#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
CDR1	1038	hgsc.bcm.edu	37	X	139866424	139866441	+	In_Frame_Del	DEL	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	GTCTTCCAACAAAGGTAC	GTCTTCCAACAAAGGTAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:139866424_139866441delGTCTTCCAACAAAGGTAC	ENST00000370532.2	-	1	282_299	c.91_108delGTACCTTTGTTGGAAGAC	c.(91-108)gtacctttgttggaagacdel	p.VPLLED31del		NM_004065.2	NP_004056.2	P51861	CDR1_HUMAN	cerebellar degeneration-related protein 1, 34kDa	31	23 X 6 AA approximate repeats.									breast(1)|endometrium(3)|large_intestine(3)|lung(11)|prostate(2)|skin(4)|urinary_tract(1)	25	Acute lymphoblastic leukemia(192;7.65e-05)	Lung SC(4;0.051)				GCCTACTTGTGTCTTCCAACAAAGGTACGTCTTCCAAC	0.44																																					p.31_37del		Atlas-Indel	.											.	CDR1	58	.	0			c.92_109del						PASS	.			205,3516		5,155,40,1432,497						-2.7	0.0			152	40,6440		8,5,19,2342,1751	no	coding	CDR1	NM_004065.2		13,160,59,3774,2248	A1A1,A1R,A1,RR,R		0.6173,5.5093,2.4017				245,9956				SO:0001651	inframe_deletion	1038	exon1			.		CCDS14670.1	Xq27.1	2013-06-13	2002-08-29		ENSG00000184258	ENSG00000184258			1798	protein-coding gene	gene with protein product	"""Cerebellar degeneration-related protein-1 (34kD)"""	302650	"""cerebellar degeneration-related protein (34kD)"""	CDR		2326268	Standard	NM_004065		Approved	CDR62A, CDR34	uc004fbg.1	P51861	OTTHUMG00000137398	ENST00000370532.2:c.91_108delGTACCTTTGTTGGAAGAC	X.37:g.139866424_139866441delGTCTTCCAACAAAGGTAC	ENSP00000359563:p.Val31_Asp36del	251.0	0.0	0		195.0	104.0	0.533333	NM_004065	Q5JXH6	In_Frame_Del	DEL	ENST00000370532.2	37	CCDS14670.1																																																																																			.	.	none		0.440	CDR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058583.1	NM_004065	
KMT2D	8085	hgsc.bcm.edu	37	12	49444214	49444214	+	Frame_Shift_Del	DEL	A	A	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49444214delA	ENST00000301067.7	-	11	3156	c.3157delT	c.(3157-3159)tccfs	p.S1053fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	1053	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)										CTCAACGGGGAGGGAACGGAC	0.572																																					p.S1053fs		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.3158delC						PASS	.						49.0	55.0	53.0					12																	49444214		2068	4208	6276	SO:0001589	frameshift_variant	8085	exon11			.	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.3157delT	12.37:g.49444214delA	ENSP00000301067:p.Ser1053fs	214.0	0.0	.		193.0	47.0	0.244	NM_003482	O14687	Frame_Shift_Del	DEL	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.572	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
APEH	327	hgsc.bcm.edu	37	3	49722525	49722525	+	IGR	DEL	A	A	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49722525delA	ENST00000296456.5	+	0	3220				MST1_ENST00000449682.2_Intron|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GGCCCTGCCTAGAGGAGTGGG	0.582																																					.		Atlas-Indel	.											.	MST1	84	.	0			c.1545-2T>-						PASS	.						11.0	12.0	12.0					3																	49722525		2187	4289	6476	SO:0001628	intergenic_variant	4485	exon15			.	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49722525delA		164.0	0.0	0		151.0	11.0	0.0728477	NM_020998	Q9BQ33|Q9P0Y2	Splice_Site	DEL	ENST00000296456.5	37	CCDS2801.1																																																																																			.	.	none		0.582	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
CFTR	1080	hgsc.bcm.edu	37	7	117144306	117144307	+	Splice_Site	INS	-	-	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:117144306_117144307insC	ENST00000003084.6	+	2	185_186		c.e2-1		CFTR_ENST00000454343.1_Splice_Site	NM_000492.3	NP_000483.3	P13569	CFTR_HUMAN	cystic fibrosis transmembrane conductance regulator (ATP-binding cassette sub-family C, member 7)						cellular response to cAMP (GO:0071320)|cellular response to hormone stimulus (GO:0032870)|chloride transmembrane transport (GO:1902476)|cholesterol biosynthetic process (GO:0006695)|cholesterol transport (GO:0030301)|intracellular pH elevation (GO:0051454)|iodide transport (GO:0015705)|lung development (GO:0030324)|membrane hyperpolarization (GO:0060081)|positive regulation of vasodilation (GO:0045909)|positive regulation of voltage-gated chloride channel activity (GO:1902943)|respiratory gaseous exchange (GO:0007585)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to peptide hormone (GO:0043434)|sperm capacitation (GO:0048240)|transepithelial chloride transport (GO:0030321)|transmembrane transport (GO:0055085)|transport (GO:0006810)|vasodilation (GO:0042311)|water transport (GO:0006833)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|chloride channel complex (GO:0034707)|cytoplasmic vesicle membrane (GO:0030659)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	ATP binding (GO:0005524)|ATP-binding and phosphorylation-dependent chloride channel activity (GO:0005224)|bicarbonate transmembrane transporter activity (GO:0015106)|channel-conductance-controlling ATPase activity (GO:0005260)|chloride channel activity (GO:0005254)|chloride channel inhibitor activity (GO:0019869)|chloride transmembrane transporter activity (GO:0015108)|enzyme binding (GO:0019899)|PDZ domain binding (GO:0030165)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(15)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(9)	69	Lung NSC(10;0.00148)|all_lung(10;0.00171)		STAD - Stomach adenocarcinoma(10;0.000534)		Bumetanide(DB00887)|Crofelemer(DB04941)|Glyburide(DB01016)|Ibuprofen(DB01050)|Ivacaftor(DB08820)	CTTTATTTTAGCTGGACCAGAC	0.381									Cystic Fibrosis																												.		Pindel,Atlas-Indel	.											.	CFTR	171	.	0			c.54-1->C						PASS	.																																			SO:0001630	splice_region_variant	1080	exon2	Familial Cancer Database	CF	.	M28668	CCDS5773.1	7q31-q32	2014-09-17	2006-09-18		ENSG00000001626	ENSG00000001626		"""Ion channels / Chloride channels : Cystic fibrosis transmembrane conductance regulators"", ""ATP binding cassette transporters / subfamily C"""	1884	protein-coding gene	gene with protein product	"""ATP-binding cassette sub-family C, member 7"""	602421	"""cystic fibrosis transmembrane conductance regulator, ATP-binding cassette (sub-family C, member 7)"""	CF, ABCC7		2772657	Standard	XM_006715842		Approved	MRP7, ABC35, TNR-CFTR, dJ760C5.1, CFTR/MRP	uc003vjd.3	P13569	OTTHUMG00000023076	ENST00000003084.6:c.54-1->C	7.37:g.117144307_117144307dupC		88.0	0.0	.		87.0	20.0	0.230	NM_000492	Q20BG8|Q20BH2|Q2I0A1|Q2I102	Splice_Site	INS	ENST00000003084.6	37	CCDS5773.1																																																																																			.	.	none		0.381	CFTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059397.3	NM_000492	Intron
MGAM	8972	hgsc.bcm.edu	37	7	141708306	141708329	+	Splice_Site	DEL	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	-	rs199885071	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCCCAGATCCTGGGACAACTGGTA	CCCCAGATCCTGGGACAACTGGTA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141708306_141708329delCCCCAGATCCTGGGACAACTGGTA	ENST00000549489.2	+	3	223_246	c.128_151delCCCCAGATCCTGGGACAACTGGTA	c.(127-153)gccccagatcctgggacaactggtacc>gcc	p.PDPGTTGT60del	MGAM_ENST00000475668.2_Splice_Site_p.PDPGTTGT60del	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	60	Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TTTGGTATAGCCCCAGATCCTGGGACAACTGGTACCCCAGATCC	0.469																																					p.43_50del		Atlas-Indel	.											.	MGAM	767	.	0			c.128_150del						PASS	.			10,3480		0,10,1735						0.4	0.0			57	7,7801		1,5,3898	no	coding-near-splice	MGAM	NM_004668.2		1,15,5633	A1A1,A1R,RR		0.0897,0.2865,0.1505				17,11281				SO:0001630	splice_region_variant	8972	exon3			.	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.128-1CCCCAGATCCTGGGACAACTGGTA>-	7.37:g.141708306_141708329delCCCCAGATCCTGGGACAACTGGTA		154.0	0.0	0		135.0	40.0	0.296296	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	ENST00000549489.2	37	CCDS47727.1																																																																																			.	.	none		0.469	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		In_Frame_Del
CYP3A5	1577	hgsc.bcm.edu	37	7	99273810	99273811	+	Frame_Shift_Ins	INS	-	-	C	rs200579169|rs28383469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99273810_99273811insC	ENST00000222982.4	-	2	191_192	c.92_93insG	c.(91-93)ggafs	p.G31fs	CYP3A5_ENST00000439761.1_Frame_Shift_Ins_p.G31fs|CYP3A5_ENST00000480723.1_5'UTR|CYP3A5_ENST00000343703.5_Frame_Shift_Ins_p.G21fs|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	31					alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	TCTTAAAAAGTCCATGTGTACG	0.46													CC|CC|CCC|insertion	17	0.00339457	0.0	0.0014	5008	,	,		20943	0.0		0.0119	False		,,,				2504	0.0041				p.G31fs		Pindel,Atlas-Indel	.											.	CYP3A5	46	.	0			c.93_94insG	GRCh37	CI067571	CYP3A5	I		PASS	.		,	6,4258		0,6,2126					,	-4.4	0.0		dbSNP_125	108	77,8175		0,77,4049	no	frameshift,frameshift	CYP3A5	NM_001190484.1,NM_000777.3	,	0,83,6175	A1A1,A1R,RR		0.9331,0.1407,0.6632	,	,		83,12433				SO:0001589	frameshift_variant	1577	exon2			.	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.93dupG	7.37:g.99273812_99273812dupC	ENSP00000222982:p.Gly31fs	92.0	0.0	.		127.0	38.0	0.299	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Frame_Shift_Ins	INS	ENST00000222982.4	37	CCDS5672.1																																																																																			-|0.994;C|0.006	0.006	strong		0.460	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
KMT2D	8085	hgsc.bcm.edu	37	12	49422949	49422950	+	Frame_Shift_Ins	INS	-	-	CA	rs376628232		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:49422949_49422950insCA	ENST00000301067.7	-	44	14144_14145	c.14145_14146insTG	c.(14143-14148)ttggggfs	p.G4716fs		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4716					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)										GCCTCCTCCCCCAAGATGCTCT	0.589																																					p.G4716fs		Pindel,Atlas-Indel	.											.	MLL2	1173	.	0			c.14146_14147insTG						PASS	.																																			SO:0001589	frameshift_variant	8085	exon44			.	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.14144_14145dupTG	12.37:g.49422950_49422951dupCA	ENSP00000301067:p.Gly4716fs	71.0	0.0	.		94.0	29.0	0.309	NM_003482	O14687	Frame_Shift_Ins	INS	ENST00000301067.7	37	CCDS44873.1																																																																																			.	.	none		0.589	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
ARHGAP30	257106	hgsc.bcm.edu	37	1	161021121	161021122	+	In_Frame_Ins	INS	-	-	GGCCAG	rs201733366		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:161021121_161021122insGGCCAG	ENST00000368013.3	-	10	1722_1723	c.1402_1403insCTGGCC	c.(1402-1404)ctt>cCTGGCCtt	p.467_468insPG	ARHGAP30_ENST00000368015.1_In_Frame_Ins_p.290_291insPG|ARHGAP30_ENST00000368016.3_In_Frame_Ins_p.467_468insPG	NM_001025598.1|NM_181720.2	NP_001020769.1|NP_859071.2	Q7Z6I6	RHG30_HUMAN	Rho GTPase activating protein 30	467					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)	GTPase activator activity (GO:0005096)			breast(2)|cervix(3)|endometrium(4)|kidney(2)|large_intestine(4)|lung(6)|ovary(4)|pancreas(1)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	37	all_cancers(52;8.05e-20)|Breast(13;0.00188)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00122)			gccagggccaaggccagggcca	0.619																																					p.L468delinsPGL		Atlas-Indel	.											.	ARHGAP30	105	.	0			c.1403_1404insCTGGCC						PASS	.																																			SO:0001652	inframe_insertion	257106	exon10			.	AL832852	CCDS1215.1, CCDS30918.1, CCDS72958.1	1q23.3	2011-06-29			ENSG00000186517	ENSG00000186517		"""Rho GTPase activating proteins"""	27414	protein-coding gene	gene with protein product		614264					Standard	NM_001287602		Approved	FLJ00267	uc001fxl.3	Q7Z6I6	OTTHUMG00000031477	ENST00000368013.3:c.1397_1402dupCTGGCC	1.37:g.161021122_161021127dupGGCCAG	ENSP00000356992:p.Pro466_Gly467dup	41.0	0.0	0		50.0	16.0	0.32	NM_181720	Q5SY52|Q5SY53|Q5SY54|Q6ZML6|Q7Z3J8|Q86XI7	In_Frame_Ins	INS	ENST00000368013.3	37	CCDS30918.1																																																																																			.	.	none		0.619	ARHGAP30-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077090.2	NM_181720	
ZNF844	284391	hgsc.bcm.edu	37	19	12187316	12187317	+	Frame_Shift_Del	DEL	CA	CA	-	rs201088213|rs61471402	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CA	CA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187316_12187317delCA	ENST00000439326.3	+	4	1556_1557	c.1381_1382delCA	c.(1381-1383)cacfs	p.H461fs	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	461					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(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AGATCTGCCTCACACCTTCAAA	0.431														57	0.0113818	0.0371	0.0029	5008	,	,		24663	0.0		0.006	False		,,,				2504	0.0				p.460_461del		Atlas-Indel	.											.	ZNF844	69	.	0			c.1380_1381del						PASS	.			196,4068		7,182,1943						-5.0	0.0		dbSNP_129	63	24,8228		1,22,4103	no	frameshift	ZNF844	NM_001136501.1		8,204,6046	A1A1,A1R,RR		0.2908,4.5966,1.7578				220,12296				SO:0001589	frameshift_variant	284391	exon4			.	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1381_1382delCA	19.37:g.12187318_12187319delCA	ENSP00000392024:p.His461fs	52.0	0.0	0		38.0	14.0	0.368421	NM_001136501	Q5JPI8	Frame_Shift_Del	DEL	ENST00000439326.3	37	CCDS45985.1																																																																																			CA|0.987;-|0.013	0.013	strong		0.431	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
ASXL3	80816	hgsc.bcm.edu	37	18	31323500	31323500	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:31323500delC	ENST00000269197.5	+	12	3688	c.3688delC	c.(3688-3690)cttfs	p.L1230fs		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1230	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						TGTGCCCATGCTTTTTAATAA	0.368																																					p.M1229fs		Atlas-Indel	.											ASXL3_ENST00000269197,NS,carcinoma,+2,2	ASXL3	405	2	0			c.3687delG						PASS	.						82.0	74.0	76.0					18																	31323500		1835	4083	5918	SO:0001589	frameshift_variant	80816	exon12			.	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.3688delC	18.37:g.31323500delC	ENSP00000269197:p.Leu1230fs	78.0	0.0	0		68.0	33.0	0.485294	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Frame_Shift_Del	DEL	ENST00000269197.5	37	CCDS45847.1																																																																																			.	.	none		0.368	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
APLF	200558	hgsc.bcm.edu	37	2	68805143	68805143	+	Frame_Shift_Del	DEL	A	A	-	rs149897324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:68805143delA	ENST00000303795.4	+	10	1696	c.1525delA	c.(1525-1527)aaafs	p.K509fs	APLF_ENST00000471727.1_Intron	NM_173545.2	NP_775816.1	Q8IW19	APLF_HUMAN	aprataxin and PNKP like factor	509					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|double-strand break repair (GO:0006302)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of DNA ligation (GO:0051106)|regulation of isotype switching (GO:0045191)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|site of double-strand break (GO:0035861)	3'-5' exonuclease activity (GO:0008408)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|endodeoxyribonuclease activity (GO:0004520)|metal ion binding (GO:0046872)|nucleotide binding (GO:0000166)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|liver(2)|lung(9)|ovary(3)|prostate(1)|skin(1)	25						AAGGTTTATGAAAAGAAAATA	0.358													AAAA|AAAA|AAA|deletion	23	0.00459265	0.0008	0.0058	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0061				p.M508fs		Pindel,Atlas-Indel	.											.	APLF	69	.	0			c.1524delG						PASS	.			15,4251		0,15,2118	68.0	74.0	72.0			2.8	1.0	2	dbSNP_134	73	121,8127		3,115,4006	no	frameshift	APLF	NM_173545.2		3,130,6124	A1A1,A1R,RR		1.467,0.3516,1.0868			68805143	136,12378	2203	4299	6502	SO:0001589	frameshift_variant	200558	exon10			.	BC030711	CCDS1888.1	2p14	2014-02-20	2008-10-01	2008-10-01	ENSG00000169621	ENSG00000169621			28724	protein-coding gene	gene with protein product	"""XRCC1-interacting protein 1"", ""zinc finger, CX5CX6HX5H motif containing 1"""	611035	"""chromosome 2 open reading frame 13"""	C2orf13		18474613, 18077224, 17353262	Standard	NM_173545		Approved	MGC47799, Xip1, ZCCHH1	uc002sep.3	Q8IW19	OTTHUMG00000129566	ENST00000303795.4:c.1525delA	2.37:g.68805143delA	ENSP00000307004:p.Lys509fs	58.0	0.0	.		64.0	26.0	0.406	NM_173545	A8K476|Q53P47|Q53PB9|Q53QU0	Frame_Shift_Del	DEL	ENST00000303795.4	37	CCDS1888.1																																																																																			A|0.991;-|0.009	0.009	strong		0.358	APLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251759.1	NM_173545	
HNRNPA0	10949	hgsc.bcm.edu	37	5	137088945	137088946	+	In_Frame_Ins	INS	-	-	GCT	rs78232709|rs201570235|rs548286503	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:137088945_137088946insGCT	ENST00000314940.4	-	1	1093_1094	c.810_811insAGC	c.(808-813)agcggc>agcAGCggc	p.270_271insS		NM_006805.3	NP_006796.1	Q13151	ROA0_HUMAN	heterogeneous nuclear ribonucleoprotein A0	270	Gly-rich.				3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|inflammatory response (GO:0006954)|mRNA processing (GO:0006397)|mRNA splicing, via spliceosome (GO:0000398)|response to lipopolysaccharide (GO:0032496)|RNA splicing (GO:0008380)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	AU-rich element binding (GO:0017091)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			large_intestine(1)|lung(2)|skin(1)	4			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ccgccgccgccgcTCTTCATGG	0.673														38	0.00758786	0.0015	0.013	5008	,	,		9196	0.0		0.0209	False		,,,				2504	0.0061				p.G271delinsSG		Pindel,Atlas-Indel	.											.	HNRNPA0	17	.	0			c.811_812insAGC						PASS	.			20,3804		3,14,1895						2.6	0.0		dbSNP_131	9	196,7418		14,168,3625	no	coding	HNRNPA0	NM_006805.3		17,182,5520	A1A1,A1R,RR		2.5742,0.523,1.8884				216,11222				SO:0001652	inframe_insertion	10949	exon1			.	U23803	CCDS4193.1	5q31	2013-02-12		2007-08-16	ENSG00000177733	ENSG00000177733		"""RNA binding motif (RRM) containing"""	5030	protein-coding gene	gene with protein product		609409		HNRPA0		7585247	Standard	NM_006805		Approved	hnRNPA0	uc003lbt.3	Q13151	OTTHUMG00000129156	ENST00000314940.4:c.808_810dupAGC	5.37:g.137088946_137088948dupGCT	ENSP00000316042:p.Ser270_Ser270dup	59.0	0.0	.		91.0	22.0	0.242	NM_006805	Q6IB18	In_Frame_Ins	INS	ENST00000314940.4	37	CCDS4193.1																																																																																			.	.	none		0.673	HNRNPA0-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251221.1	NM_006805	
PHF14	9678	hgsc.bcm.edu	37	7	11091329	11091330	+	Frame_Shift_Ins	INS	-	-	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:11091329_11091330insA	ENST00000403050.3	+	14	2855_2856	c.2403_2404insA	c.(2404-2406)aggfs	p.R802fs	PHF14_ENST00000445996.2_Frame_Shift_Ins_p.R517fs	NM_014660.3	NP_055475.2	O94880	PHF14_HUMAN	PHD finger protein 14	802					lung alveolus development (GO:0048286)|negative regulation of mesenchymal cell proliferation involved in lung development (GO:2000791)|negative regulation of platelet-derived growth factor receptor-alpha signaling pathway (GO:2000584)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	zinc ion binding (GO:0008270)			NS(2)|breast(1)|endometrium(4)|kidney(5)|large_intestine(5)|lung(14)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	35				UCEC - Uterine corpus endometrioid carcinoma (126;0.205)		AACGATCAAGGAGGCAGATTAA	0.446																																					p.R801fs		Atlas-Indel	.											.	PHF14	90	.	0			c.2403_2404insA						PASS	.																																			SO:0001589	frameshift_variant	9678	exon14			.	AB018326	CCDS47542.1	7p21.3	2013-01-28			ENSG00000106443	ENSG00000106443		"""Zinc fingers, PHD-type"""	22203	protein-coding gene	gene with protein product						9872452	Standard	NM_014660		Approved	KIAA0783	uc003sry.2	O94880	OTTHUMG00000150463	ENST00000403050.3:c.2404dupA	7.37:g.11091330_11091330dupA	ENSP00000385795:p.Arg802fs	82.0	0.0	0		76.0	16.0	0.210526	NM_014660	A7MCZ3|B4DI82	Frame_Shift_Ins	INS	ENST00000403050.3	37	CCDS47542.1																																																																																			.	.	none		0.446	PHF14-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000318212.1	NM_014660	
KIAA0586	9786	hgsc.bcm.edu	37	14	58899157	58899157	+	Frame_Shift_Del	DEL	G	G	-	rs534542684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:58899157delG	ENST00000556134.1	+	5	621	c.347delG	c.(346-348)agafs	p.R116fs	KIAA0586_ENST00000423743.3_Frame_Shift_Del_p.R46fs|KIAA0586_ENST00000261244.5_Frame_Shift_Del_p.R131fs|KIAA0586_ENST00000354386.6_Frame_Shift_Del_p.R143fs	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	116					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						GATGCTCTAAGAACAGTTTTA	0.279													G|G|-|deletion	12	0.00239617	0.0	0.0058	5008	,	,		15268	0.0		0.007	False		,,,				2504	0.001				p.R143fs		Pindel,Atlas-Indel	.											.	KIAA0586	180	.	0			c.427delA						PASS	.			3,3511		0,3,1754	44.0	43.0	43.0			5.2	1.0	14		43	25,7757		0,25,3866	no	frameshift	KIAA0586	NM_014749.3		0,28,5620	A1A1,A1R,RR		0.3213,0.0854,0.2479			58899157	28,11268	1814	4055	5869	SO:0001589	frameshift_variant	9786	exon5			.	AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.347delG	14.37:g.58899157delG	ENSP00000452351:p.Arg116fs	154.0	0.0	.		171.0	61.0	0.357	NM_001244189	B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Frame_Shift_Del	DEL	ENST00000556134.1	37	CCDS58321.1																																																																																			.	.	none		0.279	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1	NM_014749	
SLFN12L	100506736	hgsc.bcm.edu	37	17	33801989	33801990	+	Frame_Shift_Ins	INS	-	-	AAAA	rs532206571		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33801989_33801990insAAAA	ENST00000260908.7	-	4	1836_1837	c.1719_1720insTTTT	c.(1717-1722)tttcgtfs	p.R574fs	SLFN12L_ENST00000449046.1_Frame_Shift_Ins_p.R605fs|SLFN12L_ENST00000361112.4_Frame_Shift_Ins_p.R603fs	NM_001195790.1	NP_001182719.1	Q6IEE8	SN12L_HUMAN	schlafen family member 12-like	574						integral component of membrane (GO:0016021)	ATP binding (GO:0005524)			breast(1)|endometrium(4)|kidney(5)|large_intestine(2)|lung(3)|ovary(1)	16						aaacaaaaacgaaacaaacaaa	0.381																																					p.R574fs		Pindel,Atlas-Indel	.											.	SLFN12L	140	.	0			c.1720_1721insTTTT						PASS	.																																			SO:0001589	frameshift_variant	100506736	exon4			.	AK172761	CCDS56026.1	17q12	2011-05-24				ENSG00000205045			33920	protein-coding gene	gene with protein product		614956				9846487	Standard	NM_001195790		Approved		uc021tuy.1	Q6IEE8		ENST00000260908.7:c.1719_1720insTTTT	17.37:g.33801989_33801990insAAAA	ENSP00000437635:p.Arg574fs	86.0	0.0	.		61.0	25.0	0.410	NM_001195790	F5H6G3	Frame_Shift_Ins	INS	ENST00000260908.7	37	CCDS56026.1																																																																																			.	.	none		0.381	SLFN12L-004	NOVEL	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000395748.2	XM_496206	
HDGFRP2	84717	hgsc.bcm.edu	37	19	4498017	4498019	+	In_Frame_Del	DEL	AGA	AGA	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AGA	AGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:4498017_4498019delAGA	ENST00000301284.4	+	11	1455_1457	c.1391_1393delAGA	c.(1390-1395)gagaag>gag	p.K467del	HDGFRP2_ENST00000586684.1_In_Frame_Del_p.K467del	NM_001001520.1|NM_032631.2	NP_001001520|NP_116020.1	Q7Z4V5	HDGR2_HUMAN		467					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)										AGGAAGGTAGAGAAGAAGAAAGG	0.66																																					p.464_464del		Pindel,Atlas-Indel	.											.	.	.	.	0			c.1390_1392del						PASS	.																																			SO:0001651	inframe_deletion	0	exon11			.																												ENST00000301284.4:c.1391_1393delAGA	19.37:g.4498023_4498025delAGA	ENSP00000301284:p.Lys467del	78.0	0.0	.		79.0	32.0	0.405	NM_032631	I3L080|K7EQZ6|Q96GI5|Q9BW08	In_Frame_Del	DEL	ENST00000301284.4	37	CCDS42472.1																																																																																			.	.	none		0.660	HDGFRP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458642.1		
TLX1NB	100038246	hgsc.bcm.edu	37	10	102849370	102849370	+	Frame_Shift_Del	DEL	T	T	-	rs200664029	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:102849370delT	ENST00000445873.1	-	3	1569	c.293delA	c.(292-294)cagfs	p.Q98fs	TLX1NB_ENST00000425505.1_5'Flank	NM_001085398.1	NP_001078867.1	P0CAT3	TLXNB_HUMAN	TLX1 neighbor	98																	TTTCTCCAGCTGAGGTGACCT	0.572													T|T|-|deletion	7	0.00139776	0.0008	0.0014	5008	,	,		15955	0.0		0.005	False		,,,				2504	0.0				p.Q98fs		Pindel,Atlas-Indel	.											.	.	.	.	0			c.294delG						PASS	.			8,3620		0,8,1806	33.0	33.0	33.0			1.1	0.0	10		33	75,7807		1,73,3867	no	frameshift	TLX1NB	NM_001085398.1		1,81,5673	A1A1,A1R,RR		0.9515,0.2205,0.7211			102849370	83,11427	1881	4116	5997	SO:0001589	frameshift_variant	100038246	exon3			.	BC019674	CCDS60615.1	10q24	2014-04-01			ENSG00000236311	ENSG00000236311			37183	protein-coding gene	gene with protein product		612734				17303350	Standard	NM_001085398		Approved	TD1, TDI, APT-B7	uc001ksv.3	P0CAT3	OTTHUMG00000018925	ENST00000445873.1:c.293delA	10.37:g.102849370delT	ENSP00000475001:p.Gln98fs	94.0	0.0	.		97.0	33.0	0.340	NM_001085398		Frame_Shift_Del	DEL	ENST00000445873.1	37																																																																																				T|0.996;-|0.004	0.004	strong		0.572	TLX1NB-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000049925.2	NM_001085398	
E2F4	1874	hgsc.bcm.edu	37	16	67229794	67229811	+	In_Frame_Del	DEL	CAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAG	-	rs544893537|rs562856782|rs557254925|rs577742150|rs3830472|rs575614504	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CAGCAGCAGCAGCAGCAG	CAGCAGCAGCAGCAGCAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67229794_67229811delCAGCAGCAGCAGCAGCAG	ENST00000379378.3	+	7	977_994	c.918_935delCAGCAGCAGCAGCAGCAG	c.(916-936)gacagcagcagcagcagcagc>gac	p.SSSSSS313del		NM_001950.3	NP_001941.2	Q16254	E2F4_HUMAN	E2F transcription factor 4, p107/p130-binding	313	Poly-Ser.				blood circulation (GO:0008015)|cell volume homeostasis (GO:0006884)|cilium assembly (GO:0042384)|epithelial cell development (GO:0002064)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell proliferation (GO:0042127)|regulation of cell size (GO:0008361)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|protein domain specific binding (GO:0019904)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.S319_N320insS(1)		breast(4)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(2)	11		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000697)|Epithelial(162;0.00303)|all cancers(182;0.0325)		CCCTGCTGGAcagcagcagcagcagcagcagcagcagc	0.606																																					p.306_312del		Pindel,Atlas-Indel	.											.	E2F4	25	.	1	Insertion - In frame(1)	breast(1)	c.917_934del						PASS	.			119,95,114,24,205,410,3265		18,0,2,1,4,4,72,33,0,0,1,3,25,17,1,6,2,69,2,2,3,13,37,6,112,34,324,1325						4.1	0.9		dbSNP_132	47	48,74,119,62,17,1047,6793		16,0,0,2,0,3,11,16,0,0,0,1,41,6,2,0,1,104,4,0,2,48,1,0,15,34,972,2801	no	codingComplex	E2F4	NM_001950.3		34,0,2,3,4,7,83,49,0,0,1,4,66,23,3,6,3,173,6,2,5,61,38,6,127,68,1296,4126	A1A1,A1A2,A1A3,A1A4,A1A5,A1A6,A1R,A2A2,A2A3,A2A4,A2A5,A2A6,A2R,A3A3,A3A4,A3A5,A3A6,A3R,A4A4,A4A5,A4A6,A4R,A5A5,A5A6,A5R,A6A6,A6R,RR		16.7525,22.8497,18.8347				167,169,233,86,222,1457,10058				SO:0001651	inframe_deletion	1874	exon7			.	BC021050	CCDS32464.1	16q22.1	2014-05-06			ENSG00000205250	ENSG00000205250			3118	protein-coding gene	gene with protein product		600659				7958924, 7892279	Standard	NM_001950		Approved	E2F-4	uc002erz.3	Q16254	OTTHUMG00000172975	ENST00000379378.3:c.918_935delCAGCAGCAGCAGCAGCAG	16.37:g.67229794_67229811delCAGCAGCAGCAGCAGCAG	ENSP00000368686:p.Ser313_Ser318del	77.0	0.0	.		87.0	26.0	0.299	NM_001950	A6NGR8|B5BU56|Q12991|Q15328	In_Frame_Del	DEL	ENST00000379378.3	37	CCDS32464.1																																																																																			-|1.000;|0.000	1.000	alt		0.606	E2F4-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421565.1	NM_001950	
GNAI2	2771	hgsc.bcm.edu	37	3	50294456	50294458	+	In_Frame_Del	DEL	AAG	AAG	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	AAG	AAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50294456_50294458delAAG	ENST00000313601.6	+	7	1195_1197	c.811_813delAAG	c.(811-813)aagdel	p.K272del	GNAI2_ENST00000266027.5_In_Frame_Del_p.K256del|GNAI2_ENST00000491100.1_3'UTR|GNAI2_ENST00000440628.1_In_Frame_Del_p.K220del|GNAI2_ENST00000536647.1_In_Frame_Del_p.K191del|GNAI2_ENST00000422163.1_In_Frame_Del_p.K256del|GNAI2_ENST00000451956.1_In_Frame_Del_p.K235del	NM_002070.2	NP_002061.1	P04899	GNAI2_HUMAN	guanine nucleotide binding protein (G protein), alpha inhibiting activity polypeptide 2	272					activation of MAPKK activity (GO:0000186)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|blood coagulation (GO:0007596)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell proliferation (GO:0008283)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|G-protein coupled receptor signaling pathway (GO:0007186)|gamma-aminobutyric acid signaling pathway (GO:0007214)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of synaptic transmission (GO:0050805)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|regulation of calcium ion transport (GO:0051924)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|membrane (GO:0016020)|membrane raft (GO:0045121)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle (GO:0031982)	G-protein beta/gamma-subunit complex binding (GO:0031683)|G-protein coupled receptor binding (GO:0001664)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|liver(2)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	16				BRCA - Breast invasive adenocarcinoma(193;0.000288)|KIRC - Kidney renal clear cell carcinoma(197;0.00571)|Kidney(197;0.00651)		CTTCCTCAACAAGAAGGACCTGT	0.517											OREG0015582	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.270_271del		Atlas-Indel	.											.	GNAI2	42	.	0			c.810_812del						PASS	.																																			SO:0001651	inframe_deletion	2771	exon7			.	X04828	CCDS2813.1, CCDS54587.1, CCDS63642.1, CCDS63644.1	3p21.31	2010-08-27			ENSG00000114353	ENSG00000114353			4385	protein-coding gene	gene with protein product	"""GTP-binding regulatory protein Gi alpha-2 chain"""	139360		GNAI2B		3100330, 1733849	Standard	NM_001166425		Approved	GIP	uc003cyq.1	P04899	OTTHUMG00000156940	ENST00000313601.6:c.811_813delAAG	3.37:g.50294459_50294461delAAG	ENSP00000312999:p.Lys272del	160.0	0.0	0	968	174.0	18.0	0.103448	NM_002070	B3KTZ0|B4DYA0|B4E2X5|Q6B6N3|Q8IZ71	In_Frame_Del	DEL	ENST00000313601.6	37	CCDS2813.1																																																																																			.	.	none		0.517	GNAI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346688.1	NM_002070	
IRF8	3394	hgsc.bcm.edu	37	16	85954879	85954879	+	Frame_Shift_Del	DEL	C	C	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954879delC	ENST00000268638.5	+	9	1694	c.1272delC	c.(1270-1272)atcfs	p.I424fs	IRF8_ENST00000562492.1_Frame_Shift_Del_p.I220fs	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8	424					cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				ACCAACAGATCACCGTCTAAG	0.557																																					p.I424fs		Atlas-Indel	.											IRF8,NS,lymphoid_neoplasm,0,1	IRF8	65	1	0			c.1271delT						PASS	.						71.0	77.0	75.0					16																	85954879		2198	4300	6498	SO:0001589	frameshift_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	ENST00000268638.5:c.1272delC	16.37:g.85954879delC	ENSP00000268638:p.Ile424fs	39.0	0.0	0		36.0	10.0	0.277778	NM_002163	A0AV82	Frame_Shift_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.557	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
INHBE	83729	hgsc.bcm.edu	37	12	57850304	57850319	+	Frame_Shift_Del	DEL	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	-	rs536111730		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TGCGACCCCCTTATGT	TGCGACCCCCTTATGT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57850304_57850319delTGCGACCCCCTTATGT	ENST00000266646.2	+	2	942_957	c.726_741delTGCGACCCCCTTATGT	c.(724-741)cctgcgacccccttatgtfs	p.PATPLC242fs	INHBE_ENST00000551553.1_3'UTR	NM_031479.3	NP_113667.1	P58166	INHBE_HUMAN	inhibin, beta E	242					growth (GO:0040007)	extracellular region (GO:0005576)				breast(2)|central_nervous_system(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)	15						CCTGTGAGCCTGCGACCCCCTTATGTTGCAGGCGAG	0.611											OREG0021944	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.242_247del	GBM(191;1808 2166 15720 36624 50371)	Pindel,Atlas-Indel	.											.	INHBE	38	.	0			c.725_740del						PASS	.																																			SO:0001589	frameshift_variant	83729	exon2			.		CCDS8939.1	12q13.2	2008-02-05				ENSG00000139269			24029	protein-coding gene	gene with protein product		612031				12242034	Standard	NM_031479		Approved	activin, MGC4638	uc001snw.3	P58166		ENST00000266646.2:c.726_741delTGCGACCCCCTTATGT	12.37:g.57850304_57850319delTGCGACCCCCTTATGT	ENSP00000266646:p.Pro242fs	105.0	0.0	.	1026	73.0	20.0	0.274	NM_031479		Frame_Shift_Del	DEL	ENST00000266646.2	37	CCDS8939.1																																																																																			.	.	none		0.611	INHBE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406773.1	NM_031479	
DST	667	hgsc.bcm.edu	37	6	56510983	56510983	+	Intron	DEL	A	A	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56510983delA	ENST00000361203.3	-	10	929				DST_ENST00000370788.2_Intron|DST_ENST00000370754.5_Intron|DST_ENST00000312431.6_Intron|DST_ENST00000421834.2_Intron|DST_ENST00000370769.4_Intron			Q03001	DYST_HUMAN	dystonin						axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			TAAAGTGCCTAAAATAAAAAG	0.299																																					.		Pindel,Atlas-Indel	.											.	.	.	.	0			.						PASS	.						18.0	17.0	17.0					6																	56510983		1782	4017	5799	SO:0001627	intron_variant	100873774	.			.	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.922-3T>-	6.37:g.56510983delA		41.0	0.0	.		37.0	11.0	0.297	.	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	RNA	DEL	ENST00000361203.3	37																																																																																				.	.	none		0.299	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
PNPLA7	375775	hgsc.bcm.edu	37	9	140444627	140444628	+	Frame_Shift_Ins	INS	-	-	T	rs372921391|rs372038516	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:140444627_140444628insT	ENST00000277531.4	-	1	208_209	c.22_23insA	c.(22-24)agcfs	p.S8fs	PNPLA7_ENST00000406427.1_Frame_Shift_Ins_p.S8fs|MRPL41_ENST00000371443.5_5'Flank	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	49.0	0.0	.		67.0	22.0	0.328	NM_001098537	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	
IRF8	3394	hgsc.bcm.edu	37	16	85954881	85954886	+	Stop_Codon_Del	DEL	CCGTCT	CCGTCT	-	rs147057451|rs146135491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CCGTCT	CCGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954881_85954886delCCGTCT	ENST00000268638.5	+	0	1696_1701				IRF8_ENST00000562492.1_Stop_Codon_Del	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8						cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				CAACAGATCACCGTCTAAGTGCGTCG	0.558																																					p.425_426del		Atlas-Indel	.											.	IRF8	65	.	0			c.1273_1278del						PASS	.																																			SO:0001567	stop_retained_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	Exception_encountered	16.37:g.85954881_85954886delCCGTCT	ENSP00000268638:p.*427Tyrext*22	38.0	0.0	0		38.0	10.0	0.263158	NM_002163	A0AV82	In_Frame_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.558	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
CCDC63	160762	hgsc.bcm.edu	37	12	111342460	111342460	+	Frame_Shift_Del	DEL	G	G	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:111342460delG	ENST00000308208.5	+	11	1653	c.1411delG	c.(1411-1413)gggfs	p.G471fs	CCDC63_ENST00000552694.1_Frame_Shift_Del_p.G392fs|CCDC63_ENST00000545036.1_Frame_Shift_Del_p.G431fs	NM_152591.1	NP_689804.1	Q8NA47	CCD63_HUMAN	coiled-coil domain containing 63	471										NS(2)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(15)|ovary(1)|pancreas(1)|prostate(2)|skin(7)|urinary_tract(1)	39						GGAAGTGGAAGGGGCAGAGGC	0.572																																					p.E470fs		Pindel,Atlas-Indel	.											.	CCDC63	89	.	0			c.1410delA						PASS	.			1,4263		0,1,2131	82.0	78.0	79.0			-5.0	0.0	12		79	6,8248		0,6,4121	no	frameshift	CCDC63	NM_152591.1		0,7,6252	A1A1,A1R,RR		0.0727,0.0235,0.0559			111342460	7,12511	2203	4300	6503	SO:0001589	frameshift_variant	160762	exon11			.	AK093162	CCDS9151.1, CCDS66470.1, CCDS73528.1	12q24.11	2013-02-19				ENSG00000173093			26669	protein-coding gene	gene with protein product	"""outer row dynein assembly 5 homolog (Chlamydomonas)"""						Standard	NM_001286243		Approved	ODA5, FLJ35843	uc001trv.1	Q8NA47	OTTHUMG00000169534	ENST00000308208.5:c.1411delG	12.37:g.111342460delG	ENSP00000312399:p.Gly471fs	107.0	0.0	.		164.0	52.0	0.317	NM_152591	B4DY03|Q0P603|Q6P2E1	Frame_Shift_Del	DEL	ENST00000308208.5	37	CCDS9151.1																																																																																			.	.	none		0.572	CCDC63-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000404673.2	NM_152591	
IRF8	3394	hgsc.bcm.edu	37	16	85954879	85954886	+	Stop_Codon_Del	DEL	CACCGTCT	CACCGTCT	-	rs147057451|rs146135491	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	CACCGTCT	CACCGTCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:85954879_85954886delCACCGTCT	ENST00000268638.5	+	0	1694_1701				IRF8_ENST00000562492.1_Stop_Codon_Del	NM_002163.2	NP_002154.1	Q02556	IRF8_HUMAN	interferon regulatory factor 8						cellular response to lipopolysaccharide (GO:0071222)|cytokine-mediated signaling pathway (GO:0019221)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|immune response (GO:0006955)|interferon-gamma-mediated signaling pathway (GO:0060333)|myeloid cell differentiation (GO:0030099)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|phagocytosis (GO:0006909)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|transcription from RNA polymerase II promoter (GO:0006366)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|nucleus (GO:0005634)	regulatory region DNA binding (GO:0000975)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|urinary_tract(1)	24		Prostate(104;0.0771)				ACCAACAGATCACCGTCTAAGTGCGTCG	0.558																																					p.424_426del		Pindel	.											IRF8,NS,lymphoid_neoplasm,0,1	IRF8	65	1	0			c.1271_1278del						PASS	.																																			SO:0001567	stop_retained_variant	3394	exon9			.	M91196	CCDS10956.1	16q24.1	2014-09-17	2004-11-12	2004-11-12	ENSG00000140968	ENSG00000140968			5358	protein-coding gene	gene with protein product		601565	"""interferon consensus sequence binding protein 1"""	ICSBP1		1460054, 11997525	Standard	NM_002163		Approved	IRF-8, ICSBP	uc002fjh.3	Q02556	OTTHUMG00000137648	Exception_encountered	16.37:g.85954879_85954886delCACCGTCT		40.0	0.0	.		37.0	10.0	0.270	NM_002163	A0AV82	Frame_Shift_Del	DEL	ENST00000268638.5	37	CCDS10956.1																																																																																			.	.	none		0.558	IRF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269100.2	NM_002163	
ASXL3	80816	hgsc.bcm.edu	37	18	31323501	31323501	+	Frame_Shift_Del	DEL	T	T	-			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:31323501delT	ENST00000269197.5	+	12	3689	c.3689delT	c.(3688-3690)cttfs	p.L1230fs		NM_030632.1	NP_085135.1	Q9C0F0	ASXL3_HUMAN	additional sex combs like transcriptional regulator 3	1230	Ser-rich.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|endometrium(3)|kidney(3)|large_intestine(6)|lung(22)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	43						GTGCCCATGCTTTTTAATAAA	0.373																																					p.L1230fs		Pindel	.											.	ASXL3	405	.	0			c.3688delC						PASS	.						81.0	73.0	76.0					18																	31323501		1834	4083	5917	SO:0001589	frameshift_variant	80816	exon12			.	AB051500	CCDS45847.1	18q11	2014-06-17	2014-06-17	2007-02-01		ENSG00000141431			29357	protein-coding gene	gene with protein product		615115	"""KIAA1713"", ""additional sex combs like 3 (Drosophila)"""	KIAA1713		11214970	Standard	NM_030632		Approved		uc010dmg.1	Q9C0F0		ENST00000269197.5:c.3689delT	18.37:g.31323501delT	ENSP00000269197:p.Leu1230fs	76.0	0.0	.		68.0	25.0	0.368	NM_030632	Q6ZMX6|Q96MU3|Q9UFC5	Frame_Shift_Del	DEL	ENST00000269197.5	37	CCDS45847.1																																																																																			.	.	none		0.373	ASXL3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441865.2		
NUDT17	200035	hgsc.bcm.edu	37	1	145586672	145586679	+	Frame_Shift_Del	DEL	TTTTACAC	TTTTACAC	-	rs201063949|rs199513201|rs199927874|rs150364859	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	TTTTACAC	TTTTACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145586672_145586679delTTTTACAC	ENST00000334513.5	-	8	908_915	c.897_904delGTGTAAAA	c.(895-906)ccgtgtaaaagtfs	p.CKS300fs	NUDT17_ENST00000444015.2_5'Flank	NM_001012758.2	NP_001012776.1	P0C025	NUD17_HUMAN	nudix (nucleoside diphosphate linked moiety X)-type motif 17	300							hydrolase activity (GO:0016787)|metal ion binding (GO:0046872)			endometrium(3)|large_intestine(1)|lung(2)|skin(1)|urinary_tract(2)	9	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TAAGCTGCACTTTTACACGGTGGGGGTG	0.534																																					p.300_302del		Pindel	.											.	NUDT17	25	.	0			c.898_905del						PASS	.																																			SO:0001589	frameshift_variant	200035	exon8			.	BC046352	CCDS72865.1	1q21.1	2008-02-05			ENSG00000186364	ENSG00000186364		"""Nudix motif containing"""	26618	protein-coding gene	gene with protein product						12477932	Standard	NM_001012758		Approved	FLJ34433	uc001eoe.3	P0C025	OTTHUMG00000013752	ENST00000334513.5:c.897_904delGTGTAAAA	1.37:g.145586672_145586679delTTTTACAC	ENSP00000334437:p.Cys300fs	137.0	0.0	.		133.0	27.0	0.203	NM_001012758		Frame_Shift_Del	DEL	ENST00000334513.5	37	CCDS30830.1																																																																																			-|0.017;TTTTA|0.983	0.017	alt		0.534	NUDT17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038541.3	XM_496395	
CERS6	253782	hgsc.bcm.edu	37	2	169312974	169312974	+	Missense_Mutation	SNP	G	G	A	rs4496303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:169312974G>A	ENST00000305747.6	+	1	603	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	CERS6_ENST00000392687.4_Missense_Mutation_p.A6T	NM_203463.2	NP_982288.1	Q6ZMG9	CERS6_HUMAN	ceramide synthase 6	6					ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)										AGGGATCTTAGCCTGGTTCTG	0.657													G|||	39	0.00778754	0.0061	0.0101	5008	,	,		8564	0.0		0.0209	False		,,,				2504	0.0031				p.A6T		Atlas-SNP	.											.	.	.	.	0			c.G16A						PASS	.	G	THR/ALA	35,4371	40.0+/-72.8	2,31,2170	162.0	130.0	141.0		16	4.3	1.0	2	dbSNP_111	141	101,8499	56.4+/-117.6	0,101,4199	yes	missense	CERS6	NM_203463.1	58	2,132,6369	AA,AG,GG		1.1744,0.7944,1.0457	benign	6/385	169312974	136,12870	2203	4300	6503	SO:0001583	missense	253782	exon1			ATCTTAGCCTGGT	BX393696	CCDS2228.1, CCDS58734.1	2q31	2011-07-11	2011-07-08	2011-07-08	ENSG00000172292	ENSG00000172292		"""Homeoboxes / CERS class"""	23826	protein-coding gene	gene with protein product		615336	"""LAG1 longevity assurance homolog 6 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 6"""	LASS6			Standard	NM_203463		Approved		uc002uec.2	Q6ZMG9	OTTHUMG00000132183	ENST00000305747.6:c.16G>A	2.37:g.169312974G>A	ENSP00000306579:p.Ala6Thr	55.0	0.0	0		82.0	36.0	0.439024	NM_001256126	Q32M63|Q8N617	Missense_Mutation	SNP	ENST00000305747.6	37	CCDS2228.1	24	0.01098901098901099	4	0.008130081300813009	4	0.011049723756906077	0	0.0	16	0.021108179419525065	G	21.6	4.173118	0.78452	0.007944	0.011744	ENSG00000172292	ENST00000305747;ENST00000392687	T;T	0.21734	1.99;1.99	5.22	4.34	0.51931	.	0.105238	0.64402	N	0.000004	T	0.08358	0.0208	L	0.40543	1.245	0.58432	D	0.999999	B;B	0.32203	0.209;0.36	B;B	0.28465	0.045;0.09	T	0.04165	-1.0972	10	0.22706	T	0.39	-18.0462	13.4206	0.60996	0.0755:0.0:0.9245:0.0	.	6;6	Q32M63;Q6ZMG9	.;CERS6_HUMAN	T	6	ENSP00000306579:A6T;ENSP00000376453:A6T	ENSP00000306579:A6T	A	+	1	0	CERS6	169021220	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	9.346000	0.97056	1.188000	0.43014	0.467000	0.42956	GCC	A|0.008;G|0.990;T|0.002	0.008	strong		0.657	CERS6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255235.2	NM_203463	
LMAN1	3998	hgsc.bcm.edu	37	18	57026450	57026450	+	Silent	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:57026450G>C	ENST00000251047.5	-	1	744	c.27C>G	c.(25-27)ctC>ctG	p.L9L	RP11-27G24.1_ENST00000591331.1_lincRNA	NM_005570.3	NP_005561.1	P49257	LMAN1_HUMAN	lectin, mannose-binding, 1	9					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum organization (GO:0007029)|ER to Golgi vesicle-mediated transport (GO:0006888)|Golgi organization (GO:0007030)|positive regulation of organelle organization (GO:0010638)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein N-linked glycosylation via asparagine (GO:0018279)|protein transport (GO:0015031)	endoplasmic reticulum membrane (GO:0005789)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|ER to Golgi transport vesicle membrane (GO:0012507)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|sarcomere (GO:0030017)	mannose binding (GO:0005537)|metal ion binding (GO:0046872)|unfolded protein binding (GO:0051082)			breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(1)	16		Colorectal(73;0.0946)			Antihemophilic Factor(DB00025)	CTCTGGCCCGGAGACCCCTTT	0.701																																					p.L9L		Atlas-SNP	.											.	LMAN1	57	.	0			c.C27G						PASS	.						41.0	49.0	46.0					18																	57026450		2203	4300	6503	SO:0001819	synonymous_variant	3998	exon1			GGCCCGGAGACCC	X71661	CCDS11974.1	18q21.3-q22	2014-09-17	2002-08-30		ENSG00000074695	ENSG00000074695			6631	protein-coding gene	gene with protein product	"""endoplasmic reticulum-golgi intermediate compartment protein 53"""	601567	"""coagulation factor V-factor VIII combined deficiency"""	F5F8D		9546392, 8854877	Standard	NM_005570		Approved	MR60, ERGIC-53, ERGIC53, gp58, MCFD1, FMFD1	uc002lhz.3	P49257	OTTHUMG00000132758	ENST00000251047.5:c.27C>G	18.37:g.57026450G>C		80.0	0.0	0		115.0	51.0	0.443478	NM_005570	Q12895|Q8N5I7|Q9UQG1|Q9UQG2|Q9UQG3|Q9UQG4|Q9UQG5|Q9UQG6|Q9UQG7|Q9UQG8|Q9UQG9|Q9UQH0|Q9UQH1|Q9UQH2	Silent	SNP	ENST00000251047.5	37	CCDS11974.1																																																																																			.	.	none		0.701	LMAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256129.2	NM_005570	
POC1B	282809	hgsc.bcm.edu	37	12	89865394	89865394	+	Missense_Mutation	SNP	G	G	C	rs145981936		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:89865394G>C	ENST00000313546.3	-	6	801	c.673C>G	c.(673-675)Caa>Gaa	p.Q225E	POC1B_ENST00000378528.2_Intron|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Missense_Mutation_p.Q183E|POC1B_ENST00000393179.4_Missense_Mutation_p.Q95E|POC1B_ENST00000541909.1_Missense_Mutation_p.Q95E	NM_172240.2	NP_758440.1	Q8TC44	POC1B_HUMAN	POC1 centriolar protein B	225					cell proliferation (GO:0008283)|cilium assembly (GO:0042384)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|spindle pole (GO:0000922)				endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	14						TTGTTACCTTGGTAATGCTGT	0.413													G|||	1	0.000199681	0.0	0.0	5008	,	,		17728	0.0		0.001	False		,,,				2504	0.0				p.Q225E		Atlas-SNP	.											.	POC1B	41	.	0			c.C673G						PASS	.	G	GLU/GLN,GLU/GLN	0,4406		0,0,2203	147.0	137.0	140.0		547,673	6.0	1.0	12	dbSNP_134	140	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	POC1B	NM_001199777.1,NM_172240.2	29,29	0,5,6498	CC,CG,GG		0.0581,0.0,0.0384	,	183/437,225/479	89865394	5,13001	2203	4300	6503	SO:0001583	missense	282809	exon6			TACCTTGGTAATG	AL832918	CCDS31869.1, CCDS55859.1	12q21.33	2014-05-02	2013-08-21	2010-03-26	ENSG00000139323	ENSG00000139323		"""WD repeat domain containing"""	30836	protein-coding gene	gene with protein product		614784	"""WD repeat domain 51B"", ""POC1 centriolar protein homolog B (Chlamydomonas)"""	WDR51B		19109428	Standard	NM_172240		Approved	TUWD12, FLJ14923		Q8TC44	OTTHUMG00000169944	ENST00000313546.3:c.673C>G	12.37:g.89865394G>C	ENSP00000323302:p.Gln225Glu	96.0	0.0	0		101.0	34.0	0.336634	NM_172240	G3V1X0	Missense_Mutation	SNP	ENST00000313546.3	37	CCDS31869.1	.	.	.	.	.	.	.	.	.	.	G	14.22	2.471636	0.43942	0.0	5.81E-4	ENSG00000139323	ENST00000393179;ENST00000313546;ENST00000549035;ENST00000541909	T;T;T;T	0.59224	0.28;0.28;0.28;0.28	6.02	6.02	0.97574	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.155036	0.64402	D	0.000014	T	0.40719	0.1128	N	0.10972	0.075	0.80722	D	1	B	0.31655	0.334	B	0.35182	0.197	T	0.31308	-0.9948	10	0.13853	T	0.58	.	16.1501	0.81611	0.0:0.0:0.8588:0.1412	.	225	Q8TC44	POC1B_HUMAN	E	95;225;183;95	ENSP00000376877:Q95E;ENSP00000323302:Q225E;ENSP00000447916:Q183E;ENSP00000440301:Q95E	ENSP00000323302:Q225E	Q	-	1	0	POC1B	88389525	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	5.072000	0.64389	2.857000	0.98124	0.650000	0.86243	CAA	G|0.999;C|0.001	0.001	strong		0.413	POC1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406637.1	NM_172240	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751274	19751274	+	Silent	SNP	G	G	A	rs143115179	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:19751274G>A	ENST00000400113.3	-	4	953	c.849C>T	c.(847-849)caC>caT	p.H283H		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	283					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		ACAGCTGCTCGTGGTAGGCCT	0.607																																					p.H283H		Atlas-SNP	.											.	TUBA3C	166	.	0			c.C849T						PASS	.						143.0	128.0	133.0					13																	19751274		2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			CTGCTCGTGGTAG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.849C>T	13.37:g.19751274G>A		219.0	0.0	0		218.0	16.0	0.0733945	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			G|0.992;A|0.008	0.008	strong		0.607	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
CKAP2	26586	hgsc.bcm.edu	37	13	53039547	53039547	+	Missense_Mutation	SNP	C	C	T	rs143514154	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:53039547C>T	ENST00000378037.5	+	6	1516	c.1426C>T	c.(1426-1428)Cct>Tct	p.P476S	CKAP2_ENST00000378034.3_Missense_Mutation_p.P475S|CKAP2_ENST00000258607.5_Missense_Mutation_p.P475S|CKAP2_ENST00000490903.1_Missense_Mutation_p.P427S	NM_001098525.1|NM_018204.3	NP_001091995.1|NP_060674.3			cytoskeleton associated protein 2											breast(2)|kidney(3)|large_intestine(3)|lung(7)|ovary(3)|skin(1)|urinary_tract(1)	20		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;2.6e-08)		AATCACAAGTCCTATTGAAAA	0.338													c|||	17	0.00339457	0.0	0.0101	5008	,	,		16813	0.0		0.0099	False		,,,				2504	0.0				p.P476S		Atlas-SNP	.											.	CKAP2	51	.	0			c.C1426T						PASS	.	C	SER/PRO,SER/PRO	12,4394		0,12,2191	86.0	91.0	89.0		1426,1423	2.9	1.0	13	dbSNP_134	89	88,8504		0,88,4208	yes	missense,missense	CKAP2	NM_001098525.1,NM_018204.3	74,74	0,100,6399	TT,TC,CC		1.0242,0.2724,0.7693	probably-damaging,probably-damaging	476/684,475/683	53039547	100,12898	2203	4296	6499	SO:0001583	missense	26586	exon6			ACAAGTCCTATTG	AF177227	CCDS9435.1, CCDS41893.1, CCDS66557.1, CCDS73578.1	13q14	2014-03-21			ENSG00000136108	ENSG00000136108			1990	protein-coding gene	gene with protein product		611569				9771967	Standard	XM_005266343		Approved	LB1, FLJ10749, se20-10, TMAP	uc001vgv.2	Q8WWK9	OTTHUMG00000016967	ENST00000378037.5:c.1426C>T	13.37:g.53039547C>T	ENSP00000367276:p.Pro476Ser	222.0	0.0	0		182.0	78.0	0.428571	NM_001098525		Missense_Mutation	SNP	ENST00000378037.5	37	CCDS41893.1	11	0.005036630036630037	0	0.0	6	0.016574585635359115	0	0.0	5	0.006596306068601583	.	14.37	2.516023	0.44763	0.002724	0.010242	ENSG00000136108	ENST00000398044;ENST00000258607;ENST00000378034;ENST00000378037;ENST00000490903	T;T;T;T	0.22134	1.97;1.97;1.97;1.97	5.63	2.94	0.34122	.	0.512341	0.20916	N	0.083379	T	0.11922	0.0290	M	0.82056	2.57	0.36976	D	0.894063	P;P;P;P	0.40211	0.513;0.513;0.513;0.707	B;B;B;B	0.38655	0.147;0.147;0.147;0.278	T	0.08086	-1.0739	10	0.56958	D	0.05	-1.6008	3.444	0.07474	0.1396:0.5775:0.135:0.148	.	427;476;475;476	E9PD90;Q8WWK9;B2RMQ4;A8MYU4	.;CKAP2_HUMAN;.;.	S	476;475;475;476;427	ENSP00000258607:P475S;ENSP00000367273:P475S;ENSP00000367276:P476S;ENSP00000417830:P427S	ENSP00000258607:P475S	P	+	1	0	CKAP2	51937548	0.976000	0.34144	1.000000	0.80357	0.993000	0.82548	0.547000	0.23299	0.390000	0.25115	0.655000	0.94253	CCT	C|0.994;T|0.006	0.006	strong		0.338	CKAP2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355010.2		
HNRNPUL1	11100	hgsc.bcm.edu	37	19	41811706	41811706	+	Silent	SNP	C	C	T	rs372346124		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41811706C>T	ENST00000392006.3	+	14	2561	c.2388C>T	c.(2386-2388)ccC>ccT	p.P796P	HNRNPUL1_ENST00000593587.1_Silent_p.P696P|HNRNPUL1_ENST00000263367.3_Silent_p.P707P|HNRNPUL1_ENST00000602130.1_Intron|HNRNPUL1_ENST00000595018.1_Silent_p.P696P|HNRNPUL1_ENST00000378215.4_Silent_p.P692P|HNRNPUL1_ENST00000352456.3_Silent_p.P706P	NM_007040.3	NP_008971.2	Q9BUJ2	HNRL1_HUMAN	heterogeneous nuclear ribonucleoprotein U-like 1	796	Necessary for interaction with TP53.|Pro-rich.|Tyr-rich.				gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|regulation of transcription, DNA-templated (GO:0006355)|response to virus (GO:0009615)|RNA processing (GO:0006396)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|skin(1)|urinary_tract(1)	29						ACCCGGCCCCCTATACCCCAC	0.627																																					p.P796P		Atlas-SNP	.											.	HNRNPUL1	73	.	0			c.C2388T						PASS	.	C	,	1,4405	2.1+/-5.4	0,1,2202	57.0	57.0	57.0		2388,2088	-2.8	1.0	19		57	1,8599	2.2+/-6.3	0,1,4299	no	coding-synonymous,coding-synonymous	HNRNPUL1	NM_007040.3,NM_144732.2	,	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	,	796/857,696/757	41811706	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	11100	exon14			GGCCCCCTATACC	AJ007509	CCDS12576.1, CCDS12577.1	19q13.2	2013-06-12		2008-04-18	ENSG00000105323	ENSG00000105323			17011	protein-coding gene	gene with protein product	"""E1B 55kDa associated protein 5"""	605800		HNRPUL1		9733834, 12489984	Standard	XM_005258459		Approved	E1B-AP5, E1BAP5, FLJ12944	uc002oqb.4	Q9BUJ2	OTTHUMG00000182740	ENST00000392006.3:c.2388C>T	19.37:g.41811706C>T		91.0	0.0	0		128.0	62.0	0.484375	NM_007040	B3KMW7|O76022|Q6ZSZ0|Q7L8P4|Q8N6Z4|Q96G37|Q9HAL3|Q9UG75	Silent	SNP	ENST00000392006.3	37	CCDS12576.1																																																																																			.	.	weak		0.627	HNRNPUL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463406.1	NM_144732, NM_007040	
PDE4DIP	9659	hgsc.bcm.edu	37	1	145015976	145015976	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:145015976C>T	ENST00000530740.1	-	3	363	c.325G>A	c.(325-327)Gtg>Atg	p.V109M	RP11-326G21.1_ENST00000610119.1_RNA|PDE4DIP_ENST00000493130.2_Missense_Mutation_p.V38M|PDE4DIP_ENST00000478649.2_Missense_Mutation_p.V38M|PDE4DIP_ENST00000369348.3_Missense_Mutation_p.V109M|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.V38M|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.V109M			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	0				I -> M (in Ref. 1; BAB17759/BAB17760/ BAB17761/BAB17762 and 6; AAH25406/ AAI10295). {ECO:0000305}.	cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TGTGACTGCACTGGAGGGCCT	0.423			T	PDGFRB	MPD																																p.V109M		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G325A						PASS	.																																			SO:0001583	missense	9659	exon3			ACTGCACTGGAGG	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000530740.1:c.325G>A	1.37:g.145015976C>T	ENSP00000435654:p.Val109Met	174.0	0.0	0		214.0	30.0	0.140187	NM_022359	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000530740.1	37		.	.	.	.	.	.	.	.	.	.	C	9.285	1.049170	0.19827	.	.	ENSG00000178104	ENST00000313382;ENST00000530740;ENST00000369359;ENST00000532801;ENST00000530078;ENST00000369348;ENST00000531369;ENST00000493130;ENST00000478649	T;T;T;T;T;T	0.49139	4.55;4.67;4.67;0.79;2.96;1.88	5.26	-0.476	0.12100	.	.	.	.	.	T	0.09905	0.0243	N	0.14661	0.345	0.09310	N	1	B;B;B	0.18863	0.007;0.004;0.031	B;B;B	0.14023	0.003;0.002;0.01	T	0.29610	-1.0006	9	0.36615	T	0.2	.	4.6702	0.12685	0.1441:0.2711:0.4924:0.0925	.	38;109;38	Q5VU43-3;E9PJ64;E9PQH9	.;.;.	M	38;109;109;38;38;109;39;38;38	ENSP00000327209:V38M;ENSP00000435654:V109M;ENSP00000358366:V109M;ENSP00000436751:V38M;ENSP00000358354:V109M;ENSP00000435616:V39M	ENSP00000327209:V38M	V	-	1	0	PDE4DIP	143727333	0.000000	0.05858	0.002000	0.10522	0.350000	0.29205	0.037000	0.13840	0.046000	0.15833	0.655000	0.94253	GTG	.	.	none		0.423	PDE4DIP-036	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000384663.2	NM_022359	
SYCE3	644186	hgsc.bcm.edu	37	22	50989742	50989742	+	Missense_Mutation	SNP	C	C	T	rs55829948	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50989742C>T	ENST00000406915.3	-	3	246	c.199G>A	c.(199-201)Gtc>Atc	p.V67I	SYCE3_ENST00000402753.1_Missense_Mutation_p.V67I	NM_001123225.1	NP_001116697.1	A1L190	SYCE3_HUMAN	synaptonemal complex central element protein 3	67					positive regulation of apoptotic process (GO:0043065)|reciprocal meiotic recombination (GO:0007131)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)|chromosome (GO:0005694)|nucleus (GO:0005634)				endometrium(1)|kidney(1)	2						TTGCAGTTGACGAAGGCATCC	0.602													C|||	9	0.00179712	0.0	0.0	5008	,	,		20192	0.0		0.008	False		,,,				2504	0.001				p.V67I		Atlas-SNP	.											.	SYCE3	10	.	0			c.G199A						PASS	.	C	ILE/VAL	4,1380		0,4,688	50.0	50.0	50.0		199	2.4	1.0	22	dbSNP_129	50	21,3161		0,21,1570	yes	missense	C22orf41	NM_001123225.1	29	0,25,2258	TT,TC,CC		0.66,0.289,0.5475	benign	67/89	50989742	25,4541	692	1591	2283	SO:0001583	missense	644186	exon3			AGTTGACGAAGGC		CCDS46733.1	22q13.33	2011-10-05	2011-10-05	2011-10-05	ENSG00000217442	ENSG00000217442			35245	protein-coding gene	gene with protein product	"""testis highly expressed protein 2"""	615775	"""chromosome 22 open reading frame 41"""	C22orf41		21637789	Standard	NM_001123225		Approved		uc010hbe.3	A1L190	OTTHUMG00000150273	ENST00000406915.3:c.199G>A	22.37:g.50989742C>T	ENSP00000385480:p.Val67Ile	124.0	0.0	0		137.0	70.0	0.510949	NM_001123225		Missense_Mutation	SNP	ENST00000406915.3	37	CCDS46733.1	10	0.004578754578754579	1	0.0020325203252032522	0	0.0	0	0.0	9	0.011873350923482849	C	11.45	1.643125	0.29246	0.00289	0.0066	ENSG00000217442	ENST00000406915;ENST00000402753	T;T	0.42900	0.96;0.96	6.04	2.36	0.29203	.	.	.	.	.	T	0.19485	0.0468	.	.	.	0.20638	N	0.999879	B	0.23058	0.079	B	0.11329	0.006	T	0.12630	-1.0540	8	0.38643	T	0.18	-0.1893	6.0115	0.19578	0.2341:0.1521:0.6138:0.0	rs55829948	67	A1L190	SYCE3_HUMAN	I	67	ENSP00000385480:V67I;ENSP00000385122:V67I	ENSP00000385122:V67I	V	-	1	0	C22orf41	49336608	1.000000	0.71417	1.000000	0.80357	0.818000	0.46254	2.037000	0.41174	0.892000	0.36259	-0.270000	0.10280	GTC	C|0.995;T|0.005	0.005	strong		0.602	SYCE3-002	PUTATIVE	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000317660.1	NM_001123225	
OR8B4	283162	hgsc.bcm.edu	37	11	124294127	124294127	+	Missense_Mutation	SNP	A	A	G	rs370187249		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:124294127A>G	ENST00000356130.3	-	1	662	c.641T>C	c.(640-642)gTc>gCc	p.V214A		NM_001005196.1	NP_001005196.1	Q96RC9	OR8B4_HUMAN	olfactory receptor, family 8, subfamily B, member 4	214						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)		GTAAGAGATGACGATGCTTAT	0.483																																					p.V214A		Atlas-SNP	.											OR8B4,NS,carcinoma,-1,1	OR8B4	60	1	0			c.T641C						PASS	.	A	ALA/VAL	0,4402		0,0,2201	89.0	75.0	80.0		641	1.8	0.4	11		80	1,8597		0,1,4298	no	missense	OR8B4	NM_001005196.1	64	0,1,6499	GG,GA,AA		0.0116,0.0,0.0077	benign	214/310	124294127	1,12999	2201	4299	6500	SO:0001583	missense	283162	exon1			GAGATGACGATGC	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.641T>C	11.37:g.124294127A>G	ENSP00000348449:p.Val214Ala	99.0	0.0	0		88.0	46.0	0.522727	NM_001005196	B2RNF8|Q6IFQ7	Missense_Mutation	SNP	ENST00000356130.3	37	CCDS31710.1	.	.	.	.	.	.	.	.	.	.	a	5.431	0.264595	0.10294	0.0	1.16E-4	ENSG00000198657	ENST00000356130	T	0.00272	8.36	4.14	1.8	0.24995	GPCR, rhodopsin-like superfamily (1);	0.367346	0.23494	N	0.047561	T	0.00178	0.0005	L	0.33792	1.035	0.09310	N	1	B	0.16603	0.018	B	0.22601	0.04	T	0.40213	-0.9575	10	0.87932	D	0	.	6.2461	0.20818	0.7765:0.0:0.0809:0.1426	.	214	Q96RC9	OR8B4_HUMAN	A	214	ENSP00000348449:V214A	ENSP00000348449:V214A	V	-	2	0	OR8B4	123799337	0.019000	0.18553	0.397000	0.26308	0.088000	0.18126	2.931000	0.48932	0.389000	0.25086	0.533000	0.62120	GTC	.	.	weak		0.483	OR8B4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387055.1	NM_001005196	
DDX42	11325	hgsc.bcm.edu	37	17	61898928	61898928	+	IGR	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:61898928G>A	ENST00000578681.1	+	0	4337				FTSJ3_ENST00000427159.2_Missense_Mutation_p.R558W	NM_007372.2	NP_031398.2	Q86XP3	DDX42_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 42						protein localization (GO:0008104)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(3)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)	46						CCCTTCCGCCGGTTCTCAAAT	0.567																																					p.R558W		Atlas-SNP	.											FTSJ3,NS,carcinoma,0,1	FTSJ3	63	1	0			c.C1672T						PASS	.						56.0	59.0	58.0					17																	61898928		2203	4300	6503	SO:0001628	intergenic_variant	117246	exon16			TCCGCCGGTTCTC	BC015505	CCDS32704.1	17q23	2014-02-14	2013-05-13			ENSG00000198231		"""DEAD-boxes"""	18676	protein-coding gene	gene with protein product	"""splicing factor 3b, subunit 8"""	613369	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 42"""			10727850, 16397294	Standard	NM_007372		Approved	RNAHP, RHELP, SF3b125, SF3B8	uc002jbv.3	Q86XP3			17.37:g.61898928G>A		55.0	0.0	0		41.0	26.0	0.634146	NM_017647	A6NML1|A8KA43|O75619|Q68G51|Q96BK1|Q96HR7|Q9Y3V8	Missense_Mutation	SNP	ENST00000578681.1	37	CCDS32704.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.994511	0.74703	.	.	ENSG00000108592	ENST00000427159	T	0.34275	1.37	5.17	5.17	0.71159	.	0.410282	0.25651	N	0.029207	T	0.37652	0.1011	N	0.22421	0.69	0.39415	D	0.966828	D	0.69078	0.997	P	0.53490	0.727	T	0.29941	-0.9995	10	0.72032	D	0.01	-4.4553	14.0344	0.64636	0.0:0.0:1.0:0.0	.	558	Q8IY81	RRMJ3_HUMAN	W	558	ENSP00000396673:R558W	ENSP00000396673:R558W	R	-	1	2	FTSJ3	59252660	0.045000	0.20229	0.773000	0.31616	0.045000	0.14185	2.138000	0.42140	2.688000	0.91661	0.563000	0.77884	CGG	.	.	none		0.567	DDX42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444368.1	NM_007372	
PRR22	163154	hgsc.bcm.edu	37	19	5783713	5783713	+	Missense_Mutation	SNP	G	G	A	rs141874203	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5783713G>A	ENST00000419421.2	-	3	649	c.545C>T	c.(544-546)cCg>cTg	p.P182L		NM_001134316.1	NP_001127788.1	Q8IZ63	PRR22_HUMAN	proline rich 22	182	Pro-rich.									endometrium(2)|large_intestine(1)|prostate(1)|urinary_tract(1)	5						GGGTGGCAGCGGGGCCGGGCC	0.716													G|||	51	0.0101837	0.0	0.0202	5008	,	,		8447	0.0		0.0258	False		,,,				2504	0.0112				p.P182L		Atlas-SNP	.											PRR22_ENST00000419421,NS,carcinoma,+1,2	PRR22	25	2	0			c.C545T						PASS	.	G	LEU/PRO	23,3621		0,23,1799	3.0	5.0	4.0		545	2.6	0.0	19	dbSNP_134	4	224,7348		0,224,3562	no	missense	PRR22	NM_001134316.1	98	0,247,5361	AA,AG,GG		2.9583,0.6312,2.2022	possibly-damaging	182/423	5783713	247,10969	1822	3786	5608	SO:0001583	missense	163154	exon3			GGCAGCGGGGCCG	BC023278	CCDS45933.1	19p13.3	2012-12-20			ENSG00000212123	ENSG00000212123			28354	protein-coding gene	gene with protein product						12477932	Standard	NM_001134316		Approved	MGC24975	uc010xiv.1	Q8IZ63	OTTHUMG00000180553	ENST00000419421.2:c.545C>T	19.37:g.5783713G>A	ENSP00000407653:p.Pro182Leu	25.0	0.0	0		36.0	21.0	0.583333	NM_001134316	E9PB31	Missense_Mutation	SNP	ENST00000419421.2	37	CCDS45933.1	35	0.016025641025641024	0	0.0	8	0.022099447513812154	1	0.0017482517482517483	26	0.03430079155672823	G	13.85	2.360615	0.41801	0.006312	0.029583	ENSG00000212123	ENST00000419421	T	0.20200	2.09	2.58	2.58	0.30949	.	.	.	.	.	T	0.04588	0.0125	L	0.32530	0.975	0.09310	N	1	P;P	0.42161	0.772;0.772	B;B	0.34779	0.189;0.189	T	0.10800	-1.0614	9	0.62326	D	0.03	.	8.7627	0.34685	0.0:0.0:1.0:0.0	.	182;180	E9PB31;Q8IZ63	.;PRR22_HUMAN	L	182	ENSP00000407653:P182L	ENSP00000407653:P182L	P	-	2	0	PRR22	5734713	0.123000	0.22298	0.002000	0.10522	0.003000	0.03518	2.157000	0.42320	1.759000	0.51996	0.491000	0.48974	CCG	G|0.984;A|0.016	0.016	strong		0.716	PRR22-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368523.1	NM_153359	
HIST1H4D	8360	hgsc.bcm.edu	37	6	26189010	26189010	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26189010A>C	ENST00000340756.2	-	1	294	c.295T>G	c.(295-297)Tat>Gat	p.Y99D		NM_003539.3	NP_003530.1	P62805	H4_HUMAN	histone cluster 1, H4d	99					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(2)|large_intestine(2)|lung(1)|prostate(1)	8		all_hematologic(11;0.196)				CCGAAGCCATAAAGAGTGCGT	0.552																																					p.Y99D		Atlas-SNP	.											HIST1H4D,colon,carcinoma,0,1	HIST1H4D	28	1	0			c.T295G						PASS	.						119.0	102.0	108.0					6																	26189010		2203	4300	6503	SO:0001583	missense	8360	exon1			AGCCATAAAGAGT	X60482	CCDS4589.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000188987	ENSG00000277157		"""Histones / Replication-dependent"""	4782	protein-coding gene	gene with protein product		602823	"""H4 histone family, member B"", ""histone 1, H4d"""	H4FB		9119399, 12408966	Standard	NM_003539		Approved	H4/b	uc003ngu.3	P62805	OTTHUMG00000014423	ENST00000340756.2:c.295T>G	6.37:g.26189010A>C	ENSP00000343282:p.Tyr99Asp	163.0	0.0	0		152.0	71.0	0.467105	NM_003539	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000340756.2	37	CCDS4589.1	.	.	.	.	.	.	.	.	.	.	.	17.92	3.506691	0.64410	.	.	ENSG00000188987	ENST00000340756	.	.	.	5.32	5.32	0.75619	.	0.000000	0.85682	D	0.000000	T	0.68961	0.3058	.	.	.	0.46499	D	0.999071	.	.	.	.	.	.	T	0.74708	-0.3574	6	0.87932	D	0	.	14.4576	0.67428	1.0:0.0:0.0:0.0	.	.	.	.	D	99	.	ENSP00000343282:Y99D	Y	-	1	0	HIST1H4D	26296989	1.000000	0.71417	0.740000	0.30986	0.041000	0.13682	8.784000	0.91818	2.017000	0.59298	0.528000	0.53228	TAT	.	.	none		0.552	HIST1H4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040085.1	NM_003539	
RGPD8	727851	hgsc.bcm.edu	37	2	113127773	113127773	+	Silent	SNP	A	A	G	rs186330915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:113127773A>G	ENST00000302558.3	-	23	5471	c.5280T>C	c.(5278-5280)ccT>ccC	p.P1760P	RGPD8_ENST00000409750.1_Silent_p.P1620P	NM_001164463.1	NP_001157935.1	O14715	RGPD8_HUMAN	RANBP2-like and GRIP domain containing 8	1760				P -> A (in Ref. 3; CAI56757). {ECO:0000305}.	protein targeting to Golgi (GO:0000042)	nuclear pore (GO:0005643)	Ran GTPase binding (GO:0008536)			endometrium(4)|kidney(1)|lung(1)|prostate(3)|urinary_tract(1)	10						AAGAACGGGAAGGATTTTCTT	0.308													.|||	8	0.00159744	0.0	0.0029	5008	,	,		13164	0.0		0.0	False		,,,				2504	0.0061				p.P1760P		Atlas-SNP	.											RGPD8_ENST00000302558,NS,carcinoma,-2,18	RGPD8	81	18	0			c.T5280C						PASS	.	A		2,1372		0,2,685	231.0	167.0	186.0		5280	0.7	0.9	2		186	4,3110		0,4,1553	no	coding-synonymous	RGPD8	NM_001164463.1		0,6,2238	GG,GA,AA		0.1285,0.1456,0.1337		1760/1766	113127773	6,4482	687	1557	2244	SO:0001819	synonymous_variant	727851	exon23			ACGGGAAGGATTT	AF012086	CCDS46394.1	2q13	2013-01-10	2005-12-20	2005-12-20	ENSG00000169629	ENSG00000169629		"""Tetratricopeptide (TTC) repeat domain containing"""	9849	protein-coding gene	gene with protein product		602752	"""RAN binding protein 2-like 1"""	RANBP2L1		9480752	Standard	NM_001164463		Approved	RanBP2alpha	uc002ths.2	O14715	OTTHUMG00000153289	ENST00000302558.3:c.5280T>C	2.37:g.113127773A>G		621.0	0.0	0		568.0	264.0	0.464789	NM_001164463	Q5CZA8	Silent	SNP	ENST00000302558.3	37	CCDS46394.1																																																																																			A|0.999;G|0.001	0.001	strong		0.308	RGPD8-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375951.1	XM_001722279	
ANKIB1	54467	hgsc.bcm.edu	37	7	92027064	92027064	+	Missense_Mutation	SNP	G	G	T	rs200132000		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92027064G>T	ENST00000265742.3	+	19	2799	c.2423G>T	c.(2422-2424)cGc>cTc	p.R808L		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	808							zinc ion binding (GO:0008270)	p.R808L(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			AGCAGCAGCCGCAGGCCTGGC	0.473																																					p.R808L		Atlas-SNP	.											ANKIB1,NS,carcinoma,0,1	ANKIB1	92	1	1	Substitution - Missense(1)	lung(1)	c.G2423T						PASS	.						153.0	164.0	161.0					7																	92027064		1949	4164	6113	SO:0001583	missense	54467	exon19			GCAGCCGCAGGCC	AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2423G>T	7.37:g.92027064G>T	ENSP00000265742:p.Arg808Leu	59.0	0.0	0		63.0	33.0	0.52381	NM_019004	Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Missense_Mutation	SNP	ENST00000265742.3	37	CCDS47639.1	.	.	.	.	.	.	.	.	.	.	G	16.98	3.271294	0.59649	.	.	ENSG00000001629	ENST00000265742	T	0.10763	2.84	5.87	3.91	0.45181	.	0.335987	0.35615	N	0.003097	T	0.11367	0.0277	L	0.29908	0.895	0.46823	D	0.999216	P;P	0.35551	0.509;0.465	B;B	0.40165	0.321;0.069	T	0.07028	-1.0794	10	0.87932	D	0	.	12.8561	0.57886	0.1408:0.0:0.8592:0.0	.	160;808	Q4VBX8;Q9P2G1	.;AKIB1_HUMAN	L	808	ENSP00000265742:R808L	ENSP00000265742:R808L	R	+	2	0	ANKIB1	91865000	1.000000	0.71417	0.999000	0.59377	0.817000	0.46193	1.255000	0.32909	0.816000	0.34421	0.655000	0.94253	CGC	.	.	alt		0.473	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1		
PHKB	5257	hgsc.bcm.edu	37	16	47533770	47533770	+	Silent	SNP	C	C	T	rs139431568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:47533770C>T	ENST00000323584.5	+	3	294	c.270C>T	c.(268-270)tgC>tgT	p.C90C	PHKB_ENST00000299167.8_Silent_p.C90C|PHKB_ENST00000567402.1_3'UTR|PHKB_ENST00000566044.1_Silent_p.C83C|PHKB_ENST00000455779.1_Silent_p.C83C	NM_000293.2	NP_000284.1	Q93100	KPBB_HUMAN	phosphorylase kinase, beta	90					carbohydrate metabolic process (GO:0005975)|generation of precursor metabolites and energy (GO:0006091)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)|plasma membrane (GO:0005886)	hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)|phosphorylase kinase activity (GO:0004689)	p.C90C(2)|p.C83C(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(10)|liver(1)|lung(18)|ovary(1)|skin(1)	41		all_cancers(37;0.00447)|all_lung(18;0.00616)|Lung NSC(13;0.0418)|Breast(268;0.203)				GCCTATACTGCGCTGCTGGGG	0.507													C|||	3	0.000599042	0.0	0.0014	5008	,	,		19579	0.0		0.002	False		,,,				2504	0.0				p.C90C		Atlas-SNP	.											PHKB_ENST00000323584,colon,carcinoma,0,3	PHKB	298	3	3	Substitution - coding silent(3)	large_intestine(3)	c.C270T						PASS	.	C	,	0,4402		0,0,2201	137.0	124.0	128.0		270,249	0.2	1.0	16	dbSNP_134	128	12,8588	8.4+/-32.0	0,12,4288	no	coding-synonymous,coding-synonymous	PHKB	NM_000293.2,NM_001031835.2	,	0,12,6489	TT,TC,CC		0.1395,0.0,0.0923	,	90/1094,83/1087	47533770	12,12990	2201	4300	6501	SO:0001819	synonymous_variant	5257	exon3			ATACTGCGCTGCT		CCDS10729.1, CCDS42161.1	16q12-q13	2009-07-10			ENSG00000102893	ENSG00000102893	2.7.11.19		8927	protein-coding gene	gene with protein product		172490					Standard	NM_000293		Approved		uc002eev.4	Q93100	OTTHUMG00000133102	ENST00000323584.5:c.270C>T	16.37:g.47533770C>T		163.0	0.0	0		135.0	55.0	0.407407	NM_000293	Q8N4T5	Silent	SNP	ENST00000323584.5	37	CCDS10729.1																																																																																			C|0.999;T|0.001	0.001	strong		0.507	PHKB-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000430413.1		
FHAD1	114827	hgsc.bcm.edu	37	1	15723833	15723833	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:15723833G>A	ENST00000375998.4	+	30	4163	c.4163G>A	c.(4162-4164)aGa>aAa	p.R1388K	FHAD1_ENST00000471347.1_3'UTR|FHAD1_ENST00000314740.8_Missense_Mutation_p.R659K|FHAD1_ENST00000358897.4_Missense_Mutation_p.R1388K|FHAD1_ENST00000417793.1_Missense_Mutation_p.R1352K			B1AJZ9	FHAD1_HUMAN	forkhead-associated (FHA) phosphopeptide binding domain 1	1388										skin(1)|stomach(1)	2						GACCAAGAAAGAGAGATGCTG	0.473																																					p.R1388K		Atlas-SNP	.											.	FHAD1	78	.	0			c.G4163A						PASS	.						120.0	113.0	115.0					1																	15723833		692	1591	2283	SO:0001583	missense	114827	exon31			AAGAAAGAGAGAT	AK093300		1p36.21	2012-04-19			ENSG00000142621	ENSG00000142621			29408	protein-coding gene	gene with protein product						11572484	Standard	NM_052929		Approved	KIAA1937	uc001awb.2	B1AJZ9	OTTHUMG00000002088	ENST00000375998.4:c.4163G>A	1.37:g.15723833G>A	ENSP00000365166:p.Arg1388Lys	60.0	0.0	0		74.0	4.0	0.0540541	NM_052929	Q0P6F5|Q8N8D3|Q8N9T6|Q8NA05	Missense_Mutation	SNP	ENST00000375998.4	37		.	.	.	.	.	.	.	.	.	.	G	3.840	-0.033936	0.07543	.	.	ENSG00000142621	ENST00000358897;ENST00000417793;ENST00000375998;ENST00000529606;ENST00000314740;ENST00000314668	T;T;T;T;T;T	0.61510	0.83;0.83;0.83;0.1;0.11;0.86	4.54	2.69	0.31865	.	.	.	.	.	T	0.43700	0.1259	L	0.44542	1.39	0.24039	N	0.996089	B;B	0.15930	0.015;0.005	B;B	0.23419	0.046;0.004	T	0.33369	-0.9871	9	0.08599	T	0.76	.	6.7927	0.23709	0.2048:0.0:0.7952:0.0	.	659;1388	B7WPP2;B1AJZ9	.;FHAD1_HUMAN	K	1388;1352;1388;677;659;623	ENSP00000351770:R1388K;ENSP00000407615:R1352K;ENSP00000365166:R1388K;ENSP00000434909:R677K;ENSP00000322979:R659K;ENSP00000318812:R623K	ENSP00000318812:R623K	R	+	2	0	FHAD1	15596420	0.999000	0.42202	0.965000	0.40720	0.041000	0.13682	0.887000	0.28254	0.850000	0.35239	0.655000	0.94253	AGA	.	.	none		0.473	FHAD1-026	PUTATIVE	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000393400.2	NM_052929	
ZNF98	148198	hgsc.bcm.edu	37	19	22585674	22585674	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:22585674G>A	ENST00000357774.5	-	3	291	c.170C>T	c.(169-171)tCt>tTt	p.S57F	ZNF98_ENST00000601553.1_Missense_Mutation_p.S57F	NM_001098626.1	NP_001092096.1	A6NK75	ZNF98_HUMAN	zinc finger protein 98	57	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)	p.S57Y(2)		central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(8)|lung(16)|ovary(1)|prostate(4)|skin(1)|upper_aerodigestive_tract(2)	37		all_cancers(12;0.0536)|all_lung(12;0.00187)|Lung NSC(12;0.0019)|all_epithelial(12;0.00542)|Hepatocellular(1079;0.244)				GTCTGGCTTAGAGGCAGCAAT	0.393																																					p.S57F		Atlas-SNP	.											ZNF98_ENST00000357774,NS,carcinoma,0,2	ZNF98	230	2	2	Substitution - Missense(2)	prostate(2)	c.C170T						PASS	.																																			SO:0001583	missense	148198	exon3			GGCTTAGAGGCAG		CCDS46031.1	19p12	2014-02-14	2010-04-20	2008-06-12	ENSG00000197360	ENSG00000197360		"""Zinc fingers, C2H2-type"", ""-"""	13174	protein-coding gene	gene with protein product	"""zinc finger protein 739"""	603980					Standard	NM_001098626		Approved	ZNF739, F7175	uc002nqt.2	A6NK75	OTTHUMG00000182940	ENST00000357774.5:c.170C>T	19.37:g.22585674G>A	ENSP00000350418:p.Ser57Phe	43.0	0.0	0		51.0	23.0	0.45098	NM_001098626		Missense_Mutation	SNP	ENST00000357774.5	37	CCDS46031.1	.	.	.	.	.	.	.	.	.	.	.	13.75	2.330284	0.41297	.	.	ENSG00000197360	ENST00000357774	T	0.00848	5.62	0.476	0.476	0.16779	Krueppel-associated box (3);	.	.	.	.	T	0.01029	0.0034	L	0.35793	1.09	0.22389	N	0.999141	P	0.37525	0.598	B	0.37888	0.26	T	0.50923	-0.8770	8	0.45353	T	0.12	.	.	.	.	.	57	A6NK75	ZNF98_HUMAN	F	57	ENSP00000350418:S57F	ENSP00000350418:S57F	S	-	2	0	ZNF98	22377514	0.164000	0.22935	0.816000	0.32577	0.950000	0.60333	0.418000	0.21230	0.532000	0.28657	0.298000	0.19748	TCT	.	.	none		0.393	ZNF98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464398.1	NM_001098626	
TRPC4	7223	hgsc.bcm.edu	37	13	38211046	38211046	+	Silent	SNP	T	T	C	rs731860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:38211046T>C	ENST00000379705.3	-	11	3785	c.2928A>G	c.(2926-2928)agA>agG	p.R976R	TRPC4_ENST00000379673.2_Silent_p.R827R|TRPC4_ENST00000355779.2_Silent_p.R835R|TRPC4_ENST00000379681.3_Silent_p.R981R|TRPC4_ENST00000447043.1_Silent_p.R835R|TRPC4_ENST00000338947.5_Silent_p.R803R|TRPC4_ENST00000426868.2_3'UTR|TRPC4_ENST00000358477.2_Silent_p.R892R|TRPC4_ENST00000379679.1_Silent_p.R803R			Q9UBN4	TRPC4_HUMAN	transient receptor potential cation channel, subfamily C, member 4	976	Binds to ITPR1, ITPR2 and ITPR3.|PDZ-binding domain.				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)		AGTATCACAATCTTGTGGTCA	0.403													T|||	154	0.0307508	0.1112	0.0086	5008	,	,		19821	0.0		0.001	False		,,,				2504	0.0				p.R981R		Atlas-SNP	.											.	TRPC4	389	.	0			c.A2943G						PASS	.	T	,,,,,	428,3978	208.5+/-229.5	24,380,1799	118.0	111.0	114.0		2676,2481,2505,2409,2943,2928	-1.3	0.2	13	dbSNP_86	114	7,8593	5.0+/-18.6	0,7,4293	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TRPC4	NM_001135955.1,NM_001135956.1,NM_001135957.1,NM_001135958.1,NM_003306.1,NM_016179.2	,,,,,	24,387,6092	CC,CT,TT		0.0814,9.714,3.3446	,,,,,	892/894,827/829,835/837,803/805,981/983,976/978	38211046	435,12571	2203	4300	6503	SO:0001819	synonymous_variant	7223	exon11			TCACAATCTTGTG	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.2928A>G	13.37:g.38211046T>C		118.0	0.0	0		127.0	59.0	0.464567	NM_003306	B1ALE0|B1ALE1|B1ALE2|Q15721|Q3SWS6|Q96P03|Q96P04|Q96P05|Q9UIB0|Q9UIB1|Q9UIB2	Silent	SNP	ENST00000379705.3	37	CCDS9365.1																																																																																			T|0.959;C|0.041	0.041	strong		0.403	TRPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044574.2	NM_003306	
RPLP0	6175	hgsc.bcm.edu	37	12	120636498	120636498	+	Silent	SNP	G	G	A	rs138718343		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:120636498G>A	ENST00000551150.1	-	5	825	c.510C>T	c.(508-510)agC>agT	p.S170S	RPLP0_ENST00000228306.4_Silent_p.S170S|PXN-AS1_ENST00000538804.1_RNA|RPLP0_ENST00000392514.4_Silent_p.S170S|RPLP0_ENST00000313104.5_Intron|RPLP0_ENST00000546989.1_Intron|PXN-AS1_ENST00000535200.1_RNA|PXN-AS1_ENST00000542314.1_RNA|PXN-AS1_ENST00000539446.1_RNA|RPLP0_ENST00000550296.1_5'Flank|PXN-AS1_ENST00000542265.1_RNA|RPLP0_ENST00000552292.1_5'Flank			P05388	RLA0_HUMAN	ribosomal protein, large, P0	170					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|ribosome biogenesis (GO:0042254)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)	15	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCGTGGCTTCGCTGGCTCCCA	0.527																																					p.S170S		Atlas-SNP	.											.	RPLP0	27	.	0			c.C510T						PASS	.	G	,	0,4406		0,0,2203	72.0	69.0	70.0		510,510	-0.5	1.0	12	dbSNP_134	70	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous,coding-synonymous	RPLP0	NM_001002.3,NM_053275.3	,	0,3,6498	AA,AG,GG		0.0349,0.0,0.0231	,	170/318,170/318	120636498	3,12999	2203	4298	6501	SO:0001819	synonymous_variant	6175	exon6			GGCTTCGCTGGCT	AB007187	CCDS9193.1	12q24.2	2011-07-29			ENSG00000089157	ENSG00000089157		"""L ribosomal proteins"""	10371	protein-coding gene	gene with protein product	"""acidic ribosomal phosphoprotein P0"""	180510				9582194	Standard	NM_053275		Approved	PRLP0, P0, L10E, RPP0, LP0	uc001txq.3	P05388	OTTHUMG00000169317	ENST00000551150.1:c.510C>T	12.37:g.120636498G>A		153.0	0.0	0		201.0	86.0	0.427861	NM_053275	Q3B7A4|Q9BVK4	Silent	SNP	ENST00000551150.1	37	CCDS9193.1																																																																																			G|1.000;A|0.000	0.000	weak		0.527	RPLP0-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403448.3	NM_053275	
TG	7038	hgsc.bcm.edu	37	8	134145885	134145885	+	Silent	SNP	G	G	A	rs111563366		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:134145885G>A	ENST00000220616.4	+	47	8209	c.8169G>A	c.(8167-8169)tcG>tcA	p.S2723S	TG_ENST00000519543.1_Silent_p.S856S|TG_ENST00000542445.1_Silent_p.S1093S|TG_ENST00000377869.1_Silent_p.S2666S	NM_003235.4	NP_003226.4	P01266	THYG_HUMAN	thyroglobulin	2723					hormone biosynthetic process (GO:0042446)|iodide transport (GO:0015705)|regulation of myelination (GO:0031641)|signal transduction (GO:0007165)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular region (GO:0005576)|extracellular space (GO:0005615)				NS(1)|breast(11)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(34)|liver(2)|lung(59)|ovary(9)|pancreas(2)|prostate(6)|skin(7)|stomach(4)|upper_aerodigestive_tract(4)|urinary_tract(8)	168	Ovarian(258;0.00438)|Acute lymphoblastic leukemia(118;0.155)	Myeloproliferative disorder(644;0.00878)|Acute lymphoblastic leukemia(644;0.0559)|Breast(495;0.0735)	BRCA - Breast invasive adenocarcinoma(115;0.000701)	KIRC - Kidney renal clear cell carcinoma(542;0.0546)		AGTACATCTCGTCTCTGAAGA	0.562																																					p.S2723S		Atlas-SNP	.											.	TG	416	.	0			c.G8169A						PASS	.	G		1,4405	4.2+/-10.8	0,1,2202	55.0	51.0	53.0		8169	-1.1	0.2	8	dbSNP_132	53	0,8600		0,0,4300	no	coding-synonymous	TG	NM_003235.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		2723/2769	134145885	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	7038	exon47			CATCTCGTCTCTG	AU141420	CCDS34944.1	8q24	2012-10-02			ENSG00000042832	ENSG00000042832			11764	protein-coding gene	gene with protein product		188450					Standard	NM_003235		Approved	TGN, AITD3	uc003ytw.3	P01266	OTTHUMG00000164649	ENST00000220616.4:c.8169G>A	8.37:g.134145885G>A		122.0	0.0	0		152.0	52.0	0.342105	NM_003235	O15274|O43899|Q15593|Q15948|Q9NYR1|Q9NYR2|Q9UMZ0|Q9UNY3	Silent	SNP	ENST00000220616.4	37	CCDS34944.1	.	.	.	.	.	.	.	.	.	.	G	0.026	-1.372534	0.01214	2.27E-4	0.0	ENSG00000042832	ENST00000519178	.	.	.	4.84	-1.12	0.09808	.	.	.	.	.	T	0.23171	0.0560	.	.	.	0.20403	N	0.999907	.	.	.	.	.	.	T	0.28554	-1.0040	4	.	.	.	.	4.4635	0.11678	0.3929:0.0:0.4574:0.1498	.	.	.	.	I	1179	.	.	V	+	1	0	TG	134215067	0.002000	0.14202	0.191000	0.23289	0.059000	0.15707	0.558000	0.23469	-0.078000	0.12730	-1.332000	0.01269	GTC	G|0.500;A|0.500	0.500	weak		0.562	TG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379606.1	NM_003235	
CFAP57	149465	hgsc.bcm.edu	37	1	43675539	43675539	+	Silent	SNP	G	G	A	rs148341430	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43675539G>A	ENST00000372492.4	+	11	2205	c.1881G>A	c.(1879-1881)ctG>ctA	p.L627L	WDR65_ENST00000528956.1_Silent_p.L627L	NM_001195831.2	NP_001182760.2	Q96MR6	WDR65_HUMAN		627										NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(7)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	23	Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				CTCTGCCTCTGCAGAAGGAAT	0.572													g|||	2	0.000399361	0.0	0.0014	5008	,	,		18599	0.0		0.001	False		,,,				2504	0.0				p.L627L		Atlas-SNP	.											.	WDR65	76	.	0			c.G1881A						PASS	.	G	,,	0,4406		0,0,2203	176.0	149.0	158.0		1881,1881,1881	1.7	1.0	1	dbSNP_134	158	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous,coding-synonymous,coding-synonymous	WDR65	NM_001167965.1,NM_001167966.1,NM_152498.3	,,	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	,,	627/699,627/699,627/699	43675539	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	149465	exon11			GCCTCTGCAGAAG																												ENST00000372492.4:c.1881G>A	1.37:g.43675539G>A		117.0	0.0	0		117.0	58.0	0.495726	NM_152498	A6NKQ3|Q17RI9|Q5TAI0	Silent	SNP	ENST00000372492.4	37																																																																																				G|0.999;A|0.001	0.001	strong		0.572	WDR65-002	NOVEL	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000384325.1		
EPHA3	2042	hgsc.bcm.edu	37	3	89448530	89448530	+	Missense_Mutation	SNP	C	C	A	rs144696297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:89448530C>A	ENST00000336596.2	+	7	1719	c.1494C>A	c.(1492-1494)agC>agA	p.S498R	EPHA3_ENST00000494014.1_Missense_Mutation_p.S498R|EPHA3_ENST00000452448.2_Missense_Mutation_p.S498R	NM_005233.5	NP_005224.2	P29320	EPHA3_HUMAN	EPH receptor A3	498	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)|cell migration (GO:0016477)|cellular response to retinoic acid (GO:0071300)|ephrin receptor signaling pathway (GO:0048013)|fasciculation of motor neuron axon (GO:0097156)|fasciculation of sensory neuron axon (GO:0097155)|positive regulation of neuron projection development (GO:0010976)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of Rho GTPase activity (GO:0032319)	early endosome (GO:0005769)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|GPI-linked ephrin receptor activity (GO:0005004)			NS(1)|breast(4)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(26)|liver(3)|lung(67)|ovary(7)|pancreas(1)|prostate(4)|skin(8)|stomach(1)|upper_aerodigestive_tract(5)	139	all_cancers(8;0.0406)|Melanoma(1;0.00142)|all_epithelial(1;0.0612)	Lung NSC(201;0.0782)		LUSC - Lung squamous cell carcinoma(29;0.00344)|Lung(72;0.00942)		CCATCAGTAGCCTCAAGCCTG	0.423										TSP Lung(6;0.00050)			C|||	2	0.000399361	0.0	0.0	5008	,	,		15456	0.0		0.002	False		,,,				2504	0.0				p.S498R		Atlas-SNP	.											.	EPHA3	501	.	0			c.C1494A						PASS	.						93.0	90.0	91.0					3																	89448530		2203	4300	6503	SO:0001583	missense	2042	exon7			CAGTAGCCTCAAG	M83941	CCDS2922.1, CCDS46875.1	3p11.2	2013-02-11	2004-10-28		ENSG00000044524	ENSG00000044524	2.7.10.1	"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3387	protein-coding gene	gene with protein product		179611	"""EphA3"""	ETK, ETK1, TYRO4		1737782, 1311845	Standard	NM_005233		Approved	HEK, HEK4	uc003dqy.3	P29320	OTTHUMG00000159040	ENST00000336596.2:c.1494C>A	3.37:g.89448530C>A	ENSP00000337451:p.Ser498Arg	103.0	0.0	0		101.0	55.0	0.544554	NM_005233	Q9H2V3|Q9H2V4	Missense_Mutation	SNP	ENST00000336596.2	37	CCDS2922.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	17.56	3.420551	0.62622	.	.	ENSG00000044524	ENST00000336596;ENST00000452448;ENST00000494014	T;T;T	0.57595	0.39;0.39;0.39	5.35	5.35	0.76521	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.045473	0.85682	D	0.000000	T	0.38612	0.1047	N	0.20845	0.615	0.41304	D	0.987066	B;B	0.32101	0.106;0.356	B;B	0.37422	0.249;0.212	T	0.25984	-1.0116	9	.	.	.	.	10.524	0.44936	0.0:0.7909:0.1352:0.0739	.	498;498	P29320;P29320-2	EPHA3_HUMAN;.	R	498	ENSP00000337451:S498R;ENSP00000399926:S498R;ENSP00000419190:S498R	.	S	+	3	2	EPHA3	89531220	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	0.799000	0.27028	2.505000	0.84491	0.563000	0.77884	AGC	C|0.999;A|0.001	0.001	strong		0.423	EPHA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352995.1	NM_005233	
KALRN	8997	hgsc.bcm.edu	37	3	124044859	124044859	+	Silent	SNP	C	C	T	rs16835275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124044859C>T	ENST00000240874.3	+	7	1276	c.1119C>T	c.(1117-1119)tcC>tcT	p.S373S	KALRN_ENST00000360013.3_Silent_p.S373S|KALRN_ENST00000460856.1_Silent_p.S373S	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	373					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						GCATCATGTCCGTGGCTTCCC	0.547													C|||	29	0.00579073	0.0061	0.0058	5008	,	,		16950	0.0099		0.005	False		,,,				2504	0.002				p.S373S		Atlas-SNP	.											KALRN_ENST00000360013,NS,malignant_melanoma,+1,2	KALRN	556	2	0			c.C1119T						PASS	.	C	,	27,4379	32.6+/-62.9	0,27,2176	102.0	93.0	97.0		1119,1119	-9.3	0.0	3	dbSNP_123	97	73,8525	42.2+/-99.7	1,71,4227	no	coding-synonymous,coding-synonymous	KALRN	NM_001024660.3,NM_003947.4	,	1,98,6403	TT,TC,CC		0.849,0.6128,0.769	,	373/2987,373/1664	124044859	100,12904	2203	4299	6502	SO:0001819	synonymous_variant	8997	exon7			CATGTCCGTGGCT	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.1119C>T	3.37:g.124044859C>T		134.0	0.0	0		191.0	86.0	0.450262	NM_003947	A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Silent	SNP	ENST00000240874.3	37	CCDS3027.1	16	0.007326007326007326	1	0.0020325203252032522	5	0.013812154696132596	7	0.012237762237762238	3	0.00395778364116095	C	6.705	0.498764	0.12762	0.006128	0.00849	ENSG00000160145	ENST00000354186	.	.	.	4.64	-9.28	0.00656	.	.	.	.	.	T	0.49830	0.1580	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.74463	-0.3657	4	.	.	.	.	12.8333	0.57759	0.0:0.4623:0.2765:0.2612	rs16835275;rs16835275	.	.	.	L	351	.	.	P	+	2	0	KALRN	125527549	0.000000	0.05858	0.012000	0.15200	0.920000	0.55202	-5.264000	0.00136	-4.734000	0.00034	-1.876000	0.00548	CCG	C|0.992;T|0.008	0.008	strong		0.547	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947	
CFAP70	118491	hgsc.bcm.edu	37	10	75037999	75037999	+	Missense_Mutation	SNP	C	C	A	rs12256262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75037999C>A	ENST00000310715.3	-	21	2666	c.2546G>T	c.(2545-2547)tGg>tTg	p.W849L	TTC18_ENST00000394865.1_Missense_Mutation_p.W849L|TTC18_ENST00000401621.2_Missense_Mutation_p.W849L|TTC18_ENST00000493787.1_Intron|TTC18_ENST00000340329.3_Intron|DNAJC9-AS1_ENST00000440197.2_RNA|RNU6-833P_ENST00000363486.1_RNA|TTC18_ENST00000355577.3_Missense_Mutation_p.W318L	NM_145170.3	NP_660153.3	Q5T0N1	TTC18_HUMAN		849			W -> L (in dbSNP:rs12256262).			extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(13)|ovary(2)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	Prostate(51;0.0119)					ACTTGGATCCCAAGTTTGTGT	0.378													C|||	121	0.0241613	0.0847	0.013	5008	,	,		18710	0.0		0.0	False		,,,				2504	0.0				p.W849L		Atlas-SNP	.											.	TTC18	106	.	0			c.G2546T						PASS	.	C	LEU/TRP	294,4112	161.4+/-193.6	9,276,1918	184.0	180.0	181.0		2546	0.2	0.7	10	dbSNP_120	181	20,8580	14.6+/-50.1	0,20,4280	yes	missense	TTC18	NM_145170.3	61	9,296,6198	AA,AC,CC		0.2326,6.6727,2.4143	benign	849/1122	75037999	314,12692	2203	4300	6503	SO:0001583	missense	118491	exon21			GGATCCCAAGTTT																												ENST00000310715.3:c.2546G>T	10.37:g.75037999C>A	ENSP00000310829:p.Trp849Leu	224.0	1.0	0.00446429		251.0	120.0	0.478088	NM_145170	C9JIZ9|Q5T0M4|Q5T0M9|Q5T0N0|Q69YH9|Q8IYZ8|Q8N7D5|Q8NI30|Q8NI31	Missense_Mutation	SNP	ENST00000310715.3	37	CCDS7324.3	49	0.022435897435897436	36	0.07317073170731707	6	0.016574585635359115	2	0.0034965034965034965	5	0.006596306068601583	C	2.654	-0.281206	0.05642	0.066727	0.002326	ENSG00000156042	ENST00000310715;ENST00000401621;ENST00000355577;ENST00000433268;ENST00000394865	T;T;T;T	0.28666	2.03;2.03;1.6;1.63	4.56	0.152	0.14893	.	0.762705	0.11325	N	0.575616	T	0.00695	0.0023	N	0.03115	-0.41	0.25123	N	0.990622	B	0.02656	0.0	B	0.01281	0.0	T	0.31308	-0.9948	10	0.11485	T	0.65	-0.0236	3.4795	0.07597	0.4634:0.1102:0.0:0.4264	rs12256262;rs52797721;rs57681861;rs12256262	849	Q5T0N1	TTC18_HUMAN	L	849;849;849;256;849	ENSP00000310829:W849L;ENSP00000384479:W849L;ENSP00000409527:W256L;ENSP00000378334:W849L	ENSP00000310829:W849L	W	-	2	0	TTC18	74708005	0.691000	0.27709	0.746000	0.31095	0.029000	0.11900	0.181000	0.16880	-0.081000	0.12662	-0.312000	0.09012	TGG	C|0.973;A|0.027	0.027	strong		0.378	TTC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding			
ZNF516	9658	hgsc.bcm.edu	37	18	74154296	74154296	+	Missense_Mutation	SNP	C	C	T	rs12961584		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:74154296C>T	ENST00000443185.2	-	3	1032	c.715G>A	c.(715-717)Ggc>Agc	p.G239S	ZNF516_ENST00000524431.2_5'UTR	NM_014643.3	NP_055458.1	Q92618	ZN516_HUMAN	zinc finger protein 516	239			G -> S (in dbSNP:rs12961584).		regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32		Prostate(75;0.0869)|Esophageal squamous(42;0.129)		OV - Ovarian serous cystadenocarcinoma(15;7.64e-06)|BRCA - Breast invasive adenocarcinoma(31;0.238)		TCGGGCTTGCCGTTCTCCACG	0.692													C|||	1	0.000199681	0.0	0.0	5008	,	,		15391	0.0		0.001	False		,,,				2504	0.0				p.G239S		Atlas-SNP	.											.	ZNF516	102	.	0			c.G715A						PASS	.	C	SER/GLY	2,4128		0,2,2063	12.0	14.0	14.0		715	3.5	1.0	18	dbSNP_121	14	33,8345		0,33,4156	no	missense	ZNF516	NM_014643.3	56	0,35,6219	TT,TC,CC		0.3939,0.0484,0.2798	probably-damaging	239/1164	74154296	35,12473	2065	4189	6254	SO:0001583	missense	9658	exon3			GCTTGCCGTTCTC	D86975	CCDS74234.1	18q23	2013-01-08				ENSG00000101493		"""Zinc fingers, C2H2-type"""	28990	protein-coding gene	gene with protein product		615114				9039502	Standard	NM_014643		Approved	HsT287, KIAA0222	uc021ulp.1	Q92618		ENST00000443185.2:c.715G>A	18.37:g.74154296C>T	ENSP00000394757:p.Gly239Ser	22.0	0.0	0		39.0	26.0	0.666667	NM_014643		Missense_Mutation	SNP	ENST00000443185.2	37		.	.	.	.	.	.	.	.	.	.	C	16.18	3.050132	0.55218	4.84E-4	0.003939	ENSG00000101493	ENST00000443185	T	0.11063	2.81	4.39	3.5	0.40072	.	0.497156	0.19611	N	0.110146	T	0.16854	0.0405	.	.	.	0.30781	N	0.741935	D	0.69078	0.997	P	0.53760	0.734	T	0.04509	-1.0946	9	0.22109	T	0.4	-22.5334	12.8858	0.58042	0.3101:0.6899:0.0:0.0	rs12961584	239	Q92618	ZN516_HUMAN	S	239	ENSP00000394757:G239S	ENSP00000394757:G239S	G	-	1	0	ZNF516	72283284	0.628000	0.27138	0.994000	0.49952	0.971000	0.66376	1.269000	0.33074	1.187000	0.43000	0.557000	0.71058	GGC	C|0.667;T|0.333	0.333	strong		0.692	ZNF516-201	KNOWN	basic|appris_principal|exp_conf	protein_coding	protein_coding		NM_014643	
CD22	933	hgsc.bcm.edu	37	19	35832468	35832468	+	Missense_Mutation	SNP	T	T	C	rs369129095		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:35832468T>C	ENST00000085219.5	+	8	1796	c.1730T>C	c.(1729-1731)aTa>aCa	p.I577T	CD22_ENST00000536635.2_Missense_Mutation_p.I489T|CD22_ENST00000544992.2_Missense_Mutation_p.I577T|CD22_ENST00000270311.6_Missense_Mutation_p.I457T|CD22_ENST00000341773.6_Missense_Mutation_p.I400T|CD22_ENST00000419549.2_Missense_Mutation_p.I405T|CD22_ENST00000594250.1_Missense_Mutation_p.I400T	NM_001771.3	NP_001762.2	P20273	CD22_HUMAN	CD22 molecule	577	Ig-like C2-type 5.				cell adhesion (GO:0007155)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)			breast(2)|endometrium(2)|kidney(3)|large_intestine(14)|lung(21)|ovary(5)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	54	all_lung(56;9.78e-09)|Lung NSC(56;1.46e-08)|Esophageal squamous(110;0.162)		Epithelial(14;5.83e-19)|OV - Ovarian serous cystadenocarcinoma(14;3.19e-18)|all cancers(14;3.41e-16)|LUSC - Lung squamous cell carcinoma(66;0.0417)			AACAACTCCATAGGACAGACA	0.557																																					p.I577T	Ovarian(42;1009 1133 23674 26041)	Atlas-SNP	.											.	CD22	129	.	0			c.T1730C						PASS	.	T	THR/ILE,THR/ILE,THR/ILE,THR/ILE	0,4406		0,0,2203	73.0	72.0	72.0		1466,1730,1199,1730	3.5	0.0	19		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense	CD22	NM_001185099.1,NM_001185100.1,NM_001185101.1,NM_001771.3	89,89,89,89	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	489/760,577/752,400/671,577/848	35832468	1,13005	2203	4300	6503	SO:0001583	missense	933	exon8			ACTCCATAGGACA	X52785	CCDS12457.1, CCDS54247.1, CCDS54248.1, CCDS54249.1, CCDS62634.1	19q13.1	2013-01-29	2006-03-28		ENSG00000012124	ENSG00000012124		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1643	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 2"""	107266	"""CD22 antigen"""			8496602, 1691828	Standard	NM_001185099		Approved	SIGLEC-2, SIGLEC2	uc010edt.3	P20273		ENST00000085219.5:c.1730T>C	19.37:g.35832468T>C	ENSP00000085219:p.Ile577Thr	43.0	0.0	0		40.0	23.0	0.575	NM_001185100	F5GYU4|F5H7U3|O95699|O95701|O95702|O95703|Q01665|Q32M46|Q92872|Q92873|Q9UQA6|Q9UQA7|Q9UQA8|Q9UQA9|Q9UQB0|Q9Y2A6	Missense_Mutation	SNP	ENST00000085219.5	37	CCDS12457.1	.	.	.	.	.	.	.	.	.	.	T	14.05	2.420287	0.42918	0.0	1.16E-4	ENSG00000012124	ENST00000085219;ENST00000536635;ENST00000341773;ENST00000544992;ENST00000270311;ENST00000419549	T;T;T;T;T;T	0.11604	2.76;2.76;2.76;2.76;2.76;2.76	5.73	3.54	0.40534	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.679676	0.13703	N	0.368667	T	0.18882	0.0453	L	0.56124	1.755	0.09310	N	1	P;P;D;B;D	0.54964	0.931;0.9;0.969;0.223;0.96	P;P;P;B;P	0.59357	0.765;0.653;0.856;0.129;0.755	T	0.11397	-1.0589	10	0.22706	T	0.39	.	5.5235	0.16945	0.0:0.0879:0.1731:0.739	.	405;577;489;577;400	Q32M46;F5GYU4;F5H7U3;P20273;P20273-2	.;.;.;CD22_HUMAN;.	T	577;489;400;577;457;405	ENSP00000085219:I577T;ENSP00000442279:I489T;ENSP00000339349:I400T;ENSP00000441237:I577T;ENSP00000270311:I457T;ENSP00000403822:I405T	ENSP00000085219:I577T	I	+	2	0	CD22	40524308	0.002000	0.14202	0.013000	0.15412	0.133000	0.20885	1.081000	0.30791	1.001000	0.39076	-0.411000	0.06167	ATA	.	.	weak		0.557	CD22-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000466099.1	NM_001771	
ESRP2	80004	hgsc.bcm.edu	37	16	68269820	68269820	+	Silent	SNP	C	C	T	rs150603076	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68269820C>T	ENST00000565858.1	-	1	215	c.129G>A	c.(127-129)cgG>cgA	p.R43R	ESRP2_ENST00000473183.2_Silent_p.R43R|RP11-96D1.6_ENST00000564147.1_RNA	NM_024939.2	NP_079215.2	Q9H6T0	ESRP2_HUMAN	epithelial splicing regulatory protein 2	43					mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nucleus (GO:0005634)	mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|central_nervous_system(1)|kidney(2)|large_intestine(4)|lung(5)|ovary(1)|prostate(2)	16						AGCCCAGGTCCCGTCCCAGCG	0.711													C|||	15	0.00299521	0.0	0.0029	5008	,	,		7867	0.0		0.007	False		,,,				2504	0.0061				p.R43R		Atlas-SNP	.											.	ESRP2	118	.	0			c.G129A						PASS	.	C		3,4377		0,3,2187	18.0	14.0	15.0		129	-6.1	0.7	16	dbSNP_134	15	38,8532		0,38,4247	no	coding-synonymous	ESRP2	NM_024939.2		0,41,6434	TT,TC,CC		0.4434,0.0685,0.3166		43/718	68269820	41,12909	2190	4285	6475	SO:0001819	synonymous_variant	80004	exon1			CAGGTCCCGTCCC	AK025571	CCDS10863.1	16q22.1	2013-02-12	2009-03-10	2009-03-10	ENSG00000103067	ENSG00000103067		"""RNA binding motif (RRM) containing"""	26152	protein-coding gene	gene with protein product		612960	"""RNA binding motif protein 35B"""	RBM35B		12477932	Standard	NM_024939		Approved	FLJ21918	uc002evq.1	Q9H6T0	OTTHUMG00000137557	ENST00000565858.1:c.129G>A	16.37:g.68269820C>T		24.0	0.0	0		34.0	18.0	0.529412	NM_024939	Q8N6H8|Q8WZ15|Q9H6I4	Silent	SNP	ENST00000565858.1	37																																																																																				C|0.997;T|0.003	0.003	strong		0.711	ESRP2-004	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000433083.1	NM_024939	
CDK5R2	8941	hgsc.bcm.edu	37	2	219824731	219824731	+	Silent	SNP	G	G	C	rs78141300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219824731G>C	ENST00000302625.4	+	1	355	c.189G>C	c.(187-189)gcG>gcC	p.A63A	AC097468.7_ENST00000429343.1_RNA	NM_003936.4	NP_003927.1	Q13319	CD5R2_HUMAN	cyclin-dependent kinase 5, regulatory subunit 2 (p39)	63					cerebellum development (GO:0021549)|hippocampus development (GO:0021766)|layer formation in cerebral cortex (GO:0021819)|neuron migration (GO:0001764)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|superior olivary nucleus maturation (GO:0021722)	cyclin-dependent protein kinase 5 holoenzyme complex (GO:0016533)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	cyclin-dependent protein kinase 5 activator activity (GO:0016534)|lipid binding (GO:0008289)			central_nervous_system(2)|endometrium(2)|large_intestine(2)|lung(1)|ovary(1)	8		Renal(207;0.0474)		Epithelial(149;9.77e-07)|all cancers(144;0.000167)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TCATCTCGGCGCTCACCTGGA	0.716													G|||	163	0.0325479	0.0061	0.0375	5008	,	,		7620	0.0179		0.0398	False		,,,				2504	0.0726				p.A63A		Atlas-SNP	.											.	CDK5R2	17	.	0			c.G189C						PASS	.	G		22,4302		2,18,2142	10.0	14.0	13.0		189	2.5	1.0	2	dbSNP_131	13	213,8313		1,211,4051	no	coding-synonymous	CDK5R2	NM_003936.3		3,229,6193	CC,CG,GG		2.4982,0.5088,1.8288		63/368	219824731	235,12615	2162	4263	6425	SO:0001819	synonymous_variant	8941	exon1			CTCGGCGCTCACC	U34051	CCDS2427.1	2q35	2008-05-22			ENSG00000171450	ENSG00000171450			1776	protein-coding gene	gene with protein product	"""neuronal CDK5 activator isoform"""	603764				7592934	Standard	NM_003936		Approved	p39nck5ai, P39, NCK5AI	uc002vjf.4	Q13319	OTTHUMG00000133083	ENST00000302625.4:c.189G>C	2.37:g.219824731G>C		3.0	0.0	0		23.0	13.0	0.565217	NM_003936	Q4ZFW6	Silent	SNP	ENST00000302625.4	37	CCDS2427.1																																																																																			G|0.972;C|0.028	0.028	strong		0.716	CDK5R2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256728.1	NM_003936	
DSG3	1830	hgsc.bcm.edu	37	18	29049138	29049138	+	Missense_Mutation	SNP	C	C	T	rs61730311	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:29049138C>T	ENST00000257189.4	+	12	1806	c.1723C>T	c.(1723-1725)Cgg>Tgg	p.R575W		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	575					apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			TCAGAACAATCGGTGTGAGAT	0.527													C|||	23	0.00459265	0.0	0.0029	5008	,	,		20150	0.0		0.0099	False		,,,				2504	0.0112				p.R575W		Atlas-SNP	.											.	DSG3	172	.	0			c.C1723T						PASS	.	C	TRP/ARG	14,4392	21.2+/-45.6	0,14,2189	151.0	136.0	141.0		1723	0.5	0.0	18	dbSNP_129	141	98,8502	54.0+/-114.7	1,96,4203	yes	missense	DSG3	NM_001944.2	101	1,110,6392	TT,TC,CC		1.1395,0.3177,0.8611	possibly-damaging	575/1000	29049138	112,12894	2203	4300	6503	SO:0001583	missense	1830	exon12			AACAATCGGTGTG	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.1723C>T	18.37:g.29049138C>T	ENSP00000257189:p.Arg575Trp	80.0	0.0	0		89.0	41.0	0.460674	NM_001944	A8K2V2	Missense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	10	0.004578754578754579	0	0.0	2	0.0055248618784530384	0	0.0	8	0.010554089709762533	C	14.16	2.451113	0.43531	0.003177	0.011395	ENSG00000134757	ENST00000257189	T	0.59502	0.26	5.95	0.463	0.16700	.	1.487420	0.04727	N	0.420484	T	0.34019	0.0883	N	0.22421	0.69	0.09310	N	1	P	0.52316	0.952	B	0.40741	0.339	T	0.35822	-0.9773	10	0.66056	D	0.02	.	5.6006	0.17351	0.5361:0.3006:0.0:0.1633	rs61730311	575	P32926	DSG3_HUMAN	W	575	ENSP00000257189:R575W	ENSP00000257189:R575W	R	+	1	2	DSG3	27303136	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-0.080000	0.11339	0.118000	0.18165	-0.181000	0.13052	CGG	C|0.993;T|0.007	0.007	strong		0.527	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
HERC1	8925	hgsc.bcm.edu	37	15	63967170	63967170	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:63967170A>G	ENST00000443617.2	-	38	7304	c.7217T>C	c.(7216-7218)aTg>aCg	p.M2406T	RP11-317G6.1_ENST00000559303.2_RNA	NM_003922.3	NP_003913.3	Q15751	HERC1_HUMAN	HECT and RLD domain containing E3 ubiquitin protein ligase family member 1	2406					cerebellar Purkinje cell differentiation (GO:0021702)|negative regulation of autophagy (GO:0010507)|neuromuscular process controlling balance (GO:0050885)|neuron projection development (GO:0031175)|positive regulation of GTPase activity (GO:0043547)|transport (GO:0006810)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)			NS(3)|breast(9)|central_nervous_system(4)|endometrium(23)|haematopoietic_and_lymphoid_tissue(1)|kidney(12)|large_intestine(22)|liver(1)|lung(36)|ovary(7)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	132						CTGTTTGCCCATGTCTTCATG	0.502																																					p.M2406T		Atlas-SNP	.											.	HERC1	624	.	0			c.T7217C						PASS	.						152.0	144.0	146.0					15																	63967170		2042	4201	6243	SO:0001583	missense	8925	exon38			TTGCCCATGTCTT	U50078	CCDS45277.1	15q22	2013-01-10	2012-02-23			ENSG00000103657		"""WD repeat domain containing"""	4867	protein-coding gene	gene with protein product		605109	"""hect (homologous to the E6-AP (UBE3A) carboxyl terminus) domain and RCC1 (CHC1)-like domain (RLD) 1"""			8861955, 9233772	Standard	NM_003922		Approved	p532, p619	uc002amp.3	Q15751		ENST00000443617.2:c.7217T>C	15.37:g.63967170A>G	ENSP00000390158:p.Met2406Thr	275.0	0.0	0		243.0	106.0	0.436214	NM_003922	Q8IW65	Missense_Mutation	SNP	ENST00000443617.2	37	CCDS45277.1	.	.	.	.	.	.	.	.	.	.	A	7.518	0.656022	0.14580	.	.	ENSG00000103657	ENST00000443617	T	0.22743	1.94	5.51	4.39	0.52855	.	0.515835	0.20490	N	0.091313	T	0.09379	0.0231	N	0.08118	0	0.19575	N	0.999966	B	0.02656	0.0	B	0.01281	0.0	T	0.35699	-0.9778	10	0.13470	T	0.59	.	7.9035	0.29748	0.7169:0.0:0.2831:0.0	.	2406	Q15751	HERC1_HUMAN	T	2406	ENSP00000390158:M2406T	ENSP00000390158:M2406T	M	-	2	0	HERC1	61754223	0.091000	0.21658	1.000000	0.80357	0.964000	0.63967	0.681000	0.25320	0.931000	0.37242	0.528000	0.53228	ATG	.	.	none		0.502	HERC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418523.1	NM_003922	
STK11	6794	hgsc.bcm.edu	37	19	1207176	1207176	+	Silent	SNP	C	C	A	rs56354945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1207176C>A	ENST00000326873.7	+	1	1437	c.264C>A	c.(262-264)atC>atA	p.I88I	STK11_ENST00000585748.1_Intron	NM_000455.4	NP_000446.1	Q15831	STK11_HUMAN	serine/threonine kinase 11	88	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Sufficient for interaction with SIRT1.				activation of protein kinase activity (GO:0032147)|anoikis (GO:0043276)|autophagy (GO:0006914)|axonogenesis (GO:0007409)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|energy reserve metabolic process (GO:0006112)|establishment of cell polarity (GO:0030010)|glucose homeostasis (GO:0042593)|Golgi localization (GO:0051645)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epithelial cell proliferation involved in prostate gland development (GO:0060770)|positive regulation of axonogenesis (GO:0050772)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive thymic T cell selection (GO:0045059)|protein autophosphorylation (GO:0046777)|protein heterooligomerization (GO:0051291)|protein phosphorylation (GO:0006468)|regulation of cell growth (GO:0001558)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of protein kinase B signaling (GO:0051896)|regulation of Wnt signaling pathway (GO:0030111)|response to glucagon (GO:0033762)|response to ionizing radiation (GO:0010212)|response to lipid (GO:0033993)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)|T cell receptor signaling pathway (GO:0050852)|TCR signalosome assembly (GO:0036399)|tissue homeostasis (GO:0001894)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|TCR signalosome (GO:0036398)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|p53 binding (GO:0002039)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.0?(20)|p.?(3)		biliary_tract(1)|breast(3)|cervix(35)|gastrointestinal_tract_(site_indeterminate)(5)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|liver(1)|lung(219)|oesophagus(1)|ovary(4)|pancreas(6)|prostate(2)|skin(15)|small_intestine(1)|stomach(9)|testis(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	328		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Renal(1328;0.0183)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|Lung(535;0.00942)|STAD - Stomach adenocarcinoma(1328;0.18)		TGCGAAGGATCCCCAACGGGG	0.597		14	"""D, Mis, N, F, S"""		"""NSCLC, pancreatic"""	"""jejunal harmartoma, ovarian, testicular, pancreatic"""			Peutz-Jeghers syndrome	TSP Lung(3;<1E-08)			C|||	119	0.023762	0.0832	0.0086	5008	,	,		18552	0.0		0.003	False		,,,				2504	0.0				p.I88I		Atlas-SNP	.	yes	Rec	yes	Peutz-Jeghers syndrome	19	19p13.3	6794	serine/threonine kinase 11 gene (LKB1)		"""E, M, O"""	STK11,brain,glioma,0,2	STK11	410	2	23	Whole gene deletion(20)|Unknown(2)|Deletion - Frameshift(1)	cervix(15)|lung(3)|skin(1)|oesophagus(1)|ovary(1)|kidney(1)|pancreas(1)	c.C264A						PASS	.	C		255,3773		6,243,1765	29.0	32.0	31.0		264	3.9	1.0	19	dbSNP_129	31	2,8300		0,2,4149	no	coding-synonymous	STK11	NM_000455.4		6,245,5914	AA,AC,CC		0.0241,6.3307,2.0843		88/434	1207176	257,12073	2014	4151	6165	SO:0001819	synonymous_variant	6794	exon1	Familial Cancer Database	PJS, Hamartous Intestinal Polyposis	AAGGATCCCCAAC	U63333	CCDS45896.1	19p13.3	2014-09-17	2005-12-13			ENSG00000118046			11389	protein-coding gene	gene with protein product	"""polarization-related protein LKB1"""	602216	"""serine/threonine kinase 11 (Peutz-Jeghers syndrome)"""			9425897	Standard	XM_005259617		Approved	PJS, LKB1	uc002lrl.1	Q15831		ENST00000326873.7:c.264C>A	19.37:g.1207176C>A		132.0	0.0	0		133.0	69.0	0.518797	NM_000455	B2RBX7|E7EW76	Silent	SNP	ENST00000326873.7	37	CCDS45896.1																																																																																			C|0.980;A|0.020	0.020	strong		0.597	STK11-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449839.3	NM_000455	
CUBN	8029	hgsc.bcm.edu	37	10	16877110	16877110	+	Missense_Mutation	SNP	G	G	A	rs1801230	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:16877110G>A	ENST00000377833.4	-	64	10330	c.10265C>T	c.(10264-10266)aCc>aTc	p.T3422I		NM_001081.3	NP_001072.2	O60494	CUBN_HUMAN	cubilin (intrinsic factor-cobalamin receptor)	3422	CUB 26. {ECO:0000255|PROSITE- ProRule:PRU00059}.		T -> I (in dbSNP:rs1801230). {ECO:0000269|PubMed:10080186}.		cholesterol metabolic process (GO:0008203)|cobalamin metabolic process (GO:0009235)|cobalamin transport (GO:0015889)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|receptor-mediated endocytosis (GO:0006898)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|tissue homeostasis (GO:0001894)|vitamin D metabolic process (GO:0042359)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|cytosol (GO:0005829)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|Golgi apparatus (GO:0005794)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|cobalamin binding (GO:0031419)|protein homodimerization activity (GO:0042803)|receptor activity (GO:0004872)|transporter activity (GO:0005215)			breast(8)|central_nervous_system(4)|cervix(1)|endometrium(18)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(42)|liver(1)|lung(107)|ovary(9)|pancreas(2)|prostate(3)|skin(9)|stomach(3)|upper_aerodigestive_tract(11)|urinary_tract(8)	241					Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	GAGAGTAACGGTGCAATCCTT	0.458													G|||	41	0.0081869	0.0038	0.0144	5008	,	,		17717	0.0		0.0229	False		,,,				2504	0.0031				p.T3422I		Atlas-SNP	.											.	CUBN	515	.	0			c.C10265T						PASS	.	G	ILE/THR	29,4377	35.2+/-66.4	0,29,2174	178.0	151.0	160.0		10265	3.9	0.7	10	dbSNP_89	160	248,8352	98.6+/-160.1	4,240,4056	yes	missense	CUBN	NM_001081.3	89	4,269,6230	AA,AG,GG		2.8837,0.6582,2.1298	benign	3422/3624	16877110	277,12729	2203	4300	6503	SO:0001583	missense	8029	exon64			GTAACGGTGCAAT	AF034611	CCDS7113.1	10p12	2014-09-17			ENSG00000107611	ENSG00000107611			2548	protein-coding gene	gene with protein product		602997		MGA1		9572993, 9478979	Standard	NM_001081		Approved	IFCR, gp280	uc001ioo.3	O60494	OTTHUMG00000017741	ENST00000377833.4:c.10265C>T	10.37:g.16877110G>A	ENSP00000367064:p.Thr3422Ile	112.0	0.0	0		138.0	55.0	0.398551	NM_001081	B0YIZ4|Q5VTA6|Q96RU9	Missense_Mutation	SNP	ENST00000377833.4	37	CCDS7113.1	30	0.013736263736263736	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	14.17	2.455908	0.43634	0.006582	0.028837	ENSG00000107611	ENST00000377833;ENST00000545090	T	0.35421	1.31	4.84	3.94	0.45596	CUB (5);	0.538075	0.15554	N	0.256250	T	0.13243	0.0321	L	0.33753	1.03	0.80722	D	1	P	0.40000	0.698	B	0.42798	0.398	T	0.01596	-1.1316	10	0.38643	T	0.18	.	13.2177	0.59869	0.0768:0.0:0.9232:0.0	rs1801230;rs52825510	3422	O60494	CUBN_HUMAN	I	3422;263	ENSP00000367064:T3422I	ENSP00000367064:T3422I	T	-	2	0	CUBN	16917116	0.983000	0.35010	0.712000	0.30502	0.003000	0.03518	1.834000	0.39171	1.262000	0.44165	-0.258000	0.10820	ACC	G|0.982;A|0.018	0.018	strong		0.458	CUBN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047009.1	NM_001081	
MUC4	4585	hgsc.bcm.edu	37	3	195512242	195512242	+	Missense_Mutation	SNP	G	G	A	rs566214772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195512242G>A	ENST00000463781.3	-	2	6668	c.6209C>T	c.(6208-6210)cCt>cTt	p.P2070L	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P2070L|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		TGCTGAGGAAGGGTTAGTGAC	0.562													.|||	31	0.0061901	0.0061	0.0058	5008	,	,		13554	0.003		0.0099	False		,,,				2504	0.0061				p.P2070L		Atlas-SNP	.											.	MUC4	1505	.	0			c.C6209T						PASS	.																																			SO:0001583	missense	4585	exon2			GAGGAAGGGTTAG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.6209C>T	3.37:g.195512242G>A	ENSP00000417498:p.Pro2070Leu	234.0	0.0	0		176.0	29.0	0.164773	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	G	2.744	-0.261597	0.05791	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28069	1.63;1.67	.	.	.	.	.	.	.	.	T	0.11495	0.0280	N	0.08118	0	0.09310	N	1	B	0.15141	0.012	B	0.04013	0.001	T	0.28964	-1.0027	6	.	.	.	.	.	.	.	.	2070	E7ESK3	.	L	2070	ENSP00000417498:P2070L;ENSP00000420243:P2070L	.	P	-	2	0	MUC4	196996637	0.004000	0.15560	0.004000	0.12327	0.011000	0.07611	-0.008000	0.12788	-0.833000	0.04245	0.064000	0.15345	CCT	G|0.500;A|0.500	0.500	weak		0.562	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ABCG8	64241	hgsc.bcm.edu	37	2	44078913	44078913	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:44078913C>A	ENST00000272286.2	+	4	603	c.513C>A	c.(511-513)gcC>gcA	p.A171A		NM_022437.2	NP_071882.1	Q9H221	ABCG8_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 8	171	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|excretion (GO:0007588)|intestinal cholesterol absorption (GO:0030299)|negative regulation of intestinal cholesterol absorption (GO:0045796)|negative regulation of intestinal phytosterol absorption (GO:0010949)|phospholipid transport (GO:0015914)|response to drug (GO:0042493)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)|sterol transport (GO:0015918)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|protein heterodimerization activity (GO:0046982)|sterol transporter activity (GO:0015248)			NS(1)|breast(2)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(21)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	45		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)			Ezetimibe(DB00973)	CCTTCATTGCCCAGATGCGGC	0.612																																					p.A171A		Atlas-SNP	.											.	ABCG8	98	.	0			c.C513A						PASS	.						113.0	116.0	115.0					2																	44078913		2203	4300	6503	SO:0001819	synonymous_variant	64241	exon4			CATTGCCCAGATG	AF320294	CCDS1815.1	2p21	2012-03-14	2008-07-31		ENSG00000143921	ENSG00000143921		"""ATP binding cassette transporters / subfamily G"""	13887	protein-coding gene	gene with protein product	"""gallbladder disease 4"", ""sterolin 2"""	605460	"""ATP-binding cassette, sub-family G (WHITE), member 8 (sterolin 2)"""			11099417, 17626266	Standard	NM_022437		Approved	GBD4	uc002rtq.3	Q9H221	OTTHUMG00000128756	ENST00000272286.2:c.513C>A	2.37:g.44078913C>A		104.0	0.0	0		105.0	38.0	0.361905	NM_022437	Q53QN8	Silent	SNP	ENST00000272286.2	37	CCDS1815.1																																																																																			.	.	none		0.612	ABCG8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250671.1	NM_022437	
NOP58	51602	hgsc.bcm.edu	37	2	203157538	203157538	+	Silent	SNP	A	A	G	rs16839032	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:203157538A>G	ENST00000264279.5	+	9	1045	c.819A>G	c.(817-819)gaA>gaG	p.E273E	SNORD11_ENST00000459124.1_RNA|SNORD11B_ENST00000607707.1_RNA	NM_015934.3	NP_057018.1	Q9Y2X3	NOP58_HUMAN	NOP58 ribonucleoprotein	273					cell growth (GO:0016049)|rRNA processing (GO:0006364)|snRNP protein import into nucleus (GO:0006608)	box C/D snoRNP complex (GO:0031428)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|snoRNA binding (GO:0030515)	p.E273E(1)		breast(2)|cervix(1)|endometrium(3)|large_intestine(4)|lung(4)|prostate(2)	16						AGCTCTATGAATATCTACAAA	0.368													A|||	31	0.0061901	0.0	0.0187	5008	,	,		18977	0.0		0.0159	False		,,,				2504	0.002				p.E273E		Atlas-SNP	.											NOP58,NS,carcinoma,0,1	NOP58	41	1	1	Substitution - coding silent(1)	prostate(1)	c.A819G						PASS	.	A		12,4394	19.1+/-41.9	0,12,2191	159.0	160.0	160.0		819	0.3	1.0	2	dbSNP_123	160	133,8467	67.0+/-129.4	3,127,4170	no	coding-synonymous	NOP58	NM_015934.3		3,139,6361	GG,GA,AA		1.5465,0.2724,1.1149		273/530	203157538	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	51602	exon9			CTATGAATATCTA		CCDS2353.1	2q33.1	2012-12-10	2012-12-10		ENSG00000055044	ENSG00000055044			29926	protein-coding gene	gene with protein product			"""NOP58 ribonucleoprotein homolog (yeast)"""			10606270, 10925205	Standard	NM_015934		Approved	NOP5, HSPC120	uc002uzb.3	Q9Y2X3	OTTHUMG00000132840	ENST00000264279.5:c.819A>G	2.37:g.203157538A>G		117.0	0.0	0		119.0	62.0	0.521008	NM_015934	Q53SA4|Q6PK08|Q9P036|Q9UFN3	Silent	SNP	ENST00000264279.5	37	CCDS2353.1																																																																																			A|0.989;G|0.011	0.011	strong		0.368	NOP58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256313.2	NM_015934	
N4BP1	9683	hgsc.bcm.edu	37	16	48595110	48595110	+	Missense_Mutation	SNP	T	T	C	rs371090316		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:48595110T>C	ENST00000262384.3	-	2	1680	c.1444A>G	c.(1444-1446)Att>Gtt	p.I482V	RP11-44I10.3_ENST00000563994.1_RNA	NM_153029.3	NP_694574.3	O75113	N4BP1_HUMAN	NEDD4 binding protein 1	482					cellular response to UV (GO:0034644)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|negative regulation of protein ubiquitination (GO:0031397)	nucleolus (GO:0005730)|PML body (GO:0016605)				breast(3)|kidney(2)|lung(11)|urinary_tract(1)	17		all_cancers(37;0.179)|all_lung(18;0.11)				GTGTTACAAATGTAGTTCTGG	0.413																																					p.I482V		Atlas-SNP	.											.	N4BP1	121	.	0			c.A1444G						PASS	.	T	VAL/ILE	1,3799		0,1,1899	139.0	141.0	141.0		1444	-12.2	0.0	16		141	0,8216		0,0,4108	no	missense	N4BP1	NM_153029.3	29	0,1,6007	CC,CT,TT		0.0,0.0263,0.0083	benign	482/897	48595110	1,12015	1900	4108	6008	SO:0001583	missense	9683	exon2			TACAAATGTAGTT	AK026937	CCDS45479.1	16q12.1	2008-01-18				ENSG00000102921			29850	protein-coding gene	gene with protein product						9734811, 11717310	Standard	NM_153029		Approved		uc002efp.3	O75113		ENST00000262384.3:c.1444A>G	16.37:g.48595110T>C	ENSP00000262384:p.Ile482Val	145.0	0.0	0		118.0	64.0	0.542373	NM_153029	A7MD49|Q2YDX1	Missense_Mutation	SNP	ENST00000262384.3	37	CCDS45479.1	.	.	.	.	.	.	.	.	.	.	T	0.004	-2.369847	0.00209	2.63E-4	0.0	ENSG00000102921	ENST00000262384	T	0.39787	1.06	6.08	-12.2	0.00006	.	2.515080	0.01180	N	0.007078	T	0.17492	0.0420	N	0.04508	-0.205	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.10823	-1.0613	10	0.25751	T	0.34	5.5903	9.9679	0.41736	0.061:0.0984:0.1832:0.6574	.	482	O75113	N4BP1_HUMAN	V	482	ENSP00000262384:I482V	ENSP00000262384:I482V	I	-	1	0	N4BP1	47152611	0.000000	0.05858	0.000000	0.03702	0.016000	0.09150	-1.256000	0.02869	-3.027000	0.00267	-1.021000	0.02439	ATT	.	.	weak		0.413	N4BP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429920.1	NM_014664	
FMR1	2332	hgsc.bcm.edu	37	X	146993715	146993715	+	Silent	SNP	G	G	T	rs111485627	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:146993715G>T	ENST00000370475.4	+	1	146	c.18G>T	c.(16-18)gtG>gtT	p.V6V	FMR1-AS1_ENST00000598667.1_RNA|FMR1-AS1_ENST00000596112.1_RNA|FMR1_ENST00000370471.3_Silent_p.V6V|FMR1_ENST00000439526.2_Silent_p.V6V|FMR1_ENST00000370477.1_Silent_p.V6V|FMR1_ENST00000370470.1_Silent_p.V6V|FMR1-AS1_ENST00000594922.1_RNA|FMR1_ENST00000218200.8_Silent_p.V6V|FMR1_ENST00000334557.6_Silent_p.V6V	NM_002024.5	NP_002015.1	Q06787	FMR1_HUMAN	fragile X mental retardation 1	6	Agenet-like 1.				central nervous system development (GO:0007417)|mRNA transport (GO:0051028)|negative regulation of translational initiation (GO:0045947)	cytoplasm (GO:0005737)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytoplasmic stress granule (GO:0010494)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|membrane (GO:0016020)|mRNA cap binding complex (GO:0005845)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|synapse (GO:0045202)	mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)			NS(1)|breast(1)|endometrium(7)|kidney(1)|large_intestine(8)|lung(13)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)	35	Acute lymphoblastic leukemia(192;6.56e-05)					AGCTGGTGGTGGAAGTGCGGG	0.677									Fragile X syndrome				G|||	15	0.00397351	0.0	0.0029	3775	,	,		5155	0.0		0.0129	False		,,,				2504	0.0				p.V6V		Atlas-SNP	.											.	FMR1	93	.	0			c.G18T						PASS	.	G	,,,,	6,3525		0,6,0,1538,443	76.0	50.0	59.0		18,18,18,18,18	4.0	1.0	X	dbSNP_132	59	79,6026		0,62,17,2208,1548	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	FMR1	NM_001185075.1,NM_001185076.1,NM_001185081.1,NM_001185082.1,NM_002024.5	,,,,	0,68,17,3746,1991	TT,TG,T,GG,G		1.294,0.1699,0.8821	,,,,	6/538,6/612,6/517,6/587,6/633	146993715	85,9551	1987	3835	5822	SO:0001819	synonymous_variant	2332	exon1	Familial Cancer Database	Martin-Bell syndrome, FRAXA syndrome	GGTGGTGGAAGTG	X69962	CCDS14682.1, CCDS55518.1, CCDS55519.1, CCDS76039.1	Xq27.3	2014-09-17			ENSG00000102081	ENSG00000102081			3775	protein-coding gene	gene with protein product		309550	"""premature ovarian failure 1"""	POF1, POF		1572655	Standard	NM_002024		Approved	FMRP, FRAXA, MGC87458	uc010nst.3	Q06787	OTTHUMG00000022606	ENST00000370475.4:c.18G>T	X.37:g.146993715G>T		94.0	0.0	0		114.0	113.0	0.991228	NM_002024	A6NNH4|D3DWT0|D3DWT1|D3DWT2|G8JL90|Q16578|Q5PQZ6|Q99054	Silent	SNP	ENST00000370475.4	37	CCDS14682.1																																																																																			C|0.000;G|0.987;T|0.013	0.013	strong		0.677	FMR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058655.1	NM_002024	
TMEM79	84283	hgsc.bcm.edu	37	1	156255560	156255560	+	Silent	SNP	G	G	A	rs140033065	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:156255560G>A	ENST00000405535.2	+	2	714	c.543G>A	c.(541-543)ccG>ccA	p.P181P	SMG5_ENST00000361813.5_5'Flank|TMEM79_ENST00000295694.5_Silent_p.P181P|TMEM79_ENST00000495881.1_3'UTR|TMEM79_ENST00000357501.2_Intron|SMG5_ENST00000368267.5_5'Flank	NM_032323.2	NP_115699.1	Q9BSE2	TMM79_HUMAN	transmembrane protein 79	181					cornification (GO:0070268)|cuticle development (GO:0042335)|epithelial cell maturation (GO:0002070)|establishment of skin barrier (GO:0061436)|hair follicle morphogenesis (GO:0031069)|positive regulation of epidermis development (GO:0045684)|regulated secretory pathway (GO:0045055)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|trans-Golgi network membrane (GO:0032588)				breast(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|urinary_tract(1)	21	Hepatocellular(266;0.158)					TGGTGAGGCCGCCTGGCTGTT	0.682													G|||	5	0.000998403	0.0	0.0	5008	,	,		12551	0.0		0.004	False		,,,				2504	0.001				p.P181P		Atlas-SNP	.											.	TMEM79	43	.	0			c.G543A						PASS	.	G		5,4395		0,5,2195	39.0	45.0	43.0		543	-11.3	0.0	1	dbSNP_134	43	29,8569		1,27,4271	no	coding-synonymous	TMEM79	NM_032323.2		1,32,6466	AA,AG,GG		0.3373,0.1136,0.2616		181/395	156255560	34,12964	2200	4299	6499	SO:0001819	synonymous_variant	84283	exon2			GAGGCCGCCTGGC	BC005094	CCDS1138.1	1q22	2014-04-22			ENSG00000163472	ENSG00000163472			28196	protein-coding gene	gene with protein product	"""mattrin"""	615531					Standard	NM_032323		Approved	MGC13102, FLJ16057, FLJ32254, MATT	uc009wrw.3	Q9BSE2	OTTHUMG00000019788	ENST00000405535.2:c.543G>A	1.37:g.156255560G>A		81.0	0.0	0		70.0	39.0	0.557143	NM_032323	B2RE22|D3DVB8	Silent	SNP	ENST00000405535.2	37	CCDS1138.1																																																																																			G|0.997;A|0.003	0.003	strong		0.682	TMEM79-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052101.1	NM_032323	
EGFLAM	133584	hgsc.bcm.edu	37	5	38409147	38409147	+	Silent	SNP	C	C	T	rs16903964	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:38409147C>T	ENST00000354891.3	+	10	1636	c.1290C>T	c.(1288-1290)aaC>aaT	p.N430N	EGFLAM_ENST00000397202.2_Intron|EGFLAM_ENST00000322350.5_Silent_p.N430N|EGFLAM_ENST00000336740.6_Silent_p.N196N	NM_001205301.1	NP_001192230.1	Q63HQ2	EGFLA_HUMAN	EGF-like, fibronectin type III and laminin G domains	430	Laminin G-like 1. {ECO:0000255|PROSITE- ProRule:PRU00122}.				extracellular matrix organization (GO:0030198)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|positive regulation of cell-substrate adhesion (GO:0010811)	basement membrane (GO:0005604)|cell junction (GO:0030054)|interstitial matrix (GO:0005614)|synapse (GO:0045202)	glycosaminoglycan binding (GO:0005539)			NS(1)|breast(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(43)|ovary(1)|pancreas(3)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	85	all_lung(31;0.000385)					GTGGGGAGAACGAACACGGGA	0.502													C|||	235	0.0469249	0.1717	0.0101	5008	,	,		15939	0.001		0.0	False		,,,				2504	0.0				p.N430N	Colon(62;485 1295 3347 17454)	Atlas-SNP	.											.	EGFLAM	302	.	0			c.C1290T						PASS	.	C	,,	599,3807		33,533,1637	83.0	80.0	81.0		1290,1290,588	-9.4	0.0	5	dbSNP_123	81	12,8588		0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous	EGFLAM	NM_001205301.1,NM_152403.3,NM_182798.2	,,	33,545,5925	TT,TC,CC		0.1395,13.5951,4.6978	,,	430/1018,430/1010,196/776	38409147	611,12395	2203	4300	6503	SO:0001819	synonymous_variant	133584	exon10			GGAGAACGAACAC	AK097549	CCDS3924.1, CCDS3925.1, CCDS47199.1, CCDS56363.1	5p13.2-p13.1	2014-04-03			ENSG00000164318	ENSG00000164318		"""Fibronectin type III domain containing"""	26810	protein-coding gene	gene with protein product	"""pikachurin"", ""agrin-like"""					18641643, 20078962, 22760553	Standard	NM_182801		Approved	FLJ39155, AGRINL, AGRNL, PIKA	uc003jlc.2	Q63HQ2	OTTHUMG00000131139	ENST00000354891.3:c.1290C>T	5.37:g.38409147C>T		105.0	0.0	0		105.0	53.0	0.504762	NM_001205301	A8K6D7|Q5U643|Q6P3V1|Q8N124|Q8N197|Q8N7Y0|Q8N8N5|Q8NAL2	Silent	SNP	ENST00000354891.3	37	CCDS56363.1																																																																																			C|0.949;T|0.051	0.051	strong		0.502	EGFLAM-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367323.1	NM_152403	
OAS3	4940	hgsc.bcm.edu	37	12	113400593	113400593	+	Missense_Mutation	SNP	C	C	T	rs200778728		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:113400593C>T	ENST00000228928.7	+	9	2149	c.1970C>T	c.(1969-1971)aCg>aTg	p.T657M	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	657	OAS domain 2.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						GGCTTCCGGACGGTGCTGGGG	0.597																																					p.T657M		Atlas-SNP	.											OAS3,NS,carcinoma,-1,1	OAS3	63	1	0			c.C1970T						PASS	.	C	MET/THR	1,4099		0,1,2049	119.0	128.0	125.0		1970	3.2	0.0	12		125	2,8408		0,2,4203	yes	missense	OAS3	NM_006187.2	81	0,3,6252	TT,TC,CC		0.0238,0.0244,0.024	probably-damaging	657/1088	113400593	3,12507	2050	4205	6255	SO:0001583	missense	4940	exon9			TCCGGACGGTGCT	AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.1970C>T	12.37:g.113400593C>T	ENSP00000228928:p.Thr657Met	111.0	0.0	0		119.0	57.0	0.478992	NM_006187	Q2HJ14|Q9H3P5	Missense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	C	14.24	2.476130	0.44044	2.44E-4	2.38E-4	ENSG00000111331	ENST00000228928;ENST00000323881	T	0.59224	0.28	4.1	3.19	0.36642	-oligoadenylate synthetase 1, domain 2/C-terminal (2);-5&apos (2);2&apos (2);	.	.	.	.	T	0.76271	0.3964	M	0.87900	2.915	0.18873	N	0.999981	D	0.89917	1.0	D	0.77557	0.99	T	0.64415	-0.6413	9	0.87932	D	0	.	8.9438	0.35747	0.2222:0.7778:0.0:0.0	.	657	Q9Y6K5	OAS3_HUMAN	M	657;656	ENSP00000228928:T657M	ENSP00000228928:T657M	T	+	2	0	OAS3	111884976	0.568000	0.26635	0.002000	0.10522	0.012000	0.07955	2.416000	0.44644	0.917000	0.36895	0.655000	0.94253	ACG	.	.	weak		0.597	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1		
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296521	39296521	+	Silent	SNP	G	G	A	rs201084737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39296521G>A	ENST00000345847.4	-	1	218	c.219C>T	c.(217-219)acC>acT	p.T73T		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	73	30 X 5 AA repeats of C-C-[IRQVEL]-[SPTR]- [STVQRCP].					keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						TCCTGCAGCAGGTGGTCTgac	0.657																																					p.T73T		Atlas-SNP	.											.	KRTAP4-6	46	.	0			c.C219T						PASS	.																																			SO:0001819	synonymous_variant	81871	exon1			GCAGCAGGTGGTC	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.219C>T	17.37:g.39296521G>A		58.0	0.0	0		54.0	24.0	0.444444	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			G|0.996;A|0.004	0.004	strong		0.657	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
RAB3D	9545	hgsc.bcm.edu	37	19	11436221	11436221	+	Silent	SNP	A	A	G	rs12981706	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11436221A>G	ENST00000222120.3	-	5	773	c.513T>C	c.(511-513)aaT>aaC	p.N171N	CTC-510F12.4_ENST00000586356.1_RNA|TSPAN16_ENST00000316737.1_Intron|RAB3D_ENST00000589655.1_Silent_p.N171N|CTC-510F12.6_ENST00000586051.1_RNA	NM_004283.3	NP_004274.1	O95716	RAB3D_HUMAN	RAB3D, member RAS oncogene family	171					exocytosis (GO:0006887)|GTP catabolic process (GO:0006184)|peptidyl-cysteine methylation (GO:0018125)|protein transport (GO:0015031)|regulation of exocytosis (GO:0017157)|small GTPase mediated signal transduction (GO:0007264)	extracellular vesicular exosome (GO:0070062)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|transport vesicle (GO:0030133)|zymogen granule (GO:0042588)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|myosin V binding (GO:0031489)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(3)|liver(1)|lung(3)|ovary(2)	14						CCTGCTTCACATTGATGTTCT	0.557													A|||	286	0.0571086	0.1762	0.0187	5008	,	,		14659	0.0		0.0318	False		,,,				2504	0.0082				p.N171N		Atlas-SNP	.											.	RAB3D	24	.	0			c.T513C						PASS	.	A	,	617,3789	268.6+/-268.5	43,531,1629	146.0	132.0	136.0		513,	-6.2	1.0	19	dbSNP_121	136	293,8307	108.0+/-168.7	3,287,4010	no	coding-synonymous,intron	RAB3D,TSPAN16	NM_004283.3,NM_012466.2	,	46,818,5639	GG,GA,AA		3.407,14.0036,6.9968	,	171/220,	11436221	910,12096	2203	4300	6503	SO:0001819	synonymous_variant	9545	exon5			CTTCACATTGATG	AF081353	CCDS12257.1	19p13.2	2012-10-02			ENSG00000105514	ENSG00000105514		"""RAB, member RAS oncogene"""	9779	protein-coding gene	gene with protein product	"""Rab3D upregulated with myeloid differentiation"", ""glioblastoma overexpressed"""	604350		GOV		10023084, 10072586	Standard	NM_004283		Approved	RAB16, D2-2, RAD3D	uc002mqx.3	O95716	OTTHUMG00000180835	ENST00000222120.3:c.513T>C	19.37:g.11436221A>G		32.0	0.0	0		35.0	16.0	0.457143	NM_004283		Silent	SNP	ENST00000222120.3	37	CCDS12257.1																																																																																			A|0.939;G|0.061;T|0.000	0.061	strong		0.557	RAB3D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453211.1	NM_004283	
SLX4	84464	hgsc.bcm.edu	37	16	3656645	3656645	+	Missense_Mutation	SNP	A	A	G	rs147826749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3656645A>G	ENST00000294008.3	-	3	1230	c.590T>C	c.(589-591)gTg>gCg	p.V197A		NM_032444.2	NP_115820.2	Q8IY92	SLX4_HUMAN	SLX4 structure-specific endonuclease subunit	197	Interaction with SLX4IP, ERCC4 and MSH2.		V -> A (in dbSNP:rs147826749). {ECO:0000269|PubMed:22911665}.		DNA catabolic process, endonucleolytic (GO:0000737)|DNA double-strand break processing involved in repair via single-strand annealing (GO:0010792)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|double-strand break repair via homologous recombination (GO:0000724)|nucleotide-excision repair (GO:0006289)|positive regulation of catalytic activity (GO:0043085)|response to intra-S DNA damage checkpoint signaling (GO:0072429)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|Slx1-Slx4 complex (GO:0033557)	5'-flap endonuclease activity (GO:0017108)|enzyme activator activity (GO:0008047)			breast(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(20)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	76						GGGACTTGGCACTGCTGTTGT	0.527								Direct reversal of damage					A|||	2	0.000399361	0.0	0.0029	5008	,	,		19478	0.0		0.0	False		,,,				2504	0.0				p.V197A		Atlas-SNP	.											.	SLX4	173	.	0			c.T590C						PASS	.	A	ALA/VAL	1,4393	2.1+/-5.4	0,1,2196	167.0	166.0	167.0		590	-3.5	0.0	16	dbSNP_134	167	26,8574	18.5+/-59.3	0,26,4274	yes	missense	SLX4	NM_032444.2	64	0,27,6470	GG,GA,AA		0.3023,0.0228,0.2078	benign	197/1835	3656645	27,12967	2197	4300	6497	SO:0001583	missense	84464	exon3			CTTGGCACTGCTG	AB058687	CCDS10506.2	16p13.3	2014-09-17	2013-06-05	2010-09-13	ENSG00000188827	ENSG00000188827		"""Fanconi anemia, complementation groups"", ""BTB/POZ domain containing"""	23845	protein-coding gene	gene with protein product	"""Fanconi anemia, complementation group P"""	613278	"""BTB (POZ) domain containing 12"", ""SLX4 structure-specific endonuclease subunit homolog (S. cerevisiae)"""	BTBD12		11347906, 19595721	Standard	NM_032444		Approved	KIAA1784, KIAA1987, FANCP	uc002cvp.2	Q8IY92	OTTHUMG00000074089	ENST00000294008.3:c.590T>C	16.37:g.3656645A>G	ENSP00000294008:p.Val197Ala	197.0	0.0	0		186.0	90.0	0.483871	NM_032444	Q69YT8|Q8TF15|Q96JP1	Missense_Mutation	SNP	ENST00000294008.3	37	CCDS10506.2	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	A	10.77	1.443209	0.25987	2.28E-4	0.003023	ENSG00000188827	ENST00000294008	T	0.01369	4.97	5.03	-3.52	0.04682	.	2.372270	0.01586	N	0.021329	T	0.00815	0.0027	N	0.17474	0.49	0.09310	N	1	B	0.11235	0.004	B	0.08055	0.003	T	0.48068	-0.9067	10	0.18276	T	0.48	.	6.9022	0.24288	0.4116:0.1398:0.4486:0.0	.	197	Q8IY92	SLX4_HUMAN	A	197	ENSP00000294008:V197A	ENSP00000294008:V197A	V	-	2	0	SLX4	3596646	0.000000	0.05858	0.002000	0.10522	0.452000	0.32318	-0.831000	0.04405	-0.925000	0.03775	-0.441000	0.05720	GTG	A|0.997;G|0.003	0.003	strong		0.527	SLX4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157301.3	NM_032444	
ZNF333	84449	hgsc.bcm.edu	37	19	14829345	14829345	+	Silent	SNP	C	C	T	rs147332855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14829345C>T	ENST00000292530.6	+	12	1297	c.1206C>T	c.(1204-1206)gcC>gcT	p.A402A	ZNF333_ENST00000536363.1_Silent_p.A293A|ZNF333_ENST00000540689.2_Intron	NM_032433.2	NP_115809.1	Q96JL9	ZN333_HUMAN	zinc finger protein 333	402					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|pancreas(1)|prostate(1)	21						GTGGGCAAGCCTTCAAATATT	0.443													C|||	5	0.000998403	0.0	0.0043	5008	,	,		20841	0.0		0.001	False		,,,				2504	0.001				p.A402A	NSCLC(60;75 1281 16985 25154 29885)	Atlas-SNP	.											.	ZNF333	76	.	0			c.C1206T						PASS	.	C		0,4406		0,0,2203	58.0	56.0	57.0		1206	1.1	0.9	19	dbSNP_134	57	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous	ZNF333	NM_032433.2		0,13,6490	TT,TC,CC		0.1512,0.0,0.1		402/666	14829345	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	84449	exon12			GCAAGCCTTCAAA		CCDS12316.1, CCDS74298.1	19p13	2013-01-08				ENSG00000160961		"""Zinc fingers, C2H2-type"", ""-"""	15624	protein-coding gene	gene with protein product		611811				12151103	Standard	XM_005260098		Approved	KIAA1806	uc002mzn.3	Q96JL9		ENST00000292530.6:c.1206C>T	19.37:g.14829345C>T		78.0	0.0	0		81.0	43.0	0.530864	NM_032433	Q6P2E6|Q86WS6|Q8TDL0	Silent	SNP	ENST00000292530.6	37	CCDS12316.1																																																																																			C|0.999;T|0.001	0.001	strong		0.443	ZNF333-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466496.1	NM_032433	
HYI	81888	hgsc.bcm.edu	37	1	43917888	43917888	+	Silent	SNP	C	C	G	rs41270373	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43917888C>G	ENST00000372425.4	-	3	609	c.414G>C	c.(412-414)ggG>ggC	p.G138G	HYI_ENST00000372426.1_Silent_p.G90G|HYI_ENST00000583037.1_Silent_p.G65G|HYI_ENST00000486909.1_Silent_p.G138G|HYI-AS1_ENST00000444386.1_RNA|SZT2_ENST00000372442.1_3'UTR|SZT2_ENST00000562955.1_3'UTR|HYI_ENST00000372432.1_Silent_p.G138G|HYI_ENST00000372434.1_Silent_p.G163G			Q5T013	HYI_HUMAN	hydroxypyruvate isomerase (putative)	138							hydroxypyruvate isomerase activity (GO:0008903)			large_intestine(1)|lung(2)|ovary(1)|urinary_tract(2)	6	all_hematologic(146;0.0958)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)				GAGCCAAAACCCCAGCTGCAT	0.572													C|||	49	0.00978435	0.0	0.0231	5008	,	,		22722	0.0		0.0308	False		,,,				2504	0.002				p.G163G		Atlas-SNP	.											.	HYI	23	.	0			c.G489C						PASS	.	C	,,	26,4380	31.7+/-61.6	1,24,2178	174.0	153.0	160.0		414,,414	-1.0	1.0	1	dbSNP_127	160	243,8357	95.0+/-156.8	3,237,4060	no	coding-synonymous,utr-3,coding-synonymous	SZT2,HYI	NM_001190880.2,NM_015284.3,NM_031207.5	,,	4,261,6238	GG,GC,CC		2.8256,0.5901,2.0683	,,	138/278,,138/248	43917888	269,12737	2203	4300	6503	SO:0001819	synonymous_variant	81888	exon4			CAAAACCCCAGCT		CCDS488.1, CCDS488.2, CCDS53309.1, CCDS72771.1	1p34.2	2010-06-24	2010-06-24		ENSG00000178922	ENSG00000178922	5.3.1.22		26948	protein-coding gene	gene with protein product			"""hydroxypyruvate isomerase homolog (E. coli)"""			10561547	Standard	NM_031207		Approved	HT036	uc001cjo.3	Q5T013	OTTHUMG00000007502	ENST00000372425.4:c.414G>C	1.37:g.43917888C>G		87.0	0.0	0		94.0	51.0	0.542553	NM_001243526	D3DPX4|D3DPX5|Q5Q9A2|Q7Z778|Q96S83|Q9BZR3|Q9BZR4	Silent	SNP	ENST00000372425.4	37	CCDS53309.1	33	0.01510989010989011	0	0.0	9	0.024861878453038673	0	0.0	24	0.0316622691292876	C	8.031	0.761814	0.15914	0.005901	0.028256	ENSG00000178922	ENST00000470662;ENST00000487366	T;T	0.40476	1.03;1.03	5.38	-1.03	0.10102	.	0.308735	0.38111	N	0.001809	T	0.11879	0.0289	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.02654	-1.1128	7	0.18710	T	0.47	.	6.2682	0.20939	0.1866:0.2033:0.5363:0.0739	rs41270373	.	.	.	A	57;62	ENSP00000428803:G57A;ENSP00000428501:G62A	ENSP00000428803:G57A	G	-	2	0	HYI	43690475	0.752000	0.28338	0.967000	0.41034	0.766000	0.43426	0.384000	0.20668	0.028000	0.15324	0.462000	0.41574	GGG	C|0.981;G|0.019	0.019	strong		0.572	HYI-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_031207	
CRNN	49860	hgsc.bcm.edu	37	1	152383373	152383373	+	Missense_Mutation	SNP	T	T	A	rs571572587	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:152383373T>A	ENST00000271835.3	-	3	247	c.185A>T	c.(184-186)gAt>gTt	p.D62V	RP1-91G5.3_ENST00000411804.1_RNA	NM_016190.2	NP_057274.1	Q9UBG3	CRNN_HUMAN	cornulin	62	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.				response to heat (GO:0009408)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	35	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.206)			GTGGTCTTCATCCAGCAGACG	0.537													T|||	4	0.000798722	0.0	0.0	5008	,	,		18928	0.0		0.0	False		,,,				2504	0.0041				p.D62V		Atlas-SNP	.											.	CRNN	78	.	0			c.A185T						PASS	.						45.0	47.0	47.0					1																	152383373		2196	4287	6483	SO:0001583	missense	49860	exon3			TCTTCATCCAGCA	AF077831	CCDS1010.1	1q21	2014-01-28	2005-06-13	2005-06-13	ENSG00000143536	ENSG00000143536		"""EF-hand domain containing"""	1230	protein-coding gene	gene with protein product		611312	"""chromosome 1 open reading frame 10"""	C1orf10		11056050, 15854041	Standard	NM_016190		Approved	SEP53	uc001ezx.2	Q9UBG3	OTTHUMG00000012383	ENST00000271835.3:c.185A>T	1.37:g.152383373T>A	ENSP00000271835:p.Asp62Val	60.0	0.0	0		88.0	44.0	0.5	NM_016190	B2RE60|Q8N613	Missense_Mutation	SNP	ENST00000271835.3	37	CCDS1010.1	.	.	.	.	.	.	.	.	.	.	T	17.17	3.321521	0.60634	.	.	ENSG00000143536	ENST00000271835;ENST00000451038	T	0.55234	0.53	4.73	4.73	0.59995	EF-hand-like domain (1);	0.000000	0.48286	D	0.000186	T	0.77458	0.4133	H	0.97940	4.11	0.58432	D	0.999995	D	0.89917	1.0	D	0.85130	0.997	D	0.84507	0.0620	10	0.87932	D	0	.	10.5413	0.45035	0.0:0.0:0.0:1.0	.	62	Q9UBG3	CRNN_HUMAN	V	62	ENSP00000271835:D62V	ENSP00000271835:D62V	D	-	2	0	CRNN	150649997	1.000000	0.71417	1.000000	0.80357	0.669000	0.39330	3.886000	0.56190	1.983000	0.57843	0.254000	0.18369	GAT	.	.	none		0.537	CRNN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034503.1	NM_016190	
BTN2A1	11120	hgsc.bcm.edu	37	6	26458872	26458872	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26458872C>T	ENST00000312541.5	+	2	256	c.8C>T	c.(7-9)tCa>tTa	p.S3L	BTN2A1_ENST00000541522.1_Intron|BTN2A1_ENST00000429381.1_Missense_Mutation_p.S3L|BTN2A1_ENST00000469185.1_Missense_Mutation_p.S3L	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	3					lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						CTCATGGAATCAGCTGCTGCC	0.622																																					p.S3L		Atlas-SNP	.											.	BTN2A1	118	.	0			c.C8T						PASS	.						232.0	171.0	191.0					6																	26458872		2203	4300	6503	SO:0001583	missense	11120	exon2			TGGAATCAGCTGC	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.8C>T	6.37:g.26458872C>T	ENSP00000312158:p.Ser3Leu	103.0	0.0	0		111.0	6.0	0.0540541	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	C	11.00	1.510906	0.27036	.	.	ENSG00000112763	ENST00000312541;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T	0.77098	-0.48;-1.07;-1.06	3.03	0.102	0.14522	.	0.876207	0.09516	N	0.791659	T	0.41581	0.1165	L	0.27053	0.805	0.09310	N	0.999998	B;B	0.12013	0.005;0.005	B;B	0.11329	0.004;0.006	T	0.31806	-0.9930	10	0.44086	T	0.13	.	5.0586	0.14546	0.0:0.4487:0.4235:0.1277	.	3;3	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	L	3	ENSP00000312158:S3L;ENSP00000416945:S3L;ENSP00000419043:S3L	ENSP00000265424:S3L	S	+	2	0	BTN2A1	26566851	0.020000	0.18652	0.003000	0.11579	0.023000	0.10783	0.059000	0.14322	-0.006000	0.14370	0.484000	0.47621	TCA	.	.	none		0.622	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
COL15A1	1306	hgsc.bcm.edu	37	9	101804366	101804366	+	Missense_Mutation	SNP	T	T	C	rs35901514	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:101804366T>C	ENST00000375001.3	+	24	2974	c.2551T>C	c.(2551-2553)Ttt>Ctt	p.F851L		NM_001855.3	NP_001846.3	P39059	COFA1_HUMAN	collagen, type XV, alpha 1	851	Collagen-like 3.|Triple-helical region 4 (COL4).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell differentiation (GO:0030154)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|signal transduction (GO:0007165)	collagen type XV trimer (GO:0005582)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	extracellular matrix structural constituent (GO:0005201)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(20)|liver(1)|lung(42)|ovary(6)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	107		Acute lymphoblastic leukemia(62;0.0562)				TTTACCTGGCTTTCCAGGACT	0.423													T|||	16	0.00319489	0.0015	0.0058	5008	,	,		17702	0.0		0.008	False		,,,				2504	0.002				p.F851L		Atlas-SNP	.											.	COL15A1	211	.	0			c.T2551C						PASS	.	T	LEU/PHE	11,4395	17.9+/-39.9	0,11,2192	95.0	103.0	100.0		2551	5.9	1.0	9	dbSNP_126	100	108,8492	57.2+/-118.5	0,108,4192	yes	missense	COL15A1	NM_001855.3	22	0,119,6384	CC,CT,TT		1.2558,0.2497,0.915	probably-damaging	851/1389	101804366	119,12887	2203	4300	6503	SO:0001583	missense	1306	exon24			CCTGGCTTTCCAG	L25286	CCDS35081.1	9q21-q22	2013-01-16			ENSG00000204291	ENSG00000204291		"""Proteoglycans / Extracellular Matrix : Collagen proteoglycans"", ""Collagens"""	2192	protein-coding gene	gene with protein product	"""collagen type XV proteoglycan"""	120325				1427836	Standard	NM_001855		Approved		uc004azb.2	P39059	OTTHUMG00000020351	ENST00000375001.3:c.2551T>C	9.37:g.101804366T>C	ENSP00000364140:p.Phe851Leu	49.0	0.0	0		50.0	18.0	0.36	NM_001855	Q5T6J4|Q9UDC5|Q9Y4W4	Missense_Mutation	SNP	ENST00000375001.3	37	CCDS35081.1	11	0.005036630036630037	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	7	0.009234828496042216	T	19.54	3.846980	0.71603	0.002497	0.012558	ENSG00000204291	ENST00000375001	D	0.93133	-3.17	5.92	5.92	0.95590	.	0.251977	0.40818	N	0.001007	D	0.88815	0.6539	N	0.10760	0.04	0.40583	D	0.981411	D	0.69078	0.997	D	0.77004	0.989	D	0.88409	0.3020	10	0.20046	T	0.44	-12.7642	12.7552	0.57331	0.0:0.0:0.0:1.0	rs35901514	851	P39059	COFA1_HUMAN	L	851	ENSP00000364140:F851L	ENSP00000364140:F851L	F	+	1	0	COL15A1	100844187	0.997000	0.39634	1.000000	0.80357	0.986000	0.74619	2.145000	0.42207	2.270000	0.75569	0.459000	0.35465	TTT	T|0.993;C|0.007	0.007	strong		0.423	COL15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053386.3	NM_001855	
C20orf194	25943	hgsc.bcm.edu	37	20	3356878	3356878	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3356878G>A	ENST00000252032.9	-	4	422	c.355C>T	c.(355-357)Cct>Tct	p.P119S		NM_001009984.2	NP_001009984.1	Q5TEA3	CT194_HUMAN	chromosome 20 open reading frame 194	119										NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(15)|prostate(2)|skin(1)	39						GCCACATAAGGTAAGAGATAG	0.368																																					p.P119S		Atlas-SNP	.											.	C20orf194	83	.	0			c.C355T						PASS	.						148.0	134.0	138.0					20																	3356878		1869	4112	5981	SO:0001583	missense	25943	exon4			CATAAGGTAAGAG	AL110249	CCDS42851.1	20p13	2012-10-30			ENSG00000088854	ENSG00000088854			17721	protein-coding gene	gene with protein product		614146					Standard	NM_001009984		Approved	DKFZp434N061	uc002wii.3	Q5TEA3	OTTHUMG00000031742	ENST00000252032.9:c.355C>T	20.37:g.3356878G>A	ENSP00000252032:p.Pro119Ser	154.0	0.0	0		197.0	90.0	0.456853	NM_001009984	Q66K86|Q6P2R9|Q9UFX9	Missense_Mutation	SNP	ENST00000252032.9	37	CCDS42851.1	.	.	.	.	.	.	.	.	.	.	G	27.3	4.822991	0.90873	.	.	ENSG00000088854	ENST00000252032	T	0.27890	1.64	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.59432	0.2193	M	0.78801	2.425	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.62421	-0.6858	10	0.87932	D	0	.	18.4941	0.90858	0.0:0.0:1.0:0.0	.	119	Q5TEA3	CT194_HUMAN	S	119	ENSP00000252032:P119S	ENSP00000252032:P119S	P	-	1	0	C20orf194	3304878	1.000000	0.71417	0.981000	0.43875	0.981000	0.71138	7.298000	0.78815	2.740000	0.93945	0.561000	0.74099	CCT	.	.	none		0.368	C20orf194-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077734.1	NM_001009984	
ATP13A3	79572	hgsc.bcm.edu	37	3	194157937	194157937	+	Silent	SNP	G	G	A	rs369809078		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194157937G>A	ENST00000439040.1	-	20	2798	c.2007C>T	c.(2005-2007)gtC>gtT	p.V669V	ATP13A3_ENST00000256031.4_Silent_p.V669V			Q9H7F0	AT133_HUMAN	ATPase type 13A3	669						integral component of membrane (GO:0016021)|membrane (GO:0016020)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|metal ion binding (GO:0046872)			NS(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	24	all_cancers(143;6.01e-09)|Ovarian(172;0.0634)	Melanoma(1037;0.211)	OV - Ovarian serous cystadenocarcinoma(49;3.83e-18)|LUSC - Lung squamous cell carcinoma(58;3.55e-06)|Lung(62;4.19e-06)	GBM - Glioblastoma multiforme(46;5.98e-05)		TTTGAAAATCGACAGGAACTT	0.348																																					p.V669V		Atlas-SNP	.											.	ATP13A3	94	.	0			c.C2007T						PASS	.	G		0,3612		0,0,1806	98.0	93.0	94.0		2007	-1.1	0.8	3		94	1,8175		0,1,4087	no	coding-synonymous	ATP13A3	NM_024524.3		0,1,5893	AA,AG,GG		0.0122,0.0,0.0085		669/1227	194157937	1,11787	1806	4088	5894	SO:0001819	synonymous_variant	79572	exon19			AAAATCGACAGGA	AJ306929	CCDS43187.1	3q29	2010-04-20			ENSG00000133657	ENSG00000133657		"""ATPases / P-type"""	24113	protein-coding gene	gene with protein product	"""ATPase family homolog up regulated in senescence cells"""	610232				11867234	Standard	NM_024524		Approved	AFURS1	uc003fty.4	Q9H7F0	OTTHUMG00000156034	ENST00000439040.1:c.2007C>T	3.37:g.194157937G>A		95.0	0.0	0		83.0	41.0	0.493976	NM_024524	Q8NC11|Q96KS1	Silent	SNP	ENST00000439040.1	37	CCDS43187.1																																																																																			.	.	weak		0.348	ATP13A3-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342799.2	NM_024524	
STRIP2	57464	hgsc.bcm.edu	37	7	129093179	129093179	+	Missense_Mutation	SNP	T	T	C	rs201255678		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129093179T>C	ENST00000249344.2	+	5	561	c.521T>C	c.(520-522)aTg>aCg	p.M174T	STRIP2_ENST00000435494.2_Missense_Mutation_p.M174T	NM_020704.2	NP_065755.1	Q9ULQ0	STRP2_HUMAN	striatin interacting protein 2	174					cell migration (GO:0016477)|cytoskeleton organization (GO:0007010)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)											CTACTCCACATGGAAATTGAG	0.512													T|||	1	0.000199681	0.0	0.0014	5008	,	,		20828	0.0		0.0	False		,,,				2504	0.0				p.M174T		Atlas-SNP	.											.	.	.	.	0			c.T521C						PASS	.						142.0	114.0	124.0					7																	129093179		2203	4300	6503	SO:0001583	missense	57464	exon5			TCCACATGGAAAT	AB032996	CCDS34752.1, CCDS47709.1	7q32.3	2012-11-05	2012-11-05	2012-11-05	ENSG00000128578	ENSG00000128578			22209	protein-coding gene	gene with protein product	"""FAR11 factor arrest 11 homolog B (yeast)"""		"""family with sequence similarity 40, member B"""	FAM40B		22782902, 22298706, 18782753	Standard	NM_020704		Approved	KIAA1170, FAR11B	uc011koy.2	Q9ULQ0	OTTHUMG00000157695	ENST00000249344.2:c.521T>C	7.37:g.129093179T>C	ENSP00000249344:p.Met174Thr	77.0	0.0	0		110.0	46.0	0.418182	NM_020704	Q8WUZ4	Missense_Mutation	SNP	ENST00000249344.2	37	CCDS34752.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.467920	0.43839	.	.	ENSG00000128578	ENST00000249344;ENST00000435494	T;T	0.47177	0.86;0.85	5.68	5.68	0.88126	.	0.041546	0.85682	D	0.000000	T	0.56202	0.1969	M	0.62723	1.935	0.80722	D	1	B;P	0.46395	0.071;0.877	B;P	0.53861	0.062;0.736	T	0.51772	-0.8663	10	0.13108	T	0.6	-20.1919	13.8875	0.63717	0.0:0.0:0.0:1.0	.	174;174	Q9ULQ0;Q9ULQ0-2	FA40B_HUMAN;.	T	174	ENSP00000249344:M174T;ENSP00000392393:M174T	ENSP00000249344:M174T	M	+	2	0	FAM40B	128880415	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.651000	0.83577	2.179000	0.69175	0.459000	0.35465	ATG	T|0.999;C|0.001	0.001	weak		0.512	STRIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349418.1	NM_001134336	
COPG1	22820	hgsc.bcm.edu	37	3	128971751	128971751	+	Silent	SNP	C	C	T	rs73202214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:128971751C>T	ENST00000314797.6	+	5	380	c.276C>T	c.(274-276)atC>atT	p.I92I		NM_016128.3	NP_057212.1	Q9Y678	COPG1_HUMAN	coatomer protein complex, subunit gamma 1	92					COPI coating of Golgi vesicle (GO:0048205)|establishment of Golgi localization (GO:0051683)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|organelle transport along microtubule (GO:0072384)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	COPI vesicle coat (GO:0030126)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)	structural molecule activity (GO:0005198)										ACTTGACCATCAAGGAGATGT	0.542													C|||	4	0.000798722	0.0	0.0043	5008	,	,		21362	0.0		0.001	False		,,,				2504	0.0				p.I92I		Atlas-SNP	.											.	.	.	.	0			c.C276T						PASS	.	C		3,4403	6.2+/-15.9	0,3,2200	186.0	160.0	169.0		276	5.1	1.0	3	dbSNP_130	169	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous	COPG	NM_016128.3		0,17,6486	TT,TC,CC		0.1628,0.0681,0.1307		92/875	128971751	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	22820	exon5			GACCATCAAGGAG	AB047846	CCDS33851.1	3q21.3	2012-02-23	2012-02-23	2012-02-23	ENSG00000181789	ENSG00000181789			2236	protein-coding gene	gene with protein product	"""coat protein gamma-cop"""	615525	"""coatomer protein complex, subunit gamma"""	COPG		11056392	Standard	NM_016128		Approved		uc003els.3	Q9Y678	OTTHUMG00000159451	ENST00000314797.6:c.276C>T	3.37:g.128971751C>T		120.0	0.0	0		127.0	66.0	0.519685	NM_016128	A8K6M8|B3KMF6|Q54AC4	Silent	SNP	ENST00000314797.6	37	CCDS33851.1																																																																																			C|0.998;T|0.002	0.002	strong		0.542	COPG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355456.1	NM_016128	
GALNTL6	442117	hgsc.bcm.edu	37	4	172735851	172735851	+	Silent	SNP	G	G	A	rs111570068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:172735851G>A	ENST00000506823.1	+	2	777	c.120G>A	c.(118-120)gcG>gcA	p.A40A	GALNTL6_ENST00000511251.1_Silent_p.A40A	NM_001034845.2	NP_001030017.2	Q49A17	GLTL6_HUMAN	polypeptide N-acetylgalactosaminyltransferase-like 6	40					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)	p.A40A(1)		breast(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|liver(2)|lung(21)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	45						TGAAGTCAGCGGAGCCCGGGG	0.537													G|||	52	0.0103834	0.0174	0.0086	5008	,	,		17897	0.0129		0.007	False		,,,				2504	0.0031				p.A40A		Atlas-SNP	.											GALNTL6,NS,carcinoma,0,1	GALNTL6	102	1	1	Substitution - coding silent(1)	pancreas(1)	c.G120A						PASS	.	G		69,4337	61.7+/-98.7	0,69,2134	79.0	77.0	78.0		120	-10.2	0.0	4	dbSNP_132	78	24,8576	17.3+/-56.4	0,24,4276	no	coding-synonymous	GALNTL6	NM_001034845.2		0,93,6410	AA,AG,GG		0.2791,1.566,0.7151		40/602	172735851	93,12913	2203	4300	6503	SO:0001819	synonymous_variant	442117	exon2			GTCAGCGGAGCCC		CCDS34104.1	4q34.1	2014-03-13	2014-03-13		ENSG00000174473	ENSG00000174473		"""Glycosyltransferase family 2 domain containing"""	33844	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase-like 6"""	615138	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 6"""				Standard	NM_001034845		Approved	GALNT17, GalNAc-T6L	uc003isv.3	Q49A17	OTTHUMG00000160807	ENST00000506823.1:c.120G>A	4.37:g.172735851G>A		93.0	0.0	0		94.0	42.0	0.446809	NM_001034845	Q2L4S6	Silent	SNP	ENST00000506823.1	37	CCDS34104.1																																																																																			G|0.991;A|0.009	0.009	strong		0.537	GALNTL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362395.1	NM_001034845	
USHBP1	83878	hgsc.bcm.edu	37	19	17367354	17367354	+	Silent	SNP	G	G	A	rs141680124	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17367354G>A	ENST00000252597.3	-	9	1569	c.1396C>T	c.(1396-1398)Ctg>Ttg	p.L466L	USHBP1_ENST00000431146.2_Silent_p.L402L|AC010646.3_ENST00000594059.1_5'Flank	NM_031941.3	NP_114147.2			Usher syndrome 1C binding protein 1											breast(3)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(10)|liver(1)|lung(12)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	44						TGGGTCCCCAGAATGGCCTGC	0.612													G|||	21	0.00419329	0.0	0.013	5008	,	,		18612	0.0		0.007	False		,,,				2504	0.0051				p.L466L		Atlas-SNP	.											.	USHBP1	85	.	0			c.C1396T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	74.0	77.0	76.0		1396	3.8	1.0	19	dbSNP_134	76	96,8504	51.9+/-112.3	0,96,4204	no	coding-synonymous	USHBP1	NM_031941.3		0,107,6396	AA,AG,GG		1.1163,0.2497,0.8227		466/704	17367354	107,12899	2203	4300	6503	SO:0001819	synonymous_variant	83878	exon9			TCCCCAGAATGGC	AK096028	CCDS12353.1	19p13.11	2013-06-10			ENSG00000130307	ENSG00000130307			24058	protein-coding gene	gene with protein product		611810				11311560	Standard	XM_005260093		Approved	MCC2, AIEBP, FLJ38709	uc002nfs.1	Q8N6Y0	OTTHUMG00000182730	ENST00000252597.3:c.1396C>T	19.37:g.17367354G>A		70.0	0.0	0		79.0	40.0	0.506329	NM_031941		Silent	SNP	ENST00000252597.3	37	CCDS12353.1																																																																																			G|0.992;A|0.008	0.008	strong		0.612	USHBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463328.1	NM_031941	
C6	729	hgsc.bcm.edu	37	5	41161898	41161898	+	Missense_Mutation	SNP	C	C	T	rs142896559	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:41161898C>T	ENST00000263413.3	-	10	1619	c.1355G>A	c.(1354-1356)gGa>gAa	p.G452E	C6_ENST00000337836.5_Missense_Mutation_p.G452E|C6_ENST00000475349.1_5'UTR	NM_001115131.1	NP_001108603.2	P13671	CO6_HUMAN	complement component 6	452	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane attack complex (GO:0005579)				central_nervous_system(2)|cervix(2)|endometrium(2)|kidney(7)|large_intestine(16)|liver(1)|lung(51)|ovary(3)|prostate(1)|skin(9)|upper_aerodigestive_tract(2)	96		Breast(839;1.07e-05)|Ovarian(839;0.0228)|Lung SC(612;0.0548)|Lung NSC(810;0.128)|all_neural(839;0.157)				CAAAGCTGCTCCATATTCACT	0.423													C|||	11	0.00219649	0.0008	0.0014	5008	,	,		18136	0.0		0.004	False		,,,				2504	0.0051				p.G452E		Atlas-SNP	.											.	C6	197	.	0			c.G1355A						PASS	.	C	GLU/GLY,GLU/GLY	5,4401	9.9+/-24.2	0,5,2198	127.0	124.0	125.0		1355,1355	4.5	0.4	5	dbSNP_134	125	54,8546	34.3+/-88.2	0,54,4246	yes	missense,missense	C6	NM_000065.2,NM_001115131.1	98,98	0,59,6444	TT,TC,CC		0.6279,0.1135,0.4536	benign,benign	452/935,452/935	41161898	59,12947	2203	4300	6503	SO:0001583	missense	729	exon10			GCTGCTCCATATT	J05024	CCDS3936.1	5p13.1	2014-09-17			ENSG00000039537	ENSG00000039537		"""Complement system"""	1339	protein-coding gene	gene with protein product		217050					Standard	NM_001115131		Approved		uc003jmk.3	P13671	OTTHUMG00000094781	ENST00000263413.3:c.1355G>A	5.37:g.41161898C>T	ENSP00000263413:p.Gly452Glu	131.0	0.0	0		137.0	74.0	0.540146	NM_001115131		Missense_Mutation	SNP	ENST00000263413.3	37	CCDS3936.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	16.72	3.202704	0.58234	0.001135	0.006279	ENSG00000039537	ENST00000337836;ENST00000263413	D;D	0.83335	-1.71;-1.71	5.35	4.48	0.54585	Membrane attack complex component/perforin (MACPF) domain (3);	0.311897	0.38778	N	0.001563	T	0.70090	0.3184	L	0.29908	0.895	0.30383	N	0.78175	B	0.09022	0.002	B	0.06405	0.002	T	0.72811	-0.4180	10	0.72032	D	0.01	-7.7633	16.7694	0.85533	0.0:0.1292:0.8708:0.0	.	452	P13671	CO6_HUMAN	E	452	ENSP00000338861:G452E;ENSP00000263413:G452E	ENSP00000263413:G452E	G	-	2	0	C6	41197655	0.998000	0.40836	0.415000	0.26534	0.970000	0.65996	5.677000	0.68142	1.638000	0.50547	-0.128000	0.14901	GGA	C|0.996;T|0.004	0.004	strong		0.423	C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211592.1		
IQUB	154865	hgsc.bcm.edu	37	7	123152157	123152157	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:123152157C>G	ENST00000466202.1	-	2	814	c.238G>C	c.(238-240)Gaa>Caa	p.E80Q	IQUB_ENST00000488987.1_Intron|IQUB_ENST00000324698.6_Missense_Mutation_p.E80Q|IQUB_ENST00000434450.1_Missense_Mutation_p.E80Q	NM_001282855.1	NP_001269784.1	Q8NA54	IQUB_HUMAN	IQ motif and ubiquitin domain containing	80					cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	acrosomal vesicle (GO:0001669)|motile cilium (GO:0031514)				breast(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(18)|ovary(3)|prostate(2)|stomach(3)|upper_aerodigestive_tract(1)	45						ATAACCTCTTCCATGAGTTGT	0.408																																					p.E80Q		Atlas-SNP	.											.	IQUB	117	.	0			c.G238C						PASS	.						245.0	205.0	218.0					7																	123152157		2203	4300	6503	SO:0001583	missense	154865	exon2			CCTCTTCCATGAG	AK093153	CCDS5787.1	7q31.32	2010-03-19			ENSG00000164675	ENSG00000164675			21995	protein-coding gene	gene with protein product							Standard	NM_178827		Approved	FLJ35834	uc003vko.3	Q8NA54	OTTHUMG00000157347	ENST00000466202.1:c.238G>C	7.37:g.123152157C>G	ENSP00000417769:p.Glu80Gln	299.0	0.0	0		293.0	139.0	0.474403	NM_178827	A4D0X0|Q49AL6|Q4G189|Q5BJD9|Q6NUH6|Q8N9Y2	Missense_Mutation	SNP	ENST00000466202.1	37	CCDS5787.1	.	.	.	.	.	.	.	.	.	.	C	11.50	1.656291	0.29425	.	.	ENSG00000164675	ENST00000466202;ENST00000324698;ENST00000434450	T;T;T	0.48201	1.84;1.84;0.82	5.1	2.24	0.28232	.	0.791632	0.10762	N	0.637086	T	0.40546	0.1121	L	0.29908	0.895	0.09310	N	1	B;P;P	0.48016	0.244;0.904;0.718	B;P;B	0.48227	0.084;0.571;0.203	T	0.17198	-1.0377	10	0.45353	T	0.12	.	6.4052	0.21660	0.1487:0.6816:0.0:0.1697	.	80;80;80	A1A4Z1;Q8NA54-2;Q8NA54	.;.;IQUB_HUMAN	Q	80	ENSP00000417769:E80Q;ENSP00000324882:E80Q;ENSP00000388498:E80Q	ENSP00000324882:E80Q	E	-	1	0	IQUB	122939393	0.001000	0.12720	0.001000	0.08648	0.003000	0.03518	0.554000	0.23407	0.404000	0.25506	-0.813000	0.03139	GAA	.	.	none		0.408	IQUB-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348529.1	NM_178827	
KCNV1	27012	hgsc.bcm.edu	37	8	110986480	110986480	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:110986480G>A	ENST00000524391.1	-	2	1170	c.138C>T	c.(136-138)ggC>ggT	p.G46G	RP11-696P8.2_ENST00000530667.1_RNA|KCNV1_ENST00000297404.1_Silent_p.G46G			Q6PIU1	KCNV1_HUMAN	potassium channel, subfamily V, member 1	46					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|ion channel inhibitor activity (GO:0008200)|potassium channel regulator activity (GO:0015459)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(20)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	37	all_neural(195;0.219)		OV - Ovarian serous cystadenocarcinoma(57;5.35e-13)			AGCGGCTGCCGCCCACGTTGA	0.692																																					p.G46G		Atlas-SNP	.											.	KCNV1	101	.	0			c.C138T						PASS	.						8.0	7.0	8.0					8																	110986480		2140	4178	6318	SO:0001819	synonymous_variant	27012	exon1			GCTGCCGCCCACG	AF167082	CCDS6314.1	8q23.2	2011-07-05				ENSG00000164794		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18861	protein-coding gene	gene with protein product		608164				8670833, 16382104	Standard	NM_014379		Approved	Kv8.1	uc003ynr.4	Q6PIU1		ENST00000524391.1:c.138C>T	8.37:g.110986480G>A		8.0	0.0	0		14.0	7.0	0.5	NM_014379	Q9UHJ4	Silent	SNP	ENST00000524391.1	37	CCDS6314.1																																																																																			.	.	none		0.692	KCNV1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385525.1	NM_014379	
OR2AE1	81392	hgsc.bcm.edu	37	7	99474438	99474438	+	Silent	SNP	A	A	G	rs139077767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99474438A>G	ENST00000316368.2	-	1	242	c.219T>C	c.(217-219)caT>caC	p.H73H		NM_001005276.1	NP_001005276.1	Q8NHA4	O2AE1_HUMAN	olfactory receptor, family 2, subfamily AE, member 1	73						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)|large_intestine(2)|lung(3)|prostate(2)	11	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					TTGTGGAGACATGCATCAGAT	0.488													A|||	19	0.00379393	0.0008	0.0029	5008	,	,		23330	0.001		0.007	False		,,,				2504	0.0082				p.H73H		Atlas-SNP	.											.	OR2AE1	32	.	0			c.T219C						PASS	.	A		9,4397	15.5+/-35.6	0,9,2194	113.0	96.0	102.0		219	-7.2	0.0	7	dbSNP_134	102	68,8532	42.2+/-99.7	0,68,4232	no	coding-synonymous	OR2AE1	NM_001005276.1		0,77,6426	GG,GA,AA		0.7907,0.2043,0.592		73/324	99474438	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	81392	exon1			GGAGACATGCATC	AC011904	CCDS34696.1	7q22.1	2014-02-19	2002-02-28		ENSG00000244623	ENSG00000244623		"""GPCR / Class A : Olfactory receptors"""	15087	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily AE, member 2"""	OR2AE2			Standard	NM_001005276		Approved		uc003usc.1	Q8NHA4	OTTHUMG00000156650	ENST00000316368.2:c.219T>C	7.37:g.99474438A>G		100.0	0.0	0		107.0	49.0	0.457944	NM_001005276	B2RPD2	Silent	SNP	ENST00000316368.2	37	CCDS34696.1																																																																																			A|0.994;G|0.006	0.006	strong		0.488	OR2AE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345053.1		
POLR1E	64425	hgsc.bcm.edu	37	9	37498215	37498215	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:37498215C>T	ENST00000377798.4	+	9	993	c.880C>T	c.(880-882)Cgg>Tgg	p.R294W	POLR1E_ENST00000442009.2_Missense_Mutation_p.R224W|POLR1E_ENST00000377792.3_Missense_Mutation_p.R356W	NM_022490.1	NP_071935.1	O15160	RPAC1_HUMAN	polymerase (RNA) I polypeptide E, 53kDa	0					gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase I transcription (GO:0006363)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytosol (GO:0005829)|DNA-directed RNA polymerase I complex (GO:0005736)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			autonomic_ganglia(1)|endometrium(1)|kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|skin(1)|stomach(1)	12				GBM - Glioblastoma multiforme(29;0.00851)|Lung(182;0.229)		GGTAGTTAAGCGGAAAAGTAA	0.388																																					p.R294W	Ovarian(116;843 1620 18506 32459 34463)	Atlas-SNP	.											.	POLR1E	28	.	0			c.C880T						PASS	.						96.0	93.0	94.0					9																	37498215		2203	4300	6503	SO:0001583	missense	64425	exon9			GTTAAGCGGAAAA	AK091294	CCDS6611.1	9p13.1	2013-01-21	2006-03-09	2006-03-09	ENSG00000137054	ENSG00000137054		"""RNA polymerase subunits"""	17631	protein-coding gene	gene with protein product	"""RNA polymerase I associated factor 53"""		"""polymerase (RNA) I associated factor 1"""	PRAF1		8641287	Standard	XM_005251547		Approved	FLJ13390, PAF53, FLJ13970	uc003zzy.1	Q9GZS1	OTTHUMG00000019920	ENST00000377798.4:c.880C>T	9.37:g.37498215C>T	ENSP00000367029:p.Arg294Trp	110.0	0.0	0		97.0	46.0	0.474227	NM_022490	O75395|Q5JTE3	Missense_Mutation	SNP	ENST00000377798.4	37	CCDS6611.1	.	.	.	.	.	.	.	.	.	.	C	15.27	2.783965	0.49891	.	.	ENSG00000137054	ENST00000377798;ENST00000442009;ENST00000377792	T;T;T	0.24723	1.84;1.84;1.84	5.76	3.78	0.43462	.	0.538678	0.19258	N	0.118753	T	0.43612	0.1255	L	0.59436	1.845	0.35039	D	0.75957	D;D;D	0.89917	1.0;1.0;0.999	D;D;P	0.69479	0.939;0.964;0.862	T	0.56619	-0.7949	10	0.56958	D	0.05	-12.8494	11.1968	0.48717	0.1376:0.7205:0.1419:0.0	.	224;356;294	E7EX70;Q9GZS1;Q9GZS1-2	.;RPA49_HUMAN;.	W	294;224;356	ENSP00000367029:R294W;ENSP00000399887:R224W;ENSP00000367023:R356W	ENSP00000367023:R356W	R	+	1	2	POLR1E	37488215	1.000000	0.71417	1.000000	0.80357	0.155000	0.21991	2.300000	0.43620	1.534000	0.49203	0.655000	0.94253	CGG	.	.	none		0.388	POLR1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052464.1	NM_022490	
NCAPD2	9918	hgsc.bcm.edu	37	12	6634817	6634817	+	Silent	SNP	C	C	T	rs71579347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:6634817C>T	ENST00000315579.5	+	18	3082	c.2283C>T	c.(2281-2283)acC>acT	p.T761T	NCAPD2_ENST00000542492.1_3'UTR|NCAPD2_ENST00000545962.1_Silent_p.T716T	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	761					mitotic cell cycle (GO:0000278)|mitotic chromosome condensation (GO:0007076)	condensed chromosome (GO:0000793)|condensin complex (GO:0000796)|condensin core heterodimer (GO:0000797)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|pronucleus (GO:0045120)	histone binding (GO:0042393)			NS(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	48						AGCGGGCCACCGAGAAGGTCG	0.547													C|||	8	0.00159744	0.0	0.0	5008	,	,		18865	0.0		0.0	False		,,,				2504	0.0082				p.T761T		Atlas-SNP	.											.	NCAPD2	99	.	0			c.C2283T						PASS	.	C		0,4406		0,0,2203	78.0	70.0	73.0		2283	-11.7	0.0	12	dbSNP_130	73	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	NCAPD2	NM_014865.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		761/1402	6634817	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9918	exon18			GGCCACCGAGAAG	D63880	CCDS8548.1	12p13.31	2008-02-04			ENSG00000010292	ENSG00000010292			24305	protein-coding gene	gene with protein product	"""chromosome condensation related SMC associated protein 1"""	615638				8590280, 10958694	Standard	NM_014865		Approved	CNAP1, hCAP-D2, CAP-D2, KIAA0159	uc001qoo.2	Q15021	OTTHUMG00000168513	ENST00000315579.5:c.2283C>T	12.37:g.6634817C>T		116.0	0.0	0		87.0	51.0	0.586207	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	37	CCDS8548.1																																																																																			C|0.999;T|0.001	0.001	strong		0.547	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
PRKCZ	5590	hgsc.bcm.edu	37	1	2105427	2105427	+	Silent	SNP	C	C	T	rs142352833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2105427C>T	ENST00000400921.2	+	11	1511	c.828C>T	c.(826-828)gaC>gaT	p.D276D	PRKCZ_ENST00000479263.1_3'UTR|PRKCZ_ENST00000400920.1_Silent_p.D276D	NM_001033581.1	NP_001028753.1	Q05513	KPCZ_HUMAN	protein kinase C, zeta	459	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				actin cytoskeleton reorganization (GO:0031532)|activation of phospholipase D activity (GO:0031584)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell migration (GO:0016477)|establishment of cell polarity (GO:0030010)|inflammatory response (GO:0006954)|insulin receptor signaling pathway (GO:0008286)|long-term memory (GO:0007616)|long-term synaptic potentiation (GO:0060291)|membrane hyperpolarization (GO:0060081)|microtubule cytoskeleton organization (GO:0000226)|negative regulation of apoptotic process (GO:0043066)|negative regulation of hydrolase activity (GO:0051346)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of peptidyl-tyrosine phosphorylation (GO:0050732)|negative regulation of protein complex assembly (GO:0031333)|neuron projection extension (GO:1990138)|peptidyl-serine phosphorylation (GO:0018105)|platelet activation (GO:0030168)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell-matrix adhesion (GO:0001954)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of glucose import (GO:0046326)|positive regulation of insulin receptor signaling pathway (GO:0046628)|positive regulation of interleukin-10 secretion (GO:2001181)|positive regulation of interleukin-13 secretion (GO:2000667)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 secretion (GO:2000664)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of T-helper 2 cell cytokine production (GO:2000553)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|protein heterooligomerization (GO:0051291)|protein kinase C signaling (GO:0070528)|protein localization to plasma membrane (GO:0072659)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|transforming growth factor beta receptor signaling pathway (GO:0007179)|vesicle transport along microtubule (GO:0047496)	apical cortex (GO:0045179)|apical plasma membrane (GO:0016324)|axon hillock (GO:0043203)|cell junction (GO:0030054)|cell leading edge (GO:0031252)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane raft (GO:0045121)|microtubule organizing center (GO:0005815)|myelin sheath abaxonal region (GO:0035748)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)	ATP binding (GO:0005524)|insulin receptor substrate binding (GO:0043560)|potassium channel regulator activity (GO:0015459)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(4)|endometrium(1)|large_intestine(5)|lung(5)|stomach(1)	18	all_cancers(77;0.000177)|all_epithelial(69;6.41e-05)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;1.14e-19)|all_lung(118;1.22e-08)|Lung NSC(185;1.24e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Medulloblastoma(700;0.123)|Lung SC(97;0.128)		Epithelial(90;2.96e-37)|OV - Ovarian serous cystadenocarcinoma(86;3.3e-23)|GBM - Glioblastoma multiforme(42;2.85e-08)|Colorectal(212;6.15e-05)|COAD - Colon adenocarcinoma(227;0.000241)|Kidney(185;0.00294)|BRCA - Breast invasive adenocarcinoma(365;0.00493)|STAD - Stomach adenocarcinoma(132;0.00669)|KIRC - Kidney renal clear cell carcinoma(229;0.0411)|Lung(427;0.213)	Tamoxifen(DB00675)	ACAACCCGGACATGAACACAG	0.597											OREG0013007	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D459D		Atlas-SNP	.											.	PRKCZ	84	.	0			c.C1377T						PASS	.	C	,,,	0,4406	2.1+/-5.4	0,0,2203	136.0	116.0	122.0		828,828,1065,1377	3.0	1.0	1	dbSNP_134	122	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PRKCZ	NM_001033581.1,NM_001033582.1,NM_001242874.1,NM_002744.4	,,,	0,15,6488	TT,TC,CC		0.1744,0.0,0.1153	,,,	276/410,276/410,355/489,459/593	2105427	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	5590	exon14			CCCGGACATGAAC	BC014270	CCDS37.1, CCDS41229.1, CCDS55563.1	1p36.33-p36.2	2009-07-10			ENSG00000067606	ENSG00000067606	2.7.11.1		9412	protein-coding gene	gene with protein product		176982					Standard	NM_001242874		Approved	PKC2	uc001aiq.3	Q05513	OTTHUMG00000001238	ENST00000400921.2:c.828C>T	1.37:g.2105427C>T		134.0	0.0	0	601	98.0	89.0	0.908163	NM_002744	A8K4N0|A8MU64|B7Z2J7|E9PCW2|Q15207|Q5SYT5|Q969S4	Silent	SNP	ENST00000400921.2	37	CCDS41229.1																																																																																			C|0.999;T|0.001	0.001	strong		0.597	PRKCZ-009	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000098533.3	NM_002744	
UBE4A	9354	hgsc.bcm.edu	37	11	118242324	118242324	+	Silent	SNP	A	A	G	rs145949976	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118242324A>G	ENST00000431736.2	+	5	576	c.504A>G	c.(502-504)gcA>gcG	p.A168A	UBE4A_ENST00000252108.3_Silent_p.A168A					ubiquitination factor E4A											autonomic_ganglia(1)|breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(17)|large_intestine(7)|liver(2)|lung(14)|ovary(3)|prostate(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	56	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;3.28e-05)		ATCGAGATGCAGGAGAGAGGC	0.433													A|||	6	0.00119808	0.0038	0.0014	5008	,	,		16924	0.0		0.0	False		,,,				2504	0.0				p.A168A		Atlas-SNP	.											.	UBE4A	97	.	0			c.A504G						PASS	.	A	,	11,4389	17.9+/-39.9	0,11,2189	138.0	128.0	131.0		504,504	0.3	1.0	11	dbSNP_134	131	1,8591	1.2+/-3.3	0,1,4295	no	coding-synonymous,coding-synonymous	UBE4A	NM_001204077.1,NM_004788.3	,	0,12,6484	GG,GA,AA		0.0116,0.25,0.0924	,	168/1067,168/1074	118242324	12,12980	2200	4296	6496	SO:0001819	synonymous_variant	9354	exon5			AGATGCAGGAGAG	D50916	CCDS8396.1, CCDS55790.1	11q23.3	2013-01-28	2011-05-19					"""U-box domain containing"""	12499	protein-coding gene	gene with protein product		603753	"""ubiquitination factor E4A (homologous to yeast UFD2)"", ""ubiquitination factor E4A (UFD2 homolog, yeast)"""			10089879	Standard	NM_004788		Approved	UBOX2, UFD2, KIAA0126, E4	uc001psv.3	Q14139	OTTHUMG00000168100	ENST00000431736.2:c.504A>G	11.37:g.118242324A>G		79.0	0.0	0		80.0	48.0	0.6	NM_004788		Silent	SNP	ENST00000431736.2	37	CCDS8396.1																																																																																			A|0.999;G|0.001	0.001	strong		0.433	UBE4A-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000398143.1	NM_004788	
HEATR5A	25938	hgsc.bcm.edu	37	14	31856407	31856407	+	Missense_Mutation	SNP	C	C	T	rs73259359	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:31856407C>T	ENST00000389961.3	-	7	1089	c.1090G>A	c.(1090-1092)Ggt>Agt	p.G364S	HEATR5A_ENST00000543095.2_Missense_Mutation_p.G370S|HEATR5A_ENST00000404677.3_Missense_Mutation_p.G370S|HEATR5A_ENST00000439727.1_Missense_Mutation_p.G77S|HEATR5A_ENST00000439348.1_Missense_Mutation_p.G364S			Q86XA9	HTR5A_HUMAN	HEAT repeat containing 5A	364										breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)	26	Hepatocellular(127;0.0877)|Breast(36;0.137)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.0797)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.0059)		AGAAGACCACCTATAGTAGTT	0.468													C|||	145	0.0289537	0.0968	0.0187	5008	,	,		16103	0.0		0.003	False		,,,				2504	0.001				p.G370S		Atlas-SNP	.											.	HEATR5A	181	.	0			c.G1108A						PASS	.	C	SER/GLY	239,3561		9,221,1670	126.0	119.0	121.0		1108	4.7	1.0	14	dbSNP_130	121	15,8239		0,15,4112	yes	missense	HEATR5A	NM_015473.3	56	9,236,5782	TT,TC,CC		0.1817,6.2895,2.1072	probably-damaging	370/2047	31856407	254,11800	1900	4127	6027	SO:0001583	missense	25938	exon8			GACCACCTATAGT	AB037737		14q12	2012-04-19	2007-01-02	2007-01-02	ENSG00000129493	ENSG00000129493			20276	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 125"""	C14orf125			Standard	NM_015473		Approved	DKFZP434I1735	uc001wrf.4	Q86XA9	OTTHUMG00000169043	ENST00000389961.3:c.1090G>A	14.37:g.31856407C>T	ENSP00000374611:p.Gly364Ser	156.0	0.0	0		178.0	91.0	0.511236	NM_015473	Q68DD8|Q6P3S5|Q6P5R9|Q9H8D7|Q9NXB7|Q9P2N0|Q9UFQ3	Missense_Mutation	SNP	ENST00000389961.3	37		60|60	0.027472527472527472|0.027472527472527472	53|53	0.10772357723577236|0.10772357723577236	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	29.3|29.3	4.991400|4.991400	0.93106|0.93106	0.062895|0.062895	0.001817|0.001817	ENSG00000129493|ENSG00000129493	ENST00000389961;ENST00000439348;ENST00000439727;ENST00000543095;ENST00000404677|ENST00000550366	T;T;T;T;T|.	0.07567|.	3.18;3.18;3.18;3.18;3.18|.	5.53|5.53	4.65|4.65	0.58169|0.58169	.|.	0.124234|.	0.53938|.	D|.	0.000055|.	T|T	0.04907|0.04907	0.0132|0.0132	M|M	0.77313|0.77313	2.365|2.365	0.09310|0.09310	P|P	0.9999999539453|0.9999999539453	D|.	0.58970|.	0.984|.	P|.	0.59643|.	0.861|.	T|T	0.51911|0.51911	-0.8645|-0.8645	9|4	0.72032|.	D|.	0.01|.	.|.	14.2073|14.2073	0.65741|0.65741	0.0:0.9281:0.0:0.0719|0.0:0.9281:0.0:0.0719	.|.	370|.	B5MC49|.	.|.	S|K	364;364;77;370;370|28	ENSP00000374611:G364S;ENSP00000405407:G364S;ENSP00000408681:G77S;ENSP00000437968:G370S;ENSP00000384646:G370S|.	ENSP00000374611:G364S|.	G|R	-|-	1|2	0|0	HEATR5A|HEATR5A	30926158|30926158	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.901000|0.901000	0.52897|0.52897	7.632000|7.632000	0.83247|0.83247	1.339000|1.339000	0.45563|0.45563	0.491000|0.491000	0.48974|0.48974	GGT|AGG	C|0.977;T|0.023	0.023	strong		0.468	HEATR5A-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015473	
NLRP14	338323	hgsc.bcm.edu	37	11	7064560	7064560	+	Missense_Mutation	SNP	A	A	T	rs200574634		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:7064560A>T	ENST00000299481.4	+	4	1649	c.1303A>T	c.(1303-1305)Ata>Tta	p.I435L		NM_176822.3	NP_789792.1	Q86W24	NAL14_HUMAN	NLR family, pyrin domain containing 14	435	NACHT. {ECO:0000255|PROSITE- ProRule:PRU00136}.				cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)			breast(3)|large_intestine(7)|lung(1)|ovary(3)|pancreas(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	21				Epithelial(150;4.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.0871)		TGCCAAAGGAATATGGACTAT	0.428													A|||	1	0.000199681	0.0	0.0	5008	,	,		20937	0.0		0.001	False		,,,				2504	0.0				p.I435L		Atlas-SNP	.											.	NLRP14	187	.	0			c.A1303T						PASS	.						128.0	131.0	130.0					11																	7064560		2201	4296	6497	SO:0001583	missense	338323	exon4			AAAGGAATATGGA	BK001107	CCDS7776.1	11p15.4	2006-12-08	2006-12-08	2006-12-08		ENSG00000158077		"""Nucleotide-binding domain and leucine rich repeat containing"""	22939	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 14"""	609665	"""NACHT, leucine rich repeat and PYD containing 14"""	NALP14		12563287	Standard	NM_176822		Approved	NOD5, GC-LRR, Nalp-iota, PAN8, CLR11.2	uc001mfb.1	Q86W24		ENST00000299481.4:c.1303A>T	11.37:g.7064560A>T	ENSP00000299481:p.Ile435Leu	171.0	0.0	0		136.0	73.0	0.536765	NM_176822	Q7RTR6	Missense_Mutation	SNP	ENST00000299481.4	37	CCDS7776.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	5.302	0.241082	0.10077	.	.	ENSG00000158077	ENST00000299481	T	0.74421	-0.84	4.48	-0.234	0.13074	.	0.513668	0.17972	N	0.155815	T	0.49389	0.1554	N	0.12637	0.245	0.23542	N	0.997459	B	0.22800	0.075	B	0.21151	0.033	T	0.30736	-0.9968	10	0.17369	T	0.5	.	7.7052	0.28646	0.5723:0.0:0.4277:0.0	.	435	Q86W24	NAL14_HUMAN	L	435	ENSP00000299481:I435L	ENSP00000299481:I435L	I	+	1	0	NLRP14	7021136	0.888000	0.30383	0.733000	0.30861	0.937000	0.57800	0.803000	0.27083	-0.106000	0.12110	-0.256000	0.11100	ATA	A|1.000;T|0.000	0.000	strong		0.428	NLRP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384551.1	NM_176822	
ZSCAN30	100101467	hgsc.bcm.edu	37	18	32833766	32833766	+	Missense_Mutation	SNP	A	A	C	rs61731888	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:32833766A>C	ENST00000420878.3	-	5	1588	c.1133T>G	c.(1132-1134)aTc>aGc	p.I378S	ZNF397_ENST00000261333.6_Intron|ZNF397_ENST00000355632.4_Intron|ZNF397_ENST00000592264.1_Intron|ZNF397_ENST00000589420.1_Intron|ZSCAN30_ENST00000333206.5_Missense_Mutation_p.I378S	NM_001166012.1	NP_001159484.1	Q86W11	ZSC30_HUMAN	zinc finger and SCAN domain containing 30	378					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)			large_intestine(5)|lung(3)|urinary_tract(1)	9						TCCAGTGTGGATTCTCCGATG	0.453													A|||	114	0.0227636	0.0522	0.0202	5008	,	,		20229	0.001		0.0209	False		,,,				2504	0.0092				p.I378S		Atlas-SNP	.											.	ZSCAN30	34	.	0			c.T1133G						PASS	.	A	SER/ILE,SER/ILE,	147,2989		5,137,1426	96.0	90.0	92.0		1133,1133,	2.4	1.0	18	dbSNP_129	92	153,7011		2,149,3431	yes	missense,missense,intron	ZNF397,ZSCAN30	NM_001112734.2,NM_001166012.1,NM_032347.2	142,142,	7,286,4857	CC,CA,AA		2.1357,4.6875,2.9126	probably-damaging,probably-damaging,	378/495,378/495,	32833766	300,10000	1568	3582	5150	SO:0001583	missense	100101467	exon5			GTGTGGATTCTCC	AY234408	CCDS42427.1, CCDS74207.1	18q12.2	2013-01-08	2010-07-23	2010-07-23	ENSG00000186814	ENSG00000186814		"""-"", ""Zinc fingers, C2H2-type"""	33517	protein-coding gene	gene with protein product			"""zinc finger protein 397 opposite strand"", ""ZNF397 opposite strand"""	ZNF397OS		12801647	Standard	NM_001166012		Approved	ZNF917	uc002kym.3	Q86W11		ENST00000420878.3:c.1133T>G	18.37:g.32833766A>C	ENSP00000392371:p.Ile378Ser	79.0	0.0	0		80.0	42.0	0.525	NM_001166012	B4E0N0|Q6ZNB3|Q96PN3	Missense_Mutation	SNP	ENST00000420878.3	37	CCDS42427.1	63	0.028846153846153848	34	0.06910569105691057	12	0.03314917127071823	1	0.0017482517482517483	16	0.021108179419525065	A	17.36	3.370099	0.61624	0.046875	0.021357	ENSG00000186814	ENST00000420878;ENST00000333206;ENST00000360932	T;T	0.06933	3.24;3.24	4.7	2.37	0.29283	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.217388	0.23491	N	0.047605	T	0.00815	0.0027	N	0.20685	0.6	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.19095	-1.0316	10	0.59425	D	0.04	.	5.4094	0.16341	0.6984:0.0:0.3016:0.0	rs61731888	378	Q86W11	ZSC30_HUMAN	S	378;378;313	ENSP00000392371:I378S;ENSP00000329738:I378S	ENSP00000329738:I378S	I	-	2	0	ZSCAN30	31087764	0.024000	0.19004	1.000000	0.80357	0.996000	0.88848	0.796000	0.26986	0.933000	0.37291	0.533000	0.62120	ATC	A|0.975;C|0.025	0.025	strong		0.453	ZSCAN30-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442510.1	NM_001112734	
TLE3	7090	hgsc.bcm.edu	37	15	70347482	70347482	+	Missense_Mutation	SNP	G	G	A	rs200508723	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:70347482G>A	ENST00000558939.1	-	15	2870	c.1493C>T	c.(1492-1494)aCg>aTg	p.T498M	TLE3_ENST00000440567.3_Missense_Mutation_p.T488M|TLE3_ENST00000558379.1_Missense_Mutation_p.T493M|TLE3_ENST00000442299.2_Missense_Mutation_p.T490M|TLE3_ENST00000451782.2_Missense_Mutation_p.T495M|TLE3_ENST00000560589.1_Missense_Mutation_p.T442M|TLE3_ENST00000557997.1_Missense_Mutation_p.T490M|TLE3_ENST00000559929.1_Missense_Mutation_p.T508M|TLE3_ENST00000559191.1_Missense_Mutation_p.T79M|TLE3_ENST00000560939.1_Missense_Mutation_p.T500M|TLE3_ENST00000539550.1_Missense_Mutation_p.T425M|TLE3_ENST00000557907.1_Missense_Mutation_p.T490M|TLE3_ENST00000559048.1_Missense_Mutation_p.T498M|TLE3_ENST00000558201.1_Missense_Mutation_p.T504M|TLE3_ENST00000317509.8_Missense_Mutation_p.T486M	NM_001282979.1|NM_001282980.1|NM_001282981.1	NP_001269908.1|NP_001269909.1|NP_001269910.1	Q04726	TLE3_HUMAN	transducin-like enhancer of split 3	498				T -> S (in Ref. 1; AAA61194). {ECO:0000305}.	Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)				breast(1)|endometrium(4)|kidney(2)|large_intestine(4)|lung(16)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	31						GACGTGCCTCGTGGGGTTGCT	0.657													G|||	2	0.000399361	0.0	0.0	5008	,	,		18004	0.0		0.002	False		,,,				2504	0.0				p.T498M		Atlas-SNP	.											.	TLE3	104	.	0			c.C1493T						PASS	.	G	MET/THR,MET/THR,MET/THR	4,4394	6.2+/-15.9	0,4,2195	66.0	70.0	69.0		1484,1493,1457	4.5	1.0	15		69	32,8564	22.2+/-67.0	0,32,4266	yes	missense,missense,missense	TLE3	NM_001105192.1,NM_005078.2,NM_020908.1	81,81,81	0,36,6461	AA,AG,GG		0.3723,0.091,0.2771	probably-damaging,probably-damaging,probably-damaging	495/770,498/773,486/761	70347482	36,12958	2199	4298	6497	SO:0001583	missense	7090	exon15			TGCCTCGTGGGGT	M99438	CCDS45293.1, CCDS45294.1, CCDS58375.1, CCDS61689.1, CCDS61691.1, CCDS61692.1, CCDS73747.1	15q22	2014-03-07	2014-03-07			ENSG00000140332		"""WD repeat domain containing"""	11839	protein-coding gene	gene with protein product		600190	"""transducin-like enhancer of split 3, homolog of Drosophila E(sp1)"", ""transducin-like enhancer of split 3 (E(sp1) homolog, Drosophila)"""			8365415	Standard	XM_005254623		Approved	ESG, ESG3, KIAA1547, HsT18976, GRG3	uc002asm.2	Q04726		ENST00000558939.1:c.1493C>T	15.37:g.70347482G>A	ENSP00000452871:p.Thr498Met	94.0	0.0	0		109.0	56.0	0.513761	NM_005078	B4DPT0|E9PD64|F8W964|Q6PI57|Q8IVV6|Q8WVR2|Q9HCM5	Missense_Mutation	SNP	ENST00000558939.1	37	CCDS45293.1	.	.	.	.	.	.	.	.	.	.	G	23.6	4.436998	0.83885	9.1E-4	0.003723	ENSG00000140332	ENST00000442299;ENST00000451782;ENST00000317509;ENST00000440567;ENST00000539550;ENST00000542329	T;T;T;T	0.11604	2.76;2.76;2.76;2.76	4.54	4.54	0.55810	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	T	0.33673	0.0871	M	0.76170	2.325	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D	0.80764	0.978;0.987;0.935;0.987;0.989;0.994;0.985;0.965	T	0.12372	-1.0550	10	0.87932	D	0	-9.2287	16.2284	0.82315	0.0:0.0:1.0:0.0	.	488;495;490;493;486;498;498;425	F8W964;E9PD64;Q04726-3;Q6PI57;Q04726-2;Q04726;Q04726-4;F5H7D6	.;.;.;.;.;TLE3_HUMAN;.;.	M	490;495;498;488;425;165	ENSP00000390007:T490M;ENSP00000394717:T495M;ENSP00000415057:T488M;ENSP00000442594:T425M	ENSP00000319233:T498M	T	-	2	0	TLE3	68134536	1.000000	0.71417	0.968000	0.41197	0.975000	0.68041	9.530000	0.98051	2.352000	0.79861	0.462000	0.41574	ACG	G|0.999;A|0.001	0.001	weak		0.657	TLE3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416913.1	NM_005078	
AP1S3	130340	hgsc.bcm.edu	37	2	224642579	224642579	+	Missense_Mutation	SNP	A	A	C	rs116107386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:224642579A>C	ENST00000446015.2	-	2	44	c.11T>G	c.(10-12)tTc>tGc	p.F4C	AP1S3_ENST00000396653.2_Missense_Mutation_p.F4C|AP1S3_ENST00000443700.1_Missense_Mutation_p.F4C|AP1S3_ENST00000423110.1_Missense_Mutation_p.F4C|AP1S3_ENST00000409375.1_Missense_Mutation_p.F4C|AP1S3_ENST00000396654.2_Missense_Mutation_p.F4C			Q96PC3	AP1S3_HUMAN	adaptor-related protein complex 1, sigma 3 subunit	4					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	coated pit (GO:0005905)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane coat (GO:0030117)|trans-Golgi network membrane (GO:0032588)	protein transporter activity (GO:0008565)			NS(1)|breast(1)|lung(2)	4		Renal(207;0.0112)|Lung NSC(271;0.0186)|all_lung(227;0.0272)		Epithelial(121;7.6e-10)|all cancers(144;3.62e-07)|Lung(261;0.0086)|LUSC - Lung squamous cell carcinoma(224;0.00902)		GAGCAATATGAAATGTATCTA	0.408													A|||	15	0.00299521	0.0015	0.0029	5008	,	,		16772	0.0		0.0099	False		,,,				2504	0.001				p.F4C		Atlas-SNP	.											.	AP1S3	10	.	0			c.T11G						PASS	.	A	CYS/PHE	10,3754		0,10,1872	60.0	55.0	56.0		11	5.8	1.0	2	dbSNP_132	56	105,8127		0,105,4011	yes	missense	AP1S3	NM_001039569.1	205	0,115,5883	CC,CA,AA		1.2755,0.2657,0.9587	probably-damaging	4/155	224642579	115,11881	1882	4116	5998	SO:0001583	missense	130340	exon2			AATATGAAATGTA	AF393369	CCDS42827.1	2q36.3	2008-02-05			ENSG00000152056	ENSG00000152056			18971	protein-coding gene	gene with protein product		615781					Standard	NR_110905		Approved		uc002vnn.3	Q96PC3	OTTHUMG00000133165	ENST00000446015.2:c.11T>G	2.37:g.224642579A>C	ENSP00000388738:p.Phe4Cys	67.0	0.0	0		73.0	31.0	0.424658	NM_001039569	B4DQZ1|Q8WTY1|Q96DD1	Missense_Mutation	SNP	ENST00000446015.2	37		11	0.005036630036630037	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	A	22.0	4.226842	0.79576	0.002657	0.012755	ENSG00000152056	ENST00000443700;ENST00000396654;ENST00000396653;ENST00000446015;ENST00000409375;ENST00000423110	.	.	.	5.81	5.81	0.92471	Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	D	0.82747	0.5104	M	0.93594	3.435	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.85130	0.996;0.997	D	0.88388	0.3006	9	0.87932	D	0	.	16.1652	0.81750	1.0:0.0:0.0:0.0	.	4;4	Q96PC3;Q96PC3-4	AP1S3_HUMAN;.	C	4	.	ENSP00000333888:F4C	F	-	2	0	AP1S3	224350823	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	8.940000	0.92958	2.230000	0.72887	0.528000	0.53228	TTC	A|0.993;C|0.007	0.007	strong		0.408	AP1S3-008	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000383293.1		
MAML2	84441	hgsc.bcm.edu	37	11	95826485	95826485	+	Missense_Mutation	SNP	T	T	C	rs61749253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:95826485T>C	ENST00000524717.1	-	2	1994	c.710A>G	c.(709-711)cAa>cGa	p.Q237R		NM_032427.1	NP_115803.1	Q8IZL2	MAML2_HUMAN	mastermind-like 2 (Drosophila)	237					gene expression (GO:0010467)|Notch signaling pathway (GO:0007219)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription initiation from RNA polymerase II promoter (GO:0006367)	Golgi apparatus (GO:0005794)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)		CRTC3/MAML2(26)|CRTC1/MAML2(516)	breast(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(8)|lung(12)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	43		Acute lymphoblastic leukemia(157;2.63e-05)|all_hematologic(158;0.00837)				CAGGGGTGCTTGGCTCATAGG	0.478			T	"""MECT1, CRTC3"""	salivary gland mucoepidermoid								T|||	27	0.00539137	0.0015	0.0043	5008	,	,		19485	0.0		0.0209	False		,,,				2504	0.001				p.Q237R		Atlas-SNP	.		Dom	yes		11	11q22-q23	84441	mastermind-like 2 (Drosophila)		E	.	MAML2	94	.	0			c.A710G						PASS	.	T	ARG/GLN	12,3878		0,12,1933	122.0	118.0	119.0		710	5.4	0.7	11	dbSNP_129	119	166,8120		2,162,3979	yes	missense	MAML2	NM_032427.1	43	2,174,5912	CC,CT,TT		2.0034,0.3085,1.4619	probably-damaging	237/1157	95826485	178,11998	1945	4143	6088	SO:0001583	missense	84441	exon2			GGTGCTTGGCTCA	AB058722	CCDS44714.1	11q	2008-02-05	2001-11-28		ENSG00000184384	ENSG00000184384			16259	protein-coding gene	gene with protein product		607537	"""mastermind (Drosophila)-like 2"""			12370315, 12386158	Standard	NM_032427		Approved	KIAA1819, MAM3	uc001pfw.1	Q8IZL2	OTTHUMG00000167677	ENST00000524717.1:c.710A>G	11.37:g.95826485T>C	ENSP00000434552:p.Gln237Arg	307.0	0.0	0		286.0	171.0	0.597902	NM_032427	A7MD26|Q6AI23|Q6Y3A3|Q8IUL3|Q96JK6	Missense_Mutation	SNP	ENST00000524717.1	37	CCDS44714.1	17	0.007783882783882784	0	0.0	2	0.0055248618784530384	0	0.0	15	0.01978891820580475	T	8.969	0.972374	0.18736	0.003085	0.020034	ENSG00000184384	ENST00000524717;ENST00000440572	T;T	0.47869	0.83;0.83	5.42	5.42	0.78866	.	0.109437	0.42682	D	0.000666	T	0.33847	0.0877	L	0.54323	1.7	0.31335	N	0.684305	D	0.58268	0.982	P	0.52554	0.702	T	0.49283	-0.8956	10	0.17832	T	0.49	-9.134	10.6675	0.45739	0.1428:0.0:0.0:0.8572	rs61749253	237	Q8IZL2	MAML2_HUMAN	R	237	ENSP00000434552:Q237R;ENSP00000412394:Q237R	ENSP00000412394:Q237R	Q	-	2	0	MAML2	95466133	1.000000	0.71417	0.692000	0.30179	0.890000	0.51754	4.231000	0.58639	2.050000	0.60909	0.374000	0.22700	CAA	T|0.990;C|0.010	0.010	strong		0.478	MAML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395540.1		
CEP68	23177	hgsc.bcm.edu	37	2	65299330	65299330	+	Missense_Mutation	SNP	T	T	A	rs141499084	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:65299330T>A	ENST00000377990.2	+	3	1303	c.1100T>A	c.(1099-1101)tTt>tAt	p.F367Y	CEP68_ENST00000537589.1_5'UTR|CEP68_ENST00000497039.1_3'UTR|CEP68_ENST00000260569.4_Missense_Mutation_p.F367Y|RAB1A_ENST00000494188.1_Intron|CEP68_ENST00000546106.1_Missense_Mutation_p.F367Y	NM_015147.2	NP_055962.2	Q76N32	CEP68_HUMAN	centrosomal protein 68kDa	367					centriole-centriole cohesion (GO:0010457)|centrosome organization (GO:0051297)|protein localization to organelle (GO:0033365)	centrosome (GO:0005813)|cytoplasm (GO:0005737)	protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|endometrium(6)|kidney(8)|large_intestine(5)|lung(8)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	32						GCCCTGCCATTTTCTGGGCCC	0.567													T|||	21	0.00419329	0.0	0.0086	5008	,	,		18965	0.0		0.0139	False		,,,				2504	0.001				p.F367Y		Atlas-SNP	.											.	CEP68	69	.	0			c.T1100A						PASS	.	T	TYR/PHE	16,4390	22.3+/-47.3	0,16,2187	90.0	95.0	93.0		1100	2.9	0.1	2	dbSNP_134	93	169,8431	76.9+/-139.5	0,169,4131	yes	missense	CEP68	NM_015147.2	22	0,185,6318	AA,AT,TT		1.9651,0.3631,1.4224	possibly-damaging	367/758	65299330	185,12821	2203	4300	6503	SO:0001583	missense	23177	exon3			TGCCATTTTCTGG	BC004873	CCDS1880.2	2p14	2014-02-20	2005-12-01	2005-12-01	ENSG00000011523	ENSG00000011523			29076	protein-coding gene	gene with protein product			"""KIAA0582"""	KIAA0582		9628581, 9847074, 14654843	Standard	NM_015147		Approved		uc002sdl.4	Q76N32	OTTHUMG00000129538	ENST00000377990.2:c.1100T>A	2.37:g.65299330T>A	ENSP00000367229:p.Phe367Tyr	97.0	0.0	0		77.0	39.0	0.506494	NM_015147	B4DRQ1|D6W5F1|D6W5F2|O60326|Q9BQ18|Q9UDM9	Missense_Mutation	SNP	ENST00000377990.2	37	CCDS1880.2	17	0.007783882783882784	0	0.0	6	0.016574585635359115	0	0.0	11	0.014511873350923483	T	23.4	4.415682	0.83449	0.003631	0.019651	ENSG00000011523	ENST00000377990;ENST00000546106;ENST00000260569;ENST00000545501	T;T;T	0.16196	2.37;2.36;2.37	5.66	2.91	0.33838	.	0.460130	0.22130	N	0.064202	T	0.16854	0.0405	M	0.63428	1.95	0.09310	N	1	D;D;D;P;D	0.71674	0.995;0.987;0.983;0.933;0.998	P;P;P;P;P	0.62649	0.836;0.775;0.67;0.597;0.905	T	0.01863	-1.1258	10	0.62326	D	0.03	-11.404	6.9502	0.24540	0.0:0.0893:0.1532:0.7575	.	355;367;367;367;367	F5H3N9;F5H2Y2;Q76N32;Q76N32-2;Q05C09	.;.;CEP68_HUMAN;.;.	Y	367;367;367;355	ENSP00000367229:F367Y;ENSP00000438306:F367Y;ENSP00000260569:F367Y	ENSP00000260569:F367Y	F	+	2	0	CEP68	65152834	0.001000	0.12720	0.112000	0.21494	0.810000	0.45777	0.594000	0.24014	0.951000	0.37770	0.402000	0.26972	TTT	T|0.987;A|0.013	0.013	strong		0.567	CEP68-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251727.2	NM_015147	
CEP97	79598	hgsc.bcm.edu	37	3	101477214	101477214	+	Silent	SNP	C	C	A	rs368609945		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:101477214C>A	ENST00000341893.3	+	9	2516	c.1764C>A	c.(1762-1764)atC>atA	p.I588I	CEP97_ENST00000327230.4_Silent_p.I588I|CEP97_ENST00000494050.1_Silent_p.I529I			Q8IW35	CEP97_HUMAN	centrosomal protein 97kDa	588	CCP110-binding.				cell projection organization (GO:0030030)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|microtubule organizing center (GO:0005815)|protein complex (GO:0043234)				cervix(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	29						GTTACGAAATCCGGCTACGCA	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		21512	0.0		0.0	False		,,,				2504	0.001				p.I588I		Atlas-SNP	.											.	CEP97	122	.	0			c.C1764A						PASS	.	C		0,4406		0,0,2203	62.0	66.0	65.0		1764	-0.3	1.0	3		65	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CEP97	NM_024548.2		0,1,6502	AA,AC,CC		0.0116,0.0,0.0077		588/866	101477214	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	79598	exon9			CGAAATCCGGCTA	AL833269	CCDS2944.1	3q12.3	2014-02-20	2008-01-08	2008-01-08	ENSG00000182504	ENSG00000182504			26244	protein-coding gene	gene with protein product		615864	"""leucine-rich repeats and IQ motif containing 2"""	LRRIQ2		17719545, 18068367	Standard	NM_024548		Approved	FLJ23047	uc003dvk.1	Q8IW35	OTTHUMG00000159162	ENST00000341893.3:c.1764C>A	3.37:g.101477214C>A		54.0	0.0	0		65.0	21.0	0.323077	NM_024548	B5MDY8|Q8NA71|Q9H5T9	Silent	SNP	ENST00000341893.3	37	CCDS2944.1																																																																																			.	.	weak		0.463	CEP97-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353597.2	NM_024548	
SPATA6	54558	hgsc.bcm.edu	37	1	48825355	48825355	+	Missense_Mutation	SNP	G	G	A	rs1338314	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:48825355G>A	ENST00000371847.3	-	10	1161	c.997C>T	c.(997-999)Cgg>Tgg	p.R333W	SPATA6_ENST00000371843.3_Missense_Mutation_p.R333W|SPATA6_ENST00000396199.3_Missense_Mutation_p.R261W	NM_019073.2	NP_061946.1	Q9NWH7	SPAT6_HUMAN	spermatogenesis associated 6	333			R -> W (in dbSNP:rs1338314).		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)				breast(1)|endometrium(2)|large_intestine(6)|lung(7)|ovary(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	21						GCTGAATGCCGGGGCTTACTA	0.458													G|||	70	0.0139776	0.0008	0.0331	5008	,	,		14053	0.0		0.0408	False		,,,				2504	0.0051				p.R333W		Atlas-SNP	.											.	SPATA6	45	.	0			c.C997T						PASS	.	G	TRP/ARG	53,4353	52.3+/-87.9	0,53,2150	102.0	97.0	99.0		997	4.1	1.0	1	dbSNP_88	99	307,8293	109.8+/-170.3	4,299,3997	yes	missense	SPATA6	NM_019073.2	101	4,352,6147	AA,AG,GG		3.5698,1.2029,2.768	possibly-damaging	333/489	48825355	360,12646	2203	4300	6503	SO:0001583	missense	54558	exon10			AATGCCGGGGCTT	AK000869	CCDS551.1, CCDS65535.1, CCDS72787.1	1p32.3	2012-03-15			ENSG00000132122	ENSG00000132122			18309	protein-coding gene	gene with protein product	"""spermatogenesis-related factor-1"""	613947					Standard	XM_005270948		Approved	SRF1, FLJ10007, SRF-1	uc001crr.2	Q9NWH7	OTTHUMG00000007794	ENST00000371847.3:c.997C>T	1.37:g.48825355G>A	ENSP00000360913:p.Arg333Trp	74.0	0.0	0		54.0	27.0	0.5	NM_019073	Q5T3N7|Q8WUE6	Missense_Mutation	SNP	ENST00000371847.3	37	CCDS551.1	38	0.0173992673992674	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	25	0.032981530343007916	G	10.35	1.324952	0.24080	0.012029	0.035698	ENSG00000132122	ENST00000371847;ENST00000371843;ENST00000396199;ENST00000371841	T;T;T;T	0.46063	2.71;2.71;2.71;0.88	4.99	4.05	0.47172	.	1.098750	0.06782	N	0.785446	T	0.06462	0.0166	N	0.08118	0	0.19945	N	0.999948	P;P;P	0.44281	0.61;0.831;0.831	B;B;B	0.39152	0.292;0.219;0.219	T	0.06092	-1.0846	10	0.51188	T	0.08	.	8.7171	0.34419	0.0803:0.2907:0.6291:0.0	rs1338314;rs17429088;rs52805877;rs59077352;rs1338314	261;333;333	B4DX17;Q9NWH7-2;Q9NWH7	.;.;SPAT6_HUMAN	W	333;333;261;174	ENSP00000360913:R333W;ENSP00000360909:R333W;ENSP00000379502:R261W;ENSP00000360907:R174W	ENSP00000360907:R174W	R	-	1	2	SPATA6	48597942	0.971000	0.33674	1.000000	0.80357	0.015000	0.08874	1.086000	0.30853	1.278000	0.44430	0.655000	0.94253	CGG	G|0.975;A|0.025	0.025	strong		0.458	SPATA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000021347.1	NM_019073	
ATL2	64225	hgsc.bcm.edu	37	2	38537579	38537579	+	Missense_Mutation	SNP	T	T	C	rs34873284	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:38537579T>C	ENST00000378954.4	-	8	816	c.815A>G	c.(814-816)aAt>aGt	p.N272S	ATL2_ENST00000402054.1_Missense_Mutation_p.N101S|ATL2_ENST00000419554.2_Missense_Mutation_p.N272S|ATL2_ENST00000546051.1_Missense_Mutation_p.N101S|ATL2_ENST00000539122.1_Missense_Mutation_p.N101S|ATL2_ENST00000332337.4_Missense_Mutation_p.N254S|ATL2_ENST00000406122.1_Missense_Mutation_p.N101S|ATL2_ENST00000452935.2_Missense_Mutation_p.N254S	NM_001135673.1|NM_022374.2	NP_001129145.1|NP_071769.2	Q8NHH9	ATLA2_HUMAN	atlastin GTPase 2	272	GB1/RHD3-type G.		N -> S (in dbSNP:rs34873284).		endoplasmic reticulum organization (GO:0007029)|Golgi organization (GO:0007030)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	22						TTCATGTTGATTTTGTTTTAC	0.383													T|||	72	0.014377	0.0045	0.0216	5008	,	,		17843	0.0		0.0398	False		,,,				2504	0.0112				p.N272S		Atlas-SNP	.											.	ATL2	49	.	0			c.A815G						PASS	.	T	SER/ASN,SER/ASN	48,4358	48.9+/-83.8	1,46,2156	133.0	118.0	123.0		815,815	5.1	1.0	2	dbSNP_126	123	420,8180	130.8+/-188.7	10,400,3890	yes	missense,missense	ATL2	NM_001135673.1,NM_022374.2	46,46	11,446,6046	CC,CT,TT		4.8837,1.0894,3.5983	benign,benign	272/584,272/580	38537579	468,12538	2203	4300	6503	SO:0001583	missense	64225	exon8			TGTTGATTTTGTT		CCDS1795.1, CCDS46260.1	2p22.3	2008-09-17	2008-09-17	2008-09-17	ENSG00000119787	ENSG00000119787			24047	protein-coding gene	gene with protein product		609368	"""ADP-ribosylation factor-like 6 interacting protein 2"""	ARL6IP2		10508919, 18270207	Standard	NM_022374		Approved		uc002rqq.3	Q8NHH9	OTTHUMG00000102074	ENST00000378954.4:c.815A>G	2.37:g.38537579T>C	ENSP00000368237:p.Asn272Ser	93.0	0.0	0		105.0	43.0	0.409524	NM_001135673	B7Z1X2|B7Z7X8|Q4ZG30|Q7Z630|Q8NHH8|Q9H5M7	Missense_Mutation	SNP	ENST00000378954.4	37	CCDS46260.1	40|40	0.018315018315018316|0.018315018315018316	4|4	0.008130081300813009|0.008130081300813009	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	31|31	0.040897097625329816|0.040897097625329816	T|T	15.82|15.82	2.945674|2.945674	0.53079|0.53079	0.010894|0.010894	0.048837|0.048837	ENSG00000119787|ENSG00000119787	ENST00000443098|ENST00000378954;ENST00000406122;ENST00000402054;ENST00000539122;ENST00000332337;ENST00000419554;ENST00000452935;ENST00000546051;ENST00000449130	.|T;T;T;T;T;T;T;T;T	.|0.74421	.|-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84;-0.84	5.11|5.11	5.11|5.11	0.69529|0.69529	.|Guanylate-binding protein, N-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.28764|0.28764	0.0713|0.0713	L|L	0.47078|0.47078	1.49|1.49	0.80722|0.80722	D|D	1|1	.|B;B;B;B;B	.|0.17268	.|0.021;0.001;0.003;0.005;0.001	.|B;B;B;B;B	.|0.11329	.|0.006;0.001;0.001;0.002;0.002	T|T	0.53542|0.53542	-0.8424|-0.8424	5|10	.|0.44086	.|T	.|0.13	-21.5939|-21.5939	14.0983|14.0983	0.65037|0.65037	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	rs34873284;rs61754250|rs34873284;rs61754250	.|101;254;254;272;272	.|B5MCN0;B7Z7X8;Q8NHH9-4;Q8NHH9-2;Q8NHH9	.|.;.;.;.;ATLA2_HUMAN	V|S	191|272;101;101;101;254;272;254;101;90	.|ENSP00000368237:N272S;ENSP00000385446:N101S;ENSP00000384062:N101S;ENSP00000446192:N101S;ENSP00000333393:N254S;ENSP00000415336:N272S;ENSP00000390743:N254S;ENSP00000438938:N101S;ENSP00000409811:N90S	.|ENSP00000333393:N254S	I|N	-|-	1|2	0|0	ATL2|ATL2	38391083|38391083	1.000000|1.000000	0.71417|0.71417	0.973000|0.973000	0.42090|0.42090	0.982000|0.982000	0.71751|0.71751	6.134000|6.134000	0.71689|0.71689	1.917000|1.917000	0.55516|0.55516	0.455000|0.455000	0.32223|0.32223	ATC|AAT	T|0.967;C|0.033	0.033	strong		0.383	ATL2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000219886.2	NM_022374	
KTN1	3895	hgsc.bcm.edu	37	14	56105908	56105908	+	Silent	SNP	C	C	T	rs80214241	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:56105908C>T	ENST00000395314.3	+	13	1859	c.1791C>T	c.(1789-1791)tcC>tcT	p.S597S	KTN1_ENST00000395309.3_Silent_p.S597S|KTN1_ENST00000416613.1_Silent_p.S597S|KTN1_ENST00000413890.2_Silent_p.S597S|KTN1_ENST00000395311.1_Silent_p.S597S|KTN1_ENST00000395308.1_Silent_p.S597S|KTN1_ENST00000438792.2_Silent_p.S597S	NM_001079521.1	NP_001072989.1	Q86UP2	KTN1_HUMAN	kinectin 1 (kinesin receptor)	597					microtubule-based movement (GO:0007018)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(4)|central_nervous_system(1)|large_intestine(8)|lung(1)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	19						CTTAGACCTCCGCTTCAGTTC	0.313			T	RET	papillary thryoid								C|||	73	0.0145767	0.0219	0.0014	5008	,	,		17209	0.003		0.002	False		,,,				2504	0.0389				p.S597S		Atlas-SNP	.		Dom	yes		14	14q22.1	3895	kinectin 1 (kinesin receptor)		E	.	KTN1	147	.	0			c.C1791T						PASS	.	C	,,,	73,4331	65.8+/-103.3	2,69,2131	91.0	90.0	90.0		1791,1791,1791,1791	-6.3	0.9	14	dbSNP_132	90	31,8567	22.2+/-67.0	0,31,4268	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	KTN1	NM_001079521.1,NM_001079522.1,NM_004986.2,NM_182926.2	,,,	2,100,6399	TT,TC,CC		0.3605,1.6576,0.7999	,,,	597/1358,597/1307,597/1301,597/1358	56105908	104,12898	2202	4299	6501	SO:0001819	synonymous_variant	3895	exon13			GACCTCCGCTTCA		CCDS41957.1, CCDS41958.1, CCDS41959.1	14q22.1	2008-05-02			ENSG00000126777	ENSG00000126777			6467	protein-coding gene	gene with protein product		600381				9605849	Standard	NM_001079521		Approved	KIAA0004, CG1	uc001xcc.3	Q86UP2	OTTHUMG00000140312	ENST00000395314.3:c.1791C>T	14.37:g.56105908C>T		184.0	0.0	0		174.0	78.0	0.448276	NM_004986	B4DZ88|Q13999|Q14707|Q15387|Q17RZ5|Q5GGW3|Q86W57	Silent	SNP	ENST00000395314.3	37	CCDS41957.1																																																																																			C|0.991;T|0.009	0.009	strong		0.313	KTN1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276912.2		
PLA2G4A	5321	hgsc.bcm.edu	37	1	186946869	186946869	+	Missense_Mutation	SNP	A	A	G	rs28395831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186946869A>G	ENST00000367466.3	+	16	2061	c.1909A>G	c.(1909-1911)Atc>Gtc	p.I637V	PLA2G4A_ENST00000442353.2_Missense_Mutation_p.I577V	NM_024420.2	NP_077734	P47712	PA24A_HUMAN	phospholipase A2, group IVA (cytosolic, calcium-dependent)	637	PLA2c. {ECO:0000255|PROSITE- ProRule:PRU00555}.		I -> V (in dbSNP:rs28395831).		arachidonic acid metabolic process (GO:0019369)|arachidonic acid secretion (GO:0050482)|blood coagulation (GO:0007596)|cardiolipin acyl-chain remodeling (GO:0035965)|cellular response to antibiotic (GO:0071236)|glycerophospholipid biosynthetic process (GO:0046474)|icosanoid biosynthetic process (GO:0046456)|icosanoid metabolic process (GO:0006690)|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)|platelet activating factor biosynthetic process (GO:0006663)|platelet activation (GO:0030168)|regulation of cell proliferation (GO:0042127)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|calcium-dependent phospholipid binding (GO:0005544)|lysophospholipase activity (GO:0004622)|phospholipase A2 activity (GO:0004623)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(9)|lung(22)|ovary(1)|prostate(3)|skin(4)|stomach(1)	53					Aldesleukin(DB00041)|Carbachol(DB00411)|Carbenicillin(DB00578)|Epirubicin(DB00445)|Fluocinolone Acetonide(DB00591)|Fluticasone Propionate(DB00588)|Niflumic Acid(DB04552)|Orlistat(DB01083)|Quinacrine(DB01103)|Streptokinase(DB00086)|Suramin(DB04786)	TTGCCCAACCATCATCCACTT	0.418													A|||	33	0.00658946	0.0015	0.0014	5008	,	,		19824	0.0		0.0189	False		,,,				2504	0.0112				p.I637V		Atlas-SNP	.											.	PLA2G4A	125	.	0			c.A1909G						PASS	.	A	VAL/ILE	6,4400	11.4+/-27.6	0,6,2197	121.0	112.0	115.0		1909	3.7	0.6	1	dbSNP_126	115	94,8506	53.6+/-114.3	0,94,4206	yes	missense	PLA2G4A	NM_024420.2	29	0,100,6403	GG,GA,AA		1.093,0.1362,0.7689	benign	637/750	186946869	100,12906	2203	4300	6503	SO:0001583	missense	5321	exon16			CCAACCATCATCC	M72393	CCDS1372.1	1q25	2014-09-17			ENSG00000116711	ENSG00000116711	3.1.1.4, 3.1.1.5		9035	protein-coding gene	gene with protein product		600522		PLA2G4		8175726	Standard	NM_024420		Approved	cPLA2-alpha	uc001gsc.3	P47712	OTTHUMG00000035512	ENST00000367466.3:c.1909A>G	1.37:g.186946869A>G	ENSP00000356436:p.Ile637Val	248.0	0.0	0		219.0	97.0	0.442922	NM_024420	B1AKG4|Q29R80	Missense_Mutation	SNP	ENST00000367466.3	37	CCDS1372.1	15	0.006868131868131868	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	13	0.017150395778364115	A	7.587	0.670036	0.14776	0.001362	0.01093	ENSG00000116711	ENST00000367466;ENST00000442353	T;T	0.03124	4.04;4.04	5.98	3.68	0.42216	Acyl transferase/acyl hydrolase/lysophospholipase (1);Lysophospholipase, catalytic domain (3);	0.250277	0.47093	N	0.000250	T	0.00784	0.0026	N	0.03177	-0.4	0.36550	D	0.871822	B;B	0.11235	0.004;0.003	B;B	0.21708	0.036;0.026	T	0.42849	-0.9427	10	0.02654	T	1	-15.1412	8.1494	0.31132	0.7827:0.0:0.2173:0.0	rs28395831;rs45544833	577;637	E7EU42;P47712	.;PA24A_HUMAN	V	637;577	ENSP00000356436:I637V;ENSP00000406892:I577V	ENSP00000356436:I637V	I	+	1	0	PLA2G4A	185213492	0.996000	0.38824	0.615000	0.29064	0.985000	0.73830	3.247000	0.51422	0.516000	0.28340	0.533000	0.62120	ATC	A|0.992;G|0.008	0.008	strong		0.418	PLA2G4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086236.1	NM_024420	
FOXK2	3607	hgsc.bcm.edu	37	17	80545021	80545021	+	Silent	SNP	G	G	A	rs139592674		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80545021G>A	ENST00000335255.5	+	8	1833	c.1659G>A	c.(1657-1659)ccG>ccA	p.P553P	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	553					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			AGACCACCCCGGTCCAGACGG	0.532																																					p.P553P		Atlas-SNP	.											.	FOXK2	46	.	0			c.G1659A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	100.0	83.0	89.0		1659	-4.4	0.7	17	dbSNP_134	89	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	FOXK2	NM_004514.3		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		553/661	80545021	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3607	exon8			CACCCCGGTCCAG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1659G>A	17.37:g.80545021G>A		126.0	0.0	0		125.0	69.0	0.552	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			G|1.000;A|0.000	0.000	weak		0.532	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
LRPAP1	4043	hgsc.bcm.edu	37	4	3534042	3534042	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3534042C>A	ENST00000500728.2	-	1	244	c.98G>T	c.(97-99)gGc>gTc	p.G33V	LRPAP1_ENST00000296325.5_5'Flank	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	33					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)		CGAGTACTTGCCGCCGTGGCT	0.672																																					p.G33V		Atlas-SNP	.											.	LRPAP1	29	.	0			c.G98T						PASS	.						20.0	20.0	20.0					4																	3534042		2170	4270	6440	SO:0001583	missense	4043	exon1			TACTTGCCGCCGT		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.98G>T	4.37:g.3534042C>A	ENSP00000421922:p.Gly33Val	65.0	0.0	0		130.0	60.0	0.461538	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Missense_Mutation	SNP	ENST00000500728.2	37	CCDS3371.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740844	0.89573	.	.	ENSG00000163956	ENST00000500728	T	0.46451	0.87	3.8	3.8	0.43715	Alpha-2-macroglobulin receptor-associated protein, domain 1 (1);	0.120269	0.56097	D	0.000032	T	0.58395	0.2119	M	0.68317	2.08	0.80722	D	1	D	0.76494	0.999	D	0.71414	0.973	T	0.60459	-0.7259	10	0.52906	T	0.07	-30.362	11.0418	0.47835	0.0:1.0:0.0:0.0	.	33	P30533	AMRP_HUMAN	V	33	ENSP00000421922:G33V	ENSP00000421922:G33V	G	-	2	0	LRPAP1	3503840	0.998000	0.40836	1.000000	0.80357	0.924000	0.55760	4.856000	0.62932	1.937000	0.56155	0.591000	0.81541	GGC	.	.	none		0.672	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
C10orf120	399814	hgsc.bcm.edu	37	10	124457480	124457480	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124457480A>G	ENST00000329446.4	-	3	808	c.777T>C	c.(775-777)caT>caC	p.H259H		NM_001010912.1	NP_001010912.1	Q5SQS8	CJ120_HUMAN	chromosome 10 open reading frame 120	259										endometrium(1)|kidney(1)|large_intestine(6)|lung(9)|skin(2)|stomach(1)|urinary_tract(1)	21		all_neural(114;0.169)|Glioma(114;0.222)				GATCATTTCCATGGTATGTTA	0.388																																					p.H259H		Atlas-SNP	.											.	C10orf120	55	.	0			c.T777C						PASS	.						140.0	136.0	137.0					10																	124457480		2203	4300	6503	SO:0001819	synonymous_variant	399814	exon3			ATTTCCATGGTAT		CCDS31302.1	10q26.13	2012-06-12			ENSG00000183559	ENSG00000183559			25707	protein-coding gene	gene with protein product							Standard	NM_001010912		Approved	bA318C4.1	uc001lgn.3	Q5SQS8	OTTHUMG00000019187	ENST00000329446.4:c.777T>C	10.37:g.124457480A>G		132.0	0.0	0		124.0	55.0	0.443548	NM_001010912	B2RU17	Silent	SNP	ENST00000329446.4	37	CCDS31302.1																																																																																			.	.	none		0.388	C10orf120-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050803.1	NM_001010912	
MUC4	4585	hgsc.bcm.edu	37	3	195506579	195506579	+	Missense_Mutation	SNP	T	T	C	rs200317787|rs71291866	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506579T>C	ENST00000463781.3	-	2	12331	c.11872A>G	c.(11872-11874)Act>Gct	p.T3958A	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T3958A|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACTGAGGAAGTGTCGGTGACA	0.597																																					p.T3958A		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.A11872G						scavenged	.						17.0	11.0	13.0					3																	195506579		678	1521	2199	SO:0001583	missense	4585	exon2			AGGAAGTGTCGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11872A>G	3.37:g.195506579T>C	ENSP00000417498:p.Thr3958Ala	34.0	2.0	0.0588235		63.0	7.0	0.111111	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.312	-0.967054	0.02232	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33438	1.41;1.5	.	.	.	.	.	.	.	.	T	0.13586	0.0329	N	0.19112	0.55	0.09310	N	1	B	0.17465	0.022	B	0.15870	0.014	T	0.20240	-1.0281	7	.	.	.	.	4.0904	0.09967	0.0:1.0E-4:0.3498:0.6501	.	3830	E7ESK3	.	A	3958	ENSP00000417498:T3958A;ENSP00000420243:T3958A	.	T	-	1	0	MUC4	196991358	0.000000	0.05858	0.003000	0.11579	0.003000	0.03518	-0.372000	0.07504	-2.418000	0.00566	-2.418000	0.00219	ACT	CGTC|0.500;TGTT|0.500	.	alt		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
ASXL2	55252	hgsc.bcm.edu	37	2	25991689	25991689	+	Missense_Mutation	SNP	T	T	C	rs147191545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:25991689T>C	ENST00000435504.4	-	7	846	c.553A>G	c.(553-555)Agc>Ggc	p.S185G	ASXL2_ENST00000336112.4_Missense_Mutation_p.S157G|ASXL2_ENST00000272341.4_5'UTR|ASXL2_ENST00000404843.1_5'UTR|ASXL2_ENST00000497092.1_5'UTR			Q76L83	ASXL2_HUMAN	additional sex combs like transcriptional regulator 2	185	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)					ATGGATATGCTTGGCCTGCAT	0.438													T|||	3	0.000599042	0.0	0.0	5008	,	,		13298	0.0		0.003	False		,,,				2504	0.0				p.S185G		Atlas-SNP	.											.	ASXL2	217	.	0			c.A553G						PASS	.	T	GLY/SER	1,4041		0,1,2020	170.0	173.0	172.0		553	3.7	0.8	2	dbSNP_134	172	29,8385		0,29,4178	yes	missense	ASXL2	NM_018263.4	56	0,30,6198	CC,CT,TT		0.3447,0.0247,0.2408	probably-damaging	185/1436	25991689	30,12426	2021	4207	6228	SO:0001583	missense	55252	exon6			ATATGCTTGGCCT			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.553A>G	2.37:g.25991689T>C	ENSP00000391447:p.Ser185Gly	137.0	0.0	0		121.0	52.0	0.429752	NM_018263	Q53TC9|Q5H9U4|Q76L81|Q86XM1|Q9C0H8|Q9NV67	Missense_Mutation	SNP	ENST00000435504.4	37		3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	5.976	0.364036	0.11296	2.47E-4	0.003447	ENSG00000143970	ENST00000435504;ENST00000336112	T;T	0.16897	2.31;2.31	6.03	3.67	0.42095	.	0.312422	0.39544	N	0.001327	T	0.07908	0.0198	N	0.04508	-0.205	0.80722	D	1	B	0.12013	0.005	B	0.12156	0.007	T	0.16217	-1.0410	10	0.87932	D	0	-5.0436	7.3591	0.26735	0.0:0.2424:0.0:0.7576	.	185	Q76L83	ASXL2_HUMAN	G	185;157	ENSP00000391447:S185G;ENSP00000337250:S157G	ENSP00000337250:S157G	S	-	1	0	ASXL2	25845193	0.966000	0.33281	0.772000	0.31596	0.755000	0.42902	1.653000	0.37323	0.530000	0.28619	0.533000	0.62120	AGC	T|0.998;C|0.002	0.002	strong		0.438	ASXL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000325593.3	NM_018263	
BRCA2	675	hgsc.bcm.edu	37	13	32968840	32968840	+	Missense_Mutation	SNP	G	G	A	rs80359194		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32968840G>A	ENST00000380152.3	+	25	9504	c.9271G>A	c.(9271-9273)Gtc>Atc	p.V3091I	BRCA2_ENST00000544455.1_Missense_Mutation_p.V3091I			P51587	BRCA2_HUMAN	breast cancer 2, early onset	3091					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TGCCCCTTTCGTCTATTTGTC	0.323			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.V3091I	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.G9271A						PASS	.						60.0	60.0	60.0					13																	32968840		2203	4300	6503	SO:0001583	missense	675	exon25	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	CCTTTCGTCTATT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.9271G>A	13.37:g.32968840G>A	ENSP00000369497:p.Val3091Ile	73.0	0.0	0		67.0	40.0	0.597015	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	G	7.433	0.639093	0.14386	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	D;D	0.85702	-2.02;-2.02	5.9	4.16	0.48862	Nucleic acid-binding, OB-fold-like (1);BRCA2, oligonucleotide/oligosaccharide-binding 3 (1);	0.182235	0.48767	N	0.000170	D	0.84529	0.5492	M	0.70903	2.155	0.34869	D	0.74338	B	0.24043	0.096	B	0.26202	0.067	T	0.83263	-0.0047	10	0.52906	T	0.07	.	13.938	0.64036	0.1334:0.0:0.8666:0.0	.	3091	P51587	BRCA2_HUMAN	I	3091	ENSP00000369497:V3091I;ENSP00000439902:V3091I	ENSP00000369497:V3091I	V	+	1	0	BRCA2	31866840	1.000000	0.71417	0.998000	0.56505	0.025000	0.11179	2.306000	0.43673	0.409000	0.25649	-1.119000	0.02030	GTC	.	.	weak		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
ZNF781	163115	hgsc.bcm.edu	37	19	38160742	38160742	+	Missense_Mutation	SNP	T	T	C	rs149500211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:38160742T>C	ENST00000590008.1	-	5	1160	c.308A>G	c.(307-309)cAt>cGt	p.H103R	ZNF781_ENST00000593040.1_5'Flank|ZFP30_ENST00000586732.1_Intron|ZNF781_ENST00000358582.4_Missense_Mutation_p.H103R			Q8N8C0	ZN781_HUMAN	zinc finger protein 781	103					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(2)|large_intestine(5)|lung(11)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	24						TCGAATAAGATGTGCACTCCG	0.368																																					p.H103R		Atlas-SNP	.											.	ZNF781	66	.	0			c.A308G						PASS	.	T	ARG/HIS	3,4403	6.2+/-15.9	0,3,2200	122.0	119.0	120.0		308	1.2	0.0	19	dbSNP_134	120	7,8593	7.1+/-27.0	0,7,4293	yes	missense	ZNF781	NM_152605.3	29	0,10,6493	CC,CT,TT		0.0814,0.0681,0.0769	possibly-damaging	103/328	38160742	10,12996	2203	4300	6503	SO:0001583	missense	163115	exon4			ATAAGATGTGCAC	AK097019	CCDS12507.1	19q13.12	2013-01-08				ENSG00000196381		"""Zinc fingers, C2H2-type"""	26745	protein-coding gene	gene with protein product							Standard	NM_152605		Approved	FLJ37549	uc002ogy.2	Q8N8C0		ENST00000590008.1:c.308A>G	19.37:g.38160742T>C	ENSP00000466370:p.His103Arg	46.0	0.0	0		44.0	29.0	0.659091	NM_152605	Q2VPJ8	Missense_Mutation	SNP	ENST00000590008.1	37	CCDS12507.1	.	.	.	.	.	.	.	.	.	.	T	5.903	0.350770	0.11182	6.81E-4	8.14E-4	ENSG00000196381	ENST00000358582;ENST00000545586	T	0.18174	2.23	2.23	1.16	0.20824	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.13030	0.0316	N	0.25789	0.76	0.09310	N	1	B	0.29862	0.259	B	0.37601	0.254	T	0.37314	-0.9711	9	0.35671	T	0.21	.	6.1414	0.20261	0.0:0.1428:0.0:0.8572	.	103	Q8N8C0	ZN781_HUMAN	R	103	ENSP00000351391:H103R	ENSP00000351391:H103R	H	-	2	0	ZNF781	42852582	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.032000	0.12266	0.114000	0.18032	-0.410000	0.06199	CAT	T|0.999;C|0.001	0.001	strong		0.368	ZNF781-002	KNOWN	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000459495.2	NM_152605	
OPLAH	26873	hgsc.bcm.edu	37	8	145108191	145108191	+	Missense_Mutation	SNP	T	T	C	rs200702041	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145108191T>C	ENST00000426825.1	-	20	2873	c.2792A>G	c.(2791-2793)cAg>cGg	p.Q931R	CTD-3065J16.6_ENST00000528912.1_RNA|CTD-3065J16.6_ENST00000561181.1_RNA|OPLAH_ENST00000534424.1_5'UTR	NM_017570.3	NP_060040.1	O14841	OPLA_HUMAN	5-oxoprolinase (ATP-hydrolysing)	931					glutathione biosynthetic process (GO:0006750)|glutathione derivative biosynthetic process (GO:1901687)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	5-oxoprolinase (ATP-hydrolyzing) activity (GO:0017168)|ATP binding (GO:0005524)			breast(1)|central_nervous_system(1)|endometrium(1)|lung(13)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	20	all_cancers(97;1.06e-10)|all_epithelial(106;1.5e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;2.24e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			GATGCCCTTCTGGTTGGCTGC	0.657													T|||	2	0.000399361	0.0	0.0	5008	,	,		19625	0.0		0.002	False		,,,				2504	0.0				p.Q931R		Atlas-SNP	.											.	OPLAH	78	.	0			c.A2792G						PASS	.	T	ARG/GLN	2,4156		0,2,2077	50.0	56.0	54.0		2792	4.6	1.0	8		54	46,8358		0,46,4156	yes	missense	OPLAH	NM_017570.3	43	0,48,6233	CC,CT,TT		0.5474,0.0481,0.3821	benign	931/1289	145108191	48,12514	2079	4202	6281	SO:0001583	missense	26873	exon20			CCCTTCTGGTTGG	AF024672, AB122018	CCDS75802.1	8q24.3	2010-11-23			ENSG00000178814	ENSG00000178814	3.5.2.9		8149	protein-coding gene	gene with protein product		614243				14993790	Standard	NM_017570		Approved	OPLA, 5-Opase	uc003zar.3	O14841		ENST00000426825.1:c.2792A>G	8.37:g.145108191T>C	ENSP00000475943:p.Gln931Arg	124.0	0.0	0		152.0	63.0	0.414474	NM_017570	A5PKY8|Q75W65|Q9Y4Q0	Missense_Mutation	SNP	ENST00000426825.1	37		.	.	.	.	.	.	.	.	.	.	T	15.78	2.934711	0.52866	4.81E-4	0.005474	ENSG00000178814	ENST00000426825	.	.	.	4.56	4.56	0.56223	.	0.000000	0.85682	D	0.000000	T	0.40815	0.1132	.	.	.	0.42144	D	0.991525	B	0.21225	0.053	B	0.25759	0.063	T	0.57039	-0.7879	7	0.42905	T	0.14	.	11.8502	0.52407	0.0:0.0:0.0:1.0	.	931	O14841	OPLA_HUMAN	R	931	.	ENSP00000412071:Q931R	Q	-	2	0	OPLAH	145180179	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	2.215000	0.42862	1.681000	0.50988	0.368000	0.22195	CAG	T|0.996;C|0.004	0.004	weak		0.657	OPLAH-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017570	
OR5H14	403273	hgsc.bcm.edu	37	3	97869072	97869072	+	Silent	SNP	A	A	C	rs558065491		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:97869072A>C	ENST00000437310.1	+	1	903	c.843A>C	c.(841-843)atA>atC	p.I281I	RP11-343D2.11_ENST00000508964.1_RNA	NM_001005514.1	NP_001005514.1	A6NHG9	O5H14_HUMAN	olfactory receptor, family 5, subfamily H, member 14	281						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						ACACTGTCATAGTTCCTTTAT	0.378																																					p.I281I		Atlas-SNP	.											OR5H14,colon,carcinoma,+1,1	OR5H14	56	1	0			c.A843C						PASS	.						50.0	48.0	48.0					3																	97869072		2203	4297	6500	SO:0001819	synonymous_variant	403273	exon1			TGTCATAGTTCCT		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.843A>C	3.37:g.97869072A>C		276.0	0.0	0		228.0	106.0	0.464912	NM_001005514	B9EH15	Silent	SNP	ENST00000437310.1	37	CCDS33798.1																																																																																			.	.	none		0.378	OR5H14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359112.1		
PON1	5444	hgsc.bcm.edu	37	7	94940880	94940880	+	Missense_Mutation	SNP	A	A	C	rs144390653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:94940880A>C	ENST00000222381.3	-	5	611	c.380T>G	c.(379-381)aTg>aGg	p.M127R	PON1_ENST00000542556.1_Missense_Mutation_p.M127R	NM_000446.5	NP_000437.3	P27169	PON1_HUMAN	paraoxonase 1	127					aromatic compound catabolic process (GO:0019439)|carboxylic acid catabolic process (GO:0046395)|dephosphorylation (GO:0016311)|organophosphate catabolic process (GO:0046434)|phosphatidylcholine metabolic process (GO:0046470)|positive regulation of binding (GO:0051099)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of transporter activity (GO:0032411)|response to external stimulus (GO:0009605)|response to toxic substance (GO:0009636)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|high-density lipoprotein particle (GO:0034364)|intracellular membrane-bounded organelle (GO:0043231)|spherical high-density lipoprotein particle (GO:0034366)	aryldialkylphosphatase activity (GO:0004063)|arylesterase activity (GO:0004064)|calcium ion binding (GO:0005509)|phospholipid binding (GO:0005543)|protein homodimerization activity (GO:0042803)	p.M127R(1)		autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(11)|pancreas(3)|prostate(1)|stomach(1)|upper_aerodigestive_tract(2)	27	all_cancers(62;1.04e-10)|all_epithelial(64;3.67e-09)|Lung NSC(181;0.239)		STAD - Stomach adenocarcinoma(171;0.0031)		Cefazolin(DB01327)	CAGGAGGTACATGGCATTATC	0.403													A|||	13	0.00259585	0.0	0.0072	5008	,	,		18834	0.0		0.002	False		,,,				2504	0.0061				p.M127R	GBM(119;715 1622 17358 22490 33240)	Atlas-SNP	.											PON1,NS,carcinoma,0,1	PON1	55	1	1	Substitution - Missense(1)	pancreas(1)	c.T380G						PASS	.	A	ARG/MET	1,4405	2.1+/-5.4	0,1,2202	115.0	108.0	111.0		380	4.9	0.6	7	dbSNP_134	111	12,8588	8.4+/-32.0	0,12,4288	yes	missense	PON1	NM_000446.5	91	0,13,6490	CC,CA,AA		0.1395,0.0227,0.1	benign	127/356	94940880	13,12993	2203	4300	6503	SO:0001583	missense	5444	exon5			AGGTACATGGCAT	AF539592	CCDS5638.1	7q21.3	2014-03-14			ENSG00000005421	ENSG00000005421	3.1.1.2	"""Paraoxonases"""	9204	protein-coding gene	gene with protein product	"""esterase A"", ""arylesterase 1"""	168820		PON		8661009, 15450851	Standard	NM_000446		Approved	ESA	uc003uns.3	P27169	OTTHUMG00000153894	ENST00000222381.3:c.380T>G	7.37:g.94940880A>C	ENSP00000222381:p.Met127Arg	81.0	0.0	0		52.0	29.0	0.557692	NM_000446	B2RA40|Q16052|Q6B0J6|Q9UCB1	Missense_Mutation	SNP	ENST00000222381.3	37	CCDS5638.1	7	0.003205128205128205	0	0.0	5	0.013812154696132596	0	0.0	2	0.002638522427440633	A	10.59	1.391561	0.25118	2.27E-4	0.001395	ENSG00000005421	ENST00000222381;ENST00000542556	T;T	0.39406	1.08;1.08	4.88	4.88	0.63580	Six-bladed beta-propeller, TolB-like (1);	0.186666	0.47093	D	0.000258	T	0.20536	0.0494	N	0.08118	0	0.33135	D	0.543587	B;B	0.18741	0.03;0.005	B;B	0.25614	0.062;0.017	T	0.36065	-0.9763	10	0.87932	D	0	-9.4635	14.9578	0.71131	1.0:0.0:0.0:0.0	.	127;127	F5H4W9;P27169	.;PON1_HUMAN	R	127	ENSP00000222381:M127R;ENSP00000444854:M127R	ENSP00000222381:M127R	M	-	2	0	PON1	94778816	0.997000	0.39634	0.588000	0.28705	0.083000	0.17756	8.294000	0.89934	2.187000	0.69744	0.533000	0.62120	ATG	A|0.998;C|0.002	0.002	strong		0.403	PON1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000332865.2	NM_000446	
DCHS1	8642	hgsc.bcm.edu	37	11	6647596	6647596	+	Missense_Mutation	SNP	C	C	T	rs142577975		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6647596C>T	ENST00000299441.3	-	16	6791	c.6380G>A	c.(6379-6381)cGc>cAc	p.R2127H		NM_003737.2	NP_003728.1	Q96JQ0	PCD16_HUMAN	dachsous cadherin-related 1	2127	Cadherin 20. {ECO:0000255|PROSITE- ProRule:PRU00043}.				branching involved in ureteric bud morphogenesis (GO:0001658)|calcium-dependent cell-cell adhesion (GO:0016339)|cochlea development (GO:0090102)|digestive tract development (GO:0048565)|heart morphogenesis (GO:0003007)|heterophilic cell-cell adhesion (GO:0007157)|hippo signaling (GO:0035329)|homophilic cell adhesion (GO:0007156)|neural tube development (GO:0021915)|neurogenesis (GO:0022008)|ossification involved in bone maturation (GO:0043931)|post-anal tail morphogenesis (GO:0036342)	apical part of cell (GO:0045177)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(16)|liver(1)|lung(41)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(4)	103		Medulloblastoma(188;0.00263)|all_neural(188;0.026)		Epithelial(150;6.35e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		CTCTGCTGAGCGAACTGTGAT	0.587													c|||	1	0.000199681	0.0	0.0	5008	,	,		20274	0.0		0.001	False		,,,				2504	0.0				p.R2127H		Atlas-SNP	.											.	DCHS1	277	.	0			c.G6380A						PASS	.	T	HIS/ARG	0,4402		0,0,2201	58.0	57.0	57.0		6380	-1.9	0.2	11	dbSNP_134	57	1,8591	1.2+/-3.3	0,1,4295	yes	missense	DCHS1	NM_003737.2	29	0,1,6496	TT,TC,CC		0.0116,0.0,0.0077	benign	2127/3299	6647596	1,12993	2201	4296	6497	SO:0001583	missense	8642	exon16			GCTGAGCGAACTG	AB000895	CCDS7771.1	11p15.4	2013-10-04	2013-10-04	2004-09-03	ENSG00000166341	ENSG00000166341		"""Cadherins / Cadherin-related"""	13681	protein-coding gene	gene with protein product	"""cadherin-related family member 6"""	603057	"""protocadherin 16"", ""dachsous 1 (Drosophila)"""	CDH25, PCDH16		9199196	Standard	XM_005253207		Approved	FIB1, KIAA1773, FLJ11790, CDHR6	uc001mem.1	Q96JQ0	OTTHUMG00000133398	ENST00000299441.3:c.6380G>A	11.37:g.6647596C>T	ENSP00000299441:p.Arg2127His	50.0	0.0	0		67.0	40.0	0.597015	NM_003737	O15098	Missense_Mutation	SNP	ENST00000299441.3	37	CCDS7771.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	c	10.48	1.362070	0.24684	0.0	1.16E-4	ENSG00000166341	ENST00000299441	T	0.53206	0.63	4.92	-1.87	0.07737	Cadherin (4);Cadherin-like (1);	1.016160	0.07896	N	0.971952	T	0.35307	0.0927	L	0.41824	1.3	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.35500	-0.9786	10	0.52906	T	0.07	.	6.5512	0.22436	0.0:0.2635:0.1437:0.5928	.	2127	Q96JQ0	PCD16_HUMAN	H	2127	ENSP00000299441:R2127H	ENSP00000299441:R2127H	R	-	2	0	DCHS1	6604172	0.115000	0.22152	0.189000	0.23252	0.888000	0.51559	0.617000	0.24359	-0.190000	0.10465	-0.224000	0.12420	CGC	C|1.000;T|0.000	0.000	strong		0.587	DCHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257258.1	NM_003737	
FPGS	2356	hgsc.bcm.edu	37	9	130569258	130569258	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130569258C>T	ENST00000373247.2	+	5	443	c.393C>T	c.(391-393)ccC>ccT	p.P131P	FPGS_ENST00000373245.1_Silent_p.P131P|FPGS_ENST00000373225.3_Silent_p.P81P|FPGS_ENST00000460181.1_Intron|FPGS_ENST00000393706.2_Silent_p.P131P	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	131					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GCAGCTCTCCCCACCTGGTGC	0.652																																					p.P131P		Atlas-SNP	.											.	FPGS	30	.	0			c.C393T						PASS	.						58.0	59.0	59.0					9																	130569258		2203	4300	6503	SO:0001819	synonymous_variant	2356	exon5			CTCTCCCCACCTG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.393C>T	9.37:g.130569258C>T		69.0	0.0	0		84.0	42.0	0.5	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Silent	SNP	ENST00000373247.2	37	CCDS35148.1																																																																																			.	.	none		0.652	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1		
LAMA5	3911	hgsc.bcm.edu	37	20	60885978	60885978	+	Silent	SNP	G	G	T	rs201094237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:60885978G>T	ENST00000252999.3	-	74	10327	c.10261C>A	c.(10261-10263)Cgg>Agg	p.R3421R	LAMA5_ENST00000492698.1_5'Flank	NM_005560.3	NP_005551.3	O15230	LAMA5_HUMAN	laminin, alpha 5	3421	Laminin G-like 4. {ECO:0000255|PROSITE- ProRule:PRU00122}.				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)			CGGCCAGGCCGGGAGCGCTGG	0.697													.|||	3	0.000599042	0.0	0.0	5008	,	,		12759	0.0		0.001	False		,,,				2504	0.002				p.R3421R		Atlas-SNP	.											.	LAMA5	268	.	0			c.C10261A						PASS	.			0,4154		0,0,2077	12.0	16.0	14.0		10261	0.8	0.0	20		14	4,8320		0,4,4158	no	coding-synonymous	LAMA5	NM_005560.3		0,4,6235	TT,TG,GG		0.0481,0.0,0.0321		3421/3696	60885978	4,12474	2077	4162	6239	SO:0001819	synonymous_variant	3911	exon74			CAGGCCGGGAGCG	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.10261C>A	20.37:g.60885978G>T		11.0	0.0	0		42.0	30.0	0.714286	NM_005560	Q8TDF8|Q8WZA7|Q9H1P1	Silent	SNP	ENST00000252999.3	37	CCDS33502.1																																																																																			.	.	weak		0.697	LAMA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080014.2	NM_005560	
ATOH7	220202	hgsc.bcm.edu	37	10	69991099	69991099	+	Silent	SNP	G	G	A	rs201955526		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:69991099G>A	ENST00000373673.3	-	1	772	c.336C>T	c.(334-336)caC>caT	p.H112H	RP11-153K11.3_ENST00000444086.1_lincRNA	NM_145178.3	NP_660161.1	Q8N100	ATOH7_HUMAN	atonal homolog 7 (Drosophila)	112					cell differentiation (GO:0030154)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|neural retina development (GO:0003407)|optic nerve development (GO:0021554)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)										AGTGCTCACAGTGGAGACCCA	0.672																																					p.H112H		Atlas-SNP	.											.	ATOH7	4	.	0			c.C336T						PASS	.	G		0,4406		0,0,2203	33.0	34.0	34.0		336	4.1	1.0	10		34	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	ATOH7	NM_145178.2		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		112/153	69991099	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	220202	exon1			CTCACAGTGGAGA	AF418922	CCDS7276.1	10q22.2	2013-05-21			ENSG00000179774	ENSG00000179774		"""Basic helix-loop-helix proteins"""	13907	protein-coding gene	gene with protein product		609875				11889557	Standard	NM_145178		Approved	Math5, bHLHa13	uc001jnq.3	Q8N100	OTTHUMG00000018346	ENST00000373673.3:c.336C>T	10.37:g.69991099G>A		44.0	0.0	0		74.0	41.0	0.554054	NM_145178		Silent	SNP	ENST00000373673.3	37	CCDS7276.1																																																																																			G|0.999;A|0.001	0.001	weak		0.672	ATOH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048312.1		
