-	3	2	POLQ	122690139	0.943000	0.32029	1.000000	0.80357	0.899000	0.52679	-0.042000	0.12063	0.392000	0.25172	0.533000	0.62120	AAT	.	.	none		0.348	POLQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355097.1	NM_199420	
FBXO24	26261	hgsc.bcm.edu	37	7	100197690	100197690	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100197690G>A	ENST00000241071.6	+	9	1565	c.1243G>A	c.(1243-1245)Ggc>Agc	p.G415S	PCOLCE_ENST00000223061.5_5'Flank|PCOLCE-AS1_ENST00000446022.1_RNA|FBXO24_ENST00000468962.1_Missense_Mutation_p.G403S|FBXO24_ENST00000427939.2_Missense_Mutation_p.G453S|PCOLCE-AS1_ENST00000544873.1_RNA|FBXO24_ENST00000360609.2_3'UTR|PCOLCE-AS1_ENST00000442166.2_RNA	NM_033506.2	NP_277041.1	O75426	FBX24_HUMAN	F-box protein 24	415					protein ubiquitination (GO:0016567)	ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)			NS(2)|breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|ovary(3)|skin(4)|urinary_tract(2)	28	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					CCTGTGGTGCGGCCTCAACCA	0.692																																					p.G453S		Atlas-SNP	.											.	FBXO24	125	.	0			c.G1357A						PASS	.						27.0	29.0	28.0					7																	100197690		2203	4300	6503	SO:0001583	missense	26261	exon9			TGGTGCGGCCTCA	AF174604	CCDS5698.1, CCDS5699.1, CCDS5699.2, CCDS55138.1	7q22	2005-10-07	2004-06-15		ENSG00000106336	ENSG00000106336		"""F-boxes /  ""other"""""	13595	protein-coding gene	gene with protein product		609097	"""F-box only protein 24"""			10531035, 10531037	Standard	NM_012172		Approved	FBX24	uc011kjz.1	O75426	OTTHUMG00000159543	ENST00000241071.6:c.1243G>A	7.37:g.100197690G>A	ENSP00000241071:p.Gly415Ser	225.0	0.0	0		185.0	49.0	0.264865	NM_012172	A4D2D4|B4DX91|B4DY42|Q9H0G1	Missense_Mutation	SNP	ENST00000241071.6	37	CCDS5698.1	.	.	.	.	.	.	.	.	.	.	G	17.80	3.477965	0.63849	.	.	ENSG00000106336	ENST00000241071;ENST00000468962;ENST00000427939	D;D;D	0.98028	-4.67;-4.67;-4.67	4.76	4.76	0.60689	Regulator of chromosome condensation/beta-lactamase-inhibitor protein II (2);	0.000000	0.52532	D	0.000065	D	0.98317	0.9442	M	0.71036	2.16	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.76575	0.982;0.988;0.982	D	0.98525	1.0625	10	0.44086	T	0.13	-19.8922	15.2622	0.73634	0.0:0.0:1.0:0.0	.	403;453;415	B4DY42;B4DX91;O75426	.;.;FBX24_HUMAN	S	415;403;453	ENSP00000241071:G415S;ENSP00000420239:G403S;ENSP00000416558:G453S	ENSP00000241071:G415S	G	+	1	0	FBXO24	100035626	1.000000	0.71417	0.988000	0.46212	0.549000	0.35272	5.078000	0.64425	2.199000	0.70637	0.442000	0.29010	GGC	.	.	none		0.692	FBXO24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356104.1		
AHRR	57491	hgsc.bcm.edu	37	5	422858	422858	+	Missense_Mutation	SNP	C	C	G	rs562253075		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:422858C>G	ENST00000505113.1	+	6	512	c.468C>G	c.(466-468)caC>caG	p.H156Q	AHRR_ENST00000512529.1_Missense_Mutation_p.H2Q|AHRR_ENST00000506456.1_Missense_Mutation_p.H12Q|AHRR_ENST00000316418.5_Missense_Mutation_p.H156Q	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	156	PAS. {ECO:0000255|PROSITE- ProRule:PRU00140}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			ATGTAATGCACCAGAACATTT	0.522																																					p.H156Q		Atlas-SNP	.											.	AHRR	67	.	0			c.C468G						PASS	.						92.0	98.0	96.0					5																	422858		1997	4152	6149	SO:0001583	missense	57491	exon6			AATGCACCAGAAC	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.468C>G	5.37:g.422858C>G	ENSP00000424601:p.His156Gln	107.0	0.0	0		119.0	53.0	0.445378	NM_001242412	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	.	.	.	.	.	.	.	.	.	.	C	12.88	2.070730	0.36566	.	.	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000514523;ENST00000510400;ENST00000506456	T;T;T;T;T	0.36878	2.32;2.32;1.3;2.32;1.23	4.76	0.128	0.14733	PAS (2);PAS fold (1);	0.047043	0.85682	D	0.000000	T	0.51787	0.1695	M	0.72576	2.205	0.58432	D	0.999991	D;D;D	0.76494	0.999;0.993;0.99	D;D;D	0.74023	0.982;0.954;0.923	T	0.49744	-0.8907	10	0.87932	D	0	.	8.2783	0.31885	0.0:0.4437:0.0:0.5563	.	12;156;156	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	Q	156;156;2;2;152;12	ENSP00000424601:H156Q;ENSP00000323816:H156Q;ENSP00000424880:H2Q;ENSP00000428893:H152Q;ENSP00000426932:H12Q	ENSP00000323816:H156Q	H	+	3	2	AHRR	475858	0.862000	0.29867	0.994000	0.49952	0.918000	0.54935	-0.009000	0.12765	-0.051000	0.13334	0.655000	0.94253	CAC	.	.	none		0.522	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
ETS2	2114	hgsc.bcm.edu	37	21	40190408	40190408	+	Missense_Mutation	SNP	C	C	A	rs61735785	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:40190408C>A	ENST00000360214.3	+	8	1109	c.649C>A	c.(649-651)Ctc>Atc	p.L217I	ETS2_ENST00000360938.3_Missense_Mutation_p.L217I	NM_001256295.1	NP_001243224.1	P15036	ETS2_HUMAN	v-ets avian erythroblastosis virus E26 oncogene homolog 2	217					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|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)|skeletal system development (GO:0001501)|transcription from RNA polymerase II promoter (GO:0006366)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(2)|endometrium(1)|large_intestine(3)|lung(5)|ovary(1)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	18		Prostate(19;6.33e-08)|all_epithelial(19;0.123)				CAAAGGCGGCCTCCTGGACAG	0.567													C|||	17	0.00339457	0.0	0.0086	5008	,	,		17462	0.0		0.0089	False		,,,				2504	0.002				p.L357I		Atlas-SNP	.											.	ETS2	87	.	0			c.C1069A						PASS	.	C	ILE/LEU	4,4402	8.1+/-20.4	0,4,2199	149.0	155.0	153.0		649	5.3	0.9	21	dbSNP_129	153	103,8497	56.4+/-117.6	1,101,4198	yes	missense	ETS2	NM_005239.4	5	1,105,6397	AA,AC,CC		1.1977,0.0908,0.8227	probably-damaging	217/470	40190408	107,12899	2203	4300	6503	SO:0001583	missense	2114	exon8			GGCGGCCTCCTGG		CCDS13659.1	21q22.3	2013-07-09	2013-07-09		ENSG00000157557	ENSG00000157557			3489	protein-coding gene	gene with protein product		164740	"""v-ets erythroblastosis virus E26 oncogene homolog 2 (avian)"""			17986575	Standard	NM_001256295		Approved		uc002yxf.3	P15036	OTTHUMG00000090769	ENST00000360214.3:c.649C>A	21.37:g.40190408C>A	ENSP00000353344:p.Leu217Ile	61.0	0.0	0		69.0	32.0	0.463768	NM_001256295	A6NM68|D3DSH6|Q53Y89	Missense_Mutation	SNP	ENST00000360214.3	37	CCDS13659.1	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	13.05	2.120236	0.37436	9.08E-4	0.011977	ENSG00000157557	ENST00000360214;ENST00000360938;ENST00000456966	T;T;T	0.41400	2.48;2.48;1.0	6.16	5.28	0.74379	.	2.205300	0.02436	N	0.084067	T	0.42832	0.1220	M	0.69823	2.125	0.42985	D	0.994471	P;D	0.54397	0.908;0.966	B;P	0.46144	0.277;0.505	T	0.54649	-0.8262	10	0.07990	T	0.79	.	12.2106	0.54377	0.1305:0.7322:0.1373:0.0	rs61735785	217;217	P15036;C9JAG2	ETS2_HUMAN;.	I	217	ENSP00000353344:L217I;ENSP00000354194:L217I;ENSP00000411086:L217I	ENSP00000353344:L217I	L	+	1	0	ETS2	39112278	0.976000	0.34144	0.916000	0.36221	0.114000	0.19823	2.340000	0.43974	1.609000	0.50190	0.650000	0.86243	CTC	C|0.993;A|0.007	0.007	strong		0.567	ETS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207544.1		
BACE1	23621	hgsc.bcm.edu	37	11	117186506	117186506	+	Silent	SNP	G	G	A	rs28917234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:117186506G>A	ENST00000313005.6	-	1	466	c.6C>T	c.(4-6)gcC>gcT	p.A2A	BACE1_ENST00000428381.2_Silent_p.A2A|BACE1_ENST00000514464.1_5'UTR|BACE1_ENST00000528053.1_Silent_p.A2A|BACE1_ENST00000513780.1_Silent_p.A2A|BACE1_ENST00000445823.2_Silent_p.A2A|AP000892.4_ENST00000504906.1_RNA	NM_012104.4|NM_138971.3|NM_138972.3|NM_138973.3	NP_036236|NP_620427.1|NP_620428.1|NP_620429.1	P56817	BACE1_HUMAN	beta-site APP-cleaving enzyme 1	2					beta-amyloid metabolic process (GO:0050435)|membrane protein ectodomain proteolysis (GO:0006509)|proteolysis (GO:0006508)	axon (GO:0030424)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	aspartic-type endopeptidase activity (GO:0004190)|beta-amyloid binding (GO:0001540)|beta-aspartyl-peptidase activity (GO:0008798)|enzyme binding (GO:0019899)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(1)	19	all_hematologic(175;0.0487)	Breast(348;0.00908)|Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.69e-05)|Epithelial(105;0.000563)|all cancers(92;0.0032)		GCAGGGCTTGGGCCATGGTGG	0.746													G|||	92	0.0183706	0.0023	0.0159	5008	,	,		10280	0.0		0.0378	False		,,,				2504	0.0409				p.A2A		Atlas-SNP	.											.	BACE1	33	.	0			c.C6T						PASS	.	G	,,,	14,2658		0,14,1322	2.0	3.0	3.0		6,6,6,6	0.6	0.9	11	dbSNP_125	3	131,5129		1,129,2500	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BACE1	NM_012104.4,NM_138971.3,NM_138972.3,NM_138973.3	,,,	1,143,3822	AA,AG,GG		2.4905,0.524,1.828	,,,	2/502,2/458,2/477,2/433	117186506	145,7787	1336	2630	3966	SO:0001819	synonymous_variant	23621	exon1			GGCTTGGGCCATG	AF190725	CCDS8383.1, CCDS44739.1, CCDS44740.1, CCDS44741.1, CCDS55787.1, CCDS55786.1	11q23-q24	2011-07-27	2004-04-02	2004-04-02	ENSG00000186318	ENSG00000186318			933	protein-coding gene	gene with protein product		604252	"""beta-site APP-cleaving enzyme"""	BACE		10531052	Standard	NM_012104		Approved		uc001pqz.3	P56817	OTTHUMG00000160636	ENST00000313005.6:c.6C>T	11.37:g.117186506G>A		0.0	0.0	.		20.0	12.0	0.6	NM_138972	A0M8W7|B0YIU9|E9PE65|H7BXJ9|Q9BYB9|Q9BYC0|Q9BYC1|Q9UJT5|Q9ULS1	Silent	SNP	ENST00000313005.6	37	CCDS8383.1																																																																																			G|0.979;A|0.021	0.021	strong		0.746	BACE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361505.1		
HECTD4	283450	hgsc.bcm.edu	37	12	112622244	112622244	+	Missense_Mutation	SNP	A	A	G	rs369692553		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:112622244A>G	ENST00000430131.2	-	60	10405	c.9260T>C	c.(9259-9261)gTg>gCg	p.V3087A	HECTD4_ENST00000550722.1_Missense_Mutation_p.V3363A|HECTD4_ENST00000377560.5_Missense_Mutation_p.V3337A			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3087					glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)										CAGCGGATCCACAGAGAGGTC	0.677																																					p.V3375A		Atlas-SNP	.											.	.	.	.	0			c.T10124C						PASS	.	A	ALA/VAL	0,4366		0,0,2183	20.0	26.0	24.0		10010	2.1	0.7	12		24	1,8559		0,1,4279	no	missense	C12orf51	NM_001109662.2	64	0,1,6462	GG,GA,AA		0.0117,0.0,0.0077	benign	3337/4247	112622244	1,12925	2183	4280	6463	SO:0001583	missense	283450	exon61			GGATCCACAGAGA	AK091473		12q24.13	2013-07-17	2012-08-14	2012-08-14	ENSG00000173064	ENSG00000173064			26611	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 51"""	C12orf51		21270382	Standard	NM_001109662		Approved	FLJ34154, KIAA0614	uc021reb.1	Q9Y4D8	OTTHUMG00000150719	ENST00000430131.2:c.9260T>C	12.37:g.112622244A>G	ENSP00000404379:p.Val3087Ala	30.0	0.0	0		36.0	18.0	0.5	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Missense_Mutation	SNP	ENST00000430131.2	37		.	.	.	.	.	.	.	.	.	.	A	9.809	1.182707	0.21870	0.0	1.17E-4	ENSG00000173064	ENST00000377560;ENST00000430131;ENST00000550722	T;T;T	0.51325	0.71;0.71;0.71	5.82	2.06	0.26882	.	.	.	.	.	T	0.27866	0.0686	N	0.14661	0.345	0.29651	N	0.843934	B	0.02656	0.0	B	0.01281	0.0	T	0.18429	-1.0337	9	0.42905	T	0.14	.	6.5643	0.22503	0.7294:0.1299:0.1406:0.0	.	3087	Q9Y4D8	K0614_HUMAN	A	3337;3087;3363	ENSP00000366783:V3337A;ENSP00000404379:V3087A;ENSP00000449784:V3363A	ENSP00000366783:V3337A	V	-	2	0	C12orf51	111106627	0.368000	0.25031	0.678000	0.29963	0.067000	0.16453	3.175000	0.50855	0.479000	0.27511	0.533000	0.62120	GTG	.	.	weak		0.677	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
NIPBL	25836	hgsc.bcm.edu	37	5	36985274	36985274	+	Silent	SNP	C	C	T	rs116049172		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:36985274C>T	ENST00000282516.8	+	10	2491	c.1992C>T	c.(1990-1992)aaC>aaT	p.N664N	NIPBL_ENST00000448238.2_Silent_p.N664N|NIPBL_ENST00000504430.1_3'UTR	NM_015384.4|NM_133433.3	NP_056199.2|NP_597677.2	Q6KC79	NIPBL_HUMAN	Nipped-B homolog (Drosophila)	664					brain development (GO:0007420)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to X-ray (GO:0071481)|cognition (GO:0050890)|developmental growth (GO:0048589)|ear morphogenesis (GO:0042471)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic forelimb morphogenesis (GO:0035115)|embryonic viscerocranium morphogenesis (GO:0048703)|external genitalia morphogenesis (GO:0035261)|eye morphogenesis (GO:0048592)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|forelimb morphogenesis (GO:0035136)|gall bladder development (GO:0061010)|heart morphogenesis (GO:0003007)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|metanephros development (GO:0001656)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of ossification (GO:0045778)|regulation of developmental growth (GO:0048638)|regulation of embryonic development (GO:0045995)|regulation of hair cycle (GO:0042634)|sensory perception of sound (GO:0007605)|stem cell maintenance (GO:0019827)|uterus morphogenesis (GO:0061038)	extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|SMC loading complex (GO:0032116)	chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|histone deacetylase binding (GO:0042826)|protein C-terminus binding (GO:0008022)|protein N-terminus binding (GO:0047485)			autonomic_ganglia(1)|breast(4)|endometrium(9)|kidney(22)|large_intestine(21)|liver(1)|lung(47)|ovary(7)|pancreas(1)|prostate(1)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(4)	128	all_lung(31;0.000447)|Hepatocellular(1;0.108)		Epithelial(62;0.072)|COAD - Colon adenocarcinoma(61;0.14)|all cancers(62;0.191)|Colorectal(62;0.202)			GCAAACAAAACGAGAGCACCA	0.338													C|||	1	0.000199681	0.0	0.0	5008	,	,		20570	0.0		0.001	False		,,,				2504	0.0				p.N664N		Atlas-SNP	.											.	NIPBL	513	.	0			c.C1992T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	97.0	96.0	96.0		1992,1992	0.7	0.9	5	dbSNP_132	96	2,8598	3.0+/-9.4	0,2,4298	no	coding-synonymous,coding-synonymous	NIPBL	NM_015384.4,NM_133433.3	,	0,3,6500	TT,TC,CC		0.0233,0.0227,0.0231	,	664/2698,664/2805	36985274	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	25836	exon10			ACAAAACGAGAGC	AB019494	CCDS3920.1, CCDS47198.1	5p13.2	2009-08-28			ENSG00000164190	ENSG00000164190			28862	protein-coding gene	gene with protein product	"""sister chromatid cohesion 2 homolog (yeast)"""	608667				15146186, 15146185	Standard	NM_133433		Approved	IDN3, DKFZp434L1319, FLJ11203, FLJ12597, FLJ13354, FLJ13648, Scc2	uc003jkl.4	Q6KC79	OTTHUMG00000090795	ENST00000282516.8:c.1992C>T	5.37:g.36985274C>T		94.0	0.0	0		121.0	68.0	0.561983	NM_015384	Q6KCD6|Q6N080|Q6ZT92|Q7Z2E6|Q8N4M5|Q9Y6Y3|Q9Y6Y4	Silent	SNP	ENST00000282516.8	37	CCDS3920.1																																																																																			C|1.000;T|0.000	0.000	strong		0.338	NIPBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207582.1	NM_015384	
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	184.0	0.0	0		248.0	11.0	0.0443548	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	
KLHL30	377007	hgsc.bcm.edu	37	2	239059578	239059578	+	Missense_Mutation	SNP	G	G	A	rs369686635	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:239059578G>A	ENST00000409223.1	+	8	1716	c.1609G>A	c.(1609-1611)Gac>Aac	p.D537N	KLHL30_ENST00000305959.4_Missense_Mutation_p.D519N			Q0D2K2	KLH30_HUMAN	kelch-like family member 30	537										lung(4)	4		Breast(86;7.61e-05)|Renal(207;0.00183)|Ovarian(221;0.0481)|all_hematologic(139;0.158)|all_lung(227;0.198)|Melanoma(123;0.203)|Hepatocellular(293;0.244)		Epithelial(121;4.71e-24)|OV - Ovarian serous cystadenocarcinoma(60;3.02e-12)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;5.63e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000109)|Lung(119;0.0108)|LUSC - Lung squamous cell carcinoma(224;0.0253)		GGAGGCCTACGACACGGTTCG	0.672													G|||	2	0.000399361	0.0	0.0014	5008	,	,		11838	0.001		0.0	False		,,,				2504	0.0				p.D537N		Atlas-SNP	.											.	KLHL30	79	.	0			c.G1609A						PASS	.	G	ASN/ASP	1,4305		0,1,2152	19.0	27.0	24.0		1609	4.7	0.9	2		24	0,8462		0,0,4231	no	missense	KLHL30	NM_198582.3	23	0,1,6383	AA,AG,GG		0.0,0.0232,0.0078	possibly-damaging	537/579	239059578	1,12767	2153	4231	6384	SO:0001583	missense	377007	exon8			GCCTACGACACGG		CCDS46555.1, CCDS46555.2	2q37.3	2013-02-22	2013-02-22		ENSG00000168427	ENSG00000168427		"""Kelch-like"", ""BTB/POZ domain containing"""	24770	protein-coding gene	gene with protein product			"""kelch-like 30 (Drosophila)"""				Standard	NM_198582		Approved	FLJ43374	uc002vxr.2	Q0D2K2	OTTHUMG00000152905	ENST00000409223.1:c.1609G>A	2.37:g.239059578G>A	ENSP00000386389:p.Asp537Asn	138.0	0.0	0		138.0	65.0	0.471014	NM_198582	Q6ZUS1	Missense_Mutation	SNP	ENST00000409223.1	37	CCDS46555.2	.	.	.	.	.	.	.	.	.	.	G	13.29	2.192615	0.38707	2.32E-4	0.0	ENSG00000168427	ENST00000409223;ENST00000305959	T;T	0.70869	-0.52;-0.52	4.66	4.66	0.58398	Kelch-type beta propeller (1);	0.075656	0.64402	D	0.000008	T	0.61825	0.2378	L	0.52011	1.625	0.41539	D	0.988502	P	0.47841	0.901	B	0.34652	0.187	T	0.67620	-0.5624	10	0.39692	T	0.17	.	16.4605	0.84033	0.0:0.0:1.0:0.0	.	537	Q0D2K2	KLH30_HUMAN	N	537;519	ENSP00000386389:D537N;ENSP00000302386:D519N	ENSP00000302386:D519N	D	+	1	0	KLHL30	238724317	1.000000	0.71417	0.923000	0.36655	0.269000	0.26545	3.349000	0.52217	2.423000	0.82170	0.561000	0.74099	GAC	.	.	weak		0.672	KLHL30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328518.1	NM_198582	
EMR2	30817	hgsc.bcm.edu	37	19	14854338	14854338	+	Missense_Mutation	SNP	C	C	T	rs117617387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:14854338C>T	ENST00000315576.3	-	20	2808	c.2357G>A	c.(2356-2358)cGg>cAg	p.R786Q	EMR2_ENST00000353005.1_Missense_Mutation_p.R644Q|EMR2_ENST00000392965.3_Missense_Mutation_p.R728Q|EMR2_ENST00000594294.1_Missense_Mutation_p.R737Q|EMR2_ENST00000596991.2_Missense_Mutation_p.R775Q|EMR2_ENST00000601345.1_Missense_Mutation_p.R775Q|EMR2_ENST00000392967.2_Missense_Mutation_p.R775Q|EMR2_ENST00000353876.1_Missense_Mutation_p.R693Q|EMR2_ENST00000594076.1_Missense_Mutation_p.R693Q|EMR2_ENST00000346057.1_Missense_Mutation_p.R737Q|EMR2_ENST00000595839.1_Missense_Mutation_p.R644Q	NM_013447.3	NP_038475.2	Q9UHX3	EMR2_HUMAN	egf-like module containing, mucin-like, hormone receptor-like 2	786					cell adhesion (GO:0007155)|cell migration (GO:0016477)|G-protein coupled receptor signaling pathway (GO:0007186)|granulocyte chemotaxis (GO:0071621)|inflammatory response (GO:0006954)|neuropeptide signaling pathway (GO:0007218)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|G-protein coupled receptor activity (GO:0004930)			breast(1)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(1)	48						ATATTGCTCCCGGACCTGCAG	0.547													c|||	36	0.0071885	0.0015	0.0086	5008	,	,		20652	0.0		0.0089	False		,,,				2504	0.0194				p.R786Q		Atlas-SNP	.											EMR2,NS,carcinoma,+1,1	EMR2	99	1	0			c.G2357A						scavenged	.		GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	17,4389	22.3+/-47.3	0,17,2186	304.0	290.0	295.0		2357,2210,2078,1931,2324,2177,2045	-3.3	0.0	19	dbSNP_132	295	155,8445	74.2+/-136.8	2,151,4147	yes	missense,missense,missense,missense,missense,missense,missense	EMR2	NM_013447.2,NM_152916.1,NM_152917.1,NM_152918.1,NM_152919.1,NM_152920.1,NM_152921.1	43,43,43,43,43,43,43	2,168,6333	TT,TC,CC		1.8023,0.3858,1.3225	benign,benign,benign,benign,benign,benign,benign	786/824,737/775,693/731,644/682,775/813,726/764,682/720	14854338	172,12834	2203	4300	6503	SO:0001583	missense	30817	exon20			TGCTCCCGGACCT	AF114491	CCDS32935.1, CCDS59361.1	19p13.1	2014-08-08	2003-11-26			ENSG00000127507		"""CD molecules"", ""-"", ""GPCR / Class B : Orphans"""	3337	protein-coding gene	gene with protein product		606100	"""egf-like module containing, mucin-like, hormone receptor-like sequence 2"""				Standard	NM_013447		Approved	CD312	uc002mzp.2	Q9UHX3		ENST00000315576.3:c.2357G>A	19.37:g.14854338C>T	ENSP00000319883:p.Arg786Gln	169.0	1.0	0.00591716		190.0	99.0	0.521053	NM_013447	B4DQ96|E7ESD7|E9PBR1|E9PEL6|E9PFQ5|E9PG91|Q8NG96|Q9Y4B1	Missense_Mutation	SNP	ENST00000315576.3	37	CCDS32935.1	11	0.005036630036630037	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	6	0.0079155672823219	c	15.15	2.747296	0.49257	0.003858	0.018023	ENSG00000127507	ENST00000315576;ENST00000392967;ENST00000346057;ENST00000353876;ENST00000353005;ENST00000392965	T;T;T;T;T;T	0.57273	0.41;0.41;0.41;0.41;0.41;0.41	5.02	-3.26	0.05064	.	.	.	.	.	T	0.27313	0.0670	L	0.43923	1.385	0.09310	N	0.999996	B;B;B;P;B;B;B;B	0.46952	0.026;0.107;0.014;0.887;0.289;0.238;0.054;0.045	B;B;B;P;B;B;B;B	0.45794	0.006;0.08;0.011;0.493;0.141;0.103;0.022;0.099	T	0.35599	-0.9782	9	0.23891	T	0.37	.	9.6794	0.40061	0.0:0.4651:0.0:0.5349	.	728;693;786;644;737;786;786;775	E7ESD7;Q9UHX3-4;A0JNV7;Q9UHX3-5;Q9UHX3-3;A8K6W1;Q9UHX3;Q9UHX3-2	.;.;.;.;.;.;EMR2_HUMAN;.	Q	786;775;737;693;644;728	ENSP00000319883:R786Q;ENSP00000376694:R775Q;ENSP00000263380:R737Q;ENSP00000319454:R693Q;ENSP00000319838:R644Q;ENSP00000376692:R728Q	ENSP00000319883:R786Q	R	-	2	0	EMR2	14715338	0.007000	0.16637	0.033000	0.17914	0.247000	0.25773	0.266000	0.18534	-0.410000	0.07542	-0.205000	0.12727	CGG	C|0.989;T|0.011	0.011	strong		0.547	EMR2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466502.2		
FITM1	161247	hgsc.bcm.edu	37	14	24600828	24600828	+	Missense_Mutation	SNP	C	C	T	rs147792464		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24600828C>T	ENST00000267426.5	+	1	345	c.56C>T	c.(55-57)gCa>gTa	p.A19V	FITM1_ENST00000559294.1_5'Flank|RP11-468E2.6_ENST00000558325.1_Silent_p.G206G	NM_203402.2	NP_981947.1	A5D6W6	FITM1_HUMAN	fat storage-inducing transmembrane protein 1	19					lipid particle organization (GO:0034389)|positive regulation of sequestering of triglyceride (GO:0010890)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)				breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	11						CGAATCCAGGCACTGCTGGGC	0.672																																					p.A19V		Atlas-SNP	.											.	FITM1	25	.	0			c.C56T						PASS	.	C	VAL/ALA	0,4406		0,0,2203	18.0	23.0	21.0		56	1.6	0.9	14	dbSNP_134	21	6,8592		0,6,4293	yes	missense	FITM1	NM_203402.2	64	0,6,6496	TT,TC,CC		0.0698,0.0,0.0461	benign	19/293	24600828	6,12998	2203	4299	6502	SO:0001583	missense	161247	exon1			TCCAGGCACTGCT		CCDS9611.1	14q12	2009-07-09			ENSG00000139914	ENSG00000139914			33714	protein-coding gene	gene with protein product	"""fat-inducing transcript 1"""	612028				18160536	Standard	NM_203402		Approved	FIT1	uc001wmf.2	A5D6W6	OTTHUMG00000133476	ENST00000267426.5:c.56C>T	14.37:g.24600828C>T	ENSP00000267426:p.Ala19Val	123.0	0.0	0		101.0	46.0	0.455446	NM_203402	Q8IUQ7	Missense_Mutation	SNP	ENST00000267426.5	37	CCDS9611.1	.	.	.	.	.	.	.	.	.	.	c	7.996	0.754445	0.15778	0.0	6.98E-4	ENSG00000139914	ENST00000267426	.	.	.	4.6	1.58	0.23477	.	0.188323	0.32655	N	0.005818	T	0.13030	0.0316	N	0.03608	-0.345	0.25699	N	0.985606	B	0.02656	0.0	B	0.01281	0.0	T	0.20240	-1.0281	9	0.21540	T	0.41	-7.9479	5.6671	0.17700	0.0:0.6485:0.0:0.3515	.	19	A5D6W6	FITM1_HUMAN	V	19	.	ENSP00000267426:A19V	A	+	2	0	FITM1	23670668	0.001000	0.12720	0.860000	0.33809	0.460000	0.32559	0.514000	0.22786	0.567000	0.29293	-0.369000	0.07265	GCA	C|1.000;T|0.000	0.000	weak		0.672	FITM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257366.1	NM_203402	
ZNF536	9745	hgsc.bcm.edu	37	19	31039669	31039669	+	Missense_Mutation	SNP	C	C	T	rs77238711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:31039669C>T	ENST00000355537.3	+	4	3290	c.3143C>T	c.(3142-3144)gCg>gTg	p.A1048V		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	1048					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					GCCCGGGAGGCGAGTAAGATG	0.537													C|||	229	0.0457268	0.0348	0.0173	5008	,	,		19387	0.005		0.0338	False		,,,				2504	0.135				p.A1048V		Atlas-SNP	.											.	ZNF536	424	.	0			c.C3143T						PASS	.	C	VAL/ALA	161,4245	108.6+/-147.0	2,157,2044	79.0	73.0	75.0		3143	0.6	0.1	19	dbSNP_131	75	288,8312	107.0+/-167.8	5,278,4017	yes	missense	ZNF536	NM_014717.1	64	7,435,6061	TT,TC,CC		3.3488,3.6541,3.4523	benign	1048/1301	31039669	449,12557	2203	4300	6503	SO:0001583	missense	9745	exon4			GGGAGGCGAGTAA		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.3143C>T	19.37:g.31039669C>T	ENSP00000347730:p.Ala1048Val	28.0	0.0	0		35.0	22.0	0.628571	NM_014717	A2RU18	Missense_Mutation	SNP	ENST00000355537.3	37	CCDS32984.1	50	0.022893772893772892	15	0.03048780487804878	8	0.022099447513812154	0	0.0	27	0.03562005277044855	C	0.303	-0.972510	0.02215	0.036541	0.033488	ENSG00000198597	ENST00000355537	T	0.09538	2.97	5.74	0.614	0.17603	.	0.308174	0.30383	N	0.009750	T	0.01156	0.0038	N	0.14661	0.345	0.23492	N	0.99756	B;B	0.09022	0.002;0.002	B;B	0.06405	0.002;0.002	T	0.37619	-0.9698	10	0.36615	T	0.2	-16.6787	8.9777	0.35946	0.0:0.6367:0.1064:0.2569	.	1048;1048	A7E228;O15090	.;ZN536_HUMAN	V	1048	ENSP00000347730:A1048V	ENSP00000347730:A1048V	A	+	2	0	ZNF536	35731509	0.146000	0.22672	0.080000	0.20451	0.020000	0.10135	0.203000	0.17315	0.337000	0.23665	-0.768000	0.03414	GCG	C|0.970;T|0.030	0.030	strong		0.537	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
DOCK5	80005	hgsc.bcm.edu	37	8	25149612	25149612	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:25149612C>T	ENST00000276440.7	+	6	438	c.394C>T	c.(394-396)Ctg>Ttg	p.L132L	DOCK5_ENST00000481100.1_Silent_p.L132L	NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	132					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GTCCCAGATCCTGTCTGGGAC	0.493																																					p.L132L	Pancreas(145;34 1887 3271 10937 30165)	Atlas-SNP	.											.	DOCK5	167	.	0			c.C394T						PASS	.						37.0	34.0	35.0					8																	25149612		2203	4298	6501	SO:0001819	synonymous_variant	80005	exon6			CAGATCCTGTCTG		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.394C>T	8.37:g.25149612C>T		51.0	0.0	0		69.0	16.0	0.231884	NM_024940	B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	CCDS6047.1																																																																																			.	.	none		0.493	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
CDHR1	92211	hgsc.bcm.edu	37	10	85958847	85958847	+	Silent	SNP	C	C	T	rs148125234	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:85958847C>T	ENST00000372117.3	+	5	511	c.408C>T	c.(406-408)atC>atT	p.I136I	CDHR1_ENST00000332904.3_Silent_p.I136I|CDHR1_ENST00000440770.2_5'Flank	NM_033100.2	NP_149091.1	Q96JP9	CDHR1_HUMAN	cadherin-related family member 1	136	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cellular process (GO:0009987)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)	integral component of plasma membrane (GO:0005887)|photoreceptor outer segment membrane (GO:0042622)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|liver(1)|lung(21)|ovary(1)|prostate(1)|skin(1)	36						CCAGGTTCATCCAGGAGCCTT	0.597													C|||	5	0.000998403	0.0008	0.0	5008	,	,		17525	0.0		0.004	False		,,,				2504	0.0				p.I136I		Atlas-SNP	.											.	CDHR1	122	.	0			c.C408T						PASS	.	C	,	1,4047		0,1,2023	95.0	77.0	83.0		408,408	3.3	0.9	10	dbSNP_134	83	15,7755		0,15,3870	no	coding-synonymous,coding-synonymous	CDHR1	NM_001171971.1,NM_033100.2	,	0,16,5893	TT,TC,CC		0.1931,0.0247,0.1354	,	136/746,136/860	85958847	16,11802	2024	3885	5909	SO:0001819	synonymous_variant	92211	exon5			GTTCATCCAGGAG	AB053448	CCDS7372.1, CCDS53548.1	10q23.1	2014-01-28	2010-01-25	2010-01-25	ENSG00000148600	ENSG00000148600		"""Cadherins / Cadherin-related"""	14550	protein-coding gene	gene with protein product		609502	"""protocadherin 21"""	PCDH21		11597768	Standard	NM_001171971		Approved	KIAA1775, CORD15, RP65	uc001kcv.3	Q96JP9	OTTHUMG00000018634	ENST00000372117.3:c.408C>T	10.37:g.85958847C>T		98.0	0.0	0		94.0	39.0	0.414894	NM_001171971	Q69YZ8|Q8IXY5	Silent	SNP	ENST00000372117.3	37	CCDS7372.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	CDHR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049111.1	NM_033100	
PLPPR1	54886	hgsc.bcm.edu	37	9	104032338	104032338	+	Silent	SNP	C	C	T	rs7847596	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:104032338C>T	ENST00000374874.3	+	3	679	c.240C>T	c.(238-240)acC>acT	p.T80T	LPPR1_ENST00000395056.2_Silent_p.T80T	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		80					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										TGGCTGCCACCCCAACTGCTA	0.443													C|||	86	0.0171725	0.003	0.0187	5008	,	,		19611	0.001		0.0417	False		,,,				2504	0.0266				p.T80T		Atlas-SNP	.											.	.	.	.	0			c.C240T						PASS	.	C	,	32,4374	34.3+/-65.2	0,32,2171	83.0	81.0	82.0		240,240	-1.7	1.0	9	dbSNP_116	82	342,8258	112.7+/-172.9	5,332,3963	no	coding-synonymous,coding-synonymous	LPPR1	NM_017753.2,NM_207299.1	,	5,364,6134	TT,TC,CC		3.9767,0.7263,2.8756	,	80/326,80/326	104032338	374,12632	2203	4300	6503	SO:0001819	synonymous_variant	0	exon3			TGCCACCCCAACT																												ENST00000374874.3:c.240C>T	9.37:g.104032338C>T		116.0	0.0	0		110.0	61.0	0.554545	NM_207299	Q5VX23|Q9NXE2	Silent	SNP	ENST00000374874.3	37	CCDS6751.1																																																																																			C|0.973;T|0.027	0.027	strong		0.443	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
C14orf159	80017	hgsc.bcm.edu	37	14	91666248	91666248	+	Splice_Site	SNP	T	T	C	rs28715808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91666248T>C	ENST00000523771.1	+	11	2031	c.1428T>C	c.(1426-1428)acT>acC	p.T476T	C14orf159_ENST00000521077.2_Splice_Site_p.T481T|C14orf159_ENST00000428926.2_Splice_Site_p.T476T|C14orf159_ENST00000522322.1_Splice_Site_p.T476T|C14orf159_ENST00000520328.1_Splice_Site_p.T464T|C14orf159_ENST00000412671.2_Splice_Site_p.T481T|C14orf159_ENST00000518868.1_Splice_Site_p.T481T|C14orf159_ENST00000256324.10_Splice_Site_p.T481T|C14orf159_ENST00000525393.2_Splice_Site_p.T352T|C14orf159_ENST00000523816.1_Splice_Site_p.T476T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	476						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		TCTCATCAACTGGTAAGTATG	0.458													T|||	181	0.0361422	0.1067	0.0346	5008	,	,		22154	0.0		0.0109	False		,,,				2504	0.0051				p.T481T		Atlas-SNP	.											.	C14orf159	57	.	0			c.T1443C						PASS	.	T	,,,,	337,4069	176.9+/-206.0	16,305,1882	151.0	142.0	145.0		1428,1428,1443,1392,1428	-2.7	0.1	14	dbSNP_125	145	117,8483	61.0+/-122.8	0,117,4183	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	,,,,	16,422,6065	CC,CT,TT		1.3605,7.6487,3.4907	,,,,	476/617,476/617,481/622,464/565,476/617	91666248	454,12552	2203	4300	6503	SO:0001630	splice_region_variant	80017	exon11			ATCAACTGGTAAG	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1429+1T>C	14.37:g.91666248T>C		125.0	0.0	0		120.0	60.0	0.5	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Silent	SNP	ENST00000523771.1	37	CCDS32141.1	60	0.027472527472527472	41	0.08333333333333333	12	0.03314917127071823	0	0.0	7	0.009234828496042216	T	0.894	-0.724442	0.03158	0.076487	0.013605	ENSG00000133943	ENST00000522816	.	.	.	5.1	-2.71	0.05986	.	.	.	.	.	T	0.00967	0.0032	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.22173	-1.0224	3	.	.	.	.	2.29	0.04136	0.3649:0.0777:0.3565:0.2009	rs28715808	.	.	.	P	77	.	.	L	+	2	0	C14orf159	90736001	0.990000	0.36364	0.051000	0.19133	0.053000	0.15095	0.237000	0.17985	-0.360000	0.08138	-0.461000	0.05368	CTG	T|0.967;C|0.033	0.033	strong		0.458	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	Silent
WDR90	197335	hgsc.bcm.edu	37	16	703648	703648	+	Missense_Mutation	SNP	A	A	G	rs143047488	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:703648A>G	ENST00000293879.4	+	12	1357	c.1357A>G	c.(1357-1359)Atg>Gtg	p.M453V	WDR90_ENST00000549091.1_Missense_Mutation_p.M453V|LA16c-349E10.1_ENST00000573609.1_RNA			Q96KV7	WDR90_HUMAN	WD repeat domain 90	453										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				CCGGAGCCCAATGCACGTTGT	0.637													A|||	7	0.00139776	0.0	0.0014	5008	,	,		18008	0.001		0.004	False		,,,				2504	0.001				p.M453V		Atlas-SNP	.											.	WDR90	107	.	0			c.A1357G						PASS	.	A	VAL/MET	1,4113		0,1,2056	55.0	61.0	59.0		1357	-5.9	0.0	16	dbSNP_134	59	14,8368		0,14,4177	yes	missense	WDR90	NM_145294.4	21	0,15,6233	GG,GA,AA		0.167,0.0243,0.12	benign	453/1749	703648	15,12481	2057	4191	6248	SO:0001583	missense	197335	exon12			AGCCCAATGCACG	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.1357A>G	16.37:g.703648A>G	ENSP00000293879:p.Met453Val	94.0	0.0	0		61.0	34.0	0.557377	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Missense_Mutation	SNP	ENST00000293879.4	37	CCDS42092.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	0	-2.592739	0.00126	2.43E-4	0.00167	ENSG00000161996	ENST00000549091;ENST00000293879	T;T	0.01265	5.08;5.08	4.74	-5.88	0.02290	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);	0.312485	0.23962	N	0.042850	T	0.00440	0.0014	N	0.00560	-1.38	0.19300	N	0.999974	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.44997	-0.9291	10	0.20519	T	0.43	.	7.8237	0.29303	0.3658:0.2096:0.4247:0.0	.	453;454;453	Q96KV7;C9JMK1;Q96KV7-3	WDR90_HUMAN;.;.	V	453	ENSP00000448122:M453V;ENSP00000293879:M453V	ENSP00000293879:M453V	M	+	1	0	WDR90	643649	0.000000	0.05858	0.001000	0.08648	0.002000	0.02628	-0.485000	0.06520	-1.101000	0.03027	-1.545000	0.00906	ATG	A|0.997;G|0.003	0.003	strong		0.637	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
DNAH5	1767	hgsc.bcm.edu	37	5	13700783	13700783	+	Missense_Mutation	SNP	C	C	G	rs374221053		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:13700783C>G	ENST00000265104.4	-	78	13793	c.13689G>C	c.(13687-13689)ttG>ttC	p.L4563F		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4563					cilium movement (GO:0003341)|lateral ventricle development (GO:0021670)|left/right axis specification (GO:0070986)	axonemal dynein complex (GO:0005858)|axoneme (GO:0005930)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(6)|breast(14)|central_nervous_system(4)|cervix(2)|endometrium(23)|haematopoietic_and_lymphoid_tissue(8)|kidney(11)|large_intestine(85)|liver(1)|lung(129)|ovary(16)|pancreas(2)|prostate(5)|skin(48)|stomach(5)|upper_aerodigestive_tract(11)|urinary_tract(8)	378	Lung NSC(4;0.00476)					TGACAGGCATCAACTCAAAGA	0.413									Kartagener syndrome																												p.L4563F		Atlas-SNP	.											.	DNAH5	868	.	0			c.G13689C						PASS	.	C	PHE/LEU	0,4406		0,0,2203	183.0	176.0	178.0		13689	2.1	0.8	5		178	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAH5	NM_001369.2	22	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	possibly-damaging	4563/4625	13700783	1,13005	2203	4300	6503	SO:0001583	missense	1767	exon78	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	AGGCATCAACTCA	AJ132090	CCDS3882.1	5p15.2	2008-07-18	2006-09-04		ENSG00000039139	ENSG00000039139		"""Axonemal dyneins"""	2950	protein-coding gene	gene with protein product	"""dynein heavy chain 5"""	603335	"""dynein, axonemal, heavy polypeptide 5"""			9256245, 11788826	Standard	NM_001369		Approved	Dnahc5, HL1, PCD, CILD3, KTGNR	uc003jfd.2	Q8TE73	OTTHUMG00000090533	ENST00000265104.4:c.13689G>C	5.37:g.13700783C>G	ENSP00000265104:p.Leu4563Phe	173.0	0.0	0		155.0	75.0	0.483871	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.405974	0.42715	0.0	1.16E-4	ENSG00000039139	ENST00000265104	T	0.08896	3.04	5.95	2.1	0.27182	Dynein heavy chain (1);	0.167558	0.46758	D	0.000275	T	0.14013	0.0339	M	0.73430	2.235	0.36463	D	0.866823	P	0.37612	0.602	P	0.45474	0.482	T	0.04427	-1.0952	10	0.51188	T	0.08	.	5.1797	0.15154	0.0:0.4605:0.2582:0.2813	.	4563	Q8TE73	DYH5_HUMAN	F	4563	ENSP00000265104:L4563F	ENSP00000265104:L4563F	L	-	3	2	DNAH5	13753783	0.427000	0.25514	0.788000	0.31933	0.528000	0.34623	0.101000	0.15251	0.095000	0.17434	-0.182000	0.12963	TTG	.	.	weak		0.413	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
ACTR3C	653857	hgsc.bcm.edu	37	7	149981856	149981856	+	Missense_Mutation	SNP	G	G	A	rs117425825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	58.0	0.0	0		61.0	35.0	0.57377	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		
FBXW5	54461	hgsc.bcm.edu	37	9	139835558	139835558	+	Missense_Mutation	SNP	C	C	T	rs45559439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139835558C>T	ENST00000325285.3	-	9	1602	c.1523G>A	c.(1522-1524)cGg>cAg	p.R508Q	FBXW5_ENST00000483559.1_5'UTR	NM_018998.3	NP_061871.1	Q969U6	FBXW5_HUMAN	F-box and WD repeat domain containing 5	508				R -> Q (in Ref. 5; BAD92963). {ECO:0000305}.	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)		ATCCTCGTGCCGCAGCCTGGC	0.677													C|||	49	0.00978435	0.0	0.0245	5008	,	,		15182	0.0		0.0298	False		,,,				2504	0.002				p.R508Q		Atlas-SNP	.											.	FBXW5	36	.	0			c.G1523A						PASS	.	C	GLN/ARG	22,4320		0,22,2149	66.0	61.0	62.0		1523	2.2	1.0	9	dbSNP_127	62	215,8361		3,209,4076	yes	missense	FBXW5	NM_018998.2	43	3,231,6225	TT,TC,CC		2.507,0.5067,1.8346	benign	508/567	139835558	237,12681	2171	4288	6459	SO:0001583	missense	54461	exon9			TCGTGCCGCAGCC	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.1523G>A	9.37:g.139835558C>T	ENSP00000313034:p.Arg508Gln	73.0	0.0	0		81.0	39.0	0.481481	NM_018998	B2RDZ6|Q59ET5|Q5SPZ8|Q5SPZ9|Q5SQ00|Q5SQ02|Q5SQ03|Q5SQ04|Q8WY79|Q96GJ6|Q9BSU8|Q9H6A8|Q9HBQ6|Q9NSZ3	Missense_Mutation	SNP	ENST00000325285.3	37	CCDS7014.1	33	0.01510989010989011	0	0.0	10	0.027624309392265192	0	0.0	23	0.030343007915567283	C	10.25	1.298726	0.23650	0.005067	0.02507	ENSG00000159069	ENST00000325285	T	0.65549	-0.16	4.05	2.21	0.28008	WD40/YVTN repeat-like-containing domain (1);Soluble quinoprotein glucose/sorbosone dehydrogenase (1);WD40-repeat-containing domain (1);	0.432182	0.22954	N	0.053633	T	0.11922	0.0290	N	0.04705	-0.18	0.35200	D	0.774171	B	0.06786	0.001	B	0.04013	0.001	T	0.09122	-1.0689	10	0.09338	T	0.73	-16.5307	4.2639	0.10754	0.0:0.5978:0.19:0.2122	rs45559439	508	Q969U6	FBXW5_HUMAN	Q	508	ENSP00000313034:R508Q	ENSP00000313034:R508Q	R	-	2	0	FBXW5	138955379	0.994000	0.37717	1.000000	0.80357	0.857000	0.48899	1.227000	0.32576	0.403000	0.25479	-0.265000	0.10407	CGG	C|0.985;T|0.015	0.015	strong		0.677	FBXW5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055227.1	NM_018998	
WWC3	55841	hgsc.bcm.edu	37	X	10085602	10085602	+	Silent	SNP	A	A	C	rs56130457		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:10085602A>C	ENST00000380861.4	+	11	1894	c.1503A>C	c.(1501-1503)gcA>gcC	p.A501A	WWC3_ENST00000454666.1_Silent_p.A501A	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	501					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						GACTGCGGGCACACGCCTCGG	0.716													A|||	8	0.00211921	0.0008	0.0014	3775	,	,		11380	0.0		0.006	False		,,,				2504	0.0				p.A501A		Atlas-SNP	.											.	WWC3	142	.	0			c.A1503C						PASS	.	A		8,3752		0,6,2,1607,532	7.0	7.0	7.0		1503	-10.9	0.0	X	dbSNP_129	7	85,6535		0,60,25,2350,1775	no	coding-synonymous	WWC3	NM_015691.3		0,66,27,3957,2307	CC,CA,C,AA,A		1.284,0.2128,0.896		501/1093	10085602	93,10287	2147	4210	6357	SO:0001819	synonymous_variant	55841	exon11			GCGGGCACACGCC	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1503A>C	X.37:g.10085602A>C		25.0	0.0	0		27.0	27.0	1	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			A|0.995;C|0.005	0.005	strong		0.716	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
MROH7	374977	hgsc.bcm.edu	37	1	55119637	55119637	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:55119637C>G	ENST00000421030.2	+	3	1323	c.1038C>G	c.(1036-1038)agC>agG	p.S346R	MROH7_ENST00000454855.2_Intron|MROH7-TTC4_ENST00000414150.2_Missense_Mutation_p.S346R|MROH7_ENST00000472987.1_3'UTR|MROH7_ENST00000545244.1_Intron|MROH7_ENST00000339553.5_Missense_Mutation_p.S346R|MROH7_ENST00000395690.2_Missense_Mutation_p.S346R|MROH7_ENST00000409996.1_Intron	NM_001039464.2	NP_001034553	Q68CQ1	MROH7_HUMAN	maestro heat-like repeat family member 7	346	Ser-rich.					extracellular space (GO:0005615)|integral component of membrane (GO:0016021)											TCCTGTTCAGCGACACCTCCA	0.562																																					p.S346R		Atlas-SNP	.											.	.	.	.	0			c.C1038G						PASS	.						99.0	98.0	98.0					1																	55119637		2139	4231	6370	SO:0001583	missense	374977	exon3			GTTCAGCGACACC	AL832492	CCDS41342.2	1p32.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000184313	ENSG00000184313		"""maestro heat-like repeat containing"""	24802	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 175"", ""HEAT repeat containing 8"""	C1orf175, HEATR8		12477932	Standard	NM_001039464		Approved	FLJ46354	uc010ooe.1	Q68CQ1	OTTHUMG00000009890	ENST00000421030.2:c.1038C>G	1.37:g.55119637C>G	ENSP00000396622:p.Ser346Arg	171.0	0.0	0		147.0	77.0	0.52381	NM_001039464	A0AUX8|Q5TA99|Q6ZP40|Q6ZRH6|Q8N311|Q8NA14	Missense_Mutation	SNP	ENST00000421030.2	37	CCDS41342.2	.	.	.	.	.	.	.	.	.	.	C	9.694	1.152800	0.21371	.	.	ENSG00000184313	ENST00000421030;ENST00000414867;ENST00000339553;ENST00000395690	T;T;T	0.04454	3.62;3.62;3.62	3.89	-7.78	0.01223	.	0.164918	0.29113	N	0.013103	T	0.09818	0.0241	L	0.27053	0.805	0.31997	N	0.603917	D;D;D	0.89917	0.996;0.989;1.0	D;P;D	0.75484	0.944;0.875;0.986	T	0.34104	-0.9842	10	0.87932	D	0	.	19.0946	0.93244	0.0:0.7723:0.0:0.2277	.	346;346;346	F8W8P2;Q68CQ1;Q68CQ1-4	.;HEAT8_HUMAN;.	R	346	ENSP00000396622:S346R;ENSP00000343211:S346R;ENSP00000379044:S346R	ENSP00000343211:S346R	S	+	3	2	HEATR8	54892225	0.000000	0.05858	0.261000	0.24466	0.379000	0.30106	-7.901000	0.00028	-2.926000	0.00302	-1.916000	0.00518	AGC	.	.	none		0.562	MROH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346978.1	NM_198547	
PARL	55486	hgsc.bcm.edu	37	3	183580581	183580581	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183580581C>T	ENST00000317096.4	-	4	531	c.471G>A	c.(469-471)aaG>aaA	p.K157K	PARL_ENST00000311101.5_Silent_p.K157K|PARL_ENST00000435888.1_Silent_p.K157K	NM_018622.5	NP_061092.3	Q9H300	PARL_HUMAN	presenilin associated, rhomboid-like	157					membrane protein proteolysis (GO:0033619)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|proteolysis (GO:0006508)|regulation of protein targeting to mitochondrion (GO:1903214)|regulation of reactive oxygen species metabolic process (GO:2000377)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	endopeptidase activity (GO:0004175)|serine-type endopeptidase activity (GO:0004252)			endometrium(2)|large_intestine(3)|liver(1)|lung(6)|prostate(1)|skin(1)|stomach(2)|urinary_tract(1)	17	all_cancers(143;6.55e-10)|Ovarian(172;0.0303)		all cancers(12;2.21e-41)|Epithelial(37;1.34e-36)|OV - Ovarian serous cystadenocarcinoma(80;6.48e-22)			TATTCCACCACTTGTTAATCT	0.393																																					p.K157K		Atlas-SNP	.											.	PARL	32	.	0			c.G471A						PASS	.						108.0	95.0	100.0					3																	183580581		2203	4300	6503	SO:0001819	synonymous_variant	55486	exon4			CCACCACTTGTTA	AF116692	CCDS3248.1, CCDS33897.1	3q27.3	2008-02-05		2006-02-28	ENSG00000175193	ENSG00000175193			18253	protein-coding gene	gene with protein product	"""rhomboid 7 homolog 1 (Drosophila)"""	607858		PSARL			Standard	XM_005247587		Approved	PRO2207, PSARL1, RHBDS1	uc003fmd.3	Q9H300	OTTHUMG00000156890	ENST00000317096.4:c.471G>A	3.37:g.183580581C>T		46.0	0.0	0		72.0	30.0	0.416667	NM_018622	Q96CQ4|Q9BTJ6|Q9P1E3	Silent	SNP	ENST00000317096.4	37	CCDS3248.1	.	.	.	.	.	.	.	.	.	.	C	9.171	1.021044	0.19433	.	.	ENSG00000175193	ENST00000449306	.	.	.	5.45	4.51	0.55191	.	.	.	.	.	T	0.61476	0.2350	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.57774	-0.7753	4	.	.	.	-19.1355	10.6799	0.45809	0.1449:0.7143:0.1408:0.0	.	.	.	.	M	71	.	.	V	-	1	0	PARL	185063275	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.931000	0.28871	2.690000	0.91761	0.557000	0.71058	GTG	.	.	none		0.393	PARL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346465.1	NM_018622	
AGMAT	79814	hgsc.bcm.edu	37	1	15905471	15905471	+	Missense_Mutation	SNP	G	G	T	rs116813534	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:15905471G>T	ENST00000375826.3	-	4	745	c.603C>A	c.(601-603)caC>caA	p.H201Q	DNAJC16_ENST00000483270.1_Intron	NM_024758.4	NP_079034.3	Q9BSE5	SPEB_HUMAN	agmatine ureohydrolase (agmatinase)	201					agmatine biosynthetic process (GO:0097055)|cellular nitrogen compound metabolic process (GO:0034641)|polyamine metabolic process (GO:0006595)|putrescine biosynthetic process from arginine (GO:0033388)|small molecule metabolic process (GO:0044281)|spermidine biosynthetic process (GO:0008295)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	agmatinase activity (GO:0008783)|metal ion binding (GO:0046872)			endometrium(1)|kidney(2)|large_intestine(6)|lung(2)|skin(1)	12		Breast(348;0.000207)|Colorectal(325;0.000258)|Lung NSC(340;0.000359)|all_lung(284;0.000486)|Renal(390;0.000518)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;6.93e-07)|COAD - Colon adenocarcinoma(227;3.91e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000121)|KIRC - Kidney renal clear cell carcinoma(229;0.00257)|STAD - Stomach adenocarcinoma(313;0.00734)|READ - Rectum adenocarcinoma(331;0.0649)		AGGGCGCCCCGTGGTAGAGCT	0.627																																					p.H201Q	NSCLC(126;1678 1780 25805 43508 49531)	Atlas-SNP	.											.	AGMAT	25	.	0			c.C603A						PASS	.						66.0	64.0	64.0					1																	15905471		2203	4300	6503	SO:0001583	missense	79814	exon4			CGCCCCGTGGTAG	AY057097	CCDS160.1	1p36.13	2009-01-05			ENSG00000116771	ENSG00000116771			18407	protein-coding gene	gene with protein product						11804860, 14648699, 11914032	Standard	NM_024758		Approved	FLJ23384	uc001awv.2	Q9BSE5	OTTHUMG00000002357	ENST00000375826.3:c.603C>A	1.37:g.15905471G>T	ENSP00000364986:p.His201Gln	86.0	0.0	0		84.0	51.0	0.607143	NM_024758	Q5TDH1|Q9H5J3	Missense_Mutation	SNP	ENST00000375826.3	37	CCDS160.1	.	.	.	.	.	.	.	.	.	.	G	20.7	4.029886	0.75504	.	.	ENSG00000116771	ENST00000375826	D	0.88354	-2.37	5.87	-5.21	0.02815	Ureohydrolase domain (1);	0.000000	0.85682	D	0.000000	D	0.96281	0.8787	H	0.99312	4.51	0.50813	D	0.999893	D	0.89917	1.0	D	0.97110	1.0	D	0.95290	0.8394	10	0.87932	D	0	-29.7251	16.7644	0.85521	0.7501:0.0:0.2499:0.0	.	201	Q9BSE5	SPEB_HUMAN	Q	201	ENSP00000364986:H201Q	ENSP00000364986:H201Q	H	-	3	2	AGMAT	15778058	0.088000	0.21588	0.767000	0.31495	0.884000	0.51177	-0.576000	0.05854	-1.114000	0.02977	-0.142000	0.14014	CAC	A|0.007;G|0.993;T|0.000	0.000	strong		0.627	AGMAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006763.1	NM_024758	
LDB3	11155	hgsc.bcm.edu	37	10	88466465	88466465	+	Silent	SNP	C	C	T	rs45459491	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:88466465C>T	ENST00000361373.4	+	7	1095	c.1074C>T	c.(1072-1074)gcC>gcT	p.A358A	LDB3_ENST00000352360.5_Intron|LDB3_ENST00000458213.2_Intron|LDB3_ENST00000429277.2_Intron|LDB3_ENST00000263066.6_Intron	NM_007078.2	NP_009009.1			LIM domain binding 3											breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|soft_tissue(1)	25						CAAGTCCTGCCGACAGCCCAA	0.672													C|||	101	0.0201677	0.0008	0.0159	5008	,	,		18021	0.0		0.0368	False		,,,				2504	0.0532				p.A358A		Atlas-SNP	.											.	LDB3	164	.	0			c.C1074T						PASS	.	C	,,	34,4366		1,32,2167	29.0	22.0	25.0		,,1074	-0.1	0.0	10	dbSNP_127	25	317,8279		5,307,3986	no	intron,intron,coding-synonymous	LDB3	NM_001080114.1,NM_001171610.1,NM_007078.2	,,	6,339,6153	TT,TC,CC		3.6878,0.7727,2.7008	,,	,,358/728	88466465	351,12645	2200	4298	6498	SO:0001819	synonymous_variant	11155	exon7			TCCTGCCGACAGC	AB014513	CCDS7377.1, CCDS41544.1, CCDS41545.1, CCDS53549.1, CCDS53550.1	10q22.3-q23.2	2014-09-17			ENSG00000122367	ENSG00000122367			15710	protein-coding gene	gene with protein product	"""cypher"", ""oracle"", ""Z-band alternatively spliced PDZ motif protein"""	605906	"""cardiomyopathy, dilated 1C (autosomal dominant)"""	CMD1C		10427098, 23271734, 23996002, 14662268	Standard	NM_001080114		Approved	PDLIM6, KIAA0613, ZASP	uc001kdv.3	O75112	OTTHUMG00000018655	ENST00000361373.4:c.1074C>T	10.37:g.88466465C>T		139.0	0.0	0		164.0	71.0	0.432927	NM_007078		Silent	SNP	ENST00000361373.4	37	CCDS7377.1																																																																																			C|0.976;T|0.024	0.024	strong		0.672	LDB3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000049160.2		
LAMP2	3920	hgsc.bcm.edu	37	X	119576455	119576455	+	Splice_Site	SNP	G	G	A	rs73219144	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:119576455G>A	ENST00000200639.4	-	7	1063	c.927C>T	c.(925-927)tcC>tcT	p.S309S	LAMP2_ENST00000434600.2_Splice_Site_p.S309S|LAMP2_ENST00000540603.1_Splice_Site_p.S262S|LAMP2_ENST00000538785.1_Splice_Site_p.S198S|LAMP2_ENST00000371335.4_Splice_Site_p.S309S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	309	Second lumenal domain.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						TTTGCTTACCGGAGCCATTAA	0.358													G|||	50	0.013245	0.0	0.0072	3775	,	,		13506	0.0		0.0398	False		,,,				2504	0.0051				p.S309S		Atlas-SNP	.											.	LAMP2	101	.	0			c.C927T						PASS	.	G	,,	29,3806		0,24,5,1608,566	254.0	242.0	246.0		927,927,927	0.9	1.0	X	dbSNP_130	246	274,6454		6,187,75,2235,1797	yes	coding-synonymous-near-splice,coding-synonymous-near-splice,coding-synonymous-near-splice	LAMP2	NM_001122606.1,NM_002294.2,NM_013995.2	,,	6,211,80,3843,2363	AA,AG,A,GG,G		4.0725,0.7562,2.8685	,,	309/412,309/411,309/411	119576455	303,10260	2203	4300	6503	SO:0001630	splice_region_variant	3920	exon7			CTTACCGGAGCCA	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"""CD molecules"""	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.928+1C>T	X.37:g.119576455G>A		46.0	0.0	0		38.0	36.0	0.947368	NM_013995	A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Silent	SNP	ENST00000200639.4	37	CCDS14599.1																																																																																			G|0.975;A|0.025	0.025	strong		0.358	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1		Silent
CDC16	8881	hgsc.bcm.edu	37	13	115002275	115002275	+	Splice_Site	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:115002275A>G	ENST00000356221.3	+	3	213	c.105A>G	c.(103-105)gaA>gaG	p.E35E	CDC16_ENST00000252458.6_Splice_Site|CDC16_ENST00000375308.1_Splice_Site|CDC16_ENST00000360383.3_Splice_Site_p.E35E|CDC16_ENST00000375310.1_Splice_Site|CDC16_ENST00000252457.5_Splice_Site|CDC16_ENST00000375312.3_5'UTR			Q13042	CDC16_HUMAN	cell division cycle 16	35					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|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 mitosis (GO:0007088)|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)|spindle (GO:0005819)				endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	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)			TCCCTCCAGAAGAACCCCAGG	0.413																																					p.E35E		Atlas-SNP	.											.	CDC16	50	.	0			c.A105G						PASS	.						135.0	135.0	135.0					13																	115002275		2203	4300	6503	SO:0001630	splice_region_variant	8881	exon3			TCCAGAAGAACCC	U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.104-1A>G	13.37:g.115002275A>G		91.0	0.0	0		84.0	4.0	0.047619	NM_003903	A2A365|Q5T8C8|Q96AE6|Q9Y564	Silent	SNP	ENST00000356221.3	37	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	A	9.067	0.995900	0.19043	.	.	ENSG00000130177	ENST00000252457	.	.	.	5.43	2.58	0.30949	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.6961	0.40158	0.2981:0.0:0.7019:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CDC16	114020377	1.000000	0.71417	0.999000	0.59377	0.274000	0.26718	1.778000	0.38614	0.864000	0.35578	-0.146000	0.13790	.	.	.	none		0.413	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1	NM_003903	Silent
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552115	178552115	+	Silent	SNP	G	G	A	rs201215425		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178552115G>A	ENST00000251582.7	-	19	2918	c.2817C>T	c.(2815-2817)tcC>tcT	p.S939S		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	939	TSP type-1 3. {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)		TGCAGCGCACGGAGCGCACCT	0.692																																					p.S939S		Atlas-SNP	.											.	ADAMTS2	190	.	0			c.C2817T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	107.0	106.0	107.0		2817	-9.1	0.4	5		107	0,8600		0,0,4300	yes	coding-synonymous	ADAMTS2	NM_014244.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		939/1212	178552115	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9509	exon19			GCGCACGGAGCGC	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.2817C>T	5.37:g.178552115G>A		148.0	0.0	0		169.0	70.0	0.414201	NM_014244		Silent	SNP	ENST00000251582.7	37	CCDS4444.1																																																																																			.	.	weak		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16525657	16525657	+	Missense_Mutation	SNP	A	A	G	rs148325785	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16525657A>G	ENST00000270747.3	-	15	2375	c.2239T>C	c.(2239-2241)Tgg>Cgg	p.W747R	ARHGEF19-AS1_ENST00000457809.1_RNA|ARHGEF19_ENST00000478117.1_5'UTR	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	747	SH3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		TCACTGGTCCAGGTCCTCACT	0.562													A|||	25	0.00499201	0.0	0.0115	5008	,	,		19556	0.0		0.0159	False		,,,				2504	0.001				p.W747R		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.T2239C						PASS	.	A	ARG/TRP	11,4395	17.9+/-39.9	0,11,2192	125.0	98.0	107.0		2239	-0.1	1.0	1	dbSNP_134	107	106,8494	57.9+/-119.4	1,104,4195	yes	missense	ARHGEF19	NM_153213.3	101	1,115,6387	GG,GA,AA		1.2326,0.2497,0.8996	benign	747/803	16525657	117,12889	2203	4300	6503	SO:0001583	missense	128272	exon15			TGGTCCAGGTCCT	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.2239T>C	1.37:g.16525657A>G	ENSP00000270747:p.Trp747Arg	161.0	0.0	0		144.0	72.0	0.5	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	18	0.008241758241758242	0	0.0	6	0.016574585635359115	0	0.0	12	0.0158311345646438	A	4.292	0.053391	0.08291	0.002497	0.012326	ENSG00000142632	ENST00000270747	T	0.43294	0.95	4.57	-0.0683	0.13756	Src homology-3 domain (4);	0.268702	0.27604	N	0.018633	T	0.03011	0.0089	N	0.00170	-1.935	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28933	-1.0028	10	0.06236	T	0.91	.	4.4685	0.11701	0.2021:0.0:0.4709:0.327	.	747	Q8IW93	ARHGJ_HUMAN	R	747	ENSP00000270747:W747R	ENSP00000270747:W747R	W	-	1	0	ARHGEF19	16398244	0.005000	0.15991	0.963000	0.40424	0.929000	0.56500	0.455000	0.21843	0.151000	0.19162	-0.366000	0.07423	TGG	A|0.991;G|0.009	0.009	strong		0.562	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
NPAS2	4862	hgsc.bcm.edu	37	2	101541736	101541736	+	Missense_Mutation	SNP	G	G	C	rs138995271		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:101541736G>C	ENST00000335681.5	+	3	446	c.161G>C	c.(160-162)gGa>gCa	p.G54A	NPAS2_ENST00000486017.1_3'UTR|NPAS2_ENST00000542504.1_Missense_Mutation_p.G119A	NM_002518.3	NP_002509.2	Q99743	NPAS2_HUMAN	neuronal PAS domain protein 2	54	Sufficient for heterodimer formation with ARNTL/BMAL1, E-box binding and for the effect of NADPH. {ECO:0000250|UniProtKB:P97460}.|bHLH. {ECO:0000255|PROSITE- ProRule:PRU00981}.				cellular lipid metabolic process (GO:0044255)|cellular response to DNA damage stimulus (GO:0006974)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|circadian sleep/wake cycle (GO:0042745)|locomotor rhythm (GO:0045475)|negative regulation of cell death (GO:0060548)|positive regulation of DNA repair (GO:0045739)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of response to DNA damage stimulus (GO:2001020)|response to redox state (GO:0051775)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter binding (GO:0001047)|DNA binding (GO:0003677)|Hsp90 protein binding (GO:0051879)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)			cervix(1)|endometrium(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AAGGTCATCGGATTTTTGCAG	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		20410	0.0		0.001	False		,,,				2504	0.0				p.G54A		Atlas-SNP	.											.	NPAS2	88	.	0			c.G161C						PASS	.	G	ALA/GLY	0,4406		0,0,2203	108.0	101.0	104.0		161	5.7	1.0	2	dbSNP_134	104	10,8590	7.7+/-29.5	0,10,4290	yes	missense	NPAS2	NM_002518.3	60	0,10,6493	CC,CG,GG		0.1163,0.0,0.0769	benign	54/825	101541736	10,12996	2203	4300	6503	SO:0001583	missense	4862	exon3			TCATCGGATTTTT	U77970	CCDS2048.1	2q11.2	2013-05-21			ENSG00000170485	ENSG00000170485		"""Basic helix-loop-helix proteins"""	7895	protein-coding gene	gene with protein product		603347				9012850, 9079689	Standard	NM_002518		Approved	MOP4, PASD4, bHLHe9	uc002tap.1	Q99743	OTTHUMG00000130675	ENST00000335681.5:c.161G>C	2.37:g.101541736G>C	ENSP00000338283:p.Gly54Ala	145.0	0.0	0		165.0	68.0	0.412121	NM_002518	Q4ZFV9|Q53SQ3|Q86V96|Q99629	Missense_Mutation	SNP	ENST00000335681.5	37	CCDS2048.1	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	G|G	11.83|11.83	1.756142|1.756142	0.31137|0.31137	0.0|0.0	0.001163|0.001163	ENSG00000170485|ENSG00000170485	ENST00000427413|ENST00000335681;ENST00000542504;ENST00000451740	.|D;D;D	.|0.97710	.|-4.5;-4.5;-4.5	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Helix-loop-helix DNA-binding (5);	.|0.055781	.|0.64402	.|D	.|0.000001	D|D	0.93680|0.93680	0.7981|0.7981	N|N	0.02751|0.02751	-0.505|-0.505	0.58432|0.58432	D|D	0.999998|0.999998	.|P;P	.|0.37370	.|0.537;0.592	.|B;B	.|0.41174	.|0.237;0.349	D|D	0.93572|0.93572	0.6905|0.6905	5|10	.|0.41790	.|T	.|0.15	.|.	19.7272|19.7272	0.96168|0.96168	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|119;54	.|F5H027;Q99743	.|.;NPAS2_HUMAN	H|A	120|54;119;38	.|ENSP00000338283:G54A;ENSP00000438428:G119A;ENSP00000395265:G38A	.|ENSP00000338283:G54A	D|G	+|+	1|2	0|0	NPAS2|NPAS2	100908168|100908168	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.994000|0.994000	0.84299|0.84299	6.750000|6.750000	0.74888|0.74888	2.646000|2.646000	0.89796|0.89796	0.655000|0.655000	0.94253|0.94253	GAT|GGA	G|0.999;C|0.001	0.001	strong		0.498	NPAS2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253168.3		
WDR90	197335	hgsc.bcm.edu	37	16	716971	716971	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:716971C>T	ENST00000293879.4	+	40	5071	c.5071C>T	c.(5071-5073)Ctg>Ttg	p.L1691L	WDR90_ENST00000549091.1_Silent_p.L1693L|WDR90_ENST00000547944.1_Silent_p.L290L|WDR90_ENST00000315764.4_Silent_p.L242L|RHOT2_ENST00000315082.4_5'Flank			Q96KV7	WDR90_HUMAN	WD repeat domain 90	1691										endometrium(4)|kidney(3)|large_intestine(2)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	37		Hepatocellular(780;0.0218)				GACCCACCTCCTGGCTGTTGG	0.617																																					p.L1691L		Atlas-SNP	.											.	WDR90	107	.	0			c.C5071T						PASS	.						69.0	73.0	72.0					16																	716971		2108	4232	6340	SO:0001819	synonymous_variant	197335	exon40			CACCTCCTGGCTG	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.5071C>T	16.37:g.716971C>T		113.0	0.0	0		100.0	51.0	0.51	NM_145294	Q0VA87|Q0VA88|Q6P048|Q6ZMS1|Q6ZTH1|Q8N202|Q8N221|Q8NBB8|Q96PW4|Q96S18	Silent	SNP	ENST00000293879.4	37	CCDS42092.1																																																																																			.	.	none		0.617	WDR90-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404335.1	NM_145294	
CDH20	28316	hgsc.bcm.edu	37	18	59195294	59195294	+	Missense_Mutation	SNP	A	A	G	rs35923922	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:59195294A>G	ENST00000262717.4	+	7	1510	c.1112A>G	c.(1111-1113)cAg>cGg	p.Q371R	CDH20_ENST00000538374.1_Missense_Mutation_p.Q371R|CDH20_ENST00000536675.2_Missense_Mutation_p.Q371R			Q9HBT6	CAD20_HUMAN	cadherin 20, type 2	371	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.		Q -> R (in dbSNP:rs35923922).		homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|skin(3)	61		Colorectal(73;0.186)				GGCCCATTTCAGGACACAACA	0.498													A|||	43	0.00858626	0.0287	0.0058	5008	,	,		18645	0.0		0.001	False		,,,				2504	0.0				p.Q371R		Atlas-SNP	.											CDH20,NS,carcinoma,+1,1	CDH20	117	1	0			c.A1112G						PASS	.	A	ARG/GLN	88,4318	74.1+/-112.3	2,84,2117	132.0	124.0	127.0		1112	5.9	1.0	18	dbSNP_126	127	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CDH20	NM_031891.2	43	2,86,6415	GG,GA,AA		0.0233,1.9973,0.692	benign	371/802	59195294	90,12916	2203	4300	6503	SO:0001583	missense	28316	exon6			CATTTCAGGACAC	AF217289	CCDS11977.1	18q21.33	2010-01-26			ENSG00000101542	ENSG00000101542		"""Cadherins / Major cadherins"""	1760	protein-coding gene	gene with protein product		605807				10995570	Standard	NM_031891		Approved	CDH7L3, Cdh7	uc010dps.1	Q9HBT6	OTTHUMG00000132768	ENST00000262717.4:c.1112A>G	18.37:g.59195294A>G	ENSP00000262717:p.Gln371Arg	181.0	0.0	0		185.0	113.0	0.610811	NM_031891	Q495S3	Missense_Mutation	SNP	ENST00000262717.4	37	CCDS11977.1	16	0.007326007326007326	12	0.024390243902439025	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	11.09	1.535027	0.27475	0.019973	2.33E-4	ENSG00000101542	ENST00000536675;ENST00000538374;ENST00000262717	T;T;T	0.51325	0.71;0.71;0.71	5.88	5.88	0.94601	Cadherin (4);Cadherin-like (1);	0.452719	0.25270	N	0.031885	T	0.12475	0.0303	N	0.04805	-0.155	0.27597	N	0.94909	B	0.02656	0.0	B	0.06405	0.002	T	0.04400	-1.0954	10	0.33940	T	0.23	.	6.32	0.21213	0.8101:0.0:0.1899:0.0	rs35923922	371	Q9HBT6	CAD20_HUMAN	R	371	ENSP00000444767:Q371R;ENSP00000442226:Q371R;ENSP00000262717:Q371R	ENSP00000262717:Q371R	Q	+	2	0	CDH20	57346274	1.000000	0.71417	1.000000	0.80357	0.747000	0.42532	3.994000	0.56994	2.252000	0.74401	0.529000	0.55759	CAG	A|0.992;G|0.008	0.008	strong		0.498	CDH20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256141.2	NM_031891	
OR8B4	283162	hgsc.bcm.edu	37	11	124294213	124294213	+	Missense_Mutation	SNP	C	C	A	rs61736181	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124294213C>A	ENST00000356130.3	-	1	576	c.555G>T	c.(553-555)caG>caT	p.Q185H		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	185						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|large_intestine(7)|lung(15)|ovary(1)|skin(6)|stomach(1)|urinary_tract(1)	32		Breast(109;0.0115)|Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		TGCAGGAGAGCTGCAAGAGGG	0.502													C|||	41	0.0081869	0.0023	0.013	5008	,	,		22316	0.0		0.0249	False		,,,				2504	0.0041				p.Q185H		Atlas-SNP	.											.	OR8B4	60	.	0			c.G555T						PASS	.	C	HIS/GLN	23,4379	29.9+/-59.1	0,23,2178	82.0	58.0	66.0		555	3.1	1.0	11	dbSNP_129	66	220,8378	92.3+/-154.4	3,214,4082	yes	missense	OR8B4	NM_001005196.1	24	3,237,6260	AA,AC,CC		2.5587,0.5225,1.8692	possibly-damaging	185/310	124294213	243,12757	2201	4299	6500	SO:0001583	missense	283162	exon1			GGAGAGCTGCAAG	AB065831	CCDS31710.1	11q24	2012-08-09		2001-06-29	ENSG00000198657	ENSG00000198657		"""GPCR / Class A : Olfactory receptors"""	8473	protein-coding gene	gene with protein product				OR8B4P			Standard	NM_001005196		Approved		uc010sak.2	Q96RC9	OTTHUMG00000165916	ENST00000356130.3:c.555G>T	11.37:g.124294213C>A	ENSP00000348449:p.Gln185His	117.0	0.0	0		121.0	58.0	0.479339	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	28	0.01282051282051282	3	0.006097560975609756	6	0.016574585635359115	0	0.0	19	0.025065963060686015	c	14.77	2.635013	0.47049	0.005225	0.025587	ENSG00000198657	ENST00000356130	T	0.00137	8.68	4.02	3.06	0.35304	GPCR, rhodopsin-like superfamily (1);	0.495221	0.17506	N	0.171789	T	0.00109	0.0003	L	0.43757	1.38	0.32996	D	0.525657	D	0.57899	0.981	D	0.64877	0.93	T	0.68322	-0.5439	10	0.87932	D	0	.	6.7728	0.23602	0.0:0.6864:0.0:0.3136	.	185	Q96RC9	OR8B4_HUMAN	H	185	ENSP00000348449:Q185H	ENSP00000348449:Q185H	Q	-	3	2	OR8B4	123799423	0.000000	0.05858	0.994000	0.49952	0.955000	0.61496	-1.016000	0.03633	1.219000	0.43474	0.650000	0.86243	CAG	C|0.982;A|0.018	0.018	strong		0.502	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
KIF26A	26153	hgsc.bcm.edu	37	14	104640098	104640098	+	Silent	SNP	G	G	A	rs61745565	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:104640098G>A	ENST00000423312.2	+	10	1923	c.1923G>A	c.(1921-1923)gcG>gcA	p.A641A	KIF26A_ENST00000315264.7_Silent_p.A502A	NM_015656.1	NP_056471.1	Q9ULI4	KI26A_HUMAN	kinesin family member 26A	641	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|blood coagulation (GO:0007596)|enteric nervous system development (GO:0048484)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of signal transduction (GO:0009968)|regulation of cell growth by extracellular stimulus (GO:0001560)	cytosol (GO:0005829)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule binding (GO:0008017)|microtubule motor activity (GO:0003777)			autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(8)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)	21		all_cancers(154;0.109)|Melanoma(154;0.0525)|all_epithelial(191;0.0767)	Epithelial(46;0.152)	Epithelial(152;0.161)		GTGAGGCGGCGGCTGGCAGGG	0.687													G|||	83	0.0165735	0.0015	0.0288	5008	,	,		15832	0.0		0.0388	False		,,,				2504	0.0225				p.A641A		Atlas-SNP	.											.	KIF26A	84	.	0			c.G1923A						PASS	.	G		24,3842		0,24,1909	17.0	24.0	22.0		1923	-2.2	0.0	14	dbSNP_129	22	289,7937		9,271,3833	no	coding-synonymous	KIF26A	NM_015656.1		9,295,5742	AA,AG,GG		3.5133,0.6208,2.5885		641/1883	104640098	313,11779	1933	4113	6046	SO:0001819	synonymous_variant	26153	exon10			GGCGGCGGCTGGC	AB033062	CCDS45171.1	14q32.33	2009-03-19			ENSG00000066735	ENSG00000066735		"""Kinesins"""	20226	protein-coding gene	gene with protein product		613231				10574462, 11416179	Standard	NM_015656		Approved	KIAA1236, DKFZP434N178	uc001yos.4	Q9ULI4	OTTHUMG00000154986	ENST00000423312.2:c.1923G>A	14.37:g.104640098G>A		31.0	0.0	0		56.0	31.0	0.553571	NM_015656	Q8TAZ7|Q96GK3|Q9UFL3	Silent	SNP	ENST00000423312.2	37	CCDS45171.1																																																																																			G|0.981;A|0.019	0.019	strong		0.687	KIF26A-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414356.1		
MYOG	4656	hgsc.bcm.edu	37	1	203054651	203054651	+	Missense_Mutation	SNP	G	G	A	rs61745017	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:203054651G>A	ENST00000241651.4	-	1	513	c.439C>T	c.(439-441)Cgc>Tgc	p.R147C		NM_002479.5	NP_002470.2	P15173	MYOG_HUMAN	myogenin (myogenic factor 4)	147					cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to growth factor stimulus (GO:0071363)|cellular response to lithium ion (GO:0071285)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|muscle cell differentiation (GO:0042692)|muscle cell fate commitment (GO:0042693)|negative regulation of cell proliferation (GO:0008285)|ossification (GO:0001503)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of muscle atrophy (GO:0014737)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|positive regulation of myotube differentiation (GO:0010831)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of myoblast fusion (GO:1901739)|regulation of satellite cell proliferation (GO:0014842)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to electrical stimulus involved in regulation of muscle adaptation (GO:0014878)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|skeletal muscle fiber development (GO:0048741)|skeletal muscle tissue development (GO:0007519)|striated muscle atrophy (GO:0014891)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|E-box binding (GO:0070888)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(6)|skin(2)|urinary_tract(1)	12						CCCCGGTAGCGGAGGTCACGC	0.701													G|||	60	0.0119808	0.003	0.0202	5008	,	,		15296	0.0		0.0378	False		,,,				2504	0.0041				p.R147C		Atlas-SNP	.											.	MYOG	28	.	0			c.C439T						PASS	.	G	CYS/ARG	32,4374	35.2+/-66.4	0,32,2171	23.0	26.0	25.0		439	4.4	1.0	1	dbSNP_129	25	268,8332	99.9+/-161.4	5,258,4037	yes	missense	MYOG	NM_002479.4	180	5,290,6208	AA,AG,GG		3.1163,0.7263,2.3066	probably-damaging	147/225	203054651	300,12706	2203	4300	6503	SO:0001583	missense	4656	exon1			GGTAGCGGAGGTC	BC053899	CCDS1433.1	1q31-q41	2013-05-21			ENSG00000122180	ENSG00000122180		"""Basic helix-loop-helix proteins"""	7612	protein-coding gene	gene with protein product		159980		MYF4		10329008	Standard	NM_002479		Approved	bHLHc3	uc001gzd.4	P15173	OTTHUMG00000042127	ENST00000241651.4:c.439C>T	1.37:g.203054651G>A	ENSP00000241651:p.Arg147Cys	109.0	0.0	0		138.0	82.0	0.594203	NM_002479	Q53XW6	Missense_Mutation	SNP	ENST00000241651.4	37	CCDS1433.1	42	0.019230769230769232	1	0.0020325203252032522	10	0.027624309392265192	0	0.0	31	0.040897097625329816	G	18.45	3.626906	0.66901	0.007263	0.031163	ENSG00000122180	ENST00000241651	D	0.98585	-5.01	5.32	4.36	0.52297	Helix-loop-helix DNA-binding (1);	0.215520	0.47852	D	0.000208	D	0.87688	0.6240	L	0.46157	1.445	0.45567	D	0.998512	D	0.58620	0.983	B	0.38296	0.27	D	0.89363	0.3669	10	0.62326	D	0.03	-7.4351	15.9767	0.80071	0.0:0.1461:0.8539:0.0	.	147	P15173	MYOG_HUMAN	C	147	ENSP00000241651:R147C	ENSP00000241651:R147C	R	-	1	0	MYOG	201321274	1.000000	0.71417	0.999000	0.59377	0.978000	0.69477	5.946000	0.70234	2.486000	0.83907	0.563000	0.77884	CGC	G|0.979;A|0.021	0.021	strong		0.701	MYOG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000100279.1	NM_002479	
CHL1	10752	hgsc.bcm.edu	37	3	407785	407785	+	Missense_Mutation	SNP	A	A	G	rs143907501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:407785A>G	ENST00000256509.2	+	15	2380	c.1738A>G	c.(1738-1740)Aca>Gca	p.T580A	CHL1-AS1_ENST00000417612.1_RNA|CHL1_ENST00000397491.2_Missense_Mutation_p.T564A|CHL1-AS1_ENST00000608098.1_RNA	NM_001253387.1|NM_001253388.1|NM_006614.3	NP_001240316.1|NP_001240317.1|NP_006605.2	Q96FC9	DDX11_HUMAN	cell adhesion molecule L1-like	0					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			NS(1)|central_nervous_system(5)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(25)|lung(31)|ovary(1)|prostate(4)|skin(10)|stomach(1)	93		all_cancers(2;1.14e-06)|all_epithelial(2;0.00367)|all_lung(1;0.061)|Lung NSC(2;0.201)		Epithelial(13;5.36e-06)|all cancers(10;1.4e-05)|OV - Ovarian serous cystadenocarcinoma(96;0.00323)|COAD - Colon adenocarcinoma(1;0.00925)|Colorectal(20;0.0198)		AATTAATGGCACAGAAGATGG	0.363																																					p.T580A		Atlas-SNP	.											.	CHL1	242	.	0			c.A1738G						PASS	.	A	ALA/THR	0,4406		0,0,2203	115.0	111.0	112.0		1738	4.9	0.8	3	dbSNP_134	112	3,8597	3.0+/-9.4	0,3,4297	no	missense	CHL1	NM_006614.2	58	0,3,6500	GG,GA,AA		0.0349,0.0,0.0231	benign	580/1225	407785	3,13003	2203	4300	6503	SO:0001583	missense	10752	exon13			AATGGCACAGAAG	AF002246	CCDS2556.1, CCDS58812.1, CCDS74887.1	3p26	2013-05-01	2013-05-01		ENSG00000134121	ENSG00000134121		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	1939	protein-coding gene	gene with protein product	"""neural cell adhesion molecule"", ""close homolog of L1"""	607416	"""cell adhesion molecule with homology to L1CAM (close homologue of L1)"", ""cell adhesion molecule with homology to L1CAM (close homolog of L1)"""			9799093	Standard	NM_006614		Approved	CALL, L1CAM2, FLJ44930, MGC132578	uc003bot.3	O00533	OTTHUMG00000090601	ENST00000256509.2:c.1738A>G	3.37:g.407785A>G	ENSP00000256509:p.Thr580Ala	65.0	0.0	0		93.0	60.0	0.645161	NM_001253388	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000256509.2	37	CCDS2556.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.535747	0.45176	0.0	3.49E-4	ENSG00000134121	ENST00000256509;ENST00000397491	T;T	0.13778	2.56;2.56	4.94	4.94	0.65067	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.056117	0.64402	D	0.000001	T	0.19208	0.0461	L	0.55103	1.725	0.37538	D	0.918193	B;B;B	0.26363	0.003;0.004;0.147	B;B;B	0.35727	0.026;0.016;0.209	T	0.08534	-1.0717	10	0.59425	D	0.04	.	13.1152	0.59295	1.0:0.0:0.0:0.0	.	564;564;580	B3KX75;O00533;O00533-2	.;CHL1_HUMAN;.	A	580;564	ENSP00000256509:T580A;ENSP00000380628:T564A	ENSP00000256509:T580A	T	+	1	0	CHL1	382785	1.000000	0.71417	0.824000	0.32777	0.973000	0.67179	4.982000	0.63825	1.980000	0.57719	0.460000	0.39030	ACA	A|1.000;G|0.000	0.000	strong		0.363	CHL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207155.2	NM_006614	
TTN	7273	hgsc.bcm.edu	37	2	179611875	179611875	+	Intron	SNP	A	A	G	rs61233923	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611875A>G	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.Y5084Y			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)			GGGGTGTGGAATATCTCTCTA	0.547													a|||	199	0.0397364	0.1407	0.013	5008	,	,		14705	0.0		0.003	False		,,,				2504	0.001				p.Y5084Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T15252C						PASS	.	G	,,,,	406,4000	178.7+/-207.4	27,352,1824	62.0	73.0	69.0		,,15252,,	-7.1	0.0	2	dbSNP_129	69	6,8592	1.2+/-3.3	0,6,4293	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	27,358,6117	GG,GA,AA		0.0698,9.2147,3.1683	,,,,	,,5084/5605,,	179611875	412,12592	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TGTGGAATATCTC	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.10361-5227T>C	2.37:g.179611875A>G		133.0	0.0	0		162.0	20.0	0.123457	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																																																																																				A|0.963;G|0.037	0.037	strong		0.547	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
GABRA3	2556	hgsc.bcm.edu	37	X	151358333	151358333	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:151358333T>C	ENST00000370314.4	-	9	1250	c.1012A>G	c.(1012-1014)Atg>Gtg	p.M338V	GABRA3_ENST00000535043.1_Missense_Mutation_p.M338V|GABRA3_ENST00000497894.1_5'UTR	NM_000808.3	NP_000799.1	P34903	GBRA3_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 3	338					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(16)|ovary(1)|prostate(2)|skin(6)	37	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)|Zolpidem(DB00425)|Zopiclone(DB01198)	AACCAGTCCATGGCCGTCGCA	0.478																																					p.M338V	NSCLC(142;2578 2613 10251 16743)	Atlas-SNP	.											.	GABRA3	97	.	0			c.A1012G						PASS	.						86.0	81.0	83.0					X																	151358333		2203	4300	6503	SO:0001583	missense	2556	exon9			AGTCCATGGCCGT		CCDS14706.1	Xq28	2012-06-22			ENSG00000011677	ENSG00000011677		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4077	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 3"""	305660					Standard	NM_000808		Approved		uc010ntk.1	P34903	OTTHUMG00000024183	ENST00000370314.4:c.1012A>G	X.37:g.151358333T>C	ENSP00000359337:p.Met338Val	33.0	0.0	0		45.0	13.0	0.288889	NM_000808	Q8TAF9	Missense_Mutation	SNP	ENST00000370314.4	37	CCDS14706.1	.	.	.	.	.	.	.	.	.	.	T	21.0	4.089013	0.76756	.	.	ENSG00000011677	ENST00000370314;ENST00000370311;ENST00000535043	D;D;D	0.85955	-2.05;-2.05;-2.05	5.56	5.56	0.83823	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	T	0.76737	0.4029	N	0.19112	0.55	0.58432	D	0.999993	B	0.18166	0.026	B	0.22880	0.042	T	0.73972	-0.3814	10	0.87932	D	0	.	12.5432	0.56184	0.0:0.0:0.0:1.0	.	338	P34903	GBRA3_HUMAN	V	338	ENSP00000359337:M338V;ENSP00000359334:M338V;ENSP00000443527:M338V	ENSP00000359334:M338V	M	-	1	0	GABRA3	151108989	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.989000	0.88205	1.868000	0.54150	0.483000	0.47432	ATG	.	.	none		0.478	GABRA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060921.1	NM_000808	
MAP3K4	4216	hgsc.bcm.edu	37	6	161507618	161507618	+	Silent	SNP	C	C	T	rs145569434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:161507618C>T	ENST00000392142.4	+	9	2623	c.2475C>T	c.(2473-2475)gaC>gaT	p.D825D	MAP3K4_ENST00000348824.7_Silent_p.D825D|MAP3K4_ENST00000366920.2_Silent_p.D825D|MAP3K4_ENST00000366919.2_Silent_p.D825D	NM_005922.2	NP_005913	Q9Y6R4	M3K4_HUMAN	mitogen-activated protein kinase kinase kinase 4	825					activation of MAPKK activity (GO:0000186)|chorionic trophoblast cell differentiation (GO:0060718)|intracellular signal transduction (GO:0035556)|male germ-line sex determination (GO:0019100)|MAPK cascade (GO:0000165)|placenta development (GO:0001890)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of p38MAPK cascade (GO:1900745)|regulation of gene expression (GO:0010468)|response to UV-C (GO:0010225)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			breast(6)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|lung(28)|ovary(3)|skin(2)|stomach(1)	77		Breast(66;0.000776)|Ovarian(120;0.0367)|Prostate(117;0.0771)		OV - Ovarian serous cystadenocarcinoma(65;1.85e-18)|BRCA - Breast invasive adenocarcinoma(81;3.04e-05)		GATCCTAGGACCTGGAAATAG	0.353													C|||	32	0.00638978	0.0008	0.0346	5008	,	,		19983	0.0		0.006	False		,,,				2504	0.001				p.D825D		Atlas-SNP	.											.	MAP3K4	364	.	0			c.C2475T						PASS	.	C	,	15,4391	22.3+/-47.3	0,15,2188	71.0	69.0	70.0		2475,2475	4.4	1.0	6	dbSNP_134	70	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous,coding-synonymous	MAP3K4	NM_005922.2,NM_006724.2	,	0,80,6423	TT,TC,CC		0.7558,0.3404,0.6151	,	825/1609,825/1559	161507618	80,12926	2203	4300	6503	SO:0001819	synonymous_variant	4216	exon9			CTAGGACCTGGAA	AF002715	CCDS34565.1, CCDS34566.1, CCDS75544.1	6q26	2012-10-02			ENSG00000085511	ENSG00000085511		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6856	protein-coding gene	gene with protein product		602425		MEKK4		9305639	Standard	XM_005266988		Approved	MTK1, MAPKKK4, KIAA0213	uc003qtn.3	Q9Y6R4	OTTHUMG00000015968	ENST00000392142.4:c.2475C>T	6.37:g.161507618C>T		78.0	0.0	0		91.0	45.0	0.494505	NM_006724	A6H8W0|B7ZLD3|B9EG75|Q5VTT8|Q5VTT9|Q92612|Q9H408	Silent	SNP	ENST00000392142.4	37	CCDS34565.1																																																																																			C|0.994;T|0.006	0.006	strong		0.353	MAP3K4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042988.3		
CDHR2	54825	hgsc.bcm.edu	37	5	176005481	176005481	+	Missense_Mutation	SNP	G	G	A	rs61743422	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:176005481G>A	ENST00000510636.1	+	16	1964	c.1690G>A	c.(1690-1692)Ggg>Agg	p.G564R	CDHR2_ENST00000506348.1_Missense_Mutation_p.G564R|CDHR2_ENST00000261944.5_Missense_Mutation_p.G564R	NM_001171976.1	NP_001165447.1	Q9BYE9	CDHR2_HUMAN	cadherin-related family member 2	564	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|liver(1)|lung(23)|ovary(3)|prostate(5)|skin(4)|urinary_tract(1)	56						CACAGACGGCGGGAACCTGTC	0.617													G|||	53	0.0105831	0.0038	0.0043	5008	,	,		19440	0.0		0.0189	False		,,,				2504	0.0266				p.G564R		Atlas-SNP	.											.	CDHR2	152	.	0			c.G1690A						PASS	.	G	ARG/GLY,ARG/GLY	21,4385	29.0+/-57.7	0,21,2182	80.0	61.0	67.0		1690,1690	5.3	0.1	5	dbSNP_129	67	150,8450	72.9+/-135.5	2,146,4152	yes	missense,missense	CDHR2	NM_001171976.1,NM_017675.4	125,125	2,167,6334	AA,AG,GG		1.7442,0.4766,1.3148	probably-damaging,probably-damaging	564/1311,564/1311	176005481	171,12835	2203	4300	6503	SO:0001583	missense	54825	exon16			GACGGCGGGAACC	AB047004	CCDS34297.1	5q35.2	2011-07-01	2010-01-25	2010-01-25		ENSG00000074276		"""Cadherins / Cadherin-related"""	18231	protein-coding gene	gene with protein product	"""protocadherin LKC"""		"""protocadherin 24"""	PCDH24		11082270, 12117771	Standard	NM_001171976		Approved	PC-LKC, FLJ20124, FLJ20383, PCLKC	uc003mem.2	Q9BYE9		ENST00000510636.1:c.1690G>A	5.37:g.176005481G>A	ENSP00000424565:p.Gly564Arg	75.0	0.0	0		65.0	38.0	0.584615	NM_017675	A1L3U4|A6NC80|Q9NXP8	Missense_Mutation	SNP	ENST00000510636.1	37	CCDS34297.1	15	0.006868131868131868	1	0.0020325203252032522	0	0.0	0	0.0	14	0.018469656992084433	G	15.92	2.975766	0.53720	0.004766	0.017442	ENSG00000074276	ENST00000510636;ENST00000261944;ENST00000506348	T;T;T	0.68181	-0.31;-0.31;-0.31	5.33	5.33	0.75918	Cadherin (5);Cadherin-like (1);	.	.	.	.	T	0.70474	0.3228	M	0.79693	2.465	0.48452	D	0.999658	D	0.89917	1.0	D	0.70935	0.971	T	0.79969	-0.1579	9	0.72032	D	0.01	-27.052	14.6072	0.68489	0.0:0.1456:0.8544:0.0	rs61743422	564	Q9BYE9	CDHR2_HUMAN	R	564	ENSP00000424565:G564R;ENSP00000261944:G564R;ENSP00000421078:G564R	ENSP00000261944:G564R	G	+	1	0	CDHR2	175938087	1.000000	0.71417	0.098000	0.21074	0.041000	0.13682	5.345000	0.65987	2.504000	0.84457	0.542000	0.68232	GGG	G|0.987;A|0.013	0.013	strong		0.617	CDHR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372201.1	NM_017675	
ACO1	48	hgsc.bcm.edu	37	9	32433803	32433803	+	Silent	SNP	C	C	A	rs61752944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32433803C>A	ENST00000309951.6	+	16	2067	c.1929C>A	c.(1927-1929)atC>atA	p.I643I	ACO1_ENST00000379923.1_Silent_p.I643I|ACO1_ENST00000541043.1_Silent_p.I544I	NM_002197.2	NP_002188.1	P21399	ACOC_HUMAN	aconitase 1, soluble	643					cellular iron ion homeostasis (GO:0006879)|citrate metabolic process (GO:0006101)|intestinal absorption (GO:0050892)|post-embryonic development (GO:0009791)|regulation of translation (GO:0006417)|response to iron(II) ion (GO:0010040)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrion (GO:0005739)	4 iron, 4 sulfur cluster binding (GO:0051539)|aconitate hydratase activity (GO:0003994)|iron-responsive element binding (GO:0030350)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|endometrium(7)|kidney(5)|large_intestine(6)|lung(6)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	30			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;3.94e-06)		CTACGTATATCAAATCACCAC	0.328													C|||	2	0.000399361	0.0	0.0	5008	,	,		17515	0.0		0.002	False		,,,				2504	0.0				p.I643I		Atlas-SNP	.											.	ACO1	149	.	0			c.C1929A						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	107.0	107.0	107.0		1929	1.2	0.8	9	dbSNP_129	107	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous	ACO1	NM_002197.2		0,17,6486	AA,AC,CC		0.1744,0.0454,0.1307		643/890	32433803	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	48	exon16			GTATATCAAATCA	M58510	CCDS6525.1	9p21.1	2013-05-21			ENSG00000122729	ENSG00000122729	4.2.1.3		117	protein-coding gene	gene with protein product	"""aconitate hydratase, cytoplasmic"""	100880		IREB1		2172968, 2771641	Standard	NM_002197		Approved	IRP1, IREBP	uc003zqw.4	P21399	OTTHUMG00000019740	ENST00000309951.6:c.1929C>A	9.37:g.32433803C>A		68.0	0.0	0		61.0	26.0	0.42623	NM_002197	D3DRK7|Q14652|Q5VZA7	Silent	SNP	ENST00000309951.6	37	CCDS6525.1																																																																																			C|0.999;A|0.001	0.001	strong		0.328	ACO1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051998.3	NM_002197	
A4GALT	53947	hgsc.bcm.edu	37	22	43089833	43089833	+	Missense_Mutation	SNP	A	A	G	rs148881382		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:43089833A>G	ENST00000401850.1	-	2	614	c.125T>C	c.(124-126)gTt>gCt	p.V42A	A4GALT_ENST00000465765.2_5'Flank|A4GALT_ENST00000249005.2_Missense_Mutation_p.V42A|A4GALT_ENST00000381278.3_Missense_Mutation_p.V42A			Q9NPC4	A4GAT_HUMAN	alpha 1,4-galactosyltransferase	42					globoside biosynthetic process (GO:0001576)|glycosphingolipid biosynthetic process (GO:0006688)|plasma membrane organization (GO:0007009)|protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)	galactosyltransferase activity (GO:0008378)|lactosylceramide 4-alpha-galactosyltransferase activity (GO:0050512)|toxic substance binding (GO:0015643)			NS(1)|central_nervous_system(2)|large_intestine(6)|skin(1)|urinary_tract(1)	11						CTCTCCCACAACGTGCCAGTA	0.622																																					p.V42A		Atlas-SNP	.											.	A4GALT	35	.	0			c.T125C						PASS	.	A	ALA/VAL	0,4404		0,0,2202	28.0	20.0	23.0		125	2.3	0.0	22	dbSNP_134	23	4,8592		0,4,4294	yes	missense	A4GALT	NM_017436.4	64	0,4,6496	GG,GA,AA		0.0465,0.0,0.0308	benign	42/354	43089833	4,12996	2202	4298	6500	SO:0001583	missense	53947	exon3			CCCACAACGTGCC		CCDS14041.1	22q13.2	2014-07-18	2008-07-31		ENSG00000128274	ENSG00000128274	2.4.1.228		18149	protein-coding gene	gene with protein product	"""Gb3 synthase"", ""CD77 synthase"", ""globotriaosylceramide synthase"", ""lactosylceramide 4-alpha-galactosyltransferase"""	607922	"""alpha 1,4-galactosyltransferase (globotriaosylceramide synthase, P blood group)"""			10854428	Standard	XM_005261643		Approved	A14GALT, Gb3S, P(k)	uc003bdb.3	Q9NPC4	OTTHUMG00000150744	ENST00000401850.1:c.125T>C	22.37:g.43089833A>G	ENSP00000384794:p.Val42Ala	71.0	0.0	0		90.0	44.0	0.488889	NM_017436	B2R7C4|Q9P1X5	Missense_Mutation	SNP	ENST00000401850.1	37	CCDS14041.1	.	.	.	.	.	.	.	.	.	.	A	9.301	1.053038	0.19907	0.0	4.65E-4	ENSG00000128274	ENST00000401850;ENST00000249005;ENST00000381278;ENST00000535654	T;T;T	0.80393	-1.37;-1.37;-1.37	4.49	2.33	0.28932	.	0.613294	0.12950	U	0.425919	T	0.60932	0.2307	N	0.08118	0	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.47611	-0.9104	10	0.29301	T	0.29	-9.9823	8.3249	0.32151	0.8269:0.0:0.1731:0.0	.	42	Q9NPC4	A4GAT_HUMAN	A	42	ENSP00000384794:V42A;ENSP00000249005:V42A;ENSP00000370678:V42A	ENSP00000249005:V42A	V	-	2	0	A4GALT	41419777	0.020000	0.18652	0.000000	0.03702	0.056000	0.15407	2.025000	0.41059	0.324000	0.23333	-0.464000	0.05259	GTT	A|1.000;G|0.000	0.000	weak		0.622	A4GALT-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319917.1	NM_017436	
CCDC7	79741	hgsc.bcm.edu	37	10	32780886	32780886	+	Missense_Mutation	SNP	T	T	C	rs145255525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:32780886T>C	ENST00000362006.5	+	10	1376	c.833T>C	c.(832-834)aTg>aCg	p.M278T	CCDC7_ENST00000535327.1_Intron|CCDC7_ENST00000489718.1_3'UTR|CCDC7_ENST00000537047.1_3'UTR|CCDC7_ENST00000539197.1_Intron|CCDC7_ENST00000277657.6_Missense_Mutation_p.M278T|CCDC7_ENST00000545067.1_Intron	NM_145023.4	NP_659460.3	Q96M83	CCDC7_HUMAN	coiled-coil domain containing 7	278										NS(1)|breast(2)|cervix(1)|endometrium(1)|large_intestine(3)|lung(4)|prostate(2)	14		Breast(68;0.000207)|Prostate(175;0.0107)				TTTAATGCCATGTTGAAAGTA	0.249																																					p.M278T		Atlas-SNP	.											.	CCDC7	47	.	0			c.T833C						PASS	.	T	THR/MET,THR/MET	0,4406		0,0,2203	76.0	85.0	82.0		833,833	4.1	0.5	10	dbSNP_134	82	4,8586	3.7+/-12.6	0,4,4291	yes	missense,missense	CCDC7	NM_001026383.1,NM_145023.4	81,81	0,4,6494	CC,CT,TT		0.0466,0.0,0.0308	possibly-damaging,possibly-damaging	278/487,278/487	32780886	4,12992	2203	4295	6498	SO:0001583	missense	221016	exon10			ATGCCATGTTGAA	BC022020	CCDS7173.1	10p11.23	2013-12-13			ENSG00000216937	ENSG00000216937			26533	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 68"""	C10orf68		12477932	Standard	NM_024688		Approved	FLJ32762, FLJ13031	uc001iwk.3	Q96M83	OTTHUMG00000150517	ENST00000362006.5:c.833T>C	10.37:g.32780886T>C	ENSP00000355078:p.Met278Thr	86.0	0.0	0		68.0	36.0	0.529412	NM_145023	Q5VW55|Q8IVQ0|Q8NEQ0	Missense_Mutation	SNP	ENST00000362006.5	37	CCDS7173.1	.	.	.	.	.	.	.	.	.	.	T	13.47	2.248137	0.39697	0.0	4.66E-4	ENSG00000216937	ENST00000277657;ENST00000362006	T;T	0.38077	1.16;1.16	4.13	4.13	0.48395	.	.	.	.	.	T	0.40322	0.1112	L	0.36672	1.1	0.80722	D	1	D	0.54964	0.969	P	0.55087	0.768	T	0.28202	-1.0051	9	0.72032	D	0.01	-22.3335	9.8398	0.40991	0.0:0.0:0.0:1.0	.	278	Q96M83	CCDC7_HUMAN	T	278	ENSP00000277657:M278T;ENSP00000355078:M278T	ENSP00000277657:M278T	M	+	2	0	CCDC7	32820892	0.994000	0.37717	0.468000	0.27192	0.520000	0.34377	2.364000	0.44187	2.098000	0.63641	0.459000	0.35465	ATG	T|1.000;C|0.000	0.000	strong		0.249	CCDC7-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047490.1	NM_145023	
CPSF1	29894	hgsc.bcm.edu	37	8	145634452	145634452	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:145634452C>T	ENST00000349769.3	-	2	185	c.91G>A	c.(91-93)Gta>Ata	p.V31I	GS1-393G12.14_ENST00000607491.1_RNA	NM_013291.2	NP_037423.2	Q10570	CPSF1_HUMAN	cleavage and polyadenylation specific factor 1, 160kDa	31					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA cleavage (GO:0006379)|mRNA export from nucleus (GO:0006406)|mRNA polyadenylation (GO:0006378)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleoplasm (GO:0005654)	mRNA 3'-UTR binding (GO:0003730)			NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38	all_cancers(97;6.64e-12)|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;2.88e-41)|Epithelial(56;1.67e-40)|all cancers(56;1.2e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0323)|Colorectal(110;0.055)			CCGGCCACTACCAGGTTGCGC	0.652																																					p.V31I	NSCLC(133;1088 1848 27708 34777 35269)	Atlas-SNP	.											.	CPSF1	92	.	0			c.G91A						PASS	.						132.0	126.0	128.0					8																	145634452		2203	4300	6503	SO:0001583	missense	29894	exon2			CCACTACCAGGTT	U37012	CCDS34966.1	8q24	2014-05-06	2002-08-29		ENSG00000071894	ENSG00000071894			2324	protein-coding gene	gene with protein product		606027	"""cleavage and polyadenylation specific factor 1, 160kD subunit"""			7651824, 7590244	Standard	NM_013291		Approved		uc003zcj.3	Q10570	OTTHUMG00000174612	ENST00000349769.3:c.91G>A	8.37:g.145634452C>T	ENSP00000339353:p.Val31Ile	92.0	0.0	0		107.0	51.0	0.476636	NM_013291	Q96AF0	Missense_Mutation	SNP	ENST00000349769.3	37	CCDS34966.1	.	.	.	.	.	.	.	.	.	.	C	37	6.015090	0.97205	.	.	ENSG00000071894	ENST00000349769;ENST00000531042	T	0.55760	0.5	5.18	5.18	0.71444	.	0.000000	0.64402	D	0.000003	T	0.60856	0.2301	L	0.57536	1.79	0.80722	D	1	P;P	0.47545	0.675;0.897	B;P	0.51945	0.254;0.685	T	0.57894	-0.7732	10	0.31617	T	0.26	-0.1634	16.1609	0.81704	0.0:1.0:0.0:0.0	.	31;31	B4DEF4;Q10570	.;CPSF1_HUMAN	I	31	ENSP00000339353:V31I	ENSP00000339353:V31I	V	-	1	0	CPSF1	145605260	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.070000	0.76763	2.415000	0.81967	0.561000	0.74099	GTA	.	.	none		0.652	CPSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382422.2	NM_013291	
TTC39A	22996	hgsc.bcm.edu	37	1	51754619	51754619	+	Missense_Mutation	SNP	T	T	C	rs138509677	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:51754619T>C	ENST00000447632.2	-	17	1658	c.1610A>G	c.(1609-1611)aAg>aGg	p.K537R	TTC39A_ENST00000530004.1_Missense_Mutation_p.K145R|TTC39A_ENST00000413473.2_Missense_Mutation_p.K505R|TTC39A_ENST00000534098.1_5'UTR|TTC39A_ENST00000451380.1_Missense_Mutation_p.K501R|TTC39A_ENST00000262675.7_Missense_Mutation_p.K474R|TTC39A_ENST00000371750.5_Missense_Mutation_p.K502R			Q5SRH9	TT39A_HUMAN	tetratricopeptide repeat domain 39A	537								p.0?(2)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(2)|prostate(2)|skin(3)|urinary_tract(1)	17						ATATTTAATCTTCTTTTCACT	0.488													T|||	4	0.000798722	0.0	0.0029	5008	,	,		21512	0.0		0.001	False		,,,				2504	0.001				p.K505R		Atlas-SNP	.											.	TTC39A	40	.	2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	c.A1514G						PASS	.	T	ARG/LYS,ARG/LYS	2,3792		0,2,1895	44.0	45.0	45.0		1505,1514	4.6	1.0	1	dbSNP_134	45	26,8194		0,26,4084	yes	missense,missense	TTC39A	NM_001080494.2,NM_001144832.1	26,26	0,28,5979	CC,CT,TT		0.3163,0.0527,0.2331	benign,benign	502/579,505/582	51754619	28,11986	1897	4110	6007	SO:0001583	missense	22996	exon17			TTAATCTTCTTTT	AB007921	CCDS44143.1, CCDS44144.1, CCDS72789.1, CCDS72790.1	1p32.3	2013-01-11	2008-06-23	2008-06-23	ENSG00000085831	ENSG00000085831		"""Tetratricopeptide (TTC) repeat domain containing"""	18657	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 34"""	C1orf34		9455484, 9461476	Standard	XM_005270643		Approved	KIAA0452, DEME-6	uc010onf.2	Q5SRH9	OTTHUMG00000008193	ENST00000447632.2:c.1610A>G	1.37:g.51754619T>C	ENSP00000393952:p.Lys537Arg	101.0	0.0	0		130.0	70.0	0.538462	NM_001144832	B7Z782|E7EQY9|G3XAF8|O43417|O75040|Q5SRH5|Q5SRH6|Q5SRH7|Q5SRH8|Q5SRI0|Q5SRI1|Q5SRI2|Q5T7S1|Q6PIU8|Q9BT24	Missense_Mutation	SNP	ENST00000447632.2	37		2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	10.05	1.242909	0.22796	5.27E-4	0.003163	ENSG00000085831	ENST00000530004;ENST00000447632;ENST00000413473;ENST00000262675;ENST00000451380;ENST00000371750	T;T;T;T;T;T	0.63580	-0.05;0.73;0.75;0.76;0.75;0.75	5.75	4.57	0.56435	Tetratricopeptide-like helical (1);	0.146555	0.64402	N	0.000009	T	0.43144	0.1234	N	0.24115	0.695	0.33034	D	0.530583	B;B;B;B;B	0.09022	0.0;0.002;0.002;0.001;0.002	B;B;B;B;B	0.12837	0.003;0.003;0.008;0.006;0.007	T	0.46034	-0.9220	10	0.16420	T	0.52	-26.6932	8.059	0.30623	0.0:0.1678:0.0:0.8322	.	505;501;474;537;502	Q5SRH9-4;E7EQY9;D3DQ30;Q5SRH9;G3XAF8	.;.;.;TT39A_HUMAN;.	R	145;537;505;474;501;502	ENSP00000431228:K145R;ENSP00000393952:K537R;ENSP00000406144:K505R;ENSP00000262675:K474R;ENSP00000397207:K501R;ENSP00000360815:K502R	ENSP00000262675:K474R	K	-	2	0	TTC39A	51527207	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.926000	0.56491	0.938000	0.37419	0.533000	0.62120	AAG	T|0.999;C|0.001	0.001	strong		0.488	TTC39A-004	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000022434.2		
SEC16B	89866	hgsc.bcm.edu	37	1	177933344	177933344	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:177933344A>G	ENST00000308284.6	-	5	693	c.604T>C	c.(604-606)Ttt>Ctt	p.F202L	SEC16B_ENST00000464631.2_Missense_Mutation_p.F202L|RP4-798P15.3_ENST00000354921.3_RNA	NM_033127.2	NP_149118.2	Q96JE7	SC16B_HUMAN	SEC16 homolog B (S. cerevisiae)	202	Required for endoplasmic reticulum localization.				COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|peroxisome fission (GO:0016559)|peroxisome organization (GO:0007031)|positive regulation of gene expression (GO:0010628)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endoplasmic reticulum (GO:0070972)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|Golgi membrane (GO:0000139)|intracellular membrane-bounded organelle (GO:0043231)				central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(7)|lung(14)|ovary(3)|skin(1)|stomach(1)	35						CTCCCTGGAAACAGCTCCCCC	0.557																																					p.F202L		Atlas-SNP	.											.	SEC16B	92	.	0			c.T604C						PASS	.						50.0	53.0	52.0					1																	177933344		1948	4130	6078	SO:0001583	missense	89866	exon5			CTGGAAACAGCTC	AK090411	CCDS44281.1	1q25.2	2012-10-08	2007-06-20	2007-06-20	ENSG00000120341	ENSG00000120341			30301	protein-coding gene	gene with protein product	"""regucalcin gene promotor region related protein"""	612855	"""leucine zipper transcription regulator 2"""	LZTR2		11572484, 11605020	Standard	NM_033127		Approved	RGPR, PGPR-p117	uc001gli.1	Q96JE7	OTTHUMG00000167206	ENST00000308284.6:c.604T>C	1.37:g.177933344A>G	ENSP00000308339:p.Phe202Leu	61.0	0.0	0		91.0	43.0	0.472527	NM_033127	A3EYF1|Q5HYF6|Q8N7D6|Q96GX6	Missense_Mutation	SNP	ENST00000308284.6	37	CCDS44281.1	.	.	.	.	.	.	.	.	.	.	A	0.430	-0.903732	0.02453	.	.	ENSG00000120341	ENST00000308284;ENST00000464631	T;T	0.39229	2.65;1.09	4.91	-4.56	0.03431	.	1.235800	0.05332	N	0.528496	T	0.20455	0.0492	N	0.15975	0.35	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.21008	-1.0258	10	0.11485	T	0.65	2.0E-4	6.3453	0.21345	0.4249:0.0:0.4488:0.1264	.	202;202;202	E9PK14;B1AM08;Q96JE7	.;.;SC16B_HUMAN	L	202	ENSP00000308339:F202L;ENSP00000431727:F202L	ENSP00000308339:F202L	F	-	1	0	AL359075.1	176199967	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.207000	0.09384	-0.739000	0.04809	-0.290000	0.09829	TTT	.	.	none		0.557	SEC16B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084773.16	NM_033127	
MBIP	51562	hgsc.bcm.edu	37	14	36784062	36784062	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:36784062C>G	ENST00000416007.4	-	3	396	c.309G>C	c.(307-309)gaG>gaC	p.E103D	MBIP_ENST00000318473.7_Missense_Mutation_p.E103D|MBIP_ENST00000359527.7_Missense_Mutation_p.E103D|MBIP_ENST00000603913.1_5'Flank	NM_001144891.1|NM_016586.2	NP_001138363.1|NP_057670.2	Q9NS73	MBIP1_HUMAN	MAP3K12 binding inhibitory protein 1	103					chromatin organization (GO:0006325)|histone H3 acetylation (GO:0043966)|inactivation of MAPK activity involved in osmosensory signaling pathway (GO:0000173)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	identical protein binding (GO:0042802)|protein kinase inhibitor activity (GO:0004860)			breast(2)|large_intestine(1)|lung(5)	8	all_cancers(3;1.55e-52)|all_epithelial(1;2.69e-62)|Breast(36;0.0505)|Hepatocellular(127;0.158)|Esophageal squamous(585;0.164)		Lung(8;1.28e-07)|LUAD - Lung adenocarcinoma(9;3e-07)|Epithelial(34;0.0303)|all cancers(34;0.0781)	GBM - Glioblastoma multiforme(112;0.0191)		TTCTTCCTATCTCTTCAACAG	0.378																																					p.E103D		Atlas-SNP	.											.	MBIP	25	.	0			c.G309C						PASS	.						131.0	120.0	124.0					14																	36784062		2201	4300	6501	SO:0001583	missense	51562	exon3			TCCTATCTCTTCA	BC016821	CCDS9658.1, CCDS45096.1	14q13.2	2005-01-10			ENSG00000151332	ENSG00000151332			20427	protein-coding gene	gene with protein product		609431				10801814	Standard	NM_016586		Approved		uc001wtm.2	Q9NS73	OTTHUMG00000140222	ENST00000416007.4:c.309G>C	14.37:g.36784062C>G	ENSP00000399718:p.Glu103Asp	119.0	0.0	0		148.0	57.0	0.385135	NM_016586	Q86TZ2|Q96AS5|Q9BS93|Q9NZE1	Missense_Mutation	SNP	ENST00000416007.4	37	CCDS9658.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	6.648|6.648	0.488059|0.488059	0.12641|0.12641	.|.	.|.	ENSG00000151332|ENSG00000151332	ENST00000553977|ENST00000416007;ENST00000318473;ENST00000359527;ENST00000396329;ENST00000553298;ENST00000553549;ENST00000556427	.|T;T;T	.|0.46063	.|0.88;0.88;0.88	6.17|6.17	0.564|0.564	0.17302|0.17302	.|.	.|0.715788	.|0.14682	.|N	.|0.304691	T|T	0.24275|0.24275	0.0588|0.0588	L|L	0.36672|0.36672	1.1|1.1	0.25366|0.25366	N|N	0.988744|0.988744	.|B;B;B	.|0.06786	.|0.001;0.001;0.001	.|B;B;B	.|0.04013	.|0.001;0.001;0.001	T|T	0.15752|0.15752	-1.0426|-1.0426	5|10	.|0.21014	.|T	.|0.42	-2.0398|-2.0398	1.586|1.586	0.02644|0.02644	0.2059:0.402:0.2295:0.1626|0.2059:0.402:0.2295:0.1626	.|.	.|103;103;103	.|Q9NS73-5;Q9NS73-3;Q9NS73	.|.;.;MBIP1_HUMAN	H|D	100|103;103;103;110;63;82;61	.|ENSP00000399718:E103D;ENSP00000324444:E103D;ENSP00000352517:E103D	.|ENSP00000324444:E103D	D|E	-|-	1|3	0|2	MBIP|MBIP	35853813|35853813	0.597000|0.597000	0.26874|0.26874	0.995000|0.995000	0.50966|0.50966	0.821000|0.821000	0.46438|0.46438	0.313000|0.313000	0.19415|0.19415	0.089000|0.089000	0.17243|0.17243	-0.211000|-0.211000	0.12701|0.12701	GAT|GAG	.	.	none		0.378	MBIP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276685.2	NM_016586	
ELF3	1999	hgsc.bcm.edu	37	1	201981774	201981774	+	Missense_Mutation	SNP	G	G	A	rs55729978	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:201981774G>A	ENST00000359651.3	+	4	3677	c.485G>A	c.(484-486)gGc>gAc	p.G162D	ELF3_ENST00000367284.5_Missense_Mutation_p.G162D|RP11-510N19.5_ENST00000504773.1_RNA|RP11-465N4.4_ENST00000419190.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.G162D					E74-like factor 3 (ets domain transcription factor, epithelial-specific )											breast(2)|endometrium(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	20						CCAGACCAGGGCAGCCCCTTT	0.642													G|||	364	0.0726837	0.2421	0.0159	5008	,	,		14680	0.0		0.0229	False		,,,				2504	0.0102				p.G162D		Atlas-SNP	.											ELF3_ENST00000359651,NS,carcinoma,0,2	ELF3	92	2	0			c.G485A						PASS	.	G	ASP/GLY,ASP/GLY	690,3716		51,588,1564	28.0	34.0	32.0		485,485	3.3	1.0	1	dbSNP_129	32	147,8451		1,145,4153	yes	missense,missense	ELF3	NM_001114309.1,NM_004433.4	94,94	52,733,5717	AA,AG,GG		1.7097,15.6605,6.4365	benign,benign	162/372,162/372	201981774	837,12167	2203	4299	6502	SO:0001583	missense	1999	exon5			ACCAGGGCAGCCC	AF016295	CCDS1419.1	1q32.2	2008-02-05			ENSG00000163435	ENSG00000163435			3318	protein-coding gene	gene with protein product		602191		ESX		9395241, 9129154	Standard	NM_001114309		Approved	EPR-1, ESE-1, ERT	uc001gxh.4	P78545	OTTHUMG00000035867	ENST00000359651.3:c.485G>A	1.37:g.201981774G>A	ENSP00000352673:p.Gly162Asp	65.0	0.0	0		66.0	41.0	0.621212	NM_001114309		Missense_Mutation	SNP	ENST00000359651.3	37	CCDS1419.1	157	0.07188644688644688	129	0.2621951219512195	9	0.024861878453038673	0	0.0	19	0.025065963060686015	G	10.76	1.441663	0.25900	0.156605	0.017097	ENSG00000163435	ENST00000359651;ENST00000367284;ENST00000367283;ENST00000310044;ENST00000446188	T;T;T;T	0.56103	2.47;2.47;2.47;0.48	5.2	3.29	0.37713	.	0.821186	0.11026	N	0.607832	T	0.00012	0.0000	L	0.37561	1.115	0.27380	P	0.9554544	B	0.10296	0.003	B	0.09377	0.004	T	0.09796	-1.0658	9	0.37606	T	0.19	.	7.8653	0.29533	0.0862:0.164:0.7499:0.0	rs55729978	162	P78545	ELF3_HUMAN	D	162;162;162;162;160	ENSP00000352673:G162D;ENSP00000356253:G162D;ENSP00000356252:G162D;ENSP00000405162:G160D	ENSP00000311348:G162D	G	+	2	0	ELF3	200248397	0.174000	0.23070	0.988000	0.46212	0.681000	0.39784	0.316000	0.19469	1.168000	0.42723	0.655000	0.94253	GGC	G|0.938;A|0.062	0.062	strong		0.642	ELF3-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087360.1	NM_004433	
DLEC1	9940	hgsc.bcm.edu	37	3	38136476	38136476	+	Missense_Mutation	SNP	G	G	A	rs34290809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38136476G>A	ENST00000308059.6	+	13	2047	c.2026G>A	c.(2026-2028)Gag>Aag	p.E676K	DLEC1_ENST00000346219.3_Missense_Mutation_p.E676K|DLEC1_ENST00000452631.2_Missense_Mutation_p.E676K					deleted in lung and esophageal cancer 1											NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(14)|ovary(3)|pancreas(3)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	51				KIRC - Kidney renal clear cell carcinoma(284;0.0664)|Kidney(284;0.0827)		CCCCGACAAGGAGACTGCCTT	0.552													G|||	4	0.000798722	0.0	0.0	5008	,	,		23233	0.0		0.004	False		,,,				2504	0.0				p.E676K		Atlas-SNP	.											.	DLEC1	278	.	0			c.G2026A						PASS	.	G	LYS/GLU,LYS/GLU	1,4115		0,1,2057	84.0	91.0	89.0		2026,2026	5.4	0.0	3	dbSNP_126	89	21,8383		0,21,4181	yes	missense,missense	DLEC1	NM_007335.2,NM_007337.2	56,56	0,22,6238	AA,AG,GG		0.2499,0.0243,0.1757	possibly-damaging,possibly-damaging	676/1756,676/1779	38136476	22,12498	2058	4202	6260	SO:0001583	missense	9940	exon13			GACAAGGAGACTG	AB020522	CCDS2672.2	3p21.3	2014-07-31			ENSG00000008226	ENSG00000008226			2899	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 81"""	604050				10213508	Standard	XM_005265630		Approved	DLC1, CFAP81	uc003chp.1	Q9Y238	OTTHUMG00000131085	ENST00000308059.6:c.2026G>A	3.37:g.38136476G>A	ENSP00000308597:p.Glu676Lys	112.0	0.0	0		142.0	55.0	0.387324	NM_007337		Missense_Mutation	SNP	ENST00000308059.6	37	CCDS2672.2	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	11.20	1.569663	0.28003	2.43E-4	0.002499	ENSG00000008226	ENST00000308059;ENST00000346219;ENST00000452631	T;T;T	0.05513	3.45;3.43;3.67	5.39	5.39	0.77823	.	0.244689	0.40908	D	0.000992	T	0.13841	0.0335	M	0.67953	2.075	0.09310	N	1	P;D;P	0.53745	0.804;0.962;0.804	P;P;P	0.52481	0.485;0.7;0.485	T	0.13495	-1.0507	10	0.54805	T	0.06	-14.4509	8.3585	0.32344	0.1685:0.0:0.8315:0.0	rs34290809	676;676;676	F8W6T4;Q9Y238-3;Q9Y238	.;.;DLEC1_HUMAN	K	676	ENSP00000308597:E676K;ENSP00000315914:E676K;ENSP00000410427:E676K	ENSP00000308597:E676K	E	+	1	0	DLEC1	38111480	0.996000	0.38824	0.037000	0.18230	0.085000	0.17905	2.689000	0.46993	2.506000	0.84524	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.552	DLEC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253745.3	NM_007337	
ZSCAN22	342945	hgsc.bcm.edu	37	19	58850357	58850357	+	Missense_Mutation	SNP	G	G	A	rs138944686	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58850357G>A	ENST00000329665.4	+	3	1288	c.1141G>A	c.(1141-1143)Gag>Aag	p.E381K		NM_181846.2	NP_862829.1	P10073	ZSC22_HUMAN	zinc finger and SCAN domain containing 22	381					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)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|pancreas(1)|prostate(2)	16		all_cancers(17;3.11e-12)|all_epithelial(17;9.43e-09)|Colorectal(82;0.000256)|Lung NSC(17;0.000607)|all_lung(17;0.0024)|all_neural(62;0.0412)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0289)		GCGGCCCTACGAGTGTGACGC	0.607													G|||	69	0.013778	0.025	0.0202	5008	,	,		19277	0.0		0.0209	False		,,,				2504	0.001				p.E381K		Atlas-SNP	.											.	ZSCAN22	47	.	0			c.G1141A						PASS	.	G	LYS/GLU	69,4337	63.5+/-100.7	1,67,2135	68.0	64.0	65.0		1141	0.3	0.2	19	dbSNP_134	65	87,8513	51.1+/-111.2	1,85,4214	no	missense	ZSCAN22	NM_181846.2	56	2,152,6349	AA,AG,GG		1.0116,1.566,1.1994	possibly-damaging	381/492	58850357	156,12850	2203	4300	6503	SO:0001583	missense	342945	exon3			CCCTACGAGTGTG	M20675	CCDS12975.1	19q13.43	2013-01-08	2006-09-20	2006-09-20				"""-"", ""Zinc fingers, C2H2-type"""	4929	protein-coding gene	gene with protein product	"""oncogene HKR2"""	165260	"""zinc finger protein 50"", ""GLI-Kruppel family member HKR2"""	ZNF50, HKR2		2850480, 1505991	Standard	NM_181846		Approved		uc002qsc.2	P10073		ENST00000329665.4:c.1141G>A	19.37:g.58850357G>A	ENSP00000332433:p.Glu381Lys	28.0	0.0	0		47.0	20.0	0.425532	NM_181846	Q15922|Q7Z3L8	Missense_Mutation	SNP	ENST00000329665.4	37	CCDS12975.1	39	0.017857142857142856	14	0.028455284552845527	8	0.022099447513812154	0	0.0	17	0.022427440633245383	G	8.214	0.801043	0.16397	0.01566	0.010116	ENSG00000182318	ENST00000329665	T	0.06608	3.28	3.72	0.353	0.16058	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.00580	0.0019	N	0.01284	-0.91	0.09310	N	1	B	0.27117	0.168	B	0.15052	0.012	T	0.44375	-0.9332	9	0.27082	T	0.32	.	0.7237	0.00945	0.2251:0.1908:0.3878:0.1963	.	381	P10073	ZSC22_HUMAN	K	381	ENSP00000332433:E381K	ENSP00000332433:E381K	E	+	1	0	ZSCAN22	63542169	0.000000	0.05858	0.163000	0.22734	0.372000	0.29890	-2.584000	0.00904	0.344000	0.23847	-0.300000	0.09419	GAG	G|0.986;A|0.014	0.014	strong		0.607	ZSCAN22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466765.1	NM_181846	
MET	4233	hgsc.bcm.edu	37	7	116436022	116436022	+	Silent	SNP	G	G	A	rs2023748	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:116436022G>A	ENST00000318493.6	+	21	4258	c.4071G>A	c.(4069-4071)gcG>gcA	p.A1357A	MET_ENST00000397752.3_Silent_p.A1339A|MET_ENST00000539704.1_Silent_p.A209A			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					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)	p.A1357A(1)		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)			GGATATCAGCGATCTTCTCTA	0.443			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				G|||	1772	0.353834	0.034	0.4697	5008	,	,		21305	0.4673		0.4433	False		,,,				2504	0.4949				p.A1357A		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4071A						PASS	.	G	,	405,3531		16,373,1579	140.0	130.0	133.0		4017,4071	-11.4	0.0	7	dbSNP_94	133	3536,4748		773,1990,1379	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	789,2363,2958	AA,AG,GG		42.6847,10.2896,32.2504	,	1339/1391,1357/1409	116436022	3941,8279	1968	4142	6110	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ATCAGCGATCTTC	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.4071G>A	7.37:g.116436022G>A		179.0	0.0	0		174.0	174.0	1	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.618;A|0.382	0.382	strong		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
PAPLN	89932	hgsc.bcm.edu	37	14	73726151	73726151	+	Missense_Mutation	SNP	A	A	G	rs17182244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:73726151A>G	ENST00000554301.1	+	15	2046	c.1883A>G	c.(1882-1884)cAc>cGc	p.H628R	PAPLN_ENST00000555445.1_Missense_Mutation_p.H628R|PAPLN_ENST00000427855.1_Missense_Mutation_p.H628R|PAPLN_ENST00000381166.3_Missense_Mutation_p.H628R|PAPLN_ENST00000340738.5_Missense_Mutation_p.H601R			O95428	PPN_HUMAN	papilin, proteoglycan-like sulfated glycoprotein	628			H -> R (in dbSNP:rs17182244).			basement membrane (GO:0005604)	metalloendopeptidase activity (GO:0004222)|serine-type endopeptidase inhibitor activity (GO:0004867)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|lung(11)|ovary(3)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(3)	42				BRCA - Breast invasive adenocarcinoma(234;0.00394)|OV - Ovarian serous cystadenocarcinoma(108;0.0468)		TCAGGGCCCCACGACTGCAGA	0.711													A|||	55	0.0109824	0.0015	0.0115	5008	,	,		15850	0.0		0.0408	False		,,,				2504	0.0041				p.H601R		Atlas-SNP	.											.	PAPLN	180	.	0			c.A1802G						PASS	.	A	ARG/HIS	33,4373		0,33,2170	20.0	24.0	23.0		1802	-5.5	0.0	14	dbSNP_123	23	320,8268		4,312,3978	yes	missense	PAPLN	NM_173462.3	29	4,345,6148	GG,GA,AA		3.7261,0.749,2.7166	benign	601/1252	73726151	353,12641	2203	4294	6497	SO:0001583	missense	89932	exon15			GGCCCCACGACTG	BC042057	CCDS32114.1	14q24.2	2013-01-11				ENSG00000100767		"""Immunoglobulin superfamily / I-set domain containing"""	19262	protein-coding gene	gene with protein product						11076767, 19734141	Standard	NM_173462		Approved	MGC50452	uc001xnw.4	O95428		ENST00000554301.1:c.1883A>G	14.37:g.73726151A>G	ENSP00000451803:p.His628Arg	135.0	0.0	0		124.0	60.0	0.483871	NM_173462	B4DES8|B4DGE6|Q659F2|Q6UXJ4|Q6ZNM1|Q6ZUJ0|Q7Z681|Q8IVU0	Missense_Mutation	SNP	ENST00000554301.1	37		41	0.018772893772893772	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	33	0.04353562005277045	A	4.734	0.136524	0.09032	0.00749	0.037261	ENSG00000100767	ENST00000340738;ENST00000427855;ENST00000381166;ENST00000554301;ENST00000555445	T;T;T;T;T	0.61627	0.09;0.09;0.39;0.09;0.23	4.23	-5.49	0.02584	.	.	.	.	.	T	0.03871	0.0109	N	0.00436	-1.5	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.001	T	0.31081	-0.9956	9	0.11182	T	0.66	.	8.8397	0.35135	0.6381:0.1121:0.2498:0.0	rs17182244;rs17182244	628;628;601	O95428-5;O95428;O95428-6	.;PPN_HUMAN;.	R	601;628;628;628;628	ENSP00000345395:H601R;ENSP00000403403:H628R;ENSP00000370558:H628R;ENSP00000451803:H628R;ENSP00000451729:H628R	ENSP00000216658:H628R	H	+	2	0	PAPLN	72795904	0.000000	0.05858	0.000000	0.03702	0.737000	0.42083	-1.238000	0.02919	-0.688000	0.05155	0.379000	0.24179	CAC	A|0.976;G|0.024	0.024	strong		0.711	PAPLN-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000413182.1	NM_173462	
KMT2D	8085	hgsc.bcm.edu	37	12	49426818	49426818	+	Silent	SNP	G	G	A	rs376471354		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49426818G>A	ENST00000301067.7	-	39	11669	c.11670C>T	c.(11668-11670)agC>agT	p.S3890S	KMT2D_ENST00000549743.1_5'Flank	NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	3890	Gln-rich.				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)										TGGGCTGAGCGCTCAGTTTGG	0.572													G|||	1	0.000199681	0.0	0.0014	5008	,	,		19150	0.0		0.0	False		,,,				2504	0.0				p.S3890S		Atlas-SNP	.											.	MLL2	1173	.	0			c.C11670T						PASS	.	G		0,3580		0,0,1790	22.0	27.0	25.0		11670	-9.3	0.0	12		25	3,6691		0,3,3344	no	coding-synonymous	MLL2	NM_003482.3		0,3,5134	AA,AG,GG		0.0448,0.0,0.0292		3890/5538	49426818	3,10271	1790	3347	5137	SO:0001819	synonymous_variant	8085	exon39			CTGAGCGCTCAGT	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.11670C>T	12.37:g.49426818G>A		58.0	0.0	0		64.0	29.0	0.453125	NM_003482	O14687	Silent	SNP	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	weak		0.572	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
SP100	6672	hgsc.bcm.edu	37	2	231327184	231327184	+	Silent	SNP	C	C	T	rs35985492	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:231327184C>T	ENST00000264052.5	+	10	1363	c.1008C>T	c.(1006-1008)gaC>gaT	p.D336D	SP100_ENST00000409824.1_Silent_p.D311D|SP100_ENST00000341950.4_Silent_p.D336D|SP100_ENST00000409341.1_Silent_p.D336D|SP100_ENST00000409897.1_Silent_p.D301D|SP100_ENST00000340126.4_Silent_p.D336D|SP100_ENST00000427101.2_Silent_p.D311D|SP100_ENST00000409112.1_Silent_p.D336D	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	336	Sufficient to mediate interaction with ETS1.				cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of cellular component movement (GO:0051271)|negative regulation of DNA binding (GO:0043392)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of protein export from nucleus (GO:0046826)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of viral transcription (GO:0032897)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of angiogenesis (GO:0045765)|regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902041)|regulation of Fas signaling pathway (GO:1902044)|response to cytokine (GO:0034097)|response to interferon-gamma (GO:0034341)|response to retinoic acid (GO:0032526)|response to type I interferon (GO:0034340)|retinoic acid receptor signaling pathway (GO:0048384)|telomere maintenance (GO:0000723)|transcription, DNA-templated (GO:0006351)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nuclear periphery (GO:0034399)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|protein domain specific binding (GO:0019904)|protein homodimerization activity (GO:0042803)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(12)|ovary(4)|upper_aerodigestive_tract(1)	25		Renal(207;0.0112)|all_lung(227;0.0335)|all_hematologic(139;0.0749)|Lung NSC(271;0.142)|Acute lymphoblastic leukemia(138;0.167)		Epithelial(121;1.13e-12)|all cancers(144;2.71e-10)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)		GATCCACTGACGTTGATGAGC	0.493													C|||	18	0.00359425	0.0	0.0086	5008	,	,		19642	0.0		0.0089	False		,,,				2504	0.0031				p.D336D		Atlas-SNP	.											.	SP100	167	.	0			c.C1008T						PASS	.	C	,,,,,	11,4395	17.9+/-39.9	0,11,2192	126.0	110.0	115.0		1008,1008,1008,933,903,1008	-4.5	0.0	2	dbSNP_126	115	121,8479	62.8+/-124.8	1,119,4180	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SP100	NM_001080391.1,NM_001206701.1,NM_001206702.1,NM_001206703.1,NM_001206704.1,NM_003113.3	,,,,,	1,130,6372	TT,TC,CC		1.407,0.2497,1.0149	,,,,,	336/886,336/689,336/481,311/453,301/446,336/880	231327184	132,12874	2203	4300	6503	SO:0001819	synonymous_variant	6672	exon10			CACTGACGTTGAT	AF056322	CCDS2477.1, CCDS42832.1, CCDS56170.1, CCDS56171.1, CCDS56172.1, CCDS56173.1	2q37.1	2013-01-28	2005-11-30		ENSG00000067066	ENSG00000067066		"""Zinc fingers, PHD-type"""	11206	protein-coding gene	gene with protein product		604585	"""nuclear antigen Sp100"""			2258622, 8695863	Standard	NM_001080391		Approved		uc002vqu.1	P23497	OTTHUMG00000133203	ENST00000264052.5:c.1008C>T	2.37:g.231327184C>T		95.0	0.0	0		124.0	54.0	0.435484	NM_001206702	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Silent	SNP	ENST00000264052.5	37	CCDS2477.1	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	C	2.308	-0.358494	0.05138	0.002497	0.01407	ENSG00000067066	ENST00000413284	.	.	.	4.09	-4.5	0.03493	.	.	.	.	.	T	0.15176	0.0366	.	.	.	0.09310	N	0.999999	.	.	.	.	.	.	T	0.29458	-1.0011	4	.	.	.	.	5.3685	0.16127	0.0:0.3668:0.307:0.3261	rs35985492	.	.	.	M	12	.	.	T	+	2	0	SP100	231035428	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.439000	0.02414	-0.840000	0.04206	-2.265000	0.00278	ACG	C|0.992;T|0.008	0.008	strong		0.493	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
COPS7B	64708	hgsc.bcm.edu	37	2	232653358	232653358	+	Silent	SNP	C	C	T	rs11557625	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:232653358C>T	ENST00000350033.3	+	2	219	c.78C>T	c.(76-78)gcC>gcT	p.A26A	COPS7B_ENST00000410017.1_Silent_p.A26A|COPS7B_ENST00000409295.1_Intron|COPS7B_ENST00000373608.3_Silent_p.A26A|COPS7B_ENST00000409091.1_Intron|COPS7B_ENST00000410024.1_Silent_p.A26A	NM_001282949.1|NM_022730.1	NP_001269878.1|NP_073567.1	Q9H9Q2	CSN7B_HUMAN	COP9 signalosome subunit 7B	26					cullin deneddylation (GO:0010388)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				large_intestine(1)|liver(1)|lung(4)|ovary(1)|skin(1)	8		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Renal(207;0.025)		Epithelial(121;1.36e-12)|BRCA - Breast invasive adenocarcinoma(100;0.00136)|LUSC - Lung squamous cell carcinoma(224;0.0115)|Lung(119;0.0142)		GTGGCTCAGCCCTCACTGCTC	0.507													C|||	31	0.0061901	0.0	0.0086	5008	,	,		16814	0.0		0.0239	False		,,,				2504	0.001				p.A26A		Atlas-SNP	.											.	COPS7B	14	.	0			c.C78T						PASS	.	C		27,4379	33.5+/-64.1	0,27,2176	84.0	86.0	85.0		78	1.2	1.0	2	dbSNP_120	85	195,8405	85.8+/-148.2	2,191,4107	no	coding-synonymous	COPS7B	NM_022730.1		2,218,6283	TT,TC,CC		2.2674,0.6128,1.7069		26/265	232653358	222,12784	2203	4300	6503	SO:0001819	synonymous_variant	64708	exon2			CTCAGCCCTCACT	AK022674	CCDS2488.1, CCDS63152.1, CCDS63153.1, CCDS63154.1, CCDS74668.1	2q37.1	2013-03-14	2013-03-14		ENSG00000144524	ENSG00000144524			16760	protein-coding gene	gene with protein product			"""COP9 (constitutive photomorphogenic, Arabidopsis, homolog) subunit 7B"", ""COP9 constitutive photomorphogenic homolog subunit 7B (Arabidopsis)"""			9707402	Standard	NM_001282950		Approved	CSN7B	uc002vsg.1	Q9H9Q2	OTTHUMG00000133228	ENST00000350033.3:c.78C>T	2.37:g.232653358C>T		71.0	0.0	0		98.0	47.0	0.479592	NM_022730	Q53S22|Q5BJG3|Q9H7V6	Silent	SNP	ENST00000350033.3	37	CCDS2488.1																																																																																			C|0.988;T|0.012	0.012	strong		0.507	COPS7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256964.2	NM_022730	
ZNF653	115950	hgsc.bcm.edu	37	19	11598288	11598288	+	Silent	SNP	G	G	C	rs145806085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:11598288G>C	ENST00000293771.5	-	4	1126	c.990C>G	c.(988-990)ctC>ctG	p.L330L	CTC-398G3.6_ENST00000585656.1_Intron	NM_138783.3	NP_620138.2	Q96CK0	ZN653_HUMAN	zinc finger protein 653	330					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						CCTCGGCCGTGAGAGCGTCGT	0.672													G|||	7	0.00139776	0.0	0.0	5008	,	,		17152	0.0		0.007	False		,,,				2504	0.0				p.L330L	Pancreas(83;980 1446 4542 6441 43352)	Atlas-SNP	.											.	ZNF653	48	.	0			c.C990G						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	65.0	60.0	61.0		990	1.8	0.9	19	dbSNP_134	61	12,8588	9.8+/-36.6	0,12,4288	no	coding-synonymous	ZNF653	NM_138783.3		0,13,6490	CC,CG,GG		0.1395,0.0227,0.1		330/616	11598288	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	115950	exon4			GGCCGTGAGAGCG	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.990C>G	19.37:g.11598288G>C		53.0	0.0	0		43.0	23.0	0.534884	NM_138783	Q96AS7	Silent	SNP	ENST00000293771.5	37	CCDS12261.1																																																																																			G|0.998;C|0.002	0.002	strong		0.672	ZNF653-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458836.2	NM_138783	
FAM78B	149297	hgsc.bcm.edu	37	1	166039512	166039512	+	Missense_Mutation	SNP	C	C	G	rs138713518		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:166039512C>G	ENST00000338353.3	-	3	1341	c.752G>C	c.(751-753)cGg>cCg	p.R251P	FAM78B_ENST00000354422.3_Missense_Mutation_p.R251P			Q5VT40	FA78B_HUMAN	family with sequence similarity 78, member B	251										central_nervous_system(1)|endometrium(5)|large_intestine(1)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	19	all_hematologic(923;0.0813)|Acute lymphoblastic leukemia(8;0.155)					AGGTGGCCCCCGCTTGGGCCT	0.597																																					p.R251P		Atlas-SNP	.											FAM78B,NS,carcinoma,+1,1	FAM78B	51	1	0			c.G752C						PASS	.						91.0	91.0	91.0					1																	166039512		2203	4300	6503	SO:0001583	missense	149297	exon2			GGCCCCCGCTTGG	AL626787	CCDS30931.1	1q24.1	2008-02-05			ENSG00000188859	ENSG00000188859			13495	protein-coding gene	gene with protein product							Standard	NM_001017961		Approved		uc021pee.1	Q5VT40	OTTHUMG00000034705	ENST00000338353.3:c.752G>C	1.37:g.166039512C>G	ENSP00000339681:p.Arg251Pro	177.0	0.0	0		285.0	51.0	0.178947	NM_001017961	B7Z693	Missense_Mutation	SNP	ENST00000338353.3	37	CCDS30931.1	.	.	.	.	.	.	.	.	.	.	C	15.61	2.883574	0.51908	.	.	ENSG00000188859	ENST00000354422;ENST00000338353	D;D	0.94330	-3.4;-3.4	5.96	3.94	0.45596	.	0.049142	0.85682	D	0.000000	D	0.89072	0.6611	L	0.44542	1.39	0.53688	D	0.999975	D	0.53745	0.962	P	0.50049	0.629	D	0.87304	0.2307	9	0.27785	T	0.31	-16.1405	14.0529	0.64749	0.0:0.7123:0.2877:0.0	.	251	Q5VT40	FA78B_HUMAN	P	251	ENSP00000346404:R251P;ENSP00000339681:R251P	ENSP00000339681:R251P	R	-	2	0	FAM78B	164306136	1.000000	0.71417	0.990000	0.47175	0.993000	0.82548	4.646000	0.61411	1.471000	0.48121	0.650000	0.86243	CGG	C|1.000;T|0.000	.	alt		0.597	FAM78B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343108.1	NM_001017961	
CNGA2	1260	hgsc.bcm.edu	37	X	150908168	150908168	+	Missense_Mutation	SNP	G	G	T	rs144366408	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:150908168G>T	ENST00000329903.4	+	3	371	c.338G>T	c.(337-339)gGc>gTc	p.G113V		NM_005140.1	NP_005131.1	Q16280	CNGA2_HUMAN	cyclic nucleotide gated channel alpha 2	113					phototransduction, visible light (GO:0007603)|potassium ion transmembrane transport (GO:0071805)|regulation of membrane potential (GO:0042391)|sensory perception of smell (GO:0007608)	integral component of plasma membrane (GO:0005887)	cAMP binding (GO:0030552)|cGMP binding (GO:0030553)|intracellular cGMP activated cation channel activity (GO:0005223)|voltage-gated potassium channel activity (GO:0005249)			breast(4)|endometrium(4)|large_intestine(5)|lung(34)|prostate(2)	49	Acute lymphoblastic leukemia(192;6.56e-05)					GAGGGGGATGGCAAAGGCGAC	0.542													G|||	13	0.00344371	0.0015	0.0029	3775	,	,		14551	0.0		0.005	False		,,,				2504	0.0041				p.G113V		Atlas-SNP	.											.	CNGA2	136	.	0			c.G338T						PASS	.	G	VAL/GLY	2,3833		0,2,0,1630,571	128.0	96.0	107.0		338	2.8	1.0	X	dbSNP_134	107	55,6673		0,36,19,2392,1853	yes	missense	CNGA2	NM_005140.1	109	0,38,19,4022,2424	TT,TG,T,GG,G		0.8175,0.0522,0.5396	benign	113/665	150908168	57,10506	2203	4300	6503	SO:0001583	missense	1260	exon4			GGGATGGCAAAGG	S76067	CCDS14701.1	Xq27	2011-07-05			ENSG00000183862	ENSG00000183862		"""Voltage-gated ion channels / Cyclic nucleotide-regulated channels"""	2149	protein-coding gene	gene with protein product		300338		CNCA1, CNCA		7532814, 16382102	Standard	NM_005140		Approved	CNG2, OCNC1, OCNCa, OCNCALPHA, OCNCalpha, FLJ46312	uc004fey.1	Q16280	OTTHUMG00000024173	ENST00000329903.4:c.338G>T	X.37:g.150908168G>T	ENSP00000328478:p.Gly113Val	39.0	0.0	0		44.0	44.0	1	NM_005140	A0AVD0	Missense_Mutation	SNP	ENST00000329903.4	37	CCDS14701.1	7	0.004219409282700422	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	3	0.003968253968253968	G	9.795	1.178974	0.21787	5.22E-4	0.008175	ENSG00000183862	ENST00000329903	D	0.97328	-4.34	5.58	2.75	0.32379	.	0.401066	0.26948	N	0.021695	D	0.88991	0.6588	L	0.31926	0.97	0.58432	D	0.999997	B	0.15473	0.013	B	0.16289	0.015	T	0.79567	-0.1750	10	0.20519	T	0.43	.	2.2593	0.04063	0.1718:0.1496:0.5206:0.1579	.	113	Q16280	CNGA2_HUMAN	V	113	ENSP00000328478:G113V	ENSP00000328478:G113V	G	+	2	0	CNGA2	150658824	0.971000	0.33674	0.998000	0.56505	0.632000	0.37999	0.882000	0.28186	0.138000	0.18790	-0.343000	0.07986	GGC	G|0.994;T|0.006	0.006	strong		0.542	CNGA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060888.1	NM_005140	
IFNLR1	163702	hgsc.bcm.edu	37	1	24496085	24496085	+	Silent	SNP	G	G	A	rs34654982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:24496085G>A	ENST00000327535.1	-	3	201	c.189C>T	c.(187-189)ccC>ccT	p.P63P	IFNLR1_ENST00000374421.3_Silent_p.P63P|IFNLR1_ENST00000374418.3_Silent_p.P63P|IFNLR1_ENST00000327575.2_Silent_p.P63P|IFNLR1_ENST00000374419.1_5'UTR	NM_170743.3|NM_173064.2	NP_734464.1|NP_775087.1	Q8IU57	INLR1_HUMAN	interferon, lambda receptor 1	63	Fibronectin type-III. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mucosal immune response (GO:0002385)|negative regulation of cell proliferation (GO:0008285)|regulation of defense response to virus by host (GO:0050691)|response to type III interferon (GO:0034342)	integral component of membrane (GO:0016021)|interleukin-28 receptor complex (GO:0032002)											GTCTACGGGTGGGAGAGCTGG	0.552													G|||	582	0.116214	0.289	0.0432	5008	,	,		21000	0.0327		0.0417	False		,,,				2504	0.0971				p.P63P		Atlas-SNP	.											.	.	.	.	0			c.C189T						PASS	.	G	,,	1063,3343	387.5+/-326.5	126,811,1266	62.0	62.0	62.0		189,189,189	-4.2	0.0	1	dbSNP_126	62	315,8285	112.3+/-172.5	3,309,3988	no	coding-synonymous,coding-synonymous,coding-synonymous	IL28RA	NM_170743.3,NM_173064.2,NM_173065.2	,,	129,1120,5254	AA,AG,GG		3.6628,24.1262,10.5951	,,	63/521,63/492,63/245	24496085	1378,11628	2203	4300	6503	SO:0001819	synonymous_variant	163702	exon3			ACGGGTGGGAGAG	AY129153	CCDS248.1, CCDS249.1, CCDS250.1	1p36.11	2012-11-27	2012-11-26	2012-11-26	ENSG00000185436	ENSG00000185436		"""Interferons"""	18584	protein-coding gene	gene with protein product	"""interferon lambda receptor 1"""	607404	"""interleukin 28 receptor, alpha"", ""interleukin 28 receptor, alpha (interferon, lambda receptor)"""	IL28RA			Standard	NM_173064		Approved	CRF2/12, IFNLR, IL-28R1	uc001bis.3	Q8IU57	OTTHUMG00000003036	ENST00000327535.1:c.189C>T	1.37:g.24496085G>A		75.0	0.0	0		84.0	41.0	0.488095	NM_170743	Q5VTX5|Q5VTX7|Q5VTX8|Q6ZML8|Q8IV66|Q8IZI7|Q8IZI8	Silent	SNP	ENST00000327535.1	37	CCDS248.1																																																																																			G|0.897;A|0.103	0.103	strong		0.552	IFNLR1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000008402.1	NM_170743	
CCDC78	124093	hgsc.bcm.edu	37	16	775236	775236	+	Splice_Site	SNP	C	C	T	rs138669350	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:775236C>T	ENST00000293889.6	-	5	598		c.e5+1		HAGHL_ENST00000341413.4_5'Flank|HAGHL_ENST00000389703.3_5'Flank|HAGHL_ENST00000561546.1_5'Flank|HAGHL_ENST00000564537.1_5'Flank|HAGHL_ENST00000564545.1_5'Flank|HAGHL_ENST00000549114.1_5'Flank	NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78						cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)|skeletal muscle contraction (GO:0003009)	centriole (GO:0005814)|deuterosome (GO:0098536)|perinuclear region of cytoplasm (GO:0048471)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				TGCACACTCACGCCGCTCCCC	0.642													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		17690	0.0		0.003	False		,,,				2504	0.001				.		Atlas-SNP	.											.	CCDC78	26	.	0			c.492+1G>A						PASS	.	C		7,4383	11.4+/-27.6	0,7,2188	63.0	74.0	70.0			-0.3	0.0	16	dbSNP_134	70	13,8577	9.8+/-36.6	0,13,4282	yes	splice-5	CCDC78	NM_001031737.2		0,20,6470	TT,TC,CC		0.1513,0.1595,0.1541			775236	20,12960	2195	4295	6490	SO:0001630	splice_region_variant	124093	exon6			CACTCACGCCGCT	BC042110	CCDS32353.1	16p13.3	2014-07-15		2006-02-20	ENSG00000162004	ENSG00000162004			14153	protein-coding gene	gene with protein product		614666		C16orf25		24075808	Standard	NM_001031737		Approved	FLJ34512	uc002cjg.3	A2IDD5	OTTHUMG00000121176	ENST00000293889.6:c.492+1G>A	16.37:g.775236C>T		59.0	0.0	0		65.0	34.0	0.523077	NM_001031737	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Splice_Site	SNP	ENST00000293889.6	37	CCDS32353.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	4.939	0.174544	0.09391	0.001595	0.001513	ENSG00000162004	ENST00000345165;ENST00000293889	.	.	.	3.84	-0.34	0.12643	.	.	.	.	.	.	.	.	.	.	.	0.21325	N	0.999729	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.3859	0.21559	0.0:0.5601:0.0:0.4399	.	.	.	.	.	-1	.	.	.	-	.	.	CCDC78	715237	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.394000	0.07296	-0.010000	0.14271	0.561000	0.74099	.	C|0.998;T|0.002	0.002	strong		0.642	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241665.3	NM_173476	Intron
ZKSCAN5	23660	hgsc.bcm.edu	37	7	99129744	99129744	+	Missense_Mutation	SNP	G	G	C	rs150395462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99129744G>C	ENST00000394170.2	+	7	2643	c.2392G>C	c.(2392-2394)Gag>Cag	p.E798Q	ZKSCAN5_ENST00000326775.5_Missense_Mutation_p.E798Q|ZKSCAN5_ENST00000451158.1_Missense_Mutation_p.E798Q	NM_014569.3	NP_055384.1	Q9Y2L8	ZKSC5_HUMAN	zinc finger with KRAB and SCAN domains 5	798					regulation of transcription, DNA-templated (GO:0006355)|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)			breast(3)|endometrium(1)|kidney(1)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	21	all_cancers(62;2.54e-08)|all_epithelial(64;2.55e-09)|Lung NSC(181;0.0053)|all_lung(186;0.00895)|Esophageal squamous(72;0.0166)					CCATACTGGTGAGAAACCTTT	0.398													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20675	0.0		0.003	False		,,,				2504	0.0				p.E798Q		Atlas-SNP	.											.	ZKSCAN5	63	.	0			c.G2392C						PASS	.	G	GLN/GLU,GLN/GLU	5,4401	11.4+/-27.6	0,5,2198	85.0	91.0	89.0		2392,2392	5.0	1.0	7	dbSNP_134	89	61,8539	38.8+/-94.9	1,59,4240	yes	missense,missense	ZKSCAN5	NM_014569.3,NM_145102.2	29,29	1,64,6438	CC,CG,GG		0.7093,0.1135,0.5075	probably-damaging,probably-damaging	798/840,798/840	99129744	66,12940	2203	4300	6503	SO:0001583	missense	23660	exon7			ACTGGTGAGAAAC	AF170025	CCDS5667.1	7q22	2013-01-09	2007-02-20	2007-02-20	ENSG00000196652	ENSG00000196652		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	12867	protein-coding gene	gene with protein product		611272	"""zinc finger protein homologous to Zfp95 in mouse"", ""zinc finger protein 95 homolog (mouse)"""	ZFP95		10585779	Standard	NM_014569		Approved	ZNF914, ZSCAN37	uc003uqv.3	Q9Y2L8	OTTHUMG00000156749	ENST00000394170.2:c.2392G>C	7.37:g.99129744G>C	ENSP00000377725:p.Glu798Gln	54.0	0.0	0		45.0	21.0	0.466667	NM_145102	A4D280|D6W5S9	Missense_Mutation	SNP	ENST00000394170.2	37	CCDS5667.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	G	23.4	4.411517	0.83340	0.001135	0.007093	ENSG00000196652	ENST00000326775;ENST00000451158;ENST00000394170	T;T;T	0.25912	1.77;1.77;1.77	5.03	5.03	0.67393	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.116325	0.38720	N	0.001586	T	0.42177	0.1191	M	0.70595	2.14	0.50171	D	0.99985	D;D	0.76494	0.999;0.999	D;D	0.70935	0.971;0.971	T	0.45556	-0.9253	10	0.72032	D	0.01	.	16.2692	0.82607	0.0:0.0:1.0:0.0	.	798;798	Q8N718;Q9Y2L8	.;ZKSC5_HUMAN	Q	798	ENSP00000322872:E798Q;ENSP00000392104:E798Q;ENSP00000377725:E798Q	ENSP00000322872:E798Q	E	+	1	0	ZKSCAN5	98967680	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.485000	0.66850	2.782000	0.95742	0.655000	0.94253	GAG	G|0.996;C|0.004	0.004	strong		0.398	ZKSCAN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345597.1	NM_014569	
ENTPD5	957	hgsc.bcm.edu	37	14	74444009	74444009	+	Silent	SNP	G	G	A	rs143835358	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:74444009G>A	ENST00000334696.6	-	7	829	c.510C>T	c.(508-510)tcC>tcT	p.S170S	ENTPD5_ENST00000557325.1_Silent_p.S170S	NM_001249.2	NP_001240.1	O75356	ENTP5_HUMAN	ectonucleoside triphosphate diphosphohydrolase 5	170					'de novo' posttranslational protein folding (GO:0051084)|ATP metabolic process (GO:0046034)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|positive regulation of glycolytic process (GO:0045821)|protein N-linked glycosylation (GO:0006487)|regulation of phosphatidylinositol 3-kinase signaling (GO:0014066)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	guanosine-diphosphatase activity (GO:0004382)|uridine-diphosphatase activity (GO:0045134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	10				BRCA - Breast invasive adenocarcinoma(234;0.00394)		CACCTTCGTCGGATCCATCCA	0.453													G|||	5	0.000998403	0.0	0.0	5008	,	,		17509	0.0		0.005	False		,,,				2504	0.0				p.S170S		Atlas-SNP	.											.	ENTPD5	26	.	0			c.C510T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	113.0	99.0	103.0		510	2.5	1.0	14	dbSNP_134	103	17,8583	11.9+/-42.8	1,15,4284	no	coding-synonymous	ENTPD5	NM_001249.2		1,17,6485	AA,AG,GG		0.1977,0.0454,0.1461		170/429	74444009	19,12987	2203	4300	6503	SO:0001819	synonymous_variant	957	exon7			TTCGTCGGATCCA	AF039918	CCDS9825.1	14q24	2003-10-03	2003-10-03			ENSG00000187097			3367	protein-coding gene	gene with protein product		603162	"""proto-oncogene CPH"""	CD39L4, PCPH		9271669, 9676430	Standard	NM_001249		Approved	NTPDase-5	uc010tuo.2	O75356		ENST00000334696.6:c.510C>T	14.37:g.74444009G>A		25.0	0.0	0		43.0	20.0	0.465116	NM_001249	A1L4C5|Q96RX0	Silent	SNP	ENST00000334696.6	37	CCDS9825.1																																																																																			G|0.998;A|0.002	0.002	strong		0.453	ENTPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412637.1	NM_001249	
WNT16	51384	hgsc.bcm.edu	37	7	120969825	120969825	+	Silent	SNP	C	C	A	rs17143291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:120969825C>A	ENST00000222462.2	+	2	590	c.300C>A	c.(298-300)acC>acA	p.T100T	WNT16_ENST00000361301.2_Silent_p.T90T	NM_057168.1	NP_476509.1	Q9UBV4	WNT16_HUMAN	wingless-type MMTV integration site family, member 16	100					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)					CCGCCACTACCGCCCCGATGG	0.662													C|||	53	0.0105831	0.0212	0.0216	5008	,	,		13952	0.0		0.0089	False		,,,				2504	0.001				p.T100T		Atlas-SNP	.											.	WNT16	97	.	0			c.C300A						PASS	.	C	,	79,4315		0,79,2118	22.0	25.0	24.0		270,300	2.1	0.2	7	dbSNP_123	24	48,8512		0,48,4232	no	coding-synonymous,coding-synonymous	WNT16	NM_016087.2,NM_057168.1	,	0,127,6350	AA,AC,CC		0.5607,1.7979,0.9804	,	90/356,100/366	120969825	127,12827	2197	4280	6477	SO:0001819	synonymous_variant	51384	exon2			CACTACCGCCCCG	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.300C>A	7.37:g.120969825C>A		14.0	0.0	0		15.0	9.0	0.6	NM_057168	Q2M3G1|Q9Y5C0	Silent	SNP	ENST00000222462.2	37	CCDS5781.1																																																																																			C|0.988;A|0.012	0.012	strong		0.662	WNT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346843.1	NM_057168	
CATSPER1	117144	hgsc.bcm.edu	37	11	65789004	65789004	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65789004G>A	ENST00000312106.5	-	4	1791	c.1654C>T	c.(1654-1656)Cgg>Tgg	p.R552W		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	552					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)			breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						CTCAGGGCCCGCAGGCTCTTG	0.627																																					p.R552W		Atlas-SNP	.											.	CATSPER1	101	.	0			c.C1654T						PASS	.						60.0	64.0	63.0					11																	65789004		2201	4296	6497	SO:0001583	missense	117144	exon4			GGGCCCGCAGGCT	AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1654C>T	11.37:g.65789004G>A	ENSP00000309052:p.Arg552Trp	36.0	0.0	0		72.0	31.0	0.430556	NM_053054	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	G	13.91	2.378231	0.42207	.	.	ENSG00000175294	ENST00000312106	D	0.98633	-5.04	4.99	3.08	0.35506	Ion transport (1);	0.000000	0.30565	U	0.009357	D	0.99211	0.9726	H	0.95917	3.74	0.23331	N	0.997892	D	0.89917	1.0	D	0.97110	1.0	D	0.96270	0.9198	10	0.87932	D	0	-21.6854	6.1104	0.20097	0.0968:0.0:0.7178:0.1855	.	552	Q8NEC5	CTSR1_HUMAN	W	552	ENSP00000309052:R552W	ENSP00000309052:R552W	R	-	1	2	CATSPER1	65545580	1.000000	0.71417	0.893000	0.35052	0.020000	0.10135	1.757000	0.38400	0.495000	0.27882	0.561000	0.74099	CGG	.	.	none		0.627	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1	NM_053054	
RHO	6010	hgsc.bcm.edu	37	3	129247936	129247936	+	Splice_Site	SNP	C	C	T	rs79765751	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:129247936C>T	ENST00000296271.3	+	1	454	c.360C>T	c.(358-360)ggC>ggT	p.G120G		NM_000539.3	NP_000530.1	P08100	OPSD_HUMAN	rhodopsin	120	Retinal chromophore binding. {ECO:0000250}.				G-protein coupled receptor signaling pathway (GO:0007186)|phototransduction, visible light (GO:0007603)|protein phosphorylation (GO:0006468)|protein-chromophore linkage (GO:0018298)|red, far-red light phototransduction (GO:0009585)|regulation of rhodopsin mediated signaling pathway (GO:0022400)|retina development in camera-type eye (GO:0060041)|retinoid metabolic process (GO:0001523)|rhodopsin mediated signaling pathway (GO:0016056)|visual perception (GO:0007601)	cell-cell junction (GO:0005911)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|photoreceptor disc membrane (GO:0097381)|photoreceptor inner segment (GO:0001917)|photoreceptor inner segment membrane (GO:0060342)|photoreceptor outer segment (GO:0001750)|photoreceptor outer segment membrane (GO:0042622)|plasma membrane (GO:0005886)|rough endoplasmic reticulum membrane (GO:0030867)	G-protein coupled receptor activity (GO:0004930)|metal ion binding (GO:0046872)|photoreceptor activity (GO:0009881)|retinal binding (GO:0016918)			breast(1)|endometrium(1)|large_intestine(10)|lung(6)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	22		all_neural(597;0.0227)|Myeloproliferative disorder(1037;0.0255)|Prostate(884;0.183)		GBM - Glioblastoma multiforme(114;2.58e-05)|Lung(219;0.0234)	Halothane(DB01159)	CCACCCTGGGCGGTATGAGCC	0.637													C|||	7	0.00139776	0.0	0.0	5008	,	,		17167	0.001		0.006	False		,,,				2504	0.0				p.G120G	Esophageal Squamous(118;214 1623 30842 43234 46940)	Atlas-SNP	.											.	RHO	57	.	0			c.C360T						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	69.0	72.0	71.0		360	-8.9	0.8	3	dbSNP_132	71	39,8561	25.7+/-73.6	0,39,4261	yes	coding-synonymous-near-splice	RHO	NM_000539.3		0,47,6456	TT,TC,CC		0.4535,0.1816,0.3614		120/349	129247936	47,12959	2203	4300	6503	SO:0001630	splice_region_variant	6010	exon1			CCTGGGCGGTATG	AB065668	CCDS3063.1	3q21-q24	2014-01-28	2008-04-16		ENSG00000163914	ENSG00000163914		"""GPCR / Class A : Opsin receptors"""	10012	protein-coding gene	gene with protein product	"""opsin 2, rod pigment"""	180380	"""retinitis pigmentosa 4, autosomal dominant"""	RP4		2016091	Standard	NM_000539		Approved	OPN2, CSNBAD1	uc003emt.3	P08100	OTTHUMG00000159542	ENST00000296271.3:c.361+1C>T	3.37:g.129247936C>T		64.0	0.0	0		65.0	23.0	0.353846	NM_000539	Q16414|Q2M249	Silent	SNP	ENST00000296271.3	37	CCDS3063.1																																																																																			C|0.996;T|0.004	0.004	strong		0.637	RHO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356101.1	NM_000539	Silent
ANKRD35	148741	hgsc.bcm.edu	37	1	145555699	145555699	+	Missense_Mutation	SNP	G	G	A	rs141350599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:145555699G>A	ENST00000355594.4	+	2	134	c.47G>A	c.(46-48)aGa>aAa	p.R16K	ANKRD35_ENST00000544626.1_Missense_Mutation_p.R16K	NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	16										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					CAGGTGGAGAGATGGAACCGC	0.562													G|||	7	0.00139776	0.0	0.0029	5008	,	,		18080	0.0		0.005	False		,,,				2504	0.0				p.R16K	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											.	ANKRD35	96	.	0			c.G47A						PASS	.	G	LYS/ARG	1,4405	2.1+/-5.4	0,1,2202	56.0	52.0	54.0		47	0.3	1.0	1	dbSNP_134	54	42,8558	26.3+/-74.7	0,42,4258	yes	missense	ANKRD35	NM_144698.3	26	0,43,6460	AA,AG,GG		0.4884,0.0227,0.3306	benign	16/1002	145555699	43,12963	2203	4300	6503	SO:0001583	missense	148741	exon2			TGGAGAGATGGAA	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.47G>A	1.37:g.145555699G>A	ENSP00000347802:p.Arg16Lys	76.0	0.0	0		67.0	38.0	0.567164	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	10.69	1.420552	0.25639	2.27E-4	0.004884	ENSG00000198483	ENST00000355594;ENST00000544626	T;T	0.63417	-0.04;2.52	5.99	0.277	0.15668	.	0.660459	0.13934	N	0.352680	T	0.13157	0.0319	N	0.02011	-0.69	0.19775	N	0.999952	B	0.10296	0.003	B	0.10450	0.005	T	0.34800	-0.9814	10	0.30854	T	0.27	-4.0648	8.8959	0.35465	0.4511:0.0:0.5489:0.0	.	16	Q8N283	ANR35_HUMAN	K	16	ENSP00000347802:R16K;ENSP00000442671:R16K	ENSP00000347802:R16K	R	+	2	0	ANKRD35	144267056	0.998000	0.40836	0.999000	0.59377	0.978000	0.69477	0.259000	0.18405	0.126000	0.18424	0.655000	0.94253	AGA	G|0.998;A|0.002	0.002	strong		0.562	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
SPG11	80208	hgsc.bcm.edu	37	15	44890486	44890486	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:44890486G>C	ENST00000261866.7	-	23	3994	c.3978C>G	c.(3976-3978)agC>agG	p.S1326R	SPG11_ENST00000558319.1_Missense_Mutation_p.S1326R|SPG11_ENST00000427534.2_Missense_Mutation_p.S1326R|SPG11_ENST00000535302.2_Missense_Mutation_p.S1326R	NM_025137.3	NP_079413.3	Q96JI7	SPTCS_HUMAN	spastic paraplegia 11 (autosomal recessive)	1326					cell death (GO:0008219)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(24)|ovary(5)|prostate(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	72		all_cancers(109;1.29e-14)|all_epithelial(112;1.26e-12)|Lung NSC(122;1.34e-07)|all_lung(180;1.21e-06)|Melanoma(134;0.0122)		all cancers(107;2.93e-22)|GBM - Glioblastoma multiforme(94;1.55e-06)|COAD - Colon adenocarcinoma(120;0.0432)|Colorectal(105;0.0484)|Lung(196;0.104)|LUSC - Lung squamous cell carcinoma(244;0.214)		GTTGCTGAATGCTGTTCCATG	0.378																																					p.S1326R		Atlas-SNP	.											.	SPG11	207	.	0			c.C3978G						PASS	.						152.0	131.0	138.0					15																	44890486		2198	4298	6496	SO:0001583	missense	80208	exon23			CTGAATGCTGTTC		CCDS10112.1, CCDS53939.1	15q13-q15	2007-11-13			ENSG00000104133	ENSG00000104133			11226	protein-coding gene	gene with protein product	"""spatacsin"""	610844	"""KIAA1840"""	KIAA1840		10408536, 17322883	Standard	NM_001160227		Approved	FLJ21439	uc001ztx.3	Q96JI7	OTTHUMG00000131199	ENST00000261866.7:c.3978C>G	15.37:g.44890486G>C	ENSP00000261866:p.Ser1326Arg	123.0	0.0	0		152.0	68.0	0.447368	NM_025137	A8KAX9|B9EK60|F5H3N6|Q4VC11|Q58G86|Q69YG6|Q6NW01|Q8N270|Q8TBU9|Q9H734	Missense_Mutation	SNP	ENST00000261866.7	37	CCDS10112.1	.	.	.	.	.	.	.	.	.	.	G	15.07	2.725352	0.48833	.	.	ENSG00000104133	ENST00000261866;ENST00000535302;ENST00000427534	T;T;T	0.80304	-1.36;-1.36;-1.36	5.77	1.3	0.21679	.	0.489617	0.24520	N	0.037813	T	0.74550	0.3731	L	0.51422	1.61	0.80722	D	1	P;P;P	0.50443	0.773;0.935;0.773	B;P;B	0.48815	0.414;0.591;0.332	T	0.67288	-0.5708	10	0.19590	T	0.45	.	6.1682	0.20402	0.315:0.0:0.5586:0.1264	.	1326;1326;1326	C4B7M2;F5H3N6;Q96JI7	.;.;SPTCS_HUMAN	R	1326	ENSP00000261866:S1326R;ENSP00000445278:S1326R;ENSP00000396110:S1326R	ENSP00000261866:S1326R	S	-	3	2	SPG11	42677778	0.423000	0.25482	0.999000	0.59377	0.899000	0.52679	0.278000	0.18753	0.373000	0.24621	0.655000	0.94253	AGC	.	.	none		0.378	SPG11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253927.1		
SPATA31D1	389763	hgsc.bcm.edu	37	9	84608900	84608900	+	Missense_Mutation	SNP	C	C	T	rs75742550	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84608900C>T	ENST00000344803.2	+	4	3562	c.3515C>T	c.(3514-3516)aCa>aTa	p.T1172I		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1172					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TGCTCACTGACAAATGTGAAA	0.408													C|||	30	0.00599042	0.0	0.0043	5008	,	,		21271	0.005		0.0149	False		,,,				2504	0.0072				p.T1172I		Atlas-SNP	.											.	.	.	.	0			c.C3515T						PASS	.	C	ILE/THR	15,3741		0,15,1863	53.0	51.0	51.0		3515	-6.1	0.0	9	dbSNP_132	51	76,8174		1,74,4050	yes	missense	FAM75D1	NM_001001670.2	89	1,89,5913	TT,TC,CC		0.9212,0.3994,0.758	possibly-damaging	1172/1577	84608900	91,11915	1878	4125	6003	SO:0001583	missense	389763	exon4			CACTGACAAATGT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.3515C>T	9.37:g.84608900C>T	ENSP00000341988:p.Thr1172Ile	80.0	0.0	0		72.0	32.0	0.444444	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	17	0.007783882783882784	0	0.0	1	0.0027624309392265192	2	0.0034965034965034965	14	0.018469656992084433	C	0.004	-2.302874	0.00240	0.003994	0.009212	ENSG00000214929	ENST00000344803	T	0.04015	3.73	3.05	-6.11	0.02131	.	.	.	.	.	T	0.00784	0.0026	N	0.04508	-0.205	0.09310	N	1	B	0.14438	0.01	B	0.15052	0.012	T	0.43245	-0.9403	9	0.27082	T	0.32	.	0.1448	0.00087	0.2811:0.1577:0.2358:0.3254	.	1172	Q6ZQQ2	F75D1_HUMAN	I	1172	ENSP00000341988:T1172I	ENSP00000341988:T1172I	T	+	2	0	FAM75D1	83798720	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-3.244000	0.00542	-2.594000	0.00455	-1.379000	0.01178	ACA	C|0.993;T|0.007	0.007	strong		0.408	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
SH3TC2	79628	hgsc.bcm.edu	37	5	148388512	148388512	+	Missense_Mutation	SNP	C	C	T	rs139192433	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:148388512C>T	ENST00000515425.1	-	15	3481	c.3380G>A	c.(3379-3381)cGg>cAg	p.R1127Q	SH3TC2_ENST00000538184.1_Missense_Mutation_p.R674Q|SH3TC2_ENST00000512049.1_Missense_Mutation_p.R1120Q|SH3TC2_ENST00000502274.1_5'Flank	NM_024577.3	NP_078853.2	Q8TF17	S3TC2_HUMAN	SH3 domain and tetratricopeptide repeats 2	1127					cell death (GO:0008219)|peripheral nervous system myelin maintenance (GO:0032287)|regulation of ERBB signaling pathway (GO:1901184)|regulation of intracellular protein transport (GO:0033157)	cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)				breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	39			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ATTGAAAATCCGGAGCTCAGT	0.522													C|||	2	0.000399361	0.0	0.0	5008	,	,		21382	0.0		0.002	False		,,,				2504	0.0				p.R1127Q		Atlas-SNP	.											.	SH3TC2	178	.	0			c.G3380A						PASS	.	C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	134.0	133.0	133.0		3380	5.2	1.0	5	dbSNP_134	133	19,8581	14.0+/-48.4	0,19,4281	yes	missense	SH3TC2	NM_024577.3	43	0,21,6482	TT,TC,CC		0.2209,0.0454,0.1615	probably-damaging	1127/1289	148388512	21,12985	2203	4300	6503	SO:0001583	missense	79628	exon15			AAAATCCGGAGCT	AK127248	CCDS4293.1	5q32	2014-09-17			ENSG00000169247	ENSG00000169247		"""Tetratricopeptide (TTC) repeat domain containing"""	29427	protein-coding gene	gene with protein product		608206				14574644	Standard	NM_024577		Approved	KIAA1985, CMT4C	uc003lpu.3	Q8TF17	OTTHUMG00000129930	ENST00000515425.1:c.3380G>A	5.37:g.148388512C>T	ENSP00000423660:p.Arg1127Gln	93.0	0.0	0		75.0	35.0	0.466667	NM_024577	B3KWE5|Q14CC0|Q14CF5|Q9H8I5	Missense_Mutation	SNP	ENST00000515425.1	37	CCDS4293.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	33	5.223428	0.95139	4.54E-4	0.002209	ENSG00000169247	ENST00000538184;ENST00000515425;ENST00000512049	T;T;T	0.75821	-0.97;-0.97;-0.95	6.03	5.16	0.70880	Tetratricopeptide-like helical (1);	0.000000	0.64402	D	0.000002	D	0.86083	0.5848	M	0.73962	2.25	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.87578	0.998;0.998;0.998	D	0.87067	0.2157	10	0.52906	T	0.07	-21.7677	17.3176	0.87228	0.0:0.8748:0.1252:0.0	.	1120;1127;1127	Q14CC0;E9PDF1;Q8TF17	.;.;S3TC2_HUMAN	Q	674;1127;1120	ENSP00000441427:R674Q;ENSP00000423660:R1127Q;ENSP00000421860:R1120Q	ENSP00000425627:R1127Q	R	-	2	0	SH3TC2	148368705	0.978000	0.34361	0.959000	0.39883	0.995000	0.86356	7.275000	0.78548	1.530000	0.49136	0.655000	0.94253	CGG	C|0.998;T|0.002	0.002	strong		0.522	SH3TC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252186.2	NM_024577	
CNTNAP1	8506	hgsc.bcm.edu	37	17	40839829	40839829	+	Missense_Mutation	SNP	G	G	A	rs375309204		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40839829G>A	ENST00000264638.4	+	8	1353	c.1136G>A	c.(1135-1137)cGc>cAc	p.R379H	CTD-3193K9.3_ENST00000592440.1_RNA	NM_003632.2	NP_003623.1	P78357	CNTP1_HUMAN	contactin associated protein 1	379					axon cargo transport (GO:0008088)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cytoskeleton organization (GO:0007010)|neuromuscular process controlling balance (GO:0050885)|neuromuscular process controlling posture (GO:0050884)|neuron projection morphogenesis (GO:0048812)|neuronal action potential propagation (GO:0019227)|paranodal junction assembly (GO:0030913)|positive regulation of signal transduction (GO:0009967)|protein localization to paranode region of axon (GO:0002175)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|paranode region of axon (GO:0033270)|voltage-gated potassium channel complex (GO:0008076)	receptor activity (GO:0004872)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(4)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(11)|lung(15)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.143)		GGTTTCCCACGCCGTGGCCGC	0.637																																					p.R379H		Atlas-SNP	.											.	CNTNAP1	116	.	0			c.G1136A						PASS	.	G	HIS/ARG	0,4406		0,0,2203	96.0	88.0	90.0		1136	5.0	0.2	17		90	1,8599	1.2+/-3.3	0,1,4299	no	missense	CNTNAP1	NM_003632.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	379/1385	40839829	1,13005	2203	4300	6503	SO:0001583	missense	8506	exon8			TCCCACGCCGTGG	U87223	CCDS11436.1	17q21	2008-07-18				ENSG00000108797			8011	protein-coding gene	gene with protein product	"""neurexin 4"""	602346		NRXN4		9118959	Standard	NM_003632		Approved	p190, Caspr, CNTNAP	uc002iay.3	P78357		ENST00000264638.4:c.1136G>A	17.37:g.40839829G>A	ENSP00000264638:p.Arg379His	101.0	0.0	0		86.0	23.0	0.267442	NM_003632		Missense_Mutation	SNP	ENST00000264638.4	37	CCDS11436.1	.	.	.	.	.	.	.	.	.	.	G	14.77	2.634266	0.47049	0.0	1.16E-4	ENSG00000108797	ENST00000264638	T	0.79247	-1.25	5.02	5.02	0.67125	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (1);	0.187385	0.37955	N	0.001877	T	0.80773	0.4687	L	0.43152	1.355	0.44927	D	0.997946	D	0.76494	0.999	P	0.59643	0.861	T	0.80410	-0.1394	10	0.42905	T	0.14	.	13.3172	0.60413	0.0:0.0:0.8419:0.1581	.	379	P78357	CNTP1_HUMAN	H	379	ENSP00000264638:R379H	ENSP00000264638:R379H	R	+	2	0	CNTNAP1	38093355	1.000000	0.71417	0.248000	0.24265	0.483000	0.33249	7.263000	0.78421	2.302000	0.77476	0.655000	0.94253	CGC	.	.	weak		0.637	CNTNAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452342.1	NM_003632	
CRLF1	9244	hgsc.bcm.edu	37	19	18710496	18710496	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18710496G>A	ENST00000392386.3	-	2	469	c.276C>T	c.(274-276)aaC>aaT	p.N92N		NM_004750.4	NP_004741.1	O75462	CRLF1_HUMAN	cytokine receptor-like factor 1	92	Ig-like C2-type.				negative regulation of motor neuron apoptotic process (GO:2000672)|negative regulation of neuron apoptotic process (GO:0043524)|positive regulation of cell proliferation (GO:0008284)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|ureteric bud development (GO:0001657)	CRLF-CLCF1 complex (GO:0097058)|extracellular space (GO:0005615)	cytokine binding (GO:0019955)|protein heterodimerization activity (GO:0046982)|receptor activity (GO:0004872)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)	9						AGGTGGAGGCGTTGAGTACAC	0.692																																					p.N92N		Atlas-SNP	.											.	CRLF1	32	.	0			c.C276T						PASS	.						24.0	23.0	23.0					19																	18710496		2200	4298	6498	SO:0001819	synonymous_variant	9244	exon2			GGAGGCGTTGAGT	AF059293	CCDS32962.1	19p12	2013-02-11				ENSG00000006016		"""Fibronectin type III domain containing"""	2364	protein-coding gene	gene with protein product	"""cold-induced sweating syndrome"""	604237				9686600	Standard	NM_004750		Approved	CLF-1, CLF, CISS, CISS1	uc010ebt.2	O75462		ENST00000392386.3:c.276C>T	19.37:g.18710496G>A		105.0	0.0	0		135.0	69.0	0.511111	NM_004750	Q9UHH5	Silent	SNP	ENST00000392386.3	37	CCDS32962.1																																																																																			.	.	none		0.692	CRLF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465129.1		
SESTD1	91404	hgsc.bcm.edu	37	2	179986553	179986553	+	Silent	SNP	T	T	C	rs56336305	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179986553T>C	ENST00000428443.3	-	13	1702	c.1386A>G	c.(1384-1386)aaA>aaG	p.K462K		NM_178123.4	NP_835224.3	Q86VW0	SESD1_HUMAN	SEC14 and spectrin domains 1	462							phosphatidic acid binding (GO:0070300)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(2)|endometrium(4)|kidney(1)|large_intestine(9)|lung(10)|ovary(1)|skin(3)	30			OV - Ovarian serous cystadenocarcinoma(117;0.0344)|Epithelial(96;0.0531)|all cancers(119;0.147)			CCACATTTTCTTTATTTTCAA	0.383													T|||	56	0.0111821	0.0	0.0159	5008	,	,		17677	0.0		0.0278	False		,,,				2504	0.0174				p.K462K		Atlas-SNP	.											.	SESTD1	66	.	0			c.A1386G						PASS	.	T		25,4381	32.6+/-62.9	0,25,2178	110.0	105.0	107.0		1386	2.8	1.0	2	dbSNP_129	107	198,8402	86.9+/-149.2	0,198,4102	no	coding-synonymous	SESTD1	NM_178123.4		0,223,6280	CC,CT,TT		2.3023,0.5674,1.7146		462/697	179986553	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	91404	exon13			ATTTTCTTTATTT	AK096232	CCDS33338.1	2q31.3	2014-01-28			ENSG00000187231	ENSG00000187231			18379	protein-coding gene	gene with protein product						12837271	Standard	NM_178123		Approved	DKFZp434O0515, Solo	uc002uni.4	Q86VW0	OTTHUMG00000154554	ENST00000428443.3:c.1386A>G	2.37:g.179986553T>C		62.0	0.0	0		75.0	32.0	0.426667	NM_178123	Q53R38|Q53SP3|Q5GM69|Q8N6M1|Q96LQ2	Silent	SNP	ENST00000428443.3	37	CCDS33338.1																																																																																			T|0.982;C|0.018	0.018	strong		0.383	SESTD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335916.2	NM_178123	
SIRT1	23411	hgsc.bcm.edu	37	10	69644820	69644820	+	Missense_Mutation	SNP	C	C	A	rs182199697	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69644820C>A	ENST00000212015.6	+	1	394	c.341C>A	c.(340-342)cCa>cAa	p.P114Q	SIRT1_ENST00000432464.1_5'Flank	NM_012238.4	NP_036370.2	Q96EB6	SIR1_HUMAN	sirtuin 1	114	Interaction with CLOCK. {ECO:0000250|UniProtKB:Q923E4}.|Interaction with HIST1H1E.				angiogenesis (GO:0001525)|cell aging (GO:0007569)|cellular glucose homeostasis (GO:0001678)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to starvation (GO:0009267)|cellular response to tumor necrosis factor (GO:0071356)|cellular triglyceride homeostasis (GO:0035356)|cholesterol homeostasis (GO:0042632)|chromatin organization (GO:0006325)|chromatin silencing (GO:0006342)|chromatin silencing at rDNA (GO:0000183)|circadian regulation of gene expression (GO:0032922)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|DNA synthesis involved in DNA repair (GO:0000731)|establishment of chromatin silencing (GO:0006343)|fatty acid homeostasis (GO:0055089)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of chromatin silencing (GO:0006344)|methylation-dependent chromatin silencing (GO:0006346)|muscle organ development (GO:0007517)|negative regulation of androgen receptor signaling pathway (GO:0060766)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cAMP-dependent protein kinase activity (GO:2000480)|negative regulation of cell growth (GO:0030308)|negative regulation of cellular response to testosterone stimulus (GO:2000655)|negative regulation of cellular senescence (GO:2000773)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of helicase activity (GO:0051097)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of neuron death (GO:1901215)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of peptidyl-lysine acetylation (GO:2000757)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostaglandin biosynthetic process (GO:0031393)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of TOR signaling (GO:0032007)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|ovulation from ovarian follicle (GO:0001542)|peptidyl-lysine acetylation (GO:0018394)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP-dependent protein kinase activity (GO:2000481)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cellular senescence (GO:2000774)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of chromatin silencing (GO:0031937)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA repair (GO:0045739)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of macroautophagy (GO:0016239)|positive regulation of macrophage apoptotic process (GO:2000111)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein deacetylation (GO:0006476)|protein destabilization (GO:0031648)|protein ubiquitination (GO:0016567)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|regulation of bile acid biosynthetic process (GO:0070857)|regulation of cell proliferation (GO:0042127)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of glucose metabolic process (GO:0010906)|regulation of mitotic cell cycle (GO:0007346)|regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035358)|regulation of protein import into nucleus, translocation (GO:0033158)|regulation of smooth muscle cell apoptotic process (GO:0034391)|response to hydrogen peroxide (GO:0042542)|response to insulin (GO:0032868)|response to oxidative stress (GO:0006979)|rRNA processing (GO:0006364)|single strand break repair (GO:0000012)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)|triglyceride mobilization (GO:0006642)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	chromatin silencing complex (GO:0005677)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear envelope (GO:0005635)|nuclear euchromatin (GO:0005719)|nuclear heterochromatin (GO:0005720)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|rDNA heterochromatin (GO:0033553)	bHLH transcription factor binding (GO:0043425)|deacetylase activity (GO:0019213)|enzyme binding (GO:0019899)|histone binding (GO:0042393)|histone deacetylase activity (GO:0004407)|HLH domain binding (GO:0043398)|identical protein binding (GO:0042802)|keratin filament binding (GO:1990254)|metal ion binding (GO:0046872)|mitogen-activated protein kinase binding (GO:0051019)|NAD+ binding (GO:0070403)|NAD-dependent histone deacetylase activity (GO:0017136)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent protein deacetylase activity (GO:0034979)|p53 binding (GO:0002039)|protein C-terminus binding (GO:0008022)|protein deacetylase activity (GO:0033558)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(6)|lung(3)|skin(1)	14						TCTCGGGAGCCACCGCTGGCC	0.721													C|||	8	0.00159744	0.0	0.0043	5008	,	,		9467	0.0		0.005	False		,,,				2504	0.0				p.P114Q		Atlas-SNP	.											.	SIRT1	38	.	0			c.C341A						PASS	.	C	GLN/PRO	3,3319		0,3,1658	3.0	4.0	4.0		341	3.0	0.9	10		4	24,6694		0,24,3335	yes	missense	SIRT1	NM_012238.4	76	0,27,4993	AA,AC,CC		0.3572,0.0903,0.2689	benign	114/748	69644820	27,10013	1661	3359	5020	SO:0001583	missense	23411	exon1			GGGAGCCACCGCT	AF083106	CCDS7273.1, CCDS44412.1	10q21	2010-06-25	2010-06-25		ENSG00000096717	ENSG00000096717			14929	protein-coding gene	gene with protein product		604479	"""sirtuin (silent mating type information regulation 2, S. cerevisiae, homolog) 1"", ""sirtuin (silent mating type information regulation 2 homolog) 1 (S. cerevisiae)"""			10381378	Standard	NM_012238		Approved	SIR2L1	uc001jnd.3	Q96EB6	OTTHUMG00000018340	ENST00000212015.6:c.341C>A	10.37:g.69644820C>A	ENSP00000212015:p.Pro114Gln	32.0	0.0	0		43.0	27.0	0.627907	NM_012238	Q2XNF6|Q5JVQ0|Q9GZR9|Q9Y6F0	Missense_Mutation	SNP	ENST00000212015.6	37	CCDS7273.1	23	0.010531135531135532	11	0.022357723577235773	4	0.011049723756906077	0	0.0	8	0.010554089709762533	c	9.153	1.016794	0.19355	9.03E-4	0.003572	ENSG00000096717	ENST00000212015	T	0.36157	1.27	3.91	3.0	0.34707	.	1.246700	0.05789	N	0.609970	T	0.18718	0.0449	L	0.44542	1.39	0.80722	D	1	P	0.36733	0.567	B	0.37387	0.248	T	0.03000	-1.1084	10	0.35671	T	0.21	0.1106	7.5885	0.28006	0.0:0.8736:0.0:0.1264	.	114	Q96EB6	SIRT1_HUMAN	Q	114	ENSP00000212015:P114Q	ENSP00000212015:P114Q	P	+	2	0	SIRT1	69314826	0.994000	0.37717	0.940000	0.37924	0.069000	0.16628	0.498000	0.22530	0.746000	0.32786	0.556000	0.70494	CCA	C|0.989;A|0.011	0.011	strong		0.721	SIRT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048296.1		
ELL	8178	hgsc.bcm.edu	37	19	18583657	18583657	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:18583657T>C	ENST00000262809.4	-	2	242	c.171A>G	c.(169-171)caA>caG	p.Q57Q	ELL_ENST00000596124.3_5'UTR	NM_006532.3	NP_006523.1	P55199	ELL_HUMAN	elongation factor RNA polymerase II	57					gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of viral transcription (GO:0050434)|snRNA transcription from RNA polymerase II promoter (GO:0042795)|snRNA transcription from RNA polymerase III promoter (GO:0042796)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Cajal body (GO:0015030)|histone locus body (GO:0035363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|transcription elongation factor complex (GO:0008023)|transcriptionally active chromatin (GO:0035327)	phosphatase binding (GO:0019902)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(5)|prostate(1)	19				GBM - Glioblastoma multiforme(1328;7.81e-07)		CTTGGCTTCCTTGAAATCGGA	0.398			T	MLL	AL																																p.Q57Q		Atlas-SNP	.		Dom	yes		19	19p13.1	8178	ELL gene (11-19 lysine-rich leukemia gene)		L	.	ELL	52	.	0			c.A171G						PASS	.						108.0	99.0	102.0					19																	18583657		2203	4300	6503	SO:0001819	synonymous_variant	8178	exon2			GCTTCCTTGAAAT	U16282	CCDS12380.1	19p13.1	2012-04-17	2005-05-23			ENSG00000105656		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	23114	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 68"""	600284	"""chromosome 19 open reading frame 17"""	C19orf17		7991593, 8596958	Standard	NM_006532		Approved	Men, ELL1, PPP1R68	uc002njh.3	P55199		ENST00000262809.4:c.171A>G	19.37:g.18583657T>C		22.0	0.0	0		28.0	12.0	0.428571	NM_006532		Silent	SNP	ENST00000262809.4	37	CCDS12380.1																																																																																			.	.	none		0.398	ELL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466362.1	NM_006532	
ARHGEF11	9826	hgsc.bcm.edu	37	1	156941607	156941607	+	Intron	SNP	C	C	T	rs537664586		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:156941607C>T	ENST00000361409.2	-	8	1325				ARHGEF11_ENST00000368194.3_Splice_Site_p.R195H	NM_014784.3	NP_055599.1	O15085	ARHGB_HUMAN	Rho guanine nucleotide exchange factor (GEF) 11						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)					CTCACAGATACGCTAGGGATG	0.567													C|||	1	0.000199681	0.0	0.0	5008	,	,		17391	0.0		0.0	False		,,,				2504	0.001				p.R195H		Atlas-SNP	.											.	ARHGEF11	168	.	0			c.G584A						PASS	.						46.0	48.0	47.0					1																	156941607		2203	4300	6503	SO:0001627	intron_variant	9826	exon8			CAGATACGCTAGG	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.583-1772G>A	1.37:g.156941607C>T		42.0	0.0	0		64.0	33.0	0.515625	NM_198236	D3DVD0|Q5VY40|Q6PFW2	Missense_Mutation	SNP	ENST00000361409.2	37	CCDS1162.1	.	.	.	.	.	.	.	.	.	.	C	10.83	1.461360	0.26248	.	.	ENSG00000132694	ENST00000368194	T	0.66460	-0.21	5.32	1.87	0.25490	.	0.440313	0.21740	N	0.069832	T	0.32376	0.0827	.	.	.	0.80722	D	1	B	0.12013	0.005	B	0.06405	0.002	T	0.13629	-1.0502	9	0.33141	T	0.24	-4.1001	7.6746	0.28478	0.0:0.5815:0.0:0.4185	.	195	O15085-2	.	H	195	ENSP00000357177:R195H	ENSP00000357177:R195H	R	-	2	0	ARHGEF11	155208231	0.878000	0.30173	1.000000	0.80357	0.995000	0.86356	0.424000	0.21330	0.622000	0.30249	0.655000	0.94253	CGT	.	.	none		0.567	ARHGEF11-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000098931.1	NM_198236	
DNAH10	196385	hgsc.bcm.edu	37	12	124355003	124355003	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124355003C>T	ENST00000409039.3	+	43	7281	c.7256C>T	c.(7255-7257)gCc>gTc	p.A2419V		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2419	AAA 3. {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)		TATATTCATGCCCCCGAGAGG	0.433																																					p.A2419V		Atlas-SNP	.											.	DNAH10	888	.	0			c.C7256T						PASS	.						81.0	77.0	78.0					12																	124355003		1865	4114	5979	SO:0001583	missense	196385	exon43			TTCATGCCCCCGA	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.7256C>T	12.37:g.124355003C>T	ENSP00000386770:p.Ala2419Val	63.0	0.0	0		91.0	40.0	0.43956	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	12.19	1.863422	0.32884	.	.	ENSG00000197653	ENST00000409039	T	0.22134	1.97	5.06	-6.26	0.02033	.	5.622030	0.00939	U	0.002819	T	0.08935	0.0221	N	0.11364	0.135	0.09310	N	1	B	0.02656	0.0	B	0.10450	0.005	T	0.16512	-1.0400	10	0.39692	T	0.17	.	0.4362	0.00479	0.3524:0.2407:0.1472:0.2597	.	2419	Q8IVF4	DYH10_HUMAN	V	2419	ENSP00000386770:A2419V	ENSP00000386770:A2419V	A	+	2	0	DNAH10	122920956	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.150000	0.10189	-0.924000	0.03780	-0.137000	0.14449	GCC	.	.	none		0.433	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
ZNF879	345462	hgsc.bcm.edu	37	5	178455114	178455114	+	Missense_Mutation	SNP	A	A	G	rs146216019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:178455114A>G	ENST00000444149.2	+	4	430	c.242A>G	c.(241-243)cAa>cGa	p.Q81R	ZNF879_ENST00000519896.1_Silent_p.P92P	NM_001136116.1	NP_001129588.1	B4DU55	ZN879_HUMAN	zinc finger protein 879	81	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(3)|kidney(2)|pancreas(1)|stomach(1)	7						GGAGTTCCCCAAGGCGCACAT	0.532													A|||	17	0.00339457	0.0008	0.0043	5008	,	,		19179	0.0		0.0089	False		,,,				2504	0.0041				p.Q81R		Atlas-SNP	.											.	ZNF879	41	.	0			c.A242G						PASS	.	A	ARG/GLN	4,1380		0,4,688	84.0	80.0	81.0		242	-0.3	0.0	5	dbSNP_134	81	49,3133		0,49,1542	yes	missense	ZNF879	NM_001136116.1	43	0,53,2230	GG,GA,AA		1.5399,0.289,1.1608	benign	81/564	178455114	53,4513	692	1591	2283	SO:0001583	missense	345462	exon4			TTCCCCAAGGCGC	AK300504	CCDS47352.1	5q35.3	2013-01-08			ENSG00000234284	ENSG00000234284		"""Zinc fingers, C2H2-type"", ""-"""	37273	protein-coding gene	gene with protein product							Standard	NM_001136116		Approved	DKFZp686E2433	uc003mjt.4	B4DU55	OTTHUMG00000163596	ENST00000444149.2:c.242A>G	5.37:g.178455114A>G	ENSP00000414887:p.Gln81Arg	95.0	0.0	0		73.0	46.0	0.630137	NM_001136116		Missense_Mutation	SNP	ENST00000444149.2	37	CCDS47352.1	9	0.004120879120879121	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	0.237	-1.016524	0.02078	0.00289	0.015399	ENSG00000234284	ENST00000444149;ENST00000522442	T;T	0.05447	3.44;6.0	4.55	-0.285	0.12866	Krueppel-associated box (1);	.	.	.	.	T	0.01061	0.0035	N	0.03891	-0.335	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45556	-0.9253	9	0.05351	T	0.99	-9.1498	8.0252	0.30434	0.623:0.0:0.377:0.0	.	81	B4DU55	ZN879_HUMAN	R	81	ENSP00000414887:Q81R;ENSP00000428477:Q81R	ENSP00000414887:Q81R	Q	+	2	0	ZNF879	178387720	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.314000	0.08092	0.064000	0.16427	0.482000	0.46254	CAA	A|0.996;G|0.004	0.004	strong		0.532	ZNF879-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374447.1	NM_001136116	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230440	23230440	+	Splice_Site	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230440G>A	ENST00000526893.1	+	1	480		c.e1+1		IGLL5_ENST00000532223.2_Splice_Site|IGLL5_ENST00000531372.1_Splice_Site|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5							extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGTGGGGCAGGTAAGGGGCAA	0.627																																					.		Atlas-SNP	.											.	IGLL5	26	.	0			c.100+1G>A						PASS	.																																			SO:0001630	splice_region_variant	100423062	exon1			GGGCAGGTAAGGG	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.206+1G>A	22.37:g.23230440G>A		97.0	0.0	0		86.0	29.0	0.337209	NM_001256296		Splice_Site	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.15	1.271539	0.23221	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	.	.	.	3.92	3.92	0.45320	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.74	0.51788	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	IGLL5	21560440	1.000000	0.71417	1.000000	0.80357	0.199000	0.23934	1.700000	0.37815	2.481000	0.83766	0.643000	0.83706	.	.	.	none		0.627	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	Intron
SORL1	6653	hgsc.bcm.edu	37	11	121498410	121498410	+	Missense_Mutation	SNP	G	G	A	rs146742626		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:121498410G>A	ENST00000260197.7	+	47	6640	c.6511G>A	c.(6511-6513)Gcc>Acc	p.A2171T	SORL1_ENST00000534286.1_Missense_Mutation_p.A1081T|SORL1_ENST00000532694.1_Missense_Mutation_p.A1017T|SORL1_ENST00000527934.1_Missense_Mutation_p.A786T|SORL1_ENST00000525532.1_Missense_Mutation_p.A1115T	NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing	2171					cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CAGCTTCACCGCCTTCGCCAA	0.607																																					p.A2171T		Atlas-SNP	.											.	SORL1	218	.	0			c.G6511A						PASS	.	G	THR/ALA	0,4404		0,0,2202	59.0	52.0	54.0		6511	6.0	0.2	11	dbSNP_134	54	1,8597	1.2+/-3.3	0,1,4298	no	missense	SORL1	NM_003105.5	58	0,1,6500	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	2171/2215	121498410	1,13001	2202	4299	6501	SO:0001583	missense	6653	exon47			TTCACCGCCTTCG	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.6511G>A	11.37:g.121498410G>A	ENSP00000260197:p.Ala2171Thr	70.0	0.0	0		90.0	40.0	0.444444	NM_003105	B2RNX7|Q92856	Missense_Mutation	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.610245	0.87258	0.0	1.16E-4	ENSG00000137642	ENST00000260197;ENST00000525532;ENST00000532694;ENST00000534286;ENST00000527934	D;D;D;D;D	0.91464	-2.85;-2.59;-2.23;-2.26;-2.13	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	D	0.93058	0.7790	L	0.59436	1.845	0.58432	D	0.99999	D;D	0.62365	0.983;0.991	B;P	0.54629	0.397;0.757	D	0.91897	0.5528	10	0.44086	T	0.13	.	20.4008	0.98991	0.0:0.0:1.0:0.0	.	786;2171	E9PKB0;Q92673	.;SORL_HUMAN	T	2171;1115;1017;1081;786	ENSP00000260197:A2171T;ENSP00000434634:A1115T;ENSP00000432131:A1017T;ENSP00000436447:A1081T;ENSP00000435405:A786T	ENSP00000260197:A2171T	A	+	1	0	SORL1	121003620	1.000000	0.71417	0.204000	0.23530	0.947000	0.59692	5.412000	0.66392	2.826000	0.97356	0.655000	0.94253	GCC	G|1.000;A|0.000	0.000	weak		0.607	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	
SMC1B	27127	hgsc.bcm.edu	37	22	45750920	45750920	+	Silent	SNP	A	A	G	rs61748560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45750920A>G	ENST00000357450.4	-	20	3036	c.3037T>C	c.(3037-3039)Tta>Cta	p.L1013L	SMC1B_ENST00000404354.3_Silent_p.L1013L	NM_148674.3	NP_683515.3	Q8NDV3	SMC1B_HUMAN	structural maintenance of chromosomes 1B	1013					meiotic nuclear division (GO:0007126)|sister chromatid cohesion (GO:0007062)	chromosome, centromeric region (GO:0000775)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear meiotic cohesin complex (GO:0034991)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(15)|ovary(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0182)		GTTTTCAGTAAGATATCTTCC	0.443													A|||	17	0.00339457	0.0	0.0043	5008	,	,		18176	0.0		0.0129	False		,,,				2504	0.001				p.L1013L		Atlas-SNP	.											.	SMC1B	215	.	0			c.T3037C						PASS	.	A		6,3840		0,6,1917	206.0	194.0	197.0		3037	-0.4	0.0	22	dbSNP_129	197	87,8191		0,87,4052	no	coding-synonymous	SMC1B	NM_148674.3		0,93,5969	GG,GA,AA		1.051,0.156,0.7671		1013/1236	45750920	93,12031	1923	4139	6062	SO:0001819	synonymous_variant	27127	exon20			TCAGTAAGATATC	AJ504806	CCDS43027.1, CCDS74876.1	22q13	2006-07-06	2006-07-06	2006-07-06	ENSG00000077935	ENSG00000077935		"""Structural maintenance of chromosomes proteins"""	11112	protein-coding gene	gene with protein product		608685	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 2 (yeast)"""	SMC1L2		10591208, 11564881	Standard	XM_005261566		Approved	bK268H5	uc003bgc.3	Q8NDV3	OTTHUMG00000151334	ENST00000357450.4:c.3037T>C	22.37:g.45750920A>G		180.0	0.0	0		170.0	85.0	0.5	NM_148674	A0AV46|B0QY23|B0QY24|Q5TIC3|Q6ZUF9|Q9Y3G5	Silent	SNP	ENST00000357450.4	37	CCDS43027.1																																																																																			A|0.989;G|0.011	0.011	strong		0.443	SMC1B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322256.2	NM_148674	
MIPEP	4285	hgsc.bcm.edu	37	13	24443512	24443512	+	Missense_Mutation	SNP	T	T	G	rs149856612	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:24443512T>G	ENST00000382172.3	-	7	960	c.862A>C	c.(862-864)Agc>Cgc	p.S288R		NM_005932.3	NP_005923	Q99797	MIPEP_HUMAN	mitochondrial intermediate peptidase	288					protein processing involved in protein targeting to mitochondrion (GO:0006627)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(2)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|liver(1)|lung(12)|prostate(2)|skin(1)	27		all_cancers(29;1.83e-22)|all_epithelial(30;8.75e-19)|all_lung(29;9.17e-18)|Lung SC(185;0.0225)|Breast(139;0.14)		all cancers(112;0.00389)|Epithelial(112;0.0266)|OV - Ovarian serous cystadenocarcinoma(117;0.0717)|Lung(94;0.207)|GBM - Glioblastoma multiforme(144;0.232)		AGATCTCTGCTGCTGAGCAAT	0.403													T|||	5	0.000998403	0.0	0.0014	5008	,	,		17922	0.0		0.002	False		,,,				2504	0.002				p.S288R		Atlas-SNP	.											.	MIPEP	53	.	0			c.A862C						PASS	.	T	ARG/SER	1,4405	2.1+/-5.4	0,1,2202	88.0	89.0	89.0		862	3.4	0.0	13	dbSNP_134	89	3,8597	3.0+/-9.4	0,3,4297	yes	missense	MIPEP	NM_005932.3	110	0,4,6499	GG,GT,TT		0.0349,0.0227,0.0308	possibly-damaging	288/714	24443512	4,13002	2203	4300	6503	SO:0001583	missense	4285	exon7			CTCTGCTGCTGAG		CCDS9303.1	13q12	2011-01-17			ENSG00000027001	ENSG00000027001	3.4.24.59		7104	protein-coding gene	gene with protein product		602241				9073519	Standard	NM_005932		Approved	MIP	uc001uox.4	Q99797	OTTHUMG00000016573	ENST00000382172.3:c.862A>C	13.37:g.24443512T>G	ENSP00000371607:p.Ser288Arg	83.0	0.0	0		55.0	37.0	0.672727	NM_005932	Q5JV15|Q5T9Q9|Q96G65	Missense_Mutation	SNP	ENST00000382172.3	37	CCDS9303.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	11.52	1.662789	0.29515	2.27E-4	3.49E-4	ENSG00000027001	ENST00000382172	T	0.07688	3.17	5.9	3.38	0.38709	Neurolysin/Thimet oligopeptidase, domain 2 (1);	0.354147	0.38605	N	0.001630	T	0.13329	0.0323	L	0.54323	1.7	0.09310	N	0.999996	P	0.41498	0.752	P	0.45794	0.493	T	0.03473	-1.1033	10	0.44086	T	0.13	.	12.8495	0.57850	0.0:0.0:0.2573:0.7427	.	288	Q99797	MIPEP_HUMAN	R	288	ENSP00000371607:S288R	ENSP00000371607:S288R	S	-	1	0	MIPEP	23341512	0.998000	0.40836	0.010000	0.14722	0.350000	0.29205	3.528000	0.53524	0.442000	0.26555	0.459000	0.35465	AGC	T|1.000;G|0.000	0.000	strong		0.403	MIPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044169.1		
ZNF229	7772	hgsc.bcm.edu	37	19	44932704	44932704	+	Missense_Mutation	SNP	T	T	C	rs375182987	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44932704T>C	ENST00000588931.1	-	6	2685	c.2252A>G	c.(2251-2253)cAg>cGg	p.Q751R	CTC-512J12.4_ENST00000588655.1_RNA|ZNF229_ENST00000591289.1_Intron|ZNF229_ENST00000291187.4_Missense_Mutation_p.Q745R	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	751					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)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				ATGTGAGCTCTGACTATAGCC	0.512																																					p.Q751R		Atlas-SNP	.											.	ZNF229	123	.	0			c.A2252G						PASS	.	T	ARG/GLN	0,4404		0,0,2202	73.0	81.0	79.0		2252	0.6	0.0	19		79	2,8598	2.2+/-6.3	0,2,4298	no	missense	ZNF229	NM_014518.2	43	0,2,6500	CC,CT,TT		0.0233,0.0,0.0154	benign	751/826	44932704	2,13002	2202	4300	6502	SO:0001583	missense	7772	exon6			GAGCTCTGACTAT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.2252A>G	19.37:g.44932704T>C	ENSP00000466519:p.Gln751Arg	135.0	0.0	0		173.0	88.0	0.508671	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	37	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	T	14.31	2.497781	0.44455	0.0	2.33E-4	ENSG00000167383	ENST00000291187	.	.	.	4.04	0.594	0.17485	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.11196	0.0273	N	0.03294	-0.36	0.09310	N	1	P	0.39216	0.664	B	0.37267	0.245	T	0.25152	-1.0140	8	0.10902	T	0.67	.	7.7713	0.29010	0.0:0.2711:0.0:0.7289	.	751	Q9UJW7	ZN229_HUMAN	R	751	.	ENSP00000291187:Q751R	Q	-	2	0	ZNF229	49624544	0.000000	0.05858	0.000000	0.03702	0.755000	0.42902	-2.022000	0.01439	-0.284000	0.09102	0.496000	0.49642	CAG	.	.	weak		0.512	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
NFKB1	4790	hgsc.bcm.edu	37	4	103518700	103518700	+	Missense_Mutation	SNP	A	A	G	rs4648072	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:103518700A>G	ENST00000505458.1	+	15	1793	c.1516A>G	c.(1516-1518)Atg>Gtg	p.M506V	NFKB1_ENST00000394820.4_Missense_Mutation_p.M506V|NFKB1_ENST00000600343.1_Missense_Mutation_p.M326V|NFKB1_ENST00000226574.4_Missense_Mutation_p.M507V			P19838	NFKB1_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells 1	506	Interaction with CFLAR.		M -> V (in dbSNP:rs4648072). {ECO:0000269|Ref.8}.		apoptotic process (GO:0006915)|cellular response to interleukin-1 (GO:0071347)|cellular response to interleukin-6 (GO:0071354)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to mechanical stimulus (GO:0071260)|cellular response to nicotine (GO:0071316)|cellular response to peptide hormone stimulus (GO:0071375)|Fc-epsilon receptor signaling pathway (GO:0038095)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|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)|negative regulation of apoptotic process (GO:0043066)|negative regulation of calcidiol 1-monooxygenase activity (GO:0010956)|negative regulation of cellular protein metabolic process (GO:0032269)|negative regulation of cholesterol transport (GO:0032375)|negative regulation of cytokine production (GO:0001818)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interleukin-12 biosynthetic process (GO:0045083)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of vitamin D biosynthetic process (GO:0010957)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of hyaluronan biosynthetic process (GO:1900127)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|response to copper ion (GO:0046688)|response to oxidative stress (GO:0006979)|T cell receptor signaling pathway (GO:0050852)|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 from RNA polymerase II promoter (GO:0006366)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|I-kappaB/NF-kappaB complex (GO:0033256)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|nucleic acid binding transcription factor activity (GO:0001071)|regulatory region DNA binding (GO:0000975)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			biliary_tract(1)|breast(4)|endometrium(2)|large_intestine(6)|lung(7)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	27		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;6.59e-08)	Acetylsalicylic acid(DB00945)|Pranlukast(DB01411)|Thalidomide(DB01041)|Triflusal(DB08814)	AGAGAAGGCTATGCAGCTTGC	0.483													A|||	69	0.013778	0.0424	0.0072	5008	,	,		22523	0.0		0.008	False		,,,				2504	0.0				p.M507V		Atlas-SNP	.											.	NFKB1	78	.	0			c.A1519G						PASS	.	A	VAL/MET,VAL/MET	181,4225	118.0+/-155.7	4,173,2026	111.0	101.0	104.0		1516,1519	-4.9	0.0	4	dbSNP_111	104	69,8531	41.7+/-99.0	0,69,4231	yes	missense,missense	NFKB1	NM_001165412.1,NM_003998.3	21,21	4,242,6257	GG,GA,AA		0.8023,4.108,1.9222	benign,benign	506/969,507/970	103518700	250,12756	2203	4300	6503	SO:0001583	missense	4790	exon15			AAGGCTATGCAGC	M58603	CCDS3657.1, CCDS54783.1	4q24	2013-01-10	2008-07-28		ENSG00000109320	ENSG00000109320		"""Ankyrin repeat domain containing"""	7794	protein-coding gene	gene with protein product		164011				1992489	Standard	NM_003998		Approved	KBF1, p105, NFKB-p50, p50, NF-kappaB, NFkappaB, NF-kB1	uc011cep.2	P19838	OTTHUMG00000161080	ENST00000505458.1:c.1516A>G	4.37:g.103518700A>G	ENSP00000424790:p.Met506Val	72.0	0.0	0		48.0	48.0	1	NM_003998	A8K5Y5|B3KVE8|Q68D84|Q86V43|Q8N4X7|Q9NZC0	Missense_Mutation	SNP	ENST00000505458.1	37	CCDS54783.1	26	0.011904761904761904	19	0.03861788617886179	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	A	7.891	0.732244	0.15507	0.04108	0.008023	ENSG00000109320	ENST00000226574;ENST00000394820;ENST00000505458	T;T;T	0.36157	1.28;1.27;1.27	4.57	-4.88	0.03113	.	0.299368	0.33327	N	0.005038	T	0.07369	0.0186	L	0.56769	1.78	0.18873	N	0.999983	B;B;B	0.20052	0.011;0.011;0.041	B;B;B	0.20955	0.021;0.021;0.032	T	0.10245	-1.0638	10	0.48119	T	0.1	.	10.0045	0.41949	0.2584:0.6027:0.1389:0.0	rs4648072;rs4648072	326;506;507	B3KVE8;P19838;P19838-2	.;NFKB1_HUMAN;.	V	507;506;506	ENSP00000226574:M507V;ENSP00000378297:M506V;ENSP00000424790:M506V	ENSP00000226574:M507V	M	+	1	0	NFKB1	103737738	0.037000	0.19845	0.034000	0.17996	0.916000	0.54674	0.284000	0.18864	-1.114000	0.02977	0.533000	0.62120	ATG	A|0.984;G|0.016	0.016	strong		0.483	NFKB1-003	KNOWN	alternative_5_UTR|non_canonical_polymorphism|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000363411.1		
ITGAE	3682	hgsc.bcm.edu	37	17	3664361	3664361	+	Missense_Mutation	SNP	T	T	C	rs140947594	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3664361T>C	ENST00000263087.4	-	6	642	c.544A>G	c.(544-546)Aag>Gag	p.K182E		NM_002208.4	NP_002199.3	P38570	ITAE_HUMAN	integrin, alpha E (antigen CD103, human mucosal lymphocyte antigen 1; alpha polypeptide)	182	Glu-rich (acidic).|X-domain (extra domain).				cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	external side of plasma membrane (GO:0009897)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(13)|lung(14)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	41				UCEC - Uterine corpus endometrioid carcinoma (3;0.0813)		tcctcctccttctccAGAGCC	0.567													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		19977	0.0		0.0119	False		,,,				2504	0.001				p.K182E	NSCLC(182;635 2928 8995 38788)	Atlas-SNP	.											.	ITGAE	96	.	0			c.A544G						PASS	.	T	GLU/LYS	3,4403	6.2+/-15.9	0,3,2200	127.0	131.0	130.0		544	-6.0	0.0	17	dbSNP_134	130	49,8551	28.5+/-78.6	0,49,4251	yes	missense	ITGAE	NM_002208.4	56	0,52,6451	CC,CT,TT		0.5698,0.0681,0.3998	benign	182/1180	3664361	52,12954	2203	4300	6503	SO:0001583	missense	3682	exon6			CCTCCTTCTCCAG	L25851	CCDS32531.1	17p13	2010-03-23				ENSG00000083457		"""CD molecules"", ""Integrins"""	6147	protein-coding gene	gene with protein product		604682				8119947	Standard	NM_002208		Approved	CD103, HUMINAE	uc002fwo.4	P38570		ENST00000263087.4:c.544A>G	17.37:g.3664361T>C	ENSP00000263087:p.Lys182Glu	26.0	0.0	0		26.0	13.0	0.5	NM_002208	Q17RS6|Q9NZU9	Missense_Mutation	SNP	ENST00000263087.4	37	CCDS32531.1	11	0.005036630036630037	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	3.041	-0.197461	0.06259	6.81E-4	0.005698	ENSG00000083457	ENST00000263087	T	0.59772	0.24	3.57	-6.0	0.02206	.	.	.	.	.	T	0.18425	0.0442	N	0.11427	0.14	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31724	-0.9933	9	0.02654	T	1	.	5.5585	0.17129	0.0:0.215:0.2778:0.5073	.	182	P38570	ITAE_HUMAN	E	182	ENSP00000263087:K182E	ENSP00000263087:K182E	K	-	1	0	ITGAE	3611110	0.000000	0.05858	0.001000	0.08648	0.157000	0.22087	-1.083000	0.03397	-1.253000	0.02488	-0.534000	0.04291	AAG	T|0.996;C|0.004	0.004	strong		0.567	ITGAE-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438169.1	NM_002208	
PRKCB	5579	hgsc.bcm.edu	37	16	24046861	24046861	+	Silent	SNP	T	T	C	rs116345778	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:24046861T>C	ENST00000321728.7	+	5	697	c.522T>C	c.(520-522)atT>atC	p.I174I	PRKCB_ENST00000303531.7_Silent_p.I174I	NM_212535.2	NP_997700.1	P05771	KPCB_HUMAN	protein kinase C, beta	174	C2. {ECO:0000255|PROSITE- ProRule:PRU00041}.				apoptotic process (GO:0006915)|B cell activation (GO:0042113)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|cellular calcium ion homeostasis (GO:0006874)|cellular response to carbohydrate stimulus (GO:0071322)|histone H3-T6 phosphorylation (GO:0035408)|intracellular signal transduction (GO:0035556)|lipoprotein transport (GO:0042953)|negative regulation of glucose transport (GO:0010829)|negative regulation of insulin receptor signaling pathway (GO:0046627)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of B cell receptor signaling pathway (GO:0050861)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein phosphorylation (GO:0006468)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|calcium channel regulator activity (GO:0005246)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|histone kinase activity (H3-T6 specific) (GO:0035403)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			central_nervous_system(3)|large_intestine(1)|lung(2)|ovary(3)	9					Tamoxifen(DB00675)|Vitamin E(DB00163)	ACGTCCTCATTGTCCTCGGTA	0.647													T|||	48	0.00958466	0.0174	0.0029	5008	,	,		13772	0.0		0.005	False		,,,				2504	0.0184				p.I174I		Atlas-SNP	.											.	PRKCB	383	.	0			c.T522C						PASS	.	T	,	68,4326	63.5+/-100.7	1,66,2130	74.0	69.0	71.0		522,522	-4.3	0.6	16	dbSNP_132	71	16,8584	11.2+/-40.8	0,16,4284	no	coding-synonymous,coding-synonymous	PRKCB	NM_002738.6,NM_212535.2	,	1,82,6414	CC,CT,TT		0.186,1.5476,0.6465	,	174/674,174/672	24046861	84,12910	2197	4300	6497	SO:0001819	synonymous_variant	5579	exon5			CCTCATTGTCCTC	M13975	CCDS10618.1, CCDS10619.1	16p12	2009-07-10	2008-08-18	2008-08-18	ENSG00000166501	ENSG00000166501	2.7.11.1		9395	protein-coding gene	gene with protein product		176970	"""protein kinase C, beta 1"""	PRKCB2, PKCB, PRKCB1		3658678	Standard	NM_002738		Approved		uc002dme.3	P05771	OTTHUMG00000131615	ENST00000321728.7:c.522T>C	16.37:g.24046861T>C		94.0	0.0	0		121.0	47.0	0.38843	NM_212535	C5IFJ8|D3DWF5|O43744|P05127|Q15138|Q93060|Q9UE49|Q9UE50|Q9UEH8|Q9UJ30|Q9UJ33	Silent	SNP	ENST00000321728.7	37	CCDS10618.1																																																																																			T|0.993;C|0.007	0.007	strong		0.647	PRKCB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254504.2	NM_212535	
TOPORS	10210	hgsc.bcm.edu	37	9	32543801	32543801	+	Missense_Mutation	SNP	G	G	A	rs41272913	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32543801G>A	ENST00000360538.2	-	3	838	c.722C>T	c.(721-723)aCg>aTg	p.T241M	TOPORS_ENST00000379858.1_Missense_Mutation_p.T176M	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	241	Required for DNA-binding.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TTCATCTGCCGTAGTTGGCCT	0.378													G|||	2	0.000399361	0.0008	0.0	5008	,	,		21477	0.0		0.001	False		,,,				2504	0.0				p.T241M		Atlas-SNP	.											.	TOPORS	127	.	0			c.C722T						PASS	.	G	MET/THR,MET/THR	6,4400	11.4+/-27.6	0,6,2197	112.0	116.0	115.0		527,722	3.2	0.0	9	dbSNP_127	115	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	TOPORS	NM_001195622.1,NM_005802.4	81,81	0,9,6494	AA,AG,GG		0.0349,0.1362,0.0692	probably-damaging,probably-damaging	176/981,241/1046	32543801	9,12997	2203	4300	6503	SO:0001583	missense	10210	exon3			TCTGCCGTAGTTG	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.722C>T	9.37:g.32543801G>A	ENSP00000353735:p.Thr241Met	63.0	0.0	0		57.0	27.0	0.473684	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	G	13.72	2.322059	0.41096	0.001362	3.49E-4	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.15256	2.44;2.45	5.2	3.18	0.36537	.	0.543306	0.16954	N	0.192770	T	0.07188	0.0182	N	0.08118	0	0.09310	N	1	P	0.42010	0.768	B	0.33521	0.165	T	0.18085	-1.0348	10	0.52906	T	0.07	-1.9948	8.0253	0.30434	0.0:0.1386:0.467:0.3944	rs41272913	241	Q9NS56	TOPRS_HUMAN	M	241;176	ENSP00000353735:T241M;ENSP00000369187:T176M	ENSP00000353735:T241M	T	-	2	0	TOPORS	32533801	0.003000	0.15002	0.009000	0.14445	0.458000	0.32498	1.039000	0.30266	1.478000	0.48253	0.655000	0.94253	ACG	G|0.999;A|0.001	0.001	strong		0.378	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
SERPINI2	5276	hgsc.bcm.edu	37	3	167170788	167170788	+	Silent	SNP	G	G	A	rs61750373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167170788G>A	ENST00000476257.1	-	7	1198	c.900C>T	c.(898-900)gaC>gaT	p.D300D	SERPINI2_ENST00000264677.4_Silent_p.D300D|SERPINI2_ENST00000471111.1_Silent_p.D300D|SERPINI2_ENST00000461846.1_Silent_p.D300D			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	300					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						AATACAAAACGTCTTTGAAGT	0.279													G|||	7	0.00139776	0.0015	0.0	5008	,	,		15704	0.0		0.004	False		,,,				2504	0.001				p.D310D		Atlas-SNP	.											.	SERPINI2	85	.	0			c.C930T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	64.0	61.0	62.0		900	1.5	1.0	3	dbSNP_129	62	66,8532	39.8+/-96.3	1,64,4234	no	coding-synonymous	SERPINI2	NM_006217.3		1,73,6428	AA,AG,GG		0.7676,0.2043,0.5767		300/406	167170788	75,12929	2203	4299	6502	SO:0001819	synonymous_variant	5276	exon7			CAAAACGTCTTTG	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"""Serine (or cysteine) peptidase inhibitors"""	8945	protein-coding gene	gene with protein product		605587	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2"", ""serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"""	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.900C>T	3.37:g.167170788G>A		184.0	0.0	0		204.0	75.0	0.367647	NM_001012303		Silent	SNP	ENST00000476257.1	37	CCDS3200.1																																																																																			G|0.996;A|0.004	0.004	strong		0.279	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
PCDHA12	56137	hgsc.bcm.edu	37	5	140256729	140256729	+	Missense_Mutation	SNP	G	G	A	rs543806401	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140256729G>A	ENST00000398631.2	+	1	1672	c.1672G>A	c.(1672-1674)Gag>Aag	p.E558K	PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA11_ENST00000398640.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA2_ENST00000526136.1_Intron	NM_018903.2|NM_031864.2	NP_061726.1|NP_114070.1	Q9UN75	PCDAC_HUMAN	protocadherin alpha 12	558	Cadherin 5. {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(4)|breast(2)|cervix(1)|endometrium(19)|kidney(8)|large_intestine(8)|liver(2)|lung(25)|prostate(1)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGTGCTGGACGAGAACGACAA	0.701													.|||	2	0.000399361	0.0	0.0	5008	,	,		17343	0.0		0.0	False		,,,				2504	0.002				p.E558K	Pancreas(113;759 1672 13322 24104 50104)	Atlas-SNP	.											.	PCDHA12	196	.	0			c.G1672A						PASS	.						144.0	149.0	147.0					5																	140256729		2203	4299	6502	SO:0001583	missense	56137	exon1			CTGGACGAGAACG	AF152477	CCDS47285.1, CCDS75327.1	5q31	2010-11-26			ENSG00000251664	ENSG00000251664		"""Cadherins / Protocadherins : Clustered"""	8666	other	complex locus constituent	"""KIAA0345-like 2"""	606318				10380929	Standard	NM_018903		Approved	PCDH-ALPHA12	uc003lic.2	Q9UN75	OTTHUMG00000163366	ENST00000398631.2:c.1672G>A	5.37:g.140256729G>A	ENSP00000381628:p.Glu558Lys	11.0	0.0	0		21.0	8.0	0.380952	NM_018903	O75278|Q2M1N8	Missense_Mutation	SNP	ENST00000398631.2	37	CCDS47285.1	.	.	.	.	.	.	.	.	.	.	G	16.09	3.023113	0.54683	.	.	ENSG00000251664	ENST00000398631	T	0.60920	0.15	4.92	4.05	0.47172	Cadherin (4);Cadherin conserved site (1);Cadherin-like (1);	.	.	.	.	T	0.65698	0.2716	M	0.70108	2.13	0.24151	N	0.995691	D;D	0.60575	0.988;0.983	P;B	0.53760	0.734;0.284	T	0.57585	-0.7786	9	0.62326	D	0.03	.	8.9151	0.35576	0.1715:0.0:0.8285:0.0	.	558;558	Q9UN75-2;Q9UN75	.;PCDAC_HUMAN	K	558	ENSP00000381628:E558K	ENSP00000381628:E558K	E	+	1	0	PCDHA12	140236913	0.033000	0.19621	0.956000	0.39512	0.208000	0.24298	0.499000	0.22546	1.060000	0.40578	0.561000	0.74099	GAG	.	.	none		0.701	PCDHA12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372882.2	NM_018903	
DCTN1	1639	hgsc.bcm.edu	37	2	74596527	74596527	+	Missense_Mutation	SNP	C	C	T	rs17721059	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:74596527C>T	ENST00000361874.3	-	14	1801	c.1484G>A	c.(1483-1485)cGg>cAg	p.R495Q	DCTN1_ENST00000394003.3_Missense_Mutation_p.R488Q|DCTN1_ENST00000409438.1_Missense_Mutation_p.R361Q|DCTN1_ENST00000495643.1_5'Flank|DCTN1_ENST00000409567.3_Missense_Mutation_p.R475Q|DCTN1_ENST00000409240.1_Missense_Mutation_p.R458Q|DCTN1_ENST00000407639.2_Missense_Mutation_p.R361Q|DCTN1_ENST00000409868.1_Missense_Mutation_p.R478Q	NM_004082.4	NP_004073.2	Q14203	DCTN1_HUMAN	dynactin 1	495			R -> Q (in dbSNP:rs17721059).		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						CTCACGAACCCGCGCGCCTGC	0.597													C|||	39	0.00778754	0.0	0.0187	5008	,	,		16682	0.0		0.0239	False		,,,				2504	0.002				p.R495Q		Atlas-SNP	.											.	DCTN1	110	.	0			c.G1484A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	19,4387	25.3+/-52.1	0,19,2184	89.0	90.0	90.0		1424,1082,1373,1463,1484,1082	5.0	1.0	2	dbSNP_123	90	160,8440	73.2+/-135.9	1,158,4141	yes	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	43,43,43,43,43,43	1,177,6325	TT,TC,CC		1.8605,0.4312,1.3763	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	475/1254,361/1140,458/1237,488/1272,495/1279,361/1145	74596527	179,12827	2203	4300	6503	SO:0001583	missense	1639	exon14			CGAACCCGCGCGC		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.1484G>A	2.37:g.74596527C>T	ENSP00000354791:p.Arg495Gln	131.0	0.0	0		180.0	88.0	0.488889	NM_004082	A8MY36|B4DM45|E9PFS5|E9PGE1|G5E9H4|O95296|Q6IQ37|Q9BRM9|Q9UIU1|Q9UIU2	Missense_Mutation	SNP	ENST00000361874.3	37	CCDS1939.1	21	0.009615384615384616	0	0.0	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	15.10	2.731990	0.48939	0.004312	0.018605	ENSG00000204843	ENST00000361874;ENST00000394003;ENST00000393999;ENST00000407639;ENST00000409438;ENST00000409240;ENST00000409868;ENST00000409567	T;T;T;T;T;T;T	0.76578	-1.03;-1.03;-1.03;-1.03;-1.03;-0.71;-1.03	5.91	5.03	0.67393	.	0.203082	0.24587	N	0.037257	T	0.43500	0.1250	N	0.25144	0.715	0.50632	D	0.99988	B;P;P;B;B;P	0.46578	0.176;0.88;0.804;0.016;0.136;0.876	B;B;B;B;B;B	0.34138	0.022;0.122;0.123;0.008;0.04;0.176	T	0.54833	-0.8234	10	0.14252	T	0.57	-6.5169	14.0459	0.64704	0.0:0.9269:0.0:0.0731	rs17721059;rs17721059	475;458;495;488;361;361	E9PGE1;E9PFS5;Q14203;A8MY36;Q14203-2;G5E9H4	.;.;DCTN1_HUMAN;.;.;.	Q	495;488;478;361;361;458;478;475	ENSP00000354791:R495Q;ENSP00000377571:R488Q;ENSP00000384844:R361Q;ENSP00000387270:R361Q;ENSP00000386406:R458Q;ENSP00000387327:R478Q;ENSP00000386843:R475Q	ENSP00000354791:R495Q	R	-	2	0	DCTN1	74450035	0.991000	0.36638	0.970000	0.41538	0.394000	0.30568	3.179000	0.50887	1.507000	0.48752	0.655000	0.94253	CGG	C|0.985;T|0.015	0.015	strong		0.597	DCTN1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252227.3	NM_004082	
KCNJ12	3768	hgsc.bcm.edu	37	17	21318826	21318826	+	Missense_Mutation	SNP	G	G	A	rs142399667	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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						PASS	.	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	160.0	0.0	0		192.0	26.0	0.135417	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	
PCDHGC3	5098	hgsc.bcm.edu	37	5	140856349	140856349	+	Silent	SNP	A	A	G	rs115808055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140856349A>G	ENST00000308177.3	+	1	770	c.666A>G	c.(664-666)ccA>ccG	p.P222P	PCDHGA7_ENST00000518325.1_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|RN7SL68P_ENST00000488078.2_RNA|PCDHGB1_ENST00000523390.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA11_ENST00000518882.1_Intron	NM_002588.2|NM_032402.1	NP_002579.2|NP_115778.1	Q9UN70	PCDGK_HUMAN	protocadherin gamma subfamily C, 3	222	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|skin(2)|urinary_tract(1)	29			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GAGGGACCCCAGCTCTCTCCG	0.627													A|||	20	0.00399361	0.0008	0.0014	5008	,	,		15671	0.0		0.0179	False		,,,				2504	0.0				p.P222P		Atlas-SNP	.											.	PCDHGC3	173	.	0			c.A666G						PASS	.	A	,,,,,,,,,,,,,,,,,,,,,,	17,4389	23.3+/-48.9	0,17,2186	37.0	29.0	32.0		666,,,,,,,,,,,,,,,,,,,,,666,	-2.9	0.7	5	dbSNP_132	32	100,8500	51.5+/-111.7	2,96,4202	no	coding-synonymous,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,coding-synonymous,intron	PCDHGC3,PCDHGB4,PCDHGA8,PCDHGA12,PCDHGB7,PCDHGB6,PCDHGB5,PCDHGB3,PCDHGB2,PCDHGB1,PCDHGA11,PCDHGA10,PCDHGA9,PCDHGA7,PCDHGA6,PCDHGA5,PCDHGA4,PCDHGA3,PCDHGA2,PCDHGA1	NM_002588.2,NM_003735.2,NM_003736.2,NM_018912.2,NM_018913.2,NM_018914.2,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_018927.3,NM_032088.1,NM_032092.1,NM_032402.1,NM_032403.1	,,,,,,,,,,,,,,,,,,,,,,	2,113,6388	GG,GA,AA		1.1628,0.3858,0.8996	,,,,,,,,,,,,,,,,,,,,,,	222/935,,,,,,,,,,,,,,,,,,,,,222/864,	140856349	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	5098	exon1			GACCCCAGCTCTC	AF152337	CCDS4261.1, CCDS75347.1, CCDS75348.1	5q31	2010-01-26			ENSG00000240184	ENSG00000240184		"""Cadherins / Protocadherins : Clustered"""	8716	other	protocadherin	"""cadherin-like 2"", ""protocadherin 2"", ""protocadherin 43"""	603627		PCDH2		9360932, 8508762	Standard	NM_032402		Approved	PC-43, PC43, PCDH-GAMMA-C3		Q9UN70	OTTHUMG00000129613	ENST00000308177.3:c.666A>G	5.37:g.140856349A>G		40.0	0.0	0		23.0	16.0	0.695652	NM_032402	O60622|Q08192|Q9Y5C4	Silent	SNP	ENST00000308177.3	37	CCDS4261.1																																																																																			A|0.990;G|0.010	0.010	strong		0.627	PCDHGC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251808.2	NM_002588	
ZNF418	147686	hgsc.bcm.edu	37	19	58437767	58437767	+	Missense_Mutation	SNP	C	C	A	rs199612939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58437767C>A	ENST00000396147.1	-	4	2073	c.1782G>T	c.(1780-1782)agG>agT	p.R594S	ZNF418_ENST00000600989.1_Intron|ZNF418_ENST00000595830.1_Missense_Mutation_p.R594S|ZNF418_ENST00000599852.1_Missense_Mutation_p.R509S|ZNF418_ENST00000599086.1_5'Flank|ZNF418_ENST00000425570.3_Missense_Mutation_p.R615S	NM_133460.1	NP_597717.1	Q8TF45	ZN418_HUMAN	zinc finger protein 418	594					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	31		Colorectal(82;0.000256)|all_neural(62;0.0577)|Breast(46;0.147)|Ovarian(87;0.156)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0158)		TTCCACATTCCCTGCATTCAT	0.448																																					p.R594S		Atlas-SNP	.											.	ZNF418	76	.	0			c.G1782T						PASS	.	C	SER/ARG	8,4390		0,8,2191	86.0	89.0	88.0		1782	-5.5	0.0	19		88	87,8513		1,85,4214	yes	missense	ZNF418	NM_133460.1	110	1,93,6405	AA,AC,CC		1.0116,0.1819,0.7309	benign	594/677	58437767	95,12903	2199	4300	6499	SO:0001583	missense	147686	exon4			ACATTCCCTGCAT	AB075836, AY695825	CCDS42642.1	19q13.43	2013-01-08				ENSG00000196724		"""Zinc fingers, C2H2-type"", ""-"""	20647	protein-coding gene	gene with protein product						11853319	Standard	NM_133460		Approved	KIAA1956, FLJ31551	uc002qqs.1	Q8TF45		ENST00000396147.1:c.1782G>T	19.37:g.58437767C>A	ENSP00000379451:p.Arg594Ser	87.0	0.0	0		53.0	8.0	0.150943	NM_133460	Q2M1S2|Q670L5|Q96N18	Missense_Mutation	SNP	ENST00000396147.1	37	CCDS42642.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	.	0	-2.840553	0.00068	0.001819	0.010116	ENSG00000196724	ENST00000396147;ENST00000425570;ENST00000545403	T;T	0.16457	2.34;2.34	2.76	-5.51	0.02568	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02193	0.0068	N	0.01352	-0.895	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.11203	-1.0597	9	0.07813	T	0.8	.	1.0134	0.01502	0.1849:0.1646:0.3013:0.3492	.	594	Q8TF45	ZN418_HUMAN	S	594;615;560	ENSP00000379451:R594S;ENSP00000407039:R615S	ENSP00000379451:R594S	R	-	3	2	ZNF418	63129579	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-10.328000	0.00007	-4.068000	0.00076	-1.399000	0.01144	AGG	C|0.989;A|0.011	0.011	strong		0.448	ZNF418-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466693.1	NM_133460	
GJB4	127534	hgsc.bcm.edu	37	1	35226963	35226963	+	Silent	SNP	C	C	T	rs142720849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35226963C>T	ENST00000339480.1	+	2	478	c.108C>T	c.(106-108)taC>taT	p.Y36Y	RP1-34M23.5_ENST00000542839.1_RNA	NM_153212.2	NP_694944.1	Q9NTQ9	CXB4_HUMAN	gap junction protein, beta 4, 30.3kDa	36					cell communication (GO:0007154)|olfactory behavior (GO:0042048)|sensory perception of smell (GO:0007608)	connexon complex (GO:0005922)|integral component of membrane (GO:0016021)				breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(6)|ovary(2)|skin(1)	16		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.234)				TGCTGGTGTACGTGGTGGCAG	0.582													C|||	7	0.00139776	0.0008	0.0029	5008	,	,		23419	0.001		0.003	False		,,,				2504	0.0				p.Y36Y		Atlas-SNP	.											GJB4,NS,carcinoma,0,1	GJB4	51	1	0			c.C108T						PASS	.	C		2,4404	4.2+/-10.8	0,2,2201	235.0	160.0	186.0		108	0.9	1.0	1	dbSNP_134	186	53,8547	33.8+/-87.4	0,53,4247	no	coding-synonymous	GJB4	NM_153212.2		0,55,6448	TT,TC,CC		0.6163,0.0454,0.4229		36/267	35226963	55,12951	2203	4300	6503	SO:0001819	synonymous_variant	127534	exon2			GGTGTACGTGGTG		CCDS383.1	1p35-p34	2008-05-14	2007-11-06		ENSG00000189433	ENSG00000189433		"""Ion channels / Gap junction proteins (connexins)"""	4286	protein-coding gene	gene with protein product	"""connexin 30.3"""	605425	"""gap junction protein, beta 4 (connexin 30.3)"", ""gap junction protein, beta 4"""				Standard	NM_153212		Approved	CX30.3	uc001bxv.1	Q9NTQ9	OTTHUMG00000004052	ENST00000339480.1:c.108C>T	1.37:g.35226963C>T		139.0	0.0	0		125.0	63.0	0.504	NM_153212	B3KQ82	Silent	SNP	ENST00000339480.1	37	CCDS383.1																																																																																			C|0.996;T|0.004	0.004	strong		0.582	GJB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011560.1	NM_153212	
OSBPL3	26031	hgsc.bcm.edu	37	7	24905795	24905795	+	Missense_Mutation	SNP	C	C	T	rs201132926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:24905795C>T	ENST00000313367.2	-	6	894	c.443G>A	c.(442-444)cGt>cAt	p.R148H	OSBPL3_ENST00000396429.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000409069.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000353930.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000352860.1_Missense_Mutation_p.R148H|OSBPL3_ENST00000431825.2_Missense_Mutation_p.R148H|OSBPL3_ENST00000396431.1_Missense_Mutation_p.R148H	NM_015550.2	NP_056365.1	Q9H4L5	OSBL3_HUMAN	oxysterol binding protein-like 3	148					lipid transport (GO:0006869)	cytosol (GO:0005829)|membrane (GO:0016020)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	cholesterol binding (GO:0015485)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(19)|prostate(1)|skin(3)|urinary_tract(1)	43						TTCATTCTGACGATACATTCT	0.398													C|||	2	0.000399361	0.0008	0.0	5008	,	,		20987	0.0		0.0	False		,,,				2504	0.001				p.R148H		Atlas-SNP	.											.	OSBPL3	100	.	0			c.G443A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	164.0	135.0	145.0		443,443,443,443	5.6	1.0	7		145	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense,missense	OSBPL3	NM_015550.2,NM_145320.1,NM_145321.1,NM_145322.1	29,29,29,29	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	148/888,148/857,148/852,148/821	24905795	2,13004	2203	4300	6503	SO:0001583	missense	26031	exon6			TTCTGACGATACA	AB014604	CCDS5390.1, CCDS5391.1, CCDS5392.1, CCDS47564.1	7p15.3	2013-01-10			ENSG00000070882	ENSG00000070882		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16370	protein-coding gene	gene with protein product		606732		OSBP3		9734811	Standard	XM_005249698		Approved	ORP-3, ORP3, KIAA0704	uc003sxf.3	Q9H4L5	OTTHUMG00000023277	ENST00000313367.2:c.443G>A	7.37:g.24905795C>T	ENSP00000315410:p.Arg148His	98.0	0.0	0		135.0	39.0	0.288889	NM_145321	A4D167|A4D168|A4D169|A4D170|A4D171|A4D172|B8ZZ79|B8ZZP0|O14591|O43357|O43358|Q8N702|Q8N703|Q8N704|Q8NFH0|Q8NFH1|Q8NI12|Q8NI13|Q9BZF4|Q9UED6	Missense_Mutation	SNP	ENST00000313367.2	37	CCDS5390.1	.	.	.	.	.	.	.	.	.	.	C	35	5.425170	0.96131	2.27E-4	1.16E-4	ENSG00000070882	ENST00000313367;ENST00000352860;ENST00000353930;ENST00000431825;ENST00000396431;ENST00000396429;ENST00000409069	T;T;T;T;T;T;T	0.55588	1.89;0.51;0.57;1.85;0.51;0.57;1.85	5.63	5.63	0.86233	Pleckstrin homology domain (1);	0.000000	0.85682	D	0.000000	T	0.75012	0.3792	M	0.78637	2.42	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;1.0;1.0;0.999	T	0.74771	-0.3552	10	0.51188	T	0.08	-2.461	20.0499	0.97621	0.0:1.0:0.0:0.0	.	148;148;148;148	Q9H4L5-4;Q9H4L5-2;Q9H4L5-3;Q9H4L5	.;.;.;OSBL3_HUMAN	H	148	ENSP00000315410:R148H;ENSP00000315331:R148H;ENSP00000315277:R148H;ENSP00000389779:R148H;ENSP00000379708:R148H;ENSP00000379706:R148H;ENSP00000386953:R148H	ENSP00000315410:R148H	R	-	2	0	OSBPL3	24872320	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.752000	0.85141	2.798000	0.96311	0.655000	0.94253	CGT	.	.	weak		0.398	OSBPL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214085.2		
OVCH1	341350	hgsc.bcm.edu	37	12	29649191	29649191	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:29649191C>T	ENST00000318184.5	-	3	203	c.204G>A	c.(202-204)gaG>gaA	p.E68E		NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	68	Peptidase S1 1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)			NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					AGAAGTGGTGCTCATCTGATT	0.448																																					p.E68E		Atlas-SNP	.											.	OVCH1	195	.	0			c.G204A						PASS	.						67.0	67.0	67.0					12																	29649191		1951	4150	6101	SO:0001819	synonymous_variant	341350	exon3			GTGGTGCTCATCT	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.204G>A	12.37:g.29649191C>T		35.0	0.0	0		37.0	7.0	0.189189	NM_183378		Silent	SNP	ENST00000318184.5	37																																																																																				.	.	none		0.448	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
BRAF	673	hgsc.bcm.edu	37	7	140453155	140453155	+	Missense_Mutation	SNP	C	C	T	rs397516896		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140453155C>T	ENST00000288602.6	-	15	1840	c.1780G>A	c.(1780-1782)Gat>Aat	p.D594N		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	594	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> G (in NHL). {ECO:0000269|PubMed:14612909}.		activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.D594N(9)|p.D594H(2)	SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	AGACCAAAATCACCTATTTTT	0.378		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome																												p.D594N	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	BRAF,rectum,carcinoma,0,77	BRAF	36346	77	11	Substitution - Missense(11)	skin(6)|large_intestine(2)|lung(2)|haematopoietic_and_lymphoid_tissue(1)	c.G1780A						PASS	.						106.0	100.0	102.0					7																	140453155		2203	4300	6503	SO:0001583	missense	673	exon15	Familial Cancer Database	CFC, CFCS	CAAAATCACCTAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1780G>A	7.37:g.140453155C>T	ENSP00000288602:p.Asp594Asn	74.0	0.0	0		71.0	20.0	0.28169	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.	.	.	.	.	.	.	.	.	.	C	36	5.616687	0.96649	.	.	ENSG00000157764	ENST00000288602	D	0.99849	-7.15	5.65	5.65	0.86999	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	D	0.99883	0.9944	M	0.94021	3.485	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	D	0.96728	0.9537	10	0.87932	D	0	.	19.7917	0.96461	0.0:1.0:0.0:0.0	.	594	P15056	BRAF_HUMAN	N	594	ENSP00000288602:D594N	ENSP00000288602:D594N	D	-	1	0	BRAF	140099624	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.702000	0.84576	2.686000	0.91538	0.650000	0.86243	GAT	.	.	none		0.378	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
PTPRG	5793	hgsc.bcm.edu	37	3	61975387	61975387	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:61975387G>A	ENST00000474889.1	+	3	656	c.279G>A	c.(277-279)gcG>gcA	p.A93A	PTPRG_ENST00000295874.10_Silent_p.A93A	NM_002841.3	NP_002832.3	P23470	PTPRG_HUMAN	protein tyrosine phosphatase, receptor type, G	93	Alpha-carbonic anhydrase.				brain development (GO:0007420)|negative regulation of epithelial cell migration (GO:0010633)|negative regulation of neuron projection development (GO:0010977)|peptidyl-tyrosine dephosphorylation (GO:0035335)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|liver(2)|lung(15)|ovary(7)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	62				BRCA - Breast invasive adenocarcinoma(55;0.000376)|KIRC - Kidney renal clear cell carcinoma(10;0.0499)|Kidney(10;0.065)		ACCAGTATGCGCGTGTTGGGG	0.483																																					p.A93A		Atlas-SNP	.											PTPRG,NS,carcinoma,0,1	PTPRG	153	1	0			c.G279A						PASS	.						117.0	107.0	111.0					3																	61975387		2203	4300	6503	SO:0001819	synonymous_variant	5793	exon3			GTATGCGCGTGTT	L09247	CCDS2895.1	3p21-p14	2013-02-11			ENSG00000144724	ENSG00000144724		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9671	protein-coding gene	gene with protein product		176886		PTPG		1711217	Standard	NM_002841		Approved	RPTPG	uc003dlb.3	P23470	OTTHUMG00000158660	ENST00000474889.1:c.279G>A	3.37:g.61975387G>A		76.0	0.0	0		108.0	61.0	0.564815	NM_002841	B2RU12|B7ZLX5|Q15623|Q59EE0|Q68DU5	Silent	SNP	ENST00000474889.1	37	CCDS2895.1																																																																																			.	.	none		0.483	PTPRG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351674.1	NM_002841	
CLNK	116449	hgsc.bcm.edu	37	4	10502936	10502936	+	Missense_Mutation	SNP	G	G	A	rs190441710	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:10502936G>A	ENST00000226951.6	-	18	1323	c.1084C>T	c.(1084-1086)Cgc>Tgc	p.R362C	CLNK_ENST00000515667.1_Missense_Mutation_p.R100C	NM_052964.2	NP_443196.2	Q7Z7G1	CLNK_HUMAN	cytokine-dependent hematopoietic cell linker	362	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|positive regulation of signal transduction (GO:0009967)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	intracellular (GO:0005622)	SH3/SH2 adaptor activity (GO:0005070)			NS(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(1)	17						TCCAGGAAGCGTATTTTTACA	0.468													G|||	7	0.00139776	0.0	0.0	5008	,	,		19909	0.0		0.007	False		,,,				2504	0.0				p.R362C	GBM(87;402 1286 6949 13902 35851)	Atlas-SNP	.											.	CLNK	85	.	0			c.C1084T						PASS	.						82.0	78.0	79.0					4																	10502936		1884	4125	6009	SO:0001583	missense	116449	exon18			GGAAGCGTATTTT	AB032369	CCDS47024.1	4p16.1	2013-02-14			ENSG00000109684	ENSG00000109684		"""SH2 domain containing"""	17438	protein-coding gene	gene with protein product	"""mast cell immunoreceptor signal transducer"""	611434				10562326, 10744659	Standard	NM_052964		Approved	MIST	uc003gmo.4	Q7Z7G1	OTTHUMG00000160062	ENST00000226951.6:c.1084C>T	4.37:g.10502936G>A	ENSP00000226951:p.Arg362Cys	110.0	0.0	0		101.0	50.0	0.49505	NM_052964	Q05C27|Q9P2U9	Missense_Mutation	SNP	ENST00000226951.6	37	CCDS47024.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	25.4	4.637615	0.87760	.	.	ENSG00000109684	ENST00000226951;ENST00000515667;ENST00000429087	D;D	0.89196	-2.48;-2.48	5.39	5.39	0.77823	SH2 motif (4);	0.000000	0.64402	D	0.000001	D	0.91439	0.7298	M	0.64260	1.97	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.92357	0.5894	10	0.87932	D	0	-20.0915	16.6639	0.85247	0.0:0.0:1.0:0.0	.	362	Q7Z7G1	CLNK_HUMAN	C	362;100;326	ENSP00000226951:R362C;ENSP00000427256:R100C	ENSP00000226951:R362C	R	-	1	0	CLNK	10112034	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	8.149000	0.89632	2.515000	0.84797	0.650000	0.86243	CGC	G|0.998;A|0.002	0.002	strong		0.468	CLNK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359047.1	NM_052964	
GPM6A	2823	hgsc.bcm.edu	37	4	176573028	176573028	+	Silent	SNP	T	T	C	rs72702639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:176573028T>C	ENST00000280187.7	-	5	543	c.498A>G	c.(496-498)acA>acG	p.T166T	GPM6A_ENST00000515090.1_Silent_p.T159T|GPM6A_ENST00000393658.2_Silent_p.T166T|GPM6A_ENST00000506894.1_Silent_p.T155T	NM_005277.4	NP_005268.1	P51674	GPM6A_HUMAN	glycoprotein M6A	166					neural retina development (GO:0003407)|neuron migration (GO:0001764)|neuron projection morphogenesis (GO:0048812)|positive regulation of filopodium assembly (GO:0051491)|stem cell differentiation (GO:0048863)|synapse assembly (GO:0007416)	axonal growth cone (GO:0044295)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|integral component of membrane (GO:0016021)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	calcium channel activity (GO:0005262)			NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(16)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	33		Breast(14;7.35e-05)|Melanoma(52;0.00909)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;9.21e-19)|Epithelial(43;3.01e-17)|OV - Ovarian serous cystadenocarcinoma(60;2.02e-09)|STAD - Stomach adenocarcinoma(60;0.00083)|GBM - Glioblastoma multiforme(59;0.00168)|LUSC - Lung squamous cell carcinoma(193;0.0388)		CCTCCACTAATGTGGTGTTCC	0.458													T|||	138	0.0275559	0.0008	0.0072	5008	,	,		18223	0.0		0.0308	False		,,,				2504	0.1033				p.T166T		Atlas-SNP	.											.	GPM6A	70	.	0			c.A498G						PASS	.	T	,,	18,4388	25.3+/-52.1	1,16,2186	142.0	131.0	134.0		498,498,465	-11.2	0.0	4	dbSNP_130	134	174,8426	78.6+/-141.3	4,166,4130	no	coding-synonymous,coding-synonymous,coding-synonymous	GPM6A	NM_005277.3,NM_201591.1,NM_201592.1	,,	5,182,6316	CC,CT,TT		2.0233,0.4085,1.4762	,,	166/279,166/279,155/268	176573028	192,12814	2203	4300	6503	SO:0001819	synonymous_variant	2823	exon4			CACTAATGTGGTG		CCDS3824.1, CCDS54822.1, CCDS58936.1	4q34	2008-08-29				ENSG00000150625			4460	protein-coding gene	gene with protein product		601275		GPM6		8661015, 18574501	Standard	NM_005277		Approved		uc003iug.4	P51674		ENST00000280187.7:c.498A>G	4.37:g.176573028T>C		64.0	0.0	0		73.0	39.0	0.534247	NM_201591	B7Z642|E9PHI5|Q92602	Silent	SNP	ENST00000280187.7	37	CCDS3824.1																																																																																			T|0.986;C|0.014	0.014	strong		0.458	GPM6A-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362163.1		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230312	23230312	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230312C>T	ENST00000526893.1	+	1	353	c.79C>T	c.(79-81)Ctg>Ttg	p.L27L	IGLL5_ENST00000532223.2_Silent_p.L27L|IGLL5_ENST00000531372.1_Silent_p.L27L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	27						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CTGGCCCCTGCTGCTGCTGGG	0.667																																					p.L27L		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,-2,1	IGLL5	26	1	0			c.C79T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CCCCTGCTGCTGC	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.79C>T	22.37:g.23230312C>T		111.0	0.0	0		125.0	43.0	0.344	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
IL33	90865	hgsc.bcm.edu	37	9	6254467	6254467	+	Missense_Mutation	SNP	G	G	A	rs148943384		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:6254467G>A	ENST00000381434.3	+	6	539	c.526G>A	c.(526-528)Ggt>Agt	p.G176S	IL33_ENST00000417746.2_Missense_Mutation_p.G50S|IL33_ENST00000456383.2_Missense_Mutation_p.G134S	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	176					extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)			breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		GTAAGGTGACGGTGTTGATGG	0.333																																					p.G176S		Atlas-SNP	.											.	IL33	27	.	0			c.G526A						PASS	.	G	SER/GLY,SER/GLY,SER/GLY	0,4406		0,0,2203	73.0	69.0	71.0		400,148,526	1.6	0.0	9	dbSNP_134	71	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	IL33	NM_001199640.1,NM_001199641.1,NM_033439.3	56,56,56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging	134/229,50/145,176/271	6254467	1,13005	2203	4300	6503	SO:0001583	missense	90865	exon7			GGTGACGGTGTTG	AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.526G>A	9.37:g.6254467G>A	ENSP00000370842:p.Gly176Ser	73.0	0.0	0		89.0	4.0	0.0449438	NM_033439	B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Missense_Mutation	SNP	ENST00000381434.3	37	CCDS6468.1	.	.	.	.	.	.	.	.	.	.	G	15.73	2.919265	0.52546	0.0	1.16E-4	ENSG00000137033	ENST00000417746;ENST00000456383;ENST00000381434	T;T;T	0.51817	0.69;0.69;0.69	4.47	1.57	0.23409	.	2.047450	0.01906	N	0.039500	T	0.35653	0.0939	L	0.29908	0.895	0.80722	D	1	B;B;B	0.26602	0.06;0.154;0.06	B;B;B	0.13407	0.005;0.009;0.009	T	0.33727	-0.9857	10	0.72032	D	0.01	0.2295	3.6079	0.08049	0.2088:0.0:0.5934:0.1978	.	50;134;176	B4DJ35;B4E1Q9;O95760	.;.;IL33_HUMAN	S	50;134;176	ENSP00000394039:G50S;ENSP00000414238:G134S;ENSP00000370842:G176S	ENSP00000370842:G176S	G	+	1	0	IL33	6244467	0.020000	0.18652	0.000000	0.03702	0.032000	0.12392	0.634000	0.24614	0.227000	0.20999	0.655000	0.94253	GGT	G|1.000;A|0.000	0.000	weak		0.333	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1	NM_033439	
RYR3	6263	hgsc.bcm.edu	37	15	34137131	34137131	+	Silent	SNP	G	G	A	rs118177681	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:34137131G>A	ENST00000389232.4	+	93	13435	c.13365G>A	c.(13363-13365)gaG>gaA	p.E4455E	RYR3_ENST00000415757.3_Silent_p.E4450E	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	4455					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)			NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		TTAATGACGAGGAAGAGGAAG	0.463													G|||	42	0.00838658	0.0	0.013	5008	,	,		19806	0.0		0.006	False		,,,				2504	0.0276				p.E4455E		Atlas-SNP	.											.	RYR3	760	.	0			c.G13365A						PASS	.	G		11,3879		0,11,1934	135.0	126.0	129.0		13365	-0.3	1.0	15	dbSNP_132	129	88,8196		0,88,4054	no	coding-synonymous	RYR3	NM_001036.3		0,99,5988	AA,AG,GG		1.0623,0.2828,0.8132		4455/4871	34137131	99,12075	1945	4142	6087	SO:0001819	synonymous_variant	6263	exon93			TGACGAGGAAGAG		CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.13365G>A	15.37:g.34137131G>A		112.0	0.0	0		102.0	56.0	0.54902	NM_001036	O15175|Q15412	Silent	SNP	ENST00000389232.4	37	CCDS45210.1																																																																																			G|0.993;A|0.007	0.007	strong		0.463	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1		
TNS1	7145	hgsc.bcm.edu	37	2	218686643	218686643	+	Missense_Mutation	SNP	T	T	A	rs112371945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:218686643T>A	ENST00000171887.4	-	23	3532	c.3080A>T	c.(3079-3081)gAg>gTg	p.E1027V	TNS1_ENST00000430930.1_Missense_Mutation_p.E1006V|TNS1_ENST00000419504.1_Missense_Mutation_p.E1014V	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1027					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		TGCCACAGACTCCACATAGCT	0.627													T|||	3	0.000599042	0.0	0.0	5008	,	,		17582	0.0		0.003	False		,,,				2504	0.0				p.E1027V		Atlas-SNP	.											.	TNS1	251	.	0			c.A3080T						PASS	.	T	VAL/GLU	0,4400		0,0,2200	16.0	18.0	17.0		3080	4.1	1.0	2	dbSNP_132	17	12,8582		0,12,4285	yes	missense	TNS1	NM_022648.4	121	0,12,6485	AA,AT,TT		0.1396,0.0,0.0924	probably-damaging	1027/1736	218686643	12,12982	2200	4297	6497	SO:0001583	missense	7145	exon23			ACAGACTCCACAT	AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.3080A>T	2.37:g.218686643T>A	ENSP00000171887:p.Glu1027Val	95.0	0.0	0		126.0	68.0	0.539683	NM_022648	Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	22	0.010073260073260074	6	0.012195121951219513	2	0.0055248618784530384	6	0.01048951048951049	8	0.010554089709762533	T	22.7	4.320848	0.81469	0.0	0.001396	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	D;T;D;D	0.93859	-3.3;1.79;-3.19;-3.12	4.11	4.11	0.48088	.	0.793281	0.11520	N	0.555860	D	0.92675	0.7672	L	0.32530	0.975	0.80722	D	1	D;D;D	0.76494	0.999;0.999;0.984	D;D;P	0.85130	0.997;0.994;0.844	D	0.91199	0.4990	10	0.62326	D	0.03	.	13.4292	0.61044	0.0:0.0:0.0:1.0	.	1027;1006;1014	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	V	1027;165;1014;1006	ENSP00000171887:E1027V;ENSP00000394171:E165V;ENSP00000408724:E1014V;ENSP00000406016:E1006V	ENSP00000171887:E1027V	E	-	2	0	TNS1	218394888	1.000000	0.71417	0.994000	0.49952	0.792000	0.44763	7.653000	0.83643	1.631000	0.50456	0.459000	0.35465	GAG	T|0.996;A|0.004	0.004	strong		0.627	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2	NM_022648	
SORBS2	8470	hgsc.bcm.edu	37	4	186536235	186536235	+	Silent	SNP	G	G	A	rs373495088		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:186536235G>A	ENST00000284776.7	-	16	3227	c.2718C>T	c.(2716-2718)caC>caT	p.H906H	SORBS2_ENST00000437304.2_Silent_p.H630H|SORBS2_ENST00000448662.2_Silent_p.H467H|SORBS2_ENST00000449407.2_Silent_p.H450H|SORBS2_ENST00000498125.1_5'UTR|SORBS2_ENST00000393528.3_Silent_p.H472H|SORBS2_ENST00000418609.1_Silent_p.H810H|SORBS2_ENST00000355634.5_Silent_p.H1006H|SORBS2_ENST00000431808.1_Silent_p.H906H|SORBS2_ENST00000319471.9_Silent_p.H537H	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	906	SH3 1. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)			endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		CCACTCTCCCGTGGTGTTCTC	0.468																																					p.H1006H	Esophageal Squamous(153;41 2433 9491 36028)	Atlas-SNP	.											.	SORBS2	300	.	0			c.C3018T						PASS	.	G	,,,,,,,	0,4406		0,0,2203	145.0	134.0	138.0		1350,1611,1401,1890,2430,894,1416,2718	-6.9	0.3	4		138	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	SORBS2	NM_001145670.1,NM_001145671.1,NM_001145672.1,NM_001145673.1,NM_001145674.1,NM_001145675.1,NM_003603.5,NM_021069.4	,,,,,,,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,,,,,,,	450/645,537/732,467/662,630/825,810/1005,298/493,472/667,906/1101	186536235	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8470	exon19			TCTCCCGTGGTGT		CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.2718C>T	4.37:g.186536235G>A		129.0	0.0	0		142.0	71.0	0.5	NM_001270771	A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																			.	.	weak		0.468	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3	NM_003603	
KIAA1217	56243	hgsc.bcm.edu	37	10	24833407	24833407	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:24833407T>C	ENST00000376454.3	+	19	5238	c.5208T>C	c.(5206-5208)cgT>cgC	p.R1736R	KIAA1217_ENST00000396446.1_Intron|KIAA1217_ENST00000307544.6_Intron|KIAA1217_ENST00000376462.1_Intron|KIAA1217_ENST00000396445.1_Intron|KIAA1217_ENST00000458595.1_Intron|KIAA1217_ENST00000376452.3_Intron|KIAA1217_ENST00000376451.2_Silent_p.R1419R	NM_019590.3	NP_062536.2	Q5T5P2	SKT_HUMAN	KIAA1217	1736					embryonic skeletal system development (GO:0048706)	cytoplasm (GO:0005737)				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						CAGCTTCACGTAAGGTATCTT	0.493																																					p.R1736R		Atlas-SNP	.											KIAA1217,colon,carcinoma,+1,1	KIAA1217	235	1	0			c.T5208C						scavenged	.						45.0	45.0	45.0					10																	24833407		2203	4300	6503	SO:0001819	synonymous_variant	56243	exon19			TTCACGTAAGGTA	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.5208T>C	10.37:g.24833407T>C		48.0	0.0	0		65.0	3.0	0.0461538	NM_019590	A5LHW9|A6NLF3|A6PVQ5|A6PVQ6|A6PVQ7|B9EGK4|Q4KMG4|Q5T5P3|Q5T7H3|Q6MZZ6|Q6ZUI4|Q8WV45|Q9NSR2|Q9ULK3	Silent	SNP	ENST00000376454.3	37	CCDS31165.1																																																																																			.	.	none		0.493	KIAA1217-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047223.2	NM_019590	
AFAP1L2	84632	hgsc.bcm.edu	37	10	116064528	116064528	+	Missense_Mutation	SNP	G	G	A	rs73365341	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:116064528G>A	ENST00000304129.4	-	11	1263	c.1234C>T	c.(1234-1236)Ctc>Ttc	p.L412F	AFAP1L2_ENST00000491814.1_5'Flank|AFAP1L2_ENST00000545353.1_Missense_Mutation_p.L465F|AFAP1L2_ENST00000369271.3_Missense_Mutation_p.L412F			Q8N4X5	AF1L2_HUMAN	actin filament associated protein 1-like 2	412	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				inflammatory response (GO:0006954)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of interleukin-6 production (GO:0032675)|regulation of mitotic cell cycle (GO:0007346)	cytoplasm (GO:0005737)	protein tyrosine kinase activator activity (GO:0030296)|SH2 domain binding (GO:0042169)|SH3 domain binding (GO:0017124)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|liver(1)|lung(11)|ovary(1)|prostate(2)	21		Colorectal(252;0.175)|Breast(234;0.231)		Epithelial(162;0.0219)|all cancers(201;0.0561)		AAGGAGTAGAGGTGGTCGGGG	0.682													G|||	531	0.10603	0.354	0.0375	5008	,	,		12908	0.0		0.0199	False		,,,				2504	0.0174				p.L412F		Atlas-SNP	.											.	AFAP1L2	90	.	0			c.C1234T						PASS	.	G	PHE/LEU,PHE/LEU	1464,2940	461.5+/-352.9	257,950,995	39.0	38.0	38.0		1234,1234	5.3	1.0	10	dbSNP_130	38	165,8435	76.3+/-139.0	3,159,4138	yes	missense,missense	AFAP1L2	NM_001001936.1,NM_032550.2	22,22	260,1109,5133	AA,AG,GG		1.9186,33.2425,12.5269	probably-damaging,probably-damaging	412/819,412/815	116064528	1629,11375	2202	4300	6502	SO:0001583	missense	84632	exon11			AGTAGAGGTGGTC	BC024314	CCDS31286.1, CCDS31287.1	10q26.11	2013-01-10	2007-02-07	2007-02-07	ENSG00000169129	ENSG00000169129		"""Pleckstrin homology (PH) domain containing"""	25901	protein-coding gene	gene with protein product		612420	"""KIAA1914"""	KIAA1914		11572484, 17412687	Standard	XM_005270239		Approved	FLJ14564, Em:AC005383.4, XB130	uc001lbn.3	Q8N4X5	OTTHUMG00000019086	ENST00000304129.4:c.1234C>T	10.37:g.116064528G>A	ENSP00000303042:p.Leu412Phe	36.0	0.0	0		24.0	14.0	0.583333	NM_032550	A8K6P7|B3KVQ8|Q2UZW3|Q8TB54|Q96PX4|Q96SY5	Missense_Mutation	SNP	ENST00000304129.4	37	CCDS31286.1	224	0.10256410256410256	195	0.39634146341463417	15	0.04143646408839779	0	0.0	14	0.018469656992084433	G	26.3	4.722438	0.89298	0.332425	0.019186	ENSG00000169129	ENST00000369271;ENST00000304129;ENST00000392974;ENST00000545353	T;T;T	0.75589	-0.95;-0.95;-0.95	5.3	5.3	0.74995	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.85682	D	0.000000	T	0.00012	0.0000	M	0.62723	1.935	0.09310	P	0.999999814385	D;D;D;D;D	0.89917	1.0;1.0;0.997;1.0;1.0	D;D;D;D;D	0.97110	0.998;0.999;0.984;0.998;1.0	T	0.02104	-1.1213	9	0.45353	T	0.12	-16.927	18.9486	0.92632	0.0:0.0:1.0:0.0	.	465;466;440;412;412	F5GZE1;B7Z2Q0;Q8N4X5-4;Q8N4X5-2;Q8N4X5	.;.;.;.;AF1L2_HUMAN	F	412;412;439;465	ENSP00000358276:L412F;ENSP00000303042:L412F;ENSP00000444511:L465F	ENSP00000303042:L412F	L	-	1	0	AFAP1L2	116054518	1.000000	0.71417	1.000000	0.80357	0.933000	0.57130	7.973000	0.88032	2.470000	0.83445	0.563000	0.77884	CTC	G|0.884;A|0.116	0.116	strong		0.682	AFAP1L2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050462.1	NM_032550	
HDAC4	9759	hgsc.bcm.edu	37	2	240036848	240036848	+	Silent	SNP	C	C	T	rs114495208	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:240036848C>T	ENST00000345617.3	-	13	2468	c.1677G>A	c.(1675-1677)aaG>aaA	p.K559K	HDAC4_ENST00000541256.1_Silent_p.K533K|HDAC4_ENST00000543185.1_Silent_p.K143K	NM_006037.3	NP_006028.2	P56524	HDAC4_HUMAN	histone deacetylase 4	559					B cell activation (GO:0042113)|B cell differentiation (GO:0030183)|cardiac muscle hypertrophy in response to stress (GO:0014898)|chromatin remodeling (GO:0006338)|histone deacetylation (GO:0016575)|histone H3 deacetylation (GO:0070932)|histone H4 deacetylation (GO:0070933)|inflammatory response (GO:0006954)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|osteoblast development (GO:0002076)|peptidyl-lysine deacetylation (GO:0034983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein sumoylation (GO:0033235)|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 cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of gene expression, epigenetic (GO:0040029)|regulation of protein binding (GO:0043393)|regulation of skeletal muscle fiber development (GO:0048742)|response to denervation involved in regulation of muscle adaptation (GO:0014894)|response to drug (GO:0042493)|response to interleukin-1 (GO:0070555)|skeletal system development (GO:0001501)|transcription, DNA-templated (GO:0006351)	A band (GO:0031672)|actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone deacetylase complex (GO:0000118)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)|Z disc (GO:0030018)	activating transcription factor binding (GO:0033613)|core promoter binding (GO:0001047)|histone deacetylase activity (GO:0004407)|histone deacetylase binding (GO:0042826)|NAD-dependent histone deacetylase activity (H3-K14 specific) (GO:0032041)|NAD-dependent histone deacetylase activity (H3-K18 specific) (GO:0097372)|NAD-dependent histone deacetylase activity (H3-K9 specific) (GO:0046969)|NAD-dependent histone deacetylase activity (H4-K16 specific) (GO:0046970)|potassium ion binding (GO:0030955)|protein deacetylase activity (GO:0033558)|repressing transcription factor binding (GO:0070491)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|kidney(2)|large_intestine(7)|lung(27)|ovary(3)|pancreas(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(5)	62		all_epithelial(40;1.45e-17)|Breast(86;1.53e-05)|Renal(207;0.000355)|all_lung(227;0.0121)|Ovarian(221;0.0183)|Lung NSC(271;0.0413)|Melanoma(123;0.0749)|all_hematologic(139;0.159)		Epithelial(121;6.38e-25)|OV - Ovarian serous cystadenocarcinoma(60;2.48e-12)|Kidney(56;6.04e-08)|KIRC - Kidney renal clear cell carcinoma(57;1.18e-06)|BRCA - Breast invasive adenocarcinoma(100;3.99e-05)|Lung(119;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.04)		TGGGCTCCTGCTTCACCTGCA	0.687													C|||	13	0.00259585	0.0	0.0072	5008	,	,		16655	0.0		0.007	False		,,,				2504	0.001				p.K559K		Atlas-SNP	.											.	HDAC4	127	.	0			c.G1677A						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	66.0	73.0	71.0		1677	2.3	1.0	2	dbSNP_132	71	44,8554	29.0+/-79.6	0,44,4255	no	coding-synonymous	HDAC4	NM_006037.3		0,49,6453	TT,TC,CC		0.5117,0.1135,0.3768		559/1085	240036848	49,12955	2203	4299	6502	SO:0001819	synonymous_variant	9759	exon13			CTCCTGCTTCACC	AB006626	CCDS2529.1	2q37.3	2014-02-12			ENSG00000068024	ENSG00000068024			14063	protein-coding gene	gene with protein product		605314	"""brachydactyly-mental retardation syndrome"""	BDMR		10206986, 10220385, 20691407	Standard	NM_006037		Approved	KIAA0288, HDAC-A, HDACA, HD4, HA6116, HDAC-4	uc002vyk.4	P56524	OTTHUMG00000133344	ENST00000345617.3:c.1677G>A	2.37:g.240036848C>T		89.0	0.0	0		125.0	60.0	0.48	NM_006037	Q9UND6	Silent	SNP	ENST00000345617.3	37	CCDS2529.1																																																																																			C|0.996;T|0.004	0.004	strong		0.687	HDAC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257174.2	NM_006037	
KDM5B	10765	hgsc.bcm.edu	37	1	202715288	202715288	+	Missense_Mutation	SNP	G	G	A	rs144876400		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202715288G>A	ENST00000367265.3	-	15	3344	c.2180C>T	c.(2179-2181)cCt>cTt	p.P727L	KDM5B_ENST00000367264.2_Missense_Mutation_p.P763L	NM_006618.3	NP_006609.3	Q9UGL1	KDM5B_HUMAN	lysine (K)-specific demethylase 5B	727					histone H3-K4 demethylation (GO:0034720)|histone H3-K4 demethylation, trimethyl-H3-K4-specific (GO:0034721)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (H3-dimethyl-K4 specific) (GO:0034648)|histone demethylase activity (H3-trimethyl-K4 specific) (GO:0034647)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors (GO:0016706)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(2)|ovary(2)|skin(1)|urinary_tract(1)	6						ATATTTGTAAGGAGGACAGGA	0.388																																					p.P727L		Atlas-SNP	.											.	KDM5B	166	.	0			c.C2180T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	122.0	106.0	112.0		2180	5.1	0.9	1	dbSNP_134	112	2,8598	1.2+/-3.3	0,2,4298	yes	missense	KDM5B	NM_006618.3	98	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	benign	727/1545	202715288	2,13004	2203	4300	6503	SO:0001583	missense	10765	exon15			TTGTAAGGAGGAC	AJ243706	CCDS30974.1	1q32.1	2014-06-12	2009-04-06	2009-04-06	ENSG00000117139	ENSG00000117139		"""Chromatin-modifying enzymes / K-demethylases"", ""Zinc fingers, PHD-type"""	18039	protein-coding gene	gene with protein product	"""cancer/testis antigen 31"", ""protein phosphatase 1, regulatory subunit 98"""	605393	"""Jumonji, AT rich interactive domain 1B (RBP2-like)"", ""jumonji, AT rich interactive domain 1B"""	JARID1B		11483573, 11478881	Standard	NM_006618		Approved	RBBP2H1A, PLU-1, CT31, PPP1R98	uc001gyf.3	Q9UGL1	OTTHUMG00000041401	ENST00000367265.3:c.2180C>T	1.37:g.202715288G>A	ENSP00000356234:p.Pro727Leu	108.0	0.0	0		130.0	52.0	0.4	NM_006618	O95811|Q15752|Q9Y3Q5	Missense_Mutation	SNP	ENST00000367265.3	37	CCDS30974.1	.	.	.	.	.	.	.	.	.	.	G	12.37	1.916623	0.33815	0.0	2.33E-4	ENSG00000117139	ENST00000367265;ENST00000538292;ENST00000367264;ENST00000235790;ENST00000543924	D;D;D	0.88201	-2.35;-2.35;-2.35	5.97	5.06	0.68205	Zinc finger, C5HC2-type (1);	0.356049	0.34555	N	0.003863	D	0.85106	0.5621	L	0.52905	1.665	0.42064	D	0.991176	B;B	0.16396	0.017;0.005	B;B	0.19148	0.011;0.024	T	0.79704	-0.1692	10	0.34782	T	0.22	-10.6553	10.7795	0.46369	0.1402:0.0:0.8598:0.0	.	763;727	Q9UGL1-2;Q9UGL1	.;KDM5B_HUMAN	L	727;569;763;569;96	ENSP00000356234:P727L;ENSP00000356233:P763L;ENSP00000235790:P569L	ENSP00000235790:P569L	P	-	2	0	KDM5B	200981911	0.987000	0.35691	0.930000	0.37139	0.965000	0.64279	3.717000	0.54911	2.836000	0.97738	0.655000	0.94253	CCT	G|1.000;A|0.000	0.000	weak		0.388	KDM5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099184.2	NM_006618	
PCDHB13	56123	hgsc.bcm.edu	37	5	140595831	140595831	+	Silent	SNP	G	G	T	rs145378952		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140595831G>T	ENST00000341948.4	+	1	2323	c.2136G>T	c.(2134-2136)cgG>cgT	p.R712R		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	712					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TGGCGGTGCGGCTGTGTAGGA	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		15801	0.0		0.001	False		,,,				2504	0.0				p.R712R		Atlas-SNP	.											.	PCDHB13	142	.	0			c.G2136T						PASS	.	G		0,4402		0,0,2201	88.0	97.0	94.0		2136	0.2	0.8	5	dbSNP_134	94	4,8580		0,4,4288	no	coding-synonymous	PCDHB13	NM_018933.2		0,4,6489	TT,TG,GG		0.0466,0.0,0.0308		712/799	140595831	4,12982	2201	4292	6493	SO:0001819	synonymous_variant	56123	exon1			GGTGCGGCTGTGT	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.2136G>T	5.37:g.140595831G>T		67.0	0.0	0		95.0	49.0	0.515789	NM_018933	A8K9V6	Silent	SNP	ENST00000341948.4	37	CCDS4255.1																																																																																			G|1.000;T|0.000	0.000	strong		0.662	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
ANO7	50636	hgsc.bcm.edu	37	2	242144308	242144308	+	Silent	SNP	G	G	A	rs139761441	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242144308G>A	ENST00000274979.8	+	10	1183	c.1080G>A	c.(1078-1080)gcG>gcA	p.A360A	ANO7_ENST00000402430.3_Silent_p.A359A	NM_001001891.3	NP_001001891.2	Q6IWH7	ANO7_HUMAN	anoctamin 7	360					calcium activated galactosylceramide scrambling (GO:0061591)|calcium activated phosphatidylcholine scrambling (GO:0061590)|calcium activated phosphatidylserine scrambling (GO:0061589)|chloride transport (GO:0006821)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)|phospholipid scramblase activity (GO:0017128)			NS(1)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(14)|pancreas(2)|prostate(1)|skin(3)|urinary_tract(2)	32						TCCTGCCAGCGGCAGTGGTGG	0.632													G|||	4	0.000798722	0.0	0.0	5008	,	,		16608	0.0		0.004	False		,,,				2504	0.0				p.A360A		Atlas-SNP	.											.	ANO7	136	.	0			c.G1080A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	52.0	55.0	54.0		1080	-5.1	0.1	2	dbSNP_134	54	23,8577	16.6+/-54.9	0,23,4277	no	coding-synonymous	ANO7	NM_001001891.3		0,25,6478	AA,AG,GG		0.2674,0.0454,0.1922		360/934	242144308	25,12981	2203	4300	6503	SO:0001819	synonymous_variant	50636	exon10			GCCAGCGGCAGTG	AY617079	CCDS33423.1, CCDS46563.1	2q37.3	2014-04-09	2008-08-28	2008-08-28	ENSG00000146205	ENSG00000146205		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	31677	protein-coding gene	gene with protein product		605096	"""transmembrane protein 16G"""	PCANAP5, TMEM16G		14981236, 15375614, 24692353	Standard	NM_001001891		Approved	NGEP, PCANAP5L, IPCA-5	uc002wax.2	Q6IWH7	OTTHUMG00000151702	ENST00000274979.8:c.1080G>A	2.37:g.242144308G>A		64.0	0.0	0		71.0	37.0	0.521127	NM_001001891	Q6IWH6	Silent	SNP	ENST00000274979.8	37	CCDS33423.1																																																																																			G|0.998;A|0.002	0.002	strong		0.632	ANO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323509.1	NM_001001891	
TAS1R3	83756	hgsc.bcm.edu	37	1	1268462	1268462	+	Silent	SNP	G	G	A	rs138915131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1268462G>A	ENST00000339381.5	+	4	1469	c.1437G>A	c.(1435-1437)agG>agA	p.R479R		NM_152228.1	NP_689414	Q7RTX0	TS1R3_HUMAN	taste receptor, type 1, member 3	479					detection of chemical stimulus involved in sensory perception of sweet taste (GO:0001582)|G-protein coupled receptor signaling pathway (GO:0007186)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|taste receptor activity (GO:0008527)			kidney(2)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	12	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)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;3.88e-21)|Colorectal(212;0.000157)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00229)|BRCA - Breast invasive adenocarcinoma(365;0.00251)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.034)|Lung(427;0.146)		GCAGCCTCAGGACAGAGCGCC	0.667													g|||	17	0.00339457	0.0015	0.0058	5008	,	,		15673	0.0		0.0109	False		,,,				2504	0.0				p.R479R		Atlas-SNP	.											.	TAS1R3	39	.	0			c.G1437A						PASS	.	G		6,4396	14.3+/-33.2	0,6,2195	48.0	45.0	46.0		1437	-1.7	0.0	1	dbSNP_134	46	113,8475	58.7+/-120.3	0,113,4181	no	coding-synonymous	TAS1R3	NM_152228.1		0,119,6376	AA,AG,GG		1.3158,0.1363,0.9161		479/853	1268462	119,12871	2201	4294	6495	SO:0001819	synonymous_variant	83756	exon4			CCTCAGGACAGAG	AC026283	CCDS30556.1	1p36	2012-08-22			ENSG00000169962	ENSG00000169962		"""Taste receptors / Type 1"", ""GPCR / Unclassified : Taste receptors"""	15661	protein-coding gene	gene with protein product		605865				11319557	Standard	XM_006710939		Approved	T1R3	uc010nyk.2	Q7RTX0	OTTHUMG00000003071	ENST00000339381.5:c.1437G>A	1.37:g.1268462G>A		74.0	0.0	0		88.0	43.0	0.488636	NM_152228	Q5TA49|Q8NGW9	Silent	SNP	ENST00000339381.5	37	CCDS30556.1																																																																																			G|0.994;A|0.006	0.006	strong		0.667	TAS1R3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008493.1		
FBXO42	54455	hgsc.bcm.edu	37	1	16641797	16641797	+	Silent	SNP	C	C	T	rs61753288	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16641797C>T	ENST00000375592.3	-	2	333	c.117G>A	c.(115-117)gaG>gaA	p.E39E	FBXO42_ENST00000478089.1_5'UTR	NM_018994.1	NP_061867.1	Q6P3S6	FBX42_HUMAN	F-box protein 42	39										autonomic_ganglia(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	26		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00475)|all_lung(284;0.00671)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0193)|Colorectal(212;3.16e-07)|COAD - Colon adenocarcinoma(227;1.46e-05)|BRCA - Breast invasive adenocarcinoma(304;4.37e-05)|Kidney(64;0.000246)|KIRC - Kidney renal clear cell carcinoma(64;0.00336)|STAD - Stomach adenocarcinoma(313;0.0139)|READ - Rectum adenocarcinoma(331;0.0693)		GTCTAGTCTCCTCAGCCTCCA	0.502													C|||	14	0.00279553	0.0	0.0029	5008	,	,		17411	0.0		0.0119	False		,,,				2504	0.0				p.E39E		Atlas-SNP	.											.	FBXO42	53	.	0			c.G117A						PASS	.	C		8,4398	14.3+/-33.2	0,8,2195	120.0	100.0	107.0		117	-3.5	0.0	1	dbSNP_129	107	115,8485	60.2+/-122.0	0,115,4185	no	coding-synonymous	FBXO42	NM_018994.1		0,123,6380	TT,TC,CC		1.3372,0.1816,0.9457		39/718	16641797	123,12883	2203	4300	6503	SO:0001819	synonymous_variant	54455	exon2			AGTCTCCTCAGCC	BC063864	CCDS30613.1	1p36.23-p36.11	2008-02-05			ENSG00000037637	ENSG00000037637		"""F-boxes /  ""other"""""	29249	protein-coding gene	gene with protein product		609109				10718198	Standard	XM_006710698		Approved	KIAA1332, Fbx42	uc001ayg.3	Q6P3S6	OTTHUMG00000002218	ENST00000375592.3:c.117G>A	1.37:g.16641797C>T		219.0	0.0	0		246.0	110.0	0.447154	NM_018994	B3KP30|Q5TEU8|Q86XI0|Q8N3N4|Q8N5F8|Q9BRM0|Q9P2L4	Silent	SNP	ENST00000375592.3	37	CCDS30613.1																																																																																			C|0.993;T|0.007	0.007	strong		0.502	FBXO42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006285.1		
PRPF18	8559	hgsc.bcm.edu	37	10	13639490	13639490	+	Silent	SNP	C	C	T	rs2502213	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13639490C>T	ENST00000378572.3	+	2	259	c.99C>T	c.(97-99)ctC>ctT	p.L33L		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	33					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	potassium channel inhibitor activity (GO:0019870)			central_nervous_system(1)|endometrium(5)|large_intestine(5)|lung(5)|prostate(1)	17						GTAGTGAGCTCGCCAAAAAAG	0.284													C|||	136	0.0271565	0.0968	0.0072	5008	,	,		16174	0.001		0.0	False		,,,				2504	0.002				p.L33L		Atlas-SNP	.											.	PRPF18	32	.	0			c.C99T						PASS	.	C		399,4007	198.7+/-222.5	17,365,1821	92.0	93.0	93.0		99	-1.6	0.9	10	dbSNP_100	93	6,8594	4.3+/-15.6	0,6,4294	no	coding-synonymous	PRPF18	NM_003675.3		17,371,6115	TT,TC,CC		0.0698,9.0558,3.1139		33/343	13639490	405,12601	2203	4300	6503	SO:0001819	synonymous_variant	8559	exon2			TGAGCTCGCCAAA	U51990	CCDS7100.1	10p12.33	2013-06-10	2013-06-10		ENSG00000165630	ENSG00000165630			17351	protein-coding gene	gene with protein product		604993	"""PRP18 pre-mRNA processing factor 18 homolog (yeast)"", ""PRP18 pre-mRNA processing factor 18 homolog (S. cerevisiae)"""			9000057	Standard	XM_005252634		Approved	hPrp18	uc001imp.3	Q99633	OTTHUMG00000017702	ENST00000378572.3:c.99C>T	10.37:g.13639490C>T		40.0	0.0	0		43.0	22.0	0.511628	NM_003675	Q5T9P9|Q9BUI9	Silent	SNP	ENST00000378572.3	37	CCDS7100.1																																																																																			C|0.972;T|0.028	0.028	strong		0.284	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
DENND1B	163486	hgsc.bcm.edu	37	1	197482049	197482049	+	IGR	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:197482049C>A								CRB1 (34464 upstream) : DENND1B (39335 downstream)																							ATATAGAGCACCATCAAGGCT	0.368																																					p.G517V		Atlas-SNP	.											.	DENND1B	108	.	0			c.G1550T						PASS	.						115.0	99.0	105.0					1																	197482049		2203	4299	6502	SO:0001628	intergenic_variant	163486	exon21			AGAGCACCATCAA																													1.37:g.197482049C>A		108.0	0.0	0		124.0	90.0	0.725806	NM_001195215		Missense_Mutation	SNP		37		.	.	.	.	.	.	.	.	.	.	C	6.634	0.485376	0.12641	.	.	ENSG00000213047	ENST00000391979;ENST00000542760;ENST00000450419	T	0.32023	1.47	5.2	5.2	0.72013	.	0.398495	0.23317	U	0.049495	T	0.19248	0.0462	L	0.33189	0.99	0.19575	N	0.999965	B	0.21753	0.06	B	0.23574	0.047	T	0.16660	-1.0395	10	0.16896	T	0.51	.	4.781	0.13202	0.1539:0.6157:0.1487:0.0817	.	517	Q6P3S1-5	.	V	157;517;497	ENSP00000375839:G157V	ENSP00000375839:G157V	G	-	2	0	DENND1B	195748672	0.000000	0.05858	0.053000	0.19242	0.125000	0.20455	0.676000	0.25247	2.578000	0.87016	0.655000	0.94253	GGT	.	.	none	0	0.368								
VCAN	1462	hgsc.bcm.edu	37	5	82817843	82817843	+	Missense_Mutation	SNP	C	C	G	rs374590975		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:82817843C>G	ENST00000265077.3	+	7	4283	c.3718C>G	c.(3718-3720)Cct>Gct	p.P1240A	VCAN_ENST00000512590.2_Missense_Mutation_p.P1192A|VCAN_ENST00000343200.5_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.P1240A|VCAN_ENST00000502527.2_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	1240	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)			NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	CGACAGGGAACCTGGTGAAGA	0.443																																					p.P1240A		Atlas-SNP	.											.	VCAN	498	.	0			c.C3718G						PASS	.	C	ALA/PRO,ALA/PRO,,	0,4406		0,0,2203	134.0	129.0	131.0		3718,3718,,	2.5	0.0	5		131	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,intron	VCAN	NM_001164098.1,NM_004385.4,NM_001126336.2,NM_001164097.1	27,27,,	0,1,6502	GG,GC,CC		0.0116,0.0,0.0077	probably-damaging,probably-damaging,,	1240/1643,1240/3397,,	82817843	1,13005	2203	4300	6503	SO:0001583	missense	1462	exon7			AGGGAACCTGGTG	X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.3718C>G	5.37:g.82817843C>G	ENSP00000265077:p.Pro1240Ala	159.0	0.0	0		153.0	68.0	0.444444	NM_004385	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	ENST00000265077.3	37	CCDS4060.1	.	.	.	.	.	.	.	.	.	.	C	10.43	1.348713	0.24426	0.0	1.16E-4	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	D;D;D	0.87571	-2.2;-2.24;-2.27	5.39	2.49	0.30216	.	0.322422	0.27155	N	0.020667	D	0.86661	0.5986	M	0.68952	2.095	0.24807	N	0.992661	P;D	0.54397	0.944;0.966	P;P	0.50617	0.646;0.583	T	0.77571	-0.2538	10	0.40728	T	0.16	.	6.7264	0.23359	0.1164:0.5654:0.2497:0.0685	.	1240;1240	P13611-3;P13611	.;CSPG2_HUMAN	A	1240;1240;1192	ENSP00000265077:P1240A;ENSP00000342768:P1240A;ENSP00000425959:P1192A	ENSP00000265077:P1240A	P	+	1	0	VCAN	82853599	0.818000	0.29161	0.046000	0.18839	0.310000	0.27922	1.228000	0.32588	0.195000	0.20347	0.650000	0.86243	CCT	.	.	weak		0.443	VCAN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000254092.3	NM_004385	
LRRC66	339977	hgsc.bcm.edu	37	4	52862020	52862020	+	Missense_Mutation	SNP	C	C	G	rs202189181		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:52862020C>G	ENST00000343457.3	-	4	1174	c.1168G>C	c.(1168-1170)Gcc>Ccc	p.A390P		NM_001024611.1	NP_001019782.1	Q68CR7	LRC66_HUMAN	leucine rich repeat containing 66	390						integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(8)|lung(34)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	58						AGGCTGAAGGCGACAAGGAAT	0.557													C|||	1	0.000199681	0.0	0.0	5008	,	,		18727	0.0		0.0	False		,,,				2504	0.001				p.A390P		Atlas-SNP	.											.	LRRC66	128	.	0			c.G1168C						PASS	.	C	PRO/ALA	1,3953		0,1,1976	53.0	54.0	54.0		1168	4.7	1.0	4		54	4,8318		0,4,4157	yes	missense	LRRC66	NM_001024611.1	27	0,5,6133	GG,GC,CC		0.0481,0.0253,0.0407	probably-damaging	390/881	52862020	5,12271	1977	4161	6138	SO:0001583	missense	339977	exon4			TGAAGGCGACAAG	BC040414	CCDS43229.1	4q12	2008-08-08			ENSG00000188993	ENSG00000188993			34299	protein-coding gene	gene with protein product							Standard	XM_005265739		Approved		uc003gzi.3	Q68CR7	OTTHUMG00000160623	ENST00000343457.3:c.1168G>C	4.37:g.52862020C>G	ENSP00000341944:p.Ala390Pro	103.0	0.0	0		128.0	69.0	0.539062	NM_001024611		Missense_Mutation	SNP	ENST00000343457.3	37	CCDS43229.1	.	.	.	.	.	.	.	.	.	.	C	15.37	2.812710	0.50527	2.53E-4	4.81E-4	ENSG00000188993	ENST00000343457	T	0.49432	0.78	4.67	4.67	0.58626	.	0.000000	0.45867	D	0.000335	T	0.65533	0.2700	M	0.63843	1.955	0.40966	D	0.98466	D	0.89917	1.0	D	0.91635	0.999	T	0.70263	-0.4920	10	0.87932	D	0	-17.3724	14.6507	0.68794	0.0:1.0:0.0:0.0	.	390	Q68CR7	LRC66_HUMAN	P	390	ENSP00000341944:A390P	ENSP00000341944:A390P	A	-	1	0	LRRC66	52556777	0.999000	0.42202	0.997000	0.53966	0.011000	0.07611	4.870000	0.63035	2.306000	0.77630	0.467000	0.42956	GCC	.	.	weak		0.557	LRRC66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361473.1	NM_001024611	
UROS	7390	hgsc.bcm.edu	37	10	127484721	127484721	+	Missense_Mutation	SNP	A	A	G	rs17173752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:127484721A>G	ENST00000368797.4	-	8	736	c.512T>C	c.(511-513)gTt>gCt	p.V171A	UROS_ENST00000368786.1_Missense_Mutation_p.V171A|UROS_ENST00000462490.1_5'UTR	NM_000375.2	NP_000366.1	P10746	HEM4_HUMAN	uroporphyrinogen III synthase	171			V -> G (in dbSNP:rs17173752).		cellular response to amine stimulus (GO:0071418)|cellular response to arsenic-containing substance (GO:0071243)|heme biosynthetic process (GO:0006783)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to antibiotic (GO:0046677)|small molecule metabolic process (GO:0044281)|uroporphyrinogen III biosynthetic process (GO:0006780)	cytosol (GO:0005829)|mitochondrion (GO:0005739)	cofactor binding (GO:0048037)|uroporphyrinogen-III synthase activity (GO:0004852)			endometrium(2)|large_intestine(2)|lung(2)|skin(1)	7		all_lung(145;0.00756)|Lung NSC(174;0.0116)|Colorectal(57;0.0855)|all_neural(114;0.0937)|Breast(234;0.203)				TGGGTGTGCAACTGTCTGATA	0.557																																					p.V171A		Atlas-SNP	.											.	UROS	20	.	0			c.T512C						PASS	.						298.0	255.0	269.0					10																	127484721		2203	4300	6503	SO:0001583	missense	7390	exon8			TGTGCAACTGTCT	J03824	CCDS7648.1	10q25.2-q26.3	2008-07-31	2008-07-31		ENSG00000188690	ENSG00000188690	4.2.1.75		12592	protein-coding gene	gene with protein product	"""congenital erythropoietic porphyria"""	606938				2037278	Standard	NM_000375		Approved		uc001lix.4	P10746	OTTHUMG00000019236	ENST00000368797.4:c.512T>C	10.37:g.127484721A>G	ENSP00000357787:p.Val171Ala	145.0	0.0	0		131.0	62.0	0.473282	NM_000375	B2RC13|D3DRF7|Q9H2T1	Missense_Mutation	SNP	ENST00000368797.4	37	CCDS7648.1	.	.	.	.	.	.	.	.	.	.	A	0.013	-1.608054	0.00842	.	.	ENSG00000188690	ENST00000368797;ENST00000368786;ENST00000420761	D;D;D	0.93604	-3.25;-3.25;-3.25	4.98	2.59	0.31030	Tetrapyrrole biosynthesis, uroporphyrinogen III synthase (2);	0.587899	0.17904	N	0.158084	T	0.78039	0.4221	N	0.02391	-0.57	0.58432	P	1.0000000000287557E-6	B;B	0.09022	0.002;0.002	B;B	0.16722	0.005;0.016	T	0.70163	-0.4947	9	0.08599	T	0.76	-0.1402	5.5774	0.17231	0.7614:0.0:0.2386:0.0	.	171;143	P10746;E9PG85	HEM4_HUMAN;.	A	171;171;143	ENSP00000357787:V171A;ENSP00000357775:V171A;ENSP00000414833:V143A	ENSP00000357775:V171A	V	-	2	0	UROS	127474711	0.005000	0.15991	0.006000	0.13384	0.004000	0.04260	1.536000	0.36072	0.703000	0.31848	-0.417000	0.06048	GTT	A|0.994;C|0.006	.	alt		0.557	UROS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050929.1	NM_000375	
TMEM132A	54972	hgsc.bcm.edu	37	11	60701176	60701176	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:60701176G>A	ENST00000453848.2	+	8	1677	c.1519G>A	c.(1519-1521)Gag>Aag	p.E507K	TMEM132A_ENST00000005286.4_Missense_Mutation_p.E508K			Q24JP5	T132A_HUMAN	transmembrane protein 132A	507						endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				breast(1)|cervix(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(14)|ovary(3)|prostate(1)|skin(3)	32						CACCACCCTCGAGCAGGTCCG	0.701																																					p.E508K		Atlas-SNP	.											.	TMEM132A	135	.	0			c.G1522A						PASS	.						13.0	12.0	12.0					11																	60701176		2189	4283	6472	SO:0001583	missense	54972	exon8			ACCCTCGAGCAGG	AK000546	CCDS7997.1, CCDS44618.1	11q12.2	2006-03-02	2006-03-02	2006-03-02	ENSG00000006118	ENSG00000006118			31092	protein-coding gene	gene with protein product			"""heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) binding protein 1"""	HSPA5BP1		12514190, 10997877	Standard	NM_017870		Approved	GBP, FLJ20539	uc001nqi.3	Q24JP5	OTTHUMG00000167803	ENST00000453848.2:c.1519G>A	11.37:g.60701176G>A	ENSP00000405823:p.Glu507Lys	44.0	0.0	0		51.0	21.0	0.411765	NM_017870	Q69YU7|Q86VZ8|Q86W97|Q9H8K3|Q9HCI9|Q9NWY0	Missense_Mutation	SNP	ENST00000453848.2	37	CCDS44618.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	20.6|20.6	4.013820|4.013820	0.75161|0.75161	.|.	.|.	ENSG00000006118|ENSG00000006118	ENST00000444690;ENST00000453848;ENST00000005286|ENST00000536409	T;T|.	0.13538|.	2.58;2.58|.	4.25|4.25	4.25|4.25	0.50352|0.50352	.|.	0.338551|.	0.26387|.	N|.	0.024675|.	T|T	0.61553|0.61553	0.2356|0.2356	L|L	0.47716|0.47716	1.5|1.5	0.34210|0.34210	D|D	0.674176|0.674176	D;D;D|.	0.62365|.	0.989;0.991;0.991|.	P;P;P|.	0.54270|.	0.743;0.677;0.747|.	T|T	0.69416|0.69416	-0.5151|-0.5151	10|5	0.87932|.	D|.	0|.	.|.	15.3168|15.3168	0.74085|0.74085	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	258;507;508|.	Q24JP5-4;Q24JP5;Q24JP5-2|.	.;T132A_HUMAN;.|.	K|Q	258;507;508|98	ENSP00000405823:E507K;ENSP00000005286:E508K|.	ENSP00000005286:E508K|.	E|R	+|+	1|2	0|0	TMEM132A|TMEM132A	60457752|60457752	0.987000|0.987000	0.35691|0.35691	0.975000|0.975000	0.42487|0.42487	0.817000|0.817000	0.46193|0.46193	1.938000|1.938000	0.40203|0.40203	2.285000|2.285000	0.76669|0.76669	0.555000|0.555000	0.69702|0.69702	GAG|CGA	.	.	none		0.701	TMEM132A-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000396352.1	NM_017870	
WDR66	144406	hgsc.bcm.edu	37	12	122361711	122361711	+	Missense_Mutation	SNP	C	C	T	rs34703321	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122361711C>T	ENST00000288912.4	+	3	1416	c.562C>T	c.(562-564)Cgg>Tgg	p.R188W	WDR66_ENST00000397454.2_Missense_Mutation_p.R188W	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	188							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		GAAAACCGACCGGATGCCCCA	0.478													C|||	11	0.00219649	0.0	0.0029	5008	,	,		16696	0.0		0.007	False		,,,				2504	0.002				p.R188W	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											.	WDR66	143	.	0			c.C562T						PASS	.	C	TRP/ARG,TRP/ARG	8,3728		0,8,1860	104.0	100.0	101.0		562,562	2.5	0.0	12	dbSNP_126	101	68,8122		1,66,4028	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	101,101	1,74,5888	TT,TC,CC		0.8303,0.2141,0.6373	benign,benign	188/942,188/1150	122361711	76,11850	1868	4095	5963	SO:0001583	missense	144406	exon3			ACCGACCGGATGC	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.562C>T	12.37:g.122361711C>T	ENSP00000288912:p.Arg188Trp	62.0	0.0	0		75.0	36.0	0.48	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	6.949	0.544851	0.13312	0.002141	0.008303	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.17854	2.25;2.25	4.43	2.53	0.30540	.	3.743330	0.00887	N	0.002196	T	0.08358	0.0208	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.31110	-0.9955	10	0.51188	T	0.08	.	9.2319	0.37441	0.0:0.7611:0.1476:0.0914	rs34703321	188	Q8TBY9	WDR66_HUMAN	W	188	ENSP00000288912:R188W;ENSP00000380595:R188W	ENSP00000288912:R188W	R	+	1	2	WDR66	120846094	0.001000	0.12720	0.001000	0.08648	0.001000	0.01503	0.848000	0.27710	0.188000	0.20168	-1.641000	0.00772	CGG	C|0.995;T|0.005	0.005	strong		0.478	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
SMC1A	8243	hgsc.bcm.edu	37	X	53407996	53407996	+	Silent	SNP	G	G	A	rs142611198	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:53407996G>A	ENST00000322213.4	-	23	3577	c.3450C>T	c.(3448-3450)gcC>gcT	p.A1150A	SMC1A_ENST00000469129.1_5'Flank	NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	1150	Ala/Asp-rich (DA-box).				DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CGAAGAAGGGGGCTGGCTTGT	0.617													G|||	2	0.000529801	0.0	0.0014	3775	,	,		10861	0.0		0.001	False		,,,				2504	0.0				p.A1150A		Atlas-SNP	.											.	SMC1A	112	.	0			c.C3450T						PASS	.	G		0,3835		0,0,0,1632,571	67.0	58.0	61.0		3450	3.5	1.0	X	dbSNP_134	61	10,6718		0,8,2,2420,1870	no	coding-synonymous	SMC1A	NM_006306.2		0,8,2,4052,2441	AA,AG,A,GG,G		0.1486,0.0,0.0947		1150/1234	53407996	10,10553	2203	4300	6503	SO:0001819	synonymous_variant	8243	exon23			GAAGGGGGCTGGC	S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.3450C>T	X.37:g.53407996G>A		75.0	0.0	0		106.0	103.0	0.971698	NM_006306	O14995|Q16351|Q2M228	Silent	SNP	ENST00000322213.4	37	CCDS14352.1																																																																																			G|0.999;A|0.001	0.001	strong		0.617	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056756.2	NM_006306	
CHD2	1106	hgsc.bcm.edu	37	15	93557954	93557954	+	Missense_Mutation	SNP	G	G	C	rs56227200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:93557954G>C	ENST00000394196.4	+	37	5789	c.4721G>C	c.(4720-4722)gGg>gCg	p.G1574A	CHD2_ENST00000557381.1_Missense_Mutation_p.G1574A	NM_001271.3	NP_001262.3	O14647	CHD2_HUMAN	chromodomain helicase DNA binding protein 2	1574			G -> A (in dbSNP:rs56227200).		cellular response to DNA damage stimulus (GO:0006974)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|hematopoietic stem cell differentiation (GO:0060218)|muscle organ development (GO:0007517)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|core promoter sequence-specific DNA binding (GO:0001046)|DNA binding (GO:0003677)|histone binding (GO:0042393)|poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(10)|lung(17)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	47	Lung NSC(78;0.00976)|all_lung(78;0.016)		BRCA - Breast invasive adenocarcinoma(143;0.0282)|OV - Ovarian serous cystadenocarcinoma(32;0.0814)			GACGTGACTGGGGGTAAGAAA	0.483													G|||	53	0.0105831	0.0015	0.0173	5008	,	,		16711	0.0		0.0378	False		,,,				2504	0.001				p.G1574A		Atlas-SNP	.											.	CHD2	280	.	0			c.G4721C						PASS	.	G	ALA/GLY	22,4372	28.1+/-56.4	0,22,2175	96.0	101.0	99.0		4721	5.8	1.0	15	dbSNP_129	99	246,8350	97.2+/-158.9	1,244,4053	yes	missense	CHD2	NM_001271.3	60	1,266,6228	CC,CG,GG		2.8618,0.5007,2.0631	benign	1574/1829	93557954	268,12722	2197	4298	6495	SO:0001583	missense	1106	exon37			TGACTGGGGGTAA	AF006514	CCDS10374.2, CCDS45356.1	15q26	2008-07-18			ENSG00000173575	ENSG00000173575			1917	protein-coding gene	gene with protein product		602119				9326634	Standard	NM_001042572		Approved	FLJ38614, DKFZp547I1315, DKFZp781D1727, DKFZp686E01200	uc002bsp.3	O14647	OTTHUMG00000149845	ENST00000394196.4:c.4721G>C	15.37:g.93557954G>C	ENSP00000377747:p.Gly1574Ala	79.0	0.0	0		105.0	43.0	0.409524	NM_001271	C6G482|Q96IP5	Missense_Mutation	SNP	ENST00000394196.4	37	CCDS10374.2	38	0.0173992673992674	0	0.0	8	0.022099447513812154	0	0.0	30	0.0395778364116095	G	4.134	0.023158	0.08006	0.005007	0.028618	ENSG00000173575	ENST00000394196;ENST00000557381;ENST00000557759	D;D;T	0.89343	-2.5;-2.49;0.98	5.76	5.76	0.90799	.	0.239796	0.21044	U	0.081118	T	0.51958	0.1705	N	0.19112	0.55	0.80722	D	1	B;B	0.26147	0.088;0.143	B;B	0.28465	0.025;0.09	T	0.66960	-0.5791	10	0.06236	T	0.91	-18.5026	13.4137	0.60956	0.0745:0.0:0.9255:0.0	rs56227200;rs61735574	1574;1574	O14647;O14647-2	CHD2_HUMAN;.	A	1574;1574;99	ENSP00000377747:G1574A;ENSP00000451366:G1574A;ENSP00000451539:G99A	ENSP00000377747:G1574A	G	+	2	0	CHD2	91358958	1.000000	0.71417	0.994000	0.49952	0.542000	0.35054	6.743000	0.74848	2.730000	0.93505	0.591000	0.81541	GGG	G|0.981;C|0.019	0.019	strong		0.483	CHD2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313528.3	NM_001271	
ZDBF2	57683	hgsc.bcm.edu	37	2	207174559	207174559	+	Silent	SNP	A	A	G	rs13408088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207174559A>G	ENST00000374423.3	+	5	5693	c.5307A>G	c.(5305-5307)aaA>aaG	p.K1769K		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	1769							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CTGTTAAGAAAAGACACCCTT	0.413													A|||	157	0.0313498	0.1051	0.0159	5008	,	,		20253	0.0		0.006	False		,,,				2504	0.001				p.K1769K		Atlas-SNP	.											.	ZDBF2	531	.	0			c.A5307G						PASS	.	A		352,3382		17,318,1532	55.0	56.0	56.0		5307	2.6	0.0	2	dbSNP_121	56	71,8127		0,71,4028	no	coding-synonymous	ZDBF2	NM_020923.1		17,389,5560	GG,GA,AA		0.8661,9.4269,3.5451		1769/2355	207174559	423,11509	1867	4099	5966	SO:0001819	synonymous_variant	57683	exon5			TAAGAAAAGACAC	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.5307A>G	2.37:g.207174559A>G		109.0	0.0	0		114.0	54.0	0.473684	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			A|0.970;G|0.030	0.030	strong		0.413	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
GPR144	347088	hgsc.bcm.edu	37	9	127216378	127216378	+	Splice_Site	SNP	T	T	C	rs118108631	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:127216378T>C	ENST00000334810.1	+	5	1078		c.e5+2					Q7Z7M1	GP144_HUMAN	G protein-coupled receptor 144						G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(3)	4						ACCGGACAGGTGCGCCCTGGC	0.647													T|||	19	0.00379393	0.0008	0.0058	5008	,	,		13610	0.0		0.0109	False		,,,				2504	0.0031				.		Atlas-SNP	.											GPR144,NS,carcinoma,0,1	GPR144	33	1	0			c.1078+2T>C						scavenged	.	T		2,1382		0,2,690	15.0	20.0	18.0			4.3	1.0	9	dbSNP_132	18	42,3138		0,42,1548	yes	splice-5	GPR144	NM_001161808.1		0,44,2238	CC,CT,TT		1.3208,0.1445,0.9641			127216378	44,4520	692	1590	2282	SO:0001630	splice_region_variant	347088	exon5			GACAGGTGCGCCC	AY278562		9q34.11	2014-08-08			ENSG00000180264	ENSG00000180264		"""-"", ""GPCR / Class B : Orphans"""	18651	protein-coding gene	gene with protein product							Standard	XM_006710216		Approved	PGR24	uc010mwn.3	Q7Z7M1	OTTHUMG00000020652	ENST00000334810.1:c.1078+2T>C	9.37:g.127216378T>C		58.0	1.0	0.0172414		69.0	36.0	0.521739	NM_001161808	Q86SL4|Q8NH12	Splice_Site	SNP	ENST00000334810.1	37	CCDS48016.1	14	0.00641025641025641	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	16.08	3.022012	0.54576	0.001445	0.013208	ENSG00000180264	ENST00000334810	.	.	.	4.3	4.3	0.51218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	10.1411	0.42736	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	GPR144	126256199	0.995000	0.38212	0.966000	0.40874	0.606000	0.37113	0.972000	0.29409	1.707000	0.51288	0.379000	0.24179	.	T|0.993;C|0.007	0.007	strong		0.647	GPR144-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054026.2	NM_182611	Intron
PSD4	23550	hgsc.bcm.edu	37	2	113953346	113953346	+	Splice_Site	SNP	G	G	A	rs370284646	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113953346G>A	ENST00000245796.6	+	11	2419	c.2224G>A	c.(2224-2226)Gtg>Atg	p.V742M	PSD4_ENST00000441564.3_Splice_Site_p.V714M	NM_012455.2	NP_036587.2	Q8NDX1	PSD4_HUMAN	pleckstrin and Sec7 domain containing 4	742					neuron differentiation (GO:0030182)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)	cell junction (GO:0030054)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|phospholipid binding (GO:0005543)			cervix(1)|endometrium(2)|large_intestine(4)|lung(13)|ovary(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						CGAGTGGGCCGTGTGAGTGAG	0.592																																					p.V742M		Atlas-SNP	.											.	PSD4	74	.	0			c.G2224A						PASS	.	G	MET/VAL	0,4406		0,0,2203	152.0	141.0	145.0		2224	-0.4	0.1	2		145	1,8599	1.2+/-3.3	0,1,4299	no	missense-near-splice	PSD4	NM_012455.2	21	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	742/1057	113953346	1,13005	2203	4300	6503	SO:0001630	splice_region_variant	23550	exon11			TGGGCCGTGTGAG	U63127	CCDS33276.1	2q13	2013-01-10			ENSG00000125637	ENSG00000125637		"""Pleckstrin homology (PH) domain containing"""	19096	protein-coding gene	gene with protein product		614442				12082148	Standard	XM_005263634		Approved	TIC, EFA6B	uc002tjc.3	Q8NDX1	OTTHUMG00000153339	ENST00000245796.6:c.2225+1G>A	2.37:g.113953346G>A		74.0	0.0	0		57.0	11.0	0.192982	NM_012455	A6NEG7|A8K1Y0|O95621|Q4ZG34|Q6GPH8|Q8IYP4	Missense_Mutation	SNP	ENST00000245796.6	37	CCDS33276.1	.	.	.	.	.	.	.	.	.	.	G	11.40	1.627464	0.28978	0.0	1.16E-4	ENSG00000125637	ENST00000245796;ENST00000441564	T;T	0.30182	1.54;1.54	5.65	-0.402	0.12404	SEC7-like, alpha orthogonal bundle (1);SEC7-like (1);	0.449069	0.25267	N	0.031905	T	0.23210	0.0561	L	0.45581	1.43	0.80722	D	1	B;B;B	0.24882	0.113;0.027;0.016	B;B;B	0.22880	0.042;0.015;0.007	T	0.05007	-1.0912	10	0.39692	T	0.17	.	9.3598	0.38188	0.57:0.0:0.43:0.0	.	400;714;742	Q59HG0;Q8NDX1-2;Q8NDX1	.;.;PSD4_HUMAN	M	742;714	ENSP00000245796:V742M;ENSP00000413997:V714M	ENSP00000245796:V742M	V	+	1	0	PSD4	113669817	0.000000	0.05858	0.084000	0.20598	0.906000	0.53458	-0.730000	0.04915	-0.136000	0.11475	-0.140000	0.14226	GTG	.	.	weak		0.592	PSD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000330789.1	NM_012455	Missense_Mutation
NUP107	57122	hgsc.bcm.edu	37	12	69113184	69113184	+	Silent	SNP	C	C	T	rs35209116	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:69113184C>T	ENST00000229179.4	+	13	1479	c.1147C>T	c.(1147-1149)Ctg>Ttg	p.L383L	NUP107_ENST00000539906.1_Silent_p.L354L|NUP107_ENST00000378905.2_Silent_p.L232L	NM_020401.2	NP_065134.1	P57740	NU107_HUMAN	nucleoporin 107kDa	383					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	centrosome (GO:0005813)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|structural constituent of nuclear pore (GO:0017056)		NUP107/LGR5(2)	breast(3)|endometrium(4)|kidney(4)|large_intestine(12)|lung(11)|prostate(1)|skin(2)|urinary_tract(2)	39	Breast(13;6.25e-06)		Lung(24;0.000131)|LUAD - Lung adenocarcinoma(15;0.00107)|STAD - Stomach adenocarcinoma(21;0.00694)			AGGCTGGAAACTGTACCATGA	0.413													C|||	22	0.00439297	0.0	0.0072	5008	,	,		18922	0.0		0.007	False		,,,				2504	0.0102				p.L383L		Atlas-SNP	.											.	NUP107	88	.	0			c.C1147T						PASS	.	C		7,4399	11.4+/-27.6	0,7,2196	122.0	112.0	115.0		1147	1.2	0.0	12	dbSNP_126	115	47,8553	32.8+/-85.7	1,45,4254	no	coding-synonymous	NUP107	NM_020401.2		1,52,6450	TT,TC,CC		0.5465,0.1589,0.4152		383/926	69113184	54,12952	2203	4300	6503	SO:0001819	synonymous_variant	57122	exon13			TGGAAACTGTACC	AK055629	CCDS8985.1	12q14	2004-03-19			ENSG00000111581	ENSG00000111581			29914	protein-coding gene	gene with protein product		607617				12552102, 12705868	Standard	XM_005269037		Approved	NUP84	uc001suf.3	P57740	OTTHUMG00000169265	ENST00000229179.4:c.1147C>T	12.37:g.69113184C>T		146.0	0.0	0		144.0	77.0	0.534722	NM_020401	B4DZ67|Q6PJE1	Silent	SNP	ENST00000229179.4	37	CCDS8985.1																																																																																			C|0.996;T|0.004	0.004	strong		0.413	NUP107-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403195.1	NM_020401	
TYR	7299	hgsc.bcm.edu	37	11	88911575	88911575	+	Missense_Mutation	SNP	C	C	T	rs145513733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:88911575C>T	ENST00000263321.5	+	1	956	c.454C>T	c.(454-456)Ccc>Tcc	p.P152S	TYR_ENST00000526139.1_3'UTR	NM_000372.4	NP_000363.1	P14679	TYRO_HUMAN	tyrosinase	152			P -> S (in OCA1B). {ECO:0000269|PubMed:8128955}.		cell proliferation (GO:0008283)|eye pigment biosynthetic process (GO:0006726)|melanin biosynthetic process from tyrosine (GO:0006583)|thymus development (GO:0048538)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|Golgi-associated vesicle (GO:0005798)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)	copper ion binding (GO:0005507)|monophenol monooxygenase activity (GO:0004503)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(25)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	48		Acute lymphoblastic leukemia(157;2.33e-05)|all_hematologic(158;0.0033)			Azelaic Acid(DB00548)|Mimosine(DB01055)|Monobenzone(DB00600)	CTATGTCATCCCCATAGGGAC	0.403																																					p.P152S		Atlas-SNP	.											.	TYR	130	.	0			c.C454T	GRCh37	CM941344	TYR	M	rs145513733	PASS	.	C	SER/PRO	0,4402		0,0,2201	152.0	144.0	147.0		454	5.0	1.0	11	dbSNP_134	147	3,8595	3.0+/-9.4	0,3,4296	yes	missense	TYR	NM_000372.4	74	0,3,6497	TT,TC,CC		0.0349,0.0,0.0231	possibly-damaging	152/530	88911575	3,12997	2201	4299	6500	SO:0001583	missense	7299	exon1			GTCATCCCCATAG	M27160	CCDS8284.1	11q14.3	2013-09-27	2012-09-28		ENSG00000077498	ENSG00000077498	1.14.18.1		12442	protein-coding gene	gene with protein product	"""oculocutaneous albinism IA"""	606933					Standard	NM_000372		Approved	OCAIA, OCA1A, OCA1	uc001pcs.3	P14679	OTTHUMG00000167294	ENST00000263321.5:c.454C>T	11.37:g.88911575C>T	ENSP00000263321:p.Pro152Ser	61.0	0.0	0		75.0	38.0	0.506667	NM_000372	Q15675|Q15676|Q15680|Q8TAK4|Q9BYY0|Q9BZX1	Missense_Mutation	SNP	ENST00000263321.5	37	CCDS8284.1	.	.	.	.	.	.	.	.	.	.	C	17.83	3.485562	0.63962	0.0	3.49E-4	ENSG00000077498	ENST00000263321	D	0.83591	-1.74	5.97	5.01	0.66863	Uncharacterised domain, di-copper centre (2);	0.157178	0.56097	D	0.000032	T	0.80042	0.4551	L	0.41573	1.285	0.36372	D	0.861346	P	0.45078	0.85	P	0.46208	0.507	T	0.81814	-0.0760	9	.	.	.	.	14.0119	0.64503	0.0:0.6866:0.3134:0.0	.	152	P14679	TYRO_HUMAN	S	152	ENSP00000263321:P152S	.	P	+	1	0	TYR	88551223	1.000000	0.71417	1.000000	0.80357	0.880000	0.50808	4.338000	0.59316	2.828000	0.97474	0.655000	0.94253	CCC	C|0.999;T|0.001	0.001	strong		0.403	TYR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394045.2	NM_000372	
BTBD16	118663	hgsc.bcm.edu	37	10	124096014	124096014	+	Missense_Mutation	SNP	A	A	G	rs150944464	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:124096014A>G	ENST00000260723.4	+	15	1520	c.1269A>G	c.(1267-1269)atA>atG	p.I423M	BTBD16_ENST00000368994.2_Missense_Mutation_p.I424M|BTBD16_ENST00000495370.2_3'UTR	NM_144587.2	NP_653188.2	Q32M84	BTBDG_HUMAN	BTB (POZ) domain containing 16	423										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)				TGCAGAGAATAAAGCACACAG	0.542													A|||	25	0.00499201	0.0	0.0043	5008	,	,		18397	0.0		0.0209	False		,,,				2504	0.001				p.I423M		Atlas-SNP	.											.	BTBD16	44	.	0			c.A1269G						PASS	.	A	MET/ILE	13,4393	21.2+/-45.6	0,13,2190	52.0	45.0	47.0		1269	-8.5	0.0	10	dbSNP_134	47	129,8471	58.7+/-120.3	0,129,4171	yes	missense	BTBD16	NM_144587.2	10	0,142,6361	GG,GA,AA		1.5,0.2951,1.0918	benign	423/507	124096014	142,12864	2203	4300	6503	SO:0001583	missense	118663	exon15			GAGAATAAAGCAC	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.1269A>G	10.37:g.124096014A>G	ENSP00000260723:p.Ile423Met	76.0	0.0	0		63.0	17.0	0.269841	NM_144587	A6NM63|Q4VXL1|Q96LN0	Missense_Mutation	SNP	ENST00000260723.4	37	CCDS31301.1	23	0.010531135531135532	0	0.0	4	0.011049723756906077	0	0.0	19	0.025065963060686015	A	15.45	2.838596	0.51057	0.002951	0.015	ENSG00000138152	ENST00000260723;ENST00000368994	T;T	0.22134	1.97;1.97	5.68	-8.52	0.00920	.	0.900138	0.09479	N	0.796551	T	0.02807	0.0084	N	0.19112	0.55	0.09310	N	1	P;P	0.37207	0.587;0.587	B;B	0.32465	0.146;0.146	T	0.17107	-1.0380	10	0.44086	T	0.13	-1.7584	9.6517	0.39902	0.1783:0.3913:0.4304:0.0	.	424;423	Q32M84-2;Q32M84	.;BTBDG_HUMAN	M	423;424	ENSP00000260723:I423M;ENSP00000357990:I424M	ENSP00000260723:I423M	I	+	3	3	BTBD16	124086004	0.338000	0.24775	0.016000	0.15963	0.381000	0.30169	-0.278000	0.08490	-1.358000	0.02177	-0.290000	0.09829	ATA	A|0.990;G|0.010	0.010	strong		0.542	BTBD16-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050780.3	NM_144587	
PTX4	390667	hgsc.bcm.edu	37	16	1537956	1537956	+	Missense_Mutation	SNP	C	C	G	rs144904207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1537956C>G	ENST00000447419.2	-	2	182	c.157G>C	c.(157-159)Gag>Cag	p.E53Q	PTX4_ENST00000440447.2_Missense_Mutation_p.E53Q|PTX4_ENST00000293922.1_Missense_Mutation_p.E48Q			Q96A99	PTX4_HUMAN	pentraxin 4, long	53						extracellular region (GO:0005576)	metal ion binding (GO:0046872)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17						CAGGTCACCTCCTGGAATCTC	0.632													C|||	3	0.000599042	0.0	0.0	5008	,	,		16358	0.0		0.003	False		,,,				2504	0.0				p.E48Q		Atlas-SNP	.											.	PTX4	46	.	0			c.G142C						PASS	.	C	GLN/GLU	0,4236		0,0,2118	81.0	81.0	81.0		142	4.7	0.1	16	dbSNP_134	81	10,8270		0,10,4130	yes	missense	PTX4	NM_001013658.1	29	0,10,6248	GG,GC,CC		0.1208,0.0,0.0799	benign	48/474	1537956	10,12506	2118	4140	6258	SO:0001583	missense	390667	exon2			TCACCTCCTGGAA		CCDS32362.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000251692	ENSG00000251692			14171	protein-coding gene	gene with protein product		613442	"""chromosome 16 open reading frame 38"""	C16orf38			Standard	NM_001013658		Approved		uc010uvf.2	Q96A99		ENST00000447419.2:c.157G>C	16.37:g.1537956C>G	ENSP00000445277:p.Glu53Gln	43.0	0.0	0		48.0	25.0	0.520833	NM_001013658		Missense_Mutation	SNP	ENST00000447419.2	37		.	.	.	.	.	.	.	.	.	.	C	6.632	0.485074	0.12641	0.0	0.001208	ENSG00000251692	ENST00000447419;ENST00000293922	T;T	0.06768	3.39;3.26	5.68	4.71	0.59529	.	0.500926	0.20061	N	0.100088	T	0.07728	0.0194	L	0.34521	1.04	0.20196	N	0.999925	B	0.30033	0.266	B	0.30401	0.115	T	0.31475	-0.9942	10	0.23302	T	0.38	.	12.3329	0.55049	0.0:0.8226:0.1774:0.0	.	48	Q96A99-2	.	Q	53;48	ENSP00000445277:E53Q;ENSP00000293922:E48Q	ENSP00000293922:E48Q	E	-	1	0	PTX4	1477957	1.000000	0.71417	0.060000	0.19600	0.002000	0.02628	2.545000	0.45769	1.368000	0.46115	0.563000	0.77884	GAG	C|0.998;G|0.002	0.002	strong		0.632	PTX4-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000432526.1	NM_001013658	
RRN3	54700	hgsc.bcm.edu	37	16	15188018	15188018	+	Missense_Mutation	SNP	C	C	T	rs141593500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:15188018C>T	ENST00000198767.6	-	1	156	c.73G>A	c.(73-75)Ggc>Agc	p.G25S	RRN3_ENST00000429751.2_Missense_Mutation_p.G25S|RRN3_ENST00000564131.1_Missense_Mutation_p.G25S|RRN3_ENST00000563559.1_Missense_Mutation_p.G25S|RP11-72I8.1_ENST00000569858.1_RNA|PDXDC1_ENST00000535621.2_Intron|RRN3_ENST00000327307.7_5'Flank	NM_018427.3	NP_060897.3	Q9NYV6	RRN3_HUMAN	RRN3 RNA polymerase I transcription factor homolog (S. cerevisiae)	25					cell proliferation (GO:0008283)|cytoplasm organization (GO:0007028)|gene expression (GO:0010467)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902254)|nucleolus organization (GO:0007000)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, initiation (GO:2000142)|ribosome biogenesis (GO:0042254)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				NS(2)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|prostate(2)	20						CTCGACGCGCCCAGCTTCTTA	0.617													.|||	5	0.000998403	0.0	0.0	5008	,	,		9426	0.0		0.0	False		,,,				2504	0.0051				p.G25S		Atlas-SNP	.											.	RRN3	36	.	0			c.G73A						PASS	.	C	SER/GLY	0,4394		0,0,2197	26.0	23.0	24.0		73	1.1	0.0	16	dbSNP_134	24	4,8596		0,4,4296	yes	missense	RRN3	NM_018427.3	56	0,4,6493	TT,TC,CC		0.0465,0.0,0.0308	benign	25/652	15188018	4,12990	2197	4300	6497	SO:0001583	missense	54700	exon1			ACGCGCCCAGCTT	AF227156	CCDS10559.1, CCDS73833.1	16p13.11	2009-10-26	2006-04-04		ENSG00000085721	ENSG00000085721			30346	protein-coding gene	gene with protein product		605121	"""RRN3 RNA polymerase I transcription factor homolog (yeast)"""			10758157, 11250903	Standard	XM_005255375		Approved	DKFZp566E104	uc002dde.3	Q9NYV6	OTTHUMG00000129847	ENST00000198767.6:c.73G>A	16.37:g.15188018C>T	ENSP00000198767:p.Gly25Ser	124.0	0.0	0		120.0	60.0	0.5	NM_018427	A2RTY9|B4E0J7|B4E3T2|Q3MHU9|Q6IPL4|Q9H4F0	Missense_Mutation	SNP	ENST00000198767.6	37	CCDS10559.1	.	.	.	.	.	.	.	.	.	.	.	12.30	1.897935	0.33535	0.0	4.65E-4	ENSG00000085721	ENST00000198767;ENST00000429751	T;T	0.44881	1.0;0.91	3.13	1.07	0.20283	.	.	.	.	.	T	0.17195	0.0413	N	0.08118	0	0.26447	N	0.975673	B;B;B	0.13145	0.0;0.007;0.001	B;B;B	0.12156	0.003;0.007;0.003	T	0.30327	-0.9982	9	0.07813	T	0.8	.	4.8484	0.13524	0.0:0.6849:0.0:0.3151	.	25;25;25	F5H148;Q3MHU9;Q9NYV6	.;.;RRN3_HUMAN	S	25	ENSP00000198767:G25S;ENSP00000402027:G25S	ENSP00000198767:G25S	G	-	1	0	RRN3	15095519	0.000000	0.05858	0.029000	0.17559	0.160000	0.22226	-0.057000	0.11768	0.155000	0.19261	0.305000	0.20034	GGC	C|1.000;T|0.000	0.000	weak		0.617	RRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252087.2	NM_018427	
OBSCN	84033	hgsc.bcm.edu	37	1	228476420	228476420	+	Silent	SNP	C	C	T	rs56367754		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228476420C>T	ENST00000422127.1	+	38	10214	c.10170C>T	c.(10168-10170)ccC>ccT	p.P3390P	OBSCN_ENST00000570156.2_Silent_p.P3819P|OBSCN_ENST00000359599.6_Silent_p.P2237P|OBSCN_ENST00000366707.4_Silent_p.P509P|OBSCN_ENST00000284548.11_Silent_p.P3390P|OBSCN_ENST00000366709.4_Silent_p.P509P	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	3390	Ig-like 34.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AGGCGGCCCCCGTGGAGTGGA	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		21068	0.0		0.001	False		,,,				2504	0.0				p.P3819P		Atlas-SNP	.											OBSCN_ENST00000570156,colon,carcinoma,+1,4	OBSCN	2142	4	0			c.C11457T						PASS	.	C	,	2,4160		0,2,2079	88.0	98.0	95.0		10170,10170	-9.9	0.0	1	dbSNP_129	95	33,8355		0,33,4161	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,35,6240	TT,TC,CC		0.3934,0.0481,0.2789	,	3390/7969,3390/6621	228476420	35,12515	2081	4194	6275	SO:0001819	synonymous_variant	84033	exon43			GGCCCCCGTGGAG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.10170C>T	1.37:g.228476420C>T		85.0	0.0	0		113.0	56.0	0.495575	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.995;T|0.005	0.005	strong		0.637	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
COBL	23242	hgsc.bcm.edu	37	7	51093049	51093049	+	Silent	SNP	C	C	T	rs1129262	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:51093049C>T	ENST00000265136.7	-	12	3690	c.3525G>A	c.(3523-3525)gaG>gaA	p.E1175E	RP4-724E13.2_ENST00000582616.1_RNA|COBL_ENST00000395542.2_Silent_p.E1257E	NM_015198.3	NP_056013.2	O75128	COBL_HUMAN	cordon-bleu WH2 repeat protein	1175					actin filament network formation (GO:0051639)|actin filament polymerization (GO:0030041)|collateral sprouting in absence of injury (GO:0048669)|digestive tract development (GO:0048565)|embryonic axis specification (GO:0000578)|floor plate development (GO:0033504)|liver development (GO:0001889)|neural tube closure (GO:0001843)|notochord development (GO:0030903)|positive regulation of dendrite development (GO:1900006)|somite specification (GO:0001757)	actin filament (GO:0005884)|axon (GO:0030424)|axonal growth cone (GO:0044295)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic growth cone (GO:0044294)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	actin monomer binding (GO:0003785)			NS(2)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(26)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	65	Glioma(55;0.08)					TCTGGAGCTCCTCAGAAGCAG	0.527													C|||	15	0.00299521	0.0045	0.0043	5008	,	,		12853	0.0		0.005	False		,,,				2504	0.001				p.E1175E	NSCLC(189;2119 2138 12223 30818 34679)	Atlas-SNP	.											COBL,NS,haematopoietic_neoplasm,0,1	COBL	167	1	0			c.G3525A						PASS	.	C		14,4390		0,14,2188	35.0	37.0	36.0		3525	1.3	1.0	7	dbSNP_86	36	88,8508		0,88,4210	no	coding-synonymous	COBL	NM_015198.3		0,102,6398	TT,TC,CC		1.0237,0.3179,0.7846		1175/1262	51093049	102,12898	2202	4298	6500	SO:0001819	synonymous_variant	23242	exon12			GAGCTCCTCAGAA	AB014533	CCDS34637.1, CCDS75601.1, CCDS75602.1	7p12.2-p12.1	2012-12-07	2012-12-07		ENSG00000106078	ENSG00000106078			22199	protein-coding gene	gene with protein product		610317	"""cordon-bleu homolog (mouse)"""				Standard	NM_015198		Approved	KIAA0633	uc003tpr.4	O75128	OTTHUMG00000155999	ENST00000265136.7:c.3525G>A	7.37:g.51093049C>T		87.0	0.0	0		138.0	31.0	0.224638	NM_015198	A4D257|A7E2B0|B7ZLW9|B9EGF8|Q2T9J3|Q504Y4|Q86XA7|Q8N304|Q8TCM1	Silent	SNP	ENST00000265136.7	37	CCDS34637.1																																																																																			C|0.993;T|0.007	0.007	strong		0.527	COBL-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000342682.1	NM_015198	
LRPAP1	4043	hgsc.bcm.edu	37	4	3516560	3516560	+	Silent	SNP	G	G	A	rs11549512	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:3516560G>A	ENST00000500728.2	-	7	1076	c.930C>T	c.(928-930)agC>agT	p.S310S	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	310	LDL receptor binding. {ECO:0000255}.				extracellular negative regulation of signal transduction (GO:1900116)|negative regulation of beta-amyloid clearance (GO:1900222)|negative regulation of protein binding (GO:0032091)|negative regulation of very-low-density lipoprotein particle clearance (GO:0010916)|protein folding (GO:0006457)|receptor-mediated endocytosis (GO:0006898)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|rough endoplasmic reticulum lumen (GO:0048237)|vesicle (GO:0031982)	asialoglycoprotein receptor activity (GO:0004873)|heparin binding (GO:0008201)|low-density lipoprotein particle receptor binding (GO:0050750)|receptor antagonist activity (GO:0048019)|unfolded protein binding (GO:0051082)|very-low-density lipoprotein particle receptor binding (GO:0070326)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(2)	14				UCEC - Uterine corpus endometrioid carcinoma (64;0.165)		CGTCGCCCACGCTCTCTGCGT	0.637													.|||	95	0.0189696	0.0023	0.0519	5008	,	,		17011	0.001		0.0497	False		,,,				2504	0.0051				p.S310S		Atlas-SNP	.											.	LRPAP1	29	.	0			c.C930T						PASS	.	G		39,4367	43.8+/-77.6	0,39,2164	127.0	104.0	112.0		930	0.3	0.3	4	dbSNP_120	112	401,8199	127.7+/-186.0	7,387,3906	no	coding-synonymous	LRPAP1	NM_002337.3		7,426,6070	AA,AG,GG		4.6628,0.8852,3.3831		310/358	3516560	440,12566	2203	4300	6503	SO:0001819	synonymous_variant	4043	exon7			GCCCACGCTCTCT		CCDS3371.1	4p16.3	2008-05-02	2003-03-17		ENSG00000163956	ENSG00000163956			6701	protein-coding gene	gene with protein product		104225	"""low density lipoprotein-related protein-associated protein 1 (alpha-2-macroglobulin receptor-associated protein 1)"""	A2MRAP		1712782	Standard	NM_002337		Approved	HBP44	uc003ghh.4	P30533	OTTHUMG00000090299	ENST00000500728.2:c.930C>T	4.37:g.3516560G>A		96.0	0.0	0		125.0	61.0	0.488	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			G|0.971;A|0.029	0.029	strong		0.637	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
PCDHA4	56144	hgsc.bcm.edu	37	5	140188356	140188356	+	Silent	SNP	A	A	G	rs144593807	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188356A>G	ENST00000530339.1	+	1	1584	c.1584A>G	c.(1582-1584)ctA>ctG	p.L528L	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.L528L|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.L528L|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	Cadherin 5. {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)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGAGGAGCTAGAGCTGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17817	0.0		0.0755	False		,,,				2504	0.0082				p.L528L		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,+2,8	PCDHA4	419	8	0			c.A1584G						PASS	.	A	,,,,,	11,4395		0,11,2192	70.0	75.0	73.0		,,,1584,,1584	1.3	1.0	5	dbSNP_134	73	57,8543		9,39,4252	no	intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_031411.1,NM_031500.1	,,,,,	9,50,6444	GG,GA,AA		0.6628,0.2497,0.5228	,,,,,	,,,528/948,,528/799	140188356	68,12938	2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			GGAGCTAGAGCTG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1584A>G	5.37:g.140188356A>G		108.0	0.0	0		63.0	20.0	0.31746	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			A|0.976;G|0.024	0.024	strong		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
ALG1	56052	hgsc.bcm.edu	37	16	5123201	5123201	+	Missense_Mutation	SNP	A	A	C	rs113219939	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5123201A>C	ENST00000262374.5	+	3	365	c.334A>C	c.(334-336)Atg>Ctg	p.M112L	ALG1_ENST00000588623.1_Start_Codon_SNP_p.M1L|ALG1_ENST00000544428.1_Start_Codon_SNP_p.M1L	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	112					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				ACTTCAGGCTATGTACTTGCT	0.512													A|||	66	0.0131789	0.0492	0.0014	5008	,	,		19810	0.0		0.0	False		,,,				2504	0.0				p.M112L		Atlas-SNP	.											.	ALG1	35	.	0			c.A334C						PASS	.	A	LEU/MET	169,4225	112.5+/-150.6	4,161,2032	251.0	230.0	237.0		334	-2.3	0.0	16	dbSNP_132	237	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ALG1	NM_019109.4	15	4,162,6331	CC,CA,AA		0.0116,3.8462,1.3083	benign	112/465	5123201	170,12824	2197	4300	6497	SO:0001583	missense	56052	exon3			CAGGCTATGTACT	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.334A>C	16.37:g.5123201A>C	ENSP00000262374:p.Met112Leu	224.0	0.0	0		220.0	96.0	0.436364	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	22	0.010073260073260074	21	0.042682926829268296	1	0.0027624309392265192	0	0.0	0	0.0	A	0.289	-0.981205	0.02197	0.038462	1.16E-4	ENSG00000033011	ENST00000262374;ENST00000544428	T;T	0.80994	-1.44;-0.88	4.82	-2.31	0.06765	.	0.580414	0.18457	N	0.140653	T	0.08626	0.0214	N	0.00221	-1.82	0.45046	D	0.99806	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.44236	-0.9341	10	0.02654	T	1	-10.1101	0.992	0.01459	0.1831:0.3173:0.2475:0.2521	.	1;112	B4DP08;Q9BT22	.;ALG1_HUMAN	L	112;1	ENSP00000262374:M112L;ENSP00000440019:M1L	ENSP00000262374:M112L	M	+	1	0	ALG1	5063202	0.004000	0.15560	0.022000	0.16811	0.284000	0.27059	-0.033000	0.12246	-0.059000	0.13154	-0.337000	0.08149	ATG	A|0.984;C|0.016	0.016	strong		0.512	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
PPP1R18	170954	hgsc.bcm.edu	37	6	30647035	30647035	+	Missense_Mutation	SNP	G	G	T	rs115169407	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:30647035G>T	ENST00000274853.3	-	2	3619	c.1743C>A	c.(1741-1743)gaC>gaA	p.D581E	PPP1R18_ENST00000399199.3_Missense_Mutation_p.D581E|PPP1R18_ENST00000488324.1_5'UTR	NM_133471.3	NP_597728.1	Q6NYC8	PPR18_HUMAN	protein phosphatase 1, regulatory subunit 18	581						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)											CCTCTTCGTCGTCGGGTTGGG	0.667													G|||	7	0.00139776	0.0008	0.0014	5008	,	,		11756	0.0		0.005	False		,,,				2504	0.0				p.D581E		Atlas-SNP	.											KIAA1949,NS,carcinoma,0,1	.	.	1	0			c.C1743A						PASS	.	G	GLU/ASP,GLU/ASP	3,2425		0,3,1211	42.0	46.0	45.0		1743,1743	0.7	1.0	6	dbSNP_132	45	26,4986		0,26,2480	yes	missense,missense	KIAA1949	NM_001134870.1,NM_133471.3	45,45	0,29,3691	TT,TG,GG		0.5188,0.1236,0.3898	benign,benign	581/614,581/614	30647035	29,7411	1214	2506	3720	SO:0001583	missense	170954	exon3			TTCGTCGTCGGGT	AK097089	CCDS43444.1	6p21.3	2012-04-17	2011-10-11	2011-10-11	ENSG00000146112	ENSG00000146112		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	29413	protein-coding gene	gene with protein product	"""protein phosphatase 1 F-actin cytoskeleton targeting subunit"""	610990	"""KIAA1949"""	KIAA1949		11853319	Standard	NM_001134870		Approved	phostensin	uc003nra.3	Q6NYC8	OTTHUMG00000031237	ENST00000274853.3:c.1743C>A	6.37:g.30647035G>T	ENSP00000274853:p.Asp581Glu	32.0	0.0	0		38.0	17.0	0.447368	NM_001134870	A2AB01|A2AIB8|A4UBI6|A6NCB7|A8MSS7|B7ZCV7|Q68CK8|Q6ZTV1|Q6ZUJ6|Q8NDQ4|Q8TF52|Q9BRL9	Missense_Mutation	SNP	ENST00000274853.3	37	CCDS43444.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	G	15.40	2.822116	0.50739	0.001236	0.005188	ENSG00000146112	ENST00000274853;ENST00000399199	T;T	0.25579	1.79;1.79	5.08	0.679	0.17975	.	0.378241	0.23744	N	0.044992	T	0.04998	0.0134	N	0.17474	0.49	0.23076	N	0.998333	P	0.48407	0.91	P	0.45660	0.489	T	0.18366	-1.0339	10	0.34782	T	0.22	-7.4927	0.6512	0.00827	0.3521:0.1647:0.3139:0.1693	.	581	Q6NYC8	PPR18_HUMAN	E	581	ENSP00000274853:D581E;ENSP00000382150:D581E	ENSP00000274853:D581E	D	-	3	2	KIAA1949	30755014	0.253000	0.23982	0.953000	0.39169	0.881000	0.50899	-0.738000	0.04871	0.560000	0.29169	0.650000	0.86243	GAC	G|0.997;T|0.003	0.003	strong		0.667	PPP1R18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076498.2	NM_133471	
SCRN2	90507	hgsc.bcm.edu	37	17	45917703	45917703	+	Silent	SNP	C	C	T	rs11652952	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:45917703C>T	ENST00000290216.9	-	3	335	c.210G>A	c.(208-210)acG>acA	p.T70T	SCRN2_ENST00000584123.1_Silent_p.T78T|SCRN2_ENST00000407215.3_Silent_p.T70T	NM_001145023.1|NM_138355.3	NP_001138495.1|NP_612364.2	Q96FV2	SCRN2_HUMAN	secernin 2	70						extracellular vesicular exosome (GO:0070062)	dipeptidase activity (GO:0016805)			cervix(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|skin(1)	14						TCACAGCGTGCGTCTTCGACA	0.592													C|||	147	0.029353	0.0658	0.0231	5008	,	,		20332	0.0		0.0358	False		,,,				2504	0.0082				p.T70T		Atlas-SNP	.											.	SCRN2	35	.	0			c.G210A						PASS	.	C	,	237,4169	139.2+/-174.8	7,223,1973	103.0	77.0	86.0		210,210	-10.2	0.3	17	dbSNP_120	86	295,8305	108.8+/-169.4	6,283,4011	no	coding-synonymous,coding-synonymous	SCRN2	NM_001145023.1,NM_138355.3	,	13,506,5984	TT,TC,CC		3.4302,5.379,4.0904	,	70/379,70/426	45917703	532,12474	2203	4300	6503	SO:0001819	synonymous_variant	90507	exon3			AGCGTGCGTCTTC	BC002980	CCDS11519.1, CCDS45723.1	17q21	2008-02-05							30381	protein-coding gene	gene with protein product		614966				12221138	Standard	NM_001145023		Approved		uc002imd.3	Q96FV2		ENST00000290216.9:c.210G>A	17.37:g.45917703C>T		97.0	0.0	0		116.0	66.0	0.568965	NM_138355	A8K3N1|B7Z8S7|E9PBV5|Q96AC3|Q9BU04	Silent	SNP	ENST00000290216.9	37	CCDS11519.1																																																																																			C|0.963;T|0.037	0.037	strong		0.592	SCRN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441383.1	NM_138355	
EPB41L3	23136	hgsc.bcm.edu	37	18	5478295	5478295	+	Missense_Mutation	SNP	C	C	A	rs117900256	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:5478295C>A	ENST00000341928.2	-	3	666	c.326G>T	c.(325-327)aGc>aTc	p.S109I	EPB41L3_ENST00000342933.3_Missense_Mutation_p.S109I|EPB41L3_ENST00000544123.1_Missense_Mutation_p.S109I|RP11-286N3.1_ENST00000577527.1_RNA|EPB41L3_ENST00000540638.2_Missense_Mutation_p.S109I|EPB41L3_ENST00000400111.3_Missense_Mutation_p.S109I	NM_012307.2	NP_036439.2	Q9Y2J2	E41L3_HUMAN	erythrocyte membrane protein band 4.1-like 3	109					apoptotic process (GO:0006915)|cortical actin cytoskeleton organization (GO:0030866)|cortical cytoskeleton organization (GO:0030865)|cytoskeletal anchoring at plasma membrane (GO:0007016)|myelin maintenance (GO:0043217)|neuron projection morphogenesis (GO:0048812)|paranodal junction assembly (GO:0030913)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|protein localization to plasma membrane (GO:0072659)|regulation of cell shape (GO:0008360)	axolemma (GO:0030673)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extrinsic component of membrane (GO:0019898)|juxtaparanode region of axon (GO:0044224)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)	structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(52)|ovary(5)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	105						GCACTGCATGCTTTTAGGCTT	0.383													C|||	61	0.0121805	0.003	0.0101	5008	,	,		17612	0.0		0.0119	False		,,,				2504	0.0389				p.S109I		Atlas-SNP	.											.	EPB41L3	222	.	0			c.G326T						PASS	.	C	ILE/SER	12,4394	20.2+/-43.8	0,12,2191	180.0	162.0	168.0		326	4.3	1.0	18	dbSNP_132	168	107,8493	57.5+/-118.9	0,107,4193	yes	missense	EPB41L3	NM_012307.2	142	0,119,6384	AA,AC,CC		1.2442,0.2724,0.915	benign	109/1088	5478295	119,12887	2203	4300	6503	SO:0001583	missense	23136	exon3			TGCATGCTTTTAG	AB023204	CCDS11838.1, CCDS62381.1, CCDS62382.1	18p11.32	2006-06-28			ENSG00000082397	ENSG00000082397			3380	protein-coding gene	gene with protein product		605331				9828140, 9892180	Standard	NM_012307		Approved	DAL1, KIAA0987, 4.1B	uc002kmt.1	Q9Y2J2	OTTHUMG00000131562	ENST00000341928.2:c.326G>T	18.37:g.5478295C>A	ENSP00000343158:p.Ser109Ile	199.0	0.0	0		310.0	175.0	0.564516	NM_012307	B7Z4I5|F5GX05|O95713|Q9BRP5	Missense_Mutation	SNP	ENST00000341928.2	37	CCDS11838.1	18	0.008241758241758242	3	0.006097560975609756	4	0.011049723756906077	0	0.0	11	0.014511873350923483	C	13.03	2.115698	0.37339	0.002724	0.012442	ENSG00000082397	ENST00000341928;ENST00000544123;ENST00000342933;ENST00000400111;ENST00000542652	T;D;T;D	0.83075	-1.46;-1.64;-1.46;-1.68	5.16	4.27	0.50696	Band 4.1 domain (1);	0.241444	0.40385	N	0.001115	T	0.74268	0.3694	L	0.51422	1.61	0.80722	D	1	D;B;P;B	0.56746	0.977;0.002;0.858;0.002	P;B;B;B	0.47470	0.548;0.003;0.255;0.004	T	0.76814	-0.2820	10	0.42905	T	0.14	.	8.9723	0.35915	0.0:0.7703:0.0:0.2297	.	109;109;109;109	F5GX05;Q9Y2J2-3;Q9Y2J2-2;Q9Y2J2	.;.;.;E41L3_HUMAN	I	109;109;109;109;190	ENSP00000343158:S109I;ENSP00000441174:S109I;ENSP00000341138:S109I;ENSP00000382981:S109I	ENSP00000343158:S109I	S	-	2	0	EPB41L3	5468295	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.834000	0.27518	2.378000	0.81104	0.579000	0.79373	AGC	C|0.990;A|0.010	0.010	strong		0.383	EPB41L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254424.1	NM_012307	
OSBPL8	114882	hgsc.bcm.edu	37	12	76844711	76844711	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:76844711C>T	ENST00000261183.3	-	4	616	c.137G>A	c.(136-138)cGc>cAc	p.R46H	OSBPL8_ENST00000393250.4_Missense_Mutation_p.R4H|OSBPL8_ENST00000393249.2_Missense_Mutation_p.R4H	NM_020841.4	NP_065892.1	Q9BZF1	OSBL8_HUMAN	oxysterol binding protein-like 8	46					fat cell differentiation (GO:0045444)|lipid transport (GO:0006869)|negative regulation of cell migration (GO:0030336)|negative regulation of sequestering of triglyceride (GO:0010891)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of protein kinase B signaling (GO:0051897)|protein localization to nuclear pore (GO:0090204)	membrane (GO:0016020)|nuclear membrane (GO:0031965)	cholesterol binding (GO:0015485)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(2)	28						TTTTCCTTGGCGCTGACTCAT	0.443																																					p.R46H		Atlas-SNP	.											.	OSBPL8	86	.	0			c.G137A						PASS	.						160.0	139.0	146.0					12																	76844711		2203	4300	6503	SO:0001583	missense	114882	exon4			CCTTGGCGCTGAC	AF392452	CCDS31862.1, CCDS41814.1	12q14	2013-01-10				ENSG00000091039		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16396	protein-coding gene	gene with protein product		606736				1735225, 17991739	Standard	NM_020841		Approved	OSBP10, ORP8, MST120, MSTP120	uc001sye.1	Q9BZF1		ENST00000261183.3:c.137G>A	12.37:g.76844711C>T	ENSP00000261183:p.Arg46His	113.0	0.0	0		118.0	5.0	0.0423729	NM_020841	A8K1T2|E9PE66|E9PE68|Q52LQ3|Q68D75|Q8WXP8|Q9P277	Missense_Mutation	SNP	ENST00000261183.3	37	CCDS31862.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.943872	0.73672	.	.	ENSG00000091039	ENST00000393249;ENST00000261183;ENST00000446075;ENST00000393250;ENST00000438913;ENST00000547540;ENST00000548341;ENST00000553139;ENST00000549570;ENST00000551927;ENST00000547544	T;T;T;T;T;T	0.53423	1.34;2.64;1.34;2.64;2.64;0.62	5.66	5.66	0.87406	.	0.368655	0.29752	N	0.011290	T	0.37320	0.0999	N	0.19112	0.55	0.42098	D	0.991322	D	0.61080	0.989	B	0.42087	0.375	T	0.26573	-1.0099	10	0.42905	T	0.14	-3.9225	18.3033	0.90171	0.0:1.0:0.0:0.0	.	46	Q9BZF1	OSBL8_HUMAN	H	4;46;31;4;46;46;33;4;4;46;43	ENSP00000376939:R4H;ENSP00000261183:R46H;ENSP00000376940:R4H;ENSP00000450238:R46H;ENSP00000446886:R33H;ENSP00000449618:R4H	ENSP00000261183:R46H	R	-	2	0	OSBPL8	75368842	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	3.348000	0.52209	2.669000	0.90835	0.655000	0.94253	CGC	.	.	none		0.443	OSBPL8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000406357.1	NM_020841	
OBSCN	84033	hgsc.bcm.edu	37	1	228401329	228401329	+	Silent	SNP	C	C	T	rs185717159	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228401329C>T	ENST00000422127.1	+	3	1220	c.1176C>T	c.(1174-1176)cgC>cgT	p.R392R	OBSCN_ENST00000570156.2_Silent_p.R392R|OBSCN_ENST00000366707.4_5'UTR|C1orf145_ENST00000295012.5_Silent_p.L11L|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.R392R	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	392	Ig-like 4.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				TGACCGTGCGCAATGTCTCGG	0.706													C|||	17	0.00339457	0.0	0.0029	5008	,	,		6657	0.0		0.0139	False		,,,				2504	0.001				p.R392R		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C1176T						PASS	.	C	,	1,4053		0,1,2026	12.0	14.0	13.0		1176,1176	1.1	0.1	1		13	61,8229		0,61,4084	no	coding-synonymous,coding-synonymous	OBSCN	NM_001098623.1,NM_052843.2	,	0,62,6110	TT,TC,CC		0.7358,0.0247,0.5023	,	392/7969,392/6621	228401329	62,12282	2027	4145	6172	SO:0001819	synonymous_variant	84033	exon3			CGTGCGCAATGTC	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.1176C>T	1.37:g.228401329C>T		100.0	0.0	0		114.0	64.0	0.561404	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			C|0.994;T|0.006	0.006	strong		0.706	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
MYO10	4651	hgsc.bcm.edu	37	5	16676247	16676247	+	Missense_Mutation	SNP	G	G	A	rs61744227	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16676247G>A	ENST00000513610.1	-	34	5013	c.4559C>T	c.(4558-4560)tCg>tTg	p.S1520L	MYO10_ENST00000505695.1_Missense_Mutation_p.S859L|MYO10_ENST00000427430.2_Missense_Mutation_p.S877L|MYO10_ENST00000274203.9_Missense_Mutation_p.S877L|MYO10_ENST00000515803.1_Missense_Mutation_p.S859L	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	1520					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CACCACATCCGAGTTCAGGCA	0.428													G|||	19	0.00379393	0.0	0.0029	5008	,	,		17461	0.0		0.0109	False		,,,				2504	0.0061				p.S1520L		Atlas-SNP	.											.	MYO10	198	.	0			c.C4559T						PASS	.	G	LEU/SER	7,3821		0,7,1907	119.0	127.0	125.0		4559	3.3	0.0	5	dbSNP_129	125	84,8158		2,80,4039	yes	missense	MYO10	NM_012334.2	145	2,87,5946	AA,AG,GG		1.0192,0.1829,0.7539	benign	1520/2059	16676247	91,11979	1914	4121	6035	SO:0001583	missense	4651	exon34			ACATCCGAGTTCA	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.4559C>T	5.37:g.16676247G>A	ENSP00000421280:p.Ser1520Leu	117.0	0.0	0		82.0	37.0	0.451219	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	10	0.004578754578754579	0	0.0	0	0.0	0	0.0	10	0.013192612137203167	G	10.94	1.493361	0.26774	0.001829	0.010192	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.31	3.27	0.37495	.	.	.	.	.	T	0.18425	0.0442	N	0.17674	0.51	0.09310	N	1	B;B;B	0.09022	0.002;0.0;0.001	B;B;B	0.04013	0.001;0.0;0.001	T	0.17289	-1.0374	9	0.27785	T	0.31	.	6.3605	0.21425	0.1845:0.1421:0.6734:0.0	.	399;1160;1520	B4DIJ5;Q69YP8;Q9HD67	.;.;MYO10_HUMAN	L	1520;859;877;859;877	ENSP00000421280:S1520L;ENSP00000425051:S859L;ENSP00000274203:S877L;ENSP00000421170:S859L;ENSP00000391106:S877L	ENSP00000274203:S877L	S	-	2	0	MYO10	16729247	0.013000	0.17824	0.008000	0.14137	0.950000	0.60333	1.891000	0.39738	0.554000	0.29061	0.563000	0.77884	TCG	G|0.994;A|0.006	0.006	strong		0.428	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
GPR52	9293	hgsc.bcm.edu	37	1	174417941	174417941	+	Missense_Mutation	SNP	G	G	A	rs200286780	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:174417941G>A	ENST00000367685.2	+	1	730	c.692G>A	c.(691-693)cGt>cAt	p.R231H	RABGAP1L_ENST00000251507.4_Intron|RABGAP1L_ENST00000357444.6_Intron|RABGAP1L_ENST00000367689.3_Intron	NM_005684.4	NP_005675.3	Q9Y2T5	GPR52_HUMAN	G protein-coupled receptor 52	231					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)	G-protein coupled receptor activity (GO:0004930)			breast(3)|kidney(3)|large_intestine(3)|liver(1)|lung(7)|prostate(1)|skin(2)	20						AAAATTTGCCGTCAGCACACC	0.463													G|||	2	0.000399361	0.0015	0.0	5008	,	,		19971	0.0		0.0	False		,,,				2504	0.0				p.R231H	Ovarian(92;924 1390 1930 16467 40583)	Atlas-SNP	.											.	GPR52	40	.	0			c.G692A						PASS	.	G	HIS/ARG,	4,4402	8.1+/-20.4	0,4,2199	196.0	181.0	186.0		692,	6.2	1.0	1		186	2,8598	2.2+/-6.3	0,2,4298	yes	missense,intron	GPR52,RABGAP1L	NM_005684.4,NM_014857.4	29,	0,6,6497	AA,AG,GG		0.0233,0.0908,0.0461	probably-damaging,	231/362,	174417941	6,13000	2203	4300	6503	SO:0001583	missense	9293	exon1			TTTGCCGTCAGCA	AF096784	CCDS30941.1	1q24	2012-08-21			ENSG00000203737	ENSG00000203737		"""GPCR / Class A : Orphans"""	4508	protein-coding gene	gene with protein product		604106				9931487	Standard	NM_005684		Approved		uc001gka.1	Q9Y2T5	OTTHUMG00000034901	ENST00000367685.2:c.692G>A	1.37:g.174417941G>A	ENSP00000356658:p.Arg231His	99.0	0.0	0		122.0	49.0	0.401639	NM_005684	O75654|Q4VBL6|Q6ISM0	Missense_Mutation	SNP	ENST00000367685.2	37	CCDS30941.1	.	.	.	.	.	.	.	.	.	.	G	19.26	3.793374	0.70452	9.08E-4	2.33E-4	ENSG00000203737	ENST00000367685	T	0.42513	0.97	6.16	6.16	0.99307	GPCR, rhodopsin-like superfamily (1);	0.089581	0.47093	D	0.000250	T	0.55433	0.1920	L	0.54908	1.71	0.37430	D	0.913987	D	0.65815	0.995	P	0.52793	0.709	T	0.58352	-0.7651	10	0.66056	D	0.02	-9.9631	20.8598	0.99761	0.0:0.0:1.0:0.0	.	231	Q9Y2T5	GPR52_HUMAN	H	231	ENSP00000356658:R231H	ENSP00000356658:R231H	R	+	2	0	GPR52	172684564	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.126000	0.77201	2.937000	0.99478	0.650000	0.86243	CGT	.	.	weak		0.463	GPR52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084511.1	NM_005684	
DNAH2	146754	hgsc.bcm.edu	37	17	7701922	7701922	+	Silent	SNP	G	G	A	rs146210717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7701922G>A	ENST00000572933.1	+	55	9905	c.8445G>A	c.(8443-8445)acG>acA	p.T2815T	DNAH2_ENST00000389173.2_Silent_p.T2815T			Q9P225	DYH2_HUMAN	dynein, axonemal, heavy chain 2	2815	AAA 4. {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(3)|breast(11)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(2)|kidney(16)|large_intestine(53)|liver(2)|lung(49)|ovary(7)|prostate(7)|skin(15)|upper_aerodigestive_tract(1)|urinary_tract(1)	189		all_cancers(10;4.66e-07)|Prostate(122;0.081)				TCAAGACCACGTCCTTCATTT	0.547													G|||	4	0.000798722	0.0	0.0	5008	,	,		18237	0.0		0.004	False		,,,				2504	0.0				p.T2815T		Atlas-SNP	.											.	DNAH2	498	.	0			c.G8445A						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	111.0	102.0	105.0		8445	-9.6	0.9	17	dbSNP_134	105	24,8576	17.9+/-57.8	0,24,4276	no	coding-synonymous	DNAH2	NM_020877.2		0,26,6477	AA,AG,GG		0.2791,0.0454,0.1999		2815/4428	7701922	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	146754	exon54			GACCACGTCCTTC	U83570, AK128517	CCDS32551.1	17p13.1	2007-10-05	2006-09-04			ENSG00000183914		"""Axonemal dyneins"""	2948	protein-coding gene	gene with protein product		603333	"""dynein, axonemal, heavy polypeptide 2"", ""dynein heavy chain domain 3"""	DNHD3		9256245	Standard	XM_005256470		Approved	KIAA1503, FLJ46675	uc002giu.1	Q9P225		ENST00000572933.1:c.8445G>A	17.37:g.7701922G>A		48.0	0.0	0		61.0	33.0	0.540984	NM_020877	A8K992|B5MDX5|O15434|Q6PIH3|Q6ZR42	Silent	SNP	ENST00000572933.1	37	CCDS32551.1																																																																																			G|0.999;A|0.001	0.001	strong		0.547	DNAH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440241.1	NM_020877	
OR5H14	403273	hgsc.bcm.edu	37	3	97868656	97868656	+	Missense_Mutation	SNP	C	C	T	rs146577101	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:97868656C>T	ENST00000437310.1	+	1	487	c.427C>T	c.(427-429)Cgg>Tgg	p.R143W	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(3)|lung(17)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	31						ACTGTGCATCCGGCTATTAAT	0.388																																					p.R143W		Atlas-SNP	.											.	OR5H14	56	.	0			c.C427T						PASS	.	C	TRP/ARG	107,4297		0,107,2095	118.0	120.0	119.0		427	-0.7	0.0	3	dbSNP_134	119	163,8435		0,163,4136	no	missense	OR5H14	NM_001005514.1	101	0,270,6231	TT,TC,CC		1.8958,2.4296,2.0766	benign	143/311	97868656	270,12732	2202	4299	6501	SO:0001583	missense	403273	exon1			TGCATCCGGCTAT		CCDS33798.1	3q11.2	2013-09-23			ENSG00000236032	ENSG00000236032		"""GPCR / Class A : Olfactory receptors"""	31286	protein-coding gene	gene with protein product							Standard	NM_001005514		Approved		uc003dsg.1	A6NHG9	OTTHUMG00000160079	ENST00000437310.1:c.427C>T	3.37:g.97868656C>T	ENSP00000401706:p.Arg143Trp	357.0	0.0	0		529.0	72.0	0.136106	NM_001005514	B9EH15	Missense_Mutation	SNP	ENST00000437310.1	37	CCDS33798.1	.	.	.	.	.	.	.	.	.	.	C	5.787	0.329517	0.10956	0.024296	0.018958	ENSG00000236032	ENST00000437310	T	0.00130	8.69	2.49	-0.723	0.11181	GPCR, rhodopsin-like superfamily (1);	1.524830	0.04305	N	0.347965	T	0.00073	0.0002	L	0.39467	1.215	0.09310	N	1	B	0.15930	0.015	B	0.13407	0.009	T	0.23190	-1.0195	10	0.34782	T	0.22	.	3.4429	0.07470	0.0:0.3739:0.2056:0.4205	.	143	A6NHG9	O5H14_HUMAN	W	143	ENSP00000401706:R143W	ENSP00000401706:R143W	R	+	1	2	OR5H14	99351346	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-3.390000	0.00487	-0.356000	0.08187	0.195000	0.17529	CGG	C|0.936;T|0.064	0.064	strong		0.388	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
PDIA3	2923	hgsc.bcm.edu	37	15	44038850	44038850	+	Missense_Mutation	SNP	G	G	T	rs61734331	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:44038850G>T	ENST00000300289.5	+	1	261	c.113G>T	c.(112-114)cGc>cTc	p.R38L	CATSPER2P1_ENST00000381680.2_RNA|PDIA3_ENST00000538521.1_5'UTR|PDIA3_ENST00000469684.1_3'UTR	NM_005313.4	NP_005304.3	P30101	PDIA3_HUMAN	protein disulfide isomerase family A, member 3	38	Thioredoxin 1. {ECO:0000255|PROSITE- ProRule:PRU00691}.				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 peptide antigen via MHC class I (GO:0002474)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein import into nucleus (GO:0006606)|protein N-linked glycosylation via asparagine (GO:0018279)|protein retention in ER lumen (GO:0006621)|proteolysis (GO:0006508)|response to endoplasmic reticulum stress (GO:0034976)|signal transduction (GO:0007165)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	cysteine-type endopeptidase activity (GO:0004197)|phospholipase C activity (GO:0004629)|poly(A) RNA binding (GO:0044822)|protein disulfide isomerase activity (GO:0003756)			breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(9)|ovary(2)|skin(1)	17		all_cancers(109;2.61e-15)|all_epithelial(112;1.12e-12)|Lung NSC(122;2.17e-08)|all_lung(180;2.45e-07)|Melanoma(134;0.027)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;9.48e-07)		TTCGAGAGTCGCATCTCCGAC	0.682													G|||	8	0.00159744	0.0	0.0	5008	,	,		12466	0.001		0.003	False		,,,				2504	0.0041				p.R38L		Atlas-SNP	.											.	PDIA3	40	.	0			c.G113T						PASS	.	G	LEU/ARG	0,4334		0,0,2167	33.0	33.0	33.0		113	4.5	1.0	15	dbSNP_129	33	3,8511		0,3,4254	yes	missense	PDIA3	NM_005313.4	102	0,3,6421	TT,TG,GG		0.0352,0.0,0.0233	benign	38/506	44038850	3,12845	2167	4257	6424	SO:0001583	missense	2923	exon1			AGAGTCGCATCTC		CCDS10101.1	15q15	2009-11-20	2005-06-29	2005-03-03	ENSG00000167004	ENSG00000167004	5.3.4.1	"""Protein disulfide isomerases"""	4606	protein-coding gene	gene with protein product		602046	"""glucose regulated protein, 58kDa"", ""protein disulfide isomerase-associated 3"""	GRP58		8974399	Standard	NM_005313		Approved	P58, ERp61, ERp57, ERp60, GRP57, PI-PLC, HsT17083	uc001zsu.3	P30101	OTTHUMG00000044444	ENST00000300289.5:c.113G>T	15.37:g.44038850G>T	ENSP00000300289:p.Arg38Leu	59.0	0.0	0		57.0	29.0	0.508772	NM_005313	Q13453|Q14255|Q8IYF8|Q9UMU7	Missense_Mutation	SNP	ENST00000300289.5	37	CCDS10101.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	12.28	1.890128	0.33348	0.0	3.52E-4	ENSG00000167004	ENST00000300289	T	0.34667	1.35	5.46	4.53	0.55603	Thioredoxin domain (1);Thioredoxin-like fold (3);Disulphide isomerase (1);	0.293323	0.39834	N	0.001245	T	0.18173	0.0436	N	0.03324	-0.35	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.03773	-1.1005	10	0.27082	T	0.32	.	14.1256	0.65217	0.0:0.1506:0.8494:0.0	rs61734331	38	P30101	PDIA3_HUMAN	L	38	ENSP00000300289:R38L	ENSP00000300289:R38L	R	+	2	0	PDIA3	41826142	1.000000	0.71417	0.997000	0.53966	0.228000	0.25075	2.749000	0.47492	1.273000	0.44346	0.313000	0.20887	CGC	G|0.999;T|0.001	0.001	strong		0.682	PDIA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103532.3	NM_005313	
RRP12	23223	hgsc.bcm.edu	37	10	99150237	99150237	+	Silent	SNP	G	G	A	rs41300219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99150237G>A	ENST00000370992.4	-	6	807	c.696C>T	c.(694-696)ccC>ccT	p.P232P	RRP12_ENST00000315563.6_Intron|RRP12_ENST00000536831.1_Silent_p.P38P|RRP12_ENST00000414986.1_Silent_p.P171P	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	232						integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		GAAGGGTCACGGGGTAGCCCC	0.612													G|||	201	0.0401358	0.0598	0.0533	5008	,	,		19526	0.0		0.0716	False		,,,				2504	0.0133				p.P232P		Atlas-SNP	.											.	RRP12	97	.	0			c.C696T						PASS	.	G	,	254,4152	148.0+/-182.4	9,236,1958	58.0	56.0	57.0		513,696	-11.0	0.0	10	dbSNP_127	57	501,8099	144.5+/-200.4	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,703,5774	AA,AG,GG		5.8256,5.7649,5.805	,	171/1237,232/1298	99150237	755,12251	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon6			GGTCACGGGGTAG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.696C>T	10.37:g.99150237G>A		20.0	0.0	0		31.0	18.0	0.580645	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			G|0.949;A|0.051	0.051	strong		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
SCTR	6344	hgsc.bcm.edu	37	2	120194682	120194682	+	IGR	SNP	A	A	C	rs200510439		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:120194682A>C	ENST00000019103.5	-	0	1865				TMEM37_ENST00000465296.1_3'UTR|TMEM37_ENST00000306406.4_Missense_Mutation_p.H80P|TMEM37_ENST00000409826.1_Missense_Mutation_p.H92P	NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor						digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	GGCCAGGCCCATGTGCCCGGG	0.667													A|||	1	0.000199681	0.0	0.0	5008	,	,		14518	0.0		0.001	False		,,,				2504	0.0				p.H80P		Atlas-SNP	.											.	TMEM37	40	.	0			c.A239C						PASS	.	A	PRO/HIS	0,4406		0,0,2203	51.0	54.0	53.0		239	-1.9	0.0	2		53	5,8595	4.3+/-15.6	0,5,4295	no	missense	TMEM37	NM_183240.2	77	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	benign	80/191	120194682	5,13001	2203	4300	6503	SO:0001628	intergenic_variant	140738	exon2			AGGCCCATGTGCC		CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407		2.37:g.120194682A>C		48.0	0.0	0		40.0	15.0	0.375	NM_183240	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	ENST00000019103.5	37	CCDS2127.1	.	.	.	.	.	.	.	.	.	.	A	7.689	0.690644	0.15039	0.0	5.81E-4	ENSG00000171227	ENST00000409826;ENST00000306406	.	.	.	4.74	-1.88	0.07713	.	1.326400	0.04832	N	0.438832	T	0.37571	0.1008	L	0.44542	1.39	0.09310	N	1	B	0.32620	0.378	B	0.34931	0.192	T	0.39522	-0.9610	9	0.35671	T	0.21	0.0526	11.2183	0.48840	0.5495:0.0:0.4505:0.0	.	80	Q8WXS4	CCGL_HUMAN	P	92;80	.	ENSP00000303148:H80P	H	+	2	0	TMEM37	119911152	0.000000	0.05858	0.001000	0.08648	0.381000	0.30169	0.049000	0.14099	-0.500000	0.06614	0.459000	0.35465	CAT	.	.	weak		0.667	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254198.2		
RAPH1	65059	hgsc.bcm.edu	37	2	204306093	204306093	+	Missense_Mutation	SNP	G	G	A	rs541342499		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:204306093G>A	ENST00000319170.5	-	14	2119	c.1820C>T	c.(1819-1821)cCc>cTc	p.P607L	ABI2_ENST00000295851.5_3'UTR|RAPH1_ENST00000374493.3_Missense_Mutation_p.P659L|RAPH1_ENST00000457812.1_Intron	NM_213589.1	NP_998754.1	Q70E73	RAPH1_HUMAN	Ras association (RalGDS/AF-6) and pleckstrin homology domains 1	607					axon extension (GO:0048675)|cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)				breast(5)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(7)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32						GGATAAAGGGGGCACAAGTGA	0.517																																					p.P607L		Atlas-SNP	.											.	RAPH1	118	.	0			c.C1820T						PASS	.						32.0	35.0	34.0					2																	204306093		1757	3443	5200	SO:0001583	missense	65059	exon14			AAAGGGGGCACAA	AJ584699	CCDS2359.1, CCDS2360.1	2q33	2013-01-10	2003-11-25	2003-11-26	ENSG00000173166	ENSG00000173166		"""Pleckstrin homology (PH) domain containing"""	14436	protein-coding gene	gene with protein product	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 18"""	609035	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 9"""	ALS2CR9, ALS2CR18			Standard	NM_203365		Approved	KIAA1681	uc002vad.3	Q70E73	OTTHUMG00000132876	ENST00000319170.5:c.1820C>T	2.37:g.204306093G>A	ENSP00000316543:p.Pro607Leu	43.0	0.0	0		92.0	61.0	0.663043	NM_213589	Q96Q37|Q9C0I2	Missense_Mutation	SNP	ENST00000319170.5	37	CCDS2359.1	.	.	.	.	.	.	.	.	.	.	g	11.68	1.710804	0.30322	.	.	ENSG00000173166	ENST00000319170;ENST00000374493	T;T	0.75154	-0.91;-0.91	3.02	3.02	0.34903	.	1.838130	0.03300	U	0.188852	T	0.63546	0.2520	N	0.14661	0.345	0.80722	D	1	B	0.09022	0.002	B	0.06405	0.002	T	0.25187	-1.0139	10	0.34782	T	0.22	-8.7148	13.4277	0.61035	0.0:0.0:1.0:0.0	.	607	Q70E73	RAPH1_HUMAN	L	607;659	ENSP00000316543:P607L;ENSP00000363617:P659L	ENSP00000316543:P607L	P	-	2	0	RAPH1	204014338	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	4.020000	0.57189	2.008000	0.58898	0.479000	0.44913	CCC	.	.	none		0.517	RAPH1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256363.2	NM_025252	
FSTL5	56884	hgsc.bcm.edu	37	4	163032498	163032498	+	Missense_Mutation	SNP	C	C	G	rs140747357	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:163032498C>G	ENST00000306100.5	-	2	487	c.51G>C	c.(49-51)gaG>gaC	p.E17D	FSTL5_ENST00000379164.4_Missense_Mutation_p.E17D|FSTL5_ENST00000536695.1_Missense_Mutation_p.E17D|FSTL5_ENST00000427802.2_Missense_Mutation_p.E17D	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	17						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		TTCCTTCCGACTCCAGAAAAA	0.398													C|||	4	0.000798722	0.0	0.0	5008	,	,		14268	0.0		0.004	False		,,,				2504	0.0				p.E17D		Atlas-SNP	.											.	FSTL5	207	.	0			c.G51C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	7,4399	12.9+/-30.5	0,7,2196	131.0	125.0	127.0		51,51,51	-2.3	0.5	4	dbSNP_134	127	45,8555	29.0+/-79.6	0,45,4255	yes	missense,missense,missense	FSTL5	NM_001128427.1,NM_001128428.1,NM_020116.3	45,45,45	0,52,6451	GG,GC,CC		0.5233,0.1589,0.3998	benign,benign,benign	17/847,17/838,17/848	163032498	52,12954	2203	4300	6503	SO:0001583	missense	56884	exon2			TTCCGACTCCAGA	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.51G>C	4.37:g.163032498C>G	ENSP00000305334:p.Glu17Asp	101.0	0.0	0		81.0	41.0	0.506173	NM_001128428	E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	CCDS3802.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	C	2.069	-0.413600	0.04799	0.001589	0.005233	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.72725	-0.66;-0.65;-0.68;-0.65	5.51	-2.26	0.06867	.	0.753644	0.12056	N	0.503598	T	0.32556	0.0833	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;0.0	T	0.14671	-1.0464	10	0.17832	T	0.49	.	4.3997	0.11381	0.2402:0.3205:0.0:0.4394	.	17;17;17	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	D	17	ENSP00000305334:E17D;ENSP00000368462:E17D;ENSP00000389270:E17D;ENSP00000440409:E17D	ENSP00000305334:E17D	E	-	3	2	FSTL5	163251948	0.865000	0.29922	0.477000	0.27303	0.010000	0.07245	-0.188000	0.09642	-0.753000	0.04721	-1.975000	0.00460	GAG	C|0.996;G|0.004	0.004	strong		0.398	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
GALK1	2584	hgsc.bcm.edu	37	17	73751175	73751175	+	Intron	SNP	C	C	T	rs140501692		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73751175C>T	ENST00000225614.2	-	8	1301				ITGB4_ENST00000200181.3_Intron|ITGB4_ENST00000450894.3_Intron|ITGB4_ENST00000339591.3_Missense_Mutation_p.P1463L|ITGB4_ENST00000579662.1_Intron|ITGB4_ENST00000449880.2_Missense_Mutation_p.P1463L			P51570	GALK1_HUMAN	galactokinase 1						carbohydrate metabolic process (GO:0005975)|galactitol metabolic process (GO:0019402)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)|galactokinase activity (GO:0004335)|galactose binding (GO:0005534)			endometrium(2)|large_intestine(1)|lung(1)|prostate(1)	5	all_cancers(13;1.5e-07)		all cancers(21;1.03e-06)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			AGCAGGCTTCCGCTGTCCTGG	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		17871	0.001		0.0	False		,,,				2504	0.0				p.P1463L		Atlas-SNP	.											ITGB4_ENST00000339591,colon,carcinoma,+1,1	ITGB4	165	1	0			c.C4388T						PASS	.	C	,LEU/PRO,	0,4406		0,0,2203	47.0	49.0	48.0		,4388,	5.3	1.0	17	dbSNP_134	48	5,8589		0,5,4292	yes	intron,missense,intron	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	,98,	0,5,6495	TT,TC,CC		0.0582,0.0,0.0385	,,	,1463/1806,	73751175	5,12995	2203	4297	6500	SO:0001627	intron_variant	3691	exon33			GGCTTCCGCTGTC		CCDS11728.1	17q25.1	2013-09-19			ENSG00000108479	ENSG00000108479	2.7.1.6		4118	protein-coding gene	gene with protein product		604313		GALK		7670469	Standard	NM_000154		Approved		uc002jpk.3	P51570	OTTHUMG00000179832	ENST00000225614.2:c.1176+2939G>A	17.37:g.73751175C>T		50.0	0.0	0		43.0	22.0	0.511628	NM_001005619	B2RC07|B4E1G6	Missense_Mutation	SNP	ENST00000225614.2	37	CCDS11728.1	.	.	.	.	.	.	.	.	.	.	C	16.09	3.025433	0.54683	0.0	5.82E-4	ENSG00000132470	ENST00000339591;ENST00000449880	T;T	0.73152	-0.72;-0.72	5.26	5.26	0.73747	.	.	.	.	.	T	0.58323	0.2114	.	.	.	0.80722	D	1	B	0.20459	0.045	B	0.13407	0.009	T	0.53920	-0.8370	8	0.30078	T	0.28	.	11.5095	0.50486	0.0:0.9144:0.0:0.0856	.	1463	P16144-3	.	L	1463	ENSP00000344079:P1463L;ENSP00000400217:P1463L	ENSP00000344079:P1463L	P	+	2	0	ITGB4	71262770	0.989000	0.36119	1.000000	0.80357	0.996000	0.88848	1.319000	0.33655	2.455000	0.83008	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	weak		0.622	GALK1-002	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448427.1		
BMPER	168667	hgsc.bcm.edu	37	7	34091570	34091570	+	Silent	SNP	T	T	G	rs117988035	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:34091570T>G	ENST00000297161.2	+	9	1148	c.774T>G	c.(772-774)gcT>gcG	p.A258A	BMPER_ENST00000426693.1_Silent_p.A258A|BMPER_ENST00000494786.1_3'UTR	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	258	VWFC 4. {ECO:0000255|PROSITE- ProRule:PRU00220}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						ACTGCACAGCTTGTACCTGCA	0.478													T|||	36	0.0071885	0.0	0.0173	5008	,	,		22541	0.0		0.0149	False		,,,				2504	0.0092				p.A258A		Atlas-SNP	.											.	BMPER	131	.	0			c.T774G						PASS	.	T		9,4397	15.5+/-35.6	0,9,2194	168.0	147.0	154.0		774	-10.2	0.0	7	dbSNP_132	154	103,8497	57.2+/-118.5	0,103,4197	no	coding-synonymous	BMPER	NM_133468.3		0,112,6391	GG,GT,TT		1.1977,0.2043,0.8611		258/686	34091570	112,12894	2203	4300	6503	SO:0001819	synonymous_variant	168667	exon9			CACAGCTTGTACC		CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.774T>G	7.37:g.34091570T>G		97.0	0.0	0		156.0	43.0	0.275641	NM_133468	A8K1P8|Q8TF36	Silent	SNP	ENST00000297161.2	37	CCDS5442.1																																																																																			T|0.990;G|0.010	0.010	strong		0.478	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2	NM_133468	
POTEH	23784	hgsc.bcm.edu	37	22	16287538	16287538	+	Silent	SNP	G	G	A	rs200179046	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:16287538G>A	ENST00000343518.6	-	1	399	c.348C>T	c.(346-348)aaC>aaT	p.N116N		NM_001136213.1	NP_001129685.1	Q6S545	POTEH_HUMAN	POTE ankyrin domain family, member H	116										NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(20)|ovary(1)|skin(7)|urinary_tract(2)	37						AAGTGCCCACGTTGCTCTTGC	0.602													G|||	29	0.00579073	0.0113	0.0	5008	,	,		24150	0.001		0.002	False		,,,				2504	0.0112				p.N116N		Atlas-SNP	.											POTEH,colon,carcinoma,0,1	POTEH	114	1	0			c.C348T						scavenged	.						95.0	108.0	103.0					22																	16287538		2058	3900	5958	SO:0001819	synonymous_variant	23784	exon1			GCCCACGTTGCTC	AY462874	CCDS74808.1	22q11.1	2013-01-10	2008-11-26	2008-11-26	ENSG00000198062	ENSG00000198062		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	133	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 7"""	608913	"""actin, beta-like 1"", ""ANKRD26-like family C, member 3"""	ACTBL1, A26C3		10591208, 15276201, 21439273	Standard	NM_001136213		Approved	POTE22, CT104.7	uc010gqp.2	Q6S545	OTTHUMG00000140314	ENST00000343518.6:c.348C>T	22.37:g.16287538G>A		128.0	1.0	0.0078125		270.0	22.0	0.0814815	NM_001136213	A2CEK4|A6NCI1|A9Z1W0	Silent	SNP	ENST00000343518.6	37	CCDS46658.1																																																																																			A|0.008;C|0.006;G|0.986	0.008	strong		0.602	POTEH-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000276918.4	NM_001136213	
SYNGR1	9145	hgsc.bcm.edu	37	22	39777880	39777880	+	Silent	SNP	C	C	T	rs74681509	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:39777880C>T	ENST00000328933.5	+	4	678	c.663C>T	c.(661-663)ttC>ttT	p.F221F		NM_004711.4	NP_004702.2	O43759	SNG1_HUMAN	synaptogyrin 1	221					protein targeting (GO:0006605)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|synaptic vesicle membrane (GO:0030672)				endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|skin(1)	7	Melanoma(58;0.04)					CCAACACCTTCGACACCGAGC	0.701													C|||	2	0.000399361	0.0	0.0	5008	,	,		13145	0.001		0.0	False		,,,				2504	0.001				p.F221F		Atlas-SNP	.											SYNGR1,colon,carcinoma,0,1	SYNGR1	19	1	0			c.C663T						PASS	.	C		1,4405		0,1,2202	25.0	26.0	25.0		663	-6.1	0.3	22	dbSNP_131	25	0,8594		0,0,4297	no	coding-synonymous	SYNGR1	NM_004711.4		0,1,6499	TT,TC,CC		0.0,0.0227,0.0077		221/234	39777880	1,12999	2203	4297	6500	SO:0001819	synonymous_variant	9145	exon4			CACCTTCGACACC	AJ002303	CCDS13989.1, CCDS13990.1, CCDS13991.1	22q13	2008-06-10			ENSG00000100321	ENSG00000100321			11498	protein-coding gene	gene with protein product		603925				9760194, 10595519	Standard	NM_004711		Approved			O43759	OTTHUMG00000030978	ENST00000328933.5:c.663C>T	22.37:g.39777880C>T		96.0	0.0	0		90.0	34.0	0.377778	NM_004711	A6NP69|A8K0E2|O43757|O43758|Q53Y02|Q96J56|Q9UGZ4	Silent	SNP	ENST00000328933.5	37	CCDS13989.1																																																																																			C|1.000;T|0.000	0.000	strong		0.701	SYNGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075866.2	NM_004711	
WSCD1	23302	hgsc.bcm.edu	37	17	6012955	6012955	+	Nonsense_Mutation	SNP	G	G	A	rs267604993		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:6012955G>A	ENST00000574946.1	+	6	1268	c.878G>A	c.(877-879)tGg>tAg	p.W293*	WSCD1_ENST00000539421.1_Nonsense_Mutation_p.W293*|WSCD1_ENST00000574232.1_Nonsense_Mutation_p.W293*|WSCD1_ENST00000573634.1_Nonsense_Mutation_p.W177*|WSCD1_ENST00000317744.5_Nonsense_Mutation_p.W293*			Q658N2	WSCD1_HUMAN	WSC domain containing 1	293	WSC 2. {ECO:0000255|PROSITE- ProRule:PRU00558}.					integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(1)	35						CTCAGGGGCTGGGAATGCTAC	0.572																																					p.W293X		Atlas-SNP	.											.	WSCD1	84	.	0			c.G878A						PASS	.						241.0	225.0	231.0					17																	6012955		2203	4300	6503	SO:0001587	stop_gained	23302	exon6			GGGGCTGGGAATG		CCDS32538.1	17p13.2	2008-02-05				ENSG00000179314			29060	protein-coding gene	gene with protein product							Standard	XM_005256572		Approved	KIAA0523	uc002gcn.3	Q658N2		ENST00000574946.1:c.878G>A	17.37:g.6012955G>A	ENSP00000460825:p.Trp293*	65.0	0.0	0		63.0	19.0	0.301587	NM_015253	A8K0N8|D3DTM3|O60276|Q96G45	Nonsense_Mutation	SNP	ENST00000574946.1	37	CCDS32538.1	.	.	.	.	.	.	.	.	.	.	G	37	6.412301	0.97546	.	.	ENSG00000179314	ENST00000317744;ENST00000539421	.	.	.	5.91	3.83	0.44106	.	0.417502	0.27122	N	0.020825	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-23.0413	13.247	0.60028	0.0:0.4832:0.5167:0.0	.	.	.	.	X	293	.	ENSP00000323087:W293X	W	+	2	0	WSCD1	5953679	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	0.973000	0.29422	1.464000	0.47987	0.650000	0.86243	TGG	.	.	none		0.572	WSCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438965.4	NM_015253	
PIGL	9487	hgsc.bcm.edu	37	17	16203290	16203290	+	Missense_Mutation	SNP	C	C	A	rs115958467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:16203290C>A	ENST00000225609.5	+	3	441	c.424C>A	c.(424-426)Ctg>Atg	p.L142M	PIGL_ENST00000498772.2_Missense_Mutation_p.L142M|PIGL_ENST00000581006.1_Missense_Mutation_p.L142M|PIGL_ENST00000395844.4_Missense_Mutation_p.L142M	NM_004278.3	NP_004269.1	Q9Y2B2	PIGL_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class L	142					C-terminal protein lipidation (GO:0006501)|cellular protein metabolic process (GO:0044267)|GPI anchor biosynthetic process (GO:0006506)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	N-acetylglucosaminylphosphatidylinositol deacetylase activity (GO:0000225)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|skin(1)	11				UCEC - Uterine corpus endometrioid carcinoma (92;0.0934)		TGGCATCAATCTGGTAAGGGG	0.522													C|||	11	0.00219649	0.0	0.0086	5008	,	,		20273	0.0		0.005	False		,,,				2504	0.0				p.L142M		Atlas-SNP	.											.	PIGL	16	.	0			c.C424A						PASS	.	C	MET/LEU	10,4396	16.8+/-37.8	0,10,2193	133.0	115.0	121.0		424	1.3	1.0	17	dbSNP_132	121	61,8539	38.3+/-94.2	1,59,4240	yes	missense	PIGL	NM_004278.3	15	1,69,6433	AA,AC,CC		0.7093,0.227,0.5459	probably-damaging	142/253	16203290	71,12935	2203	4300	6503	SO:0001583	missense	9487	exon3			ATCAATCTGGTAA	AB017165	CCDS11176.1	17p12-p11.2	2013-02-26	2006-06-28		ENSG00000108474	ENSG00000108474	3.5.1.89	"""Phosphatidylinositol glycan anchor biosynthesis"""	8966	protein-coding gene	gene with protein product	"""N-acetylglucosaminylphosphatidylinositol deacetylase"""	605947	"""phosphatidylinositol glycan, class L"""			10085243	Standard	NM_004278		Approved		uc002gpv.3	Q9Y2B2	OTTHUMG00000059346	ENST00000225609.5:c.424C>A	17.37:g.16203290C>A	ENSP00000225609:p.Leu142Met	58.0	0.0	0		73.0	40.0	0.547945	NM_004278	A8KA67|B4DYN4	Missense_Mutation	SNP	ENST00000225609.5	37	CCDS11176.1	8	0.003663003663003663	0	0.0	4	0.011049723756906077	0	0.0	4	0.005277044854881266	C	12.67	2.008068	0.35415	0.00227	0.007093	ENSG00000108474	ENST00000225609;ENST00000395844	T;T	0.78707	-1.2;-1.2	4.47	1.28	0.21552	Putative deacetylase LmbE-like domain (2);	0.000000	0.64402	D	0.000001	T	0.73426	0.3585	M	0.66378	2.025	0.35873	D	0.828373	D;D	0.56968	0.978;0.978	P;P	0.54499	0.754;0.754	T	0.77930	-0.2403	10	0.54805	T	0.06	-14.4259	6.9712	0.24650	0.0:0.7108:0.0:0.2892	.	142;142	B4DYN4;Q9Y2B2	.;PIGL_HUMAN	M	142	ENSP00000225609:L142M;ENSP00000379185:L142M	ENSP00000225609:L142M	L	+	1	2	PIGL	16144015	0.733000	0.28132	0.962000	0.40283	0.273000	0.26683	0.159000	0.16442	0.221000	0.20879	0.460000	0.39030	CTG	C|0.996;A|0.004	0.004	strong		0.522	PIGL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131881.1		
SAFB2	9667	hgsc.bcm.edu	37	19	5590291	5590291	+	Silent	SNP	G	G	T	rs117896034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:5590291G>T	ENST00000252542.4	-	18	2787	c.2523C>A	c.(2521-2523)ccC>ccA	p.P841P		NM_014649.2	NP_055464.1	Q14151	SAFB2_HUMAN	scaffold attachment factor B2	841	Gly-rich.|Interacts with SAFB1.				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)|identical protein binding (GO:0042802)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(4)|large_intestine(7)|lung(8)|ovary(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				UCEC - Uterine corpus endometrioid carcinoma (162;0.000228)		CCACTAACCTGGGGGGAGGGG	0.677													G|||	44	0.00878594	0.0	0.0144	5008	,	,		15349	0.0089		0.0199	False		,,,				2504	0.0051				p.P841P	Ovarian(127;888 1728 23957 44128 52668)	Atlas-SNP	.											.	SAFB2	90	.	0			c.C2523A						PASS	.	G		8,4326		0,8,2159	7.0	10.0	9.0		2523	3.3	1.0	19	dbSNP_132	9	122,8386		1,120,4133	no	coding-synonymous	SAFB2	NM_014649.2		1,128,6292	TT,TG,GG		1.4339,0.1846,1.0123		841/954	5590291	130,12712	2167	4254	6421	SO:0001819	synonymous_variant	9667	exon18			TAACCTGGGGGGA	D50928	CCDS32879.1	19p13.3	2013-02-12				ENSG00000130254		"""RNA binding motif (RRM) containing"""	21605	protein-coding gene	gene with protein product		608066				12660241	Standard	NM_014649		Approved	KIAA0138	uc002mcd.3	Q14151		ENST00000252542.4:c.2523C>A	19.37:g.5590291G>T		71.0	0.0	0		60.0	28.0	0.466667	NM_014649	B4DKG3|Q8TB13	Silent	SNP	ENST00000252542.4	37	CCDS32879.1																																																																																			G|0.984;T|0.016	0.016	strong		0.677	SAFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451016.1	NM_014649	
TTN	7273	hgsc.bcm.edu	37	2	179611847	179611847	+	Intron	SNP	T	T	G	rs141105907|rs397517814	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611847T>G	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.R5094R			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)			GTGGAGTATCTCTCCAGAGTC	0.537													T|||	5	0.000998403	0.0	0.0029	5008	,	,		15680	0.0		0.003	False		,,,				2504	0.0				p.R5094R		Atlas-SNP	.											.	TTN	18412	.	0			c.A15280C						PASS	.	T	,,,,	0,4406		0,0,2203	62.0	74.0	70.0		,,15280,,	4.4	1.0	2	dbSNP_134	70	2,8596		0,2,4297	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	0,2,6500	GG,GT,TT		0.0233,0.0,0.0154	,,,,	,,5094/5605,,	179611847	2,13002	2203	4299	6502	SO:0001627	intron_variant	7273	exon46			AGTATCTCTCCAG	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.10361-5199A>C	2.37:g.179611847T>G		132.0	0.0	0		148.0	35.0	0.236486	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																																																																																				T|0.998;G|0.002	0.002	strong		0.537	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
MAPK8IP3	23162	hgsc.bcm.edu	37	16	1817855	1817855	+	Silent	SNP	C	C	T	rs118038816	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1817855C>T	ENST00000250894.4	+	28	3613	c.3456C>T	c.(3454-3456)gtC>gtT	p.V1152V	MAPK8IP3_ENST00000356010.5_Silent_p.V1146V	NM_015133.3	NP_055948.2	Q9UPT6	JIP3_HUMAN	mitogen-activated protein kinase 8 interacting protein 3	1152					activation of JUN kinase activity (GO:0007257)|axon guidance (GO:0007411)|forebrain development (GO:0030900)|in utero embryonic development (GO:0001701)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|positive regulation of neuron differentiation (GO:0045666)|post-embryonic development (GO:0009791)|protein localization (GO:0008104)|regulation of gene expression (GO:0010468)|regulation of JNK cascade (GO:0046328)|respiratory gaseous exchange (GO:0007585)|vesicle-mediated transport (GO:0016192)	axolemma (GO:0030673)|dendrite (GO:0030425)|Golgi membrane (GO:0000139)|smooth endoplasmic reticulum (GO:0005790)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(20)|ovary(1)|prostate(2)|skin(2)|urinary_tract(3)	42						CCCTGCTTGTCGCGGGCAGCC	0.667													C|||	46	0.0091853	0.0189	0.0014	5008	,	,		18035	0.0		0.005	False		,,,				2504	0.0153				p.V1152V		Atlas-SNP	.											.	MAPK8IP3	164	.	0			c.C3456T						PASS	.	C	,	63,4141		0,63,2039	61.0	73.0	69.0		3438,3456	-5.8	0.1	16	dbSNP_132	69	31,8405		0,31,4187	no	coding-synonymous,coding-synonymous	MAPK8IP3	NM_001040439.1,NM_015133.3	,	0,94,6226	TT,TC,CC		0.3675,1.4986,0.7437	,	1146/1331,1152/1337	1817855	94,12546	2102	4218	6320	SO:0001819	synonymous_variant	23162	exon28			GCTTGTCGCGGGC	AB028989	CCDS10442.2, CCDS45379.1	16p13.3	2009-11-23			ENSG00000138834	ENSG00000138834			6884	protein-coding gene	gene with protein product	"""homolog of Drosophila Sunday driver 2"""	605431				10523642, 10629060	Standard	XM_005255187		Approved	KIAA1066, JSAP1, JIP3, syd	uc002cmk.3	Q9UPT6	OTTHUMG00000128637	ENST00000250894.4:c.3456C>T	16.37:g.1817855C>T		65.0	0.0	0		84.0	47.0	0.559524	NM_015133	A2A2B3|A7E2B3|Q96RY4|Q9H4I4|Q9H7P1|Q9NUG0	Silent	SNP	ENST00000250894.4	37	CCDS10442.2																																																																																			C|0.995;T|0.005	0.005	strong		0.667	MAPK8IP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250508.2	NM_001040439	
SDCBP2	27111	hgsc.bcm.edu	37	20	1301053	1301053	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:1301053G>A	ENST00000360779.3	-	2	181	c.8C>T	c.(7-9)tCc>tTc	p.S3F	SDCBP2_ENST00000339987.3_Missense_Mutation_p.S3F|SDCBP2_ENST00000381812.1_Missense_Mutation_p.S3F	NM_080489.4	NP_536737.3	Q9H190	SDCB2_HUMAN	syndecan binding protein (syntenin) 2	3					intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|nervous system development (GO:0007399)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(1)|large_intestine(3)|lung(1)|skin(1)|stomach(1)	7						TGGGTACAGGGATGACATGGC	0.552																																					p.S3F		Atlas-SNP	.											.	SDCBP2	78	.	0			c.C8T						PASS	.						142.0	138.0	139.0					20																	1301053		1976	4166	6142	SO:0001583	missense	27111	exon2			TACAGGGATGACA	AF131809	CCDS13013.1, CCDS42848.1	20p13	2008-07-02			ENSG00000125775	ENSG00000125775			15756	protein-coding gene	gene with protein product						11152476	Standard	NM_080489		Approved	ST-2, SITAC18	uc021vzn.1	Q9H190	OTTHUMG00000031661	ENST00000360779.3:c.8C>T	20.37:g.1301053G>A	ENSP00000354013:p.Ser3Phe	85.0	0.0	0		89.0	22.0	0.247191	NM_080489	O95892|Q5W0X1|Q9BZ42|Q9H567|Q9NRY8	Missense_Mutation	SNP	ENST00000360779.3	37	CCDS42848.1	.	.	.	.	.	.	.	.	.	.	G	10.74	1.434411	0.25813	.	.	ENSG00000125775	ENST00000381812;ENST00000360779;ENST00000339987	T;T;T	0.44881	0.91;0.91;0.91	4.83	0.43	0.16515	.	1.007080	0.07972	N	0.984107	T	0.54711	0.1875	L	0.55481	1.735	0.23204	N	0.998129	P;D	0.67145	0.911;0.996	B;D	0.63033	0.382;0.91	T	0.47156	-0.9139	10	0.87932	D	0	-5.793	9.2402	0.37491	0.3788:0.0:0.6212:0.0	.	3;3	B4DKI5;Q9H190	.;SDCB2_HUMAN	F	3	ENSP00000371233:S3F;ENSP00000354013:S3F;ENSP00000342935:S3F	ENSP00000342935:S3F	S	-	2	0	SDCBP2	1249053	0.635000	0.27199	0.232000	0.24009	0.011000	0.07611	3.304000	0.51866	0.243000	0.21327	-0.258000	0.10820	TCC	.	.	none		0.552	SDCBP2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077513.2	NM_080489	
SLC23A2	9962	hgsc.bcm.edu	37	20	4855309	4855309	+	Silent	SNP	G	G	A	rs41282100	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4855309G>A	ENST00000379333.1	-	10	1250	c.858C>T	c.(856-858)taC>taT	p.Y286Y	SLC23A2_ENST00000424750.2_Silent_p.Y172Y|SLC23A2_ENST00000338244.1_Silent_p.Y286Y|SLC23A2_ENST00000468355.1_5'UTR	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	286					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)			endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						CATTTCTGGCGTATTGAGAAA	0.368													A|||	32	0.00638978	0.0129	0.0101	5008	,	,		20889	0.0		0.008	False		,,,				2504	0.0				p.Y286Y		Atlas-SNP	.											.	SLC23A2	62	.	0			c.C858T						PASS	.	A	,	55,4351	821.2+/-416.4	0,55,2148	119.0	122.0	121.0		858,858	3.7	1.0	20	dbSNP_127	121	107,8493	814.5+/-407.0	1,105,4194	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	1,160,6342	AA,AG,GG		1.2442,1.2483,1.2456	,	286/651,286/651	4855309	162,12844	2203	4300	6503	SO:0001819	synonymous_variant	9962	exon10			TCTGGCGTATTGA	AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.858C>T	20.37:g.4855309G>A		79.0	0.0	0		60.0	29.0	0.483333	NM_203327	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1	11	0.005036630036630037	3	0.006097560975609756	5	0.013812154696132596	0	0.0	3	0.00395778364116095	A	0.141	-1.102585	0.01828	0.012483	0.012442	ENSG00000089057	ENST00000423430	.	.	.	5.9	3.67	0.42095	.	.	.	.	.	T	0.50000	0.1590	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.44772	-0.9306	4	.	.	.	-10.7793	8.3011	0.32014	0.7051:0.0:0.2949:0.0	rs41282100	.	.	.	C	43	.	.	R	-	1	0	SLC23A2	4803309	1.000000	0.71417	0.982000	0.44146	0.006000	0.05464	2.001000	0.40825	0.161000	0.19458	-0.982000	0.02568	CGC	G|0.990;A|0.010	0.010	strong		0.368	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1		
MYO19	80179	hgsc.bcm.edu	37	17	34854121	34854121	+	Missense_Mutation	SNP	C	C	T	rs139565052	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:34854121C>T	ENST00000431794.3	-	25	3268	c.2746G>A	c.(2746-2748)Gcg>Acg	p.A916T	ZNHIT3_ENST00000588253.1_3'UTR|ZNHIT3_ENST00000590858.1_3'UTR|MYO19_ENST00000268852.9_Missense_Mutation_p.A716T	NM_001163735.1	NP_001157207.1	Q96H55	MYO19_HUMAN	myosin XIX	916	Mitochondrial targeting.					cytoplasm (GO:0005737)|mitochondrial outer membrane (GO:0005741)|myosin complex (GO:0016459)	ATP binding (GO:0005524)|motor activity (GO:0003774)			endometrium(6)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|urinary_tract(1)	20		Breast(25;0.00957)|Ovarian(249;0.17)	Kidney(155;0.104)	UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		TGAGGCAGCGCTCGGATGGAC	0.572													C|||	3	0.000599042	0.0	0.0014	5008	,	,		17680	0.0		0.002	False		,,,				2504	0.0				p.A916T		Atlas-SNP	.											.	MYO19	130	.	0			c.G2746A						PASS	.	C	THR/ALA,THR/ALA	1,4313		0,1,2156	74.0	76.0	75.0		2746,2146	5.9	1.0	17	dbSNP_134	75	18,8512		0,18,4247	yes	missense,missense	MYO19	NM_001163735.1,NM_025109.5	58,58	0,19,6403	TT,TC,CC		0.211,0.0232,0.1479	probably-damaging,probably-damaging	916/971,716/771	34854121	19,12825	2157	4265	6422	SO:0001583	missense	80179	exon26			GCAGCGCTCGGAT	BC008900	CCDS45654.1, CCDS54112.1, CCDS59283.1	17q12	2014-08-12	2007-09-26	2007-09-26	ENSG00000278259	ENSG00000278259		"""Myosins / Myosin superfamily : Class XIX"""	26234	protein-coding gene	gene with protein product			"""myosin head domain containing 1"""	MYOHD1		17877792, 19932026	Standard	NM_001033580		Approved	FLJ22865	uc010wcy.2	Q96H55	OTTHUMG00000188437	ENST00000431794.3:c.2746G>A	17.37:g.34854121C>T	ENSP00000409936:p.Ala916Thr	20.0	0.0	0		28.0	10.0	0.357143	NM_001163735	Q59GS4|Q9H5X2	Missense_Mutation	SNP	ENST00000431794.3	37	CCDS54112.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	C	27.1	4.800048	0.90538	2.32E-4	0.00211	ENSG00000141140	ENST00000415126;ENST00000431794;ENST00000268852	T;T	0.74002	-0.8;-0.8	5.91	5.91	0.95273	.	0.000000	0.42294	D	0.000730	D	0.85353	0.5677	M	0.65498	2.005	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	D	0.85959	0.1469	10	0.87932	D	0	.	17.0716	0.86576	0.0:1.0:0.0:0.0	.	916;716	Q96H55;Q96H55-4	MYO19_HUMAN;.	T	374;916;716	ENSP00000409936:A916T;ENSP00000268852:A716T	ENSP00000268852:A716T	A	-	1	0	MYO19	31928234	1.000000	0.71417	0.999000	0.59377	0.831000	0.47069	4.579000	0.60936	2.821000	0.97095	0.485000	0.47835	GCG	C|0.999;T|0.001	0.001	strong		0.572	MYO19-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451074.1	NM_025109	
SEMA3G	56920	hgsc.bcm.edu	37	3	52476899	52476899	+	Missense_Mutation	SNP	G	G	A	rs138988057	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:52476899G>A	ENST00000231721.2	-	2	139	c.140C>T	c.(139-141)gCc>gTc	p.A47V		NM_020163.1	NP_064548.1	Q9NS98	SEM3G_HUMAN	sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3G	47	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				multicellular organismal development (GO:0007275)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	receptor activity (GO:0004872)			kidney(1)|large_intestine(5)|lung(8)|ovary(2)|prostate(1)|skin(1)	18				BRCA - Breast invasive adenocarcinoma(193;1.69e-05)|Kidney(197;0.00173)|KIRC - Kidney renal clear cell carcinoma(197;0.00196)|OV - Ovarian serous cystadenocarcinoma(275;0.0333)		CAGAAAGATGGCAGAGCGGTT	0.617													G|||	10	0.00199681	0.0	0.0	5008	,	,		19476	0.0		0.0099	False		,,,				2504	0.0				p.A47V		Atlas-SNP	.											.	SEMA3G	58	.	0			c.C140T						PASS	.	G	VAL/ALA	0,4404		0,0,2202	54.0	55.0	54.0		140	4.1	1.0	3	dbSNP_134	54	23,8575		0,23,4276	yes	missense	SEMA3G	NM_020163.1	64	0,23,6478	AA,AG,GG		0.2675,0.0,0.1769	benign	47/783	52476899	23,12979	2202	4299	6501	SO:0001583	missense	56920	exon2			AAGATGGCAGAGC		CCDS2856.1	3p21.1	2013-01-11			ENSG00000010319	ENSG00000010319		"""Semaphorins"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	30400	protein-coding gene	gene with protein product						11214971	Standard	XM_005265327		Approved	FLJ00014, sem2	uc003dea.1	Q9NS98	OTTHUMG00000158570	ENST00000231721.2:c.140C>T	3.37:g.52476899G>A	ENSP00000231721:p.Ala47Val	67.0	0.0	0		94.0	57.0	0.606383	NM_020163	Q7L9D9|Q9H7Q3	Missense_Mutation	SNP	ENST00000231721.2	37	CCDS2856.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	G	7.761	0.705426	0.15172	0.0	0.002675	ENSG00000010319	ENST00000231721;ENST00000475739	T;T	0.20069	2.1;2.1	4.93	4.05	0.47172	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (2);	0.142087	0.47852	D	0.000201	T	0.06371	0.0164	N	0.12182	0.205	0.09310	N	1	B	0.10296	0.003	B	0.12156	0.007	T	0.30475	-0.9977	10	0.13853	T	0.58	.	5.736	0.18067	0.2264:0.0:0.7736:0.0	.	47	Q9NS98	SEM3G_HUMAN	V	47;65	ENSP00000231721:A47V;ENSP00000419181:A65V	ENSP00000231721:A47V	A	-	2	0	SEMA3G	52451939	0.000000	0.05858	0.962000	0.40283	0.733000	0.41908	0.733000	0.26087	2.302000	0.77476	0.561000	0.74099	GCC	G|0.998;A|0.002	0.002	strong		0.617	SEMA3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351354.1	NM_020163	
POLA1	5422	hgsc.bcm.edu	37	X	25014016	25014016	+	Silent	SNP	C	C	T	rs11573531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:25014016C>T	ENST00000379059.3	+	37	4353	c.4338C>T	c.(4336-4338)taC>taT	p.Y1446Y	POLA1_ENST00000379068.3_Silent_p.Y1452Y	NM_016937.3	NP_058633.2	P09884	DPOLA_HUMAN	polymerase (DNA directed), alpha 1, catalytic subunit	1446					cell proliferation (GO:0008283)|DNA replication (GO:0006260)|DNA replication initiation (GO:0006270)|DNA replication, synthesis of RNA primer (GO:0006269)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via nonhomologous end joining (GO:0006303)|G1/S transition of mitotic cell cycle (GO:0000082)|lagging strand elongation (GO:0006273)|leading strand elongation (GO:0006272)|mitotic cell cycle (GO:0000278)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|translesion synthesis (GO:0019985)|viral process (GO:0016032)	alpha DNA polymerase:primase complex (GO:0005658)|cytoplasm (GO:0005737)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	3'-5' exonuclease activity (GO:0008408)|4 iron, 4 sulfur cluster binding (GO:0051539)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed DNA polymerase activity (GO:0003887)|metal ion binding (GO:0046872)|nucleoside binding (GO:0001882)|nucleotide binding (GO:0000166)|protein kinase binding (GO:0019901)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|skin(2)	11					Cladribine(DB00242)|Clofarabine(DB00631)|Fludarabine(DB01073)|Nelarabine(DB01280)	GAAGTGGCTACTCCGAAGTGA	0.443													C|||	8	0.00211921	0.0	0.0014	3775	,	,		12343	0.0		0.007	False		,,,				2504	0.0				p.Y1446Y		Atlas-SNP	.											.	POLA1	117	.	0			c.C4338T						PASS	.	C		9,3824		0,7,2,1624,569	73.0	60.0	64.0		4338	3.3	1.0	X	dbSNP_120	64	101,6627		0,79,22,2349,1850	no	coding-synonymous	POLA1	NM_016937.3		0,86,24,3973,2419	TT,TC,T,CC,C		1.5012,0.2348,1.0416		1446/1463	25014016	110,10451	2202	4300	6502	SO:0001819	synonymous_variant	5422	exon37			TGGCTACTCCGAA		CCDS14214.1	Xp22.1-p21.3	2014-01-30	2008-08-07	2006-09-26	ENSG00000101868	ENSG00000101868	2.7.7.7	"""DNA polymerases"""	9173	protein-coding gene	gene with protein product		312040	"""polymerase (DNA directed), alpha"", ""polymerase (DNA directed), alpha 1"", ""N syndrome (mental retardation, malformations, chromosome breakage)"""	POLA, NSX		1689958	Standard	NM_016937		Approved	p180	uc004dbl.3	P09884	OTTHUMG00000021277	ENST00000379059.3:c.4338C>T	X.37:g.25014016C>T		150.0	0.0	0		139.0	139.0	1	NM_016937	Q86UQ7	Silent	SNP	ENST00000379059.3	37	CCDS14214.1																																																																																			C|0.990;T|0.010	0.010	strong		0.443	POLA1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056111.1	NM_016937	
KIAA0319L	79932	hgsc.bcm.edu	37	1	35944609	35944609	+	Missense_Mutation	SNP	T	T	C	rs34372241	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:35944609T>C	ENST00000325722.3	-	4	1105	c.871A>G	c.(871-873)Acc>Gcc	p.T291A		NM_024874.4	NP_079150.3	Q8IZA0	K319L_HUMAN	KIAA0319-like	291						cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(3)|large_intestine(7)|lung(12)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|urinary_tract(1)	34		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GCCTGGGGGGTAGGGGTAGCA	0.488													T|||	10	0.00199681	0.0	0.0014	5008	,	,		17721	0.0		0.0089	False		,,,				2504	0.0				p.T291A		Atlas-SNP	.											.	KIAA0319L	156	.	0			c.A871G						PASS	.	T	ALA/THR	9,4397	15.5+/-35.6	0,9,2194	80.0	85.0	84.0		871	-1.9	0.0	1	dbSNP_126	84	86,8514	49.4+/-109.1	1,84,4215	yes	missense	KIAA0319L	NM_024874.4	58	1,93,6409	CC,CT,TT		1.0,0.2043,0.7304	benign	291/1050	35944609	95,12911	2203	4300	6503	SO:0001583	missense	79932	exon4			GGGGGGTAGGGGT	AY163234	CCDS390.1	1p34.3	2008-10-24			ENSG00000142687	ENSG00000142687			30071	protein-coding gene	gene with protein product		613535				11347906	Standard	NM_024874		Approved	KIAA1837	uc001byx.3	Q8IZA0	OTTHUMG00000004370	ENST00000325722.3:c.871A>G	1.37:g.35944609T>C	ENSP00000318406:p.Thr291Ala	46.0	0.0	0		46.0	21.0	0.456522	NM_024874	B1AN13|D3DPR8|O95010|Q6PJJ7|Q7L1C9|Q8N2B3|Q8NDA0|Q8WY39|Q8WYZ5|Q96IC3|Q96JJ0|Q9BUW6|Q9H7V0	Missense_Mutation	SNP	ENST00000325722.3	37	CCDS390.1	7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	6|6	0.0079155672823219|0.0079155672823219	T|T	3.559|3.559	-0.090063|-0.090063	0.07053|0.07053	0.002043|0.002043	0.01|0.01	ENSG00000142687|ENSG00000142687	ENST00000325722;ENST00000426982;ENST00000440579;ENST00000373258|ENST00000431916	T;T;T;T|.	0.34667|.	3.24;3.24;2.68;1.35|.	5.65|5.65	-1.92|-1.92	0.07618|0.07618	Fibronectin, type III (1);|.	0.784679|.	0.11712|.	N|.	0.536788|.	T|T	0.18045|0.18045	0.0433|0.0433	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	B;B;B|.	0.09022|.	0.002;0.0;0.0|.	B;B;B|.	0.11329|.	0.006;0.0;0.001|.	T|T	0.27365|0.27365	-1.0076|-1.0076	10|5	0.45353|.	T|.	0.12|.	-3.0E-4|-3.0E-4	10.2654|10.2654	0.43452|0.43452	0.0:0.5192:0.0:0.4807|0.0:0.5192:0.0:0.4807	rs34372241|rs34372241	291;291;291|.	B4DYG9;B1AN14;Q8IZA0|.	.;.;K319L_HUMAN|.	A|C	291|154	ENSP00000318406:T291A;ENSP00000395883:T291A;ENSP00000407576:T291A;ENSP00000362355:T291A|.	ENSP00000318406:T291A|.	T|Y	-|-	1|2	0|0	KIAA0319L|KIAA0319L	35717196|35717196	0.012000|0.012000	0.17670|0.17670	0.001000|0.001000	0.08648|0.08648	0.016000|0.016000	0.09150|0.09150	0.013000|0.013000	0.13310|0.13310	-0.368000|-0.368000	0.08040|0.08040	-0.297000|-0.297000	0.09499|0.09499	ACC|TAC	T|0.994;C|0.006	0.006	strong		0.488	KIAA0319L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012684.2	NM_024874	
VPS18	57617	hgsc.bcm.edu	37	15	41192540	41192540	+	Silent	SNP	C	C	T	rs79536497	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41192540C>T	ENST00000220509.5	+	4	1863	c.1524C>T	c.(1522-1524)ggC>ggT	p.G508G	VPS18_ENST00000558474.1_Intron	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	508					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		CTCTGCAGGGCGACCCAGAGG	0.612													C|||	7	0.00139776	0.0008	0.0	5008	,	,		17114	0.0		0.006	False		,,,				2504	0.0				p.G508G		Atlas-SNP	.											.	VPS18	67	.	0			c.C1524T						PASS	.	C		5,4401	9.9+/-24.2	0,5,2198	76.0	86.0	82.0		1524	-5.3	0.7	15	dbSNP_131	82	65,8535	38.8+/-94.9	0,65,4235	no	coding-synonymous	VPS18	NM_020857.2		0,70,6433	TT,TC,CC		0.7558,0.1135,0.5382		508/974	41192540	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	57617	exon4			GCAGGGCGACCCA	AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.1524C>T	15.37:g.41192540C>T		61.0	0.0	0		54.0	23.0	0.425926	NM_020857	Q8TCG0|Q96DI3|Q9H268	Silent	SNP	ENST00000220509.5	37	CCDS10069.1																																																																																			C|0.996;T|0.004	0.004	strong		0.612	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2		
DHRS4	10901	hgsc.bcm.edu	37	14	24435542	24435542	+	Missense_Mutation	SNP	G	G	T	rs11556285		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24435542G>T	ENST00000313250.5	+	6	785	c.582G>T	c.(580-582)aaG>aaT	p.K194N	DHRS4_ENST00000558263.1_Intron|DHRS4_ENST00000397075.3_Intron|DHRS4_ENST00000397073.2_Intron|DHRS4_ENST00000558581.1_Missense_Mutation_p.K160N|DHRS4_ENST00000421831.1_Missense_Mutation_p.K142N|DHRS4_ENST00000382761.3_Intron|DHRS4_ENST00000559632.1_Intron|DHRS4_ENST00000543741.2_Intron|DHRS4_ENST00000308178.8_Intron|DHRS4_ENST00000397074.3_Intron	NM_021004.2	NP_066284.2	Q9BTZ2	DHRS4_HUMAN	dehydrogenase/reductase (SDR family) member 4	194					alcohol metabolic process (GO:0006066)|cellular ketone metabolic process (GO:0042180)|oxidation-reduction process (GO:0055114)|protein tetramerization (GO:0051262)|steroid metabolic process (GO:0008202)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	3-keto sterol reductase activity (GO:0000253)|alcohol dehydrogenase [NAD(P)+] activity (GO:0018455)|carbonyl reductase (NADPH) activity (GO:0004090)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|receptor binding (GO:0005102)			central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(1)|lung(4)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	14				GBM - Glioblastoma multiforme(265;0.00962)	Vitamin A(DB00162)	GCCTGACCAAGACCCTGGCCA	0.502																																					p.K194N		Atlas-SNP	.											.	DHRS4	22	.	0			c.G582T						PASS	.																																			SO:0001583	missense	10901	exon6			GACCAAGACCCTG	AF044127	CCDS9605.1, CCDS61408.1, CCDS61409.1, CCDS61410.1, CCDS61411.1, CCDS61412.1	14q11.2	2013-06-14			ENSG00000157326	ENSG00000157326	1.1.1.184	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	16985	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 25C, member 2"""	611596				10333503, 19027726	Standard	NM_021004		Approved	SCAD-SRL, SDR-SRL, humNRDR, FLJ11008, SDR25C2	uc001wla.3	Q9BTZ2	OTTHUMG00000028777	ENST00000313250.5:c.582G>T	14.37:g.24435542G>T	ENSP00000326219:p.Lys194Asn	685.0	0.0	0		751.0	38.0	0.0505992	NM_021004	B2RB10|B7WNS9|D3YTB8|E2QRL8|O95162|Q20CR0|Q2LC19|Q2LE81|Q58IU4|Q6E0Y1|Q6UWU3|Q71UQ6|Q8TD03|Q9H3N5|Q9NV08	Missense_Mutation	SNP	ENST00000313250.5	37	CCDS9605.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.739826	0.30865	.	.	ENSG00000157326	ENST00000313250;ENST00000421831	T;T	0.46063	0.88;0.88	3.53	2.63	0.31362	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.294117	0.30639	N	0.009188	T	0.54838	0.1883	M	0.82056	2.57	0.80722	D	1	B;P	0.39862	0.326;0.692	B;P	0.52823	0.238;0.71	T	0.54609	-0.8268	10	0.72032	D	0.01	.	5.9644	0.19316	0.251:0.0:0.749:0.0	rs11556285;rs11556285	160;194	Q9BTZ2-4;Q9BTZ2	.;DHRS4_HUMAN	N	194;142	ENSP00000326219:K194N;ENSP00000404147:K142N	ENSP00000326219:K194N	K	+	3	2	DHRS4	23505382	1.000000	0.71417	0.998000	0.56505	0.689000	0.40095	1.961000	0.40432	0.599000	0.29845	0.580000	0.79431	AAG	G|0.998;T|0.002	0.002	weak		0.502	DHRS4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071857.3		
KIF14	9928	hgsc.bcm.edu	37	1	200558420	200558420	+	Silent	SNP	C	C	T	rs77213709	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:200558420C>T	ENST00000367350.4	-	18	3477	c.3039G>A	c.(3037-3039)aaG>aaA	p.K1013K		NM_014875.2	NP_055690.1	Q15058	KIF14_HUMAN	kinesin family member 14	1013	Required for CIT-binding.				ATP catabolic process (GO:0006200)|cytoskeleton-dependent intracellular transport (GO:0030705)|establishment of protein localization (GO:0045184)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|negative regulation of integrin activation (GO:0033624)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of Rap protein signal transduction (GO:0032487)|substrate adhesion-dependent cell spreading (GO:0034446)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|PDZ domain binding (GO:0030165)			NS(1)|breast(5)|central_nervous_system(2)|endometrium(8)|kidney(8)|large_intestine(15)|lung(13)|ovary(3)|prostate(2)|skin(3)|urinary_tract(1)	61						GCTGCTTTGCCTTTTCTAATT	0.303													C|||	30	0.00599042	0.0	0.0	5008	,	,		19286	0.0		0.007	False		,,,				2504	0.0235				p.K1013K		Atlas-SNP	.											.	KIF14	156	.	0			c.G3039A						PASS	.	C		3,4401	6.2+/-15.9	0,3,2199	158.0	146.0	150.0		3039	3.1	0.3	1	dbSNP_132	150	33,8567	22.2+/-67.0	0,33,4267	no	coding-synonymous	KIF14	NM_014875.2		0,36,6466	TT,TC,CC		0.3837,0.0681,0.2768		1013/1649	200558420	36,12968	2202	4300	6502	SO:0001819	synonymous_variant	9928	exon18			CTTTGCCTTTTCT	D26361	CCDS30963.1	1q32.1	2008-03-03			ENSG00000118193	ENSG00000118193		"""Kinesins"""	19181	protein-coding gene	gene with protein product		611279				7584044	Standard	NM_014875		Approved	KIAA0042	uc010ppk.1	Q15058	OTTHUMG00000035723	ENST00000367350.4:c.3039G>A	1.37:g.200558420C>T		216.0	0.0	0		303.0	175.0	0.577558	NM_014875	Q14CI8|Q4G0A5|Q5T1W3	Silent	SNP	ENST00000367350.4	37	CCDS30963.1																																																																																			C|0.996;T|0.004	0.004	strong		0.303	KIF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086878.1	NM_014875	
ST5	6764	hgsc.bcm.edu	37	11	8724191	8724191	+	Missense_Mutation	SNP	A	A	G	rs113126215	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000313726.6_Missense_Mutation_p.V883A|ST5_ENST00000530991.1_Missense_Mutation_p.V355A|ST5_ENST00000530438.1_Missense_Mutation_p.V463A|ST5_ENST00000357665.1_Missense_Mutation_p.V883A|RPL27A_ENST00000531102.1_Intron|ST5_ENST00000526757.1_Missense_Mutation_p.V463A|ST5_ENST00000526099.1_Missense_Mutation_p.V396A	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	37.0	0.0	0		35.0	17.0	0.485714	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	
ARAP1	116985	hgsc.bcm.edu	37	11	72421569	72421569	+	Missense_Mutation	SNP	C	C	T	rs369752678	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:72421569C>T	ENST00000393609.3	-	10	1479	c.1277G>A	c.(1276-1278)cGg>cAg	p.R426Q	ARAP1_ENST00000393605.3_Missense_Mutation_p.R186Q|ARAP1_ENST00000455638.2_Missense_Mutation_p.R426Q|ARAP1_ENST00000429686.1_Missense_Mutation_p.R181Q|ARAP1_ENST00000426523.1_Missense_Mutation_p.R181Q|ARAP1_ENST00000359373.5_Missense_Mutation_p.R426Q|ARAP1_ENST00000334211.8_Missense_Mutation_p.R181Q	NM_001040118.2	NP_001035207.1	Q96P48	ARAP1_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 1	426					actin filament reorganization involved in cell cycle (GO:0030037)|negative regulation of stress fiber assembly (GO:0051497)|positive regulation of Cdc42 GTPase activity (GO:0043089)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of receptor recycling (GO:0001921)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of cellular component movement (GO:0051270)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			cervix(2)|endometrium(2)|large_intestine(10)|lung(8)|ovary(1)|skin(3)|urinary_tract(1)	27						GCTAGAGAGCCGGGCCCGGGC	0.632													C|||	2	0.000399361	0.0015	0.0	5008	,	,		16560	0.0		0.0	False		,,,				2504	0.0				p.R426Q	Ovarian(102;1198 1520 13195 17913 37529)	Atlas-SNP	.											.	ARAP1	168	.	0			c.G1277A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	0,4400		0,0,2200	34.0	36.0	35.0		1277,542,542	1.5	0.0	11		35	1,8585	1.2+/-3.3	0,1,4292	no	missense,missense,missense	ARAP1	NM_001040118.2,NM_001135190.1,NM_015242.4	43,43,43	0,1,6492	TT,TC,CC		0.0116,0.0,0.0077	benign,benign,benign	426/1451,181/1134,181/1206	72421569	1,12985	2200	4293	6493	SO:0001583	missense	116985	exon10			GAGAGCCGGGCCC	AF411983	CCDS8217.2, CCDS41687.1, CCDS44671.1	11q13.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000186635	ENSG00000186635		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	16925	protein-coding gene	gene with protein product		606646	"""centaurin, delta 2"""	CENTD2			Standard	NM_001040118		Approved		uc001osu.3	Q96P48	OTTHUMG00000157102	ENST00000393609.3:c.1277G>A	11.37:g.72421569C>T	ENSP00000377233:p.Arg426Gln	57.0	0.0	0		48.0	22.0	0.458333	NM_001040118	A3KLL7|B2RTS2|O94879|Q4LDD5|Q59FI7|Q6PHS3|Q8WU51|Q96HP6|Q96L71	Missense_Mutation	SNP	ENST00000393609.3	37	CCDS41687.1	.	.	.	.	.	.	.	.	.	.	C	2.665	-0.278826	0.05642	0.0	1.16E-4	ENSG00000186635	ENST00000359373;ENST00000455638;ENST00000393605;ENST00000334211;ENST00000393609;ENST00000426523;ENST00000429686;ENST00000340247	T;T;T;T;T;T;T	0.06371	3.34;3.34;3.33;3.38;3.36;3.37;3.31	5.55	1.46	0.22682	.	0.843042	0.10345	N	0.685879	T	0.04543	0.0124	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.001;0.0	B;B;B;B;B	0.06405	0.001;0.0;0.001;0.0;0.002	T	0.49113	-0.8973	10	0.08381	T	0.77	.	4.7688	0.13146	0.0:0.5092:0.148:0.3428	.	181;181;426;426;186	E7EU13;B2RTS2;Q96P48-3;Q96P48;Q96P48-1	.;.;.;ARAP1_HUMAN;.	Q	426;426;186;181;426;181;181;215	ENSP00000352332:R426Q;ENSP00000390461:R426Q;ENSP00000377230:R186Q;ENSP00000335506:R181Q;ENSP00000377233:R426Q;ENSP00000392264:R181Q;ENSP00000403127:R181Q	ENSP00000335506:R181Q	R	-	2	0	ARAP1	72099217	0.000000	0.05858	0.013000	0.15412	0.255000	0.26057	0.317000	0.19487	0.014000	0.14944	0.655000	0.94253	CGG	.	.	weak		0.632	ARAP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000347428.1	NM_001040118	
FMN1	342184	hgsc.bcm.edu	37	15	33359950	33359950	+	Intron	SNP	C	C	G	rs141655944	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:33359950C>G	ENST00000559047.1	-	3	2043				FMN1_ENST00000334528.9_Missense_Mutation_p.E46Q|FMN1_ENST00000559150.1_Intron|FMN1_ENST00000561249.1_Intron|FMN1_ENST00000558197.1_Missense_Mutation_p.E46Q			Q68DA7	FMN1_HUMAN	formin 1						actin nucleation (GO:0045010)	actin filament (GO:0005884)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|upper_aerodigestive_tract(3)	29		all_lung(180;1.14e-07)		all cancers(64;3.05e-15)|Epithelial(43;1.67e-10)|GBM - Glioblastoma multiforme(186;4.95e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0262)		TTCACAGATTCTAATTTACTC	0.443													C|||	17	0.00339457	0.0	0.0014	5008	,	,		21879	0.0		0.0149	False		,,,				2504	0.001				p.E46Q		Atlas-SNP	.											.	FMN1	174	.	0			c.G136C						PASS	.	C	GLN/GLU	12,3768		0,12,1878	71.0	68.0	69.0		136	4.9	1.0	15	dbSNP_134	69	111,8147		2,107,4020	yes	missense	FMN1	NM_001103184.2	29	2,119,5898	GG,GC,CC		1.3442,0.3175,1.0218	probably-damaging	46/1197	33359950	123,11915	1890	4129	6019	SO:0001627	intron_variant	342184	exon1			CAGATTCTAATTT	AH002864	CCDS45209.1, CCDS61581.1, CCDS61582.1	15q13.3	2013-06-13	2005-01-20	2005-01-22	ENSG00000248905	ENSG00000248905			3768	protein-coding gene	gene with protein product	"""limb deformity protein"""	136535	"""formin (limb deformity)"""	LD, FMN		1673046	Standard	NM_001277313		Approved	DKFZP686C2281, FLJ45135, MGC125288, MGC125289	uc031qrh.1	Q68DA7	OTTHUMG00000172201	ENST00000559047.1:c.2044-2675G>C	15.37:g.33359950C>G		109.0	0.0	0		84.0	43.0	0.511905	NM_001103184	Q3B7I6|Q3ZAR4|Q6ZSY1	Missense_Mutation	SNP	ENST00000559047.1	37		13	0.005952380952380952	0	0.0	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	C	11.34	1.608899	0.28623	0.003175	0.013442	ENSG00000248905	ENST00000334528	T	0.52983	0.64	4.92	4.92	0.64577	.	.	.	.	.	T	0.50616	0.1626	.	.	.	.	.	.	D;D	0.67145	0.996;0.989	P;P	0.59357	0.856;0.714	T	0.66333	-0.5950	7	0.66056	D	0.02	.	18.2894	0.90124	0.0:1.0:0.0:0.0	.	46;46	Q68DA7-3;Q68DA7-5	.;.	Q	46	ENSP00000333950:E46Q	ENSP00000333950:E46Q	E	-	1	0	FMN1	31147242	0.996000	0.38824	0.977000	0.42913	0.071000	0.16799	5.064000	0.64338	2.556000	0.86216	0.655000	0.94253	GAA	C|0.993;G|0.007	0.007	strong		0.443	FMN1-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000417414.1	NM_001103184	
LZTR1	8216	hgsc.bcm.edu	37	22	21347142	21347142	+	Silent	SNP	C	C	T	rs145833752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21347142C>T	ENST00000215739.8	+	11	1568	c.1209C>T	c.(1207-1209)ttC>ttT	p.F403F	LZTR1_ENST00000479606.1_3'UTR|LZTR1_ENST00000389355.3_Silent_p.F384F	NM_006767.3	NP_006758.2	Q8N653	LZTR1_HUMAN	leucine-zipper-like transcription regulator 1	403					anatomical structure morphogenesis (GO:0009653)|regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(13)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)	42	all_cancers(11;1.83e-25)|all_epithelial(7;9.19e-23)|Lung NSC(8;3.06e-15)|all_lung(8;5.05e-14)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|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;0.195)			TGTACATCTTCGGGGGCACGG	0.652													C|||	24	0.00479233	0.0023	0.0029	5008	,	,		19667	0.001		0.0109	False		,,,				2504	0.0072				p.F403F		Atlas-SNP	.											.	LZTR1	99	.	0			c.C1209T						PASS	.	C		7,4393	12.9+/-30.5	0,7,2193	55.0	45.0	48.0		1209	-5.1	1.0	22	dbSNP_134	48	78,8522	43.6+/-101.6	0,78,4222	no	coding-synonymous	LZTR1	NM_006767.3		0,85,6415	TT,TC,CC		0.907,0.1591,0.6538		403/841	21347142	85,12915	2200	4300	6500	SO:0001819	synonymous_variant	8216	exon11			CATCTTCGGGGGC	D38496	CCDS33606.1	22q11.21	2013-01-09	2004-12-10		ENSG00000099949	ENSG00000099949		"""BTB/POZ domain containing"""	6742	protein-coding gene	gene with protein product		600574	"""leucine-zipper-like transcriptional regulator 1"""			7633402, 16356934	Standard	NM_006767		Approved	LZTR-1, BTBD29	uc002zto.3	Q8N653	OTTHUMG00000150878	ENST00000215739.8:c.1209C>T	22.37:g.21347142C>T		93.0	0.0	0		116.0	64.0	0.551724	NM_006767	Q14776|Q20WK0	Silent	SNP	ENST00000215739.8	37	CCDS33606.1																																																																																			C|0.994;T|0.006	0.006	strong		0.652	LZTR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320387.1	NM_006767	
LRWD1	222229	hgsc.bcm.edu	37	7	102112914	102112914	+	Silent	SNP	C	C	T	rs184787600	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:102112914C>T	ENST00000292616.5	+	13	1700	c.1548C>T	c.(1546-1548)agC>agT	p.S516S	MIR4467_ENST00000578629.1_RNA	NM_152892.1	NP_690852.1	Q9UFC0	LRWD1_HUMAN	leucine-rich repeats and WD repeat domain containing 1	516					chromatin modification (GO:0016568)|chromatin organization (GO:0006325)|DNA replication initiation (GO:0006270)|establishment of protein localization to chromatin (GO:0071169)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nuclear origin of replication recognition complex (GO:0005664)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)|telomeric heterochromatin (GO:0031933)	chromatin binding (GO:0003682)|methyl-CpG binding (GO:0008327)|methylated histone binding (GO:0035064)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|skin(1)|stomach(2)	20						CCAAGGGGAGCGGCCTGGGCA	0.682													C|||	16	0.00319489	0.0008	0.0029	5008	,	,		14662	0.0		0.008	False		,,,				2504	0.0051				p.S516S		Atlas-SNP	.											LRWD1,colon,carcinoma,0,1	LRWD1	41	1	0			c.C1548T						PASS	.	C		10,4230		0,10,2110	11.0	12.0	12.0		1548	-4.2	0.0	7		12	86,8236		0,86,4075	no	coding-synonymous	LRWD1	NM_152892.1		0,96,6185	TT,TC,CC		1.0334,0.2358,0.7642		516/648	102112914	96,12466	2120	4161	6281	SO:0001819	synonymous_variant	222229	exon13			GGGGAGCGGCCTG	AL133057	CCDS34715.1	7q22.1	2013-01-10			ENSG00000161036	ENSG00000161036		"""WD repeat domain containing"""	21769	protein-coding gene	gene with protein product	"""origin recognition complex associated"", ""centromere protein 33"""	615167				20932478, 20850016, 20180869	Standard	NM_152892		Approved	DKFZp434K1815, ORCA, CENP-33	uc003uzn.3	Q9UFC0	OTTHUMG00000157718	ENST00000292616.5:c.1548C>T	7.37:g.102112914C>T		22.0	0.0	0		23.0	10.0	0.434783	NM_152892	A8K4K2|B2R9G2|Q8N0T9|Q8WV43|Q96GJ2	Silent	SNP	ENST00000292616.5	37	CCDS34715.1	10	0.004578754578754579	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	C	5.586	0.292913	0.10567	0.002358	0.010334	ENSG00000161036	ENST00000488689;ENST00000468175	.	.	.	5.1	-4.25	0.03766	.	.	.	.	.	T	0.21962	0.0529	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.34254	-0.9836	4	.	.	.	-19.7101	8.7692	0.34722	0.0949:0.4915:0.0:0.4135	.	.	.	.	V	127;102	.	.	A	+	2	0	LRWD1	101899919	0.000000	0.05858	0.001000	0.08648	0.712000	0.41017	-1.540000	0.02200	-0.725000	0.04901	0.655000	0.94253	GCG	C|0.995;T|0.005	0.005	strong		0.682	LRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349493.1	NM_152892	
MLPH	79083	hgsc.bcm.edu	37	2	238434245	238434245	+	Splice_Site	SNP	C	C	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238434245C>G	ENST00000264605.3	+	7	971	c.677C>G	c.(676-678)tCc>tGc	p.S226C	MLPH_ENST00000338530.4_Splice_Site_p.S226C|MLPH_ENST00000410032.1_Intron|MLPH_ENST00000468178.1_3'UTR|MLPH_ENST00000445024.2_Splice_Site_p.S226C|MLPH_ENST00000409373.1_Splice_Site_p.S186C	NM_024101.5	NP_077006.1	Q9BV36	MELPH_HUMAN	melanophilin	226					melanocyte differentiation (GO:0030318)|melanosome localization (GO:0032400)|protein targeting (GO:0006605)	cortical actin cytoskeleton (GO:0030864)|extracellular vesicular exosome (GO:0070062)|microtubule organizing center (GO:0005815)|microtubule plus-end (GO:0035371)|stress fiber (GO:0001725)	metal ion binding (GO:0046872)			NS(1)|breast(3)|cervix(1)|endometrium(3)|large_intestine(2)|lung(11)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	25		Breast(86;0.000381)|Renal(207;0.000966)|Ovarian(221;0.0695)|all_hematologic(139;0.095)|all_lung(227;0.17)|Melanoma(123;0.203)		Epithelial(121;1.17e-21)|OV - Ovarian serous cystadenocarcinoma(60;1.02e-10)|Kidney(56;4.23e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.15e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000439)|Lung(119;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0316)		TGTGCTTAGTCCCTCACAGAT	0.607																																					p.S226C		Atlas-SNP	.											.	MLPH	41	.	0			c.C677G						PASS	.						42.0	44.0	44.0					2																	238434245		2203	4300	6503	SO:0001630	splice_region_variant	79083	exon7			CTTAGTCCCTCAC	AY358857	CCDS2518.1, CCDS42836.1, CCDS63172.1, CCDS63173.1	2q37.2	2014-09-17			ENSG00000115648	ENSG00000115648			29643	protein-coding gene	gene with protein product		606526				11980908, 11504925	Standard	NM_024101		Approved	l1Rk3, l(1)-3Rk, Slac-2a, ln, exophilin-3	uc002vwt.3	Q9BV36	OTTHUMG00000133298	ENST00000264605.3:c.676-1C>G	2.37:g.238434245C>G		74.0	0.0	0		104.0	51.0	0.490385	NM_001042467	B3KSS2|B4DKW7|G5E9G5|Q9HA71	Missense_Mutation	SNP	ENST00000264605.3	37	CCDS2518.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.10|10.10	1.256882|1.256882	0.22965|0.22965	.|.	.|.	ENSG00000115648|ENSG00000115648	ENST00000437893|ENST00000264605;ENST00000445024;ENST00000338530;ENST00000409373	T|T;T;T;T	0.30182|0.29655	1.54|1.92;1.91;1.78;1.56	3.35|3.35	1.51|1.51	0.23008|0.23008	.|.	.|2.607010	.|0.01744	.|N	.|0.029577	T|T	0.39655|0.39655	0.1086|0.1086	L|L	0.40543|0.40543	1.245|1.245	0.35469|0.35469	D|D	0.797185|0.797185	.|B;D;B;D;B;B	.|0.71674	.|0.017;0.998;0.085;0.986;0.137;0.021	.|B;P;B;P;B;B	.|0.56216	.|0.017;0.747;0.071;0.794;0.149;0.023	T|T	0.32640|0.32640	-0.9899|-0.9899	7|10	0.87932|0.54805	D|T	0|0.06	-6.1716|-6.1716	4.7792|4.7792	0.13194|0.13194	0.0:0.6545:0.2219:0.1236|0.0:0.6545:0.2219:0.1236	.|.	.|226;110;226;186;226;226	.|B4DKW7;Q6UWC1;A8KA64;B8ZZ97;Q9BV36-2;Q9BV36	.|.;.;.;.;.;MELPH_HUMAN	A|C	33|226;226;226;186	ENSP00000412438:P33A|ENSP00000264605:S226C;ENSP00000414849:S226C;ENSP00000341845:S226C;ENSP00000386780:S186C	ENSP00000412438:P33A|ENSP00000264605:S226C	P|S	+|+	1|2	0|0	MLPH|MLPH	238098984|238098984	0.730000|0.730000	0.28100|0.28100	0.950000|0.950000	0.38849|0.38849	0.777000|0.777000	0.43975|0.43975	-0.133000|-0.133000	0.10451|0.10451	0.424000|0.424000	0.26061|0.26061	0.563000|0.563000	0.77884|0.77884	CCC|TCC	.	.	none		0.607	MLPH-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257083.2	NM_024101	Missense_Mutation
CPN1	1369	hgsc.bcm.edu	37	10	101823428	101823428	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:101823428C>T	ENST00000370418.3	-	5	1065	c.814G>A	c.(814-816)Gga>Aga	p.G272R		NM_001308.2	NP_001299.1	P15169	CBPN_HUMAN	carboxypeptidase N, polypeptide 1	272	Catalytic.				response to glucocorticoid (GO:0051384)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|lung(14)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	33		Colorectal(252;0.234)		Epithelial(162;4.77e-10)|all cancers(201;3.82e-08)		AAGTAATCTCCGCAGTTCCAA	0.502																																					p.G272R		Atlas-SNP	.											.	CPN1	62	.	0			c.G814A						PASS	.						120.0	109.0	113.0					10																	101823428		2203	4300	6503	SO:0001583	missense	1369	exon5			AATCTCCGCAGTT	X14329	CCDS7486.1	10q24.2	2012-02-10	2007-02-23		ENSG00000120054	ENSG00000120054	3.4.17.3		2312	protein-coding gene	gene with protein product	"""anaphylatoxin inactivator"", ""arginine carboxypeptidase"", ""carboxypeptidase K"", ""kininase I"", ""lysine carboxypeptidase"""	603103	"""carboxypeptidase N, polypeptide 1, 50kD"""			9628828, 2912725	Standard	NM_001308		Approved		uc001kql.2	P15169	OTTHUMG00000018896	ENST00000370418.3:c.814G>A	10.37:g.101823428C>T	ENSP00000359446:p.Gly272Arg	92.0	0.0	0		84.0	47.0	0.559524	NM_001308	B1AP59	Missense_Mutation	SNP	ENST00000370418.3	37	CCDS7486.1	.	.	.	.	.	.	.	.	.	.	C	21.4	4.143860	0.77888	.	.	ENSG00000120054	ENST00000370418;ENST00000441382	T;T	0.32023	2.15;1.47	5.61	4.7	0.59300	Peptidase M14, carboxypeptidase A (2);	0.098868	0.64402	D	0.000001	T	0.46249	0.1383	L	0.48174	1.505	0.58432	D	0.999995	D	0.71674	0.998	D	0.64144	0.922	T	0.33240	-0.9876	10	0.36615	T	0.2	-13.7978	15.9713	0.80024	0.1358:0.8642:0.0:0.0	.	272	P15169	CBPN_HUMAN	R	272;69	ENSP00000359446:G272R;ENSP00000410895:G69R	ENSP00000359446:G272R	G	-	1	0	CPN1	101813418	1.000000	0.71417	1.000000	0.80357	0.800000	0.45204	7.341000	0.79300	1.355000	0.45865	0.555000	0.69702	GGA	.	.	none		0.502	CPN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049828.1	NM_001308	
CRELD2	79174	hgsc.bcm.edu	37	22	50315382	50315382	+	Missense_Mutation	SNP	C	C	G	rs74510325	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50315382C>G	ENST00000328268.4	+	5	639	c.565C>G	c.(565-567)Cgg>Ggg	p.R189G	CRELD2_ENST00000404488.3_Missense_Mutation_p.R189G|CRELD2_ENST00000444954.1_3'UTR|CRELD2_ENST00000407217.3_Missense_Mutation_p.R189G|CRELD2_ENST00000403427.3_Missense_Mutation_p.R189G	NM_024324.3	NP_077300.3	Q6UXH1	CREL2_HUMAN	cysteine-rich with EGF-like domains 2	189						endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(1)|lung(3)|ovary(1)|stomach(3)	9		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;0.198)|LUAD - Lung adenocarcinoma(64;0.247)		CAGCTCGCTCCGGAACGAGAC	0.672													C|||	43	0.00858626	0.0015	0.0115	5008	,	,		18650	0.0		0.0288	False		,,,				2504	0.0041				p.R189G		Atlas-SNP	.											.	CRELD2	57	.	0			c.C565G						PASS	.	C	GLY/ARG,GLY/ARG	40,4366	43.1+/-76.7	0,40,2163	81.0	82.0	82.0		565,565	-1.7	0.4	22	dbSNP_132	82	341,8259	116.3+/-176.0	8,325,3967	yes	missense,missense	CRELD2	NM_001135101.1,NM_024324.3	125,125	8,365,6130	GG,GC,CC		3.9651,0.9079,2.9294	probably-damaging,probably-damaging	189/403,189/354	50315382	381,12625	2203	4300	6503	SO:0001583	missense	79174	exon5			TCGCTCCGGAACG	BC050675	CCDS14082.1, CCDS46730.1, CCDS63515.1, CCDS63516.1	22q13.33	2005-12-08			ENSG00000184164	ENSG00000184164			28150	protein-coding gene	gene with protein product		607171				12137942	Standard	XM_005261737		Approved	MGC11256	uc010hal.2	Q6UXH1	OTTHUMG00000150292	ENST00000328268.4:c.565C>G	22.37:g.50315382C>G	ENSP00000332223:p.Arg189Gly	71.0	0.0	0		96.0	45.0	0.46875	NM_024324	A5GZA2|A5GZA3|A5GZA4|A5GZA5|A5GZA6|Q4W0V0|Q86UC0|Q9BU47	Missense_Mutation	SNP	ENST00000328268.4	37	CCDS14082.1	25	0.011446886446886446	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	21	0.027704485488126648	C	12.01	1.808463	0.31961	0.009079	0.039651	ENSG00000184164	ENST00000450207;ENST00000404488;ENST00000328268;ENST00000407217;ENST00000403427	T;T;T;T;T	0.58358	2.46;0.51;0.38;0.56;0.34	4.12	-1.66	0.08265	EGF-like, laminin (1);Growth factor, receptor (1);	0.000000	0.85682	D	0.000000	T	0.21307	0.0513	N	0.20483	0.58	0.37318	D	0.90941	D;D;D;P;D;D	0.71674	0.997;0.998;0.997;0.91;0.99;0.98	D;D;D;P;P;P	0.69307	0.915;0.963;0.915;0.492;0.825;0.857	T	0.47522	-0.9111	10	0.59425	D	0.04	.	14.2293	0.65879	0.302:0.698:0.0:0.0	.	189;189;189;189;189;189	Q6UXH1-2;Q6UXH1-5;Q6UXH1-4;A5GZA6;Q6UXH1;Q6UXH1-3	.;.;.;.;CREL2_HUMAN;.	G	189	ENSP00000387769:R189G;ENSP00000383938:R189G;ENSP00000332223:R189G;ENSP00000386034:R189G;ENSP00000384111:R189G	ENSP00000332223:R189G	R	+	1	2	CRELD2	48701386	0.963000	0.33076	0.423000	0.26634	0.819000	0.46315	0.917000	0.28665	-0.606000	0.05746	-0.274000	0.10170	CGG	C|0.978;G|0.022	0.022	strong		0.672	CRELD2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000317409.1	NM_024324	
RSL1D1	26156	hgsc.bcm.edu	37	16	11935639	11935639	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11935639C>A	ENST00000571133.1	-	7	840	c.768G>T	c.(766-768)gaG>gaT	p.E256D	RSL1D1_ENST00000542106.1_Missense_Mutation_p.E36D	NM_015659.2	NP_056474.2	O76021	RL1D1_HUMAN	ribosomal L1 domain containing 1	256					osteoblast differentiation (GO:0001649)|regulation of apoptotic process (GO:0042981)|regulation of cellular senescence (GO:2000772)|regulation of protein localization (GO:0032880)	membrane (GO:0016020)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|kidney(1)|large_intestine(2)|lung(5)|prostate(1)|stomach(2)|urinary_tract(2)	15						CAGCCGATTTCTCAGTTTTCA	0.358																																					p.E256D		Atlas-SNP	.											.	RSL1D1	40	.	0			c.G768T						PASS	.						71.0	72.0	72.0					16																	11935639		2197	4300	6497	SO:0001583	missense	26156	exon7			CGATTTCTCAGTT	AY154473	CCDS10551.1	16p13.13	2011-08-12			ENSG00000171490	ENSG00000171490			24534	protein-coding gene	gene with protein product		615874				15334068, 9859858	Standard	NM_015659		Approved	PBK1, L12, DKFZP564M182, CSIG, UTP30	uc002dbp.1	O76021	OTTHUMG00000129824	ENST00000571133.1:c.768G>T	16.37:g.11935639C>A	ENSP00000460871:p.Glu256Asp	74.0	0.0	0		92.0	44.0	0.478261	NM_015659	B4DJ58|D3DUG7|Q2M1T7|Q6PL22|Q8IWS7|Q8WUZ1|Q9HDA9|Q9Y3Z9	Missense_Mutation	SNP	ENST00000571133.1	37	CCDS10551.1	.	.	.	.	.	.	.	.	.	.	C	11.36	1.615664	0.28801	.	.	ENSG00000171490	ENST00000355674;ENST00000396503;ENST00000542106	T	0.42513	0.97	4.91	2.53	0.30540	Ribosomal protein L1, 2-layer alpha/beta-sandwich (1);Ribosomal protein L1, superfamily (1);	0.556020	0.17525	N	0.171095	T	0.50718	0.1632	M	0.72479	2.2	0.19300	N	0.999975	D;P	0.55800	0.973;0.952	P;P	0.58928	0.848;0.785	T	0.35699	-0.9778	10	0.21014	T	0.42	-11.795	5.6426	0.17572	0.3284:0.5515:0.0:0.12	.	256;256	Q32Q62;O76021	.;RL1D1_HUMAN	D	255;256;36	ENSP00000347897:E255D	ENSP00000347897:E255D	E	-	3	2	RSL1D1	11843140	0.118000	0.22208	0.556000	0.28293	0.161000	0.22273	-0.318000	0.08050	0.599000	0.29845	-2.175000	0.00321	GAG	.	.	none		0.358	RSL1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252059.2	NM_015659	