SLC16A4	9122	hgsc.bcm.edu	37	1	110924316	110924316	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:110924316T>C	ENST00000369779.4	-	4	571	c.322A>G	c.(322-324)Aca>Gca	p.T108A	SLC16A4_ENST00000497687.1_Intron|LAMTOR5-AS1_ENST00000590413.1_RNA|SLC16A4_ENST00000369781.4_Missense_Mutation_p.T108A|SLC16A4_ENST00000472422.2_Intron|SLC16A4_ENST00000437429.2_Intron|SLC16A4_ENST00000541986.1_Missense_Mutation_p.T46A	NM_001201547.1|NM_004696.2	NP_001188476.1|NP_004687.1	O15374	MOT5_HUMAN	solute carrier family 16, member 4	108					monocarboxylic acid transport (GO:0015718)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	monocarboxylic acid transmembrane transporter activity (GO:0008028)|symporter activity (GO:0015293)			breast(1)|endometrium(1)|kidney(4)|large_intestine(2)|lung(2)|ovary(3)|prostate(1)|stomach(2)	16		all_cancers(81;0.000476)|all_epithelial(167;0.000401)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0251)|all cancers(265;0.0766)|Epithelial(280;0.0807)|Colorectal(144;0.112)|LUSC - Lung squamous cell carcinoma(189;0.14)	Pyruvic acid(DB00119)	GGAATACTTGTGGCCCAGCTG	0.458																																					p.T108A		Atlas-SNP	.											.	SLC16A4	47	.	0			c.A322G						PASS	.						102.0	94.0	96.0					1																	110924316		2203	4300	6503	SO:0001583	missense	9122	exon4			TACTTGTGGCCCA	U59185	CCDS823.1, CCDS55621.1, CCDS55622.1, CCDS55623.1, CCDS55624.1	1p13.3	2013-07-18	2013-07-18		ENSG00000168679	ENSG00000168679		"""Solute carriers"""	10925	protein-coding gene	gene with protein product		603878	"""solute carrier family 16 (monocarboxylic acid transporters), member 4"", ""solute carrier family 16, member 4 (monocarboxylic acid transporter 5)"""			9425115	Standard	NM_004696		Approved	MCT4, MCT5	uc001dzo.2	O15374	OTTHUMG00000011285	ENST00000369779.4:c.322A>G	1.37:g.110924316T>C	ENSP00000358794:p.Thr108Ala	259.0	0.0	0		228.0	110.0	0.482456	NM_004696	A8K3V5|B2R9C9|B4DJ67|B4DPX7|E7EPY8|G3V175|Q5T612|Q8WU09	Missense_Mutation	SNP	ENST00000369779.4	37	CCDS823.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.129800	0.77549	.	.	ENSG00000168679	ENST00000369779;ENST00000369781;ENST00000541986	T;T;T	0.55760	0.5;0.5;0.5	4.86	3.73	0.42828	Major facilitator superfamily domain, general substrate transporter (1);	0.253587	0.45867	N	0.000340	T	0.61602	0.2360	M	0.87971	2.92	0.80722	D	1	D;D;P;D	0.65815	0.995;0.994;0.947;0.992	D;D;P;D	0.68621	0.91;0.959;0.823;0.91	T	0.63633	-0.6593	10	0.30854	T	0.27	.	9.0678	0.36473	0.0:0.0848:0.0:0.9152	.	46;108;108;108	B4DJ67;Q53FH9;Q8WU09;O15374	.;.;.;MOT5_HUMAN	A	108;108;46	ENSP00000358794:T108A;ENSP00000358796:T108A;ENSP00000446087:T46A	ENSP00000358794:T108A	T	-	1	0	SLC16A4	110725839	1.000000	0.71417	0.996000	0.52242	0.991000	0.79684	5.203000	0.65174	0.994000	0.38892	0.533000	0.62120	ACA	.	.	none		0.458	SLC16A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000031115.3	NM_004696	
PCNT	5116	hgsc.bcm.edu	37	21	47850107	47850107	+	Missense_Mutation	SNP	G	G	A	rs8131693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47850107G>A	ENST00000359568.5	+	36	7981	c.7874G>A	c.(7873-7875)cGg>cAg	p.R2625Q	PCNT_ENST00000480896.1_3'UTR	NM_006031.5	NP_006022.3	O95613	PCNT_HUMAN	pericentrin	2625			R -> Q (in dbSNP:rs8131693).		brain morphogenesis (GO:0048854)|cerebellar cortex morphogenesis (GO:0021696)|cilium assembly (GO:0042384)|G2/M transition of mitotic cell cycle (GO:0000086)|in utero embryonic development (GO:0001701)|limb morphogenesis (GO:0035108)|microtubule cytoskeleton organization (GO:0000226)|mitotic cell cycle (GO:0000278)|multicellular organism growth (GO:0035264)|negative regulation of apoptotic process (GO:0043066)|neural precursor cell proliferation (GO:0061351)|neuron migration (GO:0001764)|olfactory bulb development (GO:0021772)|positive regulation of intracellular protein transport (GO:0090316)|spindle organization (GO:0007051)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intercellular bridge (GO:0045171)|membrane (GO:0016020)|microtubule (GO:0005874)|motile cilium (GO:0031514)|pericentriolar material (GO:0000242)				NS(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(15)|liver(2)|lung(41)|ovary(5)|pancreas(3)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	104	Breast(49;0.112)					CAGCTGTCCCGGTCCCTCTGC	0.622													G|||	319	0.0636981	0.2269	0.0245	5008	,	,		17998	0.0		0.002	False		,,,				2504	0.0				p.R2625Q		Atlas-SNP	.											.	PCNT	283	.	0			c.G7874A						PASS	.	G	GLN/ARG	879,3527	340.2+/-306.1	96,687,1420	67.0	65.0	66.0		7874	0.3	0.0	21	dbSNP_116	66	14,8586	8.4+/-32.0	0,14,4286	yes	missense	PCNT	NM_006031.5	43	96,701,5706	AA,AG,GG		0.1628,19.9501,6.8661	benign	2625/3337	47850107	893,12113	2203	4300	6503	SO:0001583	missense	5116	exon36			TGTCCCGGTCCCT	AB007862	CCDS33592.1	21q22.3	2014-02-20	2008-01-30	2005-11-03	ENSG00000160299	ENSG00000160299			16068	protein-coding gene	gene with protein product	"""kendrin"", ""Seckel syndrome 4"""	605925	"""pericentrin 2 (kendrin)"""	PCNT2		8812505, 9455477	Standard	NM_006031		Approved	KEN, KIAA0402, PCN, PCNTB, SCKL4	uc002zji.4	O95613	OTTHUMG00000090665	ENST00000359568.5:c.7874G>A	21.37:g.47850107G>A	ENSP00000352572:p.Arg2625Gln	93.0	0.0	0		111.0	55.0	0.495495	NM_006031	O43152|Q7Z7C9	Missense_Mutation	SNP	ENST00000359568.5	37	CCDS33592.1	95	0.043498168498168496	88	0.17886178861788618	7	0.019337016574585635	0	0.0	0	0.0	G	6.228	0.410216	0.11812	0.199501	0.001628	ENSG00000160299	ENST00000359568	T	0.01359	4.98	4.31	0.32	0.15878	.	.	.	.	.	T	0.00012	0.0000	N	0.08118	0	0.80722	P	0.0	B;B	0.17852	0.002;0.024	B;B	0.06405	0.002;0.001	T	0.43114	-0.9411	8	0.36615	T	0.2	.	5.7279	0.18022	0.5019:0.3993:0.0988:0.0	rs8131693;rs8131693	2507;2625	O95613-2;O95613	.;PCNT_HUMAN	Q	2625	ENSP00000352572:R2625Q	ENSP00000352572:R2625Q	R	+	2	0	PCNT	46674535	0.038000	0.19896	0.003000	0.11579	0.002000	0.02628	1.973000	0.40550	-0.055000	0.13244	-0.391000	0.06502	CGG	G|0.933;A|0.067	0.067	strong		0.622	PCNT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207336.1	NM_006031	
MYO7A	4647	hgsc.bcm.edu	37	11	76883797	76883797	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76883797G>A	ENST00000409709.3	+	16	2073	c.1801G>A	c.(1801-1803)Gcc>Acc	p.A601T	MYO7A_ENST00000409619.2_Missense_Mutation_p.A590T|MYO7A_ENST00000409893.1_Missense_Mutation_p.A601T|MYO7A_ENST00000458637.2_Missense_Mutation_p.A601T	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	601	Myosin motor.				actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CCCCCAGGGCGCCGAGACCAG	0.692																																					p.A601T		Atlas-SNP	.											.	MYO7A	164	.	0			c.G1801A						PASS	.						12.0	15.0	14.0					11																	76883797		1977	4041	6018	SO:0001583	missense	4647	exon16			CAGGGCGCCGAGA	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.1801G>A	11.37:g.76883797G>A	ENSP00000386331:p.Ala601Thr	105.0	0.0	0		88.0	45.0	0.511364	NM_001127179	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	.	.	.	.	.	.	.	.	.	.	G	14.98	2.697112	0.48202	.	.	ENSG00000137474	ENST00000409709;ENST00000409893;ENST00000458637;ENST00000409619;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000343419	D;D;D;D	0.87412	-2.25;-2.25;-2.25;-2.25	4.77	3.84	0.44239	Myosin head, motor domain (2);	0.000000	0.85682	D	0.000000	T	0.80654	0.4664	L	0.37466	1.105	0.46849	D	0.999226	B;B;B	0.28291	0.206;0.085;0.123	B;B;B	0.26416	0.037;0.022;0.069	T	0.74910	-0.3503	10	0.19590	T	0.45	.	15.0945	0.72223	0.0:0.1428:0.8572:0.0	.	601;601;601	B9A012;F8VUN5;Q13402	.;.;MYO7A_HUMAN	T	601;601;601;590;600;600;477;600	ENSP00000386331:A601T;ENSP00000386689:A601T;ENSP00000392185:A601T;ENSP00000386635:A590T	ENSP00000345075:A477T	A	+	1	0	MYO7A	76561445	0.993000	0.37304	0.994000	0.49952	0.906000	0.53458	5.244000	0.65400	1.107000	0.41642	0.549000	0.68633	GCC	.	.	none		0.692	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
CD276	80381	hgsc.bcm.edu	37	15	73995247	73995247	+	Missense_Mutation	SNP	C	C	T	rs142744437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:73995247C>T	ENST00000318443.5	+	4	855	c.553C>T	c.(553-555)Ccc>Tcc	p.P185S	CD276_ENST00000318424.5_Intron|CD276_ENST00000537340.2_Missense_Mutation_p.P39S|CD276_ENST00000564751.1_Intron|CD276_ENST00000561213.1_Missense_Mutation_p.P185S	NM_001024736.1	NP_001019907.1	Q5ZPR3	CD276_HUMAN	CD276 molecule	185	Ig-like C2-type 1.				cell proliferation (GO:0008283)|immune response (GO:0006955)|negative regulation of inflammatory response (GO:0050728)|negative regulation of interferon-gamma biosynthetic process (GO:0045077)|negative regulation of interleukin-2 biosynthetic process (GO:0045085)|negative regulation of T cell proliferation (GO:0042130)|positive regulation of bone mineralization (GO:0030501)|positive regulation of interferon-gamma biosynthetic process (GO:0045078)|positive regulation of interleukin-2 secretion (GO:1900042)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of T cell proliferation (GO:0042102)|regulation of immune response (GO:0050776)|T cell activation (GO:0042110)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor binding (GO:0005102)			endometrium(3)|lung(5)|ovary(1)|skin(2)|stomach(1)|urinary_tract(1)	13						GCAGGGTGTGCCCCTGACTGG	0.622													C|||	3	0.000599042	0.0	0.0	5008	,	,		19371	0.0		0.003	False		,,,				2504	0.0				p.P185S		Atlas-SNP	.											.	CD276	29	.	0			c.C553T						PASS	.	C	SER/PRO,	1,4395	2.1+/-5.4	0,1,2197	89.0	76.0	80.0		553,	-0.7	0.0	15	dbSNP_134	80	13,8577	9.1+/-34.3	0,13,4282	no	missense,intron	CD276	NM_001024736.1,NM_025240.2	74,	0,14,6479	TT,TC,CC		0.1513,0.0227,0.1078	possibly-damaging,	185/535,	73995247	14,12972	2198	4295	6493	SO:0001583	missense	80381	exon4			GGTGTGCCCCTGA	AF302102	CCDS10251.1, CCDS32288.1	15q23-q24	2013-01-11	2006-03-28		ENSG00000103855	ENSG00000103855		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"""	19137	protein-coding gene	gene with protein product		605715	"""CD276 antigen"""			11224528, 12055244	Standard	XM_005254699		Approved	B7-H3, B7H3, B7RP-2	uc002avv.1	Q5ZPR3	OTTHUMG00000137585	ENST00000318443.5:c.553C>T	15.37:g.73995247C>T	ENSP00000320084:p.Pro185Ser	204.0	0.0	0		228.0	120.0	0.526316	NM_001024736	Q6P5Y4|Q6UXI2|Q8NBI8|Q8NC34|Q8NCB6|Q9BXR1	Missense_Mutation	SNP	ENST00000318443.5	37	CCDS32288.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	0.107	-1.143273	0.01728	2.27E-4	0.001513	ENSG00000103855	ENST00000318443;ENST00000379823;ENST00000537340	T;T	0.76448	-1.02;-1.02	3.14	-0.671	0.11381	Immunoglobulin subtype 2 (1);CD80-like, immunoglobulin C2-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.55561	0.1928	N	0.12502	0.225	0.09310	N	0.999994	B;B;B	0.16396	0.017;0.017;0.013	B;B;B	0.20184	0.028;0.028;0.017	T	0.39482	-0.9612	9	0.21540	T	0.41	.	6.3988	0.21626	0.3327:0.2617:0.4056:0.0	.	131;185;185	B4DK26;Q5ZPR3;Q5ZPR3-4	.;CD276_HUMAN;.	S	185;185;39	ENSP00000320084:P185S;ENSP00000441087:P39S	ENSP00000320084:P185S	P	+	1	0	CD276	71782300	0.021000	0.18746	0.011000	0.14972	0.203000	0.24098	1.959000	0.40412	0.103000	0.17682	0.313000	0.20887	CCC	C|0.999;T|0.001	0.001	strong		0.622	CD276-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268979.1	NM_025240	
SEZ6L	23544	hgsc.bcm.edu	37	22	26692953	26692953	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26692953G>A	ENST00000248933.6	+	4	1164	c.1069G>A	c.(1069-1071)Ggg>Agg	p.G357R	SEZ6L_ENST00000402979.1_Missense_Mutation_p.G130R|SEZ6L_ENST00000360929.3_Missense_Mutation_p.G357R|SEZ6L_ENST00000403121.1_Missense_Mutation_p.G130R|SEZ6L_ENST00000404234.3_Missense_Mutation_p.G357R|SEZ6L_ENST00000529632.2_Missense_Mutation_p.G357R|SEZ6L_ENST00000343706.4_Missense_Mutation_p.G357R			Q9BYH1	SE6L1_HUMAN	seizure related 6 homolog (mouse)-like	357	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				adult locomotory behavior (GO:0008344)|cerebellar Purkinje cell layer development (GO:0021680)|regulation of protein kinase C signaling (GO:0090036)|synapse maturation (GO:0060074)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)				breast(1)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|lung(35)|ovary(4)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	80						CCTGGTGGAGGGGCAGGTAAT	0.622																																					p.G357R		Atlas-SNP	.											.	SEZ6L	174	.	0			c.G1069A						PASS	.						60.0	47.0	52.0					22																	26692953		2203	4300	6503	SO:0001583	missense	23544	exon4			GTGGAGGGGCAGG	AL050253	CCDS13833.1, CCDS54508.1, CCDS54510.1, CCDS54511.1, CCDS74837.1	22q12.1	2008-05-14	2001-11-28		ENSG00000100095	ENSG00000100095			10763	protein-coding gene	gene with protein product		607021	"""seizure related gene 6 (mouse)-like"""				Standard	NM_021115		Approved		uc003acb.3	Q9BYH1	OTTHUMG00000150870	ENST00000248933.6:c.1069G>A	22.37:g.26692953G>A	ENSP00000248933:p.Gly357Arg	104.0	0.0	0		100.0	4.0	0.04	NM_001184777	A0AUW7|B0QYG4|B0QYG5|B7ZLJ6|G8JLP3|O95917|Q5THY5|Q6IBZ4|Q6UXD4|Q9NUI3|Q9NUI4|Q9NUI5|Q9Y2E1|Q9Y3J6	Missense_Mutation	SNP	ENST00000248933.6	37	CCDS13833.1	.	.	.	.	.	.	.	.	.	.	G	31	5.087781	0.94100	.	.	ENSG00000100095	ENST00000404234;ENST00000529632;ENST00000360929;ENST00000248933;ENST00000343706;ENST00000403121;ENST00000402979	T;T;T;T;T;T;T	0.59772	0.24;0.24;0.24;0.24;0.24;0.24;0.24	5.26	5.26	0.73747	CUB (5);	0.000000	0.56097	D	0.000037	T	0.78162	0.4240	M	0.79926	2.475	0.80722	D	1	D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D	0.97110	1.0;1.0;1.0;1.0;1.0;1.0;1.0	T	0.81420	-0.0941	10	0.87932	D	0	.	17.8539	0.88756	0.0:0.0:1.0:0.0	.	357;357;130;357;357;357;357	B7ZLJ8;B7ZLJ6;B0QYH4;Q9BYH1-5;Q9BYH1-4;B0QYG3;Q9BYH1	.;.;.;.;.;.;SE6L1_HUMAN	R	357;357;357;357;357;130;130	ENSP00000384772:G357R;ENSP00000437037:G357R;ENSP00000354185:G357R;ENSP00000248933:G357R;ENSP00000342661:G357R;ENSP00000384838:G130R;ENSP00000384733:G130R	ENSP00000248933:G357R	G	+	1	0	SEZ6L	25022953	1.000000	0.71417	0.997000	0.53966	0.870000	0.49936	9.244000	0.95423	2.446000	0.82766	0.655000	0.94253	GGG	.	.	none		0.622	SEZ6L-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000320359.3		
RNF31	55072	hgsc.bcm.edu	37	14	24620821	24620821	+	Missense_Mutation	SNP	A	A	T	rs149481717	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24620821A>T	ENST00000324103.6	+	10	2185	c.1865A>T	c.(1864-1866)cAg>cTg	p.Q622L	RNF31_ENST00000382687.3_Missense_Mutation_p.Q471L|RNF31_ENST00000559275.1_Missense_Mutation_p.Q471L|RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.Q97L	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	622					CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		CCCTTCCGCCAGCGCCTCTGG	0.652													A|||	9	0.00179712	0.0	0.0029	5008	,	,		18657	0.0		0.005	False		,,,				2504	0.002				p.Q622L		Atlas-SNP	.											.	RNF31	95	.	0			c.A1865T						PASS	.	A	LEU/GLN	6,3962		0,6,1978	34.0	37.0	36.0		1865	5.4	1.0	14	dbSNP_134	36	41,8285		0,41,4122	yes	missense	RNF31	NM_017999.4	113	0,47,6100	TT,TA,AA		0.4924,0.1512,0.3823	possibly-damaging	622/1073	24620821	47,12247	1984	4163	6147	SO:0001583	missense	55072	exon10			TCCGCCAGCGCCT	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"""RING-type (C3HC4) zinc fingers"""	16031	protein-coding gene	gene with protein product	"""HOIL-1-interacting protein"""	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1865A>T	14.37:g.24620821A>T	ENSP00000315112:p.Gln622Leu	47.0	0.0	0		42.0	23.0	0.547619	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	14.27	2.485749	0.44147	0.001512	0.004924	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.47869	0.83;0.83	5.42	5.42	0.78866	.	0.068650	0.64402	D	0.000016	T	0.34395	0.0896	L	0.56769	1.78	0.46028	D	0.998828	B;B;B	0.33171	0.301;0.278;0.4	B;B;B	0.30855	0.08;0.039;0.121	T	0.42292	-0.9460	10	0.66056	D	0.02	-11.1548	9.8917	0.41294	0.8475:0.0:0.0:0.1524	.	381;622;471	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	L	622;471	ENSP00000315112:Q622L;ENSP00000372134:Q471L	ENSP00000315112:Q622L	Q	+	2	0	RNF31	23690661	1.000000	0.71417	1.000000	0.80357	0.955000	0.61496	4.311000	0.59147	2.274000	0.75844	0.533000	0.62120	CAG	A|0.998;T|0.002	0.002	strong		0.652	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999	
SLFN13	146857	hgsc.bcm.edu	37	17	33767943	33767943	+	Missense_Mutation	SNP	C	C	T	rs138317636	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:33767943C>T	ENST00000285013.6	-	6	2640	c.2365G>A	c.(2365-2367)Gtg>Atg	p.V789M	SLFN13_ENST00000534689.1_Missense_Mutation_p.V471M|SLFN13_ENST00000360502.2_Missense_Mutation_p.V471M|SLFN13_ENST00000533791.1_Missense_Mutation_p.V789M|SLFN13_ENST00000526861.1_Missense_Mutation_p.V789M|SLFN13_ENST00000542635.1_Missense_Mutation_p.V789M	NM_144682.5	NP_653283.3	Q68D06	SLN13_HUMAN	schlafen family member 13	789						intracellular (GO:0005622)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(1)|large_intestine(10)|lung(8)|ovary(3)|pancreas(1)|prostate(5)|stomach(1)	31				UCEC - Uterine corpus endometrioid carcinoma (308;0.0185)		ACATAGGTCACTATTTGCTCC	0.458																																					p.V789M		Atlas-SNP	.											.	SLFN13	79	.	0			c.G2365A						PASS	.	C	MET/VAL	0,4406		0,0,2203	78.0	76.0	77.0		2365	2.2	0.0	17	dbSNP_134	77	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SLFN13	NM_144682.5	21	0,3,6500	TT,TC,CC		0.0349,0.0,0.0231	benign	789/898	33767943	3,13003	2203	4300	6503	SO:0001583	missense	146857	exon6			AGGTCACTATTTG	AL832726	CCDS32620.1	17q12	2006-04-05				ENSG00000154760			26481	protein-coding gene	gene with protein product		614957				9846487	Standard	NM_144682		Approved	FLJ31952	uc002hjl.2	Q68D06		ENST00000285013.6:c.2365G>A	17.37:g.33767943C>T	ENSP00000285013:p.Val789Met	76.0	0.0	0		82.0	40.0	0.487805	NM_144682	E1P645|Q658M1|Q6ZS51|Q96A81	Missense_Mutation	SNP	ENST00000285013.6	37	CCDS32620.1	.	.	.	.	.	.	.	.	.	.	c	8.383	0.838010	0.16891	0.0	3.49E-4	ENSG00000154760	ENST00000285013;ENST00000360502;ENST00000526861;ENST00000542635;ENST00000534689	D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72	3.26	2.22	0.28083	.	0.899723	0.09181	N	0.837387	T	0.78972	0.4368	L	0.53780	1.695	0.09310	N	1	P;B	0.36222	0.544;0.2	B;B	0.36989	0.238;0.037	T	0.65973	-0.6038	10	0.44086	T	0.13	.	8.2184	0.31526	0.0:0.7525:0.2475:0.0	.	471;789	Q68D06-2;Q68D06	.;SLN13_HUMAN	M	789;471;789;789;471	ENSP00000285013:V789M;ENSP00000353692:V471M;ENSP00000434439:V789M;ENSP00000444016:V789M;ENSP00000435442:V471M	ENSP00000285013:V789M	V	-	1	0	SLFN13	30792056	0.000000	0.05858	0.001000	0.08648	0.062000	0.15995	0.425000	0.21346	0.637000	0.30526	0.400000	0.26472	GTG	C|1.000;T|0.000	0.000	strong		0.458	SLFN13-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381883.1	NM_144682	
HERC2	8924	hgsc.bcm.edu	37	15	28459092	28459092	+	Silent	SNP	G	G	A	rs187225254		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459092G>A	ENST00000261609.7	-	42	6690	c.6582C>T	c.(6580-6582)gaC>gaT	p.D2194D		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GGTTCTCGGAGTCGGGGAAGT	0.587																																					p.D2194D		Atlas-SNP	.											.	HERC2	501	.	0			c.C6582T						PASS	.						35.0	32.0	33.0					15																	28459092		2203	4298	6501	SO:0001819	synonymous_variant	8924	exon42			CTCGGAGTCGGGG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6582C>T	15.37:g.28459092G>A		219.0	0.0	0		194.0	12.0	0.0618557	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.993;A|0.007	0.007	strong		0.587	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
AP5Z1	9907	hgsc.bcm.edu	37	7	4827859	4827859	+	Missense_Mutation	SNP	G	G	A	rs77890266	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4827859G>A	ENST00000348624.4	+	12	1623	c.1529G>A	c.(1528-1530)cGg>cAg	p.R510Q	AP5Z1_ENST00000401897.1_Missense_Mutation_p.R510Q|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	510					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											GAGGCCTTCCGGGACCCGCAG	0.687													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		16573	0.0		0.0239	False		,,,				2504	0.0235				p.R510Q		Atlas-SNP	.											.	.	.	.	0			c.G1529A						PASS	.	G	GLN/ARG	12,3796		0,12,1892	10.0	13.0	12.0		1529	2.6	0.2	7	dbSNP_131	12	197,8015		5,187,3914	yes	missense	KIAA0415	NM_014855.2	43	5,199,5806	AA,AG,GG		2.3989,0.3151,1.7388	benign	510/808	4827859	209,11811	1904	4106	6010	SO:0001583	missense	9907	exon12			CCTTCCGGGACCC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.1529G>A	7.37:g.4827859G>A	ENSP00000297562:p.Arg510Gln	136.0	0.0	0		154.0	68.0	0.441558	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	32	0.014652014652014652	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	18	0.023746701846965697	G	13.91	2.377627	0.42105	0.003151	0.023989	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44881	0.91;0.91	4.48	2.62	0.31277	.	0.079729	0.52532	N	0.000077	T	0.10121	0.0248	L	0.45228	1.405	0.38035	D	0.93527	P	0.37864	0.61	B	0.25405	0.06	T	0.04103	-1.0977	10	0.36615	T	0.2	.	8.8683	0.35300	0.1868:0.0:0.8132:0.0	.	510	O43299	K0415_HUMAN	Q	510	ENSP00000297562:R510Q;ENSP00000384980:R510Q	ENSP00000297562:R510Q	R	+	2	0	KIAA0415	4794385	0.959000	0.32827	0.180000	0.23079	0.851000	0.48451	1.465000	0.35299	0.310000	0.22990	0.478000	0.44815	CGG	G|0.986;A|0.014	0.014	strong		0.687	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
CPED1	79974	hgsc.bcm.edu	37	7	120876835	120876835	+	Missense_Mutation	SNP	A	A	G	rs35793694	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:120876835A>G	ENST00000310396.5	+	17	2590	c.2123A>G	c.(2122-2124)gAa>gGa	p.E708G	CPED1_ENST00000450913.2_Missense_Mutation_p.E708G|CPED1_ENST00000423795.1_Missense_Mutation_p.E488G	NM_024913.4	NP_079189.4	A4D0V7	CPED1_HUMAN	cadherin-like and PC-esterase domain containing 1	708			E -> G (in dbSNP:rs35793694). {ECO:0000269|PubMed:14702039, ECO:0000269|PubMed:17974005}.			endoplasmic reticulum (GO:0005783)											GACTACATTGAAGCCATTTTA	0.348													A|||	182	0.0363419	0.0325	0.0403	5008	,	,		15919	0.0		0.0805	False		,,,				2504	0.0307				p.E708G		Atlas-SNP	.											.	.	.	.	0			c.A2123G						PASS	.	A	GLY/GLU,GLY/GLU	200,4206	124.5+/-161.8	3,194,2006	98.0	97.0	97.0		2123,2123	4.8	1.0	7	dbSNP_126	97	684,7916	169.4+/-220.8	30,624,3646	yes	missense,missense	C7orf58	NM_001105533.1,NM_024913.4	98,98	33,818,5652	GG,GA,AA		7.9535,4.5393,6.7969	benign,benign	708/784,708/1027	120876835	884,12122	2203	4300	6503	SO:0001583	missense	79974	exon16			ACATTGAAGCCAT		CCDS34739.1, CCDS47690.1	7q31.31	2012-06-12	2012-06-12	2012-06-12	ENSG00000106034	ENSG00000106034			26159	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 58"""	C7orf58		20056006	Standard	NM_024913		Approved	FLJ21986	uc003vjq.4	A4D0V7	OTTHUMG00000156982	ENST00000310396.5:c.2123A>G	7.37:g.120876835A>G	ENSP00000309772:p.Glu708Gly	93.0	0.0	0		89.0	48.0	0.539326	NM_001105533	A8K1R3|Q6UXT1|Q86T76|Q86T84|Q8N2T5|Q96NC9	Missense_Mutation	SNP	ENST00000310396.5	37	CCDS34739.1	105	0.04807692307692308	21	0.042682926829268296	16	0.04419889502762431	0	0.0	68	0.08970976253298153	A	20.3	3.965228	0.74131	0.045393	0.079535	ENSG00000106034	ENST00000310396;ENST00000450913;ENST00000423795	T;T;T	0.25085	2.15;1.82;1.83	5.86	4.75	0.60458	.	0.200573	0.43416	D	0.000573	T	0.00637	0.0021	L	0.40543	1.245	0.80722	D	1	P;P;B	0.38078	0.617;0.617;0.329	B;B;B	0.30855	0.121;0.121;0.077	T	0.03112	-1.1071	10	0.46703	T	0.11	.	10.2136	0.43156	0.6934:0.3066:0.0:0.0	rs35793694	488;708;708	G5E9U2;A4D0V7-2;A4D0V7	.;.;CG058_HUMAN	G	708;708;488	ENSP00000309772:E708G;ENSP00000406122:E708G;ENSP00000415573:E488G	ENSP00000309772:E708G	E	+	2	0	C7orf58	120664071	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	1.980000	0.40618	2.238000	0.73509	0.477000	0.44152	GAA	A|0.939;G|0.061	0.061	strong		0.348	CPED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346959.1	NM_024913	
CS	1431	hgsc.bcm.edu	37	12	56669799	56669799	+	Silent	SNP	G	G	A	rs61738833	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:56669799G>A	ENST00000351328.3	-	7	959	c.769C>T	c.(769-771)Ctg>Ttg	p.L257L	CS_ENST00000548567.1_Silent_p.L191L|CS_ENST00000542324.2_Silent_p.L244L	NM_004077.2	NP_004068.2	O75390	CISY_HUMAN	citrate synthase	257					carbohydrate metabolic process (GO:0005975)|cellular carbohydrate metabolic process (GO:0044262)|cellular metabolic process (GO:0044237)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	citrate (Si)-synthase activity (GO:0004108)|poly(A) RNA binding (GO:0044822)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(4)|ovary(1)|skin(1)	17		Myeloproliferative disorder(1001;0.000374)		BRCA - Breast invasive adenocarcinoma(357;6.17e-07)		GTGAGGTACAGGCGCGTGAGC	0.478													G|||	28	0.00559105	0.0008	0.0101	5008	,	,		20736	0.0		0.0189	False		,,,				2504	0.001				p.L257L		Atlas-SNP	.											.	CS	44	.	0			c.C769T						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	136.0	117.0	123.0		769	1.7	1.0	12	dbSNP_129	123	120,8480	62.4+/-124.4	2,116,4182	no	coding-synonymous	CS	NM_004077.2		2,127,6374	AA,AG,GG		1.3953,0.2497,1.0072		257/467	56669799	131,12875	2203	4300	6503	SO:0001819	synonymous_variant	1431	exon7			GGTACAGGCGCGT		CCDS8913.1	12q13.2	2012-10-02				ENSG00000062485	2.3.3.1		2422	protein-coding gene	gene with protein product		118950					Standard	NM_004077		Approved		uc001sks.1	O75390	OTTHUMG00000170344	ENST00000351328.3:c.769C>T	12.37:g.56669799G>A		163.0	0.0	0		215.0	104.0	0.483721	NM_004077	Q71UT9|Q7KZH0|Q96FZ8|Q9BWN8	Silent	SNP	ENST00000351328.3	37	CCDS8913.1																																																																																			G|0.991;A|0.009	0.009	strong		0.478	CS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408588.2	NM_004077	
INTS3	65123	hgsc.bcm.edu	37	1	153737498	153737498	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153737498G>T	ENST00000318967.2	+	20	2617	c.2049G>T	c.(2047-2049)caG>caT	p.Q683H	INTS3_ENST00000476843.1_3'UTR|INTS3_ENST00000512605.1_Missense_Mutation_p.Q477H|INTS3_ENST00000456435.1_Missense_Mutation_p.Q477H|INTS3_ENST00000435409.2_Missense_Mutation_p.Q683H	NM_023015.3	NP_075391.3	Q68E01	INT3_HUMAN	integrator complex subunit 3	684					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|mitotic cell cycle checkpoint (GO:0007093)|response to ionizing radiation (GO:0010212)|snRNA processing (GO:0016180)	integrator complex (GO:0032039)|nucleus (GO:0005634)|SOSS complex (GO:0070876)				breast(1)|cervix(4)|endometrium(10)|kidney(1)|large_intestine(6)|lung(9)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	38	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			ATCAGAAGCAGCCCAAGATTG	0.532																																					p.Q683H		Atlas-SNP	.											.	INTS3	83	.	0			c.G2049T						PASS	.						233.0	222.0	226.0					1																	153737498		2203	4300	6503	SO:0001583	missense	65123	exon20			GAAGCAGCCCAAG	BX640950	CCDS1052.1	1q21.3	2012-03-16	2006-03-15	2006-03-15	ENSG00000143624	ENSG00000143624			26153	protein-coding gene	gene with protein product	"""sensor of single-strand DNA complex subunit A"""	611347	"""chromosome 1 open reading frame 60"""	C1orf60		16239144	Standard	NM_023015		Approved	FLJ21919, INT3, SOSS-A	uc001fct.3	Q68E01	OTTHUMG00000037089	ENST00000318967.2:c.2049G>T	1.37:g.153737498G>T	ENSP00000318641:p.Gln683His	86.0	0.0	0		105.0	31.0	0.295238	NM_023015	A8K1W0|B4DQC8|B4E3U9|D3DV57|Q4G0E5|Q5VUQ5|Q5VUQ6|Q5VUR0|Q5VUR1|Q68DJ1|Q69YR5|Q6AI57|Q6DKG7|Q6MZQ4|Q6MZZ9|Q8NC46|Q8TB23|Q9H6S9	Missense_Mutation	SNP	ENST00000318967.2	37	CCDS1052.1	.	.	.	.	.	.	.	.	.	.	G	15.62	2.887087	0.52014	.	.	ENSG00000143624	ENST00000318967;ENST00000456435;ENST00000435409;ENST00000512605	.	.	.	4.91	1.99	0.26369	.	0.000000	0.85682	D	0.000000	T	0.57770	0.2076	M	0.64404	1.975	0.42968	D	0.994425	D;D;D	0.64830	0.994;0.98;0.988	D;D;D	0.78314	0.991;0.948;0.977	T	0.59925	-0.7362	9	0.62326	D	0.03	.	7.1424	0.25564	0.2806:0.0:0.7194:0.0	.	477;684;683	Q68E01-3;Q68E01;Q68E01-2	.;INT3_HUMAN;.	H	683;477;683;477	.	ENSP00000318641:Q683H	Q	+	3	2	INTS3	152004122	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.298000	0.43602	0.258000	0.21686	0.563000	0.77884	CAG	.	.	none		0.532	INTS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090045.2	NM_023015	
ZKSCAN2	342357	hgsc.bcm.edu	37	16	25255503	25255503	+	Missense_Mutation	SNP	G	G	C	rs116889865		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:25255503G>C	ENST00000328086.7	-	6	2387	c.1584C>G	c.(1582-1584)agC>agG	p.S528R		NM_001012981.4	NP_001012999.3	Q63HK3	ZKSC2_HUMAN	zinc finger with KRAB and SCAN domains 2	528					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(8)|lung(15)|ovary(3)|prostate(1)|stomach(2)|upper_aerodigestive_tract(1)	36				GBM - Glioblastoma multiforme(48;0.0378)		CATACAATTTGCTCTTCCGAT	0.507													G|||	1	0.000199681	0.0	0.0	5008	,	,		18493	0.0		0.001	False		,,,				2504	0.0				p.S528R		Atlas-SNP	.											.	ZKSCAN2	90	.	0			c.C1584G						PASS	.	G	ARG/SER	3,4391	6.2+/-15.9	0,3,2194	68.0	68.0	68.0		1584	4.5	1.0	16	dbSNP_133	68	7,8593	6.4+/-24.3	0,7,4293	yes	missense	ZKSCAN2	NM_001012981.4	110	0,10,6487	CC,CG,GG		0.0814,0.0683,0.077	probably-damaging	528/968	25255503	10,12984	2197	4300	6497	SO:0001583	missense	342357	exon6			CAATTTGCTCTTC	AK026852	CCDS32410.1	16p12.1	2013-01-09	2007-02-20	2007-02-20		ENSG00000155592		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	25677	protein-coding gene	gene with protein product			"""zinc finger protein 694"""	ZNF694			Standard	NM_001012981		Approved	FLJ23199, ZSCAN34	uc002dod.4	Q63HK3		ENST00000328086.7:c.1584C>G	16.37:g.25255503G>C	ENSP00000331626:p.Ser528Arg	89.0	0.0	0		94.0	41.0	0.43617	NM_001012981	A1L3B4|Q6ZN77	Missense_Mutation	SNP	ENST00000328086.7	37	CCDS32410.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	18.80	3.700874	0.68501	6.83E-4	8.14E-4	ENSG00000155592	ENST00000328086;ENST00000536768	T	0.41400	1.0	5.48	4.53	0.55603	SANT domain, DNA binding (1);	0.000000	0.85682	D	0.000000	T	0.55689	0.1936	L	0.52011	1.625	0.37889	D	0.930635	D;D	0.76494	0.999;0.999	D;D	0.87578	0.998;0.998	T	0.60596	-0.7232	10	0.51188	T	0.08	-19.0721	10.586	0.45284	0.0889:0.0:0.9111:0.0	.	324;528	B4DYF0;Q63HK3	.;ZKSC2_HUMAN	R	528	ENSP00000331626:S528R	ENSP00000331626:S528R	S	-	3	2	ZKSCAN2	25163004	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.061000	0.30542	1.457000	0.47850	0.655000	0.94253	AGC	G|0.999;C|0.001	0.001	strong		0.507	ZKSCAN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000435739.1	NM_001012981	
PKHD1	5314	hgsc.bcm.edu	37	6	51613012	51613012	+	Silent	SNP	C	C	T	rs143737660		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:51613012C>T	ENST00000371117.3	-	58	9677	c.9402G>A	c.(9400-9402)aaG>aaA	p.K3134K	PKHD1_ENST00000340994.4_Silent_p.K3134K	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3134					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)			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)					GTCCACTTTCCTTATAGAGAT	0.463													C|||	1	0.000199681	0.0	0.0	5008	,	,		21874	0.0		0.0	False		,,,				2504	0.001				p.K3134K		Atlas-SNP	.											.	PKHD1	927	.	0			c.G9402A						PASS	.	C	,	0,4406		0,0,2203	201.0	209.0	206.0		9402,9402	3.0	0.1	6	dbSNP_134	206	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous,coding-synonymous	PKHD1	NM_138694.3,NM_170724.2	,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,	3134/4075,3134/3397	51613012	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	5314	exon58			ACTTTCCTTATAG	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.9402G>A	6.37:g.51613012C>T		108.0	0.0	0		91.0	43.0	0.472527	NM_170724	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Silent	SNP	ENST00000371117.3	37	CCDS4935.1																																																																																			C|0.999;T|0.001	0.001	strong		0.463	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040893.1	NM_138694	
ADRA1D	146	hgsc.bcm.edu	37	20	4228779	4228779	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4228779G>T	ENST00000379453.4	-	1	942	c.826C>A	c.(826-828)Cgc>Agc	p.R276S		NM_000678.3	NP_000669.1	P25100	ADA1D_HUMAN	adrenoceptor alpha 1D	276					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|adrenergic receptor signaling pathway (GO:0071875)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|DNA metabolic process (GO:0006259)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)|negative regulation of the force of heart contraction involved in baroreceptor response to increased systemic arterial blood pressure (GO:0001986)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|positive regulation of cell proliferation (GO:0008284)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha1-adrenergic receptor activity (GO:0004937)			endometrium(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	14					Alfuzosin(DB00346)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Amphetamine(DB00182)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Dapiprazole(DB00298)|Desipramine(DB01151)|Doxazosin(DB00590)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|Labetalol(DB00598)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methotrimeprazine(DB01403)|Methoxamine(DB00723)|Mianserin(DB06148)|Midodrine(DB00211)|Mirtazapine(DB00370)|Nicardipine(DB00622)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Oxymetazoline(DB00935)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Phenylephrine(DB00388)|Prazosin(DB00457)|Promazine(DB00420)|Propiomazine(DB00777)|Quetiapine(DB01224)|Sertindole(DB06144)|Silodosin(DB06207)|Tamsulosin(DB00706)|Terazosin(DB01162)|Xylometazoline(DB06694)	ACGTACACGCGGCAGTACATG	0.672																																					p.R276S		Atlas-SNP	.											.	ADRA1D	36	.	0			c.C826A						PASS	.						25.0	19.0	21.0					20																	4228779		2179	4285	6464	SO:0001583	missense	146	exon1			ACACGCGGCAGTA	U03864	CCDS13079.1	20p13	2012-08-08	2012-05-09		ENSG00000171873	ENSG00000171873		"""GPCR / Class A : Adrenoceptors : alpha"""	280	protein-coding gene	gene with protein product		104219	"""adrenergic, alpha-1D-, receptor"""			8039425	Standard	NM_000678		Approved	ADRA1R, ADRA1A, ADRA1	uc002wkr.2	P25100	OTTHUMG00000031779	ENST00000379453.4:c.826C>A	20.37:g.4228779G>T	ENSP00000368766:p.Arg276Ser	32.0	0.0	0		29.0	16.0	0.551724	NM_000678	Q9NPY0	Missense_Mutation	SNP	ENST00000379453.4	37	CCDS13079.1	.	.	.	.	.	.	.	.	.	.	g	18.67	3.673764	0.67928	.	.	ENSG00000171873	ENST00000379453	T	0.38560	1.13	4.25	4.25	0.50352	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.67813	0.2933	M	0.91140	3.18	0.47862	D	0.999538	D	0.76494	0.999	D	0.80764	0.994	T	0.73895	-0.3838	10	0.87932	D	0	.	9.4862	0.38931	0.0:0.0:0.7892:0.2108	.	276	P25100	ADA1D_HUMAN	S	276	ENSP00000368766:R276S	ENSP00000368766:R276S	R	-	1	0	ADRA1D	4176779	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.525000	0.45598	2.208000	0.71279	0.552000	0.68991	CGC	.	.	none		0.672	ADRA1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077812.2	NM_000678	
GNAS	2778	hgsc.bcm.edu	37	20	57429163	57429163	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:57429163C>T	ENST00000306120.3	+	1	653	c.653C>T	c.(652-654)tCg>tTg	p.S218L	GNAS_ENST00000371102.4_Silent_p.I281I|GNAS_ENST00000371075.3_Intron|GNAS_ENST00000371100.4_Silent_p.I281I|GNAS_ENST00000313949.7_Intron|GNAS_ENST00000371099.2_Silent_p.I281I|GNAS_ENST00000464624.2_3'UTR|GNAS_ENST00000371098.2_Intron			P63092	GNAS2_HUMAN	GNAS complex locus	0					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)			CAGGCGCCATCGGCAGCCCAT	0.687			Mis		pituitary adenoma		"""McCune-Albright syndrome; pseudohypoparathyroidism, type IA"""			TSP Lung(22;0.16)																											p.S219L	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.C656T						PASS	.						14.0	15.0	15.0					20																	57429163		1811	3992	5803	SO:0001583	missense	2778	exon1			CGCCATCGGCAGC	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	ENST00000306120.3:c.653C>T	20.37:g.57429163C>T	ENSP00000302237:p.Ser218Leu	53.0	0.0	0		63.0	22.0	0.349206	NM_001077490	A6NI00|E1P5G5|P04895|Q12927|Q14433|Q32P26|Q5JWD2|Q5JWD4|Q5JWD5|Q6NR75|Q6NXS0|Q8TBC0|Q96H70	Missense_Mutation	SNP	ENST00000306120.3	37		.	.	.	.	.	.	.	.	.	.	C	2.592	-0.295042	0.05532	.	.	ENSG00000087460	ENST00000306120	.	.	.	4.03	0.906	0.19314	.	.	.	.	.	T	0.23611	0.0571	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23833	-1.0177	5	0.27082	T	0.32	.	3.761	0.08604	0.0:0.5632:0.2068:0.23	.	.	.	.	L	218	.	ENSP00000302237:S218L	S	+	2	0	GNAS	56862558	0.000000	0.05858	0.008000	0.14137	0.415000	0.31203	0.170000	0.16663	0.235000	0.21160	0.561000	0.74099	TCG	.	.	none		0.687	GNAS-050	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000267987.1	NM_000516	
POLDIP3	84271	hgsc.bcm.edu	37	22	43010821	43010821	+	Missense_Mutation	SNP	C	C	T	rs61744232	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:43010821C>T	ENST00000252115.5	-	1	147	c.43G>A	c.(43-45)Gcg>Acg	p.A15T	POLDIP3_ENST00000348657.2_Missense_Mutation_p.A15T|POLDIP3_ENST00000339677.6_Missense_Mutation_p.A15T|RNU12_ENST00000362512.1_lincRNA	NM_032311.3	NP_115687.2	Q9BY77	PDIP3_HUMAN	polymerase (DNA-directed), delta interacting protein 3	15					poly(A)+ mRNA export from nucleus (GO:0016973)|positive regulation of translation (GO:0045727)	cytoplasm (GO:0005737)|nuclear speck (GO:0016607)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(3)|upper_aerodigestive_tract(1)	16						TTCGCCGCCGCCCCGCGCTTC	0.672													C|||	19	0.00379393	0.0	0.0115	5008	,	,		12867	0.0		0.0089	False		,,,				2504	0.002				p.A15T	Ovarian(52;967 1128 5875 19997 42537)	Atlas-SNP	.											.	POLDIP3	58	.	0			c.G43A						PASS	.	C	THR/ALA,THR/ALA	13,4393	20.2+/-43.8	0,13,2190	45.0	50.0	48.0		43,43	-1.5	0.0	22	dbSNP_129	48	93,8507	51.9+/-112.3	1,91,4208	yes	missense,missense	POLDIP3	NM_032311.3,NM_178136.1	58,58	1,104,6398	TT,TC,CC		1.0814,0.2951,0.815	benign,benign	15/422,15/393	43010821	106,12900	2203	4300	6503	SO:0001583	missense	84271	exon1			CCGCCGCCCCGCG		CCDS14038.1, CCDS14039.1, CCDS74873.1	22q13.31	2013-02-12			ENSG00000100227	ENSG00000100227		"""RNA binding motif (RRM) containing"""	23782	protein-coding gene	gene with protein product		611520				12522211	Standard	NM_032311		Approved	PDIP46, KIAA1649	uc003bcu.3	Q9BY77	OTTHUMG00000150887	ENST00000252115.5:c.43G>A	22.37:g.43010821C>T	ENSP00000252115:p.Ala15Thr	52.0	0.0	0		99.0	41.0	0.414141	NM_178136	A8K6F8|A8K6V9|Q009A7|Q5H972|Q6PGN6|Q7Z6Z0|Q9NSP5|Q9NSP6	Missense_Mutation	SNP	ENST00000252115.5	37	CCDS14038.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	3.855	-0.030975	0.07543	0.002951	0.010814	ENSG00000100227	ENST00000348657;ENST00000252115;ENST00000415122;ENST00000339677;ENST00000452567	.	.	.	4.4	-1.47	0.08772	.	0.803483	0.11757	N	0.532429	T	0.08891	0.0220	N	0.04508	-0.205	0.09310	N	0.999995	B;B;B;B	0.06786	0.001;0.0;0.0;0.0	B;B;B;B	0.08055	0.001;0.003;0.001;0.0	T	0.29882	-0.9997	9	0.13470	T	0.59	-16.8684	4.6712	0.12691	0.1382:0.4646:0.0:0.3972	.	15;15;15;15	B4E0L0;Q6R954;Q9BY77-2;Q9BY77	.;.;.;PDIP3_HUMAN	T	15	.	ENSP00000252115:A15T	A	-	1	0	POLDIP3	41340765	0.001000	0.12720	0.000000	0.03702	0.689000	0.40095	0.621000	0.24418	-0.251000	0.09542	-0.259000	0.10710	GCG	C|0.995;T|0.005	0.005	strong		0.672	POLDIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320433.1	NM_032311	
TRPM5	29850	hgsc.bcm.edu	37	11	2436201	2436201	+	Missense_Mutation	SNP	C	C	T	rs202052284		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2436201C>T	ENST00000155858.6	-	10	1564	c.1556G>A	c.(1555-1557)cGg>cAg	p.R519Q	TRPM5_ENST00000528453.1_Missense_Mutation_p.R519Q|TRPM5_ENST00000533060.1_Missense_Mutation_p.R519Q|TRPM5_ENST00000452833.1_Missense_Mutation_p.R521Q	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)		GAACAGGTCCCGCCAGGGGTT	0.711																																					p.R519Q	NSCLC(1;49 61 17205 18850 43201)	Atlas-SNP	.											.	TRPM5	86	.	0			c.G1556A						PASS	.	C	GLN/ARG	1,4355		0,1,2177	23.0	29.0	27.0		1556	3.7	1.0	11		27	2,8566		0,2,4282	yes	missense	TRPM5	NM_014555.3	43	0,3,6459	TT,TC,CC		0.0233,0.023,0.0232	probably-damaging	519/1166	2436201	3,12921	2178	4284	6462	SO:0001583	missense	29850	exon10			AGGTCCCGCCAGG	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.1556G>A	11.37:g.2436201C>T	ENSP00000155858:p.Arg519Gln	13.0	0.0	0		20.0	16.0	0.8	NM_014555		Missense_Mutation	SNP	ENST00000155858.6	37	CCDS31340.1	.	.	.	.	.	.	.	.	.	.	C	19.41	3.822268	0.71028	2.3E-4	2.33E-4	ENSG00000070985	ENST00000533881;ENST00000155858;ENST00000452833;ENST00000533060;ENST00000528453;ENST00000437542	D;D;D;D;D	0.84944	-1.92;-1.92;-1.92;-1.92;-1.92	3.68	3.68	0.42216	.	0.000000	0.85682	D	0.000000	D	0.87309	0.6145	L	0.46885	1.475	0.47214	D	0.999352	D;D;D	0.89917	1.0;1.0;0.993	D;D;P	0.65443	0.935;0.935;0.837	D	0.86502	0.1804	10	0.48119	T	0.1	-29.7753	9.9877	0.41852	0.2027:0.7973:0.0:0.0	.	519;521;519	E9PRW0;Q9NZQ8-2;Q9NZQ8	.;.;TRPM5_HUMAN	Q	513;519;521;519;519;519	ENSP00000434383:R513Q;ENSP00000155858:R519Q;ENSP00000387965:R521Q;ENSP00000434121:R519Q;ENSP00000436809:R519Q	ENSP00000155858:R519Q	R	-	2	0	TRPM5	2392777	0.861000	0.29849	0.957000	0.39632	0.939000	0.58152	3.421000	0.52742	2.069000	0.61940	0.491000	0.48974	CGG	C|0.998;T|0.002	0.002	weak		0.711	TRPM5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000027378.1	NM_014555	
ENOX1	55068	hgsc.bcm.edu	37	13	43987003	43987003	+	Missense_Mutation	SNP	C	C	G	rs7338624	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:43987003C>G	ENST00000261488.6	-	4	625	c.48G>C	c.(46-48)gaG>gaC	p.E16D	ENOX1_ENST00000412891.1_Missense_Mutation_p.E16D	NM_001242863.1|NM_017993.3	NP_001229792.1|NP_060463.2	Q8TC92	ENOX1_HUMAN	ecto-NOX disulfide-thiol exchanger 1	16			E -> D (in dbSNP:rs7338624). {ECO:0000269|PubMed:19055324}.		rhythmic process (GO:0048511)	extracellular region (GO:0005576)|plasma membrane (GO:0005886)	nucleic acid binding (GO:0003676)|nucleotide binding (GO:0000166)|oxidoreductase activity (GO:0016491)			breast(1)|endometrium(3)|large_intestine(7)|lung(18)|pancreas(2)|prostate(1)|skin(1)|urinary_tract(1)	34		Lung NSC(96;0.000518)|Prostate(109;0.0233)|Hepatocellular(98;0.0268)|Lung SC(185;0.0367)|Breast(139;0.0406)		GBM - Glioblastoma multiforme(144;0.00333)|BRCA - Breast invasive adenocarcinoma(63;0.172)		TCTGAGGAAGCTCCTGGGGAA	0.498													C|||	242	0.0483227	0.1778	0.0101	5008	,	,		16486	0.0		0.0	False		,,,				2504	0.0				p.E16D		Atlas-SNP	.											.	ENOX1	158	.	0			c.G48C						PASS	.	C	ASP/GLU,ASP/GLU,ASP/GLU	677,3729	286.3+/-278.7	49,579,1575	125.0	111.0	116.0		48,48,48	2.9	0.9	13	dbSNP_116	116	9,8591	5.7+/-21.5	0,9,4291	yes	missense,missense,missense	ENOX1	NM_001127615.1,NM_001242863.1,NM_017993.3	45,45,45	49,588,5866	GG,GC,CC		0.1047,15.3654,5.2745	benign,benign,benign	16/644,16/644,16/644	43987003	686,12320	2203	4300	6503	SO:0001583	missense	55068	exon4			AGGAAGCTCCTGG	EF432052	CCDS9389.1	13q14.11	2013-02-12			ENSG00000120658	ENSG00000120658		"""RNA binding motif (RRM) containing"""	25474	protein-coding gene	gene with protein product		610914				11360993	Standard	NM_001127615		Approved	FLJ10094, PIG38, CNOX, cCNOX	uc001uza.4	Q8TC92	OTTHUMG00000016818	ENST00000261488.6:c.48G>C	13.37:g.43987003C>G	ENSP00000261488:p.Glu16Asp	80.0	0.0	0		69.0	21.0	0.304348	NM_017993	A4GU15|A6NMH9|B7Z5K1|Q2TU81|Q5VT11|Q9NWE0	Missense_Mutation	SNP	ENST00000261488.6	37	CCDS9389.1	78	0.03571428571428571	74	0.15040650406504066	4	0.011049723756906077	0	0.0	0	0.0	C	11.61	1.690096	0.29962	0.153654	0.001047	ENSG00000120658	ENST00000261488;ENST00000412891	T;T	0.44083	0.93;0.93	5.91	2.88	0.33553	.	0.688144	0.14119	N	0.340181	T	0.00109	0.0003	N	0.08118	0	0.09310	P	0.99999166027	B	0.02656	0.0	B	0.01281	0.0	T	0.18241	-1.0343	9	0.19590	T	0.45	-0.328	2.7291	0.05222	0.2036:0.4159:0.0:0.3805	rs7338624;rs52798713;rs7338624	16	Q8TC92	ENOX1_HUMAN	D	16	ENSP00000261488:E16D;ENSP00000415054:E16D	ENSP00000261488:E16D	E	-	3	2	ENOX1	42885003	0.996000	0.38824	0.871000	0.34182	0.975000	0.68041	1.058000	0.30504	0.842000	0.35045	0.655000	0.94253	GAG	C|0.955;G|0.045	0.045	strong		0.498	ENOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044717.2	NM_017993	
TXNDC2	84203	hgsc.bcm.edu	37	18	9886275	9886275	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:9886275C>T	ENST00000306084.6	+	1	303	c.104C>T	c.(103-105)gCt>gTt	p.A35V	TXNDC2_ENST00000357775.5_Intron|TXNDC2_ENST00000536353.2_Intron|TXNDC2_ENST00000426718.3_3'UTR	NM_001098529.1	NP_001091999.1	Q86VQ3	TXND2_HUMAN	thioredoxin domain containing 2 (spermatozoa)	35					cell differentiation (GO:0030154)|cell redox homeostasis (GO:0045454)|glycerol ether metabolic process (GO:0006662)|multicellular organismal development (GO:0007275)|oxidation-reduction process (GO:0055114)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|motile cilium (GO:0031514)|nucleolus (GO:0005730)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)	nutrient reservoir activity (GO:0045735)|protein disulfide isomerase activity (GO:0003756)|protein disulfide oxidoreductase activity (GO:0015035)|thioredoxin-disulfide reductase activity (GO:0004791)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(9)|ovary(2)|pancreas(1)|skin(7)|urinary_tract(1)	31						GAAGGTGATGCTAATGGTAAG	0.468																																					p.A35V		Atlas-SNP	.											.	TXNDC2	168	.	0			c.C104T						PASS	.						75.0	75.0	75.0					18																	9886275		1940	4140	6080	SO:0001583	missense	84203	exon1			GTGATGCTAATGG	AF080095	CCDS11846.1, CCDS42414.1	18p11.31-p11.2	2009-03-11	2009-03-11	2007-08-16	ENSG00000168454	ENSG00000168454			16470	protein-coding gene	gene with protein product	"""sperm-specific thioredoxin 1"""					11230166, 11399755	Standard	NM_001098529		Approved	SPTRX1	uc002koi.4	Q86VQ3	OTTHUMG00000131602	ENST00000306084.6:c.104C>T	18.37:g.9886275C>T	ENSP00000304908:p.Ala35Val	94.0	0.0	0		72.0	34.0	0.472222	NM_001098529	A5YM73|Q8N7U4|Q96RX3|Q9H0L8	Missense_Mutation	SNP	ENST00000306084.6	37	CCDS42414.1	.	.	.	.	.	.	.	.	.	.	C	9.184	1.024442	0.19433	.	.	ENSG00000168454	ENST00000306084;ENST00000426718	T	0.05199	3.48	3.92	1.03	0.20045	.	.	.	.	.	T	0.03739	0.0106	L	0.27053	0.805	0.09310	N	1	B	0.26809	0.16	B	0.23275	0.045	T	0.44982	-0.9292	8	.	.	.	1.9805	2.2617	0.04068	0.1932:0.4906:0.2043:0.1119	.	35	Q86VQ3	TXND2_HUMAN	V	35	ENSP00000304908:A35V	.	A	+	2	0	TXNDC2	9876275	0.000000	0.05858	0.004000	0.12327	0.067000	0.16453	-0.468000	0.06656	0.206000	0.20587	0.563000	0.77884	GCT	.	.	none		0.468	TXNDC2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254487.1		
TAF7L	54457	hgsc.bcm.edu	37	X	100547805	100547805	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547805C>T	ENST00000372907.3	-	1	240	c.229G>A	c.(229-231)Gcc>Acc	p.A77T	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_5'UTR	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	77					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						TTTTCTGGGGCCTGGGCAGCA	0.557																																					p.A77T	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.G229A						PASS	.						70.0	70.0	70.0					X																	100547805		2203	4300	6503	SO:0001583	missense	54457	exon1			CTGGGGCCTGGGC	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.229G>A	X.37:g.100547805C>T	ENSP00000361998:p.Ala77Thr	52.0	0.0	0		46.0	44.0	0.956522	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	9.433	1.086161	0.20390	.	.	ENSG00000102387	ENST00000372907	T	0.14391	2.51	3.17	-6.35	0.01975	.	2.099320	0.02710	N	0.112725	T	0.10380	0.0254	L	0.27053	0.805	0.09310	N	0.999998	B	0.06786	0.001	B	0.04013	0.001	T	0.24835	-1.0149	10	0.51188	T	0.08	-1.4147	9.7024	0.40196	0.0:0.5863:0.2433:0.1704	.	77	Q5H9L4	TAF7L_HUMAN	T	77	ENSP00000361998:A77T	ENSP00000361998:A77T	A	-	1	0	TAF7L	100434461	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.202000	0.03023	-2.983000	0.00282	-0.340000	0.08031	GCC	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
ODF2	4957	hgsc.bcm.edu	37	9	131245130	131245130	+	Silent	SNP	G	G	A	rs139481144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131245130G>A	ENST00000434106.3	+	10	1314	c.951G>A	c.(949-951)gaG>gaA	p.E317E	ODF2_ENST00000546203.1_Silent_p.E298E|ODF2_ENST00000372791.3_Silent_p.E298E|ODF2_ENST00000393527.3_Silent_p.E293E|ODF2_ENST00000448249.3_Silent_p.E236E|ODF2_ENST00000444119.2_Silent_p.E293E|ODF2_ENST00000372807.5_Silent_p.E312E|ODF2_ENST00000372814.3_Silent_p.E361E|ODF2_ENST00000535026.1_3'UTR|ODF2_ENST00000604420.1_Silent_p.E317E|ODF2_ENST00000351030.3_Silent_p.E312E|ODF2_ENST00000393533.2_Silent_p.E317E	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	317					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						AGGACAAGGAGGTGGAAGAGC	0.537													G|||	3	0.000599042	0.0	0.0014	5008	,	,		16148	0.0		0.002	False		,,,				2504	0.0				p.E381E		Atlas-SNP	.											.	ODF2	227	.	0			c.G1143A						PASS	.	G	,,,,,,,,,,	0,4406		0,0,2203	97.0	100.0	99.0		936,951,708,879,1083,951,1143,951,894,1026,894	1.1	1.0	9	dbSNP_134	99	21,8579	14.0+/-48.4	0,21,4279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ODF2	NM_001242352.1,NM_001242353.1,NM_001242354.1,NM_002540.4,NM_153432.1,NM_153433.1,NM_153435.1,NM_153436.1,NM_153437.2,NM_153439.1,NM_153440.1	,,,,,,,,,,	0,21,6482	AA,AG,GG		0.2442,0.0,0.1615	,,,,,,,,,,	312/825,317/830,236/577,293/806,361/702,317/830,381/894,317/658,298/639,342/654,298/639	131245130	21,12985	2203	4300	6503	SO:0001819	synonymous_variant	4957	exon10			CAAGGAGGTGGAA	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.951G>A	9.37:g.131245130G>A		57.0	0.0	0		82.0	41.0	0.5	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Silent	SNP	ENST00000434106.3	37	CCDS56588.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
COL18A1	80781	hgsc.bcm.edu	37	21	46875586	46875586	+	Missense_Mutation	SNP	C	C	G	rs61749002	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46875586C>G	ENST00000359759.4	+	1	163	c.142C>G	c.(142-144)Ccc>Gcc	p.P48A	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Missense_Mutation_p.P48A			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	48					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|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)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GATCCCTGAGCCCCAGGGGCC	0.637													C|||	99	0.0197684	0.0688	0.0115	5008	,	,		16000	0.0		0.0	False		,,,				2504	0.0				p.P48A		Atlas-SNP	.											.	COL18A1	129	.	0			c.C142G						PASS	.	C	,ALA/PRO	243,3931		6,231,1850	52.0	69.0	63.0		,142	0.2	0.0	21	dbSNP_129	63	1,8439		0,1,4219	yes	intron,missense	COL18A1	NM_130445.2,NM_030582.3	,27	6,232,6069	GG,GC,CC		0.0118,5.8218,1.9344	,benign	,48/1520	46875586	244,12370	2087	4220	6307	SO:0001583	missense	80781	exon1			CCTGAGCCCCAGG		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.142C>G	21.37:g.46875586C>G	ENSP00000352798:p.Pro48Ala	111.0	0.0	0		145.0	66.0	0.455172	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		54	0.024725274725274724	48	0.0975609756097561	4	0.011049723756906077	2	0.0034965034965034965	0	0.0	C	8.524	0.869347	0.17322	0.058218	1.18E-4	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.59906	0.23;0.23	3.33	0.153	0.14897	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	1.487630	0.05437	N	0.546948	T	0.01627	0.0052	L	0.34521	1.04	0.09310	N	1	B;B	0.14438	0.01;0.002	B;B	0.17098	0.017;0.003	T	0.15407	-1.0438	10	0.87932	D	0	.	6.156	0.20338	0.0:0.5294:0.3598:0.1108	rs61749002	48;48	P39060;P39060-1	COIA1_HUMAN;.	A	48	ENSP00000347665:P48A;ENSP00000352798:P48A	ENSP00000347665:P48A	P	+	1	0	COL18A1	45700014	0.000000	0.05858	0.049000	0.19019	0.056000	0.15407	-0.676000	0.05221	-0.110000	0.12022	0.436000	0.28706	CCC	C|0.976;G|0.024	0.024	strong		0.637	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
ZNF215	7762	hgsc.bcm.edu	37	11	6977109	6977109	+	Missense_Mutation	SNP	T	T	C	rs149189074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6977109T>C	ENST00000278319.5	+	7	1489	c.901T>C	c.(901-903)Ttt>Ctt	p.F301L	ZNF215_ENST00000527171.1_3'UTR|ZNF215_ENST00000414517.2_Missense_Mutation_p.F301L|ZNF215_ENST00000529903.1_Intron	NM_013250.2	NP_037382.2	Q9UL58	ZN215_HUMAN	zinc finger protein 215	301					regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(12)|ovary(1)|prostate(2)|skin(4)	32				Epithelial(150;6.33e-08)|BRCA - Breast invasive adenocarcinoma(625;0.134)		GGAGGAAGATTTTGAATGTAG	0.353													T|||	12	0.00239617	0.0	0.0014	5008	,	,		18696	0.0		0.0099	False		,,,				2504	0.001				p.F301L		Atlas-SNP	.											.	ZNF215	72	.	0			c.T901C						PASS	.	T	LEU/PHE	4,4398	8.1+/-20.4	0,4,2197	72.0	83.0	79.0		901	3.1	0.0	11	dbSNP_134	79	56,8530	31.7+/-84.0	0,56,4237	yes	missense	ZNF215	NM_013250.2	22	0,60,6434	CC,CT,TT		0.6522,0.0909,0.462	possibly-damaging	301/518	6977109	60,12928	2201	4293	6494	SO:0001583	missense	7762	exon7			GAAGATTTTGAAT	AF056618	CCDS7775.1	11p15.4	2013-01-09			ENSG00000149054	ENSG00000149054		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	13007	protein-coding gene	gene with protein product		605016					Standard	XM_005253130		Approved	ZKSCAN11, ZSCAN43	uc001mey.3	Q9UL58	OTTHUMG00000165507	ENST00000278319.5:c.901T>C	11.37:g.6977109T>C	ENSP00000278319:p.Phe301Leu	74.0	0.0	0		108.0	51.0	0.472222	NM_013250	Q96C84	Missense_Mutation	SNP	ENST00000278319.5	37	CCDS7775.1	10	0.004578754578754579	0	0.0	1	0.0027624309392265192	0	0.0	9	0.011873350923482849	T	10.32	1.318071	0.23994	9.09E-4	0.006522	ENSG00000149054	ENST00000278319;ENST00000414517	T;T	0.04809	3.55;3.55	4.27	3.11	0.35812	.	0.516746	0.16372	N	0.217295	T	0.02047	0.0064	N	0.14661	0.345	0.21675	N	0.999599	B	0.22346	0.068	B	0.15484	0.013	T	0.45056	-0.9287	10	0.30854	T	0.27	-2.7081	8.4029	0.32597	0.1755:0.0:0.0:0.8245	.	301	Q9UL58	ZN215_HUMAN	L	301	ENSP00000278319:F301L;ENSP00000393202:F301L	ENSP00000278319:F301L	F	+	1	0	ZNF215	6933685	0.001000	0.12720	0.001000	0.08648	0.011000	0.07611	0.972000	0.29409	0.757000	0.33036	0.533000	0.62120	TTT	T|0.996;C|0.004	0.004	strong		0.353	ZNF215-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384550.1		
RAD54B	25788	hgsc.bcm.edu	37	8	95399378	95399378	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:95399378A>G	ENST00000336148.5	-	11	1943	c.1819T>C	c.(1819-1821)Tgt>Cgt	p.C607R		NM_012415.3	NP_036547.1	Q9Y620	RA54B_HUMAN	RAD54 homolog B (S. cerevisiae)	607					ATP catabolic process (GO:0006200)|DNA duplex unwinding (GO:0032508)|double-strand break repair via homologous recombination (GO:0000724)|mitotic recombination (GO:0006312)|reciprocal meiotic recombination (GO:0007131)	nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|RNA helicase activity (GO:0003724)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(10)|lung(15)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	39	Breast(36;4.5e-05)		BRCA - Breast invasive adenocarcinoma(8;0.00217)			GTTGAGCTACATTCCTTTTCC	0.348								Direct reversal of damage;Homologous recombination																													p.C607R		Atlas-SNP	.											.	RAD54B	88	.	0			c.T1819C						PASS	.						101.0	94.0	97.0					8																	95399378		2203	4300	6503	SO:0001583	missense	25788	exon11			AGCTACATTCCTT	AF112481	CCDS6262.1, CCDS56546.1, CCDS75768.1	8q22.1	2014-08-08			ENSG00000197275	ENSG00000197275			17228	protein-coding gene	gene with protein product		604289				10362364, 10851248	Standard	NM_012415		Approved	RDH54	uc003ygk.3	Q9Y620	OTTHUMG00000133658	ENST00000336148.5:c.1819T>C	8.37:g.95399378A>G	ENSP00000336606:p.Cys607Arg	190.0	0.0	0		180.0	81.0	0.45	NM_012415	F6WBS8	Missense_Mutation	SNP	ENST00000336148.5	37	CCDS6262.1	.	.	.	.	.	.	.	.	.	.	A	7.240	0.601139	0.13939	.	.	ENSG00000197275	ENST00000336148;ENST00000546218	D	0.88586	-2.4	5.28	-0.253	0.12996	.	1.072940	0.06949	N	0.814172	T	0.81550	0.4846	L	0.60455	1.87	0.21416	N	0.999695	B	0.33413	0.411	B	0.25506	0.061	T	0.63462	-0.6632	10	0.14656	T	0.56	-24.2196	3.5354	0.07792	0.5686:0.0:0.1549:0.2765	.	607	Q9Y620	RA54B_HUMAN	R	607;279	ENSP00000336606:C607R	ENSP00000336606:C607R	C	-	1	0	RAD54B	95468554	0.224000	0.23674	0.348000	0.25681	0.965000	0.64279	0.519000	0.22862	0.025000	0.15241	0.477000	0.44152	TGT	.	.	none		0.348	RAD54B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257806.3	NM_012415	
GPRIN2	9721	hgsc.bcm.edu	37	10	46998904	46998904	+	Silent	SNP	G	G	A	rs140651048		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:46998904G>A	ENST00000374317.1	+	3	297	c.24G>A	c.(22-24)ccG>ccA	p.P8P	GPRIN2_ENST00000374314.4_Silent_p.P8P	NM_014696.3	NP_055511.2	O60269	GRIN2_HUMAN	G protein regulated inducer of neurite outgrowth 2	8										breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)	18						GCCCCGAGCCGGGTCCCTGGG	0.642													G|||	1	0.000199681	0.0	0.0	5008	,	,		31822	0.001		0.0	False		,,,				2504	0.0				p.P8P		Atlas-SNP	.											.	GPRIN2	94	.	0			c.G24A						PASS	.	G		1,4371		0,1,2185	51.0	71.0	64.0		24	-10.7	0.0	10	dbSNP_134	64	0,8544		0,0,4272	no	coding-synonymous	GPRIN2	NM_014696.3		0,1,6457	AA,AG,GG		0.0,0.0229,0.0077		8/459	46998904	1,12915	2186	4272	6458	SO:0001819	synonymous_variant	9721	exon3			CGAGCCGGGTCCC	BC011672	CCDS73101.1	10q11.22	2006-08-24	2006-08-24	2006-08-24	ENSG00000204175	ENSG00000204175			23730	protein-coding gene	gene with protein product		611240	"""KIAA0514"""	KIAA0514		9628581	Standard	NM_014696		Approved	MGC15171	uc001jec.3	O60269	OTTHUMG00000018107	ENST00000374317.1:c.24G>A	10.37:g.46998904G>A		239.0	0.0	0		140.0	32.0	0.228571	NM_014696	Q5SVF0	Silent	SNP	ENST00000374317.1	37	CCDS31192.1																																																																																			G|0.999;A|0.001	0.001	strong		0.642	GPRIN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047836.1	NM_014696	
NRG1	3084	hgsc.bcm.edu	37	8	32611970	32611970	+	Missense_Mutation	SNP	G	G	T	rs74942016	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:32611970G>T	ENST00000405005.3	+	8	781	c.781G>T	c.(781-783)Gtg>Ttg	p.V261L	NRG1_ENST00000519301.1_Missense_Mutation_p.V211L|NRG1_ENST00000341377.5_3'UTR|NRG1_ENST00000287842.3_Missense_Mutation_p.V258L|NRG1_ENST00000523079.1_Missense_Mutation_p.V258L|NRG1_ENST00000521670.1_Missense_Mutation_p.V261L|NRG1_ENST00000539990.1_Missense_Mutation_p.V104L|NRG1_ENST00000287845.5_Missense_Mutation_p.V232L|NRG1_ENST00000356819.4_Missense_Mutation_p.V266L|NRG1_ENST00000338921.4_Missense_Mutation_p.V269L			Q02297	NRG1_HUMAN	neuregulin 1	261				V -> L (in Ref. 10; ABQ53540). {ECO:0000305}.	activation of transmembrane receptor protein tyrosine kinase activity (GO:0007171)|cardiac conduction system development (GO:0003161)|cardiac muscle cell differentiation (GO:0055007)|cardiac muscle cell myoblast differentiation (GO:0060379)|cell communication (GO:0007154)|cell migration (GO:0016477)|cell morphogenesis (GO:0000902)|cell proliferation (GO:0008283)|cellular protein complex disassembly (GO:0043624)|embryo development (GO:0009790)|endocardial cell differentiation (GO:0060956)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glial cell fate commitment (GO:0021781)|innate immune response (GO:0045087)|locomotory behavior (GO:0007626)|mammary gland development (GO:0030879)|MAPK cascade (GO:0000165)|negative regulation of cardiac muscle cell apoptotic process (GO:0010667)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of protein catabolic process (GO:0042177)|negative regulation of secretion (GO:0051048)|negative regulation of transcription, DNA-templated (GO:0045892)|nervous system development (GO:0007399)|neural crest cell development (GO:0014032)|neuron fate commitment (GO:0048663)|neurotransmitter receptor metabolic process (GO:0045213)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peripheral nervous system development (GO:0007422)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell adhesion (GO:0045785)|positive regulation of cell growth (GO:0030307)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of Ras protein signal transduction (GO:0046579)|positive regulation of striated muscle cell differentiation (GO:0051155)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|synapse assembly (GO:0007416)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular trabecula myocardium morphogenesis (GO:0003222)|wound healing (GO:0042060)	apical plasma membrane (GO:0016324)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)	cytokine activity (GO:0005125)|ErbB-3 class receptor binding (GO:0043125)|growth factor activity (GO:0008083)|protein tyrosine kinase activator activity (GO:0030296)|receptor binding (GO:0005102)|receptor tyrosine kinase binding (GO:0030971)|transcription cofactor activity (GO:0003712)|transmembrane receptor protein tyrosine kinase activator activity (GO:0030297)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(18)|ovary(1)|prostate(1)|skin(1)	39		Breast(100;0.203)		KIRC - Kidney renal clear cell carcinoma(67;0.0768)|Kidney(114;0.0943)		CATCATGTGTGTGGTGGCCTA	0.527													G|||	72	0.014377	0.0008	0.0259	5008	,	,		17487	0.0		0.0467	False		,,,				2504	0.0061				p.V266L		Atlas-SNP	.											.	NRG1	260	.	0			c.G796T	GRCh37	CM066934	NRG1	M	rs74942016	PASS	.	G	LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL,LEU/VAL	47,4359	48.9+/-83.8	0,47,2156	226.0	165.0	186.0		682,319,733,631,772,772,796,772,781,781	5.6	1.0	8	dbSNP_131	186	405,8195	127.5+/-185.8	12,381,3907	yes	missense,missense,missense,missense,missense,missense,missense,missense,missense,missense	NRG1	NM_001159995.1,NM_001159996.1,NM_001159999.1,NM_001160001.1,NM_001160004.1,NM_001160008.1,NM_013956.3,NM_013957.3,NM_013960.3,NM_013964.3	32,32,32,32,32,32,32,32,32,32	12,428,6063	TT,TG,GG		4.7093,1.0667,3.4753	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	228/608,107/309,245/625,211/591,258/460,258/421,266/646,258/638,261/463,261/641	32611970	452,12554	2203	4300	6503	SO:0001583	missense	3084	exon9			ATGTGTGTGGTGG	L12261	CCDS6084.1, CCDS6085.1, CCDS6086.1, CCDS6087.1, CCDS47836.1, CCDS55218.1, CCDS55219.1, CCDS75727.1	8p21-p12	2014-06-23			ENSG00000157168	ENSG00000157168		"""Immunoglobulin superfamily / I-set domain containing"""	7997	protein-coding gene	gene with protein product		142445	"""NRG1 intronic transcript 2 (non-protein coding)"""	HGL, NRG1-IT2		1350381, 8095334	Standard	NM_013962		Approved	HRG, NDF, GGF	uc003xiu.2	Q02297	OTTHUMG00000163918	ENST00000405005.3:c.781G>T	8.37:g.32611970G>T	ENSP00000384620:p.Val261Leu	146.0	0.0	0		168.0	76.0	0.452381	NM_013956	A5YAK4|A5YAK5|A8K1L2|B7Z4Z3|E9PHH4|O14667|P98202|Q02298|Q02299|Q07110|Q07111|Q12779|Q12780|Q12781|Q12782|Q12783|Q12784|Q15491|Q7RTV9|Q7RTW0|Q7RTW1|Q7RTW2|Q8NFN1|Q8NFN2|Q8NFN3|Q9UPE3	Missense_Mutation	SNP	ENST00000405005.3	37	CCDS6085.1	40	0.018315018315018316	0	0.0	9	0.024861878453038673	0	0.0	31	0.040897097625329816	G	35	5.558867	0.96514	0.010667	0.047093	ENSG00000157168	ENST00000518104;ENST00000519301;ENST00000523534;ENST00000523079;ENST00000338921;ENST00000356819;ENST00000287840;ENST00000287845;ENST00000287842;ENST00000405005;ENST00000521670;ENST00000522402;ENST00000519240;ENST00000539990	T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.61040	0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;0.14;2.63;0.14	5.62	5.62	0.85841	Neuregulin 1-related, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.40932	0.1137	M	0.73962	2.25	0.80722	D	1	D;D;D;D;D;D;P;D;P;D;D	0.71674	0.979;0.998;0.995;0.979;0.983;0.995;0.599;0.962;0.946;0.979;0.994	D;D;D;P;D;D;B;P;P;P;D	0.85130	0.986;0.997;0.972;0.879;0.926;0.972;0.283;0.879;0.893;0.879;0.914	T	0.67722	-0.5597	10	0.72032	D	0.01	-36.9375	19.6569	0.95845	0.0:0.0:1.0:0.0	.	104;107;258;232;266;257;269;258;261;266;261	B7Z1E3;B7Z1D7;E9PHH4;F8W9E3;Q7RTW4;B0FYA9;Q02297-2;Q02297-7;Q02297;Q02297-6;Q02297-3	.;.;.;.;.;.;.;.;NRG1_HUMAN;.;.	L	228;211;334;258;269;266;261;232;258;261;261;107;104;104	ENSP00000430053:V228L;ENSP00000429582:V211L;ENSP00000429067:V334L;ENSP00000430120:V258L;ENSP00000343395:V269L;ENSP00000349275:V266L;ENSP00000287840:V261L;ENSP00000287845:V232L;ENSP00000287842:V258L;ENSP00000384620:V261L;ENSP00000428828:V261L;ENSP00000430862:V107L;ENSP00000428411:V104L;ENSP00000439276:V104L	ENSP00000287840:V261L	V	+	1	0	NRG1	32731512	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.869000	0.99810	2.639000	0.89480	0.650000	0.86243	GTG	G|0.968;T|0.032	0.032	strong		0.527	NRG1-017	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000472504.1		
IFT122	55764	hgsc.bcm.edu	37	3	129237966	129237966	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:129237966G>A	ENST00000348417.2	+	28	3485	c.3408G>A	c.(3406-3408)cgG>cgA	p.R1136R	IFT122_ENST00000349441.2_Silent_p.R1026R|IFT122_ENST00000296266.3_Silent_p.R1187R|IFT122_ENST00000440957.2_Silent_p.R927R|IFT122_ENST00000347300.2_Silent_p.R1077R|IFT122_ENST00000507564.1_Silent_p.R1129R|IFT122_ENST00000504021.1_Silent_p.R1013R|IFT122_ENST00000431818.2_Silent_p.R986R	NM_052989.1	NP_443715.1	Q9HBG6	IF122_HUMAN	intraflagellar transport 122	1136					camera-type eye morphogenesis (GO:0048593)|ciliary receptor clustering involved in smoothened signaling pathway (GO:0060830)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|embryonic digit morphogenesis (GO:0042733)|embryonic forelimb morphogenesis (GO:0035115)|embryonic heart tube development (GO:0035050)|embryonic heart tube left/right pattern formation (GO:0060971)|establishment of protein localization to organelle (GO:0072594)|intraciliary anterograde transport (GO:0035720)|intraciliary retrograde transport (GO:0035721)|limb development (GO:0060173)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of smoothened signaling pathway involved in ventral spinal cord patterning (GO:0021914)|neural tube closure (GO:0001843)|protein localization to cilium (GO:0061512)|signal transduction downstream of smoothened (GO:0007227)|smoothened signaling pathway involved in dorsal/ventral neural tube patterning (GO:0060831)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|intraciliary transport particle A (GO:0030991)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|primary cilium (GO:0072372)				breast(3)|cervix(1)|endometrium(9)|large_intestine(10)|lung(21)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	52						AGATTCTGCGGCTAGTGGAGA	0.577																																					p.R1187R		Atlas-SNP	.											.	IFT122	117	.	0			c.G3561A						PASS	.						120.0	121.0	121.0					3																	129237966		2203	4300	6503	SO:0001819	synonymous_variant	55764	exon29			TCTGCGGCTAGTG	AF244930	CCDS3059.1, CCDS3060.1, CCDS3061.1, CCDS3062.1, CCDS63770.1, CCDS63772.1, CCDS63773.1	3q21	2014-07-03	2014-07-03	2005-11-02	ENSG00000163913	ENSG00000163913		"""WD repeat domain containing"", ""Intraflagellar transport homologs"""	13556	protein-coding gene	gene with protein product		606045	"""WD repeat domain 10"", ""intraflagellar transport 122 homolog (Chlamydomonas)"""	WDR10		11242542	Standard	NM_052985		Approved	WDR140, WDR10p, SPG	uc003emm.3	Q9HBG6	OTTHUMG00000159516	ENST00000348417.2:c.3408G>A	3.37:g.129237966G>A		81.0	0.0	0		100.0	42.0	0.42	NM_052985	B3KW53|B4DEY9|B4DPW7|E7EQF4|E9PDG2|E9PDX2|G3XAB1|H7C3C0|Q53G36|Q8TC06|Q9BTB9|Q9BTY4|Q9HAT9|Q9HBG5|Q9NV68|Q9UF80	Silent	SNP	ENST00000348417.2	37	CCDS3061.1																																																																																			.	.	none		0.577	IFT122-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355852.1	NM_018262	
MAP3K9	4293	hgsc.bcm.edu	37	14	71267772	71267772	+	Silent	SNP	G	G	A	rs147891121	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:71267772G>A	ENST00000554752.2	-	2	431	c.432C>T	c.(430-432)ctC>ctT	p.L144L	MAP3K9_ENST00000381250.4_Silent_p.L144L|MAP3K9_ENST00000555993.2_Silent_p.L144L	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	144	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		CTTCCAAGGTGAGCTCCGCAA	0.438																																					p.L144L	GBM(114;411 1587 13539 28235 50070)	Atlas-SNP	.											.	MAP3K9	109	.	0			c.C432T						PASS	.	G		0,4406		0,0,2203	57.0	58.0	58.0		432	-2.0	1.0	14	dbSNP_134	58	4,8596	3.7+/-12.6	0,4,4296	no	coding-synonymous	MAP3K9	NM_033141.2		0,4,6499	AA,AG,GG		0.0465,0.0,0.0308		144/1119	71267772	4,13002	2203	4300	6503	SO:0001819	synonymous_variant	4293	exon2			CAAGGTGAGCTCC	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.432C>T	14.37:g.71267772G>A		68.0	0.0	0		75.0	35.0	0.466667	NM_033141	A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Silent	SNP	ENST00000554752.2	37																																																																																				G|1.000;A|0.000	0.000	strong		0.438	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
RADIL	55698	hgsc.bcm.edu	37	7	4843307	4843307	+	Missense_Mutation	SNP	T	T	C	rs187128776	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4843307T>C	ENST00000399583.3	-	11	2556	c.2369A>G	c.(2368-2370)aAc>aGc	p.N790S	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.N550S	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	790					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N790S(1)		NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GTCCAGGCAGTTGGCTTCCAA	0.647													T|||	63	0.0125799	0.0015	0.0187	5008	,	,		11788	0.0		0.0239	False		,,,				2504	0.0245				p.N790S		Atlas-SNP	.											RADIL,brain,glioma,0,1	RADIL	110	1	1	Substitution - Missense(1)	central_nervous_system(1)	c.A2369G						PASS	.						19.0	26.0	24.0					7																	4843307		1977	4092	6069	SO:0001583	missense	55698	exon11			AGGCAGTTGGCTT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2369A>G	7.37:g.4843307T>C	ENSP00000382492:p.Asn790Ser	97.0	0.0	0		72.0	27.0	0.375	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	33	0.01510989010989011	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	18	0.023746701846965697	T	0.543	-0.852823	0.02630	.	.	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.06449	3.37;3.3	4.27	3.12	0.35913	.	0.502188	0.20854	N	0.084468	T	0.00695	0.0023	N	0.08118	0	0.19300	N	0.999978	B;B	0.09022	0.0;0.002	B;B	0.01281	0.0;0.0	T	0.46925	-0.9156	10	0.23302	T	0.38	-15.6944	6.6406	0.22906	0.0:0.187:0.0:0.813	.	790;98	Q96JH8;Q75LH2	RADIL_HUMAN;.	S	790;761;524;550	ENSP00000382492:N790S;ENSP00000442966:N550S	ENSP00000320946:N761S	N	-	2	0	RADIL	4809833	0.936000	0.31750	0.004000	0.12327	0.026000	0.11368	3.515000	0.53429	0.692000	0.31613	0.459000	0.35465	AAC	T|0.985;C|0.015	0.015	strong		0.647	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
ASB17	127247	hgsc.bcm.edu	37	1	76387795	76387795	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:76387795C>T	ENST00000284142.6	-	2	790	c.651G>A	c.(649-651)gtG>gtA	p.V217V		NM_080868.2	NP_543144.1	Q8WXJ9	ASB17_HUMAN	ankyrin repeat and SOCS box containing 17	217					intracellular signal transduction (GO:0035556)|protein ubiquitination (GO:0016567)					breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(11)|ovary(2)|urinary_tract(1)	21						TGACAGAAAGCACTCTGGAAC	0.353																																					p.V217V		Atlas-SNP	.											.	ASB17	53	.	0			c.G651A						PASS	.						80.0	68.0	72.0					1																	76387795		2203	4300	6503	SO:0001819	synonymous_variant	127247	exon2			AGAAAGCACTCTG	AF403035	CCDS671.1	1p22.3	2013-01-11	2011-01-25		ENSG00000154007	ENSG00000154007		"""Ankyrin repeat domain containing"""	19769	protein-coding gene	gene with protein product			"""ankyrin repeat and SOCS box-containing 17"""			12076535	Standard	NM_080868		Approved		uc001dhe.2	Q8WXJ9	OTTHUMG00000009787	ENST00000284142.6:c.651G>A	1.37:g.76387795C>T		105.0	0.0	0		104.0	48.0	0.461538	NM_080868	B1APB8|Q8N0X5	Silent	SNP	ENST00000284142.6	37	CCDS671.1																																																																																			.	.	none		0.353	ASB17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026982.1	NM_080868	
CYP3A5	1577	hgsc.bcm.edu	37	7	99273815	99273815	+	Missense_Mutation	SNP	G	G	A	rs28383468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99273815G>A	ENST00000222982.4	-	2	187	c.88C>T	c.(88-90)Cat>Tat	p.H30Y	CYP3A5_ENST00000439761.1_Missense_Mutation_p.H30Y|CYP3A5_ENST00000480723.1_5'UTR|CYP3A5_ENST00000343703.5_Missense_Mutation_p.H20Y|CYP3A5_ENST00000339843.2_3'UTR	NM_000777.3	NP_000768.1	P20815	CP3A5_HUMAN	cytochrome P450, family 3, subfamily A, polypeptide 5	30			H -> Y (in dbSNP:rs28383468). {ECO:0000269|PubMed:15469410}.		alkaloid catabolic process (GO:0009822)|drug catabolic process (GO:0042737)|oxidative demethylation (GO:0070989)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxygen binding (GO:0019825)			NS(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16	all_epithelial(64;2.77e-08)|Lung NSC(181;0.00396)|all_lung(186;0.00659)|Esophageal squamous(72;0.0166)				ado-trastuzumab emtansine(DB05773)|Alfentanil(DB00802)|Alprazolam(DB00404)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Amprenavir(DB00701)|Apixaban(DB06605)|Aprepitant(DB00673)|Argatroban(DB00278)|Aripiprazole(DB01238)|Artemether(DB06697)|Astemizole(DB00637)|Atorvastatin(DB01076)|Axitinib(DB06626)|Azelastine(DB00972)|Beclomethasone(DB00394)|Boceprevir(DB08873)|Brentuximab vedotin(DB08870)|Buprenorphine(DB00921)|Buspirone(DB00490)|Cabazitaxel(DB06772)|Caffeine(DB00201)|Carbamazepine(DB00564)|Chloramphenicol(DB00446)|Chloroquine(DB00608)|Chlorphenamine(DB01114)|Cilostazol(DB01166)|Cimetidine(DB00501)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Clarithromycin(DB01211)|Clonidine(DB00575)|Clopidogrel(DB00758)|Cocaine(DB00907)|Codeine(DB00318)|Crizotinib(DB08865)|Cyclophosphamide(DB00531)|Cyclosporine(DB00091)|Dapsone(DB00250)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Dexamethasone(DB01234)|Dextromethorphan(DB00514)|Diazepam(DB00829)|Diltiazem(DB00343)|Disulfiram(DB00822)|Docetaxel(DB01248)|Dolutegravir(DB08930)|Domperidone(DB01184)|Dutasteride(DB01126)|Enzalutamide(DB08899)|Eplerenone(DB00700)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Ethosuximide(DB00593)|Etoposide(DB00773)|Felodipine(DB01023)|Fentanyl(DB00813)|Finasteride(DB01216)|Fluconazole(DB00196)|Fluoxetine(DB00472)|Flutamide(DB00499)|Fluticasone Propionate(DB00588)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Gefitinib(DB00317)|Gestodene(DB06730)|Granisetron(DB00889)|Halofantrine(DB01218)|Haloperidol(DB00502)|Hydrocortisone(DB00741)|Ifosfamide(DB01181)|Iloperidone(DB04946)|Imatinib(DB00619)|Indinavir(DB00224)|Irinotecan(DB00762)|Itraconazole(DB01167)|Ketoconazole(DB01026)|Lapatinib(DB01259)|Lercanidipine(DB00528)|Levomethadyl Acetate(DB01227)|Lidocaine(DB00281)|Losartan(DB00678)|Lovastatin(DB00227)|Methadone(DB00333)|Midazolam(DB00683)|Mifepristone(DB00834)|Modafinil(DB00745)|Mycophenolate mofetil(DB00688)|Nateglinide(DB00731)|Nefazodone(DB01149)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Norethindrone(DB00717)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ondansetron(DB00904)|Oxazepam(DB00842)|Oxcarbazepine(DB00776)|Oxybutynin(DB01062)|Oxycodone(DB00497)|Paclitaxel(DB01229)|Paliperidone(DB01267)|Pentamidine(DB00738)|Perampanel(DB08883)|Phenelzine(DB00780)|Phenobarbital(DB01174)|Phenytoin(DB00252)|Pimozide(DB01100)|Ponatinib(DB08901)|Pravastatin(DB00175)|Praziquantel(DB01058)|Progesterone(DB00396)|Propranolol(DB00571)|Quetiapine(DB01224)|Quinacrine(DB01103)|Quinine(DB00468)|Ranitidine(DB00863)|Reserpine(DB00206)|Rifampicin(DB01045)|Rifapentine(DB01201)|Risperidone(DB00734)|Ritonavir(DB00503)|Rivaroxaban(DB06228)|Rosuvastatin(DB01098)|Salmeterol(DB00938)|Saquinavir(DB01232)|Saxagliptin(DB06335)|Sildenafil(DB00203)|Simvastatin(DB00641)|Sirolimus(DB00877)|Sorafenib(DB00398)|Sulfasalazine(DB00795)|Sunitinib(DB01268)|Tacrolimus(DB00864)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Temsirolimus(DB06287)|Teniposide(DB00444)|Testosterone(DB00624)|Thalidomide(DB01041)|Trazodone(DB00656)|Tretinoin(DB00755)|Triazolam(DB00897)|Troleandomycin(DB01361)|Udenafil(DB06267)|Valproic Acid(DB00313)|Vardenafil(DB00862)|Verapamil(DB00661)|Vincristine(DB00541)|Voriconazole(DB00582)|Zalcitabine(DB00943)|Zaleplon(DB00962)|Ziprasidone(DB00246)|Zolpidem(DB00425)	AAAAGTCCATGTGTACGGGTC	0.463													G|||	17	0.00339457	0.0	0.0014	5008	,	,		20808	0.0		0.0119	False		,,,				2504	0.0041				p.H30Y		Atlas-SNP	.											.	CYP3A5	46	.	0			c.C88T						PASS	.	G	TYR/HIS,TYR/HIS	6,4400	11.4+/-27.6	0,6,2197	110.0	100.0	104.0		88,88	1.9	0.0	7	dbSNP_125	104	82,8518	48.1+/-107.5	0,82,4218	yes	missense,missense	CYP3A5	NM_000777.3,NM_001190484.1	83,83	0,88,6415	AA,AG,GG		0.9535,0.1362,0.6766	,	30/503,30/141	99273815	88,12918	2203	4300	6503	SO:0001583	missense	1577	exon2			GTCCATGTGTACG	L26985	CCDS5672.1, CCDS55134.1	7q21.1	2007-12-14	2003-01-14		ENSG00000106258	ENSG00000106258		"""Cytochrome P450s"""	2638	protein-coding gene	gene with protein product		605325	"""cytochrome P450, subfamily IIIA (niphedipine oxidase), polypeptide 5"""				Standard	NR_033808		Approved	PCN3, P450PCN3, CP35		P20815	OTTHUMG00000156724	ENST00000222982.4:c.88C>T	7.37:g.99273815G>A	ENSP00000222982:p.His30Tyr	88.0	0.0	0		124.0	50.0	0.403226	NM_001190484	A4D289|B7Z5I7|Q53WY8|Q75MV0|Q9HB56	Missense_Mutation	SNP	ENST00000222982.4	37	CCDS5672.1	13	0.005952380952380952	0	0.0	4	0.011049723756906077	0	0.0	9	0.011873350923482849	G	0.239	-1.015455	0.02078	0.001362	0.009535	ENSG00000106258	ENST00000222982;ENST00000343703;ENST00000439761	T;T;T	0.08896	3.04;3.04;3.04	3.78	1.87	0.25490	.	0.279306	0.35320	N	0.003281	T	0.04048	0.0113	L	0.34521	1.04	0.09310	N	0.999998	B;B;B	0.14012	0.002;0.009;0.004	B;B;B	0.21151	0.021;0.033;0.012	T	0.42068	-0.9473	10	0.19147	T	0.46	.	8.2763	0.31874	0.2274:0.0:0.7726:0.0	rs28383468;rs59353336	20;30;30	F5H4S0;B7Z5I7;P20815	.;.;CP3A5_HUMAN	Y	30;20;30	ENSP00000222982:H30Y;ENSP00000342969:H20Y;ENSP00000401269:H30Y	ENSP00000222982:H30Y	H	-	1	0	CYP3A5	99111751	0.350000	0.24878	0.003000	0.11579	0.009000	0.06853	1.409000	0.34680	0.209000	0.20645	-1.644000	0.00765	CAT	G|0.994;A|0.006	0.006	strong		0.463	CYP3A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345469.1		
H2AFX	3014	hgsc.bcm.edu	37	11	118965688	118965688	+	Silent	SNP	G	G	A	rs1064180	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:118965688G>A	ENST00000530167.1	-	1	489	c.417C>T	c.(415-417)gcC>gcT	p.A139A		NM_002105.2	NP_002096.1	P16104	H2AX_HUMAN	H2A histone family, member X	139					cellular response to DNA damage stimulus (GO:0006974)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|meiotic nuclear division (GO:0007126)|nucleosome assembly (GO:0006334)|positive regulation of DNA repair (GO:0045739)|response to ionizing radiation (GO:0010212)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|extracellular vesicular exosome (GO:0070062)|male germ cell nucleus (GO:0001673)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|replication fork (GO:0005657)|site of double-strand break (GO:0035861)|XY body (GO:0001741)	damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone binding (GO:0042393)			lung(3)	3	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.47e-05)		ACTCCTGGGAGGCCTGGGTGG	0.701								Chromatin Structure			OREG0021395	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	g|||	4	0.000798722	0.0	0.0	5008	,	,		10753	0.0		0.0	False		,,,				2504	0.0041				p.A139A		Atlas-SNP	.											.	H2AFX	8	.	0			c.C417T						PASS	.						17.0	21.0	20.0					11																	118965688		2196	4287	6483	SO:0001819	synonymous_variant	3014	exon1			CTGGGAGGCCTGG	X14850	CCDS8410.1	11q23.3	2011-01-27						"""Histones / Replication-independent"""	4739	protein-coding gene	gene with protein product		601772		H2AX		8076949	Standard	NM_002105		Approved		uc001pvg.3	P16104		ENST00000530167.1:c.417C>T	11.37:g.118965688G>A		9.0	0.0	0	1492	25.0	12.0	0.48	NM_002105	Q4ZGJ7|Q6IAS5	Silent	SNP	ENST00000530167.1	37	CCDS8410.1																																																																																			G|0.999;A|0.001	0.001	weak		0.701	H2AFX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388330.2	NM_002105	
C1QTNF8	390664	hgsc.bcm.edu	37	16	1143496	1143496	+	Splice_Site	SNP	C	C	A	rs150337362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1143496C>A	ENST00000328449.5	-	4	1037		c.e4+1			NM_207419.3	NP_997302.2	P60827	C1QT8_HUMAN	C1q and tumor necrosis factor related protein 8							collagen trimer (GO:0005581)|extracellular region (GO:0005576)				lung(2)|prostate(1)|skin(1)	4		Hepatocellular(780;0.00369)				GGGCCCCTCACCCGGCTACAG	0.687													C|||	51	0.0101837	0.0008	0.0187	5008	,	,		9566	0.0		0.0288	False		,,,				2504	0.0082				.		Atlas-SNP	.											.	C1QTNF8	15	.	0			c.763+1G>T						PASS	.	C		10,3934		0,10,1962	4.0	6.0	5.0			-2.6	0.0	16	dbSNP_134	5	102,7936		0,102,3917	no	splice-5	C1QTNF8	NM_207419.3		0,112,5879	AA,AC,CC		1.269,0.2535,0.9347			1143496	112,11870	1972	4019	5991	SO:0001630	splice_region_variant	390664	exon5			CCCTCACCCGGCT	AY358832	CCDS32358.1	16p13.3	2014-08-12			ENSG00000184471	ENSG00000184471			31374	protein-coding gene	gene with protein product		614147				12975309	Standard	NM_207419		Approved	UNQ5829, CTRP8	uc010uuw.1	P60827	OTTHUMG00000167756	ENST00000328449.5:c.756+1G>T	16.37:g.1143496C>A		7.0	0.0	0		17.0	13.0	0.764706	NM_207419	B7U178	Splice_Site	SNP	ENST00000328449.5	37	CCDS32358.1																																																																																			C|0.984;A|0.016	0.016	strong		0.687	C1QTNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396120.1	XM_372606	Intron
SPATA33	124045	hgsc.bcm.edu	37	16	89724755	89724755	+	Missense_Mutation	SNP	C	C	T	rs13329897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:89724755C>T	ENST00000301031.4	+	2	134	c.134C>T	c.(133-135)tCg>tTg	p.S45L	SPATA33_ENST00000579310.1_Missense_Mutation_p.S46L|SPATA33_ENST00000568929.1_Missense_Mutation_p.S15L|CHMP1A_ENST00000547614.1_5'Flank|CHMP1A_ENST00000535997.2_5'Flank|CHMP1A_ENST00000550102.1_5'Flank|CHMP1A_ENST00000397901.3_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	62.0	0.0	0		84.0	35.0	0.416667	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	
PLXNA4	91584	hgsc.bcm.edu	37	7	131864652	131864652	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:131864652G>A	ENST00000359827.3	-	20	4630	c.3668C>T	c.(3667-3669)cCg>cTg	p.P1223L	PLXNA4_ENST00000321063.4_Missense_Mutation_p.P1223L			Q9HCM2	PLXA4_HUMAN	plexin A4	1223	IPT/TIG 4.				anterior commissure morphogenesis (GO:0021960)|axon guidance (GO:0007411)|chemorepulsion of branchiomotor axon (GO:0021793)|facial nerve structural organization (GO:0021612)|glossopharyngeal nerve morphogenesis (GO:0021615)|postganglionic parasympathetic nervous system development (GO:0021784)|regulation of axon extension involved in axon guidance (GO:0048841)|regulation of negative chemotaxis (GO:0050923)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|sympathetic nervous system development (GO:0048485)|trigeminal nerve structural organization (GO:0021637)|vagus nerve morphogenesis (GO:0021644)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(1)|endometrium(3)|kidney(4)|large_intestine(14)|lung(17)|ovary(1)|prostate(2)|skin(1)|stomach(1)	45						CACCATCCCCGGGGAGTACTC	0.652																																					p.P1223L		Atlas-SNP	.											.	PLXNA4	873	.	0			c.C3668T						PASS	.						15.0	18.0	17.0					7																	131864652		2134	4237	6371	SO:0001583	missense	91584	exon20			ATCCCCGGGGAGT	AB046770, AK123428	CCDS5826.1, CCDS43646.1, CCDS43647.1	7q32.3	2007-09-26	2007-09-26	2007-09-26	ENSG00000221866	ENSG00000221866		"""Plexins"""	9102	protein-coding gene	gene with protein product		604280	"""plexin A4, A"", ""plexin A4, B"""	PLXNA4A, PLXNA4B			Standard	NM_181775		Approved	KIAA1550, DKFZp434G0625PRO34003, FAYV2820	uc003vra.4	Q9HCM2	OTTHUMG00000155108	ENST00000359827.3:c.3668C>T	7.37:g.131864652G>A	ENSP00000352882:p.Pro1223Leu	64.0	0.0	0		66.0	21.0	0.318182	NM_020911	A4D1N6|E9PAM2|Q6UWC6|Q6ZW89|Q8N969|Q8ND00|Q8NEN3|Q9NTD4	Missense_Mutation	SNP	ENST00000359827.3	37	CCDS43646.1	.	.	.	.	.	.	.	.	.	.	G	14.48	2.549153	0.45383	.	.	ENSG00000221866	ENST00000321063;ENST00000359827	T;T	0.57752	0.38;0.38	4.92	4.92	0.64577	Cell surface receptor IPT/TIG (1);Immunoglobulin E-set (1);Immunoglobulin-like fold (1);	0.097949	0.64402	D	0.000001	T	0.65133	0.2662	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.58132	-0.7690	10	0.06625	T	0.88	.	18.3041	0.90175	0.0:0.0:1.0:0.0	.	1223	Q9HCM2	PLXA4_HUMAN	L	1223	ENSP00000323194:P1223L;ENSP00000352882:P1223L	ENSP00000323194:P1223L	P	-	2	0	PLXNA4	131515192	1.000000	0.71417	0.986000	0.45419	0.951000	0.60555	9.623000	0.98386	2.582000	0.87167	0.484000	0.47621	CCG	.	.	none		0.652	PLXNA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338422.2	NM_181775	
COL14A1	7373	hgsc.bcm.edu	37	8	121357700	121357700	+	Missense_Mutation	SNP	C	C	G	rs137867605		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:121357700C>G	ENST00000297848.3	+	45	5245	c.4975C>G	c.(4975-4977)Cct>Gct	p.P1659A	COL14A1_ENST00000309791.4_Missense_Mutation_p.P1659A|COL14A1_ENST00000247781.3_Missense_Mutation_p.P1564A	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			TCCTGGGGAGCCTGGGAGGCC	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		16125	0.0		0.001	False		,,,				2504	0.0				p.P1659A		Atlas-SNP	.											.	COL14A1	292	.	0			c.C4975G						PASS	.	C	ALA/PRO	1,4405	2.1+/-5.4	0,1,2202	57.0	56.0	56.0		4975	5.8	1.0	8	dbSNP_134	56	10,8590	7.7+/-29.5	0,10,4290	yes	missense	COL14A1	NM_021110.1	27	0,11,6492	GG,GC,CC		0.1163,0.0227,0.0846	probably-damaging	1659/1797	121357700	11,12995	2203	4300	6503	SO:0001583	missense	7373	exon45			GGGGAGCCTGGGA		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.4975C>G	8.37:g.121357700C>G	ENSP00000297848:p.Pro1659Ala	99.0	0.0	0		124.0	73.0	0.58871	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	.	.	.	.	.	.	.	.	.	.	C	26.2	4.712324	0.89112	2.27E-4	0.001163	ENSG00000187955	ENST00000309791;ENST00000297848;ENST00000247781;ENST00000440844	D;D;D;D	0.93906	-3.3;-3.3;-3.3;-3.31	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.95962	0.8685	M	0.62016	1.91	0.80722	D	1	D	0.61697	0.99	D	0.77004	0.989	D	0.94953	0.8101	10	0.39692	T	0.17	.	17.7738	0.88501	0.0:1.0:0.0:0.0	.	1659	Q05707	COEA1_HUMAN	A	1659;1659;1564;6	ENSP00000311809:P1659A;ENSP00000297848:P1659A;ENSP00000247781:P1564A;ENSP00000403640:P6A	ENSP00000247781:P1564A	P	+	1	0	COL14A1	121426881	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.773000	0.55333	2.736000	0.93811	0.555000	0.69702	CCT	C|0.999;G|0.001	0.001	strong		0.637	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
PCDHB10	56126	hgsc.bcm.edu	37	5	140573956	140573956	+	Missense_Mutation	SNP	G	G	A	rs554525456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140573956G>A	ENST00000239446.4	+	1	2015	c.1831G>A	c.(1831-1833)Gag>Aag	p.E611K		NM_018930.3	NP_061753.1	Q9UN67	PCDBA_HUMAN	protocadherin beta 10	611	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				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)			breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(14)|lung(30)|ovary(4)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	76			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CAAGGCCACGGAGCCCGGGCT	0.706													G|||	11	0.00219649	0.0	0.0014	5008	,	,		15886	0.0		0.005	False		,,,				2504	0.0051				p.E611K		Atlas-SNP	.											.	PCDHB10	177	.	0			c.G1831A						PASS	.						6.0	8.0	7.0					5																	140573956		1542	3066	4608	SO:0001583	missense	56126	exon1			GCCACGGAGCCCG	AF152489	CCDS4252.1	5q31.3	2010-06-15			ENSG00000120324	ENSG00000120324		"""Cadherins / Protocadherins : Clustered"""	8681	other	protocadherin		606336				10380929	Standard	NM_018930		Approved		uc003lix.3	Q9UN67	OTTHUMG00000129626	ENST00000239446.4:c.1831G>A	5.37:g.140573956G>A	ENSP00000239446:p.Glu611Lys	5.0	0.0	0		19.0	13.0	0.684211	NM_018930	Q96T99	Missense_Mutation	SNP	ENST00000239446.4	37	CCDS4252.1	.	.	.	.	.	.	.	.	.	.	g	19.21	3.783989	0.70222	.	.	ENSG00000120324	ENST00000239446	T	0.53857	0.6	3.34	3.34	0.38264	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.72244	0.3436	M	0.79475	2.455	0.32066	N	0.595055	D	0.89917	1.0	D	0.79108	0.992	T	0.78425	-0.2209	9	0.87932	D	0	.	14.8686	0.70437	0.0:0.0:1.0:0.0	.	611	Q9UN67	PCDBA_HUMAN	K	611	ENSP00000239446:E611K	ENSP00000239446:E611K	E	+	1	0	PCDHB10	140554140	0.998000	0.40836	1.000000	0.80357	0.995000	0.86356	5.119000	0.64679	1.884000	0.54569	0.479000	0.44913	GAG	.	.	none		0.706	PCDHB10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251821.1	NM_018930	
NLRP1	22861	hgsc.bcm.edu	37	17	5442790	5442790	+	Missense_Mutation	SNP	C	C	T	rs61754791	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5442790C>T	ENST00000572272.1	-	7	2814	c.2815G>A	c.(2815-2817)Gtg>Atg	p.V939M	NLRP1_ENST00000269280.4_Missense_Mutation_p.V939M|NLRP1_ENST00000577119.1_Missense_Mutation_p.V939M|NLRP1_ENST00000262467.5_Missense_Mutation_p.V939M|NLRP1_ENST00000354411.3_Missense_Mutation_p.V939M|NLRP1_ENST00000571307.1_5'UTR|NLRP1_ENST00000345221.3_Missense_Mutation_p.V939M			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	939					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				AGCAGTCGCACGCCAACGTCA	0.622													C|||	58	0.0115815	0.0318	0.0058	5008	,	,		18777	0.0		0.0109	False		,,,				2504	0.001				p.V939M		Atlas-SNP	.											.	NLRP1	358	.	0			c.G2815A						PASS	.	C	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	105,4301	82.9+/-121.4	3,99,2101	79.0	62.0	67.0		2815,2815,2815,2815,2815	0.5	0.0	17	dbSNP_129	67	134,8466	67.7+/-130.1	2,130,4168	yes	missense,missense,missense,missense,missense	NLRP1	NM_001033053.2,NM_014922.4,NM_033004.3,NM_033006.3,NM_033007.3	21,21,21,21,21	5,229,6269	TT,TC,CC		1.5581,2.3831,1.8376	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	939/1376,939/1430,939/1474,939/1444,939/1400	5442790	239,12767	2203	4300	6503	SO:0001583	missense	22861	exon7			GTCGCACGCCAAC	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2815G>A	17.37:g.5442790C>T	ENSP00000460475:p.Val939Met	51.0	0.0	0		67.0	25.0	0.373134	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	37	CCDS42246.1	26	0.011904761904761904	14	0.028455284552845527	3	0.008287292817679558	0	0.0	9	0.011873350923482849	C	14.12	2.440438	0.43326	0.023831	0.015581	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.14766	2.48;2.48;2.48;2.48;2.48	3.7	0.477	0.16784	.	0.224064	0.22878	N	0.054551	T	0.10680	0.0261	M	0.74546	2.27	0.09310	N	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.999;0.997;1.0	D;D;D;D;P;D	0.91635	0.912;0.999;0.997;0.982;0.896;0.982	T	0.03641	-1.1017	10	0.87932	D	0	.	2.8517	0.05560	0.2212:0.5366:0.0:0.2423	rs61754791	205;939;939;939;939;939	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	M	939;939;939;939;939;205	ENSP00000442029:V939M;ENSP00000262467:V939M;ENSP00000269280:V939M;ENSP00000346390:V939M;ENSP00000324366:V939M	ENSP00000262467:V939M	V	-	1	0	NLRP1	5383514	0.000000	0.05858	0.004000	0.12327	0.009000	0.06853	0.004000	0.13106	0.155000	0.19261	0.650000	0.86243	GTG	A|0.000;C|0.986;T|0.014	0.014	strong		0.622	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057635	46057635	+	Missense_Mutation	SNP	G	G	A	rs114397261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057635G>A	ENST00000380095.1	+	1	363	c.301G>A	c.(301-303)Gtg>Atg	p.V101M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	101	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						tgtctgctgtgtgcccgtctg	0.632													A|||	306	0.0611022	0.2118	0.0173	5008	,	,		18765	0.002		0.001	False		,,,				2504	0.0112				p.V101M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.G301A						PASS	.	A	,MET/VAL	438,3968		76,286,1841	130.0	123.0	125.0		,301	-1.7	0.0	21	dbSNP_132	125	2,8594		0,2,4296	no	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,21	76,288,6137	AA,AG,GG		0.0233,9.941,3.3841	,possibly-damaging	,101/252	46057635	440,12562	2203	4298	6501	SO:0001583	missense	353333	exon1			TGCTGTGTGCCCG	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.301G>A	21.37:g.46057635G>A	ENSP00000369438:p.Val101Met	142.0	0.0	0		145.0	85.0	0.586207	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	.	.	.	.	.	.	.	.	.	.	a	1.285	-0.609223	0.03690	0.09941	2.33E-4	ENSG00000221859	ENST00000380095	T	0.01430	4.9	2.86	-1.68	0.08212	.	.	.	.	.	T	0.00073	0.0002	L	0.36672	1.1	0.09310	N	1	B	0.26195	0.144	B	0.34452	0.183	T	0.44128	-0.9348	9	0.44086	T	0.13	.	9.7593	0.40522	0.4446:0.0:0.5554:0.0	.	101	P60014	KR10A_HUMAN	M	101	ENSP00000369438:V101M	ENSP00000369438:V101M	V	+	1	0	KRTAP10-10	44882063	0.001000	0.12720	0.000000	0.03702	0.000000	0.00434	-0.140000	0.10342	-1.728000	0.01366	-2.786000	0.00116	GTG	G|0.928;A|0.072	0.072	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
ITGB4	3691	hgsc.bcm.edu	37	17	73729660	73729660	+	Missense_Mutation	SNP	G	G	A	rs61735297	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73729660G>A	ENST00000200181.3	+	13	1731	c.1544G>A	c.(1543-1545)cGt>cAt	p.R515H	ITGB4_ENST00000584558.1_3'UTR|ITGB4_ENST00000450894.3_Missense_Mutation_p.R515H|ITGB4_ENST00000579662.1_Missense_Mutation_p.R515H|ITGB4_ENST00000339591.3_Missense_Mutation_p.R515H|ITGB4_ENST00000449880.2_Missense_Mutation_p.R515H	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	515	Cysteine-rich tandem repeats.				amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			TGCTCCGGCCGTGGGGAGTGC	0.647													G|||	27	0.00539137	0.0008	0.0115	5008	,	,		13114	0.001		0.0129	False		,,,				2504	0.0041				p.R515H		Atlas-SNP	.											ITGB4,caecum,carcinoma,0,1	ITGB4	165	1	0			c.G1544A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG	15,4391	22.3+/-47.3	0,15,2188	69.0	59.0	62.0		1544,1544,1544	-0.9	0.0	17	dbSNP_129	62	163,8437	76.6+/-139.3	0,163,4137	yes	missense,missense,missense	ITGB4	NM_000213.3,NM_001005619.1,NM_001005731.1	29,29,29	0,178,6325	AA,AG,GG		1.8953,0.3404,1.3686	benign,benign,benign	515/1823,515/1806,515/1753	73729660	178,12828	2203	4300	6503	SO:0001583	missense	3691	exon13			CCGGCCGTGGGGA		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.1544G>A	17.37:g.73729660G>A	ENSP00000200181:p.Arg515His	36.0	0.0	0		53.0	23.0	0.433962	NM_001005731	A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	CCDS11727.1	16	0.007326007326007326	1	0.0020325203252032522	7	0.019337016574585635	1	0.0017482517482517483	7	0.009234828496042216	G	9.385	1.074039	0.20147	0.003404	0.018953	ENSG00000132470	ENST00000450894;ENST00000200181;ENST00000339591;ENST00000449880	D;D;D	0.97688	-4.49;-4.49;-4.49	4.78	-0.858	0.10689	.	0.072851	0.53938	N	0.000050	D	0.88764	0.6525	L	0.38531	1.155	0.42452	D	0.992753	B;B;B;B;B	0.31485	0.303;0.325;0.015;0.031;0.031	B;B;B;B;B	0.26770	0.058;0.073;0.021;0.016;0.009	T	0.82532	-0.0410	10	0.45353	T	0.12	.	9.7846	0.40668	0.4551:0.0:0.5449:0.0	rs61735297	475;515;515;515;515	B4E3N0;P16144-5;P16144-3;A0AVL6;P16144	.;.;.;.;ITB4_HUMAN	H	431;515;515;515	ENSP00000200181:R515H;ENSP00000344079:R515H;ENSP00000400217:R515H	ENSP00000200181:R515H	R	+	2	0	ITGB4	71241255	0.974000	0.33945	0.025000	0.17156	0.421000	0.31385	2.990000	0.49401	-0.424000	0.07382	-0.263000	0.10527	CGT	G|0.988;A|0.012	0.012	strong		0.647	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
MCMBP	79892	hgsc.bcm.edu	37	10	121587116	121587116	+	IGR	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:121587116C>T	ENST00000360003.3	-	0	4113				INPP5F_ENST00000361976.2_Nonsense_Mutation_p.R1075*|INPP5F_ENST00000369080.3_Nonsense_Mutation_p.R465*	NM_001256378.1|NM_001256379.1|NM_024834.3	NP_001243307.1|NP_001243308.1|NP_079110.1	Q9BTE3	MCMBP_HUMAN	minichromosome maintenance complex binding protein						DNA-dependent DNA replication (GO:0006261)|mitotic nuclear division (GO:0007067)|sister chromatid cohesion (GO:0007062)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)	p.R1075*(1)		breast(1)|endometrium(3)|large_intestine(4)|lung(9)|ovary(2)|skin(2)	21						TGCCAAGATTCGAAGTTCCAT	0.483																																					p.R1075X		Atlas-SNP	.											INPP5F,NS,carcinoma,0,1	INPP5F	112	1	1	Substitution - Nonsense(1)	endometrium(1)	c.C3223T						PASS	.						97.0	97.0	97.0					10																	121587116		2203	4300	6503	SO:0001628	intergenic_variant	22876	exon20			AAGATTCGAAGTT	BC007219	CCDS7617.1, CCDS58099.1	10q26.13	2013-10-11	2011-01-05	2011-01-05	ENSG00000197771	ENSG00000197771			25782	protein-coding gene	gene with protein product		610909	"""chromosome 10 open reading frame 119"""	C10orf119		17296731	Standard	NM_024834		Approved	FLJ13081, MCM-BP	uc001ler.3	Q9BTE3	OTTHUMG00000019159		10.37:g.121587116C>T		134.0	0.0	0		116.0	58.0	0.5	NM_014937	B3KSP7|Q6IA56|Q9BVT9|Q9H916	Nonsense_Mutation	SNP	ENST00000360003.3	37	CCDS7617.1	.	.	.	.	.	.	.	.	.	.	C	41	8.746755	0.98937	.	.	ENSG00000198825	ENST00000361976;ENST00000369080	.	.	.	6.02	3.07	0.35406	.	0.182665	0.46758	D	0.000275	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-13.7045	10.5033	0.44819	0.2383:0.6993:0.0:0.0624	.	.	.	.	X	1075;465	.	ENSP00000354519:R1075X	R	+	1	2	INPP5F	121577106	0.999000	0.42202	0.956000	0.39512	0.996000	0.88848	2.619000	0.46401	0.873000	0.35799	0.655000	0.94253	CGA	.	.	none		0.483	MCMBP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000050684.1	NM_024834	
RPL4	6124	hgsc.bcm.edu	37	15	66791920	66791920	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:66791920G>A	ENST00000307961.6	-	10	1201	c.1109C>T	c.(1108-1110)gCg>gTg	p.A370V	MIR4512_ENST00000583257.1_RNA|SNAPC5_ENST00000566658.1_5'Flank|SNAPC5_ENST00000307979.7_5'Flank|SNAPC5_ENST00000395589.2_5'Flank|SNORD18C_ENST00000362704.1_RNA|SNORD18B_ENST00000365659.1_RNA|SNAPC5_ENST00000563480.2_5'Flank|SNAPC5_ENST00000316634.5_5'Flank|RPL4_ENST00000568588.1_Missense_Mutation_p.A276V	NM_000968.3	NP_000959.2	P36578	RL4_HUMAN	ribosomal protein L4	370	Lys-rich.				cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)|translational elongation (GO:0006414)|translational initiation (GO:0006413)|translational termination (GO:0006415)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral transcription (GO:0019083)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic large ribosomal subunit (GO:0022625)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|structural constituent of ribosome (GO:0003735)			endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|skin(1)|stomach(1)|urinary_tract(1)	17						GCCTGCAACCGCCGCCTTCTC	0.512																																					p.A370V		Atlas-SNP	.											.	RPL4	29	.	0			c.C1109T						PASS	.						37.0	40.0	39.0					15																	66791920		2198	4295	6493	SO:0001583	missense	6124	exon10			GCAACCGCCGCCT	AB007167	CCDS10218.1	15q22	2011-04-06			ENSG00000174444	ENSG00000174444		"""L ribosomal proteins"""	10353	protein-coding gene	gene with protein product	"""60S ribosomal protein L4"""	180479				9582194, 8268230	Standard	NM_000968		Approved	L4	uc002apv.3	P36578	OTTHUMG00000133193	ENST00000307961.6:c.1109C>T	15.37:g.66791920G>A	ENSP00000311430:p.Ala370Val	122.0	0.0	0		89.0	33.0	0.370787	NM_000968	A8K502|P39029|Q4VBR0|Q969Z9	Missense_Mutation	SNP	ENST00000307961.6	37	CCDS10218.1	.	.	.	.	.	.	.	.	.	.	G	8.795	0.931551	0.18131	.	.	ENSG00000174444	ENST00000307961;ENST00000432669	.	.	.	5.76	-3.16	0.05217	.	.	.	.	.	T	0.13072	0.0317	N	0.08118	0	0.09310	N	1	B	0.17465	0.022	B	0.04013	0.001	T	0.22138	-1.0225	8	0.27082	T	0.32	.	0.968	0.01410	0.2269:0.1496:0.3465:0.2771	.	370	P36578	RL4_HUMAN	V	370	.	ENSP00000311430:A370V	A	-	2	0	RPL4	64578974	0.000000	0.05858	0.003000	0.11579	0.207000	0.24258	-0.538000	0.06120	-0.170000	0.10816	-0.785000	0.03343	GCG	.	.	none		0.512	RPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256903.2	NM_000968	
KAT2A	2648	hgsc.bcm.edu	37	17	40266533	40266533	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:40266533G>A	ENST00000225916.5	-	14	2162	c.2109C>T	c.(2107-2109)atC>atT	p.I703I	DHX58_ENST00000251642.3_5'Flank	NM_021078.2	NP_066564.2	Q92830	KAT2A_HUMAN	K(lysine) acetyltransferase 2A	703					cell proliferation (GO:0008283)|chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|histone deubiquitination (GO:0016578)|histone H3 acetylation (GO:0043966)|histone H3-K14 acetylation (GO:0044154)|in utero embryonic development (GO:0001701)|metencephalon development (GO:0022037)|midbrain development (GO:0030901)|multicellular organism growth (GO:0035264)|neural tube closure (GO:0001843)|positive regulation of gluconeogenesis (GO:0045722)|regulation of protein stability (GO:0031647)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|somitogenesis (GO:0001756)|telencephalon development (GO:0021537)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)|extracellular space (GO:0005615)|mitotic spindle (GO:0072686)|nucleoplasm (GO:0005654)|STAGA complex (GO:0030914)|transcription factor TFTC complex (GO:0033276)	chromatin binding (GO:0003682)|H3 histone acetyltransferase activity (GO:0010484)|histone acetyltransferase activity (GO:0004402)|histone acetyltransferase activity (H4-K12 specific) (GO:0043997)|histone deacetylase binding (GO:0042826)|transcription coactivator activity (GO:0003713)			central_nervous_system(1)|endometrium(3)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	18						TCTCCACAGGGATCTGCCTCA	0.577																																					p.I703I		Atlas-SNP	.											.	KAT2A	54	.	0			c.C2109T						PASS	.						168.0	159.0	162.0					17																	40266533		2203	4300	6503	SO:0001819	synonymous_variant	2648	exon14			CACAGGGATCTGC	AF029777	CCDS11417.1	17q12-q21	2011-07-01	2008-07-04	2008-07-04	ENSG00000108773	ENSG00000108773		"""Chromatin-modifying enzymes / K-acetyltransferases"""	4201	protein-coding gene	gene with protein product		602301	"""GCN5 general control of amino-acid synthesis 5-like 2 (yeast)"""	GCN5L2		8552087	Standard	NM_021078		Approved	GCN5, PCAF-b	uc002hyx.2	Q92830	OTTHUMG00000133504	ENST00000225916.5:c.2109C>T	17.37:g.40266533G>A		85.0	0.0	0		95.0	57.0	0.6	NM_021078	Q8N1A2|Q9UCW1	Silent	SNP	ENST00000225916.5	37	CCDS11417.1																																																																																			.	.	none		0.577	KAT2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257458.1	NM_021078	
CSNK1A1L	122011	hgsc.bcm.edu	37	13	37679120	37679120	+	Missense_Mutation	SNP	G	G	C	rs139953443	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:37679120G>C	ENST00000379800.3	-	1	683	c.274C>G	c.(274-276)Ctt>Gtt	p.L92V		NM_145203.5	NP_660204.2	Q8N752	KC1AL_HUMAN	casein kinase 1, alpha 1-like	92	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell morphogenesis (GO:0000902)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(1)|breast(3)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	37		Lung NSC(96;7.97e-05)|Breast(139;0.0615)|Lung SC(185;0.0743)|Prostate(109;0.109)		all cancers(112;3.58e-07)|Epithelial(112;1.29e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00695)|BRCA - Breast invasive adenocarcinoma(63;0.0117)|GBM - Glioblastoma multiforme(144;0.0407)		GGTCCCAGAAGGTCCATGACT	0.458													G|||	8	0.00159744	0.0053	0.0	5008	,	,		20187	0.0		0.001	False		,,,				2504	0.0				p.L92V		Atlas-SNP	.											.	CSNK1A1L	69	.	0			c.C274G						PASS	.	G	VAL/LEU	19,4387	26.2+/-53.5	0,19,2184	116.0	108.0	111.0		274	1.0	0.9	13	dbSNP_134	111	2,8598	2.2+/-6.3	0,2,4298	yes	missense	CSNK1A1L	NM_145203.5	32	0,21,6482	CC,CG,GG		0.0233,0.4312,0.1615	possibly-damaging	92/338	37679120	21,12985	2203	4300	6503	SO:0001583	missense	122011	exon1			CCAGAAGGTCCAT	BC028723	CCDS9363.1	13q13.2	2008-02-05			ENSG00000180138	ENSG00000180138			20289	protein-coding gene	gene with protein product							Standard	NM_145203		Approved	MGC33182	uc001uwm.1	Q8N752	OTTHUMG00000016748	ENST00000379800.3:c.274C>G	13.37:g.37679120G>C	ENSP00000369126:p.Leu92Val	134.0	0.0	0		127.0	65.0	0.511811	NM_145203	Q5T2N2	Missense_Mutation	SNP	ENST00000379800.3	37	CCDS9363.1	2	9.157509157509158E-4	2	0.0040650406504065045	0	0.0	0	0.0	0	0.0	G	16.63	3.176449	0.57692	0.004312	2.33E-4	ENSG00000180138	ENST00000379800	T	0.23348	1.91	1.01	1.01	0.19927	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.54727	0.1876	H	0.96996	3.92	0.44447	D	0.99737	D	0.63880	0.993	P	0.60173	0.87	T	0.63422	-0.6641	10	0.87932	D	0	.	7.8591	0.29499	0.0:0.0:1.0:0.0	.	92	Q8N752	KC1AL_HUMAN	V	92	ENSP00000369126:L92V	ENSP00000369126:L92V	L	-	1	0	CSNK1A1L	36577120	1.000000	0.71417	0.926000	0.36857	0.971000	0.66376	2.973000	0.49264	0.825000	0.34637	0.561000	0.74099	CTT	G|0.998;C|0.002	0.002	strong		0.458	CSNK1A1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044563.1	NM_145203	
COBLL1	22837	hgsc.bcm.edu	37	2	165551000	165551000	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:165551000G>A	ENST00000392717.2	-	13	3134	c.3130C>T	c.(3130-3132)Ctg>Ttg	p.L1044L	COBLL1_ENST00000194871.6_Silent_p.L1073L|COBLL1_ENST00000342193.4_Silent_p.L1006L|COBLL1_ENST00000375458.2_Silent_p.L968L|COBLL1_ENST00000409184.3_Silent_p.L1006L			Q53SF7	COBL1_HUMAN	cordon-bleu WH2 repeat protein-like 1	1044						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						AAAGTCTTCAGATTTTGTGTG	0.473																																					p.L1006L		Atlas-SNP	.											.	COBLL1	122	.	0			c.C3016T						PASS	.						107.0	106.0	106.0					2																	165551000		2203	4300	6503	SO:0001819	synonymous_variant	22837	exon12			TCTTCAGATTTTG	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.3130C>T	2.37:g.165551000G>A		137.0	0.0	0		147.0	65.0	0.442177	NM_014900	A6NMZ3|Q6IQ33|Q7Z3I6|Q9BRH4|Q9UG88|Q9Y2I3	Silent	SNP	ENST00000392717.2	37																																																																																				.	.	none		0.473	COBLL1-202	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_014900	
FYB	2533	hgsc.bcm.edu	37	5	39124367	39124367	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:39124367G>A	ENST00000351578.6	-	12	2111	c.1921C>T	c.(1921-1923)Cct>Tct	p.P641S	FYB_ENST00000505428.1_Missense_Mutation_p.P687S|FYB_ENST00000512982.1_Missense_Mutation_p.P687S|FYB_ENST00000540520.1_Missense_Mutation_p.P697S|FYB_ENST00000515010.1_Missense_Mutation_p.P641S	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	641					immune response (GO:0006955)|intracellular signal transduction (GO:0035556)|NLS-bearing protein import into nucleus (GO:0006607)|protein phosphorylation (GO:0006468)|signal transduction (GO:0007165)|T cell receptor signaling pathway (GO:0050852)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	receptor binding (GO:0005102)			endometrium(2)|kidney(4)|large_intestine(6)|liver(1)|lung(29)|ovary(2)|upper_aerodigestive_tract(1)	45	all_lung(31;0.000343)		Epithelial(62;0.235)			AATTGTTTAGGAGGAGCAGGG	0.353																																					p.P697S		Atlas-SNP	.											.	FYB	354	.	0			c.C2089T						PASS	.						93.0	84.0	86.0					5																	39124367		1850	4103	5953	SO:0001583	missense	2533	exon13			GTTTAGGAGGAGC	U93049	CCDS47200.1, CCDS54848.1	5p13.1	2012-05-04	2010-05-04		ENSG00000082074	ENSG00000082074			4036	protein-coding gene	gene with protein product		602731	"""FYN-binding protein (FYB-120/130)"""			9115214, 9207119	Standard	NM_001465		Approved	SLAP-130, FYB-120/130	uc011cpl.2	O15117	OTTHUMG00000162071	ENST00000351578.6:c.1921C>T	5.37:g.39124367G>A	ENSP00000316460:p.Pro641Ser	332.0	1.0	0.00301205		302.0	149.0	0.493377	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Missense_Mutation	SNP	ENST00000351578.6	37	CCDS47200.1	.	.	.	.	.	.	.	.	.	.	G	11.87	1.766616	0.31228	.	.	ENSG00000082074	ENST00000351578;ENST00000515010;ENST00000512982;ENST00000505428;ENST00000540520;ENST00000542542	T;T;T;T;T	0.23950	1.88;1.88;2.01;2.01;2.01	5.52	4.64	0.57946	.	0.316489	0.33419	N	0.004937	T	0.19208	0.0461	L	0.43701	1.375	0.26889	N	0.967371	B;P	0.43094	0.376;0.799	B;B	0.35931	0.186;0.214	T	0.10706	-1.0618	10	0.22706	T	0.39	-1.5143	12.0613	0.53564	0.0:0.1728:0.8272:0.0	.	697;641	B4DLN2;O15117	.;FYB_HUMAN	S	641;641;687;687;697;687	ENSP00000316460:P641S;ENSP00000426346:P641S;ENSP00000425845:P687S;ENSP00000427114:P687S;ENSP00000442840:P697S	ENSP00000316460:P641S	P	-	1	0	FYB	39160124	1.000000	0.71417	1.000000	0.80357	0.683000	0.39861	1.917000	0.39996	1.532000	0.49169	0.650000	0.86243	CCT	.	.	none		0.353	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
ZNF236	7776	hgsc.bcm.edu	37	18	74672703	74672703	+	Missense_Mutation	SNP	A	A	G	rs183845634		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:74672703A>G	ENST00000253159.8	+	30	5503	c.5305A>G	c.(5305-5307)Atg>Gtg	p.M1769V	ZNF236_ENST00000320610.9_Missense_Mutation_p.M1771V	NM_007345.3	NP_031371.3	Q9UL36	ZN236_HUMAN	zinc finger protein 236	1769					cellular response to glucose stimulus (GO:0071333)|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(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|lung(43)|ovary(7)|pancreas(1)|prostate(6)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	94		Prostate(75;0.0405)|Esophageal squamous(42;0.129)|Melanoma(33;0.132)		OV - Ovarian serous cystadenocarcinoma(15;4.36e-06)|BRCA - Breast invasive adenocarcinoma(31;0.0686)		GCAGGTGCACATGAAGAAGCA	0.552													A|||	1	0.000199681	0.0	0.0	5008	,	,		19924	0.0		0.001	False		,,,				2504	0.0				p.M1769V		Atlas-SNP	.											.	ZNF236	325	.	0			c.A5305G						PASS	.	A	VAL/MET	0,4100		0,0,2050	88.0	95.0	92.0		5305	1.8	1.0	18		92	5,8409		0,5,4202	yes	missense	ZNF236	NM_007345.3	21	0,5,6252	GG,GA,AA		0.0594,0.0,0.04	benign	1769/1846	74672703	5,12509	2050	4207	6257	SO:0001583	missense	7776	exon30			GTGCACATGAAGA	AF085243	CCDS42447.1	18q22-q23	2013-01-08				ENSG00000130856		"""Zinc fingers, C2H2-type"""	13028	protein-coding gene	gene with protein product		604760				10458916	Standard	NM_007345		Approved		uc002lmi.3	Q9UL36		ENST00000253159.8:c.5305A>G	18.37:g.74672703A>G	ENSP00000253159:p.Met1769Val	44.0	0.0	0		68.0	31.0	0.455882	NM_007345	B2RTX9|Q9UL37	Missense_Mutation	SNP	ENST00000253159.8	37	CCDS42447.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	A	11.72	1.724148	0.30593	0.0	5.94E-4	ENSG00000130856	ENST00000253159	T	0.10573	2.86	5.61	1.76	0.24704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	T	0.07773	0.0195	L	0.37750	1.13	0.28794	N	0.899167	B	0.24186	0.099	B	0.28465	0.09	T	0.27971	-1.0058	10	0.27785	T	0.31	.	4.7999	0.13292	0.6934:0.1236:0.065:0.118	.	1769	Q9UL36	ZN236_HUMAN	V	1769	ENSP00000253159:M1769V	ENSP00000253159:M1769V	M	+	1	0	ZNF236	72801691	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.024000	0.57218	0.058000	0.16222	0.533000	0.62120	ATG	A|0.999;G|0.001	0.001	strong		0.552	ZNF236-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000445776.1		
MT-ND5	4540	hgsc.bcm.edu	37	M	12633	12633	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:12633C>A	ENST00000361567.2	+	1	297	c.297C>A	c.(295-297)tcC>tcA	p.S99S	MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TG_ENST00000387429.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TR_ENST00000387439.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	99			S -> P. {ECO:0000269|PubMed:1757091}.		cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						GTTACATGGTCCATCATAGAA	0.368																																					p.S99S		Atlas-SNP	.											.	.	.	.	0			c.C297A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			ATGGTCCATCATA			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.297C>A	M.37:g.12633C>A		3.0	0.0	0		11.0	11.0	1	ENST00000361567	Q34773|Q8WCY3	Silent	SNP	ENST00000361567.2	37																																																																																				.	.	none		0.368	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
GRIN2B	2904	hgsc.bcm.edu	37	12	13724742	13724742	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:13724742T>C	ENST00000609686.1	-	10	2376	c.2167A>G	c.(2167-2169)Aca>Gca	p.T723A		NM_000834.3	NP_000825.2	Q13224	NMDE2_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2B	723					behavioral fear response (GO:0001662)|behavioral response to pain (GO:0048266)|detection of mechanical stimulus involved in sensory perception of pain (GO:0050966)|glutamate receptor signaling pathway (GO:0007215)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|learning (GO:0007612)|learning or memory (GO:0007611)|memory (GO:0007613)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of synaptic plasticity (GO:0048167)|response to ethanol (GO:0045471)|sensory organ development (GO:0007423)|startle response (GO:0001964)|suckling behavior (GO:0001967)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|cell surface (GO:0009986)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal postsynaptic density (GO:0097481)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synaptic vesicle (GO:0008021)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(12)|large_intestine(12)|liver(1)|lung(70)|ovary(4)|prostate(6)|skin(10)|upper_aerodigestive_tract(5)|urinary_tract(1)	143					Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Felbamate(DB00949)|Gabapentin(DB00996)|Haloperidol(DB00502)|Ketobemidone(DB06738)|Memantine(DB01043)|Milnacipran(DB04896)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	TCTTACCCTGTTTTCAGGGAG	0.418																																					p.T723A		Atlas-SNP	.											.	GRIN2B	303	.	0			c.A2167G						PASS	.						235.0	206.0	216.0					12																	13724742		2203	4300	6503	SO:0001583	missense	2904	exon10			ACCCTGTTTTCAG		CCDS8662.1	12p13.1	2014-07-16			ENSG00000273079			"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4586	protein-coding gene	gene with protein product		138252		NMDAR2B		1350383	Standard	NM_000834		Approved	GluN2B	uc001rbt.2	Q13224	OTTHUMG00000137373	ENST00000609686.1:c.2167A>G	12.37:g.13724742T>C	ENSP00000477455:p.Thr723Ala	144.0	0.0	0		163.0	7.0	0.0429448	NM_000834	Q12919|Q13220|Q13225|Q14CU4|Q9UM56	Missense_Mutation	SNP	ENST00000609686.1	37	CCDS8662.1	.	.	.	.	.	.	.	.	.	.	T	14.21	2.466424	0.43839	.	.	ENSG00000150086	ENST00000279593	T	0.49720	0.77	5.66	5.66	0.87406	Extracellular solute-binding protein, family 3 (1);Ionotropic glutamate receptor (2);	0.107478	0.64402	D	0.000004	T	0.40619	0.1124	L	0.33189	0.99	0.58432	D	0.999996	B	0.06786	0.001	B	0.18561	0.022	T	0.16012	-1.0417	10	0.40728	T	0.16	.	16.1922	0.82000	0.0:0.0:0.0:1.0	.	723	Q13224	NMDE2_HUMAN	A	723	ENSP00000279593:T723A	ENSP00000279593:T723A	T	-	1	0	GRIN2B	13616009	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.074000	0.57577	2.280000	0.76307	0.533000	0.62120	ACA	.	.	none		0.418	GRIN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268014.2		
MUC6	4588	hgsc.bcm.edu	37	11	1016630	1016630	+	Silent	SNP	G	G	A	rs369775657		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1016630G>A	ENST00000421673.2	-	31	6221	c.6171C>T	c.(6169-6171)tcC>tcT	p.S2057S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2057	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CTGTGTGGGTGGACCCTGTGG	0.562																																					p.S2057S		Atlas-SNP	.											.	MUC6	408	.	0			c.C6171T						PASS	.	G		32,4354	2.1+/-5.4	0,32,2161	389.0	386.0	387.0		6171	-2.5	0.0	11		387	18,8558	1.2+/-3.3	0,18,4270	no	coding-synonymous	MUC6	NM_005961.2		0,50,6431	AA,AG,GG		0.2099,0.7296,0.3857		2057/2440	1016630	50,12912	2193	4288	6481	SO:0001819	synonymous_variant	4588	exon31			GTGGGTGGACCCT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.6171C>T	11.37:g.1016630G>A		429.0	0.0	0		446.0	27.0	0.0605381	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Silent	SNP	ENST00000421673.2	37	CCDS44513.1																																																																																			.	.	weak		0.562	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
ZNF189	7743	hgsc.bcm.edu	37	9	104170227	104170227	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:104170227T>G	ENST00000339664.2	+	3	306	c.177T>G	c.(175-177)gaT>gaG	p.D59E	ZNF189_ENST00000374861.3_Missense_Mutation_p.D45E|ZNF189_ENST00000259395.4_Missense_Mutation_p.D17E	NM_001278240.1	NP_001265169.1	O75820	ZN189_HUMAN	zinc finger protein 189	59	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(10)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	26		Acute lymphoblastic leukemia(62;0.0559)				TGAACAGAGATAAGGATGAGG	0.358																																					p.D59E		Atlas-SNP	.											.	ZNF189	79	.	0			c.T177G						PASS	.						51.0	54.0	53.0					9																	104170227		2202	4300	6502	SO:0001583	missense	7743	exon3			CAGAGATAAGGAT	AF025770	CCDS6754.1, CCDS6755.1, CCDS65096.1, CCDS75867.1	9q22-q31	2013-01-08			ENSG00000136870	ENSG00000136870		"""Zinc fingers, C2H2-type"", ""-"""	12980	protein-coding gene	gene with protein product		603132				9653648	Standard	NM_003452		Approved		uc004bbh.2	O75820	OTTHUMG00000020383	ENST00000339664.2:c.177T>G	9.37:g.104170227T>G	ENSP00000342019:p.Asp59Glu	57.0	0.0	0		78.0	40.0	0.512821	NM_003452	O75802|Q5T7D7|Q5T7D8|Q5T7D9|Q9UBL4|Q9UPE9|Q9UPF0|Q9UPF1	Missense_Mutation	SNP	ENST00000339664.2	37	CCDS6754.1	.	.	.	.	.	.	.	.	.	.	T	0.024	-1.384786	0.01194	.	.	ENSG00000136870	ENST00000374861;ENST00000339664;ENST00000259395	T;T;T	0.05081	5.68;5.68;3.5	4.79	4.79	0.61399	Krueppel-associated box (3);	0.402704	0.21477	N	0.073890	T	0.03695	0.0105	N	0.11870	0.19	0.24556	N	0.993991	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.10450	0.0;0.0;0.005	T	0.38415	-0.9662	10	0.06365	T	0.9	.	12.9471	0.58379	0.0:0.0:0.0:1.0	.	44;45;59	B7ZLK9;Q5T7D8;O75820	.;.;ZN189_HUMAN	E	45;59;17	ENSP00000363995:D45E;ENSP00000342019:D59E;ENSP00000259395:D17E	ENSP00000259395:D17E	D	+	3	2	ZNF189	103210048	.	.	1.000000	0.80357	0.966000	0.64601	.	.	2.371000	0.80710	0.533000	0.62120	GAT	.	.	none		0.358	ZNF189-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053447.1	NM_003452	
LGI3	203190	hgsc.bcm.edu	37	8	22006123	22006123	+	Silent	SNP	G	G	A	rs201271501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22006123G>A	ENST00000306317.2	-	8	1486	c.1197C>T	c.(1195-1197)ccC>ccT	p.P399P	LGI3_ENST00000424267.2_Silent_p.P375P	NM_139278.2	NP_644807.1	Q8N145	LGI3_HUMAN	leucine-rich repeat LGI family, member 3	399					exocytosis (GO:0006887)|regulation of exocytosis (GO:0017157)	cell junction (GO:0030054)|extracellular region (GO:0005576)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	catalytic activity (GO:0003824)			endometrium(4)|large_intestine(3)|lung(7)|ovary(1)|upper_aerodigestive_tract(2)	17				Colorectal(74;0.00189)|COAD - Colon adenocarcinoma(73;0.0612)|READ - Rectum adenocarcinoma(644;0.0999)		GATAGATGACGGGTGCCTGGG	0.632													g|||	3	0.000599042	0.0	0.0	5008	,	,		16962	0.003		0.0	False		,,,				2504	0.0				p.P399P		Atlas-SNP	.											.	LGI3	44	.	0			c.C1197T						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	76.0	62.0	67.0		1197	-10.3	0.0	8		67	0,8600		0,0,4300	no	coding-synonymous	LGI3	NM_139278.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		399/549	22006123	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	203190	exon8			GATGACGGGTGCC	AJ487518	CCDS6025.1	8p21.2	2008-07-28			ENSG00000168481	ENSG00000168481			18711	protein-coding gene	gene with protein product		608302				12023020, 18628660	Standard	NM_139278		Approved		uc003xav.3	Q8N145	OTTHUMG00000131599	ENST00000306317.2:c.1197C>T	8.37:g.22006123G>A		55.0	0.0	0		68.0	34.0	0.5	NM_139278	A5PLP2|Q86TL4|Q8N296	Silent	SNP	ENST00000306317.2	37	CCDS6025.1																																																																																			G|1.000;A|0.000	0.000	strong		0.632	LGI3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254482.1		
SLK	9748	hgsc.bcm.edu	37	10	105762933	105762933	+	Missense_Mutation	SNP	G	G	A	rs7071400	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105762933G>A	ENST00000369755.3	+	9	2542	c.1997G>A	c.(1996-1998)gGa>gAa	p.G666E	SLK_ENST00000335753.4_Missense_Mutation_p.G666E	NM_014720.2	NP_055535.2	Q9H2G2	SLK_HUMAN	STE20-like kinase	666			G -> E (in dbSNP:rs7071400).		apoptotic process (GO:0006915)|protein autophosphorylation (GO:0046777)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|lung(1)|ovary(2)|skin(2)|stomach(2)	8		Colorectal(252;0.178)		Epithelial(162;5.81e-10)|all cancers(201;2.35e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		AAGGCTTTAGGAAGTGAAGTT	0.393													G|||	84	0.0167732	0.059	0.0086	5008	,	,		19341	0.0		0.0	False		,,,				2504	0.0				p.G666E	NSCLC(111;540 1651 1927 4474 17706)	Atlas-SNP	.											.	SLK	107	.	0			c.G1997A						PASS	.	G	GLU/GLY	206,4200	127.4+/-164.3	5,196,2002	126.0	114.0	118.0		1997	-0.6	0.0	10	dbSNP_116	118	3,8597	3.0+/-9.4	0,3,4297	yes	missense	SLK	NM_014720.2	98	5,199,6299	AA,AG,GG		0.0349,4.6754,1.607	benign	666/1236	105762933	209,12797	2203	4300	6503	SO:0001583	missense	9748	exon9			CTTTAGGAAGTGA		CCDS7553.1	10q25.1	2010-06-25	2010-06-25		ENSG00000065613	ENSG00000065613			11088	protein-coding gene	gene with protein product			"""SNF1 (sucrose nonfermenting, yeast, homolog)-like kinase, SNF1 sucrose nonfermenting like kinase (yeast)"", ""STE20-like kinase (yeast)"""			3526554	Standard	NM_014720		Approved	STK2, se20-9, KIAA0204	uc001kxo.1	Q9H2G2	OTTHUMG00000018999	ENST00000369755.3:c.1997G>A	10.37:g.105762933G>A	ENSP00000358770:p.Gly666Glu	94.0	0.0	0		101.0	44.0	0.435644	NM_014720	D3DRA0|D3DRA1|O00211|Q6P1Z4|Q86WU7|Q86WW1|Q92603|Q9NQL0|Q9NQL1	Missense_Mutation	SNP	ENST00000369755.3	37	CCDS7553.1	29	0.013278388278388278	24	0.04878048780487805	5	0.013812154696132596	0	0.0	0	0.0	G	0.021	-1.419805	0.01136	0.046754	3.49E-4	ENSG00000065613	ENST00000335753;ENST00000369755	T;T	0.66995	-0.24;-0.24	5.6	-0.619	0.11572	Protein kinase-like domain (1);	0.516601	0.20063	N	0.100027	T	0.09247	0.0228	N	0.17082	0.46	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.12156	0.005;0.007	T	0.05386	-1.0888	10	0.15499	T	0.54	.	6.5662	0.22513	0.3317:0.0:0.4868:0.1815	rs7071400;rs52824513;rs56426845;rs7071400	666;666	Q9H2G2-2;Q9H2G2	.;SLK_HUMAN	E	666	ENSP00000336824:G666E;ENSP00000358770:G666E	ENSP00000336824:G666E	G	+	2	0	SLK	105752923	0.000000	0.05858	0.000000	0.03702	0.011000	0.07611	-0.468000	0.06656	-0.380000	0.07894	-1.471000	0.01009	GGA	G|0.982;A|0.018	0.018	strong		0.393	SLK-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050188.1	NM_014720	
CASK	8573	hgsc.bcm.edu	37	X	41604809	41604809	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:41604809G>A	ENST00000378163.1	-	4	798	c.324C>T	c.(322-324)gaC>gaT	p.D108D	CASK_ENST00000378154.1_Silent_p.D108D|CASK_ENST00000442742.2_Silent_p.D108D|CASK_ENST00000318588.9_Silent_p.D108D|CASK_ENST00000378166.4_Silent_p.D108D|CASK_ENST00000378158.1_Silent_p.D108D|CASK_ENST00000421587.2_Silent_p.D108D|CASK_ENST00000361962.4_Silent_p.D108D			O14936	CSKP_HUMAN	calcium/calmodulin-dependent serine protein kinase (MAGUK family)	108	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				calcium ion import (GO:0070509)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of keratinocyte proliferation (GO:0010839)|negative regulation of wound healing (GO:0061045)|nucleotide phosphorylation (GO:0046939)|positive regulation of calcium ion import (GO:0090280)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	actin cytoskeleton (GO:0015629)|basement membrane (GO:0005604)|basolateral plasma membrane (GO:0016323)|cell-cell junction (GO:0005911)|ciliary membrane (GO:0060170)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|nuclear lamina (GO:0005652)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(5)|kidney(1)|large_intestine(6)|liver(1)|lung(11)|ovary(3)|prostate(1)|stomach(1)	32						CAAAACCAGCGTCAGCTCGCT	0.358																																					p.D108D	NSCLC(42;104 1086 3090 27189 35040)	Atlas-SNP	.											.	CASK	93	.	0			c.C324T						PASS	.						89.0	74.0	79.0					X																	41604809		2203	4300	6503	SO:0001819	synonymous_variant	8573	exon4			ACCAGCGTCAGCT	AF035582	CCDS14257.1, CCDS48094.1, CCDS48095.1	Xp11.4	2010-02-09			ENSG00000147044	ENSG00000147044			1497	protein-coding gene	gene with protein product		300172	"""trinucleotide repeat containing 8"""	TNRC8		9722958	Standard	NM_003688		Approved	LIN2, CAGH39, FGS4	uc004dfl.4	O14936	OTTHUMG00000021378	ENST00000378163.1:c.324C>T	X.37:g.41604809G>A		70.0	0.0	0		127.0	126.0	0.992126	NM_001126054	A6NES1|B7ZKY0|O43215|Q17RI4|Q59HA0|Q5VT16|Q5VT17|Q5VT18|Q5VT19|Q66T42|Q9BYH6|Q9NYB2|Q9NYB3	Silent	SNP	ENST00000378163.1	37																																																																																				.	.	none		0.358	CASK-007	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000056285.1	NM_003688	
ISM1	140862	hgsc.bcm.edu	37	20	13251325	13251325	+	Missense_Mutation	SNP	C	C	T	rs76665689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:13251325C>T	ENST00000262487.4	+	2	319	c.313C>T	c.(313-315)Ctt>Ttt	p.L105F	TASP1_ENST00000539805.1_Intron	NM_080826.1	NP_543016.1	B1AKI9	ISM1_HUMAN	isthmin 1, angiogenesis inhibitor	105						extracellular region (GO:0005576)				NS(1)|autonomic_ganglia(1)|endometrium(1)|large_intestine(8)|lung(5)|urinary_tract(1)	17						ATCCTTTCTCCTTGATCTACC	0.488													C|||	21	0.00419329	0.0045	0.0101	5008	,	,		20403	0.0		0.008	False		,,,				2504	0.0				p.L105F		Atlas-SNP	.											.	ISM1	41	.	0			c.C313T						PASS	.	C	PHE/LEU	21,3715		0,21,1847	94.0	87.0	89.0		313	3.5	1.0	20	dbSNP_131	89	7,8223		0,7,4108	yes	missense	ISM1	NM_080826.1	22	0,28,5955	TT,TC,CC		0.0851,0.5621,0.234	possibly-damaging	105/465	13251325	28,11938	1868	4115	5983	SO:0001583	missense	140862	exon2			TTTCTCCTTGATC	AL133463	CCDS46579.1	20p12.1	2013-05-15	2013-05-15	2008-12-23	ENSG00000101230	ENSG00000101230			16213	protein-coding gene	gene with protein product		615793	"""chromosome 20 open reading frame 82"", ""isthmin 1 homolog (zebrafish)"""	C20orf82			Standard	NM_080826		Approved	bA149I18.1	uc010gce.1	B1AKI9		ENST00000262487.4:c.313C>T	20.37:g.13251325C>T	ENSP00000262487:p.Leu105Phe	90.0	0.0	0		93.0	47.0	0.505376	NM_080826	Q8WVH9	Missense_Mutation	SNP	ENST00000262487.4	37	CCDS46579.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	16.02	3.005070	0.54254	0.005621	8.51E-4	ENSG00000101230	ENST00000262487;ENST00000447521	T;T	0.66638	-0.22;-0.07	5.71	3.45	0.39498	.	0.000000	0.85682	D	0.000000	T	0.54175	0.1842	L	0.57536	1.79	0.80722	D	1	B	0.06786	0.001	B	0.09377	0.004	T	0.61559	-0.7038	10	0.52906	T	0.07	3.7228	13.6816	0.62489	0.0:0.8541:0.0:0.1459	.	105	B1AKI9	ISM1_HUMAN	F	105;59	ENSP00000262487:L105F;ENSP00000409938:L59F	ENSP00000262487:L105F	L	+	1	0	ISM1	13199325	0.996000	0.38824	1.000000	0.80357	0.988000	0.76386	2.360000	0.44151	1.417000	0.47077	0.591000	0.81541	CTT	C|0.997;T|0.003	0.003	strong		0.488	ISM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078039.2		
MT-CYB	4519	hgsc.bcm.edu	37	M	14767	14767	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:14767T>C	ENST00000361789.2	+	1	21	c.21T>C	c.(19-21)acT>acC	p.T7T	MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	7			T -> I (in dbSNP:rs3135031). {ECO:0000269|PubMed:10453733, ECO:0000269|PubMed:11130070, ECO:0000269|PubMed:11553319, ECO:0000269|PubMed:12022039, ECO:0000269|PubMed:1757091, ECO:0000269|PubMed:21269460, ECO:0000269|PubMed:7530363, ECO:0000269|PubMed:7623448}.		cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						ATACGCAAAATTAACCCCCTA	0.438																																					p.T7T		Atlas-SNP	.											.	.	.	.	0			c.T21C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CAAAACTAACCCC			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.21T>C	M.37:g.14767T>C		26.0	0.0	0		50.0	49.0	0.98	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Silent	SNP	ENST00000361789.2	37																																																																																				T|0.826;C|0.174	0.174	strong		0.438	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
SDC3	9672	hgsc.bcm.edu	37	1	31349642	31349642	+	Silent	SNP	C	C	T	rs41269521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:31349642C>T	ENST00000339394.6	-	3	801	c.627G>A	c.(625-627)cgG>cgA	p.R209R	SDC3_ENST00000336798.7_Silent_p.R151R|SDC3_ENST00000471567.1_5'UTR	NM_014654.3	NP_055469.3	O75056	SDC3_HUMAN	syndecan 3	209	Ser/Thr-rich (mucin-like).				carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)	Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(5)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21		Myeloproliferative disorder(586;0.0393)|Colorectal(325;0.0466)|all_neural(195;0.0966)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)		STAD - Stomach adenocarcinoma(196;0.0197)|READ - Rectum adenocarcinoma(331;0.0649)		GCAGAAGCCTCCGTACGCCAG	0.682													C|||	75	0.014976	0.0015	0.0331	5008	,	,		13855	0.0		0.0427	False		,,,				2504	0.0072				p.R209R		Atlas-SNP	.											.	SDC3	45	.	0			c.G627A						PASS	.	C		35,4371	37.6+/-69.7	0,35,2168	26.0	29.0	28.0		627	1.8	0.8	1	dbSNP_127	28	343,8255	115.5+/-175.4	10,323,3966	no	coding-synonymous	SDC3	NM_014654.3		10,358,6134	TT,TC,CC		3.9893,0.7944,2.9068		209/443	31349642	378,12626	2203	4299	6502	SO:0001819	synonymous_variant	9672	exon3			AAGCCTCCGTACG	AF248634	CCDS30661.1	1p35.2	2013-09-19	2007-02-15		ENSG00000162512	ENSG00000162512		"""Proteoglycans / Cell Surface : Syndecans"""	10660	protein-coding gene	gene with protein product	"""syndecan proteoglycan 3"""	186357	"""syndecan 3 (N-syndecan)"""			1556152, 11527150	Standard	NM_014654		Approved	N-syndecan, SYND3	uc001bse.2	O75056	OTTHUMG00000043646	ENST00000339394.6:c.627G>A	1.37:g.31349642C>T		55.0	0.0	0		82.0	9.0	0.109756	NM_014654	Q5T1Z6|Q5T1Z7|Q96CT3|Q96PR8	Silent	SNP	ENST00000339394.6	37	CCDS30661.1																																																																																			C|0.972;G|0.000;T|0.028	0.028	strong		0.682	SDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102017.1	NM_014654	
USH2A	7399	hgsc.bcm.edu	37	1	216363590	216363590	+	Silent	SNP	C	C	T	rs56013136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:216363590C>T	ENST00000307340.3	-	20	4757	c.4371G>A	c.(4369-4371)tcG>tcA	p.S1457S	USH2A_ENST00000366942.3_Silent_p.S1457S|USH2A_ENST00000366943.2_Silent_p.S1457S	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	1457	Fibronectin type-III 4. {ECO:0000255|PROSITE-ProRule:PRU00316}.				hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		GTCCTGCTCCCGAAGCACTGG	0.368										HNSCC(13;0.011)			C|||	28	0.00559105	0.0015	0.0072	5008	,	,		17343	0.0		0.0199	False		,,,				2504	0.001				p.S1457S		Atlas-SNP	.											.	USH2A	1168	.	0			c.G4371A						PASS	.	C	,	25,4381	31.7+/-61.6	0,25,2178	101.0	98.0	99.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	4371,4371	-10.4	0.0	1	dbSNP_129	99	180,8420	81.2+/-143.8	2,176,4122	no	coding-synonymous,coding-synonymous	USH2A	NM_007123.5,NM_206933.2	,	2,201,6300	TT,TC,CC		2.093,0.5674,1.5762	,	1457/1547,1457/5203	216363590	205,12801	2203	4300	6503	SO:0001819	synonymous_variant	7399	exon20			TGCTCCCGAAGCA	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.4371G>A	1.37:g.216363590C>T		115.0	0.0	0		86.0	42.0	0.488372	NM_007123	Q5VVM9|Q6S362|Q9NS27	Silent	SNP	ENST00000307340.3	37	CCDS31025.1																																																																																			C|0.987;T|0.013	0.013	strong		0.368	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
CCDC34	91057	hgsc.bcm.edu	37	11	27379026	27379026	+	Missense_Mutation	SNP	C	C	T	rs138159804		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:27379026C>T	ENST00000328697.6	-	2	1095	c.422G>A	c.(421-423)cGc>cAc	p.R141H	CCDC34_ENST00000317945.6_Missense_Mutation_p.R141H	NM_030771.1	NP_110398.1	Q96HJ3	CCD34_HUMAN	coiled-coil domain containing 34	141										endometrium(2)|large_intestine(4)|lung(1)|prostate(1)|urinary_tract(1)	9						TGGTGTCAGGCGGCTTTCTGG	0.428																																					p.R141H		Atlas-SNP	.											.	CCDC34	48	.	0			c.G422A						PASS	.	C	HIS/ARG,HIS/ARG	0,4404		0,0,2202	150.0	139.0	143.0		422,422	1.2	0.1	11	dbSNP_134	143	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense	CCDC34	NM_030771.1,NM_080654.2	29,29	0,3,6498	TT,TC,CC		0.0349,0.0,0.0231	benign,benign	141/374,141/230	27379026	3,12999	2202	4299	6501	SO:0001583	missense	91057	exon2			GTCAGGCGGCTTT	AF382034	CCDS7863.1, CCDS31448.1	11p14.1	2010-03-30			ENSG00000109881	ENSG00000109881			25079	protein-coding gene	gene with protein product		612324				11173847	Standard	NM_080654		Approved	NY-REN-41, L15, RAMA3	uc001mrh.1	Q96HJ3	OTTHUMG00000166211	ENST00000328697.6:c.422G>A	11.37:g.27379026C>T	ENSP00000330240:p.Arg141His	187.0	0.0	0		151.0	72.0	0.476821	NM_030771	B2R8G2|Q8IX69|Q9H2A6|Q9Y599	Missense_Mutation	SNP	ENST00000328697.6	37	CCDS31448.1	.	.	.	.	.	.	.	.	.	.	C	12.06	1.825829	0.32237	0.0	3.49E-4	ENSG00000109881	ENST00000328697;ENST00000317945	T;T	0.22743	1.94;1.94	5.39	1.21	0.21127	.	0.954155	0.08803	N	0.891475	T	0.11367	0.0277	N	0.14661	0.345	0.09310	N	1	B;B	0.11235	0.004;0.001	B;B	0.04013	0.001;0.001	T	0.32322	-0.9911	10	0.38643	T	0.18	7.2849	4.8599	0.13579	0.0:0.4435:0.2345:0.322	.	141;141	Q96HJ3-2;Q96HJ3	.;CCD34_HUMAN	H	141	ENSP00000330240:R141H;ENSP00000321563:R141H	ENSP00000321563:R141H	R	-	2	0	CCDC34	27335602	0.026000	0.19158	0.117000	0.21633	0.190000	0.23558	0.086000	0.14935	0.361000	0.24292	-0.812000	0.03155	CGC	C|1.000;T|0.000	0.000	weak		0.428	CCDC34-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388396.2	NM_030771	
SDC4	6385	hgsc.bcm.edu	37	20	43964514	43964514	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43964514C>T	ENST00000372733.3	-	2	146	c.107G>A	c.(106-108)cGa>cAa	p.R36Q	SDC4_ENST00000537976.1_Intron	NM_002999.3	NP_002990.2	P31431	SDC4_HUMAN	syndecan 4	36					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|extracellular matrix organization (GO:0030198)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|phototransduction, visible light (GO:0007603)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of stress fiber assembly (GO:0051496)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|costamere (GO:0043034)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|lysosomal lumen (GO:0043202)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	thrombospondin receptor activity (GO:0070053)		SDC4/ROS1(7)	NS(1)|breast(1)|endometrium(1)|large_intestine(2)	5		Myeloproliferative disorder(115;0.0122)				GGAGAAGTATCGGCCTTCTAG	0.552			T	ROS1	NSCLC																																p.R36Q		Atlas-SNP	.		Dom	yes		20	20q12	6385	syndecan 4		E	.	SDC4	16	.	0			c.G107A						PASS	.						70.0	65.0	66.0					20																	43964514		2203	4300	6503	SO:0001583	missense	6385	exon2			AAGTATCGGCCTT	X67016, D13292	CCDS13350.1	20q12	2010-03-25	2007-02-15		ENSG00000124145	ENSG00000124145		"""Proteoglycans / Cell Surface : Syndecans"""	10661	protein-coding gene	gene with protein product	"""syndecan proteoglycan 4"""	600017	"""syndecan 4 (amphiglycan, ryudocan)"""			7916598, 1500433	Standard	NM_002999		Approved	SYND4, amphiglycan, ryudocan	uc002xnu.3	P31431	OTTHUMG00000033083	ENST00000372733.3:c.107G>A	20.37:g.43964514C>T	ENSP00000361818:p.Arg36Gln	27.0	0.0	0		52.0	24.0	0.461538	NM_002999	O00773|Q16833|Q53FN9|Q6FGN3	Missense_Mutation	SNP	ENST00000372733.3	37	CCDS13350.1	.	.	.	.	.	.	.	.	.	.	C	12.90	2.075721	0.36662	.	.	ENSG00000124145	ENST00000372733	T	0.30182	1.54	4.79	1.8	0.24995	.	0.602744	0.16677	N	0.204118	T	0.16685	0.0401	N	0.25426	0.745	0.27144	N	0.961575	B	0.16802	0.019	B	0.08055	0.003	T	0.30794	-0.9966	10	0.11485	T	0.65	-0.7809	7.1145	0.25409	0.0:0.7099:0.0:0.2901	.	36	P31431	SDC4_HUMAN	Q	36	ENSP00000361818:R36Q	ENSP00000361818:R36Q	R	-	2	0	SDC4	43397928	0.000000	0.05858	0.901000	0.35422	0.714000	0.41099	-1.122000	0.03267	0.201000	0.20466	0.561000	0.74099	CGA	.	.	none		0.552	SDC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080515.1	NM_002999	
ZNF442	79973	hgsc.bcm.edu	37	19	12463856	12463856	+	Missense_Mutation	SNP	T	T	C	rs73921445	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12463856T>C	ENST00000242804.4	-	4	733	c.151A>G	c.(151-153)Aag>Gag	p.K51E	ZNF442_ENST00000438182.1_Intron	NM_030824.2	NP_110451.1	Q9H7R0	ZN442_HUMAN	zinc finger protein 442	51	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(8)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	31						TACAGACTCTTCTGTGATGGA	0.438													T|||	63	0.0125799	0.0378	0.0058	5008	,	,		19281	0.0		0.008	False		,,,				2504	0.001				p.K51E		Atlas-SNP	.											.	ZNF442	102	.	0			c.A151G						PASS	.	T	GLU/LYS	139,4267	98.9+/-137.6	3,133,2067	142.0	139.0	140.0		151	1.0	0.1	19	dbSNP_130	140	33,8567	22.2+/-67.0	0,33,4267	yes	missense	ZNF442	NM_030824.2	56	3,166,6334	CC,CT,TT		0.3837,3.1548,1.3225	probably-damaging	51/628	12463856	172,12834	2203	4300	6503	SO:0001583	missense	79973	exon4			GACTCTTCTGTGA	AK024418	CCDS12271.1	19p13.13	2013-01-08			ENSG00000198342	ENSG00000198342		"""Zinc fingers, C2H2-type"", ""-"""	20877	protein-coding gene	gene with protein product							Standard	NM_030824		Approved	FLJ14356	uc002mtr.1	Q9H7R0	OTTHUMG00000156411	ENST00000242804.4:c.151A>G	19.37:g.12463856T>C	ENSP00000242804:p.Lys51Glu	71.0	0.0	0		87.0	38.0	0.436782	NM_030824	B4DJ48	Missense_Mutation	SNP	ENST00000242804.4	37	CCDS12271.1	25	0.011446886446886446	15	0.03048780487804878	3	0.008287292817679558	0	0.0	7	0.009234828496042216	T	16.79	3.219430	0.58560	0.031548	0.003837	ENSG00000198342	ENST00000242804	T	0.02863	4.13	1.03	1.03	0.20045	Krueppel-associated box (4);	.	.	.	.	T	0.06462	0.0166	H	0.95850	3.73	0.36021	D	0.838739	D	0.89917	1.0	D	0.87578	0.998	T	0.03202	-1.1061	9	0.87932	D	0	.	6.2028	0.20585	0.0:0.0:0.0:1.0	.	51	Q9H7R0	ZN442_HUMAN	E	51	ENSP00000242804:K51E	ENSP00000242804:K51E	K	-	1	0	ZNF442	12324856	0.683000	0.27633	0.066000	0.19879	0.547000	0.35210	1.198000	0.32223	0.710000	0.31997	0.260000	0.18958	AAG	T|0.986;C|0.014	0.014	strong		0.438	ZNF442-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344109.1	NM_030824	
NEIL1	79661	hgsc.bcm.edu	37	15	75641682	75641682	+	Splice_Site	SNP	T	T	C	rs5745908	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75641682T>C	ENST00000564784.1	+	3	1063		c.e3+2		NEIL1_ENST00000355059.4_Splice_Site|NEIL1_ENST00000569035.1_Splice_Site|NEIL1_ENST00000567959.1_Intron			Q96FI4	NEIL1_HUMAN	nei endonuclease VIII-like 1 (E. coli)						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						GCAGTTCAGGTAGGGCCAGCA	0.632								Base excision repair (BER), DNA glycosylases					T|||	14	0.00279553	0.0	0.0072	5008	,	,		14728	0.0		0.008	False		,,,				2504	0.001				.		Atlas-SNP	.											.	NEIL1	36	.	0			c.434+2T>C						PASS	.	T		7,4251		0,7,2122	18.0	20.0	20.0			5.4	1.0	15	dbSNP_114	20	105,8207		1,103,4052	yes	splice-5	NEIL1	NM_024608.2		1,110,6174	CC,CT,TT		1.2632,0.1644,0.891			75641682	112,12458	2129	4156	6285	SO:0001630	splice_region_variant	79661	exon2			TTCAGGTAGGGCC	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.434+2T>C	15.37:g.75641682T>C		23.0	0.0	0		31.0	15.0	0.483871	NM_024608	D3DW75|Q6ZRA7|Q86XW7|Q9H6C3	Splice_Site	SNP	ENST00000564784.1	37	CCDS10278.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	T	20.9	4.072179	0.76415	0.001644	0.012632	ENSG00000140398	ENST00000355059;ENST00000336572	.	.	.	5.4	5.4	0.78164	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.5906	0.68362	0.0:0.0:0.0:1.0	rs5745908;rs5745908	.	.	.	.	-1	.	.	.	+	.	.	NEIL1	73428735	1.000000	0.71417	1.000000	0.80357	0.883000	0.51084	7.327000	0.79147	2.042000	0.60477	0.459000	0.35465	.	T|0.993;C|0.007	0.007	strong		0.632	NEIL1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419885.1	NM_024608	Intron
OR52E6	390078	hgsc.bcm.edu	37	11	5862416	5862416	+	Missense_Mutation	SNP	C	C	T	rs61735020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:5862416C>T	ENST00000329322.5	-	1	711	c.712G>A	c.(712-714)Gct>Act	p.A238T	OR52E6_ENST00000379946.2_Missense_Mutation_p.A242T|TRIM5_ENST00000380027.1_Intron	NM_001005167.1	NP_001005167.1	Q96RD3	O52E6_HUMAN	olfactory receptor, family 52, subfamily E, member 6	238						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(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	27		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;2.55e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		GTGTTGAGAGCTTTGAGTCGA	0.443													C|||	43	0.00858626	0.0008	0.013	5008	,	,		19247	0.0		0.0308	False		,,,				2504	0.002				p.A238T		Atlas-SNP	.											.	OR52E6	70	.	0			c.G712A						PASS	.	C	THR/ALA	30,4364	31.7+/-61.6	0,30,2167	64.0	65.0	65.0		712	3.2	0.5	11	dbSNP_129	65	271,8317	102.3+/-163.5	5,261,4028	yes	missense	OR52E6	NM_001005167.1	58	5,291,6195	TT,TC,CC		3.1556,0.6827,2.3186	probably-damaging	238/314	5862416	301,12681	2197	4294	6491	SO:0001583	missense	390078	exon1			TGAGAGCTTTGAG	AB065815	CCDS53597.1	11p15.4	2012-08-09				ENSG00000205409		"""GPCR / Class A : Olfactory receptors"""	15215	protein-coding gene	gene with protein product							Standard	NM_001005167		Approved		uc010qzq.2	Q96RD3		ENST00000329322.5:c.712G>A	11.37:g.5862416C>T	ENSP00000328878:p.Ala238Thr	125.0	0.0	0		123.0	60.0	0.487805	NM_001005167	Q6IFF8	Missense_Mutation	SNP	ENST00000329322.5	37	CCDS53597.1	31	0.014194139194139194	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	27	0.03562005277044855	C	15.10	2.732139	0.48939	0.006827	0.031556	ENSG00000205409	ENST00000329322;ENST00000379946	T;T	0.00357	7.89;7.89	3.23	3.23	0.37069	GPCR, rhodopsin-like superfamily (1);	0.110508	0.40144	N	0.001174	T	0.00144	0.0004	M	0.67397	2.05	0.40032	D	0.975546	D	0.53462	0.96	P	0.54924	0.764	D	0.84518	0.0626	10	0.51188	T	0.08	.	13.1659	0.59571	0.0:1.0:0.0:0.0	rs61735020	238	Q96RD3	O52E6_HUMAN	T	238;242	ENSP00000328878:A238T;ENSP00000369279:A242T	ENSP00000328878:A238T	A	-	1	0	OR52E6	5818992	0.998000	0.40836	0.504000	0.27639	0.080000	0.17528	3.007000	0.49536	1.631000	0.50456	0.551000	0.68910	GCT	C|0.984;T|0.016	0.016	strong		0.443	OR52E6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401144.1	NM_001005167	
TKTL1	8277	hgsc.bcm.edu	37	X	153537783	153537783	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:153537783C>T	ENST00000369915.3	+	3	528	c.339C>T	c.(337-339)ttC>ttT	p.F113F	TKTL1_ENST00000217905.7_Intron|TKTL1_ENST00000369912.2_Silent_p.F57F	NM_001145933.1|NM_012253.3	NP_001139405.1|NP_036385.3	P51854	TKTL1_HUMAN	transketolase-like 1	113					glucose catabolic process (GO:0006007)|thiamine metabolic process (GO:0006772)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|transketolase activity (GO:0004802)	p.F113F(1)		NS(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(8)|ovary(5)|prostate(1)|skin(1)|urinary_tract(2)	34	all_cancers(53;5.05e-16)|all_epithelial(53;1.82e-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)					GCAAGTACTTCGACAGGGCCA	0.537																																					p.F113F		Atlas-SNP	.											.	TKTL1	61	.	1	Substitution - coding silent(1)	large_intestine(1)	c.C339T						PASS	.						252.0	213.0	226.0					X																	153537783		2203	4300	6503	SO:0001819	synonymous_variant	8277	exon3			GTACTTCGACAGG	X91817	CCDS35448.1, CCDS55541.1	Xq28	2008-02-05			ENSG00000007350	ENSG00000007350			11835	protein-coding gene	gene with protein product		300044				8838793	Standard	NM_012253		Approved	TKR, TKT2	uc004fkg.3	P51854	OTTHUMG00000022707	ENST00000369915.3:c.339C>T	X.37:g.153537783C>T		56.0	0.0	0		53.0	53.0	1	NM_012253	A8K896|Q5TYJ8|Q5TYJ9|Q8TC75	Silent	SNP	ENST00000369915.3	37	CCDS35448.1	.	.	.	.	.	.	.	.	.	.	C	4.122	0.020848	0.08006	.	.	ENSG00000007350	ENST00000426203	.	.	.	4.64	-1.03	0.10102	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-14.2143	4.8078	0.13328	0.0:0.2949:0.1505:0.5547	.	.	.	.	X	96	.	.	R	+	1	2	TKTL1	153190977	0.998000	0.40836	0.927000	0.36925	0.416000	0.31233	0.367000	0.20382	-0.364000	0.08088	-0.380000	0.06706	CGA	.	.	none		0.537	TKTL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058923.1	NM_012253	
FURIN	5045	hgsc.bcm.edu	37	15	91419548	91419548	+	Missense_Mutation	SNP	C	C	T	rs148110342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:91419548C>T	ENST00000268171.3	+	3	520	c.241C>T	c.(241-243)Cgc>Tgc	p.R81C		NM_002569.2	NP_002560.1	P09958	FURIN_HUMAN	furin (paired basic amino acid cleaving enzyme)	81					cell proliferation (GO:0008283)|cellular protein metabolic process (GO:0044267)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of low-density lipoprotein particle receptor catabolic process (GO:0032804)|negative regulation of transforming growth factor beta1 production (GO:0032911)|nerve growth factor processing (GO:0032455)|nerve growth factor production (GO:0032902)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch signaling pathway (GO:0007219)|peptide biosynthetic process (GO:0043043)|peptide hormone processing (GO:0016486)|peptidyl-glutamic acid carboxylation (GO:0017187)|positive regulation of membrane protein ectodomain proteolysis (GO:0051044)|post-translational protein modification (GO:0043687)|protein processing (GO:0016485)|proteolysis (GO:0006508)|regulation of endopeptidase activity (GO:0052548)|regulation of protein catabolic process (GO:0042176)|secretion by cell (GO:0032940)|signal peptide processing (GO:0006465)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	endopeptidase activity (GO:0004175)|metal ion binding (GO:0046872)|nerve growth factor binding (GO:0048406)|peptidase activity (GO:0008233)|peptide binding (GO:0042277)|protease binding (GO:0002020)|serine-type endopeptidase activity (GO:0004252)|serine-type endopeptidase inhibitor activity (GO:0004867)			breast(1)|central_nervous_system(4)|endometrium(4)|large_intestine(3)|liver(2)|lung(13)|ovary(2)|prostate(3)|skin(1)|urinary_tract(3)	36	Lung NSC(78;0.0771)|all_lung(78;0.137)		Lung(145;0.189)			GTCGCCTCACCGCCCGCGGCA	0.647													C|||	10	0.00199681	0.0	0.0101	5008	,	,		14336	0.0		0.002	False		,,,				2504	0.001				p.R81C		Atlas-SNP	.											FURIN,NS,carcinoma,-1,1	FURIN	85	1	0			c.C241T						PASS	.	C	CYS/ARG	1,4395	2.1+/-5.4	0,1,2197	62.0	69.0	66.0		241	3.7	1.0	15	dbSNP_134	66	29,8567	19.8+/-62.0	0,29,4269	yes	missense	FURIN	NM_002569.2	180	0,30,6466	TT,TC,CC		0.3374,0.0227,0.2309	probably-damaging	81/795	91419548	30,12962	2198	4298	6496	SO:0001583	missense	5045	exon3			CCTCACCGCCCGC	X17094	CCDS10364.1	15q26.1	2007-01-24	2002-12-04	2002-12-06	ENSG00000140564	ENSG00000140564			8568	protein-coding gene	gene with protein product		136950	"""paired basic amino acid cleaving enzyme (furin, membrane associated receptor protein)"""	PCSK3, FUR, PACE		2251280, 1741956	Standard	NM_002569		Approved	SPC1	uc002bpu.1	P09958	OTTHUMG00000149831	ENST00000268171.3:c.241C>T	15.37:g.91419548C>T	ENSP00000268171:p.Arg81Cys	78.0	0.0	0		83.0	37.0	0.445783	NM_002569	Q14336|Q6LBS3|Q9UCZ5	Missense_Mutation	SNP	ENST00000268171.3	37	CCDS10364.1	4	0.0018315018315018315	0	0.0	4	0.011049723756906077	0	0.0	0	0.0	C	16.37	3.103601	0.56291	2.27E-4	0.003374	ENSG00000140564	ENST00000268171	T	0.32515	1.45	4.58	3.67	0.42095	Proteinase inhibitor, propeptide (1);	0.447962	0.23209	N	0.050699	T	0.35653	0.0939	M	0.85945	2.785	0.52501	D	0.999957	D	0.61080	0.989	P	0.48677	0.586	T	0.43750	-0.9372	10	0.39692	T	0.17	-17.545	11.108	0.48214	0.0:0.9142:0.0:0.0858	.	81	P09958	FURIN_HUMAN	C	81	ENSP00000268171:R81C	ENSP00000268171:R81C	R	+	1	0	FURIN	89220552	0.624000	0.27102	0.998000	0.56505	0.701000	0.40568	1.792000	0.38754	1.170000	0.42753	-0.266000	0.10368	CGC	C|0.998;T|0.002	0.002	strong		0.647	FURIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313492.1	NM_002569	
DHODH	1723	hgsc.bcm.edu	37	16	72055078	72055078	+	Silent	SNP	G	G	A	rs148523165	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:72055078G>A	ENST00000219240.4	+	5	594	c.573G>A	c.(571-573)gcG>gcA	p.A191A	DHODH_ENST00000572887.1_Silent_p.A191A|DHODH_ENST00000573922.1_Intron	NM_001361.4	NP_001352.2	Q02127	PYRD_HUMAN	dihydroorotate dehydrogenase (quinone)	191					'de novo' pyrimidine nucleobase biosynthetic process (GO:0006207)|'de novo' UMP biosynthetic process (GO:0044205)|female pregnancy (GO:0007565)|lactation (GO:0007595)|nucleobase-containing small molecule metabolic process (GO:0055086)|positive regulation of apoptotic process (GO:0043065)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside biosynthetic process (GO:0046134)|regulation of mitochondrial fission (GO:0090140)|response to caffeine (GO:0031000)|response to drug (GO:0042493)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|neuronal cell body (GO:0043025)	dihydroorotate dehydrogenase activity (GO:0004152)|dihydroorotate oxidase activity (GO:0004158)|drug binding (GO:0008144)|FMN binding (GO:0010181)|ubiquinone binding (GO:0048039)			breast(1)|endometrium(2)|large_intestine(4)|ovary(1)|skin(1)|stomach(1)	10		Ovarian(137;0.125)			Atovaquone(DB01117)|Leflunomide(DB01097)|Teriflunomide(DB08880)	TGGACGCCGCGGAGGACTACG	0.642													G|||	17	0.00339457	0.0008	0.0	5008	,	,		16661	0.0		0.0099	False		,,,				2504	0.0061				p.A191A		Atlas-SNP	.											.	DHODH	33	.	0			c.G573A						PASS	.	G		13,4125		0,13,2056	33.0	44.0	40.0		573	-5.8	0.0	16	dbSNP_134	40	105,8249		0,105,4072	no	coding-synonymous	DHODH	NM_001361.4		0,118,6128	AA,AG,GG		1.2569,0.3142,0.9446		191/396	72055078	118,12374	2069	4177	6246	SO:0001819	synonymous_variant	1723	exon5			CGCCGCGGAGGAC		CCDS42192.1	16q22.2	2012-10-02	2011-09-05		ENSG00000102967	ENSG00000102967	1.3.5.2		2867	protein-coding gene	gene with protein product		126064	"""dihydroorotate dehydrogenase"""			8211381	Standard	NM_001361		Approved		uc002fbp.3	Q02127	OTTHUMG00000178093	ENST00000219240.4:c.573G>A	16.37:g.72055078G>A		68.0	0.0	0		82.0	45.0	0.548781	NM_001361	A8K8C8|Q6P176	Silent	SNP	ENST00000219240.4	37	CCDS42192.1																																																																																			G|0.996;A|0.004	0.004	strong		0.642	DHODH-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001361	
ASTN2	23245	hgsc.bcm.edu	37	9	119448979	119448979	+	Intron	SNP	C	C	T	rs10983304	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:119448979C>T	ENST00000313400.4	-	17	2907				ASTN2_ENST00000341734.4_Intron|ASTN2_ENST00000358637.4_Intron|ASTN2_ENST00000288520.5_Missense_Mutation_p.E36K|ASTN2_ENST00000361477.3_Intron|TRIM32_ENST00000450136.1_5'Flank|ASTN2_ENST00000373996.3_Intron|TRIM32_ENST00000373983.2_5'Flank|ASTN2_ENST00000361209.2_Intron			O75129	ASTN2_HUMAN	astrotactin 2						negative regulation of protein localization to cell surface (GO:2000009)	cell pole (GO:0060187)|endosome (GO:0005768)|integral component of membrane (GO:0016021)				breast(3)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(21)|lung(45)|ovary(4)|pancreas(2)|prostate(2)|skin(9)|stomach(1)|urinary_tract(1)	102						CGGGTACCTTCAGTCTGCAGG	0.542													C|||	60	0.0119808	0.0015	0.013	5008	,	,		19721	0.0		0.0288	False		,,,				2504	0.0204				p.E36K		Atlas-SNP	.											.	ASTN2	307	.	0			c.G106A						PASS	.																																			SO:0001627	intron_variant	23245	exon1			TACCTTCAGTCTG	AF116574	CCDS6814.1, CCDS6815.1, CCDS48009.1, CCDS48009.2, CCDS55334.1	9q33	2008-02-05			ENSG00000148219	ENSG00000148219			17021	protein-coding gene	gene with protein product		612856				9734811	Standard	NM_014010		Approved	KIAA0634	uc004bjt.2	O75129	OTTHUMG00000021013	ENST00000313400.4:c.2807-34907G>A	9.37:g.119448979C>T		55.0	0.0	0		47.0	22.0	0.468085	NM_198186	A2A2T7|A2A2T9|Q52LQ2|Q5JVX8|Q5JVX9|Q5JVY1|Q5VXG8|Q5VZX6|Q8N6P8|Q8WV47|Q96FL4|Q9UHW6	Missense_Mutation	SNP	ENST00000313400.4	37		33	0.01510989010989011	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	26	0.03430079155672823	C	13.53	2.264293	0.39995	.	.	ENSG00000148219	ENST00000288520	T	0.13307	2.6	3.9	0.998	0.19857	.	.	.	.	.	T	0.02012	0.0063	.	.	.	0.09310	N	0.999992	B	0.02656	0.0	B	0.01281	0.0	T	0.41770	-0.9490	7	.	.	.	.	4.1278	0.10134	0.0:0.5889:0.1934:0.2177	rs10983304;rs52793392;rs10983304	36	O75129-4	.	K	36	ENSP00000288520:E36K	.	E	-	1	0	ASTN2	118488800	0.041000	0.20044	0.006000	0.13384	0.020000	0.10135	0.363000	0.20301	0.224000	0.20940	0.555000	0.69702	GAA	C|0.979;T|0.021	0.021	strong		0.542	ASTN2-201	KNOWN	basic	protein_coding	protein_coding		NM_014010	
PDSS1	23590	hgsc.bcm.edu	37	10	27035396	27035396	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:27035396T>A	ENST00000376215.5	+	12	1295	c.1242T>A	c.(1240-1242)gaT>gaA	p.D414E	PDSS1_ENST00000470978.1_3'UTR|PDSS1_ENST00000376203.5_3'UTR	NM_014317.3	NP_055132.2	Q5T2R2	DPS1_HUMAN	prenyl (decaprenyl) diphosphate synthase, subunit 1	414					isoprenoid biosynthetic process (GO:0008299)|protein heterotetramerization (GO:0051290)|small molecule metabolic process (GO:0044281)|ubiquinone biosynthetic process (GO:0006744)	mitochondrial matrix (GO:0005759)	metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)|trans-hexaprenyltranstransferase activity (GO:0000010)|trans-octaprenyltranstransferase activity (GO:0050347)			autonomic_ganglia(1)|endometrium(1)|kidney(7)|large_intestine(6)|lung(5)|prostate(1)	21						TCACAAGAGATAAATGACAAC	0.403																																					p.D414E		Atlas-SNP	.											.	PDSS1	36	.	0			c.T1242A						PASS	.						91.0	79.0	83.0					10																	27035396		2203	4300	6503	SO:0001583	missense	23590	exon12			AAGAGATAAATGA	AF118395	CCDS31168.1	10p12.2	2006-04-12	2006-02-14	2006-02-14	ENSG00000148459	ENSG00000148459			17759	protein-coding gene	gene with protein product	"""coenzyme Q1 homolog (yeast)"""	607429	"""trans-prenyltransferase"""	TPRT		10972372	Standard	NM_014317		Approved	TPT, COQ1	uc001isv.3	Q5T2R2	OTTHUMG00000017844	ENST00000376215.5:c.1242T>A	10.37:g.27035396T>A	ENSP00000365388:p.Asp414Glu	82.0	0.0	0		74.0	31.0	0.418919	NM_014317	Q53F75|Q6P473|Q86WQ8|Q9Y2W5	Missense_Mutation	SNP	ENST00000376215.5	37	CCDS31168.1	.	.	.	.	.	.	.	.	.	.	T	3.921	-0.018056	0.07681	.	.	ENSG00000148459	ENST00000376215;ENST00000396343	T	0.62941	-0.01	5.54	-3.27	0.05048	Terpenoid synthase (2);	0.093864	0.64402	N	0.000001	T	0.39682	0.1087	L	0.52905	1.665	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.40478	-0.9561	10	0.02654	T	1	-16.2141	2.2506	0.04042	0.1373:0.2408:0.4191:0.2028	.	152;414	B4DJY1;Q5T2R2	.;DPS1_HUMAN	E	414;375	ENSP00000365388:D414E	ENSP00000365388:D414E	D	+	3	2	PDSS1	27075402	0.994000	0.37717	0.997000	0.53966	0.680000	0.39746	0.372000	0.20467	-0.207000	0.10187	-0.257000	0.10917	GAT	.	.	none		0.403	PDSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047276.1		
UBXN11	91544	hgsc.bcm.edu	37	1	26608849	26608849	+	Missense_Mutation	SNP	T	T	A	rs199707978		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608849T>A	ENST00000374222.1	-	16	1968	c.1504A>T	c.(1504-1506)Agt>Tgt	p.S502C	UBXN11_ENST00000357089.4_Missense_Mutation_p.S469C|UBXN11_ENST00000314675.7_Missense_Mutation_p.S382C|UBXN11_ENST00000374223.1_Missense_Mutation_p.S259C|UBXN11_ENST00000374221.3_Missense_Mutation_p.S502C|UBXN11_ENST00000374217.2_Missense_Mutation_p.S469C			Q5T124	UBX11_HUMAN	UBX domain protein 11	502	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggactggggccggga	0.731																																					p.S502C		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.A1504T						PASS	.						19.0	22.0	21.0					1																	26608849		1706	3905	5611	SO:0001583	missense	91544	exon16			CGGGACTGGGGCC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1504A>T	1.37:g.26608849T>A	ENSP00000363339:p.Ser502Cys	25.0	0.0	0		40.0	16.0	0.4	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	-	8.284	0.816212	0.16607	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.19105	2.17;2.18;2.44;2.43;2.43;2.44	.	.	.	.	.	.	.	.	T	0.10594	0.0259	N	0.08118	0	0.09310	N	0.999993	.	.	.	.	.	.	T	0.30446	-0.9978	5	0.66056	D	0.02	.	.	.	.	.	469;382;502	Q5T124-2;Q5T124-3;Q5T124	.;.;UBX11_HUMAN	C	382;259;469;502;502;469	ENSP00000324721:S382C;ENSP00000363340:S259C;ENSP00000349601:S469C;ENSP00000363338:S502C;ENSP00000363339:S502C;ENSP00000363334:S469C	ENSP00000324721:S382C	S	-	1	0	UBXN11	26481436	0.000000	0.05858	0.168000	0.22838	0.175000	0.22909	-0.694000	0.05115	0.000000	0.14550	0.000000	0.15137	AGT	.	.	weak		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
PEX13	5194	hgsc.bcm.edu	37	2	61258816	61258816	+	Missense_Mutation	SNP	G	G	A	rs147707348	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:61258816G>A	ENST00000295030.5	+	2	393	c.355G>A	c.(355-357)Gtt>Att	p.V119I	PEX13_ENST00000472678.1_3'UTR	NM_002618.3	NP_002609.1	Q92968	PEX13_HUMAN	peroxisomal biogenesis factor 13	119					cerebral cortex cell migration (GO:0021795)|fatty acid alpha-oxidation (GO:0001561)|locomotory behavior (GO:0007626)|microtubule-based peroxisome localization (GO:0060152)|neuron migration (GO:0001764)|protein import into peroxisome matrix, docking (GO:0016560)|suckling behavior (GO:0001967)	integral component of peroxisomal membrane (GO:0005779)|membrane (GO:0016020)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)				endometrium(2)|large_intestine(2)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10			LUSC - Lung squamous cell carcinoma(5;2.05e-06)|Lung(5;3.13e-05)|Epithelial(17;0.114)			CAGTAGATTTGTTCAGCAAGC	0.433													G|||	2	0.000399361	0.0	0.0	5008	,	,		20269	0.0		0.002	False		,,,				2504	0.0				p.V119I		Atlas-SNP	.											.	PEX13	27	.	0			c.G355A						PASS	.	G	ILE/VAL	2,4404	4.2+/-10.8	0,2,2201	139.0	133.0	135.0		355	5.8	1.0	2	dbSNP_134	135	22,8578	16.0+/-53.3	0,22,4278	yes	missense	PEX13	NM_002618.3	29	0,24,6479	AA,AG,GG		0.2558,0.0454,0.1845	possibly-damaging	119/404	61258816	24,12982	2203	4300	6503	SO:0001583	missense	5194	exon2			AGATTTGTTCAGC	U71374	CCDS1866.1	2p16.1	2008-08-26	2008-08-26		ENSG00000162928	ENSG00000162928			8855	protein-coding gene	gene with protein product		601789	"""peroxisome biogenesis factor 13"""			9878256	Standard	NM_002618		Approved		uc002sau.4	Q92968	OTTHUMG00000129422	ENST00000295030.5:c.355G>A	2.37:g.61258816G>A	ENSP00000295030:p.Val119Ile	157.0	0.0	0		132.0	70.0	0.530303	NM_002618	B2RCS1	Missense_Mutation	SNP	ENST00000295030.5	37	CCDS1866.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	18.70	3.679588	0.68042	4.54E-4	0.002558	ENSG00000162928	ENST00000295030	T	0.77098	-1.07	5.85	5.85	0.93711	Peroxin 13, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.77432	0.4129	L	0.31420	0.93	0.80722	D	1	P	0.45240	0.854	P	0.49361	0.608	T	0.75525	-0.3287	10	0.38643	T	0.18	-24.2526	20.1649	0.98147	0.0:0.0:1.0:0.0	.	119	Q92968	PEX13_HUMAN	I	119	ENSP00000295030:V119I	ENSP00000295030:V119I	V	+	1	0	PEX13	61112320	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.588000	0.98232	2.753000	0.94483	0.655000	0.94253	GTT	G|0.998;A|0.002	0.002	strong		0.433	PEX13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251581.3	NM_002618	
CRMP1	1400	hgsc.bcm.edu	37	4	5837708	5837708	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5837708C>T	ENST00000397890.2	-	11	1429	c.1215G>A	c.(1213-1215)tcG>tcA	p.S405S	CRMP1_ENST00000324989.7_Silent_p.S519S|CRMP1_ENST00000511535.1_5'UTR|CRMP1_ENST00000512574.1_Silent_p.S403S	NM_001313.3	NP_001304.1	Q14194	DPYL1_HUMAN	collapsin response mediator protein 1	405					axon guidance (GO:0007411)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|pyrimidine nucleobase catabolic process (GO:0006208)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendrite (GO:0030425)|neuronal cell body (GO:0043025)	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides (GO:0016812)	p.S519S(1)		NS(1)|cervix(2)|endometrium(4)|large_intestine(10)|lung(11)|ovary(2)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	36				Colorectal(103;0.0721)		CGTCGGCATCCGAGCCCACGG	0.522																																					p.S519S		Atlas-SNP	.											CRMP1,NS,carcinoma,-1,2	CRMP1	118	2	1	Substitution - coding silent(1)	stomach(1)	c.G1557A						PASS	.						149.0	135.0	140.0					4																	5837708		2203	4300	6503	SO:0001819	synonymous_variant	1400	exon11			GGCATCCGAGCCC	D78012	CCDS33950.1, CCDS43207.1, CCDS75102.1	4p16.1	2008-05-15			ENSG00000072832	ENSG00000072832			2365	protein-coding gene	gene with protein product		602462				8973361	Standard	XM_005247940		Approved	DRP-1, DPYSL1	uc003gis.3	Q14194	OTTHUMG00000125489	ENST00000397890.2:c.1215G>A	4.37:g.5837708C>T		175.0	0.0	0		183.0	77.0	0.420765	NM_001014809	A0EJG6|Q13024|Q4W5F1|Q96TC8	Silent	SNP	ENST00000397890.2	37	CCDS43207.1																																																																																			.	.	none		0.522	CRMP1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358871.1	NM_001313	
GADL1	339896	hgsc.bcm.edu	37	3	30819751	30819751	+	Missense_Mutation	SNP	C	C	T	rs143542109	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:30819751C>T	ENST00000282538.5	-	14	1462	c.1312G>A	c.(1312-1314)Gcc>Acc	p.A438T	GADL1_ENST00000498387.1_5'UTR	NM_207359.2	NP_997242.2	Q6ZQY3	GADL1_HUMAN	glutamate decarboxylase-like 1	438					carboxylic acid metabolic process (GO:0019752)		aspartate 1-decarboxylase activity (GO:0004068)|pyridoxal phosphate binding (GO:0030170)|sulfinoalanine decarboxylase activity (GO:0004782)			breast(2)|endometrium(3)|kidney(2)|lung(17)|upper_aerodigestive_tract(1)	25						CAAATATTGGCATATTCAGGC	0.328													C|||	10	0.00199681	0.0	0.0058	5008	,	,		18837	0.0		0.003	False		,,,				2504	0.0031				p.A438T		Atlas-SNP	.											.	GADL1	91	.	0			c.G1312A						PASS	.	C	THR/ALA	7,4399	9.9+/-24.2	0,7,2196	64.0	69.0	67.0		1312	3.9	1.0	3	dbSNP_134	67	57,8543	35.3+/-89.8	1,55,4244	yes	missense	GADL1	NM_207359.2	58	1,62,6440	TT,TC,CC		0.6628,0.1589,0.4921	benign	438/522	30819751	64,12942	2203	4300	6503	SO:0001583	missense	339896	exon14			TATTGGCATATTC	AK128643	CCDS2649.2	3p23-p22	2009-01-14			ENSG00000144644	ENSG00000144644			27949	protein-coding gene	gene with protein product		615601					Standard	NM_207359		Approved		uc003cep.2	Q6ZQY3	OTTHUMG00000130621	ENST00000282538.5:c.1312G>A	3.37:g.30819751C>T	ENSP00000282538:p.Ala438Thr	235.0	0.0	0		259.0	117.0	0.451737	NM_207359		Missense_Mutation	SNP	ENST00000282538.5	37	CCDS2649.2	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	6.061	0.379542	0.11466	0.001589	0.006628	ENSG00000144644	ENST00000282538	T	0.37752	1.18	6.02	3.86	0.44501	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.241129	0.41938	N	0.000786	T	0.08179	0.0204	N	0.01742	-0.745	0.80722	D	1	B	0.02656	0.0	B	0.09377	0.004	T	0.17289	-1.0374	10	0.02654	T	1	-3.3176	9.603	0.39617	0.0:0.7967:0.0:0.2033	.	438	Q6ZQY3	GADL1_HUMAN	T	438	ENSP00000282538:A438T	ENSP00000282538:A438T	A	-	1	0	GADL1	30794755	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.300000	0.51834	1.213000	0.43380	0.655000	0.94253	GCC	C|0.995;T|0.005	0.005	strong		0.328	GADL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253106.2	NM_207359	
PLK1	5347	hgsc.bcm.edu	37	16	23701313	23701313	+	Missense_Mutation	SNP	C	C	T	rs34359215		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:23701313C>T	ENST00000300093.4	+	10	1852	c.1741C>T	c.(1741-1743)Cgc>Tgc	p.R581C	CTD-2196E14.5_ENST00000566143.1_RNA	NM_005030.3	NP_005021.2	P53350	PLK1_HUMAN	polo-like kinase 1	581	POLO box 2. {ECO:0000255|PROSITE- ProRule:PRU00154}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|centrosome organization (GO:0051297)|cytokinesis (GO:0000910)|establishment of protein localization (GO:0045184)|G2 DNA damage checkpoint (GO:0031572)|G2/M transition of mitotic cell cycle (GO:0000086)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic cytokinesis (GO:0000281)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-serine phosphorylation (GO:0018105)|polar body extrusion after meiotic divisions (GO:0040038)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of proteolysis (GO:0045862)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|positive regulation of ubiquitin-protein transferase activity (GO:0051443)|protein destabilization (GO:0031648)|protein localization to chromatin (GO:0071168)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell cycle (GO:0051726)|regulation of mitotic cell cycle (GO:0007346)|regulation of mitotic metaphase/anaphase transition (GO:0030071)|regulation of protein binding (GO:0043393)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|response to antibiotic (GO:0046677)	centrosome (GO:0005813)|condensed nuclear chromosome outer kinetochore (GO:0000942)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|microtubule cytoskeleton (GO:0015630)|midbody (GO:0030496)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)|spindle midzone (GO:0051233)|spindle pole (GO:0000922)	anaphase-promoting complex binding (GO:0010997)|ATP binding (GO:0005524)|kinase activity (GO:0016301)|microtubule binding (GO:0008017)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(10)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23				GBM - Glioblastoma multiforme(48;0.0156)		CAGCCGGCTCCGCTACGCCCG	0.652																																					p.R581C	Colon(12;240 564 27038 33155)	Atlas-SNP	.											.	PLK1	67	.	0			c.C1741T						PASS	.						64.0	59.0	61.0					16																	23701313		2197	4300	6497	SO:0001583	missense	5347	exon10			CGGCTCCGCTACG		CCDS10616.1	16p	2013-01-17	2010-06-24	2004-01-28	ENSG00000166851	ENSG00000166851			9077	protein-coding gene	gene with protein product		602098	"""polo-like kinase (Drosophila)"""	PLK		8127874	Standard	NM_005030		Approved		uc002dlz.1	P53350	OTTHUMG00000096984	ENST00000300093.4:c.1741C>T	16.37:g.23701313C>T	ENSP00000300093:p.Arg581Cys	51.0	0.0	0		50.0	18.0	0.36	NM_005030	Q15153|Q99746	Missense_Mutation	SNP	ENST00000300093.4	37	CCDS10616.1	.	.	.	.	.	.	.	.	.	.	C	27.4	4.832085	0.91036	.	.	ENSG00000166851	ENST00000300093;ENST00000425844	T	0.12672	2.66	5.13	5.13	0.70059	POLO box duplicated domain (2);	0.000000	0.85682	D	0.000000	T	0.42810	0.1219	M	0.87682	2.9	0.80722	D	1	D	0.89917	1.0	D	0.69654	0.965	T	0.50448	-0.8827	10	0.87932	D	0	-25.8067	16.0722	0.80943	0.0:1.0:0.0:0.0	rs34359215	581	P53350	PLK1_HUMAN	C	581;484	ENSP00000300093:R581C	ENSP00000300093:R581C	R	+	1	0	PLK1	23608814	1.000000	0.71417	0.994000	0.49952	0.978000	0.69477	5.740000	0.68629	2.372000	0.80975	0.555000	0.69702	CGC	.	.	weak		0.652	PLK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214057.2	NM_005030	
YIPF2	78992	hgsc.bcm.edu	37	19	11036415	11036415	+	Missense_Mutation	SNP	C	C	T	rs148361413	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11036415C>T	ENST00000586748.1	-	5	486	c.314G>A	c.(313-315)cGg>cAg	p.R105Q	YIPF2_ENST00000590329.1_Missense_Mutation_p.R105Q|YIPF2_ENST00000253031.2_Missense_Mutation_p.R105Q|C19orf52_ENST00000270502.6_5'Flank			Q9BWQ6	YIPF2_HUMAN	Yip1 domain family, member 2	105						integral component of membrane (GO:0016021)|transport vesicle (GO:0030133)				cervix(1)|endometrium(1)|lung(3)|ovary(2)	7						GTGGCCAGGCCGGGGCAGCAG	0.577																																					p.R105Q		Atlas-SNP	.											.	YIPF2	13	.	0			c.G314A						PASS	.	C	GLN/ARG	0,4404		0,0,2202	90.0	74.0	80.0		314	2.5	1.0	19	dbSNP_134	80	1,8599	1.2+/-3.3	0,1,4299	no	missense	YIPF2	NM_024029.3	43	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	105/317	11036415	1,13003	2202	4300	6502	SO:0001583	missense	78992	exon5			CCAGGCCGGGGCA	BC013014	CCDS12251.1	19p13.2	2008-02-05				ENSG00000130733		"""Yip1 domain family"""	28476	protein-coding gene	gene with protein product						12477932	Standard	NM_024029		Approved	MGC3262, FinGER2	uc002mqc.3	Q9BWQ6		ENST00000586748.1:c.314G>A	19.37:g.11036415C>T	ENSP00000466055:p.Arg105Gln	58.0	0.0	0		83.0	49.0	0.590361	NM_024029		Missense_Mutation	SNP	ENST00000586748.1	37	CCDS12251.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191861	0.38707	0.0	1.16E-4	ENSG00000130733	ENST00000253031	.	.	.	4.71	2.46	0.29980	Yip1 domain (1);	0.599360	0.15816	N	0.243259	T	0.24160	0.0585	L	0.27053	0.805	0.09310	N	1	B	0.23591	0.088	B	0.14023	0.01	T	0.11060	-1.0603	9	0.27785	T	0.31	-12.2256	4.8429	0.13500	0.4337:0.4455:0.0:0.1208	.	105	Q9BWQ6	YIPF2_HUMAN	Q	105	.	ENSP00000253031:R105Q	R	-	2	0	YIPF2	10897415	0.003000	0.15002	0.998000	0.56505	0.981000	0.71138	2.003000	0.40844	0.930000	0.37217	0.542000	0.68232	CGG	C|1.000;T|0.000	0.000	strong		0.577	YIPF2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453045.1	NM_024029	
FLRT2	23768	hgsc.bcm.edu	37	14	86089032	86089032	+	Missense_Mutation	SNP	A	A	G	rs137990800	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:86089032A>G	ENST00000330753.4	+	2	1941	c.1174A>G	c.(1174-1176)Agc>Ggc	p.S392G	FLRT2_ENST00000554746.1_Missense_Mutation_p.S392G	NM_013231.4	NP_037363.1	O43155	FLRT2_HUMAN	fibronectin leucine rich transmembrane protein 2	392					axon guidance (GO:0007411)|cell adhesion (GO:0007155)|intracellular signal transduction (GO:0035556)|regulation of neuron migration (GO:2001222)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|proteinaceous extracellular matrix (GO:0005578)	chemorepellent activity (GO:0045499)|protein binding, bridging (GO:0030674)|receptor signaling protein activity (GO:0005057)			NS(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(21)|lung(27)|ovary(3)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	73				BRCA - Breast invasive adenocarcinoma(234;0.0319)		TCCAAACCCTAGCAGAAGCTA	0.572													A|||	2	0.000399361	0.0	0.0014	5008	,	,		16226	0.0		0.001	False		,,,				2504	0.0				p.S392G		Atlas-SNP	.											.	FLRT2	168	.	0			c.A1174G						PASS	.	A	GLY/SER	0,4406		0,0,2203	78.0	81.0	80.0		1174	2.6	0.1	14	dbSNP_134	80	11,8589	8.4+/-32.0	0,11,4289	yes	missense	FLRT2	NM_013231.4	56	0,11,6492	GG,GA,AA		0.1279,0.0,0.0846	benign	392/661	86089032	11,12995	2203	4300	6503	SO:0001583	missense	23768	exon2			AACCCTAGCAGAA	AF169676	CCDS9877.1	14q24-q32	2013-02-11				ENSG00000185070		"""Fibronectin type III domain containing"""	3761	protein-coding gene	gene with protein product		604807				10644439, 16872596	Standard	XM_005267490		Approved		uc001xvr.3	O43155		ENST00000330753.4:c.1174A>G	14.37:g.86089032A>G	ENSP00000332879:p.Ser392Gly	79.0	0.0	0		81.0	42.0	0.518519	NM_013231	A0AV84|B7ZLP3	Missense_Mutation	SNP	ENST00000330753.4	37	CCDS9877.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	A	0.009	-1.812472	0.00600	0.0	0.001279	ENSG00000185070	ENST00000330753;ENST00000554746;ENST00000535800	T;T	0.56941	0.43;0.43	6.17	2.57	0.30868	.	0.309770	0.41001	N	0.000969	T	0.28234	0.0697	N	0.08118	0	0.28921	N	0.892133	B	0.02656	0.0	B	0.01281	0.0	T	0.15723	-1.0427	10	0.20046	T	0.44	-12.0086	9.8404	0.40996	0.8088:0.0:0.1912:0.0	.	392	O43155	FLRT2_HUMAN	G	392;392;45	ENSP00000332879:S392G;ENSP00000451050:S392G	ENSP00000332879:S392G	S	+	1	0	FLRT2	85158785	0.870000	0.30015	0.060000	0.19600	0.021000	0.10359	1.891000	0.39738	0.207000	0.20607	0.533000	0.62120	AGC	A|0.999;G|0.001	0.001	strong		0.572	FLRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413193.1		
CREBBP	1387	hgsc.bcm.edu	37	16	3788618	3788618	+	Missense_Mutation	SNP	G	G	A	rs398124146		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3788618G>A	ENST00000262367.5	-	26	5145	c.4336C>T	c.(4336-4338)Cgc>Tgc	p.R1446C	CREBBP_ENST00000382070.3_Missense_Mutation_p.R1408C	NM_004380.2	NP_004371.2	Q92793	CBP_HUMAN	CREB binding protein	1446	Acetyl-CoA binding. {ECO:0000250|UniProtKB:Q09472}.|CBP/p300-type HAT. {ECO:0000255|PROSITE- ProRule:PRU01065}.|Cys/His-rich.				cellular lipid metabolic process (GO:0044255)|cellular response to hypoxia (GO:0071456)|chromatin organization (GO:0006325)|embryonic digit morphogenesis (GO:0042733)|gene expression (GO:0010467)|germ-line stem cell maintenance (GO:0030718)|histone acetylation (GO:0016573)|homeostatic process (GO:0042592)|innate immune response (GO:0045087)|N-terminal peptidyl-lysine acetylation (GO:0018076)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type I interferon production (GO:0032481)|protein complex assembly (GO:0006461)|regulation of smoothened signaling pathway (GO:0008589)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)|response to hypoxia (GO:0001666)|rhythmic process (GO:0048511)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|nuclear body (GO:0016604)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	acetyltransferase activity (GO:0016407)|chromatin binding (GO:0003682)|core promoter proximal region sequence-specific DNA binding (GO:0000987)|histone acetyltransferase activity (GO:0004402)|MRF binding (GO:0043426)|p53 binding (GO:0002039)|RNA polymerase II activating transcription factor binding (GO:0001102)|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 transcription coactivator activity (GO:0001105)|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)|signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)	p.R1446C(6)|p.R1446G(1)		NS(1)|breast(5)|central_nervous_system(4)|cervix(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(125)|kidney(5)|large_intestine(32)|lung(43)|ovary(18)|pancreas(2)|prostate(6)|skin(9)|soft_tissue(1)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(21)	295		Ovarian(90;0.0266)		OV - Ovarian serous cystadenocarcinoma(1;3.54e-05)		ACGGCTGTGCGGAGGCAACGT	0.413			"""T, N, F, Mis, O"""	"""MLL, MORF, RUNXBP2"""	"""ALL, AML, DLBCL, B-NHL """		Rubinstein-Taybi syndrome																														p.R1446C		Atlas-SNP	.		Dom/Rec	yes		16	16p13.3	1387	CREB binding protein (CBP)	yes	L	CREBBP,rectum,carcinoma,0,21	CREBBP	546	21	7	Substitution - Missense(7)	haematopoietic_and_lymphoid_tissue(4)|urinary_tract(1)|lung(1)|central_nervous_system(1)	c.C4336T						PASS	.						75.0	68.0	71.0					16																	3788618		2197	4300	6497	SO:0001583	missense	1387	exon26			CTGTGCGGAGGCA	U85962	CCDS10509.1, CCDS45399.1	16p13.3	2011-07-01	2008-08-01		ENSG00000005339	ENSG00000005339		"""Chromatin-modifying enzymes / K-acetyltransferases"""	2348	protein-coding gene	gene with protein product		600140	"""Rubinstein-Taybi syndrome"""	RSTS		8413673	Standard	NM_001079846		Approved	RTS, CBP, KAT3A	uc002cvv.3	Q92793	OTTHUMG00000129431	ENST00000262367.5:c.4336C>T	16.37:g.3788618G>A	ENSP00000262367:p.Arg1446Cys	54.0	0.0	0		53.0	22.0	0.415094	NM_004380	D3DUC9|O00147|Q16376|Q4LE28	Missense_Mutation	SNP	ENST00000262367.5	37	CCDS10509.1	.	.	.	.	.	.	.	.	.	.	g	17.20	3.329498	0.60743	.	.	ENSG00000005339	ENST00000262367;ENST00000543883;ENST00000382070;ENST00000323508	D;D	0.94330	-3.4;-3.4	5.28	4.29	0.51040	.	0.000000	0.64402	D	0.000004	D	0.97739	0.9258	H	0.96080	3.765	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.98988	1.0807	10	0.87932	D	0	-29.6499	15.2916	0.73870	0.0:0.0:0.8588:0.1412	.	1476;1446	Q4LE28;Q92793	.;CBP_HUMAN	C	1446;1476;1408;35	ENSP00000262367:R1446C;ENSP00000371502:R1408C	ENSP00000262367:R1446C	R	-	1	0	CREBBP	3728619	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.937000	0.63513	1.303000	0.44873	0.561000	0.74099	CGC	.	.	none		0.413	CREBBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251591.2	NM_004380	
CD1D	912	hgsc.bcm.edu	37	1	158151892	158151892	+	Silent	SNP	T	T	C	rs140563679	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:158151892T>C	ENST00000368171.3	+	4	898	c.399T>C	c.(397-399)caT>caC	p.H133H		NM_001766.3	NP_001757.1	P15813	CD1D_HUMAN	CD1d molecule	133					antigen processing and presentation, endogenous lipid antigen via MHC class Ib (GO:0048006)|detection of bacterium (GO:0016045)|heterotypic cell-cell adhesion (GO:0034113)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of T cell proliferation (GO:0042102)|T cell selection (GO:0045058)|viral process (GO:0016032)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)	beta-2-microglobulin binding (GO:0030881)|cell adhesion molecule binding (GO:0050839)|exogenous lipid antigen binding (GO:0030884)|histone binding (GO:0042393)|lipid antigen binding (GO:0030882)|receptor activity (GO:0004872)			endometrium(1)|kidney(2)|large_intestine(2)|lung(19)|ovary(1)|prostate(3)|urinary_tract(2)	30	all_hematologic(112;0.0378)					ACTTCTTCCATGTAGCATTTC	0.498													T|||	3	0.000599042	0.0	0.0	5008	,	,		19718	0.0		0.003	False		,,,				2504	0.0				p.H133H		Atlas-SNP	.											.	CD1D	60	.	0			c.T399C						PASS	.	T		0,4406		0,0,2203	130.0	143.0	138.0		399	-9.5	0.0	1	dbSNP_134	138	17,8583	12.6+/-44.7	0,17,4283	no	coding-synonymous	CD1D	NM_001766.3		0,17,6486	CC,CT,TT		0.1977,0.0,0.1307		133/336	158151892	17,12989	2203	4300	6503	SO:0001819	synonymous_variant	912	exon4			CTTCCATGTAGCA	BC027926	CCDS1173.1	1q23.1	2014-01-14	2006-03-28		ENSG00000158473	ENSG00000158473		"""CD molecules"", ""Immunoglobulin superfamily / C1-set domain containing"""	1637	protein-coding gene	gene with protein product		188410	"""CD1D antigen, d polypeptide"", ""CD1d antigen"""			2463622	Standard	NM_001766		Approved		uc001frr.3	P15813	OTTHUMG00000022436	ENST00000368171.3:c.399T>C	1.37:g.158151892T>C		201.0	0.0	0		218.0	107.0	0.490826	NM_001766	D3DVD5|Q5W0J3|Q9UMM3|Q9Y5M4	Silent	SNP	ENST00000368171.3	37	CCDS1173.1																																																																																			T|0.999;C|0.001	0.001	strong		0.498	CD1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058340.1	NM_001766	
EXOC3L1	283849	hgsc.bcm.edu	37	16	67222676	67222676	+	Silent	SNP	G	G	A	rs13334403	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67222676G>A	ENST00000314586.6	-	4	615	c.375C>T	c.(373-375)gcC>gcT	p.A125A	EXOC3L1_ENST00000562887.1_Intron	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	125	Mediates interaction with EXOC2, EXOC4 and EXOC5. {ECO:0000250}.				exocytosis (GO:0006887)|peptide hormone secretion (GO:0030072)	exocyst (GO:0000145)|secretory granule (GO:0030141)				breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(6)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	21						GCTTGTGCTGGGCAACCCGCT	0.662													G|||	405	0.0808706	0.2519	0.0187	5008	,	,		17923	0.0109		0.0268	False		,,,				2504	0.0215				p.A125A		Atlas-SNP	.											LOC283849,NS,carcinoma,-1,2	EXOC3L1	52	2	0			c.C375T						PASS	.	G		890,3506	332.5+/-302.5	96,698,1404	44.0	46.0	45.0		375	-1.6	0.1	16	dbSNP_121	45	273,8327	102.3+/-163.5	8,257,4035	no	coding-synonymous	EXOC3L1	NM_178516.3		104,955,5439	AA,AG,GG		3.1744,20.2457,8.9489		125/747	67222676	1163,11833	2198	4300	6498	SO:0001819	synonymous_variant	283849	exon4			GTGCTGGGCAACC	AK092858	CCDS10832.1	16q22.1	2011-01-31	2011-01-31	2011-01-31	ENSG00000179044	ENSG00000179044			27540	protein-coding gene	gene with protein product		614117	"""exocyst complex component 3-like"""	EXOC3L		12477932	Standard	NM_178516		Approved	FLJ35539, FLJ35587	uc002erx.1	Q86VI1	OTTHUMG00000137508	ENST00000314586.6:c.375C>T	16.37:g.67222676G>A		124.0	0.0	0		141.0	72.0	0.510638	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Silent	SNP	ENST00000314586.6	37	CCDS10832.1																																																																																			G|0.920;A|0.080	0.080	strong		0.662	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
FGFR3	2261	hgsc.bcm.edu	37	4	1803704	1803704	+	Silent	SNP	T	T	C	rs2234909	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1803704T>C	ENST00000260795.2	+	6	984	c.882T>C	c.(880-882)aaT>aaC	p.N294N	FGFR3_ENST00000340107.4_Silent_p.N294N|FGFR3_ENST00000481110.2_Silent_p.N294N|FGFR3_ENST00000474521.1_3'UTR|FGFR3_ENST00000352904.1_Silent_p.N294N|FGFR3_ENST00000440486.2_Silent_p.N294N|FGFR3_ENST00000412135.2_Silent_p.N294N			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	294	Ig-like C2-type 3.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)	p.N294N(5)		NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TGGAGGTGAATGGCAGCAAGG	0.672		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome				N|||	1039	0.207468	0.3707	0.1441	5008	,	,		12849	0.0744		0.17	False		,,,				2504	0.2076				p.N294N		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	FGFR3_ENST00000340107,caecum,carcinoma,+2,11	FGFR3	3320	11	5	Substitution - coding silent(5)	upper_aerodigestive_tract(3)|skin(2)	c.T882C						scavenged	.	C	,,	1504,2902	654.3+/-399.7	251,1002,950	47.0	42.0	44.0		882,882,882	-6.8	0.9	4	dbSNP_98	44	1278,7320	749.7+/-407.4	98,1082,3119	no	coding-synonymous,coding-synonymous,coding-synonymous	FGFR3	NM_000142.4,NM_001163213.1,NM_022965.3	,,	349,2084,4069	CC,CT,TT		14.8639,34.1353,21.3934	,,	294/807,294/809,294/695	1803704	2782,10222	2203	4299	6502	SO:0001819	synonymous_variant	2261	exon7	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	GGTGAATGGCAGC	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.882T>C	4.37:g.1803704T>C		88.0	1.0	0.0113636		108.0	45.0	0.416667	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	37	CCDS3353.1																																																																																			T|0.799;C|0.201	0.201	strong		0.672	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
HFM1	164045	hgsc.bcm.edu	37	1	91809036	91809036	+	Silent	SNP	T	T	C	rs148872247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91809036T>C	ENST00000370425.3	-	20	2384	c.2286A>G	c.(2284-2286)tcA>tcG	p.S762S	HFM1_ENST00000462405.1_5'UTR|HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Silent_p.S441S	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	762					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		AGTCCAGGGATGATAAATCAT	0.249													T|||	34	0.00678914	0.0	0.0	5008	,	,		13475	0.0		0.0	False		,,,				2504	0.0348				p.S762S		Atlas-SNP	.											.	HFM1	188	.	0			c.A2286G						PASS	.	T		1,4379		0,1,2189	27.0	27.0	27.0		2286	4.2	1.0	1	dbSNP_134	27	1,8511		0,1,4255	no	coding-synonymous	HFM1	NM_001017975.3		0,2,6444	CC,CT,TT		0.0117,0.0228,0.0155		762/1436	91809036	2,12890	2190	4256	6446	SO:0001819	synonymous_variant	164045	exon20			CAGGGATGATAAA	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2286A>G	1.37:g.91809036T>C		211.0	0.0	0		246.0	113.0	0.45935	NM_001017975	B1B0B6|Q8N9Q0	Silent	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	9.635	1.137319	0.21123	2.28E-4	1.17E-4	ENSG00000162669	ENST00000430465	.	.	.	5.35	4.18	0.49190	.	.	.	.	.	T	0.43787	0.1263	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45571	-0.9252	4	.	.	.	.	6.5979	0.22685	0.217:0.082:0.0:0.7009	.	.	.	.	R	18	.	.	H	-	2	0	HFM1	91581624	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	1.354000	0.34056	2.015000	0.59207	0.377000	0.23210	CAT	T|0.999;C|0.001	0.001	strong		0.249	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
NR4A2	4929	hgsc.bcm.edu	37	2	157184995	157184995	+	Silent	SNP	G	G	A	rs201103933	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:157184995G>A	ENST00000339562.4	-	4	1277	c.915C>T	c.(913-915)tgC>tgT	p.C305C	NR4A2_ENST00000429376.1_Silent_p.C242C|NR4A2_ENST00000426264.1_Silent_p.C242C|NR4A2_ENST00000539077.1_Silent_p.C316C|NR4A2_ENST00000409108.2_Silent_p.C305C|NR4A2_ENST00000409572.1_Silent_p.C305C	NM_006186.3	NP_006177.1	P43354	NR4A2_HUMAN	nuclear receptor subfamily 4, group A, member 2	305					adult locomotory behavior (GO:0008344)|cellular response to extracellular stimulus (GO:0031668)|cellular response to oxidative stress (GO:0034599)|central nervous system projection neuron axonogenesis (GO:0021952)|death (GO:0016265)|dopamine biosynthetic process (GO:0042416)|dopaminergic neuron differentiation (GO:0071542)|gene expression (GO:0010467)|general adaptation syndrome (GO:0051866)|habenula development (GO:0021986)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of neuron apoptotic process (GO:0043524)|neuron maturation (GO:0042551)|neuron migration (GO:0001764)|positive regulation of catalytic activity (GO:0043085)|post-embryonic development (GO:0009791)|regulation of dopamine metabolic process (GO:0042053)|regulation of respiratory gaseous exchange (GO:0043576)|response to amphetamine (GO:0001975)|response to hypoxia (GO:0001666)|response to inorganic substance (GO:0010035)|response to insecticide (GO:0017085)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|kidney(1)|large_intestine(7)|lung(15)|ovary(5)|prostate(1)|skin(3)|urinary_tract(1)	40						TGTCCACTGGGCAGTTTTTAT	0.453													G|||	2	0.000399361	0.0	0.0	5008	,	,		18722	0.0		0.0	False		,,,				2504	0.002				p.C305C		Atlas-SNP	.											.	NR4A2	82	.	0			c.C915T						PASS	.						91.0	87.0	88.0					2																	157184995		2203	4300	6503	SO:0001819	synonymous_variant	4929	exon4			CACTGGGCAGTTT	X75918	CCDS2201.1	2q22-q23	2013-01-16			ENSG00000153234	ENSG00000153234		"""Nuclear hormone receptors"""	7981	protein-coding gene	gene with protein product		601828		NURR1		7706727	Standard	NM_006186		Approved	TINUR, NOT, RNR1, HZF-3	uc002tyz.4	P43354	OTTHUMG00000131950	ENST00000339562.4:c.915C>T	2.37:g.157184995G>A		207.0	0.0	0		215.0	102.0	0.474419	NM_006186	Q16311|Q53RZ2|Q6NXU0	Silent	SNP	ENST00000339562.4	37	CCDS2201.1	.	.	.	.	.	.	.	.	.	.	G	3.579	-0.085989	0.07097	.	.	ENSG00000153234	ENST00000406048	.	.	.	6.07	5.2	0.72013	.	.	.	.	.	T	0.63248	0.2495	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.62153	-0.6914	4	.	.	.	.	11.2859	0.49222	0.138:0.0:0.862:0.0	.	.	.	.	S	87	.	.	P	-	1	0	NR4A2	156893241	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.696000	0.37773	1.584000	0.49913	0.655000	0.94253	CCC	G|0.999;A|0.001	0.001	weak		0.453	NR4A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254909.2		
PTCD1	26024	hgsc.bcm.edu	37	7	99032559	99032559	+	Missense_Mutation	SNP	G	G	A	rs150504114	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99032559G>A	ENST00000292478.4	-	2	557	c.307C>T	c.(307-309)Cgc>Tgc	p.R103C	ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.R152C|ATP5J2-PTCD1_ENST00000437572.1_5'Flank|PTCD1_ENST00000485746.1_5'UTR|PTCD1_ENST00000555673.1_Missense_Mutation_p.R152C	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	103					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	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)		STAD - Stomach adenocarcinoma(171;0.215)			GCGGATTTGCGGAATAGTCTC	0.577													G|||	36	0.0071885	0.0	0.0259	5008	,	,		19143	0.0		0.0089	False		,,,				2504	0.0092				p.R152C		Atlas-SNP	.											.	.	.	.	0			c.C454T						PASS	.	G	CYS/ARG,CYS/ARG	15,4391	22.3+/-47.3	0,15,2188	127.0	136.0	133.0		454,307	6.0	0.9	7	dbSNP_134	133	121,8479	63.5+/-125.6	1,119,4180	yes	missense,missense	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	180,180	1,134,6368	AA,AG,GG		1.407,0.3404,1.0457	probably-damaging,probably-damaging	152/750,103/701	99032559	136,12870	2203	4300	6503	SO:0001583	missense	100526740	exon3			ATTTGCGGAATAG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.307C>T	7.37:g.99032559G>A	ENSP00000292478:p.Arg103Cys	144.0	0.0	0		137.0	76.0	0.554745	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	15	0.006868131868131868	0	0.0	13	0.03591160220994475	0	0.0	2	0.002638522427440633	G	16.59	3.166435	0.57476	0.003404	0.01407	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000555673;ENST00000430982;ENST00000430029;ENST00000419981;ENST00000413834	T;T;D;D;D;T	0.85556	-0.23;-0.21;-2.0;-1.99;-1.87;-0.21	5.97	5.97	0.96955	.	0.496389	0.23896	N	0.043488	T	0.70824	0.3268	M	0.63843	1.955	0.31971	N	0.607147	D;D	0.71674	0.998;0.996	P;P	0.55667	0.781;0.564	D	0.83520	0.0085	10	0.62326	D	0.03	-2.9079	15.1788	0.72938	0.0:0.0:0.859:0.1409	.	152;103	G3V325;O75127	.;PTCD1_HUMAN	C	103;152;103;103;103;152	ENSP00000292478:R103C;ENSP00000450995:R152C;ENSP00000390530:R103C;ENSP00000408059:R103C;ENSP00000401600:R103C;ENSP00000400168:R152C	ENSP00000400168:R152C	R	-	1	0	ATP5J2-PTCD1;PTCD1	98870495	1.000000	0.71417	0.924000	0.36721	0.089000	0.18198	5.560000	0.67332	2.837000	0.97791	0.655000	0.94253	CGC	G|0.991;A|0.009	0.009	strong		0.577	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
LZIC	84328	hgsc.bcm.edu	37	1	9992024	9992024	+	Missense_Mutation	SNP	C	C	G	rs146375448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:9992024C>G	ENST00000377223.1	-	7	686	c.439G>C	c.(439-441)Gca>Cca	p.A147P	LZIC_ENST00000400903.2_Missense_Mutation_p.A147P|LZIC_ENST00000541052.1_Missense_Mutation_p.A168P|LZIC_ENST00000377213.1_Missense_Mutation_p.A147P	NM_032368.3	NP_115744.2	Q8WZA0	LZIC_HUMAN	leucine zipper and CTNNBIP1 domain containing	147					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)		TCATCATCTGCAGTCAGCTAA	0.453													C|||	5	0.000998403	0.0008	0.0014	5008	,	,		16195	0.0		0.003	False		,,,				2504	0.0				p.A147P		Atlas-SNP	.											LZIC,NS,carcinoma,+1,1	LZIC	11	1	0			c.G439C						PASS	.	C	PRO/ALA	1,4405	2.1+/-5.4	0,1,2202	83.0	75.0	78.0		439	3.4	1.0	1	dbSNP_134	78	12,8588	9.1+/-34.3	0,12,4288	yes	missense	LZIC	NM_032368.3	27	0,13,6490	GG,GC,CC		0.1395,0.0227,0.1	benign	147/191	9992024	13,12993	2203	4300	6503	SO:0001583	missense	84328	exon6			CATCTGCAGTCAG	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.439G>C	1.37:g.9992024C>G	ENSP00000366430:p.Ala147Pro	68.0	0.0	0		104.0	7.0	0.0673077	NM_032368	B2R6F0|B4E2N0|Q96IU1	Missense_Mutation	SNP	ENST00000377223.1	37	CCDS107.1	4	0.0018315018315018315	0	0.0	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	C	4.176	0.031261	0.08101	2.27E-4	0.001395	ENSG00000162441	ENST00000377223;ENST00000400903;ENST00000541052;ENST00000377213	T;T;T;T	0.42513	0.98;0.98;0.97;0.98	5.42	3.44	0.39384	.	0.625117	0.18198	N	0.148607	T	0.12817	0.0311	N	0.00642	-1.3	0.23336	N	0.997886	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.17623	-1.0363	9	.	.	.	-3.6864	10.6507	0.45647	0.1167:0.6093:0.274:0.0	.	168;147	B4E2N0;Q8WZA0	.;LZIC_HUMAN	P	147;147;168;147	ENSP00000366430:A147P;ENSP00000383695:A147P;ENSP00000437432:A168P;ENSP00000366418:A147P	.	A	-	1	0	LZIC	9914611	0.366000	0.25014	1.000000	0.80357	0.994000	0.84299	0.170000	0.16663	2.700000	0.92200	0.650000	0.86243	GCA	C|0.999;G|0.001	0.001	strong		0.453	LZIC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005037.1	NM_032368	
PKD1	5310	hgsc.bcm.edu	37	16	2161087	2161087	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:2161087G>C	ENST00000262304.4	-	15	4289	c.4081C>G	c.(4081-4083)Ctg>Gtg	p.L1361V	RP11-304L19.4_ENST00000568795.1_RNA|PKD1_ENST00000423118.1_Missense_Mutation_p.L1361V	NM_001009944.2	NP_001009944	P98161	PKD1_HUMAN	polycystic kidney disease 1 (autosomal dominant)	1361	PKD 8. {ECO:0000255|PROSITE- ProRule:PRU00151}.				anatomical structure morphogenesis (GO:0009653)|branching morphogenesis of an epithelial tube (GO:0048754)|calcium ion transmembrane transport (GO:0070588)|calcium-independent cell-matrix adhesion (GO:0007161)|cartilage condensation (GO:0001502)|cartilage development (GO:0051216)|cation transmembrane transport (GO:0098655)|cell cycle arrest (GO:0007050)|cell-matrix adhesion (GO:0007160)|cytoplasmic sequestering of transcription factor (GO:0042994)|detection of mechanical stimulus (GO:0050982)|digestive tract development (GO:0048565)|embryonic placenta development (GO:0001892)|genitalia development (GO:0048806)|heart development (GO:0007507)|homophilic cell adhesion (GO:0007156)|in utero embryonic development (GO:0001701)|JAK-STAT cascade (GO:0007259)|kidney development (GO:0001822)|liver development (GO:0001889)|lung epithelium development (GO:0060428)|mesonephric duct development (GO:0072177)|mesonephric tubule development (GO:0072164)|metanephric ascending thin limb development (GO:0072218)|metanephric collecting duct development (GO:0072205)|metanephric distal tubule morphogenesis (GO:0072287)|metanephric proximal tubule development (GO:0072237)|neural tube development (GO:0021915)|neuropeptide signaling pathway (GO:0007218)|nitrogen compound metabolic process (GO:0006807)|peptidyl-serine phosphorylation (GO:0018105)|placenta blood vessel development (GO:0060674)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein export from nucleus (GO:0006611)|regulation of mitotic spindle organization (GO:0060236)|regulation of proteasomal protein catabolic process (GO:0061136)|response to fluid shear stress (GO:0034405)|skin development (GO:0043588)|spinal cord development (GO:0021510)	basolateral plasma membrane (GO:0016323)|cilium (GO:0005929)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|motile primary cilium (GO:0031512)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|polycystin complex (GO:0002133)	calcium channel activity (GO:0005262)|carbohydrate binding (GO:0030246)|cation channel activity (GO:0005261)|ion channel binding (GO:0044325)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|kidney(6)|lung(34)|prostate(4)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	72						CGGCTGGACAGCACCAGCGCC	0.652																																					p.L1361V		Atlas-SNP	.											.	PKD1	184	.	0			c.C4081G						PASS	.						35.0	37.0	37.0					16																	2161087		2193	4295	6488	SO:0001583	missense	5310	exon15			TGGACAGCACCAG	L33243	CCDS32369.1, CCDS45385.1	16p13.3	2014-01-28			ENSG00000008710	ENSG00000008710		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	9008	protein-coding gene	gene with protein product	"""polycystin 1"", ""transient receptor potential cation channel, subfamily P, member 1"""	601313					Standard	NM_001009944		Approved	PBP, Pc-1, TRPP1	uc002cos.1	P98161	OTTHUMG00000155795	ENST00000262304.4:c.4081C>G	16.37:g.2161087G>C	ENSP00000262304:p.Leu1361Val	66.0	0.0	0		122.0	64.0	0.52459	NM_000296	Q15140|Q15141	Missense_Mutation	SNP	ENST00000262304.4	37	CCDS32369.1	.	.	.	.	.	.	.	.	.	.	g	4.600	0.111428	0.08831	.	.	ENSG00000008710	ENST00000262304;ENST00000423118;ENST00000306101	T;T	0.45276	0.9;0.9	5.58	2.51	0.30379	PKD/Chitinase domain (1);Polycystin cation channel (1);PKD domain (4);	0.236328	0.35349	N	0.003270	T	0.37128	0.0992	L	0.59436	1.845	0.21915	N	0.999479	P;P	0.40638	0.702;0.725	B;P	0.47786	0.421;0.557	T	0.16719	-1.0393	10	0.09084	T	0.74	.	2.4934	0.04615	0.2134:0.125:0.5333:0.1283	.	1361;1361	P98161-3;P98161	.;PKD1_HUMAN	V	1361;1361;1042	ENSP00000262304:L1361V;ENSP00000399501:L1361V	ENSP00000262304:L1361V	L	-	1	2	PKD1	2101088	0.548000	0.26473	0.582000	0.28627	0.017000	0.09413	0.802000	0.27069	0.705000	0.31890	0.450000	0.29827	CTG	.	.	none		0.652	PKD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341688.1		
COL17A1	1308	hgsc.bcm.edu	37	10	105836066	105836066	+	Silent	SNP	C	C	T	rs61731085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:105836066C>T	ENST00000353479.5	-	5	614	c.324G>A	c.(322-324)gcG>gcA	p.A108A	COL17A1_ENST00000369733.3_Silent_p.A108A|COL17A1_ENST00000393211.3_Silent_p.A108A	NM_000494.3	NP_000485.3	Q9UMD9	COHA1_HUMAN	collagen, type XVII, alpha 1	108	Nonhelical region (NC16).				cell junction assembly (GO:0034329)|cell-matrix adhesion (GO:0007160)|collagen catabolic process (GO:0030574)|epidermis development (GO:0008544)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|hemidesmosome (GO:0030056)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				NS(1)|breast(2)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|liver(1)|lung(22)|ovary(5)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(1)	62		Colorectal(252;0.103)|Breast(234;0.122)		Epithelial(162;2.5e-09)|all cancers(201;7.94e-08)|BRCA - Breast invasive adenocarcinoma(275;0.0165)		TACCTTCATACGCATGGCGGG	0.502													C|||	69	0.013778	0.0492	0.0043	5008	,	,		20980	0.0		0.001	False		,,,				2504	0.0				p.A108A		Atlas-SNP	.											.	COL17A1	149	.	0			c.G324A						PASS	.	C		198,4208	124.1+/-161.4	4,190,2009	203.0	202.0	202.0		324	-11.2	0.0	10	dbSNP_129	202	6,8594	5.0+/-18.6	0,6,4294	no	coding-synonymous	COL17A1	NM_000494.3		4,196,6303	TT,TC,CC		0.0698,4.4939,1.5685		108/1498	105836066	204,12802	2203	4300	6503	SO:0001819	synonymous_variant	1308	exon5			TTCATACGCATGG	M91669	CCDS7554.1	10q24.3	2013-01-16			ENSG00000065618	ENSG00000065618		"""Collagens"""	2194	protein-coding gene	gene with protein product		113811		BPAG2		7916703	Standard	NM_000494		Approved	BP180	uc001kxr.3	Q9UMD9	OTTHUMG00000018998	ENST00000353479.5:c.324G>A	10.37:g.105836066C>T		132.0	0.0	0		142.0	70.0	0.492958	NM_000494	Q02802|Q5JV36|Q99018|Q9NQK9|Q9UC14	Silent	SNP	ENST00000353479.5	37	CCDS7554.1																																																																																			C|0.988;T|0.012	0.012	strong		0.502	COL17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050181.1	NM_130778, NM_000494	
PLEKHB1	58473	hgsc.bcm.edu	37	11	73371842	73371842	+	Silent	SNP	C	C	G	rs147173613	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:73371842C>G	ENST00000354190.5	+	7	971	c.540C>G	c.(538-540)ccC>ccG	p.P180P	PLEKHB1_ENST00000227214.6_Silent_p.P126P|PLEKHB1_ENST00000543085.1_Silent_p.P75P|PLEKHB1_ENST00000398494.4_Silent_p.P161P|PLEKHB1_ENST00000398492.4_Silent_p.P145P|PLEKHB1_ENST00000535129.1_Silent_p.P126P	NM_021200.2	NP_067023.1	Q9UF11	PKHB1_HUMAN	pleckstrin homology domain containing, family B (evectins) member 1	180					multicellular organismal development (GO:0007275)|phototransduction (GO:0007602)|regulation of cell differentiation (GO:0045595)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	signal transducer activity (GO:0004871)			endometrium(2)|large_intestine(2)|lung(1)|ovary(1)|prostate(1)	7						AGGTGGTGCCCCCCAATGCAC	0.637											OREG0021217	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	24	0.00479233	0.0008	0.013	5008	,	,		17175	0.001		0.0129	False		,,,				2504	0.0				p.P180P		Atlas-SNP	.											.	PLEKHB1	16	.	0			c.C540G						PASS	.	C	,,,,	12,4134		0,12,2061	55.0	63.0	60.0		435,483,378,378,540	-6.7	0.3	11	dbSNP_134	60	121,8227		2,117,4055	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	PLEKHB1	NM_001130033.1,NM_001130034.1,NM_001130035.1,NM_001130036.1,NM_021200.2	,,,,	2,129,6116	GG,GC,CC		1.4494,0.2894,1.0645	,,,,	145/209,161/225,126/190,126/190,180/244	73371842	133,12361	2073	4174	6247	SO:0001819	synonymous_variant	58473	exon7			GGTGCCCCCCAAT	AF081583	CCDS44672.1, CCDS44673.1, CCDS44674.1, CCDS44675.1	11q13.5-q14.1	2013-01-10	2002-11-04	2002-11-08	ENSG00000021300	ENSG00000021300		"""Pleckstrin homology (PH) domain containing"""	19079	protein-coding gene	gene with protein product		607651	"""PH domain containing, retinal 1"""	PHRET1		10585447	Standard	NM_021200		Approved	PHR1, KPL1	uc001ouc.3	Q9UF11	OTTHUMG00000168030	ENST00000354190.5:c.540C>G	11.37:g.73371842C>G		69.0	0.0	0	1144	103.0	48.0	0.466019	NM_021200	A8K0Q5|B2RBP1|B7Z716|Q9UBF5|Q9UI37|Q9UI44	Silent	SNP	ENST00000354190.5	37	CCDS44672.1																																																																																			C|0.993;G|0.007	0.007	strong		0.637	PLEKHB1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000397593.1		
RADIL	55698	hgsc.bcm.edu	37	7	4876100	4876100	+	Silent	SNP	G	G	A	rs138811640	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4876100G>A	ENST00000399583.3	-	3	859	c.672C>T	c.(670-672)aaC>aaT	p.N224N	RADIL_ENST00000536091.1_Silent_p.N224N|RADIL_ENST00000538469.1_De_novo_Start_OutOfFrame	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	224					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)		p.N224N(1)		NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CGGGCAGGGCGTTCACTGGGC	0.721													G|||	60	0.0119808	0.0015	0.0173	5008	,	,		12942	0.0		0.0249	False		,,,				2504	0.0215				p.N224N		Atlas-SNP	.											RADIL,brain,glioma,0,2	RADIL	110	2	1	Substitution - coding silent(1)	lung(1)	c.C672T						PASS	.	G		16,4162		0,16,2073	11.0	18.0	16.0		672	0.3	0.1	7	dbSNP_134	16	205,8153		6,193,3980	no	coding-synonymous	RADIL	NM_018059.4		6,209,6053	AA,AG,GG		2.4527,0.383,1.7629		224/1076	4876100	221,12315	2089	4179	6268	SO:0001819	synonymous_variant	55698	exon3			CAGGGCGTTCACT	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.672C>T	7.37:g.4876100G>A		8.0	0.0	0		19.0	17.0	0.894737	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.987;A|0.013	0.013	strong		0.721	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
PBDC1	51260	hgsc.bcm.edu	37	X	75394784	75394784	+	Splice_Site	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:75394784G>T	ENST00000373358.3	+	3	359	c.156G>T	c.(154-156)aaG>aaT	p.K52N	PBDC1_ENST00000373357.3_Splice_Site_p.K52N	NM_016500.3	NP_057584.2	Q9BVG4	PBDC1_HUMAN	polysaccharide biosynthesis domain containing 1	52																	TCTATTACAAGGTGAGTTGTC	0.398																																					p.K52N		Atlas-SNP	.											.	.	.	.	0			c.G156T						PASS	.						131.0	106.0	114.0					X																	75394784		2203	4300	6503	SO:0001630	splice_region_variant	51260	exon3			TTACAAGGTGAGT	BC001220	CCDS14432.1, CCDS75995.1	Xq13.2	2012-11-28	2012-11-28	2012-11-28	ENSG00000102390	ENSG00000102390			28790	protein-coding gene	gene with protein product			"""chromosome X open reading frame 26"""	CXorf26		11042152	Standard	NM_016500		Approved	MGC874	uc004ecl.1	Q9BVG4	OTTHUMG00000021876	ENST00000373358.3:c.156+1G>T	X.37:g.75394784G>T		97.0	0.0	0		99.0	99.0	1	NM_016500		Missense_Mutation	SNP	ENST00000373358.3	37	CCDS14432.1	.	.	.	.	.	.	.	.	.	.	G	8.506	0.865350	0.17250	.	.	ENSG00000102390	ENST00000373358;ENST00000373357	.	.	.	4.8	1.69	0.24217	Yst0336-like domain (1);	0.044941	0.85682	D	0.000000	T	0.14570	0.0352	N	0.02111	-0.68	0.37122	D	0.900873	B	0.21520	0.057	B	0.23275	0.045	T	0.04242	-1.0966	9	0.15066	T	0.55	-21.0255	0.5888	0.00724	0.2492:0.1861:0.3716:0.1931	.	52	Q9BVG4	CX026_HUMAN	N	52	.	ENSP00000362455:K52N	K	+	3	2	CXorf26	75311186	1.000000	0.71417	1.000000	0.80357	0.854000	0.48673	0.813000	0.27225	0.469000	0.27268	0.600000	0.82982	AAG	.	.	none		0.398	PBDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057294.1	NM_016500	Missense_Mutation
RHPN2	85415	hgsc.bcm.edu	37	19	33482821	33482821	+	Missense_Mutation	SNP	G	G	A	rs79314177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:33482821G>A	ENST00000254260.3	-	13	1587	c.1552C>T	c.(1552-1554)Cgc>Tgc	p.R518C	RHPN2_ENST00000588683.1_5'Flank|RHPN2_ENST00000400226.4_Missense_Mutation_p.R367C	NM_033103.4	NP_149094.3	Q8IUC4	RHPN2_HUMAN	rhophilin, Rho GTPase binding protein 2	518	PDZ.				signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(5)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(3)|skin(3)|urinary_tract(1)	44	Esophageal squamous(110;0.137)					GCAGTGAAGCGGATGCTTCGA	0.547													G|||	208	0.0415335	0.0	0.0288	5008	,	,		16695	0.0169		0.0368	False		,,,				2504	0.137				p.R518C		Atlas-SNP	.											.	RHPN2	107	.	0			c.C1552T						PASS	.	G	CYS/ARG	19,4387	26.2+/-53.5	0,19,2184	69.0	62.0	64.0		1552	3.1	0.6	19	dbSNP_131	64	294,8306	107.6+/-168.3	1,292,4007	no	missense	RHPN2	NM_033103.4	180	1,311,6191	AA,AG,GG		3.4186,0.4312,2.4066	benign	518/687	33482821	313,12693	2203	4300	6503	SO:0001583	missense	85415	exon13			TGAAGCGGATGCT	AF268032	CCDS12427.1	19q13.12	2008-02-05				ENSG00000131941			19974	protein-coding gene	gene with protein product						12221077	Standard	NM_033103		Approved		uc002nuf.3	Q8IUC4		ENST00000254260.3:c.1552C>T	19.37:g.33482821G>A	ENSP00000254260:p.Arg518Cys	173.0	0.0	0		204.0	113.0	0.553922	NM_033103	B2RCG8|B3KUY8|B4DUS7|Q8N3T7|Q8N9D6|Q8NE33|Q96RU1	Missense_Mutation	SNP	ENST00000254260.3	37	CCDS12427.1	47	0.02152014652014652	0	0.0	16	0.04419889502762431	10	0.017482517482517484	21	0.027704485488126648	G	12.86	2.063219	0.36373	0.004312	0.034186	ENSG00000131941	ENST00000254260;ENST00000544458;ENST00000400226	T;T	0.30981	1.51;1.51	5.22	3.08	0.35506	PDZ/DHR/GLGF (1);	0.573078	0.19174	N	0.120873	T	0.05823	0.0152	L	0.41492	1.28	0.43761	D	0.996271	B	0.12013	0.005	B	0.08055	0.003	T	0.02805	-1.1108	10	0.33141	T	0.24	-5.1732	10.146	0.42764	0.1578:0.0:0.8422:0.0	.	518	Q8IUC4	RHPN2_HUMAN	C	518;248;367	ENSP00000254260:R518C;ENSP00000402244:R367C	ENSP00000254260:R518C	R	-	1	0	RHPN2	38174661	0.988000	0.35896	0.591000	0.28745	0.766000	0.43426	2.061000	0.41403	0.726000	0.32339	-0.119000	0.15052	CGC	G|0.974;A|0.026	0.026	strong		0.547	RHPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450828.2	NM_033103	
MMRN1	22915	hgsc.bcm.edu	37	4	90857518	90857518	+	Missense_Mutation	SNP	T	T	A	rs200343754	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:90857518T>A	ENST00000394980.1	+	7	3006	c.2687T>A	c.(2686-2688)cTg>cAg	p.L896Q	MMRN1_ENST00000394981.1_Intron|MMRN1_ENST00000264790.2_Missense_Mutation_p.L896Q|MMRN1_ENST00000508372.1_Missense_Mutation_p.L638Q			Q13201	MMRN1_HUMAN	multimerin 1	896					blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)	extracellular region (GO:0005576)|platelet alpha granule lumen (GO:0031093)				breast(2)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(12)|liver(2)|lung(34)|ovary(5)|prostate(1)|skin(6)|stomach(1)|urinary_tract(2)	72		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;6.96e-05)		GCTCTTCAACTGCAAGTATTA	0.348													T|||	3	0.000599042	0.0	0.0	5008	,	,		19216	0.0		0.001	False		,,,				2504	0.002				p.L896Q		Atlas-SNP	.											.	MMRN1	174	.	0			c.T2687A						PASS	.	T	GLN/LEU	0,4402		0,0,2201	60.0	63.0	62.0		2687	4.1	1.0	4		62	2,8594	2.2+/-6.3	0,2,4296	no	missense	MMRN1	NM_007351.2	113	0,2,6497	AA,AT,TT		0.0233,0.0,0.0154	benign	896/1229	90857518	2,12996	2201	4298	6499	SO:0001583	missense	22915	exon6			TTCAACTGCAAGT	U27109	CCDS3635.1	4q22	2008-02-05	2004-03-02	2004-03-02	ENSG00000138722	ENSG00000138722		"""EMI domain containing"""	7178	protein-coding gene	gene with protein product	"""glycoprotein Ia*"""	601456	"""multimerin"""	MMRN		7629143, 10828608	Standard	NM_007351		Approved	ECM, EMILIN4, GPIa*	uc003hst.3	Q13201	OTTHUMG00000130947	ENST00000394980.1:c.2687T>A	4.37:g.90857518T>A	ENSP00000378431:p.Leu896Gln	116.0	0.0	0		111.0	52.0	0.468468	NM_007351	Q4W5L1|Q6P3T8|Q6ZUL9	Missense_Mutation	SNP	ENST00000394980.1	37	CCDS3635.1	.	.	.	.	.	.	.	.	.	.	T	14.79	2.640952	0.47153	0.0	2.33E-4	ENSG00000138722	ENST00000394980;ENST00000264790;ENST00000508372	T;T;T	0.68624	-0.03;-0.03;-0.34	5.3	4.1	0.47936	.	0.211787	0.33290	N	0.005070	T	0.54631	0.1870	L	0.44542	1.39	0.80722	D	1	B	0.33857	0.429	B	0.27170	0.077	T	0.57423	-0.7814	10	0.72032	D	0.01	.	10.1863	0.43000	0.2658:0.0:0.0:0.7342	.	896	Q13201	MMRN1_HUMAN	Q	896;896;638	ENSP00000378431:L896Q;ENSP00000264790:L896Q;ENSP00000426461:L638Q	ENSP00000264790:L896Q	L	+	2	0	MMRN1	91076541	0.093000	0.21703	1.000000	0.80357	0.828000	0.46876	1.331000	0.33793	1.082000	0.41137	0.533000	0.62120	CTG	T|0.999;A|0.001	0.001	weak		0.348	MMRN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253546.2	NM_007351	
PCDH17	27253	hgsc.bcm.edu	37	13	58207711	58207711	+	Missense_Mutation	SNP	G	G	T	rs41292834	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:58207711G>T	ENST00000377918.3	+	1	1057	c.1031G>T	c.(1030-1032)cGc>cTc	p.R344L		NM_001040429.2	NP_001035519.1	O14917	PCD17_HUMAN	protocadherin 17	344	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(30)|liver(2)|lung(54)|ovary(4)|pancreas(2)|prostate(5)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	120		Lung NSC(96;0.027)|Prostate(109;0.0453)|Breast(118;0.128)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;1.06e-05)		CTCATCGACCGCAACGACAAT	0.647													G|||	24	0.00479233	0.0015	0.0043	5008	,	,		13628	0.0		0.0169	False		,,,				2504	0.002				p.R344L	Melanoma(72;952 1291 1619 12849 33676)	Atlas-SNP	.											.	PCDH17	304	.	0			c.G1031T						PASS	.	G	LEU/ARG	9,4397	15.5+/-35.6	0,9,2194	75.0	72.0	73.0		1031	5.6	1.0	13	dbSNP_127	73	97,8503	54.4+/-115.2	0,97,4203	yes	missense	PCDH17	NM_001040429.2	102	0,106,6397	TT,TG,GG		1.1279,0.2043,0.815	benign	344/1160	58207711	106,12900	2203	4300	6503	SO:0001583	missense	27253	exon1			TCGACCGCAACGA	AF029343	CCDS31986.1	13q21.1	2010-01-26			ENSG00000118946	ENSG00000118946		"""Cadherins / Protocadherins : Non-clustered"""	14267	protein-coding gene	gene with protein product		611760				10835267	Standard	NM_001040429		Approved	PCDH68, PCH68	uc001vhq.1	O14917	OTTHUMG00000016992	ENST00000377918.3:c.1031G>T	13.37:g.58207711G>T	ENSP00000367151:p.Arg344Leu	22.0	0.0	0		31.0	21.0	0.677419	NM_001040429	A8K1R5|Q5VVW9|Q5VVX0	Missense_Mutation	SNP	ENST00000377918.3	37	CCDS31986.1	14	0.00641025641025641	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	12	0.0158311345646438	G	11.47	1.647374	0.29246	0.002043	0.011279	ENSG00000118946	ENST00000377918	T	0.59638	0.25	5.57	5.57	0.84162	Cadherin (3);Cadherin conserved site (1);Cadherin-like (1);	0.043754	0.85682	D	0.000000	T	0.15825	0.0381	N	0.02011	-0.69	0.46149	D	0.998891	B;B	0.19935	0.016;0.04	B;B	0.17098	0.017;0.012	T	0.18777	-1.0326	9	.	.	.	.	12.8315	0.57748	0.0746:0.0:0.9254:0.0	rs41292834	344;344	O14917-2;O14917	.;PCD17_HUMAN	L	344	ENSP00000367151:R344L	.	R	+	2	0	PCDH17	57105712	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.511000	0.53400	2.640000	0.89533	0.650000	0.86243	CGC	G|0.993;T|0.007	0.007	strong		0.647	PCDH17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045139.1	NM_001040429	
HFM1	164045	hgsc.bcm.edu	37	1	91816313	91816313	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:91816313T>C	ENST00000370425.3	-	18	2286	c.2188A>G	c.(2188-2190)Aaa>Gaa	p.K730E	HFM1_ENST00000462405.1_Intron|HFM1_ENST00000294696.5_5'UTR|HFM1_ENST00000370424.3_Missense_Mutation_p.K409E	NM_001017975.3	NP_001017975.3	A2PYH4	HFM1_HUMAN	HFM1, ATP-dependent DNA helicase homolog (S. cerevisiae)	730					resolution of meiotic recombination intermediates (GO:0000712)		ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(17)|lung(33)|ovary(1)|prostate(3)|skin(2)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	75		all_lung(203;0.00961)|Lung NSC(277;0.0351)		all cancers(265;0.000481)|Epithelial(280;0.00863)|OV - Ovarian serous cystadenocarcinoma(397;0.126)|KIRC - Kidney renal clear cell carcinoma(1967;0.171)		GATGGATTTTTCAAGGCTCTG	0.343																																					p.K730E		Atlas-SNP	.											.	HFM1	188	.	0			c.A2188G						PASS	.						119.0	107.0	111.0					1																	91816313		1834	4085	5919	SO:0001583	missense	164045	exon18			GATTTTTCAAGGC	AB204867	CCDS30769.2	1p22.2	2008-03-26			ENSG00000162669	ENSG00000162669			20193	protein-coding gene	gene with protein product		615684	"""SEC63 domain containing 1"""	SEC63D1		14702039, 17286053	Standard	XM_006710395		Approved	MER3, FLJ39011, FLJ36760	uc001doa.4	A2PYH4	OTTHUMG00000010093	ENST00000370425.3:c.2188A>G	1.37:g.91816313T>C	ENSP00000359454:p.Lys730Glu	65.0	0.0	0		108.0	53.0	0.490741	NM_001017975	B1B0B6|Q8N9Q0	Missense_Mutation	SNP	ENST00000370425.3	37	CCDS30769.2	.	.	.	.	.	.	.	.	.	.	T	23.5	4.421719	0.83559	.	.	ENSG00000162669	ENST00000370425;ENST00000370424;ENST00000370421	T;T	0.68181	0.03;-0.31	5.36	5.36	0.76844	.	0.000000	0.47852	U	0.000204	T	0.80433	0.4622	M	0.88031	2.925	0.80722	D	1	D;D	0.64830	0.994;0.986	D;P	0.65874	0.939;0.904	D	0.83812	0.0242	10	0.54805	T	0.06	.	15.6548	0.77124	0.0:0.0:0.0:1.0	.	409;730	A6NGI5;A2PYH4	.;HFM1_HUMAN	E	730;409;414	ENSP00000359454:K730E;ENSP00000359453:K409E	ENSP00000359450:K414E	K	-	1	0	HFM1	91588901	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.939000	0.87685	2.162000	0.67917	0.377000	0.23210	AAA	.	.	none		0.343	HFM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316716.2	NM_001017975	
ATM	472	hgsc.bcm.edu	37	11	108163487	108163487	+	Silent	SNP	C	C	T	rs1800889	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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		164.0	0.0	0		147.0	67.0	0.455782	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	
NAT6	24142	hgsc.bcm.edu	37	3	50334592	50334592	+	Silent	SNP	G	G	A	rs374560438		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50334592G>A	ENST00000443842.1	-	2	1110	c.303C>T	c.(301-303)ttC>ttT	p.F101F	NAT6_ENST00000354862.4_Silent_p.F123F|HYAL3_ENST00000359051.3_Intron|NAT6_ENST00000417393.1_Silent_p.F101F|HYAL3_ENST00000450982.1_Intron|HYAL3_ENST00000513170.1_Intron|HYAL3_ENST00000415204.1_Intron|HYAL3_ENST00000336307.1_Intron|NAT6_ENST00000443094.2_Silent_p.F101F			Q93015	NAT6_HUMAN	N-acetyltransferase 6 (GCN5-related)	101	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					cytoplasm (GO:0005737)	N-acetyltransferase activity (GO:0008080)			endometrium(3)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		GGCAGAGGGGGAAGGCATCTG	0.652																																					p.F123F		Atlas-SNP	.											.	NAT6	14	.	0			c.C369T						PASS	.	G	,,,,,,,	2,4212		0,2,2105	27.0	34.0	32.0		303,303,,,,,,369	4.6	1.0	3		32	17,8403		0,17,4193	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	HYAL3,NAT6	NM_001200016.1,NM_001200018.1,NM_001200029.1,NM_001200030.1,NM_001200031.1,NM_001200032.1,NM_003549.3,NM_012191.3	,,,,,,,	0,19,6298	AA,AG,GG		0.2019,0.0475,0.1504	,,,,,,,	101/287,101/287,,,,,,123/309	50334592	19,12615	2107	4210	6317	SO:0001819	synonymous_variant	24142	exon2			GAGGGGGAAGGCA	AF040705	CCDS43095.1, CCDS56258.1	3p21.3	2011-11-16	2008-09-24		ENSG00000243477	ENSG00000243477	2.3.1.-		30252	protein-coding gene	gene with protein product		607073	"""N-acetyltransferase 6"""			11929860, 11085536	Standard	NM_012191		Approved	FUS2		Q93015	OTTHUMG00000156939	ENST00000443842.1:c.303C>T	3.37:g.50334592G>A		112.0	0.0	0		131.0	74.0	0.564885	NM_012191	Q93014	Silent	SNP	ENST00000443842.1	37	CCDS56258.1																																																																																			.	.	weak		0.652	NAT6-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346681.1	NM_012191	
SLFNL1	200172	hgsc.bcm.edu	37	1	41482917	41482917	+	Missense_Mutation	SNP	A	A	G	rs147062455	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41482917A>G	ENST00000359345.1	-	3	3666	c.1090T>C	c.(1090-1092)Tgg>Cgg	p.W364R	SLFNL1_ENST00000372613.2_Intron|SLFNL1_ENST00000302946.8_Missense_Mutation_p.W364R|SLFNL1_ENST00000439569.2_Missense_Mutation_p.W364R|SLFNL1_ENST00000372611.1_Missense_Mutation_p.W305R|SLFNL1_ENST00000397197.2_Intron	NM_144990.3	NP_659427.3	Q499Z3	SLNL1_HUMAN	schlafen-like 1	364							ATP binding (GO:0005524)			endometrium(3)|large_intestine(3)|lung(2)|prostate(1)|skin(1)	10	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Breast(333;0.1)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0393)				TGCCTGCACCACTCCTGGATG	0.682													A|||	10	0.00199681	0.0	0.0072	5008	,	,		17107	0.0		0.005	False		,,,				2504	0.0				p.W364R		Atlas-SNP	.											.	SLFNL1	37	.	0			c.T1090C						PASS	.	A	ARG/TRP,ARG/TRP	2,4388		0,2,2193	23.0	23.0	23.0		1090,1090	5.6	1.0	1	dbSNP_134	23	14,8572		0,14,4279	no	missense,missense	SLFNL1	NM_001168247.1,NM_144990.3	101,101	0,16,6472	GG,GA,AA		0.1631,0.0456,0.1233	probably-damaging,probably-damaging	364/408,364/408	41482917	16,12960	2195	4293	6488	SO:0001583	missense	200172	exon5			TGCACCACTCCTG	BC022037	CCDS460.1, CCDS72766.1	1p34.2	2008-02-05			ENSG00000171790	ENSG00000171790			26313	protein-coding gene	gene with protein product							Standard	NM_144990		Approved	FLJ23878	uc001cgm.2	Q499Z3	OTTHUMG00000005719	ENST00000359345.1:c.1090T>C	1.37:g.41482917A>G	ENSP00000352299:p.Trp364Arg	44.0	0.0	0		51.0	48.0	0.941176	NM_001168247	A8K8D1|Q49AG8|Q5VW72|Q5VW74|Q8N7V7|Q8TCH6|Q8WVZ8	Missense_Mutation	SNP	ENST00000359345.1	37	CCDS460.1	6	0.0027472527472527475	0	0.0	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	A	20.3	3.971902	0.74246	4.56E-4	0.001631	ENSG00000171790	ENST00000302946;ENST00000372611;ENST00000359345;ENST00000439569	T;T;T;T	0.37915	1.17;1.42;1.17;1.17	5.57	5.57	0.84162	.	0.000000	0.47852	D	0.000220	T	0.39118	0.1066	L	0.34521	1.04	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.71656	0.974;0.915	T	0.43147	-0.9409	10	0.72032	D	0.01	-16.654	12.1224	0.53900	1.0:0.0:0.0:0.0	.	305;364	Q499Z3-2;Q499Z3	.;SLNL1_HUMAN	R	364;305;364;364	ENSP00000304401:W364R;ENSP00000361694:W305R;ENSP00000352299:W364R;ENSP00000398938:W364R	ENSP00000304401:W364R	W	-	1	0	SLFNL1	41255504	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.980000	0.70516	2.117000	0.64856	0.459000	0.35465	TGG	A|0.998;G|0.002	0.002	strong		0.682	SLFNL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015650.1	NM_144990	
MSH6	2956	hgsc.bcm.edu	37	2	48027375	48027375	+	Silent	SNP	T	T	C	rs2020913	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:48027375T>C	ENST00000234420.5	+	4	2405	c.2253T>C	c.(2251-2253)aaT>aaC	p.N751N	MSH6_ENST00000538136.1_Silent_p.N449N|MSH6_ENST00000540021.1_Silent_p.N621N|FBXO11_ENST00000405808.1_Intron	NM_000179.2	NP_000170.1	P52701	MSH6_HUMAN	mutS homolog 6	751					ATP catabolic process (GO:0006200)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|positive regulation of helicase activity (GO:0051096)|reciprocal meiotic recombination (GO:0007131)|response to UV (GO:0009411)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|MutSalpha complex (GO:0032301)|nuclear chromatin (GO:0000790)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|damaged DNA binding (GO:0003684)|DNA-dependent ATPase activity (GO:0008094)|guanine/thymine mispair binding (GO:0032137)|methylated histone binding (GO:0035064)|mismatched DNA binding (GO:0030983)	p.0?(2)		breast(8)|central_nervous_system(29)|cervix(1)|endometrium(32)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(75)|lung(25)|ovary(3)|prostate(3)|skin(10)|stomach(22)|thyroid(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	229		Acute lymphoblastic leukemia(82;0.0299)|all_hematologic(82;0.0358)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			ATGGAACAAATGGTTCTACTG	0.443			"""Mis, N, F, S"""		colorectal	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				T|||	120	0.0239617	0.0885	0.0043	5008	,	,		20418	0.0		0.0	False		,,,				2504	0.0				p.N751N		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p16	2956	mutS homolog 6 (E. coli)		E	.	MSH6	341	.	2	Whole gene deletion(2)	haematopoietic_and_lymphoid_tissue(2)	c.T2253C						PASS	.	T		266,4140	150.3+/-184.3	8,250,1945	135.0	132.0	133.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2253	-0.9	1.0	2	dbSNP_98	133	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MSH6	NM_000179.2		8,251,6244	CC,CT,TT		0.0116,6.0372,2.0529		751/1361	48027375	267,12739	2203	4300	6503	SO:0001819	synonymous_variant	2956	exon4	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	AACAAATGGTTCT	U54777	CCDS1836.1, CCDS62906.1, CCDS62907.1	2p16	2014-09-17	2013-09-12		ENSG00000116062	ENSG00000116062			7329	protein-coding gene	gene with protein product		600678	"""mutS (E. coli) homolog 6"", ""mutS homolog 6 (E. coli)"""	GTBP		7604266	Standard	NM_000179		Approved		uc002rwd.4	P52701	OTTHUMG00000129129	ENST00000234420.5:c.2253T>C	2.37:g.48027375T>C		108.0	0.0	0		101.0	47.0	0.465347	NM_000179	B4DF41|B4E3I4|F5H2F9|O43706|O43917|Q8TCX4|Q9BTB5	Silent	SNP	ENST00000234420.5	37	CCDS1836.1																																																																																			T|0.980;C|0.020	0.020	strong		0.443	MSH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251180.4	NM_000179	
PCLO	27445	hgsc.bcm.edu	37	7	82785304	82785304	+	Missense_Mutation	SNP	G	G	A	rs61738783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:82785304G>A	ENST00000333891.9	-	2	990	c.653C>T	c.(652-654)cCg>cTg	p.P218L	PCLO_ENST00000423517.2_Missense_Mutation_p.P218L	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						CTTAGGAATCGGCTTGGGTGG	0.443													G|||	27	0.00539137	0.0	0.0043	5008	,	,		18249	0.0		0.0169	False		,,,				2504	0.0072				p.P218L		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,+1,5	PCLO	1506	5	0			c.C653T						PASS	.	G	LEU/PRO,LEU/PRO	11,3805		0,11,1897	83.0	88.0	86.0		653,653	4.6	0.0	7	dbSNP_129	86	141,8103		0,141,3981	yes	missense,missense	PCLO	NM_033026.5,NM_014510.2	98,98	0,152,5878	AA,AG,GG		1.7103,0.2883,1.2604	benign,benign	218/5143,218/4936	82785304	152,11908	1908	4122	6030	SO:0001583	missense	27445	exon2			GGAATCGGCTTGG	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.653C>T	7.37:g.82785304G>A	ENSP00000334319:p.Pro218Leu	235.0	1.0	0.00425532		238.0	134.0	0.563025	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	19	0.0086996336996337	0	0.0	3	0.008287292817679558	0	0.0	16	0.021108179419525065	G	4.810	0.150680	0.09185	0.002883	0.017103	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.16196	2.36;2.37	5.48	4.59	0.56863	.	.	.	.	.	T	0.06645	0.0170	N	0.22421	0.69	0.24930	N	0.991927	B;B	0.16396	0.017;0.017	B;B	0.08055	0.003;0.003	T	0.15464	-1.0436	9	0.87932	D	0	.	12.7097	0.57082	0.1393:0.0:0.8607:0.0	.	218;218	Q9Y6V0-5;Q9Y6V0-6	.;.	L	218	ENSP00000334319:P218L;ENSP00000388393:P218L	ENSP00000334319:P218L	P	-	2	0	PCLO	82623240	0.613000	0.27009	0.002000	0.10522	0.071000	0.16799	4.026000	0.57232	1.301000	0.44836	0.655000	0.94253	CCG	G|0.989;A|0.011	0.011	strong		0.443	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
ANK3	288	hgsc.bcm.edu	37	10	61832131	61832131	+	Silent	SNP	A	A	G	rs11815168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:61832131A>G	ENST00000280772.2	-	37	8699	c.8508T>C	c.(8506-8508)caT>caC	p.H2836H	ANK3_ENST00000373827.2_Intron|ANK3_ENST00000355288.2_Intron|ANK3_ENST00000503366.1_Intron	NM_020987.3	NP_066267.2	Q12955	ANK3_HUMAN	ankyrin 3, node of Ranvier (ankyrin G)	2836					axon guidance (GO:0007411)|axonogenesis (GO:0007409)|cytoskeletal anchoring at plasma membrane (GO:0007016)|establishment of protein localization (GO:0045184)|Golgi to plasma membrane protein transport (GO:0043001)|maintenance of protein location in plasma membrane (GO:0072660)|membrane assembly (GO:0071709)|mitotic cytokinesis (GO:0000281)|neuromuscular junction development (GO:0007528)|neuronal action potential (GO:0019228)|plasma membrane organization (GO:0007009)|positive regulation of cell communication by electrical coupling (GO:0010650)|positive regulation of gene expression (GO:0010628)|positive regulation of homotypic cell-cell adhesion (GO:0034112)|positive regulation of membrane depolarization during cardiac muscle cell action potential (GO:1900827)|positive regulation of membrane potential (GO:0045838)|positive regulation of protein targeting to membrane (GO:0090314)|positive regulation of sodium ion transmembrane transporter activity (GO:2000651)|positive regulation of sodium ion transport (GO:0010765)|protein localization to plasma membrane (GO:0072659)|protein targeting to plasma membrane (GO:0072661)|regulation of potassium ion transport (GO:0043266)|signal transduction (GO:0007165)	axon initial segment (GO:0043194)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|costamere (GO:0043034)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|intercalated disc (GO:0014704)|lateral plasma membrane (GO:0016328)|lysosome (GO:0005764)|neuromuscular junction (GO:0031594)|node of Ranvier (GO:0033268)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)|spectrin-associated cytoskeleton (GO:0014731)|T-tubule (GO:0030315)|Z disc (GO:0030018)	cadherin binding (GO:0045296)|cytoskeletal protein binding (GO:0008092)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)			NS(4)|breast(7)|central_nervous_system(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(5)|kidney(14)|large_intestine(30)|liver(2)|lung(59)|ovary(8)|pancreas(2)|prostate(5)|skin(26)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(7)	196						CTGAGGTTATATGACATGCCA	0.408													A|||	12	0.00239617	0.0	0.0014	5008	,	,		18183	0.0		0.007	False		,,,				2504	0.0041				p.H2836H		Atlas-SNP	.											.	ANK3	703	.	0			c.T8508C						PASS	.	A	,,,	12,4394	17.9+/-39.9	0,12,2191	102.0	102.0	102.0		,,,8508	0.7	1.0	10	dbSNP_120	102	55,8545	33.8+/-87.4	0,55,4245	no	intron,intron,intron,coding-synonymous	ANK3	NM_001149.3,NM_001204403.1,NM_001204404.1,NM_020987.3	,,,	0,67,6436	GG,GA,AA		0.6395,0.2724,0.5151	,,,	,,,2836/4378	61832131	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	288	exon37			GGTTATATGACAT	U13616	CCDS7258.1, CCDS7259.1, CCDS55711.1, CCDS55712.1	10q21	2013-01-10			ENSG00000151150	ENSG00000151150		"""Ankyrin repeat domain containing"""	494	protein-coding gene	gene with protein product	"""ankyrin-3, node of Ranvier"", ""ankyrin-G"""	600465				7665168	Standard	NM_020987		Approved		uc001jky.3	Q12955	OTTHUMG00000018288	ENST00000280772.2:c.8508T>C	10.37:g.61832131A>G		121.0	0.0	0		116.0	67.0	0.577586	NM_020987	B1AQT2|B4DIL1|E9PE32|Q13484|Q5CZH9|Q5VXD5|Q7Z3G4|Q9H0P5	Silent	SNP	ENST00000280772.2	37	CCDS7258.1																																																																																			A|0.995;G|0.005	0.005	strong		0.408	ANK3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048201.4	NM_020987	
PI16	221476	hgsc.bcm.edu	37	6	36926952	36926952	+	Missense_Mutation	SNP	A	A	G	rs113848006	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:36926952A>G	ENST00000373674.3	+	2	531	c.203A>G	c.(202-204)aAg>aGg	p.K68R		NM_001199159.1|NM_153370.2	NP_001186088.1|NP_699201.2	Q6UXB8	PI16_HUMAN	peptidase inhibitor 16	68	SCP.				negative regulation of cell growth involved in cardiac muscle cell development (GO:0061052)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	peptidase inhibitor activity (GO:0030414)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(2)|lung(13)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30						GCCTTCGCCAAGGCCTACGCA	0.652													A|||	80	0.0159744	0.0477	0.0072	5008	,	,		17606	0.0		0.0119	False		,,,				2504	0.0				p.K68R		Atlas-SNP	.											.	PI16	50	.	0			c.A203G						PASS	.	A	ARG/LYS,ARG/LYS	163,4237		2,159,2039	23.0	19.0	21.0		203,203	4.1	1.0	6	dbSNP_132	21	55,8541		0,55,4243	yes	missense,missense	PI16	NM_001199159.1,NM_153370.2	26,26	2,214,6282	GG,GA,AA		0.6398,3.7045,1.6774	probably-damaging,probably-damaging	68/464,68/464	36926952	218,12778	2200	4298	6498	SO:0001583	missense	221476	exon3			TCGCCAAGGCCTA		CCDS34440.1	6p21.31	2014-01-28	2005-08-17		ENSG00000164530	ENSG00000164530			21245	protein-coding gene	gene with protein product	"""microseminoprotein, beta-binding protein"""		"""protease inhibitor 16"""				Standard	NM_001199159		Approved	MGC45378, dJ90K10.5, MSMBBP	uc003ona.3	Q6UXB8	OTTHUMG00000014611	ENST00000373674.3:c.203A>G	6.37:g.36926952A>G	ENSP00000362778:p.Lys68Arg	96.0	0.0	0		107.0	54.0	0.504673	NM_001199159	Q6ZVG9|Q8IYL8|Q8NBK0|Q8TCB8	Missense_Mutation	SNP	ENST00000373674.3	37	CCDS34440.1	38	0.0173992673992674	28	0.056910569105691054	3	0.008287292817679558	0	0.0	7	0.009234828496042216	A	23.5	4.418054	0.83449	0.037045	0.006398	ENSG00000164530	ENST00000536757;ENST00000373674	T	0.07800	3.16	5.29	4.09	0.47781	CAP domain (3);	0.128596	0.52532	D	0.000078	T	0.05914	0.0154	N	0.20685	0.6	0.31202	N	0.699673	D;P	0.57257	0.979;0.892	P;P	0.60609	0.877;0.57	T	0.18871	-1.0323	10	0.45353	T	0.12	.	11.8387	0.52342	0.8531:0.1469:0.0:0.0	.	68;68	Q6UXB8;Q6UXB8-2	PI16_HUMAN;.	R	68	ENSP00000362778:K68R	ENSP00000362778:K68R	K	+	2	0	PI16	37034930	1.000000	0.71417	0.998000	0.56505	0.985000	0.73830	3.619000	0.54196	0.809000	0.34255	0.418000	0.28097	AAG	A|0.982;G|0.018	0.018	strong		0.652	PI16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040380.1	NM_153370	
VPS13B	157680	hgsc.bcm.edu	37	8	100443885	100443885	+	Missense_Mutation	SNP	C	C	T	rs61753722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:100443885C>T	ENST00000358544.2	+	22	3314	c.3203C>T	c.(3202-3204)aCa>aTa	p.T1068I	VPS13B_ENST00000395996.1_Missense_Mutation_p.T1068I|VPS13B_ENST00000357162.2_Missense_Mutation_p.T1068I	NM_017890.4	NP_060360.3	Q7Z7G8	VP13B_HUMAN	vacuolar protein sorting 13 homolog B (yeast)	1068					protein transport (GO:0015031)					NS(1)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(37)|lung(78)|ovary(8)|pancreas(3)|prostate(5)|skin(9)|upper_aerodigestive_tract(4)|urinary_tract(9)	193	Breast(36;3.73e-07)		OV - Ovarian serous cystadenocarcinoma(57;0.00636)			AAGCATCTCACACTACAGGTA	0.308													C|||	55	0.0109824	0.0	0.013	5008	,	,		15552	0.0		0.006	False		,,,				2504	0.0409				p.T1068I	Colon(161;2205 2542 7338 31318)	Atlas-SNP	.											.	VPS13B	811	.	0			c.C3203T						PASS	.	C	ILE/THR,ILE/THR	5,4401	8.1+/-20.4	0,5,2198	59.0	64.0	62.0		3203,3203	4.4	1.0	8	dbSNP_129	62	89,8511	49.4+/-109.1	1,87,4212	yes	missense,missense	VPS13B	NM_017890.3,NM_152564.3	89,89	1,92,6410	TT,TC,CC		1.0349,0.1135,0.7227	probably-damaging,probably-damaging	1068/4023,1068/3998	100443885	94,12912	2203	4300	6503	SO:0001583	missense	157680	exon22			ATCTCACACTACA	AJ608772	CCDS6280.1, CCDS6281.1, CCDS6283.1, CCDS47903.1	8q22-q23	2014-09-17	2006-12-19	2005-04-08	ENSG00000132549	ENSG00000132549			2183	protein-coding gene	gene with protein product		607817	"""Cohen syndrome 1"""	CHS1, COH1		7920642, 15498460	Standard	NM_181661		Approved		uc003yiv.4	Q7Z7G8	OTTHUMG00000140383	ENST00000358544.2:c.3203C>T	8.37:g.100443885C>T	ENSP00000351346:p.Thr1068Ile	17.0	0.0	0		19.0	7.0	0.368421	NM_152564	C9JD30|Q709C6|Q709C7|Q7Z7G4|Q7Z7G5|Q7Z7G6|Q7Z7G7|Q8NB77|Q9NWV1|Q9Y4E7	Missense_Mutation	SNP	ENST00000358544.2	37	CCDS6280.1	9	0.004120879120879121	0	0.0	5	0.013812154696132596	0	0.0	4	0.005277044854881266	C	11.46	1.645534	0.29246	0.001135	0.010349	ENSG00000132549	ENST00000357162;ENST00000358544;ENST00000395996	T;T;T	0.46819	0.86;0.86;0.86	4.41	4.41	0.53225	.	0.119576	0.52532	D	0.000061	T	0.45054	0.1323	N	0.24115	0.695	0.53688	D	0.999974	D;D;D;B	0.71674	0.986;0.986;0.998;0.291	P;P;D;B	0.80764	0.558;0.675;0.994;0.143	T	0.42137	-0.9469	10	0.16420	T	0.52	.	17.3622	0.87354	0.0:1.0:0.0:0.0	rs61753722	1067;1068;1068;1068	Q7Z7G8-6;Q7Z7G8-2;Q7Z7G8;Q7Z7G8-3	.;.;VP13B_HUMAN;.	I	1068	ENSP00000349685:T1068I;ENSP00000351346:T1068I;ENSP00000379318:T1068I	ENSP00000349685:T1068I	T	+	2	0	VPS13B	100513061	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.920000	0.75799	2.154000	0.67381	0.555000	0.69702	ACA	C|0.994;T|0.006	0.006	strong		0.308	VPS13B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000277138.1	NM_184042	
ASPSCR1	79058	hgsc.bcm.edu	37	17	79941511	79941511	+	Silent	SNP	C	C	T	rs11539917	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79941511C>T	ENST00000306739.4	+	3	337	c.240C>T	c.(238-240)ccC>ccT	p.P80P	ASPSCR1_ENST00000581647.1_Silent_p.P80P|ASPSCR1_ENST00000306729.7_Silent_p.P80P|ASPSCR1_ENST00000580534.1_Silent_p.P3P	NM_024083.3	NP_076988.1	Q9BZE9	ASPC1_HUMAN	alveolar soft part sarcoma chromosome region, candidate 1	80					glucose homeostasis (GO:0042593)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|regulation of glucose import (GO:0046324)	cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extrinsic component of membrane (GO:0019898)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)			ASPSCR1/TFE3(167)	breast(2)|large_intestine(2)	4	all_neural(118;0.0878)|Ovarian(332;0.12)|all_lung(278;0.246)		BRCA - Breast invasive adenocarcinoma(99;0.0114)|OV - Ovarian serous cystadenocarcinoma(97;0.0191)			AGATGGTGCCCGCTTCCCGGA	0.622			T	TFE3	alveolar soft part sarcoma								C|||	63	0.0125799	0.0015	0.0231	5008	,	,		12243	0.0		0.0209	False		,,,				2504	0.0245				p.P80P		Atlas-SNP	.		Dom	yes		17	17q25	79058	"""alveolar soft part sarcoma chromosome region, candidate 1"""		M	ASPSCR1_ENST00000306729,colon,carcinoma,0,1	ASPSCR1	27	1	0			c.C240T						PASS	.	C		22,4384	29.0+/-57.7	0,22,2181	80.0	63.0	69.0		240	-8.0	0.0	17	dbSNP_120	69	162,8438	76.3+/-139.0	2,158,4140	no	coding-synonymous	ASPSCR1	NM_024083.2		2,180,6321	TT,TC,CC		1.8837,0.4993,1.4147		80/554	79941511	184,12822	2203	4300	6503	SO:0001819	synonymous_variant	79058	exon3			GGTGCCCGCTTCC	AF324219	CCDS11796.1, CCDS58611.1	17q25	2011-06-28				ENSG00000169696		"""UBX domain containing"""	13825	protein-coding gene	gene with protein product	"""UBX domain protein 9"""	606236				11244503, 10506710	Standard	NM_024083		Approved	ASPS, ASPL, UBXD9, UBXN9	uc002kcy.3	Q9BZE9		ENST00000306739.4:c.240C>T	17.37:g.79941511C>T		55.0	0.0	0		56.0	31.0	0.553571	NM_001251888	A8K3K9|Q7Z6N7|Q8WV59|Q96LS5|Q96M40	Silent	SNP	ENST00000306739.4	37	CCDS11796.1																																																																																			C|0.988;T|0.012	0.012	strong		0.622	ASPSCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441972.1	NM_024083	
DCP2	167227	hgsc.bcm.edu	37	5	112349109	112349109	+	Silent	SNP	C	C	T	rs149633478	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:112349109C>T	ENST00000389063.2	+	11	1389	c.1191C>T	c.(1189-1191)ttC>ttT	p.F397F	DCP2_ENST00000515408.1_Silent_p.F362F|DCP2_ENST00000543319.1_Silent_p.F186F	NM_152624.5	NP_689837	Q8IU60	DCP2_HUMAN	decapping mRNA 2	397					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA catabolic process (GO:0006402)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|nucleus (GO:0005634)|RISC complex (GO:0016442)	exoribonuclease activity, producing 5'-phosphomonoesters (GO:0016896)|m7G(5')pppN diphosphatase activity (GO:0050072)|manganese ion binding (GO:0030145)|RNA binding (GO:0003723)			endometrium(3)|large_intestine(6)|lung(1)	10		all_cancers(142;4.41e-05)|all_epithelial(76;3.65e-07)|Colorectal(10;0.00115)|Prostate(80;0.00133)|Ovarian(225;0.0443)		OV - Ovarian serous cystadenocarcinoma(64;6.98e-08)|Epithelial(69;7.87e-08)|all cancers(49;1.06e-05)|COAD - Colon adenocarcinoma(37;0.0123)|Colorectal(14;0.0171)		ATTGCAAGTTCCCCTTTTCAT	0.418													C|||	9	0.00179712	0.0008	0.0	5008	,	,		19749	0.0		0.001	False		,,,				2504	0.0072				p.F397F		Atlas-SNP	.											.	DCP2	34	.	0			c.C1191T						PASS	.	C	,	0,4404		0,0,2202	233.0	204.0	214.0		1086,1191	2.8	1.0	5	dbSNP_134	214	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous,coding-synonymous	DCP2	NM_001242377.1,NM_152624.5	,	0,3,6499	TT,TC,CC		0.0349,0.0,0.0231	,	362/386,397/421	112349109	3,13001	2202	4300	6502	SO:0001819	synonymous_variant	167227	exon11			CAAGTTCCCCTTT	AY135173	CCDS34210.1, CCDS56377.1	5q22	2013-05-02	2013-05-02		ENSG00000172795	ENSG00000172795	3.6.1.62	"""Nudix motif containing"""	24452	protein-coding gene	gene with protein product	"""nudix (nucleoside diphosphate linked moiety X)-type motif 20"", ""M(7)GpppN-mRNA hydrolase"""	609844	"""DCP2 decapping enzyme homolog (S. cerevisiae)"""			12218187, 12417715	Standard	NM_152624		Approved	NUDT20	uc003kqh.3	Q8IU60	OTTHUMG00000162853	ENST00000389063.2:c.1191C>T	5.37:g.112349109C>T		84.0	0.0	0		81.0	36.0	0.444444	NM_152624	C9J778|Q6P2D4|Q7Z5W5|Q8NBG5	Silent	SNP	ENST00000389063.2	37	CCDS34210.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	0	0.0	1	0.0013192612137203166	c	9.005	0.981066	0.18812	0.0	3.49E-4	ENSG00000172795	ENST00000513585	.	.	.	5.83	2.76	0.32466	.	.	.	.	.	T	0.54598	0.1868	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.43523	-0.9386	4	.	.	.	.	6.4401	0.21845	0.0:0.6123:0.1279:0.2598	.	.	.	.	S	379	.	.	P	+	1	0	DCP2	112377008	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	0.796000	0.26986	0.242000	0.21303	0.552000	0.68991	CCC	C|0.999;T|0.001	0.001	strong		0.418	DCP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370765.3	NM_152624	