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32729618	32729618	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32729618G>A	ENST00000437316.2	-	2	246	c.183C>T	c.(181-183)aaC>aaT	p.N61N	HLA-DQB2_ENST00000411527.1_Silent_p.N61N|HLA-DQB2_ENST00000435145.2_Silent_p.N61N			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	65	Beta-1.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						ACTCCTCGCGGTTATAGATGT	0.577																																					p.N61N		Atlas-SNP	.											.	HLA-DQB2	22	.	0			c.C183T						PASS	.																																			SO:0001819	synonymous_variant	3120	exon2			CTCGCGGTTATAG	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.183C>T	6.37:g.32729618G>A		86.0	0.0	0		89.0	39.0	0.438202	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Silent	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	G	7.517	0.655922	0.14580	.	.	ENSG00000232629	ENST00000427449	.	.	.	3.48	2.59	0.31030	.	.	.	.	.	T	0.45196	0.1330	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41413	-0.9510	4	.	.	.	.	8.4756	0.33012	0.125:0.0:0.875:0.0	.	.	.	.	I	60	.	.	T	-	2	0	HLA-DQB2	32837596	0.991000	0.36638	0.792000	0.32020	0.021000	0.10359	2.255000	0.43222	1.937000	0.56155	0.491000	0.48974	ACC	.	.	none		0.577	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
WNK1	65125	hgsc.bcm.edu	37	12	998378	998378	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:998378T>A	ENST00000315939.6	+	21	6080	c.5437T>A	c.(5437-5439)Tct>Act	p.S1813T	WNK1_ENST00000340908.4_Missense_Mutation_p.S1406T|WNK1_ENST00000535572.1_Missense_Mutation_p.S1566T|WNK1_ENST00000530271.2_Missense_Mutation_p.S2311T|WNK1_ENST00000537687.1_Missense_Mutation_p.S2073T	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	1813					intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			CACAGTGACTTCTGCGGTTGG	0.363																																					p.S2073T	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.T6217A						PASS	.						166.0	161.0	163.0					12																	998378		2203	4300	6503	SO:0001583	missense	65125	exon21			GTGACTTCTGCGG	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.5437T>A	12.37:g.998378T>A	ENSP00000313059:p.Ser1813Thr	108.0	0.0	0		112.0	54.0	0.482143	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	T	11.90	1.778019	0.31502	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000252477;ENST00000530271;ENST00000340908	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	5.77	2.15	0.27550	.	0.284463	0.31092	N	0.008273	T	0.29783	0.0744	L	0.40543	1.245	0.25832	N	0.984158	B;B;B	0.13594	0.003;0.003;0.008	B;B;B	0.13407	0.006;0.009;0.004	T	0.23940	-1.0174	10	0.66056	D	0.02	-5.5426	5.5835	0.17262	0.128:0.1412:0.0:0.7307	.	1566;1566;1813	Q9H4A3-2;F5GWT4;Q9H4A3	.;.;WNK1_HUMAN	T	1566;1813;2073;986;2311;1406	ENSP00000441972:S1566T;ENSP00000313059:S1813T;ENSP00000444465:S2073T;ENSP00000433548:S2311T;ENSP00000341292:S1406T	ENSP00000252477:S986T	S	+	1	0	WNK1	868639	0.866000	0.29940	0.306000	0.25113	0.265000	0.26407	1.118000	0.31246	0.528000	0.28580	-0.336000	0.08194	TCT	.	.	none		0.363	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
DSG1	1828	hgsc.bcm.edu	37	18	28934274	28934274	+	Silent	SNP	C	C	T	rs146192657	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:28934274C>T	ENST00000257192.4	+	15	2327	c.2115C>T	c.(2113-2115)taC>taT	p.Y705Y	RP11-534N16.1_ENST00000578477.1_RNA|RP11-534N16.1_ENST00000581452.1_RNA|DSG1_ENST00000462981.2_Silent_p.Y64Y|RP11-534N16.1_ENST00000578119.1_RNA|RP11-534N16.1_ENST00000581856.1_RNA	NM_001942.2	NP_001933.2	Q02413	DSG1_HUMAN	desmoglein 1	705					apoptotic process (GO:0006915)|calcium-dependent cell-cell adhesion (GO:0016339)|cell-cell junction assembly (GO:0007043)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)|maternal process involved in female pregnancy (GO:0060135)|protein stabilization (GO:0050821)|response to progesterone (GO:0032570)|single organismal cell-cell adhesion (GO:0016337)	apical plasma membrane (GO:0016324)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lateral plasma membrane (GO:0016328)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|gamma-catenin binding (GO:0045295)|toxic substance binding (GO:0015643)	p.Y705*(2)		NS(2)|central_nervous_system(2)|endometrium(5)|kidney(7)|large_intestine(11)|lung(36)|ovary(3)|prostate(1)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)	76			OV - Ovarian serous cystadenocarcinoma(10;0.00559)			CATATGCTTACGCAGATGAAG	0.373													T|||	15	0.00299521	0.0008	0.0072	5008	,	,		17640	0.0		0.0089	False		,,,				2504	0.0				p.Y705Y		Atlas-SNP	.											.	DSG1	176	.	2	Substitution - Nonsense(2)	lung(2)	c.C2115T						PASS	.	T		7,4399	825.6+/-416.5	0,7,2196	91.0	90.0	90.0		2115	3.6	1.0	18	dbSNP_134	90	77,8523	815.9+/-406.9	0,77,4223	no	coding-synonymous	DSG1	NM_001942.2		0,84,6419	TT,TC,CC		0.8953,0.1589,0.6459		705/1050	28934274	84,12922	2203	4300	6503	SO:0001819	synonymous_variant	1828	exon15			TGCTTACGCAGAT	X56654	CCDS11896.1	18q12.1	2014-05-13			ENSG00000134760	ENSG00000134760		"""Cadherins / Major cadherins"""	3048	protein-coding gene	gene with protein product		125670		DSG		1889810	Standard	NM_001942		Approved	CDHF4	uc002kwp.3	Q02413	OTTHUMG00000131983	ENST00000257192.4:c.2115C>T	18.37:g.28934274C>T		112.0	0.0	0		135.0	87.0	0.644444	NM_001942	B7Z845	Silent	SNP	ENST00000257192.4	37	CCDS11896.1																																																																																			C|0.994;T|0.006	0.006	strong		0.373	DSG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254947.1	NM_001942	
SLC25A45	283130	hgsc.bcm.edu	37	11	65144331	65144331	+	Missense_Mutation	SNP	C	C	T	rs371949191		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:65144331C>T	ENST00000527174.1	-	5	611	c.556G>A	c.(556-558)Gaa>Aaa	p.E186K	SLC25A45_ENST00000534028.1_Missense_Mutation_p.E162K|SLC25A45_ENST00000417511.2_Missense_Mutation_p.E144K|SLC25A45_ENST00000398802.1_Missense_Mutation_p.E186K|SLC25A45_ENST00000526432.1_Missense_Mutation_p.E124K|SLC25A45_ENST00000377152.2_Missense_Mutation_p.E82K|SLC25A45_ENST00000360662.3_Missense_Mutation_p.E162K|SLC25A45_ENST00000294187.6_Missense_Mutation_p.E144K|RP11-867O8.5_ENST00000533886.1_RNA			Q8N413	S2545_HUMAN	solute carrier family 25, member 45	186					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				endometrium(2)|kidney(3)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	14						CAGAGCCCTTCATAGGTGATG	0.627																																					p.E186K		Atlas-SNP	.											.	SLC25A45	23	.	0			c.G556A						PASS	.	C	LYS/GLU,LYS/GLU	0,4070		0,0,2035	138.0	145.0	143.0		556,430	4.3	0.2	11		143	1,8389		0,1,4194	no	missense,missense	SLC25A45	NM_182556.2,NM_001077241.1	56,56	0,1,6229	TT,TC,CC		0.0119,0.0,0.0080	benign,benign	186/289,144/247	65144331	1,12459	2035	4195	6230	SO:0001583	missense	283130	exon6			GCCCTTCATAGGT	BC041100	CCDS41670.1, CCDS41671.1, CCDS60850.1	11q13.1	2013-05-22			ENSG00000162241	ENSG00000162241		"""Solute carriers"""	27442	protein-coding gene	gene with protein product		610825				16949250	Standard	XM_006718507		Approved		uc001odr.1	Q8N413	OTTHUMG00000166255	ENST00000527174.1:c.556G>A	11.37:g.65144331C>T	ENSP00000435489:p.Glu186Lys	203.0	0.0	0		211.0	89.0	0.421801	NM_182556	Q6PL49|Q8IW29	Missense_Mutation	SNP	ENST00000527174.1	37	CCDS41670.1	.	.	.	.	.	.	.	.	.	.	C	15.95	2.983275	0.53827	0.0	1.19E-4	ENSG00000162241	ENST00000527174;ENST00000534028;ENST00000398802;ENST00000360662;ENST00000377152;ENST00000294187;ENST00000417511;ENST00000526432	D;D;D;D;D;D;D;D	0.83250	-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7;-1.7	5.23	4.26	0.50523	Mitochondrial carrier domain (2);	0.116851	0.53938	D	0.000048	D	0.89336	0.6686	M	0.86343	2.81	0.39497	D	0.968142	D;B;B	0.54964	0.969;0.203;0.242	P;B;B	0.58077	0.832;0.099;0.159	D	0.88486	0.3072	10	0.27785	T	0.31	-0.3137	13.3171	0.60413	0.0:0.8399:0.1601:0.0	.	124;162;186	E9PJQ3;Q8N413-4;Q8N413	.;.;S2545_HUMAN	K	186;162;186;162;82;144;144;124	ENSP00000435489:E186K;ENSP00000431769:E162K;ENSP00000381782:E186K;ENSP00000353879:E162K;ENSP00000366357:E82K;ENSP00000294187:E144K;ENSP00000407530:E144K;ENSP00000435547:E124K	ENSP00000294187:E144K	E	-	1	0	SLC25A45	64900907	0.000000	0.05858	0.240000	0.24138	0.281000	0.26958	0.738000	0.26158	2.617000	0.88574	0.561000	0.74099	GAA	.	.	weak		0.627	SLC25A45-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388744.3	NM_182556	
CSMD3	114788	hgsc.bcm.edu	37	8	113349030	113349030	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:113349030C>A	ENST00000297405.5	-	44	7114	c.6870G>T	c.(6868-6870)atG>atT	p.M2290I	CSMD3_ENST00000352409.3_Missense_Mutation_p.M2220I|CSMD3_ENST00000343508.3_Missense_Mutation_p.M2250I|CSMD3_ENST00000455883.2_Missense_Mutation_p.M2186I	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	2290	CUB 13. {ECO:0000255|PROSITE- ProRule:PRU00059}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						TGGTGCCATTCATTGCAGTTA	0.363										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.M2290I		Atlas-SNP	.											.	CSMD3	2325	.	0			c.G6870T						PASS	.						79.0	73.0	75.0					8																	113349030		2203	4300	6503	SO:0001583	missense	114788	exon44			GCCATTCATTGCA	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.6870G>T	8.37:g.113349030C>A	ENSP00000297405:p.Met2290Ile	61.0	0.0	0		60.0	10.0	0.166667	NM_198123	Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.177692	0.38413	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.17691	2.26;2.26;2.26;2.26;2.26	5.64	5.64	0.86602	CUB (5);	0.057323	0.64402	D	0.000003	T	0.25121	0.0610	L	0.39326	1.205	0.45097	D	0.998113	B;B;P	0.37688	0.171;0.257;0.605	B;B;P	0.46076	0.193;0.216;0.503	T	0.00417	-1.1752	10	0.30078	T	0.28	.	19.8946	0.96949	0.0:1.0:0.0:0.0	.	2186;2290;2250	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	I	2250;2290;1560;2186;2220	ENSP00000345799:M2250I;ENSP00000297405:M2290I;ENSP00000341558:M1560I;ENSP00000412263:M2186I;ENSP00000343124:M2220I	ENSP00000297405:M2290I	M	-	3	0	CSMD3	113418206	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.429000	0.44758	2.937000	0.99478	0.650000	0.86243	ATG	.	.	none		0.363	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
OBSCN	84033	hgsc.bcm.edu	37	1	228554725	228554725	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228554725T>G	ENST00000422127.1	+	86	19521	c.19477T>G	c.(19477-19479)Ttg>Gtg	p.L6493V	OBSCN_ENST00000570156.2_Missense_Mutation_p.L7450V|OBSCN_ENST00000366707.4_Missense_Mutation_p.L4127V	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6493	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				AAACAAGATCTTGTGCGCTGC	0.607																																					p.L7450V		Atlas-SNP	.											.	OBSCN	2142	.	0			c.T22348G						PASS	.						47.0	50.0	49.0					1																	228554725		2026	4164	6190	SO:0001583	missense	84033	exon97			AAGATCTTGTGCG	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.19477T>G	1.37:g.228554725T>G	ENSP00000409493:p.Leu6493Val	105.0	0.0	0		106.0	46.0	0.433962	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Missense_Mutation	SNP	ENST00000422127.1	37	CCDS58065.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	10.92|10.92	1.486513|1.486513	0.26686|0.26686	.|.	.|.	ENSG00000154358|ENSG00000154358	ENST00000441106|ENST00000422127;ENST00000366707	.|T;T	.|0.66099	.|-0.19;-0.19	4.69|4.69	1.05|1.05	0.20165|0.20165	.|Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	.|.	.|.	.|.	.|.	T|T	0.36026|0.36026	0.0952|0.0952	N|N	0.13043|0.13043	0.29|0.29	0.09310|0.09310	N|N	1|1	.|B	.|0.13145	.|0.007	.|B	.|0.18871	.|0.023	T|T	0.17167|0.17167	-1.0378|-1.0378	5|9	.|0.20046	.|T	.|0.44	.|.	1.1263|1.1263	0.01736|0.01736	0.1407:0.236:0.146:0.4773|0.1407:0.236:0.146:0.4773	.|.	.|6493	.|Q5VST9	.|OBSCN_HUMAN	R|V	1109|6493;4127	.|ENSP00000409493:L6493V;ENSP00000355668:L4127V	.|ENSP00000355668:L4127V	L|L	+|+	2|1	0|2	OBSCN|OBSCN	226621348|226621348	0.003000|0.003000	0.15002|0.15002	0.016000|0.016000	0.15963|0.15963	0.385000|0.385000	0.30292|0.30292	0.243000|0.243000	0.18106|0.18106	0.018000|0.018000	0.15052|0.15052	0.402000|0.402000	0.26972|0.26972	CTT|TTG	.	.	none		0.607	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ABL1	25	hgsc.bcm.edu	37	9	133755528	133755528	+	Silent	SNP	A	A	G	rs2227985	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		79.0	0.0	0		66.0	29.0	0.439394	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	
KMT2B	9757	hgsc.bcm.edu	37	19	36223699	36223699	+	Silent	SNP	G	G	T	rs375564425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36223699G>T	ENST00000222270.7	+	28	6249	c.6249G>T	c.(6247-6249)acG>acT	p.T2083T	KMT2B_ENST00000420124.1_Silent_p.T2083T|KMT2B_ENST00000607650.1_RNA	NM_014727.1	NP_055542.1	Q9UMN6	KMT2B_HUMAN	lysine (K)-specific methyltransferase 2B	2083					chromatin-mediated maintenance of transcription (GO:0048096)|gene silencing (GO:0016458)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|oocyte differentiation (GO:0009994)|ovarian follicle development (GO:0001541)|ovulation (GO:0030728)|regulation of histone H3-K4 methylation (GO:0051569)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)										GCCAGGGCACGCCTCCTTCGG	0.687													T|||	2	0.000399361	0.0008	0.0	5008	,	,		12848	0.0		0.001	False		,,,				2504	0.0				p.T2083T		Atlas-SNP	.											.	MLL4	229	.	0			c.G6249T						PASS	.	T		1,3869		0,1,1934	11.0	13.0	12.0		6249	0.5	1.0	19		12	18,8212		0,18,4097	no	coding-synonymous	MLL4	NM_014727.1		0,19,6031	TT,TG,GG		0.2187,0.0258,0.157		2083/2716	36223699	19,12081	1935	4115	6050	SO:0001819	synonymous_variant	8085	exon28			GGGCACGCCTCCT	AJ007041	CCDS46055.1	19q13.1	2014-02-18			ENSG00000105663	ENSG00000272333		"""Chromatin-modifying enzymes / K-methyltransferases"""	15840	protein-coding gene	gene with protein product	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila) 4"""	606834				10409430, 10637508	Standard	XM_006723513		Approved	KIAA0304, MLL2, TRX2, HRX2, WBP7, MLL1B, MLL4		Q9UMN6	OTTHUMG00000048119	ENST00000222270.7:c.6249G>T	19.37:g.36223699G>T		41.0	0.0	0		80.0	41.0	0.5125	NM_014727	O15022|O95836|Q96GP2|Q96IP3|Q9UK25|Q9Y668|Q9Y669	Silent	SNP	ENST00000222270.7	37	CCDS46055.1																																																																																			.	.	weak		0.687	KMT2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_014727	
CBFA2T3	863	hgsc.bcm.edu	37	16	88951466	88951466	+	Missense_Mutation	SNP	G	G	A	rs143614023	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88951466G>A	ENST00000268679.4	-	7	1501	c.1105C>T	c.(1105-1107)Cat>Tat	p.H369Y	RP11-830F9.5_ENST00000569249.1_RNA|RP11-830F9.5_ENST00000562574.1_RNA|CBFA2T3_ENST00000327483.5_Missense_Mutation_p.H283Y|RP11-830F9.5_ENST00000562405.1_RNA|CBFA2T3_ENST00000360302.2_Missense_Mutation_p.H283Y|RP11-830F9.5_ENST00000565053.1_RNA|CBFA2T3_ENST00000436887.2_Missense_Mutation_p.H331Y|CBFA2T3_ENST00000448839.1_Missense_Mutation_p.H293Y	NM_005187.5	NP_005178.4	O75081	MTG16_HUMAN	core-binding factor, runt domain, alpha subunit 2; translocated to, 3	369	Mediates interaction with PDE7A (in isoform 2).|Mediates localization to the nucleus. {ECO:0000250}.				cell proliferation (GO:0008283)|granulocyte differentiation (GO:0030851)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17				BRCA - Breast invasive adenocarcinoma(80;0.0275)		AGCGGCCGATGGCGCTCTCGT	0.682			T	RUNX1	AML																																p.H369Y		Atlas-SNP	.		Dom	yes		16	16q24	863	"""core-binding factor, runt domain, alpha subunit 2; translocated to, 3 (MTG-16)"""		L	.	CBFA2T3	47	.	0			c.C1105T						PASS	.	G	TYR/HIS,TYR/HIS	0,4376		0,0,2188	50.0	47.0	48.0		1105,847	4.3	1.0	16	dbSNP_134	48	5,8579	4.3+/-15.6	0,5,4287	yes	missense,missense	CBFA2T3	NM_005187.5,NM_175931.2	83,83	0,5,6475	AA,AG,GG		0.0582,0.0,0.0386	benign,benign	369/654,283/568	88951466	5,12955	2188	4292	6480	SO:0001583	missense	863	exon7			GCCGATGGCGCTC	AF052213	CCDS10972.1, CCDS10973.1	16q24	2013-10-16			ENSG00000129993	ENSG00000129993		"""Zinc fingers, MYND-type"", ""A-kinase anchor proteins"""	1537	protein-coding gene	gene with protein product	"""myeloid translocation gene 8 and 16b"""	603870				9790752, 20150326	Standard	NM_005187		Approved	MTGR2, ZMYND4, MTG16	uc002fmm.2	O75081	OTTHUMG00000137864	ENST00000268679.4:c.1105C>T	16.37:g.88951466G>A	ENSP00000268679:p.His369Tyr	10.0	0.0	0		27.0	13.0	0.481481	NM_005187	D3DX78|O60615|O60616|O60617|O75082|O75107|O75108|Q0P5Z6|Q6P5W6	Missense_Mutation	SNP	ENST00000268679.4	37	CCDS10972.1	.	.	.	.	.	.	.	.	.	.	G	14.75	2.627420	0.46944	0.0	5.82E-4	ENSG00000129993	ENST00000327483;ENST00000268679;ENST00000436887;ENST00000448839;ENST00000360302	T;T;T;T;T	0.48201	1.41;0.82;0.85;1.41;1.41	4.32	4.32	0.51571	.	0.293527	0.31335	N	0.007833	T	0.52354	0.1729	M	0.61703	1.905	0.58432	D	0.999993	P;P;B;B	0.49185	0.92;0.586;0.186;0.134	P;B;B;B	0.46419	0.516;0.125;0.141;0.183	T	0.55903	-0.8067	10	0.39692	T	0.17	-1.3703	16.93	0.86188	0.0:0.0:1.0:0.0	.	331;369;369;283	E7EU24;B2RBQ7;O75081;O75081-2	.;.;MTG16_HUMAN;.	Y	283;369;331;293;283	ENSP00000332122:H283Y;ENSP00000268679:H369Y;ENSP00000395739:H331Y;ENSP00000401254:H293Y;ENSP00000353449:H283Y	ENSP00000268679:H369Y	H	-	1	0	CBFA2T3	87478967	1.000000	0.71417	1.000000	0.80357	0.305000	0.27757	7.062000	0.76706	2.386000	0.81285	0.561000	0.74099	CAT	G|1.000;A|0.000	0.000	strong		0.682	CBFA2T3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000269545.2	NM_005187	
WBSCR17	64409	hgsc.bcm.edu	37	7	70800578	70800578	+	Missense_Mutation	SNP	G	G	T	rs145721199	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:70800578G>T	ENST00000333538.5	+	2	915	c.281G>T	c.(280-282)cGg>cTg	p.R94L	WBSCR17_ENST00000498380.2_3'UTR	NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	94					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				TATGGTGGGCGGGGTAAAGGG	0.453																																					p.R94L		Atlas-SNP	.											WBSCR17,mouth,carcinoma,+1,1	WBSCR17	208	1	0			c.G281T						scavenged	.						32.0	38.0	36.0					7																	70800578		2203	4300	6503	SO:0001583	missense	64409	exon2			GTGGGCGGGGTAA	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.281G>T	7.37:g.70800578G>T	ENSP00000329654:p.Arg94Leu	29.0	0.0	0		37.0	2.0	0.0540541	NM_022479	Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	9.064	0.995119	0.19043	.	.	ENSG00000185274	ENST00000333538;ENST00000447516	T;T	0.52983	0.64;1.93	4.89	4.89	0.63831	.	0.000000	0.85682	D	0.000000	T	0.23572	0.0570	N	0.02539	-0.55	0.80722	D	1	B	0.13145	0.007	B	0.12837	0.008	T	0.13150	-1.0520	10	0.10902	T	0.67	.	17.1948	0.86890	0.0:0.0:1.0:0.0	.	94	Q6IS24	GLTL3_HUMAN	L	94;72	ENSP00000329654:R94L;ENSP00000392019:R72L	ENSP00000329654:R94L	R	+	2	0	WBSCR17	70438514	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.307000	0.78920	2.530000	0.85305	0.491000	0.48974	CGG	G|0.999;A|0.001	.	alt		0.453	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
ADAMTS12	81792	hgsc.bcm.edu	37	5	33576803	33576803	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:33576803C>T	ENST00000504830.1	-	19	3663	c.3328G>A	c.(3328-3330)Gat>Aat	p.D1110N	ADAMTS12_ENST00000504582.1_5'Flank|ADAMTS12_ENST00000352040.3_Missense_Mutation_p.D1025N	NM_030955.2	NP_112217.2	P58397	ATS12_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 12	1110	Spacer 2.				cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cellular response to BMP stimulus (GO:0071773)|cellular response to interleukin-1 (GO:0071347)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of cellular response to hepatocyte growth factor stimulus (GO:2001113)|negative regulation of cellular response to vascular endothelial growth factor stimulus (GO:1902548)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of hepatocyte growth factor receptor signaling pathway (GO:1902203)|proteoglycan catabolic process (GO:0030167)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of endothelial tube morphogenesis (GO:1901509)|regulation of inflammatory response (GO:0050727)	extracellular matrix (GO:0031012)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(11)|large_intestine(31)|liver(1)|lung(135)|ovary(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(5)	216						GGACCAGTATCTGAACTGGAA	0.507										HNSCC(64;0.19)																											p.D1110N		Atlas-SNP	.											.	ADAMTS12	464	.	0			c.G3328A						PASS	.						95.0	89.0	91.0					5																	33576803		2203	4300	6503	SO:0001583	missense	81792	exon19			CAGTATCTGAACT	AJ250725	CCDS34140.1	5q35	2008-07-18	2005-08-19		ENSG00000151388	ENSG00000151388		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14605	protein-coding gene	gene with protein product		606184	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 12"""			11279086	Standard	NM_030955		Approved		uc003jia.1	P58397	OTTHUMG00000162088	ENST00000504830.1:c.3328G>A	5.37:g.33576803C>T	ENSP00000422554:p.Asp1110Asn	83.0	0.0	0		111.0	49.0	0.441441	NM_030955	A2RRN9|A5D6V6|Q6UWL3	Missense_Mutation	SNP	ENST00000504830.1	37	CCDS34140.1	.	.	.	.	.	.	.	.	.	.	c	8.033	0.762246	0.15914	.	.	ENSG00000151388	ENST00000504830;ENST00000352040	T;T	0.59772	0.25;0.24	5.22	4.33	0.51752	.	1.532230	0.03305	N	0.189648	T	0.45637	0.1352	L	0.27053	0.805	0.21675	N	0.999593	B;B	0.34015	0.435;0.201	B;B	0.30572	0.117;0.055	T	0.35351	-0.9792	10	0.21014	T	0.42	.	8.6051	0.33769	0.0:0.7653:0.1545:0.0802	.	1025;1110	P58397-3;P58397	.;ATS12_HUMAN	N	1110;1025	ENSP00000422554:D1110N;ENSP00000344847:D1025N	ENSP00000344847:D1025N	D	-	1	0	ADAMTS12	33612560	0.000000	0.05858	0.170000	0.22879	0.143000	0.21401	-0.091000	0.11146	1.391000	0.46566	0.651000	0.88453	GAT	.	.	none		0.507	ADAMTS12-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367164.2	NM_030955	
HPS1	3257	hgsc.bcm.edu	37	10	100185638	100185638	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:100185638T>C	ENST00000325103.6	-	12	1325	c.1092A>G	c.(1090-1092)ctA>ctG	p.L364L	HPS1_ENST00000361490.4_Silent_p.L364L|HPS1_ENST00000467246.1_5'UTR	NM_000195.3	NP_000186.2	Q92902	HPS1_HUMAN	Hermansky-Pudlak syndrome 1	364					blood coagulation (GO:0007596)|eye pigmentation (GO:0048069)|lysosome organization (GO:0007040)|melanocyte differentiation (GO:0030318)|positive regulation of natural killer cell activation (GO:0032816)|retina development in camera-type eye (GO:0060041)|secretion of lysosomal enzymes (GO:0033299)|visual perception (GO:0007601)	BLOC-3 complex (GO:0031085)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	protein dimerization activity (GO:0046983)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	23		Colorectal(252;0.234)		Epithelial(162;3.87e-12)|all cancers(201;5.63e-10)		TGTGGGGCACTAGGGGGCAGT	0.612									Hermansky-Pudlak syndrome		OREG0020430	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L364L		Atlas-SNP	.											.	HPS1	65	.	0			c.A1092G						PASS	.						105.0	108.0	107.0					10																	100185638		2203	4300	6503	SO:0001819	synonymous_variant	3257	exon12	Familial Cancer Database	HPS, HPS1-8	GGGCACTAGGGGG	U79136	CCDS7475.1, CCDS7476.1	10q23.1-q23.3	2014-06-18		2002-05-01	ENSG00000107521	ENSG00000107521			5163	protein-coding gene	gene with protein product		604982	"""Hermansky-Pudlak syndrome"""	HPS		8541858, 7573033	Standard	NM_182639		Approved		uc021pwv.1	Q92902	OTTHUMG00000018876	ENST00000325103.6:c.1092A>G	10.37:g.100185638T>C		112.0	0.0	0	1349	108.0	59.0	0.546296	NM_000195	A8MRT2|O15402|O15502|Q5TAA3|Q8WXE5	Silent	SNP	ENST00000325103.6	37	CCDS7475.1																																																																																			.	.	none		0.612	HPS1-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049776.1	NM_000195, NM_182637, NM_182638, NM_182639	
CHD3	1107	hgsc.bcm.edu	37	17	7796805	7796805	+	Silent	SNP	C	C	G	rs199898244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7796805C>G	ENST00000330494.7	+	5	861	c.711C>G	c.(709-711)tcC>tcG	p.S237S	CHD3_ENST00000358181.4_Silent_p.S237S|CHD3_ENST00000380358.4_Silent_p.S296S	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	237					centrosome organization (GO:0051297)|chromatin assembly or disassembly (GO:0006333)|chromatin modification (GO:0016568)|DNA duplex unwinding (GO:0032508)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|spindle organization (GO:0007051)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|nucleolus (GO:0005730)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(11)|kidney(6)|large_intestine(13)|liver(2)|lung(14)|ovary(1)|pancreas(1)|prostate(7)|skin(3)|urinary_tract(2)	65		Prostate(122;0.202)				TAGCACCCTCCGGACCCCCCG	0.647													C|||	7	0.00139776	0.0	0.0058	5008	,	,		7723	0.0		0.003	False		,,,				2504	0.0				p.S296S		Atlas-SNP	.											.	CHD3	169	.	0			c.C888G						PASS	.	C	,,	1,4397		0,1,2198	16.0	17.0	17.0		888,711,711	-6.8	0.9	17		17	21,8559		0,21,4269	yes	coding-synonymous,coding-synonymous,coding-synonymous	CHD3	NM_001005271.2,NM_001005273.2,NM_005852.3	,,	0,22,6467	GG,GC,CC		0.2448,0.0227,0.1695	,,	296/2060,237/2001,237/1967	7796805	22,12956	2199	4290	6489	SO:0001819	synonymous_variant	1107	exon5			ACCCTCCGGACCC	U08379	CCDS32553.2, CCDS32554.1, CCDS32555.1	17p13	2013-01-28			ENSG00000170004	ENSG00000170004		"""Zinc fingers, PHD-type"""	1918	protein-coding gene	gene with protein product		602120				9326634, 7560064	Standard	NM_001005271		Approved	Mi-2a, ZFH, Mi2-ALPHA	uc002gjd.2	Q12873	OTTHUMG00000150427	ENST00000330494.7:c.711C>G	17.37:g.7796805C>G		130.0	0.0	0		105.0	46.0	0.438095	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Silent	SNP	ENST00000330494.7	37	CCDS32554.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	5.459	0.269736	0.10349	2.27E-4	0.002448	ENSG00000170004	ENST00000452447	.	.	.	4.82	-6.78	0.01721	.	.	.	.	.	T	0.45377	0.1339	.	.	.	0.46901	D	0.999246	.	.	.	.	.	.	T	0.49725	-0.8909	4	.	.	.	-19.0971	6.1106	0.20097	0.195:0.3477:0.0:0.4573	.	.	.	.	G	112	.	.	R	+	1	2	CHD3	7737530	0.596000	0.26866	0.933000	0.37362	0.882000	0.50991	-0.099000	0.11007	-0.867000	0.04063	-1.391000	0.01154	CGG	C|0.999;G|0.001	0.001	strong		0.647	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
HSD17B1	3292	hgsc.bcm.edu	37	17	40706596	40706596	+	Missense_Mutation	SNP	C	C	T	rs147402365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40706596C>T	ENST00000585807.1	+	5	4433	c.713C>T	c.(712-714)gCg>gTg	p.A238V	HSD17B1_ENST00000225929.5_Missense_Mutation_p.A239V|RP11-400F19.6_ENST00000590513.1_RNA|RP11-400F19.8_ENST00000585572.1_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	24.0	0.0	0		43.0	28.0	0.651163	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	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84607492	84607492	+	Missense_Mutation	SNP	C	C	T	rs190878253		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84607492C>T	ENST00000344803.2	+	4	2154	c.2107C>T	c.(2107-2109)Ccc>Tcc	p.P703S		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	703					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											ATGGGGCCTGCCCCGCAGAAT	0.473																																					p.P703S		Atlas-SNP	.											.	.	.	.	0			c.C2107T						PASS	.						59.0	57.0	58.0					9																	84607492		1839	4077	5916	SO:0001583	missense	389763	exon4			GGCCTGCCCCGCA		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.2107C>T	9.37:g.84607492C>T	ENSP00000341988:p.Pro703Ser	227.0	0.0	0		272.0	62.0	0.227941	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	C	14.61	2.587655	0.46110	.	.	ENSG00000214929	ENST00000344803	T	0.24151	1.87	3.51	2.51	0.30379	.	0.258257	0.27946	N	0.017208	T	0.48624	0.1510	M	0.85462	2.755	0.19945	N	0.999942	D	0.64830	0.994	D	0.71184	0.972	T	0.22173	-1.0224	10	0.66056	D	0.02	-8.1379	8.1735	0.31268	0.0:0.7513:0.2486:0.0	.	703	Q6ZQQ2	F75D1_HUMAN	S	703	ENSP00000341988:P703S	ENSP00000341988:P703S	P	+	1	0	FAM75D1	83797312	0.161000	0.22892	0.349000	0.25694	0.013000	0.08279	1.044000	0.30329	1.978000	0.57642	0.561000	0.74099	CCC	C|0.999;T|0.001	0.001	strong		0.473	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
CBL	867	hgsc.bcm.edu	37	11	119168130	119168130	+	Silent	SNP	G	G	C	rs143840974	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:119168130G>C	ENST00000264033.4	+	14	2566	c.2190G>C	c.(2188-2190)acG>acC	p.T730T		NM_005188.3	NP_005179.2	P22681	CBL_HUMAN	Cbl proto-oncogene, E3 ubiquitin protein ligase	730	Asp/Glu-rich (acidic).|Interaction with CD2AP.				cell surface receptor signaling pathway (GO:0007166)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of receptor-mediated endocytosis (GO:0048260)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|flotillin complex (GO:0016600)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|ephrin receptor binding (GO:0046875)|ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|SH3 domain binding (GO:0017124)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.T730T(1)		breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(194)|kidney(3)|large_intestine(9)|lung(30)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	251		Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.92e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.000784)		ATAGCTGTACGTATGAAGCAA	0.393			"""T, Mis S, O"""	MLL	"""AML, JMML, MDS"""				Noonan syndrome;CBL gene-associated Juvenile Myelomonocytic Leukemia and Developmental Anomalies				G|||	2	0.000399361	0.0	0.0	5008	,	,		20497	0.0		0.002	False		,,,				2504	0.0				p.T730T		Atlas-SNP	.		"""Dom, Rec"""	yes		11	11q23.3	867	Cas-Br-M (murine) ecotropic retroviral transforming		L	CBL,NS,haematopoietic_neoplasm,0,1	CBL	408	1	1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	c.G2190C						PASS	.	G		2,4396	4.2+/-10.8	0,2,2197	117.0	106.0	110.0		2190	-10.6	0.2	11	dbSNP_134	110	28,8562	19.8+/-62.0	0,28,4267	no	coding-synonymous	CBL	NM_005188.2		0,30,6464	CC,CG,GG		0.326,0.0455,0.231		730/907	119168130	30,12958	2199	4295	6494	SO:0001819	synonymous_variant	867	exon14	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CBL-associated JMML	CTGTACGTATGAA	X57110	CCDS8418.1	11q23.3	2014-09-17	2012-02-23		ENSG00000110395	ENSG00000110395		"""RING-type (C3HC4) zinc fingers"""	1541	protein-coding gene	gene with protein product	"""oncogene CBL2"""	165360	"""Cas-Br-M (murine) ecotropic retroviral transforming sequence"""	CBL2		2013228	Standard	NM_005188		Approved	RNF55, c-Cbl	uc001pwe.4	P22681	OTTHUMG00000166170	ENST00000264033.4:c.2190G>C	11.37:g.119168130G>C		95.0	0.0	0		84.0	39.0	0.464286	NM_005188	A3KMP8	Silent	SNP	ENST00000264033.4	37	CCDS8418.1																																																																																			G|0.997;C|0.003	0.003	strong		0.393	CBL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388219.4	NM_005188	
TCEA3	6920	hgsc.bcm.edu	37	1	23743859	23743859	+	Missense_Mutation	SNP	T	T	C	rs192746462	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23743859T>C	ENST00000450454.2	-	4	369	c.263A>G	c.(262-264)gAa>gGa	p.E88G	TCEA3_ENST00000461794.1_Missense_Mutation_p.E51G|TCEA3_ENST00000374601.3_Missense_Mutation_p.E88G	NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	88					regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		ctctcctttttctcctTTTGG	0.493													T|||	9	0.00179712	0.0	0.0043	5008	,	,		19825	0.0		0.004	False		,,,				2504	0.002				p.E88G		Atlas-SNP	.											.	TCEA3	20	.	0			c.A263G						PASS	.	T	GLY/GLU	2,3698		0,2,1848	92.0	90.0	90.0		263	5.0	1.0	1		90	43,8161		0,43,4059	yes	missense	TCEA3	NM_003196.1	98	0,45,5907	CC,CT,TT		0.5241,0.0541,0.378	possibly-damaging	88/349	23743859	45,11859	1850	4102	5952	SO:0001583	missense	6920	exon4			CCTTTTTCTCCTT	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.263A>G	1.37:g.23743859T>C	ENSP00000406293:p.Glu88Gly	131.0	0.0	0		143.0	71.0	0.496504	NM_003196	A8K2K7|Q5DR83	Missense_Mutation	SNP	ENST00000450454.2	37	CCDS44086.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	T	13.93	2.384002	0.42308	5.41E-4	0.005241	ENSG00000204219	ENST00000450454;ENST00000374601	.	.	.	5.02	5.02	0.67125	Transcription factor IIS, N-terminal (2);	0.911073	0.09406	N	0.806532	T	0.24661	0.0598	N	0.24115	0.695	0.24955	N	0.991769	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.09143	-1.0688	9	0.48119	T	0.1	-12.8917	11.3324	0.49484	0.0:0.0:0.0:1.0	.	88;88	A8K2K7;O75764	.;TCEA3_HUMAN	G	88	.	ENSP00000363729:E88G	E	-	2	0	TCEA3	23616446	1.000000	0.71417	1.000000	0.80357	0.810000	0.45777	1.690000	0.37711	2.244000	0.73946	0.533000	0.62120	GAA	T|0.998;C|0.002	0.002	strong		0.493	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196	
ARFGEF1	10565	hgsc.bcm.edu	37	8	68130065	68130065	+	Missense_Mutation	SNP	T	T	C	rs200528352		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:68130065T>C	ENST00000262215.3	-	32	4954	c.4565A>G	c.(4564-4566)aAa>aGa	p.K1522R	ARFGEF1_ENST00000518230.1_Missense_Mutation_p.K360R|ARFGEF1_ENST00000520381.1_Missense_Mutation_p.K976R	NM_006421.4	NP_006412.2	Q9Y6D6	BIG1_HUMAN	ADP-ribosylation factor guanine nucleotide-exchange factor 1 (brefeldin A-inhibited)	1522					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)			GTTGCAAGTTTTATCCCAGAT	0.343																																					p.K1522R		Atlas-SNP	.											.	ARFGEF1	196	.	0			c.A4565G						PASS	.						105.0	104.0	104.0					8																	68130065		2203	4300	6503	SO:0001583	missense	10565	exon32			CAAGTTTTATCCC	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.4565A>G	8.37:g.68130065T>C	ENSP00000262215:p.Lys1522Arg	114.0	0.0	0		133.0	65.0	0.488722	NM_006421	Q9NV46|Q9UFV2|Q9UNL0	Missense_Mutation	SNP	ENST00000262215.3	37	CCDS6199.1	.	.	.	.	.	.	.	.	.	.	T	17.24	3.339243	0.60963	.	.	ENSG00000066777	ENST00000520381;ENST00000262215;ENST00000518230	T;T;T	0.48522	0.81;0.81;0.81	5.48	5.48	0.80851	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.41558	0.1164	L	0.40543	1.245	0.58432	D	0.999994	B;B;B	0.19706	0.038;0.002;0.002	B;B;B	0.18561	0.022;0.003;0.003	T	0.19712	-1.0297	10	0.35671	T	0.21	.	15.8539	0.78960	0.0:0.0:0.0:1.0	.	1522;1000;976	Q9Y6D6;Q59FY5;E5RIF2	BIG1_HUMAN;.;.	R	976;1522;360	ENSP00000428429:K976R;ENSP00000262215:K1522R;ENSP00000430891:K360R	ENSP00000262215:K1522R	K	-	2	0	ARFGEF1	68292619	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.153000	0.71819	2.199000	0.70637	0.533000	0.62120	AAA	.	.	weak		0.343	ARFGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379441.4	NM_006421	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230399	23230399	+	Missense_Mutation	SNP	G	G	C	rs531309531	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:23230399G>C	ENST00000526893.1	+	1	440	c.166G>C	c.(166-168)Gtt>Ctt	p.V56L	IGLL5_ENST00000532223.2_Missense_Mutation_p.V56L|IGLL5_ENST00000531372.1_Missense_Mutation_p.V56L|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	56						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TGGAGCCTCAGTTGGAAGCAG	0.667													G|||	2	0.000399361	0.0008	0.0	5008	,	,		10555	0.0		0.001	False		,,,				2504	0.0				p.V56L		Atlas-SNP	.											.	IGLL5	26	.	0			c.G166C						PASS	.																																			SO:0001583	missense	100423062	exon1			GCCTCAGTTGGAA	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.166G>C	22.37:g.23230399G>C	ENSP00000431254:p.Val56Leu	124.0	0.0	0		108.0	35.0	0.324074	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	G	10.19	1.282876	0.23392	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00573	6.48;6.48	3.92	-7.84	0.01196	.	.	.	.	.	T	0.00412	0.0013	L	0.27053	0.805	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.47058	-0.9146	9	0.87932	D	0	.	3.3385	0.07110	0.5698:0.1407:0.1627:0.1268	.	56	B9A064	IGLL5_HUMAN	L	56	ENSP00000436353:V56L;ENSP00000431254:V56L	ENSP00000431254:V56L	V	+	1	0	IGLL5	21560399	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.883000	0.04170	-1.783000	0.01274	-0.152000	0.13540	GTT	.	.	none		0.667	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
TMPRSS9	360200	hgsc.bcm.edu	37	19	2421857	2421857	+	Silent	SNP	C	C	T	rs72971482	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2421857C>T	ENST00000332578.3	+	13	2058	c.2058C>T	c.(2056-2058)gaC>gaT	p.D686D		NM_182973.1	NP_892018.1	Q7Z410	TMPS9_HUMAN	transmembrane protease, serine 9	686	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.				plasminogen activation (GO:0031639)	integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(3)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	29				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)		TCTAGGGTGACTCTGGGGGCC	0.627													C|||	10	0.00199681	0.0	0.0014	5008	,	,		15313	0.0		0.008	False		,,,				2504	0.001				p.D686D		Atlas-SNP	.											.	TMPRSS9	79	.	0			c.C2058T						PASS	.	C		14,4390	20.2+/-43.8	0,14,2188	43.0	50.0	48.0		2058	-0.4	1.0	19	dbSNP_130	48	102,8496	52.3+/-112.8	1,100,4198	no	coding-synonymous	TMPRSS9	NM_182973.1		1,114,6386	TT,TC,CC		1.1863,0.3179,0.8922		686/1060	2421857	116,12886	2202	4299	6501	SO:0001819	synonymous_variant	360200	exon13			GGGTGACTCTGGG	AJ488946	CCDS12088.1	19p13.3	2010-04-13						"""Serine peptidases / Transmembrane"""	30079	protein-coding gene	gene with protein product	"""polyserase 1"""	610477				12886014	Standard	NM_182973		Approved		uc010xgx.2	Q7Z410		ENST00000332578.3:c.2058C>T	19.37:g.2421857C>T		64.0	0.0	0		81.0	38.0	0.469136	NM_182973	Q6ZND6|Q7Z411	Silent	SNP	ENST00000332578.3	37	CCDS12088.1																																																																																			C|0.993;T|0.007	0.007	strong		0.627	TMPRSS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451330.3	NM_182973	
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000544510.1_Silent_p.H14H|JAK2_ENST00000539801.1_Silent_p.H163H	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	163	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.|Interaction with cytokine/interferon/growth hormone receptors. {ECO:0000250}.				actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	ATTTTGTGCACGGATGGATAA	0.343		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				T|||	1794	0.358227	0.4887	0.3905	5008	,	,		15245	0.2708		0.3002	False		,,,				2504	0.3088				p.H163H		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.C489T						PASS	.	T		2047,2359	609.9+/-391.4	488,1071,644	110.0	123.0	118.0		489	-0.9	0.9	9	dbSNP_119	118	2589,6011	689.4+/-404.4	366,1857,2077	no	coding-synonymous	JAK2	NM_004972.3		854,2928,2721	TT,TC,CC		30.1047,46.4594,35.6451		163/1133	5050706	4636,8370	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon6	Familial Cancer Database		TGTGCACGGATGG		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.489C>T	9.37:g.5050706C>T		64.0	0.0	0		64.0	34.0	0.53125	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			C|0.647;T|0.353	0.353	strong		0.343	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
FMN2	56776	hgsc.bcm.edu	37	1	240256668	240256668	+	Missense_Mutation	SNP	A	A	C	rs146681532	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:240256668A>C	ENST00000319653.9	+	1	1489	c.1259A>C	c.(1258-1260)aAg>aCg	p.K420T		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	420					cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)			NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TGCTACATCAAGACCACCACC	0.677													A|||	7	0.00139776	0.0	0.0029	5008	,	,		11822	0.0		0.003	False		,,,				2504	0.002				p.K420T		Atlas-SNP	.											.	FMN2	451	.	0			c.A1259C						PASS	.	A	THR/LYS	4,4402	8.1+/-20.4	0,4,2199	48.0	56.0	54.0		1259	3.0	1.0	1	dbSNP_134	54	55,8545	33.8+/-87.4	0,55,4245	yes	missense	FMN2	NM_020066.4	78	0,59,6444	CC,CA,AA		0.6395,0.0908,0.4536	probably-damaging	420/1723	240256668	59,12947	2203	4300	6503	SO:0001583	missense	56776	exon1			ACATCAAGACCAC	AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.1259A>C	1.37:g.240256668A>C	ENSP00000318884:p.Lys420Thr	108.0	0.0	0		122.0	55.0	0.45082	NM_020066	B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Missense_Mutation	SNP	ENST00000319653.9	37	CCDS31069.2	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	A	12.29	1.892175	0.33442	9.08E-4	0.006395	ENSG00000155816	ENST00000319653	D	0.83591	-1.74	4.15	3.02	0.34903	.	0.084158	0.49305	D	0.000158	T	0.74846	0.3770	L	0.34521	1.04	0.80722	D	1	D	0.63880	0.993	P	0.53266	0.722	T	0.77611	-0.2523	10	0.87932	D	0	.	9.2617	0.37616	0.9135:0.0:0.0865:0.0	.	420	Q9NZ56	FMN2_HUMAN	T	420	ENSP00000318884:K420T	ENSP00000318884:K420T	K	+	2	0	FMN2	238323291	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.340000	0.72973	0.647000	0.30713	0.379000	0.24179	AAG	A|0.997;C|0.003	0.003	strong		0.677	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2	XM_371352	
CCDC152	100129792	hgsc.bcm.edu	37	5	42759295	42759295	+	Silent	SNP	C	C	T	rs200364347	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:42759295C>T	ENST00000361970.5	+	2	159	c.72C>T	c.(70-72)ttC>ttT	p.F24F	CCDC152_ENST00000388827.4_Silent_p.F24F	NM_001134848.1	NP_001128320.1	Q4G0S7	CC152_HUMAN	coiled-coil domain containing 152	24										endometrium(1)	1						TAAATGACTTCTCACAGATAG	0.343													C|||	6	0.00119808	0.0	0.0014	5008	,	,		17411	0.0		0.002	False		,,,				2504	0.0031				p.F24F		Atlas-SNP	.											CCDC152,NS,carcinoma,0,1	CCDC152	10	1	0			c.C72T						PASS	.						94.0	83.0	86.0					5																	42759295		692	1590	2282	SO:0001819	synonymous_variant	100129792	exon2			TGACTTCTCACAG		CCDS47203.1	5p12	2008-07-14			ENSG00000198865	ENSG00000198865			34438	protein-coding gene	gene with protein product							Standard	NM_001134848		Approved	LOC100129792	uc003jmx.3	Q4G0S7	OTTHUMG00000162141	ENST00000361970.5:c.72C>T	5.37:g.42759295C>T		160.0	0.0	0		136.0	65.0	0.477941	NM_001134848	B3KXI4|B4E0P7|Q5BLP6	Silent	SNP	ENST00000361970.5	37	CCDS47203.1																																																																																			C|0.995;T|0.005	0.005	strong		0.343	CCDC152-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367497.1	XM_001717416	
LDHA	3939	hgsc.bcm.edu	37	11	18427072	18427072	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18427072A>G	ENST00000422447.3	+	7	1060	c.787A>G	c.(787-789)Ata>Gta	p.I263V	LDHA_ENST00000227157.4_Intron|LDHA_ENST00000379412.5_Missense_Mutation_p.I263V|AC084117.3_ENST00000496975.2_RNA|LDHA_ENST00000540430.1_Missense_Mutation_p.I292V|LDHA_ENST00000542179.1_Missense_Mutation_p.I263V|LDHA_ENST00000396222.2_Intron|LDHA_ENST00000430553.2_Missense_Mutation_p.I205V	NM_001135239.1|NM_005566.3	NP_001128711.1|NP_005557.1	P00338	LDHA_HUMAN	lactate dehydrogenase A	263					cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|cellular response to extracellular stimulus (GO:0031668)|glycolytic process (GO:0006096)|pyruvate metabolic process (GO:0006090)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm fibrous sheath (GO:0035686)	L-lactate dehydrogenase activity (GO:0004459)			central_nervous_system(3)|endometrium(1)|large_intestine(4)|lung(4)	12						GGCAGAGAGTATAATGAAGAA	0.423																																					p.I292V		Atlas-SNP	.											.	LDHA	118	.	0			c.A874G						PASS	.						111.0	113.0	112.0					11																	18427072		2199	4293	6492	SO:0001583	missense	3939	exon7			GAGAGTATAATGA	X02152	CCDS7839.1, CCDS44549.1, CCDS53609.1, CCDS53610.1, CCDS53611.1	11p15.1	2012-10-02			ENSG00000134333	ENSG00000134333	1.1.1.27		6535	protein-coding gene	gene with protein product		150000				3000353	Standard	NM_005566		Approved		uc010rdd.2	P00338	OTTHUMG00000167721	ENST00000422447.3:c.787A>G	11.37:g.18427072A>G	ENSP00000395337:p.Ile263Val	71.0	0.0	0		91.0	4.0	0.043956	NM_001165414	B4DKQ2|B7Z5E3|D3DQY3|F8W819|Q53G53|Q6IBM7|Q6ZNV1|Q9UDE8|Q9UDE9	Missense_Mutation	SNP	ENST00000422447.3	37	CCDS7839.1	.	.	.	.	.	.	.	.	.	.	A	14.33	2.502896	0.44558	.	.	ENSG00000134333	ENST00000422447;ENST00000430553;ENST00000541620;ENST00000445376;ENST00000540430;ENST00000379412;ENST00000542179	T;T;T;T;T	0.66995	-0.24;-0.24;-0.24;-0.24;-0.24	5.12	5.12	0.69794	Lactate/malate dehydrogenase, C-terminal (1);Lactate dehydrogenase/glycoside hydrolase, family 4, C-terminal (2);	0.103731	0.64402	D	0.000003	T	0.66197	0.2765	L	0.55834	1.745	0.80722	D	1	B;B;B;B	0.16166	0.016;0.001;0.001;0.013	B;B;B;B	0.30251	0.113;0.025;0.026;0.056	T	0.65886	-0.6059	10	0.62326	D	0.03	-3.2056	15.205	0.73173	1.0:0.0:0.0:0.0	.	292;205;236;263	B7Z5E3;B4DKQ2;B4DJI1;P00338	.;.;.;LDHA_HUMAN	V	263;205;235;236;292;263;263	ENSP00000395337:I263V;ENSP00000406172:I205V;ENSP00000445175:I292V;ENSP00000368722:I263V;ENSP00000445331:I263V	ENSP00000368722:I263V	I	+	1	0	LDHA	18383648	1.000000	0.71417	1.000000	0.80357	0.642000	0.38348	4.095000	0.57728	2.056000	0.61249	0.374000	0.22700	ATA	.	.	none		0.423	LDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000258172.2	NM_005566	
LRRC16B	90668	hgsc.bcm.edu	37	14	24534270	24534270	+	Missense_Mutation	SNP	C	C	T	rs117833529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:24534270C>T	ENST00000342740.5	+	33	3338	c.3184C>T	c.(3184-3186)Cgg>Tgg	p.R1062W	LRRC16B_ENST00000334420.7_Missense_Mutation_p.R158W	NM_138360.3	NP_612369.3	Q8ND23	LR16B_HUMAN	leucine rich repeat containing 16B	1062				R -> W (in Ref. 2; CAD38886). {ECO:0000305}.		cytoplasm (GO:0005737)				breast(3)|central_nervous_system(2)|cervix(3)|endometrium(7)|kidney(1)|large_intestine(9)|liver(1)|lung(15)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)	52				GBM - Glioblastoma multiforme(265;0.019)		TCGCCGGCCCCGGAGCTTCAA	0.716													C|||	108	0.0215655	0.0015	0.0418	5008	,	,		8025	0.0		0.0368	False		,,,				2504	0.0409				p.R1062W		Atlas-SNP	.											.	LRRC16B	120	.	0			c.C3184T						PASS	.	C	TRP/ARG	23,3751		0,23,1864	19.0	24.0	22.0		3184	2.8	1.0	14	dbSNP_132	22	255,7637		2,251,3693	yes	missense	LRRC16B	NM_138360.3	101	2,274,5557	TT,TC,CC		3.2311,0.6094,2.383	probably-damaging	1062/1373	24534270	278,11388	1887	3946	5833	SO:0001583	missense	90668	exon33			CGGCCCCGGAGCT	AI017934	CCDS32054.1	14q11.2-q12	2010-09-10	2008-02-12	2008-02-12					20272	protein-coding gene	gene with protein product		614716	"""chromosome 14 open reading frame 121"""	C14orf121		19846667	Standard	NM_138360		Approved	BC008134, crml-1, CARMIL3	uc001wlj.2	Q8ND23		ENST00000342740.5:c.3184C>T	14.37:g.24534270C>T	ENSP00000340467:p.Arg1062Trp	21.0	0.0	0		41.0	19.0	0.463415	NM_138360	Q8TEF7|Q96HS9	Missense_Mutation	SNP	ENST00000342740.5	37	CCDS32054.1	46	0.021062271062271064	2	0.0040650406504065045	19	0.052486187845303865	0	0.0	25	0.032981530343007916	C	12.56	1.973870	0.34848	0.006094	0.032311	ENSG00000186648	ENST00000342740;ENST00000334420	T;T	0.60797	1.2;0.16	4.66	2.77	0.32553	.	0.254810	0.20948	N	0.082818	T	0.29389	0.0732	L	0.59436	1.845	0.28233	N	0.926034	D;D	0.89917	1.0;0.999	D;P	0.80764	0.994;0.876	T	0.48725	-0.9010	10	0.87932	D	0	-13.2657	9.764	0.40550	0.3756:0.6244:0.0:0.0	.	158;1062	Q8ND23-2;Q8ND23	.;LR16B_HUMAN	W	1062;158	ENSP00000340467:R1062W;ENSP00000334701:R158W	ENSP00000334701:R158W	R	+	1	2	LRRC16B	23604110	0.999000	0.42202	1.000000	0.80357	0.602000	0.36980	1.625000	0.37029	0.375000	0.24679	-0.348000	0.07805	CGG	C|0.976;T|0.024	0.024	strong		0.716	LRRC16B-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416527.1	NM_138360	
NID2	22795	hgsc.bcm.edu	37	14	52509063	52509063	+	Missense_Mutation	SNP	G	G	A	rs17831525	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:52509063G>A	ENST00000216286.5	-	7	1584	c.1585C>T	c.(1585-1587)Cct>Tct	p.P529S	NID2_ENST00000541773.1_Missense_Mutation_p.P476S	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	529	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.		P -> S (in dbSNP:rs17831525).		basement membrane organization (GO:0071711)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)	basement membrane (GO:0005604)|cell surface (GO:0009986)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)			NS(1)|breast(5)|endometrium(9)|kidney(4)|large_intestine(11)|liver(1)|lung(40)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	87	Breast(41;0.0639)|all_epithelial(31;0.123)					ACTCGGTGAGGTGCCCCTAAA	0.512													g|||	53	0.0105831	0.0008	0.0173	5008	,	,		21125	0.0		0.0398	False		,,,				2504	0.0				p.P529S		Atlas-SNP	.											.	NID2	201	.	0			c.C1585T						PASS	.	G	SER/PRO	34,4372	38.4+/-70.7	0,34,2169	104.0	105.0	105.0		1585	6.2	1.0	14	dbSNP_123	105	269,8331	103.1+/-164.3	7,255,4038	yes	missense	NID2	NM_007361.3	74	7,289,6207	AA,AG,GG		3.1279,0.7717,2.3297	probably-damaging	529/1376	52509063	303,12703	2203	4300	6503	SO:0001583	missense	22795	exon7			GGTGAGGTGCCCC	AB009799	CCDS9706.1	14q22.1	2008-05-14			ENSG00000087303	ENSG00000087303			13389	protein-coding gene	gene with protein product		605399				9733643	Standard	NM_007361		Approved		uc001wzo.3	Q14112	OTTHUMG00000140298	ENST00000216286.5:c.1585C>T	14.37:g.52509063G>A	ENSP00000216286:p.Pro529Ser	64.0	0.0	0		46.0	27.0	0.586957	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	38	0.0173992673992674	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	28	0.036939313984168866	G	19.57	3.851885	0.71719	0.007717	0.031279	ENSG00000087303	ENST00000216286;ENST00000541773;ENST00000395707	T;T	0.53640	0.61;0.61	6.16	6.16	0.99307	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.147145	0.64402	D	0.000007	T	0.37945	0.1022	M	0.79123	2.44	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	P;D;D	0.69479	0.893;0.964;0.934	T	0.60424	-0.7266	10	0.72032	D	0.01	.	16.2426	0.82423	0.0:0.1689:0.8311:0.0	rs17831525;rs52794399;rs17831525	476;531;529	Q14112-2;Q5CZI2;Q14112	.;.;NID2_HUMAN	S	529;476;531	ENSP00000216286:P529S;ENSP00000443730:P476S	ENSP00000216286:P529S	P	-	1	0	NID2	51578813	1.000000	0.71417	0.970000	0.41538	0.553000	0.35397	5.969000	0.70422	2.937000	0.99478	0.650000	0.86243	CCT	G|0.978;A|0.022	0.022	strong		0.512	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
TOPORS	10210	hgsc.bcm.edu	37	9	32542793	32542793	+	Missense_Mutation	SNP	G	G	T	rs79708790	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32542793G>T	ENST00000360538.2	-	3	1846	c.1730C>A	c.(1729-1731)tCt>tAt	p.S577Y	TOPORS_ENST00000379858.1_Missense_Mutation_p.S512Y	NM_005802.4	NP_005793.2	Q9NS56	TOPRS_HUMAN	topoisomerase I binding, arginine/serine-rich, E3 ubiquitin protein ligase	577	Interaction with SUMO1.|Interaction with TOP1.|Interaction with p53/TP53.				cellular response to DNA damage stimulus (GO:0006974)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of apoptotic process (GO:0043066)|photoreceptor cell outer segment organization (GO:0035845)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein K48-linked ubiquitination (GO:0070936)|protein localization to nucleus (GO:0034504)|protein monoubiquitination (GO:0006513)|protein sumoylation (GO:0016925)|regulation of cell proliferation (GO:0042127)|retina layer formation (GO:0010842)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|transcription, DNA-templated (GO:0006351)|ubiquitin-dependent protein catabolic process (GO:0006511)	centriole (GO:0005814)|ciliary basal body (GO:0036064)|gamma-tubulin complex (GO:0000930)|midbody (GO:0030496)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|PML body (GO:0016605)|spindle pole (GO:0000922)|ubiquitin ligase complex (GO:0000151)	antigen binding (GO:0003823)|DNA binding (GO:0003677)|DNA topoisomerase binding (GO:0044547)|SUMO ligase activity (GO:0019789)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			large_intestine(6)|ovary(3)|skin(2)|upper_aerodigestive_tract(1)	12			LUSC - Lung squamous cell carcinoma(29;0.0181)	GBM - Glioblastoma multiforme(74;0.0018)		TCCTCTTACAGATGAGTTCAG	0.378													G|||	2	0.000399361	0.0	0.0014	5008	,	,		22549	0.0		0.001	False		,,,				2504	0.0				p.S577Y		Atlas-SNP	.											.	TOPORS	127	.	0			c.C1730A						PASS	.	G	TYR/SER,TYR/SER	0,4406		0,0,2203	176.0	175.0	175.0		1535,1730	5.7	0.8	9	dbSNP_131	175	30,8570	20.4+/-63.3	0,30,4270	yes	missense,missense	TOPORS	NM_001195622.1,NM_005802.4	144,144	0,30,6473	TT,TG,GG		0.3488,0.0,0.2307	possibly-damaging,possibly-damaging	512/981,577/1046	32542793	30,12976	2203	4300	6503	SO:0001583	missense	10210	exon3			CTTACAGATGAGT	AF098300	CCDS6527.1, CCDS56566.1	9p21	2013-01-09	2010-09-17		ENSG00000197579	ENSG00000197579		"""RING-type (C3HC4) zinc fingers"""	21653	protein-coding gene	gene with protein product		609507	"""retinitis pigmentosa 31 (autosomal dominant)"", ""topoisomerase I binding, arginine/serine-rich"""	RP31		10352183, 12083797, 17924349	Standard	NM_005802		Approved	TP53BPL, LUN	uc003zrb.3	Q9NS56	OTTHUMG00000019743	ENST00000360538.2:c.1730C>A	9.37:g.32542793G>T	ENSP00000353735:p.Ser577Tyr	137.0	0.0	0		168.0	77.0	0.458333	NM_005802	O43273|Q6P987|Q9NS55|Q9UNR9	Missense_Mutation	SNP	ENST00000360538.2	37	CCDS6527.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	4.776	0.144262	0.09134	0.0	0.003488	ENSG00000197579	ENST00000360538;ENST00000379858	T;T	0.17528	2.3;2.27	5.65	5.65	0.86999	.	0.000000	0.39615	N	0.001311	T	0.18718	0.0449	N	0.24115	0.695	0.40496	D	0.980597	P	0.48407	0.91	P	0.45946	0.498	T	0.01212	-1.1417	10	0.72032	D	0.01	-10.5062	18.4994	0.90876	0.0:0.0:1.0:0.0	.	577	Q9NS56	TOPRS_HUMAN	Y	577;512	ENSP00000353735:S577Y;ENSP00000369187:S512Y	ENSP00000353735:S577Y	S	-	2	0	TOPORS	32532793	1.000000	0.71417	0.754000	0.31244	0.181000	0.23173	6.680000	0.74518	2.655000	0.90218	0.557000	0.71058	TCT	G|0.998;T|0.002	0.002	strong		0.378	TOPORS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000052007.1	NM_005802	
GREB1	9687	hgsc.bcm.edu	37	2	11750985	11750985	+	Silent	SNP	C	C	T	rs374277928		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:11750985C>T	ENST00000381486.2	+	18	3138	c.2838C>T	c.(2836-2838)caC>caT	p.H946H	GREB1_ENST00000396123.1_5'Flank|GREB1_ENST00000234142.5_Silent_p.H946H	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	946						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		CCTGCGGCCACGGGCTCATGG	0.687																																					p.H946H	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C2838T						PASS	.	C		0,4120		0,0,2060	29.0	33.0	32.0		2838	4.2	1.0	2		32	1,8383		0,1,4191	no	coding-synonymous	GREB1	NM_014668.3		0,1,6251	TT,TC,CC		0.0119,0.0,0.0080		946/1950	11750985	1,12503	2060	4192	6252	SO:0001819	synonymous_variant	9687	exon18			CGGCCACGGGCTC		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2838C>T	2.37:g.11750985C>T		60.0	0.0	0		79.0	46.0	0.582278	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	CCDS42655.1																																																																																			.	.	weak		0.687	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
SLC14A2	8170	hgsc.bcm.edu	37	18	43204739	43204739	+	Missense_Mutation	SNP	C	C	T	rs34461862	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:43204739C>T	ENST00000255226.6	+	2	926	c.110C>T	c.(109-111)aCt>aTt	p.T37I	SLC14A2_ENST00000586448.1_Missense_Mutation_p.T37I	NM_007163.3	NP_009094.3	Q15849	UT2_HUMAN	solute carrier family 14 (urea transporter), member 2	37			T -> I (in dbSNP:rs34461862).		transmembrane transport (GO:0055085)|urea transport (GO:0015840)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cell adhesion molecule binding (GO:0050839)|urea transmembrane transporter activity (GO:0015204)			NS(1)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(8)|lung(35)|ovary(1)|prostate(1)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						TCCCCGGATACTCACCCAGCT	0.582													C|||	72	0.014377	0.0015	0.0346	5008	,	,		19755	0.0		0.0417	False		,,,				2504	0.0041				p.T37I		Atlas-SNP	.											.	SLC14A2	121	.	0			c.C110T						PASS	.	C	ILE/THR,ILE/THR	26,4380	31.7+/-61.6	0,26,2177	82.0	78.0	80.0		110,110	4.5	1.0	18	dbSNP_126	80	383,8217	124.3+/-183.0	9,365,3926	yes	missense,missense	SLC14A2	NM_001242692.1,NM_007163.3	89,89	9,391,6103	TT,TC,CC		4.4535,0.5901,3.1447	benign,benign	37/921,37/921	43204739	409,12597	2203	4300	6503	SO:0001583	missense	8170	exon3			CGGATACTCACCC	X96969	CCDS11924.1	18q12.1-q21.1	2013-05-22			ENSG00000132874	ENSG00000132874		"""Solute carriers"""	10919	protein-coding gene	gene with protein product		601611				8647271	Standard	NM_007163		Approved	HUT2, UT2	uc010dnj.3	Q15849	OTTHUMG00000132616	ENST00000255226.6:c.110C>T	18.37:g.43204739C>T	ENSP00000255226:p.Thr37Ile	57.0	0.0	0		82.0	46.0	0.560976	NM_001242692	A8K8Q7|Q2TBD6|Q96PH5	Missense_Mutation	SNP	ENST00000255226.6	37	CCDS11924.1	41	0.018772893772893772	2	0.0040650406504065045	10	0.027624309392265192	0	0.0	29	0.03825857519788918	C	12.62	1.992557	0.35131	0.005901	0.044535	ENSG00000132874	ENST00000255226;ENST00000323329	T;T	0.57752	1.09;0.38	5.38	4.47	0.54385	.	0.382979	0.24666	N	0.036585	T	0.27697	0.0681	L	0.54323	1.7	0.32498	N	0.539278	D;D	0.65815	0.995;0.969	P;P	0.56278	0.795;0.585	T	0.58381	-0.7646	10	0.45353	T	0.12	-9.3842	12.1733	0.54172	0.0:0.829:0.171:0.0	rs34461862	37;37	Q15849;E7EPU1	UT2_HUMAN;.	I	37	ENSP00000255226:T37I;ENSP00000320689:T37I	ENSP00000255226:T37I	T	+	2	0	SLC14A2	41458737	0.988000	0.35896	0.998000	0.56505	0.260000	0.26232	1.538000	0.36094	2.517000	0.84864	0.462000	0.41574	ACT	C|0.973;T|0.027	0.027	strong		0.582	SLC14A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255858.1		
MCM3AP	8888	hgsc.bcm.edu	37	21	47664746	47664746	+	Silent	SNP	C	C	A	rs17183255	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47664746C>A	ENST00000397708.1	-	24	5267	c.5013G>T	c.(5011-5013)ccG>ccT	p.P1671P	MCM3AP-AS1_ENST00000591223.1_RNA|MCM3AP-AS1_ENST00000588753.1_RNA|MCM3AP-AS1_ENST00000432735.1_RNA|MCM3AP-AS1_ENST00000455567.1_RNA|MCM3AP_ENST00000467026.1_5'UTR|MCM3AP-AS1_ENST00000590829.1_RNA|MCM3AP_ENST00000291688.1_Silent_p.P1671P|MCM3AP-AS1_ENST00000421927.1_RNA|MCM3AP-AS1_ENST00000444998.1_RNA|MCM3AP-AS1_ENST00000414659.1_RNA|AP001469.7_ENST00000444966.1_RNA			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	1671	Acetyltransferase.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					GGTCCATCTGCGGAAGCTGGA	0.637																																					p.P1671P		Atlas-SNP	.											.	MCM3AP	146	.	0			c.G5013T						PASS	.						34.0	35.0	35.0					21																	47664746		2203	4300	6503	SO:0001819	synonymous_variant	8888	exon23			CATCTGCGGAAGC	AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.5013G>T	21.37:g.47664746C>A		46.0	0.0	0		54.0	20.0	0.37037	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			C|0.997;T|0.003	.	alt		0.637	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
SORCS1	114815	hgsc.bcm.edu	37	10	108339209	108339209	+	Missense_Mutation	SNP	T	T	C	rs187136160	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:108339209T>C	ENST00000263054.6	-	25	3296	c.3289A>G	c.(3289-3291)Acc>Gcc	p.T1097A	SORCS1_ENST00000369698.1_Missense_Mutation_p.T632A|SORCS1_ENST00000344440.6_Missense_Mutation_p.T1097A	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1097					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		CCACTGTGGGTTGGAGTGAGG	0.527													T|||	2	0.000399361	0.0	0.0	5008	,	,		16881	0.0		0.002	False		,,,				2504	0.0				p.T1097A		Atlas-SNP	.											SORCS1_ENST00000344440,NS,carcinoma,+2,4	SORCS1	534	4	0			c.A3289G						PASS	.	T	ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR,ALA/THR	0,4406		0,0,2203	94.0	74.0	81.0		3289,3289,3289,3289,3289,3289	3.6	0.9	10		81	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	58,58,58,58,58,58	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	benign,benign,benign,benign,benign,benign	1097/1199,1097/1180,1097/1131,1097/1160,1097/1180,1097/1169	108339209	3,13003	2203	4300	6503	SO:0001583	missense	114815	exon25			TGTGGGTTGGAGT	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3289A>G	10.37:g.108339209T>C	ENSP00000263054:p.Thr1097Ala	62.0	0.0	0		33.0	16.0	0.484848	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.840	1.190688	0.21954	0.0	3.49E-4	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.20881	2.04;2.57;2.6	5.92	3.59	0.41128	.	0.242564	0.40222	N	0.001147	T	0.09291	0.0229	N	0.08118	0	0.32196	N	0.578402	B;B;B;B;B	0.02656	0.0;0.0;0.0;0.0;0.0	B;B;B;B;B	0.06405	0.001;0.002;0.001;0.001;0.001	T	0.22661	-1.0210	9	.	.	.	-10.911	7.9891	0.30229	0.0:0.232:0.0:0.768	.	1097;1097;1097;1097;1097	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	A	632;1097;1097	ENSP00000358712:T632A;ENSP00000263054:T1097A;ENSP00000345964:T1097A	.	T	-	1	0	SORCS1	108329199	0.989000	0.36119	0.910000	0.35882	0.943000	0.58893	2.132000	0.42083	0.495000	0.27882	-0.385000	0.06624	ACC	T|0.999;C|0.001	0.001	strong		0.527	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
TRMT2A	27037	hgsc.bcm.edu	37	22	20103264	20103264	+	Silent	SNP	C	C	T	rs9605068|rs71317167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:20103264C>T	ENST00000252136.7	-	3	1027	c.639G>A	c.(637-639)ctG>ctA	p.L213L	RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000403707.3_Silent_p.L213L|TRMT2A_ENST00000439169.2_Silent_p.L213L|RANBP1_ENST00000430524.1_5'Flank|TRMT2A_ENST00000404751.3_Silent_p.L213L|RANBP1_ENST00000331821.3_5'Flank	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	213					RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						TCTGCTCGAGCAGCCAGGGCA	0.637													C|||	59	0.0117812	0.0023	0.013	5008	,	,		18163	0.0		0.0378	False		,,,				2504	0.0092				p.L213L		Atlas-SNP	.											.	TRMT2A	34	.	0			c.G639A						PASS	.	C	,	27,4377	33.5+/-64.1	1,25,2176	45.0	42.0	43.0		639,639	1.8	0.7	22	dbSNP_119	43	327,8273	114.0+/-174.0	12,303,3985	no	coding-synonymous,coding-synonymous	TRMT2A	NM_022727.4,NM_182984.3	,	13,328,6161	TT,TC,CC		3.8023,0.6131,2.7222	,	213/626,213/626	20103264	354,12650	2202	4300	6502	SO:0001819	synonymous_variant	27037	exon3			CTCGAGCAGCCAG	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"""HpaII tiny fragments locus 9C"""	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.639G>A	22.37:g.20103264C>T		191.0	0.0	0		203.0	98.0	0.482759	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Silent	SNP	ENST00000252136.7	37	CCDS13774.1																																																																																			C|0.978;T|0.022	0.022	strong		0.637	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727	
ALK	238	hgsc.bcm.edu	37	2	29416366	29416366	+	Missense_Mutation	SNP	G	G	C	rs1881421	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:29416366G>C	ENST00000389048.3	-	29	5493	c.4587C>G	c.(4585-4587)gaC>gaG	p.D1529E	ALK_ENST00000431873.1_Missense_Mutation_p.D359E	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1529			D -> E (in dbSNP:rs1881421). {ECO:0000269|PubMed:17344846, ECO:0000269|PubMed:9053841, ECO:0000269|Ref.4}.		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)	GGTTACCCCTGTCGTGTGGCT	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				C|||	2869	0.572883	0.643	0.5706	5008	,	,		17724	0.7292		0.3837	False		,,,				2504	0.5133				p.D1529E		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C4587G						PASS	.	C	GLU/ASP	2681,1725	517.7+/-369.5	834,1013,356	180.0	196.0	191.0		4587	-3.4	0.0	2	dbSNP_92	191	2957,5643	667.4+/-402.5	508,1941,1851	yes	missense	ALK	NM_004304.4	45	1342,2954,2207	CC,CG,GG		34.3837,39.1512,43.3492	benign	1529/1621	29416366	5638,7368	2203	4300	6503	SO:0001583	missense	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	ACCCCTGTCGTGT	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.4587C>G	2.37:g.29416366G>C	ENSP00000373700:p.Asp1529Glu	271.0	1.0	0.00369004		269.0	127.0	0.472119	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Missense_Mutation	SNP	ENST00000389048.3	37	CCDS33172.1	1235	0.5654761904761905	327	0.6646341463414634	191	0.5276243093922652	415	0.7255244755244755	302	0.39841688654353563	C	2.203	-0.382484	0.04966	0.608488	0.343837	ENSG00000171094	ENST00000389048;ENST00000431873	T;T	0.26957	1.7;1.7	5.11	-3.42	0.04825	.	0.428474	0.19238	N	0.119246	T	0.00012	0.0000	N	0.00246	-1.78	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.31861	-0.9928	9	0.02654	T	1	.	11.8015	0.52130	0.0:0.2641:0.5636:0.1723	rs1881421;rs3738872;rs17007643;rs52821197;rs60882094;rs1881421	1529	Q9UM73	ALK_HUMAN	E	1529;359	ENSP00000373700:D1529E;ENSP00000414027:D359E	ENSP00000373700:D1529E	D	-	3	2	ALK	29269870	0.000000	0.05858	0.000000	0.03702	0.047000	0.14425	-0.022000	0.12480	-1.464000	0.01902	-0.357000	0.07601	GAC	G|0.518;C|0.482	0.482	strong		0.547	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
OR51B5	282763	hgsc.bcm.edu	37	11	5364476	5364476	+	Silent	SNP	C	C	T	rs61738485	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364476C>T	ENST00000300773.2	-	1	333	c.279G>A	c.(277-279)gcG>gcA	p.A93A	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	93					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		AAAAGCAGGCCGCACTTCCAA	0.562													T|||	491	0.0980431	0.3071	0.049	5008	,	,		18817	0.0		0.0457	False		,,,				2504	0.0051				p.A93A		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.G279A						PASS	.	T		1240,3162	701.9+/-406.8	168,904,1129	43.0	42.0	42.0		279	-8.9	0.0	11	dbSNP_129	42	455,8139	796.1+/-407.5	13,429,3855	no	coding-synonymous	OR51B5	NM_001005567.2		181,1333,4984	TT,TC,CC		5.2944,28.169,13.0425		93/313	5364476	1695,11301	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			GCAGGCCGCACTT	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.279G>A	11.37:g.5364476C>T		32.0	0.0	0		25.0	9.0	0.36	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			C|0.885;T|0.115	0.115	strong		0.562	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
SLC1A5	6510	hgsc.bcm.edu	37	19	47280587	47280587	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47280587G>A	ENST00000542575.2	-	6	1762	c.1134C>T	c.(1132-1134)atC>atT	p.I378I	SLC1A5_ENST00000412532.2_Silent_p.I150I|SLC1A5_ENST00000594991.1_Silent_p.I202I|SLC1A5_ENST00000434726.2_Silent_p.I176I	NM_005628.2	NP_005619.1	Q15758	AAAT_HUMAN	solute carrier family 1 (neutral amino acid transporter), member 5	378					amino acid transport (GO:0006865)|extracellular amino acid transport (GO:0006860)|glutamine transport (GO:0006868)|ion transport (GO:0006811)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-glutamine transmembrane transporter activity (GO:0015186)|L-serine transmembrane transporter activity (GO:0015194)|neutral amino acid transmembrane transporter activity (GO:0015175)|receptor activity (GO:0004872)|sodium:dicarboxylate symporter activity (GO:0017153)|virus receptor activity (GO:0001618)			cervix(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(2)|stomach(1)	13		all_epithelial(76;0.00314)|Ovarian(192;0.0798)|all_neural(266;0.107)		OV - Ovarian serous cystadenocarcinoma(262;0.000338)|all cancers(93;0.000882)|Epithelial(262;0.0211)|GBM - Glioblastoma multiforme(486;0.0341)	L-Asparagine(DB00174)|L-Glutamine(DB00130)	CGATGGGCAGGATGAAACGGC	0.607																																					p.I378I		Atlas-SNP	.											.	SLC1A5	31	.	0			c.C1134T						PASS	.						67.0	56.0	60.0					19																	47280587		2203	4300	6503	SO:0001819	synonymous_variant	6510	exon6			GGGCAGGATGAAA	U53347	CCDS12692.1, CCDS46125.1, CCDS46126.1	19q13.32	2013-07-15			ENSG00000105281	ENSG00000105281		"""Solute carriers"""	10943	protein-coding gene	gene with protein product		109190		RDRC, M7V1		8702519, 10051606	Standard	NM_005628		Approved	AAAT, ASCT2	uc002pfs.3	Q15758	OTTHUMG00000183434	ENST00000542575.2:c.1134C>T	19.37:g.47280587G>A		80.0	0.0	0		90.0	34.0	0.377778	NM_005628	A8K9H5|B4DR77|B4DWS4|B7ZB81|D0EYG6|E9PC01|O95720|Q96RL9|Q9BWQ3|Q9UNP2	Silent	SNP	ENST00000542575.2	37	CCDS12692.1																																																																																			.	.	none		0.607	SLC1A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466630.1		
DNAH7	56171	hgsc.bcm.edu	37	2	196922836	196922836	+	Missense_Mutation	SNP	T	T	A	rs72917299	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:196922836T>A	ENST00000312428.6	-	2	120	c.20A>T	c.(19-21)aAa>aTa	p.K7I	DNAH7_ENST00000410072.1_Missense_Mutation_p.K7I	NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	7	Stem. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)			NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						GCTGGCCGATTTATCCTGTAT	0.313													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		16097	0.0		0.0129	False		,,,				2504	0.0				p.K7I		Atlas-SNP	.											.	DNAH7	512	.	0			c.A20T						PASS	.	T	ILE/LYS	10,3592		0,10,1791	181.0	174.0	176.0		20	4.3	0.9	2	dbSNP_130	176	108,8028		1,106,3961	yes	missense	DNAH7	NM_018897.2	102	1,116,5752	AA,AT,TT		1.3274,0.2776,1.0053	possibly-damaging	7/4025	196922836	118,11620	1801	4068	5869	SO:0001583	missense	56171	exon2			GCCGATTTATCCT	AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.20A>T	2.37:g.196922836T>A	ENSP00000311273:p.Lys7Ile	110.0	0.0	0		94.0	47.0	0.5	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	1	0.0017482517482517483	10	0.013192612137203167	T	13.85	2.361068	0.41801	0.002776	0.013274	ENSG00000118997	ENST00000312428;ENST00000410072;ENST00000312446	T;T	0.23754	1.89;2.52	4.29	4.29	0.51040	.	.	.	.	.	T	0.26919	0.0659	N	0.22421	0.69	0.31255	N	0.693556	D	0.65815	0.995	D	0.75484	0.986	T	0.19712	-1.0297	9	0.87932	D	0	.	10.1288	0.42665	0.0:0.0:0.0:1.0	.	7	Q8WXX0	DYH7_HUMAN	I	7	ENSP00000311273:K7I;ENSP00000386260:K7I	ENSP00000311273:K7I	K	-	2	0	DNAH7	196631081	0.996000	0.38824	0.876000	0.34364	0.572000	0.35998	3.399000	0.52586	2.155000	0.67459	0.460000	0.39030	AAA	T|0.991;A|0.009	0.009	strong		0.313	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
KLHL35	283212	hgsc.bcm.edu	37	11	75134832	75134832	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:75134832G>T	ENST00000539798.1	-	5	1466	c.1467C>A	c.(1465-1467)gaC>gaA	p.D489E	KLHL35_ENST00000376292.4_Missense_Mutation_p.D269E	NM_001039548.2	NP_001034637.2	Q6PF15	KLH35_HUMAN	kelch-like family member 35	489										lung(2)|stomach(1)	3						CATAGATGGTGTCCTCAAGGG	0.597																																					p.D489E	Colon(77;683 1691 18820 23811)	Atlas-SNP	.											.	KLHL35	15	.	0			c.C1467A						PASS	.						99.0	109.0	105.0					11																	75134832		2031	4177	6208	SO:0001583	missense	283212	exon5			GATGGTGTCCTCA		CCDS44685.1, CCDS44685.2	11q13.4	2013-02-22	2013-02-22		ENSG00000149243	ENSG00000149243		"""Kelch-like"", ""BTB/POZ domain containing"""	26597	protein-coding gene	gene with protein product			"""kelch-like 35 (Drosophila)"""				Standard	NM_001039548		Approved	FLJ33790	uc001owm.2	Q6PF15	OTTHUMG00000133573	ENST00000539798.1:c.1467C>A	11.37:g.75134832G>T	ENSP00000438526:p.Asp489Glu	82.0	0.0	0		81.0	4.0	0.0493827	NM_001039548	A2RU06|F5H412|Q86XM7|Q8NBB1	Missense_Mutation	SNP	ENST00000539798.1	37	CCDS44685.2	.	.	.	.	.	.	.	.	.	.	G	10.26	1.300475	0.23650	.	.	ENSG00000149243	ENST00000376292;ENST00000539798	T;T	0.68903	-0.36;-0.36	5.12	3.23	0.37069	Kelch-type beta propeller (1);	0.216802	0.37304	N	0.002158	T	0.52075	0.1712	L	0.35793	1.09	0.24569	N	0.993936	B	0.19200	0.034	B	0.23150	0.044	T	0.49244	-0.8960	10	0.66056	D	0.02	.	4.9596	0.14059	0.1754:0.0:0.658:0.1666	.	269	Q6PF15	KLH35_HUMAN	E	269;489	ENSP00000365469:D269E;ENSP00000438526:D489E	ENSP00000365469:D269E	D	-	3	2	KLHL35	74812480	1.000000	0.71417	0.986000	0.45419	0.202000	0.24057	0.617000	0.24359	0.726000	0.32339	0.650000	0.86243	GAC	.	.	none		0.597	KLHL35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_173583	
SGK223	157285	hgsc.bcm.edu	37	8	8234526	8234526	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:8234526T>A	ENST00000520004.1	-	3	1657	c.1393A>T	c.(1393-1395)Act>Tct	p.T465S	SGK223_ENST00000330777.4_Missense_Mutation_p.T465S			Q86YV5	SG223_HUMAN		467							ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										ACCTGGGGAGTTGGGTCTGGG	0.637																																					p.T465S	GBM(34;731 755 10259 33573 33867)	Atlas-SNP	.											.	.	.	.	0			c.A1393T						PASS	.						43.0	50.0	48.0					8																	8234526		2092	4227	6319	SO:0001583	missense	0	exon2			GGGGAGTTGGGTC																												ENST00000520004.1:c.1393A>T	8.37:g.8234526T>A	ENSP00000428054:p.Thr465Ser	80.0	0.0	0		91.0	30.0	0.32967	NM_001080826	Q8N3N5	Missense_Mutation	SNP	ENST00000520004.1	37	CCDS43706.1	.	.	.	.	.	.	.	.	.	.	T	11.67	1.707584	0.30322	.	.	ENSG00000182319	ENST00000330777;ENST00000520004	T;T	0.58940	0.3;0.3	5.02	1.03	0.20045	.	2.041710	0.02601	N	0.101061	T	0.43612	0.1255	N	0.19112	0.55	0.09310	N	1	B	0.14012	0.009	B	0.16289	0.015	T	0.25152	-1.0140	10	0.34782	T	0.22	.	7.1243	0.25463	0.0:0.4468:0.0:0.5532	.	465	Q86YV5	SG223_HUMAN	S	465	ENSP00000330930:T465S;ENSP00000428054:T465S	ENSP00000330930:T465S	T	-	1	0	AC068353.1	8271936	0.000000	0.05858	0.000000	0.03702	0.894000	0.52154	-0.045000	0.12003	0.249000	0.21456	-0.177000	0.13119	ACT	.	.	none		0.637	SGK223-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374864.1		
OR9K2	441639	hgsc.bcm.edu	37	12	55523833	55523833	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:55523833T>C	ENST00000305377.5	+	1	369	c.281T>C	c.(280-282)aTt>aCt	p.I94T		NM_001005243.1	NP_001005243.1	Q8NGE7	OR9K2_HUMAN	olfactory receptor, family 9, subfamily K, member 2	94						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(2)|breast(3)|central_nervous_system(1)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(2)|skin(2)	31						CTCTCCTTCATTGATCTTTTC	0.423																																					p.I94T		Atlas-SNP	.											.	OR9K2	63	.	0			c.T281C						PASS	.						181.0	179.0	180.0					12																	55523833		2203	4300	6503	SO:0001583	missense	441639	exon1			CCTTCATTGATCT	BK004326	CCDS31814.1	12q13.2	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	15339	protein-coding gene	gene with protein product							Standard	NM_001005243		Approved		uc010spe.2	Q8NGE7	OTTHUMG00000169827	ENST00000305377.5:c.281T>C	12.37:g.55523833T>C	ENSP00000307598:p.Ile94Thr	65.0	0.0	0		53.0	25.0	0.471698	NM_001005243	B9EH19|Q6IFD6	Missense_Mutation	SNP	ENST00000305377.5	37	CCDS31814.1	.	.	.	.	.	.	.	.	.	.	T	12.88	2.071507	0.36566	.	.	ENSG00000170605	ENST00000305377	T	0.03181	4.02	4.98	4.98	0.66077	GPCR, rhodopsin-like superfamily (1);	0.256644	0.27384	N	0.019611	T	0.07234	0.0183	L	0.37561	1.115	0.09310	N	1	P	0.49358	0.923	P	0.49597	0.616	T	0.09885	-1.0654	10	0.72032	D	0.01	-15.6178	14.8097	0.69985	0.0:0.0:0.0:1.0	.	94	Q8NGE7	OR9K2_HUMAN	T	94	ENSP00000307598:I94T	ENSP00000307598:I94T	I	+	2	0	OR9K2	53810100	0.007000	0.16637	0.673000	0.29887	0.816000	0.46133	1.733000	0.38156	2.223000	0.72356	0.528000	0.53228	ATT	.	.	none		0.423	OR9K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406105.1		
GCN1L1	10985	hgsc.bcm.edu	37	12	120593190	120593190	+	Missense_Mutation	SNP	G	G	A	rs183298599	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:120593190G>A	ENST00000300648.6	-	30	3497	c.3485C>T	c.(3484-3486)tCc>tTc	p.S1162F	MIR4498_ENST00000577599.1_RNA	NM_006836.1	NP_006827	Q92616	GCN1L_HUMAN	GCN1 general control of amino-acid synthesis 1-like 1 (yeast)	1162					regulation of translation (GO:0006417)|translation (GO:0006412)	cytoplasm (GO:0005737)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|translation factor activity, nucleic acid binding (GO:0008135)			NS(2)|breast(2)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(13)|liver(1)|lung(36)|ovary(4)|prostate(7)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	94	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					AATCAGCAAGGAGCAGAGGTC	0.607													G|||	3	0.000599042	0.0	0.0	5008	,	,		19268	0.0		0.003	False		,,,				2504	0.0				p.S1162F		Atlas-SNP	.											GCN1L1,NS,lymphoid_neoplasm,0,1	GCN1L1	207	1	0			c.C3485T						PASS	.	G	PHE/SER	0,4058		0,0,2029	69.0	74.0	72.0		3485	4.7	1.0	12		72	9,8377		0,9,4184	yes	missense	GCN1L1	NM_006836.1	155	0,9,6213	AA,AG,GG		0.1073,0.0,0.0723	possibly-damaging	1162/2672	120593190	9,12435	2029	4193	6222	SO:0001583	missense	10985	exon30			AGCAAGGAGCAGA	U77700	CCDS41847.1	12q24.2	2008-07-03	2001-11-28						4199	protein-coding gene	gene with protein product		605614	"""GCN1 (general control of amino-acid synthesis 1, yeast)-like 1"""			9234705	Standard	NM_006836		Approved	KIAA0219, GCN1, GCN1L	uc001txo.3	Q92616	OTTHUMG00000169338	ENST00000300648.6:c.3485C>T	12.37:g.120593190G>A	ENSP00000300648:p.Ser1162Phe	41.0	0.0	0		36.0	36.0	1	NM_006836	A8KAY1|O95001|O95651|Q6P2S3|Q86X65|Q8N5I5|Q8WU80|Q99736|Q9UE60	Missense_Mutation	SNP	ENST00000300648.6	37	CCDS41847.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	24.2	4.503043	0.85176	0.0	0.001073	ENSG00000089154	ENST00000300648	T	0.38560	1.13	5.56	4.67	0.58626	Armadillo-like helical (1);Armadillo-type fold (1);	0.111386	0.64402	N	0.000005	T	0.44222	0.1283	M	0.63843	1.955	0.80722	D	1	D	0.54397	0.966	B	0.43536	0.423	T	0.50127	-0.8864	10	0.59425	D	0.04	.	14.1912	0.65639	0.0713:0.0:0.9287:0.0	.	1162	Q92616	GCN1L_HUMAN	F	1162	ENSP00000300648:S1162F	ENSP00000300648:S1162F	S	-	2	0	GCN1L1	119077573	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	6.119000	0.71590	1.358000	0.45922	0.655000	0.94253	TCC	G|0.998;A|0.002	0.002	strong		0.607	GCN1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403592.1		
COL21A1	81578	hgsc.bcm.edu	37	6	55925801	55925801	+	Missense_Mutation	SNP	G	G	T	rs9464337	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:55925801G>T	ENST00000244728.5	-	26	2637	c.2240C>A	c.(2239-2241)gCc>gAc	p.A747D	COL21A1_ENST00000467045.1_5'UTR|COL21A1_ENST00000370808.2_Missense_Mutation_p.A147D|COL21A1_ENST00000370819.1_Missense_Mutation_p.A744D|COL21A1_ENST00000535941.1_Missense_Mutation_p.A747D	NM_030820.3	NP_110447.2	Q96P44	COLA1_HUMAN	collagen, type XXI, alpha 1	747	Collagen-like 5.		A -> D (in dbSNP:rs9464337).		extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(1)|kidney(3)|large_intestine(11)|lung(21)|ovary(2)|prostate(2)	41	Lung NSC(77;0.0483)		LUSC - Lung squamous cell carcinoma(124;0.181)			TGATCCAATGGCACCTCGGAC	0.483													G|||	209	0.0417332	0.0794	0.0173	5008	,	,		16689	0.0397		0.006	False		,,,				2504	0.047				p.A747D		Atlas-SNP	.											.	COL21A1	201	.	0			c.C2240A						PASS	.	G	ASP/ALA	284,3426		12,260,1583	58.0	56.0	57.0		2240	3.9	0.5	6	dbSNP_119	57	54,8128		1,52,4038	yes	missense	COL21A1	NM_030820.3	126	13,312,5621	TT,TG,GG		0.66,7.655,2.8422	benign	747/958	55925801	338,11554	1855	4091	5946	SO:0001583	missense	81578	exon26			CCAATGGCACCTC	AF330693	CCDS55025.1	6p12.3-p11.2	2013-01-16			ENSG00000124749	ENSG00000124749		"""Collagens"""	17025	protein-coding gene	gene with protein product		610002				11566190	Standard	XR_241922		Approved		uc003pcs.3	Q96P44	OTTHUMG00000014907	ENST00000244728.5:c.2240C>A	6.37:g.55925801G>T	ENSP00000244728:p.Ala747Asp	93.0	0.0	0		110.0	50.0	0.454545	NM_030820	A6NIX5|B2R8J9|Q49A51|Q71RF4|Q8WXV8|Q9H0V3	Missense_Mutation	SNP	ENST00000244728.5	37	CCDS55025.1	72	0.03296703296703297	45	0.09146341463414634	8	0.022099447513812154	17	0.02972027972027972	2	0.002638522427440633	G	3.291	-0.144886	0.06627	0.07655	0.0066	ENSG00000124749	ENST00000244728;ENST00000370819;ENST00000535941;ENST00000370811;ENST00000370808	D;D;D;T	0.94376	-3.41;-3.41;-3.41;-1.07	4.77	3.9	0.45041	.	0.411176	0.21246	N	0.077734	T	0.68072	0.2961	N	0.12182	0.205	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.10450	0.002;0.003;0.005;0.003	T	0.58405	-0.7642	10	0.13108	T	0.6	.	3.8636	0.09007	0.2009:0.0:0.5938:0.2053	rs9464337;rs52804762;rs9464337	147;747;747;104	Q96P44-2;B7ZLK3;Q96P44;B3KU30	.;.;COLA1_HUMAN;.	D	747;744;747;744;147	ENSP00000244728:A747D;ENSP00000359855:A744D;ENSP00000444384:A747D;ENSP00000359844:A147D	ENSP00000244728:A747D	A	-	2	0	COL21A1	56033760	0.847000	0.29606	0.523000	0.27875	0.413000	0.31143	2.015000	0.40961	1.132000	0.42129	-0.268000	0.10319	GCC	G|0.960;T|0.040	0.040	strong		0.483	COL21A1-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041004.2		
LSS	4047	hgsc.bcm.edu	37	21	47642626	47642626	+	Missense_Mutation	SNP	G	G	A	rs139003098	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47642626G>A	ENST00000397728.3	-	4	424	c.346C>T	c.(346-348)Cgc>Tgc	p.R116C	AP001469.5_ENST00000418029.1_RNA|LSS_ENST00000464357.1_5'UTR|LSS_ENST00000522411.1_Missense_Mutation_p.R116C|LSS_ENST00000457828.2_Missense_Mutation_p.R36C|LSS_ENST00000356396.4_Missense_Mutation_p.R116C	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	116					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)					AGAGGGATGCGTGCCACGTGG	0.617													G|||	4	0.000798722	0.0	0.0014	5008	,	,		20008	0.0		0.002	False		,,,				2504	0.001				p.R116C	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.C346T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG,CYS/ARG	5,4401	9.9+/-24.2	0,5,2198	115.0	91.0	99.0		346,346,106,346	0.2	0.0	21	dbSNP_134	99	16,8584	11.9+/-42.8	0,16,4284	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	180,180,180,180	0,21,6482	AA,AG,GG		0.186,0.1135,0.1615	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	116/733,116/722,36/653,116/733	47642626	21,12985	2203	4300	6503	SO:0001583	missense	4047	exon4			GGATGCGTGCCAC	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.346C>T	21.37:g.47642626G>A	ENSP00000380837:p.Arg116Cys	56.0	0.0	0		45.0	24.0	0.533333	NM_001145436	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.36	2.214719	0.39102	0.001135	0.00186	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411;ENST00000450351	T;T;T;T;T	0.44083	0.93;0.93;0.93;0.93;0.93	5.17	0.224	0.15297	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	1.046430	0.07412	N	0.892629	T	0.35799	0.0944	L	0.34521	1.04	0.09310	N	1	D;D	0.60160	0.987;0.978	B;B	0.41412	0.356;0.194	T	0.47560	-0.9108	10	0.87932	D	0	.	14.9473	0.71042	0.0:0.0:0.3631:0.6369	.	116;116	E9PEI9;P48449	.;ERG7_HUMAN	C	116;36;116;116;117	ENSP00000348762:R116C;ENSP00000409191:R36C;ENSP00000380837:R116C;ENSP00000429133:R116C;ENSP00000391368:R117C	ENSP00000348762:R116C	R	-	1	0	LSS	46467054	0.001000	0.12720	0.000000	0.03702	0.690000	0.40134	0.702000	0.25631	0.228000	0.21019	0.609000	0.83330	CGC	G|0.998;A|0.002	0.002	strong		0.617	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
BRD1	23774	hgsc.bcm.edu	37	22	50217387	50217387	+	Silent	SNP	G	G	A	rs11912787	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50217387G>A	ENST00000216267.8	-	1	1065	c.579C>T	c.(577-579)ttC>ttT	p.F193F	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.F193F|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.F193F|BRD1_ENST00000457780.2_Silent_p.F193F	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	193					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		ACTCCTTCTCGAAGCGGTCCA	0.602													G|||	508	0.101438	0.1664	0.0432	5008	,	,		21111	0.003		0.0746	False		,,,				2504	0.184				p.F193F		Atlas-SNP	.											.	BRD1	144	.	0			c.C579T						PASS	.	G		801,3605	322.9+/-297.8	69,663,1471	72.0	61.0	65.0		579	-5.2	1.0	22	dbSNP_120	65	702,7898	172.6+/-223.3	31,640,3629	no	coding-synonymous	BRD1	NM_014577.1		100,1303,5100	AA,AG,GG		8.1628,18.1798,11.5562		193/1059	50217387	1503,11503	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTTCTCGAAGCGG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.579C>T	22.37:g.50217387G>A		94.0	0.0	0		93.0	42.0	0.451613	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			G|0.899;A|0.101	0.101	strong		0.602	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
ERC1	23085	hgsc.bcm.edu	37	12	1137145	1137145	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:1137145C>T	ENST00000397203.2	+	2	482	c.76C>T	c.(76-78)Cgt>Tgt	p.R26C	ERC1_ENST00000546231.2_Missense_Mutation_p.R26C|ERC1_ENST00000355446.5_Missense_Mutation_p.R26C|ERC1_ENST00000360905.4_Missense_Mutation_p.R26C|ERC1_ENST00000543086.3_Missense_Mutation_p.R26C|ERC1_ENST00000589028.1_Missense_Mutation_p.R26C			Q8IUD2	RB6I2_HUMAN	ELKS/RAB6-interacting/CAST family member 1	26					I-kappaB phosphorylation (GO:0007252)|multicellular organismal development (GO:0007275)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|IkappaB kinase complex (GO:0008385)|presynaptic membrane (GO:0042734)	leucine zipper domain binding (GO:0043522)			NS(1)|breast(2)|cervix(2)|endometrium(2)|large_intestine(8)|lung(15)|ovary(3)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_epithelial(11;0.0698)|Ovarian(42;0.107)		OV - Ovarian serous cystadenocarcinoma(31;0.00239)|BRCA - Breast invasive adenocarcinoma(9;0.0567)			CAGGCTTCCACGTTCCCCTCG	0.572																																					p.R26C		Atlas-SNP	.											.	ERC1	95	.	0			c.C76T						PASS	.						96.0	95.0	95.0					12																	1137145		2203	4300	6503	SO:0001583	missense	23085	exon2			CTTCCACGTTCCC	AB015617	CCDS8508.1, CCDS53732.1	12p13.3	2008-02-05	2006-08-14	2006-08-14	ENSG00000082805	ENSG00000082805			17072	protein-coding gene	gene with protein product		607127	"""RAB6 interacting protein 2"""	RAB6IP2		10697956, 11929610	Standard	NM_178040		Approved	ELKS, KIAA1081, CAST2, MGC12974	uc001qjb.2	Q8IUD2	OTTHUMG00000130138	ENST00000397203.2:c.76C>T	12.37:g.1137145C>T	ENSP00000380386:p.Arg26Cys	41.0	0.0	0		34.0	12.0	0.352941	NM_178039	A2RU77|A7E295|D3DUP7|D3DUP8|Q6NVK2|Q8IUD3|Q8IUD4|Q8IUD5|Q8NAS1|Q9NXN5|Q9UIK7|Q9UPS1	Missense_Mutation	SNP	ENST00000397203.2	37	CCDS8508.1	.	.	.	.	.	.	.	.	.	.	C	18.69	3.678245	0.68042	.	.	ENSG00000082805	ENST00000347735;ENST00000397203;ENST00000454194;ENST00000537890;ENST00000299183;ENST00000543086;ENST00000542302;ENST00000545948;ENST00000546231;ENST00000355446;ENST00000360905;ENST00000440394	D;D;D;D;D;D;D;D;D	0.88818	-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43;-2.43	5.61	5.61	0.85477	.	0.000000	0.85682	D	0.000000	D	0.91267	0.7247	L	0.34521	1.04	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.994;0.952	D	0.92057	0.5653	10	0.87932	D	0	-10.8759	15.2513	0.73549	0.141:0.859:0.0:0.0	.	26;26;26	Q8IUD2-2;Q8IUD2-3;Q8IUD2	.;.;RB6I2_HUMAN	C	26	ENSP00000340054:R26C;ENSP00000380386:R26C;ENSP00000438546:R26C;ENSP00000445336:R26C;ENSP00000442976:R26C;ENSP00000442739:R26C;ENSP00000347621:R26C;ENSP00000354158:R26C;ENSP00000410064:R26C	ENSP00000299183:R26C	R	+	1	0	ERC1	1007406	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	4.827000	0.62723	2.644000	0.89710	0.655000	0.94253	CGT	.	.	none		0.572	ERC1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398380.2	NM_015064	
MORC1	27136	hgsc.bcm.edu	37	3	108723983	108723983	+	Missense_Mutation	SNP	C	C	T	rs35421732	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:108723983C>T	ENST00000483760.1	-	18	1927	c.1884G>A	c.(1882-1884)atG>atA	p.M628I	MORC1_ENST00000232603.5_Missense_Mutation_p.M649I					MORC family CW-type zinc finger 1											breast(7)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(47)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	105						GTTGAGAGTTCATTTTCTCCT	0.363													C|||	67	0.0133786	0.0	0.0231	5008	,	,		16137	0.0		0.0497	False		,,,				2504	0.001				p.M649I		Atlas-SNP	.											.	MORC1	211	.	0			c.G1947A						PASS	.	C	ILE/MET	42,4362	43.1+/-76.7	0,42,2160	102.0	105.0	104.0		1947	-2.0	0.0	3	dbSNP_126	104	401,8199	128.2+/-186.4	14,373,3913	yes	missense	MORC1	NM_014429.3	10	14,415,6073	TT,TC,CC		4.6628,0.9537,3.4066	benign	649/985	108723983	443,12561	2202	4300	6502	SO:0001583	missense	27136	exon19			AGAGTTCATTTTC	AF084946	CCDS2955.1	3q13	2011-10-26	2005-06-15	2005-06-15	ENSG00000114487	ENSG00000114487			7198	protein-coding gene	gene with protein product	"""cancer/testis antigen 33"""	603205	"""microrchidia (mouse) homolog"", ""microrchidia homolog (mouse)"""	MORC		10369865	Standard	NM_014429		Approved	ZCW6, CT33	uc003dxl.3	Q86VD1	OTTHUMG00000159209	ENST00000483760.1:c.1884G>A	3.37:g.108723983C>T	ENSP00000417282:p.Met628Ile	58.0	0.0	0		79.0	18.0	0.227848	NM_014429		Missense_Mutation	SNP	ENST00000483760.1	37		49	0.022435897435897436	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	37	0.048812664907651716	C	4.574	0.106543	0.08780	0.009537	0.046628	ENSG00000114487	ENST00000232603;ENST00000483760	T;T	0.05382	3.5;3.45	4.11	-1.98	0.07480	.	3.152720	0.00941	N	0.002824	T	0.00552	0.0018	N	0.08118	0	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.0;0.003	T	0.39251	-0.9623	10	0.31617	T	0.26	5.4385	4.2307	0.10601	0.1623:0.3617:0.0:0.476	rs35421732	628;649	E7ERX1;Q86VD1	.;MORC1_HUMAN	I	649;628	ENSP00000232603:M649I;ENSP00000417282:M628I	ENSP00000232603:M649I	M	-	3	0	MORC1	110206673	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-0.154000	0.10130	-0.447000	0.07138	0.557000	0.71058	ATG	C|0.965;T|0.035	0.035	strong		0.363	MORC1-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000353844.1		
KLHL6	89857	hgsc.bcm.edu	37	3	183273248	183273248	+	Missense_Mutation	SNP	A	A	G	rs148924291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183273248A>G	ENST00000341319.3	-	1	229	c.194T>C	c.(193-195)cTg>cCg	p.L65P		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	65					B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)			p.L65P(1)		breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			TTCCATTCGCAGGGTTTCCAG	0.498													A|||	2	0.000399361	0.0008	0.0014	5008	,	,		16106	0.0		0.0	False		,,,				2504	0.0				p.L65P		Atlas-SNP	.											KLHL6,NS,lymphoid_neoplasm,-1,2	KLHL6	100	2	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.T194C						scavenged	.	A	PRO/LEU	0,4406		0,0,2203	140.0	139.0	139.0		194	5.6	0.9	3	dbSNP_134	139	1,8599	1.2+/-3.3	0,1,4299	no	missense	KLHL6	NM_130446.2	98	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	probably-damaging	65/622	183273248	1,13005	2203	4300	6503	SO:0001583	missense	89857	exon1			ATTCGCAGGGTTT	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.194T>C	3.37:g.183273248A>G	ENSP00000341342:p.Leu65Pro	190.0	2.0	0.0105263		228.0	96.0	0.421053	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	A	17.61	3.433538	0.62955	0.0	1.16E-4	ENSG00000172578	ENST00000341319	T	0.75154	-0.91	5.56	5.56	0.83823	BTB/POZ (1);BTB/POZ fold (2);	0.066358	0.64402	D	0.000007	D	0.90487	0.7020	H	0.96142	3.775	0.80722	D	1	D	0.71674	0.998	D	0.75484	0.986	D	0.93464	0.6813	10	0.87932	D	0	.	15.7124	0.77641	1.0:0.0:0.0:0.0	.	65	Q8WZ60	KLHL6_HUMAN	P	65	ENSP00000341342:L65P	ENSP00000341342:L65P	L	-	2	0	KLHL6	184755942	1.000000	0.71417	0.941000	0.38009	0.438000	0.31896	7.483000	0.81158	2.108000	0.64289	0.533000	0.62120	CTG	A|1.000;G|0.000	0.000	weak		0.498	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
CSPG4	1464	hgsc.bcm.edu	37	15	75981765	75981765	+	Missense_Mutation	SNP	G	G	T	rs149356457	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:75981765G>T	ENST00000308508.5	-	3	1733	c.1641C>A	c.(1639-1641)aaC>aaA	p.N547K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	547	Globular or compact configuration stabilized by disulfide bonds.|Neurite growth inhibition. {ECO:0000250}.				activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|carbohydrate metabolic process (GO:0005975)|cell proliferation (GO:0008283)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|intracellular signal transduction (GO:0035556)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|small molecule metabolic process (GO:0044281)|tissue remodeling (GO:0048771)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell projection (GO:0042995)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)	protein kinase binding (GO:0019901)|signal transducer activity (GO:0004871)			breast(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(3)|liver(2)|lung(18)|ovary(2)|pancreas(2)|prostate(4)|skin(4)	48						CATTGACAGGGTTGACCTGGA	0.622													G|||	5	0.000998403	0.0	0.0	5008	,	,		20725	0.0		0.001	False		,,,				2504	0.0041				p.N547K		Atlas-SNP	.											.	CSPG4	175	.	0			c.C1641A						PASS	.	G	LYS/ASN	1,4393		0,1,2196	35.0	31.0	32.0		1641	3.2	0.1	15	dbSNP_134	32	13,8563		0,13,4275	no	missense	CSPG4	NM_001897.4	94	0,14,6471	TT,TG,GG		0.1516,0.0228,0.1079	benign	547/2323	75981765	14,12956	2197	4288	6485	SO:0001583	missense	1464	exon3			GACAGGGTTGACC	X96753, AY359468	CCDS10284.1	15q24.2	2010-04-19	2007-02-16		ENSG00000173546	ENSG00000173546		"""Proteoglycans / Cell surface : Other"""	2466	protein-coding gene	gene with protein product	"""melanoma-associated chondroitin sulfate proteoglycan"""	601172	"""chondroitin sulfate proteoglycan 4 (melanoma-associated)"""			8790396, 16407841	Standard	NM_001897		Approved	MCSPG, MEL-CSPG, MSK16, NG2, MCSP, HMW-MAA	uc002baw.3	Q6UVK1	OTTHUMG00000142836	ENST00000308508.5:c.1641C>A	15.37:g.75981765G>T	ENSP00000312506:p.Asn547Lys	69.0	0.0	0		100.0	41.0	0.41	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	2.454	-0.325794	0.05350	2.28E-4	0.001516	ENSG00000173546	ENST00000308508	T	0.45668	0.89	5.21	3.23	0.37069	.	0.608532	0.16274	N	0.221645	T	0.29288	0.0729	L	0.60455	1.87	0.41510	D	0.988332	B	0.32302	0.363	B	0.26969	0.075	T	0.08785	-1.0705	10	0.06236	T	0.91	.	5.9733	0.19365	0.1589:0.0:0.6881:0.153	.	547	Q6UVK1	CSPG4_HUMAN	K	547	ENSP00000312506:N547K	ENSP00000312506:N547K	N	-	3	2	CSPG4	73768820	0.381000	0.25140	0.100000	0.21137	0.055000	0.15305	0.522000	0.22909	0.507000	0.28148	0.555000	0.69702	AAC	G|0.998;T|0.002	0.002	strong		0.622	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
CTSH	1512	hgsc.bcm.edu	37	15	79224732	79224732	+	Silent	SNP	G	G	A	rs149231812	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:79224732G>A	ENST00000220166.5	-	6	583	c.474C>T	c.(472-474)acC>acT	p.T158T	CTSH_ENST00000534533.1_5'UTR	NM_004390.3	NP_004381.2	P09668	CATH_HUMAN	cathepsin H	158					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|adaptive immune response (GO:0002250)|antigen processing and presentation (GO:0019882)|bradykinin catabolic process (GO:0010815)|cellular response to thyroid hormone stimulus (GO:0097067)|dichotomous subdivision of terminal units involved in lung branching (GO:0060448)|ERK1 and ERK2 cascade (GO:0070371)|immune response-regulating signaling pathway (GO:0002764)|membrane protein proteolysis (GO:0033619)|metanephros development (GO:0001656)|negative regulation of apoptotic process (GO:0043066)|neuropeptide catabolic process (GO:0010813)|positive regulation of angiogenesis (GO:0045766)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidase activity (GO:0010952)|protein destabilization (GO:0031648)|proteolysis (GO:0006508)|response to retinoic acid (GO:0032526)|spermatogenesis (GO:0007283)|surfactant homeostasis (GO:0043129)|T cell mediated cytotoxicity (GO:0001913)|zymogen activation (GO:0031638)	acrosomal vesicle (GO:0001669)|alveolar lamellar body (GO:0097208)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|outer dense fiber (GO:0001520)	aminopeptidase activity (GO:0004177)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|endopeptidase activity (GO:0004175)|HLA-A specific activating MHC class I receptor activity (GO:0030108)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)|thyroid hormone binding (GO:0070324)			central_nervous_system(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(1)	10						GCATCTTTCCGGTTGCGATGG	0.622																																					p.T158T		Atlas-SNP	.											.	CTSH	23	.	0			c.C474T						PASS	.	G		0,4392		0,0,2196	73.0	72.0	73.0		474	-9.4	0.0	15	dbSNP_134	73	7,8579	5.0+/-18.6	0,7,4286	no	coding-synonymous	CTSH	NM_004390.3		0,7,6482	AA,AG,GG		0.0815,0.0,0.0539		158/336	79224732	7,12971	2196	4293	6489	SO:0001819	synonymous_variant	1512	exon6			CTTTCCGGTTGCG	X07549	CCDS10308.1	15q25.1	2014-01-28			ENSG00000103811	ENSG00000103811	3.4.22.16	"""Cathepsins"""	2535	protein-coding gene	gene with protein product		116820		CPSB		2849458	Standard	NM_004390		Approved	ACC-4, ACC-5	uc021srk.1	P09668	OTTHUMG00000144171	ENST00000220166.5:c.474C>T	15.37:g.79224732G>A		54.0	0.0	0		75.0	42.0	0.56	NM_004390	B2RBK0|Q96NY6|Q9BUM7	Silent	SNP	ENST00000220166.5	37	CCDS10308.1																																																																																			G|0.999;A|0.001	0.001	strong		0.622	CTSH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291370.1	NM_004390	
MORC3	23515	hgsc.bcm.edu	37	21	37710067	37710067	+	Missense_Mutation	SNP	G	G	A	rs370616843		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:37710067G>A	ENST00000400485.1	+	4	359	c.283G>A	c.(283-285)Gtc>Atc	p.V95I	MORC3_ENST00000487909.1_3'UTR	NM_015358.2	NP_056173.1	Q14149	MORC3_HUMAN	MORC family CW-type zinc finger 3	95					cell aging (GO:0007569)|maintenance of protein location in nucleus (GO:0051457)|negative regulation of fibroblast proliferation (GO:0048147)|peptidyl-serine phosphorylation (GO:0018105)|post-embryonic development (GO:0009791)|protein phosphorylation (GO:0006468)|protein stabilization (GO:0050821)	PML body (GO:0016605)	zinc ion binding (GO:0008270)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(9)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	35						GAATGGTCATGTCCCAGTTGG	0.348																																					p.V95I		Atlas-SNP	.											.	MORC3	78	.	0			c.G283A						PASS	.	G	ILE/VAL	0,3660		0,0,1830	90.0	79.0	82.0		283	4.3	1.0	21		82	1,8161		0,1,4080	no	missense	MORC3	NM_015358.2	29	0,1,5910	AA,AG,GG		0.0123,0.0,0.0085	possibly-damaging	95/940	37710067	1,11821	1830	4081	5911	SO:0001583	missense	23515	exon4			GGTCATGTCCCAG	AK025327	CCDS42924.1	21q22.13	2005-06-15	2005-06-15	2005-06-15	ENSG00000159256	ENSG00000159256			23572	protein-coding gene	gene with protein product		610078	"""zinc finger, CW-type with coiled-coil domain 3"", ""zinc finger, CW type with coiled-coil domain 3"""	ZCWCC3		14607086	Standard	NM_015358		Approved	ZCW5, NXP2, KIAA0136	uc002yvi.3	Q14149	OTTHUMG00000086620	ENST00000400485.1:c.283G>A	21.37:g.37710067G>A	ENSP00000383333:p.Val95Ile	108.0	0.0	0		86.0	38.0	0.44186	NM_015358	A8KA92|Q9UEZ2	Missense_Mutation	SNP	ENST00000400485.1	37	CCDS42924.1	.	.	.	.	.	.	.	.	.	.	G	19.88	3.908699	0.72868	0.0	1.23E-4	ENSG00000159256	ENST00000400485	D	0.94862	-3.54	5.21	4.33	0.51752	ATPase-like, ATP-binding domain (2);	0.187242	0.45361	D	0.000366	D	0.91533	0.7326	L	0.31664	0.95	0.47698	D	0.999497	B	0.34241	0.444	B	0.42062	0.374	D	0.88791	0.3278	10	0.24483	T	0.36	-11.2373	14.267	0.66126	0.0727:0.0:0.9273:0.0	.	95	Q14149	MORC3_HUMAN	I	95	ENSP00000383333:V95I	ENSP00000383333:V95I	V	+	1	0	MORC3	36631937	1.000000	0.71417	0.998000	0.56505	0.863000	0.49368	6.480000	0.73604	1.323000	0.45263	0.591000	0.81541	GTC	.	.	weak		0.348	MORC3-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000194640.1	NM_015358	
GCAT	23464	hgsc.bcm.edu	37	22	38211287	38211287	+	Splice_Site	SNP	G	G	A	rs200392738	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:38211287G>A	ENST00000248924.6	+	5	787	c.731G>A	c.(730-732)cGg>cAg	p.R244Q	GCAT_ENST00000323205.6_Splice_Site_p.R270Q	NM_014291.3	NP_055106.1	O75600	KBL_HUMAN	glycine C-acetyltransferase	244					biosynthetic process (GO:0009058)|cellular amino acid metabolic process (GO:0006520)|L-threonine catabolic process to glycine (GO:0019518)	mitochondrion (GO:0005739)|nucleus (GO:0005634)	glycine C-acetyltransferase activity (GO:0008890)|pyridoxal phosphate binding (GO:0030170)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(8)|skin(1)	12	Melanoma(58;0.045)				Glycine(DB00145)	CCCACAGGACGGTGGGACCAT	0.622													G|||	2	0.000399361	0.0	0.0	5008	,	,		18933	0.002		0.0	False		,,,				2504	0.0				p.R270Q		Atlas-SNP	.											.	GCAT	27	.	0			c.G809A						PASS	.	G	GLN/ARG,GLN/ARG	0,4404		0,0,2202	30.0	27.0	28.0		809,731	2.5	1.0	22		28	1,8599	1.2+/-3.3	0,1,4299	yes	missense-near-splice,missense-near-splice	GCAT	NM_001171690.1,NM_014291.3	43,43	0,1,6501	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	270/446,244/420	38211287	1,13003	2202	4300	6502	SO:0001630	splice_region_variant	23464	exon5			CAGGACGGTGGGA	AF077740	CCDS13957.1, CCDS54527.1	22q13.1	2010-01-19	2010-01-19		ENSG00000100116	ENSG00000100116	2.3.1.29		4188	protein-coding gene	gene with protein product	"""2-amino-3-ketobutyrate coenzyme A ligase"""	607422	"""glycine C-acetyltransferase (2-amino-3-ketobutyrate coenzyme A ligase)"""				Standard	NM_014291		Approved	KBL	uc003aua.2	O75600	OTTHUMG00000150664	ENST00000248924.6:c.731+1G>A	22.37:g.38211287G>A		94.0	0.0	0		91.0	62.0	0.681319	NM_001171690	E2QC23|Q6ZWF1|Q96CA9	Missense_Mutation	SNP	ENST00000248924.6	37	CCDS13957.1	.	.	.	.	.	.	.	.	.	.	G	23.5	4.426184	0.83667	0.0	1.16E-4	ENSG00000100116	ENST00000323205;ENST00000248924	D;D	0.90504	-2.68;-2.68	4.68	2.53	0.30540	Aminotransferase, class I/classII (1);Pyridoxal phosphate-dependent transferase, major region, subdomain 1 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.109395	0.64402	D	0.000014	D	0.95831	0.8643	M	0.91038	3.17	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.75020	0.985;0.922	D	0.96264	0.9193	10	0.87932	D	0	-6.0188	14.7411	0.69455	0.0:0.2752:0.7248:0.0	.	270;244	E2QC23;O75600	.;KBL_HUMAN	Q	270;244	ENSP00000371110:R270Q;ENSP00000248924:R244Q	ENSP00000248924:R244Q	R	+	2	0	GCAT	36541233	1.000000	0.71417	1.000000	0.80357	0.902000	0.53008	6.642000	0.74329	0.563000	0.29222	-0.305000	0.09177	CGG	.	.	weak		0.622	GCAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319506.1	NM_014291.2	Missense_Mutation
MST1L	11223	hgsc.bcm.edu	37	1	17084581	17084581	+	RNA	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:17084581T>C	ENST00000455405.2	-	0	308							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)										GAGAGGCATATGGCTGGGAGA	0.562																																					p.H506R		Atlas-SNP	.											.	.	.	.	0			c.A1517G						PASS	.																																					11223	exon12			GGCATATGGCTGG	U28055, AF083416		1p36.33	2013-03-27	2012-11-09	2012-11-09	ENSG00000186715	ENSG00000186715			7390	other	unknown			"""macrophage stimulating, pseudogene 7"", ""macrophage stimulating, pseudogene 9"", ""macrophage stimulating 1 (hepatocyte growth factor-like) pseudogene 9"""	MSTP7, MSTP9, MST1P9		10728827	Standard	NM_001271733		Approved	D1F15S1A, MSPL7, MSPL-7	uc010ock.3	Q2TV78	OTTHUMG00000002578		1.37:g.17084581T>C		270.0	0.0	0		317.0	42.0	0.132492	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	2.857	-0.237075	0.05944	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	0.000000	0.41396	D	0.000892	T	0.26629	0.0651	.	.	.	.	.	.	B;B	0.15141	0.012;0.001	B;B	0.13407	0.009;0.002	T	0.10660	-1.0620	6	0.24483	T	0.36	.	4.4758	0.11739	0.0:8.0E-4:0.0:0.9992	.	506;532	Q2TV78-2;Q2TV78	.;MSTP9_HUMAN	R	501;506;532	.	ENSP00000439273:H506R	H	-	2	0	MST1P9	16957168	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	4.034000	0.57289	0.000000	0.14550	0.000000	0.15137	CAT	.	.	none		0.562	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
ASXL2	55252	hgsc.bcm.edu	37	2	25991713	25991713	+	Missense_Mutation	SNP	T	T	G	rs190136878	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:25991713T>G	ENST00000435504.4	-	7	822	c.529A>C	c.(529-531)Aag>Cag	p.K177Q	ASXL2_ENST00000336112.4_Missense_Mutation_p.K149Q|ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000497092.1_5'UTR|ASXL2_ENST00000404843.1_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	177	Ser-rich.				adult heart development (GO:0007512)|embryonic skeletal system morphogenesis (GO:0048704)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of histone H3-K27 trimethylation (GO:1902466)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of peroxisome proliferator activated receptor signaling pathway (GO:0035360)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	nuclear chromatin (GO:0000790)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|peroxisome proliferator activated receptor binding (GO:0042975)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|lung(7)|pancreas(1)|prostate(4)|skin(3)|urinary_tract(3)	33	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					tgctgctgcttcttctgctgt	0.393													T|||	4	0.000798722	0.0008	0.0029	5008	,	,		14558	0.0		0.0	False		,,,				2504	0.001				p.K177Q		Atlas-SNP	.											.	ASXL2	217	.	0			c.A529C						PASS	.	T	GLN/LYS	2,4014		0,2,2006	141.0	143.0	142.0		529	6.0	1.0	2		142	11,8399		0,11,4194	yes	missense	ASXL2	NM_018263.4	53	0,13,6200	GG,GT,TT		0.1308,0.0498,0.1046	probably-damaging	177/1436	25991713	13,12413	2008	4205	6213	SO:0001583	missense	55252	exon6			GCTGCTTCTTCTG			2p24.1	2014-06-17	2014-06-17		ENSG00000143970	ENSG00000143970			23805	protein-coding gene	gene with protein product		612991	"""additional sex combs like 2 (Drosophila)"""			12888926	Standard	NM_018263		Approved	ASXH2, FLJ10898, KIAA1685	uc002rgs.2	Q76L83	OTTHUMG00000152176	ENST00000435504.4:c.529A>C	2.37:g.25991713T>G	ENSP00000391447:p.Lys177Gln	120.0	0.0	0		111.0	54.0	0.486486	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	T	18.47	3.630847	0.67015	4.98E-4	0.001308	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.19669	2.13;2.13	6.03	6.03	0.97812	.	0.168425	0.53938	D	0.000053	T	0.19604	0.0471	N	0.02011	-0.69	0.35856	D	0.827145	D	0.89917	1.0	D	0.63488	0.915	T	0.50947	-0.8767	10	0.87932	D	0	-15.1812	12.95	0.58394	0.0:0.0:0.0:1.0	.	177	Q76L83	ASXL2_HUMAN	Q	177;149	ENSP00000391447:K177Q;ENSP00000337250:K149Q	ENSP00000337250:K149Q	K	-	1	0	ASXL2	25845217	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.963000	0.49184	2.308000	0.77769	0.533000	0.62120	AAG	T|0.999;G|0.001	0.001	strong		0.393	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
CNNM1	26507	hgsc.bcm.edu	37	10	101090246	101090246	+	Missense_Mutation	SNP	G	G	A	rs144944413	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:101090246G>A	ENST00000356713.4	+	1	1391	c.1102G>A	c.(1102-1104)Gcc>Acc	p.A368T	CNNM1_ENST00000370534.4_Missense_Mutation_p.A3T|CNNM1_ENST00000446890.1_Missense_Mutation_p.A297T|CNNM1_ENST00000370528.3_Missense_Mutation_p.A297T	NM_020348.2	NP_065081.2	Q9NRU3	CNNM1_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 1	368	DUF21.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)			NS(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(5)|ovary(1)|prostate(1)|skin(1)	25		Colorectal(252;0.234)		Epithelial(162;6.82e-10)|all cancers(201;5.62e-08)		TCTGATGGCAGCCGCCTTCCC	0.657													G|||	6	0.00119808	0.0	0.0058	5008	,	,		15163	0.0		0.002	False		,,,				2504	0.0				p.A368T		Atlas-SNP	.											.	CNNM1	101	.	0			c.G1102A						PASS	.	G	THR/ALA	2,4362		0,2,2180	8.0	9.0	8.0		1102	4.7	1.0	10	dbSNP_134	8	7,8501		0,7,4247	yes	missense	CNNM1	NM_020348.2	58	0,9,6427	AA,AG,GG		0.0823,0.0458,0.0699	benign	368/952	101090246	9,12863	2182	4254	6436	SO:0001583	missense	26507	exon1			ATGGCAGCCGCCT	AF169226	CCDS7478.2	10q24.2	2014-08-08	2014-08-07		ENSG00000119946	ENSG00000119946			102	protein-coding gene	gene with protein product		607802	"""cyclin M1"""	ACDP1		21393841	Standard	NM_020348		Approved		uc001kpp.4	Q9NRU3	OTTHUMG00000018881	ENST00000356713.4:c.1102G>A	10.37:g.101090246G>A	ENSP00000349147:p.Ala368Thr	45.0	0.0	0		55.0	36.0	0.654545	NM_020348	Q4QQG7|Q4QQH8|Q4QQP9|Q9NT45	Missense_Mutation	SNP	ENST00000356713.4	37	CCDS7478.2	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	G	14.74	2.624272	0.46840	4.58E-4	8.23E-4	ENSG00000119946	ENST00000356713;ENST00000446890;ENST00000370528;ENST00000370534	D;D;D;T	0.88431	-2.38;-2.38;-2.38;-0.66	4.67	4.67	0.58626	Domain of unknown function DUF21 (1);	0.155169	0.45361	D	0.000368	T	0.78033	0.4220	N	0.19112	0.55	0.36254	D	0.854107	P;B;B;B	0.35033	0.481;0.209;0.133;0.268	B;B;B;B	0.34536	0.164;0.185;0.045;0.143	D	0.85941	0.1458	10	0.72032	D	0.01	-5.7061	17.3611	0.87350	0.0:0.0:1.0:0.0	.	3;368;3;368	F5H5J0;Q9NRU3-2;B7Z5S3;Q9NRU3	.;.;.;CNNM1_HUMAN	T	368;297;297;3	ENSP00000349147:A368T;ENSP00000406492:A297T;ENSP00000359559:A297T;ENSP00000359565:A3T	ENSP00000349147:A368T	A	+	1	0	CNNM1	101080236	0.002000	0.14202	1.000000	0.80357	0.908000	0.53690	0.819000	0.27308	2.425000	0.82216	0.462000	0.41574	GCC	G|0.999;A|0.001	0.001	strong		0.657	CNNM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049792.2	NM_020348	
TMEM63B	55362	hgsc.bcm.edu	37	6	44117619	44117619	+	Silent	SNP	C	C	T	rs75310630		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:44117619C>T	ENST00000259746.9	+	16	1620	c.1437C>T	c.(1435-1437)ttC>ttT	p.F479F	TMEM63B_ENST00000323267.6_Silent_p.F479F			Q5T3F8	CSCL2_HUMAN	transmembrane protein 63B	479					ion transport (GO:0006811)	integral component of membrane (GO:0016021)	nucleotide binding (GO:0000166)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(8)|ovary(1)|pancreas(2)|prostate(2)|stomach(4)	35	all_cancers(18;1.66e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00309)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0215)			CCCAGTTCTTCCCCACCCTGC	0.622													C|||	1	0.000199681	0.0	0.0	5008	,	,		19084	0.0		0.001	False		,,,				2504	0.0				p.F479F		Atlas-SNP	.											.	TMEM63B	77	.	0			c.C1437T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	206.0	141.0	163.0		1437	4.5	1.0	6	dbSNP_133	163	14,8586	9.1+/-34.3	0,14,4286	no	coding-synonymous	TMEM63B	NM_018426.1		0,15,6488	TT,TC,CC		0.1628,0.0227,0.1153		479/833	44117619	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	55362	exon16			GTTCTTCCCCACC	BC022095	CCDS34461.1	6p21.1	2008-02-05	2005-07-25	2005-07-25	ENSG00000137216	ENSG00000137216			17735	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 110"""	C6orf110			Standard	XM_005249211		Approved	DKFZp434P0531, dJ421H19.2	uc003owr.3	Q5T3F8	OTTHUMG00000014757	ENST00000259746.9:c.1437C>T	6.37:g.44117619C>T		126.0	0.0	0		107.0	42.0	0.392523	NM_018426	B9EGU3|Q5T3F9|Q6AHX4|Q6P5A0|Q8N219|Q8NDE1|Q9NSG5	Silent	SNP	ENST00000259746.9	37	CCDS34461.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	10.77	1.443996	0.25987	2.27E-4	0.001628	ENSG00000137216	ENST00000371893	.	.	.	4.49	4.49	0.54785	.	.	.	.	.	T	0.54062	0.1835	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53099	-0.8486	4	.	.	.	.	12.2754	0.54733	0.0:0.9139:0.0:0.0861	.	.	.	.	F	408	.	.	S	+	2	0	TMEM63B	44225597	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.121000	0.50438	2.488000	0.83962	0.549000	0.68633	TCC	C|0.999;T|0.001	0.001	strong		0.622	TMEM63B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040712.2	XM_166410	
BRF1	2972	hgsc.bcm.edu	37	14	105707747	105707747	+	Silent	SNP	C	C	T	rs144658695	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105707747C>T	ENST00000546474.1	-	6	15508	c.549G>A	c.(547-549)ccG>ccA	p.P183P	BRF1_ENST00000440513.3_Silent_p.P68P|BRF1_ENST00000446501.2_Intron|BRF1_ENST00000379937.2_Silent_p.P156P|BRF1_ENST00000392557.4_De_novo_Start_OutOfFrame|BRF1_ENST00000327359.3_Silent_p.P68P|BRF1_ENST00000551787.1_De_novo_Start_OutOfFrame|BRF1_ENST00000379932.4_De_novo_Start_OutOfFrame	NM_001242787.1|NM_001519.3	NP_001229716.1|NP_001510.2	Q92994	TF3B_HUMAN	BRF1, RNA polymerase III transcription initiation factor 90 kDa subunit	183					gene expression (GO:0010467)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|rRNA transcription (GO:0009303)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)|tRNA transcription (GO:0009304)	nucleoplasm (GO:0005654)|transcription factor TFIIIB complex (GO:0000126)	zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(1)|endometrium(5)|large_intestine(4)|lung(5)|ovary(3)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0231)|all_epithelial(191;0.0694)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00753)|all cancers(16;0.00925)|Epithelial(46;0.0221)	Epithelial(152;0.14)		TATACAGGCACGGGTCTGCGG	0.627													C|||	13	0.00259585	0.0015	0.0	5008	,	,		18733	0.0		0.006	False		,,,				2504	0.0051				p.P183P		Atlas-SNP	.											.	BRF1	102	.	0			c.G549A						PASS	.	C	,,,,,	2,4396	6.2+/-15.9	0,2,2197	82.0	67.0	72.0		204,204,468,,549,	-9.0	0.8	14	dbSNP_134	72	41,8559	27.9+/-77.7	0,41,4259	no	coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,utr-5	BRF1	NM_001242786.1,NM_001242787.1,NM_001242788.1,NM_001242789.1,NM_001519.3,NM_145685.2	,,,,,	0,43,6456	TT,TC,CC		0.4767,0.0455,0.3308	,,,,,	68/585,68/563,156/651,,183/678,	105707747	43,12955	2199	4300	6499	SO:0001819	synonymous_variant	2972	exon6			CAGGCACGGGTCT	U28838	CCDS10001.1, CCDS42001.1, CCDS55949.1, CCDS55950.1, CCDS55951.1, CCDS55952.1, CCDS55953.1	14q32.33	2014-04-02	2013-05-29	2001-12-07	ENSG00000185024	ENSG00000185024		"""General transcription factors"""	11551	protein-coding gene	gene with protein product		604902	"""TATA box binding protein (TBP)-associated factor, RNA polymerase III, GTF3B subunit 2"", ""BRF1 homolog, subunit of RNA polymerase III transcription initiation factor IIIB (S. cerevisiae)"""	TAF3B2, TAF3C, GTF3B		7624363, 8943358	Standard	NM_145685		Approved	TFIIIB90, BRF, hBRF	uc001yqp.2	Q92994	OTTHUMG00000029884	ENST00000546474.1:c.549G>A	14.37:g.105707747C>T		50.0	0.0	0		22.0	10.0	0.454545	NM_001519	B3KU36|B4DIG5|B7Z2N3|F5H5Z7|F8WA46|Q13223|Q3SYD9|Q5PR24|Q6IQ02|Q96KX3|Q9HCW6|Q9HCW7|Q9HCW8	Silent	SNP	ENST00000546474.1	37	CCDS10001.1	5	0.0022893772893772895	1	0.0020325203252032522	0	0.0	0	0.0	4	0.005277044854881266	C	3.854	-0.031251	0.07543	4.55E-4	0.004767	ENSG00000185024	ENST00000546417	.	.	.	4.51	-9.01	0.00744	.	.	.	.	.	T	0.27967	0.0689	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41324	-0.9515	4	.	.	.	.	3.9767	0.09478	0.0832:0.3485:0.3231:0.2452	.	.	.	.	M	37	.	.	V	-	1	0	BRF1	104778792	0.000000	0.05858	0.826000	0.32828	0.338000	0.28826	-4.034000	0.00309	-1.654000	0.01499	-0.191000	0.12829	GTG	C|0.997;T|0.003	0.003	strong		0.627	BRF1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000074548.4	NM_001519	
STK36	27148	hgsc.bcm.edu	37	2	219553423	219553423	+	Missense_Mutation	SNP	C	C	G	rs45586733	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:219553423C>G	ENST00000295709.3	+	12	1663	c.1384C>G	c.(1384-1386)Ctg>Gtg	p.L462V	STK36_ENST00000440309.1_Missense_Mutation_p.L462V|STK36_ENST00000392105.3_Missense_Mutation_p.L462V|STK36_ENST00000392106.2_Missense_Mutation_p.L462V	NM_015690.4	NP_056505.2			serine/threonine kinase 36											biliary_tract(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(6)|lung(20)|ovary(4)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	52		Renal(207;0.0915)		Epithelial(149;9.65e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.00813)|Lung(261;0.00984)		CACCCAGATCCTGAAAGGCAT	0.498													C|||	22	0.00439297	0.0	0.0101	5008	,	,		22309	0.0		0.0149	False		,,,				2504	0.0				p.L462V		Atlas-SNP	.											.	STK36	111	.	0			c.C1384G						PASS	.	C	VAL/LEU	17,4389	25.3+/-52.1	0,17,2186	223.0	210.0	215.0		1384	4.5	1.0	2	dbSNP_127	215	124,8476	66.0+/-128.3	0,124,4176	yes	missense	STK36	NM_015690.4	32	0,141,6362	GG,GC,CC		1.4419,0.3858,1.0841	probably-damaging	462/1316	219553423	141,12865	2203	4300	6503	SO:0001583	missense	27148	exon12			CAGATCCTGAAAG	AB033104	CCDS2421.1, CCDS58750.1	2q35	2010-06-25	2010-06-25		ENSG00000163482	ENSG00000163482			17209	protein-coding gene	gene with protein product	"""fused homolog (Drosophila)"""	607652	"""serine/threonine kinase 36 (fused homolog, Drosophila)"""			10806483	Standard	NM_001243313		Approved	KIAA1278, FU	uc002viu.3	Q9NRP7	OTTHUMG00000133079	ENST00000295709.3:c.1384C>G	2.37:g.219553423C>G	ENSP00000295709:p.Leu462Val	148.0	0.0	0		171.0	86.0	0.502924	NM_015690		Missense_Mutation	SNP	ENST00000295709.3	37	CCDS2421.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	C	17.41	3.382206	0.61845	0.003858	0.014419	ENSG00000163482	ENST00000295709;ENST00000392106;ENST00000392105;ENST00000440309	T;T;T;T	0.78126	-1.15;-1.15;-1.11;-1.15	5.38	4.51	0.55191	.	0.000000	0.34110	N	0.004245	T	0.73976	0.3656	L	0.27053	0.805	0.42723	D	0.993681	D;D	0.71674	0.998;0.997	D;D	0.68765	0.96;0.913	T	0.80125	-0.1513	10	0.72032	D	0.01	-8.883	12.2295	0.54480	0.0:0.9212:0.0:0.0788	rs45586733	462;462	Q9NRP7-2;Q9NRP7	.;STK36_HUMAN	V	462	ENSP00000295709:L462V;ENSP00000375955:L462V;ENSP00000375954:L462V;ENSP00000394095:L462V	ENSP00000295709:L462V	L	+	1	2	STK36	219261667	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	1.753000	0.38359	1.505000	0.48720	-0.140000	0.14226	CTG	C|0.990;G|0.010	0.010	strong		0.498	STK36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256723.2		
SZT2	23334	hgsc.bcm.edu	37	1	43909129	43909129	+	Missense_Mutation	SNP	C	C	T	rs372395617		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:43909129C>T	ENST00000562955.1	+	60	8435	c.8435C>T	c.(8434-8436)tCt>tTt	p.S2812F	SZT2_ENST00000372442.1_Missense_Mutation_p.S1970F	NM_015284.3	NP_056099.3	Q5T011	SZT2_HUMAN	seizure threshold 2 homolog (mouse)	2869					central nervous system development (GO:0007417)|corpus callosum morphogenesis (GO:0021540)|embryo development (GO:0009790)|pigmentation (GO:0043473)|post-embryonic development (GO:0009791)|regulation of superoxide dismutase activity (GO:1901668)	extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)				NS(2)|breast(9)|central_nervous_system(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(19)|lung(39)|ovary(4)|pancreas(3)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	113						CCAGAGACCTCTGGACCCCCT	0.617																																					p.S2812F		Atlas-SNP	.											SZT2_ENST00000562955,NS,carcinoma,-1,3	SZT2	383	3	0			c.C8435T						PASS	.	C	PHE/SER	0,4406		0,0,2203	35.0	37.0	36.0		8435	2.3	0.8	1		36	1,8599	1.2+/-3.3	0,1,4299	no	missense	SZT2	NM_015284.3	155	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	2812/3376	43909129	1,13005	2203	4300	6503	SO:0001583	missense	23334	exon60			AGACCTCTGGACC	AB007936	CCDS30694.1, CCDS30694.2	1p34.2	2012-11-19	2011-06-10	2011-06-10	ENSG00000198198	ENSG00000198198			29040	protein-coding gene	gene with protein product	"""seizure threshold 2 homolog A (mouse)"", ""seizure threshold 2 homolog B (mouse)"""	615463	"""chromosome 1 open reading frame 84"", ""KIAA0467"""	C1orf84, KIAA0467		9455484	Standard	NM_015284		Approved	FLJ10387, SZT2B, RP11-506B15.1, FLJ34502, SZT2A	uc001cjk.3	Q5T011	OTTHUMG00000007423	ENST00000562955.1:c.8435C>T	1.37:g.43909129C>T	ENSP00000457168:p.Ser2812Phe	93.0	0.0	0		81.0	33.0	0.407407	NM_015284	A0PJK5|A7E2X4|O75055|Q5JUY7|Q5T012|Q5XKC7|Q6ZNI8|Q6ZT24|Q7Z636|Q8NAY9|Q9H5H7|Q9UFQ8	Missense_Mutation	SNP	ENST00000562955.1	37	CCDS30694.2	.	.	.	.	.	.	.	.	.	.	C	9.750	1.167172	0.21621	0.0	1.16E-4	ENSG00000198198	ENST00000372442	.	.	.	5.4	2.26	0.28386	.	0.695263	0.14386	N	0.322843	T	0.25269	0.0614	N	0.08118	0	0.09310	N	1	B	0.31351	0.32	B	0.38056	0.264	T	0.24154	-1.0168	9	0.11485	T	0.65	.	12.9384	0.58329	0.0:0.52:0.48:0.0	.	2812	Q5T011-5	.	F	1970	.	ENSP00000361519:S1970F	S	+	2	0	SZT2	43681716	0.011000	0.17503	0.770000	0.31555	0.933000	0.57130	0.549000	0.23329	0.604000	0.29930	0.655000	0.94253	TCT	.	.	none		0.617	SZT2-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019517.3	NM_015284	
ACACB	32	hgsc.bcm.edu	37	12	109665242	109665242	+	Missense_Mutation	SNP	G	G	A	rs60293430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	67.0	0.0	0		73.0	38.0	0.520548	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	
AASDHPPT	60496	hgsc.bcm.edu	37	11	105962172	105962172	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:105962172G>A	ENST00000278618.4	+	4	883	c.661G>A	c.(661-663)Gat>Aat	p.D221N	RP11-677I18.3_ENST00000532422.1_RNA	NM_015423.2	NP_056238.2	Q9NRN7	ADPPT_HUMAN	aminoadipate-semialdehyde dehydrogenase-phosphopantetheinyl transferase	221					macromolecule biosynthetic process (GO:0009059)|pantothenate metabolic process (GO:0015939)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	holo-[acyl-carrier-protein] synthase activity (GO:0008897)|magnesium ion binding (GO:0000287)			endometrium(3)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)	17		Melanoma(852;0.000878)|Acute lymphoblastic leukemia(157;0.000967)|all_hematologic(158;0.0017)|Breast(348;0.0321)		BRCA - Breast invasive adenocarcinoma(274;5.78e-05)|Epithelial(105;0.00622)|all cancers(92;0.041)		TTTATTCCTGGATGGAGAGGA	0.323																																					p.D221N		Atlas-SNP	.											.	AASDHPPT	40	.	0			c.G661A						PASS	.						72.0	79.0	77.0					11																	105962172		2200	4299	6499	SO:0001583	missense	60496	exon4			TTCCTGGATGGAG	AF302110	CCDS31664.1	11q22	2010-12-09			ENSG00000149313	ENSG00000149313	1.2.1.31		14235	protein-coding gene	gene with protein product		607756				12815048, 11286508	Standard	NM_015423		Approved	LYS5, CGI-80, AASD-PPT	uc001pjc.1	Q9NRN7	OTTHUMG00000166253	ENST00000278618.4:c.661G>A	11.37:g.105962172G>A	ENSP00000278618:p.Asp221Asn	101.0	0.0	0		91.0	29.0	0.318681	NM_015423	B2R6D1|B4DDW7|Q9C068|Q9P0Q3|Q9UG80|Q9Y389	Missense_Mutation	SNP	ENST00000278618.4	37	CCDS31664.1	.	.	.	.	.	.	.	.	.	.	G	23.7	4.447623	0.84101	.	.	ENSG00000149313	ENST00000533423;ENST00000524411;ENST00000278618	.	.	.	5.77	5.77	0.91146	4&apos (2);-phosphopantetheinyl transferase (2);	0.000000	0.85682	D	0.000000	T	0.53690	0.1812	L	0.33753	1.03	0.58432	D	0.999998	P	0.51057	0.941	P	0.44647	0.456	T	0.49969	-0.8882	9	0.33141	T	0.24	.	19.981	0.97324	0.0:0.0:1.0:0.0	.	221	Q9NRN7	ADPPT_HUMAN	N	156;156;221	.	ENSP00000278618:D221N	D	+	1	0	AASDHPPT	105467382	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	8.453000	0.90349	2.729000	0.93468	0.585000	0.79938	GAT	.	.	none		0.323	AASDHPPT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388734.1	NM_015423	
ABCC10	89845	hgsc.bcm.edu	37	6	43400050	43400050	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:43400050C>T	ENST00000372530.4	+	3	547	c.332C>T	c.(331-333)gCc>gTc	p.A111V	ABCC10_ENST00000244533.3_Missense_Mutation_p.A68V|ABCC10_ENST00000443426.2_Intron	NM_001198934.1	NP_001185863.1	Q5T3U5	MRP7_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 10	111					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(8)|lung(21)|ovary(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	56	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)		Cyclosporine(DB00091)|Cytarabine(DB00987)|Daunorubicin(DB00694)|Docetaxel(DB01248)|Doxorubicin(DB00997)|Estradiol(DB00783)|Etoposide(DB00773)|Gemcitabine(DB00441)|Methotrexate(DB00563)|Paclitaxel(DB01229)|Sildenafil(DB00203)|Tenofovir(DB00300)|Verapamil(DB00661)|Vincristine(DB00541)	GCAGCTGTGGCCTGGATCAGC	0.647																																					p.A111V		Atlas-SNP	.											.	ABCC10	118	.	0			c.C332T						PASS	.						61.0	61.0	61.0					6																	43400050		2203	4300	6503	SO:0001583	missense	89845	exon3			CTGTGGCCTGGAT	U66684	CCDS4896.1, CCDS56430.1	6p12.3	2012-03-14			ENSG00000124574	ENSG00000124574		"""ATP binding cassette transporters / subfamily C"""	52	protein-coding gene	gene with protein product		612509				8894702	Standard	NM_033450		Approved	EST182763, MRP7, SIMRP7	uc003ouy.1	Q5T3U5	OTTHUMG00000014733	ENST00000372530.4:c.332C>T	6.37:g.43400050C>T	ENSP00000361608:p.Ala111Val	63.0	0.0	0		54.0	24.0	0.444444	NM_001198934	Q8NHX7|Q9H7N2|Q9NXY3|Q9UF48	Missense_Mutation	SNP	ENST00000372530.4	37	CCDS56430.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.767863	0.69878	.	.	ENSG00000124574	ENST00000372530;ENST00000244533	T;T	0.41065	1.01;1.01	5.94	5.94	0.96194	.	0.106734	0.64402	D	0.000004	T	0.37758	0.1015	L	0.32530	0.975	0.52099	D	0.999942	D;P	0.55385	0.971;0.952	P;P	0.50825	0.651;0.449	T	0.13361	-1.0512	10	0.56958	D	0.05	-20.1624	20.3633	0.98874	0.0:1.0:0.0:0.0	.	68;111	Q5T3U5-2;Q5T3U5	.;MRP7_HUMAN	V	111;68	ENSP00000361608:A111V;ENSP00000244533:A68V	ENSP00000244533:A68V	A	+	2	0	ABCC10	43508028	1.000000	0.71417	1.000000	0.80357	0.054000	0.15201	7.418000	0.80167	2.826000	0.97356	0.561000	0.74099	GCC	.	.	none		0.647	ABCC10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040603.2	NM_033450	
CNOT6L	246175	hgsc.bcm.edu	37	4	78697538	78697538	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:78697538C>T	ENST00000504123.1	-	2	144	c.14G>A	c.(13-15)gGg>gAg	p.G5E	CNOT6L_ENST00000264903.4_Missense_Mutation_p.G5E|CNOT6L_ENST00000506166.1_5'UTR			Q96LI5	CNO6L_HUMAN	CCR4-NOT transcription complex, subunit 6-like	5	Required for interaction with CNOT1, CNOT3 and CNOT7.				gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA destabilization (GO:0061157)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|transcription, DNA-templated (GO:0006351)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A)-specific ribonuclease activity (GO:0004535)			kidney(1)|large_intestine(1)|lung(6)|urinary_tract(1)	9						CTTTGGCATCCCTATTAGTCT	0.358																																					p.G5E		Atlas-SNP	.											.	CNOT6L	57	.	0			c.G14A						PASS	.						60.0	53.0	55.0					4																	78697538		1804	4080	5884	SO:0001583	missense	246175	exon2			GGCATCCCTATTA	AL133112	CCDS68731.1	4q13.3	2014-06-17				ENSG00000138767			18042	protein-coding gene	gene with protein product							Standard	NM_144571		Approved	DKFZp434K098, Ccr4b	uc003hks.3	Q96LI5		ENST00000504123.1:c.14G>A	4.37:g.78697538C>T	ENSP00000424896:p.Gly5Glu	79.0	0.0	0		79.0	32.0	0.405063	NM_144571	Q9UF92	Missense_Mutation	SNP	ENST00000504123.1	37		.	.	.	.	.	.	.	.	.	.	C	19.78	3.890592	0.72524	.	.	ENSG00000138767	ENST00000504123;ENST00000264903;ENST00000512485;ENST00000515441	T;T;T;T	0.35605	1.3;1.3;1.67;1.98	5.72	5.72	0.89469	.	0.000000	0.44285	D	0.000480	T	0.39860	0.1094	L	0.29908	0.895	0.58432	D	0.999993	D;P	0.58268	0.982;0.866	P;P	0.51550	0.622;0.673	T	0.22347	-1.0219	10	0.72032	D	0.01	-2.6931	16.1856	0.81948	0.1336:0.8664:0.0:0.0	.	5;5	B4E2S0;Q96LI5	.;CNO6L_HUMAN	E	5;5;12;5	ENSP00000424896:G5E;ENSP00000264903:G5E;ENSP00000425571:G12E;ENSP00000426269:G5E	ENSP00000264903:G5E	G	-	2	0	CNOT6L	78916562	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.037000	0.70956	2.695000	0.91970	0.557000	0.71058	GGG	.	.	none		0.358	CNOT6L-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000362515.1		
SERPINI2	5276	hgsc.bcm.edu	37	3	167159968	167159968	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:167159968T>C	ENST00000476257.1	-	10	1445	c.1147A>G	c.(1147-1149)Att>Gtt	p.I383V	SERPINI2_ENST00000264677.4_Missense_Mutation_p.I383V|SERPINI2_ENST00000471111.1_Missense_Mutation_p.I383V|SERPINI2_ENST00000461846.1_Missense_Mutation_p.I383V			O75830	SPI2_HUMAN	serpin peptidase inhibitor, clade I (pancpin), member 2	383					cellular component movement (GO:0006928)|negative regulation of endopeptidase activity (GO:0010951)|regulation of cell adhesion (GO:0030155)|regulation of proteolysis (GO:0030162)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	serine-type endopeptidase inhibitor activity (GO:0004867)			NS(1)|breast(1)|endometrium(2)|kidney(4)|large_intestine(6)|lung(20)|prostate(1)|skin(5)|urinary_tract(1)	41						ATAAACAGAATTGATTCTAGG	0.308																																					p.I393V		Atlas-SNP	.											.	SERPINI2	85	.	0			c.A1177G						PASS	.						88.0	80.0	83.0					3																	167159968		2203	4299	6502	SO:0001583	missense	5276	exon10			ACAGAATTGATTC	AB006423	CCDS3200.1, CCDS75047.1	3q26.1	2014-02-18	2005-08-18		ENSG00000114204	ENSG00000114204		"""Serine (or cysteine) peptidase inhibitors"""	8945	protein-coding gene	gene with protein product		605587	"""serine (or cysteine) proteinase inhibitor, clade I (neuroserpin), member 2"", ""serine (or cysteine) proteinase inhibitor, clade I (pancpin), member 2"""	PI14		9624529, 24172014	Standard	NM_006217		Approved	PANCPIN, TSA2004, MEPI, pancpin	uc003fes.2	O75830	OTTHUMG00000158231	ENST00000476257.1:c.1147A>G	3.37:g.167159968T>C	ENSP00000420621:p.Ile383Val	46.0	0.0	0		79.0	36.0	0.455696	NM_001012303		Missense_Mutation	SNP	ENST00000476257.1	37	CCDS3200.1	.	.	.	.	.	.	.	.	.	.	T	13.14	2.149400	0.37923	.	.	ENSG00000114204	ENST00000476257;ENST00000461846;ENST00000264677;ENST00000471111	D;D;D;D	0.85411	-1.98;-1.98;-1.98;-1.98	6.17	5.0	0.66597	Serpin domain (3);	0.102768	0.64402	D	0.000004	D	0.83496	0.5267	L	0.60845	1.875	0.80722	D	1	P;P	0.45634	0.863;0.863	P;P	0.45538	0.484;0.484	T	0.81402	-0.0949	10	0.39692	T	0.17	.	9.7406	0.40416	0.1538:0.0:0.0:0.8462	.	383;383	B4DDY9;O75830	.;SPI2_HUMAN	V	383	ENSP00000420621:I383V;ENSP00000417692:I383V;ENSP00000264677:I383V;ENSP00000419407:I383V	ENSP00000264677:I383V	I	-	1	0	SERPINI2	168642662	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	1.916000	0.39986	1.120000	0.41904	0.533000	0.62120	ATT	.	.	none		0.308	SERPINI2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350450.1	NM_006217	
MYO5A	4644	hgsc.bcm.edu	37	15	52635394	52635394	+	Splice_Site	SNP	T	T	A	rs61731219	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:52635394T>A	ENST00000399231.3	-	31	4203	c.3960A>T	c.(3958-3960)agA>agT	p.R1320S	MYO5A_ENST00000356338.6_Intron|MYO5A_ENST00000553916.1_Intron|MYO5A_ENST00000358212.6_Splice_Site_p.R1320S|MYO5A_ENST00000399233.2_Splice_Site_p.R1317S	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	1320					actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GAGCAGATGATCTTCCATGCA	0.408													T|||	58	0.0115815	0.0023	0.0072	5008	,	,		19797	0.0		0.0437	False		,,,				2504	0.0061				p.R1320S		Atlas-SNP	.											.	MYO5A	145	.	0			c.A3960T						PASS	.	T	SER/ARG,	24,3884		0,24,1930	92.0	85.0	87.0		3960,	5.9	1.0	15	dbSNP_129	87	339,7997		6,327,3835	yes	missense-near-splice,intron	MYO5A	NM_000259.3,NM_001142495.1	110,	6,351,5765	AA,AT,TT		4.0667,0.6141,2.9647	benign,	1320/1856,	52635394	363,11881	1954	4168	6122	SO:0001630	splice_region_variant	4644	exon31			AGATGATCTTCCA		CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.3960-1A>T	15.37:g.52635394T>A		67.0	0.0	0		70.0	36.0	0.514286	NM_000259	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Missense_Mutation	SNP	ENST00000399231.3	37	CCDS42037.1	37	0.01694139194139194	0	0.0	4	0.011049723756906077	0	0.0	33	0.04353562005277045	T	15.01	2.706322	0.48412	0.006141	0.040667	ENSG00000197535	ENST00000399231;ENST00000399233;ENST00000358212;ENST00000399228	T;T;T;T	0.04454	3.62;3.62;3.62;3.62	5.87	5.87	0.94306	.	0.059846	0.64402	D	0.000003	T	0.02807	0.0084	L	0.43152	1.355	0.80722	D	1	D;D;P	0.61080	0.989;0.989;0.495	D;D;B	0.75020	0.985;0.985;0.034	T	0.05566	-1.0877	10	0.38643	T	0.18	.	10.8931	0.47006	0.0:0.0783:0.0:0.9217	rs61731219	110;113;1320	Q9UES5;O95317;Q9Y4I1	.;.;MYO5A_HUMAN	S	1320;1317;1320;110	ENSP00000382177:R1320S;ENSP00000382179:R1317S;ENSP00000350945:R1320S;ENSP00000382174:R110S	ENSP00000350945:R1320S	R	-	3	2	MYO5A	50422686	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.751000	0.55165	2.236000	0.73375	0.528000	0.53228	AGA	T|0.955;A|0.045	0.045	strong		0.408	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1	NM_000259	Missense_Mutation
IGDCC4	57722	hgsc.bcm.edu	37	15	65688088	65688088	+	Splice_Site	SNP	C	C	A	rs201037111		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:65688088C>A	ENST00000352385.2	-	7	1620	c.1411G>T	c.(1411-1413)Ggc>Tgc	p.G471C		NM_020962.1	NP_066013.1	Q8TDY8	IGDC4_HUMAN	immunoglobulin superfamily, DCC subclass, member 4	471	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)	44						GCCGACGTACCCCGTGCCTTC	0.662																																					p.G471C		Atlas-SNP	.											.	IGDCC4	95	.	0			c.G1411T						PASS	.	C	CYS/GLY	1,4241		0,1,2120	7.0	7.0	7.0		1411	4.4	1.0	15		7	2,8360		0,2,4179	yes	missense-near-splice	IGDCC4	NM_020962.1	159	0,3,6299	AA,AC,CC		0.0239,0.0236,0.0238	probably-damaging	471/1251	65688088	3,12601	2121	4181	6302	SO:0001630	splice_region_variant	57722	exon7			ACGTACCCCGTGC		CCDS10206.1	15q22.31	2013-02-11			ENSG00000103742	ENSG00000103742		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	13770	protein-coding gene	gene with protein product	"""likely ortholog of mouse neighbor of Punc E11"""						Standard	NM_020962		Approved	NOPE, LOC57722	uc002aou.1	Q8TDY8	OTTHUMG00000133136	ENST00000352385.2:c.1411+1G>T	15.37:g.65688088C>A		26.0	0.0	0		35.0	17.0	0.485714	NM_020962	Q9HCE4	Missense_Mutation	SNP	ENST00000352385.2	37	CCDS10206.1	.	.	.	.	.	.	.	.	.	.	C	17.16	3.319127	0.60524	2.36E-4	2.39E-4	ENSG00000103742	ENST00000352385;ENST00000356152	T	0.59638	0.25	4.45	4.45	0.53987	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.055509	0.64402	D	0.000001	T	0.62636	0.2444	M	0.73217	2.22	0.80722	D	1	P	0.48764	0.915	P	0.45343	0.477	T	0.67499	-0.5655	9	.	.	.	-21.5089	17.4669	0.87635	0.0:1.0:0.0:0.0	.	471	Q8TDY8	IGDC4_HUMAN	C	471;200	ENSP00000319623:G471C	.	G	-	1	0	IGDCC4	63475141	1.000000	0.71417	0.981000	0.43875	0.079000	0.17450	6.706000	0.74649	2.187000	0.69744	0.462000	0.41574	GGC	.	.	weak		0.662	IGDCC4-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000256825.2	NM_020962	Missense_Mutation
PBX4	80714	hgsc.bcm.edu	37	19	19680276	19680276	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:19680276G>A	ENST00000251203.9	-	5	1036	c.750C>T	c.(748-750)ggC>ggT	p.G250G		NM_025245.2	NP_079521.1	Q9BYU1	PBX4_HUMAN	pre-B-cell leukemia homeobox 4	250					positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)|XY body (GO:0001741)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			large_intestine(1)|lung(4)|ovary(1)|prostate(3)	9						TGGTGAGGCCGCCCTTCCTGG	0.567																																					p.G250G		Atlas-SNP	.											.	PBX4	34	.	0			c.C750T						PASS	.						187.0	159.0	168.0					19																	19680276		2203	4300	6503	SO:0001819	synonymous_variant	80714	exon5			GAGGCCGCCCTTC	AJ300182	CCDS12406.1	19p13.11	2014-09-11	2007-01-30		ENSG00000105717			"""Homeoboxes / TALE class"""	13403	protein-coding gene	gene with protein product		608127	"""pre-B-cell leukemia transcription factor 4"""				Standard	NM_025245		Approved		uc002nmy.3	Q9BYU1	OTTHUMG00000172310	ENST00000251203.9:c.750C>T	19.37:g.19680276G>A		104.0	0.0	0		115.0	49.0	0.426087	NM_025245	A5D8Y0|B3KUK9	Silent	SNP	ENST00000251203.9	37	CCDS12406.1																																																																																			.	.	none		0.567	PBX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417784.6		
ZGRF1	55345	hgsc.bcm.edu	37	4	113553098	113553098	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:113553098G>A	ENST00000505019.1	-	3	215	c.90C>T	c.(88-90)caC>caT	p.H30H	C4orf21_ENST00000445203.2_5'UTR|C4orf21_ENST00000309071.5_Silent_p.H30H	NM_018392.4	NP_060862.3	Q86YA3	ZGRF1_HUMAN		30						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(6)|lung(21)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	45		Ovarian(17;0.156)		OV - Ovarian serous cystadenocarcinoma(123;0.000676)		TGTTTCCTAAGTGAGTGATCT	0.323																																					p.H30H		Atlas-SNP	.											.	C4orf21	223	.	0			c.C90T						PASS	.						103.0	94.0	97.0					4																	113553098		2202	4298	6500	SO:0001819	synonymous_variant	55345	exon3			TCCTAAGTGAGTG																												ENST00000505019.1:c.90C>T	4.37:g.113553098G>A		77.0	0.0	0		88.0	4.0	0.0454545	NM_018392	B3KQX2|B4DSN6|B4DYU8|E9PDE1|G5EA02|Q6ZU11|Q9NSW3|Q9NUJ4	Silent	SNP	ENST00000505019.1	37																																																																																				.	.	none		0.323	C4orf21-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000256413.1		
POC5	134359	hgsc.bcm.edu	37	5	74998489	74998489	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:74998489A>G	ENST00000428202.2	-	5	643	c.454T>C	c.(454-456)Tct>Cct	p.S152P	POC5_ENST00000514838.2_Missense_Mutation_p.S124P|POC5_ENST00000510798.1_Missense_Mutation_p.S35P|POC5_ENST00000380475.2_Missense_Mutation_p.S35P|POC5_ENST00000504862.1_5'UTR|POC5_ENST00000446329.2_Missense_Mutation_p.S127P	NM_001099271.1	NP_001092741.1	Q8NA72	POC5_HUMAN	POC5 centriolar protein	152					cell cycle (GO:0007049)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(4)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	15						TTTTCATCAGAAACAAGAAAA	0.378																																					p.S152P		Atlas-SNP	.											.	POC5	82	.	0			c.T454C						PASS	.						89.0	84.0	86.0					5																	74998489		1888	4109	5997	SO:0001583	missense	134359	exon5			CATCAGAAACAAG	AK093098	CCDS47236.1, CCDS47237.1	5q13.3	2013-08-05	2013-08-05	2010-03-26	ENSG00000152359	ENSG00000152359			26658	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 37"", ""POC5 centriolar protein homolog (Chlamydomonas)"""	C5orf37		19349582	Standard	NM_152408		Approved	FLJ35779, MGC120442, MGC120443, MGC120444, hPOC5	uc003keh.4	Q8NA72	OTTHUMG00000162487	ENST00000428202.2:c.454T>C	5.37:g.74998489A>G	ENSP00000410216:p.Ser152Pro	120.0	0.0	0		99.0	4.0	0.040404	NM_001099271	B4DJG7|Q494X7|Q494X9|Q6P085	Missense_Mutation	SNP	ENST00000428202.2	37	CCDS47236.1	.	.	.	.	.	.	.	.	.	.	A	12.80	2.046958	0.36085	.	.	ENSG00000152359	ENST00000428202;ENST00000514838;ENST00000380475;ENST00000510798;ENST00000446329;ENST00000503835;ENST00000502826	T;T;T;T;T	0.48836	1.84;1.42;0.8;0.8;1.84	5.78	4.51	0.55191	.	0.325126	0.38492	N	0.001678	T	0.51907	0.1702	L	0.47716	1.5	0.32491	N	0.54012	D;B;B	0.76494	0.999;0.148;0.281	D;B;B	0.64776	0.929;0.07;0.122	T	0.58457	-0.7633	10	0.26408	T	0.33	-9.7843	5.43	0.16448	0.7038:0.0:0.144:0.1522	.	35;152;127	Q8NA72-2;Q8NA72;Q8NA72-3	.;POC5_HUMAN;.	P	152;124;35;35;127;35;35	ENSP00000410216:S152P;ENSP00000420971:S124P;ENSP00000369842:S35P;ENSP00000426796:S35P;ENSP00000399481:S127P	ENSP00000369842:S35P	S	-	1	0	POC5	75034245	1.000000	0.71417	0.975000	0.42487	0.928000	0.56348	0.951000	0.29135	2.205000	0.71048	0.533000	0.62120	TCT	.	.	none		0.378	POC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369124.1	NM_152408	
PLA2G4D	283748	hgsc.bcm.edu	37	15	42363433	42363433	+	Silent	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:42363433T>A	ENST00000290472.3	-	17	1858	c.1764A>T	c.(1762-1764)gcA>gcT	p.A588A		NM_178034.3	NP_828848.3	Q86XP0	PA24D_HUMAN	phospholipase A2, group IVD (cytosolic)	588	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.				glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylcholine acyl-chain remodeling (GO:0036151)|phosphatidylethanolamine acyl-chain remodeling (GO:0036152)|phosphatidylglycerol acyl-chain remodeling (GO:0036148)|phosphatidylinositol acyl-chain remodeling (GO:0036149)|phosphatidylserine acyl-chain remodeling (GO:0036150)|phospholipid catabolic process (GO:0009395)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|membrane (GO:0016020)	metal ion binding (GO:0046872)|phospholipase A2 activity (GO:0004623)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(4)|lung(7)|ovary(1)|skin(2)|stomach(1)	27		all_cancers(109;6.37e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.019)|Ovarian(310;0.143)|Colorectal(260;0.245)		OV - Ovarian serous cystadenocarcinoma(18;4.9e-17)|GBM - Glioblastoma multiforme(94;1.02e-06)		AGCCTTTAAATGCCTGGGCCA	0.642																																					p.A588A		Atlas-SNP	.											.	PLA2G4D	72	.	0			c.A1764T						PASS	.						28.0	32.0	30.0					15																	42363433		2202	4297	6499	SO:0001819	synonymous_variant	283748	exon17			TTTAAATGCCTGG	AB090876	CCDS32203.1	15q14	2008-09-19				ENSG00000159337	3.1.1.4		30038	protein-coding gene	gene with protein product		612864				14709560	Standard	NM_178034		Approved	cPLA2delta	uc001zox.3	Q86XP0		ENST00000290472.3:c.1764A>T	15.37:g.42363433T>A		36.0	0.0	0		44.0	28.0	0.636364	NM_178034	Q8N176	Silent	SNP	ENST00000290472.3	37	CCDS32203.1																																																																																			.	.	none		0.642	PLA2G4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419317.1	NM_178034	
MYH10	4628	hgsc.bcm.edu	37	17	8413247	8413247	+	Silent	SNP	G	G	A	rs139264814		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8413247G>A	ENST00000269243.4	-	23	3018	c.2880C>T	c.(2878-2880)gaC>gaT	p.D960D	RNU7-43P_ENST00000516554.1_RNA|MYH10_ENST00000360416.3_Silent_p.D991D|MYH10_ENST00000396239.1_Silent_p.D981D|MYH10_ENST00000379980.4_Silent_p.D976D	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	960					actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						CTTCCTCCTCGTCTAGCTGTT	0.493																																					p.D991D		Atlas-SNP	.											.	MYH10	148	.	0			c.C2973T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	88.0	81.0	83.0		2880	-8.3	0.7	17	dbSNP_134	83	0,8600		0,0,4300	no	coding-synonymous	MYH10	NM_005964.1		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		960/1977	8413247	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4628	exon25			CTCCTCGTCTAGC	M69181	CCDS11144.1, CCDS58515.1, CCDS73984.1	17p13	2011-09-27	2006-09-29		ENSG00000133026	ENSG00000133026		"""Myosins / Myosin superfamily : Class II"""	7568	protein-coding gene	gene with protein product		160776	"""myosin, heavy polypeptide 10, non-muscle"""			1860190	Standard	NM_001256012		Approved	NMMHCB	uc002glm.4	P35580	OTTHUMG00000108195	ENST00000269243.4:c.2880C>T	17.37:g.8413247G>A		67.0	0.0	0		57.0	13.0	0.22807	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			G|1.000;A|0.000	0.000	weak		0.493	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
OXLD1	339229	hgsc.bcm.edu	37	17	79632327	79632327	+	Silent	SNP	C	C	T	rs137928765		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:79632327C>T	ENST00000374741.3	-	2	358	c.348G>A	c.(346-348)gaG>gaA	p.E116E	PDE6G_ENST00000571224.1_5'Flank|OXLD1_ENST00000571503.1_3'UTR|PDE6G_ENST00000574777.1_5'Flank|OXLD1_ENST00000573786.1_5'UTR|CCDC137_ENST00000329214.8_5'Flank	NM_001039842.1	NP_001034931.1	Q5BKU9	OXLD1_HUMAN	oxidoreductase-like domain containing 1	116						mitochondrion (GO:0005739)											CCAGGGCCCGCTCCCCACCGT	0.657																																					p.E116E		Atlas-SNP	.											.	.	.	.	0			c.G348A						PASS	.	C		0,4406		0,0,2203	40.0	39.0	39.0		348	2.7	1.0	17	dbSNP_134	39	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	C17orf90	NM_001039842.1		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		116/148	79632327	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	339229	exon2			GGCCCGCTCCCCA		CCDS32766.1	17q25.3	2012-07-20	2012-07-20	2012-07-20	ENSG00000204237	ENSG00000204237			27901	protein-coding gene	gene with protein product			"""chromosome 17 open reading frame 90"""	C17orf90			Standard	NM_001039842		Approved	MGC104712	uc002kba.3	Q5BKU9	OTTHUMG00000178063	ENST00000374741.3:c.348G>A	17.37:g.79632327C>T		101.0	0.0	0		96.0	40.0	0.416667	NM_001039842	A6ND24	Silent	SNP	ENST00000374741.3	37	CCDS32766.1																																																																																			C|1.000;T|0.000	0.000	strong		0.657	OXLD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440380.1	NM_001039842	
SLC5A4	6527	hgsc.bcm.edu	37	22	32647802	32647802	+	Silent	SNP	C	C	T	rs144495809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:32647802C>T	ENST00000266086.4	-	3	278	c.267G>A	c.(265-267)ggG>ggA	p.G89G	RP1-90G24.10_ENST00000434942.1_RNA	NM_014227.2	NP_055042.1	Q9NY91	SC5A4_HUMAN	solute carrier family 5 (glucose activated ion channel), member 4	89					carbohydrate transport (GO:0008643)|sodium ion transport (GO:0006814)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|pancreas(2)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36						CTGCTCCTGTCCCAGCCAGCC	0.478													c|||	11	0.00219649	0.0008	0.0072	5008	,	,		17002	0.004		0.001	False		,,,				2504	0.0				p.G89G		Atlas-SNP	.											.	SLC5A4	82	.	0			c.G267A						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	96.0	95.0	95.0		267	-2.2	0.4	22	dbSNP_134	95	29,8571	20.4+/-63.3	0,29,4271	no	coding-synonymous	SLC5A4	NM_014227.2		0,33,6470	TT,TC,CC		0.3372,0.0908,0.2537		89/660	32647802	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	6527	exon3			TCCTGTCCCAGCC	U41897	CCDS13903.1	22q12.3	2013-07-19	2013-07-19		ENSG00000100191	ENSG00000100191		"""Solute carriers"""	11039	protein-coding gene	gene with protein product			"""solute carrier family 5 (low affinity glucose cotransporter), member 4"""			9501190, 12354616	Standard	NM_014227		Approved	SAAT1, SGLT3, DJ90G24.4	uc003ami.3	Q9NY91	OTTHUMG00000150007	ENST00000266086.4:c.267G>A	22.37:g.32647802C>T		42.0	0.0	0		46.0	22.0	0.478261	NM_014227	O15279	Silent	SNP	ENST00000266086.4	37	CCDS13903.1																																																																																			C|0.997;T|0.003	0.003	strong		0.478	SLC5A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000315724.1	NM_014227	
BRD1	23774	hgsc.bcm.edu	37	22	50187853	50187853	+	Missense_Mutation	SNP	C	C	T	rs35331092	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50187853C>T	ENST00000216267.8	-	6	2674	c.2188G>A	c.(2188-2190)Gct>Act	p.A730T	BRD1_ENST00000342989.5_Missense_Mutation_p.A325T|BRD1_ENST00000404034.1_Missense_Mutation_p.A730T|BRD1_ENST00000542442.1_Missense_Mutation_p.A418T|BRD1_ENST00000404760.1_Missense_Mutation_p.A730T|BRD1_ENST00000457780.2_Missense_Mutation_p.A730T	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	730			A -> T (in dbSNP:rs35331092).		histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACTTCATAGCGCAGGTGAGG	0.607													C|||	342	0.0682907	0.0825	0.0317	5008	,	,		18559	0.003		0.0596	False		,,,				2504	0.1513				p.A730T		Atlas-SNP	.											.	BRD1	144	.	0			c.G2188A						PASS	.	C	THR/ALA	422,3984	206.5+/-228.1	21,380,1802	59.0	63.0	62.0		2188	-0.9	0.4	22	dbSNP_126	62	590,8010	156.4+/-210.3	24,542,3734	yes	missense	BRD1	NM_014577.1	58	45,922,5536	TT,TC,CC		6.8605,9.5778,7.781	benign	730/1059	50187853	1012,11994	2203	4300	6503	SO:0001583	missense	23774	exon6			TCATAGCGCAGGT	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.2188G>A	22.37:g.50187853C>T	ENSP00000216267:p.Ala730Thr	61.0	0.0	0		76.0	38.0	0.5	NM_014577	A6ZJA4	Missense_Mutation	SNP	ENST00000216267.8	37	CCDS14080.1	96	0.04395604395604396	41	0.08333333333333333	12	0.03314917127071823	0	0.0	43	0.05672823218997362	C	14.17	2.456934	0.43634	0.095778	0.068605	ENSG00000100425	ENST00000216267;ENST00000404034;ENST00000404760;ENST00000457780;ENST00000542442;ENST00000342989;ENST00000419212	T;T;T;T;T;T	0.28255	2.57;2.57;2.58;2.44;1.62;2.01	5.4	-0.94	0.10405	.	0.418477	0.26248	N	0.025479	T	0.00754	0.0025	L	0.39898	1.24	0.28355	P	0.9207138	P;P;P;D	0.54964	0.948;0.63;0.788;0.969	B;B;B;B	0.43728	0.247;0.12;0.169;0.429	T	0.07654	-1.0761	9	0.31617	T	0.26	.	21.7236	0.99959	0.1644:0.8356:0.0:0.0	rs35331092	730;325;730;730	Q86X06;B7Z926;O95696;O95696-2	.;.;BRD1_HUMAN;.	T	730;730;730;730;418;325;190	ENSP00000216267:A730T;ENSP00000384076:A730T;ENSP00000385858:A730T;ENSP00000410042:A730T;ENSP00000437514:A418T;ENSP00000345886:A325T	ENSP00000216267:A730T	A	-	1	0	BRD1	48573857	0.065000	0.20965	0.369000	0.25952	0.980000	0.70556	0.428000	0.21395	-0.460000	0.07003	0.655000	0.94253	GCT	C|0.936;T|0.064	0.064	strong		0.607	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
DEFA5	1670	hgsc.bcm.edu	37	8	6914169	6914169	+	Silent	SNP	G	G	A	rs147432781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:6914169G>A	ENST00000330590.2	-	1	87	c.51C>T	c.(49-51)gcC>gcT	p.A17A		NM_021010.1	NP_066290.1	Q01523	DEF5_HUMAN	defensin, alpha 5, Paneth cell-specific	17					antibacterial humoral response (GO:0019731)|defense response to fungus (GO:0050832)|innate immune response (GO:0045087)|killing of cells of other organism (GO:0031640)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|secretory granule lumen (GO:0034774)				NS(1)|lung(4)|skin(1)|stomach(1)	7				COAD - Colon adenocarcinoma(149;0.0572)|READ - Rectum adenocarcinoma(644;0.121)		ACTCAGCCTGGGCCTGCAGGG	0.582													.|||	10	0.00199681	0.0	0.0	5008	,	,		18658	0.0		0.008	False		,,,				2504	0.002				p.A17A		Atlas-SNP	.											.	DEFA5	17	.	0			c.C51T						PASS	.	G		13,4393		0,13,2190	109.0	99.0	102.0		51	0.8	0.1	8	dbSNP_134	102	108,8492		0,108,4192	no	coding-synonymous	DEFA5	NM_021010.1		0,121,6382	AA,AG,GG		1.2558,0.2951,0.9303		17/95	6914169	121,12885	2203	4300	6503	SO:0001819	synonymous_variant	1670	exon1			AGCCTGGGCCTGC	BC069690	CCDS5963.1	8p23.1	2007-02-20			ENSG00000164816	ENSG00000164816		"""Defensins, alpha"""	2764	protein-coding gene	gene with protein product		600472		DEF5		1429669	Standard	NM_021010		Approved	HD-5	uc003wra.1	Q01523	OTTHUMG00000090383	ENST00000330590.2:c.51C>T	8.37:g.6914169G>A		110.0	0.0	0		99.0	45.0	0.454545	NM_021010	A0JDY6|Q3KNV2	Silent	SNP	ENST00000330590.2	37	CCDS5963.1																																																																																			G|0.993;A|0.007	0.007	strong		0.582	DEFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206755.1	NM_021010	
PI4KA	5297	hgsc.bcm.edu	37	22	21064270	21064270	+	Silent	SNP	C	C	T	rs151214632		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:21064270C>T	ENST00000572273.1	-	53	6155	c.5925G>A	c.(5923-5925)gcG>gcA	p.A1975A	PI4KA_ENST00000414196.3_Silent_p.A785A|PI4KA_ENST00000255882.6_Silent_p.A2033A			P42356	PI4KA_HUMAN	phosphatidylinositol 4-kinase, catalytic, alpha	1975	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi-associated vesicle membrane (GO:0030660)|membrane (GO:0016020)|plasma membrane (GO:0005886)	1-phosphatidylinositol 4-kinase activity (GO:0004430)|ATP binding (GO:0005524)			breast(3)|endometrium(8)|kidney(9)|large_intestine(19)|lung(29)|ovary(1)|pancreas(1)|prostate(3)|salivary_gland(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	79	all_cancers(11;7.59e-25)|all_epithelial(7;1.34e-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)			GGGAGACGACCGCGTCCATGT	0.617													N|||	1	0.000199681	0.0	0.0	5008	,	,		20530	0.0		0.001	False		,,,				2504	0.0				p.A2033A	GBM(136;1332 1831 3115 23601 50806)	Atlas-SNP	.											.	PI4KA	313	.	0			c.G6099A						PASS	.	C	,	3,4403	6.2+/-15.9	0,3,2200	113.0	89.0	97.0		2355,5925	-10.5	0.2	22	dbSNP_134	97	26,8574	18.5+/-59.3	0,26,4274	no	coding-synonymous,coding-synonymous	PI4KA	NM_002650.2,NM_058004.3	,	0,29,6474	TT,TC,CC		0.3023,0.0681,0.223	,	785/855,1975/2045	21064270	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	5297	exon53			GACGACCGCGTCC	L36151	CCDS33603.1, CCDS33603.2	22q11.21	2011-05-25	2007-08-14	2007-08-02	ENSG00000241973	ENSG00000241973			8983	protein-coding gene	gene with protein product		600286		PIK4CA		7961848, 8662589	Standard	NM_002650		Approved	PI4K-ALPHA, pi4K230	uc002zsz.5	P42356	OTTHUMG00000167440	ENST00000572273.1:c.5925G>A	22.37:g.21064270C>T		429.0	0.0	0		465.0	234.0	0.503226	NM_058004	Q7Z625|Q9UPG2	Silent	SNP	ENST00000572273.1	37																																																																																				C|0.998;T|0.002	0.002	strong		0.617	PI4KA-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_058004	
MT-ND6	4541	hgsc.bcm.edu	37	M	14470	14470	+	Silent	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrM:14470T>A	ENST00000361681.2	-	1	203	c.204A>T	c.(202-204)ggA>ggT	p.G68G	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TH_ENST00000387441.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	68					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						GCTGTAGTATATCCAAAGACA	0.438																																					p.G68G		Atlas-SNP	.											.	.	.	.	0			c.A204T						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			AGTATATCCAAAG			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.204A>T	M.37:g.14470T>A		10.0	0.0	0		6.0	6.0	1	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.438	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
XDH	7498	hgsc.bcm.edu	37	2	31593230	31593230	+	Silent	SNP	C	C	T	rs557103794		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:31593230C>T	ENST00000379416.3	-	18	2019	c.1971G>A	c.(1969-1971)gcG>gcA	p.A657A		NM_000379.3	NP_000370.2	P47989	XDH_HUMAN	xanthine dehydrogenase	657					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|lactation (GO:0007595)|negative regulation of endothelial cell differentiation (GO:0045602)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of gene expression (GO:0010629)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of vascular endothelial growth factor signaling pathway (GO:1900747)|negative regulation of vasculogenesis (GO:2001213)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of p38MAPK cascade (GO:1900745)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|small molecule metabolic process (GO:0044281)|xanthine catabolic process (GO:0009115)	cytosol (GO:0005829)|extracellular space (GO:0005615)|peroxisome (GO:0005777)	2 iron, 2 sulfur cluster binding (GO:0051537)|electron carrier activity (GO:0009055)|flavin adenine dinucleotide binding (GO:0050660)|iron ion binding (GO:0005506)|molybdopterin cofactor binding (GO:0043546)|protein homodimerization activity (GO:0042803)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)|xanthine dehydrogenase activity (GO:0004854)|xanthine oxidase activity (GO:0004855)	p.A657A(1)		breast(3)|central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(31)|ovary(1)|pancreas(1)|prostate(3)|skin(9)|urinary_tract(1)	74	Acute lymphoblastic leukemia(172;0.155)				Aldesleukin(DB00041)|Allopurinol(DB00437)|Azathioprine(DB00993)|Carboplatin(DB00958)|Carvedilol(DB01136)|Chlorphenesin(DB00856)|Cisplatin(DB00515)|Daunorubicin(DB00694)|Deferoxamine(DB00746)|Doxorubicin(DB00997)|Flavin adenine dinucleotide(DB03147)|L-Carnitine(DB00583)|Menadione(DB00170)|Mercaptopurine(DB01033)|Nitrofural(DB00336)|Procarbazine(DB01168)|Pyrazinamide(DB00339)|Spermine(DB00127)|Trifluoperazine(DB00831)	CCTTATCCTTCGCAAAGACTG	0.358																																					p.A657A	Colon(66;682 1445 30109 40147)	Atlas-SNP	.											XDH,colon,carcinoma,0,1	XDH	191	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G1971A						scavenged	.						84.0	83.0	83.0					2																	31593230		2203	4300	6503	SO:0001819	synonymous_variant	7498	exon18			ATCCTTCGCAAAG	D11456	CCDS1775.1	2p23.1	2009-07-10	2003-03-20		ENSG00000158125	ENSG00000158125	1.17.1.4		12805	protein-coding gene	gene with protein product		607633	"""xanthene dehydrogenase"""			8224915	Standard	NM_000379		Approved	XOR, XO	uc002rnv.1	P47989	OTTHUMG00000099385	ENST00000379416.3:c.1971G>A	2.37:g.31593230C>T		48.0	0.0	0		63.0	3.0	0.047619	NM_000379	Q16681|Q16712|Q4PJ16	Silent	SNP	ENST00000379416.3	37	CCDS1775.1																																																																																			.	.	none		0.358	XDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216840.1	NM_000379	
ALMS1	7840	hgsc.bcm.edu	37	2	73829362	73829362	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:73829362G>A	ENST00000264448.6	+	20	12273	c.12162G>A	c.(12160-12162)cgG>cgA	p.R4054R	ALMS1_ENST00000409009.1_Silent_p.R4012R|ALMS1_ENST00000464408.2_3'UTR	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	4054	ALMS motif.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						CTGGGGAGCGGATAAAGCGCC	0.483																																					p.R4054R		Atlas-SNP	.											ALMS1,rectum,carcinoma,+2,1	ALMS1	384	1	0			c.G12162A						PASS	.						50.0	54.0	52.0					2																	73829362		2203	4300	6503	SO:0001819	synonymous_variant	7840	exon20			GGAGCGGATAAAG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.12162G>A	2.37:g.73829362G>A		189.0	0.0	0		200.0	103.0	0.515	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Silent	SNP	ENST00000264448.6	37	CCDS42697.1																																																																																			.	.	none		0.483	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
GDPD4	220032	hgsc.bcm.edu	37	11	76944178	76944178	+	Silent	SNP	G	G	A	rs17751194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:76944178G>A	ENST00000376217.2	-	13	1531	c.1281C>T	c.(1279-1281)acC>acT	p.T427T	GDPD4_ENST00000315938.4_Silent_p.T427T			Q6W3E5	GDPD4_HUMAN	glycerophosphodiester phosphodiesterase domain containing 4	427	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	integral component of membrane (GO:0016021)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|metal ion binding (GO:0046872)			breast(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(8)|prostate(1)|skin(1)	20						GCTCATTGACGGTGTATACGT	0.443													G|||	30	0.00599042	0.0	0.0058	5008	,	,		20824	0.0		0.0179	False		,,,				2504	0.0082				p.T427T		Atlas-SNP	.											.	GDPD4	49	.	0			c.C1281T						PASS	.	G		15,4385	22.3+/-47.3	1,13,2186	176.0	154.0	162.0		1281	-5.5	0.0	11	dbSNP_123	162	136,8448	68.4+/-130.8	2,132,4158	no	coding-synonymous	GDPD4	NM_182833.1		3,145,6344	AA,AG,GG		1.5843,0.3409,1.163		427/521	76944178	151,12833	2200	4292	6492	SO:0001819	synonymous_variant	220032	exon13			ATTGACGGTGTAT	AY326450	CCDS8249.1	11q13.5	2008-02-05			ENSG00000178795	ENSG00000178795			24849	protein-coding gene	gene with protein product							Standard	NM_182833		Approved	GDE6	uc001oyf.3	Q6W3E5	OTTHUMG00000165136	ENST00000376217.2:c.1281C>T	11.37:g.76944178G>A		69.0	0.0	0		62.0	36.0	0.580645	NM_182833	Q7Z5B0	Silent	SNP	ENST00000376217.2	37																																																																																				G|0.988;A|0.012	0.012	strong		0.443	GDPD4-002	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000382075.1	NM_182833	
ZNF77	58492	hgsc.bcm.edu	37	19	2934249	2934249	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:2934249T>C	ENST00000314531.4	-	4	968	c.876A>G	c.(874-876)ggA>ggG	p.G292G		NM_021217.2	NP_067040.1	Q15935	ZNF77_HUMAN	zinc finger protein 77	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(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(5)|ovary(1)	17				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)|GBM - Glioblastoma multiforme(1328;2.11e-07)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.174)|STAD - Stomach adenocarcinoma(1328;0.18)		ACGGTTTCTCTCCAGTGTGTG	0.458																																					p.G292G		Atlas-SNP	.											.	ZNF77	47	.	0			c.A876G						PASS	.						167.0	152.0	157.0					19																	2934249		2203	4300	6503	SO:0001819	synonymous_variant	58492	exon4			TTTCTCTCCAGTG	X65230	CCDS12099.1	19p13.3	2013-01-08	2006-05-12					"""Zinc fingers, C2H2-type"", ""-"""	13150	protein-coding gene	gene with protein product		194551	"""zinc finger protein 77 (pT1)"""			8478004	Standard	NM_021217		Approved	pT1	uc002lws.4	Q15935		ENST00000314531.4:c.876A>G	19.37:g.2934249T>C		76.0	0.0	0		100.0	39.0	0.39	NM_021217	Q86XJ3|Q9NPP0	Silent	SNP	ENST00000314531.4	37	CCDS12099.1																																																																																			.	.	none		0.458	ZNF77-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451924.1	NM_021217	
COL11A2	1302	hgsc.bcm.edu	37	6	33133555	33133555	+	Silent	SNP	C	C	T	rs114580597	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33133555C>T	ENST00000374708.4	-	61	4521	c.4263G>A	c.(4261-4263)caG>caA	p.Q1421Q	COL11A2_ENST00000477772.1_5'UTR|COL11A2_ENST00000374712.1_Silent_p.Q1426Q|COL11A2_ENST00000374713.1_Silent_p.Q1460Q|COL11A2_ENST00000361917.1_Silent_p.Q1400Q|COL11A2_ENST00000395197.1_Silent_p.Q1447Q|COL11A2_ENST00000341947.2_Silent_p.Q1507Q|COL11A2_ENST00000374714.1_Silent_p.Q1481Q|COL11A2_ENST00000357486.1_Silent_p.Q1486Q	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1507	Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						TCTTGGGCATCTGAATGGGCA	0.642													C|||	4	0.000798722	0.0	0.0	5008	,	,		18621	0.0		0.003	False		,,,				2504	0.001				p.Q1507Q	Melanoma(1;90 116 3946 5341 17093)	Atlas-SNP	.											.	COL11A2	124	.	0			c.G4521A						PASS	.	C	,,	4,4402	8.1+/-20.4	0,4,2199	59.0	60.0	60.0		4200,4521,4263	3.8	1.0	6	dbSNP_132	60	33,8567	19.8+/-62.0	0,33,4267	no	coding-synonymous,coding-synonymous,coding-synonymous	COL11A2	NM_080679.2,NM_080680.2,NM_080681.2	,,	0,37,6466	TT,TC,CC		0.3837,0.0908,0.2845	,,	1400/1630,1507/1737,1421/1651	33133555	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	1302	exon63			GGGCATCTGAATG	U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.4263G>A	6.37:g.33133555C>T		18.0	0.0	0		17.0	7.0	0.411765	NM_080680	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	37	CCDS43452.1																																																																																			C|0.998;T|0.002	0.002	strong		0.642	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2		
ABCC6	368	hgsc.bcm.edu	37	16	16259742	16259742	+	Missense_Mutation	SNP	C	C	T	rs373863345		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:16259742C>T	ENST00000205557.7	-	23	3073	c.3044G>A	c.(3043-3045)cGg>cAg	p.R1015Q		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	1015	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.				response to drug (GO:0042493)|transmembrane transport (GO:0055085)|transport (GO:0006810)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(6)|kidney(3)|large_intestine(10)|lung(10)|ovary(1)|skin(6)|urinary_tract(1)	43				UCEC - Uterine corpus endometrioid carcinoma (3;0.123)	Cisplatin(DB00515)|Dactinomycin(DB00970)|Daunorubicin(DB00694)|Doxorubicin(DB00997)|Etoposide(DB00773)|Indomethacin(DB00328)|Probenecid(DB01032)|Sulfinpyrazone(DB01138)|Teniposide(DB00444)|Vinblastine(DB00570)	CCTGGATGCCCGGGCCCCACC	0.617																																					p.R1015Q		Atlas-SNP	.											.	ABCC6	110	.	0			c.G3044A						PASS	.	C	GLN/ARG	0,4394		0,0,2197	36.0	37.0	36.0		3044	2.1	1.0	16		36	1,8599	1.2+/-3.3	0,1,4299	no	missense	ABCC6	NM_001171.5	43	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1015/1504	16259742	1,12993	2197	4300	6497	SO:0001583	missense	368	exon23			GATGCCCGGGCCC	AF076622	CCDS10568.1, CCDS58430.1	16p13.11	2013-01-08			ENSG00000091262	ENSG00000091262		"""ATP binding cassette transporters / subfamily C"""	57	protein-coding gene	gene with protein product		603234	"""pseudoxanthoma elasticum"""	ARA, PXE		9721217, 11439001	Standard	NM_001079528		Approved	MRP6, EST349056, MLP1, URG7	uc002den.4	O95255	OTTHUMG00000129967	ENST00000205557.7:c.3044G>A	16.37:g.16259742C>T	ENSP00000205557:p.Arg1015Gln	69.0	0.0	0		73.0	40.0	0.547945	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	.	.	.	.	.	.	.	.	.	.	C	11.82	1.751682	0.31046	0.0	1.16E-4	ENSG00000091262	ENST00000205557;ENST00000205558	D	0.91351	-2.83	5.52	2.07	0.26955	ABC transporter, transmembrane domain, type 1 (1);ABC transporter, integral membrane type 1 (1);ABC transporter, transmembrane domain (1);	0.724655	0.11525	U	0.555272	T	0.80768	0.4686	L	0.31476	0.935	0.09310	N	0.999997	B	0.30211	0.273	B	0.19946	0.027	T	0.66736	-0.5848	10	0.26408	T	0.33	.	4.8069	0.13325	0.2447:0.4906:0.0:0.2647	.	1015	O95255	MRP6_HUMAN	Q	1015;20	ENSP00000205557:R1015Q	ENSP00000205557:R1015Q	R	-	2	0	ABCC6	16167243	0.036000	0.19791	0.983000	0.44433	0.808000	0.45660	1.233000	0.32648	0.701000	0.31803	0.561000	0.74099	CGG	.	.	weak		0.617	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
HNF1A	6927	hgsc.bcm.edu	37	12	121416622	121416622	+	Silent	SNP	C	C	G	rs1169289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121416622C>G	ENST00000257555.6	+	1	277	c.51C>G	c.(49-51)ctC>ctG	p.L17L	HNF1A_ENST00000544413.1_Silent_p.L17L|HNF1A_ENST00000543427.1_Intron|HNF1A_ENST00000541395.1_Silent_p.L17L|HNF1A-AS1_ENST00000535301.1_RNA|HNF1A_ENST00000538626.1_Silent_p.L17L|HNF1A-AS1_ENST00000433033.2_RNA|HNF1A_ENST00000402929.1_Silent_p.L17L|HNF1A_ENST00000400024.2_Silent_p.L17L|HNF1A-AS1_ENST00000537361.1_RNA			P20823	HNF1A_HUMAN	HNF1 homeobox A	17	Dimerization.				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)	p.?(1)		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)					CGGCCCTGCTCGAGTCAGGGC	0.687									Hepatic Adenoma, Familial Clustering of				C|||	2146	0.428514	0.3169	0.438	5008	,	,		11818	0.3819		0.4692	False		,,,				2504	0.5787				p.L17L		Atlas-SNP	.											HNF1A,NS,carcinoma,0,1	HNF1A	302	1	1	Unknown(1)	endometrium(1)	c.C51G						scavenged	.	C		1508,2894		278,952,971	24.0	29.0	27.0		51	-3.7	0.9	12	dbSNP_87	27	3915,4673		915,2085,1294	no	coding-synonymous	HNF1A	NM_000545.5		1193,3037,2265	GG,GC,CC		45.5869,34.2572,41.7475		17/632	121416622	5423,7567	2201	4294	6495	SO:0001819	synonymous_variant	6927	exon1	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCTGCTCGAGTCA	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.51C>G	12.37:g.121416622C>G		134.0	1.0	0.00746269		135.0	72.0	0.533333	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			G|0.405;C|0.595	0.405	strong		0.687	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
KIAA1586	57691	hgsc.bcm.edu	37	6	56918933	56918933	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:56918933A>G	ENST00000370733.4	+	4	1843	c.1636A>G	c.(1636-1638)Aga>Gga	p.R546G	KIAA1586_ENST00000545356.1_Missense_Mutation_p.R519G	NM_020931.2	NP_065982.1	Q9HCI6	K1586_HUMAN	KIAA1586	546							nucleic acid binding (GO:0003676)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(9)|skin(1)	18	Lung NSC(77;0.0969)		LUSC - Lung squamous cell carcinoma(124;0.0785)|Lung(124;0.13)			ATTACAGTCAAGATCAACTAA	0.299																																					p.R546G		Atlas-SNP	.											.	KIAA1586	59	.	0			c.A1636G						PASS	.						30.0	31.0	31.0					6																	56918933		2174	4281	6455	SO:0001583	missense	57691	exon4			CAGTCAAGATCAA	AB046806	CCDS34480.1, CCDS69138.1	6p12.1	2014-03-27			ENSG00000168116	ENSG00000168116			21360	protein-coding gene	gene with protein product						10997877	Standard	NM_001286274		Approved		uc003pdj.3	Q9HCI6	OTTHUMG00000014915	ENST00000370733.4:c.1636A>G	6.37:g.56918933A>G	ENSP00000359768:p.Arg546Gly	88.0	0.0	0		90.0	4.0	0.0444444	NM_020931	A8K4M3|Q8IW25	Missense_Mutation	SNP	ENST00000370733.4	37	CCDS34480.1	.	.	.	.	.	.	.	.	.	.	a	10.50	1.368490	0.24771	.	.	ENSG00000168116	ENST00000370733;ENST00000545356	T;T	0.21191	2.02;2.02	3.84	2.66	0.31614	Ribonuclease H-like (1);	.	.	.	.	T	0.03305	0.0096	N	0.08118	0	0.23107	N	0.998283	B;B	0.11235	0.004;0.004	B;B	0.09377	0.004;0.004	T	0.40831	-0.9542	9	0.62326	D	0.03	-3.9313	5.9809	0.19407	0.8787:0.0:0.1213:0.0	.	519;546	F5H2N6;Q9HCI6	.;K1586_HUMAN	G	546;519	ENSP00000359768:R546G;ENSP00000445507:R519G	ENSP00000359768:R546G	R	+	1	2	KIAA1586	57026892	0.999000	0.42202	0.959000	0.39883	0.992000	0.81027	1.557000	0.36299	0.637000	0.30526	-0.263000	0.10527	AGA	.	.	none		0.299	KIAA1586-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041033.1	NM_020931	
RASAL2	9462	hgsc.bcm.edu	37	1	178442222	178442222	+	Missense_Mutation	SNP	G	G	A	rs371002131	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:178442222G>A	ENST00000462775.1	+	16	3393	c.3268G>A	c.(3268-3270)Gtg>Atg	p.V1090M	RASAL2_ENST00000448150.3_Missense_Mutation_p.V1220M|RASAL2_ENST00000367649.3_Missense_Mutation_p.V1231M	NM_004841.3	NP_004832.1	Q9UJF2	NGAP_HUMAN	RAS protein activator like 2	1090					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)	Ras GTPase activator activity (GO:0005099)			biliary_tract(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(2)|lung(25)|ovary(2)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	54						AAAACGGATCGTGTCCCTGGA	0.522													G|||	2	0.000399361	0.0	0.0	5008	,	,		21631	0.0		0.0	False		,,,				2504	0.002				p.V1231M		Atlas-SNP	.											.	RASAL2	334	.	0			c.G3691A						PASS	.	G	MET/VAL,MET/VAL	1,4405	2.1+/-5.4	0,1,2202	148.0	129.0	136.0		3268,3691	1.7	1.0	1		136	0,8600		0,0,4300	no	missense,missense	RASAL2	NM_004841.3,NM_170692.2	21,21	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign,benign	1090/1140,1231/1281	178442222	1,13005	2203	4300	6503	SO:0001583	missense	9462	exon18			CGGATCGTGTCCC	AF047711	CCDS1321.1, CCDS1322.1, CCDS1321.2	1q25	2013-01-10			ENSG00000075391	ENSG00000075391		"""Pleckstrin homology (PH) domain containing"""	9874	protein-coding gene	gene with protein product	"""Ras GTPase activating protein-like"", ""Ras protein activator like 1"""	606136				9877179	Standard	NM_004841		Approved	nGAP	uc001glq.3	Q9UJF2	OTTHUMG00000035022	ENST00000462775.1:c.3268G>A	1.37:g.178442222G>A	ENSP00000420558:p.Val1090Met	126.0	0.0	0		168.0	105.0	0.625	NM_170692	F8W755|O95174|Q2TB22|Q5TFU9	Missense_Mutation	SNP	ENST00000462775.1	37	CCDS1322.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	12.86|12.86	2.064109|2.064109	0.36373|0.36373	2.27E-4|2.27E-4	0.0|0.0	ENSG00000075391|ENSG00000075391	ENST00000367647|ENST00000448150;ENST00000367649;ENST00000462775	.|T;T;T	.|0.12569	.|2.67;2.67;2.67	5.79|5.79	1.68|1.68	0.24146|0.24146	.|.	.|0.649779	.|0.15466	.|N	.|0.260880	T|T	0.05364|0.05364	0.0142|0.0142	N|N	0.08118|0.08118	0|0	0.32851|0.32851	D|D	0.506687|0.506687	.|P;P	.|0.46952	.|0.842;0.887	.|B;B	.|0.39379	.|0.298;0.157	T|T	0.31420|0.31420	-0.9944|-0.9944	6|10	0.87932|0.59425	D|D	0|0.04	.|.	1.8144|1.8144	0.03097|0.03097	0.2871:0.1267:0.4559:0.1303|0.2871:0.1267:0.4559:0.1303	.|.	.|1090;1231	.|Q9UJF2;F8W755	.|NGAP_HUMAN;.	H|M	43|1220;1231;1090	.|ENSP00000407768:V1220M;ENSP00000356621:V1231M;ENSP00000420558:V1090M	ENSP00000356619:R43H|ENSP00000356621:V1231M	R|V	+|+	2|1	0|0	RASAL2|RASAL2	176708845|176708845	0.997000|0.997000	0.39634|0.39634	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	0.793000|0.793000	0.26944|0.26944	0.382000|0.382000	0.24878|0.24878	0.655000|0.655000	0.94253|0.94253	CGT|GTG	.	.	none		0.522	RASAL2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000084758.3	NM_170692	
JAK2	3717	hgsc.bcm.edu	37	9	5081780	5081780	+	Silent	SNP	G	G	A	rs2230724	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:5081780G>A	ENST00000381652.3	+	19	2984	c.2490G>A	c.(2488-2490)ctG>ctA	p.L830L	JAK2_ENST00000544510.1_Silent_p.L681L|JAK2_ENST00000539801.1_Silent_p.L830L|AL161450.1_ENST00000601793.1_Intron	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	830					actin filament polymerization (GO:0030041)|activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of cysteine-type endopeptidase activity involved in apoptotic signaling pathway (GO:0097296)|activation of JAK2 kinase activity (GO:0042977)|activation of MAPKK activity (GO:0000186)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular component movement (GO:0006928)|cytokine-mediated signaling pathway (GO:0019221)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte differentiation (GO:0030218)|extrinsic apoptotic signaling pathway (GO:0097191)|G-protein coupled receptor signaling pathway (GO:0007186)|growth hormone receptor signaling pathway (GO:0060396)|histone H3-Y41 phosphorylation (GO:0035409)|hormone-mediated signaling pathway (GO:0009755)|host programmed cell death induced by symbiont (GO:0034050)|interferon-gamma-mediated signaling pathway (GO:0060333)|interleukin-12-mediated signaling pathway (GO:0035722)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|mammary gland epithelium development (GO:0061180)|mesoderm development (GO:0007498)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of DNA binding (GO:0043392)|negative regulation of heart contraction (GO:0045822)|negative regulation of neuron apoptotic process (GO:0043524)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell activation (GO:0050867)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA binding (GO:0043388)|positive regulation of growth hormone receptor signaling pathway (GO:0060399)|positive regulation of inflammatory response (GO:0050729)|positive regulation of insulin secretion (GO:0032024)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phosphoprotein phosphatase activity (GO:0032516)|positive regulation of protein import into nucleus, translocation (GO:0033160)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of inflammatory response (GO:0050727)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|response to antibiotic (GO:0046677)|response to hydroperoxide (GO:0033194)|response to interleukin-12 (GO:0070671)|response to lipopolysaccharide (GO:0032496)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|STAT protein import into nucleus (GO:0007262)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|tyrosine phosphorylation of STAT protein (GO:0007260)|tyrosine phosphorylation of Stat1 protein (GO:0042508)|tyrosine phosphorylation of Stat3 protein (GO:0042503)|tyrosine phosphorylation of Stat5 protein (GO:0042506)	caveola (GO:0005901)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|endosome lumen (GO:0031904)|membrane raft (GO:0045121)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|heme binding (GO:0020037)|histone binding (GO:0042393)|histone kinase activity (H3-Y41 specific) (GO:0035401)|interleukin-12 receptor binding (GO:0005143)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein tyrosine kinase activity (GO:0004713)|receptor binding (GO:0005102)|SH2 domain binding (GO:0042169)		BCR/JAK2(6)|SSBP2/JAK2(4)|SEC31A/JAK2(4)|ETV6/JAK2(11)|PCM1/JAK2(30)|PAX5/JAK2(18)	breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(32944)|kidney(4)|large_intestine(10)|liver(1)|lung(20)|ovary(3)|prostate(4)|skin(2)|urinary_tract(1)	32998	all_hematologic(13;0.137)	Acute lymphoblastic leukemia(23;0.0198)|Breast(48;0.147)		GBM - Glioblastoma multiforme(50;0.0237)|Lung(218;0.133)	Ruxolitinib(DB08877)|Tofacitinib(DB08895)	TAGGTGCCCTGGGGTTTTCTG	0.348		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial				A|||	3089	0.616813	0.9312	0.5879	5008	,	,		17517	0.4395		0.5239	False		,,,				2504	0.4908				p.L830L		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.G2490A						PASS	.	A		3825,581	258.0+/-262.2	1671,483,49	109.0	110.0	110.0		2490	-3.0	0.1	9	dbSNP_98	110	4294,4306	577.7+/-390.6	1073,2148,1079	no	coding-synonymous	JAK2	NM_004972.3		2744,2631,1128	AA,AG,GG		49.9302,13.1866,37.575		830/1133	5081780	8119,4887	2203	4300	6503	SO:0001819	synonymous_variant	3717	exon19	Familial Cancer Database		TGCCCTGGGGTTT		CCDS6457.1	9p24	2014-09-17	2009-04-23		ENSG00000096968	ENSG00000096968	2.7.10.1	"""SH2 domain containing"""	6192	protein-coding gene	gene with protein product		147796				1848670	Standard	NM_004972		Approved	JTK10	uc003ziw.3	O60674	OTTHUMG00000019490	ENST00000381652.3:c.2490G>A	9.37:g.5081780G>A		75.0	0.0	0		103.0	40.0	0.38835	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	37	CCDS6457.1																																																																																			G|0.386;A|0.614	0.614	strong		0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
ERBB4	2066	hgsc.bcm.edu	37	2	212587119	212587119	+	Splice_Site	SNP	T	T	C	rs77309171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:212587119T>C	ENST00000342788.4	-	7	1192	c.882A>G	c.(880-882)ccA>ccG	p.P294P	ERBB4_ENST00000484474.1_5'Flank|ERBB4_ENST00000436443.1_Splice_Site_p.P294P|ERBB4_ENST00000402597.1_Splice_Site_p.P294P	NM_005235.2	NP_005226.1	Q15303	ERBB4_HUMAN	v-erb-b2 avian erythroblastic leukemia viral oncogene homolog 4	294	Cys-rich.				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)	GTTACTTACGTGGACATTTCT	0.313										TSP Lung(8;0.080)			T|||	10	0.00199681	0.0	0.0029	5008	,	,		16437	0.0		0.005	False		,,,				2504	0.0031				p.P294P		Atlas-SNP	.											.	ERBB4	480	.	0			c.A882G						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	146.0	133.0	138.0		882,882	1.9	1.0	2	dbSNP_131	138	46,8554	30.1+/-81.4	0,46,4254	yes	coding-synonymous-near-splice,coding-synonymous-near-splice	ERBB4	NM_001042599.1,NM_005235.2	,	0,47,6456	CC,CT,TT		0.5349,0.0227,0.3614	,	294/1293,294/1309	212587119	47,12959	2203	4300	6503	SO:0001630	splice_region_variant	2066	exon7			CTTACGTGGACAT	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.883+1A>G	2.37:g.212587119T>C		132.0	0.0	0		109.0	61.0	0.559633	NM_001042599	B7ZLD7|B7ZLE2|B7ZLE3|Q2M1W1|Q59EW4	Silent	SNP	ENST00000342788.4	37	CCDS2394.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	12.44	1.939839	0.34189	2.27E-4	0.005349	ENSG00000178568	ENST00000260943	.	.	.	5.67	1.89	0.25635	.	.	.	.	.	T	0.43765	0.1262	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.29119	-1.0022	4	.	.	.	.	4.9983	0.14251	0.2313:0.1302:0.0:0.6385	.	.	.	.	R	294	.	.	H	-	2	0	ERBB4	212295364	0.999000	0.42202	1.000000	0.80357	0.976000	0.68499	0.474000	0.22148	0.078000	0.16900	-0.344000	0.07964	CAC	T|0.997;C|0.003	0.003	strong		0.313	ERBB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256597.1	NM_001042599	Silent
LGI2	55203	hgsc.bcm.edu	37	4	25014048	25014048	+	Silent	SNP	G	G	A	rs34079294	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:25014048G>A	ENST00000382114.4	-	7	914	c.729C>T	c.(727-729)taC>taT	p.Y243Y		NM_018176.3	NP_060646.2	Q8N0V4	LGI2_HUMAN	leucine-rich repeat LGI family, member 2	243						extracellular region (GO:0005576)				breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(15)|prostate(1)|skin(3)|stomach(2)	33		Breast(46;0.173)				CGATGGCCACGTACACATCGT	0.468													G|||	12	0.00239617	0.0	0.0043	5008	,	,		21248	0.0		0.0089	False		,,,				2504	0.0				p.Y243Y		Atlas-SNP	.											.	LGI2	62	.	0			c.C729T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	145.0	122.0	130.0		729	1.0	1.0	4	dbSNP_126	130	60,8540	37.8+/-93.5	0,60,4240	no	coding-synonymous	LGI2	NM_018176.3		0,65,6438	AA,AG,GG		0.6977,0.1135,0.4998		243/546	25014048	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	55203	exon7			GGCCACGTACACA	AJ487516	CCDS3431.1	4p15.31	2008-07-28			ENSG00000153012	ENSG00000153012			18710	protein-coding gene	gene with protein product		608301				12023020, 16014869	Standard	NM_018176		Approved	KIAA1916, FLJ10675	uc003grf.2	Q8N0V4	OTTHUMG00000097749	ENST00000382114.4:c.729C>T	4.37:g.25014048G>A		110.0	0.0	0		151.0	67.0	0.443709	NM_018176	Q3MIN2|Q8NDW6|Q96PX2|Q9NVK4	Silent	SNP	ENST00000382114.4	37	CCDS3431.1																																																																																			G|0.995;A|0.005	0.005	strong		0.468	LGI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214978.1		
AKR1C1	1645	hgsc.bcm.edu	37	10	5011027	5011027	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:5011027G>A	ENST00000380872.4	+	5	653	c.461G>A	c.(460-462)tGt>tAt	p.C154Y	AKR1C1_ENST00000380859.1_Missense_Mutation_p.C156Y|AKR1C1_ENST00000434459.2_Missense_Mutation_p.C154Y|AKR1C1_ENST00000477661.1_3'UTR	NM_001353.5	NP_001344.2	Q04828	AK1C1_HUMAN	aldo-keto reductase family 1, member C1	154					bile acid and bile salt transport (GO:0015721)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|cholesterol homeostasis (GO:0042632)|daunorubicin metabolic process (GO:0044597)|digestion (GO:0007586)|doxorubicin metabolic process (GO:0044598)|epithelial cell differentiation (GO:0030855)|intestinal cholesterol absorption (GO:0030299)|oxidation-reduction process (GO:0055114)|phototransduction, visible light (GO:0007603)|progesterone metabolic process (GO:0042448)|protein homooligomerization (GO:0051260)|response to organophosphorus (GO:0046683)|retinal metabolic process (GO:0042574)|retinoid metabolic process (GO:0001523)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity (GO:0047006)|alditol:NADP+ 1-oxidoreductase activity (GO:0004032)|aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase (B-specific) activity (GO:0047042)|bile acid binding (GO:0032052)|carboxylic acid binding (GO:0031406)|indanol dehydrogenase activity (GO:0047718)|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)|trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity (GO:0047115)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(2)|ovary(3)|prostate(1)	13					Acetylsalicylic acid(DB00945)|Salicylic acid(DB00936)	GTGGAGAAGTGTAAAGATGCA	0.473																																					p.C154Y	Colon(130;2054 2316 13360 15380)	Atlas-SNP	.											.	AKR1C1	39	.	0			c.G461A						PASS	.						131.0	115.0	121.0					10																	5011027		2203	4300	6503	SO:0001583	missense	1645	exon5			AGAAGTGTAAAGA	D26124	CCDS7061.1	10p15-p14	2012-12-04	2012-12-04		ENSG00000187134	ENSG00000187134	1.3.1.20, 1.1.1.149, 1.1.1.112	"""Aldo-keto reductases"""	384	protein-coding gene	gene with protein product	"""dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase"""	600449	"""aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase)"""	DDH1		8011662	Standard	NM_001353		Approved	DDH, MBAB, DD1, HAKRC		Q04828	OTTHUMG00000017580	ENST00000380872.4:c.461G>A	10.37:g.5011027G>A	ENSP00000370254:p.Cys154Tyr	171.0	0.0	0		136.0	34.0	0.25	NM_001353	P52896|Q5SR15|Q7M4N2|Q9UCX2	Missense_Mutation	SNP	ENST00000380872.4	37	CCDS7061.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	4.273|4.273	0.049878|0.049878	0.08243|0.08243	.|.	.|.	ENSG00000187134|ENSG00000187134	ENST00000434459;ENST00000380872;ENST00000380859|ENST00000442997	T;T;T|.	0.23552|.	1.9;1.9;1.9|.	2.1|2.1	2.1|2.1	0.27182|0.27182	Aldo/keto reductase, conserved site (1);NADP-dependent oxidoreductase domain (3);|.	0.170003|.	0.42053|.	D|.	0.000762|.	T|T	0.41488|0.41488	0.1161|0.1161	L|L	0.46670|0.46670	1.46|1.46	0.28041|0.28041	N|N	0.933763|0.933763	D|.	0.62365|.	0.991|.	D|.	0.67103|.	0.949|.	T|T	0.31138|0.31138	-0.9954|-0.9954	10|5	0.87932|.	D|.	0|.	.|.	10.2386|10.2386	0.43299|0.43299	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	154|.	Q04828|.	AK1C1_HUMAN|.	Y|I	154;154;156|121	ENSP00000412248:C154Y;ENSP00000370254:C154Y;ENSP00000370240:C156Y|.	ENSP00000370240:C156Y|.	C|V	+|+	2|1	0|0	AKR1C1|AKR1C1	5001027|5001027	1.000000|1.000000	0.71417|0.71417	0.820000|0.820000	0.32676|0.32676	0.054000|0.054000	0.15201|0.15201	3.786000|3.786000	0.55431|0.55431	1.475000|1.475000	0.48197|0.48197	0.305000|0.305000	0.20034|0.20034	TGT|GTA	.	.	none		0.473	AKR1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046523.2	NM_001353	
NOLC1	9221	hgsc.bcm.edu	37	10	103912218	103912218	+	Silent	SNP	C	C	A	rs117993238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:103912218C>A	ENST00000605788.1	+	1	286	c.51C>A	c.(49-51)ctC>ctA	p.L17L	NOLC1_ENST00000488254.2_Silent_p.L17L|NOLC1_ENST00000405356.1_Silent_p.L17L|NOLC1_ENST00000603742.1_De_novo_Start_OutOfFrame	NM_001284389.1|NM_004741.3	NP_001271318.1|NP_004732.2	Q14978	NOLC1_HUMAN	nucleolar and coiled-body phosphoprotein 1	17	LisH. {ECO:0000255|PROSITE- ProRule:PRU00126}.				cell cycle (GO:0007049)|mitotic nuclear division (GO:0007067)|nucleolus organization (GO:0007000)|rRNA processing (GO:0006364)	Cajal body (GO:0015030)|cytoplasm (GO:0005737)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	31		Colorectal(252;0.122)		Epithelial(162;5.19e-08)|all cancers(201;9.43e-07)		TGTATCCCCTCGTGCTCGGCT	0.637													C|||	4	0.000798722	0.0	0.0014	5008	,	,		18450	0.0		0.003	False		,,,				2504	0.0				p.L17L		Atlas-SNP	.											.	NOLC1	61	.	0			c.C51A						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	81.0	77.0	78.0		51	-4.4	1.0	10	dbSNP_132	78	11,8589	8.4+/-32.0	0,11,4289	no	coding-synonymous	NOLC1	NM_004741.3		0,12,6491	AA,AC,CC		0.1279,0.0227,0.0923		17/700	103912218	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	9221	exon1			TCCCCTCGTGCTC	Z34289	CCDS7530.1, CCDS65925.1, CCDS65926.1	10q24.32	2008-08-01			ENSG00000166197	ENSG00000166197			15608	protein-coding gene	gene with protein product		602394				7657714, 10567578	Standard	XM_005270273		Approved	P130, KIAA0035, NOPP140, NOPP130	uc001kuo.2	Q14978	OTTHUMG00000018944	ENST00000605788.1:c.51C>A	10.37:g.103912218C>A		55.0	0.0	0		47.0	19.0	0.404255	NM_004741	Q15030|Q5VV70|Q9BUV3	Silent	SNP	ENST00000605788.1	37	CCDS7530.1																																																																																			C|0.999;A|0.001	0.001	strong		0.637	NOLC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050012.2	NM_004741	