KITLG	4254	hgsc.bcm.edu	37	12	88900891	88900891	+	Missense_Mutation	SNP	C	C	A	rs41283112	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:88900891C>A	ENST00000228280.5	-	7	810	c.628G>T	c.(628-630)Gac>Tac	p.D210Y	KITLG_ENST00000357116.4_5'UTR|KITLG_ENST00000347404.5_Missense_Mutation_p.D182Y|KITLG_ENST00000378535.4_5'UTR	NM_000899.4	NP_000890.1	P21583	SCF_HUMAN	KIT ligand	210			D -> Y (in dbSNP:rs41283112).		cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|ectopic germ cell programmed cell death (GO:0035234)|embryonic hemopoiesis (GO:0035162)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|male gonad development (GO:0008584)|negative regulation of mast cell apoptotic process (GO:0033026)|neural crest cell migration (GO:0001755)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of DNA replication (GO:0045740)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mast cell proliferation (GO:0070668)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of myeloid leukocyte differentiation (GO:0002763)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Ras protein signal transduction (GO:0046579)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	stem cell factor receptor binding (GO:0005173)			kidney(2)|large_intestine(3)|lung(1)|ovary(1)|prostate(1)|stomach(1)	9						AGGCTGGAGTCTCCAGGGGGA	0.418									Testicular Cancer, Familial Clustering of				C|||	20	0.00399361	0.0	0.0101	5008	,	,		14689	0.0		0.0099	False		,,,				2504	0.0031				p.D210Y		Atlas-SNP	.											.	KITLG	26	.	0			c.G628T						PASS	.	C	TYR/ASP,TYR/ASP	15,4391	24.3+/-50.5	0,15,2188	63.0	67.0	65.0		628,544	2.8	0.0	12	dbSNP_127	65	138,8462	68.7+/-131.2	0,138,4162	yes	missense,missense	KITLG	NM_000899.4,NM_003994.5	160,160	0,153,6350	AA,AC,CC		1.6047,0.3404,1.1764	probably-damaging,probably-damaging	210/274,182/246	88900891	153,12853	2203	4300	6503	SO:0001583	missense	4254	exon7	Familial Cancer Database		TGGAGTCTCCAGG	M59964	CCDS31867.1, CCDS31868.1	12q22	2010-11-23			ENSG00000049130	ENSG00000049130			6343	protein-coding gene	gene with protein product	"""mast cell growth factor"", ""stem cell factor"", ""steel factor"", ""familial progressive hyperpigmentation 2"""	184745		MGF		2208279, 1707188, 19375057	Standard	NM_003994		Approved	SCF, SF, Kitl, KL-1, FPH2	uc001tav.3	P21583	OTTHUMG00000169888	ENST00000228280.5:c.628G>T	12.37:g.88900891C>A	ENSP00000228280:p.Asp210Tyr	46.0	0.0	0		29.0	14.0	0.482759	NM_000899	A0AV09|A8K2Q4|B7ZLM4|Q16487|Q68DZ2|Q7M4N8|Q9UQK7	Missense_Mutation	SNP	ENST00000228280.5	37	CCDS31868.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	C|C	17.16|17.16	3.317419|3.317419	0.60524|0.60524	0.003404|0.003404	0.016047|0.016047	ENSG00000049130|ENSG00000049130	ENST00000378535;ENST00000228280;ENST00000347404|ENST00000537835	T;T|.	0.67523|.	-0.27;-0.27|.	5.68|5.68	2.84|2.84	0.33178|0.33178	.|.	0.350727|.	0.32819|.	N|.	0.005616|.	T|T	0.25419|0.25419	0.0618|0.0618	L|L	0.54323|0.54323	1.7|1.7	0.26217|0.26217	N|N	0.979217|0.979217	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.72982|.	0.964;0.979|.	T|T	0.34875|0.34875	-0.9811|-0.9811	10|6	0.59425|0.87932	D|D	0.04|0	-2.0558|-2.0558	3.7484|3.7484	0.08556|0.08556	0.0:0.5316:0.1938:0.2746|0.0:0.5316:0.1938:0.2746	rs41283112;rs61754238|rs41283112;rs61754238	182;210|.	P21583-2;P21583|.	.;SCF_HUMAN|.	Y|D	175;210;182|13	ENSP00000228280:D210Y;ENSP00000054216:D182Y|.	ENSP00000228280:D210Y|ENSP00000438889:E13D	D|E	-|-	1|3	0|2	KITLG|KITLG	87425022|87425022	0.712000|0.712000	0.27916|0.27916	0.041000|0.041000	0.18516|0.18516	0.359000|0.359000	0.29487|0.29487	1.040000|1.040000	0.30278|0.30278	0.735000|0.735000	0.32537|0.32537	0.655000|0.655000	0.94253|0.94253	GAC|GAG	C|0.991;A|0.009	0.009	strong		0.418	KITLG-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406424.2	NM_003994	
SLC25A22	79751	hgsc.bcm.edu	37	11	794790	794790	+	Silent	SNP	G	G	A	rs146402942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:794790G>A	ENST00000320230.5	-	3	613	c.132C>T	c.(130-132)cgC>cgT	p.R44R	SLC25A22_ENST00000531214.1_Silent_p.R44R	NM_001191061.1|NM_024698.5	NP_001177990.1|NP_078974.1	Q9H936	GHC1_HUMAN	solute carrier family 25 (mitochondrial carrier: glutamate), member 22	44					L-glutamate transport (GO:0015813)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	L-glutamate transmembrane transporter activity (GO:0005313)|symporter activity (GO:0015293)			endometrium(1)|kidney(1)|lung(2)|urinary_tract(1)	5		all_cancers(49;4.75e-06)|all_epithelial(84;0.00204)|Breast(177;0.00234)|Ovarian(85;0.0228)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;6.27e-26)|Epithelial(43;4.84e-25)|OV - Ovarian serous cystadenocarcinoma(40;2.72e-19)|BRCA - Breast invasive adenocarcinoma(625;4.23e-05)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TCGTGTACACGCGCTGGCCGT	0.667																																					p.R44R	Colon(93;848 1468 3270 23355 49636)	Atlas-SNP	.											.	SLC25A22	19	.	0			c.C132T						PASS	.	G	,,	0,4396		0,0,2198	39.0	37.0	37.0		132,132,132	2.3	1.0	11	dbSNP_134	37	13,8579		0,13,4283	no	coding-synonymous,coding-synonymous,coding-synonymous	SLC25A22	NM_001191060.1,NM_001191061.1,NM_024698.5	,,	0,13,6481	AA,AG,GG		0.1513,0.0,0.1001	,,	44/324,44/324,44/324	794790	13,12975	2198	4296	6494	SO:0001819	synonymous_variant	79751	exon3			GTACACGCGCTGG	AJ428202	CCDS7715.1	11p15.5	2013-05-22			ENSG00000177542	ENSG00000177542		"""Solute carriers"""	19954	protein-coding gene	gene with protein product		609302				11897791	Standard	NM_024698		Approved	GC1, FLJ13044, NET44, EIEE3	uc001lrj.3	Q9H936	OTTHUMG00000133310	ENST00000320230.5:c.132C>T	11.37:g.794790G>A		140.0	0.0	0		148.0	73.0	0.493243	NM_001191061	A8K366|C9J1H6|E9PJD3|E9PKB2|E9PL68|E9PN26|E9PNQ3|E9PP01|E9PR97|Q8TBU8	Silent	SNP	ENST00000320230.5	37	CCDS7715.1																																																																																			G|0.999;A|0.001	0.001	strong		0.667	SLC25A22-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257107.2		
DCAF4L1	285429	hgsc.bcm.edu	37	4	41984782	41984782	+	Missense_Mutation	SNP	G	G	A	rs369307123		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:41984782G>A	ENST00000333141.5	+	1	1070	c.973G>A	c.(973-975)Gaa>Aaa	p.E325K		NM_001029955.3	NP_001025126.2	Q3SXM0	DC4L1_HUMAN	DDB1 and CUL4 associated factor 4-like 1	325										breast(1)|endometrium(5)|kidney(6)|large_intestine(11)|lung(12)|prostate(1)|skin(1)	37						TGTGCACGAGGAAGAGGGAAT	0.562																																					p.E325K		Atlas-SNP	.											.	DCAF4L1	70	.	0			c.G973A						PASS	.	G	LYS/GLU	0,4406		0,0,2203	125.0	92.0	103.0		973	-0.3	0.7	4		103	1,8599	1.2+/-3.3	0,1,4299	no	missense	DCAF4L1	NM_001029955.3	56	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	325/397	41984782	1,13005	2203	4300	6503	SO:0001583	missense	285429	exon1			CACGAGGAAGAGG	BC035027	CCDS33978.1	4p13	2013-01-09	2009-07-17	2009-07-17		ENSG00000182308		"""WD repeat domain containing"""	27723	protein-coding gene	gene with protein product			"""WD repeat domain 21B"""	WDR21B			Standard	NM_001029955		Approved		uc003gwk.2	Q3SXM0		ENST00000333141.5:c.973G>A	4.37:g.41984782G>A	ENSP00000327796:p.Glu325Lys	156.0	0.0	0		205.0	86.0	0.419512	NM_001029955	B3KVI3|Q3ZCW8|Q499Y5|Q9UFI0	Missense_Mutation	SNP	ENST00000333141.5	37	CCDS33978.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.245448	0.59103	0.0	1.16E-4	ENSG00000182308	ENST00000333141	T	0.70045	-0.45	0.97	-0.348	0.12613	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.285662	0.40064	N	0.001186	T	0.63165	0.2488	L	0.60455	1.87	0.31255	N	0.693609	P	0.46578	0.88	P	0.50270	0.636	T	0.62388	-0.6865	10	0.34782	T	0.22	.	5.6253	0.17478	0.0:0.0:0.6821:0.3179	.	325	Q3SXM0	DC4L1_HUMAN	K	325	ENSP00000327796:E325K	ENSP00000327796:E325K	E	+	1	0	DCAF4L1	41679539	1.000000	0.71417	0.729000	0.30791	0.811000	0.45836	1.846000	0.39289	-0.124000	0.11724	0.313000	0.20887	GAA	.	.	weak		0.562	DCAF4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360958.1	NM_001029955	
PEBP4	157310	hgsc.bcm.edu	37	8	22570904	22570904	+	Silent	SNP	C	C	T	rs386723487|rs61732772	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22570904C>T	ENST00000256404.6	-	7	754	c.663G>A	c.(661-663)caG>caA	p.Q221Q	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	221						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		CTATCTCCGCCTGGTTTTTGT	0.587													C|||	55	0.0109824	0.0098	0.0072	5008	,	,		16308	0.004		0.0199	False		,,,				2504	0.0133				p.Q221Q		Atlas-SNP	.											.	PEBP4	23	.	0			c.G663A						PASS	.						71.0	78.0	76.0					8																	22570904		1953	4153	6106	SO:0001819	synonymous_variant	157310	exon7			CTCCGCCTGGTTT	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"""cousin-of-RKIP 1 protein"""	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.663G>A	8.37:g.22570904C>T		129.0	0.0	0		108.0	58.0	0.537037	NM_144962	Q5EVA1|Q8WW74	Silent	SNP	ENST00000256404.6	37	CCDS43724.1																																																																																			C|0.986;T|0.014	0.014	strong		0.587	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
ATAD3A	55210	hgsc.bcm.edu	37	1	1458150	1458150	+	Silent	SNP	T	T	C	rs1135025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1458150T>C	ENST00000378755.5	+	8	1015	c.921T>C	c.(919-921)gtT>gtC	p.V307V	ATAD3A_ENST00000378756.3_Silent_p.V259V|ATAD3A_ENST00000536055.1_Silent_p.V180V	NM_018188.3	NP_060658.3	Q9NVI7	ATD3A_HUMAN	ATPase family, AAA domain containing 3A	307					cell growth (GO:0016049)|negative regulation of apoptotic process (GO:0043066)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)			endometrium(4)|kidney(6)|large_intestine(1)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	20	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;1.12e-36)|OV - Ovarian serous cystadenocarcinoma(86;2.18e-22)|Colorectal(212;0.000164)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00233)|BRCA - Breast invasive adenocarcinoma(365;0.00469)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0347)|Lung(427;0.147)		TGCTGGCTGTTGGGGTCTACT	0.677													N|||	134	0.0267572	0.0507	0.0504	5008	,	,		14272	0.0109		0.0109	False		,,,				2504	0.0102				p.V307V		Atlas-SNP	.											.	ATAD3A	35	.	0			c.T921C						PASS	.	C	,,	39,4357	795.2+/-415.3	2,35,2161	40.0	52.0	48.0		777,540,921	-9.5	0.0	1	dbSNP_86	48	67,8533	811.9+/-407.1	0,67,4233	no	coding-synonymous,coding-synonymous,coding-synonymous	ATAD3A	NM_001170535.1,NM_001170536.1,NM_018188.3	,,	2,102,6394	CC,CT,TT		0.7791,0.8872,0.8156	,,	259/587,180/508,307/635	1458150	106,12890	2198	4300	6498	SO:0001819	synonymous_variant	55210	exon8			GGCTGTTGGGGTC	AK025865	CCDS31.1, CCDS53259.1, CCDS53260.1	1p36.33	2010-04-21		2007-02-08	ENSG00000197785	ENSG00000197785		"""ATPases / AAA-type"""	25567	protein-coding gene	gene with protein product		612316				12477932	Standard	NM_018188		Approved	FLJ10709	uc001afz.2	Q9NVI7	OTTHUMG00000000575	ENST00000378755.5:c.921T>C	1.37:g.1458150T>C		255.0	1.0	0.00392157		384.0	346.0	0.901042	NM_018188	B3KPB3|D2K8Q1|G3V1I6|Q5SV23|Q8N275|Q96A50	Silent	SNP	ENST00000378755.5	37	CCDS31.1	44	0.020146520146520148	13	0.026422764227642278	15	0.04143646408839779	7	0.012237762237762238	9	0.011873350923482849	c	2.002	-0.429111	0.04701	0.008872	0.007791	ENSG00000197785	ENST00000339113	.	.	.	4.92	-9.49	0.00587	.	.	.	.	.	T	0.18718	0.0449	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58255	-0.7668	4	.	.	.	.	10.7083	0.45969	0.0:0.127:0.3056:0.5674	rs1135025	.	.	.	R	245	.	.	W	+	1	0	ATAD3A	1448013	0.908000	0.30866	0.008000	0.14137	0.071000	0.16799	-0.105000	0.10907	-2.425000	0.00561	-0.768000	0.03414	TGG	T|0.991;C|0.009	0.009	strong		0.677	ATAD3A-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000001365.1	NM_018188	
C7orf33	202865	hgsc.bcm.edu	37	7	148288135	148288135	+	Silent	SNP	C	C	T	rs111320068	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:148288135C>T	ENST00000307003.2	+	1	479	c.118C>T	c.(118-120)Ctg>Ttg	p.L40L		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	40										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TGACCTTCGCCTGAGTGGGAG	0.552													C|||	131	0.0261581	0.0015	0.0908	5008	,	,		17766	0.001		0.0249	False		,,,				2504	0.0409				p.L40L		Atlas-SNP	.											.	C7orf33	28	.	0			c.C118T						PASS	.	C		39,4367	43.1+/-76.7	1,37,2165	91.0	76.0	81.0		118	1.9	0.0	7	dbSNP_132	81	296,8304	108.4+/-169.1	4,288,4008	no	coding-synonymous	C7orf33	NM_145304.2		5,325,6173	TT,TC,CC		3.4419,0.8852,2.5757		40/178	148288135	335,12671	2203	4300	6503	SO:0001819	synonymous_variant	202865	exon1			CTTCGCCTGAGTG	BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.118C>T	7.37:g.148288135C>T		89.0	0.0	0		116.0	57.0	0.491379	NM_145304		Silent	SNP	ENST00000307003.2	37	CCDS5890.1																																																																																			C|0.974;T|0.026	0.026	strong		0.552	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304	
MS4A6A	64231	hgsc.bcm.edu	37	11	59945789	59945789	+	Splice_Site	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:59945789A>G	ENST00000530839.1	-	5	775	c.283T>C	c.(283-285)Ttt>Ctt	p.F95L	MS4A6A_ENST00000412309.2_Splice_Site_p.F123L|MS4A6A_ENST00000529054.1_Splice_Site_p.F123L|MS4A6A_ENST00000426738.2_Splice_Site_p.F50L|MS4A6A_ENST00000420732.2_Splice_Site_p.F95L|MS4A6A_ENST00000533023.1_Intron|MS4A6A_ENST00000528851.1_Splice_Site_p.F95L|MS4A6A_ENST00000529906.1_5'UTR|MS4A6A_ENST00000323961.3_Splice_Site_p.F95L	NM_152852.2	NP_690591.1	Q9H2W1	M4A6A_HUMAN	membrane-spanning 4-domains, subfamily A, member 6A	95						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22						GAGATGATAAACTAAGATAAA	0.393																																					p.F123L		Atlas-SNP	.											.	MS4A6A	85	.	0			c.T367C						PASS	.						113.0	110.0	111.0					11																	59945789		2201	4295	6496	SO:0001630	splice_region_variant	64231	exon5			TGATAAACTAAGA	AB013104	CCDS7981.1, CCDS44615.1, CCDS44616.1, CCDS58134.1	11q12.1	2008-03-25			ENSG00000110077	ENSG00000110077			13375	protein-coding gene	gene with protein product		606548		MS4A6		11245982, 11401424	Standard	NM_152852		Approved	CD20L3	uc010rla.2	Q9H2W1	OTTHUMG00000167241	ENST00000530839.1:c.283-1T>C	11.37:g.59945789A>G		98.0	0.0	0		130.0	60.0	0.461538	NM_001247999	A8K755|F8W9K1|Q7Z4E8|Q8TBV7|Q8TEZ4|Q8TEZ5|Q96PG6|Q9H2L1|Q9H2N3|Q9H3V1|Q9HC76	Missense_Mutation	SNP	ENST00000530839.1	37	CCDS7981.1	.	.	.	.	.	.	.	.	.	.	A	19.17	3.775052	0.70107	.	.	ENSG00000110077	ENST00000323961;ENST00000528851;ENST00000420732;ENST00000530839;ENST00000529054;ENST00000426738;ENST00000412309	T;T;T;T;T;T;T	0.03242	4.0;4.0;4.0;4.0;4.0;4.0;4.0	4.73	3.6	0.41247	.	0.201048	0.42821	D	0.000645	T	0.12305	0.0299	M	0.81682	2.555	0.34555	D	0.711745	D;D;D;D;P	0.55385	0.971;0.964;0.971;0.971;0.703	P;P;P;P;B	0.57548	0.716;0.728;0.823;0.823;0.342	T	0.08351	-1.0726	10	0.66056	D	0.02	.	6.9541	0.24562	0.8964:0.0:0.1036:0.0	.	50;123;123;95;95	E7EMT7;F8W9K1;E9PSA9;Q9H2W1;Q9H2W1-3	.;.;.;M4A6A_HUMAN;.	L	95;95;95;95;123;50;123	ENSP00000315878:F95L;ENSP00000431901:F95L;ENSP00000392921:F95L;ENSP00000436979:F95L;ENSP00000435844:F123L;ENSP00000392770:F50L;ENSP00000403212:F123L	ENSP00000315878:F95L	F	-	1	0	MS4A6A	59702365	1.000000	0.71417	0.772000	0.31596	0.009000	0.06853	2.298000	0.43602	0.942000	0.37525	0.533000	0.62120	TTT	.	.	none		0.393	MS4A6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393848.1		Missense_Mutation
OR13A1	79290	hgsc.bcm.edu	37	10	45799451	45799451	+	Silent	SNP	C	C	T	rs17157674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45799451C>T	ENST00000553795.1	-	4	728	c.420G>A	c.(418-420)cgG>cgA	p.R140R	OR13A1_ENST00000536058.1_Silent_p.R140R|OR13A1_ENST00000374401.2_Silent_p.R140R	NM_001004297.2	NP_001004297.2	Q8NGR1	O13A1_HUMAN	olfactory receptor, family 13, subfamily A, member 1	140						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(1)|kidney(1)|large_intestine(5)|lung(9)|skin(2)|urinary_tract(1)	19						TGGCTGCGTACCGGTCATAGG	0.617													C|||	38	0.00758786	0.0265	0.0043	5008	,	,		19585	0.0		0.0	False		,,,				2504	0.0				p.R140R		Atlas-SNP	.											.	OR13A1	49	.	0			c.G420A						PASS	.	C		83,4323	69.2+/-107.0	1,81,2121	35.0	28.0	30.0		420	-6.5	0.1	10	dbSNP_123	30	0,8600		0,0,4300	no	coding-synonymous	OR13A1	NM_001004297.2		1,81,6421	TT,TC,CC		0.0,1.8838,0.6382		140/329	45799451	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	79290	exon4			TGCGTACCGGTCA	AB065728	CCDS31188.1	10q11.21	2012-10-03			ENSG00000256574	ENSG00000256574		"""GPCR / Class A : Olfactory receptors"""	14772	protein-coding gene	gene with protein product							Standard	NM_001004297		Approved		uc001jcc.1	Q8NGR1	OTTHUMG00000018080	ENST00000553795.1:c.420G>A	10.37:g.45799451C>T		59.0	0.0	0		81.0	37.0	0.45679	NM_001004297	Q2M3M4|Q5VV57|Q6IFH5|Q6ZMN6	Silent	SNP	ENST00000553795.1	37	CCDS31188.1																																																																																			C|0.992;T|0.008	0.008	strong		0.617	OR13A1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047779.2	NM_001004297	
PLEKHH1	57475	hgsc.bcm.edu	37	14	68022572	68022572	+	Missense_Mutation	SNP	G	G	A	rs200379117		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68022572G>A	ENST00000329153.5	+	3	289	c.157G>A	c.(157-159)Gca>Aca	p.A53T		NM_020715.2	NP_065766.1	Q9ULM0	PKHH1_HUMAN	pleckstrin homology domain containing, family H (with MyTH4 domain) member 1	53						cytoskeleton (GO:0005856)				endometrium(2)|kidney(4)|lung(12)|urinary_tract(1)	19				all cancers(60;0.000771)|OV - Ovarian serous cystadenocarcinoma(108;0.00502)|BRCA - Breast invasive adenocarcinoma(234;0.011)		GCTGCTGGAGGCAGAGCAGAG	0.607																																					p.A53T		Atlas-SNP	.											.	PLEKHH1	118	.	0			c.G157A						PASS	.						35.0	41.0	39.0					14																	68022572		2129	4263	6392	SO:0001583	missense	57475	exon3			CTGGAGGCAGAGC	AB033026	CCDS45128.1	14q24.1	2013-01-10				ENSG00000054690		"""Pleckstrin homology (PH) domain containing"""	17733	protein-coding gene	gene with protein product						10574462	Standard	NM_020715		Approved	KIAA1200	uc001xjl.1	Q9ULM0		ENST00000329153.5:c.157G>A	14.37:g.68022572G>A	ENSP00000330278:p.Ala53Thr	256.0	1.0	0.00390625		263.0	120.0	0.456274	NM_020715	A6H8X6|Q6PJL4|Q6ZWC7	Missense_Mutation	SNP	ENST00000329153.5	37	CCDS45128.1	.	.	.	.	.	.	.	.	.	.	G	31	5.099177	0.94197	.	.	ENSG00000054690	ENST00000329153	T	0.39229	1.09	4.44	4.44	0.53790	.	0.000000	0.85682	D	0.000000	T	0.64427	0.2597	M	0.78049	2.395	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.67237	-0.5721	10	0.52906	T	0.07	.	14.4383	0.67298	0.0:0.0:1.0:0.0	.	53	Q9ULM0	PKHH1_HUMAN	T	53	ENSP00000330278:A53T	ENSP00000330278:A53T	A	+	1	0	PLEKHH1	67092325	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	5.665000	0.68052	2.476000	0.83614	0.655000	0.94253	GCA	.	.	weak		0.607	PLEKHH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412730.3	XM_031054	
ZSCAN1	284312	hgsc.bcm.edu	37	19	58549395	58549395	+	Missense_Mutation	SNP	G	G	A	rs369859464		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58549395G>A	ENST00000282326.1	+	3	438	c.191G>A	c.(190-192)cGc>cAc	p.R64H	ZSCAN1_ENST00000601162.1_Missense_Mutation_p.R64H|ZSCAN1_ENST00000391700.1_Missense_Mutation_p.R64H	NM_182572.3	NP_872378.3	Q8NBB4	ZSCA1_HUMAN	zinc finger and SCAN domain containing 1	64	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	48		Colorectal(82;5.46e-05)|all_neural(62;0.0182)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0152)		ACGCTGTGCCGCCAGTGGCTG	0.706																																					p.R64H		Atlas-SNP	.											.	ZSCAN1	102	.	0			c.G191A						PASS	.	G	HIS/ARG	0,4342		0,0,2171	15.0	15.0	15.0		191	-0.6	0.4	19		15	1,8511		0,1,4255	no	missense	ZSCAN1	NM_182572.3	29	0,1,6426	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging	64/409	58549395	1,12853	2171	4256	6427	SO:0001583	missense	284312	exon3			TGTGCCGCCAGTG	AK091098	CCDS12969.1	19q13.43	2013-06-13	2004-04-21		ENSG00000152467	ENSG00000152467		"""-"", ""Zinc fingers, C2H2-type"""	23712	protein-coding gene	gene with protein product			"""zinc finger with SCAN domain 1"""			12477932	Standard	NM_182572		Approved	FLJ33779, ZNF915	uc002qrc.1	Q8NBB4	OTTHUMG00000183381	ENST00000282326.1:c.191G>A	19.37:g.58549395G>A	ENSP00000282326:p.Arg64His	12.0	0.0	0		24.0	12.0	0.5	NM_182572	Q3B798|Q6WLH8|Q86WS8	Missense_Mutation	SNP	ENST00000282326.1	37	CCDS12969.1	.	.	.	.	.	.	.	.	.	.	G	11.77	1.737403	0.30774	0.0	1.17E-4	ENSG00000152467	ENST00000391700;ENST00000282326	T;T	0.05786	3.39;3.39	2.09	-0.628	0.11537	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	.	.	.	.	T	0.03348	0.0097	N	0.25245	0.725	0.23126	N	0.998253	P;P	0.41102	0.738;0.584	B;B	0.36134	0.218;0.054	T	0.39187	-0.9626	9	0.35671	T	0.21	.	2.1585	0.03819	0.2018:0.0:0.4923:0.3059	.	64;64	Q8NBB4;Q8NBB4-2	ZSCA1_HUMAN;.	H	64	ENSP00000375581:R64H;ENSP00000282326:R64H	ENSP00000282326:R64H	R	+	2	0	ZSCAN1	63241207	0.000000	0.05858	0.395000	0.26283	0.143000	0.21401	0.248000	0.18198	0.216000	0.20781	0.407000	0.27541	CGC	.	.	weak		0.706	ZSCAN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466427.1	NM_182572	
MICALCL	84953	hgsc.bcm.edu	37	11	12313845	12313845	+	Splice_Site	SNP	G	G	A	rs200949393		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12313845G>A	ENST00000256186.2	+	2	420		c.e2+1			NM_032867.2	NP_116256.2	Q6ZW33	MICLK_HUMAN	MICAL C-terminal like						cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)	mitogen-activated protein kinase binding (GO:0051019)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(5)|lung(5)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)	30				Epithelial(150;0.00177)		CCCGCCTCAGGTGAGTGTCCC	0.527																																					.		Atlas-SNP	.											.	MICALCL	59	.	0			c.129+1G>A						PASS	.	G		2,3888		0,2,1943	107.0	106.0	106.0			5.4	1.0	11		106	1,8273		0,1,4136	yes	splice-5	MICALCL	NM_032867.2		0,3,6079	AA,AG,GG		0.0121,0.0514,0.0247			12313845	3,12161	1945	4137	6082	SO:0001630	splice_region_variant	84953	exon2			CCTCAGGTGAGTG	BK000463	CCDS41620.1	11p15.3	2005-11-01			ENSG00000133808	ENSG00000133808			25933	protein-coding gene	gene with protein product		612355				12110185	Standard	NM_032867		Approved	FLJ14966	uc001mkg.1	Q6ZW33	OTTHUMG00000165777	ENST00000256186.2:c.129+1G>A	11.37:g.12313845G>A		87.0	0.0	0		100.0	52.0	0.52	NM_032867	Q7RTP7|Q96JU6	Splice_Site	SNP	ENST00000256186.2	37	CCDS41620.1	.	.	.	.	.	.	.	.	.	.	G	13.36	2.212670	0.39102	5.14E-4	1.21E-4	ENSG00000133808	ENST00000256186	.	.	.	5.39	5.39	0.77823	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.0104	0.71545	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	MICALCL	12270421	1.000000	0.71417	1.000000	0.80357	0.329000	0.28539	4.368000	0.59505	2.671000	0.90904	0.591000	0.81541	.	.	.	weak		0.527	MICALCL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386164.1	NM_032867	Intron
GRIN2D	2906	hgsc.bcm.edu	37	19	48908452	48908452	+	Silent	SNP	G	G	A	rs369747884		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48908452G>A	ENST00000263269.3	+	3	1015	c.927G>A	c.(925-927)tcG>tcA	p.S309S		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	309					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CAGTGCGCTCGGCTGGCTGGC	0.716													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14132	0.0		0.0	False		,,,				2504	0.0				p.S309S		Atlas-SNP	.											.	GRIN2D	76	.	0			c.G927A						PASS	.	G		0,4306		0,0,2153	10.0	13.0	12.0		927	-8.9	0.8	19		12	2,8414		0,2,4206	no	coding-synonymous	GRIN2D	NM_000836.2		0,2,6359	AA,AG,GG		0.0238,0.0,0.0157		309/1337	48908452	2,12720	2153	4208	6361	SO:0001819	synonymous_variant	2906	exon3			GCGCTCGGCTGGC	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.927G>A	19.37:g.48908452G>A		8.0	0.0	0		21.0	13.0	0.619048	NM_000836		Silent	SNP	ENST00000263269.3	37	CCDS12719.1																																																																																			.	.	weak		0.716	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
RPRD2	23248	hgsc.bcm.edu	37	1	150445058	150445058	+	Missense_Mutation	SNP	C	C	T	rs201108869		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:150445058C>T	ENST00000369068.4	+	11	3638	c.3634C>T	c.(3634-3636)Cca>Tca	p.P1212S	RPRD2_ENST00000401000.4_Missense_Mutation_p.P1186S|RPRD2_ENST00000492220.1_3'UTR	NM_015203.3	NP_056018.2	Q5VT52	RPRD2_HUMAN	regulation of nuclear pre-mRNA domain containing 2	1212	Pro-rich.					DNA-directed RNA polymerase II, holoenzyme (GO:0016591)				central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(4)|lung(20)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	37						GCCAGTGGGGCCATCATCTGC	0.537																																					p.P1212S		Atlas-SNP	.											.	RPRD2	189	.	0			c.C3634T						PASS	.	C	SER/PRO	0,3984		0,0,1992	84.0	87.0	86.0		3634	4.6	1.0	1		86	2,8300		0,2,4149	yes	missense	RPRD2	NM_015203.3	74	0,2,6141	TT,TC,CC		0.0241,0.0,0.0163	probably-damaging	1212/1462	150445058	2,12284	1992	4151	6143	SO:0001583	missense	23248	exon11			GTGGGGCCATCAT	BX641025	CCDS44216.1, CCDS72907.1	1q21.2	2012-02-09	2008-08-15	2008-07-28	ENSG00000163125	ENSG00000163125			29039	protein-coding gene	gene with protein product		614695	"""KIAA0460"""	KIAA0460		22231121	Standard	XM_005245033		Approved	FLJ32145, HSPC099	uc009wlr.3	Q5VT52	OTTHUMG00000012808	ENST00000369068.4:c.3634C>T	1.37:g.150445058C>T	ENSP00000358064:p.Pro1212Ser	127.0	0.0	0		132.0	76.0	0.575758	NM_015203	A8K6N8|B3KPT1|B4E2Q6|O75048|Q5VT51|Q5VT53|Q6MZL4|Q86XD2|Q9P0D7	Missense_Mutation	SNP	ENST00000369068.4	37	CCDS44216.1	.	.	.	.	.	.	.	.	.	.	C	15.88	2.965007	0.53507	0.0	2.41E-4	ENSG00000163125	ENST00000401000;ENST00000369068	T;T	0.61510	0.1;0.12	4.59	4.59	0.56863	.	0.161530	0.43416	D	0.000574	T	0.57548	0.2061	N	0.24115	0.695	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.992;0.996	T	0.65537	-0.6144	10	0.72032	D	0.01	-7.9501	17.1925	0.86883	0.0:1.0:0.0:0.0	.	1212;1186	Q5VT52;Q5VT52-3	RPRD2_HUMAN;.	S	1186;1212	ENSP00000383785:P1186S;ENSP00000358064:P1212S	ENSP00000358064:P1212S	P	+	1	0	RPRD2	148711682	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.389000	0.52516	2.363000	0.80096	0.563000	0.77884	CCA	.	.	weak		0.537	RPRD2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000035844.1	NM_015203	
BTG1	694	hgsc.bcm.edu	37	12	92539246	92539246	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:92539246G>A	ENST00000256015.3	-	1	427	c.66C>T	c.(64-66)atC>atT	p.I22I	C12orf79_ENST00000546975.1_5'Flank|C12orf79_ENST00000549802.1_5'Flank|C12orf79_ENST00000551563.2_5'Flank|RP11-796E2.4_ENST00000499685.2_RNA|RP11-796E2.4_ENST00000501008.2_RNA	NM_001731.2	NP_001722.1	P62324	BTG1_HUMAN	B-cell translocation gene 1, anti-proliferative	22					cell migration (GO:0016477)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|positive regulation of angiogenesis (GO:0045766)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of fibroblast apoptotic process (GO:2000271)|positive regulation of myoblast differentiation (GO:0045663)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|transcription cofactor activity (GO:0003712)			haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(1)|lung(2)	16		Acute lymphoblastic leukemia(6;3.02e-13)|all_hematologic(6;4.32e-09)				GAAACTTGGAGATGAAGGACA	0.701			T	MYC	BCLL																																p.I22I		Atlas-SNP	.		Dom	yes		12	12q22	694	"""B-cell translocation gene 1, anti-proliferative"""		L	.	BTG1	30	.	0			c.C66T						PASS	.						44.0	48.0	47.0					12																	92539246		2203	4300	6503	SO:0001819	synonymous_variant	694	exon1			CTTGGAGATGAAG		CCDS9043.1	12q21.33	2012-10-02			ENSG00000133639	ENSG00000133639			1130	protein-coding gene	gene with protein product		109580				15033446	Standard	NM_001731		Approved		uc001tby.3	P62324	OTTHUMG00000170092	ENST00000256015.3:c.66C>T	12.37:g.92539246G>A		110.0	0.0	0		164.0	8.0	0.0487805	NM_001731	P31607	Silent	SNP	ENST00000256015.3	37	CCDS9043.1																																																																																			.	.	none		0.701	BTG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407227.1		
HIST1H4B	8366	hgsc.bcm.edu	37	6	26027286	26027286	+	Silent	SNP	G	G	A	rs115249469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26027286G>A	ENST00000377364.3	-	1	194	c.195C>T	c.(193-195)aaC>aaT	p.N65N		NM_003544.2	NP_003535.1	P62805	H4_HUMAN	histone cluster 1, H4b	65					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			large_intestine(4)|lung(6)|ovary(2)|upper_aerodigestive_tract(1)	13						CCCGGATCACGTTCTCCAGAA	0.567											OREG0017238	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	13	0.00259585	0.0008	0.0	5008	,	,		14349	0.0		0.005	False		,,,				2504	0.0072				p.N65N		Atlas-SNP	.											.	HIST1H4B	27	.	0			c.C195T						PASS	.	G		5,4401	9.9+/-24.2	0,5,2198	103.0	87.0	92.0		195	0.9	1.0	6	dbSNP_132	92	31,8569	21.6+/-65.8	0,31,4269	no	coding-synonymous	HIST1H4B	NM_003544.2		0,36,6467	AA,AG,GG		0.3605,0.1135,0.2768		65/104	26027286	36,12970	2203	4300	6503	SO:0001819	synonymous_variant	8366	exon1			GATCACGTTCTCC	X67081	CCDS4572.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000124529	ENSG00000278705		"""Histones / Replication-dependent"""	4789	protein-coding gene	gene with protein product		602829	"""H4 histone family, member I"", ""histone 1, H4b"""	H4FI		9119399, 12408966	Standard	NM_003544		Approved	H4/I	uc003nfr.3	P62805	OTTHUMG00000014417	ENST00000377364.3:c.195C>T	6.37:g.26027286G>A		87.0	0.0	0	783	116.0	66.0	0.568965	NM_003544	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Silent	SNP	ENST00000377364.3	37	CCDS4572.1																																																																																			G|0.998;A|0.002	0.002	strong		0.567	HIST1H4B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040079.2	NM_003544	
RBMX	27316	hgsc.bcm.edu	37	X	135961560	135961560	+	Missense_Mutation	SNP	C	C	G	rs80321628		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:135961560C>G	ENST00000320676.7	-	2	181	c.27G>C	c.(25-27)aaG>aaC	p.K9N	RBMX_ENST00000565438.1_Intron|RBMX_ENST00000570135.1_5'UTR|RBMX_ENST00000562646.1_Missense_Mutation_p.K9N|SNORD61_ENST00000384252.1_RNA|RBMX_ENST00000431446.3_Missense_Mutation_p.K9N	NM_002139.3	NP_002130.2	P38159	RBMX_HUMAN	RNA binding motif protein, X-linked	9	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				cellular response to interleukin-1 (GO:0071347)|gene expression (GO:0010467)|membrane protein ectodomain proteolysis (GO:0006509)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of mRNA splicing, via spliceosome (GO:0048025)|osteoblast differentiation (GO:0001649)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homooligomerization (GO:0051260)|regulation of alternative mRNA splicing, via spliceosome (GO:0000381)|RNA splicing (GO:0008380)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|supraspliceosomal complex (GO:0044530)	chromatin binding (GO:0003682)|core promoter binding (GO:0001047)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)	p.K9N(1)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|large_intestine(2)|lung(12)|ovary(2)|pancreas(1)|prostate(2)|urinary_tract(1)	33	Acute lymphoblastic leukemia(192;0.000127)					CAATGAAGAGCTTTCCTGGGC	0.413																																					p.K9N		Atlas-SNP	.											.	RBMX	149	.	1	Substitution - Missense(1)	pancreas(1)	c.G27C						PASS	.						109.0	103.0	105.0					X																	135961560		2203	4300	6503	SO:0001583	missense	27316	exon2			GAAGAGCTTTCCT		CCDS14661.1, CCDS55510.1	Xq26	2013-05-23	2003-09-12		ENSG00000147274	ENSG00000147274		"""RNA binding motif (RRM) containing"""	9910	protein-coding gene	gene with protein product	"""heterogeneous nuclear ribonucleoprotein G"""	300199	"""RNA binding motif protein, X chromosome"""			10391206, 10391207	Standard	NM_002139		Approved	RNMX, hnRNP-G, HNRNPG	uc004fae.2	P38159	OTTHUMG00000022517	ENST00000320676.7:c.27G>C	X.37:g.135961560C>G	ENSP00000359645:p.Lys9Asn	123.0	0.0	0		158.0	35.0	0.221519	NM_001164803	B4E3U4|D3DWH0|E9PG86|Q5JQ67|Q8N8Y7|Q969R3	Missense_Mutation	SNP	ENST00000320676.7	37	CCDS14661.1	.	.	.	.	.	.	.	.	.	.	.	19.30	3.801463	0.70682	.	.	ENSG00000147274	ENST00000431446;ENST00000320676;ENST00000449161	D;D	0.89050	-2.46;-2.46	4.66	3.78	0.43462	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (2);	0.000000	0.85682	U	0.000000	D	0.88507	0.6455	L	0.56340	1.77	0.09310	P	0.9999999999999992	P;B;P	0.46656	0.882;0.278;0.868	P;B;B	0.50270	0.636;0.142;0.311	D	0.91729	0.5395	9	0.72032	D	0.01	.	8.8627	0.35267	0.0:0.7507:0.0:0.2493	.	9;9;9	B4E3U4;P38159;Q8N8Y7	.;HNRPG_HUMAN;.	N	9	ENSP00000411989:K9N;ENSP00000359645:K9N	ENSP00000359645:K9N	K	-	3	2	RBMX	135789226	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	0.970000	0.29383	1.905000	0.55150	0.508000	0.49915	AAG	.	.	weak		0.413	RBMX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058507.1	NM_002139	
NXPE3	91775	hgsc.bcm.edu	37	3	101540552	101540552	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:101540552G>T	ENST00000491511.2	+	8	2390	c.1434G>T	c.(1432-1434)gtG>gtT	p.V478V	NXPE3_ENST00000273347.5_Silent_p.V478V|NXPE3_ENST00000477909.1_Silent_p.V478V|NXPE3_ENST00000422132.1_Silent_p.V478V|RP11-49I4.3_ENST00000490324.2_RNA	NM_001134456.1	NP_001127928.1	Q969Y0	NXPE3_HUMAN	neurexophilin and PC-esterase domain family, member 3	478						extracellular region (GO:0005576)											CAAAGACCGTGGTGGTCATCC	0.582																																					p.V478V		Atlas-SNP	.											.	.	.	.	0			c.G1434T						PASS	.						96.0	98.0	97.0					3																	101540552		2203	4300	6503	SO:0001819	synonymous_variant	91775	exon8			GACCGTGGTGGTC	AK054664	CCDS2945.1	3q12.3	2012-06-14	2012-06-11	2012-06-11	ENSG00000144815	ENSG00000144815			28238	protein-coding gene	gene with protein product			"""family with sequence similarity 55, member C"""	FAM55C		12975309	Standard	NM_001134456		Approved	MGC15606	uc003dvn.3	Q969Y0	OTTHUMG00000159179	ENST00000491511.2:c.1434G>T	3.37:g.101540552G>T		139.0	0.0	0		124.0	63.0	0.508065	NM_145037	A8K0X4|D3DN53|Q7Z2S8	Silent	SNP	ENST00000491511.2	37	CCDS2945.1																																																																																			.	.	none		0.582	NXPE3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353711.2	NM_145037	
MSX1	4487	hgsc.bcm.edu	37	4	4864582	4864582	+	Silent	SNP	G	G	T	rs369820958		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:4864582G>T	ENST00000382723.4	+	2	858	c.624G>T	c.(622-624)tcG>tcT	p.S208S	MSX1_ENST00000468421.1_3'UTR	NM_002448.3	NP_002439.2	P28360	MSX1_HUMAN	msh homeobox 1	208					activation of meiosis (GO:0090427)|anterior/posterior pattern specification (GO:0009952)|BMP signaling pathway involved in heart development (GO:0061312)|bone morphogenesis (GO:0060349)|cartilage morphogenesis (GO:0060536)|cell morphogenesis (GO:0000902)|cellular response to nicotine (GO:0071316)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic nail plate morphogenesis (GO:0035880)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|face morphogenesis (GO:0060325)|in utero embryonic development (GO:0001701)|mammary gland epithelium development (GO:0061180)|mesenchymal cell proliferation (GO:0010463)|midbrain development (GO:0030901)|middle ear morphogenesis (GO:0042474)|muscle organ development (GO:0007517)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of striated muscle cell differentiation (GO:0051154)|negative regulation of transcription regulatory region DNA binding (GO:2000678)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|pituitary gland development (GO:0021983)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator (GO:1902255)|positive regulation of mesenchymal cell apoptotic process (GO:2001055)|protein localization to nucleus (GO:0034504)|protein stabilization (GO:0050821)|regulation of odontogenesis (GO:0042481)|signal transduction involved in regulation of gene expression (GO:0023019)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity (GO:0000982)|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 negative regulation of transcription (GO:0001227)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			endometrium(3)|lung(5)|ovary(1)|prostate(1)|urinary_tract(1)	11				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)		TCTCCAGCTCGCTCAGCCTCA	0.632																																					p.S208S		Atlas-SNP	.											MSX1,NS,carcinoma,+1,1	MSX1	19	1	0			c.G624T						PASS	.	G		0,4406		0,0,2203	40.0	42.0	41.0		624	0.7	1.0	4		41	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MSX1	NM_002448.3		0,1,6502	TT,TG,GG		0.0116,0.0,0.0077		208/304	4864582	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4487	exon2			CAGCTCGCTCAGC	M97676	CCDS3378.2	4p16.2	2011-06-20	2006-11-21		ENSG00000163132	ENSG00000163132		"""Homeoboxes / ANTP class : NKL subclass"""	7391	protein-coding gene	gene with protein product		142983	"""msh (Drosophila) homeo box homolog 1 (formerly homeo box 7)"", ""msh homeobox homolog 1 (Drosophila)"""	HOX7		1685479, 1973146	Standard	NM_002448		Approved	HYD1, OFC5	uc003gif.3	P28360	OTTHUMG00000090335	ENST00000382723.4:c.624G>T	4.37:g.4864582G>T		100.0	0.0	0		119.0	70.0	0.588235	NM_002448	A0SZU5|A8K3M1|Q96NY4	Silent	SNP	ENST00000382723.4	37	CCDS3378.2																																																																																			.	.	weak		0.632	MSX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206700.3		
CFAP46	54777	hgsc.bcm.edu	37	10	134691496	134691496	+	Missense_Mutation	SNP	A	A	C	rs187274296		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691496A>C	ENST00000368586.5	-	30	4201	c.4101T>G	c.(4099-4101)aaT>aaG	p.N1367K	TTC40_ENST00000368582.2_Missense_Mutation_p.N1367K	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						tactcctctcattctccttct	0.448																																					p.N1367K		Atlas-SNP	.											.	TTC40	100	.	0			c.T4101G						PASS	.																																			SO:0001583	missense	54777	exon30			CCTCTCATTCTCC																												ENST00000368586.5:c.4101T>G	10.37:g.134691496A>C	ENSP00000357575:p.Asn1367Lys	265.0	0.0	0		231.0	28.0	0.121212	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	16	0.007326007326007326	0	0.0	5	0.013812154696132596	2	0.0034965034965034965	9	0.011873350923482849	A	0.010	-1.767717	0.00645	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.04758	3.56;3.56	1.72	-2.27	0.06846	.	.	.	.	.	T	0.00998	0.0033	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.44513	-0.9323	6	0.02654	T	1	.	2.8375	0.05519	0.237:0.4507:0.0:0.3123	.	.	.	.	K	1367	ENSP00000357575:N1367K;ENSP00000357571:N1367K	ENSP00000357571:N1367K	N	-	3	2	C10orf93	134541486	0.031000	0.19500	0.096000	0.21009	0.260000	0.26232	0.118000	0.15605	-0.489000	0.06716	0.102000	0.15555	AAT	A|0.993;C|0.007	0.007	strong		0.448	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
GSTA3	2940	hgsc.bcm.edu	37	6	52767193	52767193	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:52767193T>C	ENST00000211122.3	-	4	288	c.223A>G	c.(223-225)Att>Gtt	p.I75V	GSTA3_ENST00000370968.1_Missense_Mutation_p.I25V	NM_000847.4	NP_000838.3	Q16772	GSTA3_HUMAN	glutathione S-transferase alpha 3	75	GST N-terminal.				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)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)			cervix(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(2)	10	Lung NSC(77;0.0912)				Glutathione(DB00143)	TTGCTGGCAATGTAGTTGAGA	0.423																																					p.I75V		Atlas-SNP	.											.	GSTA3	21	.	0			c.A223G						PASS	.						199.0	193.0	195.0					6																	52767193		2203	4300	6503	SO:0001583	missense	2940	exon4			TGGCAATGTAGTT	AF020919	CCDS4947.1	6p12.2	2012-06-21	2008-11-26		ENSG00000174156	ENSG00000174156	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4628	protein-coding gene	gene with protein product		605449	"""glutathione S-transferase A3"""			8307579, 9480897	Standard	NM_000847		Approved		uc003pbb.3	Q16772	OTTHUMG00000014865	ENST00000211122.3:c.223A>G	6.37:g.52767193T>C	ENSP00000211122:p.Ile75Val	148.0	0.0	0		202.0	84.0	0.415842	NM_000847	O43468|Q068V6|Q8WWA8|Q9H415	Missense_Mutation	SNP	ENST00000211122.3	37	CCDS4947.1	.	.	.	.	.	.	.	.	.	.	T	12.40	1.925899	0.34002	.	.	ENSG00000174156	ENST00000370968;ENST00000211122;ENST00000431899	T;T;T	0.15487	2.42;2.42;2.42	4.16	1.75	0.24633	Glutathione S-transferase, N-terminal (2);Thioredoxin-like fold (2);	0.055329	0.64402	D	0.000001	T	0.05868	0.0153	L	0.43646	1.37	0.36011	D	0.838043	B	0.18461	0.028	B	0.24006	0.05	T	0.11891	-1.0569	10	0.46703	T	0.11	.	8.092	0.30805	0.0:0.1721:0.0:0.8279	.	75	Q16772	GSTA3_HUMAN	V	25;75;25	ENSP00000360007:I25V;ENSP00000211122:I75V;ENSP00000399142:I25V	ENSP00000211122:I75V	I	-	1	0	GSTA3	52875152	1.000000	0.71417	0.949000	0.38748	0.738000	0.42128	2.245000	0.43133	0.263000	0.21812	0.533000	0.62120	ATT	.	.	none		0.423	GSTA3-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040933.1		
SNAPC3	6619	hgsc.bcm.edu	37	9	15459821	15459821	+	Missense_Mutation	SNP	A	A	C	rs3087653	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:15459821A>C	ENST00000380821.3	+	9	1369	c.1193A>C	c.(1192-1194)gAa>gCa	p.E398A		NM_001039697.1	NP_001034786.1	Q92966	SNPC3_HUMAN	small nuclear RNA activating complex, polypeptide 3, 50kDa	398			E -> A (in dbSNP:rs3087653).		gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|snRNA transcription (GO:0009301)|transcription from RNA polymerase II promoter (GO:0006366)|transcription from RNA polymerase III promoter (GO:0006383)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(6)|lung(2)	12				GBM - Glioblastoma multiforme(50;2.15e-06)		AAACTGGGGGAATTCCTTGCT	0.413													A|||	193	0.0385383	0.0416	0.0231	5008	,	,		16799	0.0		0.0596	False		,,,				2504	0.0634				p.E398A		Atlas-SNP	.											.	SNAPC3	28	.	0			c.A1193C						PASS	.	A	ALA/GLU	145,4261	101.2+/-139.8	0,145,2058	134.0	122.0	126.0		1193	5.9	1.0	9	dbSNP_102	126	425,8175	131.8+/-189.6	13,399,3888	yes	missense	SNAPC3	NM_001039697.1	107	13,544,5946	CC,CA,AA		4.9419,3.291,4.3826	probably-damaging	398/412	15459821	570,12436	2203	4300	6503	SO:0001583	missense	6619	exon9			TGGGGGAATTCCT	U71300	CCDS6478.1	9p22.3	2008-07-21	2002-08-29		ENSG00000164975	ENSG00000164975			11136	protein-coding gene	gene with protein product		602348	"""small nuclear RNA activating complex, polypeptide 3, 50kD"""			9003788	Standard	XR_428427		Approved	SNAP50, PTFbeta, MGC33124, MGC132011	uc003zlt.3	Q92966	OTTHUMG00000019583	ENST00000380821.3:c.1193A>C	9.37:g.15459821A>C	ENSP00000370200:p.Glu398Ala	95.0	0.0	0		134.0	72.0	0.537313	NM_001039697	D3DRI8|Q2VPI6|Q5T285	Missense_Mutation	SNP	ENST00000380821.3	37	CCDS6478.1	78	0.03571428571428571	26	0.052845528455284556	11	0.03038674033149171	0	0.0	41	0.05408970976253298	A	31	5.081553	0.94050	0.03291	0.049419	ENSG00000164975	ENST00000380821	T	0.44083	0.93	5.86	5.86	0.93980	.	0.138414	0.64402	D	0.000005	T	0.17450	0.0419	M	0.65498	2.005	0.80722	D	1	D	0.57571	0.98	P	0.53224	0.721	T	0.31447	-0.9943	10	0.56958	D	0.05	-42.6534	16.5602	0.84551	1.0:0.0:0.0:0.0	rs3087653;rs3198208;rs52828246;rs3087653	398	Q92966	SNPC3_HUMAN	A	398	ENSP00000370200:E398A	ENSP00000370200:E398A	E	+	2	0	SNAPC3	15449821	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.283000	0.78640	2.367000	0.80283	0.528000	0.53228	GAA	A|0.956;C|0.044	0.044	strong		0.413	SNAPC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051763.2	NM_001039697	
MED17	9440	hgsc.bcm.edu	37	11	93529674	93529674	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:93529674C>T	ENST00000251871.3	+	7	1398	c.1111C>T	c.(1111-1113)Cta>Tta	p.L371L	snoU13_ENST00000459243.1_RNA|MED17_ENST00000533367.1_3'UTR	NM_004268.4	NP_004259.3	Q9NVC6	MED17_HUMAN	mediator complex subunit 17	371			L -> P (in MCPHSBA). {ECO:0000269|PubMed:20950787}.		androgen receptor signaling pathway (GO:0030521)|gene expression (GO:0010467)|intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|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)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|receptor activity (GO:0004872)|RNA polymerase II transcription cofactor activity (GO:0001104)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|vitamin D receptor binding (GO:0042809)			large_intestine(2)|lung(11)|ovary(1)	14		Acute lymphoblastic leukemia(157;2.31e-05)|all_hematologic(158;0.00824)				CCTTTATGTCCTAGAGCATAA	0.403																																					p.L371L		Atlas-SNP	.											.	MED17	37	.	0			c.C1111T						PASS	.						157.0	151.0	153.0					11																	93529674		2201	4298	6499	SO:0001819	synonymous_variant	9440	exon7			TATGTCCTAGAGC	AF104254	CCDS8295.1	11q21	2007-07-30	2007-07-30	2007-07-30	ENSG00000042429	ENSG00000042429			2375	protein-coding gene	gene with protein product		603810	"""cofactor required for Sp1 transcriptional activation, subunit 6 (77kD)"", ""cofactor required for Sp1 transcriptional activation, subunit 6, 77kDa"""	CRSP6		9989412, 10198638	Standard	NM_004268		Approved	CRSP77, TRAP80, DRIP80	uc001pem.4	Q9NVC6	OTTHUMG00000167497	ENST00000251871.3:c.1111C>T	11.37:g.93529674C>T		55.0	0.0	0		83.0	4.0	0.0481928	NM_004268	B3KN07|Q9HA81|Q9UNP7|Q9Y2W0|Q9Y660	Silent	SNP	ENST00000251871.3	37	CCDS8295.1																																																																																			.	.	none		0.403	MED17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394800.2	NM_004268	
FAM66D	100132923	hgsc.bcm.edu	37	8	11990882	11990882	+	RNA	SNP	C	C	T	rs9720235	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:11990882C>T	ENST00000434078.2	+	0	608					NR_027425.1				family with sequence similarity 66, member D																		GTGTCTGAAACGCCGTGGCAG	0.498													t|||	2043	0.407947	0.2897	0.5187	5008	,	,		24947	0.4077		0.4513	False		,,,				2504	0.4448				p.V213I		Atlas-SNP	.											.	.	.	.	0			c.G637A						PASS	.																																					392197	exon1			CTGAAACGCCGTG			8p23.1	2013-07-05			ENSG00000255052	ENSG00000255052		"""Long non-coding RNAs"""	24159	non-coding RNA	RNA, long non-coding							Standard	NR_027425		Approved				OTTHUMG00000165269		8.37:g.11990882C>T		5.0	0.0	0		6.0	6.0	1	NM_001256869		Missense_Mutation	SNP	ENST00000434078.2	37																																																																																				C|0.499;T|0.501	0.501	strong		0.498	FAM66D-201	KNOWN	basic	antisense	antisense		NR_027425	
FBXW8	26259	hgsc.bcm.edu	37	12	117402583	117402583	+	Missense_Mutation	SNP	G	G	C	rs141777878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117402583G>C	ENST00000309909.5	+	5	841	c.759G>C	c.(757-759)gaG>gaC	p.E253D	FBXW8_ENST00000455858.2_Missense_Mutation_p.E187D			Q8N3Y1	FBXW8_HUMAN	F-box and WD repeat domain containing 8	253					cell proliferation (GO:0008283)|Golgi organization (GO:0007030)|labyrinthine layer blood vessel development (GO:0060716)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|spongiotrophoblast layer development (GO:0060712)	Cul7-RING ubiquitin ligase complex (GO:0031467)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|SCF ubiquitin ligase complex (GO:0019005)				endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|pancreas(1)|skin(1)|stomach(1)	22	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0353)		AGGACGAGGAGGATGAGCCTG	0.532													G|||	4	0.000798722	0.0015	0.0014	5008	,	,		18740	0.0		0.0	False		,,,				2504	0.001				p.E253D		Atlas-SNP	.											.	FBXW8	53	.	0			c.G759C						PASS	.	G	ASP/GLU,ASP/GLU	4,4402	8.1+/-20.4	0,4,2199	183.0	159.0	167.0		561,759	4.3	1.0	12	dbSNP_134	167	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	FBXW8	NM_012174.1,NM_153348.2	45,45	0,9,6494	CC,CG,GG		0.0581,0.0908,0.0692	possibly-damaging,possibly-damaging	187/533,253/599	117402583	9,12997	2203	4300	6503	SO:0001583	missense	26259	exon5			CGAGGAGGATGAG	AF176707	CCDS9182.1, CCDS44988.1	12q24.23	2013-01-09	2007-02-08	2003-06-13				"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	13597	protein-coding gene	gene with protein product		609073	"""F-box only protein 29"", ""F-box and WD-40 domain protein 8"""	FBXO29		10531035, 10531037	Standard	NM_012174		Approved	FBX29, FBW6, FBW8	uc001twg.1	Q8N3Y1	OTTHUMG00000169329	ENST00000309909.5:c.759G>C	12.37:g.117402583G>C	ENSP00000310686:p.Glu253Asp	93.0	0.0	0		83.0	47.0	0.566265	NM_153348	Q9UK95	Missense_Mutation	SNP	ENST00000309909.5	37	CCDS9182.1	3	0.0013736263736263737	2	0.0040650406504065045	1	0.0027624309392265192	0	0.0	0	0.0	G	15.67	2.901463	0.52227	9.08E-4	5.81E-4	ENSG00000174989	ENST00000309909;ENST00000455858;ENST00000505227	T;T	0.09163	3.02;3.01	5.28	4.33	0.51752	WD40/YVTN repeat-like-containing domain (1);Quinonprotein alcohol dehydrogenase-like (1);WD40-repeat-containing domain (1);	0.195075	0.45126	D	0.000397	T	0.09818	0.0241	L	0.48642	1.525	0.28382	N	0.919506	P;P	0.49559	0.925;0.774	B;B	0.40285	0.325;0.236	T	0.18808	-1.0325	10	0.13108	T	0.6	-32.349	13.4249	0.61020	0.0:0.0:0.7974:0.2026	.	253;187	Q8N3Y1;Q8N3Y1-2	FBXW8_HUMAN;.	D	253;187;187	ENSP00000310686:E253D;ENSP00000389144:E187D	ENSP00000310686:E253D	E	+	3	2	FBXW8	115886966	0.999000	0.42202	1.000000	0.80357	0.924000	0.55760	0.860000	0.27871	2.906000	0.99361	0.655000	0.94253	GAG	G|0.999;C|0.001	0.001	strong		0.532	FBXW8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403561.1	NM_012174	
UBR1	197131	hgsc.bcm.edu	37	15	43299467	43299467	+	Missense_Mutation	SNP	A	A	C	rs141543407	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:43299467A>C	ENST00000290650.4	-	30	3303	c.3225T>G	c.(3223-3225)agT>agG	p.S1075R	UBR1_ENST00000382177.2_3'UTR|UBR1_ENST00000568782.1_5'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	1075					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		TAGAGTAGTCACTGACTGCTG	0.423																																					p.S1075R		Atlas-SNP	.											.	UBR1	124	.	0			c.T3225G						PASS	.	A	ARG/SER	0,4406		0,0,2203	62.0	56.0	58.0		3225	5.0	1.0	15	dbSNP_134	58	1,8597	1.2+/-3.3	0,1,4298	no	missense	UBR1	NM_174916.2	110	0,1,6501	CC,CA,AA		0.0116,0.0,0.0077	benign	1075/1750	43299467	1,13003	2203	4299	6502	SO:0001583	missense	197131	exon30			GTAGTCACTGACT		CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.3225T>G	15.37:g.43299467A>C	ENSP00000290650:p.Ser1075Arg	83.0	0.0	0		69.0	37.0	0.536232	NM_174916	O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	A	12.24	1.879865	0.33162	0.0	1.16E-4	ENSG00000159459	ENST00000290650	T	0.50277	0.75	4.99	4.99	0.66335	.	0.403021	0.31507	N	0.007537	T	0.28532	0.0706	L	0.32530	0.975	0.80722	D	1	B	0.31125	0.309	B	0.19391	0.025	T	0.10086	-1.0645	10	0.13853	T	0.58	0.1735	6.762	0.23546	0.7868:0.0:0.0763:0.1369	.	1075	Q8IWV7	UBR1_HUMAN	R	1075	ENSP00000290650:S1075R	ENSP00000290650:S1075R	S	-	3	2	UBR1	41086759	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.608000	0.46308	2.096000	0.63516	0.533000	0.62120	AGT	A|0.999;C|0.001	0.001	strong		0.423	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1	NM_174916	
AZU1	566	hgsc.bcm.edu	37	19	831865	831865	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:831865G>A	ENST00000233997.2	+	5	765	c.744G>A	c.(742-744)ccG>ccA	p.P248P		NM_001700.3	NP_001691.1	P20160	CAP7_HUMAN	azurocidin 1	248			Missing (in 50% of the molecules).		cellular extravasation (GO:0045123)|defense response to Gram-negative bacterium (GO:0050829)|glial cell migration (GO:0008347)|induction of positive chemotaxis (GO:0050930)|inflammatory response (GO:0006954)|macrophage chemotaxis (GO:0048246)|microglial cell activation (GO:0001774)|monocyte activation (GO:0042117)|negative regulation of apoptotic process (GO:0043066)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fractalkine biosynthetic process (GO:0050754)|positive regulation of interleukin-1 beta biosynthetic process (GO:0050725)|positive regulation of MHC class II biosynthetic process (GO:0045348)|positive regulation of phagocytosis (GO:0050766)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of vascular permeability (GO:0043114)	azurophil granule (GO:0042582)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	heparin binding (GO:0008201)|serine-type endopeptidase activity (GO:0004252)|toxic substance binding (GO:0015643)			NS(1)|endometrium(1)|kidney(1)|lung(4)|pancreas(1)|upper_aerodigestive_tract(2)	10		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;6.59e-06)|all_lung(49;9.97e-06)|Breast(49;0.000172)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		ACCCGGGACCGGGGCCAGCCT	0.711																																					p.P248P		Atlas-SNP	.											.	AZU1	31	.	0			c.G744A						PASS	.						27.0	33.0	31.0					19																	831865		2189	4270	6459	SO:0001819	synonymous_variant	566	exon5			GGGACCGGGGCCA	X58794	CCDS12044.1	19p13.3	2012-03-30	2008-08-01		ENSG00000172232	ENSG00000172232			913	protein-coding gene	gene with protein product	"""cationic antimicrobial protein 37"", ""heparin-binding protein"", ""neutrophil azurocidin"""	162815				1919011	Standard	NM_001700		Approved	AZU, CAP37, AZAMP, HBP, NAZC, HUMAZUR	uc002lpz.1	P20160		ENST00000233997.2:c.744G>A	19.37:g.831865G>A		41.0	0.0	0		67.0	30.0	0.447761	NM_001700	P80014|Q52LG4|Q9UCM1|Q9UCT5	Silent	SNP	ENST00000233997.2	37	CCDS12044.1																																																																																			.	.	none		0.711	AZU1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457472.2	NM_001700	
PLPPR1	54886	hgsc.bcm.edu	37	9	103947810	103947810	+	Missense_Mutation	SNP	T	T	G	rs41296085	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:103947810T>G	ENST00000374874.3	+	2	473	c.34T>G	c.(34-36)Tcc>Gcc	p.S12A	LPPR1_ENST00000395056.2_Missense_Mutation_p.S12A|LPPR1_ENST00000494890.1_3'UTR	NM_207299.1	NP_997182.1	Q8TBJ4	LPPR1_HUMAN		12					nervous system development (GO:0007399)	integral component of membrane (GO:0016021)	catalytic activity (GO:0003824)										ACGAAGTTATTCCATCATCCC	0.338													T|||	42	0.00838658	0.0	0.0144	5008	,	,		16008	0.0		0.0169	False		,,,				2504	0.0153				p.S12A		Atlas-SNP	.											.	.	.	.	0			c.T34G						PASS	.	T	ALA/SER,ALA/SER	17,4389	24.3+/-50.5	0,17,2186	221.0	202.0	208.0		34,34	5.9	1.0	9	dbSNP_127	208	133,8467	67.3+/-129.8	1,131,4168	yes	missense,missense	LPPR1	NM_017753.2,NM_207299.1	99,99	1,148,6354	GG,GT,TT		1.5465,0.3858,1.1533	benign,benign	12/326,12/326	103947810	150,12856	2203	4300	6503	SO:0001583	missense	0	exon2			AGTTATTCCATCA																												ENST00000374874.3:c.34T>G	9.37:g.103947810T>G	ENSP00000364008:p.Ser12Ala	214.0	1.0	0.0046729		207.0	99.0	0.478261	NM_207299	Q5VX23|Q9NXE2	Missense_Mutation	SNP	ENST00000374874.3	37	CCDS6751.1	20	0.009157509157509158	0	0.0	6	0.016574585635359115	0	0.0	14	0.018469656992084433	T	15.22	2.768539	0.49680	0.003858	0.015465	ENSG00000148123	ENST00000374874;ENST00000456287;ENST00000374871;ENST00000395056	T;T;T	0.38077	1.16;1.16;1.16	5.93	5.93	0.95920	.	0.431258	0.25774	N	0.028386	T	0.23094	0.0558	M	0.65498	2.005	0.34363	D	0.691192	B	0.02656	0.0	B	0.08055	0.003	T	0.40384	-0.9566	10	0.34782	T	0.22	-32.2815	14.3318	0.66561	0.0:0.0:0.0:1.0	rs41296085;rs61755095	12	Q8TBJ4	LPPR1_HUMAN	A	12	ENSP00000364008:S12A;ENSP00000410223:S12A;ENSP00000378496:S12A	ENSP00000364005:S12A	S	+	1	0	RP11-35N6.1	102987631	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.743000	0.62110	2.271000	0.75665	0.533000	0.62120	TCC	T|0.990;G|0.010	0.010	strong		0.338	LPPR1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053425.1		
IGF2BP2	10644	hgsc.bcm.edu	37	3	185542653	185542653	+	Silent	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:185542653T>A	ENST00000382199.2	-	1	191	c.96A>T	c.(94-96)ggA>ggT	p.G32G	IGF2BP2_ENST00000457616.2_Silent_p.G32G|IGF2BP2_ENST00000346192.3_Silent_p.G32G	NM_006548.4	NP_006539.3	Q9Y6M1	IF2B2_HUMAN	insulin-like growth factor 2 mRNA binding protein 2	32	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.				anatomical structure morphogenesis (GO:0009653)|gene expression (GO:0010467)|mRNA transport (GO:0051028)|negative regulation of translation (GO:0017148)|regulation of cytokine biosynthetic process (GO:0042035)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nucleus (GO:0005634)	mRNA 3'-UTR binding (GO:0003730)|mRNA 5'-UTR binding (GO:0048027)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|translation regulator activity (GO:0045182)			breast(3)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)|skin(3)	20	all_cancers(143;5.84e-11)|Ovarian(172;0.0386)		OV - Ovarian serous cystadenocarcinoma(80;7.41e-21)			GCAGGACCTGTCCCGCCAGGG	0.657																																					p.G32G		Atlas-SNP	.											.	IGF2BP2	69	.	0			c.A96T						PASS	.						24.0	25.0	25.0					3																	185542653		2197	4294	6491	SO:0001819	synonymous_variant	10644	exon1			GACCTGTCCCGCC	BC021290	CCDS3273.2, CCDS33903.1	3q27.2	2013-02-12			ENSG00000073792	ENSG00000073792		"""RNA binding motif (RRM) containing"""	28867	protein-coding gene	gene with protein product	"""IGF II mRNA binding protein 2"""	608289				10190901, 9891060	Standard	NM_001007225		Approved	IMP-2	uc003fpo.3	Q9Y6M1	OTTHUMG00000074025	ENST00000382199.2:c.96A>T	3.37:g.185542653T>A		132.0	0.0	0		187.0	81.0	0.433155	NM_001007225	A0A4Z0|B3FTN2|B3FTN3|B3FTN4	Silent	SNP	ENST00000382199.2	37	CCDS3273.2																																																																																			.	.	none		0.657	IGF2BP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157087.2	NM_006548	
TBC1D14	57533	hgsc.bcm.edu	37	4	7006636	7006636	+	Missense_Mutation	SNP	G	G	C	rs11731231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:7006636G>C	ENST00000409757.4	+	8	1460	c.1336G>C	c.(1336-1338)Gaa>Caa	p.E446Q	TBC1D14_ENST00000446947.2_Missense_Mutation_p.E59Q|TBC1D14_ENST00000451522.2_Missense_Mutation_p.E166Q|TBC1D14_ENST00000448507.1_Missense_Mutation_p.E446Q|TBC1D14_ENST00000410031.1_Missense_Mutation_p.E218Q	NM_020773.2	NP_065824.2	Q9P2M4	TBC14_HUMAN	TBC1 domain family, member 14	446	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.		E -> Q (in dbSNP:rs11731231).		negative regulation of autophagy (GO:0010507)|recycling endosome to Golgi transport (GO:0071955)|regulation of autophagic vacuole assembly (GO:2000785)	autophagic vacuole (GO:0005776)|Golgi apparatus (GO:0005794)|recycling endosome (GO:0055037)	protein kinase binding (GO:0019901)|Rab GTPase activator activity (GO:0005097)			breast(1)|endometrium(5)|large_intestine(4)|lung(9)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	22						AGGAGGCTCTGAAGTGGAGAA	0.458													G|||	8	0.00159744	0.0	0.0	5008	,	,		16696	0.0		0.006	False		,,,				2504	0.002				p.E446Q		Atlas-SNP	.											.	TBC1D14	110	.	0			c.G1336C						PASS	.	G	GLN/GLU,GLN/GLU,GLN/GLU	4,4402	8.1+/-20.4	0,4,2199	108.0	110.0	109.0		1336,496,1336	5.3	0.0	4	dbSNP_120	109	45,8555	29.6+/-80.5	0,45,4255	yes	missense,missense,missense	TBC1D14	NM_001113361.1,NM_001113363.1,NM_020773.2	29,29,29	0,49,6454	CC,CG,GG		0.5233,0.0908,0.3767	benign,benign,benign	446/694,166/414,446/694	7006636	49,12957	2203	4300	6503	SO:0001583	missense	57533	exon8			GGCTCTGAAGTGG	AL833868	CCDS3394.2, CCDS47006.1, CCDS75104.1	4p16.1	2008-01-22			ENSG00000132405	ENSG00000132405			29246	protein-coding gene	gene with protein product		614855				10718198	Standard	NM_020773		Approved	KIAA1322	uc003gjs.4	Q9P2M4	OTTHUMG00000090493	ENST00000409757.4:c.1336G>C	4.37:g.7006636G>C	ENSP00000386921:p.Glu446Gln	62.0	0.0	0		57.0	27.0	0.473684	NM_001113361	B9A6L5|D3DVT4|E9PAZ6|Q8IW15|Q8NDK3	Missense_Mutation	SNP	ENST00000409757.4	37	CCDS3394.2	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	17.41	3.381565	0.61845	9.08E-4	0.005233	ENSG00000132405	ENST00000448507;ENST00000409757;ENST00000410031;ENST00000451522;ENST00000439515;ENST00000446947	T;T;T;T;T;T	0.33216	3.46;3.46;3.43;3.44;1.42;3.0	5.27	5.27	0.74061	Rab-GAP/TBC domain (4);	0.405543	0.28718	N	0.014366	T	0.33323	0.0859	M	0.63843	1.955	0.80722	D	1	B;B;B	0.22211	0.059;0.003;0.066	B;B;B	0.36092	0.097;0.009;0.217	T	0.23583	-1.0184	10	0.49607	T	0.09	-2.7179	18.059	0.89371	0.0:0.0:1.0:0.0	rs11731231;rs52800326;rs11731231	59;166;446	F5GXK4;Q9P2M4-2;Q9P2M4	.;.;TBC14_HUMAN	Q	446;446;218;166;65;59	ENSP00000404041:E446Q;ENSP00000386921:E446Q;ENSP00000386343:E218Q;ENSP00000388886:E166Q;ENSP00000389082:E65Q;ENSP00000405875:E59Q	ENSP00000386921:E446Q	E	+	1	0	TBC1D14	7057537	0.408000	0.25360	0.029000	0.17559	0.574000	0.36063	3.009000	0.49552	2.722000	0.93159	0.655000	0.94253	GAA	G|0.997;C|0.003	0.003	strong		0.458	TBC1D14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206981.3	NM_020773	
RAD50	10111	hgsc.bcm.edu	37	5	131924538	131924538	+	Missense_Mutation	SNP	A	A	G	rs200017020	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:131924538A>G	ENST00000265335.6	+	8	1598	c.1211A>G	c.(1210-1212)cAa>cGa	p.Q404R	RAD50_ENST00000378823.3_Missense_Mutation_p.Q265R			Q92878	RAD50_HUMAN	RAD50 homolog (S. cerevisiae)	404					cellular response to DNA damage stimulus (GO:0006974)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA duplex unwinding (GO:0032508)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|positive regulation of kinase activity (GO:0033674)|positive regulation of protein autophosphorylation (GO:0031954)|reciprocal meiotic recombination (GO:0007131)|regulation of mitotic recombination (GO:0000019)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	membrane (GO:0016020)|Mre11 complex (GO:0030870)|nuclear chromosome, telomeric region (GO:0000784)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pronucleus (GO:0045120)|site of double-strand break (GO:0035861)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|nuclease activity (GO:0004518)|protein binding, bridging (GO:0030674)|zinc ion binding (GO:0008270)			breast(3)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	36		all_cancers(142;0.0368)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			AGAGAGAGACAAGAAGGGGAA	0.358								Homologous recombination					A|||	2	0.000399361	0.0	0.0	5008	,	,		16369	0.002		0.0	False		,,,				2504	0.0				p.Q404R		Atlas-SNP	.											.	RAD50	246	.	0			c.A1211G						PASS	.						77.0	77.0	77.0					5																	131924538		2203	4300	6503	SO:0001583	missense	10111	exon8			AGAGACAAGAAGG	Z75311	CCDS34233.1	5q23-q31	2008-05-30	2001-11-28		ENSG00000113522	ENSG00000113522			9816	protein-coding gene	gene with protein product		604040	"""RAD50 (S. cerevisiae) homolog"""			8756642, 9705271	Standard	NM_005732		Approved	hRad50, RAD50-2	uc003kxi.3	Q92878	OTTHUMG00000059613	ENST00000265335.6:c.1211A>G	5.37:g.131924538A>G	ENSP00000265335:p.Gln404Arg	182.0	0.0	0		174.0	95.0	0.545977	NM_005732	B9EGF5|O43254|Q6GMT7|Q6P5X3|Q9UP86	Missense_Mutation	SNP	ENST00000265335.6	37	CCDS34233.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	9.857	1.195145	0.22037	.	.	ENSG00000113522	ENST00000378823;ENST00000265335;ENST00000453394	T;T;T	0.09073	3.51;3.02;3.02	5.97	4.8	0.61643	.	0.173879	0.52532	D	0.000075	T	0.09992	0.0245	L	0.57536	1.79	0.33889	D	0.637111	B	0.30511	0.282	B	0.26517	0.07	T	0.10132	-1.0643	10	0.32370	T	0.25	-11.145	11.8328	0.52305	0.8688:0.0:0.0:0.1312	.	404	Q92878	RAD50_HUMAN	R	265;404;404	ENSP00000368100:Q265R;ENSP00000265335:Q404R;ENSP00000400049:Q404R	ENSP00000265335:Q404R	Q	+	2	0	RAD50	131952437	1.000000	0.71417	1.000000	0.80357	0.934000	0.57294	3.243000	0.51392	1.062000	0.40625	-0.333000	0.08304	CAA	A|1.000;G|0.000	0.000	strong		0.358	RAD50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132566.5	NM_005732	
FGFR2	2263	hgsc.bcm.edu	37	10	123239112	123239112	+	3'UTR	SNP	G	G	A	rs1047057	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123239112G>A	ENST00000358487.5	-	0	2997				FGFR2_ENST00000357555.5_Silent_p.L703L|FGFR2_ENST00000369060.4_3'UTR|FGFR2_ENST00000478859.1_3'UTR|FGFR2_ENST00000369061.4_3'UTR|FGFR2_ENST00000356226.4_3'UTR	NM_000141.4	NP_000132.3	P21802	FGFR2_HUMAN	fibroblast growth factor receptor 2						angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|bone development (GO:0060348)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|branch elongation involved in salivary gland morphogenesis (GO:0060667)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of a nerve (GO:0048755)|bud elongation involved in lung branching (GO:0060449)|cell fate commitment (GO:0045165)|cell-cell signaling (GO:0007267)|coronal suture morphogenesis (GO:0060365)|digestive tract development (GO:0048565)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic organ development (GO:0048568)|embryonic organ morphogenesis (GO:0048562)|embryonic pattern specification (GO:0009880)|endodermal digestive tract morphogenesis (GO:0061031)|epidermal growth factor receptor signaling pathway (GO:0007173)|epidermis morphogenesis (GO:0048730)|epithelial cell differentiation (GO:0030855)|epithelial cell proliferation involved in salivary gland morphogenesis (GO:0060664)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|fibroblast growth factor receptor signaling pathway involved in hemopoiesis (GO:0035603)|fibroblast growth factor receptor signaling pathway involved in mammary gland specification (GO:0060595)|fibroblast growth factor receptor signaling pathway involved in negative regulation of apoptotic process in bone marrow (GO:0035602)|fibroblast growth factor receptor signaling pathway involved in orbitofrontal cortex development (GO:0035607)|fibroblast growth factor receptor signaling pathway involved in positive regulation of cell proliferation in bone marrow (GO:0035604)|gland morphogenesis (GO:0022612)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|inner ear morphogenesis (GO:0042472)|insulin receptor signaling pathway (GO:0008286)|lacrimal gland development (GO:0032808)|lateral sprouting from an epithelium (GO:0060601)|lens fiber cell development (GO:0070307)|limb bud formation (GO:0060174)|lung alveolus development (GO:0048286)|lung development (GO:0030324)|lung lobe morphogenesis (GO:0060463)|lung-associated mesenchyme development (GO:0060484)|mammary gland bud formation (GO:0060615)|membranous septum morphogenesis (GO:0003149)|mesenchymal cell differentiation (GO:0048762)|mesenchymal cell differentiation involved in lung development (GO:0060915)|mesenchymal cell proliferation involved in lung development (GO:0060916)|mesodermal cell differentiation (GO:0048333)|midbrain development (GO:0030901)|morphogenesis of embryonic epithelium (GO:0016331)|multicellular organism growth (GO:0035264)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis (GO:0042476)|orbitofrontal cortex development (GO:0021769)|organ growth (GO:0035265)|organ morphogenesis (GO:0009887)|otic vesicle formation (GO:0030916)|outflow tract septum morphogenesis (GO:0003148)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell cycle (GO:0045787)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial cell proliferation involved in lung morphogenesis (GO:0060501)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|post-embryonic development (GO:0009791)|prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis (GO:0060527)|prostate epithelial cord elongation (GO:0060523)|prostate gland morphogenesis (GO:0060512)|protein autophosphorylation (GO:0046777)|pyramidal neuron development (GO:0021860)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of fibroblast growth factor receptor signaling pathway (GO:0040036)|regulation of morphogenesis of a branching structure (GO:0060688)|regulation of multicellular organism growth (GO:0040014)|regulation of osteoblast differentiation (GO:0045667)|regulation of osteoblast proliferation (GO:0033688)|regulation of smooth muscle cell differentiation (GO:0051150)|regulation of smoothened signaling pathway (GO:0008589)|reproductive structure development (GO:0048608)|skeletal system morphogenesis (GO:0048705)|squamous basal epithelial stem cell differentiation involved in prostate gland acinus development (GO:0060529)|synaptic vesicle transport (GO:0048489)|ureteric bud development (GO:0001657)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|ventricular zone neuroblast division (GO:0021847)	cell cortex (GO:0005938)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|excitatory synapse (GO:0060076)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|heparin binding (GO:0008201)|protein homodimerization activity (GO:0042803)|protein tyrosine kinase activity (GO:0004713)	p.L703L(1)		breast(3)|central_nervous_system(3)|cervix(2)|endometrium(98)|haematopoietic_and_lymphoid_tissue(4)|kidney(4)|large_intestine(7)|lung(21)|ovary(4)|skin(30)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(2)	181		Lung NSC(174;0.0841)|all_lung(145;0.106)|all_neural(114;0.107)	STAD - Stomach adenocarcinoma(1;7.52e-05)|all cancers(1;0.0722)	all cancers(201;9.73e-05)|GBM - Glioblastoma multiforme(135;0.0845)	Palifermin(DB00039)|Ponatinib(DB08901)|Regorafenib(DB08896)|Thalidomide(DB01041)	TCCACAGCCAGTACGCACGGC	0.483		5	Mis		"""gastric. NSCLC, endometrial"""		"""Crouzon, Pfeiffer, and Apert syndromes"""		Saethre-Chotzen syndrome;Apert syndrome				G|||	2075	0.414337	0.0938	0.6873	5008	,	,		15689	0.3512		0.5099	False		,,,				2504	0.6207				p.L703L		Atlas-SNP	.		Dom	yes		10	10q26	2263	fibroblast growth factor receptor 2	yes	E	FGFR2_ENST00000357555,NS,carcinoma,0,1	FGFR2	758	1	1	Substitution - coding silent(1)	stomach(1)	c.C2107T						PASS	.	G	,,,,,,	237,1147		19,199,474	86.0	84.0	85.0		,,2107,,,,	4.5	0.9	10	dbSNP_86	85	1747,1435		500,747,344	no	utr-3,utr-3,coding-synonymous,utr-3,utr-3,utr-3,utr-3	FGFR2	NM_000141.4,NM_001144914.1,NM_001144915.1,NM_001144916.1,NM_001144917.1,NM_001144918.1,NM_022970.3	,,,,,,	519,946,818	AA,AG,GG		45.0974,17.1243,43.4516	,,,,,,	,,703/708,,,,	123239112	1984,2582	692	1591	2283	SO:0001624	3_prime_UTR_variant	2263	exon17	Familial Cancer Database	Acrocephalosyndactyly type III;Acrocephalosyndactyly type I and II, ACS1. ACS2, incl Apert-Crouzon s.	CAGCCAGTACGCA	AK026508	CCDS7620.2, CCDS31298.1, CCDS44485.1, CCDS44486.1, CCDS44487.1, CCDS44488.1, CCDS44489.1, CCDS53584.1, CCDS73210.1	10q25.3-q26	2013-01-11	2008-08-01		ENSG00000066468	ENSG00000066468		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3689	protein-coding gene	gene with protein product	"""Crouzon syndrome"", ""Pfeiffer syndrome"""	176943	"""bacteria-expressed kinase"", ""keratinocyte growth factor receptor"", ""craniofacial dysostosis 1"", ""Jackson-Weiss syndrome"""	KGFR, BEK, CFD1, JWS			Standard	NM_022970		Approved	CEK3, TK14, TK25, ECT1, K-SAM, CD332	uc021pzy.1	P21802	OTTHUMG00000019175	ENST00000358487.5:c.*259C>T	10.37:g.123239112G>A		84.0	0.0	0		102.0	100.0	0.980392	NM_001144915	B4DFC2|E7EVR6|E9PCR0|P18443|Q01742|Q12922|Q14300|Q14301|Q14302|Q14303|Q14304|Q14305|Q14672|Q14718|Q14719|Q1KHY5|Q86YI4|Q8IXC7|Q96KL9|Q96KM0|Q96KM1|Q96KM2|Q9NZU2|Q9NZU3|Q9UD01|Q9UD02|Q9UIH3|Q9UIH4|Q9UIH5|Q9UIH6|Q9UIH7|Q9UIH8|Q9UM87|Q9UMC6|Q9UNS7|Q9UQH7|Q9UQH8|Q9UQH9|Q9UQI0	Silent	SNP	ENST00000358487.5	37	CCDS31298.1																																																																																			G|0.609;A|0.391	0.391	strong		0.483	FGFR2-001	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000050715.1	NM_022976, NM_000141	
MPDZ	8777	hgsc.bcm.edu	37	9	13183486	13183486	+	Silent	SNP	T	T	C	rs34704118	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:13183486T>C	ENST00000319217.7	-	19	2827	c.2580A>G	c.(2578-2580)ttA>ttG	p.L860L	MPDZ_ENST00000536827.1_Silent_p.L860L|MPDZ_ENST00000381015.4_Silent_p.L860L|MPDZ_ENST00000381022.2_Silent_p.L860L|MPDZ_ENST00000447879.1_Silent_p.L860L|MPDZ_ENST00000546205.1_Silent_p.L860L|MPDZ_ENST00000541718.1_Silent_p.L860L	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	860					cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CATGAAGAGATAAAATAGAGG	0.408													T|||	7	0.00139776	0.0	0.0072	5008	,	,		18769	0.0		0.001	False		,,,				2504	0.001				p.L860L		Atlas-SNP	.											MPDZ_ENST00000541718,colon,carcinoma,-2,2	MPDZ	324	2	0			c.A2580G						PASS	.	T		4,3782		0,4,1889	93.0	91.0	92.0		2580	0.8	0.8	9	dbSNP_126	92	55,8201		0,55,4073	no	coding-synonymous	MPDZ	NM_003829.3		0,59,5962	CC,CT,TT		0.6662,0.1057,0.49		860/2042	13183486	59,11983	1893	4128	6021	SO:0001819	synonymous_variant	8777	exon19			AAGAGATAAAATA	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.2580A>G	9.37:g.13183486T>C		109.0	0.0	0		91.0	41.0	0.450549	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Silent	SNP	ENST00000319217.7	37																																																																																				T|0.997;C|0.003	0.003	strong		0.408	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
DNMT3L	29947	hgsc.bcm.edu	37	21	45675997	45675997	+	Missense_Mutation	SNP	C	C	T	rs142917827		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45675997C>T	ENST00000418993.1	-	7	1040	c.557G>A	c.(556-558)aGg>aAg	p.R186K	DNMT3L_ENST00000270172.3_Missense_Mutation_p.R186K	NM_175867.2	NP_787063.1	Q9UJW3	DNM3L_HUMAN	DNA (cytosine-5-)-methyltransferase 3-like	186					chorionic trophoblast cell differentiation (GO:0060718)|DNA methylation (GO:0006306)|in utero embryonic development (GO:0001701)|negative regulation of transcription, DNA-templated (GO:0045892)|placenta development (GO:0001890)|positive regulation of catalytic activity (GO:0043085)|regulation of gene expression by genetic imprinting (GO:0006349)|spermatogenesis (GO:0007283)	condensed nuclear chromosome (GO:0000794)|cytosol (GO:0005829)|nuclear heterochromatin (GO:0005720)|nucleus (GO:0005634)	enzyme activator activity (GO:0008047)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)|skin(3)	11				Colorectal(79;0.0165)|READ - Rectum adenocarcinoma(84;0.0781)		TGGCTGTCTCCTCCACACAGG	0.478													C|||	1	0.000199681	0.0	0.0	5008	,	,		13853	0.0		0.001	False		,,,				2504	0.0				p.R186K		Atlas-SNP	.											.	DNMT3L	33	.	0			c.G557A						PASS	.	C	LYS/ARG,LYS/ARG	1,4405	2.1+/-5.4	0,1,2202	108.0	108.0	108.0		557,557	1.1	0.3	21	dbSNP_134	108	17,8583	12.6+/-44.7	0,17,4283	yes	missense,missense	DNMT3L	NM_013369.2,NM_175867.1	26,26	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign,benign	186/388,186/387	45675997	18,12988	2203	4300	6503	SO:0001583	missense	29947	exon7			TGTCTCCTCCACA	AF194032	CCDS13705.1	21q22.3	2008-07-31			ENSG00000142182	ENSG00000142182			2980	protein-coding gene	gene with protein product	"""cytosine-5-methyltransferase 3-like protein"", ""human cytosine-5-methyltransferase 3-like protein"""	606588				10857753	Standard	NM_013369		Approved	MGC1090	uc002zeh.2	Q9UJW3	OTTHUMG00000086914	ENST00000418993.1:c.557G>A	21.37:g.45675997C>T	ENSP00000412862:p.Arg186Lys	139.0	0.0	0		183.0	98.0	0.535519	NM_013369	E9PB42|Q9BUJ4	Missense_Mutation	SNP	ENST00000418993.1	37	CCDS46650.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	0.006	-2.100319	0.00360	2.27E-4	0.001977	ENSG00000142182	ENST00000270172;ENST00000418993;ENST00000431166	T;T;T	0.73258	-0.73;-0.73;-0.73	3.44	1.07	0.20283	.	0.493499	0.20721	N	0.086902	T	0.29620	0.0739	N	0.01091	-1.02	0.24720	N	0.993155	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.36648	-0.9739	10	0.02654	T	1	-19.7411	4.7202	0.12915	0.0:0.3025:0.0:0.6975	.	186;186	Q9UJW3-2;Q9UJW3	.;DNM3L_HUMAN	K	186;186;171	ENSP00000270172:R186K;ENSP00000412862:R186K;ENSP00000400242:R171K	ENSP00000270172:R186K	R	-	2	0	DNMT3L	44500425	0.992000	0.36948	0.271000	0.24616	0.065000	0.16274	2.203000	0.42752	0.118000	0.18165	-0.379000	0.06801	AGG	C|0.999;T|0.001	0.001	strong		0.478	DNMT3L-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000195820.1	NM_013369	
STK16	8576	hgsc.bcm.edu	37	2	220113145	220113145	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:220113145A>G	ENST00000409638.3	+	8	954	c.782A>G	c.(781-783)cAt>cGt	p.H261R	GLB1L_ENST00000392089.2_5'Flank|STK16_ENST00000396738.2_Missense_Mutation_p.H261R|GLB1L_ENST00000295759.7_5'Flank|TUBA4A_ENST00000498660.1_5'Flank|STK16_ENST00000409743.1_Missense_Mutation_p.H229R|STK16_ENST00000409516.3_Missense_Mutation_p.H143R|STK16_ENST00000409260.1_Missense_Mutation_p.H306R	NM_001008910.2	NP_001008910.1	O75716	STK16_HUMAN	serine/threonine kinase 16	261	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to transforming growth factor beta stimulus (GO:0071560)|protein autophosphorylation (GO:0046777)	Golgi-associated vesicle (GO:0005798)|membrane (GO:0016020)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein serine/threonine kinase activity (GO:0004674)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			skin(1)	1		Renal(207;0.0474)		Epithelial(149;1.2e-06)|all cancers(144;0.000197)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CTCCACAGGCATTCTTCAGCA	0.567																																					p.H261R	Pancreas(34;887 922 17165 36961 39622)	Atlas-SNP	.											.	STK16	22	.	0			c.A782G						PASS	.						128.0	135.0	133.0					2																	220113145		2088	4216	6304	SO:0001583	missense	8576	exon8			ACAGGCATTCTTC	AF060798	CCDS42822.1	2q35	2010-04-16			ENSG00000115661	ENSG00000115661			11394	protein-coding gene	gene with protein product		604719				9712705	Standard	NM_001008910		Approved	PKL12, MPSK	uc002vko.2	O75716	OTTHUMG00000154520	ENST00000409638.3:c.782A>G	2.37:g.220113145A>G	ENSP00000386928:p.His261Arg	107.0	0.0	0		91.0	42.0	0.461538	NM_001008910	A8K9H9|Q5U0F8|Q96KI2|Q9BUH4|Q9UEN3|Q9UP78	Missense_Mutation	SNP	ENST00000409638.3	37	CCDS42822.1	.	.	.	.	.	.	.	.	.	.	A	14.44	2.534997	0.45073	.	.	ENSG00000115661	ENST00000409638;ENST00000396738;ENST00000409516;ENST00000409260;ENST00000409743	T;T;T;T;T	0.73363	2.13;2.13;-0.74;-0.74;2.13	4.98	4.98	0.66077	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.301734	0.37530	N	0.002044	T	0.64405	0.2595	L	0.27944	0.81	0.48288	D	0.999628	B;B;B	0.33022	0.394;0.084;0.084	B;B;B	0.33042	0.072;0.157;0.026	T	0.68629	-0.5358	10	0.72032	D	0.01	-3.1791	14.8415	0.70230	1.0:0.0:0.0:0.0	.	143;306;261	B4DPS1;B8ZZN3;O75716	.;.;STK16_HUMAN	R	261;261;143;306;229	ENSP00000386928:H261R;ENSP00000379964:H261R;ENSP00000386309:H143R;ENSP00000387156:H306R;ENSP00000386553:H229R	ENSP00000379964:H261R	H	+	2	0	STK16	219821389	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	6.637000	0.74304	2.098000	0.63641	0.459000	0.35465	CAT	.	.	none		0.567	STK16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335679.1		
ZNF570	148268	hgsc.bcm.edu	37	19	37975379	37975379	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:37975379G>A	ENST00000330173.1	+	5	1384	c.855G>A	c.(853-855)caG>caA	p.Q285Q	ZNF570_ENST00000388801.3_Silent_p.Q82Q|ZNF570_ENST00000586475.1_Silent_p.Q341Q	NM_144694.1	NP_653295.1	Q96NI8	ZN570_HUMAN	zinc finger protein 570	285					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(3)|kidney(3)|large_intestine(6)|lung(12)|ovary(1)|prostate(1)|skin(1)	27			COAD - Colon adenocarcinoma(19;0.114)|Colorectal(19;0.177)			CCTTCAGTCAGAATGCACACC	0.423																																					p.Q285Q		Atlas-SNP	.											.	ZNF570	58	.	0			c.G855A						PASS	.						72.0	69.0	70.0					19																	37975379		2203	4300	6503	SO:0001819	synonymous_variant	148268	exon5			CAGTCAGAATGCA	AK055353	CCDS12504.1, CCDS74355.1	19q13.12	2013-09-20			ENSG00000171827	ENSG00000171827		"""Zinc fingers, C2H2-type"", ""-"""	26416	protein-coding gene	gene with protein product							Standard	XM_005258567		Approved	FLJ30791	uc002ogk.1	Q96NI8	OTTHUMG00000048176	ENST00000330173.1:c.855G>A	19.37:g.37975379G>A		35.0	0.0	0		39.0	16.0	0.410256	NM_144694	A1L472|B4DMP1	Silent	SNP	ENST00000330173.1	37	CCDS12504.1																																																																																			.	.	none		0.423	ZNF570-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109600.1	NM_144694	
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605344	84605344	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:84605344G>A	ENST00000344803.2	+	3	292	c.245G>A	c.(244-246)tGg>tAg	p.W82*		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	82					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											TTCCCAGACTGGAAAAGTTTC	0.433																																					p.W82X		Atlas-SNP	.											.	.	.	.	0			c.G245A						PASS	.						83.0	77.0	79.0					9																	84605344		1855	4089	5944	SO:0001587	stop_gained	389763	exon3			CAGACTGGAAAAG		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.245G>A	9.37:g.84605344G>A	ENSP00000341988:p.Trp82*	137.0	0.0	0		138.0	59.0	0.427536	NM_001001670		Nonsense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.828944	0.32329	.	.	ENSG00000214929	ENST00000344803	.	.	.	2.82	-3.37	0.04898	.	1.436640	0.04947	N	0.459585	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	10.638	4.091	0.09970	0.3449:0.3377:0.3174:0.0	.	.	.	.	X	82	.	ENSP00000341988:W82X	W	+	2	0	FAM75D1	83795164	0.039000	0.19947	0.000000	0.03702	0.000000	0.00434	0.316000	0.19469	-0.774000	0.04590	-0.902000	0.02854	TGG	.	.	none		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
HELZ	9931	hgsc.bcm.edu	37	17	65103373	65103373	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:65103373T>C	ENST00000358691.5	-	31	5319	c.5153A>G	c.(5152-5154)cAg>cGg	p.Q1718R	HELZ_ENST00000580168.1_Missense_Mutation_p.Q1719R	NM_014877.3	NP_055692	P42694	HELZ_HUMAN	helicase with zinc finger	1718						membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(5)|endometrium(9)|kidney(3)|large_intestine(11)|liver(1)|lung(24)|ovary(1)|pancreas(1)|prostate(1)|skin(8)|upper_aerodigestive_tract(2)|urinary_tract(2)	69	all_cancers(12;1.24e-11)|Breast(2;1.05e-17)|all_epithelial(3;3.87e-13)					TTGATGATTCTGTATTTGTAC	0.453																																					p.Q1718R		Atlas-SNP	.											.	HELZ	160	.	0			c.A5153G						PASS	.						185.0	192.0	190.0					17																	65103373		1974	4156	6130	SO:0001583	missense	9931	exon31			TGATTCTGTATTT	D29677	CCDS42374.1	17q24.2	2013-01-18			ENSG00000198265	ENSG00000198265		"""Zinc fingers, CCCH-type domain containing"""	16878	protein-coding gene	gene with protein product	"""down-regulated in human cancers"""	606699				10471385, 12691822	Standard	NM_014877		Approved	KIAA0054, HUMORF5, DHRC	uc002jfx.4	P42694	OTTHUMG00000179555	ENST00000358691.5:c.5153A>G	17.37:g.65103373T>C	ENSP00000351524:p.Gln1718Arg	306.0	0.0	0		315.0	147.0	0.466667	NM_014877	I6L9H4	Missense_Mutation	SNP	ENST00000358691.5	37	CCDS42374.1	.	.	.	.	.	.	.	.	.	.	T	12.03	1.815470	0.32145	.	.	ENSG00000198265	ENST00000358691	D	0.88201	-2.35	5.31	4.2	0.49525	.	0.067201	0.64402	D	0.000013	T	0.80909	0.4714	L	0.29908	0.895	0.44048	D	0.996786	P;P	0.37466	0.596;0.596	B;B	0.29785	0.107;0.107	T	0.79995	-0.1568	10	0.87932	D	0	-4.8142	12.192	0.54277	0.0:0.0:0.1429:0.8571	.	1719;1718	B7ZLW2;P42694	.;HELZ_HUMAN	R	1718	ENSP00000351524:Q1718R	ENSP00000351524:Q1718R	Q	-	2	0	HELZ	62533835	1.000000	0.71417	0.982000	0.44146	0.993000	0.82548	2.537000	0.45702	0.827000	0.34685	0.472000	0.43445	CAG	.	.	none		0.453	HELZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000447068.1	NM_014877	
POLR3A	11128	hgsc.bcm.edu	37	10	79744042	79744042	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:79744042G>T	ENST00000372371.3	-	25	3394	c.3257C>A	c.(3256-3258)aCa>aAa	p.T1086K		NM_007055.3	NP_008986.2	O14802	RPC1_HUMAN	polymerase (RNA) III (DNA directed) polypeptide A, 155kDa	1086					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|ribonucleoside binding (GO:0032549)|zinc ion binding (GO:0008270)			breast(1)|endometrium(7)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	59	all_cancers(46;0.0356)|all_epithelial(25;0.00102)|Breast(12;0.00124)|Prostate(51;0.0095)		Epithelial(14;0.00161)|OV - Ovarian serous cystadenocarcinoma(4;0.00323)|all cancers(16;0.00646)			TAGCTGTGCTGTGATAATTGG	0.458																																					p.T1086K		Atlas-SNP	.											.	POLR3A	104	.	0			c.C3257A						PASS	.						111.0	97.0	102.0					10																	79744042		2203	4300	6503	SO:0001583	missense	11128	exon25			TGTGCTGTGATAA	AF021351	CCDS7354.1	10q22-q23	2013-01-21			ENSG00000148606	ENSG00000148606		"""RNA polymerase subunits"""	30074	protein-coding gene	gene with protein product		614258				9331371, 12391170	Standard	NM_007055		Approved	RPC1, RPC155, hRPC155	uc001jzn.3	O14802	OTTHUMG00000018550	ENST00000372371.3:c.3257C>A	10.37:g.79744042G>T	ENSP00000361446:p.Thr1086Lys	70.0	0.0	0		77.0	34.0	0.441558	NM_007055	Q8IW34|Q8TCW5	Missense_Mutation	SNP	ENST00000372371.3	37	CCDS7354.1	.	.	.	.	.	.	.	.	.	.	G	18.88	3.717429	0.68844	.	.	ENSG00000148606	ENST00000372371;ENST00000540842	T	0.77489	-1.1	5.62	5.62	0.85841	RNA polymerase Rpb1, domain 5 (1);	0.051059	0.85682	D	0.000000	D	0.87951	0.6307	M	0.80508	2.5	0.80722	D	1	P	0.48998	0.918	P	0.60345	0.873	D	0.87312	0.2312	9	.	.	.	-17.2577	19.6607	0.95868	0.0:0.0:1.0:0.0	.	1086	O14802	RPC1_HUMAN	K	1086;1065	ENSP00000361446:T1086K	.	T	-	2	0	POLR3A	79414048	1.000000	0.71417	0.970000	0.41538	0.983000	0.72400	7.320000	0.79064	2.660000	0.90430	0.650000	0.86243	ACA	.	.	none		0.458	POLR3A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048923.1	NM_007055	
METTL4	64863	hgsc.bcm.edu	37	18	2554915	2554915	+	Silent	SNP	G	G	A	rs61749937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:2554915G>A	ENST00000574538.1	-	4	1357	c.582C>T	c.(580-582)gaC>gaT	p.D194D	METTL4_ENST00000319888.6_Silent_p.D194D|snoU109_ENST00000459316.1_RNA	NM_022840.3	NP_073751.3	Q8N3J2	METL4_HUMAN	methyltransferase like 4	194					nucleobase-containing compound metabolic process (GO:0006139)		methyltransferase activity (GO:0008168)|nucleic acid binding (GO:0003676)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						AACTGCAGGCGTCAAGTGGTA	0.393													G|||	75	0.014976	0.0318	0.0086	5008	,	,		20011	0.0		0.0239	False		,,,				2504	0.0031				p.D194D		Atlas-SNP	.											.	METTL4	40	.	0			c.C582T						PASS	.	G		124,4282	91.6+/-130.3	4,116,2083	120.0	113.0	115.0		582	2.0	0.5	18	dbSNP_129	115	95,8505	54.0+/-114.7	1,93,4206	no	coding-synonymous	METTL4	NM_022840.3		5,209,6289	AA,AG,GG		1.1047,2.8143,1.6838		194/473	2554915	219,12787	2203	4300	6503	SO:0001819	synonymous_variant	64863	exon4			GCAGGCGTCAAGT		CCDS11826.1	18p11.31	2008-02-05			ENSG00000101574	ENSG00000101574			24726	protein-coding gene	gene with protein product						12477932	Standard	NM_022840		Approved	FLJ23017, HsT661	uc002klh.4	Q8N3J2	OTTHUMG00000131482	ENST00000574538.1:c.582C>T	18.37:g.2554915G>A		201.0	0.0	0		172.0	71.0	0.412791	NM_022840	B2RNA1|Q2TAA7|Q9H5U9	Silent	SNP	ENST00000574538.1	37	CCDS11826.1																																																																																			G|0.984;A|0.016	0.016	strong		0.393	METTL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254326.3	NM_022840	
TCP10L2	401285	hgsc.bcm.edu	37	6	167592571	167592571	+	Missense_Mutation	SNP	G	G	A	rs28690444	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167592571G>A	ENST00000366832.2	+	6	861	c.730G>A	c.(730-732)Gcc>Acc	p.A244T		NM_001145121.1	NP_001138593.1	B9ZVM9	TCP2L_HUMAN	t-complex 10-like 2	244										endometrium(1)|kidney(2)|lung(3)	6						TTCCCAGGCCGCCACGCTGCA	0.592																																					p.A244T		Atlas-SNP	.											.	TCP10L2	41	.	0			c.G730A						PASS	.						23.0	28.0	27.0					6																	167592571		692	1591	2283	SO:0001583	missense	401285	exon6			CAGGCCGCCACGC		CCDS47514.1	6q27	2012-09-20	2012-09-20		ENSG00000166984	ENSG00000166984			21254	protein-coding gene	gene with protein product			"""t-complex 10-like 2 (mouse)"""				Standard	NM_001145121		Approved	bA517H2.3	uc010kkp.3	B9ZVM9	OTTHUMG00000016014	ENST00000366832.2:c.730G>A	6.37:g.167592571G>A	ENSP00000355797:p.Ala244Thr	113.0	0.0	0		61.0	15.0	0.245902	NM_001145121		Missense_Mutation	SNP	ENST00000366832.2	37	CCDS47514.1	87	0.03983516483516483	17	0.034552845528455285	12	0.03314917127071823	14	0.024475524475524476	44	0.05804749340369393	c	8.486	0.860926	0.17178	.	.	ENSG00000166984	ENST00000366832	T	0.13901	2.55	1.87	-1.19	0.09585	.	.	.	.	.	T	0.00906	0.0030	N	0.11560	0.145	0.09310	N	1	B	0.32968	0.392	B	0.17433	0.018	T	0.43718	-0.9374	9	0.02654	T	1	.	2.6095	0.04887	0.3443:0.2689:0.3868:0.0	rs28690444	244	B9ZVM9	TCP2L_HUMAN	T	244	ENSP00000355797:A244T	ENSP00000283507:A244T	A	+	1	0	TCP10L2	167512561	0.000000	0.05858	0.000000	0.03702	0.115000	0.19883	-0.863000	0.04259	-0.321000	0.08627	-1.962000	0.00476	GCC	G|0.965;A|0.035	0.035	strong		0.592	TCP10L2-001	NOVEL	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043112.5	XR_040749	
ABR	29	hgsc.bcm.edu	37	17	1028676	1028676	+	Missense_Mutation	SNP	C	C	T	rs117732533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:1028676C>T	ENST00000302538.5	-	2	234	c.88G>A	c.(88-90)Gac>Aac	p.D30N	ABR_ENST00000574437.1_5'UTR|ABR_ENST00000544583.2_5'UTR	NM_001282149.1|NM_021962.3	NP_001269078.1|NP_068781.2	Q12979	ABR_HUMAN	active BCR-related	30					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|brain development (GO:0007420)|inner ear morphogenesis (GO:0042472)|negative regulation of cell migration (GO:0030336)|negative regulation of inflammatory response (GO:0050728)|negative regulation of neutrophil degranulation (GO:0043314)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of phagocytosis (GO:0050766)|regulation of small GTPase mediated signal transduction (GO:0051056)|response to lipopolysaccharide (GO:0032496)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)|Rac GTPase activator activity (GO:0030675)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39				UCEC - Uterine corpus endometrioid carcinoma (25;0.0228)		CCCTCTCCGTCGTACTCGTCC	0.627													C|||	21	0.00419329	0.0	0.0058	5008	,	,		12183	0.0		0.0169	False		,,,				2504	0.0				p.D30N	Esophageal Squamous(197;2016 2115 4129 29033 46447)	Atlas-SNP	.											.	ABR	119	.	0			c.G88A						PASS	.	C	,ASN/ASP	8,4398	14.3+/-33.2	0,8,2195	112.0	103.0	106.0		,88	5.5	1.0	17	dbSNP_132	106	90,8510	51.5+/-111.7	1,88,4211	yes	utr-5,missense	ABR	NM_001159746.1,NM_021962.2	,23	1,96,6406	TT,TC,CC		1.0465,0.1816,0.7535	,benign	,30/860	1028676	98,12908	2203	4300	6503	SO:0001583	missense	29	exon2			CTCCGTCGTACTC	L19704	CCDS10999.1, CCDS11000.1, CCDS54060.1, CCDS58497.1, CCDS73936.1	17p13	2013-01-10	2012-02-27		ENSG00000159842	ENSG00000159842		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	81	protein-coding gene	gene with protein product		600365	"""active BCR-related gene"""			2587217, 7479768	Standard	NM_001092		Approved	MDB	uc002fsd.4	Q12979	OTTHUMG00000090313	ENST00000302538.5:c.88G>A	17.37:g.1028676C>T	ENSP00000303909:p.Asp30Asn	56.0	0.0	0		71.0	38.0	0.535211	NM_021962	B3KW89|B7Z6H7|D3DTH3|D3DTH4|F5H3S2|F5H8B3|Q13693|Q13694	Missense_Mutation	SNP	ENST00000302538.5	37	CCDS10999.1	15	0.006868131868131868	0	0.0	2	0.0055248618784530384	0	0.0	13	0.017150395778364115	C	16.51	3.142274	0.57044	0.001816	0.010465	ENSG00000159842	ENST00000302538	T	0.21361	2.01	5.46	5.46	0.80206	.	0.182095	0.48286	D	0.000187	T	0.08133	0.0203	L	0.40543	1.245	0.80722	D	1	P	0.36438	0.553	B	0.25291	0.059	T	0.05241	-1.0897	10	0.23302	T	0.38	.	16.8188	0.85740	0.0:1.0:0.0:0.0	.	30	Q12979	ABR_HUMAN	N	30	ENSP00000303909:D30N	ENSP00000303909:D30N	D	-	1	0	ABR	975426	1.000000	0.71417	1.000000	0.80357	0.613000	0.37349	5.071000	0.64382	2.567000	0.86603	0.561000	0.74099	GAC	C|0.992;T|0.008	0.008	strong		0.627	ABR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206675.4		
MUC6	4588	hgsc.bcm.edu	37	11	1017522	1017522	+	Missense_Mutation	SNP	T	T	G	rs199592093		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1017522T>G	ENST00000421673.2	-	31	5329	c.5279A>C	c.(5278-5280)gAa>gCa	p.E1760A		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1760	Approximate repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		TGAGGTGACTTCAGGATGGTG	0.567																																					p.E1760A		Atlas-SNP	.											.	MUC6	408	.	0			c.A5279C						PASS	.						751.0	715.0	727.0					11																	1017522		2200	4294	6494	SO:0001583	missense	4588	exon31			GTGACTTCAGGAT	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.5279A>C	11.37:g.1017522T>G	ENSP00000406861:p.Glu1760Ala	479.0	0.0	0		596.0	32.0	0.0536913	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	-	0.655	-0.808100	0.02819	.	.	ENSG00000184956	ENST00000421673	T	0.20332	2.08	0.235	0.235	0.15431	.	.	.	.	.	T	0.25195	0.0612	L	0.38175	1.15	0.09310	N	1	D	0.67145	0.996	D	0.70227	0.968	T	0.11966	-1.0566	8	0.05833	T	0.94	.	.	.	.	.	1760	Q6W4X9	MUC6_HUMAN	A	1760	ENSP00000406861:E1760A	ENSP00000406861:E1760A	E	-	2	0	MUC6	1007522	0.000000	0.05858	0.002000	0.10522	0.045000	0.14185	-3.356000	0.00499	0.263000	0.21812	0.260000	0.18958	GAA	.	.	weak		0.567	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
COL18A1	80781	hgsc.bcm.edu	37	21	46875683	46875683	+	Missense_Mutation	SNP	C	C	G	rs61739237	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46875683C>G	ENST00000359759.4	+	1	260	c.239C>G	c.(238-240)cCt>cGt	p.P80R	COL18A1_ENST00000400337.2_Intron|COL18A1_ENST00000355480.5_Missense_Mutation_p.P80R			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	80					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|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)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		CCTGGCAGCCCTGAGCCACCC	0.677													C|||	99	0.0197684	0.0688	0.0115	5008	,	,		16653	0.0		0.0	False		,,,				2504	0.0				p.P80R		Atlas-SNP	.											.	COL18A1	129	.	0			c.C239G						PASS	.	C	,ARG/PRO	249,3887		6,237,1825	45.0	58.0	54.0		,239	1.3	0.0	21	dbSNP_129	54	1,8375		0,1,4187	yes	intron,missense	COL18A1	NM_130445.2,NM_030582.3	,103	6,238,6012	GG,GC,CC		0.0119,6.0203,1.9981	,benign	,80/1520	46875683	250,12262	2068	4188	6256	SO:0001583	missense	80781	exon1			GCAGCCCTGAGCC		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.239C>G	21.37:g.46875683C>G	ENSP00000352798:p.Pro80Arg	107.0	0.0	0		114.0	47.0	0.412281	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		54	0.024725274725274724	50	0.1016260162601626	4	0.011049723756906077	0	0.0	0	0.0	C	7.818	0.717135	0.15372	0.060203	1.19E-4	ENSG00000182871	ENST00000355480;ENST00000359759;ENST00000539645	T;T	0.32515	1.45;1.45	3.31	1.34	0.21922	Domain of unknown function DUF959, collagen XVIII, N-terminal (1);	2.030890	0.02888	N	0.133800	T	0.00845	0.0028	L	0.42245	1.32	0.09310	N	1	B;B	0.14805	0.011;0.009	B;B	0.17433	0.018;0.011	T	0.27123	-1.0083	10	0.72032	D	0.01	.	10.5387	0.45020	0.0:0.6186:0.3814:0.0	rs61739237	80;80	P39060;P39060-1	COIA1_HUMAN;.	R	80	ENSP00000347665:P80R;ENSP00000352798:P80R	ENSP00000347665:P80R	P	+	2	0	COL18A1	45700111	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	0.377000	0.20552	0.174000	0.19809	0.491000	0.48974	CCT	C|0.976;G|0.024	0.024	strong		0.677	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
DHCR7	1717	hgsc.bcm.edu	37	11	71152459	71152459	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71152459C>T	ENST00000355527.3	-	6	716	c.440G>A	c.(439-441)gGc>gAc	p.G147D	DHCR7_ENST00000407721.2_Missense_Mutation_p.G147D	NM_001163817.1|NM_001360.2	NP_001157289.1|NP_001351.2	Q9UBM7	DHCR7_HUMAN	7-dehydrocholesterol reductase	147			G -> D (in SLOS). {ECO:0000269|PubMed:10677299}.		blood vessel development (GO:0001568)|cell differentiation (GO:0030154)|cholesterol biosynthetic process (GO:0006695)|lung development (GO:0030324)|multicellular organism growth (GO:0035264)|post-embryonic development (GO:0009791)|regulation of cell proliferation (GO:0042127)|regulation of cholesterol biosynthetic process (GO:0045540)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear outer membrane (GO:0005640)	7-dehydrocholesterol reductase activity (GO:0047598)			endometrium(2)|kidney(1)|large_intestine(3)|liver(1)|lung(10)|ovary(1)|skin(1)	19						GGCTTGCAGGCCATTGATCTG	0.547									Smith-Lemli-Opitz syndrome																												p.G147D		Atlas-SNP	.											DHCR7_ENST00000355527,NS,haematopoietic_neoplasm,-1,2	DHCR7	98	2	0			c.G440A	GRCh37	CM000680	DHCR7	M		PASS	.						135.0	105.0	115.0					11																	71152459		2200	4294	6494	SO:0001583	missense	1717	exon6	Familial Cancer Database	SLOS type I & II	TGCAGGCCATTGA	AF034544	CCDS8200.1	11q13.4	2014-09-17	2004-02-13				1.3.1.21		2860	protein-coding gene	gene with protein product		602858	"""Smith-Lemli-Opitz syndrome"""	SLOS		9465114, 9634533	Standard	NM_001360		Approved		uc001oql.3	Q9UBM7		ENST00000355527.3:c.440G>A	11.37:g.71152459C>T	ENSP00000347717:p.Gly147Asp	155.0	0.0	0		142.0	68.0	0.478873	NM_001163817	B2R6Z2|O60492|O60717	Missense_Mutation	SNP	ENST00000355527.3	37	CCDS8200.1	.	.	.	.	.	.	.	.	.	.	C	16.46	3.128197	0.56721	.	.	ENSG00000172893	ENST00000407721;ENST00000355527;ENST00000524694;ENST00000527316;ENST00000526780	D;D;D;D	0.99523	-4.85;-4.85;-4.85;-6.08	4.14	4.14	0.48551	.	0.000000	0.85682	D	0.000000	D	0.99625	0.9863	H	0.94306	3.52	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97590	1.0116	10	0.87932	D	0	-30.5655	14.271	0.66152	0.0:1.0:0.0:0.0	.	147	Q9UBM7	DHCR7_HUMAN	D	147;147;159;115;147	ENSP00000384739:G147D;ENSP00000347717:G147D;ENSP00000435047:G115D;ENSP00000435668:G147D	ENSP00000347717:G147D	G	-	2	0	DHCR7	70830107	1.000000	0.71417	0.838000	0.33150	0.133000	0.20885	6.765000	0.74965	2.035000	0.60131	0.313000	0.20887	GGC	.	.	none		0.547	DHCR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394243.1	NM_001360	
KIR3DL1	3811	hgsc.bcm.edu	37	19	55329851	55329851	+	Missense_Mutation	SNP	A	A	G	rs145262243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55329851A>G	ENST00000391728.4	+	3	185	c.152A>G	c.(151-153)tAt>tGt	p.Y51C	KIR3DL1_ENST00000538269.1_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000326542.7_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000541392.1_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000402254.2_Missense_Mutation_p.Y51C|KIR3DL1_ENST00000358178.4_Intron	NM_013289.2	NP_037421.2	P43629	KI3L1_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 1	51	Ig-like C2-type 1.				immune response (GO:0006955)|regulation of immune response (GO:0050776)|signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	HLA-B specific inhibitory MHC class I receptor activity (GO:0030109)			breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	11				GBM - Glioblastoma multiforme(193;0.0192)		CGGTGTCACTATCGTCATAGG	0.517													a|||	25	0.00499201	0.0	0.0144	5008	,	,		13050	0.0		0.008	False		,,,				2504	0.0072				p.Y51C		Atlas-SNP	.											.	KIR3DL1	174	.	0			c.A152G						PASS	.	A	CYS/TYR	6,4344		0,6,2169	101.0	102.0	101.0		152	-2.5	0.0	19	dbSNP_134	101	100,8154		20,60,4047	no	missense	KIR3DL1	NM_013289.2	194	20,66,6216	GG,GA,AA		1.2115,0.1379,0.841		51/445	55329851	106,12498	2175	4127	6302	SO:0001583	missense	3811	exon3			GTCACTATCGTCA	L41269	CCDS42621.1	19q13.4	2014-05-22			ENSG00000167633	ENSG00000167633		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6338	protein-coding gene	gene with protein product		604946		KIR		7716543, 7749980	Standard	NM_013289		Approved	cl-2, NKB1, cl-11, nkat3, NKB1B, AMB11, CD158e1/2, CD158E1, CD158e2		P43629	OTTHUMG00000065933	ENST00000391728.4:c.152A>G	19.37:g.55329851A>G	ENSP00000375608:p.Tyr51Cys	26.0	0.0	0		35.0	20.0	0.571429	NM_013289	O43473|Q14946|Q16541	Missense_Mutation	SNP	ENST00000391728.4	37	CCDS42621.1	9	0.004120879120879121	0	0.0	6	0.016574585635359115	0	0.0	3	0.00395778364116095	A	9.452	1.090889	0.20471	0.001379	0.012115	ENSG00000167633	ENST00000402254;ENST00000538269;ENST00000541392;ENST00000355608;ENST00000391728;ENST00000326542	T;T;T;T;T	0.12361	2.69;2.69;2.69;2.69;2.69	1.25	-2.51	0.06365	Immunoglobulin subtype (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.14743	0.0356	M	0.75447	2.3	0.09310	N	1	D;B	0.89917	1.0;0.022	D;B	0.91635	0.999;0.034	T	0.11591	-1.0581	9	0.66056	D	0.02	.	2.0319	0.03531	0.3118:0.4675:0.0:0.2207	.	51;51	F6QF33;P43629	.;KI3L1_HUMAN	C	51;51;51;29;51;51	ENSP00000384528:Y51C;ENSP00000443350:Y51C;ENSP00000442355:Y51C;ENSP00000375608:Y51C;ENSP00000326868:Y51C	ENSP00000326868:Y51C	Y	+	2	0	KIR3DL1	60021663	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.542000	0.06091	-0.292000	0.08999	-1.429000	0.01096	TAT	A|0.992;G|0.008	0.008	strong		0.517	KIR3DL1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000141238.1	NM_013289	
TRIM17	51127	hgsc.bcm.edu	37	1	228602459	228602459	+	Silent	SNP	G	G	A	rs142505325	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228602459G>A	ENST00000366697.2	-	1	1271	c.315C>T	c.(313-315)ccC>ccT	p.P105P	TRIM17_ENST00000366698.2_Silent_p.P105P|TRIM17_ENST00000295033.3_Silent_p.P105P|TRIM17_ENST00000456946.2_Silent_p.P105P			Q9Y577	TRI17_HUMAN	tripartite motif containing 17	105					protein autoubiquitination (GO:0051865)	intracellular (GO:0005622)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	10		Prostate(94;0.0724)				AAAGCTTGAGGGGCTCGTGGT	0.657													G|||	12	0.00239617	0.0	0.0014	5008	,	,		17247	0.0		0.004	False		,,,				2504	0.0072				p.P105P		Atlas-SNP	.											.	TRIM17	66	.	0			c.C315T						PASS	.	G	,,	0,4406		0,0,2203	77.0	84.0	82.0		315,315,315	0.3	1.0	1	dbSNP_134	82	10,8590	6.4+/-24.3	0,10,4290	no	coding-synonymous,coding-synonymous,coding-synonymous	TRIM17	NM_001024940.2,NM_001134855.1,NM_016102.3	,,	0,10,6493	AA,AG,GG		0.1163,0.0,0.0769	,,	105/478,105/344,105/478	228602459	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	51127	exon2			CTTGAGGGGCTCG	AF156271	CCDS1571.1, CCDS44327.1	1q42	2013-01-09	2011-01-25	2001-11-30	ENSG00000162931	ENSG00000162931		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	13430	protein-coding gene	gene with protein product	"""ring finger protein 16"", ""RING finger protein terf"", ""testis RING finger protein"""	606123	"""tripartite motif-containing 17"""	RNF16		9792805, 10894938	Standard	NM_016102		Approved	terf, RBCC	uc001hsv.3	Q9Y577	OTTHUMG00000039974	ENST00000366697.2:c.315C>T	1.37:g.228602459G>A		115.0	0.0	0		122.0	56.0	0.459016	NM_001024940	B4DVJ2|Q5VST8	Silent	SNP	ENST00000366697.2	37	CCDS1571.1																																																																																			G|0.999;A|0.001	0.001	strong		0.657	TRIM17-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096439.2	NM_016102	
KCNK13	56659	hgsc.bcm.edu	37	14	90651079	90651079	+	Missense_Mutation	SNP	G	G	A	rs150186575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:90651079G>A	ENST00000282146.4	+	2	1400	c.959G>A	c.(958-960)cGg>cAg	p.R320Q		NM_022054.2	NP_071337.2	Q9HB14	KCNKD_HUMAN	potassium channel, subfamily K, member 13	320					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)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(12)|prostate(1)|skin(4)	25		all_cancers(154;0.186)				GGCAGCGTCCGGAACCGCTGC	0.597																																					p.R320Q		Atlas-SNP	.											.	KCNK13	76	.	0			c.G959A						PASS	.						65.0	69.0	68.0					14																	90651079		2203	4300	6503	SO:0001583	missense	56659	exon2			GCGTCCGGAACCG	AF287303	CCDS9889.1	14q32.11	2012-03-07				ENSG00000152315		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Two-P"""	6275	protein-coding gene	gene with protein product		607367				11060316, 16382106	Standard	NM_022054		Approved	K2p13.1, THIK-1, THIK1	uc001xye.1	Q9HB14		ENST00000282146.4:c.959G>A	14.37:g.90651079G>A	ENSP00000282146:p.Arg320Gln	129.0	0.0	0		141.0	74.0	0.524823	NM_022054	B5TJL8|Q96E79	Missense_Mutation	SNP	ENST00000282146.4	37	CCDS9889.1	.	.	.	.	.	.	.	.	.	.	G	8.030	0.761526	0.15914	.	.	ENSG00000152315	ENST00000282146	T	0.12255	2.7	5.28	-0.111	0.13576	.	2.504590	0.01759	N	0.030439	T	0.11879	0.0289	L	0.36672	1.1	0.46981	D	0.999276	B	0.06786	0.001	B	0.09377	0.004	T	0.46219	-0.9207	10	0.07813	T	0.8	.	10.1408	0.42734	0.3118:0.0:0.6882:0.0	.	320	Q9HB14	KCNKD_HUMAN	Q	320	ENSP00000282146:R320Q	ENSP00000282146:R320Q	R	+	2	0	KCNK13	89720832	0.952000	0.32445	0.001000	0.08648	0.007000	0.05969	4.029000	0.57253	-0.355000	0.08199	0.655000	0.94253	CGG	G|0.999;T|0.001	.	alt		0.597	KCNK13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411251.1	NM_022054	
DST	667	hgsc.bcm.edu	37	6	56505175	56505175	+	Silent	SNP	T	T	A	rs113432929	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:56505175T>A	ENST00000361203.3	-	14	1630	c.1623A>T	c.(1621-1623)tcA>tcT	p.S541S	DST_ENST00000518935.1_Silent_p.S215S|DST_ENST00000370788.2_Silent_p.S541S|DST_ENST00000370754.5_Silent_p.S719S|DST_ENST00000446842.2_Silent_p.S215S|DST_ENST00000244364.6_Silent_p.S215S|DST_ENST00000370765.6_Silent_p.S215S|DST_ENST00000312431.6_Silent_p.S541S|DST_ENST00000421834.2_Silent_p.S541S|DST_ENST00000370769.4_Silent_p.S541S			Q03001	DYST_HUMAN	dystonin	541					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AAGTCATCCCTGATGACAGGC	0.483													T|||	11	0.00219649	0.0	0.0	5008	,	,		18999	0.0		0.005	False		,,,				2504	0.0061				p.S215S		Atlas-SNP	.											.	DST	1427	.	0			c.A645T						PASS	.	T	,	4,4402	8.1+/-20.4	0,4,2199	139.0	141.0	141.0		645,645	-4.8	0.6	6	dbSNP_132	141	36,8564	25.1+/-72.6	0,36,4264	yes	coding-synonymous,coding-synonymous	DST	NM_001723.5,NM_015548.4	,	0,40,6463	AA,AT,TT		0.4186,0.0908,0.3076	,	215/2650,215/5172	56505175	40,12966	2203	4300	6503	SO:0001819	synonymous_variant	667	exon4			CATCCCTGATGAC	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.1623A>T	6.37:g.56505175T>A		168.0	0.0	0		156.0	69.0	0.442308	NM_001723	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Silent	SNP	ENST00000361203.3	37																																																																																				T|0.997;A|0.003	0.003	strong		0.483	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
MAP4K1	11184	hgsc.bcm.edu	37	19	39101772	39101772	+	Splice_Site	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:39101772C>T	ENST00000591517.1	-	11	757	c.729G>A	c.(727-729)tgG>tgA	p.W243*	MAP4K1_ENST00000396857.2_Splice_Site_p.W243*|MAP4K1_ENST00000586296.1_Splice_Site_p.W243*|MAP4K1_ENST00000423454.2_Intron|MAP4K1_ENST00000589002.1_Intron|MAP4K1_ENST00000589130.1_Splice_Site_p.W239*	NM_007181.4	NP_009112.1	Q92918	M4K1_HUMAN	mitogen-activated protein kinase kinase kinase kinase 1	243	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|activation of MAPKKK activity (GO:0000185)|cell proliferation (GO:0008283)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|response to stress (GO:0006950)	membrane (GO:0016020)	ATP binding (GO:0005524)|MAP kinase kinase kinase kinase activity (GO:0008349)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(24)|ovary(1)|prostate(1)|skin(5)|stomach(1)|urinary_tract(1)	44	all_cancers(60;6.42e-06)|Ovarian(47;0.103)		Lung(45;0.000751)|LUSC - Lung squamous cell carcinoma(53;0.00272)			AGGCAGCCGACCTTGGGAAGA	0.577																																					p.W243X		Atlas-SNP	.											.	MAP4K1	165	.	0			c.G729A						PASS	.						99.0	110.0	106.0					19																	39101772		1982	4153	6135	SO:0001630	splice_region_variant	11184	exon11			AGCCGACCTTGGG	U66464	CCDS42564.1, CCDS59385.1	19q13.1-q13.4	2011-06-09				ENSG00000104814	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6863	protein-coding gene	gene with protein product	"""hematopoietic progenitor kinase 1"""	601983				8824585	Standard	NM_001042600		Approved	HPK1	uc002oix.1	Q92918		ENST00000591517.1:c.729-1G>A	19.37:g.39101772C>T		117.0	0.0	0		164.0	65.0	0.396341	NM_007181		Nonsense_Mutation	SNP	ENST00000591517.1	37	CCDS59385.1	.	.	.	.	.	.	.	.	.	.	C	37	6.181791	0.97352	.	.	ENSG00000104814	ENST00000396857;ENST00000221409	.	.	.	4.21	4.21	0.49690	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.4865	0.75571	0.0:1.0:0.0:0.0	.	.	.	.	X	243	.	ENSP00000221409:W243X	W	-	3	0	MAP4K1	43793612	1.000000	0.71417	0.999000	0.59377	0.823000	0.46562	7.190000	0.77755	2.175000	0.68902	0.555000	0.69702	TGG	.	.	none		0.577	MAP4K1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453390.1	NM_001042600	Nonsense_Mutation
DNAH14	127602	hgsc.bcm.edu	37	1	225155191	225155191	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:225155191C>G	ENST00000445597.2	+	7	938	c.938C>G	c.(937-939)tCc>tGc	p.S313C	DNAH14_ENST00000439375.2_Missense_Mutation_p.S186C|DNAH14_ENST00000366848.1_Missense_Mutation_p.S186C|DNAH14_ENST00000400952.3_Missense_Mutation_p.S186C|DNAH14_ENST00000366849.1_Missense_Mutation_p.S186C|DNAH14_ENST00000366850.3_Missense_Mutation_p.S186C|DNAH14_ENST00000430092.1_Missense_Mutation_p.S186C			Q0VDD8	DYH14_HUMAN	dynein, axonemal, heavy chain 14	313					microtubule-based movement (GO:0007018)	cilium (GO:0005929)|cytoplasm (GO:0005737)|dynein complex (GO:0030286)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(8)|kidney(4)|large_intestine(2)|lung(2)|skin(2)|stomach(1)	27						AGTCCTAAATCCCTTTACAAT	0.308																																					p.S186C		Atlas-SNP	.											.	DNAH14	300	.	0			c.C557G						PASS	.						152.0	144.0	147.0					1																	225155191		1824	4085	5909	SO:0001583	missense	127602	exon6			CTAAATCCCTTTA	U61741	CCDS41472.1, CCDS44322.1	1q42.13	2009-02-12	2006-09-04		ENSG00000185842	ENSG00000185842		"""Axonemal dyneins"""	2945	protein-coding gene	gene with protein product		603341	"""dynein, axonemal, heavy polypeptide 14"", ""chromosome 1 open reading frame 67"""	C1orf67		8812413	Standard	NM_144989		Approved	Dnahc14, HL-18, HL18, DKFZp781B1548, MGC27277	uc001how.2	Q0VDD8	OTTHUMG00000037447	ENST00000445597.2:c.938C>G	1.37:g.225155191C>G	ENSP00000409472:p.Ser313Cys	94.0	0.0	0		90.0	37.0	0.411111	NM_144989	A6NG62|A6NNL2|Q0VDD9|Q4VXC7|Q4VXG4|Q4VXG5|Q5VU33|Q5VU34	Missense_Mutation	SNP	ENST00000445597.2	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	9.155|9.155	1.017345|1.017345	0.19355|0.19355	.|.	.|.	ENSG00000185842|ENSG00000185842	ENST00000433124|ENST00000445597;ENST00000430092;ENST00000366850;ENST00000400952;ENST00000366849;ENST00000366848;ENST00000439375	.|T;T;T;T;T;T;T	.|0.34275	.|2.46;1.44;1.37;1.4;1.44;1.37;1.44	5.63|5.63	-2.47|-2.47	0.06442|0.06442	.|.	.|2.216230	.|0.02014	.|N	.|0.047252	T|T	0.29321|0.29321	0.0730|0.0730	.|.	.|.	.|.	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.28584	.|0.071;0.216;0.071;0.042	.|B;B;B;B	.|0.30572	.|0.117;0.117;0.117;0.054	T|T	0.35895|0.35895	-0.9770|-0.9770	4|9	.|0.48119	.|T	.|0.1	.|.	9.1048|9.1048	0.36692|0.36692	0.0:0.4285:0.4519:0.1195|0.0:0.4285:0.4519:0.1195	.|.	.|186;186;186;313	.|Q0VDD8-4;Q0VDD8-3;Q0VDD8-2;Q0VDD8	.|.;.;.;DYH14_HUMAN	A|C	84|313;186;186;186;186;186;186	.|ENSP00000409472:S313C;ENSP00000414402:S186C;ENSP00000355815:S186C;ENSP00000383737:S186C;ENSP00000355814:S186C;ENSP00000355813:S186C;ENSP00000392061:S186C	.|ENSP00000355813:S186C	P|S	+|+	1|2	0|0	DNAH14|DNAH14	223221814|223221814	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.573000|0.573000	0.36030|0.36030	0.045000|0.045000	0.14013|0.14013	-0.324000|-0.324000	0.08589|0.08589	0.543000|0.543000	0.68304|0.68304	CCC|TCC	.	.	none		0.308	DNAH14-007	PUTATIVE	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000331217.3	XM_059166	
LRIG1	26018	hgsc.bcm.edu	37	3	66432717	66432717	+	Missense_Mutation	SNP	T	T	C	rs148946048	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:66432717T>C	ENST00000273261.3	-	16	3121	c.2597A>G	c.(2596-2598)aAt>aGt	p.N866S	LRIG1_ENST00000496559.2_5'UTR|LRIG1_ENST00000383703.3_Missense_Mutation_p.N843S|SLC25A26_ENST00000536651.1_Intron	NM_015541.2	NP_056356.2	Q96JA1	LRIG1_HUMAN	leucine-rich repeats and immunoglobulin-like domains 1	866					innervation (GO:0060384)|otolith morphogenesis (GO:0032474)|sensory perception of sound (GO:0007605)	integral component of membrane (GO:0016021)				NS(2)|breast(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(12)|ovary(3)|prostate(1)|skin(4)|stomach(4)|urinary_tract(1)	42		Lung NSC(201;0.0101)		BRCA - Breast invasive adenocarcinoma(55;0.00047)		AATGTGCCCATTGGCCTGAGG	0.567													T|||	36	0.0071885	0.0265	0.0014	5008	,	,		20726	0.0		0.0	False		,,,				2504	0.0				p.N866S		Atlas-SNP	.											.	LRIG1	138	.	0			c.A2597G						PASS	.	T	SER/ASN	72,4334	67.0+/-104.6	1,70,2132	143.0	144.0	143.0		2597	1.6	0.9	3	dbSNP_134	143	3,8597	3.0+/-9.4	0,3,4297	yes	missense	LRIG1	NM_015541.2	46	1,73,6429	CC,CT,TT		0.0349,1.6341,0.5767	benign	866/1094	66432717	75,12931	2203	4300	6503	SO:0001583	missense	26018	exon16			TGCCCATTGGCCT	AB050468	CCDS33783.1	3p14	2013-01-14			ENSG00000144749	ENSG00000144749		"""Immunoglobulin superfamily / I-set domain containing"""	17360	protein-coding gene	gene with protein product	"""ortholog of mouse integral membrane glycoprotein LIG-1"", ""leucine-rich repeat protein LRIG1"""	608868				11414704, 12234026	Standard	NM_015541		Approved	LIG-1, DKFZP586O1624, LIG1	uc003dmx.3	Q96JA1	OTTHUMG00000158727	ENST00000273261.3:c.2597A>G	3.37:g.66432717T>C	ENSP00000273261:p.Asn866Ser	113.0	0.0	0		100.0	55.0	0.55	NM_015541	Q6IQ51|Q96CF9|Q9BYB8|Q9UFI4	Missense_Mutation	SNP	ENST00000273261.3	37	CCDS33783.1	9	0.004120879120879121	9	0.018292682926829267	0	0.0	0	0.0	0	0.0	T	12.51	1.960779	0.34565	0.016341	3.49E-4	ENSG00000144749	ENST00000273261;ENST00000383703;ENST00000383702	T;T	0.67171	-0.14;-0.25	5.5	1.56	0.23342	.	0.106092	0.64402	N	0.000008	T	0.36331	0.0963	L	0.45581	1.43	0.33964	D	0.645981	B;B;B	0.15141	0.009;0.001;0.012	B;B;B	0.17979	0.02;0.005;0.005	T	0.46190	-0.9209	10	0.34782	T	0.22	.	5.3801	0.16186	0.0:0.2128:0.1362:0.651	.	843;866;866	Q96JA1-2;Q5XWD3;Q96JA1	.;.;LRIG1_HUMAN	S	866;843;769	ENSP00000273261:N866S;ENSP00000373208:N843S	ENSP00000273261:N866S	N	-	2	0	LRIG1	66515407	0.940000	0.31905	0.906000	0.35671	0.814000	0.46013	0.909000	0.28558	0.373000	0.24621	-0.264000	0.10439	AAT	T|0.995;C|0.005	0.005	strong		0.567	LRIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351930.1	NM_015541	
JPH3	57338	hgsc.bcm.edu	37	16	87678302	87678302	+	Missense_Mutation	SNP	C	C	T	rs144403955	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:87678302C>T	ENST00000284262.2	+	2	1063	c.821C>T	c.(820-822)gCg>gTg	p.A274V		NM_020655.2	NP_065706.2	Q8WXH2	JPH3_HUMAN	junctophilin 3	274					calcium ion transport into cytosol (GO:0060402)|exploration behavior (GO:0035640)|learning (GO:0007612)|locomotion (GO:0040011)|memory (GO:0007613)|neuromuscular process controlling balance (GO:0050885)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of ryanodine-sensitive calcium-release channel activity (GO:0060314)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|junctional sarcoplasmic reticulum membrane (GO:0014701)|plasma membrane (GO:0005886)	calcium-release channel activity (GO:0015278)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				BRCA - Breast invasive adenocarcinoma(80;0.0287)		GCCGAGCTGGCGGTCATCGAG	0.667													C|||	4	0.000798722	0.0	0.0014	5008	,	,		12745	0.001		0.001	False		,,,				2504	0.001				p.A274V		Atlas-SNP	.											.	JPH3	95	.	0			c.C821T						PASS	.	C	VAL/ALA	0,4396		0,0,2198	75.0	68.0	70.0		821	4.9	0.9	16	dbSNP_134	70	15,8585	11.9+/-42.8	0,15,4285	yes	missense	JPH3	NM_020655.2	64	0,15,6483	TT,TC,CC		0.1744,0.0,0.1154	benign	274/749	87678302	15,12981	2198	4300	6498	SO:0001583	missense	57338	exon2			AGCTGGCGGTCAT	AB042636	CCDS10962.1	16q24.3	2008-02-05	2002-11-13		ENSG00000154118	ENSG00000154118			14203	protein-coding gene	gene with protein product		605268	"""trinucleotide repeat containing 22"""	TNRC22		10949023, 10891348	Standard	NM_020655		Approved	JP-3, CAGL237, HDL2, JP3	uc002fkd.4	Q8WXH2	OTTHUMG00000137656	ENST00000284262.2:c.821C>T	16.37:g.87678302C>T	ENSP00000284262:p.Ala274Val	46.0	0.0	0		60.0	34.0	0.566667	NM_020655	D3DUN2|Q8N471|Q9HDC3|Q9HDC4	Missense_Mutation	SNP	ENST00000284262.2	37	CCDS10962.1	3	0.0013736263736263737	0	0.0	0	0.0	1	0.0017482517482517483	2	0.002638522427440633	C	13.94	2.387189	0.42308	0.0	0.001744	ENSG00000154118	ENST00000537256;ENST00000284262	T	0.46819	0.86	4.91	4.91	0.64330	.	0.252030	0.40144	N	0.001172	T	0.28466	0.0704	N	0.08118	0	0.38661	D	0.952087	B	0.06786	0.001	B	0.09377	0.004	T	0.13926	-1.0491	10	0.13470	T	0.59	.	17.1059	0.86663	0.0:1.0:0.0:0.0	.	274	Q8WXH2	JPH3_HUMAN	V	137;274	ENSP00000284262:A274V	ENSP00000284262:A274V	A	+	2	0	JPH3	86235803	0.998000	0.40836	0.884000	0.34674	0.875000	0.50365	3.934000	0.56553	2.286000	0.76751	0.561000	0.74099	GCG	C|0.998;T|0.002	0.002	strong		0.667	JPH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269108.2		
FOXK2	3607	hgsc.bcm.edu	37	17	80543901	80543901	+	Silent	SNP	C	C	T	rs61737960	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80543901C>T	ENST00000335255.5	+	7	1575	c.1401C>T	c.(1399-1401)gtC>gtT	p.V467V	RP13-638C3.3_ENST00000575085.1_RNA	NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	467					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			AGCCACCCGTCGTGCAGACGG	0.627													C|||	58	0.0115815	0.0121	0.0202	5008	,	,		16342	0.0		0.0179	False		,,,				2504	0.0102				p.V467V		Atlas-SNP	.											.	FOXK2	46	.	0			c.C1401T						PASS	.	C		30,4370	37.6+/-69.7	0,30,2170	66.0	53.0	58.0		1401	-10.6	0.0	17	dbSNP_129	58	173,8413	79.2+/-141.9	2,169,4122	no	coding-synonymous	FOXK2	NM_004514.3		2,199,6292	TT,TC,CC		2.0149,0.6818,1.5632		467/661	80543901	203,12783	2200	4293	6493	SO:0001819	synonymous_variant	3607	exon7			ACCCGTCGTGCAG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.1401C>T	17.37:g.80543901C>T		85.0	0.0	0		98.0	48.0	0.489796	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Silent	SNP	ENST00000335255.5	37	CCDS11813.1																																																																																			C|0.986;T|0.014	0.014	strong		0.627	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
HNF1A	6927	hgsc.bcm.edu	37	12	121435342	121435342	+	Silent	SNP	C	C	T	rs544842497|rs2259820	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121435342C>T	ENST00000257555.6	+	7	1601	c.1375C>T	c.(1375-1377)Ctg>Ttg	p.L459L	HNF1A_ENST00000400024.2_Silent_p.L459L|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000538626.1_Silent_p.L41L|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Silent_p.L459L|HNF1A_ENST00000541395.1_Silent_p.L459L			P20823	HNF1A_HUMAN	HNF1 homeobox A	459					glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					CCTGACCACCCTGCAGCCCGT	0.667									Hepatic Adenoma, Familial Clustering of				c|||	1586	0.316693	0.1089	0.3501	5008	,	,		17758	0.4732		0.3161	False		,,,				2504	0.4131				p.L459L		Atlas-SNP	.											.	HNF1A	302	.	0			c.C1375T						PASS	.	C		529,3877	232.0+/-245.7	41,447,1715	33.0	35.0	34.0		1375	4.6	1.0	12	dbSNP_100	34	2675,5923	412.6+/-350.9	434,1807,2058	no	coding-synonymous	HNF1A	NM_000545.5		475,2254,3773	TT,TC,CC		31.1119,12.0064,24.6386		459/632	121435342	3204,9800	2203	4299	6502	SO:0001819	synonymous_variant	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	ACCACCCTGCAGC	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.1375C>T	12.37:g.121435342C>T		116.0	0.0	0		103.0	45.0	0.436893	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Silent	SNP	ENST00000257555.6	37	CCDS9209.1																																																																																			C|0.718;T|0.282	0.282	strong		0.667	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
CALCRL	10203	hgsc.bcm.edu	37	2	188245439	188245439	+	Missense_Mutation	SNP	A	A	G	rs61739909		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:188245439A>G	ENST00000409998.1	-	7	1041	c.260T>C	c.(259-261)cTc>cCc	p.L87P	AC007319.1_ENST00000412276.1_RNA|CALCRL_ENST00000392370.3_Missense_Mutation_p.L87P|CALCRL_ENST00000410068.1_Missense_Mutation_p.L87P|AC007319.1_ENST00000453517.1_RNA			Q16602	CALRL_HUMAN	calcitonin receptor-like	87					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|angiogenesis (GO:0001525)|calcium ion transport (GO:0006816)|cAMP biosynthetic process (GO:0006171)|cellular response to sucrose stimulus (GO:0071329)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|heart development (GO:0007507)|negative regulation of inflammatory response (GO:0050728)|positive regulation of cAMP biosynthetic process (GO:0030819)|positive regulation of smooth muscle cell proliferation (GO:0048661)|protein transport (GO:0015031)|receptor internalization (GO:0031623)|regulation of muscle contraction (GO:0006937)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	adrenomedullin receptor activity (GO:0001605)|calcitonin gene-related polypeptide receptor activity (GO:0001635)|calcitonin receptor activity (GO:0004948)|G-protein coupled receptor activity (GO:0004930)|protein transporter activity (GO:0008565)			endometrium(1)|large_intestine(7)|lung(21)|ovary(1)|prostate(1)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0554)|Epithelial(96;0.227)			ATCAGGGCAGAGCTGCATTGA	0.408													A|||	1	0.000199681	0.0	0.0	5008	,	,		13904	0.0		0.001	False		,,,				2504	0.0				p.L87P		Atlas-SNP	.											.	CALCRL	73	.	0			c.T260C						PASS	.	A	PRO/LEU	0,4406		0,0,2203	68.0	66.0	67.0		260	-0.0	1.0	2	dbSNP_129	67	21,8579	14.6+/-50.1	1,19,4280	yes	missense	CALCRL	NM_005795.4	98	1,19,6483	GG,GA,AA		0.2442,0.0,0.1615	benign	87/462	188245439	21,12985	2203	4300	6503	SO:0001583	missense	10203	exon5			GGGCAGAGCTGCA	U17473	CCDS2293.1	2q21.1-q21.3	2012-08-10			ENSG00000064989	ENSG00000064989		"""GPCR / Class B : Calcitonin receptors"""	16709	protein-coding gene	gene with protein product		114190				7818539, 8626685	Standard	NM_005795		Approved	CGRPR, CRLR	uc010frt.4	Q16602	OTTHUMG00000132636	ENST00000409998.1:c.260T>C	2.37:g.188245439A>G	ENSP00000386972:p.Leu87Pro	192.0	0.0	0		174.0	96.0	0.551724	NM_001271751	A8K6G5|A8KAD3|Q53S02|Q53TS5	Missense_Mutation	SNP	ENST00000409998.1	37	CCDS2293.1	.	.	.	.	.	.	.	.	.	.	A	13.48	2.249542	0.39797	0.0	0.002442	ENSG00000064989	ENST00000392370;ENST00000409998;ENST00000410068	T;T;T	0.46063	0.88;0.88;0.88	5.42	-0.0292	0.13919	GPCR, family 2, secretin-like, conserved site (1);GPCR, family 2, extracellular hormone receptor domain (3);	0.519591	0.18887	N	0.128407	T	0.15522	0.0374	N	0.04335	-0.225	0.47949	D	0.999551	B	0.31519	0.327	B	0.37267	0.245	T	0.25537	-1.0129	10	0.02654	T	1	.	4.3429	0.11119	0.518:0.1646:0.0:0.3174	.	87	Q16602	CALRL_HUMAN	P	87	ENSP00000376177:L87P;ENSP00000386972:L87P;ENSP00000387190:L87P	ENSP00000376177:L87P	L	-	2	0	CALCRL	187953684	0.998000	0.40836	0.996000	0.52242	0.996000	0.88848	0.409000	0.21082	-0.162000	0.10964	0.528000	0.53228	CTC	A|0.999;G|0.001	0.001	strong		0.408	CALCRL-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334648.1	NM_005795	
ERAP2	64167	hgsc.bcm.edu	37	5	96231056	96231056	+	Missense_Mutation	SNP	T	T	G	rs34261036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:96231056T>G	ENST00000437043.3	+	7	1943	c.1232T>G	c.(1231-1233)cTg>cGg	p.L411R	ERAP2_ENST00000379904.4_Missense_Mutation_p.L366R|CTD-2260A17.2_ENST00000501338.1_Intron|ERAP2_ENST00000515095.1_3'UTR	NM_001130140.1|NM_022350.3	NP_001123612.1|NP_071745.1	Q6P179	ERAP2_HUMAN	endoplasmic reticulum aminopeptidase 2	411			L -> R (in dbSNP:rs34261036).		antigen processing and presentation of endogenous peptide antigen via MHC class I (GO:0019885)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|regulation of blood pressure (GO:0008217)	endoplasmic reticulum lumen (GO:0005788)|integral component of membrane (GO:0016021)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(6)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	24		all_cancers(142;0.000311)|all_epithelial(76;1.54e-06)|all_lung(232;0.0131)|Lung NSC(167;0.0161)|Colorectal(57;0.0596)|Ovarian(225;0.105)		COAD - Colon adenocarcinoma(37;0.0703)		TATCCAGAGCTGCAATTTGTA	0.343													T|||	13	0.00259585	0.0015	0.0	5008	,	,		17876	0.0		0.002	False		,,,				2504	0.0092				p.L411R		Atlas-SNP	.											.	ERAP2	77	.	0			c.T1232G						PASS	.	T	ARG/LEU,ARG/LEU	4,4402	8.1+/-20.4	0,4,2199	136.0	133.0	134.0		1232,1232	4.7	0.7	5	dbSNP_126	134	41,8559	27.4+/-76.7	0,41,4259	yes	missense,missense	ERAP2	NM_001130140.1,NM_022350.3	102,102	0,45,6458	GG,GT,TT		0.4767,0.0908,0.346	probably-damaging,probably-damaging	411/961,411/961	96231056	45,12961	2203	4300	6503	SO:0001583	missense	64167	exon7			CAGAGCTGCAATT	AF191545	CCDS4086.1	5q15	2007-11-21			ENSG00000164308	ENSG00000164308			29499	protein-coding gene	gene with protein product	"""leukocyte-derived arginine aminopeptidase"""	609497				12799365, 15908954	Standard	NM_022350		Approved	L-RAP, LRAP	uc003kmt.3	Q6P179	OTTHUMG00000128718	ENST00000437043.3:c.1232T>G	5.37:g.96231056T>G	ENSP00000400376:p.Leu411Arg	75.0	0.0	0		91.0	40.0	0.43956	NM_001130140	Q7Z5K1|Q8TD32|Q8WVJ4|Q9HBX2	Missense_Mutation	SNP	ENST00000437043.3	37	CCDS4086.1	5	0.0022893772893772895	2	0.0040650406504065045	0	0.0	0	0.0	3	0.00395778364116095	T	18.69	3.677983	0.68042	9.08E-4	0.004767	ENSG00000164308	ENST00000437043;ENST00000510373;ENST00000513084;ENST00000379904	T;T;T;T	0.02763	4.17;4.17;4.17;4.17	4.74	4.74	0.60224	Peptidase M1, membrane alanine aminopeptidase, N-terminal (1);	0.000000	0.50627	D	0.000108	T	0.16557	0.0398	M	0.84683	2.71	0.80722	D	1	D;P	0.57571	0.98;0.915	D;D	0.72982	0.964;0.979	T	0.00380	-1.1776	10	0.87932	D	0	.	13.5065	0.61486	0.0:0.0:0.0:1.0	rs34261036	366;411	Q6P179-3;Q6P179	.;ERAP2_HUMAN	R	411;411;411;366	ENSP00000400376:L411R;ENSP00000421175:L411R;ENSP00000421849:L411R;ENSP00000369235:L366R	ENSP00000369235:L366R	L	+	2	0	ERAP2	96256812	0.989000	0.36119	0.697000	0.30258	0.966000	0.64601	5.502000	0.66956	1.904000	0.55121	0.460000	0.39030	CTG	T|0.997;G|0.003	0.003	strong		0.343	ERAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250623.2	NM_022350	
SCRIB	23513	hgsc.bcm.edu	37	8	144895018	144895018	+	Silent	SNP	C	C	T	rs75171224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144895018C>T	ENST00000320476.3	-	8	762	c.756G>A	c.(754-756)caG>caA	p.Q252Q	MIR937_ENST00000401271.1_RNA|SCRIB_ENST00000377533.3_Silent_p.Q171Q|SCRIB_ENST00000356994.2_Silent_p.Q252Q	NM_015356.4	NP_056171	Q14160	SCRIB_HUMAN	scribbled planar cell polarity protein	252	Sufficient for targeting to adherens junction and to inhibit cell proliferation.				activation of Rac GTPase activity (GO:0032863)|apoptotic process involved in morphogenesis (GO:0060561)|astrocyte cell migration (GO:0043615)|asymmetric protein localization (GO:0008105)|auditory receptor cell stereocilium organization (GO:0060088)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cochlear nucleus development (GO:0021747)|establishment of apical/basal cell polarity (GO:0035089)|mammary gland duct morphogenesis (GO:0060603)|negative regulation of mitotic cell cycle (GO:0045930)|neural tube closure (GO:0001843)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of receptor recycling (GO:0001921)|protein localization to adherens junction (GO:0071896)|single organismal cell-cell adhesion (GO:0016337)|synaptic vesicle endocytosis (GO:0048488)|synaptic vesicle targeting (GO:0016080)|viral process (GO:0016032)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|myelin sheath abaxonal region (GO:0035748)|plasma membrane (GO:0005886)|Scrib-APC-beta-catenin complex (GO:0034750)				NS(1)|autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(3)|lung(20)|ovary(2)|pancreas(1)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	42	all_cancers(97;2.31e-11)|all_epithelial(106;1.58e-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;2.46e-41)|Epithelial(56;1.23e-39)|all cancers(56;1.12e-34)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.18)			GCAGCAGGTTCTGGGACAGCA	0.706													C|||	24	0.00479233	0.0008	0.0072	5008	,	,		14449	0.0		0.0169	False		,,,				2504	0.001				p.Q252Q	Pancreas(51;966 1133 10533 14576 29674)	Atlas-SNP	.											.	SCRIB	192	.	0			c.G756A						PASS	.	C	,	8,4398	14.3+/-33.2	0,8,2195	35.0	35.0	35.0		756,756	4.2	1.0	8	dbSNP_131	35	140,8456	64.6+/-126.8	1,138,4159	no	coding-synonymous,coding-synonymous	SCRIB	NM_015356.3,NM_182706.3	,	1,146,6354	TT,TC,CC		1.6287,0.1816,1.1383	,	252/1631,252/1656	144895018	148,12854	2203	4298	6501	SO:0001819	synonymous_variant	23513	exon8			CAGGTTCTGGGAC	AY062238	CCDS6411.1, CCDS6412.1	8q24.3	2013-03-05	2013-03-05		ENSG00000180900	ENSG00000180900			30377	protein-coding gene	gene with protein product		607733	"""scribbled homolog (Drosophila)"""			11027293, 14681682	Standard	NM_182706		Approved	KIAA0147, SCRB1, Vartul	uc003yzo.1	Q14160	OTTHUMG00000165154	ENST00000320476.3:c.756G>A	8.37:g.144895018C>T		32.0	0.0	0		57.0	40.0	0.701754	NM_015356	Q6P496|Q7Z5D1|Q8WWV8|Q96C69|Q96GG1	Silent	SNP	ENST00000320476.3	37	CCDS6411.1																																																																																			C|0.991;T|0.009	0.009	strong		0.706	SCRIB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000382215.1	NM_015356	
PTCD1	26024	hgsc.bcm.edu	37	7	99022873	99022873	+	Missense_Mutation	SNP	C	C	T	rs147045279	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99022873C>T	ENST00000292478.4	-	6	1532	c.1282G>A	c.(1282-1284)Gca>Aca	p.A428T	ATP5J2-PTCD1_ENST00000413834.1_Missense_Mutation_p.A477T|PTCD1_ENST00000555673.1_Missense_Mutation_p.A477T	NM_015545.3	NP_056360.2	O75127	PTCD1_HUMAN	pentatricopeptide repeat domain 1	428					tRNA 3'-end processing (GO:0042780)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	poly(A) RNA binding (GO:0044822)|tRNA binding (GO:0000049)			endometrium(5)|large_intestine(3)|lung(16)|ovary(2)|skin(1)	27	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)		STAD - Stomach adenocarcinoma(171;0.215)			AGGGCCACTGCGGTGAGGGCT	0.662													G|||	11	0.00219649	0.0	0.0	5008	,	,		17554	0.0		0.001	False		,,,				2504	0.0102				p.A477T		Atlas-SNP	.											.	.	.	.	0			c.G1429A						PASS	.	G	THR/ALA,THR/ALA	2,4404		0,2,2201	96.0	96.0	96.0		1429,1282	2.8	0.0	7	dbSNP_134	96	13,8587		0,13,4287	yes	missense,missense	PTCD1,ATP5J2-PTCD1	NM_001198879.1,NM_015545.3	58,58	0,15,6488	TT,TC,CC		0.1512,0.0454,0.1153	benign,benign	477/750,428/701	99022873	15,12991	2203	4300	6503	SO:0001583	missense	100526740	exon7			CCACTGCGGTGAG	AB014532	CCDS34691.1	7q22.1	2006-01-27				ENSG00000106246			22198	protein-coding gene	gene with protein product		614774					Standard	NM_015545		Approved	KIAA0632		O75127		ENST00000292478.4:c.1282G>A	7.37:g.99022873C>T	ENSP00000292478:p.Ala428Thr	78.0	0.0	0		92.0	51.0	0.554348	NM_001198879	Q3ZB78|Q66K60|Q9UDV2	Missense_Mutation	SNP	ENST00000292478.4	37	CCDS34691.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	9.484	1.098951	0.20552	4.54E-4	0.001512	ENSG00000106246;ENSG00000106246;ENSG00000106246;ENSG00000248919	ENST00000292478;ENST00000438524;ENST00000555673;ENST00000413834	T;T;T	0.64803	-0.12;-0.09;-0.09	5.66	2.75	0.32379	.	0.719311	0.14379	N	0.323285	T	0.38719	0.1051	N	0.14661	0.345	0.09310	N	1	B;B	0.21753	0.06;0.036	B;B	0.18263	0.021;0.005	T	0.20806	-1.0264	10	0.15952	T	0.53	-2.2895	6.6526	0.22971	0.3204:0.1307:0.5489:0.0	.	477;428	G3V325;O75127	.;PTCD1_HUMAN	T	428;210;477;477	ENSP00000292478:A428T;ENSP00000450995:A477T;ENSP00000400168:A477T	ENSP00000400168:A477T	A	-	1	0	ATP5J2-PTCD1;PTCD1	98860809	0.005000	0.15991	0.015000	0.15790	0.007000	0.05969	0.090000	0.15025	0.275000	0.22094	-0.216000	0.12614	GCA	C|1.000;T|0.000	0.000	strong		0.662	PTCD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336391.1	NM_015545	
LAMB2	3913	hgsc.bcm.edu	37	3	49161004	49161004	+	Silent	SNP	C	C	A	rs34967349	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49161004C>A	ENST00000418109.1	-	26	4022	c.3858G>T	c.(3856-3858)gtG>gtT	p.V1286V	USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|LAMB2_ENST00000464891.1_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Silent_p.V1286V|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|USP19_ENST00000434032.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1286	Domain II.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TCTCATCTTGCACATCTGTCA	0.537													C|||	12	0.00239617	0.0	0.0058	5008	,	,		24506	0.0		0.008	False		,,,				2504	0.0				p.V1286V		Atlas-SNP	.											.	LAMB2	156	.	0			c.G3858T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	133.0	122.0	126.0		3858	0.8	1.0	3	dbSNP_126	126	50,8550	32.8+/-85.7	0,50,4250	no	coding-synonymous	LAMB2	NM_002292.3		0,57,6446	AA,AC,CC		0.5814,0.1589,0.4383		1286/1799	49161004	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	3913	exon25			ATCTTGCACATCT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.3858G>T	3.37:g.49161004C>A		134.0	0.0	0		143.0	70.0	0.48951	NM_002292	Q16321	Silent	SNP	ENST00000418109.1	37	CCDS2789.1																																																																																			C|0.996;A|0.004	0.004	strong		0.537	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
ERMP1	79956	hgsc.bcm.edu	37	9	5787439	5787439	+	Missense_Mutation	SNP	T	T	C	rs148237651		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5787439T>C	ENST00000339450.5	-	14	2630	c.2541A>G	c.(2539-2541)atA>atG	p.I847M	ERMP1_ENST00000543230.1_3'UTR|ERMP1_ENST00000381506.3_3'UTR|ERMP1_ENST00000214893.5_5'UTR	NM_024896.2	NP_079172.2	Q7Z2K6	ERMP1_HUMAN	endoplasmic reticulum metallopeptidase 1	847						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)			endometrium(2)|kidney(1)|large_intestine(9)|lung(4)|ovary(1)|prostate(2)|skin(1)	20		Acute lymphoblastic leukemia(23;0.158)		GBM - Glioblastoma multiforme(50;0.00115)|Lung(218;0.111)		CCTGCACTTCTATCCAGAACT	0.473																																					p.I847M		Atlas-SNP	.											.	ERMP1	63	.	0			c.A2541G						PASS	.	T	MET/ILE	0,4406		0,0,2203	110.0	108.0	108.0		2541	-3.8	1.0	9	dbSNP_134	108	3,8597	3.0+/-9.4	0,3,4297	yes	missense	ERMP1	NM_024896.2	10	0,3,6500	CC,CT,TT		0.0349,0.0,0.0231	probably-damaging	847/905	5787439	3,13003	2203	4300	6503	SO:0001583	missense	79956	exon14			CACTTCTATCCAG	AB058718	CCDS34983.1	9p24	2008-02-05	2007-07-05	2007-07-05	ENSG00000099219	ENSG00000099219			23703	protein-coding gene	gene with protein product	"""Felix-ina"""	611156	"""KIAA1815"""	KIAA1815		11347906	Standard	XM_005251587		Approved	FLJ23309, FXNA	uc003zjm.1	Q7Z2K6	OTTHUMG00000019508	ENST00000339450.5:c.2541A>G	9.37:g.5787439T>C	ENSP00000340427:p.Ile847Met	51.0	0.0	0		56.0	27.0	0.482143	NM_024896	B2RNA4|B3KSB1|Q8N5T5|Q9H5M1	Missense_Mutation	SNP	ENST00000339450.5	37	CCDS34983.1	.	.	.	.	.	.	.	.	.	.	T	11.10	1.538188	0.27475	0.0	3.49E-4	ENSG00000099219	ENST00000339450	T	0.53206	0.63	5.77	-3.81	0.04294	.	0.089070	0.85682	D	0.000000	T	0.50939	0.1645	L	0.55990	1.75	0.80722	D	1	D	0.71674	0.998	D	0.66602	0.945	T	0.51092	-0.8749	10	0.33940	T	0.23	-20.1147	7.7681	0.28991	0.3034:0.0:0.3774:0.3192	.	847	Q7Z2K6	ERMP1_HUMAN	M	847	ENSP00000340427:I847M	ENSP00000340427:I847M	I	-	3	3	ERMP1	5777439	0.996000	0.38824	0.989000	0.46669	0.032000	0.12392	0.236000	0.17967	-0.521000	0.06426	-0.472000	0.04984	ATA	T|1.000;C|0.000	0.000	weak		0.473	ERMP1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354877.1	NM_024896	
MET	4233	hgsc.bcm.edu	37	7	116339315	116339315	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:116339315G>A	ENST00000318493.6	+	2	364	c.177G>A	c.(175-177)gaG>gaA	p.E59E	MET_ENST00000397752.3_Silent_p.E59E|MET_ENST00000436117.2_Silent_p.E59E			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)			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)			TTCTACATGAGCATCACATTT	0.443			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)																												p.E59E		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.G177A						PASS	.						104.0	101.0	102.0					7																	116339315		1947	4135	6082	SO:0001819	synonymous_variant	4233	exon2	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	ACATGAGCATCAC	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.177G>A	7.37:g.116339315G>A		139.0	0.0	0		129.0	58.0	0.449612	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			.	.	none		0.443	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
ZWINT	11130	hgsc.bcm.edu	37	10	58118569	58118569	+	Missense_Mutation	SNP	T	T	C	rs370677108		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:58118569T>C	ENST00000373944.3	-	6	658	c.620A>G	c.(619-621)cAg>cGg	p.Q207R	ZWINT_ENST00000318387.2_Missense_Mutation_p.Q87R|ZWINT_ENST00000395405.1_Missense_Mutation_p.Q207R|ZWINT_ENST00000361148.6_Intron|ZWINT_ENST00000460654.1_5'UTR			O95229	ZWINT_HUMAN	ZW10 interacting kinetochore protein	207					establishment of localization in cell (GO:0051649)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid segregation (GO:0000070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|kinetochore (GO:0000776)|nucleus (GO:0005634)	protein N-terminus binding (GO:0047485)			NS(2)|breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(10)|prostate(1)	20						AACTTACCTCTGCAGCTTGTC	0.522																																					p.Q207R		Atlas-SNP	.											.	ZWINT	39	.	0			c.A620G						PASS	.	T	ARG/GLN,ARG/GLN,	0,4406		0,0,2203	136.0	130.0	132.0		620,620,	4.5	1.0	10		132	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron	ZWINT	NM_007057.3,NM_032997.2,NM_001005413.1	43,43,	0,1,6502	CC,CT,TT		0.0116,0.0,0.0077	probably-damaging,probably-damaging,	207/278,207/278,	58118569	1,13005	2203	4300	6503	SO:0001583	missense	11130	exon6			TACCTCTGCAGCT	AF067656	CCDS7249.1, CCDS31205.1	10q21-q22	2013-05-01	2013-05-01		ENSG00000122952	ENSG00000122952			13195	protein-coding gene	gene with protein product		609177	"""ZW10 interactor"""				Standard	XM_005269463		Approved	KNTC2AP	uc001jka.1	O95229	OTTHUMG00000018261	ENST00000373944.3:c.620A>G	10.37:g.58118569T>C	ENSP00000363055:p.Gln207Arg	278.0	0.0	0		243.0	117.0	0.481481	NM_007057	A6NNV6|Q0D2I3|Q9BWD0	Missense_Mutation	SNP	ENST00000373944.3	37	CCDS7249.1	.	.	.	.	.	.	.	.	.	.	T	11.24	1.581660	0.28180	0.0	1.16E-4	ENSG00000122952	ENST00000373944;ENST00000395405;ENST00000318387	T;T;T	0.50548	0.74;0.74;0.74	4.48	4.48	0.54585	.	0.154517	0.30911	N	0.008632	T	0.59622	0.2207	M	0.62723	1.935	0.29902	N	0.824315	D	0.63046	0.992	P	0.60541	0.876	T	0.61446	-0.7061	10	0.87932	D	0	.	10.4401	0.44460	0.0:0.0:0.0:1.0	.	207	O95229	ZWINT_HUMAN	R	207;207;87	ENSP00000363055:Q207R;ENSP00000378801:Q207R;ENSP00000322850:Q87R	ENSP00000322850:Q87R	Q	-	2	0	ZWINT	57788575	0.992000	0.36948	1.000000	0.80357	0.070000	0.16714	1.076000	0.30729	2.237000	0.73441	0.533000	0.62120	CAG	.	.	none		0.522	ZWINT-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048132.1		
NPBWR1	2831	hgsc.bcm.edu	37	8	53853160	53853160	+	Silent	SNP	T	T	C	rs75387626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:53853160T>C	ENST00000331251.3	+	1	2170	c.693T>C	c.(691-693)caT>caC	p.H231H		NM_005285.3	NP_005276.2	P48145	NPBW1_HUMAN	neuropeptides B/W receptor 1	231					G-protein coupled receptor signaling pathway (GO:0007186)|opioid receptor signaling pathway (GO:0038003)|regulation of metabolic process (GO:0019222)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|opioid receptor activity (GO:0004985)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)	17		Lung NSC(129;0.0222)|all_epithelial(80;0.0301)|all_lung(136;0.0431)				GCCGGCTGCATGCCATGCGGC	0.667													T|||	170	0.0339457	0.0023	0.0245	5008	,	,		16708	0.0079		0.0527	False		,,,				2504	0.091				p.H231H		Atlas-SNP	.											.	NPBWR1	38	.	0			c.T693C						PASS	.	T		28,4360		0,28,2166	30.0	17.0	21.0		693	-2.3	1.0	8	dbSNP_132	21	291,8255		5,281,3987	no	coding-synonymous	NPBWR1	NM_005285.3		5,309,6153	CC,CT,TT		3.4051,0.6381,2.4664		231/329	53853160	319,12615	2194	4273	6467	SO:0001819	synonymous_variant	2831	exon1			GCTGCATGCCATG	BC033145	CCDS6151.1	8p22-q21.13	2012-08-08	2006-02-15	2006-02-15		ENSG00000183729		"""GPCR / Class A : Neuropeptide receptors : W/B"""	4522	protein-coding gene	gene with protein product		600730	"""G protein-coupled receptor 7"""	GPR7		7590751, 12401809	Standard	NM_005285		Approved		uc011ldu.2	P48145		ENST00000331251.3:c.693T>C	8.37:g.53853160T>C		68.0	0.0	0		62.0	29.0	0.467742	NM_005285	Q6NTC7	Silent	SNP	ENST00000331251.3	37	CCDS6151.1																																																																																			T|0.975;C|0.025	0.025	strong		0.667	NPBWR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378047.1	NM_005285	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919231	51919231	+	Silent	SNP	A	A	G	rs112584540	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919231A>G	ENST00000339313.5	-	5	1061	c.945T>C	c.(943-945)gcT>gcC	p.A315A	SIGLEC10_ENST00000439889.2_Silent_p.A257A|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Silent_p.A267A|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000353836.5_Silent_p.A315A|SIGLEC10_ENST00000432469.2_Silent_p.A232A|SIGLEC10_ENST00000441969.3_Silent_p.A257A|SIGLEC10_ENST00000356298.5_Silent_p.A315A|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	315	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CTGAATCCCCAGCCTTCACCC	0.677													a|||	19	0.00379393	0.0015	0.0058	5008	,	,		18136	0.0		0.0089	False		,,,				2504	0.0041				p.A315A		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.T945C						PASS	.						41.0	46.0	45.0					19																	51919231		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			ATCCCCAGCCTTC	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.945T>C	19.37:g.51919231A>G		199.0	0.0	0		120.0	41.0	0.341667	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			A|0.994;G|0.006	0.006	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
LPP	4026	hgsc.bcm.edu	37	3	188478055	188478055	+	Silent	SNP	C	C	T	rs6771786	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:188478055C>T	ENST00000312675.4	+	8	1641	c.1395C>T	c.(1393-1395)tgC>tgT	p.C465C	LPP_ENST00000543006.1_Silent_p.C465C	NM_001167672.1|NM_005578.3	NP_001161144.1|NP_005569.1	Q93052	LPP_HUMAN	LIM domain containing preferred translocation partner in lipoma	465	LIM zinc-binding 1. {ECO:0000255|PROSITE- ProRule:PRU00125}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)		HMGA2/LPP(161)	NS(1)|breast(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10	all_cancers(143;1.37e-09)|all_hematologic(3;0.0429)|Ovarian(172;0.088)	all_lung(153;0.00139)|Lung NSC(153;0.00202)		GBM - Glioblastoma multiforme(93;0.00602)		AAGCATACTGCGAGCCCTGCT	0.458			T	"""HMGA2, MLL, C12orf9"""	"""lipoma, leukemia"""								C|||	15	0.00299521	0.0	0.0029	5008	,	,		19555	0.001		0.0099	False		,,,				2504	0.002				p.C465C		Atlas-SNP	.		Dom	yes		3	3q28	4026	LIM domain containing preferred translocation partner in lipoma		"""L, M"""	.	LPP	72	.	0			c.C1395T						PASS	.	C	,,	6,4400	11.4+/-27.6	0,6,2197	140.0	131.0	134.0		1395,954,1395	-5.8	0.8	3	dbSNP_116	134	80,8520	47.2+/-106.3	1,78,4221	no	coding-synonymous,coding-synonymous,coding-synonymous	LPP	NM_001167671.1,NM_001167672.1,NM_005578.3	,,	1,84,6418	TT,TC,CC		0.9302,0.1362,0.6612	,,	465/613,318/466,465/613	188478055	86,12920	2203	4300	6503	SO:0001819	synonymous_variant	4026	exon8			ATACTGCGAGCCC	AL833171	CCDS3291.1	3q27-q28	2004-03-02	2002-01-14		ENSG00000145012	ENSG00000145012			6679	protein-coding gene	gene with protein product		600700	"""LIM domain-containing preferred translocation partner in lipoma"""			8812423	Standard	XM_005247453		Approved		uc003frs.2	Q93052	OTTHUMG00000156387	ENST00000312675.4:c.1395C>T	3.37:g.188478055C>T		167.0	0.0	0		185.0	88.0	0.475676	NM_005578	A1L4L6|D3DNV6|Q8NFX5	Silent	SNP	ENST00000312675.4	37	CCDS3291.1																																																																																			C|0.994;T|0.006	0.006	strong		0.458	LPP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344030.1	NM_005578	
VENTX	27287	hgsc.bcm.edu	37	10	135053784	135053784	+	Missense_Mutation	SNP	A	A	G	rs148086757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:135053784A>G	ENST00000325980.9	+	3	1262	c.751A>G	c.(751-753)Atg>Gtg	p.M251V		NM_014468.3	NP_055283.1	O95231	VENTX_HUMAN	VENT homeobox	251					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)			NS(1)|endometrium(1)|large_intestine(1)|lung(9)|soft_tissue(1)|upper_aerodigestive_tract(1)	14		all_cancers(35;4.15e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00144)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;7.8e-06)|Epithelial(32;9.31e-06)|all cancers(32;1.19e-05)		CCTGTGTGCTATGCCACAGAC	0.667													a|||	28	0.00559105	0.0	0.013	5008	,	,		9132	0.001		0.008	False		,,,				2504	0.0102				p.M251V		Atlas-SNP	.											.	VENTX	24	.	0			c.A751G						PASS	.	A	VAL/MET	1,4105		0,1,2052	15.0	17.0	17.0		751	0.9	0.0	10	dbSNP_134	17	32,8112		0,32,4040	yes	missense	VENTX	NM_014468.2	21	0,33,6092	GG,GA,AA		0.3929,0.0244,0.2694	benign	251/259	135053784	33,12217	2053	4072	6125	SO:0001583	missense	27287	exon3			TGTGCTATGCCAC	AF068006	CCDS7675.1	10q26.3	2011-06-20	2011-06-01	2005-09-27	ENSG00000151650	ENSG00000151650		"""Homeoboxes / ANTP class : NKL subclass"""	13639	protein-coding gene	gene with protein product		607158	"""VENT-like homeobox 2"", ""VENT homeobox homolog (Xenopus laevis)"""	VENTX2		10790436	Standard	NM_014468		Approved	HPX42B	uc010quy.1	O95231	OTTHUMG00000019307	ENST00000325980.9:c.751A>G	10.37:g.135053784A>G	ENSP00000357556:p.Met251Val	19.0	0.0	0		41.0	15.0	0.365854	NM_014468	Q32MZ3	Missense_Mutation	SNP	ENST00000325980.9	37	CCDS7675.1	11	0.005036630036630037	0	0.0	5	0.013812154696132596	0	0.0	6	0.0079155672823219	a	7.807	0.714805	0.15306	2.44E-4	0.003929	ENSG00000151650	ENST00000325980	D	0.89939	-2.59	2.96	0.867	0.19085	.	0.369811	0.17386	U	0.176135	T	0.68540	0.3012	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.63152	-0.6701	10	0.62326	D	0.03	.	7.6583	0.28388	0.4764:0.5236:0.0:0.0	.	251	O95231	VENTX_HUMAN	V	251	ENSP00000357556:M251V	ENSP00000357556:M251V	M	+	1	0	VENTX	134903774	0.000000	0.05858	0.002000	0.10522	0.013000	0.08279	-0.801000	0.04550	0.052000	0.16007	-0.447000	0.05616	ATG	A|0.995;G|0.005	0.005	strong		0.667	VENTX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051116.4	NM_014468	
GSPT1	2935	hgsc.bcm.edu	37	16	11969985	11969985	+	Silent	SNP	C	C	T	rs369462446		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:11969985C>T	ENST00000563468.1	-	11	1262	c.1236G>A	c.(1234-1236)gcG>gcA	p.A412A	GSPT1_ENST00000434724.2_Silent_p.A550A|GSPT1_ENST00000439887.2_Silent_p.A549A|RP11-166B2.8_ENST00000574364.1_RNA|GSPT1_ENST00000420576.2_Silent_p.A412A			P15170	ERF3A_HUMAN	G1 to S phase transition 1	412					G1/S transition of mitotic cell cycle (GO:0000082)|GTP catabolic process (GO:0006184)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|protein methylation (GO:0006479)|translational termination (GO:0006415)	intracellular (GO:0005622)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|translation release factor activity (GO:0003747)			breast(1)|central_nervous_system(1)|kidney(4)|lung(4)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	14						TATGCAGCACCGCATTATAGC	0.333																																					p.A550A		Atlas-SNP	.											.	GSPT1	71	.	0			c.G1650A						PASS	.	C	,,	2,4392		0,2,2195	180.0	182.0	182.0		1647,1236,1650	3.0	1.0	16		182	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous	GSPT1	NM_001130006.1,NM_001130007.1,NM_002094.3	,,	0,2,6495	TT,TC,CC		0.0,0.0455,0.0154	,,	549/637,412/500,550/638	11969985	2,12992	2197	4300	6497	SO:0001819	synonymous_variant	2935	exon13			CAGCACCGCATTA	BC008391	CCDS45412.1, CCDS45413.1, CCDS45414.1	16p13.1	2008-08-01							4621	protein-coding gene	gene with protein product		139259				2511002, 17700517	Standard	NM_002094		Approved	GST1, ETF3A, eRF3a	uc002dbt.3	P15170		ENST00000563468.1:c.1236G>A	16.37:g.11969985C>T		121.0	0.0	0		122.0	56.0	0.459016	NM_002094	J3KQG6|Q96GF2	Silent	SNP	ENST00000563468.1	37	CCDS45414.1																																																																																			.	.	weak		0.333	GSPT1-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000421513.1	NM_002094	
HERC2	8924	hgsc.bcm.edu	37	15	28459227	28459227	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459227C>T	ENST00000261609.7	-	41	6658	c.6550G>A	c.(6550-6552)Gaa>Aaa	p.E2184K		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.E2184K(2)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		CCCACCCCTTCGGAAGGCCTT	0.542																																					p.E2184K		Atlas-SNP	.											HERC2,NS,carcinoma,0,1	HERC2	501	1	2	Substitution - Missense(2)	prostate(2)	c.G6550A						scavenged	.																																			SO:0001583	missense	8924	exon41			CCCCTTCGGAAGG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6550G>A	15.37:g.28459227C>T	ENSP00000261609:p.Glu2184Lys	192.0	1.0	0.00520833		245.0	22.0	0.0897959	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	6.061	0.379606	0.11466	.	.	ENSG00000128731	ENST00000261609	T	0.38077	1.16	5.43	3.53	0.40419	.	0.245102	0.40385	N	0.001107	T	0.22003	0.0530	N	0.19112	0.55	0.50171	D	0.999857	B	0.10296	0.003	B	0.06405	0.002	T	0.04242	-1.0966	10	0.24483	T	0.36	.	10.3512	0.43937	0.1352:0.7947:0.0:0.0701	.	2184	O95714	HERC2_HUMAN	K	2184	ENSP00000261609:E2184K	ENSP00000261609:E2184K	E	-	1	0	HERC2	26132822	1.000000	0.71417	0.009000	0.14445	0.018000	0.09664	5.747000	0.68689	0.640000	0.30582	0.484000	0.47621	GAA	.	.	none		0.542	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
WDR45B	56270	hgsc.bcm.edu	37	17	80573888	80573888	+	Silent	SNP	G	G	A	rs147083174	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80573888G>A	ENST00000392325.4	-	10	1136	c.942C>T	c.(940-942)gaC>gaT	p.D314D	WDR45B_ENST00000571835.1_5'Flank	NM_019613.3	NP_062559.2	Q5MNZ6	WIPI3_HUMAN	WD repeat domain 45B	314																	AGTAGCTGCCGTCTGCACAAA	0.498													G|||	19	0.00379393	0.003	0.0072	5008	,	,		18962	0.0		0.0089	False		,,,				2504	0.001				p.D314D		Atlas-SNP	.											.	.	.	.	0			c.C942T						PASS	.	G		8,4398	12.9+/-30.5	0,8,2195	119.0	100.0	107.0		942	-2.3	0.9	17	dbSNP_134	107	74,8526	44.0+/-102.2	0,74,4226	yes	coding-synonymous	WDR45L	NM_019613.3		0,82,6421	AA,AG,GG		0.8605,0.1816,0.6305		314/345	80573888	82,12924	2203	4300	6503	SO:0001819	synonymous_variant	56270	exon10			GCTGCCGTCTGCA	AF091083	CCDS11815.2	17q25.3	2013-01-11	2013-01-11	2013-01-11	ENSG00000141580	ENSG00000141580		"""WD repeat domain containing"""	25072	protein-coding gene	gene with protein product		609226	"""WDR45-like"""	WDR45L		12477932	Standard	NM_019613		Approved	WIPI3	uc002kfq.3	Q5MNZ6	OTTHUMG00000150146	ENST00000392325.4:c.942C>T	17.37:g.80573888G>A		23.0	0.0	0		53.0	24.0	0.45283	NM_019613	O95328|Q2MCP6|Q6IBN2	Silent	SNP	ENST00000392325.4	37	CCDS11815.2																																																																																			G|0.995;A|0.005	0.005	strong		0.498	WDR45B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316536.1	NM_019613	
HTR1A	3350	hgsc.bcm.edu	37	5	63257310	63257310	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:63257310C>T	ENST00000323865.3	-	1	470	c.237G>A	c.(235-237)gcG>gcA	p.A79A	RP11-158J3.2_ENST00000502882.1_RNA	NM_000524.3	NP_000515.2	P08908	5HT1A_HUMAN	5-hydroxytryptamine (serotonin) receptor 1A, G protein-coupled	79					adenylate cyclase-inhibiting serotonin receptor signaling pathway (GO:0007198)|behavioral fear response (GO:0001662)|cell proliferation (GO:0008283)|exploration behavior (GO:0035640)|G-protein coupled receptor signaling pathway (GO:0007186)|positive regulation of cell proliferation (GO:0008284)|regulation of behavior (GO:0050795)|regulation of dopamine metabolic process (GO:0042053)|regulation of hormone secretion (GO:0046883)|regulation of serotonin secretion (GO:0014062)|serotonin metabolic process (GO:0042428)|serotonin receptor signaling pathway (GO:0007210)|vasoconstriction (GO:0042310)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin receptor activity (GO:0004993)	p.A79A(1)		cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(11)|lung(29)|ovary(2)|pancreas(2)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	56		Lung NSC(810;3.55e-06)|Prostate(74;0.0352)|Ovarian(174;0.0545)|Breast(144;0.0575)|Colorectal(97;0.234)		Lung(70;0.105)	Acepromazine(DB01614)|Alprenolol(DB00866)|Alverine(DB01616)|Amitriptyline(DB00321)|Amoxapine(DB00543)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bopindolol(DB08807)|Bromocriptine(DB01200)|Buspirone(DB00490)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinitapride(DB08810)|Clozapine(DB00363)|Desipramine(DB01151)|Dopamine(DB00988)|Doxepin(DB01142)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Iloperidone(DB04946)|Imipramine(DB00458)|Ketamine(DB01221)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Methysergide(DB00247)|Mianserin(DB06148)|Molindone(DB01618)|Naratriptan(DB00952)|Nefazodone(DB01149)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Ondansetron(DB00904)|Paliperidone(DB01267)|Penbutolol(DB01359)|Pergolide(DB01186)|Pindolol(DB00960)|Pipotiazine(DB01621)|Pramipexole(DB00413)|Propranolol(DB00571)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Rotigotine(DB05271)|Sumatriptan(DB00669)|Thioproperazine(DB01622)|Trazodone(DB00656)|Trimipramine(DB00726)|Vilazodone(DB06684)|Yohimbine(DB01392)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)	GGTCGGTGACCGCCAAAGAGC	0.597																																					p.A79A		Atlas-SNP	.											HTR1A,colon,carcinoma,-1,2	HTR1A	128	2	1	Substitution - coding silent(1)	lung(1)	c.G237A						PASS	.						43.0	49.0	47.0					5																	63257310		2203	4300	6503	SO:0001819	synonymous_variant	3350	exon1			GGTGACCGCCAAA	AF498978	CCDS34168.1	5q11.2-q13	2012-08-08	2012-02-03			ENSG00000178394		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5286	protein-coding gene	gene with protein product		109760	"""5-hydroxytryptamine (serotonin) receptor 1A"""	ADRB2RL1, ADRBRL1		2591972, 12969265	Standard	NM_000524		Approved	5-HT1A	uc011cqt.3	P08908		ENST00000323865.3:c.237G>A	5.37:g.63257310C>T		125.0	0.0	0		155.0	62.0	0.4	NM_000524	Q6LAE7	Silent	SNP	ENST00000323865.3	37	CCDS34168.1																																																																																			.	.	none		0.597	HTR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368397.1	NM_000524	
NCOR2	9612	hgsc.bcm.edu	37	12	124886979	124886979	+	Silent	SNP	C	C	T	rs202047482	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124886979C>T	ENST00000405201.1	-	14	1611	c.1611G>A	c.(1609-1611)gaG>gaA	p.E537E	NCOR2_ENST00000404121.2_Silent_p.E107E|NCOR2_ENST00000397355.1_Silent_p.E537E|NCOR2_ENST00000356219.3_Silent_p.E537E|NCOR2_ENST00000404621.1_Silent_p.E536E|NCOR2_ENST00000429285.2_Silent_p.E536E			Q9Y618	NCOR2_HUMAN	nuclear receptor corepressor 2	537					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)		CGTTCTCCACCTCCGGcttct	0.637													C|||	2	0.000399361	0.0	0.0014	5008	,	,		15261	0.0		0.001	False		,,,				2504	0.0				p.E537E		Atlas-SNP	.											.	NCOR2	475	.	0			c.G1611A						PASS	.	C	,,	0,4292		0,0,2146	97.0	119.0	112.0		1608,1608,1611	-7.6	0.1	12		112	6,8488		0,6,4241	no	coding-synonymous,coding-synonymous,coding-synonymous	NCOR2	NM_001077261.3,NM_001206654.1,NM_006312.5	,,	0,6,6387	TT,TC,CC		0.0706,0.0,0.0469	,,	536/2459,536/2505,537/2515	124886979	6,12780	2146	4247	6393	SO:0001819	synonymous_variant	9612	exon16			CTCCACCTCCGGC	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.1611G>A	12.37:g.124886979C>T		101.0	0.0	0		122.0	70.0	0.57377	NM_006312	O00613|O15416|O15421|Q13354|Q56D06|Q59GM0|Q9Y5U0	Silent	SNP	ENST00000405201.1	37	CCDS41858.2																																																																																			C|0.999;T|0.001	0.001	weak		0.637	NCOR2-005	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318173.2	NM_006312	
FAM210B	116151	hgsc.bcm.edu	37	20	54940148	54940148	+	Silent	SNP	C	C	T	rs148836702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:54940148C>T	ENST00000371384.3	+	2	283	c.192C>T	c.(190-192)ccC>ccT	p.P64P		NM_080821.2	NP_543011.2	Q96KR6	F210B_HUMAN	family with sequence similarity 210, member B	64						integral component of membrane (GO:0016021)											CACAGGACCCCAGCCAGGCCA	0.498													C|||	7	0.00139776	0.0	0.0	5008	,	,		19155	0.001		0.005	False		,,,				2504	0.001				p.P64P		Atlas-SNP	.											.	.	.	.	0			c.C192T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	47.0	43.0	45.0		192	3.2	0.4	20	dbSNP_134	45	22,8578	15.3+/-51.7	0,22,4278	no	coding-synonymous	C20orf108	NM_080821.2		0,23,6480	TT,TC,CC		0.2558,0.0227,0.1768		64/193	54940148	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	116151	exon2			GGACCCCAGCCAG	AL121914	CCDS13450.1	20q13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000124098	ENSG00000124098			16102	protein-coding gene	gene with protein product	"""hypothetical protein LOC116151"""		"""chromosome 20 open reading frame 108"""	C20orf108		11780052	Standard	NM_080821		Approved	dJ1167H4.1, DKFZP434A1114	uc002xxc.3	Q96KR6	OTTHUMG00000032793	ENST00000371384.3:c.192C>T	20.37:g.54940148C>T		82.0	0.0	0		80.0	38.0	0.475	NM_080821	B2RBQ9|E1P5Y7|Q8WVN2|Q9BYL6|Q9H418	Silent	SNP	ENST00000371384.3	37	CCDS13450.1																																																																																			C|0.998;T|0.002	0.002	strong		0.498	FAM210B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079800.2	NM_080821	
USP19	10869	hgsc.bcm.edu	37	3	49146612	49146612	+	Missense_Mutation	SNP	G	G	A	rs79965514		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49146612G>A	ENST00000398888.2	-	26	4054	c.3736C>T	c.(3736-3738)Cgg>Tgg	p.R1246W	USP19_ENST00000453664.1_Intron|USP19_ENST00000398896.1_Intron|USP19_ENST00000417901.1_Intron|USP19_ENST00000398892.3_Missense_Mutation_p.R1286W|USP19_ENST00000434032.2_Missense_Mutation_p.R1347W|USP19_ENST00000398898.2_Intron	NM_006677.2	NP_006668.1	O94966	UBP19_HUMAN	ubiquitin specific peptidase 19	1246					ER-associated ubiquitin-dependent protein catabolic process (GO:0030433)|negative regulation of skeletal muscle tissue development (GO:0048642)|positive regulation of cell cycle process (GO:0090068)|protein deubiquitination (GO:0016579)|regulation of cellular response to hypoxia (GO:1900037)|regulation of protein stability (GO:0031647)|response to endoplasmic reticulum stress (GO:0034976)|skeletal muscle atrophy (GO:0014732)	cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)|ubiquitin-specific protease activity (GO:0004843)			NS(1)|breast(3)|endometrium(5)|kidney(2)|large_intestine(10)|lung(5)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	38				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGCCAAATCCGGGAAGCCTAG	0.682													G|||	1	0.000199681	0.0	0.0	5008	,	,		17126	0.001		0.0	False		,,,				2504	0.0				p.R1347W		Atlas-SNP	.											.	USP19	158	.	0			c.C4039T						PASS	.						7.0	9.0	8.0					3																	49146612		1839	3927	5766	SO:0001583	missense	10869	exon27			AAATCCGGGAAGC	AB020698	CCDS43090.1, CCDS56254.1, CCDS56255.1, CCDS56256.1	3p21.31	2005-10-13	2005-08-08		ENSG00000172046	ENSG00000172046		"""Zinc fingers, MYND-type"", ""Ubiquitin-specific peptidases"""	12617	protein-coding gene	gene with protein product		614471	"""ubiquitin specific protease 19"""			12838346	Standard	NM_001199160		Approved	KIAA0891, ZMYND9	uc011bch.2	O94966	OTTHUMG00000133611	ENST00000398888.2:c.3736C>T	3.37:g.49146612G>A	ENSP00000381863:p.Arg1246Trp	124.0	0.0	0		103.0	30.0	0.291262	NM_001199160	A5PKX8|A6H8U2|B4DGT3|B4DTZ0|E7EN22|E7ETS0|E9PEG8|Q3KQW4|Q641Q9|Q6NZY8|Q86XV9	Missense_Mutation	SNP	ENST00000398888.2	37	CCDS43090.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	19.42	3.823416	0.71143	.	.	ENSG00000172046	ENST00000398892;ENST00000398888;ENST00000434032	T;T;T	0.20463	2.07;2.17;2.17	5.3	4.43	0.53597	.	0.730358	0.12840	N	0.434921	T	0.16557	0.0398	N	0.19112	0.55	0.41423	D	0.987818	B;B;B	0.11235	0.004;0.004;0.001	B;B;B	0.08055	0.002;0.003;0.0	T	0.04078	-1.0979	10	0.59425	D	0.04	-2.2965	13.9763	0.64275	0.0724:0.0:0.9276:0.0	.	1347;1246;1286	E9PEG8;O94966;B5MEG5	.;UBP19_HUMAN;.	W	1286;1246;1347	ENSP00000381867:R1286W;ENSP00000381863:R1246W;ENSP00000401197:R1347W	ENSP00000381863:R1246W	R	-	1	2	USP19	49121616	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.009000	0.88606	1.473000	0.48159	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.682	USP19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000257721.1	NM_006677	
CR1L	1379	hgsc.bcm.edu	37	1	207870916	207870916	+	Missense_Mutation	SNP	G	G	A	rs201832831	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:207870916G>A	ENST00000508064.2	+	6	991	c.931G>A	c.(931-933)Ggg>Agg	p.G311R	CR1L_ENST00000530905.1_Intron	NM_175710.1	NP_783641.1	Q2VPA4	CR1L_HUMAN	complement component (3b/4b) receptor 1-like	311	Sushi 5. {ECO:0000255|PROSITE- ProRule:PRU00302}.					cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)|receptor complex (GO:0043235)		p.G319W(1)|p.G311W(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(15)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	22						CTTTTCACCCGGGCAGGAAGT	0.557													g|||	5	0.000998403	0.0	0.0	5008	,	,		18305	0.004		0.0	False		,,,				2504	0.001				p.G311R		Atlas-SNP	.											.	CR1L	97	.	2	Substitution - Missense(2)	lung(2)	c.G931A						PASS	.	G	ARG/GLY	1,3789		0,1,1894	151.0	149.0	149.0		931	1.5	0.0	1		149	1,8223		0,1,4111	no	missense	CR1L	NM_175710.1	125	0,2,6005	AA,AG,GG		0.0122,0.0264,0.0166	probably-damaging	311/570	207870916	2,12012	1895	4112	6007	SO:0001583	missense	1379	exon6			TCACCCGGGCAGG	AY114160	CCDS44310.1	1q32.1	2008-02-05			ENSG00000197721	ENSG00000197721		"""Complement system"""	2335	protein-coding gene	gene with protein product		605886				2295627	Standard	NM_175710		Approved		uc001hga.4	Q2VPA4	OTTHUMG00000036354	ENST00000508064.2:c.931G>A	1.37:g.207870916G>A	ENSP00000421736:p.Gly311Arg	394.0	0.0	0		480.0	231.0	0.48125	NM_175710	Q32MC9|Q8NEU7	Missense_Mutation	SNP	ENST00000508064.2	37	CCDS44310.1	3	0.0013736263736263737	0	0.0	0	0.0	3	0.005244755244755245	0	0.0	.	12.71	2.018389	0.35606	2.64E-4	1.22E-4	ENSG00000197721	ENST00000444269;ENST00000508064	T	0.71698	-0.59	2.53	1.55	0.23275	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.75295	0.3830	M	0.81614	2.55	0.09310	N	0.999996	D	0.89917	1.0	D	0.68353	0.957	T	0.64702	-0.6345	9	0.87932	D	0	.	5.7056	0.17907	0.1679:0.0:0.8321:0.0	.	311	Q2VPA4	CR1L_HUMAN	R	311	ENSP00000421736:G311R	ENSP00000434864:G255R	G	+	1	0	CR1L	205937539	0.009000	0.17119	0.001000	0.08648	0.005000	0.04900	0.673000	0.25203	0.354000	0.24105	0.298000	0.19748	GGG	G|0.999;A|0.001	0.001	strong		0.557	CR1L-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390247.1	XM_114735	
ALK	238	hgsc.bcm.edu	37	2	29449819	29449819	+	Silent	SNP	C	C	T	rs2293563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29449819C>T	ENST00000389048.3	-	18	3942	c.3036G>A	c.(3034-3036)acG>acA	p.T1012T	ALK_ENST00000431873.1_Intron	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1012			T -> M (in dbSNP:rs35073634). {ECO:0000269|PubMed:17344846}.		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)	p.T1012T(1)	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)	CAGCCAGCACCGTCCCGTGGT	0.542			"""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|||	851	0.169928	0.2277	0.147	5008	,	,		21422	0.119		0.1928	False		,,,				2504	0.137				p.T1012T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	ALK,NS,carcinoma,0,1	ALK	533	1	1	Substitution - coding silent(1)	stomach(1)	c.G3036A						PASS	.	C		974,3432	366.4+/-317.8	105,764,1334	202.0	180.0	187.0		3036	-10.8	0.1	2	dbSNP_100	187	1492,7108	283.2+/-296.0	137,1218,2945	no	coding-synonymous	ALK	NM_004304.4		242,1982,4279	TT,TC,CC		17.3488,22.1062,18.9605		1012/1621	29449819	2466,10540	2203	4300	6503	SO:0001819	synonymous_variant	238	exon18	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	CAGCACCGTCCCG	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.3036G>A	2.37:g.29449819C>T		135.0	0.0	0		109.0	109.0	1	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			C|0.816;T|0.184	0.184	strong		0.542	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
POU2F1	5451	hgsc.bcm.edu	37	1	167358837	167358837	+	Missense_Mutation	SNP	A	A	G	rs142378150	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:167358837A>G	ENST00000541643.3	+	10	919	c.757A>G	c.(757-759)Aca>Gca	p.T253A	POU2F1_ENST00000367862.5_Missense_Mutation_p.T265A|POU2F1_ENST00000452019.1_3'UTR|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000367866.2_Missense_Mutation_p.T276A|POU2F1_ENST00000429375.2_Missense_Mutation_p.T213A|POU2F1_ENST00000420254.3_Missense_Mutation_p.T253A			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	253					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						AGCAACCCCAACACGCACAAT	0.458													A|||	2	0.000399361	0.0	0.0	5008	,	,		20298	0.0		0.002	False		,,,				2504	0.0				p.T276A		Atlas-SNP	.											.	POU2F1	120	.	0			c.A826G						PASS	.	A	ALA/THR,ALA/THR,ALA/THR	6,4400	11.4+/-27.6	0,6,2197	131.0	136.0	134.0		793,637,826	5.8	1.0	1	dbSNP_134	134	35,8565	25.1+/-72.6	0,35,4265	yes	missense,missense,missense	POU2F1	NM_001198783.1,NM_001198786.1,NM_002697.3	58,58,58	0,41,6462	GG,GA,AA		0.407,0.1362,0.3152	probably-damaging,probably-damaging,probably-damaging	265/756,213/704,276/767	167358837	41,12965	2203	4300	6503	SO:0001583	missense	5451	exon9			ACCCCAACACGCA	BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"""Homeoboxes / POU class"""	9212	protein-coding gene	gene with protein product		164175	"""POU domain class 2, transcription factor 1"""	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.757A>G	1.37:g.167358837A>G	ENSP00000441285:p.Thr253Ala	115.0	0.0	0		153.0	72.0	0.470588	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Missense_Mutation	SNP	ENST00000541643.3	37		.	.	.	.	.	.	.	.	.	.	A	19.63	3.863521	0.71949	0.001362	0.00407	ENSG00000143190	ENST00000367866;ENST00000429375;ENST00000367865;ENST00000420254;ENST00000541643;ENST00000367862;ENST00000443275	T;D;T;T;T;T;T	0.86097	-1.09;-2.07;-1.09;-1.09;-1.09;-1.09;-1.09	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	D	0.88250	0.6386	L	0.54323	1.7	0.80722	D	1	D;D;D;D;D	0.61697	0.984;0.971;0.99;0.99;0.984	D;P;D;D;D	0.73380	0.935;0.79;0.971;0.98;0.935	D	0.87855	0.2660	10	0.41790	T	0.15	.	16.1747	0.81844	1.0:0.0:0.0:0.0	.	213;253;265;251;253	B4E029;P14859-4;P14859-2;P14859-3;P14859	.;.;.;.;PO2F1_HUMAN	A	276;213;251;253;253;265;161	ENSP00000356840:T276A;ENSP00000401217:T213A;ENSP00000356839:T251A;ENSP00000414660:T253A;ENSP00000441285:T253A;ENSP00000356836:T265A;ENSP00000415993:T161A	ENSP00000356836:T265A	T	+	1	0	POU2F1	165625461	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.923000	0.92808	2.225000	0.72522	0.455000	0.32223	ACA	A|0.997;G|0.003	0.003	strong		0.458	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697	
CHRNA2	1135	hgsc.bcm.edu	37	8	27327369	27327369	+	Missense_Mutation	SNP	C	C	T	rs548268816		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:27327369C>T	ENST00000520933.2	-	2	356	c.203G>A	c.(202-204)cGg>cAg	p.R68Q	CHRNA2_ENST00000240132.2_Missense_Mutation_p.R68Q|CHRNA2_ENST00000407991.1_Missense_Mutation_p.R68Q			Q15822	ACHA2_HUMAN	cholinergic receptor, nicotinic, alpha 2 (neuronal)	68					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ion transport (GO:0006811)|protein heterooligomerization (GO:0051291)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine binding (GO:0042166)|acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|drug binding (GO:0008144)	p.R68Q(1)		breast(1)|endometrium(4)|kidney(1)|large_intestine(8)|lung(5)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	23		Ovarian(32;2.61e-05)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0208)|Epithelial(17;2.77e-10)|Colorectal(74;0.136)	Atracurium(DB00732)|Biperiden(DB00810)|Carbachol(DB00411)|Cisatracurium Besylate(DB00565)|Decamethonium(DB01245)|Dextromethorphan(DB00514)|Doxacurium chloride(DB01135)|Galantamine(DB00674)|Gallamine Triethiodide(DB00483)|Mecamylamine(DB00657)|Metocurine(DB01336)|Mivacurium(DB01226)|Nicotine(DB00184)|Pancuronium(DB01337)|Pipecuronium(DB01338)|Procaine(DB00721)|Rocuronium(DB00728)|Tubocurarine(DB01199)|Vecuronium(DB01339)	GTTGTAGCCCCGGAAGAGGTG	0.632																																					p.R68Q		Atlas-SNP	.											CHRNA2,caecum,carcinoma,-1,2	CHRNA2	48	2	1	Substitution - Missense(1)	endometrium(1)	c.G203A						PASS	.						87.0	86.0	86.0					8																	27327369		2203	4300	6503	SO:0001583	missense	1135	exon3			TAGCCCCGGAAGA	U62431	CCDS6059.1, CCDS64856.1	8p21	2012-02-11	2006-02-01		ENSG00000120903	ENSG00000120903		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1956	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, alpha 2 (neuronal)"""	118502	"""cholinergic receptor, nicotinic, alpha polypeptide 2 (neuronal)"""			1505988	Standard	NM_000742		Approved		uc010lur.3	Q15822	OTTHUMG00000102083	ENST00000520933.2:c.203G>A	8.37:g.27327369C>T	ENSP00000429616:p.Arg68Gln	79.0	0.0	0		92.0	43.0	0.467391	NM_000742	A8KAX3|B4DK19|J3KMY9|Q9HAQ3	Missense_Mutation	SNP	ENST00000520933.2	37	CCDS6059.1	.	.	.	.	.	.	.	.	.	.	C	13.44	2.237311	0.39498	.	.	ENSG00000120903	ENST00000407991;ENST00000520933;ENST00000240132;ENST00000524096;ENST00000518712	T;T;T;T;T	0.62105	0.05;0.05;0.05;0.05;0.05	4.77	3.89	0.44902	Neurotransmitter-gated ion-channel ligand-binding (3);	0.410909	0.25143	N	0.032809	T	0.47488	0.1448	L	0.33753	1.03	0.09310	N	1	B;B	0.33073	0.396;0.396	B;B	0.33568	0.166;0.166	T	0.41251	-0.9519	10	0.45353	T	0.12	.	6.9775	0.24683	0.0:0.7318:0.1747:0.0935	.	68;68	B4DK19;Q15822	.;ACHA2_HUMAN	Q	68	ENSP00000385026:R68Q;ENSP00000429616:R68Q;ENSP00000240132:R68Q;ENSP00000430422:R68Q;ENSP00000430856:R68Q	ENSP00000240132:R68Q	R	-	2	0	CHRNA2	27383286	0.000000	0.05858	0.789000	0.31954	0.875000	0.50365	0.006000	0.13152	1.380000	0.46344	0.561000	0.74099	CGG	.	.	none		0.632	CHRNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376125.4		
FN3KRP	79672	hgsc.bcm.edu	37	17	80676896	80676896	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:80676896C>T	ENST00000269373.6	+	2	329	c.256C>T	c.(256-258)Ctg>Ttg	p.L86L	RP11-388C12.1_ENST00000574471.1_lincRNA|FN3KRP_ENST00000535965.1_Silent_p.L36L	NM_024619.3	NP_078895.2	Q9HA64	KT3K_HUMAN	fructosamine 3 kinase related protein	86							kinase activity (GO:0016301)			breast(1)|large_intestine(2)|lung(1)|ovary(2)|upper_aerodigestive_tract(1)	7	Breast(20;0.000523)|all_neural(118;0.0952)		BRCA - Breast invasive adenocarcinoma(99;0.0344)|OV - Ovarian serous cystadenocarcinoma(97;0.061)			CGGGAGCGTGCTGGTGATGGA	0.547																																					p.L86L		Atlas-SNP	.											.	FN3KRP	31	.	0			c.C256T						PASS	.						105.0	103.0	104.0					17																	80676896		2203	4300	6503	SO:0001819	synonymous_variant	79672	exon2			AGCGTGCTGGTGA	AY360465	CCDS11817.1	17q25.3	2014-08-12			ENSG00000141560	ENSG00000141560			25700	protein-coding gene	gene with protein product		611683				14633848	Standard	NM_024619		Approved	FLJ12171, FN3KL	uc002kfu.3	Q9HA64	OTTHUMG00000177846	ENST00000269373.6:c.256C>T	17.37:g.80676896C>T		94.0	0.0	0		109.0	59.0	0.541284	NM_024619	Q969F4|Q9H0U7	Silent	SNP	ENST00000269373.6	37	CCDS11817.1																																																																																			.	.	none		0.547	FN3KRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000439219.1	NM_024619	
MAML3	55534	hgsc.bcm.edu	37	4	140640527	140640527	+	Missense_Mutation	SNP	G	G	A	rs61743025	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:140640527G>A	ENST00000509479.2	-	5	4223	c.3367C>T	c.(3367-3369)Cca>Tca	p.P1123S	MGST2_ENST00000515137.1_Intron	NM_018717.4	NP_061187			mastermind-like 3 (Drosophila)											breast(1)|endometrium(7)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|urinary_tract(2)	25	all_hematologic(180;0.162)					TCGTCCCCTGGCCCGCCTTTG	0.537													G|||	4	0.000798722	0.0	0.0014	5008	,	,		18196	0.0		0.003	False		,,,				2504	0.0				p.P1119S		Atlas-SNP	.											.	MAML3	192	.	0			c.C3355T						PASS	.	G	,,SER/PRO	1,4041		0,1,2020	47.0	52.0	50.0		,,3367	5.0	0.8	4	dbSNP_129	50	25,8321		0,25,4148	yes	intron,intron,missense	MGST2,MAML3	NM_001204366.1,NM_001204367.1,NM_018717.4	,,74	0,26,6168	AA,AG,GG		0.2995,0.0247,0.2099	,,probably-damaging	,,1123/1139	140640527	26,12362	2021	4173	6194	SO:0001583	missense	55534	exon6			CCCCTGGCCCGCC	AB058719	CCDS54805.1	4q31.1	2014-08-12	2003-09-24		ENSG00000196782	ENSG00000196782			16272	protein-coding gene	gene with protein product	"""mastermind (drosophila)-like 3"""	608991	"""trinucleotide repeat containing 3"""	TNRC3		12370315, 12386158	Standard	NM_018717		Approved	KIAA1816, MAM2, CAGH3, GDN	uc021xsg.1	Q96JK9	OTTHUMG00000161441	ENST00000509479.2:c.3367C>T	4.37:g.140640527G>A	ENSP00000421180:p.Pro1123Ser	68.0	0.0	0		94.0	41.0	0.43617	NM_018717		Missense_Mutation	SNP	ENST00000509479.2	37	CCDS54805.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	14.26	2.483745	0.44147	2.47E-4	0.002995	ENSG00000196782	ENST00000509479;ENST00000538400	T	0.24151	1.87	4.99	4.99	0.66335	.	0.000000	0.64402	D	0.000003	T	0.50565	0.1623	M	0.76838	2.35	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.47849	-0.9085	10	0.10377	T	0.69	.	18.623	0.91327	0.0:0.0:1.0:0.0	.	1123;1119	E7EVW8;Q96JK9	.;MAML3_HUMAN	S	1123;430	ENSP00000421180:P1123S	ENSP00000421180:P1123S	P	-	1	0	MAML3	140859977	1.000000	0.71417	0.778000	0.31720	0.978000	0.69477	4.784000	0.62411	2.461000	0.83175	0.591000	0.81541	CCA	G|0.999;A|0.001	0.001	strong		0.537	MAML3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364934.2		
RALGAPB	57148	hgsc.bcm.edu	37	20	37198582	37198582	+	Missense_Mutation	SNP	C	C	T	rs142678293	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:37198582C>T	ENST00000262879.6	+	27	4290	c.4006C>T	c.(4006-4008)Ccc>Tcc	p.P1336S	RALGAPB_ENST00000397038.1_Missense_Mutation_p.P1115S|RALGAPB_ENST00000397040.1_Missense_Mutation_p.P1336S|RALGAPB_ENST00000397042.3_Missense_Mutation_p.P1333S			Q86X10	RLGPB_HUMAN	Ral GTPase activating protein, beta subunit (non-catalytic)	1336	Rap-GAP. {ECO:0000255|PROSITE- ProRule:PRU00165}.				activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)|Ral protein signal transduction (GO:0032484)|regulation of exocyst localization (GO:0060178)		protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(29)|ovary(1)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	65						CCCTGTTCCTCCCCTTGGACC	0.453													C|||	7	0.00139776	0.0015	0.0014	5008	,	,		18979	0.0		0.004	False		,,,				2504	0.0				p.P1336S		Atlas-SNP	.											.	RALGAPB	134	.	0			c.C4006T						PASS	.	C	SER/PRO	5,4401	9.9+/-24.2	0,5,2198	102.0	87.0	92.0		4006	5.6	1.0	20	dbSNP_134	92	68,8532	41.2+/-98.3	1,66,4233	yes	missense	RALGAPB	NM_020336.2	74	1,71,6431	TT,TC,CC		0.7907,0.1135,0.5613	possibly-damaging	1336/1495	37198582	73,12933	2203	4300	6503	SO:0001583	missense	57148	exon27			GTTCCTCCCCTTG	AB033045	CCDS13305.1, CCDS63272.1	20q11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000170471	ENSG00000170471			29221	protein-coding gene	gene with protein product			"""KIAA1219"""	KIAA1219		19520869	Standard	XM_005260462		Approved	DKFZp781M2411, RalGAPbeta	uc002xiw.3	Q86X10	OTTHUMG00000140270	ENST00000262879.6:c.4006C>T	20.37:g.37198582C>T	ENSP00000262879:p.Pro1336Ser	149.0	0.0	0		138.0	66.0	0.478261	NM_020336	A2A2E8|A2A2E9|Q5TG31|Q8N3D1|Q8WWC0|Q9H3X8|Q9UJR1|Q9ULK1|Q9Y3G9	Missense_Mutation	SNP	ENST00000262879.6	37	CCDS13305.1	3	0.0013736263736263737	1	0.0020325203252032522	0	0.0	0	0.0	2	0.002638522427440633	C	16.06	3.015096	0.54468	0.001135	0.007907	ENSG00000170471	ENST00000262879;ENST00000397042;ENST00000397038;ENST00000397040;ENST00000438490	D;D;D;D;D	0.93604	-3.25;-3.25;-3.25;-3.25;-3.25	5.64	5.64	0.86602	Rap/ran-GAP (1);	0.052081	0.85682	D	0.000000	D	0.87904	0.6295	L	0.28400	0.85	0.80722	D	1	P;P	0.44139	0.827;0.827	B;B	0.44044	0.439;0.439	D	0.87073	0.2161	10	0.22109	T	0.4	.	19.7154	0.96115	0.0:1.0:0.0:0.0	.	1333;1336	A2A2E9;Q86X10	.;RLGPB_HUMAN	S	1336;1333;1115;1336;1165	ENSP00000262879:P1336S;ENSP00000380235:P1333S;ENSP00000380231:P1115S;ENSP00000380233:P1336S;ENSP00000416646:P1165S	ENSP00000262879:P1336S	P	+	1	0	RALGAPB	36631996	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	7.601000	0.82783	2.664000	0.90586	0.655000	0.94253	CCC	C|0.995;T|0.005	0.005	strong		0.453	RALGAPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079191.1	NM_020336	
OTUD5	55593	hgsc.bcm.edu	37	X	48783183	48783183	+	Silent	SNP	G	G	C	rs141488277	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:48783183G>C	ENST00000156084.4	-	6	1278	c.1218C>G	c.(1216-1218)tcC>tcG	p.S406S	OTUD5_ENST00000428668.2_Silent_p.S184S|OTUD5_ENST00000484499.1_5'Flank|OTUD5_ENST00000396743.3_Silent_p.S401S|OTUD5_ENST00000376488.3_Silent_p.S401S	NM_017602.3	NP_060072.1	Q96G74	OTUD5_HUMAN	OTU deubiquitinase 5	406					innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)|response to lipopolysaccharide (GO:0032496)	cytosol (GO:0005829)	ubiquitin-specific protease activity (GO:0004843)			endometrium(2)|large_intestine(3)|lung(6)|pancreas(2)	13						ACTGCAGGTAGGATTCCCGAG	0.572													G|||	5	0.0013245	0.0	0.0014	3775	,	,		13554	0.0		0.001	False		,,,				2504	0.0031				p.S406S		Atlas-SNP	.											.	OTUD5	66	.	0			c.C1218G						PASS	.	G	,,,	0,3835		0,0,0,1632,571	102.0	75.0	85.0		1203,1203,552,1218	2.4	1.0	X	dbSNP_134	85	31,6697		0,22,9,2406,1863	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	OTUD5	NM_001136157.1,NM_001136158.1,NM_001136159.1,NM_017602.3	,,,	0,22,9,4038,2434	CC,CG,C,GG,G		0.4608,0.0,0.2935	,,,	401/567,401/567,184/350,406/572	48783183	31,10532	2203	4300	6503	SO:0001819	synonymous_variant	55593	exon6			CAGGTAGGATTCC		CCDS14313.1, CCDS48104.1, CCDS48105.1	Xp11.23	2014-06-09	2014-02-24		ENSG00000068308	ENSG00000068308		"""OTU domain containing"""	25402	protein-coding gene	gene with protein product		300713	"""OTU domain containing 5"""			24143256	Standard	NM_001136157		Approved	DKFZp761A052, DUBA	uc004dlu.3	Q96G74	OTTHUMG00000024130	ENST00000156084.4:c.1218C>G	X.37:g.48783183G>C		39.0	0.0	0		30.0	30.0	1	NM_017602	B4DGG7|G5E9D7|Q4KMN9|Q8N6T5|Q9H650|Q9H9U0|Q9NT65	Silent	SNP	ENST00000156084.4	37	CCDS14313.1																																																																																			G|0.998;C|0.002	0.002	strong		0.572	OTUD5-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000060799.1	NM_017602	
TEF	7008	hgsc.bcm.edu	37	22	41790179	41790179	+	Silent	SNP	G	G	A	rs17365991	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:41790179G>A	ENST00000266304.4	+	3	671	c.555G>A	c.(553-555)ccG>ccA	p.P185P	TEF_ENST00000406644.3_Silent_p.P155P	NM_003216.3	NP_003207.1	Q10587	TEF_HUMAN	thyrotrophic embryonic factor	185	Pro-rich (proline/acidic region (PAR)).				positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|rhythmic process (GO:0048511)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(2)|lung(2)|ovary(1)	6						ACTTCAATCCGGACCCCGCCG	0.567													G|||	90	0.0179712	0.003	0.0288	5008	,	,		16633	0.003		0.0507	False		,,,				2504	0.0123				p.P185P		Atlas-SNP	.											.	TEF	21	.	0			c.G555A						PASS	.	G	,	44,4362	46.7+/-81.2	0,44,2159	86.0	89.0	88.0		465,555	-6.4	0.9	22	dbSNP_123	88	447,8153	135.1+/-192.4	8,431,3861	no	coding-synonymous,coding-synonymous	TEF	NM_001145398.1,NM_003216.2	,	8,475,6020	AA,AG,GG		5.1977,0.9986,3.7752	,	155/274,185/304	41790179	491,12515	2203	4300	6503	SO:0001819	synonymous_variant	7008	exon3			CAATCCGGACCCC		CCDS14014.1, CCDS46716.1	22q13.2	2013-01-10			ENSG00000167074	ENSG00000167074		"""basic leucine zipper proteins"""	11722	protein-coding gene	gene with protein product		188595				7835883, 15665112	Standard	NM_001145398		Approved	KIAA1655	uc003azy.4	Q10587	OTTHUMG00000150968	ENST00000266304.4:c.555G>A	22.37:g.41790179G>A		55.0	0.0	0		71.0	23.0	0.323944	NM_003216	B0QYS8|B2RC22|Q15729|Q7Z3J7|Q8IU94|Q96TG4	Silent	SNP	ENST00000266304.4	37	CCDS14014.1	57	0.0260989010989011	2	0.0040650406504065045	10	0.027624309392265192	3	0.005244755244755245	42	0.055408970976253295	G	9.184	1.024330	0.19433	0.009986	0.051977	ENSG00000167074	ENST00000413942	.	.	.	5.78	-6.36	0.01969	.	.	.	.	.	T	0.04724	0.0128	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.31861	-0.9928	4	.	.	.	-14.0578	1.4557	0.02384	0.2829:0.3399:0.1884:0.1888	rs17365991;rs59727856;rs17365991	.	.	.	Q	151	.	.	R	+	2	0	TEF	40120125	0.000000	0.05858	0.903000	0.35520	0.978000	0.69477	-2.554000	0.00926	-1.214000	0.02614	-1.259000	0.01468	CGG	G|0.970;A|0.030	0.030	strong		0.567	TEF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320692.1	NM_003216	
ATE1	11101	hgsc.bcm.edu	37	10	123670575	123670575	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:123670575G>T	ENST00000224652.6	-	5	514	c.429C>A	c.(427-429)ctC>ctA	p.L143L	ATE1_ENST00000535655.1_5'UTR|ATE1_ENST00000369040.3_Silent_p.L47L|ATE1_ENST00000543447.1_Silent_p.L28L|ATE1_ENST00000540606.1_Silent_p.L136L|ATE1_ENST00000369043.3_Silent_p.L143L	NM_001001976.1	NP_001001976.1	O95260	ATE1_HUMAN	arginyltransferase 1	143					protein arginylation (GO:0016598)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginyltransferase activity (GO:0004057)	p.L143L(1)		endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		all_neural(114;0.061)|Lung NSC(174;0.095)|all_lung(145;0.124)|Breast(234;0.212)				TGTCATCACTGAGTGTTTTAA	0.378																																					p.L143L		Atlas-SNP	.											ATE1,mouth,carcinoma,0,1	ATE1	67	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C429A						PASS	.						136.0	139.0	138.0					10																	123670575		2203	4300	6503	SO:0001819	synonymous_variant	11101	exon5			ATCACTGAGTGTT	AF079098	CCDS31299.1, CCDS31300.1, CCDS73211.1, CCDS73212.1, CCDS73213.1	10q26	2013-05-08			ENSG00000107669	ENSG00000107669	2.3.2.8		782	protein-coding gene	gene with protein product		607103				16002466, 16943202	Standard	XM_005269458		Approved		uc001lfq.3	O95260	OTTHUMG00000019178	ENST00000224652.6:c.429C>A	10.37:g.123670575G>T		197.0	0.0	0		188.0	104.0	0.553191	NM_001001976	O95261|Q5SQQ3|Q8WW04	Silent	SNP	ENST00000224652.6	37	CCDS31300.1	.	.	.	.	.	.	.	.	.	.	G	0.199	-1.046145	0.01997	.	.	ENSG00000107669	ENST00000423243	.	.	.	5.78	-2.6	0.06190	.	.	.	.	.	T	0.18173	0.0436	.	.	.	0.28353	N	0.920826	.	.	.	.	.	.	T	0.27400	-1.0075	4	.	.	.	-12.2001	0.864	0.01199	0.242:0.2723:0.2842:0.2015	.	.	.	.	K	140	.	.	Q	-	1	0	ATE1	123660565	0.003000	0.15002	0.000000	0.03702	0.179000	0.23085	-0.111000	0.10807	-0.488000	0.06726	-0.253000	0.11424	CAG	.	.	none		0.378	ATE1-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_001001976	
C7orf33	202865	hgsc.bcm.edu	37	7	148288020	148288020	+	Start_Codon_SNP	SNP	G	G	T	rs62624492	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:148288020G>T	ENST00000307003.2	+	1	364	c.3G>T	c.(1-3)atG>atT	p.M1I		NM_145304.2	NP_660347.1	Q8WU49	CG033_HUMAN	chromosome 7 open reading frame 33	1										central_nervous_system(1)|large_intestine(4)|lung(7)|prostate(2)	14	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00291)			TTGCCAAAATGCAAGTGGAAG	0.542													G|||	137	0.0273562	0.0076	0.0893	5008	,	,		20107	0.001		0.0239	False		,,,				2504	0.0409				p.M1I		Atlas-SNP	.											.	C7orf33	28	.	0			c.G3T						PASS	.	G	ILE/MET	54,4352	52.9+/-88.7	1,52,2150	49.0	51.0	50.0		3	-3.8	0.0	7	dbSNP_129	50	291,8309	107.2+/-168.0	4,283,4013	yes	missense	C7orf33	NM_145304.2	10	5,335,6163	TT,TG,GG		3.3837,1.2256,2.6526	benign	1/178	148288020	345,12661	2203	4300	6503	SO:0001582	initiator_codon_variant	202865	exon1			CAAAATGCAAGTG	BC021251	CCDS5890.1	7q36.1	2011-11-24			ENSG00000170279	ENSG00000170279			21724	protein-coding gene	gene with protein product							Standard	NM_145304		Approved		uc003wew.3	Q8WU49	OTTHUMG00000152756	ENST00000307003.2:c.3G>T	7.37:g.148288020G>T	ENSP00000304071:p.Met1Ile	43.0	0.0	0		54.0	28.0	0.518519	NM_145304		Missense_Mutation	SNP	ENST00000307003.2	37	CCDS5890.1	41	0.018772893772893772	4	0.008130081300813009	21	0.058011049723756904	0	0.0	16	0.021108179419525065	G	6.790	0.514812	0.12944	0.012256	0.033837	ENSG00000170279	ENST00000307003	.	.	.	3.77	-3.77	0.04346	.	.	.	.	.	T	0.05502	0.0145	.	.	.	0.54753	D	0.999982	B	0.12013	0.005	B	0.12156	0.007	T	0.08827	-1.0703	7	0.87932	D	0	.	0.8787	0.01230	0.3112:0.29:0.2515:0.1473	rs62624492	1	Q8WU49	CG033_HUMAN	I	1	.	ENSP00000304071:M1I	M	+	3	0	C7orf33	147918953	0.000000	0.05858	0.000000	0.03702	0.166000	0.22503	-0.382000	0.07408	-1.036000	0.03287	0.563000	0.77884	ATG	G|0.974;T|0.026	0.026	strong		0.542	C7orf33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327684.1	NM_145304	Missense_Mutation
CSNK2A2	1459	hgsc.bcm.edu	37	16	58201631	58201631	+	Silent	SNP	G	G	A	rs55748630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58201631G>A	ENST00000262506.3	-	7	765	c.582C>T	c.(580-582)gcC>gcT	p.A194A	CSNK2A2_ENST00000566813.1_5'UTR	NM_001896.2	NP_001887.1	P19784	CSK22_HUMAN	casein kinase 2, alpha prime polypeptide	194	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|mitotic cell cycle (GO:0000278)|mitotic spindle checkpoint (GO:0071174)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein N-terminus binding (GO:0047485)|protein serine/threonine kinase activity (GO:0004674)			central_nervous_system(1)	1						AGTACCTTGAGGCTACACGAA	0.438													G|||	4	0.000798722	0.0	0.0	5008	,	,		18027	0.001		0.003	False		,,,				2504	0.0				p.A194A	Melanoma(54;119 1219 18349 35700 39738)	Atlas-SNP	.											.	CSNK2A2	25	.	0			c.C582T						PASS	.	G		2,4394	4.2+/-10.8	0,2,2196	110.0	98.0	102.0		582	0.9	1.0	16	dbSNP_129	102	51,8549	32.8+/-85.7	0,51,4249	no	coding-synonymous	CSNK2A2	NM_001896.2		0,53,6445	AA,AG,GG		0.593,0.0455,0.4078		194/351	58201631	53,12943	2198	4300	6498	SO:0001819	synonymous_variant	1459	exon7			CCTTGAGGCTACA	M55268	CCDS10794.1	16q21	2013-01-17			ENSG00000070770	ENSG00000070770			2459	protein-coding gene	gene with protein product		115442				2174700, 1766873	Standard	NM_001896		Approved	CSNK2A1	uc002enc.3	P19784	OTTHUMG00000133488	ENST00000262506.3:c.582C>T	16.37:g.58201631G>A		88.0	0.0	0		89.0	43.0	0.483146	NM_001896		Silent	SNP	ENST00000262506.3	37	CCDS10794.1																																																																																			G|0.997;A|0.003	0.003	strong		0.438	CSNK2A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257386.2	NM_001896	
EVPL	2125	hgsc.bcm.edu	37	17	74006317	74006317	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:74006317T>C	ENST00000301607.3	-	22	3222	c.2969A>G	c.(2968-2970)cAg>cGg	p.Q990R	EVPL_ENST00000586740.1_Missense_Mutation_p.Q1012R	NM_001988.2	NP_001979.2	Q92817	EVPL_HUMAN	envoplakin	990	Central fibrous rod domain.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cell junction (GO:0030054)|cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	protein binding, bridging (GO:0030674)|structural molecule activity (GO:0005198)			breast(4)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(14)|ovary(2)|pancreas(2)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	54						CAGGTCTGCCTGCAGGCCAGC	0.637																																					p.Q990R		Atlas-SNP	.											.	EVPL	155	.	0			c.A2969G						PASS	.						39.0	43.0	42.0					17																	74006317		2203	4300	6503	SO:0001583	missense	2125	exon22			TCTGCCTGCAGGC	U53786	CCDS11737.1	17q25	2008-07-18				ENSG00000167880			3503	protein-coding gene	gene with protein product		601590				8938451, 10409435	Standard	NM_001988		Approved	EVPK	uc002jqi.2	Q92817		ENST00000301607.3:c.2969A>G	17.37:g.74006317T>C	ENSP00000301607:p.Gln990Arg	105.0	0.0	0		101.0	54.0	0.534653	NM_001988	A0AUV5	Missense_Mutation	SNP	ENST00000301607.3	37	CCDS11737.1	.	.	.	.	.	.	.	.	.	.	T	12.10	1.836978	0.32421	.	.	ENSG00000167880	ENST00000301607	T	0.66815	-0.23	4.72	3.63	0.41609	.	0.198103	0.44285	D	0.000466	T	0.56877	0.2015	L	0.53780	1.695	0.33077	D	0.536119	B;B	0.16396	0.017;0.013	B;B	0.16289	0.015;0.005	T	0.64728	-0.6339	10	0.66056	D	0.02	-42.4684	5.9853	0.19430	0.1469:0.081:0.0:0.772	.	1012;990	B7ZLH8;Q92817	.;EVPL_HUMAN	R	990	ENSP00000301607:Q990R	ENSP00000301607:Q990R	Q	-	2	0	EVPL	71517912	1.000000	0.71417	1.000000	0.80357	0.713000	0.41058	5.028000	0.64115	1.887000	0.54652	0.402000	0.26972	CAG	.	.	none		0.637	EVPL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449483.1	NM_001988	
SPECC1L	23384	hgsc.bcm.edu	37	22	24718408	24718408	+	Missense_Mutation	SNP	G	G	A	rs55723436	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:24718408G>A	ENST00000314328.9	+	5	1745	c.1460G>A	c.(1459-1461)cGc>cAc	p.R487H	SPECC1L_ENST00000541492.1_Missense_Mutation_p.R487H|SPECC1L_ENST00000437398.1_Missense_Mutation_p.R487H|SPECC1L_ENST00000416735.1_Intron|SPECC1L-ADORA2A_ENST00000358654.2_Missense_Mutation_p.R487H	NM_001254733.1|NM_015330.3	NP_001241662.1|NP_056145	Q69YQ0	CYTSA_HUMAN	sperm antigen with calponin homology and coiled-coil domains 1-like	487					actin cytoskeleton organization (GO:0030036)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell migration (GO:0016477)|negative regulation of actin filament depolymerization (GO:0030835)|negative regulation of microtubule depolymerization (GO:0007026)	cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|gap junction (GO:0005921)|microtubule organizing center (GO:0005815)				breast(1)|endometrium(1)|kidney(4)|large_intestine(7)|lung(6)|ovary(1)|prostate(1)|skin(3)|stomach(2)|urinary_tract(1)	27						AAAAGTGGGCGCTATATGGAA	0.423													G|||	18	0.00359425	0.0008	0.0058	5008	,	,		22148	0.0		0.0099	False		,,,				2504	0.0031				p.R487H		Atlas-SNP	.											.	SPECC1L	85	.	0			c.G1460A						PASS	.	G	HIS/ARG,HIS/ARG	9,4397	16.8+/-37.8	0,9,2194	88.0	89.0	89.0		1460,1460	5.4	1.0	22	dbSNP_129	89	80,8520	45.8+/-104.6	0,80,4220	yes	missense,missense	SPECC1L	NM_001145468.1,NM_015330.2	29,29	0,89,6414	AA,AG,GG		0.9302,0.2043,0.6843	probably-damaging,probably-damaging	487/1118,487/1118	24718408	89,12917	2203	4300	6503	SO:0001583	missense	23384	exon4			GTGGGCGCTATAT	AK025531	CCDS33619.1, CCDS58797.1	22q11.23	2012-12-20	2010-09-17	2010-09-17	ENSG00000100014	ENSG00000100014			29022	protein-coding gene	gene with protein product	"""cytokinesis and spindle organization A"", ""cytospin A"""	614140	"""SPECC1-like"""			9205841	Standard	NM_001254733		Approved	KIAA0376, CYTSA	uc002zzv.4	Q69YQ0	OTTHUMG00000171450	ENST00000314328.9:c.1460G>A	22.37:g.24718408G>A	ENSP00000325785:p.Arg487His	105.0	0.0	0		91.0	42.0	0.461538	NM_001145468	B7Z758|F5H1H6|O15081	Missense_Mutation	SNP	ENST00000314328.9	37	CCDS33619.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	G	27.1	4.796160	0.90453	0.002043	0.009302	ENSG00000100014	ENST00000398280;ENST00000437398;ENST00000421374;ENST00000314328;ENST00000541492	T;T;T;T	0.08370	3.1;3.1;3.1;3.1	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.17280	0.0415	L	0.45581	1.43	0.80722	D	1	D;D	0.89917	1.0;0.999	D;P	0.70716	0.97;0.893	T	0.00085	-1.2098	10	0.56958	D	0.05	-15.9709	18.1791	0.89771	0.0:0.0:1.0:0.0	rs55723436	487;487	F5H1H6;Q69YQ0	.;CYTSA_HUMAN	H	515;487;487;487;487	ENSP00000393363:R487H;ENSP00000405671:R487H;ENSP00000325785:R487H;ENSP00000439633:R487H	ENSP00000325785:R487H	R	+	2	0	SPECC1L	23048408	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.647000	0.98478	2.550000	0.86006	0.591000	0.81541	CGC	G|0.993;A|0.007	0.007	strong		0.423	SPECC1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319986.2	NM_015330	
RALGAPA2	57186	hgsc.bcm.edu	37	20	20565512	20565512	+	Nonsense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:20565512T>A	ENST00000202677.7	-	19	2534	c.2527A>T	c.(2527-2529)Aag>Tag	p.K843*		NM_020343.3	NP_065076.2	Q2PPJ7	RGPA2_HUMAN	Ral GTPase activating protein, alpha subunit 2 (catalytic)	843					activation of Ral GTPase activity (GO:0032859)|membrane organization (GO:0061024)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|plasma membrane (GO:0005886)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(25)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	54						AACTTACTCTTCTGTCTTTCC	0.358																																					p.K843X		Atlas-SNP	.											.	RALGAPA2	274	.	0			c.A2527T						PASS	.						155.0	153.0	154.0					20																	20565512		1833	4097	5930	SO:0001587	stop_gained	57186	exon19			TACTCTTCTGTCT	AL078634, DQ310704	CCDS46584.1	20p11.23	2009-09-09	2009-09-09	2009-09-09	ENSG00000188559	ENSG00000188559			16207	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 74"""	C20orf74		16490346, 19520869	Standard	NM_020343		Approved	dJ1049G11.4, AS250, KIAA1272, RapGAPalpha2	uc002wrz.3	Q2PPJ7	OTTHUMG00000032010	ENST00000202677.7:c.2527A>T	20.37:g.20565512T>A	ENSP00000202677:p.Lys843*	64.0	0.0	0		75.0	36.0	0.48	NM_020343	Q4VXU6|Q5JUA3|Q5JUA4|Q5T9K3|Q96CX9|Q9BQT7|Q9H9D9|Q9ULE8	Nonsense_Mutation	SNP	ENST00000202677.7	37	CCDS46584.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	38|38	7.167061|7.167061	0.98107|0.98107	.|.	.|.	ENSG00000188559|ENSG00000188559	ENST00000202677|ENST00000430436	.|.	.|.	.|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.301070|.	0.35291|.	N|.	0.003317|.	.|T	.|0.64811	.|0.2632	.|.	.|.	.|.	0.80722|0.80722	A|A	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.71130	.|-0.4682	.|3	0.02654|.	T|.	1|.	.|.	13.4407|13.4407	0.61112|0.61112	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|.	.|.	.|.	X|S	843|659	.|.	ENSP00000202677:K843X|.	K|R	-|-	1|3	0|2	RALGAPA2|RALGAPA2	20513512|20513512	1.000000|1.000000	0.71417|0.71417	0.965000|0.965000	0.40720|0.40720	0.124000|0.124000	0.20399|0.20399	4.597000|4.597000	0.61062|0.61062	2.217000|2.217000	0.71921|0.71921	0.482000|0.482000	0.46254|0.46254	AAG|AGA	.	.	none		0.358	RALGAPA2-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000471941.1	NM_020343	
VLDLR	7436	hgsc.bcm.edu	37	9	2644799	2644799	+	Missense_Mutation	SNP	T	T	C	rs142885301	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:2644799T>C	ENST00000382100.3	+	8	1488	c.1132T>C	c.(1132-1134)Tac>Cac	p.Y378H	VLDLR_ENST00000382099.2_Missense_Mutation_p.Y378H	NM_003383.3	NP_003374.3	P98155	VLDLR_HUMAN	very low density lipoprotein receptor	378	EGF-like 1. {ECO:0000255|PROSITE- ProRule:PRU00076}.				cholesterol metabolic process (GO:0008203)|glycoprotein transport (GO:0034436)|lipid transport (GO:0006869)|memory (GO:0007613)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|positive regulation of dendrite development (GO:1900006)|positive regulation of protein kinase activity (GO:0045860)|receptor-mediated endocytosis (GO:0006898)|reelin-mediated signaling pathway (GO:0038026)|signal transduction (GO:0007165)|ventral spinal cord development (GO:0021517)|very-low-density lipoprotein particle clearance (GO:0034447)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|very-low-density lipoprotein particle (GO:0034361)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|glycoprotein binding (GO:0001948)|glycoprotein transporter activity (GO:0034437)|low-density lipoprotein receptor activity (GO:0005041)|reelin receptor activity (GO:0038025)|very-low-density lipoprotein particle binding (GO:0034189)|very-low-density lipoprotein particle receptor activity (GO:0030229)			breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	24				GBM - Glioblastoma multiforme(50;0.0668)|Lung(218;0.123)		AGTTATAGGCTACGAGTGTGA	0.413																																					p.Y378H		Atlas-SNP	.											.	VLDLR	68	.	0			c.T1132C						PASS	.	T	HIS/TYR,HIS/TYR	1,4405	2.1+/-5.4	0,1,2202	95.0	95.0	95.0		1132,1132	5.8	1.0	9	dbSNP_134	95	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense	VLDLR	NM_001018056.1,NM_003383.3	83,83	0,2,6501	CC,CT,TT		0.0116,0.0227,0.0154	possibly-damaging,possibly-damaging	378/846,378/874	2644799	2,13004	2203	4300	6503	SO:0001583	missense	7436	exon8			ATAGGCTACGAGT		CCDS6446.1, CCDS34979.1	9p24	2014-01-24			ENSG00000147852	ENSG00000147852		"""Low density lipoprotein receptors"""	12698	protein-coding gene	gene with protein product		192977				8294473	Standard	XM_006716864		Approved	CARMQ1, CHRMQ1, VLDLRCH	uc003zhk.1	P98155	OTTHUMG00000019447	ENST00000382100.3:c.1132T>C	9.37:g.2644799T>C	ENSP00000371532:p.Tyr378His	109.0	0.0	0		131.0	70.0	0.534351	NM_003383	B2RMZ7|D3DRH6|Q5VVF6	Missense_Mutation	SNP	ENST00000382100.3	37	CCDS6446.1	.	.	.	.	.	.	.	.	.	.	T	27.1	4.797534	0.90538	2.27E-4	1.16E-4	ENSG00000147852	ENST00000382100;ENST00000382099;ENST00000382092	D;D	0.96913	-4.17;-4.17	5.83	5.83	0.93111	Growth factor, receptor (1);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.48286	D	0.000194	D	0.97046	0.9035	L	0.52573	1.65	0.53688	D	0.999971	D;D;D	0.57257	0.979;0.964;0.964	D;P;P	0.65874	0.939;0.87;0.87	D	0.96766	0.9565	10	0.39692	T	0.17	.	16.1968	0.82036	0.0:0.0:0.0:1.0	.	378;378;378	P98155-2;Q5VVF5;P98155	.;.;VLDLR_HUMAN	H	378;378;257	ENSP00000371532:Y378H;ENSP00000371531:Y378H	ENSP00000371524:Y257H	Y	+	1	0	VLDLR	2634799	1.000000	0.71417	0.967000	0.41034	0.975000	0.68041	5.983000	0.70540	2.225000	0.72522	0.533000	0.62120	TAC	T|0.999;C|0.001	0.001	strong		0.413	VLDLR-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000051519.2	NM_003383	
FKBP5	2289	hgsc.bcm.edu	37	6	35544942	35544942	+	Silent	SNP	G	G	A	rs34866878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:35544942G>A	ENST00000539068.1	-	10	1297	c.1095C>T	c.(1093-1095)aaC>aaT	p.N365N	FKBP5_ENST00000357266.4_Silent_p.N365N|FKBP5_ENST00000536438.1_Silent_p.N365N|FKBP5_ENST00000540787.1_Silent_p.N186N	NM_001145776.1	NP_001139248.1	Q13451	FKBP5_HUMAN	FK506 binding protein 5	365					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	FK506 binding (GO:0005528)|heat shock protein binding (GO:0031072)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(3)|urinary_tract(2)	17						ACTCAAACTCGTTCATGAGCA	0.483													G|||	334	0.0666933	0.2239	0.0245	5008	,	,		18453	0.001		0.0179	False		,,,				2504	0.002				p.N365N		Atlas-SNP	.											.	FKBP5	64	.	0			c.C1095T						PASS	.	G	,,	815,3591	326.1+/-299.4	68,679,1456	161.0	154.0	156.0		1095,1095,1095	-3.6	0.8	6	dbSNP_126	156	225,8375	92.8+/-154.8	5,215,4080	no	coding-synonymous,coding-synonymous,coding-synonymous	FKBP5	NM_001145775.1,NM_001145776.1,NM_004117.3	,,	73,894,5536	AA,AG,GG		2.6163,18.4975,7.9963	,,	365/458,365/458,365/458	35544942	1040,11966	2203	4300	6503	SO:0001819	synonymous_variant	2289	exon11			AAACTCGTTCATG	U42031	CCDS4808.1, CCDS54996.1	6p21.31	2013-01-10	2001-11-28		ENSG00000096060	ENSG00000096060		"""Tetratricopeptide (TTC) repeat domain containing"""	3721	protein-coding gene	gene with protein product		602623	"""FK506-binding protein 5"""			9001212	Standard	NM_004117		Approved	FKBP51, FKBP54, PPIase, P54, Ptg-10	uc003okx.2	Q13451	OTTHUMG00000014576	ENST00000539068.1:c.1095C>T	6.37:g.35544942G>A		160.0	0.0	0		168.0	90.0	0.535714	NM_001145775	F5H7R1|Q59EB8|Q5TGM6	Silent	SNP	ENST00000539068.1	37	CCDS4808.1																																																																																			G|0.928;A|0.072	0.072	strong		0.483	FKBP5-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040309.2		
COL6A2	1292	hgsc.bcm.edu	37	21	47552449	47552449	+	Missense_Mutation	SNP	A	A	C	rs11910483	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47552449A>C	ENST00000300527.4	+	28	3147	c.3043A>C	c.(3043-3045)Atc>Ctc	p.I1015L		NM_001849.3	NP_001840.3	P12110	CO6A2_HUMAN	collagen, type VI, alpha 2	1015	Nonhelical region.		I -> L (in dbSNP:rs11910483).		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)		CGACCGCTTCATCCGCTGGAT	0.697													A|||	106	0.0211661	0.0756	0.0072	5008	,	,		13410	0.0		0.001	False		,,,				2504	0.0				p.I1015L		Atlas-SNP	.											.	COL6A2	351	.	0			c.A3043C						PASS	.	A	LEU/ILE	281,4115		10,261,1927	38.0	32.0	34.0		3043	4.4	1.0	21	dbSNP_120	34	4,8592		0,4,4294	yes	missense	COL6A2	NM_001849.3	5	10,265,6221	CC,CA,AA		0.0465,6.3922,2.1937	possibly-damaging	1015/1020	47552449	285,12707	2198	4298	6496	SO:0001583	missense	1292	exon28			CGCTTCATCCGCT	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.3043A>C	21.37:g.47552449A>C	ENSP00000300527:p.Ile1015Leu	24.0	0.0	0		65.0	29.0	0.446154	NM_001849	Q13909|Q13910|Q13911|Q14048|Q14049|Q16259|Q16597|Q6P0Q1|Q9UML3|Q9Y4S8	Missense_Mutation	SNP	ENST00000300527.4	37	CCDS13728.1	40	0.018315018315018316	37	0.07520325203252033	3	0.008287292817679558	0	0.0	0	0.0	A	11.98	1.799818	0.31869	0.063922	4.65E-4	ENSG00000142173	ENST00000300527	T	0.77098	-1.07	4.4	4.4	0.53042	.	0.115804	0.56097	D	0.000028	T	0.16557	0.0398	L	0.53249	1.67	0.80722	D	1	P	0.44690	0.841	P	0.45449	0.481	T	0.49835	-0.8897	10	0.32370	T	0.25	-18.2856	13.6411	0.62251	1.0:0.0:0.0:0.0	rs11910483	1015	P12110	CO6A2_HUMAN	L	1015	ENSP00000300527:I1015L	ENSP00000300527:I1015L	I	+	1	0	COL6A2	46376877	1.000000	0.71417	1.000000	0.80357	0.661000	0.39034	2.891000	0.48617	1.628000	0.50416	0.247000	0.18012	ATC	A|0.975;C|0.025	0.025	strong		0.697	COL6A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206971.1		
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919237	51919237	+	Silent	SNP	C	C	T	rs199590261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919237C>T	ENST00000339313.5	-	5	1055	c.939G>A	c.(937-939)gtG>gtA	p.V313V	SIGLEC10_ENST00000439889.2_Silent_p.V255V|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Silent_p.V265V|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000353836.5_Silent_p.V313V|SIGLEC10_ENST00000432469.2_Silent_p.V230V|SIGLEC10_ENST00000441969.3_Silent_p.V255V|SIGLEC10_ENST00000356298.5_Silent_p.V313V|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	313	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CCCCAGCCTTCACCCCGGGCA	0.677													c|||	19	0.00379393	0.0015	0.0058	5008	,	,		16746	0.0		0.0089	False		,,,				2504	0.0041				p.V313V		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.G939A						PASS	.						38.0	43.0	42.0					19																	51919237		2203	4300	6503	SO:0001819	synonymous_variant	89790	exon5			AGCCTTCACCCCG	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.939G>A	19.37:g.51919237C>T		193.0	0.0	0		109.0	33.0	0.302752	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Silent	SNP	ENST00000339313.5	37	CCDS12832.1																																																																																			C|0.994;T|0.006	0.006	strong		0.677	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
DCPS	28960	hgsc.bcm.edu	37	11	126215285	126215285	+	Missense_Mutation	SNP	G	G	A	rs140377449	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:126215285G>A	ENST00000263579.4	+	6	1120	c.791G>A	c.(790-792)cGa>cAa	p.R264Q	DCPS_ENST00000530860.1_3'UTR	NM_014026.3	NP_054745.1	Q96C86	DCPS_HUMAN	decapping enzyme, scavenger	264					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)		GACCATCTGCGAGTATACCTG	0.667													G|||	2	0.000399361	0.0	0.0	5008	,	,		18562	0.0		0.0	False		,,,				2504	0.002				p.R264Q		Atlas-SNP	.											.	DCPS	33	.	0			c.G791A						PASS	.	G	GLN/ARG	0,4402		0,0,2201	205.0	133.0	157.0		791	5.2	0.2	11	dbSNP_134	157	11,8585	8.4+/-32.0	0,11,4287	yes	missense	DCPS	NM_014026.3	43	0,11,6488	AA,AG,GG		0.128,0.0,0.0846	probably-damaging	264/338	126215285	11,12987	2201	4298	6499	SO:0001583	missense	28960	exon6			ATCTGCGAGTATA	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.791G>A	11.37:g.126215285G>A	ENSP00000263579:p.Arg264Gln	56.0	0.0	0		54.0	23.0	0.425926	NM_014026	Q8NHL8|Q9Y2S5	Missense_Mutation	SNP	ENST00000263579.4	37	CCDS8473.1	.	.	.	.	.	.	.	.	.	.	G	22.9	4.344847	0.82022	0.0	0.00128	ENSG00000110063	ENST00000263579	D	0.96200	-3.94	5.16	5.16	0.70880	Histidine triad, conserved site (1);Histidine triad-like motif (1);	0.000000	0.85682	D	0.000000	D	0.98385	0.9463	M	0.93375	3.41	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	D	0.99364	1.0918	10	0.66056	D	0.02	-12.5139	18.7289	0.91726	0.0:0.0:1.0:0.0	.	264	Q96C86	DCPS_HUMAN	Q	264	ENSP00000263579:R264Q	ENSP00000263579:R264Q	R	+	2	0	DCPS	125720495	1.000000	0.71417	0.226000	0.23910	0.260000	0.26232	9.476000	0.97823	2.421000	0.82119	0.555000	0.69702	CGA	G|0.999;A|0.001	0.001	strong		0.667	DCPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386455.1	NM_014026	
PKD1L1	168507	hgsc.bcm.edu	37	7	47925520	47925520	+	Missense_Mutation	SNP	C	C	T	rs141646493	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:47925520C>T	ENST00000289672.2	-	18	3019	c.2969G>A	c.(2968-2970)cGg>cAg	p.R990Q		NM_138295.3	NP_612152.1	Q8TDX9	PK1L1_HUMAN	polycystic kidney disease 1 like 1	990	REJ. {ECO:0000255|PROSITE- ProRule:PRU00511}.				detection of mechanical stimulus (GO:0050982)|detection of nodal flow (GO:0003127)|left/right axis specification (GO:0070986)|single organismal cell-cell adhesion (GO:0016337)	calcium channel complex (GO:0034704)|cilium (GO:0005929)|membrane (GO:0016020)|nonmotile primary cilium (GO:0031513)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)		BBS9/PKD1L1(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(27)|lung(44)|ovary(12)|prostate(5)|skin(8)|stomach(4)|upper_aerodigestive_tract(5)	142						TGAAGGTTCCCGTGAGAATGG	0.587													c|||	9	0.00179712	0.0023	0.0029	5008	,	,		15149	0.0		0.004	False		,,,				2504	0.0				p.R990Q		Atlas-SNP	.											PKD1L1,colon,carcinoma,-1,1	PKD1L1	328	1	0			c.G2969A						scavenged	.	T	GLN/ARG	14,4392	22.3+/-47.3	0,14,2189	94.0	86.0	89.0		2969	-8.7	0.0	7	dbSNP_134	89	62,8538	39.8+/-96.3	1,60,4239	yes	missense	PKD1L1	NM_138295.3	43	1,74,6428	TT,TC,CC		0.7209,0.3177,0.5843	possibly-damaging	990/2850	47925520	76,12930	2203	4300	6503	SO:0001583	missense	168507	exon18			GGTTCCCGTGAGA	AB061683	CCDS34633.1	7p12.3	2008-07-18			ENSG00000158683	ENSG00000158683			18053	protein-coding gene	gene with protein product	"""polycystin-1L1"""	609721				11863367	Standard	NM_138295		Approved	PRO19563	uc003tny.2	Q8TDX9	OTTHUMG00000155649	ENST00000289672.2:c.2969G>A	7.37:g.47925520C>T	ENSP00000289672:p.Arg990Gln	145.0	2.0	0.0137931		194.0	98.0	0.505155	NM_138295	Q6UWK1	Missense_Mutation	SNP	ENST00000289672.2	37	CCDS34633.1	5	0.0022893772893772895	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	3	0.00395778364116095	c	5.043	0.193531	0.09599	0.003177	0.007209	ENSG00000158683	ENST00000289672	T	0.19938	2.11	4.97	-8.7	0.00851	Egg jelly receptor, REJ-like (1);PKD/REJ-like protein (1);	165.707000	0.00166	N	0.000000	T	0.04588	0.0125	N	0.08118	0	0.09310	N	1	B	0.28605	0.217	B	0.14578	0.011	T	0.18366	-1.0339	10	0.19590	T	0.45	0.4961	1.9019	0.03269	0.1463:0.1646:0.3674:0.3217	.	990	Q8TDX9	PK1L1_HUMAN	Q	990	ENSP00000289672:R990Q	ENSP00000289672:R990Q	R	-	2	0	PKD1L1	47892045	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.006000	0.01459	-2.302000	0.00657	-0.835000	0.03068	CGG	C|0.995;T|0.005	0.005	strong		0.587	PKD1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340974.1	NM_138295	
FBXO45	200933	hgsc.bcm.edu	37	3	196295974	196295974	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196295974C>T	ENST00000311630.6	+	1	416	c.119C>T	c.(118-120)cCc>cTc	p.P40L	WDR53_ENST00000433160.1_5'Flank|FBXO45_ENST00000440469.1_Intron|WDR53_ENST00000332629.5_5'Flank|WDR53_ENST00000429115.1_5'Flank	NM_001105573.1	NP_001099043.1	P0C2W1	FBSP1_HUMAN	F-box protein 45	40	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.				anterior commissure morphogenesis (GO:0021960)|cellular response to DNA damage stimulus (GO:0006974)|cerebral cortex radially oriented cell migration (GO:0021799)|cerebral cortex tangential migration (GO:0021800)|corticospinal tract morphogenesis (GO:0021957)|neuron migration (GO:0001764)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|synapse assembly involved in innervation (GO:0060386)	cell junction (GO:0030054)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)				cervix(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)|upper_aerodigestive_tract(1)	7	all_cancers(143;8.88e-09)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;2.75e-23)|all cancers(36;2.47e-21)|OV - Ovarian serous cystadenocarcinoma(49;2.32e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00314)		ggccggcTGCCCAGCCGGGTG	0.771																																					p.P40L		Atlas-SNP	.											.	FBXO45	18	.	0			c.C119T						PASS	.						2.0	3.0	3.0					3																	196295974		1415	3033	4448	SO:0001583	missense	200933	exon1			GGCTGCCCAGCCG	AK025697	CCDS46985.1	3q29	2008-02-05			ENSG00000174013	ENSG00000174013		"""F-boxes /  ""other"""""	29148	protein-coding gene	gene with protein product		609112					Standard	NM_001105573		Approved	Fbx45	uc010iai.3	P0C2W1	OTTHUMG00000155571	ENST00000311630.6:c.119C>T	3.37:g.196295974C>T	ENSP00000310332:p.Pro40Leu	19.0	0.0	0		55.0	27.0	0.490909	NM_001105573	A6NF90|D3DXB5	Missense_Mutation	SNP	ENST00000311630.6	37	CCDS46985.1	.	.	.	.	.	.	.	.	.	.	c	23.0	4.361705	0.82353	.	.	ENSG00000174013	ENST00000311630	D	0.99709	-6.48	4.78	4.78	0.61160	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	0.124714	0.56097	N	0.000035	D	0.99760	0.9903	M	0.92833	3.35	0.80722	D	1	D	0.89917	1.0	D	0.75020	0.985	D	0.97050	0.9763	10	0.87932	D	0	.	16.7012	0.85349	0.0:1.0:0.0:0.0	.	40	P0C2W1	FBSP1_HUMAN	L	40	ENSP00000310332:P40L	ENSP00000310332:P40L	P	+	2	0	FBXO45	197780371	1.000000	0.71417	1.000000	0.80357	0.627000	0.37826	4.709000	0.61867	2.214000	0.71695	0.531000	0.56144	CCC	.	.	none		0.771	FBXO45-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340687.2		
EML6	400954	hgsc.bcm.edu	37	2	55119771	55119771	+	Missense_Mutation	SNP	T	T	A	rs200933456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:55119771T>A	ENST00000356458.6	+	18	3240	c.2720T>A	c.(2719-2721)tTt>tAt	p.F907Y		NM_001039753.2	NP_001034842.2	Q6ZMW3	EMAL6_HUMAN	echinoderm microtubule associated protein like 6	907						cytoplasm (GO:0005737)|microtubule (GO:0005874)				breast(1)|endometrium(6)	7						GGGCCTGTGTTTGCTATGTAT	0.413													T|||	3	0.000599042	0.0	0.0014	5008	,	,		19318	0.0		0.0	False		,,,				2504	0.002				p.F907Y		Atlas-SNP	.											.	EML6	85	.	0			c.T2720A						PASS	.	T	TYR/PHE	0,1384		0,0,692	275.0	242.0	252.0		2720	5.6	1.0	2		252	9,3173		0,9,1582	yes	missense	EML6	NM_001039753.2	22	0,9,2274	AA,AT,TT		0.2828,0.0,0.1971	possibly-damaging	907/1959	55119771	9,4557	692	1591	2283	SO:0001583	missense	400954	exon18			CTGTGTTTGCTAT		CCDS46286.1	2p16.1	2013-01-10			ENSG00000214595	ENSG00000214595		"""WD repeat domain containing"""	35412	protein-coding gene	gene with protein product							Standard	NM_001039753		Approved	FLJ42562	uc002ryb.4	Q6ZMW3	OTTHUMG00000152035	ENST00000356458.6:c.2720T>A	2.37:g.55119771T>A	ENSP00000348842:p.Phe907Tyr	87.0	0.0	0		89.0	41.0	0.460674	NM_001039753	A8MUB5|B6ZDG7	Missense_Mutation	SNP	ENST00000356458.6	37	CCDS46286.1	.	.	.	.	.	.	.	.	.	.	T	29.3	4.994989	0.93167	0.0	0.002828	ENSG00000214595	ENST00000356458	T	0.01258	5.09	5.55	5.55	0.83447	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.52532	U	0.000079	T	0.06554	0.0168	L	0.58354	1.805	0.50313	D	0.999862	D	0.67145	0.996	D	0.66084	0.941	T	0.10359	-1.0633	10	0.72032	D	0.01	.	15.6956	0.77494	0.0:0.0:0.0:1.0	.	907	Q6ZMW3	EMAL6_HUMAN	Y	907	ENSP00000348842:F907Y	ENSP00000348842:F907Y	F	+	2	0	EML6	54973275	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	7.608000	0.82898	2.110000	0.64415	0.477000	0.44152	TTT	T|0.995;A|0.005	0.005	strong		0.413	EML6-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324997.3	XM_001725002	
PDE1C	5137	hgsc.bcm.edu	37	7	31793087	31793087	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:31793087C>T	ENST00000396191.1	-	18	2496	c.2041G>A	c.(2041-2043)Gat>Aat	p.D681N	PDE1C_ENST00000396193.1_Missense_Mutation_p.D741N|PDE1C_ENST00000321453.7_Missense_Mutation_p.D681N	NM_001191057.1	NP_001177986.1	Q14123	PDE1C_HUMAN	phosphodiesterase 1C, calmodulin-dependent 70kDa	681					activation of phospholipase C activity (GO:0007202)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|metabolic process (GO:0008152)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)	cytosol (GO:0005829)	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity (GO:0004117)|metal ion binding (GO:0046872)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(38)|prostate(4)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	81			GBM - Glioblastoma multiforme(11;0.216)		Caffeine(DB00201)	GGATGCTCATCAGTTTTCTTT	0.453																																					p.D741N		Atlas-SNP	.											PDE1C_ENST00000396193,right_upper_lobe,carcinoma,0,2	PDE1C	465	2	0			c.G2221A						scavenged	.						259.0	253.0	255.0					7																	31793087		876	1991	2867	SO:0001583	missense	5137	exon19			GCTCATCAGTTTT	U40371	CCDS5437.1, CCDS55099.1, CCDS55100.1	7p15.1-p14.3	2008-05-15	2002-08-29		ENSG00000154678	ENSG00000154678	3.1.4.17	"""Phosphodiesterases"""	8776	protein-coding gene	gene with protein product		602987	"""phosphodiesterase 1C, calmodulin-dependent (70kD)"""			8557689	Standard	XM_005249769		Approved	Hcam3	uc003tco.2	Q14123	OTTHUMG00000023836	ENST00000396191.1:c.2041G>A	7.37:g.31793087C>T	ENSP00000379494:p.Asp681Asn	157.0	1.0	0.00636943		124.0	62.0	0.5	NM_001191058	B3KPC6|E9PE92|Q14124|Q8NB10	Missense_Mutation	SNP	ENST00000396191.1	37	CCDS55099.1	.	.	.	.	.	.	.	.	.	.	C	18.29	3.590817	0.66219	.	.	ENSG00000154678	ENST00000396193;ENST00000396191;ENST00000321453	T;T;T	0.73789	-0.78;-0.77;-0.77	5.36	5.36	0.76844	.	0.378221	0.29892	N	0.010933	T	0.65533	0.2700	L	0.27053	0.805	0.80722	D	1	B;B	0.17667	0.023;0.023	B;B	0.20184	0.028;0.021	T	0.63328	-0.6662	10	0.87932	D	0	.	16.103	0.81201	0.0:1.0:0.0:0.0	.	741;681	E9PE92;Q14123	.;PDE1C_HUMAN	N	741;681;681	ENSP00000379496:D741N;ENSP00000379494:D681N;ENSP00000318105:D681N	ENSP00000318105:D681N	D	-	1	0	PDE1C	31759612	0.998000	0.40836	0.996000	0.52242	0.939000	0.58152	4.150000	0.58098	2.789000	0.95967	0.591000	0.81541	GAT	.	.	none		0.453	PDE1C-006	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000328458.1		
SPATA31D1	389763	hgsc.bcm.edu	37	9	84605350	84605350	+	Missense_Mutation	SNP	G	G	C	rs367877053		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:84605350G>C	ENST00000344803.2	+	3	298	c.251G>C	c.(250-252)aGt>aCt	p.S84T		NM_001001670.2	NP_001001670.1	Q6ZQQ2	S31D1_HUMAN	SPATA31 subfamily D, member 1	84					cell differentiation (GO:0030154)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)											GACTGGAAAAGTTTCCAGAGA	0.433																																					p.S84T		Atlas-SNP	.											.	.	.	.	0			c.G251C						PASS	.	G	THR/SER	0,3710		0,0,1855	85.0	79.0	81.0		251	-5.6	0.0	9		81	1,8179		0,1,4089	no	missense	FAM75D1	NM_001001670.2	58	0,1,5944	CC,CG,GG		0.0122,0.0,0.0084	benign	84/1577	84605350	1,11889	1855	4090	5945	SO:0001583	missense	389763	exon3			GGAAAAGTTTCCA		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.251G>C	9.37:g.84605350G>C	ENSP00000341988:p.Ser84Thr	142.0	0.0	0		145.0	70.0	0.482759	NM_001001670		Missense_Mutation	SNP	ENST00000344803.2	37	CCDS47986.1	.	.	.	.	.	.	.	.	.	.	G	0.010	-1.766413	0.00651	0.0	1.22E-4	ENSG00000214929	ENST00000344803	T	0.05081	3.5	2.82	-5.63	0.02474	.	16.493900	0.00166	N	0.000000	T	0.02304	0.0071	N	0.02916	-0.46	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35574	-0.9783	10	0.18276	T	0.48	18.5219	1.232	0.01945	0.1706:0.3724:0.205:0.252	.	84	Q6ZQQ2	F75D1_HUMAN	T	84	ENSP00000341988:S84T	ENSP00000341988:S84T	S	+	2	0	FAM75D1	83795170	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.865000	0.01649	-4.130000	0.00071	-1.316000	0.01300	AGT	.	.	weak		0.433	SPATA31D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402325.1	NM_001001670	
TAF6L	10629	hgsc.bcm.edu	37	11	62543326	62543326	+	Missense_Mutation	SNP	C	C	T	rs76769410	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:62543326C>T	ENST00000294168.3	+	2	272	c.71C>T	c.(70-72)aCg>aTg	p.T24M	TMEM223_ENST00000527073.1_Intron	NM_006473.3	NP_006464.1	Q9Y6J9	TAF6L_HUMAN	TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65kDa	24					chromatin organization (GO:0006325)|chromatin remodeling (GO:0006338)|DNA-templated transcription, initiation (GO:0006352)|histone H3 acetylation (GO:0043966)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	histone deacetylase complex (GO:0000118)|STAGA complex (GO:0030914)	DNA binding (GO:0003677)|transcription coactivator activity (GO:0003713)			endometrium(2)|large_intestine(5)|lung(4)|ovary(3)|prostate(1)|skin(1)	16						GCGGAGAGCACGGGCCTGGAG	0.637													C|||	13	0.00259585	0.0015	0.0014	5008	,	,		18124	0.0		0.008	False		,,,				2504	0.002				p.T24M		Atlas-SNP	.											.	TAF6L	39	.	0			c.C71T						PASS	.	C	MET/THR	9,4393	16.8+/-37.8	0,9,2192	69.0	68.0	68.0		71	3.9	1.0	11	dbSNP_131	68	78,8520	45.4+/-104.0	2,74,4223	yes	missense	TAF6L	NM_006473.3	81	2,83,6415	TT,TC,CC		0.9072,0.2045,0.6692	possibly-damaging	24/623	62543326	87,12913	2201	4299	6500	SO:0001583	missense	10629	exon2			AGAGCACGGGCCT	BC008785	CCDS8035.1	11q12.3	2008-02-01	2002-08-29		ENSG00000162227	ENSG00000162227			17305	protein-coding gene	gene with protein product		602946	"""TAF6-like RNA polymerase II, p300/CBP-associated factor (PCAF)-associated factor, 65 kD"""			9674425	Standard	NM_006473		Approved	PAF65A	uc001nvc.3	Q9Y6J9	OTTHUMG00000167610	ENST00000294168.3:c.71C>T	11.37:g.62543326C>T	ENSP00000294168:p.Thr24Met	53.0	0.0	0		57.0	33.0	0.578947	NM_006473	B2RAT0|Q96HA6	Missense_Mutation	SNP	ENST00000294168.3	37	CCDS8035.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	12.19	1.864603	0.32977	0.002045	0.009072	ENSG00000162227	ENST00000294168;ENST00000526261;ENST00000529509	T;T;T	0.42131	0.98;0.98;0.98	4.78	3.86	0.44501	Histone-fold (2);TATA box binding protein associated factor (TAF) (2);	0.211038	0.39615	N	0.001303	T	0.15478	0.0373	N	0.11427	0.14	0.80722	D	1	B;B	0.22146	0.013;0.065	B;B	0.17098	0.006;0.017	T	0.04522	-1.0945	10	0.37606	T	0.19	1.1681	7.4374	0.27164	0.0:0.8078:0.0:0.1922	.	24;24	B4DVM4;Q9Y6J9	.;TAF6L_HUMAN	M	24	ENSP00000294168:T24M;ENSP00000435116:T24M;ENSP00000434662:T24M	ENSP00000294168:T24M	T	+	2	0	TAF6L	62299902	0.996000	0.38824	0.963000	0.40424	0.968000	0.65278	3.349000	0.52217	1.364000	0.46038	0.561000	0.74099	ACG	C|0.995;T|0.005	0.005	strong		0.637	TAF6L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395352.1	NM_006473	
CFAP46	54777	hgsc.bcm.edu	37	10	134691472	134691472	+	Missense_Mutation	SNP	C	C	A	rs181912601	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691472C>A	ENST00000368586.5	-	30	4225	c.4125G>T	c.(4123-4125)aaG>aaT	p.K1375N	TTC40_ENST00000368582.2_Missense_Mutation_p.K1375N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						tactcctctccttctccttct	0.463													C|||	47	0.00938498	0.0076	0.0086	5008	,	,		17464	0.002		0.0119	False		,,,				2504	0.0174				p.K1375N		Atlas-SNP	.											.	TTC40	100	.	0			c.G4125T						PASS	.																																			SO:0001583	missense	54777	exon30			CCTCTCCTTCTCC																												ENST00000368586.5:c.4125G>T	10.37:g.134691472C>A	ENSP00000357575:p.Lys1375Asn	301.0	0.0	0		255.0	66.0	0.258824	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	17	0.007783882783882784	5	0.01016260162601626	5	0.013812154696132596	0	0.0	7	0.009234828496042216	C	3.434	-0.115527	0.06881	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.06218	3.33;3.33	0.536	-0.606	0.11619	.	.	.	.	.	T	0.02688	0.0081	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.41413	-0.9510	5	0.32370	T	0.25	.	.	.	.	.	.	.	.	N	1375	ENSP00000357575:K1375N;ENSP00000357571:K1375N	ENSP00000357571:K1375N	K	-	3	2	C10orf93	134541462	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	-0.744000	0.04839	-1.743000	0.01340	-1.817000	0.00601	AAG	C|0.992;A|0.008	0.008	strong		0.463	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
TENM2	57451	hgsc.bcm.edu	37	5	167689162	167689162	+	Missense_Mutation	SNP	G	G	A	rs370473451		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:167689162G>A	ENST00000518659.1	+	29	7711	c.7672G>A	c.(7672-7674)Ggt>Agt	p.G2558S	TENM2_ENST00000519204.1_Missense_Mutation_p.G2437S|TENM2_ENST00000545108.1_Missense_Mutation_p.G2557S|TENM2_ENST00000403607.2_Missense_Mutation_p.G2382S|TENM2_ENST00000520394.1_Missense_Mutation_p.G2319S	NM_001122679.1	NP_001116151.1	Q9NT68	TEN2_HUMAN	teneurin transmembrane protein 2	2558					axon guidance (GO:0007411)|calcium-mediated signaling using intracellular calcium source (GO:0035584)|heterophilic cell-cell adhesion (GO:0007157)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of filopodium assembly (GO:0051491)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cell-cell junction (GO:0005911)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|endoplasmic reticulum (GO:0005783)|filopodium (GO:0030175)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|PML body (GO:0016605)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	cell adhesion molecule binding (GO:0050839)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)										AGAGAAAGCAGGTCACTGGTT	0.547																																					p.G2549S		Atlas-SNP	.											.	.	.	.	0			c.G7645A						PASS	.	G	SER/GLY	0,4040		0,0,2020	34.0	35.0	35.0		7645	5.4	1.0	5		35	1,8379		0,1,4189	no	missense	ODZ2	NM_001122679.1	56	0,1,6209	AA,AG,GG		0.0119,0.0,0.0081	probably-damaging	2549/2766	167689162	1,12419	2020	4190	6210	SO:0001583	missense	57451	exon29			AAAGCAGGTCACT	AB032953		5q35	2012-10-02	2012-10-02	2012-10-02	ENSG00000145934	ENSG00000145934			29943	protein-coding gene	gene with protein product		610119	"""odz, odd Oz/ten-m homolog 2 (Drosophila)"""	ODZ2		10625539	Standard	NM_001122679		Approved	KIAA1127, Ten-M2	uc010jjd.3	Q9NT68	OTTHUMG00000162928	ENST00000518659.1:c.7672G>A	5.37:g.167689162G>A	ENSP00000429430:p.Gly2558Ser	117.0	0.0	0		125.0	59.0	0.472	NM_001122679	Q9ULU2	Missense_Mutation	SNP	ENST00000518659.1	37		.	.	.	.	.	.	.	.	.	.	G	18.78	3.697687	0.68386	0.0	1.19E-4	ENSG00000145934	ENST00000518659;ENST00000545108;ENST00000519204;ENST00000520394;ENST00000403607	D;D;D;D;D	0.88896	-1.97;-1.96;-2.07;-2.43;-2.44	5.42	5.42	0.78866	.	0.102393	0.64402	D	0.000002	D	0.90397	0.6994	N	0.24115	0.695	0.58432	D	0.999992	D;D;D	0.89917	0.999;0.991;1.0	D;P;D	0.83275	0.974;0.842;0.996	D	0.87772	0.2606	10	0.21540	T	0.41	.	19.5868	0.95493	0.0:0.0:1.0:0.0	.	2557;2558;2319	F5H2D1;Q9NT68;F8VNQ3	.;TEN2_HUMAN;.	S	2558;2557;2437;2319;2382	ENSP00000429430:G2558S;ENSP00000438635:G2557S;ENSP00000428964:G2437S;ENSP00000427874:G2319S;ENSP00000384905:G2382S	ENSP00000384905:G2382S	G	+	1	0	ODZ2	167621740	1.000000	0.71417	0.977000	0.42913	0.886000	0.51366	9.809000	0.99208	2.694000	0.91930	0.655000	0.94253	GGT	.	.	weak		0.547	TENM2-001	KNOWN	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376096.1	NM_001122679	
PNKD	25953	hgsc.bcm.edu	37	2	219206738	219206738	+	Silent	SNP	C	C	A	rs34745867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219206738C>A	ENST00000273077.4	+	7	703	c.652C>A	c.(652-654)Cgg>Agg	p.R218R	PNKD_ENST00000258362.3_Silent_p.R194R|PNKD_ENST00000436005.2_Silent_p.R158R|AC021016.8_ENST00000411433.1_RNA	NM_015488.4	NP_056303.3	Q8N490	PNKD_HUMAN	paroxysmal nonkinesigenic dyskinesia	218					glutathione biosynthetic process (GO:0006750)|neuromuscular process controlling posture (GO:0050884)|regulation of dopamine metabolic process (GO:0042053)|regulation of synaptic transmission, dopaminergic (GO:0032225)	membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	hydroxyacylglutathione hydrolase activity (GO:0004416)|zinc ion binding (GO:0008270)			NS(1)|endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	10		Renal(207;0.0474)		Epithelial(149;7.33e-07)|all cancers(144;0.000133)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CAGCGTGGGACGGCTTCAGAT	0.597													C|||	28	0.00559105	0.0023	0.0101	5008	,	,		19253	0.0		0.0169	False		,,,				2504	0.001				p.R218R		Atlas-SNP	.											.	PNKD	58	.	0			c.C652A						PASS	.	C	,	18,4388	25.3+/-52.1	0,18,2185	132.0	109.0	117.0		652,580	2.7	1.0	2	dbSNP_126	117	222,8378	93.1+/-155.1	4,214,4082	no	coding-synonymous,coding-synonymous	PNKD	NM_015488.4,NM_022572.4	,	4,232,6267	AA,AC,CC		2.5814,0.4085,1.8453	,	218/386,194/362	219206738	240,12766	2203	4300	6503	SO:0001819	synonymous_variant	25953	exon7			GTGGGACGGCTTC		CCDS2411.1, CCDS2413.1, CCDS42816.1	2q35	2011-01-21	2007-07-12		ENSG00000127838	ENSG00000127838			9153	protein-coding gene	gene with protein product	"""myofibrillogenesis regulator 1"""	609023	"""paroxysmal nonkinesiogenic dyskinesia"""			8659518	Standard	NM_015488		Approved	DYT8, PDC, DKFZp564N1362, FPD1, MR-1, BRP17, FKSG19, TAHCCP2, KIAA1184, KIPP1184, MGC31943, PKND1	uc002vhn.3	Q8N490	OTTHUMG00000133110	ENST00000273077.4:c.652C>A	2.37:g.219206738C>A		127.0	0.0	0		102.0	47.0	0.460784	NM_015488	A8K1F2|Q96A48|Q9BU26|Q9NSX4|Q9ULN6|Q9Y4T1	Silent	SNP	ENST00000273077.4	37	CCDS2411.1																																																																																			C|0.982;A|0.018	0.018	strong		0.597	PNKD-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256775.2		
PIK3R6	146850	hgsc.bcm.edu	37	17	8733110	8733110	+	Splice_Site	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8733110C>T	ENST00000434064.2	-	9	802		c.e9-1		PIK3R6_ENST00000311434.9_Splice_Site			Q5UE93	PI3R6_HUMAN	phosphoinositide-3-kinase, regulatory subunit 6						angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|G-protein coupled receptor signaling pathway (GO:0007186)|phosphatidylinositol biosynthetic process (GO:0006661)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of angiogenesis (GO:0045766)|positive regulation of MAP kinase activity (GO:0043406)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)	1-phosphatidylinositol-4-phosphate 3-kinase, class IB complex (GO:0005944)|cytosol (GO:0005829)|membrane (GO:0016020)	1-phosphatidylinositol-3-kinase regulator activity (GO:0046935)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)										ACAAGGTCACCTGCAGAAAGG	0.632																																					.		Atlas-SNP	.											.	.	.	.	0			c.803-1G>A						PASS	.						51.0	61.0	58.0					17																	8733110		1949	3988	5937	SO:0001630	splice_region_variant	146850	exon11			GGTCACCTGCAGA	AK091819	CCDS73985.1	17p13.1	2013-01-31	2008-02-04	2008-02-04	ENSG00000174083	ENSG00000276231			27101	protein-coding gene	gene with protein product		611462	"""chromosome 17 open reading frame 38"""	C17orf38		16476736	Standard	NM_001010855		Approved	FLJ34500, HsT41028, p87PIKAP	uc002glq.1	Q5UE93	OTTHUMG00000132861	ENST00000434064.2:c.1463-1G>A	17.37:g.8733110C>T		44.0	0.0	0		35.0	12.0	0.342857	NM_001010855	Q658R3	Splice_Site	SNP	ENST00000434064.2	37																																																																																				.	.	none		0.632	PIK3R6-002	KNOWN	sequence_error|basic	processed_transcript	protein_coding	OTTHUMT00000400327.2	NM_001010855	Intron
SLC4A1	6521	hgsc.bcm.edu	37	17	42328846	42328846	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42328846G>A	ENST00000262418.6	-	18	2577	c.2422C>T	c.(2422-2424)Cgc>Tgc	p.R808C	AC003102.1_ENST00000399246.2_5'Flank	NM_000342.3	NP_000333.1	P02730	B3AT_HUMAN	solute carrier family 4 (anion exchanger), member 1 (Diego blood group)	808	Membrane (anion exchange).		R -> C (in SPH4; Jablonec). {ECO:0000269|PubMed:7530501}.|R -> H (in SPH4; Nara). {ECO:0000269|PubMed:10745622}.		anion transport (GO:0006820)|bicarbonate transport (GO:0015701)|cellular ion homeostasis (GO:0006873)|chloride transport (GO:0006821)|ion transport (GO:0006811)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cortical cytoskeleton (GO:0030863)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	anion transmembrane transporter activity (GO:0008509)|anion:anion antiporter activity (GO:0015301)|ankyrin binding (GO:0030506)|bicarbonate transmembrane transporter activity (GO:0015106)|chloride transmembrane transporter activity (GO:0015108)|inorganic anion exchanger activity (GO:0005452)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(9)|lung(16)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	40		Breast(137;0.014)|Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.115)		AGCAAGATGCGGTCAAAGAGC	0.587																																					p.R808C		Atlas-SNP	.											SLC4A1,NS,carcinoma,+1,2	SLC4A1	104	2	0			c.C2422T	GRCh37	CM951172	SLC4A1	M		PASS	.						130.0	116.0	121.0					17																	42328846		2203	4300	6503	SO:0001583	missense	6521	exon18			AGATGCGGTCAAA		CCDS11481.1	17q21.31	2014-07-19	2014-01-02		ENSG00000004939	ENSG00000004939		"""CD molecules"", ""Blood group antigens"", ""Solute carriers"""	11027	protein-coding gene	gene with protein product	"""Froese blood group"", ""Swann blood group"", ""Wright blood group"""	109270	"""Waldner blood group"", ""erythrocyte membrane protein band 3"", ""Diego blood group"", ""solute carrier family 4, anion exchanger, member 1 (erythrocyte membrane protein band 3, Diego blood group)"", ""solute carrier family 4 (anion exchanger), member 1"""	EPB3, AE1, DI, WD		8434259	Standard	NM_000342		Approved	RTA1A, CD233, FR, SW, WR	uc002igf.4	P02730	OTTHUMG00000156843	ENST00000262418.6:c.2422C>T	17.37:g.42328846G>A	ENSP00000262418:p.Arg808Cys	133.0	0.0	0		138.0	47.0	0.34058	NM_000342	G4V2I6|P78487|Q1ZZ45|Q4KKW9|Q4VB84|Q9UCY7|Q9UDJ1	Missense_Mutation	SNP	ENST00000262418.6	37	CCDS11481.1	.	.	.	.	.	.	.	.	.	.	G	23.8	4.454721	0.84209	.	.	ENSG00000004939	ENST00000262418	D	0.86694	-2.16	5.22	5.22	0.72569	Bicarbonate transporter, C-terminal (1);	0.000000	0.85682	D	0.000000	D	0.96200	0.8761	H	0.97564	4.03	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.97607	1.0127	10	0.87932	D	0	.	18.7637	0.91864	0.0:0.0:1.0:0.0	.	808	P02730	B3AT_HUMAN	C	808	ENSP00000262418:R808C	ENSP00000262418:R808C	R	-	1	0	SLC4A1	39684372	1.000000	0.71417	1.000000	0.80357	0.957000	0.61999	7.507000	0.81676	2.579000	0.87056	0.561000	0.74099	CGC	.	.	none		0.587	SLC4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346194.1	NM_000342	
SSTR5	6755	hgsc.bcm.edu	37	16	1129441	1129441	+	Silent	SNP	G	G	A	rs34608001	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1129441G>A	ENST00000293897.4	+	1	661	c.573G>A	c.(571-573)ccG>ccA	p.P191P	SSTR5_ENST00000562758.1_Silent_p.P191P|SSTR5_ENST00000397547.2_Silent_p.P191P|SSTR5-AS1_ENST00000569832.1_RNA	NM_001053.3	NP_001044.1	P35346	SSR5_HUMAN	somatostatin receptor 5	191					G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|glucose homeostasis (GO:0042593)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cytokinesis (GO:0032467)|regulation of insulin secretion (GO:0050796)|somatostatin signaling pathway (GO:0038170)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	somatostatin receptor activity (GO:0004994)			endometrium(2)|lung(5)|prostate(1)|skin(1)	9		Hepatocellular(780;0.00369)			Octreotide(DB00104)|Pasireotide(DB06663)|Vapreotide(DB04894)	CCAGCTGGCCGGAGCCCGTGG	0.687													G|||	59	0.0117812	0.0008	0.0231	5008	,	,		13403	0.0		0.0298	False		,,,				2504	0.0123				p.P191P		Atlas-SNP	.											.	SSTR5	36	.	0			c.G573A						PASS	.	G	,	19,4333		1,17,2158	23.0	27.0	26.0		573,573	-9.5	0.7	16	dbSNP_126	26	215,8347		2,211,4068	no	coding-synonymous,coding-synonymous	SSTR5	NM_001053.3,NM_001172560.1	,	3,228,6226	AA,AG,GG		2.5111,0.4366,1.812	,	191/365,191/365	1129441	234,12680	2176	4281	6457	SO:0001819	synonymous_variant	6755	exon2			CTGGCCGGAGCCC	D16827	CCDS10429.1	16p13.3	2012-08-08			ENSG00000162009	ENSG00000162009		"""GPCR / Class A : Somatostatin receptors"""	11334	protein-coding gene	gene with protein product		182455				7607700	Standard	NM_001053		Approved		uc021taf.1	P35346	OTTHUMG00000047842	ENST00000293897.4:c.573G>A	16.37:g.1129441G>A		33.0	0.0	0		70.0	37.0	0.528571	NM_001172560	P34988|Q541E0|Q9UJI5	Silent	SNP	ENST00000293897.4	37	CCDS10429.1																																																																																			G|0.983;A|0.017	0.017	strong		0.687	SSTR5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420836.1		
RTP2	344892	hgsc.bcm.edu	37	3	187419764	187419764	+	Silent	SNP	G	G	A	rs150707467		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:187419764G>A	ENST00000358241.1	-	1	581	c.153C>T	c.(151-153)caC>caT	p.H51H	RP11-211G3.3_ENST00000437407.1_5'Flank|RP11-211G3.3_ENST00000449623.1_5'Flank	NM_001004312.2	NP_001004312.2	Q5QGT7	RTP2_HUMAN	receptor (chemosensory) transporter protein 2	51					protein insertion into membrane (GO:0051205)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	olfactory receptor binding (GO:0031849)			large_intestine(3)|lung(14)|skin(1)	18	all_cancers(143;4.06e-12)|Ovarian(172;0.0418)		OV - Ovarian serous cystadenocarcinoma(80;1.76e-18)	GBM - Glioblastoma multiforme(93;0.0515)		TGCCTGAGGCGTGCTGCTCCA	0.627																																					p.H51H		Atlas-SNP	.											RTP2,right_upper_lobe,carcinoma,-2,1	RTP2	38	1	0			c.C153T						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	98.0	102.0	100.0		153	-6.0	0.9	3	dbSNP_134	100	8,8592	6.4+/-24.3	0,8,4292	no	coding-synonymous	RTP2	NM_001004312.2		0,9,6494	AA,AG,GG		0.093,0.0227,0.0692		51/226	187419764	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	344892	exon1			TGAGGCGTGCTGC	AY562236	CCDS33911.1	3q27.3	2014-02-20	2006-11-21		ENSG00000198471	ENSG00000198471		"""Receptor transporter proteins"""	32486	protein-coding gene	gene with protein product	"""receptor transporting protein 2"", ""zinc finger, 3CxxC-type 2"""	609138	"""receptor transporter protein 2"""			16271481, 15550249, 16720576	Standard	NM_001004312		Approved	MGC78665, Z3CXXC2	uc003fro.1	Q5QGT7	OTTHUMG00000156458	ENST00000358241.1:c.153C>T	3.37:g.187419764G>A		124.0	0.0	0		124.0	65.0	0.524194	NM_001004312	Q6NVH4	Silent	SNP	ENST00000358241.1	37	CCDS33911.1																																																																																			G|1.000;A|0.000	0.000	weak		0.627	RTP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344259.1	NM_001004312	