CD247	919	hgsc.bcm.edu	37	1	167407839	167407839	+	Missense_Mutation	SNP	G	G	A	rs148513413		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:167407839G>A	ENST00000362089.5	-	4	340	c.268C>T	c.(268-270)Cgt>Tgt	p.R90C	CD247_ENST00000483825.1_5'UTR|CD247_ENST00000392122.3_Missense_Mutation_p.R90C			P20963	CD3Z_HUMAN	CD247 molecule	90					Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|regulation of defense response to virus by virus (GO:0050690)|regulation of immune response (GO:0050776)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	alpha-beta T cell receptor complex (GO:0042105)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|T cell receptor complex (GO:0042101)	identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|transmembrane signaling receptor activity (GO:0004888)	p.R90C(1)		central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(1)|skin(1)	6			LUSC - Lung squamous cell carcinoma(543;0.236)		Muromonab(DB00075)	TCCCGGCCACGTCTCTTGTCC	0.552													G|||	1	0.000199681	0.0	0.0	5008	,	,		17232	0.001		0.0	False		,,,				2504	0.0				p.R90C	Ovarian(192;1815 2869 36877 43334)	Atlas-SNP	.											CD247,NS,carcinoma,+1,2	CD247	25	2	1	Substitution - Missense(1)	large_intestine(1)	c.C268T						PASS	.						151.0	141.0	145.0					1																	167407839		2203	4300	6503	SO:0001583	missense	919	exon4			GGCCACGTCTCTT	BC025703	CCDS1260.1, CCDS1261.1	1q24.2	2014-09-17	2006-03-28	2006-03-09	ENSG00000198821	ENSG00000198821		"""CD molecules"""	1677	protein-coding gene	gene with protein product		186780	"""CD3z antigen, zeta polypeptide (TiT3 complex)"", ""CD247 antigen"""	CD3Z		2974162	Standard	NM_198053		Approved	CD3H, CD3Q	uc001gei.4	P20963	OTTHUMG00000034593	ENST00000362089.5:c.268C>T	1.37:g.167407839G>A	ENSP00000354782:p.Arg90Cys	87.0	0.0	0		95.0	4.0	0.0421053	NM_198053	B1AK49|Q5VX13|Q8TAX4	Missense_Mutation	SNP	ENST00000362089.5	37	CCDS1261.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	16.10	3.026161	0.54683	.	.	ENSG00000198821	ENST00000392122;ENST00000362089	.	.	.	4.52	2.45	0.29901	.	0.137776	0.28718	U	0.014364	T	0.54224	0.1845	M	0.64997	1.995	0.35719	D	0.816966	D;D;D	0.89917	1.0;0.998;0.997	D;P;P	0.74023	0.982;0.855;0.72	T	0.58978	-0.7540	8	0.72032	D	0.01	.	8.5233	0.33289	0.0:0.1632:0.6634:0.1734	.	90;90;90	Q6KAV0;P20963-3;P20963	.;.;CD3Z_HUMAN	C	90	.	ENSP00000354782:R90C	R	-	1	0	CD247	165674463	0.000000	0.05858	0.115000	0.21578	0.951000	0.60555	0.149000	0.16243	1.096000	0.41439	0.563000	0.77884	CGT	G|1.000;A|0.000	0.000	strong		0.552	CD247-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000083707.1	NM_198053	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188353	140188353	+	Silent	SNP	G	G	A	rs561061447	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188353G>A	ENST00000530339.1	+	1	1581	c.1581G>A	c.(1579-1581)gaG>gaA	p.E527E	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Silent_p.E527E|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Silent_p.E527E|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	527	Cadherin 5. {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)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCACGAGGAGCTAGAGCTGC	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17480	0.0		0.0755	False		,,,				2504	0.0082				p.E527E		Atlas-SNP	.											.	PCDHA4	419	.	0			c.G1581A						PASS	.						71.0	76.0	74.0					5																	140188353		2203	4300	6503	SO:0001819	synonymous_variant	56144	exon1			CGAGGAGCTAGAG	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1581G>A	5.37:g.140188353G>A		112.0	0.0	0		66.0	20.0	0.30303	NM_031500	O75285|Q2M253	Silent	SNP	ENST00000530339.1	37	CCDS54916.1																																																																																			.	.	none		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
MME	4311	hgsc.bcm.edu	37	3	154859862	154859862	+	Missense_Mutation	SNP	A	A	G	rs138218277		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:154859862A>G	ENST00000460393.1	+	11	1160	c.1040A>G	c.(1039-1041)tAt>tGt	p.Y347C	MME_ENST00000462745.1_Missense_Mutation_p.Y347C|MME_ENST00000492661.1_Missense_Mutation_p.Y347C|MME_ENST00000493237.1_Missense_Mutation_p.Y347C|MME_ENST00000360490.2_Missense_Mutation_p.Y347C	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	347					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	GTGGTTGTTTATGCTCCAGAA	0.368													A|||	1	0.000199681	0.0	0.0014	5008	,	,		17690	0.0		0.0	False		,,,				2504	0.0				p.Y347C		Atlas-SNP	.											.	MME	133	.	0			c.A1040G						PASS	.	A	CYS/TYR,CYS/TYR,CYS/TYR,CYS/TYR	2,4404	4.2+/-10.8	0,2,2201	140.0	142.0	142.0		1040,1040,1040,1040	6.0	1.0	3	dbSNP_134	142	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense,missense	MME	NM_000902.3,NM_007287.2,NM_007288.2,NM_007289.2	194,194,194,194	0,8,6495	GG,GA,AA		0.0698,0.0454,0.0615	probably-damaging,probably-damaging,probably-damaging,probably-damaging	347/751,347/751,347/751,347/751	154859862	8,12998	2203	4300	6503	SO:0001583	missense	4311	exon11			TTGTTTATGCTCC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.1040A>G	3.37:g.154859862A>G	ENSP00000418525:p.Tyr347Cys	121.0	0.0	0		151.0	97.0	0.642384	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Missense_Mutation	SNP	ENST00000460393.1	37	CCDS3172.1	.	.	.	.	.	.	.	.	.	.	A	16.81	3.227122	0.58668	4.54E-4	6.98E-4	ENSG00000196549	ENST00000492661;ENST00000460393;ENST00000462745;ENST00000493237;ENST00000360490	T;T;T;T;T	0.74842	-0.88;-0.88;-0.88;-0.88;-0.88	6.02	6.02	0.97574	Peptidase M13 (1);	0.189758	0.47852	D	0.000203	T	0.80824	0.4697	M	0.85197	2.74	0.58432	D	0.999999	P	0.47350	0.894	P	0.47891	0.56	D	0.83807	0.0239	10	0.66056	D	0.02	-17.4255	11.5514	0.50723	0.931:0.0:0.069:0.0	.	347	P08473	NEP_HUMAN	C	347	ENSP00000420389:Y347C;ENSP00000418525:Y347C;ENSP00000419653:Y347C;ENSP00000417079:Y347C;ENSP00000353679:Y347C	ENSP00000353679:Y347C	Y	+	2	0	MME	156342556	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.179000	0.71974	2.306000	0.77630	0.482000	0.46254	TAT	A|0.999;G|0.001	0.001	strong		0.368	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	
TRAPPC9	83696	hgsc.bcm.edu	37	8	141461017	141461017	+	Silent	SNP	G	G	A	rs61740786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141461017G>A	ENST00000438773.2	-	2	589	c.456C>T	c.(454-456)atC>atT	p.I152I	TRAPPC9_ENST00000389327.3_Silent_p.I152I|TRAPPC9_ENST00000389328.4_Silent_p.I250I	NM_001160372.1	NP_001153844.1	Q96Q05	TPPC9_HUMAN	trafficking protein particle complex 9	152					cell differentiation (GO:0030154)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)				breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	47						ACAGTGACTCGATGAAGTCCT	0.572													G|||	26	0.00519169	0.0015	0.0101	5008	,	,		19773	0.0		0.0169	False		,,,				2504	0.0				p.I250I		Atlas-SNP	.											.	TRAPPC9	114	.	0			c.C750T						PASS	.	G	,	14,4392	21.2+/-45.6	0,14,2189	66.0	56.0	59.0		456,750	-2.4	1.0	8	dbSNP_129	59	130,8470	66.3+/-128.7	1,128,4171	no	coding-synonymous,coding-synonymous	TRAPPC9	NM_001160372.1,NM_031466.5	,	1,142,6360	AA,AG,GG		1.5116,0.3177,1.1072	,	152/1149,250/1247	141461017	144,12862	2203	4300	6503	SO:0001819	synonymous_variant	83696	exon2			TGACTCGATGAAG	BC006206	CCDS34946.1, CCDS55278.1	8q24.3	2010-10-22			ENSG00000167632	ENSG00000167632		"""Trafficking protein particle complex"""	30832	protein-coding gene	gene with protein product	"""TRAPP 120 kDa subunit"", ""tularik gene 1"""	611966				11572484	Standard	NM_031466		Approved	IKBKBBP, NIBP, KIAA1882, T1, TRS120, MRT13	uc003yvh.2	Q96Q05	OTTHUMG00000164187	ENST00000438773.2:c.456C>T	8.37:g.141461017G>A		45.0	0.0	0		51.0	27.0	0.529412	NM_031466	Q4VTT3|Q658K7|Q6P149|Q6ZQT3|Q7L5C4|Q86Y21|Q96SL2|Q9BQA2	Silent	SNP	ENST00000438773.2	37	CCDS55278.1	21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	13	0.017150395778364115	G	8.082	0.772536	0.16051	0.003177	0.015116	ENSG00000167632	ENST00000520857	.	.	.	5.61	-2.44	0.06502	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.0785	0.36536	0.538:0.1001:0.3619:0.0	.	.	.	.	X	5	.	.	R	-	1	2	TRAPPC9	141530199	0.083000	0.21467	0.973000	0.42090	0.755000	0.42902	-0.396000	0.07278	-0.397000	0.07691	-0.812000	0.03155	CGA	G|0.989;A|0.011	0.011	strong		0.572	TRAPPC9-002	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000377749.1	NM_031466	
NGFR	4804	hgsc.bcm.edu	37	17	47579567	47579567	+	Splice_Site	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:47579567G>A	ENST00000172229.3	+	2	333		c.e2+1		NGFR_ENST00000504201.1_Splice_Site	NM_002507.3	NP_002498.1	P08138	TNR16_HUMAN	nerve growth factor receptor						apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|central nervous system development (GO:0007417)|circadian regulation of gene expression (GO:0032922)|detection of temperature stimulus (GO:0016048)|glucose homeostasis (GO:0042593)|hair follicle morphogenesis (GO:0031069)|intracellular protein transport (GO:0006886)|membrane protein intracellular domain proteolysis (GO:0031293)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell cycle (GO:0045786)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of hair follicle development (GO:0051799)|nerve development (GO:0021675)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of axonogenesis (GO:0050772)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of odontogenesis of dentin-containing tooth (GO:0042488)|regulation of axonogenesis (GO:0050770)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of glucose import in response to insulin stimulus (GO:2001273)	cell surface (GO:0009986)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|neuronal postsynaptic density (GO:0097481)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)	death receptor activity (GO:0005035)|Rab GTPase binding (GO:0017137)|receptor activity (GO:0004872)|signal transducer activity (GO:0004871)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(1)|lung(7)|ovary(1)	17	all_cancers(4;1.45e-13)|Breast(4;6.34e-28)|all_epithelial(4;4.95e-17)					TGCCTGGACAGTGAGTAGAGG	0.637																																					.		Atlas-SNP	.											.	NGFR	46	.	0			c.208+1G>A						PASS	.						47.0	42.0	44.0					17																	47579567		2203	4300	6503	SO:0001630	splice_region_variant	4804	exon2			TGGACAGTGAGTA	M14764	CCDS11549.1	17q21-q22	2013-05-22	2010-04-28		ENSG00000064300	ENSG00000064300		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	7809	protein-coding gene	gene with protein product	"""low affinity nerve growth factor receptor"", ""TNFR superfamily, member 16"""	162010	"""nerve growth factor receptor (TNFR superfamily, member 16)"""			3022937, 3006050	Standard	NM_002507		Approved	TNFRSF16, CD271, p75NTR	uc002ioz.4	P08138	OTTHUMG00000161495	ENST00000172229.3:c.208+1G>A	17.37:g.47579567G>A		26.0	0.0	0		35.0	9.0	0.257143	NM_002507	B2R961|B4E096	Splice_Site	SNP	ENST00000172229.3	37	CCDS11549.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.132712	0.77662	.	.	ENSG00000064300	ENST00000172229	.	.	.	5.33	5.33	0.75918	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8004	0.88585	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NGFR	44934566	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	9.150000	0.94667	2.513000	0.84729	0.561000	0.74099	.	.	.	none		0.637	NGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365150.1		Intron
FAM171B	165215	hgsc.bcm.edu	37	2	187605000	187605000	+	Missense_Mutation	SNP	G	G	A	rs73979354	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:187605000G>A	ENST00000304698.5	+	2	487	c.284G>A	c.(283-285)cGt>cAt	p.R95H		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	95						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)			NS(1)|breast(6)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(10)|lung(22)|ovary(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						ATCATCAGTCGTCAGTACCTG	0.403													G|||	72	0.014377	0.0393	0.0115	5008	,	,		19566	0.0		0.008	False		,,,				2504	0.0041				p.R95H		Atlas-SNP	.											.	FAM171B	146	.	0			c.G284A						PASS	.	G	HIS/ARG	156,4250	105.6+/-144.1	2,152,2049	106.0	91.0	96.0		284	5.3	1.0	2	dbSNP_130	96	40,8560	26.8+/-75.7	0,40,4260	yes	missense	FAM171B	NM_177454.3	29	2,192,6309	AA,AG,GG		0.4651,3.5406,1.507	benign	95/827	187605000	196,12810	2203	4300	6503	SO:0001583	missense	165215	exon2			TCAGTCGTCAGTA	AF361495	CCDS33347.1	2q32.2	2008-06-16	2008-06-16	2008-06-16	ENSG00000144369	ENSG00000144369			29412	protein-coding gene	gene with protein product			"""KIAA1946"""	KIAA1946		11853319	Standard	NM_177454		Approved	FLJ34104	uc002ups.3	Q6P995	OTTHUMG00000154278	ENST00000304698.5:c.284G>A	2.37:g.187605000G>A	ENSP00000304108:p.Arg95His	136.0	0.0	0		107.0	55.0	0.514019	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	30	0.013736263736263736	18	0.036585365853658534	6	0.016574585635359115	0	0.0	6	0.0079155672823219	G	9.869	1.198429	0.22037	0.035406	0.004651	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.31769	1.48	6.16	5.26	0.73747	.	0.252210	0.41938	N	0.000786	T	0.03053	0.0090	N	0.08118	0	0.34129	D	0.665083	B;B	0.19583	0.037;0.037	B;B	0.12837	0.008;0.008	T	0.17623	-1.0363	10	0.22706	T	0.39	-4.6378	7.6817	0.28518	0.227:0.0:0.773:0.0	.	95;96	Q6P995;A8K122	F171B_HUMAN;.	H	95	ENSP00000304108:R95H	ENSP00000272804:R95H	R	+	2	0	FAM171B	187313245	1.000000	0.71417	0.997000	0.53966	0.892000	0.51952	2.871000	0.48459	1.557000	0.49525	0.650000	0.86243	CGT	G|0.987;A|0.013	0.013	strong		0.403	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
ARAP3	64411	hgsc.bcm.edu	37	5	141041735	141041735	+	Missense_Mutation	SNP	G	G	A	rs536504402		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:141041735G>A	ENST00000239440.4	-	20	2953	c.2888C>T	c.(2887-2889)tCg>tTg	p.S963L	ARAP3_ENST00000508305.1_Intron|ARAP3_ENST00000513878.1_Missense_Mutation_p.S625L|ARAP3_ENST00000512390.1_5'UTR	NM_022481.5	NP_071926.4	Q8WWN8	ARAP3_HUMAN	ArfGAP with RhoGAP domain, ankyrin repeat and PH domain 3	963	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				cytoskeleton organization (GO:0007010)|negative regulation of cell migration (GO:0030336)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Rho protein signal transduction (GO:0035024)|regulation of ARF GTPase activity (GO:0032312)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	ARF GTPase activator activity (GO:0008060)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			NS(1)|breast(7)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(1)|prostate(2)|skin(4)|stomach(1)	53						GAGCTTCACCGACCGGGCATC	0.617													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17730	0.0		0.0	False		,,,				2504	0.0				p.S963L		Atlas-SNP	.											.	ARAP3	139	.	0			c.C2888T						PASS	.						116.0	114.0	115.0					5																	141041735		2203	4300	6503	SO:0001583	missense	64411	exon20			TTCACCGACCGGG	AJ310567	CCDS4266.1	5q31.3	2013-01-11	2008-09-22	2008-09-22	ENSG00000120318	ENSG00000120318		"""ADP-ribosylation factor GTPase activating proteins"", ""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"", ""Ankyrin repeat domain containing"""	24097	protein-coding gene	gene with protein product		606647	"""centaurin, delta 3"""	CENTD3		11804589, 12015138	Standard	XM_005268497		Approved	FLJ21065, DRAG1	uc003llm.3	Q8WWN8	OTTHUMG00000129610	ENST00000239440.4:c.2888C>T	5.37:g.141041735G>A	ENSP00000239440:p.Ser963Leu	123.0	0.0	0		129.0	31.0	0.24031	NM_022481	B4DIT1|D3DQE3	Missense_Mutation	SNP	ENST00000239440.4	37	CCDS4266.1	.	.	.	.	.	.	.	.	.	.	G	32	5.167079	0.94768	.	.	ENSG00000120318	ENST00000239440;ENST00000513878	T;T	0.10477	2.87;2.87	5.27	5.27	0.74061	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.129855	0.45606	D	0.000345	T	0.18341	0.0440	L	0.33624	1.015	0.44155	D	0.996956	D;D	0.76494	0.995;0.999	P;P	0.61132	0.884;0.833	T	0.00202	-1.1925	10	0.49607	T	0.09	.	11.6675	0.51383	0.0:0.0:0.7116:0.2884	.	625;963	B4DIT1;Q8WWN8	.;ARAP3_HUMAN	L	963;625	ENSP00000239440:S963L;ENSP00000421468:S625L	ENSP00000239440:S963L	S	-	2	0	ARAP3	141021919	1.000000	0.71417	0.997000	0.53966	0.997000	0.91878	6.365000	0.73090	2.741000	0.93983	0.650000	0.86243	TCG	.	.	none		0.617	ARAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251805.1	NM_022481	
ZDBF2	57683	hgsc.bcm.edu	37	2	207170242	207170242	+	Silent	SNP	T	T	C	rs112075178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207170242T>C	ENST00000374423.3	+	5	1376	c.990T>C	c.(988-990)caT>caC	p.H330H		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	330							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						CAAAGAACCATGAGGAATTCT	0.358													T|||	116	0.0231629	0.0741	0.0159	5008	,	,		19800	0.0		0.006	False		,,,				2504	0.001				p.H330H		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T990C						PASS	.	T		248,3394		8,232,1581	47.0	46.0	46.0		990	-1.2	0.0	2	dbSNP_132	46	70,8096		0,70,4013	no	coding-synonymous	ZDBF2	NM_020923.1		8,302,5594	CC,CT,TT		0.8572,6.8094,2.6931		330/2355	207170242	318,11490	1821	4083	5904	SO:0001819	synonymous_variant	57683	exon5			GAACCATGAGGAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.990T>C	2.37:g.207170242T>C		74.0	0.0	0		48.0	25.0	0.520833	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			T|0.979;C|0.021	0.021	strong		0.358	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
PERP	64065	hgsc.bcm.edu	37	6	138428379	138428379	+	Silent	SNP	G	G	A	rs145663845	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:138428379G>A	ENST00000421351.3	-	1	269	c.99C>T	c.(97-99)cgC>cgT	p.R33R		NM_022121.4	NP_071404.2	Q96FX8	PERP_HUMAN	PERP, TP53 apoptosis effector	33					activation of cysteine-type endopeptidase activity (GO:0097202)|amelogenesis (GO:0097186)|desmosome organization (GO:0002934)|heterotypic cell-cell adhesion (GO:0034113)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of proteolysis (GO:0045862)	cell junction (GO:0030054)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)				breast(1)|cervix(1)|endometrium(1)|lung(1)|prostate(1)	5	Breast(32;0.0799)|Colorectal(23;0.24)			GBM - Glioblastoma multiforme(68;0.000878)|OV - Ovarian serous cystadenocarcinoma(155;0.000997)		GCAACCAGCCGCGGCCGGCCA	0.682													g|||	24	0.00479233	0.0008	0.0058	5008	,	,		11494	0.0		0.0089	False		,,,				2504	0.0102				p.R33R		Atlas-SNP	.											.	PERP	15	.	0			c.C99T						PASS	.	G		12,4260		0,12,2124	31.0	39.0	36.0		99	-0.4	1.0	6	dbSNP_134	36	95,8285		0,95,4095	no	coding-synonymous	PERP	NM_022121.4		0,107,6219	AA,AG,GG		1.1337,0.2809,0.8457		33/194	138428379	107,12545	2136	4190	6326	SO:0001819	synonymous_variant	64065	exon1			CCAGCCGCGGCCG	AF317550	CCDS5188.1	6q24	2014-04-29			ENSG00000112378	ENSG00000112378			17637	protein-coding gene	gene with protein product	"""keratinocyte associated protein 1"""	609301				11062687	Standard	NM_022121		Approved	PIGPC1, dJ496H19.1, KCP1, THW, KRTCAP1	uc003qht.2	Q96FX8	OTTHUMG00000015668	ENST00000421351.3:c.99C>T	6.37:g.138428379G>A		64.0	0.0	0		75.0	37.0	0.493333	NM_022121	B2RB73|E1P590|Q8IWS3|Q8N1J6|Q8NC16|Q9H1C5|Q9H230	Silent	SNP	ENST00000421351.3	37	CCDS5188.1																																																																																			G|0.993;A|0.007	0.007	strong		0.682	PERP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042423.2	NM_022121	
LATS2	26524	hgsc.bcm.edu	37	13	21563311	21563311	+	Missense_Mutation	SNP	G	G	A	rs77919685	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:21563311G>A	ENST00000382592.4	-	4	1013	c.608C>T	c.(607-609)gCg>gTg	p.A203V	LATS2_ENST00000472754.1_5'UTR|LATS2_ENST00000542899.1_Missense_Mutation_p.A203V	NM_014572.2	NP_055387.2			large tumor suppressor kinase 2											breast(4)|central_nervous_system(3)|endometrium(2)|kidney(2)|large_intestine(7)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(2)	45		all_cancers(29;4.74e-22)|all_epithelial(30;1.45e-18)|all_lung(29;4.69e-16)|Lung SC(185;0.0262)|Hepatocellular(188;0.244)		all cancers(112;0.000781)|Epithelial(112;0.00144)|OV - Ovarian serous cystadenocarcinoma(117;0.0183)|Lung(94;0.0375)|LUSC - Lung squamous cell carcinoma(192;0.104)		CTCCTCCAGCGCCGTGGGGCC	0.692													G|||	103	0.0205671	0.0	0.0216	5008	,	,		14848	0.0248		0.0249	False		,,,				2504	0.0389				p.A203V		Atlas-SNP	.											.	LATS2	176	.	0			c.C608T						PASS	.	G	VAL/ALA	19,4387	25.3+/-52.1	0,19,2184	50.0	45.0	46.0		608	3.0	0.0	13	dbSNP_131	46	149,8449	71.0+/-133.6	4,141,4154	yes	missense	LATS2	NM_014572.2	64	4,160,6338	AA,AG,GG		1.733,0.4312,1.2919	benign	203/1089	21563311	168,12836	2203	4299	6502	SO:0001583	missense	26524	exon4			TCCAGCGCCGTGG	AB028019	CCDS9294.1	13q11-q12	2013-04-25	2013-04-25		ENSG00000150457	ENSG00000150457			6515	protein-coding gene	gene with protein product		604861	"""LATS (large tumor suppressor, Drosophila) homolog 2"", ""LATS, large tumor suppressor, homolog 2 (Drosophila)"""			10673337	Standard	NM_014572		Approved		uc001unr.4	Q9NRM7	OTTHUMG00000016531	ENST00000382592.4:c.608C>T	13.37:g.21563311G>A	ENSP00000372035:p.Ala203Val	28.0	0.0	0		44.0	23.0	0.522727	NM_014572		Missense_Mutation	SNP	ENST00000382592.4	37	CCDS9294.1	43	0.019688644688644688	0	0.0	6	0.016574585635359115	18	0.03146853146853147	19	0.025065963060686015	G	7.001	0.554851	0.13436	0.004312	0.01733	ENSG00000150457	ENST00000382592;ENST00000542899	T;T	0.26957	1.7;1.7	5.05	3.04	0.35103	.	1.593970	0.03426	N	0.207082	T	0.03739	0.0106	N	0.02011	-0.69	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.16928	-1.0386	10	0.52906	T	0.07	.	5.4494	0.16554	0.7351:0.0:0.2649:0.0	.	203	Q9NRM7	LATS2_HUMAN	V	203	ENSP00000372035:A203V;ENSP00000441817:A203V	ENSP00000372035:A203V	A	-	2	0	LATS2	20461311	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	1.484000	0.35508	0.425000	0.26087	0.485000	0.47835	GCG	G|0.986;A|0.014	0.014	strong		0.692	LATS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044102.1		
FAM151B	167555	hgsc.bcm.edu	37	5	79797690	79797690	+	Nonsense_Mutation	SNP	G	G	A	rs149355931		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:79797690G>A	ENST00000282226.4	+	2	260	c.105G>A	c.(103-105)tgG>tgA	p.W35*	FAM151B_ENST00000511718.1_3'UTR	NM_205548.2	NP_991111.2	Q6UXP7	F151B_HUMAN	family with sequence similarity 151, member B	35										breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(1)	7		Lung NSC(167;0.0427)|all_lung(232;0.0464)|Ovarian(174;0.113)		OV - Ovarian serous cystadenocarcinoma(54;8.21e-47)|Epithelial(54;8.3e-42)|all cancers(79;1.97e-36)		AGATCACCTGGTATCATGCAG	0.358													G|||	1	0.000199681	0.0	0.0014	5008	,	,		11791	0.0		0.0	False		,,,				2504	0.0				p.W35X		Atlas-SNP	.											.	FAM151B	25	.	0			c.G105A						PASS	.	G	stop/TRP	0,4406		0,0,2203	165.0	166.0	166.0		105	5.9	1.0	5	dbSNP_134	166	5,8595	4.3+/-15.6	0,5,4295	yes	stop-gained	FAM151B	NM_205548.2		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		35/277	79797690	5,13001	2203	4300	6503	SO:0001587	stop_gained	167555	exon2			CACCTGGTATCAT		CCDS4051.1	5q14.1	2007-12-18	2007-12-18		ENSG00000152380	ENSG00000152380			33716	protein-coding gene	gene with protein product							Standard	NM_205548		Approved	UNQ9217	uc003kgv.2	Q6UXP7	OTTHUMG00000131303	ENST00000282226.4:c.105G>A	5.37:g.79797690G>A	ENSP00000282226:p.Trp35*	197.0	0.0	0		208.0	99.0	0.475962	NM_205548	A2RRE4	Nonsense_Mutation	SNP	ENST00000282226.4	37	CCDS4051.1	.	.	.	.	.	.	.	.	.	.	G	37	6.368955	0.97511	0.0	5.81E-4	ENSG00000152380	ENST00000282226	.	.	.	5.92	5.92	0.95590	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.2276	19.0783	0.93171	0.0:0.0:1.0:0.0	.	.	.	.	X	35	.	ENSP00000282226:W35X	W	+	3	0	FAM151B	79833446	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.660000	0.68018	2.803000	0.96430	0.591000	0.81541	TGG	G|1.000;A|0.000	0.000	strong		0.358	FAM151B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254072.1	NM_205548	
MEGF11	84465	hgsc.bcm.edu	37	15	66206303	66206303	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:66206303T>C	ENST00000409699.2	-	20	2654	c.2482A>G	c.(2482-2484)Atg>Gtg	p.M828V	MEGF11_ENST00000395625.2_Missense_Mutation_p.M753V|MEGF11_ENST00000395614.1_Start_Codon_SNP_p.M1V|MEGF11_ENST00000288745.3_Missense_Mutation_p.M753V|MEGF11_ENST00000478721.1_5'UTR|MEGF11_ENST00000422354.1_Missense_Mutation_p.M828V|MEGF11_ENST00000360698.4_3'UTR			A6BM72	MEG11_HUMAN	multiple EGF-like-domains 11	828					homotypic cell-cell adhesion (GO:0034109)|retina layer formation (GO:0010842)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	19						TCCTCCATCATGAGGGCAGCT	0.607																																					p.M828V		Atlas-SNP	.											.	MEGF11	70	.	0			c.A2482G						PASS	.						39.0	37.0	38.0					15																	66206303		2201	4299	6500	SO:0001583	missense	84465	exon20			CCATCATGAGGGC	AB058677	CCDS10213.2	15q22.31	2006-03-31			ENSG00000157890	ENSG00000157890			29635	protein-coding gene	gene with protein product		612454				11347906	Standard	NM_032445		Approved	KIAA1781, DKFZp434L121	uc002apm.2	A6BM72	OTTHUMG00000133175	ENST00000409699.2:c.2482A>G	15.37:g.66206303T>C	ENSP00000386908:p.Met828Val	64.0	0.0	0		56.0	25.0	0.446429	NM_032445	Q17R86|Q6UXS5|Q8ND91|Q96KG6	Missense_Mutation	SNP	ENST00000409699.2	37	CCDS10213.2	.	.	.	.	.	.	.	.	.	.	T	18.50	3.636511	0.67130	.	.	ENSG00000157890	ENST00000409699;ENST00000288745;ENST00000422354;ENST00000395625;ENST00000395614	T;T;T;T;T	0.34472	2.4;2.4;2.4;2.4;1.36	4.65	4.65	0.58169	.	0.000000	0.51477	U	0.000100	T	0.16342	0.0393	N	0.04508	-0.205	0.80722	D	1	B;B	0.25441	0.092;0.126	B;B	0.25987	0.065;0.039	T	0.10042	-1.0647	10	0.02654	T	1	.	14.2339	0.65911	0.0:0.0:0.0:1.0	.	828;753	A6BM72;A6BM72-2	MEG11_HUMAN;.	V	828;753;828;753;1	ENSP00000386908:M828V;ENSP00000288745:M753V;ENSP00000414475:M828V;ENSP00000378987:M753V;ENSP00000378976:M1V	ENSP00000288745:M753V	M	-	1	0	MEGF11	63993357	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.659000	0.61504	1.948000	0.56530	0.454000	0.30748	ATG	.	.	none		0.607	MEGF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329307.2	NM_032445	
CCDC3	83643	hgsc.bcm.edu	37	10	12940631	12940631	+	Missense_Mutation	SNP	C	C	T	rs145872952		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:12940631C>T	ENST00000378825.3	-	3	724	c.598G>A	c.(598-600)Gtc>Atc	p.V200I	CCDC3_ENST00000378839.1_Missense_Mutation_p.V75I	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	200						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			AGTTTCTTGACGTGGTCCTCC	0.602													C|||	1	0.000199681	0.0	0.0	5008	,	,		16856	0.0		0.001	False		,,,				2504	0.0				p.V200I		Atlas-SNP	.											.	CCDC3	27	.	0			c.G598A						PASS	.	C	ILE/VAL	0,4406		0,0,2203	72.0	62.0	65.0		598	5.4	1.0	10	dbSNP_134	65	4,8596	3.7+/-12.6	0,4,4296	yes	missense	CCDC3	NM_031455.3	29	0,4,6499	TT,TC,CC		0.0465,0.0,0.0308	benign	200/271	12940631	4,13002	2203	4300	6503	SO:0001583	missense	83643	exon3			TCTTGACGTGGTC	BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.598G>A	10.37:g.12940631C>T	ENSP00000368102:p.Val200Ile	83.0	0.0	0		109.0	51.0	0.46789	NM_031455	Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	37	CCDS7093.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	23.8	4.455433	0.84209	0.0	4.65E-4	ENSG00000151468	ENST00000378839;ENST00000378825	T	0.17691	2.26	5.42	5.42	0.78866	.	0.330512	0.26106	N	0.026308	T	0.18257	0.0438	M	0.64997	1.995	0.40106	D	0.976437	P	0.44946	0.846	B	0.30251	0.113	T	0.10245	-1.0638	10	0.56958	D	0.05	-25.0542	18.1996	0.89833	0.0:1.0:0.0:0.0	.	200	Q9BQI4	CCDC3_HUMAN	I	75;200	ENSP00000368116:V75I	ENSP00000368102:V200I	V	-	1	0	CCDC3	12980637	0.999000	0.42202	0.998000	0.56505	0.880000	0.50808	4.526000	0.60566	2.550000	0.86006	0.561000	0.74099	GTC	C|1.000;T|0.000	0.000	strong		0.602	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1	NM_031455	
MMP27	64066	hgsc.bcm.edu	37	11	102567522	102567522	+	Silent	SNP	G	G	A	rs201248506	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:102567522G>A	ENST00000260229.4	-	5	755	c.664C>T	c.(664-666)Ctg>Ttg	p.L222L		NM_022122.2	NP_071405.2	Q9H306	MMP27_HUMAN	matrix metallopeptidase 27	222					collagen catabolic process (GO:0030574)	proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|liver(2)|lung(12)|ovary(2)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	45	all_cancers(8;0.000843)|all_epithelial(12;0.00362)|Lung NSC(15;0.21)	all_hematologic(158;0.00092)|Acute lymphoblastic leukemia(157;0.000967)	Epithelial(9;0.0509)|Lung(13;0.0696)|LUSC - Lung squamous cell carcinoma(19;0.13)|all cancers(10;0.176)	BRCA - Breast invasive adenocarcinoma(274;0.0151)	Marimastat(DB00786)	GAGAGCCCCAGTGCATGACCA	0.423													G|||	2	0.000399361	0.0	0.0	5008	,	,		18938	0.0		0.002	False		,,,				2504	0.0				p.L222L		Atlas-SNP	.											.	MMP27	84	.	0			c.C664T						PASS	.	G		0,4406		0,0,2203	81.0	69.0	73.0		664	3.9	0.9	11		73	3,8595	3.0+/-9.4	0,3,4296	no	coding-synonymous	MMP27	NM_022122.2		0,3,6499	AA,AG,GG		0.0349,0.0,0.0231		222/514	102567522	3,13001	2203	4299	6502	SO:0001819	synonymous_variant	64066	exon5			GCCCCAGTGCATG	AF195192	CCDS8319.1	11q24	2008-07-18	2005-08-08		ENSG00000137675	ENSG00000137675			14250	protein-coding gene	gene with protein product	"""matrix metalloprotease 27"""		"""matrix metalloproteinase 27"""			10419448	Standard	NM_022122		Approved		uc001phd.1	Q9H306	OTTHUMG00000168099	ENST00000260229.4:c.664C>T	11.37:g.102567522G>A		55.0	0.0	0		72.0	36.0	0.5	NM_022122	Q6UWK6	Silent	SNP	ENST00000260229.4	37	CCDS8319.1																																																																																			G|0.999;A|0.001	0.001	strong		0.423	MMP27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398128.1	NM_022122	
UNC5C	8633	hgsc.bcm.edu	37	4	96140151	96140151	+	Silent	SNP	C	C	T	rs61741188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:96140151C>T	ENST00000453304.1	-	9	1962	c.1614G>A	c.(1612-1614)tcG>tcA	p.S538S	UNC5C_ENST00000506749.1_Silent_p.S557S	NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	538	ZU5. {ECO:0000255|PROSITE- ProRule:PRU00485}.				anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|brain development (GO:0007420)|positive regulation of apoptotic process (GO:0043065)|regulation of cell migration (GO:0030334)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)			NS(1)|breast(2)|endometrium(2)|kidney(1)|large_intestine(14)|lung(25)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	55		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;8.72e-10)		GACCTCCCAGCGAGTTGAAGC	0.443													C|||	151	0.0301518	0.0318	0.0202	5008	,	,		20428	0.0		0.0219	False		,,,				2504	0.0746				p.S538S		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1614A						PASS	.	C		134,4272	98.5+/-137.1	0,134,2069	108.0	86.0	94.0		1614	-1.9	0.9	4	dbSNP_129	94	231,8369	94.0+/-155.9	3,225,4072	no	coding-synonymous	UNC5C	NM_003728.3		3,359,6141	TT,TC,CC		2.686,3.0413,2.8064		538/932	96140151	365,12641	2203	4300	6503	SO:0001819	synonymous_variant	8633	exon9			TCCCAGCGAGTTG	AF055634	CCDS3643.1	4q21-q23	2013-01-11	2001-11-28		ENSG00000182168	ENSG00000182168		"""Immunoglobulin superfamily / I-set domain containing"""	12569	protein-coding gene	gene with protein product		603610	"""unc5 (C.elegans homolog) c"""			9126742, 9782087	Standard	NM_003728		Approved		uc003hto.3	O95185	OTTHUMG00000130989	ENST00000453304.1:c.1614G>A	4.37:g.96140151C>T		91.0	0.0	0		89.0	37.0	0.41573	NM_003728	Q8IUT0	Silent	SNP	ENST00000453304.1	37	CCDS3643.1																																																																																			C|0.977;T|0.023	0.023	strong		0.443	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
AP4M1	9179	hgsc.bcm.edu	37	7	99704104	99704104	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99704104G>A	ENST00000359593.4	+	14	1262	c.1104G>A	c.(1102-1104)gtG>gtA	p.V368V	AP4M1_ENST00000421755.1_Silent_p.V368V|AP4M1_ENST00000422582.1_Silent_p.V240V|AP4M1_ENST00000429084.1_Silent_p.V375V	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	368	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGCCTCGGGTGCAAGGAGGCT	0.632																																					p.V368V	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.G1104A						PASS	.						42.0	45.0	44.0					7																	99704104		2203	4300	6503	SO:0001819	synonymous_variant	9179	exon14			TCGGGTGCAAGGA	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"""mu-adaptin-related protein-2"", ""mu subunit of AP-4"", ""AP-4 adapter complex mu subunit"", ""adaptor-related protein complex AP-4 mu4 subunit"""	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.1104G>A	7.37:g.99704104G>A		46.0	0.0	0		47.0	22.0	0.468085	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Silent	SNP	ENST00000359593.4	37	CCDS5685.1	.	.	.	.	.	.	.	.	.	.	G	9.825	1.186877	0.21870	.	.	ENSG00000221838	ENST00000445295	.	.	.	4.81	-3.93	0.04143	.	.	.	.	.	T	0.36248	0.0960	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.33343	-0.9872	4	.	.	.	-22.5569	0.9269	0.01327	0.4879:0.1198:0.1523:0.2401	.	.	.	.	Y	94	.	.	C	+	2	0	AP4M1	99542040	0.957000	0.32711	0.976000	0.42696	0.997000	0.91878	0.023000	0.13533	-0.749000	0.04747	0.561000	0.74099	TGC	.	.	none		0.632	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	
PFAS	5198	hgsc.bcm.edu	37	17	8172506	8172506	+	Missense_Mutation	SNP	T	T	G	rs62637606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:8172506T>G	ENST00000314666.6	+	28	4074	c.3941T>G	c.(3940-3942)tTt>tGt	p.F1314C	PFAS_ENST00000545834.1_Missense_Mutation_p.F890C	NM_012393.2	NP_036525.1	O15067	PUR4_HUMAN	phosphoribosylformylglycinamidine synthase	1314					'de novo' IMP biosynthetic process (GO:0006189)|glutamine metabolic process (GO:0006541)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase metabolic process (GO:0006144)|purine ribonucleoside monophosphate biosynthetic process (GO:0009168)|response to drug (GO:0042493)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|phosphoribosylformylglycinamidine synthase activity (GO:0004642)			central_nervous_system(3)|endometrium(8)|kidney(2)|large_intestine(2)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	35					L-Glutamine(DB00130)	CCCCCTCCATTTGATACTCTG	0.637													T|||	130	0.0259585	0.0023	0.0591	5008	,	,		14648	0.0		0.0467	False		,,,				2504	0.0399				p.F1314C		Atlas-SNP	.											.	PFAS	91	.	0			c.T3941G						PASS	.	T	CYS/PHE	60,4346	57.4+/-93.9	1,58,2144	45.0	45.0	45.0		3941	5.5	1.0	17	dbSNP_129	45	549,8051	150.1+/-205.1	19,511,3770	yes	missense	PFAS	NM_012393.2	205	20,569,5914	GG,GT,TT		6.3837,1.3618,4.6825	benign	1314/1339	8172506	609,12397	2203	4300	6503	SO:0001583	missense	5198	exon28			CTCCATTTGATAC	AB002359	CCDS11136.1	17p13.1	2008-07-31	2008-07-31		ENSG00000178921	ENSG00000178921	6.3.5.3		8863	protein-coding gene	gene with protein product	"""FGAR amidotransferase"""	602133				8110788	Standard	NM_012393		Approved	PURL, FGARAT, KIAA0361	uc002gkr.3	O15067	OTTHUMG00000108188	ENST00000314666.6:c.3941T>G	17.37:g.8172506T>G	ENSP00000313490:p.Phe1314Cys	92.0	0.0	0		93.0	45.0	0.483871	NM_012393	A6H8V8	Missense_Mutation	SNP	ENST00000314666.6	37	CCDS11136.1	69	0.03159340659340659	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	36	0.047493403693931395	T	14.30	2.494705	0.44352	0.013618	0.063837	ENSG00000178921	ENST00000545834;ENST00000314666;ENST00000546020	T;T	0.30981	1.51;2.25	5.46	5.46	0.80206	Glutamine amidotransferase type 1 (1);	0.179053	0.46145	D	0.000302	T	0.01287	0.0042	L	0.55017	1.72	0.38160	D	0.939011	B	0.28998	0.23	B	0.32211	0.142	T	0.02698	-1.1122	10	0.87932	D	0	-5.1281	13.4903	0.61390	0.0:0.0:0.0:1.0	rs62637606	1314	O15067	PUR4_HUMAN	C	890;1314;723	ENSP00000441706:F890C;ENSP00000313490:F1314C	ENSP00000313490:F1314C	F	+	2	0	PFAS	8113231	0.941000	0.31946	0.969000	0.41365	0.996000	0.88848	1.167000	0.31847	2.057000	0.61298	0.533000	0.62120	TTT	T|0.957;G|0.043	0.043	strong		0.637	PFAS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000226994.2		
SORCS1	114815	hgsc.bcm.edu	37	10	108432670	108432670	+	Missense_Mutation	SNP	G	G	A	rs143914023		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:108432670G>A	ENST00000263054.6	-	15	2021	c.2014C>T	c.(2014-2016)Cgg>Tgg	p.R672W	SORCS1_ENST00000369698.1_Missense_Mutation_p.R207W|SORCS1_ENST00000344440.6_Missense_Mutation_p.R672W	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	672					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)			breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		TCGGCACACCGTCTATCAAAA	0.488																																					p.R672W		Atlas-SNP	.											.	SORCS1	534	.	0			c.C2014T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG,TRP/ARG	0,4406		0,0,2203	84.0	70.0	75.0		2014,2014,2014,2014,2014,2014	-0.1	0.8	10	dbSNP_134	75	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense,missense	SORCS1	NM_001013031.2,NM_001206569.1,NM_001206570.1,NM_001206571.1,NM_001206572.1,NM_052918.4	101,101,101,101,101,101	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	672/1199,672/1180,672/1131,672/1160,672/1180,672/1169	108432670	1,13005	2203	4300	6503	SO:0001583	missense	114815	exon15			CACACCGTCTATC	AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.2014C>T	10.37:g.108432670G>A	ENSP00000263054:p.Arg672Trp	67.0	0.0	0		72.0	26.0	0.361111	NM_001206572	A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Missense_Mutation	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	G	18.71	3.681592	0.68042	0.0	1.16E-4	ENSG00000108018	ENST00000369698;ENST00000263054;ENST00000344440	T;T;T	0.29917	1.55;1.55;1.55	5.47	-0.143	0.13444	VPS10 (1);	0.132411	0.49305	N	0.000151	T	0.47691	0.1459	M	0.67953	2.075	0.40136	D	0.976777	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.75484	0.968;0.978;0.986;0.968;0.986	T	0.42137	-0.9469	9	.	.	.	-6.2946	11.4184	0.49967	0.064:0.0:0.2926:0.6433	.	672;672;672;672;672	A8K182;Q8WY21-4;Q8WY21-3;Q8WY21;Q8WY21-2	.;.;.;SORC1_HUMAN;.	W	207;672;672	ENSP00000358712:R207W;ENSP00000263054:R672W;ENSP00000345964:R672W	.	R	-	1	2	SORCS1	108422660	0.134000	0.22483	0.849000	0.33467	0.991000	0.79684	0.199000	0.17237	-0.009000	0.14296	0.563000	0.77884	CGG	G|1.000;A|0.000	0.000	weak		0.488	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4	NM_052918	
TSC1	7248	hgsc.bcm.edu	37	9	135771682	135771682	+	Silent	SNP	C	C	T	rs140352085	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135771682C>T	ENST00000298552.3	-	23	3656	c.3435G>A	c.(3433-3435)ccG>ccA	p.P1145P	TSC1_ENST00000440111.2_Silent_p.P1145P|TSC1_ENST00000545250.1_Silent_p.P1094P	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	1145					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)	p.?(1)		NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		CAACACTGTCCGGGGTCGGGG	0.498			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis				C|||	4	0.000798722	0.0	0.0029	5008	,	,		20397	0.0		0.0	False		,,,				2504	0.002				p.P1145P		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	.	TSC1	167	.	1	Unknown(1)	bone(1)	c.G3435A						PASS	.	C	,,	0,4406		0,0,2203	177.0	153.0	161.0		3435,3432,3282	-5.2	0.0	9	dbSNP_134	161	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous,coding-synonymous	TSC1	NM_000368.4,NM_001162426.1,NM_001162427.1	,,	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	,,	1145/1165,1144/1164,1094/1114	135771682	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	7248	exon23	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	ACTGTCCGGGGTC	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.3435G>A	9.37:g.135771682C>T		151.0	0.0	0		152.0	63.0	0.414474	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																			C|1.000;T|0.000	0.000	strong		0.498	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
FASN	2194	hgsc.bcm.edu	37	17	80044214	80044214	+	Silent	SNP	G	G	A	rs530379505		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80044214G>A	ENST00000306749.2	-	22	3866	c.3648C>T	c.(3646-3648)agC>agT	p.S1216S		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	1216					acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	CCAGGAGGCCGCTGAGCAGAG	0.672																																					p.S1216S	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.C3648T						PASS	.						26.0	23.0	24.0					17																	80044214		2184	4293	6477	SO:0001819	synonymous_variant	2194	exon22			GAGGCCGCTGAGC	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.3648C>T	17.37:g.80044214G>A		71.0	0.0	0		79.0	4.0	0.0506329	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Silent	SNP	ENST00000306749.2	37	CCDS11801.1																																																																																			.	.	none		0.672	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
KLHL12	59349	hgsc.bcm.edu	37	1	202863792	202863792	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:202863792G>A	ENST00000367261.3	-	9	1439	c.1221C>T	c.(1219-1221)agC>agT	p.S407S	KLHL12_ENST00000435533.3_Silent_p.S445S|KLHL12_ENST00000367259.1_Silent_p.S140S	NM_021633.2	NP_067646.1	Q53G59	KLH12_HUMAN	kelch-like family member 12	407	Interaction with DVL3.				COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|protein monoubiquitination (GO:0006513)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|ER to Golgi transport vesicle (GO:0030134)|Golgi membrane (GO:0000139)				NS(3)|breast(2)|endometrium(1)|large_intestine(1)|lung(6)|stomach(1)	14			BRCA - Breast invasive adenocarcinoma(75;0.166)			CTCCCAGCATGCTCCACTGGT	0.517																																					p.S407S		Atlas-SNP	.											.	KLHL12	50	.	0			c.C1221T						PASS	.						153.0	147.0	149.0					1																	202863792		2203	4300	6503	SO:0001819	synonymous_variant	59349	exon9			CAGCATGCTCCAC	AF190900	CCDS1429.1	1q32.1	2013-01-30	2013-01-30		ENSG00000117153	ENSG00000117153		"""Kelch-like"", ""BTB/POZ domain containing"""	19360	protein-coding gene	gene with protein product		614522	"""kelch-like 12 (Drosophila)"""			12477932	Standard	NM_021633		Approved	C3IP1	uc001gyo.1	Q53G59	OTTHUMG00000041385	ENST00000367261.3:c.1221C>T	1.37:g.202863792G>A		144.0	0.0	0		192.0	71.0	0.369792	NM_021633	A6NEN8|B7Z7B8|Q9HBX5	Silent	SNP	ENST00000367261.3	37	CCDS1429.1																																																																																			.	.	none		0.517	KLHL12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099151.1	NM_021633	
GPR116	221395	hgsc.bcm.edu	37	6	46846060	46846060	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:46846060C>T	ENST00000283296.7	-	10	1407	c.1119G>A	c.(1117-1119)ttG>ttA	p.L373L	GPR116_ENST00000265417.7_Silent_p.L373L|GPR116_ENST00000456426.2_Intron|GPR116_ENST00000362015.4_Silent_p.L373L	NM_001098518.1	NP_001091988.1	Q8IZF2	GP116_HUMAN	G protein-coupled receptor 116	373	Ig-like 2.				energy reserve metabolic process (GO:0006112)|fat cell differentiation (GO:0045444)|G-protein coupled receptor signaling pathway (GO:0007186)|glucose homeostasis (GO:0042593)|neuropeptide signaling pathway (GO:0007218)|regulation of lipid metabolic process (GO:0019216)|surfactant homeostasis (GO:0043129)	cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			breast(2)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(21)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59			Lung(136;0.192)			CTTCATTTGCCAAAATTTGGA	0.358																																					p.L373L	NSCLC(59;410 1274 8751 36715 50546)	Atlas-SNP	.											.	GPR116	133	.	0			c.G1119A						PASS	.						138.0	123.0	128.0					6																	46846060		2202	4300	6502	SO:0001819	synonymous_variant	221395	exon10			ATTTGCCAAAATT	AB018301	CCDS4919.1	6p12.3	2014-08-08			ENSG00000069122	ENSG00000069122		"""-"", ""GPCR / Class B : Orphans"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	19030	protein-coding gene	gene with protein product						12435584	Standard	NM_001098518		Approved	DKFZp564O1923, KIAA0758	uc003oyo.3	Q8IZF2	OTTHUMG00000014793	ENST00000283296.7:c.1119G>A	6.37:g.46846060C>T		219.0	0.0	0		208.0	54.0	0.259615	NM_015234	O94858|Q5TF06|Q6RGN2|Q86SP0|Q9Y3Z2	Silent	SNP	ENST00000283296.7	37	CCDS4919.1																																																																																			.	.	none		0.358	GPR116-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040806.2	NM_015234	
SIGLEC8	27181	hgsc.bcm.edu	37	19	51961519	51961519	+	Silent	SNP	C	C	A	rs140904107	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51961519C>A	ENST00000321424.3	-	1	189	c.123G>T	c.(121-123)ctG>ctT	p.L41L	SIGLEC8_ENST00000597352.1_5'Flank|SIGLEC8_ENST00000340550.5_Silent_p.L41L|SIGLEC8_ENST00000430817.1_Silent_p.L41L	NM_014442.2	NP_055257.2	Q9NYZ4	SIGL8_HUMAN	sialic acid binding Ig-like lectin 8	41	Ig-like V-type.				cell adhesion (GO:0007155)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|central_nervous_system(3)|endometrium(2)|kidney(4)|large_intestine(11)|liver(3)|lung(15)|ovary(2)|skin(4)|stomach(3)|urinary_tract(2)	50		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000627)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CATGGACACACAGGCCCTCCT	0.597																																					p.L41L		Atlas-SNP	.											SIGLEC8,NS,carcinoma,-2,1	SIGLEC8	130	1	0			c.G123T						PASS	.	C		2,4404		0,2,2201	141.0	124.0	130.0		123	-0.2	0.8	19	dbSNP_134	130	6,8594		0,6,4294	no	coding-synonymous	SIGLEC8	NM_014442.2		0,8,6495	AA,AC,CC		0.0698,0.0454,0.0615		41/500	51961519	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	27181	exon1			GACACACAGGCCC	AF195092	CCDS33086.1	19q13.33-q13.41	2013-01-29			ENSG00000105366	ENSG00000105366		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10877	protein-coding gene	gene with protein product		605639				10625619	Standard	XR_243922		Approved	SIGLEC-8, SAF2, SIGLEC8L, MGC59785	uc002pwt.3	Q9NYZ4		ENST00000321424.3:c.123G>T	19.37:g.51961519C>A		178.0	0.0	0		196.0	89.0	0.454082	NM_014442	Q7Z728	Silent	SNP	ENST00000321424.3	37	CCDS33086.1																																																																																			C|0.999;A|0.001	0.001	strong		0.597	SIGLEC8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463648.2	NM_014442	
GRID2IP	392862	hgsc.bcm.edu	37	7	6550540	6550540	+	Splice_Site	SNP	G	G	A	rs61732373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:6550540G>A	ENST00000457091.2	-	9	1553	c.1554C>T	c.(1552-1554)tgC>tgT	p.C518C	GRID2IP_ENST00000435185.1_Splice_Site_p.C334C|GRID2IP_ENST00000452113.1_Splice_Site_p.C327C	NM_001145118.1	NP_001138590.1	A4D2P6	GRD2I_HUMAN	glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein	518					long term synaptic depression (GO:0060292)	cell junction (GO:0030054)|postsynaptic membrane (GO:0045211)				endometrium(4)	4						CAGCCTTACCGCAGCTGAGGC	0.672													G|||	43	0.00858626	0.0015	0.0014	5008	,	,		16778	0.003		0.0219	False		,,,				2504	0.0153				p.C518C		Atlas-SNP	.											.	GRID2IP	82	.	0			c.C1554T						PASS	.	G		14,1370		0,14,678	32.0	33.0	33.0		1554	-4.4	0.5	7	dbSNP_129	33	111,3071		1,109,1481	yes	coding-synonymous-near-splice	GRID2IP	NM_001145118.1		1,123,2159	AA,AG,GG		3.4884,1.0116,2.7376		518/1212	6550540	125,4441	692	1591	2283	SO:0001630	splice_region_variant	392862	exon9			CTTACCGCAGCTG		CCDS47537.1	7p22	2007-10-05	2006-03-01		ENSG00000215045	ENSG00000215045			18464	protein-coding gene	gene with protein product		610639	"""glutamate receptor, ionotropic, delta 2 (Grid2) interacting protein 1"""			14612983	Standard	NM_001145118		Approved		uc011jwx.2	A4D2P6	OTTHUMG00000155531	ENST00000457091.2:c.1555+1C>T	7.37:g.6550540G>A		87.0	0.0	0		142.0	94.0	0.661972	NM_001145118		Silent	SNP	ENST00000457091.2	37	CCDS47537.1																																																																																			G|0.984;A|0.016	0.016	strong		0.672	GRID2IP-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340534.1	XM_294249	Silent
GPR98	84059	hgsc.bcm.edu	37	5	90079811	90079811	+	Silent	SNP	C	C	T	rs41311745	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:90079811C>T	ENST00000405460.2	+	67	13686	c.13590C>T	c.(13588-13590)ccC>ccT	p.P4530P	GPR98_ENST00000425867.2_Silent_p.P191P	NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	4530	Calx-beta 31. {ECO:0000305|PubMed:11606593}.				detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)			NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		TTGCTAATCCCAATTCCACAA	0.398													C|||	28	0.00559105	0.0008	0.0043	5008	,	,		18649	0.0		0.0219	False		,,,				2504	0.002				p.P4530P		Atlas-SNP	.											.	GPR98	605	.	0			c.C13590T						PASS	.	C		21,3687		0,21,1833	41.0	41.0	41.0		13590	2.7	1.0	5	dbSNP_127	41	157,8011		2,153,3929	no	coding-synonymous	GPR98	NM_032119.3		2,174,5762	TT,TC,CC		1.9221,0.5663,1.4988		4530/6307	90079811	178,11698	1854	4084	5938	SO:0001819	synonymous_variant	84059	exon67			TAATCCCAATTCC	AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.13590C>T	5.37:g.90079811C>T		90.0	0.0	0		126.0	60.0	0.47619	NM_032119	O75171|Q8TF58|Q9H0X5|Q9UL61	Silent	SNP	ENST00000405460.2	37	CCDS47246.1																																																																																			A|0.001;C|0.992;T|0.006	0.006	strong		0.398	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2	NM_032119	
SLC6A2	6530	hgsc.bcm.edu	37	16	55690874	55690874	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:55690874G>A	ENST00000379906.2	+	1	523	c.268G>A	c.(268-270)Ggc>Agc	p.G90S	SLC6A2_ENST00000568943.1_Missense_Mutation_p.G90S|SLC6A2_ENST00000414754.3_Missense_Mutation_p.G90S|SLC6A2_ENST00000566163.1_Missense_Mutation_p.G90S|SLC6A2_ENST00000219833.8_Missense_Mutation_p.G90S|SLC6A2_ENST00000561820.1_Missense_Mutation_p.G90S	NM_001043.3	NP_001034.1	P23975	SC6A2_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 2	90					monoamine transport (GO:0015844)|norepinephrine transport (GO:0015874)|response to drug (GO:0042493)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	monoamine transmembrane transporter activity (GO:0008504)|norepinephrine:sodium symporter activity (GO:0005334)			breast(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(20)|ovary(3)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(1)	41				BRCA - Breast invasive adenocarcinoma(181;0.01)|Kidney(780;0.0267)	Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Atomoxetine(DB00289)|Bupropion(DB01156)|Chlorphenamine(DB01114)|Citalopram(DB00215)|Clomipramine(DB01242)|Cocaine(DB00907)|Debrisoquin(DB04840)|Desipramine(DB01151)|Desvenlafaxine(DB06700)|Dexmethylphenidate(DB06701)|Dextroamphetamine(DB01576)|Dextromethorphan(DB00514)|Diethylpropion(DB00937)|Dopamine(DB00988)|Doxepin(DB01142)|Droxidopa(DB06262)|Duloxetine(DB00476)|Ephedra(DB01363)|Ephedrine(DB01364)|Ergotamine(DB00696)|Escitalopram(DB01175)|Ginkgo biloba(DB01381)|Guanadrel(DB00226)|Guanethidine(DB01170)|Imipramine(DB00458)|Iobenguane(DB06704)|Ketamine(DB01221)|Levomilnacipran(DB08918)|Levonordefrin(DB06707)|Loxapine(DB00408)|Maprotiline(DB00934)|Mazindol(DB00579)|Methamphetamine(DB01577)|Methylphenidate(DB00422)|Mianserin(DB06148)|Milnacipran(DB04896)|Mirtazapine(DB00370)|Nefazodone(DB01149)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Orphenadrine(DB01173)|Paroxetine(DB00715)|Pethidine(DB00454)|Phendimetrazine(DB01579)|Phenmetrazine(DB00830)|Phentermine(DB00191)|Protriptyline(DB00344)|Pseudoephedrine(DB00852)|Reboxetine(DB00234)|Sibutramine(DB01105)|Tapentadol(DB06204)|Tramadol(DB00193)|Trimipramine(DB00726)|Venlafaxine(DB00285)	CTACAAGAACGGCGGCGGTGA	0.622																																					p.G90S		Atlas-SNP	.											SLC6A2_ENST00000219833,colon,carcinoma,0,2	SLC6A2	189	2	0			c.G268A						PASS	.						69.0	74.0	72.0					16																	55690874		2198	4300	6498	SO:0001583	missense	6530	exon2			AAGAACGGCGGCG		CCDS10754.1, CCDS54011.1, CCDS58463.1	16q12.2	2013-07-19	2013-07-19		ENSG00000103546	ENSG00000103546		"""Solute carriers"""	11048	protein-coding gene	gene with protein product	"""norepinephrine transporter"""	163970	"""solute carrier family 6 (neurotransmitter transporter, noradrenalin), member 2"""	NET1, NAT1, SLC6A5		2008212	Standard	NM_001043		Approved	NET	uc021tio.1	P23975	OTTHUMG00000133208	ENST00000379906.2:c.268G>A	16.37:g.55690874G>A	ENSP00000369237:p.Gly90Ser	67.0	0.0	0		42.0	20.0	0.47619	NM_001172501	B2R707|B4DX48|Q96KH8	Missense_Mutation	SNP	ENST00000379906.2	37	CCDS10754.1	.	.	.	.	.	.	.	.	.	.	G	19.72	3.879435	0.72294	.	.	ENSG00000103546	ENST00000414754;ENST00000379906;ENST00000219833	D;D;D	0.87491	-2.26;-2.26;-2.26	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	D	0.96775	0.8947	H	0.99169	4.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98465	1.0598	10	0.87932	D	0	.	19.2658	0.93984	0.0:0.0:1.0:0.0	.	90;90	Q96KH8;P23975	.;SC6A2_HUMAN	S	90	ENSP00000394956:G90S;ENSP00000369237:G90S;ENSP00000219833:G90S	ENSP00000219833:G90S	G	+	1	0	SLC6A2	54248375	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.728000	0.98792	2.620000	0.88729	0.563000	0.77884	GGC	.	.	none		0.622	SLC6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256922.2		
GPR113	165082	hgsc.bcm.edu	37	2	26533898	26533898	+	Missense_Mutation	SNP	C	C	T	rs72811754	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:26533898C>T	ENST00000311519.1	-	11	2697	c.2698G>A	c.(2698-2700)Gtc>Atc	p.V900I	GPR113_ENST00000459892.1_5'UTR|GPR113_ENST00000541401.1_Missense_Mutation_p.V503I|GPR113_ENST00000333478.6_Missense_Mutation_p.V701I|GPR113_ENST00000421160.2_Missense_Mutation_p.V831I	NM_001145168.1	NP_001138640.1	Q8IZF5	GP113_HUMAN	G protein-coupled receptor 113	900					G-protein coupled receptor signaling pathway (GO:0007186)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			NS(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(4)|prostate(2)|skin(1)|stomach(1)|urinary_tract(1)	24	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCAGGGTGACACCTGCCAAC	0.612													C|||	9	0.00179712	0.0	0.0	5008	,	,		17885	0.0		0.006	False		,,,				2504	0.0031				p.V900I		Atlas-SNP	.											.	GPR113	134	.	0			c.G2698A						PASS	.	C	ILE/VAL,ILE/VAL,ILE/VAL	3,4403	6.2+/-15.9	0,3,2200	38.0	36.0	36.0		2698,2491,2101	0.9	0.0	2	dbSNP_130	36	36,8564	23.4+/-69.3	0,36,4264	yes	missense,missense,missense	GPR113	NM_001145168.1,NM_001145169.1,NM_153835.3	29,29,29	0,39,6464	TT,TC,CC		0.4186,0.0681,0.2999	benign,benign,benign	900/1080,831/998,701/874	26533898	39,12967	2203	4300	6503	SO:0001583	missense	165082	exon11			GGGTGACACCTGC	AB083619	CCDS33159.2, CCDS46238.1, CCDS46239.1	2p24.1	2014-08-08			ENSG00000173567	ENSG00000173567		"""-"", ""GPCR / Class B : Orphans"""	18989	protein-coding gene	gene with protein product						12435584	Standard	NM_153835		Approved	hGPCR37, PGR23	uc002rhe.4	Q8IZF5	OTTHUMG00000150225	ENST00000311519.1:c.2698G>A	2.37:g.26533898C>T	ENSP00000307831:p.Val900Ile	65.0	0.0	0		66.0	40.0	0.606061	NM_001145168	B4DF15|E9PEV1|Q53TA5|Q6UXT7|Q6UXX3|Q86SL7|Q8IXD8|Q8TDT3	Missense_Mutation	SNP	ENST00000311519.1	37	CCDS46239.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	C	0.726	-0.781775	0.02929	6.81E-4	0.004186	ENSG00000173567	ENST00000541401;ENST00000333478;ENST00000421160;ENST00000311519	T;T;T;T	0.37058	1.22;1.22;1.22;1.22	5.78	0.853	0.19001	GPCR, family 2-like (1);	.	.	.	.	T	0.13628	0.0330	N	0.17631	0.505	0.09310	N	1	B;B;B;B	0.06786	0.001;0.001;0.0;0.001	B;B;B;B	0.18871	0.023;0.013;0.023;0.008	T	0.31447	-0.9943	9	0.11485	T	0.65	-4.2378	6.3783	0.21519	0.0:0.5889:0.1217:0.2894	.	831;701;900;503	E9PEV1;Q8IZF5-2;Q8IZF5;F5H1E4	.;.;GP113_HUMAN;.	I	503;701;831;900	ENSP00000445729:V503I;ENSP00000327396:V701I;ENSP00000388537:V831I;ENSP00000307831:V900I	ENSP00000307831:V900I	V	-	1	0	GPR113	26387402	0.000000	0.05858	0.000000	0.03702	0.992000	0.81027	0.166000	0.16583	0.093000	0.17368	0.650000	0.86243	GTC	C|0.998;T|0.002	0.002	strong		0.612	GPR113-004	PUTATIVE	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000316892.1	NM_153835	
TTN	7273	hgsc.bcm.edu	37	2	179611851	179611851	+	Intron	SNP	C	C	T	rs72648910	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611851C>T	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.L5092L			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)			AGTATCTCTCCAGAGTCTCTC	0.527													T|||	200	0.0399361	0.1407	0.013	5008	,	,		15008	0.001		0.003	False		,,,				2504	0.001				p.L5092L		Atlas-SNP	.											TTN_ENST00000360870,NS,carcinoma,-2,1	TTN	18412	1	0			c.G15276A						PASS	.	T	,,,,	323,4077	759.4+/-412.9	21,281,1898	61.0	73.0	69.0		,,15276,,	-10.5	0.0	2	dbSNP_130	69	6,8592	810.5+/-407.1	0,6,4293	no	intron,intron,coding-synonymous,intron,intron	TTN	NM_003319.4,NM_133378.4,NM_133379.3,NM_133432.3,NM_133437.3	,,,,	21,287,6191	TT,TC,CC		0.0698,7.3409,2.5312	,,,,	,,5092/5605,,	179611851	329,12669	2200	4299	6499	SO:0001627	intron_variant	7273	exon46			TCTCTCCAGAGTC	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.10361-5203G>A	2.37:g.179611851C>T		131.0	0.0	0		148.0	32.0	0.216216	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																																																																																				C|0.965;T|0.035	0.035	strong		0.527	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
IL12RB2	3595	hgsc.bcm.edu	37	1	67833643	67833643	+	Missense_Mutation	SNP	G	G	A	rs2307153	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:67833643G>A	ENST00000262345.1	+	10	2034	c.1394G>A	c.(1393-1395)gGt>gAt	p.G465D	IL12RB2_ENST00000544434.1_Missense_Mutation_p.G465D|IL12RB2_ENST00000371000.1_Missense_Mutation_p.G465D|IL12RB2_ENST00000541374.1_Missense_Mutation_p.G465D	NM_001559.2	NP_001550.1	Q99665	I12R2_HUMAN	interleukin 12 receptor, beta 2	465	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.		G -> D (in dbSNP:rs2307153). {ECO:0000269|Ref.3}.		cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma production (GO:0032609)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interferon-gamma production (GO:0032729)|response to lipopolysaccharide (GO:0032496)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	cytokine receptor activity (GO:0004896)			breast(3)|central_nervous_system(1)|endometrium(3)|large_intestine(8)|lung(21)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	45						CATCCAGGGGGTGACACACAG	0.527													G|||	37	0.00738818	0.0015	0.0101	5008	,	,		18311	0.001		0.0268	False		,,,				2504	0.0				p.G465D		Atlas-SNP	.											.	IL12RB2	94	.	0			c.G1394A						PASS	.	G	ASP/GLY	19,4387	26.2+/-53.5	0,19,2184	155.0	138.0	144.0		1394	-3.2	0.0	1	dbSNP_100	144	163,8437	77.2+/-139.8	0,163,4137	yes	missense	IL12RB2	NM_001559.2	94	0,182,6321	AA,AG,GG		1.8953,0.4312,1.3994	benign	465/863	67833643	182,12824	2203	4300	6503	SO:0001583	missense	3595	exon10			CAGGGGGTGACAC	U64198	CCDS638.1, CCDS58006.1, CCDS58007.1, CCDS72805.1	1p31.3-p31.2	2014-07-15			ENSG00000081985	ENSG00000081985		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	5972	protein-coding gene	gene with protein product		601642				9284929, 8943050	Standard	NM_001559		Approved		uc001ddu.3	Q99665	OTTHUMG00000009094	ENST00000262345.1:c.1394G>A	1.37:g.67833643G>A	ENSP00000262345:p.Gly465Asp	89.0	0.0	0		80.0	34.0	0.425	NM_001559	B1AN98|B7ZKL9|F5H7L6|Q2M3V3	Missense_Mutation	SNP	ENST00000262345.1	37	CCDS638.1	23	0.010531135531135532	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	19	0.025065963060686015	G	6.679	0.493890	0.12702	0.004312	0.018953	ENSG00000081985	ENST00000262345;ENST00000371000;ENST00000541374;ENST00000544434	T;T;T;T	0.56444	0.46;0.46;0.46;0.46	5.02	-3.19	0.05171	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.541502	0.22419	N	0.060316	T	0.14960	0.0361	L	0.58101	1.795	0.09310	N	1	B;B;B;B	0.29301	0.011;0.0;0.241;0.002	B;B;B;B	0.26693	0.025;0.002;0.072;0.014	T	0.32929	-0.9888	10	0.16896	T	0.51	0.5509	2.0862	0.03646	0.2949:0.3687:0.22:0.1163	rs2307153;rs17097322;rs52799399;rs2307153	465;465;465;465	B4DGA4;F5H7L6;Q99665-2;Q99665	.;.;.;I12R2_HUMAN	D	465	ENSP00000262345:G465D;ENSP00000360039:G465D;ENSP00000445276:G465D;ENSP00000442443:G465D	ENSP00000262345:G465D	G	+	2	0	IL12RB2	67606231	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.673000	0.05239	-0.876000	0.04017	-0.122000	0.15005	GGT	G|0.986;A|0.014	0.014	strong		0.527	IL12RB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025202.2	NM_001559	
MASTL	84930	hgsc.bcm.edu	37	10	27458886	27458886	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:27458886C>T	ENST00000375940.4	+	8	1055	c.998C>T	c.(997-999)gCa>gTa	p.A333V	MASTL_ENST00000342386.6_Missense_Mutation_p.A333V|MASTL_ENST00000375946.4_Missense_Mutation_p.A333V|MASTL_ENST00000477034.1_3'UTR			Q96GX5	GWL_HUMAN	microtubule associated serine/threonine kinase-like	333	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to DNA damage stimulus (GO:0006974)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of protein phosphatase type 2A activity (GO:0034048)|regulation of cell cycle (GO:0051726)	centrosome (GO:0005813)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein phosphatase 2A binding (GO:0051721)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|cervix(2)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						AGTGATGAAGCATTGGGCCCA	0.358																																					p.A333V		Atlas-SNP	.											.	MASTL	81	.	0			c.C998T						PASS	.						66.0	65.0	65.0					10																	27458886		2203	4300	6503	SO:0001583	missense	84930	exon8			ATGAAGCATTGGG	BC009107	CCDS7153.1, CCDS53502.1, CCDS53503.1	10p12.1	2005-11-03			ENSG00000120539	ENSG00000120539			19042	protein-coding gene	gene with protein product		608221					Standard	NM_001172303		Approved	FLJ14813, THC2	uc001itm.3	Q96GX5	OTTHUMG00000017855	ENST00000375940.4:c.998C>T	10.37:g.27458886C>T	ENSP00000365107:p.Ala333Val	73.0	0.0	0		59.0	20.0	0.338983	NM_032844	Q5T8D5|Q5T8D7|Q8NCD6|Q96SJ5	Missense_Mutation	SNP	ENST00000375940.4	37	CCDS53502.1	.	.	.	.	.	.	.	.	.	.	C	0.061	-1.224400	0.01530	.	.	ENSG00000120539	ENST00000375946;ENST00000342386;ENST00000375940	T;T;T	0.65549	-0.02;-0.16;-0.02	5.28	2.44	0.29823	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.881451	0.10156	N	0.708985	T	0.46814	0.1412	L	0.38531	1.155	0.09310	N	1	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.31194	-0.9952	10	0.25751	T	0.34	-2.2806	4.3382	0.11097	0.1893:0.5647:0.0:0.246	.	333;333;333	Q96GX5-2;Q96GX5;Q96GX5-3	.;GWL_HUMAN;.	V	333	ENSP00000365113:A333V;ENSP00000343446:A333V;ENSP00000365107:A333V	ENSP00000343446:A333V	A	+	2	0	MASTL	27498892	0.000000	0.05858	0.000000	0.03702	0.030000	0.12068	0.005000	0.13129	0.370000	0.24538	-0.133000	0.14855	GCA	.	.	none		0.358	MASTL-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047320.1	NM_032844	
WDR87	83889	hgsc.bcm.edu	37	19	38385707	38385707	+	Silent	SNP	G	G	A	rs189713744		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:38385707G>A	ENST00000303868.5	-	4	743	c.519C>T	c.(517-519)gcC>gcT	p.A173A	WDR87_ENST00000447313.2_Silent_p.A212A	NM_031951.3	NP_114157.3	Q6ZQQ6	WDR87_HUMAN	WD repeat domain 87	173										NS(4)|autonomic_ganglia(2)|breast(3)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|prostate(1)|skin(3)|stomach(1)	36						TCTCACACAGGGCCAGGAGGG	0.607													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18587	0.0		0.0	False		,,,				2504	0.0				p.A173A		Atlas-SNP	.											.	WDR87	191	.	0			c.C519T						PASS	.	G		1,1383		0,1,691	52.0	56.0	55.0		519	-0.3	0.5	19		55	4,3178		0,4,1587	no	coding-synonymous	WDR87	NM_031951.3		0,5,2278	AA,AG,GG		0.1257,0.0723,0.1095		173/2874	38385707	5,4561	692	1591	2283	SO:0001819	synonymous_variant	83889	exon4			ACACAGGGCCAGG	AK128826	CCDS46063.1, CCDS74356.1	19q13.13	2013-01-09			ENSG00000171804	ENSG00000171804		"""WD repeat domain containing"""	29934	protein-coding gene	gene with protein product							Standard	XM_005259304		Approved	NYD-SP11	uc010efu.2	Q6ZQQ6	OTTHUMG00000048187	ENST00000303868.5:c.519C>T	19.37:g.38385707G>A		57.0	0.0	0		64.0	29.0	0.453125	NM_031951	Q9BWV9	Silent	SNP	ENST00000303868.5	37	CCDS46063.1																																																																																			G|1.000;A|0.000	0.000	strong		0.607	WDR87-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314628.2	XM_940478	
NCKAP5L	57701	hgsc.bcm.edu	37	12	50186585	50186585	+	Silent	SNP	T	T	C	rs138292278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:50186585T>C	ENST00000335999.6	-	11	3726	c.3525A>G	c.(3523-3525)acA>acG	p.T1175T		NM_001037806.3	NP_001032895.2	Q9HCH0	NCK5L_HUMAN	NCK-associated protein 5-like	1171	Pro-rich.									central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(8)|prostate(2)	18						CCCGCTCCAGTGTGTGGGCGC	0.687													T|||	54	0.0107827	0.0023	0.0029	5008	,	,		11936	0.0		0.0109	False		,,,				2504	0.0389				p.T1175T		Atlas-SNP	.											.	NCKAP5L	142	.	0			c.A3525G						PASS	.	T		10,3996		0,10,1993	9.0	12.0	11.0		3525	-7.7	0.6	12	dbSNP_134	11	76,8136		0,76,4030	no	coding-synonymous	NCKAP5L	NM_001037806.3		0,86,6023	CC,CT,TT		0.9255,0.2496,0.7039		1175/1335	50186585	86,12132	2003	4106	6109	SO:0001819	synonymous_variant	57701	exon11			CTCCAGTGTGTGG	AB046822	CCDS41781.2	12q13.12	2009-08-14	2009-08-14	2009-08-14	ENSG00000167566	ENSG00000167566			29321	protein-coding gene	gene with protein product		615104	"""KIAA1602"""	KIAA1602			Standard	NM_001037806		Approved		uc009zlk.2	Q9HCH0	OTTHUMG00000156969	ENST00000335999.6:c.3525A>G	12.37:g.50186585T>C		54.0	0.0	0		78.0	34.0	0.435897	NM_001037806	Q2TB26|Q71RH1|Q8N4W1|Q96HX2	Silent	SNP	ENST00000335999.6	37	CCDS41781.2	16	0.007326007326007326	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	11	0.014511873350923483	T	7.331	0.618991	0.14129	0.002496	0.009255	ENSG00000167566	ENST00000433948	.	.	.	4.3	-7.72	0.01250	.	0.000000	0.45126	D	0.000393	T	0.43831	0.1265	.	.	.	0.48040	D	0.999577	.	.	.	.	.	.	T	0.57201	-0.7852	6	0.72032	D	0.01	-11.3794	4.1532	0.10247	0.1022:0.264:0.1016:0.5322	.	.	.	.	A	890	.	ENSP00000402619:T890A	T	-	1	0	NCKAP5L	48472852	0.000000	0.05858	0.623000	0.29173	0.865000	0.49528	-6.231000	0.00075	-1.638000	0.01529	-1.226000	0.01582	ACT	T|0.993;C|0.007	0.007	strong		0.687	NCKAP5L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346884.2	XM_035497	
ARHGEF35	445328	hgsc.bcm.edu	37	7	143884216	143884216	+	Missense_Mutation	SNP	G	G	C	rs200777966	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:143884216G>C	ENST00000378115.2	-	2	1390	c.1261C>G	c.(1261-1263)Ctg>Gtg	p.L421V	ARHGEF35_ENST00000543357.1_Missense_Mutation_p.L421V	NM_001003702.2	NP_001003702.2	A5YM69	ARG35_HUMAN	Rho guanine nucleotide exchange factor (GEF) 35	421										kidney(1)|large_intestine(1)|lung(3)|stomach(1)	6						CCTGGAAACAGGTCACAGTGA	0.587													-|||	6	0.00119808	0.0	0.0014	5008	,	,		17229	0.0		0.005	False		,,,				2504	0.0				p.L421V		Atlas-SNP	.											.	ARHGEF35	11	.	0			c.C1261G						PASS	.	G	VAL/LEU	4,4156		0,4,2076	8.0	9.0	8.0		1261	-4.7	0.0	7		8	33,8021		1,31,3995	no	missense	ARHGEF35	NM_001003702.2	32	1,35,6071	CC,CG,GG		0.4097,0.0962,0.3029	benign	421/485	143884216	37,12177	2080	4027	6107	SO:0001583	missense	445328	exon2			GAAACAGGTCACA	AK125680	CCDS34770.1	7q35	2012-07-24	2010-04-13	2010-04-13	ENSG00000213214	ENSG00000213214		"""Rho guanine nucleotide exchange factors"""	33846	protein-coding gene	gene with protein product			"""Rho guanine nucleotide exchange factor (GEF) 5-like"""	ARHGEF5L			Standard	NM_001003702		Approved	FLJ43692, CTAGE4	uc003wdz.2	A5YM69	OTTHUMG00000158010	ENST00000378115.2:c.1261C>G	7.37:g.143884216G>C	ENSP00000367355:p.Leu421Val	294.0	0.0	0		458.0	88.0	0.19214	NM_001003702	Q6ZUI2	Missense_Mutation	SNP	ENST00000378115.2	37	CCDS34770.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	.	4.049	0.006734	0.07866	9.62E-4	0.004097	ENSG00000213214	ENST00000378115;ENST00000543357	.	.	.	2.34	-4.67	0.03319	.	.	.	.	.	T	0.23688	0.0573	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.19063	-1.0317	8	0.24483	T	0.36	.	4.1258	0.10126	0.3886:0.2006:0.4109:0.0	.	421	A5YM69	ARG35_HUMAN	V	421	.	ENSP00000367355:L421V	L	-	1	2	ARHGEF35	143515149	0.000000	0.05858	0.000000	0.03702	0.110000	0.19582	-1.471000	0.02344	-1.282000	0.02396	-1.271000	0.01417	CTG	G|0.999;C|0.001	0.001	strong		0.587	ARHGEF35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349997.1	NM_001003702	
RASSF2	9770	hgsc.bcm.edu	37	20	4768282	4768282	+	Silent	SNP	G	G	A	rs6052876	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:4768282G>A	ENST00000379400.3	-	10	1005	c.810C>T	c.(808-810)taC>taT	p.Y270Y	RASSF2_ENST00000478553.1_5'UTR|RASSF2_ENST00000379376.2_Silent_p.Y270Y	NM_014737.2	NP_055552.1	P50749	RASF2_HUMAN	Ras association (RalGDS/AF-6) domain family member 2	270					bone remodeling (GO:0046849)|cell cycle (GO:0007049)|epidermal growth factor receptor signaling pathway via I-kappaB kinase/NF-kappaB cascade (GO:0038168)|homeostasis of number of cells (GO:0048872)|negative regulation of NIK/NF-kappaB signaling (GO:1901223)|ossification (GO:0001503)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(3)|kidney(2)|large_intestine(8)|lung(12)|ovary(3)|pancreas(2)|prostate(2)|skin(2)	34						AACTCACGTCGTAGGTGACTT	0.537													A|||	236	0.0471246	0.171	0.0115	5008	,	,		19617	0.0		0.0	False		,,,				2504	0.002				p.Y270Y	Melanoma(158;1891 3343 50738)	Atlas-SNP	.											.	RASSF2	75	.	0			c.C810T						PASS	.	A	,	679,3727	763.0+/-413.2	61,557,1585	117.0	94.0	102.0		810,810	1.8	1.0	20	dbSNP_114	102	9,8591	818.9+/-406.8	0,9,4291	no	coding-synonymous,coding-synonymous	RASSF2	NM_014737.2,NM_170774.1	,	61,566,5876	AA,AG,GG		0.1047,15.4108,5.2899	,	270/327,270/327	4768282	688,12318	2203	4300	6503	SO:0001819	synonymous_variant	9770	exon10			CACGTCGTAGGTG	D79990	CCDS13083.1	20p13	2011-08-12	2008-02-22		ENSG00000101265	ENSG00000101265			9883	protein-coding gene	gene with protein product	"""centromere protein 34"""	609492				8724849, 15806169	Standard	NM_014737		Approved	KIAA0168, CENP-34	uc002wld.3	P50749	OTTHUMG00000031790	ENST00000379400.3:c.810C>T	20.37:g.4768282G>A		114.0	0.0	0		98.0	36.0	0.367347	NM_014737	A6NIX9|A8K5Z3|Q17S06|Q53HD0|Q6AHZ2|Q8IZA5	Silent	SNP	ENST00000379400.3	37	CCDS13083.1																																																																																			G|0.954;A|0.046	0.046	strong		0.537	RASSF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077828.1	NM_014737	
CLIP1	6249	hgsc.bcm.edu	37	12	122825398	122825398	+	Missense_Mutation	SNP	C	C	T	rs61954403	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122825398C>T	ENST00000540338.1	-	10	2394	c.2353G>A	c.(2353-2355)Gaa>Aaa	p.E785K	CLIP1_ENST00000302528.7_Missense_Mutation_p.E774K|CLIP1_ENST00000537178.1_Missense_Mutation_p.E739K|CLIP1_ENST00000545889.1_Intron|CLIP1_ENST00000361654.4_Intron|CLIP1_ENST00000358808.2_Missense_Mutation_p.E774K			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	785					microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		GATTTACCTTCGGAACTGGCT	0.388													C|||	33	0.00658946	0.0015	0.0144	5008	,	,		21925	0.0		0.0199	False		,,,				2504	0.001				p.E785K		Atlas-SNP	.											.	CLIP1	126	.	0			c.G2353A						PASS	.	C	LYS/GLU,LYS/GLU	15,4391	22.3+/-47.3	0,15,2188	141.0	139.0	140.0		2320,2215	5.7	1.0	12	dbSNP_129	140	130,8470	66.3+/-128.7	0,130,4170	yes	missense,missense	CLIP1	NM_002956.2,NM_198240.1	56,56	0,145,6358	TT,TC,CC		1.5116,0.3404,1.1149	possibly-damaging,possibly-damaging	774/1428,739/1393	122825398	145,12861	2203	4300	6503	SO:0001583	missense	6249	exon11			TACCTTCGGAACT		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.2353G>A	12.37:g.122825398C>T	ENSP00000439093:p.Glu785Lys	175.0	0.0	0		174.0	93.0	0.534483	NM_001247997	A0AVD3|Q17RS4|Q29RG0	Missense_Mutation	SNP	ENST00000540338.1	37	CCDS58285.1	16	0.007326007326007326	0	0.0	1	0.0027624309392265192	0	0.0	15	0.01978891820580475	C	26.0	4.699526	0.88830	0.003404	0.015116	ENSG00000130779	ENST00000302528;ENST00000358808;ENST00000537178;ENST00000540338	T;T;T;T	0.56275	0.56;0.56;0.57;0.47	5.73	5.73	0.89815	.	0.052582	0.85682	D	0.000000	T	0.48466	0.1501	M	0.64997	1.995	0.53005	D	0.999968	D;D;D	0.64830	0.994;0.994;0.977	P;P;P	0.53649	0.731;0.731;0.487	T	0.52094	-0.8621	10	0.29301	T	0.29	-19.7607	20.2602	0.98440	0.0:1.0:0.0:0.0	rs61954403	739;774;785	P30622-2;P30622-1;P30622	.;.;CLIP1_HUMAN	K	774;774;739;785	ENSP00000303585:E774K;ENSP00000351665:E774K;ENSP00000445531:E739K;ENSP00000439093:E785K	ENSP00000303585:E774K	E	-	1	0	CLIP1	121391351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	4.025000	0.57225	2.861000	0.98227	0.655000	0.94253	GAA	C|0.990;T|0.010	0.010	strong		0.388	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
YARS	8565	hgsc.bcm.edu	37	1	33246709	33246709	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:33246709T>C	ENST00000373477.4	-	10	1988	c.1080A>G	c.(1078-1080)ccA>ccG	p.P360P	YARS_ENST00000469100.1_5'UTR	NM_003680.3	NP_003671.1	P54577	SYYC_HUMAN	tyrosyl-tRNA synthetase	360					apoptotic process (GO:0006915)|gene expression (GO:0010467)|signal transduction (GO:0007165)|tRNA aminoacylation for protein translation (GO:0006418)|tyrosyl-tRNA aminoacylation (GO:0006437)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|nucleus (GO:0005634)	ATP binding (GO:0005524)|interleukin-8 receptor binding (GO:0005153)|poly(A) RNA binding (GO:0044822)|signal transducer activity (GO:0004871)|tRNA binding (GO:0000049)|tyrosine-tRNA ligase activity (GO:0004831)			endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|skin(2)|urinary_tract(1)	15		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Breast(348;0.244)			L-Tyrosine(DB00135)	TGACCTCCTCTGGTTCTGAAT	0.527																																					p.P360P		Atlas-SNP	.											.	YARS	34	.	0			c.A1080G						PASS	.						128.0	117.0	120.0					1																	33246709		2203	4300	6503	SO:0001819	synonymous_variant	8565	exon10			CTCCTCTGGTTCT	U89436	CCDS368.1	1p35.1	2014-09-17			ENSG00000134684	ENSG00000134684	6.1.1.1	"""Aminoacyl tRNA synthetases / Class I"""	12840	protein-coding gene	gene with protein product	"""tyrosine tRNA ligase 1, cytoplasmic"""	603623				8552597, 9162081	Standard	NM_003680		Approved	YTS, YRS, tyrRS	uc001bvy.1	P54577	OTTHUMG00000003933	ENST00000373477.4:c.1080A>G	1.37:g.33246709T>C		53.0	0.0	0		62.0	31.0	0.5	NM_003680	B3KWK4|D3DPQ4|O43276|Q53EN1	Silent	SNP	ENST00000373477.4	37	CCDS368.1																																																																																			.	.	none		0.527	YARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011225.1	NM_003680	
HHIPL2	79802	hgsc.bcm.edu	37	1	222712108	222712108	+	Missense_Mutation	SNP	G	G	T	rs116359984	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:222712108G>T	ENST00000343410.6	-	5	1517	c.1459C>A	c.(1459-1461)Ctg>Atg	p.L487M		NM_024746.3	NP_079022.2	Q6UWX4	HIPL2_HUMAN	HHIP-like 2	487					carbohydrate metabolic process (GO:0005975)	extracellular region (GO:0005576)	oxidoreductase activity, acting on the CH-OH group of donors, quinone or similar compound as acceptor (GO:0016901)|quinone binding (GO:0048038)			NS(2)|endometrium(8)|kidney(4)|large_intestine(7)|lung(28)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59				GBM - Glioblastoma multiforme(131;0.0185)		TAGATTGGCAGAACATCATCT	0.453													G|||	12	0.00239617	0.0	0.0086	5008	,	,		19989	0.0		0.006	False		,,,				2504	0.0				p.L487M		Atlas-SNP	.											.	HHIPL2	122	.	0			c.C1459A						PASS	.	G	MET/LEU	3,4403	6.2+/-15.9	0,3,2200	118.0	97.0	104.0		1459	4.4	1.0	1	dbSNP_132	104	54,8546	33.3+/-86.6	1,52,4247	yes	missense	HHIPL2	NM_024746.3	15	1,55,6447	TT,TG,GG		0.6279,0.0681,0.4383	probably-damaging	487/725	222712108	57,12949	2203	4300	6503	SO:0001583	missense	79802	exon5			TTGGCAGAACATC	BC007638	CCDS1530.2	1q41	2008-02-05	2008-01-16	2008-01-16	ENSG00000143512	ENSG00000143512			25842	protein-coding gene	gene with protein product			"""KIAA1822-like"""	KIAA1822L		12975309	Standard	NM_024746		Approved	FLJ13840	uc001hnh.1	Q6UWX4	OTTHUMG00000037545	ENST00000343410.6:c.1459C>A	1.37:g.222712108G>T	ENSP00000342118:p.Leu487Met	119.0	0.0	0		118.0	63.0	0.533898	NM_024746	Q6GU65|Q96BT4|Q96BU5|Q9H8A0	Missense_Mutation	SNP	ENST00000343410.6	37	CCDS1530.2	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	G	17.11	3.306873	0.60305	6.81E-4	0.006279	ENSG00000143512	ENST00000343410	T	0.13778	2.56	5.35	4.43	0.53597	Soluble quinoprotein glucose/sorbosone dehydrogenase (1);Glucose/Sorbosone dehydrogenase (1);Six-bladed beta-propeller, TolB-like (1);	0.153343	0.43416	D	0.000570	T	0.19886	0.0478	L	0.49513	1.565	0.42479	D	0.992857	D	0.89917	1.0	D	0.87578	0.998	T	0.00453	-1.1730	10	0.31617	T	0.26	-6.822	9.5251	0.39160	0.1591:0.0:0.8409:0.0	.	487	Q6UWX4	HIPL2_HUMAN	M	487	ENSP00000342118:L487M	ENSP00000342118:L487M	L	-	1	2	HHIPL2	220778731	1.000000	0.71417	0.994000	0.49952	0.530000	0.34684	6.212000	0.72188	2.472000	0.83506	0.591000	0.81541	CTG	G|0.995;T|0.005	0.005	strong		0.453	HHIPL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091499.2	NM_024746	
MRPL1	65008	hgsc.bcm.edu	37	4	78792906	78792906	+	Missense_Mutation	SNP	C	C	T	rs373565703		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:78792906C>T	ENST00000315567.8	+	2	369	c.40C>T	c.(40-42)Cat>Tat	p.H14Y		NM_020236.3	NP_064621.3	Q9BYD6	RM01_HUMAN	mitochondrial ribosomal protein L1	14					translation (GO:0006412)	large ribosomal subunit (GO:0015934)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(1)	17						AGCCTTGATACATCATCAAAG	0.303																																					p.H14Y		Atlas-SNP	.											.	MRPL1	37	.	0			c.C40T						PASS	.	C	TYR/HIS	0,4406		0,0,2203	82.0	77.0	78.0		40	2.6	1.0	4		78	2,8598	2.2+/-6.3	0,2,4298	no	missense	MRPL1	NM_020236.3	83	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	benign	14/326	78792906	2,13004	2203	4300	6503	SO:0001583	missense	65008	exon2			TTGATACATCATC	AB049474	CCDS3583.2	4q21.1	2012-09-13			ENSG00000169288	ENSG00000169288		"""Mitochondrial ribosomal proteins / large subunits"""	14275	protein-coding gene	gene with protein product		611821					Standard	NM_020236		Approved	BM022	uc003hku.2	Q9BYD6	OTTHUMG00000130200	ENST00000315567.8:c.40C>T	4.37:g.78792906C>T	ENSP00000315017:p.His14Tyr	126.0	0.0	0		108.0	51.0	0.472222	NM_020236	A6NG03|Q4W5B8|Q6IAG4|Q96BW3|Q9H793|Q9NRL5	Missense_Mutation	SNP	ENST00000315567.8	37	CCDS3583.2	.	.	.	.	.	.	.	.	.	.	C	8.711	0.912058	0.17907	0.0	2.33E-4	ENSG00000169288	ENST00000315567	T	0.49139	0.79	5.27	2.62	0.31277	Ribosomal protein L1, chordata (1);	1.288150	0.06367	U	0.712771	T	0.46034	0.1372	L	0.56769	1.78	0.25979	N	0.982403	B	0.30889	0.299	B	0.35278	0.199	T	0.38585	-0.9654	10	0.31617	T	0.26	-0.8796	6.1972	0.20555	0.0:0.6775:0.1532:0.1693	.	14	Q9BYD6	RM01_HUMAN	Y	14	ENSP00000315017:H14Y	ENSP00000315017:H14Y	H	+	1	0	MRPL1	79011930	0.405000	0.25336	0.956000	0.39512	0.721000	0.41392	0.268000	0.18571	0.442000	0.26555	-0.143000	0.13931	CAT	.	.	weak		0.303	MRPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252518.3	NM_020236	
TRPC4	7223	hgsc.bcm.edu	37	13	38225406	38225406	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:38225406A>G	ENST00000379705.3	-	8	2932	c.2075T>C	c.(2074-2076)aTa>aCa	p.I692T	TRPC4_ENST00000338947.5_Missense_Mutation_p.I519T|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000379681.3_Missense_Mutation_p.I692T|TRPC4_ENST00000355779.2_Missense_Mutation_p.I692T|TRPC4_ENST00000379673.2_Intron|TRPC4_ENST00000358477.2_Missense_Mutation_p.I692T|TRPC4_ENST00000379679.1_Missense_Mutation_p.I519T|TRPC4_ENST00000447043.1_Missense_Mutation_p.I692T			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	692	Binds to ITPR1, ITPR2 and ITPR3.				axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|gamma-aminobutyric acid secretion (GO:0014051)|ion transmembrane transport (GO:0034220)|oligodendrocyte differentiation (GO:0048709)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|calcium channel complex (GO:0034704)|caveola (GO:0005901)|cell surface (GO:0009986)|cortical cytoskeleton (GO:0030863)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|cadherin binding (GO:0045296)|inositol 1,4,5 trisphosphate binding (GO:0070679)|store-operated calcium channel activity (GO:0015279)			NS(2)|breast(4)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(26)|lung(30)|ovary(4)|prostate(1)|skin(4)|urinary_tract(2)	83				all cancers(112;1.92e-08)|Epithelial(112;5.04e-06)|OV - Ovarian serous cystadenocarcinoma(117;0.000677)|GBM - Glioblastoma multiforme(144;0.00623)|BRCA - Breast invasive adenocarcinoma(63;0.0126)		TCTTACCCCTATTGTTCCAAA	0.363																																					p.I692T		Atlas-SNP	.											.	TRPC4	389	.	0			c.T2075C						PASS	.						130.0	127.0	128.0					13																	38225406		2203	4300	6503	SO:0001583	missense	7223	exon8			ACCCCTATTGTTC	U40983	CCDS9365.1, CCDS45035.1, CCDS45036.1, CCDS45038.1, CCDS45039.1	13q13.3	2013-01-10			ENSG00000133107	ENSG00000133107		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Ankyrin repeat domain containing"""	12336	protein-coding gene	gene with protein product		603651				8646775, 16382100	Standard	NM_016179		Approved	HTRP4, TRP4	uc010abx.3	Q9UBN4	OTTHUMG00000016752	ENST00000379705.3:c.2075T>C	13.37:g.38225406A>G	ENSP00000369027:p.Ile692Thr	254.0	1.0	0.00393701		237.0	112.0	0.472574	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Missense_Mutation	SNP	ENST00000379705.3	37	CCDS9365.1	.	.	.	.	.	.	.	.	.	.	A	21.1	4.097773	0.76870	.	.	ENSG00000133107	ENST00000379705;ENST00000379681;ENST00000338947;ENST00000379679;ENST00000355779;ENST00000358477;ENST00000447043	D;D;D;D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63;-1.63;-1.63;-1.63	5.7	5.7	0.88788	.	0.094472	0.64402	D	0.000001	D	0.83862	0.5346	L	0.42245	1.32	0.80722	D	1	B;P;P;P;P	0.51057	0.336;0.718;0.941;0.506;0.59	B;B;P;B;B	0.51777	0.253;0.215;0.679;0.333;0.25	D	0.83644	0.0152	10	0.40728	T	0.16	-26.2199	15.9668	0.79979	1.0:0.0:0.0:0.0	.	692;692;519;692;692	Q9UBN4-3;Q9UBN4-5;Q9UBN4-6;Q9UBN4-2;Q9UBN4	.;.;.;.;TRPC4_HUMAN	T	692;692;519;519;692;692;692	ENSP00000369027:I692T;ENSP00000369003:I692T;ENSP00000342580:I519T;ENSP00000369001:I519T;ENSP00000348025:I692T;ENSP00000351264:I692T;ENSP00000414316:I692T	ENSP00000342580:I519T	I	-	2	0	TRPC4	37123406	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.310000	0.96267	2.182000	0.69389	0.459000	0.35465	ATA	.	.	none		0.363	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
BIN1	274	hgsc.bcm.edu	37	2	127811561	127811561	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:127811561G>A	ENST00000316724.5	-	13	1570	c.1159C>T	c.(1159-1161)Cag>Tag	p.Q387*	BIN1_ENST00000348750.4_Intron|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000357970.3_Nonsense_Mutation_p.Q344*|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000409400.1_Intron|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000393041.3_Intron|BIN1_ENST00000351659.3_Intron|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000346226.3_Intron	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	387	Clathrin-binding.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		AGACTGGCCTGCTCCGAGAAA	0.642																																					p.Q387X		Atlas-SNP	.											.	BIN1	85	.	0			c.C1159T						PASS	.						22.0	24.0	23.0					2																	127811561		2107	4099	6206	SO:0001587	stop_gained	274	exon13			TGGCCTGCTCCGA	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1159C>T	2.37:g.127811561G>A	ENSP00000316779:p.Gln387*	173.0	0.0	0		162.0	67.0	0.41358	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Nonsense_Mutation	SNP	ENST00000316724.5	37	CCDS2138.1	.	.	.	.	.	.	.	.	.	.	G	41	8.932924	0.99008	.	.	ENSG00000136717	ENST00000357970;ENST00000316724	.	.	.	5.36	4.39	0.52855	.	0.765384	0.12406	N	0.471717	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.20519	T	0.43	-22.063	9.5913	0.39548	0.0:0.2271:0.6314:0.1415	.	.	.	.	X	344;387	.	ENSP00000316779:Q387X	Q	-	1	0	BIN1	127528031	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	2.211000	0.42825	2.533000	0.85409	0.456000	0.33151	CAG	.	.	none		0.642	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
SP8	221833	hgsc.bcm.edu	37	7	20824953	20824953	+	Silent	SNP	G	G	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20824953G>C	ENST00000361443.4	-	3	666	c.429C>G	c.(427-429)ggC>ggG	p.G143G	SP8_ENST00000418710.2_Silent_p.G161G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	143					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						cgccgccgccgcccccgccgc	0.736																																					p.G161G		Atlas-SNP	.											.	SP8	43	.	0			c.C483G						PASS	.						2.0	2.0	2.0					7																	20824953		584	1454	2038	SO:0001819	synonymous_variant	221833	exon2			GCCGCCGCCCCCG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.429C>G	7.37:g.20824953G>C		2.0	0.0	0		9.0	9.0	1	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.	.	none		0.736	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
CNTRL	11064	hgsc.bcm.edu	37	9	123917045	123917045	+	Missense_Mutation	SNP	A	A	G	rs149632088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:123917045A>G	ENST00000373855.1	+	27	4479	c.4219A>G	c.(4219-4221)Ata>Gta	p.I1407V	CNTRL_ENST00000238341.5_Missense_Mutation_p.I1407V|CNTRL_ENST00000373845.2_3'UTR|CNTRL_ENST00000373847.1_Missense_Mutation_p.I855V|CNTRL_ENST00000373850.1_Missense_Mutation_p.I855V			Q7Z7A1	CNTRL_HUMAN	centriolin	1407					cell division (GO:0051301)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)				haematopoietic_and_lymphoid_tissue(2)|large_intestine(9)|lung(2)|ovary(4)|skin(3)	20						TGAACTAGAAATAGAAAAATC	0.343													A|||	2	0.000399361	0.0	0.0	5008	,	,		19659	0.0		0.002	False		,,,				2504	0.0				p.I1407V		Atlas-SNP	.											.	CNTRL	161	.	0			c.A4219G						PASS	.	A	VAL/ILE	2,4404	2.1+/-5.4	0,2,2201	65.0	62.0	63.0		4219	1.9	1.0	9	dbSNP_134	63	3,8597	3.0+/-9.4	0,3,4297	yes	missense	CNTRL	NM_007018.4	29	0,5,6498	GG,GA,AA		0.0349,0.0454,0.0384	benign	1407/2326	123917045	5,13001	2203	4300	6503	SO:0001583	missense	11064	exon25			CTAGAAATAGAAA	AF513978	CCDS35118.1	9q33.2	2014-02-20	2011-05-23	2011-05-23	ENSG00000119397	ENSG00000119397			1858	protein-coding gene	gene with protein product		605496	"""centrosomal protein 1"", ""centrosomal protein 110kDa"""	CEP1, CEP110		10688839	Standard	XM_005251679		Approved		uc004bkx.1	Q7Z7A1	OTTHUMG00000020581	ENST00000373855.1:c.4219A>G	9.37:g.123917045A>G	ENSP00000362962:p.Ile1407Val	56.0	0.0	0		65.0	39.0	0.6	NM_007018	A2A2Y1|B2RP67|Q3MN79|Q5FWF8|Q5JVD0|Q6MZR3|Q6PKC1|Q8TEP3|Q9Y489	Missense_Mutation	SNP	ENST00000373855.1	37	CCDS35118.1	.	.	.	.	.	.	.	.	.	.	A	9.257	1.042151	0.19748	4.54E-4	3.49E-4	ENSG00000119397	ENST00000373855;ENST00000238341;ENST00000454238;ENST00000439778;ENST00000373850;ENST00000373847;ENST00000431571;ENST00000373845	T;T;T;T;T	0.77489	2.57;2.57;2.57;2.57;-1.1	5.58	1.93	0.25924	.	.	.	.	.	T	0.64023	0.2561	L	0.47716	1.5	0.24107	N	0.995855	B	0.20780	0.048	B	0.16289	0.015	T	0.50303	-0.8844	9	0.30078	T	0.28	.	0.594	0.00733	0.3991:0.2274:0.1411:0.2325	.	1407	Q7Z7A1	CNTRL_HUMAN	V	1407;1407;1407;163;855;855;76;76	ENSP00000362962:I1407V;ENSP00000238341:I1407V;ENSP00000362956:I855V;ENSP00000362953:I855V;ENSP00000413014:I76V	ENSP00000238341:I1407V	I	+	1	0	CNTRL	122956866	0.975000	0.34042	0.997000	0.53966	0.931000	0.56810	0.100000	0.15231	0.135000	0.18707	-0.250000	0.11733	ATA	A|0.999;G|0.001	0.001	strong		0.343	CNTRL-010	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250216.1	NM_007018	
WDR33	55339	hgsc.bcm.edu	37	2	128528508	128528508	+	Silent	SNP	C	C	T	rs55916728	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128528508C>T	ENST00000322313.4	-	2	206	c.48G>A	c.(46-48)agG>agA	p.R16R	WDR33_ENST00000409658.3_Silent_p.R16R|WDR33_ENST00000393006.1_Silent_p.R16R	NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	16					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		GGTGCTGGAACCTTGGCATAT	0.418													C|||	66	0.0131789	0.0008	0.0159	5008	,	,		16418	0.0		0.0527	False		,,,				2504	0.001				p.R16R		Atlas-SNP	.											.	WDR33	136	.	0			c.G48A						PASS	.	C	,,	45,4361	46.0+/-80.4	0,45,2158	102.0	100.0	101.0		48,48,48	5.5	1.0	2	dbSNP_129	101	389,8211	125.1+/-183.8	14,361,3925	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR33	NM_001006622.2,NM_001006623.2,NM_018383.4	,,	14,406,6083	TT,TC,CC		4.5233,1.0213,3.3369	,,	16/327,16/258,16/1337	128528508	434,12572	2203	4300	6503	SO:0001819	synonymous_variant	55339	exon2			CTGGAACCTTGGC		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.48G>A	2.37:g.128528508C>T		121.0	0.0	0		149.0	75.0	0.503356	NM_001006623	Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Silent	SNP	ENST00000322313.4	37	CCDS2150.1																																																																																			C|0.972;T|0.028	0.028	strong		0.418	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
RTN4RL1	146760	hgsc.bcm.edu	37	17	1840677	1840677	+	Missense_Mutation	SNP	C	C	T	rs181444163	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:1840677C>T	ENST00000331238.6	-	2	918	c.439G>A	c.(439-441)Ggc>Agc	p.G147S		NM_178568.2	NP_848663.1			reticulon 4 receptor-like 1									p.G147S(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|prostate(2)|skin(1)	11						CTGTGCAGGCCGCCAAAGACG	0.622													C|||	24	0.00479233	0.0091	0.0058	5008	,	,		18221	0.002		0.006	False		,,,				2504	0.0				p.G147S	GBM(68;949 1139 14865 32798 38342)	Atlas-SNP	.											RTN4RL1,NS,carcinoma,0,1	RTN4RL1	21	1	1	Substitution - Missense(1)	prostate(1)	c.G439A						PASS	.	C	SER/GLY	30,4296		0,30,2133	40.0	46.0	44.0		439	5.7	1.0	17		44	113,8417		1,111,4153	yes	missense	RTN4RL1	NM_178568.2	56	1,141,6286	TT,TC,CC		1.3247,0.6935,1.1123	probably-damaging	147/442	1840677	143,12713	2163	4265	6428	SO:0001583	missense	146760	exon2			GCAGGCCGCCAAA	AF532859	CCDS45569.1	17p13.3	2008-02-05				ENSG00000185924			21329	protein-coding gene	gene with protein product	"""nogo-66 receptor homolog 2"""	610461					Standard	NM_178568		Approved	NGRH2, NgR3, DKFZp547J144	uc002ftp.3	Q86UN2		ENST00000331238.6:c.439G>A	17.37:g.1840677C>T	ENSP00000330631:p.Gly147Ser	70.0	0.0	0		63.0	35.0	0.555556	NM_178568		Missense_Mutation	SNP	ENST00000331238.6	37	CCDS45569.1	7	0.003205128205128205	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	27.1	4.803980	0.90623	0.006935	0.013247	ENSG00000185924	ENST00000331238	T	0.61510	0.1	5.72	5.72	0.89469	.	0.000000	0.40064	N	0.001187	T	0.66684	0.2814	L	0.56280	1.765	0.80722	D	1	D	0.76494	0.999	D	0.74023	0.982	T	0.68213	-0.5468	10	0.44086	T	0.13	.	19.9443	0.97176	0.0:1.0:0.0:0.0	.	147	Q86UN2	R4RL1_HUMAN	S	147	ENSP00000330631:G147S	ENSP00000330631:G147S	G	-	1	0	RTN4RL1	1787427	1.000000	0.71417	0.964000	0.40570	0.955000	0.61496	7.484000	0.81180	2.717000	0.92951	0.644000	0.83932	GGC	C|0.995;T|0.005	0.005	strong		0.622	RTN4RL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450155.2	NM_178568	
TBX4	9496	hgsc.bcm.edu	37	17	59560751	59560751	+	Silent	SNP	G	G	A	rs117324438	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59560751G>A	ENST00000240335.1	+	8	1557	c.1512G>A	c.(1510-1512)aaG>aaA	p.K504K	TBX4_ENST00000393853.4_Silent_p.K505K	NM_018488.2	NP_060958.2	P57082	TBX4_HUMAN	T-box 4	504					angiogenesis (GO:0001525)|embryonic limb morphogenesis (GO:0030326)|limb morphogenesis (GO:0035108)|lung development (GO:0030324)|morphogenesis of an epithelium (GO:0002009)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|skeletal system morphogenesis (GO:0048705)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(15)|ovary(4)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	40						GTGAGAGGAAGCCACCCTCGC	0.552													G|||	4	0.000798722	0.0	0.0	5008	,	,		17921	0.0		0.003	False		,,,				2504	0.001				p.K504K		Atlas-SNP	.											.	TBX4	69	.	0			c.G1512A						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	69.0	69.0	69.0		1512	2.4	1.0	17	dbSNP_133	69	26,8574	17.9+/-57.8	0,26,4274	no	coding-synonymous	TBX4	NM_018488.2		0,35,6468	AA,AG,GG		0.3023,0.2043,0.2691		504/546	59560751	35,12971	2203	4300	6503	SO:0001819	synonymous_variant	9496	exon8			GAGGAAGCCACCC	AF188703	CCDS11629.1	17q21-q22	2005-10-11				ENSG00000121075		"""T-boxes"""	11603	protein-coding gene	gene with protein product		601719				10945475	Standard	NM_018488		Approved		uc002izi.3	P57082		ENST00000240335.1:c.1512G>A	17.37:g.59560751G>A		94.0	0.0	0		103.0	53.0	0.514563	NM_018488	A5PKU7|B2RMT1|B7ZLV3	Silent	SNP	ENST00000240335.1	37	CCDS11629.1																																																																																			G|0.999;A|0.001	0.001	strong		0.552	TBX4-002	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000449649.1	NM_018488	
AGPAT2	10555	hgsc.bcm.edu	37	9	139571430	139571430	+	Missense_Mutation	SNP	G	G	A	rs142993240	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:139571430G>A	ENST00000371696.2	-	3	540	c.475C>T	c.(475-477)Cgc>Tgc	p.R159C	AGPAT2_ENST00000538402.1_Missense_Mutation_p.R159C|AGPAT2_ENST00000371694.3_Missense_Mutation_p.R159C	NM_006412.3	NP_006403.2	O15120	PLCB_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 2	159					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|epidermis development (GO:0008544)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of cytokine production (GO:0001819)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			endometrium(1)|large_intestine(1)|lung(2)|prostate(2)	6	all_cancers(76;0.0893)|all_epithelial(76;0.231)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;9.87e-06)|Epithelial(140;0.000123)		CTGACCATGCGCTCGCCCAGG	0.672													g|||	15	0.00299521	0.0008	0.0014	5008	,	,		12176	0.0		0.008	False		,,,				2504	0.0051				p.R159C		Atlas-SNP	.											.	AGPAT2	17	.	0			c.C475T						PASS	.	G	CYS/ARG,CYS/ARG	6,4400	11.4+/-27.6	0,6,2197	55.0	58.0	57.0		475,475	2.7	1.0	9	dbSNP_134	57	48,8552	31.2+/-83.2	0,48,4252	yes	missense,missense	AGPAT2	NM_001012727.1,NM_006412.3	180,180	0,54,6449	AA,AG,GG		0.5581,0.1362,0.4152	possibly-damaging,possibly-damaging	159/247,159/279	139571430	54,12952	2203	4300	6503	SO:0001583	missense	10555	exon3			CCATGCGCTCGCC	AF000237	CCDS7003.1, CCDS35181.1	9q34.3	2013-02-05	2013-02-05		ENSG00000169692	ENSG00000169692	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	325	protein-coding gene	gene with protein product	"""LPAAT-beta"", ""lysophosphatidic acid acyltransferase, beta"""	603100	"""Berardinelli-Seip congenital lipodystrophy"", ""1-acylglycerol-3-phosphate O-acyltransferase 2 (lysophosphatidic acid acyltransferase, beta)"""	BSCL		9242711, 9212163	Standard	NM_006412		Approved		uc004cii.1	O15120	OTTHUMG00000020936	ENST00000371696.2:c.475C>T	9.37:g.139571430G>A	ENSP00000360761:p.Arg159Cys	81.0	0.0	0		91.0	40.0	0.43956	NM_001012727	O00516|O15106|Q5VUD3|Q5VUD4|Q9BSV7|Q9BWR7	Missense_Mutation	SNP	ENST00000371696.2	37	CCDS7003.1	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	15.73	2.920536	0.52653	0.001362	0.005581	ENSG00000169692	ENST00000371694;ENST00000371696;ENST00000538402	D;D;D	0.93604	-3.25;-3.25;-3.25	4.75	2.66	0.31614	Phospholipid/glycerol acyltransferase (2);1-acyl-sn-glycerol-3-phosphate acyltransferase (1);	0.654070	0.14876	N	0.293250	D	0.93552	0.7942	M	0.83692	2.655	0.40657	D	0.98209	D;D	0.65815	0.994;0.995	P;P	0.59595	0.827;0.86	D	0.92032	0.5634	10	0.54805	T	0.06	-9.0385	6.8996	0.24275	0.0:0.1308:0.3813:0.488	.	159;159	O15120-2;O15120	.;PLCB_HUMAN	C	159	ENSP00000360759:R159C;ENSP00000360761:R159C;ENSP00000438919:R159C	ENSP00000360759:R159C	R	-	1	0	AGPAT2	138691251	0.999000	0.42202	0.977000	0.42913	0.479000	0.33129	2.180000	0.42537	0.978000	0.38470	0.655000	0.94253	CGC	G|0.997;A|0.003	0.003	strong		0.672	AGPAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055090.1	NM_006412	
PEMT	10400	hgsc.bcm.edu	37	17	17409140	17409140	+	Missense_Mutation	SNP	G	G	A	rs140621950		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:17409140G>A	ENST00000395783.1	-	7	744	c.565C>T	c.(565-567)Cgg>Tgg	p.R189W	PEMT_ENST00000255389.5_Missense_Mutation_p.R226W|PEMT_ENST00000395782.1_Missense_Mutation_p.R189W|PEMT_ENST00000435340.2_3'UTR|PEMT_ENST00000395781.2_3'UTR|PEMT_ENST00000484838.2_5'UTR|RP11-524F11.1_ENST00000582325.1_RNA	NM_007169.2	NP_009100.2	Q9UBM1	PEMT_HUMAN	phosphatidylethanolamine N-methyltransferase	189					cell proliferation (GO:0008283)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)	phosphatidyl-N-dimethylethanolamine N-methyltransferase activity (GO:0080101)|phosphatidyl-N-methylethanolamine N-methyltransferase activity (GO:0000773)|phosphatidylethanolamine N-methyltransferase activity (GO:0004608)			endometrium(1)|kidney(1)|large_intestine(2)|prostate(3)	7				Colorectal(2;0.0157)|READ - Rectum adenocarcinoma(2;0.0891)		GCTTTCTGCCGGTAGATCTCA	0.662													G|||	1	0.000199681	0.0	0.0	5008	,	,		16588	0.0		0.001	False		,,,				2504	0.0				p.R226W		Atlas-SNP	.											.	PEMT	12	.	0			c.C676T						PASS	.	G	TRP/ARG,TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	63.0	57.0	59.0		565,676,565	2.3	1.0	17	dbSNP_134	59	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense,missense	PEMT	NM_007169.2,NM_148172.1,NM_148173.1	101,101,101	0,8,6495	AA,AG,GG		0.0698,0.0454,0.0615	probably-damaging,probably-damaging,probably-damaging	189/200,226/237,189/200	17409140	8,12998	2203	4300	6503	SO:0001583	missense	10400	exon7			TCTGCCGGTAGAT	AF176806	CCDS11186.1, CCDS11187.1, CCDS58520.1	17p11.2	2008-02-05			ENSG00000133027	ENSG00000133027	2.1.1.17		8830	protein-coding gene	gene with protein product		602391				9989271, 17881348	Standard	NM_148173		Approved	PEMPT, PEMT2	uc002grl.4	Q9UBM1	OTTHUMG00000059290	ENST00000395783.1:c.565C>T	17.37:g.17409140G>A	ENSP00000379129:p.Arg189Trp	152.0	0.0	0		151.0	64.0	0.423841	NM_148172	A8MZ66|B4DY41|D3DXC3|Q6IAQ5|Q86VL3|Q9BW86|Q9UHY6|Q9Y6V9	Missense_Mutation	SNP	ENST00000395783.1	37	CCDS11187.1	.	.	.	.	.	.	.	.	.	.	G	14.19	2.460614	0.43736	4.54E-4	6.98E-4	ENSG00000133027	ENST00000255389;ENST00000395783;ENST00000395782	T;T;T	0.44482	0.92;0.92;0.92	3.29	2.3	0.28687	.	0.487586	0.21644	N	0.071298	T	0.61185	0.2327	M	0.79805	2.47	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.68192	0.927;0.956	T	0.64322	-0.6435	10	0.66056	D	0.02	-31.4459	9.9715	0.41757	0.0:0.0:0.7954:0.2046	.	226;189	Q9UBM1-2;Q9UBM1	.;PEMT_HUMAN	W	226;189;189	ENSP00000255389:R226W;ENSP00000379129:R189W;ENSP00000379128:R189W	ENSP00000255389:R226W	R	-	1	2	PEMT	17349865	1.000000	0.71417	0.989000	0.46669	0.268000	0.26511	2.878000	0.48515	0.946000	0.37632	0.561000	0.74099	CGG	G|0.999;A|0.001	0.001	strong		0.662	PEMT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131657.1	NM_007169	
ZNF645	158506	hgsc.bcm.edu	37	X	22291942	22291942	+	Silent	SNP	G	G	A	rs138094158	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:22291942G>A	ENST00000323684.1	+	1	878	c.834G>A	c.(832-834)caG>caA	p.Q278Q		NM_152577.3	NP_689790.1	Q8N7E2	ZN645_HUMAN	zinc finger protein 645	278	Pro-rich.				protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(4)|large_intestine(8)|lung(9)|ovary(2)|pancreas(1)|skin(1)|urinary_tract(1)	27						TTATACCTCAGAAACAGCATT	0.463													G|||	1	0.000264901	0.0	0.0	3775	,	,		16433	0.0		0.001	False		,,,				2504	0.0				p.Q278Q		Atlas-SNP	.											.	ZNF645	67	.	0			c.G834A						PASS	.	G		2,3833		0,2,0,1630,571	149.0	119.0	129.0		834	-5.1	0.0	X	dbSNP_134	129	28,6700		0,19,9,2409,1863	no	coding-synonymous	ZNF645	NM_152577.3		0,21,9,4039,2434	AA,AG,A,GG,G		0.4162,0.0522,0.284		278/426	22291942	30,10533	2203	4300	6503	SO:0001819	synonymous_variant	158506	exon1			ACCTCAGAAACAG	AK098601	CCDS14205.1	Xp22.11	2014-01-21			ENSG00000175809	ENSG00000175809			26371	protein-coding gene	gene with protein product							Standard	NM_152577		Approved	FLJ25735, HAKAIL, CT138	uc004dai.2	Q8N7E2	OTTHUMG00000021242	ENST00000323684.1:c.834G>A	X.37:g.22291942G>A		156.0	0.0	0		161.0	160.0	0.993789	NM_152577	A0AV29|A0AV31|E3SBK4|Q6DJY9	Silent	SNP	ENST00000323684.1	37	CCDS14205.1																																																																																			G|0.997;A|0.003	0.003	strong		0.463	ZNF645-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056037.1	NM_152577	
SYNE1	23345	hgsc.bcm.edu	37	6	152722368	152722368	+	Missense_Mutation	SNP	A	A	G	rs138004884		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:152722368A>G	ENST00000367255.5	-	47	7535	c.6934T>C	c.(6934-6936)Ttt>Ctt	p.F2312L	SYNE1_ENST00000423061.1_Missense_Mutation_p.F2319L|RP3-398G3.5_ENST00000458194.1_RNA|SYNE1_ENST00000448038.1_Missense_Mutation_p.F2319L|SYNE1_ENST00000341594.5_Missense_Mutation_p.F2349L|SYNE1_ENST00000265368.4_Missense_Mutation_p.F2312L	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	2312					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)		TCATTAATAAACTTCTCCACT	0.393										HNSCC(10;0.0054)			A|||	1	0.000199681	0.0	0.0	5008	,	,		19585	0.0		0.001	False		,,,				2504	0.0				p.F2319L		Atlas-SNP	.											.	SYNE1	3227	.	0			c.T6955C						PASS	.	A	LEU/PHE,LEU/PHE	1,4405	2.1+/-5.4	0,1,2202	147.0	129.0	135.0		6955,6934	5.6	1.0	6	dbSNP_134	135	8,8592	6.4+/-24.3	0,8,4292	yes	missense,missense	SYNE1	NM_033071.3,NM_182961.3	22,22	0,9,6494	GG,GA,AA		0.093,0.0227,0.0692	benign,benign	2319/8750,2312/8798	152722368	9,12997	2203	4300	6503	SO:0001583	missense	23345	exon47			TAATAAACTTCTC	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.6934T>C	6.37:g.152722368A>G	ENSP00000356224:p.Phe2312Leu	159.0	0.0	0		156.0	63.0	0.403846	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	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	14.92	2.678770	0.47886	2.27E-4	9.3E-4	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	5.58	5.58	0.84498	.	0.101968	0.43919	D	0.000518	T	0.11623	0.0283	L	0.39633	1.23	0.80722	D	1	B;B;B;B	0.15141	0.012;0.002;0.002;0.002	B;B;B;B	0.13407	0.009;0.003;0.003;0.004	T	0.08848	-1.0702	10	0.16896	T	0.51	.	11.6415	0.51235	0.9288:0.0:0.0712:0.0	.	2295;2312;2312;2319	B3W695;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	L	2312;2319;2312;2319;2349	ENSP00000356224:F2312L;ENSP00000396024:F2319L;ENSP00000265368:F2312L;ENSP00000390975:F2319L;ENSP00000341887:F2349L	ENSP00000265368:F2312L	F	-	1	0	SYNE1	152764061	1.000000	0.71417	0.963000	0.40424	0.921000	0.55340	5.286000	0.65639	2.133000	0.65898	0.482000	0.46254	TTT	A|0.999;G|0.001	0.001	strong		0.393	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
BAGE2	85319	hgsc.bcm.edu	37	21	11058322	11058322	+	RNA	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:11058322C>T	ENST00000470054.1	-	0	325							Q86Y30	BAGE2_HUMAN	B melanoma antigen family, member 2							extracellular region (GO:0005576)								Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		AAATGCACATCGCTGAAAGGG	0.383																																					p.D40N		Atlas-SNP	.											.	.	.	.	0			c.G118A						PASS	.						92.0	70.0	77.0					21																	11058322		692	1591	2283			85318	exon3			GCACATCGCTGAA	AF218570		21p	2009-03-13			ENSG00000187172	ENSG00000187172			15723	protein-coding gene	gene with protein product	"""cancer/testis antigen family 2, member 2"""					12461691	Standard	NM_182482		Approved	CT2.2		Q86Y30	OTTHUMG00000074128		21.37:g.11058322C>T		200.0	0.0	0		238.0	14.0	0.0588235	NM_182481	A8K925|Q08ER0	Missense_Mutation	SNP	ENST00000470054.1	37																																																																																				C|0.750;T|0.250	0.250	strong		0.383	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
BAZ2A	11176	hgsc.bcm.edu	37	12	56995907	56995907	+	Missense_Mutation	SNP	G	G	A	rs202169462		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:56995907G>A	ENST00000551812.1	-	20	3693	c.3500C>T	c.(3499-3501)gCc>gTc	p.A1167V	BAZ2A_ENST00000549884.1_Missense_Mutation_p.A1165V|BAZ2A_ENST00000379441.3_Missense_Mutation_p.A1137V|BAZ2A_ENST00000553222.1_5'Flank|BAZ2A_ENST00000179765.5_Missense_Mutation_p.A1135V	NM_013449.3	NP_038477.2	Q9UIF9	BAZ2A_HUMAN	bromodomain adjacent to zinc finger domain, 2A	1167					chromatin remodeling (GO:0006338)|chromatin silencing at rDNA (GO:0000183)|DNA methylation (GO:0006306)|heterochromatin assembly involved in chromatin silencing (GO:0070869)|histone deacetylation (GO:0016575)|histone H3-K9 methylation (GO:0051567)|histone H4 deacetylation (GO:0070933)|histone H4-K20 methylation (GO:0034770)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromatin silencing complex (GO:0005677)|nucleolus (GO:0005730)|rDNA heterochromatin (GO:0033553)	DNA binding (GO:0003677)|ligand-dependent nuclear receptor binding (GO:0016922)|lysine-acetylated histone binding (GO:0070577)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(15)|urinary_tract(1)	31						AGAGAAGAGGGCAGGGTTGAG	0.512													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18914	0.0		0.0	False		,,,				2504	0.0				p.A1167V		Atlas-SNP	.											.	BAZ2A	263	.	0			c.C3500T						PASS	.	G	VAL/ALA	0,3988		0,0,1994	18.0	19.0	18.0		3500	1.7	0.0	12		18	3,8319		0,3,4158	yes	missense	BAZ2A	NM_013449.3	64	0,3,6152	AA,AG,GG		0.036,0.0,0.0244	benign	1167/1906	56995907	3,12307	1994	4161	6155	SO:0001583	missense	11176	exon20			AAGAGGGCAGGGT	AB032254	CCDS44924.1, CCDS73483.1	12q13.3	2013-01-28				ENSG00000076108		"""Zinc fingers, PHD-type"""	962	protein-coding gene	gene with protein product	"""TTF-I interacting peptide 5"""	605682				10662543, 11532953	Standard	XM_005268596		Approved	KIAA0314, TIP5, WALp3	uc001slq.1	Q9UIF9	OTTHUMG00000170332	ENST00000551812.1:c.3500C>T	12.37:g.56995907G>A	ENSP00000446880:p.Ala1167Val	87.0	0.0	0		87.0	45.0	0.517241	NM_013449	B3KN66|O00536|O15030|Q68DI8|Q96H26	Missense_Mutation	SNP	ENST00000551812.1	37	CCDS44924.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	2.919	-0.223686	0.06061	0.0	3.6E-4	ENSG00000076108	ENST00000379441;ENST00000179765;ENST00000551812;ENST00000549787;ENST00000549884	T;T;T;T;T	0.70164	-0.15;-0.15;-0.15;-0.46;-0.15	5.6	1.72	0.24424	.	0.512331	0.20956	N	0.082651	T	0.49133	0.1539	L	0.38531	1.155	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.0	T	0.29212	-1.0019	10	0.30854	T	0.27	.	4.9226	0.13878	0.239:0.0:0.6142:0.1468	.	1165;1167;1167	F8VU39;Q9UIF9-3;Q9UIF9	.;.;BAZ2A_HUMAN	V	1137;1135;1167;103;1165	ENSP00000368754:A1137V;ENSP00000179765:A1135V;ENSP00000446880:A1167V;ENSP00000448760:A103V;ENSP00000447941:A1165V	ENSP00000179765:A1135V	A	-	2	0	BAZ2A	55282174	0.008000	0.16893	0.000000	0.03702	0.010000	0.07245	1.643000	0.37217	0.123000	0.18342	-0.229000	0.12294	GCC	G|0.999;A|0.001	0.001	strong		0.512	BAZ2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000408561.1	NM_013449	
MEGF6	1953	hgsc.bcm.edu	37	1	3417545	3417545	+	Missense_Mutation	SNP	A	A	G	rs41303857	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:3417545A>G	ENST00000356575.4	-	20	2786	c.2560T>C	c.(2560-2562)Ttt>Ctt	p.F854L	MEGF6_ENST00000294599.4_Missense_Mutation_p.F749L	NM_001409.3	NP_001400.3	O75095	MEGF6_HUMAN	multiple EGF-like-domains 6	854	EGF-like 14. {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)		TGGCAGCTAAAGCCGGTCCAC	0.652													A|||	5	0.000998403	0.0	0.0029	5008	,	,		18548	0.0		0.003	False		,,,				2504	0.0				p.F854L	Ovarian(73;978 3658)	Atlas-SNP	.											.	MEGF6	91	.	0			c.T2560C						PASS	.	A	LEU/PHE	4,3954		0,4,1975	36.0	45.0	42.0		2560	1.7	1.0	1	dbSNP_127	42	27,8299		0,27,4136	yes	missense	MEGF6	NM_001409.3	22	0,31,6111	GG,GA,AA		0.3243,0.1011,0.2524	benign	854/1542	3417545	31,12253	1979	4163	6142	SO:0001583	missense	1953	exon20			AGCTAAAGCCGGT	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.2560T>C	1.37:g.3417545A>G	ENSP00000348982:p.Phe854Leu	83.0	0.0	0		127.0	57.0	0.448819	NM_001409	Q4AC86|Q5VV39	Missense_Mutation	SNP	ENST00000356575.4	37	CCDS41237.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	1.886	-0.456687	0.04540	0.001011	0.003243	ENSG00000162591	ENST00000294599;ENST00000356575	T;T	0.24538	1.85;1.85	4.98	1.73	0.24493	EGF-like, laminin (2);EGF-like region, conserved site (2);Epidermal growth factor-like, type 3 (1);	0.277593	0.32703	N	0.005760	T	0.06416	0.0165	N	0.00686	-1.255	0.24354	N	0.994905	B;B	0.02656	0.0;0.0	B;B	0.11329	0.006;0.002	T	0.32981	-0.9886	10	0.27082	T	0.32	-9.1415	6.1992	0.20567	0.241:0.0:0.6099:0.1491	rs41303857;rs61744087	854;749	O75095;O75095-2	MEGF6_HUMAN;.	L	749;854	ENSP00000294599:F749L;ENSP00000348982:F854L	ENSP00000294599:F749L	F	-	1	0	MEGF6	3407405	0.024000	0.19004	0.996000	0.52242	0.611000	0.37282	1.115000	0.31209	1.072000	0.40860	-0.366000	0.07423	TTT	A|0.998;G|0.002	0.002	strong		0.652	MEGF6-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354866.1	NM_001409	
PIK3CA	5290	hgsc.bcm.edu	37	3	178936082	178936082	+	Missense_Mutation	SNP	G	G	A	rs121913273		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:178936082G>A	ENST00000263967.3	+	10	1781	c.1624G>A	c.(1624-1626)Gaa>Aaa	p.E542K		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	542	PIK helical. {ECO:0000255|PROSITE- ProRule:PRU00878}.		E -> K (in CLOVE, KERSEB, CRC and BC; also found in glioblastoma multiforme and endometrial carcinoma; shows an increase in lipid kinase activity; oncogenic in vivo; occurs in the interface between the PI3K helical domain and the nSH2 (N- terminal SH2) region of the p85 regulatory subunit and may reduce the inhibitory effect of p85; requires interaction with RAS to induce cellular transformation). {ECO:0000269|PubMed:15289301, ECO:0000269|PubMed:15784156, ECO:0000269|PubMed:15924253, ECO:0000269|PubMed:15994075, ECO:0000269|PubMed:16322209, ECO:0000269|PubMed:16353168, ECO:0000269|PubMed:16533766, ECO:0000269|PubMed:17673550, ECO:0000269|PubMed:22658544}.|E -> Q (found in an endometrial carcinoma sample; unknown pathological significance). {ECO:0000269|PubMed:16322209}.|E -> V (in BC; unknown pathological significance). {ECO:0000269|PubMed:16353168}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|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)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.E542K(545)|p.E542Q(10)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TCCTCTCTCTGAAATCACTGA	0.333	E542K(BT483_BREAST)|E542K(CAL51_BREAST)|E542K(HGC27_STOMACH)|E542K(IM95_STOMACH)|E542K(JHUEM1_ENDOMETRIUM)|E542K(NCIH1341_LUNG)|E542K(SW948_LARGE_INTESTINE)|E542K(T84_LARGE_INTESTINE)|E542K(VMCUB1_URINARY_TRACT)	57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											p.E542K	Colon(199;1504 1750 3362 26421 31210 32040)	Atlas-SNP	.		Dom	yes		3	3q26.3	5290	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""		"""E, O"""	PIK3CA_ENST00000263967,NS,carcinoma,0,745	PIK3CA	8460	745	555	Substitution - Missense(555)	breast(176)|large_intestine(166)|urinary_tract(45)|endometrium(37)|skin(19)|lung(18)|stomach(16)|ovary(16)|thyroid(14)|upper_aerodigestive_tract(9)|central_nervous_system(7)|cervix(6)|liver(6)|oesophagus(5)|penis(4)|kidney(3)|soft_tissue(2)|haematopoietic_and_lymphoid_tissue(2)|prostate(2)|biliary_tract(1)|pituitary(1)	c.G1624A						scavenged	.						56.0	56.0	56.0					3																	178936082		1809	4069	5878	SO:0001583	missense	5290	exon10			CTCTCTGAAATCA		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1624G>A	3.37:g.178936082G>A	ENSP00000263967:p.Glu542Lys	275.0	1.0	0.00363636		372.0	85.0	0.228495	NM_006218	Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	G	34	5.360420	0.95877	.	.	ENSG00000121879	ENST00000263967	T	0.62105	0.05	5.78	5.78	0.91487	Phosphoinositide 3-kinase, accessory (PIK) domain (3);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.69287	0.3094	L	0.41356	1.27	0.80722	D	1	D	0.65815	0.995	D	0.63192	0.912	T	0.60296	-0.7291	10	0.09843	T	0.71	-23.9623	20.0024	0.97423	0.0:0.0:1.0:0.0	.	542	P42336	PK3CA_HUMAN	K	542	ENSP00000263967:E542K	ENSP00000263967:E542K	E	+	1	0	PIK3CA	180418776	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	9.476000	0.97823	2.722000	0.93159	0.467000	0.42956	GAA	.	.	weak		0.333	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
ADGB	79747	hgsc.bcm.edu	37	6	146977963	146977963	+	Silent	SNP	A	A	C	rs79354452	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:146977963A>C	ENST00000397944.3	+	5	535	c.459A>C	c.(457-459)ggA>ggC	p.G153G	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	153	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						TCAATGGAGGAATTTTGAGCA	0.418													A|||	37	0.00738818	0.0	0.0115	5008	,	,		16532	0.0		0.0109	False		,,,				2504	0.0184				p.G153G		Atlas-SNP	.											.	ADGB	93	.	0			c.A459C						PASS	.	A		2,1382		0,2,690	88.0	80.0	82.0		459	-4.7	0.0	6	dbSNP_132	82	73,3109		0,73,1518	no	coding-synonymous	C6orf103	NM_024694.3		0,75,2208	CC,CA,AA		2.2942,0.1445,1.6426		153/1668	146977963	75,4491	692	1591	2283	SO:0001819	synonymous_variant	79747	exon5			TGGAGGAATTTTG	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.459A>C	6.37:g.146977963A>C		139.0	0.0	0		157.0	74.0	0.471338	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				A|0.992;C|0.008	0.008	strong		0.418	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
SLC22A14	9389	hgsc.bcm.edu	37	3	38357067	38357067	+	Missense_Mutation	SNP	T	T	C	rs34256819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:38357067T>C	ENST00000273173.4	+	8	1488	c.1397T>C	c.(1396-1398)cTc>cCc	p.L466P	SLC22A14_ENST00000448498.1_Missense_Mutation_p.L466P	NM_004803.3	NP_004794.2	Q9Y267	S22AE_HUMAN	solute carrier family 22, member 14	466			L -> P (in dbSNP:rs34256819).		organic cation transport (GO:0015695)	integral component of plasma membrane (GO:0005887)	organic cation transmembrane transporter activity (GO:0015101)			central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(5)|prostate(2)|skin(1)	21				KIRC - Kidney renal clear cell carcinoma(284;0.0554)|Kidney(284;0.0696)		GGCCTCAGACTCAAGTGGCCA	0.587													T|||	4	0.000798722	0.0015	0.0	5008	,	,		19422	0.0		0.002	False		,,,				2504	0.0				p.L466P		Atlas-SNP	.											.	SLC22A14	64	.	0			c.T1397C						PASS	.	T	PRO/LEU	2,4404	4.2+/-10.8	0,2,2201	96.0	84.0	88.0		1397	3.7	0.1	3	dbSNP_126	88	32,8568	22.8+/-68.1	0,32,4268	yes	missense	SLC22A14	NM_004803.3	98	0,34,6469	CC,CT,TT		0.3721,0.0454,0.2614	probably-damaging	466/595	38357067	34,12972	2203	4300	6503	SO:0001583	missense	9389	exon8			TCAGACTCAAGTG	AB011082	CCDS2677.1	3p21.3	2013-05-22	2008-01-11	2003-10-15	ENSG00000144671	ENSG00000144671		"""Solute carriers"""	8495	protein-coding gene	gene with protein product		604048	"""organic cationic transporter-like 4"", ""solute carrier family 22 (organic cation transporter), member 14"""	ORCTL4		10072596	Standard	NM_004803		Approved	OCTL2	uc003cib.2	Q9Y267	OTTHUMG00000131082	ENST00000273173.4:c.1397T>C	3.37:g.38357067T>C	ENSP00000273173:p.Leu466Pro	64.0	0.0	0		106.0	31.0	0.292453	NM_004803	A0AVS9|A1L4H6|B2RCX3|Q6DJT3	Missense_Mutation	SNP	ENST00000273173.4	37	CCDS2677.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	14.48	2.549489	0.45383	4.54E-4	0.003721	ENSG00000144671	ENST00000448498;ENST00000273173	T;T	0.66815	-0.23;-0.23	3.66	3.66	0.41972	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.270402	0.15269	U	0.271366	T	0.56426	0.1984	N	0.02011	-0.69	0.20638	N	0.999874	D	0.76494	0.999	D	0.69307	0.963	T	0.50276	-0.8847	10	0.87932	D	0	.	8.9423	0.35738	0.0:0.0:0.0:1.0	rs34256819	466	Q9Y267	S22AE_HUMAN	P	466	ENSP00000396283:L466P;ENSP00000273173:L466P	ENSP00000273173:L466P	L	+	2	0	SLC22A14	38332071	0.184000	0.23200	0.067000	0.19924	0.003000	0.03518	0.714000	0.25808	1.873000	0.54277	0.533000	0.62120	CTC	T|0.997;C|0.003	0.003	strong		0.587	SLC22A14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253742.3	NM_004803	
HK1	3098	hgsc.bcm.edu	37	10	71142492	71142492	+	Silent	SNP	C	C	T	rs140498607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:71142492C>T	ENST00000359426.6	+	10	1619	c.1515C>T	c.(1513-1515)aaC>aaT	p.N505N	HK1_ENST00000494253.1_3'UTR|HK1_ENST00000298649.3_Silent_p.N504N|HK1_ENST00000448642.2_Silent_p.N540N|HK1_ENST00000360289.2_Silent_p.N493N|HK1_ENST00000404387.2_Silent_p.N509N	NM_000188.2	NP_000179.2	P19367	HXK1_HUMAN	hexokinase 1	505	Catalytic.|Hexokinase type-1 2.				carbohydrate metabolic process (GO:0005975)|carbohydrate phosphorylation (GO:0046835)|cell death (GO:0008219)|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)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)			breast(1)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|liver(1)|lung(14)|ovary(1)|urinary_tract(2)	35						AGACGCACAACAATGCCGTGG	0.622													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		19064	0.001		0.008	False		,,,				2504	0.001				p.N509N		Atlas-SNP	.											.	HK1	170	.	0			c.C1527T						PASS	.	C	,,,,	2,4404	4.2+/-10.8	0,2,2201	103.0	77.0	86.0		1515,1512,1527,1527,1479	-9.8	0.0	10	dbSNP_134	86	54,8546	34.3+/-88.2	0,54,4246	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HK1	NM_000188.2,NM_033496.2,NM_033497.2,NM_033498.2,NM_033500.2	,,,,	0,56,6447	TT,TC,CC		0.6279,0.0454,0.4306	,,,,	505/918,504/917,509/922,509/922,493/906	71142492	56,12950	2203	4300	6503	SO:0001819	synonymous_variant	3098	exon13			GCACAACAATGCC	M75126	CCDS7289.1, CCDS7290.1, CCDS7291.1, CCDS7292.1	10q22	2014-09-17			ENSG00000156515	ENSG00000156515	2.7.1.1		4922	protein-coding gene	gene with protein product		142600					Standard	NM_033496		Approved		uc001jpi.4	P19367	OTTHUMG00000018380	ENST00000359426.6:c.1515C>T	10.37:g.71142492C>T		51.0	0.0	0		49.0	17.0	0.346939	NM_033498	E9PCK0|O43443|O43444|O75574|Q5VTC3|Q96HC8|Q9NNZ4|Q9NNZ5	Silent	SNP	ENST00000359426.6	37	CCDS7292.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	HK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048429.2	NM_000188	
UBXN2B	137886	hgsc.bcm.edu	37	8	59329407	59329407	+	Splice_Site	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:59329407A>T	ENST00000399598.2	+	2	206		c.e2-1		UBXN2B_ENST00000522978.1_Splice_Site	NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B							endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(4)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	13						GTTATTATGTAGTTGGCCTTG	0.378																																					.		Atlas-SNP	.											.	UBXN2B	36	.	0			c.85-2A>T						PASS	.						87.0	79.0	81.0					8																	59329407		1877	4089	5966	SO:0001630	splice_region_variant	137886	exon2			TTATGTAGTTGGC	AK054658	CCDS43741.1	8q12.1	2008-08-08			ENSG00000215114	ENSG00000215114		"""UBX domain containing"""	27035	protein-coding gene	gene with protein product		610686				8619474, 9110174	Standard	NM_001077619		Approved	p37	uc003xtl.3	Q14CS0	OTTHUMG00000164300	ENST00000399598.2:c.85-1A>T	8.37:g.59329407A>T		54.0	0.0	0		33.0	10.0	0.30303	NM_001077619	B3KWZ3	Splice_Site	SNP	ENST00000399598.2	37	CCDS43741.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.063813	0.55432	.	.	ENSG00000215114	ENST00000399598	.	.	.	5.89	5.89	0.94794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.7027	0.57043	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	UBXN2B	59491961	1.000000	0.71417	0.920000	0.36463	0.789000	0.44602	4.736000	0.62059	2.257000	0.74773	0.460000	0.39030	.	.	.	none		0.378	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	Intron
ERCC1	2067	hgsc.bcm.edu	37	19	45923598	45923598	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:45923598A>G	ENST00000300853.3	-	4	1000	c.409T>C	c.(409-411)Tgt>Cgt	p.C137R	ERCC1_ENST00000423698.2_Missense_Mutation_p.C65R|ERCC1_ENST00000013807.5_Missense_Mutation_p.C137R|ERCC1_ENST00000589165.1_Missense_Mutation_p.C137R|ERCC1_ENST00000340192.7_Missense_Mutation_p.C137R|ERCC1_ENST00000591636.1_Missense_Mutation_p.C137R	NM_001983.3	NP_001974.1	P07992	ERCC1_HUMAN	excision repair cross-complementation group 1	137					cell proliferation (GO:0008283)|chromosome organization (GO:0051276)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|interstrand cross-link repair (GO:0036297)|isotype switching (GO:0045190)|male gonad development (GO:0008584)|mitotic recombination (GO:0006312)|multicellular organism growth (GO:0035264)|multicellular organismal aging (GO:0010259)|negative regulation of telomere maintenance (GO:0032205)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA damage removal (GO:0000718)|nucleotide-excision repair, DNA incision, 3'-to lesion (GO:0006295)|nucleotide-excision repair, DNA incision, 5'-to lesion (GO:0006296)|oogenesis (GO:0048477)|post-embryonic hemopoiesis (GO:0035166)|pyrimidine dimer repair by nucleotide-excision repair (GO:0000720)|replicative cell aging (GO:0001302)|response to nutrient (GO:0007584)|response to oxidative stress (GO:0006979)|response to sucrose (GO:0009744)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)|syncytium formation (GO:0006949)|transcription-coupled nucleotide-excision repair (GO:0006283)|UV protection (GO:0009650)	cytoplasm (GO:0005737)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleotide-excision repair complex (GO:0000109)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	damaged DNA binding (GO:0003684)|endonuclease activity (GO:0004519)|protein C-terminus binding (GO:0008022)|protein domain specific binding (GO:0019904)|single-stranded DNA binding (GO:0003697)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(4)|lung(2)|ovary(2)|skin(1)	15		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0247)		AACAGGGCACAGGTGCTCTGG	0.617								Nucleotide excision repair (NER)																													p.C137R		Atlas-SNP	.											.	ERCC1	46	.	0			c.T409C						PASS	.						87.0	68.0	74.0					19																	45923598		2203	4300	6503	SO:0001583	missense	2067	exon4			GGGCACAGGTGCT		CCDS12662.1, CCDS12663.1, CCDS54279.1	19q13.32	2014-03-07	2014-03-07			ENSG00000012061			3433	protein-coding gene	gene with protein product		126380	"""excision repair cross-complementing rodent repair deficiency, complementation group 1 (includes overlapping antisense sequence)"""			6462228	Standard	NM_001983		Approved	RAD10	uc002pbs.2	P07992		ENST00000300853.3:c.409T>C	19.37:g.45923598A>G	ENSP00000300853:p.Cys137Arg	68.0	0.0	0		59.0	38.0	0.644068	NM_001983	B2RC01|B3KRR0|Q7Z7F5|Q96S40	Missense_Mutation	SNP	ENST00000300853.3	37	CCDS12662.1	.	.	.	.	.	.	.	.	.	.	A	18.20	3.572338	0.65765	.	.	ENSG00000012061	ENST00000300853;ENST00000340192;ENST00000423698;ENST00000013807	T;T;T;T	0.52526	0.76;0.66;0.87;0.71	5.28	5.28	0.74379	Restriction endonuclease, type II-like (1);	0.000000	0.85682	D	0.000000	T	0.62319	0.2418	M	0.91561	3.22	0.80722	D	1	P;B;P;P	0.43973	0.731;0.054;0.681;0.823	P;B;B;B	0.45913	0.497;0.064;0.32;0.399	T	0.71210	-0.4660	10	0.66056	D	0.02	-2.2056	11.5895	0.50938	1.0:0.0:0.0:0.0	.	137;65;137;137	Q7Z7F5;B3KRR0;Q96S40;P07992	.;.;.;ERCC1_HUMAN	R	137;137;65;137	ENSP00000300853:C137R;ENSP00000345203:C137R;ENSP00000394875:C65R;ENSP00000013807:C137R	ENSP00000013807:C137R	C	-	1	0	ERCC1	50615438	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	7.739000	0.84976	2.013000	0.59113	0.374000	0.22700	TGT	.	.	none		0.617	ERCC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459542.1	NM_001983	
RABGAP1	23637	hgsc.bcm.edu	37	9	125748669	125748669	+	Silent	SNP	A	A	G	rs376096787		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:125748669A>G	ENST00000373647.4	+	4	695	c.561A>G	c.(559-561)tcA>tcG	p.S187S		NM_012197.3	NP_036329.3	Q9Y3P9	RBGP1_HUMAN	RAB GTPase activating protein 1	187	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cell cycle (GO:0007049)|positive regulation of GTPase activity (GO:0043547)|regulation of GTP catabolic process (GO:0033124)	centrosome (GO:0005813)|cytosol (GO:0005829)|microtubule associated complex (GO:0005875)	DNA binding (GO:0003677)|GTPase activator activity (GO:0005096)|Rab GTPase activator activity (GO:0005097)|Rab GTPase binding (GO:0017137)|tubulin binding (GO:0015631)			breast(3)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|prostate(4)|stomach(3)|upper_aerodigestive_tract(1)	41						TTACCCTTTCAGTGCCGAATG	0.438																																					p.S187S		Atlas-SNP	.											.	RABGAP1	164	.	0			c.A561G						PASS	.	A		0,4406		0,0,2203	185.0	179.0	181.0		561	-10.1	0.1	9		181	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RABGAP1	NM_012197.3		0,1,6502	GG,GA,AA		0.0116,0.0,0.0077		187/1070	125748669	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23637	exon4			CCTTTCAGTGCCG	AJ011679	CCDS6848.2	9q34.11	2013-07-09			ENSG00000011454	ENSG00000011454			17155	protein-coding gene	gene with protein product	"""rab6 GTPase activating protein (GAP and centrosome-associated)"", ""TBC1 domain family, member 11"""	615882				10202141	Standard	NM_012197		Approved	GAPCenA, TBC1D11	uc011lzh.2	Q9Y3P9	OTTHUMG00000020633	ENST00000373647.4:c.561A>G	9.37:g.125748669A>G		199.0	0.0	0		205.0	107.0	0.521951	NM_012197	B9A6L2|Q05CW2|Q6ZMY1|Q9HA28|Q9P0E2|Q9UG67	Silent	SNP	ENST00000373647.4	37	CCDS6848.2																																																																																			.	.	weak		0.438	RABGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053976.3	NM_012197	
MFI2	4241	hgsc.bcm.edu	37	3	196742243	196742243	+	Missense_Mutation	SNP	C	C	T	rs45625439	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:196742243C>T	ENST00000296350.5	-	9	1339	c.1226G>A	c.(1225-1227)cGg>cAg	p.R409Q		NM_005929.5	NP_005920.2	P08582	TRFM_HUMAN	antigen p97 (melanoma associated) identified by monoclonal antibodies 133.2 and 96.5	409	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				cellular iron ion homeostasis (GO:0006879)|iron ion import (GO:0097286)|negative regulation of substrate adhesion-dependent cell spreading (GO:1900025)|positive regulation of extracellular matrix disassembly (GO:0090091)|positive regulation of plasminogen activation (GO:0010756)	anchored component of plasma membrane (GO:0046658)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ferric iron binding (GO:0008199)|iron ion binding (GO:0005506)			breast(2)|endometrium(3)|kidney(2)|large_intestine(2)|lung(10)|prostate(1)	20	all_cancers(143;3.95e-09)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.55e-24)|all cancers(36;2.87e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.76e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00536)		CACCTGGATCCGCTCCATGCA	0.657													C|||	23	0.00459265	0.0	0.0043	5008	,	,		18548	0.0		0.0129	False		,,,				2504	0.0072				p.R409Q		Atlas-SNP	.											.	MFI2	88	.	0			c.G1226A						PASS	.	C	GLN/ARG	22,4348		0,22,2163	34.0	24.0	27.0		1226	-3.8	0.9	3	dbSNP_127	27	146,8408		2,142,4133	yes	missense	MFI2	NM_005929.5	43	2,164,6296	TT,TC,CC		1.7068,0.5034,1.2999	benign	409/739	196742243	168,12756	2185	4277	6462	SO:0001583	missense	4241	exon9			TGGATCCGCTCCA		CCDS3325.1, CCDS3326.1	3q28-q29	2012-10-02			ENSG00000163975	ENSG00000163975		"""CD molecules"""	7037	protein-coding gene	gene with protein product	"""melanotransferrin"", ""membrane-bound transferrin-like protein"""	155750					Standard	NM_033316		Approved	CD228, FLJ38863, MAP97, MGC4856, MTF1	uc003fxk.4	P08582	OTTHUMG00000155518	ENST00000296350.5:c.1226G>A	3.37:g.196742243C>T	ENSP00000296350:p.Arg409Gln	91.0	0.0	0		107.0	66.0	0.616822	NM_005929	Q9BQE2	Missense_Mutation	SNP	ENST00000296350.5	37	CCDS3325.1	14	0.00641025641025641	0	0.0	2	0.0055248618784530384	0	0.0	12	0.0158311345646438	C	12.39	1.923379	0.33908	0.005034	0.017068	ENSG00000163975	ENST00000296350	T	0.32272	1.46	5.72	-3.84	0.04256	.	1.025380	0.07685	N	0.937703	T	0.04907	0.0132	N	0.03177	-0.4	0.41333	D	0.987255	B	0.09022	0.002	B	0.08055	0.003	T	0.38001	-0.9681	10	0.14656	T	0.56	-10.756	5.8183	0.18514	0.183:0.3633:0.0:0.4537	rs45625439	409	P08582	TRFM_HUMAN	Q	409	ENSP00000296350:R409Q	ENSP00000296350:R409Q	R	-	2	0	MFI2	198226640	0.027000	0.19231	0.857000	0.33713	0.825000	0.46686	-0.069000	0.11542	-0.368000	0.08040	-1.320000	0.01293	CGG	C|0.991;T|0.009	0.009	strong		0.657	MFI2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340458.1		
CLEC16A	23274	hgsc.bcm.edu	37	16	11272479	11272479	+	Missense_Mutation	SNP	G	G	A	rs74163631		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:11272479G>A	ENST00000409790.1	+	24	3324	c.3094G>A	c.(3094-3096)Gcc>Acc	p.A1032T	CLEC16A_ENST00000381822.2_Missense_Mutation_p.A119T	NM_015226.2	NP_056041.1			C-type lectin domain family 16, member A									p.0?(1)		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						CACGCCGGCTGCCGCCTGCAC	0.687																																					p.A1032T		Atlas-SNP	.											.	CLEC16A	101	.	1	Whole gene deletion(1)	haematopoietic_and_lymphoid_tissue(1)	c.G3094A						PASS	.	G	THR/ALA	0,4094		0,0,2047	10.0	13.0	12.0		3094	-7.3	0.0	16	dbSNP_130	12	2,8338		0,2,4168	no	missense	CLEC16A	NM_015226.2	58	0,2,6215	AA,AG,GG		0.024,0.0,0.0161	benign	1032/1054	11272479	2,12432	2047	4170	6217	SO:0001583	missense	23274	exon23			CCGGCTGCCGCCT	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.3094G>A	16.37:g.11272479G>A	ENSP00000387122:p.Ala1032Thr	10.0	0.0	0		26.0	13.0	0.5	NM_015226		Missense_Mutation	SNP	ENST00000409790.1	37	CCDS45409.1	.	.	.	.	.	.	.	.	.	.	G	13.01	2.109842	0.37242	0.0	2.4E-4	ENSG00000038532	ENST00000409790;ENST00000542102;ENST00000381822	T	0.44083	0.93	4.4	-7.33	0.01431	.	1.036120	0.07675	N	0.936064	T	0.15089	0.0364	N	0.08118	0	0.09310	N	1	B;B	0.28350	0.208;0.002	B;B	0.22152	0.038;0.004	T	0.15723	-1.0427	10	0.49607	T	0.09	0.8435	1.4953	0.02465	0.3763:0.2341:0.2704:0.1192	.	119;1032	Q2KHT3-3;Q2KHT3	.;CL16A_HUMAN	T	1032;1032;119	ENSP00000387122:A1032T	ENSP00000371244:A119T	A	+	1	0	CLEC16A	11179980	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.117000	0.10708	-1.280000	0.02402	-0.140000	0.14226	GCC	.	.	weak		0.687	CLEC16A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328540.2	NM_015226	
PTK2	5747	hgsc.bcm.edu	37	8	141840574	141840574	+	Silent	SNP	G	G	A	rs148611560	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141840574G>A	ENST00000522684.1	-	8	874	c.645C>T	c.(643-645)gtC>gtT	p.V215V	PTK2_ENST00000519419.1_Silent_p.V259V|PTK2_ENST00000340930.3_Silent_p.V215V|PTK2_ENST00000535192.1_Silent_p.V215V|PTK2_ENST00000521059.1_Silent_p.V215V|PTK2_ENST00000395218.2_Silent_p.V215V|PTK2_ENST00000517887.1_Silent_p.V259V	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2	215	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			TAATTACCTTGACAGAATCCA	0.303													G|||	4	0.000798722	0.0	0.0029	5008	,	,		15534	0.0		0.002	False		,,,				2504	0.0				p.V237V		Atlas-SNP	.											.	PTK2	311	.	0			c.C711T						PASS	.	G	,,	3,4361		0,3,2179	30.0	31.0	30.0		645,711,645	5.2	1.0	8	dbSNP_134	30	18,8528		0,18,4255	no	coding-synonymous,coding-synonymous,coding-synonymous	PTK2	NM_001199649.1,NM_005607.4,NM_153831.3	,,	0,21,6434	AA,AG,GG		0.2106,0.0687,0.1627	,,	215/1066,237/1075,215/1053	141840574	21,12889	2182	4273	6455	SO:0001819	synonymous_variant	5747	exon8			TACCTTGACAGAA	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.645C>T	8.37:g.141840574G>A		160.0	0.0	0		165.0	82.0	0.49697	NM_005607	B4E2N6|F5H4S4|Q14291|Q9UD85	Silent	SNP	ENST00000522684.1	37	CCDS6381.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	9.907	1.208441	0.22205	6.87E-4	0.002106	ENSG00000169398	ENST00000519654	.	.	.	5.25	5.25	0.73442	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.4863	0.55874	0.0:0.1681:0.8319:0.0	.	.	.	.	X	226	.	.	Q	-	1	0	PTK2	141909756	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	1.739000	0.38217	2.618000	0.88619	0.655000	0.94253	CAA	G|0.998;A|0.002	0.002	strong		0.303	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
CCDC60	160777	hgsc.bcm.edu	37	12	119961587	119961587	+	Missense_Mutation	SNP	G	G	A	rs78218795	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:119961587G>A	ENST00000327554.2	+	11	1658	c.1193G>A	c.(1192-1194)gGc>gAc	p.G398D	RP11-768F21.1_ENST00000509470.2_lincRNA	NM_178499.3	NP_848594.2	Q8IWA6	CCD60_HUMAN	coiled-coil domain containing 60	398										endometrium(4)|kidney(3)|large_intestine(8)|lung(15)|ovary(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	40	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)			BRCA - Breast invasive adenocarcinoma(302;0.207)		CAGGAGGCTGGCTTCTGCCTG	0.483													G|||	156	0.0311502	0.0862	0.0274	5008	,	,		20637	0.001		0.0129	False		,,,				2504	0.0092				p.G398D		Atlas-SNP	.											.	CCDC60	84	.	0			c.G1193A						PASS	.	G	ASP/GLY	319,4087	170.1+/-200.6	11,297,1895	100.0	82.0	88.0		1193	4.2	1.0	12	dbSNP_131	88	148,8452	72.6+/-135.2	0,148,4152	yes	missense	CCDC60	NM_178499.3	94	11,445,6047	AA,AG,GG		1.7209,7.2401,3.5907	probably-damaging	398/551	119961587	467,12539	2203	4300	6503	SO:0001583	missense	160777	exon11			AGGCTGGCTTCTG	BC040553	CCDS9190.1	12q24.23	2006-02-03			ENSG00000183273	ENSG00000183273			28610	protein-coding gene	gene with protein product						12477932	Standard	NM_178499		Approved	MGC39827	uc001txe.3	Q8IWA6	OTTHUMG00000168943	ENST00000327554.2:c.1193G>A	12.37:g.119961587G>A	ENSP00000333374:p.Gly398Asp	68.0	0.0	0		60.0	32.0	0.533333	NM_178499		Missense_Mutation	SNP	ENST00000327554.2	37	CCDS9190.1	60	0.027472527472527472	43	0.08739837398373984	7	0.019337016574585635	1	0.0017482517482517483	9	0.011873350923482849	G	16.22	3.061173	0.55432	0.072401	0.017209	ENSG00000183273	ENST00000327554	T	0.22743	1.94	4.16	4.16	0.48862	.	0.128128	0.35407	N	0.003225	T	0.01558	0.0050	L	0.55481	1.735	0.80722	D	1	D	0.71674	0.998	D	0.68039	0.955	T	0.00032	-1.2278	9	.	.	.	-20.1692	11.8272	0.52273	0.0:0.0:1.0:0.0	.	398	Q8IWA6	CCD60_HUMAN	D	398	ENSP00000333374:G398D	.	G	+	2	0	CCDC60	118445970	1.000000	0.71417	0.999000	0.59377	0.921000	0.55340	2.598000	0.46223	2.156000	0.67533	0.655000	0.94253	GGC	G|0.968;A|0.032	0.032	strong		0.483	CCDC60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401680.1	NM_178499	
TSC1	7248	hgsc.bcm.edu	37	9	135804239	135804239	+	Silent	SNP	G	G	A	rs145987906		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:135804239G>A	ENST00000298552.3	-	3	242	c.21C>T	c.(19-21)gtC>gtT	p.V7V	TSC1_ENST00000440111.2_Silent_p.V7V|TSC1_ENST00000475903.1_5'UTR|TSC1_ENST00000545250.1_Silent_p.V7V|TSC1_ENST00000403810.1_Silent_p.V7V	NM_000368.4|NM_001162426.1|NM_001162427.1	NP_000359.1|NP_001155898.1|NP_001155899.1	Q92574	TSC1_HUMAN	tuberous sclerosis 1	7					activation of Rho GTPase activity (GO:0032862)|cardiac muscle cell differentiation (GO:0055007)|cell cycle arrest (GO:0007050)|cell projection organization (GO:0030030)|cell-matrix adhesion (GO:0007160)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|insulin receptor signaling pathway (GO:0008286)|kidney development (GO:0001822)|myelination (GO:0042552)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of TOR signaling (GO:0032007)|negative regulation of translation (GO:0017148)|neural tube closure (GO:0001843)|positive regulation of focal adhesion assembly (GO:0051894)|potassium ion transport (GO:0006813)|protein heterooligomerization (GO:0051291)|protein stabilization (GO:0050821)|regulation of cell cycle (GO:0051726)|regulation of cell-matrix adhesion (GO:0001952)|regulation of phosphoprotein phosphatase activity (GO:0043666)|regulation of protein kinase activity (GO:0045859)|regulation of stress fiber assembly (GO:0051492)|regulation of translation (GO:0006417)|response to insulin (GO:0032868)|rRNA export from nucleus (GO:0006407)|synapse organization (GO:0050808)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|lamellipodium (GO:0030027)|membrane (GO:0016020)|protein complex (GO:0043234)|TSC1-TSC2 complex (GO:0033596)	chaperone binding (GO:0051087)|GTPase regulator activity (GO:0030695)|protein N-terminus binding (GO:0047485)			NS(1)|bone(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(9)|lung(20)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	65				OV - Ovarian serous cystadenocarcinoma(145;4.32e-08)|Epithelial(140;2.72e-06)		GAAGCTCCCCGACATTTGCTT	0.527			"""D, Mis, N, F, S"""			"""hamartoma, renal cell"""			Tuberous Sclerosis																												p.V7V		Atlas-SNP	.	yes	Rec		Tuberous sclerosis 1	9	9q34	7248	tuberous sclerosis 1 gene		"""E, O"""	.	TSC1	167	.	0			c.C21T						PASS	.						104.0	84.0	91.0					9																	135804239		2203	4300	6503	SO:0001819	synonymous_variant	7248	exon3	Familial Cancer Database	TS, Tuberous Sclerosis Complex, TSC, Bourneville-Pringle disease	CTCCCCGACATTT	AF013168	CCDS6956.1, CCDS55350.1	9q34	2014-09-17			ENSG00000165699	ENSG00000165699			12362	protein-coding gene	gene with protein product		605284		TSC		9242607, 10806479	Standard	NM_000368		Approved	KIAA0243, LAM, hamartin	uc004cca.2	Q92574	OTTHUMG00000020844	ENST00000298552.3:c.21C>T	9.37:g.135804239G>A		84.0	0.0	0		82.0	52.0	0.634146	NM_000368	B7Z897|Q5VVN5	Silent	SNP	ENST00000298552.3	37	CCDS6956.1																																																																																			G|1.000;C|0.000	.	alt		0.527	TSC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054799.1		
GPER1	2852	hgsc.bcm.edu	37	7	1132384	1132384	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:1132384G>A	ENST00000297469.3	+	2	1711	c.1020G>A	c.(1018-1020)gaG>gaA	p.E340E	GPER1_ENST00000401670.1_Silent_p.E340E|GPER1_ENST00000397088.3_Silent_p.E340E|C7orf50_ENST00000357429.6_Intron|C7orf50_ENST00000397098.3_Intron|C7orf50_ENST00000488073.1_Intron|C7orf50_ENST00000397100.2_Intron|GPER1_ENST00000397092.1_Silent_p.E340E	NM_001505.2	NP_001496.1	Q99527	GPER1_HUMAN	G protein-coupled estrogen receptor 1	340					apoptotic chromosome condensation (GO:0030263)|cell cycle (GO:0007049)|cellular response to estradiol stimulus (GO:0071392)|cellular response to glucose stimulus (GO:0071333)|cellular response to mineralocorticoid stimulus (GO:0071389)|cellular response to peptide hormone stimulus (GO:0071375)|cellular response to tumor necrosis factor (GO:0071356)|cytosolic calcium ion homeostasis (GO:0051480)|G-protein coupled receptor signaling pathway (GO:0007186)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|mineralocorticoid receptor signaling pathway (GO:0031959)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA metabolic process (GO:0051053)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of gene expression (GO:0010629)|negative regulation of inflammatory response (GO:0050728)|negative regulation of leukocyte activation (GO:0002695)|negative regulation of lipid biosynthetic process (GO:0051055)|neuronal action potential (GO:0019228)|nuclear fragmentation involved in apoptotic nuclear change (GO:0030264)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of endothelial cell apoptotic process (GO:2000353)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of G-protein coupled receptor protein signaling pathway (GO:0045745)|positive regulation of gene expression (GO:0010628)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|positive regulation of insulin secretion (GO:0032024)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of neurogenesis (GO:0050769)|positive regulation of neurotransmitter secretion (GO:0001956)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of release of sequestered calcium ion into cytosol (GO:0051281)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of uterine smooth muscle contraction (GO:0070474)|positive regulation of vasodilation (GO:0045909)|steroid hormone mediated signaling pathway (GO:0043401)	axon (GO:0030424)|axon terminus (GO:0043679)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|dendritic spine head (GO:0044327)|dendritic spine membrane (GO:0032591)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|keratin filament (GO:0045095)|mitochondrial membrane (GO:0031966)|neuronal postsynaptic density (GO:0097481)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	chromatin binding (GO:0003682)|estrogen receptor activity (GO:0030284)|G-protein coupled receptor activity (GO:0004930)|mineralocorticoid receptor activity (GO:0017082)|steroid binding (GO:0005496)										TGTACATTGAGCAGAAAACAA	0.557																																					p.E340E		Atlas-SNP	.											.	GPER	25	.	0			c.G1020A						PASS	.						93.0	76.0	82.0					7																	1132384		2203	4300	6503	SO:0001819	synonymous_variant	2852	exon2			CATTGAGCAGAAA	U63917	CCDS5322.1	7p22	2013-08-14	2007-07-03	2013-08-14	ENSG00000164850	ENSG00000164850			4485	protein-coding gene	gene with protein product		601805	"""G protein-coupled receptor 30"""	CMKRL2, GPR30, GPER		9479505, 17655271	Standard	NM_001098201		Approved	FEG-1, GPCR-Br, LERGU, LERGU2, DRY12, LyGPR, CEPR	uc003skb.2	Q99527	OTTHUMG00000023680	ENST00000297469.3:c.1020G>A	7.37:g.1132384G>A		121.0	0.0	0		174.0	64.0	0.367816	NM_001505	A8K6C5|B5BUJ1|O00143|O43494|Q13631|Q6FHL1|Q96F42|Q99981	Silent	SNP	ENST00000297469.3	37	CCDS5322.1																																																																																			.	.	none		0.557	GPER1-030	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060001.1	NM_001039966	
NSUN5	55695	hgsc.bcm.edu	37	7	72721583	72721583	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:72721583G>T	ENST00000252594.6	-	3	403	c.388C>A	c.(388-390)Cca>Aca	p.P130T	NSUN5_ENST00000428206.1_Missense_Mutation_p.P92T|NSUN5_ENST00000310326.8_Missense_Mutation_p.P130T|NSUN5_ENST00000438747.2_Missense_Mutation_p.P130T			Q96P11	NSUN5_HUMAN	NOP2/Sun domain family, member 5	130					rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	methyltransferase activity (GO:0008168)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(3)|large_intestine(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	8		Lung NSC(55;0.163)				AGCTTACCTGGACCAGGCCTG	0.627																																					p.P130T		Atlas-SNP	.											.	NSUN5	47	.	0			c.C388A						PASS	.						65.0	54.0	58.0					7																	72721583		2203	4300	6503	SO:0001583	missense	55695	exon3			TACCTGGACCAGG	AF420249	CCDS5546.1, CCDS5547.1, CCDS55118.1, CCDS55119.1	7q11.23	2010-04-08	2009-11-23	2005-01-14	ENSG00000130305	ENSG00000130305		"""NOP2/Sun domain containing"""	16385	protein-coding gene	gene with protein product	"""NOP2/Sun domain family, member 5A"""	615732	"""Williams Beuren syndrome chromosome region 20A"", ""NOL1/NOP2/Sun domain family, member 5"""	WBSCR20, WBSCR20A		11978965, 12073013	Standard	NM_148956		Approved	NOL1R, p120, (NOL1), FLJ10267, NSUN5A, Ynl022cL	uc011kev.2	Q96P11	OTTHUMG00000129869	ENST00000252594.6:c.388C>A	7.37:g.72721583G>T	ENSP00000252594:p.Pro130Thr	41.0	0.0	0		62.0	4.0	0.0645161	NM_148956	B3KX04|B4DP79|G3V0G9|Q6ZUI8|Q96HT9|Q9NW70	Missense_Mutation	SNP	ENST00000252594.6	37	CCDS5547.1	.	.	.	.	.	.	.	.	.	.	G	0.150	-1.092733	0.01858	.	.	ENSG00000130305	ENST00000428206;ENST00000252594;ENST00000438747;ENST00000310326	T;T;T;T	0.13901	2.55;2.57;2.78;2.77	4.18	-3.05	0.05396	.	1.150850	0.06151	N	0.674063	T	0.08802	0.0218	L	0.39397	1.21	0.09310	N	1	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.0;0.002	T	0.40869	-0.9540	10	0.12430	T	0.62	.	3.4709	0.07567	0.2185:0.4119:0.2641:0.1055	.	130;92;130;130	B4DP79;G3V0G9;Q96P11;Q96P11-2	.;.;NSUN5_HUMAN;.	T	92;130;130;130	ENSP00000393081:P92T;ENSP00000252594:P130T;ENSP00000388464:P130T;ENSP00000309126:P130T	ENSP00000252594:P130T	P	-	1	0	NSUN5	72359519	0.000000	0.05858	0.036000	0.18154	0.102000	0.19082	-0.935000	0.03950	-0.472000	0.06881	-0.350000	0.07774	CCA	.	.	none		0.627	NSUN5-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000252113.1	NM_148956	
PTK2	5747	hgsc.bcm.edu	37	8	141685537	141685537	+	Intron	SNP	G	G	A	rs191246950	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:141685537G>A	ENST00000522684.1	-	28	2832				PTK2_ENST00000538769.1_Intron|PTK2_ENST00000519419.1_Intron|PTK2_ENST00000340930.3_Missense_Mutation_p.A875V|PTK2_ENST00000535192.1_Intron|PTK2_ENST00000430260.2_Intron|PTK2_ENST00000521059.1_Intron|PTK2_ENST00000395218.2_Missense_Mutation_p.A875V|PTK2_ENST00000517887.1_Intron|PTK2_ENST00000519465.1_Intron	NM_153831.3	NP_722560.1	Q05397	FAK1_HUMAN	protein tyrosine kinase 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell motility (GO:0048870)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|central nervous system neuron axonogenesis (GO:0021955)|embryo development (GO:0009790)|endothelial cell migration (GO:0043542)|ephrin receptor signaling pathway (GO:0048013)|establishment of cell polarity (GO:0030010)|establishment of nucleus localization (GO:0040023)|extracellular matrix organization (GO:0030198)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|growth hormone receptor signaling pathway (GO:0060396)|heart morphogenesis (GO:0003007)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of organ growth (GO:0046621)|negative regulation of synapse assembly (GO:0051964)|netrin-activated signaling pathway (GO:0038007)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|placenta development (GO:0001890)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|protein autophosphorylation (GO:0046777)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of cell proliferation (GO:0042127)|regulation of cell shape (GO:0008360)|regulation of cytoskeleton organization (GO:0051493)|regulation of endothelial cell migration (GO:0010594)|regulation of focal adhesion assembly (GO:0051893)|regulation of osteoblast differentiation (GO:0045667)|regulation of Rho GTPase activity (GO:0032319)|signal complex assembly (GO:0007172)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vasculogenesis (GO:0001570)	apical plasma membrane (GO:0016324)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|stress fiber (GO:0001725)	actin binding (GO:0003779)|ATP binding (GO:0005524)|JUN kinase binding (GO:0008432)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|SH2 domain binding (GO:0042169)|signal transducer activity (GO:0004871)			breast(1)|central_nervous_system(1)|endometrium(8)|kidney(2)|large_intestine(6)|lung(23)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	48	all_cancers(97;1.05e-15)|all_epithelial(106;2.09e-14)|Lung NSC(106;1.61e-06)|all_lung(105;2.5e-06)|Ovarian(258;0.01)|Acute lymphoblastic leukemia(118;0.155)	Ovarian(118;2.72e-05)|Breast(495;0.159)	BRCA - Breast invasive adenocarcinoma(115;0.137)			ACTTCTTTCCGCCCAATTCTT	0.368													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19290	0.0		0.003	False		,,,				2504	0.0				p.A875V		Atlas-SNP	.											.	PTK2	311	.	0			c.C2624T						PASS	.	G	VAL/ALA,,	0,4406		0,0,2203	187.0	161.0	170.0		2624,,	-0.7	0.0	8		170	3,8595	3.0+/-9.4	0,3,4296	yes	missense,intron,intron	PTK2	NM_001199649.1,NM_005607.4,NM_153831.3	64,,	0,3,6499	AA,AG,GG		0.0349,0.0,0.0231	,,	875/1066,,	141685537	3,13001	2203	4299	6502	SO:0001627	intron_variant	5747	exon28			CTTTCCGCCCAAT	L13616	CCDS6381.1, CCDS56557.1	8q24.3	2013-02-18	2013-02-18		ENSG00000169398	ENSG00000169398	2.7.10.1	"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	9611	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 71"""	600758	"""PTK2 protein tyrosine kinase 2"""			8422239	Standard	NM_153831		Approved	FAK, FADK, FAK1, PPP1R71	uc003yvt.3	Q05397	OTTHUMG00000067438	ENST00000522684.1:c.2602+21C>T	8.37:g.141685537G>A		105.0	0.0	0		132.0	54.0	0.409091	NM_001199649	B4E2N6|F5H4S4|Q14291|Q9UD85	Missense_Mutation	SNP	ENST00000522684.1	37	CCDS6381.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	7.078	0.569753	0.13560	0.0	3.49E-4	ENSG00000169398	ENST00000395218;ENST00000340930	T;T	0.75589	-0.95;-0.93	4.39	-0.655	0.11439	.	.	.	.	.	T	0.53449	0.1797	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.32455	-0.9906	8	0.28530	T	0.3	.	3.7898	0.08715	0.4383:0.2078:0.3539:0.0	.	875	B4E2N6	.	V	875	ENSP00000378644:A875V;ENSP00000341189:A875V	ENSP00000341189:A875V	A	-	2	0	PTK2	141754719	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-0.330000	0.07925	0.005000	0.14708	-0.302000	0.09304	GCG	G|0.998;A|0.002	0.002	strong		0.368	PTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378054.5	NM_005607	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84609249	84609249	+	Silent	SNP	A	A	T	rs116948895	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:84609249A>T	ENST00000344803.2	+	4	3911	c.3864A>T	c.(3862-3864)ccA>ccT	p.P1288P		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	1288					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CGAATTTCCCACCAGCTGTAA	0.557													A|||	30	0.00599042	0.0	0.0043	5008	,	,		18184	0.005		0.0149	False		,,,				2504	0.0072				p.P1288P		Atlas-SNP	.											.	.	.	.	0			c.A3864T						PASS	.	A		15,3903		0,15,1944	44.0	45.0	44.0		3864	-3.8	0.0	9	dbSNP_132	44	76,8228		1,74,4077	no	coding-synonymous	FAM75D1	NM_001001670.2		1,89,6021	TT,TA,AA		0.9152,0.3828,0.7446		1288/1577	84609249	91,12131	1959	4152	6111	SO:0001819	synonymous_variant	389763	exon4			TTTCCCACCAGCT		CCDS47986.1	9q21.32	2012-10-12	2012-10-12	2012-10-12	ENSG00000214929	ENSG00000214929			37283	protein-coding gene	gene with protein product			"""family with sequence similarity 75, member D1"""	FAM75D1			Standard	NM_001001670		Approved	FLJ46321	uc004amn.3	Q6ZQQ2	OTTHUMG00000169122	ENST00000344803.2:c.3864A>T	9.37:g.84609249A>T		65.0	0.0	0		70.0	29.0	0.414286	NM_001001670		Silent	SNP	ENST00000344803.2	37	CCDS47986.1																																																																																			A|0.993;T|0.007	0.007	strong		0.557	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
ACSS1	84532	hgsc.bcm.edu	37	20	25003705	25003705	+	Silent	SNP	A	A	C	rs41308619	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25003705A>C	ENST00000323482.4	-	5	910	c.831T>G	c.(829-831)gtT>gtG	p.V277V	ACSS1_ENST00000537502.1_Silent_p.V194V|ACSS1_ENST00000542618.1_Silent_p.V156V|ACSS1_ENST00000432802.2_Silent_p.V277V	NM_001252675.1|NM_032501.3	NP_001239604.1|NP_115890.2	Q9NUB1	ACS2L_HUMAN	acyl-CoA synthetase short-chain family member 1	277				V -> M (in Ref. 4; AAH39261). {ECO:0000305}.	acetate biosynthetic process (GO:0019413)|acetyl-CoA biosynthetic process (GO:0006085)|acetyl-CoA biosynthetic process from acetate (GO:0019427)|ethanol oxidation (GO:0006069)|propionate biosynthetic process (GO:0019542)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)	acetate-CoA ligase activity (GO:0003987)|AMP binding (GO:0016208)|ATP binding (GO:0005524)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	26					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	CTGGGGCGCAAACAGGGTCCT	0.612													C|||	176	0.0351438	0.0968	0.0274	5008	,	,		20418	0.0		0.0278	False		,,,				2504	0.001				p.V277V		Atlas-SNP	.											.	ACSS1	46	.	0			c.T831G						PASS	.	C		412,3994	787.6+/-414.9	19,374,1810	63.0	52.0	55.0		831	-1.6	0.0	20	dbSNP_127	55	188,8412	810.6+/-407.1	1,186,4113	no	coding-synonymous	ACSS1	NM_032501.2		20,560,5923	CC,CA,AA		2.186,9.3509,4.6133		277/690	25003705	600,12406	2203	4300	6503	SO:0001819	synonymous_variant	84532	exon5			GGCGCAAACAGGG		CCDS13167.1, CCDS58764.1, CCDS58765.1	20p11.23-p11.21	2012-07-13	2005-09-08	2005-09-08	ENSG00000154930	ENSG00000154930	6.2.1.1	"""Acyl-CoA synthetase family"""	16091	protein-coding gene	gene with protein product		614355	"""acetyl-Coenzyme A synthetase 2 (AMP forming)-like"""	ACAS2L			Standard	NM_032501		Approved	dJ568C11.3, AceCS2L, MGC33843	uc002wub.3	Q9NUB1	OTTHUMG00000032112	ENST00000323482.4:c.831T>G	20.37:g.25003705A>C		46.0	0.0	0		45.0	16.0	0.355556	NM_001252677	B3KXL2|B4DJZ3|D3DW48|F5H6F4|F8W7Y1|Q5TF42|Q8IV99|Q8N234|Q96JI1|Q96JX6|Q9NU28	Silent	SNP	ENST00000323482.4	37	CCDS13167.1																																																																																			A|0.960;C|0.040	0.040	strong		0.612	ACSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078386.2	NM_032501	
GSTA4	2941	hgsc.bcm.edu	37	6	52850270	52850270	+	Missense_Mutation	SNP	T	T	C	rs151284340	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:52850270T>C	ENST00000370959.1	-	4	368	c.251A>G	c.(250-252)aAg>aGg	p.K84R	GSTA4_ENST00000486559.1_5'UTR|GSTA4_ENST00000370960.1_Intron|GSTA4_ENST00000541324.1_Intron			O15217	GSTA4_HUMAN	glutathione S-transferase alpha 4	84					glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	glutathione transferase activity (GO:0004364)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(3)|skin(2)|urinary_tract(1)	7	Lung NSC(77;0.103)				Glutathione(DB00143)	CTTGAGGTTCTTGCCAAAGAG	0.488													T|||	6	0.00119808	0.0	0.0	5008	,	,		19004	0.0		0.006	False		,,,				2504	0.0				p.K84R		Atlas-SNP	.											GSTA4,right_upper_lobe,carcinoma,+1,1	GSTA4	20	1	0			c.A251G						PASS	.	T	ARG/LYS	0,4406		0,0,2203	187.0	150.0	162.0		251	-0.5	0.9	6	dbSNP_134	162	7,8593	5.7+/-21.5	0,7,4293	yes	missense	GSTA4	NM_001512.3	26	0,7,6496	CC,CT,TT		0.0814,0.0,0.0538	benign	84/223	52850270	7,12999	2203	4300	6503	SO:0001583	missense	2941	exon4			AGGTTCTTGCCAA	AF020918	CCDS4948.1	6p12.2	2012-06-21	2008-11-26		ENSG00000170899	ENSG00000170899	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4629	protein-coding gene	gene with protein product		605450	"""glutathione S-transferase A4"""			9480897	Standard	NM_001512		Approved		uc003pbf.3	O15217	OTTHUMG00000014868	ENST00000370959.1:c.251A>G	6.37:g.52850270T>C	ENSP00000359998:p.Lys84Arg	129.0	0.0	0		153.0	62.0	0.405229	NM_001512	B2RD15|Q5T7Q8|Q6P4G1|Q9BX18|Q9H414	Missense_Mutation	SNP	ENST00000370959.1	37	CCDS4948.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	T	14.82	2.649056	0.47362	0.0	8.14E-4	ENSG00000170899	ENST00000370963;ENST00000370959	T;T	0.35048	1.33;1.33	5.13	-0.516	0.11950	Glutathione S-transferase, C-terminal-like (1);Thioredoxin-like fold (1);	0.248733	0.46145	N	0.000302	T	0.16214	0.0390	M	0.62016	1.91	0.80722	D	1	B	0.09022	0.002	B	0.15052	0.012	T	0.08493	-1.0719	10	0.48119	T	0.1	-15.3197	8.5879	0.33668	0.0:0.3374:0.0:0.6626	.	84	O15217	GSTA4_HUMAN	R	84	ENSP00000360002:K84R;ENSP00000359998:K84R	ENSP00000359998:K84R	K	-	2	0	GSTA4	52958229	0.443000	0.25641	0.914000	0.36105	0.981000	0.71138	0.582000	0.23834	-0.231000	0.09825	-0.376000	0.06991	AAG	T|0.999;C|0.001	0.001	strong		0.488	GSTA4-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040946.1	NM_001512	
SLC6A13	6540	hgsc.bcm.edu	37	12	333267	333267	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:333267G>A	ENST00000343164.4	-	11	1254	c.1202C>T	c.(1201-1203)gCg>gTg	p.A401V	SLC6A13_ENST00000539668.1_5'UTR|SLC6A13_ENST00000445055.2_Missense_Mutation_p.A309V	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	401					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			GTCCACCAGCGCTGTCACCAG	0.557																																					p.A401V		Atlas-SNP	.											.	SLC6A13	62	.	0			c.C1202T						PASS	.						106.0	89.0	95.0					12																	333267		2203	4300	6503	SO:0001583	missense	6540	exon11			ACCAGCGCTGTCA	U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.1202C>T	12.37:g.333267G>A	ENSP00000339260:p.Ala401Val	79.0	0.0	0		84.0	42.0	0.5	NM_016615	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	G	31	5.059781	0.93846	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.78003	-1.14;-1.14	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	D	0.88724	0.6514	M	0.77103	2.36	0.80722	D	1	D;D;D	0.89917	1.0;0.997;0.997	D;P;D	0.76071	0.987;0.893;0.941	D	0.89618	0.3846	10	0.87932	D	0	.	19.3766	0.94512	0.0:0.0:1.0:0.0	.	309;380;401	B4DJL1;B4DJS3;Q9NSD5	.;.;S6A13_HUMAN	V	309;380;401	ENSP00000407104:A309V;ENSP00000339260:A401V	ENSP00000318097:A380V	A	-	2	0	SLC6A13	203528	1.000000	0.71417	0.994000	0.49952	0.952000	0.60782	7.876000	0.87215	2.596000	0.87737	0.491000	0.48974	GCG	.	.	none		0.557	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1	NM_016615	
VPS9D1	9605	hgsc.bcm.edu	37	16	89774870	89774870	+	Silent	SNP	C	C	T	rs369209003		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89774870C>T	ENST00000389386.3	-	14	1891	c.1767G>A	c.(1765-1767)tcG>tcA	p.S589S	VPS9D1_ENST00000565452.1_5'Flank|VPS9D1_ENST00000561976.1_Silent_p.S519S	NM_004913.2	NP_004904.2	Q9Y2B5	VP9D1_HUMAN	VPS9 domain containing 1	589	VPS9. {ECO:0000255|PROSITE- ProRule:PRU00550}.				ATP synthesis coupled proton transport (GO:0015986)		GTPase activator activity (GO:0005096)|transporter activity (GO:0005215)										CCGCGCACTCCGACACCAGCT	0.657																																					p.S589S		Atlas-SNP	.											C16orf7,colon,carcinoma,-1,1	.	.	1	0			c.G1767A						PASS	.	C		0,4254		0,0,2127	27.0	34.0	31.0		1767	-10.3	0.5	16		31	1,8465		0,1,4232	no	coding-synonymous	C16orf7	NM_004913.2		0,1,6359	TT,TC,CC		0.0118,0.0,0.0079		589/632	89774870	1,12719	2127	4233	6360	SO:0001819	synonymous_variant	9605	exon14			GCACTCCGACACC	AB018551	CCDS42220.1	16q24.3	2012-10-09	2012-10-09	2012-10-09	ENSG00000075399	ENSG00000075399			13526	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 7"""	C16orf7		10231027	Standard	NM_004913		Approved	ATP-BL	uc002fom.1	Q9Y2B5	OTTHUMG00000173219	ENST00000389386.3:c.1767G>A	16.37:g.89774870C>T		177.0	0.0	0		205.0	104.0	0.507317	NM_004913		Silent	SNP	ENST00000389386.3	37	CCDS42220.1																																																																																			.	.	weak		0.657	VPS9D1-002	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422508.1	NM_004913	
GTF2F1	2962	hgsc.bcm.edu	37	19	6392906	6392906	+	Missense_Mutation	SNP	G	G	T	rs151336104		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392906G>T	ENST00000394456.5	-	2	485	c.21C>A	c.(19-21)agC>agA	p.S7R	GTF2F1_ENST00000429701.2_5'Flank|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	7					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						CATTCTGGCTGCTAGGGCCCT	0.592											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		16554	0.0		0.001	False		,,,				2504	0.0				p.S7R		Atlas-SNP	.											.	GTF2F1	39	.	0			c.C21A						PASS	.	G	ARG/SER	0,4406		0,0,2203	138.0	139.0	139.0		21	2.9	1.0	19	dbSNP_134	139	3,8597	2.2+/-6.3	0,3,4297	yes	missense	GTF2F1	NM_002096.2	110	0,3,6500	TT,TG,GG		0.0349,0.0,0.0231	benign	7/518	6392906	3,13003	2203	4300	6503	SO:0001583	missense	2962	exon2			CTGGCTGCTAGGG		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"""General transcription factors"""	4652	protein-coding gene	gene with protein product		189968	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.21C>A	19.37:g.6392906G>T	ENSP00000377969:p.Ser7Arg	70.0	0.0	0	633	80.0	35.0	0.4375	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.51	3.143568	0.57044	0.0	3.49E-4	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.50001	0.76	5.07	2.86	0.33363	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.314292	0.37483	N	0.002061	T	0.35566	0.0936	L	0.34521	1.04	0.80722	D	1	B	0.31040	0.305	B	0.33890	0.172	T	0.29941	-0.9995	10	0.59425	D	0.04	-8.1482	8.3825	0.32479	0.086:0.156:0.758:0.0	.	7	P35269	T2FA_HUMAN	R	7	ENSP00000377969:S7R	ENSP00000377969:S7R	S	-	3	2	GTF2F1	6343906	1.000000	0.71417	0.997000	0.53966	0.686000	0.39977	2.995000	0.49441	1.334000	0.45468	-0.282000	0.10007	AGC	G|0.999;T|0.001	0.001	strong		0.592	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096	
VPS36	51028	hgsc.bcm.edu	37	13	52997751	52997751	+	Silent	SNP	G	G	A	rs148697614	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52997751G>A	ENST00000378060.4	-	10	825	c.798C>T	c.(796-798)ctC>ctT	p.L266L		NM_001282168.1|NM_001282169.1|NM_016075.2	NP_001269097.1|NP_001269098.1|NP_057159.2	Q86VN1	VPS36_HUMAN	vacuolar protein sorting 36 homolog (S. cerevisiae)	266					endosomal transport (GO:0016197)|membrane organization (GO:0061024)|protein transport (GO:0015031)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylinositol-3-phosphate binding (GO:0032266)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(7)|skin(1)|upper_aerodigestive_tract(2)	17		Breast(56;0.000207)|Lung NSC(96;0.00212)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.14e-08)		ACACCTCCGTGAGTGACATTA	0.308													G|||	10	0.00199681	0.0	0.0058	5008	,	,		15634	0.0		0.006	False		,,,				2504	0.0				p.L266L		Atlas-SNP	.											.	VPS36	38	.	0			c.C798T						PASS	.	G		8,4398		0,8,2195	113.0	116.0	115.0		798	-2.3	0.9	13	dbSNP_134	115	29,8571		0,29,4271	no	coding-synonymous	VPS36	NM_016075.2		0,37,6466	AA,AG,GG		0.3372,0.1816,0.2845		266/387	52997751	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	51028	exon10			CTCCGTGAGTGAC	AF151903	CCDS9434.1, CCDS73577.1	13q14.13	2008-02-05	2007-01-12	2005-08-02	ENSG00000136100	ENSG00000136100			20312	protein-coding gene	gene with protein product		610903	"""chromosome 13 open reading frame 9"", ""vacuolar protein sorting 36 homolog (yeast)"""	C13orf9		11278625, 15755741	Standard	NM_016075		Approved	CGI-145, Eap45	uc001vgs.3	Q86VN1	OTTHUMG00000016964	ENST00000378060.4:c.798C>T	13.37:g.52997751G>A		10.0	0.0	0		16.0	6.0	0.375	NM_016075	A8K125|Q3ZCV7|Q5H9S1|Q5VXB6|Q9H8Z5|Q9Y3E3	Silent	SNP	ENST00000378060.4	37	CCDS9434.1																																																																																			G|0.997;A|0.003	0.003	strong		0.308	VPS36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045059.3		
MYO9B	4650	hgsc.bcm.edu	37	19	17212925	17212925	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17212925G>A	ENST00000594824.1	+	2	545	c.398G>A	c.(397-399)cGg>cAg	p.R133Q	MYO9B_ENST00000397274.2_Missense_Mutation_p.R133Q|MYO9B_ENST00000595618.1_Missense_Mutation_p.R133Q|CTD-2528A14.5_ENST00000597045.1_RNA			Q13459	MYO9B_HUMAN	myosin IXB	133					actin filament-based movement (GO:0030048)|establishment of cell polarity (GO:0030010)|lamellipodium morphogenesis (GO:0072673)|macrophage chemotaxis (GO:0048246)|monocyte chemotaxis (GO:0002548)|regulation of small GTPase mediated signal transduction (GO:0051056)|Rho protein signal transduction (GO:0007266)|small GTPase mediated signal transduction (GO:0007264)	actin cytoskeleton (GO:0015629)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|filamentous actin (GO:0031941)|filopodium tip (GO:0032433)|lamellipodium (GO:0030027)|membrane (GO:0016020)|myosin complex (GO:0016459)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	actin binding (GO:0003779)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|Rho GTPase activator activity (GO:0005100)|zinc ion binding (GO:0008270)			breast(3)|endometrium(9)|kidney(2)|large_intestine(1)|lung(19)|soft_tissue(1)|urinary_tract(4)	39						ACAGCCACCCGGCGCCTAGTG	0.617																																					p.R133Q		Atlas-SNP	.											.	MYO9B	264	.	0			c.G398A						PASS	.						33.0	35.0	35.0					19																	17212925		2002	4174	6176	SO:0001583	missense	4650	exon2			CCACCCGGCGCCT		CCDS46010.1	19p13.1	2011-09-27				ENSG00000099331		"""Myosins / Myosin superfamily : Class IX"""	7609	protein-coding gene	gene with protein product		602129		CELIAC4		9226381	Standard	NM_004145		Approved		uc010eak.3	Q13459		ENST00000594824.1:c.398G>A	19.37:g.17212925G>A	ENSP00000471367:p.Arg133Gln	40.0	0.0	0		33.0	14.0	0.424242	NM_001130065	O75314|Q9NUJ2|Q9UHN0	Missense_Mutation	SNP	ENST00000594824.1	37		.	.	.	.	.	.	.	.	.	.	G	11.59	1.683444	0.29872	.	.	ENSG00000099331	ENST00000397274	D	0.84730	-1.89	5.62	3.5	0.40072	.	0.178051	0.27891	N	0.017422	T	0.79713	0.4493	L	0.52126	1.63	0.30811	N	0.738814	B;B;B	0.24651	0.108;0.108;0.064	B;B;B	0.17979	0.01;0.01;0.02	T	0.74475	-0.3653	10	0.37606	T	0.19	.	11.4579	0.50193	0.1454:0.0:0.8546:0.0	.	133;133;139	Q13459;B0I1T6;Q4LE74	MYO9B_HUMAN;.;.	Q	133	ENSP00000380444:R133Q	ENSP00000380444:R133Q	R	+	2	0	MYO9B	17073925	1.000000	0.71417	0.977000	0.42913	0.326000	0.28443	3.417000	0.52714	0.747000	0.32809	-0.119000	0.15052	CGG	.	.	none		0.617	MYO9B-002	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000463236.1		
ARFRP1	10139	hgsc.bcm.edu	37	20	62333231	62333231	+	Missense_Mutation	SNP	G	G	A	rs139547982	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62333231G>A	ENST00000359715.5	-	5	934	c.368C>T	c.(367-369)gCg>gTg	p.A123V	ARFRP1_ENST00000607873.1_Missense_Mutation_p.A76V|ARFRP1_ENST00000324228.2_Missense_Mutation_p.A123V|ARFRP1_ENST00000485858.1_5'Flank|ARFRP1_ENST00000440854.1_Missense_Mutation_p.A123V|ARFRP1_ENST00000609142.1_Missense_Mutation_p.A123V			Q13795	ARFRP_HUMAN	ADP-ribosylation factor related protein 1	123					gastrulation (GO:0007369)|Golgi to plasma membrane protein transport (GO:0043001)|GTP catabolic process (GO:0006184)|protein localization to Golgi apparatus (GO:0034067)|retrograde transport, endosome to Golgi (GO:0042147)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)			breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|skin(1)	7	all_cancers(38;9.53e-13)|all_epithelial(29;2.64e-14)|Lung NSC(23;7e-10)|all_lung(23;2.53e-09)		Epithelial(9;4.09e-08)|all cancers(9;1.7e-07)|OV - Ovarian serous cystadenocarcinoma(5;0.0102)			ACCGCACAGCGCCTCGCTGGT	0.687													G|||	2	0.000399361	0.0	0.0014	5008	,	,		15284	0.001		0.0	False		,,,				2504	0.0				p.A123V		Atlas-SNP	.											ARFRP1,colon,carcinoma,+1,1	ARFRP1	17	1	0			c.C368T						PASS	.	G	VAL/ALA,VAL/ALA	1,4167		0,1,2083	48.0	28.0	35.0		368,368	4.6	0.6	20	dbSNP_134	35	10,8152		0,10,4071	yes	missense,missense	ARFRP1	NM_001134758.1,NM_003224.3	64,64	0,11,6154	AA,AG,GG		0.1225,0.024,0.0892	benign,benign	123/174,123/202	62333231	11,12319	2084	4081	6165	SO:0001583	missense	10139	exon6			CACAGCGCCTCGC	X91504	CCDS13533.1, CCDS46630.1, CCDS68172.1, CCDS68173.1	20q13.3	2014-05-09			ENSG00000101246	ENSG00000101246		"""ADP-ribosylation factors"""	662	protein-coding gene	gene with protein product		604699				8530503	Standard	NM_003224		Approved	ARP, Arp1, ARL18	uc031rup.1	Q13795	OTTHUMG00000032993	ENST00000359715.5:c.368C>T	20.37:g.62333231G>A	ENSP00000352746:p.Ala123Val	120.0	0.0	0		123.0	59.0	0.479675	NM_001134758	B7ZKX7|E1P5J9|Q6IBQ0	Missense_Mutation	SNP	ENST00000359715.5	37	CCDS13533.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	2	0.0034965034965034965	1	0.0013192612137203166	G	11.15	1.552881	0.27739	2.4E-4	0.001225	ENSG00000101246	ENST00000440854;ENST00000359715;ENST00000324228	T;T;T	0.63913	-0.07;-0.07;-0.07	5.53	4.57	0.56435	Small GTP-binding protein domain (1);	0.234257	0.42053	D	0.000776	T	0.41351	0.1155	L	0.33624	1.015	0.50467	D	0.999877	B	0.12630	0.006	B	0.12156	0.007	T	0.44757	-0.9307	10	0.51188	T	0.08	-29.5252	10.3719	0.44060	0.1489:0.0:0.8511:0.0	.	123	Q13795	ARFRP_HUMAN	V	123	ENSP00000403942:A123V;ENSP00000352746:A123V;ENSP00000326884:A123V	ENSP00000326884:A123V	A	-	2	0	ARFRP1	61803675	0.992000	0.36948	0.594000	0.28785	0.597000	0.36814	2.904000	0.48719	2.590000	0.87494	0.462000	0.41574	GCG	G|0.999;A|0.001	0.001	strong		0.687	ARFRP1-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472024.1		
DCPS	28960	hgsc.bcm.edu	37	11	126213242	126213242	+	Missense_Mutation	SNP	G	G	A	rs35836343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126213242G>A	ENST00000263579.4	+	5	1006	c.677G>A	c.(676-678)gGc>gAc	p.G226D	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	226					cellular response to menadione (GO:0036245)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		CATCGCCGGGGCATCAGATCC	0.607													G|||	5	0.000998403	0.0	0.0043	5008	,	,		18355	0.0		0.002	False		,,,				2504	0.0				p.G226D		Atlas-SNP	.											.	DCPS	33	.	0			c.G677A						PASS	.	G	ASP/GLY	5,4397	11.4+/-27.6	0,5,2196	84.0	62.0	69.0		677	0.2	1.0	11	dbSNP_126	69	66,8530	38.8+/-94.9	0,66,4232	yes	missense	DCPS	NM_014026.3	94	0,71,6428	AA,AG,GG		0.7678,0.1136,0.5462	possibly-damaging	226/338	126213242	71,12927	2201	4298	6499	SO:0001583	missense	28960	exon5			GCCGGGGCATCAG	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.677G>A	11.37:g.126213242G>A	ENSP00000263579:p.Gly226Asp	36.0	0.0	0		37.0	19.0	0.513514	NM_014026	Q8NHL8|Q9Y2S5	Missense_Mutation	SNP	ENST00000263579.4	37	CCDS8473.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	G	11.16	1.556018	0.27827	0.001136	0.007678	ENSG00000110063	ENST00000263579	D	0.94966	-3.57	5.31	0.2	0.15181	Histidine triad-like motif (1);	0.269864	0.42548	N	0.000697	T	0.78272	0.4257	N	0.04820	-0.15	0.50171	D	0.999857	B	0.16603	0.018	B	0.30316	0.114	T	0.68667	-0.5348	10	0.02654	T	1	-8.8663	7.34	0.26632	0.3137:0.1113:0.5751:0.0	rs35836343	226	Q96C86	DCPS_HUMAN	D	226	ENSP00000263579:G226D	ENSP00000263579:G226D	G	+	2	0	DCPS	125718452	0.981000	0.34729	0.986000	0.45419	0.713000	0.41058	1.462000	0.35266	-0.091000	0.12440	-0.123000	0.14984	GGC	G|0.995;A|0.005	0.005	strong		0.607	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
KIF1B	23095	hgsc.bcm.edu	37	1	10364260	10364260	+	Intron	SNP	A	A	G	rs148481786	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:10364260A>G	ENST00000377086.1	+	22	2317				KIF1B_ENST00000377083.1_Missense_Mutation_p.E1006G|RN7SL731P_ENST00000584329.1_RNA|KIF1B_ENST00000377093.4_Missense_Mutation_p.E1006G|KIF1B_ENST00000263934.6_Intron|KIF1B_ENST00000377081.1_Intron			O60333	KIF1B_HUMAN	kinesin family member 1B						anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		GAGAGCCAAGAAAAAGGGGGT	0.423													A|||	11	0.00219649	0.0	0.0029	5008	,	,		20281	0.0		0.007	False		,,,				2504	0.002				p.E1006G		Atlas-SNP	.											.	KIF1B	242	.	0			c.A3017G						PASS	.	A	,GLY/GLU	2,4404	2.1+/-5.4	0,2,2201	108.0	117.0	114.0		,3017	4.4	0.9	1	dbSNP_134	114	52,8548	30.7+/-82.3	1,50,4249	yes	intron,missense	KIF1B	NM_015074.3,NM_183416.3	,98	1,52,6450	GG,GA,AA		0.6047,0.0454,0.4152	,	,1006/1154	10364260	54,12952	2203	4300	6503	SO:0001627	intron_variant	23095	exon21			GCCAAGAAAAAGG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.2115+6956A>G	1.37:g.10364260A>G		70.0	0.0	0		71.0	43.0	0.605634	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Missense_Mutation	SNP	ENST00000377086.1	37		7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	A	11.72	1.722702	0.30503	4.54E-4	0.006047	ENSG00000054523	ENST00000377093;ENST00000377083	T;T	0.73152	-0.72;-0.72	5.48	4.36	0.52297	.	.	.	.	.	T	0.55513	0.1925	.	.	.	0.80722	D	1	B	0.34290	0.447	B	0.33690	0.168	T	0.61038	-0.7143	8	0.66056	D	0.02	.	9.7928	0.40717	0.9228:0.0:0.0772:0.0	.	1006	O60333-3	.	G	1006	ENSP00000366297:E1006G;ENSP00000366287:E1006G	ENSP00000366287:E1006G	E	+	2	0	KIF1B	10286847	0.933000	0.31639	0.938000	0.37757	0.716000	0.41182	1.714000	0.37961	0.931000	0.37242	0.533000	0.62120	GAA	A|0.994;G|0.006	0.006	strong		0.423	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
OR10K2	391107	hgsc.bcm.edu	37	1	158390378	158390378	+	Silent	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:158390378A>T	ENST00000314902.2	-	1	278	c.279T>A	c.(277-279)tcT>tcA	p.S93S		NM_001004476.1	NP_001004476.1	Q6IF99	O10K2_HUMAN	olfactory receptor, family 10, subfamily K, member 2	93						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)|cervix(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(19)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	36	all_hematologic(112;0.0378)					AGCCCAGGAAAGAAATGGTCT	0.478																																					p.S93S		Atlas-SNP	.											OR10K2,rectum,carcinoma,-1,1	OR10K2	69	1	0			c.T279A						PASS	.						176.0	172.0	174.0					1																	158390378		2203	4300	6503	SO:0001819	synonymous_variant	391107	exon1			CAGGAAAGAAATG	AB065642	CCDS30896.1	1q23.1	2012-08-09			ENSG00000180708	ENSG00000180708		"""GPCR / Class A : Olfactory receptors"""	14826	protein-coding gene	gene with protein product							Standard	NM_001004476		Approved		uc010pii.2	Q6IF99	OTTHUMG00000019638	ENST00000314902.2:c.279T>A	1.37:g.158390378A>T		175.0	1.0	0.00571429		231.0	139.0	0.601732	NM_001004476		Silent	SNP	ENST00000314902.2	37	CCDS30896.1																																																																																			.	.	none		0.478	OR10K2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051854.1	NM_001004476	
SHANK3	85358	hgsc.bcm.edu	37	22	51160581	51160581	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:51160581C>T	ENST00000414786.2	+	21	4505	c.4278C>T	c.(4276-4278)agC>agT	p.S1426S	SHANK3_ENST00000262795.3_Silent_p.S1456S|SHANK3_ENST00000445220.2_Silent_p.S1442S			Q9BYB0	SHAN3_HUMAN	SH3 and multiple ankyrin repeat domains 3	1440					adult behavior (GO:0030534)|alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor clustering (GO:0097113)|brain morphogenesis (GO:0048854)|dendritic spine morphogenesis (GO:0060997)|guanylate kinase-associated protein clustering (GO:0097117)|learning (GO:0007612)|MAPK cascade (GO:0000165)|memory (GO:0007613)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of actin filament bundle assembly (GO:0032232)|negative regulation of cell volume (GO:0045794)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glutamate receptor signaling pathway (GO:1900451)|positive regulation of long-term neuronal synaptic plasticity (GO:0048170)|positive regulation of synapse structural plasticity (GO:0051835)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density assembly (GO:0097107)|regulation of dendritic spine morphogenesis (GO:0061001)|regulation of long term synaptic depression (GO:1900452)|regulation of long-term synaptic potentiation (GO:1900271)|social behavior (GO:0035176)|striatal medium spiny neuron differentiation (GO:0021773)|synapse assembly (GO:0007416)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	cell junction (GO:0030054)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|neuron spine (GO:0044309)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	GKAP/Homer scaffold activity (GO:0030160)|identical protein binding (GO:0042802)|ionotropic glutamate receptor binding (GO:0035255)|protein C-terminus binding (GO:0008022)|scaffold protein binding (GO:0097110)|SH3 domain binding (GO:0017124)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(5)	8		all_cancers(38;3.75e-11)|all_epithelial(38;1.82e-09)|Breast(42;0.000448)|all_lung(38;0.000665)|Lung NSC(38;0.0104)|Ovarian(80;0.104)|Lung SC(80;0.162)|Hepatocellular(38;0.178)		BRCA - Breast invasive adenocarcinoma(115;0.22)		CCTCGGACAGCGAGCTCATGG	0.682																																					p.S1426S		Atlas-SNP	.											.	SHANK3	96	.	0			c.C4278T						PASS	.						14.0	19.0	17.0					22																	51160581		2085	4202	6287	SO:0001819	synonymous_variant	85358	exon21			GGACAGCGAGCTC	AB051437		22q13.3	2013-11-14			ENSG00000251322	ENSG00000251322		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	14294	protein-coding gene	gene with protein product	"""proline rich synapse associated protein 2"", ""shank postsynaptic density protein"""	606230				11258795, 11431708, 10806096, 17173049	Standard	NM_033517		Approved	SPANK-2, prosap2, KIAA1650, PSAP2	uc031ryd.1	Q9BYB0	OTTHUMG00000150169	ENST00000414786.2:c.4278C>T	22.37:g.51160581C>T		9.0	0.0	0		14.0	9.0	0.642857	NM_033517	D7UT47|Q8TET3	Silent	SNP	ENST00000414786.2	37																																																																																				.	.	none		0.682	SHANK3-001	KNOWN	non_canonical_polymorphism|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000316674.2	NM_001080420	
HPS5	11234	hgsc.bcm.edu	37	11	18318354	18318354	+	Missense_Mutation	SNP	C	C	T	rs143784823	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18318354C>T	ENST00000349215.3	-	12	1778	c.1501G>A	c.(1501-1503)Gga>Aga	p.G501R	HPS5_ENST00000531848.1_Missense_Mutation_p.G387R|HPS5_ENST00000438420.2_Missense_Mutation_p.G387R|HPS5_ENST00000396253.3_Missense_Mutation_p.G387R|HPS5_ENST00000352460.3_5'Flank	NM_181507.1	NP_852608.1	Q9UPZ3	HPS5_HUMAN	Hermansky-Pudlak syndrome 5	501					blood coagulation (GO:0007596)|organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(1)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30						CCTTCATTTCCGTGTGAGCCA	0.458									Hermansky-Pudlak syndrome				C|||	9	0.00179712	0.0	0.0	5008	,	,		17393	0.0		0.0089	False		,,,				2504	0.0				p.G501R		Atlas-SNP	.											.	HPS5	70	.	0			c.G1501A						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY	4,4394	8.1+/-20.4	0,4,2195	260.0	249.0	253.0		1159,1501,1159	2.8	0.0	11	dbSNP_134	253	32,8554	21.6+/-65.8	1,30,4262	yes	missense,missense,missense	HPS5	NM_007216.3,NM_181507.1,NM_181508.1	125,125,125	1,34,6457	TT,TC,CC		0.3727,0.091,0.2773	benign,benign,benign	387/1016,501/1130,387/1016	18318354	36,12948	2199	4293	6492	SO:0001583	missense	11234	exon12	Familial Cancer Database	HPS, HPS1-8	CATTTCCGTGTGA	AB023234	CCDS7836.1, CCDS7837.1	11p14	2014-06-18			ENSG00000110756	ENSG00000110756			17022	protein-coding gene	gene with protein product		607521				10231032, 10094488	Standard	NM_181507		Approved		uc001mod.1	Q9UPZ3	OTTHUMG00000166612	ENST00000349215.3:c.1501G>A	11.37:g.18318354C>T	ENSP00000265967:p.Gly501Arg	145.0	0.0	0		178.0	81.0	0.455056	NM_181507	A8K6J8|A8K8S1|D3DQX9|D3DQY0|O95942|Q8N4U0	Missense_Mutation	SNP	ENST00000349215.3	37	CCDS7836.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	C	0.033	-1.322402	0.01320	9.1E-4	0.003727	ENSG00000110756	ENST00000396253;ENST00000438420;ENST00000349215;ENST00000531848	T;T;T;T	0.53423	0.63;0.63;0.62;1.6	5.71	2.83	0.33086	.	1.416520	0.04002	N	0.296561	T	0.18425	0.0442	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.20107	-1.0285	10	0.08179	T	0.78	.	7.3826	0.26864	0.0:0.6515:0.0:0.3485	.	501	Q9UPZ3	HPS5_HUMAN	R	387;387;501;387	ENSP00000379552:G387R;ENSP00000399590:G387R;ENSP00000265967:G501R;ENSP00000431758:G387R	ENSP00000265967:G501R	G	-	1	0	HPS5	18274930	0.000000	0.05858	0.002000	0.10522	0.108000	0.19459	0.521000	0.22893	0.347000	0.23924	-0.214000	0.12660	GGA	C|0.997;T|0.003	0.003	strong		0.458	HPS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390808.1	NM_181507	
SLITRK1	114798	hgsc.bcm.edu	37	13	84454391	84454391	+	Missense_Mutation	SNP	T	T	A	rs150504822		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:84454391T>A	ENST00000377084.2	-	1	2137	c.1252A>T	c.(1252-1254)Act>Tct	p.T418S		NM_001281503.1|NM_052910.1	NP_001268432.1|NP_443142.1	Q96PX8	SLIK1_HUMAN	SLIT and NTRK-like family, member 1	418				T -> S (in Ref. 4; AAH51738). {ECO:0000305}.	adult behavior (GO:0030534)|axonogenesis (GO:0007409)|homeostatic process (GO:0042592)|multicellular organism growth (GO:0035264)	integral component of membrane (GO:0016021)				NS(2)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(36)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	80	Medulloblastoma(90;0.18)	Breast(118;0.212)		GBM - Glioblastoma multiforme(99;0.07)		TTCTTGAAAGTGTTGTTCTCT	0.458													T|||	1	0.000199681	0.0	0.0	5008	,	,		21199	0.0		0.001	False		,,,				2504	0.0				p.T418S		Atlas-SNP	.											.	SLITRK1	196	.	0			c.A1252T						PASS	.	T	SER/THR	0,4406		0,0,2203	225.0	217.0	220.0		1252	5.2	1.0	13	dbSNP_134	220	12,8588	9.1+/-34.3	0,12,4288	yes	missense	SLITRK1	NM_052910.1	58	0,12,6491	AA,AT,TT		0.1395,0.0,0.0923	benign	418/697	84454391	12,12994	2203	4300	6503	SO:0001583	missense	114798	exon1			TGAAAGTGTTGTT	AB067497	CCDS9464.1	13q31.1	2004-01-08	2004-01-08		ENSG00000178235	ENSG00000178235			20297	protein-coding gene	gene with protein product		609678	"""leucine rich repeat containing 12"""	LRRC12		14557068, 12975309	Standard	NM_001281503		Approved	KIAA1910	uc001vlk.3	Q96PX8	OTTHUMG00000017149	ENST00000377084.2:c.1252A>T	13.37:g.84454391T>A	ENSP00000366288:p.Thr418Ser	110.0	0.0	0		141.0	73.0	0.51773	NM_052910	Q5U5I6|Q96SF9	Missense_Mutation	SNP	ENST00000377084.2	37	CCDS9464.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	13.37	2.215492	0.39102	0.0	0.001395	ENSG00000178235	ENST00000377084	T	0.48201	0.82	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.36799	0.0980	N	0.05177	-0.1	0.51482	D	0.999926	B	0.24963	0.115	B	0.41174	0.349	T	0.36939	-0.9727	10	0.30854	T	0.27	-8.2603	13.9445	0.64075	0.0:0.0:0.0:1.0	.	418	Q96PX8	SLIK1_HUMAN	S	418	ENSP00000366288:T418S	ENSP00000366288:T418S	T	-	1	0	SLITRK1	83352392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.270000	0.58896	1.985000	0.57927	0.459000	0.35465	ACT	T|0.999;A|0.001	0.001	strong		0.458	SLITRK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045396.1	NM_052910	
MED24	9862	hgsc.bcm.edu	37	17	38178679	38178679	+	Missense_Mutation	SNP	G	G	A	rs149459087	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:38178679G>A	ENST00000394128.2	-	22	2572	c.2491C>T	c.(2491-2493)Cgc>Tgc	p.R831C	MED24_ENST00000394127.2_Missense_Mutation_p.R818C|MED24_ENST00000394126.1_Missense_Mutation_p.R856C|MED24_ENST00000356271.3_Missense_Mutation_p.R818C|MED24_ENST00000501516.3_Missense_Mutation_p.R850C	NM_014815.3	NP_055630.2	O75448	MED24_HUMAN	mediator complex subunit 24	831					androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription, DNA-templated (GO:0045893)|protein heterooligomerization (GO:0051291)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	mediator complex (GO:0016592)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|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 cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			autonomic_ganglia(1)|breast(2)|endometrium(9)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	41	Colorectal(19;0.000442)					TTCTTCTGGCGGGTGGACGCC	0.587													G|||	3	0.000599042	0.0	0.0	5008	,	,		18089	0.0		0.003	False		,,,				2504	0.0				p.R831C		Atlas-SNP	.											.	MED24	89	.	0			c.C2491T						PASS	.	G	CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	43.0	40.0	41.0		2452,2491	5.5	1.0	17	dbSNP_134	41	27,8573	19.2+/-60.6	0,27,4273	yes	missense,missense	MED24	NM_001079518.1,NM_014815.3	180,180	0,29,6474	AA,AG,GG		0.314,0.0454,0.223	probably-damaging,probably-damaging	818/977,831/990	38178679	29,12977	2203	4300	6503	SO:0001583	missense	9862	exon22			TCTGGCGGGTGGA	AF055995	CCDS11359.1, CCDS42315.1	17q21.2	2007-07-30	2007-07-30	2007-07-30	ENSG00000008838	ENSG00000008838			22963	protein-coding gene	gene with protein product		607000	"""thyroid hormone receptor associated protein 4"", ""cofactor required for Sp1 transcriptional activation, subunit 4, 100kDa"""	THRAP4, CRSP4			Standard	NM_001079518		Approved	TRAP100, KIAA0130, DRIP100, CRSP100	uc002htt.3	O75448	OTTHUMG00000133329	ENST00000394128.2:c.2491C>T	17.37:g.38178679G>A	ENSP00000377686:p.Arg831Cys	97.0	0.0	0		109.0	60.0	0.550459	NM_014815	A8K4S5|B3KMR9|Q14143|Q9NNY5	Missense_Mutation	SNP	ENST00000394128.2	37	CCDS11359.1	2|2	9.157509157509158E-4|9.157509157509158E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	G|G	13.32|13.32	2.201336|2.201336	0.38905|0.38905	4.54E-4|4.54E-4	0.00314|0.00314	ENSG00000008838|ENSG00000008838	ENST00000422942|ENST00000394126;ENST00000356271;ENST00000394128;ENST00000535071;ENST00000394127;ENST00000536318;ENST00000431269	.|T;T;T	.|0.48836	.|0.8;0.8;0.8	5.48|5.48	5.48|5.48	0.80851|0.80851	.|Mediator complex, subunit Med24, N-terminal (1);	.|0.054745	.|0.85682	.|D	.|0.000000	T|T	0.58481|0.58481	0.2125|0.2125	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D	.|0.76494	.|0.98;0.995;0.998;0.999;0.98	.|P;P;P;P;P	.|0.60345	.|0.606;0.817;0.799;0.873;0.606	T|T	0.60321|0.60321	-0.7286|-0.7286	5|10	.|0.59425	.|D	.|0.04	-17.5546|-17.5546	10.1133|10.1133	0.42576|0.42576	0.0719:0.0:0.7899:0.1382|0.0719:0.0:0.7899:0.1382	.|.	.|741;741;818;831;773	.|F8W9R9;B4E1A5;O75448-2;O75448;F5H0K1	.|.;.;.;MED24_HUMAN;.	L|C	85|831;831;831;781;818;773;741	.|ENSP00000377686:R831C;ENSP00000443344:R781C;ENSP00000377685:R818C	.|ENSP00000348610:R831C	P|R	-|-	2|1	0|0	MED24|MED24	35432205|35432205	1.000000|1.000000	0.71417|0.71417	0.986000|0.986000	0.45419|0.45419	0.566000|0.566000	0.35808|0.35808	3.807000|3.807000	0.55591|0.55591	2.572000|2.572000	0.86782|0.86782	0.655000|0.655000	0.94253|0.94253	CCG|CGC	G|0.998;A|0.002	0.002	strong		0.587	MED24-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257147.2	NM_014815	
URB2	9816	hgsc.bcm.edu	37	1	229787055	229787055	+	Missense_Mutation	SNP	G	G	A	rs41310553	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:229787055G>A	ENST00000258243.2	+	8	4359	c.4223G>A	c.(4222-4224)cGg>cAg	p.R1408Q		NM_014777.2	NP_055592.2	Q14146	URB2_HUMAN	URB2 ribosome biogenesis 2 homolog (S. cerevisiae)	1408						aggresome (GO:0016235)|nucleolus (GO:0005730)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(33)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(6)	73						CGGGAAGGGCGGCAGAAGGAC	0.388													G|||	41	0.0081869	0.0083	0.0159	5008	,	,		17462	0.0		0.0139	False		,,,				2504	0.0051				p.R1408Q		Atlas-SNP	.											.	URB2	152	.	0			c.G4223A						PASS	.	G	GLN/ARG	58,4348	56.8+/-93.2	0,58,2145	87.0	84.0	85.0		4223	4.9	1.0	1	dbSNP_127	85	149,8451	72.9+/-135.5	1,147,4152	yes	missense	URB2	NM_014777.2	43	1,205,6297	AA,AG,GG		1.7326,1.3164,1.5916	probably-damaging	1408/1525	229787055	207,12799	2203	4300	6503	SO:0001583	missense	9816	exon8			AAGGGCGGCAGAA	D50923	CCDS31052.1	1q42.13	2009-11-06	2008-10-01	2008-10-01	ENSG00000135763	ENSG00000135763			28967	protein-coding gene	gene with protein product	"""nucleolar preribosomal-associated protein 1"""		"""KIAA0133"""	KIAA0133		8590280	Standard	NM_014777		Approved	NPA2, NET10	uc001hts.1	Q14146	OTTHUMG00000039464	ENST00000258243.2:c.4223G>A	1.37:g.229787055G>A	ENSP00000258243:p.Arg1408Gln	130.0	0.0	0		101.0	40.0	0.39604	NM_014777	Q5VYC9	Missense_Mutation	SNP	ENST00000258243.2	37	CCDS31052.1	20	0.009157509157509158	3	0.006097560975609756	7	0.019337016574585635	0	0.0	10	0.013192612137203167	G	25.7	4.661699	0.88154	0.013164	0.017326	ENSG00000135763	ENST00000258243;ENST00000434387	T;T	0.45668	0.89;0.89	5.78	4.86	0.63082	Nucleolar 27S pre-rRNA processing, Urb2/Npa2, C-terminal (1);	0.116848	0.53938	D	0.000042	T	0.46210	0.1381	M	0.69823	2.125	0.40363	D	0.97926	D	0.89917	1.0	D	0.69824	0.966	T	0.59968	-0.7354	9	.	.	.	-18.2991	14.7398	0.69445	0.0695:0.0:0.9305:0.0	rs41310553	1408	Q14146	URB2_HUMAN	Q	1408;24	ENSP00000258243:R1408Q;ENSP00000395107:R24Q	.	R	+	2	0	URB2	227853678	0.967000	0.33354	0.971000	0.41717	0.989000	0.77384	5.262000	0.65501	1.435000	0.47434	0.655000	0.94253	CGG	G|0.986;A|0.014	0.014	strong		0.388	URB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095232.1	NM_014777	
APLP1	333	hgsc.bcm.edu	37	19	36370092	36370092	+	Silent	SNP	C	C	T	rs138562956		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:36370092C>T	ENST00000221891.4	+	16	2022	c.1830C>T	c.(1828-1830)taC>taT	p.Y610Y	RN7SL402P_ENST00000465059.1_RNA|APLP1_ENST00000537454.2_Silent_p.Y570Y|APLP1_ENST00000586861.1_Silent_p.Y603Y	NM_001024807.1|NM_005166.3	NP_001019978.1|NP_005157.1	P51693	APLP1_HUMAN	amyloid beta (A4) precursor-like protein 1	609					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular response to norepinephrine stimulus (GO:0071874)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|mRNA polyadenylation (GO:0006378)|negative regulation of cAMP biosynthetic process (GO:0030818)|nervous system development (GO:0007399)|organ morphogenesis (GO:0009887)|regulation of translation (GO:0006417)	basement membrane (GO:0005604)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha-2B adrenergic receptor binding (GO:0031695)|alpha-2C adrenergic receptor binding (GO:0031696)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|transition metal ion binding (GO:0046914)			breast(4)|endometrium(2)|kidney(2)|large_intestine(12)|liver(1)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	33	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)			AGAAGCCCTACGGGGCTATCA	0.652													C|||	1	0.000199681	0.0	0.0	5008	,	,		17200	0.0		0.001	False		,,,				2504	0.0				p.Y610Y		Atlas-SNP	.											.	APLP1	77	.	0			c.C1830T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	55.0	58.0	57.0		1830,1827	-1.7	1.0	19	dbSNP_134	57	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous,coding-synonymous	APLP1	NM_001024807.1,NM_005166.3	,	0,21,6482	TT,TC,CC		0.2326,0.0227,0.1615	,	610/652,609/651	36370092	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	333	exon16			GCCCTACGGGGCT	U48437	CCDS32997.1	19q	2008-07-15							597	protein-coding gene	gene with protein product	"""amyloid-like protein 1"", ""amyloid precursor-like protein 1"""	104775				8432545	Standard	NM_001024807		Approved	APLP	uc002ocf.3	P51693		ENST00000221891.4:c.1830C>T	19.37:g.36370092C>T		35.0	0.0	0		37.0	16.0	0.432432	NM_001024807	O00113|Q96A92	Silent	SNP	ENST00000221891.4	37	CCDS32997.1																																																																																			C|0.999;T|0.001	0.001	strong		0.652	APLP1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452564.1	NM_001024807	
CALHM3	119395	hgsc.bcm.edu	37	10	105238527	105238527	+	Missense_Mutation	SNP	C	C	T	rs372176967		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:105238527C>T	ENST00000369783.4	-	1	470	c.263G>A	c.(262-264)cGg>cAg	p.R88Q	RP11-225H22.5_ENST00000453753.1_RNA	NM_001129742.1	NP_001123214.1	Q86XJ0	CAHM3_HUMAN	calcium homeostasis modulator 3	88					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				kidney(1)|large_intestine(1)	2						GTCCTTCCTCCGGTGCCCTGC	0.677																																					p.R88Q		Atlas-SNP	.											.	CALHM3	46	.	0			c.G263A						PASS	.	C	GLN/ARG	0,1384		0,0,692	18.0	23.0	21.0		263	5.7	1.0	10		21	1,3181		0,1,1590	no	missense	CALHM3	NM_001129742.1	43	0,1,2282	TT,TC,CC		0.0314,0.0,0.0219	probably-damaging	88/345	105238527	1,4565	692	1591	2283	SO:0001583	missense	119395	exon1			TTCCTCCGGTGCC	BC043367	CCDS44476.1	10q24.33	2008-07-02	2008-07-02	2008-07-02	ENSG00000183128	ENSG00000183128			23458	protein-coding gene	gene with protein product			"""family with sequence similarity 26, member A"""	FAM26A		18585350	Standard	NM_001129742		Approved	bA225H22.7	uc001kxg.4	Q86XJ0	OTTHUMG00000018989	ENST00000369783.4:c.263G>A	10.37:g.105238527C>T	ENSP00000358798:p.Arg88Gln	66.0	0.0	0		61.0	33.0	0.540984	NM_001129742	Q5W090|Q8IXR2	Missense_Mutation	SNP	ENST00000369783.4	37	CCDS44476.1	.	.	.	.	.	.	.	.	.	.	C	36	5.855923	0.97030	0.0	3.14E-4	ENSG00000183128	ENST00000369783	T	0.18502	2.21	5.65	5.65	0.86999	.	0.060452	0.64402	D	0.000006	T	0.44519	0.1297	M	0.74647	2.275	0.53688	D	0.999972	D	0.89917	1.0	D	0.72338	0.977	T	0.14783	-1.0460	10	0.40728	T	0.16	-12.0254	19.7261	0.96164	0.0:1.0:0.0:0.0	.	88	Q86XJ0-2	.	Q	88	ENSP00000358798:R88Q	ENSP00000358798:R88Q	R	-	2	0	CALHM3	105228517	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.371000	0.79600	2.667000	0.90743	0.561000	0.74099	CGG	.	.	none		0.677	CALHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050157.1	NM_182494	
HLA-DRB1	3123	hgsc.bcm.edu	37	6	32549582	32549582	+	Missense_Mutation	SNP	G	G	T	rs200516145		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	145.0	0.0	0		172.0	22.0	0.127907	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	
CPO	130749	hgsc.bcm.edu	37	2	207834049	207834049	+	Silent	SNP	G	G	C	rs139758524	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207834049G>C	ENST00000272852.3	+	9	1060	c.1014G>C	c.(1012-1014)ctG>ctC	p.L338L		NM_173077.2	NP_775100.1	Q8IVL8	CBPO_HUMAN	carboxypeptidase O	338						extracellular region (GO:0005576)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|skin(1)	14				LUSC - Lung squamous cell carcinoma(261;0.0744)|Epithelial(149;0.0807)|Lung(261;0.142)		AGGCTGTGCTGTCAGTCCTGG	0.542																																					p.L338L		Atlas-SNP	.											.	CPO	42	.	0			c.G1014C						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	164.0	129.0	141.0		1014	-0.4	0.3	2	dbSNP_134	141	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	CPO	NM_173077.2		0,5,6498	CC,CG,GG		0.0465,0.0227,0.0384		338/375	207834049	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	130749	exon9			TGTGCTGTCAGTC		CCDS2372.1	2q34	2012-02-10			ENSG00000144410	ENSG00000144410			21011	protein-coding gene	gene with protein product	"""metallocarboxypeptidase O"", ""metallocarboxypeptidase C"""	609563				11836249	Standard	NM_173077		Approved		uc002vby.2	Q8IVL8	OTTHUMG00000088987	ENST00000272852.3:c.1014G>C	2.37:g.207834049G>C		119.0	0.0	0		119.0	59.0	0.495798	NM_173077	Q2M277|Q7RTW7	Silent	SNP	ENST00000272852.3	37	CCDS2372.1																																																																																			G|1.000;C|0.000	0.000	strong		0.542	CPO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000202040.2	NM_173077	
KRT38	8687	hgsc.bcm.edu	37	17	39595537	39595537	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39595537G>A	ENST00000246646.3	-	3	649	c.650C>T	c.(649-651)gCg>gTg	p.A217V		NM_006771.3	NP_006762.3	O76015	KRT38_HUMAN	keratin 38	217	Coil 1B.|Rod.					extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(11)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)	29		Breast(137;0.000496)				GGCCAGGGTCGCATCATCCAG	0.637																																					p.A217V		Atlas-SNP	.											.	KRT38	63	.	0			c.C650T						PASS	.						83.0	75.0	78.0					17																	39595537		2203	4300	6503	SO:0001583	missense	8687	exon3			AGGGTCGCATCAT	Y16794	CCDS11392.1	17q21.2	2013-06-20	2006-07-17	2006-07-17	ENSG00000171360	ENSG00000171360		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6456	protein-coding gene	gene with protein product		604542	"""keratin, hair, acidic, 8"""	KRTHA8		9756910, 16831889	Standard	NM_006771		Approved		uc002hwq.1	O76015	OTTHUMG00000133439	ENST00000246646.3:c.650C>T	17.37:g.39595537G>A	ENSP00000246646:p.Ala217Val	63.0	0.0	0		89.0	5.0	0.0561798	NM_006771	A2RRM5|Q6A164	Missense_Mutation	SNP	ENST00000246646.3	37	CCDS11392.1	.	.	.	.	.	.	.	.	.	.	G	12.41	1.928753	0.34002	.	.	ENSG00000171360	ENST00000246646	D	0.90004	-2.6	4.31	3.11	0.35812	Filament (1);	1.672080	0.04241	N	0.336988	D	0.85961	0.5819	L	0.45051	1.395	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.71217	-0.4658	10	0.72032	D	0.01	.	7.6159	0.28158	0.8792:0.0:0.1208:0.0	.	217	O76015	KRT38_HUMAN	V	217	ENSP00000246646:A217V	ENSP00000246646:A217V	A	-	2	0	KRT38	36849063	0.044000	0.20184	0.710000	0.30468	0.780000	0.44128	3.320000	0.51991	0.590000	0.29694	0.484000	0.47621	GCG	.	.	none		0.637	KRT38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257307.2	NM_006771	
TFCP2	7024	hgsc.bcm.edu	37	12	51500329	51500329	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:51500329C>T	ENST00000257915.5	-	8	1354	c.896G>A	c.(895-897)aGc>aAc	p.S299N	TFCP2_ENST00000549867.1_Missense_Mutation_p.S299N|TFCP2_ENST00000307660.4_Missense_Mutation_p.S248N|TFCP2_ENST00000548115.1_Missense_Mutation_p.S248N	NM_001173452.1|NM_005653.4	NP_001166923.1|NP_005644.2	Q12800	TFCP2_HUMAN	transcription factor CP2	299	DNA-binding.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)	23						AGAAAAACTGCTATGGGAACT	0.368																																					p.S299N		Atlas-SNP	.											.	TFCP2	49	.	0			c.G896A						PASS	.						81.0	79.0	80.0					12																	51500329		2203	4300	6503	SO:0001583	missense	7024	exon8			AAACTGCTATGGG	U03494	CCDS8808.1, CCDS55827.1	12q13	2004-01-05				ENSG00000135457			11748	protein-coding gene	gene with protein product		189889				8157699	Standard	NM_005653		Approved	CP2, LSF, LBP-1C, TFCP2C	uc001rxw.3	Q12800	OTTHUMG00000169621	ENST00000257915.5:c.896G>A	12.37:g.51500329C>T	ENSP00000257915:p.Ser299Asn	62.0	0.0	0		59.0	4.0	0.0677966	NM_001173452	A8K5E9|Q12801|Q9UD75|Q9UD77	Missense_Mutation	SNP	ENST00000257915.5	37	CCDS8808.1	.	.	.	.	.	.	.	.	.	.	C	12.71	2.019071	0.35606	.	.	ENSG00000135457	ENST00000257915;ENST00000307660;ENST00000549867;ENST00000548115;ENST00000548108	T;T;T;T;T	0.45276	2.22;0.91;2.24;0.9;2.24	5.53	4.64	0.57946	Sterile alpha motif/pointed domain (1);	0.047786	0.85682	D	0.000000	T	0.19765	0.0475	N	0.03194	-0.395	0.40060	D	0.975885	B;B;B;B	0.23990	0.0;0.095;0.0;0.0	B;B;B;B	0.26416	0.002;0.069;0.001;0.001	T	0.09840	-1.0656	10	0.19147	T	0.46	-8.47	10.179	0.42957	0.0:0.8443:0.0:0.1557	.	248;299;299;299	Q12800-2;F8VX55;Q12800;Q12800-4	.;.;TFCP2_HUMAN;.	N	299;248;299;248;201	ENSP00000257915:S299N;ENSP00000304411:S248N;ENSP00000449742:S299N;ENSP00000447991:S248N;ENSP00000449280:S201N	ENSP00000257915:S299N	S	-	2	0	TFCP2	49786596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.788000	0.26872	1.482000	0.48325	0.655000	0.94253	AGC	.	.	none		0.368	TFCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405119.1	NM_005653	
AHCTF1	25909	hgsc.bcm.edu	37	1	247007232	247007232	+	Splice_Site	SNP	T	T	A	rs148600466	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:247007232T>A	ENST00000391829.2	-	34	6515		c.e34-2		AHCTF1_ENST00000366508.1_Splice_Site|AHCTF1_ENST00000470300.1_Splice_Site|AHCTF1_ENST00000326225.3_Splice_Site			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1						cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			TTTTTTTAGCTAAAAAAAGTT	0.303													T|||	19	0.00379393	0.0	0.0101	5008	,	,		13414	0.0		0.0109	False		,,,				2504	0.001				.	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											.	AHCTF1	187	.	0			c.6419-2A>T						PASS	.	T		19,4381	20.2+/-43.8	0,19,2181	44.0	44.0	44.0			4.2	0.9	1	dbSNP_134	44	102,8494	43.6+/-101.6	1,100,4197	no	splice-3	AHCTF1	NM_015446.4		1,119,6378	AA,AT,TT		1.1866,0.4318,0.9311			247007232	121,12875	2200	4298	6498	SO:0001630	splice_region_variant	25909	exon35			TTTAGCTAAAAAA		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.6392-2A>T	1.37:g.247007232T>A		231.0	0.0	0		209.0	102.0	0.488038	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Splice_Site	SNP	ENST00000391829.2	37		13	0.005952380952380952	1	0.0020325203252032522	3	0.008287292817679558	1	0.0017482517482517483	8	0.010554089709762533	T	13.05	2.121636	0.37436	0.004318	0.011866	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	.	.	.	5.29	4.17	0.49024	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8575	0.41094	0.0:0.0781:0.0:0.9219	.	.	.	.	.	-1	.	.	.	-	.	.	AHCTF1	245073855	1.000000	0.71417	0.937000	0.37676	0.546000	0.35178	3.504000	0.53347	0.955000	0.37878	-0.326000	0.08463	.	T|0.992;A|0.008	0.008	strong		0.303	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	Intron
BNC2	54796	hgsc.bcm.edu	37	9	16419519	16419519	+	Missense_Mutation	SNP	G	G	A	rs117452684	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:16419519G>A	ENST00000380672.4	-	7	2825	c.2768C>T	c.(2767-2769)gCc>gTc	p.A923V	BNC2_ENST00000545497.1_Missense_Mutation_p.A828V|BNC2_ENST00000380667.2_Missense_Mutation_p.A856V	NM_017637.5	NP_060107.3			basonuclin 2											NS(2)|breast(3)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(16)|liver(1)|lung(22)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(50;9.01e-08)		GGGGTGCTGGGCACCATATAT	0.572													G|||	45	0.00898562	0.0008	0.0086	5008	,	,		16876	0.0		0.0288	False		,,,				2504	0.0092				p.A923V		Atlas-SNP	.											.	BNC2	166	.	0			c.C2768T						PASS	.	G	VAL/ALA	30,4376	36.0+/-67.5	0,30,2173	83.0	87.0	86.0		2768	5.5	1.0	9	dbSNP_132	86	293,8307	107.0+/-167.8	3,287,4010	yes	missense	BNC2	NM_017637.5	64	3,317,6183	AA,AG,GG		3.407,0.6809,2.4835	benign	923/1100	16419519	323,12683	2203	4300	6503	SO:0001583	missense	54796	exon7			TGCTGGGCACCAT	AK092247	CCDS6482.2	9p22.2	2013-05-20			ENSG00000173068	ENSG00000173068		"""Zinc fingers, C2H2-type"""	30988	protein-coding gene	gene with protein product		608669				14702039	Standard	XM_006716784		Approved	BSN2, FLJ20043	uc003zml.3	Q6ZN30	OTTHUMG00000019593	ENST00000380672.4:c.2768C>T	9.37:g.16419519G>A	ENSP00000370047:p.Ala923Val	71.0	0.0	0		77.0	38.0	0.493506	NM_017637		Missense_Mutation	SNP	ENST00000380672.4	37	CCDS6482.2	26	0.011904761904761904	0	0.0	3	0.008287292817679558	0	0.0	23	0.030343007915567283	G	13.60	2.286262	0.40494	0.006809	0.03407	ENSG00000173068	ENST00000380672;ENST00000380667;ENST00000545497	T;T;T	0.31510	1.49;1.5;1.5	5.5	5.5	0.81552	.	0.166180	0.51477	D	0.000083	T	0.07954	0.0199	N	0.22421	0.69	0.80722	D	1	P;P;B	0.41673	0.578;0.759;0.18	B;B;B	0.39027	0.158;0.288;0.051	T	0.01844	-1.1262	10	0.27082	T	0.32	-9.5452	14.94	0.70986	0.0:0.1426:0.8574:0.0	.	828;923;688	F5H586;Q6ZN30;D3DRJ1	.;BNC2_HUMAN;.	V	923;856;828	ENSP00000370047:A923V;ENSP00000370042:A856V;ENSP00000444640:A828V	ENSP00000370042:A856V	A	-	2	0	BNC2	16409519	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	3.336000	0.52113	2.586000	0.87340	0.591000	0.81541	GCC	G|0.979;A|0.021	0.021	strong		0.572	BNC2-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000216901.5	NM_017637	
FAT2	2196	hgsc.bcm.edu	37	5	150947128	150947128	+	Silent	SNP	G	G	A	rs34166097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:150947128G>A	ENST00000261800.5	-	1	1377	c.1365C>T	c.(1363-1365)gcC>gcT	p.A455A		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	455	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TGAAGAGGGGGGCATGGTTGT	0.557													G|||	79	0.0157748	0.0008	0.0259	5008	,	,		19350	0.001		0.0527	False		,,,				2504	0.0061				p.A455A		Atlas-SNP	.											.	FAT2	465	.	0			c.C1365T						PASS	.	G		36,4370	41.6+/-74.8	0,36,2167	125.0	124.0	125.0		1365	2.8	1.0	5	dbSNP_126	125	414,8186	129.5+/-187.6	7,400,3893	no	coding-synonymous	FAT2	NM_001447.2		7,436,6060	AA,AG,GG		4.814,0.8171,3.4599		455/4350	150947128	450,12556	2203	4300	6503	SO:0001819	synonymous_variant	2196	exon1			GAGGGGGGCATGG	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.1365C>T	5.37:g.150947128G>A		116.0	0.0	0		152.0	62.0	0.407895	NM_001447	O75091|Q9NSR7	Silent	SNP	ENST00000261800.5	37	CCDS4317.1																																																																																			G|0.970;A|0.030	0.030	strong		0.557	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
LAMA5	3911	hgsc.bcm.edu	37	20	60899513	60899513	+	Missense_Mutation	SNP	C	C	A	rs148177752	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:60899513C>A	ENST00000252999.3	-	42	5693	c.5627G>T	c.(5626-5628)gGc>gTc	p.G1876V		NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	1876	Laminin EGF-like 17. {ECO:0000255|PROSITE-ProRule:PRU00460}.				angiogenesis (GO:0001525)|branching involved in salivary gland morphogenesis (GO:0060445)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cell recognition (GO:0008037)|cilium assembly (GO:0042384)|cytoskeleton organization (GO:0007010)|embryo development (GO:0009790)|endothelial cell differentiation (GO:0045446)|establishment of protein localization to plasma membrane (GO:0090002)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|hair follicle development (GO:0001942)|integrin-mediated signaling pathway (GO:0007229)|lung development (GO:0030324)|morphogenesis of a polarized epithelium (GO:0001738)|morphogenesis of embryonic epithelium (GO:0016331)|muscle organ development (GO:0007517)|neural crest cell migration (GO:0001755)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|regulation of embryonic development (GO:0045995)|substrate adhesion-dependent cell spreading (GO:0034446)	basal lamina (GO:0005605)|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-11 complex (GO:0043260)|laminin-5 complex (GO:0005610)|nucleus (GO:0005634)	integrin binding (GO:0005178)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|lung(40)|ovary(1)|pancreas(1)|prostate(3)|skin(6)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	81	Breast(26;1.57e-08)		BRCA - Breast invasive adenocarcinoma(19;4.36e-06)			GACGCCAGAGCCAGGGAGGCA	0.622													.|||	5	0.000998403	0.0008	0.0	5008	,	,		18736	0.0		0.004	False		,,,				2504	0.0				p.G1876V		Atlas-SNP	.											.	LAMA5	268	.	0			c.G5627T						PASS	.	C	VAL/GLY	10,4384	15.5+/-35.6	1,8,2188	42.0	36.0	38.0		5627	4.2	1.0	20	dbSNP_134	38	54,8532	31.2+/-83.2	1,52,4240	yes	missense	LAMA5	NM_005560.3	109	2,60,6428	AA,AC,CC		0.6289,0.2276,0.4931	probably-damaging	1876/3696	60899513	64,12916	2197	4293	6490	SO:0001583	missense	3911	exon42			CCAGAGCCAGGGA	AF443072	CCDS33502.1	20q13.2-q13.3	2013-03-01			ENSG00000130702	ENSG00000130702		"""Laminins"""	6485	protein-coding gene	gene with protein product		601033				9271224	Standard	NM_005560		Approved		uc002ycq.3	O15230	OTTHUMG00000032908	ENST00000252999.3:c.5627G>T	20.37:g.60899513C>A	ENSP00000252999:p.Gly1876Val	89.0	0.0	0		90.0	48.0	0.533333	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Missense_Mutation	SNP	ENST00000252999.3	37	CCDS33502.1	6	0.0027472527472527475	1	0.0020325203252032522	0	0.0	0	0.0	5	0.006596306068601583	C	18.61	3.660047	0.67586	0.002276	0.006289	ENSG00000130702	ENST00000252999	T	0.60424	0.19	4.25	4.25	0.50352	TNFR/CD27/30/40/95 cysteine-rich region (1);EGF-like, laminin (3);	0.000000	0.85682	U	0.000000	T	0.62636	0.2444	L	0.46567	1.45	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.66638	-0.5873	10	0.36615	T	0.2	.	16.9991	0.86377	0.0:1.0:0.0:0.0	.	1876	O15230	LAMA5_HUMAN	V	1876	ENSP00000252999:G1876V	ENSP00000252999:G1876V	G	-	2	0	LAMA5	60332908	1.000000	0.71417	0.995000	0.50966	0.568000	0.35870	4.553000	0.60753	2.074000	0.62210	0.579000	0.79373	GGC	C|0.996;A|0.004	0.004	strong		0.622	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
SYVN1	84447	hgsc.bcm.edu	37	11	64897292	64897292	+	Missense_Mutation	SNP	C	C	T	rs141712194	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:64897292C>T	ENST00000377190.3	-	14	1598	c.1504G>A	c.(1504-1506)Gcc>Acc	p.A502T	SYVN1_ENST00000526060.1_Missense_Mutation_p.A501T|SYVN1_ENST00000526121.1_5'Flank|SYVN1_ENST00000294256.8_Missense_Mutation_p.A501T|SYVN1_ENST00000307289.6_Missense_Mutation_p.A450T	NM_172230.2	NP_757385.1	Q86TM6	SYVN1_HUMAN	synovial apoptosis inhibitor 1, synoviolin	502					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)|in utero embryonic development (GO:0001701)|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway (GO:1902236)|protein N-linked glycosylation via asparagine (GO:0018279)|protein ubiquitination (GO:0016567)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	22						TGCAGCCGGGCCTCCAGGTGC	0.657													c|||	2	0.000399361	0.0	0.0	5008	,	,		17978	0.0		0.002	False		,,,				2504	0.0				p.A502T		Atlas-SNP	.											.	SYVN1	55	.	0			c.G1504A						PASS	.	C	THR/ALA,THR/ALA	1,4401	2.1+/-5.4	0,1,2200	40.0	45.0	43.0		1504,1501	3.8	1.0	11	dbSNP_134	43	4,8590	3.7+/-12.6	0,4,4293	yes	missense,missense	SYVN1	NM_172230.2,NM_032431.2	58,58	0,5,6493	TT,TC,CC		0.0465,0.0227,0.0385	benign,benign	502/618,501/617	64897292	5,12991	2201	4297	6498	SO:0001583	missense	84447	exon14			GCCGGGCCTCCAG	AB085847	CCDS8097.1, CCDS31605.1	11q13	2013-01-09			ENSG00000162298	ENSG00000162298		"""RING-type (C3HC4) zinc fingers"""	20738	protein-coding gene	gene with protein product	"""HMG-coA reductase degradation 1 homolog (S. cerevisiae)"""	608046				12975321	Standard	NM_032431		Approved	HRD1, DER3	uc001odb.3	Q86TM6		ENST00000377190.3:c.1504G>A	11.37:g.64897292C>T	ENSP00000366395:p.Ala502Thr	87.0	0.0	0		102.0	47.0	0.460784	NM_172230	Q8N3K3|Q8N6E8|Q96JL5|Q96PK3	Missense_Mutation	SNP	ENST00000377190.3	37	CCDS31605.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	18.41	3.616870	0.66672	2.27E-4	4.65E-4	ENSG00000162298	ENST00000377190;ENST00000294256;ENST00000434219;ENST00000307289;ENST00000526060	T;T;T;T	0.15718	2.43;2.4;2.52;2.4	4.75	3.82	0.43975	.	0.062439	0.64402	D	0.000006	T	0.40719	0.1128	M	0.78049	2.395	0.80722	D	1	D;B;B	0.67145	0.996;0.361;0.247	D;B;B	0.77557	0.99;0.293;0.153	T	0.32052	-0.9921	10	0.54805	T	0.06	-14.4894	12.007	0.53265	0.1742:0.8258:0.0:0.0	.	450;501;502	Q86TM6-2;Q86TM6-3;Q86TM6	.;.;SYVN1_HUMAN	T	502;501;502;450;501	ENSP00000366395:A502T;ENSP00000294256:A501T;ENSP00000302035:A450T;ENSP00000436984:A501T	ENSP00000294256:A501T	A	-	1	0	SYVN1	64653868	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.189000	0.77747	1.213000	0.43380	0.561000	0.74099	GCC	C|0.999;T|0.001	0.001	strong		0.657	SYVN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000385274.1	NM_032431	
LPIN2	9663	hgsc.bcm.edu	37	18	2929103	2929103	+	Missense_Mutation	SNP	G	G	A	rs104895500	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:2929103G>A	ENST00000261596.4	-	10	1748	c.1510C>T	c.(1510-1512)Ctt>Ttt	p.L504F		NM_014646.2	NP_055461.1	Q92539	LPIN2_HUMAN	lipin 2	504					cellular lipid metabolic process (GO:0044255)|dephosphorylation (GO:0016311)|fatty acid metabolic process (GO:0006631)|glycerophospholipid biosynthetic process (GO:0046474)|lipid metabolic process (GO:0006629)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)|transcription coactivator activity (GO:0003713)			autonomic_ganglia(1)|breast(1)|endometrium(2)|large_intestine(4)|lung(16)|ovary(1)|pancreas(1)|prostate(2)|skin(1)	29				READ - Rectum adenocarcinoma(2;0.0419)|Colorectal(6;0.156)		TTGTCTATAAGTCCAGGGTTT	0.294													G|||	10	0.00199681	0.0008	0.0043	5008	,	,		16858	0.0		0.005	False		,,,				2504	0.001				p.L504F		Atlas-SNP	.											.	LPIN2	75	.	0			c.C1510T	GRCh37	CM082924	LPIN2	M	rs104895500	PASS	.	G	PHE/LEU	5,4399	11.4+/-27.6	0,5,2197	126.0	139.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	1510	6.0	1.0	18	dbSNP_132	135	39,8555	25.7+/-73.6	0,39,4258	yes	missense	LPIN2	NM_014646.2	22	0,44,6455	AA,AG,GG		0.4538,0.1135,0.3385	benign	504/897	2929103	44,12954	2202	4297	6499	SO:0001583	missense	9663	exon10			CTATAAGTCCAGG	D87436	CCDS11829.1	18p	2014-09-17			ENSG00000101577	ENSG00000101577			14450	protein-coding gene	gene with protein product		605519				11138012, 9039502	Standard	NM_014646		Approved	KIAA0249	uc002klo.3	Q92539	OTTHUMG00000131508	ENST00000261596.4:c.1510C>T	18.37:g.2929103G>A	ENSP00000261596:p.Leu504Phe	48.0	0.0	0		100.0	28.0	0.28	NM_014646	A7MD25|D3DUH3	Missense_Mutation	SNP	ENST00000261596.4	37	CCDS11829.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	24.1	4.489970	0.84962	0.001135	0.004538	ENSG00000101577	ENST00000261596	D	0.83419	-1.72	6.03	6.03	0.97812	.	0.051415	0.85682	D	0.000000	D	0.83175	0.5197	M	0.75615	2.305	0.52099	D	0.99994	P	0.52842	0.956	P	0.50049	0.629	D	0.86195	0.1615	10	0.72032	D	0.01	.	15.2928	0.73879	0.0:0.0:0.86:0.14	.	504	Q92539	LPIN2_HUMAN	F	504	ENSP00000261596:L504F	ENSP00000261596:L504F	L	-	1	0	LPIN2	2919103	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	6.723000	0.74742	2.861000	0.98227	0.655000	0.94253	CTT	G|0.998;A|0.002	0.002	strong		0.294	LPIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254363.2	NM_014646	
TYRO3	7301	hgsc.bcm.edu	37	15	41857307	41857307	+	Missense_Mutation	SNP	G	G	A	rs141641556	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:41857307G>A	ENST00000263798.3	+	6	975	c.751G>A	c.(751-753)Ggc>Agc	p.G251S	TYRO3_ENST00000559066.1_Missense_Mutation_p.G206S	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase	251	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		AGGTGCTGATGGCCGAGCTCT	0.592													G|||	42	0.00838658	0.0	0.0202	5008	,	,		20484	0.0		0.0268	False		,,,				2504	0.001				p.G251S		Atlas-SNP	.											TYRO3_ENST00000263798,NS,haematopoietic_neoplasm,0,2	TYRO3	169	2	0			c.G751A						scavenged	.	G	SER/GLY	8,4398	15.5+/-35.6	0,8,2195	94.0	84.0	87.0		751	4.9	0.6	15	dbSNP_134	87	128,8472	63.5+/-125.6	0,128,4172	yes	missense	TYRO3	NM_006293.3	56	0,136,6367	AA,AG,GG		1.4884,0.1816,1.0457	probably-damaging	251/891	41857307	136,12870	2203	4300	6503	SO:0001583	missense	7301	exon6			GCTGATGGCCGAG	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.751G>A	15.37:g.41857307G>A	ENSP00000263798:p.Gly251Ser	52.0	0.0	0		44.0	6.0	0.136364	NM_006293	O14953|Q86VR3	Missense_Mutation	SNP	ENST00000263798.3	37	CCDS10080.1	14	0.00641025641025641	0	0.0	4	0.011049723756906077	0	0.0	10	0.013192612137203167	G	31	5.104713	0.94245	0.001816	0.014884	ENSG00000092445	ENST00000540218;ENST00000263798	T	0.60920	0.15	4.95	4.95	0.65309	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.000000	0.41712	D	0.000828	T	0.59266	0.2181	L	0.55103	1.725	0.58432	D	0.999997	D	0.64830	0.994	P	0.58970	0.849	T	0.64689	-0.6348	10	0.51188	T	0.08	-23.6363	13.5493	0.61723	0.0:0.0:1.0:0.0	.	251	Q06418	TYRO3_HUMAN	S	183;251	ENSP00000263798:G251S	ENSP00000263798:G251S	G	+	1	0	TYRO3	39644599	1.000000	0.71417	0.626000	0.29213	0.989000	0.77384	6.282000	0.72639	2.581000	0.87130	0.563000	0.77884	GGC	G|0.992;A|0.008	0.008	strong		0.592	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		
PRTG	283659	hgsc.bcm.edu	37	15	55965666	55965666	+	Silent	SNP	A	A	G	rs75403514	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:55965666A>G	ENST00000389286.4	-	10	1802	c.1755T>C	c.(1753-1755)agT>agC	p.S585S		NM_173814.4	NP_776175.2			protogenin											breast(1)|endometrium(6)|kidney(4)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	41				all cancers(107;0.00891)|GBM - Glioblastoma multiforme(80;0.135)		CCAGGTAGACACTGTCAGGTT	0.522													A|||	13	0.00259585	0.0	0.0014	5008	,	,		14634	0.0		0.0109	False		,,,				2504	0.001				p.S585S		Atlas-SNP	.											.	PRTG	110	.	0			c.T1755C						PASS	.	A		11,3823		0,11,1906	87.0	88.0	87.0		1755	-0.2	1.0	15	dbSNP_131	87	119,8139		4,111,4014	no	coding-synonymous	PRTG	NM_173814.4		4,122,5920	GG,GA,AA		1.441,0.2869,1.0751		585/1151	55965666	130,11962	1917	4129	6046	SO:0001819	synonymous_variant	283659	exon10			GTAGACACTGTCA	AK098622	CCDS42040.1	15q21.3	2013-02-11	2010-06-24		ENSG00000166450	ENSG00000166450		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	26373	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 5"""	613261	"""protogenin homolog (Gallus gallus)"""				Standard	NM_173814		Approved	FLJ25756, IGDCC5	uc002adg.3	Q2VWP7		ENST00000389286.4:c.1755T>C	15.37:g.55965666A>G		176.0	0.0	0		154.0	72.0	0.467532	NM_173814		Silent	SNP	ENST00000389286.4	37	CCDS42040.1																																																																																			A|0.994;G|0.006	0.006	strong		0.522	PRTG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419357.1	NM_173814	
ZNF681	148213	hgsc.bcm.edu	37	19	23927604	23927604	+	Missense_Mutation	SNP	T	T	C	rs147282314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:23927604T>C	ENST00000402377.3	-	4	889	c.748A>G	c.(748-750)Aga>Gga	p.R250G	ZNF681_ENST00000395385.3_Missense_Mutation_p.R181G	NM_138286.2	NP_612143.2	Q96N22	ZN681_HUMAN	zinc finger protein 681	250					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)			central_nervous_system(1)|endometrium(1)|large_intestine(4)|lung(10)|prostate(1)|skin(1)|urinary_tract(3)	21		all_lung(12;0.11)|Lung NSC(12;0.163)|all_epithelial(12;0.206)				AGTTTGTCTCTAGTATAAATT	0.348													T|||	4	0.000798722	0.003	0.0	5008	,	,		18422	0.0		0.0	False		,,,				2504	0.0				p.R250G		Atlas-SNP	.											.	ZNF681	76	.	0			c.A748G						PASS	.	T	GLY/ARG	10,4396		0,10,2193	97.0	96.0	97.0		748	-3.2	0.0	19	dbSNP_134	97	0,8600		0,0,4300	no	missense	ZNF681	NM_138286.2	125	0,10,6493	CC,CT,TT		0.0,0.227,0.0769	benign	250/646	23927604	10,12996	2203	4300	6503	SO:0001583	missense	148213	exon4			TGTCTCTAGTATA	AK056088	CCDS12414.2	19p12	2013-01-08			ENSG00000196172	ENSG00000196172		"""Zinc fingers, C2H2-type"", ""-"""	26457	protein-coding gene	gene with protein product	"""hypothetical protein FLJ31526"""						Standard	NM_138286		Approved	FLJ31526	uc002nrk.4	Q96N22	OTTHUMG00000150831	ENST00000402377.3:c.748A>G	19.37:g.23927604T>C	ENSP00000384000:p.Arg250Gly	61.0	0.0	0		75.0	38.0	0.506667	NM_138286	B3KVF7	Missense_Mutation	SNP	ENST00000402377.3	37	CCDS12414.2	3	0.0013736263736263737	3	0.006097560975609756	0	0.0	0	0.0	0	0.0	.	0.010	-1.745110	0.00675	0.00227	0.0	ENSG00000196172	ENST00000402377;ENST00000395385	T;T	0.07908	3.29;3.15	1.6	-3.2	0.05156	Zinc finger, C2H2 (1);	.	.	.	.	T	0.01156	0.0038	N	0.00387	-1.565	0.20703	N	0.999865	B	0.02656	0.0	B	0.01281	0.0	T	0.38607	-0.9653	9	0.02654	T	1	.	9.6115	0.39665	0.0:0.7478:0.0:0.2522	.	250	Q96N22	ZN681_HUMAN	G	250;181	ENSP00000384000:R250G;ENSP00000378783:R181G	ENSP00000378783:R181G	R	-	1	2	ZNF681	23719444	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.592000	0.23984	-1.681000	0.01448	-1.783000	0.00646	AGA	T|0.999;C|0.001	0.001	strong		0.348	ZNF681-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320248.2	NM_138286	
DPYD	1806	hgsc.bcm.edu	37	1	97547947	97547947	+	Missense_Mutation	SNP	T	T	A	rs67376798	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:97547947T>A	ENST00000370192.3	-	22	2946	c.2846A>T	c.(2845-2847)gAt>gTt	p.D949V		NM_000110.3	NP_000101	Q12882	DPYD_HUMAN	dihydropyrimidine dehydrogenase	949	4Fe-4S ferredoxin-type 2. {ECO:0000255|PROSITE-ProRule:PRU00711}.				beta-alanine biosynthetic process (GO:0019483)|nucleobase-containing small molecule metabolic process (GO:0055086)|purine nucleobase catabolic process (GO:0006145)|pyrimidine nucleobase catabolic process (GO:0006208)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|small molecule metabolic process (GO:0044281)|thymidine catabolic process (GO:0006214)|thymine catabolic process (GO:0006210)|UMP biosynthetic process (GO:0006222)|uracil catabolic process (GO:0006212)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	4 iron, 4 sulfur cluster binding (GO:0051539)|dihydroorotate dehydrogenase activity (GO:0004152)|dihydropyrimidine dehydrogenase (NADP+) activity (GO:0017113)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(18)|lung(30)|ovary(4)|prostate(6)|skin(7)|upper_aerodigestive_tract(1)	83		all_epithelial(167;0.000185)|all_lung(203;0.00318)|Lung NSC(277;0.00994)		Colorectal(170;0.0165)|Epithelial(280;0.0526)|all cancers(265;0.104)|READ - Rectum adenocarcinoma(84;0.171)|Lung(183;0.216)	Capecitabine(DB01101)|Flavin adenine dinucleotide(DB03147)|Fluorouracil(DB00544)	CATTTCTTCATCAATCATAGC	0.388													T|||	11	0.00219649	0.0008	0.0029	5008	,	,		18701	0.0		0.007	False		,,,				2504	0.001				p.D949V		Atlas-SNP	.											.	DPYD	219	.	0			c.A2846T	GRCh37	CM003590	DPYD	M	rs67376798	PASS	.	T	VAL/ASP	4,4402	9.9+/-24.2	0,4,2199	242.0	220.0	228.0		2846	5.8	1.0	1	dbSNP_130	228	47,8553	30.7+/-82.3	1,45,4254	yes	missense	DPYD	NM_000110.3	152	1,49,6453	AA,AT,TT		0.5465,0.0908,0.3921	probably-damaging	949/1026	97547947	51,12955	2203	4300	6503	SO:0001583	missense	1806	exon22			TCTTCATCAATCA	U20938	CCDS30777.1, CCDS53346.1	1p22	2014-09-17			ENSG00000188641	ENSG00000188641	1.3.1.2		3012	protein-coding gene	gene with protein product		612779				7713523	Standard	NM_000110		Approved	DPD	uc001drv.3	Q12882	OTTHUMG00000039683	ENST00000370192.3:c.2846A>T	1.37:g.97547947T>A	ENSP00000359211:p.Asp949Val	141.0	0.0	0		128.0	62.0	0.484375	NM_000110	A2RRQ2|A2RRQ3|A8K5A2|A8MWG9|B1AN21|E9PFN1|Q16694|Q16761|Q32NB0|Q96HL6|Q96TH1	Missense_Mutation	SNP	ENST00000370192.3	37	CCDS30777.1	8	0.003663003663003663	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	T	23.4	4.406204	0.83230	9.08E-4	0.005465	ENSG00000188641	ENST00000370192	D	0.93019	-3.15	5.82	5.82	0.92795	4Fe-4S ferredoxin, iron-sulpur binding domain (1);	0.000000	0.85682	D	0.000000	D	0.97170	0.9075	M	0.93763	3.455	0.80722	D	1	D	0.76494	0.999	D	0.66602	0.945	D	0.98134	1.0432	10	0.87932	D	0	-25.8976	16.1779	0.81874	0.0:0.0:0.0:1.0	.	949	Q12882	DPYD_HUMAN	V	949	ENSP00000359211:D949V	ENSP00000359211:D949V	D	-	2	0	DPYD	97320535	1.000000	0.71417	1.000000	0.80357	0.884000	0.51177	7.841000	0.86834	2.216000	0.71823	0.533000	0.62120	GAT	T|0.996;A|0.004	0.004	strong		0.388	DPYD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095698.3	NM_000110	
STAB2	55576	hgsc.bcm.edu	37	12	104025446	104025446	+	Silent	SNP	G	G	A	rs147053330	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:104025446G>A	ENST00000388887.2	+	6	762	c.558G>A	c.(556-558)gcG>gcA	p.A186A		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						GCTACTCTGCGTACACTGGCC	0.468													g|||	13	0.00259585	0.0	0.0	5008	,	,		19013	0.001		0.0119	False		,,,				2504	0.0				p.A186A		Atlas-SNP	.											.	STAB2	370	.	0			c.G558A						PASS	.	A		4,4402	8.1+/-20.4	0,4,2199	229.0	174.0	193.0		558	-9.4	0.0	12	dbSNP_134	193	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous	STAB2	NM_017564.9		0,72,6431	AA,AG,GG		0.7907,0.0908,0.5536		186/2552	104025446	72,12934	2203	4300	6503	SO:0001819	synonymous_variant	55576	exon6			CTCTGCGTACACT	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.558G>A	12.37:g.104025446G>A		137.0	0.0	0		126.0	58.0	0.460317	NM_017564		Silent	SNP	ENST00000388887.2	37	CCDS31888.1																																																																																			G|0.994;A|0.006	0.006	strong		0.468	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
FAM153B	202134	hgsc.bcm.edu	37	5	175530780	175530780	+	Missense_Mutation	SNP	C	C	T	rs200265244		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:175530780C>T	ENST00000253490.4	+	14	814	c.757C>T	c.(757-759)Cgt>Tgt	p.R253C	FAM153B_ENST00000515817.1_Missense_Mutation_p.R176C|FAM153B_ENST00000512862.1_Missense_Mutation_p.R44C|FAM153B_ENST00000510151.1_Missense_Mutation_p.R176C			P0C7A2	F153B_HUMAN	family with sequence similarity 153, member B	253										endometrium(3)|kidney(2)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)	16	all_cancers(89;0.00406)|Renal(175;0.000269)|Lung NSC(126;0.0103)|all_lung(126;0.0164)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)	Kidney(146;0.0965)		AGTTCCACAACGTGGTACGTA	0.473																																					p.R176C		Atlas-SNP	.											.	FAM153B	28	.	0			c.C526T						PASS	.	C	CYS/ARG	5,4401	8.1+/-20.4	0,5,2198	78.0	80.0	79.0		757	-2.2	0.0	5		79	29,8565	15.3+/-51.7	0,29,4268	no	missense	FAM153B	NM_001079529.2	180	0,34,6466	TT,TC,CC		0.3374,0.1135,0.2615	possibly-damaging	253/388	175530780	34,12966	2203	4297	6500	SO:0001583	missense	202134	exon13			CCACAACGTGGTA	AK055006	CCDS43401.1, CCDS43401.2	5q35.2	2010-05-12			ENSG00000182230	ENSG00000182230			27323	protein-coding gene	gene with protein product							Standard	NM_001265615		Approved		uc031smb.1	P0C7A2	OTTHUMG00000163181	ENST00000253490.4:c.757C>T	5.37:g.175530780C>T	ENSP00000253490:p.Arg253Cys	913.0	1.0	0.00109529		923.0	206.0	0.223185	NM_001265615	A8MTI1	Missense_Mutation	SNP	ENST00000253490.4	37		.	.	.	.	.	.	.	.	.	.	C	4.556	0.103267	0.08731	0.001135	0.003374	ENSG00000182230	ENST00000515817;ENST00000253490	.	.	.	1.12	-2.24	0.06909	.	.	.	.	.	T	0.16642	0.0400	N	0.14661	0.345	0.09310	N	1	B	0.19200	0.034	B	0.04013	0.001	T	0.16748	-1.0392	8	0.51188	T	0.08	.	2.2521	0.04046	0.4486:0.3196:0.2318:0.0	.	253	P0C7A2	F153B_HUMAN	C	176;253	.	ENSP00000253490:R253C	R	+	1	0	FAM153B	175463386	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-2.175000	0.01263	-0.591000	0.05859	-1.402000	0.01139	CGT	C|0.999;T|0.001	0.001	weak		0.473	FAM153B-201	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_001079529	
GNL2	29889	hgsc.bcm.edu	37	1	38061396	38061396	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:38061396T>C	ENST00000373062.3	-	1	126	c.28A>G	c.(28-30)Agc>Ggc	p.S10G		NM_013285.2	NP_037417.1	Q13823	NOG2_HUMAN	guanine nucleotide binding protein-like 2 (nucleolar)	10					GTP catabolic process (GO:0006184)|ribosome biogenesis (GO:0042254)	membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(8)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	30		Myeloproliferative disorder(586;0.0393)				TTGATGGTGCTCCGTCCTTTG	0.587																																					p.S10G		Atlas-SNP	.											.	GNL2	58	.	0			c.A28G						PASS	.						143.0	112.0	123.0					1																	38061396		2203	4300	6503	SO:0001583	missense	29889	exon1			TGGTGCTCCGTCC	L05425	CCDS421.1	1p34	2008-02-05			ENSG00000134697	ENSG00000134697			29925	protein-coding gene	gene with protein product		609365				8822211	Standard	NM_013285		Approved	Ngp-1, HUMAUANTIG	uc001cbk.3	Q13823	OTTHUMG00000004322	ENST00000373062.3:c.28A>G	1.37:g.38061396T>C	ENSP00000362153:p.Ser10Gly	156.0	0.0	0		165.0	9.0	0.0545455	NM_013285	Q9BWN7	Missense_Mutation	SNP	ENST00000373062.3	37	CCDS421.1	.	.	.	.	.	.	.	.	.	.	T	17.87	3.494496	0.64186	.	.	ENSG00000134697	ENST00000373062	T	0.24723	1.84	5.01	5.01	0.66863	.	0.073396	0.85682	D	0.000000	T	0.21186	0.0510	L	0.51422	1.61	0.54753	D	0.999985	B;B	0.06786	0.001;0.001	B;B	0.08055	0.003;0.003	T	0.08207	-1.0733	10	0.33141	T	0.24	-17.281	6.6224	0.22810	0.1386:0.0758:0.0:0.7856	.	10;10	Q5T0F3;Q13823	.;NOG2_HUMAN	G	10	ENSP00000362153:S10G	ENSP00000362153:S10G	S	-	1	0	GNL2	37833983	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.138000	0.42140	2.102000	0.63906	0.533000	0.62120	AGC	.	.	none		0.587	GNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012478.1	NM_013285	
SLC25A12	8604	hgsc.bcm.edu	37	2	172671648	172671648	+	Missense_Mutation	SNP	A	A	C	rs200754828		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:172671648A>C	ENST00000422440.2	-	10	1032	c.995T>G	c.(994-996)cTg>cGg	p.L332R	SLC25A12_ENST00000392592.4_Missense_Mutation_p.L225R	NM_003705.4	NP_003696.2	O75746	CMC1_HUMAN	solute carrier family 25 (aspartate/glutamate carrier), member 12	332					aspartate transport (GO:0015810)|carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|L-glutamate transport (GO:0015813)|malate-aspartate shuttle (GO:0043490)|response to calcium ion (GO:0051592)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|L-aspartate transmembrane transporter activity (GO:0015183)|L-glutamate transmembrane transporter activity (GO:0005313)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(10)|upper_aerodigestive_tract(1)	23			OV - Ovarian serous cystadenocarcinoma(117;0.216)		L-Aspartic Acid(DB00128)	AACTGAGCCCAGAGTGAATCT	0.473																																					p.L332R		Atlas-SNP	.											.	SLC25A12	59	.	0			c.T995G						PASS	.						86.0	81.0	83.0					2																	172671648		2203	4300	6503	SO:0001583	missense	8604	exon10			GAGCCCAGAGTGA	Y14494	CCDS33327.1	2q24	2013-05-22	2012-03-29		ENSG00000115840	ENSG00000115840		"""Solute carriers"", ""EF-hand domain containing"""	10982	protein-coding gene	gene with protein product		603667	"""solute carrier family 25 (mitochondrial carrier, Aralar), member 12"""			9722566, 10702666, 11566871	Standard	NM_003705		Approved	Aralar	uc002uhh.3	O75746	OTTHUMG00000134290	ENST00000422440.2:c.995T>G	2.37:g.172671648A>C	ENSP00000388658:p.Leu332Arg	189.0	0.0	0		215.0	95.0	0.44186	NM_003705	B3KR64|Q96AM8	Missense_Mutation	SNP	ENST00000422440.2	37	CCDS33327.1	.	.	.	.	.	.	.	.	.	.	a	23.6	4.440914	0.83993	.	.	ENSG00000115840	ENST00000422440;ENST00000392592	T;T	0.80033	-1.33;-1.33	5.47	5.47	0.80525	Mitochondrial carrier domain (2);	0.140827	0.49305	D	0.000150	D	0.88187	0.6369	M	0.63208	1.945	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.89300	0.3625	10	0.72032	D	0.01	-1.9365	15.5193	0.75854	1.0:0.0:0.0:0.0	.	225;332	B3KR64;O75746	.;CMC1_HUMAN	R	332;225	ENSP00000388658:L332R;ENSP00000376371:L225R	ENSP00000376371:L225R	L	-	2	0	SLC25A12	172379894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.869000	0.92326	2.054000	0.61138	0.482000	0.46254	CTG	A|0.999;C|0.001	0.001	weak		0.473	SLC25A12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259010.2	NM_003705	
SLC22A24	283238	hgsc.bcm.edu	37	11	62902146	62902146	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:62902146A>G	ENST00000417740.1	-	2	938	c.497T>C	c.(496-498)cTt>cCt	p.L166P	SLC22A24_ENST00000326192.5_Missense_Mutation_p.L166P	NM_001136506.2	NP_001129978.2	Q8N4F4	S22AO_HUMAN	solute carrier family 22, member 24	166					ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				kidney(1)|stomach(1)	2						CCTGTCTGAAAGATGGCCATA	0.383																																					p.L166P		Atlas-SNP	.											.	SLC22A24	31	.	0			c.T497C						PASS	.						93.0	72.0	79.0					11																	62902146		692	1591	2283	SO:0001583	missense	283238	exon2			TCTGAAAGATGGC		CCDS73308.1	11q12.3	2013-05-22			ENSG00000197658	ENSG00000197658		"""Solute carriers"""	28542	protein-coding gene	gene with protein product		611698				17714910	Standard	NM_001136506		Approved	MGC34821, NET46	uc021qkp.1	Q8N4F4	OTTHUMG00000165372	ENST00000417740.1:c.497T>C	11.37:g.62902146A>G	ENSP00000396586:p.Leu166Pro	120.0	0.0	0		160.0	49.0	0.30625	NM_001136506		Missense_Mutation	SNP	ENST00000417740.1	37		.	.	.	.	.	.	.	.	.	.	A	18.12	3.553416	0.65425	.	.	ENSG00000197658	ENST00000417740;ENST00000531535;ENST00000326192	D;T	0.85013	-1.93;-0.36	3.52	3.52	0.40303	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.237783	0.35615	U	0.003083	D	0.93631	0.7966	H	0.95043	3.615	0.35699	D	0.815434	D;D	0.89917	0.999;1.0	D;D	0.80764	0.994;0.994	D	0.95896	0.8911	10	0.87932	D	0	.	10.166	0.42879	1.0:0.0:0.0:0.0	.	166;166	Q8N4F4;C9JC66	S22AO_HUMAN;.	P	166	ENSP00000396586:L166P;ENSP00000321549:L166P	ENSP00000321549:L166P	L	-	2	0	SLC22A24	62658722	0.140000	0.22579	0.047000	0.18901	0.691000	0.40173	5.090000	0.64498	1.474000	0.48178	0.321000	0.21382	CTT	.	.	none		0.383	SLC22A24-003	PUTATIVE	non_canonical_polymorphism|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000383747.1	NM_173586	
CD300LG	146894	hgsc.bcm.edu	37	17	41926023	41926023	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:41926023G>A	ENST00000317310.4	+	2	182	c.141G>A	c.(139-141)cgG>cgA	p.R47R	CD300LG_ENST00000377203.4_Silent_p.R47R|CD300LG_ENST00000293396.8_Silent_p.R47R|CD300LG_ENST00000586233.1_Silent_p.R47R|CD300LG_ENST00000539718.1_Silent_p.R47R|CD300LG_ENST00000588884.1_Silent_p.R47R	NM_145273.3	NP_660316.2	Q6UXG3	CLM9_HUMAN	CD300 molecule-like family member g	47	Ig-like V-type.				immune system process (GO:0002376)|immunoglobulin transcytosis in epithelial cells (GO:0002414)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|skin(4)	19		Breast(137;0.0199)		BRCA - Breast invasive adenocarcinoma(366;0.115)		GGGACCACCGGAAGTACTGGT	0.577																																					p.R47R		Atlas-SNP	.											.	CD300LG	46	.	0			c.G141A						PASS	.						85.0	72.0	77.0					17																	41926023		2203	4300	6503	SO:0001819	synonymous_variant	146894	exon2			CCACCGGAAGTAC	BC025395	CCDS11470.1, CCDS54131.1, CCDS54132.1, CCDS54133.1	17q21.31	2013-01-11	2006-03-29					"""Immunoglobulin superfamily / V-set domain containing"""	30455	protein-coding gene	gene with protein product	"""nepmucin"""	610520	"""CD300 antigen like family member G"""			16876123, 16754720	Standard	NM_001168322		Approved	Trem4, CLM9	uc002iem.3	Q6UXG3		ENST00000317310.4:c.141G>A	17.37:g.41926023G>A		88.0	0.0	0		106.0	60.0	0.566038	NM_001168323	B4DNY5|F5H7P9|F8W9M3|Q8IX38|Q8IX39|Q8TA95	Silent	SNP	ENST00000317310.4	37	CCDS11470.1																																																																																			.	.	none		0.577	CD300LG-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457646.1	NM_145273	
FLNB	2317	hgsc.bcm.edu	37	3	58080639	58080639	+	Silent	SNP	C	C	T	rs141151998	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58080639C>T	ENST00000295956.4	+	5	1029	c.864C>T	c.(862-864)gaC>gaT	p.D288D	FLNB_ENST00000419752.2_Silent_p.D119D|FLNB_ENST00000358537.3_Silent_p.D288D|FLNB_ENST00000429972.2_Silent_p.D288D|FLNB_ENST00000357272.4_Silent_p.D288D|FLNB_ENST00000348383.5_Silent_p.D288D|FLNB_ENST00000493452.1_Silent_p.D119D|FLNB_ENST00000490882.1_Silent_p.D288D	NM_001457.3	NP_001448.2	O75369	FLNB_HUMAN	filamin B, beta	288					actin cytoskeleton organization (GO:0030036)|cell differentiation (GO:0030154)|cytokine-mediated signaling pathway (GO:0019221)|cytoskeletal anchoring at plasma membrane (GO:0007016)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|stress fiber (GO:0001725)	actin binding (GO:0003779)|identical protein binding (GO:0042802)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(13)|central_nervous_system(2)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(23)|liver(2)|lung(38)|ovary(6)|prostate(3)|skin(8)|upper_aerodigestive_tract(3)|urinary_tract(5)	120				BRCA - Breast invasive adenocarcinoma(55;0.000335)|KIRC - Kidney renal clear cell carcinoma(284;0.0726)|Kidney(284;0.0898)		GGCAAGGAGACGTGATGGTGT	0.542																																					p.D288D		Atlas-SNP	.											FLNB_ENST00000490882,NS,carcinoma,0,2	FLNB	430	2	0			c.C864T						PASS	.	C	,,,	0,4406		0,0,2203	213.0	194.0	201.0		864,864,864,864	-7.8	0.3	3	dbSNP_134	201	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FLNB	NM_001164317.1,NM_001164318.1,NM_001164319.1,NM_001457.3	,,,	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	,,,	288/2634,288/2592,288/2579,288/2603	58080639	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	2317	exon5			AGGAGACGTGATG	AF043045	CCDS2885.1, CCDS54599.1, CCDS54600.1, CCDS54601.1	3p14.3	2011-02-11	2009-07-23		ENSG00000136068	ENSG00000136068			3755	protein-coding gene	gene with protein product	"""actin binding protein 278"""	603381	"""filamin B, beta (actin binding protein 278)"", ""Larsen syndrome 1 (autosomal dominant)"""	FLN1L, LRS1		8327473, 10449914, 14991055, 16801345	Standard	NM_001457		Approved	TAP, TABP, ABP-278, FH1	uc010hne.2	O75369	OTTHUMG00000159158	ENST00000295956.4:c.864C>T	3.37:g.58080639C>T		78.0	0.0	0		123.0	43.0	0.349593	NM_001457	B2ZZ83|B2ZZ84|B2ZZ85|C9JKE6|C9JMC4|Q13706|Q59EC2|Q60FE7|Q6MZJ1|Q8WXS9|Q8WXT0|Q8WXT1|Q8WXT2|Q8WXT3|Q9NRB5|Q9NT26|Q9UEV9	Silent	SNP	ENST00000295956.4	37	CCDS2885.1																																																																																			C|0.999;T|0.001	0.001	strong		0.542	FLNB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000353569.1	NM_001457	
CEP170B	283638	hgsc.bcm.edu	37	14	105352910	105352910	+	Silent	SNP	G	G	A	rs373896765		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105352910G>A	ENST00000414716.3	+	12	2562	c.2334G>A	c.(2332-2334)acG>acA	p.T778T	CEP170B_ENST00000453495.1_Silent_p.T779T|CEP170B_ENST00000556508.1_Silent_p.T708T|CEP170B_ENST00000418279.1_Silent_p.T708T	NM_001112726.2	NP_001106197.1	Q9Y4F5	C170B_HUMAN	centrosomal protein 170B	778						cytoplasm (GO:0005737)|microtubule (GO:0005874)											AGGGGCCCACGTGGAGCAGGG	0.682																																					p.T778T		Atlas-SNP	.											.	.	.	.	0			c.G2334A						PASS	.	G	,	0,3656		0,0,1828	9.0	11.0	10.0		2334,2124	-6.8	0.0	14		10	3,8099		0,3,4048	no	coding-synonymous,coding-synonymous	KIAA0284	NM_001112726.2,NM_015005.2	,	0,3,5876	AA,AG,GG		0.037,0.0,0.0255	,	778/1555,708/1520	105352910	3,11755	1828	4051	5879	SO:0001819	synonymous_variant	283638	exon12			GCCCACGTGGAGC	AB006622	CCDS45175.1, CCDS45176.1, CCDS45176.2	14q32.33	2014-02-20	2012-11-30	2012-11-30	ENSG00000099814	ENSG00000099814			20362	protein-coding gene	gene with protein product	"""Cep170-related"""		"""KIAA0284"""	KIAA0284		23087211	Standard	NM_015005		Approved	FAM68C, Cep170R	uc010axb.4	Q9Y4F5	OTTHUMG00000170763	ENST00000414716.3:c.2334G>A	14.37:g.105352910G>A		19.0	0.0	0		41.0	16.0	0.390244	NM_001112726	Q2KHR7|Q86TI7	Silent	SNP	ENST00000414716.3	37	CCDS45175.1																																																																																			.	.	weak		0.682	CEP170B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000410289.2	NM_001112726	
ABL1	25	hgsc.bcm.edu	37	9	133761001	133761001	+	Silent	SNP	A	A	G	rs1056171	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:133761001A>G	ENST00000318560.5	+	11	3705	c.3324A>G	c.(3322-3324)ccA>ccG	p.P1108P		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	1108	F-actin-binding.				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)	GCAGTGGTCCAGCGGCCACTC	0.557			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""								G|||	3276	0.654153	0.882	0.6974	5008	,	,		18771	0.5952		0.4881	False		,,,				2504	0.547				p.P1127P		Atlas-SNP	.		Dom	yes		9	9q34.1	25	v-abl Abelson murine leukemia viral oncogene homolog 1		L	ABL1,scalp,carcinoma,+2,1	ABL1	1632	1	0			c.A3381G						scavenged	.	G	,	3592,814	300.1+/-286.2	1470,652,81	29.0	34.0	32.0		3324,3381	-10.5	0.2	9	dbSNP_86	32	4015,4585	586.5+/-392.0	924,2167,1209	no	coding-synonymous,coding-synonymous	ABL1	NM_005157.4,NM_007313.2	,	2394,2819,1290	GG,GA,AA		46.686,18.4748,41.5116	,	1108/1131,1127/1150	133761001	7607,5399	2203	4300	6503	SO:0001819	synonymous_variant	25	exon11			TGGTCCAGCGGCC	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.3324A>G	9.37:g.133761001A>G		108.0	2.0	0.0185185		112.0	58.0	0.517857	NM_007313	A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Silent	SNP	ENST00000318560.5	37	CCDS35166.1																																																																																			A|0.391;G|0.609	0.609	strong		0.557	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
ZNF230	7773	hgsc.bcm.edu	37	19	44515492	44515492	+	Missense_Mutation	SNP	T	T	A	rs6413542	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:44515492T>A	ENST00000429154.2	+	5	1529	c.1301T>A	c.(1300-1302)tTc>tAc	p.F434Y		NM_006300.3	NP_006291.2	Q9UIE0	ZN230_HUMAN	zinc finger protein 230	434			F -> Y (in dbSNP:rs6413542).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(1)|endometrium(2)|large_intestine(2)|lung(10)|skin(1)|stomach(3)|urinary_tract(2)	22		Prostate(69;0.0352)				CACCGGTCTTTCTGTAAAGAC	0.428													T|||	27	0.00539137	0.0	0.0014	5008	,	,		16061	0.0		0.0239	False		,,,				2504	0.002				p.F434Y	GBM(175;914 2069 22996 47111 52600)	Atlas-SNP	.											.	ZNF230	44	.	0			c.T1301A						PASS	.	T	TYR/PHE	4,4402	8.1+/-20.4	0,4,2199	53.0	58.0	56.0		1301	-1.1	0.0	19	dbSNP_116	56	95,8505	49.8+/-109.6	0,95,4205	yes	missense	ZNF230	NM_006300.3	22	0,99,6404	AA,AT,TT		1.1047,0.0908,0.7612	benign	434/475	44515492	99,12907	2203	4300	6503	SO:0001583	missense	7773	exon5			GGTCTTTCTGTAA	U95044	CCDS33044.1	19q13.31	2013-01-08				ENSG00000159882		"""Zinc fingers, C2H2-type"", ""-"""	13024	protein-coding gene	gene with protein product							Standard	NM_006300		Approved	FDZF2	uc002oyb.1	Q9UIE0		ENST00000429154.2:c.1301T>A	19.37:g.44515492T>A	ENSP00000409318:p.Phe434Tyr	41.0	0.0	0		55.0	31.0	0.563636	NM_006300	O15322|Q504X7|Q86W84|Q9P1U6	Missense_Mutation	SNP	ENST00000429154.2	37	CCDS33044.1	23	0.010531135531135532	0	0.0	0	0.0	0	0.0	23	0.030343007915567283	T	0.541	-0.853455	0.02630	9.08E-4	0.011047	ENSG00000159882	ENST00000429154	T	0.14640	2.49	2.55	-1.12	0.09808	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.01156	0.0038	N	0.02751	-0.505	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42799	-0.9430	9	0.09590	T	0.72	.	2.3511	0.04283	0.2475:0.0:0.2858:0.4666	rs6413542;rs52791695;rs6413542	434	Q9UIE0	ZN230_HUMAN	Y	434	ENSP00000409318:F434Y	ENSP00000409318:F434Y	F	+	2	0	ZNF230	49207332	0.000000	0.05858	0.000000	0.03702	0.423000	0.31445	-0.228000	0.09114	-0.182000	0.10602	-1.285000	0.01374	TTC	T|0.992;A|0.008	0.008	strong		0.428	ZNF230-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460456.1		
TRMT2A	27037	hgsc.bcm.edu	37	22	20103263	20103263	+	Missense_Mutation	SNP	G	G	T	rs9605067|rs71317167	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:20103263G>T	ENST00000252136.7	-	3	1028	c.640C>A	c.(640-642)Ctc>Atc	p.L214I	RANBP1_ENST00000402752.1_5'Flank|TRMT2A_ENST00000492988.1_5'Flank|TRMT2A_ENST00000403707.3_Missense_Mutation_p.L214I|TRMT2A_ENST00000439169.2_Missense_Mutation_p.L214I|RANBP1_ENST00000430524.1_5'Flank|TRMT2A_ENST00000404751.3_Missense_Mutation_p.L214I|RANBP1_ENST00000331821.3_5'Flank	NM_001257994.1|NM_022727.5|NM_182984.4	NP_001244923.1|NP_073564.3|NP_892029.2	Q8IZ69	TRM2A_HUMAN	tRNA methyltransferase 2 homolog A (S. cerevisiae)	214					RNA processing (GO:0006396)		nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA methyltransferase activity (GO:0008173)			breast(2)|endometrium(2)|lung(5)	9						CTCTGCTCGAGCAGCCAGGGC	0.637													G|||	59	0.0117812	0.0023	0.013	5008	,	,		17914	0.0		0.0378	False		,,,				2504	0.0092				p.L214I		Atlas-SNP	.											.	TRMT2A	34	.	0			c.C640A						PASS	.	G	ILE/LEU,ILE/LEU	27,4377	33.5+/-64.1	1,25,2176	45.0	42.0	43.0		640,640	-1.0	0.3	22	dbSNP_119	43	326,8274	113.7+/-173.7	12,302,3986	yes	missense,missense	TRMT2A	NM_022727.4,NM_182984.3	5,5	13,327,6162	TT,TG,GG		3.7907,0.6131,2.7145	benign,benign	214/626,214/626	20103263	353,12651	2202	4300	6502	SO:0001583	missense	27037	exon3			GCTCGAGCAGCCA	BC017184	CCDS13774.1, CCDS58793.1	22q11.21	2014-02-12	2012-06-12		ENSG00000099899	ENSG00000099899			24974	protein-coding gene	gene with protein product	"""HpaII tiny fragments locus 9C"""	611151				9417108, 18075473	Standard	NM_022727		Approved	HTF9C	uc002zrl.2	Q8IZ69	OTTHUMG00000150454	ENST00000252136.7:c.640C>A	22.37:g.20103263G>T	ENSP00000252136:p.Leu214Ile	189.0	0.0	0		201.0	97.0	0.482587	NM_001257994	D3DX25|Q32P57|Q96ME6|Q9H732	Missense_Mutation	SNP	ENST00000252136.7	37	CCDS13774.1	32	0.014652014652014652	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	25	0.032981530343007916	G	9.951	1.220275	0.22457	0.006131	0.037907	ENSG00000099899	ENST00000252136;ENST00000403707;ENST00000404751;ENST00000439169	T;T;T	0.44482	0.92;0.92;0.92	5.37	-1.03	0.10102	.	0.284900	0.40385	N	0.001117	T	0.05868	0.0153	L	0.43923	1.385	0.22796	N	0.998726	B;B;B;B	0.10296	0.003;0.001;0.0;0.0	B;B;B;B	0.09377	0.004;0.002;0.002;0.001	T	0.04621	-1.0938	10	0.25106	T	0.35	-17.0401	0.75	0.00989	0.4301:0.1753:0.2184:0.1762	rs9605067	214;214;214;214	B4E213;F2Z2W7;Q8IZ69-2;Q8IZ69	.;.;.;TRM2A_HUMAN	I	214	ENSP00000252136:L214I;ENSP00000385807:L214I;ENSP00000395738:L214I	ENSP00000252136:L214I	L	-	1	0	TRMT2A	18483263	1.000000	0.71417	0.273000	0.24645	0.285000	0.27093	2.279000	0.43435	0.010000	0.14839	-0.273000	0.10243	CTC	G|0.978;T|0.022	0.022	strong		0.637	TRMT2A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318168.3	NM_022727	
CSRP2BP	57325	hgsc.bcm.edu	37	20	18143261	18143261	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:18143261A>G	ENST00000435364.3	+	6	1684	c.1343A>G	c.(1342-1344)cAg>cGg	p.Q448R	CSRP2BP_ENST00000377681.3_Missense_Mutation_p.Q447R|CSRP2BP_ENST00000489634.2_Missense_Mutation_p.Q320R	NM_020536.4	NP_065397	Q9H8E8	CSR2B_HUMAN	CSRP2 binding protein	448					chromatin organization (GO:0006325)|G2/M transition of mitotic cell cycle (GO:0000086)|histone H3 acetylation (GO:0043966)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone acetyltransferase activity (GO:0004402)|LIM domain binding (GO:0030274)			NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(12)|ovary(2)|prostate(3)|skin(1)|stomach(1)	34						AGGAAGCCTCAGCTGGAGAAG	0.502																																					p.Q448R		Atlas-SNP	.											.	CSRP2BP	80	.	0			c.A1343G						PASS	.						71.0	74.0	73.0					20																	18143261		2203	4300	6503	SO:0001583	missense	57325	exon6			AGCCTCAGCTGGA	AF252257	CCDS13133.1	20p11.23	2012-06-06			ENSG00000149474	ENSG00000149474			15904	protein-coding gene	gene with protein product	"""cysteine rich protein 2 binding protein"", ""ATAC component 2 homolog (Drosophila)"""					9286703, 10924333, 19103755	Standard	NR_028402		Approved	CRP2BP, dJ717M23.1, PRO1194, ATAC2, KAT14	uc021wbb.1	Q9H8E8	OTTHUMG00000031962	ENST00000435364.3:c.1343A>G	20.37:g.18143261A>G	ENSP00000392318:p.Gln448Arg	72.0	0.0	0		63.0	30.0	0.47619	NM_020536	A2A2I5|Q96GW6|Q96IH3|Q9HBF0|Q9UIY5	Missense_Mutation	SNP	ENST00000435364.3	37	CCDS13133.1	.	.	.	.	.	.	.	.	.	.	A	4.422	0.078067	0.08485	.	.	ENSG00000149474	ENST00000278816;ENST00000377681;ENST00000435364;ENST00000489634	T;T;T;T	0.15017	2.46;2.46;2.46;2.47	6.17	0.00674	0.14068	.	0.384216	0.28859	N	0.013905	T	0.07503	0.0189	N	0.14661	0.345	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.001	T	0.38628	-0.9652	10	0.16420	T	0.52	-20.6595	7.114	0.25407	0.3473:0.3538:0.0:0.2988	.	320;448	Q9H8E8-2;Q9H8E8	.;CSR2B_HUMAN	R	448;447;448;320	ENSP00000278816:Q448R;ENSP00000366909:Q447R;ENSP00000392318:Q448R;ENSP00000425909:Q320R	ENSP00000278816:Q448R	Q	+	2	0	CSRP2BP	18091261	0.192000	0.23301	0.001000	0.08648	0.983000	0.72400	0.681000	0.25320	-0.235000	0.09767	0.533000	0.62120	CAG	.	.	none		0.502	CSRP2BP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000078152.5	NM_020536	
MUC16	94025	hgsc.bcm.edu	37	19	8995959	8995959	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8995959G>T	ENST00000397910.4	-	62	41485	c.41282C>A	c.(41281-41283)aCc>aAc	p.T13761N	MUC16_ENST00000380951.5_Missense_Mutation_p.T402N	NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	13763				Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						CTCACTGCTGGTGGTGGACAC	0.527																																					p.T13761N		Atlas-SNP	.											.	MUC16	4315	.	0			c.C41282A						PASS	.						89.0	78.0	81.0					19																	8995959		1947	4143	6090	SO:0001583	missense	94025	exon62			CTGCTGGTGGTGG	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.41282C>A	19.37:g.8995959G>T	ENSP00000381008:p.Thr13761Asn	51.0	0.0	0		45.0	14.0	0.311111	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	6.099|6.099	0.386626|0.386626	0.11524|0.11524	.|.	.|.	ENSG00000181143|ENSG00000181143	ENST00000542240|ENST00000397910;ENST00000380951	.|T;T	.|0.35973	.|1.28;1.28	1.84|1.84	0.727|0.727	0.18254|0.18254	.|.	.|.	.|.	.|.	.|.	T|T	0.53254|0.53254	0.1785|0.1785	M|M	0.81239|0.81239	2.535|2.535	.|.	.|.	.|.	.|B;D	.|0.53745	.|0.099;0.962	.|B;D	.|0.66716	.|0.007;0.946	T|T	0.58142|0.58142	-0.7688|-0.7688	4|8	.|0.44086	.|T	.|0.13	-3.0332|-3.0332	5.3761|5.3761	0.16166|0.16166	0.0:0.0:0.6654:0.3346|0.0:0.0:0.6654:0.3346	.|.	.|21406;13761	.|Q8WXI7;B5ME49	.|MUC16_HUMAN;.	T|N	601|13761;402	.|ENSP00000381008:T13761N;ENSP00000370338:T402N	.|ENSP00000370338:T402N	P|T	-|-	1|2	0|0	MUC16|MUC16	8856959|8856959	0.002000|0.002000	0.14202|0.14202	0.034000|0.034000	0.17996|0.17996	0.195000|0.195000	0.23768|0.23768	0.094000|0.094000	0.15107|0.15107	0.320000|0.320000	0.23234|0.23234	0.455000|0.455000	0.32223|0.32223	CCA|ACC	.	.	none		0.527	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DYTN	391475	hgsc.bcm.edu	37	2	207527656	207527656	+	Missense_Mutation	SNP	A	A	G	rs201792178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207527656A>G	ENST00000452335.2	-	11	1720	c.1604T>C	c.(1603-1605)aTg>aCg	p.M535T		NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	535						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GAAGGCATCCATAAGTTTTGA	0.433													A|||	2	0.000399361	0.0	0.0014	5008	,	,		21916	0.0		0.001	False		,,,				2504	0.0				p.M535T		Atlas-SNP	.											DYTN_ENST00000452335,colon,carcinoma,-1,1	DYTN	168	1	0			c.T1604C						PASS	.	A	THR/MET	5,3917		0,5,1956	277.0	273.0	274.0		1604	-2.1	0.0	2		274	42,8238		0,42,4098	yes	missense	DYTN	NM_001093730.1	81	0,47,6054	GG,GA,AA		0.5072,0.1275,0.3852	benign	535/579	207527656	47,12155	1961	4140	6101	SO:0001583	missense	391475	exon11			GCATCCATAAGTT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.1604T>C	2.37:g.207527656A>G	ENSP00000396593:p.Met535Thr	172.0	0.0	0		187.0	88.0	0.470588	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	2.601	-0.292930	0.05568	0.001275	0.005072	ENSG00000232125	ENST00000452335	T	0.14640	2.49	5.13	-2.14	0.07123	.	.	.	.	.	T	0.03695	0.0105	N	0.12182	0.205	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.44267	-0.9339	9	0.15066	T	0.55	-0.1195	4.7275	0.12948	0.392:0.0:0.4418:0.1662	.	535	A2CJ06	DYTN_HUMAN	T	535	ENSP00000396593:M535T	ENSP00000396593:M535T	M	-	2	0	DYTN	207235901	0.114000	0.22134	0.020000	0.16555	0.244000	0.25665	0.144000	0.16135	-0.124000	0.11724	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	strong		0.433	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
EVC2	132884	hgsc.bcm.edu	37	4	5642347	5642347	+	Missense_Mutation	SNP	G	G	C	rs141287105	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:5642347G>C	ENST00000344408.5	-	10	1417	c.1364C>G	c.(1363-1365)aCa>aGa	p.T455R	EVC2_ENST00000310917.2_Missense_Mutation_p.T375R|EVC2_ENST00000344938.1_Missense_Mutation_p.T455R	NM_147127.4	NP_667338.3	Q86UK5	LBN_HUMAN	Ellis van Creveld syndrome 2	455					smoothened signaling pathway (GO:0007224)	cilium (GO:0005929)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(2)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(32)|lung(28)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	81						ACATTCAGCTGTCAATGCCAC	0.433													G|||	10	0.00199681	0.0	0.0014	5008	,	,		22461	0.0		0.0089	False		,,,				2504	0.0				p.T455R		Atlas-SNP	.											.	EVC2	202	.	0			c.C1364G						PASS	.	G	ARG/THR,ARG/THR	5,4401	9.9+/-24.2	0,5,2198	367.0	327.0	341.0		1124,1364	3.3	0.8	4	dbSNP_134	341	65,8535	39.8+/-96.3	1,63,4236	yes	missense,missense	EVC2	NM_001166136.1,NM_147127.4	71,71	1,68,6434	CC,CG,GG		0.7558,0.1135,0.5382	probably-damaging,probably-damaging	375/1229,455/1309	5642347	70,12936	2203	4300	6503	SO:0001583	missense	132884	exon10			TCAGCTGTCAATG	AB083067	CCDS3382.2, CCDS54718.1	4p16.2-p16.1	2008-08-01	2008-08-01		ENSG00000173040	ENSG00000173040			19747	protein-coding gene	gene with protein product		607261				12136126, 12571802	Standard	NM_147127		Approved	LBN	uc003gij.3	Q86UK5	OTTHUMG00000125493	ENST00000344408.5:c.1364C>G	4.37:g.5642347G>C	ENSP00000342144:p.Thr455Arg	149.0	0.0	0		151.0	66.0	0.437086	NM_147127	Q86YT3|Q86YT4|Q8NG49	Missense_Mutation	SNP	ENST00000344408.5	37	CCDS3382.2	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	G	16.55	3.154339	0.57259	0.001135	0.007558	ENSG00000173040	ENST00000344938;ENST00000310917;ENST00000344408	T;T;T	0.78707	-1.2;-1.2;-1.2	4.25	3.34	0.38264	.	0.344939	0.27677	N	0.018315	T	0.75671	0.3881	M	0.67953	2.075	0.38779	D	0.954725	D	0.56746	0.977	P	0.54544	0.755	T	0.77814	-0.2448	10	0.22706	T	0.39	-4.8253	12.9472	0.58379	0.0:0.0:0.8385:0.1615	.	455	Q86UK5	LBN_HUMAN	R	455;375;455	ENSP00000339954:T455R;ENSP00000311683:T375R;ENSP00000342144:T455R	ENSP00000311683:T375R	T	-	2	0	EVC2	5693248	1.000000	0.71417	0.807000	0.32361	0.767000	0.43475	4.192000	0.58378	2.074000	0.62210	0.591000	0.81541	ACA	G|0.995;C|0.005	0.005	strong		0.433	EVC2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000289822.2	NM_147127	
EPHA2	1969	hgsc.bcm.edu	37	1	16458339	16458339	+	Silent	SNP	G	G	A	rs112285834	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16458339G>A	ENST00000358432.5	-	14	2506	c.2352C>T	c.(2350-2352)acC>acT	p.T784T		NM_004431.3	NP_004422.2	P29317	EPHA2_HUMAN	EPH receptor A2	784	Mediates interaction with ARHGEF16 and ELMO2.|Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of Rac GTPase activity (GO:0032863)|angiogenesis (GO:0001525)|axial mesoderm formation (GO:0048320)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell migration (GO:0016477)|ephrin receptor signaling pathway (GO:0048013)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|keratinocyte differentiation (GO:0030216)|lens fiber cell morphogenesis (GO:0070309)|mammary gland epithelial cell proliferation (GO:0033598)|multicellular organismal development (GO:0007275)|negative regulation of protein kinase B signaling (GO:0051898)|neural tube development (GO:0021915)|neuron differentiation (GO:0030182)|notochord cell development (GO:0060035)|notochord formation (GO:0014028)|osteoblast differentiation (GO:0001649)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|post-anal tail morphogenesis (GO:0036342)|protein kinase B signaling (GO:0043491)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of lamellipodium assembly (GO:0010591)|response to growth factor (GO:0070848)|skeletal system development (GO:0001501)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	cell projection (GO:0042995)|cell surface (GO:0009986)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|leading edge membrane (GO:0031256)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			NS(1)|biliary_tract(1)|breast(3)|central_nervous_system(3)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|pancreas(1)|prostate(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	42		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;0.0181)|Colorectal(212;3.63e-07)|COAD - Colon adenocarcinoma(227;2.25e-05)|BRCA - Breast invasive adenocarcinoma(304;9.58e-05)|Kidney(64;0.000175)|KIRC - Kidney renal clear cell carcinoma(64;0.00261)|STAD - Stomach adenocarcinoma(313;0.00669)|READ - Rectum adenocarcinoma(331;0.0649)	Dasatinib(DB01254)|Regorafenib(DB08896)	CCTCCGGGGCGGTCCAGCGGA	0.647													G|||	14	0.00279553	0.0	0.0014	5008	,	,		17168	0.0		0.0129	False		,,,				2504	0.0				p.T784T		Atlas-SNP	.											.	EPHA2	102	.	0			c.C2352T						PASS	.	G		14,4392	21.2+/-45.6	0,14,2189	49.0	46.0	47.0		2352	-8.9	0.7	1	dbSNP_132	47	138,8462	68.0+/-130.5	0,138,4162	no	coding-synonymous	EPHA2	NM_004431.3		0,152,6351	AA,AG,GG		1.6047,0.3177,1.1687		784/977	16458339	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	1969	exon14			CGGGGCGGTCCAG	BC037166	CCDS169.1	1p36	2013-02-11	2004-10-28		ENSG00000142627	ENSG00000142627	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3386	protein-coding gene	gene with protein product		176946	"""EphA2"""	ECK		9119409	Standard	NM_004431		Approved		uc001aya.2	P29317	OTTHUMG00000009527	ENST00000358432.5:c.2352C>T	1.37:g.16458339G>A		53.0	0.0	0		79.0	28.0	0.35443	NM_004431	B5A968|Q8N3Z2	Silent	SNP	ENST00000358432.5	37	CCDS169.1																																																																																			G|0.990;A|0.010	0.010	strong		0.647	EPHA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026322.1	NM_004431	
JAK3	3718	hgsc.bcm.edu	37	19	17945696	17945696	+	Missense_Mutation	SNP	C	C	T	rs3213409	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:17945696C>T	ENST00000527670.1	-	15	2193	c.2164G>A	c.(2164-2166)Gtc>Atc	p.V722I	JAK3_ENST00000534444.1_Missense_Mutation_p.V722I|JAK3_ENST00000458235.1_Missense_Mutation_p.V722I			P52333	JAK3_HUMAN	Janus kinase 3	722	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.		V -> I (in dbSNP:rs3213409). {ECO:0000269|PubMed:10982185, ECO:0000269|PubMed:14615376, ECO:0000269|PubMed:17344846, ECO:0000269|Ref.4}.		B cell differentiation (GO:0030183)|enzyme linked receptor protein signaling pathway (GO:0007167)|innate immune response (GO:0045087)|interleukin-4-mediated signaling pathway (GO:0035771)|intracellular signal transduction (GO:0035556)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of dendritic cell cytokine production (GO:0002731)|negative regulation of FasL biosynthetic process (GO:0045221)|negative regulation of interleukin-10 production (GO:0032693)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of T cell activation (GO:0050868)|negative regulation of T-helper 1 cell differentiation (GO:0045626)|negative regulation of thymocyte apoptotic process (GO:0070244)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of dendritic cell apoptotic process (GO:2000670)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of T cell apoptotic process (GO:0070232)|response to interleukin-15 (GO:0070672)|response to interleukin-2 (GO:0070669)|response to interleukin-4 (GO:0070670)|response to interleukin-9 (GO:0071104)|STAT protein import into nucleus (GO:0007262)|T cell homeostasis (GO:0043029)|tyrosine phosphorylation of STAT protein (GO:0007260)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)	p.V722I(2)		breast(5)|endometrium(4)|haematopoietic_and_lymphoid_tissue(85)|kidney(4)|large_intestine(11)|lung(22)|ovary(3)|prostate(5)|skin(1)|stomach(2)|upper_aerodigestive_tract(5)	147					Tofacitinib(DB08895)	GGCATGGTGACGCCACTAAAC	0.627		2	Mis		"""acute megakaryocytic leukemia, ETP ALL"""								C|||	18	0.00359425	0.0023	0.0014	5008	,	,		16598	0.0		0.007	False		,,,				2504	0.0072				p.V722I		Atlas-SNP	.		Dom	yes		19	19p13.1	3718	Janus kinase 3		L	JAK3,NS,haematopoietic_neoplasm,0,2	JAK3	341	2	2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	c.G2164A	GRCh37	CM000172	JAK3	M	rs3213409	PASS	.	C	ILE/VAL	9,4397	14.3+/-33.2	1,7,2195	82.0	88.0	86.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2164	0.2	0.0	19	dbSNP_106	86	114,8486	61.0+/-122.8	2,110,4188	yes	missense	JAK3	NM_000215.3	29	3,117,6383	TT,TC,CC		1.3256,0.2043,0.9457	benign	722/1125	17945696	123,12883	2203	4300	6503	SO:0001583	missense	3718	exon16			TGGTGACGCCACT	U31601	CCDS12366.1	19p13-p12	2014-09-17	2009-04-23		ENSG00000105639	ENSG00000105639	2.7.10.1		6193	protein-coding gene	gene with protein product	"""tyrosine-protein kinase JAK3"", ""leukocyte Janus kinase"""	600173				8921370, 9226382	Standard	NM_000215		Approved	L-JAK, JAKL, LJAK, JAK3_HUMAN, JAK-3	uc002nhn.4	P52333	OTTHUMG00000165648	ENST00000527670.1:c.2164G>A	19.37:g.17945696C>T	ENSP00000432511:p.Val722Ile	72.0	0.0	0		90.0	51.0	0.566667	NM_000215	Q13259|Q13260|Q13611|Q8N1E8|Q99699|Q9Y6S2	Missense_Mutation	SNP	ENST00000527670.1	37	CCDS12366.1	8	0.003663003663003663	3	0.006097560975609756	0	0.0	0	0.0	5	0.006596306068601583	C	8.473	0.857929	0.17178	0.002043	0.013256	ENSG00000105639	ENST00000458235;ENST00000527670;ENST00000534444	T;T;T	0.61980	0.06;0.06;0.06	4.89	0.248	0.15526	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.618726	0.15813	N	0.243360	T	0.33147	0.0853	N	0.17082	0.46	0.09310	N	1	B;B	0.06786	0.001;0.001	B;B	0.09377	0.003;0.004	T	0.24977	-1.0145	10	0.62326	D	0.03	-7.2327	7.7407	0.28839	0.0:0.6163:0.0:0.3837	rs3213409;rs52813014;rs3213409	722;722	P52333-2;P52333	.;JAK3_HUMAN	I	722	ENSP00000391676:V722I;ENSP00000432511:V722I;ENSP00000436421:V722I	ENSP00000391676:V722I	V	-	1	0	JAK3	17806696	0.011000	0.17503	0.000000	0.03702	0.008000	0.06430	1.524000	0.35942	-0.126000	0.11682	0.555000	0.69702	GTC	C|0.991;T|0.009	0.009	strong		0.627	JAK3-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385549.1	NM_000215	
XIRP2	129446	hgsc.bcm.edu	37	2	168099555	168099555	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:168099555C>T	ENST00000409195.1	+	9	1742	c.1653C>T	c.(1651-1653)gaC>gaT	p.D551D	XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.D551D|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409273.1_Silent_p.D329D|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409043.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	376					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						ACACAAATGACAGTTCTCAAA	0.398																																					p.D551D		Atlas-SNP	.											.	XIRP2	914	.	0			c.C1653T						PASS	.						43.0	40.0	41.0					2																	168099555		1842	4094	5936	SO:0001819	synonymous_variant	129446	exon9			AAATGACAGTTCT	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.1653C>T	2.37:g.168099555C>T		85.0	0.0	0		71.0	21.0	0.295775	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Silent	SNP	ENST00000409195.1	37	CCDS42769.1																																																																																			.	.	none		0.398	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
KIAA1598	57698	hgsc.bcm.edu	37	10	118713596	118713596	+	Silent	SNP	G	G	A	rs117277365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:118713596G>A	ENST00000355371.4	-	5	890	c.393C>T	c.(391-393)gcC>gcT	p.A131A	KIAA1598_ENST00000392901.4_Silent_p.A71A|KIAA1598_ENST00000392903.2_Silent_p.A131A|KIAA1598_ENST00000497044.1_5'UTR|KIAA1598_ENST00000260777.10_Silent_p.A131A	NM_001127211.2|NM_001258298.1|NM_001258299.1	NP_001120683.1|NP_001245227.1|NP_001245228.1	A0MZ66	SHOT1_HUMAN	KIAA1598	131					axon guidance (GO:0007411)|regulation of establishment of cell polarity (GO:2000114)|regulation of neuron migration (GO:2001222)	axonal growth cone (GO:0044295)				endometrium(1)|kidney(1)|large_intestine(5)|lung(3)	10				all cancers(201;0.00494)		AAGTCTCGGCGGCACCGTCTG	0.403													G|||	3	0.000599042	0.0	0.0	5008	,	,		17591	0.0		0.003	False		,,,				2504	0.0				p.A131A		Atlas-SNP	.											.	KIAA1598	74	.	0			c.C393T						PASS	.	G	,	4,4402	8.1+/-20.4	0,4,2199	136.0	118.0	124.0		393,393	-8.1	0.0	10	dbSNP_133	124	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous,coding-synonymous	KIAA1598	NM_001127211.1,NM_018330.5	,	0,12,6491	AA,AG,GG		0.093,0.0908,0.0923	,	131/632,131/457	118713596	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	57698	exon5			CTCGGCGGCACCG	BC022348	CCDS31293.1, CCDS44482.1, CCDS58097.1, CCDS73207.1, CCDS73208.1	10q26.12	2007-01-30			ENSG00000187164	ENSG00000187164			29319	protein-coding gene	gene with protein product		611171				10997877, 17030985	Standard	NM_001127211		Approved	shootin1, shootin-1	uc009xyw.4	A0MZ66	OTTHUMG00000019114	ENST00000355371.4:c.393C>T	10.37:g.118713596G>A		80.0	0.0	0		76.0	21.0	0.276316	NM_001258299	A8MYU7|B3KRD3|B3KRH2|B3KTE0|B3KTJ7|B3KTJ8|B4E3U1|B7Z7Z9|Q68DG1|Q6PIM5|Q9HCH4|Q9NUV0	Silent	SNP	ENST00000355371.4	37	CCDS44482.1																																																																																			G|0.999;A|0.001	0.001	strong		0.403	KIAA1598-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_018330	
JUP	3728	hgsc.bcm.edu	37	17	39925713	39925713	+	Missense_Mutation	SNP	C	C	T	rs41283425	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39925713C>T	ENST00000393931.3	-	3	543	c.425G>A	c.(424-426)cGc>cAc	p.R142H	JUP_ENST00000540235.1_Missense_Mutation_p.R142H|JUP_ENST00000310706.5_Missense_Mutation_p.R142H|JUP_ENST00000393930.1_Missense_Mutation_p.R142H	NM_002230.2	NP_002221.1	P14923	PLAK_HUMAN	junction plakoglobin	142	Interaction with DSC1 and DSG1.		R -> H (in dbSNP:rs41283425). {ECO:0000269|PubMed:19863551, ECO:0000269|PubMed:20031617}.		adherens junction organization (GO:0034332)|atrioventricular valve morphogenesis (GO:0003181)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cell junction assembly (GO:0034329)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell-cell junction organization (GO:0045216)|cellular response to indole-3-methanol (GO:0071681)|cytoskeletal anchoring at plasma membrane (GO:0007016)|desmosome assembly (GO:0002159)|detection of mechanical stimulus (GO:0050982)|ectoderm development (GO:0007398)|endothelial cell-cell adhesion (GO:0071603)|establishment of protein localization to plasma membrane (GO:0090002)|gastrulation (GO:0007369)|morphogenesis of embryonic epithelium (GO:0016331)|negative regulation of heart induction by canonical Wnt signaling pathway (GO:0003136)|negative regulation of Wnt signaling pathway involved in heart development (GO:0003308)|nervous system development (GO:0007399)|oocyte development (GO:0048599)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein heterooligomerization (GO:0051291)|regulation of cell proliferation (GO:0042127)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|skin development (GO:0043588)|ventricular cardiac muscle cell action potential (GO:0086005)	actin cytoskeleton (GO:0015629)|apicolateral plasma membrane (GO:0016327)|basolateral plasma membrane (GO:0016323)|catenin complex (GO:0016342)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|gamma-catenin-TCF7L2 complex (GO:0071665)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|lateral plasma membrane (GO:0016328)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein-DNA complex (GO:0032993)|Z disc (GO:0030018)|zonula adherens (GO:0005915)	alpha-catenin binding (GO:0045294)|cadherin binding (GO:0045296)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|structural constituent of cell wall (GO:0005199)|structural molecule activity (GO:0005198)|transcription coactivator activity (GO:0003713)			breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(4)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	23		Breast(137;0.000162)	BRCA - Breast invasive adenocarcinoma(4;0.233)	BRCA - Breast invasive adenocarcinoma(366;0.15)		GGGCAGGGCGCGAGTGGCCAG	0.652													C|||	120	0.0239617	0.0023	0.0331	5008	,	,		18035	0.0		0.0567	False		,,,				2504	0.0378				p.R142H	Colon(16;42 520 6044 17852 28530)	Atlas-SNP	.											.	JUP	64	.	0			c.G425A						PASS	.	C	HIS/ARG,HIS/ARG	49,4357	45.3+/-79.5	1,47,2155	26.0	25.0	26.0		425,425	5.5	1.0	17	dbSNP_127	26	500,8100	137.9+/-194.8	10,480,3810	yes	missense,missense	JUP	NM_002230.2,NM_021991.2	29,29	11,527,5965	TT,TC,CC		5.814,1.1121,4.2211	possibly-damaging,possibly-damaging	142/746,142/746	39925713	549,12457	2203	4300	6503	SO:0001583	missense	3728	exon3			AGGGCGCGAGTGG	AF233882	CCDS11407.1	17q21	2014-09-17	2004-08-09		ENSG00000173801	ENSG00000173801		"""Armadillo repeat containing"""	6207	protein-coding gene	gene with protein product		173325	"""catenin (cadherin-associated protein), gamma 80kDa"""	CTNNG		1889810, 7604000	Standard	NM_021991		Approved	DP3, PDGB, PKGB, DPIII	uc002hxs.2	P14923	OTTHUMG00000133494	ENST00000393931.3:c.425G>A	17.37:g.39925713C>T	ENSP00000377508:p.Arg142His	95.0	0.0	0		110.0	48.0	0.436364	NM_021991	Q15093|Q15151|Q7L3S5|Q86W21|Q9BWC4|Q9HCX9	Missense_Mutation	SNP	ENST00000393931.3	37	CCDS11407.1	61	0.027930402930402932	0	0.0	15	0.04143646408839779	0	0.0	46	0.06068601583113457	c	34	5.375802	0.95923	0.011121	0.05814	ENSG00000173801	ENST00000540235;ENST00000393930;ENST00000310706;ENST00000393931;ENST00000449889;ENST00000437187;ENST00000420370;ENST00000424457	T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	5.52	5.52	0.82312	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.35913	0.0948	M	0.73430	2.235	0.54753	D	0.999984	D;D	0.89917	1.0;1.0	D;P	0.79784	0.993;0.901	T	0.67628	-0.5622	10	0.72032	D	0.01	-47.1096	18.4331	0.90633	0.0:1.0:0.0:0.0	rs41283425	142;142	B4DE59;P14923	.;PLAK_HUMAN	H	142	ENSP00000441751:R142H;ENSP00000377507:R142H;ENSP00000311113:R142H;ENSP00000377508:R142H;ENSP00000389886:R142H;ENSP00000394146:R142H;ENSP00000411449:R142H;ENSP00000401034:R142H	ENSP00000311113:R142H	R	-	2	0	JUP	37179239	1.000000	0.71417	1.000000	0.80357	0.760000	0.43138	7.809000	0.86057	2.593000	0.87608	0.556000	0.70494	CGC	C|0.962;T|0.038	0.038	strong		0.652	JUP-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257406.1		
CUL3	8452	hgsc.bcm.edu	37	2	225365109	225365109	+	Silent	SNP	T	T	A	rs41373148	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:225365109T>A	ENST00000264414.4	-	11	1919	c.1581A>T	c.(1579-1581)gcA>gcT	p.A527A	CUL3_ENST00000409096.1_Silent_p.A503A|CUL3_ENST00000344951.4_Silent_p.A461A|CUL3_ENST00000409777.1_Silent_p.A503A	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3	527					cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CATGTCTTGGTGCTGGTGGGA	0.403													T|||	27	0.00539137	0.0015	0.0043	5008	,	,		16507	0.0		0.0169	False		,,,				2504	0.0051				p.A533A		Atlas-SNP	.											.	CUL3	96	.	0			c.A1599T						PASS	.	T		18,4388	26.2+/-53.5	0,18,2185	206.0	186.0	193.0		1581	3.6	1.0	2	dbSNP_127	193	154,8446	74.2+/-136.8	3,148,4149	no	coding-synonymous	CUL3	NM_003590.3		3,166,6334	AA,AT,TT		1.7907,0.4085,1.3225		527/769	225365109	172,12834	2203	4300	6503	SO:0001819	synonymous_variant	8452	exon11			TCTTGGTGCTGGT	U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1581A>T	2.37:g.225365109T>A		96.0	0.0	0		87.0	41.0	0.471264	NM_001257198	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	Silent	SNP	ENST00000264414.4	37	CCDS2462.1																																																																																			T|0.987;A|0.013	0.013	strong		0.403	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256871.2		
DHX38	9785	hgsc.bcm.edu	37	16	72132832	72132832	+	Silent	SNP	G	G	A	rs150221434	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:72132832G>A	ENST00000268482.3	+	6	1280	c.771G>A	c.(769-771)gtG>gtA	p.V257V	DHX38_ENST00000536867.1_Intron	NM_014003.3	NP_054722.2	Q92620	PRP16_HUMAN	DEAH (Asp-Glu-Ala-His) box polypeptide 38	257					gene expression (GO:0010467)|mRNA 3'-end processing (GO:0031124)|mRNA export from nucleus (GO:0006406)|mRNA splicing, via spliceosome (GO:0000398)|RNA splicing (GO:0008380)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			endometrium(5)|kidney(1)|large_intestine(16)|lung(15)|pancreas(1)|prostate(2)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	48		Ovarian(137;0.125)				CCAGGTCTGTGAGGGGCAAGT	0.582													G|||	4	0.000798722	0.0	0.0029	5008	,	,		19641	0.0		0.002	False		,,,				2504	0.0				p.V257V	Melanoma(97;711 1442 7855 13832 28836)	Atlas-SNP	.											.	DHX38	91	.	0			c.G771A						PASS	.	G		1,4395	2.1+/-5.4	0,1,2197	53.0	53.0	53.0		771	2.8	1.0	16	dbSNP_134	53	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	DHX38	NM_014003.3		0,18,6480	AA,AG,GG		0.1977,0.0227,0.1385		257/1228	72132832	18,12978	2198	4300	6498	SO:0001819	synonymous_variant	9785	exon6			GTCTGTGAGGGGC	AF038391	CCDS10907.1	16q22	2008-02-05	2003-06-13	2003-06-20	ENSG00000140829	ENSG00000140829		"""DEAH-boxes"""	17211	protein-coding gene	gene with protein product		605584	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 38"""	DDX38		9524131, 9039502	Standard	NM_014003		Approved	PRP16, KIAA0224, hPrp16, PRPF16	uc002fcb.3	Q92620	OTTHUMG00000137596	ENST00000268482.3:c.771G>A	16.37:g.72132832G>A		113.0	0.0	0		128.0	61.0	0.476562	NM_014003	B4DVG8|D3DWS7|O75212|Q96HN7	Silent	SNP	ENST00000268482.3	37	CCDS10907.1																																																																																			G|0.999;A|0.001	0.001	strong		0.582	DHX38-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269004.3	NM_014003	
LRP2	4036	hgsc.bcm.edu	37	2	170060670	170060670	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:170060670G>C	ENST00000263816.3	-	42	8112	c.7827C>G	c.(7825-7827)gaC>gaG	p.D2609E		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	2609					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	GTGTGTACAAGTCAGTCCAGT	0.473																																					p.D2609E		Atlas-SNP	.											.	LRP2	751	.	0			c.C7827G						PASS	.						165.0	174.0	171.0					2																	170060670		2203	4300	6503	SO:0001583	missense	4036	exon42			GTACAAGTCAGTC		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.7827C>G	2.37:g.170060670G>C	ENSP00000263816:p.Asp2609Glu	126.0	0.0	0		153.0	48.0	0.313726	NM_004525	O00711|Q16215	Missense_Mutation	SNP	ENST00000263816.3	37	CCDS2232.1	.	.	.	.	.	.	.	.	.	.	G	16.72	3.200151	0.58126	.	.	ENSG00000081479	ENST00000263816	D	0.92446	-3.04	5.78	3.01	0.34805	Six-bladed beta-propeller, TolB-like (1);	0.093401	0.64402	N	0.000001	D	0.93677	0.7980	H	0.95504	3.68	0.80722	D	1	D	0.53745	0.962	P	0.44394	0.448	D	0.91687	0.5363	10	0.87932	D	0	.	7.2942	0.26383	0.1959:0.0:0.6833:0.1207	.	2609	P98164	LRP2_HUMAN	E	2609	ENSP00000263816:D2609E	ENSP00000263816:D2609E	D	-	3	2	LRP2	169768916	1.000000	0.71417	0.553000	0.28255	0.357000	0.29423	3.438000	0.52871	0.364000	0.24374	-0.857000	0.03018	GAC	.	.	none		0.473	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
CDH13	1012	hgsc.bcm.edu	37	16	83636136	83636136	+	Silent	SNP	G	G	A	rs371581191	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:83636136G>A	ENST00000566620.1	+	8	1328	c.1038G>A	c.(1036-1038)acG>acA	p.T346T	CDH13_ENST00000268613.10_Silent_p.T393T|CDH13_ENST00000428848.3_Silent_p.T307T	NM_001220488.1|NM_001220489.1|NM_001220490.1|NM_001257.4	NP_001207417.1|NP_001207418.1|NP_001207419.1|NP_001248.1	P55290	CAD13_HUMAN	cadherin 13	346	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|calcium-dependent cell-cell adhesion (GO:0016339)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|endothelial cell migration (GO:0043542)|homophilic cell adhesion (GO:0007156)|keratinocyte proliferation (GO:0043616)|lamellipodium assembly (GO:0030032)|localization within membrane (GO:0051668)|low-density lipoprotein particle mediated signaling (GO:0055096)|mitotic cell cycle (GO:0000278)|negative regulation of cell adhesion (GO:0007162)|negative regulation of cell proliferation (GO:0008285)|positive regulation of calcium-mediated signaling (GO:0050850)|positive regulation of cell migration (GO:0030335)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of positive chemotaxis (GO:0050927)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|Rac protein signal transduction (GO:0016601)|regulation of cell growth (GO:0001558)|regulation of endocytosis (GO:0030100)|regulation of epidermal growth factor receptor signaling pathway (GO:0042058)|Rho protein signal transduction (GO:0007266)|sprouting angiogenesis (GO:0002040)	anchored component of membrane (GO:0031225)|caveola (GO:0005901)|cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	adiponectin binding (GO:0055100)|cadherin binding (GO:0045296)|calcium ion binding (GO:0005509)|lipoprotein particle binding (GO:0071813)|low-density lipoprotein particle binding (GO:0030169)			large_intestine(1)	1		all_cancers(2;1.34e-11)|all_epithelial(2;4.3e-09)		COAD - Colon adenocarcinoma(5;0.0268)		TAACAGGCACGGCCACAGCCA	0.458													G|||	4	0.000798722	0.0	0.0	5008	,	,		15867	0.0		0.003	False		,,,				2504	0.001				p.T393T		Atlas-SNP	.											.	CDH13	97	.	0			c.G1179A						PASS	.	G	,,,	1,3891		0,1,1945	182.0	184.0	183.0		1179,921,276,1038	-12.0	0.0	16		183	20,8320		0,20,4150	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	CDH13	NM_001220488.1,NM_001220489.1,NM_001220490.1,NM_001257.4	,,,	0,21,6095	AA,AG,GG		0.2398,0.0257,0.1717	,,,	393/761,307/675,92/460,346/714	83636136	21,12211	1946	4170	6116	SO:0001819	synonymous_variant	1012	exon9			AGGCACGGCCACA	U59288	CCDS56009.1, CCDS56010.1, CCDS58485.1, CCDS58486.1, CCDS58487.1	16q23.3	2013-08-27	2013-08-27			ENSG00000140945		"""Cadherins / Major cadherins"""	1753	protein-coding gene	gene with protein product	"""T-cadherin"", ""H-cadherin (heart)"""	601364				8673923, 9468307	Standard	NM_001257		Approved	CDHH	uc010vns.2	P55290		ENST00000566620.1:c.1038G>A	16.37:g.83636136G>A		101.0	0.0	0		78.0	42.0	0.538462	NM_001220488	A8W476|A8W477|B7Z590|C9JRI6|J3KN62|Q6GTW4|Q8TBX3	Silent	SNP	ENST00000566620.1	37	CCDS58486.1																																																																																			.	.	weak		0.458	CDH13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432917.1	NM_001257	
ETFB	2109	hgsc.bcm.edu	37	19	51856469	51856469	+	Missense_Mutation	SNP	G	G	A	rs147353781	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:51856469G>A	ENST00000309244.4	-	3	383	c.292C>T	c.(292-294)Cgc>Tgc	p.R98C	CTD-2616J11.9_ENST00000600974.1_RNA|ETFB_ENST00000354232.4_Missense_Mutation_p.R189C|CTD-2616J11.11_ENST00000600067.1_3'UTR	NM_001985.2	NP_001976.1	P38117	ETFB_HUMAN	electron-transfer-flavoprotein, beta polypeptide	98					cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)			kidney(2)|large_intestine(1)|lung(3)	6		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000226)|OV - Ovarian serous cystadenocarcinoma(262;0.00661)		GGACCCAAGCGTTCTGCTTCT	0.637													g|||	2	0.000399361	0.0	0.0014	5008	,	,		16497	0.0		0.001	False		,,,				2504	0.0				p.R189C		Atlas-SNP	.											ETFB_ENST00000309244,NS,carcinoma,0,2	ETFB	46	2	0			c.C565T						PASS	.		CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	112.0	99.0	104.0		565,292	3.0	0.1	19	dbSNP_134	104	13,8587	9.8+/-36.6	0,13,4287	yes	missense,missense	ETFB	NM_001014763.1,NM_001985.2	180,180	0,15,6488	AA,AG,GG		0.1512,0.0454,0.1153	probably-damaging,probably-damaging	189/347,98/256	51856469	15,12991	2203	4300	6503	SO:0001583	missense	2109	exon2			CCAAGCGTTCTGC	X71129	CCDS12828.1, CCDS33085.1	19q13.3-q13.4	2008-02-05				ENSG00000105379			3482	protein-coding gene	gene with protein product		130410					Standard	NM_001014763		Approved		uc002pwg.3	P38117		ENST00000309244.4:c.292C>T	19.37:g.51856469G>A	ENSP00000311930:p.Arg98Cys	44.0	0.0	0		49.0	28.0	0.571429	NM_001014763	A8K766|B3KNY2|Q6IBH7|Q71RF6|Q9Y3S7	Missense_Mutation	SNP	ENST00000309244.4	37	CCDS12828.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	g	13.39	2.223595	0.39300	4.54E-4	0.001512	ENSG00000105379	ENST00000309244;ENST00000354232	D;D	0.82803	-1.65;-1.65	5.18	3.0	0.34707	Electron transfer flavoprotein, alpha/beta-subunit, N-terminal (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.416981	0.27315	N	0.019921	T	0.81389	0.4812	L	0.39898	1.24	0.09310	N	0.999997	B;D	0.58620	0.218;0.983	B;P	0.55667	0.369;0.781	T	0.71774	-0.4491	10	0.72032	D	0.01	.	6.2267	0.20711	0.088:0.0:0.5739:0.3381	.	98;189	P38117;P38117-2	ETFB_HUMAN;.	C	98;189	ENSP00000311930:R98C;ENSP00000346173:R189C	ENSP00000311930:R98C	R	-	1	0	ETFB	56548281	0.020000	0.18652	0.107000	0.21349	0.673000	0.39480	1.050000	0.30404	0.561000	0.29186	-0.233000	0.12211	CGC	G|0.999;A|0.001	0.001	strong		0.637	ETFB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464273.1		
AKT1	207	hgsc.bcm.edu	37	14	105239894	105239894	+	Silent	SNP	C	C	T	rs1130233	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105239894C>T	ENST00000554581.1	-	8	2206	c.726G>A	c.(724-726)gaG>gaA	p.E242E	AKT1_ENST00000349310.3_Silent_p.E242E|AKT1_ENST00000555458.1_5'Flank|AKT1_ENST00000544168.1_Silent_p.E180E|AKT1_ENST00000402615.2_Silent_p.E242E|AKT1_ENST00000554848.1_Silent_p.E242E|AKT1_ENST00000407796.2_Silent_p.E242E|AKT1_ENST00000555528.1_Silent_p.E242E|AKT1_ENST00000554585.1_5'Flank|AKT1_ENST00000554192.1_5'Flank			P31749	AKT1_HUMAN	v-akt murine thymoma viral oncogene homolog 1	242	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation-induced cell death of T cells (GO:0006924)|aging (GO:0007568)|anagen (GO:0042640)|apoptotic mitochondrial changes (GO:0008637)|apoptotic process (GO:0006915)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cell projection organization (GO:0030030)|cell proliferation (GO:0008283)|cellular protein modification process (GO:0006464)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cellular response to hypoxia (GO:0071456)|cellular response to insulin stimulus (GO:0032869)|cellular response to mechanical stimulus (GO:0071260)|endocrine pancreas development (GO:0031018)|epidermal growth factor receptor signaling pathway (GO:0007173)|execution phase of apoptosis (GO:0097194)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|gene expression (GO:0010467)|germ cell development (GO:0007281)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycogen biosynthetic process (GO:0005978)|glycogen cell differentiation involved in embryonic placenta development (GO:0060709)|hyaluronan metabolic process (GO:0030212)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intracellular signal transduction (GO:0035556)|intrinsic apoptotic signaling pathway (GO:0097193)|labyrinthine layer blood vessel development (GO:0060716)|mammary gland epithelial cell differentiation (GO:0060644)|maternal placenta development (GO:0001893)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|negative regulation of autophagy (GO:0010507)|negative regulation of cell size (GO:0045792)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of JNK cascade (GO:0046329)|negative regulation of neuron death (GO:1901215)|negative regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902176)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of proteolysis (GO:0045861)|negative regulation of release of cytochrome c from mitochondria (GO:0090201)|neurotrophin TRK receptor signaling pathway (GO:0048011)|nitric oxide biosynthetic process (GO:0006809)|nitric oxide metabolic process (GO:0046209)|osteoblast differentiation (GO:0001649)|peptidyl-serine phosphorylation (GO:0018105)|peripheral nervous system myelin maintenance (GO:0032287)|phosphatidylinositol-mediated signaling (GO:0048015)|phosphorylation (GO:0016310)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell growth (GO:0030307)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of lipid biosynthetic process (GO:0046889)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of sodium ion transport (GO:0010765)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|protein autophosphorylation (GO:0046777)|protein catabolic process (GO:0030163)|protein import into nucleus, translocation (GO:0000060)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle checkpoint (GO:1901976)|regulation of cell migration (GO:0030334)|regulation of glycogen biosynthetic process (GO:0005979)|regulation of neuron projection development (GO:0010975)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of translation (GO:0006417)|response to fluid shear stress (GO:0034405)|response to food (GO:0032094)|response to heat (GO:0009408)|response to UV-A (GO:0070141)|RNA metabolic process (GO:0016070)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|striated muscle cell differentiation (GO:0051146)|T cell costimulation (GO:0031295)|translation (GO:0006412)	cell-cell junction (GO:0005911)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|kinase activity (GO:0016301)|nitric-oxide synthase regulator activity (GO:0030235)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)			NS(3)|breast(97)|central_nervous_system(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(7)|lung(10)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|thyroid(10)|urinary_tract(15)	176		all_cancers(154;3.77e-06)|all_lung(585;3.24e-07)|all_epithelial(191;3.45e-05)|all_neural(303;0.0459)|Melanoma(154;0.155)	all cancers(16;0.000486)|OV - Ovarian serous cystadenocarcinoma(23;0.00647)|Epithelial(46;0.0153)|GBM - Glioblastoma multiforme(11;0.116)	all cancers(159;0.0107)|OV - Ovarian serous cystadenocarcinoma(161;0.0132)|Epithelial(152;0.243)	Adenosine triphosphate(DB00171)|Arsenic trioxide(DB01169)	AGAACACACGCTCCCGGGACA	0.652		1	Mis		"""breast, colorectal, ovarian, NSCLC"""								C|||	1615	0.322484	0.0787	0.4222	5008	,	,		14497	0.6002		0.2425	False		,,,				2504	0.3773				p.E242E		Atlas-SNP	.		Dom	yes		14	14q32.32	207	v-akt murine thymoma viral oncogene homolog 1		E	.	AKT1	379	.	0			c.G726A	GRCh37	CM081515	AKT1	M	rs1130233	PASS	.	C	,,	507,3897	216.1+/-234.9	33,441,1728	31.0	26.0	28.0		726,726,726	4.8	0.9	14	dbSNP_86	28	2115,6485	334.9+/-321.2	269,1577,2454	no	coding-synonymous,coding-synonymous,coding-synonymous	AKT1	NM_001014431.1,NM_001014432.1,NM_005163.2	,,	302,2018,4182	TT,TC,CC		24.593,11.5123,20.163	,,	242/481,242/481,242/481	105239894	2622,10382	2202	4300	6502	SO:0001819	synonymous_variant	207	exon9			CACACGCTCCCGG	M63167	CCDS9994.1	14q32.33	2014-09-17			ENSG00000142208	ENSG00000142208	2.7.11.1	"""Pleckstrin homology (PH) domain containing"""	391	protein-coding gene	gene with protein product		164730					Standard	XM_005267401		Approved	RAC, PKB, PRKBA, AKT	uc001ypn.3	P31749	OTTHUMG00000170795	ENST00000554581.1:c.726G>A	14.37:g.105239894C>T		114.0	0.0	0		90.0	89.0	0.988889	NM_005163	B2RAM5|B7Z5R1|Q9BWB6	Silent	SNP	ENST00000554581.1	37	CCDS9994.1																																																																																			C|0.769;T|0.231	0.231	strong		0.652	AKT1-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410418.1	NM_005163	
MIB2	142678	hgsc.bcm.edu	37	1	1564064	1564064	+	Missense_Mutation	SNP	G	G	A	rs201947158		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:1564064G>A	ENST00000357210.4	+	16	2554	c.2338G>A	c.(2338-2340)Gcc>Acc	p.A780T	MIB2_ENST00000378712.1_Missense_Mutation_p.A657T|MIB2_ENST00000520777.1_Missense_Mutation_p.A833T|MIB2_ENST00000505820.2_Missense_Mutation_p.A837T|MIB2_ENST00000504599.1_Missense_Mutation_p.A736T|MIB2_ENST00000518681.1_Missense_Mutation_p.A772T|MIB2_ENST00000360522.4_Missense_Mutation_p.A745T|MIB2_ENST00000378708.1_Missense_Mutation_p.A686T|MIB2_ENST00000355826.5_Missense_Mutation_p.A823T|MIB2_ENST00000378710.3_Missense_Mutation_p.A744T	NM_080875.2	NP_543151.2	Q96AX9	MIB2_HUMAN	mindbomb E3 ubiquitin protein ligase 2	780					Notch signaling pathway (GO:0007219)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)	early endosome (GO:0005769)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|signal transducer activity (GO:0004871)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(5)|lung(7)|prostate(4)|upper_aerodigestive_tract(1)	18	all_cancers(77;0.000708)|all_epithelial(69;0.000943)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;6.04e-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)		Epithelial(90;5.26e-37)|OV - Ovarian serous cystadenocarcinoma(86;2.54e-23)|GBM - Glioblastoma multiforme(42;9e-08)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|STAD - Stomach adenocarcinoma(132;0.00644)|BRCA - Breast invasive adenocarcinoma(365;0.00786)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.199)		GGCTGATGGGGCCGGGGGGGA	0.716													.|||	1	0.000199681	0.0	0.0	5008	,	,		15533	0.0		0.001	False		,,,				2504	0.0				p.A837T		Atlas-SNP	.											.	MIB2	62	.	0			c.G2509A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	3,3915		0,3,1956	7.0	10.0	9.0		2497,2467,2314,1969,2509	2.9	1.0	1		9	26,8118		0,26,4046	yes	missense,missense,missense,missense,missense	MIB2	NM_001170686.1,NM_001170687.1,NM_001170688.1,NM_001170689.1,NM_080875.2	58,58,58,58,58	0,29,6002	AA,AG,GG		0.3193,0.0766,0.2404	benign,benign,benign,benign,benign	833/1067,823/1057,772/1006,657/754,837/1071	1564064	29,12033	1959	4072	6031	SO:0001583	missense	142678	exon16			GATGGGGCCGGGG	AK097106	CCDS41224.1, CCDS41224.2, CCDS53261.1, CCDS53262.1, CCDS53263.1, CCDS53264.1	1p36.33	2013-01-10	2012-02-23	2005-04-01	ENSG00000197530	ENSG00000197530		"""Zinc fingers, ZZ-type"", ""Ankyrin repeat domain containing"""	30577	protein-coding gene	gene with protein product		611141	"""zinc finger, ZZ type with ankyrin repeat domain 1"", ""mindbomb homolog 2 (Drosophila)"""	ZZANK1		12761501	Standard	NM_080875		Approved	skeletrophin, ZZZ5, FLJ39787	uc001agg.3	Q96AX9	OTTHUMG00000074647	ENST00000357210.4:c.2338G>A	1.37:g.1564064G>A	ENSP00000349741:p.Ala780Thr	102.0	0.0	0		136.0	66.0	0.485294	NM_080875	A2AGM5|A2AGM6|B3KV93|B3KVF4|B3KXY1|B4DZ57|E9PGU1|E9PHQ1|F8WA73|J3KNZ7|Q7Z437|Q8IY62|Q8N786|Q8N897|Q8N8R2|Q8N911|Q8NB36|Q8NCY1|Q8NG59|Q8NG60|Q8NG61|Q8NI59|Q8WYN1	Missense_Mutation	SNP	ENST00000357210.4	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.810|8.810	0.934982|0.934982	0.18206|0.18206	7.66E-4|7.66E-4	0.003193|0.003193	ENSG00000197530|ENSG00000197530	ENST00000520777;ENST00000357210;ENST00000360522;ENST00000378710;ENST00000355826;ENST00000518681;ENST00000505820;ENST00000378712;ENST00000504599;ENST00000378708|ENST00000514234	T;T;T;T;T;T;T;T;T;T|T	0.66995|0.35421	1.26;1.28;1.27;1.28;1.27;1.27;1.26;-0.24;1.28;1.3|1.31	3.83|3.83	2.91|2.91	0.33838|0.33838	Ankyrin repeat-containing domain (1);|.	0.626746|.	0.15520|.	N|.	0.258115|.	T|T	0.32645|0.32645	0.0836|0.0836	L|L	0.36672|0.36672	1.1|1.1	0.26411|0.26411	N|N	0.976259|0.976259	B;B;B;B;P;P;B|.	0.37122|.	0.433;0.011;0.126;0.011;0.583;0.575;0.015|.	B;B;B;B;B;B;B|.	0.36845|.	0.234;0.013;0.05;0.021;0.08;0.108;0.014|.	T|T	0.21895|0.21895	-1.0232|-1.0232	10|7	0.29301|0.56958	T|D	0.29|0.05	-2.4025|-2.4025	7.3783|7.3783	0.26841|0.26841	0.217:0.0:0.783:0.0|0.217:0.0:0.783:0.0	.|.	745;686;657;772;833;766;780|.	Q96AX9-5;F2Z2L2;B3KXY1;E9PHQ1;E9PGU1;Q96AX9-2;Q96AX9|.	.;.;.;.;.;.;MIB2_HUMAN|.	T|D	833;780;745;744;823;772;837;657;736;686|595	ENSP00000428660:A833T;ENSP00000349741:A780T;ENSP00000353713:A745T;ENSP00000367982:A744T;ENSP00000348081:A823T;ENSP00000428264:A772T;ENSP00000426103:A837T;ENSP00000367984:A657T;ENSP00000426128:A736T;ENSP00000367980:A686T|ENSP00000427680:G595D	ENSP00000348081:A823T|ENSP00000427680:G595D	A|G	+|+	1|2	0|0	MIB2|MIB2	1553927|1553927	0.894000|0.894000	0.30519|0.30519	1.000000|1.000000	0.80357|0.80357	0.988000|0.988000	0.76386|0.76386	0.434000|0.434000	0.21494|0.21494	0.817000|0.817000	0.34445|0.34445	0.491000|0.491000	0.48974|0.48974	GCC|GGC	.	.	weak		0.716	MIB2-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_080875	
OBSCN	84033	hgsc.bcm.edu	37	1	228495867	228495867	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:228495867G>A	ENST00000422127.1	+	47	12566	c.12522G>A	c.(12520-12522)gaG>gaA	p.E4174E	OBSCN_ENST00000570156.2_Silent_p.E5131E|OBSCN_ENST00000366707.4_Silent_p.E1808E|OBSCN_ENST00000284548.11_Silent_p.E4174E|OBSCN_ENST00000366709.4_Silent_p.E1293E	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	4174	Ig-like 43.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				CGGCCGATGAGGATGTTGAGT	0.597																																					p.E5131E		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G15393A						PASS	.						92.0	104.0	100.0					1																	228495867		2171	4258	6429	SO:0001819	synonymous_variant	84033	exon58			CGATGAGGATGTT	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.12522G>A	1.37:g.228495867G>A		113.0	0.0	0		118.0	53.0	0.449153	NM_001271223	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																			.	.	none		0.597	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
SCAF8	22828	hgsc.bcm.edu	37	6	155123273	155123273	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:155123273T>C	ENST00000367178.3	+	7	1351	c.775T>C	c.(775-777)Ttt>Ctt	p.F259L	SCAF8_ENST00000367186.4_Missense_Mutation_p.F325L|SCAF8_ENST00000417268.1_Missense_Mutation_p.F259L	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	259	Gln-rich.				mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)|RNA polymerase core enzyme binding (GO:0043175)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(14)|lung(15)|ovary(1)|prostate(3)|upper_aerodigestive_tract(1)	46						GGGAGTCTCCTTTAACAAGGT	0.343																																					p.F259L		Atlas-SNP	.											.	SCAF8	122	.	0			c.T775C						PASS	.						48.0	45.0	46.0					6																	155123273		2203	4300	6503	SO:0001583	missense	22828	exon7			GTCTCCTTTAACA	AB029039	CCDS5247.1, CCDS69226.1, CCDS75541.1	6q25.1-q25.3	2013-02-12	2011-01-10	2011-01-10	ENSG00000213079	ENSG00000213079		"""RNA binding motif (RRM) containing"""	20959	protein-coding gene	gene with protein product			"""RNA binding motif protein 16"""	RBM16		10470851	Standard	NM_001286189		Approved	KIAA1116	uc003qpz.3	Q9UPN6	OTTHUMG00000015877	ENST00000367178.3:c.775T>C	6.37:g.155123273T>C	ENSP00000356146:p.Phe259Leu	67.0	0.0	0		85.0	4.0	0.0470588	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	T	17.60	3.430469	0.62844	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.54675	0.6;0.6;0.56	5.75	5.75	0.90469	.	0.205984	0.41938	U	0.000799	T	0.23289	0.0563	L	0.27053	0.805	0.52501	D	0.999959	B;B;B;B	0.18610	0.029;0.029;0.006;0.015	B;B;B;B	0.17433	0.018;0.018;0.007;0.01	T	0.11131	-1.0600	10	0.35671	T	0.21	.	10.3929	0.44184	0.0:0.073:0.0:0.927	.	304;325;337;259	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	L	259;259;325	ENSP00000356146:F259L;ENSP00000413098:F259L;ENSP00000356154:F325L	ENSP00000356146:F259L	F	+	1	0	SCAF8	155164965	1.000000	0.71417	0.995000	0.50966	0.984000	0.73092	5.971000	0.70440	2.188000	0.69820	0.528000	0.53228	TTT	.	.	none		0.343	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892	
GAB2	9846	hgsc.bcm.edu	37	11	77930447	77930447	+	Silent	SNP	G	G	A	rs61749244	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:77930447G>A	ENST00000361507.4	-	10	1987	c.1902C>T	c.(1900-1902)tcC>tcT	p.S634S	GAB2_ENST00000340149.2_Silent_p.S596S	NM_080491.2	NP_536739.1	Q9UQC2	GAB2_HUMAN	GRB2-associated binding protein 2	634					cell migration (GO:0016477)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|osteoclast differentiation (GO:0030316)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell proliferation (GO:0008284)|positive regulation of mast cell degranulation (GO:0043306)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|phosphatidylinositol-3,4-bisphosphate binding (GO:0043325)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.S634S(1)	INTS4/GAB2(2)	NS(1)|breast(1)|endometrium(5)|kidney(1)|large_intestine(1)|lung(8)|ovary(5)|skin(1)|upper_aerodigestive_tract(1)	24	all_cancers(14;3.31e-18)|all_epithelial(13;5.3e-21)|Breast(9;5.6e-16)|Ovarian(111;0.152)		OV - Ovarian serous cystadenocarcinoma(8;1.58e-23)			CAGAGGTGACGGATGAAGTAG	0.567													g|||	31	0.0061901	0.0023	0.013	5008	,	,		22020	0.0		0.0149	False		,,,				2504	0.0041				p.S634S		Atlas-SNP	.											GAB2,rectum,carcinoma,-2,4	GAB2	63	4	1	Substitution - coding silent(1)	ovary(1)	c.C1902T						PASS	.	G	,	25,4375	31.7+/-61.6	0,25,2175	121.0	98.0	106.0		1788,1902	-10.7	0.0	11	dbSNP_129	106	236,8348	96.3+/-158.1	3,230,4059	no	coding-synonymous,coding-synonymous	GAB2	NM_012296.3,NM_080491.2	,	3,255,6234	AA,AG,GG		2.7493,0.5682,2.0102	,	596/639,634/677	77930447	261,12723	2200	4292	6492	SO:0001819	synonymous_variant	9846	exon10			GGTGACGGATGAA	AB011143	CCDS8259.1, CCDS8260.1	11q13.4-q13.5	2013-01-10			ENSG00000033327	ENSG00000033327		"""Pleckstrin homology (PH) domain containing"""	14458	protein-coding gene	gene with protein product	"""Grb2-associated binder 2"""	606203				10391903, 10068651	Standard	NM_080491		Approved	KIAA0571	uc001ozh.3	Q9UQC2	OTTHUMG00000166673	ENST00000361507.4:c.1902C>T	11.37:g.77930447G>A		107.0	0.0	0		95.0	52.0	0.547368	NM_080491	A2RRM2|A6NEW9|A7MD36|O60317	Silent	SNP	ENST00000361507.4	37	CCDS8259.1																																																																																			G|0.983;A|0.017	0.017	strong		0.567	GAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391085.1	NM_080491	
MYO10	4651	hgsc.bcm.edu	37	5	16877739	16877739	+	Silent	SNP	G	G	A	rs185323430		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16877739G>A	ENST00000513610.1	-	2	553	c.99C>T	c.(97-99)gtC>gtT	p.V33V	MYO10_ENST00000507288.1_Silent_p.V33V	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	33					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CTGTCCGGAAGACGACGATGC	0.498													G|||	1	0.000199681	0.0	0.0	5008	,	,		18799	0.0		0.001	False		,,,				2504	0.0				p.V33V		Atlas-SNP	.											.	MYO10	198	.	0			c.C99T						PASS	.	G		0,4024		0,0,2012	104.0	105.0	105.0		99	2.5	1.0	5		105	6,8338		0,6,4166	no	coding-synonymous	MYO10	NM_012334.2		0,6,6178	AA,AG,GG		0.0719,0.0,0.0485		33/2059	16877739	6,12362	2012	4172	6184	SO:0001819	synonymous_variant	4651	exon2			CCGGAAGACGACG	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.99C>T	5.37:g.16877739G>A		63.0	0.0	0		60.0	34.0	0.566667	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Silent	SNP	ENST00000513610.1	37	CCDS54834.1																																																																																			G|0.999;A|0.001	0.001	strong		0.498	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
ALG1	56052	hgsc.bcm.edu	37	16	5127460	5127460	+	Missense_Mutation	SNP	T	T	G	rs112668461	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5127460T>G	ENST00000262374.5	+	5	585	c.554T>G	c.(553-555)tTt>tGt	p.F185C	ALG1_ENST00000588623.1_Missense_Mutation_p.F74C|ALG1_ENST00000544428.1_Missense_Mutation_p.F74C	NM_019109.4	NP_061982.3	Q9BT22	ALG1_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase	185					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|lipopolysaccharide biosynthetic process (GO:0009103)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	chitobiosyldiphosphodolichol beta-mannosyltransferase activity (GO:0004578)|mannosyltransferase activity (GO:0000030)			breast(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	13		Ovarian(90;0.0164)				GAGAAGTTCTTTGGGCGCCTG	0.557													T|||	73	0.0145767	0.0545	0.0014	5008	,	,		15459	0.0		0.0	False		,,,				2504	0.0				p.F185C		Atlas-SNP	.											.	ALG1	35	.	0			c.T554G						PASS	.	T	CYS/PHE	179,4215	115.9+/-153.8	4,171,2022	102.0	92.0	96.0		554	-0.3	0.1	16	dbSNP_132	96	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ALG1	NM_019109.4	205	4,172,6321	GG,GT,TT		0.0116,4.0737,1.3853	benign	185/465	5127460	180,12814	2197	4300	6497	SO:0001583	missense	56052	exon5			AGTTCTTTGGGCG	AB019038	CCDS10528.1	16p13.3	2013-02-22	2013-02-22		ENSG00000033011	ENSG00000033011	2.4.1.142	"""Glycosyltransferase group 1 domain containing"""	18294	protein-coding gene	gene with protein product		605907	"""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase)"", ""asparagine-linked glycosylation 1, beta-1,4-mannosyltransferase homolog (S. cerevisiae)"""			10704531	Standard	NM_019109		Approved	HMT-1, HMAT1	uc002cym.3	Q9BT22	OTTHUMG00000129529	ENST00000262374.5:c.554T>G	16.37:g.5127460T>G	ENSP00000262374:p.Phe185Cys	62.0	0.0	0		61.0	27.0	0.442623	NM_019109	B4DP08|Q6UVZ9|Q8N5Y4|Q9P2Y2	Missense_Mutation	SNP	ENST00000262374.5	37	CCDS10528.1	23	0.010531135531135532	22	0.044715447154471545	1	0.0027624309392265192	0	0.0	0	0.0	T	10.06	1.246611	0.22796	0.040737	1.16E-4	ENSG00000033011	ENST00000262374;ENST00000544428	D;D	0.86297	-2.1;-2.1	5.79	-0.341	0.12639	.	0.364426	0.34223	N	0.004141	T	0.55529	0.1926	L	0.45422	1.42	0.54753	D	0.999989	B;B	0.22746	0.011;0.074	B;B	0.22152	0.009;0.038	T	0.64166	-0.6471	10	0.49607	T	0.09	-2.3162	14.4032	0.67063	0.0:0.0:0.338:0.662	.	74;185	B4DP08;Q9BT22	.;ALG1_HUMAN	C	185;74	ENSP00000262374:F185C;ENSP00000440019:F74C	ENSP00000262374:F185C	F	+	2	0	ALG1	5067461	0.953000	0.32496	0.133000	0.22050	0.575000	0.36095	1.537000	0.36083	-0.348000	0.08286	0.459000	0.35465	TTT	T|0.982;G|0.018	0.018	strong		0.557	ALG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251716.2	NM_019109	
ITGAX	3687	hgsc.bcm.edu	37	16	31382470	31382470	+	Silent	SNP	A	A	G	rs138137251	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:31382470A>G	ENST00000268296.4	+	15	1897	c.1776A>G	c.(1774-1776)caA>caG	p.Q592Q	ITGAX_ENST00000562522.1_Silent_p.Q592Q	NM_000887.3	NP_000878.2	P20702	ITAX_HUMAN	integrin, alpha X (complement component 3 receptor 4 subunit)	592					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|organ morphogenesis (GO:0009887)	cell surface (GO:0009986)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|receptor activity (GO:0004872)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(42)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	77						GCGGGGGTCAAGACCTCACCC	0.642													A|||	32	0.00638978	0.0015	0.0173	5008	,	,		17052	0.0		0.0169	False		,,,				2504	0.001				p.Q592Q		Atlas-SNP	.											.	ITGAX	198	.	0			c.A1776G						PASS	.	A		4,4390	8.1+/-20.4	0,4,2193	56.0	63.0	61.0		1776	3.3	1.0	16	dbSNP_134	61	112,8488	57.9+/-119.4	0,112,4188	no	coding-synonymous	ITGAX	NM_000887.3		0,116,6381	GG,GA,AA		1.3023,0.091,0.8927		592/1164	31382470	116,12878	2197	4300	6497	SO:0001819	synonymous_variant	3687	exon15			GGGTCAAGACCTC	BC038237	CCDS10711.1, CCDS67014.1	16p11.2	2010-03-23	2006-02-10		ENSG00000140678	ENSG00000140678		"""CD molecules"", ""Complement system"", ""Integrins"""	6152	protein-coding gene	gene with protein product		151510	"""integrin, alpha X (antigen CD11C (p150), alpha polypeptide)"""	CD11C		3284962, 2303426	Standard	NM_001286375		Approved	CD11c	uc002ebu.1	P20702	OTTHUMG00000132465	ENST00000268296.4:c.1776A>G	16.37:g.31382470A>G		55.0	0.0	0		48.0	25.0	0.520833	NM_000887	Q8IVA6	Silent	SNP	ENST00000268296.4	37	CCDS10711.1																																																																																			A|0.991;G|0.009	0.009	strong		0.642	ITGAX-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255628.2	NM_000887	
NUP188	23511	hgsc.bcm.edu	37	9	131768786	131768786	+	Silent	SNP	G	G	A	rs150379581	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:131768786G>A	ENST00000372577.2	+	44	5100	c.5079G>A	c.(5077-5079)acG>acA	p.T1693T	RP11-167N5.5_ENST00000594418.1_lincRNA	NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	1693					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						TGTAGAGCACGCTGCTGTCCA	0.642											OREG0019528	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	24	0.00479233	0.0008	0.0072	5008	,	,		15926	0.0		0.0169	False		,,,				2504	0.001				p.T1693T		Atlas-SNP	.											.	NUP188	140	.	0			c.G5079A						PASS	.	G		13,4393	21.2+/-45.6	0,13,2190	59.0	66.0	64.0		5079	-10.4	0.6	9	dbSNP_134	64	136,8464	67.7+/-130.1	0,136,4164	no	coding-synonymous	NUP188	NM_015354.1		0,149,6354	AA,AG,GG		1.5814,0.2951,1.1456		1693/1750	131768786	149,12857	2203	4300	6503	SO:0001819	synonymous_variant	23511	exon44			GAGCACGCTGCTG	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.5079G>A	9.37:g.131768786G>A		108.0	0.0	0	1590	109.0	53.0	0.486239	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	37	CCDS35156.1																																																																																			G|0.990;A|0.010	0.010	strong		0.642	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
COL3A1	1281	hgsc.bcm.edu	37	2	189859312	189859312	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:189859312G>A	ENST00000304636.3	+	19	1509	c.1339G>A	c.(1339-1341)Ggt>Agt	p.G447S	COL3A1_ENST00000317840.5_Missense_Mutation_p.G447S	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	447	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	CGGACCACGTGGTGAACGCGT	0.393																																					p.G447S		Atlas-SNP	.											COL3A1,NS,malignant_melanoma,-1,1	COL3A1	292	1	0			c.G1339A						PASS	.						102.0	101.0	101.0					2																	189859312		2203	4300	6503	SO:0001583	missense	1281	exon19			CCACGTGGTGAAC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.1339G>A	2.37:g.189859312G>A	ENSP00000304408:p.Gly447Ser	110.0	0.0	0		122.0	36.0	0.295082	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	28.3	4.907297	0.92107	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99607	-6.27;-6.27	6.17	6.17	0.99709	.	0.000000	0.52532	D	0.000067	D	0.99806	0.9916	H	0.96048	3.76	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97394	0.9991	10	0.87932	D	0	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	447	P02461	CO3A1_HUMAN	S	447	ENSP00000304408:G447S;ENSP00000315243:G447S	ENSP00000304408:G447S	G	+	1	0	COL3A1	189567557	1.000000	0.71417	0.983000	0.44433	0.945000	0.59286	9.550000	0.98110	2.941000	0.99782	0.655000	0.94253	GGT	.	.	none		0.393	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
APC	324	hgsc.bcm.edu	37	5	112162854	112162854	+	Silent	SNP	T	T	C	rs2229992	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112162854T>C	ENST00000457016.1	+	12	1838	c.1458T>C	c.(1456-1458)taT>taC	p.Y486Y	APC_ENST00000257430.4_Silent_p.Y486Y|APC_ENST00000508376.2_Silent_p.Y486Y|CTC-554D6.1_ENST00000520401.1_5'Flank			P25054	APC_HUMAN	adenomatous polyposis coli	486	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		GTGAAATGTATGGGCTTACTA	0.368		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			T|||	2554	0.509984	0.1619	0.6671	5008	,	,		17461	0.6647		0.5795	False		,,,				2504	0.638				p.Y486Y	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	APC,colon,carcinoma,0,1	APC	4158	1	1	Unknown(1)	skin(1)	c.T1458C	GRCh37	CM990152	APC	M	rs2229992	PASS	.	T	,,	934,3470	356.6+/-313.6	103,728,1371	131.0	117.0	122.0	http://omim.org/entry/114500	1458,1458,1404	0.7	1.0	5	dbSNP_98	122	5076,3524	632.0+/-398.6	1516,2044,740	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	1619,2772,2111	CC,CT,TT		40.9767,21.208,46.2165	,,	486/2844,486/2844,468/2826	112162854	6010,6994	2202	4300	6502	SO:0001819	synonymous_variant	324	exon13	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AATGTATGGGCTT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1458T>C	5.37:g.112162854T>C		98.0	0.0	0		119.0	119.0	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			A|0.002;C|0.475	0.475	strong		0.368	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
MUC16	94025	hgsc.bcm.edu	37	19	9015351	9015351	+	Missense_Mutation	SNP	G	G	A	rs201449501	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:9015351G>A	ENST00000397910.4	-	30	38440	c.38237C>T	c.(38236-38238)cCt>cTt	p.P12746L		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	12748	SEA 5. {ECO:0000255|PROSITE- ProRule:PRU00188}.			Missing (in Ref. 3; AAK74120). {ECO:0000305}.	cell adhesion (GO:0007155)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|vesicle (GO:0031982)				NS(9)|autonomic_ganglia(1)|breast(26)|central_nervous_system(11)|cervix(1)|endometrium(46)|haematopoietic_and_lymphoid_tissue(5)|kidney(35)|large_intestine(91)|liver(1)|lung(278)|ovary(17)|pancreas(2)|prostate(17)|skin(18)|soft_tissue(1)|stomach(8)|upper_aerodigestive_tract(16)|urinary_tract(7)	590						AGAGTACAGAGGGCCAACACT	0.512													-|||	7	0.00139776	0.0008	0.0	5008	,	,		20370	0.003		0.001	False		,,,				2504	0.002				p.P12746L		Atlas-SNP	.											.	MUC16	4315	.	0			c.C38237T						PASS	.	G	LEU/PRO	0,4000		0,0,2000	153.0	130.0	137.0		38237	-1.6	0.0	19	dbSNP_134	137	4,8338		0,4,4167	no	missense	MUC16	NM_024690.2	98	0,4,6167	AA,AG,GG		0.048,0.0,0.0324	possibly-damaging	12746/14508	9015351	4,12338	2000	4171	6171	SO:0001583	missense	94025	exon30			TACAGAGGGCCAA	AF414442	CCDS54212.1	19p13.2	2008-02-05	2006-03-14			ENSG00000181143		"""Mucins"""	15582	protein-coding gene	gene with protein product		606154				11369781	Standard	XM_006722941		Approved	CA125, FLJ14303	uc002mkp.3	Q8WXI7		ENST00000397910.4:c.38237C>T	19.37:g.9015351G>A	ENSP00000381008:p.Pro12746Leu	119.0	0.0	0		112.0	18.0	0.160714	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	.	.	.	.	.	.	.	.	.	.	.	10.49	1.365631	0.24684	0.0	4.8E-4	ENSG00000181143	ENST00000397910	T	0.38077	1.16	2.82	-1.58	0.08479	.	.	.	.	.	T	0.39759	0.1090	.	.	.	.	.	.	P	0.50710	0.938	P	0.50270	0.636	T	0.52419	-0.8578	7	0.87932	D	0	.	8.0693	0.30680	0.0:0.0:0.3447:0.6553	.	12746	B5ME49	.	L	12746	ENSP00000381008:P12746L	ENSP00000381008:P12746L	P	-	2	0	MUC16	8876351	0.000000	0.05858	0.000000	0.03702	0.046000	0.14306	0.413000	0.21148	-0.376000	0.07943	0.305000	0.20034	CCT	G|0.998;A|0.002	0.002	weak		0.512	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
SPA17	53340	hgsc.bcm.edu	37	11	124564252	124564252	+	Silent	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:124564252A>G	ENST00000532692.1	+	4	1787	c.366A>G	c.(364-366)caA>caG	p.Q122Q	SPA17_ENST00000524614.1_3'UTR|SIAE_ENST00000525730.1_5'UTR|SPA17_ENST00000227135.2_Silent_p.Q122Q			Q15506	SP17_HUMAN	sperm autoantigenic protein 17	122	IQ. {ECO:0000255|PROSITE- ProRule:PRU00116}.				binding of sperm to zona pellucida (GO:0007339)|epithelial cilium movement (GO:0003351)|single fertilization (GO:0007338)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|membrane (GO:0016020)|motile cilium (GO:0031514)|primary cilium (GO:0072372)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(2)	5	all_hematologic(175;0.215)	Breast(109;0.00109)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0223)		TCAAAATCCAAGCTGCCTTCC	0.413																																					p.Q122Q		Atlas-SNP	.											SPA17,NS,malignant_melanoma,+2,1	SPA17	16	1	0			c.A366G						PASS	.						94.0	96.0	96.0					11																	124564252		2201	4299	6500	SO:0001819	synonymous_variant	53340	exon5			AATCCAAGCTGCC	AF334735	CCDS8450.1	11q24.2	2009-03-12			ENSG00000064199	ENSG00000064199			11210	protein-coding gene	gene with protein product	"""cancer/testis antigen 22"""	608621				8688458	Standard	NM_017425		Approved	SP17, CT22	uc001qap.3	Q15506	OTTHUMG00000165927	ENST00000532692.1:c.366A>G	11.37:g.124564252A>G		112.0	0.0	0		99.0	46.0	0.464646	NM_017425	B2R4F2|Q9BXF7	Silent	SNP	ENST00000532692.1	37	CCDS8450.1																																																																																			.	.	none		0.413	SPA17-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387075.1	NM_017425	
SEMA6B	10501	hgsc.bcm.edu	37	19	4550183	4550183	+	Missense_Mutation	SNP	G	G	A	rs142864702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:4550183G>A	ENST00000586582.1	-	12	1533	c.1223C>T	c.(1222-1224)gCg>gTg	p.A408V	SEMA6B_ENST00000301293.3_Missense_Mutation_p.A408V|SEMA6B_ENST00000586965.1_Missense_Mutation_p.A408V	NM_032108.3	NP_115484.2	Q9H3T3	SEM6B_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6B	408	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)		CGAGGGCACCGCCTCGTCCAT	0.657													G|||	12	0.00239617	0.0	0.0101	5008	,	,		18713	0.002		0.003	False		,,,				2504	0.0				p.A408V		Atlas-SNP	.											SEMA6B,NS,carcinoma,+1,1	SEMA6B	51	1	0			c.C1223T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	70.0	56.0	61.0		1223	2.2	1.0	19	dbSNP_134	61	20,8580		0,20,4280	yes	missense	SEMA6B	NM_032108.3	64	0,20,6483	AA,AG,GG		0.2326,0.0,0.1538	possibly-damaging	408/889	4550183	20,12986	2203	4300	6503	SO:0001583	missense	10501	exon12			GGCACCGCCTCGT	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.1223C>T	19.37:g.4550183G>A	ENSP00000467290:p.Ala408Val	117.0	0.0	0		131.0	66.0	0.503817	NM_032108	A5PKU4|F6IB19|Q9NRK9	Missense_Mutation	SNP	ENST00000586582.1	37	CCDS12131.1	6	0.0027472527472527475	0	0.0	4	0.011049723756906077	1	0.0017482517482517483	1	0.0013192612137203166	.	21.8	4.204157	0.79127	0.0	0.002326	ENSG00000167680	ENST00000301293;ENST00000301292	T	0.10573	2.86	2.17	2.17	0.27698	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.196139	0.42964	U	0.000634	T	0.17492	0.0420	L	0.58925	1.835	0.42906	D	0.994242	D;D	0.89917	0.997;1.0	P;D	0.64321	0.484;0.924	T	0.03384	-1.1042	10	0.87932	D	0	.	12.0039	0.53248	0.0:0.0:1.0:0.0	.	408;408	B4DT36;Q9H3T3	.;SEM6B_HUMAN	V	408	ENSP00000301293:A408V	ENSP00000301292:A408V	A	-	2	0	SEMA6B	4501183	0.999000	0.42202	0.996000	0.52242	0.933000	0.57130	9.245000	0.95431	1.580000	0.49851	0.478000	0.44815	GCG	G|0.999;A|0.001	0.001	strong		0.657	SEMA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458656.2	NM_032108	
SPATA25	128497	hgsc.bcm.edu	37	20	44515322	44515322	+	Missense_Mutation	SNP	C	C	T	rs76638086	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44515322C>T	ENST00000372519.3	-	2	562	c.518G>A	c.(517-519)cGg>cAg	p.R173Q		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	173					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GTCCTCTTCCCGAACTCCTGG	0.652													C|||	12	0.00239617	0.0008	0.0072	5008	,	,		18142	0.0		0.005	False		,,,				2504	0.001				p.R173Q		Atlas-SNP	.											.	.	.	.	0			c.G518A						PASS	.	C	GLN/ARG	7,4399	11.4+/-27.6	0,7,2196	62.0	64.0	64.0		518	3.6	1.0	20	dbSNP_132	64	36,8564	25.1+/-72.6	0,36,4264	yes	missense	C20orf165	NM_080608.3	43	0,43,6460	TT,TC,CC		0.4186,0.1589,0.3306	probably-damaging	173/228	44515322	43,12963	2203	4300	6503	SO:0001583	missense	128497	exon2			TCTTCCCGAACTC	AL008726	CCDS13383.1	20q13.12	2011-11-24	2011-11-24	2011-11-24	ENSG00000149634	ENSG00000149634			16158	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 165"""	C20orf165		19240080	Standard	NM_080608		Approved	dJ337O18.8, TSG23	uc002xqf.3	Q9BR10	OTTHUMG00000032628	ENST00000372519.3:c.518G>A	20.37:g.44515322C>T	ENSP00000361597:p.Arg173Gln	110.0	0.0	0		93.0	42.0	0.451613	NM_080608		Missense_Mutation	SNP	ENST00000372519.3	37	CCDS13383.1	8	0.003663003663003663	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	4	0.005277044854881266	C	20.8	4.042836	0.75732	0.001589	0.004186	ENSG00000149634	ENST00000372519	T	0.56941	0.43	5.55	3.63	0.41609	.	0.134112	0.33515	N	0.004823	T	0.28797	0.0714	L	0.34521	1.04	0.31251	N	0.693996	B	0.30021	0.265	B	0.23852	0.049	T	0.42050	-0.9474	10	0.87932	D	0	-13.3192	6.8348	0.23931	0.0:0.6984:0.1454:0.1562	.	173	Q9BR10	CT165_HUMAN	Q	173	ENSP00000361597:R173Q	ENSP00000361597:R173Q	R	-	2	0	C20orf165	43948729	0.718000	0.27976	1.000000	0.80357	0.974000	0.67602	0.589000	0.23939	0.908000	0.36671	0.655000	0.94253	CGG	C|0.997;T|0.003	0.003	strong		0.652	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1		
HLA-DQB2	3120	hgsc.bcm.edu	37	6	32726756	32726756	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:32726756A>G	ENST00000437316.2	-	3	580	c.517T>C	c.(517-519)Tcc>Ccc	p.S173P	HLA-DQB2_ENST00000411527.1_Missense_Mutation_p.S173P|HLA-DQB2_ENST00000435145.2_Missense_Mutation_p.S173P			P05538	DQB2_HUMAN	major histocompatibility complex, class II, DQ beta 2	177	Beta-2.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|B cell affinity maturation (GO:0002344)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of alpha-beta T cell activation (GO:0046635)|positive regulation of antigen processing and presentation (GO:0002579)|positive regulation of T-helper 1 type immune response (GO:0002827)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|early endosome (GO:0005769)|endocytic vesicle membrane (GO:0030666)|ER to Golgi transport vesicle membrane (GO:0012507)|external side of plasma membrane (GO:0009897)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|MHC class II protein complex (GO:0042613)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)|toxic substance binding (GO:0015643)			endometrium(1)|kidney(1)|lung(1)|prostate(2)	5						CTAATGAGGGAGGTGGACACA	0.547																																					p.S173P		Atlas-SNP	.											.	HLA-DQB2	22	.	0			c.T517C						PASS	.																																			SO:0001583	missense	3120	exon3			TGAGGGAGGTGGA	M83890	CCDS56419.1	6p21.3	2013-01-11			ENSG00000232629	ENSG00000232629		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4945	protein-coding gene	gene with protein product		615161		HLA-DXB		2564844	Standard	NM_001198858		Approved		uc003oby.4	P05538	OTTHUMG00000031125	ENST00000437316.2:c.517T>C	6.37:g.32726756A>G	ENSP00000396330:p.Ser173Pro	116.0	0.0	0		111.0	14.0	0.126126	NM_001198858	A6NIA5|Q29826|Q29870|Q29871|Q29872|Q29873|Q5SR06	Missense_Mutation	SNP	ENST00000437316.2	37		.	.	.	.	.	.	.	.	.	.	A	0.001	-3.015517	0.00042	.	.	ENSG00000232629	ENST00000437316;ENST00000435145;ENST00000411527	T;T;T	0.00599	6.3;6.3;6.3	3.43	0.281	0.15687	.	0.777035	0.10865	N	0.625646	T	0.00039	0.0001	N	0.00221	-1.82	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.09377	0.004;0.002	T	0.10917	-1.0609	10	0.28530	T	0.3	.	4.2619	0.10745	0.2399:0.2957:0.4644:0.0	.	173;173	A2ADX3;Q5SR06	.;.	P	173	ENSP00000396330:S173P;ENSP00000410512:S173P;ENSP00000390431:S173P	ENSP00000390431:S173P	S	-	1	0	HLA-DQB2	32834734	0.000000	0.05858	0.188000	0.23233	0.053000	0.15095	0.295000	0.19065	0.267000	0.21916	-1.585000	0.00851	TCC	.	.	none		0.547	HLA-DQB2-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000076216.2		
PRR5	55615	hgsc.bcm.edu	37	22	45075741	45075741	+	Missense_Mutation	SNP	C	C	T	rs74960825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:45075741C>T	ENST00000403581.1	+	2	671	c.62C>T	c.(61-63)cCg>cTg	p.P21L	PRR5_ENST00000006251.7_Intron	NM_001198721.1	NP_001185650.1	P85299	PRR5_HUMAN	proline rich 5 (renal)	0	Interaction with RICTOR.				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)		GAAAAGATGCCGGCGCAGCCT	0.602													C|||	10	0.00199681	0.0008	0.0043	5008	,	,		15072	0.0		0.006	False		,,,				2504	0.0				p.P21L		Atlas-SNP	.											.	PRR5	75	.	0			c.C62T						PASS	.	C	,,,LEU/PRO,	0,1750		0,0,875	10.0	11.0	10.0		,,,62,	-1.5	0.0	22	dbSNP_131	10	21,3953		0,21,1966	yes	intron,intron,intron,missense,intron	PRR5	NM_001017528.2,NM_001017529.2,NM_001017530.1,NM_001198721.1,NM_015366.3	,,,98,	0,21,2841	TT,TC,CC		0.5284,0.0,0.3669	,,,,	,,,21/412,	45075741	21,5703	875	1987	2862	SO:0001583	missense	55615	exon2			AGATGCCGGCGCA	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	ENST00000403581.1:c.62C>T	22.37:g.45075741C>T	ENSP00000384848:p.Pro21Leu	105.0	0.0	0		101.0	47.0	0.465347	NM_001198721	B1AHF6|B1AHG5|B3KP73|O75983|O95695|Q5BIW2|Q5EAJ8|Q5EAJ9|Q5XKJ6|Q96RW1|Q96RW2|Q9HA49|Q9HC46|Q9NSG0|Q9NVX8|Q9NXL1|Q9UH20	Missense_Mutation	SNP	ENST00000403581.1	37	CCDS56232.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	1.807	-0.475651	0.04414	0.0	0.005284	ENSG00000186654	ENST00000403581	T	0.32515	1.45	1.09	-1.49	0.08718	.	.	.	.	.	T	0.09555	0.0235	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.20174	-1.0283	9	0.87932	D	0	.	4.4212	0.11481	0.0:0.534:0.0:0.466	.	21	B1AHF6	.	L	21	ENSP00000384848:P21L	ENSP00000384848:P21L	P	+	2	0	PRR5	43454405	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.017000	0.12590	-0.536000	0.06298	-0.474000	0.04947	CCG	C|0.996;T|0.004	0.004	strong		0.602	PRR5-003	PUTATIVE	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318199.1	NM_001017528	
DNHD1	144132	hgsc.bcm.edu	37	11	6559961	6559961	+	Silent	SNP	G	G	A	rs118078642	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:6559961G>A	ENST00000527990.2	+	14	3246	c.3246G>A	c.(3244-3246)gaG>gaA	p.E1082E	DNHD1_ENST00000254579.6_Silent_p.E1082E			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	1082					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		TCCTGGGGGAGTTTCGCAGCT	0.602													G|||	13	0.00259585	0.0	0.0072	5008	,	,		17960	0.0		0.007	False		,,,				2504	0.001				p.E1082E		Atlas-SNP	.											.	DNHD1	198	.	0			c.G3246A						PASS	.	G		6,1376		0,6,685	13.0	13.0	13.0		3246	3.2	1.0	11	dbSNP_132	13	31,3151		0,31,1560	no	coding-synonymous	DNHD1	NM_144666.2		0,37,2245	AA,AG,GG		0.9742,0.4342,0.8107		1082/4754	6559961	37,4527	691	1591	2282	SO:0001819	synonymous_variant	144132	exon16			GGGGGAGTTTCGC	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.3246G>A	11.37:g.6559961G>A		71.0	0.0	0		67.0	44.0	0.656716	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Silent	SNP	ENST00000527990.2	37	CCDS44532.1																																																																																			G|0.997;A|0.003	0.003	strong		0.602	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
HIST1H2AL	8332	hgsc.bcm.edu	37	6	27833378	27833378	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:27833378C>T	ENST00000357320.2	+	1	345	c.246C>T	c.(244-246)cgC>cgT	p.R82R		NM_003511.2	NP_003502.1	P0C0S8	H2A1_HUMAN	histone cluster 1, H2al	82						extracellular vesicular exosome (GO:0070062)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)			breast(1)|endometrium(1)|large_intestine(2)|lung(3)|urinary_tract(2)	9						TTATCCCGCGCCACTTGCAGC	0.637																																					p.R82R		Atlas-SNP	.											.	HIST1H2AL	14	.	0			c.C246T						PASS	.						112.0	113.0	113.0					6																	27833378		2203	4300	6503	SO:0001819	synonymous_variant	8332	exon1			CCCGCGCCACTTG	X83549	CCDS4634.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198374	ENSG00000276903		"""Histones / Replication-dependent"""	4730	protein-coding gene	gene with protein product		602793	"""H2A histone family, member I"", ""histone 1, H2al"""	H2AFI		9439656, 9031620, 12408966	Standard	NM_003511		Approved	H2A/i, dJ193B12.9	uc003njw.3	P0C0S8	OTTHUMG00000014492	ENST00000357320.2:c.246C>T	6.37:g.27833378C>T		108.0	0.0	0		101.0	49.0	0.485149	NM_003511	P02261|Q2M1R2|Q76PA6	Silent	SNP	ENST00000357320.2	37	CCDS4634.1																																																																																			.	.	none		0.637	HIST1H2AL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040160.1	NM_003511	
SDHA	6389	hgsc.bcm.edu	37	5	256508	256508	+	Silent	SNP	C	C	T	rs3211499		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:256508C>T	ENST00000264932.6	+	15	2083	c.1968C>T	c.(1966-1968)acC>acT	p.T656T	SDHA_ENST00000510361.1_Silent_p.T608T|SDHA_ENST00000504309.1_Silent_p.T575T|SDHA_ENST00000507522.1_3'UTR	NM_004168.2	NP_004159.2	P31040	SDHA_HUMAN	succinate dehydrogenase complex, subunit A, flavoprotein (Fp)	656					cellular metabolic process (GO:0044237)|nervous system development (GO:0007399)|oxidation-reduction process (GO:0055114)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	flavin adenine dinucleotide binding (GO:0050660)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|liver(2)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	40			Epithelial(17;0.0159)|all cancers(22;0.0236)|OV - Ovarian serous cystadenocarcinoma(19;0.0674)|Lung(60;0.113)		Succinic acid(DB00139)	ACTGTGCCACCGTCCCGCCAG	0.438									Familial Paragangliomas																												p.T656T		Atlas-SNP	.											SDHA,NS,carcinoma,+2,1	SDHA	80	1	0			c.C1968T						scavenged	.						70.0	78.0	75.0					5																	256508		2203	4300	6503	SO:0001819	synonymous_variant	6389	exon15	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss	TGCCACCGTCCCG	BC001380	CCDS3853.1	5p15	2014-09-17			ENSG00000073578	ENSG00000073578		"""Mitochondrial respiratory chain complex / Complex II"""	10680	protein-coding gene	gene with protein product		600857		SDH2		7798181	Standard	XM_005248329		Approved	FP, SDHF	uc003jao.4	P31040	OTTHUMG00000090275	ENST00000264932.6:c.1968C>T	5.37:g.256508C>T		93.0	0.0	0		102.0	7.0	0.0686275	NM_004168	A8K5J6|B4DJ60|E9PBJ5|Q16395|Q59GW8|Q8IW48|Q9UMY5	Silent	SNP	ENST00000264932.6	37	CCDS3853.1																																																																																			.	.	weak		0.438	SDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206599.1	NM_004168	
TNFRSF11A	8792	hgsc.bcm.edu	37	18	60027236	60027236	+	Silent	SNP	C	C	T	rs12721430	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:60027236C>T	ENST00000586569.1	+	6	608	c.570C>T	c.(568-570)tcC>tcT	p.S190S	TNFRSF11A_ENST00000269485.7_Silent_p.S190S	NM_001270949.1|NM_003839.3	NP_001257878.1|NP_003830.1	Q9Y6Q6	TNR11_HUMAN	tumor necrosis factor receptor superfamily, member 11a, NFKB activator	190					adaptive immune response (GO:0002250)|cell-cell signaling (GO:0007267)|circadian temperature homeostasis (GO:0060086)|lymph node development (GO:0048535)|mammary gland alveolus development (GO:0060749)|monocyte chemotaxis (GO:0002548)|ossification (GO:0001503)|osteoclast differentiation (GO:0030316)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling (GO:0071848)|positive regulation of fever generation by positive regulation of prostaglandin secretion (GO:0071812)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|response to cytokine (GO:0034097)|response to interleukin-1 (GO:0070555)|response to lipopolysaccharide (GO:0032496)|response to radiation (GO:0009314)|response to tumor necrosis factor (GO:0034612)|signal transduction (GO:0007165)|TNFSF11-mediated signaling pathway (GO:0071847)|tumor necrosis factor-mediated signaling pathway (GO:0033209)	external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)	cytokine binding (GO:0019955)|metal ion binding (GO:0046872)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|tumor necrosis factor-activated receptor activity (GO:0005031)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(13)|skin(3)|upper_aerodigestive_tract(1)	29		Colorectal(73;0.188)				CAGAGAAATCCGATGCGGTTT	0.448													C|||	8	0.00159744	0.0	0.0029	5008	,	,		19769	0.0		0.004	False		,,,				2504	0.002				p.S190S		Atlas-SNP	.											.	TNFRSF11A	51	.	0			c.C570T						PASS	.	C		4,4402	8.1+/-20.4	0,4,2199	116.0	105.0	109.0		570	-2.3	1.0	18	dbSNP_121	109	40,8560	25.7+/-73.6	0,40,4260	no	coding-synonymous	TNFRSF11A	NM_003839.2		0,44,6459	TT,TC,CC		0.4651,0.0908,0.3383		190/617	60027236	44,12962	2203	4300	6503	SO:0001819	synonymous_variant	8792	exon6			GAAATCCGATGCG	AF018253	CCDS11980.1, CCDS59324.1, CCDS74227.1, CCDS74228.1	18q22.1	2014-09-17			ENSG00000141655	ENSG00000141655		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11908	protein-coding gene	gene with protein product		603499	"""tumor necrosis factor receptor superfamily, member 11a, activator of NFKB"", ""Paget disease of bone 2"", ""loss of heterozygosity, 18, chromosomal region 1"""	PDB2, LOH18CR1		9367155, 10615125	Standard	NM_001270951		Approved	RANK, CD265, FEO	uc002lin.4	Q9Y6Q6	OTTHUMG00000132779	ENST00000586569.1:c.570C>T	18.37:g.60027236C>T		145.0	0.0	0		160.0	114.0	0.7125	NM_001270951	I4EC36|I4EC38|I4EC39|I7JE63|N0GVH0|Q59EP9	Silent	SNP	ENST00000586569.1	37	CCDS11980.1																																																																																			C|0.997;T|0.003	0.003	strong		0.448	TNFRSF11A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256186.2		
MRGPRX1	259249	hgsc.bcm.edu	37	11	18955515	18955515	+	Missense_Mutation	SNP	A	A	G	rs138263314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:18955515A>G	ENST00000302797.3	-	1	1041	c.817T>C	c.(817-819)Ttc>Ctc	p.F273L	MRGPRX1_ENST00000526914.1_5'Flank|RP11-583F24.8_ENST00000528646.1_RNA	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	273					acute-phase response (GO:0006953)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(8)|lung(12)|pancreas(2)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	36						CCCACGAAGAAGTAAATGATG	0.493													A|||	102	0.0203674	0.0015	0.0605	5008	,	,		27612	0.0		0.0318	False		,,,				2504	0.0266				p.F273L		Atlas-SNP	.											MRGPRX1,NS,carcinoma,+1,1	MRGPRX1	84	1	0			c.T817C						scavenged	.	A	LEU/PHE	23,4365		0,23,2171	78.0	76.0	77.0		817	1.1	0.4	11	dbSNP_134	77	203,8367		0,203,4082	no	missense	MRGPRX1	NM_147199.3	22	0,226,6253	GG,GA,AA		2.3687,0.5242,1.7441	possibly-damaging	273/323	18955515	226,12732	2194	4285	6479	SO:0001583	missense	259249	exon1			CGAAGAAGTAAAT		CCDS7846.1	11p15.1	2013-10-10			ENSG00000170255	ENSG00000170255		"""GPCR / Class A : Orphans"""	17962	protein-coding gene	gene with protein product		607227				11551509	Standard	NM_147199		Approved	MRGX1	uc001mpg.3	Q96LB2	OTTHUMG00000162655	ENST00000302797.3:c.817T>C	11.37:g.18955515A>G	ENSP00000305766:p.Phe273Leu	61.0	1.0	0.0163934		85.0	29.0	0.341176	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	49	0.022435897435897436	2	0.0040650406504065045	23	0.06353591160220995	0	0.0	24	0.0316622691292876	.	17.20	3.328525	0.60743	0.005242	0.023687	ENSG00000170255	ENST00000302797	T	0.35421	1.31	2.28	1.06	0.20224	.	0.210366	0.32753	N	0.005690	T	0.08179	0.0204	M	0.83692	2.655	0.25544	N	0.987152	D	0.59357	0.985	P	0.53518	0.728	T	0.04178	-1.0971	10	0.32370	T	0.25	.	6.7944	0.23717	0.7627:0.2373:0.0:0.0	.	273	Q96LB2	MRGX1_HUMAN	L	273	ENSP00000305766:F273L	ENSP00000305766:F273L	F	-	1	0	MRGPRX1	18912091	0.218000	0.23608	0.370000	0.25965	0.402000	0.30811	0.633000	0.24598	0.270000	0.21984	0.402000	0.26972	TTC	A|0.980;G|0.020	0.020	strong		0.493	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
CCND1	595	hgsc.bcm.edu	37	11	69462802	69462802	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:69462802G>A	ENST00000227507.2	+	4	842	c.615G>A	c.(613-615)gcG>gcA	p.A205A	CCND1_ENST00000536559.1_3'UTR	NM_053056.2	NP_444284.1	P24385	CCND1_HUMAN	cyclin D1	205					canonical Wnt signaling pathway (GO:0060070)|cell division (GO:0051301)|cellular response to DNA damage stimulus (GO:0006974)|endoplasmic reticulum unfolded protein response (GO:0030968)|fat cell differentiation (GO:0045444)|G1/S transition of mitotic cell cycle (GO:0000082)|lactation (GO:0007595)|Leydig cell differentiation (GO:0033327)|liver development (GO:0001889)|mammary gland alveolus development (GO:0060749)|mammary gland epithelial cell proliferation (GO:0033598)|mitotic cell cycle (GO:0000278)|mitotic G1 DNA damage checkpoint (GO:0031571)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of epithelial cell differentiation (GO:0030857)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of Wnt signaling pathway (GO:0030178)|Notch signaling pathway (GO:0007219)|organ regeneration (GO:0031100)|positive regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045737)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mammary gland epithelial cell proliferation (GO:0033601)|positive regulation of protein phosphorylation (GO:0001934)|re-entry into mitotic cell cycle (GO:0000320)|response to calcium ion (GO:0051592)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to ethanol (GO:0045471)|response to iron ion (GO:0010039)|response to magnesium ion (GO:0032026)|response to organonitrogen compound (GO:0010243)|response to UV-A (GO:0070141)|response to vitamin E (GO:0033197)|response to X-ray (GO:0010165)|transcription, DNA-templated (GO:0006351)	cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|tight junction (GO:0005923)|transcriptional repressor complex (GO:0017053)	cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)|enzyme binding (GO:0019899)|histone deacetylase binding (GO:0042826)|proline-rich region binding (GO:0070064)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|transcription corepressor activity (GO:0003714)|transcription factor binding (GO:0008134)			NS(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|lung(7)|ovary(1)|urinary_tract(1)	23	all_cancers(3;2.01e-114)|all_epithelial(3;3.59e-122)|Breast(3;5.4e-34)|all_lung(4;1.99e-21)|Lung NSC(4;4.65e-21)|Hepatocellular(3;8.22e-16)|Melanoma(5;1.89e-05)|Ovarian(3;0.0348)		Epithelial(3;7.2e-57)|all cancers(3;7.75e-51)|BRCA - Breast invasive adenocarcinoma(2;4.9e-48)|Lung(3;1.13e-16)|LUSC - Lung squamous cell carcinoma(11;3.74e-15)|STAD - Stomach adenocarcinoma(18;0.0278)|LUAD - Lung adenocarcinoma(13;0.0537)		Arsenic trioxide(DB01169)	TGGTGGCAGCGGGGAGCGTGG	0.607			T	"""IGH@, FSTL3"""	"""CLL, B-ALL, breast"""					Multiple Myeloma(6;0.086)																											p.A205A	Pancreas(65;393 884 2788 21700 24360 27795 36895)	Atlas-SNP	.		Dom	yes		11	11q13	595	cyclin D1		"""L, E"""	CCND1,NS,carcinoma,0,1	CCND1	107	1	0			c.G615A						PASS	.						112.0	111.0	112.0					11																	69462802		2200	4294	6494	SO:0001819	synonymous_variant	595	exon4			GGCAGCGGGGAGC	Z23022	CCDS8191.1	11q13	2008-07-18	2005-09-12		ENSG00000110092	ENSG00000110092			1582	protein-coding gene	gene with protein product	"""parathyroid adenomatosis 1"", ""B-cell CLL/lymphoma 1"", ""G1/S-specific cyclin D1"""	168461	"""cyclin D1 (PRAD1: parathyroid adenomatosis 1)"""	BCL1, D11S287E, PRAD1		1826542, 1833066	Standard	XM_006718653		Approved	U21B31	uc001opa.3	P24385	OTTHUMG00000167877	ENST00000227507.2:c.615G>A	11.37:g.69462802G>A		73.0	0.0	0		72.0	35.0	0.486111	NM_053056	Q6LEF0	Silent	SNP	ENST00000227507.2	37	CCDS8191.1																																																																																			.	.	none		0.607	CCND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396775.2	NM_053056	
SLC12A9	56996	hgsc.bcm.edu	37	7	100454796	100454796	+	Missense_Mutation	SNP	G	G	A	rs143666254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100454796G>A	ENST00000354161.3	+	5	880	c.755G>A	c.(754-756)gGc>gAc	p.G252D	SLC12A9_ENST00000540482.1_Missense_Mutation_p.G252D|SLC12A9_ENST00000275729.3_Missense_Mutation_p.G163D|SLC12A9_ENST00000428758.1_Missense_Mutation_p.G252D|SLC12A9_ENST00000415287.1_Missense_Mutation_p.G163D	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	252					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					GACAACTTGGGCGGTGAGCTG	0.652													G|||	7	0.00139776	0.0008	0.0029	5008	,	,		15798	0.0		0.004	False		,,,				2504	0.0				p.G252D		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G755A						PASS	.	G	ASP/GLY	6,4398		0,6,2196	43.0	48.0	46.0		755	0.7	0.2	7	dbSNP_134	46	59,8537		0,59,4239	yes	missense	SLC12A9	NM_020246.2	94	0,65,6435	AA,AG,GG		0.6864,0.1362,0.5	probably-damaging	252/915	100454796	65,12935	2202	4298	6500	SO:0001583	missense	56996	exon5			ACTTGGGCGGTGA	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.755G>A	7.37:g.100454796G>A	ENSP00000275730:p.Gly252Asp	36.0	0.0	0		44.0	21.0	0.477273	NM_001267812	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Missense_Mutation	SNP	ENST00000354161.3	37	CCDS5707.1	7	0.003205128205128205	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	G	2.002	-0.429266	0.04701	0.001362	0.006864	ENSG00000146828	ENST00000540482;ENST00000428758;ENST00000275729;ENST00000415287;ENST00000354161	D;D;D;D;D	0.98862	-5.19;-5.19;-5.19;-5.19;-5.19	4.65	0.708	0.18144	Amino acid permease domain (1);	0.458827	0.21438	N	0.074528	D	0.94470	0.8220	L	0.41710	1.295	0.19775	N	0.99995	B;B	0.24132	0.098;0.002	B;B	0.32149	0.141;0.024	D	0.89635	0.3858	10	0.36615	T	0.2	.	5.9914	0.19465	0.2529:0.3003:0.4469:0.0	.	163;252	Q9BXP2-2;Q9BXP2	.;S12A9_HUMAN	D	252;252;163;163;252	ENSP00000443702:G252D;ENSP00000408301:G252D;ENSP00000275729:G163D;ENSP00000413796:G163D;ENSP00000275730:G252D	ENSP00000275729:G163D	G	+	2	0	SLC12A9	100292732	0.059000	0.20769	0.160000	0.22671	0.005000	0.04900	0.363000	0.20301	-0.175000	0.10725	-1.943000	0.00494	GGC	G|0.996;A|0.004	0.004	strong		0.652	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
DNAJB6	10049	hgsc.bcm.edu	37	7	157202683	157202683	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:157202683G>A	ENST00000262177.4	+	9	1091	c.886G>A	c.(886-888)Gcg>Acg	p.A296T	DNAJB6_ENST00000443280.1_Missense_Mutation_p.A181T|DNAJB6_ENST00000452797.2_Missense_Mutation_p.A247T	NM_058246.3	NP_490647.1	O75190	DNJB6_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 6	296					intermediate filament organization (GO:0045109)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|protein folding (GO:0006457)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)|heat shock protein binding (GO:0031072)|unfolded protein binding (GO:0051082)			central_nervous_system(1)|lung(1)|ovary(2)|stomach(1)	5	all_neural(206;0.181)	all_epithelial(9;0.000606)|all_hematologic(28;0.00287)|Acute lymphoblastic leukemia(9;0.0647)|Ovarian(593;0.196)	OV - Ovarian serous cystadenocarcinoma(82;0.00399)	UCEC - Uterine corpus endometrioid carcinoma (81;0.172)		GGACCCCCTCGCGTCCGCAGC	0.701																																					p.A296T	Esophageal Squamous(46;195 967 1350 20350 43814)	Atlas-SNP	.											.	DNAJB6	39	.	0			c.G886A						PASS	.						6.0	5.0	5.0					7																	157202683		2018	3994	6012	SO:0001583	missense	10049	exon9			CCCCTCGCGTCCG	AB014888	CCDS5946.1, CCDS47755.1	7q36.3	2014-02-03			ENSG00000105993	ENSG00000105993		"""Heat shock proteins / DNAJ (HSP40)"""	14888	protein-coding gene	gene with protein product		611332	"""limb girdle muscular dystrophy 1D (autosomal dominant)"""	LGMD1D		10319584, 9915854, 22366786	Standard	NM_005494		Approved	MRJ	uc003wnk.3	O75190	OTTHUMG00000157242	ENST00000262177.4:c.886G>A	7.37:g.157202683G>A	ENSP00000262177:p.Ala296Thr	17.0	0.0	0		28.0	13.0	0.464286	NM_058246	A4D232|A8K7D8|A8KAG0|B4DN73|E9PCZ2|O95806|Q53EN8|Q59EF2|Q6FIC8|Q75MA2|Q9UIK6	Missense_Mutation	SNP	ENST00000262177.4	37	CCDS5946.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.226791	0.58668	.	.	ENSG00000105993	ENST00000262177;ENST00000452797;ENST00000443280	T;T;T	0.63255	0.39;-0.03;-0.02	4.5	-5.97	0.02227	.	3.940110	0.01650	N	0.024503	T	0.36054	0.0953	N	0.08118	0	0.09310	N	1	B;B;B;B	0.33494	0.0;0.414;0.001;0.001	B;B;B;B	0.24006	0.0;0.05;0.001;0.001	T	0.32107	-0.9919	10	0.45353	T	0.12	.	8.0691	0.30678	0.668:0.2188:0.1132:0.0	.	181;247;296;296	E9PH18;B4DN73;A8KAG0;O75190	.;.;.;DNJB6_HUMAN	T	296;247;181	ENSP00000262177:A296T;ENSP00000402270:A247T;ENSP00000396267:A181T	ENSP00000262177:A296T	A	+	1	0	DNAJB6	156895444	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-1.031000	0.03578	-1.112000	0.02984	-0.140000	0.14226	GCG	.	.	none		0.701	DNAJB6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000348119.2		
SEC14L5	9717	hgsc.bcm.edu	37	16	5061113	5061113	+	Silent	SNP	G	G	A	rs116849014	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:5061113G>A	ENST00000251170.7	+	15	1998	c.1818G>A	c.(1816-1818)cgG>cgA	p.R606R	RP11-165E7.1_ENST00000588778.1_RNA	NM_014692.1	NP_055507.1	O43304	S14L5_HUMAN	SEC14-like 5 (S. cerevisiae)	606	GOLD. {ECO:0000255|PROSITE- ProRule:PRU00096}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	transporter activity (GO:0005215)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(9)|ovary(1)|skin(1)	29						ATGTGACCCGGTGGCCCGGCG	0.657													G|||	28	0.00559105	0.0	0.0029	5008	,	,		15446	0.0		0.0229	False		,,,				2504	0.0031				p.R606R		Atlas-SNP	.											.	SEC14L5	79	.	0			c.G1818A						PASS	.	G		6,3994		0,6,1994	20.0	24.0	23.0		1818	-0.5	1.0	16	dbSNP_132	23	175,8173		5,165,4004	no	coding-synonymous	SEC14L5	NM_014692.1		5,171,5998	AA,AG,GG		2.0963,0.15,1.4658		606/697	5061113	181,12167	2000	4174	6174	SO:0001819	synonymous_variant	9717	exon15			GACCCGGTGGCCC	AB007880	CCDS45403.1	16p13.3	2008-02-05				ENSG00000103184			29032	protein-coding gene	gene with protein product						9455477	Standard	NM_014692		Approved	KIAA0420, PRELID4B	uc002cye.2	O43304		ENST00000251170.7:c.1818G>A	16.37:g.5061113G>A		65.0	0.0	0		55.0	26.0	0.472727	NM_014692		Silent	SNP	ENST00000251170.7	37	CCDS45403.1																																																																																			G|0.990;A|0.010	0.010	strong		0.657	SEC14L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434379.1		
SPATA21	374955	hgsc.bcm.edu	37	1	16736327	16736327	+	Missense_Mutation	SNP	G	G	A	rs41269197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16736327G>A	ENST00000335496.1	-	6	838	c.356C>T	c.(355-357)cCg>cTg	p.P119L	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Missense_Mutation_p.P96L	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	119	Pro-rich.						calcium ion binding (GO:0005509)			breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		GGTGGGCACCGGGGTCAGGGT	0.682													G|||	116	0.0231629	0.0015	0.0346	5008	,	,		13933	0.001		0.0686	False		,,,				2504	0.0204				p.P119L		Atlas-SNP	.											.	SPATA21	47	.	0			c.C356T						PASS	.	G	LEU/PRO	53,4353	49.6+/-84.7	0,53,2150	31.0	39.0	36.0		356	2.2	0.0	1	dbSNP_127	36	550,8050	148.6+/-203.8	22,506,3772	yes	missense	SPATA21	NM_198546.1	98	22,559,5922	AA,AG,GG		6.3953,1.2029,4.6363	probably-damaging	119/470	16736327	603,12403	2203	4300	6503	SO:0001583	missense	374955	exon6			GGCACCGGGGTCA		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.356C>T	1.37:g.16736327G>A	ENSP00000335612:p.Pro119Leu	48.0	0.0	0		84.0	36.0	0.428571	NM_198546	B9EK40|F5GXP5	Missense_Mutation	SNP	ENST00000335496.1	37	CCDS172.1	68	0.031135531135531136	1	0.0020325203252032522	12	0.03314917127071823	1	0.0017482517482517483	54	0.0712401055408971	G	13.99	2.401897	0.42613	0.012029	0.063953	ENSG00000187144	ENST00000335496;ENST00000540400	T;T	0.69806	-0.39;-0.43	4.07	2.16	0.27623	.	0.145674	0.32401	N	0.006141	T	0.07908	0.0198	L	0.29908	0.895	0.09310	N	1	D;P	0.57899	0.981;0.943	P;B	0.46253	0.509;0.235	T	0.08146	-1.0736	10	0.87932	D	0	-3.4136	7.2518	0.26154	0.1024:0.1774:0.7202:0.0	rs41269197	96;119	F5GXP5;Q7Z572	.;SPT21_HUMAN	L	119;96	ENSP00000335612:P119L;ENSP00000440046:P96L	ENSP00000335612:P119L	P	-	2	0	SPATA21	16608914	0.016000	0.18221	0.007000	0.13788	0.010000	0.07245	1.688000	0.37690	1.049000	0.40321	-0.527000	0.04329	CCG	G|0.960;A|0.040	0.040	strong		0.682	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
ZDBF2	57683	hgsc.bcm.edu	37	2	207170026	207170026	+	Silent	SNP	T	T	C	rs77622365	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207170026T>C	ENST00000374423.3	+	5	1160	c.774T>C	c.(772-774)aaT>aaC	p.N258N		NM_020923.1	NP_065974.1	Q9HCK1	ZDBF2_HUMAN	zinc finger, DBF-type containing 2	258							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(5)|large_intestine(28)|lung(50)|ovary(4)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	95						AAGAATCAAATAGGAAATCTT	0.368													T|||	115	0.0229633	0.0734	0.0159	5008	,	,		18712	0.0		0.006	False		,,,				2504	0.001				p.N258N		Atlas-SNP	.											.	ZDBF2	531	.	0			c.T774C						PASS	.	T		243,3413		8,227,1593	29.0	28.0	29.0		774	-3.9	0.0	2	dbSNP_132	29	71,8095		0,71,4012	no	coding-synonymous	ZDBF2	NM_020923.1		8,298,5605	CC,CT,TT		0.8695,6.6466,2.6561		258/2355	207170026	314,11508	1828	4083	5911	SO:0001819	synonymous_variant	57683	exon5			ATCAAATAGGAAA	AB046791	CCDS46501.1, CCDS74637.1	2q33.3	2013-01-10			ENSG00000204186	ENSG00000204186		"""Zinc fingers, DBF-type"""	29313	protein-coding gene	gene with protein product						10997877	Standard	XM_005246711		Approved	FLJ45338, KIAA1571	uc002vbp.2	Q9HCK1	OTTHUMG00000154648	ENST00000374423.3:c.774T>C	2.37:g.207170026T>C		160.0	0.0	0		148.0	67.0	0.452703	NM_020923	Q6ZNP7|Q6ZSN8	Silent	SNP	ENST00000374423.3	37	CCDS46501.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	ZDBF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336458.1	NM_020923	
DOLK	22845	hgsc.bcm.edu	37	9	131708710	131708710	+	Silent	SNP	G	G	A	rs148646968	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:131708710G>A	ENST00000372586.3	-	1	1188	c.873C>T	c.(871-873)ctC>ctT	p.L291L	NUP188_ENST00000372577.2_5'Flank|RP11-101E3.5_ENST00000482796.1_Intron	NM_014908.3	NP_055723.1	Q9UPQ8	DOLK_HUMAN	dolichol kinase	291					cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|dolichyl diphosphate biosynthetic process (GO:0006489)|dolichyl monophosphate biosynthetic process (GO:0043048)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)	dolichol kinase activity (GO:0004168)			breast(1)|large_intestine(5)|lung(3)|ovary(1)|urinary_tract(1)	11						CTGTCTGGAAGAGAAACTGAA	0.577													G|||	2	0.000399361	0.0	0.0	5008	,	,		18331	0.0		0.002	False		,,,				2504	0.0				p.L291L		Atlas-SNP	.											DOLK,colon,carcinoma,-2,1	DOLK	39	1	0			c.C873T						PASS	.	G		0,4406		0,0,2203	71.0	77.0	75.0		873	0.7	1.0	9	dbSNP_134	75	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	DOLK	NM_014908.3		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		291/539	131708710	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	22845	exon1			CTGGAAGAGAAAC	AB029017	CCDS6915.1	9q34.13	2014-09-17	2007-02-09	2007-02-09	ENSG00000175283	ENSG00000175283			23406	protein-coding gene	gene with protein product	"""dolichol kinase 1"""	610746	"""transmembrane protein 15"""	TMEM15		12975309, 16923818	Standard	NM_014908		Approved	KIAA1094, DK1	uc004bwr.3	Q9UPQ8	OTTHUMG00000020765	ENST00000372586.3:c.873C>T	9.37:g.131708710G>A		70.0	0.0	0		74.0	36.0	0.486486	NM_014908	Q5SRE6	Silent	SNP	ENST00000372586.3	37	CCDS6915.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	DOLK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054515.1	NM_014908	
FBN2	2201	hgsc.bcm.edu	37	5	127680130	127680130	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:127680130T>G	ENST00000508053.1	-	31	4264	c.3290A>C	c.(3289-3291)aAa>aCa	p.K1097T	FBN2_ENST00000508989.1_Missense_Mutation_p.K1064T|FBN2_ENST00000262464.4_Missense_Mutation_p.K1097T			P35556	FBN2_HUMAN	fibrillin 2	1097	EGF-like 15; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GCAACGGCATTTGAAGCTTCC	0.423																																					p.K1097T		Atlas-SNP	.											.	FBN2	858	.	0			c.A3290C						PASS	.						144.0	139.0	141.0					5																	127680130		2203	4300	6503	SO:0001583	missense	2201	exon25			CGGCATTTGAAGC	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.3290A>C	5.37:g.127680130T>G	ENSP00000424571:p.Lys1097Thr	86.0	0.0	0		72.0	31.0	0.430556	NM_001999	B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	T	9.363	1.068611	0.20067	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.86865	-2.18;-2.18;-2.18	4.26	4.26	0.50523	EGF-like calcium-binding, conserved site (1);EGF-like calcium-binding (2);Epidermal growth factor-like, type 3 (1);	0.076495	0.50627	D	0.000108	T	0.79341	0.4429	N	0.04116	-0.275	0.38313	D	0.943307	P;P	0.47677	0.899;0.503	P;B	0.51701	0.677;0.296	T	0.78884	-0.2028	10	0.17369	T	0.5	.	14.4286	0.67233	0.0:0.0:0.0:1.0	.	1064;1097	D6RJI3;P35556	.;FBN2_HUMAN	T	1097;1097;1064	ENSP00000262464:K1097T;ENSP00000424571:K1097T;ENSP00000425596:K1064T	ENSP00000262464:K1097T	K	-	2	0	FBN2	127708029	0.954000	0.32549	1.000000	0.80357	0.011000	0.07611	1.122000	0.31295	2.148000	0.66965	0.454000	0.30748	AAA	.	.	none		0.423	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
WNK1	65125	hgsc.bcm.edu	37	12	936230	936230	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:936230A>T	ENST00000315939.6	+	3	1598	c.955A>T	c.(955-957)Atg>Ttg	p.M319L	WNK1_ENST00000447667.2_Missense_Mutation_p.M319L|WNK1_ENST00000535572.1_Missense_Mutation_p.M319L|WNK1_ENST00000530271.2_Missense_Mutation_p.M319L|WNK1_ENST00000537687.1_Missense_Mutation_p.M319L	NM_018979.3	NP_061852.3	Q9H4A3	WNK1_HUMAN	WNK lysine deficient protein kinase 1	319	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				intracellular signal transduction (GO:0035556)|ion transport (GO:0006811)|negative regulation of pancreatic juice secretion (GO:0090188)|negative regulation of phosphatase activity (GO:0010923)|neuron development (GO:0048666)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of systemic arterial blood pressure (GO:0003084)|protein phosphorylation (GO:0006468)|regulation of cellular process (GO:0050794)	cytoplasm (GO:0005737)	ATP binding (GO:0005524)|chloride channel inhibitor activity (GO:0019869)|phosphatase binding (GO:0019902)|protein kinase inhibitor activity (GO:0004860)|protein serine/threonine kinase activity (GO:0004674)			breast(7)|central_nervous_system(1)|endometrium(3)|kidney(6)|large_intestine(15)|lung(43)|ovary(6)|prostate(3)|skin(7)|stomach(8)|upper_aerodigestive_tract(3)|urinary_tract(2)	104	all_cancers(10;0.00611)|all_epithelial(11;0.00825)|all_lung(10;0.0331)|Ovarian(42;0.0512)|Lung NSC(10;0.0632)		Epithelial(1;1.74e-08)|all cancers(1;7.04e-08)|OV - Ovarian serous cystadenocarcinoma(31;0.000423)|BRCA - Breast invasive adenocarcinoma(9;0.0149)|Colorectal(1;0.0197)			GTTTAAAGTGATGAAGATCAA	0.358																																					p.M319L	Colon(19;451 567 6672 12618 28860)	Atlas-SNP	.											.	WNK1	403	.	0			c.A955T						PASS	.						102.0	99.0	100.0					12																	936230		2203	4300	6503	SO:0001583	missense	65125	exon3			AAAGTGATGAAGA	AJ296290	CCDS8506.1, CCDS53731.1, CCDS73419.1	12p13.3	2014-09-17	2005-01-19	2005-01-21	ENSG00000060237	ENSG00000060237			14540	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 167"""	605232	"""protein kinase, lysine deficient 1"", ""hereditary sensory neuropathy, type II"""	PRKWNK1, HSN2			Standard	NM_001184985		Approved	HSAN2, PPP1R167	uc031qfk.1	Q9H4A3	OTTHUMG00000090321	ENST00000315939.6:c.955A>T	12.37:g.936230A>T	ENSP00000313059:p.Met319Leu	87.0	0.0	0		93.0	17.0	0.182796	NM_001184985	A1L4B0|C5HTZ5|C5HTZ6|C5HTZ7|H6WZW3|O15052|P54963|Q4VBX9|Q6IFS5|Q86WL5|Q8N673|Q96CZ6|Q9P1S9	Missense_Mutation	SNP	ENST00000315939.6	37	CCDS8506.1	.	.	.	.	.	.	.	.	.	.	A	34	5.350017	0.95830	.	.	ENSG00000060237	ENST00000535572;ENST00000315939;ENST00000537687;ENST00000447667;ENST00000530271	T;T;T;T;T	0.59638	0.25;0.25;0.25;0.25;0.25	5.54	5.54	0.83059	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.64402	D	0.000001	T	0.44644	0.1303	N	0.00337	-1.62	0.80722	D	1	P;P;B	0.52692	0.944;0.955;0.252	P;D;B	0.68353	0.866;0.957;0.157	T	0.73385	-0.3999	10	0.66056	D	0.02	-15.3692	15.6803	0.77364	1.0:0.0:0.0:0.0	.	319;319;319	F5GWT4;Q9H4A3;F6UYG0	.;WNK1_HUMAN;.	L	319	ENSP00000441972:M319L;ENSP00000313059:M319L;ENSP00000444465:M319L;ENSP00000392542:M319L;ENSP00000433548:M319L	ENSP00000313059:M319L	M	+	1	0	WNK1	806491	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.339000	0.96797	2.115000	0.64714	0.482000	0.46254	ATG	.	.	none		0.358	WNK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206683.1	NM_018979	
DENND4C	55667	hgsc.bcm.edu	37	9	19352096	19352096	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:19352096G>A	ENST00000380432.2	+	20	3699	c.3666G>A	c.(3664-3666)atG>atA	p.M1222I	DENND4C_ENST00000434457.2_Missense_Mutation_p.M1507I|DENND4C_ENST00000602925.1_Missense_Mutation_p.M1458I			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	1222					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						CAAGAGGCATGAAAGGGCAAG	0.348																																					p.M1458I		Atlas-SNP	.											.	DENND4C	120	.	0			c.G4374A						PASS	.						148.0	138.0	141.0					9																	19352096		2203	4300	6503	SO:0001583	missense	55667	exon24			AGGCATGAAAGGG	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	ENST00000380432.2:c.3666G>A	9.37:g.19352096G>A	ENSP00000369797:p.Met1222Ile	79.0	0.0	0		94.0	19.0	0.202128	NM_017925	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Missense_Mutation	SNP	ENST00000380432.2	37		.	.	.	.	.	.	.	.	.	.	G	5.514	0.279774	0.10458	.	.	ENSG00000137145	ENST00000380437;ENST00000307015;ENST00000453857;ENST00000540671;ENST00000380432;ENST00000380427;ENST00000361024;ENST00000380424	T;T	0.20881	2.05;2.04	5.27	-2.51	0.06365	.	1.303380	0.04496	N	0.380371	T	0.09818	0.0241	N	0.11560	0.145	0.28170	N	0.928596	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.0;0.001;0.0	T	0.28902	-1.0029	10	0.34782	T	0.22	-0.4352	2.7946	0.05397	0.1982:0.2628:0.4155:0.1235	.	552;1222;404;1222	B7Z660;Q5VZ89-5;Q5VZ89-3;Q5VZ89	.;.;.;DEN4C_HUMAN	I	1222;695;404;552;695;404;219;93	ENSP00000305795:M695I;ENSP00000443804:M552I	ENSP00000305795:M695I	M	+	3	0	DENND4C	19342096	0.685000	0.27652	0.809000	0.32408	0.994000	0.84299	0.215000	0.17562	-0.207000	0.10187	0.655000	0.94253	ATG	.	.	none		0.348	DENND4C-201	KNOWN	basic	protein_coding	protein_coding		NM_017925	
NFYC	4802	hgsc.bcm.edu	37	1	41232588	41232588	+	Splice_Site	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:41232588A>G	ENST00000308733.5	+	8	834		c.e8-1		NFYC_ENST00000483091.1_Splice_Site|NFYC_ENST00000425457.2_Splice_Site|NFYC_ENST00000447388.3_Intron|NFYC_ENST00000456393.2_Intron|NFYC_ENST00000440226.3_Intron|NFYC_ENST00000372652.1_Intron|NFYC_ENST00000372651.1_Intron|NFYC_ENST00000427410.2_Intron|NFYC_ENST00000372653.1_Intron|NFYC_ENST00000372654.1_Intron			Q13952	NFYC_HUMAN	nuclear transcription factor Y, gamma						cellular lipid metabolic process (GO:0044255)|positive regulation of transcription, DNA-templated (GO:0045893)|protein folding (GO:0006457)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	CCAAT-binding factor complex (GO:0016602)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(3)|lung(1)|prostate(1)|skin(2)	15	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;1.72e-17)			CTTGTTCTCAAGGGGCAAAGA	0.498																																					.		Atlas-SNP	.											.	NFYC	39	.	0			c.829-2A>G						PASS	.						85.0	83.0	84.0					1																	41232588		692	1591	2283	SO:0001630	splice_region_variant	4802	exon9			TTCTCAAGGGGCA	U78774	CCDS455.1, CCDS44120.1, CCDS44121.1, CCDS44122.1, CCDS44123.1	1p32	2008-11-11			ENSG00000066136	ENSG00000066136			7806	protein-coding gene	gene with protein product		605344				8921405, 9249075	Standard	NM_014223		Approved	CBF-C, NF-YC	uc009vwd.3	Q13952	OTTHUMG00000007729	ENST00000308733.5:c.829-1A>G	1.37:g.41232588A>G		63.0	0.0	0		69.0	5.0	0.0724638	NM_001142588	B4DUS6|B4DW63|D3DPV9|F8VWM3|Q59GY4|Q5T6K8|Q5T6K9|Q5T6L1|Q5TZR6|Q92869|Q9HBX1|Q9NXB5|Q9UM67|Q9UML0|Q9UMT7	Splice_Site	SNP	ENST00000308733.5	37		.	.	.	.	.	.	.	.	.	.	A	7.622	0.677071	0.14841	.	.	ENSG00000066136	ENST00000425457;ENST00000308733	.	.	.	5.43	1.91	0.25777	.	.	.	.	.	.	.	.	.	.	.	0.21355	N	0.999718	.	.	.	.	.	.	.	.	.	.	.	.	.	.	6.7246	0.23348	0.7231:0.0:0.2769:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NFYC	41005175	0.005000	0.15991	0.003000	0.11579	0.043000	0.13939	0.938000	0.28965	0.077000	0.16863	0.379000	0.24179	.	.	.	none		0.498	NFYC-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000020802.1	NM_014223	Intron
WDFY3	23001	hgsc.bcm.edu	37	4	85612823	85612823	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:85612823T>C	ENST00000295888.4	-	60	9572	c.9165A>G	c.(9163-9165)gcA>gcG	p.A3055A	WDFY3_ENST00000322366.6_Silent_p.A3038A	NM_014991.4	NP_055806.2	Q8IZQ1	WDFY3_HUMAN	WD repeat and FYVE domain containing 3	3055	Interaction with ATG5.|Interaction with SQSTM1.				aggrephagy (GO:0035973)|positive regulation of macroautophagy (GO:0016239)	autophagic vacuole (GO:0005776)|cytoplasm (GO:0005737)|extrinsic component of membrane (GO:0019898)|inclusion body (GO:0016234)|nuclear envelope (GO:0005635)|PML body (GO:0016605)	1-phosphatidylinositol binding (GO:0005545)|beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|metal ion binding (GO:0046872)			breast(5)|central_nervous_system(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(32)|lung(50)|ovary(3)|prostate(5)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	134		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;0.000808)		AACTGAGGTCTGCATAGCCCC	0.413																																					p.A3055A		Atlas-SNP	.											.	WDFY3	314	.	0			c.A9165G						PASS	.						121.0	108.0	113.0					4																	85612823		2203	4300	6503	SO:0001819	synonymous_variant	23001	exon60			GAGGTCTGCATAG	AB023210	CCDS3609.1	4q21.3	2013-01-09			ENSG00000163625	ENSG00000163625		"""Zinc fingers, FYVE domain containing"", ""WD repeat domain containing"""	20751	protein-coding gene	gene with protein product						10231032	Standard	NM_014991		Approved	KIAA0993, ALFY, ZFYVE25	uc003hpd.3	Q8IZQ1	OTTHUMG00000130424	ENST00000295888.4:c.9165A>G	4.37:g.85612823T>C		69.0	0.0	0		73.0	25.0	0.342466	NM_014991	Q4W5K5|Q6P0Q5|Q8N1T2|Q8NAV6|Q96BS7|Q96D33|Q96N85|Q9Y2J7	Silent	SNP	ENST00000295888.4	37	CCDS3609.1																																																																																			.	.	none		0.413	WDFY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252811.2	NM_014991	
NUDT9	53343	hgsc.bcm.edu	37	4	88344154	88344154	+	Missense_Mutation	SNP	C	C	A	rs146952902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:88344154C>A	ENST00000302174.4	+	1	421	c.97C>A	c.(97-99)Cag>Aag	p.Q33K	NUDT9_ENST00000473942.1_Intron	NM_024047.4	NP_076952.1	Q9BW91	NUDT9_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 9	33					ADP catabolic process (GO:0046032)|IDP catabolic process (GO:0046709)|nucleobase-containing small molecule catabolic process (GO:0034656)|nucleobase-containing small molecule metabolic process (GO:0055086)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|mitochondrial matrix (GO:0005759)	adenosine-diphosphatase activity (GO:0043262)|ADP-ribose diphosphatase activity (GO:0047631)|ADP-sugar diphosphatase activity (GO:0019144)			endometrium(1)|large_intestine(4)|lung(6)	11		Hepatocellular(203;0.114)|all_hematologic(202;0.21)|Acute lymphoblastic leukemia(40;0.242)		OV - Ovarian serous cystadenocarcinoma(123;0.000937)		CCGCGGCATCCAGGCGTTCAG	0.592													C|||	11	0.00219649	0.0	0.0014	5008	,	,		15253	0.0		0.006	False		,,,				2504	0.0041				p.Q33K		Atlas-SNP	.											.	NUDT9	21	.	0			c.C97A						PASS	.	C	LYS/GLN,	5,4401	9.9+/-24.2	0,5,2198	57.0	57.0	57.0		97,	2.7	0.0	4	dbSNP_134	57	32,8568	22.2+/-67.0	0,32,4268	yes	missense,intron	NUDT9	NM_024047.3,NM_198038.1	53,	0,37,6466	AA,AC,CC		0.3721,0.1135,0.2845	benign,	33/351,	88344154	37,12969	2203	4300	6503	SO:0001583	missense	53343	exon1			GGCATCCAGGCGT	AY026252	CCDS3620.1, CCDS3621.1	4q22.1	2008-08-29			ENSG00000170502	ENSG00000170502		"""Nudix motif containing"""	8056	protein-coding gene	gene with protein product		606022				11385575, 12427752	Standard	NM_024047		Approved	MGC3037	uc003hqq.3	Q9BW91	OTTHUMG00000130591	ENST00000302174.4:c.97C>A	4.37:g.88344154C>A	ENSP00000303575:p.Gln33Lys	40.0	0.0	0		40.0	11.0	0.275	NM_001248011	Q8NBN1|Q8NCB9|Q8NG25	Missense_Mutation	SNP	ENST00000302174.4	37	CCDS3620.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	C	9.675	1.147631	0.21288	0.001135	0.003721	ENSG00000170502	ENST00000302174;ENST00000440591	T;T	0.75589	-0.95;2.6	3.56	2.71	0.32032	.	0.536650	0.17871	N	0.159179	T	0.44498	0.1296	N	0.08118	0	0.21897	N	0.99949	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.44726	-0.9309	10	0.51188	T	0.08	0.1088	9.1276	0.36826	0.0:0.7534:0.2466:0.0	.	33;33	Q96KB3;Q9BW91	.;NUDT9_HUMAN	K	33	ENSP00000303575:Q33K;ENSP00000410270:Q33K	ENSP00000303575:Q33K	Q	+	1	0	NUDT9	88563178	0.004000	0.15560	0.008000	0.14137	0.004000	0.04260	0.585000	0.23879	1.048000	0.40298	0.484000	0.47621	CAG	C|0.997;A|0.003	0.003	strong		0.592	NUDT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253035.2		
FAM179A	165186	hgsc.bcm.edu	37	2	29225463	29225463	+	Silent	SNP	C	C	T	rs370488483		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:29225463C>T	ENST00000379558.4	+	5	840	c.489C>T	c.(487-489)gcC>gcT	p.A163A	FAM179A_ENST00000403861.2_Silent_p.A163A	NM_199280.2	NP_954974.2	Q6ZUX3	F179A_HUMAN	family with sequence similarity 179, member A	163										breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(5)|lung(9)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	26						TCCCCCGAGCCACCTCTCAGA	0.632																																					p.A163A		Atlas-SNP	.											.	FAM179A	106	.	0			c.C489T						PASS	.	C		1,3891		0,1,1945	23.0	28.0	27.0		489	-0.5	0.1	2		27	7,8255		0,7,4124	no	coding-synonymous	FAM179A	NM_199280.2		0,8,6069	TT,TC,CC		0.0847,0.0257,0.0658		163/1020	29225463	8,12146	1946	4131	6077	SO:0001819	synonymous_variant	165186	exon5			CCGAGCCACCTCT	AK125239, AK125744	CCDS1769.2	2p23.2	2008-10-30			ENSG00000189350	ENSG00000189350			33715	protein-coding gene	gene with protein product						16344560	Standard	NM_199280		Approved	FLJ43249, LOC165186	uc010ezl.3	Q6ZUX3	OTTHUMG00000128432	ENST00000379558.4:c.489C>T	2.37:g.29225463C>T		80.0	0.0	0		78.0	32.0	0.410256	NM_199280	Q6ZUF5	Silent	SNP	ENST00000379558.4	37	CCDS1769.2																																																																																			.	.	weak		0.632	FAM179A-003	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317848.4	NM_199280	
SERPINB10	5273	hgsc.bcm.edu	37	18	61584726	61584726	+	Missense_Mutation	SNP	G	G	T	rs143009235	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:61584726G>T	ENST00000238508.3	+	3	264	c.205G>T	c.(205-207)Gac>Tac	p.D69Y		NM_005024.1	NP_005015.1	P48595	SPB10_HUMAN	serpin peptidase inhibitor, clade B (ovalbumin), member 10	69					negative regulation of endopeptidase activity (GO:0010951)|regulation of proteolysis (GO:0030162)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(6)|prostate(1)|skin(3)|stomach(2)	24		Esophageal squamous(42;0.131)				AGTCAAATGTGACCCTGAAAG	0.274													G|||	18	0.00359425	0.003	0.0058	5008	,	,		15269	0.0		0.0099	False		,,,				2504	0.0				p.D69Y		Atlas-SNP	.											.	SERPINB10	53	.	0			c.G205T						PASS	.	G	TYR/ASP	4,4382		0,4,2189	33.0	33.0	33.0		205	-4.8	0.0	18	dbSNP_134	33	64,8478		0,64,4207	yes	missense	SERPINB10	NM_005024.1	160	0,68,6396	TT,TG,GG		0.7492,0.0912,0.526		69/398	61584726	68,12860	2193	4271	6464	SO:0001583	missense	5273	exon2			AAATGTGACCCTG	U35459	CCDS11990.1	18q21.3	2014-02-18	2005-08-18		ENSG00000242550	ENSG00000242550		"""Serine (or cysteine) peptidase inhibitors"""	8942	protein-coding gene	gene with protein product	"""protease inhibitor 10 (ovalbumin type, bomapin)"""	602058	"""serine (or cysteine) proteinase inhibitor, clade B (ovalbumin), member 10"""	PI10		9268635, 10871600, 24172014	Standard	NM_005024		Approved	bomapin		P48595	OTTHUMG00000060594	ENST00000238508.3:c.205G>T	18.37:g.61584726G>T	ENSP00000238508:p.Asp69Tyr	77.0	0.0	0		103.0	34.0	0.330097	NM_005024	Q4VAX4|Q4VAX7	Missense_Mutation	SNP	ENST00000238508.3	37	CCDS11990.1	15	0.006868131868131868	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	4.514	0.095366	0.08681	9.12E-4	0.007492	ENSG00000242550	ENST00000238508	D	0.85088	-1.94	5.1	-4.8	0.03190	Serpin domain (3);	1.218670	0.05583	N	0.573270	T	0.55305	0.1912	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.50466	-0.8825	9	.	.	.	.	7.1303	0.25497	0.3286:0.0:0.4743:0.1971	.	69;69	P48595;B2RC45	SPB10_HUMAN;.	Y	69	ENSP00000238508:D69Y	.	D	+	1	0	SERPINB10	59735706	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.633000	0.05483	-0.892000	0.03935	-0.813000	0.03139	GAC	G|0.993;T|0.007	0.007	strong		0.274	SERPINB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000134012.3	NM_005024	
ZBTB39	9880	hgsc.bcm.edu	37	12	57397250	57397250	+	Silent	SNP	G	G	C	rs145214115		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57397250G>C	ENST00000300101.2	-	2	1537	c.1452C>G	c.(1450-1452)gtC>gtG	p.V484V		NM_014830.2	NP_055645.1	O15060	ZBT39_HUMAN	zinc finger and BTB domain containing 39	484					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)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|prostate(1)	16						GCTGGTCGCAGACACTGCAGG	0.547													G|||	1	0.000199681	0.0	0.0014	5008	,	,		21109	0.0		0.0	False		,,,				2504	0.0				p.V484V		Atlas-SNP	.											.	ZBTB39	58	.	0			c.C1452G						PASS	.	G		0,4406		0,0,2203	58.0	52.0	54.0		1452	0.1	0.9	12	dbSNP_134	54	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	ZBTB39	NM_014830.2		0,2,6501	CC,CG,GG		0.0233,0.0,0.0154		484/713	57397250	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9880	exon2			GTCGCAGACACTG	AB002350	CCDS31839.1	12q13.3	2013-01-09				ENSG00000166860		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	29014	protein-coding gene	gene with protein product						9205841	Standard	NM_014830		Approved	KIAA0352, ZNF922	uc001sml.2	O15060		ENST00000300101.2:c.1452C>G	12.37:g.57397250G>C		104.0	0.0	0		93.0	44.0	0.473118	NM_014830	A7MD38|Q9UD98	Silent	SNP	ENST00000300101.2	37	CCDS31839.1																																																																																			G|0.999;C|0.001	0.001	strong		0.547	ZBTB39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411214.1	NM_014830	
RBM5	10181	hgsc.bcm.edu	37	3	50147061	50147061	+	Silent	SNP	G	G	A	rs116604207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:50147061G>A	ENST00000347869.3	+	15	1393	c.1218G>A	c.(1216-1218)gcG>gcA	p.A406A	RBM5_ENST00000441812.2_3'UTR	NM_005778.3	NP_005769.1	P52756	RBM5_HUMAN	RNA binding motif protein 5	406	Required for interaction with U2AF2.				apoptotic process (GO:0006915)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of cell proliferation (GO:0008285)|positive regulation of apoptotic process (GO:0043065)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	DNA binding (GO:0003677)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			breast(2)|cervix(2)|endometrium(3)|large_intestine(4)|lung(6)|prostate(2)	19				BRCA - Breast invasive adenocarcinoma(193;0.000121)|KIRC - Kidney renal clear cell carcinoma(197;0.00558)|Kidney(197;0.00632)		CCACCTCAGCGGCTGTAGTGT	0.488													G|||	2	0.000399361	0.0	0.0	5008	,	,		14240	0.0		0.002	False		,,,				2504	0.0				p.A406A		Atlas-SNP	.											.	RBM5	76	.	0			c.G1218A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	203.0	183.0	190.0		1218	-12.1	0.5	3	dbSNP_132	190	20,8580	14.6+/-50.1	0,20,4280	no	coding-synonymous	RBM5	NM_005778.2		0,21,6482	AA,AG,GG		0.2326,0.0227,0.1615		406/816	50147061	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	10181	exon15			CTCAGCGGCTGTA	U23946	CCDS2810.1	3p21.3	2013-08-15			ENSG00000003756	ENSG00000003756		"""G patch domain containing"", ""RNA binding motif (RRM) containing"""	9902	protein-coding gene	gene with protein product		606884				10352938, 23935508	Standard	NM_005778		Approved	LUCA15, H37	uc003cyg.3	P52756	OTTHUMG00000156785	ENST00000347869.3:c.1218G>A	3.37:g.50147061G>A		167.0	0.0	0		193.0	69.0	0.357513	NM_005778	B2RA45|B4DM16|B4DMF9|B4DZ63|Q93021|Q9BU14|Q9HDA6|Q9UKY8|Q9UL24	Silent	SNP	ENST00000347869.3	37	CCDS2810.1																																																																																			G|0.998;A|0.002	0.002	strong		0.488	RBM5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345797.3	NM_005778	
MCCC2	64087	hgsc.bcm.edu	37	5	70888804	70888804	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:70888804G>A	ENST00000340941.6	+	2	310	c.181G>A	c.(181-183)Gag>Aag	p.E61K	MCCC2_ENST00000323375.8_Missense_Mutation_p.E61K|MCCC2_ENST00000509358.2_Missense_Mutation_p.E61K	NM_022132.4	NP_071415.1	Q9HCC0	MCCB_HUMAN	methylcrotonoyl-CoA carboxylase 2 (beta)	61	Carboxyltransferase.				biotin metabolic process (GO:0006768)|branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|coenzyme A metabolic process (GO:0015936)|leucine catabolic process (GO:0006552)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytosol (GO:0005829)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|methylcrotonoyl-CoA carboxylase activity (GO:0004485)			endometrium(2)|kidney(15)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	30		Lung NSC(167;0.000697)|Prostate(74;0.0107)|Ovarian(174;0.0175)|Breast(144;0.198)		OV - Ovarian serous cystadenocarcinoma(47;2.04e-54)	Biotin(DB00121)	TGAACGAGTGGAGCATATAAA	0.348																																					p.E61K		Atlas-SNP	.											.	MCCC2	47	.	0			c.G181A						PASS	.						69.0	67.0	67.0					5																	70888804		2203	4300	6503	SO:0001583	missense	64087	exon2			CGAGTGGAGCATA	AF310971	CCDS34184.1	5q12-q13	2010-04-30	2010-04-30		ENSG00000131844	ENSG00000131844	6.4.1.4		6937	protein-coding gene	gene with protein product		609014	"""methylcrotonoyl-Coenzyme A carboxylase 2 (beta)"""				Standard	NM_022132		Approved	MCCB	uc003kbs.4	Q9HCC0	OTTHUMG00000162505	ENST00000340941.6:c.181G>A	5.37:g.70888804G>A	ENSP00000343657:p.Glu61Lys	245.0	0.0	0		256.0	137.0	0.535156	NM_022132	A6NIY9|Q96C27|Q9Y4L7	Missense_Mutation	SNP	ENST00000340941.6	37	CCDS34184.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.327666	0.24080	.	.	ENSG00000131844	ENST00000340941;ENST00000509358;ENST00000323375	D;D;D	0.98090	-4.71;-4.71;-4.71	4.73	0.197	0.15164	Acetyl-coenzyme A carboxyltransferase, N-terminal (1);	0.297876	0.35903	N	0.002915	D	0.96015	0.8702	M	0.69185	2.1	0.34463	D	0.701963	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.001	D	0.92607	0.6096	10	0.36615	T	0.2	-1.2046	16.3491	0.83195	0.0:0.3931:0.6069:0.0	.	61;61	D6RDF7;Q9HCC0	.;MCCB_HUMAN	K	61	ENSP00000343657:E61K;ENSP00000420994:E61K;ENSP00000327308:E61K	ENSP00000327308:E61K	E	+	1	0	MCCC2	70924560	0.999000	0.42202	0.001000	0.08648	0.001000	0.01503	0.986000	0.29590	0.062000	0.16340	-0.153000	0.13522	GAG	.	.	none		0.348	MCCC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369243.4		
TBX6	6911	hgsc.bcm.edu	37	16	30100401	30100401	+	Missense_Mutation	SNP	C	C	T	rs56098093	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:30100401C>T	ENST00000395224.2	-	4	543	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	TBX6_ENST00000279386.2_Missense_Mutation_p.G162S|TBX6_ENST00000553607.1_Missense_Mutation_p.G162S	NM_004608.3	NP_004599.2	O95947	TBX6_HUMAN	T-box 6	162			G -> S (in dbSNP:rs56098093).		anatomical structure morphogenesis (GO:0009653)|cell fate specification (GO:0001708)|mesoderm development (GO:0007498)|mesoderm formation (GO:0001707)|negative regulation of neuron maturation (GO:0014043)|negative regulation of neuron projection development (GO:0010977)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|signal transduction involved in regulation of gene expression (GO:0023019)|somite rostral/caudal axis specification (GO:0032525)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|pancreas(1)	9						TCTGCCTTGCCGCTGGGCTCC	0.647													C|||	4	0.000798722	0.0	0.0	5008	,	,		13926	0.0		0.004	False		,,,				2504	0.0				p.G162S		Atlas-SNP	.											.	TBX6	29	.	0			c.G484A						PASS	.	C	SER/GLY	5,4389	9.9+/-24.2	0,5,2192	47.0	52.0	50.0		484	5.8	1.0	16	dbSNP_129	50	52,8546	32.3+/-84.9	0,52,4247	yes	missense	TBX6	NM_004608.3	56	0,57,6439	TT,TC,CC		0.6048,0.1138,0.4387	probably-damaging	162/437	30100401	57,12935	2197	4299	6496	SO:0001583	missense	6911	exon4			CCTTGCCGCTGGG	AJ007989	CCDS10670.1	16p11.2	2008-02-05			ENSG00000149922	ENSG00000149922		"""T-boxes"""	11605	protein-coding gene	gene with protein product		602427				9888994, 9933572	Standard	NM_004608		Approved		uc010veh.2	O95947	OTTHUMG00000132115	ENST00000395224.2:c.484G>A	16.37:g.30100401C>T	ENSP00000378650:p.Gly162Ser	48.0	0.0	0		79.0	46.0	0.582278	NM_004608	Q8TAS4|Q9HA44	Missense_Mutation	SNP	ENST00000395224.2	37	CCDS10670.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	36	5.633723	0.96682	0.001138	0.006048	ENSG00000149922	ENST00000395224;ENST00000279386;ENST00000553607	D;D;D	0.91237	-2.81;-2.81;-2.81	5.8	5.8	0.92144	p53-like transcription factor, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.95287	0.8471	M	0.90977	3.165	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.95019	0.8159	10	0.87932	D	0	.	18.8306	0.92137	0.0:1.0:0.0:0.0	rs56098093	162;162	O95947;Q9HA44	TBX6_HUMAN;.	S	162	ENSP00000378650:G162S;ENSP00000279386:G162S;ENSP00000461223:G162S	ENSP00000279386:G162S	G	-	1	0	TBX6	30007902	0.998000	0.40836	0.997000	0.53966	0.971000	0.66376	4.819000	0.62664	2.747000	0.94245	0.462000	0.41574	GGC	C|0.997;T|0.003	0.003	strong		0.647	TBX6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255157.2	NM_004608, NM_080758	
SLC22A18	5002	hgsc.bcm.edu	37	11	2929502	2929502	+	Missense_Mutation	SNP	G	G	A	rs143044180	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:2929502G>A	ENST00000380574.1	+	3	615	c.184G>A	c.(184-186)Ggc>Agc	p.G62S	SLC22A18_ENST00000449793.2_Missense_Mutation_p.G62S|SLC22A18_ENST00000347936.2_Missense_Mutation_p.G62S|SLC22A18_ENST00000312221.5_Missense_Mutation_p.G62S			Q96BI1	S22AI_HUMAN	solute carrier family 22, member 18	62					drug transmembrane transport (GO:0006855)|drug transport (GO:0015893)|excretion (GO:0007588)|organic cation transport (GO:0015695)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	drug transmembrane transporter activity (GO:0015238)|symporter activity (GO:0015293)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(2)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)	8		all_epithelial(84;0.000124)|Medulloblastoma(188;0.00106)|Breast(177;0.00328)|Ovarian(85;0.00556)|all_neural(188;0.00681)|all_lung(207;0.198)		BRCA - Breast invasive adenocarcinoma(625;0.00256)|LUSC - Lung squamous cell carcinoma(625;0.192)		CATTGCCTTCGGCTACCTGCA	0.617																																					p.G62S		Atlas-SNP	.											SLC22A18,NS,carcinoma,0,1	SLC22A18	20	1	0			c.G184A						PASS	.						86.0	82.0	84.0					11																	2929502		2202	4299	6501	SO:0001583	missense	5002	exon3			GCCTTCGGCTACC	AF028738	CCDS7740.1	11p15.5	2013-05-22	2008-01-11	2004-01-21	ENSG00000110628	ENSG00000110628		"""Solute carriers"""	10964	protein-coding gene	gene with protein product		602631	"""solute carrier family 22 (organic cation transporter), member 1-like"""	ORCTL2, BWSCR1A, IMPT1, SLC22A1L		9499412, 9520460	Standard	NM_183233		Approved	BWR1A, TSSC5, ITM	uc001lwx.3	Q96BI1	OTTHUMG00000010037	ENST00000380574.1:c.184G>A	11.37:g.2929502G>A	ENSP00000369948:p.Gly62Ser	59.0	0.0	0		54.0	21.0	0.388889	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	.	.	.	.	.	.	.	.	.	.	G	15.78	2.935071	0.52866	.	.	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;D	0.84442	0.1;0.1;-0.06;0.1;-1.85	4.27	3.34	0.38264	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.64402	D	0.000001	D	0.87128	0.6100	L	0.56340	1.77	0.52501	D	0.999959	D;D	0.71674	0.991;0.998	P;P	0.62740	0.461;0.906	D	0.86466	0.1782	10	0.59425	D	0.04	-1.8758	7.3817	0.26859	0.1199:0.0:0.8801:0.0	.	62;62	E9PRM7;Q96BI1	.;S22AI_HUMAN	S	62	ENSP00000307859:G62S;ENSP00000311139:G62S;ENSP00000392072:G62S;ENSP00000369948:G62S;ENSP00000433019:G62S	ENSP00000311139:G62S	G	+	1	0	SLC22A18	2886078	1.000000	0.71417	0.933000	0.37362	0.037000	0.13140	2.882000	0.48546	2.105000	0.64084	0.491000	0.48974	GGC	G|0.998;T|0.002	.	alt		0.617	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
FCRLB	127943	hgsc.bcm.edu	37	1	161697068	161697068	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:161697068C>T	ENST00000367948.2	+	8	1112	c.897C>T	c.(895-897)gcC>gcT	p.A299A	FCRLB_ENST00000367946.3_Missense_Mutation_p.P251L|FCRLB_ENST00000392158.1_Silent_p.A299A|FCRLB_ENST00000495397.1_3'UTR|FCRLB_ENST00000367944.3_Missense_Mutation_p.P258S|FCRLB_ENST00000367945.1_Missense_Mutation_p.P244L|FCRLB_ENST00000336830.5_Missense_Mutation_p.P265S			Q6BAA4	FCRLB_HUMAN	Fc receptor-like B	299					negative regulation of immune response (GO:0050777)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)				central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|skin(1)	17	all_hematologic(112;0.0359)		BRCA - Breast invasive adenocarcinoma(70;0.00634)			CCACCACCGCCCCAGCTCCAT	0.662																																					p.A299A		Atlas-SNP	.											.	FCRLB	35	.	0			c.C897T						PASS	.						22.0	25.0	24.0					1																	161697068		2203	4299	6502	SO:0001819	synonymous_variant	127943	exon6			CACCGCCCCAGCT	AY670683	CCDS30927.1, CCDS72962.1, CCDS72963.1, CCDS72964.1, CCDS72965.1	1q23.3	2013-01-11	2006-09-26	2006-09-26	ENSG00000162746	ENSG00000162746		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	26431	protein-coding gene	gene with protein product		609251	"""Fc receptor-like and mucin-like 2"""	FCRLM2		15676285	Standard	NM_001288829		Approved	FLJ31052, FCRL2, FREB-2, FCRLY	uc001gbi.3	Q6BAA4	OTTHUMG00000133629	ENST00000367948.2:c.897C>T	1.37:g.161697068C>T		60.0	0.0	0		65.0	4.0	0.0615385	NM_001002901	A2A3J5|A2A3J7|Q5VXA6|Q6BAA0|Q6BAA1|Q6BAA2|Q6BAA3|Q8IXZ7	Silent	SNP	ENST00000367948.2	37	CCDS30927.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.08|17.08	3.296672|3.296672	0.60086|0.60086	.|.	.|.	ENSG00000162746|ENSG00000162746	ENST00000367946;ENST00000367945|ENST00000336830;ENST00000367944	T;T|T;T	0.02032|0.02369	4.49;4.51|4.32;4.35	4.07|4.07	-3.13|-3.13	0.05266|0.05266	.|.	.|.	.|.	.|.	.|.	T|T	0.00666|0.00666	0.0022|0.0022	.|.	.|.	.|.	0.19300|0.19300	N|N	0.999978|0.999978	B;B|B;B;B	0.06786|0.25312	0.001;0.001|0.123;0.005;0.005	B;B|B;B;B	0.04013|0.20955	0.001;0.001|0.032;0.002;0.002	T|T	0.46610|0.46610	-0.9179|-0.9179	8|8	0.62326|0.87932	D|D	0.03|0	.|.	2.4538|2.4538	0.04524|0.04524	0.143:0.2488:0.4213:0.1869|0.143:0.2488:0.4213:0.1869	.|.	244;251|302;258;265	Q6BAA4-5;Q6BAA4-4|Q96DP6;Q6BAA4-3;Q6BAA4-2	.;.|.;.;.	L|S	251;244|265;258	ENSP00000356923:P251L;ENSP00000356922:P244L|ENSP00000338598:P265S;ENSP00000356921:P258S	ENSP00000356922:P244L|ENSP00000338598:P265S	P|P	+|+	2|1	0|0	FCRLB|FCRLB	159963692|159963692	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.088000|0.088000	0.18126|0.18126	-0.913000|-0.913000	0.04042|0.04042	-0.994000|-0.994000	0.03463|0.03463	-0.519000|-0.519000	0.04390|0.04390	CCC|CCC	.	.	none		0.662	FCRLB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083585.1	NM_152378	