CFAP46	54777	hgsc.bcm.edu	37	10	134694391	134694391	+	Missense_Mutation	SNP	A	A	G	rs145022957	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134694391A>G	ENST00000368586.5	-	28	3873	c.3773T>C	c.(3772-3774)gTc>gCc	p.V1258A	TTC40_ENST00000368582.2_Missense_Mutation_p.V1258A	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TGGCTCAGGGACATCGCCGGG	0.677													a|||	47	0.00938498	0.0	0.0086	5008	,	,		15270	0.002		0.0129	False		,,,				2504	0.0266				p.V1258A		Atlas-SNP	.											.	TTC40	100	.	0			c.T3773C						PASS	.																																			SO:0001583	missense	54777	exon28			TCAGGGACATCGC																												ENST00000368586.5:c.3773T>C	10.37:g.134694391A>G	ENSP00000357575:p.Val1258Ala	15.0	0.0	0		30.0	14.0	0.466667	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	a	0.006	-2.077388	0.00375	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.40756	2.99;1.02	2.26	-1.98	0.07480	.	.	.	.	.	T	0.09247	0.0228	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.25398	-1.0133	6	0.02654	T	1	.	4.0251	0.09683	0.3732:0.3518:0.275:0.0	.	.	.	.	A	1258	ENSP00000357575:V1258A;ENSP00000357571:V1258A	ENSP00000357571:V1258A	V	-	2	0	C10orf93	134544381	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.712000	0.05013	-0.573000	0.05998	-1.948000	0.00487	GTC	A|0.993;G|0.007	0.007	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
NOTCH3	4854	hgsc.bcm.edu	37	19	15299048	15299048	+	Missense_Mutation	SNP	G	G	A	rs114207045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:15299048G>A	ENST00000263388.2	-	9	1565	c.1490C>T	c.(1489-1491)tCg>tTg	p.S497L		NM_000435.2	NP_000426.2	Q9UM47	NOTC3_HUMAN	notch 3	497	EGF-like 12; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				forebrain development (GO:0030900)|gene expression (GO:0010467)|glomerular capillary formation (GO:0072104)|negative regulation of neuron differentiation (GO:0045665)|neuron fate commitment (GO:0048663)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of smooth muscle cell proliferation (GO:0048661)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.S497L(1)		breast(4)|central_nervous_system(3)|endometrium(10)|kidney(3)|large_intestine(16)|liver(1)|lung(31)|ovary(8)|prostate(3)|skin(7)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	93			OV - Ovarian serous cystadenocarcinoma(3;2.6e-20)|Epithelial(3;1.34e-16)|all cancers(3;5.13e-15)			GTCCTCACCCGAGGGGCAGGT	0.562													G|||	37	0.00738818	0.0106	0.0086	5008	,	,		15109	0.001		0.006	False		,,,				2504	0.0102				p.S497L		Atlas-SNP	.											NOTCH3,rectum,carcinoma,0,1	NOTCH3	340	1	1	Substitution - Missense(1)	large_intestine(1)	c.C1490T						PASS	.	G	LEU/SER	46,4360		0,46,2157	27.0	26.0	26.0		1490	5.0	1.0	19	dbSNP_132	26	52,8544		0,52,4246	yes	missense	NOTCH3	NM_000435.2	145	0,98,6403	AA,AG,GG		0.6049,1.044,0.7537	benign	497/2322	15299048	98,12904	2203	4298	6501	SO:0001583	missense	4854	exon9			TCACCCGAGGGGC	U97669	CCDS12326.1	19p13.2-p13.1	2013-01-10	2010-06-24			ENSG00000074181		"""Ankyrin repeat domain containing"""	7883	protein-coding gene	gene with protein product		600276	"""Notch (Drosophila) homolog 3"", ""Notch homolog 3 (Drosophila)"""	CADASIL		7835890	Standard	NM_000435		Approved	CASIL	uc002nan.3	Q9UM47		ENST00000263388.2:c.1490C>T	19.37:g.15299048G>A	ENSP00000263388:p.Ser497Leu	51.0	0.0	0		47.0	16.0	0.340426	NM_000435	Q9UEB3|Q9UPL3|Q9Y6L8	Missense_Mutation	SNP	ENST00000263388.2	37	CCDS12326.1	15	0.006868131868131868	4	0.008130081300813009	7	0.019337016574585635	0	0.0	4	0.005277044854881266	g	13.27	2.185760	0.38609	0.01044	0.006049	ENSG00000074181	ENST00000263388;ENST00000539383	D	0.86694	-2.16	5.04	5.04	0.67666	EGF (1);EGF-like region, conserved site (2);EGF-like calcium-binding (1);Epidermal growth factor-like, type 3 (1);	0.000000	0.27705	N	0.018199	T	0.66694	0.2815	N	0.16708	0.43	0.41468	D	0.988085	B;B	0.22146	0.031;0.065	B;B	0.21708	0.02;0.036	T	0.70353	-0.4895	10	0.26408	T	0.33	.	17.1812	0.86855	0.0:0.0:1.0:0.0	.	500;497	Q59FL3;Q9UM47	.;NOTC3_HUMAN	L	497;499	ENSP00000263388:S497L	ENSP00000263388:S497L	S	-	2	0	NOTCH3	15160048	0.788000	0.28762	0.965000	0.40720	0.908000	0.53690	4.305000	0.59110	2.347000	0.79759	0.556000	0.70494	TCG	G|0.991;A|0.009	0.009	strong		0.562	NOTCH3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465714.1	NM_000435	
MOCOS	55034	hgsc.bcm.edu	37	18	33828916	33828916	+	Silent	SNP	A	A	G	rs55701019	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:33828916A>G	ENST00000261326.5	+	10	2013	c.1992A>G	c.(1990-1992)gaA>gaG	p.E664E		NM_017947.2	NP_060417.2			molybdenum cofactor sulfurase											breast(2)|endometrium(5)|kidney(1)|large_intestine(10)|liver(1)|lung(15)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	43						CTCTTGAGGAAAATAGTGAAC	0.408													A|||	34	0.00678914	0.0219	0.0058	5008	,	,		20756	0.0		0.001	False		,,,				2504	0.0				p.E664E		Atlas-SNP	.											.	MOCOS	84	.	0			c.A1992G						PASS	.	A		63,4343	59.3+/-96.0	0,63,2140	98.0	94.0	95.0		1992	-1.8	0.1	18	dbSNP_129	95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	MOCOS	NM_017947.2		0,65,6438	GG,GA,AA		0.0233,1.4299,0.4998		664/889	33828916	65,12941	2203	4300	6503	SO:0001819	synonymous_variant	55034	exon10			TGAGGAAAATAGT	AK000740	CCDS11919.1	18q12	2003-12-18			ENSG00000075643	ENSG00000075643			18234	protein-coding gene	gene with protein product		613274				11302742	Standard	NM_017947		Approved	HMCS, FLJ20733, MOS	uc002kzq.4	Q96EN8	OTTHUMG00000132590	ENST00000261326.5:c.1992A>G	18.37:g.33828916A>G		56.0	0.0	0		59.0	29.0	0.491525	NM_017947		Silent	SNP	ENST00000261326.5	37	CCDS11919.1																																																																																			A|0.995;G|0.005	0.005	strong		0.408	MOCOS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255801.1		
RXFP2	122042	hgsc.bcm.edu	37	13	32367214	32367214	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32367214G>A	ENST00000298386.2	+	16	1846	c.1775G>A	c.(1774-1776)gGa>gAa	p.G592E	RXFP2_ENST00000380314.1_Missense_Mutation_p.G568E	NM_130806.3	NP_570718.1	Q8WXD0	RXFP2_HUMAN	relaxin/insulin-like family peptide receptor 2	592					adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|male gonad development (GO:0008584)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|oocyte maturation (GO:0001556)|positive regulation of cAMP biosynthetic process (GO:0030819)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	peptide hormone binding (GO:0017046)|protein-hormone receptor activity (GO:0016500)			cervix(1)|endometrium(2)|large_intestine(15)|lung(13)|prostate(1)|stomach(1)	33		Lung SC(185;0.0262)		all cancers(112;0.000559)|Epithelial(112;0.0017)|OV - Ovarian serous cystadenocarcinoma(117;0.0145)|BRCA - Breast invasive adenocarcinoma(63;0.0535)		TATTCTCTTGGAATTTTCCTA	0.294																																					p.G592E		Atlas-SNP	.											RXFP2,colon,carcinoma,0,1	RXFP2	95	1	0			c.G1775A						scavenged	.						30.0	34.0	33.0					13																	32367214		2188	4292	6480	SO:0001583	missense	122042	exon16			CTCTTGGAATTTT	AF403384	CCDS9342.1, CCDS53862.1	13q12.3	2012-08-08	2006-05-09	2006-05-09	ENSG00000133105	ENSG00000133105		"""GPCR / Class A : Relaxin family peptide receptors"""	17318	protein-coding gene	gene with protein product		606655	"""leucine-rich repeat-containing G protein-coupled receptor 8"""	LGR8		12217959, 12970298, 15956688, 16507880	Standard	NM_130806		Approved	GREAT, GPR106, INSL3R, RXFPR2	uc001utt.3	Q8WXD0	OTTHUMG00000016690	ENST00000298386.2:c.1775G>A	13.37:g.32367214G>A	ENSP00000298386:p.Gly592Glu	50.0	0.0	0		68.0	3.0	0.0441176	NM_130806	B1ALE9|Q3KU23	Missense_Mutation	SNP	ENST00000298386.2	37	CCDS9342.1	.	.	.	.	.	.	.	.	.	.	G	18.67	3.673744	0.67928	.	.	ENSG00000133105	ENST00000380314;ENST00000298386	T;T	0.37235	1.21;1.21	5.73	4.88	0.63580	GPCR, rhodopsin-like superfamily (1);	0.102880	0.64402	D	0.000003	T	0.55401	0.1918	M	0.70275	2.135	0.80722	D	1	D;D	0.67145	0.996;0.996	D;D	0.65684	0.937;0.937	T	0.53920	-0.8370	10	0.28530	T	0.3	.	13.8607	0.63559	0.0:0.0:0.8462:0.1538	.	568;592	Q3KU23;Q8WXD0	.;RXFP2_HUMAN	E	568;592	ENSP00000369670:G568E;ENSP00000298386:G592E	ENSP00000298386:G592E	G	+	2	0	RXFP2	31265214	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	2.997000	0.49457	1.412000	0.46977	0.655000	0.94253	GGA	.	.	none		0.294	RXFP2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044399.1	NM_130806	
PRPF39	55015	hgsc.bcm.edu	37	14	45564675	45564675	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:45564675C>T	ENST00000355765.6	+	2	403	c.233C>T	c.(232-234)cCt>cTt	p.P78L		NM_017922.3	NP_060392.3	Q86UA1	PRP39_HUMAN	pre-mRNA processing factor 39	78					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)				breast(2)|endometrium(2)|kidney(4)|lung(3)|ovary(1)	12						GCAAATTTCCCTCCAGAATAT	0.398																																					p.P78L		Atlas-SNP	.											.	PRPF39	46	.	0			c.C233T						PASS	.						40.0	40.0	40.0					14																	45564675		1996	4194	6190	SO:0001583	missense	55015	exon2			ATTTCCCTCCAGA	AK000673	CCDS9682.2	14q21.1	2013-10-03	2013-10-03		ENSG00000185246	ENSG00000185246			20314	protein-coding gene	gene with protein product		614907	"""PRP39 pre-mRNA processing factor 39 homolog (yeast)"", ""PRP39 pre-mRNA processing factor 39 homolog (S. cerevisiae)"""				Standard	NM_017922		Approved	FLJ20666, FLJ11128	uc001wvz.4	Q86UA1	OTTHUMG00000140265	ENST00000355765.6:c.233C>T	14.37:g.45564675C>T	ENSP00000348010:p.Pro78Leu	84.0	0.0	0		94.0	4.0	0.0425532	NM_017922	Q08AL1|Q08AL2|Q9NUU5	Missense_Mutation	SNP	ENST00000355765.6	37	CCDS9682.2	.	.	.	.	.	.	.	.	.	.	C	18.84	3.710181	0.68730	.	.	ENSG00000185246	ENST00000355765;ENST00000553605	T	0.50548	0.74	5.72	5.72	0.89469	.	.	.	.	.	T	0.49064	0.1535	N	0.22421	0.69	0.80722	D	1	P	0.47962	0.903	P	0.53266	0.722	T	0.28427	-1.0044	9	0.23891	T	0.37	-12.9614	19.4498	0.94862	0.0:1.0:0.0:0.0	.	78	Q86UA1	PRP39_HUMAN	L	78	ENSP00000348010:P78L	ENSP00000348010:P78L	P	+	2	0	PRPF39	44634425	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.130000	0.77235	2.702000	0.92279	0.591000	0.81541	CCT	.	.	none		0.398	PRPF39-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000319683.2		
HECTD4	283450	hgsc.bcm.edu	37	12	112600883	112600883	+	Silent	SNP	C	C	T	rs183882784	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:112600883C>T	ENST00000430131.2	-	74	12962	c.11817G>A	c.(11815-11817)ccG>ccA	p.P3939P	HECTD4_ENST00000549141.1_5'Flank|HECTD4_ENST00000550722.1_Silent_p.P4215P|HECTD4_ENST00000377560.5_Silent_p.P4189P			Q9Y4D8	HECD4_HUMAN	HECT domain containing E3 ubiquitin protein ligase 4	3939	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				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)										TCATGGGGTACGGGGGCACAT	0.602													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		16711	0.001		0.006	False		,,,				2504	0.0051				p.P4227P		Atlas-SNP	.											.	.	.	.	0			c.G12681A						PASS	.	C		6,4042		0,6,2018	89.0	98.0	95.0		12567	-11.6	0.1	12		95	63,8265		0,63,4101	no	coding-synonymous	C12orf51	NM_001109662.2		0,69,6119	TT,TC,CC		0.7565,0.1482,0.5575		4189/4247	112600883	69,12307	2024	4164	6188	SO:0001819	synonymous_variant	283450	exon75			GGGGTACGGGGGC	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.11817G>A	12.37:g.112600883C>T		164.0	0.0	0		178.0	86.0	0.483146	NM_001109662	L8B0P6|Q3MJD5|Q6P0A0|Q7L530|Q8NB70|Q8WU73|Q96NT9|Q9NZS4|Q9UFT6	Silent	SNP	ENST00000430131.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.602	HECTD4-202	KNOWN	basic	protein_coding	protein_coding		NM_173813	
AXL	558	hgsc.bcm.edu	37	19	41745608	41745608	+	Missense_Mutation	SNP	A	A	C	rs199928489		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41745608A>C	ENST00000301178.4	+	10	1485	c.1295A>C	c.(1294-1296)cAg>cCg	p.Q432P	AXL_ENST00000593513.1_Missense_Mutation_p.Q164P|AXL_ENST00000359092.3_Intron	NM_001278599.1|NM_021913.3	NP_001265528.1|NP_068713	P30530	UFO_HUMAN	AXL receptor tyrosine kinase	432					apoptotic cell clearance (GO:0043277)|blood vessel remodeling (GO:0001974)|cell maturation (GO:0048469)|cellular response to extracellular stimulus (GO:0031668)|cellular response to hydrogen peroxide (GO:0070301)|cellular response to interferon-alpha (GO:0035457)|cellular response to lipopolysaccharide (GO:0071222)|dendritic cell differentiation (GO:0097028)|enzyme linked receptor protein signaling pathway (GO:0007167)|erythrocyte homeostasis (GO:0034101)|forebrain cell migration (GO:0021885)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|natural killer cell differentiation (GO:0001779)|negative regulation of dendritic cell apoptotic process (GO:2000669)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of tumor necrosis factor production (GO:0032720)|neuron migration (GO:0001764)|organ regeneration (GO:0031100)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of cytokine-mediated signaling pathway (GO:0001961)|positive regulation of natural killer cell differentiation (GO:0032825)|positive regulation of protein kinase B signaling (GO:0051897)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cell surface (GO:0009986)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|phosphatidylserine binding (GO:0001786)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(9)|lung(12)|ovary(3)|pancreas(1)|prostate(4)|skin(3)|stomach(3)|upper_aerodigestive_tract(1)	48						GGGCAAGCACAGCCAGTCCAC	0.572													a|||	1	0.000199681	0.0	0.0	5008	,	,		21079	0.0		0.001	False		,,,				2504	0.0				p.Q432P		Atlas-SNP	.											.	AXL	126	.	0			c.A1295C						PASS	.		,PRO/GLN	1,4405		0,1,2202	287.0	234.0	252.0		,1295	3.2	1.0	19		252	1,8599		0,1,4299	no	intron,missense	AXL	NM_001699.4,NM_021913.3	,76	0,2,6501	CC,CA,AA		0.0116,0.0227,0.0154	,possibly-damaging	,432/895	41745608	2,13004	2203	4300	6503	SO:0001583	missense	558	exon10			AAGCACAGCCAGT	M76125	CCDS12574.1, CCDS12575.1, CCDS62677.1	19q13.1	2013-02-11				ENSG00000167601	2.7.10.1	"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	905	protein-coding gene	gene with protein product		109135				1656220	Standard	NM_021913		Approved	UFO, JTK11	uc010ehj.3	P30530		ENST00000301178.4:c.1295A>C	19.37:g.41745608A>C	ENSP00000301178:p.Gln432Pro	109.0	0.0	0		130.0	67.0	0.515385	NM_021913	Q8N5L2|Q9UD27	Missense_Mutation	SNP	ENST00000301178.4	37	CCDS12575.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	N	8.956	0.969405	0.18659	2.27E-4	1.16E-4	ENSG00000167601	ENST00000301178	T	0.75260	-0.92	4.29	3.25	0.37280	.	0.612388	0.15184	N	0.275979	T	0.47002	0.1422	N	0.08118	0	0.80722	D	1	B	0.31931	0.347	B	0.23018	0.043	T	0.29610	-1.0006	10	0.29301	T	0.29	-5.3294	4.8946	0.13744	0.6168:0.1953:0.0:0.1879	.	432	P30530	UFO_HUMAN	P	432	ENSP00000301178:Q432P	ENSP00000301178:Q432P	Q	+	2	0	AXL	46437448	1.000000	0.71417	0.997000	0.53966	0.847000	0.48162	1.875000	0.39578	0.686000	0.31488	0.307000	0.20424	CAG	A|1.000;C|0.000	0.000	strong		0.572	AXL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000463323.2		
AP5Z1	9907	hgsc.bcm.edu	37	7	4821352	4821352	+	Missense_Mutation	SNP	G	G	C	rs11549840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4821352G>C	ENST00000348624.4	+	3	427	c.333G>C	c.(331-333)caG>caC	p.Q111H	AP5Z1_ENST00000401897.1_Missense_Mutation_p.Q111H	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	111					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											ACAGCCGGCAGCTGAGCCTGG	0.662													G|||	63	0.0125799	0.0015	0.0187	5008	,	,		17920	0.0		0.0249	False		,,,				2504	0.0235				p.Q111H		Atlas-SNP	.											.	.	.	.	0			c.G333C						PASS	.	G	HIS/GLN	13,4247		0,13,2117	21.0	26.0	24.0		333	2.1	0.8	7	dbSNP_120	24	205,8303		4,197,4053	yes	missense	KIAA0415	NM_014855.2	24	4,210,6170	CC,CG,GG		2.4095,0.3052,1.7074	possibly-damaging	111/808	4821352	218,12550	2130	4254	6384	SO:0001583	missense	9907	exon3			CCGGCAGCTGAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.333G>C	7.37:g.4821352G>C	ENSP00000297562:p.Gln111His	122.0	0.0	0		114.0	57.0	0.5	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	G	10.63	1.404230	0.25378	0.003052	0.024095	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.44482	0.92;0.92	5.08	2.13	0.27403	.	0.485095	0.20242	N	0.096270	T	0.13970	0.0338	M	0.63428	1.95	0.24747	N	0.993007	B	0.23316	0.083	B	0.20184	0.028	T	0.12941	-1.0528	10	0.27785	T	0.31	.	5.8299	0.18574	0.1763:0.2946:0.5291:0.0	rs11549840	111	O43299	K0415_HUMAN	H	111	ENSP00000297562:Q111H;ENSP00000384980:Q111H	ENSP00000297562:Q111H	Q	+	3	2	KIAA0415	4787878	0.601000	0.26907	0.815000	0.32552	0.847000	0.48162	-0.102000	0.10956	0.256000	0.21614	0.655000	0.94253	CAG	G|0.986;C|0.014	0.014	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
MSH2	4436	hgsc.bcm.edu	37	2	47637439	47637439	+	Silent	SNP	C	C	T	rs1800151	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:47637439C>T	ENST00000233146.2	+	3	796	c.573C>T	c.(571-573)ctC>ctT	p.L191L	MSH2_ENST00000406134.1_Silent_p.L191L|MSH2_ENST00000543555.1_Silent_p.L125L	NM_000251.2	NP_000242.1	P43246	MSH2_HUMAN	mutS homolog 2	191					ATP catabolic process (GO:0006200)|B cell differentiation (GO:0030183)|B cell mediated immunity (GO:0019724)|cell cycle arrest (GO:0007050)|determination of adult lifespan (GO:0008340)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|germ cell development (GO:0007281)|in utero embryonic development (GO:0001701)|intra-S DNA damage checkpoint (GO:0031573)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|isotype switching (GO:0045190)|maintenance of DNA repeat elements (GO:0043570)|male gonad development (GO:0008584)|meiotic gene conversion (GO:0006311)|meiotic mismatch repair (GO:0000710)|mismatch repair (GO:0006298)|negative regulation of DNA recombination (GO:0045910)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of reciprocal meiotic recombination (GO:0045128)|oxidative phosphorylation (GO:0006119)|positive regulation of helicase activity (GO:0051096)|postreplication repair (GO:0006301)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|somatic hypermutation of immunoglobulin genes (GO:0016446)|somatic recombination of immunoglobulin gene segments (GO:0016447)	membrane (GO:0016020)|MutSalpha complex (GO:0032301)|MutSbeta complex (GO:0032302)|nuclear chromosome (GO:0000228)	ATP binding (GO:0005524)|centromeric DNA binding (GO:0019237)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|double-strand/single-strand DNA junction binding (GO:0000406)|enzyme binding (GO:0019899)|guanine/thymine mispair binding (GO:0032137)|heteroduplex DNA loop binding (GO:0000404)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|Y-form DNA binding (GO:0000403)	p.0?(2)|p.?(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(9)|kidney(5)|large_intestine(50)|lung(18)|ovary(5)|prostate(2)|skin(3)|small_intestine(1)|stomach(2)|urinary_tract(1)	112		all_hematologic(82;0.0359)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			AGGCTCTCCTCATCCAGATTG	0.463			"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian"""	"""colorectal, endometrial, ovarian"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				C|||	97	0.019369	0.0696	0.0072	5008	,	,		15087	0.0		0.0	False		,,,				2504	0.0				p.L191L		Atlas-SNP	.	yes	Rec	yes	Hereditary non-polyposis colorectal cancer	2	2p22-p21	4436	mutS homolog 2 (E. coli)		E	.	MSH2	198	.	3	Whole gene deletion(2)|Unknown(1)	haematopoietic_and_lymphoid_tissue(3)	c.C573T						PASS	.	C		254,4152	146.9+/-181.5	4,246,1953	182.0	176.0	178.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	573	1.6	1.0	2	dbSNP_89	178	4,8596	3.0+/-9.4	0,4,4296	no	coding-synonymous	MSH2	NM_000251.1		4,250,6249	TT,TC,CC		0.0465,5.7649,1.9837		191/935	47637439	258,12748	2203	4300	6503	SO:0001819	synonymous_variant	4436	exon3	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	TCTCCTCATCCAG	U03911	CCDS1834.1, CCDS58709.1	2p21	2014-09-17	2013-09-12		ENSG00000095002	ENSG00000095002			7325	protein-coding gene	gene with protein product		609309	"""mutS (E. coli) homolog 2 (colon cancer, nonpolyposis type 1)"", ""mutS homolog 2, colon cancer, nonpolyposis type 1 (E. coli)"""	COCA1		8484120, 9843200	Standard	NM_000251		Approved	HNPCC, HNPCC1	uc002rvy.2	P43246	OTTHUMG00000128861	ENST00000233146.2:c.573C>T	2.37:g.47637439C>T		79.0	0.0	0		98.0	49.0	0.5	NM_000251	B4E2Z2|O75488	Silent	SNP	ENST00000233146.2	37	CCDS1834.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	MSH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250805.3		
KHDRBS2	202559	hgsc.bcm.edu	37	6	62390920	62390920	+	Missense_Mutation	SNP	G	G	A	rs61753606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:62390920G>A	ENST00000281156.4	-	9	1276	c.998C>T	c.(997-999)cCg>cTg	p.P333L	RP1-240B8.3_ENST00000511849.2_RNA	NM_152688.2	NP_689901.2	Q5VWX1	KHDR2_HUMAN	KH domain containing, RNA binding, signal transduction associated 2	333					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	poly(A) binding (GO:0008143)|poly(U) RNA binding (GO:0008266)			NS(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(5)|liver(1)|lung(13)|ovary(3)|prostate(3)|skin(12)|upper_aerodigestive_tract(2)|urinary_tract(1)	49				BRCA - Breast invasive adenocarcinoma(397;0.149)		TGACCTTTGCGGTGGTGCCTT	0.478													G|||	29	0.00579073	0.003	0.0086	5008	,	,		16587	0.0		0.0139	False		,,,				2504	0.0051				p.P333L		Atlas-SNP	.											KHDRBS2,NS,carcinoma,+1,2	KHDRBS2	103	2	0			c.C998T						PASS	.	G	LEU/PRO	13,4393	21.2+/-45.6	0,13,2190	186.0	130.0	149.0		998	5.1	0.8	6	dbSNP_129	149	141,8459	70.0+/-132.6	1,139,4160	no	missense	KHDRBS2	NM_152688.2	98	1,152,6350	AA,AG,GG		1.6395,0.2951,1.1841	benign	333/350	62390920	154,12852	2203	4300	6503	SO:0001583	missense	202559	exon9			CTTTGCGGTGGTG	BC034043	CCDS4963.1	6q11.1	2013-09-20			ENSG00000112232	ENSG00000112232			18114	protein-coding gene	gene with protein product	"""Sam68-like mammalian protein 1"""	610487					Standard	NM_152688		Approved	SLM1, SLM-1, MGC26664	uc003peg.2	Q5VWX1	OTTHUMG00000014936	ENST00000281156.4:c.998C>T	6.37:g.62390920G>A	ENSP00000281156:p.Pro333Leu	157.0	0.0	0		88.0	69.0	0.784091	NM_152688	A8K7M8|Q8N4I4|Q8TCZ4	Missense_Mutation	SNP	ENST00000281156.4	37	CCDS4963.1	15	0.006868131868131868	4	0.008130081300813009	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	10.68	1.419456	0.25552	0.002951	0.016395	ENSG00000112232	ENST00000281156	T	0.44083	0.93	5.13	5.13	0.70059	.	0.316534	0.34411	N	0.003988	T	0.14960	0.0361	N	0.15975	0.35	0.43959	D	0.996637	B	0.19817	0.039	B	0.11329	0.006	T	0.05241	-1.0897	10	0.56958	D	0.05	.	12.3163	0.54958	0.0783:0.0:0.9217:0.0	rs61753606	333	Q5VWX1	KHDR2_HUMAN	L	333	ENSP00000281156:P333L	ENSP00000281156:P333L	P	-	2	0	KHDRBS2	62448879	1.000000	0.71417	0.847000	0.33407	0.169000	0.22640	4.271000	0.58902	2.541000	0.85698	0.650000	0.86243	CCG	G|0.987;A|0.013	0.013	strong		0.478	KHDRBS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041066.2	NM_152688	
IGSF9B	22997	hgsc.bcm.edu	37	11	133801990	133801990	+	Silent	SNP	G	G	A	rs375960322		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:133801990G>A	ENST00000321016.8	-	8	1316	c.1086C>T	c.(1084-1086)gaC>gaT	p.D362D	IGSF9B_ENST00000533871.2_Silent_p.D362D			Q9UPX0	TUTLB_HUMAN	immunoglobulin superfamily, member 9B	362	Ig-like 4.				homophilic cell adhesion (GO:0007156)|positive regulation of inhibitory postsynaptic membrane potential (GO:0097151)	dendrite (GO:0030425)|inhibitory synapse (GO:0060077)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				breast(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(18)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	44	all_hematologic(175;0.127)	all_cancers(12;1.58e-21)|all_epithelial(12;5.17e-16)|all_lung(97;1.6e-05)|Lung NSC(97;3.86e-05)|Breast(109;0.000126)|Medulloblastoma(222;0.0245)|all_neural(223;0.0505)|Esophageal squamous(93;0.0559)		Epithelial(10;7.19e-10)|BRCA - Breast invasive adenocarcinoma(10;9.69e-09)|all cancers(11;1.23e-08)|OV - Ovarian serous cystadenocarcinoma(99;0.00328)|Lung(977;0.221)		GGGGACGGCCGTCCTTGTTCC	0.607																																					p.D362D		Atlas-SNP	.											.	IGSF9B	290	.	0			c.C1086T						PASS	.			0,4278		0,0,2139	70.0	86.0	81.0		1086	-8.2	0.8	11		81	1,8453		0,1,4226	no	coding-synonymous	IGSF9B	NM_014987.1		0,1,6365	AA,AG,GG		0.0118,0.0,0.0079		362/1350	133801990	1,12731	2139	4227	6366	SO:0001819	synonymous_variant	22997	exon8			ACGGCCGTCCTTG	AK097578	CCDS61010.1	11q25	2013-02-11	2005-10-12	2005-11-20				"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	32326	protein-coding gene	gene with protein product		613773					Standard	NM_001277285		Approved	KIAA1030	uc031qfh.1	Q9UPX0		ENST00000321016.8:c.1086C>T	11.37:g.133801990G>A		143.0	0.0	0		155.0	84.0	0.541936	NM_014987	G5EA26	Silent	SNP	ENST00000321016.8	37																																																																																				.	.	weak		0.607	IGSF9B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		XM_290502	
MRPL19	9801	hgsc.bcm.edu	37	2	75879359	75879359	+	Missense_Mutation	SNP	G	G	A	rs41382847	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:75879359G>A	ENST00000393909.2	+	3	338	c.313G>A	c.(313-315)Gta>Ata	p.V105I	MRPL19_ENST00000409374.1_Missense_Mutation_p.V105I|MRPL19_ENST00000358788.6_Missense_Mutation_p.V105I	NM_014763.3	NP_055578.2	P49406	RM19_HUMAN	mitochondrial ribosomal protein L19	105					translation (GO:0006412)	mitochondrion (GO:0005739)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			kidney(1)|large_intestine(1)|lung(6)	8						AAGGAGAAAAGTACTCCACAT	0.343													G|||	35	0.00698882	0.0008	0.0115	5008	,	,		15222	0.0		0.0149	False		,,,				2504	0.0112				p.V105I		Atlas-SNP	.											.	MRPL19	21	.	0			c.G313A						PASS	.	G	ILE/VAL	3,3617		0,3,1807	73.0	71.0	72.0		313	-0.5	1.0	2	dbSNP_127	72	74,8042		1,72,3985	yes	missense	MRPL19	NM_014763.3	29	1,75,5792	AA,AG,GG		0.9118,0.0829,0.6561	benign	105/293	75879359	77,11659	1810	4058	5868	SO:0001583	missense	9801	exon3			AGAAAAGTACTCC	AB051621	CCDS1960.2	2p11.1-q11.2	2012-09-13			ENSG00000115364	ENSG00000115364		"""Mitochondrial ribosomal proteins / large subunits"""	14052	protein-coding gene	gene with protein product	"""39S ribosomal protein L19"""	611832				11543634, 17309879	Standard	XM_006712155		Approved	MRP-L15, RPML15, KIAA0104, RLX1	uc002snl.3	P49406	OTTHUMG00000129990	ENST00000393909.2:c.313G>A	2.37:g.75879359G>A	ENSP00000377486:p.Val105Ile	371.0	0.0	0		349.0	177.0	0.507163	NM_014763	Q53TX9|Q96Q52	Missense_Mutation	SNP	ENST00000393909.2	37	CCDS1960.2	14	0.00641025641025641	0	0.0	5	0.013812154696132596	0	0.0	9	0.011873350923482849	G	12.24	1.877138	0.33162	8.29E-4	0.009118	ENSG00000115364	ENST00000393909;ENST00000409374	.	.	.	4.85	-0.463	0.12164	Translation protein SH3-like (1);	0.350899	0.32736	N	0.005705	T	0.50222	0.1603	M	0.69185	2.1	0.80722	D	1	B	0.20887	0.049	B	0.32022	0.139	T	0.48603	-0.9021	9	0.33940	T	0.23	-6.8784	10.7534	0.46221	0.3156:0.0:0.6844:0.0	rs41382847	105	P49406	RM19_HUMAN	I	105	.	ENSP00000377486:V105I	V	+	1	0	MRPL19	75732867	1.000000	0.71417	0.976000	0.42696	0.971000	0.66376	2.018000	0.40991	-0.205000	0.10219	-0.145000	0.13849	GTA	G|0.992;A|0.008	0.008	strong		0.343	MRPL19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252256.1	NM_014763	
MAK	4117	hgsc.bcm.edu	37	6	10775600	10775600	+	Missense_Mutation	SNP	G	G	A	rs567083	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:10775600G>A	ENST00000313243.2	-	12	1940	c.1558C>T	c.(1558-1560)Ccc>Tcc	p.P520S	MAK_ENST00000538030.1_3'UTR|MAK_ENST00000354489.2_Missense_Mutation_p.P520S|MAK_ENST00000474039.1_Missense_Mutation_p.P520S|SYCP2L_ENST00000543878.1_Intron|RP11-637O19.3_ENST00000480294.1_Intron			P20794	MAK_HUMAN	male germ cell-associated kinase	520			P -> S (in dbSNP:rs567083). {ECO:0000269|PubMed:17344846}.		cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|photoreceptor cell maintenance (GO:0045494)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|midbody (GO:0030496)|mitotic spindle (GO:0072686)|nucleus (GO:0005634)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)	ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(2)|kidney(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)	22	Breast(50;0.107)|Ovarian(93;0.107)	all_hematologic(90;0.117)				GCCCCAACGGGTCCCAGTGAC	0.453													G|||	99	0.0197684	0.0015	0.0908	5008	,	,		20809	0.0		0.0209	False		,,,				2504	0.0133				p.P520S		Atlas-SNP	.											.	MAK	47	.	0			c.C1558T						PASS	.	G	SER/PRO,SER/PRO	19,4387	26.2+/-53.5	0,19,2184	200.0	199.0	199.0		1558,1558	3.4	0.9	6	dbSNP_83	199	179,8421	81.8+/-144.4	2,175,4123	yes	missense,missense	MAK	NM_001242385.1,NM_005906.4	74,74	2,194,6307	AA,AG,GG		2.0814,0.4312,1.5224	benign,benign	520/584,520/624	10775600	198,12808	2203	4300	6503	SO:0001583	missense	4117	exon12			CAACGGGTCCCAG		CCDS4516.1, CCDS75398.1, CCDS75399.1	6p24.2	2014-01-28			ENSG00000111837	ENSG00000111837			6816	protein-coding gene	gene with protein product		154235				16951154	Standard	NM_005906		Approved	dJ417M14.2, RP62	uc021ylk.1	P20794	OTTHUMG00000014247	ENST00000313243.2:c.1558C>T	6.37:g.10775600G>A	ENSP00000313021:p.Pro520Ser	165.0	0.0	0		196.0	98.0	0.5	NM_005906	F1T0K6|G1FL29|Q547D0|Q9NUH7	Missense_Mutation	SNP	ENST00000313243.2	37	CCDS4516.1	43	0.019688644688644688	1	0.0020325203252032522	27	0.07458563535911603	0	0.0	15	0.01978891820580475	G	2.302	-0.359970	0.05103	0.004312	0.020814	ENSG00000111837	ENST00000313243;ENST00000354489	T;T	0.71461	-0.57;-0.57	6.17	3.36	0.38483	.	0.165506	0.53938	N	0.000048	T	0.27098	0.0664	N	0.20685	0.6	0.48571	D	0.999672	B	0.09022	0.002	B	0.09377	0.004	T	0.17137	-1.0379	10	0.08381	T	0.77	.	6.315	0.21186	0.1638:0.1538:0.6825:0.0	rs567083;rs1627871;rs17640406;rs52803991;rs567083	520	P20794	MAK_HUMAN	S	520	ENSP00000313021:P520S;ENSP00000346484:P520S	ENSP00000313021:P520S	P	-	1	0	MAK	10883586	0.831000	0.29352	0.918000	0.36340	0.161000	0.22273	0.171000	0.16685	0.884000	0.36064	0.655000	0.94253	CCC	A|0.017;C|0.006	0.017	strong		0.453	MAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039841.1	NM_005906	
PCOLCE	5118	hgsc.bcm.edu	37	7	100205365	100205365	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100205365C>T	ENST00000223061.5	+	8	1398	c.1118C>T	c.(1117-1119)tCt>tTt	p.S373F		NM_002593.3	NP_002584.2	Q15113	PCOC1_HUMAN	procollagen C-endopeptidase enhancer	373	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				multicellular organismal development (GO:0007275)|positive regulation of peptidase activity (GO:0010952)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|peptidase activator activity (GO:0016504)			breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(11)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	23	Lung NSC(181;0.0261)|all_lung(186;0.0392)|Esophageal squamous(72;0.0439)					GACCTGCCTTCTCCACCCACT	0.552																																					p.S373F		Atlas-SNP	.											.	PCOLCE	37	.	0			c.C1118T						PASS	.						154.0	146.0	149.0					7																	100205365		2203	4300	6503	SO:0001583	missense	5118	exon8			TGCCTTCTCCACC	L33799	CCDS5700.1	7q22	2008-07-18			ENSG00000106333	ENSG00000106333			8738	protein-coding gene	gene with protein product	"""procollagen, type 1, COOH-terminal proteinase enhancer"", ""procollagen C-proteinase enhancer 1"""	600270				8824813, 9799793	Standard	NM_002593		Approved	PCPE, PCPE1	uc003uvo.3	Q15113	OTTHUMG00000156675	ENST00000223061.5:c.1118C>T	7.37:g.100205365C>T	ENSP00000223061:p.Ser373Phe	140.0	0.0	0		145.0	61.0	0.42069	NM_002593	B2R9E1|O14550	Missense_Mutation	SNP	ENST00000223061.5	37	CCDS5700.1	.	.	.	.	.	.	.	.	.	.	C	14.38	2.518752	0.44763	.	.	ENSG00000106333	ENST00000223061	T	0.23552	1.9	4.42	3.5	0.40072	Tissue inhibitor of metalloproteinases-like, OB-fold (1);Netrin domain (1);Netrin module, non-TIMP type (2);	0.587059	0.17803	N	0.161488	T	0.38348	0.1037	L	0.44542	1.39	0.09310	N	1	D	0.65815	0.995	D	0.68943	0.961	T	0.07597	-1.0764	10	0.54805	T	0.06	-6.1274	9.2378	0.37477	0.2159:0.7841:0.0:0.0	.	373	Q15113	PCOC1_HUMAN	F	373	ENSP00000223061:S373F	ENSP00000223061:S373F	S	+	2	0	PCOLCE	100043301	0.082000	0.21442	0.994000	0.49952	0.730000	0.41778	1.614000	0.36911	1.017000	0.39495	0.462000	0.41574	TCT	.	.	none		0.552	PCOLCE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345285.1	NM_002593	
MZT2B	80097	hgsc.bcm.edu	37	2	130939163	130939163	+	5'Flank	SNP	G	G	T	rs146359515	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:130939163G>T	ENST00000281871.6	+	0	0				MZT2B_ENST00000409255.1_5'Flank|SMPD4_ENST00000431183.2_Missense_Mutation_p.F4L|SMPD4_ENST00000409031.1_Missense_Mutation_p.F4L|SMPD4_ENST00000452225.2_5'UTR|SMPD4_ENST00000426662.2_5'UTR|SMPD4_ENST00000339679.7_5'UTR|SMPD4_ENST00000443958.2_5'UTR|AC018804.1_ENST00000578074.1_RNA|SMPD4_ENST00000453750.1_Missense_Mutation_p.F4L|SMPD4_ENST00000473720.1_5'UTR|SMPD4_ENST00000351288.6_Missense_Mutation_p.F4L	NM_025029.3	NP_079305.2	Q6NZ67	MZT2B_HUMAN	mitotic spindle organizing protein 2B							centrosome (GO:0005813)|gamma-tubulin ring complex (GO:0008274)|spindle (GO:0005819)				lung(1)	1						CCACGGCGCCGAAAGTCGTCA	0.677													.|||	18	0.00359425	0.0	0.0086	5008	,	,		12025	0.0		0.0119	False		,,,				2504	0.0				p.F4L		Atlas-SNP	.											.	SMPD4	67	.	0			c.C12A						PASS	.	G	LEU/PHE,LEU/PHE,LEU/PHE	7,3753		0,7,1873	8.0	11.0	10.0		12,12,12	0.2	1.0	2	dbSNP_134	10	85,8099		0,85,4007	no	missense,missense,missense	SMPD4	NM_001171083.2,NM_017751.4,NM_017951.4	22,22,22	0,92,5880	TT,TG,GG		1.0386,0.1862,0.7703	benign,benign,benign	4/765,4/838,4/867	130939163	92,11852	1880	4092	5972	SO:0001631	upstream_gene_variant	55627	exon1			GGCGCCGAAAGTC	BC066296	CCDS2157.1	2q21.1	2013-10-11	2010-07-22	2010-07-22	ENSG00000152082	ENSG00000152082			25886	protein-coding gene	gene with protein product	"""mitotic-spindle organizing protein associated with a ring of gamma-tubulin 2B"""	613450	"""family with sequence similarity 128, member B"""	FAM128B		20360068	Standard	NM_025029		Approved	FLJ14346, MOZART2B	uc002tqu.3	Q6NZ67	OTTHUMG00000131625		2.37:g.130939163G>T	Exception_encountered	48.0	0.0	0		69.0	33.0	0.478261	NM_017751	Q96CG4	Missense_Mutation	SNP	ENST00000281871.6	37	CCDS2157.1	7	0.003205128205128205	0	0.0	3	0.008287292817679558	0	0.0	4	0.005277044854881266	N	8.707	0.911139	0.17833	0.001862	0.010386	ENSG00000136699	ENST00000351288;ENST00000409031;ENST00000431183;ENST00000453750	.	.	.	3.38	0.175	0.15045	.	.	.	.	.	T	0.21550	0.0519	N	0.19112	0.55	0.80722	D	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.05683	-1.0870	7	.	.	.	.	3.9534	0.09379	0.1266:0.0:0.4426:0.4308	.	4;4;4	E7ESA2;B4DM23;B1PBA3	.;.;.	L	4	.	.	F	-	3	2	SMPD4	130655633	0.722000	0.28017	0.965000	0.40720	0.152000	0.21847	-0.022000	0.12480	-0.086000	0.12550	0.455000	0.32223	TTC	G|0.996;T|0.004	0.004	strong		0.677	MZT2B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254518.1	NM_025029	
FRG1	2483	hgsc.bcm.edu	37	4	190876283	190876283	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:190876283C>A	ENST00000226798.4	+	5	631	c.409C>A	c.(409-411)Caa>Aaa	p.Q137K	FRG1_ENST00000514482.1_3'UTR	NM_004477.2	NP_004468.1	Q14331	FRG1_HUMAN	FSHD region gene 1	137					mRNA splicing, via spliceosome (GO:0000398)|muscle organ development (GO:0007517)|rRNA processing (GO:0006364)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|lung(11)|ovary(1)|pancreas(1)|prostate(5)|skin(7)|urinary_tract(1)	32		all_cancers(14;1.44e-58)|all_epithelial(14;6.32e-41)|all_lung(41;8.13e-17)|Lung NSC(41;2.13e-16)|Breast(6;2.54e-06)|Melanoma(20;0.000263)|Hepatocellular(41;0.00213)|Renal(120;0.0183)|all_hematologic(60;0.0358)|Prostate(90;0.0421)|all_neural(102;0.147)		all cancers(3;1.73e-30)|Epithelial(3;5.85e-30)|OV - Ovarian serous cystadenocarcinoma(60;5.56e-15)|BRCA - Breast invasive adenocarcinoma(30;9.14e-06)|Lung(3;3.54e-05)|STAD - Stomach adenocarcinoma(60;8.83e-05)|LUSC - Lung squamous cell carcinoma(40;0.000198)|GBM - Glioblastoma multiforme(59;0.00892)|READ - Rectum adenocarcinoma(43;0.161)		ACCAAGAGAACAATGGGAACC	0.353																																					p.Q137K		Atlas-SNP	.											.	FRG1	76	.	0			c.C409A						PASS	.						88.0	87.0	87.0					4																	190876283		2203	4300	6503	SO:0001583	missense	2483	exon5			AGAGAACAATGGG	L76159	CCDS34121.1	4q35	2008-02-05			ENSG00000109536	ENSG00000109536			3954	protein-coding gene	gene with protein product		601278				8733123	Standard	XM_005262880		Approved	FSG1, FRG1A	uc003izs.3	Q14331	OTTHUMG00000160202	ENST00000226798.4:c.409C>A	4.37:g.190876283C>A	ENSP00000226798:p.Gln137Lys	234.0	0.0	0		271.0	20.0	0.0738007	NM_004477	A8K775	Missense_Mutation	SNP	ENST00000226798.4	37	CCDS34121.1	.	.	.	.	.	.	.	.	.	.	.	16.72	3.202137	0.58234	.	.	ENSG00000109536	ENST00000226798;ENST00000531991	T;T	0.49139	2.03;0.79	4.04	4.04	0.47022	Actin cross-linking (1);	0.103449	0.64402	D	0.000002	T	0.54902	0.1887	M	0.88377	2.95	0.80722	D	1	B	0.11235	0.004	B	0.15484	0.013	T	0.60078	-0.7333	10	0.42905	T	0.14	-3.5101	14.1451	0.65347	0.0:1.0:0.0:0.0	.	137	Q14331	FRG1_HUMAN	K	137;74	ENSP00000226798:Q137K;ENSP00000435943:Q74K	ENSP00000226798:Q137K	Q	+	1	0	FRG1	191113277	1.000000	0.71417	0.998000	0.56505	0.994000	0.84299	7.292000	0.78731	1.964000	0.57103	0.567000	0.79289	CAA	.	.	none		0.353	FRG1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000359622.4	NM_004477	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57080352	57080352	+	Missense_Mutation	SNP	G	G	A	rs12801000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57080352G>A	ENST00000532437.1	-	4	2121	c.1810C>T	c.(1810-1812)Ccc>Tcc	p.P604S	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P604S|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	604	Acidic.|Pro-rich.			P -> S (in Ref. 1; AAM15531). {ECO:0000305}.	gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				GTAGCCAGGGGGAGAGGGGAC	0.637													G|||	101	0.0201677	0.0023	0.0389	5008	,	,		18898	0.002		0.0447	False		,,,				2504	0.0245				p.P604S		Atlas-SNP	.											TNKS1BP1,caecum,carcinoma,+1,1	TNKS1BP1	148	1	0			c.C1810T						PASS	.	G	SER/PRO	46,4356	46.0+/-80.4	0,46,2155	53.0	59.0	57.0		1810	1.9	0.0	11	dbSNP_121	57	399,8193	125.5+/-184.1	8,383,3905	yes	missense	TNKS1BP1	NM_033396.2	74	8,429,6060	AA,AG,GG		4.6439,1.045,3.4247	benign	604/1730	57080352	445,12549	2201	4296	6497	SO:0001583	missense	85456	exon5			CCAGGGGGAGAGG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1810C>T	11.37:g.57080352G>A	ENSP00000437271:p.Pro604Ser	112.0	0.0	0		136.0	56.0	0.411765	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	G	12.00	1.805475	0.31961	0.01045	0.046439	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.34275	1.37;1.37	3.89	1.9	0.25705	.	0.255524	0.20503	U	0.091051	T	0.03915	0.0110	L	0.27053	0.805	0.09310	N	1	P	0.36909	0.573	B	0.37780	0.258	T	0.04678	-1.0934	10	0.62326	D	0.03	-0.7947	7.0645	0.25143	0.0:0.1818:0.6143:0.2039	rs12801000	604	Q9C0C2	TB182_HUMAN	S	604	ENSP00000350990:P604S;ENSP00000437271:P604S	ENSP00000350990:P604S	P	-	1	0	TNKS1BP1	56836928	0.002000	0.14202	0.002000	0.10522	0.834000	0.47266	0.618000	0.24373	0.271000	0.22005	0.462000	0.41574	CCC	G|0.968;A|0.032	0.032	strong		0.637	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
ADAM18	8749	hgsc.bcm.edu	37	8	39468070	39468070	+	Missense_Mutation	SNP	A	A	C	rs139114737	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39468070A>C	ENST00000265707.5	+	6	412	c.367A>C	c.(367-369)Atc>Ctc	p.I123L	ADAM18_ENST00000541111.1_Intron|ADAM18_ENST00000379866.1_Missense_Mutation_p.I123L|ADAM18_ENST00000520772.1_Missense_Mutation_p.I123L	NM_014237.2	NP_055052.1	Q9Y3Q7	ADA18_HUMAN	ADAM metallopeptidase domain 18	123					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(12)|lung(31)|ovary(1)|prostate(1)|skin(12)|stomach(1)|upper_aerodigestive_tract(3)	71		all_cancers(7;1.32e-05)|all_epithelial(6;3.08e-10)|all_lung(54;0.00187)|Hepatocellular(245;0.00745)|Lung NSC(58;0.00769)|Breast(189;0.0112)	LUSC - Lung squamous cell carcinoma(45;0.000199)			GTTTGAAAATATCAGTTATGG	0.289													a|||	22	0.00439297	0.0106	0.0072	5008	,	,		16258	0.0		0.003	False		,,,				2504	0.0				p.I123L		Atlas-SNP	.											.	ADAM18	169	.	0			c.A367C						PASS	.	G	LEU/ILE,LEU/ILE	31,4357	33.5+/-64.1	0,31,2163	37.0	38.0	38.0		367,367	-3.8	0.5	8	dbSNP_134	38	11,8575	8.4+/-32.0	0,11,4282	yes	missense,missense	ADAM18	NM_001190956.1,NM_014237.2	5,5	0,42,6445	CC,CA,AA		0.1281,0.7065,0.3237	benign,benign	123/183,123/740	39468070	42,12932	2194	4293	6487	SO:0001583	missense	8749	exon6			GAAAATATCAGTT	AJ133004	CCDS6113.1, CCDS55225.1	8p11.22	2008-08-07	2005-08-18		ENSG00000168619	ENSG00000168619		"""ADAM metallopeptidase domain containing"""	196	protein-coding gene	gene with protein product			"""a disintegrin and metalloproteinase domain 18"""			12200459	Standard	NM_014237		Approved	tMDCIII, ADAM27	uc003xni.3	Q9Y3Q7	OTTHUMG00000164040	ENST00000265707.5:c.367A>C	8.37:g.39468070A>C	ENSP00000265707:p.Ile123Leu	208.0	0.0	0		225.0	93.0	0.413333	NM_001190956	B2R9Y0|Q0VAI4|Q6IRW9|Q6UXJ9	Missense_Mutation	SNP	ENST00000265707.5	37	CCDS6113.1	10	0.004578754578754579	6	0.012195121951219513	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	a	8.502	0.864400	0.17250	0.007065	0.001281	ENSG00000168619	ENST00000265707;ENST00000379866;ENST00000520772;ENST00000522198	T;T;T	0.05513	3.43;3.43;3.43	5.25	-3.75	0.04372	Peptidase M12B, propeptide (1);	0.750320	0.11876	N	0.521007	T	0.04272	0.0118	L	0.40543	1.245	0.29468	N	0.857287	B;B;B	0.26845	0.133;0.161;0.056	B;B;B	0.39152	0.192;0.292;0.042	T	0.45818	-0.9235	10	0.22109	T	0.4	.	6.7801	0.23640	0.5203:0.0:0.3672:0.1125	.	123;123;123	Q9Y3Q7-2;Q9Y3Q7;Q6IRW9	.;ADA18_HUMAN;.	L	123;123;123;79	ENSP00000265707:I123L;ENSP00000369195:I123L;ENSP00000429908:I123L	ENSP00000265707:I123L	I	+	1	0	ADAM18	39587227	0.275000	0.24201	0.488000	0.27440	0.089000	0.18198	-0.094000	0.11094	-0.734000	0.04843	-2.260000	0.00280	ATC	A|0.997;C|0.003	0.003	strong		0.289	ADAM18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376916.1	NM_014237	
PPP6R1	22870	hgsc.bcm.edu	37	19	55752662	55752662	+	Missense_Mutation	SNP	T	T	C	rs200841391	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55752662T>C	ENST00000412770.2	-	9	1672	c.1106A>G	c.(1105-1107)aAt>aGt	p.N369S	PPP6R1_ENST00000587283.1_Missense_Mutation_p.N369S	NM_014931.3	NP_055746.3	Q9UPN7	PP6R1_HUMAN	protein phosphatase 6, regulatory subunit 1	369	Interaction with PPP6C.				regulation of phosphoprotein phosphatase activity (GO:0043666)	cytoplasm (GO:0005737)	protein phosphatase binding (GO:0019903)			breast(1)	1						GGCTGCATCATTGGCGCTCAG	0.687													T|||	6	0.00119808	0.0015	0.0029	5008	,	,		11133	0.0		0.002	False		,,,				2504	0.0				p.N369S		Atlas-SNP	.											.	PPP6R1	63	.	0			c.A1106G						PASS	.	T	SER/ASN	2,4224		0,2,2111	25.0	30.0	29.0		1106	2.8	0.8	19		29	9,8481		0,9,4236	yes	missense	PPP6R1	NM_014931.3	46	0,11,6347	CC,CT,TT		0.106,0.0473,0.0865	benign	369/882	55752662	11,12705	2113	4245	6358	SO:0001583	missense	22870	exon9			GCATCATTGGCGC	AB029038	CCDS46186.1	19q13.42	2012-04-17	2010-06-28	2010-06-28	ENSG00000105063	ENSG00000105063		"""Serine/threonine phosphatases / Protein phosphatase 6, regulatory subunits"""	29195	protein-coding gene	gene with protein product		610875	"""KIAA1115"", ""SAPS domain family, member 1"""	KIAA1115, SAPS1		16769727	Standard	NM_014931		Approved	SAP190	uc002qjw.4	Q9UPN7		ENST00000412770.2:c.1106A>G	19.37:g.55752662T>C	ENSP00000414202:p.Asn369Ser	126.0	0.0	0		128.0	61.0	0.476562	NM_014931	Q2M2H3|Q504V2|Q6NVJ6|Q9BU97	Missense_Mutation	SNP	ENST00000412770.2	37	CCDS46186.1	3	0.0013736263736263737	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	T	17.04	3.286210	0.59867	4.73E-4	0.00106	ENSG00000105063	ENST00000412770	T	0.66815	-0.23	4.98	2.81	0.32909	.	0.000000	0.64402	D	0.000017	T	0.63628	0.2527	M	0.62723	1.935	0.34351	D	0.689847	P	0.45986	0.87	P	0.48334	0.574	T	0.65529	-0.6146	10	0.19590	T	0.45	-21.6412	6.5383	0.22367	0.1379:0.0786:0.0:0.7835	.	369	Q9UPN7	PP6R1_HUMAN	S	369	ENSP00000414202:N369S	ENSP00000414202:N369S	N	-	2	0	PPP6R1	60444474	0.533000	0.26354	0.751000	0.31187	0.782000	0.44232	0.629000	0.24538	0.296000	0.22592	0.379000	0.24179	AAT	T|0.998;C|0.002	0.002	strong		0.687	PPP6R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452663.1	NM_014931	
PADI2	11240	hgsc.bcm.edu	37	1	17405814	17405814	+	Missense_Mutation	SNP	C	C	T	rs148233687	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:17405814C>T	ENST00000375486.4	-	11	1318	c.1255G>A	c.(1255-1257)Gtg>Atg	p.V419M	PADI2_ENST00000444885.2_Missense_Mutation_p.V303M|PADI2_ENST00000375481.1_Missense_Mutation_p.V419M|PADI2_ENST00000466151.1_5'UTR	NM_007365.2	NP_031391.2	Q9Y2J8	PADI2_HUMAN	peptidyl arginine deiminase, type II	419					chromatin-mediated maintenance of transcription (GO:0048096)|histone H3-R26 citrullination (GO:0036413)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of lymphocyte chemotaxis (GO:1901624)|protein citrullination (GO:0018101)|regulation of chromatin disassembly (GO:0010848)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|transcriptionally active chromatin (GO:0035327)	calcium ion binding (GO:0005509)|estrogen receptor binding (GO:0030331)|protein-arginine deiminase activity (GO:0004668)			breast(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(12)|ovary(4)|pancreas(1)|skin(5)|urinary_tract(3)	29		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000422)|Renal(390;0.000518)|all_lung(284;0.000546)|Ovarian(437;0.00671)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00583)|BRCA - Breast invasive adenocarcinoma(304;1.49e-05)|COAD - Colon adenocarcinoma(227;1.54e-05)|Kidney(64;0.000258)|KIRC - Kidney renal clear cell carcinoma(64;0.00348)|STAD - Stomach adenocarcinoma(196;0.0072)|READ - Rectum adenocarcinoma(331;0.0698)|Lung(427;0.201)	L-Citrulline(DB00155)	TTGCCGTTCACGGTCACTGGG	0.597													C|||	5	0.000998403	0.0	0.0043	5008	,	,		15043	0.0		0.002	False		,,,				2504	0.0				p.V419M		Atlas-SNP	.											.	PADI2	72	.	0			c.G1255A						PASS	.	C	MET/VAL	2,4404	4.2+/-10.8	0,2,2201	65.0	65.0	65.0		1255	5.0	1.0	1	dbSNP_134	65	16,8584	11.9+/-42.8	0,16,4284	yes	missense	PADI2	NM_007365.2	21	0,18,6485	TT,TC,CC		0.186,0.0454,0.1384	probably-damaging	419/666	17405814	18,12988	2203	4300	6503	SO:0001583	missense	11240	exon11			CGTTCACGGTCAC	AB030176	CCDS177.1	1p35.2-p35.1	2008-02-05			ENSG00000117115	ENSG00000117115	3.5.3.15	"""Peptidyl arginine deiminases"""	18341	protein-coding gene	gene with protein product		607935				2768262	Standard	NM_007365		Approved	KIAA0994, PDI2	uc001baf.3	Q9Y2J8	OTTHUMG00000002295	ENST00000375486.4:c.1255G>A	1.37:g.17405814C>T	ENSP00000364635:p.Val419Met	65.0	0.0	0		57.0	48.0	0.842105	NM_007365	Q96DA7|Q9UPN2	Missense_Mutation	SNP	ENST00000375486.4	37	CCDS177.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	28.5	4.926678	0.92319	4.54E-4	0.00186	ENSG00000117115	ENST00000375486;ENST00000444885;ENST00000375481	T;T;T	0.30182	1.54;1.54;1.54	4.97	4.97	0.65823	Protein-arginine deiminase, C-terminal (1);	0.244684	0.41500	D	0.000874	T	0.52773	0.1755	M	0.85197	2.74	0.51233	D	0.999919	D;D	0.89917	1.0;0.998	D;D	0.83275	0.996;0.938	T	0.62676	-0.6804	10	0.56958	D	0.05	-20.6685	17.3265	0.87249	0.0:1.0:0.0:0.0	.	303;419	B4DIU3;Q9Y2J8	.;PADI2_HUMAN	M	419;303;419	ENSP00000364635:V419M;ENSP00000405894:V303M;ENSP00000364630:V419M	ENSP00000364630:V419M	V	-	1	0	PADI2	17278401	1.000000	0.71417	0.994000	0.49952	0.998000	0.95712	7.127000	0.77210	2.758000	0.94735	0.561000	0.74099	GTG	C|0.999;T|0.001	0.001	strong		0.597	PADI2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006624.1		
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22960654	22960654	+	Missense_Mutation	SNP	C	C	T	rs10107826|rs374790272	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22960654C>T	ENST00000356864.3	+	1	552	c.20C>T	c.(19-21)aCc>aTc	p.T7I	TNFRSF10C_ENST00000520607.1_Intron|TNFRSF10C_ENST00000540813.1_5'UTR|TNFRSF10C_ENST00000397703.2_Missense_Mutation_p.T47I	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	7					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		ATCCCCAAGACCCTAAAGTTC	0.711													C|||	208	0.0415335	0.149	0.0101	5008	,	,		14783	0.0		0.004	False		,,,				2504	0.0				p.T7I		Atlas-SNP	.											.	TNFRSF10C	30	.	0			c.C20T						PASS	.	C	ILE/THR	443,3961	170.9+/-201.2	25,393,1784	79.0	59.0	66.0		20	0.6	0.0	8	dbSNP_119	66	12,8584	5.7+/-21.5	0,12,4286	yes	missense	TNFRSF10C	NM_003841.3	89	25,405,6070	TT,TC,CC		0.1396,10.059,3.5	probably-damaging	7/260	22960654	455,12545	2202	4298	6500	SO:0001583	missense	8794	exon1			CCAAGACCCTAAA	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.20C>T	8.37:g.22960654C>T	ENSP00000349324:p.Thr7Ile	47.0	0.0	0		76.0	44.0	0.578947	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	56	0.02564102564102564	50	0.1016260162601626	4	0.011049723756906077	0	0.0	2	0.002638522427440633	C	4.995	0.184796	0.09495	0.10059	0.001396	ENSG00000173535	ENST00000397703;ENST00000356864;ENST00000544885	T	0.62364	0.03	1.76	0.639	0.17747	.	2.630870	0.02547	U	0.095275	T	0.01627	0.0052	N	0.19112	0.55	0.52099	P	5.100000000002325E-5	B	0.21225	0.053	B	0.06405	0.002	T	0.08186	-1.0734	9	0.52906	T	0.07	.	4.4054	0.11407	0.0:0.717:0.0:0.283	rs10107826;rs10107826	7	O14798	TR10C_HUMAN	I	47;7;7	ENSP00000349324:T7I	ENSP00000349324:T7I	T	+	2	0	TNFRSF10C	23016599	0.000000	0.05858	0.001000	0.08648	0.053000	0.15095	-0.737000	0.04877	-0.010000	0.14271	0.205000	0.17691	ACC	C|0.958;T|0.042	0.042	strong		0.711	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
LBR	3930	hgsc.bcm.edu	37	1	225603029	225603029	+	Silent	SNP	T	T	C	rs61749339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:225603029T>C	ENST00000338179.2	-	7	968	c.843A>G	c.(841-843)gtA>gtG	p.V281V	LBR_ENST00000487054.1_5'Flank|LBR_ENST00000272163.4_Silent_p.V281V	NM_194442.2	NP_919424.1	Q14739	LBR_HUMAN	lamin B receptor	281					cholesterol biosynthetic process (GO:0006695)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|integral component of nuclear inner membrane (GO:0005639)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)	chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|lamin binding (GO:0005521)|oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor (GO:0016628)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(5)|ovary(2)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	22	Breast(184;0.165)			GBM - Glioblastoma multiforme(131;0.117)		GCGTTCCTTCTACAACCTTAA	0.269													T|||	28	0.00559105	0.0	0.0058	5008	,	,		18270	0.0		0.0169	False		,,,				2504	0.0072				p.V281V		Atlas-SNP	.											.	LBR	54	.	0			c.A843G						PASS	.	T	,	10,4374		0,10,2182	32.0	32.0	32.0		843,843	0.4	1.0	1	dbSNP_129	32	138,8426		1,136,4145	no	coding-synonymous,coding-synonymous	LBR	NM_002296.3,NM_194442.2	,	1,146,6327	CC,CT,TT		1.6114,0.2281,1.143	,	281/616,281/616	225603029	148,12800	2192	4282	6474	SO:0001819	synonymous_variant	3930	exon7			TCCTTCTACAACC	L25931	CCDS1545.1	1q42.1	2013-01-23			ENSG00000143815	ENSG00000143815		"""Tudor domain containing"""	6518	protein-coding gene	gene with protein product	"""tudor domain containing 18"""	600024				8157663, 9878250	Standard	NM_194442		Approved	DHCR14B, TDRD18	uc001hoy.3	Q14739	OTTHUMG00000037520	ENST00000338179.2:c.843A>G	1.37:g.225603029T>C		131.0	0.0	0		177.0	82.0	0.463277	NM_194442	B2R5P3|Q14740|Q53GU7|Q59FE6	Silent	SNP	ENST00000338179.2	37	CCDS1545.1																																																																																			T|0.991;C|0.009	0.009	strong		0.269	LBR-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091398.1	NM_002296	
UGT3A1	133688	hgsc.bcm.edu	37	5	35965611	35965611	+	Silent	SNP	A	A	G	rs61733467	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:35965611A>G	ENST00000274278.3	-	4	1077	c.720T>C	c.(718-720)ctT>ctC	p.L240L	UGT3A1_ENST00000507113.1_Silent_p.L206L|UGT3A1_ENST00000513233.1_Intron|UGT3A1_ENST00000333811.4_Silent_p.L186L|UGT3A1_ENST00000503189.1_Silent_p.L240L	NM_152404.3	NP_689617.3	Q6NUS8	UD3A1_HUMAN	UDP glycosyltransferase 3 family, polypeptide A1	240						integral component of membrane (GO:0016021)|UDP-N-acetylglucosamine transferase complex (GO:0043541)	glucuronosyltransferase activity (GO:0015020)|UDP-glycosyltransferase activity (GO:0008194)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(8)|lung(28)|ovary(2)|skin(4)	46	all_lung(31;0.000197)		Epithelial(62;0.107)|Lung(74;0.111)|COAD - Colon adenocarcinoma(61;0.14)|Colorectal(62;0.202)			CTTTCAGTAGAAGATGAGACA	0.448													A|||	56	0.0111821	0.0393	0.0058	5008	,	,		20825	0.0		0.0	False		,,,				2504	0.0				p.L240L		Atlas-SNP	.											.	UGT3A1	95	.	0			c.T720C						PASS	.	A	,	155,4251	104.3+/-142.8	2,151,2050	116.0	120.0	118.0		558,720	1.8	0.9	5	dbSNP_129	118	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	UGT3A1	NM_001171873.1,NM_152404.3	,	2,152,6349	GG,GA,AA		0.0116,3.5179,1.1994	,	186/253,240/524	35965611	156,12850	2203	4300	6503	SO:0001819	synonymous_variant	133688	exon4			CAGTAGAAGATGA		CCDS3913.1, CCDS54841.1	5p13.2	2014-05-20			ENSG00000145626	ENSG00000145626		"""UDP glucuronosyltransferases"""	26625	protein-coding gene	gene with protein product							Standard	NM_152404		Approved	FLJ34658	uc003jjv.2	Q6NUS8	OTTHUMG00000131107	ENST00000274278.3:c.720T>C	5.37:g.35965611A>G		237.0	0.0	0		223.0	114.0	0.511211	NM_152404	G5E961|Q8IYS9|Q8NAW4|Q96DM6	Silent	SNP	ENST00000274278.3	37	CCDS3913.1																																																																																			A|0.988;G|0.012	0.012	strong		0.448	UGT3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253770.2	NM_152404	
CCT8	10694	hgsc.bcm.edu	37	21	30437344	30437344	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:30437344T>C	ENST00000286788.4	-	7	913	c.707A>G	c.(706-708)gAt>gGt	p.D236G	CCT8_ENST00000470450.1_5'UTR|CCT8_ENST00000542732.1_Missense_Mutation_p.D217G|CCT8_ENST00000540844.1_Missense_Mutation_p.D163G	NM_006585.2	NP_006576.2	P50990	TCPQ_HUMAN	chaperonin containing TCP1, subunit 8 (theta)	236					'de novo' posttranslational protein folding (GO:0051084)|ATP catabolic process (GO:0006200)|binding of sperm to zona pellucida (GO:0007339)|cellular protein metabolic process (GO:0044267)|protein folding (GO:0006457)	aggresome (GO:0016235)|cell body (GO:0044297)|centrosome (GO:0005813)|chaperonin-containing T-complex (GO:0005832)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|microtubule (GO:0005874)|zona pellucida receptor complex (GO:0002199)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)			breast(3)|endometrium(1)|kidney(1)|large_intestine(4)|liver(1)|lung(1)|prostate(3)	14						TATTTTTGCATCTTTGACAGA	0.378																																					p.D236G		Atlas-SNP	.											.	CCT8	38	.	0			c.A707G						PASS	.						193.0	175.0	181.0					21																	30437344		2203	4300	6503	SO:0001583	missense	10694	exon7			TTTGCATCTTTGA	Z37163	CCDS33528.1, CCDS68180.1	21q21.3	2011-09-02			ENSG00000156261	ENSG00000156261		"""Heat Shock Proteins / Chaperonins"""	1623	protein-coding gene	gene with protein product			"""chromosome 21 open reading frame 112"""	C21orf112		7890169	Standard	NM_006585		Approved	Cctq, PRED71	uc002ynb.3	P50990	OTTHUMG00000044595	ENST00000286788.4:c.707A>G	21.37:g.30437344T>C	ENSP00000286788:p.Asp236Gly	85.0	0.0	0		94.0	4.0	0.0425532	NM_006585	A6NN54|B4DEM7|B4DQH4|Q4VBP8	Missense_Mutation	SNP	ENST00000286788.4	37	CCDS33528.1	.	.	.	.	.	.	.	.	.	.	T	18.24	3.580704	0.65992	.	.	ENSG00000156261	ENST00000389159;ENST00000286788;ENST00000542732;ENST00000540844	T;T;T	0.67865	-0.29;-0.29;-0.29	5.25	5.25	0.73442	.	0.043440	0.85682	D	0.000000	T	0.58694	0.2140	L	0.38649	1.16	0.80722	D	1	B;B;B;B;B	0.32653	0.018;0.006;0.018;0.014;0.379	B;B;B;B;B	0.33339	0.043;0.007;0.027;0.016;0.162	T	0.59794	-0.7387	10	0.42905	T	0.14	-23.8735	15.6084	0.76692	0.0:0.0:0.0:1.0	.	163;217;236;235;236	B4DQH4;B4DEM7;Q53HU0;G5E9B2;P50990	.;.;.;.;TCPQ_HUMAN	G	235;236;217;163	ENSP00000286788:D236G;ENSP00000444984:D217G;ENSP00000442730:D163G	ENSP00000286788:D236G	D	-	2	0	CCT8	29359215	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.728000	0.68531	2.326000	0.78906	0.533000	0.62120	GAT	.	.	none		0.378	CCT8-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171822.1		
TENM4	26011	hgsc.bcm.edu	37	11	78565314	78565314	+	Missense_Mutation	SNP	C	C	G	rs17137261	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:78565314C>G	ENST00000278550.7	-	12	1978	c.1516G>C	c.(1516-1518)Gag>Cag	p.E506Q		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	506			E -> Q (in dbSNP:rs17137261).		cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)										CTCCGCGCCTCCTGGGTTAGG	0.587													C|||	155	0.0309505	0.0068	0.0504	5008	,	,		16854	0.0317		0.0487	False		,,,				2504	0.0307				p.E506Q		Atlas-SNP	.											.	.	.	.	0			c.G1516C						PASS	.	C	GLN/GLU	17,1367		0,17,675	12.0	14.0	14.0		1516	5.1	1.0	11	dbSNP_123	14	117,3065		5,107,1479	yes	missense	ODZ4	NM_001098816.2	29	5,124,2154	GG,GC,CC		3.6769,1.2283,2.9347	possibly-damaging	506/2770	78565314	134,4432	692	1591	2283	SO:0001583	missense	26011	exon12			GCGCCTCCTGGGT	AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.1516G>C	11.37:g.78565314C>G	ENSP00000278550:p.Glu506Gln	30.0	0.0	0		15.0	9.0	0.6	NM_001098816	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Missense_Mutation	SNP	ENST00000278550.7	37	CCDS44688.1	79	0.036172161172161175	4	0.008130081300813009	21	0.058011049723756904	17	0.02972027972027972	37	0.048812664907651716	C	20.2	3.954131	0.73902	0.012283	0.036769	ENSG00000149256	ENST00000278550	T	0.21932	1.98	5.07	5.07	0.68467	.	0.174787	0.49305	D	0.000153	T	0.01592	0.0051	L	0.34521	1.04	0.53005	D	0.999968	P	0.39391	0.671	B	0.29785	0.107	T	0.08973	-1.0696	9	.	.	.	.	18.6486	0.91421	0.0:1.0:0.0:0.0	rs17137261	506	Q6N022	TEN4_HUMAN	Q	506	ENSP00000278550:E506Q	.	E	-	1	0	ODZ4	78242962	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	7.651000	0.83577	2.631000	0.89168	0.561000	0.74099	GAG	C|0.969;G|0.031	0.031	strong		0.587	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2		
NECAB2	54550	hgsc.bcm.edu	37	16	84030848	84030848	+	Silent	SNP	C	C	T	rs7193267	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:84030848C>T	ENST00000305202.4	+	9	840	c.823C>T	c.(823-825)Ctg>Ttg	p.L275L	NECAB2_ENST00000565691.1_Silent_p.L192L|NECAB2_ENST00000567703.1_3'UTR	NM_019065.2	NP_061938.2	Q7Z6G3	NECA2_HUMAN	N-terminal EF-hand calcium binding protein 2	275						cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)			endometrium(1)|large_intestine(3)|lung(9)|ovary(2)|prostate(1)|stomach(2)|urinary_tract(1)	19						GCAGCAGCGCCTGTCAGATGA	0.607													C|||	17	0.00339457	0.0015	0.0072	5008	,	,		16661	0.0		0.0099	False		,,,				2504	0.0				p.L275L		Atlas-SNP	.											.	NECAB2	36	.	0			c.C823T						PASS	.	C		14,4386	21.2+/-45.6	0,14,2186	188.0	136.0	154.0		823	4.5	0.9	16	dbSNP_116	154	99,8501	54.4+/-115.2	1,97,4202	no	coding-synonymous	NECAB2	NM_019065.2		1,111,6388	TT,TC,CC		1.1512,0.3182,0.8692		275/387	84030848	113,12887	2200	4300	6500	SO:0001819	synonymous_variant	54550	exon9			CAGCGCCTGTCAG	AY299331	CCDS10940.1	16q23.3-q24.1	2013-01-10	2007-12-06	2007-12-06	ENSG00000103154	ENSG00000103154		"""N-terminal EF-hand calcium binding proteins"", ""EF-hand domain containing"""	23746	protein-coding gene	gene with protein product			"""EF-hand calcium binding protein 2"""	EFCBP2		12044471	Standard	NM_019065		Approved		uc002fhd.3	Q7Z6G3	OTTHUMG00000137636	ENST00000305202.4:c.823C>T	16.37:g.84030848C>T		108.0	0.0	0		133.0	64.0	0.481203	NM_019065	A2RRG3|O75547|Q6ZSK0	Silent	SNP	ENST00000305202.4	37	CCDS10940.1																																																																																			C|0.992;T|0.008	0.008	strong		0.607	NECAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269077.2	NM_019065	
FAT1	2195	hgsc.bcm.edu	37	4	187509931	187509931	+	Missense_Mutation	SNP	C	C	T	rs192609167	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187509931C>T	ENST00000441802.2	-	27	13791	c.13582G>A	c.(13582-13584)Gag>Aag	p.E4528K		NM_005245.3	NP_005236.2	Q14517	FAT1_HUMAN	FAT atypical cadherin 1	4528					actin filament organization (GO:0007015)|anatomical structure morphogenesis (GO:0009653)|cell adhesion (GO:0007155)|cell migration (GO:0016477)|cell-cell signaling (GO:0007267)|establishment or maintenance of cell polarity (GO:0007163)|homophilic cell adhesion (GO:0007156)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(38)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(33)|lung(88)|ovary(13)|pancreas(2)|prostate(16)|skin(2)|upper_aerodigestive_tract(11)|urinary_tract(4)	228						GCGGGCGCCTCGAAGTGTCTT	0.562										HNSCC(5;0.00058)			C|||	3	0.000599042	0.0	0.0014	5008	,	,		17560	0.0		0.002	False		,,,				2504	0.0				p.E4528K	Colon(197;1040 2055 4143 4984 49344)	Atlas-SNP	.											.	FAT1	500	.	0			c.G13582A						PASS	.	C	LYS/GLU	5,4159		0,5,2077	60.0	70.0	67.0		13582	5.4	0.0	4		67	67,8369		0,67,4151	yes	missense	FAT1	NM_005245.3	56	0,72,6228	TT,TC,CC		0.7942,0.1201,0.5714	benign	4528/4589	187509931	72,12528	2082	4218	6300	SO:0001583	missense	2195	exon27			GCGCCTCGAAGTG	X87241	CCDS47177.1	4q35.2	2013-05-31	2013-05-31	2008-10-30	ENSG00000083857	ENSG00000083857		"""Cadherins / Cadherin-related"""	3595	protein-coding gene	gene with protein product	"""cadherin-related family member 8"""	600976	"""FAT tumor suppressor (Drosophila) homolog"", ""FAT tumor suppressor homolog 1 (Drosophila)"""	FAT		8586420	Standard	XM_005262834		Approved	CDHF7, CDHR8	uc003izf.3	Q14517	OTTHUMG00000160320	ENST00000441802.2:c.13582G>A	4.37:g.187509931C>T	ENSP00000406229:p.Glu4528Lys	108.0	0.0	0		110.0	49.0	0.445455	NM_005245		Missense_Mutation	SNP	ENST00000441802.2	37	CCDS47177.1	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	C|C	13.46|13.46	2.243967|2.243967	0.39697|0.39697	0.001201|0.001201	0.007942|0.007942	ENSG00000083857|ENSG00000083857	ENST00000441802;ENST00000260147|ENST00000512772	T|.	0.38077|.	1.16|.	5.37|5.37	5.37|5.37	0.77165|0.77165	.|.	0.411428|.	0.30311|.	N|.	0.009906|.	T|T	0.67420|0.67420	0.2891|0.2891	M|M	0.62723|0.62723	1.935|1.935	0.58432|0.58432	D|D	0.999994|0.999994	P|.	0.42337|.	0.776|.	B|.	0.26770|.	0.073|.	T|T	0.68232|0.68232	-0.5463|-0.5463	10|5	0.21014|.	T|.	0.42|.	.|.	19.3098|19.3098	0.94182|0.94182	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	4528|.	Q14517|.	FAT1_HUMAN|.	K|Q	4528;4530|307	ENSP00000406229:E4528K|.	ENSP00000260147:E4530K|.	E|R	-|-	1|2	0|0	FAT1|FAT1	187746925|187746925	1.000000|1.000000	0.71417|0.71417	0.043000|0.043000	0.18650|0.18650	0.008000|0.008000	0.06430|0.06430	7.309000|7.309000	0.78937|0.78937	2.800000|2.800000	0.96347|0.96347	0.455000|0.455000	0.32223|0.32223	GAG|CGA	C|0.999;T|0.001	0.001	strong		0.562	FAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360209.3	NM_005245	
CFAP46	54777	hgsc.bcm.edu	37	10	134691427	134691427	+	Missense_Mutation	SNP	G	G	C	rs527530176	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691427G>C	ENST00000368586.5	-	30	4270	c.4170C>G	c.(4168-4170)gaC>gaG	p.D1390E	TTC40_ENST00000368582.2_Missense_Mutation_p.D1390E	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						ccttctccttgtccttctctt	0.507													-|||	23	0.00459265	0.0008	0.0029	5008	,	,		17437	0.002		0.007	False		,,,				2504	0.0112				p.D1390E		Atlas-SNP	.											.	TTC40	100	.	0			c.C4170G						PASS	.																																			SO:0001583	missense	54777	exon30			CTCCTTGTCCTTC																												ENST00000368586.5:c.4170C>G	10.37:g.134691427G>C	ENSP00000357575:p.Asp1390Glu	314.0	0.0	0		298.0	23.0	0.0771812	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	-	0.018	-1.468881	0.01053	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.10860	2.83;2.83	2.3	-4.61	0.03380	.	.	.	.	.	T	0.02494	0.0076	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.35549	-0.9784	6	0.02654	T	1	.	2.0591	0.03587	0.1265:0.1607:0.4006:0.3123	.	.	.	.	E	1390	ENSP00000357575:D1390E;ENSP00000357571:D1390E	ENSP00000357571:D1390E	D	-	3	2	C10orf93	134541417	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.253000	0.01184	-1.780000	0.01279	-1.213000	0.01624	GAC	.	.	none		0.507	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
GLTSCR2	29997	hgsc.bcm.edu	37	19	48254799	48254799	+	Silent	SNP	T	T	C	rs11538669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48254799T>C	ENST00000246802.5	+	5	659	c.621T>C	c.(619-621)gtT>gtC	p.V207V	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	207				SDNPLDRPLVGQDEFFLE -> LNNPDKPVVWPGCLFPG (in Ref. 3; AAG30413). {ECO:0000305}.		intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		GGCCGTTGGTTGGCCAGGATG	0.607													T|||	77	0.0153754	0.0053	0.0029	5008	,	,		18264	0.0069		0.0149	False		,,,				2504	0.047				p.V207V	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.T621C						PASS	.	T		46,4360	48.9+/-83.8	0,46,2157	84.0	76.0	79.0		621	-7.0	0.0	19	dbSNP_120	79	151,8449	73.2+/-135.9	0,151,4149	no	coding-synonymous	GLTSCR2	NM_015710.4		0,197,6306	CC,CT,TT		1.7558,1.044,1.5147		207/479	48254799	197,12809	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon5			GTTGGTTGGCCAG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.621T>C	19.37:g.48254799T>C		74.0	0.0	0		81.0	39.0	0.481481	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			T|0.987;C|0.013	0.013	strong		0.607	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
DSPP	1834	hgsc.bcm.edu	37	4	88537115	88537115	+	Missense_Mutation	SNP	G	G	A	rs201186956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:88537115G>A	ENST00000282478.7	+	4	3334	c.3301G>A	c.(3301-3303)Gac>Aac	p.D1101N	RP11-742B18.1_ENST00000506480.1_RNA|DSPP_ENST00000399271.1_Missense_Mutation_p.D1101N			Q9NZW4	DSPP_HUMAN	dentin sialophosphoprotein	1101	Asp/Ser-rich.			Missing (in Ref. 1; AAF42472 and 3; AAD16120). {ECO:0000305}.	biomineral tissue development (GO:0031214)|cellular response to cell-matrix adhesion (GO:0071460)|extracellular matrix organization (GO:0030198)|multicellular organismal development (GO:0007275)|ossification (GO:0001503)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|collagen binding (GO:0005518)|extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|skin(3)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	47		Hepatocellular(203;0.114)|all_hematologic(202;0.236)		OV - Ovarian serous cystadenocarcinoma(123;0.000508)		cgatagcagcgacagcagcga	0.542													G|||	7	0.00139776	0.0038	0.0	5008	,	,		12523	0.001		0.0	False		,,,				2504	0.001				p.D1101N		Atlas-SNP	.											.	DSPP	174	.	0			c.G3301A						PASS	.																																			SO:0001583	missense	1834	exon5			AGCAGCGACAGCA	AF163151	CCDS43248.1	4q21.3	2008-02-05			ENSG00000152591	ENSG00000152591			3054	protein-coding gene	gene with protein product		125485		DFNA39, DGI1		8995371, 9533027	Standard	NM_014208		Approved	DMP3	uc003hqu.3	Q9NZW4	OTTHUMG00000161061	ENST00000282478.7:c.3301G>A	4.37:g.88537115G>A	ENSP00000282478:p.Asp1101Asn	25.0	0.0	0		12.0	5.0	0.416667	NM_014208	A8MUI0|O95815	Missense_Mutation	SNP	ENST00000282478.7	37	CCDS43248.1	.	.	.	.	.	.	.	.	.	.	g	5.679	0.309927	0.10733	.	.	ENSG00000152591	ENST00000399271;ENST00000282478	D;D	0.90004	-2.6;-2.6	1.51	0.638	0.17742	.	.	.	.	.	T	0.78698	0.4324	L	0.34521	1.04	0.09310	N	0.999993	B	0.14438	0.01	B	0.04013	0.001	T	0.60383	-0.7274	9	0.19147	T	0.46	.	4.1914	0.10422	0.2248:0.0:0.7752:0.0	.	1101	Q9NZW4	DSPP_HUMAN	N	1101	ENSP00000382213:D1101N;ENSP00000282478:D1101N	ENSP00000282478:D1101N	D	+	1	0	DSPP	88756139	0.671000	0.27521	0.311000	0.25182	0.002000	0.02628	0.881000	0.28173	0.216000	0.20781	-0.791000	0.03333	GAC	.	.	weak		0.542	DSPP-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000363616.3	NM_014208	
RRP12	23223	hgsc.bcm.edu	37	10	99130282	99130282	+	Silent	SNP	T	T	G	rs11189170	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99130282T>G	ENST00000370992.4	-	23	2730	c.2619A>C	c.(2617-2619)gcA>gcC	p.A873A	RRP12_ENST00000414986.1_Silent_p.A812A|RRP12_ENST00000536831.1_Silent_p.A591A|RRP12_ENST00000315563.6_Silent_p.A773A|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	873						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)		CGTTCTTCCGTGCGCCCACCG	0.607													T|||	201	0.0401358	0.059	0.0548	5008	,	,		19934	0.0		0.0716	False		,,,				2504	0.0133				p.A873A		Atlas-SNP	.											RRP12,NS,carcinoma,-2,1	RRP12	97	1	0			c.A2619C						scavenged	.	T	,	254,4152	147.3+/-181.8	9,236,1958	118.0	90.0	99.0		2436,2619	-9.4	0.4	10	dbSNP_120	99	503,8097	144.7+/-200.5	17,469,3814	no	coding-synonymous,coding-synonymous	RRP12	NM_001145114.1,NM_015179.3	,	26,705,5772	GG,GT,TT		5.8488,5.7649,5.8204	,	812/1237,873/1298	99130282	757,12249	2203	4300	6503	SO:0001819	synonymous_variant	23223	exon23			CTTCCGTGCGCCC		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.2619A>C	10.37:g.99130282T>G		109.0	2.0	0.0183486		110.0	57.0	0.518182	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Silent	SNP	ENST00000370992.4	37	CCDS7457.1																																																																																			T|0.952;G|0.048	0.048	strong		0.607	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
BBX	56987	hgsc.bcm.edu	37	3	107491892	107491892	+	Missense_Mutation	SNP	G	G	A	rs138961599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:107491892G>A	ENST00000325805.8	+	11	1611	c.1324G>A	c.(1324-1326)Gca>Aca	p.A442T	BBX_ENST00000406780.1_Missense_Mutation_p.A442T|BBX_ENST00000415149.2_Missense_Mutation_p.A442T|BBX_ENST00000402543.1_Missense_Mutation_p.A442T|BBX_ENST00000416476.2_Intron			Q8WY36	BBX_HUMAN	bobby sox homolog (Drosophila)	442					bone development (GO:0060348)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|lung(18)|ovary(4)|pancreas(1)|skin(2)	49			OV - Ovarian serous cystadenocarcinoma(3;0.112)			TGAGGATCCCGCAGCATTAAA	0.358													G|||	9	0.00179712	0.0	0.0014	5008	,	,		18346	0.0		0.006	False		,,,				2504	0.002				p.A442T		Atlas-SNP	.											.	BBX	156	.	0			c.G1324A						PASS	.	G	THR/ALA,THR/ALA	9,4397	15.5+/-35.6	0,9,2194	67.0	73.0	71.0		1324,1324	0.5	1.0	3	dbSNP_134	71	84,8516	47.6+/-106.9	2,80,4218	yes	missense,missense	BBX	NM_001142568.1,NM_020235.5	58,58	2,89,6412	AA,AG,GG		0.9767,0.2043,0.7151	benign,benign	442/942,442/912	107491892	93,12913	2203	4300	6503	SO:0001583	missense	56987	exon11			GATCCCGCAGCAT	AF168718	CCDS2950.1, CCDS46881.1, CCDS63712.1	3q13.1	2008-07-18			ENSG00000114439	ENSG00000114439			14422	protein-coding gene	gene with protein product	"""x 001 protein"""					11680820	Standard	NM_001142568		Approved	MDS001, HSPC339, HBP2	uc010hpr.4	Q8WY36	OTTHUMG00000150360	ENST00000325805.8:c.1324G>A	3.37:g.107491892G>A	ENSP00000319974:p.Ala442Thr	86.0	0.0	0		112.0	58.0	0.517857	NM_001142568	A2RRM7|Q2TAJ1|Q7L3J8|Q7LBY8|Q8NDB0|Q8WY35|Q9H0J6	Missense_Mutation	SNP	ENST00000325805.8	37	CCDS46881.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	0.656	-0.807550	0.02819	0.002043	0.009767	ENSG00000114439	ENST00000415149;ENST00000325767;ENST00000402543;ENST00000325805;ENST00000402163;ENST00000406780	D;D;D;D;D	0.98192	-4.39;-4.38;-4.39;-4.78;-4.39	6.07	0.455	0.16649	.	0.817289	0.11680	N	0.539909	D	0.84584	0.5504	N	0.01874	-0.695	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.82059	-0.0645	10	0.02654	T	1	-1.6382	0.4743	0.00537	0.3839:0.1217:0.2416:0.2529	.	442;442;442	C9JA69;Q8WY36;Q8WY36-2	.;BBX_HUMAN;.	T	442;293;442;442;442;442	ENSP00000408358:A442T;ENSP00000385317:A442T;ENSP00000319974:A442T;ENSP00000385518:A442T;ENSP00000385530:A442T	ENSP00000319742:A293T	A	+	1	0	BBX	108974582	0.002000	0.14202	0.974000	0.42286	0.699000	0.40488	0.163000	0.16520	0.528000	0.28580	-0.438000	0.05819	GCA	G|0.993;A|0.007	0.007	strong		0.358	BBX-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317820.1	NM_020235	
NPAP1	23742	hgsc.bcm.edu	37	15	24923129	24923129	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:24923129T>C	ENST00000329468.2	+	1	2589	c.2115T>C	c.(2113-2115)ccT>ccC	p.P705P		NM_018958.2	NP_061831.2	Q9NZP6	NPAP1_HUMAN	nuclear pore associated protein 1	705					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)											CCACTCCTCCTTCCAAGGCTG	0.507																																					p.P705P		Atlas-SNP	.											.	.	.	.	0			c.T2115C						PASS	.						176.0	163.0	168.0					15																	24923129		2203	4300	6503	SO:0001819	synonymous_variant	23742	exon1			TCCTCCTTCCAAG	AF179681	CCDS10015.1	15q11-q13	2012-07-19	2012-06-14	2012-06-14	ENSG00000185823	ENSG00000185823			1190	protein-coding gene	gene with protein product		610922	"""chromosome 15 open reading frame 2"""	C15orf2		10783265, 22694955	Standard	NM_018958		Approved		uc001ywo.3	Q9NZP6	OTTHUMG00000129179	ENST00000329468.2:c.2115T>C	15.37:g.24923129T>C		280.0	0.0	0		271.0	110.0	0.405904	NM_018958		Silent	SNP	ENST00000329468.2	37	CCDS10015.1																																																																																			.	.	none		0.507	NPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251253.1	NM_018958	
ABCA13	154664	hgsc.bcm.edu	37	7	48318242	48318242	+	Missense_Mutation	SNP	G	G	A	rs79834369	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48318242G>A	ENST00000435803.1	+	18	7475	c.7451G>A	c.(7450-7452)aGa>aAa	p.R2484K		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	2484					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						GCTATTTCAAGAGCAAGTGAA	0.393													G|||	10	0.00199681	0.0	0.0	5008	,	,		18633	0.0		0.0099	False		,,,				2504	0.0				p.R2484K		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G7451A						PASS	.	G	LYS/ARG	10,3654		0,10,1822	149.0	150.0	150.0		7451	-0.0	0.0	7	dbSNP_132	150	73,8097		0,73,4012	yes	missense	ABCA13	NM_152701.3	26	0,83,5834	AA,AG,GG		0.8935,0.2729,0.7014	benign	2484/5059	48318242	83,11751	1832	4085	5917	SO:0001583	missense	154664	exon18			TTTCAAGAGCAAG	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.7451G>A	7.37:g.48318242G>A	ENSP00000411096:p.Arg2484Lys	108.0	0.0	0		100.0	54.0	0.54	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	9	0.004120879120879121	0	0.0	0	0.0	0	0.0	9	0.011873350923482849	G	9.467	1.094712	0.20471	0.002729	0.008935	ENSG00000179869	ENST00000435803	T	0.56611	0.45	4.11	-0.0121	0.13989	.	0.877287	0.09429	N	0.803261	T	0.24431	0.0592	N	0.24115	0.695	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.16158	-1.0412	10	0.27082	T	0.32	.	3.6594	0.08233	0.3281:0.191:0.4809:0.0	.	2484	Q86UQ4	ABCAD_HUMAN	K	2484	ENSP00000411096:R2484K	ENSP00000411096:R2484K	R	+	2	0	ABCA13	48288788	0.000000	0.05858	0.000000	0.03702	0.084000	0.17831	0.015000	0.13355	0.085000	0.17107	0.655000	0.94253	AGA	G|0.996;A|0.004	0.004	strong		0.393	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
PIGZ	80235	hgsc.bcm.edu	37	3	196675397	196675397	+	Missense_Mutation	SNP	G	G	A	rs144088027	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:196675397G>A	ENST00000412723.1	-	3	517	c.371C>T	c.(370-372)gCg>gTg	p.A124V	PIGZ_ENST00000443835.1_Intron	NM_025163.2	NP_079439.2	Q86VD9	PIGZ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Z	124					GPI anchor biosynthetic process (GO:0006506)|mannosylation (GO:0097502)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	alpha-1,2-mannosyltransferase activity (GO:0000026)|mannosyltransferase activity (GO:0000030)			breast(1)|endometrium(1)|lung(7)|ovary(3)|prostate(1)|urinary_tract(1)	14	all_cancers(143;1.05e-08)|Ovarian(172;0.0634)|Breast(254;0.0838)		Epithelial(36;4.29e-24)|all cancers(36;2.79e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.03e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00603)		CACCAGCAGCGCATAGCCGCT	0.682													g|||	12	0.00239617	0.0023	0.0	5008	,	,		14442	0.0		0.007	False		,,,				2504	0.002				p.A124V		Atlas-SNP	.											.	PIGZ	34	.	0			c.C371T						PASS	.		VAL/ALA	5,4389		0,5,2192	21.0	19.0	20.0		371	-10.5	0.0	3	dbSNP_134	20	30,8560		0,30,4265	yes	missense	PIGZ	NM_025163.2	64	0,35,6457	AA,AG,GG		0.3492,0.1138,0.2696	benign	124/580	196675397	35,12949	2197	4295	6492	SO:0001583	missense	80235	exon3			AGCAGCGCATAGC	BC018804	CCDS3324.1	3q29	2013-02-26	2006-06-28		ENSG00000119227	ENSG00000119227		"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"", ""Phosphatidylinositol glycan anchor biosynthesis"""	30596	protein-coding gene	gene with protein product	"""GPI mannosyltransferase 4"", ""dol-P-Man dependent GPI mannosyltransferase"""	611671	"""phosphatidylinositol glycan, class Z"""			15208306	Standard	NM_025163		Approved	FLJ12768, MGC52163, SMP3	uc003fxh.3	Q86VD9	OTTHUMG00000155522	ENST00000412723.1:c.371C>T	3.37:g.196675397G>A	ENSP00000413405:p.Ala124Val	47.0	0.0	0		75.0	44.0	0.586667	NM_025163	Q9H9G6	Missense_Mutation	SNP	ENST00000412723.1	37	CCDS3324.1	9	0.004120879120879121	2	0.0040650406504065045	0	0.0	0	0.0	7	0.009234828496042216	g	1.154	-0.645692	0.03531	0.001138	0.003492	ENSG00000119227	ENST00000412723	T	0.11495	2.77	5.25	-10.5	0.00291	.	2.309490	0.01740	N	0.029334	T	0.03608	0.0103	N	0.11341	0.13	0.18873	N	0.999989	B	0.09022	0.002	B	0.06405	0.002	T	0.28996	-1.0026	10	0.08381	T	0.77	3.9812	15.9089	0.79456	0.0966:0.0:0.8226:0.0808	.	124	Q86VD9	PIGZ_HUMAN	V	124	ENSP00000413405:A124V	ENSP00000413405:A124V	A	-	2	0	PIGZ	198159794	0.000000	0.05858	0.000000	0.03702	0.058000	0.15608	-0.517000	0.06275	-3.012000	0.00272	-1.122000	0.02009	GCG	G|0.997;A|0.003	0.003	strong		0.682	PIGZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340486.2	NM_025163	
SBF1	6305	hgsc.bcm.edu	37	22	50885658	50885658	+	Silent	SNP	C	C	T	rs371139013		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50885658C>T	ENST00000390679.3	-	40	5701	c.5517G>A	c.(5515-5517)acG>acA	p.T1839T	SBF1_ENST00000380817.3_Silent_p.T1865T|SBF1_ENST00000348911.6_Silent_p.T1840T			O95248	MTMR5_HUMAN	SET binding factor 1	1839	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				cell death (GO:0008219)|positive regulation of Rab GTPase activity (GO:0032851)|protein dephosphorylation (GO:0006470)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|central_nervous_system(2)|endometrium(6)|kidney(8)|large_intestine(3)|lung(18)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	43		all_cancers(38;5.78e-13)|all_epithelial(38;1.71e-11)|all_lung(38;3.89e-05)|Breast(42;0.000523)|Lung NSC(38;0.000992)|Ovarian(80;0.0221)|Hepatocellular(38;0.0691)|Lung SC(80;0.113)		BRCA - Breast invasive adenocarcinoma(115;0.206)|LUAD - Lung adenocarcinoma(64;0.247)		AAACGCGACGCGTTGTCTTCA	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		12737	0.0		0.0	False		,,,				2504	0.001				p.T1865T		Atlas-SNP	.											.	SBF1	211	.	0			c.G5595A						PASS	.	C		0,4186		0,0,2093	47.0	57.0	53.0		5595	-0.8	1.0	22		53	2,8400		0,2,4199	no	coding-synonymous	SBF1	NM_002972.2		0,2,6292	TT,TC,CC		0.0238,0.0,0.0159		1865/1894	50885658	2,12586	2093	4201	6294	SO:0001819	synonymous_variant	6305	exon41			GCGACGCGTTGTC	U93181	CCDS14091.1, CCDS14091.2	22q13.33	2013-01-10			ENSG00000100241	ENSG00000100241		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"", ""DENN/MADD domain containing"", ""Pleckstrin homology (PH) domain containing"""	10542	protein-coding gene	gene with protein product	"""myotubularin related 5"", ""DENN/MADD domain containing 7A"""	603560				9537414, 9736772	Standard	NM_002972		Approved	MTMR5, DENND7A	uc003blh.3	O95248	OTTHUMG00000150204	ENST00000390679.3:c.5517G>A	22.37:g.50885658C>T		135.0	0.0	0		178.0	80.0	0.449438	NM_002972	A6PVG9|O60228|Q5JXD8|Q5PPM2|Q96GR9|Q9UGB8	Silent	SNP	ENST00000390679.3	37		.	.	.	.	.	.	.	.	.	.	C	7.644	0.681479	0.14907	0.0	2.38E-4	ENSG00000100241	ENST00000418590	.	.	.	3.51	-0.837	0.10766	.	.	.	.	.	T	0.39886	0.1095	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.23976	-1.0173	4	.	.	.	.	1.2292	0.01940	0.1426:0.3402:0.2736:0.2437	.	.	.	.	T	387	.	.	A	-	1	0	SBF1	49232524	0.061000	0.20836	0.996000	0.52242	0.814000	0.46013	-0.957000	0.03861	-0.171000	0.10797	0.462000	0.41574	GCG	.	.	weak		0.667	SBF1-201	KNOWN	basic	protein_coding	protein_coding			
RPS6KC1	26750	hgsc.bcm.edu	37	1	213414948	213414948	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:213414948C>T	ENST00000366960.3	+	11	2279	c.2129C>T	c.(2128-2130)cCt>cTt	p.P710L	RPS6KC1_ENST00000366959.3_Missense_Mutation_p.P698L|RPS6KC1_ENST00000543470.1_Missense_Mutation_p.P498L|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543354.1_Missense_Mutation_p.P413L	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	710					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		GCAATGGGACCTACTAAGTTT	0.398																																					p.P710L		Atlas-SNP	.											.	RPS6KC1	114	.	0			c.C2129T						PASS	.						65.0	68.0	67.0					1																	213414948		2203	4300	6503	SO:0001583	missense	26750	exon11			TGGGACCTACTAA	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.2129C>T	1.37:g.213414948C>T	ENSP00000355927:p.Pro710Leu	100.0	0.0	0		93.0	4.0	0.0430108	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Missense_Mutation	SNP	ENST00000366960.3	37	CCDS1513.1	.	.	.	.	.	.	.	.	.	.	C	9.247	1.039788	0.19669	.	.	ENSG00000136643	ENST00000543470;ENST00000366960;ENST00000366959;ENST00000543354	T;T;T;T	0.39997	1.46;1.49;1.5;1.05	5.44	4.52	0.55395	.	0.244148	0.42821	D	0.000641	T	0.31606	0.0802	L	0.38838	1.175	0.38907	D	0.957457	B;B;B	0.21753	0.06;0.016;0.016	B;B;B	0.20955	0.032;0.01;0.01	T	0.23013	-1.0200	10	0.56958	D	0.05	-40.1504	8.6494	0.34025	0.1519:0.7721:0.0:0.076	.	498;710;698	F5H7T0;Q96S38;B1APS8	.;KS6C1_HUMAN;.	L	498;710;698;413	ENSP00000442306:P498L;ENSP00000355927:P710L;ENSP00000355926:P698L;ENSP00000439282:P413L	ENSP00000355926:P698L	P	+	2	0	RPS6KC1	211481571	0.936000	0.31750	0.931000	0.37212	0.967000	0.64934	1.929000	0.40114	2.541000	0.85698	0.650000	0.86243	CCT	.	.	none		0.398	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
PUS7L	83448	hgsc.bcm.edu	37	12	44130330	44130330	+	Missense_Mutation	SNP	G	G	A	rs116948464	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:44130330G>A	ENST00000416848.2	-	7	2067	c.1579C>T	c.(1579-1581)Cgc>Tgc	p.R527C	PUS7L_ENST00000431332.3_Missense_Mutation_p.R214C|PUS7L_ENST00000344862.5_Missense_Mutation_p.R527C|PUS7L_ENST00000551923.1_Missense_Mutation_p.R527C	NM_001098615.1|NM_001271826.1	NP_001092085.1|NP_001258755.1	Q9H0K6	PUS7L_HUMAN	pseudouridylate synthase 7 homolog (S. cerevisiae)-like	527	TRUD. {ECO:0000255|PROSITE- ProRule:PRU00342}.				pseudouridine synthesis (GO:0001522)|tRNA processing (GO:0008033)		pseudouridine synthase activity (GO:0009982)|RNA binding (GO:0003723)			NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(15)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	all_cancers(12;0.00027)	Lung NSC(34;0.114)|all_lung(34;0.24)		GBM - Glioblastoma multiforme(48;0.0402)		TAGAATATGCGCATGGAATGG	0.458													G|||	9	0.00179712	0.0008	0.0	5008	,	,		20268	0.001		0.006	False		,,,				2504	0.001				p.R527C		Atlas-SNP	.											PUS7L,NS,carcinoma,+1,1	PUS7L	73	1	0			c.C1579T						PASS	.	G	CYS/ARG,CYS/ARG,CYS/ARG	2,4404	4.2+/-10.8	0,2,2201	179.0	145.0	157.0		1579,1579,1579	5.0	1.0	12	dbSNP_132	157	53,8547	33.3+/-86.6	1,51,4248	yes	missense,missense,missense	PUS7L	NM_001098614.1,NM_001098615.1,NM_031292.3	180,180,180	1,53,6449	AA,AG,GG		0.6163,0.0454,0.4229	probably-damaging,probably-damaging,probably-damaging	527/702,527/702,527/702	44130330	55,12951	2203	4300	6503	SO:0001583	missense	83448	exon7			ATATGCGCATGGA	BX647494	CCDS8743.1, CCDS61104.1	12q12	2006-02-07				ENSG00000129317			25276	protein-coding gene	gene with protein product						11230166	Standard	NM_001098615		Approved	DKFZP434G1415	uc001rnr.5	Q9H0K6	OTTHUMG00000169423	ENST00000416848.2:c.1579C>T	12.37:g.44130330G>A	ENSP00000415899:p.Arg527Cys	142.0	0.0	0		168.0	74.0	0.440476	NM_001098614	B3KUJ1|Q05CU0|Q6AHZ3|Q6NUP2	Missense_Mutation	SNP	ENST00000416848.2	37	CCDS8743.1	7	0.003205128205128205	0	0.0	0	0.0	1	0.0017482517482517483	6	0.0079155672823219	G	22.0	4.231553	0.79688	4.54E-4	0.006163	ENSG00000129317	ENST00000416848;ENST00000344862;ENST00000551923;ENST00000431332	T;T;T;T	0.50548	0.74;0.74;0.74;0.74	5.02	5.02	0.67125	Pseudouridine synthase, catalytic domain (1);Pseudouridine synthase, TruD, insertion domain (1);	0.000000	0.85682	D	0.000000	T	0.72684	0.3491	H	0.94658	3.565	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.83148	-0.0105	10	0.87932	D	0	-10.4718	19.2216	0.93799	0.0:0.0:1.0:0.0	.	527	Q9H0K6	PUS7L_HUMAN	C	527;527;527;214	ENSP00000415899:R527C;ENSP00000343081:R527C;ENSP00000447706:R527C;ENSP00000398497:R214C	ENSP00000343081:R527C	R	-	1	0	PUS7L	42416597	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	5.921000	0.70028	2.723000	0.93209	0.591000	0.81541	CGC	G|0.996;A|0.004	0.004	strong		0.458	PUS7L-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403931.1	NM_031292	
CFAP46	54777	hgsc.bcm.edu	37	10	134694526	134694526	+	Missense_Mutation	SNP	A	A	G	rs148582169	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134694526A>G	ENST00000368586.5	-	28	3738	c.3638T>C	c.(3637-3639)aTg>aCg	p.M1213T	TTC40_ENST00000368582.2_Missense_Mutation_p.M1213T	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTGCCACTCCATCTCAGGCTT	0.542													G|||	47	0.00938498	0.0	0.0072	5008	,	,		18461	0.002		0.0129	False		,,,				2504	0.0276				p.M1213T		Atlas-SNP	.											.	TTC40	100	.	0			c.T3638C						PASS	.																																			SO:0001583	missense	54777	exon28			CACTCCATCTCAG																												ENST00000368586.5:c.3638T>C	10.37:g.134694526A>G	ENSP00000357575:p.Met1213Thr	58.0	0.0	0		66.0	36.0	0.545455	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	G	0	-2.644992	0.00111	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.38722	3.1;1.12	3.63	-0.816	0.10839	.	.	.	.	.	T	0.08268	0.0206	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.21724	-1.0237	6	0.02654	T	1	.	0.3205	0.00302	0.2416:0.1795:0.2888:0.2901	.	.	.	.	T	1213	ENSP00000357575:M1213T;ENSP00000357571:M1213T	ENSP00000357571:M1213T	M	-	2	0	C10orf93	134544516	0.000000	0.05858	0.015000	0.15790	0.007000	0.05969	-0.688000	0.05150	-0.490000	0.06707	-0.320000	0.08662	ATG	A|0.993;G|0.007	0.007	strong		0.542	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
TRMT6	51605	hgsc.bcm.edu	37	20	5924828	5924828	+	Silent	SNP	A	A	G	rs35861347	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5924828A>G	ENST00000203001.2	-	4	568	c.438T>C	c.(436-438)taT>taC	p.Y146Y	TRMT6_ENST00000453074.2_5'UTR|TRMT6_ENST00000473131.1_5'UTR	NM_015939.3	NP_057023.2	Q9UJA5	TRM6_HUMAN	tRNA methyltransferase 6 homolog (S. cerevisiae)	146					regulation of translational initiation (GO:0006446)|tRNA processing (GO:0008033)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|translation initiation factor activity (GO:0003743)			breast(2)|endometrium(4)|kidney(1)|large_intestine(2)|lung(5)|pancreas(1)	15						TCTTTTTAATATATTTATCTT	0.239													A|||	284	0.0567093	0.1127	0.098	5008	,	,		12906	0.001		0.0199	False		,,,				2504	0.047				p.Y146Y		Atlas-SNP	.											.	TRMT6	28	.	0			c.T438C						PASS	.	A		424,3858		22,380,1739	16.0	17.0	17.0		438	3.3	1.0	20	dbSNP_126	17	178,8304		2,174,4065	no	coding-synonymous	TRMT6	NM_015939.3		24,554,5804	GG,GA,AA		2.0986,9.9019,4.7164		146/498	5924828	602,12162	2141	4241	6382	SO:0001819	synonymous_variant	51605	exon4			TTTAATATATTTA	AK000613	CCDS13093.1, CCDS63225.1	20p12.3	2009-01-12			ENSG00000089195	ENSG00000089195			20900	protein-coding gene	gene with protein product						16043508	Standard	NM_001281467		Approved	GCD10, MGC5029, Gcd10p, CGI-09	uc002wmh.1	Q9UJA5	OTTHUMG00000031816	ENST00000203001.2:c.438T>C	20.37:g.5924828A>G		53.0	0.0	0		71.0	33.0	0.464789	NM_015939	B4DUV6|Q76P92|Q9BQV5|Q9ULR7|Q9Y2Z8	Silent	SNP	ENST00000203001.2	37	CCDS13093.1																																																																																			A|0.958;G|0.042	0.042	strong		0.239	TRMT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077889.2		
DGKI	9162	hgsc.bcm.edu	37	7	137263068	137263068	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:137263068G>T	ENST00000288490.5	-	16	1646	c.1646C>A	c.(1645-1647)gCa>gAa	p.A549E	DGKI_ENST00000446122.1_Missense_Mutation_p.A549E|DGKI_ENST00000424189.2_Missense_Mutation_p.A549E|DGKI_ENST00000453654.2_Missense_Mutation_p.A249E	NM_004717.2	NP_004708.1	O75912	DGKI_HUMAN	diacylglycerol kinase, iota	549					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|positive regulation of Ras protein signal transduction (GO:0046579)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of Rap GTPase activity (GO:0032317)	cytoplasm (GO:0005737)|guanyl-nucleotide exchange factor complex (GO:0032045)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|GTPase inhibitor activity (GO:0005095)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)			breast(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(46)|ovary(2)|prostate(4)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	84						CTCTGGATTTGCTTCTGTGAA	0.373																																					p.A549E		Atlas-SNP	.											DGKI_ENST00000288490,NS,carcinoma,-1,2	DGKI	335	2	0			c.C1646A						PASS	.						67.0	68.0	67.0					7																	137263068		2202	4299	6501	SO:0001583	missense	9162	exon16			GGATTTGCTTCTG	AF061936	CCDS5845.1	7q32.3-q33	2013-01-10			ENSG00000157680	ENSG00000157680		"""Ankyrin repeat domain containing"""	2855	protein-coding gene	gene with protein product		604072				9830018	Standard	NM_004717		Approved	DGK-IOTA	uc003vtt.3	O75912	OTTHUMG00000155697	ENST00000288490.5:c.1646C>A	7.37:g.137263068G>T	ENSP00000288490:p.Ala549Glu	120.0	0.0	0		115.0	49.0	0.426087	NM_004717	A4D1Q9|Q9NZ49	Missense_Mutation	SNP	ENST00000288490.5	37	CCDS5845.1	.	.	.	.	.	.	.	.	.	.	G	28.4	4.920853	0.92249	.	.	ENSG00000157680	ENST00000453654;ENST00000540376;ENST00000424189;ENST00000288490;ENST00000446122	T;T;T	0.27890	1.64;1.64;1.64	5.15	5.15	0.70609	Diacylglycerol kinase, accessory domain (2);	0.000000	0.85682	D	0.000000	T	0.45256	0.1333	L	0.28694	0.88	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.81914	0.987;0.995	T	0.31998	-0.9923	10	0.42905	T	0.14	.	18.6041	0.91261	0.0:0.0:1.0:0.0	.	249;549	E9PFX6;O75912	.;DGKI_HUMAN	E	249;497;549;549;549	ENSP00000392161:A249E;ENSP00000288490:A549E;ENSP00000399131:A549E	ENSP00000288490:A549E	A	-	2	0	DGKI	136913608	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.610000	0.98337	2.573000	0.86826	0.462000	0.41574	GCA	.	.	none		0.373	DGKI-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000341286.3	NM_004717	
ZNF154	7710	hgsc.bcm.edu	37	19	58213743	58213743	+	Nonsense_Mutation	SNP	G	G	A	rs74939505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58213743G>A	ENST00000512439.2	-	3	770	c.574C>T	c.(574-576)Cga>Tga	p.R192*	AC003006.7_ENST00000594684.1_Intron|ZNF154_ENST00000426889.1_Nonsense_Mutation_p.R192*|ZNF551_ENST00000596085.1_Intron|AC003006.7_ENST00000599221.1_Intron			Q13106	ZN154_HUMAN	zinc finger protein 154	192					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(1)|large_intestine(7)|lung(3)	12		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0257)		CCACACTCTCGACATTCATAA	0.428													G|||	26	0.00519169	0.0008	0.0029	5008	,	,		23939	0.001		0.0179	False		,,,				2504	0.0041				p.R192X		Atlas-SNP	.											.	ZNF154	34	.	0			c.C574T						PASS	.	G	stop/ARG	9,4345	12.9+/-30.5	0,9,2168	129.0	128.0	128.0		574	-2.7	0.0	19	dbSNP_132	128	114,8456	59.5+/-121.1	0,114,4171	yes	stop-gained	ZNF154	NM_001085384.1		0,123,6339	AA,AG,GG		1.3302,0.2067,0.9517		192/438	58213743	123,12801	2177	4285	6462	SO:0001587	stop_gained	7710	exon3			ACTCTCGACATTC	U20648	CCDS42639.1	19q13.4	2013-01-08	2006-08-22		ENSG00000179909	ENSG00000179909		"""Zinc fingers, C2H2-type"", ""-"""	12939	protein-coding gene	gene with protein product		604085	"""zinc finger protein 154 (pHZ-92)"""			7557990	Standard	XR_243957		Approved	pHZ-92	uc010euf.3	Q13106	OTTHUMG00000140375	ENST00000512439.2:c.574C>T	19.37:g.58213743G>A	ENSP00000421258:p.Arg192*	169.0	0.0	0		207.0	101.0	0.487923	NM_001085384	A7MCY3|Q8IVG7|Q8NAR0	Nonsense_Mutation	SNP	ENST00000512439.2	37	CCDS42639.1	16	0.007326007326007326	0	0.0	2	0.0055248618784530384	0	0.0	14	0.018469656992084433	G	14.30	2.495078	0.44352	0.002067	0.013302	ENSG00000179909	ENST00000512439;ENST00000426889	.	.	.	2.82	-2.67	0.06059	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.54805	T	0.06	.	2.8458	0.05542	0.2637:0.2107:0.4239:0.1018	.	.	.	.	X	192	.	ENSP00000442370:R192X	R	-	1	2	ZNF154	62905555	0.000000	0.05858	0.001000	0.08648	0.112000	0.19704	-8.748000	0.00017	-0.786000	0.04516	-1.268000	0.01426	CGA	G|0.993;A|0.007	0.007	strong		0.428	ZNF154-002	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277102.2		
PRSS53	339105	hgsc.bcm.edu	37	16	31095999	31095999	+	Silent	SNP	G	G	A	rs138417092	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31095999G>A	ENST00000280606.6	-	9	1458	c.1305C>T	c.(1303-1305)ccC>ccT	p.P435P		NM_001039503.2	NP_001034592.1	Q2L4Q9	PRS53_HUMAN	protease, serine, 53	435	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)			large_intestine(1)|lung(3)	4						GGAGGGTCACGGGCACTGTCT	0.667													G|||	43	0.00858626	0.0008	0.0187	5008	,	,		17066	0.0		0.0268	False		,,,				2504	0.002				p.P435P		Atlas-SNP	.											PRSS53,NS,haematopoietic_neoplasm,0,1	PRSS53	29	1	0			c.C1305T						scavenged	.	G		9,4091		0,9,2041	15.0	19.0	18.0		1305	0.3	1.0	16	dbSNP_134	18	95,8309		0,95,4107	no	coding-synonymous	PRSS53	NM_001039503.2		0,104,6148	AA,AG,GG		1.1304,0.2195,0.8317		435/554	31095999	104,12400	2050	4202	6252	SO:0001819	synonymous_variant	339105	exon9			GGTCACGGGCACT		CCDS42153.1	16p11.2	2010-05-07			ENSG00000151006	ENSG00000151006		"""Serine peptidases / Serine peptidases"""	34407	protein-coding gene	gene with protein product	"""polyserase 3"""	610561				16566820	Standard	NM_001039503		Approved	POL3S	uc002eaq.3	Q2L4Q9	OTTHUMG00000047358	ENST00000280606.6:c.1305C>T	16.37:g.31095999G>A		177.0	1.0	0.00564972		177.0	65.0	0.367232	NM_001039503		Silent	SNP	ENST00000280606.6	37	CCDS42153.1																																																																																			G|0.988;A|0.012	0.012	strong		0.667	PRSS53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108580.4	NM_001081268	
BRSK1	84446	hgsc.bcm.edu	37	19	55817694	55817694	+	Silent	SNP	C	C	T	rs200320831		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55817694C>T	ENST00000309383.1	+	17	2242	c.1965C>T	c.(1963-1965)tcC>tcT	p.S655S	BRSK1_ENST00000590333.1_Silent_p.S671S|BRSK1_ENST00000326848.7_Silent_p.S350S	NM_032430.1	NP_115806.1	Q8TDC3	BRSK1_HUMAN	BR serine/threonine kinase 1	655					axonogenesis (GO:0007409)|cellular response to DNA damage stimulus (GO:0006974)|centrosome duplication (GO:0051298)|establishment of cell polarity (GO:0030010)|G2 DNA damage checkpoint (GO:0031572)|neuron differentiation (GO:0030182)|neurotransmitter secretion (GO:0007269)|protein phosphorylation (GO:0006468)|response to UV (GO:0009411)	cell junction (GO:0030054)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	ATP binding (GO:0005524)|gamma-tubulin binding (GO:0043015)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)|tau-protein kinase activity (GO:0050321)	p.S655S(2)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(15)|ovary(2)|prostate(2)|skin(6)|stomach(1)	48		Renal(1328;0.245)	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0474)		GCGGCCCCTCCGTCTTCCAAA	0.637																																					p.S655S		Atlas-SNP	.											BRSK1_ENST00000309383,NS,carcinoma,0,2	BRSK1	192	2	2	Substitution - coding silent(2)	endometrium(2)	c.C1965T						PASS	.						59.0	58.0	58.0					19																	55817694		2203	4300	6503	SO:0001819	synonymous_variant	84446	exon17			CCCCTCCGTCTTC	AB058714	CCDS12921.1	19q13.4	2008-02-05				ENSG00000160469			18994	protein-coding gene	gene with protein product		609235				14976552	Standard	NM_032430		Approved	KIAA1811	uc002qkg.3	Q8TDC3		ENST00000309383.1:c.1965C>T	19.37:g.55817694C>T		56.0	0.0	0		71.0	35.0	0.492958	NM_032430	F1DG44|Q5J5B5|Q8NDD0|Q8NDR4|Q8TDC2|Q96AV4|Q96JL4	Silent	SNP	ENST00000309383.1	37	CCDS12921.1																																																																																			C|0.999;T|0.001	0.001	weak		0.637	BRSK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452787.1	NM_032430	
EGFR	1956	hgsc.bcm.edu	37	7	55259450	55259450	+	Silent	SNP	C	C	T	rs2229066	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55259450C>T	ENST00000275493.2	+	21	2685	c.2508C>T	c.(2506-2508)cgC>cgT	p.R836R	EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000454757.2_Silent_p.R783R|EGFR_ENST00000455089.1_Silent_p.R791R|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	836	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.R836R(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	TGGTGCACCGCGACCTGGCAG	0.542		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			C|||	27	0.00539137	0.0008	0.0058	5008	,	,		20375	0.0		0.0169	False		,,,				2504	0.0051				p.R836R		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	EGFR,NS,carcinoma,0,8	EGFR	20426	8	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.C2508T						scavenged	.	C		25,4381	31.7+/-61.6	0,25,2178	112.0	97.0	102.0		2508	-11.6	0.0	7	dbSNP_123	102	196,8404	86.9+/-149.2	3,190,4107	no	coding-synonymous	EGFR	NM_005228.3		3,215,6285	TT,TC,CC		2.2791,0.5674,1.6992		836/1211	55259450	221,12785	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon21	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	GCACCGCGACCTG		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2508C>T	7.37:g.55259450C>T		20.0	0.0	0		19.0	3.0	0.157895	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			C|0.986;T|0.014	0.014	strong		0.542	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
MAPK15	225689	hgsc.bcm.edu	37	8	144804000	144804000	+	Missense_Mutation	SNP	C	C	T	rs536928468		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144804000C>T	ENST00000338033.4	+	13	1527	c.1408C>T	c.(1408-1410)Cgg>Tgg	p.R470W	RP11-429J17.5_ENST00000527908.1_RNA	NM_139021.2	NP_620590.2	Q8TD08	MK15_HUMAN	mitogen-activated protein kinase 15	470					MAPK cascade (GO:0000165)|negative regulation of DNA replication (GO:0008156)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein ubiquitination (GO:0031398)|protein autophosphorylation (GO:0046777)|response to estradiol (GO:0032355)	extracellular region (GO:0005576)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|MAP kinase activity (GO:0004707)|SH3 domain binding (GO:0017124)			endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|skin(1)|stomach(1)	12	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)			GGCCCTGATCCGGGGTGACTG	0.687													c|||	1	0.000199681	0.0008	0.0	5008	,	,		13081	0.0		0.0	False		,,,				2504	0.0				p.R470W		Atlas-SNP	.											.	MAPK15	32	.	0			c.C1408T						PASS	.						30.0	39.0	36.0					8																	144804000		1960	4118	6078	SO:0001583	missense	225689	exon13			CTGATCCGGGGTG	AY065978	CCDS6409.2	8q24.3	2011-06-09			ENSG00000181085	ENSG00000181085		"""Mitogen-activated protein kinase cascade / Kinases"""	24667	protein-coding gene	gene with protein product	"""extracellular signal regulated kinase 8"""					11875070	Standard	XM_006716528		Approved	ERK8, ERK7	uc003yzj.3	Q8TD08	OTTHUMG00000146450	ENST00000338033.4:c.1408C>T	8.37:g.144804000C>T	ENSP00000337691:p.Arg470Trp	75.0	0.0	0		69.0	22.0	0.318841	NM_139021	Q2TCF9|Q8N362	Missense_Mutation	SNP	ENST00000338033.4	37	CCDS6409.2	.	.	.	.	.	.	.	.	.	.	c	12.80	2.045324	0.36085	.	.	ENSG00000181085	ENST00000338033	T	0.81330	-1.48	3.23	2.31	0.28768	.	0.000000	0.85682	U	0.000000	T	0.81884	0.4917	L	0.32530	0.975	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.80761	-0.1238	10	0.87932	D	0	-20.9811	9.0646	0.36455	0.2217:0.7783:0.0:0.0	.	470	Q8TD08	MK15_HUMAN	W	470	ENSP00000337691:R470W	ENSP00000337691:R470W	R	+	1	2	MAPK15	144875988	0.017000	0.18338	0.486000	0.27416	0.049000	0.14656	1.449000	0.35123	0.519000	0.28406	0.306000	0.20318	CGG	.	.	none		0.687	MAPK15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000300348.1	NM_139021	
GPR153	387509	hgsc.bcm.edu	37	1	6314758	6314758	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:6314758G>A	ENST00000377893.2	-	2	467	c.208C>T	c.(208-210)Cgg>Tgg	p.R70W		NM_207370.2	NP_997253.2	Q6NV75	GP153_HUMAN	G protein-coupled receptor 153	70						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(2)|liver(1)|lung(7)|skin(1)	14	Ovarian(185;0.0634)	all_cancers(23;8.07e-33)|all_epithelial(116;4.45e-18)|all_lung(118;1.09e-06)|all_neural(13;3.68e-06)|Lung NSC(185;1.52e-05)|all_hematologic(16;2.39e-05)|Acute lymphoblastic leukemia(12;0.000372)|Glioma(11;0.00127)|Renal(390;0.00188)|Colorectal(325;0.00342)|Breast(487;0.00475)|Hepatocellular(190;0.0218)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.15)		Epithelial(90;1.91e-37)|GBM - Glioblastoma multiforme(13;4.87e-29)|OV - Ovarian serous cystadenocarcinoma(86;3.03e-19)|Colorectal(212;1.33e-07)|COAD - Colon adenocarcinoma(227;1.36e-05)|Kidney(185;4.89e-05)|KIRC - Kidney renal clear cell carcinoma(229;0.000911)|BRCA - Breast invasive adenocarcinoma(365;0.00109)|STAD - Stomach adenocarcinoma(132;0.00313)|READ - Rectum adenocarcinoma(331;0.0642)|Lung(427;0.246)		CGCTGCCGCCGCAGCTGCACC	0.607																																					p.R70W		Atlas-SNP	.											.	GPR153	44	.	0			c.C208T						PASS	.						119.0	107.0	111.0					1																	6314758		2203	4300	6503	SO:0001583	missense	387509	exon2			GCCGCCGCAGCTG	AY255529	CCDS64.1	1p36.31	2012-08-21			ENSG00000158292	ENSG00000158292		"""GPCR / Class A : Orphans"""	23618	protein-coding gene	gene with protein product		614269				12679517	Standard	NM_207370		Approved	PGR1	uc001amp.2	Q6NV75	OTTHUMG00000001272	ENST00000377893.2:c.208C>T	1.37:g.6314758G>A	ENSP00000367125:p.Arg70Trp	115.0	0.0	0		115.0	9.0	0.0782609	NM_207370	Q5TGR5|Q6AHW8|Q86SP8	Missense_Mutation	SNP	ENST00000377893.2	37	CCDS64.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.546288	0.86022	.	.	ENSG00000158292	ENST00000377893	T	0.37584	1.19	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.000000	0.85682	D	0.000000	T	0.48447	0.1500	L	0.32530	0.975	0.58432	D	0.99999	D	0.89917	1.0	D	0.97110	1.0	T	0.48625	-0.9019	10	0.87932	D	0	-53.1149	12.8394	0.57793	0.0:0.0:0.8368:0.1632	.	70	Q6NV75	GP153_HUMAN	W	70	ENSP00000367125:R70W	ENSP00000367125:R70W	R	-	1	2	GPR153	6237345	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.795000	0.85887	2.534000	0.85438	0.557000	0.71058	CGG	.	.	none		0.607	GPR153-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000003717.2		
RBMXL1	494115	hgsc.bcm.edu	37	1	89449037	89449037	+	Missense_Mutation	SNP	C	C	A	rs200081893		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:89449037C>A	ENST00000321792.5	-	2	900	c.473G>T	c.(472-474)gGg>gTg	p.G158V	CCBL2_ENST00000260508.4_Intron|RBMXL1_ENST00000413769.1_5'UTR|CCBL2_ENST00000370491.3_Intron|CCBL2_ENST00000446900.2_Intron|CCBL2_ENST00000370485.2_Intron|RBMXL1_ENST00000399794.2_Missense_Mutation_p.G158V	NM_019610.5	NP_062556.2	Q96E39	RMXL1_HUMAN	RNA binding motif protein, X-linked-like 1	158					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)										AGAAGGACCCCCACTTCTTGG	0.493																																					p.G158V		Atlas-SNP	.											.	.	.	.	0			c.G473T						PASS	.						146.0	153.0	151.0					1																	89449037		2203	4300	6503	SO:0001583	missense	494115	exon3			GGACCCCCACTTC	BC012942	CCDS716.1	1p22.2	2013-02-12	2007-01-04	2007-01-04	ENSG00000213516	ENSG00000213516		"""RNA binding motif (RRM) containing"""	25073	protein-coding gene	gene with protein product	"""kynurenine aminotransferase III"""					10441733	Standard	NM_019610		Approved	KAT3	uc001dms.3	Q96E39	OTTHUMG00000010661	ENST00000321792.5:c.473G>T	1.37:g.89449037C>A	ENSP00000318415:p.Gly158Val	473.0	0.0	0		486.0	23.0	0.0473251	NM_001162536		Missense_Mutation	SNP	ENST00000321792.5	37	CCDS716.1	.	.	.	.	.	.	.	.	.	.	C	15.99	2.995423	0.54147	.	.	ENSG00000213516	ENST00000321792;ENST00000399794	T;T	0.78924	-1.22;-1.22	1.76	0.711	0.18162	.	0.000000	0.85682	U	0.000000	T	0.57888	0.2084	M	0.72894	2.215	0.80722	D	1	B	0.23316	0.083	B	0.19391	0.025	T	0.55483	-0.8134	10	0.51188	T	0.08	-9.2612	6.8205	0.23855	0.2788:0.7212:0.0:0.0	.	158	Q96E39	RBMXL_HUMAN	V	158	ENSP00000318415:G158V;ENSP00000446099:G158V	ENSP00000318415:G158V	G	-	2	0	RBMXL1	89221625	0.997000	0.39634	0.791000	0.31998	0.903000	0.53119	2.436000	0.44819	0.049000	0.15920	0.306000	0.20318	GGG	C|0.997;A|0.003	0.003	weak		0.493	RBMXL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029403.3	NM_019610	
BOC	91653	hgsc.bcm.edu	37	3	112989763	112989763	+	Silent	SNP	C	C	T	rs9819129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:112989763C>T	ENST00000495514.1	+	6	1343	c.639C>T	c.(637-639)tcC>tcT	p.S213S	BOC_ENST00000355385.3_Silent_p.S213S|BOC_ENST00000273395.4_Silent_p.S213S			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	213	Ig-like C2-type 2.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)				NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			TGAAAACCTCCGGCTCCAGCG	0.607													C|||	113	0.0225639	0.0484	0.0173	5008	,	,		20556	0.0		0.0258	False		,,,				2504	0.0112				p.S213S		Atlas-SNP	.											.	BOC	139	.	0			c.C639T						PASS	.	C		167,4239	110.4+/-148.6	2,163,2038	126.0	126.0	126.0		639	-11.6	0.5	3	dbSNP_119	126	209,8391	89.7+/-151.9	2,205,4093	no	coding-synonymous	BOC	NM_033254.2		4,368,6131	TT,TC,CC		2.4302,3.7903,2.891		213/1115	112989763	376,12630	2203	4300	6503	SO:0001819	synonymous_variant	91653	exon6			AACCTCCGGCTCC	AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.639C>T	3.37:g.112989763C>T		82.0	0.0	0		65.0	21.0	0.323077	NM_033254	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Silent	SNP	ENST00000495514.1	37	CCDS2971.1																																																																																			C|0.974;T|0.026	0.026	strong		0.607	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3	NM_033254	
ADAMTS7	11173	hgsc.bcm.edu	37	15	79065483	79065483	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:79065483G>A	ENST00000388820.4	-	14	2283	c.2073C>T	c.(2071-2073)caC>caT	p.H691H	ADAMTS7_ENST00000566303.1_Intron	NM_014272.3	NP_055087.2	Q9UKP4	ATS7_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 7	691	Cys-rich.				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 chondrocyte differentiation (GO:0032331)|proteolysis involved in cellular protein catabolic process (GO:0051603)	cell surface (GO:0009986)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(2)|lung(23)|ovary(1)|prostate(8)|skin(9)	54						AGCCGTTGCCGTGGCACACAC	0.652																																					p.H691H		Atlas-SNP	.											.	ADAMTS7	142	.	0			c.C2073T						PASS	.						10.0	10.0	10.0					15																	79065483		2113	4023	6136	SO:0001819	synonymous_variant	11173	exon14			GTTGCCGTGGCAC	AF140675	CCDS32303.1	15q25.1	2012-05-16	2005-08-19		ENSG00000136378	ENSG00000136378		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	223	protein-coding gene	gene with protein product	"""COMPase"", ""a disintegrin and metalloprotease with thrombospondin motifs-7 preproprotein"""	605009	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 7"""			10464288	Standard	NM_014272		Approved	ADAM-TS7, DKFZp434H204	uc002bej.4	Q9UKP4	OTTHUMG00000172907	ENST00000388820.4:c.2073C>T	15.37:g.79065483G>A		610.0	0.0	0		709.0	69.0	0.0973202	NM_014272	Q14F51|Q6P7J9	Silent	SNP	ENST00000388820.4	37	CCDS32303.1																																																																																			.	.	none		0.652	ADAMTS7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421331.1	NM_014272	
SLC11A2	4891	hgsc.bcm.edu	37	12	51390685	51390685	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:51390685C>T	ENST00000262051.7	-	9	833	c.746G>A	c.(745-747)cGc>cAc	p.R249H	SLC11A2_ENST00000262052.5_Missense_Mutation_p.R249H|SLC11A2_ENST00000541174.2_Missense_Mutation_p.R249H|SLC11A2_ENST00000547688.1_Missense_Mutation_p.R278H|SLC11A2_ENST00000547198.1_Missense_Mutation_p.R249H|SLC11A2_ENST00000394904.3_Missense_Mutation_p.R278H|SLC11A2_ENST00000545993.2_Missense_Mutation_p.R245H|SLC11A2_ENST00000546743.1_Missense_Mutation_p.R170H	NM_001174126.1|NM_001174127.1	NP_001167597.1|NP_001167598.1	P49281	NRAM2_HUMAN	solute carrier family 11 (proton-coupled divalent metal ion transporter), member 2	249					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cadmium ion transmembrane transport (GO:0070574)|cation transmembrane transport (GO:0098655)|cellular iron ion homeostasis (GO:0006879)|cellular response to hypoxia (GO:0071456)|cellular response to iron ion (GO:0071281)|cellular response to oxidative stress (GO:0034599)|cellular response to tumor necrosis factor (GO:0071356)|cobalt ion transport (GO:0006824)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detection of oxygen (GO:0003032)|erythrocyte development (GO:0048821)|ferrous iron import (GO:0070627)|ferrous iron transport (GO:0015684)|heme biosynthetic process (GO:0006783)|lead ion transport (GO:0015692)|learning or memory (GO:0007611)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organismal iron ion homeostasis (GO:0060586)|nickel cation transmembrane transport (GO:0035444)|nickel cation transport (GO:0015675)|response to cadmium ion (GO:0046686)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to lead ion (GO:0010288)|response to manganese ion (GO:0010042)|transmembrane transport (GO:0055085)|vanadium ion transport (GO:0015676)|zinc ion transmembrane transport (GO:0071577)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basal part of cell (GO:0045178)|brush border (GO:0005903)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|nucleus (GO:0005634)|paraferritin complex (GO:0070826)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)|vacuole (GO:0005773)	cadmium ion binding (GO:0046870)|cadmium ion transmembrane transporter activity (GO:0015086)|cobalt ion binding (GO:0050897)|cobalt ion transmembrane transporter activity (GO:0015087)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|ferrous iron transmembrane transporter activity (GO:0015093)|hydrogen ion transmembrane transporter activity (GO:0015078)|inorganic cation transmembrane transporter activity (GO:0022890)|iron ion binding (GO:0005506)|lead ion transmembrane transporter activity (GO:0015094)|manganese ion binding (GO:0030145)|manganese ion transmembrane transporter activity (GO:0005384)|nickel cation binding (GO:0016151)|nickel cation transmembrane transporter activity (GO:0015099)|solute:proton symporter activity (GO:0015295)|vanadium ion transmembrane transporter activity (GO:0015100)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(2)|cervix(1)|endometrium(3)|kidney(16)|large_intestine(4)|lung(9)|upper_aerodigestive_tract(1)	36						CTGTGGAGTGCGACAGCCTGA	0.498																																					p.R278H		Atlas-SNP	.											SLC11A2,caecum,carcinoma,0,1	SLC11A2	51	1	0			c.G833A						PASS	.						233.0	148.0	177.0					12																	51390685		2203	4300	6503	SO:0001583	missense	4891	exon9			GGAGTGCGACAGC	AB015355	CCDS8805.1, CCDS53791.1, CCDS53792.1, CCDS53793.1	12q13	2013-07-18	2013-07-18		ENSG00000110911	ENSG00000110911		"""Solute carriers"""	10908	protein-coding gene	gene with protein product		600523		NRAMP2		7613023	Standard	NM_000617		Approved	DCT1, DMT1	uc001rxk.2	P49281	OTTHUMG00000169493	ENST00000262051.7:c.746G>A	12.37:g.51390685C>T	ENSP00000262051:p.Arg249His	132.0	0.0	0		148.0	63.0	0.425676	NM_001174125	B3KT08|B4DK84|F5H741|O43288|O60932|O94801|Q498Z5|Q8IUD7|Q96J35	Missense_Mutation	SNP	ENST00000262051.7	37	CCDS53792.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.170540	0.38315	.	.	ENSG00000110911	ENST00000262051;ENST00000547198;ENST00000262052;ENST00000394904;ENST00000547688;ENST00000541174;ENST00000545993;ENST00000546743	T;T;T;T;T;T;T;T	0.30714	1.93;1.93;1.93;1.93;1.93;1.93;1.93;1.52	5.79	-5.03	0.02973	.	1.323470	0.04699	N	0.415517	T	0.18964	0.0455	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.06786	0.0;0.001;0.001;0.0;0.0;0.0	B;B;B;B;B;B	0.10450	0.003;0.003;0.005;0.003;0.003;0.003	T	0.34453	-0.9828	10	0.48119	T	0.1	8.703	8.5091	0.33206	0.0:0.402:0.0991:0.4989	.	212;245;278;249;98;249	B7Z9M2;F5H741;P49281-3;P49281-2;B3KY44;P49281	.;.;.;.;.;NRAM2_HUMAN	H	249;249;249;278;278;249;245;170	ENSP00000262051:R249H;ENSP00000446769:R249H;ENSP00000262052:R249H;ENSP00000378364:R278H;ENSP00000449200:R278H;ENSP00000444542:R249H;ENSP00000442810:R245H;ENSP00000446914:R170H	ENSP00000262051:R249H	R	-	2	0	SLC11A2	49676952	0.000000	0.05858	0.001000	0.08648	0.493000	0.33554	0.566000	0.23593	-0.836000	0.04229	-0.140000	0.14226	CGC	.	.	none		0.498	SLC11A2-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404383.1		
CCDC171	203238	hgsc.bcm.edu	37	9	15874585	15874585	+	Missense_Mutation	SNP	T	T	G	rs149814894	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:15874585T>G	ENST00000380701.3	+	24	3852	c.3524T>G	c.(3523-3525)cTa>cGa	p.L1175R	CCDC171_ENST00000486641.2_3'UTR|CCDC171_ENST00000297641.3_Missense_Mutation_p.L1175R	NM_173550.2	NP_775821.2	Q6TFL3	CC171_HUMAN	coiled-coil domain containing 171	1175																	GACTTCACCCTACAGCTACCC	0.493													T|||	34	0.00678914	0.0	0.0058	5008	,	,		17965	0.0		0.0109	False		,,,				2504	0.0194				p.L1175R		Atlas-SNP	.											C9orf93_ENST00000380689,NS,lymphoid_neoplasm,0,2	.	.	2	0			c.T3524G						PASS	.	T	ARG/LEU	5,4401	9.9+/-24.2	0,5,2198	139.0	125.0	130.0		3524	5.7	1.0	9	dbSNP_134	130	61,8539	37.8+/-93.5	0,61,4239	yes	missense	C9orf93	NM_173550.2	102	0,66,6437	GG,GT,TT		0.7093,0.1135,0.5075	probably-damaging	1175/1327	15874585	66,12940	2203	4300	6503	SO:0001583	missense	203238	exon24			TCACCCTACAGCT	AY422473	CCDS6481.1	9p22.2	2012-03-26	2012-03-26	2012-03-26	ENSG00000164989	ENSG00000164989			29828	protein-coding gene	gene with protein product	"""myosin tail domain containing protein"""		"""chromosome 9 open reading frame 93"""	C9orf93		14702039	Standard	NM_173550		Approved	FLJ39267, FLJ46740, Em:AL513423.1, bA778P13.1, bA536D16.1	uc003zmd.3	Q6TFL3	OTTHUMG00000019584	ENST00000380701.3:c.3524T>G	9.37:g.15874585T>G	ENSP00000370077:p.Leu1175Arg	175.0	0.0	0		196.0	92.0	0.469388	NM_173550	B7ZM22|Q5SU58|Q6P1W1|Q6ZR13|Q8N1Z4|Q8N8L3|Q8TBR2	Missense_Mutation	SNP	ENST00000380701.3	37	CCDS6481.1	11|11	0.005036630036630037|0.005036630036630037	0|0	0.0|0.0	3|3	0.008287292817679558|0.008287292817679558	0|0	0.0|0.0	8|8	0.010554089709762533|0.010554089709762533	T|T	18.34|18.34	3.602189|3.602189	0.66445|0.66445	0.001135|0.001135	0.007093|0.007093	ENSG00000164989|ENSG00000164989	ENST00000297641;ENST00000380689;ENST00000380701;ENST00000359391|ENST00000449575;ENST00000432954	T;T|.	0.19938|.	2.14;2.11|.	5.74|5.74	5.74|5.74	0.90152|0.90152	.|.	0.000000|.	0.64402|.	D|.	0.000020|.	T|T	0.46889|0.46889	0.1416|0.1416	L|L	0.27053|0.27053	0.805|0.805	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.91635|.	0.999;0.998;0.999|.	T|T	0.48031|0.48031	-0.9070|-0.9070	10|5	0.45353|.	T|.	0.12|.	-5.9924|-5.9924	16.1053|16.1053	0.81216|0.81216	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	1183;442;1175|.	B7ZM22;A6NK04;Q6TFL3|.	.;.;CI093_HUMAN|.	R|D	1175;442;1175;29|415;229	ENSP00000297641:L1175R;ENSP00000370077:L1175R|.	ENSP00000297641:L1175R|.	L|Y	+|+	2|1	0|0	C9orf93|C9orf93	15864585|15864585	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.986000|0.986000	0.74619|0.74619	5.172000|5.172000	0.65003|0.65003	2.205000|2.205000	0.71048|0.71048	0.524000|0.524000	0.50904|0.50904	CTA|TAC	T|0.993;G|0.007	0.007	strong		0.493	CCDC171-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051768.4	NM_173550	
USP31	57478	hgsc.bcm.edu	37	16	23079408	23079408	+	Missense_Mutation	SNP	T	T	C	rs114976439	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:23079408T>C	ENST00000219689.7	-	16	4017	c.4018A>G	c.(4018-4020)Agc>Ggc	p.S1340G	USP31_ENST00000567975.1_Missense_Mutation_p.S633G	NM_020718.3	NP_065769.3	Q86UV5	UBP48_HUMAN	ubiquitin specific peptidase 31	0					ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	ubiquitin-specific protease activity (GO:0004843)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(17)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(2)	57				GBM - Glioblastoma multiforme(48;0.0187)		GTTTGCATGCTAGAAGATAAC	0.448													T|||	4	0.000798722	0.0	0.0029	5008	,	,		19237	0.0		0.002	False		,,,				2504	0.0				p.S1340G		Atlas-SNP	.											.	USP31	122	.	0			c.A4018G						PASS	.	T	GLY/SER	2,4392	4.2+/-10.8	0,2,2195	66.0	70.0	69.0		4018	4.6	1.0	16	dbSNP_132	69	30,8570	19.8+/-62.0	0,30,4270	yes	missense	USP31	NM_020718.3	56	0,32,6465	CC,CT,TT		0.3488,0.0455,0.2463	possibly-damaging	1340/1353	23079408	32,12962	2197	4300	6497	SO:0001583	missense	57478	exon16			GCATGCTAGAAGA	AB033029	CCDS10607.1	16p12.3	2008-02-05	2005-08-08		ENSG00000103404	ENSG00000103404		"""Ubiquitin-specific peptidases"""	20060	protein-coding gene	gene with protein product			"""ubiquitin specific protease 31"""			12838346	Standard	NM_020718		Approved	KIAA1203	uc002dll.3	Q70CQ4	OTTHUMG00000094793	ENST00000219689.7:c.4018A>G	16.37:g.23079408T>C	ENSP00000219689:p.Ser1340Gly	99.0	0.0	0		106.0	44.0	0.415094	NM_020718	B7ZKS7|Q2M3I4|Q5SZI4|Q5T3T5|Q6NX53|Q8N3F6|Q96F64|Q96IQ3|Q9H5N3|Q9H5T7|Q9NUJ6|Q9NXR0	Missense_Mutation	SNP	ENST00000219689.7	37	CCDS10607.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	T	17.73	3.460859	0.63513	4.55E-4	0.003488	ENSG00000103404	ENST00000219689	T	0.13420	2.59	5.68	4.6	0.57074	.	0.381647	0.25164	N	0.032643	T	0.15912	0.0383	L	0.60455	1.87	0.48135	D	0.999591	B;B	0.19583	0.012;0.037	B;B	0.19148	0.006;0.024	T	0.01966	-1.1238	10	0.72032	D	0.01	-9.5109	10.6397	0.45586	0.0:0.0746:0.0:0.9253	.	1340;633	Q70CQ4;B3KS48	UBP31_HUMAN;.	G	1340	ENSP00000219689:S1340G	ENSP00000219689:S1340G	S	-	1	0	USP31	22986909	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.848000	0.55903	0.989000	0.38761	0.533000	0.62120	AGC	T|0.997;C|0.003	0.003	strong		0.448	USP31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211607.1	NM_020718	
KLHL3	26249	hgsc.bcm.edu	37	5	136975604	136975604	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:136975604G>A	ENST00000309755.4	-	9	1409	c.966C>T	c.(964-966)ttC>ttT	p.F322F	KLHL3_ENST00000541417.1_Intron|KLHL3_ENST00000506873.1_5'UTR|KLHL3_ENST00000508657.1_Silent_p.F290F|KLHL3_ENST00000506491.1_Silent_p.F240F	NM_017415.2	NP_059111.2	Q9UH77	KLHL3_HUMAN	kelch-like family member 3	322			F -> C (in PHA2D). {ECO:0000269|PubMed:22266938}.		distal tubule morphogenesis (GO:0072156)|ion homeostasis (GO:0050801)|protein K48-linked ubiquitination (GO:0070936)|protein ubiquitination (GO:0016567)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|renal sodium ion absorption (GO:0070294)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)	structural molecule activity (GO:0005198)			breast(2)|endometrium(3)|kidney(2)|large_intestine(4)|lung(8)|stomach(1)|upper_aerodigestive_tract(1)	21		all_hematologic(541;3.67e-07)|Breast(839;7.61e-05)|Prostate(281;0.000825)|Ovarian(839;0.0481)|all_lung(232;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)	GBM - Glioblastoma multiforme(465;0.0223)		GGTCCTCCTCGAAATCATAGC	0.577																																					p.F322F		Atlas-SNP	.											.	KLHL3	54	.	0			c.C966T						PASS	.						104.0	90.0	95.0					5																	136975604		2203	4300	6503	SO:0001819	synonymous_variant	26249	exon9			CTCCTCGAAATCA	AB032955	CCDS4192.1, CCDS58969.1, CCDS58970.1	5q31	2013-01-30	2013-01-30		ENSG00000146021	ENSG00000146021		"""Kelch-like"", ""BTB/POZ domain containing"""	6354	protein-coding gene	gene with protein product		605775	"""kelch (Drosophila)-like 3"", ""kelch-like 3 (Drosophila)"""			10843806	Standard	NM_017415		Approved	KIAA1129	uc010jek.3	Q9UH77	OTTHUMG00000129155	ENST00000309755.4:c.966C>T	5.37:g.136975604G>A		150.0	0.0	0		139.0	58.0	0.417266	NM_017415	B2RBK7|Q9UH75|Q9UH76|Q9ULU0|Q9Y6V6	Silent	SNP	ENST00000309755.4	37	CCDS4192.1																																																																																			.	.	none		0.577	KLHL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251220.2		
UNC13C	440279	hgsc.bcm.edu	37	15	54838957	54838957	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:54838957C>A	ENST00000260323.11	+	26	5734	c.5734C>A	c.(5734-5736)Cta>Ata	p.L1912I	UNC13C_ENST00000537900.1_Missense_Mutation_p.L1910I|UNC13C_ENST00000545554.1_Missense_Mutation_p.L1912I	NM_001080534.1	NP_001074003.1	Q8NB66	UN13C_HUMAN	unc-13 homolog C (C. elegans)	1912	MHD2. {ECO:0000255|PROSITE- ProRule:PRU00588}.				exocytosis (GO:0006887)|intracellular signal transduction (GO:0035556)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|presynaptic active zone (GO:0048786)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)			breast(3)|endometrium(5)|kidney(5)|large_intestine(20)|lung(70)|ovary(6)|pancreas(2)|prostate(2)|upper_aerodigestive_tract(4)|urinary_tract(4)	121				GBM - Glioblastoma multiforme(80;0.0789)|all cancers(107;0.124)		GAAAACAGTCCTAAAGCGAGT	0.294																																					p.L1912I		Atlas-SNP	.											.	UNC13C	674	.	0			c.C5734A						PASS	.						37.0	32.0	33.0					15																	54838957		1748	4012	5760	SO:0001583	missense	440279	exon25			ACAGTCCTAAAGC	AK091491	CCDS45264.1	15q21.3	2012-10-02			ENSG00000137766	ENSG00000137766			23149	protein-coding gene	gene with protein product		614568					Standard	NM_001080534		Approved	Munc13-3, DKFZp547H074	uc021smr.1	Q8NB66	OTTHUMG00000172542	ENST00000260323.11:c.5734C>A	15.37:g.54838957C>A	ENSP00000260323:p.Leu1912Ile	112.0	0.0	0		133.0	54.0	0.406015	NM_001080534	Q0P613|Q8ND48|Q96NP3	Missense_Mutation	SNP	ENST00000260323.11	37	CCDS45264.1	.	.	.	.	.	.	.	.	.	.	C	14.35	2.509347	0.44660	.	.	ENSG00000137766	ENST00000260323;ENST00000545554;ENST00000537900	D;D;D	0.81996	-1.56;-1.56;-1.56	5.59	4.68	0.58851	Mammalian uncoordinated homology 13, domain 2 (1);Mammalian uncoordinated homology 13, subgroup, domain 2 (1);	0.000000	0.64402	D	0.000002	D	0.90830	0.7120	M	0.87682	2.9	0.42046	D	0.991092	D	0.76494	0.999	D	0.87578	0.998	D	0.91027	0.4861	10	0.54805	T	0.06	.	9.6213	0.39723	0.0:0.8427:0.0:0.1573	.	1912	Q8NB66	UN13C_HUMAN	I	1912;1912;1910	ENSP00000260323:L1912I;ENSP00000438156:L1912I;ENSP00000442569:L1910I	ENSP00000260323:L1912I	L	+	1	2	UNC13C	52626249	0.999000	0.42202	0.571000	0.28486	0.201000	0.24016	2.469000	0.45110	1.364000	0.46038	0.561000	0.74099	CTA	.	.	none		0.294	UNC13C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000419028.3	NM_173166	
RASSF4	83937	hgsc.bcm.edu	37	10	45488738	45488738	+	Silent	SNP	G	G	A	rs145503557	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45488738G>A	ENST00000340258.5	+	11	1040	c.927G>A	c.(925-927)acG>acA	p.T309T	RASSF4_ENST00000334940.6_Silent_p.T318T|RASSF4_ENST00000374417.2_3'UTR|RASSF4_ENST00000472561.1_3'UTR	NM_032023.3	NP_114412.2	Q8WYP3	RIN2_HUMAN	Ras association (RalGDS/AF-6) domain family member 4	0	Poly-Pro.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of catalytic activity (GO:0050790)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	GTPase activator activity (GO:0005096)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)|small GTPase regulator activity (GO:0005083)			NS(1)|endometrium(2)|large_intestine(6)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16						TGCGTCTGACGATGCTGCAGC	0.627													G|||	5	0.000998403	0.0038	0.0	5008	,	,		19979	0.0		0.0	False		,,,				2504	0.0				p.T309T		Atlas-SNP	.											.	RASSF4	33	.	0			c.G927A						PASS	.	G		11,4395	19.1+/-41.9	0,11,2192	67.0	51.0	56.0		927	-8.1	1.0	10	dbSNP_134	56	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RASSF4	NM_032023.3		0,12,6491	AA,AG,GG		0.0116,0.2497,0.0923		309/322	45488738	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	83937	exon11			TCTGACGATGCTG	BC032593	CCDS7208.1	10q11.1	2008-02-22	2008-02-22		ENSG00000107551	ENSG00000107551			20793	protein-coding gene	gene with protein product		610559					Standard	NM_032023		Approved	AD037, MGC44914	uc001jbo.3	Q9H2L5	OTTHUMG00000018060	ENST00000340258.5:c.927G>A	10.37:g.45488738G>A		31.0	0.0	0		20.0	11.0	0.55	NM_032023	Q00425|Q5TFT8|Q9BQL3|Q9H071	Silent	SNP	ENST00000340258.5	37	CCDS7208.1																																																																																			G|0.999;A|0.001	0.001	strong		0.627	RASSF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047745.2	NM_032023	
TBC1D4	9882	hgsc.bcm.edu	37	13	75861001	75861001	+	Missense_Mutation	SNP	A	A	G	rs557337	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:75861001A>G	ENST00000377636.3	-	21	4170	c.3824T>C	c.(3823-3825)gTc>gCc	p.V1275A	TBC1D4_ENST00000425511.1_Missense_Mutation_p.V439A|TBC1D4_ENST00000377625.2_Missense_Mutation_p.V1212A|TBC1D4_ENST00000431480.2_Missense_Mutation_p.V1267A	NM_014832.2	NP_055647.2	O60343	TBCD4_HUMAN	TBC1 domain family, member 4	1275			V -> A (in dbSNP:rs557337). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:19077034, ECO:0000269|PubMed:9628581}.		cellular response to insulin stimulus (GO:0032869)|membrane organization (GO:0061024)|negative regulation of vesicle fusion (GO:0031339)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytoplasmic vesicle membrane (GO:0030659)|extracellular vesicular exosome (GO:0070062)	Rab GTPase activator activity (GO:0005097)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(12)|lung(18)|ovary(4)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Prostate(6;0.014)|Breast(118;0.0982)		GBM - Glioblastoma multiforme(99;0.0116)		GTCACAATTGACTAGAGCATC	0.463													G|||	873	0.174321	0.556	0.0778	5008	,	,		16760	0.0		0.0666	False		,,,				2504	0.0174				p.V1275A		Atlas-SNP	.											.	TBC1D4	142	.	0			c.T3824C						PASS	.	G	ALA/VAL	1770,2058		428,914,572	104.0	107.0	106.0		3824	3.9	0.0	13	dbSNP_83	106	484,7778		13,458,3660	yes	missense	TBC1D4	NM_014832.2	64	441,1372,4232	GG,GA,AA		5.8581,46.2382,18.6435	benign	1275/1299	75861001	2254,9836	1914	4131	6045	SO:0001583	missense	9882	exon21			CAATTGACTAGAG	AB011175	CCDS41901.1, CCDS66563.1, CCDS66564.1	13q22.2	2013-07-09			ENSG00000136111	ENSG00000136111			19165	protein-coding gene	gene with protein product	"""Akt substrate of 160 kDa"""	612465				11829485, 11994271, 15304337	Standard	XM_005266603		Approved	KIAA0603, AS160, DKFZp779C0666	uc001vjl.1	O60343	OTTHUMG00000017088	ENST00000377636.3:c.3824T>C	13.37:g.75861001A>G	ENSP00000366863:p.Val1275Ala	307.0	0.0	0		305.0	163.0	0.534426	NM_014832	A7E2X8|B4DU25|B4E235|B6ETN8|B6ETN9|Q5W0B9|Q68D14	Missense_Mutation	SNP	ENST00000377636.3	37	CCDS41901.1	333	0.15247252747252749	256	0.5203252032520326	32	0.08839779005524862	0	0.0	45	0.059366754617414245	G	0.218	-1.030972	0.02029	0.462382	0.058581	ENSG00000136111	ENST00000377636;ENST00000431480;ENST00000377625;ENST00000425511	T;T;T;T	0.03358	4.23;4.23;4.23;3.96	5.63	3.87	0.44632	.	0.297360	0.28841	N	0.013979	T	0.00012	0.0000	N	0.02011	-0.69	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.001;0.0;0.0	T	0.38329	-0.9666	9	0.02654	T	1	-5.6523	10.4567	0.44555	0.2148:0.0:0.7852:0.0	rs557337;rs52811417;rs60191388;rs557337	439;1212;1267;1275	O60343-4;O60343-2;O60343-3;O60343	.;.;.;TBCD4_HUMAN	A	1275;1267;1212;439	ENSP00000366863:V1275A;ENSP00000395986:V1267A;ENSP00000366852:V1212A;ENSP00000390654:V439A	ENSP00000366852:V1212A	V	-	2	0	TBC1D4	74759002	1.000000	0.71417	0.008000	0.14137	0.004000	0.04260	4.134000	0.57990	0.847000	0.35167	-0.119000	0.15052	GTC	A|0.827;G|0.173	0.173	strong		0.463	TBC1D4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045283.1	NM_014832	
CAPN2	824	hgsc.bcm.edu	37	1	223949900	223949900	+	Missense_Mutation	SNP	G	G	A	rs145816861		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:223949900G>A	ENST00000295006.5	+	14	1888	c.1579G>A	c.(1579-1581)Gag>Aag	p.E527K	CAPN2_ENST00000474026.1_3'UTR|CAPN2_ENST00000433674.2_Missense_Mutation_p.E449K	NM_001748.4	NP_001739	P17655	CAN2_HUMAN	calpain 2, (m/II) large subunit	527	Linker.				blastocyst development (GO:0001824)|cellular response to amino acid stimulus (GO:0071230)|myoblast fusion (GO:0007520)|protein autoprocessing (GO:0016540)|proteolysis (GO:0006508)|proteolysis involved in cellular protein catabolic process (GO:0051603)|regulation of cytoskeleton organization (GO:0051493)|response to hypoxia (GO:0001666)	chromatin (GO:0000785)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)|pseudopodium (GO:0031143)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|cysteine-type peptidase activity (GO:0008234)|cytoskeletal protein binding (GO:0008092)			breast(3)|endometrium(1)|kidney(1)|large_intestine(9)|lung(10)|prostate(1)|skin(1)|stomach(3)	29				GBM - Glioblastoma multiforme(131;0.109)		CGACATCAGCGAGGATGACAT	0.517																																					p.E527K		Atlas-SNP	.											.	CAPN2	69	.	0			c.G1579A						PASS	.	G	LYS/GLU,LYS/GLU	1,4405	2.1+/-5.4	0,1,2202	174.0	128.0	143.0		1345,1579	4.7	0.9	1	dbSNP_134	143	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense	CAPN2	NM_001146068.1,NM_001748.4	56,56	0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231	probably-damaging,probably-damaging	449/623,527/701	223949900	3,13003	2203	4300	6503	SO:0001583	missense	824	exon14			ATCAGCGAGGATG	J04700	CCDS31035.1, CCDS53478.1	1q41-q42	2013-01-10			ENSG00000162909	ENSG00000162909	3.4.22.52	"""EF-hand domain containing"""	1479	protein-coding gene	gene with protein product		114230				2852952, 2539381	Standard	NM_001748		Approved	mCANP, CANPml, CANPL2	uc001hob.4	P17655	OTTHUMG00000037376	ENST00000295006.5:c.1579G>A	1.37:g.223949900G>A	ENSP00000295006:p.Glu527Lys	64.0	0.0	0		83.0	36.0	0.433735	NM_001748	A6NDG7|B7ZA96|E7ES58|Q16738|Q6PJT3|Q8WU26|Q9HBB1	Missense_Mutation	SNP	ENST00000295006.5	37	CCDS31035.1	.	.	.	.	.	.	.	.	.	.	G	13.78	2.339343	0.41398	2.27E-4	2.33E-4	ENSG00000162909	ENST00000433674;ENST00000295006;ENST00000366869	T;T	0.30714	1.52;1.52	5.63	4.71	0.59529	.	0.442904	0.27284	N	0.020073	T	0.30448	0.0765	L	0.57536	1.79	0.80722	D	1	B;B;B	0.28128	0.003;0.201;0.036	B;B;B	0.20184	0.005;0.028;0.007	T	0.04946	-1.0916	10	0.33141	T	0.24	.	14.7507	0.69522	0.0:0.0:0.8544:0.1456	.	449;110;527	B7ZA96;B3KUH9;P17655	.;.;CAN2_HUMAN	K	449;527;556	ENSP00000413158:E449K;ENSP00000295006:E527K	ENSP00000295006:E527K	E	+	1	0	CAPN2	222016523	1.000000	0.71417	0.853000	0.33588	0.071000	0.16799	9.176000	0.94839	1.364000	0.46038	0.655000	0.94253	GAG	G|1.000;A|0.000	0.000	weak		0.517	CAPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090973.1	NM_001748	
KNTC1	9735	hgsc.bcm.edu	37	12	123032478	123032478	+	Missense_Mutation	SNP	C	C	T	rs61751321	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:123032478C>T	ENST00000333479.7	+	12	1126	c.949C>T	c.(949-951)Ctc>Ttc	p.L317F	KNTC1_ENST00000450485.2_Missense_Mutation_p.L280F	NM_014708.4	NP_055523.1	P50748	KNTC1_HUMAN	kinetochore associated 1	317					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|protein complex assembly (GO:0006461)|regulation of exit from mitosis (GO:0007096)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle pole (GO:0000922)				breast(1)|central_nervous_system(1)|cervix(2)|endometrium(12)|kidney(8)|large_intestine(12)|lung(20)|ovary(7)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(4)	72	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;7.21e-05)|Epithelial(86;0.000178)|BRCA - Breast invasive adenocarcinoma(302;0.217)		AATTACAAATCTCAAATTAAT	0.259													C|||	5	0.000998403	0.0	0.0	5008	,	,		15154	0.0		0.001	False		,,,				2504	0.0041				p.L317F		Atlas-SNP	.											.	KNTC1	182	.	0			c.C949T						PASS	.	C	PHE/LEU	1,3563		0,1,1781	43.0	40.0	41.0		949	5.3	1.0	12	dbSNP_129	41	27,8073		0,27,4023	yes	missense	KNTC1	NM_014708.4	22	0,28,5804	TT,TC,CC		0.3333,0.0281,0.2401	possibly-damaging	317/2210	123032478	28,11636	1782	4050	5832	SO:0001583	missense	9735	exon12			ACAAATCTCAAAT		CCDS45002.1	12q24.31	2013-01-17			ENSG00000184445	ENSG00000184445			17255	protein-coding gene	gene with protein product	"""rough deal homolog (Drosophila)"""	607363				11146660, 11590237	Standard	NM_014708		Approved	KIAA0166, ROD	uc001ucv.3	P50748	OTTHUMG00000168861	ENST00000333479.7:c.949C>T	12.37:g.123032478C>T	ENSP00000328236:p.Leu317Phe	43.0	0.0	0		40.0	14.0	0.35	NM_014708	A7E2C4|B3KSG2	Missense_Mutation	SNP	ENST00000333479.7	37	CCDS45002.1	.	.	.	.	.	.	.	.	.	.	C	12.64	2.000039	0.35320	2.81E-4	0.003333	ENSG00000184445	ENST00000450485;ENST00000333479	T;T	0.17054	2.3;2.3	5.35	5.35	0.76521	.	0.201753	0.44483	D	0.000444	T	0.32285	0.0824	L	0.56769	1.78	0.80722	D	1	D;D	0.63880	0.983;0.993	P;P	0.59288	0.799;0.855	T	0.00722	-1.1594	10	0.46703	T	0.11	-12.1835	12.9217	0.58237	0.0:0.8244:0.1756:0.0	rs61751321	280;317	E7ES84;P50748	.;KNTC1_HUMAN	F	280;317	ENSP00000397992:L280F;ENSP00000328236:L317F	ENSP00000328236:L317F	L	+	1	0	KNTC1	121598431	1.000000	0.71417	1.000000	0.80357	0.577000	0.36160	3.241000	0.51376	2.668000	0.90789	0.573000	0.79308	CTC	C|0.991;T|0.008	0.008	strong		0.259	KNTC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396110.2		
NOTCH1	4851	hgsc.bcm.edu	37	9	139391636	139391636	+	Silent	SNP	G	G	A	rs2229974	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139391636G>A	ENST00000277541.6	-	34	6630	c.6555C>T	c.(6553-6555)gaC>gaT	p.D2185D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2185					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.K2182fs*61(1)|p.S2163_T2283del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		AGCCCTTGCCGTCCTGGGACT	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	3481	0.695088	0.6278	0.6542	5008	,	,		16337	0.9494		0.5775	False		,,,				2504	0.6738				p.D2185D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	.	NOTCH1	1980	.	2	Deletion - Frameshift(1)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(2)	c.C6555T						PASS	.	G		2777,1589		891,995,297	47.0	54.0	52.0		6555	-0.8	1.0	9	dbSNP_98	52	4726,3816		1319,2088,864	no	coding-synonymous	NOTCH1	NM_017617.3		2210,3083,1161	AA,AG,GG		44.6734,36.3949,41.8733		2185/2556	139391636	7503,5405	2183	4271	6454	SO:0001819	synonymous_variant	4851	exon34			CTTGCCGTCCTGG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.6555C>T	9.37:g.139391636G>A		115.0	0.0	0		107.0	107.0	1	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.341;A|0.659	0.659	strong		0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
C3orf20	84077	hgsc.bcm.edu	37	3	14769980	14769980	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:14769980G>A	ENST00000253697.3	+	12	2177	c.1725G>A	c.(1723-1725)gaG>gaA	p.E575E	C3orf20_ENST00000435614.1_Silent_p.E453E|C3orf20_ENST00000412910.1_Silent_p.E453E	NM_032137.4	NP_115513.4	Q8ND61	CC020_HUMAN	chromosome 3 open reading frame 20	575	Poly-Glu.					cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(13)|lung(11)|ovary(4)|skin(2)	40						CCAAAAAGGAGGAGGAAGAAT	0.473																																					p.E575E		Atlas-SNP	.											.	C3orf20	109	.	0			c.G1725A						PASS	.						81.0	82.0	82.0					3																	14769980		2203	4300	6503	SO:0001819	synonymous_variant	84077	exon12			AAAGGAGGAGGAA	AL136781	CCDS33706.1, CCDS54555.1	3p25.1	2011-01-25			ENSG00000131379	ENSG00000131379			25320	protein-coding gene	gene with protein product						11230166	Standard	NM_032137		Approved	DKFZP434N1817	uc003byy.3	Q8ND61	OTTHUMG00000155545	ENST00000253697.3:c.1725G>A	3.37:g.14769980G>A		165.0	0.0	0		150.0	49.0	0.326667	NM_032137	Q7L0U6|Q8NCP2|Q9H0I7	Silent	SNP	ENST00000253697.3	37	CCDS33706.1																																																																																			.	.	none		0.473	C3orf20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340586.1	NM_032137	
FRY	10129	hgsc.bcm.edu	37	13	32768428	32768428	+	Missense_Mutation	SNP	G	G	A	rs41292163	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32768428G>A	ENST00000380250.3	+	29	4236	c.3740G>A	c.(3739-3741)gGa>gAa	p.G1247E		NM_023037.2	NP_075463.2	Q5TBA9	FRY_HUMAN	furry homolog (Drosophila)	1247						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)				NS(3)|breast(4)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(31)|lung(50)|ovary(5)|pancreas(1)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	132		Lung SC(185;0.0271)		all cancers(112;4.81e-05)|Epithelial(112;0.000656)|OV - Ovarian serous cystadenocarcinoma(117;0.0123)|BRCA - Breast invasive adenocarcinoma(63;0.0295)|GBM - Glioblastoma multiforme(144;0.104)		ACTGTGTGTGGAAGCAGGTAC	0.413													G|||	6	0.00119808	0.0	0.0014	5008	,	,		19625	0.0		0.005	False		,,,				2504	0.0				p.G1247E		Atlas-SNP	.											.	FRY	312	.	0			c.G3740A						PASS	.	G	GLU/GLY	7,3831		0,7,1912	97.0	92.0	93.0		3740	5.2	1.0	13	dbSNP_127	93	45,8251		0,45,4103	yes	missense	FRY	NM_023037.2	98	0,52,6015	AA,AG,GG		0.5424,0.1824,0.4285	benign	1247/3014	32768428	52,12082	1919	4148	6067	SO:0001583	missense	10129	exon29			TGTGTGGAAGCAG	AL049784	CCDS41875.1	13q13.1	2008-02-05	2005-11-24	2005-11-24	ENSG00000073910	ENSG00000073910			20367	protein-coding gene	gene with protein product		614818	"""chromosome 13 open reading frame 14"""	C13orf14		14702039, 8812419	Standard	NM_023037		Approved	bA37E23.1, 13CDNA73, CG003	uc001utx.3	Q5TBA9	OTTHUMG00000016696	ENST00000380250.3:c.3740G>A	13.37:g.32768428G>A	ENSP00000369600:p.Gly1247Glu	93.0	0.0	0		106.0	58.0	0.54717	NM_023037	Q9Y3N6	Missense_Mutation	SNP	ENST00000380250.3	37	CCDS41875.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	21.1	4.104845	0.77096	0.001824	0.005424	ENSG00000073910	ENST00000380250;ENST00000380257	T	0.65549	-0.16	5.2	5.2	0.72013	.	0.112550	0.64402	D	0.000008	T	0.53206	0.1782	L	0.50333	1.59	0.80722	D	1	P	0.41848	0.763	P	0.46208	0.507	T	0.56341	-0.7995	10	0.05436	T	0.98	.	19.0865	0.93204	0.0:0.0:1.0:0.0	rs41292163	1247	Q5TBA9	FRY_HUMAN	E	1247;86	ENSP00000369600:G1247E	ENSP00000369600:G1247E	G	+	2	0	FRY	31666428	1.000000	0.71417	1.000000	0.80357	0.889000	0.51656	7.659000	0.83766	2.567000	0.86603	0.563000	0.77884	GGA	G|0.996;A|0.004	0.004	strong		0.413	FRY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044405.1	NM_023037	
CACHD1	57685	hgsc.bcm.edu	37	1	65142686	65142686	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:65142686G>A	ENST00000371073.2	+	22	3084	c.3084G>A	c.(3082-3084)ctG>ctA	p.L1028L	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Silent_p.L977L			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1028					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)				breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GTCAGAGGCTGGAAAGTGGGT	0.453																																					p.L977L		Atlas-SNP	.											.	CACHD1	125	.	0			c.G2931A						PASS	.						74.0	69.0	71.0					1																	65142686		2203	4300	6503	SO:0001819	synonymous_variant	57685	exon22			GAGGCTGGAAAGT	AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3084G>A	1.37:g.65142686G>A		161.0	0.0	0		169.0	67.0	0.39645	NM_020925	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																				.	.	none		0.453	CACHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_020925	
LRFN2	57497	hgsc.bcm.edu	37	6	40360492	40360492	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:40360492C>T	ENST00000338305.6	-	3	2102	c.1560G>A	c.(1558-1560)ccG>ccA	p.P520P		NM_020737.1	NP_065788.1	Q9ULH4	LRFN2_HUMAN	leucine rich repeat and fibronectin type III domain containing 2	520						cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(13)|lung(25)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	58	Ovarian(28;0.0418)|Colorectal(47;0.196)					ACTGGCACTGCGGGTAGTCAG	0.602																																					p.P520P		Atlas-SNP	.											.	LRFN2	133	.	0			c.G1560A						PASS	.						78.0	55.0	63.0					6																	40360492		2203	4300	6503	SO:0001819	synonymous_variant	57497	exon3			GCACTGCGGGTAG	AB033072	CCDS34443.1	6p21.2-p21.1	2013-02-11	2004-02-02	2004-02-04	ENSG00000156564	ENSG00000156564		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	21226	protein-coding gene	gene with protein product	"""fibronectin type III, immunoglobulin and leucine rich repeat domains 2"""	612808	"""KIAA1246"""	KIAA1246, SALM1		16495444, 16828986	Standard	NM_020737		Approved	FIGLER2	uc003oph.1	Q9ULH4	OTTHUMG00000014662	ENST00000338305.6:c.1560G>A	6.37:g.40360492C>T		106.0	0.0	0		119.0	67.0	0.563025	NM_020737	A5PKU3|Q5SYP9	Silent	SNP	ENST00000338305.6	37	CCDS34443.1																																																																																			.	.	none		0.602	LRFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040488.1	XM_166372	
UBXN11	91544	hgsc.bcm.edu	37	1	26608853	26608853	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608853G>A	ENST00000374222.1	-	16	1964	c.1500C>T	c.(1498-1500)ggC>ggT	p.G500G	UBXN11_ENST00000357089.4_Silent_p.G467G|UBXN11_ENST00000314675.7_Silent_p.G380G|UBXN11_ENST00000374223.1_Silent_p.G257G|UBXN11_ENST00000374221.3_Silent_p.G500G|UBXN11_ENST00000374217.2_Silent_p.G467G			Q5T124	UBX11_HUMAN	UBX domain protein 11	500	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						cgggactggggccgggaccgg	0.731																																					p.G500G		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.C1500T						PASS	.						20.0	23.0	22.0					1																	26608853		1694	3910	5604	SO:0001819	synonymous_variant	91544	exon16			ACTGGGGCCGGGA	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1500C>T	1.37:g.26608853G>A		24.0	0.0	0		38.0	15.0	0.394737	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Silent	SNP	ENST00000374222.1	37	CCDS41288.1																																																																																			.	.	none		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
LAMB2	3913	hgsc.bcm.edu	37	3	49159152	49159152	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49159152C>A	ENST00000418109.1	-	31	5229	c.5065G>T	c.(5065-5067)Ggc>Tgc	p.G1689C	USP19_ENST00000453664.1_5'Flank|USP19_ENST00000398888.2_5'Flank|USP19_ENST00000488993.1_5'Flank|LAMB2_ENST00000305544.4_Missense_Mutation_p.G1689C|USP19_ENST00000417901.1_5'Flank|USP19_ENST00000398892.3_5'Flank|USP19_ENST00000434032.2_5'Flank|USP19_ENST00000398898.2_5'Flank	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	1689	Domain I.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		TGGGCACTGCCTGCCGTTTCT	0.597																																					p.G1689C		Atlas-SNP	.											.	LAMB2	156	.	0			c.G5065T						PASS	.						71.0	74.0	73.0					3																	49159152		2203	4300	6503	SO:0001583	missense	3913	exon30			CACTGCCTGCCGT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.5065G>T	3.37:g.49159152C>A	ENSP00000388325:p.Gly1689Cys	77.0	0.0	0		103.0	36.0	0.349515	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	.	.	.	.	.	.	.	.	.	.	C	17.39	3.378244	0.61735	.	.	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34859	1.34;1.34	5.79	1.37	0.22104	.	0.448886	0.23889	N	0.043563	T	0.36413	0.0966	L	0.40543	1.245	0.37970	D	0.93324	D	0.69078	0.997	P	0.55667	0.781	T	0.29305	-1.0016	10	0.59425	D	0.04	.	5.0677	0.14591	0.0:0.4547:0.1499:0.3954	.	1689	P55268	LAMB2_HUMAN	C	1689	ENSP00000388325:G1689C;ENSP00000307156:G1689C	ENSP00000307156:G1689C	G	-	1	0	LAMB2	49134156	0.288000	0.24324	0.990000	0.47175	0.978000	0.69477	0.697000	0.25556	0.342000	0.23796	0.655000	0.94253	GGC	.	.	none		0.597	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
OPTN	10133	hgsc.bcm.edu	37	10	13168025	13168025	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13168025C>A	ENST00000378748.3	+	12	1590	c.1228C>A	c.(1228-1230)Cta>Ata	p.L410I	OPTN_ENST00000263036.5_Missense_Mutation_p.L410I|OPTN_ENST00000378752.3_Missense_Mutation_p.L404I|OPTN_ENST00000378764.2_Missense_Mutation_p.L404I|OPTN_ENST00000378757.2_Missense_Mutation_p.L410I|OPTN_ENST00000378747.3_Missense_Mutation_p.L410I	NM_001008211.1|NM_001008213.1	NP_001008212|NP_001008214	Q96CV9	OPTN_HUMAN	optineurin	410					cell death (GO:0008219)|defense response to Gram-negative bacterium (GO:0050829)|G2/M transition of mitotic cell cycle (GO:0000086)|Golgi organization (GO:0007030)|Golgi ribbon formation (GO:0090161)|Golgi to plasma membrane protein transport (GO:0043001)|macroautophagy (GO:0016236)|mitotic cell cycle (GO:0000278)|negative regulation of receptor recycling (GO:0001920)|protein targeting to Golgi (GO:0000042)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|nucleoplasm (GO:0005654)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)	polyubiquitin binding (GO:0031593)|protein C-terminus binding (GO:0008022)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|large_intestine(5)|lung(9)|ovary(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	22						AATTGAGGAACTAACAAGAAA	0.294																																					p.L410I		Atlas-SNP	.											.	OPTN	57	.	0			c.C1228A						PASS	.						75.0	74.0	74.0					10																	13168025		2203	4298	6501	SO:0001583	missense	10133	exon11			GAGGAACTAACAA	AF420371	CCDS7094.1	10p14	2014-01-28	2003-09-08		ENSG00000123240	ENSG00000123240			17142	protein-coding gene	gene with protein product		602432	"""glaucoma 1, open angle, E (adult-onset)"""	GLC1E		11834836, 9488477	Standard	NM_001008211		Approved	FIP2, HYPL, FIP-2, TFIIIA-INTP, NRP, HIP7	uc001ilx.1	Q96CV9	OTTHUMG00000017690	ENST00000378748.3:c.1228C>A	10.37:g.13168025C>A	ENSP00000368022:p.Leu410Ile	79.0	0.0	0		64.0	26.0	0.40625	NM_001008212	B3KP00|D3DRS4|D3DRS8|Q5T672|Q5T673|Q5T674|Q5T675|Q7LDL9|Q8N562|Q9UET9|Q9UEV4|Q9Y218	Missense_Mutation	SNP	ENST00000378748.3	37	CCDS7094.1	.	.	.	.	.	.	.	.	.	.	C	13.12	2.141179	0.37825	.	.	ENSG00000123240	ENST00000263036;ENST00000378764;ENST00000378757;ENST00000378752;ENST00000378748;ENST00000378747	D;D;D;D;D;D	0.87809	-2.28;-2.3;-2.28;-2.3;-2.28;-2.28	5.57	4.67	0.58626	.	0.427472	0.25981	N	0.027066	D	0.87896	0.6293	L	0.59436	1.845	0.27698	N	0.945886	P;P	0.46457	0.878;0.807	P;P	0.52481	0.7;0.504	T	0.81267	-0.1010	10	0.40728	T	0.16	-2.6754	8.8732	0.35330	0.0:0.83:0.0:0.17	.	404;410	Q96CV9-2;Q96CV9	.;OPTN_HUMAN	I	410;404;410;404;410;410	ENSP00000263036:L410I;ENSP00000368040:L404I;ENSP00000368032:L410I;ENSP00000368027:L404I;ENSP00000368022:L410I;ENSP00000368021:L410I	ENSP00000263036:L410I	L	+	1	2	OPTN	13208031	1.000000	0.71417	0.730000	0.30809	0.374000	0.29953	1.614000	0.36911	1.490000	0.48466	0.650000	0.86243	CTA	.	.	none		0.294	OPTN-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000046834.1	NM_021980	
KRAS	3845	hgsc.bcm.edu	37	12	25398284	25398284	+	Missense_Mutation	SNP	C	C	A	rs121913529		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:25398284C>A	ENST00000256078.4	-	2	98	c.35G>T	c.(34-36)gGt>gTt	p.G12V	KRAS_ENST00000311936.3_Missense_Mutation_p.G12V|KRAS_ENST00000557334.1_Missense_Mutation_p.G12V|KRAS_ENST00000556131.1_Missense_Mutation_p.G12V	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	12			G -> A (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.|G -> C (in lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:6320174}.|G -> D (in pancreatic carcinoma, GASC and lung carcinoma; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929, ECO:0000269|PubMed:8439212}.|G -> R (in lung cancer and bladder cancer; somatic mutation). {ECO:0000269|PubMed:6695174}.|G -> S (in lung carcinoma and GASC; somatic mutation). {ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:7773929}.|G -> V (in lung carcinoma, pancreatic carcinoma, colon cancer and GASC; somatic mutation, constitutively activated). {ECO:0000269|PubMed:14534542, ECO:0000269|PubMed:16533793, ECO:0000269|PubMed:16959974, ECO:0000269|PubMed:22711838, ECO:0000269|PubMed:3034404, ECO:0000269|PubMed:6092920, ECO:0000269|PubMed:8439212}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.G12D(8562)|p.G12V(5775)|p.G12A(1407)|p.G12F(46)|p.G12L(8)|p.G12I(4)|p.G12E(3)|p.G12W(3)|p.G12Y(2)|p.G12fs*3(1)|p.G12C(1)|p.G12N(1)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			GCCTACGCCACCAGCTCCAAC	0.348	G12A(KMS28BM_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(KPNSI9S_AUTONOMIC_GANGLIA)|G12A(MM1S_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(NCIH1573_LUNG)|G12A(NCIH2009_LUNG)|G12A(RERFLCAD1_LUNG)|G12A(RPMI8226_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12A(SW1116_LARGE_INTESTINE)|G12D(AGS_STOMACH)|G12D(ASPC1_PANCREAS)|G12D(COLO678_LARGE_INTESTINE)|G12D(HEC1A_ENDOMETRIUM)|G12D(HEC50B_ENDOMETRIUM)|G12D(HEYA8_OVARY)|G12D(HPAC_PANCREAS)|G12D(HPAFII_PANCREAS)|G12D(KARPAS620_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KOPN8_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|G12D(KP4_PANCREAS)|G12D(L33_PANCREAS)|G12D(LS180_LARGE_INTESTINE)|G12D(LS513_LARGE_INTESTINE)|G12D(MCAS_OVARY)|G12D(PANC0203_PANCREAS)|G12D(PANC0403_PANCREAS)|G12D(PANC0504_PANCREAS)|G12D(PANC0813_PANCREAS)|G12D(PANC1_PANCREAS)|G12D(PK1_PANCREAS)|G12D(PK59_PANCREAS)|G12D(SKLU1_LUNG)|G12D(SNUC2A_LARGE_INTESTINE)|G12D(SU8686_PANCREAS)|G12D(SUIT2_PANCREAS)|G12D(SW1990_PANCREAS)|G12V(A498_KIDNEY)|G12V(CAPAN2_PANCREAS)|G12V(CFPAC1_PANCREAS)|G12V(COLO668_LUNG)|G12V(CORL23_LUNG)|G12V(DANG_PANCREAS)|G12V(HCC56_LARGE_INTESTINE)|G12V(HUPT4_PANCREAS)|G12V(KP3_PANCREAS)|G12V(LCLC97TM1_LUNG)|G12V(NCIH2444_LUNG)|G12V(NCIH441_LUNG)|G12V(NCIH727_LUNG)|G12V(PANC0327_PANCREAS)|G12V(PATU8902_PANCREAS)|G12V(PATU8988S_PANCREAS)|G12V(QGP1_PANCREAS)|G12V(RCM1_LARGE_INTESTINE)|G12V(RERFLCAD2_LUNG)|G12V(RKN_OVARY)|G12V(SH10TC_STOMACH)|G12V(SHP77_LUNG)|G12V(SNGM_ENDOMETRIUM)|G12V(SW403_LARGE_INTESTINE)|G12V(SW480_LARGE_INTESTINE)|G12V(SW620_LARGE_INTESTINE)|G12V(SW900_LUNG)|G12V(YAPC_PANCREAS)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											p.G12V	Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	Atlas-SNP	.		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	KRAS_ENST00000256078,NS,adenocarcinoma,0,25136	KRAS	30930	25136	15813	Substitution - Missense(15812)|Deletion - Frameshift(1)	large_intestine(9453)|pancreas(3002)|lung(1512)|ovary(500)|biliary_tract(369)|endometrium(319)|haematopoietic_and_lymphoid_tissue(163)|stomach(124)|prostate(59)|thyroid(55)|small_intestine(43)|upper_aerodigestive_tract(30)|urinary_tract(30)|soft_tissue(28)|skin(27)|cervix(22)|liver(16)|breast(11)|testis(9)|oesophagus(8)|central_nervous_system(7)|peritoneum(5)|kidney(4)|eye(4)|gastrointestinal_tract_(site_indeterminate)(3)|NS(3)|thymus(3)|autonomic_ganglia(2)|salivary_gland(1)|bone(1)	c.G35T						PASS	.						91.0	81.0	85.0					12																	25398284		2203	4300	6503	SO:0001583	missense	3845	exon2	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	ACGCCACCAGCTC	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.35G>T	12.37:g.25398284C>A	ENSP00000256078:p.Gly12Val	165.0	0.0	0		211.0	89.0	0.421801	NM_004985	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	ENST00000256078.4	37	CCDS8703.1	.	.	.	.	.	.	.	.	.	.	C	27.2	4.808637	0.90707	.	.	ENSG00000133703	ENST00000311936;ENST00000557334;ENST00000256078;ENST00000556131	T;T;T;T	0.78707	-1.2;-1.2;-1.2;-1.2	5.68	5.68	0.88126	Small GTP-binding protein domain (1);	0.000000	0.85682	D	0.000000	D	0.90373	0.6987	M	0.90650	3.135	0.80722	D	1	D;D	0.76494	0.997;0.999	D;D	0.72625	0.969;0.978	D	0.91773	0.5429	10	0.72032	D	0.01	.	18.3719	0.90409	0.0:1.0:0.0:0.0	.	12;12	P01116-2;P01116	.;RASK_HUMAN	V	12	ENSP00000308495:G12V;ENSP00000452512:G12V;ENSP00000256078:G12V;ENSP00000451856:G12V	ENSP00000256078:G12V	G	-	2	0	KRAS	25289551	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.743000	0.85020	2.668000	0.90789	0.563000	0.77884	GGT	.	.	weak		0.348	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000412232.1	NM_033360	
FAM209B	388799	hgsc.bcm.edu	37	20	55108589	55108589	+	Missense_Mutation	SNP	G	G	T	rs386815439		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:55108589G>T	ENST00000371325.1	+	1	288	c.192G>T	c.(190-192)ttG>ttT	p.L64F		NM_001013646.2	NP_001013668.2	Q5JX69	F209B_HUMAN	family with sequence similarity 209, member B	64						integral component of membrane (GO:0016021)|nucleus (GO:0005634)											TCTGGCTTTTGTTTGCTGTTG	0.483																																					p.L64F		Atlas-SNP	.											.	.	.	.	0			c.G192T						PASS	.						168.0	146.0	153.0					20																	55108589		2203	4300	6503	SO:0001583	missense	388799	exon1			GCTTTTGTTTGCT	AL109806	CCDS33494.1	20q13.31	2011-11-24	2011-11-24	2011-11-24	ENSG00000213714	ENSG00000213714			16101	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 107"""	C20orf107			Standard	NM_001013646		Approved	dJ1153D9.4	uc002xxz.4	Q5JX69	OTTHUMG00000032800	ENST00000371325.1:c.192G>T	20.37:g.55108589G>T	ENSP00000360376:p.Leu64Phe	203.0	0.0	0		260.0	19.0	0.0730769	NM_001013646	Q3KRB5	Missense_Mutation	SNP	ENST00000371325.1	37	CCDS33494.1	.	.	.	.	.	.	.	.	.	.	G	0.325	-0.959853	0.02267	.	.	ENSG00000213714	ENST00000371325	T	0.08896	3.04	2.8	-3.7	0.04437	.	1.580090	0.04046	N	0.303922	T	0.04137	0.0115	N	0.17474	0.49	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.38090	-0.9677	10	0.07990	T	0.79	0.1847	4.0099	0.09618	0.0:0.2385:0.3799:0.3817	.	64	Q5JX69	CT107_HUMAN	F	64	ENSP00000360376:L64F	ENSP00000360376:L64F	L	+	3	2	C20orf107	54541996	0.000000	0.05858	0.000000	0.03702	0.033000	0.12548	-1.684000	0.01932	-1.037000	0.03283	-0.782000	0.03352	TTG	.	.	none		0.483	FAM209B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079816.1		
SCNN1D	6339	hgsc.bcm.edu	37	1	1222622	1222622	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1222622G>A	ENST00000338555.2	+	6	1905	c.761G>A	c.(760-762)aGc>aAc	p.S254N	SCNN1D_ENST00000400928.3_Missense_Mutation_p.S254N|SCNN1D_ENST00000379116.5_Missense_Mutation_p.S418N|SCNN1D_ENST00000325425.8_Missense_Mutation_p.S320N			P51172	SCNND_HUMAN	sodium channel, non-voltage-gated 1, delta subunit	254					ion transmembrane transport (GO:0034220)|response to stimulus (GO:0050896)|sensory perception of taste (GO:0050909)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)	actin cytoskeleton (GO:0015629)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ligand-gated sodium channel activity (GO:0015280)			lung(6)|skin(1)	7	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		Epithelial(90;3.01e-35)|OV - Ovarian serous cystadenocarcinoma(86;2.46e-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;0.199)	Amiloride(DB00594)|Triamterene(DB00384)	AGCCACGGGAGCCAGGACGGC	0.677																																					p.S418N		Atlas-SNP	.											.	SCNN1D	60	.	0			c.G1253A						PASS	.						22.0	20.0	21.0					1																	1222622		2169	4249	6418	SO:0001583	missense	6339	exon9			ACGGGAGCCAGGA	U38254	CCDS44037.1, CCDS44037.2	1p36.3-p36.2	2012-02-28	2012-02-28		ENSG00000162572	ENSG00000162572		"""Ion channels / Sodium channel, nonvoltage-gated"", ""Sodium channels"""	10601	protein-coding gene	gene with protein product		601328	"""sodium channel, nonvoltage-gated 1, delta"", ""sodium channel, non-voltage-gated 1, delta"""			8661065	Standard	NM_001130413		Approved	ENaCdelta, dNaCh	uc001adt.1	P51172	OTTHUMG00000002081	ENST00000338555.2:c.761G>A	1.37:g.1222622G>A	ENSP00000339504:p.Ser254Asn	77.0	0.0	0		79.0	75.0	0.949367	NM_001130413	A9Z1X6|B1PS44|Q08AQ3|Q09HT0|Q5T7L3|Q8NA24	Missense_Mutation	SNP	ENST00000338555.2	37		.	.	.	.	.	.	.	.	.	.	G	8.390	0.839506	0.16891	.	.	ENSG00000162572	ENST00000379110;ENST00000379116;ENST00000338555;ENST00000325425;ENST00000400928;ENST00000379099	T;T;T;T	0.63417	-0.04;-0.04;-0.04;-0.04	4.4	-0.589	0.11683	.	8.235220	0.00166	N	0.000001	T	0.53286	0.1787	L	0.51422	1.61	0.09310	N	1	B;B	0.32968	0.392;0.003	B;B	0.33960	0.173;0.001	T	0.26360	-1.0105	10	0.27785	T	0.31	.	2.8715	0.05618	0.2348:0.1198:0.5233:0.1222	.	254;418	P51172;A6NNF7	SCNND_HUMAN;.	N	285;418;254;320;254;45	ENSP00000368411:S418N;ENSP00000339504:S254N;ENSP00000321594:S320N;ENSP00000383717:S254N	ENSP00000321594:S320N	S	+	2	0	SCNN1D	1212485	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.212000	0.09319	0.280000	0.22209	0.313000	0.20887	AGC	.	.	none		0.677	SCNN1D-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000005802.2	NM_002978	
HERC2	8924	hgsc.bcm.edu	37	15	28420676	28420676	+	Silent	SNP	C	C	T	rs139728053	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28420676C>T	ENST00000261609.7	-	64	9921	c.9813G>A	c.(9811-9813)gcG>gcA	p.A3271A		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		AGTCCGTGACCGCCAGGCAGT	0.662													C|||	5	0.000998403	0.0	0.0	5008	,	,		16999	0.005		0.0	False		,,,				2504	0.0				p.A3271A		Atlas-SNP	.											.	HERC2	501	.	0			c.G9813A						PASS	.	C		0,4406		0,0,2203	38.0	30.0	33.0		9813	-7.9	0.9	15	dbSNP_134	33	1,8587		0,1,4293	no	coding-synonymous	HERC2	NM_004667.4		0,1,6496	TT,TC,CC		0.0116,0.0,0.0077		3271/4835	28420676	1,12993	2203	4294	6497	SO:0001819	synonymous_variant	8924	exon64			CGTGACCGCCAGG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.9813G>A	15.37:g.28420676C>T		73.0	0.0	0		91.0	49.0	0.538462	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			C|1.000;T|0.000	0.000	weak		0.662	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
GRID2	2895	hgsc.bcm.edu	37	4	94137954	94137954	+	Silent	SNP	G	G	A	rs75225211	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:94137954G>A	ENST00000282020.4	+	6	1113	c.855G>A	c.(853-855)cgG>cgA	p.R285R	GRID2_ENST00000510992.1_Silent_p.R190R|GRID2_ENST00000505687.1_3'UTR	NM_001510.2	NP_001501.2	O43424	GRID2_HUMAN	glutamate receptor, ionotropic, delta 2	285					cellular protein localization (GO:0034613)|cerebellar granule cell differentiation (GO:0021707)|glutamate receptor signaling pathway (GO:0007215)|heterophilic cell-cell adhesion (GO:0007157)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of neuron apoptotic process (GO:0043523)|regulation of neuron projection development (GO:0010975)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|dendritic spine (GO:0043197)|integral component of plasma membrane (GO:0005887)|ionotropic glutamate receptor complex (GO:0008328)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	extracellular-glutamate-gated ion channel activity (GO:0005234)|glutamate receptor activity (GO:0008066)|ionotropic glutamate receptor activity (GO:0004970)|PDZ domain binding (GO:0030165)|scaffold protein binding (GO:0097110)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(4)|large_intestine(18)|lung(45)|ovary(3)|prostate(6)|skin(9)|upper_aerodigestive_tract(3)|urinary_tract(1)	100		Hepatocellular(203;0.114)|all_hematologic(202;0.177)		OV - Ovarian serous cystadenocarcinoma(123;3.22e-06)|LUSC - Lung squamous cell carcinoma(81;0.185)|Lung(65;0.191)		CGATTATTCGGCAGACATTTC	0.408													G|||	20	0.00399361	0.0008	0.0014	5008	,	,		16944	0.0		0.0179	False		,,,				2504	0.0				p.R285R		Atlas-SNP	.											GRID2,NS,malignant_melanoma,+2,1	GRID2	233	1	0			c.G855A						PASS	.	G		12,4394	19.1+/-41.9	0,12,2191	157.0	150.0	152.0		855	-2.1	1.0	4	dbSNP_131	152	105,8495	57.2+/-118.5	0,105,4195	no	coding-synonymous	GRID2	NM_001510.2		0,117,6386	AA,AG,GG		1.2209,0.2724,0.8996		285/1008	94137954	117,12889	2203	4300	6503	SO:0001819	synonymous_variant	2895	exon6			TATTCGGCAGACA	AF009014	CCDS3637.1, CCDS68758.1	4q22	2012-08-29			ENSG00000152208	ENSG00000152208		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4576	protein-coding gene	gene with protein product		602368				9465309	Standard	NM_001510		Approved	GluD2, GluR-delta-2	uc011cdt.2	O43424	OTTHUMG00000130975	ENST00000282020.4:c.855G>A	4.37:g.94137954G>A		112.0	0.0	0		96.0	48.0	0.5	NM_001510	E9PH24|Q4KKU8|Q4KKU9|Q4KKV0|Q59FZ1	Silent	SNP	ENST00000282020.4	37	CCDS3637.1																																																																																			G|0.990;A|0.010	0.010	strong		0.408	GRID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253588.2		
GPR133	283383	hgsc.bcm.edu	37	12	131471699	131471699	+	Missense_Mutation	SNP	G	G	A	rs61732860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:131471699G>A	ENST00000261654.5	+	6	1109	c.550G>A	c.(550-552)Gtc>Atc	p.V184I	GPR133_ENST00000535015.1_Missense_Mutation_p.V216I|RP11-76C10.5_ENST00000542980.1_lincRNA	NM_198827.3	NP_942122.2	Q6QNK2	GP133_HUMAN	G protein-coupled receptor 133	184					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)	p.V184I(1)		NS(2)|breast(2)|endometrium(6)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|pancreas(6)|prostate(6)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(4)	67	all_neural(191;0.0982)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.68e-06)|all cancers(50;2.71e-06)|Epithelial(86;6.75e-06)		GAAAGTCTACGTCAACGGGAC	0.517													G|||	44	0.00878594	0.0008	0.0202	5008	,	,		20919	0.0		0.0209	False		,,,				2504	0.0082				p.V184I		Atlas-SNP	.											GPR133,NS,carcinoma,0,1	GPR133	136	1	1	Substitution - Missense(1)	prostate(1)	c.G550A						PASS	.	G	ILE/VAL	15,4391	22.3+/-47.3	0,15,2188	115.0	107.0	110.0		550	3.7	1.0	12	dbSNP_129	110	173,8427	79.5+/-142.1	3,167,4130	yes	missense	GPR133	NM_198827.3	29	3,182,6318	AA,AG,GG		2.0116,0.3404,1.4455	possibly-damaging	184/875	131471699	188,12818	2203	4300	6503	SO:0001583	missense	283383	exon6			GTCTACGTCAACG	AY278561	CCDS9272.1	12q24.33	2014-08-08			ENSG00000111452	ENSG00000111452		"""-"", ""GPCR / Class B : Orphans"""	19893	protein-coding gene	gene with protein product		613639					Standard	NM_198827		Approved	DKFZp434B1272, PGR25	uc001uit.4	Q6QNK2	OTTHUMG00000168339	ENST00000261654.5:c.550G>A	12.37:g.131471699G>A	ENSP00000261654:p.Val184Ile	133.0	0.0	0		129.0	63.0	0.488372	NM_198827	B2CKK9|B7ZLF7|Q2M1L3|Q6ZMQ1|Q7Z7M2|Q86SM4	Missense_Mutation	SNP	ENST00000261654.5	37	CCDS9272.1	23	0.010531135531135532	0	0.0	7	0.019337016574585635	0	0.0	16	0.021108179419525065	G	9.840	1.190859	0.21954	0.003404	0.020116	ENSG00000111452	ENST00000261654;ENST00000542091;ENST00000535015	T;T;T	0.74526	-0.85;-0.85;-0.85	4.55	3.67	0.42095	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);	0.146844	0.46442	N	0.000283	T	0.43478	0.1249	L	0.28014	0.82	0.80722	D	1	B;B	0.28512	0.003;0.214	B;B	0.24006	0.01;0.05	T	0.48917	-0.8992	10	0.33141	T	0.24	.	11.9058	0.52711	0.0852:0.0:0.9148:0.0	rs61732860	216;184	B7ZLF7;Q6QNK2	.;GP133_HUMAN	I	184;124;216	ENSP00000261654:V184I;ENSP00000442501:V124I;ENSP00000444425:V216I	ENSP00000261654:V184I	V	+	1	0	GPR133	130037652	0.991000	0.36638	0.999000	0.59377	0.690000	0.40134	2.351000	0.44071	0.912000	0.36772	-0.126000	0.14955	GTC	G|0.985;A|0.015	0.015	strong		0.517	GPR133-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399356.1	NM_198827	
SCAF8	22828	hgsc.bcm.edu	37	6	155152262	155152262	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:155152262A>G	ENST00000367178.3	+	19	2923	c.2347A>G	c.(2347-2349)Aac>Gac	p.N783D	TIAM2_ENST00000461783.3_5'Flank|SCAF8_ENST00000367186.4_Missense_Mutation_p.N849D|SCAF8_ENST00000417268.1_Missense_Mutation_p.N783D	NM_014892.3	NP_055707.3	Q9UPN6	SCAF8_HUMAN	SR-related CTD-associated factor 8	783	Pro-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						TTCTGGTGAAAACACCAGATC	0.383																																					p.N783D		Atlas-SNP	.											.	SCAF8	122	.	0			c.A2347G						PASS	.						28.0	27.0	28.0					6																	155152262		2203	4300	6503	SO:0001583	missense	22828	exon19			GGTGAAAACACCA	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.2347A>G	6.37:g.155152262A>G	ENSP00000356146:p.Asn783Asp	25.0	0.0	0		21.0	20.0	0.952381	NM_014892	B7Z888|Q5TBU6|Q6NSK3|Q9BQN8|Q9BX43	Missense_Mutation	SNP	ENST00000367178.3	37	CCDS5247.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.731115	0.48939	.	.	ENSG00000213079	ENST00000367178;ENST00000417268;ENST00000367186	T;T;T	0.47528	0.87;0.87;0.84	5.32	4.08	0.47627	.	0.189894	0.24940	U	0.034400	T	0.20047	0.0482	L	0.44542	1.39	0.29468	N	0.857268	B;B;P;P	0.37864	0.094;0.094;0.61;0.61	B;B;B;B	0.35510	0.016;0.016;0.204;0.145	T	0.04579	-1.0941	10	0.26408	T	0.33	.	10.1615	0.42855	0.8517:0.0:0.0:0.1483	.	828;849;861;783	B7Z876;B7Z888;B7Z3A4;Q9UPN6	.;.;.;SCAF8_HUMAN	D	783;783;849	ENSP00000356146:N783D;ENSP00000413098:N783D;ENSP00000356154:N849D	ENSP00000356146:N783D	N	+	1	0	SCAF8	155193954	0.999000	0.42202	1.000000	0.80357	0.992000	0.81027	3.825000	0.55730	2.136000	0.66102	0.533000	0.62120	AAC	.	.	none		0.383	SCAF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042798.1	NM_014892	
MROH9	80133	hgsc.bcm.edu	37	1	170952652	170952652	+	Missense_Mutation	SNP	C	C	A	rs112394419	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:170952652C>A	ENST00000367758.3	+	9	805	c.706C>A	c.(706-708)Caa>Aaa	p.Q236K	MROH9_ENST00000367759.4_Missense_Mutation_p.Q236K	NM_025063.2	NP_079339.2	Q5TGP6	MROH9_HUMAN	maestro heat-like repeat family member 9	236																	GGAGTTTCAACAAGACGAAAG	0.358													C|||	14	0.00279553	0.0008	0.0014	5008	,	,		16447	0.0		0.0099	False		,,,				2504	0.002				p.Q236K		Atlas-SNP	.											.	.	.	.	0			c.C706A						PASS	.	C	LYS/GLN,LYS/GLN	8,3616		0,8,1804	80.0	73.0	76.0		706,706	-5.2	0.0	1	dbSNP_132	76	71,8085		0,71,4007	yes	missense,missense	C1orf129	NM_001163629.1,NM_025063.2	53,53	0,79,5811	AA,AC,CC		0.8705,0.2208,0.6706	benign,benign	236/862,236/574	170952652	79,11701	1812	4078	5890	SO:0001583	missense	80133	exon9			TTTCAACAAGACG	AK027203	CCDS41436.1, CCDS53429.1	1q24.3	2012-12-19	2012-12-19	2012-12-19	ENSG00000117501	ENSG00000117501		"""maestro heat-like repeat containing"""	26287	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 129"""	C1orf129			Standard	NM_025063		Approved	FLJ23550, ARMC11	uc010plz.2	Q5TGP6	OTTHUMG00000041456	ENST00000367758.3:c.706C>A	1.37:g.170952652C>A	ENSP00000356732:p.Gln236Lys	27.0	0.0	0		36.0	16.0	0.444444	NM_025063	A0PJM0|A0PJM2|F5GWX6|Q9H5D7	Missense_Mutation	SNP	ENST00000367758.3	37	CCDS41436.1	7	0.003205128205128205	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	5	0.006596306068601583	C	0.018	-1.467182	0.01053	0.002208	0.008705	ENSG00000117501	ENST00000367759;ENST00000367758	T;T	0.31769	4.08;1.48	3.86	-5.21	0.02815	.	2.159800	0.02223	N	0.064196	T	0.05227	0.0139	L	0.34521	1.04	0.09310	N	1	B;B	0.13594	0.008;0.008	B;B	0.11329	0.006;0.006	T	0.10337	-1.0634	10	0.02654	T	1	6.0798	7.38	0.26849	0.4342:0.1874:0.3784:0.0	.	236;236	F5GWX6;Q5TGP6	.;CA129_HUMAN	K	236	ENSP00000356733:Q236K;ENSP00000356732:Q236K	ENSP00000356732:Q236K	Q	+	1	0	C1orf129	169219276	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.168000	0.09925	-0.676000	0.05238	-0.499000	0.04595	CAA	C|0.996;A|0.004	0.004	strong		0.358	MROH9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000099327.1	NM_025063	
FAM63B	54629	hgsc.bcm.edu	37	15	59064214	59064214	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:59064214G>A	ENST00000559228.1	+	1	702	c.620G>A	c.(619-621)gGc>gAc	p.G207D	RP11-30K9.6_ENST00000500929.2_lincRNA|FAM63B_ENST00000450403.2_Missense_Mutation_p.G207D			Q8NBR6	FA63B_HUMAN	family with sequence similarity 63, member B	207										central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(1)|liver(2)|lung(4)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	15						GAGGAGGAGGGCGCGGCGGTG	0.622																																					p.G207D		Atlas-SNP	.											.	FAM63B	33	.	0			c.G620A						PASS	.						31.0	35.0	34.0					15																	59064214		1929	4117	6046	SO:0001583	missense	54629	exon1			AGGAGGGCGCGGC	AK075319	CCDS42046.1, CCDS45268.1	15q21.3	2005-08-09							26954	protein-coding gene	gene with protein product						10574461	Standard	NM_001040450		Approved	KIAA1164	uc002afj.3	Q8NBR6		ENST00000559228.1:c.620G>A	15.37:g.59064214G>A	ENSP00000452885:p.Gly207Asp	79.0	0.0	0		82.0	36.0	0.439024	NM_001040450	B2RTT8|Q9ULQ6	Missense_Mutation	SNP	ENST00000559228.1	37	CCDS42046.1	.	.	.	.	.	.	.	.	.	.	G	14.67	2.603459	0.46423	.	.	ENSG00000128923	ENST00000316848;ENST00000450403	T	0.51574	0.7	3.92	2.95	0.34219	.	0.870346	0.10083	N	0.718159	T	0.36331	0.0963	N	0.22421	0.69	0.41810	D	0.989967	P;P	0.41131	0.483;0.739	B;B	0.43082	0.084;0.407	T	0.06789	-1.0807	10	0.12430	T	0.62	-14.985	12.3052	0.54898	0.0:0.2553:0.7447:0.0	.	207;207	Q8NBR6;Q8NBR6-2	FA63B_HUMAN;.	D	207	ENSP00000393231:G207D	ENSP00000326194:G207D	G	+	2	0	FAM63B	56851506	0.985000	0.35326	0.961000	0.40146	0.496000	0.33645	0.082000	0.14847	2.024000	0.59613	0.543000	0.68304	GGC	.	.	none		0.622	FAM63B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000416230.1	NM_019092	
SLC4A11	83959	hgsc.bcm.edu	37	20	3208967	3208967	+	Missense_Mutation	SNP	C	C	T	rs34224785	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3208967C>T	ENST00000380056.3	-	18	2591	c.2544G>A	c.(2542-2544)atG>atA	p.M848I	SLC4A11_ENST00000539553.2_Missense_Mutation_p.M832I|SLC4A11_ENST00000380059.3_Missense_Mutation_p.M875I|SLC4A11_ENST00000488544.1_5'Flank	NM_032034.3	NP_114423.1	Q8NBS3	S4A11_HUMAN	solute carrier family 4, sodium borate transporter, member 11	848	Membrane (bicarbonate transporter).		M -> I (in dbSNP:rs34224785).		bicarbonate transport (GO:0015701)|borate transmembrane transport (GO:0035445)|borate transport (GO:0046713)|cellular cation homeostasis (GO:0030003)|fluid transport (GO:0042044)|proton transport (GO:0015992)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	basolateral plasma membrane (GO:0016323)|integral component of membrane (GO:0016021)	bicarbonate transmembrane transporter activity (GO:0015106)|borate transmembrane transporter activity (GO:0046715)|hydrogen ion channel activity (GO:0015252)|inorganic anion exchanger activity (GO:0005452)|protein dimerization activity (GO:0046983)|sodium channel activity (GO:0005272)|symporter activity (GO:0015293)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(4)|soft_tissue(1)|urinary_tract(1)	40						GCAGGGAGCTCATGCCGAAGG	0.617													C|||	57	0.0113818	0.0386	0.0058	5008	,	,		13939	0.0		0.002	False		,,,				2504	0.0				p.M875I	NSCLC(190;922 2139 10266 10292 38692)	Atlas-SNP	.											.	SLC4A11	188	.	0			c.G2625A						PASS	.	C	ILE/MET,ILE/MET,ILE/MET	120,4286	90.2+/-128.9	2,116,2085	106.0	94.0	98.0		2496,2625,2544	4.4	1.0	20	dbSNP_126	98	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,missense	SLC4A11	NM_001174089.1,NM_001174090.1,NM_032034.3	10,10,10	2,117,6384	TT,TC,CC		0.0116,2.7236,0.9303	probably-damaging,probably-damaging,probably-damaging	832/876,875/919,848/892	3208967	121,12885	2203	4300	6503	SO:0001583	missense	83959	exon19			GGAGCTCATGCCG	AF336127	CCDS13052.1, CCDS54445.1, CCDS54446.1	20p13	2014-02-14	2007-08-03		ENSG00000088836	ENSG00000088836		"""Solute carriers"""	16438	protein-coding gene	gene with protein product		610206	"""corneal endothelial dystrophy 2 (autosomal recessive)"", ""solute carrier family 4, sodium bicarbonate transporter-like, member 11"", ""corneal dystrophy and perceptive deafness 1"""	CHED2, CDPD1		10843999, 11302728, 16767101	Standard	NM_001174089		Approved	dJ794I6.2, BTR1, NaBC1, FECD4	uc010zqe.2	Q8NBS3	OTTHUMG00000031740	ENST00000380056.3:c.2544G>A	20.37:g.3208967C>T	ENSP00000369396:p.Met848Ile	170.0	0.0	0		156.0	64.0	0.410256	NM_001174090	B4DKC8|B4DKX9|G3V1M3|Q2TB62|Q2TB63|Q9BXF4|Q9NTW9	Missense_Mutation	SNP	ENST00000380056.3	37	CCDS13052.1	30	0.013736263736263736	23	0.046747967479674794	5	0.013812154696132596	0	0.0	2	0.002638522427440633	C	14.38	2.517442	0.44763	0.027236	1.16E-4	ENSG00000088836	ENST00000380059;ENST00000380056;ENST00000539553	T;T;T	0.79454	-1.27;-1.27;-1.26	5.37	4.41	0.53225	.	0.000000	0.85682	D	0.000000	T	0.42585	0.1209	M	0.81682	2.555	0.58432	D	0.999999	B;B;B	0.29766	0.122;0.256;0.043	B;B;B	0.31614	0.133;0.063;0.035	T	0.65372	-0.6184	10	0.24483	T	0.36	.	15.9593	0.79914	0.0:0.8646:0.1354:0.0	rs34224785	832;875;848	G3V1M3;B4DKC8;Q8NBS3	.;.;S4A11_HUMAN	I	875;848;832	ENSP00000369399:M875I;ENSP00000369396:M848I;ENSP00000441370:M832I	ENSP00000369396:M848I	M	-	3	0	SLC4A11	3156967	1.000000	0.71417	1.000000	0.80357	0.841000	0.47740	3.253000	0.51469	1.239000	0.43787	0.455000	0.32223	ATG	C|0.988;T|0.012	0.012	strong		0.617	SLC4A11-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000077728.1		
PRMT2	3275	hgsc.bcm.edu	37	21	48071901	48071901	+	Intron	SNP	C	C	T	rs77776707	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:48071901C>T	ENST00000397637.1	+	6	1608				PRMT2_ENST00000334494.4_Missense_Mutation_p.P280S|PRMT2_ENST00000397638.2_Intron|PRMT2_ENST00000458387.2_Intron|PRMT2_ENST00000355680.3_Intron|PRMT2_ENST00000440086.1_Intron|PRMT2_ENST00000451211.2_Intron|PRMT2_ENST00000291705.6_Intron			P55345	ANM2_HUMAN	protein arginine methyltransferase 2						developmental cell growth (GO:0048588)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of transcription, DNA-templated (GO:0045892)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|protein methylation (GO:0006479)|regulation of androgen receptor signaling pathway (GO:0060765)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (GO:0042054)|histone-arginine N-methyltransferase activity (GO:0008469)|peroxisome proliferator activated receptor binding (GO:0042975)|progesterone receptor binding (GO:0033142)|protein homodimerization activity (GO:0042803)|protein-arginine N-methyltransferase activity (GO:0016274)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|retinoic acid receptor binding (GO:0042974)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)			NS(1)|breast(3)|endometrium(2)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	16	Breast(49;0.247)	Lung NSC(3;0.245)		Epithelial(3;1.03e-07)|OV - Ovarian serous cystadenocarcinoma(3;4.68e-07)|all cancers(3;7.48e-07)|Colorectal(79;0.167)|Lung(125;0.203)|LUSC - Lung squamous cell carcinoma(216;0.23)|READ - Rectum adenocarcinoma(84;0.248)		TCTCTCCTGGCCCATCTTCCT	0.552													C|||	41	0.0081869	0.0008	0.0072	5008	,	,		20121	0.0159		0.007	False		,,,				2504	0.0123				p.P280S		Atlas-SNP	.											.	PRMT2	48	.	0			c.C838T						PASS	.	C	,SER/PRO,,,	2,1750		0,2,874	75.0	68.0	70.0		,838,,,	-1.7	0.0	21	dbSNP_131	70	11,3971		0,11,1980	no	intron,missense,intron,intron,intron	PRMT2	NM_001242864.1,NM_001242865.1,NM_001242866.1,NM_001535.3,NM_206962.2	,74,,,	0,13,2854	TT,TC,CC		0.2762,0.1142,0.2267	,,,,	,280/285,,,	48071901	13,5721	876	1991	2867	SO:0001627	intron_variant	3275	exon7			TCCTGGCCCATCT	U80213	CCDS13737.1, CCDS56219.1, CCDS56220.1, CCDS68230.1, CCDS68231.1, CCDS74806.1	21q22.3	2014-06-12	2006-02-16	2006-02-16	ENSG00000160310	ENSG00000160310	2.1.1.125	"""Protein arginine methyltransferases"""	5186	protein-coding gene	gene with protein product		601961	"""HMT1 (hnRNP methyltransferase, S. cerevisiae)-like 1"", ""HMT1 hnRNP methyltransferase-like 1 (S. cerevisiae)"""	HRMT1L1		9545638	Standard	XM_005261111		Approved	MGC111373	uc002zjy.3	P55345	OTTHUMG00000048806	ENST00000397637.1:c.654+2250C>T	21.37:g.48071901C>T		93.0	0.0	0		154.0	70.0	0.454545	NM_001242865	B7U630|B7U631|B7U632|P78350|Q498Y5|Q5U7D4|Q6FHF0|Q99781|Q9BW15|Q9UMC2	Missense_Mutation	SNP	ENST00000397637.1	37	CCDS13737.1	20	0.009157509157509158	0	0.0	2	0.0055248618784530384	11	0.019230769230769232	7	0.009234828496042216	.	8.123	0.781437	0.16120	0.001142	0.002762	ENSG00000160310	ENST00000334494	T	0.66280	-0.2	0.852	-1.7	0.08159	.	.	.	.	.	T	0.40839	0.1133	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.50118	-0.8865	6	0.87932	D	0	.	6.4147	0.21710	0.0:0.6399:0.0:0.3601	.	.	.	.	S	280	ENSP00000335490:P280S	ENSP00000335490:P280S	P	+	1	0	PRMT2	46896329	0.003000	0.15002	0.000000	0.03702	0.001000	0.01503	-0.364000	0.07583	-1.587000	0.01630	-1.786000	0.00637	CCC	C|0.992;T|0.008	0.008	strong		0.552	PRMT2-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207401.1	NM_001535	
RTN4	57142	hgsc.bcm.edu	37	2	55253973	55253973	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:55253973T>G	ENST00000337526.6	-	3	1505	c.1262A>C	c.(1261-1263)gAt>gCt	p.D421A	RTN4_ENST00000357732.4_Intron|RTN4_ENST00000405240.1_Missense_Mutation_p.D215A|RTN4_ENST00000394611.2_Missense_Mutation_p.D215A|RTN4_ENST00000402434.2_Intron|RTN4_ENST00000404909.1_Missense_Mutation_p.D215A|RTN4_ENST00000357376.3_Missense_Mutation_p.D215A|RTN4_ENST00000354474.6_Missense_Mutation_p.D189A|RTN4_ENST00000317610.7_Intron	NM_020532.4	NP_065393.1	Q9NQC3	RTN4_HUMAN	reticulon 4	421					angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|axonal fasciculation (GO:0007413)|cardiac epithelial to mesenchymal transition (GO:0060317)|cerebral cortex radial glia guided migration (GO:0021801)|endoplasmic reticulum tubular network organization (GO:0071786)|negative regulation of axon extension (GO:0030517)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell growth (GO:0030308)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of apoptotic process (GO:0042981)|regulation of axonogenesis (GO:0050770)|regulation of branching morphogenesis of a nerve (GO:2000172)|regulation of cell migration (GO:0030334)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of endoplasmic reticulum membrane (GO:0030176)|intracellular (GO:0005622)|neuronal cell body (GO:0043025)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)			NS(2)|breast(4)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(11)|lung(9)|ovary(2)|prostate(1)|skin(1)|stomach(1)	36						ACATTTTTTATCCACTTTACT	0.383																																					p.D421A		Atlas-SNP	.											.	RTN4	189	.	0			c.A1262C						PASS	.						236.0	233.0	234.0					2																	55253973		2202	4300	6502	SO:0001583	missense	57142	exon3			TTTTTATCCACTT	AF087901	CCDS1851.1, CCDS1852.1, CCDS42683.1, CCDS42684.1, CCDS42685.1	2p14-p13	2008-05-23			ENSG00000115310	ENSG00000115310			14085	protein-coding gene	gene with protein product		604475				10667797, 10773680	Standard	NM_020532		Approved	NSP-CL, KIAA0886, NOGO, ASY	uc002rye.3	Q9NQC3	OTTHUMG00000129337	ENST00000337526.6:c.1262A>C	2.37:g.55253973T>G	ENSP00000337838:p.Asp421Ala	232.0	0.0	0		227.0	120.0	0.528634	NM_020532	O94962|Q7L7Q5|Q7L7Q6|Q7L7Q8|Q8IUA4|Q96B16|Q9BXG5|Q9H212|Q9H3I3|Q9UQ42|Q9Y293|Q9Y2Y7|Q9Y5U6	Missense_Mutation	SNP	ENST00000337526.6	37	CCDS42684.1	.	.	.	.	.	.	.	.	.	.	t	10.97	1.500459	0.26861	.	.	ENSG00000115310	ENST00000405240;ENST00000357376;ENST00000337526;ENST00000394611;ENST00000404909;ENST00000354474	T;T;T;T;T;T	0.27557	1.66;1.66;2.34;1.66;1.66;1.72	6.06	0.962	0.19643	.	0.933951	0.09057	N	0.854885	T	0.33876	0.0878	M	0.66939	2.045	0.33241	D	0.557225	P	0.48294	0.908	P	0.44422	0.449	T	0.48139	-0.9061	10	0.87932	D	0	-1.8717	6.2376	0.20772	0.0:0.1944:0.148:0.6577	.	421	Q9NQC3	RTN4_HUMAN	A	215;215;421;215;215;189	ENSP00000384471:D215A;ENSP00000349944:D215A;ENSP00000337838:D421A;ENSP00000378109:D215A;ENSP00000385650:D215A;ENSP00000346465:D189A	ENSP00000337838:D421A	D	-	2	0	RTN4	55107477	0.005000	0.15991	0.153000	0.22517	0.300000	0.27592	0.122000	0.15687	-0.072000	0.12864	-0.266000	0.10368	GAT	.	.	none		0.383	RTN4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000251484.1		
C8B	732	hgsc.bcm.edu	37	1	57409459	57409459	+	Missense_Mutation	SNP	C	C	A	rs139498867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:57409459C>A	ENST00000371237.4	-	8	1210	c.1144G>T	c.(1144-1146)Gat>Tat	p.D382Y	C8B_ENST00000543257.1_Missense_Mutation_p.D330Y|C8B_ENST00000535057.1_Missense_Mutation_p.D320Y	NM_000066.2	NP_000057	P07358	CO8B_HUMAN	complement component 8, beta polypeptide	382	MACPF. {ECO:0000255|PROSITE- ProRule:PRU00745}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|complement activation, classical pathway (GO:0006958)|cytolysis (GO:0019835)|immune response (GO:0006955)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|membrane attack complex (GO:0005579)|vesicle (GO:0031982)				breast(2)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|liver(1)|lung(20)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)	52						ATTTTAAAATCATTTTTGGCA	0.403													C|||	14	0.00279553	0.0	0.0058	5008	,	,		21667	0.0		0.0099	False		,,,				2504	0.0				p.D382Y		Atlas-SNP	.											.	C8B	107	.	0			c.G1144T						PASS	.	C	TYR/ASP	4,4402	8.1+/-20.4	0,4,2199	187.0	166.0	173.0		1144	3.7	0.0	1	dbSNP_134	173	73,8527	44.5+/-102.8	0,73,4227	yes	missense	C8B	NM_000066.2	160	0,77,6426	AA,AC,CC		0.8488,0.0908,0.592	possibly-damaging	382/592	57409459	77,12929	2203	4300	6503	SO:0001583	missense	732	exon8			TAAAATCATTTTT	M16973	CCDS30730.1, CCDS60151.1, CCDS60152.1	1p32.2	2014-09-17			ENSG00000021852	ENSG00000021852		"""Complement system"""	1353	protein-coding gene	gene with protein product		120960					Standard	NM_000066		Approved		uc001cyp.3	P07358	OTTHUMG00000008305	ENST00000371237.4:c.1144G>T	1.37:g.57409459C>A	ENSP00000360281:p.Asp382Tyr	159.0	0.0	0		173.0	74.0	0.427746	NM_000066	A1L4K7	Missense_Mutation	SNP	ENST00000371237.4	37	CCDS30730.1	8	0.003663003663003663	0	0.0	2	0.0055248618784530384	0	0.0	6	0.0079155672823219	C	26.5	4.741358	0.89573	9.08E-4	0.008488	ENSG00000021852	ENST00000371237;ENST00000543257;ENST00000535057	D;D;D	0.84146	-1.81;-1.81;-1.81	4.59	3.66	0.41972	Membrane attack complex component/perforin (MACPF) domain (3);	0.458353	0.25651	N	0.029202	D	0.83977	0.5371	L	0.51422	1.61	0.29294	N	0.869162	P;D;D	0.61080	0.874;0.974;0.989	P;P;P	0.58331	0.568;0.66;0.837	T	0.81992	-0.0678	10	0.72032	D	0.01	-3.603	12.8556	0.57884	0.0:0.9173:0.0:0.0827	.	330;320;382	F5H7G1;F5GY80;P07358	.;.;CO8B_HUMAN	Y	382;330;320	ENSP00000360281:D382Y;ENSP00000442548:D330Y;ENSP00000440113:D320Y	ENSP00000360281:D382Y	D	-	1	0	C8B	57182047	0.013000	0.17824	0.013000	0.15412	0.915000	0.54546	2.152000	0.42272	1.507000	0.48752	0.655000	0.94253	GAT	C|0.994;A|0.006	0.006	strong		0.403	C8B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022886.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1264795	1264795	+	Missense_Mutation	SNP	G	G	C	rs200138247	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1264795G>C	ENST00000529681.1	+	31	6743	c.6685G>C	c.(6685-6687)Gag>Cag	p.E2229Q	MUC5B_ENST00000447027.1_Missense_Mutation_p.E2232Q|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2229	7 X Cys-rich subdomain repeats.|Thr-rich.				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)		CCACATCACAGAGCCTTCCAC	0.652													g|||	19	0.00379393	0.0008	0.0058	5008	,	,		13832	0.0		0.0119	False		,,,				2504	0.002				p.E2229Q		Atlas-SNP	.											.	MUC5B	473	.	0			c.G6685C						PASS	.	G	GLN/GLU	5,4165		0,5,2080	95.0	120.0	112.0		6685	-1.5	0.0	11		112	55,8297		0,55,4121	no	missense	MUC5B	NM_002458.2	29	0,60,6201	CC,CG,GG		0.6585,0.1199,0.4792	possibly-damaging	2229/5763	1264795	60,12462	2085	4176	6261	SO:0001583	missense	727897	exon31			ATCACAGAGCCTT	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.6685G>C	11.37:g.1264795G>C	ENSP00000436812:p.Glu2229Gln	347.0	0.0	0		322.0	117.0	0.363354	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	g	4.475	0.088061	0.08583	0.001199	0.006585	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21031	2.03;2.21	1.87	-1.45	0.08828	.	.	.	.	.	T	0.06280	0.0162	L	0.36672	1.1	0.09310	N	1	P;P	0.47604	0.813;0.898	B;B	0.28784	0.053;0.094	T	0.24512	-1.0158	9	0.87932	D	0	.	0.5061	0.00588	0.4066:0.1743:0.2245:0.1945	.	2867;2232	A7Y9J9;E9PBJ0	.;.	Q	2229;2232;2230;2244	ENSP00000436812:E2229Q;ENSP00000415793:E2232Q	ENSP00000343037:E2230Q	E	+	1	0	MUC5B	1221371	0.000000	0.05858	0.000000	0.03702	0.024000	0.10985	-0.475000	0.06599	-0.394000	0.07727	0.305000	0.20034	GAG	.	.	weak		0.652	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PEBP4	157310	hgsc.bcm.edu	37	8	22570905	22570905	+	Missense_Mutation	SNP	T	T	G	rs386723487|rs79936857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22570905T>G	ENST00000256404.6	-	7	753	c.662A>C	c.(661-663)cAg>cCg	p.Q221P	RP11-459E5.1_ENST00000523627.1_RNA	NM_144962.2	NP_659399.2	Q96S96	PEBP4_HUMAN	phosphatidylethanolamine-binding protein 4	221						extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)				breast(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)|stomach(2)	10		Prostate(55;0.0453)|Breast(100;0.103)		Colorectal(74;0.0434)|COAD - Colon adenocarcinoma(73;0.124)		TATCTCCGCCTGGTTTTTGTG	0.592													T|||	374	0.0746805	0.2428	0.0231	5008	,	,		16389	0.004		0.0199	False		,,,				2504	0.0133				p.Q221P		Atlas-SNP	.											.	PEBP4	23	.	0			c.A662C						PASS	.						72.0	79.0	77.0					8																	22570905		1953	4151	6104	SO:0001583	missense	157310	exon7			TCCGCCTGGTTTT	BC020779	CCDS43724.1	8p21.3	2009-08-13			ENSG00000134020	ENSG00000134020			28319	protein-coding gene	gene with protein product	"""cousin-of-RKIP 1 protein"""	612473				15302887, 16865237	Standard	NM_144962		Approved	MGC22776, CORK1, hPEBP4	uc003xcn.1	Q96S96	OTTHUMG00000163749	ENST00000256404.6:c.662A>C	8.37:g.22570905T>G	ENSP00000256404:p.Gln221Pro	131.0	0.0	0		108.0	59.0	0.546296	NM_144962	Q5EVA1|Q8WW74	Missense_Mutation	SNP	ENST00000256404.6	37	CCDS43724.1	114	0.0521978021978022	96	0.1951219512195122	6	0.016574585635359115	5	0.008741258741258742	7	0.009234828496042216	T	11.07	1.531292	0.27387	.	.	ENSG00000134020	ENST00000256404	T	0.33438	1.41	5.01	-1.92	0.07618	.	47.664200	0.00166	N	0.000000	T	0.00039	0.0001	N	0.14661	0.345	0.80722	P	0.0	D	0.65815	0.995	P	0.56278	0.795	T	0.02539	-1.1144	9	0.59425	D	0.04	8.4188	4.2246	0.10574	0.1617:0.3762:0.0:0.4621	.	221	Q96S96	PEBP4_HUMAN	P	221	ENSP00000256404:Q221P	ENSP00000256404:Q221P	Q	-	2	0	PEBP4	22626850	0.000000	0.05858	0.001000	0.08648	0.012000	0.07955	-0.839000	0.04368	-0.336000	0.08438	0.459000	0.35465	CAG	T|0.962;G|0.038	0.038	strong		0.592	PEBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375141.2	NM_144962	
PJA1	64219	hgsc.bcm.edu	37	X	68382422	68382422	+	Silent	SNP	C	C	T	rs149179614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:68382422C>T	ENST00000361478.1	-	2	1037	c.660G>A	c.(658-660)tcG>tcA	p.S220S	PJA1_ENST00000374584.3_Intron|PJA1_ENST00000374583.1_Silent_p.S220S|PJA1_ENST00000477231.1_5'UTR|PJA1_ENST00000374571.4_Silent_p.S165S	NM_001032396.2|NM_022368.4|NM_145119.3	NP_001027568.1|NP_071763.2|NP_660095.1	Q8NG27	PJA1_HUMAN	praja ring finger 1, E3 ubiquitin protein ligase	220					protein catabolic process (GO:0030163)	cytoplasm (GO:0005737)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			endometrium(3)|large_intestine(5)|lung(12)|ovary(1)	21						TCTCCCTCTCCGAGCTGTCAC	0.532													c|||	6	0.0015894	0.0	0.0	3775	,	,		14255	0.0		0.0	False		,,,				2504	0.0061				p.S220S		Atlas-SNP	.											.	PJA1	106	.	0			c.G660A						PASS	.		,,	1,3834		0,1,0,1631,571	47.0	38.0	41.0		495,,660	1.0	0.0	X	dbSNP_134	41	4,6724		0,3,1,2425,1871	no	coding-synonymous,intron,coding-synonymous	PJA1	NM_001032396.2,NM_022368.4,NM_145119.3	,,	0,4,1,4056,2442	TT,TC,T,CC,C		0.0595,0.0261,0.0473	,,	165/589,,220/644	68382422	5,10558	2203	4300	6503	SO:0001819	synonymous_variant	64219	exon2			CCTCTCCGAGCTG	AK021892	CCDS14392.1, CCDS14393.1, CCDS35316.1	Xq13.1	2013-01-09	2012-02-23		ENSG00000181191	ENSG00000181191		"""RING-type (C3HC4) zinc fingers"""	16648	protein-coding gene	gene with protein product		300420	"""praja 1"", ""praja ring finger 1"""			12036302	Standard	NM_001032396		Approved	FLJ11830, RNF70	uc004dxh.3	Q8NG27	OTTHUMG00000021753	ENST00000361478.1:c.660G>A	X.37:g.68382422C>T		89.0	0.0	0		92.0	91.0	0.98913	NM_145119	A2A322|Q5JUT8|Q5JUT9|Q8NG28|Q9HAC1	Silent	SNP	ENST00000361478.1	37	CCDS14393.1																																																																																			C|0.999;T|0.001	0.001	strong		0.532	PJA1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057031.2	NM_145119	
EYS	346007	hgsc.bcm.edu	37	6	65622420	65622420	+	Silent	SNP	G	G	A	rs183814213		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:65622420G>A	ENST00000370621.3	-	16	3124	c.2598C>T	c.(2596-2598)tgC>tgT	p.C866C	EYS_ENST00000370616.2_Silent_p.C866C|EYS_ENST00000503581.1_Silent_p.C866C			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	866	EGF-like 12. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCAAAGCTAAGCATGTTGAGT	0.353													G|||	1	0.000199681	0.0	0.0014	5008	,	,		17718	0.0		0.0	False		,,,				2504	0.0				p.C866C		Atlas-SNP	.											.	EYS	527	.	0			c.C2598T						PASS	.	G		0,1384		0,0,692	156.0	129.0	137.0		2598	2.6	0.0	6		137	1,3181		0,1,1590	no	coding-synonymous	EYS	NM_001142800.1		0,1,2282	AA,AG,GG		0.0314,0.0,0.0219		866/3145	65622420	1,4565	692	1591	2283	SO:0001819	synonymous_variant	346007	exon16			AGCTAAGCATGTT		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2598C>T	6.37:g.65622420G>A		291.0	0.0	0		167.0	19.0	0.113772	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	37																																																																																				G|1.000;A|0.000	0.000	strong		0.353	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
HNF1A	6927	hgsc.bcm.edu	37	12	121435427	121435427	+	Missense_Mutation	SNP	G	G	A	rs2464196	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:121435427G>A	ENST00000257555.6	+	7	1686	c.1460G>A	c.(1459-1461)aGc>aAc	p.S487N	HNF1A_ENST00000400024.2_Missense_Mutation_p.S487N|HNF1A_ENST00000402929.1_3'UTR|HNF1A_ENST00000538626.1_Missense_Mutation_p.S69N|RP11-216P16.2_ENST00000606238.1_RNA|HNF1A_ENST00000544413.1_Missense_Mutation_p.S487N|HNF1A_ENST00000541395.1_Missense_Mutation_p.S487N			P20823	HNF1A_HUMAN	HNF1 homeobox A	487			S -> N (in dbSNP:rs2464196). {ECO:0000269|PubMed:9112026, ECO:0000269|PubMed:9133564, ECO:0000269|PubMed:9287055, ECO:0000269|PubMed:9604876, ECO:0000269|PubMed:9621514, ECO:0000269|Ref.6}.		glucose homeostasis (GO:0042593)|glucose import (GO:0046323)|insulin secretion (GO:0030073)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|renal glucose absorption (GO:0035623)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein dimerization activity (GO:0046983)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(3)|central_nervous_system(2)|cervix(1)|endometrium(8)|large_intestine(19)|liver(175)|lung(9)|ovary(2)|prostate(1)|urinary_tract(1)	221	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					GTGACCCAGAGCCCCTTCATG	0.637									Hepatic Adenoma, Familial Clustering of				g|||	1591	0.317692	0.112	0.3501	5008	,	,		18114	0.4732		0.3161	False		,,,				2504	0.4141				p.S487N		Atlas-SNP	.											.	HNF1A	302	.	0			c.G1460A	GRCh37	CM067474	HNF1A	M	rs2464196	PASS	.	G	ASN/SER	541,3865	230.4+/-244.6	42,457,1704	29.0	28.0	29.0		1460	3.5	1.0	12	dbSNP_100	29	2676,5924	411.0+/-350.3	431,1814,2055	yes	missense	HNF1A	NM_000545.5	46	473,2271,3759	AA,AG,GG		31.1163,12.2787,24.7347	possibly-damaging	487/632	121435427	3217,9789	2203	4300	6503	SO:0001583	missense	6927	exon7	Familial Cancer Database	incl. Maturity-Onset Diabetes of the Young type 3, MODY3	CCCAGAGCCCCTT	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.1460G>A	12.37:g.121435427G>A	ENSP00000257555:p.Ser487Asn	148.0	0.0	0		133.0	62.0	0.466165	NM_000545	A5Z2R8|E0YMJ5|E0YMK0|E0YMK1|E2I9R4|E2I9R5|F5H5U3|Q2M3H2|Q99861	Missense_Mutation	SNP	ENST00000257555.6	37	CCDS9209.1	715	0.3273809523809524	54	0.10975609756097561	132	0.36464088397790057	296	0.5174825174825175	233	0.3073878627968338	G	12.39	1.924644	0.34002	0.122787	0.311163	ENSG00000135100	ENST00000257555;ENST00000535125;ENST00000537424;ENST00000543027;ENST00000541395;ENST00000340577;ENST00000544413	D;D;D	0.97455	-4.39;-4.39;-4.39	4.49	3.53	0.40419	Hepatocyte nuclear factor 1, beta isoform, C-terminal (1);	0.068781	0.64402	N	0.000014	T	0.00012	0.0000	L	0.40543	1.245	0.09310	P	0.99999999123403	B;B;B	0.24576	0.0;0.014;0.106	B;B;B	0.32533	0.005;0.085;0.147	T	0.04153	-1.0973	9	0.42905	T	0.14	-9.2011	10.4952	0.44772	0.104:0.0:0.896:0.0	rs2464196;rs2708085;rs16950667;rs17847503;rs56962510;rs2464196	487;487;487	F5H0K0;P20823;E7EUQ4	.;HNF1A_HUMAN;.	N	487;379;487;308;487;487;487	ENSP00000257555:S487N;ENSP00000443112:S487N;ENSP00000438804:S487N	ENSP00000257555:S487N	S	+	2	0	HNF1A	119919810	0.950000	0.32346	0.992000	0.48379	0.944000	0.59088	1.527000	0.35975	0.976000	0.38417	0.655000	0.94253	AGC	G|0.725;A|0.275	0.275	strong		0.637	HNF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320957.5	NM_000545	
UNC5C	8633	hgsc.bcm.edu	37	4	96127799	96127799	+	Missense_Mutation	SNP	C	C	T	rs146123204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:96127799C>T	ENST00000453304.1	-	11	2230	c.1882G>A	c.(1882-1884)Gca>Aca	p.A628T		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	628	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)		CCCTGTGCTGCCTGGTTCTTG	0.537													C|||	3	0.000599042	0.0	0.0014	5008	,	,		15911	0.0		0.002	False		,,,				2504	0.0				p.A628T		Atlas-SNP	.											.	UNC5C	141	.	0			c.G1882A						PASS	.	C	THR/ALA	1,4405	2.1+/-5.4	0,1,2202	106.0	94.0	98.0		1882	-2.4	0.8	4	dbSNP_134	98	17,8583	10.5+/-38.8	0,17,4283	yes	missense	UNC5C	NM_003728.3	58	0,18,6485	TT,TC,CC		0.1977,0.0227,0.1384	benign	628/932	96127799	18,12988	2203	4300	6503	SO:0001583	missense	8633	exon11			GTGCTGCCTGGTT	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.1882G>A	4.37:g.96127799C>T	ENSP00000406022:p.Ala628Thr	119.0	0.0	0		118.0	51.0	0.432203	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	7.398	0.632177	0.14322	2.27E-4	0.001977	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.41400	1.0;1.0	5.28	-2.41	0.06562	ZU5 (3);	0.761342	0.12964	N	0.424732	T	0.13628	0.0330	N	0.02225	-0.63	0.35230	D	0.776799	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.38779	-0.9645	10	0.09338	T	0.73	.	8.1752	0.31278	0.1126:0.2927:0.0:0.5947	.	628;628	A8K385;O95185	.;UNC5C_HUMAN	T	628;587;647	ENSP00000406022:A628T;ENSP00000426924:A647T	ENSP00000328673:A587T	A	-	1	0	UNC5C	96346822	0.002000	0.14202	0.791000	0.31998	0.797000	0.45037	-0.626000	0.05527	-0.391000	0.07763	-0.251000	0.11542	GCA	C|0.998;T|0.002	0.002	strong		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
CLSPN	63967	hgsc.bcm.edu	37	1	36202125	36202125	+	Missense_Mutation	SNP	C	C	T	rs115320551		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:36202125C>T	ENST00000318121.3	-	25	4049	c.3992G>A	c.(3991-3993)cGa>cAa	p.R1331Q	CLSPN_ENST00000466308.1_5'UTR|RP11-435D7.3_ENST00000373226.2_RNA|CLSPN_ENST00000251195.5_Intron|CLSPN_ENST00000373220.3_Missense_Mutation_p.R1267Q|CLSPN_ENST00000520551.1_Missense_Mutation_p.R1278Q	NM_022111.3	NP_071394.2	Q9HAW4	CLSPN_HUMAN	claspin	1331					activation of protein kinase activity (GO:0032147)|apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|DNA damage checkpoint (GO:0000077)|DNA repair (GO:0006281)|DNA replication (GO:0006260)|G2 DNA damage checkpoint (GO:0031572)|mitotic DNA replication checkpoint (GO:0033314)|peptidyl-serine phosphorylation (GO:0018105)	nucleoplasm (GO:0005654)	anaphase-promoting complex binding (GO:0010997)|DNA binding (GO:0003677)	p.R1331Q(1)		NS(2)|breast(3)|central_nervous_system(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(8)|lung(20)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0887)				GAAGATGCTTCGCGTCAATCC	0.423													C|||	1	0.000199681	0.0008	0.0	5008	,	,		18800	0.0		0.0	False		,,,				2504	0.0				p.R1331Q		Atlas-SNP	.											CLSPN,colon,carcinoma,-1,4	CLSPN	248	4	1	Substitution - Missense(1)	ovary(1)	c.G3992A						PASS	.						150.0	141.0	144.0					1																	36202125		2203	4300	6503	SO:0001583	missense	63967	exon25			ATGCTTCGCGTCA	AF297866	CCDS396.1, CCDS53297.1	1p34.3	2010-06-24	2010-06-24		ENSG00000092853	ENSG00000092853			19715	protein-coding gene	gene with protein product		605434	"""claspin homolog (Xenopus laevis)"""			11090622, 12766152	Standard	NM_022111		Approved		uc001bzi.3	Q9HAW4	OTTHUMG00000004168	ENST00000318121.3:c.3992G>A	1.37:g.36202125C>T	ENSP00000312995:p.Arg1331Gln	133.0	0.0	0		144.0	132.0	0.916667	NM_022111	A6NFL4|Q1RMC6|Q2KHM3|Q5VYG0|Q6P6H5|Q8IWI1	Missense_Mutation	SNP	ENST00000318121.3	37	CCDS396.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.64	2.298942	0.40694	.	.	ENSG00000092853	ENST00000318121;ENST00000373220;ENST00000520551	T;T;T	0.27557	1.66;1.71;1.72	5.29	-1.26	0.09376	.	0.312008	0.29046	N	0.013319	T	0.14960	0.0361	N	0.12746	0.255	0.24776	N	0.992842	B;B	0.25007	0.116;0.068	B;B	0.15052	0.012;0.012	T	0.13176	-1.0519	10	0.32370	T	0.25	0.0185	13.1085	0.59261	0.0:0.8736:0.0:0.1264	.	1267;1331	Q9HAW4-2;Q9HAW4	.;CLSPN_HUMAN	Q	1331;1267;1278	ENSP00000312995:R1331Q;ENSP00000362317:R1267Q;ENSP00000428848:R1278Q	ENSP00000312995:R1331Q	R	-	2	0	CLSPN	35974712	0.998000	0.40836	0.974000	0.42286	0.967000	0.64934	0.428000	0.21395	-0.357000	0.08175	-0.290000	0.09829	CGA	C|0.999;T|0.001	0.001	strong		0.423	CLSPN-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377857.1	NM_022111	
MCM8	84515	hgsc.bcm.edu	37	20	5974265	5974265	+	Missense_Mutation	SNP	A	A	G	rs16991638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5974265A>G	ENST00000378896.3	+	18	2731	c.2354A>G	c.(2353-2355)aAc>aGc	p.N785S	MCM8_ENST00000265187.4_Missense_Mutation_p.N769S|MCM8_ENST00000378886.2_Missense_Mutation_p.N825S|MCM8_ENST00000378883.1_Missense_Mutation_p.N738S	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	785			N -> S (in dbSNP:rs16991638).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						GCTCTCAACAACGTTGCTGAA	0.358													A|||	378	0.0754792	0.1853	0.1009	5008	,	,		18096	0.001		0.0199	False		,,,				2504	0.0429				p.N785S		Atlas-SNP	.											.	MCM8	125	.	0			c.A2354G						PASS	.	A	SER/ASN,SER/ASN	703,3703	283.4+/-277.1	58,587,1558	57.0	62.0	61.0		2354,2306	0.4	1.0	20	dbSNP_123	61	181,8419	82.3+/-144.9	2,177,4121	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	46,46	60,764,5679	GG,GA,AA		2.1047,15.9555,6.7969	benign,benign	785/841,769/825	5974265	884,12122	2203	4300	6503	SO:0001583	missense	84515	exon18			TCAACAACGTTGC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.2354A>G	20.37:g.5974265A>G	ENSP00000368174:p.Asn785Ser	44.0	0.0	0		52.0	20.0	0.384615	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	128	0.05860805860805861	86	0.17479674796747968	26	0.0718232044198895	1	0.0017482517482517483	15	0.01978891820580475	A	9.100	1.003892	0.19199	0.159555	0.021047	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000378886;ENST00000265187	T;T;T;T	0.02812	4.25;4.15;4.23;4.25	5.82	0.411	0.16392	.	0.769958	0.13000	N	0.421768	T	0.00012	0.0000	N	0.01576	-0.805	0.54753	P	1.3000000000040757E-5	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.45056	-0.9287	9	0.17832	T	0.49	-3.3433	6.6121	0.22757	0.2319:0.3374:0.4307:0.0	rs16991638;rs56419414;rs16991638	738;825;769;785	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	S	785;738;825;769	ENSP00000368174:N785S;ENSP00000368161:N738S;ENSP00000368164:N825S;ENSP00000265187:N769S	ENSP00000265187:N769S	N	+	2	0	MCM8	5922265	0.001000	0.12720	0.997000	0.53966	0.995000	0.86356	-0.073000	0.11468	0.055000	0.16094	0.533000	0.62120	AAC	A|0.934;G|0.066	0.066	strong		0.358	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
FAM129B	64855	hgsc.bcm.edu	37	9	130270782	130270782	+	Silent	SNP	G	G	A	rs11545937	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130270782G>A	ENST00000373312.3	-	11	1566	c.1353C>T	c.(1351-1353)ctC>ctT	p.L451L	FAM129B_ENST00000373314.3_Silent_p.L438L|FAM129B_ENST00000468379.1_Intron	NM_022833.2	NP_073744.2	Q96TA1	NIBL1_HUMAN	family with sequence similarity 129, member B	451					negative regulation of apoptotic process (GO:0043066)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(2)|endometrium(4)|kidney(1)|large_intestine(5)|liver(1)|lung(7)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	25						CCTGGTGCAGGAGGGTCTCGA	0.652													G|||	118	0.0235623	0.0045	0.0389	5008	,	,		17611	0.0		0.0596	False		,,,				2504	0.0256				p.L451L		Atlas-SNP	.											.	FAM129B	84	.	0			c.C1353T						PASS	.	G	,	56,4350	55.5+/-91.7	0,56,2147	137.0	133.0	135.0		1314,1353	-1.5	1.0	9	dbSNP_120	135	570,8030	153.9+/-208.2	20,530,3750	no	coding-synonymous,coding-synonymous	FAM129B	NM_001035534.1,NM_022833.2	,	20,586,5897	AA,AG,GG		6.6279,1.271,4.8132	,	438/734,451/747	130270782	626,12380	2203	4300	6503	SO:0001819	synonymous_variant	64855	exon11			GTGCAGGAGGGTC	AF151783	CCDS35144.1, CCDS35145.1	9q34.13	2010-02-01	2006-11-23	2006-11-23	ENSG00000136830	ENSG00000136830			25282	protein-coding gene	gene with protein product		614045	"""chromosome 9 open reading frame 88"""	C9orf88		14702039, 19362540	Standard	XM_005252135		Approved	DKFZP434H0820, FLJ13518, FLJ22151, FLJ22298, bA356B19.6, MINERVA	uc004brh.3	Q96TA1	OTTHUMG00000020705	ENST00000373312.3:c.1353C>T	9.37:g.130270782G>A		28.0	0.0	0		37.0	12.0	0.324324	NM_022833	Q4LE55|Q5VVW6|Q5VVW7|Q9BUS2|Q9NT35	Silent	SNP	ENST00000373312.3	37	CCDS35145.1																																																																																			G|0.957;C|0.000;A|0.043	0.043	strong		0.652	FAM129B-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054196.1	NM_022833	
DTX2	113878	hgsc.bcm.edu	37	7	76112299	76112299	+	Missense_Mutation	SNP	A	A	G	rs145151450	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:76112299A>G	ENST00000324432.5	+	5	1253	c.743A>G	c.(742-744)aAc>aGc	p.N248S	DTX2_ENST00000446600.1_Missense_Mutation_p.N157S|DTX2_ENST00000413936.2_Missense_Mutation_p.N248S|DTX2_ENST00000307569.8_Missense_Mutation_p.N248S|DTX2_ENST00000446820.2_Missense_Mutation_p.N248S|DTX2_ENST00000430490.2_Missense_Mutation_p.N248S	NM_020892.2	NP_065943.2	Q86UW9	DTX2_HUMAN	deltex 2, E3 ubiquitin ligase	248					Notch signaling pathway (GO:0007219)|protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			NS(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(14)|ovary(1)|skin(1)|stomach(2)	27						GCACCGTACAACAAACCCTCA	0.672													.|||	11	0.00219649	0.0	0.0029	5008	,	,		18951	0.001		0.008	False		,,,				2504	0.0				p.N248S		Atlas-SNP	.											.	DTX2	64	.	0			c.A743G						PASS	.	A	SER/ASN,SER/ASN,SER/ASN,SER/ASN	3,4403		0,3,2200	151.0	159.0	157.0		743,743,743,743	1.4	1.0	7	dbSNP_134	157	46,8554		0,46,4254	yes	missense,missense,missense,missense	DTX2	NM_001102594.1,NM_001102595.1,NM_001102596.1,NM_020892.2	46,46,46,46	0,49,6454	GG,GA,AA		0.5349,0.0681,0.3767	benign,benign,benign,benign	248/623,248/623,248/576,248/623	76112299	49,12957	2203	4300	6503	SO:0001583	missense	113878	exon2			CGTACAACAAACC		CCDS5587.1, CCDS43605.1	7q11.23	2014-01-28	2014-01-28		ENSG00000091073	ENSG00000091073		"""RING-type (C3HC4) zinc fingers"""	15973	protein-coding gene	gene with protein product		613141	"""deltex (Drosophila) homolog 2"", ""deltex homolog 2 (Drosophila)"""			12670957	Standard	NM_020892		Approved	RNF58, KIAA1528	uc003ufh.4	Q86UW9	OTTHUMG00000162594	ENST00000324432.5:c.743A>G	7.37:g.76112299A>G	ENSP00000322885:p.Asn248Ser	329.0	1.0	0.00303951		266.0	116.0	0.43609	NM_001102596	Q6XM87|Q6XM88|Q96H69|Q9H890|Q9P200	Missense_Mutation	SNP	ENST00000324432.5	37	CCDS5587.1	4	0.0018315018315018315	0	0.0	0	0.0	2	0.0034965034965034965	2	0.002638522427440633	.	0.016	-1.528964	0.00951	6.81E-4	0.005349	ENSG00000091073	ENST00000324432;ENST00000307569;ENST00000541989;ENST00000446600;ENST00000413936;ENST00000430490;ENST00000446820	T;T;T;T;T;T	0.10668	2.85;2.86;2.85;2.85;2.85;2.86	5.18	1.39	0.22231	.	0.598456	0.18389	N	0.142736	T	0.02688	0.0081	N	0.08118	0	0.24585	N	0.993856	B;B;B	0.11235	0.004;0.001;0.0	B;B;B	0.12837	0.006;0.008;0.002	T	0.45716	-0.9242	10	0.08381	T	0.77	-14.9182	6.4167	0.21719	0.5953:0.1273:0.2774:0.0	.	157;248;248	F5GX89;Q86UW9-2;Q86UW9	.;.;DTX2_HUMAN	S	248;248;157;157;248;248;248	ENSP00000322885:N248S;ENSP00000305242:N248S;ENSP00000397648:N157S;ENSP00000390218:N248S;ENSP00000411986:N248S;ENSP00000392545:N248S	ENSP00000305242:N248S	N	+	2	0	AC005522.1	75950235	0.994000	0.37717	0.993000	0.49108	0.282000	0.26991	0.532000	0.23067	0.005000	0.14708	-1.447000	0.01057	AAC	A|0.997;G|0.003	0.003	strong		0.672	DTX2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253104.2		
LAMP2	3920	hgsc.bcm.edu	37	X	119576455	119576455	+	Splice_Site	SNP	G	G	A	rs73219144	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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		44.0	0.0	0		44.0	44.0	1	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
DUOX2	50506	hgsc.bcm.edu	37	15	45398797	45398797	+	Missense_Mutation	SNP	C	C	T	rs373620034		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:45398797C>T	ENST00000603300.1	-	16	2076	c.1874G>A	c.(1873-1875)cGa>cAa	p.R625Q	DUOX2_ENST00000389039.6_Missense_Mutation_p.R625Q	NM_014080.4	NP_054799.4	Q9NRD8	DUOX2_HUMAN	dual oxidase 2	625					adenohypophysis morphogenesis (GO:0048855)|bone mineralization (GO:0030282)|cuticle development (GO:0042335)|cytokine-mediated signaling pathway (GO:0019221)|fertilization (GO:0009566)|hormone biosynthetic process (GO:0042446)|hydrogen peroxide catabolic process (GO:0042744)|inner ear development (GO:0048839)|multicellular organism growth (GO:0035264)|oxidation-reduction process (GO:0055114)|response to cAMP (GO:0051591)|response to virus (GO:0009615)|thyroid gland development (GO:0030878)|thyroid hormone generation (GO:0006590)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|heme binding (GO:0020037)|NAD(P)H oxidase activity (GO:0016174)|peroxidase activity (GO:0004601)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(7)|urinary_tract(1)	63		all_cancers(109;3.79e-11)|all_epithelial(112;2.92e-09)|Lung NSC(122;3.55e-06)|all_lung(180;2.56e-05)|Melanoma(134;0.027)		all cancers(107;1.05e-18)|GBM - Glioblastoma multiforme(94;4.23e-07)|COAD - Colon adenocarcinoma(120;0.0668)|Colorectal(133;0.068)		CTTGTGTTCTCGGCCCCGGAA	0.557																																					p.R625Q		Atlas-SNP	.											DUOX2,NS,carcinoma,-1,1	DUOX2	137	1	0			c.G1874A						PASS	.	C	GLN/ARG	0,4396		0,0,2198	154.0	150.0	151.0		1874	-1.0	1.0	15		151	1,8595	1.2+/-3.3	0,1,4297	no	missense	DUOX2	NM_014080.4	43	0,1,6495	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging	625/1549	45398797	1,12991	2198	4298	6496	SO:0001583	missense	50506	exon16			TGTTCTCGGCCCC	AF181972	CCDS10117.1	15q15.3-q21	2013-01-10			ENSG00000140279	ENSG00000140279		"""EF-hand domain containing"""	13273	protein-coding gene	gene with protein product	"""dual oxidase-like domains 2"", ""nicotinamide adenine dinucleotide phosphate oxidase"", ""flavoprotein NADPH oxidase"", ""NADPH thyroid oxidase 2"", ""NADH/NADPH thyroid oxidase p138-tox"", ""NADPH oxidase/peroxidase DUOX2"""	606759				10601291, 10806195	Standard	NM_014080		Approved	P138-TOX, P138(TOX), THOX2, LNOX2	uc010bea.3	Q9NRD8	OTTHUMG00000131355	ENST00000603300.1:c.1874G>A	15.37:g.45398797C>T	ENSP00000475084:p.Arg625Gln	158.0	0.0	0		154.0	72.0	0.467532	NM_014080	A8MQ13|D2XI64|Q9NR02|Q9UHF9	Missense_Mutation	SNP	ENST00000603300.1	37	CCDS10117.1	.	.	.	.	.	.	.	.	.	.	C	13.84	2.357373	0.41801	0.0	1.16E-4	ENSG00000140279	ENST00000389039	.	.	.	5.42	-1.02	0.10135	.	0.584816	0.18081	N	0.152290	T	0.49287	0.1548	M	0.72894	2.215	0.40470	D	0.980336	B;B	0.31931	0.188;0.347	B;B	0.24701	0.023;0.055	T	0.44467	-0.9326	9	0.42905	T	0.14	-3.1592	9.9682	0.41738	0.0:0.6012:0.0:0.3988	.	625;187	Q9NRD8;Q59GU9	DUOX2_HUMAN;.	Q	625	.	ENSP00000373691:R625Q	R	-	2	0	DUOX2	43186089	0.024000	0.19004	0.990000	0.47175	0.648000	0.38561	-0.235000	0.09016	-0.185000	0.10550	0.455000	0.32223	CGA	.	.	weak		0.557	DUOX2-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_014080	
GLTSCR2	29997	hgsc.bcm.edu	37	19	48259787	48259787	+	Silent	SNP	C	C	T	rs11538664	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48259787C>T	ENST00000246802.5	+	11	1337	c.1299C>T	c.(1297-1299)ccC>ccT	p.P433P	CTD-2571L23.6_ENST00000602048.1_RNA|GLTSCR2_ENST00000598681.1_3'UTR|SNORD23_ENST00000408876.1_RNA	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	433				PEGNILRDRFKSFQRRNMIEPRERAKFKRKYKVKLVEKRAF REIQ -> VLTVSCRGAPCPVMTPSLLPVPPRGYGRHHGCP WAGPVGPMPRG (in Ref. 5). {ECO:0000305}.		intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		TCCTGTAGCCCGAGGGCAACA	0.642													C|||	80	0.0159744	0.0053	0.0043	5008	,	,		17005	0.0069		0.0149	False		,,,				2504	0.0491				p.P433P	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.C1299T						PASS	.	C		49,4357	49.6+/-84.7	0,49,2154	32.0	34.0	33.0		1299	-7.4	0.9	19	dbSNP_120	33	168,8432	77.2+/-139.8	0,168,4132	no	coding-synonymous	GLTSCR2	NM_015710.4		0,217,6286	TT,TC,CC		1.9535,1.1121,1.6685		433/479	48259787	217,12789	2203	4300	6503	SO:0001819	synonymous_variant	29997	exon11			GTAGCCCGAGGGC	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.1299C>T	19.37:g.48259787C>T		40.0	0.0	0		48.0	21.0	0.4375	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Silent	SNP	ENST00000246802.5	37	CCDS12705.1																																																																																			C|0.984;T|0.016	0.016	strong		0.642	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
ZNF587	84914	hgsc.bcm.edu	37	19	58371212	58371212	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:58371212A>T	ENST00000339656.5	+	3	1614	c.1432A>T	c.(1432-1434)Agc>Tgc	p.S478C	ZNF587_ENST00000423137.1_Missense_Mutation_p.S477C|ZNF587_ENST00000419854.1_Missense_Mutation_p.S435C|ZNF814_ENST00000597652.1_5'Flank|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597832.1_Intron	NM_001204817.1|NM_032828.3	NP_001191746.1|NP_116217.1	Q96SQ5	ZN587_HUMAN	zinc finger protein 587	478					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|pancreas(1)|stomach(1)	15		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;0.0264)		CAATAAGCACAGCGTGACTAT	0.423																																					p.S478C	Pancreas(59;641 1233 1885 20055 50741)	Atlas-SNP	.											.	ZNF587	53	.	0			c.A1432T						PASS	.						156.0	149.0	152.0					19																	58371212		2203	4300	6503	SO:0001583	missense	84914	exon3			AAGCACAGCGTGA	AF294842	CCDS12964.1, CCDS56110.1	19q13.43	2013-01-08				ENSG00000198466		"""Zinc fingers, C2H2-type"", ""-"""	30955	protein-coding gene	gene with protein product						10520746	Standard	NM_032828		Approved	ZF6, FLJ14710, UBF-fl, FLJ20813	uc002qql.3	Q96SQ5	OTTHUMG00000154901	ENST00000339656.5:c.1432A>T	19.37:g.58371212A>T	ENSP00000345479:p.Ser478Cys	199.0	0.0	0		250.0	17.0	0.068	NM_032828	A0AV72|G3V0H5|Q6ZMK8	Missense_Mutation	SNP	ENST00000339656.5	37	CCDS12964.1	.	.	.	.	.	.	.	.	.	.	.	7.068	0.567735	0.13560	.	.	ENSG00000198466	ENST00000376209;ENST00000423137;ENST00000339656;ENST00000540851;ENST00000419854	T;T;T	0.08008	3.14;3.14;3.14	0.882	-0.521	0.11931	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08980	0.0222	M	0.64630	1.985	0.24750	N	0.992985	B;B	0.27140	0.169;0.025	B;B	0.29598	0.104;0.033	T	0.20773	-1.0265	8	0.38643	T	0.18	.	4.8451	0.13510	0.7267:0.0:0.0:0.2733	.	477;478	G3V0H5;Q96SQ5	.;ZN587_HUMAN	C	435;477;478;478;435	ENSP00000393865:S477C;ENSP00000345479:S478C;ENSP00000406999:S435C	ENSP00000345479:S478C	S	+	1	0	ZNF587	63063024	0.000000	0.05858	0.000000	0.03702	0.344000	0.29017	-2.794000	0.00765	-0.256000	0.09473	0.164000	0.16699	AGC	.	.	none		0.423	ZNF587-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337594.2	NM_032828	
PRIMPOL	201973	hgsc.bcm.edu	37	4	185578337	185578337	+	Nonsense_Mutation	SNP	C	C	T	rs145651098		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:185578337C>T	ENST00000314970.6	+	3	476	c.43C>T	c.(43-45)Cga>Tga	p.R15*	PRIMPOL_ENST00000512834.1_Nonsense_Mutation_p.R15*|PRIMPOL_ENST00000503752.1_Nonsense_Mutation_p.R15*|PRIMPOL_ENST00000515774.1_Intron	NM_152683.2	NP_689896	Q96LW4	PRIPO_HUMAN	primase and polymerase (DNA-directed)	15					mitochondrial DNA replication (GO:0006264)|replication fork processing (GO:0031297)|response to UV (GO:0009411)|translesion synthesis (GO:0019985)	mitochondrial matrix (GO:0005759)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA primase activity (GO:0003896)|DNA-directed DNA polymerase activity (GO:0003887)|manganese ion binding (GO:0030145)										AATTGAAGAACGAGCATCTCA	0.398																																					p.R15X		Atlas-SNP	.											.	CCDC111	43	.	0			c.C43T						PASS	.	C	stop/ARG	1,4405	2.1+/-5.4	0,1,2202	118.0	109.0	112.0		43	5.6	0.9	4	dbSNP_134	112	0,8600		0,0,4300	no	stop-gained	CCDC111	NM_152683.2		0,1,6502	TT,TC,CC		0.0,0.0227,0.0077		15/561	185578337	1,13005	2203	4300	6503	SO:0001587	stop_gained	201973	exon3			GAAGAACGAGCAT	AK057729	CCDS3837.1, CCDS75211.1, CCDS75212.1	4q35.1	2013-09-27	2013-09-27	2013-09-27	ENSG00000164306	ENSG00000164306			26575	protein-coding gene	gene with protein product		615421	"""coiled-coil domain containing 111"""	CCDC111		12477932	Standard	XM_005262814		Approved	FLJ33167	uc003iwk.2	Q96LW4	OTTHUMG00000160495	ENST00000314970.6:c.43C>T	4.37:g.185578337C>T	ENSP00000313816:p.Arg15*	67.0	0.0	0		63.0	31.0	0.492063	NM_152683	D3DP55|D6RDM1|Q5HYJ9	Nonsense_Mutation	SNP	ENST00000314970.6	37	CCDS3837.1	.	.	.	.	.	.	.	.	.	.	C	37	6.625279	0.97714	2.27E-4	0.0	ENSG00000164306	ENST00000314970;ENST00000503752;ENST00000512834	.	.	.	5.64	5.64	0.86602	.	0.353602	0.27362	N	0.019716	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07990	T	0.79	-2.1277	19.7127	0.96102	0.0:1.0:0.0:0.0	.	.	.	.	X	15	.	ENSP00000313816:R15X	R	+	1	2	CCDC111	185815331	0.999000	0.42202	0.894000	0.35097	0.999000	0.98932	3.362000	0.52314	2.652000	0.90054	0.655000	0.94253	CGA	C|1.000;T|0.000	0.000	weak		0.398	PRIMPOL-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000360827.1	NM_152683	
MAGEB3	4114	hgsc.bcm.edu	37	X	30254064	30254064	+	Missense_Mutation	SNP	C	C	T	rs201131077		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:30254064C>T	ENST00000361644.2	+	5	760	c.23C>T	c.(22-24)aCg>aTg	p.T8M		NM_002365.4	NP_002356.2	O15480	MAGB3_HUMAN	melanoma antigen family B, 3	8										NS(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(12)|prostate(2)|skin(2)	25						CAGAAGAGTACGCTCCATGCA	0.542																																					p.T8M		Atlas-SNP	.											.	MAGEB3	54	.	0			c.C23T						PASS	.	A	MET/THR	0,3833		0,0,1631,571	61.0	51.0	55.0		23	-1.8	0.0	X		55	1,6727		0,1,2427,1872	yes	missense	MAGEB3	NM_002365.4	81	0,1,4058,2443	TT,TC,CC,C		0.0149,0.0,0.0095	possibly-damaging	8/347	30254064	1,10560	2202	4300	6502	SO:0001583	missense	4114	exon5			AGAGTACGCTCCA	AK057441	CCDS14220.1	Xp21.3	2009-03-17			ENSG00000198798	ENSG00000198798			6810	protein-coding gene	gene with protein product	"""cancer/testis antigen family 3, member 5"""	300152				9441743	Standard	NM_002365		Approved	CT3.5	uc004dca.2	O15480	OTTHUMG00000021320	ENST00000361644.2:c.23C>T	X.37:g.30254064C>T	ENSP00000355198:p.Thr8Met	122.0	1.0	0.00819672		130.0	129.0	0.992308	NM_002365	A0AVE4|B3KQ52|O75861	Missense_Mutation	SNP	ENST00000361644.2	37	CCDS14220.1	.	.	.	.	.	.	.	.	.	.	c	13.20	2.166490	0.38217	0.0	1.49E-4	ENSG00000198798	ENST00000378986;ENST00000361644	T;T	0.04360	3.64;3.64	3.77	-1.77	0.07982	Melanoma associated antigen, MAGE, N-terminal (1);	11.449600	0.01612	U	0.022560	T	0.07052	0.0179	N	0.22421	0.69	0.09310	N	1	D	0.54397	0.966	P	0.51701	0.677	T	0.22591	-1.0212	10	0.87932	D	0	.	5.614	0.17420	0.5656:0.3294:0.1051:0.0	.	8	O15480	MAGB3_HUMAN	M	8	ENSP00000368271:T8M;ENSP00000355198:T8M	ENSP00000355198:T8M	T	+	2	0	MAGEB3	30163985	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.113000	0.15499	-0.461000	0.06993	-1.548000	0.00902	ACG	.	.	weak		0.542	MAGEB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056158.2	NM_002365	
KRT26	353288	hgsc.bcm.edu	37	17	38927462	38927462	+	Silent	SNP	G	G	A	rs113285472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:38927462G>A	ENST00000335552.4	-	2	516	c.468C>T	c.(466-468)gcC>gcT	p.A156A		NM_181539.4	NP_853517.2			keratin 26											central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(5)	16		Breast(137;0.00526)				GAACAATGCTGGCATTGCAGA	0.348													G|||	6	0.00119808	0.0	0.0014	5008	,	,		15657	0.0		0.005	False		,,,				2504	0.0				p.A156A		Atlas-SNP	.											.	KRT26	49	.	0			c.C468T						PASS	.	G		7,4399	11.4+/-27.6	0,7,2196	43.0	43.0	43.0		468	5.3	1.0	17	dbSNP_132	43	41,8559	25.7+/-73.6	0,41,4259	no	coding-synonymous	KRT26	NM_181539.4		0,48,6455	AA,AG,GG		0.4767,0.1589,0.3691		156/469	38927462	48,12958	2203	4300	6503	SO:0001819	synonymous_variant	353288	exon2			AATGCTGGCATTG	AJ564205	CCDS11374.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000186393	ENSG00000186393		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	30840	protein-coding gene	gene with protein product			"""keratin 25B"""	KRT25B		16831889	Standard	NM_181539		Approved		uc002hvf.3	Q7Z3Y9	OTTHUMG00000133370	ENST00000335552.4:c.468C>T	17.37:g.38927462G>A		118.0	0.0	0		128.0	66.0	0.515625	NM_181539		Silent	SNP	ENST00000335552.4	37	CCDS11374.1																																																																																			G|0.997;A|0.003	0.003	strong		0.348	KRT26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257215.1	NM_181539	
TESC	54997	hgsc.bcm.edu	37	12	117486947	117486947	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:117486947G>T	ENST00000335209.7	-	4	412	c.226C>A	c.(226-228)Ccc>Acc	p.P76T	TESC_ENST00000541210.1_Missense_Mutation_p.P49T|TESC_ENST00000392545.4_Missense_Mutation_p.P129T|TESC_ENST00000535198.1_5'UTR			Q96BS2	CHP3_HUMAN	tescalcin	76					cell differentiation (GO:0030154)|cellular response to retinoic acid (GO:0071300)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell proliferation (GO:0008285)|positive regulation of gene expression (GO:0010628)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of megakaryocyte differentiation (GO:0045654)|positive regulation of sodium:proton antiporter activity (GO:0032417)|positive regulation of transcription, DNA-templated (GO:0045893)|protein maturation (GO:0051604)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of cell adhesion mediated by integrin (GO:0033628)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphatase inhibitor activity (GO:0019212)|protein homodimerization activity (GO:0042803)|protein kinase inhibitor activity (GO:0004860)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|upper_aerodigestive_tract(1)	6	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0297)		AGGCCACTGGGTCCCTTGCGC	0.537																																					p.P76T		Atlas-SNP	.											.	TESC	16	.	0			c.C226A						PASS	.						131.0	119.0	123.0					12																	117486947		2203	4300	6503	SO:0001583	missense	54997	exon4			CACTGGGTCCCTT	AF443207	CCDS9183.2, CCDS9183.3, CCDS53835.1	12q24.22	2013-01-10			ENSG00000088992	ENSG00000088992		"""EF-hand domain containing"""	26065	protein-coding gene	gene with protein product	"""calcineurin-like EF hand protein 3"""	611585				11145610, 11696366, 12809501, 14661968	Standard	NM_017899		Approved	TSC, FLJ20607, CHP3	uc001twh.3	Q96BS2	OTTHUMG00000144168	ENST00000335209.7:c.226C>A	12.37:g.117486947G>T	ENSP00000334785:p.Pro76Thr	66.0	0.0	0		73.0	31.0	0.424658	NM_017899	F5H1Y5|Q9NWT9	Missense_Mutation	SNP	ENST00000335209.7	37	CCDS9183.3	.	.	.	.	.	.	.	.	.	.	G	7.196	0.592551	0.13875	.	.	ENSG00000088992	ENST00000335209;ENST00000392545;ENST00000541210	T;T;T	0.39997	1.05;1.05;1.13	5.92	0.671	0.17929	EF-hand-like domain (1);	0.691593	0.14781	N	0.298762	T	0.18635	0.0447	N	0.13043	0.29	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.22243	-1.0222	10	0.14252	T	0.57	-11.9903	2.8483	0.05550	0.3475:0.109:0.4322:0.1112	.	76	Q96BS2	TESC_HUMAN	T	76;129;49	ENSP00000334785:P76T;ENSP00000376328:P129T;ENSP00000445689:P49T	ENSP00000334785:P76T	P	-	1	0	TESC	115971330	0.000000	0.05858	0.478000	0.27316	0.638000	0.38207	-0.280000	0.08468	-0.381000	0.07882	-1.164000	0.01763	CCC	.	.	none		0.537	TESC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291363.2	NM_017899	
AMT	275	hgsc.bcm.edu	37	3	49459683	49459683	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49459683G>A	ENST00000273588.3	-	2	414	c.112C>T	c.(112-114)Ctc>Ttc	p.L38F	AMT_ENST00000458307.2_Missense_Mutation_p.L38F|AMT_ENST00000538581.1_Intron|AMT_ENST00000395338.2_Missense_Mutation_p.L38F|NICN1-AS1_ENST00000424915.1_RNA|AMT_ENST00000546031.1_Intron|NICN1_ENST00000422593.1_5'Flank|AMT_ENST00000476226.1_5'UTR	NM_000481.3	NP_000472.2	P48728	GCST_HUMAN	aminomethyltransferase	38					glycine catabolic process (GO:0006546)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|transaminase activity (GO:0008483)			endometrium(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	6				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	Tetrahydrofolic acid(DB00116)	AAGTCATAGAGCGGTGTCCTG	0.657																																					p.L38F		Atlas-SNP	.											.	AMT	22	.	0			c.C112T						PASS	.						101.0	105.0	103.0					3																	49459683		2203	4300	6503	SO:0001583	missense	275	exon2			CATAGAGCGGTGT	D13811	CCDS2797.1, CCDS54583.1, CCDS54584.1, CCDS54585.1	3p21.2-p21.1	2014-09-17	2006-05-22		ENSG00000145020	ENSG00000145020	2.1.2.10		473	protein-coding gene	gene with protein product	"""glycine cleavage system protein T"""	238310	"""aminomethyltransferase (glycine cleavage system protein T)"""			1993704, 8188235	Standard	NM_000481		Approved	GCST, NKH	uc003cww.3	P48728	OTTHUMG00000156847	ENST00000273588.3:c.112C>T	3.37:g.49459683G>A	ENSP00000273588:p.Leu38Phe	111.0	0.0	0		95.0	23.0	0.242105	NM_001164712	A8K3I5|B4DE61|B4DJQ0|E9PBG1|Q96IG6	Missense_Mutation	SNP	ENST00000273588.3	37	CCDS2797.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.53|15.53	2.861431|2.861431	0.51482|0.51482	.|.	.|.	ENSG00000145020|ENSG00000145020	ENST00000427987|ENST00000395338;ENST00000458307;ENST00000273588	.|D;D;D	.|0.86097	.|-2.07;-2.07;-2.07	5.22|5.22	4.33|4.33	0.51752|0.51752	.|.	.|0.148983	.|0.46145	.|D	.|0.000309	D|D	0.90089|0.90089	0.6904|0.6904	L|L	0.56769|0.56769	1.78|1.78	0.80722|0.80722	D|D	1|1	.|D;D;D	.|0.89917	.|1.0;1.0;1.0	.|D;D;D	.|0.97110	.|1.0;1.0;1.0	D|D	0.90373|0.90373	0.4382|0.4382	5|10	.|0.59425	.|D	.|0.04	-14.4114|-14.4114	13.1666|13.1666	0.59575|0.59575	0.0:0.0:0.8386:0.1614|0.0:0.0:0.8386:0.1614	.|.	.|38;38;38	.|B4DJQ0;E9PBG1;P48728	.|.;.;GCST_HUMAN	V|F	35|38	.|ENSP00000378747:L38F;ENSP00000415619:L38F;ENSP00000273588:L38F	.|ENSP00000273588:L38F	A|L	-|-	2|1	0|0	AMT|AMT	49434687|49434687	1.000000|1.000000	0.71417|0.71417	0.034000|0.034000	0.17996|0.17996	0.003000|0.003000	0.03518|0.03518	9.009000|9.009000	0.93606|0.93606	1.299000|1.299000	0.44798|0.44798	-0.181000|-0.181000	0.13052|0.13052	GCT|CTC	.	.	none		0.657	AMT-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346216.2	NM_000481	
CD2BP2	10421	hgsc.bcm.edu	37	16	30364805	30364805	+	Missense_Mutation	SNP	C	C	T	rs13330462	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30364805C>T	ENST00000305596.3	-	5	867	c.692G>A	c.(691-693)gGt>gAt	p.G231D	CD2BP2_ENST00000569466.1_Missense_Mutation_p.G231D|RP11-347C12.10_ENST00000563252.1_lincRNA	NM_006110.2	NP_006101.1	O95400	CD2B2_HUMAN	CD2 (cytoplasmic tail) binding protein 2	231			G -> D (in dbSNP:rs13330462).		gene expression (GO:0010467)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of phosphatase activity (GO:0010923)|RNA splicing (GO:0008380)|spliceosomal tri-snRNP complex assembly (GO:0000244)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|U5 snRNP (GO:0005682)	ribonucleoprotein complex binding (GO:0043021)			breast(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)	15						ACACCCCAAACCCTTCAGACG	0.632													c|||	517	0.103235	0.3359	0.0432	5008	,	,		16256	0.001		0.0119	False		,,,				2504	0.0307				p.G231D		Atlas-SNP	.											.	CD2BP2	30	.	0			c.G692A						PASS	.	C	ASP/GLY	1197,3197	418.5+/-338.3	163,871,1163	65.0	64.0	65.0		692	3.4	1.0	16	dbSNP_121	65	119,8481	61.7+/-123.6	1,117,4182	yes	missense	CD2BP2	NM_006110.2	94	164,988,5345	TT,TC,CC		1.3837,27.2417,10.1278	benign	231/342	30364805	1316,11678	2197	4300	6497	SO:0001583	missense	10421	exon5			CCCAAACCCTTCA	AF104222	CCDS10675.1	16p11.2	2012-04-17	2006-03-28		ENSG00000169217	ENSG00000169217		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	1656	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 59"""	604470	"""CD2 antigen (cytoplasmic tail)-binding protein 2"""			9843987	Standard	NM_006110		Approved	LIN1, Snu40, PPP1R59	uc002dxs.3	O95400	OTTHUMG00000132397	ENST00000305596.3:c.692G>A	16.37:g.30364805C>T	ENSP00000304903:p.Gly231Asp	57.0	0.0	0		56.0	30.0	0.535714	NM_006110	B2RDX2|Q9ULP2	Missense_Mutation	SNP	ENST00000305596.3	37	CCDS10675.1	184	0.08424908424908426	154	0.3130081300813008	20	0.055248618784530384	1	0.0017482517482517483	9	0.011873350923482849	c	10.63	1.405572	0.25378	0.272417	0.013837	ENSG00000169217	ENST00000305596	T	0.28666	1.6	5.51	3.4	0.38934	.	0.446171	0.27631	N	0.018511	T	0.00012	0.0000	L	0.27053	0.805	0.31159	P	0.704604	B	0.27559	0.181	B	0.18561	0.022	T	0.39961	-0.9588	9	0.13108	T	0.6	-0.0537	14.0925	0.65000	0.0:0.6336:0.3664:0.0	rs13330462;rs13330462	231	O95400	CD2B2_HUMAN	D	231	ENSP00000304903:G231D	ENSP00000304903:G231D	G	-	2	0	CD2BP2	30272306	0.332000	0.24722	0.977000	0.42913	0.887000	0.51463	0.830000	0.27462	1.314000	0.45095	0.643000	0.83706	GGT	C|0.892;T|0.108	0.108	strong		0.632	CD2BP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255528.1	NM_006110	
ACOXL	55289	hgsc.bcm.edu	37	2	111551725	111551725	+	Missense_Mutation	SNP	G	G	A	rs150003283	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:111551725G>A	ENST00000389811.4	+	5	543	c.319G>A	c.(319-321)Gaa>Aaa	p.E107K	ACOXL_ENST00000439055.1_Missense_Mutation_p.E107K|ACOXL_ENST00000340561.4_Missense_Mutation_p.E107K			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	107					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						GATCCAGACCGAAGCCACCTT	0.537													G|||	43	0.00858626	0.0	0.0043	5008	,	,		19322	0.001		0.007	False		,,,				2504	0.0327				p.E107K		Atlas-SNP	.											ACOXL_ENST00000439055,colon,carcinoma,0,2	ACOXL	93	2	0			c.G319A						PASS	.	G	LYS/GLU	1,3935		0,1,1967	88.0	96.0	94.0		319	3.5	0.1	2	dbSNP_134	94	37,8249		0,37,4106	yes	missense	ACOXL	NM_001142807.1	56	0,38,6073	AA,AG,GG		0.4465,0.0254,0.3109	probably-damaging	107/581	111551725	38,12184	1968	4143	6111	SO:0001583	missense	55289	exon5			CAGACCGAAGCCA		CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"""acyl-Coenzyme A oxidase-like"""				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.319G>A	2.37:g.111551725G>A	ENSP00000374461:p.Glu107Lys	100.0	0.0	0		109.0	57.0	0.522936	NM_001142807	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	ENST00000389811.4	37		11	0.005036630036630037	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	7	0.009234828496042216	G	22.8	4.335963	0.81801	2.54E-4	0.004465	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000340561	D;D;D	0.94862	-3.54;-3.54;-3.54	5.33	3.53	0.40419	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (2);	0.269326	0.27787	N	0.017858	D	0.87529	0.6200	N	0.04162	-0.26	0.33945	D	0.643766	D;D;D	0.71674	0.998;0.997;0.963	P;P;P	0.58130	0.833;0.742;0.49	D	0.90091	0.4177	10	0.59425	D	0.04	-7.9556	9.0146	0.36161	0.0824:0.1491:0.7686:0.0	.	107;107;107	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	K	107	ENSP00000374461:E107K;ENSP00000407761:E107K;ENSP00000343717:E107K	ENSP00000343717:E107K	E	+	1	0	ACOXL	111268196	0.988000	0.35896	0.122000	0.21767	0.936000	0.57629	2.001000	0.40825	0.615000	0.30124	0.655000	0.94253	GAA	G|0.995;A|0.005	0.005	strong		0.537	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000254024.2	NM_018308	
ADAMTS19	171019	hgsc.bcm.edu	37	5	129001247	129001247	+	Silent	SNP	G	G	A	rs77945368	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:129001247G>A	ENST00000274487.4	+	16	2608	c.2463G>A	c.(2461-2463)gaG>gaA	p.E821E	CTC-575N7.1_ENST00000503616.1_RNA	NM_133638.3	NP_598377.3	Q8TE59	ATS19_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 19	821	Spacer.					proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|endometrium(10)|kidney(9)|large_intestine(14)|lung(34)|ovary(6)|pancreas(1)|prostate(6)|skin(6)	91		all_cancers(142;0.0148)|Prostate(80;0.0494)|Breast(839;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.222)		AAGTTGTGGAGGAAAAGCCGG	0.428													G|||	18	0.00359425	0.0136	0.0	5008	,	,		13404	0.0		0.0	False		,,,				2504	0.0				p.E821E		Atlas-SNP	.											ADAMTS19,NS,carcinoma,0,1	ADAMTS19	216	1	0			c.G2463A						PASS	.	G		79,4327	68.1+/-105.8	0,79,2124	119.0	107.0	111.0		2463	0.8	1.0	5	dbSNP_132	111	0,8600		0,0,4300	no	coding-synonymous	ADAMTS19	NM_133638.3		0,79,6424	AA,AG,GG		0.0,1.793,0.6074		821/1208	129001247	79,12927	2203	4300	6503	SO:0001819	synonymous_variant	171019	exon16			TGTGGAGGAAAAG	AJ311904	CCDS4146.1	5q23.3	2009-04-27	2005-08-19		ENSG00000145808	ENSG00000145808		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17111	protein-coding gene	gene with protein product		607513	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 19"""			11867212	Standard	NM_133638		Approved		uc003kvb.1	Q8TE59	OTTHUMG00000128990	ENST00000274487.4:c.2463G>A	5.37:g.129001247G>A		83.0	0.0	0		62.0	25.0	0.403226	NM_133638		Silent	SNP	ENST00000274487.4	37	CCDS4146.1																																																																																			G|0.993;A|0.007	0.007	strong		0.428	ADAMTS19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250979.2	NM_133638	
TM4SF20	79853	hgsc.bcm.edu	37	2	228228462	228228462	+	Missense_Mutation	SNP	T	T	G	rs137891000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:228228462T>G	ENST00000304568.3	-	4	705	c.668A>C	c.(667-669)aAg>aCg	p.K223T		NM_024795.3	NP_079071.2	Q53R12	T4S20_HUMAN	transmembrane 4 L six family member 20	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(4)|stomach(2)	10		Renal(207;0.025)|all_lung(227;0.123)|Esophageal squamous(248;0.23)|all_hematologic(139;0.248)		Epithelial(121;3.8e-11)|all cancers(144;2.57e-08)|Lung(261;0.00942)|LUSC - Lung squamous cell carcinoma(224;0.0115)		ACTTCTTCGCTTAGAGACTCC	0.373													T|||	27	0.00539137	0.0008	0.0072	5008	,	,		19702	0.0		0.006	False		,,,				2504	0.0153				p.K223T		Atlas-SNP	.											.	TM4SF20	24	.	0			c.A668C						PASS	.	T	THR/LYS	5,4401	9.9+/-24.2	0,5,2198	104.0	107.0	106.0		668	2.0	0.0	2	dbSNP_134	106	41,8559	27.9+/-77.7	0,41,4259	yes	missense	TM4SF20	NM_024795.3	78	0,46,6457	GG,GT,TT		0.4767,0.1135,0.3537	possibly-damaging	223/230	228228462	46,12960	2203	4300	6503	SO:0001583	missense	79853	exon4			CTTCGCTTAGAGA	AK026453	CCDS2466.1	2q36.3	2008-02-05			ENSG00000168955	ENSG00000168955			26230	protein-coding gene	gene with protein product		615404				12975309	Standard	NM_024795		Approved	FLJ22800, TCCE518	uc002vpb.2	Q53R12	OTTHUMG00000133187	ENST00000304568.3:c.668A>C	2.37:g.228228462T>G	ENSP00000303028:p.Lys223Thr	70.0	0.0	0		84.0	42.0	0.5	NM_024795	B2RP42|Q5U609|Q6UWS1|Q9H5X9	Missense_Mutation	SNP	ENST00000304568.3	37	CCDS2466.1	9	0.004120879120879121	1	0.0020325203252032522	5	0.013812154696132596	0	0.0	3	0.00395778364116095	T	16.53	3.150382	0.57151	0.001135	0.004767	ENSG00000168955	ENST00000304568	T	0.30448	1.53	5.62	1.98	0.26296	.	0.601254	0.17265	N	0.180637	T	0.33177	0.0854	M	0.72118	2.19	0.09310	N	1	P	0.52577	0.954	P	0.57057	0.812	T	0.19484	-1.0304	10	0.20519	T	0.43	-6.6529	7.0811	0.25231	0.0:0.2599:0.0:0.7401	.	223	Q53R12	T4S20_HUMAN	T	223	ENSP00000303028:K223T	ENSP00000303028:K223T	K	-	2	0	TM4SF20	227936706	0.000000	0.05858	0.004000	0.12327	0.576000	0.36127	-0.112000	0.10791	0.109000	0.17891	0.533000	0.62120	AAG	T|0.995;G|0.005	0.005	strong		0.373	TM4SF20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256896.2	NM_024795	
PCDHB12	56124	hgsc.bcm.edu	37	5	140590641	140590641	+	Missense_Mutation	SNP	C	C	G	rs150562956	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140590641C>G	ENST00000239450.2	+	1	2351	c.2162C>G	c.(2161-2163)cCg>cGg	p.P721R	PCDHB12_ENST00000541609.1_Missense_Mutation_p.P384R|PCDHB13_ENST00000341948.4_5'Flank	NM_018932.3	NP_061755.1	Q9Y5F1	PCDBC_HUMAN	protocadherin beta 12	721					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)|breast(3)|endometrium(10)|large_intestine(17)|lung(38)|ovary(3)|pancreas(1)|prostate(2)|skin(7)|stomach(1)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			AGGGCGGCCCCGGTCGGTCGC	0.657													C|||	36	0.0071885	0.0	0.0014	5008	,	,		14069	0.001		0.005	False		,,,				2504	0.0297				p.P721R		Atlas-SNP	.											PCDHB12,colon,carcinoma,0,1	PCDHB12	179	1	0			c.C2162G						PASS	.	C	ARG/PRO	2,4404		0,2,2201	70.0	79.0	76.0		2162	1.7	0.0	5	dbSNP_134	76	47,8553		0,47,4253	no	missense	PCDHB12	NM_018932.3	103	0,49,6454	GG,GC,CC		0.5465,0.0454,0.3767	benign	721/796	140590641	49,12957	2203	4300	6503	SO:0001583	missense	56124	exon1			CGGCCCCGGTCGG	AF152491	CCDS4254.1	5q31	2010-01-26			ENSG00000120328	ENSG00000120328		"""Cadherins / Protocadherins : Clustered"""	8683	other	protocadherin		606338				10380929	Standard	NM_018932		Approved	PCDH-BETA12	uc003liz.3	Q9Y5F1	OTTHUMG00000129620	ENST00000239450.2:c.2162C>G	5.37:g.140590641C>G	ENSP00000239450:p.Pro721Arg	53.0	0.0	0		90.0	46.0	0.511111	NM_018932	B4DDU1	Missense_Mutation	SNP	ENST00000239450.2	37	CCDS4254.1	.	.	.	.	.	.	.	.	.	.	C	8.354	0.831566	0.16820	4.54E-4	0.005465	ENSG00000120328	ENST00000541609;ENST00000239450;ENST00000507840	T;T	0.52295	0.67;0.85	3.67	1.7	0.24286	.	.	.	.	.	T	0.27384	0.0672	L	0.38838	1.175	0.09310	N	1	B	0.21821	0.061	B	0.21360	0.034	T	0.18745	-1.0327	9	0.38643	T	0.18	.	7.7474	0.28877	0.2725:0.3123:0.4152:0.0	.	721	Q9Y5F1	PCDBC_HUMAN	R	384;721;341	ENSP00000440199:P384R;ENSP00000239450:P721R	ENSP00000239450:P721R	P	+	2	0	PCDHB12	140570825	0.006000	0.16342	0.002000	0.10522	0.053000	0.15095	0.784000	0.26816	0.128000	0.18479	0.479000	0.44913	CCG	C|0.998;G|0.002;T|0.000	0.002	strong		0.657	PCDHB12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251815.2	NM_018932	