TIAF1	9220	hgsc.bcm.edu	37	17	27401176	27401176	+	Silent	SNP	G	G	C	rs1049848	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:27401176G>C	ENST00000359450.6	-	1	4699	c.42C>G	c.(40-42)ctC>ctG	p.L14L	MYO18A_ENST00000533112.1_3'UTR|TIAF1_ENST00000408971.2_Silent_p.L14L|MYO18A_ENST00000527372.1_3'UTR|MYO18A_ENST00000354329.4_3'UTR|MYO18A_ENST00000531253.1_3'UTR|MYO18A_ENST00000529578.1_5'UTR	NM_004740.3	NP_004731.2	O95411	TIAF1_HUMAN	TGFB1-induced anti-apoptotic factor 1	14					apoptotic process (GO:0006915)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|negative regulation of apoptotic process (GO:0043066)	nucleus (GO:0005634)				kidney(1)|lung(1)|urinary_tract(1)	3	Lung NSC(42;0.015)		Epithelial(11;1.19e-05)|all cancers(11;6.57e-05)|BRCA - Breast invasive adenocarcinoma(11;0.000153)|Colorectal(6;0.0102)|COAD - Colon adenocarcinoma(6;0.031)			CAGCTGCACAGAGAAAGGACT	0.597													G|||	24	0.00479233	0.0	0.0	5008	,	,		16628	0.001		0.0209	False		,,,				2504	0.002				p.L14L		Atlas-SNP	.											.	TIAF1	9	.	0			c.C42G						PASS	.	G	,,	18,4388	25.3+/-52.1	0,18,2185	50.0	51.0	51.0		42,,	1.7	0.0	17	dbSNP_86	51	135,8465	68.7+/-131.2	1,133,4166	no	coding-synonymous,utr-3,utr-3	TIAF1,MYO18A	NM_004740.3,NM_078471.3,NM_203318.1	,,	1,151,6351	CC,CG,GG		1.5698,0.4085,1.1764	,,	14/116,,	27401176	153,12853	2203	4300	6503	SO:0001819	synonymous_variant	9220	exon1			TGCACAGAGAAAG	AF105277	CCDS32599.1	17q11.2	2006-08-07				ENSG00000221995			11803	protein-coding gene	gene with protein product		609517				9918798	Standard	NM_004740		Approved		uc002hdv.1	O95411		ENST00000359450.6:c.42C>G	17.37:g.27401176G>C		48.0	0.0	0		55.0	27.0	0.490909	NM_004740	A2RRE2|Q6PEG2	Silent	SNP	ENST00000359450.6	37	CCDS32599.1																																																																																			G|0.988;C|0.012	0.012	strong		0.597	TIAF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372394.2	NM_004740	
TEP1	7011	hgsc.bcm.edu	37	14	20871901	20871901	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:20871901C>T	ENST00000262715.5	-	6	1215	c.1175G>A	c.(1174-1176)cGc>cAc	p.R392H	TEP1_ENST00000556935.1_Intron	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	392	TROVE. {ECO:0000255|PROSITE- ProRule:PRU00343}.				RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GGGTGGCCGGCGGGGGTGTCT	0.627																																					p.R392H		Atlas-SNP	.											TEP1,NS,carcinoma,-1,1	TEP1	224	1	0			c.G1175A						PASS	.						57.0	69.0	65.0					14																	20871901		2203	4300	6503	SO:0001583	missense	7011	exon6			GGCCGGCGGGGGT		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.1175G>A	14.37:g.20871901C>T	ENSP00000262715:p.Arg392His	64.0	0.0	0		55.0	34.0	0.618182	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	37	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	c	12.44	1.939881	0.34189	.	.	ENSG00000129566	ENST00000262715;ENST00000359243	T	0.19250	2.16	5.54	-2.45	0.06481	TROVE (2);	0.558259	0.18672	N	0.134420	T	0.19446	0.0467	M	0.74258	2.255	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.19811	-1.0294	10	0.51188	T	0.08	-0.5193	5.7588	0.18188	0.0:0.4309:0.2237:0.3453	.	392	Q99973	TEP1_HUMAN	H	392	ENSP00000262715:R392H	ENSP00000262715:R392H	R	-	2	0	TEP1	19941741	0.000000	0.05858	0.000000	0.03702	0.012000	0.07955	-1.167000	0.03126	-0.499000	0.06623	-0.119000	0.15052	CGC	.	.	none		0.627	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
TRIM66	9866	hgsc.bcm.edu	37	11	8671296	8671296	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:8671296C>T	ENST00000299550.6	-	3	342	c.148G>A	c.(148-150)Gga>Aga	p.G50R	TRIM66_ENST00000402157.2_Missense_Mutation_p.G50R|TRIM66_ENST00000531498.1_5'UTR	NM_014818.1	NP_055633.1	O15016	TRI66_HUMAN	tripartite motif containing 66	50						aggresome (GO:0016235)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			autonomic_ganglia(1)|breast(4)|kidney(1)|lung(1)|skin(2)	9						CCTGGAGATCCCTTCTGGGCC	0.587																																					p.G50R		Atlas-SNP	.											.	TRIM66	45	.	0			c.G148A						PASS	.						57.0	61.0	60.0					11																	8671296		692	1591	2283	SO:0001583	missense	9866	exon3			GAGATCCCTTCTG	AB002296		11p15.4	2013-01-28	2011-01-25		ENSG00000166436	ENSG00000166436		"""Tripartite motif containing / Tripartite motif containing"", ""Zinc fingers, PHD-type"""	29005	protein-coding gene	gene with protein product		612000	"""chromosome 11 open reading frame 29"", ""tripartite motif-containing 66"""	C11orf29		9205841	Standard	NM_014818		Approved	KIAA0298, TIF1D	uc010rbo.2	O15016	OTTHUMG00000150481	ENST00000299550.6:c.148G>A	11.37:g.8671296C>T	ENSP00000299550:p.Gly50Arg	51.0	0.0	0		37.0	18.0	0.486486	NM_014818	Q9BQQ4	Missense_Mutation	SNP	ENST00000299550.6	37		.	.	.	.	.	.	.	.	.	.	C	12.59	1.984321	0.35036	.	.	ENSG00000166436	ENST00000299550;ENST00000402157	T;T	0.65549	-0.16;-0.15	5.69	4.78	0.61160	Zinc finger, PHD-type (1);	0.108635	0.41712	N	0.000827	T	0.50377	0.1612	L	0.27053	0.805	0.32346	N	0.559062	B;B	0.24768	0.047;0.111	B;B	0.24269	0.052;0.039	T	0.54214	-0.8327	10	0.25106	T	0.35	-4.1626	16.8115	0.85722	0.0:0.8713:0.1286:0.0	.	50;50	O15016;B5MCJ9	TRI66_HUMAN;.	R	50	ENSP00000299550:G50R;ENSP00000384876:G50R	ENSP00000299550:G50R	G	-	1	0	TRIM66	8627872	1.000000	0.71417	0.999000	0.59377	0.392000	0.30506	2.886000	0.48578	1.393000	0.46605	0.655000	0.94253	GGA	.	.	none		0.587	TRIM66-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_084529	
STAT3	6774	hgsc.bcm.edu	37	17	40498635	40498635	+	Silent	SNP	C	C	T	rs146184566	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:40498635C>T	ENST00000264657.5	-	3	537	c.225G>A	c.(223-225)tcG>tcA	p.S75S	STAT3_ENST00000404395.3_Silent_p.S75S|STAT3_ENST00000389272.3_5'UTR|STAT3_ENST00000588969.1_Silent_p.S75S|STAT3_ENST00000585517.1_Silent_p.S75S	NM_003150.3|NM_139276.2	NP_003141.2|NP_644805.1	P40763	STAT3_HUMAN	signal transducer and activator of transcription 3 (acute-phase response factor)	75					acute-phase response (GO:0006953)|astrocyte differentiation (GO:0048708)|cell proliferation (GO:0008283)|cellular component movement (GO:0006928)|cellular response to hormone stimulus (GO:0032870)|cytokine-mediated signaling pathway (GO:0019221)|eating behavior (GO:0042755)|eye photoreceptor cell differentiation (GO:0001754)|glucose homeostasis (GO:0042593)|growth hormone receptor signaling pathway (GO:0060396)|interleukin-6-mediated signaling pathway (GO:0070102)|intracellular receptor signaling pathway (GO:0030522)|JAK-STAT cascade (GO:0007259)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of glycolytic process (GO:0045820)|negative regulation of neuron migration (GO:2001223)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphorylation (GO:0016310)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein import into nucleus (GO:0006606)|radial glial cell differentiation (GO:0060019)|regulation of multicellular organism growth (GO:0040014)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|sexual reproduction (GO:0019953)|signal transduction (GO:0007165)|stem cell maintenance (GO:0019827)|temperature homeostasis (GO:0001659)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|protein kinase binding (GO:0019901)|protein phosphatase binding (GO:0019903)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|signal transducer activity (GO:0004871)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(3)|lung(12)|ovary(1)|prostate(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	35		all_cancers(22;1.39e-06)|all_epithelial(22;2.95e-05)|Breast(137;0.000135)		BRCA - Breast invasive adenocarcinoma(366;0.139)		AGAGAACATTCGACTCTTGCA	0.478									Hyperimmunoglobulin E Recurrent Infection Syndrome				C|||	10	0.00199681	0.0076	0.0	5008	,	,		19275	0.0		0.0	False		,,,				2504	0.0				p.S75S		Atlas-SNP	.											STAT3,NS,carcinoma,0,1	STAT3	268	1	0			c.G225A						PASS	.	C	,,	7,4399	11.4+/-27.6	0,7,2196	225.0	220.0	222.0		225,225,225	-11.0	0.7	17	dbSNP_134	222	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	STAT3	NM_003150.3,NM_139276.2,NM_213662.1	,,	0,7,6496	TT,TC,CC		0.0,0.1589,0.0538	,,	75/770,75/771,75/723	40498635	7,12999	2203	4300	6503	SO:0001819	synonymous_variant	6774	exon3	Familial Cancer Database	HIES, Hyper IgE syndrome, autosomal dominant (Job syndrome) / recessive	AACATTCGACTCT	BC014482	CCDS32656.1, CCDS32657.1, CCDS59288.1	17q21	2014-09-17			ENSG00000168610	ENSG00000168610		"""SH2 domain containing"""	11364	protein-coding gene	gene with protein product		102582				7512451	Standard	NM_139276		Approved	APRF	uc002hzl.1	P40763	OTTHUMG00000150645	ENST00000264657.5:c.225G>A	17.37:g.40498635C>T		128.0	0.0	0		100.0	42.0	0.42	NM_003150	A8K7B8|K7ENL3|O14916|Q9BW54	Silent	SNP	ENST00000264657.5	37	CCDS32656.1																																																																																			C|0.999;T|0.001	0.001	strong		0.478	STAT3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000319353.3	NM_139276, NM_003150	
HELZ2	85441	hgsc.bcm.edu	37	20	62193733	62193733	+	Missense_Mutation	SNP	C	C	T	rs370768380		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:62193733C>T	ENST00000467148.1	-	9	6374	c.6305G>A	c.(6304-6306)cGc>cAc	p.R2102H	HELZ2_ENST00000427522.2_Missense_Mutation_p.R1533H	NM_001037335.2	NP_001032412.2	Q9BYK8	HELZ2_HUMAN	helicase with zinc finger 2, transcriptional coactivator	2102					cellular lipid metabolic process (GO:0044255)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)	membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)										TTCCTCCTTGCGGCTGGGGGT	0.682																																					p.R2102H		Atlas-SNP	.											PRIC285,colon,carcinoma,0,1	.	.	1	0			c.G6305A						PASS	.	C	HIS/ARG,HIS/ARG	0,4222		0,0,2111	8.0	9.0	9.0		6305,4598	4.2	1.0	20		9	1,8395		0,1,4197	no	missense,missense	PRIC285	NM_001037335.2,NM_033405.3	29,29	0,1,6308	TT,TC,CC		0.0119,0.0,0.0079	probably-damaging,probably-damaging	2102/2650,1533/2081	62193733	1,12617	2111	4198	6309	SO:0001583	missense	85441	exon10			TCCTTGCGGCTGG	AB201715	CCDS13527.1, CCDS33508.1	20q13.33	2012-09-26			ENSG00000130589	ENSG00000130589			30021	protein-coding gene	gene with protein product	"""peroxisomal proliferator activated receptor A interacting complex 285"", ""PPARG-DBD-interacting protein 1"""	611265				11214970, 12189208, 16239304	Standard	NM_001037335		Approved	PDIP1, PRIC285, KIAA1769	uc002yfm.2	Q9BYK8	OTTHUMG00000032969	ENST00000467148.1:c.6305G>A	20.37:g.62193733C>T	ENSP00000417401:p.Arg2102His	53.0	0.0	0		48.0	23.0	0.479167	NM_001037335	Q3C2G2|Q4VXQ1|Q8TEF3|Q96ND3|Q9C094	Missense_Mutation	SNP	ENST00000467148.1	37	CCDS33508.1	.	.	.	.	.	.	.	.	.	.	C	22.0	4.227358	0.79576	0.0	1.19E-4	ENSG00000130589	ENST00000427522;ENST00000467148	D;D	0.84800	-1.9;-1.72	4.15	4.15	0.48705	.	0.311695	0.30043	N	0.010556	D	0.91233	0.7237	M	0.74258	2.255	0.53688	D	0.999977	D;D	0.89917	1.0;1.0	D;D	0.74348	0.961;0.983	D	0.92378	0.5911	10	0.87932	D	0	-31.3164	13.9239	0.63950	0.0:1.0:0.0:0.0	.	2102;1533	Q9BYK8;Q9BYK8-2	PR285_HUMAN;.	H	1533;2102	ENSP00000393257:R1533H;ENSP00000417401:R2102H	ENSP00000393257:R1533H	R	-	2	0	RP4-697K14.7	61664177	1.000000	0.71417	1.000000	0.80357	0.750000	0.42670	2.523000	0.45580	1.867000	0.54127	0.313000	0.20887	CGC	.	.	weak		0.682	HELZ2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354127.1	NM_001037335	
DLX5	1749	hgsc.bcm.edu	37	7	96653684	96653684	+	Silent	SNP	G	G	C	rs61753628	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:96653684G>C	ENST00000222598.4	-	1	725	c.252C>G	c.(250-252)gcC>gcG	p.A84A	DLX5_ENST00000493764.1_5'UTR|DLX5_ENST00000486603.2_Silent_p.A84A	NM_005221.5	NP_005212.1	P56178	DLX5_HUMAN	distal-less homeobox 5	84					anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|cell proliferation (GO:0008283)|cellular response to BMP stimulus (GO:0071773)|embryonic limb morphogenesis (GO:0030326)|endochondral ossification (GO:0001958)|epithelial cell differentiation (GO:0030855)|face morphogenesis (GO:0060325)|inner ear morphogenesis (GO:0042472)|nervous system development (GO:0007399)|olfactory pit development (GO:0060166)|osteoblast differentiation (GO:0001649)|palate development (GO:0060021)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus (GO:1901522)|positive regulation of transcription, DNA-templated (GO:0045893)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)	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)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|endometrium(1)|large_intestine(7)|lung(9)|ovary(1)|prostate(1)	20	all_cancers(62;9.56e-09)|all_epithelial(64;7.38e-09)|Esophageal squamous(72;0.0125)|all_lung(186;0.0855)|Lung NSC(181;0.0858)					GGTAGCTCCCGGCGGAGCCGT	0.627													G|||	4	0.000798722	0.0	0.0014	5008	,	,		14915	0.0		0.002	False		,,,				2504	0.001				p.A84A		Atlas-SNP	.											DLX5,caecum,carcinoma,0,1	DLX5	52	1	0			c.C252G						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	51.0	52.0	52.0		252	3.1	1.0	7	dbSNP_129	52	7,8593	5.7+/-21.5	0,7,4293	no	coding-synonymous	DLX5	NM_005221.5		0,8,6495	CC,CG,GG		0.0814,0.0227,0.0615		84/290	96653684	8,12998	2203	4300	6503	SO:0001819	synonymous_variant	1749	exon1			GCTCCCGGCGGAG		CCDS5647.1	7q21.3	2011-06-20	2005-12-22		ENSG00000105880	ENSG00000105880		"""Homeoboxes / ANTP class : NKL subclass"""	2918	protein-coding gene	gene with protein product		600028	"""distal-less homeo box 5"""			7907794	Standard	XM_005250185		Approved		uc003uon.3	P56178	OTTHUMG00000154200	ENST00000222598.4:c.252C>G	7.37:g.96653684G>C		120.0	1.0	0.00833333		119.0	61.0	0.512605	NM_005221	B7Z4P3|Q9UPL1	Silent	SNP	ENST00000222598.4	37	CCDS5647.1																																																																																			G|0.994;C|0.006	0.006	strong		0.627	DLX5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334371.2		
TMC7	79905	hgsc.bcm.edu	37	16	19056695	19056695	+	Silent	SNP	C	C	T	rs137989665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:19056695C>T	ENST00000304381.5	+	11	1618	c.1488C>T	c.(1486-1488)taC>taT	p.Y496Y	TMC7_ENST00000569532.1_Silent_p.Y496Y|TMC7_ENST00000421369.3_Silent_p.Y386Y	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7	496					ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						AGGAAATGTACAAGCTGATGA	0.493																																					p.Y496Y		Atlas-SNP	.											.	TMC7	75	.	0			c.C1488T						PASS	.	C	,	0,4394		0,0,2197	163.0	131.0	142.0		1158,1488	2.9	1.0	16	dbSNP_134	142	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	TMC7	NM_001160364.1,NM_024847.3	,	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	,	386/614,496/724	19056695	1,12993	2197	4300	6497	SO:0001819	synonymous_variant	79905	exon11			AATGTACAAGCTG	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.1488C>T	16.37:g.19056695C>T		172.0	0.0	0		156.0	69.0	0.442308	NM_024847	E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Silent	SNP	ENST00000304381.5	37	CCDS10573.1																																																																																			C|1.000;T|0.000	0.000	strong		0.493	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847	
SH3TC1	54436	hgsc.bcm.edu	37	4	8229378	8229378	+	Silent	SNP	C	C	A	rs139890356	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:8229378C>A	ENST00000245105.3	+	12	2024	c.1957C>A	c.(1957-1959)Cgg>Agg	p.R653R	SH3TC1_ENST00000539824.1_Silent_p.R577R	NM_018986.3	NP_061859	Q8TE82	S3TC1_HUMAN	SH3 domain and tetratricopeptide repeats 1	653										NS(1)|breast(3)|endometrium(4)|kidney(4)|large_intestine(6)|lung(10)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						GCTGGCGCTGCGGCGGGCGGT	0.726																																					p.R653R	NSCLC(145;2298 2623 35616 37297)	Atlas-SNP	.											.	SH3TC1	105	.	0			c.C1957A						PASS	.						12.0	13.0	13.0					4																	8229378		1842	3696	5538	SO:0001819	synonymous_variant	54436	exon12			GCGCTGCGGCGGG	AK074093	CCDS3399.1	4p16.1	2013-01-11			ENSG00000125089	ENSG00000125089		"""Tetratricopeptide (TTC) repeat domain containing"""	26009	protein-coding gene	gene with protein product							Standard	NM_018986		Approved	FLJ20356	uc003gkv.4	Q8TE82	OTTHUMG00000160934	ENST00000245105.3:c.1957C>A	4.37:g.8229378C>A		24.0	0.0	0		38.0	21.0	0.552632	NM_018986	Q4W5G5	Silent	SNP	ENST00000245105.3	37	CCDS3399.1																																																																																			C|0.996;T|0.004	.	alt		0.726	SH3TC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206991.2	NM_018986	
APC	324	hgsc.bcm.edu	37	5	112176559	112176559	+	Silent	SNP	T	T	G	rs866006	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176559T>G	ENST00000457016.1	+	16	5648	c.5268T>G	c.(5266-5268)tcT>tcG	p.S1756S	APC_ENST00000257430.4_Silent_p.S1756S|APC_ENST00000508376.2_Silent_p.S1756S|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1756	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		CATCTGCGTCTTCTTCTGCAC	0.398		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			t|||	3340	0.666933	0.5197	0.7161	5008	,	,		19571	0.8165		0.6004	False		,,,				2504	0.7454				p.S1756S	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.T5268G						PASS	.	G	,,	2326,2078	584.6+/-386.1	621,1084,497	55.0	54.0	54.0	http://omim.org/entry/114500	5268,5268,5214	-2.5	0.2	5	dbSNP_86	54	5319,3279	623.8+/-397.5	1680,1959,660	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2301,3043,1157	GG,GT,TT		38.1368,47.1844,41.2014	,,	1756/2844,1756/2844,1738/2826	112176559	7645,5357	2202	4299	6501	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TGCGTCTTCTTCT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5268T>G	5.37:g.112176559T>G		95.0	0.0	0		111.0	111.0	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			T|0.384;G|0.616	0.616	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
ADCY6	112	hgsc.bcm.edu	37	12	49162439	49162439	+	Missense_Mutation	SNP	C	C	G	rs200204618		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49162439C>G	ENST00000307885.4	-	21	4136	c.3442G>C	c.(3442-3444)Gtg>Ctg	p.V1148L	RP11-579D7.2_ENST00000548742.1_RNA|ADCY6_ENST00000357869.3_Missense_Mutation_p.V1095L|ADCY6_ENST00000550422.1_Missense_Mutation_p.V1095L	NM_015270.3	NP_056085.1	O43306	ADCY6_HUMAN	adenylate cyclase 6	1148					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)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|dopamine receptor signaling pathway (GO:0007212)|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)|negative regulation of neuron projection development (GO:0010977)|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)	cilium (GO:0005929)|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)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(1)|large_intestine(2)|lung(16)|prostate(1)|skin(1)|urinary_tract(1)	29						ACCTTGACCACCCCTCGACAC	0.607																																					p.V1148L		Atlas-SNP	.											.	ADCY6	81	.	0			c.G3442C						PASS	.	C	LEU/VAL,LEU/VAL	0,4406		0,0,2203	104.0	88.0	93.0		3442,3283	4.2	1.0	12		93	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	ADCY6	NM_015270.3,NM_020983.2	32,32	0,2,6501	GG,GC,CC		0.0233,0.0,0.0154	benign,benign	1148/1169,1095/1116	49162439	2,13004	2203	4300	6503	SO:0001583	missense	112	exon21			TGACCACCCCTCG		CCDS8767.1, CCDS8768.1	12q12-q13	2013-02-04				ENSG00000174233	4.6.1.1	"""Adenylate cyclases"""	237	protein-coding gene	gene with protein product		600294					Standard	NM_015270		Approved	AC6	uc001rsh.4	O43306		ENST00000307885.4:c.3442G>C	12.37:g.49162439C>G	ENSP00000311405:p.Val1148Leu	92.0	0.0	0		96.0	51.0	0.53125	NM_015270	Q9NR75|Q9UDB0	Missense_Mutation	SNP	ENST00000307885.4	37	CCDS8767.1	.	.	.	.	.	.	.	.	.	.	C	11.76	1.735662	0.30774	0.0	2.33E-4	ENSG00000174233	ENST00000357869;ENST00000550422;ENST00000307885	T;T;T	0.80738	-1.41;-1.41;-1.41	5.12	4.23	0.50019	Adenylyl cyclase class-3/4/guanylyl cyclase (3);	0.246243	0.32563	N	0.005938	T	0.56834	0.2012	N	0.01679	-0.765	0.47778	D	0.999511	B;B	0.13594	0.007;0.008	B;B	0.15484	0.012;0.013	T	0.53165	-0.8477	10	0.19590	T	0.45	.	15.4765	0.75485	0.0:0.86:0.14:0.0	.	1095;1148	O43306-2;O43306	.;ADCY6_HUMAN	L	1095;1095;1148	ENSP00000350536:V1095L;ENSP00000446730:V1095L;ENSP00000311405:V1148L	ENSP00000311405:V1148L	V	-	1	0	ADCY6	47448706	0.944000	0.32072	1.000000	0.80357	0.994000	0.84299	1.300000	0.33436	1.491000	0.48482	-0.223000	0.12442	GTG	.	.	weak		0.607	ADCY6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408863.1	NM_020983	
NOD2	64127	hgsc.bcm.edu	37	16	50753892	50753892	+	Missense_Mutation	SNP	G	G	A	rs201831159		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:50753892G>A	ENST00000300589.2	+	7	2792	c.2687G>A	c.(2686-2688)cGa>cAa	p.R896Q		NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	896					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)				GAGGGGCTCCGAGGCAACACC	0.597													G|||	1	0.000199681	0.0	0.0	5008	,	,		18894	0.0		0.001	False		,,,				2504	0.0				p.R896Q		Atlas-SNP	.											.	NOD2	118	.	0			c.G2687A						PASS	.						75.0	80.0	78.0					16																	50753892		2198	4300	6498	SO:0001583	missense	64127	exon7			GGCTCCGAGGCAA	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.2687G>A	16.37:g.50753892G>A	ENSP00000300589:p.Arg896Gln	51.0	0.0	0		67.0	41.0	0.61194	NM_022162	E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	CCDS10746.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	8.658	0.899935	0.17686	.	.	ENSG00000167207	ENST00000526417;ENST00000300589;ENST00000431240	T	0.52983	0.64	5.91	3.31	0.37934	.	0.369818	0.23142	N	0.051460	T	0.30479	0.0766	L	0.47716	1.5	0.09310	N	1	P;P	0.50066	0.788;0.931	B;B	0.37267	0.245;0.091	T	0.13282	-1.0515	10	0.18710	T	0.47	.	5.1538	0.15025	0.367:0.0:0.633:0.0	.	869;896	Q9HC29-2;Q9HC29	.;NOD2_HUMAN	Q	869;896;36	ENSP00000300589:R896Q	ENSP00000300589:R896Q	R	+	2	0	NOD2	49311393	0.115000	0.22152	0.283000	0.24790	0.014000	0.08584	0.496000	0.22499	1.161000	0.42604	0.655000	0.94253	CGA	G|1.000;A|0.000	0.000	strong		0.597	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
PRRC2B	84726	hgsc.bcm.edu	37	9	134340444	134340444	+	Missense_Mutation	SNP	A	A	G	rs201633009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134340444A>G	ENST00000357304.4	+	11	1754	c.1699A>G	c.(1699-1701)Aac>Gac	p.N567D	PRRC2B_ENST00000458550.1_Missense_Mutation_p.N567D|PRRC2B_ENST00000405995.1_Missense_Mutation_p.N567D|PRRC2B_ENST00000372249.1_5'UTR	NM_013318.3	NP_037450.2	Q5JSZ5	PRC2B_HUMAN	proline-rich coiled-coil 2B	567							poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(7)|lung(20)|ovary(2)	44						TCCCCAGGAAAACGGCCCTGC	0.572													A|||	2	0.000399361	0.0	0.0029	5008	,	,		17186	0.0		0.0	False		,,,				2504	0.0				p.N567D		Atlas-SNP	.											.	PRRC2B	266	.	0			c.A1699G						PASS	.	A	ASP/ASN	0,3984		0,0,1992	41.0	47.0	45.0		1699	5.5	1.0	9		45	13,8289		1,11,4139	yes	missense	PRRC2B	NM_013318.3	23	1,11,6131	GG,GA,AA		0.1566,0.0,0.1058	probably-damaging	567/2230	134340444	13,12273	1992	4151	6143	SO:0001583	missense	84726	exon11			CAGGAAAACGGCC	AB011087	CCDS48044.1	9q34.13	2010-12-09	2010-12-09	2010-12-09	ENSG00000130723	ENSG00000130723			28121	protein-coding gene	gene with protein product			"""KIAA0515"", ""HLA-B associated transcript 2-like"", ""HLA-B associated transcript 2-like 1"""	KIAA0515, BAT2L, BAT2L1		9628581	Standard	NM_013318		Approved	MGC10526, LQFBS-1	uc004can.4	Q5JSZ5	OTTHUMG00000020827	ENST00000357304.4:c.1699A>G	9.37:g.134340444A>G	ENSP00000349856:p.Asn567Asp	63.0	0.0	0		70.0	37.0	0.528571	NM_013318	O60270|Q5JSZ7|Q66VZ2|Q68CR0|Q96EI9|Q9H683	Missense_Mutation	SNP	ENST00000357304.4	37	CCDS48044.1	.	.	.	.	.	.	.	.	.	.	A	16.66	3.185233	0.57909	0.0	0.001566	ENSG00000130723	ENST00000405995;ENST00000357304;ENST00000458550;ENST00000422467	T;T;T;T	0.12672	2.66;2.66;2.66;2.66	5.48	5.48	0.80851	.	0.000000	0.44483	U	0.000450	T	0.31827	0.0809	L	0.57536	1.79	0.80722	D	1	D	0.69078	0.997	D	0.73380	0.98	T	0.01914	-1.1248	10	0.26408	T	0.33	-2.5709	14.7458	0.69490	1.0:0.0:0.0:0.0	.	567	Q5JSZ5	PRC2B_HUMAN	D	567;567;567;107	ENSP00000384606:N567D;ENSP00000349856:N567D;ENSP00000398853:N567D;ENSP00000391063:N107D	ENSP00000349856:N567D	N	+	1	0	PRRC2B	133330265	1.000000	0.71417	0.998000	0.56505	0.221000	0.24807	4.399000	0.59703	2.075000	0.62263	0.459000	0.35465	AAC	A|0.994;G|0.006	0.006	strong		0.572	PRRC2B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
SPPL2A	84888	hgsc.bcm.edu	37	15	51041909	51041909	+	Missense_Mutation	SNP	C	C	T	rs145832874	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:51041909C>T	ENST00000261854.5	-	2	375	c.101G>A	c.(100-102)gGa>gAa	p.G34E	RP11-507J18.2_ENST00000558317.1_RNA	NM_032802.3	NP_116191.2	Q8TCT8	SPP2A_HUMAN	signal peptide peptidase like 2A	34					membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|regulation of immune response (GO:0050776)	extracellular vesicular exosome (GO:0070062)|Golgi-associated vesicle membrane (GO:0030660)|integral component of cytoplasmic side of endoplasmic reticulum membrane (GO:0071458)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	aspartic-type endopeptidase activity (GO:0004190)|protein homodimerization activity (GO:0042803)			endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	15				all cancers(107;0.000712)|GBM - Glioblastoma multiforme(94;0.00314)		TGTGCCATTTCCAGACGCATG	0.403													C|||	13	0.00259585	0.0	0.0043	5008	,	,		20240	0.0		0.002	False		,,,				2504	0.0082				p.G34E	Melanoma(50;790 1209 4069 22965 33125)	Atlas-SNP	.											.	SPPL2A	26	.	0			c.G101A						PASS	.	C	GLU/GLY	0,4392		0,0,2196	137.0	129.0	132.0		101	3.8	1.0	15	dbSNP_134	132	14,8574	11.2+/-40.8	0,14,4280	yes	missense	SPPL2A	NM_032802.3	98	0,14,6476	TT,TC,CC		0.163,0.0,0.1079	benign	34/521	51041909	14,12966	2196	4294	6490	SO:0001583	missense	84888	exon2			CCATTTCCAGACG		CCDS10138.1	15q21.2	2012-02-21			ENSG00000138600	ENSG00000138600			30227	protein-coding gene	gene with protein product	"""intramembrane protease 3"", ""presenilin-like protein 2"""	608238				12077416, 12139484	Standard	NM_032802		Approved	IMP3, PSL2	uc001zyv.3	Q8TCT8	OTTHUMG00000131647	ENST00000261854.5:c.101G>A	15.37:g.51041909C>T	ENSP00000261854:p.Gly34Glu	73.0	0.0	0		88.0	46.0	0.522727	NM_032802	B2RDS0|Q8TAW1|Q96SZ8	Missense_Mutation	SNP	ENST00000261854.5	37	CCDS10138.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	15.84	2.951845	0.53293	0.0	0.00163	ENSG00000138600	ENST00000261854	T	0.10960	2.82	5.72	3.8	0.43715	.	0.291695	0.39909	N	0.001238	T	0.06050	0.0157	L	0.36672	1.1	0.32630	N	0.522116	B	0.17038	0.02	B	0.16289	0.015	T	0.04413	-1.0953	10	0.45353	T	0.12	-4.7508	8.2699	0.31838	0.0:0.7246:0.1402:0.1353	.	34	Q8TCT8	PSL2_HUMAN	E	34	ENSP00000261854:G34E	ENSP00000261854:G34E	G	-	2	0	AC012100.1	48829201	0.998000	0.40836	0.995000	0.50966	0.954000	0.61252	1.261000	0.32980	1.384000	0.46424	0.650000	0.86243	GGA	C|0.998;T|0.002	0.002	strong		0.403	SPPL2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254543.3	NM_032802	
TGFB2	7042	hgsc.bcm.edu	37	1	218520315	218520315	+	Missense_Mutation	SNP	G	G	A	rs10482721	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:218520315G>A	ENST00000366930.4	+	1	739	c.272G>A	c.(271-273)cGc>cAc	p.R91H	TGFB2_ENST00000366929.4_Missense_Mutation_p.R91H|RP11-224O19.2_ENST00000414452.1_RNA	NM_003238.3	NP_003229.1	P61812	TGFB2_HUMAN	transforming growth factor, beta 2	91			R -> H (in dbSNP:rs10482721). {ECO:0000269|PubMed:11528528, ECO:0000269|Ref.4}.		activation of protein kinase activity (GO:0032147)|angiogenesis (GO:0001525)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|blood vessel remodeling (GO:0001974)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac muscle cell proliferation (GO:0060038)|cardioblast differentiation (GO:0010002)|cartilage condensation (GO:0001502)|catagen (GO:0042637)|cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cell-cell junction organization (GO:0045216)|cell-cell signaling (GO:0007267)|collagen fibril organization (GO:0030199)|dopamine biosynthetic process (GO:0042416)|embryo development (GO:0009790)|embryonic digestive tract development (GO:0048566)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway (GO:0097191)|eye development (GO:0001654)|face morphogenesis (GO:0060325)|generation of neurons (GO:0048699)|glial cell migration (GO:0008347)|hair follicle development (GO:0001942)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart morphogenesis (GO:0003007)|hemopoiesis (GO:0030097)|menstrual cycle phase (GO:0022601)|negative regulation of alkaline phosphatase activity (GO:0010693)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of immune response (GO:0050777)|negative regulation of macrophage cytokine production (GO:0010936)|neuron development (GO:0048666)|neuron fate commitment (GO:0048663)|neutrophil chemotaxis (GO:0030593)|odontogenesis (GO:0042476)|pathway-restricted SMAD protein phosphorylation (GO:0060389)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of activation-induced cell death of T cells (GO:0070237)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of catagen (GO:0051795)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of gene expression (GO:0010628)|positive regulation of heart contraction (GO:0045823)|positive regulation of immune response (GO:0050778)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of ossification (GO:0045778)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein secretion (GO:0050714)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of transforming growth factor beta2 production (GO:0032909)|response to drug (GO:0042493)|response to hypoxia (GO:0001666)|response to progesterone (GO:0032570)|response to wounding (GO:0009611)|salivary gland morphogenesis (GO:0007435)|signal transduction by phosphorylation (GO:0023014)|SMAD protein import into nucleus (GO:0007184)|somatic stem cell division (GO:0048103)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	axon (GO:0030424)|endosome (GO:0005768)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|platelet alpha granule lumen (GO:0031093)	beta-amyloid binding (GO:0001540)|cytokine activity (GO:0005125)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta receptor binding (GO:0005160)|type II transforming growth factor beta receptor binding (GO:0005114)			breast(1)|endometrium(1)|large_intestine(11)|lung(15)|upper_aerodigestive_tract(2)|urinary_tract(1)	31				all cancers(67;0.0459)|OV - Ovarian serous cystadenocarcinoma(81;0.049)|GBM - Glioblastoma multiforme(131;0.0776)		GCCTGCGAGCGCGAGAGGAGC	0.577													G|||	4	0.000798722	0.0	0.0029	5008	,	,		17473	0.0		0.002	False		,,,				2504	0.0				p.R91H		Atlas-SNP	.											.	TGFB2	102	.	0			c.G272A						PASS	.	G	HIS/ARG,HIS/ARG	5,4393		0,5,2194	23.0	21.0	22.0		272,272	5.4	1.0	1	dbSNP_119	22	43,8543		1,41,4251	yes	missense,missense	TGFB2	NM_001135599.2,NM_003238.3	29,29	1,46,6445	AA,AG,GG		0.5008,0.1137,0.3697	possibly-damaging,possibly-damaging	91/443,91/415	218520315	48,12936	2199	4293	6492	SO:0001583	missense	7042	exon1			GCGAGCGCGAGAG	M19154	CCDS1521.1, CCDS44318.1	1q41	2014-01-30			ENSG00000092969	ENSG00000092969		"""Endogenous ligands"""	11768	protein-coding gene	gene with protein product	"""prepro-transforming growth factor beta-2"""	190220					Standard	NM_003238		Approved		uc001hln.3	P61812	OTTHUMG00000039521	ENST00000366930.4:c.272G>A	1.37:g.218520315G>A	ENSP00000355897:p.Arg91His	99.0	0.0	0		116.0	56.0	0.482759	NM_003238	B4DKC5|P08112|Q15579|Q15581|Q4VAV9	Missense_Mutation	SNP	ENST00000366930.4	37	CCDS1521.1	3	0.0013736263736263737	0	0.0	2	0.0055248618784530384	0	0.0	1	0.0013192612137203166	G	29.8	5.041172	0.93685	0.001137	0.005008	ENSG00000092969	ENST00000366930;ENST00000366929	T;T	0.64618	-0.11;-0.11	5.45	5.45	0.79879	Transforming growth factor-beta, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.68311	0.2987	L	0.60455	1.87	0.80722	D	1	D;D;D	0.89917	0.995;0.984;1.0	P;P;D	0.81914	0.855;0.767;0.995	T	0.71941	-0.4440	10	0.52906	T	0.07	.	13.7098	0.62661	0.0732:0.0:0.9268:0.0	rs10482721	91;91;92	P61812-2;P61812;Q59EG9	.;TGFB2_HUMAN;.	H	91	ENSP00000355897:R91H;ENSP00000355896:R91H	ENSP00000355896:R91H	R	+	2	0	TGFB2	216586938	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.548000	0.73896	2.837000	0.97791	0.591000	0.81541	CGC	G|0.996;A|0.004	0.004	strong		0.577	TGFB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095359.2	NM_003238	
BRAF	673	hgsc.bcm.edu	37	7	140449150	140449150	+	Silent	SNP	T	T	C	rs9648696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:140449150T>C	ENST00000288602.6	-	16	1989	c.1929A>G	c.(1927-1929)ggA>ggG	p.G643G		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	643	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPKK activity (GO:0000186)|CD4-positive, alpha-beta T cell differentiation (GO:0043367)|cellular response to calcium ion (GO:0071277)|cellular response to drug (GO:0035690)|fibroblast growth factor receptor signaling pathway (GO:0008543)|long-term synaptic potentiation (GO:0060291)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of fibroblast migration (GO:0010764)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic vesicle exocytosis (GO:2000301)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gene expression (GO:0010628)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|positive T cell selection (GO:0043368)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell proliferation (GO:0042127)|response to cAMP (GO:0051591)|response to epidermal growth factor (GO:0070849)|response to peptide hormone (GO:0043434)|small GTPase mediated signal transduction (GO:0007264)|somatic stem cell maintenance (GO:0035019)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cell body (GO:0044297)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)		SLC45A3/BRAF(2)|AGTRAP/BRAF(2)|FAM131B_ENST00000443739/BRAF(7)|AKAP9_ENST00000356239/BRAF(10)|KIAA1549/BRAF(703)|FCHSD1/BRAF(2)	NS(588)|adrenal_gland(3)|autonomic_ganglia(3)|biliary_tract(29)|bone(7)|breast(21)|central_nervous_system(99)|cervix(6)|endometrium(33)|eye(72)|gastrointestinal_tract_(site_indeterminate)(2)|genital_tract(4)|haematopoietic_and_lymphoid_tissue(436)|kidney(3)|large_intestine(6953)|liver(17)|lung(192)|oesophagus(4)|ovary(275)|pancreas(15)|pituitary(1)|prostate(25)|salivary_gland(1)|skin(6285)|small_intestine(12)|soft_tissue(40)|stomach(11)|testis(7)|thyroid(12220)|upper_aerodigestive_tract(13)|urinary_tract(3)	27380	Melanoma(164;0.00956)				Dabrafenib(DB08912)|Regorafenib(DB08896)|Sorafenib(DB00398)|Vemurafenib(DB08881)	ACAGAACAATTCCAAATGCAT	0.348		61	"""Mis, T, O"""	"""AKAP9, KIAA1549"""	"""melanoma, colorectal, papillary thyroid, borderline ov, Non small-cell lung cancer (NSCLC), cholangiocarcinoma, pilocytic astrocytoma"""		Cardio-facio-cutaneous syndrome		Cardiofaciocutaneous syndrome				C|||	1758	0.351038	0.7451	0.1585	5008	,	,		17576	0.1825		0.1531	False		,,,				2504	0.3323				p.G643G	Colon(40;35 892 2973 5743 27438)	Atlas-SNP	.		Dom	yes		7	7q34	673	v-raf murine sarcoma viral oncogene homolog B1	yes	E	.	BRAF	36346	.	0			c.A1929G						PASS	.	C		2904,1502	476.8+/-357.7	963,978,262	105.0	108.0	107.0		1929	2.1	1.0	7	dbSNP_119	107	1258,7342	758.6+/-407.5	114,1030,3156	no	coding-synonymous	BRAF	NM_004333.4		1077,2008,3418	CC,CT,TT		14.6279,34.0899,32.0006		643/767	140449150	4162,8844	2203	4300	6503	SO:0001819	synonymous_variant	673	exon16	Familial Cancer Database	CFC, CFCS	AACAATTCCAAAT	M95712	CCDS5863.1	7q34	2014-09-17	2014-06-26		ENSG00000157764	ENSG00000157764			1097	protein-coding gene	gene with protein product		164757	"""v-raf murine sarcoma viral oncogene homolog B"""			2284096, 1565476	Standard	NM_004333		Approved	BRAF1	uc003vwc.4	P15056	OTTHUMG00000157457	ENST00000288602.6:c.1929A>G	7.37:g.140449150T>C		121.0	0.0	0		141.0	84.0	0.595745	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Silent	SNP	ENST00000288602.6	37	CCDS5863.1	611	0.27976190476190477	355	0.7215447154471545	58	0.16022099447513813	91	0.1590909090909091	107	0.14116094986807387	C	9.723	1.160251	0.21454	0.659101	0.146279	ENSG00000157764	ENST00000496384	.	.	.	5.02	2.11	0.27256	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	1.0	.	.	.	.	.	.	T	0.33317	-0.9873	3	.	.	.	.	5.8585	0.18732	0.0:0.5864:0.1264:0.2872	rs9648696;rs10238189;rs60896634	.	.	.	G	251	.	.	E	-	2	0	BRAF	140095619	1.000000	0.71417	0.998000	0.56505	0.947000	0.59692	1.503000	0.35715	-0.010000	0.14271	-0.355000	0.07637	GAA	T|0.696;C|0.304	0.304	strong		0.348	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
ZNF324	25799	hgsc.bcm.edu	37	19	58983321	58983321	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:58983321C>T	ENST00000536459.2	+	4	2171	c.1462C>T	c.(1462-1464)Cgc>Tgc	p.R488C	ZNF324_ENST00000196482.3_Missense_Mutation_p.R488C|ZNF324_ENST00000535298.1_Missense_Mutation_p.R265C|ZNF446_ENST00000596341.1_5'Flank			O75467	Z324A_HUMAN	zinc finger protein 324	488					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(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|liver(1)|lung(2)|prostate(2)|urinary_tract(2)	16		all_cancers(17;1.81e-17)|all_epithelial(17;1.21e-12)|Lung NSC(17;2.8e-05)|all_lung(17;0.000139)|Colorectal(82;0.000147)|Renal(17;0.00528)|all_neural(62;0.0133)|Ovarian(87;0.156)|Medulloblastoma(540;0.232)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0164)|Lung(386;0.179)		GCAGTGTGGCCGCGCCTTCCG	0.692																																					p.R488C		Atlas-SNP	.											ZNF324,NS,carcinoma,-2,1	ZNF324	46	1	0			c.C1462T						PASS	.						32.0	34.0	34.0					19																	58983321		2201	4299	6500	SO:0001583	missense	25799	exon4			TGTGGCCGCGCCT	AF060503	CCDS12981.1	19q13.43	2013-01-08				ENSG00000083812		"""Zinc fingers, C2H2-type"", ""-"""	14096	protein-coding gene	gene with protein product							Standard	NM_014347		Approved	ZF5128, ZNF324A	uc002qsw.2	O75467		ENST00000536459.2:c.1462C>T	19.37:g.58983321C>T	ENSP00000444812:p.Arg488Cys	27.0	0.0	0		36.0	14.0	0.388889	NM_014347	B3KRX1	Missense_Mutation	SNP	ENST00000536459.2	37	CCDS12981.1	.	.	.	.	.	.	.	.	.	.	C	13.54	2.268427	0.40095	.	.	ENSG00000083812	ENST00000196482;ENST00000536459;ENST00000539101;ENST00000535298	T;T;T	0.19806	2.12;2.12;2.12	3.84	3.84	0.44239	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.39475	N	0.001353	T	0.46386	0.1390	M	0.87547	2.89	0.45108	D	0.998126	D	0.69078	0.997	P	0.62740	0.906	T	0.53933	-0.8368	10	0.87932	D	0	.	11.5508	0.50719	0.0:1.0:0.0:0.0	.	488	O75467	Z324A_HUMAN	C	488;488;478;265	ENSP00000196482:R488C;ENSP00000444812:R488C;ENSP00000439588:R265C	ENSP00000196482:R488C	R	+	1	0	ZNF324	63675133	0.016000	0.18221	0.998000	0.56505	0.157000	0.22087	0.719000	0.25881	2.433000	0.82419	0.400000	0.26472	CGC	.	.	none		0.692	ZNF324-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467044.1	NM_014347	
SDR42E1	93517	hgsc.bcm.edu	37	16	82033022	82033022	+	Silent	SNP	A	A	G	rs11861598	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:82033022A>G	ENST00000328945.5	-	3	1003	c.876T>C	c.(874-876)ttT>ttC	p.F292F	SDR42E1_ENST00000534209.1_5'Flank	NM_145168.2	NP_660151.2	Q8WUS8	D42E1_HUMAN	short chain dehydrogenase/reductase family 42E, member 1	292					steroid biosynthetic process (GO:0006694)	integral component of membrane (GO:0016021)	3-beta-hydroxy-delta5-steroid dehydrogenase activity (GO:0003854)			NS(2)|endometrium(1)|lung(4)|skin(3)	10						TCTCTGTTAGAAAAGCAAAGC	0.483													A|||	243	0.0485224	0.1596	0.0173	5008	,	,		20516	0.001		0.0129	False		,,,				2504	0.0061				p.F292F		Atlas-SNP	.											.	SDR42E1	26	.	0			c.T876C						PASS	.	A		538,3326		32,474,1426	70.0	68.0	69.0		876	4.3	1.0	16	dbSNP_120	69	77,8211		0,77,4067	no	coding-synonymous	SDR42E1	NM_145168.2		32,551,5493	GG,GA,AA		0.9291,13.9234,5.0609		292/394	82033022	615,11537	1932	4144	6076	SO:0001819	synonymous_variant	93517	exon3			TGTTAGAAAAGCA	AF161368	CCDS42205.1	16q23.3	2011-09-14				ENSG00000184860	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Extended SDR fold"""	29834	protein-coding gene	gene with protein product						19027726	Standard	NM_145168		Approved	HSPC105	uc002fgu.3	Q8WUS8		ENST00000328945.5:c.876T>C	16.37:g.82033022A>G		56.0	0.0	0		51.0	31.0	0.607843	NM_145168	B2RDS1|Q9P0D1	Silent	SNP	ENST00000328945.5	37	CCDS42205.1																																																																																			A|0.956;G|0.044	0.044	strong		0.483	SDR42E1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388081.2	NM_145168	
NLRP7	199713	hgsc.bcm.edu	37	19	55451256	55451256	+	Missense_Mutation	SNP	G	G	T	rs79513034	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451256G>T	ENST00000590030.1	-	3	971	c.931C>A	c.(931-933)Ctc>Atc	p.L311I	NLRP7_ENST00000448121.2_Missense_Mutation_p.L311I|NLRP7_ENST00000340844.2_Missense_Mutation_p.L311I|NLRP7_ENST00000328092.5_Missense_Mutation_p.L311I|NLRP7_ENST00000446217.1_Missense_Mutation_p.L339I|NLRP7_ENST00000588756.1_Missense_Mutation_p.L311I|NLRP7_ENST00000592784.1_Missense_Mutation_p.L311I			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	311	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.			QL -> RI (in Ref. 4; AAI09126). {ECO:0000305}.			ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		TGCGCCAGGAGCTGGAGGTCC	0.627													.|||	26	0.00519169	0.0015	0.0029	5008	,	,		16625	0.0		0.0219	False		,,,				2504	0.0				p.L311I		Atlas-SNP	.											.	NLRP7	411	.	0			c.C931A						PASS	.	G	ILE/LEU,ILE/LEU,ILE/LEU	3,4403	6.2+/-15.9	0,3,2200	38.0	38.0	38.0		931,931,931	-1.9	0.0	19	dbSNP_131	38	135,8465	60.2+/-122.0	1,133,4166	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	5,5,5	1,136,6366	TT,TG,GG		1.5698,0.0681,1.061	benign,benign,benign	311/1038,311/1010,311/981	55451256	138,12868	2203	4300	6503	SO:0001583	missense	199713	exon4			CCAGGAGCTGGAG	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.931C>A	19.37:g.55451256G>T	ENSP00000465520:p.Leu311Ile	92.0	0.0	0		92.0	37.0	0.402174	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	4.165	0.029214	0.08054	6.81E-4	0.015698	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.78246	-1.16;-1.16;-1.16;-1.16	1.77	-1.85	0.07784	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.46678	0.1405	L	0.39397	1.21	0.09310	N	1	P;P;P	0.39601	0.68;0.68;0.63	B;B;B	0.40066	0.318;0.318;0.212	T	0.47045	-0.9147	9	0.17369	T	0.5	.	3.7385	0.08520	0.2934:0.4095:0.2972:0.0	.	339;311;311	E7EPM2;Q8WX94;Q8WX94-2	.;NALP7_HUMAN;.	I	311;311;311;339	ENSP00000329568:L311I;ENSP00000409137:L311I;ENSP00000339491:L311I;ENSP00000414273:L339I	ENSP00000329568:L311I	L	-	1	0	NLRP7	60143068	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.029000	0.12329	-0.432000	0.07297	-0.368000	0.07277	CTC	G|0.989;T|0.011	0.011	strong		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
TCEA3	6920	hgsc.bcm.edu	37	1	23720501	23720501	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:23720501C>T	ENST00000450454.2	-	8	796	c.690G>A	c.(688-690)acG>acA	p.T230T		NM_003196.1	NP_003187.1	O75764	TCEA3_HUMAN	transcription elongation factor A (SII), 3	230	TFIIS central. {ECO:0000255|PROSITE- ProRule:PRU00651}.				regulation of DNA-templated transcription, elongation (GO:0032784)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	7		Colorectal(325;3.46e-05)|Lung NSC(340;4.16e-05)|all_lung(284;6.68e-05)|Renal(390;0.000219)|Breast(348;0.00262)|Ovarian(437;0.0054)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|OV - Ovarian serous cystadenocarcinoma(117;1.6e-25)|Colorectal(126;8.32e-08)|COAD - Colon adenocarcinoma(152;4.29e-06)|GBM - Glioblastoma multiforme(114;9e-05)|BRCA - Breast invasive adenocarcinoma(304;0.00112)|KIRC - Kidney renal clear cell carcinoma(1967;0.00424)|STAD - Stomach adenocarcinoma(196;0.0145)|READ - Rectum adenocarcinoma(331;0.0686)|Lung(427;0.0963)|LUSC - Lung squamous cell carcinoma(448;0.198)		ACTTCATGTCCGTGCTCTTGA	0.632																																					p.T230T		Atlas-SNP	.											.	TCEA3	20	.	0			c.G690A						PASS	.						68.0	69.0	69.0					1																	23720501		1970	4143	6113	SO:0001819	synonymous_variant	6920	exon8			CATGTCCGTGCTC	AJ223473	CCDS44086.1	1p36.11	2011-01-25			ENSG00000204219	ENSG00000204219			11615	protein-coding gene	gene with protein product		604128				9790746	Standard	NM_003196		Approved	TFIIS.H	uc021oig.1	O75764	OTTHUMG00000003233	ENST00000450454.2:c.690G>A	1.37:g.23720501C>T		92.0	0.0	0		109.0	26.0	0.238532	NM_003196	A8K2K7|Q5DR83	Silent	SNP	ENST00000450454.2	37	CCDS44086.1																																																																																			.	.	none		0.632	TCEA3-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000008911.2	NM_003196	
COL6A2	1292	hgsc.bcm.edu	37	21	47537804	47537804	+	Missense_Mutation	SNP	C	C	G	rs199929757	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:47537804C>G	ENST00000300527.4	+	12	1174	c.1070C>G	c.(1069-1071)cCg>cGg	p.P357R	COL6A2_ENST00000397763.1_Missense_Mutation_p.P357R|COL6A2_ENST00000310645.5_Missense_Mutation_p.P357R|COL6A2_ENST00000357838.4_Missense_Mutation_p.P357R|COL6A2_ENST00000409416.1_Missense_Mutation_p.P357R	NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	357	Triple-helical region.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|protein heterotrimerization (GO:0070208)|response to glucose (GO:0009749)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)|vesicle (GO:0031982)				NS(1)|breast(1)|central_nervous_system(7)|endometrium(7)|kidney(5)|liver(1)|lung(15)|ovary(2)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	43	Breast(49;0.245)			Colorectal(79;0.0303)|READ - Rectum adenocarcinoma(84;0.0649)		GACGGTTACCCGGGGGAAGCA	0.682													C|||	3	0.000599042	0.0	0.0014	5008	,	,		16264	0.0		0.002	False		,,,				2504	0.0				p.P357R		Atlas-SNP	.											.	COL6A2	351	.	0			c.C1070G						PASS	.	C	ARG/PRO,ARG/PRO,ARG/PRO	2,4388	2.1+/-5.4	0,2,2193	50.0	48.0	48.0		1070,1070,1070	2.6	0.1	21		48	14,8574	9.1+/-34.3	0,14,4280	yes	missense,missense,missense	COL6A2	NM_001849.3,NM_058174.2,NM_058175.2	103,103,103	0,16,6473	GG,GC,CC		0.163,0.0456,0.1233	benign,benign,benign	357/1020,357/919,357/829	47537804	16,12962	2195	4294	6489	SO:0001583	missense	1292	exon12			GTTACCCGGGGGA	M20777	CCDS13728.1, CCDS13729.1, CCDS13730.1	21q22.3	2014-09-17			ENSG00000142173	ENSG00000142173		"""Collagens"""	2212	protein-coding gene	gene with protein product		120240					Standard	NM_001849		Approved		uc002zia.1	P12110	OTTHUMG00000090489	ENST00000300527.4:c.1070C>G	21.37:g.47537804C>G	ENSP00000300527:p.Pro357Arg	48.0	0.0	0		45.0	31.0	0.688889	NM_058175	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	.	.	.	.	.	.	.	.	.	.	C	2.941	-0.218840	0.06101	4.56E-4	0.00163	ENSG00000142173	ENST00000300527;ENST00000357838;ENST00000310645;ENST00000409416;ENST00000397763	D;D;D;D;D	0.96885	-4.16;-4.16;-4.16;-4.16;-4.16	4.46	2.59	0.31030	.	0.302904	0.36303	N	0.002665	D	0.94463	0.8218	L	0.46741	1.465	0.49915	D	0.999832	P;P;B	0.44877	0.81;0.845;0.111	P;P;B	0.47626	0.552;0.504;0.103	D	0.91557	0.5261	10	0.44086	T	0.13	-0.2304	9.7478	0.40457	0.0:0.8421:0.0:0.1579	.	357;357;357	P12110;P12110-2;P12110-3	CO6A2_HUMAN;.;.	R	357	ENSP00000300527:P357R;ENSP00000350497:P357R;ENSP00000312529:P357R;ENSP00000387115:P357R;ENSP00000380870:P357R	ENSP00000300527:P357R	P	+	2	0	COL6A2	46362232	0.902000	0.30710	0.087000	0.20705	0.104000	0.19210	2.090000	0.41682	0.411000	0.25702	0.305000	0.20034	CCG	C|0.996;G|0.005	0.005	strong		0.682	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
PPIE	10450	hgsc.bcm.edu	37	1	40207580	40207580	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:40207580C>T	ENST00000324379.5	+	4	207	c.188C>T	c.(187-189)gCt>gTt	p.A63V	PPIE_ENST00000470213.1_Missense_Mutation_p.A63V|PPIE_ENST00000372830.1_Missense_Mutation_p.A63V|PPIE_ENST00000480169.1_3'UTR|PPIE_ENST00000356511.2_Missense_Mutation_p.A63V	NM_006112.3	NP_006103.1	Q9UNP9	PPIE_HUMAN	peptidylprolyl isomerase E (cyclophilin E)	63	Poly-Ala.|RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mRNA splicing, via spliceosome (GO:0000398)|positive regulation of viral genome replication (GO:0045070)|protein folding (GO:0006457)|regulation of transcription, DNA-templated (GO:0006355)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	cyclosporin A binding (GO:0016018)|nucleotide binding (GO:0000166)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			kidney(3)|large_intestine(2)|lung(2)|prostate(1)|urinary_tract(1)	9	all_cancers(7;1.63e-13)|all_lung(5;2.27e-16)|all_epithelial(6;1.35e-15)|Lung NSC(20;1.49e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.87e-18)|Epithelial(16;2.7e-17)|all cancers(16;5.5e-16)|LUSC - Lung squamous cell carcinoma(16;0.000261)|Lung(16;0.000457)			GCTGCAGCAGCTATCGACAAC	0.423																																					p.A63V		Atlas-SNP	.											.	PPIE	33	.	0			c.C188T						PASS	.						146.0	146.0	146.0					1																	40207580		2203	4300	6503	SO:0001583	missense	10450	exon4			CAGCAGCTATCGA	AF042385	CCDS442.1, CCDS443.1, CCDS53299.1	1p32	2013-02-12			ENSG00000084072	ENSG00000084072		"""RNA binding motif (RRM) containing"""	9258	protein-coding gene	gene with protein product	"""peptidyl-prolyl cis-trans isomerase E"", ""cyclophilin 33"", ""cyclophilin E"", ""PPIase E"", ""rotamase E"", ""peptidylprolyl isomerase E, isoform 1"""	602435				9747881	Standard	NM_203456		Approved	CyP-33, MGC3736, MGC111222	uc001cdw.3	Q9UNP9	OTTHUMG00000009248	ENST00000324379.5:c.188C>T	1.37:g.40207580C>T	ENSP00000312769:p.Ala63Val	149.0	0.0	0		182.0	81.0	0.445055	NM_006112	B2R971|O43634|O43635|Q32Q72|Q3S611|Q5TGA0|Q5TGA2|Q5TGA3|Q9UIZ5	Missense_Mutation	SNP	ENST00000324379.5	37	CCDS443.1	.	.	.	.	.	.	.	.	.	.	C	33	5.255577	0.95336	.	.	ENSG00000084072	ENST00000324379;ENST00000356511;ENST00000470213;ENST00000372830	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	4.7	4.7	0.59300	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	0.000000	0.85682	D	0.000000	D	0.93716	0.7992	M	0.84082	2.675	0.80722	D	1	D;D;D	0.76494	0.999;0.971;0.995	D;P;D	0.74023	0.982;0.783;0.951	D	0.94503	0.7711	10	0.87932	D	0	-15.1861	17.7685	0.88485	0.0:1.0:0.0:0.0	.	63;63;63	Q5TGA3;Q9UNP9-2;Q9UNP9	.;.;PPIE_HUMAN	V	63	ENSP00000312769:A63V;ENSP00000348904:A63V;ENSP00000431714:A63V;ENSP00000361918:A63V	ENSP00000312769:A63V	A	+	2	0	PPIE	39980167	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	6.808000	0.75206	2.619000	0.88677	0.561000	0.74099	GCT	.	.	none		0.423	PPIE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025642.2	NM_006112	
SPATA25	128497	hgsc.bcm.edu	37	20	44515244	44515244	+	Missense_Mutation	SNP	C	C	T	rs146744825	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:44515244C>T	ENST00000372519.3	-	2	640	c.596G>A	c.(595-597)cGg>cAg	p.R199Q		NM_080608.3	NP_542175.1	Q9BR10	SPT25_HUMAN	spermatogenesis associated 25	199					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											CTGCTCCCACCGCGCCCCCTC	0.612													c|||	57	0.0113818	0.0015	0.0764	5008	,	,		16944	0.0		0.002	False		,,,				2504	0.0				p.R199Q		Atlas-SNP	.											.	.	.	.	0			c.G596A						PASS	.	T	GLN/ARG	13,4393	20.2+/-43.8	0,13,2190	65.0	70.0	68.0		596	-5.7	0.0	20	dbSNP_134	68	22,8578	16.6+/-54.9	0,22,4278	yes	missense	C20orf165	NM_080608.3	43	0,35,6468	TT,TC,CC		0.2558,0.2951,0.2691	benign	199/228	44515244	35,12971	2203	4300	6503	SO:0001583	missense	128497	exon2			TCCCACCGCGCCC	AL008726	CCDS13383.1	20q13.12	2011-11-24	2011-11-24	2011-11-24	ENSG00000149634	ENSG00000149634			16158	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 165"""	C20orf165		19240080	Standard	NM_080608		Approved	dJ337O18.8, TSG23	uc002xqf.3	Q9BR10	OTTHUMG00000032628	ENST00000372519.3:c.596G>A	20.37:g.44515244C>T	ENSP00000361597:p.Arg199Gln	72.0	0.0	0		84.0	41.0	0.488095	NM_080608		Missense_Mutation	SNP	ENST00000372519.3	37	CCDS13383.1	34	0.015567765567765568	1	0.0020325203252032522	32	0.08839779005524862	0	0.0	1	0.0013192612137203166	c	0.495	-0.873413	0.02570	0.002951	0.002558	ENSG00000149634	ENST00000372519	T	0.40756	1.02	5.55	-5.74	0.02391	.	1.042410	0.07602	N	0.923760	T	0.00754	0.0025	N	0.11560	0.145	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.33085	-0.9882	10	0.09338	T	0.73	-0.1318	15.7642	0.78114	0.0:0.2044:0.0:0.7956	.	199	Q9BR10	CT165_HUMAN	Q	199	ENSP00000361597:R199Q	ENSP00000361597:R199Q	R	-	2	0	C20orf165	43948651	0.000000	0.05858	0.002000	0.10522	0.099000	0.18886	-1.573000	0.02134	-1.357000	0.02180	-1.552000	0.00895	CGG	C|0.994;T|0.006	0.006	strong		0.612	SPATA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079541.1		
SLC30A4	7782	hgsc.bcm.edu	37	15	45778828	45778828	+	Silent	SNP	G	G	A	rs145466606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:45778828G>A	ENST00000261867.4	-	7	1430	c.1116C>T	c.(1114-1116)gcC>gcT	p.A372A	RP11-519G16.3_ENST00000558536.1_RNA|RP11-519G16.3_ENST00000560647.1_RNA	NM_013309.4	NP_037441.2	O14863	ZNT4_HUMAN	solute carrier family 30 (zinc transporter), member 4	372					regulation of sequestering of zinc ion (GO:0061088)|response to toxic substance (GO:0009636)|zinc ion homeostasis (GO:0055069)|zinc ion transmembrane transport (GO:0071577)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	zinc ion transmembrane transporter activity (GO:0005385)			endometrium(3)|large_intestine(2)|lung(8)|prostate(1)|stomach(1)	15		Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.58e-16)|GBM - Glioblastoma multiforme(94;2.15e-06)		TGTGAACTATGGCAGTAGATT	0.373																																					p.A372A		Atlas-SNP	.											.	SLC30A4	25	.	0			c.C1116T						PASS	.	G		1,4395		0,1,2197	131.0	135.0	134.0		1116	4.6	1.0	15	dbSNP_134	134	8,8588	6.4+/-24.3	0,8,4290	no	coding-synonymous	SLC30A4	NM_013309.4		0,9,6487	AA,AG,GG		0.0931,0.0227,0.0693		372/430	45778828	9,12983	2198	4298	6496	SO:0001819	synonymous_variant	7782	exon7			AACTATGGCAGTA		CCDS10125.1	15q21.1	2013-05-22			ENSG00000104154	ENSG00000104154		"""Solute carriers"""	11015	protein-coding gene	gene with protein product		602095		ZNT4			Standard	NM_013309		Approved		uc001zvj.3	O14863	OTTHUMG00000131439	ENST00000261867.4:c.1116C>T	15.37:g.45778828G>A		58.0	0.0	0		55.0	25.0	0.454545	NM_013309	Q8TC39	Silent	SNP	ENST00000261867.4	37	CCDS10125.1																																																																																			G|0.999;A|0.001	0.001	strong		0.373	SLC30A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254236.1		
MYO9A	4649	hgsc.bcm.edu	37	15	72170400	72170400	+	Missense_Mutation	SNP	G	G	A	rs148435644	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:72170400G>A	ENST00000356056.5	-	31	6384	c.5912C>T	c.(5911-5913)tCa>tTa	p.S1971L	MYO9A_ENST00000444904.1_Missense_Mutation_p.S1952L|MYO9A_ENST00000564571.1_Missense_Mutation_p.S1971L|MYO9A_ENST00000424560.1_Missense_Mutation_p.S2042L	NM_006901.3	NP_008832.2	B2RTY4	MYO9A_HUMAN	myosin IXA	1971	Tail.				regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|visual perception (GO:0007601)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|motor activity (GO:0003774)			NS(4)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(29)|lung(27)|ovary(1)|pancreas(1)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	88						TGTGCAATCTGAAGTCTTGAA	0.343													G|||	56	0.0111821	0.0	0.0317	5008	,	,		16355	0.0		0.0338	False		,,,				2504	0.0				p.S1971L		Atlas-SNP	.											.	MYO9A	203	.	0			c.C5912T						PASS	.	G	LEU/SER	24,4374	29.9+/-59.1	1,22,2176	62.0	64.0	63.0		5912	0.1	0.5	15	dbSNP_134	63	287,8307	105.6+/-166.5	6,275,4016	yes	missense	MYO9A	NM_006901.2	145	7,297,6192	AA,AG,GG		3.3395,0.5457,2.3938	benign	1971/2549	72170400	311,12681	2199	4297	6496	SO:0001583	missense	4649	exon31			CAATCTGAAGTCT	AF117888	CCDS10239.1	15q22-q23	2011-09-27			ENSG00000066933	ENSG00000066933		"""Myosins / Myosin superfamily : Class IX"""	7608	protein-coding gene	gene with protein product		604875				10409426	Standard	NM_006901		Approved	FLJ11061, FLJ13244, MGC71859	uc002atl.5	B2RTY4	OTTHUMG00000133440	ENST00000356056.5:c.5912C>T	15.37:g.72170400G>A	ENSP00000348349:p.Ser1971Leu	141.0	0.0	0		118.0	47.0	0.398305	NM_006901	B0I1T5|C9IYB3|C9JA86|Q14787|Q3YLD7|Q3YLD8|Q6P986|Q9H8T5|Q9NTG2|Q9NUY2|Q9UEP3|Q9UNJ2	Missense_Mutation	SNP	ENST00000356056.5	37	CCDS10239.1	36	0.016483516483516484	0	0.0	11	0.03038674033149171	0	0.0	25	0.032981530343007916	G	1.667	-0.509968	0.04231	0.005457	0.033395	ENSG00000066933	ENST00000356056;ENST00000424560;ENST00000444904	D;D;D	0.83591	-1.74;-1.73;-1.74	5.21	0.132	0.14762	.	.	.	.	.	T	0.31544	0.0800	N	0.01297	-0.9	0.20926	N	0.999826	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33979	-0.9847	9	0.22706	T	0.39	.	9.0444	0.36338	0.8015:0.0:0.1985:0.0	.	2042;1971	B2RTY4-4;B2RTY4	.;MYO9A_HUMAN	L	1971;2042;1952	ENSP00000348349:S1971L;ENSP00000399162:S2042L;ENSP00000398250:S1952L	ENSP00000348349:S1971L	S	-	2	0	MYO9A	69957454	0.999000	0.42202	0.470000	0.27216	0.826000	0.46750	2.312000	0.43726	0.174000	0.19809	0.591000	0.81541	TCA	G|0.977;A|0.023	0.023	strong		0.343	MYO9A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257308.1	NM_006901	
BEND7	222389	hgsc.bcm.edu	37	10	13481466	13481466	+	Silent	SNP	C	C	T	rs76298779	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:13481466C>T	ENST00000396900.2	-	9	1265	c.1266G>A	c.(1264-1266)ccG>ccA	p.P422P	BEND7_ENST00000486542.1_5'UTR|BEND7_ENST00000341083.3_Silent_p.P371P			Q8N7W2	BEND7_HUMAN	BEN domain containing 7	422						extracellular vesicular exosome (GO:0070062)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(2)|ovary(2)|prostate(1)|stomach(1)	17						CACTCCCACCCGGCAGAACAG	0.527													C|||	142	0.0283546	0.1036	0.0072	5008	,	,		21405	0.0		0.0	False		,,,				2504	0.0				p.P371P		Atlas-SNP	.											.	BEND7	85	.	0			c.G1113A						PASS	.	C		389,4017	193.6+/-218.7	15,359,1829	56.0	50.0	52.0		1113	1.2	0.0	10	dbSNP_131	52	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	BEND7	NM_152751.2		15,361,6127	TT,TC,CC		0.0233,8.8289,3.0063		371/469	13481466	391,12615	2203	4300	6503	SO:0001819	synonymous_variant	222389	exon9			CCCACCCGGCAGA	BC031618	CCDS7099.1, CCDS41490.1	10p14	2012-11-22	2008-10-03	2008-10-03	ENSG00000165626	ENSG00000165626		"""BEN domain containing"""	23514	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 30"""	C10orf30			Standard	NM_152751		Approved	FLJ40283	uc001imm.2	Q8N7W2	OTTHUMG00000017699	ENST00000396900.2:c.1266G>A	10.37:g.13481466C>T		60.0	0.0	0		66.0	30.0	0.454545	NM_152751	Q5SYY7|Q5SYY8|Q5SYY9|Q8N5T7	Silent	SNP	ENST00000396900.2	37																																																																																				C|0.965;T|0.035	0.035	strong		0.527	BEND7-202	KNOWN	basic	protein_coding	protein_coding		NM_152751	
BSN	8927	hgsc.bcm.edu	37	3	49689642	49689642	+	Missense_Mutation	SNP	C	C	T	rs150021639	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49689642C>T	ENST00000296452.4	+	5	2767	c.2653C>T	c.(2653-2655)Cct>Tct	p.P885S		NM_003458.3	NP_003449.2	Q9UPA5	BSN_HUMAN	bassoon presynaptic cytomatrix protein	885					synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|dendrite (GO:0030425)|neuron projection terminus (GO:0044306)|nucleus (GO:0005634)|presynaptic cytoskeletal matrix assembled at active zones (GO:0048788)	metal ion binding (GO:0046872)			breast(8)|central_nervous_system(2)|cervix(2)|endometrium(16)|kidney(3)|large_intestine(17)|lung(37)|ovary(7)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	106				BRCA - Breast invasive adenocarcinoma(193;6.66e-05)|KIRC - Kidney renal clear cell carcinoma(197;0.0032)|Kidney(197;0.00336)		CAGGCCTGAGCCTAGCCAAGA	0.652													C|||	34	0.00678914	0.0023	0.0058	5008	,	,		17544	0.0		0.0249	False		,,,				2504	0.002				p.P885S		Atlas-SNP	.											.	BSN	272	.	0			c.C2653T						PASS	.	C	SER/PRO	12,4394	19.1+/-41.9	0,12,2191	25.0	26.0	26.0		2653	1.3	1.0	3	dbSNP_134	26	152,8446	71.6+/-134.2	0,152,4147	yes	missense	BSN	NM_003458.3	74	0,164,6338	TT,TC,CC		1.7679,0.2724,1.2612	benign	885/3927	49689642	164,12840	2203	4299	6502	SO:0001583	missense	8927	exon5			CCTGAGCCTAGCC	AF052224	CCDS2800.1	3p21	2013-01-07	2013-01-07		ENSG00000164061	ENSG00000164061			1117	protein-coding gene	gene with protein product	"""zinc finger protein 231"", ""neuronal double zinc finger protein"""	604020	"""bassoon (presynaptic cytomatrix protein)"""	ZNF231		9806829, 10329005	Standard	NM_003458		Approved		uc003cxe.4	Q9UPA5	OTTHUMG00000133750	ENST00000296452.4:c.2653C>T	3.37:g.49689642C>T	ENSP00000296452:p.Pro885Ser	105.0	0.0	0		154.0	87.0	0.564935	NM_003458	O43161|Q7LGH3	Missense_Mutation	SNP	ENST00000296452.4	37	CCDS2800.1	24	0.01098901098901099	2	0.0040650406504065045	4	0.011049723756906077	0	0.0	18	0.023746701846965697	C	5.535	0.283703	0.10458	0.002724	0.017679	ENSG00000164061	ENST00000296452	T	0.15256	2.44	4.81	1.26	0.21427	.	1.048100	0.07469	N	0.901973	T	0.02083	0.0065	N	0.02011	-0.69	0.09310	N	0.99999	B	0.02656	0.0	B	0.04013	0.001	T	0.40757	-0.9546	10	0.08179	T	0.78	.	0.9669	0.01407	0.2611:0.3854:0.1373:0.2161	.	885	Q9UPA5	BSN_HUMAN	S	885	ENSP00000296452:P885S	ENSP00000296452:P885S	P	+	1	0	BSN	49664646	0.991000	0.36638	0.979000	0.43373	0.947000	0.59692	1.573000	0.36472	0.253000	0.21552	-0.225000	0.12378	CCT	C|0.987;T|0.013	0.013	strong		0.652	BSN-001	KNOWN	NMD_exception|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258164.1	NM_003458	
POMC	5443	hgsc.bcm.edu	37	2	25384113	25384113	+	Missense_Mutation	SNP	T	T	C	rs80326661	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:25384113T>C	ENST00000405623.1	-	3	1096	c.641A>G	c.(640-642)gAg>gGg	p.E214G	POMC_ENST00000380794.1_Missense_Mutation_p.E214G|POMC_ENST00000395826.2_Missense_Mutation_p.E214G|RP11-509E16.1_ENST00000567599.1_lincRNA|POMC_ENST00000264708.3_Missense_Mutation_p.E214G			P01189	COLI_HUMAN	proopiomelanocortin	214			E -> G (in dbSNP:rs80326661). {ECO:0000269|PubMed:9768693}.		cell-cell signaling (GO:0007267)|cellular pigmentation (GO:0033059)|cellular protein metabolic process (GO:0044267)|generation of precursor metabolites and energy (GO:0006091)|glucose homeostasis (GO:0042593)|negative regulation of tumor necrosis factor production (GO:0032720)|neuropeptide signaling pathway (GO:0007218)|peptide hormone processing (GO:0016486)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of appetite (GO:0032098)|regulation of blood pressure (GO:0008217)|regulation of corticosterone secretion (GO:2000852)|regulation of glycogen metabolic process (GO:0070873)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|peroxisomal matrix (GO:0005782)|secretory granule (GO:0030141)|secretory granule lumen (GO:0034774)	G-protein coupled receptor binding (GO:0001664)|hormone activity (GO:0005179)|receptor binding (GO:0005102)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(5)|ovary(1)	12	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)				Loperamide(DB00836)	GTCCTTCTTCTCGGCCGCCAC	0.697													T|||	7	0.00139776	0.0	0.0	5008	,	,		15787	0.0		0.007	False		,,,				2504	0.0				p.E214G	Colon(110;1515 1566 8452 10082 43216)	Atlas-SNP	.											POMC,colon,carcinoma,-1,1	POMC	33	1	0			c.A641G	GRCh37	CM984056	POMC	M	rs80326661	scavenged	.	T	GLY/GLU,GLY/GLU	6,4400	8.1+/-20.4	0,6,2197	24.0	26.0	25.0		641,641	-2.6	0.3	2	dbSNP_131	25	62,8538	35.9+/-90.5	0,62,4238	yes	missense,missense	POMC	NM_000939.2,NM_001035256.1	98,98	0,68,6435	CC,CT,TT		0.7209,0.1362,0.5228	possibly-damaging,possibly-damaging	214/268,214/268	25384113	68,12938	2203	4300	6503	SO:0001583	missense	5443	exon4			TTCTTCTCGGCCG		CCDS1717.1	2p23	2013-02-25	2008-07-31		ENSG00000115138	ENSG00000115138		"""Endogenous ligands"""	9201	protein-coding gene	gene with protein product	"""adrenocorticotropin"", ""beta-lipotropin"", ""alpha-melanocyte stimulating hormone"", ""beta-melanocyte stimulating hormone"", ""beta-endorphin"", ""adrenocorticotropic hormone"", ""opiomelanocortin prepropeptide"""	176830				6254047, 9620771	Standard	NM_001035256		Approved	MSH, POC, CLIP, ACTH, NPP, LPH	uc002rfz.1	P01189	OTTHUMG00000094764	ENST00000405623.1:c.641A>G	2.37:g.25384113T>C	ENSP00000384092:p.Glu214Gly	25.0	1.0	0.04		58.0	29.0	0.5	NM_001035256	P78442|Q53T23|Q9UD39|Q9UD40	Missense_Mutation	SNP	ENST00000405623.1	37	CCDS1717.1	6	0.0027472527472527475	0	0.0	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	T	8.778	0.927470	0.18056	0.001362	0.007209	ENSG00000115138	ENST00000380794;ENST00000405623;ENST00000264708;ENST00000395826;ENST00000449220	T;T;T;T;T	0.80033	-1.32;-1.32;-1.32;-1.32;-1.33	4.94	-2.56	0.06268	.	0.859913	0.10550	N	0.661521	T	0.65281	0.2676	M	0.80183	2.485	0.23657	N	0.997187	P	0.36086	0.536	B	0.27380	0.079	T	0.62685	-0.6802	10	0.87932	D	0	-23.9239	1.564	0.02601	0.3754:0.0782:0.2568:0.2896	.	214	P01189	COLI_HUMAN	G	214	ENSP00000370171:E214G;ENSP00000384092:E214G;ENSP00000264708:E214G;ENSP00000379170:E214G;ENSP00000387993:E214G	ENSP00000264708:E214G	E	-	2	0	POMC	25237617	0.001000	0.12720	0.348000	0.25681	0.190000	0.23558	-0.012000	0.12699	-0.317000	0.08677	-0.379000	0.06801	GAG	T|0.996;C|0.004	0.004	strong		0.697	POMC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211573.3	NM_001035256	
FLNA	2316	hgsc.bcm.edu	37	X	153594535	153594535	+	Missense_Mutation	SNP	G	G	A	rs36051194		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:153594535G>A	ENST00000369850.3	-	9	1522	c.1286C>T	c.(1285-1287)aCg>aTg	p.T429M	FLNA_ENST00000360319.4_Missense_Mutation_p.T429M|FLNA_ENST00000344736.4_Missense_Mutation_p.T429M|FLNA_ENST00000422373.1_Missense_Mutation_p.T429M	NM_001110556.1	NP_001104026.1	P21333	FLNA_HUMAN	filamin A, alpha	429			T -> M. {ECO:0000269|PubMed:12612583}.		actin crosslink formation (GO:0051764)|actin cytoskeleton reorganization (GO:0031532)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|cilium assembly (GO:0042384)|cytoplasmic sequestering of protein (GO:0051220)|early endosome to late endosome transport (GO:0045022)|epithelial to mesenchymal transition (GO:0001837)|establishment of protein localization (GO:0045184)|mRNA transcription from RNA polymerase II promoter (GO:0042789)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription factor import into nucleus (GO:0042993)|protein localization to cell surface (GO:0034394)|protein stabilization (GO:0050821)|receptor clustering (GO:0043113)|spindle assembly involved in mitosis (GO:0090307)	actin cytoskeleton (GO:0015629)|actin filament (GO:0005884)|apical dendrite (GO:0097440)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|Myb complex (GO:0031523)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)	actin filament binding (GO:0051015)|Fc-gamma receptor I complex binding (GO:0034988)|glycoprotein binding (GO:0001948)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|Rac GTPase binding (GO:0048365)|Ral GTPase binding (GO:0017160)|Rho GTPase binding (GO:0017048)|signal transducer activity (GO:0004871)|small GTPase binding (GO:0031267)|transcription factor binding (GO:0008134)			breast(6)	6	all_cancers(53;3.7e-16)|all_epithelial(53;2.97e-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)					AGGCTCTACCGTGCCCTTCTG	0.682													G|||	16	0.00423841	0.0	0.0058	3775	,	,		12254	0.0		0.0119	False		,,,				2504	0.0				p.T429M		Atlas-SNP	.											.	FLNA	373	.	0			c.C1286T	GRCh37	CM065185	FLNA	M	rs36051194	PASS	.		MET/THR,MET/THR	9,3653		0,7,2,1539,568	48.0	53.0	51.0		1286,1286	3.8	0.3	X	dbSNP_126	51	107,6462		0,74,33,2305,1778	yes	missense,missense	FLNA	NM_001110556.1,NM_001456.3	81,81	0,81,35,3844,2346	AA,AG,A,GG,G		1.6289,0.2458,1.1338	probably-damaging,probably-damaging	429/2648,429/2640	153594535	116,10115	2116	4190	6306	SO:0001583	missense	2316	exon9			TCTACCGTGCCCT	X70082	CCDS44021.1, CCDS48194.1	Xq28	2009-07-23	2009-07-23		ENSG00000196924	ENSG00000196924			3754	protein-coding gene	gene with protein product	"""actin binding protein 280"""	300017	"""filamin A, alpha (actin binding protein 280)"""	FLN1, FLN, OPD2, OPD1		8406501, 12612583	Standard	NM_001456		Approved	ABP-280	uc004fkk.2	P21333	OTTHUMG00000022712	ENST00000369850.3:c.1286C>T	X.37:g.153594535G>A	ENSP00000358866:p.Thr429Met	52.0	0.0	0		56.0	52.0	0.928571	NM_001456	E9KL45|Q5HY53|Q5HY55|Q8NF52	Missense_Mutation	SNP	ENST00000369850.3	37	CCDS48194.1	8	0.004822182037371911	0	0.0	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	G	4.764	0.142126	0.09083	0.002458	0.016289	ENSG00000196924	ENST00000360319;ENST00000369852;ENST00000422373;ENST00000369850;ENST00000344736	D;D;D;D	0.84800	-1.9;-1.9;-1.9;-1.9	4.68	3.81	0.43845	Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	D	0.83626	0.5295	M	0.78285	2.405	0.80722	D	1	P;D	0.69078	0.839;0.997	B;D	0.62955	0.281;0.909	D	0.84840	0.0807	10	0.40728	T	0.16	.	11.1083	0.48216	0.096:0.0:0.904:0.0	rs36051194	429;429	P21333-2;P21333	.;FLNA_HUMAN	M	429;402;429;429;429	ENSP00000353467:T429M;ENSP00000416926:T429M;ENSP00000358866:T429M;ENSP00000358863:T429M	ENSP00000358863:T429M	T	-	2	0	FLNA	153247729	1.000000	0.71417	0.266000	0.24541	0.038000	0.13279	3.356000	0.52269	0.763000	0.33175	0.464000	0.42555	ACG	G|0.995;A|0.005	0.005	strong		0.682	FLNA-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058942.3		
USP4	7375	hgsc.bcm.edu	37	3	49321424	49321424	+	Missense_Mutation	SNP	T	T	C	rs41290700	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:49321424T>C	ENST00000265560.4	-	19	2582	c.2536A>G	c.(2536-2538)Atc>Gtc	p.I846V	USP4_ENST00000351842.4_Missense_Mutation_p.I799V	NM_003363.3	NP_003354.2	Q13107	UBP4_HUMAN	ubiquitin specific peptidase 4 (proto-oncogene)	846	USP.				negative regulation of protein ubiquitination (GO:0031397)|protein deubiquitination (GO:0016579)|protein localization to cell surface (GO:0034394)|regulation of protein stability (GO:0031647)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	adenosine receptor binding (GO:0031685)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|liver(1)|lung(10)|ovary(3)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	33		Ovarian(412;0.00308)|Myeloproliferative disorder(1037;0.0255)|Hepatocellular(537;0.121)		OV - Ovarian serous cystadenocarcinoma(275;4.74e-26)|Kidney(197;2.22e-07)|KIRC - Kidney renal clear cell carcinoma(197;5.14e-06)|BRCA - Breast invasive adenocarcinoma(193;9.46e-05)		ACCCACCTGATTGGGAATTCT	0.463													T|||	15	0.00299521	0.0008	0.0058	5008	,	,		22007	0.0		0.005	False		,,,				2504	0.0051				p.I846V		Atlas-SNP	.											.	USP4	72	.	0			c.A2536G						PASS	.	T	VAL/ILE,VAL/ILE	8,4398	14.3+/-33.2	0,8,2195	133.0	130.0	131.0		2536,2395	3.3	1.0	3	dbSNP_127	131	59,8541	36.9+/-92.0	0,59,4241	yes	missense,missense	USP4	NM_003363.3,NM_199443.2	29,29	0,67,6436	CC,CT,TT		0.686,0.1816,0.5151	benign,benign	846/964,799/917	49321424	67,12939	2203	4300	6503	SO:0001583	missense	7375	exon19			ACCTGATTGGGAA	U20657	CCDS2793.1, CCDS2794.1, CCDS58832.1	3p21.3	2005-10-11	2005-08-08		ENSG00000114316	ENSG00000114316		"""Ubiquitin-specific peptidases"""	12627	protein-coding gene	gene with protein product		603486	"""ubiquitin specific protease 4 (proto-oncogene)"""	UNP		12838346, 9464533	Standard	NM_199443		Approved	Unph	uc003cwq.2	Q13107	OTTHUMG00000156825	ENST00000265560.4:c.2536A>G	3.37:g.49321424T>C	ENSP00000265560:p.Ile846Val	114.0	0.0	0		147.0	54.0	0.367347	NM_003363	A8K6Y0|C9IY91|O43452|O43453|Q08AK8	Missense_Mutation	SNP	ENST00000265560.4	37	CCDS2793.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	T|T	12.07|12.07	1.827377|1.827377	0.32329|0.32329	0.001816|0.001816	0.00686|0.00686	ENSG00000114316|ENSG00000114316	ENST00000351842;ENST00000265560|ENST00000431357	T;T|.	0.33654|.	1.4;1.4|.	5.63|5.63	3.35|3.35	0.38373|0.38373	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);|.	0.097121|.	0.64402|.	N|.	0.000002|.	T|T	0.31104|0.31104	0.0786|0.0786	N|N	0.26092|0.26092	0.79|0.79	0.80722|0.80722	D|D	1|1	B;B;B|.	0.02656|.	0.0;0.0;0.0|.	B;B;B|.	0.12156|.	0.003;0.007;0.003|.	T|T	0.10200|0.10200	-1.0640|-1.0640	10|5	0.29301|.	T|.	0.29|.	.|.	4.7623|4.7623	0.13113|0.13113	0.0:0.5066:0.0:0.4934|0.0:0.5066:0.0:0.4934	rs41290700|rs41290700	799;846;846|.	Q13107-2;Q13107;Q08AK7|.	.;UBP4_HUMAN;.|.	V|S	799;846|584	ENSP00000341028:I799V;ENSP00000265560:I846V|.	ENSP00000265560:I846V|.	I|N	-|-	1|2	0|0	USP4|USP4	49296428|49296428	0.963000|0.963000	0.33076|0.33076	0.998000|0.998000	0.56505|0.56505	0.743000|0.743000	0.42351|0.42351	1.848000|1.848000	0.39309|0.39309	1.176000|1.176000	0.42840|0.42840	-0.408000|-0.408000	0.06270|0.06270	ATC|AAT	T|0.995;C|0.005	0.005	strong		0.463	USP4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346069.1	NM_199443	
KY	339855	hgsc.bcm.edu	37	3	134369767	134369767	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:134369767G>A	ENST00000423778.2	-	1	97	c.36C>T	c.(34-36)atC>atT	p.I12I	KY_ENST00000503669.1_Silent_p.I12I|KY_ENST00000508956.1_Silent_p.I12I	NM_178554.4	NP_848649.3	Q8NBH2	KY_HUMAN	kyphoscoliosis peptidase	12					muscle organ development (GO:0007517)|neuromuscular junction development (GO:0007528)	cytoskeleton (GO:0005856)|Z disc (GO:0030018)	peptidase activity (GO:0008233)			central_nervous_system(1)|endometrium(3)|kidney(1)|lung(12)|ovary(2)|upper_aerodigestive_tract(2)	21						GCAGCATGTCGATAGATACAG	0.647																																					p.I12I		Atlas-SNP	.											.	KY	92	.	0			c.C36T						PASS	.						58.0	65.0	63.0					3																	134369767		2131	4236	6367	SO:0001819	synonymous_variant	339855	exon1			CATGTCGATAGAT	AK090526	CCDS46920.1	3q22.1	2010-11-23			ENSG00000174611	ENSG00000174611			26576	protein-coding gene	gene with protein product		605739					Standard	NM_178554		Approved	FLJ33207	uc010hty.3	Q8NBH2	OTTHUMG00000159788	ENST00000423778.2:c.36C>T	3.37:g.134369767G>A		107.0	0.0	0		190.0	37.0	0.194737	NM_178554	B7Z1S4|Q6ZT15	Silent	SNP	ENST00000423778.2	37	CCDS46920.1																																																																																			.	.	none		0.647	KY-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357320.1	NM_178554	
CDH9	1007	hgsc.bcm.edu	37	5	26885964	26885964	+	Silent	SNP	T	T	G	rs35328154	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:26885964T>G	ENST00000231021.4	-	11	1813	c.1641A>C	c.(1639-1641)gcA>gcC	p.A547A		NM_016279.3	NP_057363.3	Q9ULB4	CADH9_HUMAN	cadherin 9, type 2 (T1-cadherin)	547	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(25)|lung(80)|ovary(5)|prostate(4)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	137						TCATGATTCCTGCTGTATTAT	0.318													T|||	49	0.00978435	0.0	0.0187	5008	,	,		17688	0.0		0.0109	False		,,,				2504	0.0256				p.A547A	Melanoma(8;187 585 15745 40864 52829)	Atlas-SNP	.											.	CDH9	305	.	0			c.A1641C						PASS	.	T		7,4399	11.4+/-27.6	0,7,2196	55.0	58.0	57.0		1641	-4.3	1.0	5	dbSNP_126	57	82,8518	44.0+/-102.2	0,82,4218	no	coding-synonymous	CDH9	NM_016279.3		0,89,6414	GG,GT,TT		0.9535,0.1589,0.6843		547/790	26885964	89,12917	2203	4300	6503	SO:0001819	synonymous_variant	1007	exon11			GATTCCTGCTGTA	AB035302	CCDS3893.1	5p14	2010-01-26			ENSG00000113100	ENSG00000113100		"""Cadherins / Major cadherins"""	1768	protein-coding gene	gene with protein product		609974				2059658	Standard	NM_016279		Approved		uc003jgs.1	Q9ULB4	OTTHUMG00000090671	ENST00000231021.4:c.1641A>C	5.37:g.26885964T>G		72.0	0.0	0		60.0	26.0	0.433333	NM_016279	Q3B7I5	Silent	SNP	ENST00000231021.4	37	CCDS3893.1																																																																																			T|0.992;G|0.008	0.008	strong		0.318	CDH9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207352.1	NM_016279	
UGT2B17	7367	hgsc.bcm.edu	37	4	69433479	69433479	+	Splice_Site	SNP	C	C	G	rs145791375	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:69433479C>G	ENST00000317746.2	-	1	766	c.724G>C	c.(724-726)Gga>Cga	p.G242R		NM_001077.3	NP_001068.1	O75795	UDB17_HUMAN	UDP glucuronosyltransferase 2 family, polypeptide B17	242					cellular glucuronidation (GO:0052695)|steroid metabolic process (GO:0008202)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	glucuronosyltransferase activity (GO:0015020)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(14)|ovary(2)|prostate(1)	30					Losartan(DB00678)	CACGACTTACCTAGAACTTCA	0.323													C|||	2	0.000399361	0.0	0.0	5008	,	,		10536	0.0		0.002	False		,,,				2504	0.0				p.G242R	Melanoma(18;649 833 28984 37818 38500)	Atlas-SNP	.											.	UGT2B17	34	.	0			c.G724C						PASS	.	C	ARG/GLY	2,4188		0,2,2093	100.0	109.0	106.0		724	2.7	0.7	4	dbSNP_134	106	6,7868		2,2,3933	yes	missense-near-splice	UGT2B17	NM_001077.3	125	2,4,6026	GG,GC,CC		0.0762,0.0477,0.0663		242/531	69433479	8,12056	2095	3937	6032	SO:0001630	splice_region_variant	7367	exon1			ACTTACCTAGAAC	U59209	CCDS3523.1	4q13	2008-02-05	2005-07-20		ENSG00000197888	ENSG00000197888		"""UDP glucuronosyltransferases"""	12547	protein-coding gene	gene with protein product		601903	"""UDP glycosyltransferase 2 family, polypeptide B17"""			8798464	Standard	NM_001077		Approved		uc021xov.1	O75795	OTTHUMG00000129305	ENST00000317746.2:c.724+1G>C	4.37:g.69433479C>G		0.0	0.0	.		127.0	59.0	0.464567	NM_001077		Missense_Mutation	SNP	ENST00000317746.2	37	CCDS3523.1	.	.	.	.	.	.	.	.	.	.	c	14.66	2.602420	0.46423	4.77E-4	7.62E-4	ENSG00000197888	ENST00000317746	T	0.60424	0.19	2.66	2.66	0.31614	.	0.000000	0.64402	U	0.000005	T	0.69967	0.3170	M	0.85777	2.775	0.30173	N	0.801107	.	.	.	.	.	.	T	0.70927	-0.4739	7	.	.	.	.	11.1206	0.48287	0.0:1.0:0.0:0.0	.	.	.	.	R	242	ENSP00000320401:G242R	.	G	-	1	0	UGT2B17	69116074	1.000000	0.71417	0.673000	0.29887	0.022000	0.10575	6.023000	0.70848	1.516000	0.48900	0.499000	0.49734	GGA	C|0.999;G|0.001	0.001	strong		0.323	UGT2B17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251436.1	NM_001077	Missense_Mutation
APC	324	hgsc.bcm.edu	37	5	112176756	112176756	+	Missense_Mutation	SNP	T	T	A	rs459552	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176756T>A	ENST00000457016.1	+	16	5845	c.5465T>A	c.(5464-5466)gTc>gAc	p.V1822D	APC_ENST00000257430.4_Missense_Mutation_p.V1822D|APC_ENST00000508376.2_Missense_Mutation_p.V1822D|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1822	Ser-rich.		V -> D (in dbSNP:rs459552). {ECO:0000269|PubMed:1651562, ECO:0000269|PubMed:1678319, ECO:0000269|PubMed:9950360, ECO:0000269|Ref.4}.		anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AATTCCAAGGTCTTCAATGAT	0.328		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			A|||	4334	0.865415	0.9909	0.8184	5008	,	,		19820	0.9008		0.7654	False		,,,				2504	0.7955				p.V1822D	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.T5465A	GRCh37	CM990164	APC	M	rs459552	PASS	.	A	ASP/VAL,ASP/VAL,ASP/VAL	4164,238	135.3+/-171.4	1973,218,10	67.0	63.0	64.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	5465,5465,5411	3.6	1.0	5	dbSNP_80	64	6579,2021	339.4+/-323.1	2529,1521,250	yes	missense,missense,missense	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	152,152,152	4502,1739,260	AA,AT,TT		23.5,5.4066,17.3743	benign,benign,benign	1822/2844,1822/2844,1804/2826	112176756	10743,2259	2201	4300	6501	SO:0001583	missense	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	CCAAGGTCTTCAA	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5465T>A	5.37:g.112176756T>A	ENSP00000413133:p.Val1822Asp	71.0	0.0	0		86.0	84.0	0.976744	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Missense_Mutation	SNP	ENST00000457016.1	37	CCDS4107.1	1883	0.8621794871794872	486	0.9878048780487805	296	0.8176795580110497	514	0.8986013986013986	587	0.7744063324538258	A	0.069	-1.206578	0.01568	0.945934	0.765	ENSG00000134982	ENST00000457016;ENST00000257430;ENST00000508376	D;D;D	0.87809	-2.3;-2.3;-2.3	6.07	3.59	0.41128	.	0.187419	0.47093	N	0.000244	T	0.00012	0.0000	N	0.01352	-0.895	0.40534	P	0.019048999999999983	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42085	-0.9472	8	.	.	.	-1.4078	9.3995	0.38424	0.6507:0.2365:0.0:0.1128	rs459552;rs52814776;rs56587573;rs459552	1824;1822	Q4LE70;P25054	.;APC_HUMAN	D	1822	ENSP00000413133:V1822D;ENSP00000257430:V1822D;ENSP00000427089:V1822D	.	V	+	2	0	APC	112204655	1.000000	0.71417	0.987000	0.45799	0.796000	0.44982	3.653000	0.54446	0.139000	0.18822	-0.265000	0.10407	GTC	T|0.151;A|0.849	0.849	strong		0.328	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
POLR1B	84172	hgsc.bcm.edu	37	2	113333238	113333238	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:113333238T>C	ENST00000263331.5	+	15	3920	c.3340T>C	c.(3340-3342)Tat>Cat	p.Y1114H	POLR1B_ENST00000409894.3_Missense_Mutation_p.Y931H|POLR1B_ENST00000417433.2_Missense_Mutation_p.Y1058H|POLR1B_ENST00000541869.1_Missense_Mutation_p.Y1152H|POLR1B_ENST00000537335.1_Missense_Mutation_p.Y903H	NM_019014.4	NP_061887.2	Q9H9Y6	RPA2_HUMAN	polymerase (RNA) I polypeptide B, 128kDa	1114					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(3)|endometrium(9)|kidney(2)|large_intestine(9)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42						TTCTGTGCCTTATGTTTTTCG	0.423																																					p.Y1114H	Ovarian(16;256 576 9537 23969 41147)	Atlas-SNP	.											.	POLR1B	95	.	0			c.T3340C						PASS	.						122.0	114.0	117.0					2																	113333238		2203	4300	6503	SO:0001583	missense	84172	exon15			GTGCCTTATGTTT	AK001678	CCDS2097.1, CCDS46395.1, CCDS62988.1, CCDS62989.1, CCDS62990.1	2q13	2013-01-21			ENSG00000125630	ENSG00000125630		"""RNA polymerase subunits"""	20454	protein-coding gene	gene with protein product		602000					Standard	NM_001137604		Approved	Rpo1-2, FLJ21921, FLJ10816, RPA2	uc002thw.2	Q9H9Y6	OTTHUMG00000131314	ENST00000263331.5:c.3340T>C	2.37:g.113333238T>C	ENSP00000263331:p.Tyr1114His	79.0	0.0	0		77.0	4.0	0.0519481	NM_019014	B7Z6Y7|B7Z823|F5GZX4|F8W898|Q2TAM4|Q585T5|Q6ZRR2|Q9H9D3	Missense_Mutation	SNP	ENST00000263331.5	37	CCDS2097.1	.	.	.	.	.	.	.	.	.	.	T	15.75	2.925462	0.52759	.	.	ENSG00000125630	ENST00000263331;ENST00000541869;ENST00000409894;ENST00000537335;ENST00000417433	T;T;T;T;T	0.79141	-1.24;-1.24;-1.24;-1.24;-1.24	5.37	5.37	0.77165	RNA polymerase Rpb2, domain 7 (1);	0.108910	0.64402	D	0.000004	D	0.87669	0.6235	M	0.78637	2.42	0.80722	D	1	P;D;B;B	0.76494	0.476;0.999;0.274;0.183	B;D;B;B	0.83275	0.178;0.996;0.225;0.2	D	0.88914	0.3361	10	0.62326	D	0.03	-21.3681	14.3792	0.66900	0.0:0.0:0.0:1.0	.	1152;931;1058;1114	F5GZX4;F8W898;Q9H9Y6-2;Q9H9Y6	.;.;.;RPA2_HUMAN	H	1114;1152;931;903;1058	ENSP00000263331:Y1114H;ENSP00000444136:Y1152H;ENSP00000387143:Y931H;ENSP00000437914:Y903H;ENSP00000405358:Y1058H	ENSP00000263331:Y1114H	Y	+	1	0	POLR1B	113049709	1.000000	0.71417	0.978000	0.43139	0.995000	0.86356	5.887000	0.69751	2.030000	0.59900	0.455000	0.32223	TAT	.	.	none		0.423	POLR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254083.1	NM_019014	
LCP2	3937	hgsc.bcm.edu	37	5	169675739	169675739	+	Missense_Mutation	SNP	A	A	G	rs187889192	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169675739A>G	ENST00000046794.5	-	21	2179	c.1564T>C	c.(1564-1566)Tac>Cac	p.Y522H	LCP2_ENST00000521416.1_Missense_Mutation_p.Y317H|C5orf58_ENST00000517575.1_Intron	NM_005565.3	NP_005556.1	Q13094	LCP2_HUMAN	lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)	522	SH2. {ECO:0000255|PROSITE- ProRule:PRU00191}.				blood coagulation (GO:0007596)|cytokine secretion (GO:0050663)|Fc-epsilon receptor signaling pathway (GO:0038095)|immune response (GO:0006955)|innate immune response (GO:0045087)|mast cell activation (GO:0045576)|platelet activation (GO:0030168)|T cell receptor signaling pathway (GO:0050852)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)				cervix(1)|endometrium(1)|kidney(3)|large_intestine(4)|lung(12)|ovary(1)|upper_aerodigestive_tract(1)	23	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0109)|all_neural(177;0.0146)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	OV - Ovarian serous cystadenocarcinoma(192;0.247)		GTGCACTGGTATCTGGAACCT	0.458													A|||	3	0.000599042	0.0008	0.0	5008	,	,		17968	0.0		0.002	False		,,,				2504	0.0				p.Y522H		Atlas-SNP	.											.	LCP2	133	.	0			c.T1564C						PASS	.	A	HIS/TYR	1,3959		0,1,1979	308.0	298.0	302.0		1564	3.1	1.0	5		302	42,8248		0,42,4103	yes	missense	LCP2	NM_005565.3	83	0,43,6082	GG,GA,AA		0.5066,0.0253,0.351	possibly-damaging	522/534	169675739	43,12207	1980	4145	6125	SO:0001583	missense	3937	exon21			ACTGGTATCTGGA		CCDS47339.1	5q35.1	2013-02-14	2002-08-29		ENSG00000043462	ENSG00000043462		"""SH2 domain containing"""	6529	protein-coding gene	gene with protein product	"""76 kDa tyrosine phosphoprotein"", ""SH2 domain-containing leukocyte protein of 76kD"""	601603	"""lymphocyte cytosolic protein 2 (SH2 domain-containing leukocyte protein of 76kD)"""	SLP76		7706237	Standard	NM_005565		Approved	SLP-76	uc003man.1	Q13094	OTTHUMG00000163121	ENST00000046794.5:c.1564T>C	5.37:g.169675739A>G	ENSP00000046794:p.Tyr522His	157.0	0.0	0		159.0	83.0	0.522013	NM_005565	A8KA25|Q53XV4	Missense_Mutation	SNP	ENST00000046794.5	37	CCDS47339.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	16.03	3.006340	0.54361	2.53E-4	0.005066	ENSG00000043462	ENST00000046794;ENST00000521416	T;T	0.42513	0.97;0.98	5.82	3.07	0.35406	SH2 motif (1);	0.191452	0.43260	D	0.000595	T	0.12050	0.0293	N	0.01874	-0.695	0.31418	N	0.674662	P;P	0.47910	0.902;0.902	B;B	0.44278	0.445;0.445	T	0.04216	-1.0968	10	0.29301	T	0.29	-19.8141	5.4042	0.16312	0.5846:0.0:0.0818:0.3337	.	317;522	E7ESF6;Q13094	.;LCP2_HUMAN	H	522;317	ENSP00000046794:Y522H;ENSP00000428871:Y317H	ENSP00000046794:Y522H	Y	-	1	0	LCP2	169608317	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	2.042000	0.41222	0.971000	0.38288	0.482000	0.46254	TAC	A|0.999;G|0.001	0.001	strong		0.458	LCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371727.1	NM_005565	
GPD1L	23171	hgsc.bcm.edu	37	3	32181723	32181723	+	Missense_Mutation	SNP	A	A	G	rs72552293	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:32181723A>G	ENST00000282541.5	+	4	571	c.370A>G	c.(370-372)Ata>Gta	p.I124V		NM_015141.3	NP_055956.1	Q8N335	GPD1L_HUMAN	glycerol-3-phosphate dehydrogenase 1-like	124			I -> V (in SIDS; significant reduction of sodium current when coexpressed with SCN5A in HEK cells; dbSNP:rs72552293). {ECO:0000269|PubMed:17967976}.		carbohydrate metabolic process (GO:0005975)|cellular lipid metabolic process (GO:0044255)|glycerol-3-phosphate catabolic process (GO:0046168)|glycerophospholipid biosynthetic process (GO:0046474)|NAD metabolic process (GO:0019674)|NADH metabolic process (GO:0006734)|negative regulation of peptidyl-serine phosphorylation (GO:0033137)|negative regulation of protein kinase C signaling (GO:0090038)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid metabolic process (GO:0006644)|positive regulation of protein localization to cell surface (GO:2000010)|positive regulation of sodium ion transport (GO:0010765)|regulation of heart rate (GO:0002027)|regulation of sodium ion transmembrane transporter activity (GO:2000649)|regulation of ventricular cardiac muscle cell membrane depolarization (GO:0060373)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|ventricular cardiac muscle cell action potential (GO:0086005)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycerol-3-phosphate dehydrogenase complex (GO:0009331)|plasma membrane (GO:0005886)	glycerol-3-phosphate dehydrogenase [NAD+] activity (GO:0004367)|ion channel binding (GO:0044325)|NAD binding (GO:0051287)|sodium channel regulator activity (GO:0017080)			large_intestine(4)|lung(7)|ovary(1)	12						CTTGTAGGGCATAGACGAGGG	0.483													A|||	4	0.000798722	0.0	0.0014	5008	,	,		20191	0.0		0.003	False		,,,				2504	0.0				p.I124V		Atlas-SNP	.											.	GPD1L	25	.	0			c.A370G	GRCh37	CM074889	GPD1L	M	rs72552293	PASS	.	A	VAL/ILE	0,4406		0,0,2203	172.0	184.0	180.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	370	3.9	1.0	3	dbSNP_130	180	14,8586	10.5+/-38.8	0,14,4286	yes	missense	GPD1L	NM_015141.3	29	0,14,6489	GG,GA,AA		0.1628,0.0,0.1076	benign	124/352	32181723	14,12992	2203	4300	6503	SO:0001583	missense	23171	exon4			TAGGGCATAGACG	D42047	CCDS33729.1	3p22.3	2014-09-17			ENSG00000152642	ENSG00000152642			28956	protein-coding gene	gene with protein product		611778				7788527	Standard	NM_015141		Approved	KIAA0089	uc003cew.3	Q8N335	OTTHUMG00000155846	ENST00000282541.5:c.370A>G	3.37:g.32181723A>G	ENSP00000282541:p.Ile124Val	92.0	0.0	0		110.0	42.0	0.381818	NM_015141	A8K9U3|Q14702|Q9BRM5	Missense_Mutation	SNP	ENST00000282541.5	37	CCDS33729.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	A	1.632	-0.518627	0.04171	0.0	0.001628	ENSG00000152642	ENST00000429432;ENST00000282541;ENST00000425459;ENST00000431009	T;T;T;T	0.59772	0.24;0.24;0.42;0.24	5.06	3.87	0.44632	Glycerol-3-phosphate dehydrogenase, NAD-dependent, N-terminal (1);NAD(P)-binding domain (1);	0.042492	0.85682	D	0.000000	T	0.31979	0.0814	N	0.11818	0.18	0.54753	A	0.999988	B	0.02656	0.0	B	0.04013	0.001	T	0.30679	-0.9970	9	0.10377	T	0.69	-17.6846	7.0731	0.25189	0.7746:0.15:0.0753:0.0	.	124	Q8N335	GPD1L_HUMAN	V	85;124;77;85	ENSP00000393861:I85V;ENSP00000282541:I124V;ENSP00000408770:I77V;ENSP00000416518:I85V	ENSP00000282541:I124V	I	+	1	0	GPD1L	32156727	0.908000	0.30866	0.992000	0.48379	0.825000	0.46686	2.058000	0.41374	0.979000	0.38497	0.533000	0.62120	ATA	A|0.998;G|0.002	0.002	strong		0.483	GPD1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341975.2	NM_015141	
MYPN	84665	hgsc.bcm.edu	37	10	69902800	69902800	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:69902800A>T	ENST00000358913.5	+	3	1494	c.1006A>T	c.(1006-1008)Aca>Tca	p.T336S	MYPN_ENST00000354393.2_Missense_Mutation_p.T61S|MYPN_ENST00000373675.3_Missense_Mutation_p.T336S|MYPN_ENST00000540630.1_Missense_Mutation_p.T336S	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	336	Ig-like 1.|Interaction with CARP.				sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)			breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						TGAAGAGGACACAGGACGCTA	0.443																																					p.T336S		Atlas-SNP	.											.	MYPN	189	.	0			c.A1006T						PASS	.						118.0	107.0	111.0					10																	69902800		2203	4300	6503	SO:0001583	missense	84665	exon3			GAGGACACAGGAC	AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1006A>T	10.37:g.69902800A>T	ENSP00000351790:p.Thr336Ser	58.0	0.0	0		64.0	33.0	0.515625	NM_032578	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	A	32	5.115153	0.94339	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630;ENST00000373675	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.59	5.59	0.84812	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.53286	0.1787	N	0.01188	-0.97	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;0.999;0.999	D;D;D;D	0.87578	0.987;0.996;0.998;0.996	T	0.64706	-0.6344	9	.	.	.	.	15.7811	0.78260	1.0:0.0:0.0:0.0	.	336;336;61;336	F5GWA6;Q86TC9-3;Q86TC9-2;Q86TC9	.;.;.;MYPN_HUMAN	S	61;61;336;336;336	ENSP00000346369:T61S;ENSP00000351790:T336S;ENSP00000441668:T336S;ENSP00000362779:T336S	.	T	+	1	0	MYPN	69572806	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.253000	0.95501	2.123000	0.65237	0.533000	0.62120	ACA	.	.	none		0.443	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1	NM_032578	
KIF1A	547	hgsc.bcm.edu	37	2	241702599	241702599	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:241702599G>A	ENST00000320389.7	-	20	2064	c.1906C>T	c.(1906-1908)Cag>Tag	p.Q636*	KIF1A_ENST00000498729.2_Nonsense_Mutation_p.Q645*	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	636					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		TCCATCTCCTGCTTCATGTCG	0.672																																					p.Q645X		Atlas-SNP	.											.	KIF1A	152	.	0			c.C1933T						PASS	.						24.0	27.0	26.0					2																	241702599		2151	4252	6403	SO:0001587	stop_gained	547	exon21			TCTCCTGCTTCAT	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.1906C>T	2.37:g.241702599G>A	ENSP00000322791:p.Gln636*	37.0	0.0	0		52.0	16.0	0.307692	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Nonsense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	G	42	9.413377	0.99164	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308;ENST00000404283	.	.	.	3.81	2.91	0.33838	.	0.000000	0.85682	U	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.05833	T	0.94	.	11.8555	0.52435	0.089:0.0:0.911:0.0	.	.	.	.	X	636;645;645;645	.	ENSP00000322791:Q636X	Q	-	1	0	KIF1A	241351272	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	7.644000	0.83416	0.695000	0.31675	0.467000	0.42956	CAG	.	.	none		0.672	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
PAK6	56924	hgsc.bcm.edu	37	15	40564441	40564441	+	Missense_Mutation	SNP	G	G	A	rs150100570	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40564441G>A	ENST00000542403.2	+	4	986	c.875G>A	c.(874-876)cGa>cAa	p.R292Q	PAK6_ENST00000455577.2_Missense_Mutation_p.R292Q|PAK6_ENST00000453867.1_Missense_Mutation_p.R292Q|PAK6_ENST00000441369.1_Missense_Mutation_p.R292Q|RP11-133K1.2_ENST00000558658.1_3'UTR|PAK6_ENST00000560346.1_Missense_Mutation_p.R292Q|PAK6_ENST00000260404.4_Missense_Mutation_p.R292Q	NM_001276717.1	NP_001263646.1	Q9NQU5	PAK6_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 6	292	Linker.				apoptotic process (GO:0006915)|cytoskeleton organization (GO:0007010)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|cervix(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(11)|ovary(2)|prostate(1)|skin(2)	24		all_cancers(109;1.13e-18)|all_epithelial(112;1.62e-15)|Lung NSC(122;5.67e-11)|all_lung(180;1.41e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0823)|Colorectal(260;0.117)		GBM - Glioblastoma multiforme(113;1.51e-05)|BRCA - Breast invasive adenocarcinoma(123;0.0544)		TCCTCTTTCCGACCGCCGCAG	0.637																																					p.R292Q		Atlas-SNP	.											PAK6,NS,adenocarcinoma,+1,1	PAK6	49	1	0			c.G875A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	0,4406		0,0,2203	68.0	84.0	79.0		875,875,875	3.1	0.9	15	dbSNP_134	79	16,8584	10.5+/-38.8	0,16,4284	yes	missense,missense,missense	PAK6	NM_001128628.1,NM_001128629.1,NM_020168.4	43,43,43	0,16,6487	AA,AG,GG		0.186,0.0,0.123	possibly-damaging,possibly-damaging,possibly-damaging	292/682,292/682,292/682	40564441	16,12990	2203	4300	6503	SO:0001583	missense	56924	exon5			CTTTCCGACCGCC	AF276893	CCDS10054.1, CCDS61590.1	15q14	2008-06-17	2008-06-17		ENSG00000137843	ENSG00000137843			16061	protein-coding gene	gene with protein product		608110	"""p21(CDKN1A)-activated kinase 6"""			11278661	Standard	NM_020168		Approved	PAK5	uc001zlb.3	Q9NQU5	OTTHUMG00000129921	ENST00000542403.2:c.875G>A	15.37:g.40564441G>A	ENSP00000439597:p.Arg292Gln	64.0	0.0	0		81.0	39.0	0.481481	NM_001128629	A8K2G2|B3KYB0|G5E9R2	Missense_Mutation	SNP	ENST00000542403.2	37	CCDS10054.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.529004	0.27387	0.0	0.00186	ENSG00000137843	ENST00000441369;ENST00000453867;ENST00000455577;ENST00000260404;ENST00000542403	T;T;T;T;T	0.74842	-0.81;-0.81;-0.88;-0.81;-0.81	5.02	3.14	0.36123	.	0.683340	0.13547	N	0.379732	T	0.57799	0.2078	L	0.27053	0.805	0.37769	D	0.926619	B;B	0.21905	0.037;0.062	B;B	0.10450	0.002;0.005	T	0.47947	-0.9077	10	0.15499	T	0.54	.	9.1394	0.36894	0.2362:0.0:0.7638:0.0	.	292;292	Q9NQU5;G5E9R2	PAK6_HUMAN;.	Q	292	ENSP00000406873:R292Q;ENSP00000401153:R292Q;ENSP00000409465:R292Q;ENSP00000260404:R292Q;ENSP00000439597:R292Q	ENSP00000260404:R292Q	R	+	2	0	PAK6	38351733	0.340000	0.24792	0.917000	0.36280	0.835000	0.47333	0.975000	0.29449	0.632000	0.30432	0.555000	0.69702	CGA	G|0.999;A|0.001	0.001	strong		0.637	PAK6-004	NOVEL	alternative_3_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000418355.1		
ANKS1A	23294	hgsc.bcm.edu	37	6	35048829	35048829	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:35048829G>A	ENST00000360359.3	+	17	2741	c.2603G>A	c.(2602-2604)gGg>gAg	p.G868E	ANKS1A_ENST00000470698.1_3'UTR|ANKS1A_ENST00000535627.1_Intron	NM_015245.2	NP_056060.2	Q92625	ANS1A_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1A	868					ephrin receptor signaling pathway (GO:0048013)|neuron remodeling (GO:0016322)|substrate-dependent cell migration (GO:0006929)	cytoplasm (GO:0005737)|neuron projection (GO:0043005)|nucleus (GO:0005634)				cervix(2)|endometrium(3)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	31						TCCTGCACTGGGCGGTCGGCA	0.617																																					p.G868E		Atlas-SNP	.											.	ANKS1A	123	.	0			c.G2603A						PASS	.						119.0	102.0	108.0					6																	35048829		2203	4300	6503	SO:0001583	missense	23294	exon17			GCACTGGGCGGTC	D86982	CCDS4798.1	6p21.31	2013-01-10	2006-02-17	2006-02-17	ENSG00000064999	ENSG00000064999		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	20961	protein-coding gene	gene with protein product		608994	"""ankyrin repeat and SAM domain containing 1"", ""ankyrin repeat and sterile alpha motif domain containing 1"""	ANKS1		9039502	Standard	NM_015245		Approved	KIAA0229	uc003ojx.4	Q92625	OTTHUMG00000014559	ENST00000360359.3:c.2603G>A	6.37:g.35048829G>A	ENSP00000353518:p.Gly868Glu	80.0	0.0	0		100.0	27.0	0.27	NM_015245	A2RUC1|B4DQW8|Q5JYI9|Q5SYR2|Q86WQ7	Missense_Mutation	SNP	ENST00000360359.3	37	CCDS4798.1	.	.	.	.	.	.	.	.	.	.	G	15.46	2.838812	0.51057	.	.	ENSG00000064999	ENST00000360359;ENST00000373990	T	0.40756	1.02	5.28	2.37	0.29283	.	0.133303	0.33591	N	0.004742	T	0.49508	0.1561	M	0.68952	2.095	0.80722	D	1	D;B;P	0.67145	0.996;0.104;0.884	D;B;B	0.63703	0.917;0.04;0.432	T	0.59521	-0.7439	10	0.87932	D	0	-8.113	15.4348	0.75137	0.0:0.4714:0.5286:0.0	.	194;194;868	Q49AR9;E7EM84;Q92625	.;.;ANS1A_HUMAN	E	868;194	ENSP00000353518:G868E	ENSP00000353518:G868E	G	+	2	0	ANKS1A	35156807	0.765000	0.28485	0.008000	0.14137	0.101000	0.19017	0.901000	0.28445	0.561000	0.29186	-0.211000	0.12701	GGG	.	.	none		0.617	ANKS1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040262.1	XM_166478	
DISP2	85455	hgsc.bcm.edu	37	15	40656724	40656724	+	Silent	SNP	C	C	T	rs72733418	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:40656724C>T	ENST00000267889.3	+	4	669	c.582C>T	c.(580-582)ccC>ccT	p.P194P		NM_033510.1	NP_277045.1	A7MBM2	DISP2_HUMAN	dispatched homolog 2 (Drosophila)	194					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)		CCCGGCTGCCCGACTTCTCCA	0.637													C|||	38	0.00758786	0.0212	0.0014	5008	,	,		18401	0.0		0.008	False		,,,				2504	0.001				p.P194P		Atlas-SNP	.											.	DISP2	86	.	0			c.C582T						PASS	.	C		120,4286	88.2+/-126.9	0,120,2083	56.0	59.0	58.0		582	-9.8	0.0	15	dbSNP_130	58	66,8534	40.8+/-97.7	0,66,4234	no	coding-synonymous	DISP2	NM_033510.1		0,186,6317	TT,TC,CC		0.7674,2.7236,1.4301		194/1402	40656724	186,12820	2203	4300	6503	SO:0001819	synonymous_variant	85455	exon4			GCTGCCCGACTTC	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.582C>T	15.37:g.40656724C>T		40.0	0.0	0		70.0	43.0	0.614286	NM_033510	Q6AHW3|Q9C0C1	Silent	SNP	ENST00000267889.3	37	CCDS10056.1																																																																																			C|0.987;T|0.013	0.013	strong		0.637	DISP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252249.1	NM_033510	
SLC7A5	8140	hgsc.bcm.edu	37	16	87885369	87885369	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:87885369C>T	ENST00000261622.4	-	2	690	c.625G>A	c.(625-627)Gcc>Acc	p.A209T	SLC7A5_ENST00000565644.1_5'UTR	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	209					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	ATGATCAGGGCCAGGGCCAGG	0.667																																					p.A209T		Atlas-SNP	.											.	SLC7A5	28	.	0			c.G625A						PASS	.						40.0	38.0	38.0					16																	87885369		2197	4300	6497	SO:0001583	missense	8140	exon2			TCAGGGCCAGGGC	AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"""CD molecules"", ""Solute carriers"""	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.625G>A	16.37:g.87885369C>T	ENSP00000261622:p.Ala209Thr	175.0	0.0	0		171.0	48.0	0.280702	NM_003486	Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Missense_Mutation	SNP	ENST00000261622.4	37	CCDS10964.1	.	.	.	.	.	.	.	.	.	.	C	17.40	3.378913	0.61735	.	.	ENSG00000103257	ENST00000261622	D	0.90620	-2.7	5.17	5.17	0.71159	Amino acid permease domain (1);	0.499292	0.20200	N	0.097117	D	0.88157	0.6361	L	0.56280	1.765	0.23361	N	0.997833	B	0.22003	0.063	B	0.19666	0.026	T	0.81609	-0.0855	10	0.72032	D	0.01	.	12.7141	0.57105	0.1645:0.8355:0.0:0.0	.	209	Q01650	LAT1_HUMAN	T	209	ENSP00000261622:A209T	ENSP00000261622:A209T	A	-	1	0	SLC7A5	86442870	0.088000	0.21588	0.710000	0.30468	0.944000	0.59088	1.045000	0.30341	2.386000	0.81285	0.655000	0.94253	GCC	.	.	none		0.667	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486	
DCPS	28960	hgsc.bcm.edu	37	11	126215507	126215507	+	Silent	SNP	G	G	A	rs139354381	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:126215507G>A	ENST00000263579.4	+	6	1342	c.1013G>A	c.(1012-1014)tGa>tAa	p.*338*	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	0					cellular response to menadione (GO:0036245)|deadenylation-dependent decapping of nuclear-transcribed mRNA (GO:0000290)|exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA cis splicing, via spliceosome (GO:0045292)|mRNA metabolic process (GO:0016071)|negative regulation of programmed cell death (GO:0043069)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	m7G(5')pppN diphosphatase activity (GO:0050072)|RNA 7-methylguanosine cap binding (GO:0000340)			endometrium(3)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|urinary_tract(1)	17	all_hematologic(175;0.145)	Breast(109;0.00156)|Lung NSC(97;0.00949)|all_lung(97;0.0101)|Medulloblastoma(222;0.0425)|all_neural(223;0.0604)		BRCA - Breast invasive adenocarcinoma(274;1.15e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.08)		CAGCAAAGCTGAATTAACTCA	0.502													G|||	5	0.000998403	0.0	0.0043	5008	,	,		18179	0.0		0.002	False		,,,				2504	0.0				p.X338X		Atlas-SNP	.											.	DCPS	33	.	0			c.G1013A						PASS	.	G		5,4397	8.1+/-20.4	0,5,2196	73.0	78.0	76.0		1013	5.2	1.0	11	dbSNP_134	76	73,8523	39.8+/-96.3	0,73,4225	no	coding-synonymous	DCPS	NM_014026.3		0,78,6421	AA,AG,GG		0.8492,0.1136,0.6001		338/338	126215507	78,12920	2201	4298	6499	SO:0001819	synonymous_variant	28960	exon6			AAAGCTGAATTAA	AF077201	CCDS8473.1	11q24	2008-02-05			ENSG00000110063	ENSG00000110063			29812	protein-coding gene	gene with protein product		610534				12198172, 14523240	Standard	NM_014026		Approved	HSPC015, HINT-5, HSL1	uc001qdp.3	Q96C86	OTTHUMG00000165829	ENST00000263579.4:c.1013G>A	11.37:g.126215507G>A		23.0	0.0	0		21.0	10.0	0.47619	NM_014026	Q8NHL8|Q9Y2S5	Silent	SNP	ENST00000263579.4	37	CCDS8473.1																																																																																			G|0.995;A|0.005	0.005	strong		0.502	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
WWC3	55841	hgsc.bcm.edu	37	X	10085227	10085227	+	Silent	SNP	T	T	C	rs7058143	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:10085227T>C	ENST00000380861.4	+	11	1519	c.1128T>C	c.(1126-1128)cgT>cgC	p.R376R	WWC3_ENST00000454666.1_Silent_p.R376R	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	376	Ser-rich.				negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CCTCCAGCCGTGGGTCTCTGG	0.672													C|||	774	0.205033	0.5401	0.0648	3775	,	,		12301	0.0		0.0149	False		,,,				2504	0.0				p.R376R		Atlas-SNP	.											.	WWC3	142	.	0			c.T1128C						PASS	.	C		2272,1558		575,780,342,277,224	36.0	44.0	41.0		1128	-3.3	0.3	X	dbSNP_116	41	142,6583		0,105,37,2323,1832	no	coding-synonymous	WWC3	NM_015691.3		575,885,379,2600,2056	CC,CT,C,TT,T		2.1115,40.6789,22.8707		376/1093	10085227	2414,8141	2198	4297	6495	SO:0001819	synonymous_variant	55841	exon11			CAGCCGTGGGTCT	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.1128T>C	X.37:g.10085227T>C		49.0	0.0	0		39.0	39.0	1	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	37	CCDS14136.1																																																																																			0|0.004;C|0.221	0.221	strong		0.672	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
TPO	7173	hgsc.bcm.edu	37	2	1426844	1426844	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:1426844G>T	ENST00000345913.4	+	3	213	c.122G>T	c.(121-123)aGc>aTc	p.S41I	TPO_ENST00000382201.3_Missense_Mutation_p.S41I|TPO_ENST00000349624.3_Missense_Mutation_p.S41I|TPO_ENST00000382198.1_Missense_Mutation_p.S41I|TPO_ENST00000329066.4_Missense_Mutation_p.S41I|TPO_ENST00000346956.3_Missense_Mutation_p.S41I|TPO_ENST00000539820.1_Missense_Mutation_p.S41I|TPO_ENST00000382269.3_Missense_Mutation_p.S41I|TPO_ENST00000497517.2_Intron|TPO_ENST00000337415.3_Missense_Mutation_p.S41I	NM_000547.5	NP_000538.3	P07202	PERT_HUMAN	thyroid peroxidase	41					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)	CGTGTCTCTAGCGTCTTGGAG	0.572																																					p.S41I		Atlas-SNP	.											.	TPO	224	.	0			c.G122T						PASS	.						124.0	99.0	108.0					2																	1426844		2203	4300	6503	SO:0001583	missense	7173	exon3			TCTCTAGCGTCTT		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.122G>T	2.37:g.1426844G>T	ENSP00000318820:p.Ser41Ile	75.0	0.0	0		58.0	37.0	0.637931	NM_175719	P09934|P09935|Q8IUL0|Q8NF94|Q8NF95|Q8NF96|Q8NF97|Q8TCI9	Missense_Mutation	SNP	ENST00000345913.4	37	CCDS1643.1	.	.	.	.	.	.	.	.	.	.	G	10.16	1.274665	0.23307	.	.	ENSG00000115705	ENST00000382269;ENST00000337415;ENST00000345913;ENST00000346956;ENST00000349624;ENST00000539820;ENST00000329066;ENST00000382201;ENST00000423320;ENST00000382198	T;T;T;T;T;T;T;T;T;T	0.58358	0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34;0.34	3.72	-0.276	0.12902	.	2.391560	0.01734	N	0.029009	T	0.59865	0.2225	L	0.54323	1.7	0.09310	N	1	P;P;D;P;P	0.65815	0.846;0.545;0.995;0.911;0.761	P;B;P;P;B	0.58172	0.466;0.206;0.834;0.563;0.276	T	0.40001	-0.9586	10	0.33940	T	0.23	-1.8372	3.7622	0.08609	0.3281:0.185:0.4869:0.0	.	41;41;41;41;41	P07202-4;P07202-5;E9PFM6;P07202-2;P07202	.;.;.;.;PERT_HUMAN	I	41	ENSP00000371704:S41I;ENSP00000337263:S41I;ENSP00000318820:S41I;ENSP00000263886:S41I;ENSP00000332044:S41I;ENSP00000444840:S41I;ENSP00000329869:S41I;ENSP00000371636:S41I;ENSP00000390994:S41I;ENSP00000371633:S41I	ENSP00000329869:S41I	S	+	2	0	TPO	1405851	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.511000	0.22739	-0.075000	0.12798	-0.373000	0.07131	AGC	.	.	none		0.572	TPO-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000206594.2	NM_000547	
ZHX2	22882	hgsc.bcm.edu	37	8	123964819	123964819	+	Missense_Mutation	SNP	G	G	A	rs9649951	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:123964819G>A	ENST00000314393.4	+	3	1904	c.1069G>A	c.(1069-1071)Gtg>Atg	p.V357M		NM_014943.3	NP_055758.1	Q9Y6X8	ZHX2_HUMAN	zinc fingers and homeoboxes 2	357	Required for homodimerization.|Required for interaction with NFYA.|Required for nuclear localization.|Required for repressor activity.		V -> M (in dbSNP:rs9649951).		mRNA catabolic process (GO:0006402)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(15)|ovary(1)|prostate(1)|skin(4)|stomach(3)|urinary_tract(1)	45	Lung NSC(37;2e-09)|Ovarian(258;0.0205)|Hepatocellular(40;0.105)		STAD - Stomach adenocarcinoma(47;0.00527)			CCCCACAAAGGTGACGCAGCC	0.617													G|||	50	0.00998403	0.0015	0.0144	5008	,	,		17314	0.001		0.0258	False		,,,				2504	0.0112				p.V357M	Esophageal Squamous(94;1056 1388 11767 13799 49639)	Atlas-SNP	.											.	ZHX2	106	.	0			c.G1069A						PASS	.	G	MET/VAL	41,4365	45.3+/-79.5	0,41,2162	77.0	64.0	69.0		1069	1.4	0.4	8	dbSNP_119	69	373,8227	123.1+/-182.0	6,361,3933	yes	missense	ZHX2	NM_014943.3	21	6,402,6095	AA,AG,GG		4.3372,0.9305,3.1831	benign	357/838	123964819	414,12592	2203	4300	6503	SO:0001583	missense	22882	exon3			ACAAAGGTGACGC	AB020661	CCDS6336.1	8q24.13	2012-03-09	2004-01-23		ENSG00000178764	ENSG00000178764		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	18513	protein-coding gene	gene with protein product		609185	"""zinc-fingers and homeoboxes 2"""			10048485, 12741956	Standard	XM_005250837		Approved	KIAA0854	uc003ypk.1	Q9Y6X8	OTTHUMG00000165077	ENST00000314393.4:c.1069G>A	8.37:g.123964819G>A	ENSP00000314709:p.Val357Met	69.0	0.0	0		83.0	36.0	0.433735	NM_014943		Missense_Mutation	SNP	ENST00000314393.4	37	CCDS6336.1	29	0.013278388278388278	1	0.0020325203252032522	10	0.027624309392265192	1	0.0017482517482517483	17	0.022427440633245383	G	6.657	0.489767	0.12702	0.009305	0.043372	ENSG00000178764	ENST00000314393	T	0.17370	2.28	5.62	1.42	0.22433	.	0.551628	0.20995	N	0.081968	T	0.02119	0.0066	N	0.22421	0.69	0.09310	N	0.999999	B	0.02656	0.0	B	0.04013	0.001	T	0.24404	-1.0161	10	0.40728	T	0.16	-6.6533	8.5687	0.33556	0.636:0.0:0.364:0.0	rs9649951;rs9649951	357	Q9Y6X8	ZHX2_HUMAN	M	357	ENSP00000314709:V357M	ENSP00000314709:V357M	V	+	1	0	ZHX2	124034000	1.000000	0.71417	0.392000	0.26245	0.782000	0.44232	1.466000	0.35310	0.008000	0.14787	-0.361000	0.07541	GTG	G|0.974;A|0.026	0.026	strong		0.617	ZHX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381709.1	NM_014943	
PSMD7	5713	hgsc.bcm.edu	37	16	74334016	74334016	+	Silent	SNP	C	C	T	rs140080000	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:74334016C>T	ENST00000219313.4	+	2	218	c.78C>T	c.(76-78)atC>atT	p.I26I	PSMD7_ENST00000540379.1_5'UTR|PSMD7_ENST00000568615.2_Silent_p.I26I|PSMD7_ENST00000567958.1_Silent_p.I26I	NM_002811.4	NP_002802.2	P51665	PSMD7_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 7	26	MPN.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|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 peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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 polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)	protein homodimerization activity (GO:0042803)			breast(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(6)|prostate(1)	15						CATTCAGAATCGGCAAGGTTG	0.418													C|||	3	0.000599042	0.0	0.0	5008	,	,		19257	0.0		0.002	False		,,,				2504	0.001				p.I26I		Atlas-SNP	.											.	PSMD7	29	.	0			c.C78T						PASS	.	C		1,4395	2.1+/-5.4	0,1,2197	129.0	108.0	115.0		78	-0.2	1.0	16	dbSNP_134	115	14,8586	11.2+/-40.8	0,14,4286	no	coding-synonymous	PSMD7	NM_002811.4		0,15,6483	TT,TC,CC		0.1628,0.0227,0.1154		26/325	74334016	15,12981	2198	4300	6498	SO:0001819	synonymous_variant	5713	exon2			CAGAATCGGCAAG	D50063	CCDS10910.1	16q22.3	2010-10-15	2007-07-06		ENSG00000103035	ENSG00000103035		"""Proteasome (prosome, macropain) subunits"""	9565	protein-coding gene	gene with protein product	"""Mov34 homolog"""	157970	"""proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 (Mov34 homolog)"""			7755639	Standard	NM_002811		Approved	S12, P40, MOV34, Rpn8	uc002fcq.3	P51665	OTTHUMG00000137601	ENST00000219313.4:c.78C>T	16.37:g.74334016C>T		84.0	0.0	0		81.0	37.0	0.45679	NM_002811	D3DWS9|Q6PKI2|Q96E97	Silent	SNP	ENST00000219313.4	37	CCDS10910.1																																																																																			C|0.999;T|0.001	0.001	strong		0.418	PSMD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269010.2	NM_002811	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134501410	134501410	+	Missense_Mutation	SNP	C	C	T	rs200547421		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:134501410C>T	ENST00000372189.3	-	10	1673	c.1550G>A	c.(1549-1551)gGt>gAt	p.G517D	RAPGEF1_ENST00000372195.1_Missense_Mutation_p.G534D|RAPGEF1_ENST00000481260.1_5'Flank|RAPGEF1_ENST00000372190.3_Missense_Mutation_p.G535D	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1	517					activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		GGCTGAGGAACCTCCATGCTG	0.537													C|||	1	0.000199681	0.0	0.0014	5008	,	,		18229	0.0		0.0	False		,,,				2504	0.0				p.G535D		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.G1604A						PASS	.	C	ASP/GLY,ASP/GLY	0,4064		0,0,2032	79.0	84.0	82.0		1550,1604	1.9	0.5	9		82	12,8340		1,10,4165	yes	missense,missense	RAPGEF1	NM_005312.2,NM_198679.1	94,94	1,10,6197	TT,TC,CC		0.1437,0.0,0.0966	benign,benign	517/1078,535/1096	134501410	12,12404	2032	4176	6208	SO:0001583	missense	2889	exon10			GAGGAACCTCCAT	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.1550G>A	9.37:g.134501410C>T	ENSP00000361263:p.Gly517Asp	118.0	0.0	0		111.0	48.0	0.432432	NM_198679	Q5JUE4|Q8IV73	Missense_Mutation	SNP	ENST00000372189.3	37	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	13.98	2.397773	0.42512	0.0	0.001437	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000372191;ENST00000357686	T;T;T	0.25749	1.78;1.78;1.78	5.07	1.9	0.25705	.	0.158578	0.56097	D	0.000029	T	0.10937	0.0267	N	0.03608	-0.345	0.22675	N	0.998864	B;B;B	0.25235	0.121;0.072;0.118	B;B;B	0.32980	0.031;0.046;0.156	T	0.39057	-0.9632	10	0.13853	T	0.58	.	9.0597	0.36427	0.0:0.4277:0.4828:0.0895	.	534;517;535	Q68DL3;Q13905;Q13905-3	.;RPGF1_HUMAN;.	D	517;534;411;517;535;497;443;212;534	ENSP00000361269:G534D;ENSP00000361263:G517D;ENSP00000361264:G535D	ENSP00000266110:G517D	G	-	2	0	RAPGEF1	133491231	0.026000	0.19158	0.521000	0.27850	0.981000	0.71138	0.914000	0.28624	0.488000	0.27723	0.655000	0.94253	GGT	C|0.993;T|0.007	0.007	strong		0.537	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	
FOXP1	27086	hgsc.bcm.edu	37	3	71096114	71096114	+	Missense_Mutation	SNP	G	G	C	rs146606219		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:71096114G>C	ENST00000318789.4	-	10	1168	c.643C>G	c.(643-645)Ccc>Gcc	p.P215A	FOXP1_ENST00000493089.1_Missense_Mutation_p.P215A|FOXP1_ENST00000491238.1_Missense_Mutation_p.P217A|FOXP1_ENST00000498215.1_Missense_Mutation_p.P215A|FOXP1_ENST00000468577.1_Missense_Mutation_p.P215A|FOXP1_ENST00000472382.1_5'UTR|FOXP1_ENST00000475937.1_Missense_Mutation_p.P215A|FOXP1_ENST00000484350.1_Missense_Mutation_p.P139A	NM_001244810.1|NM_001244813.1|NM_032682.5	NP_001231739.1|NP_001231742.1|NP_116071.2	Q9H334	FOXP1_HUMAN	forkhead box P1	215	Gln-rich.		P -> A (in dbSNP:rs146606219). {ECO:0000269|PubMed:19352412, ECO:0000269|PubMed:20848658, ECO:0000269|PubMed:20950788}.		negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P215S(1)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(7)|lung(8)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	31		Lung NSC(201;4.62e-05)|Prostate(10;0.0181)|Hepatocellular(537;0.186)|Myeloproliferative disorder(1037;0.209)		BRCA - Breast invasive adenocarcinoma(55;1.17e-05)|Epithelial(33;1.39e-05)|LUSC - Lung squamous cell carcinoma(21;2.35e-05)|Lung(16;4.26e-05)		GGTTGAAGGGGAAGGGCAGGC	0.517			T	PAX5	ALL								G|||	1	0.000199681	0.0	0.0	5008	,	,		19705	0.0		0.001	False		,,,				2504	0.0				p.P217A		Atlas-SNP	.		Dom	yes		3	3p14.1	27086	forkhead box P1		L	FOXP1,NS,carcinoma,0,1	FOXP1	104	1	1	Substitution - Missense(1)	endometrium(1)	c.C649G						PASS	.	G	ALA/PRO	2,4404	4.2+/-10.8	0,2,2201	177.0	181.0	180.0		643	6.0	1.0	3	dbSNP_134	180	22,8578	15.3+/-51.7	0,22,4278	yes	missense	FOXP1	NM_032682.5	27	0,24,6479	CC,CG,GG		0.2558,0.0454,0.1845	benign	215/678	71096114	24,12982	2203	4300	6503	SO:0001583	missense	27086	exon5			GAAGGGGAAGGGC	AF146696	CCDS2914.1, CCDS33785.1, CCDS58837.1, CCDS58838.1, CCDS58839.1, CCDS74963.1, CCDS74964.1	3p14.1	2008-07-18			ENSG00000114861	ENSG00000114861		"""Forkhead boxes"""	3823	protein-coding gene	gene with protein product	"""fork head-related protein like B"", ""glutamine-rich factor 1"", ""PAX5/FOXP1 fusion protein"""	605515				8265594, 11751404	Standard	NM_032682		Approved	QRF1, 12CC4, HSPC215, hFKH1B	uc003doj.3	Q9H334	OTTHUMG00000158803	ENST00000318789.4:c.643C>G	3.37:g.71096114G>C	ENSP00000318902:p.Pro215Ala	124.0	0.0	0		161.0	90.0	0.559006	NM_001244815	A3QVP8|B3KV70|G5E9V8|Q8NAN6|Q9BSG9|Q9H332|Q9H333|Q9P0R1	Missense_Mutation	SNP	ENST00000318789.4	37	CCDS2914.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	24.6	4.554029	0.86231	4.54E-4	0.002558	ENSG00000114861	ENST00000318789;ENST00000318796;ENST00000475937;ENST00000339693;ENST00000497355;ENST00000491238;ENST00000493089;ENST00000498215;ENST00000484350;ENST00000468577;ENST00000485326;ENST00000497553	T;T;T;T;T;T;T;T;T;T	0.48836	0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;0.8;1.13	6.03	6.03	0.97812	.	0.195111	0.56097	D	0.000031	T	0.64483	0.2602	L	0.44542	1.39	0.80722	D	1	D;D;D;D	0.67145	0.996;0.996;0.993;0.993	D;D;D;D	0.76071	0.987;0.981;0.956;0.956	T	0.61322	-0.7086	10	0.52906	T	0.07	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	214;215;139;215	A3KMG1;G5E9V8;Q8NAN6;Q9H334	.;.;.;FOXP1_HUMAN	A	215;115;215;215;111;217;215;215;139;215;115;115	ENSP00000318902:P215A;ENSP00000419393:P215A;ENSP00000418225:P111A;ENSP00000420736:P217A;ENSP00000418524:P215A;ENSP00000418102:P215A;ENSP00000417857:P139A;ENSP00000418883:P215A;ENSP00000417941:P115A;ENSP00000418784:P115A	ENSP00000318902:P215A	P	-	1	0	FOXP1	71178804	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.878000	0.92393	2.854000	0.98071	0.655000	0.94253	CCC	G|0.998;C|0.002	0.002	strong		0.517	FOXP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352250.1	NM_032682	
TTLL5	23093	hgsc.bcm.edu	37	14	76232469	76232469	+	Silent	SNP	C	C	T	rs61741261	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:76232469C>T	ENST00000298832.9	+	20	1978	c.1773C>T	c.(1771-1773)gtC>gtT	p.V591V	TTLL5_ENST00000556893.1_Silent_p.V142V|TTLL5_ENST00000554510.1_Silent_p.V100V|TTLL5_ENST00000557636.1_Silent_p.V605V|TTLL5_ENST00000555422.1_3'UTR	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	591					fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		AGGAAGAAGTCGCATTAGATA	0.398													c|||	6	0.00119808	0.0	0.0	5008	,	,		16548	0.0		0.006	False		,,,				2504	0.0				p.V591V		Atlas-SNP	.											.	TTLL5	102	.	0			c.C1773T						PASS	.			0,4406		0,0,2203	86.0	82.0	83.0		1773	-3.9	0.1	14	dbSNP_129	83	17,8583	13.3+/-46.6	0,17,4283	no	coding-synonymous	TTLL5	NM_015072.4		0,17,6486	TT,TC,CC		0.1977,0.0,0.1307		591/1282	76232469	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	23093	exon20			AGAAGTCGCATTA	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.1773C>T	14.37:g.76232469C>T		61.0	0.0	0		47.0	22.0	0.468085	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Silent	SNP	ENST00000298832.9	37	CCDS32124.1																																																																																			C|0.998;T|0.002	0.002	strong		0.398	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
LZIC	84328	hgsc.bcm.edu	37	1	9995633	9995633	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:9995633G>A	ENST00000377223.1	-	4	401	c.154C>T	c.(154-156)Caa>Taa	p.Q52*	LZIC_ENST00000541052.1_Nonsense_Mutation_p.Q73*|LZIC_ENST00000400903.2_Nonsense_Mutation_p.Q52*|LZIC_ENST00000377213.1_Nonsense_Mutation_p.Q52*	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	52					response to ionizing radiation (GO:0010212)					breast(1)|endometrium(2)|large_intestine(2)|lung(1)|skin(1)	7		all_lung(284;0.000407)|Renal(390;0.000469)|Lung NSC(185;0.000577)|Colorectal(325;0.0062)|Breast(348;0.00686)|Hepatocellular(190;0.0305)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.104)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;5.29e-08)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(185;0.000242)|BRCA - Breast invasive adenocarcinoma(304;0.000299)|KIRC - Kidney renal clear cell carcinoma(229;0.000896)|STAD - Stomach adenocarcinoma(132;0.00842)|READ - Rectum adenocarcinoma(331;0.0419)		TCACTTAGTTGCTCCAGAGTT	0.333																																					p.Q52X		Atlas-SNP	.											.	LZIC	11	.	0			c.C154T						PASS	.						151.0	157.0	155.0					1																	9995633		2203	4299	6502	SO:0001587	stop_gained	84328	exon3			TTAGTTGCTCCAG	AB060688	CCDS107.1	1p36.22	2008-02-05			ENSG00000162441	ENSG00000162441			17497	protein-coding gene	gene with protein product		610458				11712074	Standard	NM_032368		Approved	MGC15436	uc001aqm.3	Q8WZA0	OTTHUMG00000001804	ENST00000377223.1:c.154C>T	1.37:g.9995633G>A	ENSP00000366430:p.Gln52*	100.0	0.0	0		98.0	5.0	0.0510204	NM_032368	B2R6F0|B4E2N0|Q96IU1	Nonsense_Mutation	SNP	ENST00000377223.1	37	CCDS107.1	.	.	.	.	.	.	.	.	.	.	G	39	7.297898	0.98196	.	.	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	.	.	.	5.63	5.63	0.86233	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.6655	0.95891	0.0:0.0:1.0:0.0	.	.	.	.	X	52;52;73;52	.	.	Q	-	1	0	LZIC	9918220	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.716000	0.98752	2.652000	0.90054	0.491000	0.48974	CAA	.	.	none		0.333	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368	
CARD11	84433	hgsc.bcm.edu	37	7	2983886	2983886	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:2983886T>G	ENST00000396946.4	-	5	1047	c.644A>C	c.(643-645)aAg>aCg	p.K215T	AC004906.3_ENST00000423194.1_RNA	NM_032415.4	NP_115791.3	Q9BXL7	CAR11_HUMAN	caspase recruitment domain family, member 11	215					Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|nucleotide phosphorylation (GO:0046939)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cytokine production (GO:0001819)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T cell proliferation (GO:0042102)|regulation of apoptotic process (GO:0042981)|regulation of B cell differentiation (GO:0045577)|regulation of T cell differentiation (GO:0045580)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|thymic T cell selection (GO:0045061)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	CARD domain binding (GO:0050700)|guanylate kinase activity (GO:0004385)			NS(1)|breast(3)|central_nervous_system(1)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(62)|kidney(11)|large_intestine(13)|lung(31)|ovary(4)|prostate(5)|skin(7)|upper_aerodigestive_tract(2)	150		Ovarian(82;0.0115)		OV - Ovarian serous cystadenocarcinoma(56;8.44e-14)		CGCCATGTTCTTCTCCTCACT	0.572			Mis		DLBCL																																p.K215T		Atlas-SNP	.		Dom	yes		7	7p22	84433	"""caspase recruitment domain family, member 11"""		L	CARD11,colon,carcinoma,-1,6	CARD11	339	6	0			c.A644C						PASS	.						187.0	114.0	139.0					7																	2983886		2203	4300	6503	SO:0001583	missense	84433	exon5			ATGTTCTTCTCCT	AF322641	CCDS5336.2	7p22	2014-09-17			ENSG00000198286	ENSG00000198286			16393	protein-coding gene	gene with protein product	"""card-maguk protein 1"", ""bcl10-interacting maguk protein 3"""	607210				11278692, 11356195	Standard	NM_032415		Approved	CARMA1, BIMP3	uc003smv.3	Q9BXL7	OTTHUMG00000023023	ENST00000396946.4:c.644A>C	7.37:g.2983886T>G	ENSP00000380150:p.Lys215Thr	178.0	0.0	0		251.0	36.0	0.143426	NM_032415	A4D1Z7|Q2NKN7|Q548H3	Missense_Mutation	SNP	ENST00000396946.4	37	CCDS5336.2	.	.	.	.	.	.	.	.	.	.	T	18.82	3.705011	0.68615	.	.	ENSG00000198286	ENST00000396946	T	0.37915	1.17	4.16	4.16	0.48862	.	0.000000	0.85682	D	0.000000	T	0.55016	0.1894	L	0.57536	1.79	0.58432	D	0.999995	D	0.89917	1.0	D	0.83275	0.996	T	0.58836	-0.7566	10	0.66056	D	0.02	-28.1579	13.4982	0.61438	0.0:0.0:0.0:1.0	.	215	Q9BXL7	CAR11_HUMAN	T	215	ENSP00000380150:K215T	ENSP00000380150:K215T	K	-	2	0	CARD11	2950412	1.000000	0.71417	0.991000	0.47740	0.982000	0.71751	5.720000	0.68470	1.650000	0.50662	0.459000	0.35465	AAG	.	.	none		0.572	CARD11-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059344.4	NM_032415	
TAF6	6878	hgsc.bcm.edu	37	7	99711386	99711386	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:99711386A>C	ENST00000344095.4	-	4	775	c.250T>G	c.(250-252)Tat>Gat	p.Y84D	TAF6_ENST00000497233.1_5'Flank|TAF6_ENST00000452041.1_Missense_Mutation_p.Y84D|RP11-506M12.1_ENST00000494221.1_RNA|TAF6_ENST00000418432.2_Missense_Mutation_p.Y27D|TAF6_ENST00000437822.2_Missense_Mutation_p.Y121D|TAF6_ENST00000472509.1_Missense_Mutation_p.Y141D|TAF6_ENST00000453269.2_Missense_Mutation_p.Y84D	NM_005641.3	NP_005632.1	P49848	TAF6_HUMAN	TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80kDa	84					DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)|transcription factor TFTC complex (GO:0033276)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|urinary_tract(2)	26	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TGGAAGCCATAGAGTGGCTGT	0.607																																					p.Y121D		Atlas-SNP	.											.	TAF6	55	.	0			c.T361G						PASS	.						33.0	35.0	35.0					7																	99711386		2203	4300	6503	SO:0001583	missense	6878	exon4			AGCCATAGAGTGG		CCDS5686.1, CCDS55135.1	7q	2010-02-26	2002-08-29	2001-12-07	ENSG00000106290	ENSG00000106290			11540	protein-coding gene	gene with protein product	"""TAF6 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 80 kD"", ""transcription initiation factor TFIID 70 kD subunit"""	602955	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, E, 70/85kD"""	TAF2E		826207	Standard	NM_139315		Approved	TAFII70, TAFII80, MGC:8964, TAFII85	uc011kji.2	P49848	OTTHUMG00000154771	ENST00000344095.4:c.250T>G	7.37:g.99711386A>C	ENSP00000344537:p.Tyr84Asp	52.0	0.0	0		52.0	8.0	0.153846	NM_001190415	A4D2B2|A4D2B3|B4DT11|D6W5U2|Q6AI29	Missense_Mutation	SNP	ENST00000344095.4	37	CCDS5686.1	.	.	.	.	.	.	.	.	.	.	A	19.08	3.758276	0.69763	.	.	ENSG00000106290	ENST00000453269;ENST00000472509;ENST00000452041;ENST00000344095;ENST00000418432;ENST00000437822;ENST00000493322;ENST00000440225;ENST00000452438;ENST00000523306;ENST00000449571;ENST00000520135;ENST00000451699	T;T;T;T;T;T;T;T;T;T;T;T	0.49432	0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78;0.78	5.5	4.35	0.52113	Histone-fold (1);	0.057225	0.64402	D	0.000001	T	0.69006	0.3063	M	0.92219	3.285	0.58432	D	0.99999	P;P;P;P;D;P	0.58970	0.865;0.753;0.639;0.491;0.984;0.919	P;P;P;P;P;P	0.58520	0.642;0.71;0.516;0.54;0.84;0.516	T	0.73493	-0.3965	10	0.62326	D	0.03	-2.7986	9.3794	0.38304	0.9156:0.0:0.0844:0.0	.	121;84;74;84;84;27	B4DT11;P49848-2;A4D299;P49848;C9JTY6;B3KUR4	.;.;.;TAF6_HUMAN;.;.	D	84;141;84;84;27;121;84;84;84;74;84;74;84	ENSP00000389575:Y84D;ENSP00000419760:Y141D;ENSP00000416396:Y84D;ENSP00000344537:Y84D;ENSP00000399982:Y121D;ENSP00000419555:Y84D;ENSP00000410012:Y84D;ENSP00000412346:Y84D;ENSP00000428639:Y74D;ENSP00000390073:Y84D;ENSP00000428071:Y74D;ENSP00000406315:Y84D	ENSP00000344537:Y84D	Y	-	1	0	TAF6	99549322	1.000000	0.71417	0.821000	0.32701	0.907000	0.53573	8.627000	0.90974	0.939000	0.37446	0.456000	0.33151	TAT	.	.	none		0.607	TAF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337024.2	NM_005641	
THOC1	9984	hgsc.bcm.edu	37	18	264039	264039	+	Silent	SNP	C	C	A	rs376944925		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:264039C>A	ENST00000261600.6	-	4	250	c.243G>T	c.(241-243)ggG>ggT	p.G81G	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	81					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				CAGTTACTCCCCCAATAGCAA	0.358																																					p.G81G		Atlas-SNP	.											.	THOC1	43	.	0			c.G243T						PASS	.	C		0,3690		0,0,1845	86.0	74.0	78.0		243	4.3	1.0	18		78	5,8171		0,5,4083	no	coding-synonymous	THOC1	NM_005131.2		0,5,5928	AA,AC,CC		0.0612,0.0,0.0421		81/658	264039	5,11861	1845	4088	5933	SO:0001819	synonymous_variant	9984	exon4			TACTCCCCCAATA	AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"""THO complex subunits"""	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.243G>T	18.37:g.264039C>A		162.0	0.0	0		179.0	62.0	0.346369	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Silent	SNP	ENST00000261600.6	37	CCDS45820.1																																																																																			.	.	weak		0.358	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131	
ZNF536	9745	hgsc.bcm.edu	37	19	31039256	31039256	+	Silent	SNP	C	C	T	rs111707808	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:31039256C>T	ENST00000355537.3	+	4	2877	c.2730C>T	c.(2728-2730)aaC>aaT	p.N910N		NM_014717.1	NP_055532.1	O15090	ZN536_HUMAN	zinc finger protein 536	910					negative regulation of neuron differentiation (GO:0045665)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|retinoic acid-responsive element binding (GO:0044323)			NS(3)|breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|lung(119)|ovary(7)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	182	Esophageal squamous(110;0.0834)					TTGTGAGCAACGGTGTGAATT	0.498													C|||	229	0.0457268	0.0348	0.0173	5008	,	,		21120	0.005		0.0338	False		,,,				2504	0.135				p.N910N		Atlas-SNP	.											ZNF536,colon,carcinoma,+1,1	ZNF536	424	1	0			c.C2730T						scavenged	.	C		161,4245	108.6+/-147.0	2,157,2044	178.0	183.0	181.0		2730	-0.6	1.0	19	dbSNP_132	181	287,8313	106.8+/-167.6	5,277,4018	no	coding-synonymous	ZNF536	NM_014717.1		7,434,6062	TT,TC,CC		3.3372,3.6541,3.4446		910/1301	31039256	448,12558	2203	4300	6503	SO:0001819	synonymous_variant	9745	exon4			GAGCAACGGTGTG		CCDS32984.1	19q13.11	2013-01-08				ENSG00000198597		"""Zinc fingers, C2H2-type"""	29025	protein-coding gene	gene with protein product						9205841	Standard	XM_005259445		Approved	KIAA0390	uc002nsu.1	O15090		ENST00000355537.3:c.2730C>T	19.37:g.31039256C>T		43.0	1.0	0.0232558		44.0	28.0	0.636364	NM_014717	A2RU18	Silent	SNP	ENST00000355537.3	37	CCDS32984.1																																																																																			C|0.970;T|0.030	0.030	strong		0.498	ZNF536-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459667.2	NM_014717	
HSPG2	3339	hgsc.bcm.edu	37	1	22214040	22214040	+	Silent	SNP	G	G	A	rs41310388	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:22214040G>A	ENST00000374695.3	-	8	910	c.831C>T	c.(829-831)ccC>ccT	p.P277P		NM_005529.5	NP_005520.4	P98160	PGBM_HUMAN	heparan sulfate proteoglycan 2	277					angiogenesis (GO:0001525)|brain development (GO:0007420)|carbohydrate metabolic process (GO:0005975)|cardiac muscle tissue development (GO:0048738)|cartilage development involved in endochondral bone morphogenesis (GO:0060351)|chondrocyte differentiation (GO:0002062)|chondroitin sulfate metabolic process (GO:0030204)|embryonic skeletal system morphogenesis (GO:0048704)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lipoprotein metabolic process (GO:0042157)|phototransduction, visible light (GO:0007603)|protein localization (GO:0008104)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	basal lamina (GO:0005605)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)	p.P277P(1)		breast(6)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(15)|liver(1)|lung(44)|ovary(10)|pancreas(1)|prostate(10)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(3)	127		Colorectal(325;3.46e-05)|all_lung(284;7.93e-05)|Lung NSC(340;8.71e-05)|Renal(390;0.000219)|Breast(348;0.00222)|Ovarian(437;0.00308)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0498)|OV - Ovarian serous cystadenocarcinoma(117;1.14e-26)|Colorectal(126;4.18e-07)|COAD - Colon adenocarcinoma(152;1.82e-05)|GBM - Glioblastoma multiforme(114;3.13e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000756)|STAD - Stomach adenocarcinoma(196;0.00656)|KIRC - Kidney renal clear cell carcinoma(1967;0.00942)|READ - Rectum adenocarcinoma(331;0.0721)|Lung(427;0.223)	Palifermin(DB00039)	TGACGGAACCGGGAAGCAGGG	0.647													G|||	29	0.00579073	0.0008	0.0029	5008	,	,		14680	0.0		0.0179	False		,,,				2504	0.0082				p.P277P		Atlas-SNP	.											HSPG2,NS,carcinoma,0,1	HSPG2	311	1	1	Substitution - coding silent(1)	prostate(1)	c.C831T						PASS	.	G		14,4392	20.2+/-43.8	0,14,2189	81.0	99.0	93.0		831	-4.3	0.0	1	dbSNP_127	93	138,8462	66.7+/-129.0	1,136,4163	no	coding-synonymous	HSPG2	NM_005529.5		1,150,6352	AA,AG,GG		1.6047,0.3177,1.1687		277/4392	22214040	152,12854	2203	4300	6503	SO:0001819	synonymous_variant	3339	exon8			GGAACCGGGAAGC	M85289	CCDS30625.1	1p36.1-p35	2013-01-29	2007-02-16	2007-02-16	ENSG00000142798	ENSG00000142798		"""Proteoglycans / Extracellular Matrix : Other"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5273	protein-coding gene	gene with protein product	"""perlecan proteoglycan"""	142461	"""Schwartz-Jampel syndrome 1 (chondrodystrophic myotonia)"""	SJS1		1685141, 11941538	Standard	XM_005245863		Approved	perlecan, PRCAN	uc001bfj.3	P98160	OTTHUMG00000002674	ENST00000374695.3:c.831C>T	1.37:g.22214040G>A		145.0	0.0	0		129.0	58.0	0.449612	NM_005529	Q16287|Q5SZI3|Q9H3V5	Silent	SNP	ENST00000374695.3	37	CCDS30625.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	G	16.74	3.206474	0.58343	0.003177	0.016047	ENSG00000142798	ENST00000412328;ENST00000374673	T;D	0.92249	0.51;-3.0	4.62	-4.32	0.03688	.	0.000000	0.37623	N	0.002018	T	0.72503	0.3468	.	.	.	0.49915	D	0.999833	B	0.20780	0.048	B	0.17098	0.017	T	0.55805	-0.8083	9	0.27785	T	0.31	.	7.5881	0.28004	0.6013:0.1275:0.2712:0.0	rs41310388	200	Q5SZI5	.	L	200;104	ENSP00000405412:P200L;ENSP00000363805:P104L	ENSP00000363805:P104L	P	-	2	0	HSPG2	22086627	0.011000	0.17503	0.000000	0.03702	0.013000	0.08279	-0.065000	0.11617	-1.198000	0.02669	-0.379000	0.06801	CCG	G|0.989;A|0.011	0.011	strong		0.647	HSPG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007598.1	NM_005529	
LAMA3	3909	hgsc.bcm.edu	37	18	21496533	21496533	+	Silent	SNP	C	C	T	rs61751706	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000587184.1_Silent_p.D934D|LAMA3_ENST00000269217.6_Silent_p.D990D|LAMA3_ENST00000588770.1_3'UTR	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		63.0	0.0	0		103.0	59.0	0.572816	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	
GSG2	83903	hgsc.bcm.edu	37	17	3628759	3628759	+	Missense_Mutation	SNP	A	A	G	rs146480185		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:3628759A>G	ENST00000325418.4	+	1	1549	c.1530A>G	c.(1528-1530)atA>atG	p.I510M	ITGAE_ENST00000571185.1_Intron|CTD-3195I5.3_ENST00000571741.1_RNA|ITGAE_ENST00000263087.4_Intron	NM_031965.2	NP_114171.2	Q8TF76	HASP_HUMAN	germ cell associated 2 (haspin)	510	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159, ECO:0000305}.				histone H3-T3 phosphorylation involved in chromosome passenger complex localization to kinetochore (GO:2000751)|intracellular signal transduction (GO:0035556)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|protein localization to chromosome, centromeric region (GO:0071459)|protein phosphorylation (GO:0006468)|regulation of spindle checkpoint (GO:0090231)	centrosome (GO:0005813)|chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|spindle (GO:0005819)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|histone kinase activity (H3-T3 specific) (GO:0072354)|protein kinase activity (GO:0004672)										CCGTAGCCATAAAAATCATTG	0.443																																					p.I510M		Atlas-SNP	.											.	GSG2	48	.	0			c.A1530G						PASS	.	A	,MET/ILE	0,4406		0,0,2203	68.0	66.0	67.0		,1530	2.6	1.0	17	dbSNP_134	67	1,8599	1.2+/-3.3	0,1,4299	no	intron,missense	ITGAE,GSG2	NM_002208.4,NM_031965.2	,10	0,1,6502	GG,GA,AA		0.0116,0.0,0.0077	,benign	,510/799	3628759	1,13005	2203	4300	6503	SO:0001583	missense	83903	exon1			AGCCATAAAAATC	AB039834	CCDS11036.1	17p13	2005-01-19			ENSG00000177602	ENSG00000177602			19682	protein-coding gene	gene with protein product		609240					Standard	NM_031965		Approved	haspin	uc002fwp.3	Q8TF76	OTTHUMG00000090703	ENST00000325418.4:c.1530A>G	17.37:g.3628759A>G	ENSP00000325290:p.Ile510Met	90.0	0.0	0		137.0	65.0	0.474453	NM_031965	Q5U5K3|Q96MN1|Q9BXS7	Missense_Mutation	SNP	ENST00000325418.4	37	CCDS11036.1	.	.	.	.	.	.	.	.	.	.	A	9.753	1.167938	0.21621	0.0	1.16E-4	ENSG00000177602	ENST00000325418	T	0.68624	-0.34	4.87	2.62	0.31277	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.249150	0.20240	N	0.096308	T	0.56202	0.1969	L	0.33093	0.98	0.30357	N	0.784223	B	0.13145	0.007	B	0.31946	0.138	T	0.57625	-0.7779	10	0.87932	D	0	-37.732	7.5752	0.27931	0.8258:0.0:0.1742:0.0	.	510	Q8TF76	HASP_HUMAN	M	510	ENSP00000325290:I510M	ENSP00000325290:I510M	I	+	3	3	GSG2	3575508	1.000000	0.71417	0.997000	0.53966	0.594000	0.36715	0.746000	0.26275	0.420000	0.25954	0.533000	0.62120	ATA	A|1.000;G|0.000	0.000	weak		0.443	GSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207391.1	NM_031965	
FDFT1	2222	hgsc.bcm.edu	37	8	11667253	11667253	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:11667253A>G	ENST00000220584.4	+	3	497	c.275A>G	c.(274-276)aAg>aGg	p.K92R	FDFT1_ENST00000530664.1_Missense_Mutation_p.K28R|FDFT1_ENST00000525777.1_Missense_Mutation_p.K7R|FDFT1_ENST00000446331.2_Intron|FDFT1_ENST00000528643.1_Missense_Mutation_p.K7R|FDFT1_ENST00000538689.1_5'UTR|FDFT1_ENST00000528812.1_Missense_Mutation_p.K28R|FDFT1_ENST00000443614.2_Missense_Mutation_p.K92R|FDFT1_ENST00000525900.1_Missense_Mutation_p.K85R	NM_004462.3	NP_004453.3	P37268	FDFT_HUMAN	farnesyl-diphosphate farnesyltransferase 1	92					cellular lipid metabolic process (GO:0044255)|cholesterol biosynthetic process (GO:0006695)|isoprenoid biosynthetic process (GO:0008299)|small molecule metabolic process (GO:0044281)|steroid biosynthetic process (GO:0006694)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	farnesyl-diphosphate farnesyltransferase activity (GO:0004310)|oxidoreductase activity (GO:0016491)|squalene synthase activity (GO:0051996)			breast(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(2)|upper_aerodigestive_tract(2)	12	all_epithelial(15;0.234)		STAD - Stomach adenocarcinoma(15;0.00225)	COAD - Colon adenocarcinoma(149;0.18)		AGTGTGGAAAAGAAGGTCCCG	0.473																																					p.K92R		Atlas-SNP	.											.	FDFT1	25	.	0			c.A275G						PASS	.						138.0	115.0	123.0					8																	11667253		2203	4300	6503	SO:0001583	missense	2222	exon3			TGGAAAAGAAGGT	X69141	CCDS5985.1, CCDS75696.1, CCDS75697.1	8p23.1-p22	2005-03-07			ENSG00000079459	ENSG00000079459	2.5.1.21		3629	protein-coding gene	gene with protein product	"""squalene synthase"""	184420					Standard	NM_001287742		Approved		uc003wui.3	P37268	OTTHUMG00000090801	ENST00000220584.4:c.275A>G	8.37:g.11667253A>G	ENSP00000220584:p.Lys92Arg	99.0	0.0	0		123.0	55.0	0.447154	NM_004462	B3KQ95|B4DJE5|B4DT56|B7Z1J3|Q96GT0	Missense_Mutation	SNP	ENST00000220584.4	37	CCDS5985.1	.	.	.	.	.	.	.	.	.	.	A	10.89	1.479017	0.26511	.	.	ENSG00000079459	ENST00000530337;ENST00000220584;ENST00000443614;ENST00000525900;ENST00000528812;ENST00000530664;ENST00000528643;ENST00000525777	D;D;D;D;D;D;T;T	0.81996	-1.56;-1.56;-1.56;-1.56;-1.56;-1.56;-0.57;-0.57	4.91	-1.99	0.07457	Terpenoid synthase (2);	0.360845	0.31760	N	0.007118	T	0.66436	0.2789	L	0.42245	1.32	0.09310	N	0.999998	B;B;B;B	0.06786	0.0;0.001;0.0;0.0	B;B;B;B	0.06405	0.002;0.002;0.001;0.001	T	0.47100	-0.9143	10	0.25106	T	0.35	-7.7419	0.1655	0.00108	0.2664:0.2386:0.2384:0.2566	.	92;149;85;92	B4DJE5;B4DND3;E9PNM1;P37268	.;.;.;FDFT_HUMAN	R	92;92;92;85;28;28;7;7	ENSP00000431852:K92R;ENSP00000220584:K92R;ENSP00000390367:K92R;ENSP00000434714:K85R;ENSP00000431749:K28R;ENSP00000432331:K28R;ENSP00000431649:K7R;ENSP00000436069:K7R	ENSP00000220584:K92R	K	+	2	0	FDFT1	11704662	0.008000	0.16893	0.000000	0.03702	0.943000	0.58893	0.527000	0.22987	-0.398000	0.07679	0.402000	0.26972	AAG	.	.	none		0.473	FDFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207588.2		
TRMT1	55621	hgsc.bcm.edu	37	19	13218417	13218417	+	Silent	SNP	T	T	C	rs148858467	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:13218417T>C	ENST00000592062.1	-	15	2124	c.1554A>G	c.(1552-1554)ccA>ccG	p.P518P	TRMT1_ENST00000221504.8_Silent_p.P489P|TRMT1_ENST00000437766.1_Silent_p.P518P|TRMT1_ENST00000357720.4_Silent_p.P518P			Q9NXH9	TRM1_HUMAN	tRNA methyltransferase 1 homolog (S. cerevisiae)	518							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)		TGCGGAACGCTGGGCTAGTCT	0.592													T|||	9	0.00179712	0.0	0.0043	5008	,	,		20409	0.0		0.006	False		,,,				2504	0.0				p.P518P		Atlas-SNP	.											.	TRMT1	31	.	0			c.A1554G						PASS	.	T	,,	4,4402	8.1+/-20.4	0,4,2199	64.0	39.0	48.0		1554,1467,1554	-8.0	0.0	19	dbSNP_134	48	75,8523	41.2+/-98.3	0,75,4224	no	coding-synonymous,coding-synonymous,coding-synonymous	TRMT1	NM_001136035.2,NM_001142554.1,NM_017722.3	,,	0,79,6423	CC,CT,TT		0.8723,0.0908,0.6075	,,	518/660,489/631,518/660	13218417	79,12925	2203	4299	6502	SO:0001819	synonymous_variant	55621	exon14			GAACGCTGGGCTA	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.1554A>G	19.37:g.13218417T>C		75.0	0.0	0		64.0	21.0	0.328125	NM_001136035	O76103|Q548Y5|Q8WVA6	Silent	SNP	ENST00000592062.1	37	CCDS12293.1																																																																																			T|0.995;C|0.005	0.005	strong		0.592	TRMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452780.2	NM_017722	
TTN	7273	hgsc.bcm.edu	37	2	179455352	179455352	+	Missense_Mutation	SNP	C	C	T	rs141973925	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179455352C>T	ENST00000591111.1	-	254	56401	c.56177G>A	c.(56176-56178)cGg>cAg	p.R18726Q	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.R11302Q|TTN_ENST00000342992.6_Missense_Mutation_p.R17799Q|TTN_ENST00000589042.1_Missense_Mutation_p.R20367Q|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.R11494Q|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.R11427Q|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590743.1_RNA			Q8WZ42	TITIN_HUMAN	titin	18726	Fibronectin type-III 35. {ECO:0000255|PROSITE-ProRule:PRU00316}.		R -> Q. {ECO:0000269|PubMed:17344846}.		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)			TTTGATGGGCCGGCAAGCTTT	0.433													C|||	6	0.00119808	0.0008	0.0029	5008	,	,		22262	0.0		0.003	False		,,,				2504	0.0				p.R20367Q		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,+1,5	TTN	18412	5	0			c.G61100A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG,GLN/ARG	5,3765		0,5,1880	109.0	107.0	107.0		33905,53396,34280,34481	6.1	1.0	2	dbSNP_134	107	35,8191		0,35,4078	yes	missense,missense,missense,missense	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	43,43,43,43	0,40,5958	TT,TC,CC		0.4255,0.1326,0.3334	probably-damaging,probably-damaging,probably-damaging,probably-damaging	11302/26927,17799/33424,11427/27052,11494/27119	179455352	40,11956	1885	4113	5998	SO:0001583	missense	7273	exon304			ATGGGCCGGCAAG	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.56177G>A	2.37:g.179455352C>T	ENSP00000465570:p.Arg18726Gln	330.0	0.0	0		344.0	179.0	0.520349	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		3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	15.40	2.821552	0.50633	0.001326	0.004255	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.39056	1.1;1.1;1.1;1.1	6.11	6.11	0.99139	Fibronectin, type III (2);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.60818	0.2298	L	0.43923	1.385	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.79108	0.992;0.992;0.992;0.992	T	0.59101	-0.7517	9	0.87932	D	0	.	20.7342	0.99715	0.0:1.0:0.0:0.0	.	11302;11427;11494;18726	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	Q	17799;11302;11494;11427;11300	ENSP00000343764:R17799Q;ENSP00000434586:R11302Q;ENSP00000340554:R11494Q;ENSP00000352154:R11427Q	ENSP00000340554:R11494Q	R	-	2	0	TTN	179163598	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	5.976000	0.70484	2.906000	0.99361	0.655000	0.94253	CGG	C|0.999;T|0.001	0.001	strong		0.433	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZNF268	10795	hgsc.bcm.edu	37	12	133778887	133778887	+	Silent	SNP	G	G	A	rs75772856	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:133778887G>A	ENST00000536435.2	+	6	945	c.615G>A	c.(613-615)acG>acA	p.T205T	ZNF268_ENST00000537565.1_Silent_p.T44T|ZNF268_ENST00000228289.5_Silent_p.T205T|ZNF268_ENST00000416488.1_3'UTR|ZNF268_ENST00000539248.2_Missense_Mutation_p.R131H|ZNF268_ENST00000536899.2_Missense_Mutation_p.R64H|ZNF268_ENST00000592241.1_3'UTR|ZNF268_ENST00000542711.2_Missense_Mutation_p.R96H|ZNF268_ENST00000542986.2_3'UTR|ZNF268_ENST00000541009.2_3'UTR|ZNF268_ENST00000541211.2_Missense_Mutation_p.R163H|CTD-2140B24.4_ENST00000540096.2_3'UTR	NM_001165885.1|NM_003415.2	NP_001159357.1|NP_003406.1	Q14587	ZN268_HUMAN	zinc finger protein 268	205					cell differentiation (GO:0030154)|cellular response to tumor necrosis factor (GO:0071356)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell cycle arrest (GO:0071157)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein homodimerization activity (GO:0090073)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter during mitosis (GO:0046022)|regulation of mitotic cell cycle (GO:0007346)|regulation of protein heterodimerization activity (GO:0043497)|regulation of transcription, DNA-templated (GO:0006355)|release of cytoplasmic sequestered NF-kappaB (GO:0008588)|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(2)|breast(3)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(1)	24	all_neural(191;0.0982)|Medulloblastoma(191;0.163)	all_cancers(7;0.000215)|all_epithelial(31;0.096)		OV - Ovarian serous cystadenocarcinoma(86;3.58e-08)|Epithelial(86;6.6e-07)|all cancers(50;2.28e-05)		AATGTGGCACGCATGGAAAGA	0.338													g|||	48	0.00958466	0.0	0.0072	5008	,	,		21313	0.0		0.0278	False		,,,				2504	0.0153				p.R163H		Atlas-SNP	.											.	ZNF268	71	.	0			c.G488A						PASS	.	G	,,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,,,	9,3651		0,9,1821	67.0	68.0	67.0		615,366,392,191,488,287,,615,	-4.6	0.0	12	dbSNP_132	67	160,7998		1,158,3920	yes	coding-synonymous,coding-synonymous,missense,missense,missense,missense,utr-3,coding-synonymous,utr-3	ZNF268	NM_001165881.2,NM_001165882.2,NM_001165883.1,NM_001165884.2,NM_001165885.1,NM_001165886.1,NM_001165887.1,NM_003415.2,NM_152943.2	,,29,29,29,29,,,	1,167,5741	AA,AG,GG		1.9613,0.2459,1.43	,,,,,,,,	205/948,122/865,131/136,64/69,163/168,96/101,,205/948,	133778887	169,11649	1830	4079	5909	SO:0001819	synonymous_variant	10795	exon5			TGGCACGCATGGA	X78926	CCDS45012.1, CCDS53851.1, CCDS53852.1, CCDS53853.1, CCDS53854.1, CCDS59239.1, CCDS59240.1	12q24.33	2013-01-08				ENSG00000090612		"""Zinc fingers, C2H2-type"", ""-"""	13061	protein-coding gene	gene with protein product		604753				7865130	Standard	NM_003415		Approved	HZF3	uc010tcf.2	Q14587	OTTHUMG00000167946	ENST00000536435.2:c.615G>A	12.37:g.133778887G>A		86.0	0.0	0		54.0	18.0	0.333333	NM_001165885	Q8TDG8|Q96RH4|Q9BZJ9	Missense_Mutation	SNP	ENST00000536435.2	37	CCDS45012.1	25	0.011446886446886446	0	0.0	1	0.0027624309392265192	0	0.0	24	0.0316622691292876	G	11.82	1.751871	0.31046	0.002459	0.019613	ENSG00000090612	ENST00000536435;ENST00000542711;ENST00000536899	.	.	.	3.79	-4.56	0.03431	.	.	.	.	.	T	0.07098	0.0180	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23440	-1.0188	4	.	.	.	.	4.4841	0.11781	0.191:0.0:0.2934:0.5157	.	.	.	.	H	163;96;64	.	.	R	+	2	0	ZNF268	132288960	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.052000	0.03503	-0.961000	0.03609	-0.387000	0.06579	CGC	G|0.988;A|0.012	0.012	strong		0.338	ZNF268-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397191.2	NM_152943	
IL6ST	3572	hgsc.bcm.edu	37	5	55251889	55251889	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:55251889C>T	ENST00000381298.2	-	10	1543	c.1231G>A	c.(1231-1233)Gca>Aca	p.A411T	IL6ST_ENST00000381294.3_Missense_Mutation_p.A411T|IL6ST_ENST00000381293.2_Intron|IL6ST_ENST00000502326.3_Missense_Mutation_p.A411T|IL6ST_ENST00000336909.5_Missense_Mutation_p.A411T|IL6ST_ENST00000522633.2_3'UTR|IL6ST_ENST00000381286.3_Intron|IL6ST_ENST00000536319.1_3'UTR|IL6ST_ENST00000381287.4_3'UTR	NM_001190981.1|NM_002184.3|NM_175767.2	NP_001177910.1|NP_002175.2|NP_786943.1	P40189	IL6RB_HUMAN	interleukin 6 signal transducer	411	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				ciliary neurotrophic factor-mediated signaling pathway (GO:0070120)|cytokine-mediated signaling pathway (GO:0019221)|glycogen metabolic process (GO:0005977)|interleukin-27-mediated signaling pathway (GO:0070106)|interleukin-6-mediated signaling pathway (GO:0070102)|leukemia inhibitory factor signaling pathway (GO:0048861)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-6-mediated signaling pathway (GO:0070104)|oncostatin-M-mediated signaling pathway (GO:0038165)|positive regulation of acute inflammatory response (GO:0002675)|positive regulation of adaptive immune response (GO:0002821)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cell proliferation (GO:0008284)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation vascular endothelial growth factor production (GO:0010575)|regulation of Notch signaling pathway (GO:0008593)|response to cytokine (GO:0034097)|viral process (GO:0016032)	ciliary neurotrophic factor receptor complex (GO:0070110)|dendrite (GO:0030425)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|interleukin-6 receptor complex (GO:0005896)|membrane (GO:0016020)|neuronal cell body (GO:0043025)|oncostatin-M receptor complex (GO:0005900)|plasma membrane (GO:0005886)	ciliary neurotrophic factor receptor activity (GO:0004897)|ciliary neurotrophic factor receptor binding (GO:0005127)|growth factor binding (GO:0019838)|interleukin-11 receptor activity (GO:0004921)|interleukin-27 receptor activity (GO:0045509)|protein homodimerization activity (GO:0042803)			breast(2)|endometrium(5)|kidney(5)|large_intestine(4)|liver(2)|lung(1)|ovary(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	26		Lung NSC(810;8.69e-05)|Prostate(74;0.00308)|Breast(144;0.0544)|Ovarian(174;0.223)				AAAACAGCTGCATCTGATTTG	0.413			O		hepatocellular ca																																p.A411T		Atlas-SNP	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.G1231A						PASS	.						142.0	131.0	135.0					5																	55251889		2203	4300	6503	SO:0001583	missense	3572	exon10			CAGCTGCATCTGA	M57230	CCDS3971.1, CCDS47209.1, CCDS54856.1	5q11.2	2014-04-04	2014-04-04		ENSG00000134352	ENSG00000134352		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Fibronectin type III domain containing"""	6021	protein-coding gene	gene with protein product	"""gp130, oncostatin M receptor"""	600694	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""			2261637	Standard	NM_002184		Approved	GP130, CD130	uc003jqq.3	P40189	OTTHUMG00000097043	ENST00000381298.2:c.1231G>A	5.37:g.55251889C>T	ENSP00000370698:p.Ala411Thr	119.0	0.0	0		141.0	61.0	0.432624	NM_002184	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	.	.	.	.	.	.	.	.	.	.	C	1.910	-0.450848	0.04572	.	.	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294	T;T;T	0.43688	0.94;0.94;0.94	5.86	0.727	0.18254	Long hematopoietin receptor, Gp130 family 2, conserved site (1);Fibronectin, type III (2);	0.981590	0.08384	N	0.954070	T	0.40956	0.1138	M	0.71036	2.16	0.09310	N	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.06405	0.0;0.002;0.0	T	0.41251	-0.9519	10	0.56958	D	0.05	.	6.7334	0.23395	0.0:0.3836:0.3238:0.2926	.	411;411;411	Q17RA0;Q5FC04;P40189	.;.;IL6RB_HUMAN	T	411	ENSP00000370698:A411T;ENSP00000338799:A411T;ENSP00000370694:A411T	ENSP00000338799:A411T	A	-	1	0	IL6ST	55287646	0.007000	0.16637	0.002000	0.10522	0.162000	0.22319	-0.060000	0.11712	0.166000	0.19597	-0.145000	0.13849	GCA	.	.	none		0.413	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
ATM	472	hgsc.bcm.edu	37	11	108163487	108163487	+	Silent	SNP	C	C	T	rs1800889	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:108163487C>T	ENST00000452508.2	+	31	4767	c.4578C>T	c.(4576-4578)ccC>ccT	p.P1526P	ATM_ENST00000278616.4_Silent_p.P1526P			Q13315	ATM_HUMAN	ATM serine/threonine kinase	1526					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)			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)	CACTTATACCCCTTGTGTATG	0.358			"""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)			C|||	77	0.0153754	0.003	0.0288	5008	,	,		18654	0.0		0.0398	False		,,,				2504	0.0133				p.P1526P		Atlas-SNP	.	yes	Rec	yes	Ataxia-telangiectasia	11	11q22.3	472	ataxia telangiectasia mutated		"""L, O"""	.	ATM	1657	.	0			c.C4578T						PASS	.	C		43,4359	44.6+/-78.6	0,43,2158	197.0	173.0	181.0		4578	-0.5	0.9	11	dbSNP_89	181	438,8158	133.0+/-190.5	21,396,3881	no	coding-synonymous	ATM	NM_000051.3		21,439,6039	TT,TC,CC		5.0954,0.9768,3.7006		1526/3057	108163487	481,12517	2201	4298	6499	SO:0001819	synonymous_variant	472	exon30	Familial Cancer Database	AT, Louis-Bar syndrome	TATACCCCTTGTG	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.4578C>T	11.37:g.108163487C>T		122.0	0.0	0		139.0	69.0	0.496403	NM_000051	B2RNX5|O15429|Q12758|Q16551|Q93007|Q9NP02|Q9UCX7	Silent	SNP	ENST00000452508.2	37	CCDS31669.1																																																																																			C|0.972;T|0.028	0.028	strong		0.358	ATM-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389938.1	NM_000051	
TTC39C	125488	hgsc.bcm.edu	37	18	21662974	21662974	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:21662974C>T	ENST00000317571.3	+	6	1149	c.913C>T	c.(913-915)Ctt>Ttt	p.L305F	TTC39C_ENST00000304621.6_Missense_Mutation_p.L244F|RP11-403A21.3_ENST00000578443.1_RNA	NM_001135993.1	NP_001129465.1	Q8N584	TT39C_HUMAN	tetratricopeptide repeat domain 39C	305										breast(1)|endometrium(3)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|skin(1)	19						GGAAATTCTCCTTAAAAAAGA	0.413																																					p.L305F		Atlas-SNP	.											.	TTC39C	83	.	0			c.C913T						PASS	.						135.0	138.0	137.0					18																	21662974		2203	4300	6503	SO:0001583	missense	125488	exon6			ATTCTCCTTAAAA	AK091080	CCDS32804.1, CCDS45839.1, CCDS58616.1	18q11.2	2014-02-07	2008-06-23	2008-06-23	ENSG00000168234	ENSG00000168234		"""Tetratricopeptide (TTC) repeat domain containing"""	26595	protein-coding gene	gene with protein product			"""chromosome 18 open reading frame 17"""	C18orf17		14702039	Standard	NM_153211		Approved	FLJ33761, HsT2697	uc002kuw.3	Q8N584	OTTHUMG00000179403	ENST00000317571.3:c.913C>T	18.37:g.21662974C>T	ENSP00000323645:p.Leu305Phe	135.0	0.0	0		163.0	34.0	0.208589	NM_001135993	B7WP63|J3QRR1|Q0VAJ2|Q8N284	Missense_Mutation	SNP	ENST00000317571.3	37	CCDS45839.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831199	0.50845	.	.	ENSG00000168234	ENST00000304621;ENST00000317571	T;T	0.76578	-1.03;-1.03	5.7	5.7	0.88788	.	0.377714	0.30556	N	0.009377	T	0.58708	0.2141	N	0.08118	0	0.80722	D	1	B	0.26002	0.139	B	0.18263	0.021	T	0.59857	-0.7375	10	0.56958	D	0.05	-23.3579	11.3611	0.49644	0.1316:0.725:0.1435:0.0	.	305	Q8N584	TT39C_HUMAN	F	244;305	ENSP00000306598:L244F;ENSP00000323645:L305F	ENSP00000306598:L244F	L	+	1	0	TTC39C	19916972	0.889000	0.30405	0.998000	0.56505	0.994000	0.84299	1.412000	0.34714	2.681000	0.91329	0.557000	0.71058	CTT	.	.	none		0.413	TTC39C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446107.1	NM_153211	
LRP1	4035	hgsc.bcm.edu	37	12	57579390	57579390	+	Silent	SNP	C	C	T	rs149556819	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57579390C>T	ENST00000243077.3	+	41	7006	c.6540C>T	c.(6538-6540)tgC>tgT	p.C2180C		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	2180	EGF-like 9. {ECO:0000255|PROSITE- ProRule:PRU00076}.				aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	AGCGGGCCTGCGCCTGTGCCC	0.672																																					p.C2180C		Atlas-SNP	.											.	LRP1	428	.	0			c.C6540T						PASS	.	C		2,4402	4.2+/-10.8	0,2,2200	31.0	28.0	29.0		6540	-4.2	1.0	12	dbSNP_134	29	0,8594		0,0,4297	no	coding-synonymous	LRP1	NM_002332.2		0,2,6497	TT,TC,CC		0.0,0.0454,0.0154		2180/4545	57579390	2,12996	2202	4297	6499	SO:0001819	synonymous_variant	4035	exon41			GGCCTGCGCCTGT	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.6540C>T	12.37:g.57579390C>T		24.0	0.0	0		50.0	30.0	0.6	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.999;T|0.001	0.001	strong		0.672	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
LRRFIP1	9208	hgsc.bcm.edu	37	2	238662005	238662005	+	Silent	SNP	T	T	C	rs200278632		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:238662005T>C	ENST00000392000.4	+	8	654	c.537T>C	c.(535-537)gcT>gcC	p.A179A	LRRFIP1_ENST00000244815.5_Silent_p.A155A|LRRFIP1_ENST00000289175.6_Silent_p.A123A|LRRFIP1_ENST00000308482.9_Silent_p.A307A	NM_001137552.1	NP_001131024.1	Q32MZ4	LRRF1_HUMAN	leucine rich repeat (in FLII) interacting protein 1	179					innate immune response (GO:0045087)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of type I interferon production (GO:0032481)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	DNA binding (GO:0003677)|double-stranded RNA binding (GO:0003725)|protein homodimerization activity (GO:0042803)			NS(1)|breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(10)|ovary(1)|upper_aerodigestive_tract(1)	29		Breast(86;0.00257)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;9.75e-23)|OV - Ovarian serous cystadenocarcinoma(60;1.01e-10)|Kidney(56;4.85e-09)|KIRC - Kidney renal clear cell carcinoma(57;1.31e-07)|BRCA - Breast invasive adenocarcinoma(100;0.000151)|Lung(119;0.0137)|LUSC - Lung squamous cell carcinoma(224;0.0325)|COAD - Colon adenocarcinoma(134;0.228)		TTTCCAATGCTCAGCTAGACA	0.388																																					p.A307A		Atlas-SNP	.											.	LRRFIP1	171	.	0			c.T921C						PASS	.						89.0	88.0	89.0					2																	238662005		2203	4300	6503	SO:0001819	synonymous_variant	9208	exon15			CAATGCTCAGCTA	AJ223075	CCDS2521.1, CCDS46551.1, CCDS46552.1, CCDS46553.1	2q37.3	2010-09-30			ENSG00000124831	ENSG00000124831			6702	protein-coding gene	gene with protein product	"""GC-binding factor 2"""	603256				9705290, 9525888, 16199883	Standard	NM_004735		Approved	FLAP-1, FLIIAP1, TRIP, GCF-2, HUFI-1	uc002vxe.3	Q32MZ4	OTTHUMG00000133339	ENST00000392000.4:c.537T>C	2.37:g.238662005T>C		50.0	0.0	0		45.0	12.0	0.266667	NM_001137550	E9PGZ2|O75766|O75799|Q32MZ5|Q53T49|Q6PKG2|Q9Y607	Silent	SNP	ENST00000392000.4	37	CCDS46552.1																																																																																			T|1.000;C|0.000	0.000	strong		0.388	LRRFIP1-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317198.1	NM_004735	
PHYHIPL	84457	hgsc.bcm.edu	37	10	61005204	61005204	+	Silent	SNP	C	C	T	rs138490289	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:61005204C>T	ENST00000373880.4	+	5	1248	c.984C>T	c.(982-984)gtC>gtT	p.V328V	PHYHIPL_ENST00000373878.3_Silent_p.V302V	NM_032439.3	NP_115815.2	Q96FC7	PHIPL_HUMAN	phytanoyl-CoA 2-hydroxylase interacting protein-like	328						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				NS(1)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(3)|liver(2)|lung(3)|skin(1)|urinary_tract(1)	18						CCCAGGATGTCATTTTAGAAG	0.433													C|||	2	0.000399361	0.0	0.0029	5008	,	,		18642	0.0		0.0	False		,,,				2504	0.0				p.V328V		Atlas-SNP	.											.	PHYHIPL	44	.	0			c.C984T						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	75.0	70.0	72.0		906,984	2.7	1.0	10	dbSNP_134	72	18,8582	14.6+/-50.1	0,18,4282	no	coding-synonymous,coding-synonymous	PHYHIPL	NM_001143774.1,NM_032439.3	,	0,20,6483	TT,TC,CC		0.2093,0.0454,0.1538	,	302/351,328/377	61005204	20,12986	2203	4300	6503	SO:0001819	synonymous_variant	84457	exon5			GGATGTCATTTTA	AL834339	CCDS7254.1, CCDS44405.1	10q21.1	2013-02-11	2006-01-09		ENSG00000165443	ENSG00000165443		"""Fibronectin type III domain containing"""	29378	protein-coding gene	gene with protein product			"""phytanoyl-CoA hydroxylase interacting protein-like"""			11347906	Standard	NM_032439		Approved	KIAA1796, Em:AC025038.1	uc001jkk.4	Q96FC7	OTTHUMG00000018276	ENST00000373880.4:c.984C>T	10.37:g.61005204C>T		99.0	0.0	0		109.0	44.0	0.40367	NM_032439	B7WP61|Q68DF3|Q6UXY3|Q8N3W3|Q96JM9|Q96NP7	Silent	SNP	ENST00000373880.4	37	CCDS7254.1																																																																																			C|0.998;T|0.002	0.002	strong		0.433	PHYHIPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048156.1	NM_032439	
SPDYE1	285955	hgsc.bcm.edu	37	7	44046900	44046900	+	Silent	SNP	G	G	A	rs147853765	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:44046900G>A	ENST00000258704.3	+	5	803	c.666G>A	c.(664-666)gaG>gaA	p.E222E	RP5-1165K10.2_ENST00000454572.1_RNA|AC004951.6_ENST00000447643.1_lincRNA|POLR2J4_ENST00000427076.1_RNA	NM_001099435.2|NM_175064.2	NP_001092905.2|NP_778234.2	Q8NFV5	SPDE1_HUMAN	speedy/RINGO cell cycle regulator family member E1	222										endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(1)|prostate(1)	11						AGGACGACGAGGACTCCAAAC	0.552													g|||	26	0.00519169	0.0	0.0115	5008	,	,		19923	0.0		0.0159	False		,,,				2504	0.002				p.E222E		Atlas-SNP	.											.	SPDYE1	29	.	0			c.G666A						PASS	.	G		18,4388		0,18,2185	110.0	109.0	110.0		666		0.4	7	dbSNP_134	110	148,8442		1,146,4148	no	coding-synonymous	SPDYE1	NM_175064.2		1,164,6333	AA,AG,GG		1.7229,0.4085,1.2773		222/337	44046900	166,12830	2203	4295	6498	SO:0001819	synonymous_variant	285955	exon5			CGACGAGGACTCC	AF412027	CCDS5475.1	7q11.23	2013-05-08	2013-05-08	2009-02-17	ENSG00000136206	ENSG00000136206		"""Speedy homologs"""	16408	protein-coding gene	gene with protein product	"""Speedy E"""		"""Williams Beuren syndrome chromosome region 19"", ""speedy homolog E1 (Xenopus laevis)"""	WBSCR19		12073013	Standard	NM_175064		Approved	Ringo1, SPDYE	uc003tjf.3	Q8NFV5	OTTHUMG00000128985	ENST00000258704.3:c.666G>A	7.37:g.44046900G>A		144.0	0.0	0		235.0	55.0	0.234043	NM_175064	Q9NTH5	Silent	SNP	ENST00000258704.3	37	CCDS5475.1																																																																																			G|0.984;A|0.016	0.016	strong		0.552	SPDYE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250974.1	NM_175064	
FAM219A	203259	hgsc.bcm.edu	37	9	34401049	34401049	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:34401049C>T	ENST00000445726.1	-	6	777	c.471G>A	c.(469-471)gaG>gaA	p.E157E	FAM219A_ENST00000379081.1_Silent_p.E128E|FAM219A_ENST00000379080.1_Silent_p.E144E|FAM219A_ENST00000297620.4_Silent_p.E140E|FAM219A_ENST00000379087.1_Silent_p.E138E|FAM219A_ENST00000379084.1_Silent_p.E139E|FAM219A_ENST00000379089.1_Silent_p.E155E	NM_001184940.1|NM_001184941.1	NP_001171869.1|NP_001171870.1	Q8IW50	F219A_HUMAN	family with sequence similarity 219, member A	157																	GGTCTAGGTCCTCGTCGTCGG	0.617																																					p.E157E		Atlas-SNP	.											.	FAM219A	3	.	0			c.G471A						PASS	.						119.0	105.0	110.0					9																	34401049		2203	4300	6503	SO:0001819	synonymous_variant	203259	exon6			TAGGTCCTCGTCG	AK096350	CCDS6556.1, CCDS55304.1	9p11.2	2012-03-06	2012-03-06	2012-03-06	ENSG00000164970	ENSG00000164970			19920	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 25"""	C9orf25		9110174, 8619474	Standard	NM_147202		Approved	bA573M23.5, FLJ39031	uc011lok.2	Q8IW50	OTTHUMG00000019822	ENST00000445726.1:c.471G>A	9.37:g.34401049C>T		37.0	0.0	0		48.0	4.0	0.0833333	NM_001184940	A2A364|B4DFE1|B4DSR8|Q5T590|Q5T591|Q5T592|Q5T594|Q5T595|Q8TAZ8	Silent	SNP	ENST00000445726.1	37	CCDS55304.1																																																																																			.	.	none		0.617	FAM219A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001184940	
DYTN	391475	hgsc.bcm.edu	37	2	207564562	207564562	+	Missense_Mutation	SNP	T	T	A	rs112735024	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207564562T>A	ENST00000452335.2	-	7	724	c.608A>T	c.(607-609)gAg>gTg	p.E203V	DYTN_ENST00000477734.1_5'UTR|Y_RNA_ENST00000384589.1_RNA	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	203						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GATGGGAGGCTCAGATTGGAC	0.507													T|||	16	0.00319489	0.0076	0.0058	5008	,	,		18067	0.0		0.002	False		,,,				2504	0.0				p.E203V		Atlas-SNP	.											.	DYTN	168	.	0			c.A608T						PASS	.	T	VAL/GLU	44,3860		1,42,1909	76.0	82.0	80.0		608	3.6	1.0	2	dbSNP_132	80	51,8255		0,51,4102	yes	missense	DYTN	NM_001093730.1	121	1,93,6011	AA,AT,TT		0.614,1.127,0.7781	probably-damaging	203/579	207564562	95,12115	1952	4153	6105	SO:0001583	missense	391475	exon7			GGAGGCTCAGATT	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.608A>T	2.37:g.207564562T>A	ENSP00000396593:p.Glu203Val	139.0	0.0	0		166.0	81.0	0.487952	NM_001093730		Missense_Mutation	SNP	ENST00000452335.2	37	CCDS46502.1	4	0.0018315018315018315	3	0.006097560975609756	1	0.0027624309392265192	0	0.0	0	0.0	T	16.99	3.273329	0.59649	0.01127	0.00614	ENSG00000232125	ENST00000452335	T	0.77620	-1.11	5.89	3.58	0.41010	EF-hand domain, type 2 (1);	.	.	.	.	D	0.83450	0.5257	M	0.84433	2.695	0.36672	D	0.878551	D	0.89917	1.0	D	0.79784	0.993	D	0.88043	0.2782	9	0.87932	D	0	-12.5875	9.3049	0.37870	0.0:0.1712:0.0:0.8288	.	203	A2CJ06	DYTN_HUMAN	V	203	ENSP00000396593:E203V	ENSP00000396593:E203V	E	-	2	0	DYTN	207272807	1.000000	0.71417	0.998000	0.56505	0.413000	0.31143	2.499000	0.45372	2.254000	0.74563	0.459000	0.35465	GAG	T|0.997;A|0.003	0.003	strong		0.507	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
SIN3B	23309	hgsc.bcm.edu	37	19	16973724	16973724	+	Silent	SNP	G	G	A	rs143287291	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:16973724G>A	ENST00000379803.1	+	10	1310	c.1296G>A	c.(1294-1296)tcG>tcA	p.S432S	SIN3B_ENST00000595541.1_5'Flank|SIN3B_ENST00000248054.5_Intron	NM_015260.2	NP_056075.1			SIN3 transcription regulator family member B											endometrium(4)|kidney(2)|large_intestine(8)|lung(8)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26						TCCAGGGTTCGTGGACAGACG	0.527													.|||	22	0.00439297	0.0	0.0072	5008	,	,		19490	0.0		0.0119	False		,,,				2504	0.0051				p.S432S		Atlas-SNP	.											SIN3B,NS,malignant_melanoma,+1,1	SIN3B	90	1	0			c.G1296A						PASS	.	G		9,4397	16.8+/-37.8	0,9,2194	254.0	236.0	242.0		1296	-0.3	0.0	19	dbSNP_134	242	86,8514	49.8+/-109.6	1,84,4215	no	coding-synonymous	SIN3B	NM_015260.2		1,93,6409	AA,AG,GG		1.0,0.2043,0.7304		432/1163	16973724	95,12911	2203	4300	6503	SO:0001819	synonymous_variant	23309	exon10			GGGTTCGTGGACA	AB014600	CCDS32946.1, CCDS74308.1	19p13.12	2013-08-21	2013-08-21						19354	protein-coding gene	gene with protein product		607777	"""SIN3 homolog B, transcription regulator (yeast)"", ""SIN3 transcription regulator homolog B (yeast)"""			9734811	Standard	XM_005259832		Approved	KIAA0700	uc002ney.2	O75182		ENST00000379803.1:c.1296G>A	19.37:g.16973724G>A		157.0	0.0	0		188.0	87.0	0.462766	NM_015260		Silent	SNP	ENST00000379803.1	37	CCDS32946.1																																																																																			G|0.992;A|0.008	0.008	strong		0.527	SIN3B-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000462848.1	NM_015260	
KMT2D	8085	hgsc.bcm.edu	37	12	49445949	49445949	+	Missense_Mutation	SNP	G	G	T	rs367925817		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:49445949G>T	ENST00000301067.7	-	10	1516	c.1517C>A	c.(1516-1518)cCa>cAa	p.P506Q		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	506	15 X 5 AA repeats of S/P-P-P-E/P-E/A.|Pro-rich.				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)										TGATTCAGGTGGGGGAGACAG	0.612																																					p.P506Q		Atlas-SNP	.											.	MLL2	1173	.	0			c.C1517A						PASS	.	G	GLN/PRO	0,4072		0,0,2036	48.0	55.0	52.0		1517	-0.0	1.0	12		52	1,8375		0,1,4187	no	missense	MLL2	NM_003482.3	76	0,1,6223	TT,TG,GG		0.0119,0.0,0.0080	possibly-damaging	506/5538	49445949	1,12447	2036	4188	6224	SO:0001583	missense	8085	exon10			TCAGGTGGGGGAG	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.1517C>A	12.37:g.49445949G>T	ENSP00000301067:p.Pro506Gln	86.0	0.0	0		97.0	49.0	0.505155	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	G	6.497	0.459924	0.12342	0.0	1.19E-4	ENSG00000167548	ENST00000301067	T	0.79653	-1.29	4.2	-0.0106	0.13996	.	.	.	.	.	T	0.57301	0.2044	N	0.08118	0	0.09310	N	1	P	0.34462	0.454	B	0.34722	0.188	T	0.53851	-0.8380	9	0.87932	D	0	.	0.6454	0.00817	0.2995:0.1688:0.3582:0.1735	.	506	O14686	MLL2_HUMAN	Q	506	ENSP00000301067:P506Q	ENSP00000301067:P506Q	P	-	2	0	MLL2	47732216	0.015000	0.18098	0.993000	0.49108	0.853000	0.48598	0.189000	0.17037	0.178000	0.19917	-0.678000	0.03780	CCA	.	.	weak		0.612	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
SIGLEC12	89858	hgsc.bcm.edu	37	19	52000192	52000192	+	Missense_Mutation	SNP	A	A	G	rs144032115	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:52000192A>G	ENST00000291707.3	-	7	1596	c.1541T>C	c.(1540-1542)gTg>gCg	p.V514A	SIGLEC12_ENST00000598614.1_Missense_Mutation_p.V396A	NM_053003.2	NP_443729.1	Q96PQ1	SIG12_HUMAN	sialic acid binding Ig-like lectin 12 (gene/pseudogene)	514					cell adhesion (GO:0007155)	integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)			NS(2)|biliary_tract(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(8)|liver(1)|lung(23)|ovary(4)|prostate(2)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)	61		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.00161)|OV - Ovarian serous cystadenocarcinoma(262;0.0102)		CCCCACGCCCACTGCTGGCCT	0.582													N|||	5	0.000998403	0.0015	0.0	5008	,	,		19279	0.0		0.001	False		,,,				2504	0.002				p.V514A		Atlas-SNP	.											SIGLEC12,NS,haematopoietic_neoplasm,0,1	SIGLEC12	243	1	0			c.T1541C						PASS	.	G	ALA/VAL,ALA/VAL	0,4406		0,0,2203	164.0	127.0	140.0		1187,1541	-2.7	0.0	19	dbSNP_134	140	5,8595		0,5,4295	no	missense,missense	SIGLEC12	NM_033329.1,NM_053003.2	64,64	0,5,6498	GG,GA,AA		0.0581,0.0,0.0384	benign,benign	396/478,514/596	52000192	5,13001	2203	4300	6503	SO:0001583	missense	89858	exon7			ACGCCCACTGCTG	AF282256	CCDS12833.1, CCDS59416.1	19q13.41	2013-01-29	2011-06-29	2004-10-20	ENSG00000254521	ENSG00000254521		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15482	protein-coding gene	gene with protein product		606094	"""SIGLEC-like 1"", ""sialic acid binding Ig-like lectin 12"""	SIGLECL1		11409877, 11328818, 21555517	Standard	NM_053003		Approved	SLG, S2V, Siglec-XII, Siglec-12, Siglec-L1	uc002pwx.1	Q96PQ1	OTTHUMG00000165524	ENST00000291707.3:c.1541T>C	19.37:g.52000192A>G	ENSP00000291707:p.Val514Ala	95.0	0.0	0		132.0	15.0	0.113636	NM_053003	Q8IYH7	Missense_Mutation	SNP	ENST00000291707.3	37	CCDS12833.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	.	0.001	-3.340068	0.00017	0.0	5.81E-4	ENSG00000254521	ENST00000291707	T	0.35789	1.29	1.34	-2.69	0.06022	.	.	.	.	.	T	0.10981	0.0268	N	0.03194	-0.395	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.10894	-1.0610	9	0.11485	T	0.65	.	0.7864	0.01049	0.2935:0.3354:0.2021:0.169	.	514;396	Q96PQ1;Q96PQ1-2	SIG12_HUMAN;.	A	514	ENSP00000291707:V514A	ENSP00000291707:V514A	V	-	2	0	SIGLEC12	56692004	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-5.050000	0.00156	-3.045000	0.00262	-1.416000	0.01114	GTG	A|1.000;G|0.000	0.000	strong		0.582	SIGLEC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384641.2	NM_053003	
SCUBE2	57758	hgsc.bcm.edu	37	11	9082068	9082068	+	Missense_Mutation	SNP	G	G	A	rs35703942|rs72547298	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:9082068G>A	ENST00000309263.3	-	8	926	c.854C>T	c.(853-855)aCg>aTg	p.T285M	SCUBE2_ENST00000450649.2_Missense_Mutation_p.T285M|SCUBE2_ENST00000520467.1_Missense_Mutation_p.T285M|RP11-467K18.2_ENST00000521394.2_RNA|SCUBE2_ENST00000457346.2_Missense_Mutation_p.T285M			Q9NQ36	SCUB2_HUMAN	signal peptide, CUB domain, EGF-like 2	285						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			breast(1)|endometrium(5)|kidney(3)|large_intestine(15)|liver(1)|lung(10)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	42				all cancers(16;8.57e-09)|Epithelial(150;4.42e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0116)		GACAGCACACGTTTCTGGCAA	0.498													G|||	14	0.00279553	0.0	0.0029	5008	,	,		23726	0.0		0.0089	False		,,,				2504	0.0031				p.T285M		Atlas-SNP	.											.	SCUBE2	102	.	0			c.C854T						PASS	.	G	MET/THR,MET/THR	12,4390	19.1+/-41.9	0,12,2189	143.0	133.0	136.0		854,854	5.9	1.0	11	dbSNP_130	136	92,8500	51.9+/-112.3	3,86,4207	yes	missense,missense	SCUBE2	NM_001170690.1,NM_020974.2	81,81	3,98,6396	AA,AG,GG		1.0708,0.2726,0.8004	probably-damaging,probably-damaging	285/808,285/972	9082068	104,12890	2201	4296	6497	SO:0001583	missense	57758	exon8			GCACACGTTTCTG	AK131552	CCDS7797.1, CCDS7797.2, CCDS53599.1	11p15.4	2014-09-04			ENSG00000175356	ENSG00000175356			30425	protein-coding gene	gene with protein product		611747				12270931, 11528127	Standard	NM_020974		Approved	Cegf1, Cegb1, FLJ16792	uc001mhi.2	Q9NQ36	OTTHUMG00000163880	ENST00000309263.3:c.854C>T	11.37:g.9082068G>A	ENSP00000310658:p.Thr285Met	41.0	0.0	0		52.0	26.0	0.5	NM_001170690	Q2NKQ8|Q6ZWI1	Missense_Mutation	SNP	ENST00000309263.3	37		7|7	0.003205128205128205|0.003205128205128205	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	7|7	0.009234828496042216|0.009234828496042216	G|G	23.8|23.8	4.462764|4.462764	0.84425|0.84425	0.002726|0.002726	0.010708|0.010708	ENSG00000175356|ENSG00000175356	ENST00000519788;ENST00000531429|ENST00000457346;ENST00000309263;ENST00000450649;ENST00000520467	.|T;T;D;D	.|0.84589	.|-1.34;-1.41;-1.87;-1.53	5.94|5.94	5.94|5.94	0.96194|0.96194	.|Epidermal growth factor-like (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91885|0.91885	0.7431|0.7431	M|M	0.86953|0.86953	2.85|2.85	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|0.999;1.0;0.999	D|D	0.92305|0.92305	0.5853|0.5853	5|10	.|0.72032	.|D	.|0.01	.|.	20.3736|20.3736	0.98901|0.98901	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|285;285;285	.|Q9NQ36-3;Q9NQ36-2;Q9NQ36	.|.;.;SCUB2_HUMAN	C|M	9;50|285	.|ENSP00000390481:T285M;ENSP00000310658:T285M;ENSP00000415187:T285M;ENSP00000429969:T285M	.|ENSP00000310658:T285M	R|T	-|-	1|2	0|0	SCUBE2|SCUBE2	9038644|9038644	1.000000|1.000000	0.71417|0.71417	0.968000|0.968000	0.41197|0.41197	0.916000|0.916000	0.54674|0.54674	9.869000|9.869000	0.99810|0.99810	2.820000|2.820000	0.97059|0.97059	0.650000|0.650000	0.86243|0.86243	CGT|ACG	G|0.994;A|0.006	0.006	strong		0.498	SCUBE2-005	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000385812.2	NM_020974	
NAA25	80018	hgsc.bcm.edu	37	12	112486213	112486213	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:112486213C>T	ENST00000261745.4	-	16	2011	c.1763G>A	c.(1762-1764)gGt>gAt	p.G588D		NM_024953.3	NP_079229.2	Q14CX7	NAA25_HUMAN	N(alpha)-acetyltransferase 25, NatB auxiliary subunit	588						cytoplasm (GO:0005737)				autonomic_ganglia(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|liver(1)|lung(14)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(4)	46						CTCAAATGCACCATATTTGTA	0.388																																					p.G588D		Atlas-SNP	.											.	NAA25	105	.	0			c.G1763A						PASS	.						111.0	106.0	108.0					12																	112486213		2203	4300	6503	SO:0001583	missense	80018	exon16			AATGCACCATATT	AB054990	CCDS9159.1	12q24.13	2013-10-11	2010-01-14	2010-01-14		ENSG00000111300		"""N(alpha)-acetyltransferase subunits"""	25783	protein-coding gene	gene with protein product		612755	"""chromosome 12 open reading frame 30"""	C12orf30		19660095	Standard	NM_024953		Approved	FLJ13089	uc001ttm.3	Q14CX7	OTTHUMG00000169638	ENST00000261745.4:c.1763G>A	12.37:g.112486213C>T	ENSP00000261745:p.Gly588Asp	49.0	0.0	0		57.0	4.0	0.0701754	NM_024953	A0JLU7|Q6MZH1|Q7Z4N6|Q9H911	Missense_Mutation	SNP	ENST00000261745.4	37	CCDS9159.1	.	.	.	.	.	.	.	.	.	.	C	24.6	4.545698	0.86022	.	.	ENSG00000111300	ENST00000261745	T	0.53857	0.6	5.58	5.58	0.84498	.	0.000000	0.85682	D	0.000000	T	0.75722	0.3888	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.77004	0.989;0.989	T	0.75442	-0.3316	10	0.40728	T	0.16	-12.8941	19.5841	0.95484	0.0:1.0:0.0:0.0	.	588;588	A8K8X0;Q14CX7	.;NAA25_HUMAN	D	588	ENSP00000261745:G588D	ENSP00000261745:G588D	G	-	2	0	NAA25	110970596	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.604000	0.88044	0.655000	0.94253	GGT	.	.	none		0.388	NAA25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405205.1	NM_024953	
OTUD7A	161725	hgsc.bcm.edu	37	15	31776837	31776837	+	Missense_Mutation	SNP	C	C	G	rs76704217	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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	81.0	0.0	0		84.0	46.0	0.547619	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	
KIAA1958	158405	hgsc.bcm.edu	37	9	115337154	115337154	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:115337154A>G	ENST00000337530.6	+	2	1090	c.794A>G	c.(793-795)gAc>gGc	p.D265G	KIAA1958_ENST00000536272.1_Missense_Mutation_p.D265G|KIAA1958_ENST00000374244.3_Missense_Mutation_p.D265G	NM_133465.2	NP_597722.1	Q8N8K9	K1958_HUMAN	KIAA1958	265										endometrium(1)|large_intestine(9)|lung(10)|prostate(2)|skin(3)	25						ACGGAGCTAGACCCACACGGT	0.547																																					p.D265G		Atlas-SNP	.											KIAA1958_ENST00000374244,NS,carcinoma,+1,3	KIAA1958	52	3	0			c.A794G						PASS	.						239.0	211.0	221.0					9																	115337154		2203	4300	6503	SO:0001583	missense	158405	exon2			AGCTAGACCCACA	AB075838	CCDS35108.1, CCDS69642.1	9q33.1	2009-09-22			ENSG00000165185	ENSG00000165185			23427	protein-coding gene	gene with protein product							Standard	NM_001287038		Approved	FLJ39294	uc004bgf.1	Q8N8K9	OTTHUMG00000020508	ENST00000337530.6:c.794A>G	9.37:g.115337154A>G	ENSP00000336940:p.Asp265Gly	99.0	0.0	0		102.0	5.0	0.0490196	NM_133465	B7ZKW6|Q2M336|Q5T252|Q8TF43|Q96N02	Missense_Mutation	SNP	ENST00000337530.6	37	CCDS35108.1	.	.	.	.	.	.	.	.	.	.	A	16.00	2.999186	0.54147	.	.	ENSG00000165185	ENST00000337530;ENST00000374244;ENST00000536272	T;T;T	0.41758	0.99;0.99;0.99	6.07	6.07	0.98685	.	0.067648	0.64402	D	0.000011	T	0.33059	0.0850	N	0.14661	0.345	0.58432	D	0.999991	P;P	0.46395	0.877;0.734	B;B	0.43194	0.411;0.321	T	0.24297	-1.0164	10	0.66056	D	0.02	-10.9977	16.6288	0.85011	1.0:0.0:0.0:0.0	.	265;265	B7ZKW6;Q8N8K9	.;K1958_HUMAN	G	265	ENSP00000336940:D265G;ENSP00000363362:D265G;ENSP00000440504:D265G	ENSP00000336940:D265G	D	+	2	0	KIAA1958	114376975	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.696000	0.74598	2.326000	0.78906	0.533000	0.62120	GAC	.	.	none		0.547	KIAA1958-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053690.1	NM_133465	
KCNIP4	80333	hgsc.bcm.edu	37	4	20751343	20751343	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:20751343T>C	ENST00000382152.2	-	5	538	c.371A>G	c.(370-372)tAt>tGt	p.Y124C	PACRGL_ENST00000507634.1_Intron|KCNIP4_ENST00000509207.1_Missense_Mutation_p.Y62C|KCNIP4_ENST00000447367.2_Missense_Mutation_p.Y90C|KCNIP4_ENST00000382148.3_Missense_Mutation_p.Y99C|KCNIP4_ENST00000359001.5_Missense_Mutation_p.Y62C|KCNIP4_ENST00000382149.4_5'UTR|KCNIP4_ENST00000382150.4_Missense_Mutation_p.Y103C	NM_025221.5	NP_079497.2	Q6PIL6	KCIP4_HUMAN	Kv channel interacting protein 4	124	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.					dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(6)|prostate(1)|upper_aerodigestive_tract(1)	13		Breast(46;0.134)				AAAATGTGCATATGTTGTAGA	0.368																																					p.Y104C		Atlas-SNP	.											.	KCNIP4	85	.	0			c.A311G						PASS	.						114.0	105.0	108.0					4																	20751343		2203	4300	6503	SO:0001583	missense	80333	exon4			TGTGCATATGTTG	AF453244	CCDS3428.1, CCDS43215.1, CCDS43216.1, CCDS43217.1, CCDS47035.1	4p15.32	2013-01-10			ENSG00000185774	ENSG00000185774		"""EF-hand domain containing"""	30083	protein-coding gene	gene with protein product		608182				11805342, 11847232	Standard	XM_005248190		Approved	CALP, KCHIP4, MGC44947	uc003gqh.1	Q6PIL6	OTTHUMG00000128557	ENST00000382152.2:c.371A>G	4.37:g.20751343T>C	ENSP00000371587:p.Tyr124Cys	53.0	0.0	0		48.0	4.0	0.0833333	NM_025221	Q3YAB8|Q3YAB9|Q3YAC0|Q3YAC1|Q3YAC2|Q4W5G8|Q8NEU0|Q9BWT2|Q9H294|Q9H2A4	Missense_Mutation	SNP	ENST00000382152.2	37	CCDS43216.1	.	.	.	.	.	.	.	.	.	.	T	18.46	3.628173	0.66901	.	.	ENSG00000185774	ENST00000382148;ENST00000447367;ENST00000382150;ENST00000413487;ENST00000382152;ENST00000509207;ENST00000359001	T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98	5.24	5.24	0.73138	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	T	0.55862	0.1947	M	0.92880	3.355	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.998;0.998;0.999;0.999	T	0.67715	-0.5599	10	0.87932	D	0	.	14.1041	0.65078	0.0:0.0:0.0:1.0	.	99;103;107;124	Q3YAB9;Q3YAC0;Q3YAB7;Q6PIL6	.;.;.;KCIP4_HUMAN	C	99;90;103;62;124;62;62	ENSP00000371583:Y99C;ENSP00000399080:Y90C;ENSP00000371585:Y103C;ENSP00000371587:Y124C;ENSP00000423257:Y62C;ENSP00000351892:Y62C	ENSP00000351892:Y62C	Y	-	2	0	KCNIP4	20360441	1.000000	0.71417	0.997000	0.53966	0.725000	0.41563	7.662000	0.83803	1.974000	0.57490	0.482000	0.46254	TAT	.	.	none		0.368	KCNIP4-004	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000360407.3	NM_025221	
SRRM4	84530	hgsc.bcm.edu	37	12	119568596	119568596	+	Missense_Mutation	SNP	G	G	A	rs7297606	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:119568596G>A	ENST00000267260.4	+	8	1116	c.728G>A	c.(727-729)aGt>aAt	p.S243N	SRRM4_ENST00000537597.1_3'UTR	NM_194286.3	NP_919262.2	A7MD48	SRRM4_HUMAN	serine/arginine repetitive matrix 4	243	Ser-rich.		S -> N (in dbSNP:rs7297606).		cell differentiation (GO:0030154)|mRNA processing (GO:0006397)|nervous system development (GO:0007399)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|sensory perception of sound (GO:0007605)	nucleus (GO:0005634)	mRNA binding (GO:0003729)			breast(2)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	24						CGCCCGCCCAGTCAACCCCTC	0.627													G|||	500	0.0998403	0.2042	0.1124	5008	,	,		15715	0.0268		0.0547	False		,,,				2504	0.0716				p.S243N		Atlas-SNP	.											.	SRRM4	131	.	0			c.G728A						PASS	.	G	ASN/SER	638,3266		55,528,1369	25.0	31.0	29.0		728	3.3	1.0	12	dbSNP_116	29	626,7648		17,592,3528	yes	missense	SRRM4	NM_194286.3	46	72,1120,4897	AA,AG,GG		7.5659,16.3422,10.3794	benign	243/612	119568596	1264,10914	1952	4137	6089	SO:0001583	missense	84530	exon8			CGCCCAGTCAACC	AB058756	CCDS44994.1	12q24.23	2009-09-22	2009-09-21	2009-09-21	ENSG00000139767	ENSG00000139767			29389	protein-coding gene	gene with protein product	"""neural-specific SR-related protein of 100 kDa"""	613103	"""KIAA1853"""	KIAA1853		19737518	Standard	NM_194286		Approved	nSR100	uc001txa.2	A7MD48	OTTHUMG00000168928	ENST00000267260.4:c.728G>A	12.37:g.119568596G>A	ENSP00000267260:p.Ser243Asn	18.0	0.0	0		26.0	14.0	0.538462	NM_194286	A8K5P6|B2RZH7|Q7Z5F0|Q96JH4	Missense_Mutation	SNP	ENST00000267260.4	37	CCDS44994.1	191	0.08745421245421245	94	0.1910569105691057	36	0.09944751381215469	20	0.03496503496503497	41	0.05408970976253298	G	7.164	0.586356	0.13749	0.163422	0.075659	ENSG00000139767	ENST00000267260	T	0.24538	1.85	5.21	3.34	0.38264	.	0.747332	0.13340	N	0.395235	T	0.00039	0.0001	L	0.44542	1.39	0.41880	P	0.009688999999999948	B	0.30281	0.275	B	0.29942	0.109	T	0.23440	-1.0188	9	0.12430	T	0.62	-8.2941	11.354	0.49605	0.0752:0.1274:0.7974:0.0	rs7297606;rs52809663;rs58175205;rs7297606	243	A7MD48	SRRM4_HUMAN	N	243	ENSP00000267260:S243N	ENSP00000267260:S243N	S	+	2	0	SRRM4	118052979	1.000000	0.71417	0.992000	0.48379	0.053000	0.15095	1.326000	0.33735	0.207000	0.20607	-1.688000	0.00730	AGT	G|0.908;A|0.092	0.092	strong		0.627	SRRM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401640.2	NM_194286	
WWC2	80014	hgsc.bcm.edu	37	4	184207192	184207192	+	Missense_Mutation	SNP	C	C	T	rs148189381		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:184207192C>T	ENST00000403733.3	+	20	3320	c.3121C>T	c.(3121-3123)Cgc>Tgc	p.R1041C	WWC2_ENST00000508747.1_Missense_Mutation_p.R169C|WWC2_ENST00000504005.1_Missense_Mutation_p.R723C|WWC2_ENST00000448232.2_Missense_Mutation_p.R1065C|WWC2_ENST00000513834.1_Missense_Mutation_p.R992C	NM_024949.5	NP_079225.5	Q6AWC2	WWC2_HUMAN	WW and C2 domain containing 2	1041					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(2)|prostate(1)|stomach(1)|urinary_tract(3)	32		all_lung(41;5.28e-14)|Lung NSC(41;1.35e-13)|Colorectal(36;0.00681)|Hepatocellular(41;0.00886)|Renal(120;0.00992)|Prostate(90;0.0237)|all_hematologic(60;0.0592)|Esophageal squamous(56;0.179)|all_neural(102;0.202)		all cancers(43;3.38e-24)|Epithelial(43;1.4e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.09e-09)|GBM - Glioblastoma multiforme(59;3.33e-05)|Colorectal(24;3.58e-05)|STAD - Stomach adenocarcinoma(60;4.21e-05)|COAD - Colon adenocarcinoma(29;0.000171)|LUSC - Lung squamous cell carcinoma(40;0.0145)|READ - Rectum adenocarcinoma(43;0.242)		CACCGAACGCCGCAGTTTGAG	0.448																																					p.R1041C		Atlas-SNP	.											.	WWC2	78	.	0			c.C3121T						PASS	.	C	CYS/ARG	0,4404		0,0,2202	73.0	63.0	67.0		3121	4.4	1.0	4	dbSNP_134	67	1,8599		0,1,4299	no	missense	WWC2	NM_024949.5	180	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	1041/1193	184207192	1,13003	2202	4300	6502	SO:0001583	missense	80014	exon20			GAACGCCGCAGTT	BC017957	CCDS34109.2	4q35.1	2010-08-05	2006-11-09		ENSG00000151718	ENSG00000151718		"""WW, C2 and coiled-coil domain containing"""	24148	protein-coding gene	gene with protein product			"""WW, C2 and coiled-coil domain containing 2"""			12477932	Standard	NM_024949		Approved	BOMB, FLJ22029	uc010irx.3	Q6AWC2	OTTHUMG00000150685	ENST00000403733.3:c.3121C>T	4.37:g.184207192C>T	ENSP00000384222:p.Arg1041Cys	52.0	0.0	0		80.0	40.0	0.5	NM_024949	Q32Q84|Q69YQ1|Q6AWB8|Q6ZSY9|Q6ZU09|Q7Z620|Q8TEB8|Q9H6P0	Missense_Mutation	SNP	ENST00000403733.3	37	CCDS34109.2	.	.	.	.	.	.	.	.	.	.	C	19.81	3.897272	0.72639	0.0	1.16E-4	ENSG00000151718	ENST00000403733;ENST00000513834;ENST00000448232;ENST00000504005;ENST00000508747	T;T;T;T;T	0.56103	0.48;0.48;0.48;0.48;0.48	5.23	4.39	0.52855	.	0.082358	0.50627	D	0.000117	T	0.71350	0.3329	M	0.82823	2.61	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.998;1.0;0.998;0.998	T	0.73672	-0.3909	10	0.54805	T	0.06	-15.2741	9.6331	0.39791	0.1967:0.7307:0.0:0.0726	.	1065;1041;169;992	Q6AWC2-6;Q6AWC2;Q6AWC2-7;Q6AWC2-4	.;WWC2_HUMAN;.;.	C	1041;992;1065;723;169	ENSP00000384222:R1041C;ENSP00000425054:R992C;ENSP00000398577:R1065C;ENSP00000427569:R723C;ENSP00000420835:R169C	ENSP00000384222:R1041C	R	+	1	0	WWC2	184444186	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.516000	0.45520	1.443000	0.47586	0.655000	0.94253	CGC	C|1.000;T|0.000	0.000	weak		0.448	WWC2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319608.1	NM_024949	
GRAP2	9402	hgsc.bcm.edu	37	22	40366924	40366924	+	Missense_Mutation	SNP	C	C	T	rs149718626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:40366924C>T	ENST00000344138.4	+	8	1092	c.829C>T	c.(829-831)Cgg>Tgg	p.R277W	GRAP2_ENST00000540310.1_Missense_Mutation_p.R211W|GRAP2_ENST00000544756.1_Missense_Mutation_p.R205W|GRAP2_ENST00000543252.1_Missense_Mutation_p.R237W|GRAP2_ENST00000407075.3_Missense_Mutation_p.R277W|GRAP2_ENST00000399090.2_Missense_Mutation_p.R164W	NM_004810.2	NP_004801.1	O75791	GRAP2_HUMAN	GRB2-related adaptor protein 2	277	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				cell-cell signaling (GO:0007267)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of signal transduction (GO:0009967)|Ras protein signal transduction (GO:0007265)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|nucleus (GO:0005634)	SH3/SH2 adaptor activity (GO:0005070)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	14						GCGGTGGGCCCGGGCGCTGTA	0.657																																					p.R277W		Atlas-SNP	.											.	GRAP2	29	.	0			c.C829T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	42.0	44.0	43.0		829	0.6	0.9	22	dbSNP_134	43	2,8598	2.2+/-6.3	0,2,4298	yes	missense	GRAP2	NM_004810.2	101	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging	277/331	40366924	2,13004	2203	4300	6503	SO:0001583	missense	9402	exon8			TGGGCCCGGGCGC	AF102694	CCDS13999.1	22q13.2	2013-02-14			ENSG00000100351	ENSG00000100351		"""SH2 domain containing"""	4563	protein-coding gene	gene with protein product		604518				9878555, 10224278	Standard	XM_005261836		Approved	Grf40, GrbX, GRBLG, GADS, Mona	uc003ayh.2	O75791	OTTHUMG00000151097	ENST00000344138.4:c.829C>T	22.37:g.40366924C>T	ENSP00000339186:p.Arg277Trp	61.0	0.0	0		39.0	18.0	0.461538	NM_004810	B7Z8I3|O43726|Q9NRB7	Missense_Mutation	SNP	ENST00000344138.4	37	CCDS13999.1	.	.	.	.	.	.	.	.	.	.	C	19.22	3.786068	0.70337	0.0	2.33E-4	ENSG00000100351	ENST00000344138;ENST00000543252;ENST00000544006;ENST00000540310;ENST00000544756;ENST00000399090;ENST00000407075	T;T;T;T;T;T	0.52983	0.64;1.37;0.64;0.64;0.64;0.64	5.45	0.607	0.17564	Src homology-3 domain (5);	0.508670	0.20690	N	0.087471	T	0.69513	0.3119	M	0.92649	3.33	0.40772	D	0.983098	D;D;D;D;D	0.89917	1.0;0.998;0.999;0.999;0.998	D;P;D;P;P	0.68765	0.96;0.817;0.921;0.877;0.817	T	0.73257	-0.4040	10	0.66056	D	0.02	-14.6978	8.7497	0.34609	0.5226:0.4077:0.0:0.0697	.	164;277;211;251;277	B7Z8I3;Q6FI14;F5H548;B7Z8F8;O75791	.;.;.;.;GRAP2_HUMAN	W	277;237;251;211;205;164;277	ENSP00000339186:R277W;ENSP00000446350:R237W;ENSP00000444734:R211W;ENSP00000442195:R205W;ENSP00000382040:R164W;ENSP00000385607:R277W	ENSP00000339186:R277W	R	+	1	2	GRAP2	38696870	0.999000	0.42202	0.932000	0.37286	0.880000	0.50808	0.823000	0.27366	0.593000	0.29745	0.557000	0.71058	CGG	C|1.000;T|0.000	0.000	strong		0.657	GRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321295.1	NM_004810	
PDCD4	27250	hgsc.bcm.edu	37	10	112654238	112654238	+	Silent	SNP	C	C	T	rs41292602	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:112654238C>T	ENST00000280154.7	+	10	1441	c.1167C>T	c.(1165-1167)tcC>tcT	p.S389S	PDCD4_ENST00000393104.2_Silent_p.S378S	NM_001199492.1|NM_014456.4	NP_001186421.1|NP_055271.2	Q53EL6	PDCD4_HUMAN	programmed cell death 4 (neoplastic transformation inhibitor)	389	MI 2. {ECO:0000255|PROSITE- ProRule:PRU00698}.				apoptotic process (GO:0006915)|cell aging (GO:0007569)|negative regulation of cell cycle (GO:0045786)|negative regulation of JUN kinase activity (GO:0043508)|negative regulation of transcription, DNA-templated (GO:0045892)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	RNA binding (GO:0003723)			breast(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	13		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.000526)|all cancers(201;0.00794)|BRCA - Breast invasive adenocarcinoma(275;0.125)		TATTAAAGTCCCTTTGGAAGT	0.284													C|||	9	0.00179712	0.0008	0.0014	5008	,	,		17286	0.0		0.007	False		,,,				2504	0.0				p.S389S	Ovarian(115;1498 1603 9363 40056 40885)	Atlas-SNP	.											.	PDCD4	39	.	0			c.C1167T						PASS	.	C	,,	3,4399	2.1+/-5.4	0,3,2198	87.0	97.0	93.0		1125,1167,1134	-7.2	0.5	10	dbSNP_127	93	45,8529	27.9+/-77.7	0,45,4242	no	coding-synonymous,coding-synonymous,coding-synonymous	PDCD4	NM_001199492.1,NM_014456.4,NM_145341.3	,,	0,48,6440	TT,TC,CC		0.5248,0.0682,0.3699	,,	375/456,389/470,378/459	112654238	48,12928	2201	4287	6488	SO:0001819	synonymous_variant	27250	exon10			AAAGTCCCTTTGG	U83908	CCDS7567.1, CCDS44478.1	10q24	2008-08-01			ENSG00000150593	ENSG00000150593			8763	protein-coding gene	gene with protein product	"""nuclear antigen H731"""	608610				9759869	Standard	NM_014456		Approved	H731	uc001kzh.3	Q53EL6	OTTHUMG00000019048	ENST00000280154.7:c.1167C>T	10.37:g.112654238C>T		31.0	0.0	0		30.0	15.0	0.5	NM_014456	B2RCV4|B5ME91|O15501|Q5VZS6|Q6PJI5|Q8TAR5|Q99834	Silent	SNP	ENST00000280154.7	37	CCDS7567.1																																																																																			C|0.997;T|0.003	0.003	strong		0.284	PDCD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050361.1	NM_014456	
FAM83G	644815	hgsc.bcm.edu	37	17	18907198	18907198	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:18907198C>T	ENST00000388995.6	-	2	380	c.157G>A	c.(157-159)Gag>Aag	p.E53K	SLC5A10_ENST00000395643.2_Intron|SLC5A10_ENST00000395647.2_Intron|FAM83G_ENST00000585154.2_Missense_Mutation_p.E53K|FAM83G_ENST00000345041.4_Missense_Mutation_p.E53K|SLC5A10_ENST00000395642.1_Intron|SLC5A10_ENST00000317977.6_Intron|SLC5A10_ENST00000417251.2_Intron|SLC5A10_ENST00000395645.3_Intron			A6ND36	FA83G_HUMAN	family with sequence similarity 83, member G	53					BMP signaling pathway (GO:0030509)	cytosol (GO:0005829)|nucleus (GO:0005634)				central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(2)|prostate(3)|stomach(1)	22						CGGATGTTCTCCCGCTTGAGC	0.672																																					p.E53K		Atlas-SNP	.											.	FAM83G	51	.	0			c.G157A						PASS	.						35.0	41.0	39.0					17																	18907198		2015	4183	6198	SO:0001583	missense	644815	exon2			TGTTCTCCCGCTT	AK123558	CCDS42276.1	17p11.2	2014-05-01	2006-03-22		ENSG00000188522	ENSG00000188522			32554	protein-coding gene	gene with protein product	"""protein associated with SMAD1"""	615886				24554596	Standard	NM_001039999		Approved	FLJ41564, PAWS1	uc002guw.3	A6ND36	OTTHUMG00000059411	ENST00000388995.6:c.157G>A	17.37:g.18907198C>T	ENSP00000373647:p.Glu53Lys	110.0	0.0	0		116.0	60.0	0.517241	NM_001039999	Q3KQZ4|Q6ZW60	Missense_Mutation	SNP	ENST00000388995.6	37	CCDS42276.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.658749	0.47467	.	.	ENSG00000188522	ENST00000388995;ENST00000345041;ENST00000399096	T;T	0.15487	2.42;2.42	5.01	5.01	0.66863	.	0.392245	0.26746	N	0.022701	T	0.31040	0.0784	M	0.84511	2.7	0.34765	D	0.733098	P	0.34934	0.476	B	0.36186	0.219	T	0.53732	-0.8397	10	0.87932	D	0	-36.4032	18.3131	0.90207	0.0:1.0:0.0:0.0	.	53	A6ND36	FA83G_HUMAN	K	53	ENSP00000373647:E53K;ENSP00000343279:E53K	ENSP00000343279:E53K	E	-	1	0	FAM83G	18847923	0.905000	0.30787	1.000000	0.80357	0.987000	0.75469	1.035000	0.30216	2.332000	0.79248	0.491000	0.48974	GAG	.	.	none		0.672	FAM83G-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253108.4		
HBP1	26959	hgsc.bcm.edu	37	7	106836344	106836344	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:106836344G>A	ENST00000222574.4	+	9	1319	c.1133G>A	c.(1132-1134)cGt>cAt	p.R378H	HBP1_ENST00000468410.1_Missense_Mutation_p.R378H|HBP1_ENST00000485846.1_Missense_Mutation_p.R378H|HBP1_ENST00000461963.1_3'UTR|CTA-363E19.2_ENST00000607036.1_RNA	NM_012257.3	NP_036389.2	O60381	HBP1_HUMAN	HMG-box transcription factor 1	378					cell cycle arrest (GO:0007050)|positive regulation of potassium ion transport (GO:0043268)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			large_intestine(4)|lung(3)|prostate(1)|skin(2)	10						CGCCAGCGTCGTGCATCTTTG	0.388																																					p.R388H		Atlas-SNP	.											.	HBP1	31	.	0			c.G1163A						PASS	.						87.0	85.0	86.0					7																	106836344		2203	4300	6503	SO:0001583	missense	26959	exon9			AGCGTCGTGCATC	BC017069	CCDS5741.1	7q22-q31	2003-10-08			ENSG00000105856	ENSG00000105856			23200	protein-coding gene	gene with protein product						9030690, 11500377	Standard	NM_001244262		Approved		uc011klv.2	O60381	OTTHUMG00000157642	ENST00000222574.4:c.1133G>A	7.37:g.106836344G>A	ENSP00000222574:p.Arg378His	102.0	0.0	0		109.0	55.0	0.504587	NM_001244262	B3KVB7|Q8TBM1|Q8TE93|Q96AJ2	Missense_Mutation	SNP	ENST00000222574.4	37	CCDS5741.1	.	.	.	.	.	.	.	.	.	.	G	34	5.355207	0.95854	.	.	ENSG00000105856	ENST00000468410;ENST00000222574;ENST00000485846;ENST00000498408	D;D;D	0.99369	-5.78;-5.78;-5.78	5.96	5.96	0.96718	.	0.044632	0.85682	D	0.000000	D	0.98896	0.9626	L	0.29908	0.895	0.58432	D	0.999999	D;D;D	0.89917	0.999;1.0;0.999	D;D;P	0.65773	0.913;0.938;0.869	D	0.99925	1.1280	10	0.72032	D	0.01	-14.0183	20.4084	0.99013	0.0:0.0:1.0:0.0	.	388;378;378	B4DJ36;O60381-3;O60381	.;.;HBP1_HUMAN	H	378;378;378;370	ENSP00000420500:R378H;ENSP00000222574:R378H;ENSP00000418738:R378H	ENSP00000222574:R378H	R	+	2	0	HBP1	106623580	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.950000	0.87804	2.833000	0.97629	0.650000	0.86243	CGT	.	.	none		0.388	HBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349297.1	NM_012257	
APC	324	hgsc.bcm.edu	37	5	112176325	112176325	+	Silent	SNP	G	G	A	rs42427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112176325G>A	ENST00000457016.1	+	16	5414	c.5034G>A	c.(5032-5034)ggG>ggA	p.G1678G	APC_ENST00000257430.4_Silent_p.G1678G|APC_ENST00000508376.2_Silent_p.G1678G|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1678	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.K1192fs*3(1)|p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		TTAGAGGAGGGGCACAGTCAG	0.443		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			g|||	3339	0.666733	0.5189	0.7176	5008	,	,		20292	0.8165		0.6024	False		,,,				2504	0.7423				p.G1678G	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	2	Unknown(1)|Deletion - Frameshift(1)	soft_tissue(1)|skin(1)	c.G5034A						PASS	.	T	,,	2333,2071	603.2+/-390.1	625,1083,494	60.0	59.0	59.0	http://omim.org/entry/114500	5034,5034,4980	1.3	0.2	5	dbSNP_76	59	5341,3259	648.4+/-400.5	1692,1957,651	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2317,3040,1145	AA,AG,GG		37.8953,47.0254,40.9874	,,	1678/2844,1678/2844,1660/2826	112176325	7674,5330	2202	4300	6502	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	AGGAGGGGCACAG	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5034G>A	5.37:g.112176325G>A		107.0	0.0	0		80.0	80.0	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.379;A|0.621	0.621	strong		0.443	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
NEK3	4752	hgsc.bcm.edu	37	13	52707924	52707924	+	Missense_Mutation	SNP	A	A	C	rs200805375		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:52707924A>C	ENST00000400357.2	-	13	2579	c.1286T>G	c.(1285-1287)cTg>cGg	p.L429R	NEK3_ENST00000378101.2_Missense_Mutation_p.L446R|NEK3_ENST00000452082.2_Missense_Mutation_p.L450R|NEK3_ENST00000339406.3_Missense_Mutation_p.L446R			P51956	NEK3_HUMAN	NIMA-related kinase 3	446					mitotic nuclear division (GO:0007067)|protein phosphorylation (GO:0006468)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|stomach(2)	18		Breast(56;0.000207)|Lung NSC(96;0.00145)|Prostate(109;0.034)|Hepatocellular(98;0.065)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;2.81e-08)		TTCTTCAGACAGGGGGCCTTT	0.418																																					p.L446R		Atlas-SNP	.											.	NEK3	41	.	0			c.T1337G						PASS	.	A	ARG/LEU,ARG/LEU	0,3778		0,0,1889	43.0	40.0	41.0		1286,1336	3.8	1.0	13		41	2,8224		0,2,4111	yes	missense,missense	NEK3	NM_001146099.1,NM_152720.2	102,102	0,2,6000	CC,CA,AA		0.0243,0.0,0.0167	probably-damaging,probably-damaging	429/490,446/507	52707924	2,12002	1889	4113	6002	SO:0001583	missense	4752	exon15			TCAGACAGGGGGC	AK290259, BC019916	CCDS73576.1	13q14.2-q21.1	2014-07-17	2012-11-15		ENSG00000136098	ENSG00000136098	2.7.11.1		7746	protein-coding gene	gene with protein product	"""serine/threonine-protein kinase NEK3"", ""phosphorylase B kinase kinase"", ""glycogen synthase A kinase"", ""hydroxyalkyl-protein kinase"""	604044	"""NIMA (never in mitosis gene a)-related kinase 3"""			8274451, 7522034	Standard	NM_002498		Approved	HSPK36, MGC29949	uc010tgy.2	P51956	OTTHUMG00000016958	ENST00000400357.2:c.1286T>G	13.37:g.52707924A>C	ENSP00000383210:p.Leu429Arg	104.0	0.0	0		72.0	30.0	0.416667	NM_002498	A8K2J4|Q5TAP2|Q8J023|Q8WUN5	Missense_Mutation	SNP	ENST00000400357.2	37	CCDS53871.1	.	.	.	.	.	.	.	.	.	.	A	16.05	3.012638	0.54468	0.0	2.43E-4	ENSG00000136098	ENST00000339406;ENST00000378101;ENST00000400357;ENST00000452082;ENST00000547422	T;T;T;T;T	0.78816	-1.03;-1.03;-1.21;-1.11;-1.04	4.99	3.78	0.43462	.	0.141261	0.48767	D	0.000177	D	0.85796	0.5780	M	0.74258	2.255	0.34463	D	0.702004	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;0.999;1.0	D	0.89208	0.3562	10	0.87932	D	0	.	9.7246	0.40324	0.8455:0.0:0.0:0.1545	.	446;450;423	P51956;Q6ZN64;F8VS47	NEK3_HUMAN;.;.	R	446;446;429;450;423	ENSP00000339429:L446R;ENSP00000367341:L446R;ENSP00000383210:L429R;ENSP00000404197:L450R;ENSP00000448716:L423R	ENSP00000339429:L446R	L	-	2	0	NEK3	51605925	1.000000	0.71417	0.998000	0.56505	0.625000	0.37756	5.553000	0.67287	0.807000	0.34208	0.383000	0.25322	CTG	A|0.999;C|0.001	0.001	weak		0.418	NEK3-002	KNOWN	upstream_ATG|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000045047.3		
CDC45	8318	hgsc.bcm.edu	37	22	19482035	19482035	+	Intron	SNP	C	C	G	rs151216373	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:19482035C>G	ENST00000407835.1	+	7	798				CDC45_ENST00000483431.1_3'UTR|CDC45_ENST00000437685.2_Missense_Mutation_p.S183C|CDC45_ENST00000404724.3_Intron|CDC45_ENST00000263201.1_Intron			O75419	CDC45_HUMAN	cell division cycle 45						DNA replication (GO:0006260)|DNA replication checkpoint (GO:0000076)|DNA replication initiation (GO:0006270)|DNA strand elongation involved in DNA replication (GO:0006271)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)	19						GCCAGTGGCTCTGGGAGTGAA	0.562													C|||	19	0.00379393	0.0	0.0159	5008	,	,		14122	0.0		0.008	False		,,,				2504	0.0				p.S183C		Atlas-SNP	.											.	CDC45	48	.	0			c.C548G						PASS	.																																			SO:0001627	intron_variant	8318	exon7			GTGGCTCTGGGAG	AF053074	CCDS13762.1, CCDS54499.1, CCDS54500.1	22q11.21	2013-01-17	2013-01-17	2010-03-24	ENSG00000093009	ENSG00000093009			1739	protein-coding gene	gene with protein product	"""human CDC45"""	603465	"""CDC45 (cell division cycle 45, S.cerevisiae, homolog)-like"", ""CDC45 cell division cycle 45-like (S. cerevisiae)"", ""cell division cycle 45 homolog (S. cerevisiae)"""	CDC45L2, CDC45L		9660782, 9724329, 17608804	Standard	NM_001178010		Approved		uc011aha.2	O75419	OTTHUMG00000150386	ENST00000407835.1:c.542+130C>G	22.37:g.19482035C>G		49.0	0.0	0		32.0	10.0	0.3125	NM_001178010	B4DDB4|B4DDU3|E9PDH7|O60856|Q20WK8|Q6UW54|Q9UP68	Missense_Mutation	SNP	ENST00000407835.1	37	CCDS13762.1	16	0.007326007326007326	0	0.0	8	0.022099447513812154	0	0.0	8	0.010554089709762533	C	10.30	1.312792	0.23908	.	.	ENSG00000093009	ENST00000437685	T	0.23754	1.89	4.21	-2.11	0.07187	.	.	.	.	.	T	0.07908	0.0198	L	0.32530	0.975	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25363	-1.0134	9	0.59425	D	0.04	.	4.7364	0.12989	0.0:0.4021:0.3216:0.2763	.	183	E9PDH7	.	C	183	ENSP00000405726:S183C	ENSP00000405726:S183C	S	+	2	0	CDC45	17862035	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.293000	0.08320	-0.352000	0.08237	-0.136000	0.14681	TCT	C|0.993;G|0.007	0.007	strong		0.562	CDC45-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317903.1	NM_003504	
TNKS	8658	hgsc.bcm.edu	37	8	9584176	9584176	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:9584176T>C	ENST00000310430.6	+	13	1973	c.1947T>C	c.(1945-1947)gaT>gaC	p.D649D	TNKS_ENST00000518281.1_Silent_p.D412D	NM_003747.2	NP_003738.2	O95271	TNKS1_HUMAN	tankyrase, TRF1-interacting ankyrin-related ADP-ribose polymerase	649					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)			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)		GTACTTCTGATGTTGATTATC	0.373																																					p.D649D		Atlas-SNP	.											.	TNKS	198	.	0			c.T1947C						PASS	.						257.0	262.0	260.0					8																	9584176		2203	4300	6503	SO:0001819	synonymous_variant	8658	exon13			TTCTGATGTTGAT	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.1947T>C	8.37:g.9584176T>C		71.0	0.0	0		84.0	41.0	0.488095	NM_003747	O95272|Q4G0F2	Silent	SNP	ENST00000310430.6	37	CCDS5974.1																																																																																			.	.	none		0.373	TNKS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206935.1	NM_003747	
TSPYL6	388951	hgsc.bcm.edu	37	2	54482271	54482271	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:54482271T>C	ENST00000317802.7	-	1	1138	c.1018A>G	c.(1018-1020)Att>Gtt	p.I340V	ACYP2_ENST00000303536.4_Intron|ACYP2_ENST00000606865.1_Intron|ACYP2_ENST00000394666.3_Intron|ACYP2_ENST00000607452.1_Intron	NM_001003937.2	NP_001003937.2	Q8N831	TSYL6_HUMAN	TSPY-like 6	340					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(1)|ovary(1)|skin(1)|stomach(2)	20						TTCCTATGAATGAAGGACTGG	0.498																																					p.I340V		Atlas-SNP	.											.	TSPYL6	54	.	0			c.A1018G						PASS	.						74.0	79.0	77.0					2																	54482271		2124	4267	6391	SO:0001583	missense	388951	exon1			TATGAATGAAGGA	AK097417	CCDS42682.1	2p16.3	2007-10-22			ENSG00000178021	ENSG00000178021			14521	protein-coding gene	gene with protein product							Standard	NM_001003937		Approved		uc002rxr.2	Q8N831	OTTHUMG00000151823	ENST00000317802.7:c.1018A>G	2.37:g.54482271T>C	ENSP00000417919:p.Ile340Val	106.0	0.0	0		92.0	47.0	0.51087	NM_001003937	Q6NUJ3	Missense_Mutation	SNP	ENST00000317802.7	37	CCDS42682.1	.	.	.	.	.	.	.	.	.	.	T	7.246	0.602182	0.13939	.	.	ENSG00000178021	ENST00000317802	T	0.28666	1.6	1.52	0.306	0.15806	.	.	.	.	.	T	0.16938	0.0407	N	0.05177	-0.1	0.09310	N	1	P	0.35192	0.489	P	0.45232	0.474	T	0.36432	-0.9748	9	0.12430	T	0.62	.	5.7092	0.17925	0.0:0.0:0.3027:0.6972	.	340	Q8N831	TSYL6_HUMAN	V	340	ENSP00000417919:I340V	ENSP00000417919:I340V	I	-	1	0	TSPYL6	54335775	0.000000	0.05858	0.006000	0.13384	0.349000	0.29174	-0.527000	0.06200	0.071000	0.16664	0.383000	0.25322	ATT	.	.	none		0.498	TSPYL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324069.3	XM_371494	
TTN	7273	hgsc.bcm.edu	37	2	179453429	179453429	+	Missense_Mutation	SNP	G	G	A	rs72646850	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179453429G>A	ENST00000591111.1	-	254	58324	c.58100C>T	c.(58099-58101)aCa>aTa	p.T19367I	TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.T11943I|TTN_ENST00000342992.6_Missense_Mutation_p.T18440I|TTN_ENST00000589042.1_Missense_Mutation_p.T21008I|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.T12135I|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000589234.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.T12068I|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000590743.1_RNA			Q8WZ42	TITIN_HUMAN	titin	19367	Fibronectin type-III 40. {ECO:0000255|PROSITE-ProRule:PRU00316}.		T -> I. {ECO:0000269|PubMed:17344846}.		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)			GACCCATCGTGTTGAATGCTT	0.428													G|||	29	0.00579073	0.0008	0.0159	5008	,	,		20616	0.0		0.0169	False		,,,				2504	0.0				p.T21008I		Atlas-SNP	.											.	TTN	18412	.	0			c.C63023T						PASS	.	G	ILE/THR,ILE/THR,ILE/THR,ILE/THR	12,3802		0,12,1895	162.0	152.0	155.0		36404,36203,55319,35828	-6.5	0.0	2	dbSNP_130	155	134,8108		2,130,3989	yes	missense,missense,missense,missense	TTN	NM_133437.3,NM_133432.3,NM_133378.4,NM_003319.4	89,89,89,89	2,142,5884	AA,AG,GG		1.6258,0.3146,1.211	benign,benign,benign,benign	12135/27119,12068/27052,18440/33424,11943/26927	179453429	146,11910	1907	4121	6028	SO:0001583	missense	7273	exon304			CATCGTGTTGAAT	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.58100C>T	2.37:g.179453429G>A	ENSP00000465570:p.Thr19367Ile	195.0	0.0	0		208.0	119.0	0.572115	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		21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	13	0.017150395778364115	G	9.129	1.011021	0.19277	0.003146	0.016258	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.57907	0.37;0.37;0.37;0.37	6.16	-6.48	0.01896	Fibronectin, type III (4);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.19765	0.0475	N	0.10874	0.06	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.08764	-1.0706	9	0.87932	D	0	.	19.6396	0.95753	0.9305:0.0:0.0695:0.0	.	11943;12068;12135;19367	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	I	18440;11943;12135;12068;11941	ENSP00000343764:T18440I;ENSP00000434586:T11943I;ENSP00000340554:T12135I;ENSP00000352154:T12068I	ENSP00000340554:T12135I	T	-	2	0	TTN	179161675	0.000000	0.05858	0.000000	0.03702	0.925000	0.55904	1.233000	0.32648	-1.316000	0.02295	-0.312000	0.09012	ACA	G|0.988;A|0.012	0.012	strong		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
C5AR2	27202	hgsc.bcm.edu	37	19	47844383	47844383	+	Silent	SNP	G	G	T	rs373920189		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:47844383G>T	ENST00000595464.1	+	2	545	c.327G>T	c.(325-327)gcG>gcT	p.A109A	C5AR2_ENST00000257267.2_Silent_p.A109A|C5AR2_ENST00000600626.1_Silent_p.A109A	NM_001271749.1	NP_001258678.1	Q9P296	C5AR2_HUMAN	complement component 5a receptor 2	109					chemotaxis (GO:0006935)|inflammatory response (GO:0006954)|negative regulation of interleukin-6 secretion (GO:1900165)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of tumor necrosis factor production (GO:0032720)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of interleukin-8 secretion (GO:2000482)	apical part of cell (GO:0045177)|basal plasma membrane (GO:0009925)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	C5a anaphylatoxin receptor activity (GO:0004944)										GCTGTCGGGCGCTGCCCTCCA	0.647																																					p.A109A		Atlas-SNP	.											.	.	.	.	0			c.G327T						PASS	.						96.0	91.0	93.0					19																	47844383		2203	4300	6503	SO:0001819	synonymous_variant	27202	exon2			TCGGGCGCTGCCC	AB038237	CCDS12699.1	19q13.33	2013-01-28	2013-01-28	2013-01-28		ENSG00000134830		"""GPCR / Class A : Complement component receptors"""	4527	protein-coding gene	gene with protein product		609949	"""G protein-coupled receptor 77"""	GPR77		11165367	Standard	NM_018485		Approved	C5L2	uc010ela.1	Q9P296		ENST00000595464.1:c.327G>T	19.37:g.47844383G>T		26.0	0.0	0		33.0	17.0	0.515152	NM_001271750	B2RA09	Silent	SNP	ENST00000595464.1	37	CCDS12699.1																																																																																			.	.	alt		0.647	C5AR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466926.1	NM_018485	
NLRP7	199713	hgsc.bcm.edu	37	19	55451258	55451258	+	Missense_Mutation	SNP	T	T	C	rs77812009	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451258T>C	ENST00000590030.1	-	3	969	c.929A>G	c.(928-930)cAg>cGg	p.Q310R	NLRP7_ENST00000448121.2_Missense_Mutation_p.Q310R|NLRP7_ENST00000340844.2_Missense_Mutation_p.Q310R|NLRP7_ENST00000328092.5_Missense_Mutation_p.Q310R|NLRP7_ENST00000446217.1_Missense_Mutation_p.Q338R|NLRP7_ENST00000588756.1_Missense_Mutation_p.Q310R|NLRP7_ENST00000592784.1_Missense_Mutation_p.Q310R			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	310	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.			QL -> RI (in Ref. 4; AAI09126). {ECO:0000305}.			ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CGCCAGGAGCTGGAGGTCCCT	0.627													.|||	26	0.00519169	0.0015	0.0029	5008	,	,		16817	0.0		0.0219	False		,,,				2504	0.0				p.Q310R		Atlas-SNP	.											NLRP7_ENST00000328092,NS,lymphoid_neoplasm,+1,2	NLRP7	411	2	0			c.A929G						PASS	.	T	ARG/GLN,ARG/GLN,ARG/GLN	3,4403	6.2+/-15.9	0,3,2200	38.0	38.0	38.0		929,929,929	-3.5	0.0	19	dbSNP_131	38	136,8464	59.8+/-121.6	1,134,4165	no	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	43,43,43	1,137,6365	CC,CT,TT		1.5814,0.0681,1.0687	benign,benign,benign	310/1038,310/1010,310/981	55451258	139,12867	2203	4300	6503	SO:0001583	missense	199713	exon4			AGGAGCTGGAGGT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.929A>G	19.37:g.55451258T>C	ENSP00000465520:p.Gln310Arg	92.0	0.0	0		92.0	38.0	0.413043	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	T	0.005	-2.144416	0.00332	6.81E-4	0.015814	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.80824	-1.42;-1.42;-1.42;-1.42	1.77	-3.54	0.04653	NACHT nucleoside triphosphatase (1);	.	.	.	.	T	0.30293	0.0760	N	0.02539	-0.55	0.09310	N	1	B;B;B	0.09022	0.002;0.002;0.002	B;B;B	0.12156	0.007;0.007;0.002	T	0.37596	-0.9699	9	0.06099	T	0.92	.	3.6467	0.08187	0.1766:0.364:0.0:0.4594	.	338;310;310	E7EPM2;Q8WX94;Q8WX94-2	.;NALP7_HUMAN;.	R	310;310;310;338	ENSP00000329568:Q310R;ENSP00000409137:Q310R;ENSP00000339491:Q310R;ENSP00000414273:Q338R	ENSP00000329568:Q310R	Q	-	2	0	NLRP7	60143070	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.617000	0.24359	-1.039000	0.03275	-1.457000	0.01029	CAG	T|0.989;C|0.011	0.011	strong		0.627	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
FHDC1	85462	hgsc.bcm.edu	37	4	153886104	153886104	+	Silent	SNP	G	G	A	rs2018007	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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		383.0	1.0	0.00261097		330.0	166.0	0.50303	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	
KDM2B	84678	hgsc.bcm.edu	37	12	121877738	121877738	+	Missense_Mutation	SNP	C	C	T	rs200642027		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:121877738C>T	ENST00000377071.4	-	22	3823	c.3751G>A	c.(3751-3753)Gtc>Atc	p.V1251I	KDM2B_ENST00000542973.1_Missense_Mutation_p.V619I|KDM2B_ENST00000536437.1_Intron|KDM2B_ENST00000377069.4_Missense_Mutation_p.V1182I	NM_032590.4	NP_115979.3	Q8NHM5	KDM2B_HUMAN	lysine (K)-specific demethylase 2B	1251					embryonic camera-type eye morphogenesis (GO:0048596)|forebrain development (GO:0030900)|fourth ventricle development (GO:0021592)|hindbrain development (GO:0030902)|histone demethylation (GO:0016577)|histone H2A monoubiquitination (GO:0035518)|initiation of neural tube closure (GO:0021993)|lateral ventricle development (GO:0021670)|midbrain development (GO:0030901)|midbrain-hindbrain boundary morphogenesis (GO:0021555)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|spermatogenesis (GO:0007283)|third ventricle development (GO:0021678)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|histone demethylase activity (GO:0032452)|histone demethylase activity (H3-K36 specific) (GO:0051864)|rRNA binding (GO:0019843)|zinc ion binding (GO:0008270)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(8)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	19						TGGTCGGTGACGTGGTTACAG	0.607																																					p.V1251I		Atlas-SNP	.											.	KDM2B	218	.	0			c.G3751A						PASS	.	C	ILE/VAL,ILE/VAL	0,4368		0,0,2184	125.0	148.0	140.0		3544,3751	3.9	0.6	12		140	4,8542		0,4,4269	yes	missense,missense	KDM2B	NM_001005366.1,NM_032590.4	29,29	0,4,6453	TT,TC,CC		0.0468,0.0,0.031	benign,benign	1182/1266,1251/1337	121877738	4,12910	2184	4273	6457	SO:0001583	missense	84678	exon22			CGGTGACGTGGTT	AJ459424	CCDS41849.1, CCDS41850.1	12q24.31	2014-02-18	2009-04-06	2009-04-06	ENSG00000089094	ENSG00000089094		"""F-boxes / Leucine-rich repeats"", ""Chromatin-modifying enzymes / K-demethylases"""	13610	protein-coding gene	gene with protein product	"""jumonji C domain-containing histone demethylase 1B"""	609078	"""F-box and leucine-rich repeat protein 10"""	FBXL10		10799292	Standard	NM_032590		Approved	PCCX2, CXXC2, Fbl10, JHDM1B	uc001uat.3	Q8NHM5	OTTHUMG00000169071	ENST00000377071.4:c.3751G>A	12.37:g.121877738C>T	ENSP00000366271:p.Val1251Ile	67.0	0.0	0		73.0	33.0	0.452055	NM_032590	A8MRS1|Q8NCI2|Q96HC7|Q96SL0|Q96T03|Q9NS96|Q9UF75	Missense_Mutation	SNP	ENST00000377071.4	37	CCDS41850.1	.	.	.	.	.	.	.	.	.	.	C	13.16	2.154362	0.38021	0.0	4.68E-4	ENSG00000089094	ENST00000397480;ENST00000542973;ENST00000377069;ENST00000377071;ENST00000540043;ENST00000261824	T;T;T	0.01172	5.23;5.23;5.23	5.73	3.88	0.44766	.	0.145937	0.30575	N	0.009338	T	0.00468	0.0015	N	0.01624	-0.795	0.80722	D	1	B;B;B;B	0.30114	0.103;0.001;0.269;0.037	B;B;B;B	0.15484	0.008;0.001;0.013;0.008	T	0.52343	-0.8588	10	0.02654	T	1	-15.9978	10.6917	0.45875	0.0:0.7916:0.0:0.2084	.	691;1251;1182;694	B7ZB05;Q8NHM5;A8MRS1;B4DSN4	.;KDM2B_HUMAN;.;.	I	1241;619;1182;1251;694;1254	ENSP00000437821:V619I;ENSP00000366269:V1182I;ENSP00000366271:V1251I	ENSP00000261824:V1254I	V	-	1	0	KDM2B	120362121	1.000000	0.71417	0.613000	0.29037	0.983000	0.72400	1.995000	0.40767	0.742000	0.32697	0.655000	0.94253	GTC	.	.	weak		0.607	KDM2B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000402132.2	NM_032590	
SYNGAP1	8831	hgsc.bcm.edu	37	6	33391270	33391270	+	Silent	SNP	T	T	C	rs587780476|rs142359891	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:33391270T>C	ENST00000418600.2	+	2	185	c.84T>C	c.(82-84)tcT>tcC	p.S28S	SYNGAP1_ENST00000293748.5_Silent_p.S28S|SYNGAP1_ENST00000496374.1_3'UTR	NM_006772.2	NP_006763.2	Q96PV0	SYGP1_HUMAN	synaptic Ras GTPase activating protein 1	28					dendrite development (GO:0016358)|negative regulation of axonogenesis (GO:0050771)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Ras protein signal transduction (GO:0046580)|pattern specification process (GO:0007389)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|receptor clustering (GO:0043113)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of MAPK cascade (GO:0043408)|regulation of synapse structure and activity (GO:0050803)|regulation of synaptic plasticity (GO:0048167)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	Rab GTPase activator activity (GO:0005097)|Ras GTPase activator activity (GO:0005099)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(15)|ovary(7)|pancreas(1)|stomach(1)|urinary_tract(1)	43						GGGGACCCTCTATGCACCGAA	0.527													T|||	10	0.00199681	0.0	0.0	5008	,	,		20532	0.0		0.006	False		,,,				2504	0.0041				p.S28S		Atlas-SNP	.											.	SYNGAP1	202	.	0			c.T84C						PASS	.	T		16,4390	23.3+/-48.9	0,16,2187	255.0	222.0	233.0		84	3.7	1.0	6	dbSNP_134	233	101,8499	55.2+/-116.2	0,101,4199	no	coding-synonymous	SYNGAP1	NM_006772.2		0,117,6386	CC,CT,TT		1.1744,0.3631,0.8996		28/1344	33391270	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	8831	exon2			ACCCTCTATGCAC	AB067525	CCDS34434.2	6p21.3	2010-06-25	2010-06-25		ENSG00000197283	ENSG00000197283			11497	protein-coding gene	gene with protein product		603384	"""synaptic Ras GTPase activating protein 1 homolog (rat)"""			9581761, 18323856	Standard	NM_006772		Approved	SYNGAP, RASA5, KIAA1938	uc011dri.2	Q96PV0	OTTHUMG00000031096	ENST00000418600.2:c.84T>C	6.37:g.33391270T>C		89.0	0.0	0		104.0	52.0	0.5	NM_006772	A2AB17|A2BEL6|A2BEL7|A8MQC4|Q8TCS2|Q9UGE2	Silent	SNP	ENST00000418600.2	37	CCDS34434.2																																																																																			T|0.993;C|0.007	0.007	strong		0.527	SYNGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076151.4	XM_166407	
OR51B5	282763	hgsc.bcm.edu	37	11	5364295	5364295	+	Missense_Mutation	SNP	C	C	T	rs12273630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364295C>T	ENST00000300773.2	-	1	514	c.460G>A	c.(460-462)Gtt>Att	p.V154I	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	154			V -> I (in dbSNP:rs12273630).		detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GGGGGAACAACGGATACAAAT	0.438													C|||	487	0.0972444	0.3026	0.0476	5008	,	,		19117	0.0		0.0467	False		,,,				2504	0.0072				p.V154I		Atlas-SNP	.											.	OR51B5	60	.	0			c.G460A						PASS	.	C	ILE/VAL	1218,3184	414.4+/-336.8	162,894,1145	53.0	59.0	57.0		460	-1.3	0.0	11	dbSNP_120	57	453,8141	135.1+/-192.4	13,427,3857	yes	missense	OR51B5	NM_001005567.2	29	175,1321,5002	TT,TC,CC		5.2711,27.6692,12.8578	benign	154/313	5364295	1671,11325	2201	4297	6498	SO:0001583	missense	282763	exon5			GAACAACGGATAC	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.460G>A	11.37:g.5364295C>T	ENSP00000300773:p.Val154Ile	49.0	0.0	0		43.0	25.0	0.581395	NM_001005567	B2RN59	Missense_Mutation	SNP	ENST00000300773.2	37	CCDS31378.1	188	0.08608058608058608	134	0.27235772357723576	20	0.055248618784530384	0	0.0	34	0.044854881266490766	C	0.678	-0.799441	0.02841	0.276692	0.052711	ENSG00000242180	ENST00000300773	T	0.37411	1.2	4.76	-1.28	0.09318	GPCR, rhodopsin-like superfamily (1);	0.194438	0.24818	N	0.035344	T	0.00012	0.0000	N	0.01789	-0.72	0.80722	P	0.0	B	0.16166	0.016	B	0.15870	0.014	T	0.32402	-0.9908	9	0.02654	T	1	.	5.2403	0.15467	0.0:0.4688:0.239:0.2922	rs12273630;rs52831752;rs59964283;rs12273630	154	Q9H339	O51B5_HUMAN	I	154	ENSP00000300773:V154I	ENSP00000300773:V154I	V	-	1	0	OR51B5	5320871	0.000000	0.05858	0.002000	0.10522	0.868000	0.49771	-3.516000	0.00445	-0.111000	0.12001	0.650000	0.86243	GTT	C|0.888;T|0.112	0.112	strong		0.438	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
TECPR2	9895	hgsc.bcm.edu	37	14	102916966	102916966	+	Missense_Mutation	SNP	C	C	A	rs139247564		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:102916966C>A	ENST00000359520.7	+	15	3612	c.3386C>A	c.(3385-3387)tCt>tAt	p.S1129Y	TECPR2_ENST00000558678.1_Missense_Mutation_p.S1129Y	NM_014844.3	NP_055659.2	O15040	TCPR2_HUMAN	tectonin beta-propeller repeat containing 2	1129					autophagy (GO:0006914)|cell death (GO:0008219)					breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(7)|lung(21)|ovary(2)|prostate(3)|skin(4)|stomach(1)|urinary_tract(1)	50						GTGTTGGCTTCTGCAGCTCCC	0.498																																					p.S1129Y		Atlas-SNP	.											.	TECPR2	114	.	0			c.C3386A						PASS	.						104.0	83.0	90.0					14																	102916966		2203	4300	6503	SO:0001583	missense	9895	exon15			TGGCTTCTGCAGC	AB019441	CCDS32162.1, CCDS58337.1	14q32.33	2009-02-27	2009-02-27	2009-02-27		ENSG00000196663			19957	protein-coding gene	gene with protein product		615000	"""KIAA0329"""	KIAA0329		9205841	Standard	NM_014844		Approved		uc001ylw.2	O15040		ENST00000359520.7:c.3386C>A	14.37:g.102916966C>A	ENSP00000352510:p.Ser1129Tyr	169.0	0.0	0		170.0	72.0	0.423529	NM_001172631	A5PKY3|A6NFY9|A7E2X3|H0YMM9|Q9UEG6	Missense_Mutation	SNP	ENST00000359520.7	37	CCDS32162.1	.	.	.	.	.	.	.	.	.	.	C	24.1	4.493237	0.84962	.	.	ENSG00000196663	ENST00000359520	T	0.20598	2.06	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.37019	0.0988	L	0.27053	0.805	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.997;0.997;0.998	T	0.20207	-1.0282	10	0.87932	D	0	.	19.3784	0.94521	0.0:1.0:0.0:0.0	.	312;1129;1129	B4DSD3;A5PKY3;O15040	.;.;TCPR2_HUMAN	Y	1129	ENSP00000352510:S1129Y	ENSP00000352510:S1129Y	S	+	2	0	TECPR2	101986719	1.000000	0.71417	0.172000	0.22920	0.842000	0.47809	6.757000	0.74924	2.585000	0.87301	0.655000	0.94253	TCT	C|0.999;A|0.001	0.001	weak		0.498	TECPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415056.2	NM_014844	
LRP1	4035	hgsc.bcm.edu	37	12	57592067	57592067	+	Silent	SNP	G	G	A	rs143423493	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:57592067G>A	ENST00000243077.3	+	59	9877	c.9411G>A	c.(9409-9411)acG>acA	p.T3137T		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	3137					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)			NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	CCTATCGGACGGTGCTGGTCA	0.637													G|||	11	0.00219649	0.0008	0.0014	5008	,	,		21534	0.0		0.006	False		,,,				2504	0.0031				p.T3137T		Atlas-SNP	.											LRP1,colon,carcinoma,+2,1	LRP1	428	1	0			c.G9411A						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	78.0	79.0	78.0		9411	-6.1	0.7	12	dbSNP_134	78	36,8564	25.1+/-72.6	0,36,4264	no	coding-synonymous	LRP1	NM_002332.2		0,37,6466	AA,AG,GG		0.4186,0.0227,0.2845		3137/4545	57592067	37,12969	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon59			TCGGACGGTGCTG	X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.9411G>A	12.37:g.57592067G>A		47.0	1.0	0.0212766		55.0	26.0	0.472727	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			G|0.996;A|0.004	0.004	strong		0.637	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
CNR1	1268	hgsc.bcm.edu	37	6	88854166	88854166	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:88854166C>T	ENST00000537554.1	-	2	4390	c.828G>A	c.(826-828)ctG>ctA	p.L276L	CNR1_ENST00000369499.2_Silent_p.L276L|CNR1_ENST00000428600.2_Silent_p.L276L|CNR1_ENST00000549890.1_Silent_p.L276L|CNR1_ENST00000549716.1_Silent_p.L215L|CNR1_ENST00000468898.1_Silent_p.L243L|CNR1_ENST00000362094.5_3'UTR|CNR1_ENST00000535130.1_Silent_p.L276L|CNR1_ENST00000369501.2_Silent_p.L276L	NM_001160226.1|NM_001160258.1	NP_001153698.1|NP_001153730.1	P21554	CNR1_HUMAN	cannabinoid receptor 1 (brain)	276					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|aging (GO:0007568)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|negative regulation of action potential (GO:0045759)|negative regulation of blood pressure (GO:0045776)|negative regulation of dopamine secretion (GO:0033602)|negative regulation of fatty acid beta-oxidation (GO:0031999)|negative regulation of mast cell activation (GO:0033004)|negative regulation of nitric-oxide synthase activity (GO:0051001)|positive regulation of acute inflammatory response to antigenic stimulus (GO:0002866)|positive regulation of apoptotic process (GO:0043065)|positive regulation of blood pressure (GO:0045777)|positive regulation of fever generation (GO:0031622)|positive regulation of neuron projection development (GO:0010976)|regulation of feeding behavior (GO:0060259)|regulation of insulin secretion (GO:0050796)|regulation of penile erection (GO:0060405)|regulation of synaptic transmission, GABAergic (GO:0032228)|regulation of synaptic transmission, glutamatergic (GO:0051966)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|response to lipopolysaccharide (GO:0032496)|response to morphine (GO:0043278)|response to nicotine (GO:0035094)|response to nutrient (GO:0007584)|sensory perception of pain (GO:0019233)|spermatogenesis (GO:0007283)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	cannabinoid receptor activity (GO:0004949)|drug binding (GO:0008144)			breast(2)|endometrium(3)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|prostate(1)|skin(10)|urinary_tract(1)	37		all_cancers(76;8.24e-09)|Acute lymphoblastic leukemia(125;2.15e-10)|Prostate(29;4.11e-10)|all_hematologic(105;1.08e-06)|all_epithelial(107;0.00011)		BRCA - Breast invasive adenocarcinoma(108;0.15)	Dronabinol(DB00470)|Nabilone(DB00486)|Rimonabant(DB06155)	TCCAGAACATCAGGTAGGTTT	0.512																																					p.L276L		Atlas-SNP	.											.	CNR1	91	.	0			c.G828A						PASS	.						83.0	72.0	76.0					6																	88854166		2203	4300	6503	SO:0001819	synonymous_variant	1268	exon4			GAACATCAGGTAG	AF107262	CCDS5015.1, CCDS5016.1, CCDS5016.2	6q14-q15	2012-08-08			ENSG00000118432	ENSG00000118432		"""GPCR / Class A : Cannabinoid receptors"""	2159	protein-coding gene	gene with protein product		114610		CNR			Standard	NM_016083		Approved	CB1K5, CB-R, CB1, CANN6, CB1A	uc003pmq.4	P21554	OTTHUMG00000015184	ENST00000537554.1:c.828G>A	6.37:g.88854166C>T		64.0	0.0	0		68.0	34.0	0.5	NM_001160258	B2R9T4|E1P512|Q13949|Q495Z0|Q4PLI4|Q4VBM6|Q5JVL5|Q5UB37|Q9UNN0	Silent	SNP	ENST00000537554.1	37	CCDS5015.1																																																																																			.	.	none		0.512	CNR1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354204.2		
WDR41	55255	hgsc.bcm.edu	37	5	76728996	76728996	+	Silent	SNP	T	T	C	rs72769029	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:76728996T>C	ENST00000296679.4	-	13	1719	c.1344A>G	c.(1342-1344)aaA>aaG	p.K448K	WDR41_ENST00000512033.1_5'UTR|WDR41_ENST00000507029.1_Silent_p.K393K|WDR41_ENST00000414719.2_Silent_p.K194K	NM_018268.2	NP_060738.2	Q9HAD4	WDR41_HUMAN	WD repeat domain 41	448						lysosomal membrane (GO:0005765)				NS(1)|autonomic_ganglia(1)|endometrium(3)|kidney(1)|large_intestine(3)|lung(5)	14		all_lung(232;0.000961)|Lung NSC(167;0.0011)|Ovarian(174;0.0105)|Prostate(461;0.059)		OV - Ovarian serous cystadenocarcinoma(54;6.3e-50)|Epithelial(54;2.04e-44)|all cancers(79;6.84e-40)		TCTCCTCTAATTTTTGAAATA	0.368													T|||	83	0.0165735	0.0015	0.0245	5008	,	,		17492	0.0		0.0338	False		,,,				2504	0.0307				p.K448K		Atlas-SNP	.											.	WDR41	29	.	0			c.A1344G						PASS	.	T		21,4383	27.2+/-55.0	0,21,2181	118.0	121.0	120.0		1344	-0.2	1.0	5	dbSNP_130	120	238,8362	96.8+/-158.5	5,228,4067	no	coding-synonymous	WDR41	NM_018268.2		5,249,6248	CC,CT,TT		2.7674,0.4768,1.9917		448/460	76728996	259,12745	2202	4300	6502	SO:0001819	synonymous_variant	55255	exon13			CTCTAATTTTTGA	AF115511	CCDS4038.1	5q14	2013-01-09			ENSG00000164253	ENSG00000164253		"""WD repeat domain containing"""	25601	protein-coding gene	gene with protein product						12477932	Standard	NM_018268		Approved	FLJ10904	uc003kff.1	Q9HAD4	OTTHUMG00000102169	ENST00000296679.4:c.1344A>G	5.37:g.76728996T>C		135.0	0.0	0		201.0	101.0	0.502488	NM_018268	B4DT55|Q7Z792|Q8IWG3|Q8IXA9|Q8NDA7|Q9NV62	Silent	SNP	ENST00000296679.4	37	CCDS4038.1																																																																																			T|0.979;C|0.021	0.021	strong		0.368	WDR41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220014.2	NM_018268	
PRDM1	639	hgsc.bcm.edu	37	6	106554343	106554343	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:106554343T>A	ENST00000369096.4	+	6	2105	c.1871T>A	c.(1870-1872)gTa>gAa	p.V624E	PRDM1_ENST00000369089.3_Missense_Mutation_p.V490E|PRDM1_ENST00000369091.2_Missense_Mutation_p.V588E	NM_001198.3	NP_001189.2	O75626	PRDM1_HUMAN	PR domain containing 1, with ZNF domain	624					cell fate commitment (GO:0045165)|eye photoreceptor cell development (GO:0042462)|germ cell development (GO:0007281)|intestinal epithelial cell development (GO:0060576)|maternal placenta development (GO:0001893)|negative regulation of B cell proliferation (GO:0030889)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of B cell differentiation (GO:0045579)|positive regulation of gene expression (GO:0010628)|post-embryonic development (GO:0009791)|transcription, DNA-templated (GO:0006351)|trophoblast giant cell differentiation (GO:0060707)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(59)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(5)|urinary_tract(2)	94	Breast(9;0.022)	all_cancers(87;2.2e-31)|all_epithelial(87;2.03e-21)|Acute lymphoblastic leukemia(125;4.99e-11)|all_lung(197;7.55e-09)|all_hematologic(75;5.82e-08)|Lung NSC(302;1.28e-06)|Colorectal(196;0.0112)|Ovarian(999;0.0365)		all cancers(137;1.83e-46)|Epithelial(106;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(136;1.99e-20)|GBM - Glioblastoma multiforme(226;3.72e-11)|BRCA - Breast invasive adenocarcinoma(108;1.38e-05)		CACTACCTGGTACACACGGGA	0.512			"""D, N, Mis, F, S"""		DLBCL																																p.V624E		Atlas-SNP	.		Rec	yes		6	6q21	639	"""PR domain containing 1, with ZNF domain"""		L	.	PRDM1	195	.	0			c.T1871A						PASS	.						116.0	96.0	103.0					6																	106554343		2203	4300	6503	SO:0001583	missense	639	exon6			ACCTGGTACACAC		CCDS5054.2, CCDS34505.1	6q21	2013-01-08			ENSG00000057657	ENSG00000057657		"""Zinc fingers, C2H2-type"""	9346	protein-coding gene	gene with protein product		603423		BLIMP1		1851123	Standard	NM_001198		Approved	PRDI-BF1	uc003prd.2	O75626	OTTHUMG00000015299	ENST00000369096.4:c.1871T>A	6.37:g.106554343T>A	ENSP00000358092:p.Val624Glu	54.0	0.0	0		57.0	13.0	0.22807	NM_001198	B2REA6|E1P5E0|Q86WM7	Missense_Mutation	SNP	ENST00000369096.4	37	CCDS5054.2	.	.	.	.	.	.	.	.	.	.	T	25.0	4.589481	0.86851	.	.	ENSG00000057657	ENST00000369091;ENST00000369096;ENST00000456278;ENST00000369089	T;T;T	0.07688	3.17;3.17;3.17	5.55	5.55	0.83447	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.052469	0.85682	D	0.000000	T	0.14700	0.0355	L	0.50993	1.605	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.87578	0.994;0.998	T	0.00613	-1.1644	10	0.87932	D	0	-13.8246	12.4582	0.55716	0.0:0.0:0.1492:0.8508	.	490;624	Q86WM7;O75626	.;PRDM1_HUMAN	E	588;624;587;490	ENSP00000358087:V588E;ENSP00000358092:V624E;ENSP00000358085:V490E	ENSP00000358085:V490E	V	+	2	0	PRDM1	106661036	1.000000	0.71417	0.999000	0.59377	0.999000	0.98932	6.180000	0.71981	2.118000	0.64928	0.533000	0.62120	GTA	.	.	none		0.512	PRDM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041661.3		
ACTN2	88	hgsc.bcm.edu	37	1	236908053	236908053	+	Silent	SNP	C	C	T	rs34827377	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:236908053C>T	ENST00000366578.4	+	12	1549	c.1383C>T	c.(1381-1383)atC>atT	p.I461I	ACTN2_ENST00000492634.1_3'UTR|ACTN2_ENST00000542672.1_Silent_p.I461I|ACTN2_ENST00000546208.1_5'UTR	NM_001103.2|NM_001278343.1	NP_001094.1|NP_001265272.1	P35609	ACTN2_HUMAN	actinin, alpha 2	461					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|focal adhesion assembly (GO:0048041)|microspike assembly (GO:0030035)|muscle filament sliding (GO:0030049)|negative regulation of potassium ion transmembrane transporter activity (GO:1901017)|negative regulation of potassium ion transport (GO:0043267)|negative regulation of protein localization to cell surface (GO:2000009)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein homotetramerization (GO:0051289)|regulation of apoptotic process (GO:0042981)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	actin filament (GO:0005884)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|cytoskeletal protein binding (GO:0008092)|FATZ binding (GO:0051373)|identical protein binding (GO:0042802)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|protein dimerization activity (GO:0046983)|structural constituent of muscle (GO:0008307)|thyroid hormone receptor coactivator activity (GO:0030375)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			endometrium(4)|kidney(2)|large_intestine(15)|lung(55)|ovary(4)|prostate(3)|skin(3)	86	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.00661)|Acute lymphoblastic leukemia(190;0.109)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00168)			TGGAGCAGATCGCAGCCATCG	0.652													C|||	5	0.000998403	0.0	0.0029	5008	,	,		18183	0.0		0.003	False		,,,				2504	0.0				p.I461I		Atlas-SNP	.											.	ACTN2	191	.	0			c.C1383T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	61.0	52.0	55.0		1383	-9.9	0.1	1	dbSNP_126	55	16,8584	11.9+/-42.8	0,16,4284	yes	coding-synonymous	ACTN2	NM_001103.2		0,17,6486	TT,TC,CC		0.186,0.0227,0.1307		461/895	236908053	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	88	exon12			GCAGATCGCAGCC	BC047901	CCDS1613.1, CCDS60455.1, CCDS73053.1	1q42-q43	2014-09-17			ENSG00000077522	ENSG00000077522		"""EF-hand domain containing"""	164	protein-coding gene	gene with protein product		102573				1339456	Standard	NM_001103		Approved		uc001hyf.2	P35609	OTTHUMG00000040059	ENST00000366578.4:c.1383C>T	1.37:g.236908053C>T		100.0	0.0	0		110.0	59.0	0.536364	NM_001103	B1ANE4|B2RCS5|Q86TF4|Q86TI8	Silent	SNP	ENST00000366578.4	37	CCDS1613.1																																																																																			C|0.998;T|0.002	0.002	strong		0.652	ACTN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000096628.1	NM_001103	
GREB1	9687	hgsc.bcm.edu	37	2	11758536	11758536	+	Missense_Mutation	SNP	C	C	A	rs61741332	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:11758536C>A	ENST00000381486.2	+	22	3835	c.3535C>A	c.(3535-3537)Ccc>Acc	p.P1179T	GREB1_ENST00000396123.1_Missense_Mutation_p.P177T|GREB1_ENST00000234142.5_Missense_Mutation_p.P1179T	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	1179	Ser-rich.					integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		GAAACAGAGGCCCCGGGCAAG	0.721													C|||	32	0.00638978	0.0008	0.0159	5008	,	,		14493	0.001		0.0159	False		,,,				2504	0.0031				p.P1179T	Ovarian(39;850 945 2785 23371 33093)	Atlas-SNP	.											.	GREB1	308	.	0			c.C3535A						PASS	.	C	THR/PRO	17,3853		0,17,1918	9.0	12.0	11.0		3535	1.9	0.0	2	dbSNP_129	11	145,8019		3,139,3940	no	missense	GREB1	NM_014668.3	38	3,156,5858	AA,AC,CC		1.7761,0.4393,1.3462	benign	1179/1950	11758536	162,11872	1935	4082	6017	SO:0001583	missense	9687	exon22			CAGAGGCCCCGGG		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.3535C>A	2.37:g.11758536C>A	ENSP00000370896:p.Pro1179Thr	84.0	0.0	0		86.0	43.0	0.5	NM_014668	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Missense_Mutation	SNP	ENST00000381486.2	37	CCDS42655.1	21	0.009615384615384616	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	12	0.0158311345646438	C	9.915	1.210717	0.22289	0.004393	0.017761	ENSG00000196208	ENST00000381486;ENST00000234142;ENST00000396123	T;T;T	0.21543	3.34;3.34;2.0	4.84	1.93	0.25924	.	2.089630	0.01658	N	0.024926	T	0.04998	0.0134	N	0.03608	-0.345	0.09310	N	1	B	0.22211	0.066	B	0.23419	0.046	T	0.24083	-1.0170	10	0.22109	T	0.4	-25.9697	5.8172	0.18500	0.1667:0.6621:0.0:0.1712	rs61741332	1179	Q4ZG55	GREB1_HUMAN	T	1179;1179;177	ENSP00000370896:P1179T;ENSP00000234142:P1179T;ENSP00000379429:P177T	ENSP00000234142:P1179T	P	+	1	0	GREB1	11675987	0.036000	0.19791	0.000000	0.03702	0.357000	0.29423	1.934000	0.40163	0.084000	0.17077	0.643000	0.83706	CCC	C|0.989;A|0.011	0.011	strong		0.721	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
SP8	221833	hgsc.bcm.edu	37	7	20824956	20824956	+	Silent	SNP	C	C	G	rs201180283		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:20824956C>G	ENST00000361443.4	-	3	663	c.426G>C	c.(424-426)ggG>ggC	p.G142G	SP8_ENST00000418710.2_Silent_p.G160G	NM_198956.2	NP_945194.1	Q8IXZ3	SP8_HUMAN	Sp8 transcription factor	142					dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|proximal/distal pattern formation (GO:0009954)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	8						cgccgccgcccccgccgccgc	0.741																																					p.G160G		Atlas-SNP	.											.	SP8	43	.	0			c.G480C						PASS	.						2.0	2.0	2.0					7																	20824956		542	1367	1909	SO:0001819	synonymous_variant	221833	exon2			GCCGCCCCCGCCG		CCDS5372.1, CCDS43555.1	7p21.2	2013-01-08			ENSG00000164651	ENSG00000164651		"""Specificity protein transcription factors"", ""Zinc fingers, C2H2-type"""	19196	protein-coding gene	gene with protein product		608306					Standard	NM_182700		Approved		uc003suz.3	Q8IXZ3	OTTHUMG00000094788	ENST00000361443.4:c.426G>C	7.37:g.20824956C>G		2.0	0.0	0		7.0	7.0	1	NM_182700	Q7Z615|Q7Z616|Q96MJ1	Silent	SNP	ENST00000361443.4	37	CCDS5372.1																																																																																			.	.	weak		0.741	SP8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000326904.2		
POM121L12	285877	hgsc.bcm.edu	37	7	53103370	53103370	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:53103370C>T	ENST00000408890.4	+	1	22	c.6C>T	c.(4-6)ggC>ggT	p.G2G		NM_182595.3	NP_872401.3	Q8N7R1	P1L12_HUMAN	POM121 transmembrane nucleoporin-like 12	2										endometrium(5)|kidney(1)|large_intestine(5)|lung(44)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	61						CAGCCATGGGCGCTGCAGCTC	0.701																																					p.G2G		Atlas-SNP	.											.	POM121L12	146	.	0			c.C6T						PASS	.																																			SO:0001819	synonymous_variant	285877	exon1			CATGGGCGCTGCA		CCDS43584.1	7p12.1	2012-03-13	2012-03-13		ENSG00000221900	ENSG00000221900			25369	protein-coding gene	gene with protein product			"""POM121 membrane glycoprotein-like 12"""				Standard	NM_182595		Approved	DKFZp564N2472	uc003tpz.3	Q8N7R1	OTTHUMG00000155995	ENST00000408890.4:c.6C>T	7.37:g.53103370C>T		59.0	0.0	0		72.0	53.0	0.736111	NM_182595	Q8NDI9	Silent	SNP	ENST00000408890.4	37	CCDS43584.1																																																																																			.	.	none		0.701	POM121L12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342656.1	NM_182595	
KRTAP10-9	386676	hgsc.bcm.edu	37	21	46047105	46047105	+	Missense_Mutation	SNP	T	T	C	rs200504844		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:46047105T>C	ENST00000397911.3	+	1	66	c.17T>C	c.(16-18)aTg>aCg	p.M6T	KRTAP10-9_ENST00000484861.1_3'UTR|TSPEAR_ENST00000323084.4_Intron	NM_198690.2	NP_941963.2	P60411	KR109_HUMAN	keratin associated protein 10-9	6						keratin filament (GO:0045095)				endometrium(1)|kidney(1)|large_intestine(1)|lung(6)	9						GCGTCCACCATGTCCATCCGC	0.642													T|||	1	0.000199681	0.0	0.0	5008	,	,		16835	0.0		0.001	False		,,,				2504	0.0				p.M6T		Atlas-SNP	.											.	KRTAP10-9	24	.	0			c.T17C						PASS	.	T	,THR/MET	0,4406		0,0,2203	73.0	85.0	81.0		,17	-1.0	0.9	21		81	8,8592	5.7+/-21.5	0,8,4292	no	intron,missense	TSPEAR,KRTAP10-9	NM_144991.2,NM_198690.2	,81	0,8,6495	CC,CT,TT		0.093,0.0,0.0615	,benign	,6/293	46047105	8,12998	2203	4300	6503	SO:0001583	missense	386676	exon1			CCACCATGTCCAT	AJ566386	CCDS42961.1	21q22.3	2007-10-05			ENSG00000221837	ENSG00000221837		"""Keratin associated proteins"""	22971	protein-coding gene	gene with protein product				KRTAP18-9			Standard	NM_198690		Approved	KAP10.9, KAP18.9	uc002zfp.4	P60411	OTTHUMG00000057637	ENST00000397911.3:c.17T>C	21.37:g.46047105T>C	ENSP00000381009:p.Met6Thr	91.0	0.0	0		90.0	47.0	0.522222	NM_198690	A2RRG1|A6NIR9|Q70LJ1	Missense_Mutation	SNP	ENST00000397911.3	37	CCDS42961.1	.	.	.	.	.	.	.	.	.	.	t	3.359	-0.130818	0.06753	0.0	9.3E-4	ENSG00000221837	ENST00000397911	T	0.13196	2.61	3.67	-0.997	0.10215	.	.	.	.	.	T	0.09158	0.0226	L	0.41573	1.285	0.09310	N	0.999999	B	0.02656	0.0	B	0.01281	0.0	T	0.39440	-0.9614	9	0.66056	D	0.02	.	0.7715	0.01024	0.16:0.2466:0.1626:0.4307	.	6	P60411	KR109_HUMAN	T	6	ENSP00000381009:M6T	ENSP00000381009:M6T	M	+	2	0	KRTAP10-9	44871533	0.058000	0.20735	0.903000	0.35520	0.008000	0.06430	0.077000	0.14738	0.001000	0.14605	-0.408000	0.06270	ATG	T|0.999;C|0.001	0.001	weak		0.642	KRTAP10-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128040.1		
GTF2F1	2962	hgsc.bcm.edu	37	19	6392908	6392908	+	Missense_Mutation	SNP	T	T	C	rs140541374		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392908T>C	ENST00000394456.5	-	2	483	c.19A>G	c.(19-21)Agc>Ggc	p.S7G	GTF2F1_ENST00000429701.2_5'Flank|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	7					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						TTCTGGCTGCTAGGGCCCTGC	0.597											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	T|||	1	0.000199681	0.0	0.0	5008	,	,		16539	0.0		0.001	False		,,,				2504	0.0				p.S7G		Atlas-SNP	.											.	GTF2F1	39	.	0			c.A19G						PASS	.						135.0	136.0	136.0					19																	6392908		2203	4300	6503	SO:0001583	missense	2962	exon2			GGCTGCTAGGGCC		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"""General transcription factors"""	4652	protein-coding gene	gene with protein product		189968	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.19A>G	19.37:g.6392908T>C	ENSP00000377969:p.Ser7Gly	70.0	0.0	0	633	80.0	37.0	0.4625	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	T	11.77	1.737992	0.30774	.	.	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.49720	0.77	5.07	-2.96	0.05547	Transcription Factor IIF, Rap30/Rap74, interaction (1);	0.314292	0.37483	N	0.002061	T	0.26593	0.0650	N	0.14661	0.345	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.02512	-1.1148	10	0.46703	T	0.11	-8.1482	12.3718	0.55260	0.0:0.1636:0.0:0.8364	.	7	P35269	T2FA_HUMAN	G	7	ENSP00000377969:S7G	ENSP00000377969:S7G	S	-	1	0	GTF2F1	6343908	0.999000	0.42202	0.929000	0.37066	0.680000	0.39746	0.351000	0.20096	-0.625000	0.05604	-0.353000	0.07706	AGC	T|0.999;C|0.001	0.001	strong		0.597	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096	
CNDP1	84735	hgsc.bcm.edu	37	18	72228154	72228154	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:72228154A>C	ENST00000358821.3	+	4	595	c.367A>C	c.(367-369)Acg>Ccg	p.T123P	CNDP1_ENST00000585136.1_Intron|CNDP1_ENST00000582365.1_Missense_Mutation_p.T80P|RP11-231E4.3_ENST00000583702.1_RNA	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	123						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		GAGCGATCCCACGAAAGGCAC	0.577																																					p.T123P	Melanoma(32;1029 1042 25286 38395 44237)	Atlas-SNP	.											CNDP1,NS,carcinoma,-1,1	CNDP1	98	1	0			c.A367C						PASS	.						124.0	121.0	122.0					18																	72228154		2203	4300	6503	SO:0001583	missense	84735	exon4			GATCCCACGAAAG		CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.367A>C	18.37:g.72228154A>C	ENSP00000351682:p.Thr123Pro	87.0	0.0	0		113.0	34.0	0.300885	NM_032649	Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	.	.	.	.	.	.	.	.	.	.	A	8.474	0.858173	0.17178	.	.	ENSG00000150656	ENST00000358821	T	0.14893	2.47	4.93	-2.86	0.05717	.	0.808128	0.11858	N	0.522700	T	0.07908	0.0198	N	0.08118	0	0.09310	N	1	B	0.18610	0.029	B	0.23716	0.048	T	0.33727	-0.9857	10	0.51188	T	0.08	-4.9001	7.9888	0.30229	0.3867:0.4619:0.1513:0.0	.	123	Q96KN2	CNDP1_HUMAN	P	123	ENSP00000351682:T123P	ENSP00000351682:T123P	T	+	1	0	CNDP1	70379134	0.000000	0.05858	0.002000	0.10522	0.128000	0.20619	-0.201000	0.09464	-0.375000	0.07955	0.533000	0.62120	ACG	.	.	none		0.577	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1	NM_032649	
ABCF2	10061	hgsc.bcm.edu	37	7	150920891	150920891	+	Silent	SNP	G	G	A	rs41273648	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:150920891G>A	ENST00000287844.2	-	5	704	c.595C>T	c.(595-597)Ctg>Ttg	p.L199L	ABCF2_ENST00000473874.1_5'Flank|ABCF2_ENST00000222388.2_Silent_p.L199L	NM_007189.1	NP_009120.1	Q9UG63	ABCF2_HUMAN	ATP-binding cassette, sub-family F (GCN20), member 2	199	ABC transporter 1. {ECO:0000255|PROSITE- ProRule:PRU00434}.				transport (GO:0006810)	ATP-binding cassette (ABC) transporter complex (GO:0043190)|membrane (GO:0016020)|mitochondrial envelope (GO:0005740)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|transporter activity (GO:0005215)			breast(1)|central_nervous_system(1)|large_intestine(4)|lung(15)|ovary(1)|skin(2)	24			OV - Ovarian serous cystadenocarcinoma(82;0.00448)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		TCGGCATCCAGCTCCTCCAGG	0.602													G|||	37	0.00738818	0.0015	0.0115	5008	,	,		19099	0.0		0.0209	False		,,,				2504	0.0061				p.L199L		Atlas-SNP	.											.	ABCF2	54	.	0			c.C595T						PASS	.	G	,	21,4385	28.1+/-56.4	0,21,2182	41.0	36.0	38.0		595,595	2.2	1.0	7	dbSNP_127	38	238,8362	96.8+/-158.5	6,226,4068	no	coding-synonymous,coding-synonymous	ABCF2	NM_005692.3,NM_007189.1	,	6,247,6250	AA,AG,GG		2.7674,0.4766,1.9914	,	199/635,199/624	150920891	259,12747	2203	4300	6503	SO:0001819	synonymous_variant	10061	exon5			CATCCAGCTCCTC	AJ005016	CCDS5922.1, CCDS5923.1	7q36.1	2012-03-14			ENSG00000033050	ENSG00000033050		"""ATP binding cassette transporters / subfamily F"""	71	protein-coding gene	gene with protein product		612510				8894702	Standard	NM_007189		Approved	EST133090, ABC28, M-ABC1, HUSSY-18	uc003wjo.1	Q9UG63	OTTHUMG00000154570	ENST00000287844.2:c.595C>T	7.37:g.150920891G>A		67.0	0.0	0		54.0	25.0	0.462963	NM_007189	O60864|Q75MJ0|Q75MJ1|Q96TE8	Silent	SNP	ENST00000287844.2	37	CCDS5923.1																																																																																			G|0.985;A|0.015	0.015	strong		0.602	ABCF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336086.1	NM_005692	
DMXL1	1657	hgsc.bcm.edu	37	5	118454599	118454599	+	Missense_Mutation	SNP	T	T	C	rs200933738		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:118454599T>C	ENST00000311085.8	+	8	913	c.833T>C	c.(832-834)cTa>cCa	p.L278P	DMXL1_ENST00000539542.1_Missense_Mutation_p.L278P	NM_005509.4	NP_005500.4	Q9Y485	DMXL1_HUMAN	Dmx-like 1	278										breast(3)|central_nervous_system(1)|endometrium(14)|kidney(4)|large_intestine(20)|liver(6)|lung(28)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(1)	86		all_cancers(142;0.0314)|all_epithelial(76;0.00559)|Prostate(80;0.11)|Breast(839;0.231)		OV - Ovarian serous cystadenocarcinoma(64;0.000563)|Epithelial(69;0.00179)|all cancers(49;0.0243)		GATTGTTTGCTATACGGAGGT	0.363																																					p.L278P		Atlas-SNP	.											.	DMXL1	268	.	0			c.T833C						PASS	.	T	PRO/LEU	0,4404		0,0,2202	158.0	151.0	154.0		833	5.4	0.4	5		154	3,8597	3.0+/-9.4	0,3,4297	yes	missense	DMXL1	NM_005509.4	98	0,3,6499	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	278/3028	118454599	3,13001	2202	4300	6502	SO:0001583	missense	1657	exon8			GTTTGCTATACGG	AJ005821	CCDS4125.1, CCDS75289.1	5q22	2013-01-10			ENSG00000172869	ENSG00000172869		"""WD repeat domain containing"""	2937	protein-coding gene	gene with protein product		605671				10708522	Standard	NM_005509		Approved		uc003ksd.2	Q9Y485	OTTHUMG00000128898	ENST00000311085.8:c.833T>C	5.37:g.118454599T>C	ENSP00000309690:p.Leu278Pro	95.0	0.0	0		125.0	54.0	0.432	NM_005509		Missense_Mutation	SNP	ENST00000311085.8	37	CCDS4125.1	.	.	.	.	.	.	.	.	.	.	T	15.22	2.770171	0.49680	0.0	3.49E-4	ENSG00000172869	ENST00000503802;ENST00000311085;ENST00000539542	T;T;T	0.28069	1.63;2.67;2.67	5.38	5.38	0.77491	WD40 repeat-like-containing domain (1);	0.000000	0.64402	D	0.000002	T	0.56001	0.1956	M	0.73962	2.25	0.80722	D	1	D;D	0.89917	1.0;0.998	D;D	0.72338	0.977;0.931	T	0.60905	-0.7170	10	0.72032	D	0.01	-1.619	15.3913	0.74747	0.0:0.0:0.0:1.0	.	278;278	F5H269;Q9Y485	.;DMXL1_HUMAN	P	278	ENSP00000427692:L278P;ENSP00000309690:L278P;ENSP00000439479:L278P	ENSP00000309690:L278P	L	+	2	0	DMXL1	118482498	0.940000	0.31905	0.396000	0.26296	0.137000	0.21094	5.757000	0.68766	2.046000	0.60703	0.533000	0.62120	CTA	T|0.999;C|0.001	0.001	weak		0.363	DMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250862.1	NM_005509	
LY75	4065	hgsc.bcm.edu	37	2	160661704	160661704	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:160661704C>T	ENST00000263636.4	-	35	5047	c.5020G>A	c.(5020-5022)Gtt>Att	p.V1674I	LY75_ENST00000554112.1_Intron|LY75_ENST00000553424.1_Intron|LY75-CD302_ENST00000504764.1_Intron|LY75-CD302_ENST00000505052.1_Intron	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	1674					endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AGTGTGGCAACTATGATAGCT	0.423																																					p.V1674I		Atlas-SNP	.											.	LY75	151	.	0			c.G5020A						PASS	.						107.0	98.0	101.0					2																	160661704		2203	4300	6503	SO:0001583	missense	4065	exon35			TGGCAACTATGAT	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.5020G>A	2.37:g.160661704C>T	ENSP00000263636:p.Val1674Ile	117.0	0.0	0		99.0	16.0	0.161616	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	37	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	C	8.786	0.929415	0.18131	.	.	ENSG00000054219	ENST00000263636	T	0.08634	3.07	5.38	-5.11	0.02901	.	1.327090	0.05825	N	0.616489	T	0.02970	0.0088	N	0.08118	0	0.24881	N	0.992224	B	0.02656	0.0	B	0.01281	0.0	T	0.44590	-0.9318	10	0.12766	T	0.61	.	2.3409	0.04260	0.3665:0.2775:0.066:0.29	.	1674	O60449	LY75_HUMAN	I	1674	ENSP00000263636:V1674I	ENSP00000263636:V1674I	V	-	1	0	LY75	160369950	0.000000	0.05858	0.001000	0.08648	0.000000	0.00434	-0.555000	0.05999	-0.516000	0.06470	-2.451000	0.00208	GTT	.	.	none		0.423	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
FRYL	285527	hgsc.bcm.edu	37	4	48542671	48542671	+	Silent	SNP	G	G	A	rs373260615		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:48542671G>A	ENST00000503238.1	-	43	5993	c.5994C>T	c.(5992-5994)aaC>aaT	p.N1998N	FRYL_ENST00000264319.7_5'UTR|FRYL_ENST00000507873.2_5'UTR|FRYL_ENST00000358350.4_Silent_p.N1998N|FRYL_ENST00000537810.1_Silent_p.N1998N			O94915	FRYL_HUMAN	FRY-like	1998					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)					breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(21)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	91						TGGCCATCAAGTTGGTAGGCT	0.423																																					p.N1998N		Atlas-SNP	.											.	FRYL	242	.	0			c.C5994T						PASS	.	G		0,3846		0,0,1923	79.0	78.0	79.0		5994	5.3	1.0	4		79	2,8232		0,2,4115	no	coding-synonymous	FRYL	NM_015030.1		0,2,6038	AA,AG,GG		0.0243,0.0,0.0166		1998/3014	48542671	2,12078	1923	4117	6040	SO:0001819	synonymous_variant	285527	exon46			CATCAAGTTGGTA	AL833170	CCDS43227.1	4p12	2011-08-03	2006-11-17	2005-11-24	ENSG00000075539	ENSG00000075539			29127	protein-coding gene	gene with protein product			"""KIAA0826"", ""furry homolog-like (Drosophila)"""	KIAA0826		10048485	Standard	NM_015030		Approved	DKFZp686E205	uc003gyh.1	O94915	OTTHUMG00000160608	ENST00000503238.1:c.5994C>T	4.37:g.48542671G>A		132.0	0.0	0		117.0	57.0	0.487179	NM_015030	O95640|Q8WTZ5|Q9NT40	Silent	SNP	ENST00000503238.1	37	CCDS43227.1	.	.	.	.	.	.	.	.	.	.	G	2.279	-0.365058	0.05103	0.0	2.43E-4	ENSG00000075539	ENST00000514617	.	.	.	6.16	5.33	0.75918	.	.	.	.	.	T	0.62696	0.2449	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.61594	-0.7031	4	.	.	.	.	10.6144	0.45441	0.1986:0.0:0.8014:0.0	.	.	.	.	F	868	.	.	L	-	1	0	FRYL	48237428	1.000000	0.71417	0.978000	0.43139	0.571000	0.35966	3.050000	0.49877	1.628000	0.50416	0.650000	0.86243	CTT	.	.	weak		0.423	FRYL-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000369265.2		
VAV3	10451	hgsc.bcm.edu	37	1	108417534	108417534	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:108417534C>T	ENST00000370056.4	-	2	584	c.310G>A	c.(310-312)Gac>Aac	p.D104N	VAV3_ENST00000371846.4_Missense_Mutation_p.D39N|VAV3_ENST00000527011.1_Missense_Mutation_p.D104N	NM_006113.4	NP_006104.4	Q9UKW4	VAV3_HUMAN	vav 3 guanine nucleotide exchange factor	104	CH. {ECO:0000255|PROSITE- ProRule:PRU00044}.				angiogenesis (GO:0001525)|apoptotic signaling pathway (GO:0097190)|B cell receptor signaling pathway (GO:0050853)|blood coagulation (GO:0007596)|cellular response to DNA damage stimulus (GO:0006974)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|neutrophil chemotaxis (GO:0030593)|platelet activation (GO:0030168)|positive regulation of apoptotic process (GO:0043065)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell adhesion (GO:0045785)|positive regulation of GTPase activity (GO:0043547)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of signal transduction (GO:0009967)|regulation of Rac GTPase activity (GO:0032314)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to drug (GO:0042493)|small GTPase mediated signal transduction (GO:0007264)|vesicle fusion (GO:0006906)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|SH3/SH2 adaptor activity (GO:0005070)			NS(2)|breast(5)|endometrium(4)|kidney(2)|large_intestine(14)|lung(20)|ovary(6)|prostate(3)|stomach(1)|urinary_tract(1)	58		all_epithelial(167;5.38e-05)|all_lung(203;0.000314)|Lung NSC(277;0.000594)		Colorectal(144;0.0331)|Lung(183;0.128)|Epithelial(280;0.204)		TTTCCAAAGTCACGAACATCA	0.353																																					p.D104N		Atlas-SNP	.											.	VAV3	176	.	0			c.G310A						PASS	.						78.0	74.0	76.0					1																	108417534		2203	4300	6503	SO:0001583	missense	10451	exon2			CAAAGTCACGAAC	AF118886	CCDS785.1, CCDS44181.1	1p13.3	2013-02-14	2007-07-25		ENSG00000134215	ENSG00000134215		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	12659	protein-coding gene	gene with protein product		605541	"""vav 3 oncogene"""				Standard	NM_001079874		Approved		uc001dvk.1	Q9UKW4	OTTHUMG00000010995	ENST00000370056.4:c.310G>A	1.37:g.108417534C>T	ENSP00000359073:p.Asp104Asn	151.0	0.0	0		190.0	92.0	0.484211	NM_006113	B1AMM0|B1APV5|B4E232|B7ZLR1|E9PQ97|O60498|O95230|Q9Y5X8	Missense_Mutation	SNP	ENST00000370056.4	37	CCDS785.1	.	.	.	.	.	.	.	.	.	.	C	27.7	4.850961	0.91277	.	.	ENSG00000134215	ENST00000370056;ENST00000527011;ENST00000371846	T;T;T	0.41758	0.99;0.99;0.99	6.08	6.08	0.98989	Calponin homology domain (5);	0.229124	0.43416	D	0.000580	T	0.40423	0.1116	N	0.20328	0.56	0.58432	D	0.99999	B;B;D	0.54397	0.004;0.272;0.966	B;B;D	0.70487	0.023;0.322;0.969	T	0.09773	-1.0659	10	0.22706	T	0.39	.	19.2273	0.93822	0.0:1.0:0.0:0.0	.	104;104;104	B7ZLR1;E9PQ97;Q9UKW4	.;.;VAV3_HUMAN	N	104;104;39	ENSP00000359073:D104N;ENSP00000432540:D104N;ENSP00000360912:D39N	ENSP00000359073:D104N	D	-	1	0	VAV3	108219057	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.302000	0.78861	2.894000	0.99253	0.655000	0.94253	GAC	.	.	none		0.353	VAV3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030242.2	NM_006113	
TGM2	7052	hgsc.bcm.edu	37	20	36766591	36766591	+	Silent	SNP	G	G	A	rs140171902	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:36766591G>A	ENST00000361475.2	-	10	1712	c.1539C>T	c.(1537-1539)acC>acT	p.T513T	TGM2_ENST00000536701.1_Silent_p.T432T|TGM2_ENST00000536724.1_Silent_p.T453T	NM_004613.2|NM_198951.1	NP_004604.2|NP_945189.1	P21980	TGM2_HUMAN	transglutaminase 2	513					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|branching involved in salivary gland morphogenesis (GO:0060445)|isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine (GO:0018153)|negative regulation of endoplasmic reticulum calcium ion concentration (GO:0032471)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cytosolic calcium ion concentration involved in phospholipase C-activating G-protein coupled signaling pathway (GO:0051482)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of inflammatory response (GO:0050729)|positive regulation of mitochondrial calcium ion concentration (GO:0051561)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein homooligomerization (GO:0051260)|salivary gland cavitation (GO:0060662)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			endometrium(2)|large_intestine(11)|liver(1)|lung(7)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		Myeloproliferative disorder(115;0.00878)			L-Glutamine(DB00130)	TGTAGCTGACGGTGCGGGCAC	0.577													G|||	3	0.000599042	0.0	0.0029	5008	,	,		17458	0.0		0.001	False		,,,				2504	0.0				p.T513T		Atlas-SNP	.											.	TGM2	88	.	0			c.C1539T						PASS	.	G	,	0,4406		0,0,2203	93.0	70.0	78.0		1539,1539	-7.9	0.8	20	dbSNP_134	78	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	TGM2	NM_004613.2,NM_198951.1	,	0,5,6498	AA,AG,GG		0.0581,0.0,0.0384	,	513/688,513/549	36766591	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	7052	exon10			GCTGACGGTGCGG	M98478	CCDS13302.1	20q12	2013-05-02	2013-05-02		ENSG00000198959	ENSG00000198959	2.3.2.13	"""Transglutaminases"""	11778	protein-coding gene	gene with protein product	"""C polypeptide, protein-glutamine-gamma-glutamyltransferase"""	190196	"""transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)"""			7912692, 11390390	Standard	NM_004613		Approved	TGC	uc002xhr.3	P21980	OTTHUMG00000032437	ENST00000361475.2:c.1539C>T	20.37:g.36766591G>A		127.0	0.0	0		154.0	75.0	0.487013	NM_198951	E1P5V9|Q16436|Q6B838|Q9BTN7|Q9UH35	Silent	SNP	ENST00000361475.2	37	CCDS13302.1																																																																																			G|1.000;A|0.000	0.000	strong		0.577	TGM2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079151.2	NM_198951	
FAM83H	286077	hgsc.bcm.edu	37	8	144810346	144810346	+	Missense_Mutation	SNP	C	C	A	rs144418186	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr8:144810346C>A	ENST00000388913.3	-	5	1410	c.1285G>T	c.(1285-1287)Gtg>Ttg	p.V429L		NM_198488.3	NP_940890	Q6ZRV2	FA83H_HUMAN	family with sequence similarity 83, member H	429					biomineral tissue development (GO:0031214)					central_nervous_system(2)|endometrium(1)|large_intestine(1)|lung(12)|pancreas(1)|prostate(3)|urinary_tract(1)	21	all_cancers(97;3.74e-11)|all_epithelial(106;2.62e-09)|Lung NSC(106;0.00013)|all_lung(105;0.000374)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;3.38e-41)|Epithelial(56;6.8e-40)|all cancers(56;6.43e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.146)			TGCCGCGACACCTGCCGCGCG	0.682													C|||	21	0.00419329	0.0	0.013	5008	,	,		6410	0.0		0.008	False		,,,				2504	0.0041				p.V429L		Atlas-SNP	.											.	FAM83H	68	.	0			c.G1285T						PASS	.	C	LEU/VAL	8,4120		0,8,2056	15.0	24.0	21.0		1285	4.0	1.0	8	dbSNP_134	21	137,8219		2,133,4043	yes	missense	FAM83H	NM_198488.3	32	2,141,6099	AA,AC,CC		1.6395,0.1938,1.1615	possibly-damaging	429/1180	144810346	145,12339	2064	4178	6242	SO:0001583	missense	286077	exon5			GCGACACCTGCCG	AK127960	CCDS6410.2	8q24.3	2014-03-13			ENSG00000180921	ENSG00000180921			24797	protein-coding gene	gene with protein product		611927				18252228	Standard	NM_198488		Approved	FLJ46072	uc003yzk.3	Q6ZRV2	OTTHUMG00000133559	ENST00000388913.3:c.1285G>T	8.37:g.144810346C>A	ENSP00000373565:p.Val429Leu	11.0	0.0	0		24.0	13.0	0.541667	NM_198488	A0JLS2|Q8N4W0	Missense_Mutation	SNP	ENST00000388913.3	37	CCDS6410.2	9	0.004120879120879121	0	0.0	3	0.008287292817679558	0	0.0	6	0.0079155672823219	c	8.338	0.828008	0.16749	0.001938	0.016395	ENSG00000180921	ENST00000388913	T	0.15017	2.46	4.96	4.02	0.46733	.	0.947136	0.08665	N	0.911838	T	0.05731	0.0150	L	0.27053	0.805	0.25299	N	0.9893	B	0.31581	0.329	B	0.25987	0.065	T	0.11372	-1.0590	10	0.21014	T	0.42	.	10.4754	0.44661	0.361:0.639:0.0:0.0	.	429	Q6ZRV2	FA83H_HUMAN	L	429	ENSP00000373565:V429L	ENSP00000373565:V429L	V	-	1	0	FAM83H	144882334	0.976000	0.34144	0.995000	0.50966	0.035000	0.12851	2.070000	0.41491	2.277000	0.76020	0.555000	0.69702	GTG	C|0.991;A|0.009	0.009	strong		0.682	FAM83H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257632.2	NM_198488	
PROC	5624	hgsc.bcm.edu	37	2	128186156	128186156	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:128186156G>A	ENST00000234071.3	+	9	1107	c.1020G>A	c.(1018-1020)acG>acA	p.T340T	PROC_ENST00000422777.3_Silent_p.T340T|PROC_ENST00000409048.1_Silent_p.T374T|PROC_ENST00000453608.2_Silent_p.T395T	NM_000312.3	NP_000303.1	P04070	PROC_HUMAN	protein C (inactivator of coagulation factors Va and VIIIa)	340	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.		T -> M (in THPH3; Vermont-2). {ECO:0000269|PubMed:8292730, ECO:0000269|PubMed:9798967}.		blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of blood coagulation (GO:0030195)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)	p.T340T(1)		endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)	15	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0673)	Antihemophilic Factor(DB00025)|Menadione(DB00170)|Sodium Tetradecyl Sulfate(DB00464)	CCCTCGTGACGGGCTGGGGCT	0.632																																					p.T340T		Atlas-SNP	.											.	PROC	31	.	1	Substitution - coding silent(1)	lung(1)	c.G1020A						PASS	.						85.0	99.0	94.0					2																	128186156		2203	4300	6503	SO:0001819	synonymous_variant	5624	exon9			CGTGACGGGCTGG	X02750	CCDS2145.1	2q13-q14	2014-01-30			ENSG00000115718	ENSG00000115718		"""Endogenous ligands"""	9451	protein-coding gene	gene with protein product	"""prepro-protein C"""	612283				2991887, 2437584	Standard	NM_000312		Approved		uc002tok.3	P04070	OTTHUMG00000131528	ENST00000234071.3:c.1020G>A	2.37:g.128186156G>A		84.0	0.0	0		99.0	42.0	0.424242	NM_000312	B4DPQ7|Q15189|Q15190|Q16001|Q53S74|Q9UC55	Silent	SNP	ENST00000234071.3	37	CCDS2145.1	.	.	.	.	.	.	.	.	.	.	G	0.108	-1.142460	0.01728	.	.	ENSG00000115718	ENST00000402125	.	.	.	5.23	-10.5	0.00291	.	.	.	.	.	T	0.32224	0.0822	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.41016	-0.9532	4	.	.	.	.	1.6144	0.02700	0.4409:0.2044:0.1371:0.2175	.	.	.	.	Q	115	.	.	R	+	2	0	PROC	127902626	0.000000	0.05858	0.263000	0.24496	0.026000	0.11368	-5.090000	0.00152	-2.914000	0.00307	-1.036000	0.02392	CGG	.	.	none		0.632	PROC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254385.2	NM_000312	
FAM126A	84668	hgsc.bcm.edu	37	7	23030692	23030692	+	Silent	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:23030692C>T	ENST00000432176.2	-	2	271	c.39G>A	c.(37-39)ttG>ttA	p.L13L	FAM126A_ENST00000409923.1_Silent_p.L13L|FAM126A_ENST00000409763.1_Silent_p.L13L	NM_032581.3	NP_115970.2	Q9BYI3	HYCCI_HUMAN	family with sequence similarity 126, member A	13					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(8)|urinary_tract(2)	23						TAAACTCTGACAACCATTCCT	0.308																																					p.L13L		Atlas-SNP	.											.	FAM126A	53	.	0			c.G39A						PASS	.						107.0	108.0	108.0					7																	23030692		2203	4294	6497	SO:0001819	synonymous_variant	84668	exon2			CTCTGACAACCAT	BC018710	CCDS5377.1	7p15.3	2008-10-02			ENSG00000122591	ENSG00000122591			24587	protein-coding gene	gene with protein product	"""down regulated by Ctnnb1, a"""	610531				10910037, 16951682	Standard	NM_032581		Approved	DRCTNNB1A, HCC, HYCC1, hyccin	uc003svm.4	Q9BYI3	OTTHUMG00000128435	ENST00000432176.2:c.39G>A	7.37:g.23030692C>T		71.0	0.0	0		139.0	106.0	0.76259	NM_032581	A4D145|Q6N010|Q75MR4|Q7LDZ4|Q96MX1|Q96NQ6	Silent	SNP	ENST00000432176.2	37	CCDS5377.1																																																																																			.	.	none		0.308	FAM126A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250230.1	NM_032581	
GATA6	2627	hgsc.bcm.edu	37	18	19762989	19762989	+	Silent	SNP	A	A	G	rs117646477	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:19762989A>G	ENST00000269216.3	+	6	1882	c.1605A>G	c.(1603-1605)caA>caG	p.Q535Q	GATA6_ENST00000581694.1_Silent_p.Q535Q|RNU6-702P_ENST00000364982.1_RNA	NM_005257.4	NP_005248.2	Q92908	GATA6_HUMAN	GATA binding protein 6	535					blood coagulation (GO:0007596)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac vascular smooth muscle cell differentiation (GO:0060947)|cellular response to BMP stimulus (GO:0071773)|cellular response to gonadotropin stimulus (GO:0071371)|cellular response to hypoxia (GO:0071456)|Clara cell differentiation (GO:0060486)|endodermal cell fate determination (GO:0007493)|in utero embryonic development (GO:0001701)|intestinal epithelial cell differentiation (GO:0060575)|liver development (GO:0001889)|lung saccule development (GO:0060430)|male gonad development (GO:0008584)|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)|negative regulation of transforming growth factor beta1 production (GO:0032911)|negative regulation of transforming growth factor beta2 production (GO:0032912)|organ formation (GO:0048645)|outflow tract septum morphogenesis (GO:0003148)|pancreatic A cell differentiation (GO:0003310)|phospholipid metabolic process (GO:0006644)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cardioblast differentiation (GO:0051891)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to growth factor (GO:0070848)|smooth muscle cell differentiation (GO:0051145)|transcription from RNA polymerase II promoter (GO:0006366)|tube morphogenesis (GO:0035239)|type B pancreatic cell differentiation (GO:0003309)|Type II pneumocyte differentiation (GO:0060510)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin binding (GO:0003682)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			NS(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(8)|prostate(1)|skin(1)	18	all_cancers(21;0.00271)|all_epithelial(16;7.31e-05)|Ovarian(2;0.116)|Lung NSC(20;0.123)|all_lung(20;0.246)		STAD - Stomach adenocarcinoma(5;0.106)			CCACAACACAACCTACAGCCT	0.393													A|||	3	0.000599042	0.0	0.0	5008	,	,		15678	0.0		0.002	False		,,,				2504	0.001				p.Q535Q	Colon(8;48 282 46199 46856)|Melanoma(177;170 2725 12489 26999)	Atlas-SNP	.											.	GATA6	35	.	0			c.A1605G						PASS	.	A		0,4406		0,0,2203	104.0	92.0	96.0		1605	2.4	1.0	18	dbSNP_133	96	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	GATA6	NM_005257.3		0,4,6499	GG,GA,AA		0.0465,0.0,0.0308		535/596	19762989	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	2627	exon6			AACACAACCTACA	U66075	CCDS11872.1	18q11-q12	2013-01-25	2001-11-28		ENSG00000141448	ENSG00000141448		"""GATA zinc finger domain containing"""	4174	protein-coding gene	gene with protein product		601656	"""GATA-binding protein 6"""			8975704	Standard	XM_005258248		Approved		uc002ktt.2	Q92908	OTTHUMG00000131767	ENST00000269216.3:c.1605A>G	18.37:g.19762989A>G		134.0	0.0	0		160.0	97.0	0.60625	NM_005257	B0YJ17|P78327	Silent	SNP	ENST00000269216.3	37	CCDS11872.1																																																																																			A|0.999;G|0.001	0.001	strong		0.393	GATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254696.1	NM_005257	
ZADH2	284273	hgsc.bcm.edu	37	18	72913920	72913920	+	Silent	SNP	C	C	T	rs61910717	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:72913920C>T	ENST00000322342.3	-	2	874	c.585G>A	c.(583-585)aaG>aaA	p.K195K	ZADH2_ENST00000537114.2_Silent_p.K72K	NM_175907.4	NP_787103.1	Q8N4Q0	ZADH2_HUMAN	zinc binding alcohol dehydrogenase domain containing 2	195						mitochondrion (GO:0005739)|peroxisome (GO:0005777)	oxidoreductase activity (GO:0016491)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(3)|lung(8)|skin(1)	15		Esophageal squamous(42;0.131)|Prostate(75;0.155)		READ - Rectum adenocarcinoma(2;0.0276)|BRCA - Breast invasive adenocarcinoma(31;0.216)		GGCACTTTGCCTTCTTTGAAA	0.478													C|||	127	0.0253594	0.003	0.0202	5008	,	,		21275	0.0		0.0358	False		,,,				2504	0.0746				p.K195K		Atlas-SNP	.											.	ZADH2	25	.	0			c.G585A						PASS	.	C		38,4368	41.6+/-74.8	0,38,2165	177.0	189.0	185.0		585	2.3	0.6	18	dbSNP_129	185	317,8283	111.0+/-171.3	5,307,3988	no	coding-synonymous	ZADH2	NM_175907.4		5,345,6153	TT,TC,CC		3.686,0.8625,2.7295		195/378	72913920	355,12651	2203	4300	6503	SO:0001819	synonymous_variant	284273	exon2			CTTTGCCTTCTTT	BC033780	CCDS12008.1	18q22.3	2008-05-29	2008-05-29		ENSG00000180011	ENSG00000180011			28697	protein-coding gene	gene with protein product						12477932	Standard	NM_175907		Approved	MGC45594	uc002llx.3	Q8N4Q0	OTTHUMG00000132858	ENST00000322342.3:c.585G>A	18.37:g.72913920C>T		76.0	0.0	0		84.0	59.0	0.702381	NM_175907	A8KA15|B4DZ91	Silent	SNP	ENST00000322342.3	37	CCDS12008.1																																																																																			C|0.973;T|0.027	0.027	strong		0.478	ZADH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256332.1	NM_175907	
APC	324	hgsc.bcm.edu	37	5	112177171	112177171	+	Silent	SNP	G	G	A	rs465899|rs587779801	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112177171G>A	ENST00000457016.1	+	16	6260	c.5880G>A	c.(5878-5880)ccG>ccA	p.P1960P	APC_ENST00000257430.4_Silent_p.P1960P|APC_ENST00000508376.2_Silent_p.P1960P|CTC-554D6.1_ENST00000520401.1_Intron			P25054	APC_HUMAN	adenomatous polyposis coli	1960	Ser-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AAAATACTCCGGTTTGCTTTT	0.398		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			A|||	3338	0.666534	0.5212	0.7161	5008	,	,		20489	0.8165		0.5994	False		,,,				2504	0.7423				p.P1960P	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	1	Unknown(1)	skin(1)	c.G5880A						PASS	.	A	,,	2328,2076	560.3+/-380.4	623,1082,497	66.0	64.0	65.0	http://omim.org/entry/114500	5880,5880,5826	-3.7	1.0	5	dbSNP_80	65	5303,3295	486.2+/-371.8	1668,1967,664	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2291,3049,1161	AA,AG,GG		38.3229,47.139,41.309	,,	1960/2844,1960/2844,1942/2826	112177171	7631,5371	2202	4299	6501	SO:0001819	synonymous_variant	324	exon17	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TACTCCGGTTTGC	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.5880G>A	5.37:g.112177171G>A		119.0	0.0	0		141.0	139.0	0.985816	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.332;A|0.668	0.668	strong		0.398	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
GABRA6	2559	hgsc.bcm.edu	37	5	161117243	161117243	+	Missense_Mutation	SNP	A	A	G	rs76773579	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:161117243A>G	ENST00000274545.5	+	7	1143	c.710A>G	c.(709-711)cAa>cGa	p.Q237R	GABRA6_ENST00000523217.1_Missense_Mutation_p.Q227R|RP11-348M17.2_ENST00000521984.1_RNA			Q16445	GBRA6_HUMAN	gamma-aminobutyric acid (GABA) A receptor, alpha 6	237					gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			breast(1)|central_nervous_system(2)|endometrium(6)|large_intestine(9)|liver(2)|lung(22)|ovary(7)|skin(6)|urinary_tract(2)	57	Renal(175;0.00259)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		Acamprosate(DB00659)|Alprazolam(DB00404)|Amobarbital(DB01351)|Amoxapine(DB00543)|Aprobarbital(DB01352)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flunitrazepam(DB01544)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methylphenobarbital(DB00849)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Secobarbital(DB00418)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Thiopental(DB00599)|Topiramate(DB00273)|Triazolam(DB00897)	TTCCACTTGCAAAGGAAGATG	0.393										TCGA Ovarian(5;0.080)			A|||	4	0.000798722	0.0	0.0014	5008	,	,		19724	0.0		0.002	False		,,,				2504	0.001				p.Q237R		Atlas-SNP	.											.	GABRA6	139	.	0			c.A710G						PASS	.	A	ARG/GLN	1,4405	2.1+/-5.4	0,1,2202	152.0	135.0	141.0		710	5.3	1.0	5	dbSNP_131	141	35,8565	24.6+/-71.5	0,35,4265	yes	missense	GABRA6	NM_000811.2	43	0,36,6467	GG,GA,AA		0.407,0.0227,0.2768	benign	237/454	161117243	36,12970	2203	4300	6503	SO:0001583	missense	2559	exon7			ACTTGCAAAGGAA		CCDS4356.1	5q34	2012-06-22			ENSG00000145863	ENSG00000145863		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4080	protein-coding gene	gene with protein product	"""GABA(A) receptor, alpha 6"""	137143				8020978	Standard	NM_000811		Approved		uc003lyu.2	Q16445	OTTHUMG00000130351	ENST00000274545.5:c.710A>G	5.37:g.161117243A>G	ENSP00000274545:p.Gln237Arg	112.0	0.0	0		131.0	65.0	0.496183	NM_000811	A8K096|Q4VAV2	Missense_Mutation	SNP	ENST00000274545.5	37	CCDS4356.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	A|A	14.82|14.82	2.648356|2.648356	0.47258|0.47258	2.27E-4|2.27E-4	0.00407|0.00407	ENSG00000145863|ENSG00000145863	ENST00000520000|ENST00000274545;ENST00000523217;ENST00000517823;ENST00000523691	.|T;T;T;T	.|0.75589	.|-0.95;-0.95;-0.95;-0.95	5.31|5.31	5.31|5.31	0.75309|0.75309	.|Neurotransmitter-gated ion-channel ligand-binding (3);	.|0.053501	.|0.85682	.|D	.|0.000000	T|T	0.57257|0.57257	0.2041|0.2041	N|N	0.04959|0.04959	-0.14|-0.14	0.47778|0.47778	D|D	0.999516|0.999516	.|B	.|0.20052	.|0.041	.|B	.|0.25405	.|0.06	T|T	0.55547|0.55547	-0.8124|-0.8124	5|10	.|0.39692	.|T	.|0.17	.|.	15.2733|15.2733	0.73723|0.73723	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	.|237	.|Q16445	.|GBRA6_HUMAN	E|R	177|237;227;184;157	.|ENSP00000274545:Q237R;ENSP00000430527:Q227R;ENSP00000430212:Q184R;ENSP00000427989:Q157R	.|ENSP00000274545:Q237R	K|Q	+|+	1|2	0|0	GABRA6|GABRA6	161049821|161049821	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.995000|0.995000	0.86356|0.86356	7.423000|7.423000	0.80229|0.80229	2.016000|2.016000	0.59253|0.59253	0.533000|0.533000	0.62120|0.62120	AAA|CAA	A|0.997;G|0.003	0.003	strong		0.393	GABRA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252707.2		
DDX60	55601	hgsc.bcm.edu	37	4	169227551	169227551	+	Silent	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:169227551T>C	ENST00000393743.3	-	5	876	c.585A>G	c.(583-585)agA>agG	p.R195R		NM_017631.5	NP_060101.3	Q8IY21	DDX60_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 60	195					defense response to virus (GO:0051607)|innate immune response (GO:0045087)|positive regulation of MDA-5 signaling pathway (GO:1900245)|positive regulation of RIG-I signaling pathway (GO:1900246)|response to virus (GO:0009615)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|single-stranded RNA binding (GO:0003727)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(15)|liver(1)|lung(21)|ovary(1)|pancreas(2)|prostate(1)|skin(4)|urinary_tract(4)	63		Prostate(90;0.00876)|Renal(120;0.0183)|all_neural(102;0.0837)|Melanoma(52;0.132)		GBM - Glioblastoma multiforme(119;0.0485)		AAATCTGGTGTCTGTACATGC	0.378																																					p.R195R		Atlas-SNP	.											.	DDX60	304	.	0			c.A585G						PASS	.						59.0	59.0	59.0					4																	169227551		2203	4300	6503	SO:0001819	synonymous_variant	55601	exon5			CTGGTGTCTGTAC	AK001649	CCDS34097.1	4q32.3	2010-02-17			ENSG00000137628	ENSG00000137628			25942	protein-coding gene	gene with protein product		613974				12477932	Standard	NM_017631		Approved	FLJ20035	uc003irp.3	Q8IY21	OTTHUMG00000161350	ENST00000393743.3:c.585A>G	4.37:g.169227551T>C		61.0	0.0	0		38.0	4.0	0.105263	NM_017631	Q6PK35|Q9NVE3	Silent	SNP	ENST00000393743.3	37	CCDS34097.1																																																																																			.	.	none		0.378	DDX60-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364622.1	NM_017631	
MET	4233	hgsc.bcm.edu	37	7	116435768	116435768	+	Silent	SNP	C	C	T	rs41736	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:116435768C>T	ENST00000318493.6	+	20	4099	c.3912C>T	c.(3910-3912)gaC>gaT	p.D1304D	MET_ENST00000397752.3_Silent_p.D1286D|MET_ENST00000539704.1_Silent_p.D156D			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					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)	p.D1304D(1)		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)			CTTATCCTGACGTAAACACCT	0.473			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)		OREG0003446	type=REGULATORY REGION|Gene=MET|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay	c|||	1764	0.352236	0.034	0.464	5008	,	,		18610	0.4673		0.4414	False		,,,				2504	0.4928				p.D1304D		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.C3912T						PASS	.	T	,	393,3383		15,363,1510	245.0	238.0	240.0		3858,3912	-10.9	0.0	7	dbSNP_76	240	3487,4731		756,1975,1378	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	771,2338,2888	TT,TC,CC		42.4312,10.4078,32.3495	,	1286/1391,1304/1409	116435768	3880,8114	1888	4109	5997	SO:0001819	synonymous_variant	4233	exon20	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	TCCTGACGTAAAC	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.3912C>T	7.37:g.116435768C>T		123.0	1.0	0.00813008	1473	123.0	122.0	0.99187	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			C|0.624;T|0.376	0.376	strong		0.473	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
THOC1	9984	hgsc.bcm.edu	37	18	264030	264030	+	Silent	SNP	A	A	G	rs371643145		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:264030A>G	ENST00000261600.6	-	4	259	c.252T>C	c.(250-252)acT>acC	p.T84T	THOC1_ENST00000582313.1_5'UTR	NM_005131.2	NP_005122.2	Q96FV9	THOC1_HUMAN	THO complex 1	84					apoptotic process (GO:0006915)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of isotype switching to IgA isotypes (GO:0048297)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|regulation of DNA recombination (GO:0000018)|regulation of DNA-templated transcription, elongation (GO:0032784)|replication fork processing (GO:0031297)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	DNA binding (GO:0003677)|RNA binding (GO:0003723)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|skin(1)|stomach(1)|urinary_tract(1)	20		all_cancers(4;0.0896)|Myeloproliferative disorder(11;0.0412)				ACTTACCTTCAGTTACTCCCC	0.353																																					p.T84T		Atlas-SNP	.											.	THOC1	43	.	0			c.T252C						PASS	.	A		0,3698		0,0,1849	86.0	73.0	77.0		252	1.0	1.0	18		77	5,8177		0,5,4086	no	coding-synonymous	THOC1	NM_005131.2		0,5,5935	GG,GA,AA		0.0611,0.0,0.0421		84/658	264030	5,11875	1849	4091	5940	SO:0001819	synonymous_variant	9984	exon4			ACCTTCAGTTACT	AK055354	CCDS45820.1	18p11.32	2013-02-11			ENSG00000079134	ENSG00000079134		"""THO complex subunits"""	19070	protein-coding gene	gene with protein product		606930				11979277	Standard	NM_005131		Approved	P84, HPR1	uc002kkj.4	Q96FV9		ENST00000261600.6:c.252T>C	18.37:g.264030A>G		162.0	0.0	0		182.0	61.0	0.335165	NM_005131	B2RBP6|Q15219|Q64I72|Q64I73	Silent	SNP	ENST00000261600.6	37	CCDS45820.1																																																																																			.	.	weak		0.353	THOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440348.5	NM_005131	
EPG5	57724	hgsc.bcm.edu	37	18	43523997	43523997	+	Missense_Mutation	SNP	T	T	C	rs61734402	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:43523997T>C	ENST00000282041.5	-	8	1800	c.1766A>G	c.(1765-1767)cAg>cGg	p.Q589R		NM_020964.2	NP_066015.2	Q9HCE0	EPG5_HUMAN	ectopic P-granules autophagy protein 5 homolog (C. elegans)	589					autophagic vacuole maturation (GO:0097352)|autophagy (GO:0006914)|endocytic recycling (GO:0032456)					NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(22)|lung(35)|ovary(2)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	95						AAGAAGATGCTGAAAGAGTTC	0.398													T|||	16	0.00319489	0.0008	0.0029	5008	,	,		20382	0.0		0.0129	False		,,,				2504	0.0				p.Q589R		Atlas-SNP	.											.	EPG5	199	.	0			c.A1766G						PASS	.	T	ARG/GLN	10,3706		0,10,1848	150.0	134.0	139.0		1766	5.2	0.9	18	dbSNP_129	139	147,8069		1,145,3962	yes	missense	EPG5	NM_020964.2	43	1,155,5810	CC,CT,TT		1.7892,0.2691,1.3158	benign	589/2580	43523997	157,11775	1858	4108	5966	SO:0001583	missense	57724	exon8			AGATGCTGAAAGA	AK023817	CCDS11926.2	18q12.3	2011-03-02	2011-03-02	2011-03-02	ENSG00000152223	ENSG00000152223			29331	protein-coding gene	gene with protein product		615068	"""KIAA1632"""	KIAA1632		10997877, 20550938	Standard	XM_005258323		Approved	hEPG5	uc002lbm.3	Q9HCE0	OTTHUMG00000132626	ENST00000282041.5:c.1766A>G	18.37:g.43523997T>C	ENSP00000282041:p.Gln589Arg	75.0	0.0	0		90.0	42.0	0.466667	NM_020964	A2BDF3|Q9H8C8	Missense_Mutation	SNP	ENST00000282041.5	37	CCDS11926.2	13	0.005952380952380952	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	9.853	1.194070	0.22037	0.002691	0.017892	ENSG00000152223	ENST00000282041	T	0.09817	2.94	5.25	5.25	0.73442	.	0.170822	0.38720	N	0.001587	T	0.04998	0.0134	L	0.40543	1.245	0.29097	N	0.881736	P;B	0.34724	0.465;0.4	B;B	0.34242	0.178;0.085	T	0.08868	-1.0701	10	0.22109	T	0.4	-10.7121	15.1999	0.73126	0.0:0.0:0.0:1.0	.	589;589	Q9HCE0-2;Q9HCE0	.;EPG5_HUMAN	R	589	ENSP00000282041:Q589R	ENSP00000282041:Q589R	Q	-	2	0	EPG5	41777995	1.000000	0.71417	0.894000	0.35097	0.212000	0.24457	4.972000	0.63756	1.991000	0.58162	0.374000	0.22700	CAG	T|0.994;C|0.006	0.006	strong		0.398	EPG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445081.1	NM_020964	
GSTZ1	2954	hgsc.bcm.edu	37	14	77793237	77793237	+	Missense_Mutation	SNP	G	G	A	rs7972	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	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_ENST00000557053.1_5'UTR|GSTZ1_ENST00000349555.3_Missense_Mutation_p.G42R|GSTZ1_ENST00000216465.5_Missense_Mutation_p.G42R|GSTZ1_ENST00000393734.1_5'UTR|GSTZ1_ENST00000361389.4_5'UTR|GSTZ1_ENST00000557639.1_5'UTR|GSTZ1_ENST00000553586.1_Missense_Mutation_p.G43R			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	38.0	0.0	0		54.0	22.0	0.407407	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	
SLC12A9	56996	hgsc.bcm.edu	37	7	100463492	100463492	+	Silent	SNP	G	G	A	rs34433055	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:100463492G>A	ENST00000354161.3	+	14	2135	c.2010G>A	c.(2008-2010)cgG>cgA	p.R670R	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	670					chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation:chloride symporter activity (GO:0015377)			breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(20)|ovary(1)|skin(3)|stomach(1)|urinary_tract(1)	41	Lung NSC(181;0.041)|all_lung(186;0.0581)					CTCCTCCCCGGGCTCCTGGGA	0.667													G|||	26	0.00519169	0.0008	0.0043	5008	,	,		14655	0.0		0.0159	False		,,,				2504	0.0061				p.R670R		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2010A						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	30.0	36.0	34.0		2010	3.3	1.0	7	dbSNP_126	34	132,8466	64.9+/-127.2	1,130,4168	no	coding-synonymous	SLC12A9	NM_020246.2		1,143,6358	AA,AG,GG		1.5352,0.2951,1.115		670/915	100463492	145,12859	2203	4299	6502	SO:0001819	synonymous_variant	56996	exon14			TCCCCGGGCTCCT	AF284422	CCDS5707.1, CCDS59068.1, CCDS59069.1	7q22	2013-07-18	2013-07-18		ENSG00000146828	ENSG00000146828		"""Solute carriers"""	17435	protein-coding gene	gene with protein product	"""cation-chloride cotransporter-interacting protein"""					10871601, 11239002	Standard	NM_020246		Approved	CIP1	uc003uwp.4	Q9BXP2	OTTHUMG00000156045	ENST00000354161.3:c.2010G>A	7.37:g.100463492G>A		100.0	0.0	0		98.0	41.0	0.418367	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1																																																																																			G|0.991;A|0.009	0.009	strong		0.667	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
VSX1	30813	hgsc.bcm.edu	37	20	25060143	25060143	+	Missense_Mutation	SNP	G	G	C	rs140122268	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:25060143G>C	ENST00000376709.4	-	2	695	c.432C>G	c.(430-432)gaC>gaG	p.D144E	VSX1_ENST00000424574.1_Missense_Mutation_p.D144E|VSX1_ENST00000451258.1_Missense_Mutation_p.D144E|VSX1_ENST00000444511.2_Missense_Mutation_p.D144E|VSX1_ENST00000429762.3_Missense_Mutation_p.D144E|VSX1_ENST00000376707.3_Missense_Mutation_p.D144E	NM_014588.5	NP_055403.2	Q9NZR4	VSX1_HUMAN	visual system homeobox 1	144	Asp/Glu-rich (acidic).		D -> E (in PPCD1 and KTCN1; dbSNP:rs140122268). {ECO:0000269|PubMed:11978762, ECO:0000269|PubMed:15623752}.		neuron maturation (GO:0042551)|response to stimulus (GO:0050896)|retinal bipolar neuron differentiation (GO:0060040)|transcription, DNA-templated (GO:0006351)|visual perception (GO:0007601)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(3)|lung(2)	6						CAGACTGGCTGTCCTCATCTG	0.502													G|||	11	0.00219649	0.0	0.0029	5008	,	,		19019	0.001		0.005	False		,,,				2504	0.0031				p.D144E		Atlas-SNP	.											.	VSX1	20	.	0			c.C432G	GRCh37	CM020983	VSX1	M	rs140122268	PASS	.	G	GLU/ASP,GLU/ASP	4,4402	8.1+/-20.4	0,4,2199	59.0	46.0	50.0		432,432	1.8	0.9	20	dbSNP_134	50	31,8569	21.6+/-65.8	0,31,4269	yes	missense,missense	VSX1	NM_014588.4,NM_199425.1	45,45	0,35,6468	CC,CG,GG		0.3605,0.0908,0.2691	possibly-damaging,possibly-damaging	144/366,144/240	25060143	35,12971	2203	4300	6503	SO:0001583	missense	30813	exon2			CTGGCTGTCCTCA	AF176797	CCDS13168.1, CCDS13169.1, CCDS58766.1, CCDS58767.1	20p11.21	2014-02-14	2007-07-12		ENSG00000100987	ENSG00000100987		"""Homeoboxes / PRD class"""	12723	protein-coding gene	gene with protein product		605020	"""posterior polymorphous corneal dystrophy"", ""visual system homeobox 1 homolog, CHX10-like (zebrafish)"""	PPCD		10673340	Standard	NM_001256272		Approved	PPD, PPCD1	uc002wuf.4	Q9NZR4	OTTHUMG00000032111	ENST00000376709.4:c.432C>G	20.37:g.25060143G>C	ENSP00000365899:p.Asp144Glu	29.0	0.0	0		39.0	20.0	0.512821	NM_014588	B9EGJ4|D1MF28|Q0GM60|Q0GM61|Q0GM62|Q0GM63|Q0GM64|Q0GM65|Q5TF40|Q5TF41|Q9HCU3|Q9NU27	Missense_Mutation	SNP	ENST00000376709.4	37	CCDS13168.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	11.20	1.568006	0.28003	9.08E-4	0.003605	ENSG00000100987	ENST00000429762;ENST00000444511;ENST00000424574;ENST00000451258;ENST00000376709;ENST00000376707	D;D;D;D;D;D	0.92965	-2.89;-3.14;-2.88;-2.99;-2.99;-3.05	5.01	1.75	0.24633	.	0.158273	0.56097	N	0.000035	D	0.85124	0.5625	L	0.47716	1.5	0.80722	D	1	B;B;B;B	0.29136	0.234;0.027;0.122;0.023	B;B;B;B	0.35859	0.212;0.013;0.16;0.016	T	0.80099	-0.1524	10	0.44086	T	0.13	.	9.0206	0.36198	0.0:0.1814:0.5437:0.2748	.	144;144;144;144	Q9NZR4-7;Q9NZR4-8;Q9NZR4-2;Q9NZR4	.;.;.;VSX1_HUMAN	E	144	ENSP00000401690:D144E;ENSP00000387720:D144E;ENSP00000399496:D144E;ENSP00000389654:D144E;ENSP00000365899:D144E;ENSP00000365897:D144E	ENSP00000365897:D144E	D	-	3	2	VSX1	25008143	1.000000	0.71417	0.933000	0.37362	0.545000	0.35147	0.397000	0.20883	0.188000	0.20168	0.462000	0.41574	GAC	G|0.997;C|0.003	0.003	strong		0.502	VSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078384.3		
TSPYL4	23270	hgsc.bcm.edu	37	6	116574977	116574977	+	Missense_Mutation	SNP	A	A	C	rs187133419	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:116574977A>C	ENST00000420283.1	-	1	284	c.195T>G	c.(193-195)gaT>gaG	p.D65E	RP3-486I3.7_ENST00000448740.2_lincRNA|DSE_ENST00000540275.1_5'Flank	NM_021648.4	NP_067680.3	Q9UJ04	TSYL4_HUMAN	TSPY-like 4	65					nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(2)	11		all_cancers(87;0.0144)|all_epithelial(87;0.021)|Colorectal(196;0.234)		all cancers(137;0.045)|OV - Ovarian serous cystadenocarcinoma(136;0.0666)|GBM - Glioblastoma multiforme(226;0.095)|Epithelial(106;0.125)		AGTCGACAGGATCCTGGGATG	0.667													A|||	8	0.00159744	0.0	0.0086	5008	,	,		15829	0.0		0.002	False		,,,				2504	0.0				p.D65E		Atlas-SNP	.											.	TSPYL4	18	.	0			c.T195G						PASS	.	A	GLU/ASP	3,4039		0,3,2018	19.0	22.0	21.0		195	-7.5	0.0	6		21	36,8334		0,36,4149	yes	missense	TSPYL4	NM_021648.4	45	0,39,6167	CC,CA,AA		0.4301,0.0742,0.3142	possibly-damaging	65/415	116574977	39,12373	2021	4185	6206	SO:0001583	missense	23270	exon1			GACAGGATCCTGG		CCDS5106.1	6q22.1	2010-05-12			ENSG00000187189	ENSG00000187189			21559	protein-coding gene	gene with protein product							Standard	NM_021648		Approved	dJ486I3.2, KIAA0721	uc003pwn.3	Q9UJ04	OTTHUMG00000015429	ENST00000420283.1:c.195T>G	6.37:g.116574977A>C	ENSP00000410943:p.Asp65Glu	34.0	0.0	0		35.0	15.0	0.428571	NM_021648	B4DYQ2|O94828|Q96GW8	Missense_Mutation	SNP	ENST00000420283.1	37	CCDS5106.1	4	0.0018315018315018315	0	0.0	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	A	10.13	1.264700	0.23136	7.42E-4	0.004301	ENSG00000187189	ENST00000420283	T	0.18810	2.19	3.75	-7.5	0.01351	.	.	.	.	.	T	0.03220	0.0094	M	0.63843	1.955	0.09310	N	1	B	0.15930	0.015	B	0.15052	0.012	T	0.43718	-0.9374	9	0.02654	T	1	-2.0876	2.3433	0.04265	0.1299:0.3779:0.1165:0.3757	.	65	Q9UJ04	TSYL4_HUMAN	E	65	ENSP00000410943:D65E	ENSP00000410943:D65E	D	-	3	2	TSPYL4	116681670	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.061000	0.11693	-1.631000	0.01543	-0.648000	0.03929	GAT	A|0.998;C|0.002	0.002	strong		0.667	TSPYL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041934.2		
FAM3D	131177	hgsc.bcm.edu	37	3	58639418	58639418	+	Missense_Mutation	SNP	C	C	T	rs13097314	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:58639418C>T	ENST00000358781.2	-	3	414	c.104G>A	c.(103-105)cGt>cAt	p.R35H		NM_138805.2	NP_620160.1	Q96BQ1	FAM3D_HUMAN	family with sequence similarity 3, member D	35					negative regulation of insulin secretion (GO:0046676)	extracellular region (GO:0005576)	cytokine activity (GO:0005125)			large_intestine(1)|lung(2)	3				BRCA - Breast invasive adenocarcinoma(55;0.000225)|Kidney(10;0.000667)|KIRC - Kidney renal clear cell carcinoma(10;0.000802)|OV - Ovarian serous cystadenocarcinoma(275;0.169)		GCGTGGCAGACGGATGGTTTT	0.572													C|||	13	0.00259585	0.0008	0.0014	5008	,	,		22521	0.0		0.0109	False		,,,				2504	0.0				p.R35H		Atlas-SNP	.											FAM3D,colon,carcinoma,-1,1	FAM3D	29	1	0			c.G104A						PASS	.	C	HIS/ARG	9,4397	15.5+/-35.6	0,9,2194	132.0	128.0	129.0		104	3.4	1.0	3	dbSNP_121	129	79,8521	45.8+/-104.6	1,77,4222	yes	missense	FAM3D	NM_138805.2	29	1,86,6416	TT,TC,CC		0.9186,0.2043,0.6766	possibly-damaging	35/225	58639418	88,12918	2203	4300	6503	SO:0001583	missense	131177	exon3			GGCAGACGGATGG	AF494381	CCDS2893.1	3p21.1	2008-07-18			ENSG00000198643	ENSG00000198643			18665	protein-coding gene	gene with protein product		608619				12160727	Standard	NM_138805		Approved	EF7, OIT1	uc003dkq.3	Q96BQ1	OTTHUMG00000159148	ENST00000358781.2:c.104G>A	3.37:g.58639418C>T	ENSP00000351632:p.Arg35His	35.0	0.0	0		39.0	17.0	0.435897	NM_138805	Q547G2	Missense_Mutation	SNP	ENST00000358781.2	37	CCDS2893.1	9	0.004120879120879121	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	16.58	3.163527	0.57476	0.002043	0.009186	ENSG00000198643	ENST00000358781;ENST00000483787;ENST00000498347	T;T;T	0.53857	0.6;1.85;1.44	4.26	3.38	0.38709	.	0.262588	0.30920	N	0.008602	T	0.41190	0.1148	L	0.54323	1.7	0.33744	D	0.619856	D	0.63046	0.992	P	0.49047	0.599	T	0.55611	-0.8114	10	0.13470	T	0.59	-5.3718	9.7791	0.40637	0.2049:0.795:0.0:0.0	rs13097314	35	Q96BQ1	FAM3D_HUMAN	H	35	ENSP00000351632:R35H;ENSP00000417099:R35H;ENSP00000418982:R35H	ENSP00000351632:R35H	R	-	2	0	FAM3D	58614458	0.956000	0.32656	0.971000	0.41717	0.801000	0.45260	1.522000	0.35921	1.156000	0.42514	0.435000	0.28638	CGT	C|0.994;T|0.006	0.006	strong		0.572	FAM3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353494.1	NM_138805	
TRIM22	10346	hgsc.bcm.edu	37	11	5730343	5730343	+	Missense_Mutation	SNP	G	G	A	rs12364019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5730343G>A	ENST00000379965.3	+	8	1239	c.962G>A	c.(961-963)aGa>aAa	p.R321K	TRIM5_ENST00000380027.1_Intron	NM_001199573.1|NM_006074.4	NP_001186502.1|NP_006065.2	Q8IYM9	TRI22_HUMAN	tripartite motif containing 22	321	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.		R -> K (in dbSNP:rs12364019).		defense response to virus (GO:0051607)|immune response (GO:0006955)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|protein trimerization (GO:0070206)|protein ubiquitination (GO:0016567)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			kidney(3)|large_intestine(8)|lung(9)|prostate(1)|stomach(2)	23		Medulloblastoma(188;0.00225)|Breast(177;0.0204)|all_neural(188;0.0212)		Epithelial(150;7.54e-09)|BRCA - Breast invasive adenocarcinoma(625;0.14)		GTGGATCAGAGACAAGTGAAA	0.418													G|||	58	0.0115815	0.0008	0.0144	5008	,	,		20306	0.0		0.0308	False		,,,				2504	0.0164				p.R321K	GBM(104;491 2336 5222)	Atlas-SNP	.											.	TRIM22	66	.	0			c.G962A						PASS	.	G	LYS/ARG,LYS/ARG	16,3874		0,16,1929	148.0	139.0	142.0		950,962	2.8	0.7	11	dbSNP_120	142	338,7968		9,320,3824	yes	missense,missense	TRIM22	NM_001199573.1,NM_006074.4	26,26	9,336,5753	AA,AG,GG		4.0693,0.4113,2.9026	probably-damaging,probably-damaging	317/495,321/499	5730343	354,11842	1945	4153	6098	SO:0001583	missense	10346	exon8			ATCAGAGACAAGT	X82200	CCDS41612.1	11p15	2013-01-09	2011-01-25		ENSG00000132274	ENSG00000132274		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	16379	protein-coding gene	gene with protein product		606559	"""tripartite motif-containing 22"""			11331580, 11096452	Standard	NM_006074		Approved	STAF50, GPSTAF50, RNF94	uc001mbr.3	Q8IYM9	OTTHUMG00000066904	ENST00000379965.3:c.962G>A	11.37:g.5730343G>A	ENSP00000369299:p.Arg321Lys	75.0	0.0	0		98.0	40.0	0.408163	NM_006074	Q05CQ0|Q15521	Missense_Mutation	SNP	ENST00000379965.3	37	CCDS41612.1	32	0.014652014652014652	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	24	0.0316622691292876	G	20.4	3.976912	0.74360	0.004113	0.040693	ENSG00000132274	ENST00000379965;ENST00000545338;ENST00000454828;ENST00000455293	T;T	0.59638	2.71;0.25	3.72	2.77	0.32553	Concanavalin A-like lectin/glucanase (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.34658	0.0905	L	0.43152	1.355	0.23411	N	0.997739	D;D;D	0.89917	0.99;1.0;0.999	D;D;D	0.83275	0.979;0.991;0.996	T	0.38178	-0.9673	9	0.87932	D	0	.	9.9749	0.41777	0.1096:0.0:0.8904:0.0	rs12364019;rs52821696;rs12364019	243;317;321	F8WAP8;Q8IYM9-2;Q8IYM9	.;.;TRI22_HUMAN	K	321;132;289;243	ENSP00000369299:R321K;ENSP00000393250:R289K	ENSP00000369299:R321K	R	+	2	0	TRIM22	5686919	0.118000	0.22208	0.678000	0.29963	0.381000	0.30169	0.558000	0.23469	0.825000	0.34637	0.460000	0.39030	AGA	G|0.976;A|0.024	0.024	strong		0.418	TRIM22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143387.2	NM_006074	
MPZL2	10205	hgsc.bcm.edu	37	11	118134830	118134830	+	Silent	SNP	G	G	A	rs36040758	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:118134830G>A	ENST00000278937.2	-	1	167	c.39C>T	c.(37-39)ctC>ctT	p.L13L	MPZL2_ENST00000438295.2_Silent_p.L13L|MPZL2_ENST00000525647.1_5'UTR	NM_005797.3	NP_005788.1	O60487	MPZL2_HUMAN	myelin protein zero-like 2	13					anatomical structure morphogenesis (GO:0009653)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)|T cell differentiation in thymus (GO:0033077)	cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|kidney(2)|large_intestine(5)|lung(2)|skin(1)	11	all_hematologic(175;0.046)	Medulloblastoma(222;0.0425)|Breast(348;0.181)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;3.04e-05)		GTATGCCAAGGAGAAGAAGCA	0.547													G|||	8	0.00159744	0.0008	0.0014	5008	,	,		17565	0.0		0.005	False		,,,				2504	0.001				p.L13L		Atlas-SNP	.											.	MPZL2	20	.	0			c.C39T						PASS	.	G	,	9,4391	15.5+/-35.6	0,9,2191	81.0	75.0	77.0		39,39	-1.1	0.1	11	dbSNP_126	77	74,8518	44.0+/-102.2	0,74,4222	no	coding-synonymous,coding-synonymous	MPZL2	NM_005797.3,NM_144765.2	,	0,83,6413	AA,AG,GG		0.8613,0.2045,0.6389	,	13/216,13/216	118134830	83,12909	2200	4296	6496	SO:0001819	synonymous_variant	10205	exon1			GCCAAGGAGAAGA	AF275945	CCDS8393.1	11q24	2013-01-11	2007-08-01	2007-08-01		ENSG00000149573		"""Immunoglobulin superfamily / V-set domain containing"""	3496	protein-coding gene	gene with protein product		604873	"""epithelial V-like antigen 1"""	EVA1		9585423	Standard	NM_005797		Approved	EVA	uc001psn.3	O60487		ENST00000278937.2:c.39C>T	11.37:g.118134830G>A		38.0	0.0	0		72.0	33.0	0.458333	NM_005797	A8K2R1	Silent	SNP	ENST00000278937.2	37	CCDS8393.1																																																																																			G|0.993;A|0.007	0.007	strong		0.547	MPZL2-001	PUTATIVE	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392113.1	NM_005797	
ALS2CL	259173	hgsc.bcm.edu	37	3	46717175	46717175	+	Splice_Site	SNP	C	C	T	rs142971127	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46717175C>T	ENST00000318962.4	-	20	2271	c.2188G>A	c.(2188-2190)Ggt>Agt	p.G730S	ALS2CL_ENST00000383742.3_Splice_Site_p.G77S|ALS2CL_ENST00000415953.1_Splice_Site_p.G730S	NM_147129.3	NP_667340.2	Q60I27	AL2CL_HUMAN	ALS2 C-terminal like	730					endosome organization (GO:0007032)|protein localization (GO:0008104)	cytoplasmic membrane-bounded vesicle (GO:0016023)	GTPase activator activity (GO:0005096)|identical protein binding (GO:0042802)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(2)|central_nervous_system(3)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(3)|stomach(2)	29				BRCA - Breast invasive adenocarcinoma(193;0.000726)|KIRC - Kidney renal clear cell carcinoma(197;0.0171)|Kidney(197;0.0202)		CGCAGCAGACCCCTGTGAGTC	0.577													C|||	17	0.00339457	0.0008	0.0086	5008	,	,		20439	0.0		0.0089	False		,,,				2504	0.001				p.G730S		Atlas-SNP	.											.	ALS2CL	78	.	0			c.G2188A						PASS	.	C	SER/GLY,SER/GLY,SER/GLY	9,4397	15.5+/-35.6	0,9,2194	81.0	76.0	78.0		2188,2188,229	4.7	1.0	3	dbSNP_134	78	89,8511	49.4+/-109.1	1,87,4212	yes	missense-near-splice,missense-near-splice,missense-near-splice	ALS2CL	NM_001190707.1,NM_147129.3,NM_182775.2	56,56,56	1,96,6406	TT,TC,CC		1.0349,0.2043,0.7535	probably-damaging,probably-damaging,probably-damaging	730/954,730/954,77/301	46717175	98,12908	2203	4300	6503	SO:0001630	splice_region_variant	259173	exon20			GCAGACCCCTGTG	AK074118	CCDS2743.1, CCDS43080.1	3p21.31	2008-01-30			ENSG00000178038	ENSG00000178038			20605	protein-coding gene	gene with protein product		612402				15388334, 8889548, 17239822	Standard	NM_147129		Approved	FLJ36525, RN49018, DKFZp686I0110	uc003cqb.2	Q60I27	OTTHUMG00000128673	ENST00000318962.4:c.2187-1G>A	3.37:g.46717175C>T		33.0	0.0	0		44.0	15.0	0.340909	NM_001190707	Q32MA1|Q6AI56|Q6ZNC5|Q6ZNC7|Q6ZTL4|Q86YD2|Q8N9U1|Q8NAL7	Missense_Mutation	SNP	ENST00000318962.4	37	CCDS2743.1	12	0.005494505494505495	0	0.0	4	0.011049723756906077	0	0.0	8	0.010554089709762533	C	12.27	1.886260	0.33348	0.002043	0.010349	ENSG00000178038	ENST00000318962;ENST00000415953;ENST00000383742	T;T;T	0.30182	1.54;1.54;1.54	4.66	4.66	0.58398	.	0.195229	0.35970	N	0.002863	T	0.31638	0.0803	L	0.60455	1.87	0.45541	D	0.998496	D	0.62365	0.991	P	0.55785	0.784	T	0.06643	-1.0815	10	0.10377	T	0.69	.	13.236	0.59969	0.0:1.0:0.0:0.0	.	730	Q60I27	AL2CL_HUMAN	S	730;730;77	ENSP00000313670:G730S;ENSP00000413223:G730S;ENSP00000373248:G77S	ENSP00000313670:G730S	G	-	1	0	ALS2CL	46692179	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	1.715000	0.37971	2.592000	0.87571	0.561000	0.74099	GGT	C|0.993;T|0.007	0.007	strong		0.577	ALS2CL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250567.3	NM_147129	Missense_Mutation
TNFSF13B	10673	hgsc.bcm.edu	37	13	108955609	108955609	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr13:108955609A>G	ENST00000375887.4	+	4	668	c.490A>G	c.(490-492)Aca>Gca	p.T164A	TNFSF13B_ENST00000479435.1_3'UTR|TNFSF13B_ENST00000542136.1_Intron|TNFSF13B_ENST00000430559.1_Missense_Mutation_p.T145A|RNA5SP39_ENST00000411245.1_RNA	NM_006573.4	NP_006564.1	Q9Y275	TN13B_HUMAN	tumor necrosis factor (ligand) superfamily, member 13b	164					B cell costimulation (GO:0031296)|B cell homeostasis (GO:0001782)|cell proliferation (GO:0008283)|immune response (GO:0006955)|immunoglobulin secretion (GO:0048305)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell proliferation (GO:0008284)|positive regulation of germinal center formation (GO:0002636)|positive regulation of T cell proliferation (GO:0042102)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			large_intestine(1)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	10	all_lung(23;0.000396)|all_neural(89;0.00256)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00902)|Lung SC(71;0.104)		all cancers(43;0.184)|BRCA - Breast invasive adenocarcinoma(86;0.19)		Belimumab(DB08879)	AGGATCTTACACATTTGTTCC	0.343																																					p.T164A		Atlas-SNP	.											.	TNFSF13B	25	.	0			c.A490G						PASS	.						52.0	54.0	53.0					13																	108955609		2199	4298	6497	SO:0001583	missense	10673	exon4			TCTTACACATTTG	AF136293	CCDS9509.1, CCDS45067.1	13q32-q34	2008-05-14			ENSG00000102524	ENSG00000102524		"""Tumor necrosis factor (ligand) superfamily"", ""CD molecules"""	11929	protein-coding gene	gene with protein product		603969		TNFSF20		10331498, 10359578	Standard	NM_006573		Approved	BAFF, THANK, BLYS, TALL-1, TALL1, CD257	uc001vqr.3	Q9Y275	OTTHUMG00000017329	ENST00000375887.4:c.490A>G	13.37:g.108955609A>G	ENSP00000365048:p.Thr164Ala	74.0	0.0	0		46.0	11.0	0.23913	NM_006573	E0ADT7|Q6FHD6|Q7Z5J2	Missense_Mutation	SNP	ENST00000375887.4	37	CCDS9509.1	.	.	.	.	.	.	.	.	.	.	A	16.50	3.141866	0.57044	.	.	ENSG00000102524	ENST00000430559;ENST00000375887	T;T	0.31769	1.48;1.48	5.95	5.95	0.96441	Tumour necrosis factor (2);Tumour necrosis factor-like (2);	0.101283	0.64402	D	0.000003	T	0.27629	0.0679	L	0.39898	1.24	0.80722	D	1	B;B	0.34399	0.452;0.299	B;B	0.36719	0.231;0.164	T	0.09079	-1.0691	10	0.62326	D	0.03	-22.6206	9.8726	0.41185	0.9173:0.0:0.0827:0.0	.	145;164	Q9Y275-2;Q9Y275	.;TN13B_HUMAN	A	145;164	ENSP00000389540:T145A;ENSP00000365048:T164A	ENSP00000365048:T164A	T	+	1	0	TNFSF13B	107753610	1.000000	0.71417	0.987000	0.45799	0.977000	0.68977	7.198000	0.77823	2.281000	0.76405	0.528000	0.53228	ACA	.	.	none		0.343	TNFSF13B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045739.3		
PKHD1	5314	hgsc.bcm.edu	37	6	51771044	51771044	+	Silent	SNP	G	G	A	rs140065359	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:51771044G>A	ENST00000371117.3	-	41	7052	c.6777C>T	c.(6775-6777)ttC>ttT	p.F2259F	PKHD1_ENST00000340994.4_Silent_p.F2259F	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	2259					cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)	p.F2259L(2)		NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AAATATTGTAGAATACATTAC	0.438													G|||	11	0.00219649	0.0	0.0014	5008	,	,		17456	0.0		0.0099	False		,,,				2504	0.0				p.F2259F		Atlas-SNP	.											PKHD1_ENST00000340994,NS,carcinoma,0,2	PKHD1	927	2	2	Substitution - Missense(2)	lung(2)	c.C6777T						PASS	.	G	,	3,4403	6.2+/-15.9	0,3,2200	80.0	79.0	79.0		6777,6777	3.7	1.0	6	dbSNP_134	79	50,8550	32.8+/-85.7	0,50,4250	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,53,6450	AA,AG,GG		0.5814,0.0681,0.4075	,	2259/4075,2259/3397	51771044	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon41			ATTGTAGAATACA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.6777C>T	6.37:g.51771044G>A		36.0	0.0	0		20.0	7.0	0.35	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			G|0.996;A|0.004	0.004	strong		0.438	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
GNAS	2778	hgsc.bcm.edu	37	20	57478807	57478807	+	Silent	SNP	C	C	T	rs7121	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:57478807C>T	ENST00000371085.3	+	5	817	c.393C>T	c.(391-393)atC>atT	p.I131I	GNAS_ENST00000371100.4_Silent_p.I774I|GNAS_ENST00000313949.7_3'UTR|GNAS_ENST00000371102.4_Silent_p.I760I|GNAS_ENST00000371075.3_3'UTR|GNAS_ENST00000354359.7_Silent_p.I132I|GNAS_ENST00000371095.3_Silent_p.I117I|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000306090.10_Silent_p.I117I|GNAS_ENST00000265620.7_Silent_p.I116I	NM_000516.4	NP_000507.1	P63092	GNAS2_HUMAN	GNAS complex locus	131					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating adrenergic receptor signaling pathway (GO:0071880)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|blood coagulation (GO:0007596)|bone development (GO:0060348)|cAMP biosynthetic process (GO:0006171)|cellular response to catecholamine stimulus (GO:0071870)|cellular response to glucagon stimulus (GO:0071377)|cellular response to prostaglandin E stimulus (GO:0071380)|cognition (GO:0050890)|developmental growth (GO:0048589)|energy reserve metabolic process (GO:0006112)|hair follicle placode formation (GO:0060789)|intracellular transport (GO:0046907)|platelet aggregation (GO:0070527)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of insulin secretion (GO:0050796)|sensory perception of smell (GO:0007608)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|intrinsic component of membrane (GO:0031224)|membrane (GO:0016020)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)	adenylate cyclase activity (GO:0004016)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			adrenal_gland(12)|autonomic_ganglia(1)|biliary_tract(5)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(37)|liver(9)|lung(9)|ovary(16)|pancreas(56)|parathyroid(5)|pituitary(228)|prostate(2)|small_intestine(1)|stomach(1)|testis(2)|thyroid(35)|upper_aerodigestive_tract(3)|urinary_tract(1)	441	all_lung(29;0.0104)		BRCA - Breast invasive adenocarcinoma(13;2.19e-08)|Colorectal(105;0.109)			TGGACTACATCCTGAGTGTGA	0.557			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)			T|||	3227	0.644369	0.8139	0.6124	5008	,	,		18620	0.6716		0.4742	False		,,,				2504	0.5849				p.I774I	Colon(117;935 1597 6045 8307 46442)	Atlas-SNP	.		Dom	yes		20	20q13.2	2778	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	yes	E	.	GNAS	867	.	0			c.C2322T	GRCh37	CM023931	GNAS	M	rs7121	PASS	.	T	,,,,,,	3298,1108	398.3+/-330.8	1234,830,139	247.0	224.0	232.0		393,396,348,,,2322,351	-9.2	0.2	20	dbSNP_52	232	4238,4362	582.0+/-391.3	1060,2118,1122	no	coding-synonymous,coding-synonymous,coding-synonymous,utr-3,utr-3,coding-synonymous,coding-synonymous	GNAS	NM_000516.4,NM_001077488.2,NM_001077489.2,NM_001077490.1,NM_016592.2,NM_080425.2,NM_080426.2	,,,,,,	2294,2948,1261	TT,TC,CC		49.2791,25.1475,42.0575	,,,,,,	131/395,132/396,116/380,,,774/1038,117/381	57478807	7536,5470	2203	4300	6503	SO:0001819	synonymous_variant	2778	exon5			CTACATCCTGAGT	M21142	CCDS13471.1, CCDS13472.1, CCDS42892.1, CCDS46622.1, CCDS46623.1, CCDS46624.1	20q13.2-q13.3	2010-03-01	2001-12-19	2001-12-20	ENSG00000087460	ENSG00000087460			4392	protein-coding gene	gene with protein product	"""secretogranin VI"""	139320	"""guanine nucleotide binding protein (G protein), alpha stimulating activity polypeptide 1"""	GNAS1			Standard	NM_000516		Approved	NESP55, NESP, GNASXL, GPSA, SCG6	uc002xzw.3	O95467	OTTHUMG00000033069	ENST00000371085.3:c.393C>T	20.37:g.57478807C>T		194.0	0.0	0		209.0	94.0	0.449761	NM_080425	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Silent	SNP	ENST00000371085.3	37	CCDS13472.1	1341	0.614010989010989	407	0.8272357723577236	227	0.6270718232044199	366	0.6398601398601399	341	0.449868073878628	T	10.08	1.252619	0.22880	0.748525	0.492791	ENSG00000087460	ENST00000450130	.	.	.	5.81	-9.18	0.00688	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.09310	P	0.999999101873	.	.	.	.	.	.	T	0.04400	-1.0954	3	.	.	.	.	21.0308	0.99944	0.0914:0.759:0.0:0.1496	rs7121;rs1053389;rs3171206;rs3730167;rs17829840;rs61041002;rs7121	.	.	.	S	146	.	.	P	+	1	0	GNAS	56912202	0.382000	0.25148	0.173000	0.22940	0.924000	0.55760	-0.313000	0.08103	-2.651000	0.00424	-1.760000	0.00671	CCT	C|0.395;T|0.605	0.605	strong		0.557	GNAS-015	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000080431.2	NM_000516	
ZNF718	255403	hgsc.bcm.edu	37	4	155411	155411	+	lincRNA	SNP	A	A	T	rs142742436	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:155411A>T	ENST00000510175.1	+	0	846							Q3SXZ3	ZN718_HUMAN	zinc finger protein 718						regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)						all_cancers(4;0.0738)|all_epithelial(65;0.139)		Lung(54;0.0681)|Epithelial(2;0.0838)|all cancers(2;0.135)|LUSC - Lung squamous cell carcinoma(95;0.18)		AACCCTTCTCATGCGAAGAAT	0.383													A|||	20	0.00399361	0.0	0.0014	5008	,	,		20733	0.0		0.0189	False		,,,				2504	0.0				p.S312S		Atlas-SNP	.											.	.	.	.	0			c.A936T						PASS	.	A		8,4220		0,8,2106	30.0	34.0	33.0		747	-0.9	0.0	4	dbSNP_134	33	95,8429		3,89,4170	no	coding-synonymous	ZNF718	NM_001039127.3		3,97,6276	TT,TA,AA		1.1145,0.1892,0.8077		249/416	155411	103,12649	2114	4262	6376			255403	exon4			CTTCTCATGCGAA	AK096662	CCDS75078.1, CCDS75079.1	4p16.3	2011-05-24			ENSG00000250312	ENSG00000250312		"""Zinc fingers, C2H2-type"""	26889	protein-coding gene	gene with protein product							Standard	XM_005278364		Approved	FLJ90036	uc003fzt.4	Q3SXZ3	OTTHUMG00000159873		4.37:g.155411A>T		28.0	0.0	0		21.0	9.0	0.428571	NM_001039127	Q3SXZ4|Q3SXZ5	Silent	SNP	ENST00000510175.1	37																																																																																				A|0.992;T|0.008	0.008	strong		0.383	ZNF718-002	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000357865.3	NM_001039127	
PCDHA5	56143	hgsc.bcm.edu	37	5	140203463	140203463	+	Silent	SNP	C	C	A	rs142924665	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140203463C>A	ENST00000529859.1	+	1	2103	c.2103C>A	c.(2101-2103)atC>atA	p.I701I	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Silent_p.I701I|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000378126.3_Silent_p.I701I|PCDHA2_ENST00000526136.1_Intron	NM_018908.2	NP_061731.1	Q9Y5H7	PCDA5_HUMAN	protocadherin alpha 5	701					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(1)|autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(6)|large_intestine(8)|liver(1)|lung(22)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(3)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACCTGATCATCGCCATCTGTG	0.692													.|||	2	0.000399361	0.0	0.0	5008	,	,		16849	0.0		0.002	False		,,,				2504	0.0				p.I701I		Atlas-SNP	.											.	PCDHA5	361	.	0			c.C2103A						PASS	.	C	,,,,,,	4,4402	8.1+/-20.4	0,4,2199	63.0	62.0	62.0		,,,,2103,,2103	2.2	1.0	5	dbSNP_134	62	35,8561	23.4+/-69.3	0,35,4263	no	intron,intron,intron,intron,coding-synonymous,intron,coding-synonymous	PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018905.2,NM_018906.2,NM_018907.2,NM_018908.2,NM_031411.1,NM_031501.1	,,,,,,	0,39,6462	AA,AC,CC		0.4072,0.0908,0.3	,,,,,,	,,,,701/937,,701/817	140203463	39,12963	2203	4298	6501	SO:0001819	synonymous_variant	56143	exon1			GATCATCGCCATC	AF152483	CCDS54917.1	5q31	2010-11-26				ENSG00000204965		"""Cadherins / Protocadherins : Clustered"""	8671	other	complex locus constituent	"""ortholog of mouse CNR6"", ""KIAA0345-like 9"""	606311		CNRS6		10380929, 10662547	Standard	NM_018908		Approved	CNR6, CRNR6, CNRN6, PCDH-ALPHA5		Q9Y5H7		ENST00000529859.1:c.2103C>A	5.37:g.140203463C>A		154.0	0.0	0		159.0	76.0	0.477987	NM_018908	O75284|Q8N4R3	Silent	SNP	ENST00000529859.1	37	CCDS54917.1																																																																																			C|0.997;A|0.003	0.003	strong		0.692	PCDHA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372883.2	NM_018908	
CACNA1H	8912	hgsc.bcm.edu	37	16	1256127	1256127	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:1256127C>T	ENST00000348261.5	+	12	2875	c.2627C>T	c.(2626-2628)gCg>gTg	p.A876V	CACNA1H_ENST00000358590.4_Missense_Mutation_p.A876V|CACNA1H_ENST00000565831.1_Missense_Mutation_p.A876V|RP11-616M22.3_ENST00000564700.1_RNA	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	876					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)	GTGGGGCAGGCGGACGGTGGC	0.701																																					p.A876V		Atlas-SNP	.											.	CACNA1H	317	.	0			c.C2627T						PASS	.																																			SO:0001583	missense	8912	exon12			GGCAGGCGGACGG	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.2627C>T	16.37:g.1256127C>T	ENSP00000334198:p.Ala876Val	54.0	0.0	0		49.0	12.0	0.244898	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Missense_Mutation	SNP	ENST00000348261.5	37	CCDS45375.1	.	.	.	.	.	.	.	.	.	.	C	18.36	3.607711	0.66558	.	.	ENSG00000196557	ENST00000348261;ENST00000358590	D;D	0.98419	-4.92;-4.92	3.96	3.96	0.45880	Ion transport (1);	0.416444	0.21210	N	0.078324	D	0.97782	0.9272	L	0.39467	1.215	0.37503	D	0.91685	D;D	0.69078	0.997;0.989	P;P	0.61658	0.892;0.805	D	0.99229	1.0881	10	0.46703	T	0.11	.	15.1886	0.73025	0.0:1.0:0.0:0.0	.	876;876	O95180-2;O95180	.;CAC1H_HUMAN	V	876	ENSP00000334198:A876V;ENSP00000351401:A876V	ENSP00000334198:A876V	A	+	2	0	CACNA1H	1196128	1.000000	0.71417	0.943000	0.38184	0.404000	0.30871	4.442000	0.59988	2.050000	0.60909	0.561000	0.74099	GCG	.	.	none		0.701	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
TNRC18	84629	hgsc.bcm.edu	37	7	5396866	5396866	+	Missense_Mutation	SNP	C	C	G	rs200950320		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:5396866C>G	ENST00000430969.1	-	16	5223	c.4875G>C	c.(4873-4875)caG>caC	p.Q1625H	TNRC18_ENST00000399537.4_Missense_Mutation_p.Q1625H	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	1625							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		TGCTTGCCAACTGCTCCTGGT	0.498																																					p.Q1625H		Atlas-SNP	.											.	TNRC18	311	.	0			c.G4875C						PASS	.	C	HIS/GLN	0,4034		0,0,2017	48.0	48.0	48.0		4875	3.4	0.9	7		48	1,8387		0,1,4193	yes	missense	TNRC18	NM_001080495.2	24	0,1,6210	GG,GC,CC		0.0119,0.0,0.0081	probably-damaging	1625/2969	5396866	1,12421	2017	4194	6211	SO:0001583	missense	84629	exon16			TGCCAACTGCTCC	U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.4875G>C	7.37:g.5396866C>G	ENSP00000395538:p.Gln1625His	65.0	0.0	0		124.0	47.0	0.379032	NM_001080495	A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	c	11.99	1.803262	0.31869	0.0	1.19E-4	ENSG00000182095	ENST00000399537;ENST00000430969;ENST00000399544;ENST00000440081	T;T;T	0.55052	2.34;2.4;0.54	5.25	3.37	0.38596	.	0.000000	0.37483	N	0.002071	T	0.61123	0.2322	L	0.47016	1.485	0.39858	D	0.973332	D;D	0.71674	0.997;0.998	D;D	0.79784	0.993;0.956	T	0.61441	-0.7062	10	0.66056	D	0.02	.	7.4435	0.27198	0.0:0.7123:0.0:0.2877	.	680;1625	A8MSW5;O15417	.;TNC18_HUMAN	H	1625;1625;680;115	ENSP00000382452:Q1625H;ENSP00000395538:Q1625H;ENSP00000395990:Q115H	ENSP00000382452:Q1625H	Q	-	3	2	TNRC18	5363392	0.999000	0.42202	0.878000	0.34440	0.983000	0.72400	1.017000	0.29989	0.550000	0.28991	0.561000	0.74099	CAG	.	.	weak		0.498	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
SSC5D	284297	hgsc.bcm.edu	37	19	56029621	56029621	+	Silent	SNP	A	A	C	rs202012508		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:56029621A>C	ENST00000389623.6	+	14	4001	c.3978A>C	c.(3976-3978)acA>acC	p.T1326T		NM_001144950.1	NP_001138422.1	A1L4H1	SRCRL_HUMAN	scavenger receptor cysteine rich family, 5 domains	1326	Pro-rich.|Thr-rich.				defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterial lipoprotein (GO:0042494)|innate immune response (GO:0045087)|multicellular organismal development (GO:0007275)|negative regulation of interleukin-8 secretion (GO:2000483)|receptor-mediated endocytosis (GO:0006898)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|intracellular (GO:0005622)|membrane (GO:0016020)	extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|laminin binding (GO:0043236)|scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|skin(2)	4						ctcaccccACAACTCCTGACC	0.597																																					p.T1326T		Atlas-SNP	.											.	SSC5D	65	.	0			c.A3978C						PASS	.						332.0	320.0	323.0					19																	56029621		692	1591	2283	SO:0001819	synonymous_variant	284297	exon14			CCCCACAACTCCT		CCDS46196.1, CCDS59424.1	19q13.42	2014-07-09	2014-07-09		ENSG00000179954	ENSG00000179954			26641	protein-coding gene	gene with protein product	"""soluble scavenger with 5 domains"""		"""scavenger receptor cysteine rich domain containing (5 domains)"""			19535143	Standard	NM_001144950		Approved	FLJ35258	uc002qlg.4	A1L4H1		ENST00000389623.6:c.3978A>C	19.37:g.56029621A>C		47.0	0.0	0		64.0	6.0	0.09375	NM_001144950	B5MDQ5|C7S7T9|C7S7U0|K7EP70	Silent	SNP	ENST00000389623.6	37	CCDS46196.1																																																																																			.	.	weak		0.597	SSC5D-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000453345.2	XM_001718392	
CCDC57	284001	hgsc.bcm.edu	37	17	80146154	80146154	+	Silent	SNP	G	G	C	rs201504809	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80146154G>C	ENST00000389641.4	-	7	1029	c.993C>G	c.(991-993)ctC>ctG	p.L331L	CCDC57_ENST00000392347.1_Silent_p.L331L|CCDC57_ENST00000392343.3_Silent_p.L331L			Q2TAC2	CCD57_HUMAN	coiled-coil domain containing 57	331										endometrium(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	16	Breast(20;0.00285)|all_neural(118;0.0878)|all_lung(278;0.0949)|Lung NSC(278;0.128)|Ovarian(332;0.227)		BRCA - Breast invasive adenocarcinoma(99;0.0232)|OV - Ovarian serous cystadenocarcinoma(97;0.0253)			CTGCCCTGCGGAGCTGCGCCT	0.667													G|||	5	0.000998403	0.0	0.0	5008	,	,		16916	0.0		0.005	False		,,,				2504	0.0				p.L331L		Atlas-SNP	.											.	CCDC57	102	.	0			c.C993G						PASS	.	G		0,4394		0,0,2197	22.0	25.0	24.0		993	-1.5	0.9	17		24	28,8552		0,28,4262	no	coding-synonymous	CCDC57	NM_198082.2		0,28,6459	CC,CG,GG		0.3263,0.0,0.2158		331/916	80146154	28,12946	2197	4290	6487	SO:0001819	synonymous_variant	284001	exon7			CCTGCGGAGCTGC	BC040264		17q25.3	2006-03-08			ENSG00000176155	ENSG00000176155			27564	protein-coding gene	gene with protein product						12477932	Standard	XM_006722279		Approved	FLJ00130, FLJ23754	uc002kdx.1	Q2TAC2	OTTHUMG00000140396	ENST00000389641.4:c.993C>G	17.37:g.80146154G>C		50.0	0.0	0		55.0	23.0	0.418182	NM_198082	A6NP51|A8MQC7|Q8IWG2|Q8TER3	Silent	SNP	ENST00000389641.4	37																																																																																				G|0.994;C|0.006	0.006	weak		0.667	CCDC57-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000277182.3	NM_198082	
FAM172A	83989	hgsc.bcm.edu	37	5	93159971	93159971	+	Silent	SNP	T	T	C	rs141777861	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:93159971T>C	ENST00000395965.3	-	8	931	c.789A>G	c.(787-789)gaA>gaG	p.E263E	FAM172A_ENST00000509163.1_Silent_p.E217E|FAM172A_ENST00000505869.1_Silent_p.E153E|FAM172A_ENST00000509739.1_Silent_p.E116E	NM_032042.5	NP_114431.2	Q8WUF8	F172A_HUMAN	family with sequence similarity 172, member A	263						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)				endometrium(2)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9						GAGAACCATTTTCCTATAAGG	0.343													T|||	42	0.00838658	0.0	0.0086	5008	,	,		11615	0.0		0.0199	False		,,,				2504	0.0164				p.E263E		Atlas-SNP	.											.	FAM172A	38	.	0			c.A789G						PASS	.	T	,,	28,4378	32.6+/-62.9	0,28,2175	102.0	100.0	101.0		651,459,789	2.3	1.0	5	dbSNP_134	101	195,8405	84.2+/-146.7	3,189,4108	no	coding-synonymous,coding-synonymous,coding-synonymous	FAM172A	NM_001163417.1,NM_001163418.1,NM_032042.5	,,	3,217,6283	CC,CT,TT		2.2674,0.6355,1.7146	,,	217/371,153/307,263/417	93159971	223,12783	2203	4300	6503	SO:0001819	synonymous_variant	83989	exon8			ACCATTTTCCTAT		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.789A>G	5.37:g.93159971T>C		162.0	0.0	0		128.0	66.0	0.515625	NM_032042	B2R7C6|B4DJ14|B4DLG5|Q9H0U8	Silent	SNP	ENST00000395965.3	37	CCDS4069.1																																																																																			T|0.986;C|0.015	0.015	strong		0.343	FAM172A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254100.3	NM_032042	
ANKS4B	257629	hgsc.bcm.edu	37	16	21261302	21261302	+	Missense_Mutation	SNP	G	G	A	rs539999603		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:21261302G>A	ENST00000311620.5	+	2	488	c.415G>A	c.(415-417)Gct>Act	p.A139T		NM_145865.2	NP_665872.2	Q8N8V4	ANS4B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 4B	139					response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)				NS(1)|central_nervous_system(2)|endometrium(2)|kidney(2)|lung(11)|ovary(2)	20				GBM - Glioblastoma multiforme(48;0.0565)		GAAGGAGCAGGCTCAGAAGAA	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		21059	0.0		0.0	False		,,,				2504	0.001				p.A139T		Atlas-SNP	.											.	ANKS4B	43	.	0			c.G415A						PASS	.						49.0	50.0	50.0					16																	21261302		2088	4223	6311	SO:0001583	missense	257629	exon2			GAGCAGGCTCAGA	AK096138	CCDS42130.1	16p12.2	2013-01-10				ENSG00000175311		"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	26795	protein-coding gene	gene with protein product		609901					Standard	NM_145865		Approved	FLJ38819, HARP	uc010bwp.1	Q8N8V4		ENST00000311620.5:c.415G>A	16.37:g.21261302G>A	ENSP00000308772:p.Ala139Thr	80.0	0.0	0		91.0	49.0	0.538462	NM_145865		Missense_Mutation	SNP	ENST00000311620.5	37	CCDS42130.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.609379	0.87258	.	.	ENSG00000175311	ENST00000311620	T	0.51071	0.72	5.77	4.81	0.61882	Ankyrin repeat-containing domain (2);	0.000000	0.85682	D	0.000000	T	0.69169	0.3081	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.73946	-0.3822	10	0.66056	D	0.02	-10.602	15.2442	0.73493	0.0:0.0:0.8584:0.1416	.	139	Q8N8V4	ANS4B_HUMAN	T	139	ENSP00000308772:A139T	ENSP00000308772:A139T	A	+	1	0	ANKS4B	21168803	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.776000	0.99001	1.422000	0.47177	-0.282000	0.10007	GCT	.	.	none		0.542	ANKS4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000436535.1	NM_145865	
C14orf159	80017	hgsc.bcm.edu	37	14	91681784	91681784	+	Missense_Mutation	SNP	G	G	A	rs115874122	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:91681784G>A	ENST00000523771.1	+	13	2188	c.1585G>A	c.(1585-1587)Gca>Aca	p.A529T	C14orf159_ENST00000521077.2_Missense_Mutation_p.A494T|C14orf159_ENST00000428926.2_Missense_Mutation_p.A529T|C14orf159_ENST00000522322.1_Missense_Mutation_p.A529T|C14orf159_ENST00000520328.1_Missense_Mutation_p.A477T|C14orf159_ENST00000412671.2_Missense_Mutation_p.A534T|C14orf159_ENST00000518868.1_Missense_Mutation_p.A534T|C14orf159_ENST00000256324.10_Missense_Mutation_p.A534T|C14orf159_ENST00000525393.2_Missense_Mutation_p.A405T|C14orf159_ENST00000523816.1_Missense_Mutation_p.A529T			Q7Z3D6	CN159_HUMAN	chromosome 14 open reading frame 159	529						mitochondrion (GO:0005739)				NS(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(5)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	21		all_cancers(154;0.0191)|all_epithelial(191;0.241)		Epithelial(152;0.141)|OV - Ovarian serous cystadenocarcinoma(161;0.207)		CCTGGCCTGCGCACTCTACAT	0.542													G|||	20	0.00399361	0.0	0.0245	5008	,	,		17334	0.001		0.001	False		,,,				2504	0.001				p.A534T		Atlas-SNP	.											.	C14orf159	57	.	0			c.G1600A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	2,4404	4.2+/-10.8	0,2,2201	132.0	118.0	123.0		1585,1585,1600,1429,1585	1.3	0.0	14	dbSNP_132	123	11,8589	8.4+/-32.0	0,11,4289	yes	missense,missense,missense,missense,missense	C14orf159	NM_001102366.1,NM_001102367.1,NM_001102368.1,NM_001102369.1,NM_024952.6	58,58,58,58,58	0,13,6490	AA,AG,GG		0.1279,0.0454,0.1	benign,benign,benign,benign,benign	529/617,529/617,534/622,477/565,529/617	91681784	13,12993	2203	4300	6503	SO:0001583	missense	80017	exon13			GCCTGCGCACTCT	AK097294	CCDS32141.1, CCDS41979.1, CCDS45150.1, CCDS66693.1, CCDS73677.1	14q32.11	2012-09-26			ENSG00000133943	ENSG00000133943			20498	protein-coding gene	gene with protein product							Standard	NM_001102367		Approved	FLJ39975	uc001xze.2	Q7Z3D6	OTTHUMG00000164980	ENST00000523771.1:c.1585G>A	14.37:g.91681784G>A	ENSP00000429655:p.Ala529Thr	61.0	0.0	0		56.0	27.0	0.482143	NM_001102368	B3KUI7|Q86SW3|Q86SX8|Q86SX9|Q86T08|Q86TV5|Q96GW5|Q9H7G0|Q9H8Y9|Q9H9W6	Missense_Mutation	SNP	ENST00000523771.1	37	CCDS32141.1	10	0.004578754578754579	0	0.0	9	0.024861878453038673	1	0.0017482517482517483	0	0.0	G	9.610	1.130943	0.21041	4.54E-4	0.001279	ENSG00000133943	ENST00000520328;ENST00000256324;ENST00000521077;ENST00000518868;ENST00000523816;ENST00000525393;ENST00000428926;ENST00000522322;ENST00000523771;ENST00000412671	T;T;T;T;T;T;T;T;T;T	0.20598	2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06;2.06	5.34	1.28	0.21552	.	0.240499	0.41097	N	0.000955	T	0.07728	0.0194	M	0.62088	1.915	0.09310	N	1	B;P;B;B;B	0.43662	0.202;0.814;0.168;0.41;0.168	B;B;B;B;B	0.34931	0.034;0.192;0.02;0.033;0.02	T	0.14615	-1.0466	10	0.54805	T	0.06	.	4.7277	0.12948	0.2495:0.0:0.5999:0.1506	.	529;405;477;534;494	Q7Z3D6;Q8NB88;Q7Z3D6-5;Q7Z3D6-2;Q7Z3D6-3	CN159_HUMAN;.;.;.;.	T	477;534;494;534;529;405;529;529;529;534	ENSP00000429453:A477T;ENSP00000256324:A534T;ENSP00000430137:A494T;ENSP00000428263:A534T;ENSP00000428974:A529T;ENSP00000435459:A405T;ENSP00000404343:A529T;ENSP00000427953:A529T;ENSP00000429655:A529T;ENSP00000404196:A534T	ENSP00000256324:A534T	A	+	1	0	C14orf159	90751537	0.408000	0.25360	0.014000	0.15608	0.002000	0.02628	2.292000	0.43549	0.265000	0.21872	-0.136000	0.14681	GCA	G|0.998;A|0.002	0.002	strong		0.542	C14orf159-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381273.1	NM_024952	
ALPP	250	hgsc.bcm.edu	37	2	233245982	233245982	+	Missense_Mutation	SNP	G	G	A	rs143205011	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:233245982G>A	ENST00000392027.2	+	10	1483	c.1214G>A	c.(1213-1215)cGg>cAg	p.R405Q	AC068134.8_ENST00000441266.1_RNA|AC068134.8_ENST00000439072.1_RNA	NM_001632.3	NP_001623.3	P05187	PPB1_HUMAN	alkaline phosphatase, placental	405					dephosphorylation (GO:0016311)	anchored component of membrane (GO:0031225)|cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alkaline phosphatase activity (GO:0004035)|magnesium ion binding (GO:0000287)|zinc ion binding (GO:0008270)			NS(1)|biliary_tract(1)|endometrium(1)|kidney(4)|large_intestine(2)|liver(1)|lung(10)|ovary(2)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;4.45e-22)|Kidney(3;4.42e-11)|KIRC - Kidney renal clear cell carcinoma(3;1.9e-09)|BRCA - Breast invasive adenocarcinoma(100;0.000767)|Lung(119;0.00566)|LUSC - Lung squamous cell carcinoma(224;0.00746)|STAD - Stomach adenocarcinoma(3;0.0181)|GBM - Glioblastoma multiforme(43;0.196)		GGCAAGGCCCGGGACAGGAAG	0.637													G|||	5	0.000998403	0.0	0.0029	5008	,	,		19588	0.0		0.001	False		,,,				2504	0.002				p.R405Q		Atlas-SNP	.											.	ALPP	53	.	0			c.G1214A						PASS	.	A	GLN/ARG	3,4395		0,3,2196	24.0	30.0	28.0		1214	-4.7	0.0	2	dbSNP_134	28	41,8505		0,41,4232	no	missense	ALPP	NM_001632.3	43	0,44,6428	AA,AG,GG		0.4798,0.0682,0.3399	benign	405/536	233245982	44,12900	2199	4273	6472	SO:0001583	missense	250	exon10			AGGCCCGGGACAG	M14169	CCDS2490.1	2q37.1	2010-06-24	2010-06-24		ENSG00000163283	ENSG00000163283	3.1.3.1		439	protein-coding gene	gene with protein product	"""Regan isozyme"""	171800	"""alkaline phosphatase, placental (Regan isozyme)"""			3001717, 3461452	Standard	XM_005246439		Approved		uc002vsq.3	P05187	OTTHUMG00000133255	ENST00000392027.2:c.1214G>A	2.37:g.233245982G>A	ENSP00000375881:p.Arg405Gln	342.0	0.0	0		393.0	121.0	0.307888	NM_001632	P05188|P06861|Q53S78|Q96DB7	Missense_Mutation	SNP	ENST00000392027.2	37	CCDS2490.1	.	.	.	.	.	.	.	.	.	.	g	1.358	-0.589485	0.03799	6.82E-4	0.004798	ENSG00000163283	ENST00000392027	D	0.96491	-4.03	2.35	-4.69	0.03299	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	2.308210	0.01558	N	0.019990	D	0.85084	0.5616	N	0.02368	-0.58	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.81695	-0.0816	10	0.13108	T	0.6	.	0.4192	0.00453	0.392:0.1279:0.2136:0.2665	.	405	P05187	PPB1_HUMAN	Q	405	ENSP00000375881:R405Q	ENSP00000375881:R405Q	R	+	2	0	ALPP	232954226	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-6.351000	0.00069	-3.004000	0.00275	-3.289000	0.00047	CGG	G|0.999;A|0.001	0.001	strong		0.637	ALPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257032.3	NM_001632	
SPACA3	124912	hgsc.bcm.edu	37	17	31323886	31323886	+	Silent	SNP	C	C	T	rs200596990	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:31323886C>T	ENST00000269053.3	+	3	439	c.369C>T	c.(367-369)agC>agT	p.S123S	SPACA3_ENST00000394637.2_3'UTR|SPACA3_ENST00000580599.1_Silent_p.S54S|SPACA3_ENST00000394638.1_Silent_p.S20S	NM_173847.3	NP_776246.1	Q8IXA5	SACA3_HUMAN	sperm acrosome associated 3	123					cell wall macromolecule catabolic process (GO:0016998)|defense response to Gram-positive bacterium (GO:0050830)|monocyte activation (GO:0042117)|peptidoglycan catabolic process (GO:0009253)|positive regulation of macrophage activation (GO:0043032)|positive regulation of phagocytosis (GO:0050766)|response to virus (GO:0009615)|sperm-egg recognition (GO:0035036)	acrosomal vesicle (GO:0001669)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|secretory granule (GO:0030141)	lysozyme activity (GO:0003796)			breast(1)|endometrium(1)|large_intestine(3)|lung(10)|ovary(2)|urinary_tract(1)	18			BRCA - Breast invasive adenocarcinoma(9;0.193)			ATTTCACAAGCGGTTTCAACG	0.582																																					p.S123S		Atlas-SNP	.											SPACA3,NS,carcinoma,+1,1	SPACA3	35	1	0			c.C369T						PASS	.	C		0,4406		0,0,2203	104.0	92.0	96.0		369	0.9	1.0	17		96	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	SPACA3	NM_173847.3		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		123/216	31323886	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	124912	exon3			CACAAGCGGTTTC	AF216311, AF099029	CCDS11275.1	17q12	2014-07-23			ENSG00000141316	ENSG00000141316			16260	protein-coding gene	gene with protein product	"""cancer/testis antigen 54"", ""sperm lyzozyme-like acrosomal protein 1"""	612749				12606493	Standard	NM_173847		Approved	ALLP17, SLLP1, LYC3, LYZL3, CT54	uc002hhs.1	Q8IXA5	OTTHUMG00000132886	ENST00000269053.3:c.369C>T	17.37:g.31323886C>T		56.0	0.0	0		59.0	37.0	0.627119	NM_173847	Q7Z4Y5	Silent	SNP	ENST00000269053.3	37	CCDS11275.1																																																																																			C|0.998;T|0.002	0.002	strong		0.582	SPACA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256380.1	NM_173847	
PRDM15	63977	hgsc.bcm.edu	37	21	43230669	43230669	+	Silent	SNP	C	C	T	rs146699277	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:43230669C>T	ENST00000269844.3	-	28	3701	c.3591G>A	c.(3589-3591)acG>acA	p.T1197T	PRDM15_ENST00000398548.1_Silent_p.T868T|PRDM15_ENST00000422911.1_Silent_p.T888T|PRDM15_ENST00000538201.1_Silent_p.T851T|PRDM15_ENST00000470586.1_5'UTR|PRDM15_ENST00000447207.2_Silent_p.T831T	NM_022115.3	NP_071398.3	P57071	PRD15_HUMAN	PR domain containing 15	1197					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(11)|ovary(3)|skin(2)|stomach(2)|urinary_tract(1)	43						ACACGGAGCACGTCCACTGCT	0.582													c|||	9	0.00179712	0.0008	0.0043	5008	,	,		20936	0.0		0.003	False		,,,				2504	0.002				p.T1197T		Atlas-SNP	.											.	PRDM15	110	.	0			c.G3591A						PASS	.		,	0,4406		0,0,2203	134.0	78.0	97.0		2604,3591	-4.3	1.0	21	dbSNP_134	97	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous	PRDM15	NM_001040424.1,NM_022115.3	,	0,12,6491	TT,TC,CC		0.1395,0.0,0.0923	,	868/1179,1197/1508	43230669	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	63977	exon28			GGAGCACGTCCAC	AF276513	CCDS13676.1, CCDS42932.1, CCDS63370.1	21q22.3	2013-01-08	2002-07-31		ENSG00000141956	ENSG00000141956		"""Zinc fingers, C2H2-type"""	13999	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 83"""	ZNF298, C21orf83		12036297, 12036298	Standard	NM_022115		Approved		uc002yzq.1	P57071	OTTHUMG00000086781	ENST00000269844.3:c.3591G>A	21.37:g.43230669C>T		41.0	0.0	0		52.0	19.0	0.365385	NM_022115	E9PDJ6|E9PF37|E9PGL3|Q4W8S0|Q4W8S3|Q4W8S4|Q4W8S5|Q8N0X3|Q8NEX0|Q9NQV3	Silent	SNP	ENST00000269844.3	37	CCDS13676.1																																																																																			C|0.999;T|0.001	0.001	strong		0.582	PRDM15-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_022115	
ARHGEF19	128272	hgsc.bcm.edu	37	1	16535487	16535487	+	Missense_Mutation	SNP	G	G	C	rs143314517	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16535487G>C	ENST00000270747.3	-	2	199	c.63C>G	c.(61-63)caC>caG	p.H21Q	ARHGEF19_ENST00000478117.1_5'Flank	NM_153213.3	NP_694945.2	Q8IW93	ARHGJ_HUMAN	Rho guanine nucleotide exchange factor (GEF) 19	21					regulation of actin cytoskeleton organization (GO:0032956)|wound healing (GO:0042060)		GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(1)|lung(3)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	12		Colorectal(325;0.000147)|Renal(390;0.00145)|Breast(348;0.00224)|Lung NSC(340;0.00566)|all_lung(284;0.00831)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.018)|Colorectal(212;3.48e-07)|COAD - Colon adenocarcinoma(227;2.19e-05)|BRCA - Breast invasive adenocarcinoma(304;9.46e-05)|Kidney(64;0.000171)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.0117)|READ - Rectum adenocarcinoma(331;0.0649)		CTACAGGGTGGTGGGCAGTGC	0.642													G|||	14	0.00279553	0.0	0.0029	5008	,	,		17289	0.0		0.0119	False		,,,				2504	0.0				p.H21Q		Atlas-SNP	.											.	ARHGEF19	49	.	0			c.C63G						PASS	.	G	GLN/HIS	9,4395		0,9,2193	17.0	19.0	18.0		63	1.0	0.0	1	dbSNP_134	18	114,8482		0,114,4184	no	missense	ARHGEF19	NM_153213.3	24	0,123,6377	CC,CG,GG		1.3262,0.2044,0.9462	benign	21/803	16535487	123,12877	2202	4298	6500	SO:0001583	missense	128272	exon2			AGGGTGGTGGGCA	BC012982	CCDS170.1	1p36.13	2011-11-16			ENSG00000142632	ENSG00000142632		"""Rho guanine nucleotide exchange factors"""	26604	protein-coding gene	gene with protein product		612496				12477932	Standard	NM_153213		Approved	FLJ33962, WGEF	uc001ayc.1	Q8IW93	OTTHUMG00000002219	ENST00000270747.3:c.63C>G	1.37:g.16535487G>C	ENSP00000270747:p.His21Gln	62.0	0.0	0		72.0	35.0	0.486111	NM_153213	A6NJ04|Q5TEV2|Q6PJQ4|Q8N244	Missense_Mutation	SNP	ENST00000270747.3	37	CCDS170.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	G	5.788	0.329777	0.10956	0.002044	0.013262	ENSG00000142632	ENST00000270747;ENST00000421561;ENST00000375607	T;T	0.39592	1.07;1.07	5.12	1.02	0.19986	.	0.844696	0.10118	N	0.713769	T	0.16471	0.0396	N	0.14661	0.345	0.09310	N	1	B	0.17667	0.023	B	0.14023	0.01	T	0.19516	-1.0303	10	0.52906	T	0.07	.	3.3172	0.07038	0.3042:0.0:0.5128:0.1829	.	21	Q8IW93	ARHGJ_HUMAN	Q	21	ENSP00000270747:H21Q;ENSP00000396001:H21Q	ENSP00000270747:H21Q	H	-	3	2	ARHGEF19	16408074	0.761000	0.28439	0.015000	0.15790	0.010000	0.07245	0.817000	0.27281	-0.076000	0.12775	0.462000	0.41574	CAC	G|0.993;C|0.007	0.007	strong		0.642	ARHGEF19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006289.1	NM_153213	
ZNF486	90649	hgsc.bcm.edu	37	19	20308207	20308207	+	Missense_Mutation	SNP	A	A	T	rs148497901	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:20308207A>T	ENST00000335117.8	+	4	745	c.688A>T	c.(688-690)Ata>Tta	p.I230L	CTC-260E6.6_ENST00000585498.1_RNA|CTC-260E6.6_ENST00000586657.1_RNA|CTC-260E6.6_ENST00000593655.1_RNA	NM_052852.3	NP_443084.2	Q96H40	ZN486_HUMAN	zinc finger protein 486	230					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)			endometrium(3)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11						TACACATAAGATAACTCATAC	0.363													A|||	31	0.0061901	0.0008	0.0058	5008	,	,		19318	0.0		0.0249	False		,,,				2504	0.001				p.I230L		Atlas-SNP	.											.	ZNF486	74	.	0			c.A688T						PASS	.	A	LEU/ILE	16,4292		0,16,2138	40.0	43.0	42.0		688	0.8	0.0	19	dbSNP_134	42	187,8375		6,175,4100	no	missense	ZNF486	NM_052852.2	5	6,191,6238	TT,TA,AA		2.1841,0.3714,1.5773	benign	230/464	20308207	203,12667	2154	4281	6435	SO:0001583	missense	90649	exon4			CATAAGATAACTC	BC008936	CCDS46029.1	19p12	2014-02-13	2003-12-16	2003-12-17	ENSG00000256229	ENSG00000256229		"""Zinc fingers, C2H2-type"", ""-"""	20807	protein-coding gene	gene with protein product			"""KRAB domain only 2"""	KRBO2			Standard	NM_052852		Approved	MGC2396	uc002nou.3	Q96H40	OTTHUMG00000179731	ENST00000335117.8:c.688A>T	19.37:g.20308207A>T	ENSP00000335042:p.Ile230Leu	25.0	0.0	0		36.0	27.0	0.75	NM_052852	Q0VG00	Missense_Mutation	SNP	ENST00000335117.8	37	CCDS46029.1	24	0.01098901098901099	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	19	0.025065963060686015	a	9.789	1.177288	0.21787	0.003714	0.021841	ENSG00000256229	ENST00000545779;ENST00000335117	T	0.18016	2.24	0.814	0.814	0.18756	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.02267	0.0070	N	0.01076	-1.035	0.19575	N	0.999961	B	0.32467	0.372	B	0.42959	0.403	T	0.36311	-0.9753	9	0.66056	D	0.02	.	5.4337	0.16469	1.0:0.0:0.0:0.0	.	230	Q96H40	ZN486_HUMAN	L	269;230	ENSP00000335042:I230L	ENSP00000335042:I230L	I	+	1	0	ZNF486	20169207	0.000000	0.05858	0.037000	0.18230	0.036000	0.12997	-0.471000	0.06631	0.158000	0.19367	0.156000	0.16432	ATA	A|0.986;T|0.014	0.014	strong		0.363	ZNF486-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447843.2	NM_052852	
SLC2A4	6517	hgsc.bcm.edu	37	17	7188459	7188459	+	Missense_Mutation	SNP	C	C	T	rs8192702	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7188459C>T	ENST00000317370.8	+	9	1341	c.1073C>T	c.(1072-1074)gCg>gTg	p.A358V	RP1-4G17.2_ENST00000576271.1_RNA|SLC2A4_ENST00000424875.2_Missense_Mutation_p.A348V|SLC2A4_ENST00000571308.1_Missense_Mutation_p.A358V	NM_001042.2	NP_001033.1	P14672	GTR4_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 4	358			A -> V (in dbSNP:rs8192702).		amylopectin biosynthetic process (GO:0010021)|brown fat cell differentiation (GO:0050873)|carbohydrate metabolic process (GO:0005975)|cellular response to insulin stimulus (GO:0032869)|cellular response to osmotic stress (GO:0071470)|glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|membrane organization (GO:0061024)|response to ethanol (GO:0045471)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|endomembrane system (GO:0012505)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|insulin-responsive compartment (GO:0032593)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|multivesicular body (GO:0005771)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|trans-Golgi network transport vesicle (GO:0030140)|vesicle membrane (GO:0012506)	D-glucose transmembrane transporter activity (GO:0055056)|glucose transmembrane transporter activity (GO:0005355)			breast(1)|endometrium(3)|large_intestine(7)|lung(2)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	17						CTGGGCCTGGCGGGCATGTGT	0.662													C|||	8	0.00159744	0.0	0.0	5008	,	,		17560	0.0		0.007	False		,,,				2504	0.001				p.A358V		Atlas-SNP	.											.	SLC2A4	44	.	0			c.C1073T						PASS	.	C	VAL/ALA	5,4401		1,3,2199	34.0	36.0	35.0		1073	5.9	1.0	17	dbSNP_117	35	61,8539		0,61,4239	yes	missense	SLC2A4	NM_001042.2	64	1,64,6438	TT,TC,CC		0.7093,0.1135,0.5075	benign	358/510	7188459	66,12940	2203	4300	6503	SO:0001583	missense	6517	exon9			GCCTGGCGGGCAT	M20747	CCDS11097.1	17p13	2013-05-22			ENSG00000181856	ENSG00000181856		"""Solute carriers"""	11009	protein-coding gene	gene with protein product		138190		GLUT4			Standard	NM_001042		Approved		uc002gfp.3	P14672	OTTHUMG00000102181	ENST00000317370.8:c.1073C>T	17.37:g.7188459C>T	ENSP00000320935:p.Ala358Val	36.0	0.0	0		57.0	31.0	0.54386	NM_001042	Q05BQ3|Q14CX2	Missense_Mutation	SNP	ENST00000317370.8	37	CCDS11097.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	C	15.10	2.733429	0.48939	0.001135	0.007093	ENSG00000181856	ENST00000317370;ENST00000424875	T;T	0.80480	0.35;-1.38	5.92	5.92	0.95590	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.209191	0.41712	D	0.000827	T	0.65709	0.2717	L	0.37800	1.135	0.36892	D	0.889926	B;B	0.31351	0.175;0.32	B;B	0.29524	0.103;0.024	T	0.72437	-0.4294	10	0.41790	T	0.15	.	13.4065	0.60915	0.0:0.8425:0.1575:0.0	rs8192702	358;348	P14672;F5H081	GTR4_HUMAN;.	V	358;348	ENSP00000320935:A358V;ENSP00000396887:A348V	ENSP00000320935:A358V	A	+	2	0	SLC2A4	7129183	0.040000	0.19996	0.983000	0.44433	0.909000	0.53808	0.267000	0.18552	2.813000	0.96785	0.561000	0.74099	GCG	C|0.996;T|0.004	0.004	strong		0.662	SLC2A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000220031.3		
NUP37	79023	hgsc.bcm.edu	37	12	102494849	102494849	+	Silent	SNP	T	T	C	rs17438178	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:102494849T>C	ENST00000552283.1	-	4	454	c.315A>G	c.(313-315)agA>agG	p.R105R	NUP37_ENST00000251074.1_Silent_p.R105R|NUP37_ENST00000543021.1_5'UTR			Q8NFH4	NUP37_HUMAN	nucleoporin 37kDa	105					carbohydrate metabolic process (GO:0005975)|chromosome segregation (GO:0007059)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|kinetochore (GO:0000776)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)|nucleus (GO:0005634)				endometrium(3)|large_intestine(3)|lung(10)|ovary(1)	17						AAGTAAATAATCTAATTTTCA	0.308													T|||	110	0.0219649	0.0401	0.0058	5008	,	,		16106	0.0		0.0308	False		,,,				2504	0.0225				p.R105R		Atlas-SNP	.											.	NUP37	26	.	0			c.A315G						PASS	.	T		130,4262		4,122,2070	29.0	31.0	31.0		315	0.3	1.0	12	dbSNP_123	31	211,8361		2,207,4077	no	coding-synonymous	NUP37	NM_024057.2		6,329,6147	CC,CT,TT		2.4615,2.9599,2.6304		105/327	102494849	341,12623	2196	4286	6482	SO:0001819	synonymous_variant	79023	exon3			AAATAATCTAATT	AF514994	CCDS9089.1	12q23.2	2014-08-12			ENSG00000075188	ENSG00000075188		"""WD repeat domain containing"""	29929	protein-coding gene	gene with protein product		609264				12196509	Standard	NM_024057		Approved	MGC5585, FLJ22618	uc001tjc.3	Q8NFH4	OTTHUMG00000170478	ENST00000552283.1:c.315A>G	12.37:g.102494849T>C		164.0	0.0	0		130.0	66.0	0.507692	NM_024057	Q9H644	Silent	SNP	ENST00000552283.1	37	CCDS9089.1																																																																																			T|0.976;C|0.024	0.024	strong		0.308	NUP37-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409330.1	NM_024057	
SYTL2	54843	hgsc.bcm.edu	37	11	85445365	85445365	+	Missense_Mutation	SNP	G	G	C	rs74718633	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:85445365G>C	ENST00000528231.1	-	6	1281	c.1004C>G	c.(1003-1005)tCt>tGt	p.S335C	SYTL2_ENST00000527523.1_Missense_Mutation_p.S287C|SYTL2_ENST00000389960.4_Missense_Mutation_p.S335C|SYTL2_ENST00000316356.4_Missense_Mutation_p.S336C|SYTL2_ENST00000524452.1_Missense_Mutation_p.S335C	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	335					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)		CTTCACTGCAGAGAATCTCAC	0.443													G|||	19	0.00379393	0.0008	0.0058	5008	,	,		19642	0.0		0.0139	False		,,,				2504	0.0				p.S336C		Atlas-SNP	.											.	SYTL2	231	.	0			c.C1007G						PASS	.	G	CYS/SER,CYS/SER,CYS/SER	10,4396	16.8+/-37.8	0,10,2193	104.0	107.0	106.0		1004,1007,1004	5.2	1.0	11	dbSNP_131	106	113,8485	61.0+/-122.8	1,111,4187	yes	missense,missense,missense	SYTL2	NM_001162951.1,NM_001162953.1,NM_032943.3	112,112,112	1,121,6380	CC,CG,GG		1.3143,0.227,0.9459	,,	335/935,336/936,335/911	85445365	123,12881	2203	4299	6502	SO:0001583	missense	54843	exon6			ACTGCAGAGAATC	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.1004C>G	11.37:g.85445365G>C	ENSP00000431701:p.Ser335Cys	116.0	0.0	0		102.0	51.0	0.5	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	37	CCDS53688.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	20.5	4.002879	0.74932	0.00227	0.013143	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.59083	0.29;0.69;0.62;0.49;0.29	6.06	5.15	0.70609	.	.	.	.	.	T	0.67011	0.2848	M	0.66939	2.045	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.97110	0.997;0.999;0.999;0.994;1.0	T	0.71836	-0.4472	8	.	.	.	.	14.79	0.69833	0.0694:0.0:0.9306:0.0	.	287;335;335;336;193	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	C	335;336;335;287;335	ENSP00000374610:S335C;ENSP00000318803:S336C;ENSP00000431701:S335C;ENSP00000434010:S287C;ENSP00000435238:S335C	.	S	-	2	0	SYTL2	85123013	1.000000	0.71417	1.000000	0.80357	0.963000	0.63663	6.541000	0.73865	1.567000	0.49668	0.650000	0.86243	TCT	G|0.993;C|0.007	0.007	strong		0.443	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
BIN1	274	hgsc.bcm.edu	37	2	127809840	127809840	+	Silent	SNP	C	C	A	rs61748155	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:127809840C>A	ENST00000316724.5	-	15	1773	c.1362G>T	c.(1360-1362)ggG>ggT	p.G454G	BIN1_ENST00000348750.4_Intron|BIN1_ENST00000352848.3_Intron|BIN1_ENST00000259238.4_Intron|BIN1_ENST00000357970.3_Silent_p.G411G|BIN1_ENST00000466111.1_Intron|BIN1_ENST00000409400.1_Intron|BIN1_ENST00000376113.2_Intron|BIN1_ENST00000393041.3_Silent_p.G336G|BIN1_ENST00000351659.3_Silent_p.G367G|BIN1_ENST00000393040.3_Intron|BIN1_ENST00000346226.3_Silent_p.G379G	NM_139343.2	NP_647593.1	O00499	BIN1_HUMAN	bridging integrator 1	454					cell proliferation (GO:0008283)|endocytosis (GO:0006897)|lipid tube assembly (GO:0060988)|muscle cell differentiation (GO:0042692)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of endocytosis (GO:0045807)|positive regulation of GTPase activity (GO:0043547)|regulation of cell cycle arrest (GO:0071156)|regulation of neuron differentiation (GO:0045664)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|axon initial segment (GO:0043194)|axon terminus (GO:0043679)|cerebellar mossy fiber (GO:0044300)|cytoplasm (GO:0005737)|I band (GO:0031674)|lipid tube (GO:0060987)|node of Ranvier (GO:0033268)|nucleus (GO:0005634)|synaptic vesicle (GO:0008021)|T-tubule (GO:0030315)|varicosity (GO:0043196)|Z disc (GO:0030018)	identical protein binding (GO:0042802)|tau protein binding (GO:0048156)			NS(1)|breast(1)|central_nervous_system(2)|endometrium(2)|large_intestine(3)|lung(6)|ovary(3)|prostate(3)|skin(3)	24	Colorectal(110;0.0831)			BRCA - Breast invasive adenocarcinoma(221;0.073)		CTTGGGCAGGCCCCGGCTCGG	0.692													C|||	73	0.0145767	0.0	0.0144	5008	,	,		14417	0.0		0.0159	False		,,,				2504	0.0481				p.G454G		Atlas-SNP	.											BIN1,brain,glioma,0,1	BIN1	85	1	0			c.G1362T						scavenged	.	C	,,,,,,,,,	14,4288		0,14,2137	9.0	12.0	11.0		,1362,1233,1101,,1137,,1008,,	3.8	1.0	2	dbSNP_129	11	149,8367		1,147,4110	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron,coding-synonymous,intron,coding-synonymous,intron,intron	BIN1	NM_004305.3,NM_139343.2,NM_139344.2,NM_139345.2,NM_139346.2,NM_139347.2,NM_139348.2,NM_139349.2,NM_139350.2,NM_139351.2	,,,,,,,,,	1,161,6247	AA,AC,CC		1.7496,0.3254,1.2716	,,,,,,,,,	,454/594,411/551,367/507,,379/519,,336/476,,	127809840	163,12655	2151	4258	6409	SO:0001819	synonymous_variant	274	exon15			GGCAGGCCCCGGC	U68485	CCDS2137.1, CCDS2138.1, CCDS2139.1, CCDS2140.1, CCDS2141.1, CCDS2142.1, CCDS2143.1, CCDS42743.1, CCDS42744.1, CCDS46403.1	2q14	2014-09-17			ENSG00000136717	ENSG00000136717			1052	protein-coding gene	gene with protein product	"""amphiphysin II"""	601248		AMPHL		8725406, 8782822, 17676042	Standard	NM_004305		Approved	SH3P9, AMPH2	uc002tns.2	O00499	OTTHUMG00000131465	ENST00000316724.5:c.1362G>T	2.37:g.127809840C>A		64.0	1.0	0.015625		67.0	35.0	0.522388	NM_139343	O00297|O00545|O43867|O60552|O60553|O60554|O60555|O75514|O75515|O75516|O75517|O75518|Q659B7|Q92944|Q99688	Silent	SNP	ENST00000316724.5	37	CCDS2138.1																																																																																			C|0.990;A|0.010	0.010	strong		0.692	BIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254298.2	NM_139343	
SFXN1	94081	hgsc.bcm.edu	37	5	174936102	174936102	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:174936102G>T	ENST00000321442.5	+	3	486	c.232G>T	c.(232-234)Gct>Tct	p.A78S	SFXN1_ENST00000502393.1_Missense_Mutation_p.A78S	NM_022754.5	NP_073591.2	Q9H9B4	SFXN1_HUMAN	sideroflexin 1	78					erythrocyte differentiation (GO:0030218)|iron ion homeostasis (GO:0055072)|iron ion transport (GO:0006826)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			endometrium(1)|large_intestine(3)|lung(7)|ovary(1)|skin(3)	15	all_cancers(89;0.00922)|Renal(175;0.000269)|Lung NSC(126;0.00515)|all_lung(126;0.00873)	Medulloblastoma(196;0.0399)|all_neural(177;0.0663)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CTATGATTCAGCTTTTCATCC	0.393																																					p.A78S		Atlas-SNP	.											.	SFXN1	23	.	0			c.G232T						PASS	.						204.0	192.0	196.0					5																	174936102		2203	4300	6503	SO:0001583	missense	94081	exon3			GATTCAGCTTTTC	AF327346	CCDS4394.1	5q35.3	2008-02-05			ENSG00000164466	ENSG00000164466		"""Sideroflexins"""	16085	protein-coding gene	gene with protein product		615569					Standard	NM_022754		Approved	FLJ12876	uc003mda.2	Q9H9B4	OTTHUMG00000130555	ENST00000321442.5:c.232G>T	5.37:g.174936102G>T	ENSP00000316905:p.Ala78Ser	166.0	0.0	0		204.0	9.0	0.0441176	NM_022754	B3KPW3|D3DQN2|Q9HA53	Missense_Mutation	SNP	ENST00000321442.5	37	CCDS4394.1	.	.	.	.	.	.	.	.	.	.	G	28.5	4.923734	0.92319	.	.	ENSG00000164466	ENST00000507017;ENST00000321442;ENST00000506963	T;T;T	0.36157	1.27;1.27;1.27	5.23	5.23	0.72850	.	0.000000	0.85682	D	0.000000	T	0.59362	0.2188	M	0.69248	2.105	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.993	T	0.57277	-0.7839	10	0.39692	T	0.17	-21.0535	17.8038	0.88596	0.0:0.0:1.0:0.0	.	78;78	D6RFI0;Q9H9B4	.;SFXN1_HUMAN	S	78	ENSP00000420961:A78S;ENSP00000316905:A78S;ENSP00000421467:A78S	ENSP00000316905:A78S	A	+	1	0	SFXN1	174868708	1.000000	0.71417	0.048000	0.18961	0.968000	0.65278	9.731000	0.98807	2.444000	0.82710	0.555000	0.69702	GCT	.	.	none		0.393	SFXN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252980.2	NM_022754	
SPATA33	124045	hgsc.bcm.edu	37	16	89724755	89724755	+	Missense_Mutation	SNP	C	C	T	rs13329897	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:89724755C>T	ENST00000301031.4	+	2	134	c.134C>T	c.(133-135)tCg>tTg	p.S45L	SPATA33_ENST00000568929.1_Missense_Mutation_p.S15L|CHMP1A_ENST00000397901.3_5'Flank|SPATA33_ENST00000579310.1_Missense_Mutation_p.S46L|CHMP1A_ENST00000550102.1_5'Flank|CHMP1A_ENST00000547614.1_5'Flank|CHMP1A_ENST00000535997.2_5'Flank|CHMP1A_ENST00000253475.5_5'Flank	NM_001271908.1|NM_153025.1	NP_001258837.1|NP_694570.1	Q96N06	SPT33_HUMAN	spermatogenesis associated 33	45			S -> L (in dbSNP:rs13329897).			cytoplasm (GO:0005737)|nucleus (GO:0005634)											GACAGGGAGTCGGAGAAGCCT	0.612													C|||	37	0.00738818	0.0	0.013	5008	,	,		13663	0.0		0.0249	False		,,,				2504	0.0031				p.S46L		Atlas-SNP	.											.	C16orf55	6	.	0			c.C137T						PASS	.		LEU/SER	24,4370	29.9+/-59.1	0,24,2173	34.0	38.0	37.0		134	-1.5	0.0	16	dbSNP_121	37	174,8426	79.5+/-142.1	2,170,4128	yes	missense	C16orf55	NM_153025.1	145	2,194,6301	TT,TC,CC		2.0233,0.5462,1.5238	possibly-damaging	45/140	89724755	198,12796	2197	4300	6497	SO:0001583	missense	124045	exon2			GGGAGTCGGAGAA	AK056168	CCDS10983.1, CCDS62012.1, CCDS73929.1	16q24.3	2013-07-16	2013-07-05	2013-07-05	ENSG00000167523	ENSG00000167523			26463	protein-coding gene	gene with protein product		615409	"""chromosome 16 open reading frame 55"""	C16orf55		23844118	Standard	NM_153025		Approved	FLJ31606	uc010vpk.2	Q96N06	OTTHUMG00000138048	ENST00000301031.4:c.134C>T	16.37:g.89724755C>T	ENSP00000301031:p.Ser45Leu	64.0	0.0	0		69.0	28.0	0.405797	NM_001271910	A8WFL2|B4DZN8	Missense_Mutation	SNP	ENST00000301031.4	37	CCDS10983.1	23	0.010531135531135532	0	0.0	6	0.016574585635359115	0	0.0	17	0.022427440633245383	C	6.839	0.524082	0.13066	0.005462	0.020233	ENSG00000167523	ENST00000301031;ENST00000457689	T	0.40225	1.04	1.95	-1.52	0.08637	.	.	.	.	.	T	0.11665	0.0284	L	0.27053	0.805	0.09310	N	1	B;B;B	0.22851	0.004;0.076;0.008	B;B;B	0.08055	0.001;0.003;0.001	T	0.12426	-1.0548	9	0.36615	T	0.2	.	2.8748	0.05628	0.0:0.4326:0.2424:0.325	rs13329897;rs52799200;rs13329897	46;59;45	B4DZN8;Q86XC3;Q96N06	.;.;CP055_HUMAN	L	45;46	ENSP00000301031:S45L	ENSP00000301031:S45L	S	+	2	0	C16orf55	88252256	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.868000	0.04236	-0.356000	0.08187	-2.290000	0.00267	TCG	C|0.987;T|0.013	0.013	strong		0.612	SPATA33-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269924.2	NM_153025	
NLRP7	199713	hgsc.bcm.edu	37	19	55451613	55451613	+	Missense_Mutation	SNP	T	T	G	rs104895529	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:55451613T>G	ENST00000590030.1	-	3	614	c.574A>C	c.(574-576)Atg>Ctg	p.M192L	NLRP7_ENST00000448121.2_Missense_Mutation_p.M192L|NLRP7_ENST00000340844.2_Missense_Mutation_p.M192L|NLRP7_ENST00000328092.5_Missense_Mutation_p.M192L|NLRP7_ENST00000446217.1_Missense_Mutation_p.M220L|NLRP7_ENST00000588756.1_Missense_Mutation_p.M192L|NLRP7_ENST00000592784.1_Missense_Mutation_p.M192L			Q8WX94	NALP7_HUMAN	NLR family, pyrin domain containing 7	192	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.						ATP binding (GO:0005524)			autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(17)|liver(1)|lung(33)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	73				GBM - Glioblastoma multiforme(193;0.0325)		CAGTCCAGCATACACTTTTTG	0.582													.|||	4	0.000798722	0.0	0.0	5008	,	,		19202	0.0		0.003	False		,,,				2504	0.001				p.M192L		Atlas-SNP	.											.	NLRP7	411	.	0			c.A574C						PASS	.	T	LEU/MET,LEU/MET,LEU/MET	3,4403	6.2+/-15.9	0,3,2200	124.0	122.0	122.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	574,574,574	-0.6	0.0	19	dbSNP_132	122	36,8564	25.1+/-72.6	1,34,4265	yes	missense,missense,missense	NLRP7	NM_001127255.1,NM_139176.3,NM_206828.3	15,15,15	1,37,6465	GG,GT,TT		0.4186,0.0681,0.2999	benign,benign,benign	192/1038,192/1010,192/981	55451613	39,12967	2203	4300	6503	SO:0001583	missense	199713	exon4			CCAGCATACACTT	AF464765	CCDS12912.1, CCDS33109.1, CCDS46183.1	19q13.42	2008-02-05	2006-12-08	2006-12-08		ENSG00000167634		"""Nucleotide-binding domain and leucine rich repeat containing"""	22947	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 7"""	609661	"""NACHT, leucine rich repeat and PYD containing 7"""	NALP7		12563287, 12019269	Standard	NM_139176		Approved	PYPAF3, NOD12, PAN7, CLR19.4	uc002qii.4	Q8WX94		ENST00000590030.1:c.574A>C	19.37:g.55451613T>G	ENSP00000465520:p.Met192Leu	125.0	0.0	0		108.0	56.0	0.518519	NM_001127255	E9PE16|Q32MH8|Q7RTR1	Missense_Mutation	SNP	ENST00000590030.1	37	CCDS33109.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	T	9.712	1.157458	0.21454	6.81E-4	0.004186	ENSG00000167634	ENST00000328092;ENST00000448121;ENST00000340844;ENST00000446217	T;T;T;T	0.80033	-1.33;-1.33;-1.33;-1.33	1.88	-0.548	0.11833	NACHT nucleoside triphosphatase (1);	0.000000	0.38837	N	0.001543	T	0.68393	0.2996	L	0.41632	1.29	0.09310	N	1	B;B;B;B	0.34147	0.438;0.438;0.438;0.384	B;B;B;B	0.40782	0.34;0.34;0.34;0.23	T	0.59423	-0.7457	10	0.49607	T	0.09	.	0.1778	0.00120	0.2414:0.1591:0.2466:0.3529	.	220;192;192;192	E7EPM2;Q32MH9;Q8WX94;Q8WX94-2	.;.;NALP7_HUMAN;.	L	192;192;192;220	ENSP00000329568:M192L;ENSP00000409137:M192L;ENSP00000339491:M192L;ENSP00000414273:M220L	ENSP00000329568:M192L	M	-	1	0	NLRP7	60143425	0.008000	0.16893	0.016000	0.15963	0.144000	0.21451	0.142000	0.16096	-0.222000	0.09958	0.379000	0.24179	ATG	T|0.998;G|0.002	0.002	strong		0.582	NLRP7-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451396.1	NM_139176	
PRSS50	29122	hgsc.bcm.edu	37	3	46784532	46784532	+	Intron	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:46784532C>T	ENST00000460241.1	-	4	1129				PRSS45_ENST00000442359.2_Silent_p.E108E			Q9UI38	TSP50_HUMAN	protease, serine, 50						proteolysis (GO:0006508)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)	serine-type endopeptidase activity (GO:0004252)|threonine-type endopeptidase activity (GO:0004298)			endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	11						ACACCTCAGCCTCCTGCAGCT	0.577																																					p.E108E	Pancreas(41;915 1239 11561 17469)	Atlas-SNP	.											.	PRSS45	12	.	0			c.G324A						PASS	.						61.0	69.0	66.0					3																	46784532		2133	4258	6391	SO:0001627	intron_variant	377047	exon3			CTCAGCCTCCTGC	AF100707	CCDS2745.1	3p21.31	2011-05-24			ENSG00000206549	ENSG00000206549		"""Serine peptidases / Serine peptidases"""	17910	protein-coding gene	gene with protein product	"""cancer/testis antigen 20"", ""testes specific protease 50"""	607950				10397268	Standard	NM_013270		Approved	TSP50, CT20	uc003cqe.1	Q9UI38	OTTHUMG00000164067	ENST00000460241.1:c.541+5582G>A	3.37:g.46784532C>T		60.0	0.0	0		78.0	45.0	0.576923	NM_199183		Silent	SNP	ENST00000460241.1	37	CCDS2745.1																																																																																			.	.	none		0.577	PRSS50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354544.1		
TBX2	6909	hgsc.bcm.edu	37	17	59480547	59480547	+	Silent	SNP	C	C	T	rs140013823		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:59480547C>T	ENST00000240328.3	+	3	1070	c.789C>T	c.(787-789)gtC>gtT	p.V263V	RP11-332H18.4_ENST00000592009.1_RNA|RP11-332H18.5_ENST00000585765.1_RNA	NM_005994.3	NP_005985.3	Q13207	TBX2_HUMAN	T-box 2	263					aorta morphogenesis (GO:0035909)|atrioventricular canal development (GO:0036302)|cardiac muscle tissue development (GO:0048738)|cell aging (GO:0007569)|cellular senescence (GO:0090398)|developmental growth involved in morphogenesis (GO:0060560)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|endocardial cushion morphogenesis (GO:0003203)|mammary placode formation (GO:0060596)|muscle cell fate determination (GO:0007521)|negative regulation of cardiac chamber formation (GO:1901211)|negative regulation of heart looping (GO:1901208)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|outflow tract morphogenesis (GO:0003151)|outflow tract septum morphogenesis (GO:0003148)|palate development (GO:0060021)|pharynx development (GO:0060465)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell proliferation (GO:0008284)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|lung(7)|ovary(1)	9						TCATCGCCGTCACTGCCTACC	0.637													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14472	0.0		0.0	False		,,,				2504	0.0				p.V263V	GBM(3;187 253 11467 14965 23079)	Atlas-SNP	.											.	TBX2	30	.	0			c.C789T						PASS	.	C		0,4406		0,0,2203	90.0	76.0	81.0		789	4.8	1.0	17	dbSNP_134	81	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	TBX2	NM_005994.3		0,13,6490	TT,TC,CC		0.1512,0.0,0.1		263/713	59480547	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	6909	exon3			CGCCGTCACTGCC	AB209378	CCDS11627.2	17q23.2	2012-01-23			ENSG00000121068	ENSG00000121068		"""T-boxes"""	11597	protein-coding gene	gene with protein product		600747				8530034	Standard	NM_005994		Approved		uc010wox.2	Q13207	OTTHUMG00000156986	ENST00000240328.3:c.789C>T	17.37:g.59480547C>T		38.0	0.0	0		44.0	24.0	0.545455	NM_005994	Q16424|Q7Z647	Silent	SNP	ENST00000240328.3	37	CCDS11627.2																																																																																			C|0.999;T|0.001	0.001	strong		0.637	TBX2-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346977.2	NM_005994	
PKD1L2	114780	hgsc.bcm.edu	37	16	81209325	81209325	+	RNA	SNP	G	G	A	rs145948343	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:81209325G>A	ENST00000527937.1	-	0	349				PKD1L2_ENST00000531391.1_RNA|PKD1L2_ENST00000533478.1_RNA|PKD1L2_ENST00000525539.1_RNA|PKD1L2_ENST00000337114.4_RNA			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						TGATGGGAGGGCAGGTTCAGG	0.547													G|||	2	0.000399361	0.0	0.0	5008	,	,		18881	0.0		0.002	False		,,,				2504	0.0				p.A823V		Atlas-SNP	.											.	PKD1L2	361	.	0			c.C2468T						PASS	.	G	VAL/ALA,VAL/ALA	1,4073		0,1,2036	85.0	87.0	86.0		2468,2468	-0.1	0.9	16	dbSNP_134	86	4,8360		0,4,4178	yes	missense,missense	PKD1L2	NM_001076780.1,NM_052892.3	64,64	0,5,6214	AA,AG,GG		0.0478,0.0245,0.0402	benign,benign	823/992,823/2460	81209325	5,12433	2037	4182	6219			114780	exon15			GGGAGGGCAGGTT	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.81209325G>A		89.0	0.0	0		73.0	36.0	0.493151	NM_001076780	Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Missense_Mutation	SNP	ENST00000527937.1	37		2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	10.51	1.369906	0.24771	2.45E-4	4.78E-4	ENSG00000166473	ENST00000531391;ENST00000337114;ENST00000527937	T;T;T	0.70631	-0.5;-0.5;2.14	4.82	-0.11	0.13580	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	0.500926	0.19769	N	0.106485	T	0.44307	0.1287	.	.	.	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.09377	0.004;0.001;0.002	T	0.08973	-1.0696	9	0.18710	T	0.47	-8.2539	2.0758	0.03623	0.225:0.1363:0.4838:0.1549	.	79;823;823	Q7Z442-6;Q7Z442-3;Q7Z442	.;.;PK1L2_HUMAN	V	138;823;79	ENSP00000436309:A138V;ENSP00000337397:A823V;ENSP00000432818:A79V	ENSP00000337397:A823V	A	-	2	0	PKD1L2	79766826	0.386000	0.25180	0.907000	0.35723	0.962000	0.63368	-0.022000	0.12480	0.331000	0.23511	-0.611000	0.04053	GCC	G|0.999;A|0.001	0.001	strong		0.547	PKD1L2-007	KNOWN	basic|exp_conf	protein_coding	polymorphic_pseudogene	OTTHUMT00000387978.1		
MYO10	4651	hgsc.bcm.edu	37	5	16701796	16701796	+	Missense_Mutation	SNP	A	A	G	rs112696559	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:16701796A>G	ENST00000513610.1	-	25	3162	c.2708T>C	c.(2707-2709)aTg>aCg	p.M903T	MYO10_ENST00000505695.1_Missense_Mutation_p.M242T|MYO10_ENST00000427430.2_Missense_Mutation_p.M260T|MYO10_ENST00000274203.9_Missense_Mutation_p.M260T|MYO10_ENST00000512061.1_5'Flank|MYO10_ENST00000515803.1_Missense_Mutation_p.M242T	NM_012334.2	NP_036466.2	Q9HD67	MYO10_HUMAN	myosin X	903	Mediates antiparallel dimerization.				ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cytoskeleton-dependent intracellular transport (GO:0030705)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|regulation of cell shape (GO:0008360)|regulation of filopodium assembly (GO:0051489)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|filopodium tip (GO:0032433)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|plus-end directed microfilament motor activity (GO:0060002)|spectrin binding (GO:0030507)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(19)|lung(28)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	86						CTGCTCCTTCATGCGCTGCAG	0.587													A|||	28	0.00559105	0.0	0.0029	5008	,	,		18003	0.0		0.0129	False		,,,				2504	0.0133				p.M903T		Atlas-SNP	.											.	MYO10	198	.	0			c.T2708C						PASS	.	A	THR/MET	6,4234		0,6,2114	40.0	44.0	43.0		2708	3.8	1.0	5	dbSNP_132	43	79,8425		2,75,4175	yes	missense	MYO10	NM_012334.2	81	2,81,6289	GG,GA,AA		0.929,0.1415,0.667	benign	903/2059	16701796	85,12659	2120	4252	6372	SO:0001583	missense	4651	exon25			TCCTTCATGCGCT	AF247457	CCDS54834.1	5p15.1-p14.3	2013-01-10				ENSG00000145555		"""Myosins / Myosin superfamily : Class X"", ""Pleckstrin homology (PH) domain containing"""	7593	protein-coding gene	gene with protein product		601481				8884266	Standard	NM_012334		Approved	KIAA0799	uc003jft.4	Q9HD67		ENST00000513610.1:c.2708T>C	5.37:g.16701796A>G	ENSP00000421280:p.Met903Thr	131.0	0.0	0		133.0	62.0	0.466165	NM_012334	A7E2D1|O94893|Q8IVX5|Q9NYM7|Q9P110|Q9P111|Q9UHF6	Missense_Mutation	SNP	ENST00000513610.1	37	CCDS54834.1	11	0.005036630036630037	0	0.0	0	0.0	0	0.0	11	0.014511873350923483	A	9.654	1.142336	0.21205	0.001415	0.00929	ENSG00000145555	ENST00000513610;ENST00000515803;ENST00000274203;ENST00000505695;ENST00000427430	T;T;T;T;T	0.03982	3.74;3.74;3.74;3.74;3.74	5.0	3.82	0.43975	.	.	.	.	.	T	0.02047	0.0064	N	0.14661	0.345	0.29659	N	0.843378	B;B	0.17667	0.01;0.023	B;B	0.11329	0.004;0.006	T	0.40289	-0.9571	9	0.19147	T	0.46	.	7.2935	0.26380	0.7044:0.1512:0.0:0.1444	.	544;903	Q69YP8;Q9HD67	.;MYO10_HUMAN	T	903;242;260;242;260	ENSP00000421280:M903T;ENSP00000425051:M242T;ENSP00000274203:M260T;ENSP00000421170:M242T;ENSP00000391106:M260T	ENSP00000274203:M260T	M	-	2	0	MYO10	16754796	1.000000	0.71417	1.000000	0.80357	0.929000	0.56500	3.753000	0.55180	0.733000	0.32492	-0.460000	0.05396	ATG	A|0.994;G|0.006;T|0.000	0.006	strong		0.587	MYO10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366167.1	NM_012334	
KDM6B	23135	hgsc.bcm.edu	37	17	7749972	7749972	+	Missense_Mutation	SNP	G	G	T	rs148641957	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:7749972G>T	ENST00000448097.2	+	8	956	c.625G>T	c.(625-627)Gtg>Ttg	p.V209L	KDM6B_ENST00000254846.5_Missense_Mutation_p.V209L			O15054	KDM6B_HUMAN	lysine (K)-specific demethylase 6B	209	Pro-rich.				cardiac muscle cell differentiation (GO:0055007)|cellular response to hydrogen peroxide (GO:0070301)|endothelial cell differentiation (GO:0045446)|inflammatory response (GO:0006954)|mesodermal cell differentiation (GO:0048333)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	dioxygenase activity (GO:0051213)|histone demethylase activity (H3-K27 specific) (GO:0071558)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)			central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|skin(5)	37						GGTGCAGCCTGTGCCTCCTGC	0.607													G|||	10	0.00199681	0.0	0.0058	5008	,	,		9853	0.0		0.006	False		,,,				2504	0.0				p.V209L		Atlas-SNP	.											.	KDM6B	95	.	0			c.G625T						PASS	.	G	LEU/VAL	6,4400	11.4+/-27.6	0,6,2197	53.0	60.0	58.0		625	1.4	1.0	17	dbSNP_134	58	34,8566	23.4+/-69.3	0,34,4266	yes	missense	KDM6B	NM_001080424.1	32	0,40,6463	TT,TG,GG		0.3953,0.1362,0.3076	benign	209/1683	7749972	40,12966	2203	4300	6503	SO:0001583	missense	23135	exon8			CAGCCTGTGCCTC	AB002344	CCDS32552.1	17p13.1	2011-07-01	2009-04-17	2009-04-17		ENSG00000132510		"""Chromatin-modifying enzymes / K-demethylases"""	29012	protein-coding gene	gene with protein product		611577	"""jumonji domain containing 3"", ""jumonji domain containing 3, histone lysine demethylase"""	JMJD3		10662545, 9205841	Standard	NM_001080424		Approved	KIAA0346	uc002giw.1	O15054		ENST00000448097.2:c.625G>T	17.37:g.7749972G>T	ENSP00000412513:p.Val209Leu	62.0	0.0	0		68.0	28.0	0.411765	NM_001080424	C9IZ40|Q96G33	Missense_Mutation	SNP	ENST00000448097.2	37		5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	G	10.41	1.342148	0.24339	0.001362	0.003953	ENSG00000132510	ENST00000254846;ENST00000448097	T;T	0.06933	3.24;3.24	5.14	1.42	0.22433	.	0.725657	0.12197	N	0.490623	T	0.02380	0.0073	N	0.08118	0	0.23440	N	0.997671	B	0.06786	0.001	B	0.06405	0.002	T	0.47275	-0.9130	10	0.19147	T	0.46	-1.9231	4.5059	0.11887	0.3322:0.1581:0.5097:0.0	.	209	O15054-1	.	L	209	ENSP00000254846:V209L;ENSP00000412513:V209L	ENSP00000254846:V209L	V	+	1	0	KDM6B	7690697	0.994000	0.37717	0.996000	0.52242	0.991000	0.79684	0.849000	0.27723	0.108000	0.17862	0.561000	0.74099	GTG	G|0.997;T|0.003	0.003	strong		0.607	KDM6B-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000440248.1	XM_043272	
AMOT	154796	hgsc.bcm.edu	37	X	112053138	112053138	+	Silent	SNP	C	C	T	rs57201849	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chrX:112053138C>T	ENST00000524145.1	-	5	1688	c.1614G>A	c.(1612-1614)tcG>tcA	p.S538S	AMOT_ENST00000371962.1_Silent_p.S306S|AMOT_ENST00000304758.1_Silent_p.S129S|AMOT_ENST00000371958.1_Silent_p.S306S|AMOT_ENST00000371959.3_Silent_p.S538S			Q4VCS5	AMOT_HUMAN	angiomotin	538					actin cytoskeleton organization (GO:0030036)|blood vessel endothelial cell migration (GO:0043534)|cell migration involved in gastrulation (GO:0042074)|cell-cell junction assembly (GO:0007043)|cellular protein localization (GO:0034613)|chemotaxis (GO:0006935)|establishment of cell polarity involved in ameboidal cell migration (GO:0003365)|gastrulation with mouth forming second (GO:0001702)|hippo signaling (GO:0035329)|in utero embryonic development (GO:0001701)|negative regulation of angiogenesis (GO:0016525)|negative regulation of GTPase activity (GO:0034260)|negative regulation of vascular permeability (GO:0043116)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell size (GO:0045793)|positive regulation of embryonic development (GO:0040019)|positive regulation of stress fiber assembly (GO:0051496)|regulation of cell migration (GO:0030334)|regulation of small GTPase mediated signal transduction (GO:0051056)|vasculogenesis (GO:0001570)	actin filament (GO:0005884)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|external side of plasma membrane (GO:0009897)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|ruffle (GO:0001726)|stress fiber (GO:0001725)|tight junction (GO:0005923)	angiostatin binding (GO:0043532)|receptor activity (GO:0004872)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	43						CAAAGAGCTGCGAGATGGTTT	0.458													C|||	85	0.0225166	0.062	0.0043	3775	,	,		14472	0.0		0.0	False		,,,				2504	0.0				p.S538S		Atlas-SNP	.											.	AMOT	204	.	0			c.G1614A						PASS	.	C	,	221,3614		4,173,40,1455,531	254.0	220.0	231.0		1614,387	-0.6	1.0	X	dbSNP_129	231	4,6724		0,4,0,2424,1872	no	coding-synonymous,coding-synonymous	AMOT	NM_001113490.1,NM_133265.2	,	4,177,40,3879,2403	TT,TC,T,CC,C		0.0595,5.7627,2.1301	,	538/1085,129/676	112053138	225,10338	2203	4300	6503	SO:0001819	synonymous_variant	154796	exon4			GAGCTGCGAGATG	AB028994	CCDS14563.1, CCDS48154.1	Xq23	2006-02-08			ENSG00000126016	ENSG00000126016			17810	protein-coding gene	gene with protein product		300410				11257124, 16043488, 12406577	Standard	NM_001113490		Approved	KIAA1071	uc004epr.3	Q4VCS5	OTTHUMG00000022216	ENST00000524145.1:c.1614G>A	X.37:g.112053138C>T		36.0	0.0	0		31.0	31.0	1	NM_001113490	Q504X5|Q9HD27|Q9UPT1	Silent	SNP	ENST00000524145.1	37	CCDS48154.1																																																																																			C|0.980;T|0.020	0.020	strong		0.458	AMOT-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000378570.1	NM_133265	
LAMA1	284217	hgsc.bcm.edu	37	18	7010233	7010233	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:7010233C>T	ENST00000389658.3	-	26	3932	c.3839G>A	c.(3838-3840)gGa>gAa	p.G1280E		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1280	Laminin IV type A 2. {ECO:0000255|PROSITE-ProRule:PRU00458}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				CTGTCTCACTCCATTCTCTGG	0.443																																					p.G1280E		Atlas-SNP	.											.	LAMA1	458	.	0			c.G3839A						PASS	.						193.0	164.0	174.0					18																	7010233		2203	4300	6503	SO:0001583	missense	284217	exon26			CTCACTCCATTCT	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.3839G>A	18.37:g.7010233C>T	ENSP00000374309:p.Gly1280Glu	211.0	0.0	0		254.0	52.0	0.204724	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	.	.	.	.	.	.	.	.	.	.	C	17.96	3.516908	0.64634	.	.	ENSG00000101680	ENST00000389658	T	0.31247	1.5	5.57	5.57	0.84162	Laminin B type IV (2);Laminin B, subgroup (1);	0.059894	0.64402	D	0.000003	T	0.55561	0.1928	M	0.64080	1.96	0.58432	D	0.999993	D	0.89917	1.0	D	0.85130	0.997	T	0.51926	-0.8643	10	0.48119	T	0.1	.	19.5479	0.95307	0.0:1.0:0.0:0.0	.	1280	P25391	LAMA1_HUMAN	E	1280	ENSP00000374309:G1280E	ENSP00000374309:G1280E	G	-	2	0	LAMA1	7000233	0.987000	0.35691	0.982000	0.44146	0.385000	0.30292	5.643000	0.67895	2.632000	0.89209	0.579000	0.79373	GGA	.	.	none		0.443	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
RRP12	23223	hgsc.bcm.edu	37	10	99126513	99126513	+	Silent	SNP	C	C	T	rs45527941	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr10:99126513C>T	ENST00000370992.4	-	27	3312	c.3201G>A	c.(3199-3201)caG>caA	p.Q1067Q	RRP12_ENST00000315563.6_Silent_p.Q967Q|RRP12_ENST00000536831.1_Silent_p.Q785Q|RRP12_ENST00000414986.1_Silent_p.Q1006Q|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1067	Glu-rich.					integral component of membrane (GO:0016021)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(5)|large_intestine(2)|lung(13)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	37		Colorectal(252;0.162)		Epithelial(162;2.72e-09)|all cancers(201;1.76e-07)		CACCTTTGCCCTGGGCGGGct	0.672													C|||	128	0.0255591	0.0038	0.0548	5008	,	,		15272	0.0		0.0716	False		,,,				2504	0.0133				p.Q1067Q		Atlas-SNP	.											.	RRP12	97	.	0			c.G3201A						PASS	.	C	,	58,4348	56.2+/-92.4	0,58,2145	70.0	82.0	78.0		3018,3201	4.8	1.0	10	dbSNP_127	78	501,8099	143.6+/-199.6	17,467,3816	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	17,525,5961	TT,TC,CC		5.8256,1.3164,4.298	,	1006/1237,1067/1298	99126513	559,12447	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon27			TTTGCCCTGGGCG		CCDS7457.1, CCDS44467.1, CCDS60605.1	10q24.2	2006-11-06	2006-11-06	2006-11-06	ENSG00000052749	ENSG00000052749			29100	protein-coding gene	gene with protein product			"""KIAA0690"""	KIAA0690		9734811	Standard	NM_015179		Approved		uc001knf.3	Q5JTH9	OTTHUMG00000018855	ENST00000370992.4:c.3201G>A	10.37:g.99126513C>T		43.0	0.0	0		37.0	18.0	0.486486	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			C|0.962;T|0.038	0.038	strong		0.672	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