NEK1	4750	hgsc.bcm.edu	37	4	170506525	170506525	+	Missense_Mutation	SNP	C	C	T	rs200161705	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:170506525C>T	ENST00000439128.2	-	9	1422	c.782G>A	c.(781-783)cGc>cAc	p.R261H	NEK1_ENST00000510533.1_Missense_Mutation_p.R261H|NEK1_ENST00000512193.1_Missense_Mutation_p.R261H|NEK1_ENST00000511633.1_Missense_Mutation_p.R261H|NEK1_ENST00000507142.1_Missense_Mutation_p.R261H	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	261					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)	p.R261L(2)		NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		CTTTTCAATGCGTTTGGCTAT	0.388													C|||	4	0.000798722	0.0	0.0029	5008	,	,		18346	0.0		0.001	False		,,,				2504	0.001				p.R261H		Atlas-SNP	.											NEK1_ENST00000507142,NS,carcinoma,0,2	NEK1	203	2	2	Substitution - Missense(2)	breast(2)	c.G782A						PASS	.	C	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	3,3653		0,3,1825	72.0	68.0	69.0		782,782,782,782,782	5.8	1.0	4		69	31,8137		0,31,4053	yes	missense,missense,missense,missense,missense	NEK1	NM_001199397.1,NM_001199398.1,NM_001199399.1,NM_001199400.1,NM_012224.2	29,29,29,29,29	0,34,5878	TT,TC,CC		0.3795,0.0821,0.2876	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	261/1287,261/1243,261/1190,261/1215,261/1259	170506525	34,11790	1828	4084	5912	SO:0001583	missense	4750	exon10			TCAATGCGTTTGG	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.782G>A	4.37:g.170506525C>T	ENSP00000408020:p.Arg261His	172.0	0.0	0		133.0	63.0	0.473684	NM_001199399	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	33	5.219726	0.95139	8.21E-4	0.003795	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.24350	1.86;1.86;1.86;1.86;1.86	5.82	5.82	0.92795	Protein kinase-like domain (1);	0.000000	0.64402	D	0.000004	T	0.42471	0.1204	M	0.62016	1.91	0.80722	D	1	D;D;D;D;D;D	0.89917	0.972;1.0;1.0;1.0;1.0;1.0	P;D;D;D;D;D	0.97110	0.55;0.999;1.0;1.0;0.997;0.999	T	0.11108	-1.0601	10	0.30078	T	0.28	.	20.0909	0.97817	0.0:1.0:0.0:0.0	.	261;261;261;261;261;261	Q96PY6-5;Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;.;NEK1_HUMAN	H	261	ENSP00000408020:R261H;ENSP00000423332:R261H;ENSP00000427653:R261H;ENSP00000424757:R261H;ENSP00000424938:R261H	ENSP00000408020:R261H	R	-	2	0	NEK1	170743100	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	7.709000	0.84645	2.756000	0.94617	0.591000	0.81541	CGC	C|0.999;T|0.001	0.001	strong		0.388	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
TMEM38B	55151	hgsc.bcm.edu	37	9	108536246	108536246	+	Missense_Mutation	SNP	G	G	C	rs35232724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:108536246G>C	ENST00000374692.3	+	6	878	c.761G>C	c.(760-762)tGt>tCt	p.C254S	TMEM38B_ENST00000374688.1_Missense_Mutation_p.C200S	NM_018112.1	NP_060582.1	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	254			C -> S (in dbSNP:rs35232724).			integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13						TTTTCATCATGTGAGAAGAAA	0.418													G|||	142	0.0283546	0.0968	0.0101	5008	,	,		16874	0.0		0.005	False		,,,				2504	0.002				p.C254S		Atlas-SNP	.											.	TMEM38B	31	.	0			c.G761C						PASS	.	G	SER/CYS	488,3918	227.8+/-242.9	29,430,1744	105.0	101.0	103.0		761	1.3	0.0	9	dbSNP_126	103	80,8520	46.3+/-105.2	0,80,4220	yes	missense	TMEM38B	NM_018112.1	112	29,510,5964	CC,CG,GG		0.9302,11.0758,4.3672	benign	254/292	108536246	568,12438	2203	4300	6503	SO:0001583	missense	55151	exon6			CATCATGTGAGAA	BC031938	CCDS6768.1	9q31.3	2013-05-23	2004-12-21	2004-12-22	ENSG00000095209	ENSG00000095209			25535	protein-coding gene	gene with protein product		611236	"""chromosome 9 open reading frame 87"""	C9orf87		17611541, 23316006	Standard	NM_018112		Approved	FLJ10493, bA219P18.1, D4Ertd89e, TRIC-B	uc004bcu.2	Q9NVV0	OTTHUMG00000020429	ENST00000374692.3:c.761G>C	9.37:g.108536246G>C	ENSP00000363824:p.Cys254Ser	79.0	0.0	0		65.0	37.0	0.569231	NM_018112	Q5JR63|Q5SVN5|Q5SVN6|Q5VTE2|Q6IA97	Missense_Mutation	SNP	ENST00000374692.3	37	CCDS6768.1	62	0.028388278388278388	54	0.10975609756097561	3	0.008287292817679558	0	0.0	5	0.006596306068601583	G	0.255	-1.003554	0.02128	0.110758	0.009302	ENSG00000095209	ENST00000374692;ENST00000374688	T;T	0.39056	1.1;1.1	4.25	1.3	0.21679	.	0.987695	0.08274	N	0.970939	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.12502	-1.0545	10	0.07990	T	0.79	-3.46	7.6203	0.28181	0.0:0.3465:0.4746:0.1789	rs35232724	254	Q9NVV0	TM38B_HUMAN	S	254;200	ENSP00000363824:C254S;ENSP00000363820:C200S	ENSP00000363820:C200S	C	+	2	0	TMEM38B	107576067	0.178000	0.23122	0.014000	0.15608	0.185000	0.23345	0.189000	0.17037	0.289000	0.22422	-0.234000	0.12200	TGT	G|0.960;C|0.040	0.040	strong		0.418	TMEM38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053517.1	NM_018112	
SLC23A2	9962	hgsc.bcm.edu	37	20	4855309	4855309	+	Silent	SNP	G	G	A	rs41282100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:4855309G>A	ENST00000379333.1	-	10	1250	c.858C>T	c.(856-858)taC>taT	p.Y286Y	SLC23A2_ENST00000468355.1_5'UTR|SLC23A2_ENST00000338244.1_Silent_p.Y286Y|SLC23A2_ENST00000424750.2_Silent_p.Y172Y	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		58.0	0.0	0		80.0	36.0	0.45	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		
CRACR2A	84766	hgsc.bcm.edu	37	12	3805977	3805977	+	Missense_Mutation	SNP	A	A	C	rs144314920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:3805977A>C	ENST00000252322.1	-	4	657	c.189T>G	c.(187-189)gaT>gaG	p.D63E	EFCAB4B_ENST00000440314.2_Missense_Mutation_p.D63E|EFCAB4B_ENST00000444507.1_Missense_Mutation_p.D63E	NM_032680.3	NP_116069.1	Q9BSW2	EFC4B_HUMAN		63	EF-hand 1. {ECO:0000255|PROSITE- ProRule:PRU00448}.				activation of store-operated calcium channel activity (GO:0032237)|immune system process (GO:0002376)|positive regulation of calcium ion transport (GO:0051928)|store-operated calcium entry (GO:0002115)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)			breast(1)|endometrium(3)|large_intestine(2)|liver(1)|lung(12)|ovary(1)|pancreas(2)|prostate(1)|upper_aerodigestive_tract(1)	24			OV - Ovarian serous cystadenocarcinoma(31;0.00287)|COAD - Colon adenocarcinoma(12;0.0264)			TGCCTTCAGCATCACAGGTCT	0.567													A|||	2	0.000399361	0.0	0.0014	5008	,	,		20268	0.0		0.001	False		,,,				2504	0.0				p.D63E		Atlas-SNP	.											.	EFCAB4B	100	.	0			c.T189G						PASS	.	A	GLU/ASP,GLU/ASP	0,4406		0,0,2203	133.0	96.0	108.0		189,189	-4.5	0.0	12	dbSNP_134	108	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	EFCAB4B	NM_001144958.1,NM_032680.3	45,45	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	probably-damaging,probably-damaging	63/732,63/396	3805977	5,13001	2203	4300	6503	SO:0001583	missense	84766	exon4			TTCAGCATCACAG																												ENST00000252322.1:c.189T>G	12.37:g.3805977A>C	ENSP00000252322:p.Asp63Glu	66.0	0.0	0		85.0	42.0	0.494118	NM_001144958	B4E1X0|B9EK63	Missense_Mutation	SNP	ENST00000252322.1	37	CCDS8522.1	.	.	.	.	.	.	.	.	.	.	A	18.58	3.653645	0.67472	0.0	5.81E-4	ENSG00000130038	ENST00000440314;ENST00000444507;ENST00000252322	T;D;T	0.95821	-0.03;-3.82;-0.03	5.57	-4.47	0.03525	EF-hand-like domain (1);	0.000000	0.85682	D	0.000000	D	0.97430	0.9159	M	0.89904	3.07	0.21553	N	0.999645	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.97110	1.0;0.996;0.991	D	0.94659	0.7846	10	0.87932	D	0	-24.417	15.1484	0.72677	0.2367:0.0:0.7633:0.0	.	63;63;63	D7UEQ6;Q9BSW2-2;Q9BSW2	.;.;EFC4B_HUMAN	E	63	ENSP00000409382:D63E;ENSP00000412496:D63E;ENSP00000252322:D63E	ENSP00000252322:D63E	D	-	3	2	EFCAB4B	3676238	0.001000	0.12720	0.009000	0.14445	0.854000	0.48673	-0.320000	0.08028	-0.748000	0.04753	-0.263000	0.10527	GAT	A|1.000;C|0.000	0.000	strong		0.567	EFCAB4B-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000398673.1		
NUTM1	256646	hgsc.bcm.edu	37	15	34649336	34649336	+	Missense_Mutation	SNP	G	G	A	rs149177074	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:34649336G>A	ENST00000333756.4	+	7	3198	c.3043G>A	c.(3043-3045)Gag>Aag	p.E1015K	NUTM1_ENST00000537011.1_Missense_Mutation_p.E1043K|NUTM1_ENST00000438749.3_Missense_Mutation_p.E1033K	NM_175741.1	NP_786883	Q86Y26	NUTM1_HUMAN	NUT midline carcinoma, family member 1	1015						cytoplasm (GO:0005737)|nucleus (GO:0005634)											GGAAGAGGATGAGGAACTCTC	0.498													G|||	8	0.00159744	0.0	0.0029	5008	,	,		20984	0.0		0.006	False		,,,				2504	0.0				p.E1015K		Atlas-SNP	.											C15orf55_ENST00000333756,NS,lymphoid_neoplasm,0,1	C15orf55	110	1	0			c.G3043A						PASS	.	G	LYS/GLU	4,4398	9.9+/-24.2	0,4,2197	76.0	61.0	66.0		3043	4.3	1.0	15	dbSNP_134	66	31,8565	22.8+/-68.1	0,31,4267	yes	missense	C15orf55	NM_175741.1	56	0,35,6464	AA,AG,GG		0.3606,0.0909,0.2693	benign	1015/1133	34649336	35,12963	2201	4298	6499	SO:0001583	missense	256646	exon7			GAGGATGAGGAAC	AF482429	CCDS32190.1, CCDS61584.1, CCDS61585.1	15q14	2014-01-28	2013-03-14	2013-03-14	ENSG00000184507	ENSG00000184507			29919	protein-coding gene	gene with protein product	"""nuclear protein in testis"""	608963	"""chromosome 15 open reading frame 55"""	C15orf55		12543779	Standard	NM_175741		Approved	NUT, DKFZp434O192, FAM22H	uc001zif.3	Q86Y26	OTTHUMG00000172348	ENST00000333756.4:c.3043G>A	15.37:g.34649336G>A	ENSP00000329448:p.Glu1015Lys	56.0	0.0	0		55.0	26.0	0.472727	NM_175741	B4DZ00|B7Z7Y4|E7EVE8|F5H4I6|Q86YS8|Q8N7F2|Q9NTB3	Missense_Mutation	SNP	ENST00000333756.4	37	CCDS32190.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	15.74	2.923315	0.52653	9.09E-4	0.003606	ENSG00000184507	ENST00000537011;ENST00000438749;ENST00000333756	T;T;T	0.13307	2.62;2.6;2.61	5.2	4.28	0.50868	.	0.557345	0.16563	N	0.208980	T	0.11324	0.0276	L	0.61387	1.9	0.33479	D	0.58722	B;B;B	0.29085	0.232;0.154;0.192	B;B;B	0.27076	0.059;0.076;0.031	T	0.10222	-1.0639	10	0.66056	D	0.02	.	9.6167	0.39696	0.0944:0.0:0.9056:0.0	.	1033;1043;1015	E7EVE8;F5H4I6;Q86Y26	.;.;NUT_HUMAN	K	1043;1033;1015	ENSP00000444896:E1043K;ENSP00000407031:E1033K;ENSP00000329448:E1015K	ENSP00000329448:E1015K	E	+	1	0	C15orf55	32436628	0.965000	0.33210	0.991000	0.47740	0.842000	0.47809	1.928000	0.40104	1.422000	0.47177	0.655000	0.94253	GAG	G|0.998;A|0.002	0.002	strong		0.498	NUTM1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418026.1	NM_175741	
PGAM1	5223	hgsc.bcm.edu	37	10	99190185	99190185	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99190185G>A	ENST00000334828.5	+	2	337	c.189G>A	c.(187-189)gcG>gcA	p.A63A	PGAM1_ENST00000467867.1_3'UTR	NM_002629.2	NP_002620.1	P18669	PGAM1_HUMAN	phosphoglycerate mutase 1 (brain)	63					carbohydrate metabolic process (GO:0005975)|gluconeogenesis (GO:0006094)|glucose metabolic process (GO:0006006)|glycolytic process (GO:0006096)|regulation of glycolytic process (GO:0006110)|regulation of pentose-phosphate shunt (GO:0043456)|respiratory burst (GO:0045730)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	bisphosphoglycerate 2-phosphatase activity (GO:0004083)|bisphosphoglycerate mutase activity (GO:0004082)|phosphoglycerate mutase activity (GO:0004619)|protein kinase binding (GO:0019901)			endometrium(1)|kidney(1)|large_intestine(3)|lung(1)	6		Colorectal(252;0.162)		Epithelial(162;8.36e-10)|all cancers(201;5.62e-08)		AGAAGAGAGCGATCCGGACCC	0.522																																					p.A63A		Atlas-SNP	.											PGAM1,caecum,carcinoma,+1,1	PGAM1	11	1	0			c.G189A						PASS	.						101.0	105.0	104.0					10																	99190185		2203	4297	6500	SO:0001819	synonymous_variant	5223	exon2			GAGAGCGATCCGG	BC010038	CCDS7458.1	10q25.3	2012-10-02			ENSG00000171314	ENSG00000171314	5.4.2.1		8888	protein-coding gene	gene with protein product	"""Phosphoglycerate mutase A, nonmuscle form"""	172250		PGAMA		2846553	Standard	NM_002629		Approved	PGAM-B	uc001knh.3	P18669	OTTHUMG00000018846	ENST00000334828.5:c.189G>A	10.37:g.99190185G>A		82.0	0.0	0		81.0	41.0	0.506173	NM_002629	Q9BWC0	Silent	SNP	ENST00000334828.5	37	CCDS7458.1																																																																																			.	.	none		0.522	PGAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049652.1	NM_002629	
MUC17	140453	hgsc.bcm.edu	37	7	100686291	100686291	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100686291G>A	ENST00000306151.4	+	3	11658	c.11594G>A	c.(11593-11595)cGt>cAt	p.R3865H		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	3865					cellular homeostasis (GO:0019725)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|PDZ domain binding (GO:0030165)			NS(3)|breast(14)|central_nervous_system(2)|cervix(2)|endometrium(27)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(28)|lung(179)|ovary(19)|pancreas(1)|prostate(13)|skin(26)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(4)	343	Lung NSC(181;0.136)|all_lung(186;0.182)					ACTACCATACGTATTTCAATT	0.488																																					p.R3865H		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.G11594A						PASS	.						143.0	130.0	135.0					7																	100686291		2203	4300	6503	SO:0001583	missense	140453	exon3			CCATACGTATTTC	AJ606307	CCDS34711.1	7q22	2007-01-17	2006-03-14		ENSG00000169876	ENSG00000169876		"""Mucins"""	16800	protein-coding gene	gene with protein product		608424				11855812	Standard	NM_001040105		Approved		uc003uxp.1	Q685J3	OTTHUMG00000157030	ENST00000306151.4:c.11594G>A	7.37:g.100686291G>A	ENSP00000302716:p.Arg3865His	99.0	0.0	0		101.0	55.0	0.544554	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	g	3.518	-0.098385	0.07010	.	.	ENSG00000169876	ENST00000306151	T	0.02140	4.43	0.558	-1.12	0.09808	.	.	.	.	.	T	0.02571	0.0078	N	0.08118	0	0.09310	N	1	D	0.76494	0.999	D	0.65443	0.935	T	0.40001	-0.9586	8	0.38643	T	0.18	.	.	.	.	.	3865	Q685J3	MUC17_HUMAN	H	3865	ENSP00000302716:R3865H	ENSP00000302716:R3865H	R	+	2	0	MUC17	100473011	0.000000	0.05858	0.000000	0.03702	0.018000	0.09664	-1.161000	0.03144	-1.475000	0.01876	-1.089000	0.02181	CGT	.	.	none		0.488	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
ATAD3B	83858	hgsc.bcm.edu	37	1	1431048	1431048	+	Missense_Mutation	SNP	A	A	G	rs201429000		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:1431048A>G	ENST00000308647.7	+	16	1914	c.1798A>G	c.(1798-1800)Acg>Gcg	p.T600A		NM_031921.4	NP_114127.3	Q5T9A4	ATD3B_HUMAN	ATPase family, AAA domain containing 3B	600						mitochondrial inner membrane (GO:0005743)	ATP binding (GO:0005524)			endometrium(2)|large_intestine(1)|lung(3)|ovary(1)|skin(2)|urinary_tract(1)	10	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;1.79e-36)|OV - Ovarian serous cystadenocarcinoma(86;3.94e-22)|Colorectal(212;0.000155)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.00227)|BRCA - Breast invasive adenocarcinoma(365;0.00461)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0339)|Lung(427;0.145)		GAGCCTGGCCACGGACCCCTC	0.672																																					p.T600A		Atlas-SNP	.											ATAD3B,NS,neuroblastoma,0,1	ATAD3B	68	1	0			c.A1798G						scavenged	.																																			SO:0001583	missense	83858	exon16			CTGGCCACGGACC	AL834179	CCDS30.1	1p36.33	2010-04-21		2007-02-08	ENSG00000160072	ENSG00000160072		"""ATPases / AAA-type"""	24007	protein-coding gene	gene with protein product		612317				10574462	Standard	XM_005244806		Approved	TOB3, KIAA1273	uc001afv.3	Q5T9A4	OTTHUMG00000000577	ENST00000308647.7:c.1798A>G	1.37:g.1431048A>G	ENSP00000311766:p.Thr600Ala	119.0	2.0	0.0168067		147.0	9.0	0.0612245	NM_031921	A8K3H1|Q6ZRB5|Q9BUK4|Q9ULE7	Missense_Mutation	SNP	ENST00000308647.7	37	CCDS30.1	.	.	.	.	.	.	.	.	.	.	g	0.005	-2.129716	0.00338	.	.	ENSG00000160072	ENST00000378737;ENST00000308647	D	0.93189	-3.18	1.2	-1.67	0.08238	.	0.186138	0.20546	N	0.090207	T	0.78220	0.4249	N	0.08118	0	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.65792	-0.6082	10	0.12766	T	0.61	.	2.0444	0.03557	0.4037:0.0:0.3428:0.2535	.	554;600	Q5T9A4-3;Q5T9A4	.;ATD3B_HUMAN	A	434;600	ENSP00000311766:T600A	ENSP00000311766:T600A	T	+	1	0	ATAD3B	1420911	0.007000	0.16637	0.000000	0.03702	0.003000	0.03518	0.259000	0.18405	-1.264000	0.02452	-1.032000	0.02404	ACG	.	.	weak		0.672	ATAD3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001369.2	NM_031921	
MANEAL	149175	hgsc.bcm.edu	37	1	38265653	38265653	+	Silent	SNP	T	T	C	rs41267339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:38265653T>C	ENST00000373045.6	+	4	1533	c.1152T>C	c.(1150-1152)taT>taC	p.Y384Y	MANEAL_ENST00000329006.5_Silent_p.Y162Y|MANEAL_ENST00000397631.3_3'UTR|MANEAL_ENST00000525897.1_Silent_p.Y190Y|RP11-109P14.9_ENST00000433474.1_RNA	NM_001113482.1	NP_001106954.1	Q5VSG8	MANEL_HUMAN	mannosidase, endo-alpha-like	384						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	hydrolase activity (GO:0016787)			endometrium(1)|large_intestine(1)|liver(1)|lung(1)|prostate(3)	7	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)				GCAAGTACTATGAGACGGCCC	0.567													T|||	28	0.00559105	0.0	0.0115	5008	,	,		19471	0.0		0.0189	False		,,,				2504	0.001				p.Y384Y		Atlas-SNP	.											.	MANEAL	43	.	0			c.T1152C						PASS	.	T	,,	30,4376	35.2+/-66.4	0,30,2173	79.0	86.0	83.0		,1152,486	-0.6	1.0	1	dbSNP_127	83	232,8368	94.5+/-156.4	3,226,4071	no	utr-3,coding-synonymous,coding-synonymous	MANEAL	NM_001031740.2,NM_001113482.1,NM_152496.2	,,	3,256,6244	CC,CT,TT		2.6977,0.6809,2.0145	,,	,384/458,162/236	38265653	262,12744	2203	4300	6503	SO:0001819	synonymous_variant	149175	exon4			GTACTATGAGACG	AK055996	CCDS426.1, CCDS44110.1, CCDS44111.1	1p34.3	2008-02-05			ENSG00000185090	ENSG00000185090			26452	protein-coding gene	gene with protein product							Standard	NM_152496		Approved	FLJ31434	uc001cby.2	Q5VSG8	OTTHUMG00000004317	ENST00000373045.6:c.1152T>C	1.37:g.38265653T>C		128.0	1.0	0.0078125		125.0	118.0	0.944	NM_001113482	Q6DD86|Q6P497|Q8N5P8|Q96G55|Q96N42	Silent	SNP	ENST00000373045.6	37	CCDS44110.1																																																																																			T|0.982;C|0.018	0.018	strong		0.567	MANEAL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012469.2	NM_152496	
OR2H1	26716	hgsc.bcm.edu	37	6	29429766	29429766	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29429766A>G	ENST00000377136.1	+	4	685	c.220A>G	c.(220-222)Agt>Ggt	p.S74G	OR2H1_ENST00000442615.1_Missense_Mutation_p.S74G|OR2H1_ENST00000377132.1_Missense_Mutation_p.S74G|OR2H1_ENST00000396792.2_Missense_Mutation_p.S74G|OR2H1_ENST00000473369.1_Splice_Site|OR2H1_ENST00000377133.1_Missense_Mutation_p.S74G			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	74						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						CTTTACCACAAGTTGTGTCCC	0.537																																					p.S74G		Atlas-SNP	.											.	OR2H1	38	.	0			c.A220G						PASS	.						108.0	107.0	107.0					6																	29429766		1511	2709	4220	SO:0001583	missense	26716	exon3			ACCACAAGTTGTG	AF044491	CCDS4660.1	6p22.1	2014-02-19	2002-02-28		ENSG00000204688	ENSG00000204688		"""GPCR / Class A : Olfactory receptors"""	8252	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily H, member 8"""	OR2H6, OR2H8			Standard	NM_030883		Approved	OR6-2	uc003nmi.3	Q9GZK4	OTTHUMG00000031050	ENST00000377136.1:c.220A>G	6.37:g.29429766A>G	ENSP00000366340:p.Ser74Gly	206.0	0.0	0		203.0	93.0	0.458128	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Missense_Mutation	SNP	ENST00000377136.1	37	CCDS4660.1	.	.	.	.	.	.	.	.	.	.	A	0.142	-1.100996	0.01843	.	.	ENSG00000204688	ENST00000377136;ENST00000377133;ENST00000442615;ENST00000377132;ENST00000396792	T;T;T;T;T	0.01933	4.55;4.55;4.55;4.55;4.55	2.92	2.92	0.33932	GPCR, rhodopsin-like superfamily (1);	0.149339	0.31257	N	0.007964	T	0.02012	0.0063	M	0.90977	3.165	0.09310	N	1	P	0.47962	0.903	B	0.39876	0.312	T	0.31752	-0.9932	10	0.56958	D	0.05	.	6.2425	0.20800	0.8763:0.0:0.1237:0.0	.	74	Q9GZK4	OR2H1_HUMAN	G	74	ENSP00000366340:S74G;ENSP00000366337:S74G;ENSP00000393254:S74G;ENSP00000366336:S74G;ENSP00000380010:S74G	ENSP00000366336:S74G	S	+	1	0	OR2H1	29537745	0.000000	0.05858	0.013000	0.15412	0.048000	0.14542	-0.288000	0.08377	1.582000	0.49881	0.491000	0.48974	AGT	.	.	none		0.537	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
CUL9	23113	hgsc.bcm.edu	37	6	43193877	43193877	+	IGR	SNP	G	G	A	rs7832	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:43193877G>A	ENST00000252050.4	+	0	7780				DNPH1_ENST00000230431.6_Silent_p.V90V|RP3-330M21.5_ENST00000500590.1_RNA|DNPH1_ENST00000393987.2_Silent_p.V90V	NM_015089.2	NP_055904.1	Q8IWT3	CUL9_HUMAN	cullin 9						microtubule cytoskeleton organization (GO:0000226)|protein ubiquitination (GO:0016567)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|liver(1)|lung(30)|ovary(5)|prostate(3)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(4)	92						CTTCTGCCACGACCACTGGGA	0.592													G|||	208	0.0415335	0.0023	0.0908	5008	,	,		21379	0.003		0.0706	False		,,,				2504	0.0695				p.V90V		Atlas-SNP	.											C6orf108_ENST00000393987,NS,carcinoma,0,2	.	.	2	0			c.C270T						PASS	.	G	,	85,4303		1,83,2110	30.0	24.0	26.0		270,270	-9.2	0.0	6	dbSNP_52	26	882,7688		43,796,3446	no	coding-synonymous,coding-synonymous	C6orf108	NM_006443.2,NM_199184.1	,	44,879,5556	AA,AG,GG		10.2917,1.9371,7.4626	,	90/175,90/149	43193877	967,11991	2194	4285	6479	SO:0001628	intergenic_variant	10591	exon3			TGCCACGACCACT	AB014608	CCDS4890.1	6p21.1	2011-05-24			ENSG00000112659	ENSG00000112659			15982	protein-coding gene	gene with protein product	"""parkin-like cytoplasmic p53 binding protein"", ""p53-associated parkin-like cytoplasmic protein"""	607489				17332328, 10521492, 12526791	Standard	NM_015089		Approved	H7AP1, KIAA0708, PARC	uc003ouk.3	Q8IWT3	OTTHUMG00000014723		6.37:g.43193877G>A		34.0	0.0	0		31.0	16.0	0.516129	NM_006443	O75188|Q5TCY3|Q68CP2|Q68D92|Q8N3W9|Q9BU56	Silent	SNP	ENST00000252050.4	37	CCDS4890.1																																																																																			G|0.942;A|0.058	0.058	strong		0.592	CUL9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040582.2	NM_015089	
MTUS1	57509	hgsc.bcm.edu	37	8	17513484	17513484	+	Missense_Mutation	SNP	T	T	C	rs61733708	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17513484T>C	ENST00000262102.6	-	9	3220	c.2996A>G	c.(2995-2997)gAa>gGa	p.E999G	MTUS1_ENST00000381861.3_Missense_Mutation_p.E246G|MTUS1_ENST00000381869.3_Missense_Mutation_p.E945G|MTUS1_ENST00000297488.6_Missense_Mutation_p.E165G|MTUS1_ENST00000518713.1_5'UTR|MTUS1_ENST00000400046.1_Missense_Mutation_p.E71G|MTUS1_ENST00000544260.1_Missense_Mutation_p.E144G|MTUS1_ENST00000519263.1_Missense_Mutation_p.E945G	NM_001001924.2	NP_001001924.1	Q9ULD2	MTUS1_HUMAN	microtubule associated tumor suppressor 1	999				E -> G (in Ref. 5; CAH56128). {ECO:0000305}.	cellular response to peptide hormone stimulus (GO:0071375)|regulation of macrophage chemotaxis (GO:0010758)	extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(14)|lung(8)|ovary(1)|skin(2)|urinary_tract(1)	36				Colorectal(111;0.0778)		TTCTGTTTTTTCAGCCTGGTG	0.418													T|||	15	0.00299521	0.0	0.0029	5008	,	,		19675	0.0		0.0129	False		,,,				2504	0.0				p.E999G		Atlas-SNP	.											.	MTUS1	144	.	0			c.A2996G						PASS	.	T	GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU,GLY/GLU	8,3748		0,8,1870	190.0	173.0	178.0		2996,2834,737,431,494	5.1	0.1	8	dbSNP_129	178	76,8168		1,74,4047	yes	missense,missense,missense,missense,missense	MTUS1	NM_001001924.2,NM_001001925.2,NM_001001931.2,NM_001166393.1,NM_020749.4	98,98,98,98,98	1,82,5917	CC,CT,TT		0.9219,0.213,0.7	benign,benign,benign,benign,benign	999/1271,945/1217,246/518,144/416,165/437	17513484	84,11916	1878	4122	6000	SO:0001583	missense	57509	exon9			GTTTTTTCAGCCT	AL096842	CCDS43716.1, CCDS43717.1, CCDS43718.1, CCDS43719.1, CCDS55204.1	8p22	2013-01-17	2009-10-20		ENSG00000129422	ENSG00000129422			29789	protein-coding gene	gene with protein product	"""AT2 receptor-interacting protein"", ""AT2R binding protein"", ""mitochondrial tumor suppressor gene 1"""	609589	"""mitochondrial tumor suppressor 1"""			10574462, 12692079	Standard	NM_001001931		Approved	MTSG1, KIAA1288, DKFZp586D1519, FLJ14295, ATIP1, MP44, ATBP, ICIS	uc003wxv.3	Q9ULD2	OTTHUMG00000163756	ENST00000262102.6:c.2996A>G	8.37:g.17513484T>C	ENSP00000262102:p.Glu999Gly	245.0	0.0	0		209.0	110.0	0.526316	NM_001001924	A8K135|B2RBJ6|B3KWJ9|B4DH03|B9EGA1|D3DSP8|Q63HJ6|Q659F4|Q6PK49|Q6URW7|Q8N4M6|Q8WTT9|Q9H7T2	Missense_Mutation	SNP	ENST00000262102.6	37	CCDS43717.1	12	0.005494505494505495	0	0.0	1	0.0027624309392265192	0	0.0	11	0.014511873350923483	T	18.28	3.589263	0.66105	0.00213	0.009219	ENSG00000129422	ENST00000381869;ENST00000544260;ENST00000400046;ENST00000297488;ENST00000381861;ENST00000262102;ENST00000519263	T;T;T;T;T;T;T	0.39056	1.1;1.1;1.6;1.1;1.1;1.1;1.1	5.13	5.13	0.70059	.	0.199759	0.51477	D	0.000098	T	0.45337	0.1337	M	0.79258	2.445	0.80722	D	1	P;P;B;B	0.40970	0.734;0.734;0.411;0.246	B;P;B;B	0.44946	0.302;0.465;0.281;0.157	T	0.58504	-0.7625	10	0.87932	D	0	-18.4737	15.2621	0.73631	0.0:0.0:0.0:1.0	rs61733708	945;999;246;165	Q9ULD2-2;Q9ULD2;Q9ULD2-6;Q9ULD2-3	.;MTUS1_HUMAN;.;.	G	945;144;71;165;246;999;945	ENSP00000371293:E945G;ENSP00000445738:E144G;ENSP00000382921:E71G;ENSP00000297488:E165G;ENSP00000371285:E246G;ENSP00000262102:E999G;ENSP00000430167:E945G	ENSP00000262102:E999G	E	-	2	0	MTUS1	17557764	1.000000	0.71417	0.086000	0.20670	0.802000	0.45316	7.411000	0.80078	2.079000	0.62486	0.482000	0.46254	GAA	T|0.992;C|0.008	0.008	strong		0.418	MTUS1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000375247.1	XM_372031	
LOXHD1	125336	hgsc.bcm.edu	37	18	44157746	44157746	+	Missense_Mutation	SNP	C	C	A	rs35088381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:44157746C>A	ENST00000398722.4	-	7	1059	c.1060G>T	c.(1060-1062)Ggc>Tgc	p.G354C	LOXHD1_ENST00000536736.1_Missense_Mutation_p.G632C|LOXHD1_ENST00000441551.2_Missense_Mutation_p.G632C			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	354	PLAT 3. {ECO:0000255|PROSITE- ProRule:PRU00152}.		G -> C (in dbSNP:rs35088381).		calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						AGGTACCAGCCGCTGCCGGAG	0.602													C|||	62	0.0123802	0.0113	0.013	5008	,	,		18925	0.0		0.0129	False		,,,				2504	0.0256				p.G632C		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G1894T						PASS	.	C	CYS/GLY	21,1363		0,21,671	36.0	49.0	45.0		1894	4.8	0.9	18	dbSNP_126	45	45,3137		0,45,1546	yes	missense	LOXHD1	NM_144612.6	159	0,66,2217	AA,AC,CC		1.4142,1.5173,1.4455	probably-damaging	632/2212	44157746	66,4500	692	1591	2283	SO:0001583	missense	125336	exon14			ACCAGCCGCTGCC	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1060G>T	18.37:g.44157746C>A	ENSP00000381707:p.Gly354Cys	85.0	0.0	0		88.0	45.0	0.511364	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		29|29	0.013278388278388278|0.013278388278388278	13|13	0.026422764227642278|0.026422764227642278	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	11.42|11.42	1.634805|1.634805	0.29068|0.29068	0.015173|0.015173	0.014142|0.014142	ENSG00000167210|ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000335730|ENST00000441551	T;T|.	0.65732|.	-0.17;-0.17|.	5.66|5.66	4.79|4.79	0.61399|0.61399	.|.	0.107620|.	0.64402|.	D|.	0.000008|.	T|T	0.70894|0.70894	0.3276|0.3276	H|H	0.94658|0.94658	3.565|3.565	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.83275|.	0.991;0.996|.	D|D	0.84597|0.84597	0.0670|0.0670	10|5	0.45353|.	T|.	0.12|.	.|.	14.4404|14.4404	0.67311|0.67311	0.0:0.9295:0.0:0.0705|0.0:0.9295:0.0:0.0705	rs35088381|rs35088381	632;354|.	F5GZB4;Q8IVV2-2|.	.;.|.	C|L	354;632;354|612	ENSP00000381707:G354C;ENSP00000444586:G632C|.	ENSP00000338222:G354C|.	G|R	-|-	1|2	0|0	LOXHD1|LOXHD1	42411744|42411744	1.000000|1.000000	0.71417|0.71417	0.894000|0.894000	0.35097|0.35097	0.335000|0.335000	0.28730|0.28730	7.701000|7.701000	0.84566|0.84566	1.391000|1.391000	0.46566|0.46566	0.561000|0.561000	0.74099|0.74099	GGC|CGG	C|0.984;A|0.016	0.016	strong		0.602	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
RECK	8434	hgsc.bcm.edu	37	9	36107981	36107981	+	Missense_Mutation	SNP	C	C	G	rs148296262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:36107981C>G	ENST00000377966.3	+	14	2151	c.1585C>G	c.(1585-1587)Ctg>Gtg	p.L529V		NM_021111.2	NP_066934.1	O95980	RECK_HUMAN	reversion-inducing-cysteine-rich protein with kazal motifs	529					blood vessel maturation (GO:0001955)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|negative regulation of endopeptidase activity (GO:0010951)	anchored component of membrane (GO:0031225)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase inhibitor activity (GO:0004866)|metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(7)|kidney(3)|large_intestine(6)|lung(10)|ovary(1)|pancreas(1)|skin(2)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(32;0.112)|STAD - Stomach adenocarcinoma(86;0.228)			AGGTTGCAAACTGGGAGAAGC	0.383													C|||	2	0.000399361	0.0	0.0	5008	,	,		17308	0.0		0.002	False		,,,				2504	0.0				p.L529V		Atlas-SNP	.											.	RECK	73	.	0			c.C1585G						PASS	.	C	VAL/LEU	6,4400	9.9+/-24.2	0,6,2197	92.0	84.0	87.0		1585	0.6	1.0	9	dbSNP_134	87	22,8578	16.0+/-53.3	0,22,4278	yes	missense	RECK	NM_021111.2	32	0,28,6475	GG,GC,CC		0.2558,0.1362,0.2153	possibly-damaging	529/972	36107981	28,12978	2203	4300	6503	SO:0001583	missense	8434	exon14			TGCAAACTGGGAG	E13833	CCDS6597.1	9p13.3	2008-05-15			ENSG00000122707	ENSG00000122707			11345	protein-coding gene	gene with protein product		605227		ST15		9789069	Standard	NM_021111		Approved	hRECK	uc003zyv.3	O95980	OTTHUMG00000019898	ENST00000377966.3:c.1585C>G	9.37:g.36107981C>G	ENSP00000367202:p.Leu529Val	97.0	0.0	0		92.0	45.0	0.48913	NM_021111	B2RNS1|Q5W0K6|Q8WX37	Missense_Mutation	SNP	ENST00000377966.3	37	CCDS6597.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	C	16.95	3.264660	0.59431	0.001362	0.002558	ENSG00000122707	ENST00000377966	T	0.56941	0.43	5.45	0.56	0.17279	.	0.000000	0.64402	D	0.000002	T	0.41282	0.1152	L	0.53561	1.675	0.39944	D	0.974446	P;P	0.48407	0.91;0.91	B;B	0.39217	0.294;0.294	T	0.34950	-0.9808	10	0.52906	T	0.07	-9.0488	8.2357	0.31625	0.0:0.3492:0.0:0.6508	.	529;529	A8K9D8;O95980	.;RECK_HUMAN	V	529	ENSP00000367202:L529V	ENSP00000367202:L529V	L	+	1	2	RECK	36097981	0.999000	0.42202	1.000000	0.80357	0.989000	0.77384	0.655000	0.24933	0.125000	0.18397	-0.302000	0.09304	CTG	C|0.997;G|0.003	0.003	strong		0.383	RECK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052409.1		
CAPN1	823	hgsc.bcm.edu	37	11	64981818	64981818	+	IGR	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:64981818C>T	ENST00000527323.1	+	0	3086				SLC22A20_ENST00000525437.1_RNA			P07384	CAN1_HUMAN	calpain 1, (mu/I) large subunit						extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell proliferation (GO:0008284)|proteolysis (GO:0006508)|receptor catabolic process (GO:0032801)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)			breast(2)|endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(1)|skin(1)	13		Lung NSC(402;0.094)|Melanoma(852;0.16)		Lung(977;0.00168)|LUSC - Lung squamous cell carcinoma(976;0.00813)		GTGTGAGGCCCGCACTCTCCG	0.662																																					p.R135C		Atlas-SNP	.											.	SLC22A20	36	.	0			c.C403T						PASS	.						35.0	39.0	38.0					11																	64981818		2065	4197	6262	SO:0001628	intergenic_variant	440044	exon2			GAGGCCCGCACTC	X04366	CCDS44644.1	11q13	2013-01-10			ENSG00000014216	ENSG00000014216	3.4.22.52	"""EF-hand domain containing"""	1476	protein-coding gene	gene with protein product		114220				3017764, 2209092	Standard	NM_005186		Approved	muCANP, muCL, CANP, CANPL1	uc009yqd.2	P07384	OTTHUMG00000165614		11.37:g.64981818C>T		62.0	0.0	0		72.0	45.0	0.625	NM_001004326	Q2TTR0|Q6DHV4	Missense_Mutation	SNP	ENST00000527323.1	37	CCDS44644.1																																																																																			.	.	none		0.662	CAPN1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385325.1		
KCNH4	23415	hgsc.bcm.edu	37	17	40312349	40312349	+	Silent	SNP	G	G	A	rs138917401	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:40312349G>A	ENST00000264661.3	-	16	3095	c.2763C>T	c.(2761-2763)tcC>tcT	p.S921S	KCNH4_ENST00000607371.1_Silent_p.S921S	NM_012285.2	NP_036417.1	Q9UQ05	KCNH4_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 4	921					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	phosphorelay sensor kinase activity (GO:0000155)|voltage-gated potassium channel activity (GO:0005249)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(6)|lung(15)|skin(2)|urinary_tract(1)	32		all_cancers(22;1.24e-06)|all_epithelial(22;4.33e-05)|Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.126)		GGGTCCAAGCGGAGCCTGCTG	0.647													G|||	11	0.00219649	0.0008	0.0043	5008	,	,		16423	0.0		0.004	False		,,,				2504	0.0031				p.S921S	NSCLC(117;707 1703 2300 21308 31858)	Atlas-SNP	.											.	KCNH4	105	.	0			c.C2763T						PASS	.	G		7,4399	12.9+/-30.5	0,7,2196	53.0	48.0	49.0		2763	-9.9	0.0	17	dbSNP_134	49	60,8540	36.9+/-92.0	1,58,4241	no	coding-synonymous	KCNH4	NM_012285.2		1,65,6437	AA,AG,GG		0.6977,0.1589,0.5151		921/1018	40312349	67,12939	2203	4300	6503	SO:0001819	synonymous_variant	23415	exon16			CCAAGCGGAGCCT	AB022698	CCDS11420.1	17q21	2012-07-05				ENSG00000089558		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6253	protein-coding gene	gene with protein product		604528				10455180, 16382104	Standard	NM_012285		Approved	Kv12.3, elk1	uc002hzb.2	Q9UQ05		ENST00000264661.3:c.2763C>T	17.37:g.40312349G>A		122.0	0.0	0		110.0	50.0	0.454545	NM_012285		Silent	SNP	ENST00000264661.3	37	CCDS11420.1																																																																																			G|0.996;A|0.004	0.004	strong		0.647	KCNH4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000449791.2	NM_012285	
MYO1E	4643	hgsc.bcm.edu	37	15	59500970	59500970	+	Silent	SNP	C	C	T	rs117265950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:59500970C>T	ENST00000288235.4	-	14	1839	c.1440G>A	c.(1438-1440)acG>acA	p.T480T		NM_004998.3	NP_004989.2	Q12965	MYO1E_HUMAN	myosin IE	480	Myosin motor.				actin filament-based movement (GO:0030048)|ATP catabolic process (GO:0006200)|endocytosis (GO:0006897)|glomerular basement membrane development (GO:0032836)|glomerular filtration (GO:0003094)|glomerular visceral epithelial cell development (GO:0072015)|in utero embryonic development (GO:0001701)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|post-embryonic hemopoiesis (GO:0035166)|vasculogenesis (GO:0001570)	actin cytoskeleton (GO:0015629)|adherens junction (GO:0005912)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(6)|lung(10)|pancreas(2)|prostate(1)|urinary_tract(1)	33				all cancers(107;0.207)		TCTGGAGCAGCGTCTGATCTG	0.532													c|||	47	0.00938498	0.0015	0.0086	5008	,	,		19011	0.0		0.0149	False		,,,				2504	0.0245				p.T480T		Atlas-SNP	.											.	MYO1E	99	.	0			c.G1440A						PASS	.	T		10,4372	16.8+/-37.8	0,10,2181	176.0	148.0	157.0		1440	-10.7	0.2	15	dbSNP_132	157	116,8464	61.0+/-122.8	2,112,4176	no	coding-synonymous	MYO1E	NM_004998.2		2,122,6357	TT,TC,CC		1.352,0.2282,0.9721		480/1109	59500970	126,12836	2191	4290	6481	SO:0001819	synonymous_variant	4643	exon14			GAGCAGCGTCTGA	U14391	CCDS32254.1	15q21-q22	2011-09-27				ENSG00000157483		"""Myosins / Myosin superfamily : Class I"""	7599	protein-coding gene	gene with protein product	"""myosin-IC"""	601479				8884266	Standard	NM_004998		Approved	MYO1C, HuncM-IC, MGC104638	uc002aga.4	Q12965		ENST00000288235.4:c.1440G>A	15.37:g.59500970C>T		152.0	0.0	0		158.0	63.0	0.398734	NM_004998	Q14778	Silent	SNP	ENST00000288235.4	37	CCDS32254.1																																																																																			C|0.991;T|0.009	0.009	strong		0.532	MYO1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416024.1	NM_004998	
EPB41L2	2037	hgsc.bcm.edu	37	6	131186718	131186718	+	Silent	SNP	T	T	A	rs149001048		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:131186718T>A	ENST00000337057.3	-	17	2968	c.2787A>T	c.(2785-2787)acA>acT	p.T929T	EPB41L2_ENST00000525271.1_Intron|EPB41L2_ENST00000527659.1_Silent_p.T735T|EPB41L2_ENST00000529208.1_Silent_p.T859T|EPB41L2_ENST00000368128.2_Silent_p.T929T|EPB41L2_ENST00000530757.1_Intron|EPB41L2_ENST00000527411.1_Silent_p.T859T|EPB41L2_ENST00000392427.3_Intron|EPB41L2_ENST00000524581.1_Silent_p.T307T|EPB41L2_ENST00000531410.1_Silent_p.T50T|EPB41L2_ENST00000528282.1_Silent_p.T671T|EPB41L2_ENST00000445890.2_Silent_p.T671T|EPB41L2_ENST00000530481.1_Silent_p.T776T|EPB41L2_ENST00000525193.1_Silent_p.T630T	NM_001431.3	NP_001422.1	O43491	E41L2_HUMAN	erythrocyte membrane protein band 4.1-like 2	929	C-terminal (CTD).				cortical actin cytoskeleton organization (GO:0030866)	extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|focal adhesion (GO:0005925)|plasma membrane (GO:0005886)|spectrin (GO:0008091)	structural molecule activity (GO:0005198)			autonomic_ganglia(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(7)|lung(23)|prostate(1)|skin(2)	44	Breast(56;0.0639)			OV - Ovarian serous cystadenocarcinoma(155;0.0271)|GBM - Glioblastoma multiforme(226;0.0355)		CGGACTCAGATGTGATGGTTT	0.458													T|||	1	0.000199681	0.0	0.0	5008	,	,		5461	0.0		0.001	False		,,,				2504	0.0				p.T929T		Atlas-SNP	.											.	EPB41L2	96	.	0			c.A2787T						PASS	.						357.0	260.0	293.0					6																	131186718		2203	4300	6503	SO:0001819	synonymous_variant	2037	exon17			CTCAGATGTGATG	AF027299	CCDS5141.1, CCDS47474.1, CCDS56450.1, CCDS59037.1	6q23	2008-08-29			ENSG00000079819	ENSG00000079819			3379	protein-coding gene	gene with protein product		603237				9598318, 9828140	Standard	NM_001431		Approved	4.1-G	uc003qch.2	O43491	OTTHUMG00000015560	ENST00000337057.3:c.2787A>T	6.37:g.131186718T>A		247.0	0.0	0		154.0	19.0	0.123377	NM_001431	B4DHI8|E9PPD9|Q5T4F0|Q68DV2	Silent	SNP	ENST00000337057.3	37	CCDS5141.1																																																																																			T|1.000;A|0.000	0.000	strong		0.458	EPB41L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042204.3		
HEG1	57493	hgsc.bcm.edu	37	3	124746237	124746237	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124746237A>T	ENST00000311127.4	-	3	792	c.725T>A	c.(724-726)cTg>cAg	p.L242Q		NM_020733.1	NP_065784.1	Q9ULI3	HEG1_HUMAN	heart development protein with EGF-like domains 1	242					cardiac atrium morphogenesis (GO:0003209)|cell-cell junction assembly (GO:0007043)|endothelial cell morphogenesis (GO:0001886)|in utero embryonic development (GO:0001701)|lung development (GO:0030324)|lymph circulation (GO:0003017)|lymph vessel development (GO:0001945)|multicellular organism growth (GO:0035264)|pericardium development (GO:0060039)|post-embryonic development (GO:0009791)|regulation of body fluid levels (GO:0050878)|vasculogenesis (GO:0001570)|venous blood vessel morphogenesis (GO:0048845)|ventricular septum development (GO:0003281)	cell-cell junction (GO:0005911)|external side of plasma membrane (GO:0009897)|extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(24)|ovary(2)|urinary_tract(4)	47						TTCTTCTGACAGCCCCATCGC	0.547																																					p.L242Q		Atlas-SNP	.											.	HEG1	109	.	0			c.T725A						PASS	.						66.0	67.0	66.0					3																	124746237		1989	4156	6145	SO:0001583	missense	57493	exon3			TCTGACAGCCCCA	AK074987	CCDS46898.1	3q21.2	2013-03-08	2013-03-08		ENSG00000173706	ENSG00000173706			29227	protein-coding gene	gene with protein product	"""heart of glass"""	614182	"""HEG homolog 1 (zebrafish)"""			10574462, 19151727, 23007647	Standard	NM_020733		Approved	KIAA1237, HEG	uc003ehs.4	Q9ULI3	OTTHUMG00000159486	ENST00000311127.4:c.725T>A	3.37:g.124746237A>T	ENSP00000311502:p.Leu242Gln	199.0	0.0	0		213.0	106.0	0.497653	NM_020733	Q6NX66|Q8NC40|Q9BSV0	Missense_Mutation	SNP	ENST00000311127.4	37	CCDS46898.1	.	.	.	.	.	.	.	.	.	.	A	18.45	3.626598	0.66901	.	.	ENSG00000173706	ENST00000311127	T	0.42513	0.97	4.69	3.54	0.40534	.	.	.	.	.	T	0.53334	0.1790	L	0.60455	1.87	0.26084	N	0.981056	D;D	0.67145	0.996;0.994	D;D	0.69479	0.964;0.922	T	0.37267	-0.9713	9	0.27785	T	0.31	.	6.9296	0.24434	0.8966:0.0:0.1034:0.0	.	242;242	Q9ULI3-2;Q9ULI3	.;HEG1_HUMAN	Q	242	ENSP00000311502:L242Q	ENSP00000311502:L242Q	L	-	2	0	HEG1	126228927	0.000000	0.05858	0.750000	0.31169	0.261000	0.26267	0.557000	0.23454	0.931000	0.37242	0.528000	0.53228	CTG	.	.	none		0.547	HEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355732.2	XM_087386	
MRPL40	64976	hgsc.bcm.edu	37	22	19423257	19423257	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19423257G>A	ENST00000333130.3	+	4	1046	c.393G>A	c.(391-393)atG>atA	p.M131I	MRPL40_ENST00000443660.1_3'UTR|HIRA_ENST00000546308.1_Intron|HIRA_ENST00000541063.1_Intron	NM_003776.2	NP_003767.2	Q9NQ50	RM40_HUMAN	mitochondrial ribosomal protein L40	131					anatomical structure morphogenesis (GO:0009653)	mitochondrial ribosome (GO:0005761)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|upper_aerodigestive_tract(1)	2	Colorectal(54;0.0993)					AGCGTAAGATGGAGAGGGACA	0.567																																					p.M131I		Atlas-SNP	.											.	MRPL40	13	.	0			c.G393A						PASS	.						145.0	147.0	146.0					22																	19423257		2203	4300	6503	SO:0001583	missense	64976	exon4			TAAGATGGAGAGG	AB051624	CCDS13760.1	22q11.2	2012-09-13	2002-11-13		ENSG00000185608	ENSG00000185608		"""Mitochondrial ribosomal proteins / large subunits"""	14491	protein-coding gene	gene with protein product		605089	"""nuclear localization signal deleted in velocardiofacial syndrome"""	NLVCF		9790763, 11543634	Standard	NM_003776		Approved	MRP-L22	uc002zpg.3	Q9NQ50	OTTHUMG00000150136	ENST00000333130.3:c.393G>A	22.37:g.19423257G>A	ENSP00000333401:p.Met131Ile	118.0	0.0	0		120.0	5.0	0.0416667	NM_003776	B3KVZ7|O95134	Missense_Mutation	SNP	ENST00000333130.3	37	CCDS13760.1	.	.	.	.	.	.	.	.	.	.	G	8.714	0.912730	0.17907	.	.	ENSG00000185608	ENST00000333130	T	0.43294	0.95	5.22	-0.486	0.12064	.	0.620008	0.17767	N	0.162711	T	0.28433	0.0703	L	0.56769	1.78	0.35764	D	0.820406	B	0.14012	0.009	B	0.17098	0.017	T	0.11941	-1.0567	10	0.17832	T	0.49	-1.0103	1.306	0.02088	0.445:0.1498:0.2525:0.1527	.	131	Q9NQ50	RM40_HUMAN	I	131	ENSP00000333401:M131I	ENSP00000333401:M131I	M	+	3	0	MRPL40	17803257	0.988000	0.35896	0.439000	0.26833	0.259000	0.26198	0.659000	0.24994	0.366000	0.24427	-0.251000	0.11542	ATG	.	.	none		0.567	MRPL40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316491.2	NM_003776	
OTOP3	347741	hgsc.bcm.edu	37	17	72943184	72943184	+	Missense_Mutation	SNP	C	C	T	rs142183564	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:72943184C>T	ENST00000328801.4	+	6	1234	c.1234C>T	c.(1234-1236)Cgc>Tgc	p.R412C		NM_178233.1	NP_839947.1	Q7RTS5	OTOP3_HUMAN	otopetrin 3	412						integral component of membrane (GO:0016021)	metal ion binding (GO:0046872)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(5)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	23	all_lung(278;0.151)|Lung NSC(278;0.185)					GAACCCTACCCGCAGCCTGGA	0.622																																					p.R412C		Atlas-SNP	.											.	OTOP3	64	.	0			c.C1234T						PASS	.	C	CYS/ARG	1,4405	2.1+/-5.4	0,1,2202	94.0	92.0	93.0		1234	4.5	1.0	17	dbSNP_134	93	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OTOP3	NM_178233.1	180	0,5,6498	TT,TC,CC		0.0465,0.0227,0.0384	probably-damaging	412/597	72943184	5,13001	2203	4300	6503	SO:0001583	missense	347741	exon6			CCTACCCGCAGCC	BK000568	CCDS11709.1	17q25	2004-01-19				ENSG00000182938			19658	protein-coding gene	gene with protein product		607828				12651873	Standard	NM_178233		Approved		uc010wrr.3	Q7RTS5		ENST00000328801.4:c.1234C>T	17.37:g.72943184C>T	ENSP00000328090:p.Arg412Cys	66.0	0.0	0		83.0	42.0	0.506024	NM_178233		Missense_Mutation	SNP	ENST00000328801.4	37	CCDS11709.1	.	.	.	.	.	.	.	.	.	.	C	17.93	3.508979	0.64410	2.27E-4	4.65E-4	ENSG00000182938	ENST00000328801	T	0.22743	1.94	4.54	4.54	0.55810	.	0.000000	0.64402	D	0.000001	T	0.52208	0.1720	M	0.86028	2.79	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.62793	-0.6779	10	0.87932	D	0	-16.6297	17.2793	0.87124	0.0:1.0:0.0:0.0	.	412	Q7RTS5	OTOP3_HUMAN	C	412	ENSP00000328090:R412C	ENSP00000328090:R412C	R	+	1	0	OTOP3	70454779	1.000000	0.71417	1.000000	0.80357	0.834000	0.47266	4.414000	0.59802	2.073000	0.62155	0.462000	0.41574	CGC	C|0.999;T|0.001	0.001	strong		0.622	OTOP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445308.1	NM_178233	
ABLIM3	22885	hgsc.bcm.edu	37	5	148596547	148596547	+	Missense_Mutation	SNP	C	C	T	rs116226381	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:148596547C>T	ENST00000506113.1	+	7	1177	c.695C>T	c.(694-696)aCc>aTc	p.T232I	RP11-331K21.1_ENST00000522685.1_RNA|RP11-331K21.1_ENST00000512647.2_RNA|AC012613.2_ENST00000523176.1_RNA|ABLIM3_ENST00000326685.7_Missense_Mutation_p.T232I|ABLIM3_ENST00000508983.1_Missense_Mutation_p.T232I|ABLIM3_ENST00000504238.1_Missense_Mutation_p.T232I|ABLIM3_ENST00000356541.3_Missense_Mutation_p.T232I|ABLIM3_ENST00000309868.7_Missense_Mutation_p.T232I			O94929	ABLM3_HUMAN	actin binding LIM protein family, member 3	232	LIM zinc-binding 4. {ECO:0000255|PROSITE- ProRule:PRU00125}.				actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|cilium assembly (GO:0042384)|lamellipodium assembly (GO:0030032)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|lamellipodium (GO:0030027)|stress fiber (GO:0001725)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(7)|lung(13)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	34			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TACCACCCAACCTGTGCCAGG	0.522													C|||	10	0.00199681	0.0008	0.0	5008	,	,		21664	0.0		0.005	False		,,,				2504	0.0041				p.T232I		Atlas-SNP	.											.	ABLIM3	91	.	0			c.C695T						PASS	.	C	ILE/THR	2,4404	4.2+/-10.8	0,2,2201	94.0	81.0	85.0		695	2.6	1.0	5	dbSNP_132	85	46,8554	30.1+/-81.4	0,46,4254	yes	missense	ABLIM3	NM_014945.2	89	0,48,6455	TT,TC,CC		0.5349,0.0454,0.3691	benign	232/684	148596547	48,12958	2203	4300	6503	SO:0001583	missense	22885	exon8			ACCCAACCTGTGC	AB020650	CCDS4294.1	5q33.1	2008-02-05			ENSG00000173210	ENSG00000173210			29132	protein-coding gene	gene with protein product		611305					Standard	XM_005268392		Approved	KIAA0843	uc003lpy.2	O94929	OTTHUMG00000129932	ENST00000506113.1:c.695C>T	5.37:g.148596547C>T	ENSP00000425394:p.Thr232Ile	106.0	0.0	0		79.0	39.0	0.493671	NM_014945	A8K121|Q19VH3|Q658S1|Q68CI5|Q9BV32	Missense_Mutation	SNP	ENST00000506113.1	37	CCDS4294.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	C	15.76	2.928929	0.52759	4.54E-4	0.005349	ENSG00000173210	ENST00000326685;ENST00000356541;ENST00000309868;ENST00000506113;ENST00000504238;ENST00000508983	D;D;D;D;D;D	0.87491	-2.26;-2.26;-2.26;-2.26;-2.26;-2.26	5.49	2.56	0.30785	Zinc finger, LIM-type (5);	0.416904	0.28192	N	0.016242	T	0.81851	0.4910	M	0.77820	2.39	0.28363	N	0.920359	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.13407	0.001;0.001;0.009	T	0.79105	-0.1940	10	0.72032	D	0.01	.	10.4399	0.44460	0.0:0.6783:0.2521:0.0696	.	232;232;232	O94929-3;O94929-2;O94929	.;.;ABLM3_HUMAN	I	232	ENSP00000315841:T232I;ENSP00000348938:T232I;ENSP00000310309:T232I;ENSP00000425394:T232I;ENSP00000421183:T232I;ENSP00000420855:T232I	ENSP00000310309:T232I	T	+	2	0	ABLIM3	148576740	0.957000	0.32711	0.991000	0.47740	0.991000	0.79684	3.543000	0.53633	0.790000	0.33803	0.655000	0.94253	ACC	C|0.997;T|0.003	0.003	strong		0.522	ABLIM3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373435.1	NM_014945	
USP6	9098	hgsc.bcm.edu	37	17	5039138	5039138	+	Silent	SNP	C	C	T	rs3213878	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5039138C>T	ENST00000574788.1	+	17	2809	c.579C>T	c.(577-579)acC>acT	p.T193T	USP6_ENST00000304328.5_5'UTR|USP6_ENST00000332776.4_Silent_p.T193T|USP6_ENST00000250066.6_Silent_p.T193T			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	193	Rab-GAP TBC. {ECO:0000255|PROSITE- ProRule:PRU00163}.				cellular protein modification process (GO:0006464)|protein deubiquitination (GO:0016579)|regulation of vesicle-mediated transport (GO:0060627)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	calmodulin binding (GO:0005516)|cysteine-type endopeptidase activity (GO:0004197)|nucleic acid binding (GO:0003676)|Rab GTPase activator activity (GO:0005097)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	34						GCCACATCACCGCCTTGTTCC	0.607			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts								C|||	490	0.0978435	0.1853	0.0375	5008	,	,		20475	0.0774		0.1143	False		,,,				2504	0.0266				p.T193T		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C579T						PASS	.	C		682,3724	287.2+/-279.2	60,562,1581	126.0	110.0	115.0		579	-1.7	0.2	17	dbSNP_106	115	949,7651	208.0+/-249.6	52,845,3403	no	coding-synonymous	USP6	NM_004505.2		112,1407,4984	TT,TC,CC		11.0349,15.4789,12.5404		193/1407	5039138	1631,11375	2203	4300	6503	SO:0001819	synonymous_variant	9098	exon9			CATCACCGCCTTG	X63547	CCDS11069.2	17p13	2014-06-12	2014-06-12		ENSG00000129204	ENSG00000129204	3.4.19.12	"""Ubiquitin-specific peptidases"""	12629	protein-coding gene	gene with protein product	"""ubiquitin carboxyl-terminal hydrolase 6"", ""TBC1D3 and USP32 fusion"", ""Tre-2 oncogene"""	604334	"""ubiquitin specific protease 6 (Tre-2 oncogene)"", ""TRE oncogene, Smith Magenis syndrome chromosome region"", ""ubiquitin specific peptidase 6 (Tre-2 oncogene)"""	HRP1, TRESMCR		12838346, 1349106	Standard	NM_004505		Approved	Tre-2, TRE17, Tre2	uc002gav.1	P35125	OTTHUMG00000099449	ENST00000574788.1:c.579C>T	17.37:g.5039138C>T		12.0	0.0	0		14.0	7.0	0.5	NM_004505	Q15634|Q86WP6|Q8IWT4	Silent	SNP	ENST00000574788.1	37	CCDS11069.2																																																																																			C|0.883;T|0.117	0.117	strong		0.607	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
ART3	419	hgsc.bcm.edu	37	4	77003484	77003484	+	Missense_Mutation	SNP	G	G	A	rs142545952	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:77003484G>A	ENST00000355810.4	+	3	696	c.577G>A	c.(577-579)Gct>Act	p.A193T	ART3_ENST00000513494.1_3'UTR|ART3_ENST00000341029.5_Missense_Mutation_p.A193T|ART3_ENST00000349321.3_Missense_Mutation_p.A193T	NM_001130016.2	NP_001123488.1	Q13508	NAR3_HUMAN	ADP-ribosyltransferase 3	193					protein ADP-ribosylation (GO:0006471)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	NAD(P)+-protein-arginine ADP-ribosyltransferase activity (GO:0003956)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.A193T(1)		autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|stomach(1)	16			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			CAAACCTCAGGCTGCTAATGA	0.403																																					p.A193T		Atlas-SNP	.											ART3,NS,carcinoma,0,1	ART3	34	1	1	Substitution - Missense(1)	lung(1)	c.G577A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA	0,4406		0,0,2203	46.0	43.0	44.0		577,577,577	1.0	0.0	4	dbSNP_134	44	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense,missense	ART3	NM_001130016.1,NM_001130017.1,NM_001179.4	58,58,58	0,4,6499	AA,AG,GG		0.0465,0.0,0.0308	benign,benign,benign	193/390,193/368,193/379	77003484	4,13002	2203	4300	6503	SO:0001583	missense	419	exon3			CCTCAGGCTGCTA	X95827	CCDS3575.1, CCDS47079.1, CCDS47080.1	4q21.1	2008-05-15			ENSG00000156219	ENSG00000156219			725	protein-coding gene	gene with protein product		603086				9119374	Standard	NM_001130017		Approved		uc003hjo.3	Q13508	OTTHUMG00000130110	ENST00000355810.4:c.577G>A	4.37:g.77003484G>A	ENSP00000348064:p.Ala193Thr	77.0	0.0	0		96.0	40.0	0.416667	NM_001130017	Q53XW3|Q6FHT7|Q8WVJ7|Q93069|Q96HL1	Missense_Mutation	SNP	ENST00000355810.4	37	CCDS47079.1	.	.	.	.	.	.	.	.	.	.	G	3.557	-0.090400	0.07053	0.0	4.65E-4	ENSG00000156219	ENST00000341029;ENST00000513122;ENST00000355810;ENST00000349321	T;T;T;T	0.14766	2.48;2.48;2.48;2.48	6.04	1.03	0.20045	.	0.443020	0.25575	N	0.029735	T	0.10121	0.0248	L	0.46157	1.445	0.09310	N	1	B;B;P;B;B;B	0.34977	0.007;0.003;0.478;0.015;0.023;0.254	B;B;B;B;B;B	0.31390	0.019;0.007;0.129;0.038;0.016;0.098	T	0.21518	-1.0243	9	.	.	.	-6.6012	7.7094	0.28669	0.2965:0.1213:0.5823:0.0	.	163;193;193;193;193;193	D6RBN3;E7ESB3;B4DHX3;Q13508;Q13508-3;Q13508-2	.;.;.;NAR3_HUMAN;.;.	T	193	ENSP00000343843:A193T;ENSP00000422287:A193T;ENSP00000348064:A193T;ENSP00000304313:A193T	.	A	+	1	0	ART3	77222508	0.002000	0.14202	0.000000	0.03702	0.015000	0.08874	0.959000	0.29240	0.154000	0.19237	-0.251000	0.11542	GCT	G|1.000;A|0.000	0.000	strong		0.403	ART3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252416.2	NM_001179	
SLC12A9	56996	hgsc.bcm.edu	37	7	100464053	100464053	+	Silent	SNP	G	G	A	rs199582669	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100464053G>A	ENST00000354161.3	+	14	2696	c.2571G>A	c.(2569-2571)gaG>gaA	p.E857E	TRIP6_ENST00000200457.4_5'Flank	NM_020246.3	NP_064631.2	Q9BXP2	S12A9_HUMAN	solute carrier family 12, member 9	857				E -> K (in Ref. 3; BAB40456). {ECO:0000305}.	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)					GTGGGCCGGAGGGTGGGGATG	0.736													G|||	19	0.00379393	0.0	0.0058	5008	,	,		9921	0.001		0.0089	False		,,,				2504	0.0051				p.E857E		Atlas-SNP	.											.	SLC12A9	81	.	0			c.G2571A						PASS	.	G		7,4113		0,7,2053	11.0	12.0	12.0		2571	-0.8	0.0	7		12	77,7943		0,77,3933	no	coding-synonymous	SLC12A9	NM_020246.2		0,84,5986	AA,AG,GG		0.9601,0.1699,0.6919		857/915	100464053	84,12056	2060	4010	6070	SO:0001819	synonymous_variant	56996	exon14			GCCGGAGGGTGGG	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.2571G>A	7.37:g.100464053G>A		16.0	0.0	0		18.0	8.0	0.444444	NM_020246	B7Z740|D6W5X0|D6W5X2|F5H8C2|Q9BWL2|Q9BXP1|Q9BYI0|Q9NQR5	Silent	SNP	ENST00000354161.3	37	CCDS5707.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	1	0.0017482517482517483	6	0.0079155672823219	G	2.646	-0.283100	0.05642	0.001699	0.009601	ENSG00000146828	ENST00000539308	.	.	.	4.7	-0.816	0.10839	.	.	.	.	.	T	0.50086	0.1595	.	.	.	0.40595	D	0.981521	.	.	.	.	.	.	T	0.57195	-0.7853	5	0.87932	D	0	.	5.1517	0.15013	0.2797:0.2866:0.4337:0.0	.	.	.	.	R	483	.	ENSP00000442859:G483R	G	+	1	0	SLC12A9	100301989	0.977000	0.34250	0.023000	0.16930	0.499000	0.33736	0.261000	0.18442	-0.044000	0.13491	0.555000	0.69702	GGG	G|0.995;A|0.005	0.005	strong		0.736	SLC12A9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342837.1	NM_020246	
MT-ND6	4541	hgsc.bcm.edu	37	M	14311	14311	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrM:14311T>C	ENST00000361681.2	-	1	362	c.363A>G	c.(361-363)gtA>gtG	p.V121V	MT-CYB_ENST00000361789.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03923	NU6M_HUMAN	mitochondrially encoded NADH dehydrogenase 6	121					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						ATTCAGCTTCCTACACTATTA	0.468																																					p.V121V		Atlas-SNP	.											.	.	.	.	0			c.A363G						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			GCTTCCTACACTA			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.363A>G	M.37:g.14311T>C		7.0	0.0	0		8.0	8.0	1	ENST00000361681	Q34774|Q8HG30	Silent	SNP	ENST00000361681.2	37																																																																																				.	.	none		0.468	MT-ND6-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024037	
PRDM16	63976	hgsc.bcm.edu	37	1	3329037	3329037	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:3329037G>A	ENST00000270722.5	+	9	2325	c.2276G>A	c.(2275-2277)cGg>cAg	p.R759Q	PRDM16_ENST00000512462.1_3'UTR|PRDM16_ENST00000442529.2_Missense_Mutation_p.R759Q|PRDM16_ENST00000511072.1_Missense_Mutation_p.R760Q|PRDM16_ENST00000378391.2_Missense_Mutation_p.R759Q|PRDM16_ENST00000514189.1_Missense_Mutation_p.R760Q|PRDM16_ENST00000378398.3_Missense_Mutation_p.R760Q|PRDM16_ENST00000441472.2_Missense_Mutation_p.R759Q			Q9HAZ2	PRD16_HUMAN	PR domain containing 16	759	Interaction with CTBP1 and CTBP2. {ECO:0000250}.|Mediates interaction with SKI and regulation of TGF-beta signaling.				brown fat cell differentiation (GO:0050873)|negative regulation of granulocyte differentiation (GO:0030853)|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)|neurogenesis (GO:0022008)|palate development (GO:0060021)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cellular respiration (GO:0043457)|somatic stem cell maintenance (GO:0035019)|tongue development (GO:0043586)|transcription, DNA-templated (GO:0006351)|white fat cell differentiation (GO:0050872)	nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)			breast(4)|central_nervous_system(1)|endometrium(5)|kidney(4)|large_intestine(7)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(3)	59	all_cancers(77;0.00208)|all_epithelial(69;0.000732)|Ovarian(185;0.0634)|Lung NSC(156;0.109)|all_lung(157;0.111)	all_epithelial(116;2.03e-21)|all_lung(118;7.55e-09)|Lung NSC(185;1.28e-06)|Breast(487;0.000792)|Renal(390;0.00137)|Hepatocellular(190;0.00515)|Myeloproliferative disorder(586;0.0267)|Ovarian(437;0.0365)|Lung SC(97;0.114)|Medulloblastoma(700;0.134)		Epithelial(90;5.59e-35)|OV - Ovarian serous cystadenocarcinoma(86;1.99e-20)|GBM - Glioblastoma multiforme(42;3.72e-11)|Colorectal(212;0.000425)|BRCA - Breast invasive adenocarcinoma(365;0.000946)|COAD - Colon adenocarcinoma(227;0.000968)|Kidney(185;0.00155)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0175)|Lung(427;0.137)		AAGTCACCCCGGGACGCCCTC	0.652			T	EVI1	"""MDS, AML"""																																p.R759Q		Atlas-SNP	.		Dom	yes		1	1p36.23-p33	63976	PR domain containing 16		L	PRDM16,NS,lymphoid_neoplasm,+1,1	PRDM16	147	1	0			c.G2276A						PASS	.						53.0	61.0	58.0					1																	3329037		2015	4158	6173	SO:0001583	missense	63976	exon9			CACCCCGGGACGC	AF294278	CCDS41236.1, CCDS44048.1, CCDS41236.2, CCDS44048.2	1p36.23-p33	2013-01-08			ENSG00000142611	ENSG00000142611		"""Zinc fingers, C2H2-type"""	14000	protein-coding gene	gene with protein product	"""MDS1/EVI1-like"", ""PR-domain zinc finger protein 16"", ""transcription factor MEL1"""	605557				11050005	Standard	NM_199454		Approved	MEL1, PFM13, KIAA1675, MGC166915	uc001akf.3	Q9HAZ2	OTTHUMG00000000581	ENST00000270722.5:c.2276G>A	1.37:g.3329037G>A	ENSP00000270722:p.Arg759Gln	70.0	0.0	0		85.0	77.0	0.905882	NM_022114	A6NHQ8|B1AJP7|B1AJP8|B1AJP9|B1WB48|Q8WYJ9|Q9C0I8	Missense_Mutation	SNP	ENST00000270722.5	37	CCDS41236.2	.	.	.	.	.	.	.	.	.	.	G	14.09	2.433145	0.43224	.	.	ENSG00000142611	ENST00000511072;ENST00000378398;ENST00000441472;ENST00000442529;ENST00000378391;ENST00000514189;ENST00000270722;ENST00000512462;ENST00000408992;ENST00000509860	T;T;T;T;T;T;T;T;T	0.05649	3.41;3.44;3.46;3.44;3.43;3.44;3.46;3.41;3.41	4.41	4.41	0.53225	.	0.000000	0.46758	U	0.000280	T	0.19208	0.0461	M	0.67953	2.075	0.51012	D	0.999903	D;D;D;D	0.76494	0.999;0.998;0.999;0.997	P;P;P;P	0.62184	0.75;0.821;0.899;0.667	T	0.10382	-1.0632	10	0.16420	T	0.52	.	17.3359	0.87281	0.0:0.0:1.0:0.0	.	759;759;759;759	Q9HAZ2;Q9HAZ2-2;F8WEV3;D3YTA5	PRD16_HUMAN;.;.;.	Q	760;760;759;759;759;760;759;575;575;568	ENSP00000426975:R760Q;ENSP00000367651:R760Q;ENSP00000407968:R759Q;ENSP00000405253:R759Q;ENSP00000367643:R759Q;ENSP00000421400:R760Q;ENSP00000270722:R759Q;ENSP00000422504:R575Q;ENSP00000425796:R568Q	ENSP00000270722:R759Q	R	+	2	0	PRDM16	3318897	1.000000	0.71417	1.000000	0.80357	0.557000	0.35523	4.285000	0.58989	2.169000	0.68431	0.453000	0.30009	CGG	.	.	none		0.652	PRDM16-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000001382.3	NM_022114	
IKBIP	121457	hgsc.bcm.edu	37	12	99007411	99007411	+	Silent	SNP	C	C	T	rs201283576	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:99007411C>T	ENST00000342502.2	-	3	1416	c.1005G>A	c.(1003-1005)gaG>gaA	p.E335E	IKBIP_ENST00000420861.1_Silent_p.E229E|IKBIP_ENST00000393042.3_3'UTR	NM_201612.2	NP_963906.1	Q70UQ0	IKIP_HUMAN	IKBKB interacting protein	335					response to X-ray (GO:0010165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|kidney(1)|large_intestine(1)|lung(1)|prostate(2)	6						TATCCTTAATCTCAGCTTGGA	0.308																																					p.E335E		Atlas-SNP	.											.	IKBIP	46	.	0			c.G1005A						PASS	.						52.0	58.0	56.0					12																	99007411		2199	4297	6496	SO:0001819	synonymous_variant	121457	exon3			CTTAATCTCAGCT	AJ539425	CCDS9067.1, CCDS9068.1, CCDS41822.1	12q23.1	2010-02-17			ENSG00000166130	ENSG00000166130			26430	protein-coding gene	gene with protein product	"""I kappa B kinase interacting protein"""	609861				15389287	Standard	NM_153687		Approved	FLJ31051, IKIP	uc001tfx.4	Q70UQ0	OTTHUMG00000170213	ENST00000342502.2:c.1005G>A	12.37:g.99007411C>T		45.0	0.0	0		47.0	15.0	0.319149	NM_201612	Q6ZWH4|Q70UP9|Q86V91|Q96ND2	Silent	SNP	ENST00000342502.2	37	CCDS9067.1																																																																																			C|0.999;A|0.001	.	alt		0.308	IKBIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000408003.2	NM_153687	
BRCA2	675	hgsc.bcm.edu	37	13	32914126	32914126	+	Missense_Mutation	SNP	C	C	G	rs80358784		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:32914126C>G	ENST00000380152.3	+	11	5867	c.5634C>G	c.(5632-5634)aaC>aaG	p.N1878K	BRCA2_ENST00000544455.1_Missense_Mutation_p.N1878K			P51587	BRCA2_HUMAN	breast cancer 2, early onset	1878					brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		AGGAAAACAACGAGAATAAAT	0.323			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											p.N1878K	Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	Atlas-SNP	.	yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	familial breast/ovarian cancer gene 2		"""L, E"""	.	BRCA2	812	.	0			c.C5634G						PASS	.						44.0	43.0	43.0					13																	32914126		2203	4300	6503	SO:0001583	missense	675	exon11	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	AAACAACGAGAAT	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.5634C>G	13.37:g.32914126C>G	ENSP00000369497:p.Asn1878Lys	81.0	0.0	0		61.0	27.0	0.442623	NM_000059	O00183|O15008|Q13879|Q5TBJ7	Missense_Mutation	SNP	ENST00000380152.3	37	CCDS9344.1	.	.	.	.	.	.	.	.	.	.	C	4.413	0.076344	0.08485	.	.	ENSG00000139618	ENST00000380152;ENST00000544455	T;T	0.68181	-0.31;-0.31	5.71	-5.99	0.02213	.	0.505217	0.19599	N	0.110421	T	0.29588	0.0738	N	0.08118	0	0.09310	N	1	B	0.15930	0.015	B	0.14578	0.011	T	0.32903	-0.9889	10	0.12766	T	0.61	.	0.9378	0.01348	0.3907:0.1216:0.2013:0.2864	.	1878	P51587	BRCA2_HUMAN	K	1878	ENSP00000369497:N1878K;ENSP00000439902:N1878K	ENSP00000369497:N1878K	N	+	3	2	BRCA2	31812126	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.132000	0.10467	-1.353000	0.02191	-0.295000	0.09555	AAC	C|0.999;T|0.001	.	weak		0.323	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
SMYD3	64754	hgsc.bcm.edu	37	1	246078851	246078851	+	Missense_Mutation	SNP	C	C	T	rs61762672	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:246078851C>T	ENST00000388985.4	-	8	793	c.794G>A	c.(793-795)cGt>cAt	p.R265H	SMYD3_ENST00000490107.1_Missense_Mutation_p.R206H|SMYD3_ENST00000366517.1_5'UTR|SMYD3_ENST00000541742.1_Missense_Mutation_p.R206H			Q9H7B4	SMYD3_HUMAN	SET and MYND domain containing 3	265					cellular response to dexamethasone stimulus (GO:0071549)|establishment of protein localization (GO:0045184)|myotube cell development (GO:0014904)|negative regulation of protein kinase activity (GO:0006469)|nucleosome assembly (GO:0006334)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|metal ion binding (GO:0046872)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II intronic transcription regulatory region sequence-specific DNA binding (GO:0001162)			breast(3)|large_intestine(5)|lung(8)|skin(1)	17	all_cancers(71;0.000291)|all_epithelial(71;0.000174)|Ovarian(71;0.0377)|all_lung(81;0.0568)|Lung NSC(105;0.0804)|Breast(184;0.173)|Melanoma(84;0.242)	all_cancers(173;0.0496)|Acute lymphoblastic leukemia(190;0.164)	OV - Ovarian serous cystadenocarcinoma(106;0.0129)	all cancers(4;0.028)|GBM - Glioblastoma multiforme(49;0.0537)		GGTTTGGCAACGGAAACAGTC	0.488													C|||	5	0.000998403	0.0	0.0029	5008	,	,		17129	0.0		0.003	False		,,,				2504	0.0				p.R265H		Atlas-SNP	.											.	SMYD3	77	.	0			c.G794A						PASS	.	C	HIS/ARG,HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	145.0	120.0	128.0		794,617	5.0	0.2	1	dbSNP_129	128	12,8588	8.4+/-32.0	0,12,4288	yes	missense,missense	SMYD3	NM_001167740.1,NM_022743.2	29,29	0,13,6490	TT,TC,CC		0.1395,0.0227,0.1	probably-damaging,probably-damaging	265/429,206/370	246078851	13,12993	2203	4300	6503	SO:0001583	missense	64754	exon8			TGGCAACGGAAAC	AK023594	CCDS31083.1	1q44	2011-07-01	2003-05-14	2003-05-16	ENSG00000185420	ENSG00000185420		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	15513	protein-coding gene	gene with protein product		608783	"""zinc finger, MYND domain containing 1"""	ZNFN3A1, ZMYND1			Standard	NM_022743		Approved	KMT3E	uc001ibl.3	Q9H7B4	OTTHUMG00000040508	ENST00000388985.4:c.794G>A	1.37:g.246078851C>T	ENSP00000373637:p.Arg265His	83.0	0.0	0		103.0	43.0	0.417476	NM_001167740	A8K0P0|B1AN38|Q86TL8|Q8N5Z6|Q96AI5	Missense_Mutation	SNP	ENST00000388985.4	37	CCDS53486.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	16.78	3.217791	0.58560	2.27E-4	0.001395	ENSG00000185420	ENST00000541742;ENST00000490107;ENST00000544586;ENST00000388985;ENST00000391836	T;T;T;T	0.30714	1.52;1.52;1.52;1.52	5.97	5.03	0.67393	.	0.287715	0.33438	N	0.004906	T	0.31765	0.0807	L	0.28400	0.85	0.20489	N	0.999892	D;D	0.89917	1.0;1.0	P;D	0.69142	0.865;0.962	T	0.09796	-1.0658	10	0.37606	T	0.19	-18.4741	12.7104	0.57086	0.1631:0.8369:0.0:0.0	rs61762672	265;76	Q9H7B4;B3KN46	SMYD3_HUMAN;.	H	206;206;95;265;76	ENSP00000444184:R206H;ENSP00000419184:R206H;ENSP00000373637:R265H;ENSP00000375712:R76H	ENSP00000373637:R265H	R	-	2	0	SMYD3	244145474	0.032000	0.19561	0.156000	0.22583	0.785000	0.44390	0.472000	0.22116	2.836000	0.97738	0.655000	0.94253	CGT	C|0.999;T|0.001	0.001	strong		0.488	SMYD3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_022743	
ZNF407	55628	hgsc.bcm.edu	37	18	72346701	72346701	+	Silent	SNP	T	T	C	rs146635665	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:72346701T>C	ENST00000299687.5	+	1	3726	c.3726T>C	c.(3724-3726)ggT>ggC	p.G1242G	ZNF407_ENST00000582337.1_Silent_p.G1242G|ZNF407_ENST00000577538.1_Silent_p.G1242G|ZNF407_ENST00000309902.6_Silent_p.G1242G	NM_017757.2	NP_060227.2	Q9C0G0	ZN407_HUMAN	zinc finger protein 407	1242					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(6)|kidney(7)|large_intestine(21)|lung(23)|ovary(4)|prostate(3)|upper_aerodigestive_tract(2)	67		Esophageal squamous(42;0.131)|Prostate(75;0.173)		BRCA - Breast invasive adenocarcinoma(31;0.184)		ACGGTGGAGGTGTTGTCCCCC	0.537													T|||	15	0.00299521	0.0	0.0058	5008	,	,		17029	0.0		0.007	False		,,,				2504	0.0041				p.G1242G		Atlas-SNP	.											.	ZNF407	231	.	0			c.T3726C						PASS	.	T	,,	5,4097		0,5,2046	53.0	61.0	58.0		3726,3726,3726	-6.3	0.0	18	dbSNP_134	58	48,8320		0,48,4136	yes	coding-synonymous,coding-synonymous,coding-synonymous	ZNF407	NM_001146189.1,NM_001146190.1,NM_017757.2	,,	0,53,6182	CC,CT,TT		0.5736,0.1219,0.425	,,	1242/1816,1242/1661,1242/2249	72346701	53,12417	2051	4184	6235	SO:0001819	synonymous_variant	55628	exon1			TGGAGGTGTTGTC	AB051490	CCDS45885.1, CCDS54191.1, CCDS58634.1	18q23	2013-01-08			ENSG00000215421	ENSG00000215421		"""Zinc fingers, C2H2-type"""	19904	protein-coding gene	gene with protein product		615894				11214970	Standard	NM_017757		Approved	FLJ20307, FLJ13839, KIAA1703	uc002llw.2	Q9C0G0		ENST00000299687.5:c.3726T>C	18.37:g.72346701T>C		72.0	0.0	0		58.0	27.0	0.465517	NM_001146190	B5MD54|Q96MY0|Q9H8A1|Q9NXD4|Q9NXD7	Silent	SNP	ENST00000299687.5	37	CCDS45885.1																																																																																			T|0.997;C|0.003	0.003	strong		0.537	ZNF407-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444903.1	NM_017757	
CFAP46	54777	hgsc.bcm.edu	37	10	134680921	134680921	+	Silent	SNP	A	A	G	rs141926275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134680921A>G	ENST00000368586.5	-	34	4801	c.4701T>C	c.(4699-4701)ccT>ccC	p.P1567P		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CAGGCTGGACAGGAAGTGTCT	0.537													a|||	145	0.0289537	0.0703	0.0144	5008	,	,		16426	0.002		0.0139	False		,,,				2504	0.0266				p.P1567P		Atlas-SNP	.											.	TTC40	100	.	0			c.T4701C						PASS	.																																			SO:0001819	synonymous_variant	54777	exon34			CTGGACAGGAAGT																												ENST00000368586.5:c.4701T>C	10.37:g.134680921A>G		143.0	0.0	0		152.0	71.0	0.467105	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			A|0.985;G|0.015	0.015	strong		0.537	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
DNAH7	56171	hgsc.bcm.edu	37	2	196825256	196825256	+	Silent	SNP	G	G	C	rs115124743	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:196825256G>C	ENST00000312428.6	-	18	2719	c.2619C>G	c.(2617-2619)gtC>gtG	p.V873V		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	873	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						AAAAAGAGGAGACTGTGGAGT	0.448													G|||	94	0.01877	0.0045	0.0389	5008	,	,		19851	0.0		0.0507	False		,,,				2504	0.0102				p.V873V		Atlas-SNP	.											.	DNAH7	512	.	0			c.C2619G						PASS	.	G		30,3736		0,30,1853	105.0	103.0	104.0		2619	2.4	0.8	2	dbSNP_132	104	347,7895		8,331,3782	no	coding-synonymous	DNAH7	NM_018897.2		8,361,5635	CC,CG,GG		4.2101,0.7966,3.1396		873/4025	196825256	377,11631	1883	4121	6004	SO:0001819	synonymous_variant	56171	exon18			AGAGGAGACTGTG	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.2619C>G	2.37:g.196825256G>C		161.0	0.0	0		163.0	74.0	0.453988	NM_018897	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Silent	SNP	ENST00000312428.6	37	CCDS42794.1																																																																																			G|0.969;C|0.031	0.031	strong		0.448	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3	NM_018897	
ERC2	26059	hgsc.bcm.edu	37	3	55922561	55922561	+	Missense_Mutation	SNP	T	T	G	rs61745935	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:55922561T>G	ENST00000288221.6	-	14	2675	c.2420A>C	c.(2419-2421)aAt>aCt	p.N807T		NM_015576.1	NP_056391.1	O15083	ERC2_HUMAN	ELKS/RAB6-interacting/CAST family member 2	807						cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|growth cone (GO:0030426)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)				breast(2)|endometrium(5)|large_intestine(6)|liver(1)|lung(14)|ovary(2)|urinary_tract(1)	31				KIRC - Kidney renal clear cell carcinoma(284;0.0667)|Kidney(284;0.0873)|OV - Ovarian serous cystadenocarcinoma(275;0.219)		CTCCAGTGCATTCATCAGTTC	0.502													T|||	2	0.000399361	0.0	0.0	5008	,	,		18713	0.0		0.002	False		,,,				2504	0.0				p.N805T		Atlas-SNP	.											ERC2_ENST00000288221,NS,carcinoma,+1,2	ERC2	221	2	0			c.A2414C						PASS	.	T	THR/ASN	2,4176		0,2,2087	220.0	226.0	224.0		2420	4.8	0.9	3	dbSNP_129	224	18,8410		0,18,4196	yes	missense	ERC2	NM_015576.1	65	0,20,6283	GG,GT,TT		0.2136,0.0479,0.1587	benign	807/958	55922561	20,12586	2089	4214	6303	SO:0001583	missense	26059	exon13			AGTGCATTCATCA	AB002376	CCDS46851.1	3p14.3	2006-08-14			ENSG00000187672	ENSG00000187672			31922	protein-coding gene	gene with protein product							Standard	NM_015576		Approved	CAST, CAST1, KIAA0378, SPBC110, Spc110, ELKSL	uc003dhr.1	O15083	OTTHUMG00000158390	ENST00000288221.6:c.2420A>C	3.37:g.55922561T>G	ENSP00000288221:p.Asn807Thr	213.0	0.0	0		226.0	117.0	0.517699	NM_015576	Q2T9F6|Q86TK4	Missense_Mutation	SNP	ENST00000288221.6	37	CCDS46851.1	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	T|T	3.251|3.251	-0.153272|-0.153272	0.06585|0.06585	4.79E-4|4.79E-4	0.002136|0.002136	ENSG00000187672|ENSG00000187672	ENST00000492584|ENST00000288221	.|T	.|0.42131	.|0.98	5.93|5.93	4.76|4.76	0.60689|0.60689	.|.	.|0.171337	.|0.51477	.|N	.|0.000089	T|T	0.30198|0.30198	0.0757|0.0757	L|L	0.34521|0.34521	1.04|1.04	0.35402|0.35402	D|D	0.791684|0.791684	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	T|T	0.28073|0.28073	-1.0055|-1.0055	5|10	.|0.14252	.|T	.|0.57	-14.0227|-14.0227	12.0725|12.0725	0.53624|0.53624	0.0:0.0:0.2732:0.7268|0.0:0.0:0.2732:0.7268	.|.	.|807	.|O15083	.|ERC2_HUMAN	L|T	454|807	.|ENSP00000288221:N807T	.|ENSP00000288221:N807T	M|N	-|-	1|2	0|0	ERC2|ERC2	55897601|55897601	0.378000|0.378000	0.25114|0.25114	0.875000|0.875000	0.34327|0.34327	0.574000|0.574000	0.36063|0.36063	0.622000|0.622000	0.24433|0.24433	1.037000|1.037000	0.40024|0.40024	-0.316000|-0.316000	0.08728|0.08728	ATG|AAT	T|0.999;G|0.001	0.001	strong		0.502	ERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350884.2	NM_015576	
IL31RA	133396	hgsc.bcm.edu	37	5	55147405	55147405	+	Missense_Mutation	SNP	A	A	C	rs75528518		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:55147405A>C	ENST00000447346.2	+	1	72	c.7A>C	c.(7-9)Atc>Ctc	p.I3L	IL31RA_ENST00000297015.3_5'Flank|IL31RA_ENST00000359040.5_Missense_Mutation_p.I3L|IL31RA_ENST00000354961.4_5'Flank|IL31RA_ENST00000396836.2_Missense_Mutation_p.I3L|IL31RA_ENST00000396834.1_5'UTR|IL31RA_ENST00000490985.1_5'Flank	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	0					cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				gggaatgtgcatcaggcaact	0.438																																					p.I3L		Atlas-SNP	.											.	IL31RA	84	.	0			c.A7C						PASS	.						133.0	138.0	136.0					5																	55147405		2024	4184	6208	SO:0001583	missense	133396	exon1			ATGTGCATCAGGC	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.7A>C	5.37:g.55147405A>C	ENSP00000415900:p.Ile3Leu	133.0	0.0	0		160.0	69.0	0.43125	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	.	4.977	0.181530	0.09495	.	.	ENSG00000164509	ENST00000396836;ENST00000447346;ENST00000359040	T;T;T	0.37915	1.33;1.2;1.17	2.33	-2.34	0.06704	.	1.884850	0.02918	N	0.137637	T	0.25865	0.0630	.	.	.	0.09310	N	1	B;B;B	0.19583	0.037;0.037;0.037	B;B;B	0.24541	0.036;0.054;0.054	T	0.28713	-1.0035	9	0.87932	D	0	.	2.59	0.04840	0.4946:0.0:0.1516:0.3539	.	3;3;3	Q8NI17-5;Q8NI17-2;Q8NI17-8	.;.;.	L	3	ENSP00000380048:I3L;ENSP00000415900:I3L;ENSP00000351935:I3L	ENSP00000351935:I3L	I	+	1	0	IL31RA	55183162	0.000000	0.05858	0.000000	0.03702	0.040000	0.13550	-0.332000	0.07904	-0.487000	0.06735	-0.415000	0.06103	ATC	.	.	alt		0.438	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
RDH8	50700	hgsc.bcm.edu	37	19	10124257	10124257	+	Silent	SNP	C	C	T	rs150712129	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10124257C>T	ENST00000171214.1	+	1	333	c.84C>T	c.(82-84)gaC>gaT	p.D28D	RDH8_ENST00000591589.1_Silent_p.D48D	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	28					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	TGGCCCATGACCCCAAGAAGC	0.612																																					p.D48D		Atlas-SNP	.											.	RDH8	51	.	0			c.C144T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	83.0	76.0	78.0		84	1.5	0.9	19	dbSNP_134	78	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	RDH8	NM_015725.2		0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154		28/312	10124257	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	50700	exon1			CCATGACCCCAAG	AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	14423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 28C, member 2"""	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.84C>T	19.37:g.10124257C>T		28.0	0.0	0		37.0	16.0	0.432432	NM_015725	Q9H838	Silent	SNP	ENST00000171214.1	37																																																																																				C|1.000;T|0.000	0.000	strong		0.612	RDH8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
CFAP46	54777	hgsc.bcm.edu	37	10	134671154	134671154	+	Silent	SNP	G	G	A	rs189775198	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134671154G>A	ENST00000368586.5	-	39	5614	c.5514C>T	c.(5512-5514)ggC>ggT	p.G1838G	TTC40_ENST00000263170.5_5'UTR	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CAGCCATGGCGCCCTGGGCCA	0.587													G|||	46	0.0091853	0.0	0.0072	5008	,	,		16138	0.002		0.0129	False		,,,				2504	0.0266				p.G1838G		Atlas-SNP	.											.	TTC40	100	.	0			c.C5514T						PASS	.	G		9,4397	15.5+/-35.6	0,9,2194	125.0	83.0	97.0		450	-1.4	0.0	10		97	82,8518	46.3+/-105.2	0,82,4218	no	coding-synonymous	C10orf92	NM_001200049.1		0,91,6412	AA,AG,GG		0.9535,0.2043,0.6997		150/1028	134671154	91,12915	2203	4300	6503	SO:0001819	synonymous_variant	54777	exon39			CATGGCGCCCTGG																												ENST00000368586.5:c.5514C>T	10.37:g.134671154G>A		131.0	0.0	0		132.0	60.0	0.454545	NM_001200049		Silent	SNP	ENST00000368586.5	37	CCDS58101.1																																																																																			G|0.991;A|0.009	0.009	strong		0.587	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
XIRP2	129446	hgsc.bcm.edu	37	2	168104679	168104679	+	Silent	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:168104679T>G	ENST00000409195.1	+	9	6866	c.6777T>G	c.(6775-6777)acT>acG	p.T2259T	XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron|XIRP2_ENST00000295237.9_Silent_p.T2259T|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000409273.1_Silent_p.T2037T	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2084					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						AAACAAATACTTCCACAGGCT	0.388																																					p.T2259T		Atlas-SNP	.											.	XIRP2	914	.	0			c.T6777G						PASS	.						68.0	64.0	65.0					2																	168104679		1834	4085	5919	SO:0001819	synonymous_variant	129446	exon9			AAATACTTCCACA	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.6777T>G	2.37:g.168104679T>G		196.0	0.0	0		176.0	60.0	0.340909	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		0.388	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
MFSD3	113655	hgsc.bcm.edu	37	8	145737123	145737123	+	IGR	SNP	G	G	A	rs35346077	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145737123G>A	ENST00000301327.4	+	0	1548				RECQL4_ENST00000428558.2_Missense_Mutation_p.S1148F|CTD-2517M22.17_ENST00000580385.1_RNA|RECQL4_ENST00000532237.1_5'UTR	NM_138431.1	NP_612440.1	Q96ES6	MFSD3_HUMAN	major facilitator superfamily domain containing 3						transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)				central_nervous_system(2)|endometrium(1)|kidney(1)|lung(4)	8	all_cancers(97;5.56e-11)|all_epithelial(106;3.54e-10)|Lung NSC(106;5.7e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;1.48e-41)|Epithelial(56;1.85e-40)|all cancers(56;3.59e-35)|BRCA - Breast invasive adenocarcinoma(115;0.0483)|Colorectal(110;0.055)			TGGCCTCAGGGACAGGAACTG	0.662													G|||	4	0.000798722	0.0	0.0	5008	,	,		18429	0.0		0.002	False		,,,				2504	0.002				p.S1148F		Atlas-SNP	.											.	RECQL4	75	.	0			c.C3443T						PASS	.	G	PHE/SER	1,4329		0,1,2164	66.0	79.0	75.0		3444	5.0	1.0	8	dbSNP_126	75	13,8505		0,13,4246	no	missense	RECQL4	NM_004260.3	155	0,14,6410	AA,AG,GG		0.1526,0.0231,0.109	possibly-damaging	1148/1209	145737123	14,12834	2165	4259	6424	SO:0001628	intergenic_variant	9401	exon21			CTCAGGGACAGGA		CCDS6431.1	8q24.3	2005-11-17			ENSG00000167700	ENSG00000167700			25157	protein-coding gene	gene with protein product							Standard	NM_138431		Approved		uc003zdi.1	Q96ES6	OTTHUMG00000165177		8.37:g.145737123G>A		57.0	0.0	0		79.0	50.0	0.632911	NM_004260		Missense_Mutation	SNP	ENST00000301327.4	37	CCDS6431.1																																																																																			G|0.995;A|0.005	0.005	weak		0.662	MFSD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382478.2	NM_138431	
AQP11	282679	hgsc.bcm.edu	37	11	77301385	77301385	+	Silent	SNP	G	G	A	rs145642525	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:77301385G>A	ENST00000313578.3	+	1	706	c.348G>A	c.(346-348)acG>acA	p.T116T	AQP11_ENST00000528638.1_Intron	NM_173039.2	NP_766627.1	Q8NBQ7	AQP11_HUMAN	aquaporin 11	116					endosomal lumen acidification (GO:0048388)|protein homooligomerization (GO:0051260)|proximal tubule development (GO:0072014)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cell surface (GO:0009986)|cytosol (GO:0005829)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			kidney(2)|large_intestine(1)|lung(5)	8	all_cancers(14;1.75e-17)|all_epithelial(13;4.7e-20)|Ovarian(111;0.249)		Epithelial(5;4.73e-49)|BRCA - Breast invasive adenocarcinoma(5;1.4e-30)			CCCCCGAGACGGGTGCGGTGA	0.612													G|||	6	0.00119808	0.0015	0.0014	5008	,	,		19669	0.0		0.003	False		,,,				2504	0.0				p.T116T		Atlas-SNP	.											.	AQP11	14	.	0			c.G348A						PASS	.	G		1,4399	2.1+/-5.4	0,1,2199	88.0	70.0	76.0		348	0.2	0.0	11	dbSNP_134	76	12,8572	9.1+/-34.3	0,12,4280	no	coding-synonymous	AQP11	NM_173039.2		0,13,6479	AA,AG,GG		0.1398,0.0227,0.1001		116/272	77301385	13,12971	2200	4292	6492	SO:0001819	synonymous_variant	282679	exon1			CGAGACGGGTGCG	AB028147	CCDS8251.1	11q13.5	2008-02-05			ENSG00000178301	ENSG00000178301		"""Ion channels / Aquaporins"""	19940	protein-coding gene	gene with protein product		609914				16107722	Standard	NM_173039		Approved		uc001oyj.3	Q8NBQ7	OTTHUMG00000165194	ENST00000313578.3:c.348G>A	11.37:g.77301385G>A		85.0	0.0	0		113.0	51.0	0.451327	NM_173039		Silent	SNP	ENST00000313578.3	37	CCDS8251.1																																																																																			G|0.998;A|0.002	0.002	strong		0.612	AQP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382582.1	NM_173039	
ADAMTS9	56999	hgsc.bcm.edu	37	3	64606840	64606840	+	Silent	SNP	C	C	A	rs149253049	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:64606840C>A	ENST00000498707.1	-	19	3105	c.2763G>T	c.(2761-2763)ctG>ctT	p.L921L	ADAMTS9_ENST00000295903.4_Silent_p.L893L	NM_182920.1	NP_891550.1	Q9P2N4	ATS9_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 9	921	TSP type-1 2. {ECO:0000255|PROSITE- ProRule:PRU00210}.				glycoprotein catabolic process (GO:0006516)|multicellular organismal development (GO:0007275)|positive regulation of melanocyte differentiation (GO:0045636)|protein transport (GO:0015031)|proteolysis (GO:0006508)|vesicle-mediated transport (GO:0016192)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(3)|central_nervous_system(4)|cervix(1)|endometrium(9)|kidney(4)|large_intestine(17)|liver(4)|lung(43)|ovary(3)|prostate(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(3)	100		Lung NSC(201;0.00682)		BRCA - Breast invasive adenocarcinoma(55;0.00142)|Kidney(15;0.00202)|KIRC - Kidney renal clear cell carcinoma(15;0.00221)		CAGGCTGGGGCAGCCGATCGC	0.463													C|||	5	0.000998403	0.0023	0.0014	5008	,	,		16289	0.0		0.001	False		,,,				2504	0.0				p.L921L		Atlas-SNP	.											.	ADAMTS9	206	.	0			c.G2763T						PASS	.	C		7,4399	14.3+/-33.2	0,7,2196	70.0	71.0	71.0		2763	3.0	1.0	3	dbSNP_134	71	3,8597	3.0+/-9.4	0,3,4297	no	coding-synonymous	ADAMTS9	NM_182920.1		0,10,6493	AA,AC,CC		0.0349,0.1589,0.0769		921/1936	64606840	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	56999	exon19			CTGGGGCAGCCGA	AF261918	CCDS2903.1	3p14.1	2008-05-15	2005-08-19		ENSG00000163638	ENSG00000163638		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	13202	protein-coding gene	gene with protein product		605421	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 9"""			10936055	Standard	NM_182920		Approved	KIAA1312	uc003dmg.3	Q9P2N4	OTTHUMG00000158722	ENST00000498707.1:c.2763G>T	3.37:g.64606840C>A		170.0	0.0	0		208.0	98.0	0.471154	NM_182920	A1L4L0|B7ZVX9|B9ZVN0|Q9NR29	Silent	SNP	ENST00000498707.1	37	CCDS2903.1																																																																																			A|0.001;C|0.999;G|0.000	0.001	strong		0.463	ADAMTS9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351891.1		
PPFIA4	8497	hgsc.bcm.edu	37	1	203044777	203044777	+	Missense_Mutation	SNP	G	G	A	rs12130501	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:203044777G>A	ENST00000447715.2	+	34	3841	c.3400G>A	c.(3400-3402)Ggc>Agc	p.G1134S	PPFIA4_ENST00000599966.1_Missense_Mutation_p.G641S|PPFIA4_ENST00000414050.2_Missense_Mutation_p.G863S|PPFIA4_ENST00000367240.2_Missense_Mutation_p.G1135S|PPFIA4_ENST00000272198.6_Missense_Mutation_p.G650S|PPFIA4_ENST00000295706.4_Missense_Mutation_p.G641S			O75335	LIPA4_HUMAN	protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interacting protein (liprin), alpha 4	1134				G -> A (in Ref. 5; AAC26102). {ECO:0000305}.	cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)				NS(1)|autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(8)|lung(20)|ovary(4)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	50						CCACGGTCGCGGCGGCATGCT	0.716													g|||	32	0.00638978	0.0	0.0115	5008	,	,		11140	0.0		0.0189	False		,,,				2504	0.0051				p.G650S		Atlas-SNP	.											PPFIA4_ENST00000272198,colon,carcinoma,-1,2	PPFIA4	139	2	0			c.G1948A						PASS	.		SER/GLY	15,3733		0,15,1859	11.0	14.0	13.0		1948	-0.2	0.0	1	dbSNP_120	13	228,7910		2,224,3843	no	missense	PPFIA4	NM_015053.1	56	2,239,5702	AA,AG,GG		2.8017,0.4002,2.0444	benign	650/702	203044777	243,11643	1874	4069	5943	SO:0001583	missense	8497	exon16			GGTCGCGGCGGCA	AF034801	CCDS44296.1	1q32.1	2013-01-10			ENSG00000143847	ENSG00000143847		"""Sterile alpha motif (SAM) domain containing"""	9248	protein-coding gene	gene with protein product	"""Liprin-alpha4"""	603145				9624153	Standard	XM_005245553		Approved		uc009xaj.3	O75335	OTTHUMG00000042123	ENST00000447715.2:c.3400G>A	1.37:g.203044777G>A	ENSP00000402576:p.Gly1134Ser	14.0	0.0	0		11.0	6.0	0.545455	NM_015053	A2RUJ5|B1APN8|B1N949|B7ZM43|O94971	Missense_Mutation	SNP	ENST00000447715.2	37		16	0.007326007326007326	0	0.0	5	0.013812154696132596	0	0.0	11	0.014511873350923483	g	12.32	1.901775	0.33535	0.004002	0.028017	ENSG00000143847	ENST00000367240;ENST00000447715;ENST00000295706;ENST00000414050;ENST00000272198	T;T;T;T;T	0.21734	2.32;2.0;1.99;2.0;1.99	4.58	-0.158	0.13383	.	1.035160	0.07805	U	0.957214	T	0.03564	0.0102	N	0.17474	0.49	0.09310	N	1	B;B;B;B;B	0.17038	0.0;0.0;0.005;0.02;0.012	B;B;B;B;B	0.16722	0.0;0.0;0.002;0.016;0.007	T	0.34875	-0.9811	10	0.32370	T	0.25	-0.3686	4.4121	0.11438	0.4118:0.2651:0.3231:0.0	rs12130501	863;1134;336;641;650	B4DIS5;B1N949;B3KN22;O75335-2;O75335	.;.;.;.;LIPA4_HUMAN	S	1135;1134;641;863;650	ENSP00000356209:G1135S;ENSP00000402576:G1134S;ENSP00000295706:G641S;ENSP00000400379:G863S;ENSP00000272198:G650S	ENSP00000272198:G650S	G	+	1	0	PPFIA4	201311400	0.948000	0.32251	0.014000	0.15608	0.413000	0.31143	1.380000	0.34351	-0.369000	0.08028	0.298000	0.19748	GGC	G|0.992;A|0.008	0.008	strong		0.716	PPFIA4-005	NOVEL	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000462949.1	NM_015053	
MYO16	23026	hgsc.bcm.edu	37	13	109613929	109613929	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:109613929C>T	ENST00000357550.2	+	17	2055	c.2014C>T	c.(2014-2016)Ctt>Ttt	p.L672F	MYO16_ENST00000356711.2_Missense_Mutation_p.L672F|MYO16_ENST00000251041.5_Missense_Mutation_p.L672F|MYO16_ENST00000457511.2_Missense_Mutation_p.L184F	NM_001198950.1	NP_001185879.1			myosin XVI											NS(3)|breast(4)|central_nervous_system(2)|endometrium(10)|kidney(8)|large_intestine(27)|lung(51)|ovary(9)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	121	all_lung(23;0.000332)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung NSC(43;0.00751)|Lung SC(71;0.104)		BRCA - Breast invasive adenocarcinoma(86;0.19)|all cancers(43;0.201)			AATATTGCACCTTGGAGACAT	0.453																																					p.L694F		Atlas-SNP	.											.	MYO16	285	.	0			c.C2080T						PASS	.						191.0	153.0	166.0					13																	109613929		2203	4300	6503	SO:0001583	missense	23026	exon18			TTGCACCTTGGAG		CCDS32008.1, CCDS73598.1	13q33.3	2014-06-12			ENSG00000041515	ENSG00000041515		"""Myosins / Myosin superfamily : Class XVI"", ""Ankyrin repeat domain containing"""	29822	protein-coding gene	gene with protein product	"""neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 3"", ""protein phosphatase 1, regulatory subunit 107"""	615479				11588169, 17029291, 21946561	Standard	NM_001198950		Approved	MYR8, KIAA0865, Myo16b, NYAP3, PPP1R107	uc001vqt.1	Q9Y6X6	OTTHUMG00000017333	ENST00000357550.2:c.2014C>T	13.37:g.109613929C>T	ENSP00000350160:p.Leu672Phe	137.0	0.0	0		99.0	4.0	0.040404	NM_001198950		Missense_Mutation	SNP	ENST00000357550.2	37	CCDS32008.1	.	.	.	.	.	.	.	.	.	.	C	11.79	1.743813	0.30865	.	.	ENSG00000041515	ENST00000356711;ENST00000397258;ENST00000357550;ENST00000251041;ENST00000375857;ENST00000457511	D;D;D;D	0.97959	-4.63;-4.63;-4.63;-4.63	5.07	-8.68	0.00859	Myosin head, motor domain (2);	0.760287	0.10614	U	0.654105	D	0.96253	0.8778	M	0.74389	2.26	0.23913	N	0.996482	P;P;P	0.46987	0.888;0.888;0.733	P;P;B	0.46885	0.474;0.53;0.375	D	0.93439	0.6792	9	.	.	.	.	11.4832	0.50337	0.2328:0.5853:0.182:0.0	.	184;672;672	F8W883;Q9Y6X6-2;Q9Y6X6	.;.;MYO16_HUMAN	F	672;672;672;672;460;184	ENSP00000349145:L672F;ENSP00000350160:L672F;ENSP00000251041:L672F;ENSP00000401633:L184F	.	L	+	1	0	MYO16	108411930	0.881000	0.30235	0.010000	0.14722	0.052000	0.14988	-0.121000	0.10643	-1.924000	0.01064	-1.513000	0.00942	CTT	.	.	none		0.453	MYO16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045746.1	NM_015011	
GNB2	2783	hgsc.bcm.edu	37	7	100276355	100276355	+	Silent	SNP	C	C	T	rs17850902	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100276355C>T	ENST00000303210.4	+	10	1436	c.954C>T	c.(952-954)ctC>ctT	p.L318L	GNB2_ENST00000427895.1_Silent_p.L218L|GNB2_ENST00000419828.1_Silent_p.L218L|GNB2_ENST00000436220.1_Silent_p.L274L|GNB2_ENST00000393926.1_Silent_p.L318L|GNB2_ENST00000424361.1_Silent_p.L274L|GNB2_ENST00000393924.1_Silent_p.L318L	NM_005273.3	NP_005264.2	P62879	GBB2_HUMAN	guanine nucleotide binding protein (G protein), beta polypeptide 2	318					cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|GTP catabolic process (GO:0006184)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cell body (GO:0044297)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	calcium channel regulator activity (GO:0005246)|GTPase activity (GO:0003924)|GTPase binding (GO:0051020)|protein complex binding (GO:0032403)|signal transducer activity (GO:0004871)			endometrium(1)|lung(3)|ovary(2)|prostate(1)	7	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)	Ovarian(593;0.238)				TGAGCTGCCTCGGGGTCACCG	0.652													C|||	17	0.00339457	0.0008	0.0029	5008	,	,		16180	0.001		0.005	False		,,,				2504	0.0082				p.L318L		Atlas-SNP	.											.	GNB2	29	.	0			c.C954T						PASS	.	C		7,4399		0,7,2196	60.0	63.0	62.0		954	-6.0	0.9	7	dbSNP_123	62	76,8524		0,76,4224	no	coding-synonymous	GNB2	NM_005273.3		0,83,6420	TT,TC,CC		0.8837,0.1589,0.6382		318/341	100276355	83,12923	2203	4300	6503	SO:0001819	synonymous_variant	2783	exon10			CTGCCTCGGGGTC	M16514	CCDS5703.1	7q21.3-q22.1	2013-01-10			ENSG00000172354	ENSG00000172354		"""WD repeat domain containing"""	4398	protein-coding gene	gene with protein product	"""G protein, beta-2 subunit"", ""guanine nucleotide-binding protein G(I)/G(S)/G(T) beta subunit 2"", ""signal-transducing guanine nucleotide-binding regulatory protein beta subunit"", ""transducin beta chain 2"""	139390				9799793	Standard	NM_005273		Approved		uc003uwb.3	P62879	OTTHUMG00000137419	ENST00000303210.4:c.954C>T	7.37:g.100276355C>T		145.0	0.0	0		147.0	83.0	0.564626	NM_005273	B3KPU1|P11016|P54312	Silent	SNP	ENST00000303210.4	37	CCDS5703.1																																																																																			C|0.995;T|0.005	0.005	strong		0.652	GNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268391.2	NM_005273	
POU2F2	5452	hgsc.bcm.edu	37	19	42600030	42600030	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:42600030T>C	ENST00000526816.2	-	9	730	c.715A>G	c.(715-717)Acg>Gcg	p.T239A	POU2F2_ENST00000529067.1_Missense_Mutation_p.T223A|POU2F2_ENST00000342301.4_Missense_Mutation_p.T239A|POU2F2_ENST00000560558.1_Missense_Mutation_p.T184A|POU2F2_ENST00000529952.1_Missense_Mutation_p.T239A|POU2F2_ENST00000389341.5_Missense_Mutation_p.T223A|POU2F2_ENST00000533720.1_Missense_Mutation_p.T223A|POU2F2_ENST00000560398.1_Missense_Mutation_p.T245A			P09086	PO2F2_HUMAN	POU class 2 homeobox 2	239	POU-specific. {ECO:0000255|PROSITE- ProRule:PRU00530}.				cell maturation (GO:0048469)|humoral immune response (GO:0006959)|immunoglobulin secretion involved in immune response (GO:0002380)|mature B cell differentiation (GO:0002335)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			kidney(1)|large_intestine(5)|lung(4)|ovary(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		Prostate(69;0.059)			Dolutegravir(DB08930)	GAAATGGTCGTCTGGCTGAAG	0.627																																					p.T239A		Atlas-SNP	.											POU2F2_ENST00000292077,NS,lymphoid_neoplasm,0,8	POU2F2	106	8	0			c.A715G						PASS	.						119.0	118.0	118.0					19																	42600030		2203	4300	6503	SO:0001583	missense	5452	exon9			TGGTCGTCTGGCT		CCDS33035.1, CCDS56094.1, CCDS56095.1, CCDS58665.1	19q13.2	2011-06-20	2007-07-13					"""Homeoboxes / POU class"""	9213	protein-coding gene	gene with protein product		164176	"""POU domain class 2, transcription factor 2"""	OTF2			Standard	NM_001207026		Approved	OCT2	uc002osp.3	P09086		ENST00000526816.2:c.715A>G	19.37:g.42600030T>C	ENSP00000431603:p.Thr239Ala	30.0	0.0	0		79.0	31.0	0.392405	NM_001207025	Q16648|Q7M4M8|Q9BRS4	Missense_Mutation	SNP	ENST00000526816.2	37	CCDS56095.1	.	.	.	.	.	.	.	.	.	.	T	20.2	3.957613	0.73902	.	.	ENSG00000028277	ENST00000389341;ENST00000342301;ENST00000292077;ENST00000533720;ENST00000526816;ENST00000529067;ENST00000529952	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	4.38	2.18	0.27775	POU-specific (4);Lambda repressor-like, DNA-binding (2);POU (1);	0.247967	0.39834	N	0.001250	D	0.91492	0.7314	M	0.88310	2.945	0.52501	D	0.999956	D;P;B	0.76494	0.999;0.953;0.262	D;D;B	0.79784	0.993;0.938;0.37	D	0.89325	0.3643	10	0.87932	D	0	.	6.8485	0.24003	0.15:0.0:0.1568:0.6932	.	223;239;223	P09086-4;P09086;P09086-3	.;PO2F2_HUMAN;.	A	223;239;239;223;238;223;239	ENSP00000373992:T223A;ENSP00000339369:T239A;ENSP00000437221:T223A;ENSP00000437224:T223A;ENSP00000436988:T239A	ENSP00000292077:T239A	T	-	1	0	POU2F2	47291870	1.000000	0.71417	0.972000	0.41901	0.994000	0.84299	7.819000	0.86621	0.269000	0.21961	0.454000	0.30748	ACG	.	.	none		0.627	POU2F2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387329.3		
ACADL	33	hgsc.bcm.edu	37	2	211085491	211085491	+	Missense_Mutation	SNP	G	G	A	rs61731470	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211085491G>A	ENST00000233710.3	-	2	340	c.113C>T	c.(112-114)aCt>aTt	p.T38I	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	38					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		AGCAGAAGGAGTTTCTAGACG	0.333													G|||	78	0.0155751	0.0015	0.0274	5008	,	,		18116	0.001		0.0358	False		,,,				2504	0.0204				p.T38I		Atlas-SNP	.											.	ACADL	38	.	0			c.C113T						PASS	.	G	ILE/THR	25,4381	29.0+/-57.7	0,25,2178	60.0	59.0	60.0		113	1.5	0.3	2	dbSNP_129	60	310,8290	108.0+/-168.7	2,306,3992	yes	missense	ACADL	NM_001608.3	89	2,331,6170	AA,AG,GG		3.6047,0.5674,2.5757	benign	38/431	211085491	335,12671	2203	4300	6503	SO:0001583	missense	33	exon2			GAAGGAGTTTCTA	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"""acyl-Coenzyme A dehydrogenase, long chain"""			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.113C>T	2.37:g.211085491G>A	ENSP00000233710:p.Thr38Ile	44.0	0.0	0		39.0	25.0	0.641026	NM_001608	B2R8T3|Q8IUN8	Missense_Mutation	SNP	ENST00000233710.3	37	CCDS2389.1	39	0.017857142857142856	1	0.0020325203252032522	11	0.03038674033149171	0	0.0	27	0.03562005277044855	G	12.72	2.022726	0.35701	0.005674	0.036047	ENSG00000115361	ENST00000233710	D	0.97553	-4.43	5.69	1.46	0.22682	.	0.233058	0.42294	D	0.000738	T	0.76147	0.3947	N	0.08118	0	0.34426	D	0.697969	B	0.15141	0.012	B	0.12156	0.007	T	0.81678	-0.0824	10	0.48119	T	0.1	.	13.294	0.60286	0.0639:0.3386:0.5975:0.0	rs61731470	38	P28330	ACADL_HUMAN	I	38	ENSP00000233710:T38I	ENSP00000233710:T38I	T	-	2	0	ACADL	210793736	0.999000	0.42202	0.338000	0.25549	0.833000	0.47200	1.967000	0.40491	0.319000	0.23209	-0.126000	0.14955	ACT	G|0.976;A|0.024	0.024	strong		0.333	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	
PTPRN2	5799	hgsc.bcm.edu	37	7	157369324	157369324	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:157369324A>G	ENST00000389418.4	-	19	2773	c.2764T>C	c.(2764-2766)Tcc>Ccc	p.S922P	PTPRN2_ENST00000389413.3_Missense_Mutation_p.S893P|PTPRN2_ENST00000389416.4_Missense_Mutation_p.S905P|PTPRN2_ENST00000409483.1_Missense_Mutation_p.S884P|PTPRN2_ENST00000404321.2_Missense_Mutation_p.S945P|MIR153-2_ENST00000385225.1_RNA	NM_002847.3	NP_002838.2	Q92932	PTPR2_HUMAN	protein tyrosine phosphatase, receptor type, N polypeptide 2	922	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of GTPase activity (GO:0034260)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	endoplasmic reticulum lumen (GO:0005788)|integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)|secretory granule (GO:0030141)|terminal bouton (GO:0043195)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(1)|lung(42)|ovary(4)|pleura(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	86	all_neural(206;0.181)	all_cancers(7;8.99e-13)|all_epithelial(9;2.4e-06)|all_hematologic(28;0.0155)|Breast(660;0.132)	OV - Ovarian serous cystadenocarcinoma(82;0.00463)	STAD - Stomach adenocarcinoma(7;0.0875)		TCCAGGAGGGACCTTGAGGAG	0.647																																					p.S922P		Atlas-SNP	.											.	PTPRN2	243	.	0			c.T2764C						PASS	.						62.0	49.0	54.0					7																	157369324		2203	4300	6503	SO:0001583	missense	5799	exon19			GGAGGGACCTTGA	AB002385	CCDS5947.1, CCDS5948.1, CCDS5949.1	7q36	2011-06-09			ENSG00000155093	ENSG00000155093		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9677	protein-coding gene	gene with protein product	"""IAR PTPRP"""	601698				8954911, 9220540	Standard	NM_130842		Approved	KIAA0387, phogrin, ICAAR, IA-2beta	uc003wno.3	Q92932	OTTHUMG00000152646	ENST00000389418.4:c.2764T>C	7.37:g.157369324A>G	ENSP00000374069:p.Ser922Pro	45.0	0.0	0		57.0	20.0	0.350877	NM_002847	E9PC57|Q8N4I5|Q92662|Q9Y4F8|Q9Y4I6	Missense_Mutation	SNP	ENST00000389418.4	37	CCDS5947.1	.	.	.	.	.	.	.	.	.	.	A	8.190	0.795727	0.16327	.	.	ENSG00000155093	ENST00000409483;ENST00000389413;ENST00000389416;ENST00000389418;ENST00000404321	D;D;D;D;D	0.84298	-1.83;-1.83;-1.83;-1.83;-1.83	5.44	1.67	0.24075	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.066743	0.64402	D	0.000012	T	0.57814	0.2079	N	0.02266	-0.62	0.80722	D	1	B;B;B;B;B	0.29301	0.203;0.241;0.203;0.208;0.241	B;B;B;B;B	0.30495	0.071;0.116;0.071;0.044;0.116	T	0.55224	-0.8174	10	0.02654	T	1	.	5.9778	0.19391	0.7094:0.1376:0.153:0.0	.	945;884;893;905;922	Q92932-3;E7EM83;Q92932-2;E9PC57;Q92932	.;.;.;.;PTPR2_HUMAN	P	884;893;905;922;945	ENSP00000387114:S884P;ENSP00000374064:S893P;ENSP00000374067:S905P;ENSP00000374069:S922P;ENSP00000385464:S945P	ENSP00000374064:S893P	S	-	1	0	PTPRN2	157062085	1.000000	0.71417	0.100000	0.21137	0.015000	0.08874	2.455000	0.44988	0.041000	0.15688	0.528000	0.53228	TCC	.	.	none		0.647	PTPRN2-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000353214.1		
ATP8B4	79895	hgsc.bcm.edu	37	15	50212572	50212572	+	Silent	SNP	G	G	T	rs72733094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:50212572G>T	ENST00000284509.6	-	18	1935	c.1794C>A	c.(1792-1794)atC>atA	p.I598I	ATP8B4_ENST00000559829.1_Silent_p.I598I	NM_024837.2	NP_079113.2	Q8TF62	AT8B4_HUMAN	ATPase, class I, type 8B, member 4	598						Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cation-transporting ATPase activity (GO:0019829)|magnesium ion binding (GO:0000287)|phospholipid-translocating ATPase activity (GO:0004012)			breast(6)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(14)|lung(27)|ovary(2)|pancreas(1)|prostate(1)|skin(7)|urinary_tract(1)	73		all_lung(180;0.00183)		all cancers(107;2.41e-07)|GBM - Glioblastoma multiforme(94;8.28e-05)		CTCTGTATGCGATGGCCAAGG	0.458													G|||	7	0.00139776	0.0	0.0	5008	,	,		20424	0.0		0.007	False		,,,				2504	0.0				p.I598I		Atlas-SNP	.											.	ATP8B4	173	.	0			c.C1794A						PASS	.	G		6,4386	9.9+/-24.2	0,6,2190	84.0	76.0	79.0		1794	-11.3	0.0	15	dbSNP_130	79	85,8505	48.5+/-108.0	0,85,4210	no	coding-synonymous	ATP8B4	NM_024837.2		0,91,6400	TT,TG,GG		0.9895,0.1366,0.701		598/1193	50212572	91,12891	2196	4295	6491	SO:0001819	synonymous_variant	79895	exon18			GTATGCGATGGCC	AB075819	CCDS32238.1	15q21.2	2010-04-20	2007-09-19		ENSG00000104043	ENSG00000104043		"""ATPases / P-type"""	13536	protein-coding gene	gene with protein product		609123	"""ATPase, Class I, type 8B, member 4"""			11015572	Standard	NM_024837		Approved	ATPIM, KIAA1939	uc001zxu.3	Q8TF62		ENST00000284509.6:c.1794C>A	15.37:g.50212572G>T		199.0	1.0	0.00502513		174.0	92.0	0.528736	NM_024837	Q9H727	Silent	SNP	ENST00000284509.6	37	CCDS32238.1																																																																																			G|0.994;T|0.006	0.006	strong		0.458	ATP8B4-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418100.1	NM_024837	
RIN3	79890	hgsc.bcm.edu	37	14	93118790	93118790	+	Missense_Mutation	SNP	A	A	C	rs139248637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:93118790A>C	ENST00000216487.7	+	6	1555	c.1396A>C	c.(1396-1398)Atc>Ctc	p.I466L	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	466	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				GAAAAAACGGATCTCTCGACA	0.627													A|||	15	0.00299521	0.0	0.0014	5008	,	,		16397	0.0		0.007	False		,,,				2504	0.0072				p.I466L		Atlas-SNP	.											.	RIN3	81	.	0			c.A1396C						PASS	.	A	LEU/ILE	0,4406		0,0,2203	94.0	118.0	110.0		1396	-3.2	0.7	14	dbSNP_134	110	32,8568	22.2+/-67.0	0,32,4268	yes	missense	RIN3	NM_024832.3	5	0,32,6471	CC,CA,AA		0.3721,0.0,0.246	benign	466/986	93118790	32,12974	2203	4300	6503	SO:0001583	missense	79890	exon6			AAACGGATCTCTC	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1396A>C	14.37:g.93118790A>C	ENSP00000216487:p.Ile466Leu	85.0	0.0	0		83.0	34.0	0.409639	NM_024832	Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	CCDS32144.1	6	0.0027472527472527475	0	0.0	0	0.0	0	0.0	6	0.0079155672823219	A	6.565	0.472587	0.12461	0.0	0.003721	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.05199	3.48	4.22	-3.16	0.05217	.	1.726180	0.03309	N	0.190221	T	0.03263	0.0095	L	0.38531	1.155	0.22591	N	0.99896	P;B;B;B	0.42518	0.782;0.0;0.001;0.001	B;B;B;B	0.41813	0.367;0.001;0.001;0.001	T	0.35126	-0.9801	10	0.02654	T	1	-7.5443	4.3078	0.10956	0.1825:0.2771:0.438:0.1024	.	466;512;391;466	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	L	466;390	ENSP00000216487:I466L	ENSP00000216487:I466L	I	+	1	0	RIN3	92188543	0.047000	0.20315	0.692000	0.30179	0.814000	0.46013	-0.512000	0.06313	-1.044000	0.03254	0.260000	0.18958	ATC	A|0.998;C|0.002	0.002	strong		0.627	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
HLA-C	3107	hgsc.bcm.edu	37	6	31239622	31239622	+	Missense_Mutation	SNP	C	C	G	rs9264668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31239622C>G	ENST00000376228.5	-	2	111	c.97G>C	c.(97-99)Gac>Cac	p.D33H	HLA-C_ENST00000383329.3_Missense_Mutation_p.D33H	NM_002117.5	NP_002108.4	Q95604	1C17_HUMAN	major histocompatibility complex, class I, C	33	Alpha-1.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)|viral process (GO:0016032)	cell surface (GO:0009986)|early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)			central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(4)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)	17						ACGGCGGTGTCGAAATACCTC	0.726													a|||	20	0.00399361	0.0113	0.0	5008	,	,		11654	0.001		0.003	False		,,,				2504	0.001				p.D33H		Atlas-SNP	.											HLA-C_ENST00000383329,NS,neuroblastoma,0,2	HLA-C	92	2	0			c.G97C						scavenged	.						16.0	17.0	17.0					6																	31239622		1477	2676	4153	SO:0001583	missense	3107	exon2			CGGTGTCGAAATA	M11886	CCDS34393.1	6p21.3	2014-01-30			ENSG00000204525	ENSG00000204525		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4933	protein-coding gene	gene with protein product		142840	"""psoriasis susceptibility 1"""	HLA-JY3, D6S204, PSORS1		3863816, 16642438	Standard	NM_001243042		Approved		uc003nsy.3	P04222	OTTHUMG00000031154	ENST00000376228.5:c.97G>C	6.37:g.31239622C>G	ENSP00000365402:p.Asp33His	25.0	0.0	0		58.0	11.0	0.189655	NM_002117	O02864|O02958|Q29643|Q9MY30	Missense_Mutation	SNP	ENST00000376228.5	37	CCDS34393.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	0.003|0.003	-2.468672|-2.468672	0.00169|0.00169	.|.	.|.	ENSG00000204525|ENSG00000204525	ENST00000376228;ENST00000383329;ENST00000396254;ENST00000539307|ENST00000415537	T;T|.	0.00009|.	9.5;9.5|.	2.16|2.16	-4.32|-4.32	0.03688|0.03688	MHC class I, alpha chain, alpha1/alpha2 (1);MHC classes I/II-like antigen recognition protein (1);MHC class I-like antigen recognition (1);|.	10.311600|.	0.00879|.	N|.	0.002109|.	T|T	0.03390|0.03390	0.0098|0.0098	L|L	0.31578|0.31578	0.945|0.945	0.09310|0.09310	N|N	1|1	P;P;P;P|.	0.51351|.	0.944;0.822;0.822;0.888|.	P;P;P;D|.	0.68483|.	0.904;0.904;0.829;0.958|.	T|T	0.58504|0.58504	-0.7625|-0.7625	10|5	0.42905|.	T|.	0.14|.	.|.	0.4543|0.4543	0.00506|0.00506	0.2454:0.267:0.2544:0.2332|0.2454:0.267:0.2544:0.2332	.|.	33;33;33;33|.	A2AEA4;A6H578;A2AEA2;P10321|.	.;.;.;1C07_HUMAN|.	H|P	33;33;33;70|32	ENSP00000365402:D33H;ENSP00000372819:D33H|.	ENSP00000365402:D33H|.	D|R	-|-	1|2	0|0	HLA-C|HLA-C	31347601|31347601	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.001000|0.001000	0.01503|0.01503	-13.217000|-13.217000	0.00001|0.00001	-7.736000|-7.736000	0.00000|0.00000	-4.008000|-4.008000	0.00013|0.00013	GAC|CGA	A|0.575;C|0.423;G|0.002	0.002	strong		0.726	HLA-C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076281.3	NM_002117	
AP5Z1	9907	hgsc.bcm.edu	37	7	4830971	4830971	+	Silent	SNP	G	G	T	rs77393809	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4830971G>T	ENST00000348624.4	+	17	2473	c.2379G>T	c.(2377-2379)acG>acT	p.T793T	AP5Z1_ENST00000490487.1_3'UTR|MIR4656_ENST00000579503.1_RNA	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	793					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CCCTGCGCACGGTCAGCCGGC	0.677													G|||	62	0.0123802	0.0015	0.0187	5008	,	,		17357	0.0		0.0239	False		,,,				2504	0.0235				p.T793T		Atlas-SNP	.											.	.	.	.	0			c.G2379T						PASS	.	G		12,4080		0,12,2034	15.0	20.0	18.0		2379	-9.4	0.0	7	dbSNP_133	18	204,8148		4,196,3976	no	coding-synonymous	KIAA0415	NM_014855.2		4,208,6010	TT,TG,GG		2.4425,0.2933,1.7358		793/808	4830971	216,12228	2046	4176	6222	SO:0001819	synonymous_variant	9907	exon17			GCGCACGGTCAGC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.2379G>T	7.37:g.4830971G>T		109.0	0.0	0		137.0	73.0	0.532847	NM_014855	Q8N3X2|Q96H80	Silent	SNP	ENST00000348624.4	37	CCDS47528.1																																																																																			G|0.985;T|0.015	0.015	strong		0.677	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
PLXND1	23129	hgsc.bcm.edu	37	3	129303236	129303236	+	Missense_Mutation	SNP	G	G	C	rs201334507	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:129303236G>C	ENST00000324093.4	-	6	2199	c.2021C>G	c.(2020-2022)cCc>cGc	p.P674R	PLXND1_ENST00000393239.1_Missense_Mutation_p.P674R	NM_015103.2	NP_055918	Q9Y4D7	PLXD1_HUMAN	plexin D1	674					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						ACCCTGGTTGGGGGGGAAGGG	0.637													G|||	2	0.000399361	0.0008	0.0	5008	,	,		19988	0.001		0.0	False		,,,				2504	0.0				p.P674R	Ovarian(97;366 1484 3738 22084 39045)	Atlas-SNP	.											.	PLXND1	149	.	0			c.C2021G						PASS	.	G	ARG/PRO	0,4406		0,0,2203	53.0	53.0	53.0		2021	2.9	0.0	3		53	3,8597	3.0+/-9.4	0,3,4297	yes	missense	PLXND1	NM_015103.2	103	0,3,6500	CC,CG,GG		0.0349,0.0,0.0231	benign	674/1926	129303236	3,13003	2203	4300	6503	SO:0001583	missense	23129	exon6			TGGTTGGGGGGGA	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.2021C>G	3.37:g.129303236G>C	ENSP00000317128:p.Pro674Arg	93.0	0.0	0		70.0	40.0	0.571429	NM_015103	A7E2C6|C9JPZ6|Q6PJS9|Q8IZJ2|Q9BTQ2	Missense_Mutation	SNP	ENST00000324093.4	37	CCDS33854.1	.	.	.	.	.	.	.	.	.	.	G	1.556	-0.538035	0.04082	0.0	3.49E-4	ENSG00000004399	ENST00000324093;ENST00000393239	T;T	0.34275	1.42;1.37	4.77	2.94	0.34122	.	0.473004	0.19301	N	0.117635	T	0.33644	0.0870	M	0.65975	2.015	0.09310	N	1	B	0.21688	0.059	B	0.26310	0.068	T	0.31530	-0.9940	10	0.12103	T	0.63	.	10.1176	0.42601	0.0:0.1326:0.593:0.2744	.	674	Q9Y4D7	PLXD1_HUMAN	R	674	ENSP00000317128:P674R;ENSP00000376931:P674R	ENSP00000317128:P674R	P	-	2	0	PLXND1	130785926	0.013000	0.17824	0.002000	0.10522	0.049000	0.14656	1.150000	0.31639	0.528000	0.28580	-0.218000	0.12543	CCC	.	.	weak		0.637	PLXND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356132.4	NM_015103	
UNC5C	8633	hgsc.bcm.edu	37	4	96127798	96127798	+	Missense_Mutation	SNP	G	G	T	rs141976218	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:96127798G>T	ENST00000453304.1	-	11	2231	c.1883C>A	c.(1882-1884)gCa>gAa	p.A628E		NM_003728.3	NP_003719.3	O95185	UNC5C_HUMAN	unc-5 homolog C (C. elegans)	628	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)		TCCCTGTGCTGCCTGGTTCTT	0.537													G|||	3	0.000599042	0.0	0.0014	5008	,	,		15925	0.0		0.002	False		,,,				2504	0.0				p.A628E		Atlas-SNP	.											.	UNC5C	141	.	0			c.C1883A						PASS	.	G	GLU/ALA	1,4405	2.1+/-5.4	0,1,2202	106.0	94.0	98.0		1883	3.5	0.8	4	dbSNP_134	98	19,8581	10.5+/-38.8	0,19,4281	yes	missense	UNC5C	NM_003728.3	107	0,20,6483	TT,TG,GG		0.2209,0.0227,0.1538	benign	628/932	96127798	20,12986	2203	4300	6503	SO:0001583	missense	8633	exon11			TGTGCTGCCTGGT	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.1883C>A	4.37:g.96127798G>T	ENSP00000406022:p.Ala628Glu	119.0	0.0	0		117.0	50.0	0.42735	NM_003728	Q8IUT0	Missense_Mutation	SNP	ENST00000453304.1	37	CCDS3643.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	10.51	1.369746	0.24771	2.27E-4	0.002209	ENSG00000182168	ENST00000453304;ENST00000331502;ENST00000513796	T;T	0.40476	1.03;1.03	5.28	3.45	0.39498	ZU5 (3);	0.761342	0.12964	N	0.424732	T	0.28433	0.0703	N	0.19112	0.55	0.28023	N	0.934452	B;B	0.17852	0.004;0.024	B;B	0.19391	0.01;0.025	T	0.19844	-1.0293	10	0.34782	T	0.22	.	9.8179	0.40865	0.0805:0.1393:0.7802:0.0	.	628;628	A8K385;O95185	.;UNC5C_HUMAN	E	628;587;647	ENSP00000406022:A628E;ENSP00000426924:A647E	ENSP00000328673:A587E	A	-	2	0	UNC5C	96346821	0.714000	0.27936	0.807000	0.32361	0.801000	0.45260	3.981000	0.56902	0.633000	0.30452	-0.300000	0.09419	GCA	G|0.998;T|0.002	0.002	strong		0.537	UNC5C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253607.1	NM_003728	
NACAD	23148	hgsc.bcm.edu	37	7	45123859	45123859	+	Silent	SNP	G	G	A	rs72497819	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:45123859G>A	ENST00000490531.2	-	2	1939	c.1920C>T	c.(1918-1920)tcC>tcT	p.S640S		NM_001146334.1	NP_001139806.1	O15069	NACAD_HUMAN	NAC alpha domain containing	640					protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(1)|endometrium(2)|skin(2)	5						GTGTCATAACGGAGTCCTGGG	0.602													G|||	1213	0.242212	0.1505	0.3415	5008	,	,		16852	0.2391		0.2853	False		,,,				2504	0.2546				p.S640S		Atlas-SNP	.											.	NACAD	44	.	0			c.C1920T						PASS	.						5.0	6.0	5.0					7																	45123859		630	1536	2166	SO:0001819	synonymous_variant	23148	exon2			CATAACGGAGTCC	AB002361	CCDS47582.1	7p13	2010-07-14			ENSG00000136274	ENSG00000136274			22196	protein-coding gene	gene with protein product							Standard	NM_001146334		Approved	KIAA0363	uc003tmt.3	O15069	OTTHUMG00000159170	ENST00000490531.2:c.1920C>T	7.37:g.45123859G>A		19.0	0.0	0		19.0	6.0	0.315789	NM_001146334		Silent	SNP	ENST00000490531.2	37	CCDS47582.1																																																																																			G|0.792;A|0.208	0.208	strong		0.602	NACAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353652.2	NM_001146334	
MYO18B	84700	hgsc.bcm.edu	37	22	26423477	26423477	+	Missense_Mutation	SNP	G	G	A	rs7284177	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26423477G>A	ENST00000407587.2	+	43	7709	c.7540G>A	c.(7540-7542)Ggc>Agc	p.G2514S	MYO18B_ENST00000335473.7_Missense_Mutation_p.G2513S|MYO18B_ENST00000536101.1_Missense_Mutation_p.G2513S			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2513	Poly-Ser.					cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						CTCATCCTCCGGCTCCATCGT	0.587													A|||	352	0.0702875	0.2005	0.0259	5008	,	,		18932	0.004		0.0179	False		,,,				2504	0.0481				p.G2513S		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7537A						PASS	.	A	SER/GLY	695,3407		58,579,1414	53.0	55.0	55.0		7537	1.8	1.0	22	dbSNP_116	55	146,8242		1,144,4049	yes	missense	MYO18B	NM_032608.5	56	59,723,5463	AA,AG,GG		1.7406,16.943,6.7334	benign	2513/2568	26423477	841,11649	2051	4194	6245	SO:0001583	missense	84700	exon43			TCCTCCGGCTCCA	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7540G>A	22.37:g.26423477G>A	ENSP00000386096:p.Gly2514Ser	60.0	0.0	0		49.0	19.0	0.387755	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		123	0.05631868131868132	92	0.18699186991869918	13	0.03591160220994475	4	0.006993006993006993	14	0.018469656992084433	A	4.656	0.121893	0.08931	0.16943	0.017406	ENSG00000133454	ENST00000536101;ENST00000335473;ENST00000407587	D;D;D	0.85088	-1.92;-1.92;-1.94	5.17	1.8	0.24995	.	0.170297	0.37437	N	0.002083	T	0.00109	0.0003	N	0.00729	-1.24	0.54753	P	1.0999999999983245E-5	B;B;B;B;B	0.06786	0.001;0.0;0.0;0.0;0.001	B;B;B;B;B	0.06405	0.002;0.001;0.001;0.002;0.002	T	0.12426	-1.0548	9	0.02654	T	1	.	4.0444	0.09766	0.4128:0.0:0.4136:0.1736	rs7284177;rs52837742;rs59696890;rs7284177	2026;2515;2513;2514;2513	Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.;.;MY18B_HUMAN;.;.	S	2513;2513;2514	ENSP00000441229:G2513S;ENSP00000334563:G2513S;ENSP00000386096:G2514S	ENSP00000334563:G2513S	G	+	1	0	MYO18B	24753477	0.459000	0.25768	0.958000	0.39756	0.893000	0.52053	0.694000	0.25512	-0.007000	0.14345	-0.361000	0.07541	GGC	G|0.931;A|0.069	0.069	strong		0.587	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
COL8A2	1296	hgsc.bcm.edu	37	1	36563509	36563509	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:36563509G>A	ENST00000397799.1	-	4	1997	c.1773C>T	c.(1771-1773)ccC>ccT	p.P591P	COL8A2_ENST00000481785.1_Silent_p.P526P|COL8A2_ENST00000303143.4_Silent_p.P591P			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	591	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Nonhelical region (NC1).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CAAATTTCACGGGCATGCCCG	0.632																																					p.P591P		Atlas-SNP	.											.	COL8A2	41	.	0			c.C1773T						PASS	.						39.0	36.0	37.0					1																	36563509		2202	4300	6502	SO:0001819	synonymous_variant	1296	exon2			TTTCACGGGCATG	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"""Collagens"""	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.1773C>T	1.37:g.36563509G>A		46.0	0.0	0		69.0	67.0	0.971014	NM_005202	Q5JV31|Q8TEJ5	Silent	SNP	ENST00000397799.1	37	CCDS403.1																																																																																			.	.	none		0.632	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202	
AGRP	181	hgsc.bcm.edu	37	16	67516605	67516605	+	Silent	SNP	G	G	C	rs34730014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67516605G>C	ENST00000290953.2	-	4	632	c.333C>G	c.(331-333)cgC>cgG	p.R111R	ATP6V0D1_ENST00000290949.3_5'Flank|ATP6V0D1_ENST00000540149.1_5'Flank|RP11-297D21.4_ENST00000602596.1_RNA	NM_001138.1	NP_001129.1	O00253	AGRP_HUMAN	agouti related neuropeptide	111	Agouti. {ECO:0000255|PROSITE- ProRule:PRU00494}.|Interaction with melanocortin receptors.				adult feeding behavior (GO:0008343)|eating behavior (GO:0042755)|feeding behavior (GO:0007631)|hormone-mediated signaling pathway (GO:0009755)|maternal process involved in female pregnancy (GO:0060135)|neuropeptide signaling pathway (GO:0007218)|photoperiodism (GO:0009648)|positive regulation of feeding behavior (GO:2000253)|regulation of feeding behavior (GO:0060259)|response to insulin (GO:0032868)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|neuronal cell body (GO:0043025)	neuropeptide hormone activity (GO:0005184)|receptor binding (GO:0005102)			endometrium(1)	1		Acute lymphoblastic leukemia(13;0.00263)|all_hematologic(13;0.0274)|Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.0717)|Epithelial(162;0.16)		CATTGAAGAAGCGGCAGTAGC	0.637													G|||	4	0.000798722	0.0	0.0014	5008	,	,		19478	0.0		0.003	False		,,,				2504	0.0				p.R111R		Atlas-SNP	.											.	AGRP	8	.	0			c.C333G						PASS	.	G		6,4390	9.9+/-24.2	0,6,2192	106.0	99.0	101.0		333	0.6	1.0	16	dbSNP_126	101	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous	AGRP	NM_001138.1		0,50,6448	CC,CG,GG		0.5116,0.1365,0.3847		111/133	67516605	50,12946	2198	4300	6498	SO:0001819	synonymous_variant	181	exon4			GAAGAAGCGGCAG	U88063	CCDS10839.1	16q22	2014-07-15	2014-07-15		ENSG00000159723	ENSG00000159723		"""Endogenous ligands"""	330	protein-coding gene	gene with protein product		602311	"""agouti (mouse) related protein"", ""agouti related protein homolog (mouse)"""			9119224, 9311920	Standard	NM_001138		Approved	Agrt, ART, ASIP2	uc002etg.1	O00253	OTTHUMG00000137509	ENST00000290953.2:c.333C>G	16.37:g.67516605G>C		138.0	0.0	0		147.0	63.0	0.428571	NM_001138	O15459|Q2TBD9	Silent	SNP	ENST00000290953.2	37	CCDS10839.1																																																																																			G|0.997;C|0.003	0.003	strong		0.637	AGRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268828.1		
TAF7L	54457	hgsc.bcm.edu	37	X	100547804	100547804	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547804G>C	ENST00000372907.3	-	1	241	c.230C>G	c.(229-231)gCc>gGc	p.A77G	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_5'UTR	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	77					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						GTTTTCTGGGGCCTGGGCAGC	0.557																																					p.A77G	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.C230G						PASS	.						69.0	70.0	70.0					X																	100547804		2203	4300	6503	SO:0001583	missense	54457	exon1			TCTGGGGCCTGGG	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.230C>G	X.37:g.100547804G>C	ENSP00000361998:p.Ala77Gly	52.0	0.0	0		47.0	45.0	0.957447	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	G	8.991	0.977721	0.18812	.	.	ENSG00000102387	ENST00000372907	T	0.15834	2.39	3.06	2.19	0.27852	.	2.099320	0.02710	N	0.112725	T	0.12305	0.0299	L	0.27053	0.805	0.09310	N	0.999996	B	0.33694	0.421	B	0.24006	0.05	T	0.24476	-1.0159	10	0.72032	D	0.01	-1.4147	5.2676	0.15607	0.165:0.0:0.8349:0.0	.	77	Q5H9L4	TAF7L_HUMAN	G	77	ENSP00000361998:A77G	ENSP00000361998:A77G	A	-	2	0	TAF7L	100434460	0.006000	0.16342	0.001000	0.08648	0.009000	0.06853	1.723000	0.38053	0.681000	0.31386	0.600000	0.82982	GCC	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
SPATC1L	84221	hgsc.bcm.edu	37	21	47588427	47588427	+	Silent	SNP	G	G	A	rs74486947	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47588427G>A	ENST00000291672.5	-	3	1400	c.339C>T	c.(337-339)ccC>ccT	p.P113P	SPATC1L_ENST00000330205.6_5'UTR	NM_001142854.1	NP_001136326.1	Q9H0A9	SPC1L_HUMAN	spermatogenesis and centriole associated 1-like	113			P -> L (in dbSNP:rs884134).														AGGCCTTGAAGGGTGCCTGGG	0.652													G|||	278	0.0555112	0.1982	0.0202	5008	,	,		15628	0.0		0.002	False		,,,				2504	0.0				p.P113P		Atlas-SNP	.											.	.	.	.	0			c.C339T						PASS	.	G	,	227,1157		18,191,483	41.0	43.0	42.0		339,	1.4	0.9	21	dbSNP_132	42	6,3176		0,6,1585	no	coding-synonymous,utr-5	C21orf56	NM_001142854.1,NM_032261.4	,	18,197,2068	AA,AG,GG		0.1886,16.4017,5.1029	,	113/341,	47588427	233,4333	692	1591	2283	SO:0001819	synonymous_variant	84221	exon3			CTTGAAGGGTGCC	BC009497	CCDS13732.1, CCDS46653.1	21q22.3	2013-01-21	2012-11-12	2012-11-12	ENSG00000160284	ENSG00000160284			1298	protein-coding gene	gene with protein product	"""speriolin-like protein"""	612412	"""chromosome 21 open reading frame 56"""	C21orf56			Standard	NM_032261		Approved		uc011afu.2	Q9H0A9	OTTHUMG00000090487	ENST00000291672.5:c.339C>T	21.37:g.47588427G>A		52.0	0.0	0		90.0	42.0	0.466667	NM_001142854	B4E323|Q52LS9|Q6FIH5|Q6P0L3|Q9NSE5	Silent	SNP	ENST00000291672.5	37	CCDS46653.1																																																																																			G|0.966;A|0.034	0.034	strong		0.652	SPATC1L-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376654.1	NM_032261	
TSPAN16	26526	hgsc.bcm.edu	37	19	11407019	11407019	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11407019T>C	ENST00000316737.1	+	1	196	c.46T>C	c.(46-48)Tct>Cct	p.S16P	TSPAN16_ENST00000592955.1_Missense_Mutation_p.S16P|TSPAN16_ENST00000590327.1_Missense_Mutation_p.S16P	NM_012466.2	NP_036598.1	Q9UKR8	TSN16_HUMAN	tetraspanin 16	16						integral component of membrane (GO:0016021)				breast(1)|endometrium(3)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)|skin(2)|stomach(1)	12						GAAACTGTTATCTTTACTCAA	0.463																																					p.S16P		Atlas-SNP	.											.	TSPAN16	22	.	0			c.T46C						PASS	.						122.0	114.0	117.0					19																	11407019		2203	4300	6503	SO:0001583	missense	26526	exon1			CTGTTATCTTTAC	BC029908	CCDS12256.1, CCDS62549.1, CCDS62550.1	19p13.2	2013-02-14	2005-03-21	2005-03-21	ENSG00000130167	ENSG00000130167		"""Tetraspanins"""	30725	protein-coding gene	gene with protein product			"""transmembrane 4 superfamily member 16"""	TM4SF16		10500248	Standard	NM_012466		Approved	TM4-B, TM-8	uc002mqv.1	Q9UKR8	OTTHUMG00000180833	ENST00000316737.1:c.46T>C	19.37:g.11407019T>C	ENSP00000319486:p.Ser16Pro	126.0	0.0	0		121.0	57.0	0.471074	NM_012466	K7EN22|K7EPD8|Q8N6J7	Missense_Mutation	SNP	ENST00000316737.1	37	CCDS12256.1	.	.	.	.	.	.	.	.	.	.	T	14.76	2.630464	0.46944	.	.	ENSG00000130167	ENST00000316737;ENST00000337994	T;T	0.79554	-1.28;-1.28	3.78	-0.82	0.10826	.	2.367380	0.02315	N	0.072502	T	0.65260	0.2674	N	0.12182	0.205	0.09310	N	1	B	0.15719	0.014	B	0.18263	0.021	T	0.54410	-0.8298	10	0.66056	D	0.02	-0.0342	3.9199	0.09239	0.0:0.3253:0.192:0.4827	.	16	Q9UKR8	TSN16_HUMAN	P	16	ENSP00000319486:S16P;ENSP00000338759:S16P	ENSP00000319486:S16P	S	+	1	0	TSPAN16	11268019	0.000000	0.05858	0.000000	0.03702	0.298000	0.27526	0.403000	0.20982	-0.257000	0.09459	-0.379000	0.06801	TCT	.	.	none		0.463	TSPAN16-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000453204.1	NM_012466	
LSS	4047	hgsc.bcm.edu	37	21	47635686	47635686	+	Missense_Mutation	SNP	C	C	T	rs143692945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47635686C>T	ENST00000397728.3	-	8	883	c.805G>A	c.(805-807)Gcc>Acc	p.A269T	LSS_ENST00000464357.1_5'UTR|LSS_ENST00000356396.4_Missense_Mutation_p.A269T|LSS_ENST00000522411.1_Missense_Mutation_p.A258T|LSS_ENST00000457828.2_Missense_Mutation_p.A189T	NM_001145436.1|NM_002340.5	NP_001138908.1|NP_002331.3	P48449	ERG7_HUMAN	lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase)	269					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)					TCAATGCTGGCGAAGTCCTCC	0.652													C|||	19	0.00379393	0.0136	0.0014	5008	,	,		15065	0.0		0.0	False		,,,				2504	0.0				p.A269T	Pancreas(114;955 2313 34923 50507)	Atlas-SNP	.											.	LSS	50	.	0			c.G805A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA	40,4366	43.1+/-76.7	0,40,2163	28.0	33.0	31.0		805,772,565,805	0.9	0.2	21	dbSNP_134	31	1,8597		0,1,4298	yes	missense,missense,missense,missense	LSS	NM_001001438.2,NM_001145436.1,NM_001145437.1,NM_002340.5	58,58,58,58	0,41,6461	TT,TC,CC		0.0116,0.9079,0.3153	benign,benign,benign,benign	269/733,258/722,189/653,269/733	47635686	41,12963	2203	4299	6502	SO:0001583	missense	4047	exon8			TGCTGGCGAAGTC	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.805G>A	21.37:g.47635686C>T	ENSP00000380837:p.Ala269Thr	87.0	0.0	0		118.0	64.0	0.542373	NM_001001438	B4DJZ9|D3DSN0|E9PEI9|G5E9Q9|Q8IYL6|Q9UEZ1	Missense_Mutation	SNP	ENST00000397728.3	37	CCDS13733.1	5	0.0022893772893772895	5	0.01016260162601626	0	0.0	0	0.0	0	0.0	C	7.049	0.564068	0.13498	0.009079	1.16E-4	ENSG00000160285	ENST00000356396;ENST00000457828;ENST00000397728;ENST00000522411	T;T;T;T	0.29397	1.57;1.57;1.57;1.57	5.32	0.867	0.19085	Terpenoid cylases/protein prenyltransferase alpha-alpha toroid (1);	0.573488	0.18205	N	0.148380	T	0.11410	0.0278	L	0.35542	1.07	0.20873	N	0.999835	B;B	0.31153	0.31;0.206	B;B	0.18561	0.022;0.01	T	0.12268	-1.0554	10	0.28530	T	0.3	.	5.0794	0.14649	0.3294:0.4293:0.0:0.2412	.	258;269	E9PEI9;P48449	.;ERG7_HUMAN	T	269;189;269;258	ENSP00000348762:A269T;ENSP00000409191:A189T;ENSP00000380837:A269T;ENSP00000429133:A258T	ENSP00000348762:A269T	A	-	1	0	LSS	46460114	0.011000	0.17503	0.155000	0.22561	0.080000	0.17528	0.200000	0.17257	0.226000	0.20979	-0.258000	0.10820	GCC	C|0.997;T|0.003	0.003	strong		0.652	LSS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207274.2		
MUC5B	727897	hgsc.bcm.edu	37	11	1258184	1258184	+	Silent	SNP	C	C	T	rs55703838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1258184C>T	ENST00000529681.1	+	25	3145	c.3087C>T	c.(3085-3087)ttC>ttT	p.F1029F	MUC5B_ENST00000447027.1_Silent_p.F1032F	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	1029	VWFD 3. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCGGGAACTTCGACGACAATG	0.672													c|||	25	0.00499201	0.0008	0.0058	5008	,	,		17982	0.0		0.0139	False		,,,				2504	0.0061				p.F1029F		Atlas-SNP	.											.	MUC5B	473	.	0			c.C3087T						PASS	.	C		11,4265		0,11,2127	26.0	34.0	32.0		3087	-4.5	0.8	11	dbSNP_129	32	107,8349		0,107,4121	no	coding-synonymous	MUC5B	NM_002458.2		0,118,6248	TT,TC,CC		1.2654,0.2572,0.9268		1029/5763	1258184	118,12614	2138	4228	6366	SO:0001819	synonymous_variant	727897	exon25			GAACTTCGACGAC	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.3087C>T	11.37:g.1258184C>T		48.0	0.0	0		44.0	21.0	0.477273	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			C|0.993;T|0.007	0.007	strong		0.672	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PSMC4	5704	hgsc.bcm.edu	37	19	40478362	40478362	+	Silent	SNP	T	T	C	rs35555615	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40478362T>C	ENST00000157812.2	+	3	420	c.222T>C	c.(220-222)caT>caC	p.H74H	PSMC4_ENST00000455878.2_Intron	NM_006503.3|NM_153001.2	NP_006494.1|NP_694546.1	P43686	PRS6B_HUMAN	proteasome (prosome, macropain) 26S subunit, ATPase, 4	74					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)|ATP catabolic process (GO:0006200)|blastocyst development (GO:0001824)|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)|proteolysis (GO:0006508)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|cytosolic proteasome complex (GO:0031597)|inclusion body (GO:0016234)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|urinary_tract(1)	19	all_cancers(60;9.55e-06)|all_lung(34;1.17e-07)|Lung NSC(34;1.41e-07)|Ovarian(47;0.0925)					AATTTCTCCATGCCCAGGAGG	0.517													T|||	93	0.0185703	0.0008	0.0115	5008	,	,		16447	0.0		0.0249	False		,,,				2504	0.0603				p.H74H	Colon(105;1478 1543 4034 6132 38638)	Atlas-SNP	.											.	PSMC4	48	.	0			c.T222C						PASS	.	T	,	35,4371	40.0+/-72.8	0,35,2168	77.0	77.0	77.0		222,	-5.6	0.9	19	dbSNP_126	77	297,8303	108.6+/-169.2	10,277,4013	no	coding-synonymous,intron	PSMC4	NM_006503.2,NM_153001.1	,	10,312,6181	CC,CT,TT		3.4535,0.7944,2.5527	,	74/419,	40478362	332,12674	2203	4300	6503	SO:0001819	synonymous_variant	5704	exon3			TCTCCATGCCCAG	U27515	CCDS12547.1, CCDS46076.1	19q13.11-q13.13	2010-04-21			ENSG00000013275	ENSG00000013275		"""Proteasome (prosome, macropain) subunits"", ""ATPases / AAA-type"""	9551	protein-coding gene	gene with protein product	"""protease 26S subunit 6"", ""Tat-binding protein 7"", ""MB67 interacting protein"""	602707		MIP224		9473509, 8603043	Standard	NM_006503		Approved	TBP7, S6, MGC8570, MGC13687, MGC23214, TBP-7	uc002omq.4	P43686		ENST00000157812.2:c.222T>C	19.37:g.40478362T>C		43.0	0.0	0		45.0	15.0	0.333333	NM_006503	Q96FV5|Q9UBM3|Q9UEX3	Silent	SNP	ENST00000157812.2	37	CCDS12547.1																																																																																			T|0.976;C|0.024	0.024	strong		0.517	PSMC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462485.1	NM_006503	
DYDC1	143241	hgsc.bcm.edu	37	10	82098881	82098881	+	Missense_Mutation	SNP	A	A	T	rs35605779	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:82098881A>T	ENST00000372204.3	-	6	535	c.371T>A	c.(370-372)gTt>gAt	p.V124D	DYDC1_ENST00000372202.1_Missense_Mutation_p.V124D|DYDC1_ENST00000421924.2_Missense_Mutation_p.V124D	NM_138812.3	NP_620167.1	Q8WWB3	DYDC1_HUMAN	DPY30 domain containing 1	124										kidney(1)|large_intestine(3)|skin(1)	5			Colorectal(32;0.229)			TTCATTCCTAACTAGATTTTC	0.254													A|||	10	0.00199681	0.0	0.0014	5008	,	,		13230	0.0		0.008	False		,,,				2504	0.001				p.V124D		Atlas-SNP	.											.	DYDC1	15	.	0			c.T371A						PASS	.	A	ASP/VAL	9,4361		0,9,2176	59.0	53.0	55.0		371	-3.6	0.0	10	dbSNP_126	55	106,8454		0,106,4174	yes	missense	DYDC1	NM_138812.2	152	0,115,6350	TT,TA,AA		1.2383,0.2059,0.8894	benign	124/178	82098881	115,12815	2185	4280	6465	SO:0001583	missense	143241	exon5			TTCCTAACTAGAT	BC019250	CCDS7366.1	10q22.3	2006-02-01			ENSG00000170788	ENSG00000170788			23460	protein-coding gene	gene with protein product		615154					Standard	NM_138812		Approved	bA36D19.5, DPY30D1	uc031pwj.1	Q8WWB3	OTTHUMG00000018609	ENST00000372204.3:c.371T>A	10.37:g.82098881A>T	ENSP00000361278:p.Val124Asp	111.0	0.0	0		112.0	51.0	0.455357	NM_001269053	A8K927|Q5QP03|Q5QP04|Q6WNP4|Q6ZU87	Missense_Mutation	SNP	ENST00000372204.3	37	CCDS7366.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	A	3.197	-0.164454	0.06502	0.002059	0.012383	ENSG00000170788	ENST00000372204;ENST00000372202;ENST00000421924;ENST00000454362	.	.	.	4.56	-3.64	0.04515	.	2.257240	0.01811	N	0.033424	T	0.12646	0.0307	N	0.08118	0	0.09310	N	1	B;B	0.24092	0.097;0.057	B;B	0.18871	0.023;0.014	T	0.10405	-1.0631	9	0.30078	T	0.28	5.9472	5.9793	0.19399	0.3843:0.4372:0.1785:0.0	rs35605779	124;124	A8K927;Q8WWB3	.;DYDC1_HUMAN	D	124	.	ENSP00000361276:V124D	V	-	2	0	DYDC1	82088861	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.099000	0.15210	-0.644000	0.05465	-1.276000	0.01395	GTT	A|0.994;T|0.006	0.006	strong		0.254	DYDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049059.1	NM_138812	
GIPR	2696	hgsc.bcm.edu	37	19	46177997	46177997	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46177997G>T	ENST00000590918.1	+	7	645	c.546G>T	c.(544-546)ctG>ctT	p.L182L	MIR642A_ENST00000385039.1_RNA|GIPR_ENST00000263281.3_Silent_p.L182L|GIPR_ENST00000304207.8_Silent_p.L146L	NM_000164.2	NP_000155.1	P48546	GIPR_HUMAN	gastric inhibitory polypeptide receptor	182					activation of adenylate cyclase activity (GO:0007190)|cell surface receptor signaling pathway (GO:0007166)|desensitization of G-protein coupled receptor protein signaling pathway (GO:0002029)|endocrine pancreas development (GO:0031018)|generation of precursor metabolites and energy (GO:0006091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of insulin secretion (GO:0032024)|response to axon injury (GO:0048678)|response to calcium ion (GO:0051592)|response to fatty acid (GO:0070542)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	gastric inhibitory peptide receptor activity (GO:0016519)|peptide hormone binding (GO:0017046)|transmembrane signaling receptor activity (GO:0004888)			endometrium(1)|kidney(2)|lung(5)|prostate(1)|skin(2)|urinary_tract(1)	12		Ovarian(192;0.051)|all_neural(266;0.112)		OV - Ovarian serous cystadenocarcinoma(262;0.0056)|GBM - Glioblastoma multiforme(486;0.0832)|Epithelial(262;0.199)		CTTTCATGCTGCGAGCTGCGG	0.597																																					p.L182L		Atlas-SNP	.											.	GIPR	36	.	0			c.G546T						PASS	.						76.0	67.0	70.0					19																	46177997		2203	4300	6503	SO:0001819	synonymous_variant	2696	exon7			CATGCTGCGAGCT		CCDS12671.1	19q13.2-q13.3	2012-08-10				ENSG00000010310		"""GPCR / Class B : Glucagon receptors"""	4271	protein-coding gene	gene with protein product		137241				7490109	Standard	NM_000164		Approved		uc002pcu.1	P48546		ENST00000590918.1:c.546G>T	19.37:g.46177997G>T		89.0	0.0	0		96.0	48.0	0.5	NM_000164	B7WP14|B7ZKQ0|Q14401|Q16400|Q52M04|Q9UPI1	Silent	SNP	ENST00000590918.1	37	CCDS12671.1																																																																																			.	.	none		0.597	GIPR-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000459640.1		
HNF4A	3172	hgsc.bcm.edu	37	20	43048368	43048368	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:43048368C>T	ENST00000316099.4	+	7	833	c.744C>T	c.(742-744)gaC>gaT	p.D248D	HNF4A_ENST00000443598.2_Silent_p.D248D|HNF4A_ENST00000609795.1_Silent_p.D226D|HNF4A_ENST00000457232.1_Silent_p.D226D|HNF4A_ENST00000316673.4_Silent_p.D226D|HNF4A_ENST00000415691.2_Silent_p.D248D	NM_000457.4|NM_001258355.1|NM_178849.2	NP_000448.3|NP_001245284.1|NP_849180.1	P41235	HNF4A_HUMAN	hepatocyte nuclear factor 4, alpha	248					blood coagulation (GO:0007596)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|glucose homeostasis (GO:0042593)|lipid homeostasis (GO:0055088)|lipid metabolic process (GO:0006629)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|ornithine metabolic process (GO:0006591)|phospholipid homeostasis (GO:0055091)|positive regulation of cholesterol homeostasis (GO:2000189)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gastrulation (GO:0010470)|regulation of growth hormone receptor signaling pathway (GO:0060398)|regulation of insulin secretion (GO:0050796)|regulation of lipid metabolic process (GO:0019216)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|sex differentiation (GO:0007548)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|transcription initiation from RNA polymerase II promoter (GO:0006367)|triglyceride homeostasis (GO:0070328)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|fatty acid binding (GO:0005504)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			endometrium(4)|large_intestine(7)|lung(17)|ovary(1)|pancreas(1)|skin(2)|urinary_tract(2)	34		Myeloproliferative disorder(115;0.0122)	COAD - Colon adenocarcinoma(18;0.00189)			CAGGCAATGACTACATTGTCC	0.582																																					p.D248D	Colon(79;2 1269 8820 14841 52347)	Atlas-SNP	.											.	HNF4A	150	.	0			c.C744T						PASS	.						89.0	79.0	83.0					20																	43048368		2203	4300	6503	SO:0001819	synonymous_variant	3172	exon7			CAATGACTACATT	X76930	CCDS13330.1, CCDS13331.1, CCDS42876.1, CCDS46604.1, CCDS46605.1, CCDS68131.1, CCDS74728.1	20q13.12	2014-09-17			ENSG00000101076	ENSG00000101076		"""Nuclear hormone receptors"""	5024	protein-coding gene	gene with protein product		600281		TCF14, MODY, MODY1		7926813, 9048927	Standard	NM_001030003		Approved	NR2A1, HNF4	uc010zwo.1	P41235	OTTHUMG00000032531	ENST00000316099.4:c.744C>T	20.37:g.43048368C>T		58.0	0.0	0		54.0	24.0	0.444444	NM_178849	A5JW41|B2RPP8|O00659|O00723|Q14540|Q5QPB8|Q6B4V5|Q6B4V6|Q6B4V7|Q92653|Q92654|Q92655|Q99864|Q9NQH0	Silent	SNP	ENST00000316099.4	37	CCDS13330.1																																																																																			.	.	none		0.582	HNF4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079363.3		
BNC2	54796	hgsc.bcm.edu	37	9	16419519	16419519	+	Missense_Mutation	SNP	G	G	A	rs117452684	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	116.0	0.0	0		89.0	46.0	0.516854	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	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7505147	7505147	+	Missense_Mutation	SNP	G	G	T	rs201598844		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7505147G>T	ENST00000359920.6	+	1	574	c.321G>T	c.(319-321)caG>caT	p.Q107H	ARHGEF18_ENST00000319670.9_Intron|CTD-2207O23.3_ENST00000593531.1_Intron	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	107					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				TGCGGCCGCAGTCGGAGCGGG	0.602													G|||	1	0.000199681	0.0	0.0	5008	,	,		13103	0.0		0.0	False		,,,				2504	0.001				p.Q107H		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.G321T						PASS	.						27.0	35.0	33.0					19																	7505147		692	1591	2283	SO:0001583	missense	23370	exon1			GCCGCAGTCGGAG	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.321G>T	19.37:g.7505147G>T	ENSP00000352995:p.Gln107His	74.0	0.0	0		116.0	52.0	0.448276	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	G	7.449	0.642374	0.14451	.	.	ENSG00000104880	ENST00000359920	T	0.30182	1.54	5.23	4.17	0.49024	.	0.187822	0.25607	U	0.029507	T	0.15565	0.0375	N	0.11560	0.145	0.09310	N	0.999997	B	0.10296	0.003	B	0.08055	0.003	T	0.13791	-1.0496	10	0.16896	T	0.51	-7.5996	11.9999	0.53224	0.0:0.0:0.7921:0.2079	.	107	Q6ZSZ5	ARHGI_HUMAN	H	107	ENSP00000352995:Q107H	ENSP00000352995:Q107H	Q	+	3	2	ARHGEF18	7411147	0.006000	0.16342	0.034000	0.17996	0.874000	0.50279	0.359000	0.20233	2.442000	0.82660	0.561000	0.74099	CAG	G|0.999;T|0.001	0.001	weak		0.602	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
PKN1	5585	hgsc.bcm.edu	37	19	14580197	14580197	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14580197G>T	ENST00000242783.6	+	16	2186	c.2021G>T	c.(2020-2022)gGa>gTa	p.G674V	PKN1_ENST00000342216.4_Missense_Mutation_p.G680V	NM_002741.3	NP_002732.3	Q16512	PKN1_HUMAN	protein kinase N1	674	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|epithelial cell migration (GO:0010631)|histone H3-T11 phosphorylation (GO:0035407)|hyperosmotic response (GO:0006972)|protein phosphorylation (GO:0006468)|regulation of cell motility (GO:2000145)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|endosome (GO:0005768)|midbody (GO:0030496)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	androgen receptor binding (GO:0050681)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|GTP-Rho binding (GO:0017049)|histone binding (GO:0042393)|histone deacetylase binding (GO:0042826)|histone kinase activity (H3-T11 specific) (GO:0035402)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein kinase C binding (GO:0005080)|protein serine/threonine kinase activity (GO:0004674)|Rac GTPase binding (GO:0048365)			breast(3)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(6)|lung(11)|ovary(4)|skin(2)|upper_aerodigestive_tract(1)	31						ACCAGTGCGGGACACCCCTTC	0.602																																					p.G680V	NSCLC(185;2539 2965 10733 52867)	Atlas-SNP	.											.	PKN1	99	.	0			c.G2039T						PASS	.						106.0	120.0	116.0					19																	14580197		2123	4227	6350	SO:0001583	missense	5585	exon16			GTGCGGGACACCC	S75546	CCDS42513.1, CCDS42514.1	19p13.12	2008-05-14	2004-07-01	2004-07-01	ENSG00000123143	ENSG00000123143			9405	protein-coding gene	gene with protein product		601032	"""protein kinase C-like 1"""	PRKCL1		9570957	Standard	NM_002741		Approved	DBK, PRK1, PKN, MGC46204, PAK1	uc002myq.3	Q16512	OTTHUMG00000039611	ENST00000242783.6:c.2021G>T	19.37:g.14580197G>T	ENSP00000242783:p.Gly674Val	150.0	0.0	0		142.0	82.0	0.577465	NM_213560	A8K7W5|B2R9R4|B3KVN3|Q15143|Q504U4|Q8IUV5|Q9UD44	Missense_Mutation	SNP	ENST00000242783.6	37	CCDS42513.1	.	.	.	.	.	.	.	.	.	.	G	4.532	0.098772	0.08681	.	.	ENSG00000123143	ENST00000242783;ENST00000342216	T;T	0.25912	1.77;1.77	3.45	3.45	0.39498	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.356188	0.26407	U	0.024542	T	0.20170	0.0485	L	0.39514	1.22	0.28256	N	0.925049	B;B	0.26744	0.131;0.158	B;B	0.26310	0.04;0.068	T	0.13522	-1.0506	10	0.56958	D	0.05	-18.5356	8.9541	0.35807	0.0:0.2289:0.7711:0.0	.	680;674	Q16512-2;Q16512	.;PKN1_HUMAN	V	674;680	ENSP00000242783:G674V;ENSP00000343325:G680V	ENSP00000242783:G674V	G	+	2	0	PKN1	14441197	0.001000	0.12720	0.885000	0.34714	0.129000	0.20672	1.374000	0.34283	1.926000	0.55796	0.491000	0.48974	GGA	.	.	none		0.602	PKN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095510.1	NM_002741, NM_213560	
MCM3AP	8888	hgsc.bcm.edu	37	21	47695220	47695220	+	Silent	SNP	A	A	G	rs2839190	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47695220A>G	ENST00000397708.1	-	7	2132	c.1878T>C	c.(1876-1878)gaT>gaC	p.D626D	MCM3AP_ENST00000291688.1_Silent_p.D626D			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	626					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)					CTTTGTCCAGATCGGTTCTCT	0.473													A|||	700	0.139776	0.4251	0.0591	5008	,	,		19284	0.004		0.0129	False		,,,				2504	0.0818				p.D626D		Atlas-SNP	.											.	MCM3AP	146	.	0			c.T1878C						PASS	.	A		1581,2825	492.9+/-362.5	271,1039,893	97.0	76.0	83.0		1878	-3.5	0.6	21	dbSNP_100	83	114,8486	59.5+/-121.1	1,112,4187	yes	coding-synonymous	MCM3AP	NM_003906.3		272,1151,5080	GG,GA,AA		1.3256,35.8829,13.0324		626/1981	47695220	1695,11311	2203	4300	6503	SO:0001819	synonymous_variant	8888	exon6			GTCCAGATCGGTT	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.1878T>C	21.37:g.47695220A>G		65.0	0.0	0		88.0	42.0	0.477273	NM_003906	C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Silent	SNP	ENST00000397708.1	37	CCDS13734.1																																																																																			A|0.864;G|0.136	0.136	strong		0.473	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1	NM_003906	
MCM8	84515	hgsc.bcm.edu	37	20	5935303	5935303	+	Missense_Mutation	SNP	A	A	C	rs6117014	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:5935303A>C	ENST00000378896.3	+	4	680	c.303A>C	c.(301-303)aaA>aaC	p.K101N	MCM8_ENST00000265187.4_Missense_Mutation_p.K101N|MCM8_ENST00000378886.2_Missense_Mutation_p.K101N|MCM8_ENST00000378883.1_Missense_Mutation_p.K101N	NM_001281520.1|NM_032485.4|NM_182802.1	NP_001268449.1|NP_115874.3|NP_877954.1	Q9UJA3	MCM8_HUMAN	minichromosome maintenance complex component 8	101			K -> N (in dbSNP:rs6117014).		cellular response to DNA damage stimulus (GO:0006974)|DNA replication (GO:0006260)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair via homologous recombination (GO:0000724)|female gamete generation (GO:0007292)|G1/S transition of mitotic cell cycle (GO:0000082)|male gamete generation (GO:0048232)|mitotic cell cycle (GO:0000278)	MCM8-MCM9 complex (GO:0097362)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(9)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	23						CATTTGAAAAATTTTTCACAA	0.373													A|||	351	0.0700879	0.1626	0.1009	5008	,	,		19997	0.001		0.0199	False		,,,				2504	0.046				p.K101N		Atlas-SNP	.											.	MCM8	125	.	0			c.A303C						PASS	.	A	ASN/LYS,ASN/LYS	652,3750	276.0+/-272.9	51,550,1600	101.0	97.0	98.0		303,303	-10.4	0.5	20	dbSNP_114	98	183,8417	83.1+/-145.7	2,179,4119	yes	missense,missense	MCM8	NM_032485.4,NM_182802.1	94,94	53,729,5719	CC,CA,AA		2.1279,14.8114,6.4221	benign,benign	101/841,101/825	5935303	835,12167	2201	4300	6501	SO:0001583	missense	84515	exon4			TGAAAAATTTTTC	AJ439063	CCDS13094.1, CCDS13095.1, CCDS63226.1, CCDS63227.1	20p12.3	2007-04-04	2007-04-04	2003-07-09	ENSG00000125885	ENSG00000125885			16147	protein-coding gene	gene with protein product	"""REC homolog (Drosophila)"""	608187	"""chromosome 20 open reading frame 154"""	C20orf154		12527764	Standard	NM_032485		Approved	MGC4816, MGC12866, MGC119522, MGC119523, dJ967N21.5, REC	uc002wmi.3	Q9UJA3	OTTHUMG00000031822	ENST00000378896.3:c.303A>C	20.37:g.5935303A>C	ENSP00000368174:p.Lys101Asn	87.0	0.0	0		100.0	36.0	0.36	NM_032485	B2RBG7|D3DW08|E7EQU7|Q495R4|Q495R6|Q495R7|Q86US4|Q969I5	Missense_Mutation	SNP	ENST00000378896.3	37	CCDS13094.1	145	0.06639194139194139	92	0.18699186991869918	29	0.08011049723756906	2	0.0034965034965034965	22	0.029023746701846966	A	11.02	1.515159	0.27123	0.148114	0.021279	ENSG00000125885	ENST00000378896;ENST00000378883;ENST00000399350;ENST00000378886;ENST00000265187	T;T;T;T	0.04119	3.7;3.7;3.7;3.7	5.37	-10.4	0.00318	Nucleic acid-binding, OB-fold-like (1);	0.302307	0.39475	N	0.001357	T	0.00012	0.0000	L	0.29908	0.895	0.27511	P	0.9516967	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.06405	0.002;0.001;0.002;0.001	T	0.38265	-0.9669	9	0.11485	T	0.65	-1.2423	2.7834	0.05367	0.2356:0.137:0.3949:0.2325	rs6117014;rs52802444;rs6117014	101;101;101;101	Q9UJA3-2;E7EQU7;Q9UJA3-3;Q9UJA3	.;.;.;MCM8_HUMAN	N	101	ENSP00000368174:K101N;ENSP00000368161:K101N;ENSP00000368164:K101N;ENSP00000265187:K101N	ENSP00000265187:K101N	K	+	3	2	MCM8	5883303	0.041000	0.20044	0.522000	0.27862	0.993000	0.82548	-1.262000	0.02852	-1.754000	0.01321	-0.250000	0.11733	AAA	A|0.936;C|0.064	0.064	strong		0.373	MCM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000077900.1	NM_032485	
IL6ST	3572	hgsc.bcm.edu	37	5	55272085	55272085	+	Missense_Mutation	SNP	G	G	C	rs1063560	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:55272085G>C	ENST00000381298.2	-	3	334	c.22C>G	c.(22-24)Cta>Gta	p.L8V	IL6ST_ENST00000577363.1_5'UTR|IL6ST_ENST00000336909.5_Missense_Mutation_p.L8V|IL6ST_ENST00000381287.4_Missense_Mutation_p.L8V|IL6ST_ENST00000522633.2_Missense_Mutation_p.L8V|IL6ST_ENST00000381286.3_Missense_Mutation_p.L8V|IL6ST_ENST00000502326.3_Missense_Mutation_p.L8V|IL6ST_ENST00000381293.2_Missense_Mutation_p.L8V|IL6ST_ENST00000396816.1_Missense_Mutation_p.L8V|IL6ST_ENST00000536319.1_Missense_Mutation_p.L8V|IL6ST_ENST00000381294.3_Missense_Mutation_p.L8V	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	8			L -> V (in dbSNP:rs1063560). {ECO:0000269|PubMed:10880057, ECO:0000269|PubMed:2261637}.		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)				GCTTGCACTAGCCAAGTCTGC	0.323			O		hepatocellular ca								g|||	42	0.00838658	0.0015	0.0	5008	,	,		12985	0.001		0.0129	False		,,,				2504	0.0266				p.L8V		Atlas-SNP	.		Dom	yes		5	5q11	3572	"""interleukin 6 signal transducer (gp130, oncostatin M receptor)"""		E	.	IL6ST	75	.	0			c.C22G						PASS	.	A	VAL/LEU,VAL/LEU,VAL/LEU	5,4401	9.9+/-24.2	0,5,2198	70.0	64.0	66.0		22,22,22	-1.1	0.0	5	dbSNP_86	66	99,8501	54.4+/-115.2	1,97,4202	yes	missense,missense,missense	IL6ST	NM_001190981.1,NM_002184.3,NM_175767.2	32,32,32	1,102,6400	CC,CG,GG		1.1512,0.1135,0.7996	benign,benign,benign	8/858,8/919,8/330	55272085	104,12902	2203	4300	6503	SO:0001583	missense	3572	exon3			GCACTAGCCAAGT	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.22C>G	5.37:g.55272085G>C	ENSP00000370698:p.Leu8Val	163.0	0.0	0		180.0	82.0	0.455556	NM_175767	A0N0L4|Q5FC04|Q9UQ41	Missense_Mutation	SNP	ENST00000381298.2	37	CCDS3971.1	12	0.005494505494505495	1	0.0020325203252032522	0	0.0	0	0.0	11	0.014511873350923483	g	0.001	-3.108750	0.00033	0.001135	0.011512	ENSG00000134352	ENST00000381298;ENST00000336909;ENST00000381294;ENST00000381287;ENST00000536319;ENST00000381293;ENST00000381286;ENST00000522633;ENST00000542298	T;T;T;T;T;T;T;T	0.61980	1.52;1.52;1.27;1.49;1.49;1.88;0.06;1.49	4.85	-1.07	0.09968	.	0.996520	0.08132	N	0.993050	T	0.35451	0.0932	L	0.40543	1.245	0.09310	N	1	B;B;B;B	0.06786	0.0;0.0;0.001;0.0	B;B;B;B	0.04013	0.001;0.001;0.001;0.0	T	0.17289	-1.0374	10	0.20519	T	0.43	.	0.7244	0.00946	0.2881:0.1764:0.3444:0.1911	rs1063560;rs3204590;rs52794902;rs1063560	8;8;8;8	Q5FC05;Q5FC04;P40189-2;P40189	.;.;.;IL6RB_HUMAN	V	8	ENSP00000370698:L8V;ENSP00000338799:L8V;ENSP00000370694:L8V;ENSP00000370687:L8V;ENSP00000444456:L8V;ENSP00000370693:L8V;ENSP00000370686:L8V;ENSP00000435399:L8V	ENSP00000338799:L8V	L	-	1	2	IL6ST	55307842	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-0.516000	0.06282	-0.573000	0.05998	-3.277000	0.00047	CTA	G|0.989;C|0.011	0.011	strong		0.323	IL6ST-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000214146.3	NM_002184	
BAGE2	85319	hgsc.bcm.edu	37	21	11049616	11049616	+	RNA	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:11049616C>T	ENST00000470054.1	-	0	492							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)		TTTGCATCTTCCTTCGCTATA	0.368																																					p.R95R		Atlas-SNP	.											.	.	.	.	0			c.G285A						PASS	.						135.0	96.0	108.0					21																	11049616		692	1591	2283			85318	exon4			CATCTTCCTTCGC	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.11049616C>T		430.0	0.0	0		388.0	27.0	0.0695876	NM_182481	A8K925|Q08ER0	Silent	SNP	ENST00000470054.1	37																																																																																				.	.	none		0.368	BAGE2-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000157417.3	NM_182482	
SSRP1	6749	hgsc.bcm.edu	37	11	57099661	57099661	+	Silent	SNP	T	T	C	rs2230648	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57099661T>C	ENST00000278412.2	-	8	1232	c.966A>G	c.(964-966)gtA>gtG	p.V322V		NM_003146.2	NP_003137.1	Q08945	SSRP1_HUMAN	structure specific recognition protein 1	322					DNA repair (GO:0006281)|DNA replication (GO:0006260)|gene expression (GO:0010467)|positive regulation of viral transcription (GO:0050434)|regulation of transcription, DNA-templated (GO:0006355)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	chromosome (GO:0005694)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(6)|ovary(2)|prostate(4)	23						TCTTGCGGTTTACCAGTGCTT	0.542													C|||	110	0.0219649	0.0136	0.0389	5008	,	,		22838	0.001		0.0388	False		,,,				2504	0.0256				p.V322V	Colon(89;1000 1340 6884 23013 41819)	Atlas-SNP	.											.	SSRP1	75	.	0			c.A966G						PASS	.	C		104,4298	816.5+/-416.3	1,102,2098	113.0	91.0	98.0		966	0.6	1.0	11	dbSNP_98	98	391,8201	801.2+/-407.4	8,375,3913	no	coding-synonymous	SSRP1	NM_003146.2		9,477,6011	CC,CT,TT		4.5507,2.3626,3.8095		322/710	57099661	495,12499	2201	4296	6497	SO:0001819	synonymous_variant	6749	exon8			GCGGTTTACCAGT	M86737	CCDS7952.1	11q12	2008-02-05			ENSG00000149136	ENSG00000149136			11327	protein-coding gene	gene with protein product	"""facilitates chromatin remodeling 80 kDa subunit"""	604328				1372440	Standard	NM_003146		Approved	FACT80	uc001njt.3	Q08945	OTTHUMG00000167024	ENST00000278412.2:c.966A>G	11.37:g.57099661T>C		73.0	0.0	0		48.0	19.0	0.395833	NM_003146	Q5BJG8	Silent	SNP	ENST00000278412.2	37	CCDS7952.1																																																																																			T|0.967;C|0.033;A|0.000	0.033	strong		0.542	SSRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392460.1	NM_003146	
CENPB	1059	hgsc.bcm.edu	37	20	3766885	3766885	+	Silent	SNP	G	G	A	rs140023764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:3766885G>A	ENST00000379751.4	-	1	452	c.246C>T	c.(244-246)atC>atT	p.I82I	CDC25B_ENST00000379598.5_5'Flank|CDC25B_ENST00000344256.6_5'Flank	NM_001810.5	NP_001801.1	P07199	CENPB_HUMAN	centromere protein B, 80kDa	82	HTH CENPB-type. {ECO:0000255|PROSITE- ProRule:PRU00583}.				regulation of transcription, DNA-templated (GO:0006355)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|nucleus (GO:0005634)	centromeric DNA binding (GO:0019237)|chromatin binding (GO:0003682)|satellite DNA binding (GO:0003696)|sequence-specific DNA binding (GO:0043565)			kidney(1)|large_intestine(2)|lung(4)|skin(1)	8						GGAACCAGGCGATGAGCAAGC	0.657													g|||	16	0.00319489	0.0121	0.0	5008	,	,		8145	0.0		0.0	False		,,,				2504	0.0				p.I82I		Atlas-SNP	.											.	CENPB	24	.	0			c.C246T						PASS	.	G		28,4378	33.5+/-64.1	0,28,2175	67.0	66.0	67.0		246	-0.4	1.0	20	dbSNP_134	67	4,8596	4.3+/-15.6	0,4,4296	no	coding-synonymous	CENPB	NM_001810.5		0,32,6471	AA,AG,GG		0.0465,0.6355,0.246		82/600	3766885	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	1059	exon1			CCAGGCGATGAGC	X05299	CCDS13064.1	20p13	2013-11-05	2002-08-29		ENSG00000125817	ENSG00000125817			1852	protein-coding gene	gene with protein product		117140	"""centromere protein B (80kD)"""			8406460, 11884609	Standard	NM_001810		Approved		uc002wjk.3	P07199	OTTHUMG00000031761	ENST00000379751.4:c.246C>T	20.37:g.3766885G>A		29.0	0.0	0		35.0	16.0	0.457143	NM_001810	Q96EI4	Silent	SNP	ENST00000379751.4	37	CCDS13064.1																																																																																			G|0.997;A|0.003	0.003	strong		0.657	CENPB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077772.2	NM_001810	
PARD6B	84612	hgsc.bcm.edu	37	20	49366879	49366879	+	Silent	SNP	C	C	T	rs41283606	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:49366879C>T	ENST00000371610.2	+	3	1216	c.973C>T	c.(973-975)Cta>Tta	p.L325L	PARD6B_ENST00000396039.1_Intron	NM_032521.2	NP_115910.1	Q9BYG5	PAR6B_HUMAN	par-6 family cell polarity regulator beta	325					axonogenesis (GO:0007409)|cell cycle (GO:0007049)|cell division (GO:0051301)|cell junction assembly (GO:0034329)|cell-cell junction assembly (GO:0007043)|cell-cell junction organization (GO:0045216)|establishment or maintenance of cell polarity (GO:0007163)|protein complex assembly (GO:0006461)|regulation of cell migration (GO:0030334)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				NS(1)|breast(1)|endometrium(1)|kidney(4)|lung(3)|urinary_tract(1)	11						ACAGATAGAGCTAAGCTTTGA	0.433													C|||	6	0.00119808	0.0	0.0	5008	,	,		20869	0.0		0.006	False		,,,				2504	0.0				p.L325L		Atlas-SNP	.											.	PARD6B	31	.	0			c.C973T						PASS	.	C		14,4392	20.2+/-43.8	0,14,2189	109.0	102.0	104.0		973	4.8	0.5	20	dbSNP_127	104	56,8544	35.9+/-90.5	1,54,4245	no	coding-synonymous	PARD6B	NM_032521.2		1,68,6434	TT,TC,CC		0.6512,0.3177,0.5382		325/373	49366879	70,12936	2203	4300	6503	SO:0001819	synonymous_variant	84612	exon3			ATAGAGCTAAGCT	AB044555	CCDS33485.1	20q13.13	2013-08-28	2013-08-28		ENSG00000124171	ENSG00000124171			16245	protein-coding gene	gene with protein product		608975	"""par-6 (partitioning defective 6, C.elegans) homolog beta"", ""par-6 partitioning defective 6 homolog beta (C. elegans)"""			11260256	Standard	NM_032521		Approved	PAR-6B	uc002xvo.3	Q9BYG5	OTTHUMG00000032732	ENST00000371610.2:c.973C>T	20.37:g.49366879C>T		165.0	0.0	0		194.0	98.0	0.505155	NM_032521	A2A2A7|Q9Y510	Silent	SNP	ENST00000371610.2	37	CCDS33485.1																																																																																			C|0.996;T|0.004	0.004	strong		0.433	PARD6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079697.2	NM_032521	
SGCD	6444	hgsc.bcm.edu	37	5	155935708	155935708	+	Missense_Mutation	SNP	G	G	A	rs45559835	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:155935708G>A	ENST00000435422.3	+	3	774	c.287G>A	c.(286-288)cGa>cAa	p.R96Q	SGCD_ENST00000337851.4_Missense_Mutation_p.R97Q|SGCD_ENST00000447401.1_Missense_Mutation_p.R97Q|SGCD_ENST00000517913.1_Missense_Mutation_p.R97Q	NM_001128209.1	NP_001121681.1	Q92629	SGCD_HUMAN	sarcoglycan, delta (35kDa dystrophin-associated glycoprotein)	96			R -> Q (in dbSNP:rs1801194). {ECO:0000269|PubMed:8842738}.		muscle organ development (GO:0007517)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dystrophin-associated glycoprotein complex (GO:0016010)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcoglycan complex (GO:0016012)|sarcolemma (GO:0042383)				breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(16)|prostate(1)	24	Renal(175;0.00488)	Medulloblastoma(196;0.0378)|all_neural(177;0.106)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			ATCCAGTCCCGACCAGTAAGT	0.438													G|||	95	0.0189696	0.003	0.0317	5008	,	,		17897	0.0		0.0517	False		,,,				2504	0.0174				p.R97Q		Atlas-SNP	.											SGCD,NS,carcinoma,+1,1	SGCD	52	1	0			c.G290A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	44,3666		0,44,1811	76.0	69.0	71.0		290,287,290	5.5	1.0	5	dbSNP_127	71	527,7677		14,499,3589	yes	missense,missense,missense	SGCD	NM_000337.5,NM_001128209.1,NM_172244.2	43,43,43	14,543,5400	AA,AG,GG		6.4237,1.186,4.7927	benign,benign,benign	97/291,96/290,97/257	155935708	571,11343	1855	4102	5957	SO:0001583	missense	6444	exon4			AGTCCCGACCAGT	BX537948	CCDS47325.1, CCDS47326.1, CCDS47327.1	5q33-q34	2014-09-17	2002-08-29						10807	protein-coding gene	gene with protein product		601411	"""sarcoglycan, delta (35kD dystrophin-associated glycoprotein)"""			8776597, 8841194, 10974018	Standard	NM_000337		Approved	DAGD, LGMD2F, CMD1L	uc003lwd.4	Q92629		ENST00000435422.3:c.287G>A	5.37:g.155935708G>A	ENSP00000403003:p.Arg96Gln	60.0	0.0	0		61.0	26.0	0.42623	NM_000337	A8K9S9|Q53XA5|Q99644	Missense_Mutation	SNP	ENST00000435422.3	37	CCDS47327.1	49	0.022435897435897436	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	34	0.044854881266490766	G	26.3	4.727809	0.89390	0.01186	0.064237	ENSG00000170624	ENST00000517913;ENST00000435422;ENST00000337851;ENST00000447401	D;D;D;D	0.95656	-3.77;-3.77;-3.77;-3.77	5.49	5.49	0.81192	.	0.127312	0.53938	D	0.000051	T	0.71685	0.3369	M	0.78049	2.395	0.43559	D	0.99587	P;P;D	0.56287	0.826;0.792;0.975	B;B;B	0.39738	0.105;0.063;0.308	T	0.80774	-0.1232	10	0.27082	T	0.32	-2.0249	12.2832	0.54776	0.0783:0.0:0.9217:0.0	rs45559835;rs61742485	96;97;97	Q92629;Q92629-2;Q92629-3	SGCD_HUMAN;.;.	Q	97;96;97;97	ENSP00000429378:R97Q;ENSP00000403003:R96Q;ENSP00000338343:R97Q;ENSP00000408324:R97Q	ENSP00000338343:R97Q	R	+	2	0	SGCD	155868286	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.094000	0.57721	2.732000	0.93576	0.585000	0.79938	CGA	G|0.972;A|0.028	0.028	strong		0.438	SGCD-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000373469.3		
SPICE1	152185	hgsc.bcm.edu	37	3	113175984	113175984	+	Splice_Site	SNP	G	G	A	rs146846950	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:113175984G>A	ENST00000295872.4	-	13	1915	c.1656C>T	c.(1654-1656)gaC>gaT	p.D552D		NM_144718.3	NP_653319.1	Q8N0Z3	SPICE_HUMAN	spindle and centriole associated protein 1	552					metaphase plate congression (GO:0051310)|regulation of centriole replication (GO:0046599)|spindle assembly involved in mitosis (GO:0090307)	centriole (GO:0005814)|centrosome (GO:0005813)|spindle (GO:0005819)				NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(3)|large_intestine(9)|lung(10)|ovary(2)|skin(2)|urinary_tract(1)	33						AAGACTTACCGTCCTGAAGAG	0.353													g|||	46	0.0091853	0.0008	0.0014	5008	,	,		19525	0.0		0.0119	False		,,,				2504	0.0327				p.D552D		Atlas-SNP	.											SPICE1_ENST00000295872,NS,carcinoma,0,2	SPICE1	130	2	0			c.C1656T						PASS	.	A		3,4403	6.2+/-15.9	0,3,2200	55.0	55.0	55.0		1656	-11.3	0.8	3	dbSNP_134	55	46,8554	30.7+/-82.3	0,46,4254	yes	coding-synonymous-near-splice	SPICE1	NM_144718.3		0,49,6454	AA,AG,GG		0.5349,0.0681,0.3767		552/856	113175984	49,12957	2203	4300	6503	SO:0001630	splice_region_variant	152185	exon13			CTTACCGTCCTGA	AY099107	CCDS2973.1	3q13.2	2010-09-01	2010-09-01	2010-09-01	ENSG00000163611	ENSG00000163611			25083	protein-coding gene	gene with protein product	"""spindle and centriole protein"""	613447	"""coiled-coil domain containing 52"""	CCDC52		20736305	Standard	NM_144718		Approved	SPICE	uc003eag.4	Q8N0Z3	OTTHUMG00000159261	ENST00000295872.4:c.1657+1C>T	3.37:g.113175984G>A		46.0	0.0	0		45.0	24.0	0.533333	NM_144718	D3DN72|Q8WUX6	Silent	SNP	ENST00000295872.4	37	CCDS2973.1																																																																																			G|0.995;A|0.005	0.005	strong		0.353	SPICE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354177.2	NM_144718	Silent
PTCRA	171558	hgsc.bcm.edu	37	6	42893254	42893254	+	Missense_Mutation	SNP	G	G	A	rs146531157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42893254G>A	ENST00000304672.1	+	4	761	c.680G>A	c.(679-681)cGg>cAg	p.R227Q	PTCRA_ENST00000446507.1_Missense_Mutation_p.R120Q|PTCRA_ENST00000441198.1_Missense_Mutation_p.R202Q	NM_001243168.1|NM_138296.2	NP_001230097.1|NP_612153.2	Q6ISU1	PTCRA_HUMAN	pre T-cell antigen receptor alpha	227					negative regulation of thymocyte apoptotic process (GO:0070244)	integral component of membrane (GO:0016021)				large_intestine(2)|lung(4)|ovary(2)	8	Colorectal(47;0.196)		all cancers(41;0.000731)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|KIRC - Kidney renal clear cell carcinoma(15;0.02)|OV - Ovarian serous cystadenocarcinoma(102;0.0218)|Kidney(15;0.0388)			CCTCCGGGTCGGAAGCCCGGG	0.682													G|||	6	0.00119808	0.0	0.0014	5008	,	,		14322	0.0		0.005	False		,,,				2504	0.0				p.R242Q		Atlas-SNP	.											.	PTCRA	24	.	0			c.G725A						PASS	.	G	GLN/ARG	1,4387		0,1,2193	15.0	14.0	14.0		680	-6.3	0.0	6	dbSNP_134	14	41,8511		0,41,4235	yes	missense	PTCRA	NM_138296.2	43	0,42,6428	AA,AG,GG		0.4794,0.0228,0.3246	benign	227/282	42893254	42,12898	2194	4276	6470	SO:0001583	missense	171558	exon4			CGGGTCGGAAGCC	AF084941	CCDS4874.1, CCDS59019.1, CCDS59020.1, CCDS75457.1	6p21.3	2008-02-05			ENSG00000171611	ENSG00000171611			21290	protein-coding gene	gene with protein product		606817				8618853, 9842925	Standard	NM_138296		Approved	PTA, PT-ALPHA	uc021yzp.1	Q6ISU1	OTTHUMG00000014709	ENST00000304672.1:c.680G>A	6.37:g.42893254G>A	ENSP00000304447:p.Arg227Gln	52.0	0.0	0		45.0	25.0	0.555556	NM_001243168	Q5TFZ7	Missense_Mutation	SNP	ENST00000304672.1	37	CCDS4874.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	7.257	0.604442	0.14002	2.28E-4	0.004794	ENSG00000171611	ENST00000304672;ENST00000441198;ENST00000446507;ENST00000418903	T;T;T	0.55234	1.21;1.18;0.53	3.14	-6.28	0.02020	.	1.969100	0.03135	N	0.165837	T	0.10423	0.0255	N	0.14661	0.345	0.09310	N	1	B;B;B	0.15930	0.015;0.006;0.002	B;B;B	0.08055	0.003;0.003;0.003	T	0.03315	-1.1049	10	0.59425	D	0.04	.	1.8301	0.03128	0.3078:0.3482:0.2246:0.1194	.	120;202;227	Q6ISU1-2;Q6ISU1-3;Q6ISU1	.;.;PTCRA_HUMAN	Q	227;202;120;73	ENSP00000304447:R227Q;ENSP00000409550:R202Q;ENSP00000392288:R120Q	ENSP00000304447:R227Q	R	+	2	0	PTCRA	43001232	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-2.350000	0.01092	-2.666000	0.00416	-0.175000	0.13238	CGG	G|0.999;A|0.001	0.001	strong		0.682	PTCRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040565.2	NM_138296	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057666	46057666	+	Missense_Mutation	SNP	A	A	T	rs116100696	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057666A>T	ENST00000380095.1	+	1	394	c.332A>T	c.(331-333)aAg>aTg	p.K111M	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	111	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						gtctgtaacaagcctgtgtgc	0.632													A|||	91	0.0181709	0.0651	0.0072	5008	,	,		20883	0.0		0.0	False		,,,				2504	0.0				p.K111M		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.A332T						PASS	.	A	,MET/LYS	231,4175	136.5+/-172.5	10,211,1982	222.0	189.0	200.0		,332	-6.2	0.0	21	dbSNP_132	200	0,8600		0,0,4300	yes	intron,missense	TSPEAR,KRTAP10-10	NM_144991.2,NM_181688.1	,95	10,211,6282	TT,TA,AA		0.0,5.2429,1.7761	,benign	,111/252	46057666	231,12775	2203	4300	6503	SO:0001583	missense	353333	exon1			GTAACAAGCCTGT	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.332A>T	21.37:g.46057666A>T	ENSP00000369438:p.Lys111Met	140.0	0.0	0		150.0	90.0	0.6	NM_181688		Missense_Mutation	SNP	ENST00000380095.1	37	CCDS33585.1	35	0.016025641025641024	32	0.06504065040650407	3	0.008287292817679558	0	0.0	0	0.0	a	6.984	0.551656	0.13374	0.052429	0.0	ENSG00000221859	ENST00000380095	T	0.01438	4.89	3.13	-6.25	0.02039	.	.	.	.	.	T	0.00241	0.0007	M	0.84846	2.72	0.09310	N	1	P	0.47302	0.893	P	0.46543	0.52	T	0.00529	-1.1687	9	0.52906	T	0.07	.	0.1928	0.00136	0.2301:0.2328:0.1914:0.3458	.	111	P60014	KR10A_HUMAN	M	111	ENSP00000369438:K111M	ENSP00000369438:K111M	K	+	2	0	KRTAP10-10	44882094	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.719000	0.04974	-2.037000	0.00920	-0.711000	0.03637	AAG	A|0.982;T|0.018	0.018	strong		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
ACSL3	2181	hgsc.bcm.edu	37	2	223799388	223799388	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:223799388C>T	ENST00000357430.3	+	16	2519	c.1988C>T	c.(1987-1989)tCc>tTc	p.S663F	ACSL3_ENST00000392066.3_Missense_Mutation_p.S663F|AC013476.1_ENST00000582868.1_RNA	NM_004457.3	NP_004448.2	O95573	ACSL3_HUMAN	acyl-CoA synthetase long-chain family member 3	663					brain development (GO:0007420)|fatty acid biosynthetic process (GO:0006633)|long-chain fatty acid import (GO:0044539)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)|positive regulation of phosphatidylcholine biosynthetic process (GO:2001247)|positive regulation of secretion (GO:0051047)|response to nutrient (GO:0007584)|response to organic cyclic compound (GO:0014070)|very-low-density lipoprotein particle assembly (GO:0034379)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lipid particle (GO:0005811)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|perinuclear region of cytoplasm (GO:0048471)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|long-chain fatty acid-CoA ligase activity (GO:0004467)|protein domain specific binding (GO:0019904)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)|skin(2)	22		Renal(207;0.0183)		Epithelial(121;1.28e-10)|all cancers(144;8.06e-08)|Lung(261;0.00834)|LUSC - Lung squamous cell carcinoma(224;0.00864)	Icosapent(DB00159)	AAAGTGCTTTCCGAAGCTGCT	0.398			T	ETV1	prostate																																p.S663F		Atlas-SNP	.		Dom	yes		2	2q36	2181	acyl-CoA synthetase long-chain family member 3		E	.	ACSL3	107	.	0			c.C1988T						PASS	.						123.0	111.0	115.0					2																	223799388		2203	4300	6503	SO:0001583	missense	2181	exon15			TGCTTTCCGAAGC	D89053	CCDS2455.1	2q34-q35	2008-02-05	2004-02-19	2004-02-20	ENSG00000123983	ENSG00000123983		"""Acyl-CoA synthetase family"""	3570	protein-coding gene	gene with protein product		602371	"""fatty-acid-Coenzyme A ligase, long-chain 3"""	FACL3			Standard	NM_004457		Approved	ACS3, PRO2194	uc002vnj.3	O95573	OTTHUMG00000133160	ENST00000357430.3:c.1988C>T	2.37:g.223799388C>T	ENSP00000350012:p.Ser663Phe	113.0	0.0	0		101.0	44.0	0.435644	NM_203372	Q60I92|Q8IUM9	Missense_Mutation	SNP	ENST00000357430.3	37	CCDS2455.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.26|19.26	3.793730|3.793730	0.70452|0.70452	.|.	.|.	ENSG00000123983|ENSG00000123983	ENST00000407441|ENST00000357430;ENST00000392066	.|T;T	.|0.11277	.|2.79;2.79	5.79|5.79	5.79|5.79	0.91817|0.91817	.|.	.|0.106594	.|0.64402	.|D	.|0.000004	T|T	0.15825|0.15825	0.0381|0.0381	L|L	0.43152|0.43152	1.355|1.355	0.58432|0.58432	D|D	0.999991|0.999991	.|B	.|0.27625	.|0.183	.|B	.|0.33392	.|0.163	T|T	0.02539|0.02539	-1.1144|-1.1144	5|10	.|0.56958	.|D	.|0.05	-17.9388|-17.9388	20.0411|20.0411	0.97590|0.97590	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|663	.|O95573	.|ACSL3_HUMAN	S|F	164|663	.|ENSP00000350012:S663F;ENSP00000375918:S663F	.|ENSP00000350012:S663F	P|S	+|+	1|2	0|0	ACSL3|ACSL3	223507632|223507632	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.987000|0.987000	0.75469|0.75469	3.908000|3.908000	0.56355|0.56355	2.739000|2.739000	0.93911|0.93911	0.655000|0.655000	0.94253|0.94253	CCG|TCC	.	.	none		0.398	ACSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256862.2	NM_004457	
TMEM30A	55754	hgsc.bcm.edu	37	6	75965985	75965985	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:75965985G>A	ENST00000230461.6	-	7	1248	c.919C>T	c.(919-921)Cga>Tga	p.R307*	TMEM30A_ENST00000475111.2_Nonsense_Mutation_p.R271*|TMEM30A_ENST00000370050.5_Nonsense_Mutation_p.R188*	NM_018247.3	NP_060717.1	Q9NV96	CC50A_HUMAN	transmembrane protein 30A	307					drug transmembrane transport (GO:0006855)|phospholipid translocation (GO:0045332)|positive regulation of neuron projection development (GO:0010976)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|protein localization to endosome (GO:0036010)	cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(8)|kidney(1)|large_intestine(4)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						ATCCGTTTTCGTCCATCAAAA	0.378																																					p.R307X		Atlas-SNP	.											TMEM30A,NS,carcinoma,+1,3	TMEM30A	40	3	0			c.C919T						PASS	.						105.0	101.0	102.0					6																	75965985		2203	4300	6503	SO:0001587	stop_gained	55754	exon7			GTTTTCGTCCATC	AK001718	CCDS4983.1, CCDS47453.1	6q14.1	2014-01-28	2004-06-17	2004-06-18	ENSG00000112697	ENSG00000112697			16667	protein-coding gene	gene with protein product		611028	"""chromosome 6 open reading frame 67"""	C6orf67		15375526	Standard	NM_001143958		Approved	FLJ10856, CDC50A	uc003phw.2	Q9NV96	OTTHUMG00000015050	ENST00000230461.6:c.919C>T	6.37:g.75965985G>A	ENSP00000230461:p.Arg307*	83.0	0.0	0		55.0	41.0	0.745455	NM_018247	A8K9V8|E1P539|Q658Z3|Q96H09|Q9NSL9	Nonsense_Mutation	SNP	ENST00000230461.6	37	CCDS4983.1	.	.	.	.	.	.	.	.	.	.	G	39	7.619958	0.98393	.	.	ENSG00000112697	ENST00000230461;ENST00000545449;ENST00000370050;ENST00000475111	.	.	.	5.88	5.88	0.94601	.	0.055311	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	.	13.6255	0.62161	0.0:0.0:0.7294:0.2706	.	.	.	.	X	307;291;188;271	.	ENSP00000230461:R307X	R	-	1	2	TMEM30A	76022705	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.821000	0.55700	2.780000	0.95670	0.655000	0.94253	CGA	.	.	none		0.378	TMEM30A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041248.2	NM_018247	
WDR17	116966	hgsc.bcm.edu	37	4	177089839	177089839	+	Missense_Mutation	SNP	C	C	G	rs375753370|rs140459637	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:177089839C>G	ENST00000280190.4	+	25	3280	c.3124C>G	c.(3124-3126)Ctt>Gtt	p.L1042V	WDR17_ENST00000508596.1_Missense_Mutation_p.L1003V|WDR17_ENST00000393643.2_Missense_Mutation_p.L1018V|WDR17_ENST00000507824.2_Missense_Mutation_p.L1017V			Q8IZU2	WDR17_HUMAN	WD repeat domain 17	1042										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(18)|lung(46)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	92		Breast(14;0.00015)|Melanoma(52;0.00886)|Prostate(90;0.00996)|Renal(120;0.0183)|all_hematologic(60;0.107)|all_neural(102;0.164)		all cancers(43;2.21e-20)|Epithelial(43;9.71e-18)|OV - Ovarian serous cystadenocarcinoma(60;2.38e-09)|GBM - Glioblastoma multiforme(59;0.000295)|STAD - Stomach adenocarcinoma(60;0.000703)|LUSC - Lung squamous cell carcinoma(193;0.0232)		GGCAGCTGATCTTCTTCTGAT	0.348													C|||	16	0.00319489	0.0	0.0029	5008	,	,		17511	0.0		0.0129	False		,,,				2504	0.001				p.L1042V		Atlas-SNP	.											.	WDR17	198	.	0			c.C3124G						PASS	.	C	VAL/LEU,VAL/LEU	4,4402	8.1+/-20.4	0,4,2199	140.0	134.0	136.0		3124,3007	5.1	1.0	4	dbSNP_134	136	50,8550	33.3+/-86.6	0,50,4250	yes	missense,missense	WDR17	NM_170710.4,NM_181265.3	32,32	0,54,6449	GG,GC,CC		0.5814,0.0908,0.4152	possibly-damaging,possibly-damaging	1042/1323,1003/1284	177089839	54,12952	2203	4300	6503	SO:0001583	missense	116966	exon25			GCTGATCTTCTTC	AF492460	CCDS3825.1, CCDS43284.1, CCDS43284.2	4q34	2013-01-09			ENSG00000150627	ENSG00000150627		"""WD repeat domain containing"""	16661	protein-coding gene	gene with protein product		609005				12401215	Standard	NM_170710		Approved		uc003iuj.3	Q8IZU2	OTTHUMG00000160791	ENST00000280190.4:c.3124C>G	4.37:g.177089839C>G	ENSP00000280190:p.Leu1042Val	150.0	0.0	0		131.0	51.0	0.389313	NM_170710	E7EQX0|Q0QD35	Missense_Mutation	SNP	ENST00000280190.4	37	CCDS3825.1	10|10	0.004578754578754579|0.004578754578754579	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	9|9	0.011873350923482849|0.011873350923482849	C|C	12.08|12.08	1.831352|1.831352	0.32329|0.32329	9.08E-4|9.08E-4	0.005814|0.005814	ENSG00000150627|ENSG00000150627	ENST00000508596;ENST00000393643;ENST00000280190;ENST00000507824|ENST00000443118	T;T;T|.	0.61392|.	0.31;0.18;0.11|.	5.1|5.1	5.1|5.1	0.69264|0.69264	.|.	0.000000|.	0.64402|.	D|.	0.000001|.	T|T	0.68302|0.68302	0.2986|0.2986	M|M	0.68317|0.68317	2.08|2.08	0.53688|0.53688	D|D	0.999974|0.999974	D;D;D|.	0.76494|.	0.97;0.999;0.999|.	P;D;D|.	0.77557|.	0.591;0.99;0.99|.	T|T	0.70857|0.70857	-0.4758|-0.4758	10|5	0.56958|.	D|.	0.05|.	-22.4333|-22.4333	18.6954|18.6954	0.91599|0.91599	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	1018;1003;1042|.	E7EP77;E7EQX0;Q8IZU2|.	.;.;WDR17_HUMAN|.	V|C	1003;1018;1042;1018|276	ENSP00000422763:L1003V;ENSP00000377258:L1018V;ENSP00000280190:L1042V|.	ENSP00000280190:L1042V|.	L|S	+|+	1|2	0|0	WDR17|WDR17	177326833|177326833	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.055000|0.055000	0.15305|0.15305	4.228000|4.228000	0.58619|0.58619	2.647000|2.647000	0.89833|0.89833	0.591000|0.591000	0.81541|0.81541	CTT|TCT	C|0.995;G|0.005	0.005	strong		0.348	WDR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362334.2		
DUXA	503835	hgsc.bcm.edu	37	19	57669827	57669827	+	Missense_Mutation	SNP	G	G	A	rs140589597	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:57669827G>A	ENST00000554048.2	-	4	306	c.307C>T	c.(307-309)Cgg>Tgg	p.R103W		NM_001012729.1	NP_001012747.1	A6NLW8	DUXA_HUMAN	double homeobox A	103					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(2)|central_nervous_system(1)|endometrium(1)|large_intestine(2)|lung(9)|ovary(1)|upper_aerodigestive_tract(1)	17		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Ovarian(87;0.0822)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0123)		GTACGACACCGTCTGGCTTCT	0.468																																					p.R103W		Atlas-SNP	.											DUXA,NS,carcinoma,+1,3	DUXA	46	3	0			c.C307T						PASS	.	G	TRP/ARG	0,4406		0,0,2203	64.0	64.0	64.0		307	2.8	0.1	19	dbSNP_134	64	6,8594	4.3+/-15.6	0,6,4294	yes	missense	DUXA	NM_001012729.1	101	0,6,6497	AA,AG,GG		0.0698,0.0,0.0461	probably-damaging	103/205	57669827	6,13000	2203	4300	6503	SO:0001583	missense	503835	exon4			GACACCGTCTGGC		CCDS33126.1	19q13.43	2012-10-04			ENSG00000258873	ENSG00000258873		"""Homeoboxes / PRD class"""	32179	protein-coding gene	gene with protein product		611168					Standard	NM_001012729		Approved		uc002qoa.1	A6NLW8	OTTHUMG00000170714	ENST00000554048.2:c.307C>T	19.37:g.57669827G>A	ENSP00000452398:p.Arg103Trp	100.0	0.0	0		80.0	37.0	0.4625	NM_001012729		Missense_Mutation	SNP	ENST00000554048.2	37	CCDS33126.1	.	.	.	.	.	.	.	.	.	.	G	14.63	2.593578	0.46214	0.0	6.98E-4	ENSG00000258873	ENST00000554048	D	0.96940	-4.18	2.85	2.85	0.33270	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.281548	0.19295	N	0.117793	D	0.98213	0.9409	M	0.93507	3.425	0.09310	N	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92627	0.6113	10	0.87932	D	0	-12.0051	9.41	0.38485	0.0:0.0:1.0:0.0	.	103	A6NLW8	DUXA_HUMAN	W	103	ENSP00000452398:R103W	ENSP00000365415:R103W	R	-	1	2	DUXA	62361639	0.030000	0.19436	0.064000	0.19789	0.033000	0.12548	0.925000	0.28791	1.900000	0.55004	0.655000	0.94253	CGG	G|0.999;A|0.001	0.001	strong		0.468	DUXA-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410075.3	NM_001012729	
SLC22A18	5002	hgsc.bcm.edu	37	11	2929502	2929502	+	Missense_Mutation	SNP	G	G	T	rs143044180	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2929502G>T	ENST00000380574.1	+	3	615	c.184G>T	c.(184-186)Ggc>Tgc	p.G62C	SLC22A18_ENST00000312221.5_Missense_Mutation_p.G62C|SLC22A18_ENST00000347936.2_Missense_Mutation_p.G62C|SLC22A18_ENST00000449793.2_Missense_Mutation_p.G62C			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													G|||	5	0.000998403	0.0	0.0029	5008	,	,		15811	0.0		0.002	False		,,,				2504	0.001				p.G62C		Atlas-SNP	.											SLC22A18,NS,carcinoma,0,1	SLC22A18	20	1	0			c.G184T						PASS	.	G	CYS/GLY,CYS/GLY	2,4402	4.2+/-10.8	0,2,2200	86.0	82.0	84.0		184,184	3.3	0.9	11	dbSNP_134	84	33,8565	22.8+/-68.1	0,33,4266	yes	missense,missense	SLC22A18	NM_002555.5,NM_183233.2	159,159	0,35,6466	TT,TG,GG		0.3838,0.0454,0.2692	probably-damaging,probably-damaging	62/425,62/425	2929502	35,12967	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>T	11.37:g.2929502G>T	ENSP00000369948:p.Gly62Cys	92.0	0.0	0		81.0	45.0	0.555556	NM_002555	O14906|O43562|O60485|O60680|Q7LDS5|Q7LGF7	Missense_Mutation	SNP	ENST00000380574.1	37	CCDS7740.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	13.97	2.395838	0.42512	4.54E-4	0.003838	ENSG00000110628	ENST00000347936;ENST00000312221;ENST00000449793;ENST00000380574;ENST00000485423	T;T;T;T;D	0.86097	-0.21;-0.21;-0.21;-0.21;-2.07	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	0.90861	0.7129	M	0.83953	2.67	0.58432	D	0.99999	D;D	0.89917	1.0;1.0	D;D	0.97110	0.986;1.0	D	0.90662	0.4591	10	0.87932	D	0	-1.8758	7.3817	0.26859	0.1199:0.0:0.8801:0.0	.	62;62	E9PRM7;Q96BI1	.;S22AI_HUMAN	C	62	ENSP00000307859:G62C;ENSP00000311139:G62C;ENSP00000392072:G62C;ENSP00000369948:G62C;ENSP00000433019:G62C	ENSP00000311139:G62C	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	0.002	strong		0.617	SLC22A18-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027770.1	NM_183233	
MTUS2	23281	hgsc.bcm.edu	37	13	29675049	29675049	+	Silent	SNP	A	A	T	rs140464903	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:29675049A>T	ENST00000431530.3	+	3	2674	c.2616A>T	c.(2614-2616)tcA>tcT	p.S872S		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	862	Localization to the growing distal tip of microtubules.|Mediates interaction with MAPRE1.|Sufficient for interaction with KIF2C.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						GCGTCTCCTCAGTCTCCAGCA	0.632													A|||	114	0.0227636	0.0053	0.0259	5008	,	,		12307	0.002		0.0596	False		,,,				2504	0.0276				p.S872S		Atlas-SNP	.											MTUS2_ENST00000431530,NS,carcinoma,0,1	MTUS2	279	1	0			c.A2616T						PASS	.	A		41,4015		1,39,1988	8.0	9.0	9.0		2616	-10.5	0.0	13	dbSNP_134	9	361,8001		4,353,3824	no	coding-synonymous	MTUS2	NM_001033602.2		5,392,5812	TT,TA,AA		4.3171,1.0108,3.2372		872/1380	29675049	402,12016	2028	4181	6209	SO:0001819	synonymous_variant	23281	exon3			CTCCTCAGTCTCC	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2616A>T	13.37:g.29675049A>T		72.0	0.0	0		87.0	40.0	0.45977	NM_001033602	A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Silent	SNP	ENST00000431530.3	37	CCDS45022.1																																																																																			A|0.965;T|0.035	0.035	strong		0.632	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
GLTSCR1L	23506	hgsc.bcm.edu	37	6	42832683	42832683	+	Silent	SNP	G	G	A	rs10456519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:42832683G>A	ENST00000314073.5	+	13	2915	c.2739G>A	c.(2737-2739)caG>caA	p.Q913Q	GLTSCR1L_ENST00000394168.1_Silent_p.Q913Q			Q6AI39	GSC1L_HUMAN	GLTSCR1-like	913																	GCTTAGTGCAGTACCAGAGCA	0.517													G|||	36	0.0071885	0.0053	0.0101	5008	,	,		19729	0.001		0.0129	False		,,,				2504	0.0082				p.Q913Q		Atlas-SNP	.											.	.	.	.	0			c.G2739A						PASS	.	G		30,4376	36.8+/-68.6	0,30,2173	51.0	50.0	50.0		2739	-3.0	0.1	6	dbSNP_119	50	96,8504	52.7+/-113.3	3,90,4207	no	coding-synonymous	KIAA0240	NM_015349.1		3,120,6380	AA,AG,GG		1.1163,0.6809,0.9688		913/1080	42832683	126,12880	2203	4300	6503	SO:0001819	synonymous_variant	23506	exon12			AGTGCAGTACCAG	AL833540	CCDS34451.1	6p21.1	2012-11-29	2012-11-29	2012-11-29	ENSG00000112624	ENSG00000112624			21111	protein-coding gene	gene with protein product			"""KIAA0240"""	KIAA0240			Standard	XM_005248972		Approved		uc003osp.1	Q6AI39	OTTHUMG00000014706	ENST00000314073.5:c.2739G>A	6.37:g.42832683G>A		40.0	0.0	0		59.0	28.0	0.474576	NM_015349	A1L3W2|Q5TFZ3|Q92514	Silent	SNP	ENST00000314073.5	37	CCDS34451.1																																																																																			G|0.989;A|0.011	0.011	strong		0.517	GLTSCR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040562.3	NM_015349	
NSD1	64324	hgsc.bcm.edu	37	5	176721879	176721879	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176721879G>A	ENST00000439151.2	+	23	7555	c.7510G>A	c.(7510-7512)Gtt>Att	p.V2504I	NSD1_ENST00000354179.4_Missense_Mutation_p.V2235I|NSD1_ENST00000347982.4_Missense_Mutation_p.V2235I|NSD1_ENST00000361032.4_Missense_Mutation_p.V2401I	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	2504					gastrulation with mouth forming second (GO:0001702)|histone H3-K36 methylation (GO:0010452)|histone H4-K20 methylation (GO:0034770)|histone methylation (GO:0016571)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|estrogen receptor binding (GO:0030331)|histone methyltransferase activity (H3-K36 specific) (GO:0046975)|histone methyltransferase activity (H4-K20 specific) (GO:0042799)|retinoic acid receptor binding (GO:0042974)|retinoid X receptor binding (GO:0046965)|thyroid hormone receptor binding (GO:0046966)|transcription cofactor activity (GO:0003712)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(13)|large_intestine(18)|lung(24)|ovary(2)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(7)|urinary_tract(3)	96	all_cancers(89;1.57e-05)|Renal(175;0.000269)|Lung NSC(126;0.00111)|all_lung(126;0.002)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.198)	Kidney(146;0.235)		GCCGAGAGCTGTTGAGAAAGG	0.542			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.V2504I		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.G7510A						PASS	.						125.0	121.0	123.0					5																	176721879		2203	4300	6503	SO:0001583	missense	64324	exon23	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	AGAGCTGTTGAGA	AK026066	CCDS4412.1, CCDS4413.1	5q35	2014-09-17	2003-03-12		ENSG00000165671	ENSG00000165671		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	14234	protein-coding gene	gene with protein product		606681	"""Sotos syndrome"""	STO		9628876, 11896389	Standard	NM_022455		Approved	ARA267, FLJ22263, KMT3B	uc003mfr.4	Q96L73	OTTHUMG00000130846	ENST00000439151.2:c.7510G>A	5.37:g.176721879G>A	ENSP00000395929:p.Val2504Ile	34.0	0.0	0		42.0	17.0	0.404762	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	37	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	G	4.395	0.072998	0.08485	.	.	ENSG00000165671	ENST00000354179;ENST00000439151;ENST00000347982;ENST00000361032	D;D;D;D	0.93366	-3.11;-3.11;-3.11;-3.21	4.33	-0.92	0.10475	.	1.377650	0.04932	N	0.457076	D	0.84415	0.5467	N	0.14661	0.345	0.09310	N	1	B;B	0.23249	0.082;0.008	B;B	0.18561	0.022;0.006	T	0.71461	-0.4586	10	0.42905	T	0.14	.	2.489	0.04606	0.2231:0.3057:0.3602:0.111	.	2235;2504	Q96L73-2;Q96L73	.;NSD1_HUMAN	I	2235;2504;2235;2401	ENSP00000346111:V2235I;ENSP00000395929:V2504I;ENSP00000343209:V2235I;ENSP00000354310:V2401I	ENSP00000343209:V2235I	V	+	1	0	NSD1	176654485	0.000000	0.05858	0.008000	0.14137	0.469000	0.32828	-0.079000	0.11357	-0.438000	0.07232	0.462000	0.41574	GTT	.	.	none		0.542	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
POLRMT	5442	hgsc.bcm.edu	37	19	621148	621148	+	Silent	SNP	C	C	T	rs143192895	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:621148C>T	ENST00000588649.2	-	10	2634	c.2550G>A	c.(2548-2550)ggG>ggA	p.G850G	LLNLR-299G3.1_ENST00000607288.1_RNA	NM_005035.3	NP_005026.3	O00411	RPOM_HUMAN	polymerase (RNA) mitochondrial (DNA directed)	850	Mediates interaction with TEFM.				gene expression (GO:0010467)|transcription from mitochondrial promoter (GO:0006390)|transcription initiation from mitochondrial promoter (GO:0006391)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|poly(A) RNA binding (GO:0044822)			cervix(2)|endometrium(3)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)|prostate(1)|stomach(1)	20		all_epithelial(18;2.78e-22)|Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;3.55e-06)|all_lung(49;5.41e-06)|Breast(49;4.08e-05)|Hepatocellular(1079;0.137)|Renal(1328;0.228)		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)		GCTTCTTCAACCCCGTGAGAT	0.687													C|||	15	0.00299521	0.0	0.0014	5008	,	,		5814	0.0		0.007	False		,,,				2504	0.0072				p.G850G		Atlas-SNP	.											.	POLRMT	91	.	0			c.G2550A						PASS	.	C		7,4399		0,7,2196	28.0	33.0	32.0		2550	-5.4	0.6	19	dbSNP_134	32	35,8555		1,33,4261	no	coding-synonymous	POLRMT	NM_005035.3		1,40,6457	TT,TC,CC		0.4075,0.1589,0.3232		850/1231	621148	42,12954	2203	4295	6498	SO:0001819	synonymous_variant	5442	exon10			CTTCAACCCCGTG		CCDS12036.1	19p13.3	2010-10-22			ENSG00000099821	ENSG00000099821	2.7.7.6		9200	protein-coding gene	gene with protein product		601778				9097968	Standard	NM_005035		Approved	h-mtRPOL, APOLMT, MTRNAP, MTRPOL	uc002lpf.1	O00411		ENST00000588649.2:c.2550G>A	19.37:g.621148C>T		74.0	0.0	0		86.0	26.0	0.302326	NM_005035	O60370	Silent	SNP	ENST00000588649.2	37	CCDS12036.1																																																																																			C|0.997;T|0.003	0.003	strong		0.687	POLRMT-001	KNOWN	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452172.3	NM_005035	
ZFYVE9	9372	hgsc.bcm.edu	37	1	52803595	52803595	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:52803595C>T	ENST00000371591.1	+	15	3953	c.3822C>T	c.(3820-3822)aaC>aaT	p.N1274N	ZFYVE9_ENST00000287727.3_Silent_p.N1274N|ZFYVE9_ENST00000357206.2_Silent_p.N1215N	NM_004799.2|NM_007324.2	NP_004790.2|NP_015563.2	O95405	ZFYV9_HUMAN	zinc finger, FYVE domain containing 9	1274					endocytosis (GO:0006897)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|proteolysis (GO:0006508)|SMAD protein complex assembly (GO:0007183)|SMAD protein import into nucleus (GO:0007184)|transforming growth factor beta receptor signaling pathway (GO:0007179)	early endosome (GO:0005769)|early endosome membrane (GO:0031901)	1-phosphatidylinositol binding (GO:0005545)|metal ion binding (GO:0046872)|serine-type peptidase activity (GO:0008236)			breast(1)|central_nervous_system(4)|endometrium(3)|kidney(1)|large_intestine(12)|lung(17)|ovary(2)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(6)	53						ATGACAAGAACGTTAGCAAGG	0.502																																					p.N1274N		Atlas-SNP	.											.	ZFYVE9	131	.	0			c.C3822T						PASS	.						83.0	61.0	69.0					1																	52803595		2203	4300	6503	SO:0001819	synonymous_variant	9372	exon16			CAAGAACGTTAGC	AF104304	CCDS563.1, CCDS564.1	1p32.3	2014-06-13	2004-05-21	2004-05-26	ENSG00000157077	ENSG00000157077		"""Zinc fingers, FYVE domain containing"""	6775	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 173"""	603755	"""MAD, mothers against decapentaplegic homolog (Drosophila) interacting protein, receptor activation anchor"""	MADHIP		9865696	Standard	NM_007324		Approved	SMADIP, SARA, PPP1R173	uc001cto.4	O95405	OTTHUMG00000008061	ENST00000371591.1:c.3822C>T	1.37:g.52803595C>T		145.0	0.0	0		128.0	73.0	0.570312	NM_004799	Q5T0F6|Q5T0F7|Q9UNE1|Q9Y5R7	Silent	SNP	ENST00000371591.1	37	CCDS563.1																																																																																			.	.	none		0.502	ZFYVE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022083.1	NM_007324	
AP5Z1	9907	hgsc.bcm.edu	37	7	4821300	4821300	+	Missense_Mutation	SNP	C	C	G	rs11549839	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4821300C>G	ENST00000348624.4	+	3	375	c.281C>G	c.(280-282)tCc>tGc	p.S94C	AP5Z1_ENST00000401897.1_Missense_Mutation_p.S94C	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	94			S -> C (in dbSNP:rs11549839).		cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CGAGAGATGTCCCCCTCTGAC	0.662													C|||	63	0.0125799	0.0015	0.0187	5008	,	,		18244	0.0		0.0249	False		,,,				2504	0.0235				p.S94C		Atlas-SNP	.											.	.	.	.	0			c.C281G						PASS	.	C	CYS/SER	12,4262		0,12,2125	25.0	30.0	28.0		281	5.1	0.6	7	dbSNP_120	28	208,8290		5,198,4046	yes	missense	KIAA0415	NM_014855.2	112	5,210,6171	GG,GC,CC		2.4476,0.2808,1.7225	benign	94/808	4821300	220,12552	2137	4249	6386	SO:0001583	missense	9907	exon3			AGATGTCCCCCTC	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.281C>G	7.37:g.4821300C>G	ENSP00000297562:p.Ser94Cys	130.0	0.0	0		126.0	70.0	0.555556	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	33	0.01510989010989011	2	0.0040650406504065045	12	0.03314917127071823	0	0.0	19	0.025065963060686015	C	12.67	2.008321	0.35415	0.002808	0.024476	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.64085	-0.08;0.67	5.08	5.08	0.68730	.	0.645959	0.15127	N	0.279052	T	0.38585	0.1046	M	0.65975	2.015	0.18873	N	0.999984	B	0.22080	0.064	B	0.21917	0.037	T	0.46665	-0.9175	10	0.41790	T	0.15	.	15.7732	0.78187	0.0:1.0:0.0:0.0	rs11549839;rs11549839	94	O43299	K0415_HUMAN	C	94	ENSP00000297562:S94C;ENSP00000384980:S94C	ENSP00000297562:S94C	S	+	2	0	KIAA0415	4787826	0.990000	0.36364	0.650000	0.29550	0.856000	0.48823	3.089000	0.50183	2.640000	0.89533	0.655000	0.94253	TCC	C|0.987;G|0.013	0.013	strong		0.662	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
GNRH1	2796	hgsc.bcm.edu	37	8	25279148	25279148	+	Missense_Mutation	SNP	G	G	A	rs574867408		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:25279148G>A	ENST00000276414.4	-	2	1501	c.178C>T	c.(178-180)Cgc>Tgc	p.R60C	GNRH1_ENST00000421054.2_Missense_Mutation_p.R60C	NM_000825.3	NP_000816.4	P01148	GON1_HUMAN	gonadotropin-releasing hormone 1 (luteinizing-releasing hormone)	60					cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|ovulation cycle (GO:0042698)|regulation of gene expression (GO:0010468)|regulation of ovarian follicle development (GO:2000354)|response to corticosteroid (GO:0031960)|response to ethanol (GO:0045471)|signal transduction (GO:0007165)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	gonadotropin hormone-releasing hormone activity (GO:0005183)|hormone activity (GO:0005179)			large_intestine(1)	1		all_cancers(63;0.0423)|Ovarian(32;0.000626)|all_epithelial(46;0.0186)|Hepatocellular(4;0.114)|Breast(100;0.14)|Prostate(55;0.191)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0201)|Epithelial(17;1.25e-12)|Colorectal(74;0.0113)|COAD - Colon adenocarcinoma(73;0.0385)		CATTCGAAGCGTTGGGTTTCT	0.448													G|||	1	0.000199681	0.0	0.0014	5008	,	,		14545	0.0		0.0	False		,,,				2504	0.0				p.R64C		Atlas-SNP	.											.	GNRH1	8	.	0			c.C190T						PASS	.						102.0	110.0	107.0					8																	25279148		2033	4193	6226	SO:0001583	missense	2796	exon2			CGAAGCGTTGGGT	X01059	CCDS43725.1	8p21-p11.2	2013-02-26	2004-10-13		ENSG00000147437	ENSG00000147437		"""Endogenous ligands"""	4419	protein-coding gene	gene with protein product		152760	"""gonadotropin-releasing hormone 1 (leutinizing-releasing hormone)"""	GRH, GNRH, LHRH		6090951	Standard	NM_000825		Approved		uc003xem.4	P01148	OTTHUMG00000163852	ENST00000276414.4:c.178C>T	8.37:g.25279148G>A	ENSP00000276414:p.Arg60Cys	195.0	0.0	0		150.0	67.0	0.446667	NM_000825	A0AVP0	Missense_Mutation	SNP	ENST00000276414.4	37	CCDS43725.1	.	.	.	.	.	.	.	.	.	.	G	5.063	0.197253	0.09599	.	.	ENSG00000147437	ENST00000421054;ENST00000276414	T;T	0.47528	0.84;0.84	4.91	2.09	0.27110	.	1.839800	0.02297	N	0.070879	T	0.38214	0.1032	.	.	.	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.25047	-1.0143	9	0.46703	T	0.11	0.5379	7.6257	0.28210	0.0774:0.0:0.5127:0.4099	.	60	P01148	GON1_HUMAN	C	60	ENSP00000391280:R60C;ENSP00000276414:R60C	ENSP00000276414:R60C	R	-	1	0	GNRH1	25335065	0.003000	0.15002	0.000000	0.03702	0.003000	0.03518	1.075000	0.30716	0.250000	0.21479	0.561000	0.74099	CGC	.	.	none		0.448	GNRH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375982.1	NM_001083111	
FAM171B	165215	hgsc.bcm.edu	37	2	187615953	187615953	+	Missense_Mutation	SNP	G	G	A	rs201119796		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:187615953G>A	ENST00000304698.5	+	5	1020	c.817G>A	c.(817-819)Gtt>Att	p.V273I		NM_177454.3	NP_803237.3	Q6P995	F171B_HUMAN	family with sequence similarity 171, member B	273						integral component of membrane (GO:0016021)	DNA binding (GO:0003677)	p.V273F(1)		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						CTCTATTCAAGTTTCTCTTCC	0.363																																					p.V273I		Atlas-SNP	.											FAM171B,rectum,carcinoma,-1,2	FAM171B	146	2	1	Substitution - Missense(1)	breast(1)	c.G817A						PASS	.						108.0	115.0	113.0					2																	187615953		2203	4300	6503	SO:0001583	missense	165215	exon5			ATTCAAGTTTCTC	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.817G>A	2.37:g.187615953G>A	ENSP00000304108:p.Val273Ile	83.0	0.0	0		77.0	29.0	0.376623	NM_177454	Q53SK3|Q8N1Y4|Q8N3K1|Q8N970|Q8NB81|Q8TF55|Q8WYR8	Missense_Mutation	SNP	ENST00000304698.5	37	CCDS33347.1	.	.	.	.	.	.	.	.	.	.	A	7.399	0.632436	0.14322	.	.	ENSG00000144369	ENST00000304698;ENST00000272804	T	0.38401	1.14	5.53	-4.51	0.03483	.	0.550372	0.20261	N	0.095865	T	0.10208	0.0250	N	0.02202	-0.64	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.06405	0.002;0.002	T	0.28554	-1.0040	10	0.05436	T	0.98	-0.8584	11.0846	0.48080	0.5502:0.0853:0.3645:0.0	.	273;274	Q6P995;A8K122	F171B_HUMAN;.	I	273	ENSP00000304108:V273I	ENSP00000272804:V273I	V	+	1	0	FAM171B	187324198	0.694000	0.27738	0.178000	0.23040	0.632000	0.37999	0.201000	0.17276	-1.197000	0.02673	-1.372000	0.01188	GTT	G|0.999;A|0.001	0.001	weak		0.363	FAM171B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334679.1	NM_177454	
MYB	4602	hgsc.bcm.edu	37	6	135518402	135518402	+	Intron	SNP	G	G	A	rs547508696		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:135518402G>A	ENST00000367814.4	+	9	1389				MYB-AS1_ENST00000455534.1_RNA|MYB_ENST00000533624.1_Intron|MYB_ENST00000534121.1_Missense_Mutation_p.V487I|MYB_ENST00000527615.1_Intron|MYB_ENST00000534044.1_Intron|MYB_ENST00000531845.1_Intron|MYB_ENST00000528774.1_Missense_Mutation_p.V500I|MYB_ENST00000341911.5_Missense_Mutation_p.V503I|MYB_ENST00000316528.8_Intron|MYB_ENST00000525369.1_Intron|MYB_ENST00000442647.2_Intron	NM_001161659.1|NM_005375.2	NP_001155131.1|NP_005366.2	P10242	MYB_HUMAN	v-myb avian myeloblastosis viral oncogene homolog						B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|chromatin remodeling (GO:0006338)|embryonic digestive tract development (GO:0048566)|G1/S transition of mitotic cell cycle (GO:0000082)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of histone H3-K9 methylation (GO:0051574)|positive regulation of T-helper cell differentiation (GO:0045624)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|thymus development (GO:0048538)	nuclear matrix (GO:0016363)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(4)|endometrium(1)|kidney(2)|large_intestine(3)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	28	all_epithelial(2;0.109)|Breast(56;0.158)|Colorectal(23;0.221)	Lung NSC(302;3.08e-05)|Ovarian(999;0.208)		OV - Ovarian serous cystadenocarcinoma(155;0.0079)|GBM - Glioblastoma multiforme(68;0.0117)		ATTTGCTGACGTCAGCAGTTC	0.507			T	NFIB	adenoid cystic carcinoma								G|||	1	0.000199681	0.0	0.0	5008	,	,		20039	0.001		0.0	False		,,,				2504	0.0				p.V503I		Atlas-SNP	.		Dom	yes		6	6q22-23	4602	v-myb myeloblastosis viral oncogene homolog		E	.	MYB	137	.	0			c.G1507A						PASS	.						77.0	72.0	73.0					6																	135518402		1568	3582	5150	SO:0001627	intron_variant	4602	exon10			GCTGACGTCAGCA		CCDS5174.1, CCDS47481.1, CCDS47482.1, CCDS55058.1, CCDS55059.1, CCDS55060.1, CCDS55061.1, CCDS55062.1	6q22-q23	2013-07-09	2013-07-09		ENSG00000118513	ENSG00000118513			7545	protein-coding gene	gene with protein product		189990				17599807	Standard	NM_001130172		Approved	c-myb	uc003qfh.3	P10242	OTTHUMG00000015629	ENST00000367814.4:c.1203+1262G>A	6.37:g.135518402G>A		105.0	0.0	0		72.0	70.0	0.972222	NM_001130173	E9PI07|E9PLZ5|E9PNA4|E9PNL6|E9PRS2|P78391|P78392|P78525|P78526|Q14023|Q14024|Q708E4|Q708E7|Q9UE83	Missense_Mutation	SNP	ENST00000367814.4	37	CCDS5174.1	.	.	.	.	.	.	.	.	.	.	G	11.15	1.553390	0.27739	.	.	ENSG00000118513	ENST00000341911;ENST00000528774;ENST00000534121	T;T;T	0.11277	2.79;2.79;2.8	5.78	2.96	0.34315	.	0.514050	0.19050	N	0.124064	T	0.01976	0.0062	N	0.22421	0.69	0.80722	D	1	B;B;B	0.15719	0.004;0.005;0.014	B;B;B	0.11329	0.002;0.002;0.006	T	0.40683	-0.9550	10	0.17369	T	0.5	-0.0596	6.0033	0.19533	0.2267:0.1344:0.6389:0.0	.	500;487;503	E9PNL6;E9PNA4;P10242-4	.;.;.	I	503;500;487	ENSP00000339992:V503I;ENSP00000434723:V500I;ENSP00000432851:V487I	ENSP00000339992:V503I	V	+	1	0	MYB	135560095	0.999000	0.42202	0.999000	0.59377	0.999000	0.98932	0.652000	0.24888	0.337000	0.23665	0.655000	0.94253	GTC	.	.	none		0.507	MYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042347.4		
ATF4	468	hgsc.bcm.edu	37	22	39917787	39917787	+	Missense_Mutation	SNP	T	T	G	rs141575018		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39917787T>G	ENST00000337304.2	+	2	1118	c.236T>G	c.(235-237)tTc>tGc	p.F79C	ATF4_ENST00000396680.1_Missense_Mutation_p.F79C|ATF4_ENST00000404241.2_Missense_Mutation_p.F79C	NM_001675.2	NP_001666.2	P18848	ATF4_HUMAN	activating transcription factor 4	79					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular amino acid metabolic process (GO:0006520)|cellular protein metabolic process (GO:0044267)|circadian regulation of gene expression (GO:0032922)|endoplasmic reticulum unfolded protein response (GO:0030968)|gamma-aminobutyric acid signaling pathway (GO:0007214)|gluconeogenesis (GO:0006094)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of oxidative stress-induced neuron death (GO:1903204)|negative regulation of potassium ion transport (GO:0043267)|positive regulation of apoptotic process (GO:0043065)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress (GO:1990440)|positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress (GO:0036091)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|response to endoplasmic reticulum stress (GO:0034976)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|dendrite membrane (GO:0032590)|Lewy body core (GO:1990037)|neuron projection (GO:0043005)|nuclear periphery (GO:0034399)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	core promoter sequence-specific DNA binding (GO:0001046)|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 positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(2)|large_intestine(2)|lung(5)|skin(1)	11	Melanoma(58;0.04)				Pseudoephedrine(DB00852)	GAGGATGCCTTCTCCGGGACA	0.502																																					p.F79C		Atlas-SNP	.											.	ATF4	27	.	0			c.T236G						PASS	.	T	CYS/PHE,CYS/PHE	0,4406		0,0,2203	100.0	103.0	102.0		236,236	4.7	1.0	22	dbSNP_134	102	4,8596	3.7+/-12.6	0,4,4296	yes	missense,missense	ATF4	NM_001675.2,NM_182810.1	205,205	0,4,6499	GG,GT,TT		0.0465,0.0,0.0308	probably-damaging,probably-damaging	79/352,79/352	39917787	4,13002	2203	4300	6503	SO:0001583	missense	468	exon2			ATGCCTTCTCCGG	D90209	CCDS13996.1	22q13.1	2013-05-23	2013-05-23		ENSG00000128272	ENSG00000128272		"""basic leucine zipper proteins"""	786	protein-coding gene	gene with protein product	"""tax-responsive enhancer element B67"""	604064	"""activating transcription factor 4 (tax-responsive enhancer element B67)"""	TXREB		1847461, 1534408	Standard	NM_182810		Approved	TAXREB67, CREB-2	uc003axz.3	P18848	OTTHUMG00000151099	ENST00000337304.2:c.236T>G	22.37:g.39917787T>G	ENSP00000336790:p.Phe79Cys	76.0	0.0	0		61.0	30.0	0.491803	NM_001675	Q9UH31	Missense_Mutation	SNP	ENST00000337304.2	37	CCDS13996.1	.	.	.	.	.	.	.	.	.	.	T	19.58	3.853455	0.71719	0.0	4.65E-4	ENSG00000128272	ENST00000404241;ENST00000337304;ENST00000396680	T;T;T	0.49432	0.78;0.78;0.78	4.74	4.74	0.60224	.	0.052105	0.85682	D	0.000000	T	0.68869	0.3048	M	0.79475	2.455	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.74144	-0.3760	10	0.87932	D	0	-24.7248	14.269	0.66140	0.0:0.0:0.0:1.0	.	79	P18848	ATF4_HUMAN	C	79	ENSP00000384587:F79C;ENSP00000336790:F79C;ENSP00000379912:F79C	ENSP00000336790:F79C	F	+	2	0	ATF4	38247733	1.000000	0.71417	0.998000	0.56505	0.902000	0.53008	7.654000	0.83653	1.770000	0.52166	0.459000	0.35465	TTC	T|1.000;G|0.000	0.000	weak		0.502	ATF4-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321305.1	NM_001675	
GYLTL1B	120071	hgsc.bcm.edu	37	11	45948962	45948962	+	Silent	SNP	C	C	T	rs138897549		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:45948962C>T	ENST00000531526.1	+	11	1533	c.1422C>T	c.(1420-1422)ttC>ttT	p.F474F	GYLTL1B_ENST00000401752.1_Silent_p.F474F|GYLTL1B_ENST00000389968.3_Silent_p.F201F|GYLTL1B_ENST00000325468.5_Silent_p.F474F|GYLTL1B_ENST00000529052.1_Silent_p.F443F|GYLTL1B_ENST00000536139.1_Silent_p.F443F	NM_152312.3	NP_689525.3	Q8N3Y3	LARG2_HUMAN	glycosyltransferase-like 1B	474				HF -> IS (in Ref. 5; AAG23791). {ECO:0000305}.	muscle cell cellular homeostasis (GO:0046716)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(2)|endometrium(6)|large_intestine(4)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)	22				GBM - Glioblastoma multiforme(35;0.226)		TCCTGCATTTCGTCGAGGCCT	0.617													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20898	0.0		0.0	False		,,,				2504	0.0				p.F474F		Atlas-SNP	.											.	GYLTL1B	45	.	0			c.C1422T						PASS	.	C		0,4406		0,0,2203	89.0	74.0	79.0		1422	-1.3	0.7	11	dbSNP_134	79	1,8597	1.2+/-3.3	0,1,4298	no	coding-synonymous	GYLTL1B	NM_152312.3		0,1,6501	TT,TC,CC		0.0116,0.0,0.0077		474/722	45948962	1,13003	2203	4299	6502	SO:0001819	synonymous_variant	120071	exon11			GCATTTCGTCGAG		CCDS31473.1	11p11.12	2013-02-22			ENSG00000165905	ENSG00000165905		"""Glycosyltransferase family 8 domain containing"""	16522	protein-coding gene	gene with protein product		609709				15661757, 15958417	Standard	XM_005252785		Approved	PP5656, FLJ35207, LARGE2	uc001nbv.1	Q8N3Y3	OTTHUMG00000167037	ENST00000531526.1:c.1422C>T	11.37:g.45948962C>T		84.0	0.0	0		83.0	32.0	0.385542	NM_152312	A6NN75|Q8N8Y6|Q8NAK3|Q8WY62	Silent	SNP	ENST00000531526.1	37	CCDS31473.1																																																																																			C|1.000;T|0.000	0.000	strong		0.617	GYLTL1B-002	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000392572.1	NM_152312	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57076895	57076895	+	Missense_Mutation	SNP	T	T	C	rs35950335	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57076895T>C	ENST00000532437.1	-	5	3601	c.3290A>G	c.(3289-3291)cAg>cGg	p.Q1097R	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.Q1097R|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1097	Acidic.|Gly-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TGCCTCTCGCTGGGGGCCAAC	0.617													C|||	101	0.0201677	0.0023	0.0389	5008	,	,		19520	0.002		0.0447	False		,,,				2504	0.0245				p.Q1097R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A3290G						PASS	.	C	ARG/GLN	46,4356	821.9+/-416.4	0,46,2155	76.0	66.0	69.0		3290	2.6	0.1	11	dbSNP_126	69	402,8190	800.7+/-407.4	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	43	8,432,6057	CC,CT,TT		4.6788,1.045,3.4477	benign	1097/1730	57076895	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon6			TCTCGCTGGGGGC	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.3290A>G	11.37:g.57076895T>C	ENSP00000437271:p.Gln1097Arg	75.0	0.0	0		60.0	34.0	0.566667	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	C	0.621	-0.821246	0.02755	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.31769	1.48;1.48	5.05	2.58	0.30949	.	0.438549	0.19467	N	0.113554	T	0.03220	0.0094	L	0.29908	0.895	0.09310	N	1	B	0.24576	0.106	B	0.29353	0.101	T	0.16512	-1.0400	10	0.25751	T	0.34	-6.1023	7.9512	0.30017	0.0:0.1873:0.0:0.8127	rs35950335	1097	Q9C0C2	TB182_HUMAN	R	1097	ENSP00000350990:Q1097R;ENSP00000437271:Q1097R	ENSP00000350990:Q1097R	Q	-	2	0	TNKS1BP1	56833471	0.125000	0.22332	0.082000	0.20525	0.005000	0.04900	0.530000	0.23036	0.270000	0.21984	-1.694000	0.00725	CAG	T|0.968;C|0.032	0.032	strong		0.617	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
TECTA	7007	hgsc.bcm.edu	37	11	121030874	121030874	+	Missense_Mutation	SNP	A	A	G	rs147354818		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:121030874A>G	ENST00000392793.1	+	15	4991	c.4720A>G	c.(4720-4722)Ata>Gta	p.I1574V	TECTA_ENST00000264037.2_Missense_Mutation_p.I1574V			O75443	TECTA_HUMAN	tectorin alpha	1574	VWFD 4. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cell-matrix adhesion (GO:0007160)|sensory perception of sound (GO:0007605)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)			TECTA/TBCEL(2)	NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(38)|liver(1)|lung(46)|ovary(3)|prostate(4)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	135	all_hematologic(175;0.208)	Breast(109;0.000766)|Medulloblastoma(222;0.0427)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;8.04e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.166)		TGTTCCATTTATAACTGGTTT	0.413													A|||	1	0.000199681	0.0	0.0014	5008	,	,		23199	0.0		0.0	False		,,,				2504	0.0				p.I1574V		Atlas-SNP	.											.	TECTA	329	.	0			c.A4720G						PASS	.	A	VAL/ILE	0,4406		0,0,2203	88.0	91.0	90.0		4720	1.2	1.0	11	dbSNP_134	90	14,8584	10.5+/-38.8	0,14,4285	yes	missense	TECTA	NM_005422.2	29	0,14,6488	GG,GA,AA		0.1628,0.0,0.1077	benign	1574/2156	121030874	14,12990	2203	4299	6502	SO:0001583	missense	7007	exon14			CCATTTATAACTG	AF055136	CCDS8434.1	11q22-q24	2008-02-05			ENSG00000109927	ENSG00000109927			11720	protein-coding gene	gene with protein product		602574		DFNA12, DFNA8, DFNB21		9503015, 9590290	Standard	NM_005422		Approved		uc010rzo.2	O75443	OTTHUMG00000149908	ENST00000392793.1:c.4720A>G	11.37:g.121030874A>G	ENSP00000376543:p.Ile1574Val	97.0	0.0	0		124.0	65.0	0.524194	NM_005422		Missense_Mutation	SNP	ENST00000392793.1	37	CCDS8434.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	A	1.012	-0.687529	0.03328	0.0	0.001628	ENSG00000109927	ENST00000392793;ENST00000264037	T;T	0.58652	0.32;0.32	4.87	1.2	0.21068	von Willebrand factor, type D domain (3);	0.304381	0.32273	N	0.006326	T	0.23766	0.0575	N	0.02802	-0.49	0.27653	N	0.947345	B	0.06786	0.001	B	0.08055	0.003	T	0.31613	-0.9937	10	0.02654	T	1	.	8.3001	0.32008	0.4982:0.0:0.5018:0.0	.	1574	O75443	TECTA_HUMAN	V	1574	ENSP00000376543:I1574V;ENSP00000264037:I1574V	ENSP00000264037:I1574V	I	+	1	0	TECTA	120536084	0.926000	0.31397	0.991000	0.47740	0.997000	0.91878	1.014000	0.29950	0.033000	0.15463	0.533000	0.62120	ATA	A|0.999;G|0.001	0.001	strong		0.413	TECTA-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313850.1	NM_005422	
APOBEC1	339	hgsc.bcm.edu	37	12	7805154	7805154	+	Missense_Mutation	SNP	G	G	A	rs61753204	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:7805154G>A	ENST00000229304.4	-	3	342	c.322C>T	c.(322-324)Cct>Tct	p.P108S		NM_001644.3	NP_001635.2	P41238	ABEC1_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide 1	108					cellular response to insulin stimulus (GO:0032869)|cytidine deamination (GO:0009972)|cytidine to uridine editing (GO:0016554)|defense response to virus (GO:0051607)|DNA demethylation (GO:0080111)|gene expression (GO:0010467)|lipid metabolic process (GO:0006629)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein transport (GO:0042953)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|mRNA stabilization (GO:0048255)|negative regulation of methylation-dependent chromatin silencing (GO:0090310)|regulation of cell proliferation (GO:0042127)|response to calcium ion (GO:0051592)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gamma radiation (GO:0010332)|response to osmotic stress (GO:0006970)|response to zinc ion (GO:0010043)|RNA processing (GO:0006396)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)	AU-rich element binding (GO:0017091)|cytidine deaminase activity (GO:0004126)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			kidney(2)|large_intestine(2)|lung(10)|prostate(1)|skin(1)|stomach(1)	17						GTCACACCAGGGTGCCGACTC	0.498													G|||	45	0.00898562	0.0015	0.0072	5008	,	,		-128	0.002		0.0139	False		,,,				2504	0.0225				p.P108S	Pancreas(135;929 1826 4531 10527 41012)	Atlas-SNP	.											.	APOBEC1	43	.	0			c.C322T						PASS	.	G	SER/PRO	14,4392	21.2+/-45.6	1,12,2190	65.0	64.0	64.0		322	3.2	0.2	12	dbSNP_129	64	129,8471	66.7+/-129.0	1,127,4172	yes	missense	APOBEC1	NM_001644.3	74	2,139,6362	AA,AG,GG		1.5,0.3177,1.0995	probably-damaging	108/237	7805154	143,12863	2203	4300	6503	SO:0001583	missense	339	exon3			CACCAGGGTGCCG	U72891	CCDS8579.1	12p13.1	2007-02-01			ENSG00000111701	ENSG00000111701		"""Apolipoprotein B mRNA editing enzymes"""	604	protein-coding gene	gene with protein product		600130					Standard	XM_005253355		Approved	BEDP, CDAR1, APOBEC-1, HEPR	uc001qtb.3	P41238	OTTHUMG00000141288	ENST00000229304.4:c.322C>T	12.37:g.7805154G>A	ENSP00000229304:p.Pro108Ser	86.0	0.0	0		80.0	44.0	0.55	NM_001644	Q9UE64|Q9UM71	Missense_Mutation	SNP	ENST00000229304.4	37	CCDS8579.1	15	0.006868131868131868	2	0.0040650406504065045	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	10.29	1.309349	0.23821	0.003177	0.015	ENSG00000111701	ENST00000229304	T	0.64991	-0.13	4.12	3.23	0.37069	APOBEC-like, N-terminal (1);	0.000000	0.56097	D	0.000039	T	0.66934	0.2840	M	0.73319	2.225	0.26925	N	0.966593	D	0.89917	1.0	D	0.81914	0.995	T	0.60880	-0.7175	10	0.54805	T	0.06	-14.1848	7.9106	0.29789	0.1139:0.0:0.8861:0.0	rs61753204	108	P41238	ABEC1_HUMAN	S	108	ENSP00000229304:P108S	ENSP00000229304:P108S	P	-	1	0	APOBEC1	7696421	0.975000	0.34042	0.171000	0.22900	0.014000	0.08584	2.996000	0.49449	1.105000	0.41606	0.462000	0.41574	CCT	G|0.989;A|0.011	0.011	strong		0.498	APOBEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280523.1	NM_001644	
LRRC29	26231	hgsc.bcm.edu	37	16	67241930	67241930	+	Missense_Mutation	SNP	C	C	T	rs34595673	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67241930C>T	ENST00000409037.1	-	3	1245	c.349G>A	c.(349-351)Ggc>Agc	p.G117S	LRRC29_ENST00000393992.1_Missense_Mutation_p.G117S|LRRC29_ENST00000409509.1_Missense_Mutation_p.G117S|LRRC29_ENST00000462169.1_5'Flank|LRRC29_ENST00000341546.3_Missense_Mutation_p.G117S			Q8WV35	LRC29_HUMAN	leucine rich repeat containing 29	117			G -> S (in dbSNP:rs34595673).							autonomic_ganglia(1)|breast(1)|endometrium(1)|large_intestine(1)|lung(2)|urinary_tract(1)	7		Ovarian(137;0.0563)		OV - Ovarian serous cystadenocarcinoma(108;0.000691)|Epithelial(162;0.00462)|all cancers(182;0.0434)		GCAACCAAGCCGTTGTCTGTG	0.612													C|||	455	0.0908546	0.2844	0.0288	5008	,	,		19362	0.0099		0.0278	False		,,,				2504	0.0215				p.G117S		Atlas-SNP	.											.	LRRC29	13	.	0			c.G349A						PASS	.	C	SER/GLY,SER/GLY	1023,3373		129,765,1304	22.0	20.0	21.0		349,349	5.6	0.5	16	dbSNP_126	21	273,8327		8,257,4035	yes	missense,missense	LRRC29	NM_001004055.1,NM_012163.2	56,56	137,1022,5339	TT,TC,CC		3.1744,23.2712,9.9723	possibly-damaging,possibly-damaging	117/224,117/224	67241930	1296,11700	2198	4300	6498	SO:0001583	missense	26231	exon5			CCAAGCCGTTGTC	AF176701	CCDS32465.1	16q22.1	2008-02-05	2004-08-23	2004-08-26	ENSG00000125122	ENSG00000125122			13605	protein-coding gene	gene with protein product			"""F-box and leucine-rich repeat protein 9"""	FBXL9		10531037	Standard	NM_012163		Approved	FBL9	uc002esf.3	Q8WV35	OTTHUMG00000154403	ENST00000409037.1:c.349G>A	16.37:g.67241930C>T	ENSP00000387318:p.Gly117Ser	90.0	0.0	0		111.0	54.0	0.486486	NM_001004055	B2RE92|Q9UKA0	Missense_Mutation	SNP	ENST00000409037.1	37	CCDS32465.1	157	0.07188644688644688	124	0.25203252032520324	10	0.027624309392265192	4	0.006993006993006993	19	0.025065963060686015	C	19.59	3.855436	0.71719	0.232712	0.031744	ENSG00000125122	ENST00000409509;ENST00000393992;ENST00000409037;ENST00000341546;ENST00000433915;ENST00000424285	T;T;T;T;T;T	0.01172	5.23;5.23;5.23;5.23;5.23;5.23	5.57	5.57	0.84162	.	0.603229	0.17346	N	0.177597	T	0.00012	0.0000	L	0.55103	1.725	0.47584	P	5.309999999999482E-4	P	0.37824	0.609	B	0.21546	0.035	T	0.62751	-0.6788	9	0.35671	T	0.21	.	15.0432	0.71807	0.0:1.0:0.0:0.0	rs34595673	117	Q8WV35	LRC29_HUMAN	S	117;117;117;117;69;117	ENSP00000386622:G117S;ENSP00000377561:G117S;ENSP00000387318:G117S;ENSP00000344364:G117S;ENSP00000413129:G69S;ENSP00000409459:G117S	ENSP00000344364:G117S	G	-	1	0	LRRC29	65799431	0.968000	0.33430	0.482000	0.27366	0.824000	0.46624	2.258000	0.43249	2.617000	0.88574	0.655000	0.94253	GGC	C|0.909;T|0.091	0.091	strong		0.612	LRRC29-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335073.1	NM_012163	
MACF1	23499	hgsc.bcm.edu	37	1	39549942	39549942	+	Missense_Mutation	SNP	C	C	T	rs369843705		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:39549942C>T	ENST00000372915.3	+	1	139	c.52C>T	c.(52-54)Cgg>Tgg	p.R18W	MACF1_ENST00000317713.7_Missense_Mutation_p.R18W|MACF1_ENST00000484793.1_Missense_Mutation_p.R18W|MACF1_ENST00000361689.2_Missense_Mutation_p.R18W|MACF1_ENST00000545844.1_Missense_Mutation_p.R18W|MACF1_ENST00000539005.1_Missense_Mutation_p.R18W|MACF1_ENST00000602421.1_Missense_Mutation_p.R18W|MACF1_ENST00000567887.1_Missense_Mutation_p.R18W			Q9UPN3	MACF1_HUMAN	microtubule-actin crosslinking factor 1	18	Actin-binding.				ATP catabolic process (GO:0006200)|cell cycle arrest (GO:0007050)|Golgi to plasma membrane protein transport (GO:0043001)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of epithelial cell migration (GO:0010632)|regulation of focal adhesion assembly (GO:0051893)|regulation of microtubule-based process (GO:0032886)|Wnt signaling pathway (GO:0016055)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			breast(11)|central_nervous_system(5)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(36)|lung(78)|ovary(12)|prostate(2)|skin(9)|stomach(2)|upper_aerodigestive_tract(8)|urinary_tract(10)	203	Lung NSC(20;5.57e-06)|Ovarian(52;0.00769)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;7.78e-19)|Epithelial(16;1.73e-17)|all cancers(16;2.49e-16)|LUSC - Lung squamous cell carcinoma(16;0.00146)|Lung(16;0.00204)			TCGGAGTGAGCGGTCTTGTCG	0.642													C|||	1	0.000199681	0.0	0.0014	5008	,	,		16833	0.0		0.0	False		,,,				2504	0.0				p.R18W		Atlas-SNP	.											MACF1_ENST00000361689,caecum,carcinoma,-1,1	MACF1	909	1	0			c.C52T						PASS	.	C	TRP/ARG	0,4406		0,0,2203	68.0	61.0	64.0		52	0.7	1.0	1		64	1,8599	1.2+/-3.3	0,1,4299	no	missense	MACF1	NM_012090.4	101	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077		18/5431	39549942	1,13005	2203	4300	6503	SO:0001583	missense	23499	exon3			AGTGAGCGGTCTT	AB007934	CCDS435.1	1p32-p31	2013-01-10			ENSG00000127603	ENSG00000127603		"""EF-hand domain containing"""	13664	protein-coding gene	gene with protein product	"""actin cross-linking factor"", ""620 kDa actin binding protein"", ""macrophin 1"", ""trabeculin-alpha"", ""actin cross-linking family protein 7"""	608271				7635207, 10529403	Standard	NM_012090		Approved	KIAA0465, ACF7, ABP620, KIAA1251, MACF, FLJ45612, FLJ46776	uc031pmc.1	Q9UPN3	OTTHUMG00000007754	ENST00000372915.3:c.52C>T	1.37:g.39549942C>T	ENSP00000362006:p.Arg18Trp	76.0	0.0	0		80.0	74.0	0.925	NM_012090	B1ALC5|E9PJT0|O75053|Q5VW20|Q8WXY1|Q8WXY2|Q96PK2|Q9H540|Q9UKP0|Q9ULG9	Missense_Mutation	SNP	ENST00000372915.3	37		.	.	.	.	.	.	.	.	.	.	C	16.64	3.178377	0.57692	0.0	1.16E-4	ENSG00000127603	ENST00000484793;ENST00000545844;ENST00000372915;ENST00000361689;ENST00000404645;ENST00000317713;ENST00000539005	T;T;T;T;T	0.66099	-0.15;-0.13;-0.15;-0.19;0.0	5.35	0.69	0.18039	.	.	.	.	.	T	0.58466	0.2124	N	0.08118	0	0.80722	D	1	D	0.89917	1.0	D	0.70227	0.968	T	0.63598	-0.6601	9	0.62326	D	0.03	.	12.8938	0.58087	0.6321:0.3679:0.0:0.0	.	18	F8W8Q1	.	W	18;18;18;18;34;18;18	ENSP00000439537:R18W;ENSP00000362006:R18W;ENSP00000354573:R18W;ENSP00000313438:R18W;ENSP00000444364:R18W	ENSP00000313438:R18W	R	+	1	2	MACF1	39322529	0.998000	0.40836	0.998000	0.56505	0.963000	0.63663	0.510000	0.22723	0.559000	0.29153	0.655000	0.94253	CGG	.	.	none		0.642	MACF1-028	NOVEL	not_organism_supported|basic|appris_candidate|exp_conf	protein_coding	protein_coding	OTTHUMT00000392096.1	NM_033044	
ZNF491	126069	hgsc.bcm.edu	37	19	11916914	11916914	+	Missense_Mutation	SNP	A	A	G	rs141870350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11916914A>G	ENST00000323169.5	+	3	477	c.146A>G	c.(145-147)tAt>tGt	p.Y49C	ZNF491_ENST00000492230.1_Intron	NM_152356.3	NP_689569.2	Q8N8L2	ZN491_HUMAN	zinc finger protein 491	49					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(14)|lung(6)|ovary(2)|skin(1)	26						TTCATGGGATATTCATCCTTT	0.383													A|||	3	0.000599042	0.0	0.0014	5008	,	,		18120	0.0		0.002	False		,,,				2504	0.0				p.Y49C		Atlas-SNP	.											.	ZNF491	61	.	0			c.A146G						PASS	.	A	CYS/TYR	6,4400	9.9+/-24.2	0,6,2197	72.0	76.0	75.0		146	1.0	0.0	19	dbSNP_134	75	66,8534	41.2+/-98.3	1,64,4235	yes	missense	ZNF491	NM_152356.3	194	1,70,6432	GG,GA,AA		0.7674,0.1362,0.5536	benign	49/438	11916914	72,12934	2203	4300	6503	SO:0001583	missense	126069	exon3			TGGGATATTCATC	AK092110	CCDS12267.1	19p13.2	2013-01-08			ENSG00000177599	ENSG00000177599		"""Zinc fingers, C2H2-type"""	23706	protein-coding gene	gene with protein product							Standard	XM_005259730		Approved	FLJ34791	uc002mso.1	Q8N8L2	OTTHUMG00000156529	ENST00000323169.5:c.146A>G	19.37:g.11916914A>G	ENSP00000313443:p.Tyr49Cys	78.0	0.0	0		76.0	38.0	0.5	NM_152356	Q3MJ35|Q8NAT8	Missense_Mutation	SNP	ENST00000323169.5	37	CCDS12267.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	a	9.874	1.199678	0.22121	0.001362	0.007674	ENSG00000177599	ENST00000323169;ENST00000455048;ENST00000450087	T;T	0.15256	2.44;2.44	1.01	1.01	0.19927	Zinc finger, C2H2 (1);	.	.	.	.	T	0.05273	0.0140	N	0.12831	0.26	0.09310	N	1	B	0.28900	0.227	B	0.19148	0.024	T	0.30851	-0.9964	9	0.37606	T	0.19	.	5.9285	0.19126	1.0:0.0:0.0:0.0	.	49	Q8N8L2	ZN491_HUMAN	C	49	ENSP00000313443:Y49C;ENSP00000392176:Y49C	ENSP00000313443:Y49C	Y	+	2	0	ZNF491	11777914	0.000000	0.05858	0.007000	0.13788	0.007000	0.05969	-1.435000	0.02423	0.710000	0.31997	0.413000	0.27773	TAT	A|0.997;G|0.003	0.003	strong		0.383	ZNF491-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344518.1	NM_152356	
KRT9	3857	hgsc.bcm.edu	37	17	39724810	39724810	+	Missense_Mutation	SNP	G	G	A	rs116216460	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39724810G>A	ENST00000246662.4	-	5	1185	c.1120C>T	c.(1120-1122)Cgg>Tgg	p.R374W	KRT9_ENST00000588431.1_Missense_Mutation_p.R141W	NM_000226.3	NP_000217.2	P35527	K1C9_HUMAN	keratin 9	374	Coil 2.|Rod.				epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(4)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25		Breast(137;0.000307)				ACACCGTGCCGGAGCTGGGTC	0.547																																					p.R374W		Atlas-SNP	.											.	KRT9	78	.	0			c.C1120T						PASS	.	G	TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	287.0	271.0	277.0		1120	0.6	0.1	17	dbSNP_132	277	17,8583	12.6+/-44.7	0,17,4283	yes	missense	KRT9	NM_000226.3	101	0,19,6484	AA,AG,GG		0.1977,0.0454,0.1461	probably-damaging	374/624	39724810	19,12987	2203	4300	6503	SO:0001583	missense	3857	exon5			CGTGCCGGAGCTG		CCDS32654.1	17q21.2	2013-06-20	2008-08-01		ENSG00000171403	ENSG00000171403		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6447	protein-coding gene	gene with protein product	"""cytokeratin 9"", ""type I cytoskeletal 9"", ""epidermolytic palmoplantar keratoderma"""	607606				7512862, 16831889	Standard	NM_000226		Approved	EPPK, K9, CK-9	uc002hxe.4	P35527	OTTHUMG00000133599	ENST00000246662.4:c.1120C>T	17.37:g.39724810G>A	ENSP00000246662:p.Arg374Trp	114.0	0.0	0		124.0	68.0	0.548387	NM_000226	O00109|Q0IJ47|Q14665	Missense_Mutation	SNP	ENST00000246662.4	37	CCDS32654.1	.	.	.	.	.	.	.	.	.	.	G	18.04	3.535278	0.64972	4.54E-4	0.001977	ENSG00000171403	ENST00000246662	D	0.92149	-2.98	5.15	0.585	0.17428	Filament (1);	0.304329	0.18190	N	0.148859	D	0.91202	0.7228	M	0.92649	3.33	0.09310	N	1	B	0.30236	0.274	B	0.26094	0.066	D	0.85544	0.1217	10	0.87932	D	0	.	4.1908	0.10419	0.2528:0.0:0.4257:0.3215	.	374	P35527	K1C9_HUMAN	W	374	ENSP00000246662:R374W	ENSP00000246662:R374W	R	-	1	2	KRT9	36978336	0.000000	0.05858	0.061000	0.19648	0.351000	0.29236	0.349000	0.20055	0.133000	0.18654	-0.224000	0.12420	CGG	G|0.998;A|0.002	0.002	strong		0.547	KRT9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257707.1	NM_000226	
FPGS	2356	hgsc.bcm.edu	37	9	130566678	130566678	+	Missense_Mutation	SNP	C	C	T	rs41306702	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:130566678C>T	ENST00000373247.2	+	2	303	c.253C>T	c.(253-255)Cgg>Tgg	p.R85W	FPGS_ENST00000373245.1_Missense_Mutation_p.R85W|FPGS_ENST00000373225.3_Missense_Mutation_p.R35W|FPGS_ENST00000460181.1_3'UTR|FPGS_ENST00000393706.2_Missense_Mutation_p.R85W	NM_004957.4	NP_004948.4	Q05932	FOLC_HUMAN	folylpolyglutamate synthase	85					brain development (GO:0007420)|folic acid metabolic process (GO:0046655)|liver development (GO:0001889)|nucleobase-containing compound metabolic process (GO:0006139)|one-carbon metabolic process (GO:0006730)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|tetrahydrofolylpolyglutamate synthase activity (GO:0004326)			endometrium(2)|kidney(1)|lung(3)|ovary(1)	7					Methotrexate(DB00563)|Pralatrexate(DB06813)|Raltitrexed(DB00293)	GTACCTGGCACGGAGTGGGCT	0.607													C|||	7	0.00139776	0.0008	0.0	5008	,	,		19694	0.0		0.006	False		,,,				2504	0.0				p.R85W		Atlas-SNP	.											.	FPGS	30	.	0			c.C253T						PASS	.	C	TRP/ARG,TRP/ARG	2,4404	4.2+/-10.8	0,2,2201	116.0	98.0	104.0		103,253	4.2	1.0	9	dbSNP_127	104	30,8570	21.0+/-64.5	0,30,4270	yes	missense,missense	FPGS	NM_001018078.1,NM_004957.4	101,101	0,32,6471	TT,TC,CC		0.3488,0.0454,0.246	probably-damaging,probably-damaging	35/538,85/588	130566678	32,12974	2203	4300	6503	SO:0001583	missense	2356	exon2			CTGGCACGGAGTG		CCDS35148.1, CCDS35149.1, CCDS75905.1	9q34.11	2013-09-19			ENSG00000136877	ENSG00000136877	6.3.2.17		3824	protein-coding gene	gene with protein product		136510					Standard	NM_004957		Approved		uc004bsg.1	Q05932	OTTHUMG00000020716	ENST00000373247.2:c.253C>T	9.37:g.130566678C>T	ENSP00000362344:p.Arg85Trp	96.0	0.0	0		93.0	54.0	0.580645	NM_004957	B3KPW4|B7Z2Z3|F5H0K6|Q5JU19|Q5JU22|Q6P2P6	Missense_Mutation	SNP	ENST00000373247.2	37	CCDS35148.1	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	0	0.0	6	0.0079155672823219	C	18.11	3.550644	0.65311	4.54E-4	0.003488	ENSG00000136877	ENST00000373247;ENST00000373245;ENST00000393706;ENST00000373228;ENST00000373225;ENST00000431857;ENST00000423577	T;T;T;T;T	0.38722	2.53;1.12;2.57;1.12;2.15	5.17	4.25	0.50352	Mur ligase, central (2);	0.062573	0.64402	D	0.000005	T	0.64427	0.2597	H	0.94964	3.605	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.80764	0.992;0.994	T	0.75414	-0.3326	10	0.87932	D	0	-1.3396	10.6558	0.45673	0.3481:0.6519:0.0:0.0	rs41306702	85;85	Q05932-4;Q05932	.;FOLC_HUMAN	W	85;85;85;85;35;35;35	ENSP00000362344:R85W;ENSP00000362342:R85W;ENSP00000377309:R85W;ENSP00000362325:R85W;ENSP00000362322:R35W	ENSP00000362322:R35W	R	+	1	2	FPGS	129606499	1.000000	0.71417	1.000000	0.80357	0.588000	0.36517	1.130000	0.31393	1.124000	0.41980	0.563000	0.77884	CGG	C|0.997;T|0.003	0.003	strong		0.607	FPGS-011	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054251.1		
DNAJC9	23234	hgsc.bcm.edu	37	10	75006932	75006932	+	Missense_Mutation	SNP	G	G	T	rs201308148	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75006932G>T	ENST00000372950.4	-	1	1688	c.16C>A	c.(16-18)Ctt>Att	p.L6I	MRPS16_ENST00000479005.1_5'Flank|DNAJC9-AS1_ENST00000440197.2_RNA|DNAJC9-AS1_ENST00000513954.1_RNA|MRPS16_ENST00000416782.2_3'UTR	NM_015190.3	NP_056005.1	Q8WXX5	DNJC9_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 9	6					social behavior (GO:0035176)	nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|stomach(1)	6	Prostate(51;0.0119)					TCCTCGCAAAGGTCCAGCAGC	0.672													G|||	3	0.000599042	0.0	0.0043	5008	,	,		14564	0.0		0.0	False		,,,				2504	0.0				p.L6I		Atlas-SNP	.											.	DNAJC9	19	.	0			c.C16A						PASS	.	G	ILE/LEU	1,4373		0,1,2186	10.0	12.0	11.0		16	5.0	1.0	10		11	3,8543		0,3,4270	no	missense	DNAJC9	NM_015190.3	5	0,4,6456	TT,TG,GG		0.0351,0.0229,0.031	possibly-damaging	6/261	75006932	4,12916	2187	4273	6460	SO:0001583	missense	23234	exon1			CGCAAAGGTCCAG	AF327347	CCDS7322.1	10q22.3	2011-09-02			ENSG00000213551	ENSG00000213551		"""Heat shock proteins / DNAJ (HSP40)"""	19123	protein-coding gene	gene with protein product		611206					Standard	NM_015190		Approved	JDD1, SB73	uc001jtr.3	Q8WXX5	OTTHUMG00000018461	ENST00000372950.4:c.16C>A	10.37:g.75006932G>T	ENSP00000362041:p.Leu6Ile	42.0	0.0	0		61.0	27.0	0.442623	NM_015190	B2RMW6	Missense_Mutation	SNP	ENST00000372950.4	37	CCDS7322.1	.	.	.	.	.	.	.	.	.	.	g	20.4	3.980759	0.74474	2.29E-4	3.51E-4	ENSG00000213551	ENST00000372950	T	0.19250	2.16	5.93	5.02	0.67125	Heat shock protein DnaJ, N-terminal (1);	0.546225	0.18936	N	0.127072	T	0.18087	0.0434	L	0.39898	1.24	0.80722	D	1	B	0.25955	0.138	B	0.24541	0.054	T	0.03608	-1.1020	10	0.33141	T	0.24	-12.0946	11.1756	0.48596	0.0844:0.0:0.9156:0.0	.	6	Q8WXX5	DNJC9_HUMAN	I	6	ENSP00000362041:L6I	ENSP00000362041:L6I	L	-	1	0	DNAJC9	74676938	0.996000	0.38824	1.000000	0.80357	0.989000	0.77384	2.876000	0.48498	1.518000	0.48934	0.586000	0.80456	CTT	.	.	weak		0.672	DNAJC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048643.1	NM_015190	
ZSWIM8	23053	hgsc.bcm.edu	37	10	75552298	75552298	+	Silent	SNP	T	T	C	rs200674189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75552298T>C	ENST00000605216.1	+	10	2218	c.2001T>C	c.(1999-2001)taT>taC	p.Y667Y	ZSWIM8_ENST00000398706.2_Silent_p.Y667Y|ZSWIM8_ENST00000603114.1_Intron|ZSWIM8_ENST00000604524.1_Silent_p.Y667Y|ZSWIM8_ENST00000604729.1_Silent_p.Y667Y|ZSWIM8_ENST00000431225.1_3'UTR	NM_001242487.1	NP_001229416.1	A7E2V4	ZSWM8_HUMAN	zinc finger, SWIM-type containing 8	667							zinc ion binding (GO:0008270)										CAGATACTTATGAAGAAGATG	0.622													T|||	7	0.00139776	0.003	0.0043	5008	,	,		16349	0.0		0.0	False		,,,				2504	0.0				p.Y667Y		Atlas-SNP	.											.	.	.	.	0			c.T2001C						PASS	.	T	,,	2,3828		0,2,1913	46.0	49.0	48.0		2001,2001,2001	1.6	1.0	10		48	5,8241		0,5,4118	no	coding-synonymous,coding-synonymous,coding-synonymous	KIAA0913	NM_001242487.1,NM_001242488.1,NM_015037.3	,,	0,7,6031	CC,CT,TT		0.0606,0.0522,0.058	,,	667/1838,667/1893,667/1843	75552298	7,12069	1915	4123	6038	SO:0001819	synonymous_variant	23053	exon10			TACTTATGAAGAA	BC151206, BC040726	CCDS44440.1, CCDS60560.1	10q22.3	2012-11-02	2012-11-02	2012-11-02	ENSG00000214655	ENSG00000214655		"""Zinc fingers, SWIM-type"""	23528	protein-coding gene	gene with protein product			"""KIAA0913"""	KIAA0913			Standard	NM_015037		Approved	4832404P21Rik	uc001jvj.3	A7E2V4	OTTHUMG00000018486	ENST00000605216.1:c.2001T>C	10.37:g.75552298T>C		144.0	0.0	0		141.0	63.0	0.446809	NM_001242488	B2RP37|O94987|Q17RS8|Q2TAB8|Q6P439|Q8IW81|Q8NB34|Q9H8F3	Silent	SNP	ENST00000605216.1	37		4|4	0.0018315018315018315|0.0018315018315018315	3|3	0.006097560975609756|0.006097560975609756	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	0|0	0.0|0.0	T|T	4.874|4.874	0.162425|0.162425	0.09287|0.09287	5.22E-4|5.22E-4	6.06E-4|6.06E-4	ENSG00000214655|ENSG00000214655	ENST00000431225|ENST00000433366	.|.	.|.	.|.	5.4|5.4	1.63|1.63	0.23807|0.23807	.|.	.|.	.|.	.|.	.|.	T|.	0.49389|.	0.1554|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.44620|.	-0.9316|.	4|.	.|.	.|.	.|.	-4.1973|-4.1973	9.2674|9.2674	0.37650|0.37650	0.0:0.2171:0.0:0.7829|0.0:0.2171:0.0:0.7829	.|.	.|.	.|.	.|.	T|R	164|390	.|.	.|.	M|X	+|+	2|1	0|0	KIAA0913|KIAA0913	75222304|75222304	0.236000|0.236000	0.23804|0.23804	1.000000|1.000000	0.80357|0.80357	0.977000|0.977000	0.68977|0.68977	-0.663000|-0.663000	0.05299|0.05299	0.112000|0.112000	0.17975|0.17975	-0.256000|-0.256000	0.11100|0.11100	ATG|TGA	T|0.997;C|0.003	0.003	strong		0.622	ZSWIM8-012	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000468545.1	NM_001242487	
LRPAP1	4043	hgsc.bcm.edu	37	4	3520701	3520701	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3520701T>C	ENST00000500728.2	-	4	635	c.489A>G	c.(487-489)aaA>aaG	p.K163K	LRPAP1_ENST00000296325.5_5'UTR	NM_002337.3	NP_002328.1	P30533	AMRP_HUMAN	low density lipoprotein receptor-related protein associated protein 1	163					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)		CGCCGGAGAATTTCCCAGAGG	0.597																																					p.K163K		Atlas-SNP	.											.	LRPAP1	29	.	0			c.A489G						PASS	.						49.0	53.0	51.0					4																	3520701		2203	4300	6503	SO:0001819	synonymous_variant	4043	exon4			GGAGAATTTCCCA		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.489A>G	4.37:g.3520701T>C		97.0	0.0	0		84.0	43.0	0.511905	NM_002337	D3DVR9|Q2M310|Q53HQ3|Q53HS6	Silent	SNP	ENST00000500728.2	37	CCDS3371.1																																																																																			.	.	none		0.597	LRPAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206659.4		
NID2	22795	hgsc.bcm.edu	37	14	52508842	52508842	+	Missense_Mutation	SNP	C	C	A	rs61747585	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:52508842C>A	ENST00000216286.5	-	7	1805	c.1806G>T	c.(1804-1806)gaG>gaT	p.E602D	NID2_ENST00000541773.1_Missense_Mutation_p.E549D	NM_007361.3	NP_031387.3	Q14112	NID2_HUMAN	nidogen 2 (osteonidogen)	602	Nidogen G2 beta-barrel. {ECO:0000255|PROSITE-ProRule:PRU00348}.				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)					TGAAGCCGTTCTCAGAGCCAG	0.577													c|||	161	0.0321486	0.062	0.0303	5008	,	,		19175	0.0		0.0517	False		,,,				2504	0.0061				p.E602D		Atlas-SNP	.											NID2,NS,carcinoma,-2,1	NID2	201	1	0			c.G1806T						scavenged	.	C	ASP/GLU	249,4157	142.3+/-177.5	9,231,1963	75.0	83.0	80.0		1806	4.1	0.8	14	dbSNP_129	80	371,8229	121.7+/-180.7	4,363,3933	yes	missense	NID2	NM_007361.3	45	13,594,5896	AA,AC,CC		4.314,5.6514,4.767	probably-damaging	602/1376	52508842	620,12386	2203	4300	6503	SO:0001583	missense	22795	exon7			GCCGTTCTCAGAG	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.1806G>T	14.37:g.52508842C>A	ENSP00000216286:p.Glu602Asp	85.0	1.0	0.0117647		77.0	35.0	0.454545	NM_007361	A8K6I7|B4DU19|O43710	Missense_Mutation	SNP	ENST00000216286.5	37	CCDS9706.1	88	0.040293040293040296	33	0.06707317073170732	13	0.03591160220994475	0	0.0	42	0.055408970976253295	C	13.76	2.334393	0.41297	0.056514	0.04314	ENSG00000087303	ENST00000216286;ENST00000316204;ENST00000541773;ENST00000395707	T;T	0.31247	1.5;1.5	5.93	4.11	0.48088	G2 nidogen/fibulin G2F (3);Green fluorescent protein-like (1);	0.473992	0.25319	N	0.031528	T	0.03095	0.0091	M	0.68952	2.095	0.29539	N	0.85222	P;P;P;P	0.48998	0.542;0.799;0.918;0.741	B;B;P;P	0.49140	0.348;0.158;0.601;0.491	T	0.03103	-1.1072	10	0.25751	T	0.34	.	6.2035	0.20590	0.0:0.6512:0.1381:0.2107	.	196;549;604;602	E7EPP3;Q14112-2;Q5CZI2;Q14112	.;.;.;NID2_HUMAN	D	602;196;549;604	ENSP00000216286:E602D;ENSP00000443730:E549D	ENSP00000216286:E602D	E	-	3	2	NID2	51578592	0.990000	0.36364	0.769000	0.31535	0.920000	0.55202	0.896000	0.28377	0.853000	0.35312	0.655000	0.94253	GAG	C|0.953;A|0.047	0.047	strong		0.577	NID2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276888.1		
LAMB2	3913	hgsc.bcm.edu	37	3	49166460	49166460	+	Missense_Mutation	SNP	C	C	T	rs61729152	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:49166460C>T	ENST00000418109.1	-	14	1888	c.1724G>A	c.(1723-1725)cGa>cAa	p.R575Q	LAMB2_ENST00000305544.4_Missense_Mutation_p.R575Q	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	575	Laminin IV type B. {ECO:0000255|PROSITE- ProRule:PRU00462}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CACCTGCCCTCGGGTGTCCTC	0.622													C|||	32	0.00638978	0.0	0.013	5008	,	,		18383	0.0		0.0209	False		,,,				2504	0.002				p.R575Q		Atlas-SNP	.											LAMB2,NS,carcinoma,-1,1	LAMB2	156	1	0			c.G1724A						scavenged	.	C	GLN/ARG	17,4389	26.2+/-53.5	0,17,2186	52.0	55.0	54.0		1724	-1.9	0.0	3	dbSNP_129	54	139,8461	63.5+/-125.6	2,135,4163	yes	missense	LAMB2	NM_002292.3	43	2,152,6349	TT,TC,CC		1.6163,0.3858,1.1994	benign	575/1799	49166460	156,12850	2203	4300	6503	SO:0001583	missense	3913	exon13			TGCCCTCGGGTGT		CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.1724G>A	3.37:g.49166460C>T	ENSP00000388325:p.Arg575Gln	33.0	1.0	0.030303		34.0	14.0	0.411765	NM_002292	Q16321	Missense_Mutation	SNP	ENST00000418109.1	37	CCDS2789.1	22	0.010073260073260074	0	0.0	7	0.019337016574585635	0	0.0	15	0.01978891820580475	C	3.211	-0.161592	0.06502	0.003858	0.016163	ENSG00000172037	ENST00000418109;ENST00000305544	T;T	0.34275	1.37;1.37	5.18	-1.88	0.07713	Laminin IV (1);	0.609454	0.16134	N	0.228066	T	0.07052	0.0179	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.29027	-1.0025	10	0.10377	T	0.69	.	9.9192	0.41453	0.0:0.5495:0.0:0.4505	.	575	P55268	LAMB2_HUMAN	Q	575	ENSP00000388325:R575Q;ENSP00000307156:R575Q	ENSP00000307156:R575Q	R	-	2	0	LAMB2	49141464	0.000000	0.05858	0.014000	0.15608	0.012000	0.07955	-1.165000	0.03132	-0.448000	0.07128	-0.423000	0.05987	CGA	C|0.991;T|0.009	0.009	strong		0.622	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345939.1	NM_002292	
NEK11	79858	hgsc.bcm.edu	37	3	130947466	130947466	+	Silent	SNP	G	G	A	rs138864243	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:130947466G>A	ENST00000510769.1	+	11	1432	c.1179G>A	c.(1177-1179)gcG>gcA	p.A393A	NEK11_ENST00000412440.2_Silent_p.A314A|NEK11_ENST00000429253.2_Silent_p.A498A|NEK11_ENST00000508196.1_Silent_p.A498A|NEK11_ENST00000383366.4_Silent_p.A498A|NEK11_ENST00000510688.1_Silent_p.A498A					NIMA-related kinase 11											breast(2)|central_nervous_system(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(14)|stomach(1)|urinary_tract(2)	33						AAGAAATAGCGTTAGAAAGAC	0.453													G|||	5	0.000998403	0.0023	0.0014	5008	,	,		19611	0.0		0.001	False		,,,				2504	0.0				p.A498A		Atlas-SNP	.											.	NEK11	76	.	0			c.G1494A						PASS	.	G	,	6,4400	11.4+/-27.6	0,6,2197	117.0	109.0	112.0		1494,1494	1.6	0.0	3	dbSNP_134	112	10,8590	7.7+/-29.5	0,10,4290	no	coding-synonymous,coding-synonymous	NEK11	NM_001146003.1,NM_024800.4	,	0,16,6487	AA,AG,GG		0.1163,0.1362,0.123	,	498/600,498/646	130947466	16,12990	2203	4300	6503	SO:0001819	synonymous_variant	79858	exon15			AATAGCGTTAGAA	AK027148	CCDS3069.1, CCDS46915.1, CCDS54639.1	3q22.1	2012-11-15	2012-11-15		ENSG00000114670	ENSG00000114670			18593	protein-coding gene	gene with protein product		609779	"""NIMA (never in mitosis gene a)- related kinase 11"""				Standard	NM_024800		Approved	FLJ23495	uc003eny.3	Q8NG66	OTTHUMG00000159654	ENST00000510769.1:c.1179G>A	3.37:g.130947466G>A		51.0	0.0	0		42.0	21.0	0.5	NM_024800		Silent	SNP	ENST00000510769.1	37																																																																																				G|0.998;A|0.002	0.002	strong		0.453	NEK11-005	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000356757.1	NM_024800	
WFIKKN2	124857	hgsc.bcm.edu	37	17	48918275	48918275	+	Silent	SNP	C	C	T	rs139049586	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48918275C>T	ENST00000311378.4	+	2	2154	c.1626C>T	c.(1624-1626)ccC>ccT	p.P542P	RP11-506D12.5_ENST00000572491.2_RNA|WFIKKN2_ENST00000426127.1_Silent_p.P449P	NM_175575.5	NP_783165.1	Q8TEU8	WFKN2_HUMAN	WAP, follistatin/kazal, immunoglobulin, kunitz and netrin domain containing 2	542	NTR. {ECO:0000255|PROSITE- ProRule:PRU00295}.				muscle fiber development (GO:0048747)|negative regulation of DNA binding (GO:0043392)|negative regulation of protein binding (GO:0032091)|palate development (GO:0060021)|skeletal system development (GO:0001501)|transforming growth factor beta receptor signaling pathway (GO:0007179)	extracellular region (GO:0005576)	metalloendopeptidase inhibitor activity (GO:0008191)|serine-type endopeptidase inhibitor activity (GO:0004867)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(3)|lung(13)|ovary(4)|skin(1)	29			BRCA - Breast invasive adenocarcinoma(22;1.09e-08)			TGCTGCGCCCCGATAGCTTTG	0.622													C|||	12	0.00239617	0.0008	0.0115	5008	,	,		16132	0.0		0.002	False		,,,				2504	0.001				p.P542P		Atlas-SNP	.											WFIKKN2,colon,carcinoma,0,1	WFIKKN2	69	1	0			c.C1626T						scavenged	.	C		3,4403	2.1+/-5.4	0,3,2200	50.0	42.0	45.0		1626	-10.2	0.2	17	dbSNP_134	45	42,8558	27.4+/-76.7	0,42,4258	no	coding-synonymous	WFIKKN2	NM_175575.5		0,45,6458	TT,TC,CC		0.4884,0.0681,0.346		542/577	48918275	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	124857	exon2			GCGCCCCGATAGC	AY358142	CCDS11575.1	17q21.33	2013-01-21			ENSG00000173714	ENSG00000173714		"""Immunoglobulin superfamily / I-set domain containing"", ""WAP four-disulfide core domain containing"""	30916	protein-coding gene	gene with protein product	"""WAP four-disulfide core domain 20B"""	610895				11928817, 12709070	Standard	NM_175575		Approved	WFIKKNRP, WFDC20B	uc002isv.4	Q8TEU8	OTTHUMG00000162274	ENST00000311378.4:c.1626C>T	17.37:g.48918275C>T		139.0	1.0	0.00719424		116.0	56.0	0.482759	NM_175575	Q6UXZ9	Silent	SNP	ENST00000311378.4	37	CCDS11575.1																																																																																			C|0.997;T|0.003	0.003	strong		0.622	WFIKKN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000368358.1	NM_175575	
RADIL	55698	hgsc.bcm.edu	37	7	4874729	4874729	+	Missense_Mutation	SNP	C	C	G	rs144507770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4874729C>G	ENST00000399583.3	-	4	1112	c.925G>C	c.(925-927)Ggc>Cgc	p.G309R	RADIL_ENST00000536091.1_Missense_Mutation_p.G309R|RADIL_ENST00000538469.1_Missense_Mutation_p.G69R	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	309					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		GCGGCCTGGCCGCTGTCCGGG	0.711													C|||	60	0.0119808	0.0015	0.0173	5008	,	,		10553	0.0		0.0249	False		,,,				2504	0.0215				p.G309R		Atlas-SNP	.											.	RADIL	110	.	0			c.G925C						PASS	.	C	ARG/GLY	8,3996		0,8,1994	9.0	13.0	12.0		925	-1.8	0.0	7	dbSNP_134	12	168,8110		4,160,3975	yes	missense	RADIL	NM_018059.4	125	4,168,5969	GG,GC,CC		2.0295,0.1998,1.433	possibly-damaging	309/1076	4874729	176,12106	2002	4139	6141	SO:0001583	missense	55698	exon4			CCTGGCCGCTGTC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.925G>C	7.37:g.4874729C>G	ENSP00000382492:p.Gly309Arg	27.0	0.0	0		41.0	21.0	0.512195	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	29	0.013278388278388278	2	0.0040650406504065045	9	0.024861878453038673	0	0.0	18	0.023746701846965697	-	4.272	0.049630	0.08243	0.001998	0.020295	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000536091;ENST00000538469	T;T;T	0.06068	3.35;3.35;3.35	4.3	-1.83	0.07833	Forkhead-associated (FHA) domain (1);SMAD/FHA domain (1);	1.742530	0.03218	N	0.177080	T	0.02193	0.0068	L	0.40543	1.245	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.39643	-0.9604	10	0.18710	T	0.47	-0.7787	0.4916	0.00565	0.1804:0.2431:0.2692:0.3073	.	309	Q96JH8	RADIL_HUMAN	R	309;280;309;69	ENSP00000382492:G309R;ENSP00000442533:G309R;ENSP00000442966:G69R	ENSP00000320946:G280R	G	-	1	0	RADIL	4841255	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.164000	0.16542	-0.261000	0.09405	-0.759000	0.03464	GGC	C|0.987;G|0.013	0.013	strong		0.711	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
ZDHHC1	29800	hgsc.bcm.edu	37	16	67434917	67434917	+	Missense_Mutation	SNP	C	C	T	rs34229857	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67434917C>T	ENST00000348579.2	-	4	712	c.371G>A	c.(370-372)cGa>cAa	p.R124Q		NM_013304.2	NP_037436.1	Q8WTX9	ZDHC1_HUMAN	zinc finger, DHHC-type containing 1	124			R -> Q (in dbSNP:rs34229857).		protein palmitoylation (GO:0018345)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	DNA binding (GO:0003677)|palmitoyltransferase activity (GO:0016409)|protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|urinary_tract(1)	10		Ovarian(137;0.223)		UCEC - Uterine corpus endometrioid carcinoma (183;0.0178)|all cancers(182;5.71e-53)|Epithelial(162;4.73e-52)|OV - Ovarian serous cystadenocarcinoma(108;1.53e-29)|Kidney(780;4.37e-05)|BRCA - Breast invasive adenocarcinoma(181;5.8e-05)|GBM - Glioblastoma multiforme(240;0.0022)		GTGCTGGCTTCGGTTGAAGAT	0.602													C|||	51	0.0101837	0.0	0.0014	5008	,	,		20071	0.0089		0.0249	False		,,,				2504	0.0164				p.R124Q		Atlas-SNP	.											.	ZDHHC1	28	.	0			c.G371A						PASS	.	C	GLN/ARG	22,4374	28.1+/-56.4	0,22,2176	131.0	113.0	119.0		371	5.1	1.0	16	dbSNP_126	119	229,8371	93.5+/-155.5	5,219,4076	yes	missense	ZDHHC1	NM_013304.2	43	5,241,6252	TT,TC,CC		2.6628,0.5005,1.9314	probably-damaging	124/486	67434917	251,12745	2198	4300	6498	SO:0001583	missense	29800	exon4			TGGCTTCGGTTGA	U90653	CCDS10836.1	16q22.1	2010-03-25	2003-01-27		ENSG00000159714	ENSG00000159714		"""Zinc fingers, DHHC-type"""	17916	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 1"""	C16orf1		10395086	Standard	NM_013304		Approved	HSU90653, ZNF377	uc010vjm.2	Q8WTX9	OTTHUMG00000137522	ENST00000348579.2:c.371G>A	16.37:g.67434917C>T	ENSP00000340299:p.Arg124Gln	120.0	0.0	0		164.0	89.0	0.542683	NM_013304	O15461	Missense_Mutation	SNP	ENST00000348579.2	37	CCDS10836.1	20	0.009157509157509158	0	0.0	1	0.0027624309392265192	3	0.005244755244755245	16	0.021108179419525065	C	26.2	4.710737	0.89112	0.005005	0.026628	ENSG00000159714	ENST00000348579	T	0.37411	1.2	6.06	5.1	0.69264	.	0.081104	0.53938	D	0.000060	T	0.26011	0.0634	L	0.55834	1.745	0.51482	D	0.999921	D	0.89917	1.0	D	0.75484	0.986	T	0.21484	-1.0244	10	0.23302	T	0.38	.	9.8809	0.41233	0.0:0.7878:0.1405:0.0716	rs34229857	124	Q8WTX9	ZDHC1_HUMAN	Q	124	ENSP00000340299:R124Q	ENSP00000340299:R124Q	R	-	2	0	ZDHHC1	65992418	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	4.674000	0.61612	1.557000	0.49525	0.655000	0.94253	CGA	C|0.983;T|0.017	0.017	strong		0.602	ZDHHC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268845.1	NM_013304	
LETM2	137994	hgsc.bcm.edu	37	8	38250202	38250202	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:38250202A>G	ENST00000379957.4	+	3	317	c.190A>G	c.(190-192)Aat>Gat	p.N64D	LETM2_ENST00000297720.5_Missense_Mutation_p.N17D|LETM2_ENST00000519476.2_Missense_Mutation_p.N64D|LETM2_ENST00000524874.1_Missense_Mutation_p.N64D|LETM2_ENST00000523983.2_Missense_Mutation_p.N17D	NM_001199659.1	NP_001186588.1	Q2VYF4	LETM2_HUMAN	leucine zipper-EF-hand containing transmembrane protein 2	64						integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)				NS(1)|large_intestine(1)|lung(3)|prostate(2)	7	all_cancers(2;6.77e-47)|all_epithelial(2;1.01e-50)|all_lung(3;1.25e-23)|Lung NSC(2;2.76e-23)|Colorectal(12;0.000442)|Esophageal squamous(3;0.00202)	all_lung(54;0.0657)|Hepatocellular(245;0.152)|Lung NSC(58;0.175)	Epithelial(3;1.17e-42)|all cancers(3;5.44e-38)|BRCA - Breast invasive adenocarcinoma(5;5.44e-27)|LUSC - Lung squamous cell carcinoma(2;7.12e-25)|Lung(2;4.49e-22)|COAD - Colon adenocarcinoma(9;0.114)			TCAGCCAGGCAATACAGTACT	0.453																																					p.N17D		Atlas-SNP	.											.	LETM2	57	.	0			c.A49G						PASS	.						86.0	89.0	88.0					8																	38250202		2203	4300	6503	SO:0001583	missense	137994	exon3			CCAGGCAATACAG	AK058138	CCDS6106.1, CCDS56534.1, CCDS69466.1, CCDS75731.1	8p12	2013-01-11						"""EF-hand domain containing"""	14648	protein-coding gene	gene with protein product						11549311	Standard	NM_001286821		Approved	FLJ25409	uc003xlm.2	Q2VYF4		ENST00000379957.4:c.190A>G	8.37:g.38250202A>G	ENSP00000369291:p.Asn64Asp	79.0	0.0	0		71.0	37.0	0.521127	NM_001199659	A6NMG3|Q8NCR2|Q96LL1	Missense_Mutation	SNP	ENST00000379957.4	37		.	.	.	.	.	.	.	.	.	.	A	6.285	0.420678	0.11928	.	.	ENSG00000165046	ENST00000527334;ENST00000519476;ENST00000297720;ENST00000524874;ENST00000379957;ENST00000523983;ENST00000526356	.	.	.	5.75	1.81	0.25067	.	1.355500	0.04352	N	0.355909	T	0.30386	0.0763	L	0.56769	1.78	0.09310	N	0.999997	B;B;P	0.34462	0.201;0.094;0.454	B;B;B	0.30401	0.016;0.016;0.115	T	0.14504	-1.0470	9	0.18276	T	0.48	.	2.9332	0.05805	0.3552:0.4136:0.098:0.1332	.	64;64;64	Q2VYF4;E9PMA4;A8K1M9	LETM2_HUMAN;.;.	D	64;64;17;64;64;17;64	.	ENSP00000297720:N17D	N	+	1	0	LETM2	38369359	0.000000	0.05858	0.020000	0.16555	0.053000	0.15095	-0.173000	0.09854	0.059000	0.16252	0.533000	0.62120	AAT	.	.	none		0.453	LETM2-013	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000381816.1	NM_144652	
RTBDN	83546	hgsc.bcm.edu	37	19	12936693	12936693	+	Missense_Mutation	SNP	C	C	T	rs148952767	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12936693C>T	ENST00000458671.2	-	6	669	c.517G>A	c.(517-519)Gtg>Atg	p.V173M	RTBDN_ENST00000592204.1_Missense_Mutation_p.V183M|RTBDN_ENST00000589272.1_3'UTR|RTBDN_ENST00000393233.2_3'UTR|RTBDN_ENST00000322912.5_Missense_Mutation_p.V205M|CTD-2265O21.3_ENST00000588469.1_RNA	NM_001080997.2	NP_001074466.1	Q9BSG5	RTBDN_HUMAN	retbindin	173						extracellular region (GO:0005576)				kidney(1)|large_intestine(5)|liver(1)|lung(4)|prostate(1)	12						GGAGCAGCCACCGGTAGGGCG	0.647											OREG0025275	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	C|||	19	0.00379393	0.0	0.0086	5008	,	,		13754	0.0		0.0109	False		,,,				2504	0.002				p.V205M		Atlas-SNP	.											.	RTBDN	26	.	0			c.G613A						PASS	.	C	MET/VAL,MET/VAL	4,4396		0,4,2196	29.0	26.0	27.0		517,613	1.9	0.0	19	dbSNP_134	27	77,8513		0,77,4218	yes	missense,missense	RTBDN	NM_001080997.1,NM_031429.1	21,21	0,81,6414	TT,TC,CC		0.8964,0.0909,0.6236	probably-damaging,probably-damaging	173/230,205/262	12936693	81,12909	2200	4295	6495	SO:0001583	missense	83546	exon7			CAGCCACCGGTAG	AY028917	CCDS12283.1, CCDS45994.1, CCDS59355.1, CCDS59356.1	19p13	2006-03-22				ENSG00000132026			30310	protein-coding gene	gene with protein product		609553				12107411	Standard	NM_001080997		Approved	FLJ36353	uc002mvj.4	Q9BSG5		ENST00000458671.2:c.517G>A	19.37:g.12936693C>T	ENSP00000416375:p.Val173Met	84.0	0.0	0	683	127.0	59.0	0.464567	NM_031429	F1T0I8|Q9BWT5	Missense_Mutation	SNP	ENST00000458671.2	37	CCDS45994.1	13	0.005952380952380952	0	0.0	3	0.008287292817679558	0	0.0	10	0.013192612137203167	C	16.73	3.204950	0.58234	9.09E-4	0.008964	ENSG00000132026	ENST00000322912;ENST00000458671	T;T	0.79033	-1.23;-1.23	4.36	1.89	0.25635	Folate receptor-like (1);	0.581337	0.14332	N	0.326316	T	0.79673	0.4486	M	0.70595	2.14	0.19300	N	0.999978	D;D	0.89917	1.0;1.0	D;D	0.74674	0.973;0.984	T	0.68949	-0.5274	10	0.72032	D	0.01	-26.9761	5.851	0.18694	0.0:0.7037:0.0:0.2963	.	205;173	Q9BSG5-2;Q9BSG5	.;RTBDN_HUMAN	M	205;173	ENSP00000326253:V205M;ENSP00000416375:V173M	ENSP00000326253:V205M	V	-	1	0	RTBDN	12797693	0.043000	0.20138	0.045000	0.18777	0.048000	0.14542	0.110000	0.15437	0.404000	0.25506	0.591000	0.81541	GTG	C|0.993;T|0.007	0.007	strong		0.647	RTBDN-003	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000451513.1	NM_031429	
LGALS14	56891	hgsc.bcm.edu	37	19	40195183	40195183	+	Splice_Site	SNP	C	C	T	rs117106744	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:40195183C>T	ENST00000392052.3	+	1	238	c.15C>T	c.(13-15)ccC>ccT	p.P5P	LGALS14_ENST00000360675.3_5'UTR	NM_020129.2	NP_064514.1	Q8TCE9	PPL13_HUMAN	lectin, galactoside-binding, soluble, 14	5				SLPV -> ITPG (in Ref. 1; AAP97241). {ECO:0000305}.	apoptotic process (GO:0006915)	nucleus (GO:0005634)	carbohydrate binding (GO:0030246)			breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|skin(2)|stomach(2)	14	all_cancers(60;4.39e-06)|all_lung(34;6.76e-08)|Lung NSC(34;7.98e-08)|Ovarian(47;0.06)	Myeloproliferative disorder(2;0.0741)	Epithelial(26;1.08e-24)|OV - Ovarian serous cystadenocarcinoma(5;1.92e-24)|all cancers(26;4.12e-22)			CATCACTACCCGTGAGTTGAA	0.423													C|||	7	0.00139776	0.0	0.0014	5008	,	,		22816	0.0		0.006	False		,,,				2504	0.0				p.P5P		Atlas-SNP	.											.	LGALS14	38	.	0			c.C15T						PASS	.	C	,	14,4336		0,14,2161	62.0	63.0	63.0		15,	-1.8	0.0	19	dbSNP_132	63	73,8495		0,73,4211	yes	coding-synonymous-near-splice,utr-5	LGALS14	NM_020129.2,NM_203471.1	,	0,87,6372	TT,TC,CC		0.852,0.3218,0.6735	,	5/140,	40195183	87,12831	2175	4284	6459	SO:0001630	splice_region_variant	56891	exon1			ACTACCCGTGAGT	AF267852	CCDS12542.1, CCDS46073.1	19q13.2	2014-03-19			ENSG00000006659	ENSG00000006659		"""Lectins, galactoside-binding"""	30054	protein-coding gene	gene with protein product		607260				11997112	Standard	NM_020129		Approved	PPL13, CLC2	uc002omg.3	Q8TCE9	OTTHUMG00000183143	ENST00000392052.3:c.15+1C>T	19.37:g.40195183C>T		199.0	0.0	0		214.0	103.0	0.481308	NM_020129	A8MPV8|B2R530|C5HZ19|Q7Z4X8|Q96KD4|Q96KD5|Q96KD6|Q9NR03	Silent	SNP	ENST00000392052.3	37	CCDS46073.1																																																																																			C|0.996;T|0.004	0.004	strong		0.423	LGALS14-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465222.1	NM_020129	Silent
MORC4	79710	hgsc.bcm.edu	37	X	106221323	106221323	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:106221323C>A	ENST00000355610.4	-	8	1317	c.1043G>T	c.(1042-1044)gGg>gTg	p.G348V	MORC4_ENST00000255495.7_Missense_Mutation_p.G348V|MORC4_ENST00000535534.1_Missense_Mutation_p.G96V	NM_001085354.2|NM_024657.4	NP_001078823.1|NP_078933.3	Q8TE76	MORC4_HUMAN	MORC family CW-type zinc finger 4	348						nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(7)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	28						CACCTGGCACCCCACCTTCTC	0.383																																					p.G348V		Atlas-SNP	.											.	MORC4	155	.	0			c.G1043T						PASS	.						160.0	159.0	160.0					X																	106221323		2203	4300	6503	SO:0001583	missense	79710	exon8			TGGCACCCCACCT	AK021627	CCDS14525.2, CCDS48146.1	Xq22.3	2008-02-05	2005-06-15	2005-06-15	ENSG00000133131	ENSG00000133131			23485	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 2"", ""zinc finger, CW type with coiled-coil domain 2"""	ZCWCC2		14607086	Standard	NM_024657		Approved	ZCW4, FLJ11565	uc004emp.4	Q8TE76	OTTHUMG00000022155	ENST00000355610.4:c.1043G>T	X.37:g.106221323C>A	ENSP00000347821:p.Gly348Val	67.0	0.0	0		71.0	61.0	0.859155	NM_001085354	A1YR23|A1YR24|H7BXF1|Q5JUK7|Q96MZ2|Q9HAI7	Missense_Mutation	SNP	ENST00000355610.4	37	CCDS14525.2	.	.	.	.	.	.	.	.	.	.	C	19.17	3.775432	0.70107	.	.	ENSG00000133131	ENST00000355610;ENST00000535534;ENST00000255495	T;T;T	0.37752	2.41;1.18;2.41	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.59582	0.2204	M	0.72118	2.19	0.58432	D	0.999999	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	T	0.63739	-0.6569	10	0.87932	D	0	-13.769	15.1835	0.72978	0.0:1.0:0.0:0.0	.	96;348;348	A1YR24;A1YR23;Q8TE76	.;.;MORC4_HUMAN	V	348;96;348	ENSP00000347821:G348V;ENSP00000440359:G96V;ENSP00000255495:G348V	ENSP00000255495:G348V	G	-	2	0	MORC4	106107979	1.000000	0.71417	0.997000	0.53966	0.987000	0.75469	5.777000	0.68931	2.393000	0.81446	0.538000	0.68166	GGG	.	.	none		0.383	MORC4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057816.3	NM_024657	
KCNQ1	3784	hgsc.bcm.edu	37	11	2869086	2869086	+	Silent	SNP	C	C	T	rs144610043|rs397508102		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:2869086C>T	ENST00000155840.5	+	16	1992	c.1884C>T	c.(1882-1884)ggC>ggT	p.G628G	KCNQ1-AS1_ENST00000440887.2_RNA|KCNQ1_ENST00000335475.5_Silent_p.G501G|KCNQ1_ENST00000526095.1_3'UTR	NM_000218.2	NP_000209.2	P51787	KCNQ1_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 1	628				LHGGSTPGSGGPPREGGAHITQPCGS -> MQQGGPTCNSR SQVVASNE (in Ref. 4; AAM94040). {ECO:0000305}.	atrial cardiac muscle cell action potential (GO:0086014)|cardiac muscle contraction (GO:0060048)|cardiovascular system development (GO:0072358)|cellular response to cAMP (GO:0071320)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|gene silencing (GO:0016458)|male gonad development (GO:0008584)|membrane repolarization during action potential (GO:0086011)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of insulin secretion (GO:0046676)|positive regulation of gastric acid secretion (GO:0060454)|positive regulation of potassium ion transmembrane transport (GO:1901381)|potassium ion export (GO:0071435)|potassium ion transmembrane transport (GO:0071805)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of heart contraction (GO:0008016)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of membrane repolarization (GO:0060306)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)|ventricular cardiac muscle cell action potential (GO:0086005)	basolateral plasma membrane (GO:0016323)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated potassium channel complex (GO:0008076)|zymogen granule membrane (GO:0042589)	calmodulin binding (GO:0005516)|delayed rectifier potassium channel activity (GO:0005251)|ion channel binding (GO:0044325)|outward rectifier potassium channel activity (GO:0015271)|protein kinase A catalytic subunit binding (GO:0034236)|protein kinase A regulatory subunit binding (GO:0034237)|protein phosphatase 1 binding (GO:0008157)|scaffold protein binding (GO:0097110)|voltage-gated potassium channel activity (GO:0005249)|voltage-gated potassium channel activity involved in atrial cardiac muscle cell action potential repolarization (GO:0086089)|voltage-gated potassium channel activity involved in cardiac muscle cell action potential repolarization (GO:0086008)|voltage-gated potassium channel activity involved in ventricular cardiac muscle cell action potential repolarization (GO:1902282)			endometrium(1)|kidney(1)|large_intestine(2)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(2)	21		all_epithelial(84;3.26e-05)|Breast(177;0.001)|Medulloblastoma(188;0.00111)|Ovarian(85;0.00158)|all_neural(188;0.00725)|all_lung(207;0.11)|Lung NSC(207;0.159)		BRCA - Breast invasive adenocarcinoma(625;0.00251)|Lung(200;0.131)	Bepridil(DB01244)|Indapamide(DB00808)	CCGGCAGCGGCGGCCCCCCCA	0.701																																					p.G628G		Atlas-SNP	.											.	KCNQ1	60	.	0			c.C1884T						PASS	.						10.0	10.0	10.0					11																	2869086		2141	4219	6360	SO:0001819	synonymous_variant	3784	exon16			CAGCGGCGGCCCC	AF000571	CCDS7736.1	11p15.5	2014-09-17			ENSG00000053918	ENSG00000053918		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6294	protein-coding gene	gene with protein product	"""Jervell and Lange-Nielsen syndrome 1"""	607542		LQT, KCNA9		8528244, 16382104	Standard	NM_181798		Approved	Kv7.1, KCNA8, KVLQT1, JLNS1, LQT1	uc001lwn.3	P51787	OTTHUMG00000009900	ENST00000155840.5:c.1884C>T	11.37:g.2869086C>T		31.0	0.0	0		66.0	36.0	0.545455	NM_000218	O00347|O60607|O94787|Q14D14|Q7Z6G9|Q92960|Q9UMN8|Q9UMN9	Silent	SNP	ENST00000155840.5	37	CCDS7736.1																																																																																			.	.	none		0.701	KCNQ1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027382.2	NM_000218	
IL17RC	84818	hgsc.bcm.edu	37	3	9965582	9965582	+	Missense_Mutation	SNP	G	G	A	rs75692599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9965582G>A	ENST00000295981.3	+	8	1071	c.853G>A	c.(853-855)Gtg>Atg	p.V285M	IL17RC_ENST00000498214.1_3'UTR|IL17RC_ENST00000403601.3_Missense_Mutation_p.V214M|IL17RC_ENST00000413608.1_Missense_Mutation_p.V214M|IL17RC_ENST00000383812.4_Missense_Mutation_p.V199M|IL17RC_ENST00000455057.1_Missense_Mutation_p.V199M|IL17RC_ENST00000416074.2_Missense_Mutation_p.V70M	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	285					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						CTGGCTCAACGTGTCAGCAGA	0.567													G|||	24	0.00479233	0.003	0.0058	5008	,	,		19241	0.0		0.0159	False		,,,				2504	0.0				p.V285M		Atlas-SNP	.											.	IL17RC	55	.	0			c.G853A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	10,4396	16.8+/-37.8	0,10,2193	83.0	76.0	78.0		640,640,595,595,640,853	2.2	0.1	3	dbSNP_131	78	202,8398	87.9+/-150.2	5,192,4103	yes	missense,missense,missense,missense,missense,missense	IL17RC	NM_001203263.1,NM_001203264.1,NM_001203265.1,NM_032732.5,NM_153460.3,NM_153461.3	21,21,21,21,21,21	5,202,6296	AA,AG,GG		2.3488,0.227,1.63	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	214/708,214/691,199/689,199/706,214/721,285/792	9965582	212,12794	2203	4300	6503	SO:0001583	missense	84818	exon8			CTCAACGTGTCAG	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.853G>A	3.37:g.9965582G>A	ENSP00000295981:p.Val285Met	117.0	0.0	0		125.0	54.0	0.432	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Missense_Mutation	SNP	ENST00000295981.3	37	CCDS2590.1	15	0.006868131868131868	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	11	0.014511873350923483	G	8.788	0.929765	0.18131	0.00227	0.023488	ENSG00000163702	ENST00000383812;ENST00000438091;ENST00000295981;ENST00000436503;ENST00000403601;ENST00000416074;ENST00000455057;ENST00000413608	T;T;T;T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1;2.1;2.1;2.1	5.47	2.2	0.27929	.	0.636179	0.13137	N	0.410970	T	0.17577	0.0422	M	0.64997	1.995	0.09310	N	1	D;D;P;P;D;D;D;D;D	0.76494	0.981;0.999;0.943;0.943;0.994;0.99;0.966;0.997;0.997	B;P;B;B;P;P;B;P;P	0.57283	0.428;0.817;0.246;0.246;0.557;0.557;0.428;0.654;0.704	T	0.06625	-1.0816	10	0.62326	D	0.03	-8.7325	4.2685	0.10775	0.0961:0.1562:0.5875:0.1602	.	199;70;199;214;214;214;199;285;214	Q8NAC3-4;F5H4Z2;E9PHG1;A8BWD5;E9PHJ6;A8BWC9;Q8NAC3-3;Q8NAC3;Q8NAC3-2	.;.;.;.;.;.;.;I17RC_HUMAN;.	M	199;174;285;189;214;70;199;214	ENSP00000373323:V199M;ENSP00000414609:V174M;ENSP00000295981:V285M;ENSP00000401128:V189M;ENSP00000384969:V214M;ENSP00000395315:V70M;ENSP00000407894:V199M;ENSP00000396064:V214M	ENSP00000295981:V285M	V	+	1	0	IL17RC	9940582	0.951000	0.32395	0.104000	0.21259	0.258000	0.26162	1.493000	0.35605	0.687000	0.31509	0.638000	0.83543	GTG	G|0.988;A|0.012	0.012	strong		0.567	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
MUC4	4585	hgsc.bcm.edu	37	3	195506752	195506752	+	Missense_Mutation	SNP	C	C	T	rs554841787	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506752C>T	ENST00000463781.3	-	2	12158	c.11699G>A	c.(11698-11700)cGt>cAt	p.R3900H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.R3900H|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GGTGGCGTGACGTGTGGATGC	0.587													.|||	63	0.0125799	0.0	0.0086	5008	,	,		8251	0.003		0.0149	False		,,,				2504	0.0399				p.R3900H		Atlas-SNP	.											.	MUC4	1505	.	0			c.G11699A						PASS	.						10.0	9.0	9.0					3																	195506752		525	990	1515	SO:0001583	missense	4585	exon2			GCGTGACGTGTGG	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11699G>A	3.37:g.195506752C>T	ENSP00000417498:p.Arg3900His	25.0	0.0	0		70.0	23.0	0.328571	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	c	6.268	0.417524	0.11870	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.30714	1.52;1.57	.	.	.	.	.	.	.	.	T	0.10981	0.0268	N	0.14661	0.345	0.09310	N	1	P	0.35793	0.521	B	0.11329	0.006	T	0.18147	-1.0346	7	.	.	.	.	2.8356	0.05513	0.4983:0.5012:2.0E-4:3.0E-4	.	3772	E7ESK3	.	H	3900	ENSP00000417498:R3900H;ENSP00000420243:R3900H	.	R	-	2	0	MUC4	196991531	0.000000	0.05858	0.002000	0.10522	0.002000	0.02628	-0.055000	0.11807	0.064000	0.16427	0.064000	0.15345	CGT	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
FSD1L	83856	hgsc.bcm.edu	37	9	108230553	108230553	+	Missense_Mutation	SNP	G	G	T	rs41316532	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:108230553G>T	ENST00000481272.1	+	4	406	c.287G>T	c.(286-288)aGt>aTt	p.S96I	FSD1L_ENST00000495708.1_Missense_Mutation_p.S96I|FSD1L_ENST00000394926.3_Missense_Mutation_p.S64I|FSD1L_ENST00000484973.1_Missense_Mutation_p.S64I|FSD1L_ENST00000374716.4_Missense_Mutation_p.S64I|FSD1L_ENST00000539376.1_5'UTR|FSD1L_ENST00000374710.3_Missense_Mutation_p.S64I|FSD1L_ENST00000480279.1_3'UTR	NM_001145313.1	NP_001138785.1	Q9BXM9	FSD1L_HUMAN	fibronectin type III and SPRY domain containing 1-like	96										NS(1)|endometrium(1)	2						GTAAAAGAAAGTATGATTAAC	0.303													G|||	21	0.00419329	0.0008	0.0029	5008	,	,		15362	0.0		0.0119	False		,,,				2504	0.0061				p.S96I		Atlas-SNP	.											.	FSD1L	31	.	0			c.G287T						PASS	.	G	ILE/SER,ILE/SER,ILE/SER	3,1381		0,3,689	105.0	97.0	99.0		287,191,191	6.0	1.0	9	dbSNP_127	99	29,3143		0,29,1557	yes	missense,missense,missense	FSD1L	NM_001145313.1,NM_031919.3,NM_207647.2	142,142,142	0,32,2246	TT,TG,GG		0.9142,0.2168,0.7024	benign,benign,benign	96/531,64/146,64/499	108230553	32,4524	692	1586	2278	SO:0001583	missense	83856	exon4			AAGAAAGTATGAT	AF316830	CCDS6765.2, CCDS47999.1, CCDS6765.3, CCDS75870.1	9q31	2013-02-11	2006-03-10	2006-03-10	ENSG00000106701	ENSG00000106701		"""Fibronectin type III domain containing"""	13753	protein-coding gene	gene with protein product		609829	"""cystatin and DUF19 domain containing 1"", ""coiled-coil domain containing 10"""	CSDUFD1, CCDC10, FSD1NL, FSD1CL		11267680	Standard	XM_005252254		Approved		uc004bcq.2	Q9BXM9	OTTHUMG00000020426	ENST00000481272.1:c.287G>T	9.37:g.108230553G>T	ENSP00000417492:p.Ser96Ile	109.0	0.0	0		156.0	77.0	0.49359	NM_001145313	A2A338|A6NKH7|B7Z5S6|B7Z5W3|Q5T879|Q5T880	Missense_Mutation	SNP	ENST00000481272.1	37	CCDS47999.1	13	0.005952380952380952	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	10	0.013192612137203167	G	21.6	4.170296	0.78452	0.002168	0.009142	ENSG00000106701	ENST00000495708;ENST00000374716;ENST00000374710;ENST00000481272;ENST00000484973;ENST00000394926	T;T;T;T;T;T	0.45668	0.89;0.89;0.89;0.89;0.89;0.89	5.98	5.98	0.97165	.	0.000000	0.64402	U	0.000001	T	0.47691	0.1459	L	0.51422	1.61	0.80722	D	1	B;D;D;D	0.57257	0.222;0.964;0.979;0.958	B;P;P;P	0.57960	0.405;0.68;0.83;0.731	T	0.33548	-0.9864	10	0.33141	T	0.24	.	19.208	0.93742	0.0:0.0:1.0:0.0	rs41316532;rs62575097	64;96;64;64	F8W946;Q9BXM9;Q9BXM9-2;Q9BXM9-3	.;FSD1L_HUMAN;.;.	I	96;64;64;96;64;64	ENSP00000420624:S96I;ENSP00000363848:S64I;ENSP00000363842:S64I;ENSP00000417492:S96I;ENSP00000419691:S64I;ENSP00000378384:S64I	ENSP00000363842:S64I	S	+	2	0	FSD1L	107270374	1.000000	0.71417	0.988000	0.46212	0.996000	0.88848	5.539000	0.67199	2.843000	0.97960	0.585000	0.79938	AGT	G|0.992;T|0.008	0.008	strong		0.303	FSD1L-007	NOVEL	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000349935.1	NM_207647	
HLA-F	3134	hgsc.bcm.edu	37	6	29693019	29693019	+	Silent	SNP	G	G	A	rs201844059		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:29693019G>A	ENST00000376861.1	+	5	1206	c.822G>A	c.(820-822)gaG>gaA	p.E274E	HLA-F_ENST00000334668.4_Silent_p.E274E|HLA-F_ENST00000434407.2_Intron|HLA-F_ENST00000440587.2_Silent_p.E156E|HLA-F_ENST00000259951.7_Silent_p.E274E			P30511	HLAF_HUMAN	major histocompatibility complex, class I, F	274	Alpha-3.|Ig-like C1-type.				antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cytokine-mediated signaling pathway (GO:0019221)|interferon-gamma-mediated signaling pathway (GO:0060333)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|regulation of immune response (GO:0050776)|type I interferon signaling pathway (GO:0060337)	early endosome membrane (GO:0031901)|endoplasmic reticulum (GO:0005783)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|membrane (GO:0016020)|MHC class I protein complex (GO:0042612)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)	peptide antigen binding (GO:0042605)|TAP1 binding (GO:0046978)|TAP2 binding (GO:0046979)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	8						CTCCTGGAGAGGAACAGAGAT	0.612													.|||	1	0.000199681	0.0	0.0014	5008	,	,		18491	0.0		0.0	False		,,,				2504	0.0				p.E274E		Atlas-SNP	.											.	HLA-F	41	.	0			c.G822A						PASS	.	G	,,	2,4404		0,2,2201	53.0	47.0	49.0		,822,822	-0.1	0.9	6		49	8,8592		0,8,4292	no	intron,coding-synonymous,coding-synonymous	HLA-F	NM_001098478.1,NM_001098479.1,NM_018950.2	,,	0,10,6493	AA,AG,GG		0.093,0.0454,0.0769	,,	,274/443,274/347	29693019	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	3134	exon4			TGGAGAGGAACAG	AY253269	CCDS43437.1, CCDS43438.1, CCDS43439.1	6p21.3	2013-01-11			ENSG00000204642	ENSG00000204642		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4963	protein-coding gene	gene with protein product		143110				1688605	Standard	NM_018950		Approved		uc003nno.4	P30511	OTTHUMG00000031156	ENST00000376861.1:c.822G>A	6.37:g.29693019G>A		191.0	0.0	0		156.0	60.0	0.384615	NM_001098479	Q5JQI8|Q5JQJ1|Q5SPT5|Q860R0|Q8MGQ1|Q8WLP5|Q95HC0|Q9TP68	Silent	SNP	ENST00000376861.1	37	CCDS43438.1	.	.	.	.	.	.	.	.	.	.	.	0.413	-0.912347	0.02415	4.54E-4	9.3E-4	ENSG00000204642	ENST00000429294	.	.	.	1.92	-0.104	0.13605	.	.	.	.	.	T	0.28466	0.0704	.	.	.	0.39086	D	0.961008	.	.	.	.	.	.	T	0.15464	-1.0436	4	.	.	.	.	4.3592	0.11194	0.3972:0.0:0.6028:0.0	.	.	.	.	K	153	.	.	R	+	2	0	HLA-F	29800998	0.000000	0.05858	0.855000	0.33649	0.268000	0.26511	-0.944000	0.03913	-0.248000	0.09583	-0.436000	0.05848	AGG	G|0.999;A|0.001	0.001	weak		0.612	HLA-F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195083.1	NM_018950	
CEBPZ	10153	hgsc.bcm.edu	37	2	37441091	37441091	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37441091C>A	ENST00000234170.5	-	10	2606	c.2461G>T	c.(2461-2463)Gtt>Ttt	p.V821F	RP11-423P10.2_ENST00000606229.1_RNA|AC007390.5_ENST00000438935.2_Intron	NM_005760.2	NP_005751.2	Q03701	CEBPZ_HUMAN	CCAAT/enhancer binding protein (C/EBP), zeta	821					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)			breast(3)|endometrium(2)|large_intestine(7)|lung(12)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28		all_hematologic(82;0.21)				TTAACAGCAACTTTTTTATAA	0.299																																					p.V821F		Atlas-SNP	.											.	CEBPZ	68	.	0			c.G2461T						PASS	.						132.0	128.0	130.0					2																	37441091		2201	4299	6500	SO:0001583	missense	10153	exon10			CAGCAACTTTTTT	M37197	CCDS1787.1	2p22.3	2008-09-03	2008-09-03		ENSG00000115816	ENSG00000115816			24218	protein-coding gene	gene with protein product		612828				2247079, 12534345	Standard	NM_005760		Approved	CBF2, CTF2	uc002rpz.3	Q03701	OTTHUMG00000100960	ENST00000234170.5:c.2461G>T	2.37:g.37441091C>A	ENSP00000234170:p.Val821Phe	121.0	0.0	0		76.0	32.0	0.421053	NM_005760	Q8NE75	Missense_Mutation	SNP	ENST00000234170.5	37	CCDS1787.1	.	.	.	.	.	.	.	.	.	.	C	6.869	0.529703	0.13127	.	.	ENSG00000115816	ENST00000234170;ENST00000545744	T	0.14640	2.49	5.41	3.53	0.40419	Armadillo-type fold (1);	0.871941	0.10183	N	0.705591	T	0.13713	0.0332	L	0.47716	1.5	0.29558	N	0.850814	B	0.09022	0.002	B	0.08055	0.003	T	0.15925	-1.0420	10	0.87932	D	0	.	7.0108	0.24861	0.5827:0.3154:0.0:0.1019	.	821	Q03701	CEBPZ_HUMAN	F	821	ENSP00000234170:V821F	ENSP00000234170:V821F	V	-	1	0	CEBPZ	37294595	0.982000	0.34865	1.000000	0.80357	0.994000	0.84299	1.441000	0.35035	0.577000	0.29470	-0.181000	0.13052	GTT	.	.	none		0.299	CEBPZ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218569.2	NM_005760	
NOTCH1	4851	hgsc.bcm.edu	37	9	139399213	139399213	+	Silent	SNP	G	G	A	rs568700183	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139399213G>A	ENST00000277541.6	-	26	5005	c.4930C>T	c.(4930-4932)Ctg>Ttg	p.L1644L		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1644					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.A1641fs*2(2)|p.E1637_Q1648del(1)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGGCCCAGCAGGGCGTCAGGT	0.711			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2	0.000399361	0.0	0.0	5008	,	,		14356	0.0		0.002	False		,,,				2504	0.0				p.L1644L		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1,NS,lymphoid_neoplasm,+2,1	NOTCH1	1980	1	3	Deletion - Frameshift(2)|Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(3)	c.C4930T						PASS	.						6.0	7.0	7.0					9																	139399213		1882	3984	5866	SO:0001819	synonymous_variant	4851	exon26			CCAGCAGGGCGTC	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.4930C>T	9.37:g.139399213G>A		25.0	0.0	0		20.0	10.0	0.5	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			.	.	none		0.711	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
LAMA1	284217	hgsc.bcm.edu	37	18	6978233	6978233	+	Missense_Mutation	SNP	C	C	T	rs145781920	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:6978233C>T	ENST00000389658.3	-	43	6245	c.6152G>A	c.(6151-6153)cGa>cAa	p.R2051Q		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	2051	Domain II and I.				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)				GTGTGTCTCTCGTAATGTGGT	0.602													C|||	2	0.000399361	0.0	0.0	5008	,	,		17990	0.0		0.002	False		,,,				2504	0.0				p.R2051Q		Atlas-SNP	.											.	LAMA1	458	.	0			c.G6152A						PASS	.	C	GLN/ARG	0,4406		0,0,2203	231.0	199.0	210.0		6152	-10.1	0.0	18	dbSNP_134	210	10,8590	7.1+/-27.0	0,10,4290	yes	missense	LAMA1	NM_005559.3	43	0,10,6493	TT,TC,CC		0.1163,0.0,0.0769	benign	2051/3076	6978233	10,12996	2203	4300	6503	SO:0001583	missense	284217	exon43			GTCTCTCGTAATG	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.6152G>A	18.37:g.6978233C>T	ENSP00000374309:p.Arg2051Gln	179.0	0.0	0		174.0	85.0	0.488506	NM_005559		Missense_Mutation	SNP	ENST00000389658.3	37	CCDS32787.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	6.111	0.388642	0.11581	0.0	0.001163	ENSG00000101680	ENST00000389658	T	0.40756	1.02	5.64	-10.1	0.00402	Laminin II (1);	0.727738	0.12726	N	0.444249	T	0.14184	0.0343	N	0.03253	-0.375	0.09310	N	1	B	0.06786	0.001	B	0.06405	0.002	T	0.35649	-0.9780	10	0.10902	T	0.67	.	14.4677	0.67494	0.0841:0.5919:0.0:0.324	.	2051	P25391	LAMA1_HUMAN	Q	2051	ENSP00000374309:R2051Q	ENSP00000374309:R2051Q	R	-	2	0	LAMA1	6968233	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.580000	0.02121	-1.900000	0.01097	-1.874000	0.00550	CGA	C|0.999;T|0.001	0.001	strong		0.602	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
CCT8L2	150160	hgsc.bcm.edu	37	22	17072411	17072411	+	Missense_Mutation	SNP	G	G	T	rs41277596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:17072411G>T	ENST00000359963.3	-	1	1289	c.1030C>A	c.(1030-1032)Cca>Aca	p.P344T		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	344					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)			breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CACTTGCCTGGCCTCTGGGGA	0.547													g|||	17	0.00339457	0.0	0.0072	5008	,	,		19488	0.0		0.0109	False		,,,				2504	0.001				p.P344T		Atlas-SNP	.											.	CCT8L2	150	.	0			c.C1030A						PASS	.	G	THR/PRO	3,4403	6.2+/-15.9	0,3,2200	101.0	100.0	100.0		1030	0.7	0.7	22	dbSNP_127	100	69,8531	41.2+/-98.3	0,69,4231	no	missense	CCT8L2	NM_014406.4	38	0,72,6431	TT,TG,GG		0.8023,0.0681,0.5536	probably-damaging	344/558	17072411	72,12934	2203	4300	6503	SO:0001583	missense	150160	exon1			TGCCTGGCCTCTG	AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.1030C>A	22.37:g.17072411G>T	ENSP00000353048:p.Pro344Thr	95.0	0.0	0		95.0	52.0	0.547368	NM_014406	A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	15	0.006868131868131868	0	0.0	5	0.013812154696132596	0	0.0	10	0.013192612137203167	g	1.736	-0.492944	0.04322	6.81E-4	0.008023	ENSG00000198445	ENST00000359963	T	0.77877	-1.13	1.98	0.711	0.18162	.	0.201946	0.24693	U	0.036363	T	0.61726	0.2370	L	0.41236	1.265	0.24066	N	0.99599	B	0.34255	0.445	B	0.41723	0.365	T	0.60367	-0.7277	10	0.72032	D	0.01	-14.4681	5.6792	0.17765	0.0:0.347:0.653:0.0	rs41277596	344	Q96SF2	TCPQM_HUMAN	T	344	ENSP00000353048:P344T	ENSP00000353048:P344T	P	-	1	0	CCT8L2	15452411	0.005000	0.15991	0.710000	0.30468	0.079000	0.17450	0.660000	0.25009	1.115000	0.41800	0.379000	0.24179	CCA	G|0.994;T|0.006	0.006	strong		0.547	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1		
DCK	1633	hgsc.bcm.edu	37	4	71888240	71888240	+	Missense_Mutation	SNP	C	C	T	rs67437265	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:71888240C>T	ENST00000286648.5	+	3	761	c.364C>T	c.(364-366)Cct>Tct	p.P122S	DCK_ENST00000504730.1_Missense_Mutation_p.P122S|DCK_ENST00000504952.1_Missense_Mutation_p.P122S	NM_000788.2	NP_000779.1	P27707	DCK_HUMAN	deoxycytidine kinase	122				P -> S (in Ref. 4; AAV38744/AAV38745). {ECO:0000305}.	deoxyribonucleoside monophosphate biosynthetic process (GO:0009157)|nucleobase-containing small molecule metabolic process (GO:0055086)|nucleotide biosynthetic process (GO:0009165)|purine nucleobase metabolic process (GO:0006144)|purine-containing compound salvage (GO:0043101)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside salvage (GO:0043097)|pyrimidine nucleotide metabolic process (GO:0006220)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|deoxycytidine kinase activity (GO:0004137)|drug binding (GO:0008144)|nucleoside kinase activity (GO:0019206)|protein homodimerization activity (GO:0042803)			endometrium(2)|large_intestine(3)|lung(3)|ovary(1)	9			Lung(101;0.235)		Cladribine(DB00242)|Clofarabine(DB00631)|Cytarabine(DB00987)|Decitabine(DB01262)|Emtricitabine(DB00879)|Fludarabine(DB01073)|Gemcitabine(DB00441)|Lamivudine(DB00709)|Nelarabine(DB01280)|Pemetrexed(DB00642)|Zalcitabine(DB00943)	TGCAGAGAAACCTGTATTATT	0.388													C|||	165	0.0329473	0.0635	0.0216	5008	,	,		18820	0.0387		0.0099	False		,,,				2504	0.0174				p.P122S		Atlas-SNP	.											.	DCK	23	.	0			c.C364T	GRCh37	CM076146	DCK	M	rs67437265	PASS	.	C	SER/PRO	209,4197	128.6+/-165.4	7,195,2001	110.0	111.0	111.0		364	5.8	1.0	4	dbSNP_130	111	87,8513	48.9+/-108.6	0,87,4213	yes	missense	DCK	NM_000788.2	74	7,282,6214	TT,TC,CC		1.0116,4.7435,2.2759	benign	122/261	71888240	296,12710	2203	4300	6503	SO:0001583	missense	1633	exon3			GAGAAACCTGTAT	M60527	CCDS3548.1	4q13.3-q21.1	2008-02-05			ENSG00000156136	ENSG00000156136	2.7.1.74		2704	protein-coding gene	gene with protein product		125450				8406512	Standard	NM_000788		Approved		uc003hfx.3	P27707	OTTHUMG00000129908	ENST00000286648.5:c.364C>T	4.37:g.71888240C>T	ENSP00000286648:p.Pro122Ser	44.0	0.0	0		29.0	14.0	0.482759	NM_000788	B2R8V6|Q5TZY7|Q6FI11	Missense_Mutation	SNP	ENST00000286648.5	37	CCDS3548.1	73	0.033424908424908424	29	0.05894308943089431	9	0.024861878453038673	25	0.043706293706293704	10	0.013192612137203167	C	31	5.089919	0.94149	0.047435	0.010116	ENSG00000156136	ENST00000286648;ENST00000504730;ENST00000504952	D;D;D	0.97811	-4.55;-4.55;-4.55	5.83	5.83	0.93111	.	0.000000	0.85682	D	0.000000	D	0.89989	0.6875	L	0.57536	1.79	0.09310	P	0.999999999887503	D	0.89917	1.0	D	0.81914	0.995	D	0.86615	0.1875	8	.	.	.	.	20.1162	0.97934	0.0:1.0:0.0:0.0	.	122	P27707	DCK_HUMAN	S	122	ENSP00000286648:P122S;ENSP00000425578:P122S;ENSP00000421508:P122S	.	P	+	1	0	DCK	72107104	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	7.625000	0.83145	2.757000	0.94681	0.563000	0.77884	CCT	C|0.975;T|0.025	0.025	strong		0.388	DCK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252159.2		
ZNF33A	7581	hgsc.bcm.edu	37	10	38345455	38345455	+	Silent	SNP	A	A	G	rs12242343	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38345455A>G	ENST00000458705.2	+	5	2558	c.2400A>G	c.(2398-2400)ggA>ggG	p.G800G	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000432900.2_Silent_p.G807G|ZNF33A_ENST00000307441.9_Silent_p.G800G|ZNF33A_ENST00000374618.3_Silent_p.G801G			Q06730	ZN33A_HUMAN	zinc finger protein 33A	800					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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CACACTGTGGAGAAAGCCCTG	0.388													A|||	140	0.0279553	0.0915	0.013	5008	,	,		18836	0.0		0.0099	False		,,,				2504	0.0				p.G801G		Atlas-SNP	.											.	ZNF33A	103	.	0			c.A2403G						PASS	.	A	,	359,4047	175.9+/-205.1	19,321,1863	61.0	59.0	60.0		2403,2400	1.9	0.1	10	dbSNP_120	60	53,8547	32.3+/-84.9	0,53,4247	no	coding-synonymous,coding-synonymous	ZNF33A	NM_006954.1,NM_006974.2	,	19,374,6110	GG,GA,AA		0.6163,8.148,3.1678	,	801/812,800/811	38345455	412,12594	2203	4300	6503	SO:0001819	synonymous_variant	7581	exon5			CTGTGGAGAAAGC	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.2400A>G	10.37:g.38345455A>G		84.0	0.0	0		71.0	40.0	0.56338	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Silent	SNP	ENST00000458705.2	37	CCDS31182.1																																																																																			A|0.968;G|0.032	0.032	strong		0.388	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
CDC37L1	55664	hgsc.bcm.edu	37	9	4679847	4679847	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:4679847A>C	ENST00000381854.3	+	1	282	c.80A>C	c.(79-81)gAc>gCc	p.D27A	RP11-6J24.6_ENST00000607997.1_lincRNA|CDC37L1_ENST00000381858.1_Missense_Mutation_p.D27A|CDC37L1_ENST00000479095.1_3'UTR	NM_017913.2	NP_060383.2	Q7L3B6	CD37L_HUMAN	cell division cycle 37-like 1	27	Self-association.					cytoplasm (GO:0005737)				breast(1)|kidney(1)|lung(2)	4	all_hematologic(13;0.137)	Breast(48;0.238)		GBM - Glioblastoma multiforme(50;0.0318)		AGTGACTTCGACGTGTTCCCC	0.697											OREG0019085	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.D27A		Atlas-SNP	.											.	CDC37L1	19	.	0			c.A80C						PASS	.						43.0	49.0	47.0					9																	4679847		2202	4299	6501	SO:0001583	missense	55664	exon1			ACTTCGACGTGTT	AK000497	CCDS6454.1	9p24.1	2013-01-17	2013-01-17		ENSG00000106993	ENSG00000106993			17179	protein-coding gene	gene with protein product		610346	"""CDC37 cell division cycle 37 homolog (S. cerevisiae)-like 1"", ""cell division cycle 37 homolog (S. cerevisiae)-like 1"""				Standard	NM_017913		Approved	HARC, FLJ20639, CDC37B	uc003zio.3	Q7L3B6	OTTHUMG00000019465	ENST00000381854.3:c.80A>C	9.37:g.4679847A>C	ENSP00000371278:p.Asp27Ala	78.0	0.0	0	620	105.0	38.0	0.361905	NM_017913	B1AL70|Q9NWS3|Q9NX16	Missense_Mutation	SNP	ENST00000381854.3	37	CCDS6454.1	.	.	.	.	.	.	.	.	.	.	A	12.29	1.894709	0.33442	.	.	ENSG00000106993	ENST00000381858;ENST00000381854	T;T	0.44083	0.93;0.93	5.09	5.09	0.68999	.	0.233816	0.37053	N	0.002269	T	0.46908	0.1417	N	0.19112	0.55	0.32054	N	0.596549	D	0.63880	0.993	D	0.70227	0.968	T	0.57300	-0.7835	10	0.72032	D	0.01	-13.2073	11.1808	0.48627	1.0:0.0:0.0:0.0	.	27	Q7L3B6	CD37L_HUMAN	A	27	ENSP00000371282:D27A;ENSP00000371278:D27A	ENSP00000371278:D27A	D	+	2	0	CDC37L1	4669847	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	3.755000	0.55197	2.139000	0.66308	0.455000	0.32223	GAC	.	.	none		0.697	CDC37L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051564.1	NM_017913	
SORCS3	22986	hgsc.bcm.edu	37	10	106974224	106974224	+	Missense_Mutation	SNP	C	C	A	rs200098588	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:106974224C>A	ENST00000369701.3	+	18	2627	c.2400C>A	c.(2398-2400)aaC>aaA	p.N800K	SORCS3_ENST00000369699.4_Missense_Mutation_p.N86K	NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	800					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		TGTCCAACAACTGCACAGATG	0.522													c|||	5	0.000998403	0.0038	0.0	5008	,	,		18731	0.0		0.0	False		,,,				2504	0.0				p.N800K	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-SNP	.											.	SORCS3	282	.	0			c.C2400A						PASS	.		LYS/ASN	20,4386	26.2+/-53.5	0,20,2183	124.0	104.0	111.0		2400	5.0	1.0	10		111	0,8600		0,0,4300	yes	missense	SORCS3	NM_014978.1	94	0,20,6483	AA,AC,CC		0.0,0.4539,0.1538	possibly-damaging	800/1223	106974224	20,12986	2203	4300	6503	SO:0001583	missense	22986	exon18			CAACAACTGCACA	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.2400C>A	10.37:g.106974224C>A	ENSP00000358715:p.Asn800Lys	112.0	0.0	0		123.0	62.0	0.504065	NM_014978	Q5VXF9|Q9NQJ2	Missense_Mutation	SNP	ENST00000369701.3	37	CCDS7558.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	c	13.79	2.343489	0.41498	0.004539	0.0	ENSG00000156395	ENST00000369701;ENST00000369699	T;T	0.68025	-0.3;-0.3	5.89	4.98	0.66077	VPS10 (1);PKD domain (1);	0.151901	0.56097	N	0.000021	T	0.74921	0.3780	L	0.41573	1.285	0.54753	D	0.999989	D	0.76494	0.999	D	0.70935	0.971	T	0.74000	-0.3805	9	.	.	.	.	17.0953	0.86633	0.0:0.8732:0.1268:0.0	.	800	Q9UPU3	SORC3_HUMAN	K	800;86	ENSP00000358715:N800K;ENSP00000358713:N86K	.	N	+	3	2	SORCS3	106964214	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	3.828000	0.55753	1.482000	0.48325	0.558000	0.71614	AAC	C|1.000;A|0.000	0.000	strong		0.522	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
CUL5	8065	hgsc.bcm.edu	37	11	107965639	107965639	+	Silent	SNP	G	G	A	rs146843253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:107965639G>A	ENST00000393094.2	+	15	2284	c.1668G>A	c.(1666-1668)ccG>ccA	p.P556P		NM_003478.3	NP_003469.2	Q93034	CUL5_HUMAN	cullin 5	556					calcium ion transmembrane transport (GO:0070588)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cytosolic calcium ion homeostasis (GO:0051480)|G1/S transition of mitotic cell cycle (GO:0000082)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|protein ubiquitination (GO:0016567)|response to osmotic stress (GO:0006970)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	Cul5-RING ubiquitin ligase complex (GO:0031466)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|receptor activity (GO:0004872)|ubiquitin protein ligase binding (GO:0031625)			endometrium(2)|kidney(1)|large_intestine(8)|lung(9)|ovary(1)|prostate(1)|skin(1)	23		all_cancers(61;7.09e-10)|all_epithelial(67;2.97e-06)|Acute lymphoblastic leukemia(157;3.95e-05)|Melanoma(852;4.48e-05)|all_hematologic(158;0.00014)|Breast(348;0.0258)|all_neural(303;0.072)		BRCA - Breast invasive adenocarcinoma(274;3.58e-05)|Epithelial(105;4.68e-05)|all cancers(92;0.00122)|OV - Ovarian serous cystadenocarcinoma(223;0.217)		ACTTGATACCGGAAGTAGAAG	0.353													G|||	5	0.000998403	0.0038	0.0	5008	,	,		16265	0.0		0.0	False		,,,				2504	0.0				p.P556P		Atlas-SNP	.											.	CUL5	71	.	0			c.G1668A						PASS	.	G		4,4398	8.1+/-20.4	0,4,2197	58.0	63.0	61.0		1668	0.6	1.0	11	dbSNP_134	61	0,8596		0,0,4298	no	coding-synonymous	CUL5	NM_003478.3		0,4,6495	AA,AG,GG		0.0,0.0909,0.0308		556/781	107965639	4,12994	2201	4298	6499	SO:0001819	synonymous_variant	8065	exon15			GATACCGGAAGTA	X81882	CCDS31668.1	11q22.3	2011-05-24			ENSG00000166266	ENSG00000166266			2556	protein-coding gene	gene with protein product		601741				8681378, 9037604	Standard	XM_005271682		Approved	VACM-1	uc001pjv.3	Q93034	OTTHUMG00000166369	ENST00000393094.2:c.1668G>A	11.37:g.107965639G>A		72.0	0.0	0		92.0	53.0	0.576087	NM_003478	A8K960|O14766|Q9BZC6	Silent	SNP	ENST00000393094.2	37	CCDS31668.1																																																																																			G|1.000;A|0.000	0.000	strong		0.353	CUL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389429.1		
TEX43	389320	hgsc.bcm.edu	37	5	125968301	125968301	+	Silent	SNP	C	C	T	rs6887295	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:125968301C>T	ENST00000357147.3	+	2	163	c.150C>T	c.(148-150)gtC>gtT	p.V50V		NM_207408.1	NP_997291.1	Q6ZNM6	TEX43_HUMAN		50										large_intestine(1)|lung(1)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	7						GACGTTATGTCATGCCTTGGA	0.368													T|||	676	0.134984	0.4818	0.0375	5008	,	,		21723	0.001		0.0	False		,,,				2504	0.0123				p.V50V		Atlas-SNP	.											.	C5orf48	21	.	0			c.C150T						PASS	.	T		1693,2713	652.3+/-399.4	334,1025,844	109.0	104.0	105.0		150	-6.3	0.1	5	dbSNP_116	105	12,8588	818.7+/-406.8	0,12,4288	no	coding-synonymous	C5orf48	NM_207408.1		334,1037,5132	TT,TC,CC		0.1395,38.4249,13.1093		50/135	125968301	1705,11301	2203	4300	6503	SO:0001819	synonymous_variant	389320	exon2			TTATGTCATGCCT																												ENST00000357147.3:c.150C>T	5.37:g.125968301C>T		89.0	0.0	0		78.0	43.0	0.551282	NM_207408		Silent	SNP	ENST00000357147.3	37	CCDS4139.1																																																																																			C|0.870;T|0.130	0.130	strong		0.368	C5orf48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250923.1		
C1QTNF8	390664	hgsc.bcm.edu	37	16	1143605	1143605	+	Missense_Mutation	SNP	C	C	A	rs116934818	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:1143605C>A	ENST00000328449.5	-	4	928	c.655G>T	c.(655-657)Gtg>Ttg	p.V219L		NM_207419.3	NP_997302.2	P60827	C1QT8_HUMAN	C1q and tumor necrosis factor related protein 8	219	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.					collagen trimer (GO:0005581)|extracellular region (GO:0005576)				lung(2)|prostate(1)|skin(1)	4		Hepatocellular(780;0.00369)				AACATGCGCACCCAGACGGCG	0.716													C|||	54	0.0107827	0.0008	0.0187	5008	,	,		8643	0.0		0.0298	False		,,,				2504	0.0102				p.V219L		Atlas-SNP	.											.	C1QTNF8	15	.	0			c.G655T						PASS	.	C	LEU/VAL	17,4307		1,15,2146	12.0	13.0	13.0		655	3.2	1.0	16	dbSNP_132	13	170,8368		1,168,4100	yes	missense	C1QTNF8	NM_207419.3	32	2,183,6246	AA,AC,CC		1.9911,0.3932,1.4539	possibly-damaging	219/253	1143605	187,12675	2162	4269	6431	SO:0001583	missense	390664	exon4			TGCGCACCCAGAC	AY358832	CCDS32358.1	16p13.3	2014-08-12			ENSG00000184471	ENSG00000184471			31374	protein-coding gene	gene with protein product		614147				12975309	Standard	NM_207419		Approved	UNQ5829, CTRP8	uc010uuw.1	P60827	OTTHUMG00000167756	ENST00000328449.5:c.655G>T	16.37:g.1143605C>A	ENSP00000330426:p.Val219Leu	13.0	0.0	0		36.0	15.0	0.416667	NM_207419	B7U178	Missense_Mutation	SNP	ENST00000328449.5	37	CCDS32358.1	32	0.014652014652014652	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	22	0.029023746701846966	C	12.81	2.050482	0.36181	0.003932	0.019911	ENSG00000184471	ENST00000328449	D	0.82711	-1.64	3.24	3.24	0.37175	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.46442	D	0.000298	T	0.53190	0.1781	L	0.52759	1.655	0.36281	D	0.855751	P	0.43231	0.801	P	0.45610	0.487	T	0.71265	-0.4644	10	0.02654	T	1	.	5.9986	0.19507	0.0:0.6915:0.1956:0.1129	.	219	P60827	C1QT8_HUMAN	L	219	ENSP00000330426:V219L	ENSP00000330426:V219L	V	-	1	0	C1QTNF8	1083606	1.000000	0.71417	0.979000	0.43373	0.865000	0.49528	1.250000	0.32850	1.654000	0.50703	0.557000	0.71058	GTG	C|0.987;A|0.013	0.013	strong		0.716	C1QTNF8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000396120.1	XM_372606	
UBXN2B	137886	hgsc.bcm.edu	37	8	59358556	59358556	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:59358556G>A	ENST00000399598.2	+	7	884	c.762G>A	c.(760-762)gtG>gtA	p.V254V		NM_001077619.1	NP_001071087.1	Q14CS0	UBX2B_HUMAN	UBX domain protein 2B	254	UBX. {ECO:0000255|PROSITE- ProRule:PRU00215}.					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						ATGATTCAGTGCCAACAACAA	0.373																																					p.V254V		Atlas-SNP	.											.	UBXN2B	36	.	0			c.G762A						PASS	.						139.0	122.0	128.0					8																	59358556		1863	4092	5955	SO:0001819	synonymous_variant	137886	exon7			TTCAGTGCCAACA	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.762G>A	8.37:g.59358556G>A		78.0	0.0	0		62.0	30.0	0.483871	NM_001077619	B3KWZ3	Silent	SNP	ENST00000399598.2	37	CCDS43741.1																																																																																			.	.	none		0.373	UBXN2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378184.1	NM_001077619	
DNAH17	8632	hgsc.bcm.edu	37	17	76567708	76567708	+	Silent	SNP	G	G	A	rs555197985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76567708G>A	ENST00000585328.1	-	4	820	c.696C>T	c.(694-696)gaC>gaT	p.D232D	DNAH17_ENST00000389840.5_Silent_p.D232D	NM_173628.3	NP_775899.3	Q9UFH2	DYH17_HUMAN	dynein, axonemal, heavy chain 17	232	Stem. {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(2)|breast(7)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(13)|large_intestine(8)|lung(37)|ovary(8)|prostate(7)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	116			BRCA - Breast invasive adenocarcinoma(99;0.00294)|OV - Ovarian serous cystadenocarcinoma(97;0.0656)			GCAGCCGAGTGTCCCAGAACT	0.642													G|||	2	0.000399361	0.0008	0.0014	5008	,	,		17482	0.0		0.0	False		,,,				2504	0.0				p.D232D		Atlas-SNP	.											.	DNAH17	347	.	0			c.C696T						PASS	.						60.0	66.0	64.0					17																	76567708		2030	4179	6209	SO:0001819	synonymous_variant	8632	exon4			CCGAGTGTCCCAG	AJ000522		17q25.3	2012-04-19	2006-09-04		ENSG00000187775	ENSG00000187775		"""Axonemal dyneins"""	2946	protein-coding gene	gene with protein product		610063	"""dynein, axonemal, heavy polypeptide 17"", ""dynein, axonemal, heavy chain like 1"", ""dynein, axonemal, heavy like 1"""	DNAHL1		9545504	Standard	NM_173628		Approved	DNEL2, FLJ40457	uc010dhp.2	Q9UFH2		ENST00000585328.1:c.696C>T	17.37:g.76567708G>A		111.0	0.0	0		143.0	73.0	0.51049	NM_173628	O00431|O15206|Q2M2Y1|Q6ZRQ2|Q8N7Q7	Silent	SNP	ENST00000585328.1	37																																																																																				.	.	none		0.642	DNAH17-001	PUTATIVE	not_organism_supported|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000318962.2	NM_173628	
KIAA1671	85379	hgsc.bcm.edu	37	22	25577667	25577667	+	Splice_Site	SNP	G	G	A	rs199924926		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:25577667G>A	ENST00000406486.4	+	11	5463	c.5076G>A	c.(5074-5076)gaG>gaA	p.E1692E	KIAA1671_ENST00000401395.1_Splice_Site_p.E199E|KIAA1671_ENST00000358431.3_Splice_Site_p.E1692E			Q9BY89	K1671_HUMAN	KIAA1671	1692										autonomic_ganglia(1)|breast(1)|endometrium(2)|lung(2)|prostate(1)|stomach(2)	9						TTGCAACAGAGGAGAAATCAC	0.512													G|||	1	0.000199681	0.0	0.0	5008	,	,		19953	0.0		0.001	False		,,,				2504	0.0				p.E1692E		Atlas-SNP	.											.	KIAA1671	28	.	0			c.G5076A						PASS	.						55.0	57.0	56.0					22																	25577667		692	1591	2283	SO:0001630	splice_region_variant	85379	exon8			AACAGAGGAGAAA		CCDS46676.1	22q11.23	2009-07-09			ENSG00000197077	ENSG00000197077			29345	protein-coding gene	gene with protein product						15289310	Standard	NM_001145206		Approved		uc003abn.3	Q9BY89	OTTHUMG00000150841	ENST00000406486.4:c.5075-1G>A	22.37:g.25577667G>A		98.0	0.0	0		93.0	49.0	0.526882	NM_001145206	B0QYF2|B7ZW08|Q5THZ5	Silent	SNP	ENST00000406486.4	37	CCDS46676.1																																																																																			.	.	weak		0.512	KIAA1671-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320306.6	NM_001145206	Silent
KIAA1755	85449	hgsc.bcm.edu	37	20	36842086	36842086	+	Silent	SNP	G	G	A	rs112401596	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36842086G>A	ENST00000279024.4	-	14	3232	c.2961C>T	c.(2959-2961)acC>acT	p.T987T		NM_001029864.1	NP_001025035.1	Q5JYT7	K1755_HUMAN	KIAA1755	987										breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(31)|ovary(5)|pancreas(2)|skin(4)|stomach(1)	54		Myeloproliferative disorder(115;0.00874)				TGACCCTTGAGGTCTTGTCCA	0.642													G|||	31	0.0061901	0.003	0.0058	5008	,	,		17289	0.0		0.0169	False		,,,				2504	0.0061				p.T987T		Atlas-SNP	.											.	KIAA1755	145	.	0			c.C2961T						PASS	.	G		19,4387		0,19,2184	21.0	19.0	20.0		2961	-0.3	0.0	20	dbSNP_132	20	179,8421		2,175,4123	no	coding-synonymous	KIAA1755	NM_001029864.1		2,194,6307	AA,AG,GG		2.0814,0.4312,1.5224		987/1201	36842086	198,12808	2203	4300	6503	SO:0001819	synonymous_variant	85449	exon14			CCTTGAGGTCTTG	AB051542	CCDS33467.1	20q11.23	2007-12-07			ENSG00000149633	ENSG00000149633			29372	protein-coding gene	gene with protein product						11214970	Standard	NM_001029864		Approved	RP5-1054A22.3	uc002xhy.1	Q5JYT7	OTTHUMG00000032436	ENST00000279024.4:c.2961C>T	20.37:g.36842086G>A		73.0	0.0	0		82.0	39.0	0.47561	NM_001029864	Q9C0A8	Silent	SNP	ENST00000279024.4	37	CCDS33467.1																																																																																			G|0.986;A|0.014	0.014	strong		0.642	KIAA1755-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079144.3	NM_001029864	
GPR156	165829	hgsc.bcm.edu	37	3	119886101	119886101	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:119886101G>A	ENST00000464295.1	-	10	2668	c.2223C>T	c.(2221-2223)caC>caT	p.H741H	GPR156_ENST00000315843.3_Silent_p.H741H|GPR156_ENST00000461057.1_Silent_p.H737H			Q8NFN8	GP156_HUMAN	G protein-coupled receptor 156	741						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled GABA receptor activity (GO:0004965)			breast(2)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|ovary(1)|prostate(1)|skin(1)	32				GBM - Glioblastoma multiforme(114;0.19)		CAAAATAGCTGTGTTGAGAAG	0.567																																					p.H741H		Atlas-SNP	.											.	GPR156	85	.	0			c.C2223T						PASS	.						58.0	65.0	63.0					3																	119886101		2203	4300	6503	SO:0001819	synonymous_variant	165829	exon9			ATAGCTGTGTTGA	AF488739	CCDS2997.1, CCDS54629.1	3q13.33	2012-08-21			ENSG00000175697	ENSG00000175697		"""GPCR / Class C : Orphans"""	20844	protein-coding gene	gene with protein product		610464				12591167	Standard	NM_153002		Approved	PGR28, GABABL	uc011bjf.2	Q8NFN8	OTTHUMG00000159406	ENST00000464295.1:c.2223C>T	3.37:g.119886101G>A		81.0	0.0	0		95.0	46.0	0.484211	NM_153002	B7ZL66|E9PFZ4|Q14CM1|Q86SN6	Silent	SNP	ENST00000464295.1	37	CCDS2997.1																																																																																			.	.	none		0.567	GPR156-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355139.1	NM_153002	
RRBP1	6238	hgsc.bcm.edu	37	20	17602571	17602571	+	Missense_Mutation	SNP	A	A	G	rs2229886	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:17602571A>G	ENST00000377813.1	-	14	3472	c.3169T>C	c.(3169-3171)Tgt>Cgt	p.C1057R	RRBP1_ENST00000360807.4_Missense_Mutation_p.C624R|RRBP1_ENST00000377807.2_Missense_Mutation_p.C624R|RRBP1_ENST00000246043.4_Missense_Mutation_p.C1057R|RRBP1_ENST00000470422.1_5'UTR|RRBP1_ENST00000455029.2_Missense_Mutation_p.C398R			Q9P2E9	RRBP1_HUMAN	ribosome binding protein 1	1057					osteoblast differentiation (GO:0001649)|protein transport (GO:0015031)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|integral component of endoplasmic reticulum membrane (GO:0030176)|membrane (GO:0016020)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|receptor activity (GO:0004872)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(9)|ovary(2)|prostate(6)	28						TCAATCAGACAGAGCTGCTTC	0.617													A|||	99	0.0197684	0.0008	0.0303	5008	,	,		15560	0.001		0.0477	False		,,,				2504	0.0286				p.C624R		Atlas-SNP	.											.	RRBP1	157	.	0			c.T1870C						PASS	.	A	ARG/CYS,ARG/CYS	52,4354	50.2+/-85.5	2,48,2153	63.0	70.0	68.0		1870,1870	-0.2	0.0	20	dbSNP_98	68	479,8121	139.5+/-196.2	5,469,3826	yes	missense,missense	RRBP1	NM_001042576.1,NM_004587.2	180,180	7,517,5979	GG,GA,AA		5.5698,1.1802,4.0827	benign,benign	624/978,624/978	17602571	531,12475	2203	4300	6503	SO:0001583	missense	6238	exon14			TCAGACAGAGCTG	AB037819	CCDS13128.1	20p12	2012-12-07	2012-12-07		ENSG00000125844	ENSG00000125844			10448	protein-coding gene	gene with protein product		601418	"""ribosome binding protein 1 (dog 180kD homolog)"", ""ribosome binding protein 1 homolog 180kDa (dog)"""			8812507	Standard	NM_001042576		Approved	ES/130, hES	uc002wpw.1	Q9P2E9	OTTHUMG00000031945	ENST00000377813.1:c.3169T>C	20.37:g.17602571A>G	ENSP00000367044:p.Cys1057Arg	44.0	0.0	0		63.0	36.0	0.571429	NM_004587	A2A2S6|A6NCN6|O75300|O75301|Q5W165|Q96SB2|Q9BWP1|Q9H476	Missense_Mutation	SNP	ENST00000377813.1	37		51	0.023351648351648352	1	0.0020325203252032522	12	0.03314917127071823	0	0.0	38	0.05013192612137203	A	0.010	-1.795706	0.00617	0.011802	0.055698	ENSG00000125844	ENST00000360807;ENST00000377813;ENST00000377807;ENST00000246043;ENST00000455029	T;T;T;T;T	0.32515	1.45;1.45;1.45;1.45;1.45	4.98	-0.19	0.13256	.	2.041510	0.02459	N	0.086394	T	0.00998	0.0033	N	0.01352	-0.895	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.14420	-1.0473	10	0.17832	T	0.49	2.3478	3.1217	0.06393	0.0856:0.1954:0.3645:0.3545	rs2229886;rs34246888	581;624	A1A5C4;Q9P2E9-3	.;.	R	624;1057;624;1057;398	ENSP00000354045:C624R;ENSP00000367044:C1057R;ENSP00000367038:C624R;ENSP00000246043:C1057R;ENSP00000401206:C398R	ENSP00000246043:C1057R	C	-	1	0	RRBP1	17550571	0.000000	0.05858	0.009000	0.14445	0.003000	0.03518	-0.055000	0.11807	0.106000	0.17784	-0.232000	0.12228	TGT	A|0.964;G|0.036	0.036	strong		0.617	RRBP1-002	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000078125.1	NM_001042576	
AMBRA1	55626	hgsc.bcm.edu	37	11	46431914	46431914	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:46431914A>C	ENST00000458649.2	-	16	3539	c.3121T>G	c.(3121-3123)Tta>Gta	p.L1041V	AMBRA1_ENST00000528950.1_Missense_Mutation_p.L1012V|AMBRA1_ENST00000298834.3_Missense_Mutation_p.L981V|AMBRA1_ENST00000314845.3_Missense_Mutation_p.L951V|AMBRA1_ENST00000534300.1_Missense_Mutation_p.L981V|AMBRA1_ENST00000426438.1_Missense_Mutation_p.L1012V|AMBRA1_ENST00000533727.1_Missense_Mutation_p.L922V			Q9C0C7	AMRA1_HUMAN	autophagy/beclin-1 regulator 1	1041					autophagy (GO:0006914)|cell differentiation (GO:0030154)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron apoptotic process (GO:0043524)|neural tube development (GO:0021915)	axoneme (GO:0005930)|cytoplasm (GO:0005737)|phagocytic vesicle (GO:0045335)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|prostate(1)|skin(1)|urinary_tract(2)	39				GBM - Glioblastoma multiforme(35;0.0435)|Lung(87;0.182)		CCAGAGTTTAAGGCCCTAAAA	0.507																																					p.L1044V		Atlas-SNP	.											.	AMBRA1	201	.	0			c.T3130G						PASS	.						91.0	81.0	84.0					11																	46431914		2201	4299	6500	SO:0001583	missense	55626	exon18			AGTTTAAGGCCCT	AB051523	CCDS31475.1, CCDS58132.1, CCDS73281.1	11p11.2	2013-01-09			ENSG00000110497	ENSG00000110497		"""WD repeat domain containing"", ""DDB1 and CUL4 associated factors"""	25990	protein-coding gene	gene with protein product	"""WD repeat domain 94"", ""DDB1 and CUL4 associated factor 3"""	611359				17622796, 17603510, 17589504	Standard	NM_001267782		Approved	FLJ20294, KIAA1736, WDR94, DCAF3	uc001ncv.3	Q9C0C7	OTTHUMG00000166500	ENST00000458649.2:c.3121T>G	11.37:g.46431914A>C	ENSP00000415327:p.Leu1041Val	56.0	0.0	0		87.0	34.0	0.390805	NM_001267782	A6XN33|D3DQP8|G3V193|Q86XD6|Q9H8Z0|Q9NXE7	Missense_Mutation	SNP	ENST00000458649.2	37		.	.	.	.	.	.	.	.	.	.	A	18.00	3.526152	0.64860	.	.	ENSG00000110497	ENST00000314845;ENST00000533727;ENST00000534300;ENST00000426438;ENST00000298834;ENST00000458649;ENST00000528950	T;T;T;T;T;T;T	0.71222	-0.37;-0.55;-0.14;-0.27;-0.14;-0.24;-0.27	5.86	5.86	0.93980	.	0.249598	0.35436	N	0.003219	T	0.54415	0.1857	N	0.12182	0.205	0.41696	D	0.989373	B;B;B;B;P;B	0.34639	0.012;0.116;0.106;0.25;0.461;0.116	B;B;B;B;B;B	0.32393	0.006;0.103;0.042;0.103;0.145;0.103	T	0.62300	-0.6883	10	0.87932	D	0	.	14.8261	0.70113	1.0:0.0:0.0:0.0	.	1041;1012;981;922;1044;951	Q9C0C7;Q9C0C7-3;Q9C0C7-2;G3V193;Q9C0C7-5;Q9C0C7-4	AMRA1_HUMAN;.;.;.;.;.	V	951;922;981;1012;981;1041;1012	ENSP00000318313:L951V;ENSP00000433372:L922V;ENSP00000431926:L981V;ENSP00000410899:L1012V;ENSP00000298834:L981V;ENSP00000415327:L1041V;ENSP00000433945:L1012V	ENSP00000298834:L981V	L	-	1	2	AMBRA1	46388490	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	4.398000	0.59697	2.240000	0.73641	0.533000	0.62120	TTA	.	.	none		0.507	AMBRA1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000390103.1	NM_017749	
COL18A1	80781	hgsc.bcm.edu	37	21	46895427	46895427	+	Missense_Mutation	SNP	G	G	T	rs62000965	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46895427G>T	ENST00000359759.4	+	4	2042	c.2021G>T	c.(2020-2022)cGg>cTg	p.R674L	COL18A1_ENST00000400337.2_Missense_Mutation_p.R259L|COL18A1_ENST00000355480.5_Missense_Mutation_p.R439L			P39060	COIA1_HUMAN	collagen, type XVIII, alpha 1	674	Nonhelical region 1 (NC1).				angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|collagen catabolic process (GO:0030574)|endothelial cell morphogenesis (GO:0001886)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|organ morphogenesis (GO:0009887)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell apoptotic process (GO:2000353)|response to drug (GO:0042493)|response to hydrostatic pressure (GO:0051599)|visual perception (GO:0007601)	basement membrane (GO:0005604)|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)	identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|structural molecule activity (GO:0005198)			breast(1)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	25				Colorectal(79;0.0157)|READ - Rectum adenocarcinoma(84;0.0929)		GGGGACGCCCGGGAGCTTCTC	0.692													G|||	96	0.0191693	0.0666	0.0115	5008	,	,		14324	0.0		0.0	False		,,,				2504	0.0				p.R439L		Atlas-SNP	.											.	COL18A1	129	.	0			c.G1316T						PASS	.	G	LEU/ARG,LEU/ARG	231,3473		6,219,1627	13.0	16.0	15.0		776,1316	-4.6	0.0	21	dbSNP_129	15	1,8171		0,1,4085	no	missense,missense	COL18A1	NM_130445.2,NM_030582.3	102,102	6,220,5712	TT,TG,GG		0.0122,6.2365,1.9535	benign,benign	259/1340,439/1520	46895427	232,11644	1852	4086	5938	SO:0001583	missense	80781	exon4			ACGCCCGGGAGCT		CCDS42971.1, CCDS42972.1	21q22.3	2013-01-16			ENSG00000182871	ENSG00000182871		"""Collagens"""	2195	protein-coding gene	gene with protein product	"""endostatin"""	120328	"""Knobloch syndrome, type 1"""	KNO		8188291, 8776601, 10942434, 17546652	Standard	NM_130445		Approved	KS, KNO1	uc002zhi.3	P39060	OTTHUMG00000090407	ENST00000359759.4:c.2021G>T	21.37:g.46895427G>T	ENSP00000352798:p.Arg674Leu	141.0	0.0	0		148.0	65.0	0.439189	NM_030582	A8MVI4|Q58EX6|Q6RZ39|Q6RZ40|Q6RZ41|Q8N4S4|Q8WXI5|Q96T70|Q9UK38|Q9Y6Q7|Q9Y6Q8	Missense_Mutation	SNP	ENST00000359759.4	37		53	0.024267399267399268	48	0.0975609756097561	5	0.013812154696132596	0	0.0	0	0.0	G	9.059	0.994091	0.19043	0.062365	1.22E-4	ENSG00000182871	ENST00000400337;ENST00000400347;ENST00000355480;ENST00000359759;ENST00000539645	D;D;D	0.90563	-2.66;-2.69;-2.57	2.98	-4.62	0.03370	.	1.760170	0.02944	N	0.140855	T	0.11452	0.0279	N	0.24115	0.695	0.09310	N	1	B;B;B	0.29716	0.166;0.255;0.255	B;B;B	0.25614	0.028;0.062;0.045	T	0.57528	-0.7796	10	0.25751	T	0.34	.	5.8286	0.18568	0.6231:0.1574:0.2195:0.0	rs62000965	674;439;259	P39060;P39060-1;P39060-2	COIA1_HUMAN;.;.	L	259;259;439;674;674	ENSP00000383191:R259L;ENSP00000347665:R439L;ENSP00000352798:R674L	ENSP00000347665:R439L	R	+	2	0	COL18A1	45719855	0.000000	0.05858	0.000000	0.03702	0.056000	0.15407	-2.199000	0.01238	-1.208000	0.02634	0.196000	0.17591	CGG	G|0.976;T|0.024	0.024	strong		0.692	COL18A1-201	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000206827.1		
TTC8	123016	hgsc.bcm.edu	37	14	89319359	89319359	+	Silent	SNP	G	G	A	rs141304350	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:89319359G>A	ENST00000345383.5	+	7	723	c.639G>A	c.(637-639)aaG>aaA	p.K213K	TTC8_ENST00000358622.5_Silent_p.K25K|TTC8_ENST00000346301.4_Silent_p.K183K|TTC8_ENST00000380656.2_Silent_p.K223K|TTC8_ENST00000338104.6_Silent_p.K239K|TTC8_ENST00000354441.6_Intron|TTC8_ENST00000536576.1_5'UTR	NM_198309.2	NP_938051.1	Q8TAM2	TTC8_HUMAN	tetratricopeptide repeat domain 8	249					axon guidance (GO:0007411)|camera-type eye photoreceptor cell differentiation (GO:0060219)|cilium assembly (GO:0042384)|establishment of anatomical structure orientation (GO:0048560)|fat cell differentiation (GO:0045444)|multicellular organism growth (GO:0035264)|nonmotile primary cilium assembly (GO:0035058)|olfactory bulb development (GO:0021772)|protein transport (GO:0015031)|regulation of protein localization (GO:0032880)|renal tubule development (GO:0061326)|sensory perception of smell (GO:0007608)|sensory processing (GO:0050893)	BBSome (GO:0034464)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|photoreceptor connecting cilium (GO:0032391)|plasma membrane (GO:0005886)	RNA polymerase II repressing transcription factor binding (GO:0001103)			endometrium(2)|kidney(1)|large_intestine(4)|lung(7)|prostate(1)	15						CTCAGTACAAGGACTGGTGGT	0.378													G|||	5	0.000998403	0.0	0.0029	5008	,	,		16565	0.0		0.001	False		,,,				2504	0.002				p.K223K		Atlas-SNP	.											.	TTC8	42	.	0			c.G669A						PASS	.	G	,,	1,4405	2.1+/-5.4	0,1,2202	91.0	80.0	84.0		669,639,549	5.3	1.0	14	dbSNP_134	84	5,8595	3.7+/-12.6	0,5,4295	no	coding-synonymous,coding-synonymous,coding-synonymous	TTC8	NM_144596.2,NM_198309.2,NM_198310.2	,,	0,6,6497	AA,AG,GG		0.0581,0.0227,0.0461	,,	223/516,213/506,183/476	89319359	6,13000	2203	4300	6503	SO:0001819	synonymous_variant	123016	exon8			GTACAAGGACTGG	AK093891	CCDS9885.1, CCDS9886.1, CCDS32137.1, CCDS73674.1, CCDS73675.1	14q31.3	2013-02-14				ENSG00000165533		"""Tetratricopeptide (TTC) repeat domain containing"""	20087	protein-coding gene	gene with protein product		608132				14520415, 20451172	Standard	NM_144596		Approved	BBS8, RP51	uc001xxi.3	Q8TAM2		ENST00000345383.5:c.639G>A	14.37:g.89319359G>A		139.0	0.0	0		151.0	73.0	0.483444	NM_144596	A6NFG2|B3KWA5|Q67B97|Q86SY0|Q86TV9|Q86U26|Q8NDH9|Q96DG8	Silent	SNP	ENST00000345383.5	37	CCDS9885.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	G	9.139	1.013312	0.19277	2.27E-4	5.81E-4	ENSG00000165533	ENST00000554686	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	T	0.60907	0.2305	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.58317	-0.7657	4	.	.	.	-26.5066	9.7161	0.40276	0.1556:0.0:0.8444:0.0	.	.	.	.	K	173	.	.	R	+	2	0	TTC8	88389112	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.332000	0.65911	2.660000	0.90430	0.655000	0.94253	AGG	G|1.000;A|0.000	0.000	strong		0.378	TTC8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410861.1	NM_144596	
CXXC1	30827	hgsc.bcm.edu	37	18	47813157	47813157	+	Silent	SNP	C	C	A	rs375253589		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:47813157C>A	ENST00000285106.6	-	2	789	c.75G>T	c.(73-75)gcG>gcT	p.A25A	CXXC1_ENST00000589940.1_Silent_p.A25A|CXXC1_ENST00000412036.2_Silent_p.A25A|CXXC1_ENST00000587396.1_5'UTR	NM_001101654.1|NM_014593.3	NP_001095124.1|NP_055408.2	Q9P0U4	CXXC1_HUMAN	CXXC finger protein 1	25					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)|histone H3-K4 methylation (GO:0051568)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(5)|kidney(1)|large_intestine(3)|lung(8)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	24						AGTAGATGGGCGCATTCTCCC	0.612																																					p.A25A		Atlas-SNP	.											.	CXXC1	50	.	0			c.G75T						PASS	.	C	,	0,4406		0,0,2203	115.0	91.0	99.0		75,75	-4.2	1.0	18		99	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	CXXC1	NM_001101654.1,NM_014593.3	,	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	,	25/661,25/657	47813157	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	30827	exon2			GATGGGCGCATTC	BC014940	CCDS11945.1, CCDS45866.1	18q12	2014-02-20	2014-02-20		ENSG00000154832	ENSG00000154832		"""Zinc fingers, PHD-type"""	24343	protein-coding gene	gene with protein product	"""CpG binding protein"", ""DNA-binding protein with PHD finger and CXXC domain"", ""zinc finger, CpG binding-type containing 1"""	609150	"""CXXC finger 1 (PHD domain)"""			10799292, 10688657	Standard	NM_014593		Approved	HsT2645, PCCX1, hCGBP, PHF18, CGBP, SPP1, CFP1, ZCGPC1	uc002ler.4	Q9P0U4	OTTHUMG00000132670	ENST00000285106.6:c.75G>T	18.37:g.47813157C>A		114.0	0.0	0		138.0	62.0	0.449275	NM_001101654	B2RC03|Q8N2W4|Q96BC8|Q9P2V7	Silent	SNP	ENST00000285106.6	37	CCDS11945.1																																																																																			.	.	weak		0.612	CXXC1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000255927.2	NM_014593	
CLTCL1	8218	hgsc.bcm.edu	37	22	19263266	19263266	+	Missense_Mutation	SNP	C	C	A	rs34869740	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:19263266C>A	ENST00000263200.10	-	2	202	c.130G>T	c.(130-132)Gtt>Ttt	p.V44F	CLTCL1_ENST00000353891.5_Missense_Mutation_p.V44F|CLTCL1_ENST00000427926.1_Missense_Mutation_p.V44F	NM_007098.3	NP_009029.3	P53675	CLH2_HUMAN	clathrin, heavy chain-like 1	44	Globular terminal domain.|WD40-like repeat 1.				anatomical structure morphogenesis (GO:0009653)|intracellular protein transport (GO:0006886)|mitotic nuclear division (GO:0007067)|positive regulation of glucose import (GO:0046326)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	clathrin coat of coated pit (GO:0030132)|clathrin coat of trans-Golgi network vesicle (GO:0030130)|clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|coated vesicle (GO:0030135)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|spindle (GO:0005819)|trans-Golgi network (GO:0005802)	signal transducer activity (GO:0004871)|structural molecule activity (GO:0005198)			breast(2)|central_nervous_system(3)|cervix(2)|endometrium(9)|kidney(3)|large_intestine(11)|lung(9)|ovary(5)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49	Colorectal(54;0.0993)					TGCTCACCAACTTTCTCTCGG	0.468			T	?	ALCL								C|||	45	0.00898562	0.0	0.0058	5008	,	,		17693	0.001		0.004	False		,,,				2504	0.0368				p.V44F		Atlas-SNP	.		Dom	yes		22	22q11.21	8218	"""clathrin, heavy polypeptide-like 1"""		L	.	CLTCL1	115	.	0			c.G130T						PASS	.	C	PHE/VAL,PHE/VAL	2,3930		0,2,1964	64.0	64.0	64.0		130,130	1.9	0.0	22	dbSNP_126	64	71,8235		0,71,4082	yes	missense,missense	CLTCL1	NM_001835.3,NM_007098.3	50,50	0,73,6046	AA,AC,CC		0.8548,0.0509,0.5965	possibly-damaging,possibly-damaging	44/1584,44/1641	19263266	73,12165	1966	4153	6119	SO:0001583	missense	8218	exon2			CACCAACTTTCTC		CCDS46662.1, CCDS54497.1, CCDS46662.2, CCDS54497.2	22q11.2	2008-06-10	2006-09-29		ENSG00000070371	ENSG00000070371			2093	protein-coding gene	gene with protein product		601273	"""clathrin, heavy polypeptide-like 1"""	CLTCL		8844170, 15133132	Standard	NM_007098		Approved	CLTD, CLH22, CHC22	uc021wle.1	P53675	OTTHUMG00000150109	ENST00000263200.10:c.130G>T	22.37:g.19263266C>A	ENSP00000445677:p.Val44Phe	124.0	0.0	0		128.0	58.0	0.453125	NM_001835	B7Z7U5|Q14017|Q15808|Q15809	Missense_Mutation	SNP	ENST00000263200.10	37	CCDS46662.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	14.65	2.600102	0.46423	5.09E-4	0.008548	ENSG00000070371	ENST00000353891;ENST00000263200;ENST00000427926;ENST00000449918	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	4.07	1.93	0.25924	Clathrin, heavy chain, propeller, N-terminal (1);Clathrin, heavy chain, linker/propeller domain (1);	0.078972	0.50627	D	0.000108	T	0.53642	0.1809	M	0.87827	2.91	0.45914	D	0.998752	B;D	0.54047	0.177;0.964	B;D	0.64321	0.325;0.924	T	0.59053	-0.7526	10	0.56958	D	0.05	-6.7814	8.2311	0.31599	0.1561:0.7604:0.0:0.0836	rs34869740	44;44	P53675-2;P53675	.;CLH2_HUMAN	F	44	ENSP00000439662:V44F;ENSP00000445677:V44F;ENSP00000441158:V44F;ENSP00000443264:V44F	ENSP00000445677:V44F	V	-	1	0	CLTCL1	17643266	1.000000	0.71417	0.009000	0.14445	0.231000	0.25187	3.255000	0.51484	0.367000	0.24454	-0.142000	0.14014	GTT	C|0.994;A|0.006	0.006	strong		0.468	CLTCL1-001	KNOWN	non_canonical_genome_sequence_error|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316397.5	NM_007098	
MLC1	23209	hgsc.bcm.edu	37	22	50512732	50512732	+	Silent	SNP	G	G	A	rs138153307		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50512732G>A	ENST00000311597.5	-	8	1233	c.627C>T	c.(625-627)gcC>gcT	p.A209A	MLC1_ENST00000535444.1_Silent_p.A130A|MLC1_ENST00000395876.2_Silent_p.A209A|MLC1_ENST00000538737.1_Silent_p.A175A|MLC1_ENST00000450140.2_Silent_p.A157A|MLC1_ENST00000431262.2_Silent_p.A179A|MLC1_ENST00000483836.1_5'Flank	NM_015166.3	NP_055981.1	Q15049	MLC1_HUMAN	megalencephalic leukoencephalopathy with subcortical cysts 1	209					caveolin-mediated endocytosis (GO:0072584)|cellular response to cholesterol (GO:0071397)|ion transport (GO:0006811)|positive regulation of intracellular transport (GO:0032388)|protein oligomerization (GO:0051259)|regulation of response to osmotic stress (GO:0047484)|transport (GO:0006810)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	protein complex binding (GO:0032403)|protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			endometrium(1)|kidney(1)|large_intestine(5)|lung(7)|pancreas(1)|prostate(3)	18		all_cancers(38;7.69e-11)|all_epithelial(38;9.52e-10)|all_lung(38;3.67e-05)|Breast(42;0.000776)|Lung NSC(38;0.000946)|Ovarian(80;0.0365)|Lung SC(80;0.113)		READ - Rectum adenocarcinoma(2;0.000669)|Colorectal(2;0.00242)|LUAD - Lung adenocarcinoma(64;0.0695)|BRCA - Breast invasive adenocarcinoma(115;0.216)		CCCCGAGGACGGCAGAGATGC	0.572													G|||	1	0.000199681	0.0	0.0	5008	,	,		16208	0.0		0.001	False		,,,				2504	0.0				p.A209A		Atlas-SNP	.											.	MLC1	48	.	0			c.C627T						PASS	.	G	,	1,4405	2.1+/-5.4	0,1,2202	108.0	76.0	87.0		627,627	-10.2	0.1	22	dbSNP_134	87	14,8586	10.5+/-38.8	0,14,4286	no	coding-synonymous,coding-synonymous	MLC1	NM_015166.3,NM_139202.2	,	0,15,6488	AA,AG,GG		0.1628,0.0227,0.1153	,	209/378,209/378	50512732	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	23209	exon8			GAGGACGGCAGAG	D25217	CCDS14083.1	22q13.33	2007-03-20			ENSG00000100427	ENSG00000100427			17082	protein-coding gene	gene with protein product		605908				7584026, 7584028	Standard	XR_430476		Approved	MLC, KIAA0027, LVM, VL	uc003bjg.1	Q15049	OTTHUMG00000150236	ENST00000311597.5:c.627C>T	22.37:g.50512732G>A		82.0	0.0	0		66.0	32.0	0.484848	NM_015166	B3KW61|B7Z659|Q5JZ83|Q8TAG4|Q96RP5|Q9UGY8	Silent	SNP	ENST00000311597.5	37	CCDS14083.1																																																																																			G|0.999;A|0.001	0.001	strong		0.572	MLC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316979.2	NM_015166	
SCN9A	6335	hgsc.bcm.edu	37	2	167128972	167128972	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:167128972G>A	ENST00000409435.1	-	16	3287	c.3288C>T	c.(3286-3288)tcC>tcT	p.S1096S	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.S1097S|SCN9A_ENST00000409672.1_Silent_p.S1085S|SCN9A_ENST00000375387.4_Silent_p.S1097S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1096					behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.S1085S(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TTTCCAAATCGGATTCCCCAG	0.413																																					p.S1085S		Atlas-SNP	.											SCN9A,colon,carcinoma,0,1	SCN9A	296	1	1	Substitution - coding silent(1)	large_intestine(1)	c.C3255T						PASS	.						71.0	65.0	67.0					2																	167128972		1897	4121	6018	SO:0001819	synonymous_variant	6335	exon17			CAAATCGGATTCC	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.3288C>T	2.37:g.167128972G>A		180.0	0.0	0		150.0	78.0	0.52	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	37	CCDS46441.1																																																																																			.	.	none		0.413	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
KRT33B	3884	hgsc.bcm.edu	37	17	39521058	39521058	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39521058C>G	ENST00000251646.3	-	6	1119	c.1070G>C	c.(1069-1071)cGg>cCg	p.R357P		NM_002279.4	NP_002270.1	Q14525	KT33B_HUMAN	keratin 33B	357	Coil 2.|Rod.				aging (GO:0007568)|hair cycle (GO:0042633)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(6)|lung(6)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)	21		Breast(137;0.000496)				CAGCAGGCTCCGGTATGTGTT	0.597																																					p.R357P		Atlas-SNP	.											KRT33B,NS,carcinoma,-1,1	KRT33B	46	1	0			c.G1070C						PASS	.						74.0	83.0	80.0					17																	39521058		2191	4300	6491	SO:0001583	missense	3884	exon6			AGGCTCCGGTATG	X82634	CCDS11389.1	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000131738	ENSG00000131738		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6451	protein-coding gene	gene with protein product	"""hard keratin type I 3II"""	602762	"""keratin, hair, acidic, 3B"""	KRTHA3B		7565656, 16831889	Standard	NM_002279		Approved	Ha-3II	uc002hwl.4	Q14525	OTTHUMG00000133429	ENST00000251646.3:c.1070G>C	17.37:g.39521058C>G	ENSP00000251646:p.Arg357Pro	118.0	0.0	0		115.0	57.0	0.495652	NM_002279	O76010	Missense_Mutation	SNP	ENST00000251646.3	37	CCDS11389.1	.	.	.	.	.	.	.	.	.	.	c	14.69	2.609786	0.46527	.	.	ENSG00000131738	ENST00000251646	D	0.94793	-3.52	4.72	2.74	0.32292	Filament (1);Intermediate filament protein, conserved site (1);	0.000000	0.64402	D	0.000012	D	0.98197	0.9404	H	0.99454	4.575	0.31011	N	0.71926	D	0.64830	0.994	D	0.77557	0.99	D	0.94737	0.7915	10	0.87932	D	0	.	8.178	0.31294	0.0:0.7468:0.0:0.2532	.	357	Q14525	KT33B_HUMAN	P	357	ENSP00000251646:R357P	ENSP00000251646:R357P	R	-	2	0	KRT33B	36774584	0.992000	0.36948	1.000000	0.80357	0.118000	0.20060	2.344000	0.44010	1.341000	0.45600	0.555000	0.69702	CGG	.	.	none		0.597	KRT33B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257292.1	NM_002279	
PLEKHF1	79156	hgsc.bcm.edu	37	19	30165157	30165157	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:30165157G>T	ENST00000436066.3	+	2	877	c.411G>T	c.(409-411)acG>acT	p.T137T	PLEKHF1_ENST00000592810.1_Silent_p.T137T	NM_024310.4	NP_077286.3	Q96S99	PKHF1_HUMAN	pleckstrin homology domain containing, family F (with FYVE domain) member 1	137					apoptotic process (GO:0006915)|endosome organization (GO:0007032)|positive regulation of autophagy (GO:0010508)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|protein localization to plasma membrane (GO:0072659)|vesicle organization (GO:0016050)	endosome membrane (GO:0010008)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)|phosphatidylinositol-4-phosphate binding (GO:0070273)|phosphatidylinositol-5-phosphate binding (GO:0010314)			breast(1)|lung(3)|ovary(1)|prostate(1)	6	Ovarian(5;0.000567)|Breast(6;0.0602)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0623)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.225)			TGAGGGCCACGGGCCGCCCGC	0.682																																					p.T137T		Atlas-SNP	.											.	PLEKHF1	16	.	0			c.G411T						PASS	.						23.0	26.0	25.0					19																	30165157		2200	4296	6496	SO:0001819	synonymous_variant	79156	exon2			GGCCACGGGCCGC	AF434818	CCDS12417.1	19q11	2013-01-10				ENSG00000166289		"""Zinc fingers, FYVE domain containing"", ""Pleckstrin homology (PH) domain containing"""	20764	protein-coding gene	gene with protein product		615200					Standard	NM_024310		Approved	APPD, MGC4090, PHAFIN1, ZFYVE15	uc002nsh.4	Q96S99		ENST00000436066.3:c.411G>T	19.37:g.30165157G>T		10.0	0.0	0		15.0	7.0	0.466667	NM_024310	Q96K11|Q9BUB9	Silent	SNP	ENST00000436066.3	37	CCDS12417.1																																																																																			.	.	none		0.682	PLEKHF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459323.1	NM_024310	
PRMT9	90826	hgsc.bcm.edu	37	4	148560193	148560193	+	Missense_Mutation	SNP	C	C	T	rs11557361	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:148560193C>T	ENST00000322396.6	-	11	2482	c.2240G>A	c.(2239-2241)tGt>tAt	p.C747Y	PRMT10_ENST00000541232.1_Missense_Mutation_p.C634Y|TMEM184C_ENST00000508208.1_Intron	NM_138364.2	NP_612373.2	Q6P2P2	ANM9_HUMAN		747	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.		C -> Y (in dbSNP:rs11557361).			cytoplasm (GO:0005737)	protein methyltransferase activity (GO:0008276)			breast(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(8)|lung(10)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28						TAAAGGTATACAGGGCAATGA	0.368													C|||	41	0.0081869	0.0	0.0101	5008	,	,		16840	0.0		0.0338	False		,,,				2504	0.0				p.C747Y		Atlas-SNP	.											.	PRMT10	68	.	0			c.G2240A						PASS	.	C	TYR/CYS	21,4385	26.2+/-53.5	0,21,2182	98.0	99.0	98.0		2240	5.2	0.7	4	dbSNP_120	98	245,8355	97.7+/-159.3	1,243,4056	yes	missense	PRMT10	NM_138364.2	194	1,264,6238	TT,TC,CC		2.8488,0.4766,2.0452	probably-damaging	747/846	148560193	266,12740	2203	4300	6503	SO:0001583	missense	90826	exon11			GGTATACAGGGCA																												ENST00000322396.6:c.2240G>A	4.37:g.148560193C>T	ENSP00000314396:p.Cys747Tyr	104.0	0.0	0		103.0	47.0	0.456311	NM_138364	A8KA39|B3KU92|Q6ZR58|Q8N383|Q9BT55|Q9NT98	Missense_Mutation	SNP	ENST00000322396.6	37	CCDS3771.1	31	0.014194139194139194	0	0.0	2	0.0055248618784530384	0	0.0	29	0.03825857519788918	C	8.851	0.944484	0.18356	0.004766	0.028488	ENSG00000164169	ENST00000322396;ENST00000541232	T;T	0.33438	1.41;1.41	5.25	5.25	0.73442	.	0.000000	0.85682	D	0.000000	T	0.06645	0.0170	L	0.54323	1.7	0.58432	D	0.999996	P	0.51653	0.947	B	0.42282	0.382	T	0.08330	-1.0727	10	0.02654	T	1	-33.0667	13.1858	0.59680	0.0:0.9234:0.0:0.0766	rs11557361;rs52794661;rs11557361	747	Q6P2P2	ANM10_HUMAN	Y	747;634	ENSP00000314396:C747Y;ENSP00000439508:C634Y	ENSP00000314396:C747Y	C	-	2	0	PRMT10	148779643	1.000000	0.71417	0.665000	0.29768	0.998000	0.95712	5.321000	0.65846	2.428000	0.82296	0.650000	0.86243	TGT	C|0.981;T|0.019	0.019	strong		0.368	PRMT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364650.1		
ETFDH	2110	hgsc.bcm.edu	37	4	159627845	159627845	+	Silent	SNP	T	T	C	rs77484245	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:159627845T>C	ENST00000511912.1	+	12	1865	c.1533T>C	c.(1531-1533)gaT>gaC	p.D511D	ETFDH_ENST00000307738.5_Silent_p.D464D	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	511					cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		CAAAACCCGATGGACAGATCA	0.433													T|||	10	0.00199681	0.0	0.0	5008	,	,		16740	0.0		0.0099	False		,,,				2504	0.0				p.D511D		Atlas-SNP	.											.	ETFDH	57	.	0			c.T1533C						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	203.0	192.0	196.0		1533	-1.0	0.9	4	dbSNP_132	196	54,8546	33.8+/-87.4	0,54,4246	no	coding-synonymous	ETFDH	NM_004453.2		0,57,6446	CC,CT,TT		0.6279,0.0681,0.4383		511/618	159627845	57,12949	2203	4300	6503	SO:0001819	synonymous_variant	2110	exon12			ACCCGATGGACAG	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.1533T>C	4.37:g.159627845T>C		91.0	0.0	0		91.0	38.0	0.417582	NM_004453	B4E3R9|J3KND9|Q7Z347	Silent	SNP	ENST00000511912.1	37	CCDS3800.1																																																																																			T|0.996;C|0.004	0.004	strong		0.433	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2		
CPAMD8	27151	hgsc.bcm.edu	37	19	17062905	17062905	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:17062905G>A	ENST00000443236.1	-	20	2554	c.2523C>T	c.(2521-2523)gcC>gcT	p.A841A		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	794						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						GGGAGGGCTCGGCGATGCCTA	0.617																																					p.A841A		Atlas-SNP	.											.	CPAMD8	192	.	0			c.C2523T						PASS	.						27.0	30.0	29.0					19																	17062905		2015	4149	6164	SO:0001819	synonymous_variant	27151	exon20			GGGCTCGGCGATG	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.2523C>T	19.37:g.17062905G>A		63.0	0.0	0		57.0	31.0	0.54386	NM_015692	Q8NC09|Q9ULD7	Silent	SNP	ENST00000443236.1	37	CCDS42519.1	.	.	.	.	.	.	.	.	.	.	G	12.31	1.899355	0.33535	.	.	ENSG00000160111	ENST00000443236	.	.	.	3.14	-6.29	0.02013	.	.	.	.	.	T	0.35278	0.0926	.	.	.	0.50467	D	0.999877	.	.	.	.	.	.	T	0.37619	-0.9698	4	.	.	.	.	1.5938	0.02659	0.4277:0.1287:0.2994:0.1442	.	.	.	.	L	852	.	.	P	-	2	0	CPAMD8	16923905	0.005000	0.15991	0.000000	0.03702	0.825000	0.46686	-0.070000	0.11523	-1.304000	0.02329	0.491000	0.48974	CCG	.	.	none		0.617	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
BANP	54971	hgsc.bcm.edu	37	16	88071611	88071611	+	Silent	SNP	C	C	T	rs149196674	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88071611C>T	ENST00000393207.1	+	11	1493	c.1272C>T	c.(1270-1272)gaC>gaT	p.D424D	BANP_ENST00000355163.5_Silent_p.D402D|BANP_ENST00000479780.2_Silent_p.D393D|BANP_ENST00000286122.7_Silent_p.D424D|BANP_ENST00000538234.1_Silent_p.D435D|BANP_ENST00000355022.4_Silent_p.D396D|BANP_ENST00000393208.2_Silent_p.D396D	NM_001173543.1	NP_001167014.1	Q8N9N5	BANP_HUMAN	BTG3 associated nuclear protein	424	Gln-rich.				cell cycle (GO:0007049)|chromatin modification (GO:0016568)|multicellular organismal development (GO:0007275)|negative regulation of protein catabolic process (GO:0042177)|protein localization to nucleus (GO:0034504)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|endometrium(2)|large_intestine(3)|lung(5)|prostate(1)	12				BRCA - Breast invasive adenocarcinoma(80;0.00551)		TGGGGCAGGACGGTCAGGTGA	0.612													c|||	2	0.000399361	0.0015	0.0	5008	,	,		11861	0.0		0.0	False		,,,				2504	0.0				p.D435D		Atlas-SNP	.											.	BANP	67	.	0			c.C1305T						PASS	.	C	,,,,,,	4,4392	8.1+/-20.4	0,4,2194	118.0	99.0	106.0		1296,1206,1179,1305,1272,1188,1188	-6.3	0.7	16	dbSNP_134	106	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	BANP	NM_001173539.1,NM_001173540.1,NM_001173541.1,NM_001173542.1,NM_001173543.1,NM_017869.3,NM_079837.2	,,,,,,	0,4,6494	TT,TC,CC		0.0,0.091,0.0308	,,,,,,	432/506,402/498,393/467,435/509,424/520,396/470,396/492	88071611	4,12992	2198	4300	6498	SO:0001819	synonymous_variant	54971	exon11			GCAGGACGGTCAG	AK094158	CCDS10966.2, CCDS42215.1, CCDS54052.1, CCDS54053.1, CCDS54054.1	16q24	2012-11-22			ENSG00000172530	ENSG00000172530		"""BEN domain containing"""	13450	protein-coding gene	gene with protein product	"""BEN domain containing 1"""	611564				10940556, 10950932	Standard	NM_017869		Approved	SMARBP1, SMAR1, FLJ20538, DKFZp761H172, FLJ10177, BEND1	uc010vow.2	Q8N9N5	OTTHUMG00000137678	ENST00000393207.1:c.1272C>T	16.37:g.88071611C>T		151.0	0.0	0		130.0	69.0	0.530769	NM_001173542	A8MU25|A8MX25|B2RCF7|B4DNJ9|F5GZM0|Q96GJ7|Q9NWY1	Silent	SNP	ENST00000393207.1	37	CCDS54054.1																																																																																			C|0.999;T|0.001	0.001	strong		0.612	BANP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000269166.1	NM_017869	
ALK	238	hgsc.bcm.edu	37	2	29416615	29416615	+	Silent	SNP	G	G	A	rs56132472	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29416615G>A	ENST00000389048.3	-	29	5244	c.4338C>T	c.(4336-4338)acC>acT	p.T1446T	ALK_ENST00000431873.1_Silent_p.T276T	NM_004304.4	NP_004295.2	Q9UM73	ALK_HUMAN	anaplastic lymphoma receptor tyrosine kinase	1446					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)	CAGAGGAGGTGGTAGGCAGAG	0.617			"""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				G|||	296	0.0591054	0.0779	0.0648	5008	,	,		15538	0.001		0.1233	False		,,,				2504	0.0235				p.T1446T		Atlas-SNP	.	yes	Dom	yes	Familial neuroblastoma	2	2p23	238	anaplastic lymphoma kinase (Ki-1)		"""L, E, M"""	.	ALK	533	.	0			c.C4338T						PASS	.			375,4031	187.8+/-214.3	15,345,1843	76.0	80.0	78.0		4338	1.4	0.0	2	dbSNP_129	78	968,7632	210.7+/-251.5	48,872,3380	no	coding-synonymous	ALK	NM_004304.4		63,1217,5223	AA,AG,GG		11.2558,8.5111,10.326		1446/1621	29416615	1343,11663	2203	4300	6503	SO:0001819	synonymous_variant	238	exon29	Familial Cancer Database	Familial Neuroblastoma;CCHS, Ondine Curse, incl. Ondine-Hirschsprung Disease	GGAGGTGGTAGGC	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.4338C>T	2.37:g.29416615G>A		133.0	0.0	0		86.0	40.0	0.465116	NM_004304	Q4ZFX9|Q53QQ6|Q53RZ4|Q59FI3|Q9Y4K6	Silent	SNP	ENST00000389048.3	37	CCDS33172.1																																																																																			G|0.903;A|0.097	0.097	strong		0.617	ALK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324994.1	NM_004304	
DNAH10	196385	hgsc.bcm.edu	37	12	124366300	124366300	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:124366300G>T	ENST00000409039.3	+	50	8434	c.8409G>T	c.(8407-8409)ggG>ggT	p.G2803G		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	2803	AAA 4. {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)		TGCTGGTCGGGGTAGGGGGCT	0.582																																					p.G2803G		Atlas-SNP	.											.	DNAH10	888	.	0			c.G8409T						PASS	.						17.0	20.0	19.0					12																	124366300		1775	3736	5511	SO:0001819	synonymous_variant	196385	exon50			GGTCGGGGTAGGG	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.8409G>T	12.37:g.124366300G>T		101.0	0.0	0		92.0	43.0	0.467391	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Silent	SNP	ENST00000409039.3	37	CCDS9255.2																																																																																			.	.	none		0.582	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
INO80C	125476	hgsc.bcm.edu	37	18	33048617	33048617	+	Silent	SNP	G	G	A	rs34130630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:33048617G>A	ENST00000334598.7	-	5	653	c.537C>T	c.(535-537)acC>acT	p.T179T	RP11-322E11.5_ENST00000591141.1_lincRNA|INO80C_ENST00000590757.1_Silent_p.T82T|INO80C_ENST00000592173.1_Intron|INO80C_ENST00000586489.1_Silent_p.T124T|INO80C_ENST00000441607.2_Silent_p.T215T|RP11-322E11.6_ENST00000589258.1_Intron	NM_194281.3	NP_919257.2	Q6PI98	IN80C_HUMAN	INO80 complex subunit C	179					chromatin remodeling (GO:0006338)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ino80 complex (GO:0031011)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)				central_nervous_system(1)|endometrium(1)|lung(3)|prostate(2)|skin(1)	8						CCAGGTAGCCGGTGACGACGT	0.542													G|||	64	0.0127796	0.0461	0.0043	5008	,	,		15661	0.0		0.0	False		,,,				2504	0.0				p.T215T		Atlas-SNP	.											.	INO80C	18	.	0			c.C645T						PASS	.	G	,	174,4232	115.0+/-153.0	6,162,2035	136.0	138.0	137.0		645,537	-10.5	1.0	18	dbSNP_126	137	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	INO80C	NM_001098817.1,NM_194281.3	,	6,167,6330	AA,AG,GG		0.0581,3.9492,1.3763	,	215/229,179/193	33048617	179,12827	2203	4300	6503	SO:0001819	synonymous_variant	125476	exon7			GTAGCCGGTGACG		CCDS11914.1, CCDS45853.1	18q12.2	2011-07-06	2008-08-07	2008-08-07	ENSG00000153391	ENSG00000153391		"""INO80 complex subunits"""	26994	protein-coding gene	gene with protein product	"""IES6 homolog (S. cerevisiae)"""		"""chromosome 18 open reading frame 37"""	C18orf37		16230350	Standard	NM_001098817		Approved	FLJ38183, hIes6, IES6	uc010dmt.3	Q6PI98	OTTHUMG00000132564	ENST00000334598.7:c.537C>T	18.37:g.33048617G>A		80.0	0.0	0		65.0	38.0	0.584615	NM_001098817	B4DUI4|E9PCS7|Q86WR1|Q8N994	Silent	SNP	ENST00000334598.7	37	CCDS11914.1																																																																																			G|0.986;A|0.014	0.014	strong		0.542	INO80C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255768.1	NM_194281	
AGRN	375790	hgsc.bcm.edu	37	1	978800	978800	+	Silent	SNP	C	C	T	rs375687903		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:978800C>T	ENST00000379370.2	+	8	1616	c.1566C>T	c.(1564-1566)ctC>ctT	p.L522L		NM_198576.3	NP_940978.2	O00468	AGRIN_HUMAN	agrin	522	Kazal-like 5. {ECO:0000255|PROSITE- ProRule:PRU00798}.				axon guidance (GO:0007411)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|clustering of voltage-gated sodium channels (GO:0045162)|extracellular matrix organization (GO:0030198)|G-protein coupled acetylcholine receptor signaling pathway (GO:0007213)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|neuromuscular junction development (GO:0007528)|neurotransmitter receptor metabolic process (GO:0045213)|phototransduction, visible light (GO:0007603)|plasma membrane organization (GO:0007009)|positive regulation of filopodium assembly (GO:0051491)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of synaptic growth at neuromuscular junction (GO:0045887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|receptor clustering (GO:0043113)|retinoid metabolic process (GO:0001523)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synapse organization (GO:0050808)	basal lamina (GO:0005605)|cell junction (GO:0030054)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|lysosomal lumen (GO:0043202)|plasma membrane (GO:0005886)|synapse (GO:0045202)	acetylcholine receptor regulator activity (GO:0030548)|calcium ion binding (GO:0005509)|chondroitin sulfate binding (GO:0035374)|dystroglycan binding (GO:0002162)|heparan sulfate proteoglycan binding (GO:0043395)|laminin binding (GO:0043236)|sialic acid binding (GO:0033691)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(3)|large_intestine(2)|lung(20)|ovary(1)|prostate(1)|skin(3)|urinary_tract(1)	42	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;8.75e-19)|all_lung(118;2.3e-08)|Lung NSC(185;2.38e-06)|Renal(390;0.00183)|Breast(487;0.00354)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.128)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00462)|Epithelial(90;5.98e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.43e-23)|Colorectal(212;5.97e-05)|COAD - Colon adenocarcinoma(227;0.000201)|Kidney(185;0.0024)|BRCA - Breast invasive adenocarcinoma(365;0.00246)|STAD - Stomach adenocarcinoma(132;0.00645)|KIRC - Kidney renal clear cell carcinoma(229;0.0354)|Lung(427;0.201)		CCTGTACCCTCGGGCGGGAGA	0.682																																					p.L522L		Atlas-SNP	.											.	AGRN	110	.	0			c.C1566T						PASS	.	C		0,4374		0,0,2187	35.0	35.0	35.0		1566	-7.6	0.1	1		35	2,8588		0,2,4293	no	coding-synonymous	AGRN	NM_198576.3		0,2,6480	TT,TC,CC		0.0233,0.0,0.0154		522/2046	978800	2,12962	2187	4295	6482	SO:0001819	synonymous_variant	375790	exon8			TACCCTCGGGCGG	XM_372195	CCDS30551.1	1p36.33	2014-09-17		2007-02-16	ENSG00000188157	ENSG00000188157		"""Proteoglycans / Extracellular Matrix : Other"""	329	protein-coding gene	gene with protein product	"""agrin proteoglycan"""	103320				1851019, 12270958	Standard	NM_198576		Approved	AGRIN	uc001ack.2	O00468	OTTHUMG00000040778	ENST00000379370.2:c.1566C>T	1.37:g.978800C>T		43.0	0.0	0		80.0	4.0	0.05	NM_198576	Q5SVA1|Q5SVA2|Q60FE1|Q7KYS8|Q8N4J5|Q96IC1|Q9BTD4	Silent	SNP	ENST00000379370.2	37	CCDS30551.1																																																																																			.	.	none		0.682	AGRN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097990.2	NM_198576	
CLCNKA	1187	hgsc.bcm.edu	37	1	16349137	16349137	+	Missense_Mutation	SNP	G	G	A	rs9442189	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:16349137G>A	ENST00000331433.4	+	2	42	c.23G>A	c.(22-24)cGt>cAt	p.R8H	CLCNKA_ENST00000420078.1_Missense_Mutation_p.R8H|CLCNKA_ENST00000375692.1_Missense_Mutation_p.R8H|CLCNKA_ENST00000464764.1_3'UTR|CLCNKA_ENST00000439316.2_Missense_Mutation_p.R8H			P51800	CLCKA_HUMAN	chloride channel, voltage-sensitive Ka	8			R -> H (in dbSNP:rs9442189).		excretion (GO:0007588)|ion transmembrane transport (GO:0034220)|regulation of anion transport (GO:0044070)|transmembrane transport (GO:0055085)|transport (GO:0006810)	chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)|metal ion binding (GO:0046872)|voltage-gated chloride channel activity (GO:0005247)			breast(1)|kidney(1)|large_intestine(2)|lung(12)|ovary(2)|skin(1)	19		Colorectal(325;3.46e-05)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0221)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|Colorectal(212;8.04e-08)|COAD - Colon adenocarcinoma(227;5.46e-06)|BRCA - Breast invasive adenocarcinoma(304;9.02e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(313;0.00655)|READ - Rectum adenocarcinoma(331;0.0649)	Niflumic Acid(DB04552)	GTGGGGCTGCGTGAGGGCTTC	0.667													G|||	61	0.0121805	0.0	0.0058	5008	,	,		17257	0.001		0.0278	False		,,,				2504	0.0286				p.R8H		Atlas-SNP	.											.	CLCNKA	56	.	0			c.G23A						PASS	.	G	HIS/ARG,HIS/ARG	12,4378		1,10,2184	48.0	42.0	44.0		23,23	2.2	0.6	1	dbSNP_119	44	182,8400		2,178,4111	yes	missense,missense	CLCNKA	NM_001042704.1,NM_004070.3	29,29	3,188,6295	AA,AG,GG		2.1207,0.2733,1.4955	benign,benign	8/687,8/688	16349137	194,12778	2195	4291	6486	SO:0001583	missense	1187	exon2			GGCTGCGTGAGGG		CCDS167.1, CCDS41269.1, CCDS57973.1	1p36	2012-09-26	2012-02-23		ENSG00000186510	ENSG00000186510		"""Ion channels / Chloride channels : Voltage-sensitive"""	2026	protein-coding gene	gene with protein product		602024	"""chloride channel Ka"""			8544406	Standard	NM_004070		Approved	hClC-Ka	uc001axu.3	P51800	OTTHUMG00000009529	ENST00000331433.4:c.23G>A	1.37:g.16349137G>A	ENSP00000332771:p.Arg8His	95.0	0.0	0		128.0	7.0	0.0546875	NM_004070	B4DPD3|E7EPH6|Q5T5P8|Q5T5Q4|Q7Z6D1|Q86VT1	Missense_Mutation	SNP	ENST00000331433.4	37	CCDS167.1	21	0.009615384615384616	0	0.0	2	0.0055248618784530384	0	0.0	19	0.025065963060686015	G	10.27	1.304871	0.23736	0.002733	0.021207	ENSG00000186510	ENST00000375692;ENST00000420078;ENST00000439316;ENST00000331433	D;D;D;D	0.86562	-1.93;-1.93;-2.14;-1.93	4.12	2.15	0.27550	.	0.835714	0.10474	U	0.670447	T	0.68595	0.3018	M	0.75447	2.3	0.23138	N	0.998237	B;B;B	0.29671	0.254;0.254;0.254	B;B;B	0.25614	0.062;0.062;0.062	T	0.69221	-0.5202	10	0.62326	D	0.03	.	6.152	0.20316	0.2539:0.0:0.7461:0.0	rs9442189;rs9442189	8;8;8	E7EPH6;Q5T5Q4;P51800	.;.;CLCKA_HUMAN	H	8	ENSP00000364844:R8H;ENSP00000410353:R8H;ENSP00000414445:R8H;ENSP00000332771:R8H	ENSP00000332771:R8H	R	+	2	0	CLCNKA	16221724	0.001000	0.12720	0.588000	0.28705	0.445000	0.32107	-0.259000	0.08721	0.337000	0.23665	-0.657000	0.03884	CGT	G|0.989;A|0.011	0.011	strong		0.667	CLCNKA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026326.1		
MUC5B	727897	hgsc.bcm.edu	37	11	1264941	1264941	+	Silent	SNP	G	G	A	rs200834421	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1264941G>A	ENST00000529681.1	+	31	6889	c.6831G>A	c.(6829-6831)acG>acA	p.T2277T	MUC5B_ENST00000447027.1_Silent_p.T2280T|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2277	7 X Cys-rich subdomain repeats.|Thr-rich.				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)		GCCACACCACGGCCACCTCCA	0.682													g|||	24	0.00479233	0.0008	0.0058	5008	,	,		15879	0.0		0.0129	False		,,,				2504	0.0061				p.T2277T		Atlas-SNP	.											MUC5B,NS,carcinoma,+1,2	MUC5B	473	2	0			c.G6831A						PASS	.	G		9,4263		0,9,2127	98.0	136.0	123.0		6831	-6.0	0.0	11		123	100,8354		0,100,4127	no	coding-synonymous	MUC5B	NM_002458.2		0,109,6254	AA,AG,GG		1.1829,0.2107,0.8565		2277/5763	1264941	109,12617	2136	4227	6363	SO:0001819	synonymous_variant	727897	exon31			CACCACGGCCACC	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.6831G>A	11.37:g.1264941G>A		537.0	0.0	0		607.0	179.0	0.294893	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Silent	SNP	ENST00000529681.1	37	CCDS44515.2																																																																																			G|0.988;A|0.012	0.012	strong		0.682	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
CD2AP	23607	hgsc.bcm.edu	37	6	47563608	47563608	+	Missense_Mutation	SNP	A	A	G	rs138727736	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:47563608A>G	ENST00000359314.5	+	12	1576	c.1120A>G	c.(1120-1122)Aca>Gca	p.T374A		NM_012120.2	NP_036252.1	Q9Y5K6	CD2AP_HUMAN	CD2-associated protein	374	Pro-rich.				mitotic nuclear division (GO:0007067)|negative regulation of transforming growth factor beta1 production (GO:0032911)|positive regulation of protein localization to nucleus (GO:1900182)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein complex assembly (GO:0006461)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of receptor-mediated endocytosis (GO:0048259)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|substrate-dependent cell migration, cell extension (GO:0006930)|vesicle organization (GO:0016050)	actin cytoskeleton (GO:0015629)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|filamentous actin (GO:0031941)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			kidney(1)|large_intestine(9)|lung(5)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	20			Lung(136;0.105)|LUSC - Lung squamous cell carcinoma(51;0.138)			TGAAAAATCAACACTGGAACA	0.353													A|||	23	0.00459265	0.0	0.0115	5008	,	,		14171	0.001		0.003	False		,,,				2504	0.0112				p.T374A		Atlas-SNP	.											.	CD2AP	43	.	0			c.A1120G	GRCh37	CM090139	CD2AP	M	rs138727736	PASS	.	A	ALA/THR	2,4404	4.2+/-10.8	0,2,2201	149.0	169.0	162.0		1120	-5.2	0.0	6	dbSNP_134	162	46,8554	28.5+/-78.6	0,46,4254	yes	missense	CD2AP	NM_012120.2	58	0,48,6455	GG,GA,AA		0.5349,0.0454,0.3691	benign	374/640	47563608	48,12958	2203	4300	6503	SO:0001583	missense	23607	exon12			AAATCAACACTGG	AF146277	CCDS34472.1	6p12	2008-02-05			ENSG00000198087	ENSG00000198087			14258	protein-coding gene	gene with protein product		604241				10339567	Standard	NM_012120		Approved	CMS	uc003oyw.3	Q9Y5K6	OTTHUMG00000014799	ENST00000359314.5:c.1120A>G	6.37:g.47563608A>G	ENSP00000352264:p.Thr374Ala	24.0	0.0	0		29.0	16.0	0.551724	NM_012120	A6NL34|Q5VYA3|Q9UG97	Missense_Mutation	SNP	ENST00000359314.5	37	CCDS34472.1	8	0.003663003663003663	0	0.0	6	0.016574585635359115	0	0.0	2	0.002638522427440633	A	3.633	-0.075108	0.07184	4.54E-4	0.005349	ENSG00000198087	ENST00000359314	T	0.22945	1.93	5.57	-5.18	0.02840	.	5.281300	0.00481	N	0.000133	T	0.01627	0.0052	N	0.02011	-0.69	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.21690	-1.0238	10	0.07644	T	0.81	4.6781	2.2995	0.04159	0.4573:0.1057:0.271:0.166	.	374	Q9Y5K6	CD2AP_HUMAN	A	374	ENSP00000352264:T374A	ENSP00000352264:T374A	T	+	1	0	CD2AP	47671567	0.000000	0.05858	0.011000	0.14972	0.933000	0.57130	-1.282000	0.02799	-0.673000	0.05259	-0.467000	0.05162	ACA	A|0.995;G|0.005	0.005	strong		0.353	CD2AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040817.2		
ACADL	33	hgsc.bcm.edu	37	2	211068100	211068100	+	Silent	SNP	A	A	G	rs148069105	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:211068100A>G	ENST00000233710.3	-	8	1166	c.939T>C	c.(937-939)taT>taC	p.Y313Y	AC006994.2_ENST00000412065.1_RNA	NM_001608.3	NP_001599.1	P28330	ACADL_HUMAN	acyl-CoA dehydrogenase, long chain	313					carnitine catabolic process (GO:0042413)|carnitine metabolic process, CoA-linked (GO:0019254)|cellular lipid catabolic process (GO:0044242)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|long-chain fatty acid catabolic process (GO:0042758)|negative regulation of fatty acid biosynthetic process (GO:0045717)|negative regulation of fatty acid oxidation (GO:0046322)|oxidation-reduction process (GO:0055114)|protein homotetramerization (GO:0051289)|regulation of cholesterol metabolic process (GO:0090181)|small molecule metabolic process (GO:0044281)|temperature homeostasis (GO:0001659)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)|mitochondrion (GO:0005739)	acyl-CoA dehydrogenase activity (GO:0003995)|fatty-acyl-CoA binding (GO:0000062)|flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|palmitoyl-CoA oxidase activity (GO:0016401)			central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(1)|skin(1)	14		Renal(323;0.202)		Epithelial(149;0.00631)|Lung(261;0.0438)|LUSC - Lung squamous cell carcinoma(261;0.0466)|all cancers(144;0.0621)		TTTGTTTAACATAGTTCCTGG	0.343																																					p.Y313Y		Atlas-SNP	.											.	ACADL	38	.	0			c.T939C						PASS	.	A		1,4405	2.1+/-5.4	0,1,2202	113.0	98.0	103.0		939	-5.7	0.9	2	dbSNP_134	103	12,8586	9.1+/-34.3	0,12,4287	no	coding-synonymous	ACADL	NM_001608.3		0,13,6489	GG,GA,AA		0.1396,0.0227,0.1		313/431	211068100	13,12991	2203	4299	6502	SO:0001819	synonymous_variant	33	exon8			TTTAACATAGTTC	M74096	CCDS2389.1	2q34	2012-07-13	2010-04-30		ENSG00000115361	ENSG00000115361	1.3.99.13		88	protein-coding gene	gene with protein product		609576	"""acyl-Coenzyme A dehydrogenase, long chain"""			1774065	Standard	NM_001608		Approved	LCAD, ACAD4	uc002vdz.4	P28330	OTTHUMG00000132989	ENST00000233710.3:c.939T>C	2.37:g.211068100A>G		64.0	0.0	0		80.0	30.0	0.375	NM_001608	B2R8T3|Q8IUN8	Silent	SNP	ENST00000233710.3	37	CCDS2389.1																																																																																			A|0.999;G|0.001	0.001	strong		0.343	ACADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256561.2	NM_001608	
POMGNT2	84892	hgsc.bcm.edu	37	3	43121743	43121743	+	Missense_Mutation	SNP	C	C	T	rs199612856	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:43121743C>T	ENST00000344697.2	-	2	1526	c.1181G>A	c.(1180-1182)cGg>cAg	p.R394Q	POMGNT2_ENST00000441964.1_Missense_Mutation_p.R394Q	NM_032806.5	NP_116195.2	Q8NAT1	PMGT2_HUMAN	protein O-linked mannose N-acetylglucosaminyltransferase 2 (beta 1,4-)	394					protein O-linked glycosylation (GO:0006493)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein O-GlcNAc transferase activity (GO:0097363)										CATCATGTTCCGCCAGGCTAC	0.587													C|||	5	0.000998403	0.0	0.0	5008	,	,		22992	0.002		0.0	False		,,,				2504	0.0031				p.R394Q		Atlas-SNP	.											.	.	.	.	0			c.G1181A						PASS	.						80.0	71.0	74.0					3																	43121743		2203	4300	6503	SO:0001583	missense	84892	exon2			ATGTTCCGCCAGG	AK092147	CCDS2709.1	3p22.1	2014-07-15	2013-08-22	2013-08-22	ENSG00000144647	ENSG00000144647			25902	protein-coding gene	gene with protein product		614828	"""chromosome 3 open reading frame 39"", ""glycosyltransferase-like domain containing 2"""	C3orf39, GTDC2		12477932	Standard	NM_032806		Approved	FLJ14566, AGO61	uc003cmr.2	Q8NAT1	OTTHUMG00000133038	ENST00000344697.2:c.1181G>A	3.37:g.43121743C>T	ENSP00000344125:p.Arg394Gln	184.0	0.0	0		185.0	92.0	0.497297	NM_032806	B3KWC3|Q96SY3	Missense_Mutation	SNP	ENST00000344697.2	37	CCDS2709.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	11.87	1.767376	0.31320	.	.	ENSG00000144647	ENST00000441964;ENST00000344697	T;T	0.77229	-1.08;-1.08	5.53	1.22	0.21188	.	0.363726	0.31233	N	0.008011	T	0.57946	0.2088	N	0.17278	0.47	0.37391	D	0.912468	B	0.09022	0.002	B	0.10450	0.005	T	0.48127	-0.9062	10	0.30078	T	0.28	-25.7255	7.9623	0.30079	0.0:0.4895:0.0:0.5105	.	394	Q8NAT1	AGO61_HUMAN	Q	394	ENSP00000408992:R394Q;ENSP00000344125:R394Q	ENSP00000344125:R394Q	R	-	2	0	C3orf39	43096747	0.970000	0.33590	0.988000	0.46212	0.986000	0.74619	0.528000	0.23002	0.318000	0.23185	0.650000	0.86243	CGG	C|1.000;T|0.000	0.000	strong		0.587	POMGNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256643.1	NM_032806	
ESPN	83715	hgsc.bcm.edu	37	1	6500762	6500762	+	Missense_Mutation	SNP	G	G	A	rs200602012		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:6500762G>A	ENST00000377828.1	+	4	920	c.752G>A	c.(751-753)gGc>gAc	p.G251D	RP1-202O8.2_ENST00000419034.1_RNA	NM_031475.2	NP_113663.2	B1AK53	ESPN_HUMAN	espin	251					locomotory behavior (GO:0007626)|negative regulation of cytoskeleton organization (GO:0051494)|parallel actin filament bundle assembly (GO:0030046)|positive regulation of filopodium assembly (GO:0051491)|sensory perception of sound (GO:0007605)	brush border (GO:0005903)|cytoplasm (GO:0005737)|filamentous actin (GO:0031941)|microvillus (GO:0005902)|stereocilium bundle tip (GO:0032426)	actin filament binding (GO:0051015)|SH3 domain binding (GO:0017124)			NS(1)|breast(2)|cervix(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(1)|skin(1)	17	Ovarian(185;0.0386)|all_lung(157;0.154)	all_cancers(23;3.6e-37)|all_epithelial(116;2.56e-22)|all_lung(118;7.57e-07)|Lung NSC(185;4.26e-06)|all_hematologic(16;6.92e-06)|Colorectal(325;4.47e-05)|Acute lymphoblastic leukemia(12;4.92e-05)|Breast(487;7.61e-05)|Renal(390;0.0007)|Hepatocellular(190;0.00308)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0392)		Epithelial(90;1.82e-35)|GBM - Glioblastoma multiforme(13;3e-28)|Kidney(185;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(229;5.63e-08)|Colorectal(212;7e-08)|COAD - Colon adenocarcinoma(227;1.41e-05)|BRCA - Breast invasive adenocarcinoma(365;0.000109)|STAD - Stomach adenocarcinoma(132;0.00167)|Lung(427;0.0108)|LUSC - Lung squamous cell carcinoma(448;0.0253)|READ - Rectum adenocarcinoma(331;0.0419)		GCGAGCCGCGGCCACACCAAG	0.726																																					p.G251D		Atlas-SNP	.											.	ESPN	32	.	0			c.G752A						PASS	.						5.0	6.0	5.0					1																	6500762		1942	3927	5869	SO:0001583	missense	83715	exon4			GCCGCGGCCACAC	AF134401	CCDS70.1	1p36.31	2013-01-10			ENSG00000187017	ENSG00000187017		"""Ankyrin repeat domain containing"""	13281	protein-coding gene	gene with protein product		606351	"""deafness, autosomal recessive 36"""	DFNB36		10975527, 15286153	Standard	NM_031475		Approved		uc001amy.3	B1AK53	OTTHUMG00000000753	ENST00000377828.1:c.752G>A	1.37:g.6500762G>A	ENSP00000367059:p.Gly251Asp	7.0	0.0	0		16.0	11.0	0.6875	NM_031475	Q6XYB2|Q9H0A2|Q9Y329	Missense_Mutation	SNP	ENST00000377828.1	37	CCDS70.1	.	.	.	.	.	.	.	.	.	.	G	25.6	4.650081	0.87958	.	.	ENSG00000187017	ENST00000377828;ENST00000418286	T;T	0.72394	-0.65;0.89	3.84	3.84	0.44239	Ankyrin repeat-containing domain (5);	0.233607	0.34959	N	0.003544	T	0.81772	0.4893	M	0.80982	2.52	0.80722	D	1	D	0.65815	0.995	D	0.63283	0.913	D	0.83857	0.0266	10	0.54805	T	0.06	-5.9744	12.6418	0.56714	0.0:0.0:1.0:0.0	.	251	B1AK53	ESPN_HUMAN	D	251;36	ENSP00000367059:G251D;ENSP00000401793:G36D	ENSP00000367059:G251D	G	+	2	0	ESPN	6423349	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	8.972000	0.93424	1.989000	0.58080	0.430000	0.28490	GGC	G|0.991;A|0.010	0.010	weak		0.726	ESPN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000001887.3	NM_031475	
LGALS3BP	3959	hgsc.bcm.edu	37	17	76970803	76970803	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:76970803G>A	ENST00000262776.3	-	4	651	c.343C>T	c.(343-345)Cac>Tac	p.H115Y	LGALS3BP_ENST00000585407.1_Missense_Mutation_p.H115Y|LGALS3BP_ENST00000591778.1_Missense_Mutation_p.H115Y	NM_005567.3	NP_005558.1	Q08380	LG3BP_HUMAN	lectin, galactoside-binding, soluble, 3 binding protein	115	SRCR. {ECO:0000255|PROSITE- ProRule:PRU00196}.				cell adhesion (GO:0007155)|cellular defense response (GO:0006968)|receptor-mediated endocytosis (GO:0006898)|signal transduction (GO:0007165)	blood microparticle (GO:0072562)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	scavenger receptor activity (GO:0005044)			NS(1)|breast(1)|central_nervous_system(5)|endometrium(3)|large_intestine(1)|lung(3)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	17			BRCA - Breast invasive adenocarcinoma(99;0.0677)|OV - Ovarian serous cystadenocarcinoma(97;0.139)			TCTCTCTCGTGCCTGCAGTTG	0.677																																					p.H115Y	GBM(89;1105 1755 18102 21513)	Atlas-SNP	.											.	LGALS3BP	47	.	0			c.C343T						PASS	.						76.0	56.0	63.0					17																	76970803		2203	4300	6503	SO:0001583	missense	3959	exon4			TCTCGTGCCTGCA	L13210	CCDS11759.1	17q25	2014-07-09				ENSG00000108679		"""BTB/POZ domain containing"", ""Endogenous ligands"""	6564	protein-coding gene	gene with protein product	"""L3 antigen"", ""Mac-2-binding protein"", ""serum protein 90K"", ""transport and golgi organization 10 homolog B (Drosophila)"""	600626				7698018, 8034587, 8390986	Standard	NM_005567		Approved	MAC-2-BP, 90K, BTBD17B, TANGO10B, M2BP, gp90, CyCAP	uc002jwh.3	Q08380		ENST00000262776.3:c.343C>T	17.37:g.76970803G>A	ENSP00000262776:p.His115Tyr	126.0	0.0	0		117.0	46.0	0.393162	NM_005567	Q7M4S0|Q9UCH8|Q9UCH9|Q9UCI0	Missense_Mutation	SNP	ENST00000262776.3	37	CCDS11759.1	.	.	.	.	.	.	.	.	.	.	G	15.15	2.748237	0.49257	.	.	ENSG00000108679	ENST00000262776;ENST00000536190	T	0.34072	1.38	3.22	3.22	0.36961	Speract/scavenger receptor (3);Speract/scavenger receptor-related (2);	0.000000	0.35615	N	0.003090	T	0.67420	0.2891	H	0.95114	3.625	0.41107	D	0.985716	D	0.89917	1.0	D	0.91635	0.999	T	0.75961	-0.3133	10	0.87932	D	0	-44.0802	10.1799	0.42961	0.0:0.0:1.0:0.0	.	115	Q08380	LG3BP_HUMAN	Y	115;103	ENSP00000262776:H115Y	ENSP00000262776:H115Y	H	-	1	0	LGALS3BP	74482398	1.000000	0.71417	0.034000	0.17996	0.284000	0.27059	8.854000	0.92228	2.091000	0.63221	0.313000	0.20887	CAC	.	.	none		0.677	LGALS3BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437785.3	NM_005567	
AMY2A	279	hgsc.bcm.edu	37	1	104166590	104166590	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:104166590C>G	ENST00000414303.2	+	8	1268	c.1204C>G	c.(1204-1206)Cga>Gga	p.R402G	AMY2A_ENST00000497748.1_3'UTR	NM_000699.2	NP_000690.1	P04746	AMYP_HUMAN	amylase, alpha 2A (pancreatic)	402					carbohydrate catabolic process (GO:0016052)|carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|calcium ion binding (GO:0005509)|chloride ion binding (GO:0031404)	p.R402*(1)		endometrium(3)|kidney(1)|large_intestine(5)|liver(3)|lung(5)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	22		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)	Acarbose(DB00284)|Icodextrin(DB00702)|Miglitol(DB00491)	CTGTGAACATCGATGGCGCCA	0.343																																					p.R402G		Atlas-SNP	.											AMY2A,colon,carcinoma,0,1	AMY2A	36	1	1	Substitution - Nonsense(1)	large_intestine(1)	c.C1204G						scavenged	.						9.0	9.0	9.0					1																	104166590		1665	3373	5038	SO:0001583	missense	279	exon8			GAACATCGATGGC	BC007060	CCDS783.1	1p21.1	2012-10-02	2007-05-03		ENSG00000243480	ENSG00000243480	3.2.1.1		477	protein-coding gene	gene with protein product		104650	"""amylase, alpha 2A; pancreatic"""	AMY2		3260028	Standard	NM_000699		Approved		uc001dut.3	P04746	OTTHUMG00000011023	ENST00000414303.2:c.1204C>G	1.37:g.104166590C>G	ENSP00000397582:p.Arg402Gly	468.0	0.0	0		492.0	93.0	0.189024	NM_000699	B9EJG1|Q9UBH3	Missense_Mutation	SNP	ENST00000414303.2	37	CCDS783.1	.	.	.	.	.	.	.	.	.	.	-	13.88	2.369406	0.42003	.	.	ENSG00000243480	ENST00000414303;ENST00000393932	.	.	.	2.94	1.99	0.26369	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);Glycosyl hydrolase, family 13, subfamily, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.81384	0.4811	H	0.96239	3.79	0.80722	D	1	D	0.89917	1.0	D	0.76575	0.988	D	0.83784	0.0227	9	0.87932	D	0	.	9.5171	0.39113	0.3781:0.6219:0.0:0.0	.	402	P04746	AMYP_HUMAN	G	402	.	ENSP00000377509:R402G	R	+	1	2	AMY2A	103968113	0.999000	0.42202	0.992000	0.48379	0.892000	0.51952	1.860000	0.39428	0.540000	0.28808	0.305000	0.20034	CGA	.	.	weak		0.343	AMY2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030315.1	NM_000699	
GAS2L3	283431	hgsc.bcm.edu	37	12	101017839	101017839	+	Missense_Mutation	SNP	C	C	T	rs148236676	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101017839C>T	ENST00000539410.1	+	9	1642	c.1256C>T	c.(1255-1257)cCa>cTa	p.P419L	GAS2L3_ENST00000547754.1_Missense_Mutation_p.P419L|GAS2L3_ENST00000266754.5_Missense_Mutation_p.P419L|GAS2L3_ENST00000537247.1_Missense_Mutation_p.P315L			Q86XJ1	GA2L3_HUMAN	growth arrest-specific 2 like 3	419					actin cytoskeleton organization (GO:0030036)|cell cycle arrest (GO:0007050)|microtubule cytoskeleton organization (GO:0000226)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	actin binding (GO:0003779)|microtubule binding (GO:0008017)			endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(15)|pancreas(1)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	35						ACTTCTTCACCAGCTTTACCA	0.423													C|||	17	0.00339457	0.0008	0.0115	5008	,	,		19471	0.0		0.006	False		,,,				2504	0.002				p.P419L		Atlas-SNP	.											.	GAS2L3	76	.	0			c.C1256T						PASS	.	C	LEU/PRO	7,4399	12.9+/-30.5	0,7,2196	91.0	93.0	92.0		1256	4.1	0.0	12	dbSNP_134	92	61,8539	37.8+/-93.5	0,61,4239	yes	missense	GAS2L3	NM_174942.1	98	0,68,6435	TT,TC,CC		0.7093,0.1589,0.5228	benign	419/695	101017839	68,12938	2203	4300	6503	SO:0001583	missense	283431	exon10			CTTCACCAGCTTT	AK095594	CCDS9079.1	12q23.1	2014-09-11			ENSG00000139354	ENSG00000139354			27475	protein-coding gene	gene with protein product							Standard	NM_174942		Approved		uc001thu.3	Q86XJ1	OTTHUMG00000170439	ENST00000539410.1:c.1256C>T	12.37:g.101017839C>T	ENSP00000439672:p.Pro419Leu	102.0	0.0	0		102.0	44.0	0.431373	NM_174942	B2RCN2	Missense_Mutation	SNP	ENST00000539410.1	37	CCDS9079.1	8	0.003663003663003663	1	0.0020325203252032522	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	C	4.648	0.120536	0.08881	0.001589	0.007093	ENSG00000139354	ENST00000266754;ENST00000547754;ENST00000537247;ENST00000539410	T;T;T;T	0.25085	1.86;1.86;1.82;1.86	4.95	4.06	0.47325	.	0.368200	0.25089	N	0.033227	T	0.16041	0.0386	L	0.43152	1.355	0.28581	N	0.910137	B	0.09022	0.002	B	0.08055	0.003	T	0.11966	-1.0566	10	0.62326	D	0.03	-3.2328	10.2064	0.43116	0.0:0.7873:0.1365:0.0761	.	419	Q86XJ1	GA2L3_HUMAN	L	419;419;315;419	ENSP00000266754:P419L;ENSP00000448955:P419L;ENSP00000442406:P315L;ENSP00000439672:P419L	ENSP00000266754:P419L	P	+	2	0	GAS2L3	99541970	0.005000	0.15991	0.008000	0.14137	0.047000	0.14425	2.030000	0.41108	1.080000	0.41073	0.603000	0.83216	CCA	C|0.995;T|0.005	0.005	strong		0.423	GAS2L3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409143.1	NM_174942	
KCTD19	146212	hgsc.bcm.edu	37	16	67327642	67327642	+	Missense_Mutation	SNP	C	C	T	rs145649592	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67327642C>T	ENST00000304372.5	-	12	2078	c.2023G>A	c.(2023-2025)Gag>Aag	p.E675K		NM_001100915.1	NP_001094385.1	Q17RG1	KCD19_HUMAN	potassium channel tetramerization domain containing 19	675					protein homooligomerization (GO:0051260)					endometrium(3)|large_intestine(7)|lung(8)|ovary(1)|prostate(1)|skin(3)	23		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0311)|Epithelial(162;0.0906)		GAAGCAGCCTCGCTTCCCAAG	0.617													C|||	14	0.00279553	0.0	0.0029	5008	,	,		17949	0.0		0.006	False		,,,				2504	0.0061				p.E675K		Atlas-SNP	.											.	KCTD19	82	.	0			c.G2023A						PASS	.	C	LYS/GLU	2,4160		0,2,2079	76.0	86.0	83.0		2023	4.9	0.9	16	dbSNP_134	83	43,8353		0,43,4155	yes	missense	KCTD19	NM_001100915.1	56	0,45,6234	TT,TC,CC		0.5121,0.0481,0.3583	probably-damaging	675/927	67327642	45,12513	2081	4198	6279	SO:0001583	missense	146212	exon12			CAGCCTCGCTTCC	AK097481	CCDS42179.1	16q22.1	2013-06-20	2013-06-20			ENSG00000168676			24753	protein-coding gene	gene with protein product			"""potassium channel tetramerisation domain containing 19"""				Standard	NM_001100915		Approved	FLJ40162	uc002esu.2	Q17RG1		ENST00000304372.5:c.2023G>A	16.37:g.67327642C>T	ENSP00000305702:p.Glu675Lys	96.0	0.0	0		70.0	30.0	0.428571	NM_001100915	B4DZ49|Q8N804	Missense_Mutation	SNP	ENST00000304372.5	37	CCDS42179.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	C	13.27	2.187741	0.38609	4.81E-4	0.005121	ENSG00000168676	ENST00000304372	T	0.58940	0.3	5.86	4.92	0.64577	.	0.101032	0.43747	D	0.000539	T	0.37945	0.1022	N	0.24115	0.695	0.27940	N	0.937539	D	0.67145	0.996	P	0.48063	0.565	T	0.31052	-0.9957	10	0.32370	T	0.25	-21.685	9.3289	0.38010	0.0:0.8369:0.0:0.1631	.	675	Q17RG1	KCD19_HUMAN	K	675	ENSP00000305702:E675K	ENSP00000305702:E675K	E	-	1	0	KCTD19	65885143	0.747000	0.28283	0.940000	0.37924	0.914000	0.54420	1.272000	0.33109	1.493000	0.48517	-0.244000	0.11960	GAG	C|0.997;T|0.003	0.003	strong		0.617	KCTD19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000422061.1	XM_085367	
ADAMTS18	170692	hgsc.bcm.edu	37	16	77327042	77327042	+	Silent	SNP	C	C	T	rs61754842	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:77327042C>T	ENST00000282849.5	-	20	3538	c.3120G>A	c.(3118-3120)caG>caA	p.Q1040Q	RP11-538I12.3_ENST00000561672.1_RNA	NM_199355.2	NP_955387.1	Q8TE60	ATS18_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 18	1040	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				eye development (GO:0001654)|negative regulation of platelet aggregation (GO:0090331)	proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(9)|large_intestine(26)|lung(44)|ovary(2)|pancreas(1)|prostate(1)|skin(19)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	118						CACAGCCCTCCTGCAGCTCAG	0.607													C|||	10	0.00199681	0.0008	0.0014	5008	,	,		15978	0.0		0.005	False		,,,				2504	0.0031				p.Q1040Q		Atlas-SNP	.											ADAMTS18,breast,lymphoid_neoplasm,-2,1	ADAMTS18	270	1	0			c.G3120A						PASS	.	C		8,4388	14.3+/-33.2	0,8,2190	86.0	81.0	82.0		3120	3.0	1.0	16	dbSNP_129	82	65,8535	40.8+/-97.7	1,63,4236	no	coding-synonymous	ADAMTS18	NM_199355.2		1,71,6426	TT,TC,CC		0.7558,0.182,0.5617		1040/1222	77327042	73,12923	2198	4300	6498	SO:0001819	synonymous_variant	170692	exon20			GCCCTCCTGCAGC	AJ311903	CCDS10926.1	16q23	2008-07-29	2005-08-19		ENSG00000140873	ENSG00000140873		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	17110	protein-coding gene	gene with protein product		607512	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 18"""	ADAMTS21		11867212, 17546048	Standard	NM_199355		Approved		uc002ffc.4	Q8TE60	OTTHUMG00000137619	ENST00000282849.5:c.3120G>A	16.37:g.77327042C>T		59.0	0.0	0		61.0	39.0	0.639344	NM_199355	Q6P4R5|Q6ZWJ9	Silent	SNP	ENST00000282849.5	37	CCDS10926.1																																																																																			C|0.995;T|0.005	0.005	strong		0.607	ADAMTS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269037.1		
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57076080	57076080	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57076080C>T	ENST00000532437.1	-	5	4416	c.4105G>A	c.(4105-4107)Ggg>Agg	p.G1369R	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.G1369R|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1369	Acidic.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				TGGCTCACCCCGCCCACCCCA	0.667																																					p.G1369R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4105A						PASS	.						59.0	69.0	65.0					11																	57076080		2201	4296	6497	SO:0001583	missense	85456	exon6			TCACCCCGCCCAC	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4105G>A	11.37:g.57076080C>T	ENSP00000437271:p.Gly1369Arg	45.0	0.0	0		64.0	26.0	0.40625	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	.	.	.	.	.	.	.	.	.	.	C	8.708	0.911309	0.17833	.	.	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.28666	1.6;1.6	4.78	1.35	0.21983	.	1.049680	0.07553	N	0.915820	T	0.12944	0.0314	N	0.03608	-0.345	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.31916	-0.9926	10	0.20046	T	0.44	-1.079	6.365	0.21449	0.0:0.4339:0.4537:0.1124	.	1369	Q9C0C2	TB182_HUMAN	R	1369	ENSP00000350990:G1369R;ENSP00000437271:G1369R	ENSP00000350990:G1369R	G	-	1	0	TNKS1BP1	56832656	0.000000	0.05858	0.000000	0.03702	0.013000	0.08279	0.405000	0.21015	0.512000	0.28257	0.462000	0.41574	GGG	.	.	none		0.667	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
DOC2A	8448	hgsc.bcm.edu	37	16	30017536	30017536	+	Missense_Mutation	SNP	G	G	C	rs202062683	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30017536G>C	ENST00000350119.4	-	11	1364	c.1174C>G	c.(1174-1176)Cct>Gct	p.P392A	DOC2A_ENST00000564944.1_Missense_Mutation_p.P392A|DOC2A_ENST00000564979.1_Missense_Mutation_p.P392A	NM_001282062.1|NM_001282063.1|NM_001282068.1|NM_003586.2	NP_001268991.1|NP_001268992.1|NP_001268997.1|NP_003577.2	Q14183	DOC2A_HUMAN	double C2-like domains, alpha	392	Interaction with UNC13D.				nervous system development (GO:0007399)|regulation of calcium ion-dependent exocytosis (GO:0017158)|synaptic transmission (GO:0007268)|synaptic vesicle exocytosis (GO:0016079)	cell junction (GO:0030054)|lysosome (GO:0005764)|membrane (GO:0016020)|neuron projection (GO:0043005)|synaptic vesicle (GO:0008021)	calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			central_nervous_system(1)|endometrium(1)|large_intestine(3)|lung(2)|ovary(2)	9						CCGGCCGCAGGGGGCAGCTCA	0.692													G|||	12	0.00239617	0.0023	0.0029	5008	,	,		15719	0.0		0.006	False		,,,				2504	0.001				p.P392A		Atlas-SNP	.											.	DOC2A	40	.	0			c.C1174G						PASS	.	G	ALA/PRO	3,4359		0,3,2178	9.0	9.0	9.0		1174	1.9	0.3	16		9	73,8487		0,73,4207	no	missense	DOC2A	NM_003586.2	27	0,76,6385	CC,CG,GG		0.8528,0.0688,0.5881	possibly-damaging	392/401	30017536	76,12846	2181	4280	6461	SO:0001583	missense	8448	exon11			CCGCAGGGGGCAG	D31897	CCDS10666.1	16p11.2	2014-07-02			ENSG00000149927	ENSG00000149927		"""Synaptotagmins"""	2985	protein-coding gene	gene with protein product		604567				7826360, 9736751	Standard	NM_003586		Approved		uc002dvn.3	Q14183	OTTHUMG00000132109	ENST00000350119.4:c.1174C>G	16.37:g.30017536G>C	ENSP00000340017:p.Pro392Ala	72.0	0.0	0		90.0	50.0	0.555556	NM_003586	B4DEJ2|H3BNH6|Q6P4G4|Q7Z5G0|Q8IVX0	Missense_Mutation	SNP	ENST00000350119.4	37	CCDS10666.1	.	.	.	.	.	.	.	.	.	.	G	0.003	-2.413386	0.00191	6.88E-4	0.008528	ENSG00000149927	ENST00000350119	T	0.61040	0.14	5.09	1.85	0.25348	.	0.263699	0.27048	N	0.021185	T	0.31765	0.0807	L	0.44542	1.39	0.25635	N	0.986269	P	0.35745	0.518	B	0.30316	0.114	T	0.34153	-0.9840	10	0.02654	T	1	.	12.9913	0.58620	0.0:0.4802:0.5198:0.0	.	392	Q14183	DOC2A_HUMAN	A	392	ENSP00000340017:P392A	ENSP00000340017:P392A	P	-	1	0	DOC2A	29925037	0.913000	0.31002	0.274000	0.24659	0.075000	0.17131	-0.678000	0.05209	0.214000	0.20742	0.491000	0.48974	CCT	.	.	weak		0.692	DOC2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255148.2	NM_003586	
KCNQ3	3786	hgsc.bcm.edu	37	8	133153451	133153451	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:133153451C>T	ENST00000388996.4	-	10	1810	c.1390G>A	c.(1390-1392)Gtt>Att	p.V464I	KCNQ3_ENST00000519445.1_Missense_Mutation_p.V464I|KCNQ3_ENST00000521134.1_Missense_Mutation_p.V344I	NM_004519.3	NP_004510.1	O43525	KCNQ3_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 3	464					axon guidance (GO:0007411)|membrane hyperpolarization (GO:0060081)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	axon initial segment (GO:0043194)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)|voltage-gated potassium channel activity (GO:0005249)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(21)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	70	Esophageal squamous(12;0.00507)|Ovarian(258;0.00579)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.000311)		Amitriptyline(DB00321)|Diclofenac(DB00586)|Ezogabine(DB04953)|Meclofenamic acid(DB00939)	TTTAAGCCAACAGGCTTTGGT	0.448																																					p.V464I		Atlas-SNP	.											.	KCNQ3	164	.	0			c.G1390A						PASS	.						135.0	140.0	138.0					8																	133153451		2203	4300	6503	SO:0001583	missense	3786	exon10			AGCCAACAGGCTT	AB208890	CCDS34943.1, CCDS56554.1	8q24	2012-07-05			ENSG00000184156	ENSG00000184156		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6297	protein-coding gene	gene with protein product		602232		EBN2		9425900, 16382104	Standard	NM_004519		Approved	Kv7.3	uc003ytj.3	O43525	OTTHUMG00000137472	ENST00000388996.4:c.1390G>A	8.37:g.133153451C>T	ENSP00000373648:p.Val464Ile	97.0	0.0	0		124.0	41.0	0.330645	NM_004519	A2VCT8|B4DJY4|E7EQ89	Missense_Mutation	SNP	ENST00000388996.4	37	CCDS34943.1	.	.	.	.	.	.	.	.	.	.	C	18.21	3.573918	0.65765	.	.	ENSG00000184156	ENST00000388996;ENST00000521134;ENST00000519445;ENST00000542679;ENST00000423790	D;D;D	0.99594	-6.25;-6.25;-6.25	5.63	5.63	0.86233	Potassium channel, voltage dependent, KCNQ, C-terminal (1);	0.189166	0.45606	D	0.000344	D	0.97102	0.9053	N	0.03608	-0.345	0.32328	N	0.561483	P;P	0.42123	0.771;0.771	B;B	0.39971	0.315;0.315	D	0.98773	1.0729	10	0.41790	T	0.15	-9.8868	13.6375	0.62230	0.1545:0.8455:0.0:0.0	.	464;464	E7ET42;O43525	.;KCNQ3_HUMAN	I	464;344;464;453;343	ENSP00000373648:V464I;ENSP00000429799:V344I;ENSP00000428790:V464I	ENSP00000373648:V464I	V	-	1	0	KCNQ3	133222633	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.046000	0.49846	2.652000	0.90054	0.655000	0.94253	GTT	.	.	none		0.448	KCNQ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268621.2	NM_004519	
SEMA6D	80031	hgsc.bcm.edu	37	15	48056050	48056050	+	Missense_Mutation	SNP	G	G	A	rs151039709	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:48056050G>A	ENST00000316364.5	+	10	1190	c.751G>A	c.(751-753)Gtg>Atg	p.V251M	SEMA6D_ENST00000355997.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000537942.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000558014.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000389433.2_Missense_Mutation_p.V251M|SEMA6D_ENST00000389428.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000558816.1_Missense_Mutation_p.V251M|SEMA6D_ENST00000354744.4_Missense_Mutation_p.V251M|SEMA6D_ENST00000389425.3_Missense_Mutation_p.V251M|SEMA6D_ENST00000358066.4_Missense_Mutation_p.V251M|SEMA6D_ENST00000536845.2_Missense_Mutation_p.V251M|SEMA6D_ENST00000389432.2_Missense_Mutation_p.V251M	NM_153618.1	NP_705871.1	Q8NFY4	SEM6D_HUMAN	sema domain, transmembrane domain (TM), and cytoplasmic domain, (semaphorin) 6D	251	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|negative regulation of smooth muscle cell migration (GO:0014912)|positive regulation of smooth muscle cell migration (GO:0014911)|ventricular system development (GO:0021591)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			biliary_tract(1)|breast(4)|endometrium(4)|kidney(5)|large_intestine(10)|lung(42)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	77		all_lung(180;0.000635)|Myeloproliferative disorder(241;0.116)|Melanoma(134;0.18)		all cancers(107;1.2e-11)|GBM - Glioblastoma multiforme(94;1.2e-06)		TGGGCAGGCTGTGTATTCCCG	0.473																																					p.V251M		Atlas-SNP	.											.	SEMA6D	322	.	0			c.G751A						PASS	.	G	MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL,MET/VAL	2,4394	4.2+/-10.8	0,2,2196	132.0	131.0	131.0		751,751,751,751,751,751,751	4.9	0.9	15	dbSNP_134	131	1,8593	1.2+/-3.3	0,1,4296	yes	missense,missense,missense,missense,missense,missense,missense	SEMA6D	NM_001198999.1,NM_020858.1,NM_024966.2,NM_153616.1,NM_153617.1,NM_153618.1,NM_153619.1	21,21,21,21,21,21,21	0,3,6492	AA,AG,GG		0.0116,0.0455,0.0231	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	251/1012,251/1012,251/477,251/999,251/1018,251/1074,251/598	48056050	3,12987	2198	4297	6495	SO:0001583	missense	80031	exon10			CAGGCTGTGTATT	AF389430	CCDS32224.1, CCDS32225.1, CCDS32226.1, CCDS32227.1, CCDS32228.1, CCDS32229.1	15q21.1	2006-09-18				ENSG00000137872		"""Semaphorins"""	16770	protein-coding gene	gene with protein product		609295				12110693, 14977921	Standard	NM_020858		Approved	KIAA1479, FLJ11598	uc001zvy.3	Q8NFY4		ENST00000316364.5:c.751G>A	15.37:g.48056050G>A	ENSP00000324857:p.Val251Met	133.0	0.0	0		131.0	62.0	0.473282	NM_153617	A6NF10|A6NM95|A6NNK1|A7E2A0|Q8NFY3|Q8NFY5|Q8NFY6|Q8NFY7|Q9P249	Missense_Mutation	SNP	ENST00000316364.5	37	CCDS32225.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.513526	0.85389	4.55E-4	1.16E-4	ENSG00000137872	ENST00000537942;ENST00000536845;ENST00000316364;ENST00000389433;ENST00000389432;ENST00000354744;ENST00000358066;ENST00000389428;ENST00000355997;ENST00000389425	T;T;T;T;T;T;T;T;T;T	0.12672	2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66;2.66	5.87	4.93	0.64822	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.105633	0.64402	D	0.000005	T	0.37489	0.1005	M	0.71581	2.175	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.999;1.0;0.98;1.0	D;D;D;P;D	0.71870	0.975;0.952;0.975;0.821;0.975	T	0.25641	-1.0126	10	0.66056	D	0.02	.	16.8154	0.85733	0.0:0.1288:0.8712:0.0	.	251;251;251;251;251	Q8NFY4-3;A6NM95;Q8NFY4-4;Q8NFY4;Q8NFY4-2	.;.;.;SEM6D_HUMAN;.	M	251	ENSP00000442040:V251M;ENSP00000446152:V251M;ENSP00000324857:V251M;ENSP00000374084:V251M;ENSP00000374083:V251M;ENSP00000346786:V251M;ENSP00000350770:V251M;ENSP00000374079:V251M;ENSP00000348276:V251M;ENSP00000374076:V251M	ENSP00000324857:V251M	V	+	1	0	SEMA6D	45843342	1.000000	0.71417	0.918000	0.36340	0.881000	0.50899	6.757000	0.74924	1.452000	0.47756	0.655000	0.94253	GTG	G|1.000;A|0.000	0.000	strong		0.473	SEMA6D-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416868.1	NM_024966	
HEATR5B	54497	hgsc.bcm.edu	37	2	37289177	37289177	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:37289177G>T	ENST00000233099.5	-	11	1696	c.1601C>A	c.(1600-1602)gCt>gAt	p.A534D	HEATR5B_ENST00000354531.2_Missense_Mutation_p.A534D	NM_019024.1	NP_061897.1	Q9P2D3	HTR5B_HUMAN	HEAT repeat containing 5B	534						extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)				breast(3)|cervix(3)|endometrium(3)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|pancreas(1)|prostate(1)|skin(10)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	77		all_hematologic(82;0.21)				AAGATCTTCAGCAATACTAAC	0.348																																					p.A534D		Atlas-SNP	.											.	HEATR5B	185	.	0			c.C1601A						PASS	.						96.0	99.0	98.0					2																	37289177		2203	4300	6503	SO:0001583	missense	54497	exon11			TCTTCAGCAATAC	AB037835	CCDS33181.1	2p22.2	2007-01-02			ENSG00000008869	ENSG00000008869			29273	protein-coding gene	gene with protein product						10718198	Standard	XM_005264379		Approved	KIAA1414, DKFZp686P15184	uc002rpp.1	Q9P2D3	OTTHUMG00000152158	ENST00000233099.5:c.1601C>A	2.37:g.37289177G>T	ENSP00000233099:p.Ala534Asp	52.0	0.0	0		40.0	11.0	0.275	NM_019024	B5MDU8|Q7Z3B2|Q9NVL7	Missense_Mutation	SNP	ENST00000233099.5	37	CCDS33181.1	.	.	.	.	.	.	.	.	.	.	G	32	5.127527	0.94473	.	.	ENSG00000008869	ENST00000233099;ENST00000354531;ENST00000424416	T;T	0.08458	3.09;3.09	5.7	5.7	0.88788	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.40767	0.1130	M	0.91300	3.195	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.49082	-0.8976	10	0.87932	D	0	-21.1412	19.8411	0.96685	0.0:0.0:1.0:0.0	.	534	Q9P2D3	HTR5B_HUMAN	D	534	ENSP00000233099:A534D;ENSP00000346531:A534D	ENSP00000233099:A534D	A	-	2	0	HEATR5B	37142681	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.624000	0.98398	2.683000	0.91414	0.655000	0.94253	GCT	.	.	none		0.348	HEATR5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325492.1	NM_019024	
SLC17A1	6568	hgsc.bcm.edu	37	6	25820126	25820126	+	Missense_Mutation	SNP	C	C	A	rs149708935		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:25820126C>A	ENST00000244527.4	-	4	340	c.225G>T	c.(223-225)tgG>tgT	p.W75C	SLC17A1_ENST00000476801.1_Missense_Mutation_p.W75C|SLC17A1_ENST00000468082.1_Missense_Mutation_p.W75C|SLC17A1_ENST00000427328.1_Missense_Mutation_p.W75C	NM_005074.3	NP_005065.2	Q14916	NPT1_HUMAN	solute carrier family 17 (organic anion transporter), member 1	75					ion transport (GO:0006811)|phosphate ion transport (GO:0006817)|sodium ion transport (GO:0006814)|sodium-dependent phosphate transport (GO:0044341)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	sodium-dependent phosphate transmembrane transporter activity (GO:0015321)|symporter activity (GO:0015293)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(14)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	36						TATCTGGGCTCCAATTATACA	0.408													C|||	1	0.000199681	0.0	0.0	5008	,	,		19051	0.0		0.001	False		,,,				2504	0.0				p.W75C		Atlas-SNP	.											.	SLC17A1	71	.	0			c.G225T						PASS	.	C	CYS/TRP	1,4403	2.1+/-5.4	0,1,2201	63.0	68.0	66.0		225	4.3	1.0	6	dbSNP_134	66	9,8591	7.1+/-27.0	0,9,4291	yes	missense	SLC17A1	NM_005074.3	215	0,10,6492	AA,AC,CC		0.1047,0.0227,0.0769	probably-damaging	75/468	25820126	10,12994	2202	4300	6502	SO:0001583	missense	6568	exon4			TGGGCTCCAATTA		CCDS4565.1	6p22.2	2013-07-18	2013-07-18		ENSG00000124568	ENSG00000124568		"""Solute carriers"""	10929	protein-coding gene	gene with protein product		182308	"""solute carrier family 17 (sodium phosphate), member 1"""	NPT1		8288239	Standard	NM_005074		Approved	NAPI-1	uc003nfh.4	Q14916	OTTHUMG00000016297	ENST00000244527.4:c.225G>T	6.37:g.25820126C>A	ENSP00000244527:p.Trp75Cys	53.0	0.0	0		68.0	27.0	0.397059	NM_005074	A8K418|O60761|Q13783|Q3MIP5|Q5MJP8|Q5TB83|Q96KL8	Missense_Mutation	SNP	ENST00000244527.4	37	CCDS4565.1	.	.	.	.	.	.	.	.	.	.	C	12.63	1.994860	0.35226	2.27E-4	0.001047	ENSG00000124568	ENST00000244527;ENST00000427328;ENST00000476801;ENST00000468082	T;T;T;T	0.59083	0.29;0.29;0.29;0.29	4.33	4.33	0.51752	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.43110	D	0.000602	T	0.77350	0.4117	M	0.93241	3.395	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	T	0.82697	-0.0329	10	0.87932	D	0	.	12.53	0.56109	0.0:1.0:0.0:0.0	.	75;75	Q14916-2;Q14916	.;NPT1_HUMAN	C	75	ENSP00000244527:W75C;ENSP00000410549:W75C;ENSP00000420614:W75C;ENSP00000420546:W75C	ENSP00000244527:W75C	W	-	3	0	SLC17A1	25928105	1.000000	0.71417	1.000000	0.80357	0.280000	0.26924	4.467000	0.60155	2.423000	0.82170	0.650000	0.86243	TGG	C|1.000;A|0.000	0.000	weak		0.408	SLC17A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043647.2		
KIFC3	3801	hgsc.bcm.edu	37	16	57794643	57794643	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:57794643C>T	ENST00000379655.4	-	16	2484	c.2227G>A	c.(2227-2229)Gta>Ata	p.V743I	KIFC3_ENST00000421376.2_Missense_Mutation_p.V604I|KIFC3_ENST00000562903.1_Missense_Mutation_p.V604I|KIFC3_ENST00000543930.1_Missense_Mutation_p.V601I|KIFC3_ENST00000445690.2_Missense_Mutation_p.V743I|KIFC3_ENST00000541240.1_Missense_Mutation_p.V765I|KIFC3_ENST00000539578.1_Missense_Mutation_p.V685I|KIFC3_ENST00000465878.2_Missense_Mutation_p.V604I|KIFC3_ENST00000540079.2_Missense_Mutation_p.V641I	NM_005550.3	NP_005541.3	Q9BVG8	KIFC3_HUMAN	kinesin family member C3	743	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|epithelial cell-cell adhesion (GO:0090136)|Golgi organization (GO:0007030)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|visual perception (GO:0007601)|zonula adherens maintenance (GO:0045218)	centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|zonula adherens (GO:0005915)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(2)|central_nervous_system(3)|endometrium(4)|large_intestine(3)|lung(6)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23		all_neural(199;0.224)				CTCACCTGTACCACCATGAGG	0.622																																					p.V743I		Atlas-SNP	.											.	KIFC3	55	.	0			c.G2227A						PASS	.						49.0	52.0	51.0					16																	57794643		2198	4299	6497	SO:0001583	missense	3801	exon16			CCTGTACCACCAT	BC001211	CCDS10789.2, CCDS45493.1, CCDS45494.1	16q13-q21	2008-02-05			ENSG00000140859	ENSG00000140859		"""Kinesins"""	6326	protein-coding gene	gene with protein product		604535				9782090	Standard	NM_001130099		Approved		uc002emp.3	Q9BVG8	OTTHUMG00000133455	ENST00000379655.4:c.2227G>A	16.37:g.57794643C>T	ENSP00000368976:p.Val743Ile	87.0	0.0	0		87.0	4.0	0.045977	NM_001130100	A8K6S2|B7Z484|O75299|Q49A29|Q49AQ0|Q59G19|Q8IUT3|Q96HW6	Missense_Mutation	SNP	ENST00000379655.4	37	CCDS10789.2	.	.	.	.	.	.	.	.	.	.	C	17.13	3.311199	0.60414	.	.	ENSG00000140859	ENST00000379655;ENST00000445690;ENST00000421376;ENST00000541240;ENST00000540079;ENST00000543930;ENST00000539578	T;T;T;T;T;T;T	0.77098	-1.07;-1.07;-1.07;-1.07;-1.07;-1.07;-1.07	4.99	4.99	0.66335	Kinesin, motor domain (3);	0.061337	0.64402	D	0.000004	D	0.83321	0.5229	M	0.69823	2.125	0.54753	D	0.999987	P;P;P;P;P;P	0.42692	0.571;0.747;0.787;0.554;0.571;0.52	B;B;P;B;B;B	0.52386	0.428;0.411;0.697;0.377;0.312;0.346	D	0.85208	0.1019	10	0.72032	D	0.01	.	13.0651	0.59028	0.0:0.8385:0.1614:0.0	.	765;685;601;641;743;604	B7Z484;F5H4I9;B7Z896;F5H3M2;Q9BVG8;A8K6S2	.;.;.;.;KIFC3_HUMAN;.	I	743;743;604;765;641;601;685	ENSP00000368976:V743I;ENSP00000401696:V743I;ENSP00000396399:V604I;ENSP00000442008:V765I;ENSP00000438805:V641I;ENSP00000444012:V601I;ENSP00000444884:V685I	ENSP00000368976:V743I	V	-	1	0	KIFC3	56352144	1.000000	0.71417	1.000000	0.80357	0.463000	0.32649	4.881000	0.63114	2.341000	0.79615	0.205000	0.17691	GTA	.	.	none		0.622	KIFC3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257329.2	NM_005550	
HOXC6	3223	hgsc.bcm.edu	37	12	54422479	54422479	+	Silent	SNP	G	G	A	rs145731630	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:54422479G>A	ENST00000243108.4	+	1	338	c.174G>A	c.(172-174)caG>caA	p.Q58Q	HOXC4_ENST00000303406.4_Intron|HOXC6_ENST00000394331.3_5'UTR|RP11-834C11.14_ENST00000512206.1_RNA|RP11-834C11.12_ENST00000513209.1_Intron	NM_004503.3	NP_004494.1	P09630	HXC6_HUMAN	homeobox C6	58					anterior/posterior pattern specification (GO:0009952)|embryonic skeletal system development (GO:0048706)|multicellular organismal development (GO:0007275)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						ATTCGCCACAGGAGAATGTCG	0.512													G|||	6	0.00119808	0.0	0.0	5008	,	,		17413	0.0		0.002	False		,,,				2504	0.0041				p.Q58Q		Atlas-SNP	.											.	HOXC6	30	.	0			c.G174A						PASS	.	G	,,	7,4399	12.9+/-30.5	0,7,2196	87.0	81.0	83.0		174,,	2.5	1.0	12	dbSNP_134	83	46,8554	30.1+/-81.4	0,46,4254	no	coding-synonymous,intron,utr-5	HOXC4,HOXC6	NM_004503.3,NM_014620.4,NM_153693.3	,,	0,53,6450	AA,AG,GG		0.5349,0.1589,0.4075	,,	58/236,,	54422479	53,12953	2203	4300	6503	SO:0001819	synonymous_variant	3223	exon1			GCCACAGGAGAAT		CCDS8871.1, CCDS41792.1	12q13.13	2011-06-20	2005-12-22		ENSG00000197757	ENSG00000197757		"""Homeoboxes / ANTP class : HOXL subclass"""	5128	protein-coding gene	gene with protein product		142972	"""homeo box C6"""	HOX3C, HOX3		1973146, 1358459	Standard	NM_153693		Approved		uc001sev.3	P09630	OTTHUMG00000160027	ENST00000243108.4:c.174G>A	12.37:g.54422479G>A		97.0	0.0	0		112.0	58.0	0.517857	NM_004503	B2RBV2|Q6DK09	Silent	SNP	ENST00000243108.4	37	CCDS8871.1																																																																																			G|0.997;A|0.003	0.003	strong		0.512	HOXC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358943.2		
SWSAP1	126074	hgsc.bcm.edu	37	19	11486514	11486514	+	Missense_Mutation	SNP	A	A	G	rs317926	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:11486514A>G	ENST00000312423.2	+	2	571	c.512A>G	c.(511-513)gAt>gGt	p.D171G	CTD-2342J14.6_ENST00000590399.1_RNA	NM_175871.3	NP_787067.2	Q6NVH7	SWAP1_HUMAN	SWIM-type zinc finger 7 associated protein 1	171			D -> G (in dbSNP:rs317926).		ATP catabolic process (GO:0006200)|double-strand break repair via homologous recombination (GO:0000724)|protein stabilization (GO:0050821)	nucleus (GO:0005634)|Shu complex (GO:0097196)	ATPase activity (GO:0016887)|single-stranded DNA binding (GO:0003697)										CTGCAGCCAGATGCACCAGGT	0.642													A|||	69	0.013778	0.0507	0.0029	5008	,	,		16689	0.0		0.0	False		,,,				2504	0.0				p.D171G		Atlas-SNP	.											C19orf39,NS,carcinoma,0,1	.	.	1	0			c.A512G						PASS	.	A	GLY/ASP	196,4210	117.5+/-155.4	3,190,2010	42.0	40.0	41.0		512	0.5	0.0	19	dbSNP_79	41	3,8597	3.0+/-9.4	0,3,4297	no	missense	C19orf39	NM_175871.3	94	3,193,6307	GG,GA,AA		0.0349,4.4485,1.5301	possibly-damaging	171/230	11486514	199,12807	2203	4300	6503	SO:0001583	missense	126074	exon2			AGCCAGATGCACC	AK092438	CCDS12259.1	19p13.2	2011-11-24	2011-11-24	2011-11-24	ENSG00000173928	ENSG00000173928			26638	protein-coding gene	gene with protein product	"""zinc finger, SWIM-type containing 7 associated protein 1"", ""SWS1-associated protein 1"""	614536	"""chromosome 19 open reading frame 39"""	C19orf39		21965664	Standard	NM_175871		Approved	FLJ35119, ZSWIM7AP1, SWS1AP1	uc002mrg.1	Q6NVH7		ENST00000312423.2:c.512A>G	19.37:g.11486514A>G	ENSP00000310008:p.Asp171Gly	49.0	0.0	0		60.0	26.0	0.433333	NM_175871	Q8NAM1	Missense_Mutation	SNP	ENST00000312423.2	37	CCDS12259.1	19	0.0086996336996337	19	0.03861788617886179	0	0.0	0	0.0	0	0.0	A	9.198	1.027667	0.19512	0.044485	3.49E-4	ENSG00000173928	ENST00000312423	T	0.48522	0.81	5.15	0.528	0.17089	.	1.321610	0.04957	N	0.461333	T	0.13072	0.0317	L	0.60455	1.87	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.16778	-1.0391	10	0.48119	T	0.1	1.0742	1.487	0.02449	0.5539:0.1458:0.16:0.1402	rs317926;rs318715;rs317926	171	Q6NVH7	CS039_HUMAN	G	171	ENSP00000310008:D171G	ENSP00000310008:D171G	D	+	2	0	C19orf39	11347514	0.000000	0.05858	0.000000	0.03702	0.315000	0.28087	0.288000	0.18939	-0.287000	0.09064	0.533000	0.62120	GAT	A|0.984;G|0.016	0.016	strong		0.642	SWSAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458789.1	NM_175871	
BCKDHA	593	hgsc.bcm.edu	37	19	41920030	41920030	+	Missense_Mutation	SNP	C	C	T	rs34442879	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:41920030C>T	ENST00000269980.2	+	4	820	c.452C>T	c.(451-453)aCg>aTg	p.T151M	BCKDHA_ENST00000595085.1_Missense_Mutation_p.T185M|BCKDHA_ENST00000457836.2_Missense_Mutation_p.T129M|CTC-435M10.3_ENST00000540732.1_Missense_Mutation_p.T185M	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide	151			T -> M (in dbSNP:rs34442879).		branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						CTGGACAACACGGACCTGGTG	0.602													C|||	21	0.00419329	0.0	0.0058	5008	,	,		18861	0.001		0.0139	False		,,,				2504	0.002				p.T151M		Atlas-SNP	.											.	BCKDHA	36	.	0			c.C452T	GRCh37	CM021497	BCKDHA	M	rs34442879	PASS	.	C	MET/THR,MET/THR	7,4399	14.3+/-33.2	0,7,2196	73.0	57.0	63.0		452,452	4.7	0.9	19	dbSNP_126	63	91,8509	50.6+/-110.7	2,87,4211	yes	missense,missense	BCKDHA	NM_000709.3,NM_001164783.1	81,81	2,94,6407	TT,TC,CC		1.0581,0.1589,0.7535	possibly-damaging,possibly-damaging	151/446,151/445	41920030	98,12908	2203	4300	6503	SO:0001583	missense	593	exon4			ACAACACGGACCT	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128	ENST00000269980.2:c.452C>T	19.37:g.41920030C>T	ENSP00000269980:p.Thr151Met	86.0	0.0	0		107.0	60.0	0.560748	NM_000709	B4DP47|E7EW46|Q16034|Q16472	Missense_Mutation	SNP	ENST00000269980.2	37	CCDS12581.1	12|12	0.005494505494505495|0.005494505494505495	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	20.7|20.7	4.042043|4.042043	0.75732|0.75732	0.001589|0.001589	0.010581|0.010581	ENSG00000248098|ENSG00000255730;ENSG00000248098;ENSG00000248098;ENSG00000248098;ENSG00000248098	ENST00000541315|ENST00000540732;ENST00000269980;ENST00000542943;ENST00000457836;ENST00000378196	.|D;D;D;D	.|0.96011	.|-3.88;-3.88;-3.88;-3.88	4.66|4.66	4.66|4.66	0.58398|0.58398	.|Dehydrogenase, E1 component (1);	.|0.167160	.|0.51477	.|D	.|0.000089	D|D	0.94961|0.94961	0.8370|0.8370	L|L	0.57536|0.57536	1.79|1.79	0.40759|0.40759	D|D	0.98298|0.98298	.|D;D;D;P	.|0.54964	.|0.969;0.962;0.963;0.953	.|P;P;P;P	.|0.56788	.|0.806;0.622;0.622;0.488	D|D	0.94832|0.94832	0.7997|0.7997	5|10	.|0.62326	.|D	.|0.03	-23.707|-23.707	16.8305|16.8305	0.85943|0.85943	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34442879|rs34442879	.|129;151;151;185	.|B4DP47;Q59EI3;P12694;F5H5P2	.|.;.;ODBA_HUMAN;.	W|M	87|185;151;122;129;151	.|ENSP00000443246:T185M;ENSP00000269980:T151M;ENSP00000440345:T122M;ENSP00000416000:T129M	.|ENSP00000269980:T151M	R|T	+|+	1|2	2|0	BCKDHA|BCKDHA;CTC-435M10.3	46611870|46611870	0.488000|0.488000	0.25996|0.25996	0.874000|0.874000	0.34290|0.34290	0.931000|0.931000	0.56810|0.56810	1.755000|1.755000	0.38379|0.38379	2.578000|2.578000	0.87016|0.87016	0.563000|0.563000	0.77884|0.77884	CGG|ACG	C|0.993;T|0.007	0.007	strong		0.602	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57070170	57070170	+	Silent	SNP	C	C	T	rs34905018	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57070170C>T	ENST00000532437.1	-	6	4757	c.4446G>A	c.(4444-4446)ttG>ttA	p.L1482L	TNKS1BP1_ENST00000358252.3_Silent_p.L1482L			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1482	Acidic.|Tankyrase-binding.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CTTCCTCCTCCAACAGGCCCC	0.706													c|||	47	0.00938498	0.0015	0.0288	5008	,	,		13982	0.0		0.0229	False		,,,				2504	0.002				p.L1482L		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4446A						PASS	.			23,4377		0,23,2177	14.0	15.0	14.0		4446	-2.7	0.0	11	dbSNP_126	14	196,8390		2,192,4099	no	coding-synonymous	TNKS1BP1	NM_033396.2		2,215,6276	TT,TC,CC		2.2828,0.5227,1.6864		1482/1730	57070170	219,12767	2200	4293	6493	SO:0001819	synonymous_variant	85456	exon7			CTCCTCCAACAGG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4446G>A	11.37:g.57070170C>T		39.0	0.0	0		52.0	29.0	0.557692	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.987;T|0.013	0.013	strong		0.706	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
MAGEA6	4105	hgsc.bcm.edu	37	X	151870117	151870117	+	Silent	SNP	T	T	C	rs369345489		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:151870117T>C	ENST00000329342.5	+	3	1032	c.807T>C	c.(805-807)taT>taC	p.Y269Y		NM_005363.2	NP_005354.1	P43360	MAGA6_HUMAN	melanoma antigen family A, 6	269	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.									breast(1)|endometrium(3)|large_intestine(3)|lung(16)|prostate(3)|skin(1)|urinary_tract(1)	28	Acute lymphoblastic leukemia(192;6.56e-05)					CTGCATGCTATGAGTTCCTGT	0.527																																					p.Y269Y		Atlas-SNP	.											.	MAGEA6	53	.	0			c.T807C						PASS	.	T	,	0,3834		0,0,0,1632,570	139.0	136.0	137.0		807,807	-1.8	0.0	X		137	2,6726		0,1,1,2427,1871	no	coding-synonymous,coding-synonymous	MAGEA6	NM_005363.2,NM_175868.1	,	0,1,1,4059,2441	CC,CT,C,TT,T		0.0297,0.0,0.0189	,	269/315,269/315	151870117	2,10560	2202	4300	6502	SO:0001819	synonymous_variant	4105	exon3			ATGCTATGAGTTC		CCDS76050.1	Xq28	2009-03-13			ENSG00000197172	ENSG00000197172			6804	protein-coding gene	gene with protein product	"""MAGE-6 antigen"", ""melanoma-associated antigen 6"", ""melanoma antigen family A 6"", ""cancer/testis antigen family 1, member 6"""	300176		MAGE6		8575766	Standard	NM_005363		Approved	CT1.6	uc004ffq.1	P43360	OTTHUMG00000022642	ENST00000329342.5:c.807T>C	X.37:g.151870117T>C		119.0	0.0	0		92.0	91.0	0.98913	NM_005363	A8IF93|Q6NW44	Silent	SNP	ENST00000329342.5	37	CCDS14708.1																																																																																			.	.	weak		0.527	MAGEA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058747.2	NM_005363	
DUSP4	1846	hgsc.bcm.edu	37	8	29197685	29197685	+	Missense_Mutation	SNP	G	G	A	rs371579846		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:29197685G>A	ENST00000240100.2	-	2	898	c.509C>T	c.(508-510)cCg>cTg	p.P170L	DUSP4_ENST00000240101.2_Missense_Mutation_p.P79L	NM_001394.6	NP_001385.1	Q13115	DUS4_HUMAN	dual specificity phosphatase 4	170					endoderm formation (GO:0001706)|innate immune response (GO:0045087)|MAPK cascade (GO:0000165)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neurotrophin TRK receptor signaling pathway (GO:0048011)|protein dephosphorylation (GO:0006470)|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)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	MAP kinase tyrosine/serine/threonine phosphatase activity (GO:0017017)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)|protein tyrosine/threonine phosphatase activity (GO:0008330)			endometrium(1)|large_intestine(1)|lung(4)	6				KIRC - Kidney renal clear cell carcinoma(542;0.094)|Kidney(114;0.113)		GGGGGGAACCGGGGGTGGGAT	0.602											OREG0018686	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P170L		Atlas-SNP	.											.	DUSP4	58	.	0			c.C509T						PASS	.	G	LEU/PRO,LEU/PRO	2,4404		0,2,2201	17.0	22.0	21.0		509,236	4.1	0.0	8		21	0,8600		0,0,4300	no	missense,missense	DUSP4	NM_001394.6,NM_057158.3	98,98	0,2,6501	AA,AG,GG		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging	170/395,79/304	29197685	2,13004	2203	4300	6503	SO:0001583	missense	1846	exon2			GGAACCGGGGGTG	U21108	CCDS6072.1, CCDS6073.1	8p12-p11	2011-06-09			ENSG00000120875	ENSG00000120875		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : MAP kinase phosphatases"""	3070	protein-coding gene	gene with protein product	"""VH1 homologous phosphatase 2"", ""MAP kinase phosphatase 2"""	602747				7535768, 9205128	Standard	NM_001394		Approved	HVH2, MKP-2, TYP	uc003xhm.3	Q13115	OTTHUMG00000133395	ENST00000240100.2:c.509C>T	8.37:g.29197685G>A	ENSP00000240100:p.Pro170Leu	47.0	0.0	0	807	52.0	20.0	0.384615	NM_001394	B2RBU5|D3DSU4|G5E930|Q13524	Missense_Mutation	SNP	ENST00000240100.2	37	CCDS6072.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.237221	0.39498	4.54E-4	0.0	ENSG00000120875	ENST00000240100;ENST00000240101	T;T	0.03413	4.17;3.94	5.01	4.13	0.48395	Rhodanese-like (1);	0.585786	0.16408	N	0.215753	T	0.03739	0.0106	L	0.42245	1.32	0.58432	D	0.999995	P;P	0.35774	0.458;0.519	B;B	0.24974	0.017;0.057	T	0.48433	-0.9036	10	0.59425	D	0.04	.	9.9081	0.41388	0.0962:0.0:0.9038:0.0	.	170;79	Q13115;G5E930	DUS4_HUMAN;.	L	170;79	ENSP00000240100:P170L;ENSP00000240101:P79L	ENSP00000240100:P170L	P	-	2	0	DUSP4	29253604	1.000000	0.71417	0.019000	0.16419	0.332000	0.28634	5.751000	0.68720	1.427000	0.47276	0.650000	0.86243	CCG	.	.	weak		0.602	DUSP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257249.1	NM_001394	
CHD3	1107	hgsc.bcm.edu	37	17	7807904	7807904	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:7807904G>A	ENST00000330494.7	+	25	4189	c.4039G>A	c.(4039-4041)Gtt>Att	p.V1347I	SCARNA21_ENST00000517026.1_RNA|CHD3_ENST00000358181.4_Missense_Mutation_p.V1347I|CHD3_ENST00000380358.4_Missense_Mutation_p.V1406I	NM_001005273.2	NP_001005273.1	Q12873	CHD3_HUMAN	chromodomain helicase DNA binding protein 3	1347					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)				TCGCAAGCAAGTTAACTACAA	0.547																																					p.V1406I		Atlas-SNP	.											.	CHD3	169	.	0			c.G4216A						PASS	.						98.0	82.0	87.0					17																	7807904		2203	4300	6503	SO:0001583	missense	1107	exon25			AAGCAAGTTAACT	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.4039G>A	17.37:g.7807904G>A	ENSP00000332628:p.Val1347Ile	95.0	0.0	0		102.0	55.0	0.539216	NM_001005271	D3DTQ9|E9PG89|Q9Y4I0	Missense_Mutation	SNP	ENST00000330494.7	37	CCDS32554.1	.	.	.	.	.	.	.	.	.	.	G	21.6	4.177879	0.78564	.	.	ENSG00000170004	ENST00000380358;ENST00000358181;ENST00000330494	D;D;D	0.91631	-2.88;-2.81;-2.82	4.9	4.9	0.64082	Domain of unknown function DUF1087 (1);	0.000000	0.41712	D	0.000823	D	0.95284	0.8470	M	0.64404	1.975	0.80722	D	1	D;D;D	0.69078	0.99;0.992;0.997	D;D;D	0.79108	0.98;0.989;0.992	D	0.95219	0.8332	10	0.54805	T	0.06	-19.8382	18.2591	0.90028	0.0:0.0:1.0:0.0	.	1347;1347;1406	Q12873-2;Q12873;E9PG89	.;CHD3_HUMAN;.	I	1406;1347;1347	ENSP00000369716:V1406I;ENSP00000350907:V1347I;ENSP00000332628:V1347I	ENSP00000332628:V1347I	V	+	1	0	CHD3	7748629	1.000000	0.71417	0.869000	0.34112	0.998000	0.95712	9.263000	0.95617	2.539000	0.85634	0.561000	0.74099	GTT	.	.	none		0.547	CHD3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000318050.1	NM_001005273	
POFUT2	23275	hgsc.bcm.edu	37	21	46707778	46707778	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46707778T>C	ENST00000349485.5	-	1	35	c.9A>G	c.(7-9)acA>acG	p.T3T	BX322557.10_ENST00000454115.2_RNA|POFUT2_ENST00000331343.7_Silent_p.T3T	NM_133635.4	NP_598368.2	Q9Y2G5	OFUT2_HUMAN	protein O-fucosyltransferase 2	3					fucose metabolic process (GO:0006004)|mesoderm formation (GO:0001707)|protein O-linked fucosylation (GO:0036066)|regulation of epithelial to mesenchymal transition (GO:0010717)|regulation of gene expression (GO:0010468)|regulation of secretion (GO:0051046)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)	peptide-O-fucosyltransferase activity (GO:0046922)			breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|liver(1)|lung(9)|skin(2)|upper_aerodigestive_tract(2)	20				Colorectal(79;0.243)		CGAAGCTGAGTGTCGCCATGG	0.706																																					p.T3T		Atlas-SNP	.											.	POFUT2	77	.	0			c.A9G						PASS	.						5.0	6.0	6.0					21																	46707778		2017	3977	5994	SO:0001819	synonymous_variant	23275	exon1			GCTGAGTGTCGCC	AJ203079	CCDS13719.1, CCDS13721.1	21q22.3	2013-03-06	2004-06-07	2004-06-09	ENSG00000186866	ENSG00000186866	2.4.1.221	"""Fucosyltransferases"""	14683	protein-coding gene	gene with protein product	"""peptide-O-fucosyltransferase"", ""GDP-fucose protein O-fucosyltransferase 2"""	610249	"""chromosome 21 open reading frame 80"""	C21orf80			Standard	NM_133635		Approved	KIAA0958, FUT13	uc002zhc.3	Q9Y2G5	OTTHUMG00000084874	ENST00000349485.5:c.9A>G	21.37:g.46707778T>C		11.0	0.0	0		20.0	12.0	0.6	NM_015227	Q6PJV1|Q7Z4N0|Q8WWU6|Q9BQS4|Q9BQS5|Q9UFY3	Silent	SNP	ENST00000349485.5	37	CCDS13719.1																																																																																			.	.	none		0.706	POFUT2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000192573.2	NM_015227	
P2RX3	5024	hgsc.bcm.edu	37	11	57114109	57114109	+	Missense_Mutation	SNP	G	G	A	rs34572680	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57114109G>A	ENST00000263314.2	+	2	245	c.211G>A	c.(211-213)Gcc>Acc	p.A71T		NM_002559.3	NP_002550.2	P56373	P2RX3_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 3	71					behavioral response to pain (GO:0048266)|cation transmembrane transport (GO:0098655)|neuromuscular synaptic transmission (GO:0007274)|neuronal action potential (GO:0019228)|peristalsis (GO:0030432)|positive regulation of calcium ion transport into cytosol (GO:0010524)|positive regulation of calcium-mediated signaling (GO:0050850)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of synaptic plasticity (GO:0048167)|response to ATP (GO:0033198)|response to carbohydrate (GO:0009743)|response to cold (GO:0009409)|response to heat (GO:0009408)|response to hypoxia (GO:0001666)|response to mechanical stimulus (GO:0009612)|sensory perception of taste (GO:0050909)|signal transduction (GO:0007165)|transport (GO:0006810)|urinary bladder smooth muscle contraction (GO:0014832)	dendritic spine (GO:0043197)|Golgi apparatus (GO:0005794)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuronal cell body (GO:0043025)|receptor complex (GO:0043235)|rough endoplasmic reticulum (GO:0005791)|terminal bouton (GO:0043195)	ATP binding (GO:0005524)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)			endometrium(4)|kidney(2)|large_intestine(4)|lung(15)|prostate(1)	26						CGGACTCTACGCCAACAGAGT	0.567													G|||	96	0.0191693	0.003	0.0375	5008	,	,		21427	0.004		0.0368	False		,,,				2504	0.0256				p.A71T		Atlas-SNP	.											.	P2RX3	55	.	0			c.G211A						PASS	.	G	THR/ALA	50,4352	50.2+/-85.5	0,50,2151	136.0	95.0	109.0		211	4.7	1.0	11	dbSNP_126	109	371,8221	123.1+/-182.0	8,355,3933	yes	missense	P2RX3	NM_002559.3	58	8,405,6084	AA,AG,GG		4.318,1.1358,3.24	possibly-damaging	71/398	57114109	421,12573	2201	4296	6497	SO:0001583	missense	5024	exon2			CTCTACGCCAACA	Y07683	CCDS7953.1	11q12	2012-01-17			ENSG00000109991	ENSG00000109991		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8534	protein-coding gene	gene with protein product		600843				9221902	Standard	NM_002559		Approved	P2X3	uc001nju.3	P56373	OTTHUMG00000167025	ENST00000263314.2:c.211G>A	11.37:g.57114109G>A	ENSP00000263314:p.Ala71Thr	92.0	0.0	0		83.0	39.0	0.46988	NM_002559	Q6DK37|Q9UQB6	Missense_Mutation	SNP	ENST00000263314.2	37	CCDS7953.1	48	0.02197802197802198	2	0.0040650406504065045	12	0.03314917127071823	4	0.006993006993006993	30	0.0395778364116095	G	13.93	2.384147	0.42308	0.011358	0.04318	ENSG00000109991	ENST00000439993;ENST00000263314	T	0.04156	3.69	4.66	4.66	0.58398	.	0.243784	0.41605	D	0.000844	T	0.00580	0.0019	N	0.04508	-0.205	0.29540	N	0.852188	P	0.45212	0.853	B	0.38106	0.265	T	0.34054	-0.9844	10	0.56958	D	0.05	-25.3858	8.6535	0.34049	0.1014:0.0:0.8986:0.0	rs34572680;rs58315342	71	P56373	P2RX3_HUMAN	T	71	ENSP00000263314:A71T	ENSP00000263314:A71T	A	+	1	0	P2RX3	56870685	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	3.662000	0.54510	2.408000	0.81797	0.561000	0.74099	GCC	G|0.971;A|0.029	0.029	strong		0.567	P2RX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392465.1	NM_002559	
NUMA1	4926	hgsc.bcm.edu	37	11	71725281	71725281	+	Silent	SNP	G	G	A	rs200298289		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:71725281G>A	ENST00000393695.3	-	15	3599	c.3268C>T	c.(3268-3270)Ctg>Ttg	p.L1090L	NUMA1_ENST00000351960.6_Intron|NUMA1_ENST00000358965.6_Silent_p.L1090L|RP11-849H4.4_ENST00000502284.1_RNA	NM_006185.2	NP_006176.2			nuclear mitotic apparatus protein 1											central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(12)|lung(20)|ovary(5)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(3)	65						TGTTCCTTCAGTTGCTTCACG	0.562			T	RARA	APL																																p.L1090L		Atlas-SNP	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.C3268T						PASS	.						127.0	139.0	135.0					11																	71725281		2200	4293	6493	SO:0001819	synonymous_variant	4926	exon15			CCTTCAGTTGCTT	Z11584	CCDS31633.1, CCDS66156.1	11q13	2008-02-05				ENSG00000137497			8059	protein-coding gene	gene with protein product		164009				8406455	Standard	NM_006185		Approved		uc001orl.1	Q14980		ENST00000393695.3:c.3268C>T	11.37:g.71725281G>A		167.0	0.0	0		209.0	104.0	0.497608	NM_006185		Silent	SNP	ENST00000393695.3	37	CCDS31633.1																																																																																			A|0.001;G|0.999	0.001	weak		0.562	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
ELF3	1999	hgsc.bcm.edu	37	1	201981774	201981774	+	Missense_Mutation	SNP	G	G	A	rs55729978	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:201981774G>A	ENST00000359651.3	+	4	3677	c.485G>A	c.(484-486)gGc>gAc	p.G162D	RP11-510N19.5_ENST00000504773.1_RNA|ELF3_ENST00000367283.3_Missense_Mutation_p.G162D|ELF3_ENST00000367284.5_Missense_Mutation_p.G162D|RP11-465N4.4_ENST00000419190.1_RNA					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	71.0	0.0	0		96.0	40.0	0.416667	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	
EVC	2121	hgsc.bcm.edu	37	4	5733236	5733236	+	Missense_Mutation	SNP	C	C	G	rs146729456	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:5733236C>G	ENST00000264956.6	+	4	653	c.469C>G	c.(469-471)Cct>Gct	p.P157A	EVC_ENST00000509451.1_Missense_Mutation_p.P157A|EVC_ENST00000382674.2_Missense_Mutation_p.P157A	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	157					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				AGAGGCCTCTCCTTCCAGCAG	0.612													C|||	15	0.00299521	0.0008	0.0014	5008	,	,		17399	0.0		0.0119	False		,,,				2504	0.001				p.P157A		Atlas-SNP	.											.	EVC	90	.	0			c.C469G						PASS	.	C	ALA/PRO	8,4398	14.3+/-33.2	0,8,2195	71.0	74.0	73.0		469	4.0	0.0	4	dbSNP_134	73	64,8536	39.3+/-95.6	1,62,4237	yes	missense	EVC	NM_153717.2	27	1,70,6432	GG,GC,CC		0.7442,0.1816,0.5536	probably-damaging	157/993	5733236	72,12934	2203	4300	6503	SO:0001583	missense	2121	exon4			GCCTCTCCTTCCA	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.469C>G	4.37:g.5733236C>G	ENSP00000264956:p.Pro157Ala	181.0	0.0	0		166.0	76.0	0.457831	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	37	CCDS3383.1	8	0.003663003663003663	1	0.0020325203252032522	0	0.0	0	0.0	7	0.009234828496042216	C	5.980	0.364833	0.11296	0.001816	0.007442	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.52295	0.67;0.67;0.75	3.95	3.95	0.45737	.	0.216956	0.40385	N	0.001110	T	0.29093	0.0723	L	0.50333	1.59	0.09310	N	1	B	0.25312	0.123	B	0.21360	0.034	T	0.12344	-1.0551	10	0.35671	T	0.21	.	7.1792	0.25763	0.2043:0.625:0.1707:0.0	.	157	P57679	EVC_HUMAN	A	157	ENSP00000264956:P157A;ENSP00000372120:P157A;ENSP00000426774:P157A	ENSP00000264956:P157A	P	+	1	0	EVC	5784137	0.115000	0.22152	0.019000	0.16419	0.172000	0.22775	1.547000	0.36190	2.206000	0.71126	0.561000	0.74099	CCT	C|0.995;G|0.005	0.005	strong		0.612	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
ZNF700	90592	hgsc.bcm.edu	37	19	12060627	12060627	+	Silent	SNP	A	A	G	rs78201704	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12060627A>G	ENST00000254321.5	+	4	1931	c.1788A>G	c.(1786-1788)caA>caG	p.Q596Q	CTD-2006C1.12_ENST00000586394.1_RNA|ZNF763_ENST00000538752.1_Intron|ZNF763_ENST00000591944.1_Intron|ZNF700_ENST00000482090.1_Silent_p.Q578Q|ZNF763_ENST00000590798.1_Intron	NM_001271848.1|NM_144566.1	NP_001258777.1|NP_653167.1	Q9H0M5	ZN700_HUMAN	zinc finger protein 700	596					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q596Q(1)	ZNF700/MAST1_ENST00000251472(2)	breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(9)|lung(13)|pancreas(1)|prostate(1)|urinary_tract(1)	33						AGTGTAAGCAATGTGGGAAAG	0.473													a|||	75	0.014976	0.0492	0.0058	5008	,	,		23157	0.0		0.006	False		,,,				2504	0.0				p.Q599Q		Atlas-SNP	.											ZNF700,NS,carcinoma,0,1	ZNF700	81	1	1	Substitution - coding silent(1)	pancreas(1)	c.A1797G						PASS	.	A		254,4152	145.4+/-180.2	8,238,1957	105.0	103.0	104.0		1788	-1.0	0.0	19	dbSNP_131	104	30,8570	21.0+/-64.5	0,30,4270	no	coding-synonymous	ZNF700	NM_144566.1		8,268,6227	GG,GA,AA		0.3488,5.7649,2.1836		596/743	12060627	284,12722	2203	4300	6503	SO:0001819	synonymous_variant	90592	exon4			TAAGCAATGTGGG	AL136732	CCDS32915.1, CCDS74289.1	19p13.2	2013-01-08			ENSG00000196757	ENSG00000196757		"""Zinc fingers, C2H2-type"", ""-"""	25292	protein-coding gene	gene with protein product							Standard	NM_144566		Approved	DKFZp434I1610	uc031rjk.1	Q9H0M5	OTTHUMG00000156421	ENST00000254321.5:c.1788A>G	19.37:g.12060627A>G		34.0	0.0	0		39.0	21.0	0.538462	NM_001271848	B9EGU4	Silent	SNP	ENST00000254321.5	37	CCDS32915.1																																																																																			A|0.979;G|0.021	0.021	strong		0.473	ZNF700-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344126.2	NM_144566	
SEC16A	9919	hgsc.bcm.edu	37	9	139371700	139371700	+	Missense_Mutation	SNP	G	G	A	rs371074782		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139371700G>A	ENST00000313050.7	-	1	441	c.368C>T	c.(367-369)cCg>cTg	p.P123L	SEC16A_ENST00000290037.6_5'Flank|SEC16A_ENST00000431893.2_5'Flank|SEC16A_ENST00000371706.3_5'Flank	NM_014866.1	NP_055681.1	O15027	SC16A_HUMAN	SEC16 homolog A (S. cerevisiae)	0					COPII vesicle coating (GO:0048208)|endoplasmic reticulum organization (GO:0007029)|protein transport (GO:0015031)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)				breast(1)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(15)|lung(14)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Myeloproliferative disorder(178;0.0511)		Epithelial(140;2.9e-06)|OV - Ovarian serous cystadenocarcinoma(145;5.88e-06)		ACCAGAAAACGGACTGGCATG	0.577																																					p.P123L		Atlas-SNP	.											.	SEC16A	249	.	0			c.C368T						PASS	.	G	LEU/PRO	0,4068		0,0,2034	82.0	86.0	85.0		368	-7.8	0.0	9		85	1,8361		0,1,4180	no	missense	SEC16A	NM_014866.1	98	0,1,6214	AA,AG,GG		0.012,0.0,0.0080	benign	123/2358	139371700	1,12429	2034	4181	6215	SO:0001583	missense	9919	exon3			GAAAACGGACTGG	AK074565	CCDS55351.1, CCDS75936.1	9q34.3	2007-06-20	2007-06-20	2007-06-20	ENSG00000148396	ENSG00000148396			29006	protein-coding gene	gene with protein product		612854	"""KIAA0310"""	KIAA0310		9205841	Standard	NM_014866		Approved	p250	uc004chx.3	O15027	OTTHUMG00000020932	ENST00000313050.7:c.368C>T	9.37:g.139371700G>A	ENSP00000325827:p.Pro123Leu	140.0	0.0	0		118.0	10.0	0.0847458	NM_014866	A1YCA4|Q4G0D7|Q5SXP0|Q5SXP1|Q8N347|Q96HP1	Missense_Mutation	SNP	ENST00000313050.7	37	CCDS55351.1	.	.	.	.	.	.	.	.	.	.	G	8.006	0.756537	0.15846	0.0	1.2E-4	ENSG00000148396	ENST00000313050	T	0.21031	2.03	5.02	-7.76	0.01232	.	.	.	.	.	T	0.06645	0.0170	N	0.04508	-0.205	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.38090	-0.9677	8	.	.	.	.	6.51	0.22216	0.607:0.0887:0.2148:0.0895	.	123	F1T0I1	.	L	123	ENSP00000325827:P123L	.	P	-	2	0	SEC16A	138491521	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	0.064000	0.14437	-1.641000	0.01523	-0.794000	0.03295	CCG	.	.	weak		0.577	SEC16A-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		XM_088459	
TUBA8	51807	hgsc.bcm.edu	37	22	18613739	18613739	+	Missense_Mutation	SNP	G	G	T	rs146821364		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:18613739G>T	ENST00000330423.3	+	5	1259	c.1186G>T	c.(1186-1188)Gac>Tac	p.D396Y	TUBA8_ENST00000316027.6_Missense_Mutation_p.D330Y	NM_018943.2	NP_061816.1	Q9NY65	TBA8_HUMAN	tubulin, alpha 8	396					microtubule-based process (GO:0007017)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|prostate(1)	14						CCACAAGTTCGACCTCATGTA	0.622																																					p.D396Y		Atlas-SNP	.											TUBA8,NS,carcinoma,0,1	TUBA8	36	1	0			c.G1186T						PASS	.	G	TYR/ASP,TYR/ASP	1,4405		0,1,2202	63.0	58.0	60.0		988,1186	5.2	1.0	22	dbSNP_134	60	0,8600		0,0,4300	no	missense,missense	TUBA8	NM_001193414.1,NM_018943.2	160,160	0,1,6502	TT,TG,GG		0.0,0.0227,0.0077	probably-damaging,probably-damaging	330/384,396/450	18613739	1,13005	2203	4300	6503	SO:0001583	missense	51807	exon5			AAGTTCGACCTCA	AJ245922	CCDS13751.1, CCDS54495.1	22q11	2005-06-11			ENSG00000183785	ENSG00000183785		"""Tubulins"""	12410	protein-coding gene	gene with protein product		605742		TUBAL2		10772959, 10591208	Standard	NM_001193414		Approved		uc002znv.2	Q9NY65	OTTHUMG00000150097	ENST00000330423.3:c.1186G>T	22.37:g.18613739G>T	ENSP00000333326:p.Asp396Tyr	130.0	0.0	0		143.0	61.0	0.426573	NM_018943	B2RCX2|B3KPW9|B4DWG3|Q2M3N4	Missense_Mutation	SNP	ENST00000330423.3	37	CCDS13751.1	.	.	.	.	.	.	.	.	.	.	.	18.66	3.671959	0.67928	2.27E-4	0.0	ENSG00000183785	ENST00000316027;ENST00000330423;ENST00000416740	D;D;D	0.86097	-2.07;-2.07;-2.07	5.19	5.19	0.71726	Tubulin, C-terminal (1);Tubulin/FtsZ, C-terminal (1);	0.097032	0.64402	D	0.000002	D	0.95089	0.8409	H	0.96489	3.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.991;0.989;1.0	D	0.96490	0.9363	10	0.87932	D	0	.	18.0766	0.89428	0.0:0.0:1.0:0.0	.	330;420;396	B3KPW9;C9J2C0;Q9NY65	.;.;TBA8_HUMAN	Y	330;396;420	ENSP00000318575:D330Y;ENSP00000333326:D396Y;ENSP00000412646:D420Y	ENSP00000318575:D330Y	D	+	1	0	TUBA8	16993739	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	9.835000	0.99442	2.569000	0.86673	0.655000	0.94253	GAC	G|1.000;T|0.000	0.000	weak		0.622	TUBA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316232.3	NM_018943	
LEPRE1	64175	hgsc.bcm.edu	37	1	43228049	43228049	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:43228049G>A	ENST00000296388.5	-	2	614	c.563C>T	c.(562-564)aCc>aTc	p.T188I	LEPRE1_ENST00000397054.3_Missense_Mutation_p.T188I|LEPRE1_ENST00000236040.4_Missense_Mutation_p.T188I			Q32P28	P3H1_HUMAN	leucine proline-enriched proteoglycan (leprecan) 1	188					bone development (GO:0060348)|cell growth (GO:0016049)|chaperone-mediated protein folding (GO:0061077)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|negative regulation of post-translational protein modification (GO:1901874)|peptidyl-proline hydroxylation (GO:0019511)|protein folding (GO:0006457)|protein hydroxylation (GO:0018126)|protein stabilization (GO:0050821)|regulation of ossification (GO:0030278)|regulation of protein secretion (GO:0050708)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|macromolecular complex (GO:0032991)|membrane (GO:0016020)|nucleus (GO:0005634)|proteinaceous extracellular matrix (GO:0005578)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)|protein complex binding (GO:0032403)			large_intestine(2)|lung(15)|ovary(5)|prostate(1)|urinary_tract(3)	26	Ovarian(52;0.00744)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0505)			L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TCCAGACATGGTTTGGTAATA	0.428																																					p.T188I		Atlas-SNP	.											.	LEPRE1	130	.	0			c.C563T						PASS	.						168.0	159.0	162.0					1																	43228049		2203	4300	6503	SO:0001583	missense	64175	exon2			GACATGGTTTGGT	AK027648	CCDS472.2, CCDS53307.1, CCDS57986.1	1p34.1	2014-09-17			ENSG00000117385	ENSG00000117385			19316	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 1"", ""growth suppressor 1"""	610339				10951563	Standard	NM_022356		Approved	GROS1, P3H1, LEPRECAN, MGC117314	uc001chx.4	Q32P28	OTTHUMG00000007525	ENST00000296388.5:c.563C>T	1.37:g.43228049G>A	ENSP00000296388:p.Thr188Ile	102.0	0.0	0		117.0	51.0	0.435897	NM_001146289	Q7KZR4|Q96BR8|Q96SK8|Q96SL5|Q96SN3|Q9H6K3|Q9HC86|Q9HC87	Missense_Mutation	SNP	ENST00000296388.5	37	CCDS472.2	.	.	.	.	.	.	.	.	.	.	G	14.28	2.489214	0.44249	.	.	ENSG00000117385	ENST00000397054;ENST00000236040;ENST00000296388;ENST00000540027	T;T;T	0.32988	1.43;1.43;1.43	5.82	4.88	0.63580	Tetratricopeptide-like helical (1);	0.083955	0.85682	D	0.000000	T	0.21962	0.0529	L	0.40543	1.245	0.29400	N	0.862025	P;P;B;P	0.45283	0.855;0.708;0.391;0.544	B;B;B;B	0.37480	0.251;0.251;0.116;0.162	T	0.17077	-1.0381	10	0.45353	T	0.12	-25.5115	7.968	0.30111	0.0835:0.1631:0.7534:0.0	.	188;188;53;188	Q32P28-2;Q32P28-3;B4DNM8;Q32P28	.;.;.;P3H1_HUMAN	I	188;188;188;53	ENSP00000380245:T188I;ENSP00000236040:T188I;ENSP00000296388:T188I	ENSP00000236040:T188I	T	-	2	0	LEPRE1	43000636	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.101000	0.41787	1.400000	0.46741	0.563000	0.77884	ACC	.	.	none		0.428	LEPRE1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000019790.2	NM_022356	
PLD2	5338	hgsc.bcm.edu	37	17	4720522	4720522	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4720522A>T	ENST00000263088.6	+	17	1914	c.1783A>T	c.(1783-1785)Aca>Tca	p.T595S	PLD2_ENST00000572940.1_Missense_Mutation_p.T595S	NM_001243108.1|NM_002663.4	NP_001230037.1|NP_002654.3	O14939	PLD2_HUMAN	phospholipase D2	595	Catalytic.				cytoskeleton organization (GO:0007010)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|G-protein coupled receptor internalization (GO:0002031)|glycerophospholipid biosynthetic process (GO:0046474)|innate immune response (GO:0045087)|lipid catabolic process (GO:0016042)|phosphatidic acid biosynthetic process (GO:0006654)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	brush border membrane (GO:0031526)|endoplasmic reticulum membrane (GO:0005789)|plasma membrane (GO:0005886)	N-acylphosphatidylethanolamine-specific phospholipase D activity (GO:0070290)|phosphatidylinositol binding (GO:0035091)|phospholipase D activity (GO:0004630)			autonomic_ganglia(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(3)|lung(10)|ovary(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)	31					Choline(DB00122)	GCTCCCCTTCACACTTCCAGG	0.602																																					p.T595S		Atlas-SNP	.											.	PLD2	138	.	0			c.A1783T						PASS	.						225.0	193.0	204.0					17																	4720522		2203	4300	6503	SO:0001583	missense	5338	exon17			CCCTTCACACTTC	AF035483	CCDS11057.1, CCDS58507.1	17p13.3	2008-04-14			ENSG00000129219	ENSG00000129219	3.1.4.4		9068	protein-coding gene	gene with protein product	"""choline phosphatase 2"""	602384				9858823, 9582313	Standard	NM_002663		Approved		uc002fzc.3	O14939	OTTHUMG00000090779	ENST00000263088.6:c.1783A>T	17.37:g.4720522A>T	ENSP00000263088:p.Thr595Ser	129.0	0.0	0		187.0	79.0	0.42246	NM_001243108	I3L2C9|O43540|O43579|O43580|Q6PGR0|Q96BY3	Missense_Mutation	SNP	ENST00000263088.6	37	CCDS11057.1	.	.	.	.	.	.	.	.	.	.	A	2.773	-0.255213	0.05829	.	.	ENSG00000129219	ENST00000263088	T	0.05447	3.44	4.48	2.18	0.27775	.	0.430330	0.25572	N	0.029760	T	0.03053	0.0090	N	0.13327	0.33	0.27520	N	0.951422	B;B;B	0.06786	0.001;0.0;0.0	B;B;B	0.11329	0.001;0.006;0.002	T	0.40232	-0.9574	10	0.21540	T	0.41	0.6258	3.2221	0.06719	0.6276:0.0:0.1983:0.1741	.	452;595;595	B7Z905;O14939-2;O14939	.;.;PLD2_HUMAN	S	595	ENSP00000263088:T595S	ENSP00000263088:T595S	T	+	1	0	PLD2	4667488	0.016000	0.18221	0.659000	0.29680	0.288000	0.27193	0.396000	0.20867	0.747000	0.32809	0.454000	0.30748	ACA	.	.	none		0.602	PLD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207561.3	NM_002663	
MNX1	3110	hgsc.bcm.edu	37	7	156802363	156802363	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:156802363C>T	ENST00000252971.6	-	1	982	c.682G>A	c.(682-684)Gac>Aac	p.D228N	MNX1-AS1_ENST00000480284.1_RNA|MNX1_ENST00000543409.1_5'Flank|MNX1-AS2_ENST00000429228.1_RNA|MNX1_ENST00000469500.1_5'Flank	NM_005515.3	NP_005506.3	P50219	MNX1_HUMAN	motor neuron and pancreas homeobox 1	228					anatomical structure morphogenesis (GO:0009653)|diaphragm development (GO:0060539)|dorsal/ventral neural tube patterning (GO:0021904)|endocrine pancreas development (GO:0031018)|humoral immune response (GO:0006959)|motor neuron axon guidance (GO:0008045)|nerve development (GO:0021675)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|large_intestine(1)|lung(4)|skin(1)	7	Ovarian(565;0.218)	all_hematologic(28;0.0592)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)		CAGTTGAAGTCGGGCATCTTA	0.716																																					p.D228N		Atlas-SNP	.											.	MNX1	17	.	0			c.G682A						PASS	.						11.0	12.0	12.0					7																	156802363		2137	4195	6332	SO:0001583	missense	3110	exon1			TGAAGTCGGGCAT	AF107457	CCDS34788.1, CCDS55187.1	7q36	2012-03-09	2007-08-09	2007-08-09	ENSG00000130675	ENSG00000130675		"""Homeoboxes / ANTP class : HOXL subclass"""	4979	protein-coding gene	gene with protein product		142994	"""homeo box HB9"", ""homeobox HB9"""	HLXB9		9843207	Standard	NM_001165255		Approved	HB9, HOXHB9, SCRA1	uc003wmz.4	P50219	OTTHUMG00000157181	ENST00000252971.6:c.682G>A	7.37:g.156802363C>T	ENSP00000252971:p.Asp228Asn	15.0	0.0	0		43.0	22.0	0.511628	NM_005515	F5H401|Q9Y648	Missense_Mutation	SNP	ENST00000252971.6	37	CCDS34788.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.603729	0.87157	.	.	ENSG00000130675	ENST00000252971;ENST00000542972	D	0.95656	-3.77	3.12	2.21	0.28008	Homeodomain-like (1);	0.000000	0.40222	U	0.001156	D	0.96034	0.8708	M	0.65498	2.005	0.80722	D	1	D	0.71674	0.998	P	0.59115	0.852	D	0.95038	0.8175	10	0.66056	D	0.02	-25.9529	11.1823	0.48636	0.0:0.8115:0.1885:0.0	.	228	P50219	MNX1_HUMAN	N	228;58	ENSP00000252971:D228N	ENSP00000252971:D228N	D	-	1	0	MNX1	156495124	1.000000	0.71417	0.996000	0.52242	0.993000	0.82548	4.845000	0.62853	0.536000	0.28733	0.549000	0.68633	GAC	.	.	none		0.716	MNX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347796.3		
COL14A1	7373	hgsc.bcm.edu	37	8	121222046	121222046	+	Missense_Mutation	SNP	G	G	A	rs61753752	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:121222046G>A	ENST00000297848.3	+	12	1643	c.1373G>A	c.(1372-1374)aGc>aAc	p.S458N	COL14A1_ENST00000309791.4_Missense_Mutation_p.S458N|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000537875.1_Missense_Mutation_p.S458N|COL14A1_ENST00000247781.3_Missense_Mutation_p.S363N	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			ACTGAGAACAGCATGCGAGTC	0.468													G|||	5	0.000998403	0.0	0.0029	5008	,	,		14372	0.0		0.003	False		,,,				2504	0.0				p.S458N		Atlas-SNP	.											COL14A1,NS,carcinoma,-1,1	COL14A1	292	1	0			c.G1373A						PASS	.	G	ASN/SER	2,4404	2.1+/-5.4	0,2,2201	119.0	111.0	114.0		1373	5.3	1.0	8	dbSNP_129	114	26,8574	18.5+/-59.3	0,26,4274	yes	missense	COL14A1	NM_021110.1	46	0,28,6475	AA,AG,GG		0.3023,0.0454,0.2153	probably-damaging	458/1797	121222046	28,12978	2203	4300	6503	SO:0001583	missense	7373	exon12			AGAACAGCATGCG		CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.1373G>A	8.37:g.121222046G>A	ENSP00000297848:p.Ser458Asn	93.0	0.0	0		114.0	56.0	0.491228	NM_021110		Missense_Mutation	SNP	ENST00000297848.3	37	CCDS34938.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	17.53	3.412148	0.62511	4.54E-4	0.003023	ENSG00000187955	ENST00000537875;ENST00000309791;ENST00000297848;ENST00000247781;ENST00000434620	T;T;T;T;T	0.62639	0.01;0.01;0.01;0.01;0.01	5.31	5.31	0.75309	Fibronectin, type III (4);	0.148564	0.64402	D	0.000013	T	0.79616	0.4476	M	0.84156	2.68	0.48135	D	0.999599	D;D	0.67145	0.996;0.99	P;P	0.60173	0.857;0.87	T	0.82534	-0.0409	10	0.87932	D	0	.	19.1802	0.93620	0.0:0.0:1.0:0.0	rs61753752	458;458	Q05707-2;Q05707	.;COEA1_HUMAN	N	458;458;458;363;271	ENSP00000443974:S458N;ENSP00000311809:S458N;ENSP00000297848:S458N;ENSP00000247781:S363N;ENSP00000409461:S271N	ENSP00000247781:S363N	S	+	2	0	COL14A1	121291227	1.000000	0.71417	0.960000	0.40013	0.256000	0.26092	4.592000	0.61027	2.748000	0.94277	0.650000	0.86243	AGC	G|0.998;A|0.002	0.002	strong		0.468	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2	NM_021110	
SLCO1C1	53919	hgsc.bcm.edu	37	12	20854303	20854303	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:20854303G>T	ENST00000266509.2	+	3	549	c.181G>T	c.(181-183)Ggc>Tgc	p.G61C	SLCO1C1_ENST00000545604.1_Missense_Mutation_p.G61C|SLCO1C1_ENST00000545102.1_Intron|SLCO1C1_ENST00000540354.1_Missense_Mutation_p.G61C|SLCO1C1_ENST00000381552.1_Missense_Mutation_p.G61C	NM_017435.4	NP_059131.1	Q9NYB5	SO1C1_HUMAN	solute carrier organic anion transporter family, member 1C1	61					sodium-independent organic anion transport (GO:0043252)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)			NS(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	60	Esophageal squamous(101;0.149)				Conjugated Estrogens(DB00286)|Dextrothyroxine(DB00509)|Diclofenac(DB00586)|Digoxin(DB00390)|Dinoprostone(DB00917)|Estradiol(DB00783)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Liotrix(DB01583)|Meclofenamic acid(DB00939)|Methotrexate(DB00563)|Ouabain(DB01092)|Phenytoin(DB00252)|Probenecid(DB01032)	ATTGGCAGAAGGCTATCTGAA	0.418																																					p.G61C		Atlas-SNP	.											.	SLCO1C1	216	.	0			c.G181T						PASS	.						272.0	207.0	229.0					12																	20854303		2203	4300	6503	SO:0001583	missense	53919	exon3			GCAGAAGGCTATC	AF260704	CCDS8683.1, CCDS53757.1, CCDS53758.1, CCDS53759.1	12p12.2	2013-05-22	2003-11-25	2003-11-26	ENSG00000139155	ENSG00000139155		"""Solute carriers"""	13819	protein-coding gene	gene with protein product		613389	"""solute carrier family 21 (organic anion transporter), member 14"""	SLC21A14			Standard	NM_017435		Approved	OATP-F, OATP1C1, OATP1	uc010sii.2	Q9NYB5	OTTHUMG00000168966	ENST00000266509.2:c.181G>T	12.37:g.20854303G>T	ENSP00000266509:p.Gly61Cys	179.0	0.0	0		179.0	74.0	0.413408	NM_017435	B7Z251|B7Z3Q3|B7Z8P1|F5GZD6|Q5JPA4	Missense_Mutation	SNP	ENST00000266509.2	37	CCDS8683.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.981799	0.74474	.	.	ENSG00000139155	ENST00000545604;ENST00000540354;ENST00000266509;ENST00000381552	T;T;T;T	0.60299	0.2;0.2;0.2;0.2	5.09	5.09	0.68999	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.046510	0.85682	D	0.000000	T	0.70996	0.3288	M	0.80183	2.485	0.41867	D	0.990257	D;D;D	0.62365	0.973;0.98;0.991	P;P;D	0.64506	0.852;0.852;0.926	T	0.74435	-0.3666	10	0.66056	D	0.02	.	6.0855	0.19964	0.2193:0.0:0.7807:0.0	.	61;61;61	B7Z3Q3;Q5JPA4;Q9NYB5	.;.;SO1C1_HUMAN	C	61	ENSP00000444149:G61C;ENSP00000438665:G61C;ENSP00000266509:G61C;ENSP00000370964:G61C	ENSP00000266509:G61C	G	+	1	0	SLCO1C1	20745570	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.764000	0.62264	2.652000	0.90054	0.655000	0.94253	GGC	.	.	none		0.418	SLCO1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401765.1	NM_017435	
FIP1L1	81608	hgsc.bcm.edu	37	4	54324914	54324914	+	Nonsense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:54324914C>T	ENST00000337488.6	+	17	1788	c.1594C>T	c.(1594-1596)Cga>Tga	p.R532*	FIP1L1_ENST00000358575.5_Nonsense_Mutation_p.R526*|FIP1L1_ENST00000306932.6_Nonsense_Mutation_p.R458*|FIP1L1_ENST00000507166.1_Intron	NM_030917.3	NP_112179.2	Q6UN15	FIP1_HUMAN	factor interacting with PAPOLA and CPSF1	532	Arg-rich.|Glu-rich.|Sufficient for interaction with CPSF1 and CSTF3.				mRNA processing (GO:0006397)	mRNA cleavage and polyadenylation specificity factor complex (GO:0005847)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			large_intestine(3)|liver(1)|ovary(1)|skin(1)	6			GBM - Glioblastoma multiforme(3;3.31e-36)|LUSC - Lung squamous cell carcinoma(32;0.0134)			TAGAGAAAGACGACACAGGGA	0.393			T	PDGFRA	idiopathic hypereosinophilic syndrome																																p.R532X		Atlas-SNP	.		Dom	yes		4	4q12	81608	FIP1 like 1 (S. cerevisiae)		L	.	FIP1L1	60	.	0			c.C1594T						PASS	.						98.0	110.0	106.0					4																	54324914		2203	4300	6503	SO:0001587	stop_gained	81608	exon17			GAAAGACGACACA	AF161429	CCDS3491.1, CCDS47055.1, CCDS47056.1	4q12	2013-06-18	2013-06-18		ENSG00000145216	ENSG00000145216			19124	protein-coding gene	gene with protein product		607686	"""FIP1 like 1 (S. cerevisiae)"", ""FIP1L1 cleavage and polyadenylation specific factor subunit"""			11230166, 14749727	Standard	NM_030917		Approved	DKFZp586K0717, FIP1	uc003hae.3	Q6UN15	OTTHUMG00000128701	ENST00000337488.6:c.1594C>T	4.37:g.54324914C>T	ENSP00000336752:p.Arg532*	194.0	0.0	0		213.0	92.0	0.431925	NM_030917	B4DIR3|G3XAD6|Q0VGE0|Q499Y4|Q49AU3|Q7Z608|Q8WVN3|Q96F80|Q9H077	Nonsense_Mutation	SNP	ENST00000337488.6	37	CCDS3491.1	.	.	.	.	.	.	.	.	.	.	C	29.9	5.044750	0.93685	.	.	ENSG00000145216	ENST00000337488;ENST00000358575;ENST00000306932;ENST00000504094	.	.	.	4.93	4.02	0.46733	.	0.000000	0.64402	D	0.000004	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-9.7173	10.9749	0.47461	0.3547:0.6453:0.0:0.0	.	.	.	.	X	532;526;458;192	.	ENSP00000302993:R458X	R	+	1	2	FIP1L1	54019671	1.000000	0.71417	0.953000	0.39169	0.010000	0.07245	1.951000	0.40333	2.706000	0.92434	0.591000	0.81541	CGA	.	.	none		0.393	FIP1L1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250602.1	NM_030917	
CFAP46	54777	hgsc.bcm.edu	37	10	134671150	134671150	+	Missense_Mutation	SNP	T	T	C	rs148181302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134671150T>C	ENST00000368586.5	-	39	5618	c.5518A>G	c.(5518-5520)Atg>Gtg	p.M1840V	TTC40_ENST00000263170.5_Start_Codon_SNP_p.M1V	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCCTCAGCCATGGCGCCCTGG	0.587													T|||	46	0.0091853	0.0	0.0072	5008	,	,		16300	0.002		0.0129	False		,,,				2504	0.0266				p.M1840V		Atlas-SNP	.											.	TTC40	100	.	0			c.A5518G						PASS	.	T	VAL/MET	5,4401	8.1+/-20.4	0,5,2198	138.0	91.0	107.0		454	-1.8	0.0	10	dbSNP_134	107	54,8546	22.8+/-68.1	0,54,4246	no	missense	C10orf92	NM_001200049.1	21	0,59,6444	CC,CT,TT		0.6279,0.1135,0.4536	benign	152/1028	134671150	59,12947	2203	4300	6503	SO:0001583	missense	54777	exon39			CAGCCATGGCGCC																												ENST00000368586.5:c.5518A>G	10.37:g.134671150T>C	ENSP00000357575:p.Met1840Val	131.0	0.0	0		125.0	55.0	0.44	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	T	0	-2.868758	0.00063	0.001135	0.006279	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.12465	3.08;2.68	0.924	-1.8	0.07907	.	.	.	.	.	T	0.01870	0.0059	N	0.01048	-1.04	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39482	-0.9612	9	0.02654	T	1	.	4.0252	0.09683	0.0:0.4768:0.0:0.5232	.	1	Q8IYW2	CJ092_HUMAN	V	1840;1	ENSP00000357575:M1840V;ENSP00000263170:M1V	ENSP00000263170:M1V	M	-	1	0	C10orf93	134521140	0.379000	0.25123	0.002000	0.10522	0.048000	0.14542	-0.121000	0.10643	-0.572000	0.06006	0.055000	0.15244	ATG	T|0.991;C|0.009	0.009	strong		0.587	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
HIST4H4	121504	hgsc.bcm.edu	37	12	14923988	14923988	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:14923988G>T	ENST00000539745.1	-	1	77	c.31C>A	c.(31-33)Ctg>Atg	p.L11M	HIST4H4_ENST00000541592.1_5'Flank	NM_175054.2	NP_778224.1	P62805	H4_HUMAN	histone cluster 4, H4	11					CENP-A containing nucleosome assembly (GO:0034080)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|DNA replication-independent nucleosome assembly (GO:0006336)|histone H4-K20 demethylation (GO:0035574)|mitotic cell cycle (GO:0000278)|negative regulation of megakaryocyte differentiation (GO:0045653)|nucleosome assembly (GO:0006334)|telomere maintenance (GO:0000723)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|histone demethylase activity (H4-K20 specific) (GO:0035575)|poly(A) RNA binding (GO:0044822)			haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(2)	6						CCCTTACCCAGCCCCTTGCCA	0.617																																					p.L11M		Atlas-SNP	.											.	HIST4H4	13	.	0			c.C31A						PASS	.						46.0	52.0	50.0					12																	14923988		2203	4300	6503	SO:0001583	missense	121504	exon1			TACCCAGCCCCTT	AY128653	CCDS8665.1	12p12.3	2011-01-27	2006-10-11			ENSG00000197837		"""Histones / Replication-dependent"""	20510	protein-coding gene	gene with protein product		615069	"""histone 4, H4"""			12408966	Standard	NM_175054		Approved	MGC24116	uc001rcf.4	P62805		ENST00000539745.1:c.31C>A	12.37:g.14923988G>T	ENSP00000443017:p.Leu11Met	69.0	0.0	0		75.0	38.0	0.506667	NM_175054	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000539745.1	37	CCDS8665.1	.	.	.	.	.	.	.	.	.	.	G	11.51	1.660167	0.29515	.	.	ENSG00000197837	ENST00000539745	.	.	.	4.07	4.07	0.47477	.	0.000000	0.43260	U	0.000587	T	0.64080	0.2566	.	.	.	0.51482	D	0.999927	.	.	.	.	.	.	T	0.67409	-0.5678	6	0.87932	D	0	.	7.8764	0.29597	0.1106:0.0:0.8894:0.0	.	.	.	.	M	11	.	ENSP00000350767:L11M	L	-	1	2	HIST4H4	14815255	1.000000	0.71417	0.737000	0.30932	0.392000	0.30506	3.606000	0.54095	2.275000	0.75901	0.650000	0.86243	CTG	.	.	none		0.617	HIST4H4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400844.1	NM_175054	
C21orf58	54058	hgsc.bcm.edu	37	21	47734777	47734777	+	Silent	SNP	G	G	A	rs56036022	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47734777G>A	ENST00000291691.7	-	5	1598	c.462C>T	c.(460-462)gaC>gaT	p.D154D	C21orf58_ENST00000397683.1_Silent_p.D48D|C21orf58_ENST00000397679.1_Silent_p.D48D|C21orf58_ENST00000397682.3_Silent_p.D48D|C21orf58_ENST00000397680.1_Silent_p.D48D	NM_058180.3	NP_478060.2	P58505	CU058_HUMAN	chromosome 21 open reading frame 58	154										breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|lung(1)|pancreas(1)	9	Breast(49;0.112)			Colorectal(79;0.239)		GAGAGAGCTCGTCCAGGAGGT	0.701													G|||	174	0.0347444	0.1248	0.0101	5008	,	,		14424	0.0		0.002	False		,,,				2504	0.0				p.D154D		Atlas-SNP	.											.	C21orf58	25	.	0			c.C462T						PASS	.	G		383,3735		17,349,1693	9.0	11.0	10.0		462	-9.5	0.2	21	dbSNP_129	10	8,8092		0,8,4042	no	coding-synonymous	C21orf58	NM_058180.3		17,357,5735	AA,AG,GG		0.0988,9.3006,3.2002		154/323	47734777	391,11827	2059	4050	6109	SO:0001819	synonymous_variant	54058	exon5			GAGCTCGTCCAGG		CCDS13735.1, CCDS68229.1	21q22.3	2008-07-07			ENSG00000160298	ENSG00000160298			1300	protein-coding gene	gene with protein product							Standard	XM_005261149		Approved		uc002zjf.3	P58505	OTTHUMG00000090634	ENST00000291691.7:c.462C>T	21.37:g.47734777G>A		74.0	0.0	0		91.0	40.0	0.43956	NM_058180	B3KPI1	Silent	SNP	ENST00000291691.7	37	CCDS13735.1																																																																																			G|0.975;A|0.025	0.025	strong		0.701	C21orf58-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207283.1	NM_058180	
GRID1	2894	hgsc.bcm.edu	37	10	88126071	88126071	+	Splice_Site	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:88126071C>T	ENST00000327946.7	-	1	164	c.79G>A	c.(79-81)Ggt>Agt	p.G27S		NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	27					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						CCGCGCTTACCGATGTGGATG	0.716										Multiple Myeloma(13;0.14)																											p.G27S		Atlas-SNP	.											.	GRID1	204	.	0			c.G79A						PASS	.						9.0	9.0	9.0					10																	88126071		2110	4138	6248	SO:0001630	splice_region_variant	2894	exon1			GCTTACCGATGTG	AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.79+1G>A	10.37:g.88126071C>T		3.0	0.0	0		20.0	13.0	0.65	NM_017551	B3KXD5|B7Z7L0|Q8IXT3	Missense_Mutation	SNP	ENST00000327946.7	37	CCDS31236.1	.	.	.	.	.	.	.	.	.	.	C	17.85	3.491269	0.64074	.	.	ENSG00000182771	ENST00000327946	D	0.95588	-3.75	2.24	2.24	0.28232	.	0.288147	0.21374	U	0.075581	D	0.94198	0.8138	L	0.27053	0.805	0.80722	D	1	D	0.89917	1.0	D	0.65684	0.937	D	0.91741	0.5404	9	.	.	.	.	9.8853	0.41257	0.0:1.0:0.0:0.0	.	27	Q9ULK0	GRID1_HUMAN	S	27	ENSP00000330148:G27S	.	G	-	1	0	GRID1	88116051	1.000000	0.71417	0.972000	0.41901	0.495000	0.33615	6.014000	0.70784	1.228000	0.43614	0.305000	0.20034	GGT	.	.	none		0.716	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049148.3	XM_043613	Missense_Mutation
ELMO2	63916	hgsc.bcm.edu	37	20	45003211	45003211	+	Silent	SNP	C	C	T	rs8124302	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:45003211C>T	ENST00000290246.6	-	14	1328	c.1134G>A	c.(1132-1134)ctG>ctA	p.L378L	ELMO2_ENST00000372176.1_Silent_p.L290L|ELMO2_ENST00000439931.2_Silent_p.L390L|ELMO2_ENST00000454865.2_Silent_p.L110L|ELMO2_ENST00000488853.1_5'UTR|ELMO2_ENST00000396391.1_Silent_p.L378L|ELMO2_ENST00000445496.2_Silent_p.L195L|ELMO2_ENST00000352077.2_Silent_p.L376L	NM_133171.3	NP_573403.1	Q96JJ3	ELMO2_HUMAN	engulfment and cell motility 2	378	ELMO. {ECO:0000255|PROSITE- ProRule:PRU00664}.				apoptotic process (GO:0006915)|cell chemotaxis (GO:0060326)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|membrane (GO:0016020)	receptor tyrosine kinase binding (GO:0030971)			breast(1)|endometrium(1)|large_intestine(4)|lung(8)|ovary(1)|urinary_tract(1)	16		Myeloproliferative disorder(115;0.0122)				TAGCCAAGTACAGCATGTTGT	0.517													C|||	5	0.000998403	0.0	0.0	5008	,	,		21226	0.0		0.004	False		,,,				2504	0.001				p.L378L		Atlas-SNP	.											.	ELMO2	51	.	0			c.G1134A						PASS	.	C	,	5,4401	9.9+/-24.2	0,5,2198	120.0	99.0	106.0		1134,1134	0.4	1.0	20	dbSNP_116	106	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous,coding-synonymous	ELMO2	NM_133171.3,NM_182764.1	,	0,32,6471	TT,TC,CC		0.314,0.1135,0.246	,	378/721,378/721	45003211	32,12974	2203	4300	6503	SO:0001819	synonymous_variant	63916	exon13			CAAGTACAGCATG	AF398886	CCDS13398.1	20q13	2010-03-18	2006-01-20		ENSG00000062598	ENSG00000062598		"""Engulfment and cell motility proteins"""	17233	protein-coding gene	gene with protein product		606421	"""engulfment and cell motility 2 (ced-12 homolog, C. elegans)"""			11595183	Standard	NM_133171		Approved	CED12, ELMO-2, CED-12, KIAA1834, FLJ11656	uc002xru.1	Q96JJ3	OTTHUMG00000033070	ENST00000290246.6:c.1134G>A	20.37:g.45003211C>T		106.0	0.0	0		120.0	60.0	0.5	NM_182764	E1P5T3|Q5JVZ6|Q7Z5G9|Q96CJ2|Q96ME5|Q96PA9|Q9H938|Q9H9L5|Q9HAH0|Q9NQQ6	Silent	SNP	ENST00000290246.6	37	CCDS13398.1																																																																																			C|0.997;T|0.003	0.003	strong		0.517	ELMO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080466.1	NM_022086	
VKORC1	79001	hgsc.bcm.edu	37	16	31106015	31106015	+	Silent	SNP	C	C	T	rs55894764	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31106015C>T	ENST00000394975.2	-	1	263	c.36G>A	c.(34-36)cgG>cgA	p.R12R	VKORC1_ENST00000394971.3_5'Flank|VKORC1_ENST00000498155.1_Intron|RP11-196G11.1_ENST00000529564.1_Silent_p.R12R|VKORC1_ENST00000354895.4_Silent_p.R12R|VKORC1_ENST00000319788.7_Silent_p.R12R|VKORC1_ENST00000300851.6_Silent_p.R12R	NM_024006.4	NP_076869.1	Q9BQB6	VKOR1_HUMAN	vitamin K epoxide reductase complex, subunit 1	12					blood coagulation (GO:0007596)|bone development (GO:0060348)|cellular protein metabolic process (GO:0044267)|drug metabolic process (GO:0017144)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|vitamin K metabolic process (GO:0042373)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	quinone binding (GO:0048038)|vitamin-K-epoxide reductase (warfarin-sensitive) activity (GO:0047057)			lung(3)|urinary_tract(1)	4					Acenocoumarol(DB01418)|Dicoumarol(DB00266)|Menadione(DB00170)|Phenindione(DB00498)|Phenprocoumon(DB00946)|Warfarin(DB00682)	AAAGAGCGAGCCGCACCCAGC	0.721													C|||	43	0.00858626	0.0008	0.0187	5008	,	,		13567	0.0		0.0268	False		,,,				2504	0.002				p.R12R		Atlas-SNP	.											.	VKORC1	9	.	0			c.G36A						PASS	.	C	,	12,4280		0,12,2134	13.0	13.0	13.0		36,36	2.5	1.0	16	dbSNP_129	13	92,8316		0,92,4112	no	coding-synonymous,coding-synonymous	VKORC1	NM_024006.4,NM_206824.1	,	0,104,6246	TT,TC,CC		1.0942,0.2796,0.8189	,	12/164,12/93	31106015	104,12596	2146	4204	6350	SO:0001819	synonymous_variant	79001	exon1			AGCGAGCCGCACC		CCDS10703.1, CCDS10704.1	16p11.2	2008-02-05	2004-07-23		ENSG00000167397	ENSG00000167397			23663	protein-coding gene	gene with protein product		608547	"""vitamin K dependent clotting factors deficiency 2"""	VKCFD2			Standard	NM_024006		Approved		uc002eas.3	Q9BQB6	OTTHUMG00000047408	ENST00000394975.2:c.36G>A	16.37:g.31106015C>T		18.0	0.0	0		47.0	27.0	0.574468	NM_024006	A6NIQ6|B2R4Z6|Q6UX90|Q7Z2R4	Silent	SNP	ENST00000394975.2	37	CCDS10703.1																																																																																			C|0.990;T|0.010	0.010	strong		0.721	VKORC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000108582.1	NM_024006	
ZNF713	349075	hgsc.bcm.edu	37	7	56007498	56007498	+	Silent	SNP	A	A	G	rs112798657	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:56007498A>G	ENST00000429591.2	+	4	1130	c.1092A>G	c.(1090-1092)aaA>aaG	p.K364K	MRPS17_ENST00000426595.1_Intron	NM_182633.1	NP_872439.1	Q8N859	ZN713_HUMAN	zinc finger protein 713	364					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(1)|kidney(1)|large_intestine(4)|lung(10)|ovary(2)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	25	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			TCTGTGGCAAAGCCTTCAGTC	0.423													A|||	6	0.00119808	0.0	0.0029	5008	,	,		18360	0.0		0.002	False		,,,				2504	0.002				p.K364K		Atlas-SNP	.											.	ZNF713	47	.	0			c.A1092G						PASS	.	A		2,4404	4.2+/-10.8	0,2,2201	65.0	66.0	66.0		1092	0.8	1.0	7	dbSNP_132	66	20,8580	14.0+/-48.4	0,20,4280	no	coding-synonymous	ZNF713	NM_182633.1		0,22,6481	GG,GA,AA		0.2326,0.0454,0.1692		364/431	56007498	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	349075	exon4			TGGCAAAGCCTTC	AK097282	CCDS34639.1	7p11.2	2013-01-08			ENSG00000178665	ENSG00000178665		"""Zinc fingers, C2H2-type"", ""-"""	22043	protein-coding gene	gene with protein product							Standard	NM_182633		Approved	FLJ39963	uc003trc.1	Q8N859	OTTHUMG00000156175	ENST00000429591.2:c.1092A>G	7.37:g.56007498A>G		63.0	0.0	0		72.0	41.0	0.569444	NM_182633		Silent	SNP	ENST00000429591.2	37	CCDS34639.1																																																																																			A|0.998;G|0.002	0.002	strong		0.423	ZNF713-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343297.1	NM_182633	
CCDC85C	317762	hgsc.bcm.edu	37	14	99988570	99988570	+	Missense_Mutation	SNP	C	C	G	rs75827961	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:99988570C>G	ENST00000380243.4	-	3	941	c.875G>C	c.(874-876)gGc>gCc	p.G292A	CCDC85C_ENST00000555822.1_5'UTR|CCDC85C_ENST00000557769.1_5'UTR|CCNK_ENST00000555049.1_Intron	NM_001144995.1	NP_001138467.1	A6NKD9	CC85C_HUMAN	coiled-coil domain containing 85C	292					cerebral cortex development (GO:0021987)	apical junction complex (GO:0043296)|tight junction (GO:0005923)				endometrium(1)|skin(1)	2						CTCTCCGGAGCCTGCCTGCTG	0.672													C|||	434	0.0866613	0.2723	0.036	5008	,	,		17507	0.004		0.0149	False		,,,				2504	0.0307				p.G292A		Atlas-SNP	.											.	CCDC85C	3	.	0			c.G875C						PASS	.	C	ALA/GLY	297,1087		38,221,433	52.0	54.0	53.0		875	3.9	0.6	14	dbSNP_131	53	62,3120		1,60,1530	yes	missense	CCDC85C	NM_001144995.1	60	39,281,1963	GG,GC,CC		1.9485,21.4595,7.8625	benign	292/420	99988570	359,4207	692	1591	2283	SO:0001583	missense	317762	exon3			CCGGAGCCTGCCT		CCDS45161.1	14q32.31	2009-02-18				ENSG00000205476			35459	protein-coding gene	gene with protein product							Standard	NM_001144995		Approved		uc010avr.3	A6NKD9		ENST00000380243.4:c.875G>C	14.37:g.99988570C>G	ENSP00000369592:p.Gly292Ala	22.0	0.0	0		27.0	14.0	0.518519	NM_001144995		Missense_Mutation	SNP	ENST00000380243.4	37	CCDS45161.1	150|150	0.06868131868131869|0.06868131868131869	120|120	0.24390243902439024|0.24390243902439024	16|16	0.04419889502762431|0.04419889502762431	3|3	0.005244755244755245|0.005244755244755245	11|11	0.014511873350923483|0.014511873350923483	C|C	14.01|14.01	2.408809|2.408809	0.42715|0.42715	0.214595|0.214595	0.019485|0.019485	ENSG00000205476|ENSG00000205476	ENST00000557576|ENST00000380243;ENST00000554996;ENST00000556348	.|.	.|.	.|.	4.83|4.83	3.87|3.87	0.44632|0.44632	.|.	.|0.218004	.|0.34435	.|U	.|0.003978	T|T	0.00012|0.00012	0.0000|0.0000	N|N	0.08118|0.08118	0|0	0.45005|0.45005	P|P	0.0019780000000000353|0.0019780000000000353	.|B	.|0.30406	.|0.278	.|B	.|0.30179	.|0.112	T|T	0.26643|0.26643	-1.0097|-1.0097	4|8	.|0.19147	.|T	.|0.46	-19.1362|-19.1362	7.8087|7.8087	0.29217|0.29217	0.162:0.5454:0.2926:0.0|0.162:0.5454:0.2926:0.0	.|.	.|292	.|A6NKD9	.|CC85C_HUMAN	P|A	28|292;63;44	.|.	.|ENSP00000369592:G292A	A|G	-|-	1|2	0|0	CCDC85C|CCDC85C	99058323|99058323	0.441000|0.441000	0.25626|0.25626	0.560000|0.560000	0.28344|0.28344	0.439000|0.439000	0.31926|0.31926	1.727000|1.727000	0.38095|0.38095	2.212000|2.212000	0.71576|0.71576	0.655000|0.655000	0.94253|0.94253	GCT|GGC	C|0.930;G|0.070	0.070	strong		0.672	CCDC85C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413802.1	NM_001144995	
ADAMTS5	11096	hgsc.bcm.edu	37	21	28315841	28315841	+	Silent	SNP	G	G	A	rs61088614	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:28315841G>A	ENST00000284987.5	-	3	1384	c.1263C>T	c.(1261-1263)gaC>gaT	p.D421D		NM_007038.3	NP_008969.2	Q9UNA0	ATS5_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 5	421	Peptidase M12B. {ECO:0000255|PROSITE- ProRule:PRU00276}.				defense response to bacterium (GO:0042742)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|proteolysis (GO:0006508)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(3)	72						ATTTGGAATCGTCATGGGAGA	0.418													G|||	251	0.0501198	0.1755	0.0144	5008	,	,		20735	0.0		0.006	False		,,,				2504	0.0031				p.D421D	Esophageal Squamous(53;683 1080 10100 14424 45938)	Atlas-SNP	.											.	ADAMTS5	184	.	0			c.C1263T						PASS	.	G		601,3805	262.8+/-265.1	44,513,1646	75.0	70.0	72.0		1263	-10.1	0.1	21	dbSNP_129	72	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	ADAMTS5	NM_007038.3		44,541,5918	AA,AG,GG		0.3256,13.6405,4.8362		421/931	28315841	629,12377	2203	4300	6503	SO:0001819	synonymous_variant	11096	exon3			GGAATCGTCATGG	AF142099	CCDS13579.1	21q21.3	2008-07-31	2008-07-31		ENSG00000154736	ENSG00000154736		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	221	protein-coding gene	gene with protein product	"""aggrecanase-2"""	605007	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 5 (aggrecanase-2)"""			10438522	Standard	NM_007038		Approved	ADMP-2, ADAMTS11	uc002ymg.3	Q9UNA0	OTTHUMG00000078686	ENST00000284987.5:c.1263C>T	21.37:g.28315841G>A		100.0	0.0	0		114.0	55.0	0.482456	NM_007038	Q52LV4|Q9UKP2	Silent	SNP	ENST00000284987.5	37	CCDS13579.1																																																																																			G|0.957;A|0.043	0.043	strong		0.418	ADAMTS5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171648.1		
IL17RC	84818	hgsc.bcm.edu	37	3	9962634	9962634	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:9962634C>T	ENST00000295981.3	+	7	1034	c.816C>T	c.(814-816)aaC>aaT	p.N272N	IL17RC_ENST00000498214.1_Intron|IL17RC_ENST00000403601.3_Silent_p.N201N|IL17RC_ENST00000413608.1_Silent_p.N201N|RNU6-882P_ENST00000391025.1_RNA|IL17RC_ENST00000383812.4_Intron|IL17RC_ENST00000455057.1_Intron|IL17RC_ENST00000416074.2_Intron	NM_153461.3	NP_703191	Q8NAC3	I17RC_HUMAN	interleukin 17 receptor C	272					cytokine-mediated signaling pathway (GO:0019221)|positive regulation of cytokine production involved in inflammatory response (GO:1900017)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-17 receptor activity (GO:0030368)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(3)|ovary(3)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22						AAGTCTGGAACAGCATCCCGA	0.612																																					p.N272N		Atlas-SNP	.											.	IL17RC	55	.	0			c.C816T						PASS	.						27.0	30.0	29.0					3																	9962634		2203	4300	6503	SO:0001819	synonymous_variant	84818	exon7			CTGGAACAGCATC	BC006411	CCDS2590.1, CCDS2591.2, CCDS46746.1, CCDS56240.1, CCDS56241.1, CCDS74898.1	3p25.3	2008-02-05			ENSG00000163702	ENSG00000163702		"""Interleukins and interleukin receptors"""	18358	protein-coding gene	gene with protein product		610925				11706037	Standard	NM_153460		Approved	IL17-RL	uc003bua.3	Q8NAC3	OTTHUMG00000128648	ENST00000295981.3:c.816C>T	3.37:g.9962634C>T		317.0	0.0	0		332.0	176.0	0.53012	NM_153461	E9PHG1|E9PHJ6|Q6UVY3|Q6UWD4|Q8NFS1|Q9BR97	Silent	SNP	ENST00000295981.3	37	CCDS2590.1																																																																																			.	.	none		0.612	IL17RC-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250526.2	NM_032732	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57070089	57070089	+	Silent	SNP	C	C	T	rs34498883	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57070089C>T	ENST00000532437.1	-	6	4838	c.4527G>A	c.(4525-4527)ccG>ccA	p.P1509P	TNKS1BP1_ENST00000358252.3_Silent_p.P1509P			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1509	Acidic.|Tankyrase-binding.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CATCAGGCTGCGGCCTCCAGG	0.677													G|||	102	0.0203674	0.0023	0.0389	5008	,	,		15780	0.002		0.0457	False		,,,				2504	0.0245				p.P1509P		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.G4527A						PASS	.	G		46,4356		0,46,2155	26.0	26.0	26.0		4527	-4.9	0.9	11	dbSNP_126	26	401,8191		8,385,3903	no	coding-synonymous	TNKS1BP1	NM_033396.2		8,431,6058	TT,TC,CC		4.6671,1.045,3.44		1509/1730	57070089	447,12547	2201	4296	6497	SO:0001819	synonymous_variant	85456	exon7			AGGCTGCGGCCTC	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4527G>A	11.37:g.57070089C>T		57.0	0.0	0		59.0	24.0	0.40678	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Silent	SNP	ENST00000532437.1	37	CCDS7951.1																																																																																			C|0.969;T|0.031	0.031	strong		0.677	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
GAREML	150946	hgsc.bcm.edu	37	2	26407120	26407120	+	Missense_Mutation	SNP	A	A	T	rs116239749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:26407120A>T	ENST00000401533.2	+	4	533	c.403A>T	c.(403-405)Agc>Tgc	p.S135C	GAREML_ENST00000407684.1_Missense_Mutation_p.S58C	NM_001168241.1	NP_001161713.1	Q75VX8	GAREL_HUMAN	GRB2 associated, regulator of MAPK1-like	135	CABIT.					extracellular vesicular exosome (GO:0070062)											GGGCGAGTTCAGCGAGGACAG	0.637													A|||	10	0.00199681	0.0	0.0	5008	,	,		14452	0.0		0.0089	False		,,,				2504	0.001				p.S135C		Atlas-SNP	.											.	.	.	.	0			c.A403T						PASS	.	A	CYS/SER,CYS/SER	2,1382		0,2,690	35.0	32.0	33.0		403,172	4.6	1.0	2	dbSNP_132	33	35,3147		0,35,1556	yes	missense,missense	FAM59B	NM_001168241.1,NM_001191033.1	112,112	0,37,2246	TT,TA,AA		1.0999,0.1445,0.8103	probably-damaging,probably-damaging	135/875,58/665	26407120	37,4529	692	1591	2283	SO:0001583	missense	150946	exon4			GAGTTCAGCGAGG	AK090454, AB015349, AB124552	CCDS54336.1, CCDS54337.1	2p23.3	2012-11-30	2012-11-30	2012-11-30	ENSG00000157833	ENSG00000157833			27172	protein-coding gene	gene with protein product			"""family with sequence similarity 59, member B"""	FAM59B			Standard	NM_001168241		Approved	KIAA2038, FLJ00375	uc002rgw.2	Q75VX8	OTTHUMG00000151935	ENST00000401533.2:c.403A>T	2.37:g.26407120A>T	ENSP00000384593:p.Ser135Cys	135.0	0.0	0		142.0	77.0	0.542253	NM_001168241	B5MC97|B7WNK9|Q8NF27|Q9UIK8	Missense_Mutation	SNP	ENST00000401533.2	37	CCDS54336.1	7	0.003205128205128205	0	0.0	0	0.0	0	0.0	7	0.009234828496042216	A	22.5	4.302172	0.81136	0.001445	0.010999	ENSG00000157833	ENST00000401533;ENST00000407684	T;T	0.16743	2.32;2.32	4.55	4.55	0.56014	.	0.000000	0.85682	D	0.000000	T	0.29355	0.0731	M	0.61703	1.905	0.46798	D	0.999206	D;D	0.76494	0.999;0.999	D;D	0.77004	0.975;0.989	T	0.08953	-1.0697	10	0.87932	D	0	-15.1645	12.1651	0.54125	1.0:0.0:0.0:0.0	.	58;135	B7WNK9;Q75VX8	.;FA59B_HUMAN	C	135;58	ENSP00000384593:S135C;ENSP00000384581:S58C	ENSP00000384593:S135C	S	+	1	0	FAM59B	26260624	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	8.718000	0.91430	1.813000	0.52934	0.528000	0.53228	AGC	A|0.997;T|0.003	0.003	strong		0.637	GAREML-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324498.2	NM_001168241	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144922252	144922252	+	Missense_Mutation	SNP	C	C	G	rs147451175	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:144922252C>G	ENST00000369354.3	-	8	1105	c.916G>C	c.(916-918)Ggt>Cgt	p.G306R	PDE4DIP_ENST00000530740.1_Missense_Mutation_p.G443R|PDE4DIP_ENST00000529945.1_Missense_Mutation_p.G469R|PDE4DIP_ENST00000369356.4_Missense_Mutation_p.G306R|PDE4DIP_ENST00000369351.3_Missense_Mutation_p.G306R|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.G372R|PDE4DIP_ENST00000479408.2_Missense_Mutation_p.G93R|PDE4DIP_ENST00000369349.3_Missense_Mutation_p.G306R|PDE4DIP_ENST00000313431.9_Missense_Mutation_p.G469R|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.G443R			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	306					cellular protein complex assembly (GO:0043623)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|myofibril (GO:0030016)|nucleus (GO:0005634)	enzyme binding (GO:0019899)			NS(1)|breast(3)|central_nervous_system(2)|cervix(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(9)|large_intestine(12)|lung(106)|ovary(8)|prostate(7)|skin(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	176				Colorectal(2;0.0829)|COAD - Colon adenocarcinoma(2;0.126)		TCATTTTGACCTTCAATTACC	0.398			T	PDGFRB	MPD								C|||	19	0.00379393	0.0	0.0072	5008	,	,		45130	0.0		0.0089	False		,,,				2504	0.0051				p.G469R		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	.	PDE4DIP	817	.	0			c.G1405C						PASS	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	3,4403	6.2+/-15.9	0,3,2200	163.0	141.0	148.0		1405,916,1114,916,916	3.1	1.0	1	dbSNP_134	148	52,8548	29.6+/-80.5	0,52,4248	yes	missense,missense,missense,missense,missense	PDE4DIP	NM_001002811.1,NM_001002812.1,NM_001198832.1,NM_001198834.2,NM_014644.4	125,125,125,125,125	0,55,6448	GG,GC,CC		0.6047,0.0681,0.4229	probably-damaging,probably-damaging,probably-damaging,probably-damaging,probably-damaging	469/1133,306/970,372/2241,306/2363,306/2347	144922252	55,12951	2203	4300	6503	SO:0001583	missense	9659	exon4			TTTGACCTTCAAT	AB007923, AB007946	CCDS72887.1, CCDS72888.1, CCDS72889.1, CCDS72890.1, CCDS72891.1, CCDS72892.1, CCDS72893.1, CCDS72894.1	1q21.1	2008-07-31	2008-07-31		ENSG00000178104	ENSG00000178104			15580	protein-coding gene	gene with protein product	"""myomegalin"""	608117	"""cardiomyopathy associated 2"""	CMYA2		9455484, 11134006	Standard	NM_022359		Approved	KIAA0477, KIAA0454, MMGL	uc021ouh.1	Q5VU43	OTTHUMG00000013846	ENST00000369354.3:c.916G>C	1.37:g.144922252C>G	ENSP00000358360:p.Gly306Arg	132.0	0.0	0		144.0	26.0	0.180556	NM_001002811	A2RU15|O75042|O75065|Q2YDC1|Q5VU42|Q5VU44|Q5VU45|Q5VU46|Q5VU47|Q5VU48|Q5VU49|Q68DU2|Q6AZ93|Q6PK88|Q86T40|Q86TB2|Q8N3W0|Q8TAY9|Q9HCP2|Q9HCP3|Q9HCP4|Q9HCP5	Missense_Mutation	SNP	ENST00000369354.3	37	CCDS30824.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	C	19.82	3.898738	0.72639	6.81E-4	0.006047	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000369353;ENST00000530740;ENST00000369359;ENST00000369351;ENST00000369349;ENST00000313431;ENST00000529945;ENST00000479408	T;T;T;T;T;T;T;T;T;T	0.12774	4.6;4.69;4.69;4.7;4.69;3.72;3.72;2.67;2.67;2.65	5.92	3.07	0.35406	.	.	.	.	.	T	0.18964	0.0455	M	0.67953	2.075	0.80722	D	1	D;D;D;D;D	0.71674	0.997;0.985;0.997;0.998;0.994	D;P;D;D;D	0.71870	0.931;0.859;0.954;0.975;0.929	T	0.00931	-1.1510	9	0.48119	T	0.1	.	9.4783	0.38884	0.0:0.7702:0.0:0.2298	.	469;306;469;372;306	E9PL24;Q5VU43-7;Q5VU43-2;Q5VU43-3;Q5VU43	.;.;.;.;MYOME_HUMAN	R	372;306;306;469;443;443;306;306;469;469;93	ENSP00000327209:G372R;ENSP00000358360:G306R;ENSP00000358363:G306R;ENSP00000435654:G443R;ENSP00000358366:G443R;ENSP00000358357:G306R;ENSP00000358355:G306R;ENSP00000316434:G469R;ENSP00000433392:G469R;ENSP00000436791:G93R	ENSP00000327209:G372R	G	-	1	0	PDE4DIP	143633609	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	1.718000	0.38001	0.411000	0.25702	0.650000	0.86243	GGT	C|0.996;G|0.004	0.004	strong		0.398	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
FAM208B	54906	hgsc.bcm.edu	37	10	5790738	5790738	+	Missense_Mutation	SNP	G	G	A	rs183849963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:5790738G>A	ENST00000328090.5	+	15	5979	c.5354G>A	c.(5353-5355)tGt>tAt	p.C1785Y		NM_017782.4	NP_060252	Q5VWN6	F208B_HUMAN	family with sequence similarity 208, member B	1785																	ACTTCTGTTTGTGGAATAGCC	0.498													G|||	5	0.000998403	0.0	0.0029	5008	,	,		20410	0.0		0.003	False		,,,				2504	0.0				p.C1785Y		Atlas-SNP	.											.	.	.	.	0			c.G5354A						PASS	.	G	TYR/CYS	2,3712		0,2,1855	82.0	79.0	80.0		5354	3.0	0.1	10		80	26,8222		1,24,4099	yes	missense	FAM208B	NM_017782.4	194	1,26,5954	AA,AG,GG		0.3152,0.0539,0.2341	probably-damaging	1785/2431	5790738	28,11934	1857	4124	5981	SO:0001583	missense	54906	exon15			CTGTTTGTGGAAT	BX649177	CCDS41485.1	10p15.1	2011-09-14	2011-09-14	2011-09-14	ENSG00000108021	ENSG00000108021			23484	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 18"""	C10orf18		12477932	Standard	NM_017782		Approved	FLJ20360, bA318E3.2, KIAA2006	uc001iij.3	Q5VWN6	OTTHUMG00000017605	ENST00000328090.5:c.5354G>A	10.37:g.5790738G>A	ENSP00000328426:p.Cys1785Tyr	91.0	0.0	0		106.0	41.0	0.386792	NM_017782	Q2YD91|Q5VWN5|Q6ZRQ8|Q8IVG4|Q9BUZ7|Q9H5J9|Q9H7A4|Q9H996|Q9NXA1	Missense_Mutation	SNP	ENST00000328090.5	37	CCDS41485.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	3.608	-0.080146	0.07141	5.39E-4	0.003152	ENSG00000108021	ENST00000328090;ENST00000442808	T	0.05258	3.47	5.82	2.98	0.34508	.	0.369488	0.27000	N	0.021434	T	0.04272	0.0118	L	0.29908	0.895	0.09310	N	1	B	0.19583	0.037	B	0.20184	0.028	T	0.45920	-0.9228	10	0.14252	T	0.57	.	5.9626	0.19308	0.1676:0.1569:0.6754:0.0	.	1785	Q5VWN6	F208B_HUMAN	Y	1785;980	ENSP00000328426:C1785Y	ENSP00000328426:C1785Y	C	+	2	0	C10orf18	5830744	0.330000	0.24705	0.086000	0.20670	0.005000	0.04900	0.357000	0.20199	0.383000	0.24910	-0.302000	0.09304	TGT	G|0.999;A|0.001	0.001	strong		0.498	FAM208B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046571.2	NM_017782	
DENND6B	414918	hgsc.bcm.edu	37	22	50755782	50755782	+	Silent	SNP	G	G	A	rs145811594	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:50755782G>A	ENST00000413817.3	-	5	464	c.393C>T	c.(391-393)ttC>ttT	p.F131F	XX-C283C717.1_ENST00000453835.1_RNA	NM_001001794.3	NP_001001794.3	Q8NEG7	DEN6B_HUMAN	DENN/MADD domain containing 6B	131					positive regulation of Rab GTPase activity (GO:0032851)	endosome (GO:0005768)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)										ACACGTAGCCGAAGTAGTGTG	0.637													G|||	28	0.00559105	0.0	0.0043	5008	,	,		12216	0.0		0.0129	False		,,,				2504	0.0123				p.F131F		Atlas-SNP	.											FAM116B,colon,carcinoma,0,1	.	.	1	0			c.C393T						scavenged	.	G		4,4192		0,4,2094	54.0	62.0	60.0		393	-9.6	0.6	22	dbSNP_134	60	63,8363		1,61,4151	no	coding-synonymous	FAM116B	NM_001001794.3		1,65,6245	AA,AG,GG		0.7477,0.0953,0.5308		131/586	50755782	67,12555	2098	4213	6311	SO:0001819	synonymous_variant	414918	exon5			GTAGCCGAAGTAG	AK054743	CCDS46732.1	22q13.33	2012-10-03	2012-10-03	2012-10-03	ENSG00000205593	ENSG00000205593		"""DENN/MADD domain containing"""	32690	protein-coding gene	gene with protein product			"""family with sequence similarity 116, member B"""	FAM116B		21330364	Standard	NM_001001794		Approved	MGC33692, AFI1B	uc011arv.1	Q8NEG7	OTTHUMG00000150210	ENST00000413817.3:c.393C>T	22.37:g.50755782G>A		87.0	1.0	0.0114943		82.0	41.0	0.5	NM_001001794	A6X8I5	Silent	SNP	ENST00000413817.3	37	CCDS46732.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	G	1.803	-0.476686	0.04414	9.53E-4	0.007477	ENSG00000205593	ENST00000433760	.	.	.	4.8	-9.6	0.00553	.	.	.	.	.	T	0.41696	0.1170	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.60712	-0.7209	4	.	.	.	-6.8758	10.8518	0.46775	0.3823:0.1029:0.5148:0.0	.	.	.	.	L	103	.	.	S	-	2	0	FAM116B	49098354	0.005000	0.15991	0.579000	0.28588	0.026000	0.11368	-0.863000	0.04259	-2.344000	0.00622	-1.855000	0.00564	TCG	G|0.992;A|0.008	0.008	strong		0.637	DENND6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316845.3	NM_001001794	
CCDC28B	79140	hgsc.bcm.edu	37	1	32669645	32669645	+	Splice_Site	SNP	C	C	T	rs41263993	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:32669645C>T	ENST00000373602.5	+	3	677	c.330C>T	c.(328-330)ttC>ttT	p.F110F	IQCC_ENST00000291358.6_5'Flank|CCDC28B_ENST00000483009.1_3'UTR|CCDC28B_ENST00000421922.2_Splice_Site_p.F110F|RP4-622L5.7_ENST00000373604.4_RNA|IQCC_ENST00000537469.1_5'Flank|RP4-622L5.7_ENST00000421616.1_RNA	NM_024296.3	NP_077272.2	Q9BUN5	CC28B_HUMAN	coiled-coil domain containing 28B	110					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cytoplasm (GO:0005737)				large_intestine(4)|lung(3)|ovary(1)|upper_aerodigestive_tract(2)	10		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0837)|Ovarian(437;0.101)|Breast(348;0.174)				TGCAGGCCTTCGGTGAGTCCT	0.607													C|||	28	0.00559105	0.0015	0.0115	5008	,	,		18193	0.0		0.0139	False		,,,				2504	0.0041				p.F110F		Atlas-SNP	.											.	CCDC28B	21	.	0			c.C330T	GRCh37	CS066273	CCDC28B	S	rs41263993	PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	45.0	46.0	46.0		330	-9.5	0.7	1	dbSNP_127	46	169,8431	78.1+/-140.7	4,161,4135	yes	coding-synonymous-near-splice	CCDC28B	NM_024296.3		4,168,6331	TT,TC,CC		1.9651,0.1589,1.3532		110/201	32669645	176,12830	2203	4300	6503	SO:0001630	splice_region_variant	79140	exon3			GGCCTTCGGTGAG	BC022848	CCDS354.2, CCDS72749.1	1p36.11-p34.2	2008-02-05			ENSG00000160050	ENSG00000160050			28163	protein-coding gene	gene with protein product		610162				16327777	Standard	XM_006710892		Approved	MGC1203, RP4-622L5.5	uc001bul.1	Q9BUN5	OTTHUMG00000005738	ENST00000373602.5:c.331+1C>T	1.37:g.32669645C>T		56.0	0.0	0		49.0	5.0	0.102041	NM_024296	A8K789|Q8TBV8	Silent	SNP	ENST00000373602.5	37	CCDS354.2																																																																																			C|0.987;T|0.013	0.013	strong		0.607	CCDC28B-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015723.4	NM_024296	Silent
COL4A4	1286	hgsc.bcm.edu	37	2	227920747	227920747	+	Missense_Mutation	SNP	C	C	T	rs150979437	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:227920747C>T	ENST00000396625.3	-	30	2837	c.2630G>A	c.(2629-2631)cGg>cAg	p.R877Q	COL4A4_ENST00000329662.7_Missense_Mutation_p.R877Q	NM_000092.4	NP_000083.3	P53420	CO4A4_HUMAN	collagen, type IV, alpha 4	877	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glomerular basement membrane development (GO:0032836)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)			breast(2)|central_nervous_system(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(15)|lung(35)|ovary(5)|pancreas(3)|prostate(2)|skin(12)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	98		Renal(207;0.00844)|all_lung(227;0.0187)|Lung NSC(271;0.0879)|all_hematologic(139;0.21)|Esophageal squamous(248;0.242)		Epithelial(121;6.7e-11)|all cancers(144;5.39e-08)|Lung(261;0.0132)|LUSC - Lung squamous cell carcinoma(224;0.0181)		TGCCCCAGGCCGTCCTGGGAG	0.627													C|||	26	0.00519169	0.0	0.0	5008	,	,		15399	0.0258		0.0	False		,,,				2504	0.0				p.R877Q		Atlas-SNP	.											.	COL4A4	215	.	0			c.G2630A						PASS	.	C	GLN/ARG	4,3654		0,4,1825	36.0	39.0	39.0		2630	-1.9	0.0	2	dbSNP_134	39	27,8121		0,27,4047	no	missense	COL4A4	NM_000092.4	43	0,31,5872	TT,TC,CC		0.3314,0.1093,0.2626	benign	877/1691	227920747	31,11775	1829	4074	5903	SO:0001583	missense	1286	exon30			CCAGGCCGTCCTG		CCDS42828.1	2q35-q37	2014-09-17			ENSG00000081052	ENSG00000081052		"""Collagens"""	2206	protein-coding gene	gene with protein product	"""collagen of basement membrane, alpha-4 chain"""	120131				1639407	Standard	NM_000092		Approved	CA44	uc021vxs.1	P53420	OTTHUMG00000149892	ENST00000396625.3:c.2630G>A	2.37:g.227920747C>T	ENSP00000379866:p.Arg877Gln	95.0	0.0	0		108.0	57.0	0.527778	NM_000092	A8MTZ1|Q53RW9|Q53S42|Q53WR1	Missense_Mutation	SNP	ENST00000396625.3	37	CCDS42828.1	224	0.10256410256410256	71	0.1443089430894309	23	0.06353591160220995	44	0.07692307692307693	86	0.11345646437994723	C	3.151	-0.174203	0.06421	0.001093	0.003314	ENSG00000081052	ENST00000396625;ENST00000329662	D;D	0.93307	-3.2;-3.2	5.63	-1.9	0.07665	.	.	.	.	.	T	0.02533	0.0077	N	0.16743	0.435	0.09310	N	1	B	0.13145	0.007	B	0.09377	0.004	T	0.40701	-0.9549	9	0.13470	T	0.59	.	2.2257	0.03983	0.2432:0.4338:0.1032:0.2199	.	877	P53420	CO4A4_HUMAN	Q	877	ENSP00000379866:R877Q;ENSP00000328553:R877Q	ENSP00000328553:R877Q	R	-	2	0	COL4A4	227628991	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	0.006000	0.13152	-0.756000	0.04703	-0.271000	0.10264	CGG	C|0.930;T|0.070	0.070	strong		0.627	COL4A4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000313770.1	NM_000092	
ANKHD1	54882	hgsc.bcm.edu	37	5	139838786	139838786	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:139838786A>C	ENST00000360839.2	+	9	1672	c.1518A>C	c.(1516-1518)gaA>gaC	p.E506D	ANKHD1_ENST00000297183.6_Missense_Mutation_p.E506D|ANKHD1_ENST00000394722.3_Missense_Mutation_p.E495D|ANKHD1-EIF4EBP3_ENST00000532219.1_Missense_Mutation_p.E506D|ANKHD1_ENST00000394723.3_Missense_Mutation_p.E506D	NM_017747.2	NP_060217.1	Q8IWZ3	ANKH1_HUMAN	ankyrin repeat and KH domain containing 1	506						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(8)|kidney(6)|large_intestine(14)|lung(18)|ovary(5)|prostate(2)|skin(3)|urinary_tract(2)	60			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AAACTCAAGAAACTGCTCTTA	0.363																																					p.E506D		Atlas-SNP	.											ANKHD1-EIF4EBP3,rectum,carcinoma,+2,2	ANKHD1	233	2	0			c.A1518C						PASS	.						75.0	77.0	76.0					5																	139838786		2203	4300	6503	SO:0001583	missense	54882	exon9			TCAAGAAACTGCT	AF521882	CCDS4225.1, CCDS43371.1, CCDS43372.1, CCDS75319.1	5q31.3	2013-01-10			ENSG00000131503	ENSG00000131503		"""Ankyrin repeat domain containing"""	24714	protein-coding gene	gene with protein product		610500				10470851, 11230166, 16098192	Standard	NM_017747		Approved	MASK, FLJ20288, FLJ11979, FLJ10042, FLJ14127, KIAA1085		Q8IWZ3	OTTHUMG00000161610	ENST00000360839.2:c.1518A>C	5.37:g.139838786A>C	ENSP00000354085:p.Glu506Asp	188.0	0.0	0		150.0	70.0	0.466667	NM_024668	A6NH85|Q149P2|Q8IWZ2|Q8WY90|Q96G77|Q96GK0|Q9H2U0|Q9HA95|Q9NWG4|Q9UPR7	Missense_Mutation	SNP	ENST00000360839.2	37	CCDS4225.1	.	.	.	.	.	.	.	.	.	.	A	19.90	3.912101	0.72983	.	.	ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000131503;ENSG00000254996	ENST00000360839;ENST00000422011;ENST00000297183;ENST00000253810;ENST00000310356;ENST00000421134;ENST00000394723;ENST00000394722;ENST00000532219	T;T;T;T;T;T	0.64618	-0.11;-0.11;2.39;2.39;2.39;-0.11	5.51	5.51	0.81932	Ankyrin repeat-containing domain (4);	0.000000	0.85682	D	0.000000	T	0.61565	0.2357	N	0.11927	0.2	0.58432	D	0.999997	D;D;D;D;D	0.89917	0.999;0.997;0.992;0.971;1.0	D;D;D;P;D	0.80764	0.98;0.992;0.989;0.77;0.994	T	0.66826	-0.5825	10	0.62326	D	0.03	.	9.8994	0.41338	0.879:0.0:0.121:0.0	.	506;506;506;495;506	Q8IWZ3-5;Q8IWZ2;Q8IWZ3;Q8IWZ3-3;Q8IWZ3-2	.;.;ANKH1_HUMAN;.;.	D	506;520;506;506;21;506;506;495;506	ENSP00000354085:E506D;ENSP00000297183:E506D;ENSP00000394489:E506D;ENSP00000378212:E506D;ENSP00000378211:E495D;ENSP00000432016:E506D	ENSP00000432016:E506D	E	+	3	2	ANKHD1-EIF4EBP3;ANKHD1	139818970	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	3.935000	0.56560	2.105000	0.64084	0.454000	0.30748	GAA	.	.	none		0.363	ANKHD1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000251672.1	NM_017747	
BPIFB6	128859	hgsc.bcm.edu	37	20	31619515	31619515	+	Missense_Mutation	SNP	G	G	A	rs41293138	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:31619515G>A	ENST00000349552.1	+	1	62	c.62G>A	c.(61-63)gGg>gAg	p.G21E		NM_174897.2	NP_777557.1	Q8NFQ5	BPIB6_HUMAN	BPI fold containing family B, member 6	21						extracellular region (GO:0005576)	lipid binding (GO:0008289)										GCTGACCCTGGGGCACTGCTG	0.662													G|||	10	0.00199681	0.0008	0.0014	5008	,	,		17401	0.0		0.008	False		,,,				2504	0.0				p.G21E		Atlas-SNP	.											.	.	.	.	0			c.G62A						PASS	.	G	GLU/GLY	9,4397	15.5+/-35.6	0,9,2194	43.0	33.0	37.0		62	4.8	1.0	20	dbSNP_127	37	62,8538	36.4+/-91.3	1,60,4239	yes	missense	BPIFB6	NM_174897.2	98	1,69,6433	AA,AG,GG		0.7209,0.2043,0.5459	possibly-damaging	21/454	31619515	71,12935	2203	4300	6503	SO:0001583	missense	128859	exon1			ACCCTGGGGCACT	AF465767	CCDS13211.1	20q11.21	2011-08-04	2011-07-29	2011-07-29	ENSG00000167104	ENSG00000167104		"""BPI fold containing"""	16504	protein-coding gene	gene with protein product		614110	"""bactericidal/permeability-increasing protein-like 3"""	BPIL3		12185532, 21787333	Standard	NM_174897		Approved	LPLUNC6	uc010zuc.2	Q8NFQ5	OTTHUMG00000032238	ENST00000349552.1:c.62G>A	20.37:g.31619515G>A	ENSP00000344929:p.Gly21Glu	138.0	0.0	0		165.0	50.0	0.30303	NM_174897		Missense_Mutation	SNP	ENST00000349552.1	37	CCDS13211.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	G	17.66	3.445168	0.63178	0.002043	0.007209	ENSG00000167104	ENST00000349552	T	0.02498	4.27	4.85	4.85	0.62838	.	0.117103	0.38111	N	0.001818	T	0.06325	0.0163	L	0.57536	1.79	0.38042	D	0.935492	D	0.62365	0.991	P	0.56823	0.807	T	0.03587	-1.1022	10	0.59425	D	0.04	.	13.4708	0.61281	0.0:0.0:1.0:0.0	rs41293138	21	Q8NFQ5	BPIB6_HUMAN	E	21	ENSP00000344929:G21E	ENSP00000344929:G21E	G	+	2	0	BPIFB6	31083176	1.000000	0.71417	0.981000	0.43875	0.451000	0.32288	4.825000	0.62708	2.240000	0.73641	0.561000	0.74099	GGG	G|0.995;A|0.005	0.005	strong		0.662	BPIFB6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078658.2	NM_174897	
GBGT1	26301	hgsc.bcm.edu	37	9	136029138	136029138	+	Silent	SNP	G	G	A	rs35902535	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136029138G>A	ENST00000372040.3	-	7	1181	c.870C>T	c.(868-870)ggC>ggT	p.G290G	RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000540636.1_Silent_p.G273G|GBGT1_ENST00000372043.3_Missense_Mutation_p.A284V|GBGT1_ENST00000472281.1_5'UTR	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	290					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		CAGCCATGATGCCATTGGCCT	0.587													G|||	210	0.0419329	0.0333	0.0403	5008	,	,		17659	0.002		0.0795	False		,,,				2504	0.0573				p.G290G		Atlas-SNP	.											.	GBGT1	25	.	0			c.C870T						PASS	.	G		200,4206	124.9+/-162.1	8,184,2011	121.0	113.0	116.0		870	2.3	1.0	9	dbSNP_126	116	618,7982	160.3+/-213.4	16,586,3698	no	coding-synonymous	GBGT1	NM_021996.4		24,770,5709	AA,AG,GG		7.186,4.5393,6.2894		290/348	136029138	818,12188	2203	4300	6503	SO:0001819	synonymous_variant	26301	exon7			CATGATGCCATTG	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.870C>T	9.37:g.136029138G>A		102.0	0.0	0		100.0	52.0	0.52	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Silent	SNP	ENST00000372040.3	37	CCDS6960.1	105	0.04807692307692308	21	0.042682926829268296	15	0.04143646408839779	2	0.0034965034965034965	67	0.08839050131926121	G	12.72	2.022220	0.35701	0.045393	0.07186	ENSG00000148288	ENST00000372043	T	0.23348	1.91	5.38	2.31	0.28768	.	.	.	.	.	T	0.01287	0.0042	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.00460	-1.1726	6	0.87932	D	0	-15.1162	5.0909	0.14708	0.2677:0.3054:0.4269:0.0	rs35902535;rs62638711	.	.	.	V	284	ENSP00000361113:A284V	ENSP00000361113:A284V	A	-	2	0	GBGT1	135018959	0.629000	0.27146	0.992000	0.48379	0.929000	0.56500	0.761000	0.26489	0.542000	0.28846	0.561000	0.74099	GCA	G|0.944;A|0.056	0.056	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
ZNF232	7775	hgsc.bcm.edu	37	17	5012935	5012935	+	Missense_Mutation	SNP	A	A	C	rs200108859		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:5012935A>C	ENST00000250076.3	-	3	906	c.252T>G	c.(250-252)caT>caG	p.H84Q	ZNF232_ENST00000416429.2_Missense_Mutation_p.H57Q|ZNF232_ENST00000575898.1_Missense_Mutation_p.H84Q|ZNF232_ENST00000575538.1_Intron|AC012146.7_ENST00000413077.1_RNA|AC012146.7_ENST00000571138.1_RNA	NM_014519.2	NP_055334.2	Q9UNY5	ZN232_HUMAN	zinc finger protein 232	57	SCAN box. {ECO:0000255|PROSITE- ProRule:PRU00187}.				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)			kidney(1)|large_intestine(2)|liver(1)|lung(4)|ovary(1)|prostate(2)	11						GGTAGCGGAGATGCCTGAAGC	0.557																																					p.H84Q		Atlas-SNP	.											.	ZNF232	42	.	0			c.T252G						PASS	.	A	GLN/HIS	0,4406		0,0,2203	154.0	125.0	135.0		252	-6.3	0.8	17		135	1,8599	1.2+/-3.3	0,1,4299	yes	missense	ZNF232	NM_014519.2	24	0,1,6502	CC,CA,AA		0.0116,0.0,0.0077	benign	84/445	5012935	1,13005	2203	4300	6503	SO:0001583	missense	7775	exon3			GCGGAGATGCCTG	AF080169	CCDS11068.1	17p13.2	2013-01-09			ENSG00000167840	ENSG00000167840		"""-"", ""Zinc fingers, C2H2-type"""	13026	protein-coding gene	gene with protein product						11311944	Standard	NM_014519		Approved	ZSCAN11	uc002gat.3	Q9UNY5	OTTHUMG00000099450	ENST00000250076.3:c.252T>G	17.37:g.5012935A>C	ENSP00000250076:p.His84Gln	186.0	0.0	0		184.0	86.0	0.467391	NM_014519		Missense_Mutation	SNP	ENST00000250076.3	37	CCDS11068.1	.	.	.	.	.	.	.	.	.	.	A	0.344	-0.948705	0.02304	0.0	1.16E-4	ENSG00000167840	ENST00000250076;ENST00000416429	T;T	0.03772	3.81;3.81	3.15	-6.3	0.02007	Retrovirus capsid, C-terminal (1);Transcription regulator SCAN (3);	0.277051	0.19503	N	0.112683	T	0.00998	0.0033	N	0.01096	-1.015	0.23581	N	0.997361	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.11329	0.006;0.001;0.0;0.0	T	0.25433	-1.0132	10	0.02654	T	1	.	5.1735	0.15122	0.419:0.432:0.0:0.1491	.	84;57;57;57	B4DNA7;B4DP49;Q9UNY5;Q9UNY5-2	.;.;ZN232_HUMAN;.	Q	84;57	ENSP00000250076:H84Q;ENSP00000416430:H57Q	ENSP00000250076:H84Q	H	-	3	2	ZNF232	4953659	0.000000	0.05858	0.841000	0.33234	0.923000	0.55619	-1.797000	0.01749	-1.716000	0.01387	-0.472000	0.04984	CAT	.	.	weak		0.557	ZNF232-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216915.1	NM_014519	