DDOST	1650	hgsc.bcm.edu	37	1	20980799	20980799	+	Silent	SNP	G	G	A	rs34189097	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:20980799G>A	ENST00000375048.3	-	7	867	c.762C>T	c.(760-762)cgC>cgT	p.R254R	DDOST_ENST00000602624.2_Silent_p.R237R|PINK1-AS_ENST00000451424.1_RNA|DDOST_ENST00000415136.2_Silent_p.R217R	NM_005216.4	NP_005207	P39656	OST48_HUMAN	dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit (non-catalytic)	254					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|innate immune response (GO:0045087)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|response to cytokine (GO:0034097)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|T cell activation (GO:0042110)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|oligosaccharyltransferase complex (GO:0008250)|protein complex (GO:0043234)	dolichyl-diphosphooligosaccharide-protein glycotransferase activity (GO:0004579)			endometrium(2)|kidney(1)|large_intestine(6)|lung(2)|ovary(1)|skin(1)	13		all_lung(284;2.98e-05)|Lung NSC(340;3.25e-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;0.0181)|COAD - Colon adenocarcinoma(152;1.17e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000141)|Kidney(64;0.000177)|GBM - Glioblastoma multiforme(114;0.00046)|KIRC - Kidney renal clear cell carcinoma(64;0.00262)|STAD - Stomach adenocarcinoma(196;0.00303)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.199)		TGAAGATGACGCGGGCATTGT	0.602													G|||	3	0.000599042	0.0008	0.0014	5008	,	,		17003	0.0		0.0	False		,,,				2504	0.001				p.R254R		Atlas-SNP	.											DDOST,caecum,carcinoma,-1,1	DDOST	30	1	0			c.C762T						PASS	.	G		1,4391		0,1,2195	50.0	42.0	45.0		762	-2.0	1.0	1	dbSNP_126	45	9,8553		0,9,4272	no	coding-synonymous	DDOST	NM_005216.4		0,10,6467	AA,AG,GG		0.1051,0.0228,0.0772		254/457	20980799	10,12944	2196	4281	6477	SO:0001819	synonymous_variant	1650	exon7			GATGACGCGGGCA	D29643	CCDS212.1	1p36.1	2013-03-06	2013-03-06		ENSG00000244038	ENSG00000244038	2.4.1.119		2728	protein-coding gene	gene with protein product	"""oligosaccharyltransferase subunit 48"""	602202	"""dolichyl-diphosphooligosaccharide-protein glycosyltransferase"", ""dolichyl-diphosphooligosaccharide--protein glycosyltransferase"""			9367678	Standard	NM_005216		Approved	OST, KIAA0115, OST48, WBP1	uc001bdo.1	P39656	OTTHUMG00000002844	ENST00000375048.3:c.762C>T	1.37:g.20980799G>A		104.0	0.0	0		106.0	31.0	0.292453	NM_005216	B2RDQ4|B4DJE3|B4DLI2|O43244|Q5VWA5|Q8NI93|Q9BUI2	Silent	SNP	ENST00000375048.3	37	CCDS212.1																																																																																			G|0.999;A|0.001	0.001	strong		0.602	DDOST-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000007961.2	NM_005216	
DNM2	1785	hgsc.bcm.edu	37	19	10939884	10939884	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:10939884T>C	ENST00000355667.6	+	19	2311	c.2231T>C	c.(2230-2232)gTg>gCg	p.V744A	DNM2_ENST00000389253.4_Missense_Mutation_p.V744A|DNM2_ENST00000359692.6_Missense_Mutation_p.V740A|DNM2_ENST00000408974.4_Missense_Mutation_p.V740A|DNM2_ENST00000314646.5_Missense_Mutation_p.V744A|DNM2_ENST00000585892.1_Missense_Mutation_p.V744A	NM_001005360.2|NM_001190716.1	NP_001005360.1|NP_001177645.1	P50570	DYN2_HUMAN	dynamin 2	744	GED. {ECO:0000255|PROSITE- ProRule:PRU00720}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|endocytosis (GO:0006897)|G2/M transition of mitotic cell cycle (GO:0000086)|GTP catabolic process (GO:0006184)|membrane organization (GO:0061024)|nitric oxide metabolic process (GO:0046209)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|post-Golgi vesicle-mediated transport (GO:0006892)|receptor internalization (GO:0031623)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic vesicle transport (GO:0048489)|transferrin transport (GO:0033572)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	enzyme binding (GO:0019899)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|microtubule binding (GO:0008017)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(2)|skin(3)|upper_aerodigestive_tract(2)	42			Epithelial(33;4.17e-05)|all cancers(31;8.48e-05)			ACCAGCACTGTGTCCACGCCT	0.637			"""F, N, Splice, Mis, O"""		ETP ALL																																p.V744A		Atlas-SNP	.		Rec	yes		19	19p13.2	1785	dynamin 2		L	.	DNM2	175	.	0			c.T2231C						PASS	.						86.0	64.0	71.0					19																	10939884		2203	4300	6503	SO:0001583	missense	1785	exon19			GCACTGTGTCCAC		CCDS32907.1, CCDS32908.1, CCDS45968.1, CCDS45969.1, CCDS59351.1	19p	2014-09-17						"""Pleckstrin homology (PH) domain containing"""	2974	protein-coding gene	gene with protein product	"""dynamin II"", ""cytoskeletal protein"""	602378				7590285, 9143510	Standard	NM_001190716		Approved	DYNII, DYN2, CMTDIB, CMTDI1, DI-CMTB	uc002mps.2	P50570		ENST00000355667.6:c.2231T>C	19.37:g.10939884T>C	ENSP00000347890:p.Val744Ala	76.0	0.0	0		79.0	44.0	0.556962	NM_001005361	A8K1B6|E7EV30|E9PEQ4|K7ESI9|Q5I0Y0|Q7Z5S3|Q9UPH4	Missense_Mutation	SNP	ENST00000355667.6	37	CCDS45968.1	.	.	.	.	.	.	.	.	.	.	T	10.09	1.254187	0.22965	.	.	ENSG00000079805	ENST00000408974;ENST00000355667;ENST00000359692;ENST00000389253;ENST00000314646;ENST00000545324	D;D;D;D	0.92911	-3.13;-3.06;-3.12;-3.12	4.83	4.83	0.62350	GTPase effector domain, GED (1);	0.361801	0.25241	N	0.032084	D	0.87485	0.6189	L	0.42245	1.32	0.37324	D	0.909672	B;B;B;B;B;B;B	0.14012	0.009;0.004;0.005;0.002;0.002;0.0;0.002	B;B;B;B;B;B;B	0.15052	0.005;0.012;0.009;0.005;0.008;0.005;0.003	D	0.85541	0.1215	10	0.59425	D	0.04	.	8.187	0.31346	0.0:0.0927:0.0:0.9073	.	338;744;473;740;740;744;744	Q8N1K8;F5H4R9;B4DJ53;A8K1B6;P50570-2;P50570;E9PEQ4	.;.;.;.;.;DYN2_HUMAN;.	A	740;740;744;744;744;351	ENSP00000386192:V740A;ENSP00000352721:V744A;ENSP00000373905:V744A;ENSP00000313164:V744A	ENSP00000313164:V744A	V	+	2	0	DNM2	10800884	0.996000	0.38824	0.990000	0.47175	0.005000	0.04900	5.022000	0.64078	1.808000	0.52836	0.377000	0.23210	GTG	.	.	none		0.637	DNM2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000452592.1	NM_004945	
TBCD	6904	hgsc.bcm.edu	37	17	80899349	80899349	+	Missense_Mutation	SNP	T	T	C	rs2292969	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80899349T>C	ENST00000355528.4	+	38	3684	c.3554T>C	c.(3553-3555)cTg>cCg	p.L1185P	TBCD_ENST00000576691.1_3'UTR|TBCD_ENST00000539345.2_Missense_Mutation_p.L1223P	NM_005993.4	NP_005984.3	Q9BTW9	TBCD_HUMAN	tubulin folding cofactor D	1185			L -> P (in dbSNP:rs2292969).		'de novo' posttranslational protein folding (GO:0051084)|adherens junction assembly (GO:0034333)|cellular protein metabolic process (GO:0044267)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of microtubule polymerization (GO:0031115)|positive regulation of GTPase activity (GO:0043547)|post-chaperonin tubulin folding pathway (GO:0007023)|protein folding (GO:0006457)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cytoplasm (GO:0005737)|lateral plasma membrane (GO:0016328)|microtubule (GO:0005874)|tight junction (GO:0005923)	beta-tubulin binding (GO:0048487)|chaperone binding (GO:0051087)|GTPase activator activity (GO:0005096)					Breast(20;0.000523)|all_neural(118;0.0779)	all_cancers(8;0.0266)|all_epithelial(8;0.0696)	OV - Ovarian serous cystadenocarcinoma(97;0.0868)|BRCA - Breast invasive adenocarcinoma(99;0.18)			AGGCCCCAGCTGGTGCCCCAG	0.622													T|||	23	0.00459265	0.0	0.0058	5008	,	,		18723	0.002		0.0089	False		,,,				2504	0.0082				p.L1185P		Atlas-SNP	.											.	TBCD	94	.	0			c.T3554C						PASS	.	T	PRO/LEU	6,4162		0,6,2078	44.0	58.0	53.0		3554	5.0	1.0	17	dbSNP_100	53	48,8376		1,46,4165	yes	missense	TBCD	NM_005993.4	98	1,52,6243	CC,CT,TT		0.5698,0.144,0.4288	probably-damaging	1185/1193	80899349	54,12538	2084	4212	6296	SO:0001583	missense	6904	exon38			CCCAGCTGGTGCC	BC003094	CCDS45818.1	17q25.3	2006-11-21	2006-11-21			ENSG00000141556			11581	protein-coding gene	gene with protein product		604649	"""tubulin-specific chaperone d"""				Standard	NM_005993		Approved		uc002kfz.3	Q9BTW9		ENST00000355528.4:c.3554T>C	17.37:g.80899349T>C	ENSP00000347719:p.Leu1185Pro	31.0	0.0	0		25.0	12.0	0.48	NM_005993	O95458|Q7L8K1|Q8IXP6|Q8NAX0|Q8WYH4|Q96E74|Q9UF82|Q9UG46|Q9Y2J3	Missense_Mutation	SNP	ENST00000355528.4	37	CCDS45818.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	2|2	0.0034965034965034965|0.0034965034965034965	5|5	0.006596306068601583|0.006596306068601583	T|T	13.78|13.78	2.340685|2.340685	0.41498|0.41498	0.00144|0.00144	0.005698|0.005698	ENSG00000141556|ENSG00000141556	ENST00000355528;ENST00000539345|ENST00000334614	T|.	0.22336|.	1.96|.	4.96|4.96	4.96|4.96	0.65561|0.65561	.|.	.|0.369474	.|0.21711	.|N	.|0.070272	T|T	0.65481|0.65481	0.2695|0.2695	M|M	0.75777|0.75777	2.31|2.31	0.80722|0.80722	D|D	1|1	B|.	0.26744|.	0.158|.	B|.	0.26202|.	0.067|.	T|T	0.70096|0.70096	-0.4966|-0.4966	8|6	.|.	.|.	.|.	.|.	11.3315|11.3315	0.49479|0.49479	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs2292969;rs2292969|rs2292969;rs2292969	1185|.	Q9BTW9|.	TBCD_HUMAN|.	P|R	1185;177|973	ENSP00000347719:L1185P|.	.|.	L|W	+|+	2|1	0|0	TBCD|TBCD	78492638|78492638	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.664000|0.664000	0.39144|0.39144	3.885000|3.885000	0.56182|0.56182	2.015000|2.015000	0.59207|0.59207	0.460000|0.460000	0.39030|0.39030	CTG|TGG	T|0.994;C|0.006	0.006	strong		0.622	TBCD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439415.1	NM_005993	
PCDHA10	56139	hgsc.bcm.edu	37	5	140237158	140237158	+	Missense_Mutation	SNP	G	G	A	rs142356019	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140237158G>A	ENST00000307360.5	+	1	1525	c.1525G>A	c.(1525-1527)Gtg>Atg	p.V509M	PCDHA8_ENST00000531613.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA10_ENST00000506939.2_Missense_Mutation_p.V509M|PCDHA3_ENST00000522353.2_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000527624.1_Intron	NM_018901.2	NP_061724.1	Q9Y5I2	PCDAA_HUMAN	protocadherin alpha 10	509	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(11)|cervix(1)|endometrium(11)|kidney(5)|large_intestine(13)|liver(2)|lung(20)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(2)	79			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTACGTGTCGGTGCACGCGGA	0.697													.|||	119	0.023762	0.0121	0.0346	5008	,	,		14546	0.0		0.0716	False		,,,				2504	0.0072				p.V509M		Atlas-SNP	.											.	PCDHA10	358	.	0			c.G1525A						PASS	.	G	,MET/VAL,,,,,,,,,,,MET/VAL,MET/VAL	120,4272		4,112,2080	66.0	73.0	71.0		,1525,,,,,,,,,,,1525,1525	3.6	1.0	5	dbSNP_134	71	477,8069		47,383,3843	no	intron,missense,intron,intron,intron,intron,intron,intron,intron,intron,intron,intron,missense,missense	PCDHA9,PCDHA10,PCDHA8,PCDHA7,PCDHA6,PCDHA5,PCDHA4,PCDHA3,PCDHA2,PCDHA1	NM_018900.2,NM_018901.2,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_031859.1,NM_031860.1	,21,,,,,,,,,,,21,21	51,495,5923	AA,AG,GG		5.5816,2.7322,4.6143	,,,,,,,,,,,,,	,509/949,,,,,,,,,,,509/845,509/686	140237158	597,12341	2196	4273	6469	SO:0001583	missense	56139	exon1			GTGTCGGTGCACG	AF152475	CCDS34255.1, CCDS54921.1, CCDS75325.1	5q31	2010-11-26			ENSG00000250120	ENSG00000250120		"""Cadherins / Protocadherins : Clustered"""	8664	other	complex locus constituent	"""KIAA0345-like 4"", ""ortholog to mouse CNR8"""	606316		CNRS8		10380929	Standard	NM_018901		Approved	CNR8, CRNR8, CNRN8, PCDH-ALPHA10		Q9Y5I2	OTTHUMG00000163372	ENST00000307360.5:c.1525G>A	5.37:g.140237158G>A	ENSP00000304234:p.Val509Met	73.0	0.0	0		160.0	79.0	0.49375	NM_031859	A1L493|O75280|Q9NRU2	Missense_Mutation	SNP	ENST00000307360.5	37	CCDS54921.1	87	0.03983516483516483	9	0.018292682926829267	19	0.052486187845303865	0	0.0	59	0.07783641160949868	G	14.28	2.487603	0.44249	0.027322	0.055816	ENSG00000250120	ENST00000506939;ENST00000307360	T;T	0.67698	-0.28;-0.28	3.63	3.63	0.41609	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.17323	0.0416	M	0.64404	1.975	0.43489	P	0.004271000000000025	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.993	T	0.65446	-0.6166	8	0.59425	D	0.04	.	9.6727	0.40021	0.0974:0.0:0.9026:0.0	.	509;509;509	Q9Y5I2-3;Q9Y5I2;Q9Y5I2-2	.;PCDAA_HUMAN;.	M	509	ENSP00000421030:V509M;ENSP00000304234:V509M	ENSP00000304234:V509M	V	+	1	0	PCDHA10	140217342	.	.	0.998000	0.56505	0.648000	0.38561	.	.	2.007000	0.58848	0.561000	0.74099	GTG	G|0.957;A|0.043	0.043	strong		0.697	PCDHA10-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372895.2	NM_018901	
TTN	7273	hgsc.bcm.edu	37	2	179611809	179611809	+	Intron	SNP	A	A	G	rs397517815|rs569499266		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611809A>G	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.Y5106Y			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)			GGGGTGTGGAATATCGCTCTA	0.498																																					p.Y5106Y		Atlas-SNP	.											.	TTN	18412	.	0			c.T15318C						PASS	.																																			SO:0001627	intron_variant	7273	exon46			TGTGGAATATCGC	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.10361-5161T>C	2.37:g.179611809A>G		168.0	0.0	0		164.0	12.0	0.0731707	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																																																																																				.	.	none		0.498	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
KALRN	8997	hgsc.bcm.edu	37	3	124157798	124157798	+	Silent	SNP	C	C	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:124157798C>A	ENST00000240874.3	+	18	3263	c.3106C>A	c.(3106-3108)Cga>Aga	p.R1036R	KALRN_ENST00000360013.3_Silent_p.R1036R|KALRN_ENST00000460856.1_Silent_p.R1027R	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	1036					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)	p.R1036*(2)		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						GTGTGGTGGACGAGATAAGCT	0.468																																					p.R1036R		Atlas-SNP	.											KALRN_ENST00000360013,caecum,carcinoma,0,2	KALRN	556	2	2	Substitution - Nonsense(2)	large_intestine(2)	c.C3106A						PASS	.						197.0	186.0	190.0					3																	124157798		2203	4300	6503	SO:0001819	synonymous_variant	8997	exon18			GGTGGACGAGATA	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.3106C>A	3.37:g.124157798C>A		95.0	0.0	0		131.0	72.0	0.549618	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.292179	0.23564	.	.	ENSG00000160145	ENST00000354186	.	.	.	5.54	3.54	0.40534	.	.	.	.	.	T	0.72011	0.3408	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.71182	-0.4668	4	.	.	.	.	16.5605	0.84565	0.1516:0.8484:0.0:0.0	.	.	.	.	E	1004	.	.	D	+	3	2	KALRN	125640488	0.957000	0.32711	1.000000	0.80357	0.997000	0.91878	1.191000	0.32138	0.683000	0.31428	0.655000	0.94253	GAC	.	.	none		0.468	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
PIEZO1	9780	hgsc.bcm.edu	37	16	88789709	88789709	+	Missense_Mutation	SNP	C	C	T	rs191656121	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:88789709C>T	ENST00000301015.9	-	32	4609	c.4363G>A	c.(4363-4365)Gcc>Acc	p.A1455T	RP5-1142A6.9_ENST00000564984.1_RNA	NM_001142864.2	NP_001136336.2	Q92508	PIEZ1_HUMAN	piezo-type mechanosensitive ion channel component 1	1455					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						ACCGCCTGGGCGTTGGTCACC	0.701													C|||	6	0.00119808	0.0	0.0	5008	,	,		13017	0.001		0.001	False		,,,				2504	0.0041				p.A1455T		Atlas-SNP	.											.	PIEZO1	79	.	0			c.G4363A						PASS	.						22.0	27.0	25.0					16																	88789709		691	1585	2276	SO:0001583	missense	9780	exon32			CCTGGGCGTTGGT	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.4363G>A	16.37:g.88789709C>T	ENSP00000301015:p.Ala1455Thr	19.0	0.0	0		38.0	18.0	0.473684	NM_001142864	A6NHT9|A7E2B7|Q0KKZ9	Missense_Mutation	SNP	ENST00000301015.9	37	CCDS54058.1	3|3	0.0013736263736263737|0.0013736263736263737	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0017482517482517483|0.0017482517482517483	2|2	0.002638522427440633|0.002638522427440633	C|C	20.1|20.1	3.934414|3.934414	0.73442|0.73442	.|.	.|.	ENSG00000103335|ENSG00000103335	ENST00000301015|ENST00000451779	T|.	0.73047|.	-0.71|.	5.1|5.1	4.09|4.09	0.47781|0.47781	.|.	0.200054|.	0.41396|.	D|.	0.000890|.	T|T	0.57519|0.57519	0.2059|0.2059	L|L	0.48362|0.48362	1.52|1.52	0.80722|0.80722	D|D	1|1	B|.	0.31859|.	0.343|.	B|.	0.21546|.	0.035|.	T|T	0.53308|0.53308	-0.8457|-0.8457	10|5	0.13853|.	T|.	0.58|.	-40.0355|-40.0355	9.4442|9.4442	0.38688|0.38688	0.0:0.7677:0.1478:0.0845|0.0:0.7677:0.1478:0.0845	.|.	1455|.	Q92508|.	PIEZ1_HUMAN|.	T|H	1455|1400	ENSP00000301015:A1455T|.	ENSP00000301015:A1455T|.	A|R	-|-	1|2	0|0	FAM38A|FAM38A	87317210|87317210	0.558000|0.558000	0.26554|0.26554	0.801000|0.801000	0.32222|0.32222	0.978000|0.978000	0.69477|0.69477	1.004000|1.004000	0.29822|0.29822	2.545000|2.545000	0.85829|0.85829	0.561000|0.561000	0.74099|0.74099	GCC|CGC	C|0.999;T|0.001	0.001	strong		0.701	PIEZO1-001	NOVEL	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000345699.4	NM_014745	
DYTN	391475	hgsc.bcm.edu	37	2	207564537	207564537	+	Silent	SNP	C	C	T	rs113447424	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:207564537C>T	ENST00000452335.2	-	7	749	c.633G>A	c.(631-633)ccG>ccA	p.P211P	DYTN_ENST00000477734.1_5'UTR|Y_RNA_ENST00000384589.1_RNA	NM_001093730.1	NP_001087199.1	A2CJ06	DYTN_HUMAN	dystrotelin	211						plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(6)|lung(24)|ovary(1)|upper_aerodigestive_tract(1)	36				LUSC - Lung squamous cell carcinoma(261;0.082)|Epithelial(149;0.129)|Lung(261;0.153)		GGTGGCAGGTCGGGAGCCACA	0.532													C|||	16	0.00319489	0.0076	0.0058	5008	,	,		16997	0.0		0.002	False		,,,				2504	0.0				p.P211P		Atlas-SNP	.											DYTN,medulla,primitive_neuroectodermal_tumour-medulloblastoma,-1,1	DYTN	168	1	0			c.G633A						scavenged	.	C		46,3908		1,44,1932	70.0	76.0	74.0		633	-11.8	0.0	2	dbSNP_132	74	52,8280		0,52,4114	no	coding-synonymous	DYTN	NM_001093730.1		1,96,6046	TT,TC,CC		0.6241,1.1634,0.7977		211/579	207564537	98,12188	1977	4166	6143	SO:0001819	synonymous_variant	391475	exon7			GCAGGTCGGGAGC	ABF55377	CCDS46502.1	2q33.3	2007-01-22			ENSG00000232125	ENSG00000232125			23279	protein-coding gene	gene with protein product						17233888	Standard	NM_001093730		Approved		uc002vbr.1	A2CJ06	OTTHUMG00000154729	ENST00000452335.2:c.633G>A	2.37:g.207564537C>T		125.0	1.0	0.008		146.0	71.0	0.486301	NM_001093730		Silent	SNP	ENST00000452335.2	37	CCDS46502.1																																																																																			C|0.997;T|0.003	0.003	strong		0.532	DYTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336799.1		
KCNK17	89822	hgsc.bcm.edu	37	6	39267230	39267230	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:39267230G>A	ENST00000373231.4	-	5	1204	c.972C>T	c.(970-972)caC>caT	p.H324H	KCNK17_ENST00000453413.2_3'UTR	NM_031460.3	NP_113648.2	Q96T54	KCNKH_HUMAN	potassium channel, subfamily K, member 17	324					potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)			endometrium(1)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|skin(2)	14						aGCCTGCAGCGTGAGCAGAAG	0.547																																					p.H324H		Atlas-SNP	.											.	KCNK17	61	.	0			c.C972T						PASS	.						68.0	60.0	63.0					6																	39267230		2203	4300	6503	SO:0001819	synonymous_variant	89822	exon5			TGCAGCGTGAGCA	AF358910	CCDS4842.1, CCDS47419.1	6p21	2012-03-07			ENSG00000124780	ENSG00000124780		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	14465	protein-coding gene	gene with protein product		607370				16382106	Standard	NM_031460		Approved	K2p17.1, TALK-2, TALK2, TASK4, TASK-4	uc003ooo.3	Q96T54	OTTHUMG00000014646	ENST00000373231.4:c.972C>T	6.37:g.39267230G>A		82.0	0.0	0		72.0	43.0	0.597222	NM_031460	E9PB46|Q5TCF4|Q8TAW4|Q9BXD1|Q9H592	Silent	SNP	ENST00000373231.4	37	CCDS4842.1																																																																																			.	.	none		0.547	KCNK17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040453.2	NM_031460	
HEXDC	284004	hgsc.bcm.edu	37	17	80393704	80393704	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:80393704T>C	ENST00000327949.9	+	5	598	c.587T>C	c.(586-588)gTg>gCg	p.V196A	HEXDC_ENST00000577944.1_Missense_Mutation_p.V196A|HEXDC_ENST00000337014.6_Missense_Mutation_p.V196A			Q8WVB3	HEXDC_HUMAN	hexosaminidase (glycosyl hydrolase family 20, catalytic domain) containing	196					carbohydrate metabolic process (GO:0005975)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	beta-N-acetylhexosaminidase activity (GO:0004563)			breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|lung(7)|ovary(1)|prostate(1)|skin(1)	16	Breast(20;0.00106)|all_neural(118;0.0804)		OV - Ovarian serous cystadenocarcinoma(97;0.0143)|BRCA - Breast invasive adenocarcinoma(99;0.0369)			ACACCCCTGGTGTGGGACGAC	0.682																																					p.V196A		Atlas-SNP	.											.	HEXDC	43	.	0			c.T587C						PASS	.						50.0	60.0	57.0					17																	80393704		2060	4155	6215	SO:0001583	missense	284004	exon6			CCCTGGTGTGGGA	AK074405	CCDS42402.1	17q25.3	2011-12-19			ENSG00000169660	ENSG00000169660			26307	protein-coding gene	gene with protein product						12477932	Standard	NM_173620		Approved	FLJ23825	uc002kev.4	Q8WVB3		ENST00000327949.9:c.587T>C	17.37:g.80393704T>C	ENSP00000332634:p.Val196Ala	30.0	0.0	0		42.0	15.0	0.357143	NM_173620	B7UUP6|Q8IYN4|Q8TE81	Missense_Mutation	SNP	ENST00000327949.9	37		.	.	.	.	.	.	.	.	.	.	T	10.28	1.306572	0.23736	.	.	ENSG00000169660	ENST00000337014;ENST00000327949	D;D	0.95821	-3.82;-3.82	5.72	4.65	0.58169	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycoside hydrolase, family 20, catalytic core (1);	0.286925	0.43110	N	0.000601	D	0.87474	0.6186	N	0.05592	-0.015	0.36187	D	0.849809	B;B	0.22276	0.027;0.067	B;B	0.20955	0.026;0.032	D	0.83518	0.0084	10	0.30854	T	0.27	-18.7938	8.2399	0.31654	0.0:0.152:0.0:0.848	.	196;196	Q8WVB3;Q8WVB3-2	HEXDC_HUMAN;.	A	196	ENSP00000337854:V196A;ENSP00000332634:V196A	ENSP00000332634:V196A	V	+	2	0	HEXDC	77986993	1.000000	0.71417	1.000000	0.80357	0.289000	0.27227	4.183000	0.58317	0.995000	0.38917	-0.376000	0.06991	GTG	.	.	none		0.682	HEXDC-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000443513.1	NM_173620	
HTR3C	170572	hgsc.bcm.edu	37	3	183777328	183777328	+	Silent	SNP	C	C	T	rs138181384	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:183777328C>T	ENST00000318351.1	+	7	859	c.825C>T	c.(823-825)agC>agT	p.S275S		NM_130770.2	NP_570126.2	Q8WXA8	5HT3C_HUMAN	5-hydroxytryptamine (serotonin) receptor 3C, ionotropic	275					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	extracellular ligand-gated ion channel activity (GO:0005230)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(1)|prostate(1)|skin(2)|stomach(2)	32	all_cancers(143;2.33e-10)|Ovarian(172;0.0303)		Epithelial(37;1.74e-35)|OV - Ovarian serous cystadenocarcinoma(80;3.11e-22)		Ergoloid mesylate(DB01049)	CAGCAGAGAGCGAGAATCGTG	0.547													C|||	3	0.000599042	0.0	0.0	5008	,	,		17250	0.002		0.001	False		,,,				2504	0.0				p.S275S		Atlas-SNP	.											.	HTR3C	65	.	0			c.C825T						PASS	.	C		0,4406		0,0,2203	150.0	133.0	139.0		825	-3.0	0.0	3	dbSNP_134	139	5,8595		0,5,4295	no	coding-synonymous	HTR3C	NM_130770.2		0,5,6498	TT,TC,CC		0.0581,0.0,0.0384		275/448	183777328	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	170572	exon7			AGAGAGCGAGAAT	AF459285	CCDS3250.1	3q27	2012-05-22	2012-02-03		ENSG00000178084	ENSG00000178084		"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	24003	protein-coding gene	gene with protein product		610121	"""5-hydroxytryptamine (serotonin) receptor 3, family member C"""			12801637, 15157181	Standard	NM_130770		Approved		uc003fmk.3	Q8WXA8	OTTHUMG00000156862	ENST00000318351.1:c.825C>T	3.37:g.183777328C>T		122.0	0.0	0		134.0	44.0	0.328358	NM_130770	A2RRR5	Silent	SNP	ENST00000318351.1	37	CCDS3250.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	HTR3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346296.1	NM_130770	
ZBTB7B	51043	hgsc.bcm.edu	37	1	154987363	154987363	+	Missense_Mutation	SNP	G	G	T	rs145349387	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:154987363G>T	ENST00000368426.3	+	3	364	c.227G>T	c.(226-228)gGt>gTt	p.G76V	ZBTB7B_ENST00000417934.2_Missense_Mutation_p.G110V|ZBTB7B_ENST00000487542.1_3'UTR|ZBTB7B_ENST00000535420.1_Missense_Mutation_p.G76V|ZBTB7B_ENST00000292176.2_Missense_Mutation_p.G76V	NM_001256455.1	NP_001243384.1	O15156	ZBT7B_HUMAN	zinc finger and BTB domain containing 7B	76	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				cell differentiation (GO:0030154)|ectoderm development (GO:0007398)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			endometrium(4)|kidney(1)|large_intestine(2)|liver(1)|lung(14)|ovary(1)|prostate(3)|skin(3)	29	all_epithelial(22;2.77e-30)|all_lung(78;4.1e-28)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		BRCA - Breast invasive adenocarcinoma(34;0.00034)			GGGGCCGGGGGTAGCGGGACG	0.622													G|||	7	0.00139776	0.0	0.0101	5008	,	,		15973	0.0		0.0	False		,,,				2504	0.0				p.G110V		Atlas-SNP	.											.	ZBTB7B	69	.	0			c.G329T						PASS	.	G	VAL/GLY	0,4406		0,0,2203	33.0	39.0	37.0		227	3.7	0.9	1	dbSNP_134	37	14,8586	8.4+/-32.0	0,14,4286	yes	missense	ZBTB7B	NM_015872.2	109	0,14,6489	TT,TG,GG		0.1628,0.0,0.1076	benign	76/540	154987363	14,12992	2203	4300	6503	SO:0001583	missense	51043	exon4			CCGGGGGTAGCGG	AF007833	CCDS1081.1, CCDS58030.1	1q21.2	2013-01-08		2005-04-07	ENSG00000160685	ENSG00000160685		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	18668	protein-coding gene	gene with protein product	"""zinc finger and BTB domain containing 15"""	607646	"""zinc finger protein 67 homolog (mouse)"""	ZFP67		9370309, 7937772	Standard	NR_045515		Approved	ZBTB15, c-Krox, hcKrox, ZNF857B	uc010peq.3	O15156	OTTHUMG00000037414	ENST00000368426.3:c.227G>T	1.37:g.154987363G>T	ENSP00000357411:p.Gly76Val	50.0	0.0	0		77.0	30.0	0.38961	NM_001252406	B4E3K5|D3DV83|J3KQQ3|Q68DR2|Q96EP2	Missense_Mutation	SNP	ENST00000368426.3	37	CCDS1081.1	3	0.0013736263736263737	0	0.0	3	0.008287292817679558	0	0.0	0	0.0	G	8.561	0.877867	0.17395	0.0	0.001628	ENSG00000160685	ENST00000535420;ENST00000368426;ENST00000417934;ENST00000292176	T;T;T;T	0.10099	2.96;2.96;2.91;2.96	3.66	3.66	0.41972	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.847359	0.09620	N	0.777684	T	0.10380	0.0254	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;0.998;1.0	D;D;D	0.76071	0.987;0.966;0.987	T	0.24905	-1.0147	10	0.39692	T	0.17	.	10.7167	0.46017	0.0:0.0:1.0:0.0	.	76;76;110	A8K6F4;O15156;B4E3K5	.;ZBT7B_HUMAN;.	V	76;76;110;76	ENSP00000438647:G76V;ENSP00000357411:G76V;ENSP00000406286:G110V;ENSP00000292176:G76V	ENSP00000292176:G76V	G	+	2	0	ZBTB7B	153253987	0.978000	0.34361	0.893000	0.35052	0.005000	0.04900	0.651000	0.24873	1.867000	0.54127	0.455000	0.32223	GGT	G|0.999;T|0.001	0.001	strong		0.622	ZBTB7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091083.1	NM_015872	
DDX58	23586	hgsc.bcm.edu	37	9	32481339	32481339	+	Splice_Site	SNP	C	C	T	rs61752945	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:32481339C>T	ENST00000379883.2	-	11	1794	c.1637G>A	c.(1636-1638)cGg>cAg	p.R546Q	DDX58_ENST00000379882.1_Splice_Site_p.R501Q|DDX58_ENST00000545044.1_Splice_Site_p.R343Q|DDX58_ENST00000542096.1_Splice_Site_p.R475Q|DDX58_ENST00000379868.1_Splice_Site_p.R343Q	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	546	Interaction with ZC3HAV1.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		GGAACGTACCCGCAAATGTGA	0.443													C|||	57	0.0113818	0.0204	0.0101	5008	,	,		17585	0.0		0.0089	False		,,,				2504	0.0143				p.R546Q		Atlas-SNP	.											DDX58,colon,carcinoma,-1,1	DDX58	82	1	0			c.G1637A						scavenged	.	C	GLN/ARG	83,4323	70.3+/-108.2	1,81,2121	139.0	117.0	124.0		1637	3.9	1.0	9	dbSNP_129	124	113,8487	59.8+/-121.6	1,111,4188	yes	missense-near-splice	DDX58	NM_014314.3	43	2,192,6309	TT,TC,CC		1.314,1.8838,1.507	probably-damaging	546/926	32481339	196,12810	2203	4300	6503	SO:0001630	splice_region_variant	23586	exon11			CGTACCCGCAAAT	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.1638+1G>A	9.37:g.32481339C>T		88.0	1.0	0.0113636		78.0	38.0	0.487179	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Missense_Mutation	SNP	ENST00000379883.2	37	CCDS6526.1	21	0.009615384615384616	11	0.022357723577235773	4	0.011049723756906077	0	0.0	6	0.0079155672823219	C	24.3	4.511527	0.85389	0.018838	0.01314	ENSG00000107201	ENST00000379882;ENST00000379883;ENST00000379868;ENST00000542096;ENST00000545044	T;T;T;T;T	0.53857	0.6;0.6;0.6;0.6;0.6	4.77	3.87	0.44632	.	0.000000	0.64402	D	0.000002	T	0.59810	0.2221	M	0.88775	2.98	0.45284	D	0.998289	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	1.0;0.995;0.952;0.985	T	0.70561	-0.4838	10	0.30078	T	0.28	-5.8222	12.4045	0.55432	0.0:0.915:0.0:0.085	rs61752945	343;501;475;546	F5H5W6;O95786-2;B3KWW1;O95786	.;.;.;DDX58_HUMAN	Q	501;546;343;475;343	ENSP00000369212:R501Q;ENSP00000369213:R546Q;ENSP00000369197:R343Q;ENSP00000442160:R475Q;ENSP00000443055:R343Q	ENSP00000369197:R343Q	R	-	2	0	DDX58	32471339	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	2.447000	0.44917	1.308000	0.44962	0.655000	0.94253	CGG	C|0.987;T|0.013	0.013	strong		0.443	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	Missense_Mutation
JAG2	3714	hgsc.bcm.edu	37	14	105615514	105615514	+	Silent	SNP	G	G	A	rs368778866		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:105615514G>A	ENST00000331782.3	-	13	2149	c.1746C>T	c.(1744-1746)gcC>gcT	p.A582A	JAG2_ENST00000347004.2_Silent_p.A544A	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	582	EGF-like 10; atypical. {ECO:0000255|PROSITE-ProRule:PRU00076}.				auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		CACCTCTGCAGGCCCCGCCAG	0.657																																					p.A582A		Atlas-SNP	.											.	JAG2	69	.	0			c.C1746T						PASS	.	G	,	0,4400		0,0,2200	43.0	50.0	47.0		1746,1632	1.0	1.0	14		47	2,8578		0,2,4288	no	coding-synonymous,coding-synonymous	JAG2	NM_002226.3,NM_145159.1	,	0,2,6488	AA,AG,GG		0.0233,0.0,0.0154	,	582/1239,544/1201	105615514	2,12978	2200	4290	6490	SO:0001819	synonymous_variant	3714	exon13			TCTGCAGGCCCCG	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1746C>T	14.37:g.105615514G>A		52.0	0.0	0		103.0	53.0	0.514563	NM_002226	Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	CCDS9998.1																																																																																			.	.	weak		0.657	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
KCNK12	56660	hgsc.bcm.edu	37	2	47748388	47748388	+	Silent	SNP	G	G	A	rs115862926	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:47748388G>A	ENST00000327876.4	-	2	1558	c.951C>T	c.(949-951)tgC>tgT	p.C317C	MSH2_ENST00000461394.1_Intron	NM_022055.1	NP_071338.1	Q9HB15	KCNKC_HUMAN	potassium channel, subfamily K, member 12	317						integral component of membrane (GO:0016021)	potassium channel activity (GO:0005267)|voltage-gated ion channel activity (GO:0005244)	p.0?(2)|p.?(2)		NS(1)|endometrium(1)|lung(3)|ovary(1)	6		all_hematologic(82;0.0495)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGCGCGCGCAGCAGCGGCAGC	0.697													G|||	3	0.000599042	0.0	0.0014	5008	,	,		11033	0.0		0.001	False		,,,				2504	0.001				p.C317C		Atlas-SNP	.											.	KCNK12	11	.	4	Whole gene deletion(2)|Unknown(2)	haematopoietic_and_lymphoid_tissue(3)|prostate(1)	c.C951T						PASS	.	G		5,4319		0,5,2157	13.0	15.0	14.0		951	3.4	1.0	2	dbSNP_132	14	15,8443		0,15,4214	no	coding-synonymous	KCNK12	NM_022055.1		0,20,6371	AA,AG,GG		0.1773,0.1156,0.1565		317/431	47748388	20,12762	2162	4229	6391	SO:0001819	synonymous_variant	56660	exon2			CGCGCAGCAGCGG	AF287302	CCDS1835.1	2p16.3	2012-03-07			ENSG00000184261	ENSG00000184261		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6274	protein-coding gene	gene with protein product		607366				11060316	Standard	NM_022055		Approved	THIK-2, THIK2, K2p12.1	uc002rwb.3	Q9HB15	OTTHUMG00000129131	ENST00000327876.4:c.951C>T	2.37:g.47748388G>A		16.0	0.0	0		19.0	12.0	0.631579	NM_022055		Silent	SNP	ENST00000327876.4	37	CCDS1835.1																																																																																			G|0.998;A|0.002	0.002	strong		0.697	KCNK12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251182.2	NM_022055	
PRRG2	5639	hgsc.bcm.edu	37	19	50091763	50091763	+	Missense_Mutation	SNP	G	G	A	rs117225796	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:50091763G>A	ENST00000246794.5	+	5	480	c.311G>A	c.(310-312)cGa>cAa	p.R104Q	PRRG2_ENST00000596700.1_Intron	NM_000951.2	NP_000942.1	O14669	TMG2_HUMAN	proline rich Gla (G-carboxyglutamic acid) 2	104						extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			lung(1)|skin(1)|soft_tissue(1)	3		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.196)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00295)|GBM - Glioblastoma multiforme(134;0.0121)		GGGCGTGGACGAGTGGATGTG	0.607													G|||	16	0.00319489	0.0	0.0029	5008	,	,		17535	0.0		0.0089	False		,,,				2504	0.0051				p.R104Q		Atlas-SNP	.											.	PRRG2	13	.	0			c.G311A						PASS	.	G	GLN/ARG	4,4398		0,4,2197	35.0	29.0	31.0		311	2.4	0.2	19	dbSNP_132	31	68,8532		0,68,4232	yes	missense	PRRG2	NM_000951.2	43	0,72,6429	AA,AG,GG		0.7907,0.0909,0.5538	benign	104/203	50091763	72,12930	2201	4300	6501	SO:0001583	missense	5639	exon5			GTGGACGAGTGGA		CCDS12773.1	19q13.33	2008-02-05	2004-05-27						9470	protein-coding gene	gene with protein product		604429	"""proline-rich Gla (G-carboxyglutamic acid) polypeptide 2"""			9256434	Standard	NM_000951		Approved	PRGP2	uc002pon.3	O14669		ENST00000246794.5:c.311G>A	19.37:g.50091763G>A	ENSP00000246794:p.Arg104Gln	58.0	0.0	0		62.0	37.0	0.596774	NM_000951	Q6IBF8	Missense_Mutation	SNP	ENST00000246794.5	37	CCDS12773.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	10.82	1.459638	0.26248	9.09E-4	0.007907	ENSG00000126460	ENST00000246794;ENST00000543867	D	0.99773	-6.72	5.62	2.36	0.29203	Gamma-carboxyglutamic acid-rich (GLA) domain (1);	0.544550	0.17501	N	0.171991	D	0.98061	0.9361	L	0.50333	1.59	0.09310	N	1	B;B	0.20052	0.028;0.041	B;B	0.13407	0.009;0.002	D	0.97650	1.0154	10	0.23302	T	0.38	-7.5056	6.9565	0.24574	0.276:0.0:0.724:0.0	.	81;104	F5GZ13;O14669	.;TMG2_HUMAN	Q	104;81	ENSP00000246794:R104Q	ENSP00000246794:R104Q	R	+	2	0	PRRG2	54783575	0.740000	0.28207	0.163000	0.22734	0.416000	0.31233	1.066000	0.30604	0.738000	0.32606	0.563000	0.77884	CGA	G|0.995;A|0.005	0.005	strong		0.607	PRRG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465257.1	NM_000951	
KRT16	3868	hgsc.bcm.edu	37	17	39767731	39767731	+	Missense_Mutation	SNP	G	G	A	rs148173278	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:39767731G>A	ENST00000301653.4	-	3	701	c.637C>T	c.(637-639)Cgg>Tgg	p.R213W		NM_005557.3	NP_005548.2	P08779	K1C16_HUMAN	keratin 16	213	Coil 1B.|Rod.				aging (GO:0007568)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|epidermis development (GO:0008544)|hair cycle (GO:0042633)|intermediate filament cytoskeleton organization (GO:0045104)|negative regulation of cell migration (GO:0030336)	cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	23		Breast(137;0.000307)				ACAGTCTGCCGCAGGGCCAGT	0.637													g|||	10	0.00199681	0.0076	0.0	5008	,	,		19186	0.0		0.0	False		,,,				2504	0.0				p.R213W		Atlas-SNP	.											.	KRT16	45	.	0			c.C637T						PASS	.	G	TRP/ARG	34,4372	38.4+/-70.7	0,34,2169	47.0	48.0	48.0		637	0.3	1.0	17	dbSNP_134	48	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KRT16	NM_005557.3	101	0,35,6468	AA,AG,GG		0.0116,0.7717,0.2691	probably-damaging	213/474	39767731	35,12971	2203	4300	6503	SO:0001583	missense	3868	exon3			TCTGCCGCAGGGC	S79867	CCDS11401.1	17q21.2	2013-01-16	2008-08-01		ENSG00000186832	ENSG00000186832		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6423	protein-coding gene	gene with protein product	"""focal non-epidermolytic palmoplantar keratoderma"""	148067				2451124, 16831889	Standard	NM_005557		Approved	NEPPK	uc002hxg.4	P08779	OTTHUMG00000133495	ENST00000301653.4:c.637C>T	17.37:g.39767731G>A	ENSP00000301653:p.Arg213Trp	128.0	0.0	0		147.0	70.0	0.47619	NM_005557	A8K488|P30654|Q16402|Q9UBG8	Missense_Mutation	SNP	ENST00000301653.4	37	CCDS11401.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	17.20	3.329471	0.60743	0.007717	1.16E-4	ENSG00000186832	ENST00000301653	D	0.92099	-2.97	4.84	0.345	0.16011	Filament (1);	0.000000	0.47852	D	0.000203	D	0.95567	0.8559	H	0.98199	4.17	0.50171	D	0.999858	D	0.89917	1.0	D	0.85130	0.997	D	0.93019	0.6438	10	0.87932	D	0	.	6.7407	0.23435	0.141:0.0:0.6081:0.251	.	213	P08779	K1C16_HUMAN	W	213	ENSP00000301653:R213W	ENSP00000301653:R213W	R	-	1	2	KRT16	37021257	1.000000	0.71417	0.999000	0.59377	0.584000	0.36387	2.574000	0.46016	0.338000	0.23692	0.561000	0.74099	CGG	G|0.997;A|0.003	0.003	strong		0.637	KRT16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257408.1	NM_005557	
MED22	6837	hgsc.bcm.edu	37	9	136208442	136208442	+	Silent	SNP	C	C	T	rs78711238	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr9:136208442C>T	ENST00000491289.1	-	5	1097	c.516G>A	c.(514-516)gcG>gcA	p.A172A	MED22_ENST00000343730.5_Silent_p.A172A|MED22_ENST00000344469.5_3'UTR|MED22_ENST00000471524.1_5'Flank|MED22_ENST00000476080.1_3'UTR			Q15528	MED22_HUMAN	mediator complex subunit 22	172						cytoplasm (GO:0005737)|mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			endometrium(1)|large_intestine(1)|ovary(1)|urinary_tract(1)	4				OV - Ovarian serous cystadenocarcinoma(145;1.14e-06)|Epithelial(140;8.2e-06)|all cancers(34;6.94e-05)		GCTCCGGGGACGCCAGCAGAG	0.677													C|||	37	0.00738818	0.0038	0.0043	5008	,	,		15768	0.0		0.0258	False		,,,				2504	0.0031				p.A172A		Atlas-SNP	.											.	MED22	13	.	0			c.G516A						PASS	.	C	,	25,4381	31.7+/-61.6	0,25,2178	32.0	35.0	34.0		516,	-5.3	0.4	9	dbSNP_133	34	122,8478	62.1+/-124.0	1,120,4179	no	coding-synonymous,utr-3	MED22	NM_133640.3,NM_181491.1	,	1,145,6357	TT,TC,CC		1.4186,0.5674,1.1302	,	172/201,	136208442	147,12859	2203	4300	6503	SO:0001819	synonymous_variant	6837	exon5			CGGGGACGCCAGC		CCDS6963.1, CCDS6964.1	9q34.1	2008-02-05	2007-07-30	2007-07-30	ENSG00000148297	ENSG00000148297			11477	protein-coding gene	gene with protein product		185641	"""surfeit 5"""	SURF5		8499913, 15175163	Standard	NM_133640		Approved	Med24	uc004cdc.3	Q15528	OTTHUMG00000020869	ENST00000491289.1:c.516G>A	9.37:g.136208442C>T		120.0	0.0	0		133.0	62.0	0.466165	NM_133640	B3KW83|B3KWX4|O76072|Q5T8U0	Silent	SNP	ENST00000491289.1	37	CCDS6963.1																																																																																			C|0.988;T|0.012	0.012	strong		0.677	MED22-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054898.2	NM_133640	
EP300	2033	hgsc.bcm.edu	37	22	41574383	41574383	+	Missense_Mutation	SNP	A	A	C	rs1046088	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:41574383A>C	ENST00000263253.7	+	31	7887	c.6668A>C	c.(6667-6669)cAg>cCg	p.Q2223P	RP1-85F18.6_ENST00000415054.1_RNA|RP1-85F18.5_ENST00000420537.1_RNA	NM_001429.3	NP_001420.2	Q09472	EP300_HUMAN	E1A binding protein p300	2223	Interaction with NCOA2.		Q -> P (in dbSNP:rs1046088). {ECO:0000269|PubMed:7523245}.		apoptotic process (GO:0006915)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|circadian rhythm (GO:0007623)|G2/M transition of mitotic cell cycle (GO:0000086)|heart development (GO:0007507)|histone H2B acetylation (GO:0043969)|histone H4 acetylation (GO:0043967)|innate immune response (GO:0045087)|internal peptidyl-lysine acetylation (GO:0018393)|internal protein amino acid acetylation (GO:0006475)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|lung development (GO:0030324)|mitotic cell cycle (GO:0000278)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of protein binding (GO:0032092)|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 type I interferon production (GO:0032481)|regulation of androgen receptor signaling pathway (GO:0060765)|regulation of cell cycle (GO:0051726)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|regulation of tubulin deacetylation (GO:0090043)|response to estrogen (GO:0043627)|response to hypoxia (GO:0001666)|skeletal muscle tissue development (GO:0007519)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|activating transcription factor binding (GO:0033613)|androgen receptor binding (GO:0050681)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0004468)|nuclear hormone receptor binding (GO:0035257)|pre-mRNA intronic binding (GO:0097157)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|transferase activity, transferring acyl groups (GO:0016746)|zinc ion binding (GO:0008270)			NS(2)|breast(11)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(31)|kidney(5)|large_intestine(31)|liver(2)|lung(33)|ovary(2)|pancreas(4)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(16)	171						CCACCACAGCAGCAGCAGCGG	0.577			"""T,  N, F, Mis, O"""	"""MLL, RUNXBP2"""	"""colorectal, breast, pancreatic, AML, ALL, DLBCL"""				Rubinstein-Taybi syndrome				A|||	57	0.0113818	0.0015	0.0173	5008	,	,		21238	0.0		0.0388	False		,,,				2504	0.0041				p.Q2223P		Atlas-SNP	.		Rec	yes		22	22q13	2033	300 kd E1A-Binding protein gene		"""L, E"""	.	EP300	367	.	0			c.A6668C						PASS	.	A	PRO/GLN	25,4381	32.6+/-62.9	0,25,2178	60.0	60.0	60.0		6668	3.3	1.0	22	dbSNP_86	60	312,8288	111.4+/-171.7	5,302,3993	yes	missense	EP300	NM_001429.3	76	5,327,6171	CC,CA,AA		3.6279,0.5674,2.5911	benign	2223/2415	41574383	337,12669	2203	4300	6503	SO:0001583	missense	2033	exon31	Familial Cancer Database	Broad Thumb-Hallux syndrome	CACAGCAGCAGCA	U01877	CCDS14010.1	22q13.2	2011-07-01			ENSG00000100393	ENSG00000100393		"""Chromatin-modifying enzymes / K-acetyltransferases"""	3373	protein-coding gene	gene with protein product	"""histone acetyltransferase p300"""	602700				7523245	Standard	NM_001429		Approved	p300, KAT3B	uc003azl.4	Q09472	OTTHUMG00000150937	ENST00000263253.7:c.6668A>C	22.37:g.41574383A>C	ENSP00000263253:p.Gln2223Pro	91.0	0.0	0		108.0	43.0	0.398148	NM_001429	B1AKC2	Missense_Mutation	SNP	ENST00000263253.7	37	CCDS14010.1	42	0.019230769230769232	2	0.0040650406504065045	7	0.019337016574585635	0	0.0	33	0.04353562005277045	A	7.129	0.579572	0.13686	0.005674	0.036279	ENSG00000100393	ENST00000263253	D	0.84944	-1.92	5.5	3.27	0.37495	.	0.532986	0.15322	N	0.268513	T	0.45337	0.1337	N	0.22421	0.69	0.39836	D	0.973045	B	0.02656	0.0	B	0.01281	0.0	T	0.58561	-0.7615	10	0.27082	T	0.32	.	12.1846	0.54231	0.7172:0.2828:0.0:0.0	rs1046088;rs60456996;rs1046088	2223	Q09472	EP300_HUMAN	P	2223	ENSP00000263253:Q2223P	ENSP00000263253:Q2223P	Q	+	2	0	EP300	39904329	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.250000	0.58772	0.920000	0.36970	0.533000	0.62120	CAG	A|0.977;C|0.023	0.023	strong		0.577	EP300-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320600.1	NM_001429	
ANGPTL4	51129	hgsc.bcm.edu	37	19	8431131	8431131	+	Missense_Mutation	SNP	C	C	G	rs547981454		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:8431131C>G	ENST00000301455.2	+	3	646	c.475C>G	c.(475-477)Cct>Gct	p.P159A	ANGPTL4_ENST00000393962.2_Missense_Mutation_p.P159A|ANGPTL4_ENST00000541807.1_5'UTR	NM_139314.1	NP_647475.1	Q9BY76	ANGL4_HUMAN	angiopoietin-like 4	159					angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|cellular lipid metabolic process (GO:0044255)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of lipoprotein lipase activity (GO:0051005)|positive regulation of angiogenesis (GO:0045766)|protein homooligomerization (GO:0051260)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)|triglyceride homeostasis (GO:0070328)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	enzyme inhibitor activity (GO:0004857)			large_intestine(1)|lung(1)|ovary(2)|skin(2)	6						GGTGGCCAAGCCTGCCCGAAG	0.652																																					p.P159A		Atlas-SNP	.											.	ANGPTL4	21	.	0			c.C475G						PASS	.						83.0	85.0	84.0					19																	8431131		2203	4300	6503	SO:0001583	missense	51129	exon3			GCCAAGCCTGCCC	AF202636	CCDS12200.1, CCDS42493.1	19p13.3	2013-10-07				ENSG00000167772		"""Fibrinogen C domain containing"""	16039	protein-coding gene	gene with protein product	"""fasting-induced adipose factor"", ""hepatic angiopoietin-related protein"", ""PPARG angiopoietin related protein"", ""hepatic fibrinogen/angiopoietin-related protein"", ""peroxisome proliferator-activated receptor (PPAR) gamma induced angiopoietin-related protein"", ""angiopoietin-related protein 4"""	605910				10698685, 10866690, 23960078	Standard	NM_139314		Approved	pp1158, PGAR, ARP4, HFARP, FIAF, NL2	uc002mjq.1	Q9BY76		ENST00000301455.2:c.475C>G	19.37:g.8431131C>G	ENSP00000301455:p.Pro159Ala	77.0	0.0	0		64.0	25.0	0.390625	NM_001039667	A8MY84|B4E089|D6W670|F5H0I2|Q53HQ6|Q53HU1|Q6UXN0|Q9HBV4|Q9NZU4|Q9Y5B3	Missense_Mutation	SNP	ENST00000301455.2	37	CCDS12200.1	.	.	.	.	.	.	.	.	.	.	C	8.367	0.834379	0.16820	.	.	ENSG00000167772	ENST00000301455;ENST00000393962	T;T	0.54866	0.71;0.55	4.09	-1.04	0.10068	.	613.611000	0.00166	N	0.000000	T	0.28167	0.0695	N	0.08118	0	0.09310	N	0.999992	B;B	0.06786	0.001;0.001	B;B	0.09377	0.001;0.004	T	0.06463	-1.0825	10	0.25106	T	0.35	.	0.667	0.00852	0.1966:0.3829:0.1774:0.2431	.	159;159	A8MY84;Q9BY76	.;ANGL4_HUMAN	A	159	ENSP00000301455:P159A;ENSP00000377534:P159A	ENSP00000301455:P159A	P	+	1	0	ANGPTL4	8337131	0.001000	0.12720	0.004000	0.12327	0.796000	0.44982	-0.456000	0.06754	-0.190000	0.10465	0.655000	0.94253	CCT	.	.	none		0.652	ANGPTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460322.1	NM_139314	
NFATC2	4773	hgsc.bcm.edu	37	20	50092193	50092193	+	Missense_Mutation	SNP	T	T	C	rs12479626	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr20:50092193T>C	ENST00000396009.3	-	4	1556	c.1337A>G	c.(1336-1338)cAt>cGt	p.H446R	NFATC2_ENST00000414705.1_Missense_Mutation_p.H426R|NFATC2_ENST00000371564.3_Missense_Mutation_p.H446R|NFATC2_ENST00000609943.1_Missense_Mutation_p.H426R|NFATC2_ENST00000610033.1_Missense_Mutation_p.H227R|NFATC2_ENST00000609507.1_Missense_Mutation_p.H227R	NM_001258297.1|NM_173091.3	NP_001245226.1|NP_775114.1	Q13469	NFAC2_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 2	446	RHD. {ECO:0000255|PROSITE- ProRule:PRU00265}.		H -> R (in dbSNP:rs12479626).		B cell receptor signaling pathway (GO:0050853)|cell migration (GO:0016477)|cellular response to DNA damage stimulus (GO:0006974)|cytokine production (GO:0001816)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to drug (GO:0042493)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear transcription factor complex (GO:0044798)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ribonucleoprotein complex (GO:0030529)	DNA binding (GO:0003677)|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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H446R(1)	EWSR1/NFATC2(9)	breast(2)|endometrium(7)|kidney(1)|large_intestine(7)|lung(25)|ovary(2)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	53	Hepatocellular(150;0.248)					CATGTAGCCATGGAGCTGGTG	0.502													T|||	65	0.0129792	0.0023	0.0274	5008	,	,		17874	0.0387		0.0	False		,,,				2504	0.0041				p.H446R		Atlas-SNP	.											NFATC2,NS,carcinoma,0,1	NFATC2	112	1	1	Substitution - Missense(1)	stomach(1)	c.A1337G						scavenged	.	T	ARG/HIS,ARG/HIS,ARG/HIS	5,4401	8.1+/-20.4	0,5,2198	65.0	60.0	61.0		1277,1337,1337	5.4	1.0	20	dbSNP_120	61	8,8592	7.1+/-27.0	0,8,4292	yes	missense,missense,missense	NFATC2	NM_001136021.1,NM_012340.3,NM_173091.2	29,29,29	0,13,6490	CC,CT,TT		0.093,0.1135,0.1	benign,benign,benign	426/902,446/922,446/926	50092193	13,12993	2203	4300	6503	SO:0001583	missense	4773	exon4			TAGCCATGGAGCT	U43342, U43341	CCDS13437.1, CCDS33488.1, CCDS46614.1, CCDS68156.1, CCDS68157.1	20q13.2	2009-11-24			ENSG00000101096	ENSG00000101096		"""Nuclear factor of activated T-cells"""	7776	protein-coding gene	gene with protein product		600490				8202141	Standard	NM_012340		Approved	NF-ATP, NFATp, NFAT1	uc002xwd.4	Q13469	OTTHUMG00000032747	ENST00000396009.3:c.1337A>G	20.37:g.50092193T>C	ENSP00000379330:p.His446Arg	129.0	1.0	0.00775194		124.0	53.0	0.427419	NM_012340	B5B2N8|B5B2N9|B5B2P0|B5B2P2|B5B2P3|Q13468|Q5TFW7|Q5TFW8|Q9NPX6|Q9NQH3|Q9UJR2	Missense_Mutation	SNP	ENST00000396009.3	37	CCDS13437.1	34	0.015567765567765568	3	0.006097560975609756	3	0.008287292817679558	28	0.04895104895104895	0	0.0	T	23.5	4.419816	0.83559	0.001135	9.3E-4	ENSG00000101096	ENST00000371564;ENST00000396009;ENST00000371567;ENST00000414705	T;T;T	0.42900	0.96;0.96;0.96	5.44	5.44	0.79542	Rel homology (3);p53-like transcription factor, DNA-binding (1);	0.048788	0.85682	D	0.000000	T	0.04907	0.0132	N	0.08118	0	0.58432	D	0.999991	B;P;B;B	0.51351	0.114;0.944;0.068;0.068	B;P;B;B	0.44394	0.032;0.448;0.058;0.032	T	0.02691	-1.1123	10	0.29301	T	0.29	-19.6058	15.5154	0.75818	0.0:0.0:0.0:1.0	rs12479626;rs52802474;rs12479626	426;426;446;446	B5B2N9;B5B2P2;Q13469;B5B2N8	.;.;NFAC2_HUMAN;.	R	446;446;227;426	ENSP00000360619:H446R;ENSP00000379330:H446R;ENSP00000396471:H426R	ENSP00000360619:H446R	H	-	2	0	NFATC2	49525600	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	6.153000	0.71819	2.063000	0.61619	0.528000	0.53228	CAT	T|0.992;C|0.008	0.008	strong		0.502	NFATC2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079730.2	NM_012340	
AHRR	57491	hgsc.bcm.edu	37	5	434546	434546	+	Missense_Mutation	SNP	C	C	T	rs61757546	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:434546C>T	ENST00000505113.1	+	11	1747	c.1703C>T	c.(1702-1704)gCc>gTc	p.A568V	AHRR_ENST00000512529.1_Missense_Mutation_p.A414V|AHRR_ENST00000506456.1_Missense_Mutation_p.A424V|AHRR_ENST00000316418.5_Missense_Mutation_p.A586V	NM_001242412.1	NP_001229341.1	A9YTQ3	AHRR_HUMAN	aryl-hydrocarbon receptor repressor	568	Needed for transcriptional repression. {ECO:0000250}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein sumoylation (GO:0033235)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)|signal transducer activity (GO:0004871)			breast(2)|endometrium(4)|large_intestine(1)|lung(12)|prostate(1)	20			Epithelial(17;0.0011)|OV - Ovarian serous cystadenocarcinoma(19;0.00353)|all cancers(22;0.00354)|Lung(60;0.0863)			AGCCACCCAGCCACCTTCCCT	0.637													C|||	16	0.00319489	0.0	0.0029	5008	,	,		16396	0.0		0.0129	False		,,,				2504	0.001				p.A586V		Atlas-SNP	.											.	AHRR	67	.	0			c.C1757T						PASS	.	C	VAL/ALA,VAL/ALA	2,4254		0,2,2126	51.0	58.0	56.0		1703,1757	-2.3	0.0	5	dbSNP_129	56	40,8438		0,40,4199	yes	missense,missense	AHRR	NM_001242412.1,NM_020731.4	64,64	0,42,6325	TT,TC,CC		0.4718,0.047,0.3298	benign,benign	568/702,586/720	434546	42,12692	2128	4239	6367	SO:0001583	missense	57491	exon12			ACCCAGCCACCTT	AB033060	CCDS43297.1, CCDS56355.1	5p15.33	2013-05-21	2003-09-11	2003-09-12	ENSG00000063438	ENSG00000063438		"""Basic helix-loop-helix proteins"""	346	protein-coding gene	gene with protein product		606517	"""aryl hydrocarbon receptor regulator"""	AHH, AHHR		1070014, 11423533	Standard	NM_020731		Approved	KIAA1234, bHLHe77	uc003jaw.3	A9YTQ3	OTTHUMG00000162171	ENST00000505113.1:c.1703C>T	5.37:g.434546C>T	ENSP00000424601:p.Ala568Val	44.0	0.0	0		43.0	19.0	0.44186	NM_020731	A7MBN5|D6RAZ1|Q9HAZ3|Q9ULI6	Missense_Mutation	SNP	ENST00000505113.1	37	CCDS56355.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	0.008	-1.892504	0.00522	4.7E-4	0.004718	ENSG00000063438	ENST00000505113;ENST00000316418;ENST00000512529;ENST00000506456	T;T;T;T	0.20069	2.44;2.43;2.11;2.1	4.43	-2.29	0.06805	.	0.629100	0.15903	N	0.238965	T	0.03095	0.0091	N	0.01168	-0.975	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.0;0.0	T	0.39860	-0.9593	10	0.09590	T	0.72	.	5.5855	0.17272	0.1478:0.4627:0.0:0.3895	rs61757546	424;568;586	D6RE68;A9YTQ3;A9YTQ3-2	.;AHRR_HUMAN;.	V	568;586;414;424	ENSP00000424601:A568V;ENSP00000323816:A586V;ENSP00000424880:A414V;ENSP00000426932:A424V	ENSP00000323816:A586V	A	+	2	0	AHRR	487546	0.000000	0.05858	0.000000	0.03702	0.179000	0.23085	0.002000	0.13061	-0.364000	0.08088	-0.263000	0.10527	GCC	C|0.996;T|0.004	0.004	strong		0.637	AHRR-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367720.1	NM_020731	
HFE	3077	hgsc.bcm.edu	37	6	26093141	26093141	+	Missense_Mutation	SNP	G	G	A	rs1800562	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:26093141G>A	ENST00000357618.5	+	4	967	c.845G>A	c.(844-846)tGc>tAc	p.C282Y	HFE_ENST00000470149.1_Missense_Mutation_p.C279Y|HFE_ENST00000397022.3_Missense_Mutation_p.C259Y|HFE_ENST00000461397.1_Missense_Mutation_p.C268Y|HFE_ENST00000353147.5_Missense_Mutation_p.C102Y|HFE_ENST00000352392.4_Intron|HFE_ENST00000336625.8_Missense_Mutation_p.C176Y|HFE_ENST00000349999.4_Missense_Mutation_p.C194Y|HFE_ENST00000309234.6_Missense_Mutation_p.C282Y|HFE_ENST00000488199.1_Missense_Mutation_p.C180Y|HFE_ENST00000317896.7_Missense_Mutation_p.C190Y	NM_000410.3|NM_139006.2	NP_000401.1|NP_620575.1	Q30201	HFE_HUMAN	hemochromatosis	282	Alpha-3.|Ig-like C1-type.		C -> Y (in HFE1; associated with susceptibility to porphyria cutanea tarda; associated with increased serum transferrin levels; higher frequency in patients with type 2 diabetes than in controls; dbSNP:rs1800562). {ECO:0000269|PubMed:10094552, ECO:0000269|PubMed:10194428, ECO:0000269|PubMed:11069625, ECO:0000269|PubMed:11423500, ECO:0000269|PubMed:12542741, ECO:0000269|PubMed:14633868, ECO:0000269|PubMed:18157833, ECO:0000269|PubMed:8696333, ECO:0000269|PubMed:9024376, ECO:0000269|PubMed:9106528, ECO:0000269|PubMed:9620340, ECO:0000269|Ref.8}.		antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular iron ion homeostasis (GO:0006879)|cellular response to iron ion starvation (GO:0010106)|female pregnancy (GO:0007565)|hormone biosynthetic process (GO:0042446)|immune response (GO:0006955)|iron ion import into cell (GO:0097459)|multicellular organismal iron ion homeostasis (GO:0060586)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein complex assembly (GO:0006461)	apical part of cell (GO:0045177)|basal part of cell (GO:0045178)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|MHC class I protein complex (GO:0042612)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	peptide antigen binding (GO:0042605)|receptor binding (GO:0005102)			endometrium(3)|large_intestine(3)|liver(2)|lung(7)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						AGATATACGTGCCAGGTGGAG	0.547									Hemochromatosis				G|||	63	0.0125799	0.0023	0.0216	5008	,	,		19430	0.0		0.0427	False		,,,				2504	0.002				p.C282Y		Atlas-SNP	.											.	HFE	37	.	0			c.G845A	GRCh37	CM004391|CM960828	HFE	M	rs1800562	PASS	.	G	TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,TYR/CYS,	67,4339		1,65,2137	84.0	81.0	82.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	845,527,569,803,581,539,776,305,	5.3	1.0	6	dbSNP_89	82	551,8049		18,515,3767	yes	missense,missense,missense,missense,missense,missense,missense,missense,intron	HFE	NM_000410.3,NM_139003.2,NM_139004.2,NM_139006.2,NM_139007.2,NM_139008.2,NM_139009.2,NM_139010.2,NM_139011.2	194,194,194,194,194,194,194,194,	19,580,5904	AA,AG,GG	http://www.ncbi.nlm.nih.gov/pubmed?term	6.407,1.5207,4.7517	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,	282/349,176/243,190/257,268/335,194/261,180/247,259/326,102/169,	26093141	618,12388	2203	4300	6503	SO:0001583	missense	3077	exon4	Familial Cancer Database		ATACGTGCCAGGT		CCDS4578.1, CCDS4579.1, CCDS4580.1, CCDS4581.1, CCDS4582.1, CCDS47386.1, CCDS47387.1, CCDS54974.1, CCDS54975.1, CCDS75412.1	6p21.3	2014-09-17			ENSG00000010704	ENSG00000010704		"""Immunoglobulin superfamily / C1-set domain containing"""	4886	protein-coding gene	gene with protein product	"""high Fe"""	613609				3460331	Standard	XR_241893		Approved	HLA-H	uc003nfx.1	Q30201	OTTHUMG00000016348	ENST00000357618.5:c.845G>A	6.37:g.26093141G>A	ENSP00000417404:p.Cys282Tyr	152.0	0.0	0		138.0	77.0	0.557971	NM_000410	B2CKL0|O75929|O75930|O75931|Q17RT0|Q96KU5|Q96KU6|Q96KU7|Q96KU8|Q9HC64|Q9HC68|Q9HC70|Q9HC83	Missense_Mutation	SNP	ENST00000357618.5	37	CCDS4578.1	43	0.019688644688644688	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	35	0.04617414248021108	.	17.19	3.326013	0.60743	0.015207	0.06407	ENSG00000010704	ENST00000349999;ENST00000397022;ENST00000317896;ENST00000353147;ENST00000357618;ENST00000470149;ENST00000336625;ENST00000461397;ENST00000488199;ENST00000309234	D;D;D;D;D;D;D;D;D;D	0.95342	-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68;-3.68	5.35	5.35	0.76521	Immunoglobulin/major histocompatibility complex, conserved site (1);Immunoglobulin-like (1);Immunoglobulin C1-set (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000003	D	0.98557	0.9518	H	0.99143	4.445	0.80722	A	1	D;D;D;D;D;P;D;D;D	0.89917	0.982;1.0;1.0;1.0;1.0;0.951;0.996;0.993;0.961	P;D;D;D;D;P;P;D;P	0.91635	0.756;0.999;0.999;0.999;0.999;0.56;0.826;0.917;0.667	D	0.98784	1.0733	9	0.87932	D	0	.	14.7506	0.69522	0.0:0.0:1.0:0.0	rs1800562;rs4134660;rs17530654;rs58044250;rs1800562	279;102;180;190;176;268;194;259;282	Q6B0J5;Q30201-6;Q30201-4;Q30201-7;Q30201-10;Q30201-3;Q30201-2;Q30201-5;Q30201	.;.;.;.;.;.;.;.;HFE_HUMAN	Y	194;259;190;102;282;279;176;268;180;282	ENSP00000259699:C194Y;ENSP00000380217:C259Y;ENSP00000313776:C190Y;ENSP00000312342:C102Y;ENSP00000417404:C282Y;ENSP00000419725:C279Y;ENSP00000337819:C176Y;ENSP00000420802:C268Y;ENSP00000420559:C180Y;ENSP00000311698:C282Y	ENSP00000311698:C282Y	C	+	2	0	HFE	26201120	1.000000	0.71417	0.993000	0.49108	0.351000	0.29236	4.282000	0.58971	2.941000	0.99782	0.655000	0.94253	TGC	G|0.966;A|0.034	0.034	strong		0.547	HFE-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356133.1		
APC	324	hgsc.bcm.edu	37	5	112164561	112164561	+	Silent	SNP	G	G	A	rs351771	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:112164561G>A	ENST00000457016.1	+	14	2015	c.1635G>A	c.(1633-1635)gcG>gcA	p.A545A	APC_ENST00000257430.4_Silent_p.A545A|APC_ENST00000508376.2_Silent_p.A545A|CTC-554D6.1_ENST00000520401.1_Missense_Mutation_p.R41Q			P25054	APC_HUMAN	adenomatous polyposis coli	545	Leu-rich.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|axis specification (GO:0009798)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in negative regulation of apoptotic process (GO:0044336)|canonical Wnt signaling pathway involved in positive regulation of apoptotic process (GO:0044337)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to DNA damage stimulus (GO:0006974)|chromosome organization (GO:0051276)|cytoplasmic microtubule organization (GO:0031122)|dorsal/ventral pattern formation (GO:0009953)|hair follicle development (GO:0001942)|kidney development (GO:0001822)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cytokinesis (GO:0000281)|mitotic spindle assembly checkpoint (GO:0007094)|muscle cell cellular homeostasis (GO:0046716)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of odontogenesis (GO:0042483)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell division (GO:0051781)|positive regulation of cell migration (GO:0030335)|positive regulation of epithelial cell differentiation (GO:0030858)|positive regulation of microtubule polymerization (GO:0031116)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of pseudopodium assembly (GO:0031274)|protein complex assembly (GO:0006461)|proximal/distal pattern formation (GO:0009954)|regulation of attachment of spindle microtubules to kinetochore (GO:0051988)|regulation of microtubule-based process (GO:0032886)|regulation of nitrogen compound metabolic process (GO:0051171)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoclast differentiation (GO:0045670)|retina development in camera-type eye (GO:0060041)|somatic stem cell maintenance (GO:0035019)|T cell differentiation in thymus (GO:0033077)|thymus development (GO:0048538)|tight junction assembly (GO:0070830)	axonal growth cone (GO:0044295)|beta-catenin destruction complex (GO:0030877)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|kinetochore (GO:0000776)|lamellipodium (GO:0030027)|lateral plasma membrane (GO:0016328)|microtubule plus-end (GO:0035371)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	beta-catenin binding (GO:0008013)|gamma-catenin binding (GO:0045295)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|protein kinase binding (GO:0019901)|protein kinase regulator activity (GO:0019887)	p.?(1)		NS(7)|adrenal_gland(6)|biliary_tract(5)|bone(6)|breast(29)|central_nervous_system(12)|cervix(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(6)|kidney(8)|large_intestine(2768)|liver(15)|lung(39)|oesophagus(1)|ovary(12)|pancreas(27)|prostate(15)|salivary_gland(2)|skin(14)|small_intestine(34)|soft_tissue(55)|stomach(136)|thyroid(22)|upper_aerodigestive_tract(8)|urinary_tract(20)	3261		all_cancers(142;3.01e-27)|all_epithelial(76;2.3e-18)|all_hematologic(541;4.32e-09)|Ovarian(225;1.78e-06)|Lung NSC(167;0.000195)|Breast(839;0.000231)|all_lung(232;0.000247)|Colorectal(10;0.000355)|Prostate(80;0.00133)		OV - Ovarian serous cystadenocarcinoma(64;1.09e-113)|Epithelial(69;3.79e-112)|all cancers(49;1.67e-104)|BRCA - Breast invasive adenocarcinoma(61;0.00136)|COAD - Colon adenocarcinoma(37;0.00155)|Colorectal(14;0.00191)		AGGTTATTGCGAGTGTTTTGA	0.313		12	"""D, Mis, N, F, S"""		"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""	"""colorectal, pancreatic, desmoid, hepatoblastoma, glioma, other CNS"""			Turcot syndrome;Hereditary Desmoid Disease;Familial Adenomatous Polyposis	TSP Lung(16;0.13)			A|||	3336	0.666134	0.5166	0.7161	5008	,	,		17820	0.8165		0.5994	False		,,,				2504	0.7464				p.A545A	NSCLC(107;854 1218 9699 17025 28335 47076 52975)|Esophageal Squamous(32;282 584 32991 36563 39392 49665 50115)	Atlas-SNP	.	yes	Rec	yes	Adenomatous polyposis coli; Turcot syndrome	5	5q21	324	adenomatous polyposis of the colon gene		"""E, M, O"""	.	APC	4158	.	1	Unknown(1)	skin(1)	c.G1635A						PASS	.	A	,,	2321,2083	570.8+/-382.9	619,1083,500	101.0	105.0	104.0	http://omim.org/entry/114500	1635,1635,1581	4.5	1.0	5	dbSNP_79	104	5305,3295	491.5+/-373.1	1671,1963,666	no	coding-synonymous,coding-synonymous,coding-synonymous	APC	NM_000038.5,NM_001127510.2,NM_001127511.2	,,	2290,3046,1166	AA,AG,GG		38.314,47.2979,41.3565	,,	545/2844,545/2844,527/2826	112164561	7626,5378	2202	4300	6502	SO:0001819	synonymous_variant	324	exon15	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome;Familial Infiltrative Mesenteric Fibromatosis;FAP, incl.: Gardner s., Attenuated FAP, Flat Adenoma s., Oldfield s,	TATTGCGAGTGTT	M74088	CCDS4107.1	5q21-q22	2014-09-17	2008-01-08		ENSG00000134982	ENSG00000134982		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Armadillo repeat containing"""	583	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 46"""	611731	"""adenomatosis polyposis coli"""			1651563	Standard	NM_001127511		Approved	DP2, DP3, DP2.5, PPP1R46	uc003kpy.4	P25054	OTTHUMG00000128806	ENST00000457016.1:c.1635G>A	5.37:g.112164561G>A		134.0	0.0	0		111.0	111.0	1	NM_001127510	D3DT03|Q15162|Q15163|Q93042	Silent	SNP	ENST00000457016.1	37	CCDS4107.1																																																																																			G|0.388;A|0.612	0.612	strong		0.313	APC-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250738.2	NM_000038	
DDX55	57696	hgsc.bcm.edu	37	12	124086736	124086736	+	Missense_Mutation	SNP	T	T	G	rs141195308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124086736T>G	ENST00000238146.4	+	1	91	c.41T>G	c.(40-42)gTg>gGg	p.V14G	DDX55_ENST00000538744.1_Missense_Mutation_p.V14G	NM_020936.1	NP_065987.1	Q8NHQ9	DDX55_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 55	14						membrane (GO:0016020)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(3)|liver(1)|lung(4)|ovary(1)|prostate(1)|skin(1)	14	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000142)|Epithelial(86;0.000637)|all cancers(50;0.00772)		TCGCTGCCTGTGCCGCTGCAC	0.706													T|||	6	0.00119808	0.0	0.0029	5008	,	,		15400	0.0		0.004	False		,,,				2504	0.0				p.V14G		Atlas-SNP	.											DDX55,NS,lymphoid_neoplasm,0,1	DDX55	51	1	0			c.T41G						scavenged	.	T	GLY/VAL	3,4375		0,3,2186	12.0	13.0	13.0		41	3.9	0.3	12	dbSNP_134	13	25,8541		0,25,4258	yes	missense	DDX55	NM_020936.1	109	0,28,6444	GG,GT,TT		0.2919,0.0685,0.2163	benign	14/601	124086736	28,12916	2189	4283	6472	SO:0001583	missense	57696	exon1			TGCCTGTGCCGCT	AB046815	CCDS9251.1	12q24.31	2003-06-13			ENSG00000111364	ENSG00000111364		"""DEAD-boxes"""	20085	protein-coding gene	gene with protein product						10997877	Standard	NM_020936		Approved	KIAA1595	uc001ufi.3	Q8NHQ9	OTTHUMG00000168695	ENST00000238146.4:c.41T>G	12.37:g.124086736T>G	ENSP00000238146:p.Val14Gly	45.0	1.0	0.0222222		48.0	21.0	0.4375	NM_020936	Q658L6|Q8IYH0|Q9HCH7	Missense_Mutation	SNP	ENST00000238146.4	37	CCDS9251.1	8	0.003663003663003663	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	3	0.00395778364116095	T	8.130	0.782942	0.16189	6.85E-4	0.002919	ENSG00000111364	ENST00000238146;ENST00000538449;ENST00000538744	T;T	0.04234	3.95;3.67	5.03	3.89	0.44902	RNA helicase, DEAD-box type, Q motif (1);	0.578293	0.17416	N	0.175019	T	0.04679	0.0127	M	0.72894	2.215	0.80722	D	1	B	0.25850	0.136	B	0.19391	0.025	T	0.16600	-1.0397	10	0.22109	T	0.4	-20.8964	9.5249	0.39158	0.0:0.0796:0.0:0.9204	.	14	Q8NHQ9	DDX55_HUMAN	G	14	ENSP00000238146:V14G;ENSP00000443114:V14G	ENSP00000238146:V14G	V	+	2	0	DDX55	122652689	0.995000	0.38212	0.349000	0.25694	0.004000	0.04260	2.926000	0.48892	0.941000	0.37499	0.533000	0.62120	GTG	T|0.998;G|0.002	0.002	strong		0.706	DDX55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400616.2		
GLTSCR1	29998	hgsc.bcm.edu	37	19	48183748	48183748	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48183748G>A	ENST00000396720.3	+	6	1515	c.1321G>A	c.(1321-1323)Ggg>Agg	p.G441R	CTD-2571L23.8_ENST00000599924.1_lincRNA	NM_015711.3	NP_056526.3	Q9NZM4	GSCR1_HUMAN	glioma tumor suppressor candidate region gene 1	441										breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(3)|pancreas(3)|prostate(4)|skin(2)	20		all_cancers(25;1.8e-07)|all_lung(116;5.73e-06)|Lung NSC(112;9.69e-06)|all_epithelial(76;2.42e-05)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000358)|OV - Ovarian serous cystadenocarcinoma(262;0.000576)|Epithelial(262;0.0212)|GBM - Glioblastoma multiforme(486;0.0355)		gcagccccccggggcccTGAG	0.687																																					p.G441R		Atlas-SNP	.											.	GLTSCR1	79	.	0			c.G1321A						PASS	.						12.0	17.0	16.0					19																	48183748		1779	3787	5566	SO:0001583	missense	29998	exon6			CCCCCCGGGGCCC	AF182077	CCDS46134.1	19q13.3	2012-11-29			ENSG00000063169	ENSG00000063169			4332	protein-coding gene	gene with protein product		605690				10708517	Standard	NM_015711		Approved		uc002phh.4	Q9NZM4		ENST00000396720.3:c.1321G>A	19.37:g.48183748G>A	ENSP00000379946:p.Gly441Arg	14.0	0.0	0		22.0	12.0	0.545455	NM_015711	A8MW01	Missense_Mutation	SNP	ENST00000396720.3	37	CCDS46134.1	.	.	.	.	.	.	.	.	.	.	G	6.411	0.443896	0.12164	.	.	ENSG00000063169	ENST00000396720	T	0.33216	1.42	3.93	3.93	0.45458	.	.	.	.	.	T	0.25419	0.0618	N	0.14661	0.345	0.32728	N	0.50933	D	0.62365	0.991	P	0.52856	0.711	T	0.05989	-1.0852	9	0.16420	T	0.52	.	11.3225	0.49430	0.0:0.0:1.0:0.0	.	441	Q9NZM4	GSCR1_HUMAN	R	441	ENSP00000379946:G441R	ENSP00000379946:G441R	G	+	1	0	GLTSCR1	52875560	0.914000	0.31030	0.859000	0.33776	0.345000	0.29048	2.650000	0.46665	2.018000	0.59344	0.491000	0.48974	GGG	.	.	none		0.687	GLTSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465846.1	NM_015711	
PRRT4	401399	hgsc.bcm.edu	37	7	127999459	127999459	+	Missense_Mutation	SNP	G	G	A	rs145413607	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:127999459G>A	ENST00000446477.2	-	3	900	c.587C>T	c.(586-588)aCg>aTg	p.T196M	PRRT4_ENST00000535159.1_Missense_Mutation_p.T196M|PRRT4_ENST00000489835.2_Missense_Mutation_p.T196M|PRRT4_ENST00000435512.1_Missense_Mutation_p.T196M	NM_001174164.1	NP_001167635.1	C9JH25	PRRT4_HUMAN	proline-rich transmembrane protein 4	196						integral component of membrane (GO:0016021)		p.T196M(1)		endometrium(4)|prostate(1)	5						CAGGGGCAGCGTTCGATGCCC	0.652													G|||	28	0.00559105	0.0	0.0072	5008	,	,		16449	0.0		0.0199	False		,,,				2504	0.0031				p.T196M		Atlas-SNP	.											PRRT4,NS,carcinoma,0,1	PRRT4	31	1	1	Substitution - Missense(1)	endometrium(1)	c.C587T						PASS	.	G	MET/THR,MET/THR	5,1379		0,5,687	19.0	23.0	22.0		587,587	2.8	0.9	7	dbSNP_134	22	55,3127		2,51,1538	yes	missense,missense	PRRT4	NM_001174164.1,NM_001114726.2	81,81	2,56,2225	AA,AG,GG		1.7285,0.3613,1.3141	benign,benign	196/900,196/430	127999459	60,4506	692	1591	2283	SO:0001583	missense	401399	exon3			GGCAGCGTTCGAT	BC063892	CCDS47698.1, CCDS47698.2, CCDS55160.1	7q32.1	2011-10-10			ENSG00000224940	ENSG00000224940		"""Proline-rich transmembrane proteins"""	37280	protein-coding gene	gene with protein product							Standard	NM_001114726		Approved		uc022aky.1	C9JH25	OTTHUMG00000157714	ENST00000446477.2:c.587C>T	7.37:g.127999459G>A	ENSP00000415026:p.Thr196Met	69.0	0.0	0		56.0	30.0	0.535714	NM_001174164	A4D0Z9|C9JVW7	Missense_Mutation	SNP	ENST00000446477.2	37	CCDS55160.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	9.816	1.184515	0.21870	0.003613	0.017285	ENSG00000224940	ENST00000489835;ENST00000446477;ENST00000535159;ENST00000435512;ENST00000489517;ENST00000464607;ENST00000495931	.	.	.	4.97	2.78	0.32641	.	.	.	.	.	T	0.08537	0.0212	N	0.08118	0	0.09310	N	1	B;B	0.32893	0.077;0.389	B;B	0.23716	0.01;0.048	T	0.09250	-1.0683	8	0.87932	D	0	-13.8848	7.9713	0.30130	0.2241:0.0:0.7759:0.0	.	196;196	C9JH25;C9JH25-2	PRRT4_HUMAN;.	M	196	.	ENSP00000410779:T196M	T	-	2	0	PRRT4	127786695	0.137000	0.22531	0.873000	0.34254	0.521000	0.34408	1.775000	0.38584	1.115000	0.41800	0.585000	0.79938	ACG	G|0.991;A|0.009	0.009	strong		0.652	PRRT4-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001114726	
MYH9	4627	hgsc.bcm.edu	37	22	36681272	36681272	+	Missense_Mutation	SNP	T	T	C	rs141440715	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36681272T>C	ENST00000216181.5	-	38	5608	c.5378A>G	c.(5377-5379)aAg>aGg	p.K1793R	MYH9_ENST00000475726.1_5'UTR	NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	1793					actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						CTCCTGCAGCTTGACCTTAAG	0.587			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.K1793R		Atlas-SNP	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.A5378G						PASS	.	T	ARG/LYS	1,4405	2.1+/-5.4	0,1,2202	144.0	115.0	125.0		5378	5.0	1.0	22	dbSNP_134	125	3,8597	3.7+/-12.6	0,3,4297	yes	missense	MYH9	NM_002473.4	26	0,4,6499	CC,CT,TT		0.0349,0.0227,0.0308	benign	1793/1961	36681272	4,13002	2203	4300	6503	SO:0001583	missense	4627	exon38	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	TGCAGCTTGACCT		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.5378A>G	22.37:g.36681272T>C	ENSP00000216181:p.Lys1793Arg	97.0	0.0	0		122.0	60.0	0.491803	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Missense_Mutation	SNP	ENST00000216181.5	37	CCDS13927.1	.	.	.	.	.	.	.	.	.	.	T	16.04	3.011097	0.54361	2.27E-4	3.49E-4	ENSG00000100345	ENST00000337818;ENST00000397231;ENST00000216181	T	0.75154	-0.91	5.03	5.03	0.67393	Myosin tail (1);Regulator of G protein signalling superfamily (1);	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	N	0.25647	0.755	0.80722	D	1	B	0.24651	0.108	B	0.31016	0.123	T	0.56001	-0.8051	10	0.02654	T	1	.	14.7562	0.69567	0.0:0.0:0.0:1.0	.	1793	P35579	MYH9_HUMAN	R	1215;395;1793	ENSP00000216181:K1793R	ENSP00000216181:K1793R	K	-	2	0	MYH9	35011218	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.692000	0.84203	1.879000	0.54435	0.455000	0.32223	AAG	T|1.000;C|0.000	0.000	strong		0.587	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
OGDH	4967	hgsc.bcm.edu	37	7	44715599	44715599	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:44715599A>T	ENST00000222673.5	+	9	1099	c.1057A>T	c.(1057-1059)Atg>Ttg	p.M353L	OGDH_ENST00000439616.2_Missense_Mutation_p.M203L|OGDH_ENST00000444676.1_Missense_Mutation_p.M368L|OGDH_ENST00000447398.1_Missense_Mutation_p.M364L|OGDH_ENST00000543843.1_Missense_Mutation_p.M304L|OGDH_ENST00000443864.2_Missense_Mutation_p.M353L|OGDH_ENST00000449767.1_Missense_Mutation_p.M349L	NM_002541.3	NP_002532.2	Q02218	ODO1_HUMAN	oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide)	353					2-oxoglutarate metabolic process (GO:0006103)|cellular metabolic process (GO:0044237)|cellular nitrogen compound metabolic process (GO:0034641)|cerebellar cortex development (GO:0021695)|generation of precursor metabolites and energy (GO:0006091)|glycolytic process (GO:0006096)|hippocampus development (GO:0021766)|lysine catabolic process (GO:0006554)|NADH metabolic process (GO:0006734)|olfactory bulb mitral cell layer development (GO:0061034)|pyramidal neuron development (GO:0021860)|small molecule metabolic process (GO:0044281)|striatum development (GO:0021756)|succinyl-CoA metabolic process (GO:0006104)|tangential migration from the subventricular zone to the olfactory bulb (GO:0022028)|thalamus development (GO:0021794)|tricarboxylic acid cycle (GO:0006099)	mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)|oxoglutarate dehydrogenase complex (GO:0045252)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (NAD+) activity (GO:0034602)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			breast(2)|endometrium(5)|kidney(2)|large_intestine(6)|lung(13)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	36					Valproic Acid(DB00313)	CCACCTGGGCATGTATCACCG	0.547																																					p.M353L		Atlas-SNP	.											.	OGDH	145	.	0			c.A1057T						PASS	.						111.0	98.0	102.0					7																	44715599		2203	4300	6503	SO:0001583	missense	4967	exon9			CTGGGCATGTATC	D10523	CCDS34627.1, CCDS47580.1, CCDS55107.1	7p13-p11.2	2010-11-23			ENSG00000105953	ENSG00000105953	1.2.4.2		8124	protein-coding gene	gene with protein product		613022				8020988, 1542694	Standard	NM_002541		Approved	E1k	uc003tln.3	Q02218	OTTHUMG00000155304	ENST00000222673.5:c.1057A>T	7.37:g.44715599A>T	ENSP00000222673:p.Met353Leu	78.0	0.0	0		130.0	85.0	0.653846	NM_002541	B4E2U9|D3DVL0|E9PBM1|Q96DD3|Q9UDX0	Missense_Mutation	SNP	ENST00000222673.5	37	CCDS34627.1	.	.	.	.	.	.	.	.	.	.	A	17.45	3.392130	0.62066	.	.	ENSG00000105953	ENST00000439616;ENST00000443864;ENST00000449767;ENST00000447398;ENST00000444676;ENST00000222673;ENST00000543843	D;T;D;D;D;D;D	0.95724	-3.79;2.71;-3.79;-3.79;-3.79;-3.79;-3.79	5.14	5.14	0.70334	Dehydrogenase, E1 component (1);	0.000000	0.85682	D	0.000000	D	0.93582	0.7951	L	0.52905	1.665	0.58432	D	0.99999	B;B;B;B;B;B;B	0.18310	0.004;0.004;0.002;0.002;0.002;0.002;0.027	B;B;B;B;B;B;B	0.24006	0.029;0.02;0.029;0.029;0.02;0.029;0.05	D	0.91106	0.4918	10	0.37606	T	0.19	-47.9559	14.9242	0.70862	1.0:0.0:0.0:0.0	.	148;203;349;364;255;353;353	B4E3E9;E9PFG7;E9PBM1;E9PDF2;A2VCT2;Q02218;Q96DD3	.;.;.;.;.;ODO1_HUMAN;.	L	203;353;349;364;368;353;304	ENSP00000398576:M203L;ENSP00000388084:M353L;ENSP00000392878:M349L;ENSP00000388183:M364L;ENSP00000414662:M368L;ENSP00000222673:M353L;ENSP00000443821:M304L	ENSP00000222673:M353L	M	+	1	0	OGDH	44682124	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	9.043000	0.93799	2.063000	0.61619	0.379000	0.24179	ATG	.	.	none		0.547	OGDH-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000339391.1		
TMED8	283578	hgsc.bcm.edu	37	14	77810133	77810133	+	Missense_Mutation	SNP	C	C	T	rs142882254	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:77810133C>T	ENST00000216468.7	-	4	416	c.361G>A	c.(361-363)Gac>Aac	p.D121N		NM_213601.1	NP_998766.1	Q6PL24	TMED8_HUMAN	transmembrane emp24 protein transport domain containing 8	121					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)	15			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		ATAACGATGTCCCCAGACCTC	0.438													C|||	5	0.000998403	0.0	0.0	5008	,	,		19285	0.0		0.005	False		,,,				2504	0.0				p.D121N		Atlas-SNP	.											.	TMED8	27	.	0			c.G361A						PASS	.	C	ASN/ASP	2,4404	4.2+/-10.8	0,2,2201	143.0	136.0	138.0		361	6.0	1.0	14	dbSNP_134	138	33,8567	22.2+/-67.0	0,33,4267	yes	missense	TMED8	NM_213601.1	23	0,35,6468	TT,TC,CC		0.3837,0.0454,0.2691	probably-damaging	121/326	77810133	35,12971	2203	4300	6503	SO:0001583	missense	283578	exon4			CGATGTCCCCAGA	AK095650	CCDS32125.1	14q24.3	2005-08-26	2005-08-26	2005-01-07		ENSG00000100580			18633	protein-coding gene	gene with protein product			"""family with sequence similarity 15, member B"", ""transmembrane emp24 domain containing 8"""	FAM15B			Standard	NM_213601		Approved		uc001xto.1	Q6PL24		ENST00000216468.7:c.361G>A	14.37:g.77810133C>T	ENSP00000216468:p.Asp121Asn	101.0	0.0	0		85.0	37.0	0.435294	NM_213601	B3KTI6|Q3MJB0|Q9P1V9	Missense_Mutation	SNP	ENST00000216468.7	37	CCDS32125.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	C	29.0	4.971209	0.92919	4.54E-4	0.003837	ENSG00000100580	ENST00000216468	T	0.29142	1.58	5.98	5.98	0.97165	.	0.051631	0.85682	D	0.000000	T	0.39682	0.1087	L	0.34521	1.04	0.52099	D	0.999945	D	0.89917	1.0	D	0.83275	0.996	T	0.10359	-1.0633	10	0.36615	T	0.2	-2.0029	20.4293	0.99080	0.0:1.0:0.0:0.0	.	121	Q6PL24	TMED8_HUMAN	N	121	ENSP00000216468:D121N	ENSP00000216468:D121N	D	-	1	0	TMED8	76879886	0.999000	0.42202	1.000000	0.80357	0.988000	0.76386	5.026000	0.64103	2.833000	0.97629	0.655000	0.94253	GAC	C|0.996;T|0.004	0.004	strong		0.438	TMED8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414100.1	NM_213601	
FNDC4	64838	hgsc.bcm.edu	37	2	27716823	27716823	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:27716823C>T	ENST00000264703.3	-	4	819	c.428G>A	c.(427-429)cGg>cAg	p.R143Q	GCKR_ENST00000264717.2_5'Flank|GCKR_ENST00000424318.2_5'Flank	NM_022823.2	NP_073734.1	Q9H6D8	FNDC4_HUMAN	fibronectin type III domain containing 4	143						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(2)|kidney(1)|large_intestine(1)|liver(2)|prostate(1)|skin(1)	9	Acute lymphoblastic leukemia(172;0.155)					TGAAGGTAGCCGGTCAGAACC	0.562																																					p.R143Q		Atlas-SNP	.											FNDC4,NS,carcinoma,-1,1	FNDC4	21	1	0			c.G428A						PASS	.						75.0	81.0	79.0					2																	27716823		2203	4300	6503	SO:0001583	missense	64838	exon4			GGTAGCCGGTCAG	AK026015	CCDS1756.1	2p23.3	2013-02-11			ENSG00000115226	ENSG00000115226		"""Fibronectin type III domain containing"""	20239	protein-coding gene	gene with protein product		611905				12384288	Standard	NM_022823		Approved	FLJ22362, FRCP1	uc002rkx.3	Q9H6D8	OTTHUMG00000097787	ENST00000264703.3:c.428G>A	2.37:g.27716823C>T	ENSP00000264703:p.Arg143Gln	73.0	0.0	0		76.0	24.0	0.315789	NM_022823	D6W560	Missense_Mutation	SNP	ENST00000264703.3	37	CCDS1756.1	.	.	.	.	.	.	.	.	.	.	C	13.08	2.129221	0.37533	.	.	ENSG00000115226	ENST00000264703	T	0.07444	3.19	5.46	3.68	0.42216	.	0.057087	0.64402	D	0.000002	T	0.04092	0.0114	N	0.24115	0.695	0.44660	D	0.997647	P	0.41710	0.76	B	0.26770	0.073	T	0.54200	-0.8329	10	0.28530	T	0.3	-10.0669	8.5567	0.33485	0.0:0.7609:0.0:0.2391	.	143	Q9H6D8	FNDC4_HUMAN	Q	143	ENSP00000264703:R143Q	ENSP00000264703:R143Q	R	-	2	0	FNDC4	27570327	1.000000	0.71417	1.000000	0.80357	0.524000	0.34500	2.017000	0.40981	0.682000	0.31407	-0.244000	0.11960	CGG	.	.	none		0.562	FNDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215031.1	NM_022823	
FOXN2	3344	hgsc.bcm.edu	37	2	48573875	48573875	+	Silent	SNP	A	A	G	rs35742253	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:48573875A>G	ENST00000340553.3	+	3	783	c.522A>G	c.(520-522)gaA>gaG	p.E174E		NM_002158.3	NP_002149.2	P32314	FOXN2_HUMAN	forkhead box N2	174					transcription, DNA-templated (GO:0006351)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)|skin(1)|urinary_tract(1)	13		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.0272)|LUSC - Lung squamous cell carcinoma(58;0.036)			AGAAAGTGGAAAGAAGCCATG	0.418													A|||	16	0.00319489	0.0008	0.0072	5008	,	,		16893	0.0		0.0099	False		,,,				2504	0.0				p.E174E		Atlas-SNP	.											.	FOXN2	39	.	0			c.A522G						PASS	.	A		13,4363		1,11,2176	52.0	54.0	53.0		522	2.9	1.0	2	dbSNP_126	53	91,8483		0,91,4196	no	coding-synonymous	FOXN2	NM_002158.3		1,102,6372	GG,GA,AA		1.0613,0.2971,0.8031		174/432	48573875	104,12846	2188	4287	6475	SO:0001819	synonymous_variant	3344	exon3			AGTGGAAAGAAGC		CCDS1838.1	2p22-p16	2008-02-05	2006-10-02	2006-10-02	ENSG00000170802	ENSG00000170802		"""Forkhead boxes"""	5281	protein-coding gene	gene with protein product		143089	"""human T-cell leukemia virus enhancer factor"""	HTLF		1639393	Standard	NM_002158		Approved		uc002rwh.1	P32314	OTTHUMG00000129168	ENST00000340553.3:c.522A>G	2.37:g.48573875A>G		30.0	0.0	0		21.0	11.0	0.52381	NM_002158	Q15769|Q6P4Q2	Silent	SNP	ENST00000340553.3	37	CCDS1838.1																																																																																			A|0.992;G|0.008	0.008	strong		0.418	FOXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251240.3	NM_002158	
XKR8	55113	hgsc.bcm.edu	37	1	28290132	28290132	+	Silent	SNP	T	T	C	rs61743136	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:28290132T>C	ENST00000373884.5	+	2	1026	c.418T>C	c.(418-420)Ttg>Ctg	p.L140L		NM_018053.2	NP_060523.2	Q9H6D3	XKR8_HUMAN	XK, Kell blood group complex subunit-related family, member 8	140					engulfment of apoptotic cell (GO:0043652)|phosphatidylserine exposure on apoptotic cell surface (GO:0070782)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(1)|large_intestine(2)|lung(1)	4		Colorectal(325;0.000147)|Renal(390;0.00357)|Lung NSC(340;0.00588)|all_lung(284;0.00645)|Breast(348;0.0174)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0545)|all_neural(195;0.0557)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;4.72e-24)|Colorectal(126;1.52e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00269)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00572)|READ - Rectum adenocarcinoma(331;0.0526)		CGAGACCTTCTTGGAGACGGC	0.632													T|||	40	0.00798722	0.0129	0.0101	5008	,	,		17747	0.0		0.0159	False		,,,				2504	0.0				p.L140L		Atlas-SNP	.											.	XKR8	15	.	0			c.T418C						PASS	.	T		79,4327	64.7+/-102.0	1,77,2125	29.0	25.0	27.0		418	-3.5	0.9	1	dbSNP_129	27	90,8510	47.2+/-106.3	0,90,4210	no	coding-synonymous	XKR8	NM_018053.2		1,167,6335	CC,CT,TT		1.0465,1.793,1.2994		140/396	28290132	169,12837	2203	4300	6503	SO:0001819	synonymous_variant	55113	exon2			ACCTTCTTGGAGA	AK091615	CCDS315.1	1p35.3	2008-02-05	2006-01-12		ENSG00000158156	ENSG00000158156			25508	protein-coding gene	gene with protein product			"""X Kell blood group precursor-related family, member 8"""			12477932	Standard	NM_018053		Approved	FLJ10307	uc001bph.1	Q9H6D3	OTTHUMG00000003912	ENST00000373884.5:c.418T>C	1.37:g.28290132T>C		100.0	0.0	0		106.0	45.0	0.424528	NM_018053		Silent	SNP	ENST00000373884.5	37	CCDS315.1																																																																																			T|0.987;C|0.013	0.013	strong		0.632	XKR8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000011175.1	NM_018053	
NTN3	4917	hgsc.bcm.edu	37	16	2522536	2522536	+	Silent	SNP	T	T	C	rs148996457		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:2522536T>C	ENST00000293973.1	+	1	1037	c.834T>C	c.(832-834)caT>caC	p.H278H	TBC1D24_ENST00000293970.5_5'Flank|TBC1D24_ENST00000567020.1_5'Flank	NM_006181.2	NP_006172.1	O00634	NET3_HUMAN	netrin 3	278	Laminin EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00460}.				axon guidance (GO:0007411)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)	Golgi apparatus (GO:0005794)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|central_nervous_system(2)|lung(3)|prostate(1)	7						ACTGTCGGCATGGCACCGAGG	0.687																																					p.H278H		Atlas-SNP	.											.	NTN3	28	.	0			c.T834C						PASS	.	T		0,4370		0,0,2185	26.0	26.0	26.0		834	-6.5	0.7	16	dbSNP_134	26	3,8559		0,3,4278	no	coding-synonymous	NTN3	NM_006181.2		0,3,6463	CC,CT,TT		0.035,0.0,0.0232		278/581	2522536	3,12929	2185	4281	6466	SO:0001819	synonymous_variant	4917	exon1			TCGGCATGGCACC	U86759	CCDS10469.1	16p13.3	2013-03-01	2008-10-29	2008-10-29	ENSG00000162068	ENSG00000162068		"""Netrins"""	8030	protein-coding gene	gene with protein product	"""Netrin-3"""	602349	"""netrin 2 (chicken)-like"", ""netrin 2-like (chicken)"""	NTN2L		9143507, 10366627	Standard	NM_006181		Approved		uc002cqj.3	O00634	OTTHUMG00000128867	ENST00000293973.1:c.834T>C	16.37:g.2522536T>C		31.0	0.0	0		33.0	17.0	0.515152	NM_006181		Silent	SNP	ENST00000293973.1	37	CCDS10469.1																																																																																			T|1.000;C|0.000	0.000	weak		0.687	NTN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250812.1	NM_006181	
MUC5B	727897	hgsc.bcm.edu	37	11	1274209	1274209	+	Splice_Site	SNP	G	G	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:1274209G>T	ENST00000529681.1	+	33	15274	c.15216G>T	c.(15214-15216)gaG>gaT	p.E5072D	MUC5B_ENST00000447027.1_Splice_Site_p.E5075D	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	5072					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)		ATGAGTGCGAGTGTGAGTGCG	0.642																																					p.E5072D		Atlas-SNP	.											.	MUC5B	473	.	0			c.G15216T						PASS	.						53.0	59.0	57.0					11																	1274209		2132	4227	6359	SO:0001630	splice_region_variant	727897	exon33			GTGCGAGTGTGAG	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.15217+1G>T	11.37:g.1274209G>T		70.0	0.0	0		100.0	44.0	0.44	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	10.24	1.295134	0.23564	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.15487	2.42;2.61	4.64	-4.49	0.03504	.	.	.	.	.	T	0.09949	0.0244	L	0.28274	0.84	0.20873	N	0.999838	P;P	0.43094	0.799;0.799	B;B	0.36845	0.234;0.234	T	0.20672	-1.0268	9	0.87932	D	0	.	9.6818	0.40074	0.7156:0.0:0.1642:0.1202	.	5394;5075	A7Y9J9;E9PBJ0	.;.	D	5072;5075;5016;4771	ENSP00000436812:E5072D;ENSP00000415793:E5075D	ENSP00000343037:E5016D	E	+	3	2	MUC5B	1230785	0.001000	0.12720	0.574000	0.28523	0.561000	0.35649	-2.094000	0.01351	-0.851000	0.04147	-0.258000	0.10820	GAG	.	.	none		0.642	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	Missense_Mutation
BRD1	23774	hgsc.bcm.edu	37	22	50217300	50217300	+	Silent	SNP	G	G	A	rs374070979		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:50217300G>A	ENST00000216267.8	-	1	1152	c.666C>T	c.(664-666)gaC>gaT	p.D222D	BRD1_ENST00000342989.5_5'Flank|BRD1_ENST00000459821.1_5'Flank|BRD1_ENST00000404034.1_Silent_p.D222D|BRD1_ENST00000542442.1_5'Flank|BRD1_ENST00000404760.1_Silent_p.D222D|BRD1_ENST00000457780.2_Silent_p.D222D	NM_014577.1	NP_055392.1	O95696	BRD1_HUMAN	bromodomain containing 1	222					histone H3 acetylation (GO:0043966)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleus (GO:0005634)	histone binding (GO:0042393)|zinc ion binding (GO:0008270)			endometrium(6)|kidney(3)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(3)|skin(1)	37		all_cancers(38;6.11e-10)|all_epithelial(38;8.06e-09)|all_lung(38;6.64e-05)|Lung NSC(38;0.0011)|Breast(42;0.00235)|Ovarian(80;0.0139)|Lung SC(80;0.164)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0369)|BRCA - Breast invasive adenocarcinoma(115;0.21)		GACACTCCCCGTCCATGCAGA	0.612																																					p.D222D		Atlas-SNP	.											.	BRD1	144	.	0			c.C666T						PASS	.	G		2,4404	4.2+/-10.8	0,2,2201	62.0	49.0	53.0		666	-4.3	1.0	22		53	0,8600		0,0,4300	no	coding-synonymous	BRD1	NM_014577.1		0,2,6501	AA,AG,GG		0.0,0.0454,0.0154		222/1059	50217300	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	23774	exon1			CTCCCCGTCCATG	AF005067	CCDS14080.1	22q13.33	2008-07-01	2002-01-14		ENSG00000100425	ENSG00000100425			1102	protein-coding gene	gene with protein product	"""BR140-like"""	604589	"""bromodomain-containing 1"""			10591208, 10602503	Standard	NM_014577		Approved	BRL, BRPF2	uc003biv.3	O95696	OTTHUMG00000150288	ENST00000216267.8:c.666C>T	22.37:g.50217300G>A		46.0	0.0	0		57.0	33.0	0.578947	NM_014577	A6ZJA4	Silent	SNP	ENST00000216267.8	37	CCDS14080.1																																																																																			.	.	weak		0.612	BRD1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317402.1	NM_014577	
COBLL1	22837	hgsc.bcm.edu	37	2	165578602	165578602	+	Missense_Mutation	SNP	C	C	T	rs74459242	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:165578602C>T	ENST00000392717.2	-	7	1097	c.1093G>A	c.(1093-1095)Gtg>Atg	p.V365M	COBLL1_ENST00000409184.3_Missense_Mutation_p.V365M|COBLL1_ENST00000375458.2_Missense_Mutation_p.V327M|COBLL1_ENST00000342193.4_Missense_Mutation_p.V327M|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	81.0	0.0	0		102.0	58.0	0.568627	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	
ZBTB16	7704	hgsc.bcm.edu	37	11	114121182	114121182	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:114121182T>A	ENST00000335953.4	+	7	2307	c.1927T>A	c.(1927-1929)Tcc>Acc	p.S643T	RP11-64D24.2_ENST00000544925.1_RNA|ZBTB16_ENST00000535379.1_3'UTR|ZBTB16_ENST00000392996.2_Missense_Mutation_p.S643T	NM_006006.4	NP_005997.2	Q05516	ZBT16_HUMAN	zinc finger and BTB domain containing 16	643					anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|cartilage development (GO:0051216)|central nervous system development (GO:0007417)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic pattern specification (GO:0009880)|forelimb morphogenesis (GO:0035136)|hemopoiesis (GO:0030097)|male germ-line stem cell asymmetric division (GO:0048133)|mesonephros development (GO:0001823)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of myeloid cell differentiation (GO:0045638)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cartilage development (GO:0061036)|positive regulation of chondrocyte differentiation (GO:0032332)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of NK T cell differentiation (GO:0051138)|positive regulation of ossification (GO:0045778)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|protein ubiquitination (GO:0016567)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nuclear body (GO:0016604)|nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|transcriptional repressor complex (GO:0017053)	DNA binding (GO:0003677)|double-stranded DNA binding (GO:0003690)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)			central_nervous_system(1)|large_intestine(2)|skin(1)|upper_aerodigestive_tract(2)	6		all_cancers(61;3.79e-18)|all_epithelial(67;2.32e-10)|all_hematologic(158;2.96e-05)|Melanoma(852;0.000362)|Acute lymphoblastic leukemia(157;0.00108)|Breast(348;0.0104)|all_neural(223;0.0294)|Prostate(24;0.0318)|Medulloblastoma(222;0.0438)		BRCA - Breast invasive adenocarcinoma(274;6.75e-06)|Epithelial(105;0.000181)|all cancers(92;0.0018)		CCCCAGCCTCTCCTCCATGCA	0.602																																					p.S643T		Atlas-SNP	.											ZBTB16_ENST00000335953,NS,carcinoma,0,1	ZBTB16	101	1	0			c.T1927A						scavenged	.						76.0	68.0	71.0					11																	114121182		2201	4296	6497	SO:0001583	missense	7704	exon7			AGCCTCTCCTCCA	Z19002	CCDS8367.1	11q23	2013-10-17	2004-07-16	2004-07-16	ENSG00000109906	ENSG00000109906		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	12930	protein-coding gene	gene with protein product	"""promyelocytic leukaemia zinc finger"""	176797	"""zinc finger protein 145 (Kruppel-like, expressed in promyelocytic leukemia)"""	ZNF145			Standard	XM_006718899		Approved	PLZF	uc001poq.3	Q05516	OTTHUMG00000168243	ENST00000335953.4:c.1927T>A	11.37:g.114121182T>A	ENSP00000338157:p.Ser643Thr	59.0	0.0	0		38.0	2.0	0.0526316	NM_006006	Q8TAL4	Missense_Mutation	SNP	ENST00000335953.4	37	CCDS8367.1	.	.	.	.	.	.	.	.	.	.	t	18.33	3.599781	0.66332	.	.	ENSG00000109906	ENST00000335953;ENST00000392996;ENST00000310883	T;T	0.62232	0.04;0.04	5.39	5.39	0.77823	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.066981	0.64402	D	0.000008	T	0.47040	0.1424	N	0.14661	0.345	0.45272	D	0.998277	P	0.38767	0.646	B	0.36464	0.225	T	0.54925	-0.8220	10	0.59425	D	0.04	-13.3009	15.4492	0.75259	0.0:0.0:0.0:1.0	.	643	Q05516	ZBT16_HUMAN	T	643;643;520	ENSP00000338157:S643T;ENSP00000376721:S643T	ENSP00000309507:S520T	S	+	1	0	ZBTB16	113626392	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.924000	0.63418	2.047000	0.60756	0.358000	0.22013	TCC	.	.	none		0.602	ZBTB16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398940.1	NM_006006	
KLHDC7A	127707	hgsc.bcm.edu	37	1	18807523	18807523	+	Silent	SNP	G	G	A	rs377259272		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:18807523G>A	ENST00000400664.1	+	1	100	c.48G>A	c.(46-48)caG>caA	p.Q16Q		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	16						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		TGGATATGCAGCTGACCGGCA	0.592																																					p.Q16Q		Atlas-SNP	.											.	KLHDC7A	60	.	0			c.G48A						PASS	.	G		1,4111		0,1,2055	51.0	57.0	55.0		48	4.9	1.0	1		55	0,8434		0,0,4217	no	coding-synonymous	KLHDC7A	NM_152375.2		0,1,6272	AA,AG,GG		0.0,0.0243,0.0080		16/778	18807523	1,12545	2056	4217	6273	SO:0001819	synonymous_variant	127707	exon1			TATGCAGCTGACC	AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.48G>A	1.37:g.18807523G>A		236.0	1.0	0.00423729		218.0	113.0	0.518349	NM_152375	Q8N8W6	Silent	SNP	ENST00000400664.1	37	CCDS185.2																																																																																			.	.	none		0.592	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006923.3	NM_152375	
PCDHA4	56144	hgsc.bcm.edu	37	5	140188354	140188354	+	Missense_Mutation	SNP	C	C	G	rs142480630	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:140188354C>G	ENST00000530339.1	+	1	1582	c.1582C>G	c.(1582-1584)Cta>Gta	p.L528V	PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Missense_Mutation_p.L528V|PCDHA1_ENST00000394633.3_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000356878.4_Missense_Mutation_p.L528V|PCDHA2_ENST00000526136.1_Intron	NM_018907.2	NP_061730.1	Q9UN74	PCDA4_HUMAN	protocadherin alpha 4	528	Cadherin 5. {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)			breast(6)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(6)|pancreas(1)|prostate(3)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CCACGAGGAGCTAGAGCTGCT	0.652													.|||	115	0.0229633	0.003	0.0389	5008	,	,		17618	0.0		0.0755	False		,,,				2504	0.0082				p.L528V		Atlas-SNP	.											PCDHA4_ENST00000530339,NS,carcinoma,0,8	PCDHA4	419	8	0			c.C1582G						PASS	.						70.0	75.0	74.0					5																	140188354		2203	4300	6503	SO:0001583	missense	56144	exon1			GAGGAGCTAGAGC	AF152482	CCDS54916.1	5q31	2010-11-26				ENSG00000204967		"""Cadherins / Protocadherins : Clustered"""	8670	other	complex locus constituent	"""ortholog of mouse CNR1, KIAA0345-like 10"""	606310				10380929, 10662547	Standard	NM_018907		Approved	CNR1, CRNR1, PCDH-ALPHA4, CNRN1		Q9UN74		ENST00000530339.1:c.1582C>G	5.37:g.140188354C>G	ENSP00000435300:p.Leu528Val	110.0	0.0	0		65.0	20.0	0.307692	NM_031500	O75285|Q2M253	Missense_Mutation	SNP	ENST00000530339.1	37	CCDS54916.1	.	.	.	.	.	.	.	.	.	.	c	11.23	1.577307	0.28092	.	.	ENSG00000204967	ENST00000512229;ENST00000356878;ENST00000530339	T;T;T	0.51325	0.71;0.71;0.71	4.18	2.19	0.27852	Cadherin (5);Cadherin-like (1);	0.000000	0.28952	U	0.013601	T	0.34948	0.0915	N	0.25332	0.735	0.20764	N	0.999854	P;B;B	0.43662	0.814;0.101;0.207	B;B;B	0.43508	0.422;0.421;0.214	T	0.15150	-1.0447	10	0.51188	T	0.08	.	8.8809	0.35374	0.2588:0.4914:0.2498:0.0	.	528;528;528	Q9UN74-2;Q9UN74;D6RA20	.;PCDA4_HUMAN;.	V	528	ENSP00000423470:L528V;ENSP00000349344:L528V;ENSP00000435300:L528V	ENSP00000349344:L528V	L	+	1	2	PCDHA4	140168538	0.000000	0.05858	1.000000	0.80357	0.984000	0.73092	-1.847000	0.01675	0.874000	0.35823	0.580000	0.79431	CTA	C|0.999;G|0.001	0.001	weak		0.652	PCDHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372864.2	NM_018907	
DOCK2	1794	hgsc.bcm.edu	37	5	169267839	169267839	+	Missense_Mutation	SNP	C	C	T	rs200070944		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr5:169267839C>T	ENST00000256935.8	+	27	2862	c.2782C>T	c.(2782-2784)Cgg>Tgg	p.R928W	DOCK2_ENST00000540750.1_5'UTR|DOCK2_ENST00000523351.1_3'UTR|DOCK2_ENST00000520908.1_Missense_Mutation_p.R420W	NM_004946.2	NP_004937.1	Q92608	DOCK2_HUMAN	dedicator of cytokinesis 2	928					actin cytoskeleton organization (GO:0030036)|alpha-beta T cell proliferation (GO:0046633)|chemotaxis (GO:0006935)|establishment of T cell polarity (GO:0001768)|immunological synapse formation (GO:0001771)|macropinocytosis (GO:0044351)|membrane raft polarization (GO:0001766)|myeloid dendritic cell activation involved in immune response (GO:0002277)|negative thymic T cell selection (GO:0045060)|positive regulation of phagocytosis (GO:0050766)|positive thymic T cell selection (GO:0045059)|regulation of defense response to virus by virus (GO:0050690)|small GTPase mediated signal transduction (GO:0007264)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	Rac GTPase activator activity (GO:0030675)|Rac guanyl-nucleotide exchange factor activity (GO:0030676)|T cell receptor binding (GO:0042608)			NS(2)|breast(5)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(42)|liver(2)|lung(63)|ovary(5)|pancreas(3)|prostate(7)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)	160	Renal(175;0.000159)|Lung NSC(126;0.0221)|all_lung(126;0.0337)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CACCATGGGCCGGGATCACAT	0.458																																					p.R928W		Atlas-SNP	.											.	DOCK2	389	.	0			c.C2782T						PASS	.						126.0	108.0	114.0					5																	169267839		2203	4300	6503	SO:0001583	missense	1794	exon27			ATGGGCCGGGATC	BC016996	CCDS4371.1	5q35.1	2008-02-05			ENSG00000134516	ENSG00000134516			2988	protein-coding gene	gene with protein product		603122	"""dedicator of cyto-kinesis 2"""				Standard	NM_004946		Approved	KIAA0209	uc003maf.3	Q92608	OTTHUMG00000130437	ENST00000256935.8:c.2782C>T	5.37:g.169267839C>T	ENSP00000256935:p.Arg928Trp	91.0	0.0	0		75.0	42.0	0.56	NM_004946	Q2M3I0|Q96AK7	Missense_Mutation	SNP	ENST00000256935.8	37	CCDS4371.1	.	.	.	.	.	.	.	.	.	.	C	18.01	3.527368	0.64860	.	.	ENSG00000134516	ENST00000256935;ENST00000343291;ENST00000520908;ENST00000519628	T;T	0.69306	-0.39;-0.39	5.28	5.28	0.74379	.	0.120890	0.56097	D	0.000022	T	0.70518	0.3233	M	0.71036	2.16	0.80722	D	1	D;D	0.65815	0.995;0.959	P;B	0.49387	0.609;0.245	T	0.73202	-0.4057	10	0.49607	T	0.09	.	11.5168	0.50526	0.1792:0.8208:0.0:0.0	.	420;928	E7ERW7;Q92608	.;DOCK2_HUMAN	W	928;309;420;132	ENSP00000256935:R928W;ENSP00000429283:R420W	ENSP00000256935:R928W	R	+	1	2	DOCK2	169200417	0.994000	0.37717	1.000000	0.80357	0.778000	0.44026	3.353000	0.52247	2.460000	0.83146	0.585000	0.79938	CGG	C|0.999;A|0.001	.	alt		0.458	DOCK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252828.2	NM_004946	
IDH1	3417	hgsc.bcm.edu	37	2	209108317	209108317	+	Missense_Mutation	SNP	C	C	T	rs34218846	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:209108317C>T	ENST00000415913.1	-	6	913	c.532G>A	c.(532-534)Gtt>Att	p.V178I	IDH1_ENST00000345146.2_Missense_Mutation_p.V178I|IDH1_ENST00000446179.1_Missense_Mutation_p.V178I	NM_001282387.1	NP_001269316.1	O75874	IDHC_HUMAN	isocitrate dehydrogenase 1 (NADP+), soluble	178			V -> I (in dbSNP:rs34218846).		2-oxoglutarate metabolic process (GO:0006103)|cellular lipid metabolic process (GO:0044255)|female gonad development (GO:0008585)|glutathione metabolic process (GO:0006749)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|NADPH regeneration (GO:0006740)|response to oxidative stress (GO:0006979)|response to steroid hormone (GO:0048545)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)	p.V178I(8)		NS(1)|autonomic_ganglia(2)|biliary_tract(24)|bone(237)|central_nervous_system(3764)|endometrium(3)|haematopoietic_and_lymphoid_tissue(794)|kidney(2)|large_intestine(7)|lung(7)|prostate(6)|skin(5)|soft_tissue(12)|thyroid(22)|urinary_tract(1)	4887				Epithelial(149;0.0322)|LUSC - Lung squamous cell carcinoma(261;0.0711)|Lung(261;0.136)		CCCATGGCAACACCACCACCT	0.418			Mis		gliobastoma								C|||	247	0.0493211	0.0893	0.0447	5008	,	,		18161	0.0069		0.0477	False		,,,				2504	0.044				p.V178I	Pancreas(158;264 1958 3300 35450 36047)	Atlas-SNP	.		Dom	yes		2	2q33.3	3417	"""isocitrate dehydrogenase 1 (NADP+), soluble"""		O	IDH1,colon,carcinoma,0,9	IDH1	6310	9	8	Substitution - Missense(8)	thyroid(8)	c.G532A						PASS	.	C	ILE/VAL	356,4050	182.6+/-210.3	12,332,1859	69.0	65.0	66.0		532	5.5	1.0	2	dbSNP_126	66	457,8143	137.1+/-194.1	7,443,3850	yes	missense	IDH1	NM_005896.2	29	19,775,5709	TT,TC,CC		5.314,8.0799,6.251	possibly-damaging	178/415	209108317	813,12193	2203	4300	6503	SO:0001583	missense	3417	exon6			TGGCAACACCACC		CCDS2381.1	2q34	2014-09-17			ENSG00000138413	ENSG00000138413	1.1.1.42		5382	protein-coding gene	gene with protein product		147700					Standard	NM_005896		Approved		uc002vcu.3	O75874	OTTHUMG00000132943	ENST00000415913.1:c.532G>A	2.37:g.209108317C>T	ENSP00000390265:p.Val178Ile	70.0	0.0	0		66.0	33.0	0.5	NM_005896	Q567U4|Q6FHQ6|Q7Z3V0|Q93090|Q9NTJ9|Q9UKW8	Missense_Mutation	SNP	ENST00000415913.1	37	CCDS2381.1	90	0.04120879120879121	38	0.07723577235772358	16	0.04419889502762431	2	0.0034965034965034965	34	0.044854881266490766	C	20.3	3.968029	0.74131	0.080799	0.05314	ENSG00000138413	ENST00000345146;ENST00000446179;ENST00000415913	T;T;T	0.77229	-1.08;-1.08;-1.08	5.52	5.52	0.82312	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	T	0.32376	0.0827	L	0.54863	1.705	0.80722	D	1	D	0.63046	0.992	D	0.74674	0.984	T	0.66701	-0.5857	10	0.44086	T	0.13	-13.6312	19.7971	0.96490	0.0:1.0:0.0:0.0	rs34218846	178	O75874	IDHC_HUMAN	I	178	ENSP00000260985:V178I;ENSP00000410513:V178I;ENSP00000390265:V178I	ENSP00000260985:V178I	V	-	1	0	IDH1	208816562	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	6.126000	0.71635	2.762000	0.94881	0.484000	0.47621	GTT	C|0.946;T|0.054	0.054	strong		0.418	IDH1-006	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336672.1		
UGT1A10	54575	hgsc.bcm.edu	37	2	234545932	234545932	+	Missense_Mutation	SNP	C	C	T	rs45574333	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:234545932C>T	ENST00000344644.5	+	1	833	c.764C>T	c.(763-765)aCg>aTg	p.T255M	UGT1A10_ENST00000373445.1_Missense_Mutation_p.T255M|UGT1A1_ENST00000373450.4_Intron	NM_019075.2	NP_061948.1	Q9HAW8	UD110_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A10	255					cellular glucuronidation (GO:0052695)|flavone metabolic process (GO:0051552)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase C binding (GO:0005080)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(15)|ovary(2)|skin(3)	32		Breast(86;0.000766)|all_lung(227;0.00271)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0334)|Lung NSC(271;0.0461)|Lung SC(224;0.128)		Epithelial(121;1.96e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000468)|Lung(119;0.00381)|LUSC - Lung squamous cell carcinoma(224;0.008)	Acetaminophen(DB00316)|Etodolac(DB00749)|Losartan(DB00678)|Mycophenolate mofetil(DB00688)|Valproic Acid(DB00313)	TTGTTGCGAACGGACTTTGTT	0.433																																					p.T255M		Atlas-SNP	.											.	UGT1A10	71	.	0			c.C764T						PASS	.	C	MET/THR,	1,4405	2.1+/-5.4	0,1,2202	254.0	253.0	253.0		764,	1.5	0.5	2	dbSNP_127	253	11,8589	8.4+/-32.0	0,11,4289	no	missense,intron	UGT1A10,UGT1A8	NM_019075.2,NM_019076.4	81,	0,12,6491	TT,TC,CC		0.1279,0.0227,0.0923	,	255/531,	234545932	12,12994	2203	4300	6503	SO:0001583	missense	54575	exon1			TGCGAACGGACTT	U39550	CCDS33403.1	2q37	2010-03-05	2005-07-20		ENSG00000242515	ENSG00000242515		"""UDP glucuronosyltransferases"""	12531	other	complex locus constituent		606435	"""UDP glycosyltransferase 1 family, polypeptide A10"""			9295054, 9325166	Standard	NM_019075		Approved	UGT1J		Q9HAW8	OTTHUMG00000059121	ENST00000344644.5:c.764C>T	2.37:g.234545932C>T	ENSP00000343838:p.Thr255Met	133.0	0.0	0		153.0	71.0	0.464052	NM_019075	O00474|Q6NT91|Q7Z6H8	Missense_Mutation	SNP	ENST00000344644.5	37	CCDS33403.1	.	.	.	.	.	.	.	.	.	.	C	7.102	0.574235	0.13623	2.27E-4	0.001279	ENSG00000242515	ENST00000344644;ENST00000373445	T;T	0.67345	-0.26;-0.26	3.52	1.53	0.23141	.	.	.	.	.	T	0.69726	0.3143	M	0.84433	2.695	0.09310	N	1	B;B	0.34147	0.234;0.438	B;B	0.42163	0.269;0.378	T	0.63418	-0.6642	9	0.51188	T	0.08	.	3.4103	0.07356	0.3801:0.3993:0.1324:0.0881	rs45574333	255;255	Q9HAW8;Q7Z6H8	UD110_HUMAN;.	M	255	ENSP00000343838:T255M;ENSP00000362544:T255M	ENSP00000343838:T255M	T	+	2	0	UGT1A10	234210671	0.000000	0.05858	0.532000	0.27989	0.802000	0.45316	-2.845000	0.00735	0.254000	0.21573	0.405000	0.27470	ACG	C|0.999;T|0.001	0.001	strong		0.433	UGT1A10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000130986.1	NM_019075	
GTF2F1	2962	hgsc.bcm.edu	37	19	6392910	6392910	+	Missense_Mutation	SNP	G	G	A	rs150462935		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:6392910G>A	ENST00000394456.5	-	2	481	c.17C>T	c.(16-18)cCt>cTt	p.P6L	GTF2F1_ENST00000429701.2_5'Flank|CTB-180A7.6_ENST00000599584.1_RNA	NM_002096.2	NP_002087.2	P35269	T2FA_HUMAN	general transcription factor IIF, polypeptide 1, 74kDa	6					7-methylguanosine mRNA capping (GO:0006370)|gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|positive regulation of catalytic activity (GO:0043085)|positive regulation of transcription elongation from RNA polymerase II promoter (GO:0032968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to virus (GO:0009615)|RNA splicing (GO:0008380)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cell junction (GO:0030054)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIIF complex (GO:0005674)	catalytic activity (GO:0003824)|DNA binding (GO:0003677)|phosphatase activator activity (GO:0019211)|poly(A) RNA binding (GO:0044822)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)			breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(4)	16						CTGGCTGCTAGGGCCCTGCGG	0.602											OREG0025199	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	1	0.000199681	0.0	0.0	5008	,	,		16382	0.0		0.001	False		,,,				2504	0.0				p.P6L		Atlas-SNP	.											.	GTF2F1	39	.	0			c.C17T						PASS	.	G	LEU/PRO	0,4406		0,0,2203	134.0	135.0	134.0		17	5.1	1.0	19	dbSNP_134	134	4,8596	1.2+/-3.3	0,4,4296	yes	missense	GTF2F1	NM_002096.2	98	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign	6/518	6392910	4,13002	2203	4300	6503	SO:0001583	missense	2962	exon2			CTGCTAGGGCCCT		CCDS12165.1	19p13.3	2010-03-23	2002-08-29		ENSG00000125651	ENSG00000125651		"""General transcription factors"""	4652	protein-coding gene	gene with protein product		189968	"""general transcription factor IIF, polypeptide 1 (74kD subunit)"""			1734284	Standard	NM_002096		Approved	TFIIF, BTF4, RAP74, TF2F1	uc002meq.2	P35269	OTTHUMG00000168087	ENST00000394456.5:c.17C>T	19.37:g.6392910G>A	ENSP00000377969:p.Pro6Leu	71.0	0.0	0	633	79.0	35.0	0.443038	NM_002096	B2RCS0|Q9BWN0	Missense_Mutation	SNP	ENST00000394456.5	37	CCDS12165.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	16.23	3.063678	0.55432	0.0	4.65E-4	ENSG00000125651	ENST00000394456;ENST00000541263	T	0.46451	0.87	5.07	5.07	0.68467	.	0.397846	0.25529	N	0.030059	T	0.26521	0.0648	N	0.08118	0	0.80722	D	1	B	0.21225	0.053	B	0.16289	0.015	T	0.10177	-1.0641	10	0.72032	D	0.01	-21.0264	15.4688	0.75426	0.0:0.0:1.0:0.0	.	6	P35269	T2FA_HUMAN	L	6	ENSP00000377969:P6L	ENSP00000377969:P6L	P	-	2	0	GTF2F1	6343910	1.000000	0.71417	0.997000	0.53966	0.751000	0.42716	2.686000	0.46968	2.629000	0.89072	0.591000	0.81541	CCT	G|0.999;A|0.001	0.001	strong		0.602	GTF2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398033.1	NM_002096	
CHD5	26038	hgsc.bcm.edu	37	1	6188596	6188596	+	Silent	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:6188596G>A	ENST00000262450.3	-	24	3792	c.3693C>T	c.(3691-3693)gcC>gcT	p.A1231A	CHD5_ENST00000378021.1_Silent_p.A88A	NM_015557.2	NP_056372.1	O00258	WRB_HUMAN	chromodomain helicase DNA binding protein 5	0					tail-anchored membrane protein insertion into ER membrane (GO:0071816)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				breast(3)|central_nervous_system(3)|liver(1)|lung(1)|ovary(4)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)	16	Ovarian(185;0.0634)	all_cancers(23;5.36e-32)|all_epithelial(116;2.32e-17)|all_neural(13;3.68e-06)|all_lung(118;3.94e-06)|all_hematologic(16;2.39e-05)|Lung NSC(185;5.33e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00373)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;3.08e-37)|GBM - Glioblastoma multiforme(13;1.36e-31)|OV - Ovarian serous cystadenocarcinoma(86;7.7e-19)|Colorectal(212;9.97e-08)|COAD - Colon adenocarcinoma(227;1.07e-05)|Kidney(185;6.16e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.00109)|BRCA - Breast invasive adenocarcinoma(365;0.0012)|STAD - Stomach adenocarcinoma(132;0.00346)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.193)		TTGCACTGGCGGCCAAGTTCC	0.627																																					p.A1231A		Atlas-SNP	.											.	CHD5	267	.	0			c.C3693T						PASS	.						59.0	62.0	61.0					1																	6188596		2203	4300	6503	SO:0001819	synonymous_variant	26038	exon24			ACTGGCGGCCAAG	AF425231	CCDS57.1	1p36.3	2013-01-28			ENSG00000116254	ENSG00000116254		"""Zinc fingers, PHD-type"""	16816	protein-coding gene	gene with protein product		610771				11889561, 12592387	Standard	NM_015557		Approved		uc001amb.2	Q8TDI0	OTTHUMG00000000952	ENST00000262450.3:c.3693C>T	1.37:g.6188596G>A		75.0	0.0	0		75.0	41.0	0.546667	NM_015557	A8KAP8|A8MQ44|D3DSH9|O60740	Silent	SNP	ENST00000262450.3	37	CCDS57.1																																																																																			.	.	none		0.627	CHD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002823.2	NM_015557	
ZNF521	25925	hgsc.bcm.edu	37	18	22804942	22804942	+	Silent	SNP	C	C	T	rs187705938	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr18:22804942C>T	ENST00000361524.3	-	4	3088	c.2940G>A	c.(2938-2940)acG>acA	p.T980T	ZNF521_ENST00000538137.2_Silent_p.T980T|ZNF521_ENST00000579111.1_5'Flank|ZNF521_ENST00000584787.1_Silent_p.T760T	NM_015461.2	NP_056276.1	Q96K83	ZN521_HUMAN	zinc finger protein 521	980					cell differentiation (GO:0030154)|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)|protein domain specific binding (GO:0019904)			NS(1)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(21)|lung(97)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	149	all_cancers(21;0.0025)|all_epithelial(16;3.62e-05)|Ovarian(20;0.0991)					TCTTACTATGCGTGACTTTGT	0.468			T	PAX5	ALL								C|||	2	0.000399361	0.0	0.0	5008	,	,		21326	0.0		0.002	False		,,,				2504	0.0				p.T980T		Atlas-SNP	.		Dom	yes		18	18q11.2	25925	zinc finger protein 521		L	ZNF521,NS,carcinoma,-1,1	ZNF521	269	1	0			c.G2940A						PASS	.	C		0,4406		0,0,2203	69.0	67.0	68.0		2940	-11.9	0.2	18		68	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	ZNF521	NM_015461.2		0,4,6499	TT,TC,CC		0.0465,0.0,0.0308		980/1312	22804942	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	25925	exon4			ACTATGCGTGACT	AK027354	CCDS32806.1	18q11.2	2013-01-08				ENSG00000198795		"""Zinc fingers, C2H2-type"""	24605	protein-coding gene	gene with protein product	"""early hematopoietic zinc finger"""	610974				11984006, 14630787	Standard	NM_015461		Approved	EHZF, Evi3	uc002kvk.2	Q96K83		ENST00000361524.3:c.2940G>A	18.37:g.22804942C>T		68.0	0.0	0		81.0	28.0	0.345679	NM_015461	A3QVP7|B0YJB7|Q8IXI0|Q8TES6|Q9C065|Q9HAL5|Q9UFK4	Silent	SNP	ENST00000361524.3	37	CCDS32806.1																																																																																			C|0.999;T|0.001	0.001	strong		0.468	ZNF521-001	KNOWN	overlapping_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446781.2	NM_015461	
PDIA6	10130	hgsc.bcm.edu	37	2	10929938	10929938	+	Silent	SNP	G	G	A	rs138712410	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:10929938G>A	ENST00000272227.3	-	8	924	c.777C>T	c.(775-777)tcC>tcT	p.S259S	PDIA6_ENST00000404371.2_Silent_p.S311S|PDIA6_ENST00000381611.4_Silent_p.S264S|PDIA6_ENST00000404824.2_Silent_p.S307S|PDIA6_ENST00000540494.1_Silent_p.S256S	NM_001282707.1|NM_005742.2	NP_001269636.1|NP_005733.1	Q15084	PDIA6_HUMAN	protein disulfide isomerase family A, member 6	259	Thioredoxin 2. {ECO:0000255|PROSITE- ProRule:PRU00691}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|apoptotic cell clearance (GO:0043277)|cell redox homeostasis (GO:0045454)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|protein folding (GO:0006457)|response to endoplasmic reticulum stress (GO:0034976)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)	protein disulfide isomerase activity (GO:0003756)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(8)|prostate(2)	18	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.191)			Epithelial(75;0.149)|OV - Ovarian serous cystadenocarcinoma(76;0.15)		ACACGATGTCGGATCTTGTCC	0.458													G|||	40	0.00798722	0.0008	0.0058	5008	,	,		14648	0.0		0.008	False		,,,				2504	0.0276				p.S259S	GBM(73;509 1219 34219 41343 41551)	Atlas-SNP	.											PDIA6,NS,carcinoma,0,1	PDIA6	31	1	0			c.C777T						PASS	.	G		3,4403	6.2+/-15.9	0,3,2200	85.0	83.0	84.0		777	-11.3	0.0	2	dbSNP_134	84	68,8532	41.7+/-99.0	0,68,4232	no	coding-synonymous	PDIA6	NM_005742.2		0,71,6432	AA,AG,GG		0.7907,0.0681,0.5459		259/441	10929938	71,12935	2203	4300	6503	SO:0001819	synonymous_variant	10130	exon8			GATGTCGGATCTT	BC001312	CCDS1675.1, CCDS62852.1, CCDS62853.1, CCDS62854.1, CCDS62855.1	2p25.1	2009-11-20	2005-06-29	2005-03-03	ENSG00000143870	ENSG00000143870	5.3.4.1	"""Protein disulfide isomerases"""	30168	protein-coding gene	gene with protein product	"""protein disulfide isomerase-related protein"""	611099	"""thioredoxin domain containing 7 (protein disulfide isomerase)"", ""protein disulfide isomerase-associated 6"""	TXNDC7		7590364, 12204115	Standard	XM_005246145		Approved	P5, ERp5	uc002rau.3	Q15084	OTTHUMG00000090479	ENST00000272227.3:c.777C>T	2.37:g.10929938G>A		68.0	0.0	0		77.0	39.0	0.506494	NM_005742	B3KY95|B5MCQ5|B7Z254|B7Z4M8|F8WA83|Q53RC7|Q6ZSH5|Q99778	Silent	SNP	ENST00000272227.3	37	CCDS1675.1																																																																																			G|0.994;A|0.006	0.006	strong		0.458	PDIA6-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206933.1	NM_005742	
PAXBP1	94104	hgsc.bcm.edu	37	21	34132288	34132288	+	Silent	SNP	G	G	A	rs149224793	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr21:34132288G>A	ENST00000331923.4	-	6	1182	c.993C>T	c.(991-993)ccC>ccT	p.P331P	PAXBP1_ENST00000472588.1_5'UTR|PAXBP1_ENST00000290178.4_Silent_p.P331P	NM_016631.3	NP_057715.2	Q9Y5B6	PAXB1_HUMAN	PAX3 and PAX7 binding protein 1	331					muscle organ development (GO:0007517)|positive regulation of histone methylation (GO:0031062)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of satellite cell proliferation (GO:0014842)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)										TCACTTCTGCGGGTTGACTGG	0.373													G|||	3	0.000599042	0.0	0.0014	5008	,	,		18563	0.0		0.002	False		,,,				2504	0.0				p.P331P		Atlas-SNP	.											.	.	.	.	0			c.C993T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	100.0	103.0	102.0		993,993	0.4	0.2	21	dbSNP_134	102	25,8575	17.3+/-56.4	0,25,4275	no	coding-synonymous,coding-synonymous	GCFC1	NM_013329.3,NM_016631.3	,	0,26,6477	AA,AG,GG		0.2907,0.0227,0.1999	,	331/816,331/918	34132288	26,12980	2203	4300	6503	SO:0001819	synonymous_variant	94104	exon6			TTCTGCGGGTTGA	AF231920	CCDS13619.1, CCDS33541.1	21q22.11	2014-01-23	2013-01-08	2013-01-08	ENSG00000159086	ENSG00000159086			13579	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 105"", ""GC-rich sequence DNA-binding factor candidate"""		"""chromosome 21 open reading frame 66"", ""GC-rich sequence DNA-binding factor 1"""	C21orf66, GCFC1		11707072, 22862948	Standard	NM_016631		Approved	GCFC, fSAP105	uc002yqn.3	Q9Y5B6	OTTHUMG00000064980	ENST00000331923.4:c.993C>T	21.37:g.34132288G>A		104.0	0.0	0		96.0	43.0	0.447917	NM_013329	D3DSE7|Q96DU8|Q9NYQ0	Silent	SNP	ENST00000331923.4	37	CCDS13619.1																																																																																			G|0.999;A|0.001	0.001	strong		0.373	PAXBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139563.1	NM_013329	
CMTM2	146225	hgsc.bcm.edu	37	16	66613725	66613725	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:66613725G>A	ENST00000268595.2	+	1	366	c.215G>A	c.(214-216)cGg>cAg	p.R72Q	CMTM2_ENST00000379486.2_Missense_Mutation_p.R72Q|RP11-403P17.2_ENST00000568430.1_RNA	NM_144673.2	NP_653274.1	Q8TAZ6	CKLF2_HUMAN	CKLF-like MARVEL transmembrane domain containing 2	72					chemotaxis (GO:0006935)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|kidney(1)|large_intestine(4)|lung(6)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	17		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.068)|Epithelial(162;0.212)		CGCCGCTACCGGTGGGAATTA	0.562																																					p.R72Q		Atlas-SNP	.											.	CMTM2	33	.	0			c.G215A						PASS	.						48.0	52.0	51.0					16																	66613725		2201	4300	6501	SO:0001583	missense	146225	exon1			GCTACCGGTGGGA	BC025354	CCDS10814.1, CCDS56001.1	16q22.1-q22.3	2008-02-05	2005-11-08	2005-11-08	ENSG00000140932	ENSG00000140932			19173	protein-coding gene	gene with protein product		607885	"""chemokine-like factor super family 2"", ""chemokine-like factor superfamily 2"""	CKLFSF2			Standard	NM_001199317		Approved	MGC39436, FLJ25732	uc002ept.3	Q8TAZ6	OTTHUMG00000137501	ENST00000268595.2:c.215G>A	16.37:g.66613725G>A	ENSP00000268595:p.Arg72Gln	69.0	0.0	0		80.0	40.0	0.5	NM_001199317	Q5I2A4|Q8N7E5	Missense_Mutation	SNP	ENST00000268595.2	37	CCDS10814.1	.	.	.	.	.	.	.	.	.	.	G	19.20	3.781718	0.70222	.	.	ENSG00000140932	ENST00000379486;ENST00000268595	T;T	0.49139	0.79;1.37	4.51	-7.19	0.01500	.	1.889910	0.02580	N	0.098726	T	0.26955	0.0660	L	0.36672	1.1	0.09310	N	1	P;B	0.38167	0.621;0.447	B;B	0.27608	0.081;0.045	T	0.21415	-1.0246	10	0.28530	T	0.3	1.8102	4.3444	0.11126	0.2588:0.0:0.2537:0.4874	.	72;72	Q5I2A4;Q8TAZ6	.;CKLF2_HUMAN	Q	72	ENSP00000368800:R72Q;ENSP00000268595:R72Q	ENSP00000268595:R72Q	R	+	2	0	CMTM2	65171226	0.001000	0.12720	0.000000	0.03702	0.848000	0.48234	-1.284000	0.02793	-1.329000	0.02258	0.561000	0.74099	CGG	.	.	none		0.562	CMTM2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268808.1		
TAF1A	9015	hgsc.bcm.edu	37	1	222732051	222732051	+	Missense_Mutation	SNP	C	C	T	rs143557200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:222732051C>T	ENST00000352967.4	-	11	1492	c.1304G>A	c.(1303-1305)cGg>cAg	p.R435Q	TAF1A_ENST00000350027.4_Missense_Mutation_p.R435Q|TAF1A_ENST00000391882.1_Missense_Mutation_p.R321Q|TAF1A_ENST00000366890.1_Missense_Mutation_p.R321Q	NM_005681.3	NP_005672.1	Q15573	TAF1A_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kDa	435					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	intracellular membrane-bounded organelle (GO:0043231)|microtubule cytoskeleton (GO:0015630)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|RNA polymerase I transcription factor complex (GO:0000120)	DNA binding (GO:0003677)			kidney(3)|large_intestine(3)|lung(11)|urinary_tract(1)	18				GBM - Glioblastoma multiforme(131;0.0186)		TCTCTTCATCCGCTTAATTTT	0.303													C|||	20	0.00399361	0.0	0.0144	5008	,	,		12618	0.0		0.007	False		,,,				2504	0.0031				p.R435Q		Atlas-SNP	.											TAF1A,NS,carcinoma,0,1	TAF1A	35	1	0			c.G1304A						PASS	.	C	GLN/ARG,GLN/ARG,GLN/ARG	2,4400	4.2+/-10.8	0,2,2199	82.0	84.0	83.0		1304,1304,962	-3.5	0.8	1	dbSNP_134	83	72,8498	40.8+/-97.7	1,70,4214	yes	missense,missense,missense	TAF1A	NM_001201536.1,NM_005681.3,NM_139352.2	43,43,43	1,72,6413	TT,TC,CC		0.8401,0.0454,0.5705	benign,benign,benign	435/451,435/451,321/337	222732051	74,12898	2201	4285	6486	SO:0001583	missense	9015	exon11			TTCATCCGCTTAA	L39060	CCDS1531.1, CCDS1532.1	1q42	2008-02-05	2002-08-29		ENSG00000143498	ENSG00000143498			11532	protein-coding gene	gene with protein product		604903	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, A, 48kD"""			7801123	Standard	NM_005681		Approved	TAFI48, SL1	uc009xdz.2	Q15573	OTTHUMG00000037544	ENST00000352967.4:c.1304G>A	1.37:g.222732051C>T	ENSP00000327072:p.Arg435Gln	90.0	0.0	0		90.0	43.0	0.477778	NM_001201536	B2RDZ8|D3DTB7|Q9NWA1	Missense_Mutation	SNP	ENST00000352967.4	37	CCDS1531.1	10	0.004578754578754579	0	0.0	5	0.013812154696132596	0	0.0	5	0.006596306068601583	C	10.77	1.444536	0.25987	4.54E-4	0.008401	ENSG00000143498	ENST00000366890;ENST00000350027;ENST00000352967;ENST00000391882	T;T;T;T	0.43294	0.95;0.95;0.95;0.95	5.34	-3.51	0.04696	.	0.878450	0.10066	N	0.720352	T	0.16214	0.0390	N	0.21583	0.68	0.38468	D	0.947394	B	0.15141	0.012	B	0.10450	0.005	T	0.21965	-1.0230	10	0.18276	T	0.48	-18.2737	7.0687	0.25167	0.0:0.2261:0.1415:0.6324	.	435	Q15573	TAF1A_HUMAN	Q	321;435;435;321	ENSP00000355856:R321Q;ENSP00000339976:R435Q;ENSP00000327072:R435Q;ENSP00000375754:R321Q	ENSP00000339976:R435Q	R	-	2	0	TAF1A	220798674	0.035000	0.19736	0.844000	0.33320	0.826000	0.46750	-1.046000	0.03525	-0.257000	0.09459	-0.345000	0.07892	CGG	C|0.994;T|0.006	0.006	strong		0.303	TAF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091493.2	NM_005681	
LIG1	3978	hgsc.bcm.edu	37	19	48664687	48664687	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:48664687C>T	ENST00000263274.7	-	4	604	c.185G>A	c.(184-186)cGg>cAg	p.R62Q	LIG1_ENST00000536218.1_Missense_Mutation_p.R62Q|LIG1_ENST00000427526.2_Missense_Mutation_p.R32Q|LIG1_ENST00000599165.1_Intron	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	62			R -> W (in dbSNP:rs3730863). {ECO:0000269|Ref.2}.		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)	GCCCAGGACCCGGGCCGCCTT	0.602								Nucleotide excision repair (NER)																													p.R62Q		Atlas-SNP	.											.	LIG1	151	.	0			c.G185A						PASS	.						124.0	120.0	121.0					19																	48664687		2203	4300	6503	SO:0001583	missense	3978	exon4			AGGACCCGGGCCG		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.185G>A	19.37:g.48664687C>T	ENSP00000263274:p.Arg62Gln	55.0	0.0	0		38.0	24.0	0.631579	NM_000234	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	C	12.86	2.063708	0.36373	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218;ENST00000542460	T;T;T;T	0.58652	0.45;0.32;0.46;1.98	4.62	-1.03	0.10102	.	0.681137	0.14004	N	0.347948	T	0.39545	0.1082	L	0.39397	1.21	0.20975	N	0.999815	B;B;B	0.18013	0.008;0.025;0.008	B;B;B	0.09377	0.001;0.004;0.001	T	0.25710	-1.0124	10	0.12766	T	0.61	-5.9785	7.7073	0.28657	0.0:0.5183:0.0:0.4817	.	32;62;62	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	Q	62;94;32;62;62	ENSP00000263274:R62Q;ENSP00000442841:R32Q;ENSP00000441531:R62Q;ENSP00000445928:R62Q	ENSP00000263274:R62Q	R	-	2	0	LIG1	53356499	0.489000	0.26004	0.781000	0.31783	0.827000	0.46813	-0.049000	0.11924	-0.188000	0.10499	-0.369000	0.07265	CGG	.	.	none		0.602	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465575.1	NM_000234	
DYSF	8291	hgsc.bcm.edu	37	2	71778829	71778829	+	Silent	SNP	G	G	A	rs35984374	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:71778829G>A	ENST00000258104.3	+	19	2008	c.1731G>A	c.(1729-1731)gcG>gcA	p.A577A	DYSF_ENST00000409582.3_Silent_p.A594A|DYSF_ENST00000413539.2_Silent_p.A608A|DYSF_ENST00000409744.1_Silent_p.A564A|DYSF_ENST00000429174.2_Silent_p.A577A|DYSF_ENST00000409762.1_Silent_p.A594A|DYSF_ENST00000410020.3_Silent_p.A595A|DYSF_ENST00000409366.1_Silent_p.A578A|DYSF_ENST00000394120.2_Silent_p.A578A|DYSF_ENST00000410041.1_Silent_p.A595A|DYSF_ENST00000409651.1_Silent_p.A609A	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	577					plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						ACCTTCCTGCGGATGACATCC	0.652													G|||	30	0.00599042	0.0008	0.0058	5008	,	,		15341	0.0		0.0249	False		,,,				2504	0.0				p.A609A		Atlas-SNP	.											.	DYSF	536	.	0			c.G1827A						PASS	.	G	,,,,,,,,,,,,,	17,4389	23.3+/-48.9	1,15,2187	73.0	61.0	65.0		1734,1689,1689,1731,1824,1782,1782,1827,1734,1692,1785,1692,1785,1731	-10.9	0.0	2	dbSNP_126	65	168,8432	76.9+/-139.5	1,166,4133	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	DYSF	NM_001130455.1,NM_001130976.1,NM_001130977.1,NM_001130978.1,NM_001130979.1,NM_001130980.1,NM_001130981.1,NM_001130982.1,NM_001130983.1,NM_001130984.1,NM_001130985.1,NM_001130986.1,NM_001130987.1,NM_003494.3	,,,,,,,,,,,,,	2,181,6320	AA,AG,GG		1.9535,0.3858,1.4224	,,,,,,,,,,,,,	578/2082,563/2067,563/2088,577/2102,608/2112,594/2098,594/2119,609/2113,578/2103,564/2089,595/2099,564/2068,595/2120,577/2081	71778829	185,12821	2203	4300	6503	SO:0001819	synonymous_variant	8291	exon20			TCCTGCGGATGAC	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.1731G>A	2.37:g.71778829G>A		42.0	0.0	0		47.0	26.0	0.553191	NM_001130982	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	Silent	SNP	ENST00000258104.3	37	CCDS1918.1																																																																																			G|0.987;A|0.013	0.013	strong		0.652	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
SLC2A14	144195	hgsc.bcm.edu	37	12	7985318	7985318	+	Splice_Site	SNP	C	C	A	rs10846018	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:7985318C>A	ENST00000543909.1	-	8	939	c.180G>T	c.(178-180)acG>acT	p.T60T	SLC2A14_ENST00000431042.2_Splice_Site_p.T37T|SLC2A14_ENST00000542505.1_Intron|SLC2A14_ENST00000542546.1_Splice_Site_p.R5L|SLC2A14_ENST00000535295.1_Splice_Site_p.R5L|SLC2A14_ENST00000539924.1_Splice_Site_p.T75T|SLC2A14_ENST00000340749.5_Splice_Site_p.T37T|SLC2A14_ENST00000396589.2_Splice_Site_p.T60T			Q8TDB8	GTR14_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 14	60					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	glucose transmembrane transporter activity (GO:0005355)			central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(12)|ovary(2)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(1)	38				Kidney(36;0.0883)		TGGCACTCACCGTCTCAGGAG	0.478											OREG0021654	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	c|||	55	0.0109824	0.0015	0.0144	5008	,	,		-128	0.0		0.0398	False		,,,				2504	0.0031				p.T60T		Atlas-SNP	.											.	SLC2A14	78	.	0			c.G180T						PASS	.	C		40,4366	43.8+/-77.6	0,40,2163	96.0	92.0	93.0		180	0.5	0.4	12	dbSNP_120	93	276,8324	104.6+/-165.6	4,268,4028	yes	coding-synonymous-near-splice	SLC2A14	NM_153449.2		4,308,6191	AA,AC,CC		3.2093,0.9079,2.4296		60/521	7985318	316,12690	2203	4300	6503	SO:0001630	splice_region_variant	144195	exon4			ACTCACCGTCTCA	AF481878	CCDS8585.1, CCDS66300.1, CCDS66301.1, CCDS66302.1	12p13.31	2013-07-15			ENSG00000173262	ENSG00000173262		"""Solute carriers"""	18301	protein-coding gene	gene with protein product		611039	"""solute carrier family 2 (facilitated glucose transporter), member 3 pseudogene 3"""	SLC2A3P3		12504846	Standard	NM_001286234		Approved	GLUT14	uc001qtn.3	Q8TDB8	OTTHUMG00000168463	ENST00000543909.1:c.180+1G>T	12.37:g.7985318C>A		97.0	0.0	0	645	93.0	50.0	0.537634	NM_153449	B3KVB5|B3KWW7|B7Z844|B7ZAC3|Q6UY84|Q8TDB9	Silent	SNP	ENST00000543909.1	37	CCDS8585.1	42	0.019230769230769232	2	0.0040650406504065045	6	0.016574585635359115	0	0.0	34	0.044854881266490766	C	14.99	2.701667	0.48307	0.009079	0.032093	ENSG00000173262	ENST00000535295;ENST00000542546	D;D	0.83837	-1.77;-1.77	2.59	0.538	0.17150	.	.	.	.	.	T	0.69187	0.3083	.	.	.	0.53688	D	0.999972	D	0.64830	0.994	D	0.68943	0.961	T	0.77040	-0.2735	7	.	.	.	.	8.4863	0.33074	0.0:0.7381:0.0:0.2619	rs10846018;rs10846018	5	B7Z844	.	L	5	ENSP00000440492:R5L;ENSP00000443903:R5L	.	R	-	2	0	SLC2A14	7876585	0.256000	0.24012	0.446000	0.26920	0.094000	0.18550	0.809000	0.27168	-0.343000	0.08351	-1.641000	0.00772	CGG	C|0.979;A|0.021	0.021	strong		0.478	SLC2A14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399836.2	NM_153449	Silent
ARPP21	10777	hgsc.bcm.edu	37	3	35780947	35780947	+	Missense_Mutation	SNP	G	G	A	rs151173813	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:35780947G>A	ENST00000187397.4	+	17	2239	c.1783G>A	c.(1783-1785)Gcc>Acc	p.A595T	ARPP21_ENST00000444190.1_Missense_Mutation_p.A576T|ARPP21_ENST00000458225.1_Missense_Mutation_p.A596T|ARPP21_ENST00000337271.5_Missense_Mutation_p.A576T|ARPP21_ENST00000417925.1_Missense_Mutation_p.A596T	NM_016300.4	NP_057384.2	Q9UBL0	ARP21_HUMAN	cAMP-regulated phosphoprotein, 21kDa	595	Gln-rich.				cellular response to heat (GO:0034605)	cytoplasm (GO:0005737)	nucleic acid binding (GO:0003676)	p.A595T(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|lung(31)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	61						CTATGTAATCGCCTCTACAGG	0.627													G|||	7	0.00139776	0.0	0.0029	5008	,	,		15714	0.0		0.003	False		,,,				2504	0.002				p.A596T		Atlas-SNP	.											ARPP21,NS,NS,0,1	ARPP21	153	1	1	Substitution - Missense(1)	large_intestine(1)	c.G1786A						PASS	.	G	THR/ALA	3,4403	6.2+/-15.9	0,3,2200	58.0	59.0	58.0		1783	4.1	0.4	3	dbSNP_134	58	37,8563	25.7+/-73.6	0,37,4263	yes	missense	ARPP21	NM_016300.4	58	0,40,6463	AA,AG,GG		0.4302,0.0681,0.3076	benign	595/813	35780947	40,12966	2203	4300	6503	SO:0001583	missense	10777	exon16			GTAATCGCCTCTA	AA733082	CCDS2661.1, CCDS43063.1, CCDS58823.1, CCDS58824.1	3p24.3	2010-08-12			ENSG00000172995	ENSG00000172995			16968	protein-coding gene	gene with protein product	"""R3H domain containing 3"""	605488				8120638	Standard	NM_198399		Approved	ARPP-21, TARPP, R3HDM3	uc011axy.2	Q9UBL0	OTTHUMG00000130795	ENST00000187397.4:c.1783G>A	3.37:g.35780947G>A	ENSP00000187397:p.Ala595Thr	108.0	0.0	0		135.0	76.0	0.562963	NM_001267619	B4DG96|Q49AK3|Q49AS6|Q4G0V4|Q6NYC3|Q86V31|Q9UF93	Missense_Mutation	SNP	ENST00000187397.4	37	CCDS2661.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	11.71	1.719677	0.30503	6.81E-4	0.004302	ENSG00000172995	ENST00000458225;ENST00000337271;ENST00000444190;ENST00000187397;ENST00000417925	T;T;T;T;T	0.40476	1.03;1.03;1.03;1.03;1.03	5.96	4.14	0.48551	.	0.068903	0.56097	N	0.000036	T	0.19127	0.0459	L	0.31476	0.935	0.31779	N	0.631164	B;B;B;B	0.32543	0.067;0.375;0.011;0.067	B;B;B;B	0.28385	0.023;0.089;0.006;0.023	T	0.19418	-1.0306	10	0.12103	T	0.63	-7.922	10.8408	0.46715	0.1502:0.0:0.8498:0.0	.	596;118;595;576	Q9UBL0-3;Q9UBL0-5;Q9UBL0;Q9UBL0-4	.;.;ARP21_HUMAN;.	T	596;576;576;595;596	ENSP00000414351:A596T;ENSP00000337792:A576T;ENSP00000405276:A576T;ENSP00000187397:A595T;ENSP00000412326:A596T	ENSP00000187397:A595T	A	+	1	0	ARPP21	35755951	1.000000	0.71417	0.406000	0.26421	0.573000	0.36030	4.374000	0.59543	1.499000	0.48617	0.655000	0.94253	GCC	G|0.997;A|0.003	0.003	strong		0.627	ARPP21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253334.2	NM_198399	
ADGB	79747	hgsc.bcm.edu	37	6	146993392	146993392	+	Silent	SNP	A	A	G	rs77104188	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:146993392A>G	ENST00000397944.3	+	8	952	c.876A>G	c.(874-876)aaA>aaG	p.K292K	ADGB_ENST00000367493.3_5'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	292	Calpain catalytic. {ECO:0000255|PROSITE- ProRule:PRU00239}.				oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						AGCTCCTGAAAGAAATATTGC	0.378													A|||	111	0.0221645	0.003	0.0274	5008	,	,		17411	0.0		0.0437	False		,,,				2504	0.045				p.K292K		Atlas-SNP	.											.	ADGB	93	.	0			c.A876G						PASS	.	A		13,1371		0,13,679	57.0	51.0	53.0		876	1.3	1.0	6	dbSNP_132	53	206,2976		9,188,1394	no	coding-synonymous	C6orf103	NM_024694.3		9,201,2073	GG,GA,AA		6.4739,0.9393,4.7963		292/1668	146993392	219,4347	692	1591	2283	SO:0001819	synonymous_variant	79747	exon8			CCTGAAAGAAATA	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.876A>G	6.37:g.146993392A>G		118.0	0.0	0		118.0	51.0	0.432203	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				A|0.976;G|0.024	0.024	strong		0.378	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
TFIP11	24144	hgsc.bcm.edu	37	22	26899695	26899695	+	Silent	SNP	G	G	A	rs74334826	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:26899695G>A	ENST00000407690.1	-	7	868	c.585C>T	c.(583-585)tcC>tcT	p.S195S	TFIP11_ENST00000496523.1_5'UTR|TFIP11_ENST00000407431.1_Silent_p.S195S|TFIP11_ENST00000407148.1_Silent_p.S195S|TFIP11_ENST00000405938.1_Silent_p.S195S	NM_012143.2	NP_036275.1	Q9UBB9	TFP11_HUMAN	tuftelin interacting protein 11	195	G-patch. {ECO:0000255|PROSITE- ProRule:PRU00092}.				biomineral tissue development (GO:0031214)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|RNA processing (GO:0006396)|spliceosomal complex disassembly (GO:0000390)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|nuclear speck (GO:0016607)|proteinaceous extracellular matrix (GO:0005578)|spliceosomal complex (GO:0005681)|U2-type post-mRNA release spliceosomal complex (GO:0071008)	DNA binding (GO:0003677)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	25						TGGTGCGCTCGGATCCATAAG	0.483													G|||	22	0.00439297	0.0008	0.0072	5008	,	,		19610	0.0		0.0149	False		,,,				2504	0.001				p.S195S		Atlas-SNP	.											.	TFIP11	72	.	0			c.C585T						PASS	.	G	,	12,4394	17.9+/-39.9	0,12,2191	154.0	135.0	141.0		585,585	-11.4	0.0	22	dbSNP_132	141	143,8457	71.3+/-133.9	0,143,4157	no	coding-synonymous,coding-synonymous	TFIP11	NM_001008697.1,NM_012143.2	,	0,155,6348	AA,AG,GG		1.6628,0.2724,1.1918	,	195/838,195/838	26899695	155,12851	2203	4300	6503	SO:0001819	synonymous_variant	24144	exon8			GCGCTCGGATCCA	AL050258	CCDS13838.1	22q12.1	2013-01-28			ENSG00000100109	ENSG00000100109		"""G patch domain containing"""	17165	protein-coding gene	gene with protein product		612747				10806191, 11230166	Standard	NM_012143		Approved	TIP39, DKFZP434B194, Spp382	uc003acs.2	Q9UBB9	OTTHUMG00000150883	ENST00000407690.1:c.585C>T	22.37:g.26899695G>A		74.0	0.0	0		88.0	44.0	0.5	NM_001008697	O95908|Q20WL0|Q5H8V8|Q9UGV7|Q9Y2Q8	Silent	SNP	ENST00000407690.1	37	CCDS13838.1	12	0.005494505494505495	0	0.0	3	0.008287292817679558	0	0.0	9	0.011873350923482849	G	0.332	-0.955568	0.02267	0.002724	0.016628	ENSG00000100109	ENST00000450493	.	.	.	5.68	-11.4	0.00090	.	.	.	.	.	T	0.17789	0.0427	.	.	.	0.51012	D	0.999905	.	.	.	.	.	.	T	0.45542	-0.9254	4	.	.	.	-16.0333	1.8375	0.03143	0.1951:0.1397:0.2425:0.4227	.	.	.	.	L	32	.	.	P	-	2	0	TFIP11	25229695	0.000000	0.05858	0.008000	0.14137	0.031000	0.12232	-7.970000	0.00027	-3.591000	0.00136	-0.867000	0.03001	CCG	G|0.991;A|0.009	0.009	strong		0.483	TFIP11-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320750.1	NM_001008697	
WDR66	144406	hgsc.bcm.edu	37	12	122404946	122404946	+	Missense_Mutation	SNP	C	C	T	rs146415200	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:122404946C>T	ENST00000288912.4	+	16	3432	c.2578C>T	c.(2578-2580)Cgc>Tgc	p.R860C	WDR66_ENST00000545752.1_3'UTR|WDR66_ENST00000397454.2_Missense_Mutation_p.R860C	NM_144668.5	NP_653269.3	Q8TBY9	WDR66_HUMAN	WD repeat domain 66	860							calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(11)|liver(2)|lung(13)|ovary(2)|prostate(2)|skin(2)|soft_tissue(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	all_neural(191;0.0496)|Medulloblastoma(191;0.0922)			OV - Ovarian serous cystadenocarcinoma(86;0.000155)|Epithelial(86;0.000634)|BRCA - Breast invasive adenocarcinoma(302;0.248)		GCTACAGAAACGCTACTTGGT	0.483													C|||	13	0.00259585	0.0	0.0043	5008	,	,		14206	0.001		0.007	False		,,,				2504	0.002				p.R860C	Esophageal Squamous(85;849 1794 49757 52143)	Atlas-SNP	.											WDR66,NS,carcinoma,-1,1	WDR66	143	1	0			c.C2578T						PASS	.	C	CYS/ARG,CYS/ARG	8,3860		0,8,1926	110.0	111.0	111.0		2578,2578	4.6	1.0	12	dbSNP_134	111	69,8201		1,67,4067	yes	missense,missense	WDR66	NM_001178003.1,NM_144668.5	180,180	1,75,5993	TT,TC,CC		0.8343,0.2068,0.6344	possibly-damaging,possibly-damaging	860/942,860/1150	122404946	77,12061	1934	4135	6069	SO:0001583	missense	144406	exon16			CAGAAACGCTACT	AL833930	CCDS41853.1, CCDS53840.1	12q24.31	2014-07-31			ENSG00000158023	ENSG00000158023		"""WD repeat domain containing"""	28506	protein-coding gene	gene with protein product						17967944	Standard	NM_001178003		Approved	MGC33630, CaM-IP4	uc009zxk.3	Q8TBY9	OTTHUMG00000168948	ENST00000288912.4:c.2578C>T	12.37:g.122404946C>T	ENSP00000288912:p.Arg860Cys	82.0	0.0	0		83.0	42.0	0.506024	NM_001178003	C9J1W2|Q8IYA3|Q8N898|Q8NDE7	Missense_Mutation	SNP	ENST00000288912.4	37	CCDS41853.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	14.97	2.695530	0.48202	0.002068	0.008343	ENSG00000158023	ENST00000288912;ENST00000397454	T;T	0.56776	0.44;1.19	4.61	4.61	0.57282	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);	0.385177	0.27415	N	0.019473	T	0.49304	0.1549	M	0.78916	2.43	0.42205	D	0.991785	P	0.52316	0.952	P	0.44561	0.453	T	0.64592	-0.6371	10	0.66056	D	0.02	.	13.2823	0.60222	0.0:0.8409:0.1591:0.0	.	860	Q8TBY9	WDR66_HUMAN	C	860	ENSP00000288912:R860C;ENSP00000380595:R860C	ENSP00000288912:R860C	R	+	1	0	WDR66	120889329	0.923000	0.31300	0.999000	0.59377	0.216000	0.24613	1.620000	0.36976	2.124000	0.65301	0.551000	0.68910	CGC	C|0.995;T|0.005	0.005	strong		0.483	WDR66-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401700.1	NM_144668	
PDXDC1	23042	hgsc.bcm.edu	37	16	15127249	15127249	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr16:15127249A>G	ENST00000396410.4	+	19	1902	c.1805A>G	c.(1804-1806)aAc>aGc	p.N602S	PDXDC1_ENST00000447912.2_Missense_Mutation_p.N511S|PDXDC1_ENST00000569715.1_Missense_Mutation_p.N575S|PDXDC1_ENST00000325823.7_Missense_Mutation_p.N587S|PDXDC1_ENST00000563679.1_Missense_Mutation_p.N620S|PDXDC1_ENST00000535621.2_Intron|PDXDC1_ENST00000450288.2_Missense_Mutation_p.N574S	NM_015027.2	NP_055842.2	Q6P996	PDXD1_HUMAN	pyridoxal-dependent decarboxylase domain containing 1	602					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						ATAGAGGAGAACTCGAGGGTC	0.572																																					p.N602S		Atlas-SNP	.											.	PDXDC1	59	.	0			c.A1805G						PASS	.						120.0	112.0	115.0					16																	15127249		2197	4300	6497	SO:0001583	missense	23042	exon19			AGGAGAACTCGAG	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.1805A>G	16.37:g.15127249A>G	ENSP00000379691:p.Asn602Ser	62.0	0.0	0		72.0	46.0	0.638889	NM_015027	B4DR55|B4DSL3|E7EMH5|E7EPL4|H3BNZ1|O00236|Q4F6X7|Q6PID7|Q86YF1|Q8N4Q9|Q8TBS5	Missense_Mutation	SNP	ENST00000396410.4	37	CCDS32393.1	.	.	.	.	.	.	.	.	.	.	A	9.764	1.170997	0.21621	.	.	ENSG00000179889	ENST00000325823;ENST00000447912;ENST00000396410;ENST00000450288	T;T;T;T	0.71698	-0.59;-0.59;-0.59;-0.59	5.83	5.83	0.93111	.	0.077261	0.85682	D	0.000000	T	0.54806	0.1881	N	0.17631	0.505	0.80722	D	1	B;B;B;B	0.26400	0.021;0.148;0.021;0.037	B;B;B;B	0.23574	0.029;0.047;0.029;0.029	T	0.52902	-0.8513	10	0.12103	T	0.63	-25.0955	15.3837	0.74681	1.0:0.0:0.0:0.0	.	574;511;574;602	E7EPL4;E7EMH5;B4DR55;Q6P996	.;.;.;PDXD1_HUMAN	S	587;511;602;574	ENSP00000322807:N587S;ENSP00000400310:N511S;ENSP00000379691:N602S;ENSP00000391147:N574S	ENSP00000322807:N587S	N	+	2	0	PDXDC1	15034750	1.000000	0.71417	0.994000	0.49952	0.218000	0.24690	4.530000	0.60595	2.231000	0.72958	0.459000	0.35465	AAC	.	.	none		0.572	PDXDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389065.2	NM_015027	
MARK3	4140	hgsc.bcm.edu	37	14	103941454	103941454	+	Silent	SNP	G	G	A	rs56126530	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr14:103941454G>A	ENST00000429436.2	+	13	1899	c.1389G>A	c.(1387-1389)aaG>aaA	p.K463K	MARK3_ENST00000440884.3_Silent_p.K384K|MARK3_ENST00000416682.2_Silent_p.K486K|MARK3_ENST00000335102.5_Silent_p.K486K|MARK3_ENST00000561071.1_Intron|MARK3_ENST00000553942.1_Silent_p.K463K|MARK3_ENST00000303622.9_Silent_p.K463K|MARK3_ENST00000216288.7_Silent_p.K447K	NM_001128918.1|NM_001128919.1	NP_001122390.1|NP_001122391.1	P27448	MARK3_HUMAN	MAP/microtubule affinity-regulating kinase 3	463						plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			autonomic_ganglia(1)|breast(1)|central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	30		Melanoma(154;0.155)	Epithelial(46;0.241)			TTGGAGGAAAGGGAATTGCTC	0.488													G|||	20	0.00399361	0.0	0.0029	5008	,	,		18604	0.001		0.0169	False		,,,				2504	0.0				p.K463K		Atlas-SNP	.											.	MARK3	86	.	0			c.G1389A						PASS	.	G	,,,,	3,3887		0,3,1942	78.0	77.0	77.0		1389,1389,1341,1152,1389	3.9	1.0	14	dbSNP_129	77	95,8197		2,91,4053	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	MARK3	NM_001128918.1,NM_001128919.1,NM_001128920.1,NM_001128921.1,NM_002376.5	,,,,	2,94,5995	AA,AG,GG		1.1457,0.0771,0.8045	,,,,	463/754,463/745,447/714,384/660,463/730	103941454	98,12084	1945	4146	6091	SO:0001819	synonymous_variant	4140	exon13			AGGAAAGGGAATT	M80359	CCDS41993.1, CCDS45165.1, CCDS45166.1, CCDS45167.1, CCDS55947.1	14q32.32	2014-04-07			ENSG00000075413	ENSG00000075413			6897	protein-coding gene	gene with protein product		602678				9533022	Standard	NM_002376		Approved	CTAK1, KP78, PAR-1A	uc001ymz.4	P27448	OTTHUMG00000171789	ENST00000429436.2:c.1389G>A	14.37:g.103941454G>A		95.0	0.0	0		105.0	51.0	0.485714	NM_001128919	O60219|Q86TT8|Q8TB41|Q8WX83|Q96RG1|Q9UMY9|Q9UN34	Silent	SNP	ENST00000429436.2	37	CCDS45165.1	18	0.008241758241758242	0	0.0	0	0.0	1	0.0017482517482517483	17	0.022427440633245383	G	9.682	1.149478	0.21288	7.71E-4	0.011457	ENSG00000075413	ENST00000554627	.	.	.	5.78	3.91	0.45181	.	.	.	.	.	T	0.31040	0.0784	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.25882	-1.0119	4	.	.	.	.	3.6647	0.08252	0.2736:0.0:0.5486:0.1777	rs56126530	.	.	.	K	215	.	.	R	+	2	0	MARK3	103011207	1.000000	0.71417	0.960000	0.40013	0.953000	0.61014	1.561000	0.36342	0.744000	0.32741	0.655000	0.94253	AGG	G|0.989;A|0.011	0.011	strong		0.488	MARK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000415144.1	NM_001128918	
VWA3B	200403	hgsc.bcm.edu	37	2	98797660	98797660	+	Silent	SNP	C	C	T	rs375244468		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:98797660C>T	ENST00000477737.1	+	9	1500	c.1296C>T	c.(1294-1296)tcC>tcT	p.S432S	VWA3B_ENST00000435344.1_Silent_p.S432S|VWA3B_ENST00000451075.2_Silent_p.S282S	NM_144992.4	NP_659429.4	Q502W6	VWA3B_HUMAN	von Willebrand factor A domain containing 3B	432										NS(3)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	70						AGAATGAGTCCGTGCAGACCA	0.592																																					p.S432S		Atlas-SNP	.											.	VWA3B	138	.	0			c.C1296T						PASS	.	C		0,4068		0,0,2034	87.0	90.0	89.0		1296	-2.5	0.1	2		89	1,8365		0,1,4182	no	coding-synonymous	VWA3B	NM_144992.4		0,1,6216	TT,TC,CC		0.012,0.0,0.0080		432/1295	98797660	1,12433	2034	4183	6217	SO:0001819	synonymous_variant	200403	exon9			TGAGTCCGTGCAG	AL832761	CCDS42718.1	2q11.2	2008-02-05			ENSG00000168658	ENSG00000168658			28385	protein-coding gene	gene with protein product						12477932	Standard	NM_144992		Approved	DKFZp686F2227, MGC26733	uc002syo.3	Q502W6	OTTHUMG00000153104	ENST00000477737.1:c.1296C>T	2.37:g.98797660C>T		154.0	0.0	0		168.0	68.0	0.404762	NM_144992	B9EK71|Q86T73|Q8N2D0|Q8N770|Q8NA79|Q8ND63|Q8ND65|Q8WW02	Silent	SNP	ENST00000477737.1	37	CCDS42718.1																																																																																			.	.	weak		0.592	VWA3B-020	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353469.2	NM_144992	
CASP8AP2	9994	hgsc.bcm.edu	37	6	90577650	90577650	+	RNA	SNP	T	T	G	rs200433993	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr6:90577650T>G	ENST00000551025.1	+	0	6078									caspase 8 associated protein 2											NS(1)|endometrium(7)|kidney(6)|large_intestine(12)|lung(21)|ovary(2)|urinary_tract(2)	51		all_cancers(76;3.64e-09)|Prostate(29;1.16e-10)|Acute lymphoblastic leukemia(125;1.45e-10)|all_hematologic(105;7.74e-07)|all_epithelial(107;4.69e-05)|Lung NSC(302;0.238)		BRCA - Breast invasive adenocarcinoma(108;0.0953)		AAATACGACGTGCAACACCAT	0.443													T|||	5	0.000998403	0.0	0.0	5008	,	,		21746	0.0		0.005	False		,,,				2504	0.0				p.R1547R	Colon(187;1656 2025 17045 31481 39901)	Atlas-SNP	.											CASP8AP2,caecum,carcinoma,+2,1	CASP8AP2	108	1	0			c.T4641G						PASS	.	T	,,	5,3875		0,5,1935	142.0	128.0	133.0		4641,4641,4641	4.3	1.0	6		133	22,8250		0,22,4114	no	coding-synonymous,coding-synonymous,coding-synonymous	CASP8AP2	NM_001137667.1,NM_001137668.1,NM_012115.3	,,	0,27,6049	GG,GT,TT		0.266,0.1289,0.2222	,,	1547/1967,1547/1967,1547/1967	90577650	27,12125	1940	4136	6076			9994	exon8			ACGACGTGCAACA	AB037736		6q15	2012-04-19	2008-10-30		ENSG00000118412	ENSG00000118412			1510	protein-coding gene	gene with protein product	"""FLICE-associated huge protein"""	606880	"""CASP8 associated protein 2"""			10235259, 17245429, 17003126	Standard	NM_001137668		Approved	FLASH, CED-4, RIP25, FLJ11208, KIAA1315	uc011dzz.2	Q9UKL3	OTTHUMG00000015212		6.37:g.90577650T>G		89.0	0.0	0		96.0	37.0	0.385417	NM_001137667		Silent	SNP	ENST00000551025.1	37																																																																																				T|0.996;G|0.004	0.004	strong		0.443	CASP8AP2-202	KNOWN	basic	processed_transcript	processed_transcript		NM_001137667	
ZNF100	163227	hgsc.bcm.edu	37	19	21910621	21910621	+	Silent	SNP	A	A	G	rs11556742	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr19:21910621A>G	ENST00000358296.6	-	5	691	c.493T>C	c.(493-495)Tta>Cta	p.L165L	ZNF100_ENST00000305570.6_Silent_p.L101L	NM_173531.3	NP_775802.2	Q8IYN0	ZN100_HUMAN	zinc finger protein 100	165					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(11)|skin(1)|upper_aerodigestive_tract(1)	21						CACTGGTTTAATTTGTTATCA	0.313													N|||	92	0.0183706	0.0023	0.0576	5008	,	,		16971	0.0		0.0249	False		,,,				2504	0.0245				p.L165L		Atlas-SNP	.											.	ZNF100	62	.	0			c.T493C						PASS	.	A		16,4080		0,16,2032	168.0	169.0	169.0		493	1.4	0.0	19	dbSNP_120	169	178,8286		1,176,4055	no	coding-synonymous	ZNF100	NM_173531.3		1,192,6087	GG,GA,AA		2.103,0.3906,1.5446		165/543	21910621	194,12366	2048	4232	6280	SO:0001819	synonymous_variant	163227	exon5			GGTTTAATTTGTT	BC035579	CCDS42538.1	19p13.1	2013-01-08	2003-12-19		ENSG00000197020	ENSG00000197020		"""Zinc fingers, C2H2-type"", ""-"""	12880	protein-coding gene	gene with protein product		603982	"""zinc finger protein 100 (Y1)"""			12477932	Standard	NM_173531		Approved		uc002nqi.3	Q8IYN0		ENST00000358296.6:c.493T>C	19.37:g.21910621A>G		95.0	0.0	0		111.0	48.0	0.432432	NM_173531	Q7M4M0	Silent	SNP	ENST00000358296.6	37	CCDS42538.1																																																																																			A|0.980;G|0.020	0.020	strong		0.313	ZNF100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464087.1	NM_173531	
FOXRED2	80020	hgsc.bcm.edu	37	22	36886112	36886112	+	Silent	SNP	G	G	A	rs34949308	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr22:36886112G>A	ENST00000397224.4	-	9	2091	c.1998C>T	c.(1996-1998)tcC>tcT	p.S666S	FOXRED2_ENST00000216187.6_Silent_p.S666S|FOXRED2_ENST00000397223.4_Silent_p.S666S|FOXRED2_ENST00000366463.3_Silent_p.S218S	NM_001102371.1	NP_001095841.1	Q8IWF2	FXRD2_HUMAN	FAD-dependent oxidoreductase domain containing 2	666					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)	endoplasmic reticulum lumen (GO:0005788)	flavin adenine dinucleotide binding (GO:0050660)|glycoprotein binding (GO:0001948)|oxidoreductase activity (GO:0016491)			breast(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						GAGCCAGGGGGGAACCTAGTG	0.642													G|||	40	0.00798722	0.0	0.0	5008	,	,		18397	0.0		0.0099	False		,,,				2504	0.0307				p.S666S		Atlas-SNP	.											.	FOXRED2	48	.	0			c.C1998T						PASS	.	G	,	12,4394	17.9+/-39.9	0,12,2191	33.0	37.0	36.0		1998,1998	-4.8	0.0	22	dbSNP_126	36	123,8477	61.0+/-122.8	1,121,4178	no	coding-synonymous,coding-synonymous	FOXRED2	NM_001102371.1,NM_024955.5	,	1,133,6369	AA,AG,GG		1.4302,0.2724,1.038	,	666/685,666/685	36886112	135,12871	2203	4300	6503	SO:0001819	synonymous_variant	80020	exon9			CAGGGGGGAACCT	BC027716	CCDS13929.1	22q12.3	2006-07-05			ENSG00000100350	ENSG00000100350			26264	protein-coding gene	gene with protein product		613777				12477932	Standard	NM_024955		Approved	FLJ23322	uc003app.4	Q8IWF2	OTTHUMG00000044614	ENST00000397224.4:c.1998C>T	22.37:g.36886112G>A		63.0	0.0	0		64.0	24.0	0.375	NM_001102371	B2RDI4|Q8N378|Q96BD1|Q9H5L5|Q9H6M8	Silent	SNP	ENST00000397224.4	37	CCDS13929.1																																																																																			G|0.991;A|0.009	0.009	strong		0.642	FOXRED2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104098.2	NM_024955	
BBOX1	8424	hgsc.bcm.edu	37	11	27148847	27148847	+	Silent	SNP	G	G	A	rs77035197	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:27148847G>A	ENST00000529202.1	+	8	1350	c.1011G>A	c.(1009-1011)gtG>gtA	p.V337V	BBOX1_ENST00000528583.1_Silent_p.V337V|BBOX1_ENST00000525090.1_Silent_p.V337V|BBOX1_ENST00000263182.3_Silent_p.V337V|RP11-1L12.3_ENST00000526061.1_RNA|RP11-1L12.3_ENST00000530430.1_RNA|RP11-1L12.3_ENST00000525302.1_RNA			O75936	BODG_HUMAN	butyrobetaine (gamma), 2-oxoglutarate dioxygenase (gamma-butyrobetaine hydroxylase) 1	337					carnitine biosynthetic process (GO:0045329)|cellular nitrogen compound metabolic process (GO:0034641)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)	gamma-butyrobetaine dioxygenase activity (GO:0008336)|iron ion binding (GO:0005506)|zinc ion binding (GO:0008270)			breast(1)|kidney(3)|large_intestine(3)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	23					Succinic acid(DB00139)|Vitamin C(DB00126)	TAGGTGATGTGATTACTTTTG	0.398													G|||	104	0.0207668	0.0008	0.0375	5008	,	,		18591	0.0		0.0507	False		,,,				2504	0.0266				p.V337V		Atlas-SNP	.											.	BBOX1	46	.	0			c.G1011A						PASS	.	G		26,4378	32.6+/-62.9	0,26,2176	104.0	93.0	96.0		1011	4.0	1.0	11	dbSNP_132	96	366,8232	121.1+/-180.3	9,348,3942	no	coding-synonymous	BBOX1	NM_003986.2		9,374,6118	AA,AG,GG		4.2568,0.5904,3.0149		337/388	27148847	392,12610	2202	4299	6501	SO:0001819	synonymous_variant	8424	exon9			TGATGTGATTACT	AF082868	CCDS7862.1	11p	2008-02-01			ENSG00000129151	ENSG00000129151	1.14.11.1		964	protein-coding gene	gene with protein product		603312		BBOX		9753662	Standard	XM_005253159		Approved	gamma-BBH, G-BBH, BBH	uc001mre.1	O75936	OTTHUMG00000166121	ENST00000529202.1:c.1011G>A	11.37:g.27148847G>A		67.0	0.0	0		55.0	30.0	0.545455	NM_003986	B2R8L7|D3DQZ1|Q6IBJ2	Silent	SNP	ENST00000529202.1	37	CCDS7862.1																																																																																			G|0.968;A|0.032	0.032	strong		0.398	BBOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387946.1	NM_003986	
RECQL5	9400	hgsc.bcm.edu	37	17	73624466	73624466	+	Silent	SNP	G	G	A	rs140010427	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:73624466G>A	ENST00000317905.5	-	18	2796	c.2637C>T	c.(2635-2637)gtC>gtT	p.V879V	RECQL5_ENST00000443199.2_5'UTR|RECQL5_ENST00000423245.2_Silent_p.V852V	NM_004259.6	NP_004250.4	O94762	RECQ5_HUMAN	RecQ protein-like 5	879					chromosome separation (GO:0051304)|DNA duplex unwinding (GO:0032508)|DNA metabolic process (GO:0006259)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|mitotic nuclear division (GO:0007067)|negative regulation of transcription elongation from RNA polymerase II promoter (GO:0034244)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase II, holoenzyme (GO:0016591)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|DNA helicase activity (GO:0003678)|nucleic acid binding (GO:0003676)|RNA polymerase II core binding (GO:0000993)			breast(1)|cervix(3)|endometrium(3)|kidney(7)|large_intestine(7)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	36	all_cancers(13;2.73e-08)|Breast(9;6.04e-09)|all_epithelial(9;6.79e-09)		all cancers(21;1.15e-06)|Epithelial(20;2.19e-06)|Lung(188;0.101)|LUSC - Lung squamous cell carcinoma(166;0.112)			CCTCAGCTACGACGGAGGGCT	0.637								Other identified genes with known or suspected DNA repair function					G|||	16	0.00319489	0.0008	0.0	5008	,	,		17331	0.0149		0.0	False		,,,				2504	0.0				p.V879V		Atlas-SNP	.											.	RECQL5	77	.	0			c.C2637T						PASS	.	G		0,4128		0,0,2064	60.0	71.0	67.0		2637	3.0	0.0	17	dbSNP_134	67	6,8362		0,6,4178	no	coding-synonymous	RECQL5	NM_004259.6		0,6,6242	AA,AG,GG		0.0717,0.0,0.048		879/992	73624466	6,12490	2064	4184	6248	SO:0001819	synonymous_variant	9400	exon18			AGCTACGACGGAG	AB006533	CCDS32735.1, CCDS42380.1, CCDS45777.1	17q25	2014-03-07	2014-03-07	2014-03-07	ENSG00000108469	ENSG00000108469			9950	protein-coding gene	gene with protein product	"""RecQ protein 5"""	603781				9878247	Standard	NM_004259		Approved	RecQ5, FLJ90603	uc010dgl.3	O94762		ENST00000317905.5:c.2637C>T	17.37:g.73624466G>A		87.0	0.0	0		67.0	30.0	0.447761	NM_004259	Q9H0B1|Q9P1W7|Q9UNC8	Silent	SNP	ENST00000317905.5	37	CCDS42380.1																																																																																			G|0.997;A|0.003	0.003	strong		0.637	RECQL5-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448207.1	NM_004259	
PPP3CA	5530	hgsc.bcm.edu	37	4	101984390	101984390	+	Splice_Site	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr4:101984390T>C	ENST00000394854.3	-	9	1763	c.1080A>G	c.(1078-1080)aaA>aaG	p.K360K	PPP3CA_ENST00000523694.2_Splice_Site_p.K293K|PPP3CA_ENST00000394853.4_Splice_Site_p.K360K|PPP3CA_ENST00000512215.1_Splice_Site_p.K128K|PPP3CA_ENST00000323055.6_Intron|PPP3CA_ENST00000507176.1_Splice_Site_p.K262K	NM_000944.4	NP_000935.1	Q08209	PP2BA_HUMAN	protein phosphatase 3, catalytic subunit, alpha isozyme	360					calcineurin-NFAT signaling cascade (GO:0033173)|calcium ion transport (GO:0006816)|cellular response to drug (GO:0035690)|cellular response to glucose stimulus (GO:0071333)|dephosphorylation (GO:0016311)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|innate immune response (GO:0045087)|multicellular organismal response to stress (GO:0033555)|negative regulation of insulin secretion (GO:0046676)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein dephosphorylation (GO:0006470)|protein import into nucleus (GO:0006606)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic transmission (GO:0050804)|response to amphetamine (GO:0001975)|response to calcium ion (GO:0051592)|skeletal muscle fiber development (GO:0048741)|T cell activation (GO:0042110)|transition between fast and slow fiber (GO:0014883)	calcineurin complex (GO:0005955)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|calmodulin-dependent protein phosphatase activity (GO:0033192)|drug binding (GO:0008144)|enzyme binding (GO:0019899)|protein dimerization activity (GO:0046983)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|urinary_tract(1)	20				OV - Ovarian serous cystadenocarcinoma(123;6.79e-08)		ACAACATACCTTTTTCCCCAA	0.383																																					p.K360K		Atlas-SNP	.											.	PPP3CA	51	.	0			c.A1080G						PASS	.						86.0	86.0	86.0					4																	101984390		2203	4300	6503	SO:0001630	splice_region_variant	5530	exon9			CATACCTTTTTCC		CCDS34037.1, CCDS47113.1, CCDS47114.1	4q24	2010-03-17	2010-03-05		ENSG00000138814	ENSG00000138814	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase, catalytic subunits"""	9314	protein-coding gene	gene with protein product	"""calcineurin A alpha"", ""protein phosphatase 2B, catalytic subunit, alpha isoform"""	114105	"""protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform (calcineurin A alpha)"", ""protein phosphatase 3 (formerly 2B), catalytic subunit, alpha isoform"""	CALN, CALNA		2848250, 1659808	Standard	NM_000944		Approved	CNA1, PPP2B	uc011cen.1	Q08209	OTTHUMG00000133839	ENST00000394854.3:c.1081+1A>G	4.37:g.101984390T>C		146.0	0.0	0		124.0	26.0	0.209677	NM_000944	A1A441|A8K3B7|A8W6Z7|A8W6Z8|B5BUA2|Q8TAW9	Silent	SNP	ENST00000394854.3	37	CCDS34037.1																																																																																			.	.	none		0.383	PPP3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000258379.2	NM_000944	Silent
NCOR2	9612	hgsc.bcm.edu	37	12	124856830	124856830	+	Missense_Mutation	SNP	C	C	T	rs142292731	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr12:124856830C>T	ENST00000405201.1	-	20	2545	c.2545G>A	c.(2545-2547)Gag>Aag	p.E849K	NCOR2_ENST00000397355.1_Missense_Mutation_p.E832K|NCOR2_ENST00000356219.3_Missense_Mutation_p.E849K|NCOR2_ENST00000404121.2_Missense_Mutation_p.E402K|NCOR2_ENST00000429285.2_Missense_Mutation_p.E831K|NCOR2_ENST00000404621.1_Missense_Mutation_p.E831K			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	849					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)		GCCAGCTCCTCAGCCGCGGGG	0.701													C|||	21	0.00419329	0.0	0.0101	5008	,	,		10880	0.0		0.0129	False		,,,				2504	0.001				p.E849K		Atlas-SNP	.											.	NCOR2	475	.	0			c.G2545A						PASS	.	C	LYS/GLU,LYS/GLU,LYS/GLU	15,3945		0,15,1965	19.0	23.0	22.0		2491,2491,2545	0.7	0.0	12	dbSNP_134	22	226,8042		3,220,3911	yes	missense,missense,missense	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	56,56,56	3,235,5876	TT,TC,CC		2.7334,0.3788,1.9709	benign,benign,benign	831/2459,831/2505,849/2515	124856830	241,11987	1980	4134	6114	SO:0001583	missense	9612	exon22			GCTCCTCAGCCGC	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.2545G>A	12.37:g.124856830C>T	ENSP00000384018:p.Glu849Lys	32.0	0.0	0		62.0	23.0	0.370968	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Missense_Mutation	SNP	ENST00000405201.1	37	CCDS41858.2	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	10.89	1.477039	0.26511	0.003788	0.027334	ENSG00000196498	ENST00000405201;ENST00000404621;ENST00000356219;ENST00000397355;ENST00000447011;ENST00000404121;ENST00000429285;ENST00000458234	T;T;T;T;T;T;T	0.31769	1.48;1.48;1.48;1.48;1.48;1.48;1.48	4.77	0.655	0.17839	.	0.491076	0.15915	N	0.238404	T	0.05273	0.0140	N	0.22421	0.69	0.09310	N	0.99999	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.06405	0.001;0.001;0.002	T	0.17868	-1.0355	10	0.27785	T	0.31	-1.4997	4.0561	0.09818	0.2308:0.4004:0.2913:0.0776	.	831;832;849	C9J0Q5;C9J239;C9JFD3	.;.;.	K	849;831;849;832;848;402;831;849	ENSP00000384018:E849K;ENSP00000384202:E831K;ENSP00000348551:E849K;ENSP00000380513:E832K;ENSP00000385618:E402K;ENSP00000400281:E831K;ENSP00000402808:E849K	ENSP00000348551:E849K	E	-	1	0	NCOR2	123422783	0.527000	0.26306	0.001000	0.08648	0.004000	0.04260	2.329000	0.43876	-0.171000	0.10797	-0.310000	0.09108	GAG	C|0.988;T|0.012	0.012	strong		0.701	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
SCN4A	6329	hgsc.bcm.edu	37	17	62049749	62049749	+	Missense_Mutation	SNP	C	C	T	rs41280110	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:62049749C>T	ENST00000435607.1	-	2	431	c.355G>A	c.(355-357)Gta>Ata	p.V119I	SCN4A_ENST00000578147.1_Missense_Mutation_p.V119I|CTC-264K15.6_ENST00000577329.1_lincRNA	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	119					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CGCCTGACTACGCTGAAGGGG	0.607													C|||	6	0.00119808	0.0	0.0	5008	,	,		21598	0.0		0.004	False		,,,				2504	0.002				p.V119I		Atlas-SNP	.											SCN4A,NS,carcinoma,+1,1	SCN4A	205	1	0			c.G355A						PASS	.	C	ILE/VAL	2,4316		0,2,2157	66.0	72.0	70.0		355	-1.0	0.1	17	dbSNP_127	70	36,8498		0,36,4231	yes	missense	SCN4A	NM_000334.4	29	0,38,6388	TT,TC,CC		0.4218,0.0463,0.2957	benign	119/1837	62049749	38,12814	2159	4267	6426	SO:0001583	missense	6329	exon2			TGACTACGCTGAA	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.355G>A	17.37:g.62049749C>T	ENSP00000396320:p.Val119Ile	119.0	0.0	0		146.0	85.0	0.582192	NM_000334	Q15478|Q16447|Q7Z6B1	Missense_Mutation	SNP	ENST00000435607.1	37	CCDS45761.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	3.276	-0.148162	0.06627	4.63E-4	0.004218	ENSG00000007314	ENST00000435607	D	0.95918	-3.85	4.23	-0.98	0.10272	.	1.351180	0.04536	N	0.387199	D	0.82296	0.5006	N	0.00801	-1.175	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.74624	-0.3603	10	0.33141	T	0.24	.	2.0281	0.03523	0.1273:0.1785:0.4109:0.2833	rs41280110	119	P35499	SCN4A_HUMAN	I	119	ENSP00000396320:V119I	ENSP00000396320:V119I	V	-	1	0	SCN4A	59403481	0.000000	0.05858	0.116000	0.21606	0.196000	0.23810	-0.152000	0.10159	-0.405000	0.07599	-2.222000	0.00295	GTA	C|0.998;T|0.002	0.002	strong		0.607	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ERICH6	131831	hgsc.bcm.edu	37	3	150398311	150398311	+	Missense_Mutation	SNP	C	C	A	rs144597450	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:150398311C>A	ENST00000295910.6	-	9	1107	c.1055G>T	c.(1054-1056)cGa>cTa	p.R352L	FAM194A_ENST00000491361.1_Missense_Mutation_p.R206L	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						TCTGGCCATTCGTTGCTCCTG	0.383													C|||	20	0.00399361	0.0008	0.0014	5008	,	,		18752	0.0		0.0089	False		,,,				2504	0.0092				p.R352L		Atlas-SNP	.											.	FAM194A	91	.	0			c.G1055T						PASS	.	C	LEU/ARG	17,4389	23.3+/-48.9	0,17,2186	203.0	181.0	189.0		1055	-0.5	0.3	3	dbSNP_134	189	155,8445	73.8+/-136.5	0,155,4145	yes	missense	FAM194A	NM_152394.3	102	0,172,6331	AA,AC,CC		1.8023,0.3858,1.3225	benign	352/664	150398311	172,12834	2203	4300	6503	SO:0001583	missense	131831	exon9			GCCATTCGTTGCT																												ENST00000295910.6:c.1055G>T	3.37:g.150398311C>A	ENSP00000295910:p.Arg352Leu	95.0	0.0	0		112.0	47.0	0.419643	NM_152394		Missense_Mutation	SNP	ENST00000295910.6	37	CCDS3151.2	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	C	6.981	0.551108	0.13374	0.003858	0.018023	ENSG00000163645	ENST00000295910;ENST00000491361;ENST00000313811	T;T	0.14144	2.73;2.53	4.93	-0.458	0.12182	.	0.483859	0.19089	N	0.123014	T	0.03053	0.0090	N	0.22421	0.69	0.20638	N	0.999872	B	0.13594	0.008	B	0.13407	0.009	T	0.26292	-1.0107	10	0.42905	T	0.14	-6.1936	2.7584	0.05299	0.321:0.1879:0.0:0.491	.	352	Q7L0X2	F194A_HUMAN	L	352;206;310	ENSP00000295910:R352L;ENSP00000419366:R206L	ENSP00000295910:R352L	R	-	2	0	FAM194A	151881001	0.994000	0.37717	0.258000	0.24420	0.019000	0.09904	0.567000	0.23608	-0.140000	0.11394	-0.471000	0.05019	CGA	C|0.990;A|0.010	0.010	strong		0.383	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1		
MET	4233	hgsc.bcm.edu	37	7	116436097	116436097	+	Silent	SNP	G	G	A	rs41737	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:116436097G>A	ENST00000318493.6	+	21	4333	c.4146G>A	c.(4144-4146)ccG>ccA	p.P1382P	MET_ENST00000397752.3_Silent_p.P1364P|MET_ENST00000539704.1_Silent_p.P234P			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0					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)	p.P1382P(1)		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)			GTGTCGCTCCGTATCCTTCTC	0.468			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	1776	0.354633	0.0356	0.4726	5008	,	,		19834	0.4673		0.4433	False		,,,				2504	0.4949				p.P1382P		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	MET,NS,carcinoma,0,1	MET	412	1	1	Substitution - coding silent(1)	stomach(1)	c.G4146A						PASS	.	A	,	418,3602		15,388,1607	193.0	176.0	181.0		4092,4146	-3.1	1.0	7	dbSNP_76	181	3563,4817		777,2009,1404	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	792,2397,3011	AA,AG,GG		42.5179,10.398,32.1048	,	1364/1391,1382/1409	116436097	3981,8419	2010	4190	6200	SO:0001819	synonymous_variant	4233	exon21	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	CGCTCCGTATCCT	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.4146G>A	7.37:g.116436097G>A		126.0	0.0	0		148.0	148.0	1	NM_001127500	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			G|0.615;A|0.385	0.385	strong		0.468	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
RLBP1	6017	hgsc.bcm.edu	37	15	89753546	89753546	+	Silent	SNP	G	G	C	rs144615495	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr15:89753546G>C	ENST00000268125.5	-	9	1363	c.924C>G	c.(922-924)ccC>ccG	p.P308P		NM_000326.4	NP_000317.1	P12271	RLBP1_HUMAN	retinaldehyde binding protein 1	308					phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|visual perception (GO:0007601)|vitamin A metabolic process (GO:0006776)	cell body (GO:0044297)|cytosol (GO:0005829)	11-cis retinal binding (GO:0005502)|retinol binding (GO:0019841)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(1)|prostate(1)|skin(1)	18	Lung NSC(78;0.0472)|all_lung(78;0.089)				Vitamin A(DB00162)	CTTGGGCCTGGGGGCCAAAGA	0.562													G|||	2	0.000399361	0.0	0.0	5008	,	,		20947	0.0		0.002	False		,,,				2504	0.0				p.P308P		Atlas-SNP	.											.	RLBP1	34	.	0			c.C924G						PASS	.	G		1,4399	2.1+/-5.4	0,1,2199	94.0	92.0	93.0		924	-0.9	0.1	15	dbSNP_134	93	15,8583	11.2+/-40.8	0,15,4284	no	coding-synonymous	RLBP1	NM_000326.4		0,16,6483	CC,CG,GG		0.1745,0.0227,0.1231		308/318	89753546	16,12982	2200	4299	6499	SO:0001819	synonymous_variant	6017	exon9			GGCCTGGGGGCCA	BC004199	CCDS32324.1	15q26.1	2007-07-16	2001-11-28			ENSG00000140522			10024	protein-coding gene	gene with protein product		180090	"""retinaldehyde-binding protein 1"""			1733864, 9326942	Standard	NM_000326		Approved	CRALBP	uc002bnl.3	P12271		ENST00000268125.5:c.924C>G	15.37:g.89753546G>C		44.0	0.0	0		35.0	19.0	0.542857	NM_000326	B2R667	Silent	SNP	ENST00000268125.5	37	CCDS32324.1																																																																																			G|0.999;C|0.001	0.001	strong		0.562	RLBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421135.1	NM_000326	
PPFIA1	8500	hgsc.bcm.edu	37	11	70189892	70189892	+	Missense_Mutation	SNP	A	A	G	rs146858711	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:70189892A>G	ENST00000253925.7	+	15	2040	c.1825A>G	c.(1825-1827)Act>Gct	p.T609A	AP000487.6_ENST00000528607.1_RNA|PPFIA1_ENST00000389547.3_Missense_Mutation_p.T609A	NM_003626.3	NP_003617.1	Q13136	LIPA1_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 1	609					cell-matrix adhesion (GO:0007160)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of stress fiber assembly (GO:0051497)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|presynaptic active zone (GO:0048786)	signal transducer activity (GO:0004871)			breast(3)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(11)|lung(31)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	65			BRCA - Breast invasive adenocarcinoma(2;1.04e-44)|LUSC - Lung squamous cell carcinoma(11;1.46e-14)|STAD - Stomach adenocarcinoma(18;0.0513)			TGACAGGGACACTCTCCTCAG	0.557													A|||	7	0.00139776	0.0	0.0	5008	,	,		17819	0.0		0.007	False		,,,				2504	0.0				p.T609A		Atlas-SNP	.											.	PPFIA1	114	.	0			c.A1825G						PASS	.	A	ALA/THR,ALA/THR	1,4399	2.1+/-5.4	0,1,2199	139.0	95.0	110.0		1825,1825	1.7	0.7	11	dbSNP_134	110	13,8575	9.8+/-36.6	0,13,4281	yes	missense,missense	PPFIA1	NM_003626.2,NM_177423.1	58,58	0,14,6480	GG,GA,AA		0.1514,0.0227,0.1078	benign,benign	609/1203,609/1186	70189892	14,12974	2200	4294	6494	SO:0001583	missense	8500	exon15			AGGGACACTCTCC	U22816	CCDS31627.1, CCDS31628.1	11q13.3	2013-01-10			ENSG00000131626	ENSG00000131626		"""Sterile alpha motif (SAM) domain containing"""	9245	protein-coding gene	gene with protein product	"""Liprin-alpha1"""	611054				7796809, 9624153	Standard	NM_003626		Approved	LIP.1, LIPRIN	uc001opo.3	Q13136	OTTHUMG00000167266	ENST00000253925.7:c.1825A>G	11.37:g.70189892A>G	ENSP00000253925:p.Thr609Ala	76.0	0.0	0		72.0	36.0	0.5	NM_177423	A6NLE3|Q13135|Q14567|Q8N4I2	Missense_Mutation	SNP	ENST00000253925.7	37	CCDS31627.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	9.790	1.177733	0.21787	2.27E-4	0.001514	ENSG00000131626	ENST00000253925;ENST00000389547;ENST00000544950	T;T	0.23950	1.88;1.88	5.3	1.66	0.24008	.	0.134893	0.49305	N	0.000153	T	0.17789	0.0427	M	0.72118	2.19	0.42471	D	0.992829	B;B	0.15473	0.001;0.013	B;B	0.17979	0.009;0.02	T	0.04041	-1.0982	10	0.37606	T	0.19	.	6.1866	0.20500	0.7209:0.1362:0.1429:0.0	.	609;609	Q13136;Q13136-2	LIPA1_HUMAN;.	A	609;609;96	ENSP00000253925:T609A;ENSP00000374198:T609A	ENSP00000253925:T609A	T	+	1	0	PPFIA1	69867540	1.000000	0.71417	0.739000	0.30968	0.957000	0.61999	2.204000	0.42761	0.033000	0.15463	0.459000	0.35465	ACT	A|0.998;G|0.002	0.002	strong		0.557	PPFIA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000393905.1	NM_003626	
TRIM50	135892	hgsc.bcm.edu	37	7	72738638	72738638	+	Missense_Mutation	SNP	C	C	T	rs138877207	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr7:72738638C>T	ENST00000333149.2	-	2	348	c.148G>A	c.(148-150)Gag>Aag	p.E50K	TRIM50_ENST00000453152.1_Missense_Mutation_p.E50K|TRIM50_ENST00000493498.1_5'UTR	NM_178125.2	NP_835226.2	Q86XT4	TRI50_HUMAN	tripartite motif containing 50	50						cytoplasm (GO:0005737)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(3)|kidney(1)|large_intestine(2)|lung(11)|ovary(1)|skin(2)	20						CAGCGCAGCTCGGCATCCAGG	0.667											OREG0018105	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	2	0.000399361	0.0015	0.0	5008	,	,		15859	0.0		0.0	False		,,,				2504	0.0				p.E50K		Atlas-SNP	.											.	TRIM50	78	.	0			c.G148A						PASS	.						52.0	52.0	52.0					7																	72738638		2203	4300	6503	SO:0001583	missense	135892	exon2			GCAGCTCGGCATC	AY081948	CCDS34654.1	7q11.23	2013-01-09	2011-01-25	2006-03-31	ENSG00000146755	ENSG00000146755		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19017	protein-coding gene	gene with protein product		612548	"""tripartite motif-containing 50A"", ""tripartite motif-containing 50"""	TRIM50A			Standard	NM_001281450		Approved	FLJ32804	uc003txy.1	Q86XT4	OTTHUMG00000156805	ENST00000333149.2:c.148G>A	7.37:g.72738638C>T	ENSP00000327994:p.Glu50Lys	156.0	0.0	0	1139	150.0	82.0	0.546667	NM_178125	Q86XT3	Missense_Mutation	SNP	ENST00000333149.2	37	CCDS34654.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.430	-0.903959	0.02453	.	.	ENSG00000146755	ENST00000333149;ENST00000453152	T;T	0.08546	3.08;3.08	3.94	-0.221	0.13126	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	0.408805	0.22937	N	0.053826	T	0.04003	0.0112	N	0.19112	0.55	0.18873	N	0.999982	B;B	0.20780	0.038;0.048	B;B	0.16289	0.009;0.015	T	0.39375	-0.9617	10	0.25106	T	0.35	.	4.0294	0.09701	0.0:0.4312:0.2394:0.3294	.	50;50	Q86XT4-2;Q86XT4	.;TRI50_HUMAN	K	50	ENSP00000327994:E50K;ENSP00000413875:E50K	ENSP00000327994:E50K	E	-	1	0	TRIM50	72376574	0.702000	0.27816	0.244000	0.24202	0.021000	0.10359	1.858000	0.39408	0.127000	0.18452	-1.166000	0.01754	GAG	A|0.000;C|1.000;T|0.000	0.000	strong		0.667	TRIM50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345925.1	NM_178125	
NPHP3	27031	hgsc.bcm.edu	37	3	132441143	132441143	+	Silent	SNP	C	C	G	rs192633696	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr3:132441143C>G	ENST00000337331.5	-	1	143	c.57G>C	c.(55-57)acG>acC	p.T19T	NPHP3_ENST00000383282.2_Silent_p.T19T|NPHP3-AS1_ENST00000504440.1_RNA|NPHP3_ENST00000326682.8_Silent_p.T19T|NPHP3-AS1_ENST00000489343.1_RNA|NPHP3_ENST00000343113.4_Silent_p.T19T	NM_153240.4	NP_694972.3	Q7Z494	NPHP3_HUMAN	nephronophthisis 3 (adolescent)	19					atrial septum development (GO:0003283)|cilium morphogenesis (GO:0060271)|convergent extension involved in gastrulation (GO:0060027)|determination of intestine left/right asymmetry (GO:0071908)|determination of left/right symmetry (GO:0007368)|determination of liver left/right asymmetry (GO:0071910)|determination of pancreatic left/right asymmetry (GO:0035469)|determination of stomach left/right asymmetry (GO:0071909)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|establishment or maintenance of cell polarity (GO:0007163)|extracellular matrix organization (GO:0030198)|heart looping (GO:0001947)|kidney development (GO:0001822)|kidney morphogenesis (GO:0060993)|lipid metabolic process (GO:0006629)|lung development (GO:0030324)|maintenance of organ identity (GO:0048496)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|photoreceptor cell maintenance (GO:0045494)|regulation of cAMP metabolic process (GO:0030814)|regulation of planar cell polarity pathway involved in neural tube closure (GO:2000167)|regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000095)|ureter development (GO:0072189)|Wnt signaling pathway (GO:0016055)	cilium (GO:0005929)|primary cilium (GO:0072372)				NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(5)|lung(15)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	42						CCGCCCCGTACGTGTCCTCGA	0.721													c|||	46	0.0091853	0.0008	0.0202	5008	,	,		6716	0.001		0.0179	False		,,,				2504	0.0123				p.T19T		Atlas-SNP	.											.	NPHP3	110	.	0			c.G57C						PASS	.			13,3561		0,13,1774	10.0	12.0	12.0		57	0.6	1.0	3		12	120,7108		3,114,3497	no	coding-synonymous	NPHP3	NM_153240.4		3,127,5271	GG,GC,CC		1.6602,0.3637,1.2313		19/1331	132441143	133,10669	1787	3614	5401	SO:0001819	synonymous_variant	27031	exon1			CCCGTACGTGTCC	AB056657	CCDS3078.1	3q22	2014-07-18			ENSG00000113971	ENSG00000113971		"""Tetratricopeptide (TTC) repeat domain containing"""	7907	protein-coding gene	gene with protein product	"""nephrocystin-3"", ""Meckel syndrome, type 7"", ""cilia and flagella associated protein 31"""	608002				12872122, 15381417	Standard	NM_153240		Approved	NPH3, KIAA2000, FLJ30691, FLJ36696, MKS7, SLSN3, CFAP31	uc003epe.2	Q7Z494	OTTHUMG00000159713	ENST00000337331.5:c.57G>C	3.37:g.132441143C>G		7.0	0.0	0		19.0	8.0	0.421053	NM_153240	Q5JPE3|Q5JPE6|Q68D99|Q6NVH3|Q7Z492|Q7Z493|Q8N9R2|Q8NCM5|Q96N70|Q96NK2	Silent	SNP	ENST00000337331.5	37	CCDS3078.1																																																																																			C|0.991;G|0.009	0.009	strong		0.721	NPHP3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357020.2	NM_153240	
SPATA21	374955	hgsc.bcm.edu	37	1	16748432	16748432	+	Silent	SNP	C	C	T	rs114456729	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr1:16748432C>T	ENST00000335496.1	-	4	551	c.69G>A	c.(67-69)acG>acA	p.T23T	SPATA21_ENST00000466212.1_5'UTR|SPATA21_ENST00000540400.1_Intron	NM_198546.1	NP_940948.1	Q7Z572	SPT21_HUMAN	spermatogenesis associated 21	23							calcium ion binding (GO:0005509)	p.T23T(1)		breast(1)|endometrium(2)|lung(8)|ovary(2)|pancreas(3)|stomach(1)|urinary_tract(2)	19		Colorectal(325;0.000147)|Renal(390;0.00145)|Lung NSC(340;0.00215)|Breast(348;0.00224)|all_lung(284;0.00351)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0646)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(227;1.15e-05)|BRCA - Breast invasive adenocarcinoma(304;4.2e-05)|Kidney(64;0.000183)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(313;0.0122)|READ - Rectum adenocarcinoma(331;0.0651)		TAGGTCCAGGCGTGGATGGCA	0.562													C|||	122	0.024361	0.0015	0.036	5008	,	,		19316	0.001		0.0726	False		,,,				2504	0.0215				p.T23T		Atlas-SNP	.											SPATA21,NS,carcinoma,-1,2	SPATA21	47	2	1	Substitution - coding silent(1)	pancreas(1)	c.G69A						PASS	.	C		57,4349	54.9+/-90.9	0,57,2146	219.0	207.0	211.0		69	-2.2	0.0	1	dbSNP_132	211	600,8000	158.9+/-212.3	23,554,3723	no	coding-synonymous	SPATA21	NM_198546.1		23,611,5869	TT,TC,CC		6.9767,1.2937,5.0515		23/470	16748432	657,12349	2203	4300	6503	SO:0001819	synonymous_variant	374955	exon4			TCCAGGCGTGGAT		CCDS172.1	1p36.13	2013-01-10			ENSG00000187144	ENSG00000187144		"""EF-hand domain containing"""	28026	protein-coding gene	gene with protein product							Standard	NM_198546		Approved	spergen-2, spergen2	uc001ayn.3	Q7Z572	OTTHUMG00000002312	ENST00000335496.1:c.69G>A	1.37:g.16748432C>T		109.0	0.0	0		93.0	46.0	0.494624	NM_198546	B9EK40|F5GXP5	Silent	SNP	ENST00000335496.1	37	CCDS172.1																																																																																			C|0.954;T|0.046	0.046	strong		0.562	SPATA21-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000006677.2	NM_198546	
FARP2	9855	hgsc.bcm.edu	37	2	242380734	242380734	+	Missense_Mutation	SNP	G	G	A	rs146443541	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:242380734G>A	ENST00000264042.3	+	13	1344	c.1174G>A	c.(1174-1176)Gag>Aag	p.E392K	FARP2_ENST00000545004.1_Missense_Mutation_p.E392K|FARP2_ENST00000373287.4_Missense_Mutation_p.E392K	NM_014808.2	NP_055623.1	O94887	FARP2_HUMAN	FERM, RhoGEF and pleckstrin domain protein 2	392					actin cytoskeleton reorganization (GO:0031532)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|neuron remodeling (GO:0016322)|osteoclast differentiation (GO:0030316)|podosome assembly (GO:0071800)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rho GTPase activity (GO:0032321)|Rac protein signal transduction (GO:0016601)|regulation of integrin activation (GO:0033623)|regulation of Rac GTPase activity (GO:0032314)|semaphorin-plexin signaling pathway (GO:0071526)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)	Rac guanyl-nucleotide exchange factor activity (GO:0030676)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(18)|ovary(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	43		all_cancers(19;4.88e-34)|all_epithelial(40;4.81e-14)|Breast(86;0.000141)|Renal(207;0.0143)|all_lung(227;0.0344)|Lung NSC(271;0.0886)|Ovarian(221;0.0905)|Esophageal squamous(248;0.131)|all_hematologic(139;0.182)|Melanoma(123;0.238)		Epithelial(32;1.81e-33)|all cancers(36;1.61e-30)|OV - Ovarian serous cystadenocarcinoma(60;6.83e-15)|Kidney(56;1.19e-08)|KIRC - Kidney renal clear cell carcinoma(57;8.98e-08)|BRCA - Breast invasive adenocarcinoma(100;1.49e-06)|Lung(119;0.000152)|LUSC - Lung squamous cell carcinoma(224;0.00125)|Colorectal(34;0.0199)|COAD - Colon adenocarcinoma(134;0.121)		CTCATTCCCCGAGGGATTGAG	0.473													G|||	6	0.00119808	0.0	0.0	5008	,	,		17915	0.0		0.005	False		,,,				2504	0.001				p.E392K		Atlas-SNP	.											.	FARP2	92	.	0			c.G1174A						PASS	.	G	LYS/GLU	2,4404	4.2+/-10.8	0,2,2201	104.0	98.0	100.0		1174	5.3	0.5	2	dbSNP_134	100	19,8581	14.0+/-48.4	0,19,4281	yes	missense	FARP2	NM_014808.2	56	0,21,6482	AA,AG,GG		0.2209,0.0454,0.1615	benign	392/1055	242380734	21,12985	2203	4300	6503	SO:0001583	missense	9855	exon13			TTCCCCGAGGGAT	AB018336	CCDS33424.1, CCDS63197.1	2q37.3	2013-01-10			ENSG00000006607	ENSG00000006607		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	16460	protein-coding gene	gene with protein product						9872452, 12351724	Standard	NM_001282984		Approved	KIAA0793, FIR, PLEKHC3, FRG	uc002wbi.2	O94887	OTTHUMG00000151574	ENST00000264042.3:c.1174G>A	2.37:g.242380734G>A	ENSP00000264042:p.Glu392Lys	74.0	0.0	0		74.0	25.0	0.337838	NM_014808	B7Z6J8|F5GZ84|Q53QM5|Q8WU27|Q9UFE7	Missense_Mutation	SNP	ENST00000264042.3	37	CCDS33424.1	5	0.0022893772893772895	0	0.0	0	0.0	0	0.0	5	0.006596306068601583	G	12.87	2.068509	0.36470	4.54E-4	0.002209	ENSG00000006607	ENST00000264042;ENST00000545004;ENST00000373287;ENST00000413432	T;T;T;D	0.81739	-0.88;-1.46;-1.46;-1.53	5.28	5.28	0.74379	.	0.652894	0.15957	N	0.236471	T	0.64605	0.2613	L	0.34521	1.04	0.47153	D	0.999336	P;P;P	0.52577	0.954;0.907;0.76	B;B;B	0.39840	0.311;0.246;0.091	T	0.68179	-0.5477	10	0.09843	T	0.71	.	18.9095	0.92477	0.0:0.0:1.0:0.0	.	392;392;392	O94887-2;F5GZ84;O94887	.;.;FARP2_HUMAN	K	392;392;392;79	ENSP00000264042:E392K;ENSP00000443876:E392K;ENSP00000362384:E392K;ENSP00000412772:E79K	ENSP00000264042:E392K	E	+	1	0	FARP2	242029407	1.000000	0.71417	0.484000	0.27391	0.024000	0.10985	8.223000	0.89779	2.472000	0.83506	0.655000	0.94253	GAG	G|0.999;A|0.001	0.001	strong		0.473	FARP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323153.1		
KIAA0100	9703	hgsc.bcm.edu	37	17	26961735	26961735	+	Missense_Mutation	SNP	G	G	A	rs118181996		TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr17:26961735G>A	ENST00000528896.2	-	16	2944	c.2870C>T	c.(2869-2871)aCa>aTa	p.T957I	KIAA0100_ENST00000544884.1_Missense_Mutation_p.T814I|KIAA0100_ENST00000389003.3_Missense_Mutation_p.T814I|RP11-192H23.7_ENST00000577814.1_RNA|RP11-192H23.7_ENST00000583787.1_RNA	NM_014680.3	NP_055495.2	Q14667	K0100_HUMAN	KIAA0100	957						extracellular region (GO:0005576)				breast(3)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|lung(23)|ovary(2)|prostate(2)|skin(6)|stomach(2)|urinary_tract(3)	68	Lung NSC(42;0.00431)					GCGCATGGGTGTGTTGCCATA	0.527													G|||	1	0.000199681	0.0	0.0	5008	,	,		19628	0.0		0.001	False		,,,				2504	0.0				p.T957I		Atlas-SNP	.											.	KIAA0100	175	.	0			c.C2870T						PASS	.	G	ILE/THR	0,4406		0,0,2203	113.0	112.0	113.0		2870	5.9	1.0	17	dbSNP_132	113	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KIAA0100	NM_014680.3	89	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	probably-damaging	957/2236	26961735	3,13003	2203	4300	6503	SO:0001583	missense	9703	exon16			ATGGGTGTGTTGC	D43947	CCDS32595.1	17q11.2	2012-11-29			ENSG00000007202	ENSG00000007202			28960	protein-coding gene	gene with protein product	"""cancer/testis antigen 101"", ""breast cancer overexpressed gene 1"""	610664				16289875	Standard	NM_014680		Approved	DKFZp686M0843, MGC111488, BCOX1, CT101, BCOX	uc002hbu.3	Q14667	OTTHUMG00000166587	ENST00000528896.2:c.2870C>T	17.37:g.26961735G>A	ENSP00000436773:p.Thr957Ile	66.0	0.0	0		72.0	22.0	0.305556	NM_014680	A6NCX3|Q3SYN5|Q49A07|Q5H9T4|Q6WG74|Q6ZP51|Q96HH8	Missense_Mutation	SNP	ENST00000528896.2	37	CCDS32595.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	21.4	4.139429	0.77775	0.0	3.49E-4	ENSG00000007202	ENST00000005905;ENST00000389003;ENST00000528896;ENST00000544884	T;T	0.25085	1.83;1.82	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	T	0.46347	0.1388	L	0.47716	1.5	0.80722	D	1	D	0.76494	0.999	D	0.83275	0.996	T	0.04537	-1.0944	10	0.25106	T	0.35	.	20.2651	0.98459	0.0:0.0:1.0:0.0	.	957	Q14667	K0100_HUMAN	I	957;927;957;814	ENSP00000436773:T957I;ENSP00000446443:T814I	ENSP00000005905:T957I	T	-	2	0	KIAA0100	23985862	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	7.328000	0.79160	2.796000	0.96246	0.563000	0.77884	ACA	G|0.999;A|0.001	0.001	strong		0.527	KIAA0100-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390571.3	NM_014680	
OR51B5	282763	hgsc.bcm.edu	37	11	5364431	5364431	+	Silent	SNP	G	G	A	rs58233587	byFrequency	TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr11:5364431G>A	ENST00000300773.2	-	1	378	c.324C>T	c.(322-324)ctC>ctT	p.L108L	HBG2_ENST00000380252.1_Intron|AC104389.28_ENST00000415970.1_RNA|HBE1_ENST00000380237.1_Intron|HBG2_ENST00000380259.2_Intron	NM_001005567.2	NP_001005567.2	Q9H339	O51B5_HUMAN	olfactory receptor, family 51, subfamily B, member 5	108					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(13)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	28		Medulloblastoma(188;0.0075)|all_neural(188;0.0572)|Breast(177;0.0675)		Epithelial(150;3.05e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TGCCAGACTCGAGAAAGGAAA	0.493													G|||	486	0.0970447	0.3041	0.0476	5008	,	,		20358	0.0		0.0457	False		,,,				2504	0.0051				p.L108L		Atlas-SNP	.											OR51B5,NS,carcinoma,-1,1	OR51B5	60	1	0			c.C324T						PASS	.	G		1214,3188	413.5+/-336.5	164,886,1151	46.0	45.0	46.0		324	-8.8	0.1	11	dbSNP_129	46	454,8140	135.6+/-192.8	13,428,3856	no	coding-synonymous	OR51B5	NM_001005567.2		177,1314,5007	AA,AG,GG		5.2828,27.5784,12.8347		108/313	5364431	1668,11328	2201	4297	6498	SO:0001819	synonymous_variant	282763	exon5			AGACTCGAGAAAG	BK004430	CCDS31378.1	11p15.4	2012-08-09			ENSG00000242180	ENSG00000242180		"""GPCR / Class A : Olfactory receptors"""	19599	protein-coding gene	gene with protein product							Standard	NM_001005567		Approved		uc001maq.2	Q9H339	OTTHUMG00000066676	ENST00000300773.2:c.324C>T	11.37:g.5364431G>A		27.0	0.0	0		23.0	9.0	0.391304	NM_001005567	B2RN59	Silent	SNP	ENST00000300773.2	37	CCDS31378.1																																																																																			G|0.886;A|0.114	0.114	strong		0.493	OR51B5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142975.1	NM_001005567	
TTN	7273	hgsc.bcm.edu	37	2	179611884	179611884	+	Intron	SNP	T	T	C			TCGA-G8-6914-01A-11D-2210-10	TCGA-G8-6914-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	16ea266a-69ef-42a9-81c7-affe59adb1ce	366ac237-58d3-45ae-bf82-9f85fc562612	g.chr2:179611884T>C	ENST00000591111.1	-	46	10585				TTN_ENST00000460472.2_Intron|TTN_ENST00000342992.6_Intron|TTN_ENST00000589042.1_Intron|TTN_ENST00000342175.6_Intron|TTN-AS1_ENST00000590773.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000359218.5_Intron|TTN-AS1_ENST00000578746.1_RNA|TTN_ENST00000360870.5_Silent_p.L5081L			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)			AATATCTCTCTAGAGTCTCTC	0.552																																					p.L5081L		Atlas-SNP	.											.	TTN	18412	.	0			c.A15243G						PASS	.						63.0	72.0	69.0					2																	179611884		2203	4299	6502	SO:0001627	intron_variant	7273	exon46			TCTCTCTAGAGTC	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.10361-5236A>G	2.37:g.179611884T>C		137.0	0.0	0		165.0	17.0	0.10303	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																																																																																				.	.	none		0.552	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