SLIRP	81892	hgsc.bcm.edu	37	14	78182188	78182188	+	Missense_Mutation	SNP	T	T	A	rs199752740		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:78182188T>A	ENST00000557342.1	+	3	271	c.230T>A	c.(229-231)cTa>cAa	p.L77Q	SLIRP_ENST00000238688.5_Missense_Mutation_p.L77Q|SLIRP_ENST00000557623.1_Missense_Mutation_p.L77Q|SLIRP_ENST00000557431.1_Missense_Mutation_p.L77Q	NM_001267864.1|NM_031210.5	NP_001254793.1|NP_112487.1	Q9GZT3	SLIRP_HUMAN	SRA stem-loop interacting RNA binding protein	77	RRM. {ECO:0000255|PROSITE- ProRule:PRU00176}.				mitochondrion morphogenesis (GO:0070584)|negative regulation of mitochondrial RNA catabolic process (GO:0000961)|regulation of transcription, DNA-templated (GO:0006355)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|spermatid development (GO:0007286)|transcription, DNA-templated (GO:0006351)	acrosomal vesicle (GO:0001669)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ribonucleoprotein complex (GO:0030529)|sperm flagellum (GO:0036126)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			kidney(1)|prostate(1)	2						CGGAATGCACTACAACAGGAA	0.328																																					p.L77Q		Atlas-SNP	.											.	SLIRP	6	.	0			c.T230A						PASS	.	T	GLN/LEU	0,4398		0,0,2199	75.0	89.0	84.0		230	5.8	1.0	14		84	2,8594	1.2+/-3.3	0,2,4296	no	missense	SLIRP	NM_031210.4	113	0,2,6495	AA,AT,TT		0.0233,0.0,0.0154	probably-damaging	77/110	78182188	2,12992	2199	4298	6497	SO:0001583	missense	81892	exon3			ATGCACTACAACA	AF253980	CCDS9866.1, CCDS58331.1, CCDS73668.1	14q24.3	2013-02-12	2011-06-17	2011-06-17	ENSG00000119705	ENSG00000119705		"""RNA binding motif (RRM) containing"""	20495	protein-coding gene	gene with protein product		610211	"""chromosome 14 open reading frame 156"""	C14orf156		16762838	Standard	NM_031210		Approved	DC50	uc001xue.5	Q9GZT3		ENST00000557342.1:c.230T>A	14.37:g.78182188T>A	ENSP00000450909:p.Leu77Gln	238.0	0.0	0		222.0	102.0	0.459459	NM_001267864	J3KMY7	Missense_Mutation	SNP	ENST00000557342.1	37	CCDS9866.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.2|20.2	3.956115|3.956115	0.73902|0.73902	0.0|0.0	2.33E-4|2.33E-4	ENSG00000119705|ENSG00000119705	ENST00000557342;ENST00000238688;ENST00000557623;ENST00000557431|ENST00000556831;ENST00000553981	T;T;T;T|.	0.21734|.	1.99;1.99;1.99;1.99|.	5.77|5.77	5.77|5.77	0.91146|0.91146	Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);|.	0.162010|.	0.41396|.	D|.	0.000897|.	T|T	0.77631|0.77631	0.4159|0.4159	M|M	0.79693|0.79693	2.465|2.465	0.44247|0.44247	D|D	0.997098|0.997098	D|.	0.89917|.	1.0|.	D|.	0.80764|.	0.994|.	T|T	0.78669|0.78669	-0.2114|-0.2114	10|5	0.87932|.	D|.	0|.	-5.4684|-5.4684	16.3818|16.3818	0.83467|0.83467	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	77|.	Q9GZT3|.	SLIRP_HUMAN|.	Q|N	77|75;50	ENSP00000450909:L77Q;ENSP00000238688:L77Q;ENSP00000452057:L77Q;ENSP00000450849:L77Q|.	ENSP00000238688:L77Q|.	L|Y	+|+	2|1	0|0	SLIRP|SLIRP	77251941|77251941	0.839000|0.839000	0.29477|0.29477	0.998000|0.998000	0.56505|0.56505	0.946000|0.946000	0.59487|0.59487	6.378000|6.378000	0.73150|0.73150	2.330000|2.330000	0.79161|0.79161	0.528000|0.528000	0.53228|0.53228	CTA|TAC	T|0.999;A|0.001	0.001	weak		0.328	SLIRP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000413901.1	NM_031210	
ZNF25	219749	hgsc.bcm.edu	37	10	38241220	38241220	+	Silent	SNP	T	T	C	rs146555827	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:38241220T>C	ENST00000302609.7	-	6	1418	c.1206A>G	c.(1204-1206)gaA>gaG	p.E402E	AL117337.1_ENST00000582458.1_RNA|ZNF25_ENST00000374633.1_5'UTR	NM_145011.2	NP_659448.1	P17030	ZNF25_HUMAN	zinc finger protein 25	402					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)|central_nervous_system(1)|endometrium(3)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	28		all_neural(218;0.0218)|Breast(68;0.0389)|Ovarian(717;0.0443)|Renal(717;0.157)				ACTTCCCACATTCCTTGCATG	0.433																																					p.E402E		Atlas-SNP	.											.	ZNF25	66	.	0			c.A1206G						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	92.0	90.0	90.0		1206	-4.1	0.7	10	dbSNP_134	90	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	ZNF25	NM_145011.2		0,10,6493	CC,CT,TT		0.1047,0.0227,0.0769		402/457	38241220	10,12996	2203	4300	6503	SO:0001819	synonymous_variant	219749	exon6			CCCACATTCCTTG	AK056452	CCDS7195.1	10p11.2	2013-01-08	2006-05-10		ENSG00000175395	ENSG00000175395		"""Zinc fingers, C2H2-type"", ""-"""	13043	protein-coding gene	gene with protein product		194528	"""zinc finger protein 25 (KOX 19)"""			1639412, 8464732	Standard	NM_145011		Approved	KOX19, FLJ31890, Zfp9	uc001ize.1	P17030	OTTHUMG00000019344	ENST00000302609.7:c.1206A>G	10.37:g.38241220T>C		78.0	0.0	0		92.0	51.0	0.554348	NM_145011	A9Z1X5|Q8IYE3|Q8NDD6|Q96MU2	Silent	SNP	ENST00000302609.7	37	CCDS7195.1																																																																																			T|0.999;C|0.001	0.001	strong		0.433	ZNF25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051214.1	NM_145011, NM_006966	
PODXL2	50512	hgsc.bcm.edu	37	3	127379635	127379635	+	Missense_Mutation	SNP	C	C	T	rs34691761	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:127379635C>T	ENST00000342480.6	+	3	803	c.764C>T	c.(763-765)cCg>cTg	p.P255L		NM_015720.2	NP_056535.1	Q9NZ53	PDXL2_HUMAN	podocalyxin-like 2	255					leukocyte tethering or rolling (GO:0050901)	integral component of plasma membrane (GO:0005887)	glycosaminoglycan binding (GO:0005539)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	26						ACAGTGACTCCGGGGGACCAG	0.627													C|||	13	0.00259585	0.0	0.0058	5008	,	,		18265	0.0		0.0089	False		,,,				2504	0.0				p.P255L		Atlas-SNP	.											.	PODXL2	53	.	0			c.C764T						PASS	.	C	LEU/PRO	3,4403	6.2+/-15.9	0,3,2200	35.0	39.0	37.0		764	-0.9	0.0	3	dbSNP_126	37	47,8553	30.1+/-81.4	1,45,4254	yes	missense	PODXL2	NM_015720.2	98	1,48,6454	TT,TC,CC		0.5465,0.0681,0.3844	benign	255/606	127379635	50,12956	2203	4300	6503	SO:0001583	missense	50512	exon3			TGACTCCGGGGGA	AF219137	CCDS3044.1	3q21.3	2005-02-18			ENSG00000114631	ENSG00000114631			17936	protein-coding gene	gene with protein product	"""endoglycan"""					10722749	Standard	NM_015720		Approved	PODLX2, endoglycan	uc003ejq.3	Q9NZ53	OTTHUMG00000159642	ENST00000342480.6:c.764C>T	3.37:g.127379635C>T	ENSP00000345359:p.Pro255Leu	127.0	0.0	0		123.0	49.0	0.398374	NM_015720	Q6UVY4|Q8WUV6	Missense_Mutation	SNP	ENST00000342480.6	37	CCDS3044.1	7	0.003205128205128205	0	0.0	1	0.0027624309392265192	0	0.0	6	0.0079155672823219	C	0	-2.607312	0.00121	6.81E-4	0.005465	ENSG00000114631	ENST00000342480;ENST00000302192	T	0.20738	2.05	4.67	-0.937	0.10415	.	1.475550	0.04280	N	0.343618	T	0.07863	0.0197	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.31806	-0.9930	10	0.20519	T	0.43	0.0338	9.3502	0.38133	0.0:0.4699:0.0:0.5301	rs34691761	255	Q9NZ53	PDXL2_HUMAN	L	255	ENSP00000345359:P255L	ENSP00000304498:P255L	P	+	2	0	PODXL2	128862325	0.000000	0.05858	0.001000	0.08648	0.025000	0.11179	-0.299000	0.08254	-0.341000	0.08376	-0.573000	0.04149	CCG	C|0.995;T|0.005	0.005	strong		0.627	PODXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356638.1	NM_015720	
C2orf71	388939	hgsc.bcm.edu	37	2	29295476	29295476	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29295476C>T	ENST00000331664.5	-	1	1651	c.1652G>A	c.(1651-1653)aGg>aAg	p.R551K		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	551					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						AAACTTGATCCTTTCGCTGAT	0.592																																					p.R551K		Atlas-SNP	.											.	C2orf71	146	.	0			c.G1652A						PASS	.						48.0	51.0	50.0					2																	29295476		2016	4170	6186	SO:0001583	missense	388939	exon1			TTGATCCTTTCGC		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.1652G>A	2.37:g.29295476C>T	ENSP00000332809:p.Arg551Lys	115.0	0.0	0		103.0	52.0	0.504854	NM_001029883		Missense_Mutation	SNP	ENST00000331664.5	37	CCDS42669.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.386668	0.25031	.	.	ENSG00000179270	ENST00000331664	T	0.20738	2.05	5.17	2.4	0.29515	.	0.258207	0.38111	N	0.001807	T	0.10035	0.0246	N	0.25647	0.755	0.27894	N	0.939233	B	0.32040	0.353	B	0.25884	0.064	T	0.25606	-1.0127	10	0.12766	T	0.61	-19.7104	5.7968	0.18392	0.0:0.4904:0.0:0.5096	.	551	A6NGG8	CB071_HUMAN	K	551	ENSP00000332809:R551K	ENSP00000332809:R551K	R	-	2	0	C2orf71	29148980	1.000000	0.71417	0.999000	0.59377	0.868000	0.49771	2.616000	0.46376	0.593000	0.29745	0.561000	0.74099	AGG	.	.	none		0.592	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
CILP2	148113	hgsc.bcm.edu	37	19	19653231	19653231	+	Missense_Mutation	SNP	T	T	A	rs186322474		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:19653231T>A	ENST00000291495.5	+	5	725	c.640T>A	c.(640-642)Tcg>Acg	p.S214T	CILP2_ENST00000588333.2_3'UTR|CILP2_ENST00000586018.1_Missense_Mutation_p.S220T	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	214						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CCTCCTGGGCTCGGTGGTCAC	0.627																																					p.S214T		Atlas-SNP	.											.	CILP2	84	.	0			c.T640A						PASS	.	T	THR/SER	0,4406		0,0,2203	34.0	31.0	32.0		640	1.5	0.1	19		32	2,8598	2.2+/-6.3	0,2,4298	no	missense	CILP2	NM_153221.2	58	0,2,6501	AA,AT,TT		0.0233,0.0,0.0154	benign	214/1157	19653231	2,13004	2203	4300	6503	SO:0001583	missense	148113	exon5			CTGGGCTCGGTGG	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.640T>A	19.37:g.19653231T>A	ENSP00000291495:p.Ser214Thr	56.0	0.0	0		62.0	33.0	0.532258	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	37	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	T	1.434	-0.569499	0.03910	0.0	2.33E-4	ENSG00000160161	ENST00000291495	T	0.39229	1.09	5.23	1.46	0.22682	Carboxypeptidase-like, regulatory domain (1);Carboxypeptidase, regulatory domain (1);	0.617705	0.16243	N	0.223061	T	0.17577	0.0422	N	0.13235	0.315	0.09310	N	1	B;B	0.14012	0.009;0.009	B;B	0.18871	0.023;0.014	T	0.18871	-1.0323	10	0.10902	T	0.67	-14.2755	0.421	0.00456	0.4059:0.1494:0.1428:0.3019	.	214;214	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	T	214	ENSP00000291495:S214T	ENSP00000291495:S214T	S	+	1	0	CILP2	19514231	0.001000	0.12720	0.086000	0.20670	0.209000	0.24338	0.967000	0.29344	-0.119000	0.11830	0.454000	0.30748	TCG	T|0.999;A|0.001	0.001	weak		0.627	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
OTOGL	283310	hgsc.bcm.edu	37	12	80764360	80764360	+	Missense_Mutation	SNP	C	C	T	rs146572555	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:80764360C>T	ENST00000547103.1	+	55	6569	c.6563C>T	c.(6562-6564)aCc>aTc	p.T2188I	OTOGL_ENST00000458043.2_Missense_Mutation_p.T2200I|OTOGL_ENST00000546620.1_Missense_Mutation_p.T219I			Q3ZCN5	OTOGL_HUMAN	otogelin-like	2188					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						GTAGGGAGTACCTGGCACTAC	0.308													C|||	14	0.00279553	0.0068	0.0029	5008	,	,		13968	0.0		0.003	False		,,,				2504	0.0				p.T2200I		Atlas-SNP	.											.	OTOGL	235	.	0			c.C6599T						PASS	.	C	ILE/THR	12,4394	17.9+/-39.9	0,12,2191	132.0	129.0	130.0		6599	0.1	0.0	12	dbSNP_134	130	4,8596	3.7+/-12.6	0,4,4296	yes	missense	OTOGL	NM_173591.3	89	0,16,6487	TT,TC,CC		0.0465,0.2724,0.123	benign	2200/2345	80764360	16,12990	2203	4300	6503	SO:0001583	missense	283310	exon55			GGAGTACCTGGCA	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.6563C>T	12.37:g.80764360C>T	ENSP00000447211:p.Thr2188Ile	67.0	0.0	0		47.0	29.0	0.617021	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		15|15	0.006868131868131868|0.006868131868131868	9|9	0.018292682926829267|0.018292682926829267	4|4	0.011049723756906077|0.011049723756906077	0|0	0.0|0.0	2|2	0.002638522427440633|0.002638522427440633	C|C	6.727|6.727	0.502843|0.502843	0.12822|0.12822	0.002724|0.002724	4.65E-4|4.65E-4	ENSG00000165899|ENSG00000165899	ENST00000298820|ENST00000547103;ENST00000458043;ENST00000546620;ENST00000550182	.|T;T;T;T	.|0.46063	.|2.23;2.23;2.13;0.88	5.44|5.44	0.118|0.118	0.14667|0.14667	.|.	.|0.315004	.|0.30869	.|N	.|0.008710	T|T	0.21801|0.21801	0.0525|0.0525	M|M	0.62723|0.62723	1.935|1.935	0.09310|0.09310	N|N	1|1	.|B	.|0.14012	.|0.009	.|B	.|0.16289	.|0.015	T|T	0.30357|0.30357	-0.9981|-0.9981	5|10	.|0.72032	.|D	.|0.01	.|.	9.8313|9.8313	0.40944|0.40944	0.0:0.6306:0.0:0.3694|0.0:0.6306:0.0:0.3694	.|.	.|565	.|Q3ZCN5	.|OTOGL_HUMAN	S|I	608|2188;2200;219;217	.|ENSP00000447211:T2188I;ENSP00000400895:T2200I;ENSP00000449094:T219I;ENSP00000449641:T217I	.|ENSP00000400895:T2200I	P|T	+|+	1|2	0|0	OTOGL|OTOGL	79288491|79288491	0.990000|0.990000	0.36364|0.36364	0.019000|0.019000	0.16419|0.16419	0.184000|0.184000	0.23303|0.23303	2.773000|2.773000	0.47686|0.47686	-0.268000|-0.268000	0.09312|0.09312	-0.229000|-0.229000	0.12294|0.12294	CCT|ACC	C|0.997;T|0.003	0.003	strong		0.308	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
SIGLEC7	27036	hgsc.bcm.edu	37	19	51650520	51650520	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51650520C>T	ENST00000317643.6	+	6	1236	c.1167C>T	c.(1165-1167)gaC>gaT	p.D389D	SIGLEC7_ENST00000305628.7_Silent_p.D296D|SIGLEC7_ENST00000600577.1_Intron	NM_014385.2	NP_055200.1	Q9Y286	SIGL7_HUMAN	sialic acid binding Ig-like lectin 7	389					cell adhesion (GO:0007155)	integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(11)|skin(2)|stomach(1)	29		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000836)|OV - Ovarian serous cystadenocarcinoma(262;0.00297)		CAGCAGCGGACGTGGGAGACA	0.577																																					p.D389D		Atlas-SNP	.											.	SIGLEC7	74	.	0			c.C1167T						PASS	.						124.0	99.0	107.0					19																	51650520		2203	4300	6503	SO:0001819	synonymous_variant	27036	exon6			AGCGGACGTGGGA	AF170485	CCDS12826.1, CCDS42601.1, CCDS62771.1	19q13.41	2014-03-20			ENSG00000168995	ENSG00000168995		"""Sialic acid binding Ig-like lectins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	10876	protein-coding gene	gene with protein product		604410	"""sialic acid binding Ig-like lectin 19, pseudogene"", ""sialic acid binding Ig-like lectin, pseudogene 2"""	SIGLEC19P, SIGLECP2		10567377	Standard	NM_001277201		Approved	SIGLEC-7, p75/AIRM1, QA79, CD328	uc002pvv.1	Q9Y286	OTTHUMG00000182895	ENST00000317643.6:c.1167C>T	19.37:g.51650520C>T		134.0	0.0	0		154.0	79.0	0.512987	NM_014385	Q9NZQ1|Q9UJ86|Q9UJ87|Q9Y502	Silent	SNP	ENST00000317643.6	37	CCDS12826.1																																																																																			.	.	none		0.577	SIGLEC7-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464226.2	NM_016543	
TNFRSF14	8764	hgsc.bcm.edu	37	1	2493168	2493168	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2493168G>A	ENST00000355716.4	+	6	907	c.608G>A	c.(607-609)tGg>tAg	p.W203*		NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	203					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell migration (GO:2000406)|T cell costimulation (GO:0031295)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			kidney(1)	1	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;1.11e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000326)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.199)		CACTGGGTATGGTGGTTTCTC	0.607			"""Mis, N, F"""		follicular lymphoma																																p.W203X		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""		L	.	TNFRSF14	89	.	0			c.G608A						PASS	.						91.0	83.0	86.0					1																	2493168		2203	4300	6503	SO:0001587	stop_gained	8764	exon6			GGGTATGGTGGTT	U70321	CCDS44046.1	1p36.32	2012-02-27	2011-08-11		ENSG00000157873	ENSG00000157873		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11912	protein-coding gene	gene with protein product	"""herpesvirus entry mediator"""	602746	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""			8898196, 9162061	Standard	XM_006711018		Approved	HVEM, ATAR, TR2, LIGHTR, HVEA, CD270	uc001ajt.1	Q92956	OTTHUMG00000000792	ENST00000355716.4:c.608G>A	1.37:g.2493168G>A	ENSP00000347948:p.Trp203*	67.0	0.0	0		72.0	47.0	0.652778	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Nonsense_Mutation	SNP	ENST00000355716.4	37	CCDS44046.1	.	.	.	.	.	.	.	.	.	.	G	16.88	3.243726	0.58995	.	.	ENSG00000157873	ENST00000434817;ENST00000435221;ENST00000451778;ENST00000355716	.	.	.	1.34	1.34	0.21922	.	.	.	.	.	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	-4.8029	6.0814	0.19942	0.0:0.0:1.0:0.0	.	.	.	.	X	203	.	ENSP00000347948:W203X	W	+	2	0	TNFRSF14	2481250	0.000000	0.05858	0.005000	0.12908	0.025000	0.11179	-0.033000	0.12246	1.091000	0.41335	0.205000	0.17691	TGG	.	.	none		0.607	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1		
RADIL	55698	hgsc.bcm.edu	37	7	4841614	4841614	+	Missense_Mutation	SNP	C	C	T	rs117943885	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4841614C>T	ENST00000399583.3	-	12	2699	c.2512G>A	c.(2512-2514)Gtg>Atg	p.V838M	RADIL_ENST00000536091.1_3'UTR|RADIL_ENST00000538469.1_Missense_Mutation_p.V598M	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	838					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		TCAAGGACCACGTGGTGCATA	0.677													C|||	64	0.0127796	0.0015	0.0187	5008	,	,		13575	0.0		0.0249	False		,,,				2504	0.0245				p.V838M		Atlas-SNP	.											.	RADIL	110	.	0			c.G2512A						PASS	.	C	MET/VAL	10,3304		0,10,1647	5.0	6.0	6.0		2512	-3.5	0.0	7	dbSNP_132	6	139,6811		3,133,3339	yes	missense	RADIL	NM_018059.4	21	3,143,4986	TT,TC,CC		2.0,0.3018,1.4517	benign	838/1076	4841614	149,10115	1657	3475	5132	SO:0001583	missense	55698	exon12			GGACCACGTGGTG	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.2512G>A	7.37:g.4841614C>T	ENSP00000382492:p.Val838Met	66.0	0.0	0		78.0	33.0	0.423077	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Missense_Mutation	SNP	ENST00000399583.3	37	CCDS43544.1	34	0.015567765567765568	2	0.0040650406504065045	13	0.03591160220994475	0	0.0	19	0.025065963060686015	C	8.995	0.978733	0.18812	0.003018	0.02	ENSG00000157927	ENST00000399583;ENST00000316919;ENST00000544486;ENST00000538469	T;T	0.07114	3.29;3.22	4.15	-3.5	0.04710	.	0.941613	0.08946	N	0.870830	T	0.00815	0.0027	N	0.08118	0	0.09310	N	1	B;B	0.16396	0.017;0.004	B;B	0.06405	0.002;0.0	T	0.41645	-0.9497	10	0.51188	T	0.08	-1.412	5.9949	0.19489	0.0:0.1746:0.2538:0.5716	.	838;146	Q96JH8;Q75LH2	RADIL_HUMAN;.	M	838;809;572;598	ENSP00000382492:V838M;ENSP00000442966:V598M	ENSP00000320946:V809M	V	-	1	0	RADIL	4808140	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.693000	0.05121	-1.147000	0.02851	-1.340000	0.01251	GTG	C|0.984;T|0.016	0.016	strong		0.677	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
EPPK1	83481	hgsc.bcm.edu	37	8	144944225	144944225	+	Missense_Mutation	SNP	C	C	T	rs118079568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144944225C>T	ENST00000525985.1	-	2	3268	c.3197G>A	c.(3196-3198)cGt>cAt	p.R1066H				P58107	EPIPL_HUMAN	epiplakin 1	1066						cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	poly(A) RNA binding (GO:0044822)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(5)|cervix(1)|endometrium(8)|kidney(4)|large_intestine(2)|lung(30)|ovary(2)|pancreas(1)|prostate(10)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(97;1.42e-10)|all_epithelial(106;1.99e-09)|Lung NSC(106;0.000126)|all_lung(105;0.000354)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;2.46e-41)|Epithelial(56;2.88e-40)|all cancers(56;1.82e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			AACATAGCCACGCTGAATGGC	0.642													C|||	26	0.00519169	0.0008	0.0144	5008	,	,		18612	0.001		0.0139	False		,,,				2504	0.0				p.R1066H		Atlas-SNP	.											.	EPPK1	199	.	0			c.G3197A						PASS	.	C	HIS/ARG	10,4230		1,8,2111	36.0	40.0	39.0		3197	3.6	0.9	8	dbSNP_132	39	145,8341		1,143,4099	yes	missense	EPPK1	NM_031308.1	29	2,151,6210	TT,TC,CC		1.7087,0.2358,1.218	probably-damaging	1066/2420	144944225	155,12571	2120	4243	6363	SO:0001583	missense	83481	exon1			TAGCCACGCTGAA	AB051895	CCDS75800.1	8q24.3	2014-09-17				ENSG00000261150			15577	protein-coding gene	gene with protein product	"""epidermal autoantigen 450K"""	607553				11278896, 15671067	Standard	NM_031308		Approved	EPIPL1	uc003zaa.1	P58107		ENST00000525985.1:c.3197G>A	8.37:g.144944225C>T	ENSP00000436337:p.Arg1066His	154.0	0.0	0		167.0	90.0	0.538922	NM_031308	Q76E58|Q9NSU9	Missense_Mutation	SNP	ENST00000525985.1	37		22	0.010073260073260074	1	0.0020325203252032522	6	0.016574585635359115	0	0.0	15	0.01978891820580475	C	17.80	3.478453	0.63849	0.002358	0.017087	ENSG00000227184	ENST00000525985	T	0.79247	-1.25	4.54	3.64	0.41730	.	.	.	.	.	T	0.79227	0.4410	M	0.79693	2.465	0.28124	N	0.930474	D	0.89917	1.0	D	0.72338	0.977	T	0.75428	-0.3321	9	0.66056	D	0.02	.	11.5171	0.50529	0.1804:0.8195:0.0:0.0	.	1066	E9PPU0	.	H	1066	ENSP00000436337:R1066H	ENSP00000436337:R1066H	R	-	2	0	EPPK1	145016213	0.117000	0.22190	0.871000	0.34182	0.301000	0.27625	0.709000	0.25734	1.067000	0.40740	0.563000	0.77884	CGT	C|0.990;T|0.010	0.010	strong		0.642	EPPK1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000382675.1	NM_031308	
MYRIP	25924	hgsc.bcm.edu	37	3	40231810	40231810	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:40231810C>T	ENST00000302541.6	+	10	1863	c.1521C>T	c.(1519-1521)acC>acT	p.T507T	MYRIP_ENST00000539167.1_Silent_p.T320T|MYRIP_ENST00000444716.1_Silent_p.T507T|MYRIP_ENST00000396217.3_Silent_p.T418T|MYRIP_ENST00000425621.1_Silent_p.T507T|MYRIP_ENST00000459828.1_3'UTR	NM_001284423.1|NM_001284426.1|NM_015460.2	NP_001271352.1|NP_001271355.1|NP_056275.2	Q8NFW9	MYRIP_HUMAN	myosin VIIA and Rab interacting protein	507	Actin-binding.|Myosin-binding.				intracellular protein transport (GO:0006886)|positive regulation of insulin secretion (GO:0032024)	actin cytoskeleton (GO:0015629)|dense core granule (GO:0031045)|exocyst (GO:0000145)|melanosome (GO:0042470)|perinuclear region of cytoplasm (GO:0048471)|photoreceptor outer segment (GO:0001750)|synapse (GO:0045202)	zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(9)|liver(2)|lung(10)|ovary(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34				KIRC - Kidney renal clear cell carcinoma(284;0.174)|Kidney(284;0.206)		GCAGGGAGACCTCGGACAGCA	0.642																																					p.T507T		Atlas-SNP	.											.	MYRIP	98	.	0			c.C1521T						PASS	.						60.0	67.0	65.0					3																	40231810		2203	4300	6503	SO:0001819	synonymous_variant	25924	exon10			GGAGACCTCGGAC	AF396687	CCDS2689.1, CCDS68390.1, CCDS68391.1, CCDS68392.1	3p21.33	2010-08-20			ENSG00000170011	ENSG00000170011		"""A-kinase anchor proteins"""	19156	protein-coding gene	gene with protein product	"""synaptotagmin-like protein homologue lacking C2 domains-c"", ""rab effector MYRIP"", ""Slp homologue lacking C2 domains"""	611790				11964381, 12221080	Standard	NM_001284425		Approved	DKFZp586F1018, exophilin-8, MyRIP, SLAC2-C, SLAC2C	uc003cka.3	Q8NFW9	OTTHUMG00000131392	ENST00000302541.6:c.1521C>T	3.37:g.40231810C>T		146.0	0.0	0		186.0	86.0	0.462366	NM_015460	B3KWM3|B3KWW4|B7Z2H1|B7Z9V3|G3XAI8|Q32M41|Q32M42|Q569F7|Q8IUF5|Q9Y3V4	Silent	SNP	ENST00000302541.6	37	CCDS2689.1																																																																																			.	.	none		0.642	MYRIP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254181.2	NM_015460	
ABCC12	94160	hgsc.bcm.edu	37	16	48139232	48139232	+	Nonsense_Mutation	SNP	G	G	A	rs151150316	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:48139232G>A	ENST00000311303.3	-	19	2836	c.2491C>T	c.(2491-2493)Cag>Tag	p.Q831*	ABCC12_ENST00000416054.1_3'UTR|ABCC12_ENST00000448542.1_Nonsense_Mutation_p.Q828*	NM_033226.2	NP_150229.2	Q96J65	MRP9_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	831	ABC transmembrane type-1 2. {ECO:0000255|PROSITE-ProRule:PRU00441}.					integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)			NS(1)|breast(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(15)|liver(1)|lung(43)|ovary(2)|prostate(3)|skin(7)|urinary_tract(1)	90		all_cancers(37;0.0474)|all_lung(18;0.047)				CTGTTGCCCTGGGGCCCACAG	0.517													G|||	3	0.000599042	0.0008	0.0	5008	,	,		20402	0.0		0.002	False		,,,				2504	0.0				p.Q831X		Atlas-SNP	.											.	ABCC12	190	.	0			c.C2491T						PASS	.	G	stop/GLN	5,4397	8.1+/-20.4	0,5,2196	61.0	49.0	53.0		2491	3.2	0.0	16	dbSNP_134	53	37,8563	22.8+/-68.1	0,37,4263	yes	stop-gained	ABCC12	NM_033226.2		0,42,6459	AA,AG,GG		0.4302,0.1136,0.323		831/1360	48139232	42,12960	2201	4300	6501	SO:0001587	stop_gained	94160	exon19			TGCCCTGGGGCCC	AY040220	CCDS10730.1	16q12.1	2012-03-14			ENSG00000140798	ENSG00000140798		"""ATP binding cassette transporters / subfamily C"""	14640	protein-coding gene	gene with protein product		607041				11435397, 11483364	Standard	NM_033226		Approved	MRP9	uc002efc.1	Q96J65	OTTHUMG00000133143	ENST00000311303.3:c.2491C>T	16.37:g.48139232G>A	ENSP00000311030:p.Gln831*	42.0	0.0	0		39.0	25.0	0.641026	NM_033226	Q49AL2|Q8TAF0|Q8TEY2	Nonsense_Mutation	SNP	ENST00000311303.3	37	CCDS10730.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	35	5.497679	0.96355	0.001136	0.004302	ENSG00000140798	ENST00000311303;ENST00000448542;ENST00000449939	.	.	.	5.21	3.23	0.37069	.	1.089020	0.06851	N	0.797314	.	.	.	.	.	.	0.09310	N	0.999995	.	.	.	.	.	.	.	.	.	.	0.27082	T	0.32	.	9.3552	0.38161	0.1553:0.0:0.8447:0.0	.	.	.	.	X	831;828;749	.	ENSP00000311030:Q831X	Q	-	1	0	ABCC12	46696733	0.001000	0.12720	0.009000	0.14445	0.127000	0.20565	0.706000	0.25690	2.405000	0.81733	0.655000	0.94253	CAG	G|0.998;A|0.002	0.002	strong		0.517	ABCC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256837.1	NM_033226	
FREM2	341640	hgsc.bcm.edu	37	13	39261784	39261784	+	Silent	SNP	C	C	A	rs8002488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39261784C>A	ENST00000280481.7	+	1	519	c.303C>A	c.(301-303)ccC>ccA	p.P101P		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	101					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		AGGTGCAGCCCGGGGACCGCT	0.677													C|||	289	0.0577077	0.2073	0.0216	5008	,	,		14748	0.0		0.0	False		,,,				2504	0.0				p.P101P		Atlas-SNP	.											.	FREM2	385	.	0			c.C303A						PASS	.	C		759,3645		77,605,1520	16.0	17.0	17.0		303	-5.8	0.9	13	dbSNP_116	17	11,8585		0,11,4287	no	coding-synonymous	FREM2	NM_207361.4		77,616,5807	AA,AC,CC		0.128,17.2343,5.9231		101/3170	39261784	770,12230	2202	4298	6500	SO:0001819	synonymous_variant	341640	exon1			GCAGCCCGGGGAC	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.303C>A	13.37:g.39261784C>A		36.0	0.0	0		66.0	38.0	0.575758	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Silent	SNP	ENST00000280481.7	37	CCDS31960.1																																																																																			C|0.944;A|0.056	0.056	strong		0.677	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
NOTCH1	4851	hgsc.bcm.edu	37	9	139397707	139397707	+	Silent	SNP	G	G	A	rs10521	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:139397707G>A	ENST00000277541.6	-	27	5169	c.5094C>T	c.(5092-5094)gaC>gaT	p.D1698D		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1698					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D1699D(11)		breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		ATGCGGCCACGTCGGTGGCAC	0.632			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)			G|||	2772	0.553514	0.5552	0.5115	5008	,	,		17626	0.9018		0.4046	False		,,,				2504	0.3753				p.D1698D		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1_ENST00000277541,colon,carcinoma,0,19	NOTCH1	1980	19	11	Substitution - coding silent(11)	haematopoietic_and_lymphoid_tissue(11)	c.C5094T						PASS	.	G		2208,2062		587,1034,514	57.0	67.0	64.0		5094	-4.9	0.8	9	dbSNP_52	64	3010,5508		545,1920,1794	no	coding-synonymous	NOTCH1	NM_017617.3		1132,2954,2308	AA,AG,GG		35.3369,48.2904,40.8039		1698/2556	139397707	5218,7570	2135	4259	6394	SO:0001819	synonymous_variant	4851	exon27			GGCCACGTCGGTG	AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.5094C>T	9.37:g.139397707G>A		73.0	0.0	0		84.0	30.0	0.357143	NM_017617	Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																			G|0.466;A|0.534	0.534	strong		0.632	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
CPB1	1360	hgsc.bcm.edu	37	3	148575250	148575250	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:148575250C>T	ENST00000491148.1	+	11	1322	c.988C>T	c.(988-990)Ctg>Ttg	p.L330L	RP11-680B3.2_ENST00000488190.1_RNA|CPB1_ENST00000282957.4_Silent_p.L330L|CPB1_ENST00000498639.1_3'UTR			P15086	CBPB1_HUMAN	carboxypeptidase B1 (tissue)	330						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			NS(1)|breast(3)|central_nervous_system(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	38			LUSC - Lung squamous cell carcinoma(72;0.0934)|Lung(72;0.115)			GCAGAATGCCCTGGCTAAAGC	0.423																																					p.L330L		Atlas-SNP	.											.	CPB1	74	.	0			c.C988T						PASS	.						111.0	102.0	105.0					3																	148575250		2203	4300	6503	SO:0001819	synonymous_variant	1360	exon10			AATGCCCTGGCTA	AJ224866	CCDS33874.1	3q24	2012-02-10			ENSG00000153002	ENSG00000153002	3.4.17.2		2299	protein-coding gene	gene with protein product	"""pancreatic carboxypeptidase B"", ""tissue carboxypeptidase B"", ""protaminase"""	114852					Standard	XM_005247124		Approved		uc003ewl.3	P15086	OTTHUMG00000159520	ENST00000491148.1:c.988C>T	3.37:g.148575250C>T		130.0	0.0	0		126.0	56.0	0.444444	NM_001871	O60834|Q53XJ0|Q96BQ8	Silent	SNP	ENST00000491148.1	37	CCDS33874.1																																																																																			.	.	none		0.423	CPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355928.1	NM_001871	
PLA2G5	5322	hgsc.bcm.edu	37	1	20417066	20417066	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:20417066G>A	ENST00000375108.3	+	5	566	c.298G>A	c.(298-300)Ggg>Agg	p.G100R	PLA2G5_ENST00000486277.1_3'UTR	NM_000929.2	NP_000920.1	P39877	PA2G5_HUMAN	phospholipase A2, group V	100					arachidonic acid secretion (GO:0050482)|glycerophospholipid biosynthetic process (GO:0046474)|leukotriene biosynthetic process (GO:0019370)|lipid catabolic process (GO:0016042)|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 metabolic process (GO:0006644)|platelet activating factor biosynthetic process (GO:0006663)|response to cAMP (GO:0051591)|response to cytokine (GO:0034097)|small molecule metabolic process (GO:0044281)	cell surface (GO:0009986)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|calcium-dependent phospholipase A2 activity (GO:0047498)|heparin binding (GO:0008201)			NS(1)|large_intestine(1)|lung(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	14		Colorectal(325;3.46e-05)|Renal(390;0.000147)|all_lung(284;0.000249)|Lung NSC(340;0.000287)|Breast(348;0.000812)|Ovarian(437;0.00328)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0182)|COAD - Colon adenocarcinoma(152;1.22e-05)|BRCA - Breast invasive adenocarcinoma(304;8.15e-05)|Kidney(64;0.000184)|GBM - Glioblastoma multiforme(114;0.00089)|KIRC - Kidney renal clear cell carcinoma(64;0.0027)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0652)		TGCAGAGCCCGGGCCCTTCTG	0.557																																					p.G100R		Atlas-SNP	.											.	PLA2G5	21	.	0			c.G298A						PASS	.						145.0	127.0	133.0					1																	20417066		2203	4300	6503	SO:0001583	missense	5322	exon5			GAGCCCGGGCCCT	U03090	CCDS202.1	1p36-p34	2008-09-19			ENSG00000127472	ENSG00000127472	3.1.1.4		9038	protein-coding gene	gene with protein product		601192				8838795, 8300559	Standard	NM_000929		Approved		uc001bcy.3	P39877	OTTHUMG00000002698	ENST00000375108.3:c.298G>A	1.37:g.20417066G>A	ENSP00000364249:p.Gly100Arg	134.0	0.0	0		174.0	65.0	0.373563	NM_000929	Q8N435	Missense_Mutation	SNP	ENST00000375108.3	37	CCDS202.1	.	.	.	.	.	.	.	.	.	.	G	17.88	3.498320	0.64186	.	.	ENSG00000127472	ENST00000375108	T	0.26223	1.75	5.77	5.77	0.91146	Phospholipase A2 (3);	0.847373	0.10252	N	0.697050	T	0.46639	0.1403	L	0.48642	1.525	0.09310	N	1	D;D	0.89917	1.0;1.0	D;D	0.71656	0.974;0.939	T	0.39251	-0.9623	10	0.51188	T	0.08	-16.3128	15.4945	0.75637	0.0:0.0:1.0:0.0	.	100;73	P39877;B3KUQ4	PA2G5_HUMAN;.	R	100	ENSP00000364249:G100R	ENSP00000364249:G100R	G	+	1	0	PLA2G5	20289653	0.484000	0.25964	0.010000	0.14722	0.004000	0.04260	3.297000	0.51810	2.720000	0.93068	0.557000	0.71058	GGG	.	.	none		0.557	PLA2G5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000007668.1	NM_000929	
NAT6	24142	hgsc.bcm.edu	37	3	50334568	50334568	+	Silent	SNP	G	G	A	rs199554290		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:50334568G>A	ENST00000443842.1	-	2	1134	c.327C>T	c.(325-327)agC>agT	p.S109S	NAT6_ENST00000354862.4_Silent_p.S131S|HYAL3_ENST00000359051.3_Intron|NAT6_ENST00000417393.1_Silent_p.S109S|HYAL3_ENST00000450982.1_Intron|HYAL3_ENST00000513170.1_Intron|HYAL3_ENST00000415204.1_Intron|HYAL3_ENST00000336307.1_Intron|NAT6_ENST00000443094.2_Silent_p.S109S			Q93015	NAT6_HUMAN	N-acetyltransferase 6 (GCN5-related)	109	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.					cytoplasm (GO:0005737)	N-acetyltransferase activity (GO:0008080)			endometrium(3)|lung(1)|skin(1)	5				BRCA - Breast invasive adenocarcinoma(193;0.000272)|KIRC - Kidney renal clear cell carcinoma(197;0.00544)|Kidney(197;0.00605)		TGGGGTGGGGGCTTAGCAGCA	0.647																																					p.S131S		Atlas-SNP	.											.	NAT6	14	.	0			c.C393T						PASS	.	G	,,,,,,,	3,4157		0,3,2077	20.0	25.0	23.0		327,327,,,,,,393	1.6	0.9	3		23	20,8362		0,20,4171	no	coding-synonymous,coding-synonymous,intron,intron,intron,intron,intron,coding-synonymous	HYAL3,NAT6	NM_001200016.1,NM_001200018.1,NM_001200029.1,NM_001200030.1,NM_001200031.1,NM_001200032.1,NM_003549.3,NM_012191.3	,,,,,,,	0,23,6248	AA,AG,GG		0.2386,0.0721,0.1834	,,,,,,,	109/287,109/287,,,,,,131/309	50334568	23,12519	2080	4191	6271	SO:0001819	synonymous_variant	24142	exon2			GTGGGGGCTTAGC	AF040705	CCDS43095.1, CCDS56258.1	3p21.3	2011-11-16	2008-09-24		ENSG00000243477	ENSG00000243477	2.3.1.-		30252	protein-coding gene	gene with protein product		607073	"""N-acetyltransferase 6"""			11929860, 11085536	Standard	NM_012191		Approved	FUS2		Q93015	OTTHUMG00000156939	ENST00000443842.1:c.327C>T	3.37:g.50334568G>A		91.0	0.0	0		113.0	66.0	0.584071	NM_012191	Q93014	Silent	SNP	ENST00000443842.1	37	CCDS56258.1																																																																																			G|0.997;A|0.003	0.003	weak		0.647	NAT6-002	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000346681.1	NM_012191	
TFAP2D	83741	hgsc.bcm.edu	37	6	50682935	50682935	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:50682935C>G	ENST00000008391.3	+	2	374	c.146C>G	c.(145-147)tCc>tGc	p.S49C		NM_172238.3	NP_758438.2			transcription factor AP-2 delta (activating enhancer binding protein 2 delta)											NS(1)|biliary_tract(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(26)|ovary(6)|pancreas(1)|prostate(5)|stomach(1)	60	Lung NSC(77;0.0334)					TTAACTTACTCCACCACCGGC	0.547																																					p.S49C		Atlas-SNP	.											.	TFAP2D	144	.	0			c.C146G						PASS	.						245.0	195.0	212.0					6																	50682935		2203	4300	6503	SO:0001583	missense	83741	exon2			CTTACTCCACCAC	AY028376	CCDS4933.1	6p12.3	2008-02-05	2004-10-26	2004-10-27		ENSG00000008197			15581	protein-coding gene	gene with protein product		610161	"""transcription factor AP-2 beta (activating enhancer-binding protein 2 beta)-like 1"""	TFAP2BL1		11733187	Standard	NM_172238		Approved		uc003paf.3	Q7Z6R9		ENST00000008391.3:c.146C>G	6.37:g.50682935C>G	ENSP00000008391:p.Ser49Cys	196.0	0.0	0		206.0	10.0	0.0485437	NM_172238		Missense_Mutation	SNP	ENST00000008391.3	37	CCDS4933.1	.	.	.	.	.	.	.	.	.	.	C	14.00	2.404207	0.42613	.	.	ENSG00000008197	ENST00000008391	D	0.97505	-4.41	5.07	5.07	0.68467	.	0.127543	0.53938	D	0.000045	D	0.91112	0.7202	N	0.08118	0	0.54753	D	0.999988	B	0.28713	0.22	B	0.33846	0.171	D	0.90227	0.4276	10	0.87932	D	0	0.3288	18.8076	0.92045	0.0:1.0:0.0:0.0	.	49	Q7Z6R9	AP2D_HUMAN	C	49	ENSP00000008391:S49C	ENSP00000008391:S49C	S	+	2	0	TFAP2D	50790894	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.763000	0.68818	2.498000	0.84270	0.655000	0.94253	TCC	.	.	none		0.547	TFAP2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040881.1	NM_172238	
OBSCN	84033	hgsc.bcm.edu	37	1	228437757	228437757	+	Silent	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228437757C>A	ENST00000422127.1	+	14	4169	c.4125C>A	c.(4123-4125)gcC>gcA	p.A1375A	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Silent_p.A1375A|OBSCN_ENST00000570156.2_Silent_p.A1467A	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	1375	Ig-like 14.				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)				GCGAGGTGGCCCAGGCCCAGA	0.642																																					p.A1467A		Atlas-SNP	.											.	OBSCN	2142	.	0			c.C4401A						PASS	.						69.0	72.0	71.0					1																	228437757		2065	4189	6254	SO:0001819	synonymous_variant	84033	exon15			GGTGGCCCAGGCC	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.4125C>A	1.37:g.228437757C>A		290.0	1.0	0.00344828		258.0	95.0	0.368217	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		0.642	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
KCNJ16	3773	hgsc.bcm.edu	37	17	68128417	68128417	+	Silent	SNP	C	C	T	rs34408089	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:68128417C>T	ENST00000589377.1	+	2	352	c.189C>T	c.(187-189)acC>acT	p.T63T	KCNJ16_ENST00000392671.1_Silent_p.T63T|KCNJ16_ENST00000392670.1_Silent_p.T63T|KCNJ16_ENST00000585558.1_Silent_p.T98T|KCNJ16_ENST00000586462.1_Silent_p.T102T|KCNJ16_ENST00000283936.1_Silent_p.T63T	NM_001270422.1	NP_001257351.1	Q9NPI9	KCJ16_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 16	63					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	32	Breast(10;2.96e-09)					ACATCTTCACCACTCTTGTGG	0.413													C|||	84	0.0167732	0.0159	0.0115	5008	,	,		21473	0.0		0.0288	False		,,,				2504	0.0266				p.T63T		Atlas-SNP	.											.	KCNJ16	72	.	0			c.C189T						PASS	.	C	,,	73,4333	65.3+/-102.7	1,71,2131	283.0	249.0	261.0		189,189,189	3.1	1.0	17	dbSNP_126	261	220,8380	92.6+/-154.6	2,216,4082	no	coding-synonymous,coding-synonymous,coding-synonymous	KCNJ16	NM_018658.1,NM_170741.1,NM_170742.1	,,	3,287,6213	TT,TC,CC		2.5581,1.6568,2.2528	,,	63/419,63/419,63/419	68128417	293,12713	2203	4300	6503	SO:0001819	synonymous_variant	3773	exon6			CTTCACCACTCTT	AF153815	CCDS11687.1, CCDS74141.1	17q24.3	2011-07-05				ENSG00000153822		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6262	protein-coding gene	gene with protein product		605722				11240146, 16382105	Standard	NM_018658		Approved	Kir5.1, BIR9	uc002jio.4	Q9NPI9		ENST00000589377.1:c.189C>T	17.37:g.68128417C>T		149.0	0.0	0		137.0	69.0	0.50365	NM_001270422		Silent	SNP	ENST00000589377.1	37	CCDS11687.1																																																																																			C|0.976;T|0.024	0.024	strong		0.413	KCNJ16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450880.1	NM_018658	
MYO7A	4647	hgsc.bcm.edu	37	11	76924066	76924066	+	Missense_Mutation	SNP	G	G	A	rs1132036	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:76924066G>A	ENST00000409709.3	+	47	6696	c.6424G>A	c.(6424-6426)Gat>Aat	p.D2142N	MYO7A_ENST00000605744.1_3'UTR|MYO7A_ENST00000409619.2_Missense_Mutation_p.D2093N|MYO7A_ENST00000458637.2_Missense_Mutation_p.D2102N	NM_000260.3	NP_000251.3	Q13402	MYO7A_HUMAN	myosin VIIA	2142	FERM 2. {ECO:0000255|PROSITE- ProRule:PRU00084}.		D -> N (in dbSNP:rs1132036).		actin filament-based movement (GO:0030048)|auditory receptor cell stereocilium organization (GO:0060088)|equilibrioception (GO:0050957)|eye photoreceptor cell development (GO:0042462)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|metabolic process (GO:0008152)|phagolysosome assembly (GO:0001845)|pigment granule transport (GO:0051904)|post-embryonic organ morphogenesis (GO:0048563)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|melanosome (GO:0042470)|myosin VII complex (GO:0031477)|photoreceptor connecting cilium (GO:0032391)|photoreceptor inner segment (GO:0001917)|photoreceptor outer segment (GO:0001750)|stereocilium (GO:0032420)|synapse (GO:0045202)	actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|microfilament motor activity (GO:0000146)|spectrin binding (GO:0030507)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	64						CAGCCTCATCGATCCCAAAAC	0.532													G|||	151	0.0301518	0.1089	0.0086	5008	,	,		20348	0.0		0.001	False		,,,				2504	0.0				p.D2142N		Atlas-SNP	.											MYO7A,rectum,carcinoma,0,1	MYO7A	164	1	0			c.G6424A						scavenged	.	G	ASN/ASP,ASN/ASP	312,3634		18,276,1679	61.0	55.0	57.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	6424,6304	3.8	0.9	11	dbSNP_86	57	2,8300		0,2,4149	yes	missense,missense	MYO7A	NM_000260.3,NM_001127180.1	23,23	18,278,5828	AA,AG,GG		0.0241,7.9067,2.5637	benign,benign	2142/2216,2102/2176	76924066	314,11934	1973	4151	6124	SO:0001583	missense	4647	exon47			CTCATCGATCCCA	U39226	CCDS53683.1, CCDS53684.1, CCDS53685.1	11q13.5	2013-01-08	2005-09-12		ENSG00000137474	ENSG00000137474		"""A-kinase anchor proteins"", ""Myosins / Myosin superfamily : Class VII"""	7606	protein-coding gene	gene with protein product		276903	"""myosin VIIA (Usher syndrome 1B (autosomal recessive, severe))"""	USH1B, DFNB2, DFNA11		8884266	Standard	NM_000260		Approved	NSRD2	uc001oyb.2	Q13402	OTTHUMG00000152822	ENST00000409709.3:c.6424G>A	11.37:g.76924066G>A	ENSP00000386331:p.Asp2142Asn	86.0	1.0	0.0116279		67.0	23.0	0.343284	NM_000260	B9A011|F8VUN5|P78427|Q13321|Q14785|Q92821|Q92822	Missense_Mutation	SNP	ENST00000409709.3	37	CCDS53683.1	57	0.0260989010989011	52	0.10569105691056911	4	0.011049723756906077	0	0.0	1	0.0013192612137203166	G	13.65	2.300715	0.40694	0.079067	2.41E-4	ENSG00000137474	ENST00000409709;ENST00000458637;ENST00000409619;ENST00000545136;ENST00000358342;ENST00000343356;ENST00000341717;ENST00000458169	T;T;T;T	0.80123	-1.34;-1.34;-1.34;-1.34	4.74	3.83	0.44106	FERM domain (1);Pleckstrin homology-type (1);	0.201491	0.49916	D	0.000122	T	0.02649	0.0080	N	0.20328	0.56	0.58432	D	0.999998	B;B	0.31485	0.068;0.325	B;B	0.20384	0.014;0.029	T	0.05146	-1.0903	10	0.24483	T	0.36	.	13.242	0.60002	0.0776:0.0:0.9224:0.0	rs1132036;rs3192425;rs7117511;rs11546951;rs17417614;rs52822228;rs1132036	2102;2142	F8VUN5;Q13402	.;MYO7A_HUMAN	N	2142;2102;2093;1315;2141;2111;2018;1284	ENSP00000386331:D2142N;ENSP00000392185:D2102N;ENSP00000386635:D2093N;ENSP00000417017:D1284N	ENSP00000345075:D2018N	D	+	1	0	MYO7A	76601714	1.000000	0.71417	0.932000	0.37286	0.858000	0.48976	5.057000	0.64294	1.117000	0.41842	0.585000	0.79938	GAT	G|0.966;A|0.034	0.034	strong		0.532	MYO7A-001	KNOWN	non_canonical_conserved|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000328133.1	NM_000260	
F11	2160	hgsc.bcm.edu	37	4	187195373	187195373	+	Silent	SNP	C	C	T	rs5973	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:187195373C>T	ENST00000403665.2	+	5	781	c.429C>T	c.(427-429)gaC>gaT	p.D143D	F11_ENST00000264692.4_Intron|F11_ENST00000492972.2_Silent_p.D143D	NM_000128.3	NP_000119.1	P03951	FA11_HUMAN	coagulation factor XI	143	Apple 2. {ECO:0000255|PROSITE- ProRule:PRU00315}.				blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|plasminogen activation (GO:0031639)|positive regulation of fibrinolysis (GO:0051919)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	heparin binding (GO:0008201)|serine-type aminopeptidase activity (GO:0070009)|serine-type endopeptidase activity (GO:0004252)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(15)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)	32		all_cancers(14;6.2e-52)|all_epithelial(14;1.62e-38)|all_lung(41;1.34e-13)|Lung NSC(41;3.58e-13)|Melanoma(20;1.91e-06)|Hepatocellular(41;0.00886)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|Colorectal(36;0.0161)|all_neural(102;0.202)		OV - Ovarian serous cystadenocarcinoma(60;2.13e-11)|BRCA - Breast invasive adenocarcinoma(30;4.59e-06)|GBM - Glioblastoma multiforme(59;0.000149)|STAD - Stomach adenocarcinoma(60;0.000314)|LUSC - Lung squamous cell carcinoma(40;0.00112)|READ - Rectum adenocarcinoma(43;0.176)	Coagulation Factor IX(DB00100)	GCACGGATGACGTCCACTGCC	0.483													C|||	315	0.0628994	0.1853	0.0418	5008	,	,		18531	0.0		0.0358	False		,,,				2504	0.0051				p.D143D		Atlas-SNP	.											.	F11	65	.	0			c.C429T						PASS	.	C		647,3759	277.2+/-273.6	51,545,1607	171.0	139.0	150.0		429	-1.3	0.0	4	dbSNP_52	150	249,8351	98.4+/-159.9	5,239,4056	no	coding-synonymous	F11	NM_000128.3		56,784,5663	TT,TC,CC		2.8953,14.6845,6.8891		143/626	187195373	896,12110	2203	4300	6503	SO:0001819	synonymous_variant	2160	exon5			GGATGACGTCCAC	M13142	CCDS3847.1	4q35	2008-08-01	2008-08-01		ENSG00000088926	ENSG00000088926	3.4.21.27		3529	protein-coding gene	gene with protein product	"""plasma thromboplastin antecedent"""	264900					Standard	NM_000128		Approved	FXI	uc003iza.1	P03951	OTTHUMG00000150311	ENST00000403665.2:c.429C>T	4.37:g.187195373C>T		169.0	0.0	0		198.0	94.0	0.474747	NM_000128	D3DP64|Q4W5C2|Q9Y495	Silent	SNP	ENST00000403665.2	37	CCDS3847.1																																																																																			C|0.938;T|0.062	0.062	strong		0.483	F11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317519.4		
MICAL2	9645	hgsc.bcm.edu	37	11	12248590	12248590	+	Missense_Mutation	SNP	A	A	G	rs35228638	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12248590A>G	ENST00000256194.4	+	15	2195	c.1907A>G	c.(1906-1908)tAt>tGt	p.Y636C	MICAL2_ENST00000527546.1_Missense_Mutation_p.Y636C|MICAL2_ENST00000537344.1_Missense_Mutation_p.Y636C|MICAL2_ENST00000379612.3_Missense_Mutation_p.Y636C|MICAL2_ENST00000342902.5_Missense_Mutation_p.Y636C	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	636					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		CGCAAAAACTATGGAGAAAAT	0.453													A|||	12	0.00239617	0.0	0.0014	5008	,	,		21389	0.0		0.0109	False		,,,				2504	0.0				p.Y636C		Atlas-SNP	.											.	MICAL2	114	.	0			c.A1907G						PASS	.	A	CYS/TYR	13,4389	19.1+/-41.9	0,13,2188	111.0	101.0	104.0		1907	3.8	1.0	11	dbSNP_126	104	97,8491	54.0+/-114.7	2,93,4199	yes	missense	MICAL2	NM_014632.2	194	2,106,6387	GG,GA,AA		1.1295,0.2953,0.8468	benign	636/1125	12248590	110,12880	2201	4294	6495	SO:0001583	missense	9645	exon15			AAAACTATGGAGA	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.1907A>G	11.37:g.12248590A>G	ENSP00000256194:p.Tyr636Cys	130.0	0.0	0		124.0	51.0	0.41129	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	8	0.003663003663003663	0	0.0	1	0.0027624309392265192	0	0.0	7	0.009234828496042216	A	7.192	0.591637	0.13812	0.002953	0.011295	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.60920	0.15;0.15;0.15;0.15;0.24	4.88	3.75	0.43078	.	0.567421	0.17466	N	0.173256	T	0.40222	0.1108	L	0.44542	1.39	0.31618	N	0.650676	B;B;B;B;B;B	0.10296	0.003;0.001;0.001;0.0;0.001;0.0	B;B;B;B;B;B	0.04013	0.001;0.001;0.001;0.0;0.001;0.001	T	0.50457	-0.8826	10	0.46703	T	0.11	.	10.4565	0.44553	0.9224:0.0:0.0776:0.0	rs35228638	169;636;636;636;636;636	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	C	636;169;636;636;636;636	ENSP00000441689:Y636C;ENSP00000256194:Y636C;ENSP00000433965:Y636C;ENSP00000344894:Y636C;ENSP00000368932:Y636C	ENSP00000256194:Y636C	Y	+	2	0	MICAL2	12205166	1.000000	0.71417	0.977000	0.42913	0.336000	0.28762	4.903000	0.63272	0.881000	0.35993	0.533000	0.62120	TAT	A|0.992;G|0.008	0.008	strong		0.453	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
ACOX2	8309	hgsc.bcm.edu	37	3	58517520	58517520	+	Silent	SNP	A	A	G	rs57216393	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:58517520A>G	ENST00000302819.5	-	6	894	c.603T>C	c.(601-603)caT>caC	p.H201H	ACOX2_ENST00000459701.2_Silent_p.H201H	NM_003500.3	NP_003491.1	Q99424	ACOX2_HUMAN	acyl-CoA oxidase 2, branched chain	201					bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	3alpha,7alpha,12alpha-trihydroxy-5beta-cholestanoyl-CoA 24-hydroxylase activity (GO:0033791)|acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(8)|prostate(1)|skin(3)|urinary_tract(1)	25				BRCA - Breast invasive adenocarcinoma(55;0.000194)|Kidney(10;0.00255)|KIRC - Kidney renal clear cell carcinoma(10;0.00268)|OV - Ovarian serous cystadenocarcinoma(275;0.156)		GGACCAGGGCATGGGTGGCTG	0.627													G|||	355	0.0708866	0.2262	0.0375	5008	,	,		18088	0.0		0.0189	False		,,,				2504	0.0112				p.H201H		Atlas-SNP	.											.	ACOX2	53	.	0			c.T603C						PASS	.	G		884,3522	741.6+/-411.3	92,700,1411	59.0	53.0	55.0		603	-9.4	0.1	3	dbSNP_129	55	184,8416	810.9+/-407.1	3,178,4119	no	coding-synonymous	ACOX2	NM_003500.3		95,878,5530	GG,GA,AA		2.1395,20.0635,8.2116		201/682	58517520	1068,11938	2203	4300	6503	SO:0001819	synonymous_variant	8309	exon6			CAGGGCATGGGTG	X95190	CCDS33775.1	3p14.3	2012-07-13	2010-04-30		ENSG00000168306	ENSG00000168306	1.17.99.3		120	protein-coding gene	gene with protein product	"""trihydroxycoprostanoyl-CoA oxidase"", ""3-alpha,7-alpha,12-alpha-trihydroxy-5-beta-cholestanoyl-CoA 24-hydroxylase"""	601641	"""acyl-Coenzyme A oxidase 2, branched chain"""			8943006, 9070889	Standard	NM_003500		Approved	BRCACOX, BRCOX, THCCox	uc003dkl.3	Q99424	OTTHUMG00000159154	ENST00000302819.5:c.603T>C	3.37:g.58517520A>G		57.0	0.0	0		53.0	28.0	0.528302	NM_003500	A6NF16|B2R8U5	Silent	SNP	ENST00000302819.5	37	CCDS33775.1																																																																																			A|0.923;G|0.077	0.077	strong		0.627	ACOX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353541.1		
OR5AK2	390181	hgsc.bcm.edu	37	11	56757056	56757056	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:56757056C>T	ENST00000326855.2	+	1	710	c.668C>T	c.(667-669)gCc>gTc	p.A223V		NM_001005323.1	NP_001005323.1	Q8NH90	O5AK2_HUMAN	olfactory receptor, family 5, subfamily AK, member 2	223						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(3)|endometrium(1)|large_intestine(4)|lung(3)|ovary(3)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	21						TACATCATGGCCACCATCCTG	0.433																																					p.A223V		Atlas-SNP	.											.	OR5AK2	45	.	0			c.C668T						PASS	.						175.0	160.0	165.0					11																	56757056		2201	4296	6497	SO:0001583	missense	390181	exon1			TCATGGCCACCAT	AB065496	CCDS31538.1	11q11	2012-08-09			ENSG00000181273	ENSG00000181273		"""GPCR / Class A : Olfactory receptors"""	15251	protein-coding gene	gene with protein product							Standard	NM_001005323		Approved		uc010rjp.2	Q8NH90	OTTHUMG00000167019	ENST00000326855.2:c.668C>T	11.37:g.56757056C>T	ENSP00000322784:p.Ala223Val	290.0	0.0	0		313.0	118.0	0.376997	NM_001005323	B2RNZ9	Missense_Mutation	SNP	ENST00000326855.2	37	CCDS31538.1	.	.	.	.	.	.	.	.	.	.	C	0.011	-1.735318	0.00681	.	.	ENSG00000181273	ENST00000326855	T	0.36157	1.27	3.97	2.05	0.26809	GPCR, rhodopsin-like superfamily (1);	0.590959	0.13870	N	0.357078	T	0.16811	0.0404	N	0.12853	0.265	0.09310	N	1	B	0.15719	0.014	B	0.24006	0.05	T	0.25779	-1.0122	10	0.19147	T	0.46	-0.0979	2.6585	0.05019	0.1802:0.5133:0.1997:0.1068	.	223	Q8NH90	O5AK2_HUMAN	V	223	ENSP00000322784:A223V	ENSP00000322784:A223V	A	+	2	0	OR5AK2	56513632	0.000000	0.05858	0.001000	0.08648	0.044000	0.14063	-0.408000	0.07169	0.435000	0.26365	0.400000	0.26472	GCC	.	.	none		0.433	OR5AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392446.1	NM_001005323	
BAG4	9530	hgsc.bcm.edu	37	8	38034402	38034402	+	Silent	SNP	G	G	A	rs61731143	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:38034402G>A	ENST00000287322.4	+	1	286	c.15G>A	c.(13-15)agG>agA	p.R5R	LSM1_ENST00000311351.4_5'Flank|LSM1_ENST00000520755.1_5'Flank|BAG4_ENST00000521282.1_Intron|BAG4_ENST00000432471.2_Silent_p.R5R|LSM1_ENST00000522515.1_5'Flank	NM_004874.3	NP_004865.1	O95429	BAG4_HUMAN	BCL2-associated athanogene 4	5					cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to tumor necrosis factor (GO:0071356)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of mRNA modification (GO:0090367)|negative regulation of phosphatidylinositol-3,4,5-trisphosphate 5-phosphatase activity (GO:2001145)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cell adhesion (GO:0045785)|positive regulation of fibroblast migration (GO:0010763)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein localization to plasma membrane (GO:0072659)|ruffle assembly (GO:0097178)	cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|receptor signaling protein activity (GO:0005057)			breast(1)|kidney(2)|large_intestine(2)|liver(2)|lung(2)|ovary(1)|urinary_tract(1)	11	Colorectal(12;0.000442)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.121)				CGGCCCTGAGGCGCTCGGGCT	0.701													G|||	16	0.00319489	0.0	0.0144	5008	,	,		12933	0.0		0.006	False		,,,				2504	0.0				p.R5R		Atlas-SNP	.											.	BAG4	32	.	0			c.G15A						PASS	.	G	,	3,4047		0,3,2022	12.0	10.0	11.0		15,15	3.6	1.0	8	dbSNP_129	11	56,7836		0,56,3890	no	coding-synonymous,coding-synonymous	BAG4	NM_001204878.1,NM_004874.3	,	0,59,5912	AA,AG,GG		0.7096,0.0741,0.4941	,	5/422,5/458	38034402	59,11883	2025	3946	5971	SO:0001819	synonymous_variant	9530	exon1			CCTGAGGCGCTCG	AF095194	CCDS6104.1, CCDS56533.1	8p11.23	2008-08-07			ENSG00000156735	ENSG00000156735			940	protein-coding gene	gene with protein product	"""silencer of death domains"""	603884				9873016, 9915703	Standard	NM_004874		Approved	SODD	uc003xky.2	O95429	OTTHUMG00000164064	ENST00000287322.4:c.15G>A	8.37:g.38034402G>A		39.0	0.0	0		72.0	36.0	0.5	NM_001204878	B4E217|O95818	Silent	SNP	ENST00000287322.4	37	CCDS6104.1																																																																																			G|0.995;A|0.005	0.005	strong		0.701	BAG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377038.2	NM_004874	
FAM53B	9679	hgsc.bcm.edu	37	10	126370638	126370638	+	Silent	SNP	G	G	A	rs148943049		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:126370638G>A	ENST00000337318.3	-	4	655	c.444C>T	c.(442-444)agC>agT	p.S148S	FAM53B_ENST00000392754.3_Silent_p.S148S|RP11-12J10.3_ENST00000494792.1_3'UTR|FAM53B_ENST00000280780.6_Silent_p.S148S	NM_014661.3	NP_055476.3	Q14153	FA53B_HUMAN	family with sequence similarity 53, member B	148										cervix(1)|lung(5)|ovary(2)|pancreas(1)	9		all_lung(145;0.0191)|Lung NSC(174;0.0301)|Colorectal(57;0.106)|all_neural(114;0.117)		COAD - Colon adenocarcinoma(40;0.141)|Colorectal(40;0.15)		CGCTGCCCCCGCTGTAGCAGC	0.612													G|||	1	0.000199681	0.0	0.0	5008	,	,		19147	0.0		0.0	False		,,,				2504	0.001				p.S148S		Atlas-SNP	.											.	FAM53B	22	.	0			c.C444T						PASS	.	G		0,4406		0,0,2203	28.0	29.0	28.0		444	-8.4	0.2	10	dbSNP_134	28	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous	FAM53B	NM_014661.3		0,9,6494	AA,AG,GG		0.1047,0.0,0.0692		148/423	126370638	9,12997	2203	4300	6503	SO:0001819	synonymous_variant	9679	exon4			GCCCCCGCTGTAG	D50930	CCDS7641.1	10q26.13	2004-11-24	2004-11-24	2004-11-24	ENSG00000189319	ENSG00000189319			28968	protein-coding gene	gene with protein product			"""KIAA0140"""	KIAA0140		8590280	Standard	NM_014661		Approved	bA12J10.2	uc001lhv.1	Q14153	OTTHUMG00000019215	ENST00000337318.3:c.444C>T	10.37:g.126370638G>A		90.0	0.0	0		61.0	29.0	0.47541	NM_014661	D3DRF1|Q5VUW1|Q5VUW2|Q8N5S6	Silent	SNP	ENST00000337318.3	37	CCDS7641.1																																																																																			G|0.999;A|0.001	0.001	strong		0.612	FAM53B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050879.1	NM_014661	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57069568	57069568	+	Missense_Mutation	SNP	T	T	C	rs35272228	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57069568T>C	ENST00000532437.1	-	7	5125	c.4814A>G	c.(4813-4815)cAc>cGc	p.H1605R	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.H1605R			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1605	Arg/Glu/Lys-rich (charged).				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				CTGGAACAGGTGTGCATCCGA	0.597													C|||	101	0.0201677	0.0023	0.0389	5008	,	,		18503	0.002		0.0447	False		,,,				2504	0.0245				p.H1605R		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.A4814G						PASS	.	C	ARG/HIS	46,4356	822.0+/-416.4	0,46,2155	118.0	117.0	117.0		4814	4.3	0.7	11	dbSNP_126	117	402,8190	800.9+/-407.4	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	29	8,432,6057	CC,CT,TT		4.6788,1.045,3.4477	benign	1605/1730	57069568	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon8			AACAGGTGTGCAT	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4814A>G	11.37:g.57069568T>C	ENSP00000437271:p.His1605Arg	55.0	0.0	0		58.0	23.0	0.396552	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	C	2.177	-0.388487	0.04932	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.27402	1.67;1.67	5.22	4.31	0.51392	.	0.082812	0.51477	N	0.000091	T	0.00936	0.0031	N	0.00289	-1.7	0.09310	N	0.999997	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.33701	-0.9858	10	0.05959	T	0.93	-9.0253	9.3555	0.38164	0.0:0.8307:0.0:0.1693	rs35272228	1605;187	Q9C0C2;Q86TK2	TB182_HUMAN;.	R	1605	ENSP00000350990:H1605R;ENSP00000437271:H1605R	ENSP00000350990:H1605R	H	-	2	0	TNKS1BP1	56826144	0.228000	0.23718	0.705000	0.30386	0.649000	0.38597	0.896000	0.28377	0.608000	0.30000	-0.974000	0.02594	CAC	T|0.969;C|0.031	0.031	strong		0.597	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
ZNF326	284695	hgsc.bcm.edu	37	1	90484253	90484253	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:90484253G>A	ENST00000340281.4	+	9	1227	c.1084G>A	c.(1084-1086)Gtg>Atg	p.V362M	ZNF326_ENST00000370447.3_Missense_Mutation_p.V273M|ZNF326_ENST00000455342.2_Missense_Mutation_p.V156M	NM_182976.2	NP_892021.1	Q5BKZ1	ZN326_HUMAN	zinc finger protein 326	362					mRNA processing (GO:0006397)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of DNA-templated transcription, elongation (GO:0032784)|RNA splicing (GO:0008380)|transcription, DNA-templated (GO:0006351)	DBIRD complex (GO:0044609)|nuclear matrix (GO:0016363)	DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)|RNA polymerase II core binding (GO:0000993)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(12)|lung(7)|ovary(1)	25		all_lung(203;0.0116)|Lung NSC(277;0.0417)		all cancers(265;0.00728)|Epithelial(280;0.0265)		GGAGTGTATGGTGAATAAATT	0.289																																					p.V362M		Atlas-SNP	.											.	ZNF326	60	.	0			c.G1084A						PASS	.						52.0	57.0	55.0					1																	90484253		2198	4280	6478	SO:0001583	missense	284695	exon9			TGTATGGTGAATA	BC013102	CCDS727.1, CCDS728.1	1p22	2012-04-19			ENSG00000162664	ENSG00000162664		"""Zinc fingers, C2H2-type"""	14104	protein-coding gene	gene with protein product	"""ZNF-protein interacting with nuclear mRNPs and DBC1"""	614601				22446626	Standard	NM_182976		Approved	Zfp326, ZAN75, FLJ20403, ZIRD	uc001dnq.2	Q5BKZ1	OTTHUMG00000010675	ENST00000340281.4:c.1084G>A	1.37:g.90484253G>A	ENSP00000340796:p.Val362Met	131.0	0.0	0		148.0	66.0	0.445946	NM_182976	A8MYX1|B4DLN0|B4E179|Q5VW93|Q5VW94|Q5VW96|Q5VW97|Q6NSA2|Q7Z638|Q7Z6C2	Missense_Mutation	SNP	ENST00000340281.4	37	CCDS727.1	.	.	.	.	.	.	.	.	.	.	G	21.1	4.094288	0.76870	.	.	ENSG00000162664	ENST00000394590;ENST00000340281;ENST00000370447;ENST00000455342	T;T;T	0.17528	2.27;2.27;2.27	5.56	5.56	0.83823	.	0.066635	0.64402	D	0.000018	T	0.32496	0.0831	M	0.62723	1.935	0.50313	D	0.999865	D;D	0.63046	0.992;0.992	D;P	0.66847	0.947;0.9	T	0.02457	-1.1156	10	0.62326	D	0.03	-10.1859	19.1298	0.93400	0.0:0.0:1.0:0.0	.	362;362	A8MYX1;Q5BKZ1	.;ZN326_HUMAN	M	362;362;273;156	ENSP00000340796:V362M;ENSP00000359476:V273M;ENSP00000403470:V156M	ENSP00000340796:V362M	V	+	1	0	ZNF326	90256841	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.778000	0.75043	2.620000	0.88729	0.650000	0.86243	GTG	.	.	none		0.289	ZNF326-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029428.2	NM_181781	
AGPAT3	56894	hgsc.bcm.edu	37	21	45389034	45389034	+	Silent	SNP	C	C	T	rs61737069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45389034C>T	ENST00000398063.2	+	4	876	c.384C>T	c.(382-384)taC>taT	p.Y128Y	AGPAT3_ENST00000398061.1_Silent_p.Y128Y|AGPAT3_ENST00000479117.1_3'UTR|AGPAT3_ENST00000291572.8_Silent_p.Y128Y|AGPAT3_ENST00000398058.1_Silent_p.Y128Y|AGPAT3_ENST00000546158.1_Silent_p.Y128Y|AGPAT3_ENST00000327505.2_Silent_p.Y128Y	NM_001037553.1	NP_001032642.1	Q9NRZ7	PLCC_HUMAN	1-acylglycerol-3-phosphate O-acyltransferase 3	128					CDP-diacylglycerol biosynthetic process (GO:0016024)|cellular lipid metabolic process (GO:0044255)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidic acid biosynthetic process (GO:0006654)|phospholipid biosynthetic process (GO:0008654)|phospholipid metabolic process (GO:0006644)|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)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	1-acylglycerol-3-phosphate O-acyltransferase activity (GO:0003841)			large_intestine(4)|lung(5)|ovary(1)|prostate(1)	11				STAD - Stomach adenocarcinoma(101;0.18)|Colorectal(79;0.24)		AGCTGCTCTACGTGCCCCTCA	0.632													C|||	42	0.00838658	0.0023	0.0072	5008	,	,		19868	0.0		0.0179	False		,,,				2504	0.0164				p.Y128Y	Pancreas(60;623 1650 5574 52796)	Atlas-SNP	.											.	AGPAT3	37	.	0			c.C384T						PASS	.	C	,	18,4388	25.3+/-52.1	0,18,2185	130.0	105.0	113.0		384,384	0.4	1.0	21	dbSNP_129	113	171,8429	78.9+/-141.6	1,169,4130	no	coding-synonymous,coding-synonymous	AGPAT3	NM_001037553.1,NM_020132.4	,	1,187,6315	TT,TC,CC		1.9884,0.4085,1.4532	,	128/377,128/377	45389034	189,12817	2203	4300	6503	SO:0001819	synonymous_variant	56894	exon4			GCTCTACGTGCCC	AF156774	CCDS13703.1	21q22.3	2013-02-05			ENSG00000160216	ENSG00000160216	2.3.1.51	"""1-acylglycerol-3-phosphate O-acyltransferases"""	326	protein-coding gene	gene with protein product		614794					Standard	XM_005261159		Approved	LPAAT-gamma	uc002zdw.3	Q9NRZ7	OTTHUMG00000086892	ENST00000398063.2:c.384C>T	21.37:g.45389034C>T		145.0	0.0	0		167.0	93.0	0.556886	NM_001037553	D3DSL2|Q3ZCU2|Q6UWP6|Q6ZUC6|Q8N3Q7|Q9NRZ6	Silent	SNP	ENST00000398063.2	37	CCDS13703.1																																																																																			C|0.986;T|0.014	0.014	strong		0.632	AGPAT3-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195722.1	NM_020132	
XYLT1	64131	hgsc.bcm.edu	37	16	17353090	17353090	+	Missense_Mutation	SNP	G	G	C	rs113276942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:17353090G>C	ENST00000261381.6	-	3	752	c.668C>G	c.(667-669)gCc>gGc	p.A223G		NM_022166.3	NP_071449.1	Q86Y38	XYLT1_HUMAN	xylosyltransferase I	223					cellular response to heat (GO:0034605)|chondroitin sulfate biosynthetic process (GO:0030206)|glycosaminoglycan biosynthetic process (GO:0006024)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)	endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	acetylglucosaminyltransferase activity (GO:0008375)|protein xylosyltransferase activity (GO:0030158)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(2)|large_intestine(7)|lung(35)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						GTTGGCTGCGGCTCTGTCCCC	0.592													G|||	265	0.0529153	0.1914	0.0173	5008	,	,		17039	0.0		0.0	False		,,,				2504	0.0				p.A223G		Atlas-SNP	.											XYLT1,NS,carcinoma,+1,1	XYLT1	147	1	0			c.C668G						PASS	.	G	GLY/ALA	697,3697	288.1+/-279.7	67,563,1567	106.0	117.0	113.0		668	4.5	0.0	16	dbSNP_132	113	19,8581	11.2+/-40.8	0,19,4281	yes	missense	XYLT1	NM_022166.3	60	67,582,5848	CC,CG,GG		0.2209,15.8625,5.5102	benign	223/960	17353090	716,12278	2197	4300	6497	SO:0001583	missense	64131	exon3			GCTGCGGCTCTGT	AJ277441	CCDS10569.1	16p12	2013-02-25			ENSG00000103489	ENSG00000103489	2.4.2.26	"""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	15516	protein-coding gene	gene with protein product	"""protein xylosyltransferase 1"""	608124				11099377	Standard	NM_022166		Approved	XT-I, PXYLT1	uc002dfa.3	Q86Y38	OTTHUMG00000129975	ENST00000261381.6:c.668C>G	16.37:g.17353090G>C	ENSP00000261381:p.Ala223Gly	169.0	0.0	0		144.0	78.0	0.541667	NM_022166	Q9H1B6	Missense_Mutation	SNP	ENST00000261381.6	37	CCDS10569.1	89	0.04075091575091575	81	0.16463414634146342	8	0.022099447513812154	0	0.0	0	0.0	G	9.870	1.198774	0.22121	0.158625	0.002209	ENSG00000103489	ENST00000261381	T	0.04809	3.55	5.43	4.47	0.54385	.	0.429861	0.27500	N	0.019098	T	0.00039	0.0001	L	0.44542	1.39	0.09310	N	1	B	0.32245	0.361	B	0.19148	0.024	T	0.49021	-0.8982	10	0.31617	T	0.26	-19.7884	11.4244	0.50001	0.1501:0.0:0.8499:0.0	.	223	Q86Y38	XYLT1_HUMAN	G	223	ENSP00000261381:A223G	ENSP00000261381:A223G	A	-	2	0	XYLT1	17260591	0.015000	0.18098	0.011000	0.14972	0.446000	0.32137	1.886000	0.39688	1.296000	0.44742	0.655000	0.94253	GCC	G|0.950;C|0.050	0.050	strong		0.592	XYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252241.2	NM_022166	
PDLIM2	64236	hgsc.bcm.edu	37	8	22442908	22442908	+	Missense_Mutation	SNP	G	G	A	rs11989168	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22442908G>A	ENST00000397760.4	+	6	936	c.536G>A	c.(535-537)cGa>cAa	p.R179Q	PDLIM2_ENST00000409417.1_Missense_Mutation_p.R179Q|PDLIM2_ENST00000448520.1_3'UTR|PDLIM2_ENST00000409141.1_Missense_Mutation_p.R179Q|PDLIM2_ENST00000397761.2_Missense_Mutation_p.R179Q|PDLIM2_ENST00000339162.7_Missense_Mutation_p.R179Q|PDLIM2_ENST00000308354.7_Missense_Mutation_p.R429Q|PDLIM2_ENST00000265810.4_Missense_Mutation_p.R179Q			Q96JY6	PDLI2_HUMAN	PDZ and LIM domain 2 (mystique)	179						actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|urinary_tract(1)	9		Prostate(55;0.0421)|Breast(100;0.102)|all_epithelial(46;0.142)		BRCA - Breast invasive adenocarcinoma(99;0.00579)|Colorectal(74;0.0152)|COAD - Colon adenocarcinoma(73;0.0626)		CCTGGAAGCCGACAGGTGAGG	0.667													G|||	25	0.00499201	0.0144	0.0072	5008	,	,		11606	0.0		0.001	False		,,,				2504	0.0				p.R429Q		Atlas-SNP	.											PDLIM2_ENST00000308354,colon,carcinoma,+1,2	PDLIM2	42	2	0			c.G1286A						PASS	.	G	GLN/ARG,GLN/ARG,GLN/ARG	57,4345		0,57,2144	26.0	20.0	22.0		1286,536,536	-2.1	0.1	8	dbSNP_120	22	4,8590		0,4,4293	yes	missense,missense,missense	PDLIM2	NM_021630.5,NM_176871.3,NM_198042.3	43,43,43	0,61,6437	AA,AG,GG		0.0465,1.2949,0.4694	benign,benign,benign	429/603,179/367,179/279	22442908	61,12935	2201	4297	6498	SO:0001583	missense	64236	exon6			GAAGCCGACAGGT	AY007729	CCDS34860.1, CCDS6032.1, CCDS34861.1, CCDS6032.2	8p21.3	2012-06-27			ENSG00000120913	ENSG00000120913			13992	protein-coding gene	gene with protein product		609722					Standard	NM_021630		Approved		uc003xby.4	Q96JY6	OTTHUMG00000164270	ENST00000397760.4:c.536G>A	8.37:g.22442908G>A	ENSP00000380867:p.Arg179Gln	77.0	0.0	0		98.0	46.0	0.469388	NM_021630	D3DSR5|J3KNH4|Q7Z584|Q86WM8|Q8WZ29|Q9H4L9|Q9H7I2	Missense_Mutation	SNP	ENST00000397760.4	37		15	0.006868131868131868	10	0.02032520325203252	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	8.308	0.821380	0.16678	0.012949	4.65E-4	ENSG00000120913	ENST00000456545;ENST00000308354;ENST00000452226;ENST00000397760;ENST00000339162;ENST00000397761;ENST00000429812;ENST00000409141;ENST00000265810;ENST00000409417	T;T;T;T;T;T;T;T;T;T	0.25749	2.06;3.57;2.65;2.65;2.64;2.65;1.78;2.64;2.74;2.65	4.75	-2.07	0.07276	.	0.808770	0.10844	N	0.627938	T	0.01730	0.0055	N	0.00162	-1.95	0.09310	N	1	B;B;B;B	0.23490	0.005;0.086;0.007;0.052	B;B;B;B	0.15052	0.003;0.012;0.002;0.007	T	0.39623	-0.9605	10	0.11485	T	0.65	-0.0402	4.6558	0.12617	0.477:0.0:0.3754:0.1476	rs11989168	179;179;179;179	Q96JY6-3;Q96JY6-4;Q96JY6;C9JS55	.;.;PDLI2_HUMAN;.	Q	179;429;179;179;179;179;179;179;179;179	ENSP00000401992:R179Q;ENSP00000312634:R429Q;ENSP00000394376:R179Q;ENSP00000380867:R179Q;ENSP00000342035:R179Q;ENSP00000380868:R179Q;ENSP00000407643:R179Q;ENSP00000386868:R179Q;ENSP00000265810:R179Q;ENSP00000387084:R179Q	ENSP00000265810:R179Q	R	+	2	0	PDLIM2	22498853	0.000000	0.05858	0.068000	0.19968	0.166000	0.22503	-0.518000	0.06267	-0.292000	0.08999	-0.448000	0.05591	CGA	G|0.993;A|0.007	0.007	strong		0.667	PDLIM2-202	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000334167.1		
TNFRSF10C	8794	hgsc.bcm.edu	37	8	22974405	22974405	+	Missense_Mutation	SNP	C	C	T	rs61736406	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:22974405C>T	ENST00000356864.3	+	5	1173	c.641C>T	c.(640-642)aCc>aTc	p.T214I	TNFRSF10C_ENST00000540813.1_Missense_Mutation_p.T112I	NM_003841.3	NP_003832	O14798	TR10C_HUMAN	tumor necrosis factor receptor superfamily, member 10c, decoy without an intracellular domain	214					apoptotic process (GO:0006915)|signal transduction (GO:0007165)	anchored component of membrane (GO:0031225)|integral component of plasma membrane (GO:0005887)	transmembrane signaling receptor activity (GO:0004888)	p.T214N(7)		endometrium(1)|large_intestine(6)|lung(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	15		Prostate(55;0.0421)|Breast(100;0.067)		Colorectal(74;0.0147)|COAD - Colon adenocarcinoma(73;0.0612)		GAGACAATGACCACCAGCCCG	0.612																																					p.T214I		Atlas-SNP	.											TNFRSF10C,NS,carcinoma,0,5	TNFRSF10C	30	5	7	Substitution - Missense(7)	prostate(4)|large_intestine(3)	c.C641T						PASS	.						63.0	71.0	68.0					8																	22974405		2203	4298	6501	SO:0001583	missense	8794	exon5			CAATGACCACCAG	AF012536	CCDS6037.1	8p22-p21	2006-02-22			ENSG00000173535	ENSG00000173535		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11906	protein-coding gene	gene with protein product		603613				9314565, 9325248	Standard	NM_003841		Approved	DcR1, TRAILR3, LIT, TRID, CD263	uc003xcy.3	O14798	OTTHUMG00000097844	ENST00000356864.3:c.641C>T	8.37:g.22974405C>T	ENSP00000349324:p.Thr214Ile	126.0	0.0	0		152.0	35.0	0.230263	NM_003841	O14755|Q08AS6|Q6FH98|Q6UXM5	Missense_Mutation	SNP	ENST00000356864.3	37	CCDS6037.1	32	0.014652014652014652	27	0.054878048780487805	3	0.008287292817679558	0	0.0	2	0.002638522427440633	c	0.284	-0.984715	0.02180	.	.	ENSG00000173535	ENST00000356864;ENST00000540813;ENST00000544885	T;T	0.62498	0.02;0.38	.	.	.	.	7739.210000	0.00166	U	0.000000	T	0.06872	0.0175	N	0.03608	-0.345	0.09310	N	1	B	0.22909	0.077	B	0.06405	0.002	T	0.19031	-1.0318	9	0.62326	D	0.03	.	5.2848	0.15696	0.3272:0.6728:0.0:0.0	.	214	O14798	TR10C_HUMAN	I	214;112;214	ENSP00000349324:T214I;ENSP00000437612:T112I	ENSP00000349324:T214I	T	+	2	0	TNFRSF10C	23030350	0.033000	0.19621	0.001000	0.08648	0.141000	0.21300	0.550000	0.23345	-2.089000	0.00860	-2.399000	0.00225	ACC	A|0.000;C|0.990;T|0.009	0.009	strong		0.612	TNFRSF10C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215134.3		
MUC16	94025	hgsc.bcm.edu	37	19	9070873	9070873	+	Missense_Mutation	SNP	A	A	G	rs79202331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:9070873A>G	ENST00000397910.4	-	3	16776	c.16573T>C	c.(16573-16575)Tcc>Ccc	p.S5525P		NM_024690.2	NP_078966.2	Q8WXI7	MUC16_HUMAN	mucin 16, cell surface associated	5527	Thr-rich.				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						CTGCTAGAGGAGATTTCTGTT	0.507													A|||	24	0.00479233	0.0015	0.0043	5008	,	,		20120	0.0		0.0149	False		,,,				2504	0.0041				p.S5525P		Atlas-SNP	.											.	MUC16	4315	.	0			c.T16573C						PASS	.		PRO/SER	3,3913		0,3,1955	157.0	142.0	147.0		16573	0.9	0.0	19	dbSNP_131	147	59,8275		0,59,4108	yes	missense	MUC16	NM_024690.2	74	0,62,6063	GG,GA,AA		0.7079,0.0766,0.5061	benign	5525/14508	9070873	62,12188	1958	4167	6125	SO:0001583	missense	94025	exon3			TAGAGGAGATTTC	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.16573T>C	19.37:g.9070873A>G	ENSP00000381008:p.Ser5525Pro	236.0	1.0	0.00423729		248.0	115.0	0.46371	NM_024690	Q6ZQW5|Q96RK2	Missense_Mutation	SNP	ENST00000397910.4	37	CCDS54212.1	14	0.00641025641025641	1	0.0020325203252032522	4	0.011049723756906077	0	0.0	9	0.011873350923482849	a	3.455	-0.111140	0.06881	7.66E-4	0.007079	ENSG00000181143	ENST00000397910	T	0.02709	4.19	1.89	0.851	0.18989	.	.	.	.	.	T	0.01730	0.0055	L	0.32530	0.975	.	.	.	B	0.06786	0.001	B	0.04013	0.001	T	0.33471	-0.9867	8	0.87932	D	0	.	3.8711	0.09036	0.8048:0.0:0.1952:0.0	.	5525	B5ME49	.	P	5525	ENSP00000381008:S5525P	ENSP00000381008:S5525P	S	-	1	0	MUC16	8931873	0.005000	0.15991	0.001000	0.08648	0.086000	0.17979	0.206000	0.17375	0.192000	0.20272	-0.933000	0.02702	TCC	A|0.993;G|0.007	0.007	strong		0.507	MUC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402806.1	NM_024690	
DNHD1	144132	hgsc.bcm.edu	37	11	6592951	6592951	+	Missense_Mutation	SNP	T	T	C	rs11604362	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6592951T>C	ENST00000527990.2	+	41	13997	c.13997T>C	c.(13996-13998)aTa>aCa	p.I4666T	DNHD1_ENST00000254579.6_Missense_Mutation_p.I4666T			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	4666			I -> T (in dbSNP:rs11604362).		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)		TGGGACCCAATAGCTGGAGCC	0.632													T|||	10	0.00199681	0.0	0.0058	5008	,	,		17689	0.0		0.006	False		,,,				2504	0.0				p.I4666T		Atlas-SNP	.											.	DNHD1	198	.	0			c.T13997C						PASS	.	T	THR/ILE	10,4218		0,10,2104	38.0	49.0	45.0		13997	-0.8	0.0	11	dbSNP_120	45	65,8389		0,65,4162	yes	missense	DNHD1	NM_144666.2	89	0,75,6266	CC,CT,TT		0.7689,0.2365,0.5914	benign	4666/4754	6592951	75,12607	2114	4227	6341	SO:0001583	missense	144132	exon43			ACCCAATAGCTGG	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.13997T>C	11.37:g.6592951T>C	ENSP00000436180:p.Ile4666Thr	94.0	0.0	0		127.0	75.0	0.590551	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	37	CCDS44532.1	11	0.005036630036630037	2	0.0040650406504065045	3	0.008287292817679558	2	0.0034965034965034965	4	0.005277044854881266	T	0.823	-0.748044	0.03065	0.002365	0.007689	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000530197	T;T	0.07444	3.19;3.19	4.75	-0.827	0.10802	Dynein heavy chain (1);	1.500610	0.03937	N	0.286257	T	0.01489	0.0048	N	0.00538	-1.39	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.001;0.001;0.001	T	0.40001	-0.9586	10	0.14252	T	0.57	0.038	3.778	0.08668	0.3386:0.1861:0.0:0.4753	rs11604362;rs11604362	3754;719;4666	B0I1S4;Q9NSW8;Q96M86	.;.;DNHD1_HUMAN	T	4666;4666;934	ENSP00000254579:I4666T;ENSP00000436180:I4666T	ENSP00000254579:I4666T	I	+	2	0	DNHD1	6549527	0.000000	0.05858	0.003000	0.11579	0.389000	0.30415	-0.299000	0.08254	0.009000	0.14813	-0.274000	0.10170	ATA	T|0.994;C|0.006	0.006	strong		0.632	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
MYO1D	4642	hgsc.bcm.edu	37	17	30980871	30980871	+	Missense_Mutation	SNP	T	T	A	rs138039699	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:30980871T>A	ENST00000318217.5	-	19	2889	c.2585A>T	c.(2584-2586)cAc>cTc	p.H862L	RP11-220C2.1_ENST00000582272.1_RNA|MYO1D_ENST00000579584.1_Missense_Mutation_p.H862L|MYO1D_ENST00000394649.4_Missense_Mutation_p.H774L	NM_015194.1	NP_056009.1	O94832	MYO1D_HUMAN	myosin ID	862	Myosin tail. {ECO:0000255}.				early endosome to recycling endosome transport (GO:0061502)|negative regulation of phosphatase activity (GO:0010923)	axolemma (GO:0030673)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|myosin complex (GO:0016459)|smooth endoplasmic reticulum (GO:0005790)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(14)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39			BRCA - Breast invasive adenocarcinoma(9;0.0362)			CTTACGGACGTGACAGGAAAA	0.408													T|||	5	0.000998403	0.0	0.0	5008	,	,		22025	0.0		0.003	False		,,,				2504	0.002				p.H862L		Atlas-SNP	.											.	MYO1D	93	.	0			c.A2585T						PASS	.	T	LEU/HIS	2,4404	4.2+/-10.8	0,2,2201	135.0	109.0	118.0		2585	5.9	1.0	17	dbSNP_134	118	28,8572	20.4+/-63.3	0,28,4272	yes	missense	MYO1D	NM_015194.1	99	0,30,6473	AA,AT,TT		0.3256,0.0454,0.2307	benign	862/1007	30980871	30,12976	2203	4300	6503	SO:0001583	missense	4642	exon19			CGGACGTGACAGG	AB018270	CCDS32615.1	17q11-q12	2014-06-12				ENSG00000176658		"""Myosins / Myosin superfamily : Class I"""	7598	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 108"""	606539				8884266	Standard	NM_015194		Approved	KIAA0727, myr4, PPP1R108	uc002hho.1	O94832		ENST00000318217.5:c.2585A>T	17.37:g.30980871T>A	ENSP00000324527:p.His862Leu	58.0	0.0	0		45.0	22.0	0.488889	NM_015194	A6H8V3|Q8NHP9	Missense_Mutation	SNP	ENST00000318217.5	37	CCDS32615.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	T	16.55	3.153297	0.57259	4.54E-4	0.003256	ENSG00000176658	ENST00000318217;ENST00000394649	T	0.35421	1.31	5.89	5.89	0.94794	Myosin tail 2 (1);	0.000000	0.40554	U	0.001063	T	0.41026	0.1141	M	0.65498	2.005	0.80722	D	1	P;B	0.35033	0.481;0.292	B;B	0.40982	0.345;0.186	T	0.21415	-1.0246	10	0.12103	T	0.63	.	14.2432	0.65971	0.0:0.0:0.0:1.0	.	773;862	Q7Z3N6;O94832	.;MYO1D_HUMAN	L	862;54	ENSP00000324527:H862L	ENSP00000324527:H862L	H	-	2	0	MYO1D	28004984	1.000000	0.71417	0.994000	0.49952	0.931000	0.56810	7.278000	0.78587	2.251000	0.74343	0.482000	0.46254	CAC	T|0.998;A|0.002	0.002	strong		0.408	MYO1D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447457.1		
PLAC8L1	153770	hgsc.bcm.edu	37	5	145464130	145464130	+	Silent	SNP	T	T	C	rs1859897	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145464130T>C	ENST00000311450.4	-	4	456	c.399A>G	c.(397-399)acA>acG	p.T133T		NM_001029869.1	NP_001025040.1	A1L4L8	PL8L1_HUMAN	PLAC8-like 1	133										autonomic_ganglia(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|pancreas(1)|prostate(1)|stomach(2)	10			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			CTTCACACAGTGTGCCCTAGG	0.527													T|||	178	0.0355431	0.1218	0.0216	5008	,	,		17606	0.0		0.002	False		,,,				2504	0.0				p.T133T		Atlas-SNP	.											.	PLAC8L1	17	.	0			c.A399G						PASS	.	T		480,3926	226.5+/-242.0	28,424,1751	95.0	93.0	93.0		399	-10.1	0.0	5	dbSNP_92	93	16,8584	11.9+/-42.8	0,16,4284	no	coding-synonymous	PLAC8L1	NM_001029869.1		28,440,6035	CC,CT,TT		0.186,10.8942,3.8136		133/178	145464130	496,12510	2203	4300	6503	SO:0001819	synonymous_variant	153770	exon4			ACACAGTGTGCCC		CCDS34264.1	5q32	2008-02-05			ENSG00000173261	ENSG00000173261			31746	protein-coding gene	gene with protein product							Standard	XM_005268381		Approved		uc003lnv.3	A1L4L8	OTTHUMG00000163418	ENST00000311450.4:c.399A>G	5.37:g.145464130T>C		64.0	0.0	0		70.0	42.0	0.6	NM_001029869		Silent	SNP	ENST00000311450.4	37	CCDS34264.1																																																																																			T|0.967;C|0.033	0.033	strong		0.527	PLAC8L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373290.1	XM_087761	
UTP20	27340	hgsc.bcm.edu	37	12	101761753	101761753	+	Splice_Site	SNP	A	A	G	rs117476305	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:101761753A>G	ENST00000261637.4	+	48	6557	c.6383A>G	c.(6382-6384)aAg>aGg	p.K2128R		NM_014503.2	NP_055318.2	O75691	UTP20_HUMAN	UTP20, small subunit (SSU) processome component, homolog (yeast)	2128					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						ATGGATGTGAAGGTAAGCATC	0.433													A|||	15	0.00299521	0.0	0.0043	5008	,	,		19984	0.0		0.0099	False		,,,				2504	0.002				p.K2128R		Atlas-SNP	.											.	UTP20	222	.	0			c.A6383G						PASS	.	A	ARG/LYS	3,4403	6.2+/-15.9	0,3,2200	240.0	211.0	221.0		6383	4.4	1.0	12	dbSNP_132	221	99,8501	54.4+/-115.2	0,99,4201	yes	missense-near-splice	UTP20	NM_014503.2	26	0,102,6401	GG,GA,AA		1.1512,0.0681,0.7843	possibly-damaging	2128/2786	101761753	102,12904	2203	4300	6503	SO:0001630	splice_region_variant	27340	exon48			ATGTGAAGGTAAG	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.6384+1A>G	12.37:g.101761753A>G		136.0	0.0	0		125.0	58.0	0.464	NM_014503	Q9H3H4	Missense_Mutation	SNP	ENST00000261637.4	37	CCDS9081.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	A	14.07	2.424265	0.43020	6.81E-4	0.011512	ENSG00000120800	ENST00000261637	T	0.65364	-0.15	5.59	4.44	0.53790	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.43322	0.1242	L	0.52126	1.63	0.58432	D	0.999997	P	0.40431	0.717	B	0.35039	0.194	T	0.38866	-0.9641	10	0.25751	T	0.34	-13.9985	11.5039	0.50454	0.9298:0.0:0.0702:0.0	.	2128	O75691	UTP20_HUMAN	R	2128	ENSP00000261637:K2128R	ENSP00000261637:K2128R	K	+	2	0	UTP20	100285884	1.000000	0.71417	1.000000	0.80357	0.225000	0.24961	5.758000	0.68776	0.942000	0.37525	0.528000	0.53228	AAG	A|0.991;G|0.009	0.009	strong		0.433	UTP20-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408242.1	NM_014503	Missense_Mutation
TTI1	9675	hgsc.bcm.edu	37	20	36642101	36642101	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:36642101C>T	ENST00000373448.2	-	3	356	c.118G>A	c.(118-120)Gtg>Atg	p.V40M	TTI1_ENST00000373447.3_Missense_Mutation_p.V40M|TTI1_ENST00000449821.1_Missense_Mutation_p.V40M|TTI1_ENST00000487362.1_Splice_Site	NM_014657.1	NP_055472.1	O43156	TTI1_HUMAN	TELO2 interacting protein 1	40					regulation of TOR signaling (GO:0032006)	cytoplasm (GO:0005737)|TORC1 complex (GO:0031931)|TORC2 complex (GO:0031932)				breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(6)|liver(1)|lung(18)|ovary(3)|pancreas(1)|prostate(3)|skin(3)	47						CTGTCACTCACAGCTTGTAGT	0.517																																					p.V40M		Atlas-SNP	.											.	TTI1	104	.	0			c.G118A						PASS	.						143.0	117.0	126.0					20																	36642101		2203	4300	6503	SO:0001583	missense	9675	exon3			CACTCACAGCTTG	BC013121	CCDS13300.1	20q11.23	2011-11-10	2011-11-10	2010-06-22	ENSG00000101407	ENSG00000101407			29029	protein-coding gene	gene with protein product	"""smg-10 homolog, nonsense mediated mRNA decay factor (C. elegans)"""	614425	"""KIAA0406"", ""Tel2 interacting protein 1 homolog (S. pombe)"""	KIAA0406		9455477, 20427287, 20371770	Standard	NM_014657		Approved	smg-10	uc002xhl.3	O43156	OTTHUMG00000032433	ENST00000373448.2:c.118G>A	20.37:g.36642101C>T	ENSP00000362547:p.Val40Met	106.0	0.0	0		102.0	47.0	0.460784	NM_014657	D6W4K3|Q5JX67|Q96A38|Q9BR47|Q9H4K0	Missense_Mutation	SNP	ENST00000373448.2	37	CCDS13300.1	.	.	.	.	.	.	.	.	.	.	C	15.02	2.710534	0.48517	.	.	ENSG00000101407	ENST00000373448;ENST00000373447;ENST00000449821	T;T;T	0.68181	-0.31;-0.31;-0.31	5.33	3.35	0.38373	Armadillo-type fold (1);	0.247212	0.40908	D	0.000983	T	0.69522	0.3120	M	0.62723	1.935	0.40385	D	0.979489	P	0.46512	0.879	P	0.51385	0.668	T	0.69624	-0.5095	10	0.36615	T	0.2	-9.5996	10.6162	0.45451	0.0:0.8401:0.0:0.1599	.	40	O43156	TTI1_HUMAN	M	40	ENSP00000362547:V40M;ENSP00000362546:V40M;ENSP00000407270:V40M	ENSP00000362546:V40M	V	-	1	0	TTI1	36075515	0.976000	0.34144	0.815000	0.32552	0.871000	0.50021	2.440000	0.44855	1.457000	0.47850	0.655000	0.94253	GTG	.	.	none		0.517	TTI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079138.2	NM_014657	
ALAS2	212	hgsc.bcm.edu	37	X	55039959	55039959	+	Silent	SNP	G	G	T	rs150055592	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:55039959G>T	ENST00000330807.5	-	10	1697	c.1560C>A	c.(1558-1560)ccC>ccA	p.P520P	ALAS2_ENST00000498636.1_Intron|ALAS2_ENST00000335854.4_Silent_p.P483P|ALAS2_ENST00000396198.3_Silent_p.P507P	NM_000032.4	NP_000023.2	P22557	HEM0_HUMAN	aminolevulinate, delta-, synthase 2	520			P -> L (in dbSNP:rs201062903). {ECO:0000269|PubMed:21309041}.		cellular iron ion homeostasis (GO:0006879)|erythrocyte differentiation (GO:0030218)|heme biosynthetic process (GO:0006783)|hemoglobin biosynthetic process (GO:0042541)|oxygen homeostasis (GO:0032364)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX biosynthetic process (GO:0006782)|response to hypoxia (GO:0001666)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	5-aminolevulinate synthase activity (GO:0003870)|coenzyme binding (GO:0050662)|glycine binding (GO:0016594)|pyridoxal phosphate binding (GO:0030170)			central_nervous_system(1)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(2)|skin(1)	17					Glycine(DB00145)	GGTGGGGGGAGGGTGCCAAGC	0.577													G|||	10	0.00264901	0.0	0.0029	3775	,	,		12458	0.0		0.008	False		,,,				2504	0.0				p.P520P		Atlas-SNP	.											.	ALAS2	163	.	0			c.C1560A						PASS	.	G	,,	1,3834		0,1,0,1631,571	62.0	51.0	55.0		1560,1449,1521	1.4	1.0	X	dbSNP_134	55	42,6686		0,25,17,2403,1855	no	coding-synonymous,coding-synonymous,coding-synonymous	ALAS2	NM_000032.4,NM_001037967.3,NM_001037968.3	,,	0,26,17,4034,2426	TT,TG,T,GG,G		0.6243,0.0261,0.4071	,,	520/588,483/551,507/575	55039959	43,10520	2203	4300	6503	SO:0001819	synonymous_variant	212	exon10			GGGGGAGGGTGCC		CCDS14366.1, CCDS35303.1, CCDS43960.1	Xp11.21	2008-02-05	2008-02-04		ENSG00000158578	ENSG00000158578	2.3.1.37		397	protein-coding gene	gene with protein product	"""sideroblastic/hypochromic anemia"""	301300	"""aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia)"""	ASB		1577484	Standard	NM_000032		Approved		uc004dua.4	P22557	OTTHUMG00000021641	ENST00000330807.5:c.1560C>A	X.37:g.55039959G>T		65.0	0.0	0		66.0	64.0	0.969697	NM_000032	A8K3F0|A8K6C4|Q13735|Q5JZF5|Q8N6H3	Silent	SNP	ENST00000330807.5	37	CCDS14366.1																																																																																			G|0.997;T|0.003	0.003	strong		0.577	ALAS2-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056843.3	NM_000032	
DNAJB8	165721	hgsc.bcm.edu	37	3	128181964	128181964	+	Missense_Mutation	SNP	G	G	A	rs142768827		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:128181964G>A	ENST00000469083.1	-	2	2682	c.125C>T	c.(124-126)gCg>gTg	p.A42V	DNAJB8_ENST00000319153.3_Missense_Mutation_p.A42V|DNAJB8-AS1_ENST00000471626.1_RNA			Q8NHS0	DNJB8_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 8	42	J. {ECO:0000255|PROSITE- ProRule:PRU00286}.				chaperone-mediated protein folding (GO:0061077)|negative regulation of inclusion body assembly (GO:0090084)	cytosol (GO:0005829)|nucleus (GO:0005634)	chaperone binding (GO:0051087)|protein binding involved in protein folding (GO:0044183)|unfolded protein binding (GO:0051082)			kidney(1)|large_intestine(4)|lung(4)|prostate(1)|skin(1)	11				GBM - Glioblastoma multiforme(114;0.177)		CTTCTTCTCCGCCTCCTCCTT	0.592																																					p.A42V		Atlas-SNP	.											.	DNAJB8	34	.	0			c.C125T						PASS	.	G	VAL/ALA	0,4406		0,0,2203	162.0	160.0	161.0		125	4.4	0.8	3	dbSNP_134	161	1,8599	1.2+/-3.3	0,1,4299	no	missense	DNAJB8	NM_153330.2	64	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging	42/233	128181964	1,13005	2203	4300	6503	SO:0001583	missense	165721	exon3			TTCTCCGCCTCCT		CCDS3048.1	3q21.3	2014-01-21			ENSG00000179407	ENSG00000179407		"""Heat shock proteins / DNAJ (HSP40)"""	23699	protein-coding gene	gene with protein product		611337					Standard	NM_153330		Approved	MGC33884, CT156	uc003ekk.2	Q8NHS0	OTTHUMG00000159690	ENST00000469083.1:c.125C>T	3.37:g.128181964G>A	ENSP00000417418:p.Ala42Val	185.0	0.0	0		203.0	75.0	0.369458	NM_153330	B3KWV7	Missense_Mutation	SNP	ENST00000469083.1	37	CCDS3048.1	.	.	.	.	.	.	.	.	.	.	G	15.83	2.949383	0.53186	0.0	1.16E-4	ENSG00000179407	ENST00000469083;ENST00000319153	T;T	0.39056	1.1;1.1	4.42	4.42	0.53409	Heat shock protein DnaJ, N-terminal (5);	0.000000	0.85682	D	0.000000	T	0.68540	0.3012	M	0.84683	2.71	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.76391	-0.2976	10	0.87932	D	0	.	17.0136	0.86413	0.0:0.0:1.0:0.0	.	42	Q8NHS0	DNJB8_HUMAN	V	42	ENSP00000417418:A42V;ENSP00000316053:A42V	ENSP00000316053:A42V	A	-	2	0	DNAJB8	129664654	1.000000	0.71417	0.844000	0.33320	0.003000	0.03518	7.784000	0.85713	2.003000	0.58678	0.561000	0.74099	GCG	G|1.000;A|0.000	0.000	weak		0.592	DNAJB8-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356933.1	NM_153330	
SUCNR1	56670	hgsc.bcm.edu	37	3	151599267	151599267	+	Silent	SNP	C	C	T	rs139804843		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:151599267C>T	ENST00000362032.5	+	3	1041	c.936C>T	c.(934-936)caC>caT	p.H312H	RP11-454C18.2_ENST00000475855.1_RNA|RP11-454C18.2_ENST00000483843.2_RNA	NM_033050.4	NP_149039.2	Q9BXA5	SUCR1_HUMAN	succinate receptor 1	312						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)			endometrium(2)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	14			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		Succinic acid(DB00139)	AACTGAGACACAACTTCAAAT	0.433																																					p.H312H		Atlas-SNP	.											.	SUCNR1	31	.	0			c.C936T						PASS	.	C		0,4406		0,0,2203	93.0	94.0	93.0		936	-7.4	0.0	3	dbSNP_134	93	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	SUCNR1	NM_033050.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		312/335	151599267	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	56670	exon3			GAGACACAACTTC	AF348078	CCDS3162.1	3q25.1	2012-08-21	2004-07-08	2004-07-09	ENSG00000198829	ENSG00000198829		"""GPCR / Class A : Orphans"""	4542	protein-coding gene	gene with protein product		606381	"""G protein-coupled receptor 91"""	GPR91		11273702, 15141213, 17192395	Standard	NM_033050		Approved		uc003ezf.2	Q9BXA5	OTTHUMG00000159880	ENST00000362032.5:c.936C>T	3.37:g.151599267C>T		101.0	0.0	0		103.0	49.0	0.475728	NM_033050	A8K305|Q8TDQ8	Silent	SNP	ENST00000362032.5	37	CCDS3162.1																																																																																			C|1.000;T|0.000	0.000	weak		0.433	SUCNR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357897.2	NM_033050	
TYK2	7297	hgsc.bcm.edu	37	19	10472452	10472452	+	Silent	SNP	G	G	A	rs12720355	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10472452G>A	ENST00000525621.1	-	13	2434	c.1953C>T	c.(1951-1953)atC>atT	p.I651I	TYK2_ENST00000529370.1_Silent_p.I651I|TYK2_ENST00000264818.6_Silent_p.I651I|TYK2_ENST00000524462.1_Silent_p.I466I	NM_003331.4	NP_003322.3	P29597	TYK2_HUMAN	tyrosine kinase 2	651	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|intracellular signal transduction (GO:0035556)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|growth hormone receptor binding (GO:0005131)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(11)|kidney(6)|large_intestine(3)|lung(19)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	64			OV - Ovarian serous cystadenocarcinoma(20;1.77e-09)|Epithelial(33;3.92e-06)|all cancers(31;8.95e-06)			TCACCAGGGCGATGTCATGGT	0.652													g|||	25	0.00499201	0.0008	0.0058	5008	,	,		15733	0.0		0.0139	False		,,,				2504	0.0061				p.I651I		Atlas-SNP	.											.	TYK2	126	.	0			c.C1953T						PASS	.	G		13,4393	20.2+/-43.8	0,13,2190	83.0	81.0	82.0		1953	-3.9	0.4	19	dbSNP_121	82	132,8468	66.7+/-129.0	1,130,4169	no	coding-synonymous	TYK2	NM_003331.4		1,143,6359	AA,AG,GG		1.5349,0.2951,1.1149		651/1188	10472452	145,12861	2203	4300	6503	SO:0001819	synonymous_variant	7297	exon13			CAGGGCGATGTCA		CCDS12236.1	19p13.2	2014-09-17			ENSG00000105397	ENSG00000105397	2.7.10.1		12440	protein-coding gene	gene with protein product		176941				2156206	Standard	NM_003331		Approved	JTK1	uc002moc.4	P29597	OTTHUMG00000166373	ENST00000525621.1:c.1953C>T	19.37:g.10472452G>A		69.0	0.0	0		68.0	34.0	0.5	NM_003331	Q6QB10|Q96CH0	Silent	SNP	ENST00000525621.1	37	CCDS12236.1																																																																																			G|0.992;A|0.008	0.008	strong		0.652	TYK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389443.1		
MYO18B	84700	hgsc.bcm.edu	37	22	26423124	26423124	+	Missense_Mutation	SNP	G	G	C	rs6004901	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26423124G>C	ENST00000407587.2	+	43	7356	c.7187G>C	c.(7186-7188)gGc>gCc	p.G2396A	MYO18B_ENST00000335473.7_Missense_Mutation_p.G2395A|MYO18B_ENST00000536101.1_Missense_Mutation_p.G2395A			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2395						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						GACGATGCGGGCTGTCCAGAC	0.592													G|||	488	0.0974441	0.2663	0.0476	5008	,	,		15885	0.004		0.0348	False		,,,				2504	0.0654				p.G2395A		Atlas-SNP	.											.	MYO18B	322	.	0			c.G7184C						PASS	.	G	ALA/GLY	855,3101		95,665,1218	66.0	72.0	70.0		7184	-1.6	0.0	22	dbSNP_114	70	253,8029		6,241,3894	yes	missense	MYO18B	NM_032608.5	60	101,906,5112	CC,CG,GG		3.0548,21.6127,9.0538	benign	2395/2568	26423124	1108,11130	1978	4141	6119	SO:0001583	missense	84700	exon43			ATGCGGGCTGTCC	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.7187G>C	22.37:g.26423124G>C	ENSP00000386096:p.Gly2396Ala	76.0	0.0	0		87.0	37.0	0.425287	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Missense_Mutation	SNP	ENST00000407587.2	37		166|166	0.076007326007326|0.076007326007326	119|119	0.241869918699187|0.241869918699187	22|22	0.06077348066298342|0.06077348066298342	4|4	0.006993006993006993|0.006993006993006993	21|21	0.027704485488126648|0.027704485488126648	G|G	0.007|0.007	-1.985354|-1.985354	0.00443|0.00443	0.216127|0.216127	0.030548|0.030548	ENSG00000133454|ENSG00000133454	ENST00000543971|ENST00000536101;ENST00000335473;ENST00000407587	.|D;D;D	.|0.86956	.|-2.17;-2.17;-2.19	5.12|5.12	-1.6|-1.6	0.08426|0.08426	.|.	.|0.491877	.|0.18417	.|N	.|0.141867	T|T	0.00073|0.00073	0.0002|0.0002	L|L	0.45581|0.45581	1.43|1.43	0.80722|0.80722	P|P	0.0|0.0	.|B;B;B;B;B	.|0.06786	.|0.001;0.001;0.001;0.001;0.001	.|B;B;B;B;B	.|0.08055	.|0.003;0.001;0.001;0.003;0.003	T|T	0.02877|0.02877	-1.1099|-1.1099	4|9	.|0.19147	.|T	.|0.46	.|.	1.509|1.509	0.02492|0.02492	0.1649:0.2383:0.3545:0.2424|0.1649:0.2383:0.3545:0.2424	rs6004901;rs52824215;rs6004901|rs6004901;rs52824215;rs6004901	.|1908;2397;2395;2396;2395	.|Q8IUG5-2;B0QYF5;Q8IUG5;F5GXR6;F5GYU7	.|.;.;MY18B_HUMAN;.;.	P|A	345|2395;2395;2396	.|ENSP00000441229:G2395A;ENSP00000334563:G2395A;ENSP00000386096:G2396A	.|ENSP00000334563:G2395A	A|G	+|+	1|2	0|0	MYO18B|MYO18B	24753124|24753124	0.003000|0.003000	0.15002|0.15002	0.011000|0.011000	0.14972|0.14972	0.130000|0.130000	0.20726|0.20726	0.135000|0.135000	0.15952|0.15952	0.154000|0.154000	0.19237|0.19237	-0.264000|-0.264000	0.10439|0.10439	GCT|GGC	G|0.912;C|0.088	0.088	strong		0.592	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
SSPO	23145	hgsc.bcm.edu	37	7	149479935	149479935	+	RNA	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:149479935G>A	ENST00000378016.2	+	0	1901							A2VEC9	SSPO_HUMAN	SCO-spondin						cell adhesion (GO:0007155)	extracellular space (GO:0005615)	peptidase inhibitor activity (GO:0030414)					Melanoma(164;0.165)|Ovarian(565;0.177)		OV - Ovarian serous cystadenocarcinoma(82;0.00625)			CCTGTTCCAGGAGCTGTGCTG	0.612																																					p.G634E		Atlas-SNP	.											.	.	.	.	0			c.G1901A						PASS	.						36.0	40.0	39.0					7																	149479935		2080	4195	6275			23145	exon15			TTCCAGGAGCTGT	AK093431		7q36.1	2013-08-07	2013-08-06		ENSG00000197558	ENSG00000197558			21998	protein-coding gene	gene with protein product	"""subcommissural organ spondin"", ""SCO protein, thrombospondin domain containing"""		"""SCO-spondin homolog (Bos taurus)"""			8743952, 11008217	Standard	NM_198455		Approved	SCO-spondin, KIAA0543, FLJ36112	uc010lpk.3	A2VEC9	OTTHUMG00000157884		7.37:g.149479935G>A		118.0	0.0	0		108.0	38.0	0.351852	NM_198455	Q76B61	Missense_Mutation	SNP	ENST00000378016.2	37																																																																																				.	.	none		0.612	SSPO-202	KNOWN	basic	processed_transcript	processed_transcript			
SYP	6855	hgsc.bcm.edu	37	X	49047924	49047924	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:49047924A>G	ENST00000263233.4	-	6	984	c.912T>C	c.(910-912)ggT>ggC	p.G304G	SYP_ENST00000479808.1_Silent_p.G304G|SYP_ENST00000538567.1_Silent_p.G186G	NM_003179.2	NP_003170.1	P08247	SYPH_HUMAN	synaptophysin	304	Repeats, Gly-rich.				cellular response to organic substance (GO:0071310)|endocytosis (GO:0006897)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of opioid receptor signaling pathway (GO:2000474)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|synaptic vesicle maturation (GO:0016188)|synaptic vesicle membrane organization (GO:0048499)	cell junction (GO:0030054)|excitatory synapse (GO:0060076)|integral component of synaptic vesicle membrane (GO:0030285)|neuron projection (GO:0043005)|neuron projection terminus (GO:0044306)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|protein complex (GO:0043234)|synaptic vesicle (GO:0008021)	cholesterol binding (GO:0015485)|protein self-association (GO:0043621)|transporter activity (GO:0005215)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|large_intestine(2)|lung(4)|ovary(1)|pancreas(1)	15		all_lung(315;0.00016)				AGGTGGGTGCACCCTGCGGGC	0.647																																					p.G304G		Atlas-SNP	.											.	SYP	71	.	0			c.T912C						PASS	.						20.0	19.0	19.0					X																	49047924		2203	4296	6499	SO:0001819	synonymous_variant	6855	exon6			GGGTGCACCCTGC	X06389	CCDS14321.1	Xp11.23-p11.22	2014-02-19			ENSG00000102003	ENSG00000102003			11506	protein-coding gene	gene with protein product		313475				3120152, 19377476	Standard	NM_003179		Approved	MRX96	uc004dmz.1	P08247	OTTHUMG00000034557	ENST00000263233.4:c.912T>C	X.37:g.49047924A>G		28.0	0.0	0		31.0	30.0	0.967742	NM_003179	B2R7L6|B7Z359|Q6P2F7	Silent	SNP	ENST00000263233.4	37	CCDS14321.1	.	.	.	.	.	.	.	.	.	.	A	11.63	1.694606	0.30052	.	.	ENSG00000102003	ENST00000472598	.	.	.	5.5	0.389	0.16269	.	.	.	.	.	T	0.40040	0.1101	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32929	-0.9888	4	.	.	.	-9.7988	0.3716	0.00380	0.2718:0.3005:0.1615:0.2662	.	.	.	.	A	194	.	.	V	-	2	0	SYP	48934868	0.083000	0.21467	1.000000	0.80357	0.997000	0.91878	-0.907000	0.04067	0.693000	0.31634	0.486000	0.48141	GTG	.	.	none		0.647	SYP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083625.2	NM_003179	
PRMT7	54496	hgsc.bcm.edu	37	16	68390697	68390697	+	Silent	SNP	C	C	T	rs61733486	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:68390697C>T	ENST00000339507.5	+	18	2735	c.1905C>T	c.(1903-1905)ccC>ccT	p.P635P	PRMT7_ENST00000441236.1_Silent_p.P585P|PRMT7_ENST00000348497.4_Silent_p.P487P|PRMT7_ENST00000449359.3_Silent_p.P585P			Q9NVM4	ANM7_HUMAN	protein arginine methyltransferase 7	635	SAM-dependent MTase PRMT-type 2. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell differentiation (GO:0030154)|DNA methylation involved in gamete generation (GO:0043046)|histone arginine methylation (GO:0034969)|histone methylation (GO:0016571)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to asymmetrical-dimethyl arginine (GO:0019919)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|regulation of gene expression by genetic imprinting (GO:0006349)|regulation of protein binding (GO:0043393)|regulation of transcription, DNA-templated (GO:0006355)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	[myelin basic protein]-arginine N-methyltransferase activity (GO:0016277)|histone binding (GO:0042393)|histone methyltransferase activity (H4-R3 specific) (GO:0044020)|histone-arginine N-methyltransferase activity (GO:0008469)|protein-arginine omega-N asymmetric methyltransferase activity (GO:0035242)|protein-arginine omega-N monomethyltransferase activity (GO:0035241)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|S-adenosylmethionine-dependent methyltransferase activity (GO:0008757)			endometrium(3)|kidney(2)|large_intestine(3)|lung(10)|pancreas(1)|urinary_tract(1)	20		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0155)|Epithelial(162;0.0629)		CTGCAGACCCCGAGGTAGTGC	0.687													c|||	226	0.0451278	0.0688	0.0533	5008	,	,		16243	0.0		0.0477	False		,,,				2504	0.0511				p.P635P		Atlas-SNP	.											.	PRMT7	51	.	0			c.C1905T						PASS	.		,	302,4088		13,276,1906	20.0	20.0	20.0		1755,1905	3.8	0.2	16	dbSNP_129	20	492,8106		12,468,3819	no	coding-synonymous,coding-synonymous	PRMT7	NM_001184824.1,NM_019023.2	,	25,744,5725	TT,TC,CC		5.7223,6.8793,6.1133	,	585/643,635/693	68390697	794,12194	2195	4299	6494	SO:0001819	synonymous_variant	54496	exon18			AGACCCCGAGGTA	AK001502	CCDS10866.1, CCDS54033.1	16q22.1	2008-02-05			ENSG00000132600	ENSG00000132600		"""Protein arginine methyltransferases"""	25557	protein-coding gene	gene with protein product		610087				15044439	Standard	NM_001184824		Approved	FLJ10640, KIAA1933	uc002evy.2	Q9NVM4	OTTHUMG00000137556	ENST00000339507.5:c.1905C>T	16.37:g.68390697C>T		116.0	0.0	0		128.0	52.0	0.40625	NM_019023	B3KPR0|B3KUG9|B4E379|Q96PV5|Q9H9L0	Silent	SNP	ENST00000339507.5	37	CCDS10866.1																																																																																			C|0.941;T|0.059	0.059	strong		0.687	PRMT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268892.3	NM_019023	
ACSS3	79611	hgsc.bcm.edu	37	12	81627215	81627215	+	Missense_Mutation	SNP	G	G	T	rs145641313	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:81627215G>T	ENST00000548058.1	+	13	2594	c.1684G>T	c.(1684-1686)Gca>Tca	p.A562S	ACSS3_ENST00000548324.1_Missense_Mutation_p.A244S|ACSS3_ENST00000261206.3_Missense_Mutation_p.A561S			Q9H6R3	ACSS3_HUMAN	acyl-CoA synthetase short-chain family member 3	562						mitochondrion (GO:0005739)	acetate-CoA ligase activity (GO:0003987)|ATP binding (GO:0005524)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(5)|kidney(2)|large_intestine(7)|liver(3)|lung(20)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)	51						AATAAATGTTGCAGGTCACAG	0.393													G|||	2	0.000399361	0.0015	0.0	5008	,	,		18493	0.0		0.0	False		,,,				2504	0.0				p.A562S		Atlas-SNP	.											.	ACSS3	118	.	0			c.G1684T						PASS	.	G	SER/ALA	3,4403	6.2+/-15.9	0,3,2200	227.0	221.0	223.0		1684	5.8	1.0	12	dbSNP_134	223	0,8600		0,0,4300	yes	missense	ACSS3	NM_024560.2	99	0,3,6500	TT,TG,GG		0.0,0.0681,0.0231	possibly-damaging	562/687	81627215	3,13003	2203	4300	6503	SO:0001583	missense	79611	exon13			AATGTTGCAGGTC		CCDS9022.1	12q21.31	2014-08-08			ENSG00000111058	ENSG00000111058		"""Acyl-CoA synthetase family"""	24723	protein-coding gene	gene with protein product		614356				17762044	Standard	NM_024560		Approved	FLJ21963	uc001szl.1	Q9H6R3	OTTHUMG00000170179	ENST00000548058.1:c.1684G>T	12.37:g.81627215G>T	ENSP00000449535:p.Ala562Ser	144.0	0.0	0		154.0	63.0	0.409091	NM_024560	Q8NC66	Missense_Mutation	SNP	ENST00000548058.1	37	CCDS9022.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	32	5.163767	0.94727	6.81E-4	0.0	ENSG00000111058	ENST00000548058;ENST00000261206;ENST00000548324	T;T;T	0.46451	2.94;2.94;0.87	5.84	5.84	0.93424	AMP-dependent synthetase/ligase (1);	0.000000	0.85682	D	0.000000	T	0.53706	0.1813	N	0.26130	0.795	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.998	T	0.44667	-0.9313	10	0.30854	T	0.27	-15.5203	19.7715	0.96367	0.0:0.0:1.0:0.0	.	244;562	Q9H6R3-2;Q9H6R3	.;ACSS3_HUMAN	S	562;561;244	ENSP00000449535:A562S;ENSP00000261206:A561S;ENSP00000448965:A244S	ENSP00000261206:A561S	A	+	1	0	ACSS3	80151346	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	7.315000	0.78998	2.777000	0.95525	0.650000	0.86243	GCA	G|0.999;T|0.001	0.001	strong		0.393	ACSS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407794.1	NM_024560	
LSM6	11157	hgsc.bcm.edu	37	4	147110790	147110790	+	Silent	SNP	A	A	T	rs41280529	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:147110790A>T	ENST00000502781.1	+	4	944	c.225A>T	c.(223-225)acA>acT	p.T75T	LSM6_ENST00000296581.5_Silent_p.T75T			P62312	LSM6_HUMAN	LSM6 homolog, U6 small nuclear RNA associated (S. cerevisiae)	75					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|rRNA processing (GO:0006364)|tRNA processing (GO:0008033)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|small nuclear ribonucleoprotein complex (GO:0030532)|spliceosomal complex (GO:0005681)	poly(A) RNA binding (GO:0044822)					all_hematologic(180;0.151)					ACATCAGTACACAGAAGAGAC	0.299													A|||	23	0.00459265	0.0015	0.0043	5008	,	,		18321	0.0		0.0179	False		,,,				2504	0.0				p.T75T	Ovarian(181;1591 2748 12147 31551)	Atlas-SNP	.											.	LSM6	5	.	0			c.A225T						PASS	.	A		9,4397	12.9+/-30.5	0,9,2194	68.0	75.0	72.0		225	-1.0	1.0	4	dbSNP_127	72	115,8483	61.7+/-123.6	0,115,4184	no	coding-synonymous	LSM6	NM_007080.2		0,124,6378	TT,TA,AA		1.3375,0.2043,0.9536		75/81	147110790	124,12880	2203	4299	6502	SO:0001819	synonymous_variant	11157	exon4			CAGTACACAGAAG	AF182292	CCDS3767.1	4q31.21	2008-02-05				ENSG00000164167			17017	protein-coding gene	gene with protein product		607286				10369684, 10523320	Standard	NM_007080		Approved	YDR378C	uc003ikq.4	P62312		ENST00000502781.1:c.225A>T	4.37:g.147110790A>T		118.0	0.0	0		119.0	49.0	0.411765	NM_007080	Q4W5J5|Q9Y4Y8	Silent	SNP	ENST00000502781.1	37	CCDS3767.1																																																																																			A|0.991;T|0.009	0.009	strong		0.299	LSM6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364929.1		
BYSL	705	hgsc.bcm.edu	37	6	41895153	41895153	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41895153G>A	ENST00000230340.4	+	2	685	c.310G>A	c.(310-312)Gag>Aag	p.E104K		NM_004053.3	NP_004044.3	Q13895	BYST_HUMAN	bystin-like	104					cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|female pregnancy (GO:0007565)|maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000462)|trophectodermal cell differentiation (GO:0001829)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(5)|skin(1)	8	Colorectal(47;0.121)		STAD - Stomach adenocarcinoma(11;0.000204)|Epithelial(12;0.000473)|Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)			CGAGGACGAGGAGTGGCCCAC	0.542																																					p.E104K		Atlas-SNP	.											.	BYSL	17	.	0			c.G310A						PASS	.						127.0	115.0	119.0					6																	41895153		2203	4300	6503	SO:0001583	missense	705	exon2			GACGAGGAGTGGC	L36720	CCDS34450.1	6p21.1	2008-08-29			ENSG00000112578	ENSG00000112578			1157	protein-coding gene	gene with protein product		603871				9925933, 17381424	Standard	NM_004053		Approved		uc003orl.3	Q13895	OTTHUMG00000014687	ENST00000230340.4:c.310G>A	6.37:g.41895153G>A	ENSP00000230340:p.Glu104Lys	144.0	0.0	0		135.0	52.0	0.385185	NM_004053	Q6P5W4|Q86W44|Q96IP8	Missense_Mutation	SNP	ENST00000230340.4	37	CCDS34450.1	.	.	.	.	.	.	.	.	.	.	G	34	5.317664	0.95682	.	.	ENSG00000112578	ENST00000230340	T	0.21734	1.99	5.37	4.5	0.54988	.	0.049967	0.85682	D	0.000000	T	0.12732	0.0309	M	0.74647	2.275	0.80722	D	1	B	0.12013	0.005	B	0.09377	0.004	T	0.04522	-1.0945	10	0.24483	T	0.36	-14.342	13.8124	0.63270	0.0747:0.0:0.9253:0.0	.	104	Q13895	BYST_HUMAN	K	104	ENSP00000230340:E104K	ENSP00000230340:E104K	E	+	1	0	BYSL	42003131	1.000000	0.71417	0.998000	0.56505	0.966000	0.64601	9.177000	0.94849	1.267000	0.44247	0.643000	0.83706	GAG	.	.	none		0.542	BYSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040535.2		
ALDH1A3	220	hgsc.bcm.edu	37	15	101432798	101432798	+	Nonsense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:101432798C>G	ENST00000329841.5	+	4	961	c.429C>G	c.(427-429)taC>taG	p.Y143*	ALDH1A3_ENST00000346623.6_Intron|RP11-66B24.4_ENST00000560351.1_RNA	NM_000693.2	NP_000684.2	P47895	AL1A3_HUMAN	aldehyde dehydrogenase 1 family, member A3	143					embryonic eye morphogenesis (GO:0048048)|face development (GO:0060324)|inner ear morphogenesis (GO:0042472)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|nucleus accumbens development (GO:0021768)|olfactory pit development (GO:0060166)|optic cup morphogenesis involved in camera-type eye development (GO:0002072)|positive regulation of apoptotic process (GO:0043065)|retinal metabolic process (GO:0042574)|retinoic acid biosynthetic process (GO:0002138)|retinoic acid metabolic process (GO:0042573)|retinol metabolic process (GO:0042572)|righting reflex (GO:0060013)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	aldehyde dehydrogenase (NAD) activity (GO:0004029)|aldehyde dehydrogenase [NAD(P)+] activity (GO:0004030)|NAD+ binding (GO:0070403)|protein homodimerization activity (GO:0042803)|thyroid hormone binding (GO:0070324)			NS(1)|central_nervous_system(2)|endometrium(3)|large_intestine(7)|lung(9)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	27	Lung NSC(78;0.00144)|all_lung(78;0.0018)|Melanoma(26;0.00852)		OV - Ovarian serous cystadenocarcinoma(32;0.000932)|LUSC - Lung squamous cell carcinoma(107;0.0766)|Lung(145;0.103)		Vitamin A(DB00162)	CCCTCAGATACTTTGCAGGGT	0.478																																					p.Y143X		Atlas-SNP	.											.	ALDH1A3	61	.	0			c.C429G						PASS	.						131.0	131.0	131.0					15																	101432798		2203	4300	6503	SO:0001587	stop_gained	220	exon4			CAGATACTTTGCA	U07919	CCDS10389.1	15q26	2010-05-07			ENSG00000184254	ENSG00000184254	1.2.1.5	"""Aldehyde dehydrogenases"""	409	protein-coding gene	gene with protein product	"""retinaldehyde dehydrogenase 3"""	600463		ALDH6		7698756	Standard	XR_111558		Approved	RALDH3	uc002bwn.4	P47895	OTTHUMG00000149870	ENST00000329841.5:c.429C>G	15.37:g.101432798C>G	ENSP00000332256:p.Tyr143*	136.0	0.0	0		127.0	70.0	0.551181	NM_000693	Q6NT64	Nonsense_Mutation	SNP	ENST00000329841.5	37	CCDS10389.1	.	.	.	.	.	.	.	.	.	.	C	26.1	4.702411	0.88924	.	.	ENSG00000184254	ENST00000329841	.	.	.	5.52	2.11	0.27256	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	10.2979	0.43635	0.0:0.7892:0.0:0.2108	.	.	.	.	X	143	.	ENSP00000332256:Y143X	Y	+	3	2	ALDH1A3	99250321	0.827000	0.29292	0.998000	0.56505	0.980000	0.70556	-0.072000	0.11486	0.120000	0.18254	0.555000	0.69702	TAC	.	.	none		0.478	ALDH1A3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313620.2		
ADAM2	2515	hgsc.bcm.edu	37	8	39695677	39695677	+	Missense_Mutation	SNP	C	C	A	rs34800519	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:39695677C>A	ENST00000265708.4	-	1	131	c.28G>T	c.(28-30)Ggg>Tgg	p.G10W	ADAM2_ENST00000379853.2_Missense_Mutation_p.G10W|ADAM2_ENST00000523181.1_5'UTR|ADAM2_ENST00000521880.1_Missense_Mutation_p.G10W|ADAM2_ENST00000347580.4_Missense_Mutation_p.G10W	NM_001464.3	NP_001455.3	Q99965	ADAM2_HUMAN	ADAM metallopeptidase domain 2	10			G -> W (in dbSNP:rs34800519).		adult behavior (GO:0030534)|binding of sperm to zona pellucida (GO:0007339)|cell adhesion (GO:0007155)|fusion of sperm to egg plasma membrane (GO:0007342)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)|visual learning (GO:0008542)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(11)|lung(29)|ovary(3)|prostate(1)|skin(5)|urinary_tract(1)	53		all_cancers(7;2.38e-28)|all_epithelial(6;8.85e-21)|all_lung(54;1.24e-07)|Lung NSC(58;1.94e-07)|Hepatocellular(245;0.00745)|Breast(189;0.00908)|Renal(179;0.0183)|Colorectal(162;0.246)	LUSC - Lung squamous cell carcinoma(45;0.000149)	READ - Rectum adenocarcinoma(644;0.0689)|Kidney(114;0.162)		CCGCCGAGCCCGCTGAGCAGA	0.572													C|||	132	0.0263578	0.0923	0.0101	5008	,	,		16527	0.0		0.003	False		,,,				2504	0.0				p.G10W		Atlas-SNP	.											ADAM2,NS,carcinoma,+1,1	ADAM2	124	1	0			c.G28T						PASS	.	C	TRP/GLY	299,4107	164.4+/-196.0	19,261,1923	80.0	80.0	80.0		28	3.3	0.3	8	dbSNP_126	80	16,8584	11.9+/-42.8	0,16,4284	yes	missense	ADAM2	NM_001464.3	184	19,277,6207	AA,AC,CC		0.186,6.7862,2.422	probably-damaging	10/736	39695677	315,12691	2203	4300	6503	SO:0001583	missense	2515	exon1			CGAGCCCGCTGAG	U52370	CCDS34884.1, CCDS64882.1, CCDS64883.1	8p11.2	2009-03-25	2008-07-31		ENSG00000104755	ENSG00000104755		"""ADAM metallopeptidase domain containing"""	198	protein-coding gene	gene with protein product	"""cancer/testis antigen 15"""	601533	"""fertilin beta"""	FTNB		8702389, 9070941	Standard	NM_001278113		Approved	PH-30b, PH30, CT15	uc003xnj.4	Q99965	OTTHUMG00000164041	ENST00000265708.4:c.28G>T	8.37:g.39695677C>A	ENSP00000265708:p.Gly10Trp	113.0	0.0	0		124.0	49.0	0.395161	NM_001464	P78326|Q9UQQ8	Missense_Mutation	SNP	ENST00000265708.4	37	CCDS34884.1	54	0.024725274725274724	47	0.09552845528455285	4	0.011049723756906077	0	0.0	3	0.00395778364116095	C	15.16	2.751827	0.49362	0.067862	0.00186	ENSG00000104755	ENST00000347580;ENST00000379853;ENST00000265708;ENST00000521880	T;T;T;T	0.02258	5.01;4.37;5.24;5.21	3.26	3.26	0.37387	.	.	.	.	.	T	0.00300	0.0009	M	0.80982	2.52	0.19300	N	0.999973	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.91635	0.98;0.999;0.991;0.971	T	0.04053	-1.0981	8	.	.	.	.	10.2854	0.43564	0.0:1.0:0.0:0.0	rs34800519	10;10;10;10	B4DWY7;Q6P2G0;Q99965-2;Q99965	.;.;.;ADAM2_HUMAN	W	10	ENSP00000343854:G10W;ENSP00000369182:G10W;ENSP00000265708:G10W;ENSP00000429352:G10W	.	G	-	1	0	ADAM2	39814834	0.048000	0.20356	0.275000	0.24674	0.128000	0.20619	1.104000	0.31074	2.114000	0.64651	0.460000	0.39030	GGG	C|0.977;A|0.023	0.023	strong		0.572	ADAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376926.1	NM_001464	
MUC4	4585	hgsc.bcm.edu	37	3	195515100	195515100	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195515100G>A	ENST00000463781.3	-	2	3810	c.3351C>T	c.(3349-3351)caC>caT	p.H1117H	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.H1117H|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	556					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		GAGGGGTGGTGTGACCTGTGG	0.567																																					p.H1117H		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-2,1	MUC4	1505	1	0			c.C3351T						scavenged	.						14.0	8.0	9.0					3																	195515100		671	1543	2214	SO:0001819	synonymous_variant	4585	exon2			GGTGGTGTGACCT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3351C>T	3.37:g.195515100G>A		137.0	0.0	0		98.0	5.0	0.0510204	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	none		0.567	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KIF11	3832	hgsc.bcm.edu	37	10	94369247	94369247	+	Silent	SNP	C	C	T	rs145656661		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:94369247C>T	ENST00000260731.3	+	6	769	c.679C>T	c.(679-681)Ctg>Ttg	p.L227L		NM_004523.3	NP_004514.2	P52732	KIF11_HUMAN	kinesin family member 11	227	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|ATP catabolic process (GO:0006200)|blood coagulation (GO:0007596)|chromosome segregation (GO:0007059)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic centrosome separation (GO:0007100)|mitotic nuclear division (GO:0007067)|mitotic spindle organization (GO:0007052)|spindle assembly involved in mitosis (GO:0090307)|spindle organization (GO:0007051)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinesin complex (GO:0005871)|membrane (GO:0016020)|microtubule (GO:0005874)|spindle (GO:0005819)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)			breast(1)|endometrium(5)|kidney(2)|large_intestine(9)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29						TGCAGCTACTCTGATGAATGC	0.378																																					p.L227L	Colon(47;212 1003 2764 4062 8431)	Atlas-SNP	.											.	KIF11	58	.	0			c.C679T						PASS	.	C		0,4406		0,0,2203	201.0	222.0	215.0		679	-4.9	0.0	10	dbSNP_134	215	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	KIF11	NM_004523.3		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		227/1057	94369247	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	3832	exon6			GCTACTCTGATGA	X85137	CCDS7422.1	10q24.1	2008-03-03	2003-01-09	2003-01-10	ENSG00000138160	ENSG00000138160		"""Kinesins"""	6388	protein-coding gene	gene with protein product		148760	"""kinesin-like 1"""	KNSL1		1505978, 8548803	Standard	NM_004523		Approved	Eg5, HKSP, TRIP5	uc001kic.3	P52732	OTTHUMG00000018761	ENST00000260731.3:c.679C>T	10.37:g.94369247C>T		49.0	0.0	0		54.0	20.0	0.37037	NM_004523	A0AV49|B2RMV3|Q15716|Q5VWX0	Silent	SNP	ENST00000260731.3	37	CCDS7422.1																																																																																			C|1.000;T|0.000	0.000	weak		0.378	KIF11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049401.1	NM_004523	
GPATCH8	23131	hgsc.bcm.edu	37	17	42475670	42475670	+	Missense_Mutation	SNP	T	T	C	rs760339	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:42475670T>C	ENST00000591680.1	-	8	3805	c.3775A>G	c.(3775-3777)Agc>Ggc	p.S1259G	GPATCH8_ENST00000434000.1_Missense_Mutation_p.S1181G	NM_001002909.2	NP_001002909.1	Q9UKJ3	GPTC8_HUMAN	G patch domain containing 8	1259			S -> G (in dbSNP:rs760339). {ECO:0000269|PubMed:10477733}.				metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			breast(4)|endometrium(7)|kidney(6)|large_intestine(4)|liver(2)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	50		Prostate(33;0.0181)		BRCA - Breast invasive adenocarcinoma(366;0.206)		GGCTGACTGCTGCTATCCAGG	0.582													T|||	21	0.00419329	0.0	0.0043	5008	,	,		18567	0.0		0.003	False		,,,				2504	0.0153				p.S1259G		Atlas-SNP	.											.	GPATCH8	114	.	0			c.A3775G						PASS	.	T	GLY/SER	0,4406		0,0,2203	126.0	124.0	125.0		3775	-1.1	0.8	17	dbSNP_86	125	32,8568	22.2+/-67.0	0,32,4268	yes	missense	GPATCH8	NM_001002909.2	56	0,32,6471	CC,CT,TT		0.3721,0.0,0.246	benign	1259/1503	42475670	32,12974	2203	4300	6503	SO:0001583	missense	23131	exon8			GACTGCTGCTATC	AB011125	CCDS32666.1	17q21.31	2013-01-28	2006-08-22	2006-12-13	ENSG00000186566	ENSG00000186566		"""G patch domain containing"""	29066	protein-coding gene	gene with protein product		614396	"""KIAA0553"""	KIAA0553, GPATC8		9628581	Standard	NM_001002909		Approved		uc002igw.2	Q9UKJ3	OTTHUMG00000181818	ENST00000591680.1:c.3775A>G	17.37:g.42475670T>C	ENSP00000467556:p.Ser1259Gly	49.0	0.0	0		47.0	24.0	0.510638	NM_001002909	B9EGP9|O60300|Q8TB99	Missense_Mutation	SNP	ENST00000591680.1	37	CCDS32666.1	4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	T	0.003	-2.450966	0.00175	0.0	0.003721	ENSG00000186566	ENST00000335500;ENST00000434000	T	0.11169	2.8	4.76	-1.12	0.09808	.	0.595775	0.18361	N	0.143579	T	0.02012	0.0063	N	0.02539	-0.55	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.45131	-0.9282	10	0.06365	T	0.9	-4.6956	9.4564	0.38758	0.0:0.6109:0.0:0.3891	rs760339;rs760339	1259	Q9UKJ3	GPTC8_HUMAN	G	1259;1181	ENSP00000395016:S1181G	ENSP00000335486:S1259G	S	-	1	0	GPATCH8	39831196	0.060000	0.20803	0.835000	0.33067	0.534000	0.34807	0.338000	0.19858	-0.063000	0.13065	-0.479000	0.04858	AGC	T|0.997;C|0.003	0.003	strong		0.582	GPATCH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457797.1	NM_001002909	
TGM6	343641	hgsc.bcm.edu	37	20	2377204	2377204	+	Silent	SNP	C	C	T	rs16984872	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:2377204C>T	ENST00000202625.2	+	4	538	c.477C>T	c.(475-477)agC>agT	p.S159S	TGM6_ENST00000477505.1_Intron|TGM6_ENST00000381423.1_Silent_p.S159S	NM_198994.2	NP_945345.2	O95932	TGM3L_HUMAN	transglutaminase 6	159					cell death (GO:0008219)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			breast(1)|endometrium(6)|kidney(2)|large_intestine(2)|lung(32)|ovary(4)|prostate(1)|skin(4)	52					L-Glutamine(DB00130)	ACGTGCTCAGCGACAGCGGCA	0.612													C|||	193	0.0385383	0.1225	0.0259	5008	,	,		19129	0.0		0.0099	False		,,,				2504	0.0031				p.S159S		Atlas-SNP	.											TGM6,NS,carcinoma,0,1	TGM6	126	1	0			c.C477T						PASS	.	C		447,3959	215.8+/-234.7	28,391,1784	96.0	85.0	89.0		477	-5.3	0.9	20	dbSNP_123	89	87,8513	49.4+/-109.1	0,87,4213	no	coding-synonymous	TGM6	NM_198994.2		28,478,5997	TT,TC,CC		1.0116,10.1453,4.1058		159/707	2377204	534,12472	2203	4300	6503	SO:0001819	synonymous_variant	343641	exon4			GCTCAGCGACAGC	AF540970	CCDS13025.1, CCDS58761.1	20p13	2010-12-19	2004-07-05	2004-07-07	ENSG00000166948	ENSG00000166948		"""Transglutaminases"""	16255	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 35"""	613900	"""transglutaminase 3-like"""	TGM3L		11390390, 21106500	Standard	NM_198994		Approved	dJ734P14.3, TGY, SCA35	uc002wfy.1	O95932	OTTHUMG00000031692	ENST00000202625.2:c.477C>T	20.37:g.2377204C>T		217.0	0.0	0		250.0	115.0	0.46	NM_198994	Q5JXU4|Q5JXU5|Q719M2|Q719M3|Q9Y4U8	Silent	SNP	ENST00000202625.2	37	CCDS13025.1																																																																																			C|0.960;T|0.040	0.040	strong		0.612	TGM6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077581.2	NM_198994	
RADIL	55698	hgsc.bcm.edu	37	7	4876064	4876064	+	Silent	SNP	G	G	A	rs150209652	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:4876064G>A	ENST00000399583.3	-	3	895	c.708C>T	c.(706-708)ccC>ccT	p.P236P	RADIL_ENST00000536091.1_Silent_p.P236P|RADIL_ENST00000538469.1_5'UTR	NM_018059.4	NP_060529.4	Q96JH8	RADIL_HUMAN	Ras association and DIL domains	236					multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|substrate adhesion-dependent cell spreading (GO:0034446)	microtubule (GO:0005874)				NS(1)|biliary_tract(2)|breast(1)|central_nervous_system(3)|endometrium(2)|large_intestine(2)|lung(22)|pancreas(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	41		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0986)|OV - Ovarian serous cystadenocarcinoma(56;7.41e-15)		CGTCGGGGCCGGGCTCCTCGG	0.706													G|||	60	0.0119808	0.0015	0.0173	5008	,	,		12929	0.0		0.0249	False		,,,				2504	0.0215				p.P236P		Atlas-SNP	.											.	RADIL	110	.	0			c.C708T						PASS	.	G		15,4077		0,15,2031	12.0	19.0	17.0		708	-9.7	0.0	7	dbSNP_134	17	196,8144		5,186,3979	no	coding-synonymous	RADIL	NM_018059.4		5,201,6010	AA,AG,GG		2.3501,0.3666,1.6972		236/1076	4876064	211,12221	2046	4170	6216	SO:0001819	synonymous_variant	55698	exon3			GGGGCCGGGCTCC	AB058752	CCDS43544.1	7p22.1	2010-08-27			ENSG00000157927	ENSG00000157927			22226	protein-coding gene	gene with protein product		611491				16051602, 17704304	Standard	NM_018059		Approved	FLJ10324, KIAA1849, RASIP2	uc003snj.1	Q96JH8	OTTHUMG00000151753	ENST00000399583.3:c.708C>T	7.37:g.4876064G>A		34.0	0.0	0		55.0	34.0	0.618182	NM_018059	A4D1Z5|A5YM49|B7ZL20|Q0VFZ9|Q75LH3|Q9BSP5|Q9H0M6|Q9NW43|Q9NWC4	Silent	SNP	ENST00000399583.3	37	CCDS43544.1																																																																																			G|0.987;A|0.013	0.013	strong		0.706	RADIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323769.2	NM_018059	
GOLGA4	2803	hgsc.bcm.edu	37	3	37368600	37368600	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:37368600A>T	ENST00000361924.2	+	14	5597	c.5223A>T	c.(5221-5223)ttA>ttT	p.L1741F	GOLGA4_ENST00000356847.4_Missense_Mutation_p.L1763F|GOLGA4_ENST00000444882.1_Intron	NM_002078.4	NP_002069.2	Q13439	GOGA4_HUMAN	golgin A4	1741	Glu-rich.				Golgi to plasma membrane protein transport (GO:0043001)|protein targeting to Golgi (GO:0000042)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	GTPase binding (GO:0051020)			NS(2)|breast(3)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(17)|liver(2)|lung(16)|ovary(4)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	65						TCAGTGTTTTACAAAGAAACT	0.388																																					p.L1763F		Atlas-SNP	.											.	GOLGA4	173	.	0			c.A5289T						PASS	.						103.0	109.0	107.0					3																	37368600		2203	4299	6502	SO:0001583	missense	2803	exon15			TGTTTTACAAAGA	U31906	CCDS2666.1, CCDS54564.1	3p22-p21.3	2010-02-12	2010-02-12		ENSG00000144674	ENSG00000144674			4427	protein-coding gene	gene with protein product	"""golgin 245"""	602509	"""golgi autoantigen, golgin subfamily a, 4"""			8626529	Standard	NM_002078		Approved	GOLG, GCP2, p230, golgin-240	uc003cgw.3	Q13439	OTTHUMG00000130799	ENST00000361924.2:c.5223A>T	3.37:g.37368600A>T	ENSP00000354486:p.Leu1741Phe	146.0	0.0	0		126.0	50.0	0.396825	NM_001172713	F8W8Q7|Q13270|Q13654|Q14436|Q59EW8	Missense_Mutation	SNP	ENST00000361924.2	37	CCDS2666.1	.	.	.	.	.	.	.	.	.	.	A	15.09	2.729120	0.48833	.	.	ENSG00000144674	ENST00000361924;ENST00000356847;ENST00000437131	T;T;T	0.34472	1.36;1.36;1.37	4.39	-3.04	0.05412	.	0.000000	0.27636	N	0.018486	T	0.48642	0.1511	M	0.76002	2.32	0.18873	N	0.999985	D;D;D;D	0.89917	0.96;0.96;0.96;1.0	P;P;P;D	0.85130	0.731;0.684;0.684;0.997	T	0.35919	-0.9769	10	0.48119	T	0.1	.	5.1769	0.15139	0.4641:0.0:0.3958:0.1401	.	1741;1741;1763;1741	Q13439-3;Q13439-4;F8W8Q7;Q13439	.;.;.;GOGA4_HUMAN	F	1741;1763;1612	ENSP00000354486:L1741F;ENSP00000349305:L1763F;ENSP00000405842:L1612F	ENSP00000349305:L1763F	L	+	3	2	GOLGA4	37343604	0.979000	0.34478	0.002000	0.10522	0.888000	0.51559	0.310000	0.19356	-0.410000	0.07542	-0.379000	0.06801	TTA	.	.	none		0.388	GOLGA4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000253339.2	NM_002078	
PTPRJ	5795	hgsc.bcm.edu	37	11	48157625	48157625	+	Silent	SNP	C	C	T	rs148782546	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:48157625C>T	ENST00000418331.2	+	9	2002	c.1650C>T	c.(1648-1650)taC>taT	p.Y550Y		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	550	Fibronectin type-III 6. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)			breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						ACGTGGTCTACGTCACCACCA	0.512													C|||	12	0.00239617	0.0	0.0	5008	,	,		21414	0.0		0.0119	False		,,,				2504	0.0				p.Y550Y		Atlas-SNP	.											PTPRJ_ENST00000418331,caecum,carcinoma,0,2	PTPRJ	225	2	0			c.C1650T						PASS	.	C		3,4399	6.2+/-15.9	0,3,2198	184.0	160.0	168.0		1650	-11.2	0.0	11	dbSNP_134	168	3,8593	3.0+/-9.4	0,3,4295	no	coding-synonymous	PTPRJ	NM_002843.3		0,6,6493	TT,TC,CC		0.0349,0.0682,0.0462		550/1338	48157625	6,12992	2201	4298	6499	SO:0001819	synonymous_variant	5795	exon9			GGTCTACGTCACC	U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.1650C>T	11.37:g.48157625C>T		212.0	0.0	0		246.0	127.0	0.51626	NM_002843	Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Silent	SNP	ENST00000418331.2	37	CCDS7945.1																																																																																			C|0.998;T|0.002	0.002	strong		0.512	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1		
KIR3DL2	3812	hgsc.bcm.edu	37	19	55367311	55367311	+	Missense_Mutation	SNP	G	G	A	rs113800142	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:55367311G>A	ENST00000326321.3	+	5	926	c.893G>A	c.(892-894)cGt>cAt	p.R298H	KIR3DL1_ENST00000402254.2_Intron|KIR3DL2_ENST00000270442.5_Missense_Mutation_p.R298H	NM_006737.3	NP_006728.2	P43630	KI3L2_HUMAN	killer cell immunoglobulin-like receptor, three domains, long cytoplasmic tail, 2	298	Ig-like C2-type 3.				cellular defense response (GO:0006968)|regulation of immune response (GO:0050776)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(2)|endometrium(1)|kidney(3)|large_intestine(4)|lung(5)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	23				GBM - Glioblastoma multiforme(193;0.0192)		GGCTCTTTCCGTGCCCTGCCC	0.567													.|||	348	0.0694888	0.0794	0.0591	5008	,	,		10257	0.0397		0.0636	False		,,,				2504	0.1002				p.R298H		Atlas-SNP	.											KIR3DL2,NS,carcinoma,0,1	KIR3DL2	55	1	0			c.G893A						scavenged	.	G	HIS/ARG	173,3101		9,155,1473	5.0	6.0	6.0		893	-2.0	0.0	19	dbSNP_132	6	521,6479		39,443,3018	no	missense	KIR3DL2	NM_006737.3	29	48,598,4491	AA,AG,GG		7.4429,5.2841,6.7549	benign	298/456	55367311	694,9580	1637	3500	5137	SO:0001583	missense	3812	exon5			CTTTCCGTGCCCT	L41270	CCDS12906.1, CCDS58677.1	19q13.4	2014-05-22			ENSG00000240403	ENSG00000240403		"""Killer cell immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6339	protein-coding gene	gene with protein product		604947				7716543, 8662091	Standard	NM_006737		Approved	cl-5, nkat4, nkat4a, nkat4b, CD158K	uc002qho.4	P43630	OTTHUMG00000065935	ENST00000326321.3:c.893G>A	19.37:g.55367311G>A	ENSP00000325525:p.Arg298His	78.0	0.0	0		69.0	31.0	0.449275	NM_001242867	Q13238|Q14947|Q14948|Q92684|Q95366|Q95367|Q95368	Missense_Mutation	SNP	ENST00000326321.3	37	CCDS12906.1	.	.	.	.	.	.	.	.	.	.	g	0.311	-0.967828	0.02232	0.052841	0.074429	ENSG00000240403	ENST00000326321;ENST00000270442	T;T	0.00768	5.72;5.72	0.993	-1.99	0.07457	Immunoglobulin subtype (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.00073	0.0002	L	0.43701	1.375	0.09310	N	1	B;B;B	0.15930	0.015;0.011;0.013	B;B;B	0.06405	0.002;0.001;0.0	T	0.44544	-0.9321	9	0.52906	T	0.07	.	2.9371	0.05818	0.3559:0.2417:0.4024:0.0	.	298;298;103	Q95366;P43630;B5MCJ6	.;KI3L2_HUMAN;.	H	298	ENSP00000325525:R298H;ENSP00000270442:R298H	ENSP00000270442:R298H	R	+	2	0	KIR3DL2	60059123	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-4.304000	0.00256	-1.364000	0.02161	-1.254000	0.01491	CGT	G|0.910;A|0.091	0.091	strong		0.567	KIR3DL2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000141241.1		
MUC1	4582	hgsc.bcm.edu	37	1	155161833	155161833	+	Silent	SNP	C	C	G	rs147687610	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:155161833C>G	ENST00000368395.1	-	2	371	c.300G>C	c.(298-300)tcG>tcC	p.S100S	MUC1_ENST00000342482.4_Intron|MUC1_ENST00000338684.5_Intron|MUC1_ENST00000457295.2_Intron|MUC1_ENST00000343256.5_Intron|MUC1_ENST00000337604.5_Intron|RP11-201K10.3_ENST00000473363.2_5'Flank|MUC1_ENST00000368389.2_Intron|MUC1_ENST00000462215.1_Intron|MUC1_ENST00000368398.3_Intron|MUC1_ENST00000368393.3_Intron|MUC1_ENST00000438413.1_Intron|MUC1_ENST00000368396.4_Intron|MUC1_ENST00000368392.3_Intron|MUC1_ENST00000368390.3_Intron	NM_001204285.1|NM_001204286.1	NP_001191214.1|NP_001191215.1	P15941	MUC1_HUMAN	mucin 1, cell surface associated	880					cellular protein metabolic process (GO:0044267)|cellular response to retinoic acid (GO:0071300)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|epithelial cell differentiation (GO:0030855)|female pregnancy (GO:0007565)|negative regulation of intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:1902166)|negative regulation of transcription by competitive promoter binding (GO:0010944)|O-glycan processing (GO:0016266)|positive regulation of histone H4 acetylation (GO:0090240)|positive regulation of transcription from RNA polymerase II promoter in response to stress (GO:0036003)|post-translational protein modification (GO:0043687)|regulation of transcription from RNA polymerase II promoter in response to stress (GO:0043618)|response to hypoxia (GO:0001666)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|nuclear chromatin (GO:0000790)|vesicle (GO:0031982)	p53 binding (GO:0002039)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|transcription cofactor activity (GO:0003712)			breast(1)|kidney(1)|large_intestine(1)|lung(3)|ovary(1)|pancreas(1)|skin(2)	10	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;5.31e-10)|all cancers(21;2.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TGACTGGGACCGAGGTGACAT	0.687			T	IGH@	B-NHL								C|||	30	0.00599042	0.0008	0.0072	5008	,	,		9990	0.0		0.0109	False		,,,				2504	0.0133				p.S109S		Atlas-SNP	.		Dom	yes		1	1q21	4582	"""mucin 1, transmembrane"""		L	.	MUC1	94	.	0			c.G327C						PASS	.																																			SO:0001819	synonymous_variant	4582	exon2			TGGGACCGAGGTG	J05581	CCDS1098.1, CCDS30882.1, CCDS30883.1, CCDS41408.1, CCDS41409.1, CCDS55640.1, CCDS55641.1, CCDS55642.1, CCDS55640.2, CCDS72933.1, CCDS72934.1, CCDS72935.1, CCDS72936.1	1q22	2014-01-31	2006-03-14		ENSG00000185499	ENSG00000185499		"""CD molecules"", ""Mucins"""	7508	protein-coding gene	gene with protein product		158340	"""mucin 1, transmembrane"", ""medullary cystic kidney disease 1 (autosomal dominant)"""	PUM, MCKD1		1697589, 23396133	Standard	NM_002456		Approved	CD227, PEM, ADMCKD, ADMCKD1, MCKD, MCD	uc031ppv.1	P15941	OTTHUMG00000035681	ENST00000368395.1:c.300G>C	1.37:g.155161833C>G		38.0	0.0	0		41.0	19.0	0.463415	NM_001204286	A5YRV1|A6ZID9|A6ZIE0|B1AVQ8|B1AVR0|B6ECA1|E7ESE5|E7EUG9|P13931|P15942|P17626|Q0VAP5|Q0VAP6|Q14128|Q14876|Q16437|Q16442|Q16615|Q6S4Y3|Q7Z547|Q7Z548|Q7Z550|Q7Z552|Q9BXA4|Q9UE75|Q9UE76|Q9UQL1|Q9Y4J2	Silent	SNP	ENST00000368395.1	37	CCDS55640.1																																																																																			C|0.995;G|0.005	0.005	strong		0.687	MUC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086735.1	NM_002456	
PPA2	27068	hgsc.bcm.edu	37	4	106345379	106345379	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:106345379T>C	ENST00000341695.5	-	7	659	c.629A>G	c.(628-630)aAt>aGt	p.N210S	PPA2_ENST00000310267.7_Missense_Mutation_p.N131S|PPA2_ENST00000380004.2_Missense_Mutation_p.N192S|PPA2_ENST00000432483.2_Missense_Mutation_p.N108S|PPA2_ENST00000357415.4_Missense_Mutation_p.N225S|PPA2_ENST00000509426.1_5'UTR|PPA2_ENST00000354147.3_Intron|PPA2_ENST00000348706.5_Missense_Mutation_p.N181S	NM_176869.2	NP_789845.1	Q9H2U2	IPYR2_HUMAN	pyrophosphatase (inorganic) 2	210					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)|protein serine/threonine phosphatase activity (GO:0004722)			breast(1)|endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|pancreas(1)	11		Myeloproliferative disorder(5;0.0255)|Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;2.03e-07)		TTCAGGATCATTCGCATTGAT	0.348																																					p.N210S		Atlas-SNP	.											.	PPA2	23	.	0			c.A629G						PASS	.						136.0	134.0	134.0					4																	106345379		2203	4300	6503	SO:0001583	missense	27068	exon7			GGATCATTCGCAT		CCDS3667.1, CCDS3668.2, CCDS3669.2, CCDS34043.1	4q25	2005-10-07			ENSG00000138777	ENSG00000138777			28883	protein-coding gene	gene with protein product		609988				11042152	Standard	NM_176869		Approved	FLJ20459	uc003hxl.3	Q9H2U2	OTTHUMG00000128781	ENST00000341695.5:c.629A>G	4.37:g.106345379T>C	ENSP00000343885:p.Asn210Ser	43.0	0.0	0		75.0	31.0	0.413333	NM_176869	B4DLP7|F8WDN9|I6L9B6|Q4W5E9|Q6PG51|Q8TBW0|Q96E55|Q9H0T0|Q9NX37|Q9P033|Q9ULX0	Missense_Mutation	SNP	ENST00000341695.5	37	CCDS3667.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.95|14.95	2.687529|2.687529	0.48097|0.48097	.|.	.|.	ENSG00000138777|ENSG00000138777	ENST00000508518|ENST00000341695;ENST00000348706;ENST00000432483;ENST00000357415;ENST00000380004;ENST00000510015;ENST00000310267	.|T;T;T;T;T;T;T	.|0.43688	.|0.94;0.94;0.94;0.94;0.94;0.94;0.94	5.4|5.4	4.14|4.14	0.48551|0.48551	.|.	.|0.202955	.|0.50627	.|D	.|0.000102	T|T	0.39708|0.39708	0.1088|0.1088	L|L	0.53671|0.53671	1.685|1.685	0.38017|0.38017	D|D	0.934732|0.934732	.|B;B;B;B;B	.|0.31680	.|0.009;0.335;0.182;0.181;0.023	.|B;B;B;B;B	.|0.34991	.|0.01;0.109;0.193;0.079;0.073	T|T	0.49214|0.49214	-0.8963|-0.8963	5|10	.|0.52906	.|T	.|0.07	-2.6133|-2.6133	11.196|11.196	0.48713|0.48713	0.0:0.0:0.1536:0.8464|0.0:0.0:0.1536:0.8464	.|.	.|131;108;181;192;210	.|B4DFH3;F8WDN9;Q9H2U2-3;E2QRM6;Q9H2U2	.|.;.;.;.;IPYR2_HUMAN	V|S	189|210;181;108;225;192;137;131	.|ENSP00000343885:N210S;ENSP00000313061:N181S;ENSP00000389957:N108S;ENSP00000349996:N225S;ENSP00000369340:N192S;ENSP00000423363:N137S;ENSP00000311150:N131S	.|ENSP00000311150:N131S	M|N	-|-	1|2	0|0	PPA2|PPA2	106564828|106564828	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.794000|0.794000	0.44872|0.44872	5.215000|5.215000	0.65241|0.65241	2.045000|2.045000	0.60652|0.60652	0.459000|0.459000	0.35465|0.35465	ATG|AAT	.	.	none		0.348	PPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250704.4	NM_176869	
KMT2C	58508	hgsc.bcm.edu	37	7	151962289	151962289	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:151962289C>T	ENST00000262189.6	-	8	1236	c.1018G>A	c.(1018-1020)Gaa>Aaa	p.E340K	KMT2C_ENST00000355193.2_Missense_Mutation_p.E340K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	340					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|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)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)										TTTGCATCTTCCTTCGCTATA	0.363																																					p.E340K		Atlas-SNP	.											MLL3_ENST00000355193,NS,carcinoma,+2,2	MLL3	1564	2	0			c.G1018A						scavenged	.						80.0	74.0	76.0					7																	151962289		2203	4299	6502	SO:0001583	missense	58508	exon8			CATCTTCCTTCGC	AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.1018G>A	7.37:g.151962289C>T	ENSP00000262189:p.Glu340Lys	177.0	0.0	0		172.0	11.0	0.0639535	NM_170606	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	C	14.11	2.437062	0.43224	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.98947	-5.26;-5.26	4.65	4.65	0.58169	Zinc finger, RING/FYVE/PHD-type (1);Protein kinase C-like, phorbol ester/diacylglycerol binding (1);Zinc finger, FYVE/PHD-type (1);	0.000000	0.42821	U	0.000650	D	0.97688	0.9242	N	0.25890	0.77	0.80722	D	1	D	0.60575	0.988	P	0.54759	0.76	D	0.98897	1.0775	10	0.62326	D	0.03	.	17.9157	0.88950	0.0:1.0:0.0:0.0	.	340	Q8NEZ4	MLL3_HUMAN	K	340	ENSP00000262189:E340K;ENSP00000347325:E340K	ENSP00000262189:E340K	E	-	1	0	MLL3	151593222	1.000000	0.71417	1.000000	0.80357	0.009000	0.06853	7.772000	0.85439	2.271000	0.75665	0.557000	0.71058	GAA	.	.	none		0.363	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3		
ABCG4	64137	hgsc.bcm.edu	37	11	119025270	119025270	+	Silent	SNP	G	G	A	rs200058802	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:119025270G>A	ENST00000449422.2	+	5	713	c.525G>A	c.(523-525)gaG>gaA	p.E175E	ABCG4_ENST00000531739.1_Silent_p.E175E|ABCG4_ENST00000307417.3_Silent_p.E175E	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	175	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		AGAAGCAGGAGGTGAAGAAGG	0.592													G|||	4	0.000798722	0.0	0.0	5008	,	,		18764	0.0		0.0	False		,,,				2504	0.0041				p.E175E		Atlas-SNP	.											.	ABCG4	77	.	0			c.G525A						PASS	.	G	,	0,4400		0,0,2200	62.0	60.0	61.0		525,525	1.2	1.0	11		61	2,8588	2.2+/-6.3	0,2,4293	no	coding-synonymous,coding-synonymous	ABCG4	NM_001142505.1,NM_022169.4	,	0,2,6493	AA,AG,GG		0.0233,0.0,0.0154	,	175/647,175/647	119025270	2,12988	2200	4295	6495	SO:0001819	synonymous_variant	64137	exon5			GCAGGAGGTGAAG	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.525G>A	11.37:g.119025270G>A		66.0	0.0	0		52.0	20.0	0.384615	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Silent	SNP	ENST00000449422.2	37	CCDS8415.1																																																																																			G|0.999;A|0.001	0.001	weak		0.592	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
DNAJC13	23317	hgsc.bcm.edu	37	3	132166302	132166302	+	Silent	SNP	T	T	G	rs116489157	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132166302T>G	ENST00000260818.6	+	4	530	c.282T>G	c.(280-282)ctT>ctG	p.L94L	DNAJC13_ENST00000486798.1_3'UTR	NM_015268.3	NP_056083.3	O75165	DJC13_HUMAN	DnaJ (Hsp40) homolog, subfamily C, member 13	94					osteoblast differentiation (GO:0001649)	extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)				breast(4)|endometrium(2)|kidney(2)|large_intestine(5)|lung(15)|ovary(1)|pancreas(2)|prostate(2)|urinary_tract(1)	34						CAGAACTTCTTACAGAAGCAT	0.318													T|||	22	0.00439297	0.0008	0.0058	5008	,	,		14614	0.0		0.0129	False		,,,				2504	0.0041				p.L94L		Atlas-SNP	.											.	DNAJC13	253	.	0			c.T282G						PASS	.	T		10,4396	16.8+/-37.8	0,10,2193	34.0	37.0	36.0		282	2.1	1.0	3	dbSNP_132	36	158,8432	71.6+/-134.2	2,154,4139	no	coding-synonymous	DNAJC13	NM_015268.3		2,164,6332	GG,GT,TT		1.8393,0.227,1.2927		94/2244	132166302	168,12828	2203	4295	6498	SO:0001819	synonymous_variant	23317	exon4			ACTTCTTACAGAA	AB014578	CCDS33857.1	3q22.1	2011-09-02			ENSG00000138246	ENSG00000138246		"""Heat shock proteins / DNAJ (HSP40)"""	30343	protein-coding gene	gene with protein product		614334				12438707	Standard	NM_015268		Approved	RME8, KIAA0678	uc003eor.3	O75165	OTTHUMG00000159674	ENST00000260818.6:c.282T>G	3.37:g.132166302T>G		130.0	0.0	0		137.0	76.0	0.554745	NM_015268	Q3L0T1|Q6PI82|Q6UJ77|Q6ZSW1|Q6ZUT5|Q86XG3|Q96DC1|Q9BWK9	Silent	SNP	ENST00000260818.6	37	CCDS33857.1																																																																																			T|0.990;G|0.010	0.010	strong		0.318	DNAJC13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356807.2	NM_015268	
CDH8	1006	hgsc.bcm.edu	37	16	61935330	61935330	+	Silent	SNP	T	T	C	rs368241476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:61935330T>C	ENST00000577390.1	-	3	1254	c.300A>G	c.(298-300)ctA>ctG	p.L100L	CDH8_ENST00000577730.1_Silent_p.L100L|CDH8_ENST00000584337.1_Silent_p.L100L|CDH8_ENST00000299345.6_Silent_p.L100L	NM_001796.4	NP_001787.2	P55286	CADH8_HUMAN	cadherin 8, type 2	100	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				adherens junction organization (GO:0034332)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|homophilic cell adhesion (GO:0007156)|response to cold (GO:0009409)|synaptic transmission, glutamatergic (GO:0035249)	axon terminus (GO:0043679)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|synaptic cleft (GO:0043083)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(3)|cervix(1)|endometrium(7)|kidney(6)|large_intestine(22)|liver(2)|lung(49)|ovary(6)|pancreas(2)|prostate(5)|skin(4)|urinary_tract(4)	112		Ovarian(137;0.0799)|Melanoma(118;0.16)		UCEC - Uterine corpus endometrioid carcinoma (183;0.196)|Epithelial(162;0.0155)|all cancers(182;0.0305)|OV - Ovarian serous cystadenocarcinoma(108;0.0499)|BRCA - Breast invasive adenocarcinoma(181;0.249)		CATCACCTGATAGGATATACT	0.388																																					p.L100L		Atlas-SNP	.											.	CDH8	273	.	0			c.A300G						PASS	.	T		0,4406		0,0,2203	93.0	89.0	90.0		300	-3.0	1.0	16		90	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	CDH8	NM_001796.4		0,1,6502	CC,CT,TT		0.0116,0.0,0.0077		100/800	61935330	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	1006	exon3			ACCTGATAGGATA	L34060	CCDS10802.1	16q22.1	2010-01-26			ENSG00000150394	ENSG00000150394		"""Cadherins / Major cadherins"""	1767	protein-coding gene	gene with protein product		603008				9615235, 2059658	Standard	NM_001796		Approved		uc002eog.2	P55286	OTTHUMG00000137493	ENST00000577390.1:c.300A>G	16.37:g.61935330T>C		117.0	0.0	0		109.0	44.0	0.40367	NM_001796	B3KWC1|Q14DC6|Q9ULB2	Silent	SNP	ENST00000577390.1	37	CCDS10802.1																																																																																			.	.	weak		0.388	CDH8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268754.3	NM_001796	
CFAP46	54777	hgsc.bcm.edu	37	10	134691424	134691424	+	Missense_Mutation	SNP	C	C	A	rs541673671	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134691424C>A	ENST00000368586.5	-	30	4273	c.4173G>T	c.(4171-4173)aaG>aaT	p.K1391N	TTC40_ENST00000368582.2_Missense_Mutation_p.K1391N	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						ttcccttctccttgtccttct	0.512													C|||	21	0.00419329	0.0008	0.0029	5008	,	,		17453	0.001		0.007	False		,,,				2504	0.0102				p.K1391N		Atlas-SNP	.											.	TTC40	100	.	0			c.G4173T						PASS	.																																			SO:0001583	missense	54777	exon30			CTTCTCCTTGTCC																												ENST00000368586.5:c.4173G>T	10.37:g.134691424C>A	ENSP00000357575:p.Lys1391Asn	315.0	0.0	0		301.0	16.0	0.0531561	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	.	.	.	.	.	.	.	.	.	.	C	1.664	-0.510681	0.04231	.	.	ENSG00000171811	ENST00000368586;ENST00000368582	T;T	0.05996	3.36;3.36	2.37	-3.18	0.05186	.	.	.	.	.	T	0.07593	0.0191	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.31530	-0.9940	6	0.46703	T	0.11	.	9.5036	0.39033	0.0:0.7879:0.0:0.2121	.	.	.	.	N	1391	ENSP00000357575:K1391N;ENSP00000357571:K1391N	ENSP00000357571:K1391N	K	-	3	2	C10orf93	134541414	0.078000	0.21339	0.000000	0.03702	0.019000	0.09904	-0.209000	0.09358	-0.946000	0.03677	-0.229000	0.12294	AAG	.	.	none		0.512	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
GLTSCR2	29997	hgsc.bcm.edu	37	19	48248907	48248907	+	Missense_Mutation	SNP	G	G	C	rs78530808	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:48248907G>C	ENST00000246802.5	+	1	129	c.91G>C	c.(91-93)Gac>Cac	p.D31H	GLTSCR2_ENST00000598681.1_3'UTR	NM_015710.4	NP_056525.2	Q9NZM5	GSCR2_HUMAN	glioma tumor suppressor candidate region gene 2	31						intracellular (GO:0005622)|intracellular membrane-bounded organelle (GO:0043231)|nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)	15		all_cancers(25;1.47e-06)|all_lung(116;6.89e-05)|all_epithelial(76;0.000108)|Lung NSC(112;0.000117)|all_neural(266;0.0332)|Ovarian(192;0.086)		all cancers(93;0.000301)|OV - Ovarian serous cystadenocarcinoma(262;0.00031)|Epithelial(262;0.0149)|GBM - Glioblastoma multiforme(486;0.0278)		CACTTCGGTGGACCCAGCGCT	0.657													G|||	79	0.0157748	0.0053	0.0029	5008	,	,		9702	0.0069		0.0149	False		,,,				2504	0.0491				p.D31H	Colon(58;613 1041 9473 10089 15241)	Atlas-SNP	.											.	GLTSCR2	45	.	0			c.G91C						PASS	.	G	HIS/ASP	45,4361	48.2+/-83.0	0,45,2158	49.0	58.0	55.0		91	4.6	1.0	19	dbSNP_131	55	151,8449	70.7+/-133.2	0,151,4149	yes	missense	GLTSCR2	NM_015710.4	81	0,196,6307	CC,CG,GG		1.7558,1.0213,1.507	probably-damaging	31/479	48248907	196,12810	2203	4300	6503	SO:0001583	missense	29997	exon1			TCGGTGGACCCAG	AF182076	CCDS12705.1	19q13.3	2014-01-20				ENSG00000105373			4333	protein-coding gene	gene with protein product		605691				10708517, 16971513, 17657248	Standard	NM_015710		Approved	PICT-1	uc002phm.2	Q9NZM5		ENST00000246802.5:c.91G>C	19.37:g.48248907G>C	ENSP00000246802:p.Asp31His	98.0	0.0	0		147.0	81.0	0.55102	NM_015710	Q9BTC6|Q9HAX6|Q9NPP1|Q9NPR4|Q9UFI2	Missense_Mutation	SNP	ENST00000246802.5	37	CCDS12705.1	20	0.009157509157509158	6	0.012195121951219513	1	0.0027624309392265192	2	0.0034965034965034965	11	0.014511873350923483	G	23.9	4.465428	0.84425	0.010213	0.017558	ENSG00000105373	ENST00000246802;ENST00000325566;ENST00000446535	T	0.34472	1.36	4.55	4.55	0.56014	.	0.276137	0.34133	N	0.004227	T	0.29945	0.0749	L	0.34521	1.04	0.52501	D	0.999954	D;D;D	0.76494	0.999;0.999;0.999	D;D;D	0.65573	0.936;0.936;0.936	T	0.34625	-0.9821	10	0.87932	D	0	-24.6863	13.1558	0.59516	0.0:0.0:1.0:0.0	.	31;31;29	Q53YP0;Q9NZM5;Q96CS0	.;GSCR2_HUMAN;.	H	31	ENSP00000246802:D31H	ENSP00000246802:D31H	D	+	1	0	GLTSCR2	52940719	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	4.935000	0.63498	2.227000	0.72691	0.655000	0.94253	GAC	G|0.987;C|0.013	0.013	strong		0.657	GLTSCR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000464870.1	NM_015710	
KRT80	144501	hgsc.bcm.edu	37	12	52579315	52579315	+	Silent	SNP	C	C	T	rs151324530	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52579315C>T	ENST00000394815.2	-	2	454	c.357G>A	c.(355-357)caG>caA	p.Q119Q	KRT80_ENST00000313234.5_Silent_p.Q119Q	NM_182507.2	NP_872313.2	Q6KB66	K2C80_HUMAN	keratin 80	119	Linker 1.|Rod.					cytoplasm (GO:0005737)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(2)|large_intestine(2)|lung(1)	5				BRCA - Breast invasive adenocarcinoma(357;0.108)		AGTCCTGGCCCTGCAGGAAGC	0.632													C|||	3	0.000599042	0.0	0.0	5008	,	,		17710	0.0		0.003	False		,,,				2504	0.0				p.Q119Q	GBM(178;2309 2916 15678 35873)	Atlas-SNP	.											.	KRT80	68	.	0			c.G357A						PASS	.	C	,	3,4403	8.1+/-20.4	0,3,2200	46.0	45.0	45.0		357,357	4.2	1.0	12	dbSNP_134	45	9,8591	7.1+/-27.0	0,9,4291	no	coding-synonymous,coding-synonymous	KRT80	NM_001081492.1,NM_182507.2	,	0,12,6491	TT,TC,CC		0.1047,0.0681,0.0923	,	119/423,119/453	52579315	12,12994	2203	4300	6503	SO:0001819	synonymous_variant	144501	exon2			CTGGCCCTGCAGG	BX537567	CCDS8821.2, CCDS41784.1	12q13.13	2013-01-16			ENSG00000167767	ENSG00000167767		"""-"", ""Intermediate filaments type II, keratins (basic)"""	27056	protein-coding gene	gene with protein product		611161				16831889	Standard	NM_001081492		Approved	KB20	uc001rzx.3	Q6KB66	OTTHUMG00000150193	ENST00000394815.2:c.357G>A	12.37:g.52579315C>T		33.0	0.0	0		33.0	19.0	0.575758	NM_182507	Q6P1A5|Q7Z3Q0	Silent	SNP	ENST00000394815.2	37	CCDS8821.2																																																																																			C|0.999;T|0.001	0.001	strong		0.632	KRT80-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000316757.1	NM_182507	
UBXN11	91544	hgsc.bcm.edu	37	1	26608855	26608855	+	Missense_Mutation	SNP	C	C	T	rs201756933		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:26608855C>T	ENST00000374222.1	-	16	1962	c.1498G>A	c.(1498-1500)Ggc>Agc	p.G500S	UBXN11_ENST00000357089.4_Missense_Mutation_p.G467S|UBXN11_ENST00000314675.7_Missense_Mutation_p.G380S|UBXN11_ENST00000374223.1_Missense_Mutation_p.G257S|UBXN11_ENST00000374221.3_Missense_Mutation_p.G500S|UBXN11_ENST00000374217.2_Missense_Mutation_p.G467S			Q5T124	UBX11_HUMAN	UBX domain protein 11	500	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.		Missing.			cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggactggggccgggaccggga	0.731																																					p.G500S		Atlas-SNP	.											.	UBXN11	54	.	1	Deletion - In frame(1)	ovary(1)	c.G1498A						PASS	.						20.0	24.0	23.0					1																	26608855		1677	3891	5568	SO:0001583	missense	91544	exon16			TGGGGCCGGGACC	AF521017	CCDS41286.1, CCDS41287.1, CCDS41288.1	1p36.11	2008-07-25	2008-07-25	2008-07-25	ENSG00000158062	ENSG00000158062		"""UBX domain containing"""	30600	protein-coding gene	gene with protein product	"""socius"""	609151	"""UBX domain containing 5"""	UBXD5		11940653	Standard	NM_183008		Approved	SOC, SOCI	uc001blw.3	Q5T124	OTTHUMG00000003382	ENST00000374222.1:c.1498G>A	1.37:g.26608855C>T	ENSP00000363339:p.Gly500Ser	26.0	0.0	0		40.0	15.0	0.375	NM_183008	D3DPK6|Q5T117|Q5T120|Q5T125|Q5T126|Q5T129|Q5T131|Q5T133|Q63HM6|Q71RB3|Q8IY27|Q8N1L6|Q8N9M4|Q8NA18|Q8NFE3|Q8NFE4|Q8NFE6	Missense_Mutation	SNP	ENST00000374222.1	37	CCDS41288.1	.	.	.	.	.	.	.	.	.	.	-	0.087	-1.172989	0.01646	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.18174	2.23;2.24;2.54;2.51;2.51;2.54	.	.	.	.	.	.	.	.	T	0.07143	0.0181	N	0.08118	0	0.18873	N	0.999989	.	.	.	.	.	.	T	0.37979	-0.9682	6	0.28530	T	0.3	.	4.1991	0.10457	0.0:0.6625:0.0:0.3375	.	467;462;380;500	Q5T124-2;Q5T124-4;Q5T124-3;Q5T124	.;.;.;UBX11_HUMAN	S	380;257;467;500;500;467	ENSP00000324721:G380S;ENSP00000363340:G257S;ENSP00000349601:G467S;ENSP00000363338:G500S;ENSP00000363339:G500S;ENSP00000363334:G467S	ENSP00000324721:G380S	G	-	1	0	UBXN11	26481442	0.000000	0.05858	0.163000	0.22734	0.170000	0.22686	-0.959000	0.03853	-0.000000	0.14550	0.000000	0.15137	GGC	.	.	weak		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
ODF2	4957	hgsc.bcm.edu	37	9	131262512	131262512	+	Missense_Mutation	SNP	G	G	A	rs142129915	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:131262512G>A	ENST00000434106.3	+	21	2831	c.2468G>A	c.(2467-2469)cGc>cAc	p.R823H	ODF2_ENST00000393527.3_Missense_Mutation_p.R799H|ODF2_ENST00000444119.2_Missense_Mutation_p.R799H|ODF2_ENST00000372807.5_Missense_Mutation_p.R818H|ODF2_ENST00000604420.1_Missense_Mutation_p.R823H|ODF2_ENST00000351030.3_Missense_Mutation_p.R818H	NM_153433.1	NP_702911.1	Q5BJF6	ODFP2_HUMAN	outer dense fiber of sperm tails 2	823					G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|multicellular organismal development (GO:0007275)|regulation of cilium assembly (GO:1902017)|spermatid development (GO:0007286)	centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytosol (GO:0005829)|microtubule (GO:0005874)|nucleus (GO:0005634)|outer dense fiber (GO:0001520)|primary cilium (GO:0072372)	Rab GTPase binding (GO:0017137)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(7)|cervix(1)|endometrium(4)|kidney(5)|large_intestine(7)|lung(8)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(1)	37						TCTCCCATCCGCTCCCGATCT	0.557													G|||	13	0.00259585	0.0	0.0014	5008	,	,		17126	0.001		0.005	False		,,,				2504	0.0061				p.R887H		Atlas-SNP	.											ODF2,NS,carcinoma,+1,1	ODF2	227	1	0			c.G2660A						PASS	.	G	HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG,HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	181.0	152.0	162.0		2453,2468,2396,2468,2660	5.5	1.0	9	dbSNP_134	162	66,8534	40.3+/-97.0	1,64,4235	yes	missense,missense,missense,missense,missense	ODF2	NM_001242352.1,NM_001242353.1,NM_002540.4,NM_153433.1,NM_153435.1	29,29,29,29,29	1,76,6426	AA,AG,GG		0.7674,0.2724,0.5997	benign,benign,benign,benign,benign	818/825,823/830,799/806,823/830,887/894	131262512	78,12928	2203	4300	6503	SO:0001583	missense	4957	exon21			CCATCCGCTCCCG	AF012549	CCDS6902.1, CCDS56585.1, CCDS56586.1, CCDS56587.1, CCDS56588.1, CCDS56589.1, CCDS56590.1	9q34	2010-04-23	2002-10-21		ENSG00000136811	ENSG00000136811			8114	protein-coding gene	gene with protein product	"""cancer/testis antigen 134"""	602015	"""outer dense fibre of sperm tails 2"""			9045620, 10072582	Standard	NM_153435		Approved	ODF84, CT134	uc004bvc.3	Q5BJF6	OTTHUMG00000020748	ENST00000434106.3:c.2468G>A	9.37:g.131262512G>A	ENSP00000403453:p.Arg823His	105.0	0.0	0		111.0	58.0	0.522523	NM_153435	B1AND3|B4DRK4|B4DX73|B4DZ02|E7EWL2|F5H6J4|O14721|O60631|Q1W2J6|Q6UN26|Q7Z5I6|Q96FN2	Missense_Mutation	SNP	ENST00000434106.3	37	CCDS56588.1	5	0.0022893772893772895	0	0.0	0	0.0	1	0.0017482517482517483	4	0.005277044854881266	G	18.25	3.581992	0.65992	0.002724	0.007674	ENSG00000136811	ENST00000351030;ENST00000372796;ENST00000303890	T;T;T	0.28666	1.64;1.6;1.65	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	T	0.15609	0.0376	L	0.32530	0.975	0.80722	D	1	P;B;B;B	0.44690	0.841;0.231;0.054;0.016	B;B;B;B	0.34536	0.185;0.04;0.018;0.002	T	0.02138	-1.1207	10	0.45353	T	0.12	-4.1319	13.6785	0.62469	0.0762:0.0:0.9238:0.0	.	818;168;823;799	Q5BJF6-4;Q6PJQ8;Q5BJF6;Q5BJF6-3	.;.;ODFP2_HUMAN;.	H	818;823;799	ENSP00000342581:R818H;ENSP00000361882:R823H;ENSP00000307781:R799H	ENSP00000307781:R799H	R	+	2	0	ODF2	130302333	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.562000	0.53777	2.581000	0.87130	0.561000	0.74099	CGC	G|0.996;A|0.004	0.004	strong		0.557	ODF2-011	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054449.3		
TTLL2	83887	hgsc.bcm.edu	37	6	167754360	167754360	+	Silent	SNP	C	C	T	rs77767783	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:167754360C>T	ENST00000239587.5	+	3	1060	c.972C>T	c.(970-972)ctC>ctT	p.L324L		NM_031949.4	NP_114155.4	Q9BWV7	TTLL2_HUMAN	tubulin tyrosine ligase-like family, member 2	324	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				cellular protein modification process (GO:0006464)		ligase activity (GO:0016874)			central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(66;7.8e-06)|Ovarian(120;0.024)		OV - Ovarian serous cystadenocarcinoma(33;2.22e-20)|BRCA - Breast invasive adenocarcinoma(81;6.17e-07)|GBM - Glioblastoma multiforme(31;0.00492)		AATGGACGCTCAGCAGATTTT	0.438													C|||	9	0.00179712	0.0	0.0043	5008	,	,		20069	0.0		0.006	False		,,,				2504	0.0				p.L324L		Atlas-SNP	.											.	TTLL2	82	.	0			c.C972T						PASS	.	C		1,4405	2.1+/-5.4	0,1,2202	159.0	168.0	165.0		972	0.3	0.5	6	dbSNP_132	165	28,8572	19.8+/-62.0	0,28,4272	no	coding-synonymous	TTLL2	NM_031949.4		0,29,6474	TT,TC,CC		0.3256,0.0227,0.223		324/593	167754360	29,12977	2203	4300	6503	SO:0001819	synonymous_variant	83887	exon3			GACGCTCAGCAGA	AK093039	CCDS5301.1	6q27	2013-02-14		2004-01-14	ENSG00000120440	ENSG00000120440		"""Tubulin tyrosine ligase-like family"""	21211	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 104"""	C6orf104		11054573	Standard	XM_006715572		Approved	NYD-TSPG, dJ366N23.3	uc003qvs.1	Q9BWV7	OTTHUMG00000016023	ENST00000239587.5:c.972C>T	6.37:g.167754360C>T		174.0	0.0	0		90.0	80.0	0.888889	NM_031949	B2RB11|B3KS77|Q7Z6R8|Q86X22	Silent	SNP	ENST00000239587.5	37	CCDS5301.1																																																																																			C|0.998;T|0.002	0.002	strong		0.438	TTLL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043127.3	NM_031949	
OTOGL	283310	hgsc.bcm.edu	37	12	80665473	80665473	+	Missense_Mutation	SNP	C	C	T	rs183159689	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:80665473C>T	ENST00000547103.1	+	23	2543	c.2537C>T	c.(2536-2538)cCt>cTt	p.P846L	OTOGL_ENST00000458043.2_Missense_Mutation_p.P846L			Q3ZCN5	OTOGL_HUMAN	otogelin-like	846					L-arabinose metabolic process (GO:0046373)	extracellular region (GO:0005576)	alpha-L-arabinofuranosidase activity (GO:0046556)			breast(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(14)|prostate(1)	23						TGCAGGTTTCCTGACCCTGAA	0.458													C|||	3	0.000599042	0.0	0.0	5008	,	,		17643	0.0		0.003	False		,,,				2504	0.0				p.P846L		Atlas-SNP	.											.	OTOGL	235	.	0			c.C2537T						PASS	.	C	LEU/PRO	4,3910		0,4,1953	97.0	100.0	99.0		2537	5.1	1.0	12		99	3,8259		0,3,4128	yes	missense	OTOGL	NM_173591.3	98	0,7,6081	TT,TC,CC		0.0363,0.1022,0.0575		846/2345	80665473	7,12169	1957	4131	6088	SO:0001583	missense	283310	exon23			GGTTTCCTGACCC	AK096852		12q21.31	2011-02-11	2011-02-11	2011-02-11	ENSG00000165899	ENSG00000165899			26901	protein-coding gene	gene with protein product		614925	"""chromosome 12 open reading frame 64"""	C12orf64			Standard	NM_173591		Approved	FLJ90579	uc001szd.3	Q3ZCN5	OTTHUMG00000150509	ENST00000547103.1:c.2537C>T	12.37:g.80665473C>T	ENSP00000447211:p.Pro846Leu	133.0	0.0	0		156.0	74.0	0.474359	NM_173591	F8W0C3|Q495U8|Q8N8G5|Q8NC28	Missense_Mutation	SNP	ENST00000547103.1	37		4	0.0018315018315018315	0	0.0	2	0.0055248618784530384	0	0.0	2	0.002638522427440633	C	15.16	2.751832	0.49362	0.001022	3.63E-4	ENSG00000165899	ENST00000547103;ENST00000458043	T;T	0.16324	2.35;2.35	5.14	5.14	0.70334	.	.	.	.	.	T	0.22475	0.0542	L	0.59912	1.85	0.58432	D	0.999999	.	.	.	.	.	.	T	0.00420	-1.1750	7	0.29301	T	0.29	.	14.6719	0.68951	0.1459:0.8541:0.0:0.0	.	.	.	.	L	846	ENSP00000447211:P846L;ENSP00000400895:P846L	ENSP00000400895:P846L	P	+	2	0	OTOGL	79189604	0.962000	0.33011	1.000000	0.80357	0.977000	0.68977	1.923000	0.40055	2.551000	0.86045	0.655000	0.94253	CCT	C|0.998;T|0.002	0.002	strong		0.458	OTOGL-001	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000407438.1	NM_173591	
TOP1MT	116447	hgsc.bcm.edu	37	8	144399993	144399993	+	Silent	SNP	G	G	A	rs146827342	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:144399993G>A	ENST00000329245.4	-	10	1264	c.1230C>T	c.(1228-1230)aaC>aaT	p.N410N	TOP1MT_ENST00000523676.1_Silent_p.N312N|TOP1MT_ENST00000519148.1_Silent_p.N312N|AC087793.1_ENST00000585120.1_RNA|TOP1MT_ENST00000521193.1_Silent_p.N312N	NM_052963.2	NP_443195.1	Q969P6	TOP1M_HUMAN	topoisomerase (DNA) I, mitochondrial	410		Interaction with DNA. {ECO:0000250}.			DNA replication (GO:0006260)|DNA topological change (GO:0006265)	chromosome (GO:0005694)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase type I activity (GO:0003917)|DNA topoisomerase type II (ATP-hydrolyzing) activity (GO:0003918)			endometrium(5)|kidney(1)|large_intestine(6)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	23	all_cancers(97;1.01e-10)|all_epithelial(106;4.86e-09)|Lung NSC(106;0.000167)|all_lung(105;0.000459)|Ovarian(258;0.0212)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.156)|Colorectal(110;0.173)		Irinotecan(DB00762)|Topotecan(DB01030)	GGAGGTGCTTGTTCAGGCTGG	0.617													G|||	5	0.000998403	0.0	0.0014	5008	,	,		16371	0.0		0.004	False		,,,				2504	0.0				p.N410N		Atlas-SNP	.											.	TOP1MT	63	.	0			c.C1230T						PASS	.	G		6,4400	12.9+/-30.5	0,6,2197	65.0	60.0	62.0		1230	1.9	0.4	8	dbSNP_134	62	27,8573	19.2+/-60.6	0,27,4273	no	coding-synonymous	TOP1MT	NM_052963.1		0,33,6470	AA,AG,GG		0.314,0.1362,0.2537		410/602	144399993	33,12973	2203	4300	6503	SO:0001819	synonymous_variant	116447	exon10			GTGCTTGTTCAGG	AF349018	CCDS6400.1, CCDS59115.1	8q24.3	2006-04-12				ENSG00000184428			29787	protein-coding gene	gene with protein product		606387				11526219	Standard	NM_052963		Approved		uc003yxz.4	Q969P6		ENST00000329245.4:c.1230C>T	8.37:g.144399993G>A		83.0	0.0	0		98.0	43.0	0.438776	NM_052963	B7ZAR5|E7ES89|Q86ST4|Q86V82	Silent	SNP	ENST00000329245.4	37	CCDS6400.1																																																																																			G|0.997;A|0.003	0.003	strong		0.617	TOP1MT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381247.3	NM_052963	
MRGPRX1	259249	hgsc.bcm.edu	37	11	18956210	18956210	+	Missense_Mutation	SNP	C	C	G	rs139433266		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18956210C>G	ENST00000302797.3	-	1	346	c.122G>C	c.(121-123)gGg>gCg	p.G41A	RP11-583F24.8_ENST00000528646.1_RNA|MRGPRX1_ENST00000526914.1_5'UTR	NM_147199.3	NP_671732.3	Q96LB2	MRGX1_HUMAN	MAS-related GPR, member X1	41					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						TCCTGTCAGCCCGACAAGGGA	0.562																																					p.G41A		Atlas-SNP	.											MRGPRX1,NS,carcinoma,-1,1	MRGPRX1	84	1	0			c.G122C						PASS	.	C	ALA/GLY	1,4387		0,1,2193	187.0	176.0	180.0		122	0.3	0.0	11	dbSNP_134	180	1,8571		0,1,4285	no	missense	MRGPRX1	NM_147199.3	60	0,2,6478	GG,GC,CC		0.0117,0.0228,0.0154	possibly-damaging	41/323	18956210	2,12958	2194	4286	6480	SO:0001583	missense	259249	exon1			GTCAGCCCGACAA		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.122G>C	11.37:g.18956210C>G	ENSP00000305766:p.Gly41Ala	112.0	0.0	0		127.0	73.0	0.574803	NM_147199	Q4V9L2|Q8TDD8|Q8TDD9	Missense_Mutation	SNP	ENST00000302797.3	37	CCDS7846.1	.	.	.	.	.	.	.	.	.	.	.	11.92	1.781660	0.31502	2.28E-4	1.17E-4	ENSG00000170255	ENST00000302797	T	0.18016	2.24	2.43	0.304	0.15796	.	0.000000	0.64402	D	0.000005	T	0.19765	0.0475	L	0.52905	1.665	0.09310	N	1	P	0.39003	0.654	P	0.47162	0.54	T	0.09100	-1.0690	10	0.66056	D	0.02	.	4.8899	0.13722	0.2076:0.6607:0.0:0.1317	.	41	Q96LB2	MRGX1_HUMAN	A	41	ENSP00000305766:G41A	ENSP00000305766:G41A	G	-	2	0	MRGPRX1	18912786	0.950000	0.32346	0.000000	0.03702	0.004000	0.04260	2.750000	0.47500	0.075000	0.16796	0.491000	0.48974	GGG	C|1.000;G|0.000	0.000	weak		0.562	MRGPRX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369913.1	NM_147199	
PDGFRL	5157	hgsc.bcm.edu	37	8	17447018	17447018	+	Missense_Mutation	SNP	C	C	A	rs374832042		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:17447018C>A	ENST00000541323.1	+	3	542	c.97C>A	c.(97-99)Cca>Aca	p.P33T	PDGFRL_ENST00000251630.6_Missense_Mutation_p.P33T|PDGFRL_ENST00000398074.3_Missense_Mutation_p.P33T	NM_006207.2	NP_006198.1	Q15198	PGFRL_HUMAN	platelet-derived growth factor receptor-like	33					G-protein coupled receptor signaling pathway (GO:0007186)|platelet-derived growth factor receptor-beta signaling pathway (GO:0035791)	extracellular region (GO:0005576)	platelet activating factor receptor activity (GO:0004992)|platelet-derived growth factor beta-receptor activity (GO:0005019)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(5)	9				Colorectal(111;0.0752)		TCCAAAAGAACCAGGAGAGAA	0.433																																					p.P33T		Atlas-SNP	.											.	PDGFRL	27	.	0			c.C97A						PASS	.	C	THR/PRO	0,4406		0,0,2203	146.0	148.0	147.0		97	4.5	0.9	8		147	1,8599	1.2+/-3.3	0,1,4299	no	missense	PDGFRL	NM_006207.2	38	0,1,6502	AA,AC,CC		0.0116,0.0,0.0077	benign	33/376	17447018	1,13005	2203	4300	6503	SO:0001583	missense	5157	exon3			AAAGAACCAGGAG	D37965	CCDS6003.1	8p22-p21.3	2013-01-29			ENSG00000104213	ENSG00000104213		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	8805	protein-coding gene	gene with protein product		604584					Standard	NM_006207		Approved	PRLTS	uc003wxr.3	Q15198	OTTHUMG00000130818	ENST00000541323.1:c.97C>A	8.37:g.17447018C>A	ENSP00000444211:p.Pro33Thr	37.0	0.0	0		31.0	21.0	0.677419	NM_006207	A8K085|Q6FH04	Missense_Mutation	SNP	ENST00000541323.1	37	CCDS6003.1	.	.	.	.	.	.	.	.	.	.	C	11.77	1.737518	0.30774	0.0	1.16E-4	ENSG00000104213	ENST00000251630;ENST00000541323;ENST00000398074	T;T;T	0.32272	1.46;1.46;1.46	4.52	4.52	0.55395	.	0.256475	0.39146	N	0.001451	T	0.32102	0.0818	L	0.56769	1.78	0.32797	N	0.500418	B	0.27559	0.181	B	0.26969	0.075	T	0.37174	-0.9717	10	0.22706	T	0.39	-18.4186	17.8077	0.88606	0.0:1.0:0.0:0.0	.	33	Q15198	PGFRL_HUMAN	T	33	ENSP00000251630:P33T;ENSP00000444211:P33T;ENSP00000381149:P33T	ENSP00000251630:P33T	P	+	1	0	PDGFRL	17491278	0.996000	0.38824	0.943000	0.38184	0.677000	0.39632	2.992000	0.49417	2.503000	0.84419	0.591000	0.81541	CCA	.	.	weak		0.433	PDGFRL-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253366.3	NM_006207	
MYH10	4628	hgsc.bcm.edu	37	17	8455419	8455419	+	Silent	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:8455419T>C	ENST00000269243.4	-	8	972	c.834A>G	c.(832-834)gaA>gaG	p.E278E	MYH10_ENST00000360416.3_Silent_p.E288E|MYH10_ENST00000396239.1_Silent_p.E278E|MYH10_ENST00000379980.4_Silent_p.E294E	NM_005964.3	NP_005955.3	P35580	MYH10_HUMAN	myosin, heavy chain 10, non-muscle	278	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|cardiac myofibril assembly (GO:0055003)|cell adhesion (GO:0007155)|cell proliferation (GO:0008283)|cerebellar Purkinje cell layer development (GO:0021680)|exocytosis (GO:0006887)|fourth ventricle development (GO:0021592)|in utero embryonic development (GO:0001701)|lateral ventricle development (GO:0021670)|mitotic cytokinesis (GO:0000281)|neuromuscular process controlling balance (GO:0050885)|neuron migration (GO:0001764)|nuclear migration (GO:0007097)|plasma membrane repair (GO:0001778)|regulation of cell shape (GO:0008360)|retina development in camera-type eye (GO:0060041)|substrate-dependent cell migration, cell extension (GO:0006930)|third ventricle development (GO:0021678)|ventricular cardiac muscle cell development (GO:0055015)	actomyosin (GO:0042641)|axon (GO:0030424)|cell cortex (GO:0005938)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|dendritic spine (GO:0043197)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|midbody (GO:0030496)|myosin complex (GO:0016459)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spindle (GO:0005819)|stress fiber (GO:0001725)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			breast(5)|endometrium(9)|kidney(2)|large_intestine(16)|lung(9)|ovary(3)|prostate(3)|skin(4)|stomach(1)	52						GAAAAGTACGTTCATCTTTTG	0.308																																					p.E288E		Atlas-SNP	.											.	MYH10	148	.	0			c.A864G						PASS	.						48.0	49.0	49.0					17																	8455419		2203	4300	6503	SO:0001819	synonymous_variant	4628	exon9			AGTACGTTCATCT	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.834A>G	17.37:g.8455419T>C		107.0	0.0	0		131.0	6.0	0.0458015	NM_001256012	B2RWP9|D3DTS1|F8VTL3|Q12989|Q149N3|Q149N4|Q16087|Q4LE45|Q6PK16|Q9BWG0	Silent	SNP	ENST00000269243.4	37	CCDS11144.1																																																																																			.	.	none		0.308	MYH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000227001.2		
IFT81	28981	hgsc.bcm.edu	37	12	110600841	110600841	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:110600841G>C	ENST00000242591.5	+	11	1665	c.1159G>C	c.(1159-1161)Gat>Cat	p.D387H	IFT81_ENST00000361948.4_Missense_Mutation_p.D387H|IFT81_ENST00000552912.1_Missense_Mutation_p.D387H|IFT81_ENST00000549009.1_3'UTR	NM_014055.3	NP_054774.2	Q8WYA0	IFT81_HUMAN	intraflagellar transport 81	387					cilium assembly (GO:0042384)|intraciliary transport involved in cilium morphogenesis (GO:0035735)|spermatogenesis (GO:0007283)	centrosome (GO:0005813)|cilium (GO:0005929)|intraciliary transport particle B (GO:0030992)|motile cilium (GO:0031514)|sperm midpiece (GO:0097225)|sperm principal piece (GO:0097228)	tubulin binding (GO:0015631)			endometrium(1)|large_intestine(2)|lung(5)|ovary(1)|stomach(1)	10						CCGTGAATTTGATGGTACTGA	0.413																																					p.D387H		Atlas-SNP	.											.	IFT81	86	.	0			c.G1159C						PASS	.						131.0	124.0	126.0					12																	110600841		2203	4300	6503	SO:0001583	missense	28981	exon11			GAATTTGATGGTA	AF139540	CCDS9142.1, CCDS41831.1	12q24.13	2014-07-03	2014-07-03	2005-11-02		ENSG00000122970		"""Intraflagellar transport homologs"""	14313	protein-coding gene	gene with protein product		605489	"""carnitine deficiency-associated, expressed in ventricle 1"", ""intraflagellar transport 81 homolog (Chlamydomonas)"""	CDV1		11130971	Standard	NM_014055		Approved	CDV-1R, MGC4027	uc001tqi.3	Q8WYA0	OTTHUMG00000169326	ENST00000242591.5:c.1159G>C	12.37:g.110600841G>C	ENSP00000242591:p.Asp387His	77.0	0.0	0		74.0	29.0	0.391892	NM_014055	Q2YDY1|Q8NB51|Q9BSV2|Q9UNY8	Missense_Mutation	SNP	ENST00000242591.5	37	CCDS41831.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.756569	0.49362	.	.	ENSG00000122970	ENST00000361948;ENST00000552912;ENST00000242591;ENST00000546374	T	0.30714	1.52	5.42	5.42	0.78866	.	0.356693	0.31601	N	0.007377	T	0.32010	0.0815	L	0.50333	1.59	0.80722	D	1	B;P	0.46220	0.343;0.874	B;B	0.44224	0.398;0.444	T	0.03773	-1.1005	10	0.45353	T	0.12	-5.4288	11.8083	0.52169	0.0804:0.0:0.9196:0.0	.	387;387	Q8WYA0;Q8WYA0-3	IFT81_HUMAN;.	H	387;387;387;357	ENSP00000355372:D387H	ENSP00000242591:D387H	D	+	1	0	IFT81	109085224	1.000000	0.71417	0.621000	0.29145	0.917000	0.54804	6.328000	0.72915	2.553000	0.86117	0.655000	0.94253	GAT	.	.	none		0.413	IFT81-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403529.1	NM_014055	
TRPM2	7226	hgsc.bcm.edu	37	21	45826486	45826486	+	Missense_Mutation	SNP	G	G	A	rs56379273	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:45826486G>A	ENST00000397928.1	+	19	3245	c.2800G>A	c.(2800-2802)Gtc>Atc	p.V934I	TRPM2_ENST00000498430.1_3'UTR|TRPM2_ENST00000397932.2_Missense_Mutation_p.V934I|TRPM2_ENST00000300482.5_Missense_Mutation_p.V934I|TRPM2_ENST00000300481.9_Missense_Mutation_p.V914I	NM_003307.3	NP_003298	O94759	TRPM2_HUMAN	transient receptor potential cation channel, subfamily M, member 2	934					calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|ion transmembrane transport (GO:0034220)|response to hydroperoxide (GO:0033194)|transmembrane transport (GO:0055085)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	ADP-ribose diphosphatase activity (GO:0047631)|calcium channel activity (GO:0005262)|manganese ion transmembrane transporter activity (GO:0005384)|sodium channel activity (GO:0005272)			breast(3)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(15)|lung(29)|ovary(3)|pancreas(1)|prostate(5)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(1)	76						GATGAAGGACGTCTTCTTCTT	0.627													g|||	30	0.00599042	0.0015	0.0086	5008	,	,		16988	0.0		0.0199	False		,,,				2504	0.002				p.V934I		Atlas-SNP	.											.	TRPM2	196	.	0			c.G2800A						PASS	.	G	ILE/VAL	12,4372	21.2+/-45.6	0,12,2180	41.0	39.0	40.0		2800	3.2	1.0	21	dbSNP_129	40	133,8439	66.7+/-129.0	0,133,4153	yes	missense	TRPM2	NM_003307.3	29	0,145,6333	AA,AG,GG		1.5516,0.2737,1.1192	possibly-damaging	934/1504	45826486	145,12811	2192	4286	6478	SO:0001583	missense	7226	exon19			AAGGACGTCTTCT	AB001535	CCDS13710.1	21q22.3	2011-12-14		2002-01-18	ENSG00000142185	ENSG00000142185		"""Voltage-gated ion channels / Transient receptor potential cation channels"", ""Nudix motif containing"""	12339	protein-coding gene	gene with protein product		603749		TRPC7		9806837, 11385575, 16382100	Standard	NR_038257		Approved	KNP3, LTRPC2, NUDT9L1, NUDT9H, EREG1	uc002zew.1	O94759	OTTHUMG00000040840	ENST00000397928.1:c.2800G>A	21.37:g.45826486G>A	ENSP00000381023:p.Val934Ile	16.0	0.0	0		29.0	14.0	0.482759	NM_003307	D3DSL6|Q5KTC2|Q6J3P5|Q96KN6|Q96Q93	Missense_Mutation	SNP	ENST00000397928.1	37	CCDS13710.1	19	0.0086996336996337	0	0.0	4	0.011049723756906077	0	0.0	15	0.01978891820580475	g	12.27	1.888364	0.33348	0.002737	0.015516	ENSG00000142185	ENST00000300482;ENST00000397928;ENST00000300481;ENST00000397932	T;T;T;T	0.74209	-0.82;-0.82;-0.82;-0.82	4.12	3.23	0.37069	Ion transport (1);	0.453240	0.21370	N	0.075647	T	0.49558	0.1564	L	0.41632	1.29	0.37070	D	0.898505	B;B;B	0.24043	0.096;0.056;0.056	B;B;B	0.19391	0.025;0.025;0.025	T	0.63382	-0.6650	10	0.62326	D	0.03	-29.5505	12.4046	0.55432	0.0842:0.0:0.9158:0.0	rs56379273	934;720;934	E9PGK7;Q5KTC1;O94759	.;.;TRPM2_HUMAN	I	934;934;914;934	ENSP00000300482:V934I;ENSP00000381023:V934I;ENSP00000300481:V914I;ENSP00000381026:V934I	ENSP00000300481:V914I	V	+	1	0	TRPM2	44650914	0.998000	0.40836	1.000000	0.80357	0.981000	0.71138	2.350000	0.44063	0.861000	0.35504	0.536000	0.68110	GTC	G|0.988;A|0.012	0.012	strong		0.627	TRPM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098086.1	NM_003307	
CCDC108	255101	hgsc.bcm.edu	37	2	219900300	219900300	+	Silent	SNP	A	A	C	rs77746575	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:219900300A>C	ENST00000341552.5	-	5	527	c.444T>G	c.(442-444)gcT>gcG	p.A148A	CCDC108_ENST00000409865.3_Silent_p.A137A|CCDC108_ENST00000410037.1_Silent_p.A83A|CCDC108_ENST00000441968.1_Silent_p.A148A|CCDC108_ENST00000295729.2_Silent_p.A83A|CCDC108_ENST00000453220.1_Silent_p.A148A|CCDC108_ENST00000324264.6_Silent_p.A83A	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	148						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		GCAGCTCCTCAGCCACCTCAA	0.517													A|||	2	0.000399361	0.0	0.0	5008	,	,		18210	0.0		0.002	False		,,,				2504	0.0				p.A148A		Atlas-SNP	.											CCDC108_ENST00000295729,colon,carcinoma,-2,2	CCDC108	208	2	0			c.T444G						PASS	.	A	,	0,4406		0,0,2203	167.0	151.0	156.0		249,444	-10.8	0.0	2	dbSNP_132	156	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous,coding-synonymous	CCDC108	NM_152389.2,NM_194302.2	,	0,5,6498	CC,CA,AA		0.0581,0.0,0.0384	,	83/165,148/1926	219900300	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	255101	exon5			CTCCTCAGCCACC	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.444T>G	2.37:g.219900300A>C		277.0	1.0	0.00361011		310.0	150.0	0.483871	NM_194302	A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Silent	SNP	ENST00000341552.5	37	CCDS2430.2																																																																																			A|0.999;C|0.001	0.001	strong		0.517	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
SETD6	79918	hgsc.bcm.edu	37	16	58550386	58550386	+	Missense_Mutation	SNP	G	G	A	rs147467868	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:58550386G>A	ENST00000219315.4	+	4	531	c.481G>A	c.(481-483)Gag>Aag	p.E161K	SETD6_ENST00000418480.1_3'UTR|SETD6_ENST00000310682.2_Missense_Mutation_p.E137K|SETD6_ENST00000394266.4_Intron			Q8TBK2	SETD6_HUMAN	SET domain containing 6	161	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of NF-kappaB transcription factor activity (GO:0032088)|peptidyl-lysine monomethylation (GO:0018026)|regulation of inflammatory response (GO:0050727)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	NF-kappaB binding (GO:0051059)|protein-lysine N-methyltransferase activity (GO:0016279)			endometrium(1)|kidney(1)|large_intestine(1)|lung(2)|ovary(1)|skin(1)	7						CTGCAGGCCAGAGGAGGAGCG	0.617													G|||	3	0.000599042	0.0	0.0014	5008	,	,		14632	0.0		0.002	False		,,,				2504	0.0				p.E161K		Atlas-SNP	.											.	SETD6	27	.	0			c.G481A						PASS	.	G	LYS/GLU,LYS/GLU	0,4396		0,0,2198	78.0	92.0	87.0		481,409	3.4	1.0	16	dbSNP_134	87	5,8595	4.3+/-15.6	0,5,4295	yes	missense,missense	SETD6	NM_001160305.1,NM_024860.2	56,56	0,5,6493	AA,AG,GG		0.0581,0.0,0.0385	benign,benign	161/474,137/450	58550386	5,12991	2198	4300	6498	SO:0001583	missense	79918	exon4			AGGCCAGAGGAGG	AK024801	CCDS10798.1, CCDS54013.1	16q21	2008-02-05			ENSG00000103037	ENSG00000103037			26116	protein-coding gene	gene with protein product						12477932	Standard	NM_024860		Approved	FLJ21148	uc002ens.3	Q8TBK2	OTTHUMG00000150276	ENST00000219315.4:c.481G>A	16.37:g.58550386G>A	ENSP00000219315:p.Glu161Lys	53.0	0.0	0		70.0	30.0	0.428571	NM_001160305	A8K380|B5ME38|Q9H787	Missense_Mutation	SNP	ENST00000219315.4	37	CCDS54013.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	G	15.38	2.815025	0.50527	0.0	5.81E-4	ENSG00000103037	ENST00000310682;ENST00000219315	T;T	0.15603	2.41;2.41	5.37	3.37	0.38596	SET domain (2);	0.113840	0.64402	D	0.000016	T	0.13628	0.0330	L	0.49455	1.56	0.49483	D	0.999793	B;B;B	0.30914	0.14;0.3;0.004	B;B;B	0.22152	0.018;0.038;0.006	T	0.06698	-1.0812	10	0.33940	T	0.23	-20.8516	8.6244	0.33881	0.0812:0.2933:0.6254:0.0	.	137;161;137	E9PC53;Q8TBK2;Q8TBK2-2	.;SETD6_HUMAN;.	K	137;161	ENSP00000310082:E137K;ENSP00000219315:E161K	ENSP00000219315:E161K	E	+	1	0	SETD6	57107887	0.999000	0.42202	0.956000	0.39512	0.884000	0.51177	2.924000	0.48876	1.215000	0.43411	0.313000	0.20887	GAG	G|0.999;A|0.001	0.001	strong		0.617	SETD6-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000317274.2	NM_024860	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57069375	57069375	+	Missense_Mutation	SNP	A	A	G	rs34069781	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57069375A>G	ENST00000532437.1	-	8	5188	c.4877T>C	c.(4876-4878)gTg>gCg	p.V1626A	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.V1626A			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	1626	Arg/Glu/Lys-rich (charged).				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)			breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				AGGTTCCTCCACTACCTCTTC	0.612													A|||	101	0.0201677	0.0023	0.0389	5008	,	,		17084	0.002		0.0447	False		,,,				2504	0.0245				p.V1626A		Atlas-SNP	.											.	TNKS1BP1	148	.	0			c.T4877C						PASS	.	A	ALA/VAL	46,4356	46.7+/-81.2	0,46,2155	78.0	72.0	74.0		4877	1.2	0.1	11	dbSNP_126	74	402,8190	128.3+/-186.6	8,386,3902	yes	missense	TNKS1BP1	NM_033396.2	64	8,432,6057	GG,GA,AA		4.6788,1.045,3.4477	benign	1626/1730	57069375	448,12546	2201	4296	6497	SO:0001583	missense	85456	exon9			TCCTCCACTACCT	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.4877T>C	11.37:g.57069375A>G	ENSP00000437271:p.Val1626Ala	55.0	0.0	0		60.0	18.0	0.3	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	56	0.02564102564102564	2	0.0040650406504065045	14	0.03867403314917127	2	0.0034965034965034965	38	0.05013192612137203	A	1.725	-0.495729	0.04291	0.01045	0.046788	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.29917	1.55;1.55	4.94	1.18	0.20946	.	0.844445	0.10282	N	0.693393	T	0.03053	0.0090	L	0.35723	1.085	0.09310	N	1	B;B	0.15930	0.015;0.0	B;B	0.16722	0.016;0.002	T	0.26744	-1.0094	10	0.20519	T	0.43	-7.5445	4.0079	0.09610	0.595:0.0:0.2591:0.1459	rs34069781	1626;208	Q9C0C2;Q86TK2	TB182_HUMAN;.	A	1626	ENSP00000350990:V1626A;ENSP00000437271:V1626A	ENSP00000350990:V1626A	V	-	2	0	TNKS1BP1	56825951	0.003000	0.15002	0.065000	0.19835	0.987000	0.75469	0.402000	0.20965	0.226000	0.20979	0.459000	0.35465	GTG	A|0.968;G|0.032;T|0.000	0.032	strong		0.612	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
CLRN3	119467	hgsc.bcm.edu	37	10	129690990	129690990	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:129690990G>T	ENST00000368671.3	-	1	221	c.59C>A	c.(58-60)tCc>tAc	p.S20Y		NM_152311.3	NP_689524.1	Q8NCR9	CLRN3_HUMAN	clarin 3	20						extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(2)|skin(1)|upper_aerodigestive_tract(1)	6		all_epithelial(44;0.00168)|all_lung(145;0.0586)|Lung NSC(174;0.0765)|all_neural(114;0.201)|Glioma(114;0.222)|Colorectal(57;0.235)				TACAATGAAGGACCCAAGGCT	0.383																																					p.S20Y		Atlas-SNP	.											.	CLRN3	27	.	0			c.C59A						PASS	.						114.0	102.0	106.0					10																	129690990		2203	4300	6503	SO:0001583	missense	119467	exon1			ATGAAGGACCCAA	BC029478	CCDS7656.1	10q26.2	2006-11-24	2006-11-23	2006-11-23	ENSG00000180745	ENSG00000180745			20795	protein-coding gene	gene with protein product			"""transmembrane protein 12"""	TMEM12		12145752, 12080385	Standard	NM_152311		Approved	MGC32871, USH3AL1	uc001lka.1	Q8NCR9	OTTHUMG00000019253	ENST00000368671.3:c.59C>A	10.37:g.129690990G>T	ENSP00000357660:p.Ser20Tyr	63.0	0.0	0		46.0	20.0	0.434783	NM_152311	Q6MZX8	Missense_Mutation	SNP	ENST00000368671.3	37	CCDS7656.1	.	.	.	.	.	.	.	.	.	.	G	17.06	3.291288	0.59976	.	.	ENSG00000180745	ENST00000368671	T	0.71103	-0.54	5.52	5.52	0.82312	.	0.222808	0.38837	N	0.001554	T	0.81631	0.4863	M	0.62723	1.935	0.19945	N	0.999946	D	0.65815	0.995	D	0.66716	0.946	T	0.74615	-0.3606	10	0.66056	D	0.02	-14.6668	16.4802	0.84156	0.0:0.0:1.0:0.0	.	20	Q8NCR9	CLRN3_HUMAN	Y	20	ENSP00000357660:S20Y	ENSP00000357660:S20Y	S	-	2	0	CLRN3	129580980	0.324000	0.24652	0.009000	0.14445	0.104000	0.19210	4.040000	0.57333	2.880000	0.98712	0.655000	0.94253	TCC	.	.	none		0.383	CLRN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050987.1	NM_152311	
LRRC28	123355	hgsc.bcm.edu	37	15	99892589	99892589	+	Missense_Mutation	SNP	G	G	A	rs139516247		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:99892589G>A	ENST00000301981.3	+	7	848	c.608G>A	c.(607-609)cGa>cAa	p.R203Q	LRRC28_ENST00000447360.2_Missense_Mutation_p.R203Q|LRRC28_ENST00000442993.2_3'UTR|LRRC28_ENST00000558879.1_Intron|LRRC28_ENST00000331450.5_Intron|LRRC28_ENST00000422500.2_Missense_Mutation_p.R134Q	NM_144598.2	NP_653199.2	Q86X40	LRC28_HUMAN	leucine rich repeat containing 28	203										endometrium(2)|large_intestine(3)|lung(6)|prostate(1)	12	Lung NSC(78;0.00175)|all_lung(78;0.00351)|Melanoma(26;0.00778)|Medulloblastoma(229;0.163)		OV - Ovarian serous cystadenocarcinoma(32;0.00106)			GGTCGATCTCGAGAACTACAG	0.353																																					p.R203Q		Atlas-SNP	.											LRRC28,NS,malignant_melanoma,+1,1	LRRC28	38	1	0			c.G608A						PASS	.	G	GLN/ARG	0,4394		0,0,2197	166.0	157.0	160.0		608	5.5	1.0	15	dbSNP_134	160	1,8593	1.2+/-3.3	0,1,4296	no	missense	LRRC28	NM_144598.2	43	0,1,6493	AA,AG,GG		0.0116,0.0,0.0077	benign	203/368	99892589	1,12987	2197	4297	6494	SO:0001583	missense	123355	exon7			GATCTCGAGAACT	AK091588	CCDS10380.1, CCDS66873.1	15q26.3	2004-06-29			ENSG00000168904	ENSG00000168904			28355	protein-coding gene	gene with protein product						12975309	Standard	XM_005254861		Approved	MGC24976, FLJ34269, FLJ45242	uc002bva.1	Q86X40	OTTHUMG00000149854	ENST00000301981.3:c.608G>A	15.37:g.99892589G>A	ENSP00000304923:p.Arg203Gln	39.0	0.0	0		33.0	16.0	0.484848	NM_144598	A8KA22|Q6UY49|Q6ZSS6	Missense_Mutation	SNP	ENST00000301981.3	37	CCDS10380.1	.	.	.	.	.	.	.	.	.	.	G	17.23	3.336020	0.60853	0.0	1.16E-4	ENSG00000168904	ENST00000301981;ENST00000447360;ENST00000422500	T;T;T	0.31247	2.23;2.23;1.5	5.52	5.52	0.82312	.	0.131334	0.49916	D	0.000129	T	0.51856	0.1699	M	0.62723	1.935	0.80722	D	1	D;D;B	0.76494	0.999;0.999;0.046	D;D;B	0.77557	0.984;0.99;0.003	T	0.35500	-0.9786	10	0.15499	T	0.54	.	18.4386	0.90656	0.0:0.0:1.0:0.0	.	134;203;203	B4DHL3;Q86X40-2;Q86X40	.;.;LRC28_HUMAN	Q	203;203;134	ENSP00000304923:R203Q;ENSP00000404520:R203Q;ENSP00000398606:R134Q	ENSP00000304923:R203Q	R	+	2	0	LRRC28	97710112	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	4.864000	0.62990	2.597000	0.87782	0.655000	0.94253	CGA	G|1.000;A|0.000	0.000	weak		0.353	LRRC28-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313546.1	NM_144598	
GALNT13	114805	hgsc.bcm.edu	37	2	155102403	155102403	+	Silent	SNP	T	T	C	rs375635744		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:155102403T>C	ENST00000392825.3	+	7	1332	c.765T>C	c.(763-765)taT>taC	p.Y255Y	GALNT13_ENST00000409237.1_Silent_p.Y255Y	NM_052917.2	NP_443149.2	Q8IUC8	GLT13_HUMAN	polypeptide N-acetylgalactosaminyltransferase 13	255					cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(2)|central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(6)|lung(37)|ovary(3)|pancreas(2)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	65						ACATGACTTATGGGGGTTTTA	0.413																																					p.Y255Y		Atlas-SNP	.											.	GALNT13	170	.	0			c.T765C						PASS	.	T		0,4406		0,0,2203	109.0	108.0	108.0		765	0.3	1.0	2		108	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	GALNT13	NM_052917.2		0,2,6501	CC,CT,TT		0.0233,0.0,0.0154		255/557	155102403	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	114805	exon7			GACTTATGGGGGT	AB067505	CCDS2199.1	2q24.1	2014-03-13	2014-03-13		ENSG00000144278	ENSG00000144278	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23242	protein-coding gene	gene with protein product	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13"", ""polypeptide GalNAc transferase 13"""	608369	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 13 (GalNAc-T13)"""			11572484, 12407114	Standard	XM_005246267		Approved	KIAA1918, GalNAc-T13	uc002tyr.4	Q8IUC8	OTTHUMG00000131917	ENST00000392825.3:c.765T>C	2.37:g.155102403T>C		77.0	0.0	0		48.0	23.0	0.479167	NM_052917	Q08ER7|Q68VI8|Q6ZWG1|Q96PX0|Q9UIE5	Silent	SNP	ENST00000392825.3	37	CCDS2199.1																																																																																			.	.	weak		0.413	GALNT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254870.2	NM_052917	
CSPG4	1464	hgsc.bcm.edu	37	15	75980159	75980159	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:75980159G>T	ENST00000308508.5	-	3	3339	c.3247C>A	c.(3247-3249)Cag>Aag	p.Q1083K		NM_001897.4	NP_001888.2	Q6UVK1	CSPG4_HUMAN	chondroitin sulfate proteoglycan 4	1083	Gly/Ser-rich (glycosaminoglycan attachment domain).|Interaction with COL5A1. {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						AGGTCCTCCTGGGTGAAGCGG	0.637																																					p.Q1083K		Atlas-SNP	.											.	CSPG4	175	.	0			c.C3247A						PASS	.						67.0	64.0	65.0					15																	75980159		2197	4292	6489	SO:0001583	missense	1464	exon3			CCTCCTGGGTGAA	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.3247C>A	15.37:g.75980159G>T	ENSP00000312506:p.Gln1083Lys	123.0	0.0	0		184.0	92.0	0.5	NM_001897	D3DW77|Q92675	Missense_Mutation	SNP	ENST00000308508.5	37	CCDS10284.1	.	.	.	.	.	.	.	.	.	.	.	25.0	4.590308	0.86851	.	.	ENSG00000173546	ENST00000308508	T	0.52754	0.65	5.07	5.07	0.68467	.	0.000000	0.64402	D	0.000006	T	0.69815	0.3153	M	0.78456	2.415	0.80722	D	1	D	0.69078	0.997	D	0.77004	0.989	T	0.72246	-0.4349	10	0.49607	T	0.09	.	17.4549	0.87604	0.0:0.0:1.0:0.0	.	1083	Q6UVK1	CSPG4_HUMAN	K	1083	ENSP00000312506:Q1083K	ENSP00000312506:Q1083K	Q	-	1	0	CSPG4	73767214	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	9.869000	0.99810	2.356000	0.79943	0.555000	0.69702	CAG	.	.	none		0.637	CSPG4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286472.1	NM_001897	
DIRC1	116093	hgsc.bcm.edu	37	2	189599497	189599497	+	Missense_Mutation	SNP	A	A	C	rs72902678	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:189599497A>C	ENST00000308100.4	-	2	421	c.151T>G	c.(151-153)Tct>Gct	p.S51A	AC079613.1_ENST00000431708.1_RNA	NM_052952.2	NP_443184.1	Q969H9	DIRC1_HUMAN	disrupted in renal carcinoma 1	51			S -> A (in dbSNP:rs72902678). {ECO:0000269|PubMed:11587072}.							large_intestine(1)|lung(6)	7			OV - Ovarian serous cystadenocarcinoma(117;0.00842)|Epithelial(96;0.102)			GCAGCAGCAGAAGAACAATTT	0.438													C|||	46	0.0091853	0.0015	0.0043	5008	,	,		19145	0.0		0.0258	False		,,,				2504	0.0153				p.S51A		Atlas-SNP	.											.	DIRC1	13	.	0			c.T151G						PASS	.	C	ALA/SER	20,4386	824.4+/-416.5	0,20,2183	163.0	153.0	156.0		151	-1.0	0.0	2	dbSNP_130	156	197,8403	810.5+/-407.1	4,189,4107	yes	missense	DIRC1	NM_052952.2	99	4,209,6290	CC,CA,AA		2.2907,0.4539,1.6685	benign	51/105	189599497	217,12789	2203	4300	6503	SO:0001583	missense	116093	exon2			CAGCAGAAGAACA	AY039011	CCDS2296.1	2q33	2008-05-22			ENSG00000174325	ENSG00000174325			15760	protein-coding gene	gene with protein product		606423				11587072	Standard	NM_052952		Approved		uc002uqi.1	Q969H9	OTTHUMG00000132646	ENST00000308100.4:c.151T>G	2.37:g.189599497A>C	ENSP00000307860:p.Ser51Ala	209.0	0.0	0		166.0	87.0	0.524096	NM_052952	Q08AK1	Missense_Mutation	SNP	ENST00000308100.4	37	CCDS2296.1	26	0.011904761904761904	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	24	0.0316622691292876	C	3.267	-0.149923	0.06585	0.004539	0.022907	ENSG00000174325	ENST00000308100	T	0.34667	1.35	3.32	-0.974	0.10293	.	.	.	.	.	T	0.05181	0.0138	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.16808	-1.0390	9	0.87932	D	0	.	2.3607	0.04307	0.1301:0.428:0.2831:0.1587	.	51	Q969H9	DIRC1_HUMAN	A	51	ENSP00000307860:S51A	ENSP00000307860:S51A	S	-	1	0	DIRC1	189307742	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.093000	0.03362	-0.472000	0.06881	-2.196000	0.00310	TCT	A|0.985;C|0.015	0.015	strong		0.438	DIRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255897.2	NM_052952	
FAIM	55179	hgsc.bcm.edu	37	3	138347988	138347988	+	Missense_Mutation	SNP	T	T	C	rs13043	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:138347988T>C	ENST00000393035.2	+	4	489	c.380T>C	c.(379-381)tTg>tCg	p.L127S	FAIM_ENST00000360570.3_Missense_Mutation_p.L149S|FAIM_ENST00000464668.1_Missense_Mutation_p.L127S|FAIM_ENST00000393034.2_Missense_Mutation_p.L127S|FAIM_ENST00000338446.4_Missense_Mutation_p.L161S	NM_001033032.1	NP_001028204.1	Q9NVQ4	FAIM1_HUMAN	Fas apoptotic inhibitory molecule	127			L -> S (in dbSNP:rs13043). {ECO:0000269|PubMed:12107411}.		apoptotic process (GO:0006915)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)	cytoplasm (GO:0005737)				kidney(1)|upper_aerodigestive_tract(1)	2						GGTAAAAAATTGGAGACAGCG	0.313													T|||	893	0.178315	0.6256	0.0735	5008	,	,		17281	0.0		0.0139	False		,,,				2504	0.001				p.L161S		Atlas-SNP	.											.	FAIM	27	.	0			c.T482C						PASS	.	T	SER/LEU,SER/LEU,SER/LEU,SER/LEU	2378,2028	610.6+/-391.6	646,1086,471	134.0	150.0	144.0		482,446,380,380	4.9	0.9	3	dbSNP_52	144	131,8469	65.3+/-127.6	1,129,4170	yes	missense,missense,missense,missense	FAIM	NM_001033030.1,NM_001033031.1,NM_001033032.1,NM_018147.3	145,145,145,145	647,1215,4641	CC,CT,TT		1.5233,46.0281,19.2911	benign,benign,benign,benign	161/214,149/202,127/180,127/180	138347988	2509,10497	2203	4300	6503	SO:0001583	missense	55179	exon5			AAAAATTGGAGAC	AK001444	CCDS3103.1, CCDS33864.1, CCDS33865.1	3q23	2008-07-18			ENSG00000158234	ENSG00000158234			18703	protein-coding gene	gene with protein product						10075978	Standard	NM_018147		Approved	FLJ10582, FAIM1	uc003esq.3	Q9NVQ4	OTTHUMG00000159885	ENST00000393035.2:c.380T>C	3.37:g.138347988T>C	ENSP00000376755:p.Leu127Ser	95.0	0.0	0		149.0	77.0	0.516779	NM_001033030	Q6IAN2	Missense_Mutation	SNP	ENST00000393035.2	37	CCDS3103.1	338	0.15476190476190477	301	0.6117886178861789	26	0.0718232044198895	0	0.0	11	0.014511873350923483	T	15.38	2.816084	0.50527	0.539719	0.015233	ENSG00000158234	ENST00000338446;ENST00000360570;ENST00000393035;ENST00000393034;ENST00000464668;ENST00000479848	T;T;T;T;T;T	0.28895	1.59;1.59;1.59;1.59;1.59;1.59	4.94	4.94	0.65067	.	0.123452	0.64402	D	0.000001	T	0.00012	0.0000	L	0.29908	0.895	0.32280	P	0.567723	B;B;B;P	0.36647	0.008;0.007;0.023;0.563	B;B;B;P	0.45610	0.043;0.019;0.069;0.487	T	0.42565	-0.9444	9	0.52906	T	0.07	-9.8443	12.8554	0.57882	0.0:0.0:0.0:1.0	rs13043;rs640979;rs1136174;rs1672960;rs3199418;rs11556767;rs16848257;rs52837206;rs56519713;rs57680134;rs13043	127;149;161;127	Q9NVQ4;Q9NVQ4-3;Q9NVQ4-2;C9JDZ2	FAIM1_HUMAN;.;.;.	S	161;149;127;127;127;127	ENSP00000342805:L161S;ENSP00000353775:L149S;ENSP00000376755:L127S;ENSP00000376754:L127S;ENSP00000417642:L127S;ENSP00000420543:L127S	ENSP00000342805:L161S	L	+	2	0	FAIM	139830678	1.000000	0.71417	0.921000	0.36526	0.937000	0.57800	7.513000	0.81739	2.195000	0.70347	0.533000	0.62120	TTG	T|0.810;C|0.190	0.190	strong		0.313	FAIM-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357979.1	NM_001033032	
TMEM132D	121256	hgsc.bcm.edu	37	12	130184947	130184947	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:130184947T>A	ENST00000422113.2	-	2	702	c.376A>T	c.(376-378)Aac>Tac	p.N126Y	RP11-174M13.2_ENST00000544036.1_lincRNA	NM_133448.2	NP_597705.2	Q14C87	T132D_HUMAN	transmembrane protein 132D	126					negative regulation of phosphatase activity (GO:0010923)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(33)|liver(1)|lung(69)|ovary(10)|pancreas(2)|prostate(2)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(2)	152	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.0934)|Breast(359;0.133)		OV - Ovarian serous cystadenocarcinoma(86;0.000288)|Epithelial(86;0.0116)|all cancers(50;0.0246)		AGTTTCCAGTTAAGAGAAAAT	0.517																																					p.N126Y		Atlas-SNP	.											.	TMEM132D	299	.	0			c.A376T						PASS	.						56.0	56.0	56.0					12																	130184947		2203	4300	6503	SO:0001583	missense	121256	exon2			TCCAGTTAAGAGA	AB061814	CCDS9266.1	12q24.32-q24.33	2014-06-13			ENSG00000151952	ENSG00000151952			29411	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 153"""	611257				11853319, 12966072	Standard	NM_133448		Approved	KIAA1944, MOLT, PPP1R153	uc009zyl.1	Q14C87	OTTHUMG00000168400	ENST00000422113.2:c.376A>T	12.37:g.130184947T>A	ENSP00000408581:p.Asn126Tyr	82.0	0.0	0		88.0	34.0	0.386364	NM_133448	Q14C96|Q76M59|Q8N1W9|Q8N3Q5|Q8TF57	Missense_Mutation	SNP	ENST00000422113.2	37	CCDS9266.1	.	.	.	.	.	.	.	.	.	.	T	17.73	3.462540	0.63513	.	.	ENSG00000151952	ENST00000422113	T	0.13307	2.6	5.33	5.33	0.75918	.	0.082670	0.48767	D	0.000166	T	0.38878	0.1057	M	0.79123	2.44	0.44754	D	0.997754	D	0.89917	1.0	D	0.78314	0.991	T	0.21075	-1.0256	9	.	.	.	-44.5477	15.3082	0.74011	0.0:0.0:0.0:1.0	.	126	Q14C87	T132D_HUMAN	Y	126	ENSP00000408581:N126Y	.	N	-	1	0	TMEM132D	128750900	1.000000	0.71417	0.881000	0.34555	0.437000	0.31866	4.073000	0.57570	2.001000	0.58596	0.454000	0.30748	AAC	.	.	none		0.517	TMEM132D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399592.1	NM_133448	
PPARGC1B	133522	hgsc.bcm.edu	37	5	149216095	149216095	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:149216095G>A	ENST00000309241.5	+	8	2109	c.2077G>A	c.(2077-2079)Gac>Aac	p.D693N	PPARGC1B_ENST00000403750.1_Missense_Mutation_p.D629N|PPARGC1B_ENST00000360453.4_Missense_Mutation_p.D654N|PPARGC1B_ENST00000394320.3_Missense_Mutation_p.D693N	NM_133263.3	NP_573570.3	Q86YN6	PRGC2_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator 1 beta	693					actin filament organization (GO:0007015)|bone trabecula formation (GO:0060346)|cellular lipid metabolic process (GO:0044255)|cellular response to reactive oxygen species (GO:0034614)|intracellular estrogen receptor signaling pathway (GO:0030520)|negative regulation of transcription, DNA-templated (GO:0045892)|ossification (GO:0001503)|positive regulation of alkaline phosphatase activity (GO:0010694)|positive regulation of bone resorption (GO:0045780)|positive regulation of osteoclast differentiation (GO:0045672)|positive regulation of phosphorylation (GO:0042327)|positive regulation of receptor activity (GO:2000273)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|small molecule metabolic process (GO:0044281)|transcription from mitochondrial promoter (GO:0006390)|transcription from RNA polymerase II promoter (GO:0006366)	mediator complex (GO:0016592)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AF-2 domain binding (GO:0050682)|estrogen receptor binding (GO:0030331)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nucleotide binding (GO:0000166)|receptor activator activity (GO:0030546)|RNA binding (GO:0003723)|RNA polymerase II transcription cofactor activity (GO:0001104)			NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(1)|liver(2)|lung(15)|ovary(3)|prostate(2)|stomach(1)	30			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)			TGGAGACCATGACTACTGCCA	0.632																																					p.D693N		Atlas-SNP	.											.	PPARGC1B	74	.	0			c.G2077A						PASS	.						53.0	56.0	55.0					5																	149216095		2203	4300	6503	SO:0001583	missense	133522	exon8			GACCATGACTACT	AF468496	CCDS4298.1, CCDS54933.1, CCDS54934.1	5q33.1	2013-02-12	2006-10-17		ENSG00000155846	ENSG00000155846		"""RNA binding motif (RRM) containing"""	30022	protein-coding gene	gene with protein product		608886	"""peroxisome proliferative activated receptor, gamma, coactivator 1, beta"""			11793024, 11854298	Standard	NM_133263		Approved	PERC, PGC1B	uc003lrc.3	Q86YN6	OTTHUMG00000130055	ENST00000309241.5:c.2077G>A	5.37:g.149216095G>A	ENSP00000312649:p.Asp693Asn	97.0	0.0	0		63.0	34.0	0.539683	NM_133263	A2RUM8|A2RUN0|B3KVW0|Q86YN3|Q86YN4|Q86YN5|Q8N1N9|Q8TDE4|Q8TDE5	Missense_Mutation	SNP	ENST00000309241.5	37	CCDS4298.1	.	.	.	.	.	.	.	.	.	.	G	26.4	4.737115	0.89482	.	.	ENSG00000155846	ENST00000360453;ENST00000394320;ENST00000309241;ENST00000403750	T;T;T;T	0.50813	0.77;0.73;0.81;0.75	4.47	4.47	0.54385	.	0.282850	0.37623	N	0.002014	T	0.66436	0.2789	M	0.81341	2.54	0.50632	D	0.99988	D;P;D;P;D	0.60575	0.976;0.948;0.976;0.93;0.988	P;P;P;P;P	0.57101	0.799;0.558;0.799;0.634;0.813	T	0.74300	-0.3710	10	0.87932	D	0	-13.9513	17.5766	0.87952	0.0:0.0:1.0:0.0	.	672;672;654;693;693	Q86YN6-2;Q86YN6-4;Q86YN6-5;Q86YN6;Q86YN6-3	.;.;.;PRGC2_HUMAN;.	N	654;693;693;629	ENSP00000353638:D654N;ENSP00000377855:D693N;ENSP00000312649:D693N;ENSP00000384403:D629N	ENSP00000312649:D693N	D	+	1	0	PPARGC1B	149196288	1.000000	0.71417	0.986000	0.45419	0.993000	0.82548	8.449000	0.90337	2.212000	0.71576	0.456000	0.33151	GAC	.	.	none		0.632	PPARGC1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252334.1	NM_133263	
EGFR	1956	hgsc.bcm.edu	37	7	55238874	55238874	+	Silent	SNP	T	T	A	rs2227984	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55238874T>A	ENST00000275493.2	+	16	2064	c.1887T>A	c.(1885-1887)acT>acA	p.T629T	EGFR_ENST00000454757.2_Silent_p.T576T|EGFR_ENST00000455089.1_Silent_p.T584T|EGFR_ENST00000442591.1_Silent_p.T629T	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	629					activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	ACAGATGCACTGGGCCAGGTC	0.398		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			T|||	1955	0.390375	0.2678	0.3977	5008	,	,		21298	0.5347		0.3559	False		,,,				2504	0.4376				p.T629T		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.T1887A						PASS	.	T		1213,3193	422.3+/-339.7	168,877,1158	135.0	120.0	125.0		1887	-5.9	0.0	7	dbSNP_123	125	2981,5619	461.9+/-365.5	537,1907,1856	no	coding-synonymous	EGFR	NM_005228.3		705,2784,3014	AA,AT,TT		34.6628,27.5306,32.2467		629/1211	55238874	4194,8812	2203	4300	6503	SO:0001819	synonymous_variant	1956	exon16	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	ATGCACTGGGCCA		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1887T>A	7.37:g.55238874T>A		65.0	0.0	0		54.0	54.0	1	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Silent	SNP	ENST00000275493.2	37	CCDS5514.1																																																																																			T|0.645;A|0.355	0.355	strong		0.398	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
ADGB	79747	hgsc.bcm.edu	37	6	147045358	147045358	+	Missense_Mutation	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:147045358T>G	ENST00000397944.3	+	18	2208	c.2132T>G	c.(2131-2133)cTt>cGt	p.L711R	ADGB_ENST00000367493.3_Missense_Mutation_p.L130R	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	711					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						GAGCCTGGACTTCTCACAGCT	0.413																																					p.L711R		Atlas-SNP	.											.	ADGB	93	.	0			c.T2132G						PASS	.						156.0	128.0	136.0					6																	147045358		692	1591	2283	SO:0001583	missense	79747	exon18			CTGGACTTCTCAC	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.2132T>G	6.37:g.147045358T>G	ENSP00000381036:p.Leu711Arg	133.0	0.0	0		73.0	55.0	0.753425	NM_024694	Q5T402|Q5T904|Q5T905	Missense_Mutation	SNP	ENST00000397944.3	37		.	.	.	.	.	.	.	.	.	.	T	15.88	2.962879	0.53507	.	.	ENSG00000118492	ENST00000397944;ENST00000367493	T	0.36520	1.25	5.58	5.58	0.84498	.	0.433362	0.21605	N	0.071881	T	0.46249	0.1383	M	0.70275	2.135	0.09310	N	1	D	0.71674	0.998	D	0.67103	0.949	T	0.47381	-0.9122	10	0.72032	D	0.01	-5.0251	13.2886	0.60258	0.0:0.0:0.0:1.0	.	711	Q8N7X0	CAN7L_HUMAN	R	711;130	ENSP00000381036:L711R	ENSP00000356463:L130R	L	+	2	0	C6orf103	147087051	0.116000	0.22171	0.349000	0.25694	0.380000	0.30137	2.892000	0.48625	2.127000	0.65507	0.533000	0.62120	CTT	.	.	none		0.413	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
ARHGEF18	23370	hgsc.bcm.edu	37	19	7505146	7505146	+	Missense_Mutation	SNP	A	A	C	rs200643326		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:7505146A>C	ENST00000359920.6	+	1	573	c.320A>C	c.(319-321)cAg>cCg	p.Q107P	ARHGEF18_ENST00000319670.9_Intron|CTD-2207O23.3_ENST00000593531.1_Intron	NM_001130955.1	NP_001124427.1	Q6ZSZ5	ARHGI_HUMAN	Rho/Rac guanine nucleotide exchange factor (GEF) 18	107					actin cytoskeleton organization (GO:0030036)|apoptotic signaling pathway (GO:0097190)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transforming growth factor beta receptor signaling pathway (GO:0007179)	apical part of cell (GO:0045177)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(4)|ovary(2)|prostate(2)|stomach(1)|urinary_tract(1)	23		Renal(5;0.0902)				CTGCGGCCGCAGTCGGAGCGG	0.602													A|||	1	0.000199681	0.0	0.0	5008	,	,		13226	0.0		0.0	False		,,,				2504	0.001				p.Q107P		Atlas-SNP	.											.	ARHGEF18	129	.	0			c.A320C						PASS	.						27.0	34.0	32.0					19																	7505146		692	1591	2283	SO:0001583	missense	23370	exon1			GGCCGCAGTCGGA	AK074372	CCDS12177.1, CCDS45946.1	19p13.3	2013-01-10	2009-06-12			ENSG00000104880		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	17090	protein-coding gene	gene with protein product	"""Rho-specific guanine nucleotide exchange factor p114"""		"""rho/rac guanine nucleotide exchange factor (GEF) 18"""			9628581, 11318610	Standard	NM_015318		Approved	P114-RhoGEF, KIAA0521, MGC15913	uc002mgi.3	Q6ZSZ5		ENST00000359920.6:c.320A>C	19.37:g.7505146A>C	ENSP00000352995:p.Gln107Pro	74.0	0.0	0		118.0	53.0	0.449153	NM_001130955	A8MV62|B5ME81|O60274|Q6DD92	Missense_Mutation	SNP	ENST00000359920.6	37	CCDS45946.1	.	.	.	.	.	.	.	.	.	.	A	12.64	1.999042	0.35226	.	.	ENSG00000104880	ENST00000359920	T	0.32988	1.43	5.23	1.88	0.25563	.	0.187822	0.25607	U	0.029507	T	0.17023	0.0409	N	0.24115	0.695	0.09310	N	0.999999	P	0.44521	0.837	B	0.37451	0.25	T	0.10382	-1.0632	10	0.62326	D	0.03	-7.5996	7.6096	0.28122	0.7026:0.0:0.2974:0.0	.	107	Q6ZSZ5	ARHGI_HUMAN	P	107	ENSP00000352995:Q107P	ENSP00000352995:Q107P	Q	+	2	0	ARHGEF18	7411146	0.023000	0.18921	0.031000	0.17742	0.874000	0.50279	0.774000	0.26675	0.330000	0.23485	0.459000	0.35465	CAG	A|0.999;C|0.001	0.001	weak		0.602	ARHGEF18-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000436340.1	NM_015318	
SMPD1	6609	hgsc.bcm.edu	37	11	6413108	6413108	+	Silent	SNP	T	T	C	rs61876771	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:6413108T>C	ENST00000342245.4	+	2	981	c.813T>C	c.(811-813)ccT>ccC	p.P271P	SMPD1_ENST00000533196.1_Intron|SMPD1_ENST00000299397.3_Silent_p.P271P|SMPD1_ENST00000356761.2_Silent_p.P271P|SMPD1_ENST00000527275.1_Silent_p.P270P	NM_000543.4|NM_001007593.2	NP_000534.3|NP_001007594.2	P17405	ASM_HUMAN	sphingomyelin phosphodiesterase 1, acid lysosomal	269					cell death (GO:0008219)|ceramide biosynthetic process (GO:0046513)|glycosphingolipid metabolic process (GO:0006687)|negative regulation of MAP kinase activity (GO:0043407)|nervous system development (GO:0007399)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein dephosphorylation (GO:0035307)|response to cocaine (GO:0042220)|response to drug (GO:0042493)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)|sphingomyelin catabolic process (GO:0006685)|sphingomyelin metabolic process (GO:0006684)|termination of signal transduction (GO:0023021)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lamellar body (GO:0042599)|lysosomal lumen (GO:0043202)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			breast(1)|central_nervous_system(2)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(3)	23		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;4.9e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)	Amlodipine(DB00381)|Chlorpromazine(DB00477)|Desipramine(DB01151)	CAGCCGGCCCTTTTGATATGG	0.622													T|||	13	0.00259585	0.0008	0.0029	5008	,	,		12884	0.0		0.0099	False		,,,				2504	0.0				p.P271P		Atlas-SNP	.											.	SMPD1	108	.	0			c.T813C						PASS	.	T	,	3,4399	6.2+/-15.9	0,3,2198	85.0	102.0	96.0		813,810	-1.8	1.0	11	dbSNP_129	96	55,8537	30.1+/-81.4	0,55,4241	no	coding-synonymous,coding-synonymous	SMPD1	NM_000543.4,NM_001007593.2	,	0,58,6439	CC,CT,TT		0.6401,0.0682,0.4464	,	271/632,270/631	6413108	58,12936	2201	4296	6497	SO:0001819	synonymous_variant	6609	exon2			CGGCCCTTTTGAT	AB209775	CCDS31409.1, CCDS44531.1, CCDS31409.2	11p15.4-p15.1	2010-04-28	2008-02-04		ENSG00000166311	ENSG00000166311	3.1.4.12		11120	protein-coding gene	gene with protein product	"""acid sphingomyelinase"""	607608				1711683	Standard	NM_000543		Approved	ASM	uc001mcw.3	P17405	OTTHUMG00000165453	ENST00000342245.4:c.813T>C	11.37:g.6413108T>C		68.0	0.0	0		71.0	43.0	0.605634	NM_000543	A8K8M3|E9PKS3|P17406|Q13811|Q16837|Q16841	Silent	SNP	ENST00000342245.4	37	CCDS44531.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	T	10.10	1.258006	0.22965	6.82E-4	0.006401	ENSG00000166311	ENST00000526280	.	.	.	5.02	-1.8	0.07907	.	.	.	.	.	T	0.39784	0.1091	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.32561	-0.9902	4	.	.	.	-21.0652	4.6701	0.12685	0.0:0.3147:0.3048:0.3805	rs61876771	.	.	.	P	1	.	.	L	+	2	0	SMPD1	6369684	0.796000	0.28864	0.992000	0.48379	0.966000	0.64601	-0.140000	0.10342	-0.243000	0.09653	0.459000	0.35465	CTT	A|0.000;C|0.006;T|0.993	0.006	strong		0.622	SMPD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384205.1	NM_000543	
DDR1	780	hgsc.bcm.edu	37	6	30860313	30860313	+	Missense_Mutation	SNP	A	A	T	rs143367160	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:30860313A>T	ENST00000324771.8	+	10	1641	c.1093A>T	c.(1093-1095)Atc>Ttc	p.I365F	DDR1_ENST00000454612.2_Missense_Mutation_p.I365F|DDR1_ENST00000452441.1_Missense_Mutation_p.I365F|MIR4640_ENST00000581824.1_RNA|DDR1_ENST00000513240.1_Missense_Mutation_p.I365F|DDR1_ENST00000361741.4_Missense_Mutation_p.I96F|DDR1_ENST00000376575.3_Missense_Mutation_p.I365F|DDR1_ENST00000418800.2_Missense_Mutation_p.I365F|DDR1_ENST00000446312.1_3'UTR|DDR1_ENST00000376569.3_Missense_Mutation_p.I365F|DDR1_ENST00000508312.1_Missense_Mutation_p.I383F|DDR1_ENST00000376568.3_Missense_Mutation_p.I365F|DDR1_ENST00000376567.2_Missense_Mutation_p.I365F|DDR1_ENST00000376570.4_Missense_Mutation_p.I365F			Q08345	DDR1_HUMAN	discoidin domain receptor tyrosine kinase 1	365	DS-like domain.				branching involved in mammary gland duct morphogenesis (GO:0060444)|cell adhesion (GO:0007155)|collagen-activated tyrosine kinase receptor signaling pathway (GO:0038063)|ear development (GO:0043583)|embryo implantation (GO:0007566)|extracellular matrix organization (GO:0030198)|lactation (GO:0007595)|mammary gland alveolus development (GO:0060749)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine autophosphorylation (GO:0038083)|protein autophosphorylation (GO:0046777)|regulation of cell growth (GO:0001558)|regulation of cell-matrix adhesion (GO:0001952)|regulation of extracellular matrix disassembly (GO:0010715)|smooth muscle cell migration (GO:0014909)|smooth muscle cell-matrix adhesion (GO:0061302)|wound healing, spreading of cells (GO:0044319)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|collagen binding (GO:0005518)|metal ion binding (GO:0046872)|protein tyrosine kinase collagen receptor activity (GO:0038062)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(3)|endometrium(2)|kidney(1)|large_intestine(5)|liver(1)|lung(14)|ovary(1)|prostate(1)|skin(1)	29					Imatinib(DB00619)	AATCTCCTTCATCTCTGGTAA	0.547													A|||	13	0.00259585	0.0	0.0086	5008	,	,		16593	0.0		0.003	False		,,,				2504	0.0041				p.I383F		Atlas-SNP	.											.	DDR1	213	.	0			c.A1147T						PASS	.	A	PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE,PHE/ILE	2,4404	4.2+/-10.8	0,2,2201	63.0	69.0	67.0		1093,1093,1147,1093,1093,1093	3.1	1.0	6	dbSNP_134	67	50,8550	31.2+/-83.2	0,50,4250	yes	missense,missense,missense,missense,missense,missense	DDR1	NM_001202521.1,NM_001202522.1,NM_001202523.1,NM_001954.4,NM_013993.2,NM_013994.2	21,21,21,21,21,21	0,52,6451	TT,TA,AA		0.5814,0.0454,0.3998	benign,benign,benign,benign,benign,benign	365/509,365/768,383/895,365/877,365/914,365/920	30860313	52,12954	2203	4300	6503	SO:0001583	missense	780	exon8			TCCTTCATCTCTG	X99031	CCDS4690.1, CCDS34385.1, CCDS47396.1, CCDS56411.1, CCDS75419.1	6p21.33	2010-02-17	2008-01-23		ENSG00000204580	ENSG00000204580	2.7.10.1	"""CD molecules"""	2730	protein-coding gene	gene with protein product		600408	"""discoidin domain receptor family, member 1"""	NTRK4, PTK3A, NEP, CAK, EDDR1		7789998	Standard	NM_001954		Approved	RTK6, CD167	uc003nrv.3	Q08345	OTTHUMG00000031236	ENST00000324771.8:c.1093A>T	6.37:g.30860313A>T	ENSP00000318217:p.Ile365Phe	42.0	0.0	0		63.0	23.0	0.365079	NM_001202523	B5A975|B5A976|B7Z2K0|Q14196|Q16562|Q2L6H3|Q4LE50|Q5ST11|Q5ST12|Q6NSK4|Q9UD35|Q9UD36|Q9UD37|Q9UD86|Q9UDL2	Missense_Mutation	SNP	ENST00000324771.8	37	CCDS34385.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	0	0.0	1	0.0013192612137203166	A	13.80	2.344152	0.41498	4.54E-4	0.005814	ENSG00000204580	ENST00000324771;ENST00000418800;ENST00000454612;ENST00000376569;ENST00000376575;ENST00000376570;ENST00000376568;ENST00000452441;ENST00000508312;ENST00000376567;ENST00000513240;ENST00000417521;ENST00000361741;ENST00000451954	T;T;T;T;T;T;T;T;T;T;T;T;T	0.21734	1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99;1.99	4.23	3.12	0.35913	.	0.077437	0.51477	D	0.000083	T	0.08313	0.0207	L	0.43923	1.385	0.41933	D	0.990575	B;P;B;B	0.48230	0.045;0.907;0.004;0.005	B;B;B;B	0.44224	0.021;0.444;0.038;0.007	T	0.09885	-1.0654	9	.	.	.	.	4.0728	0.09891	0.5736:0.2983:0.1282:0.0	.	383;161;365;365	B7Z2K0;A2ABM8;Q08345-5;Q08345	.;.;.;DDR1_HUMAN	F	365;365;365;365;365;365;365;365;383;365;365;161;96;48	ENSP00000318217:I365F;ENSP00000407699:I365F;ENSP00000406091:I365F;ENSP00000365753:I365F;ENSP00000365759:I365F;ENSP00000365754:I365F;ENSP00000365752:I365F;ENSP00000405039:I365F;ENSP00000422442:I383F;ENSP00000365751:I365F;ENSP00000427552:I365F;ENSP00000398682:I161F;ENSP00000354844:I96F	.	I	+	1	0	DDR1	30968292	0.967000	0.33354	1.000000	0.80357	0.979000	0.70002	2.245000	0.43133	1.559000	0.49555	0.379000	0.24179	ATC	A|0.997;T|0.003	0.003	strong		0.547	DDR1-005	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076494.3	NM_013994	
PROSER3	148137	hgsc.bcm.edu	37	19	36259415	36259415	+	Missense_Mutation	SNP	G	G	A	rs35178229	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:36259415G>A	ENST00000396908.4	+	12	1481	c.1408G>A	c.(1408-1410)Gaa>Aaa	p.E470K	C19orf55_ENST00000544099.1_3'UTR|C19orf55_ENST00000536037.1_3'UTR|AC002398.13_ENST00000589397.1_RNA	NM_001039887.2	NP_001034976.2	Q2NL68	PRSR3_HUMAN		471										cervix(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(3)|ovary(2)|prostate(1)	15	all_lung(56;2.87e-07)|Lung NSC(56;4.32e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			GCTAAGAAGGGAAGGAGATTC	0.498													G|||	693	0.138379	0.2042	0.1628	5008	,	,		14706	0.1498		0.0895	False		,,,				2504	0.0706				p.E471K		Atlas-SNP	.											.	C19orf55	39	.	0			c.G1411A						PASS	.	G	LYS/GLU	321,1431		26,269,581	112.0	119.0	117.0		1412	4.1	0.9	19	dbSNP_126	117	413,3569		23,367,1601	yes	missense	C19orf55	NM_001039887.2	56	49,636,2182	AA,AG,GG		10.3717,18.3219,12.8008		471/481	36259415	734,5000	876	1991	2867	SO:0001583	missense	148137	exon12			AGAAGGGAAGGAG																												ENST00000396908.4:c.1408G>A	19.37:g.36259415G>A	ENSP00000380116:p.Glu470Lys	0.0	0.0	.		4.0	4.0	1	NM_001039887	Q8NDI3|Q8WWC8|Q96NL4	Missense_Mutation	SNP	ENST00000396908.4	37		308	0.14102564102564102	94	0.1910569105691057	62	0.1712707182320442	78	0.13636363636363635	74	0.09762532981530343	G	36	5.706541	0.96821	0.183219	0.103717	ENSG00000167595	ENST00000396908	T	0.39229	1.09	4.09	4.09	0.47781	.	.	.	.	.	T	0.00109	0.0003	.	.	.	0.37590	P	0.07984800000000003	.	.	.	.	.	.	T	0.04976	-1.0914	5	0.87932	D	0	-2.3027	12.1094	0.53830	0.0:0.0:1.0:0.0	rs35178229	.	.	.	K	470	ENSP00000380116:E470K	ENSP00000380116:E470K	E	+	1	0	C19orf55	40951255	1.000000	0.71417	0.902000	0.35471	0.735000	0.41995	1.705000	0.37867	2.567000	0.86603	0.563000	0.77884	GAA	G|0.872;A|0.128	0.128	strong		0.498	C19orf55-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			
FREM2	341640	hgsc.bcm.edu	37	13	39263772	39263772	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39263772C>T	ENST00000280481.7	+	1	2507	c.2291C>T	c.(2290-2292)aCt>aTt	p.T764I		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	764					cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		TTGGTCTTGACTGACAACCCC	0.532																																					p.T764I		Atlas-SNP	.											.	FREM2	385	.	0			c.C2291T						PASS	.						84.0	89.0	87.0					13																	39263772		2203	4300	6503	SO:0001583	missense	341640	exon1			TCTTGACTGACAA	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.2291C>T	13.37:g.39263772C>T	ENSP00000280481:p.Thr764Ile	132.0	0.0	0		99.0	50.0	0.50505	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	.	.	.	.	.	.	.	.	.	.	C	14.36	2.512067	0.44660	.	.	ENSG00000150893	ENST00000280481	T	0.42131	0.98	5.8	4.95	0.65309	.	0.222181	0.45606	D	0.000354	T	0.44767	0.1309	M	0.69523	2.12	0.53688	D	0.999972	P	0.42161	0.772	B	0.40864	0.342	T	0.48080	-0.9066	10	0.54805	T	0.06	.	11.9366	0.52876	0.1368:0.7317:0.1316:0.0	.	764	Q5SZK8	FREM2_HUMAN	I	764	ENSP00000280481:T764I	ENSP00000280481:T764I	T	+	2	0	FREM2	38161772	0.998000	0.40836	0.895000	0.35142	0.761000	0.43186	3.899000	0.56288	1.437000	0.47472	0.655000	0.94253	ACT	.	.	none		0.532	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
RRP12	23223	hgsc.bcm.edu	37	10	99150237	99150237	+	Silent	SNP	G	G	A	rs41300219	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99150237G>A	ENST00000370992.4	-	6	807	c.696C>T	c.(694-696)ccC>ccT	p.P232P	RRP12_ENST00000414986.1_Silent_p.P171P|RRP12_ENST00000536831.1_Silent_p.P38P|RRP12_ENST00000315563.6_Intron	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		42.0	0.0	0		48.0	19.0	0.395833	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	
C2orf71	388939	hgsc.bcm.edu	37	2	29293837	29293837	+	Silent	SNP	C	C	T	rs183536545	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:29293837C>T	ENST00000331664.5	-	1	3290	c.3291G>A	c.(3289-3291)caG>caA	p.Q1097Q		NM_001029883.2	NP_001025054.1	A6NGG8	CB071_HUMAN	chromosome 2 open reading frame 71	1097					response to stimulus (GO:0050896)|visual perception (GO:0007601)	primary cilium (GO:0072372)				NS(2)|breast(5)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(11)|lung(20)|ovary(2)|prostate(6)|skin(3)|stomach(1)	60						CCTTGTGCTCCTGAGAAGGGG	0.562													C|||	24	0.00479233	0.0008	0.0115	5008	,	,		12777	0.0		0.0119	False		,,,				2504	0.0031				p.Q1097Q		Atlas-SNP	.											.	C2orf71	146	.	0			c.G3291A						PASS	.	C		13,3861		0,13,1924	62.0	69.0	66.0		3291	2.7	0.0	2		66	114,8170		0,114,4028	no	coding-synonymous	C2orf71	NM_001029883.1		0,127,5952	TT,TC,CC		1.3761,0.3356,1.0446		1097/1289	29293837	127,12031	1937	4142	6079	SO:0001819	synonymous_variant	388939	exon1			GTGCTCCTGAGAA		CCDS42669.1	2p23.2	2014-01-28			ENSG00000179270	ENSG00000179270			34383	protein-coding gene	gene with protein product		613425				20398886	Standard	NM_001029883		Approved	FLJ34931, RP54	uc002rmt.2	A6NGG8	OTTHUMG00000152024	ENST00000331664.5:c.3291G>A	2.37:g.29293837C>T		117.0	0.0	0		114.0	48.0	0.421053	NM_001029883		Silent	SNP	ENST00000331664.5	37	CCDS42669.1																																																																																			C|0.990;T|0.010	0.010	strong		0.562	C2orf71-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000324924.3	NM_001029883	
MAP3K15	389840	hgsc.bcm.edu	37	X	19387318	19387318	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:19387318C>A	ENST00000338883.4	-	25	3419	c.3420G>T	c.(3418-3420)gaG>gaT	p.E1140D	MAP3K15_ENST00000469203.2_Missense_Mutation_p.E972D|MAP3K15_ENST00000518578.1_5'UTR|MAP3K15_ENST00000359173.3_Missense_Mutation_p.E575D	NM_001001671.3	NP_001001671.3	Q6ZN16	M3K15_HUMAN	mitogen-activated protein kinase kinase kinase 15	1140							ATP binding (GO:0005524)|MAP kinase kinase kinase activity (GO:0004709)|metal ion binding (GO:0046872)			NS(2)|cervix(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(8)|lung(13)|ovary(3)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	Hepatocellular(33;0.183)					CACAGGTAGGCTCAAAGTGGG	0.602																																					p.E1140D		Atlas-SNP	.											.	MAP3K15	108	.	0			c.G3420T						PASS	.						71.0	64.0	66.0					X																	19387318		2203	4300	6503	SO:0001583	missense	389840	exon25			GGTAGGCTCAAAG	AK131412		Xp22.12	2011-06-09			ENSG00000180815	ENSG00000180815		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	31689	protein-coding gene	gene with protein product		300820					Standard	NM_001001671		Approved	bA723P2.3, FLJ16518	uc022btq.1	Q6ZN16	OTTHUMG00000022724	ENST00000338883.4:c.3420G>T	X.37:g.19387318C>A	ENSP00000345629:p.Glu1140Asp	24.0	0.0	0		36.0	36.0	1	NM_001001671	A2AI49|A2AI50|A6NJ61|Q5JPR4|Q6ZMV3	Missense_Mutation	SNP	ENST00000338883.4	37		.	.	.	.	.	.	.	.	.	.	C	11.19	1.564365	0.27915	.	.	ENSG00000180815	ENST00000338883;ENST00000359173;ENST00000469203	T;T;T	0.73047	-0.67;-0.71;-0.67	5.34	3.51	0.40186	.	0.104397	0.64402	N	0.000005	T	0.64294	0.2585	M	0.63428	1.95	0.25693	N	0.985669	P;D	0.56521	0.68;0.976	B;P	0.45913	0.431;0.497	T	0.58544	-0.7618	10	0.37606	T	0.19	.	2.7745	0.05344	0.1497:0.5478:0.1421:0.1604	.	615;1140	Q6ZN16-3;Q6ZN16	.;M3K15_HUMAN	D	1140;575;972	ENSP00000345629:E1140D;ENSP00000352093:E575D;ENSP00000428356:E972D	ENSP00000345629:E1140D	E	-	3	2	MAP3K15	19297239	0.032000	0.19561	0.063000	0.19743	0.727000	0.41649	-0.364000	0.07583	0.430000	0.26230	0.506000	0.49869	GAG	.	.	none		0.602	MAP3K15-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001001671	
ZNF844	284391	hgsc.bcm.edu	37	19	12187907	12187907	+	Missense_Mutation	SNP	G	G	A	rs55703333	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:12187907G>A	ENST00000439326.3	+	4	2147	c.1972G>A	c.(1972-1974)Gta>Ata	p.V658I	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	658			V -> I (in dbSNP:rs55703333).		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(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						GGTTCCTTTCGTAGACATAAA	0.403													.|||	76	0.0151757	0.0378	0.0086	5008	,	,		22386	0.001		0.0179	False		,,,				2504	0.001				p.V658I		Atlas-SNP	.											.	ZNF844	69	.	0			c.G1972A						PASS	.	G	ILE/VAL	71,1313		4,63,625	47.0	51.0	50.0		1972	-5.8	0.0	19	dbSNP_129	50	50,3132		2,46,1543	yes	missense	ZNF844	NM_001136501.1	29	6,109,2168	AA,AG,GG		1.5713,5.1301,2.65	benign	658/667	12187907	121,4445	692	1591	2283	SO:0001583	missense	284391	exon4			CCTTTCGTAGACA	AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.1972G>A	19.37:g.12187907G>A	ENSP00000392024:p.Val658Ile	43.0	0.0	0		64.0	28.0	0.4375	NM_001136501	Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	43	0.019688644688644688	23	0.046747967479674794	4	0.011049723756906077	1	0.0017482517482517483	15	0.01978891820580475	G	9.085	1.000237	0.19121	0.051301	0.015713	ENSG00000223547	ENST00000439326	T	0.05996	3.36	2.92	-5.83	0.02325	.	.	.	.	.	T	0.00356	0.0011	N	0.08118	0	0.09310	N	1	P	0.40476	0.718	B	0.21917	0.037	T	0.41233	-0.9520	9	0.87932	D	0	.	4.1975	0.10450	0.1349:0.1113:0.5622:0.1917	rs55703333	658	Q08AG5	ZN844_HUMAN	I	658	ENSP00000392024:V658I	ENSP00000392024:V658I	V	+	1	0	ZNF844	12048907	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-4.792000	0.00185	-1.709000	0.01399	-0.300000	0.09419	GTA	G|0.980;A|0.020	0.020	strong		0.403	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2		
RALGDS	5900	hgsc.bcm.edu	37	9	135982493	135982493	+	Silent	SNP	C	C	T	rs45487303	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:135982493C>T	ENST00000372050.3	-	7	1413	c.1392G>A	c.(1390-1392)gaG>gaA	p.E464E	RALGDS_ENST00000542690.1_Silent_p.E535E|RALGDS_ENST00000372062.3_Silent_p.E435E|RALGDS_ENST00000393157.3_Silent_p.E463E|RALGDS_ENST00000372047.3_Silent_p.E452E|RALGDS_ENST00000393160.3_Silent_p.E409E|RALGDS_ENST00000469972.1_5'UTR	NM_006266.2	NP_006257.1	Q12967	GNDS_HUMAN	ral guanine nucleotide dissociation stimulator	464	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				neurotrophin TRK receptor signaling pathway (GO:0048011)|Ras protein signal transduction (GO:0007265)|regulation of catalytic activity (GO:0050790)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytosol (GO:0005829)	guanyl-nucleotide exchange factor activity (GO:0005085)|small GTPase regulator activity (GO:0005083)			endometrium(1)|large_intestine(4)|lung(2)|ovary(1)|upper_aerodigestive_tract(2)	10				OV - Ovarian serous cystadenocarcinoma(145;3.66e-06)|Epithelial(140;2.77e-05)		CGATCCAGTGCTCCACCACCC	0.617			T	CIITA	"""PMBL, Hodgkin Lymphona, """								C|||	50	0.00998403	0.0	0.0144	5008	,	,		18802	0.0		0.0288	False		,,,				2504	0.0112				p.E464E	Melanoma(189;762 2088 15384 21931 52515)	Atlas-SNP	.		Dom	yes		9	9q34.3	5900	ral guanine nucleotide dissociation stimulator		L	.	RALGDS	75	.	0			c.G1392A						PASS	.	C	,	20,4386	27.2+/-55.0	0,20,2183	80.0	74.0	76.0		1227,1392	0.1	1.0	9	dbSNP_127	76	158,8442	73.5+/-136.2	0,158,4142	no	coding-synonymous,coding-synonymous	RALGDS	NM_001042368.1,NM_006266.2	,	0,178,6325	TT,TC,CC		1.8372,0.4539,1.3686	,	409/860,464/915	135982493	178,12828	2203	4300	6503	SO:0001819	synonymous_variant	5900	exon7			CCAGTGCTCCACC	AB037729	CCDS6959.1, CCDS43897.1, CCDS65172.1, CCDS65173.1, CCDS65174.1	9q34.3	2009-04-08			ENSG00000160271	ENSG00000160271			9842	protein-coding gene	gene with protein product		601619				7972015	Standard	NM_006266		Approved	RGF, RalGEF, RGDS	uc004ccr.3	Q12967	OTTHUMG00000020858	ENST00000372050.3:c.1392G>A	9.37:g.135982493C>T		151.0	0.0	0		132.0	132.0	1	NM_006266	B7Z753|E7ER93|E7ERZ0|Q5T7V4|Q6KH11|Q6PCE1|Q6ZSD5|Q9HAX7|Q9HAY1|Q9HCT1|Q9P2N8	Silent	SNP	ENST00000372050.3	37	CCDS6959.1																																																																																			C|0.985;T|0.015	0.015	strong		0.617	RALGDS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000054837.1	NM_006266	
SEC24C	9632	hgsc.bcm.edu	37	10	75523634	75523634	+	Missense_Mutation	SNP	A	A	G	rs35528438	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:75523634A>G	ENST00000339365.2	+	9	1282	c.1120A>G	c.(1120-1122)Atc>Gtc	p.I374V	SEC24C_ENST00000345254.4_Missense_Mutation_p.I374V|SEC24C_ENST00000546025.1_Intron|SEC24C_ENST00000411652.2_Missense_Mutation_p.I255V|SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000540668.1_Intron	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	374					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					TCCCCGATACATCCGATGTAC	0.542													A|||	40	0.00798722	0.0008	0.0202	5008	,	,		15779	0.0		0.0219	False		,,,				2504	0.0031				p.I374V		Atlas-SNP	.											.	SEC24C	86	.	0			c.A1120G						PASS	.	A	VAL/ILE,VAL/ILE	24,4382	29.0+/-57.7	0,24,2179	84.0	71.0	75.0		1120,1120	5.8	1.0	10	dbSNP_126	75	219,8381	91.9+/-153.9	4,211,4085	yes	missense,missense	SEC24C	NM_004922.3,NM_198597.2	29,29	4,235,6264	GG,GA,AA		2.5465,0.5447,1.8684	benign,benign	374/1095,374/1095	75523634	243,12763	2203	4300	6503	SO:0001583	missense	9632	exon8			CGATACATCCGAT	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.1120A>G	10.37:g.75523634A>G	ENSP00000343405:p.Ile374Val	143.0	0.0	0		158.0	76.0	0.481013	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	37	CCDS7332.1	25	0.011446886446886446	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	17	0.022427440633245383	A	15.89	2.965859	0.53507	0.005447	0.025465	ENSG00000176986	ENST00000345254;ENST00000339365;ENST00000411652	T;T;T	0.20200	2.09;2.09;2.09	5.77	5.77	0.91146	.	0.093915	0.64402	D	0.000001	T	0.08670	0.0215	L	0.52266	1.64	0.80722	D	1	B;B;B	0.31209	0.189;0.313;0.209	B;B;B	0.36378	0.064;0.223;0.111	T	0.03384	-1.1042	10	0.14656	T	0.56	-14.7248	16.1024	0.81184	1.0:0.0:0.0:0.0	rs35528438	255;374;374	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	V	374;374;255	ENSP00000321845:I374V;ENSP00000343405:I374V;ENSP00000402913:I255V	ENSP00000343405:I374V	I	+	1	0	SEC24C	75193640	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.393000	0.59665	2.200000	0.70718	0.459000	0.35465	ATC	A|0.983;G|0.017	0.017	strong		0.542	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
TRRAP	8295	hgsc.bcm.edu	37	7	98592335	98592335	+	Silent	SNP	G	G	A	rs56282945		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:98592335G>A	ENST00000359863.4	+	66	10340	c.10131G>A	c.(10129-10131)acG>acA	p.T3377T	TRRAP_ENST00000446306.3_Silent_p.T3366T|TRRAP_ENST00000355540.3_Silent_p.T3348T	NM_001244580.1	NP_001231509.1	Q9Y4A5	TRRAP_HUMAN	transformation/transcription domain-associated protein	3377					chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone deubiquitination (GO:0016578)|histone H2A acetylation (GO:0043968)|histone H4 acetylation (GO:0043967)|mitotic cell cycle checkpoint (GO:0007093)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	NuA4 histone acetyltransferase complex (GO:0035267)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PCAF complex (GO:0000125)|STAGA complex (GO:0030914)|Swr1 complex (GO:0000812)|transcription factor TFTC complex (GO:0033276)	phosphotransferase activity, alcohol group as acceptor (GO:0016773)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)			NS(3)|breast(1)|central_nervous_system(10)|endometrium(16)|kidney(7)|large_intestine(36)|liver(1)|lung(54)|ovary(10)|pancreas(1)|prostate(8)|skin(16)|stomach(5)|upper_aerodigestive_tract(6)|urinary_tract(2)	176	all_cancers(62;6.96e-09)|all_epithelial(64;4.86e-09)|Lung NSC(181;0.01)|all_lung(186;0.016)|Esophageal squamous(72;0.0274)		STAD - Stomach adenocarcinoma(171;0.215)			TGGTGAGCACGTTTGGGGTGG	0.567													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18543	0.0		0.0	False		,,,				2504	0.0				p.T3377T		Atlas-SNP	.											.	TRRAP	863	.	0			c.G10131A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	187.0	180.0	182.0		10044	-9.6	0.1	7	dbSNP_129	182	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TRRAP	NM_003496.3		0,3,6500	AA,AG,GG		0.0233,0.0227,0.0231		3348/3831	98592335	3,13003	2203	4300	6503	SO:0001819	synonymous_variant	8295	exon66			GAGCACGTTTGGG	AF076974	CCDS5659.1, CCDS59066.1	7q21.2-q22.1	2010-06-22			ENSG00000196367	ENSG00000196367			12347	protein-coding gene	gene with protein product		603015				9708738, 9885574	Standard	NM_003496		Approved	TR-AP, PAF400, Tra1	uc003upp.3	Q9Y4A5	OTTHUMG00000150403	ENST00000359863.4:c.10131G>A	7.37:g.98592335G>A		152.0	0.0	0		171.0	76.0	0.444444	NM_001244580	A4D265|O75218|Q9Y631|Q9Y6H4	Silent	SNP	ENST00000359863.4	37	CCDS59066.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	8.130	0.782960	0.16189	2.27E-4	2.33E-4	ENSG00000196367	ENST00000456197	.	.	.	5.29	-9.63	0.00544	.	.	.	.	.	T	0.35248	0.0925	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.42582	-0.9443	4	.	.	.	.	3.8434	0.08925	0.5236:0.2218:0.107:0.1476	rs56282945	.	.	.	H	3106	.	.	R	+	2	0	TRRAP	98430271	0.000000	0.05858	0.094000	0.20943	0.949000	0.60115	-2.691000	0.00830	-1.767000	0.01300	-0.502000	0.04539	CGT	G|1.000;A|0.000	0.000	strong		0.567	TRRAP-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317978.1	NM_003496	
NFATC1	4772	hgsc.bcm.edu	37	18	77170505	77170505	+	Missense_Mutation	SNP	C	C	T	rs143045693	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:77170505C>T	ENST00000427363.2	+	2	230	c.230C>T	c.(229-231)cCg>cTg	p.P77L	NFATC1_ENST00000586434.1_Missense_Mutation_p.P64L|NFATC1_ENST00000592223.1_Missense_Mutation_p.P64L|NFATC1_ENST00000397790.2_Intron|NFATC1_ENST00000587635.1_Missense_Mutation_p.P77L|NFATC1_ENST00000591814.1_Missense_Mutation_p.P77L|NFATC1_ENST00000329101.4_Missense_Mutation_p.P64L|NFATC1_ENST00000542384.1_Missense_Mutation_p.P77L|NFATC1_ENST00000545796.1_Intron|NFATC1_ENST00000253506.5_Missense_Mutation_p.P77L|NFATC1_ENST00000318065.5_Missense_Mutation_p.P64L			O95644	NFAC1_HUMAN	nuclear factor of activated T-cells, cytoplasmic, calcineurin-dependent 1	77					calcium ion transport (GO:0006816)|epithelial to mesenchymal transition (GO:0001837)|Fc-epsilon receptor signaling pathway (GO:0038095)|G1/S transition of mitotic cell cycle (GO:0000082)|heart development (GO:0007507)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|osteoclast differentiation (GO:0030316)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	FK506 binding (GO:0005528)|mitogen-activated protein kinase p38 binding (GO:0048273)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II distal enhancer sequence-specific DNA binding (GO:0000980)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(7)|kidney(1)|large_intestine(4)|lung(17)|ovary(2)|prostate(4)|skin(1)|soft_tissue(1)	40		Esophageal squamous(42;0.0157)|Melanoma(33;0.144)		OV - Ovarian serous cystadenocarcinoma(15;3.73e-07)|BRCA - Breast invasive adenocarcinoma(31;0.0257)	Pseudoephedrine(DB00852)	ACCTCCACACCGGGCATCATC	0.692													C|||	2	0.000399361	0.0	0.0	5008	,	,		13489	0.0		0.002	False		,,,				2504	0.0				p.P77L	GBM(151;1210 2593 28719 45011)	Atlas-SNP	.											.	NFATC1	105	.	0			c.C230T						PASS	.	C	LEU/PRO,LEU/PRO,,LEU/PRO,LEU/PRO	1,4405	2.1+/-5.4	0,1,2202	50.0	56.0	54.0		230,191,,191,230	4.4	0.0	18	dbSNP_134	54	3,8595	3.0+/-9.4	0,3,4296	yes	missense,missense,intron,missense,missense	NFATC1	NM_006162.3,NM_172387.1,NM_172388.1,NM_172389.1,NM_172390.1	98,98,,98,98	0,4,6498	TT,TC,CC		0.0349,0.0227,0.0308	benign,benign,,benign,benign	77/826,64/931,,64/813,77/717	77170505	4,13000	2203	4299	6502	SO:0001583	missense	4772	exon2			CCACACCGGGCAT	U08015	CCDS12015.1, CCDS12016.1, CCDS32850.1, CCDS59326.1, CCDS59327.1, CCDS62467.1, CCDS62468.1, CCDS62469.1, CCDS62470.1, CCDS62471.1	18q23	2009-11-24			ENSG00000131196	ENSG00000131196		"""Nuclear factor of activated T-cells"""	7775	protein-coding gene	gene with protein product		600489				8202141	Standard	NM_001278669		Approved	NF-ATC, NFATc, NFAT2	uc002lnf.3	O95644	OTTHUMG00000132897	ENST00000427363.2:c.230C>T	18.37:g.77170505C>T	ENSP00000389377:p.Pro77Leu	49.0	0.0	0		81.0	44.0	0.54321	NM_172390	B5B2M4|B5B2M5|B5B2M6|B5B2M7|B5B2M8|B5B2M9|B5B2N1|Q12865|Q15793|Q2M1S3	Missense_Mutation	SNP	ENST00000427363.2	37		0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	C	22.8	4.334065	0.81801	2.27E-4	3.49E-4	ENSG00000131196	ENST00000318065;ENST00000253506;ENST00000542384;ENST00000329101;ENST00000427363;ENST00000397794	T;T;T	0.39229	1.09;1.09;1.09	4.39	4.39	0.52855	.	0.400014	0.28146	N	0.016430	T	0.46386	0.1390	M	0.61703	1.905	0.80722	D	1	P;P;P;D;D;P;P	0.55605	0.904;0.904;0.946;0.972;0.972;0.773;0.946	B;B;B;B;B;B;B	0.43916	0.344;0.23;0.344;0.436;0.436;0.121;0.436	T	0.57894	-0.7732	10	0.87932	D	0	-17.9221	17.1373	0.86743	0.0:1.0:0.0:0.0	.	64;64;77;77;77;64;77	B5B2M7;B5B2N1;B5B2M6;O95644;B5B2M4;B5B2M5;Q2M1S3	.;.;.;NFAC1_HUMAN;.;.;.	L	77;77;77;64;64;41	ENSP00000253506:P77L;ENSP00000442435:P77L;ENSP00000327850:P64L	ENSP00000253506:P77L	P	+	2	0	NFATC1	75271493	0.997000	0.39634	0.025000	0.17156	0.028000	0.11728	6.807000	0.75201	2.267000	0.75376	0.561000	0.74099	CCG	C|1.000;T|0.000	0.000	strong		0.692	NFATC1-007	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000450507.1	NM_172390	
MET	4233	hgsc.bcm.edu	37	7	116397572	116397572	+	Silent	SNP	A	A	G	rs13223756	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:116397572A>G	ENST00000318493.6	+	7	2131	c.1944A>G	c.(1942-1944)caA>caG	p.Q648Q	MET_ENST00000397752.3_Silent_p.Q648Q|MET_ENST00000436117.2_Silent_p.Q648Q			Q9NWH9	SLTM_HUMAN	MET proto-oncogene, receptor tyrosine kinase	0	Arg/Glu-rich.				apoptotic process (GO:0006915)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(10)|breast(4)|central_nervous_system(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(5)|kidney(25)|large_intestine(8)|liver(3)|lung(70)|ovary(10)|pleura(2)|prostate(4)|skin(5)|stomach(6)|testis(1)|thyroid(4)|upper_aerodigestive_tract(64)|urinary_tract(3)	233	all_cancers(3;1.25e-07)|all_epithelial(6;4.07e-08)|Lung NSC(10;0.00108)|all_lung(10;0.00125)	Ovarian(593;0.133)	GBM - Glioblastoma multiforme(2;2.31e-07)|all cancers(2;0.000419)|STAD - Stomach adenocarcinoma(10;0.000512)			GGACAACACAATACAGTACAT	0.318			Mis		"""papillary renal, head-neck squamous cell """	papillary renal			Hereditary Papillary Renal Carcinoma (type 1)				A|||	941	0.187899	0.1089	0.1254	5008	,	,		17860	0.2728		0.2048	False		,,,				2504	0.2342				p.Q648Q		Atlas-SNP	.		Dom	yes	Familial Papillary Renal Cancer	7	7q31	4233	met proto-oncogene (hepatocyte growth factor receptor)		E	.	MET	412	.	0			c.A1944G						PASS	.	A	,	486,3224		27,432,1396	93.0	92.0	92.0		1944,1944	-6.5	0.0	7	dbSNP_121	92	1521,6665		129,1263,2701	no	coding-synonymous,coding-synonymous	MET	NM_000245.2,NM_001127500.1	,	156,1695,4097	GG,GA,AA		18.5805,13.0997,16.8712	,	648/1391,648/1409	116397572	2007,9889	1855	4093	5948	SO:0001819	synonymous_variant	4233	exon7	Familial Cancer Database	HPRC, Hereditary Papillary Renal Cell Cancer	AACACAATACAGT	M35073	CCDS43636.1, CCDS47689.1	7q31	2014-09-17	2014-06-26		ENSG00000105976	ENSG00000105976	2.7.10.1		7029	protein-coding gene	gene with protein product	"""hepatocyte growth factor receptor"""	164860	"""met proto-oncogene"""			1846706, 1611909	Standard	NM_001127500		Approved	HGFR, RCCP2	uc010lkh.3	P08581	OTTHUMG00000023299	ENST00000318493.6:c.1944A>G	7.37:g.116397572A>G		74.0	0.0	0		72.0	39.0	0.541667	NM_000245	A8K5V8|B2RTX3|Q2VPK7|Q52MB3|Q658J7|Q6ZNF2|Q86TK6|Q9H7C3|Q9H8U9	Silent	SNP	ENST00000318493.6	37	CCDS47689.1																																																																																			A|0.817;G|0.183	0.183	strong		0.318	MET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059620.3		
ARHGAP22	58504	hgsc.bcm.edu	37	10	49658842	49658842	+	Missense_Mutation	SNP	C	C	G	rs34940331	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:49658842C>G	ENST00000249601.4	-	9	1626	c.1330G>C	c.(1330-1332)Ggg>Cgg	p.G444R	ARHGAP22_ENST00000417247.2_Missense_Mutation_p.G354R|ARHGAP22_ENST00000417912.2_Missense_Mutation_p.G460R|ARHGAP22_ENST00000374172.1_Missense_Mutation_p.G335R|ARHGAP22_ENST00000477708.2_Missense_Mutation_p.G277R|ARHGAP22_ENST00000374170.1_Missense_Mutation_p.G285R|ARHGAP22_ENST00000435790.2_Missense_Mutation_p.G450R	NM_001256024.1|NM_021226.3	NP_001242953.1|NP_067049.2	Q7Z5H3	RHG22_HUMAN	Rho GTPase activating protein 22	444	Ser-rich.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|regulation of small GTPase mediated signal transduction (GO:0051056)|regulation of transcription, DNA-templated (GO:0006355)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|nucleus (GO:0005634)	GTPase activator activity (GO:0005096)			endometrium(3)|large_intestine(3)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	18						GAGCCGCCCCCCTTCGGGCTT	0.701													C|||	29	0.00579073	0.0	0.0115	5008	,	,		14381	0.0		0.0169	False		,,,				2504	0.0041				p.G460R		Atlas-SNP	.											.	ARHGAP22	94	.	0			c.G1378C						PASS	.	C	ARG/GLY	18,4346		0,18,2164	16.0	16.0	16.0		1330	1.9	0.1	10	dbSNP_126	16	120,8452		0,120,4166	yes	missense	ARHGAP22	NM_021226.2	125	0,138,6330	GG,GC,CC		1.3999,0.4125,1.0668	benign	444/699	49658842	138,12798	2182	4286	6468	SO:0001583	missense	58504	exon9			CGCCCCCCTTCGG	AY324801	CCDS7227.1, CCDS58079.1, CCDS58080.1, CCDS58081.1	10q11.23	2013-01-10			ENSG00000128805	ENSG00000128805		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	30320	protein-coding gene	gene with protein product		610585				8619474	Standard	NM_021226		Approved	RhoGAP2	uc010qgm.3	Q7Z5H3	OTTHUMG00000018176	ENST00000249601.4:c.1330G>C	10.37:g.49658842C>G	ENSP00000249601:p.Gly444Arg	84.0	0.0	0		90.0	39.0	0.433333	NM_001256024	A0AVP7|A5YM75|B4DED8|B9EGA0|C9JDM2|O00152|Q6ZSB0	Missense_Mutation	SNP	ENST00000249601.4	37	CCDS7227.1	16	0.007326007326007326	0	0.0	4	0.011049723756906077	0	0.0	12	0.0158311345646438	C	1.420	-0.573198	0.03882	0.004125	0.013999	ENSG00000128805	ENST00000249601;ENST00000374172;ENST00000374170;ENST00000477708;ENST00000417247;ENST00000435790;ENST00000417912	T;T;T;T;T;T;T	0.25250	2.93;2.6;1.81;2.22;2.59;2.89;2.93	4.94	1.9	0.25705	.	1.698030	0.02544	N	0.094901	T	0.10852	0.0265	L	0.36672	1.1	0.09310	N	1	B;B;B;B;B;B	0.17038	0.001;0.0;0.0;0.0;0.0;0.02	B;B;B;B;B;B	0.13407	0.002;0.001;0.001;0.001;0.002;0.009	T	0.16689	-1.0394	10	0.15952	T	0.53	.	7.5489	0.27783	0.2549:0.3359:0.4092:0.0	rs34940331	450;444;460;444;354;277	B4DED8;A6NDI7;Q7Z5H3-2;Q7Z5H3;Q7Z5H3-3;D6R9V6	.;.;.;RHG22_HUMAN;.;.	R	444;335;285;277;354;450;460	ENSP00000249601:G444R;ENSP00000363287:G335R;ENSP00000363285:G285R;ENSP00000422868:G277R;ENSP00000410054:G354R;ENSP00000416701:G450R;ENSP00000412461:G460R	ENSP00000249601:G444R	G	-	1	0	ARHGAP22	49328848	0.001000	0.12720	0.081000	0.20488	0.304000	0.27724	-0.001000	0.12947	1.074000	0.40909	-0.226000	0.12346	GGG	C|0.991;G|0.009	0.009	strong		0.701	ARHGAP22-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358767.1	NM_021226	
SALL1	6299	hgsc.bcm.edu	37	16	51172786	51172786	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:51172786G>A	ENST00000251020.4	-	2	3380	c.3347C>T	c.(3346-3348)tCt>tTt	p.S1116F	SALL1_ENST00000541611.1_Intron|SALL1_ENST00000440970.1_Missense_Mutation_p.S1019F|SALL1_ENST00000566102.1_Intron	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1116					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GGATGTGGCAGAGGAAGACAG	0.567																																					p.S1116F	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.C3347T						PASS	.						91.0	76.0	81.0					16																	51172786		2198	4300	6498	SO:0001583	missense	6299	exon2			GTGGCAGAGGAAG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3347C>T	16.37:g.51172786G>A	ENSP00000251020:p.Ser1116Phe	119.0	0.0	0		114.0	46.0	0.403509	NM_002968	Q99881|Q9NSC3|Q9P1R0	Missense_Mutation	SNP	ENST00000251020.4	37	CCDS10747.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.576037	0.86645	.	.	ENSG00000103449	ENST00000251020;ENST00000440970;ENST00000457559	T;T	0.07800	3.16;3.17	5.42	5.42	0.78866	.	0.104526	0.64402	D	0.000003	T	0.07683	0.0193	N	0.14661	0.345	0.58432	D	0.999999	P	0.44478	0.836	B	0.40329	0.326	T	0.26430	-1.0103	10	0.59425	D	0.04	.	19.2277	0.93824	0.0:0.0:1.0:0.0	.	1116	Q9NSC2	SALL1_HUMAN	F	1116;1019;1080	ENSP00000251020:S1116F;ENSP00000407914:S1019F	ENSP00000251020:S1116F	S	-	2	0	SALL1	49730287	1.000000	0.71417	0.994000	0.49952	0.970000	0.65996	7.866000	0.87056	2.529000	0.85273	0.563000	0.77884	TCT	.	.	none		0.567	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
EPHB4	2050	hgsc.bcm.edu	37	7	100403131	100403131	+	Missense_Mutation	SNP	C	C	A	rs35638378	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:100403131C>A	ENST00000358173.3	-	15	3138	c.2670G>T	c.(2668-2670)gaG>gaT	p.E890D	EPHB4_ENST00000360620.3_Missense_Mutation_p.E890D	NM_004444.4	NP_004435.3	P54760	EPHB4_HUMAN	EPH receptor B4	890	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		E -> D (in dbSNP:rs35638378). {ECO:0000269|PubMed:17344846}.		angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|ephrin receptor signaling pathway (GO:0048013)|heart morphogenesis (GO:0003007)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(20)|ovary(3)|prostate(2)|skin(3)|stomach(3)	47	Lung NSC(181;0.041)|all_lung(186;0.0581)					ACCCGCCATTCTCCCGGGCCA	0.652													C|||	13	0.00259585	0.0	0.0043	5008	,	,		15943	0.0		0.006	False		,,,				2504	0.0041				p.E890D	GBM(200;2113 3072 25865 52728)	Atlas-SNP	.											.	EPHB4	106	.	0			c.G2670T						PASS	.	C	ASP/GLU	7,4399	14.3+/-33.2	0,7,2196	53.0	60.0	58.0		2670	2.3	1.0	7	dbSNP_126	58	80,8520	44.9+/-103.4	1,78,4221	yes	missense	EPHB4	NM_004444.4	45	1,85,6417	AA,AC,CC		0.9302,0.1589,0.6689	benign	890/988	100403131	87,12919	2203	4300	6503	SO:0001583	missense	2050	exon15			GCCATTCTCCCGG	AY056047	CCDS5706.1	7q22	2013-02-11	2004-10-28		ENSG00000196411	ENSG00000196411		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3395	protein-coding gene	gene with protein product		600011	"""EphB4"""	HTK		8188704	Standard	NM_004444		Approved	Tyro11	uc003uwn.1	P54760	OTTHUMG00000157040	ENST00000358173.3:c.2670G>T	7.37:g.100403131C>A	ENSP00000350896:p.Glu890Asp	79.0	0.0	0		100.0	46.0	0.46	NM_004444	B5A970|B5A971|B5A972|Q7Z635|Q9BTA5|Q9BXP0	Missense_Mutation	SNP	ENST00000358173.3	37	CCDS5706.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	C	9.167	1.020236	0.19433	0.001589	0.009302	ENSG00000196411	ENST00000360620;ENST00000358173	T;T	0.76316	-1.01;-0.79	5.28	2.33	0.28932	Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.120844	0.36972	N	0.002303	T	0.41488	0.1161	N	0.05031	-0.125	0.28430	N	0.917311	B;B	0.09022	0.002;0.001	B;B	0.12156	0.007;0.002	T	0.23261	-1.0193	10	0.13470	T	0.59	.	4.4028	0.11395	0.0:0.5648:0.1653:0.2699	rs35638378	890;890	Q96L35;P54760	.;EPHB4_HUMAN	D	890	ENSP00000353833:E890D;ENSP00000350896:E890D	ENSP00000350896:E890D	E	-	3	2	EPHB4	100241067	0.733000	0.28132	1.000000	0.80357	0.923000	0.55619	0.224000	0.17738	0.625000	0.30304	-0.258000	0.10820	GAG	C|0.993;A|0.007	0.007	strong		0.652	EPHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347222.1	NM_004444	
DENND1C	79958	hgsc.bcm.edu	37	19	6468907	6468907	+	Missense_Mutation	SNP	G	G	A	rs35001260	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:6468907G>A	ENST00000381480.2	-	20	1577	c.1465C>T	c.(1465-1467)Cgc>Tgc	p.R489C	DENND1C_ENST00000543576.1_Missense_Mutation_p.R445C	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	489			R -> C (in dbSNP:rs35001260).		positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						CGGTCTGAGCGGCTGGGGAGG	0.607													G|||	50	0.00998403	0.0015	0.0058	5008	,	,		13199	0.0		0.0229	False		,,,				2504	0.0215				p.R489C		Atlas-SNP	.											.	DENND1C	93	.	0			c.C1465T						PASS	.	G	CYS/ARG	10,3842		0,10,1916	25.0	29.0	28.0		1465	4.7	1.0	19	dbSNP_126	28	170,8058		3,164,3947	yes	missense	DENND1C	NM_024898.2	180	3,174,5863	AA,AG,GG		2.0661,0.2596,1.4901	probably-damaging	489/802	6468907	180,11900	1926	4114	6040	SO:0001583	missense	79958	exon20			CTGAGCGGCTGGG	AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1465C>T	19.37:g.6468907G>A	ENSP00000370889:p.Arg489Cys	40.0	0.0	0		60.0	28.0	0.466667	NM_024898	B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	20	0.009157509157509158	0	0.0	1	0.0027624309392265192	0	0.0	19	0.025065963060686015	G	16.60	3.168788	0.57584	0.002596	0.020661	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.11821	2.91;2.74	4.69	4.69	0.59074	.	0.327353	0.28815	N	0.014059	T	0.09598	0.0236	L	0.53249	1.67	0.47123	D	0.999325	D	0.89917	1.0	P	0.56278	0.795	T	0.00171	-1.1959	10	0.62326	D	0.03	-15.0887	13.1025	0.59228	0.0:0.0:1.0:0.0	rs35001260;rs35001260	489	Q8IV53	DEN1C_HUMAN	C	489;445	ENSP00000370889:R489C;ENSP00000437805:R445C	ENSP00000370889:R489C	R	-	1	0	DENND1C	6419907	1.000000	0.71417	1.000000	0.80357	0.062000	0.15995	2.749000	0.47492	2.167000	0.68274	0.491000	0.48974	CGC	G|0.983;A|0.017	0.017	strong		0.607	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2	NM_024898	
ZEB2	9839	hgsc.bcm.edu	37	2	145157593	145157593	+	Silent	SNP	T	T	C	rs146673563	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:145157593T>C	ENST00000558170.2	-	8	2345	c.1161A>G	c.(1159-1161)ttA>ttG	p.L387L	ZEB2_ENST00000303660.4_Silent_p.L387L|ZEB2_ENST00000539609.3_Silent_p.L363L|ZEB2_ENST00000409487.3_Silent_p.L387L	NM_014795.3	NP_055610.1	O60315	ZEB2_HUMAN	zinc finger E-box binding homeobox 2	387					cell proliferation in forebrain (GO:0021846)|developmental pigmentation (GO:0048066)|hippocampus development (GO:0021766)|melanocyte migration (GO:0097324)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|neural crest cell migration (GO:0001755)|neural tube closure (GO:0001843)|positive regulation of JUN kinase activity (GO:0043507)|positive regulation of melanin biosynthetic process (GO:0048023)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of melanosome organization (GO:1903056)|somitogenesis (GO:0001756)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|phosphatase regulator activity (GO:0019208)			breast(3)|central_nervous_system(1)|cervix(2)|endometrium(7)|kidney(6)|large_intestine(23)|lung(45)|ovary(5)|pancreas(2)|prostate(6)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(3)	107				BRCA - Breast invasive adenocarcinoma(221;0.112)		TAATTTTAAGTAAGCCTGTCT	0.383													T|||	4	0.000798722	0.0	0.0029	5008	,	,		20112	0.0		0.002	False		,,,				2504	0.0				p.L387L	Melanoma(33;1235 1264 5755 16332)	Atlas-SNP	.											ZEB2,NS,carcinoma,0,1	ZEB2	218	1	0			c.A1161G						PASS	.	T	,	0,4406		0,0,2203	101.0	103.0	102.0		1089,1161	1.8	1.0	2	dbSNP_134	102	13,8587	9.8+/-36.6	0,13,4287	no	coding-synonymous,coding-synonymous	ZEB2	NM_001171653.1,NM_014795.3	,	0,13,6490	CC,CT,TT		0.1512,0.0,0.1	,	363/1191,387/1215	145157593	13,12993	2203	4300	6503	SO:0001819	synonymous_variant	9839	exon8			TTTAAGTAAGCCT	AB011141	CCDS2186.1, CCDS54403.1	2q22.3	2013-01-08	2007-02-15	2007-02-15	ENSG00000169554	ENSG00000169554		"""Zinc fingers, C2H2-type"", ""Homeoboxes / ZF class"""	14881	protein-coding gene	gene with protein product	"""SMAD interacting protein 1"""	605802	"""zinc finger homeobox 1b"""	ZFHX1B			Standard	NM_014795		Approved	KIAA0569, SIP-1, SIP1	uc002tvu.3	O60315	OTTHUMG00000131834	ENST00000558170.2:c.1161A>G	2.37:g.145157593T>C		105.0	0.0	0		101.0	48.0	0.475248	NM_014795	A0JP09|B7Z2P2|F5H814|Q9UED1	Silent	SNP	ENST00000558170.2	37	CCDS2186.1																																																																																			T|0.999;C|0.001	0.001	strong		0.383	ZEB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254778.5	NM_014795	
MYH6	4624	hgsc.bcm.edu	37	14	23852443	23852443	+	Silent	SNP	G	G	A	rs200662317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:23852443G>A	ENST00000356287.3	-	36	5681	c.5652C>T	c.(5650-5652)gcC>gcT	p.A1884A	MYH6_ENST00000405093.3_Silent_p.A1884A			P13533	MYH6_HUMAN	myosin, heavy chain 6, cardiac muscle, alpha	1884					adult heart development (GO:0007512)|ATP catabolic process (GO:0006200)|atrial cardiac muscle tissue morphogenesis (GO:0055009)|BMP signaling pathway (GO:0030509)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle fiber development (GO:0048739)|in utero embryonic development (GO:0001701)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|myofibril assembly (GO:0030239)|regulation of ATPase activity (GO:0043462)|regulation of blood pressure (GO:0008217)|regulation of heart contraction (GO:0008016)|regulation of heart growth (GO:0060420)|regulation of heart rate (GO:0002027)|regulation of the force of heart contraction (GO:0002026)|sarcomere organization (GO:0045214)|striated muscle contraction (GO:0006941)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visceral muscle development (GO:0007522)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|muscle myosin complex (GO:0005859)|myofibril (GO:0030016)|myosin complex (GO:0016459)|myosin filament (GO:0032982)|nucleus (GO:0005634)|sarcomere (GO:0030017)|stress fiber (GO:0001725)|Z disc (GO:0030018)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|protein kinase binding (GO:0019901)			breast(4)|cervix(2)|endometrium(8)|kidney(2)|large_intestine(16)|liver(1)|lung(60)|ovary(2)|pancreas(3)|prostate(6)|skin(6)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	119	all_cancers(95;2.54e-05)			GBM - Glioblastoma multiforme(265;0.00764)|READ - Rectum adenocarcinoma(4;0.0289)|Colorectal(4;0.0441)		CCGCCTCCTCGGCCTGGCGCT	0.532													G|||	2	0.000399361	0.0	0.0	5008	,	,		12269	0.002		0.0	False		,,,				2504	0.0				p.A1884A		Atlas-SNP	.											.	MYH6	274	.	0			c.C5652T						PASS	.	G		0,4406		0,0,2203	84.0	74.0	78.0		5652	-7.8	0.9	14		78	5,8595	4.3+/-15.6	0,5,4295	no	coding-synonymous	MYH6	NM_002471.3		0,5,6498	AA,AG,GG		0.0581,0.0,0.0384		1884/1940	23852443	5,13001	2203	4300	6503	SO:0001819	synonymous_variant	4624	exon37			CTCCTCGGCCTGG	D00943	CCDS9600.1	14q11.2-q13	2014-09-17	2008-08-01		ENSG00000197616	ENSG00000197616		"""Myosins / Myosin superfamily : Class II"""	7576	protein-coding gene	gene with protein product	"""cardiomyopathy, hypertrophic 1"""	160710	"""myosin, heavy polypeptide 6, cardiac muscle, alpha (cardiomyopathy, hypertrophic 1)"""			2144212	Standard	NM_002471		Approved		uc001wjv.3	P13533	OTTHUMG00000028753	ENST00000356287.3:c.5652C>T	14.37:g.23852443G>A		113.0	0.0	0		97.0	47.0	0.484536	NM_002471	A2RTX1|D9YZU2|Q13943|Q14906|Q14907	Silent	SNP	ENST00000356287.3	37	CCDS9600.1																																																																																			G|0.997;A|0.003	0.003	strong		0.532	MYH6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071796.3		
OR7A5	26659	hgsc.bcm.edu	37	19	14938190	14938190	+	Silent	SNP	A	A	G	rs2240561	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:14938190A>G	ENST00000322301.3	-	2	951	c.864T>C	c.(862-864)ttT>ttC	p.F288F	OR7A5_ENST00000594432.1_Silent_p.F288F|OR7A5_ENST00000601611.1_Intron			Q15622	OR7A5_HUMAN	olfactory receptor, family 7, subfamily A, member 5	288					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)			breast(1)|central_nervous_system(4)|endometrium(2)|kidney(4)|large_intestine(3)|lung(6)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	26						GACTATAGATAAAGGGGTTCA	0.473																																					p.F288F		Atlas-SNP	.											.	OR7A5	43	.	0			c.T864C						PASS	.						73.0	71.0	71.0					19																	14938190		2203	4300	6503	SO:0001819	synonymous_variant	26659	exon1			ATAGATAAAGGGG	X64976	CCDS12318.1	19p13.1	2012-08-09	2003-12-09			ENSG00000188269		"""GPCR / Class A : Olfactory receptors"""	8368	protein-coding gene	gene with protein product			"""olfactory receptor, family 7, subfamily A, member 5 pseudogene"""				Standard	XM_006722722		Approved	HTPCR2	uc002mzw.3	Q15622		ENST00000322301.3:c.864T>C	19.37:g.14938190A>G		69.0	0.0	0		115.0	9.0	0.0782609	NM_017506	B2R682|Q6IFP1|Q96R96	Silent	SNP	ENST00000322301.3	37	CCDS12318.1																																																																																			A|0.999;G|0.001	0.001	strong		0.473	OR7A5-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466518.1	NM_017506	
ZFP36L1	677	hgsc.bcm.edu	37	14	69259661	69259661	+	5'UTR	SNP	G	G	A	rs529200428		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:69259661G>A	ENST00000439696.2	-	0	296				ZFP36L1_ENST00000336440.3_5'UTR|ZFP36L1_ENST00000555997.1_5'Flank	NM_001244701.1|NM_004926.3	NP_001231630.1|NP_004917.2	Q07352	TISB_HUMAN	ZFP36 ring finger protein-like 1						gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|regulation of mRNA stability (GO:0043488)|regulation of transcription, DNA-templated (GO:0006355)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|T cell differentiation in thymus (GO:0033077)|vasculogenesis (GO:0001570)	cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|mRNA binding (GO:0003729)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|kidney(1)|large_intestine(1)|liver(2)|lung(9)|ovary(1)|prostate(2)|urinary_tract(1)	21				all cancers(60;0.00203)|BRCA - Breast invasive adenocarcinoma(234;0.00205)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		GTCATCCTGTGCGTTCGCGCG	0.597													G|||	1	0.000199681	0.0008	0.0	5008	,	,		11745	0.0		0.0	False		,,,				2504	0.0				p.H68Y		Atlas-SNP	.											.	ZFP36L1	47	.	0			c.C202T						PASS	.						121.0	118.0	119.0					14																	69259661		2203	4300	6503	SO:0001623	5_prime_UTR_variant	677	exon2			TCCTGTGCGTTCG	X79066	CCDS9791.1	14q22-q24	2012-11-27	2012-11-27	2001-11-23		ENSG00000185650		"""RING-type (C3HC4) zinc fingers"""	1107	protein-coding gene	gene with protein product		601064	"""zinc finger protein, C3H type, 36-like 1"", ""zinc finger protein 36, C3H type-like 1"""	BRF1		8024689	Standard	NM_004926		Approved	RNF162B, Berg36, ERF1, TIS11B, cMG1	uc021rve.1	Q07352		ENST00000439696.2:c.-6C>T	14.37:g.69259661G>A		79.0	0.0	0		114.0	51.0	0.447368	NM_001244701	Q13851	Missense_Mutation	SNP	ENST00000439696.2	37	CCDS9791.1	.	.	.	.	.	.	.	.	.	.	G	10.92	1.485806	0.26686	.	.	ENSG00000185650	ENST00000553375	.	.	.	4.56	3.43	0.39272	.	.	.	.	.	T	0.56963	0.2021	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53933	-0.8368	4	.	.	.	.	7.8188	0.29276	0.1044:0.0:0.729:0.1666	.	.	.	.	Y	68	.	.	H	-	1	0	ZFP36L1	68329414	0.999000	0.42202	1.000000	0.80357	0.798000	0.45092	3.149000	0.50655	2.065000	0.61736	0.561000	0.74099	CAC	.	.	none		0.597	ZFP36L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413227.1		
HGS	9146	hgsc.bcm.edu	37	17	79658569	79658569	+	Silent	SNP	C	C	T	rs148002494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:79658569C>T	ENST00000329138.4	+	8	765	c.630C>T	c.(628-630)cgC>cgT	p.R210R		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	210					endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			AGGAGGTGCGCGTGTGTGAGC	0.592																																					p.R210R		Atlas-SNP	.											.	HGS	54	.	0			c.C630T						PASS	.	C		0,4406		0,0,2203	141.0	120.0	127.0		630	-3.2	1.0	17	dbSNP_134	127	2,8598	1.2+/-3.3	0,2,4298	no	coding-synonymous	HGS	NM_004712.4		0,2,6501	TT,TC,CC		0.0233,0.0,0.0154		210/778	79658569	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	9146	exon8			GGTGCGCGTGTGT	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.630C>T	17.37:g.79658569C>T		110.0	0.0	0		120.0	58.0	0.483333	NM_004712	Q9NR36	Silent	SNP	ENST00000329138.4	37	CCDS11784.1																																																																																			C|0.999;T|0.001	0.001	strong		0.592	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
KCNB2	9312	hgsc.bcm.edu	37	8	73849768	73849768	+	Silent	SNP	A	A	C	rs142525254	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:73849768A>C	ENST00000523207.1	+	3	2766	c.2178A>C	c.(2176-2178)gcA>gcC	p.A726A		NM_004770.2	NP_004761.2	Q92953	KCNB2_HUMAN	potassium voltage-gated channel, Shab-related subfamily, member 2	726					potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of smooth muscle contraction (GO:0006940)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(20)|liver(2)|lung(31)|ovary(2)|pancreas(3)|prostate(2)|skin(8)|upper_aerodigestive_tract(4)|urinary_tract(1)	85	Breast(64;0.137)		Epithelial(68;0.105)		Dalfampridine(DB06637)	GAGGCAGTGCACCACAGACCC	0.522													A|||	49	0.00978435	0.0083	0.0058	5008	,	,		17236	0.0		0.0139	False		,,,				2504	0.0204				p.A726A		Atlas-SNP	.											.	KCNB2	228	.	0			c.A2178C						PASS	.	A		43,4363	45.3+/-79.5	0,43,2160	94.0	99.0	98.0		2178	-10.1	0.2	8	dbSNP_134	98	132,8468	66.0+/-128.3	0,132,4168	no	coding-synonymous	KCNB2	NM_004770.2		0,175,6328	CC,CA,AA		1.5349,0.9759,1.3455		726/912	73849768	175,12831	2203	4300	6503	SO:0001819	synonymous_variant	9312	exon3			CAGTGCACCACAG	U69962	CCDS6209.1	8q13.2	2012-07-05			ENSG00000182674	ENSG00000182674		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6232	protein-coding gene	gene with protein product		607738				9612272, 16382104	Standard	NM_004770		Approved	Kv2.2	uc003xzb.3	Q92953	OTTHUMG00000164498	ENST00000523207.1:c.2178A>C	8.37:g.73849768A>C		63.0	0.0	0		56.0	23.0	0.410714	NM_004770	Q7Z7D0|Q9BXD3	Silent	SNP	ENST00000523207.1	37	CCDS6209.1																																																																																			A|0.989;C|0.011	0.011	strong		0.522	KCNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378998.1	NM_004770	
PNMAL1	55228	hgsc.bcm.edu	37	19	46974077	46974077	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:46974077C>T	ENST00000313683.10	-	2	521	c.216G>A	c.(214-216)gaG>gaA	p.E72E	PNMAL1_ENST00000602246.1_Splice_Site_p.E72E|PNMAL1_ENST00000438932.2_Silent_p.E72E	NM_001103149.1|NM_018215.3	NP_001096619.1|NP_060685.2	Q86V59	PNML1_HUMAN	paraneoplastic Ma antigen family-like 1	72										cervix(1)|endometrium(2)|large_intestine(8)|lung(8)|prostate(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	25		Ovarian(192;0.00965)|all_neural(266;0.0459)		OV - Ovarian serous cystadenocarcinoma(262;0.000166)|all cancers(93;0.0014)|GBM - Glioblastoma multiforme(486;0.0421)|Epithelial(262;0.0427)		cttcaccaacctcaatgaggg	0.547																																					p.E72E		Atlas-SNP	.											.	PNMAL1	87	.	0			c.G216A						PASS	.						65.0	52.0	56.0					19																	46974077		2203	4300	6503	SO:0001819	synonymous_variant	55228	exon2			ACCAACCTCAATG	BC026026	CCDS33059.1, CCDS46124.1	19q13.32	2014-02-12	2012-02-09			ENSG00000182013		"""Paraneoplastic Ma antigens"""	25578	protein-coding gene	gene with protein product			"""PNMA-like 1"""			12477932	Standard	NM_018215		Approved	KIAA1183L, FLJ10781	uc002peq.4	Q86V59		ENST00000313683.10:c.216G>A	19.37:g.46974077C>T		66.0	0.0	0		77.0	31.0	0.402597	NM_018215	A8K2F3|Q5U638|Q8N3H4|Q9NVE8	Silent	SNP	ENST00000313683.10	37	CCDS33059.1																																																																																			.	.	none		0.547	PNMAL1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000403929.1	NM_018215	
NPR1	4881	hgsc.bcm.edu	37	1	153662423	153662423	+	Missense_Mutation	SNP	G	G	A	rs35479618	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:153662423G>A	ENST00000368680.3	+	19	3371	c.2899G>A	c.(2899-2901)Gag>Aag	p.E967K		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	967	Guanylate cyclase. {ECO:0000255|PROSITE- ProRule:PRU00099}.		E -> K (in dbSNP:rs35479618). {ECO:0000269|PubMed:17344846}.		body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CCGGCCCCAGGAGCAGCTGCG	0.662													G|||	17	0.00339457	0.0	0.0014	5008	,	,		14197	0.0		0.0139	False		,,,				2504	0.002				p.E967K	Pancreas(141;1349 1870 15144 15830 40702)	Atlas-SNP	.											.	NPR1	104	.	0			c.G2899A						PASS	.	G	LYS/GLU	11,4311		0,11,2150	15.0	16.0	15.0		2899	2.9	1.0	1	dbSNP_126	15	105,8313		1,103,4105	yes	missense	NPR1	NM_000906.3	56	1,114,6255	AA,AG,GG		1.2473,0.2545,0.9105	possibly-damaging	967/1062	153662423	116,12624	2161	4209	6370	SO:0001583	missense	4881	exon19			CCCCAGGAGCAGC	BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2899G>A	1.37:g.153662423G>A	ENSP00000357669:p.Glu967Lys	79.0	0.0	0		85.0	33.0	0.388235	NM_000906	B0ZBF0|Q5SR08|Q6P4Q3	Missense_Mutation	SNP	ENST00000368680.3	37	CCDS1051.1	10	0.004578754578754579	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	15.02	2.709779	0.48517	0.002545	0.012473	ENSG00000169418	ENST00000368680;ENST00000428723;ENST00000368677	D	0.81739	-1.53	2.87	2.87	0.33458	Adenylyl cyclase class-3/4/guanylyl cyclase (5);	0.294578	0.26324	N	0.025023	T	0.55178	0.1904	L	0.34521	1.04	0.38332	D	0.943827	B;P	0.35628	0.201;0.513	B;B	0.36922	0.236;0.134	T	0.58358	-0.7650	10	0.37606	T	0.19	.	5.8634	0.18760	0.1433:0.0:0.8567:0.0	rs35479618;rs61758573	446;967	B7Z4Y7;P16066	.;ANPRA_HUMAN	K	967;446;148	ENSP00000357669:E967K	ENSP00000357666:E148K	E	+	1	0	NPR1	151929047	0.886000	0.30341	1.000000	0.80357	0.912000	0.54170	1.368000	0.34216	1.907000	0.55213	0.462000	0.41574	GAG	G|0.993;A|0.007	0.007	strong		0.662	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1	NM_000906	
COL6A1	1291	hgsc.bcm.edu	37	21	47422174	47422174	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:47422174G>A	ENST00000361866.3	+	32	2223	c.2109G>A	c.(2107-2109)acG>acA	p.T703T	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	703	C-terminal globular domain.|VWFA 2. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		GCACCTTCACGGGGGAGGCCC	0.697																																					p.T703T		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2109A						PASS	.						12.0	12.0	12.0					21																	47422174		2176	4278	6454	SO:0001819	synonymous_variant	1291	exon32			CTTCACGGGGGAG	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2109G>A	21.37:g.47422174G>A		36.0	0.0	0		40.0	20.0	0.5	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Silent	SNP	ENST00000361866.3	37	CCDS13727.1																																																																																			.	.	none		0.697	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
NKTR	4820	hgsc.bcm.edu	37	3	42662976	42662976	+	Silent	SNP	A	A	C	rs35419602	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:42662976A>C	ENST00000232978.8	+	6	530	c.342A>C	c.(340-342)cgA>cgC	p.R114R	RP4-613B23.1_ENST00000438017.1_RNA|RP4-613B23.1_ENST00000445452.1_RNA	NM_005385.3	NP_005376.2	P30414	NKTR_HUMAN	natural killer cell triggering receptor	114	PPIase cyclophilin-type. {ECO:0000255|PROSITE-ProRule:PRU00156}.				protein folding (GO:0006457)	membrane (GO:0016020)	cyclosporin A binding (GO:0016018)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			breast(3)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	41				KIRC - Kidney renal clear cell carcinoma(284;0.24)		TGGCAAATCGAGGGAAACATA	0.358													A|||	35	0.00698882	0.0083	0.0072	5008	,	,		15576	0.0		0.0179	False		,,,				2504	0.001				p.R114R		Atlas-SNP	.											.	NKTR	116	.	0			c.A342C						PASS	.	A		32,4374	39.2+/-71.8	0,32,2171	76.0	73.0	74.0		342	-1.8	1.0	3	dbSNP_126	74	128,8470	65.6+/-127.9	1,126,4172	no	coding-synonymous	NKTR	NM_005385.3		1,158,6343	CC,CA,AA		1.4887,0.7263,1.2304		114/1463	42662976	160,12844	2203	4299	6502	SO:0001819	synonymous_variant	4820	exon6			AAATCGAGGGAAA		CCDS2702.1	3p22.1	2014-01-20	2014-01-20		ENSG00000114857	ENSG00000114857			7833	protein-coding gene	gene with protein product	"""NK-tumor recognition protein"", ""natural-killer cells cyclophilin-related protein"", ""NK-TR protein"""	161565	"""natural killer-tumor recognition sequence"""			8314596, 8144875	Standard	XM_005265173		Approved	p104	uc003clo.3	P30414	OTTHUMG00000133037	ENST00000232978.8:c.342A>C	3.37:g.42662976A>C		109.0	0.0	0		79.0	30.0	0.379747	NM_005385		Silent	SNP	ENST00000232978.8	37	CCDS2702.1																																																																																			A|0.988;C|0.012	0.012	strong		0.358	NKTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256642.2	NM_005385	
SLC15A1	6564	hgsc.bcm.edu	37	13	99340578	99340578	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:99340578G>A	ENST00000376503.5	-	20	1662	c.1607C>T	c.(1606-1608)cCg>cTg	p.P536L		NM_005073.3	NP_005064.1	P46059	S15A1_HUMAN	solute carrier family 15 (oligopeptide transporter), member 1	536					digestion (GO:0007586)|ion transport (GO:0006811)|protein transport (GO:0015031)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	peptide:proton symporter activity (GO:0015333)|proton-dependent oligopeptide secondary active transmembrane transporter activity (GO:0005427)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(6)|lung(10)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	30	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)				Aminolevulinic acid(DB00855)|Amoxicillin(DB01060)|Ampicillin(DB00415)|Azidocillin(DB08795)|Benazepril(DB00542)|Benzylpenicillin(DB01053)|Captopril(DB01197)|Cefaclor(DB00833)|Cefadroxil(DB01140)|Cefalotin(DB00456)|Cefdinir(DB00535)|Cefepime(DB01413)|Cefixime(DB00671)|Cefmetazole(DB00274)|Cefotaxime(DB00493)|Cefradine(DB01333)|Ceftazidime(DB00438)|Ceftibuten(DB01415)|Ceftizoxime(DB01332)|Ceftriaxone(DB01212)|Cefuroxime(DB01112)|Cephalexin(DB00567)|Chlorpropamide(DB00672)|Cilazapril(DB01340)|Cloxacillin(DB01147)|Cyclacillin(DB01000)|Dicloxacillin(DB00485)|Enalapril(DB00584)|Fluvastatin(DB01095)|Fosinopril(DB00492)|Glyburide(DB01016)|L-DOPA(DB01235)|Lisinopril(DB00722)|Methyldopa(DB00968)|Midodrine(DB00211)|Moexipril(DB00691)|Nateglinide(DB00731)|Oseltamivir(DB00198)|Oxacillin(DB00713)|Perindopril(DB00790)|Quinapril(DB00881)|Ramipril(DB00178)|Spirapril(DB01348)|Tolbutamide(DB01124)|Trandolapril(DB00519)|Valaciclovir(DB00577)|Valganciclovir(DB01610)	ACATTGTGGCGGAATCTCTGT	0.308																																					p.P536L		Atlas-SNP	.											.	SLC15A1	92	.	0			c.C1607T						PASS	.						78.0	78.0	78.0					13																	99340578		2203	4300	6503	SO:0001583	missense	6564	exon20			TGTGGCGGAATCT	U13173	CCDS9489.1	13q32.3	2013-05-22			ENSG00000088386	ENSG00000088386		"""Solute carriers"""	10920	protein-coding gene	gene with protein product	"""peptide transporter HPEPT1"", ""bA551M18.1.1 (solute carrier family 15 (oligopeptide transporter) member 1)"", ""solute carrier family 15 oligopeptide transporter member 1"""	600544				7896779	Standard	NM_005073		Approved	PEPT1, HPECT1, HPEPT1	uc001vno.3	P46059	OTTHUMG00000017255	ENST00000376503.5:c.1607C>T	13.37:g.99340578G>A	ENSP00000365686:p.Pro536Leu	107.0	0.0	0		97.0	38.0	0.391753	NM_005073	Q5VW82	Missense_Mutation	SNP	ENST00000376503.5	37	CCDS9489.1	.	.	.	.	.	.	.	.	.	.	G	6.435	0.448320	0.12223	.	.	ENSG00000088386	ENST00000376503	T	0.01963	4.53	5.09	1.21	0.21127	Major facilitator superfamily domain, general substrate transporter (1);	1.449500	0.03719	N	0.251497	T	0.01695	0.0054	N	0.14661	0.345	0.09310	N	1	B	0.25486	0.127	B	0.20384	0.029	T	0.44832	-0.9302	10	0.23891	T	0.37	-9.85	3.6908	0.08346	0.3572:0.1832:0.4596:0.0	.	536	P46059	S15A1_HUMAN	L	536	ENSP00000365686:P536L	ENSP00000365686:P536L	P	-	2	0	SLC15A1	98138579	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.380000	0.20602	0.674000	0.31244	-0.768000	0.03414	CCG	.	.	none		0.308	SLC15A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045560.3	NM_005073	
LRRC19	64922	hgsc.bcm.edu	37	9	26998122	26998122	+	Silent	SNP	T	T	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:26998122T>G	ENST00000380055.5	-	3	309	c.199A>C	c.(199-201)Aga>Cga	p.R67R	IFT74_ENST00000433700.1_Intron|LRRC19_ENST00000482770.1_5'Flank|IFT74_ENST00000380062.5_Intron|IFT74_ENST00000429045.2_Intron|IFT74_ENST00000443698.1_Intron	NM_022901.2	NP_075052.1	Q9H756	LRC19_HUMAN	leucine rich repeat containing 19	67						integral component of membrane (GO:0016021)				breast(1)|endometrium(2)|kidney(1)|lung(2)	6		all_neural(11;1.81e-09)		Lung(218;1.06e-05)|LUSC - Lung squamous cell carcinoma(38;0.0001)		TGTAGAACTCTTGTGTCTGTA	0.328																																					p.R67R		Atlas-SNP	.											.	LRRC19	24	.	0			c.A199C						PASS	.						73.0	81.0	78.0					9																	26998122		2203	4296	6499	SO:0001819	synonymous_variant	64922	exon3			GAACTCTTGTGTC	AK024955	CCDS6518.1	9p21.1	2008-02-05			ENSG00000184434	ENSG00000184434			23379	protein-coding gene	gene with protein product							Standard	NM_022901		Approved	FLJ21302	uc003zqh.3	Q9H756	OTTHUMG00000019710	ENST00000380055.5:c.199A>C	9.37:g.26998122T>G		95.0	0.0	0		80.0	38.0	0.475	NM_022901	A0AV00|B9EG91	Silent	SNP	ENST00000380055.5	37	CCDS6518.1																																																																																			.	.	none		0.328	LRRC19-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051961.2	NM_022901	
FAM104B	90736	hgsc.bcm.edu	37	X	55172630	55172630	+	Nonsense_Mutation	SNP	G	G	A	rs113263757		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:55172630G>A	ENST00000358460.4	-	3	388	c.235C>T	c.(235-237)Cag>Tag	p.Q79*	FAM104B_ENST00000477847.2_Nonsense_Mutation_p.Q76*|FAM104B_ENST00000332132.4_Nonsense_Mutation_p.Q80*|FAM104B_ENST00000472571.2_3'UTR|FAM104B_ENST00000425133.2_Nonsense_Mutation_p.Q80*|FAM104B_ENST00000489298.1_Nonsense_Mutation_p.Q78*|FAM104B_ENST00000478918.1_5'Flank			Q5XKR9	F104B_HUMAN	family with sequence similarity 104, member B	79										endometrium(3)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	8						TGCAAGAACTGGGGAAAGTTT	0.493																																					p.Q80X		Atlas-SNP	.											.	FAM104B	28	.	0			c.C238T						PASS	.						127.0	104.0	112.0					X																	55172630		2203	4300	6503	SO:0001587	stop_gained	90736	exon3			AGAACTGGGGAAA	BC000919	CCDS35305.1, CCDS35305.2, CCDS55422.1, CCDS55423.1, CCDS55424.1, CCDS55425.1, CCDS55426.1	Xp11.22	2008-02-05	2006-05-16	2006-05-16	ENSG00000182518	ENSG00000182518			25085	protein-coding gene	gene with protein product			"""chromosome X open reading frame 44"""	CXorf44		12477932	Standard	NM_138362		Approved	FLJ20434	uc004dug.2	Q5XKR9	OTTHUMG00000021646	ENST00000358460.4:c.235C>T	X.37:g.55172630G>A	ENSP00000364101:p.Gln79*	33.0	0.0	0		46.0	4.0	0.0869565	NM_001166699	A6NEH1|B4DSV6|D6R9S5|D6RDJ5|E9PH40|Q8WVU5|Q9BRA1	Nonsense_Mutation	SNP	ENST00000358460.4	37	CCDS35305.2	.	.	.	.	.	.	.	.	.	.	g	11.17	1.559418	0.27827	.	.	ENSG00000182518	ENST00000358460;ENST00000332132;ENST00000425133;ENST00000477847;ENST00000489298	.	.	.	1.6	1.6	0.23607	.	0.325359	0.21941	U	0.066869	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.62326	D	0.03	-0.2487	6.0913	0.19995	0.0:0.0:1.0:0.0	.	.	.	.	X	79;80;80;76;78	.	ENSP00000333394:Q80X	Q	-	1	0	FAM104B	55189355	0.905000	0.30787	0.015000	0.15790	0.033000	0.12548	1.600000	0.36762	1.084000	0.41184	0.436000	0.28706	CAG	.	.	weak		0.493	FAM104B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000056851.1	NM_138362	
SAMD4A	23034	hgsc.bcm.edu	37	14	55227152	55227152	+	Missense_Mutation	SNP	G	G	T	rs149416017	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:55227152G>T	ENST00000554335.1	+	7	2113	c.1450G>T	c.(1450-1452)Gcc>Tcc	p.A484S	SAMD4A_ENST00000392067.3_Missense_Mutation_p.A484S|SAMD4A_ENST00000357634.3_Missense_Mutation_p.A483S|SAMD4A_ENST00000555192.1_Missense_Mutation_p.A75S|SAMD4A_ENST00000251091.5_Missense_Mutation_p.A396S			Q9UPU9	SMAG1_HUMAN	sterile alpha motif domain containing 4A	484					negative regulation of translation (GO:0017148)|positive regulation of translation (GO:0045727)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)|synapse (GO:0045202)	poly(A) RNA binding (GO:0044822)|translation repressor activity (GO:0030371)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(10)|prostate(1)|skin(1)	29						TGGGGAGCTGGCCGTCGCCCC	0.682													G|||	40	0.00798722	0.0023	0.0159	5008	,	,		13068	0.0		0.0249	False		,,,				2504	0.001				p.A484S		Atlas-SNP	.											.	SAMD4A	68	.	0			c.G1450T						PASS	.	G	SER/ALA,SER/ALA,SER/ALA	21,3909		0,21,1944	4.0	6.0	5.0		1183,223,1447	5.2	1.0	14	dbSNP_134	5	153,7591		3,147,3722	no	missense,missense,missense	SAMD4A	NM_001161576.2,NM_001161577.1,NM_015589.5	99,99,99	3,168,5666	TT,TG,GG		1.9757,0.5344,1.4905	benign,benign,benign	395/630,75/346,483/718	55227152	174,11500	1965	3872	5837	SO:0001583	missense	23034	exon6			GAGCTGGCCGTCG	AB028976	CCDS32084.1, CCDS55917.1, CCDS55918.1, CCDS32084.2, CCDS55917.2	14q22.2	2013-01-10	2006-01-27	2006-01-27	ENSG00000020577	ENSG00000020577		"""Sterile alpha motif (SAM) domain containing"""	23023	protein-coding gene	gene with protein product	"""smaug homolog (Drosophila)"""	610747	"""sterile alpha motif domain containing 4"""	SAMD4		16221671	Standard	NM_001161577		Approved	KIAA1053, DKFZP434H0350, Smaug, SMG, SMGA, hSmaug1	uc001xbb.4	Q9UPU9	OTTHUMG00000170999	ENST00000554335.1:c.1450G>T	14.37:g.55227152G>T	ENSP00000452535:p.Ala484Ser	0.0	0.0	.		6.0	4.0	0.666667	NM_015589	A8MPZ5|Q0VA96|Q6PEW4	Missense_Mutation	SNP	ENST00000554335.1	37	CCDS32084.2	29	0.013278388278388278	1	0.0020325203252032522	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	15.72	2.917871	0.52546	0.005344	0.019757	ENSG00000020577	ENST00000554335;ENST00000392067;ENST00000305831;ENST00000251091;ENST00000357634;ENST00000555192	.	.	.	5.22	5.22	0.72569	.	0.112512	0.64402	D	0.000017	T	0.20251	0.0487	N	0.12182	0.205	0.34882	D	0.744671	B;B;B	0.16802	0.019;0.011;0.003	B;B;B	0.23574	0.047;0.037;0.002	T	0.34650	-0.9820	9	0.28530	T	0.3	-24.0747	18.9689	0.92707	0.0:0.0:1.0:0.0	.	75;396;484	G3V2R1;Q9UPU9-3;Q9UPU9	.;.;SMAG1_HUMAN	S	484;484;396;395;483;75	.	ENSP00000251091:A113S	A	+	1	0	SAMD4A	54296902	1.000000	0.71417	0.999000	0.59377	0.774000	0.43823	5.707000	0.68370	2.711000	0.92665	0.609000	0.83330	GCC	G|0.987;T|0.013	0.013	strong		0.682	SAMD4A-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000411186.1	NM_015589	
PLG	5340	hgsc.bcm.edu	37	6	161159619	161159619	+	Silent	SNP	T	T	C	rs4252195	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:161159619T>C	ENST00000308192.9	+	15	1915	c.1852T>C	c.(1852-1854)Ttg>Ctg	p.L618L		NM_000301.3	NP_000292.1	P00747	PLMN_HUMAN	plasminogen	618	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|fibrinolysis (GO:0042730)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion mediated by cadherin (GO:2000048)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of fibrinolysis (GO:0051918)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of fibrinolysis (GO:0051919)|tissue remodeling (GO:0048771)	blood microparticle (GO:0072562)|cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of external side of plasma membrane (GO:0031232)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)	apolipoprotein binding (GO:0034185)|protein domain specific binding (GO:0019904)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(12)|lung(19)|ovary(1)|prostate(3)|skin(9)|upper_aerodigestive_tract(1)	59				OV - Ovarian serous cystadenocarcinoma(65;5.24e-17)|BRCA - Breast invasive adenocarcinoma(81;7.08e-06)	Alteplase(DB00009)|Aminocaproic Acid(DB00513)|Anistreplase(DB00029)|Aprotinin(DB06692)|Reteplase(DB00015)|Streptokinase(DB00086)|Tenecteplase(DB00031)|Tranexamic Acid(DB00302)|Urokinase(DB00013)	AGAGTGGGTGTTGACTGCTGC	0.413													T|||	3	0.000599042	0.0	0.0014	5008	,	,		21373	0.0		0.002	False		,,,				2504	0.0				p.L618L		Atlas-SNP	.											.	PLG	150	.	0			c.T1852C						PASS	.	T		9,4397		0,9,2194	150.0	139.0	143.0		1852	-4.5	1.0	6	dbSNP_111	143	55,8545		0,55,4245	no	coding-synonymous	PLG	NM_000301.3		0,64,6439	CC,CT,TT		0.6395,0.2043,0.4921		618/811	161159619	64,12942	2203	4300	6503	SO:0001819	synonymous_variant	5340	exon15			TGGGTGTTGACTG	M74220	CCDS5279.1, CCDS55074.1	6q26	2012-10-02			ENSG00000122194	ENSG00000122194			9071	protein-coding gene	gene with protein product		173350					Standard	NM_000301		Approved		uc003qtm.4	P00747	OTTHUMG00000015957	ENST00000308192.9:c.1852T>C	6.37:g.161159619T>C		175.0	0.0	0		93.0	81.0	0.870968	NM_000301	Q15146|Q5TEH4|Q6PA00	Silent	SNP	ENST00000308192.9	37	CCDS5279.1																																																																																			T|0.996;C|0.004	0.004	strong		0.413	PLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042959.2	NM_000301	
LTF	4057	hgsc.bcm.edu	37	3	46490456	46490456	+	Silent	SNP	G	G	A	rs61737000	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:46490456G>A	ENST00000231751.4	-	9	1405	c.1110C>T	c.(1108-1110)ggC>ggT	p.G370G	LTF_ENST00000426532.2_Silent_p.G326G|LTF_ENST00000417439.1_Silent_p.G370G	NM_002343.3	NP_002334.2	P02788	TRFL_HUMAN	lactotransferrin	370	Transferrin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00741}.				antibacterial humoral response (GO:0019731)|antifungal humoral response (GO:0019732)|bone morphogenesis (GO:0060349)|humoral immune response (GO:0006959)|innate immune response in mucosa (GO:0002227)|interaction with host (GO:0051701)|iron assimilation by chelation and transport (GO:0033214)|iron ion transport (GO:0006826)|negative regulation of apoptotic process (GO:0043066)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of osteoclast development (GO:2001205)|negative regulation of single-species biofilm formation in or on host organism (GO:1900229)|negative regulation of tumor necrosis factor (ligand) superfamily member 11 production (GO:2000308)|ossification (GO:0001503)|phagosome maturation (GO:0090382)|positive regulation of bone mineralization involved in bone maturation (GO:1900159)|positive regulation of chondrocyte proliferation (GO:1902732)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|regulation of cytokine production (GO:0001817)|regulation of tumor necrosis factor production (GO:0032680)|response to host immune response (GO:0052572)|retina homeostasis (GO:0001895)|transcription, DNA-templated (GO:0006351)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|phagocytic vesicle lumen (GO:0097013)|secretory granule (GO:0030141)|specific granule (GO:0042581)	DNA binding (GO:0003677)|ferric iron binding (GO:0008199)|heparin binding (GO:0008201)|iron ion binding (GO:0005506)|protein serine/threonine kinase activator activity (GO:0043539)|serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(3)|central_nervous_system(3)|endometrium(4)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	40				all cancers(1;7.55e-14)|GBM - Glioblastoma multiforme(1;2.1e-09)|Epithelial(1;9.25e-07)|Colorectal(1;3.81e-05)|BRCA - Breast invasive adenocarcinoma(193;0.00129)|COAD - Colon adenocarcinoma(1;0.00308)|KIRC - Kidney renal clear cell carcinoma(197;0.0205)|Kidney(197;0.0242)|OV - Ovarian serous cystadenocarcinoma(275;0.089)		GCTCCTGCTCGCCCACCGCAC	0.667													G|||	300	0.0599042	0.2057	0.0187	5008	,	,		15791	0.001		0.003	False		,,,				2504	0.0112				p.G370G		Atlas-SNP	.											.	LTF	98	.	0			c.C1110T						PASS	.	G	,	837,3569	321.5+/-297.2	71,695,1437	42.0	37.0	39.0		978,1110	3.0	0.6	3	dbSNP_129	39	49,8543	30.1+/-81.4	0,49,4247	no	coding-synonymous,coding-synonymous	LTF	NM_001199149.1,NM_002343.3	,	71,744,5684	AA,AG,GG		0.5703,18.9968,6.8164	,	326/667,370/711	46490456	886,12112	2203	4296	6499	SO:0001819	synonymous_variant	4057	exon9			CTGCTCGCCCACC		CCDS33747.1, CCDS56251.1	3p21.31	2012-10-02			ENSG00000012223	ENSG00000012223			6720	protein-coding gene	gene with protein product		150210				17476971, 3356163	Standard	NM_001199149		Approved	HLF2	uc003cpq.3	P02788	OTTHUMG00000156325	ENST00000231751.4:c.1110C>T	3.37:g.46490456G>A		136.0	0.0	0		106.0	54.0	0.509434	NM_002343	A8K9U8|B2MV13|B7Z4X2|E7EQH5|O00756|Q16780|Q16785|Q16786|Q16789|Q5DSM0|Q8IU92|Q8IZH6|Q8TCD2|Q96KZ4|Q96KZ5|Q9H1Z3|Q9UCY5	Silent	SNP	ENST00000231751.4	37	CCDS33747.1																																																																																			G|0.929;A|0.071	0.071	strong		0.667	LTF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000343951.2	NM_002343	
PLEKHN1	84069	hgsc.bcm.edu	37	1	906122	906122	+	Silent	SNP	C	C	T	rs41285812	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:906122C>T	ENST00000379409.2	+	5	498	c.468C>T	c.(466-468)caC>caT	p.H156H	PLEKHN1_ENST00000379407.3_Silent_p.H156H|PLEKHN1_ENST00000379410.3_Silent_p.H156H			Q494U1	PKHN1_HUMAN	pleckstrin homology domain containing, family N member 1	156	PH 1.									central_nervous_system(1)|endometrium(3)|kidney(1)|lung(2)|skin(1)|urinary_tract(1)	9	all_cancers(77;0.00164)|all_epithelial(69;0.000959)|all_lung(157;0.00963)|Lung NSC(156;0.0232)|Ovarian(185;0.0634)	all_epithelial(116;9.48e-15)|all_lung(118;9.67e-07)|Lung NSC(185;5.59e-05)|Renal(390;0.00571)|Breast(487;0.0183)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Lung SC(97;0.217)		UCEC - Uterine corpus endometrioid carcinoma (11;0.00459)|Epithelial(90;4.31e-38)|OV - Ovarian serous cystadenocarcinoma(86;5.93e-23)|Colorectal(212;0.000159)|COAD - Colon adenocarcinoma(227;0.000193)|BRCA - Breast invasive adenocarcinoma(365;0.00095)|Kidney(185;0.0023)|STAD - Stomach adenocarcinoma(132;0.00644)|KIRC - Kidney renal clear cell carcinoma(229;0.0342)|Lung(427;0.199)		CCCGAGAGCACGCCTTCCAGA	0.662													C|||	9	0.00179712	0.0023	0.0	5008	,	,		15705	0.0		0.005	False		,,,				2504	0.001				p.H156H		Atlas-SNP	.											.	PLEKHN1	49	.	0			c.C468T						PASS	.	C	,	7,4399	12.9+/-30.5	1,5,2197	50.0	59.0	56.0		468,468	-3.5	0.9	1	dbSNP_127	56	68,8532	40.8+/-97.7	0,68,4232	no	coding-synonymous,coding-synonymous	PLEKHN1	NM_001160184.1,NM_032129.2	,	1,73,6429	TT,TC,CC		0.7907,0.1589,0.5767	,	156/577,156/612	906122	75,12931	2203	4300	6503	SO:0001819	synonymous_variant	84069	exon5			AGAGCACGCCTTC	AL136730	CCDS4.1, CCDS53256.1	1p36.33	2013-01-11			ENSG00000187583	ENSG00000187583		"""Pleckstrin homology (PH) domain containing"""	25284	protein-coding gene	gene with protein product						11230166	Standard	NM_032129		Approved	DKFZP434H2010	uc001acd.3	Q494U1	OTTHUMG00000040756	ENST00000379409.2:c.468C>T	1.37:g.906122C>T		118.0	1.0	0.00847458		106.0	99.0	0.933962	NM_001160184	Q494U2|Q5SV98|Q9H0M7	Silent	SNP	ENST00000379409.2	37																																																																																				C|0.995;T|0.005	0.005	strong		0.662	PLEKHN1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000473256.1	NM_032129	
TPR	7175	hgsc.bcm.edu	37	1	186330768	186330768	+	Missense_Mutation	SNP	T	T	C	rs201760745		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:186330768T>C	ENST00000367478.4	-	9	1240	c.944A>G	c.(943-945)aAa>aGa	p.K315R	TPR_ENST00000474852.1_5'UTR	NM_003292.2	NP_003283.2	P12270	TPR_HUMAN	translocated promoter region, nuclear basket protein	315					carbohydrate metabolic process (GO:0005975)|cellular response to heat (GO:0034605)|cellular response to interferon-alpha (GO:0035457)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|MAPK import into nucleus (GO:0000189)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic nuclear envelope disassembly (GO:0007077)|mitotic spindle assembly checkpoint (GO:0007094)|mRNA export from nucleus in response to heat stress (GO:0031990)|negative regulation of RNA export from nucleus (GO:0046832)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of translational initiation (GO:0045947)|nuclear pore organization (GO:0006999)|positive regulation of heterochromatin assembly (GO:0031453)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of mitotic cell cycle spindle assembly checkpoint (GO:0090267)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein import into nucleus (GO:0042307)|protein import into nucleus (GO:0006606)|regulation of glucose transport (GO:0010827)|regulation of mitotic sister chromatid separation (GO:0010965)|regulation of spindle assembly involved in mitosis (GO:1901673)|response to epidermal growth factor (GO:0070849)|RNA export from nucleus (GO:0006405)|RNA import into nucleus (GO:0006404)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoplasmic dynein complex (GO:0005868)|extrinsic component of membrane (GO:0019898)|kinetochore (GO:0000776)|mitotic spindle (GO:0072686)|nuclear envelope (GO:0005635)|nuclear inclusion body (GO:0042405)|nuclear membrane (GO:0031965)|nuclear periphery (GO:0034399)|nuclear pore (GO:0005643)|nuclear pore nuclear basket (GO:0044615)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|dynein complex binding (GO:0070840)|heat shock protein binding (GO:0031072)|mitogen-activated protein kinase binding (GO:0051019)|mRNA binding (GO:0003729)|nucleocytoplasmic transporter activity (GO:0005487)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)			autonomic_ganglia(1)|breast(5)|central_nervous_system(4)|cervix(2)|endometrium(9)|kidney(12)|large_intestine(23)|liver(1)|lung(45)|ovary(2)|pancreas(1)|prostate(6)|skin(3)|stomach(1)|urinary_tract(8)	123		Breast(1374;0.000659)|Lung SC(1967;0.0262)|Prostate(1639;0.157)		Colorectal(1306;1.12e-05)|KIRC - Kidney renal clear cell carcinoma(1967;0.00553)		ACCAGCTTCTTTCAAAAGTTT	0.343			T	NTRK1	papillary thyroid								T|||	1	0.000199681	0.0	0.0	5008	,	,		16594	0.0		0.001	False		,,,				2504	0.0				p.K315R		Atlas-SNP	.		Dom	yes		1	1q25	7175	translocated promoter region		E	.	TPR	441	.	0			c.A944G						PASS	.	T	ARG/LYS	0,3662		0,0,1831	128.0	119.0	122.0		944	5.5	1.0	1		122	2,8168		0,2,4083	yes	missense	TPR	NM_003292.2	26	0,2,5914	CC,CT,TT		0.0245,0.0,0.0169	probably-damaging	315/2364	186330768	2,11830	1831	4085	5916	SO:0001583	missense	7175	exon9			GCTTCTTTCAAAA	U69668	CCDS41446.1	1q25	2012-03-13	2012-03-13		ENSG00000047410	ENSG00000047410			12017	protein-coding gene	gene with protein product		189940	"""translocated promoter region (to activated MET oncogene)"""			1611909, 15229283	Standard	NM_003292		Approved		uc001grv.3	P12270	OTTHUMG00000035580	ENST00000367478.4:c.944A>G	1.37:g.186330768T>C	ENSP00000356448:p.Lys315Arg	239.0	0.0	0		202.0	97.0	0.480198	NM_003292	Q15655|Q5SWY0|Q99968	Missense_Mutation	SNP	ENST00000367478.4	37	CCDS41446.1	.	.	.	.	.	.	.	.	.	.	T	24.8	4.567818	0.86439	0.0	2.45E-4	ENSG00000047410	ENST00000367478	T	0.24723	1.84	5.49	5.49	0.81192	.	0.000000	0.85682	D	0.000000	T	0.46658	0.1404	L	0.60455	1.87	0.42919	D	0.994283	D;D	0.69078	0.976;0.997	P;D	0.75020	0.693;0.985	T	0.39333	-0.9619	10	0.45353	T	0.12	.	14.7725	0.69691	0.0:0.0:0.0:1.0	.	315;315	Q15624;P12270	.;TPR_HUMAN	R	315	ENSP00000356448:K315R	ENSP00000356448:K315R	K	-	2	0	TPR	184597391	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.877000	0.69675	2.076000	0.62316	0.533000	0.62120	AAA	.	.	weak		0.343	TPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086353.2	NM_003292	
KCNJ4	3761	hgsc.bcm.edu	37	22	38823676	38823676	+	Silent	SNP	C	C	G	rs77032485	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:38823676C>G	ENST00000303592.3	-	2	720	c.462G>C	c.(460-462)gtG>gtC	p.V154V	RP3-434P1.6_ENST00000433230.1_RNA	NM_004981.1|NM_152868.2	NP_004972.1|NP_690607.1	P48050	KCNJ4_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 4	154					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|synaptic transmission (GO:0007268)	basolateral plasma membrane (GO:0016323)|cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|voltage-gated potassium channel complex (GO:0008076)	inward rectifier potassium channel activity (GO:0005242)|PDZ domain binding (GO:0030165)			endometrium(7)|kidney(1)|large_intestine(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	23	Melanoma(58;0.0286)					TGGACTGGACCACCACAGCGA	0.617													C|||	6	0.00119808	0.0	0.0014	5008	,	,		17014	0.0		0.003	False		,,,				2504	0.002				p.V154V		Atlas-SNP	.											.	KCNJ4	74	.	0			c.G462C						PASS	.	C	,	2,4404	4.2+/-10.8	0,2,2201	78.0	69.0	72.0		462,462	2.6	1.0	22	dbSNP_131	72	57,8543	35.9+/-90.5	0,57,4243	no	coding-synonymous,coding-synonymous	KCNJ4	NM_004981.1,NM_152868.1	,	0,59,6444	GG,GC,CC		0.6628,0.0454,0.4536	,	154/446,154/446	38823676	59,12947	2203	4300	6503	SO:0001819	synonymous_variant	3761	exon2			CTGGACCACCACA	U07364	CCDS13971.1	22q13.1	2011-07-05			ENSG00000168135	ENSG00000168135		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6265	protein-coding gene	gene with protein product		600504				8016146, 16382105	Standard	NM_152868		Approved	Kir2.3, HIR, HRK1, hIRK2, IRK3	uc003avs.1	P48050	OTTHUMG00000151131	ENST00000303592.3:c.462G>C	22.37:g.38823676C>G		54.0	0.0	0		89.0	36.0	0.404494	NM_004981	Q14D44	Silent	SNP	ENST00000303592.3	37	CCDS13971.1																																																																																			C|0.995;G|0.005	0.005	strong		0.617	KCNJ4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321447.1	NM_004981	
MYBBP1A	10514	hgsc.bcm.edu	37	17	4451570	4451570	+	Missense_Mutation	SNP	G	G	A	rs142700966	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:4451570G>A	ENST00000254718.4	-	12	1898	c.1592C>T	c.(1591-1593)gCa>gTa	p.A531V	MYBBP1A_ENST00000381556.2_Missense_Mutation_p.A531V			Q9BQG0	MBB1A_HUMAN	MYB binding protein (P160) 1a	531	Interaction with MYB. {ECO:0000250}.				cellular response to glucose starvation (GO:0042149)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleocytoplasmic transport (GO:0006913)|osteoblast differentiation (GO:0001649)|positive regulation of cell cycle arrest (GO:0071158)|regulation of transcription, DNA-templated (GO:0006355)|respiratory electron transport chain (GO:0022904)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|NLS-dependent protein nuclear import complex (GO:0042564)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed DNA polymerase activity (GO:0003887)|poly(A) RNA binding (GO:0044822)|sequence-specific DNA binding (GO:0043565)|transcription factor binding (GO:0008134)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|lung(7)|ovary(3)|prostate(2)|skin(2)|stomach(1)	24						CTGGCCCGGTGCCTGCTTGAA	0.632													G|||	4	0.000798722	0.0	0.0	5008	,	,		17643	0.0		0.004	False		,,,				2504	0.0				p.A531V		Atlas-SNP	.											.	MYBBP1A	69	.	0			c.C1592T						PASS	.						66.0	65.0	65.0					17																	4451570		2203	4300	6503	SO:0001583	missense	10514	exon12			CCCGGTGCCTGCT	AF147709	CCDS11046.1, CCDS42238.1	17p13.3	2008-07-18			ENSG00000132382	ENSG00000132382			7546	protein-coding gene	gene with protein product	"""p53-activated protein-2"""	604885				10644447	Standard	NM_014520		Approved	P160, PAP2, FLJ37886	uc002fxz.4	Q9BQG0	OTTHUMG00000090747	ENST00000254718.4:c.1592C>T	17.37:g.4451570G>A	ENSP00000254718:p.Ala531Val	62.0	0.0	0		65.0	34.0	0.523077	NM_014520	Q86VM3|Q9BW49|Q9P0V5|Q9UF99	Missense_Mutation	SNP	ENST00000254718.4	37	CCDS11046.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	3.338	-0.135261	0.06711	.	.	ENSG00000132382	ENST00000381556;ENST00000254718	T;T	0.50813	0.73;0.73	5.48	-0.24	0.13047	Armadillo-type fold (1);	0.643159	0.16655	N	0.205055	T	0.21186	0.0510	L	0.35414	1.06	0.09310	N	1	B;B	0.09022	0.002;0.002	B;B	0.12156	0.007;0.004	T	0.11155	-1.0599	10	0.22706	T	0.39	-5.7941	4.1307	0.10148	0.4189:0.1728:0.4083:0.0	.	531;531	Q9BQG0;Q9BQG0-2	MBB1A_HUMAN;.	V	531	ENSP00000370968:A531V;ENSP00000254718:A531V	ENSP00000254718:A531V	A	-	2	0	MYBBP1A	4398319	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.430000	0.21428	0.040000	0.15660	0.655000	0.94253	GCA	G|0.998;A|0.002	0.002	strong		0.632	MYBBP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000207488.2	NM_014520	
KRTAP29-1	100533177	hgsc.bcm.edu	37	17	39458772	39458772	+	Missense_Mutation	SNP	G	G	A	rs117847625	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:39458772G>A	ENST00000391353.1	-	1	331	c.332C>T	c.(331-333)tCg>tTg	p.S111L		NM_001257309.1	NP_001244238.1	A8MX34	KR291_HUMAN	keratin associated protein 29-1	111	7 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)											AGTAGATTCCGAGCAGGATGG	0.537													G|||	87	0.0173722	0.0015	0.0418	5008	,	,		24603	0.0		0.0537	False		,,,				2504	0.002				p.S111L		Atlas-SNP	.											.	KRTAP29-1	2	.	0			c.C332T						PASS	.																																			SO:0001583	missense	100533177	exon1			GATTCCGAGCAGG		CCDS62183.1	17q21.2	2013-06-20			ENSG00000212658	ENSG00000212658		"""Keratin associated proteins"""	34211	protein-coding gene	gene with protein product							Standard	NM_001257309		Approved	KAP29.2	uc031rai.1	A8MX34	OTTHUMG00000133662	ENST00000391353.1:c.332C>T	17.37:g.39458772G>A	ENSP00000375148:p.Ser111Leu	61.0	0.0	0		59.0	23.0	0.38983	NM_001257309		Missense_Mutation	SNP	ENST00000391353.1	37		53	0.024267399267399268	1	0.0020325203252032522	14	0.03867403314917127	0	0.0	38	0.05013192612137203	G	0.058	-1.231533	0.01505	.	.	ENSG00000212658	ENST00000391353	.	.	.	5.38	-7.21	0.01490	.	.	.	.	.	T	0.06325	0.0163	.	.	.	.	.	.	.	.	.	.	.	.	T	0.40924	-0.9537	4	0.66056	D	0.02	.	5.1253	0.14880	0.6068:0.1009:0.1906:0.1018	.	.	.	.	L	111	.	ENSP00000375148:S111L	S	-	2	0	KRTAP29-1	36712298	0.000000	0.05858	0.002000	0.10522	0.020000	0.10135	-0.838000	0.04372	-1.373000	0.02134	-1.223000	0.01593	TCG	G|0.969;A|0.031	0.031	strong		0.537	KRTAP29-1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000257828.2		
RRP12	23223	hgsc.bcm.edu	37	10	99118716	99118716	+	Missense_Mutation	SNP	G	G	T	rs143870774	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99118716G>T	ENST00000370992.4	-	32	3803	c.3692C>A	c.(3691-3693)gCt>gAt	p.A1231D	RRP12_ENST00000414986.1_Missense_Mutation_p.A1170D|RRP12_ENST00000536831.1_Missense_Mutation_p.A949D|RRP12_ENST00000315563.6_Missense_Mutation_p.A1131D|RRP12_ENST00000479481.1_5'UTR	NM_015179.3	NP_055994.2	Q5JTH9	RRP12_HUMAN	ribosomal RNA processing 12 homolog (S. cerevisiae)	1231						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)		CTTGTATTCAGCCCCAGGCAT	0.612																																					p.A1231D		Atlas-SNP	.											.	RRP12	97	.	0			c.C3692A						PASS	.						91.0	65.0	74.0					10																	99118716		2203	4300	6503	SO:0001583	missense	23223	exon32			TATTCAGCCCCAG		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.3692C>A	10.37:g.99118716G>T	ENSP00000360031:p.Ala1231Asp	44.0	0.0	0		45.0	27.0	0.6	NM_015179	B4DK00|E9PCK7|Q5JTH8|Q69YK4|Q96E87|Q9BUH3|Q9Y4C7	Missense_Mutation	SNP	ENST00000370992.4	37	CCDS7457.1	.	.	.	.	.	.	.	.	.	.	G	15.09	2.730886	0.48939	.	.	ENSG00000052749	ENST00000370992;ENST00000315563;ENST00000414986;ENST00000536831	T;T;T;T	0.29917	1.55;1.55;1.55;1.55	5.58	5.58	0.84498	.	0.228748	0.45126	D	0.000387	T	0.34454	0.0898	L	0.43923	1.385	0.48762	D	0.999708	P;P;D;P	0.53745	0.937;0.935;0.962;0.937	B;P;P;B	0.51833	0.276;0.681;0.528;0.218	T	0.02498	-1.1150	10	0.12103	T	0.63	-6.7512	13.8164	0.63295	0.0733:0.0:0.9267:0.0	.	1170;1131;949;1231	E9PCK7;Q5JTH9-2;F5H456;Q5JTH9	.;.;.;RRP12_HUMAN	D	1231;1131;1170;949	ENSP00000360031:A1231D;ENSP00000324315:A1131D;ENSP00000414863:A1170D;ENSP00000446184:A949D	ENSP00000324315:A1131D	A	-	2	0	RRP12	99108706	0.963000	0.33076	0.875000	0.34327	0.341000	0.28922	3.020000	0.49643	2.635000	0.89317	0.561000	0.74099	GCT	G|0.998;A|0.002	.	alt		0.612	RRP12-007	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000049699.4	NM_015179	
TDP2	51567	hgsc.bcm.edu	37	6	24667074	24667074	+	Missense_Mutation	SNP	C	C	A	rs61760186	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:24667074C>A	ENST00000378198.4	-	1	187	c.17G>T	c.(16-18)tGc>tTc	p.C6F	TDP2_ENST00000545995.1_Missense_Mutation_p.C36F|ACOT13_ENST00000230048.4_5'Flank|TDP2_ENST00000341060.3_5'Flank|ACOT13_ENST00000537591.1_5'Flank			O95551	TYDP2_HUMAN	tyrosyl-DNA phosphodiesterase 2	6					cell surface receptor signaling pathway (GO:0007166)|double-strand break repair (GO:0006302)|regulation of RNA biosynthetic process (GO:2001141)	cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|PML body (GO:0016605)	5'-tyrosyl-DNA phosphodiesterase activity (GO:0070260)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|nuclease activity (GO:0004518)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)|tyrosyl-RNA phosphodiesterase activity (GO:0036317)			kidney(2)|large_intestine(1)|lung(5)|ovary(1)	9						GCCCTCCAGGCAACTCCCCAA	0.657								Direct reversal of damage					C|||	11	0.00219649	0.003	0.0029	5008	,	,		14407	0.0		0.005	False		,,,				2504	0.0				p.C6F		Atlas-SNP	.											.	TDP2	29	.	0			c.G17T						PASS	.	C	PHE/CYS	11,4395	17.9+/-39.9	0,11,2192	92.0	107.0	102.0		17	0.6	0.0	6	dbSNP_129	102	28,8572	20.4+/-63.3	1,26,4273	yes	missense	TDP2	NM_016614.2	205	1,37,6465	AA,AC,CC		0.3256,0.2497,0.2999	probably-damaging	6/363	24667074	39,12967	2203	4300	6503	SO:0001583	missense	51567	exon1			TCCAGGCAACTCC	AJ269473	CCDS4557.1	6p22.3-p22.1	2010-05-07	2010-05-07	2010-05-07	ENSG00000111802	ENSG00000111802	3.1.4.-		17768	protein-coding gene	gene with protein product		605764	"""TRAF and TNF receptor associated protein"""	TTRAP		11478795	Standard	NM_016614		Approved		uc003nej.3	O95551	OTTHUMG00000014360	ENST00000378198.4:c.17G>T	6.37:g.24667074C>A	ENSP00000367440:p.Cys6Phe	43.0	0.0	0		48.0	29.0	0.604167	NM_016614	B4DKL8|B4DQ95|Q2TBE2|Q5JYM0|Q7Z6U5|Q9NUK5|Q9NYY9	Missense_Mutation	SNP	ENST00000378198.4	37	CCDS4557.1	9	0.004120879120879121	3	0.006097560975609756	2	0.0055248618784530384	0	0.0	4	0.005277044854881266	C	11.65	1.701925	0.30232	0.002497	0.003256	ENSG00000111802	ENST00000378198;ENST00000545995;ENST00000545780	T;T	0.25085	1.93;1.82	4.51	0.603	0.17541	.	2.748860	0.00807	N	0.001479	T	0.05547	0.0146	N	0.22421	0.69	0.09310	N	1	B;B	0.28783	0.222;0.122	B;B	0.25759	0.063;0.025	T	0.22906	-1.0203	10	0.40728	T	0.16	-12.8014	3.1399	0.06452	0.1875:0.4951:0.0:0.3174	rs61760186	36;6	O95551-2;O95551	.;TYDP2_HUMAN	F	6;36;6	ENSP00000367440:C6F;ENSP00000437637:C36F	ENSP00000367440:C6F	C	-	2	0	TDP2	24775053	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.717000	0.04986	0.218000	0.20820	-0.127000	0.14921	TGC	C|0.997;A|0.003	0.003	strong		0.657	TDP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000040012.1		
CYP2A6	1548	hgsc.bcm.edu	37	19	41351321	41351321	+	Missense_Mutation	SNP	C	C	T	rs200267449		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	220.0	0.0	0		306.0	30.0	0.0980392	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	
PCDHB2	56133	hgsc.bcm.edu	37	5	140475665	140475665	+	Missense_Mutation	SNP	C	C	A	rs116177548	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140475665C>A	ENST00000194155.4	+	1	1439	c.1291C>A	c.(1291-1293)Ccc>Acc	p.P431T		NM_018936.2	NP_061759.1	Q9Y5E7	PCDB2_HUMAN	protocadherin beta 2	431	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(22)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(7)|upper_aerodigestive_tract(3)|urinary_tract(2)	71			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CTTCGGGACACCCAGGCTGAA	0.557													C|||	48	0.00958466	0.0	0.0043	5008	,	,		19536	0.001		0.003	False		,,,				2504	0.0419				p.P431T		Atlas-SNP	.											PCDHB2,NS,carcinoma,-2,1	PCDHB2	163	1	0			c.C1291A						PASS	.	C	THR/PRO	2,4404	4.2+/-10.8	0,2,2201	138.0	127.0	131.0		1291	5.1	0.9	5	dbSNP_132	131	48,8552	31.2+/-83.2	0,48,4252	yes	missense	PCDHB2	NM_018936.2	38	0,50,6453	AA,AC,CC		0.5581,0.0454,0.3844	probably-damaging	431/799	140475665	50,12956	2203	4300	6503	SO:0001583	missense	56133	exon1			GGGACACCCAGGC	AF152495	CCDS4244.1	5q31	2010-01-26			ENSG00000112852	ENSG00000112852		"""Cadherins / Protocadherins : Clustered"""	8687	other	protocadherin		606328				10380929	Standard	NM_018936		Approved	PCDH-BETA2	uc003lil.3	Q9Y5E7	OTTHUMG00000129606	ENST00000194155.4:c.1291C>A	5.37:g.140475665C>A	ENSP00000194155:p.Pro431Thr	153.0	0.0	0		239.0	113.0	0.472803	NM_018936	Q4KMU1	Missense_Mutation	SNP	ENST00000194155.4	37	CCDS4244.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	C	13.48	2.249833	0.39797	4.54E-4	0.005581	ENSG00000112852	ENST00000194155	T	0.56275	0.47	5.11	5.11	0.69529	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.77631	0.4159	H	0.98133	4.155	0.45284	D	0.998288	D	0.89917	1.0	D	0.91635	0.999	D	0.86973	0.2099	9	0.87932	D	0	.	14.5945	0.68395	0.1465:0.8535:0.0:0.0	.	431	Q9Y5E7	PCDB2_HUMAN	T	431	ENSP00000194155:P431T	ENSP00000194155:P431T	P	+	1	0	PCDHB2	140455849	0.889000	0.30405	0.880000	0.34516	0.050000	0.14768	2.396000	0.44468	2.542000	0.85734	0.650000	0.86243	CCC	C|0.996;A|0.004	0.004	strong		0.557	PCDHB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251801.2	NM_018936	
HAPLN3	145864	hgsc.bcm.edu	37	15	89422353	89422353	+	Missense_Mutation	SNP	G	G	A	rs569695538	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:89422353G>A	ENST00000359595.3	-	4	855	c.641C>T	c.(640-642)gCg>gTg	p.A214V	HAPLN3_ENST00000562889.1_Missense_Mutation_p.A276V	NM_178232.2	NP_839946.1	Q96S86	HPLN3_HUMAN	hyaluronan and proteoglycan link protein 3	214	Link 1. {ECO:0000255|PROSITE- ProRule:PRU00323, ECO:0000305}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	hyaluronic acid binding (GO:0005540)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)	17	Lung NSC(78;0.0392)|all_lung(78;0.077)				Hyaluronan(DB08818)	CAGCCAGCCCGCGTTGCACCA	0.701											OREG0023445	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	G|||	2	0.000399361	0.0	0.0	5008	,	,		15072	0.001		0.0	False		,,,				2504	0.001				p.A214V		Atlas-SNP	.											.	HAPLN3	43	.	0			c.C641T						PASS	.						29.0	33.0	32.0					15																	89422353		2199	4299	6498	SO:0001583	missense	145864	exon4			CAGCCCGCGTTGC	AY262759	CCDS10346.1	15q26.1	2013-01-11			ENSG00000140511	ENSG00000140511		"""Immunoglobulin superfamily / V-set domain containing"""	21446	protein-coding gene	gene with protein product			"""extracellular link domain containing, 1"""	EXLD1		12663660	Standard	NM_178232		Approved	HsT19883	uc002bnc.3	Q96S86	OTTHUMG00000148680	ENST00000359595.3:c.641C>T	15.37:g.89422353G>A	ENSP00000352606:p.Ala214Val	23.0	0.0	0	1267	54.0	26.0	0.481481	NM_178232	A8K7P0	Missense_Mutation	SNP	ENST00000359595.3	37	CCDS10346.1	.	.	.	.	.	.	.	.	.	.	G	14.09	2.432313	0.43122	.	.	ENSG00000140511	ENST00000359595	T	0.13778	2.56	4.36	3.44	0.39384	C-type lectin fold (1);Link (5);C-type lectin-like (1);	0.054620	0.64402	D	0.000001	T	0.33000	0.0848	M	0.79123	2.44	0.54753	D	0.999987	D;D	0.65815	0.995;0.995	P;P	0.62184	0.899;0.899	T	0.09530	-1.0670	10	0.72032	D	0.01	-15.2009	11.1418	0.48406	0.0927:0.0:0.9073:0.0	.	214;214	A8K7T8;Q96S86	.;HPLN3_HUMAN	V	214	ENSP00000352606:A214V	ENSP00000352606:A214V	A	-	2	0	HAPLN3	87223357	1.000000	0.71417	0.066000	0.19879	0.986000	0.74619	9.207000	0.95064	0.940000	0.37473	0.655000	0.94253	GCG	.	.	none		0.701	HAPLN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309070.1	NM_178232	
RIC8A	60626	hgsc.bcm.edu	37	11	205398	205398	+	5'Flank	SNP	G	G	A	rs190584141	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:205398G>A	ENST00000526104.1	+	0	0				BET1L_ENST00000410108.1_Intron|BET1L_ENST00000382762.3_Silent_p.S80S|BET1L_ENST00000486280.1_Silent_p.S57S|BET1L_ENST00000325147.9_3'UTR|RP11-304M2.5_ENST00000526963.1_RNA|BET1L_ENST00000332865.6_3'UTR|BET1L_ENST00000529614.2_Silent_p.S61S			Q9NPQ8	RIC8A_HUMAN	RIC8 guanine nucleotide exchange factor A						adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|basement membrane organization (GO:0071711)|cell migration involved in gastrulation (GO:0042074)|cell-cell adhesion involved in gastrulation (GO:0070586)|in utero embryonic development (GO:0001701)|vasculature development (GO:0001944)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|pancreas(1)|prostate(1)|skin(1)	13		all_cancers(49;9.23e-07)|all_epithelial(84;0.000315)|Breast(177;0.00122)|Ovarian(85;0.0202)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		all cancers(45;4.45e-27)|Epithelial(43;2.94e-26)|OV - Ovarian serous cystadenocarcinoma(40;5.86e-21)|BRCA - Breast invasive adenocarcinoma(625;3.57e-05)|Lung(200;0.105)|LUSC - Lung squamous cell carcinoma(625;0.122)		TGTCTTGTCCGGACCTTGCCA	0.537													G|||	4	0.000798722	0.0	0.0	5008	,	,		21271	0.0		0.004	False		,,,				2504	0.0				p.S80S		Atlas-SNP	.											.	BET1L	7	.	0			c.C240T						PASS	.	G	,	5,4401	9.9+/-24.2	0,5,2198	84.0	88.0	87.0		240,	-4.5	1.0	11		87	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,utr-3	BET1L	NM_001098787.1,NM_016526.4	,	0,20,6483	AA,AG,GG		0.1744,0.1135,0.1538	,	80/112,	205398	20,12986	2203	4300	6503	SO:0001631	upstream_gene_variant	51272	exon4			TTGTCCGGACCTT	AK022870	CCDS7690.1, CCDS65982.1	11p15.5	2013-08-05	2013-08-05		ENSG00000177963	ENSG00000177963			29550	protein-coding gene	gene with protein product		609146	"""resistance to inhibitors of cholinesterase 8 homolog A (C. elegans)"""			10985349, 11230166	Standard	XM_005253052		Approved	synembryn, synembryn-A	uc001lof.3	Q9NPQ8	OTTHUMG00000119069		11.37:g.205398G>A	Exception_encountered	118.0	0.0	0		161.0	90.0	0.559006	NM_001098787	Q0P508|Q2T9J1|Q7Z352|Q96EZ1|Q96SZ2|Q9H064|Q9H5H3|Q9H9E7	Silent	SNP	ENST00000526104.1	37																																																																																				G|0.998;A|0.002	0.002	strong		0.537	RIC8A-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000384761.1	NM_021932	
EGFR	1956	hgsc.bcm.edu	37	7	55229255	55229255	+	Missense_Mutation	SNP	G	G	A	rs2227983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:55229255G>A	ENST00000275493.2	+	13	1739	c.1562G>A	c.(1561-1563)aGg>aAg	p.R521K	EGFR_ENST00000454757.2_Missense_Mutation_p.R468K|EGFR_ENST00000455089.1_Missense_Mutation_p.R476K|EGFR_ENST00000442591.1_Missense_Mutation_p.R521K|EGFR_ENST00000342916.3_Missense_Mutation_p.R521K|EGFR_ENST00000344576.2_Missense_Mutation_p.R521K	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	521			R -> K (in dbSNP:rs2227983). {ECO:0000269|PubMed:17344846, ECO:0000269|Ref.7}.		activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)			NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	CCGGAGCCCAGGGACTGCGTC	0.617		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)			G|||	1463	0.292133	0.0643	0.33	5008	,	,		17432	0.5238		0.2763	False		,,,				2504	0.3507				p.R521K		Atlas-SNP	.	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""		"""E, O"""	.	EGFR	20426	.	0			c.G1562A	GRCh37	CM942312	EGFR	M	rs2227983	PASS	.	G	LYS/ARG,LYS/ARG,LYS/ARG	391,4015	196.0+/-220.5	12,367,1824	111.0	114.0	113.0		1562,1562,1562	-5.8	0.0	7	dbSNP_98	113	2245,6355	380.6+/-339.7	317,1611,2372	yes	missense,missense,missense	EGFR	NM_005228.3,NM_201282.1,NM_201284.1	26,26,26	329,1978,4196	AA,AG,GG		26.1047,8.8743,20.2676	benign,benign,benign	521/1211,521/629,521/706	55229255	2636,10370	2203	4300	6503	SO:0001583	missense	1956	exon13	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	AGCCCAGGGACTG		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.1562G>A	7.37:g.55229255G>A	ENSP00000275493:p.Arg521Lys	69.0	0.0	0		65.0	65.0	1	NM_005228	O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	Missense_Mutation	SNP	ENST00000275493.2	37	CCDS5514.1	652	0.29853479853479853	29	0.05894308943089431	108	0.2983425414364641	302	0.527972027972028	213	0.28100263852242746	G	1.353	-0.590998	0.03799	0.088743	0.261047	ENSG00000146648	ENST00000455089;ENST00000342916;ENST00000395504;ENST00000344576;ENST00000275493;ENST00000442591;ENST00000454757;ENST00000533450	T;T;T;T;T;T	0.28069	1.63;1.63;1.63;1.63;1.63;1.63	6.07	-5.79	0.02354	Growth factor, receptor (1);	1.067450	0.06989	N	0.821201	T	0.00012	0.0000	N	0.16368	0.405	0.80722	P	0.0	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.48043	-0.9069	9	0.10377	T	0.69	.	2.4933	0.04615	0.5094:0.1722:0.17:0.1484	rs2227983;rs3752650;rs11543848;rs12234746;rs17336807;rs11543848	476;521;521;521	Q504U8;P00533;P00533-3;P00533-4	.;EGFR_HUMAN;.;.	K	476;521;391;521;521;521;468;315	ENSP00000415559:R476K;ENSP00000342376:R521K;ENSP00000345973:R521K;ENSP00000275493:R521K;ENSP00000410031:R521K;ENSP00000395243:R468K	ENSP00000275493:R521K	R	+	2	0	EGFR	55196749	0.000000	0.05858	0.000000	0.03702	0.265000	0.26407	-0.793000	0.04589	-1.106000	0.03008	-0.165000	0.13383	AGG	A|0.243;C|0.000;G|0.757;T|0.000	0.243	strong		0.617	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
SAPCD1	401251	hgsc.bcm.edu	37	6	31731301	31731301	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:31731301G>A	ENST00000425424.1	+	2	283	c.224G>A	c.(223-225)cGa>cAa	p.R75Q	MSH5-SAPCD1_ENST00000493662.2_3'UTR|SAPCD1-AS1_ENST00000419679.1_RNA|VWA7_ENST00000467576.1_5'Flank|SAPCD1_ENST00000415669.2_Missense_Mutation_p.R75Q|MSH5_ENST00000534153.4_3'UTR			Q5SSQ6	SAPC1_HUMAN	suppressor APC domain containing 1	75																	GAGGCACAGCGACAGCAGCTG	0.607																																					p.R75Q		Atlas-SNP	.											.	.	.	.	0			c.G224A						PASS	.						76.0	78.0	77.0					6																	31731301		1509	2708	4217	SO:0001583	missense	401251	exon2			CACAGCGACAGCA		CCDS34411.1	6p21	2011-12-13	2011-12-13	2011-12-13	ENSG00000228727	ENSG00000228727			13938	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 26"""	C6orf26			Standard	NM_001039651		Approved	NG23		Q5SSQ6	OTTHUMG00000031131	ENST00000425424.1:c.224G>A	6.37:g.31731301G>A	ENSP00000413372:p.Arg75Gln	54.0	0.0	0		76.0	38.0	0.5	NM_001039651	A2ABF2|A2ABS9|Q9Y335	Missense_Mutation	SNP	ENST00000425424.1	37		.	.	.	.	.	.	.	.	.	.	G	1.914	-0.450071	0.04572	.	.	ENSG00000228727	ENST00000433778;ENST00000415669;ENST00000425424	T;T	0.79845	-1.31;-1.31	5.01	-3.43	0.04810	.	.	.	.	.	T	0.44519	0.1297	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.04013	0.001	T	0.36480	-0.9746	8	0.18710	T	0.47	-5.3272	12.7855	0.57502	0.2885:0.0:0.7115:0.0	.	75	Q5SSQ6-2	.	Q	75	ENSP00000411948:R75Q;ENSP00000413372:R75Q	ENSP00000411948:R75Q	R	+	2	0	C6orf26	31839280	0.000000	0.05858	0.330000	0.25442	0.801000	0.45260	-0.272000	0.08560	-0.674000	0.05253	-1.004000	0.02495	CGA	.	.	none		0.607	SAPCD1-203	KNOWN	basic	protein_coding	protein_coding		NM_001039651	
WBP4	11193	hgsc.bcm.edu	37	13	41639377	41639377	+	Silent	SNP	C	C	T	rs61740513	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:41639377C>T	ENST00000379487.3	+	4	616	c.216C>T	c.(214-216)gcC>gcT	p.A72A	WBP4_ENST00000542082.1_Silent_p.A51A	NM_007187.3	NP_009118.1	O75554	WBP4_HUMAN	WW domain binding protein 4	72					mRNA cis splicing, via spliceosome (GO:0045292)	nuclear speck (GO:0016607)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|spliceosomal complex (GO:0005681)	nucleic acid binding (GO:0003676)|proline-rich region binding (GO:0070064)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(1)|liver(2)|lung(2)|prostate(1)|skin(1)	12		Lung NSC(96;3.55e-06)|Breast(139;0.00123)|Prostate(109;0.0181)|Lung SC(185;0.0262)|Hepatocellular(98;0.114)		all cancers(112;3.11e-09)|Epithelial(112;3.37e-06)|OV - Ovarian serous cystadenocarcinoma(117;8.3e-05)|GBM - Glioblastoma multiforme(144;0.00102)|BRCA - Breast invasive adenocarcinoma(63;0.07)		AGGCAGCTGCCCTGAAAGCAT	0.368													C|||	126	0.0251597	0.0908	0.0072	5008	,	,		14418	0.0		0.001	False		,,,				2504	0.0				p.A72A		Atlas-SNP	.											.	WBP4	40	.	0			c.C216T						PASS	.	C		411,3995	201.5+/-224.5	14,383,1806	64.0	69.0	67.0		216	2.8	1.0	13	dbSNP_129	67	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	WBP4	NM_007187.3		14,385,6104	TT,TC,CC		0.0233,9.3282,3.1755		72/377	41639377	413,12593	2203	4300	6503	SO:0001819	synonymous_variant	11193	exon4			AGCTGCCCTGAAA	AF071185	CCDS9375.1	13q13.3	2012-10-17	2012-10-17		ENSG00000120688	ENSG00000120688			12739	protein-coding gene	gene with protein product	"""formin binding protein 21"""	604981				9724750	Standard	NM_007187		Approved	FBP21, MGC117310	uc001uxt.3	O75554	OTTHUMG00000016784	ENST00000379487.3:c.216C>T	13.37:g.41639377C>T		54.0	0.0	0		71.0	39.0	0.549296	NM_007187	B7Z4M2|Q32P29	Silent	SNP	ENST00000379487.3	37	CCDS9375.1																																																																																			C|0.967;T|0.033	0.033	strong		0.368	WBP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044655.2	NM_007187	
OBSCN	84033	hgsc.bcm.edu	37	1	228557755	228557755	+	Missense_Mutation	SNP	G	G	A	rs145597580	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:228557755G>A	ENST00000422127.1	+	91	20124	c.20080G>A	c.(20080-20082)Gcc>Acc	p.A6694T	OBSCN_ENST00000366707.4_Missense_Mutation_p.A4328T|OBSCN_ENST00000570156.2_Missense_Mutation_p.A7651T	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	6694	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)				CAGCGAAGACGCCAAAGACTT	0.667													G|||	12	0.00239617	0.0	0.0014	5008	,	,		19459	0.0		0.004	False		,,,				2504	0.0072				p.A7651T		Atlas-SNP	.											.	OBSCN	2142	.	0			c.G22951A						PASS	.	G	THR/ALA	0,3934		0,0,1967	59.0	62.0	61.0		20080	4.7	0.8	1	dbSNP_134	61	10,8296		0,10,4143	yes	missense	OBSCN	NM_001098623.1	58	0,10,6110	AA,AG,GG		0.1204,0.0,0.0817	probably-damaging	6694/7969	228557755	10,12230	1967	4153	6120	SO:0001583	missense	84033	exon102			GAAGACGCCAAAG	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.20080G>A	1.37:g.228557755G>A	ENSP00000409493:p.Ala6694Thr	80.0	0.0	0		74.0	45.0	0.608108	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	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	G|G	16.97|16.97	3.269577|3.269577	0.59540|0.59540	0.0|0.0	0.001204|0.001204	ENSG00000154358|ENSG00000154358	ENST00000422127;ENST00000366707|ENST00000441106	T;T|.	0.68025|.	-0.3;-0.3|.	4.72|4.72	4.72|4.72	0.59763|0.59763	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	0.73281|0.73281	0.3567|0.3567	M|M	0.85710|0.85710	2.77|2.77	0.80722|0.80722	D|D	1|1	D|.	0.76494|.	0.999|.	D|.	0.64410|.	0.925|.	T|T	0.79752|0.79752	-0.1671|-0.1671	9|5	0.87932|.	D|.	0|.	.|.	16.025|16.025	0.80536|0.80536	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	6694|.	Q5VST9|.	OBSCN_HUMAN|.	T|H	6694;4328|1310	ENSP00000409493:A6694T;ENSP00000355668:A4328T|.	ENSP00000355668:A4328T|.	A|R	+|+	1|2	0|0	OBSCN|OBSCN	226624378|226624378	1.000000|1.000000	0.71417|0.71417	0.819000|0.819000	0.32651|0.32651	0.185000|0.185000	0.23345|0.23345	6.988000|6.988000	0.76212|0.76212	2.459000|2.459000	0.83118|0.83118	0.455000|0.455000	0.32223|0.32223	GCC|CGC	G|0.998;A|0.002	0.002	strong		0.667	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ABCA13	154664	hgsc.bcm.edu	37	7	48312084	48312084	+	Missense_Mutation	SNP	G	G	C	rs78575608	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:48312084G>C	ENST00000435803.1	+	17	2845	c.2821G>C	c.(2821-2823)Gtt>Ctt	p.V941L		NM_152701.3	NP_689914.2	Q86UQ4	ABCAD_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 13	941					transport (GO:0006810)	integral component of membrane (GO:0016021)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)			breast(13)|central_nervous_system(8)|endometrium(25)|haematopoietic_and_lymphoid_tissue(4)|kidney(20)|large_intestine(51)|lung(100)|ovary(5)|pancreas(2)|prostate(22)|skin(10)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(4)	270						AAAACAAGAAGTTGATAAAAT	0.368													G|||	126	0.0251597	0.003	0.0202	5008	,	,		17420	0.0		0.0557	False		,,,				2504	0.0532				p.V941L		Atlas-SNP	.											.	ABCA13	1192	.	0			c.G2821C						PASS	.	G	LEU/VAL	45,3611		0,45,1783	58.0	56.0	56.0		2821	-6.4	0.0	7	dbSNP_131	56	532,7648		14,504,3572	yes	missense	ABCA13	NM_152701.3	32	14,549,5355	CC,CG,GG		6.5037,1.2309,4.875	benign	941/5059	48312084	577,11259	1828	4090	5918	SO:0001583	missense	154664	exon17			CAAGAAGTTGATA	AY204751	CCDS47584.1	7p12.3	2012-03-14			ENSG00000179869	ENSG00000179869		"""ATP binding cassette transporters / subfamily A"""	14638	protein-coding gene	gene with protein product		607807				12697998	Standard	NM_152701		Approved	FLJ33876, FLJ33951	uc003toq.2	Q86UQ4	OTTHUMG00000155840	ENST00000435803.1:c.2821G>C	7.37:g.48312084G>C	ENSP00000411096:p.Val941Leu	214.0	0.0	0		200.0	85.0	0.425	NM_152701	K9LC76|K9LC79|K9LCX7|K9LDK8|K9LDY4|Q6ZTT7|Q86WI2|Q8N248	Missense_Mutation	SNP	ENST00000435803.1	37	CCDS47584.1	47	0.02152014652014652	1	0.0020325203252032522	9	0.024861878453038673	0	0.0	37	0.048812664907651716	G	4.662	0.123148	0.08931	0.012309	0.065037	ENSG00000179869	ENST00000435803	D	0.82984	-1.67	5.81	-6.43	0.01926	.	1.110050	0.06993	N	0.821921	T	0.09202	0.0227	N	0.16368	0.405	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.45775	-0.9238	10	0.05525	T	0.97	.	1.2609	0.02001	0.3788:0.2867:0.186:0.1485	.	941	Q86UQ4	ABCAD_HUMAN	L	941	ENSP00000411096:V941L	ENSP00000411096:V941L	V	+	1	0	ABCA13	48282630	0.000000	0.05858	0.000000	0.03702	0.986000	0.74619	-1.314000	0.02715	-0.919000	0.03803	0.655000	0.94253	GTT	G|0.974;C|0.026	0.026	strong		0.368	ABCA13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341964.2	NM_152701	
HRCT1	646962	hgsc.bcm.edu	37	9	35906583	35906583	+	Missense_Mutation	SNP	T	T	A	rs112821450|rs143611048|rs79156963	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35906583T>A	ENST00000354323.2	+	1	395	c.299T>A	c.(298-300)cTc>cAc	p.L100H	LINC00961_ENST00000443779.1_lincRNA	NM_001039792.1	NP_001034881.1	Q6UXD1	HRCT1_HUMAN	histidine rich carboxyl terminus 1	100	His-rich.					integral component of membrane (GO:0016021)		p.L100H(1)		NS(1)|haematopoietic_and_lymphoid_tissue(1)|lung(1)|prostate(1)	4						cctcaccacctccaccaccac	0.667																																					p.L100H		Atlas-SNP	.											HRCT1,NS,malignant_melanoma,0,1	HRCT1	14	1	1	Substitution - Missense(1)	NS(1)	c.T299A						scavenged	.						13.0	10.0	11.0					9																	35906583		1961	3863	5824	SO:0001583	missense	646962	exon1			ACCACCTCCACCA		CCDS35012.1	9p13.3	2008-09-30			ENSG00000196196	ENSG00000196196			33872	protein-coding gene	gene with protein product						12975309	Standard	NM_001039792		Approved	LGLL338, PRO537, UNQ338	uc003zyr.1	Q6UXD1	OTTHUMG00000154146	ENST00000354323.2:c.299T>A	9.37:g.35906583T>A	ENSP00000346283:p.Leu100His	20.0	0.0	0		34.0	3.0	0.0882353	NM_001039792	B7ZBJ1	Missense_Mutation	SNP	ENST00000354323.2	37	CCDS35012.1	.	.	.	.	.	.	.	.	.	.	T	9.866	1.197686	0.22037	.	.	ENSG00000196196	ENST00000354323	.	.	.	3.43	-0.386	0.12466	.	.	.	.	.	T	0.09730	0.0239	N	0.01874	-0.695	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.25117	-1.0141	8	0.87932	D	0	-5.7925	0.5802	0.00711	0.4571:0.1878:0.1238:0.2312	.	100	Q6UXD1	HRCT1_HUMAN	H	100	.	ENSP00000346283:L100H	L	+	2	0	HRCT1	35896583	0.000000	0.05858	0.107000	0.21349	0.466000	0.32739	-0.309000	0.08145	-0.078000	0.12730	-0.376000	0.06991	CTC	T|0.500;A|0.500	0.500	weak		0.667	HRCT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334099.1	NM_001039792	
RNF40	9810	hgsc.bcm.edu	37	16	30780861	30780861	+	Silent	SNP	C	C	T	rs142343572	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:30780861C>T	ENST00000324685.6	+	17	2961	c.2526C>T	c.(2524-2526)ctC>ctT	p.L842L	RNF40_ENST00000567365.1_3'UTR|RNF40_ENST00000402121.3_Silent_p.L534L|RNF40_ENST00000357890.5_Silent_p.L742L|RNF40_ENST00000563683.1_Silent_p.L802L	NM_001207033.1|NM_014771.3	NP_001193962.1|NP_055586	O75150	BRE1B_HUMAN	ring finger protein 40, E3 ubiquitin protein ligase	842					histone H2B ubiquitination (GO:0033523)|histone monoubiquitination (GO:0010390)|ubiquitin-dependent protein catabolic process (GO:0006511)	HULC complex (GO:0033503)|membrane (GO:0016020)|neuron projection (GO:0043005)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ligase activity (GO:0016874)|protein homodimerization activity (GO:0042803)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(6)|lung(10)|prostate(2)	30			Colorectal(24;0.198)			AGGGCAGCCTCGGGGGTGTGG	0.647													c|||	2	0.000399361	0.0	0.0014	5008	,	,		19891	0.0		0.001	False		,,,				2504	0.0				p.L842L		Atlas-SNP	.											.	RNF40	83	.	0			c.C2526T						PASS	.		,,	2,4392	4.2+/-10.8	0,2,2195	28.0	26.0	27.0		2526,2226,2526	-12.1	0.0	16	dbSNP_134	27	7,8591	4.3+/-15.6	0,7,4292	no	coding-synonymous,coding-synonymous,coding-synonymous	RNF40	NM_001207033.1,NM_001207034.1,NM_014771.3	,,	0,9,6487	TT,TC,CC		0.0814,0.0455,0.0693	,,	842/1001,742/902,842/1002	30780861	9,12983	2197	4299	6496	SO:0001819	synonymous_variant	9810	exon17			CAGCCTCGGGGGT	AB014561	CCDS10691.1, CCDS55994.1	16p11.2-p11.1	2012-02-23	2012-02-23		ENSG00000103549	ENSG00000103549		"""RING-type (C3HC4) zinc fingers"""	16867	protein-coding gene	gene with protein product	"""BRE1 E3 ubiquitin ligase homolog B (S. cerevisiae)"""	607700	"""ring finger protein 40"""			9734811, 10944455, 12121982	Standard	NM_014771		Approved	KIAA0661, RBP95, BRE1B, STARING	uc002dzq.3	O75150	OTTHUMG00000132394	ENST00000324685.6:c.2526C>T	16.37:g.30780861C>T		71.0	0.0	0		58.0	25.0	0.431034	NM_014771	Q6AHZ6|Q6N005|Q7L3T6|Q8N615|Q96T18|Q9BSV9|Q9HC82	Silent	SNP	ENST00000324685.6	37	CCDS10691.1																																																																																			C|0.997;T|0.003	0.003	strong		0.647	RNF40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255524.2	NM_014771	
APOBEC3G	60489	hgsc.bcm.edu	37	22	39482557	39482557	+	Missense_Mutation	SNP	A	A	G	rs139265278		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:39482557A>G	ENST00000407997.3	+	6	1366	c.1009A>G	c.(1009-1011)Ata>Gta	p.I337V	APOBEC3G_ENST00000452957.2_Missense_Mutation_p.I337V	NM_021822.3	NP_068594.1	Q9HC16	ABC3G_HUMAN	apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 3G	337					base conversion or substitution editing (GO:0016553)|cytidine deamination (GO:0009972)|defense response to virus (GO:0051607)|DNA cytosine deamination (GO:0070383)|innate immune response (GO:0045087)|negative regulation of single stranded viral RNA replication via double stranded DNA intermediate (GO:0045869)|negative regulation of transposition (GO:0010529)|negative regulation of viral genome replication (GO:0045071)|negative regulation of viral process (GO:0048525)|positive regulation of defense response to virus by host (GO:0002230)|viral process (GO:0016032)	apolipoprotein B mRNA editing enzyme complex (GO:0030895)|cytoplasm (GO:0005737)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|ribonucleoprotein complex (GO:0030529)	cytidine deaminase activity (GO:0004126)|deoxycytidine deaminase activity (GO:0047844)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)|zinc ion binding (GO:0008270)			central_nervous_system(1)|large_intestine(4)|lung(5)|skin(1)|stomach(1)	12	Melanoma(58;0.04)					CAAAATTTCAATAATGACATA	0.572																																					p.I337V		Atlas-SNP	.											.	APOBEC3G	69	.	0			c.A1009G						PASS	.		VAL/ILE	0,4406		0,0,2203	85.0	95.0	91.0		1009	1.5	0.0	22	dbSNP_134	91	2,8598		0,2,4298	no	missense	APOBEC3G	NM_021822.3	29	0,2,6501	GG,GA,AA		0.0233,0.0,0.0154	benign	337/385	39482557	2,13004	2203	4300	6503	SO:0001583	missense	60489	exon6			ATTTCAATAATGA	AF182420	CCDS13984.1	22q13.1-q13.2	2008-05-15			ENSG00000239713	ENSG00000239713		"""Apolipoprotein B mRNA editing enzymes"""	17357	protein-coding gene	gene with protein product		607113				11863358	Standard	NM_021822		Approved	CEM15, MDS019, dJ494G10.1, FLJ12740, bK150C2.7		Q9HC16	OTTHUMG00000151081	ENST00000407997.3:c.1009A>G	22.37:g.39482557A>G	ENSP00000385057:p.Ile337Val	96.0	0.0	0		72.0	37.0	0.513889	NM_021822	B2RDR9|Q45F02|Q5TF77|Q7Z2N1|Q7Z2N4|Q9H9H8	Missense_Mutation	SNP	ENST00000407997.3	37	CCDS13984.1	.	.	.	.	.	.	.	.	.	.	.	3.799	-0.042054	0.07452	0.0	2.33E-4	ENSG00000239713	ENST00000452957;ENST00000407997	T;T	0.64438	-0.1;-0.1	1.51	1.51	0.23008	APOBEC-like, C-terminal (1);Cytidine deaminase-like (1);	.	.	.	.	T	0.43765	0.1262	L	0.38175	1.15	0.09310	N	1	B	0.02656	0.0	B	0.08055	0.003	T	0.19778	-1.0295	9	0.18276	T	0.48	.	3.2677	0.06870	0.7742:0.0:0.2258:0.0	.	337	Q9HC16	ABC3G_HUMAN	V	337	ENSP00000413376:I337V;ENSP00000385057:I337V	ENSP00000385057:I337V	I	+	1	0	APOBEC3G	37812503	0.070000	0.21116	0.024000	0.17045	0.002000	0.02628	0.249000	0.18216	0.946000	0.37632	0.373000	0.22412	ATA	A|1.000;G|0.000	0.000	weak		0.572	APOBEC3G-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321219.1	NM_021822	
ZNF469	84627	hgsc.bcm.edu	37	16	88504204	88504204	+	Missense_Mutation	SNP	G	G	C	rs56236932	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:88504204G>C	ENST00000437464.1	+	2	10242	c.10242G>C	c.(10240-10242)agG>agC	p.R3414S	ZNF469_ENST00000565624.1_Missense_Mutation_p.R3442S	NM_001127464.1	NP_001120936.1	Q96JG9	ZN469_HUMAN	zinc finger protein 469	3414					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(6)|kidney(3)|large_intestine(1)|skin(6)	20						AGCACCTCAGGGGGGGGCGGC	0.667													G|||	20	0.00399361	0.0008	0.0058	5008	,	,		13737	0.0		0.0139	False		,,,				2504	0.001				p.R3414S		Atlas-SNP	.											ZNF469,NS,carcinoma,+1,1	ZNF469	121	1	0			c.G10242C						PASS	.	G	SER/ARG	3,1349		0,3,673	4.0	5.0	5.0		10242	-1.3	0.0	16	dbSNP_129	5	38,3064		0,38,1513	yes	missense	ZNF469	NM_001127464.1	110	0,41,2186	CC,CG,GG		1.225,0.2219,0.9205	possibly-damaging	3414/3926	88504204	41,4413	676	1551	2227	SO:0001583	missense	84627	exon2			CCTCAGGGGGGGG	AB058761	CCDS45544.1	16q24	2010-08-04				ENSG00000225614		"""Zinc fingers, C2H2-type"""	23216	protein-coding gene	gene with protein product		612078				11347906	Standard	NM_001127464		Approved	KIAA1858	uc002fku.2	Q96JG9		ENST00000437464.1:c.10242G>C	16.37:g.88504204G>C	ENSP00000402343:p.Arg3414Ser	22.0	0.0	0		17.0	9.0	0.529412	NM_001127464		Missense_Mutation	SNP	ENST00000437464.1	37	CCDS45544.1	12	0.005494505494505495	1	0.0020325203252032522	3	0.008287292817679558	0	0.0	8	0.010554089709762533	G	10.54	1.378878	0.24944	0.002219	0.01225	ENSG00000225614	ENST00000437464	T	0.06218	3.33	5.14	-1.31	0.09230	Zinc finger, C2H2 (1);	.	.	.	.	T	0.01835	0.0058	N	0.24115	0.695	0.09310	N	1	B	0.30824	0.296	B	0.26202	0.067	T	0.41142	-0.9525	9	0.06365	T	0.9	.	1.7855	0.03040	0.2306:0.1127:0.4274:0.2292	rs56236932	3414	Q96JG9	ZN469_HUMAN	S	3414	ENSP00000402343:R3414S	ENSP00000402343:R3414S	R	+	3	2	ZNF469	87031705	0.000000	0.05858	0.003000	0.11579	0.007000	0.05969	-1.172000	0.03112	-0.065000	0.13021	0.561000	0.74099	AGG	G|0.994;C|0.006	0.006	strong		0.667	ZNF469-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NG_012236	
ITGA3	3675	hgsc.bcm.edu	37	17	48151296	48151296	+	Silent	SNP	T	T	C	rs117783166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:48151296T>C	ENST00000320031.8	+	8	1503	c.1173T>C	c.(1171-1173)gcT>gcC	p.A391A	ITGA3_ENST00000544892.1_Silent_p.A166A|ITGA3_ENST00000007722.7_Silent_p.A391A	NM_002204.2|NM_005501.2	NP_002195.1|NP_005492.1	P26006	ITA3_HUMAN	integrin, alpha 3 (antigen CD49C, alpha 3 subunit of VLA-3 receptor)	391					blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|lung development (GO:0030324)|maternal process involved in female pregnancy (GO:0060135)|memory (GO:0007613)|mesodermal cell differentiation (GO:0048333)|negative regulation of cell projection organization (GO:0031345)|nephron development (GO:0072006)|neuron migration (GO:0001764)|positive regulation of cell-substrate adhesion (GO:0010811)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of gene expression (GO:0010628)|positive regulation of neuron projection development (GO:0010976)|regulation of BMP signaling pathway (GO:0030510)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|regulation of Wnt signaling pathway (GO:0030111)|renal filtration (GO:0097205)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|skin development (GO:0043588)	basolateral plasma membrane (GO:0016323)|cell periphery (GO:0071944)|cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integrin alpha3-beta1 complex (GO:0034667)|integrin complex (GO:0008305)|invadopodium membrane (GO:0071438)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|synapse (GO:0045202)	glycoprotein binding (GO:0001948)|metal ion binding (GO:0046872)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)			endometrium(3)|kidney(2)|large_intestine(7)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(2)	31						CTGTGGGAGCTCCGTTTGAAG	0.557													T|||	10	0.00199681	0.0	0.0014	5008	,	,		17926	0.0		0.0089	False		,,,				2504	0.0				p.A391A		Atlas-SNP	.											.	ITGA3	128	.	0			c.T1173C						PASS	.	T	,	1,4405	2.1+/-5.4	0,1,2202	120.0	115.0	117.0		1173,1173	-3.8	0.9	17	dbSNP_133	117	44,8556	29.0+/-79.6	0,44,4256	no	coding-synonymous,coding-synonymous	ITGA3	NM_002204.2,NM_005501.2	,	0,45,6458	CC,CT,TT		0.5116,0.0227,0.346	,	391/1052,391/1067	48151296	45,12961	2203	4300	6503	SO:0001819	synonymous_variant	3675	exon8			GGGAGCTCCGTTT	M59911	CCDS11557.1, CCDS11558.1	17q21.33	2010-03-23	2003-10-13		ENSG00000005884	ENSG00000005884		"""CD molecules"", ""Integrins"""	6139	protein-coding gene	gene with protein product		605025	"""antigen identified by monoclonal antibody J143"""	MSK18		1655803, 9704023	Standard	NM_005501		Approved	CD49c, VLA3a, VCA-2, GAP-B3	uc010dbm.3	P26006	OTTHUMG00000161890	ENST00000320031.8:c.1173T>C	17.37:g.48151296T>C		78.0	0.0	0		62.0	20.0	0.322581	NM_005501	A7E246|B7ZM80|B9EGQ1|D3DTX4|D3DTX5	Silent	SNP	ENST00000320031.8	37	CCDS11558.1																																																																																			T|0.997;C|0.003	0.003	strong		0.557	ITGA3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000366298.1	NM_005501	
ZPR1	8882	hgsc.bcm.edu	37	11	116652892	116652892	+	Missense_Mutation	SNP	A	A	T	rs11550892	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:116652892A>T	ENST00000227322.3	-	12	1220	c.1161T>A	c.(1159-1161)ttT>ttA	p.F387L		NM_003904.3	NP_003895.1	O75312	ZPR1_HUMAN		387					apoptotic process involved in development (GO:1902742)|axon development (GO:0061564)|Cajal body organization (GO:0030576)|cell proliferation (GO:0008283)|cellular response to epidermal growth factor stimulus (GO:0071364)|DNA endoreduplication (GO:0042023)|inner cell mass cell proliferation (GO:0001833)|microtubule cytoskeleton organization (GO:0000226)|mRNA processing (GO:0006397)|negative regulation of motor neuron apoptotic process (GO:2000672)|positive regulation of gene expression (GO:0010628)|positive regulation of growth (GO:0045927)|positive regulation of protein import into nucleus (GO:0042307)|positive regulation of RNA splicing (GO:0033120)|positive regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071931)|pre-mRNA catabolic process (GO:1990261)|regulation of myelination (GO:0031641)|RNA splicing (GO:0008380)|signal transduction (GO:0007165)|spinal cord development (GO:0021510)|trophectodermal cell proliferation (GO:0001834)	axon (GO:0030424)|Cajal body (GO:0015030)|cytoplasm (GO:0005737)|Gemini of coiled bodies (GO:0097504)|growth cone (GO:0030426)|neuronal cell body (GO:0043025)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perikaryon (GO:0043204)|SMN complex (GO:0032797)	translation initiation factor binding (GO:0031369)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|large_intestine(2)|lung(4)|upper_aerodigestive_tract(1)	9	all_hematologic(175;0.0487)	all_cancers(61;1.72e-06)|all_epithelial(67;0.000735)|Melanoma(852;0.022)|Acute lymphoblastic leukemia(157;0.0255)|Medulloblastoma(222;0.0523)|Breast(348;0.056)|all_hematologic(158;0.0588)		BRCA - Breast invasive adenocarcinoma(274;1.49e-06)|Epithelial(105;5.61e-06)|all cancers(92;0.000139)|OV - Ovarian serous cystadenocarcinoma(223;0.153)		TCTTCTGGCTAAACTCCTGTA	0.478													A|||	3	0.000599042	0.0	0.0014	5008	,	,		17633	0.0		0.002	False		,,,				2504	0.0				p.F387L		Atlas-SNP	.											.	ZNF259	27	.	0			c.T1161A						PASS	.	A	LEU/PHE	4,4398	8.1+/-20.4	0,4,2197	114.0	93.0	100.0		1161	1.1	1.0	11	dbSNP_120	100	69,8523	41.7+/-99.0	0,69,4227	yes	missense	ZNF259	NM_003904.3	22	0,73,6424	TT,TA,AA		0.8031,0.0909,0.5618	probably-damaging	387/460	116652892	73,12921	2201	4296	6497	SO:0001583	missense	8882	exon12			CTGGCTAAACTCC																												ENST00000227322.3:c.1161T>A	11.37:g.116652892A>T	ENSP00000227322:p.Phe387Leu	115.0	0.0	0		99.0	47.0	0.474747	NM_003904	Q2TAA0	Missense_Mutation	SNP	ENST00000227322.3	37	CCDS8375.1	5|5	0.0022893772893772895|0.0022893772893772895	0|0	0.0|0.0	1|1	0.0027624309392265192|0.0027624309392265192	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	A|A	24.5|24.5	4.534777|4.534777	0.85812|0.85812	9.09E-4|9.09E-4	0.008031|0.008031	ENSG00000109917|ENSG00000109917	ENST00000227322|ENST00000429220	T|.	0.45276|.	0.9|.	6.02|6.02	1.12|1.12	0.20585|0.20585	Zinc finger, ZPR1-type (3);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|.	0.63046|.	0.2478|.	M|M	0.79011|0.79011	2.435|2.435	0.80722|0.80722	D|D	1|1	D|.	0.56035|.	0.974|.	P|.	0.61201|.	0.885|.	T|.	0.64193|.	-0.6465|.	10|.	0.62326|.	D|.	0.03|.	-11.3214|-11.3214	10.2019|10.2019	0.43089|0.43089	0.63:0.0:0.37:0.0|0.63:0.0:0.37:0.0	rs11550892;rs35417469|rs11550892;rs35417469	387|.	O75312|.	ZPR1_HUMAN|.	L|K	387|314	ENSP00000227322:F387L|.	ENSP00000227322:F387L|.	F|X	-|-	3|1	2|0	ZNF259|ZNF259	116158102|116158102	0.888000|0.888000	0.30383|0.30383	0.998000|0.998000	0.56505|0.56505	0.935000|0.935000	0.57460|0.57460	0.349000|0.349000	0.20055|0.20055	-0.047000|-0.047000	0.13423|0.13423	0.533000|0.533000	0.62120|0.62120	TTT|TAG	A|0.996;T|0.004	0.004	strong		0.478	ZNF259-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106283.2		
TPTE	7179	hgsc.bcm.edu	37	21	10920086	10920086	+	Missense_Mutation	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:10920086G>T	ENST00000361285.4	-	19	1497	c.1168C>A	c.(1168-1170)Cag>Aag	p.Q390K	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000298232.7_Missense_Mutation_p.Q372K|TPTE_ENST00000342420.5_Missense_Mutation_p.Q352K	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	390	Phosphatase tensin-type. {ECO:0000255|PROSITE-ProRule:PRU00590}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.Q390K(1)|p.Q372K(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			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)		AAACTTACCTGAGAAGGAGTT	0.378																																					p.Q390K		Atlas-SNP	.											TPTE_ENST00000361285,NS,carcinoma,0,3	TPTE	513	3	2	Substitution - Missense(2)	lung(2)	c.C1168A						PASS	.						70.0	70.0	70.0					21																	10920086		2202	4300	6502	SO:0001583	missense	7179	exon19			TTACCTGAGAAGG	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1168C>A	21.37:g.10920086G>T	ENSP00000355208:p.Gln390Lys	99.0	0.0	0		127.0	30.0	0.23622	NM_199261	B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	12.26	1.885014	0.33255	.	.	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.99488	-6.0;-6.0;-6.0	2.32	2.32	0.28847	Phosphatase tensin type (1);	0.000000	0.85682	D	0.000000	D	0.99629	0.9864	H	0.97962	4.115	0.46798	D	0.999209	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.996;0.996;0.999	D	0.98186	1.0460	10	0.87932	D	0	-18.4997	8.1818	0.31315	0.0:0.0:1.0:0.0	.	352;372;390	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	K	372;390;352	ENSP00000298232:Q372K;ENSP00000355208:Q390K;ENSP00000344441:Q352K	ENSP00000298232:Q372K	Q	-	1	0	TPTE	9941957	1.000000	0.71417	0.997000	0.53966	0.311000	0.27955	5.387000	0.66243	1.313000	0.45069	0.184000	0.17185	CAG	.	.	none		0.378	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
MGAM	8972	hgsc.bcm.edu	37	7	141752154	141752154	+	Missense_Mutation	SNP	A	A	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:141752154A>T	ENST00000549489.2	+	25	2961	c.2866A>T	c.(2866-2868)Ata>Tta	p.I956L	MGAM_ENST00000475668.2_Missense_Mutation_p.I956L	NM_004668.2	NP_004659.2	O43451	MGA_HUMAN	maltase-glucoamylase (alpha-glucosidase)	956	P-type 2. {ECO:0000255|PROSITE- ProRule:PRU00779}.				carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			cervix(1)|endometrium(1)|large_intestine(4)|lung(3)|ovary(2)|skin(2)	13	Melanoma(164;0.0272)				Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	GGAATGGAGCATAAAGATAAG	0.428																																					p.I956L		Atlas-SNP	.											.	MGAM	767	.	0			c.A2866T						PASS	.						72.0	64.0	67.0					7																	141752154		1893	4125	6018	SO:0001583	missense	8972	exon25			TGGAGCATAAAGA	AF016833	CCDS47727.1	7q34	2012-10-03			ENSG00000257335	ENSG00000257335			7043	protein-coding gene	gene with protein product		154360				9446624	Standard	NM_004668		Approved	MGA	uc003vwy.3	O43451	OTTHUMG00000158395	ENST00000549489.2:c.2866A>T	7.37:g.141752154A>T	ENSP00000447378:p.Ile956Leu	52.0	0.0	0		52.0	30.0	0.576923	NM_004668	Q0VAX6|Q75ME7|Q86UM5	Missense_Mutation	SNP	ENST00000549489.2	37	CCDS47727.1	.	.	.	.	.	.	.	.	.	.	A	4.008	-0.001239	0.07819	.	.	ENSG00000257335	ENST00000549489;ENST00000475668;ENST00000548812	D	0.88431	-2.38	4.64	-9.28	0.00656	P-type trefoil (2);	5.617280	0.00166	N	0.000008	T	0.66636	0.2809	N	0.03608	-0.345	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.64676	-0.6351	10	0.11485	T	0.65	.	1.9557	0.03375	0.2744:0.3783:0.0822:0.2652	.	956	O43451	MGA_HUMAN	L	956;956;833	ENSP00000447378:I956L	ENSP00000316431:I833L	I	+	1	0	MGAM	141398623	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.999000	0.01467	-1.559000	0.01688	-0.661000	0.03856	ATA	.	.	none		0.428	MGAM-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000351244.3		
MUC5B	727897	hgsc.bcm.edu	37	11	1251357	1251357	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1251357G>C	ENST00000529681.1	+	11	1401	c.1343G>C	c.(1342-1344)aGc>aCc	p.S448T	MUC5B_ENST00000447027.1_Missense_Mutation_p.S451T	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	448	VWFD 2. {ECO:0000255|PROSITE- ProRule:PRU00580}.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GGTGACTGCAGCTACGTTCTG	0.637																																					p.S448T		Atlas-SNP	.											.	MUC5B	473	.	0			c.G1343C						PASS	.						112.0	115.0	114.0					11																	1251357		1991	4140	6131	SO:0001583	missense	727897	exon11			ACTGCAGCTACGT	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.1343G>C	11.37:g.1251357G>C	ENSP00000436812:p.Ser448Thr	66.0	0.0	0		71.0	34.0	0.478873	NM_002458	O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	G	3.587	-0.084422	0.07097	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.59638	0.25;0.25	4.26	2.37	0.29283	von Willebrand factor, type D domain (3);VWC out (1);	.	.	.	.	T	0.44286	0.1286	N	0.21617	0.685	0.25405	N	0.988402	B;P;P	0.39094	0.051;0.659;0.659	B;B;B	0.42882	0.049;0.401;0.401	T	0.35375	-0.9791	9	0.87932	D	0	.	4.8917	0.13730	0.2846:0.2117:0.5037:0.0	.	448;1107;451	Q9HC84;A7Y9J9;E9PBJ0	MUC5B_HUMAN;.;.	T	448;451;449;484	ENSP00000436812:S448T;ENSP00000415793:S451T	ENSP00000343037:S449T	S	+	2	0	MUC5B	1207933	0.001000	0.12720	1.000000	0.80357	0.111000	0.19643	-0.241000	0.08940	0.270000	0.21984	0.313000	0.20887	AGC	.	.	none		0.637	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
PPAN	56342	hgsc.bcm.edu	37	19	10221227	10221227	+	Missense_Mutation	SNP	C	C	T	rs139737427		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10221227C>T	ENST00000253107.7	+	10	1074	c.968C>T	c.(967-969)gCg>gTg	p.A323V	P2RY11_ENST00000321826.4_5'Flank|SNORD105_ENST00000386910.1_RNA|SNORD105B_ENST00000458770.1_RNA|PPAN-P2RY11_ENST00000393796.4_Missense_Mutation_p.A323V|PPAN-P2RY11_ENST00000428358.1_Missense_Mutation_p.A323V|PPAN_ENST00000556468.1_Missense_Mutation_p.A323V|PPAN_ENST00000393793.1_Missense_Mutation_p.A270V	NM_020230.5	NP_064615.3	Q9NQ55	SSF1_HUMAN	peter pan homolog (Drosophila)	323					RNA splicing (GO:0008380)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(3)|liver(2)|lung(7)|prostate(1)|skin(1)|urinary_tract(1)	15			OV - Ovarian serous cystadenocarcinoma(20;2.19e-08)|Epithelial(33;1.76e-05)|all cancers(31;3.54e-05)			CGGCTGAAGGCGCAGAGGCAG	0.667													C|||	1	0.000199681	0.0	0.0	5008	,	,		15026	0.0		0.001	False		,,,				2504	0.0				p.A323V		Atlas-SNP	.											.	PPAN	43	.	0			c.C968T						PASS	.	C	VAL/ALA,VAL/ALA,VAL/ALA	1,4399		0,1,2199	14.0	17.0	16.0		968,968,968	3.8	0.4	19	dbSNP_134	16	18,8574		0,18,4278	yes	missense,missense,missense	PPAN,PPAN-P2RY11	NM_001040664.2,NM_001198690.1,NM_020230.5	64,64,64	0,19,6477	TT,TC,CC		0.2095,0.0227,0.1462	possibly-damaging,possibly-damaging,possibly-damaging	323/795,323/521,323/474	10221227	19,12973	2200	4296	6496	SO:0001583	missense	56342	exon10			TGAAGGCGCAGAG	BC033202	CCDS12225.1	19p13.2	2008-02-05	2001-11-28		ENSG00000130810	ENSG00000130810			9227	protein-coding gene	gene with protein product		607793	"""peter pan (Drosophila) homolog"""			10873382	Standard	NM_020230		Approved	SSF1, SSF2, SSF, BXDC3		Q9NQ55	OTTHUMG00000156826	ENST00000253107.7:c.968C>T	19.37:g.10221227C>T	ENSP00000253107:p.Ala323Val	89.0	0.0	0		82.0	43.0	0.52439	NM_020230	C9J3F9|Q9BW97|Q9H170	Missense_Mutation	SNP	ENST00000253107.7	37	CCDS12225.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	C|C	12.64|12.64	1.999423|1.999423	0.35320|0.35320	2.27E-4|2.27E-4	0.002095|0.002095	ENSG00000243207;ENSG00000243207;ENSG00000130810;ENSG00000130810;ENSG00000130810;ENSG00000130810|ENSG00000130810	ENST00000428358;ENST00000393796;ENST00000253107;ENST00000556468;ENST00000342696;ENST00000393793|ENST00000444703	T;T;T;T;T|.	0.63255|.	1.39;-0.03;1.42;-0.03;1.44|.	4.78|4.78	3.75|3.75	0.43078|0.43078	.|.	.|.	.|.	.|.	.|.	T|T	0.49677|0.49677	0.1571|0.1571	L|L	0.61036|0.61036	1.89|1.89	0.29207|0.29207	N|N	0.874799|0.874799	P;P;P|.	0.50710|.	0.931;0.87;0.938|.	B;B;B|.	0.33960|.	0.173;0.101;0.146|.	T|T	0.47971|0.47971	-0.9075|-0.9075	9|5	0.51188|.	T|.	0.08|.	-14.6112|-14.6112	7.0518|7.0518	0.25077|0.25077	0.1706:0.7394:0.0:0.09|0.1706:0.7394:0.0:0.09	.|.	323;323;323|.	C9J3F9;C9JW41;Q9NQ55|.	.;.;SSF1_HUMAN|.	V|C	323;323;323;323;323;270|83	ENSP00000411918:A323V;ENSP00000377385:A323V;ENSP00000253107:A323V;ENSP00000450710:A323V;ENSP00000377382:A270V|.	ENSP00000253107:A323V|.	A|R	+|+	2|1	0|0	PPAN;PPAN-P2RY11|PPAN	10082227|10082227	0.950000|0.950000	0.32346|0.32346	0.433000|0.433000	0.26760|0.26760	0.029000|0.029000	0.11900|0.11900	2.089000|2.089000	0.41672|0.41672	1.008000|1.008000	0.39264|0.39264	0.561000|0.561000	0.74099|0.74099	GCG|CGC	C|0.999;T|0.001	0.001	strong		0.667	PPAN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316658.1	NM_020230	
HPSE	10855	hgsc.bcm.edu	37	4	84222208	84222208	+	Silent	SNP	A	A	G	rs11031	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:84222208A>G	ENST00000405413.2	-	12	1513	c.1377T>C	c.(1375-1377)aaT>aaC	p.N459N	HPSE_ENST00000512196.1_Silent_p.N385N|HPSE_ENST00000513463.1_Silent_p.N401N|HPSE_ENST00000311412.5_Silent_p.N459N	NM_006665.5	NP_006656.2	Q9Y251	HPSE_HUMAN	heparanase	459					carbohydrate metabolic process (GO:0005975)|cell-matrix adhesion (GO:0007160)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan catabolic process (GO:0030200)|positive regulation of blood coagulation (GO:0030194)|positive regulation of hair follicle development (GO:0051798)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation vascular endothelial growth factor production (GO:0010575)|proteoglycan metabolic process (GO:0006029)|regulation of hair follicle development (GO:0051797)|small molecule metabolic process (GO:0044281)|vascular wound healing (GO:0061042)	extracellular region (GO:0005576)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)	beta-glucuronidase activity (GO:0004566)|heparanase activity (GO:0030305)|protein dimerization activity (GO:0046983)|syndecan binding (GO:0045545)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(2)|skin(1)|urinary_tract(2)	20		Hepatocellular(203;0.114)		COAD - Colon adenocarcinoma(81;0.141)	Dalteparin(DB06779)|Heparin(DB01109)	ACTTGGTGACATTATGGAGGT	0.353													A|||	426	0.0850639	0.3064	0.0259	5008	,	,		18825	0.0		0.003	False		,,,				2504	0.0				p.N459N		Atlas-SNP	.											.	HPSE	55	.	0			c.T1377C						PASS	.	A	,,,	1123,3283	402.2+/-332.3	156,811,1236	119.0	126.0	123.0		1377,1155,1203,1377	-3.8	1.0	4	dbSNP_52	123	18,8582	11.9+/-42.8	0,18,4282	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	HPSE	NM_001098540.2,NM_001166498.2,NM_001199830.1,NM_006665.5	,,,	156,829,5518	GG,GA,AA		0.2093,25.488,8.7729	,,,	459/544,385/470,401/486,459/544	84222208	1141,11865	2203	4300	6503	SO:0001819	synonymous_variant	10855	exon11			GGTGACATTATGG	AF144325	CCDS3602.1, CCDS54774.1, CCDS56337.1	4q21.3	2008-02-05			ENSG00000173083	ENSG00000173083			5164	protein-coding gene	gene with protein product		604724				10395325, 10395326	Standard	NM_006665		Approved	HPA, HSE1, HPSE1	uc003hoj.4	Q9Y251	OTTHUMG00000130425	ENST00000405413.2:c.1377T>C	4.37:g.84222208A>G		143.0	0.0	0		94.0	47.0	0.5	NM_001098540	A9JIG7|C7F7I3|C7F7I4|E9PCA9|E9PGR1|Q53GE5|Q9UL39	Silent	SNP	ENST00000405413.2	37	CCDS3602.1																																																																																			A|0.911;G|0.089	0.089	strong		0.353	HPSE-001	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000252812.2	NM_006665	
RFT1	91869	hgsc.bcm.edu	37	3	53159970	53159970	+	Missense_Mutation	SNP	A	A	G	rs146354877	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:53159970A>G	ENST00000296292.3	-	2	165	c.104T>C	c.(103-105)aTt>aCt	p.I35T	RFT1_ENST00000394738.3_Missense_Mutation_p.I35T	NM_052859.3	NP_443091.1	Q96AA3	RFT1_HUMAN	RFT1 homolog (S. cerevisiae)	35					carbohydrate transport (GO:0008643)|cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	integral component of membrane (GO:0016021)	lipid transporter activity (GO:0005319)			NS(1)|breast(1)|kidney(1)|lung(5)|skin(2)|urinary_tract(2)	12				BRCA - Breast invasive adenocarcinoma(193;6.98e-05)|Kidney(197;0.0017)|KIRC - Kidney renal clear cell carcinoma(197;0.00192)|OV - Ovarian serous cystadenocarcinoma(275;0.104)		GAAGCGAAGAATAAATGCATT	0.413																																					p.I35T		Atlas-SNP	.											.	RFT1	34	.	0			c.T104C						PASS	.	A	THR/ILE	1,4405	2.1+/-5.4	0,1,2202	114.0	92.0	99.0		104	3.7	1.0	3	dbSNP_134	99	0,8600		0,0,4300	yes	missense	RFT1	NM_052859.3	89	0,1,6502	GG,GA,AA		0.0,0.0227,0.0077	benign	35/542	53159970	1,13005	2203	4300	6503	SO:0001583	missense	91869	exon2			CGAAGAATAAATG	AJ318099	CCDS2869.1	3p21.1	2014-02-06	2005-01-26		ENSG00000163933	ENSG00000163933			30220	protein-coding gene	gene with protein product	"""congenital disorder of glycosylation 1N"""	611908	"""RFT1, requiring fifty three 1 homolog (S. cerevisiae)"""			12477932	Standard	NM_052859		Approved	CDG1N	uc003dgj.3	Q96AA3	OTTHUMG00000074035	ENST00000296292.3:c.104T>C	3.37:g.53159970A>G	ENSP00000296292:p.Ile35Thr	143.0	0.0	0		92.0	35.0	0.380435	NM_052859	Q96J03	Missense_Mutation	SNP	ENST00000296292.3	37	CCDS2869.1	.	.	.	.	.	.	.	.	.	.	A	12.89	2.073820	0.36566	2.27E-4	0.0	ENSG00000163933	ENST00000296292;ENST00000394738;ENST00000467048	D;D;D	0.86497	-2.13;-2.13;-2.13	6.02	3.71	0.42584	.	0.103749	0.64402	D	0.000005	T	0.73799	0.3633	N	0.16790	0.44	0.33518	D	0.591968	B;B	0.17465	0.022;0.003	B;B	0.17433	0.018;0.01	T	0.72178	-0.4369	10	0.35671	T	0.21	.	6.0431	0.19746	0.7465:0.0:0.2535:0.0	.	35;35	B5MDE0;Q96AA3	.;RFT1_HUMAN	T	35	ENSP00000296292:I35T;ENSP00000378223:I35T;ENSP00000420325:I35T	ENSP00000296292:I35T	I	-	2	0	RFT1	53135010	1.000000	0.71417	1.000000	0.80357	0.941000	0.58515	4.784000	0.62411	2.304000	0.77564	0.528000	0.53228	ATT	A|0.999;G|0.001	0.001	strong		0.413	RFT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000157136.2	NM_052859	
SMURF2	64750	hgsc.bcm.edu	37	17	62587204	62587204	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:62587204A>G	ENST00000262435.9	-	5	585	c.398T>C	c.(397-399)gTa>gCa	p.V133A	SMURF2_ENST00000578200.1_Intron	NM_022739.3	NP_073576.1	Q9HAU4	SMUF2_HUMAN	SMAD specific E3 ubiquitin protein ligase 2	133					BMP signaling pathway (GO:0030509)|gene expression (GO:0010467)|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)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|regulation of transforming growth factor beta receptor signaling pathway (GO:0017015)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)|ubiquitin-dependent SMAD protein catabolic process (GO:0030579)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|ubiquitin ligase complex (GO:0000151)	identical protein binding (GO:0042802)|ligase activity (GO:0016874)|SMAD binding (GO:0046332)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(2)|lung(6)|prostate(1)|skin(4)	22	Breast(5;1.32e-14)		BRCA - Breast invasive adenocarcinoma(8;9.88e-12)			ACACTTACCTACTATCTGTCC	0.318																																					p.V133A		Atlas-SNP	.											.	SMURF2	63	.	0			c.T398C						PASS	.						130.0	116.0	121.0					17																	62587204		2203	4299	6502	SO:0001583	missense	64750	exon5			TTACCTACTATCT	AF301463	CCDS32707.1	17q22-q23	2012-10-05			ENSG00000108854	ENSG00000108854			16809	protein-coding gene	gene with protein product		605532				11016919	Standard	XM_005257585		Approved		uc002jep.1	Q9HAU4	OTTHUMG00000179189	ENST00000262435.9:c.398T>C	17.37:g.62587204A>G	ENSP00000262435:p.Val133Ala	120.0	0.0	0		101.0	5.0	0.049505	NM_022739	Q52LL1|Q9H260	Missense_Mutation	SNP	ENST00000262435.9	37	CCDS32707.1	.	.	.	.	.	.	.	.	.	.	A	15.64	2.892338	0.52121	.	.	ENSG00000108854	ENST00000262435	T	0.67171	-0.25	5.41	5.41	0.78517	C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.78477	0.4289	M	0.68593	2.085	0.80722	D	1	D	0.76494	0.999	D	0.87578	0.998	T	0.74509	-0.3642	10	0.14656	T	0.56	.	15.7378	0.77859	1.0:0.0:0.0:0.0	.	133	Q9HAU4	SMUF2_HUMAN	A	133	ENSP00000262435:V133A	ENSP00000262435:V133A	V	-	2	0	SMURF2	60017666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.971000	0.93419	2.184000	0.69523	0.477000	0.44152	GTA	.	.	none		0.318	SMURF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445227.1	NM_022739	
ARMC5	79798	hgsc.bcm.edu	37	16	31471283	31471283	+	Silent	SNP	G	G	A	rs201280100	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:31471283G>A	ENST00000563544.1	+	2	984	c.438G>A	c.(436-438)cgG>cgA	p.R146R	ARMC5_ENST00000538189.1_Silent_p.R178R|RP11-452L6.5_ENST00000564629.1_RNA|ARMC5_ENST00000412665.2_5'UTR|ARMC5_ENST00000457010.2_Silent_p.R146R|ARMC5_ENST00000408912.3_Silent_p.R241R|ARMC5_ENST00000268314.4_Silent_p.R146R			Q96C12	ARMC5_HUMAN	armadillo repeat containing 5	146										central_nervous_system(1)|endometrium(4)|large_intestine(3)|liver(2)|lung(12)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	28						GGGCGTGCCGGACCGAAGTGC	0.602													G|||	19	0.00379393	0.0	0.0043	5008	,	,		14517	0.0		0.0159	False		,,,				2504	0.0				p.R146R		Atlas-SNP	.											.	ARMC5	94	.	0			c.G438A						PASS	.	G	,	8,4040		0,8,2016	52.0	55.0	54.0		438,438	2.5	1.0	16		54	80,8282		1,78,4102	no	coding-synonymous,coding-synonymous	ARMC5	NM_001105247.1,NM_024742.2	,	1,86,6118	AA,AG,GG		0.9567,0.1976,0.7091	,	146/936,146/726	31471283	88,12322	2024	4181	6205	SO:0001819	synonymous_variant	79798	exon1			GTGCCGGACCGAA	AY217348	CCDS42155.1, CCDS45472.1, CCDS73874.1	16p11	2013-02-14			ENSG00000140691	ENSG00000140691		"""Armadillo repeat containing"""	25781	protein-coding gene	gene with protein product		615549					Standard	NM_024742		Approved	FLJ13063	uc002ecc.3	Q96C12	OTTHUMG00000176618	ENST00000563544.1:c.438G>A	16.37:g.31471283G>A		24.0	0.0	0		21.0	12.0	0.571429	NM_024742	Q86WM9|Q9H7P8|Q9H925	Silent	SNP	ENST00000563544.1	37	CCDS45472.1																																																																																			G|0.993;A|0.007	0.007	strong		0.602	ARMC5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000432847.1	NM_024742	
MESDC1	59274	hgsc.bcm.edu	37	15	81294774	81294774	+	Silent	SNP	G	G	C	rs11541231	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:81294774G>C	ENST00000267984.2	+	1	1480	c.162G>C	c.(160-162)tcG>tcC	p.S54S		NM_022566.2	NP_072088.1	Q9H1K6	MESD1_HUMAN	mesoderm development candidate 1	54										endometrium(1)|lung(2)	3						TGCTGCTGTCGAGCGAGGCGC	0.701													G|||	137	0.0273562	0.003	0.0951	5008	,	,		9514	0.0		0.0457	False		,,,				2504	0.0215				p.S54S		Atlas-SNP	.											.	MESDC1	7	.	0			c.G162C						PASS	.	G		48,3752		2,44,1854	11.0	9.0	10.0		162	-8.7	0.9	15	dbSNP_120	10	281,7351		5,271,3540	no	coding-synonymous	MESDC1	NM_022566.2		7,315,5394	CC,CG,GG		3.6819,1.2632,2.8779		54/363	81294774	329,11103	1900	3816	5716	SO:0001819	synonymous_variant	59274	exon1			GCTGTCGAGCGAG	AY007810	CCDS10316.1	15q13	2008-07-18			ENSG00000140406	ENSG00000140406			13519	protein-coding gene	gene with protein product		615466				11247670	Standard	NM_022566		Approved	MGC99595	uc002bfz.3	Q9H1K6	OTTHUMG00000144185	ENST00000267984.2:c.162G>C	15.37:g.81294774G>C		5.0	0.0	0		12.0	10.0	0.833333	NM_022566		Silent	SNP	ENST00000267984.2	37	CCDS10316.1																																																																																			G|0.972;C|0.028	0.028	strong		0.701	MESDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000291390.1	NM_022566	
ALPK3	57538	hgsc.bcm.edu	37	15	85400564	85400564	+	Silent	SNP	C	C	T	rs114957070	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:85400564C>T	ENST00000258888.5	+	6	3368	c.3201C>T	c.(3199-3201)ccC>ccT	p.P1067P		NM_020778.4	NP_065829.3	Q96L96	ALPK3_HUMAN	alpha-kinase 3	1067					heart development (GO:0007507)	nucleus (GO:0005634)	ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			NS(3)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(4)|large_intestine(9)|lung(27)|ovary(3)|prostate(5)|skin(8)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	81			BRCA - Breast invasive adenocarcinoma(143;0.0587)			AGGAGGTACCCACGATGCCTT	0.647													C|||	9	0.00179712	0.0	0.0	5008	,	,		19517	0.0		0.0089	False		,,,				2504	0.0				p.P1067P		Atlas-SNP	.											.	ALPK3	289	.	0			c.C3201T						PASS	.	C		7,4399	12.9+/-30.5	0,7,2196	69.0	54.0	59.0		3201	0.4	0.0	15	dbSNP_132	59	53,8545	34.3+/-88.2	0,53,4246	no	coding-synonymous	ALPK3	NM_020778.4		0,60,6442	TT,TC,CC		0.6164,0.1589,0.4614		1067/1908	85400564	60,12944	2203	4299	6502	SO:0001819	synonymous_variant	57538	exon6			GGTACCCACGATG	AY044449	CCDS10333.1	15q25.2	2013-01-29			ENSG00000136383	ENSG00000136383		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	17574	protein-coding gene	gene with protein product	"""myocyte induction differentiation originator"", ""muscle alpha-kinase"""					10021370	Standard	NM_020778		Approved	MAK, KIAA1330, Midori	uc002ble.3	Q96L96	OTTHUMG00000148667	ENST00000258888.5:c.3201C>T	15.37:g.85400564C>T		54.0	0.0	0		65.0	42.0	0.646154	NM_020778	Q9P2L6	Silent	SNP	ENST00000258888.5	37	CCDS10333.1																																																																																			C|0.996;T|0.004	0.004	strong		0.647	ALPK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000308997.1	NM_020778	
ZCWPW1	55063	hgsc.bcm.edu	37	7	99998750	99998750	+	Silent	SNP	G	G	A	rs145308367	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:99998750G>A	ENST00000398027.2	-	18	2081	c.1834C>T	c.(1834-1836)Ctg>Ttg	p.L612L	ZCWPW1_ENST00000360951.4_3'UTR|ZCWPW1_ENST00000490721.1_Silent_p.L441L|ZCWPW1_ENST00000324725.6_Silent_p.L441L	NM_017984.4	NP_060454.3	Q9H0M4	ZCPW1_HUMAN	zinc finger, CW type with PWWP domain 1	612							zinc ion binding (GO:0008270)			breast(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)	16	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					TCCAGGTCCAGGTCACTGGAG	0.637													g|||	12	0.00239617	0.0	0.0043	5008	,	,		16848	0.0		0.006	False		,,,				2504	0.0031				p.L612L		Atlas-SNP	.											.	ZCWPW1	41	.	0			c.C1834T						PASS	.	G		4,4012		0,4,2004	49.0	51.0	51.0		1834	4.1	1.0	7	dbSNP_134	51	76,8316		1,74,4121	no	coding-synonymous	ZCWPW1	NM_017984.3		1,78,6125	AA,AG,GG		0.9056,0.0996,0.6447		612/649	99998750	80,12328	2008	4196	6204	SO:0001819	synonymous_variant	55063	exon18			GGTCCAGGTCACT	AK000919	CCDS43623.1, CCDS59067.1	7q22.1	2012-02-10	2004-11-03		ENSG00000078487	ENSG00000078487			23486	protein-coding gene	gene with protein product			"""zinc finger, CW-type with PWWP domain 1"""			11230166, 14607086, 20826339	Standard	NM_017984		Approved	FLJ10057, DKFZp434N0510, ZCW1	uc003uut.4	Q9H0M4	OTTHUMG00000159537	ENST00000398027.2:c.1834C>T	7.37:g.99998750G>A		82.0	0.0	0		111.0	49.0	0.441441	NM_017984	A8MVF5|B4DUQ2|Q8NA98|Q9BUD0|Q9NWF7	Silent	SNP	ENST00000398027.2	37	CCDS43623.1	7	0.003205128205128205	0	0.0	2	0.0055248618784530384	0	0.0	5	0.006596306068601583	G	10.34	1.323458	0.24080	9.96E-4	0.009056	ENSG00000233389	ENST00000449355	.	.	.	5.04	4.12	0.48240	.	.	.	.	.	T	0.50274	0.1606	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.52939	-0.8508	4	.	.	.	-5.4653	8.2412	0.31660	0.1153:0.0:0.8847:0.0	.	.	.	.	K	7	.	.	R	+	2	0	AC005071.3	99836686	0.998000	0.40836	1.000000	0.80357	0.228000	0.25075	0.143000	0.16115	1.416000	0.47057	0.655000	0.94253	AGG	G|0.994;A|0.006	0.006	strong		0.637	ZCWPW1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000356083.1	NM_017984	
SIGLEC10	89790	hgsc.bcm.edu	37	19	51919244	51919244	+	Missense_Mutation	SNP	G	G	C	rs200798488	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:51919244G>C	ENST00000339313.5	-	5	1048	c.932C>G	c.(931-933)cCc>cGc	p.P311R	SIGLEC10_ENST00000439889.2_Missense_Mutation_p.P253R|SIGLEC10_ENST00000525998.1_Intron|SIGLEC10_ENST00000436984.2_Missense_Mutation_p.P263R|SIGLEC10_ENST00000442846.3_Intron|CTD-2616J11.2_ENST00000532688.1_RNA|SIGLEC10_ENST00000353836.5_Missense_Mutation_p.P311R|SIGLEC10_ENST00000432469.2_Missense_Mutation_p.P228R|SIGLEC10_ENST00000441969.3_Missense_Mutation_p.P253R|SIGLEC10_ENST00000356298.5_Missense_Mutation_p.P311R|CTD-2616J11.2_ENST00000526996.1_RNA|CTD-2616J11.3_ENST00000532473.1_RNA			Q96LC7	SIG10_HUMAN	sialic acid binding Ig-like lectin 10	311	Ig-like C2-type 2.				cell adhesion (GO:0007155)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(10)|lung(27)|ovary(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	58		all_neural(266;0.0199)		GBM - Glioblastoma multiforme(134;0.000668)|OV - Ovarian serous cystadenocarcinoma(262;0.0101)		CTTCACCCCGGGCAGCTCCAG	0.667																																					p.P311R		Atlas-SNP	.											.	SIGLEC10	112	.	0			c.C932G						PASS	.						33.0	38.0	37.0					19																	51919244		2203	4300	6503	SO:0001583	missense	89790	exon5			ACCCCGGGCAGCT	AF310233	CCDS12832.1, CCDS54301.1, CCDS54302.1, CCDS54303.1, CCDS54304.1, CCDS54305.1	19q13.3	2013-01-29			ENSG00000142512	ENSG00000142512		"""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15620	protein-coding gene	gene with protein product	"""sialic acid binding Ig-like lectin 10 Ig-like lectin 7"", ""siglec-like gene 2"""	606091				11284738	Standard	NM_033130		Approved	SIGLEC-10, SLG2, PRO940, MGC126774	uc002pwo.3	Q96LC7	OTTHUMG00000165521	ENST00000339313.5:c.932C>G	19.37:g.51919244G>C	ENSP00000345243:p.Pro311Arg	176.0	0.0	0		108.0	39.0	0.361111	NM_001171157	A8K1I5|A8K3C7|C9JJ33|C9JM10|F8W917|Q3MIR5|Q6UXI8|Q96G54|Q96LC8	Missense_Mutation	SNP	ENST00000339313.5	37	CCDS12832.1	.	.	.	.	.	.	.	.	.	.	.	5.587	0.293054	0.10567	.	.	ENSG00000142512	ENST00000353836;ENST00000432469;ENST00000356298;ENST00000441969;ENST00000439889;ENST00000436984;ENST00000339313;ENST00000529627	T;T;T;T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16;-0.16	4.37	1.01	0.19927	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.141960	0.32868	N	0.005554	T	0.54631	0.1870	L	0.45051	1.395	0.23834	N	0.996719	B;P;P;B;B;B	0.41848	0.383;0.763;0.72;0.332;0.332;0.395	P;P;P;B;B;B	0.48571	0.464;0.582;0.447;0.333;0.333;0.208	T	0.44892	-0.9298	10	0.44086	T	0.13	.	3.6772	0.08297	0.2098:0.0:0.5964:0.1939	.	263;311;311;253;253;311	C9JM10;B7ZL04;Q96LC7-2;Q96LC7-6;Q96LC7-3;Q96LC7	.;.;.;.;.;SIG10_HUMAN	R	311;228;311;253;253;263;311;125	ENSP00000342389:P311R;ENSP00000396742:P228R;ENSP00000348646:P311R;ENSP00000408387:P253R;ENSP00000389132:P253R;ENSP00000414324:P263R;ENSP00000345243:P311R;ENSP00000435281:P125R	ENSP00000345243:P311R	P	-	2	0	SIGLEC10	56611056	0.544000	0.26441	0.193000	0.23327	0.071000	0.16799	0.847000	0.27696	0.130000	0.18549	0.313000	0.20887	CCC	G|0.993;C|0.007	0.007	strong		0.667	SIGLEC10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384620.2	NM_033130	
LRP1	4035	hgsc.bcm.edu	37	12	57571249	57571249	+	Silent	SNP	C	C	T	rs2228187	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:57571249C>T	ENST00000243077.3	+	26	4702	c.4236C>T	c.(4234-4236)cgC>cgT	p.R1412R		NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	1412					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)	GCCTGCCCCGCATTGAGGCAG	0.677													C|||	18	0.00359425	0.0008	0.0101	5008	,	,		15185	0.0		0.007	False		,,,				2504	0.0031				p.R1412R		Atlas-SNP	.											.	LRP1	428	.	0			c.C4236T						PASS	.	C		1,4405		0,1,2202	36.0	39.0	38.0		4236	-7.2	0.8	12	dbSNP_98	38	73,8527	41.7+/-99.0	0,73,4227	no	coding-synonymous	LRP1	NM_002332.2		0,74,6429	TT,TC,CC		0.8488,0.0227,0.569		1412/4545	57571249	74,12932	2203	4300	6503	SO:0001819	synonymous_variant	4035	exon26			GCCCCGCATTGAG	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.4236C>T	12.37:g.57571249C>T		149.0	0.0	0		175.0	94.0	0.537143	NM_002332	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																			C|0.994;T|0.006	0.006	strong		0.677	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2	NM_002332	
PCDHB4	56131	hgsc.bcm.edu	37	5	140502433	140502433	+	Missense_Mutation	SNP	G	G	C	rs149340599	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140502433G>C	ENST00000194152.1	+	1	853	c.853G>C	c.(853-855)Gat>Cat	p.D285H	AC005754.8_ENST00000606030.1_lincRNA	NM_018938.2	NP_061761.1	Q9Y5E5	PCDB4_HUMAN	protocadherin beta 4	285	Cadherin 3. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intermediate filament cytoskeleton (GO:0045111)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			autonomic_ganglia(1)|breast(2)|endometrium(4)|kidney(2)|large_intestine(12)|lung(35)|ovary(1)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	67			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CCAAGCATCAGATGAAATTAA	0.348													G|||	48	0.00958466	0.0	0.0043	5008	,	,		20653	0.001		0.003	False		,,,				2504	0.0419				p.D285H		Atlas-SNP	.											.	PCDHB4	177	.	0			c.G853C						PASS	.	G	HIS/ASP	2,4398	4.2+/-10.8	0,2,2198	92.0	107.0	102.0		853	4.4	1.0	5	dbSNP_134	102	46,8554	29.6+/-80.5	0,46,4254	yes	missense	PCDHB4	NM_018938.2	81	0,48,6452	CC,CG,GG		0.5349,0.0455,0.3692	possibly-damaging	285/796	140502433	48,12952	2200	4300	6500	SO:0001583	missense	56131	exon1			GCATCAGATGAAA	AF152497	CCDS4246.1	5q31	2010-01-26			ENSG00000081818	ENSG00000081818		"""Cadherins / Protocadherins : Clustered"""	8689	other	protocadherin		606330				10380929	Standard	NM_018938		Approved	PCDH-BETA4	uc003lip.1	Q9Y5E5	OTTHUMG00000129617	ENST00000194152.1:c.853G>C	5.37:g.140502433G>C	ENSP00000194152:p.Asp285His	112.0	0.0	0		115.0	53.0	0.46087	NM_018938	Q4V761	Missense_Mutation	SNP	ENST00000194152.1	37	CCDS4246.1	5	0.0022893772893772895	0	0.0	3	0.008287292817679558	0	0.0	2	0.002638522427440633	G	15.05	2.718902	0.48622	4.55E-4	0.005349	ENSG00000081818	ENST00000194152	T	0.66099	-0.19	4.41	4.41	0.53225	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.66257	0.2771	L	0.45285	1.41	0.43448	D	0.995638	P	0.37370	0.592	P	0.57620	0.824	T	0.72107	-0.4390	9	0.56958	D	0.05	.	17.5536	0.87884	0.0:0.0:1.0:0.0	.	285	Q9Y5E5	PCDB4_HUMAN	H	285	ENSP00000194152:D285H	ENSP00000194152:D285H	D	+	1	0	PCDHB4	140482617	0.015000	0.18098	0.996000	0.52242	0.671000	0.39405	1.433000	0.34947	2.449000	0.82847	0.650000	0.86243	GAT	G|0.996;C|0.004	0.004	strong		0.348	PCDHB4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251812.2	NM_018938	
BCL2	596	hgsc.bcm.edu	37	18	60985833	60985833	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:60985833G>A	ENST00000398117.1	-	1	1528	c.67C>T	c.(67-69)Ctg>Ttg	p.L23L	BCL2_ENST00000333681.4_Silent_p.L23L|BCL2_ENST00000444484.1_Silent_p.L23L|BCL2_ENST00000589955.1_Silent_p.L23L	NM_000633.2	NP_000624.2	P10415	BCL2_HUMAN	B-cell CLL/lymphoma 2	23					actin filament organization (GO:0007015)|apoptotic process (GO:0006915)|axon regeneration (GO:0031103)|axonogenesis (GO:0007409)|B cell homeostasis (GO:0001782)|B cell lineage commitment (GO:0002326)|B cell proliferation (GO:0042100)|B cell receptor signaling pathway (GO:0050853)|behavioral fear response (GO:0001662)|branching involved in ureteric bud morphogenesis (GO:0001658)|CD8-positive, alpha-beta T cell lineage commitment (GO:0043375)|cell aging (GO:0007569)|cell growth (GO:0016049)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to organic substance (GO:0071310)|cochlear nucleus development (GO:0021747)|defense response to virus (GO:0051607)|developmental growth (GO:0048589)|digestive tract morphogenesis (GO:0048546)|ear development (GO:0043583)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|female pregnancy (GO:0007565)|focal adhesion assembly (GO:0048041)|gland morphogenesis (GO:0022612)|glomerulus development (GO:0032835)|hair follicle morphogenesis (GO:0031069)|homeostasis of number of cells within a tissue (GO:0048873)|humoral immune response (GO:0006959)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|intrinsic apoptotic signaling pathway in response to oxidative stress (GO:0008631)|lymphoid progenitor cell differentiation (GO:0002320)|male gonad development (GO:0008584)|melanin metabolic process (GO:0006582)|melanocyte differentiation (GO:0030318)|mesenchymal cell development (GO:0014031)|metanephros development (GO:0001656)|negative regulation of anoikis (GO:2000811)|negative regulation of apoptotic process (GO:0043066)|negative regulation of apoptotic signaling pathway (GO:2001234)|negative regulation of autophagy (GO:0010507)|negative regulation of calcium ion transport into cytosol (GO:0010523)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cellular pH reduction (GO:0032848)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of mitochondrial depolarization (GO:0051902)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of myeloid cell apoptotic process (GO:0033033)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast proliferation (GO:0033689)|negative regulation of retinal cell programmed cell death (GO:0046671)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|oocyte development (GO:0048599)|organ growth (GO:0035265)|ossification (GO:0001503)|ovarian follicle development (GO:0001541)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|pigment granule organization (GO:0048753)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of catalytic activity (GO:0043085)|positive regulation of cell growth (GO:0030307)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of melanocyte differentiation (GO:0045636)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of neuron maturation (GO:0014042)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of skeletal muscle fiber development (GO:0048743)|positive regulation of smooth muscle cell migration (GO:0014911)|post-embryonic development (GO:0009791)|protein dephosphorylation (GO:0006470)|protein polyubiquitination (GO:0000209)|reactive oxygen species metabolic process (GO:0072593)|regulation of calcium ion transport (GO:0051924)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glycoprotein biosynthetic process (GO:0010559)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of nitrogen utilization (GO:0006808)|regulation of protein heterodimerization activity (GO:0043497)|regulation of protein homodimerization activity (GO:0043496)|regulation of protein stability (GO:0031647)|regulation of transmembrane transporter activity (GO:0022898)|regulation of viral genome replication (GO:0045069)|release of cytochrome c from mitochondria (GO:0001836)|renal system process (GO:0003014)|response to acid chemical (GO:0001101)|response to cytokine (GO:0034097)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to glucocorticoid (GO:0051384)|response to hydrogen peroxide (GO:0042542)|response to iron ion (GO:0010039)|response to ischemia (GO:0002931)|response to nicotine (GO:0035094)|response to radiation (GO:0009314)|response to toxic substance (GO:0009636)|response to UV-B (GO:0010224)|single organismal cell-cell adhesion (GO:0016337)|spleen development (GO:0048536)|T cell differentiation in thymus (GO:0033077)|T cell homeostasis (GO:0043029)|thymus development (GO:0048538)|transmembrane transport (GO:0055085)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)|myelin sheath (GO:0043209)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|pore complex (GO:0046930)	BH3 domain binding (GO:0051434)|channel activity (GO:0015267)|channel inhibitor activity (GO:0016248)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding (GO:0043565)|ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(106)|kidney(1)|large_intestine(1)|lung(3)	113		all_hematologic(56;1.18e-20)|Prostate(75;0.0872)		Lung(128;0.0234)|READ - Rectum adenocarcinoma(59;0.0935)	Docetaxel(DB01248)|Ibuprofen(DB01050)|Paclitaxel(DB01229)|Rasagiline(DB01367)	CTCTGCGACAGCTTATAATGG	0.652			T	IGH@	"""NHL, CLL"""																																p.L23L		Atlas-SNP	.		Dom	yes		18	18q21.3	596	B-cell CLL/lymphoma 2		L	.	BCL2	272	.	0			c.C67T						PASS	.						68.0	76.0	73.0					18																	60985833		1972	4119	6091	SO:0001819	synonymous_variant	596	exon2			GCGACAGCTTATA	M14745	CCDS11981.1, CCDS45882.1	18q21.3	2014-03-07			ENSG00000171791	ENSG00000171791		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	990	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 50"""	151430					Standard	XM_006722523		Approved	Bcl-2, PPP1R50	uc002lit.1	P10415	OTTHUMG00000132791	ENST00000398117.1:c.67C>T	18.37:g.60985833G>A		28.0	0.0	0		33.0	17.0	0.515152	NM_000633	C9JHD5|P10416|Q13842|Q16197	Silent	SNP	ENST00000398117.1	37	CCDS11981.1																																																																																			.	.	none		0.652	BCL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256199.1	NM_000633, NM_000657	
TNKS1BP1	85456	hgsc.bcm.edu	37	11	57081048	57081048	+	Missense_Mutation	SNP	G	G	C	rs79638626	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:57081048G>C	ENST00000532437.1	-	4	1425	c.1114C>G	c.(1114-1116)Cct>Gct	p.P372A	TNKS1BP1_ENST00000358252.3_Missense_Mutation_p.P372A|TNKS1BP1_ENST00000530920.1_5'Flank			Q9C0C2	TB182_HUMAN	tankyrase 1 binding protein 1, 182kDa	372	Acidic.|Pro-rich.				gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|RNA metabolic process (GO:0016070)|telomere maintenance via telomerase (GO:0007004)	CCR4-NOT complex (GO:0030014)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|nuclear telomeric heterochromatin (GO:0005724)|nucleus (GO:0005634)	ankyrin binding (GO:0030506)|enzyme binding (GO:0019899)	p.P372A(1)		breast(3)|central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(11)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	64		all_epithelial(135;0.21)				AAGACCTCAGGGGGTGGGCTG	0.701													G|||	108	0.0215655	0.0023	0.0418	5008	,	,		13311	0.002		0.0487	False		,,,				2504	0.0256				p.P372A		Atlas-SNP	.											TNKS1BP1,NS,haematopoietic_neoplasm,0,1	TNKS1BP1	148	1	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C1114G						PASS	.	G	ALA/PRO	48,4254		1,46,2104	7.0	10.0	9.0		1114	-6.0	0.0	11	dbSNP_132	9	403,8029		9,385,3822	yes	missense	TNKS1BP1	NM_033396.2	27	10,431,5926	CC,CG,GG		4.7794,1.1158,3.5417	benign	372/1730	57081048	451,12283	2151	4216	6367	SO:0001583	missense	85456	exon5			CCTCAGGGGGTGG	AB051528	CCDS7951.1	11q12.2	2008-07-21			ENSG00000149115	ENSG00000149115			19081	protein-coding gene	gene with protein product		607104				11854288	Standard	NM_033396		Approved	TAB182, KIAA1741, FLJ45975	uc001njs.3	Q9C0C2	OTTHUMG00000167022	ENST00000532437.1:c.1114C>G	11.37:g.57081048G>C	ENSP00000437271:p.Pro372Ala	40.0	0.0	0		44.0	23.0	0.522727	NM_033396	A7E2F8|Q6PJ35|Q6ZV74	Missense_Mutation	SNP	ENST00000532437.1	37	CCDS7951.1	63	0.028846153846153848	2	0.0040650406504065045	16	0.04419889502762431	2	0.0034965034965034965	43	0.05672823218997362	G	8.473	0.857895	0.17178	0.011158	0.047794	ENSG00000149115	ENST00000358252;ENST00000532437	T;T	0.29397	1.57;1.57	4.18	-6.04	0.02178	.	.	.	.	.	T	0.00906	0.0030	N	0.08118	0	0.09310	N	1	B	0.09022	0.002	B	0.08055	0.003	T	0.28170	-1.0052	9	0.08381	T	0.77	0.8305	1.441	0.02354	0.1918:0.3296:0.267:0.2116	.	372	Q9C0C2	TB182_HUMAN	A	372	ENSP00000350990:P372A;ENSP00000437271:P372A	ENSP00000350990:P372A	P	-	1	0	TNKS1BP1	56837624	0.001000	0.12720	0.000000	0.03702	0.644000	0.38419	-0.111000	0.10807	-1.098000	0.03038	0.462000	0.41574	CCT	G|0.970;C|0.030	0.030	strong		0.701	TNKS1BP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392455.1	NM_033396	
ATP2A2	488	hgsc.bcm.edu	37	12	110765378	110765378	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:110765378G>A	ENST00000539276.2	+	8	760	c.651G>A	c.(649-651)ggG>ggA	p.G217G	ATP2A2_ENST00000395494.2_Silent_p.G190G|ATP2A2_ENST00000308664.6_Silent_p.G217G			P16615	AT2A2_HUMAN	ATPase, Ca++ transporting, cardiac muscle, slow twitch 2	217					blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cell adhesion (GO:0007155)|cellular calcium ion homeostasis (GO:0006874)|epidermis development (GO:0008544)|ER-nucleus signaling pathway (GO:0006984)|ion transmembrane transport (GO:0034220)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart rate (GO:0010460)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|transmembrane transport (GO:0055085)|transport (GO:0006810)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|platelet dense tubular network membrane (GO:0031095)|sarcoplasmic reticulum (GO:0016529)|sarcoplasmic reticulum membrane (GO:0033017)	ATP binding (GO:0005524)|calcium-transporting ATPase activity (GO:0005388)|calcium-transporting ATPase activity involved in regulation of cardiac muscle cell membrane potential (GO:0086039)|enzyme binding (GO:0019899)|metal ion binding (GO:0046872)|protein C-terminus binding (GO:0008022)|S100 protein binding (GO:0044548)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(10)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	38						TTGCTGCTGGGAAAGCTATGG	0.483																																					p.G217G		Atlas-SNP	.											.	ATP2A2	78	.	0			c.G651A						PASS	.						186.0	186.0	186.0					12																	110765378		2203	4300	6503	SO:0001819	synonymous_variant	488	exon8			TGCTGGGAAAGCT		CCDS9143.1, CCDS9144.1	12q24.11	2012-10-22			ENSG00000174437	ENSG00000174437	3.6.3.8	"""ATPases / P-type"""	812	protein-coding gene	gene with protein product	"""sarcoplasmic/endoplasmic reticulum calcium ATPase 2"", ""calcium pump 2"""	108740		ATP2B, DAR		10080178	Standard	NM_170665		Approved	SERCA2	uc001tqk.4	P16615	OTTHUMG00000169327	ENST00000539276.2:c.651G>A	12.37:g.110765378G>A		134.0	0.0	0		127.0	45.0	0.354331	NM_001681	A6NDN7|B4DF05|P16614|Q86VJ2	Silent	SNP	ENST00000539276.2	37	CCDS9144.1	.	.	.	.	.	.	.	.	.	.	G	9.772	1.172980	0.21704	.	.	ENSG00000174437	ENST00000548169	.	.	.	5.38	-0.366	0.12545	.	.	.	.	.	T	0.43233	0.1238	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.22173	-1.0224	4	.	.	.	.	3.2414	0.06782	0.2326:0.4733:0.1189:0.1752	.	.	.	.	K	108	.	.	E	+	1	0	ATP2A2	109249761	0.385000	0.25172	0.994000	0.49952	0.998000	0.95712	-0.274000	0.08537	-0.198000	0.10333	0.585000	0.79938	GAA	.	.	none		0.483	ATP2A2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000403539.1	NM_001681	
XXYLT1	152002	hgsc.bcm.edu	37	3	194790782	194790782	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:194790782G>A	ENST00000310380.6	-	4	952	c.844C>T	c.(844-846)Ccc>Tcc	p.P282S	XXYLT1_ENST00000429994.1_Missense_Mutation_p.P136S|XXYLT1_ENST00000460582.1_5'UTR|XXYLT1_ENST00000437101.1_Missense_Mutation_p.P79S|XXYLT1_ENST00000355729.4_Missense_Mutation_p.P79S|XXYLT1_ENST00000356740.5_Missense_Mutation_p.P76S	NM_152531.4	NP_689744.3	Q8NBI6	XXLT1_HUMAN	xyloside xylosyltransferase 1	282						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	transferase activity, transferring pentosyl groups (GO:0016763)										AGCCCCTCGGGGGGCGGGCCC	0.672																																					p.P282S		Atlas-SNP	.											C3orf21,bladder,carcinoma,+2,1	.	.	1	0			c.C844T						scavenged	.						22.0	27.0	26.0					3																	194790782		1802	3994	5796	SO:0001583	missense	152002	exon4			CCTCGGGGGGCGG	AK075551	CCDS43188.1	3q29	2013-02-22	2011-10-19	2011-10-19	ENSG00000173950	ENSG00000173950		"""Glycosyltransferase family 8 domain containing"""	26639	protein-coding gene	gene with protein product		614552	"""chromosome 3 open reading frame 21"""	C3orf21		22117070	Standard	NM_152531		Approved	FLJ35155	uc003fum.4	Q8NBI6	OTTHUMG00000155915	ENST00000310380.6:c.844C>T	3.37:g.194790782G>A	ENSP00000309640:p.Pro282Ser	5.0	0.0	0		14.0	2.0	0.142857	NM_152531	D3DNW5|Q8NAL3|Q8WV03|Q96ME0	Missense_Mutation	SNP	ENST00000310380.6	37	CCDS43188.1	.	.	.	.	.	.	.	.	.	.	G	22.0	4.232940	0.79688	.	.	ENSG00000173950	ENST00000310380;ENST00000437101;ENST00000355729;ENST00000429994;ENST00000356740	T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98	5.89	5.89	0.94794	.	0.000000	0.85682	D	0.000000	T	0.50051	0.1593	M	0.81497	2.545	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.976;0.975	T	0.32134	-0.9918	10	0.24483	T	0.36	-21.2021	19.2443	0.93896	0.0:0.0:1.0:0.0	.	282;79;76	Q8NBI6;Q8NBI6-2;Q8NBI6-3	XXLT1_HUMAN;.;.	S	282;79;79;136;76	ENSP00000309640:P282S;ENSP00000409865:P79S;ENSP00000347967:P79S;ENSP00000399422:P136S;ENSP00000349179:P76S	ENSP00000309640:P282S	P	-	1	0	C3orf21	196272071	1.000000	0.71417	0.712000	0.30502	0.863000	0.49368	7.752000	0.85141	2.797000	0.96272	0.563000	0.77884	CCC	.	.	none		0.672	XXYLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342290.1	NM_152531	
NCOA3	8202	hgsc.bcm.edu	37	20	46279860	46279860	+	Silent	SNP	G	G	A	rs151060280	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:46279860G>A	ENST00000371998.3	+	20	3977	c.3786G>A	c.(3784-3786)caG>caA	p.Q1262Q	NCOA3_ENST00000371997.3_Silent_p.Q1253Q|NCOA3_ENST00000341724.6_Silent_p.Q1188Q|NCOA3_ENST00000372004.3_Silent_p.Q1258Q			Q9Y6Q9	NCOA3_HUMAN	nuclear receptor coactivator 3	1262	Acetyltransferase.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|developmental growth (GO:0048589)|histone acetylation (GO:0016573)|labyrinthine layer morphogenesis (GO:0060713)|mammary gland branching involved in thelarche (GO:0060744)|multicellular organism growth (GO:0035264)|positive regulation of gene expression (GO:0010628)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|receptor transactivation (GO:0035624)|regulation of RNA biosynthetic process (GO:2001141)|transcription, DNA-templated (GO:0006351)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	androgen receptor binding (GO:0050681)|chromatin binding (GO:0003682)|histone acetyltransferase activity (GO:0004402)|ligand-dependent nuclear receptor binding (GO:0016922)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|nuclear hormone receptor binding (GO:0035257)|protein N-terminus binding (GO:0047485)|signal transducer activity (GO:0004871)|thyroid hormone receptor binding (GO:0046966)|transcription coactivator activity (GO:0003713)	p.Q1262Q(1)		breast(3)|endometrium(3)|kidney(4)|large_intestine(12)|lung(19)|ovary(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						agcagcagcagcagcaacagc	0.567																																					p.Q1262Q		Atlas-SNP	.											NCOA3,bladder,carcinoma,0,6	NCOA3	156	6	1	Substitution - coding silent(1)	endometrium(1)	c.G3786A						PASS	.	G	,,,	10,4396	11.4+/-27.6	1,8,2194	53.0	58.0	56.0		3783,3759,3774,3786	-0.1	0.1	20	dbSNP_134	56	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	NCOA3	NM_001174087.1,NM_001174088.1,NM_006534.3,NM_181659.2	,,,	1,20,6482	AA,AG,GG		0.1395,0.227,0.1692	,,,	1261/1424,1253/1416,1258/1421,1262/1425	46279860	22,12984	2203	4300	6503	SO:0001819	synonymous_variant	8202	exon20			GCAGCAGCAGCAA	AF012108	CCDS13406.1, CCDS13407.1, CCDS54472.1	20q12	2011-07-01			ENSG00000124151	ENSG00000124151		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Basic helix-loop-helix proteins"""	7670	protein-coding gene	gene with protein product	"""receptor-associated coactivator 3"", ""thyroid hormone receptor activator molecule 1"""	601937				9252329, 9346901	Standard	NM_181659		Approved	RAC3, AIB1, ACTR, p/CIP, TRAM-1, CAGH16, TNRC16, KAT13B, bHLHe42, SRC-3, SRC3	uc002xtk.3	Q9Y6Q9	OTTHUMG00000033061	ENST00000371998.3:c.3786G>A	20.37:g.46279860G>A		93.0	0.0	0		80.0	4.0	0.05	NM_181659	A4LAZ5|Q0VF45|Q5JYD9|Q5JYE0|Q9BR49|Q9UPC9|Q9UPG4|Q9UPG7	Silent	SNP	ENST00000371998.3	37	CCDS13407.1																																																																																			G|0.997;A|0.003	0.003	strong		0.567	NCOA3-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000080405.1	NM_006534	
MEGF10	84466	hgsc.bcm.edu	37	5	126746147	126746147	+	Silent	SNP	C	C	T	rs35550094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:126746147C>T	ENST00000274473.6	+	10	1251	c.984C>T	c.(982-984)aaC>aaT	p.N328N	MEGF10_ENST00000508365.1_Silent_p.N328N|MEGF10_ENST00000418761.2_Silent_p.N328N|MEGF10_ENST00000503335.2_Silent_p.N328N	NM_032446.2	NP_115822.1	Q96KG7	MEG10_HUMAN	multiple EGF-like-domains 10	328	EGF-like 6. {ECO:0000255|PROSITE- ProRule:PRU00076}.|Necessary for interaction with AP2M1, self-assembly and formation of the irregular, mosaic-like adhesion pattern.				homotypic cell-cell adhesion (GO:0034109)|muscle cell development (GO:0055001)|recognition of apoptotic cell (GO:0043654)|regulation of muscle cell differentiation (GO:0051147)|regulation of skeletal muscle tissue development (GO:0048641)|skeletal muscle satellite cell activation (GO:0014719)|skeletal muscle satellite cell differentiation (GO:0014816)|skeletal muscle satellite cell proliferation (GO:0014841)	cell projection (GO:0042995)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)				breast(2)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(10)|lung(28)|ovary(4)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	68		Prostate(80;0.165)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0657)|Epithelial(69;0.123)		AGTGTGTCAACGGAGGGAAGT	0.587													T|||	82	0.0163738	0.0582	0.0072	5008	,	,		20739	0.0		0.0	False		,,,				2504	0.0				p.N328N		Atlas-SNP	.											.	MEGF10	152	.	0			c.C984T						PASS	.	T		194,4212	808.7+/-415.9	4,186,2013	123.0	103.0	110.0		984	-0.9	0.9	5	dbSNP_126	110	20,8580	818.4+/-406.9	0,20,4280	no	coding-synonymous	MEGF10	NM_032446.2		4,206,6293	TT,TC,CC		0.2326,4.4031,1.6454		328/1141	126746147	214,12792	2203	4300	6503	SO:0001819	synonymous_variant	84466	exon10			TGTCAACGGAGGG	AK021631	CCDS4142.1	5q33	2008-02-05			ENSG00000145794	ENSG00000145794			29634	protein-coding gene	gene with protein product		612453				11347906	Standard	NM_032446		Approved	KIAA1780	uc003kui.4	Q96KG7	OTTHUMG00000128984	ENST00000274473.6:c.984C>T	5.37:g.126746147C>T		132.0	0.0	0		145.0	68.0	0.468966	NM_032446	Q68DE5|Q8WUL3	Silent	SNP	ENST00000274473.6	37	CCDS4142.1																																																																																			C|0.983;T|0.017	0.017	strong		0.587	MEGF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250973.2	NM_032446	
PLEKHA4	57664	hgsc.bcm.edu	37	19	49340661	49340661	+	Missense_Mutation	SNP	C	C	A	rs35965411	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49340661C>A	ENST00000263265.6	-	20	2780	c.2225G>T	c.(2224-2226)gGa>gTa	p.G742V	PLEKHA4_ENST00000355496.5_3'UTR|HSD17B14_ENST00000263278.4_5'Flank|HSD17B14_ENST00000599157.1_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	742			G -> V (in dbSNP:rs35965411).			cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGGACCTCCTCCACGCCCACT	0.706													.|||	489	0.0976438	0.2716	0.0375	5008	,	,		11132	0.001		0.0159	False		,,,				2504	0.089				p.G742V		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.G2225T						PASS	.		,VAL/GLY	832,3560		77,678,1441	24.0	28.0	26.0		,2225	4.2	0.1	19	dbSNP_126	26	92,8490		0,92,4199	yes	utr-3,missense	PLEKHA4	NM_001161354.1,NM_020904.2	,109	77,770,5640	AA,AC,CC		1.072,18.9435,7.1219	,possibly-damaging	,742/780	49340661	924,12050	2196	4291	6487	SO:0001583	missense	57664	exon20			CCTCCTCCACGCC	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.2225G>T	19.37:g.49340661C>A	ENSP00000263265:p.Gly742Val	98.0	0.0	0		79.0	39.0	0.493671	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	149	0.06822344322344322	120	0.24390243902439024	17	0.04696132596685083	0	0.0	12	0.0158311345646438	c	15.22	2.769097	0.49680	0.189435	0.01072	ENSG00000105559	ENST00000263265	T	0.10477	2.87	4.22	4.22	0.49857	.	0.000000	0.38381	N	0.001702	T	0.00012	0.0000	N	0.24115	0.695	0.19575	P	0.9999659469	P	0.41313	0.745	B	0.37346	0.247	T	0.44667	-0.9313	9	0.87932	D	0	.	12.3514	0.55151	0.0:1.0:0.0:0.0	rs35965411;rs61755450	742	Q9H4M7	PKHA4_HUMAN	V	742	ENSP00000263265:G742V	ENSP00000263265:G742V	G	-	2	0	PLEKHA4	54032473	0.000000	0.05858	0.056000	0.19401	0.173000	0.22820	-0.053000	0.11846	2.385000	0.81259	0.450000	0.29827	GGA	C|0.932;A|0.068	0.068	strong		0.706	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
SETBP1	26040	hgsc.bcm.edu	37	18	42530295	42530295	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:42530295G>A	ENST00000282030.5	+	4	1286	c.990G>A	c.(988-990)acG>acA	p.T330T		NM_015559.2	NP_056374.2	Q9Y6X0	SETBP_HUMAN	SET binding protein 1	330						nucleus (GO:0005634)	DNA binding (GO:0003677)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(20)|lung(47)|prostate(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	104				Colorectal(1;0.0622)|COAD - Colon adenocarcinoma(74;0.201)		AACCACCTACGGTGGGCAGCA	0.527									Schinzel-Giedion syndrome																												p.T330T		Atlas-SNP	.											.	SETBP1	577	.	0			c.G990A						PASS	.						68.0	74.0	72.0					18																	42530295		2202	4300	6502	SO:0001819	synonymous_variant	26040	exon4	Familial Cancer Database	SGC, Schinzel-Giedion Midface Retraction syndrome	ACCTACGGTGGGC	AB022660	CCDS11923.2, CCDS45859.1	18q21.1	2008-08-01			ENSG00000152217	ENSG00000152217			15573	protein-coding gene	gene with protein product		611060				11231286	Standard	NM_015559		Approved	SEB, KIAA0437	uc010dni.3	Q9Y6X0	OTTHUMG00000132613	ENST00000282030.5:c.990G>A	18.37:g.42530295G>A		59.0	0.0	0		60.0	35.0	0.583333	NM_015559	A6H8W5|Q6P6C3|Q9UEF3	Silent	SNP	ENST00000282030.5	37	CCDS11923.2																																																																																			.	.	none		0.527	SETBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255854.4	NM_001130110	
SOS2	6655	hgsc.bcm.edu	37	14	50585109	50585109	+	Missense_Mutation	SNP	G	G	A	rs140995728	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:50585109G>A	ENST00000216373.5	-	23	4226	c.3952C>T	c.(3952-3954)Cca>Tca	p.P1318S	VCPKMT_ENST00000395860.2_5'Flank|VCPKMT_ENST00000395859.2_5'Flank|SOS2_ENST00000543680.1_Missense_Mutation_p.P1285S	NM_006939.2	NP_008870.2	Q07890	SOS2_HUMAN	son of sevenless homolog 2 (Drosophila)	1318					apoptotic signaling pathway (GO:0097190)|axon guidance (GO:0007411)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	DNA binding (GO:0003677)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(13)|lung(16)|ovary(2)|skin(1)	39	all_epithelial(31;0.000822)|Breast(41;0.0065)					CTGTACAATGGGGGGTGCGAA	0.463													G|||	4	0.000798722	0.0	0.0014	5008	,	,		17130	0.0		0.003	False		,,,				2504	0.0				p.P1318S		Atlas-SNP	.											.	SOS2	195	.	0			c.C3952T						PASS	.	G	SER/PRO	2,4404	4.2+/-10.8	0,2,2201	74.0	72.0	72.0		3952	5.4	0.8	14	dbSNP_134	72	11,8589	8.4+/-32.0	0,11,4289	yes	missense	SOS2	NM_006939.2	74	0,13,6490	AA,AG,GG		0.1279,0.0454,0.1	benign	1318/1333	50585109	13,12993	2203	4300	6503	SO:0001583	missense	6655	exon23			ACAATGGGGGGTG	L13858	CCDS9697.1	14q21	2013-01-10	2001-12-04		ENSG00000100485	ENSG00000100485		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	11188	protein-coding gene	gene with protein product		601247	"""son of sevenless (Drosophilia) homolog 2"""			8276400	Standard	NM_006939		Approved		uc001wxs.4	Q07890	OTTHUMG00000140292	ENST00000216373.5:c.3952C>T	14.37:g.50585109G>A	ENSP00000216373:p.Pro1318Ser	206.0	0.0	0		165.0	73.0	0.442424	NM_006939	B7ZKT6|D3DSB4|Q15503|Q17RN1	Missense_Mutation	SNP	ENST00000216373.5	37	CCDS9697.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	3.971	-0.008341	0.07727	4.54E-4	0.001279	ENSG00000100485	ENST00000216373;ENST00000543680	T;T	0.78003	-1.14;-1.01	5.37	5.37	0.77165	.	0.056414	0.64402	D	0.000001	T	0.81293	0.4792	L	0.33485	1.01	0.58432	D	0.999999	D;D	0.63880	0.993;0.993	D;D	0.70227	0.968;0.968	T	0.75099	-0.3437	10	0.10636	T	0.68	.	19.1021	0.93277	0.0:0.0:1.0:0.0	.	1285;1318	B7ZKT6;Q07890	.;SOS2_HUMAN	S	1318;1285	ENSP00000216373:P1318S;ENSP00000445328:P1285S	ENSP00000216373:P1318S	P	-	1	0	SOS2	49654859	1.000000	0.71417	0.829000	0.32907	0.982000	0.71751	3.088000	0.50175	2.490000	0.84030	0.563000	0.77884	CCA	G|0.999;A|0.001	0.001	strong		0.463	SOS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276878.2		
LMO7	4008	hgsc.bcm.edu	37	13	76370887	76370887	+	Splice_Site	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:76370887T>C	ENST00000321797.8	+	4	484		c.e4+2		RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Splice_Site|LMO7_ENST00000377534.3_Splice_Site|LMO7_ENST00000341547.4_Splice_Site|LMO7_ENST00000465261.2_Splice_Site|LMO7_ENST00000526202.1_Splice_Site			Q8WWI1	LMO7_HUMAN	LIM domain 7						protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		CTGACGAAGGTAAGTAAACTA	0.398																																					.		Atlas-SNP	.											.	LMO7	334	.	0			c.618+2T>C						PASS	.						112.0	99.0	103.0					13																	76370887		2203	4300	6503	SO:0001630	splice_region_variant	4008	exon7			CGAAGGTAAGTAA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.-238+2T>C	13.37:g.76370887T>C		60.0	0.0	0		100.0	26.0	0.26	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Splice_Site	SNP	ENST00000321797.8	37		.	.	.	.	.	.	.	.	.	.	T	9.699	1.153939	0.21371	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000526202	.	.	.	5.11	3.89	0.44902	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.397	0.49847	0.1357:0.0:0.0:0.8643	.	.	.	.	.	-1	.	.	.	+	.	.	LMO7	75268888	1.000000	0.71417	1.000000	0.80357	0.040000	0.13550	7.075000	0.76798	0.844000	0.35094	0.459000	0.35465	.	.	.	none		0.398	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	Intron
PLEKHA4	57664	hgsc.bcm.edu	37	19	49340746	49340746	+	Missense_Mutation	SNP	T	T	C	rs34460869	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:49340746T>C	ENST00000263265.6	-	20	2695	c.2140A>G	c.(2140-2142)Acg>Gcg	p.T714A	PLEKHA4_ENST00000355496.5_3'UTR|HSD17B14_ENST00000263278.4_5'Flank|HSD17B14_ENST00000599157.1_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	714			T -> A (in dbSNP:rs34460869).			cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		TCCTGGCGCGTGGGGTCCGAA	0.652													.|||	489	0.0976438	0.2716	0.0375	5008	,	,		12165	0.001		0.0159	False		,,,				2504	0.089				p.T714A		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.A2140G						PASS	.		,ALA/THR	867,3535		87,693,1421	31.0	38.0	36.0		,2140	1.5	0.0	19	dbSNP_126	36	94,8506		0,94,4206	yes	utr-3,missense	PLEKHA4	NM_001161354.1,NM_020904.2	,58	87,787,5627	CC,CT,TT		1.093,19.6956,7.3912	,benign	,714/780	49340746	961,12041	2201	4300	6501	SO:0001583	missense	57664	exon20			GGCGCGTGGGGTC	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.2140A>G	19.37:g.49340746T>C	ENSP00000263265:p.Thr714Ala	146.0	0.0	0		143.0	76.0	0.531469	NM_020904	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	37	CCDS12737.1	149	0.06822344322344322	120	0.24390243902439024	17	0.04696132596685083	0	0.0	12	0.0158311345646438	t	12.76	2.033282	0.35893	0.196956	0.01093	ENSG00000105559	ENST00000263265	T	0.08634	3.07	3.76	1.51	0.23008	.	1.395420	0.04808	N	0.434704	T	0.00012	0.0000	N	0.24115	0.695	0.58432	P	4.000000000004E-6	B	0.26002	0.139	B	0.19391	0.025	T	0.47983	-0.9074	9	0.20519	T	0.43	.	8.0169	0.30387	0.0:0.0:0.4338:0.5662	rs34460869	714	Q9H4M7	PKHA4_HUMAN	A	714	ENSP00000263265:T714A	ENSP00000263265:T714A	T	-	1	0	PLEKHA4	54032558	0.001000	0.12720	0.001000	0.08648	0.315000	0.28087	0.381000	0.20619	0.142000	0.18901	0.249000	0.18162	ACG	T|0.929;C|0.071	0.071	strong		0.652	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
JAK2	3717	hgsc.bcm.edu	37	9	5050706	5050706	+	Silent	SNP	C	C	T	rs2230722	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:5050706C>T	ENST00000381652.3	+	6	983	c.489C>T	c.(487-489)caC>caT	p.H163H	JAK2_ENST00000539801.1_Silent_p.H163H|JAK2_ENST00000544510.1_Silent_p.H14H	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		75.0	0.0	0		83.0	82.0	0.987952	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		
DMBT1	1755	hgsc.bcm.edu	37	10	124330421	124330421	+	Missense_Mutation	SNP	C	C	G	rs75209396	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:124330421C>G	ENST00000338354.3	+	4	261	c.155C>G	c.(154-156)tCg>tGg	p.S52W	DMBT1_ENST00000344338.3_Missense_Mutation_p.S52W|DMBT1_ENST00000330163.4_Missense_Mutation_p.S52W|DMBT1_ENST00000368956.2_Missense_Mutation_p.S52W|DMBT1_ENST00000359586.6_Missense_Mutation_p.S52W|DMBT1_ENST00000368909.3_Missense_Mutation_p.S52W|DMBT1_ENST00000368955.3_Missense_Mutation_p.S52W			Q9UGM3	DMBT1_HUMAN	deleted in malignant brain tumors 1	52			S -> W (in dbSNP:rs75209396). {ECO:0000269|PubMed:12185598, ECO:0000269|PubMed:12353266}.		defense response to virus (GO:0051607)|epithelial cell differentiation (GO:0030855)|induction of bacterial agglutination (GO:0043152)|innate immune response (GO:0045087)|inner cell mass cell proliferation (GO:0001833)|pattern recognition receptor signaling pathway (GO:0002221)|positive regulation of epithelial cell differentiation (GO:0030858)|protein transport (GO:0015031)|receptor-mediated endocytosis (GO:0006898)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|phagocytic vesicle membrane (GO:0030670)|proteinaceous extracellular matrix (GO:0005578)|zymogen granule membrane (GO:0042589)	calcium-dependent protein binding (GO:0048306)|scavenger receptor activity (GO:0005044)|signaling pattern recognition receptor activity (GO:0008329)|zymogen binding (GO:0035375)			breast(2)|central_nervous_system(7)|cervix(3)|endometrium(8)|kidney(1)|large_intestine(1)|lung(46)|prostate(1)|urinary_tract(3)	72		all_neural(114;0.0765)|Lung NSC(174;0.132)|all_lung(145;0.163)|Breast(234;0.238)				CCATTTCCCTCGGAGTCGACC	0.537													c|||	329	0.0656949	0.23	0.0231	5008	,	,		22102	0.001		0.007	False		,,,				2504	0.001				p.S52W	Ovarian(182;93 2026 18125 22222 38972)	Atlas-SNP	.											.	DMBT1	677	.	0			c.C155G						PASS	.	C	TRP/SER,TRP/SER,TRP/SER	658,3106		51,556,1275	168.0	167.0	167.0		155,155,155	1.0	0.0	10	dbSNP_132	167	51,8185		0,51,4067	yes	missense,missense,missense	DMBT1	NM_004406.2,NM_007329.2,NM_017579.2	177,177,177	51,607,5342	GG,GC,CC		0.6192,17.4814,5.9083	probably-damaging,probably-damaging,probably-damaging	52/1786,52/2414,52/2404	124330421	709,11291	1882	4118	6000	SO:0001583	missense	1755	exon4			TTCCCTCGGAGTC		CCDS44490.1, CCDS44491.1, CCDS44492.1	10q25.3-q26.1	2008-08-01			ENSG00000187908	ENSG00000187908			2926	protein-coding gene	gene with protein product		601969				9288095, 17548659	Standard	NM_004406		Approved	GP340, muclin	uc001lgk.1	Q9UGM3	OTTHUMG00000019185	ENST00000338354.3:c.155C>G	10.37:g.124330421C>G	ENSP00000342210:p.Ser52Trp	188.0	0.0	0		185.0	81.0	0.437838	NM_007329	A6NDG4|A6NDJ5|A8E4R5|B1ARE7|B1ARE8|B1ARE9|B1ARF0|B7Z8Y2|F8WEF7|Q59EX0|Q5JR26|Q6MZN4|Q96DU4|Q9UGM2|Q9UJ57|Q9UKJ4|Q9Y211|Q9Y4V9	Missense_Mutation	SNP	ENST00000338354.3	37		130	0.05952380952380952	118	0.23983739837398374	9	0.024861878453038673	0	0.0	3	0.00395778364116095	C	10.71	1.426167	0.25726	0.174814	0.006192	ENSG00000187908	ENST00000338354;ENST00000368915;ENST00000341278;ENST00000368953;ENST00000339871;ENST00000368942;ENST00000327438;ENST00000344338;ENST00000339712;ENST00000330163;ENST00000368909;ENST00000368955;ENST00000368956;ENST00000359586	T;T;T;T;T;T;T	0.26223	1.85;1.84;1.78;1.85;1.84;1.78;1.75	1.9	0.968	0.19680	.	.	.	.	.	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	D;P;P;P;D	0.76494	0.997;0.572;0.922;0.529;0.999	D;B;B;B;P	0.65443	0.935;0.152;0.206;0.202;0.902	T	0.24476	-1.0159	8	0.66056	D	0.02	.	4.3987	0.11376	0.0:0.7908:0.0:0.2092	.	52;52;52;52;52	F8WEF7;Q9UGM3-6;Q9UGM3-2;Q9UGM3-3;Q9UGM3	.;.;.;.;DMBT1_HUMAN	W	52	ENSP00000342210:S52W;ENSP00000343175:S52W;ENSP00000327747:S52W;ENSP00000357905:S52W;ENSP00000357951:S52W;ENSP00000357952:S52W;ENSP00000352593:S52W	ENSP00000331522:S52W	S	+	2	0	DMBT1	124320411	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	0.122000	0.15687	0.337000	0.23665	0.205000	0.17691	TCG	C|0.950;G|0.050	0.050	strong		0.537	DMBT1-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000050792.2	NM_004406	
BTN2A1	11120	hgsc.bcm.edu	37	6	26458871	26458871	+	Missense_Mutation	SNP	T	T	C	rs146399224	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:26458871T>C	ENST00000312541.5	+	2	255	c.7T>C	c.(7-9)Tca>Cca	p.S3P	BTN2A1_ENST00000541522.1_Intron|BTN2A1_ENST00000429381.1_Missense_Mutation_p.S3P|BTN2A1_ENST00000469185.1_Missense_Mutation_p.S3P	NM_007049.3|NM_078476.2	NP_008980.1|NP_510961.1	Q7KYR7	BT2A1_HUMAN	butyrophilin, subfamily 2, member A1	3					lipid metabolic process (GO:0006629)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				breast(3)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)|skin(3)|urinary_tract(3)	27						GCTCATGGAATCAGCTGCTGC	0.617													T|||	2	0.000399361	0.0	0.0	5008	,	,		15890	0.0		0.002	False		,,,				2504	0.0				p.S3P		Atlas-SNP	.											.	BTN2A1	118	.	0			c.T7C						PASS	.						233.0	171.0	192.0					6																	26458871		2203	4300	6503	SO:0001583	missense	11120	exon2			ATGGAATCAGCTG	U90543	CCDS4613.1, CCDS47390.1, CCDS56404.1, CCDS56405.1	6p22.1	2014-01-14			ENSG00000112763	ENSG00000112763		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Butyrophilins"""	1136	protein-coding gene	gene with protein product		613590				9382921, 9149941	Standard	NM_007049		Approved	BT2.1, BTF1, BTN2.1	uc003nib.2	Q7KYR7	OTTHUMG00000014457	ENST00000312541.5:c.7T>C	6.37:g.26458871T>C	ENSP00000312158:p.Ser3Pro	101.0	0.0	0		111.0	6.0	0.0540541	NM_001197234	B4DLP9|E9PGR4|O00475|P78408|Q59EN4|Q7KYQ7|Q7Z386|Q96AV7|Q9NU62	Missense_Mutation	SNP	ENST00000312541.5	37	CCDS4613.1	.	.	.	.	.	.	.	.	.	.	T	0.016	-1.519967	0.00967	.	.	ENSG00000112763	ENST00000312541;ENST00000429381;ENST00000265424;ENST00000469185	T;T;T	0.76448	-0.46;-1.02;-1.01	3.03	0.0692	0.14373	.	0.876207	0.09516	N	0.791659	T	0.24392	0.0591	N	0.01668	-0.77	0.09310	N	0.999992	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.18053	-1.0349	10	0.42905	T	0.14	.	3.2421	0.06784	0.0:0.505:0.2251:0.2699	.	3;3	Q96AV7;Q7KYR7	.;BT2A1_HUMAN	P	3	ENSP00000312158:S3P;ENSP00000416945:S3P;ENSP00000419043:S3P	ENSP00000265424:S3P	S	+	1	0	BTN2A1	26566850	0.150000	0.22732	0.014000	0.15608	0.022000	0.10575	0.087000	0.14958	-0.002000	0.14469	-0.354000	0.07668	TCA	T|0.999;C|0.001	0.001	weak		0.617	BTN2A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040122.2	NM_007049	
KRTAP10-10	353333	hgsc.bcm.edu	37	21	46057634	46057634	+	Silent	SNP	T	T	C	rs61029972	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr21:46057634T>C	ENST00000380095.1	+	1	362	c.300T>C	c.(298-300)tgT>tgC	p.C100C	TSPEAR_ENST00000323084.4_Intron	NM_181688.1	NP_859016.1	P60014	KR10A_HUMAN	keratin associated protein 10-10	100	15 X 5 AA repeats of C-C-X(3).					keratin filament (GO:0045095)				NS(1)|endometrium(2)|kidney(1)|lung(6)|prostate(1)|skin(2)	13						ctgtctgctgtgtgcccgtct	0.632													C|||	539	0.107628	0.2383	0.0591	5008	,	,		18755	0.0109		0.0557	False		,,,				2504	0.1186				p.C100C		Atlas-SNP	.											.	KRTAP10-10	37	.	0			c.T300C						PASS	.						126.0	121.0	123.0					21																	46057634		2203	4298	6501	SO:0001819	synonymous_variant	353333	exon1			CTGCTGTGTGCCC	AJ566387	CCDS33585.1	21q22.3	2006-03-13			ENSG00000221859	ENSG00000221859		"""Keratin associated proteins"""	22972	protein-coding gene	gene with protein product							Standard	NM_181688		Approved	KAP10.10, KAP18.10, KRTAP18-10	uc002zfq.3	P60014	OTTHUMG00000057631	ENST00000380095.1:c.300T>C	21.37:g.46057634T>C		142.0	0.0	0		145.0	84.0	0.57931	NM_181688		Silent	SNP	ENST00000380095.1	37	CCDS33585.1																																																																																			C|1.000;|0.000	1.000	weak		0.632	KRTAP10-10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128034.1	NM_181688	
MLH1	4292	hgsc.bcm.edu	37	3	37053568	37053568	+	Missense_Mutation	SNP	A	A	G	rs1799977	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:37053568A>G	ENST00000231790.2	+	8	871	c.655A>G	c.(655-657)Atc>Gtc	p.I219V	MLH1_ENST00000458205.2_5'UTR|MLH1_ENST00000455445.2_5'UTR|MLH1_ENST00000536378.1_5'UTR|MLH1_ENST00000539477.1_5'UTR|MLH1_ENST00000435176.1_Missense_Mutation_p.I121V	NM_000249.3|NM_001258273.1	NP_000240.1|NP_001245202.1	P40692	MLH1_HUMAN	mutL homolog 1	219			I -> V (common polymorphism; found in 37% of alleles; dbSNP:rs1799977). {ECO:0000269|PubMed:10375096, ECO:0000269|PubMed:10777691, ECO:0000269|PubMed:11754112, ECO:0000269|PubMed:12115348, ECO:0000269|PubMed:12200596, ECO:0000269|PubMed:12362047, ECO:0000269|PubMed:9032648, ECO:0000269|PubMed:9067757, ECO:0000269|PubMed:9087566, ECO:0000269|PubMed:9218993, ECO:0000269|PubMed:9833759, ECO:0000269|Ref.5}.		ATP catabolic process (GO:0006200)|double-strand break repair via nonhomologous end joining (GO:0006303)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|isotype switching (GO:0045190)|male meiosis chromosome segregation (GO:0007060)|meiotic metaphase I plate congression (GO:0043060)|mismatch repair (GO:0006298)|negative regulation of mitotic recombination (GO:0045950)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|oogenesis (GO:0048477)|resolution of meiotic recombination intermediates (GO:0000712)|somatic hypermutation of immunoglobulin genes (GO:0016446)|spermatogenesis (GO:0007283)|spindle midzone assembly involved in meiosis (GO:0051257)|synapsis (GO:0007129)	chiasma (GO:0005712)|male germ cell nucleus (GO:0001673)|membrane (GO:0016020)|MutLalpha complex (GO:0032389)|nucleus (GO:0005634)|synaptonemal complex (GO:0000795)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|guanine/thymine mispair binding (GO:0032137)	p.I219V(1)|p.0?(1)		NS(1)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(12)|kidney(2)|large_intestine(54)|lung(13)|oesophagus(7)|ovary(6)|pancreas(5)|prostate(5)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	127						TATTCGCTCCATCTTTGGAAA	0.368		1	"""D, Mis, N, F, S"""		"""colorectal, endometrial, ovarian, CNS"""	"""colorectal, endometrial, ovarian, CNS"""		Mismatch excision repair (MMR)	Turcot syndrome;Muir-Torre syndrome;Lynch syndrome;Constitutional Mismatch Repair Deficiency Syndrome				A|||	649	0.129593	0.0386	0.1686	5008	,	,		18149	0.0258		0.325	False		,,,				2504	0.1309				p.I219V		Atlas-SNP	.	yes	Rec	yes	"""Hereditary non-polyposis colorectal cancer, Turcot syndrome"""	3	3p21.3	4292	E.coli MutL homolog gene		"""E, O"""	MLH1,NS,carcinoma,0,1	MLH1	226	1	2	Substitution - Missense(1)|Whole gene deletion(1)	ovary(1)|prostate(1)	c.A655G	GRCh37	CM970958	MLH1	M	rs1799977	PASS	.	A	VAL/ILE,VAL/ILE,,	406,4000	199.4+/-223.0	27,352,1824	145.0	129.0	135.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	655,361,,	4.6	1.0	3	dbSNP_89	135	2754,5846	438.0+/-358.8	442,1870,1988	yes	missense,missense,utr-5,utr-5	MLH1	NM_000249.3,NM_001167617.1,NM_001167618.1,NM_001167619.1	29,29,,	469,2222,3812	GG,GA,AA		32.0233,9.2147,24.2965	benign,benign,,	219/757,121/659,,	37053568	3160,9846	2203	4300	6503	SO:0001583	missense	4292	exon8	Familial Cancer Database	Brain tumor-colorectal polyp(osis) syndrome; ;Hereditary Non-Polyposis Colorectal Cancer, HNPCC, Lynch syndromes 1 and 2 (= Cancer Family Syndrome), Hereditary Mismatch Repair Deficiency syndrome, HMRDS;Mismatch Repair Cancer syndrome, MMRCS, Childhood Cancer Syndrome, CCS, Biallelic Mismatch Repair Gene Mutations Associated Early Onset Cancer, Lynch syndrome type III	CGCTCCATCTTTG	U07418	CCDS2663.1, CCDS54562.1, CCDS54563.1	3p22.3	2014-09-17	2013-09-12		ENSG00000076242	ENSG00000076242			7127	protein-coding gene	gene with protein product		120436	"""mutL (E. coli) homolog 1 (colon cancer, nonpolyposis type 2)"", ""mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli)"""	COCA2		7903889	Standard	NM_000249		Approved	HNPCC, FCC2, HNPCC2	uc003cgl.3	P40692	OTTHUMG00000130797	ENST00000231790.2:c.655A>G	3.37:g.37053568A>G	ENSP00000231790:p.Ile219Val	118.0	0.0	0		101.0	44.0	0.435644	NM_000249	B4DI13|B4DQ11|E9PCU2	Missense_Mutation	SNP	ENST00000231790.2	37	CCDS2663.1	374	0.17124542124542125	28	0.056910569105691054	72	0.19889502762430938	16	0.027972027972027972	258	0.3403693931398417	A	14.01	2.408011	0.42715	0.092147	0.320233	ENSG00000076242	ENST00000231790;ENST00000436867;ENST00000537937;ENST00000383761;ENST00000435176	D;D	0.83591	-1.74;-1.74	5.76	4.61	0.57282	Ribosomal protein S5 domain 2-type fold (1);DNA mismatch repair protein, N-terminal (1);ATPase-like, ATP-binding domain (1);Ribosomal protein S5 domain 2-type fold, subgroup (1);DNA mismatch repair protein, C-terminal (1);	0.113678	0.64402	D	0.000010	T	0.00012	0.0000	N	0.25992	0.78	0.09310	P	1.0	B;B;B	0.16603	0.018;0.018;0.018	B;B;B	0.26864	0.028;0.074;0.06	T	0.07424	-1.0773	9	0.12430	T	0.62	-17.9526	7.4844	0.27423	0.7886:0.0:0.2114:0.0	rs1799977;rs2229023;rs11541861;rs17809298;rs52803721;rs56722302;rs1799977	121;219;219	E9PCU2;Q53GX1;P40692	.;.;MLH1_HUMAN	V	219;185;185;83;121	ENSP00000231790:I219V;ENSP00000402564:I121V	ENSP00000231790:I219V	I	+	1	0	MLH1	37028572	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.446000	0.44908	2.209000	0.71365	0.533000	0.62120	ATC	A|0.799;G|0.201	0.201	strong		0.368	MLH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253337.2	NM_000249	
ADAMTS14	140766	hgsc.bcm.edu	37	10	72520417	72520417	+	Silent	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:72520417A>G	ENST00000373207.1	+	22	3480	c.3480A>G	c.(3478-3480)ccA>ccG	p.P1160P	ADAMTS14_ENST00000373208.1_Silent_p.P1163P	NM_080722.3	NP_542453.2	Q8WXS8	ATS14_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 14	1160	Pro-rich.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(11)|lung(15)|ovary(7)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	50						CAAGCTCCCCAGGGACCCAGC	0.632																																					p.P1163P		Atlas-SNP	.											ADAMTS14,rectum,carcinoma,+2,2	ADAMTS14	148	2	0			c.A3489G						PASS	.						61.0	60.0	60.0					10																	72520417		2203	4300	6503	SO:0001819	synonymous_variant	140766	exon22			CTCCCCAGGGACC	AF358666	CCDS7306.1, CCDS7307.1	10q21	2008-08-01	2005-08-19		ENSG00000138316	ENSG00000138316		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	14899	protein-coding gene	gene with protein product		607506	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 14"""			11779638	Standard	NM_139155		Approved		uc001jrg.3	Q8WXS8	OTTHUMG00000018414	ENST00000373207.1:c.3480A>G	10.37:g.72520417A>G		70.0	0.0	0		75.0	38.0	0.506667	NM_139155	Q5T4G0|Q5T4G1|Q8TE55|Q8TEY8	Silent	SNP	ENST00000373207.1	37	CCDS7306.1																																																																																			.	.	none		0.632	ADAMTS14-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000048522.1	NM_080722	
C11orf24	53838	hgsc.bcm.edu	37	11	68029738	68029738	+	Missense_Mutation	SNP	G	G	A	rs143548724	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:68029738G>A	ENST00000304271.6	-	4	1127	c.725C>T	c.(724-726)gCg>gTg	p.A242V	C11orf24_ENST00000533310.1_Intron|C11orf24_ENST00000530166.1_5'Flank	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	242	Pro-rich.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						AGGGCTTGCCGCGGTGTCACT	0.562													G|||	12	0.00239617	0.0	0.0043	5008	,	,		17040	0.0		0.005	False		,,,				2504	0.0041				p.A242V	NSCLC(21;855 905 4198 36694)	Atlas-SNP	.											.	C11orf24	35	.	0			c.C725T						PASS	.	G	VAL/ALA	1,4399	4.2+/-10.8	0,1,2199	110.0	108.0	108.0		725	2.7	0.0	11	dbSNP_134	108	41,8547	26.3+/-74.7	1,39,4254	yes	missense	C11orf24	NM_022338.3	64	1,40,6453	AA,AG,GG		0.4774,0.0227,0.3234	benign	242/450	68029738	42,12946	2200	4294	6494	SO:0001583	missense	53838	exon4			CTTGCCGCGGTGT	AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.725C>T	11.37:g.68029738G>A	ENSP00000307264:p.Ala242Val	452.0	0.0	0		475.0	238.0	0.501053	NM_022338	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	G	12.16	1.854439	0.32791	2.27E-4	0.004774	ENSG00000171067	ENST00000304271	T	0.30448	1.53	4.61	2.73	0.32206	.	1.566200	0.04540	N	0.387933	T	0.20251	0.0487	N	0.14661	0.345	0.21984	N	0.999436	B	0.29862	0.259	B	0.22880	0.042	T	0.26503	-1.0101	10	0.33940	T	0.23	0.7561	9.9733	0.41768	0.1699:0.0:0.8301:0.0	.	242	Q96F05	CK024_HUMAN	V	242	ENSP00000307264:A242V	ENSP00000307264:A242V	A	-	2	0	C11orf24	67786314	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	0.126000	0.15769	0.487000	0.27698	-0.459000	0.05422	GCG	G|0.998;A|0.002	0.002	strong		0.562	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1	NM_022338	
SP100	6672	hgsc.bcm.edu	37	2	231379967	231379967	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:231379967C>T	ENST00000264052.5	+	25	2607	c.2252C>T	c.(2251-2253)aCc>aTc	p.T751I	SP100_ENST00000340126.4_Intron	NM_003113.3	NP_003104.2	P23497	SP100_HUMAN	SP100 nuclear antigen	751					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)		GAAATGAAAACCTATATCCCT	0.428																																					p.T751I		Atlas-SNP	.											.	SP100	167	.	0			c.C2252T						PASS	.						53.0	57.0	55.0					2																	231379967		2201	4297	6498	SO:0001583	missense	6672	exon25			TGAAAACCTATAT	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.2252C>T	2.37:g.231379967C>T	ENSP00000264052:p.Thr751Ile	81.0	0.0	0		78.0	36.0	0.461538	NM_003113	B4DDX5|B8ZZD8|E7EUA7|E9PH61|F8WFE2|O75450|Q13343|Q8TE34|Q96F70|Q96T24|Q96T95|Q9NP33|Q9UE32	Missense_Mutation	SNP	ENST00000264052.5	37	CCDS2477.1	.	.	.	.	.	.	.	.	.	.	C	7.765	0.706193	0.15239	.	.	ENSG00000067066	ENST00000264052	T	0.17854	2.25	0.158	0.158	0.14942	High mobility group, superfamily (1);High mobility group, HMG1/HMG2 (4);	.	.	.	.	T	0.18635	0.0447	M	0.66297	2.02	0.80722	D	1	B	0.34313	0.448	B	0.38156	0.266	T	0.05402	-1.0887	9	0.54805	T	0.06	.	6.0348	0.19702	0.0:0.9995:0.0:5.0E-4	.	751	P23497	SP100_HUMAN	I	751	ENSP00000264052:T751I	ENSP00000264052:T751I	T	+	2	0	SP100	231088211	0.593000	0.26840	0.022000	0.16811	0.022000	0.10575	-0.367000	0.07553	0.202000	0.20498	0.205000	0.17691	ACC	.	.	none		0.428	SP100-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256914.2	NM_003113	
RNF31	55072	hgsc.bcm.edu	37	14	24620710	24620710	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:24620710C>G	ENST00000324103.6	+	10	2074	c.1754C>G	c.(1753-1755)tCt>tGt	p.S585C	RNF31_ENST00000382687.3_Missense_Mutation_p.S434C|RNF31_ENST00000559275.1_Missense_Mutation_p.S434C|RP11-468E2.4_ENST00000558468.1_Missense_Mutation_p.S60C	NM_017999.4	NP_060469.4	Q96EP0	RNF31_HUMAN	ring finger protein 31	585	Interaction with RBCK1.|UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				CD40 signaling pathway (GO:0023035)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein linear polyubiquitination (GO:0097039)|protein polyubiquitination (GO:0000209)|T cell receptor signaling pathway (GO:0050852)	CD40 receptor complex (GO:0035631)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|LUBAC complex (GO:0071797)	ligase activity (GO:0016874)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(6)|kidney(1)|large_intestine(6)|lung(15)|ovary(1)|prostate(4)|skin(2)|soft_tissue(1)	39				GBM - Glioblastoma multiforme(265;0.00861)		GAGCTCCAGTCTCTAGGCTTT	0.587																																					p.S585C		Atlas-SNP	.											RNF31,NS,carcinoma,0,1	RNF31	95	1	0			c.C1754G						PASS	.						53.0	55.0	55.0					14																	24620710		2021	4210	6231	SO:0001583	missense	55072	exon10			TCCAGTCTCTAGG	AK000973	CCDS41931.1	14q11.2	2012-09-20			ENSG00000092098	ENSG00000092098		"""RING-type (C3HC4) zinc fingers"""	16031	protein-coding gene	gene with protein product	"""HOIL-1-interacting protein"""	612487				10422847	Standard	NM_017999		Approved	ZIBRA, FLJ10111, FLJ23501, HOIP	uc001wmn.1	Q96EP0	OTTHUMG00000028798	ENST00000324103.6:c.1754C>G	14.37:g.24620710C>G	ENSP00000315112:p.Ser585Cys	88.0	0.0	0		81.0	37.0	0.45679	NM_017999	A0A962|Q86VI2|Q8TEI0|Q96GB4|Q96NF1|Q9H5F1|Q9NWD2	Missense_Mutation	SNP	ENST00000324103.6	37	CCDS41931.1	.	.	.	.	.	.	.	.	.	.	C	9.929	1.214179	0.22289	.	.	ENSG00000092098	ENST00000324103;ENST00000382687	T;T	0.47869	0.83;0.83	5.42	3.47	0.39725	Ubiquitin-associated/translation elongation factor EF1B, N-terminal, eukaryote (1);UBA-like (1);	0.583409	0.18022	N	0.154194	T	0.37461	0.1004	N	0.19112	0.55	0.09310	N	1	D;P;D	0.54964	0.969;0.947;0.969	P;B;P	0.49683	0.619;0.36;0.563	T	0.14364	-1.0475	10	0.72032	D	0.01	-7.8769	6.4608	0.21956	0.0:0.6637:0.1566:0.1797	.	344;585;434	B3KV71;Q96EP0;Q96EP0-3	.;RNF31_HUMAN;.	C	585;434	ENSP00000315112:S585C;ENSP00000372134:S434C	ENSP00000315112:S585C	S	+	2	0	RNF31	23690550	0.059000	0.20769	0.991000	0.47740	0.196000	0.23810	1.449000	0.35123	1.523000	0.49018	0.655000	0.94253	TCT	.	.	none		0.587	RNF31-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071921.3	NM_017999	
OTUD7B	56957	hgsc.bcm.edu	37	1	149916118	149916118	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:149916118G>C	ENST00000369135.4	-	12	2464	c.2170C>G	c.(2170-2172)Cta>Gta	p.L724V		NM_020205.2	NP_064590.2	Q6GQQ9	OTU7B_HUMAN	OTU deubiquitinase 7B	724					mucosal immune response (GO:0002385)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of protein localization to nucleus (GO:1900181)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein K11-linked deubiquitination (GO:0035871)|protein K48-linked deubiquitination (GO:0071108)|protein K63-linked deubiquitination (GO:0070536)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	cysteine-type peptidase activity (GO:0008234)|DNA binding (GO:0003677)|Lys48-specific deubiquitinase activity (GO:1990380)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			breast(1)|endometrium(6)|kidney(2)|large_intestine(5)|lung(18)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39	Breast(34;0.0009)|Ovarian(49;0.0265)|all_hematologic(923;0.0597)|Hepatocellular(266;0.161)|Colorectal(459;0.171)		LUSC - Lung squamous cell carcinoma(543;0.171)|STAD - Stomach adenocarcinoma(528;0.247)			TATGGTGGTAGGCCCCCGACA	0.652																																					p.L724V		Atlas-SNP	.											.	OTUD7B	76	.	0			c.C2170G						PASS	.						28.0	32.0	31.0					1																	149916118		1961	4133	6094	SO:0001583	missense	56957	exon12			GTGGTAGGCCCCC	AJ293573	CCDS72903.1	1q21.2	2014-02-24	2014-02-24	2006-07-07	ENSG00000163113	ENSG00000264522		"""OTU domain containing"""	16683	protein-coding gene	gene with protein product		611748	"""zinc finger, A20 domain containing 1"", ""OTU domain containing 7B"""	ZA20D1		11463333, 23827681	Standard	NM_020205		Approved	CEZANNE	uc001etn.3	Q6GQQ9	OTTHUMG00000012291	ENST00000369135.4:c.2170C>G	1.37:g.149916118G>C	ENSP00000358131:p.Leu724Val	38.0	0.0	0		65.0	34.0	0.523077	NM_020205	B7Z643|D3DUZ8|Q5SZ60|Q8WWA7|Q9NQ53|Q9UFF4	Missense_Mutation	SNP	ENST00000369135.4	37	CCDS41389.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.710511	0.30322	.	.	ENSG00000163113	ENST00000369135;ENST00000543330	T	0.35789	1.29	4.37	3.44	0.39384	.	0.146689	0.45606	D	0.000347	T	0.13756	0.0333	L	0.50333	1.59	0.41982	D	0.990803	P	0.44241	0.829	B	0.33254	0.16	T	0.03157	-1.1066	9	.	.	.	-23.4143	10.4837	0.44708	0.098:0.0:0.902:0.0	.	724	Q6GQQ9	OTU7B_HUMAN	V	724	ENSP00000358131:L724V	.	L	-	1	2	OTUD7B	148182742	0.998000	0.40836	0.903000	0.35520	0.767000	0.43475	3.982000	0.56909	1.027000	0.39758	0.455000	0.32223	CTA	.	.	none		0.652	OTUD7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034146.3	NM_020205	
AKAP11	11215	hgsc.bcm.edu	37	13	42876103	42876103	+	Missense_Mutation	SNP	C	C	T	rs61756566	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:42876103C>T	ENST00000025301.2	+	8	3396	c.3221C>T	c.(3220-3222)tCt>tTt	p.S1074F		NM_016248.3	NP_057332.1	Q9UKA4	AKA11_HUMAN	A kinase (PRKA) anchor protein 11	1074					intracellular signal transduction (GO:0035556)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)	protein kinase A binding (GO:0051018)|protein phosphatase 1 binding (GO:0008157)	p.S1074F(1)		breast(3)|central_nervous_system(4)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(10)|liver(1)|lung(22)|ovary(1)|skin(3)|stomach(2)	56		Lung NSC(96;1.86e-05)|Prostate(109;0.0165)|Lung SC(185;0.0262)|Breast(139;0.0707)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;0.000365)|GBM - Glioblastoma multiforme(144;0.00116)|BRCA - Breast invasive adenocarcinoma(63;0.19)		ACTTTCTCATCTACAGCACTT	0.398													C|||	113	0.0225639	0.0136	0.0	5008	,	,		22265	0.0813		0.004	False		,,,				2504	0.0092				p.S1074F		Atlas-SNP	.											AKAP11,NS,carcinoma,0,1	AKAP11	146	1	1	Substitution - Missense(1)	stomach(1)	c.C3221T						PASS	.	C	PHE/SER	51,4355	51.6+/-87.1	1,49,2153	159.0	151.0	153.0		3221	5.8	0.4	13	dbSNP_129	153	3,8597	3.0+/-9.4	0,3,4297	yes	missense	AKAP11	NM_016248.3	155	1,52,6450	TT,TC,CC		0.0349,1.1575,0.4152	possibly-damaging	1074/1902	42876103	54,12952	2203	4300	6503	SO:0001583	missense	11215	exon8			TCTCATCTACAGC	AB014529	CCDS9383.1	13q	2012-04-17			ENSG00000023516	ENSG00000023516		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	369	protein-coding gene	gene with protein product	"""AKAP 220"", ""A-kinase anchoring protein, 220kDa"", ""protein kinase A anchoring protein 11"", ""protein phosphatase 1, regulatory subunit 44"""	604696				9734811, 8621616	Standard	NM_016248		Approved	KIAA0629, AKAP220, PRKA11, FLJ11304, DKFZp781I12161, PPP1R44	uc001uys.2	Q9UKA4	OTTHUMG00000016805	ENST00000025301.2:c.3221C>T	13.37:g.42876103C>T	ENSP00000025301:p.Ser1074Phe	86.0	0.0	0		78.0	40.0	0.512821	NM_016248	O75124|Q9NUK7	Missense_Mutation	SNP	ENST00000025301.2	37	CCDS9383.1	54	0.024725274725274724	7	0.014227642276422764	0	0.0	43	0.07517482517482517	4	0.005277044854881266	C	13.10	2.136954	0.37728	0.011575	3.49E-4	ENSG00000023516	ENST00000025301	T	0.18502	2.21	5.8	5.8	0.92144	.	0.527839	0.19579	N	0.110907	T	0.02727	0.0082	M	0.67953	2.075	0.43054	D	0.994668	D	0.64830	0.994	P	0.60473	0.875	T	0.00020	-1.2350	10	0.62326	D	0.03	.	20.0706	0.97721	0.0:1.0:0.0:0.0	rs61756566	1074	Q9UKA4	AKA11_HUMAN	F	1074	ENSP00000025301:S1074F	ENSP00000025301:S1074F	S	+	2	0	AKAP11	41774103	0.269000	0.24143	0.389000	0.26208	0.087000	0.18053	3.666000	0.54540	2.744000	0.94065	0.655000	0.94253	TCT	C|0.988;T|0.012	0.012	strong		0.398	AKAP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044700.2	NM_016248	
MRC1	4360	hgsc.bcm.edu	37	10	17875762	17875762	+	Silent	SNP	G	G	A	rs374113136	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:17875762G>A	ENST00000331429.2	+	4	829	c.726G>A	c.(724-726)caG>caA	p.Q242Q	MRC1L1_ENST00000457317.1_Silent_p.Q242Q														p.Q242Q(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(8)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	14						CGTGGCACCAGGCGAGGAAAA	0.468													g|||	178	0.0355431	0.0431	0.0346	5008	,	,		10278	0.0238		0.0497	False		,,,				2504	0.0235				p.Q242Q		Atlas-SNP	.											MRC1L1,rectum,carcinoma,0,2	MRC1	13	2	1	Substitution - coding silent(1)	large_intestine(1)	c.G726A						scavenged	.						100.0	91.0	94.0					10																	17875762		1955	3878	5833	SO:0001819	synonymous_variant	4360	exon4			GCACCAGGCGAGG																												ENST00000331429.2:c.726G>A	10.37:g.17875762G>A		185.0	1.0	0.00540541		80.0	4.0	0.05	NM_002438		Silent	SNP	ENST00000331429.2	37																																																																																				G|0.750;A|0.250	0.250	weak		0.468	MRC1L1-001	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000047054.1		
CLUAP1	23059	hgsc.bcm.edu	37	16	3554799	3554799	+	Silent	SNP	T	T	C	rs34672214	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:3554799T>C	ENST00000576634.1	+	2	246	c.102T>C	c.(100-102)ctT>ctC	p.L34L	CLUAP1_ENST00000417763.2_5'UTR|CLUAP1_ENST00000341633.5_Silent_p.L34L|LA16c-306E5.3_ENST00000574423.2_RNA|CLUAP1_ENST00000571025.1_Silent_p.L34L	NM_015041.2	NP_055856.1	Q96AJ1	CLUA1_HUMAN	clusterin associated protein 1	34					cilium assembly (GO:0042384)	centrosome (GO:0005813)|cilium (GO:0005929)|intracellular membrane-bounded organelle (GO:0043231)|intraciliary transport particle B (GO:0030992)|nucleus (GO:0005634)				breast(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(1)|ovary(1)|pancreas(1)|urinary_tract(2)	16						ATTTTGGACTTGTATCTGAAG	0.383													T|||	283	0.0565096	0.115	0.0331	5008	,	,		19316	0.0556		0.0159	False		,,,				2504	0.0368				p.L34L		Atlas-SNP	.											.	CLUAP1	32	.	0			c.T102C						PASS	.	T		427,3967	207.5+/-228.8	19,389,1789	111.0	109.0	110.0		102	3.1	1.0	16	dbSNP_126	110	138,8462	69.0+/-131.5	0,138,4162	no	coding-synonymous	CLUAP1	NM_015041.1		19,527,5951	CC,CT,TT		1.6047,9.7178,4.3482		34/414	3554799	565,12429	2197	4300	6497	SO:0001819	synonymous_variant	23059	exon2			TGGACTTGTATCT	BC017070	CCDS32381.1, CCDS45398.1	16p13.3	2014-07-18				ENSG00000103351		"""Intraflagellar transport homologs"""	19009	protein-coding gene	gene with protein product	"""flagellar associated protein 22, qilin-like protein, homolog (Chlamydomonas)"", ""cilia and flagella associated protein 22"""					15480429, 9734811, 19253336	Standard	NM_015041		Approved	FLJ13297, KIAA0643, FAP22, CFAP22	uc002cvk.2	Q96AJ1		ENST00000576634.1:c.102T>C	16.37:g.3554799T>C		218.0	0.0	0		203.0	91.0	0.448276	NM_015041	O75138|Q65ZA3|Q9H8R4|Q9H8T1	Silent	SNP	ENST00000576634.1	37	CCDS32381.1																																																																																			T|0.955;C|0.045	0.045	strong		0.383	CLUAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437883.2	NM_024793	
ZFYVE26	23503	hgsc.bcm.edu	37	14	68229051	68229051	+	Missense_Mutation	SNP	T	T	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:68229051T>C	ENST00000347230.4	-	34	6376	c.6238A>G	c.(6238-6240)Act>Gct	p.T2080A	ZFYVE26_ENST00000555452.1_Missense_Mutation_p.T2080A|ZFYVE26_ENST00000557306.1_5'Flank	NM_015346.3	NP_056161.2	Q68DK2	ZFY26_HUMAN	zinc finger, FYVE domain containing 26	2080					cell death (GO:0008219)|cytokinesis (GO:0000910)|double-strand break repair via homologous recombination (GO:0000724)	centrosome (GO:0005813)|lysosomal membrane (GO:0005765)|midbody (GO:0030496)	metal ion binding (GO:0046872)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(8)|large_intestine(8)|lung(39)|ovary(12)|pancreas(1)|prostate(7)|skin(3)|stomach(1)|upper_aerodigestive_tract(4)	94				all cancers(60;0.000763)|OV - Ovarian serous cystadenocarcinoma(108;0.0011)|BRCA - Breast invasive adenocarcinoma(234;0.0115)		CGTGCAGCAGTGAGGTTCCCG	0.562																																					p.T2080A		Atlas-SNP	.											.	ZFYVE26	223	.	0			c.A6238G						PASS	.						93.0	76.0	82.0					14																	68229051		2203	4300	6503	SO:0001583	missense	23503	exon34			CAGCAGTGAGGTT	AB002319	CCDS9788.1	14q23.3	2012-11-23				ENSG00000072121		"""Zinc fingers, FYVE domain containing"""	20761	protein-coding gene	gene with protein product	"""spastizin"", ""FYVE-CENT"""	612012	"""spastic paraplegia 15 (complicated, autosomal recessive)"""	SPG15		9205841, 18394578	Standard	NM_015346		Approved	KIAA0321	uc001xka.2	Q68DK2		ENST00000347230.4:c.6238A>G	14.37:g.68229051T>C	ENSP00000251119:p.Thr2080Ala	89.0	0.0	0		105.0	45.0	0.428571	NM_015346	B1B5Y3|B4E2U3|O15035|Q68DT9|Q6AW90|Q6ZR50|Q7Z3A4|Q7Z3I1|Q8N4W7	Missense_Mutation	SNP	ENST00000347230.4	37	CCDS9788.1	.	.	.	.	.	.	.	.	.	.	T	3.183	-0.167539	0.06461	.	.	ENSG00000072121	ENST00000347230;ENST00000411699;ENST00000555452	T;T	0.26518	1.88;1.73	5.55	0.543	0.17179	.	0.468395	0.22794	N	0.055575	T	0.06872	0.0175	N	0.02011	-0.69	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.09377	0.004;0.001	T	0.36335	-0.9752	10	0.11182	T	0.66	-0.8863	4.9027	0.13782	0.0:0.23:0.2765:0.4935	.	2080;2080	G3V2D8;Q68DK2	.;ZFY26_HUMAN	A	2080;2059;2080	ENSP00000251119:T2080A;ENSP00000450603:T2080A	ENSP00000251119:T2080A	T	-	1	0	ZFYVE26	67298804	0.979000	0.34478	0.895000	0.35142	0.474000	0.32979	0.238000	0.18004	0.071000	0.16664	-0.313000	0.08912	ACT	.	.	none		0.562	ZFYVE26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412736.2	NM_015346	
PIK3AP1	118788	hgsc.bcm.edu	37	10	98369563	98369563	+	Silent	SNP	T	T	C	rs141067860	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:98369563T>C	ENST00000339364.5	-	14	2195	c.2076A>G	c.(2074-2076)ggA>ggG	p.G692G	PIK3AP1_ENST00000371110.2_Silent_p.G514G|PIK3AP1_ENST00000371109.3_Silent_p.G291G	NM_152309.2	NP_689522.2	Q6ZUJ8	BCAP_HUMAN	phosphoinositide-3-kinase adaptor protein 1	692					negative regulation of toll-like receptor signaling pathway (GO:0034122)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of toll-like receptor signaling pathway (GO:0034123)|regulation of inflammatory response (GO:0050727)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 7 signaling pathway (GO:0034154)|toll-like receptor 9 signaling pathway (GO:0034162)	cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	phosphatidylinositol 3-kinase regulatory subunit binding (GO:0036312)			NS(1)|autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(27)|ovary(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(4)	52		Colorectal(252;0.0442)		Epithelial(162;6.29e-08)|all cancers(201;3.18e-06)		TCTCATAGACTCCAAACTCCA	0.532													T|||	4	0.000798722	0.0	0.0029	5008	,	,		6366	0.0		0.002	False		,,,				2504	0.0				p.G692G		Atlas-SNP	.											.	PIK3AP1	111	.	0			c.A2076G						PASS	.	T		3,4403	6.2+/-15.9	0,3,2200	236.0	242.0	240.0		2076	-2.2	1.0	10	dbSNP_134	240	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	PIK3AP1	NM_152309.2		0,15,6488	CC,CT,TT		0.1395,0.0681,0.1153		692/806	98369563	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	118788	exon14			ATAGACTCCAAAC	AK092883	CCDS31259.1	10q24.2	2008-10-23			ENSG00000155629	ENSG00000155629			30034	protein-coding gene	gene with protein product		607942				1251844, 11163197	Standard	NM_152309		Approved	BCAP, FLJ35564	uc001kmq.3	Q6ZUJ8	OTTHUMG00000018838	ENST00000339364.5:c.2076A>G	10.37:g.98369563T>C		119.0	0.0	0		144.0	59.0	0.409722	NM_152309	Q5TB56|Q5VXJ9|Q8N6J6|Q8NAC8	Silent	SNP	ENST00000339364.5	37	CCDS31259.1																																																																																			T|0.999;C|0.001	0.001	strong		0.532	PIK3AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049619.2	NM_152309	
S1PR5	53637	hgsc.bcm.edu	37	19	10624863	10624863	+	Silent	SNP	C	C	T	rs75861469	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10624863C>T	ENST00000439028.3	-	2	950	c.825G>A	c.(823-825)gtG>gtA	p.V275V	S1PR5_ENST00000333430.4_Silent_p.V275V	NM_001166215.1	NP_001159687.1	Q9H228	S1PR5_HUMAN	sphingosine-1-phosphate receptor 5	275					regulation of neuron differentiation (GO:0045664)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	sphingosine-1-phosphate receptor activity (GO:0038036)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(5)|ovary(1)|pancreas(1)|prostate(1)	12					Fingolimod(DB08868)	CCGGGCACGCCACGTCGAGCA	0.652													C|||	96	0.0191693	0.0711	0.0029	5008	,	,		15206	0.0		0.0	False		,,,				2504	0.0				p.V275V		Atlas-SNP	.											.	S1PR5	33	.	0			c.G825A						PASS	.	C	,	236,4150	125.7+/-162.9	9,218,1966	31.0	29.0	29.0		825,825	1.2	1.0	19	dbSNP_132	29	3,8593	1.2+/-3.3	0,3,4295	no	coding-synonymous,coding-synonymous	S1PR5	NM_001166215.1,NM_030760.4	,	9,221,6261	TT,TC,CC		0.0349,5.3808,1.841	,	275/399,275/399	10624863	239,12743	2193	4298	6491	SO:0001819	synonymous_variant	53637	exon2			GCACGCCACGTCG	AK074661	CCDS12240.1	19p13.2	2012-08-08	2008-04-30	2008-04-30		ENSG00000180739		"""GPCR / Class A : Lysophospholipid receptors : Sphingosine 1-phosphate"""	14299	protein-coding gene	gene with protein product		605146	"""endothelial differentiation, sphingolipid G-protein-coupled receptor, 8"""	EDG8		10799507	Standard	NM_030760		Approved	Edg-8	uc002mou.2	Q9H228		ENST00000439028.3:c.825G>A	19.37:g.10624863C>T		46.0	0.0	0		56.0	31.0	0.553571	NM_030760	Q6NW11	Silent	SNP	ENST00000439028.3	37	CCDS12240.1	35	0.016025641025641024	32	0.06504065040650407	1	0.0027624309392265192	0	0.0	2	0.002638522427440633	C	9.558	1.117787	0.20877	0.053808	3.49E-4	ENSG00000180739	ENST00000359134	.	.	.	5.15	1.24	0.21308	.	.	.	.	.	T	0.05456	0.0144	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.09228	-1.0684	5	0.41790	T	0.15	.	1.7012	0.02873	0.1474:0.4422:0.1546:0.2558	.	.	.	.	S	244	.	ENSP00000352045:G244S	G	-	1	0	S1PR5	10485863	0.002000	0.14202	1.000000	0.80357	0.816000	0.46133	-0.292000	0.08332	0.541000	0.28827	0.491000	0.48974	GGC	C|0.981;T|0.019	0.019	strong		0.652	S1PR5-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452015.1	NM_030760	
TAF7L	54457	hgsc.bcm.edu	37	X	100547806	100547806	+	Missense_Mutation	SNP	C	C	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:100547806C>A	ENST00000372907.3	-	1	239	c.228G>T	c.(226-228)caG>caT	p.Q76H	TAF7L_ENST00000356784.1_5'Flank|TAF7L_ENST00000372905.2_De_novo_Start_OutOfFrame	NM_024885.3	NP_079161.3	Q5H9L4	TAF7L_HUMAN	TAF7-like RNA polymerase II, TATA box binding protein (TBP)-associated factor, 50kDa	76					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|spermatogenesis (GO:0007283)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|transcription factor TFIID complex (GO:0005669)				NS(1)|breast(4)|kidney(4)|large_intestine(4)|lung(7)|ovary(1)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	29						TTTCTGGGGCCTGGGCAGCAG	0.557																																					p.Q76H	Ovarian(104;431 1530 3210 15406 18594)	Atlas-SNP	.											.	TAF7L	64	.	0			c.G228T						PASS	.						70.0	71.0	71.0					X																	100547806		2203	4300	6503	SO:0001583	missense	54457	exon1			TGGGGCCTGGGCA	AF285595	CCDS35347.1, CCDS55466.1	Xq22.1	2009-03-25	2002-08-29	2001-12-07	ENSG00000102387	ENSG00000102387			11548	protein-coding gene	gene with protein product	"""cancer/testis antigen 40"""	300314	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, Q"""	TAF2Q		11279525	Standard	NM_024885		Approved	CT40	uc004ehb.3	Q5H9L4	OTTHUMG00000022021	ENST00000372907.3:c.228G>T	X.37:g.100547806C>A	ENSP00000361998:p.Gln76His	53.0	0.0	0		46.0	44.0	0.956522	NM_024885	Q5H9L6|Q86XI4|Q9BXU5|Q9H5R0	Missense_Mutation	SNP	ENST00000372907.3	37	CCDS35347.1	.	.	.	.	.	.	.	.	.	.	C	8.598	0.886065	0.17540	.	.	ENSG00000102387	ENST00000372907	T	0.16597	2.33	3.17	-2.29	0.06805	.	5.716450	0.00953	N	0.002982	T	0.08714	0.0216	N	0.14661	0.345	0.09310	N	0.999993	P	0.39964	0.697	B	0.32465	0.146	T	0.13683	-1.0500	10	0.51188	T	0.08	6.1498	3.8568	0.08979	0.0:0.284:0.4115:0.3044	.	76	Q5H9L4	TAF7L_HUMAN	H	76	ENSP00000361998:Q76H	ENSP00000361998:Q76H	Q	-	3	2	TAF7L	100434462	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.793000	0.04589	-0.640000	0.05495	-0.340000	0.08031	CAG	.	.	none		0.557	TAF7L-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057526.2		
HSPB8	26353	hgsc.bcm.edu	37	12	119617350	119617350	+	Missense_Mutation	SNP	G	G	T	rs55826713		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:119617350G>T	ENST00000281938.2	+	1	904	c.233G>T	c.(232-234)aGg>aTg	p.R78M	RP11-64B16.4_ENST00000535921.1_RNA	NM_014365.2	NP_055180.1	Q9UJY1	HSPB8_HUMAN	heat shock 22kDa protein 8	78			R -> M (in dbSNP:rs55826713). {ECO:0000269|PubMed:17344846}.		cell death (GO:0008219)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(1)|lung(9)|skin(1)	14	all_neural(191;0.0804)|Medulloblastoma(191;0.0922)					GCCACCGCCAGGTTTGGGGTG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		14955	0.0		0.001	False		,,,				2504	0.0				p.R78M		Atlas-SNP	.											.	HSPB8	45	.	0			c.G233T						PASS	.	G	MET/ARG	0,4404		0,0,2202	26.0	31.0	30.0		233	4.4	0.9	12	dbSNP_129	30	8,8592	6.4+/-24.3	0,8,4292	no	missense	HSPB8	NM_014365.2	91	0,8,6494	TT,TG,GG		0.093,0.0,0.0615	benign	78/197	119617350	8,12996	2202	4300	6502	SO:0001583	missense	26353	exon1			CCGCCAGGTTTGG	AF191017	CCDS9189.1	12q24.23	2014-09-17	2004-04-23					"""Heat shock proteins / HSPB"""	30171	protein-coding gene	gene with protein product		608014	"""heat shock 27kDa protein 8"""			10833516, 11085516	Standard	NM_014365		Approved	H11, E2IG1, HSP22, HspB8	uc001txb.3	Q9UJY1		ENST00000281938.2:c.233G>T	12.37:g.119617350G>T	ENSP00000281938:p.Arg78Met	25.0	0.0	0		42.0	22.0	0.52381	NM_014365	B2R6A6|Q6FIH3|Q9UKS3	Missense_Mutation	SNP	ENST00000281938.2	37	CCDS9189.1	.	.	.	.	.	.	.	.	.	.	G	14.24	2.476262	0.44044	0.0	9.3E-4	ENSG00000152137	ENST00000281938	D	0.87650	-2.28	4.42	4.42	0.53409	HSP20-like chaperone (1);	0.414383	0.24285	N	0.039876	D	0.83968	0.5369	L	0.53249	1.67	0.47183	D	0.999349	P	0.44578	0.838	B	0.41691	0.364	D	0.83545	0.0098	9	.	.	.	.	12.7024	0.57041	0.0823:0.0:0.9177:0.0	rs55826713	78	Q9UJY1	HSPB8_HUMAN	M	78	ENSP00000281938:R78M	.	R	+	2	0	HSPB8	118101733	1.000000	0.71417	0.938000	0.37757	0.256000	0.26092	5.565000	0.67365	2.294000	0.77228	0.563000	0.77884	AGG	G|0.999;T|0.001	0.001	strong		0.672	HSPB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401647.1	NM_014365	
ABCC6	368	hgsc.bcm.edu	37	16	16263662	16263662	+	Missense_Mutation	SNP	G	G	T	rs74315152|rs61340537	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:16263662G>T	ENST00000205557.7	-	22	2865	c.2836C>A	c.(2836-2838)Ctc>Atc	p.L946I		NM_001171.5	NP_001162	O95255	MRP6_HUMAN	ATP-binding cassette, sub-family C (CFTR/MRP), member 6	946			L -> I (in dbSNP:rs61340537). {ECO:0000269|PubMed:16086317, ECO:0000269|PubMed:19339160}.		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)	TAGAGGCAGAGGGGGGTGCCC	0.662													G|||	54	0.0107827	0.0008	0.0202	5008	,	,		16733	0.0		0.0219	False		,,,				2504	0.0174				p.L946I		Atlas-SNP	.											.	ABCC6	110	.	0			c.C2836A	GRCh37	CM034642	ABCC6	M	rs61340537	PASS	.	G	ILE/LEU	20,4332		0,20,2156	20.0	17.0	18.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	2836	-1.1	0.0	16	dbSNP_129	18	131,8445		0,131,4157	yes	missense	ABCC6	NM_001171.5	5	0,151,6313	TT,TG,GG		1.5275,0.4596,1.168	benign	946/1504	16263662	151,12777	2176	4288	6464	SO:0001583	missense	368	exon22			GGCAGAGGGGGGT	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.2836C>A	16.37:g.16263662G>T	ENSP00000205557:p.Leu946Ile	113.0	0.0	0		100.0	41.0	0.41	NM_001171	A2RRN8|A8KIG6|A8Y988|E7ESW8|P78420|Q8TCY8|Q9UMZ7	Missense_Mutation	SNP	ENST00000205557.7	37	CCDS10568.1	27	0.012362637362637362	1	0.0020325203252032522	7	0.019337016574585635	0	0.0	19	0.025065963060686015	G	0.010	-1.770641	0.00645	0.004596	0.015275	ENSG00000091262	ENST00000205557	D	0.95103	-3.61	5.0	-1.06	0.10002	ABC transporter, transmembrane domain, type 1 (1);	1.097620	0.07160	N	0.850486	T	0.72946	0.3524	N	0.25957	0.775	0.31769	N	0.632287	B	0.26363	0.147	B	0.24541	0.054	T	0.74583	-0.3617	10	0.20046	T	0.44	.	3.4997	0.07668	0.0871:0.3098:0.3635:0.2396	rs61340537	946	O95255	MRP6_HUMAN	I	946	ENSP00000205557:L946I	ENSP00000205557:L946I	L	-	1	0	ABCC6	16171163	0.001000	0.12720	0.015000	0.15790	0.057000	0.15508	-0.218000	0.09240	0.121000	0.18284	-0.904000	0.02843	CTC	G|0.989;T|0.011	0.011	strong		0.662	ABCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252232.2		
UST	10090	hgsc.bcm.edu	37	6	149395197	149395197	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:149395197T>A	ENST00000367463.4	+	8	1269	c.1166T>A	c.(1165-1167)aTc>aAc	p.I389N	UST_ENST00000466695.1_3'UTR	NM_005715.2	NP_005706.1	Q9Y2C2	UST_HUMAN	uronyl-2-sulfotransferase	389					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|glycosaminoglycan metabolic process (GO:0030203)|protein sulfation (GO:0006477)|small molecule metabolic process (GO:0044281)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sulfotransferase activity (GO:0008146)			breast(1)|endometrium(3)|large_intestine(4)|lung(2)|ovary(2)	12		Ovarian(120;0.0907)		OV - Ovarian serous cystadenocarcinoma(155;1.78e-10)|GBM - Glioblastoma multiforme(68;0.138)		GAGGAGCCAATCGACGATGAA	0.483																																					p.I389N		Atlas-SNP	.											UST,right_upper_lobe,carcinoma,0,2	UST	42	2	0			c.T1166A						PASS	.						95.0	95.0	95.0					6																	149395197		2203	4300	6503	SO:0001583	missense	10090	exon8			AGCCAATCGACGA	AB020316	CCDS5213.1	6q25.1	2008-02-05			ENSG00000111962	ENSG00000111962		"""Sulfotransferases, membrane-bound"""	17223	protein-coding gene	gene with protein product		610752				10187838	Standard	NM_005715		Approved	2OST	uc003qmg.3	Q9Y2C2	OTTHUMG00000016135	ENST00000367463.4:c.1166T>A	6.37:g.149395197T>A	ENSP00000356433:p.Ile389Asn	126.0	0.0	0		86.0	14.0	0.162791	NM_005715	B2RCX6	Missense_Mutation	SNP	ENST00000367463.4	37	CCDS5213.1	.	.	.	.	.	.	.	.	.	.	T	15.45	2.835824	0.50951	.	.	ENSG00000111962	ENST00000367463	T	0.53857	0.6	5.3	5.3	0.74995	.	0.184757	0.48767	D	0.000180	T	0.18467	0.0443	N	0.14661	0.345	0.40188	D	0.977379	P	0.35982	0.531	B	0.27796	0.083	T	0.20974	-1.0259	10	0.72032	D	0.01	-6.0612	10.7296	0.46089	0.0:0.0747:0.0:0.9252	.	389	Q9Y2C2	UST_HUMAN	N	389	ENSP00000356433:I389N	ENSP00000356433:I389N	I	+	2	0	UST	149436890	0.272000	0.24172	0.034000	0.17996	0.910000	0.53928	2.116000	0.41930	2.127000	0.65507	0.460000	0.39030	ATC	.	.	none		0.483	UST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043363.1	NM_005715	
TMEM86A	144110	hgsc.bcm.edu	37	11	18723210	18723210	+	Missense_Mutation	SNP	C	C	T	rs144559255	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:18723210C>T	ENST00000280734.2	+	3	473	c.377C>T	c.(376-378)gCg>gTg	p.A126V	TMEM86A_ENST00000527002.1_3'UTR	NM_153347.1	NP_699178.1	Q8N2M4	TM86A_HUMAN	transmembrane protein 86A	126						integral component of membrane (GO:0016021)				endometrium(2)|kidney(1)|large_intestine(4)|lung(1)|ovary(1)|skin(2)	11						GTGATGGCAGCGCTGTCGGGC	0.602													C|||	46	0.0091853	0.0	0.0173	5008	,	,		17494	0.0		0.0249	False		,,,				2504	0.0092				p.A126V		Atlas-SNP	.											TMEM86A,caecum,carcinoma,-1,1	TMEM86A	29	1	0			c.C377T						PASS	.	C	VAL/ALA	23,4375	29.0+/-57.7	0,23,2176	97.0	85.0	89.0		377	2.6	1.0	11	dbSNP_134	89	155,8431	75.1+/-137.7	1,153,4139	yes	missense	TMEM86A	NM_153347.1	64	1,176,6315	TT,TC,CC		1.8053,0.523,1.3709	benign	126/241	18723210	178,12806	2199	4293	6492	SO:0001583	missense	144110	exon3			TGGCAGCGCTGTC	BC035692	CCDS7844.1	11p15.1	2005-10-28				ENSG00000151117			26890	protein-coding gene	gene with protein product							Standard	NM_153347		Approved	FLJ90119	uc001moz.1	Q8N2M4		ENST00000280734.2:c.377C>T	11.37:g.18723210C>T	ENSP00000280734:p.Ala126Val	131.0	0.0	0		112.0	52.0	0.464286	NM_153347	Q96AJ0	Missense_Mutation	SNP	ENST00000280734.2	37	CCDS7844.1	22	0.010073260073260074	0	0.0	6	0.016574585635359115	0	0.0	16	0.021108179419525065	C	0.322	-0.961477	0.02249	0.00523	0.018053	ENSG00000151117	ENST00000535380;ENST00000280734	T	0.20069	2.1	5.03	2.64	0.31445	.	0.537430	0.19759	N	0.106710	T	0.02848	0.0085	N	0.02403	-0.565	0.19300	N	0.999975	B	0.02656	0.0	B	0.04013	0.001	T	0.39482	-0.9612	10	0.06891	T	0.86	-2.3684	8.0781	0.30729	0.0:0.0707:0.1359:0.7934	.	126	Q8N2M4	TM86A_HUMAN	V	126	ENSP00000280734:A126V	ENSP00000280734:A126V	A	+	2	0	TMEM86A	18679786	0.054000	0.20591	0.984000	0.44739	0.608000	0.37181	2.275000	0.43399	0.477000	0.27464	-1.402000	0.01139	GCG	C|0.987;T|0.013	0.013	strong		0.602	TMEM86A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387812.1	NM_153347	
C10orf10	11067	hgsc.bcm.edu	37	10	45473432	45473432	+	Missense_Mutation	SNP	C	C	T	rs149255069	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45473432C>T	ENST00000298295.3	-	2	264	c.47G>A	c.(46-48)cGg>cAg	p.R16Q	C10orf10_ENST00000496638.1_Intron|RASSF4_ENST00000340258.5_Intron|RASSF4_ENST00000334940.6_Intron|RASSF4_ENST00000374417.2_Intron|RASSF4_ENST00000472561.1_Intron	NM_007021.3	NP_008952.1	Q9NTK1	DEPP_HUMAN	chromosome 10 open reading frame 10	16						mitochondrion (GO:0005739)				lung(1)	1						CGTGGTCTCCCGAATTGTGGG	0.607													C|||	5	0.000998403	0.0038	0.0	5008	,	,		16956	0.0		0.0	False		,,,				2504	0.0				p.R16Q		Atlas-SNP	.											.	C10orf10	6	.	0			c.G47A						PASS	.	C	GLN/ARG,	11,4393		0,11,2191	44.0	50.0	48.0		47,	2.7	1.0	10	dbSNP_134	48	0,8596		0,0,4298	yes	missense,intron	C10orf10,RASSF4	NM_007021.3,NM_032023.3	43,	0,11,6489	TT,TC,CC		0.0,0.2498,0.0846	benign,	16/213,	45473432	11,12989	2202	4298	6500	SO:0001583	missense	11067	exon2			GTCTCCCGAATTG	AB022718	CCDS7210.1	10q11.21	2014-07-31			ENSG00000165507	ENSG00000165507			23355	protein-coding gene	gene with protein product	"""decidual protein induced by progesterone"", ""fasting induced"", ""fat-specific expressed gene"""	611309				24530860, 19937567, 16123073	Standard	NM_007021		Approved	DEPP, FIG, Fseg	uc001jbr.4	Q9NTK1	OTTHUMG00000018063	ENST00000298295.3:c.47G>A	10.37:g.45473432C>T	ENSP00000298295:p.Arg16Gln	101.0	0.0	0		91.0	36.0	0.395604	NM_007021	B2R6A1|O94997|Q5T735|Q76MX8	Missense_Mutation	SNP	ENST00000298295.3	37	CCDS7210.1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.249917	0.80024	0.002498	0.0	ENSG00000165507	ENST00000298295;ENST00000432283;ENST00000448778	T;T	0.51574	0.73;0.7	5.63	2.73	0.32206	.	0.512064	0.16368	N	0.217438	T	0.22627	0.0546	N	0.12746	0.255	0.28270	N	0.924451	B	0.32800	0.385	B	0.21546	0.035	T	0.10064	-1.0646	10	0.37606	T	0.19	-18.3777	5.2281	0.15406	0.1628:0.6657:0.0:0.1715	.	16	Q9NTK1	DEPP_HUMAN	Q	16	ENSP00000298295:R16Q;ENSP00000414494:R16Q	ENSP00000298295:R16Q	R	-	2	0	C10orf10	44793438	0.989000	0.36119	0.982000	0.44146	0.994000	0.84299	0.343000	0.19944	0.302000	0.22762	0.561000	0.74099	CGG	C|0.999;T|0.001	0.001	strong		0.607	C10orf10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047758.1	NM_007021	
PXDNL	137902	hgsc.bcm.edu	37	8	52321966	52321966	+	Missense_Mutation	SNP	G	G	A	rs201280324	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:52321966G>A	ENST00000356297.4	-	17	2318	c.2218C>T	c.(2218-2220)Ccc>Tcc	p.P740S	PXDNL_ENST00000543296.1_Missense_Mutation_p.P740S	NM_144651.4	NP_653252	A1KZ92	PXDNL_HUMAN	peroxidasin homolog (Drosophila)-like	740					hydrogen peroxide catabolic process (GO:0042744)|oxidation-reduction process (GO:0055114)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)	endonuclease activity (GO:0004519)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|peroxidase activity (GO:0004601)			NS(1)|breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(6)|lung(25)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	48		all_cancers(86;0.107)|Lung NSC(129;0.00641)|all_epithelial(80;0.00716)|all_lung(136;0.015)				CCCCACGTGGGCTGCTGCAGG	0.701													G|||	7	0.00139776	0.0	0.0014	5008	,	,		8293	0.0		0.005	False		,,,				2504	0.001				p.P740S		Atlas-SNP	.											PXDNL_ENST00000356297,NS,carcinoma,+2,1	PXDNL	414	1	0			c.C2218T						scavenged	.	G	SER/PRO	8,4010		0,8,2001	17.0	19.0	18.0		2218	1.8	0.0	8		18	58,8254		0,58,4098	yes	missense	PXDNL	NM_144651.4	74	0,66,6099	AA,AG,GG		0.6978,0.1991,0.5353	probably-damaging	740/1464	52321966	66,12264	2009	4156	6165	SO:0001583	missense	137902	exon17			ACGTGGGCTGCTG		CCDS47855.1	8q11.21-q11.22	2013-02-18	2007-01-12		ENSG00000147485	ENSG00000147485		"""Immunoglobulin superfamily / I-set domain containing"""	26359	protein-coding gene	gene with protein product	"""polysomal ribonuclease 1 homolog (Xenopus)"""	615904	"""peroxidasin homolog-like (Drosophila)"""			22543864	Standard	NM_144651		Approved	FLJ25471, PMR1	uc003xqu.4	A1KZ92	OTTHUMG00000164244	ENST00000356297.4:c.2218C>T	8.37:g.52321966G>A	ENSP00000348645:p.Pro740Ser	28.0	0.0	0		34.0	14.0	0.411765	NM_144651	B5ME43|B6CGZ3|H0YBM9|Q6ZMR2|Q96LH9	Missense_Mutation	SNP	ENST00000356297.4	37	CCDS47855.1	5	0.0022893772893772895	0	0.0	2	0.0055248618784530384	0	0.0	3	0.00395778364116095	G	16.46	3.130556	0.56828	0.001991	0.006978	ENSG00000147485	ENST00000356297;ENST00000543296	T;T	0.78246	-1.16;-1.16	3.71	1.79	0.24919	.	.	.	.	.	T	0.79736	0.4497	M	0.76727	2.345	0.36838	D	0.887265	D	0.65815	0.995	D	0.70016	0.967	T	0.81002	-0.1130	9	0.72032	D	0.01	.	5.8018	0.18417	0.1109:0.0:0.6977:0.1914	.	740	A1KZ92	PXDNL_HUMAN	S	740	ENSP00000348645:P740S;ENSP00000444865:P740S	ENSP00000348645:P740S	P	-	1	0	PXDNL	52484519	1.000000	0.71417	0.042000	0.18584	0.667000	0.39255	8.437000	0.90302	0.153000	0.19213	0.555000	0.69702	CCC	G|0.998;A|0.002	0.002	strong		0.701	PXDNL-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000377905.1	NM_144651	
TRIP11	9321	hgsc.bcm.edu	37	14	92460176	92460176	+	Missense_Mutation	SNP	C	C	G	rs137974620	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr14:92460176C>G	ENST00000267622.4	-	15	5510	c.5137G>C	c.(5137-5139)Gaa>Caa	p.E1713Q		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	1713					protein targeting to Golgi (GO:0000042)|regulation of RNA biosynthetic process (GO:2001141)|transcription from RNA polymerase II promoter (GO:0006366)|ventricular septum development (GO:0003281)	acrosomal membrane (GO:0002080)|cis-Golgi network (GO:0005801)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			breast(3)|central_nervous_system(2)|endometrium(1)|kidney(8)|large_intestine(12)|lung(17)|ovary(7)|pancreas(1)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	58				COAD - Colon adenocarcinoma(157;0.223)		ACTTTTCCTTCCAGATTTTCT	0.328			T	PDGFRB	AML								C|||	4	0.000798722	0.0	0.0	5008	,	,		18129	0.0		0.004	False		,,,				2504	0.0				p.E1713Q	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	.	TRIP11	184	.	0			c.G5137C						PASS	.	C	GLN/GLU	3,4401	6.2+/-15.9	0,3,2199	141.0	128.0	133.0		5137	4.5	1.0	14	dbSNP_134	133	29,8567	21.0+/-64.5	0,29,4269	yes	missense	TRIP11	NM_004239.3	29	0,32,6468	GG,GC,CC		0.3374,0.0681,0.2462	probably-damaging	1713/1980	92460176	32,12968	2202	4298	6500	SO:0001583	missense	9321	exon15			TTCCTTCCAGATT	L40380	CCDS9899.1	14q31-q32	2008-05-02				ENSG00000100815			12305	protein-coding gene	gene with protein product		604505				7776974, 9373237	Standard	NM_004239		Approved	CEV14, Trip230, GMAP-210	uc001xzy.3	Q15643		ENST00000267622.4:c.5137G>C	14.37:g.92460176C>G	ENSP00000267622:p.Glu1713Gln	136.0	0.0	0		158.0	86.0	0.544304	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	4|4	0.0018315018315018315|0.0018315018315018315	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	4|4	0.005277044854881266|0.005277044854881266	C|C	17.47|17.47	3.397608|3.397608	0.62177|0.62177	6.81E-4|6.81E-4	0.003374|0.003374	ENSG00000100815|ENSG00000100815	ENST00000267622;ENST00000542257|ENST00000554357	T|.	0.04862|.	3.54|.	5.41|5.41	4.51|4.51	0.55191|0.55191	.|.	0.050641|.	0.85682|.	N|.	0.000000|.	T|T	0.66228|0.66228	0.2768|0.2768	M|M	0.70275|0.70275	2.135|2.135	0.44899|0.44899	D|D	0.99791|0.99791	D;D|.	0.58970|.	0.976;0.984|.	P;P|.	0.62435|.	0.799;0.902|.	T|T	0.70749|0.70749	-0.4787|-0.4787	10|5	0.42905|.	T|.	0.14|.	.|.	15.1012|15.1012	0.72279|0.72279	0.0:0.8575:0.1425:0.0|0.0:0.8575:0.1425:0.0	.|.	1449;1713|.	F5H1Z0;Q15643|.	.;TRIPB_HUMAN|.	Q|A	1713;1449|1428	ENSP00000267622:E1713Q|.	ENSP00000267622:E1713Q|.	E|G	-|-	1|2	0|0	TRIP11|TRIP11	91529929|91529929	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.985000|0.985000	0.73830|0.73830	3.187000|3.187000	0.50950|0.50950	1.363000|1.363000	0.46019|0.46019	0.655000|0.655000	0.94253|0.94253	GAA|GGA	C|0.998;G|0.002	0.002	strong		0.328	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
FREM2	341640	hgsc.bcm.edu	37	13	39452993	39452993	+	Missense_Mutation	SNP	C	C	T	rs7996253	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:39452993C>T	ENST00000280481.7	+	23	9101	c.8885C>T	c.(8884-8886)gCg>gTg	p.A2962V		NM_207361.4	NP_997244.3	Q5SZK8	FREM2_HUMAN	FRAS1 related extracellular matrix protein 2	2962			A -> V (in dbSNP:rs7996253).		cell communication (GO:0007154)|homophilic cell adhesion (GO:0007156)|inner ear development (GO:0048839)|morphogenesis of an epithelium (GO:0002009)	basement membrane (GO:0005604)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(8)|large_intestine(35)|lung(39)|ovary(9)|pancreas(2)|prostate(12)|skin(11)|upper_aerodigestive_tract(7)|urinary_tract(2)	148		Lung NSC(96;1.04e-07)|Prostate(109;0.00384)|Breast(139;0.00396)|Lung SC(185;0.0565)|Hepatocellular(188;0.114)		all cancers(112;3.32e-07)|Epithelial(112;1.66e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00154)|BRCA - Breast invasive adenocarcinoma(63;0.00631)|GBM - Glioblastoma multiforme(144;0.0312)		GAGACACAAGCGACCAGTTTT	0.438													C|||	113	0.0225639	0.0817	0.0058	5008	,	,		18911	0.0		0.001	False		,,,				2504	0.0				p.A2962V		Atlas-SNP	.											.	FREM2	385	.	0			c.C8885T						PASS	.	C	VAL/ALA	291,4115	158.5+/-191.2	6,279,1918	152.0	139.0	144.0		8885	2.8	1.0	13	dbSNP_116	144	0,8600		0,0,4300	yes	missense	FREM2	NM_207361.4	64	6,279,6218	TT,TC,CC		0.0,6.6046,2.2374	benign	2962/3170	39452993	291,12715	2203	4300	6503	SO:0001583	missense	341640	exon23			CACAAGCGACCAG	BX538150	CCDS31960.1	13q13.3	2004-12-15			ENSG00000150893	ENSG00000150893			25396	protein-coding gene	gene with protein product		608945				15345741	Standard	NM_207361		Approved	DKFZp686J0811	uc001uwv.3	Q5SZK8	OTTHUMG00000016759	ENST00000280481.7:c.8885C>T	13.37:g.39452993C>T	ENSP00000280481:p.Ala2962Val	158.0	0.0	0		155.0	66.0	0.425806	NM_207361	Q4QQG1|Q5H9N8|Q5T6Q1|Q6N057|Q6ZSB4|Q7Z305|Q7Z341	Missense_Mutation	SNP	ENST00000280481.7	37	CCDS31960.1	39	0.017857142857142856	35	0.07113821138211382	3	0.008287292817679558	0	0.0	1	0.0013192612137203166	C	15.76	2.927535	0.52759	0.066046	0.0	ENSG00000150893	ENST00000280481	T	0.63580	-0.05	5.71	2.83	0.33086	.	0.227351	0.44902	N	0.000401	T	0.07954	0.0199	M	0.69823	2.125	0.58432	D	0.999992	P	0.43750	0.816	B	0.37198	0.243	T	0.04333	-1.0959	10	0.26408	T	0.33	.	9.1802	0.37136	0.2607:0.6709:0.0:0.0683	rs7996253;rs52813429;rs7996253	2962	Q5SZK8	FREM2_HUMAN	V	2962	ENSP00000280481:A2962V	ENSP00000280481:A2962V	A	+	2	0	FREM2	38350993	0.994000	0.37717	0.999000	0.59377	0.713000	0.41058	3.132000	0.50523	0.723000	0.32274	0.563000	0.77884	GCG	C|0.978;T|0.022	0.022	strong		0.438	FREM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044599.2	NM_207361	
ULK4	54986	hgsc.bcm.edu	37	3	41877410	41877410	+	Missense_Mutation	SNP	T	T	G	rs192218045	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:41877410T>G	ENST00000301831.4	-	18	2172	c.1710A>C	c.(1708-1710)ttA>ttC	p.L570F		NM_017886.2	NP_060356.2	Q96C45	ULK4_HUMAN	unc-51 like kinase 4	570				AIVLLTELIRENFRNSKLKQCLLPTLGE -> TTSSIGIGI LNCLVQHSTPVPRQCLVYV (in Ref. 3; AAH14794). {ECO:0000305}.	cilium morphogenesis (GO:0060271)|epithelial cilium movement (GO:0003351)|microtubule cytoskeleton organization (GO:0000226)|regulation of JNK cascade (GO:0046328)|regulation of MAPK cascade (GO:0043408)|regulation of neuron migration (GO:2001222)|regulation of neuron projection development (GO:0010975)|regulation of p38MAPK cascade (GO:1900744)|regulation of protein kinase C signaling (GO:0090036)|ventricular system development (GO:0021591)		ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			breast(2)|cervix(1)|large_intestine(6)|lung(7)|prostate(5)|skin(1)	22				KIRC - Kidney renal clear cell carcinoma(284;0.214)		GGCACTGTTTTAATTTGCTGT	0.363													T|||	5	0.000998403	0.0008	0.0014	5008	,	,		14639	0.0		0.003	False		,,,				2504	0.0				p.L570F		Atlas-SNP	.											.	ULK4	150	.	0			c.A1710C						PASS	.	T	PHE/LEU	2,3672		0,2,1835	136.0	136.0	136.0		1710	1.3	1.0	3		136	29,8139		0,29,4055	yes	missense	ULK4	NM_017886.2	22	0,31,5890	GG,GT,TT		0.355,0.0544,0.2618	probably-damaging	570/1276	41877410	31,11811	1837	4084	5921	SO:0001583	missense	54986	exon18			CTGTTTTAATTTG	AK000581	CCDS43071.1	3p22.1	2013-07-02	2013-07-02		ENSG00000168038	ENSG00000168038			15784	protein-coding gene	gene with protein product			"""unc-51-like kinase 4 (C. elegans)"""			12477932	Standard	NM_017886		Approved	FLJ20574, REC01035, FAM7C1	uc003ckv.4	Q96C45	OTTHUMG00000156210	ENST00000301831.4:c.1710A>C	3.37:g.41877410T>G	ENSP00000301831:p.Leu570Phe	215.0	0.0	0		255.0	118.0	0.462745	NM_017886	A6NF15|Q8IW79|Q9NWV6|Q9UF96	Missense_Mutation	SNP	ENST00000301831.4	37	CCDS43071.1	4	0.0018315018315018315	1	0.0020325203252032522	0	0.0	0	0.0	3	0.00395778364116095	T	19.99	3.928909	0.73327	5.44E-4	0.00355	ENSG00000168038	ENST00000301831	T	0.67171	-0.25	5.37	1.28	0.21552	Armadillo-like helical (1);Armadillo-type fold (2);	0.091392	0.45361	U	0.000380	T	0.71762	0.3378	L	0.57536	1.79	0.80722	D	1	D;D	0.65815	0.991;0.995	P;P	0.61800	0.894;0.894	T	0.70063	-0.4975	10	0.62326	D	0.03	.	8.263	0.31797	0.0:0.4472:0.0:0.5528	.	570;570	B4E2M4;Q96C45	.;ULK4_HUMAN	F	570	ENSP00000301831:L570F	ENSP00000301831:L570F	L	-	3	2	ULK4	41852414	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	0.467000	0.22035	0.316000	0.23135	0.528000	0.53228	TTA	T|0.997;G|0.003	0.003	strong		0.363	ULK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343490.1	XM_929989	
FBN2	2201	hgsc.bcm.edu	37	5	127595153	127595153	+	Silent	SNP	G	G	C	rs34383505	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:127595153G>C	ENST00000508053.1	-	71	9707	c.8733C>G	c.(8731-8733)ctC>ctG	p.L2911L	FBN2_ENST00000262464.4_Silent_p.L2911L			P35556	FBN2_HUMAN	fibrillin 2	2911					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)		AGGGTTAATAGAGCTGAATCT	0.458													G|||	138	0.0275559	0.0998	0.0086	5008	,	,		15857	0.0		0.0	False		,,,				2504	0.0				p.L2911L		Atlas-SNP	.											.	FBN2	858	.	0			c.C8733G						PASS	.	G		323,4083	171.9+/-202.1	11,301,1891	96.0	95.0	95.0		8733	3.7	1.0	5	dbSNP_126	95	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	FBN2	NM_001999.3		11,303,6189	CC,CG,GG		0.0233,7.3309,2.4988		2911/2913	127595153	325,12681	2203	4300	6503	SO:0001819	synonymous_variant	2201	exon65			TTAATAGAGCTGA	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.8733C>G	5.37:g.127595153G>C		197.0	0.0	0		220.0	111.0	0.504545	NM_001999	B4DU01|Q59ES6	Silent	SNP	ENST00000508053.1	37	CCDS34222.1																																																																																			G|0.973;C|0.027	0.027	strong		0.458	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
SMG1	23049	hgsc.bcm.edu	37	16	18882775	18882775	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:18882775G>A	ENST00000446231.2	-	16	2625	c.2213C>T	c.(2212-2214)gCa>gTa	p.A738V	SMG1_ENST00000389467.3_Missense_Mutation_p.A738V|snoU13_ENST00000459248.1_RNA			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	738	Interaction with SMG8 and SMG9.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						TAAAACAGCTGCTTCCAAAGC	0.348																																					p.A738V		Atlas-SNP	.											.	SMG1	401	.	0			c.C2213T						PASS	.						59.0	54.0	55.0					16																	18882775		1816	4081	5897	SO:0001583	missense	23049	exon16			ACAGCTGCTTCCA	AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.2213C>T	16.37:g.18882775G>A	ENSP00000402515:p.Ala738Val	282.0	0.0	0		295.0	118.0	0.4	NM_015092	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	A	10.24	1.295768	0.23564	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.64803	-0.12;-0.12	5.21	5.21	0.72293	Armadillo-type fold (1);	0.096968	0.41823	N	0.000802	T	0.27663	0.0680	N	0.00926	-1.1	0.24424	N	0.99461	B	0.02656	0.0	B	0.01281	0.0	T	0.23261	-1.0193	10	0.05436	T	0.98	.	11.34	0.49527	0.9281:0.0:0.0719:0.0	.	738	Q96Q15	SMG1_HUMAN	V	738	ENSP00000402515:A738V;ENSP00000374118:A738V	ENSP00000374118:A738V	A	-	2	0	SMG1	18790276	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.236000	0.78154	0.925000	0.37094	-0.381000	0.06696	GCA	.	.	none		0.348	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391817.1	NM_015092	
TMEM72	643236	hgsc.bcm.edu	37	10	45430153	45430153	+	Silent	SNP	G	G	A	rs17157262	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:45430153G>A	ENST00000544540.1	+	4	529	c.45G>A	c.(43-45)cgG>cgA	p.R15R	TMEM72-AS1_ENST00000450287.2_RNA|RP11-285G1.9_ENST00000425541.2_lincRNA			A0PK05	TMM72_HUMAN	transmembrane protein 72	133						integral component of membrane (GO:0016021)				breast(2)|kidney(1)|large_intestine(2)|lung(10)	15						TGAGCAAGCGGAAGAAGAGGA	0.602													G|||	57	0.0113818	0.0386	0.0086	5008	,	,		17472	0.0		0.0	False		,,,				2504	0.0				p.R133R		Atlas-SNP	.											.	TMEM72	25	.	0			c.G399A						PASS	.	G		91,3045		1,89,1478	77.0	81.0	80.0		399	-3.8	0.9	10	dbSNP_123	80	2,7162		0,2,3580	no	coding-synonymous	TMEM72	NM_001123376.1		1,91,5058	AA,AG,GG		0.0279,2.9018,0.9029		133/276	45430153	93,10207	1568	3582	5150	SO:0001819	synonymous_variant	643236	exon5			CAAGCGGAAGAAG	AB235418	CCDS41504.1	10q11.21	2008-10-24	2008-08-21	2008-08-21	ENSG00000187783	ENSG00000187783			31658	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 127"""	C10orf127			Standard	NM_001123376		Approved	bA285G1.3, KSP37	uc001jbn.2	A0PK05	OTTHUMG00000018067	ENST00000544540.1:c.45G>A	10.37:g.45430153G>A		67.0	0.0	0		80.0	38.0	0.475	NM_001123376	A1L181|Q5T740	Silent	SNP	ENST00000544540.1	37																																																																																				G|0.990;A|0.010	0.010	strong		0.602	TMEM72-201	KNOWN	basic	protein_coding	protein_coding		NM_001123376	
MICAL2	9645	hgsc.bcm.edu	37	11	12281414	12281414	+	Missense_Mutation	SNP	G	G	A	rs148517207		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:12281414G>A	ENST00000256194.4	+	26	3592	c.3304G>A	c.(3304-3306)Gcc>Acc	p.A1102T	MICAL2_ENST00000527546.1_Missense_Mutation_p.A912T|MICAL2_ENST00000537344.1_Missense_Mutation_p.A912T|MICAL2_ENST00000379612.3_Missense_Mutation_p.A876T|RP11-265D17.2_ENST00000527288.1_RNA|MICAL2_ENST00000342902.5_Missense_Mutation_p.A1081T	NM_001282663.1|NM_014632.2	NP_001269592.1|NP_055447.1	O94851	MICA2_HUMAN	microtubule associated monooxygenase, calponin and LIM domain containing 2	1102					actin filament depolymerization (GO:0030042)|cytoskeleton organization (GO:0007010)|heart development (GO:0007507)|heart looping (GO:0001947)|oxidation-reduction process (GO:0055114)|positive regulation of transcription via serum response element binding (GO:0010735)|sulfur oxidation (GO:0019417)	nucleus (GO:0005634)	actin binding (GO:0003779)|FAD binding (GO:0071949)|NADPH:sulfur oxidoreductase activity (GO:0043914)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen (GO:0016709)|zinc ion binding (GO:0008270)			breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(6)|lung(12)|ovary(2)|prostate(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(4)	47				Epithelial(150;0.00552)		CGCAGTGGCCGCCATTGGCAC	0.597																																					p.A1102T		Atlas-SNP	.											.	MICAL2	114	.	0			c.G3304A						PASS	.	G	THR/ALA	1,4401	2.1+/-5.4	0,1,2200	43.0	43.0	43.0		3304	3.7	0.4	11	dbSNP_134	43	0,8588		0,0,4294	no	missense	MICAL2	NM_014632.2	58	0,1,6494	AA,AG,GG		0.0,0.0227,0.0077	possibly-damaging	1102/1125	12281414	1,12989	2201	4294	6495	SO:0001583	missense	9645	exon26			GTGGCCGCCATTG	AB018293	CCDS7809.1, CCDS60726.1, CCDS60727.1, CCDS60728.1	11p15.3	2014-08-12	2013-03-26		ENSG00000133816	ENSG00000133816			24693	protein-coding gene	gene with protein product		608881				12110185	Standard	XM_005253249		Approved	KIAA0750	uc001mjz.3	O94851	OTTHUMG00000165744	ENST00000256194.4:c.3304G>A	11.37:g.12281414G>A	ENSP00000256194:p.Ala1102Thr	108.0	0.0	0		141.0	53.0	0.375887	NM_014632	B4DGZ0|B7Z849|D3DQW5|G3XAC8|Q5KTR3|Q5KTR4|Q7Z3A8	Missense_Mutation	SNP	ENST00000256194.4	37	CCDS7809.1	.	.	.	.	.	.	.	.	.	.	G	6.866	0.529211	0.13127	2.27E-4	0.0	ENSG00000133816	ENST00000537344;ENST00000544073;ENST00000256194;ENST00000527546;ENST00000342902;ENST00000379612	T;T;T;T;T	0.61040	0.14;0.15;0.14;0.15;0.15	5.56	3.68	0.42216	.	0.230508	0.30940	N	0.008579	T	0.40570	0.1122	N	0.24115	0.695	0.09310	N	1	B;D;B;B;B;D	0.67145	0.224;0.972;0.007;0.209;0.007;0.996	B;B;B;B;B;P	0.44518	0.016;0.367;0.003;0.015;0.003;0.452	T	0.22208	-1.0223	10	0.15499	T	0.54	.	9.8179	0.40865	0.2194:0.0:0.7806:0.0	.	445;1081;912;855;876;1102	B4DYS3;G3XAC8;B7Z849;Q5KTR3;Q5KTR4;O94851	.;.;.;.;.;MICA2_HUMAN	T	912;445;1102;912;1081;876	ENSP00000441689:A912T;ENSP00000256194:A1102T;ENSP00000433965:A912T;ENSP00000344894:A1081T;ENSP00000368932:A876T	ENSP00000256194:A1102T	A	+	1	0	MICAL2	12237990	0.987000	0.35691	0.433000	0.26760	0.023000	0.10783	2.954000	0.49113	1.333000	0.45449	0.591000	0.81541	GCC	G|1.000;A|0.000	0.000	weak		0.597	MICAL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385993.1	NM_014632	
TRPC4AP	26133	hgsc.bcm.edu	37	20	33665969	33665969	+	Silent	SNP	C	C	T	rs139800499	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr20:33665969C>T	ENST00000252015.2	-	2	266	c.177G>A	c.(175-177)gaG>gaA	p.E59E	TRPC4AP_ENST00000451813.2_Silent_p.E59E|TRPC4AP_ENST00000432634.2_Silent_p.E59E			Q8TEL6	TP4AP_HUMAN	transient receptor potential cation channel, subfamily C, member 4 associated protein	59	Interaction with TNFRSF1A. {ECO:0000250}.				calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|protein ubiquitination (GO:0016567)|transmembrane transport (GO:0055085)|ubiquitin-dependent protein catabolic process (GO:0006511)	Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)			breast(3)|central_nervous_system(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(13)|skin(1)|stomach(1)|urinary_tract(1)	32			BRCA - Breast invasive adenocarcinoma(18;0.00936)			TCAAAAAAGTCTCAGTGAACT	0.458													C|||	6	0.00119808	0.0008	0.0014	5008	,	,		17571	0.0		0.004	False		,,,				2504	0.0				p.E59E		Atlas-SNP	.											.	TRPC4AP	64	.	0			c.G177A						PASS	.	C	,	12,4394	19.1+/-41.9	0,12,2191	99.0	90.0	93.0		177,177	0.4	1.0	20	dbSNP_134	93	65,8535	39.3+/-95.6	0,65,4235	no	coding-synonymous,coding-synonymous	TRPC4AP	NM_015638.2,NM_199368.1	,	0,77,6426	TT,TC,CC		0.7558,0.2724,0.592	,	59/798,59/790	33665969	77,12929	2203	4300	6503	SO:0001819	synonymous_variant	26133	exon2			AAAAGTCTCAGTG	AF055022	CCDS13246.1, CCDS46591.1	20q11.23	2014-06-13	2003-10-06	2003-10-08	ENSG00000100991	ENSG00000100991			16181	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 158"""	608430	"""chromosome 20 open reading frame 188"""	C20orf188			Standard	NM_015638		Approved	DKFZP727M231, DKFZp586C1223, dJ756N5.2, TRRP4AP, PPP1R158	uc002xbk.3	Q8TEL6	OTTHUMG00000032319	ENST00000252015.2:c.177G>A	20.37:g.33665969C>T		83.0	0.0	0		77.0	32.0	0.415584	NM_199368	E1P5Q0|E1P5Q1|Q96H82|Q9BVB8|Q9H429|Q9UFS6	Silent	SNP	ENST00000252015.2	37	CCDS13246.1																																																																																			C|0.995;T|0.005	0.005	strong		0.458	TRPC4AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078832.2	NM_015638	
DENND5B	160518	hgsc.bcm.edu	37	12	31600503	31600503	+	Missense_Mutation	SNP	T	T	C	rs34129725	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:31600503T>C	ENST00000389082.5	-	6	2094	c.1830A>G	c.(1828-1830)atA>atG	p.I610M	DENND5B_ENST00000306833.6_Missense_Mutation_p.I645M|DENND5B_ENST00000354285.4_Missense_Mutation_p.I632M|snoU13_ENST00000458765.1_RNA|DENND5B_ENST00000536562.1_Missense_Mutation_p.I645M	NM_144973.3	NP_659410.3	Q6ZUT9	DEN5B_HUMAN	DENN/MADD domain containing 5B	610					positive regulation of Rab GTPase activity (GO:0032851)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			NS(2)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(8)|lung(17)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	38						ATTTCTGATATATAGATGTCC	0.398													T|||	8	0.00159744	0.0	0.0	5008	,	,		18530	0.0		0.005	False		,,,				2504	0.0031				p.I610M		Atlas-SNP	.											.	DENND5B	114	.	0			c.A1830G						PASS	.	T	MET/ILE	13,3669		0,13,1828	60.0	57.0	58.0		1830	-4.4	1.0	12	dbSNP_126	58	86,8100		1,84,4008	yes	missense	DENND5B	NM_144973.3	10	1,97,5836	CC,CT,TT		1.0506,0.3531,0.8342	benign	610/1275	31600503	99,11769	1841	4093	5934	SO:0001583	missense	160518	exon6			CTGATATATAGAT	AF086301	CCDS44857.1	12p11.21	2012-10-03			ENSG00000170456	ENSG00000170456		"""DENN/MADD domain containing"""	28338	protein-coding gene	gene with protein product						12477932	Standard	NM_144973		Approved	MGC24039	uc001rki.1	Q6ZUT9	OTTHUMG00000169034	ENST00000389082.5:c.1830A>G	12.37:g.31600503T>C	ENSP00000373734:p.Ile610Met	109.0	0.0	0		152.0	69.0	0.453947	NM_144973	B5ME75|Q59FW8|Q68CZ7|Q6NUJ0|Q7Z3F9|Q8N973|Q8WUC8	Missense_Mutation	SNP	ENST00000389082.5	37	CCDS44857.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	T	8.110	0.778637	0.16120	0.003531	0.010506	ENSG00000170456	ENST00000389082;ENST00000306833;ENST00000536562;ENST00000354285	T;T;T;T	0.44482	0.92;0.92;0.92;0.92	5.05	-4.42	0.03579	.	0.231333	0.35903	N	0.002910	T	0.09379	0.0231	N	0.03115	-0.41	0.24313	N	0.99507	B;B;B	0.13145	0.007;0.001;0.003	B;B;B	0.16289	0.015;0.004;0.009	T	0.06303	-1.0834	10	0.40728	T	0.16	-11.2663	3.3897	0.07285	0.3423:0.0629:0.3752:0.2196	rs34129725	632;610;645	Q6ZUT9-4;Q6ZUT9;G3V1S3	.;DEN5B_HUMAN;.	M	610;645;645;632	ENSP00000373734:I610M;ENSP00000306482:I645M;ENSP00000444889:I645M;ENSP00000346238:I632M	ENSP00000306482:I645M	I	-	3	3	DENND5B	31491770	0.000000	0.05858	0.988000	0.46212	0.994000	0.84299	-2.825000	0.00747	-0.495000	0.06659	0.460000	0.39030	ATA	T|0.995;C|0.005	0.005	strong		0.398	DENND5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402040.1	NM_144973	
ZNF596	169270	hgsc.bcm.edu	37	8	194695	194695	+	Missense_Mutation	SNP	C	C	A	rs148383942	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:194695C>A	ENST00000398612.1	+	5	683	c.300C>A	c.(298-300)agC>agA	p.S100R	ZNF596_ENST00000308811.4_Missense_Mutation_p.S100R|ZNF596_ENST00000320552.2_Intron	NM_001042415.1|NM_001042416.1	NP_001035880.1|NP_001035881.1	Q8TC21	ZN596_HUMAN	zinc finger protein 596	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			autonomic_ganglia(1)|endometrium(2)|large_intestine(6)|lung(5)	14		all_cancers(2;4.81e-29)|all_epithelial(2;5.03e-19)|Lung NSC(2;8.68e-08)|all_lung(2;1.52e-07)|Ovarian(12;0.00965)|Colorectal(14;0.0367)|all_neural(12;0.0837)|Myeloproliferative disorder(644;0.116)|all_hematologic(2;0.138)|Acute lymphoblastic leukemia(644;0.242)		Epithelial(5;3.77e-18)|all cancers(2;5.2e-17)|OV - Ovarian serous cystadenocarcinoma(5;5.37e-09)|BRCA - Breast invasive adenocarcinoma(11;1.7e-06)|Colorectal(2;6.51e-05)|READ - Rectum adenocarcinoma(2;0.0276)|COAD - Colon adenocarcinoma(149;0.0702)		CCACCATCAGCACAATGGTAA	0.358													.|||	10	0.00199681	0.0008	0.0014	5008	,	,		19470	0.0		0.002	False		,,,				2504	0.0061				p.S100R		Atlas-SNP	.											.	ZNF596	34	.	0			c.C300A						PASS	.	C	ARG/SER,ARG/SER,ARG/SER	0,4406		0,0,2203	120.0	101.0	108.0		300,300,300	-3.2	0.0	8	dbSNP_134	108	20,8580		0,20,4280	yes	missense,missense,missense	ZNF596	NM_001042415.1,NM_001042416.1,NM_173539.2	110,110,110	0,20,6483	AA,AC,CC		0.2326,0.0,0.1538	benign,benign,benign	100/505,100/505,100/505	194695	20,12986	2203	4300	6503	SO:0001583	missense	169270	exon5			CATCAGCACAATG	BC026190	CCDS5951.2	8p23.3	2013-01-08			ENSG00000172748	ENSG00000172748		"""Zinc fingers, C2H2-type"", ""-"""	27268	protein-coding gene	gene with protein product						12477932	Standard	NM_001287256		Approved		uc003wot.3	Q8TC21	OTTHUMG00000086931	ENST00000398612.1:c.300C>A	8.37:g.194695C>A	ENSP00000381613:p.Ser100Arg	212.0	1.0	0.00471698		219.0	117.0	0.534247	NM_173539	B2R8P4|O95015|Q8N9X0	Missense_Mutation	SNP	ENST00000398612.1	37	CCDS5951.2	6	0.0027472527472527475	1	0.0020325203252032522	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	.	6.943	0.543844	0.13312	0.0	0.002326	ENSG00000172748	ENST00000521145;ENST00000308811;ENST00000522866;ENST00000398612	T;T;T	0.13778	2.56;3.47;3.47	2.91	-3.16	0.05217	.	.	.	.	.	T	0.02342	0.0072	N	0.03194	-0.395	0.09310	N	1	B	0.21381	0.055	B	0.12837	0.008	T	0.40757	-0.9546	9	0.10111	T	0.7	.	1.2469	0.01974	0.2252:0.2777:0.3413:0.1559	.	100	Q8TC21	ZN596_HUMAN	R	100	ENSP00000429671:S100R;ENSP00000310033:S100R;ENSP00000381613:S100R	ENSP00000310033:S100R	S	+	3	2	ZNF596	184695	0.000000	0.05858	0.000000	0.03702	0.242000	0.25591	-1.119000	0.03276	-0.755000	0.04709	0.591000	0.81541	AGC	C|0.997;A|0.003	0.003	strong		0.358	ZNF596-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195858.4	NM_173539	
TMEM230	29058	hgsc.bcm.edu	37	20	5086918	5086918	+	Silent	SNP	G	G	A	rs147693982	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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_ENST00000379277.2_Silent_p.I46I|TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379283.2_Silent_p.I46I|TMEM230_ENST00000379279.2_Silent_p.I46I|TMEM230_ENST00000342308.5_Silent_p.I109I	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		93.0	0.0	0		94.0	53.0	0.56383	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		
MYO18B	84700	hgsc.bcm.edu	37	22	26422651	26422651	+	Silent	SNP	G	G	A	rs199593757	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:26422651G>A	ENST00000407587.2	+	43	6883	c.6714G>A	c.(6712-6714)ccG>ccA	p.P2238P	MYO18B_ENST00000335473.7_Silent_p.P2237P|MYO18B_ENST00000536101.1_Silent_p.P2237P			Q8IUG5	MY18B_HUMAN	myosin XVIIIB	2237						cytoplasm (GO:0005737)|nucleus (GO:0005634)|unconventional myosin complex (GO:0016461)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(6)|central_nervous_system(3)|endometrium(12)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(27)|liver(2)|lung(60)|ovary(7)|prostate(8)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	146						ATACATCCCCGCTGTCGAGGG	0.597													G|||	13	0.00259585	0.0	0.0014	5008	,	,		18385	0.0		0.001	False		,,,				2504	0.0112				p.P2237P		Atlas-SNP	.											.	MYO18B	322	.	0			c.G6711A						PASS	.	G		2,3830		0,2,1914	25.0	27.0	26.0		6711	-4.2	0.0	22		26	25,8189		0,25,4082	no	coding-synonymous	MYO18B	NM_032608.5		0,27,5996	AA,AG,GG		0.3044,0.0522,0.2241		2237/2568	26422651	27,12019	1916	4107	6023	SO:0001819	synonymous_variant	84700	exon43			ATCCCCGCTGTCG	AJ310931	CCDS54507.1	22q12.1	2011-09-27			ENSG00000133454	ENSG00000133454		"""Myosins / Myosin superfamily : Class XVIII"""	18150	protein-coding gene	gene with protein product		607295				12209013, 12547197	Standard	NM_032608		Approved	BK125H2.1	uc003abz.1	Q8IUG5	OTTHUMG00000151129	ENST00000407587.2:c.6714G>A	22.37:g.26422651G>A		66.0	0.0	0		86.0	48.0	0.55814	NM_032608	B2RWP3|F5GYU7|Q8NDI8|Q8TE65|Q8WWS0|Q96KH2|Q96KR8|Q96KR9	Silent	SNP	ENST00000407587.2	37		.	.	.	.	.	.	.	.	.	.	G	11.64	1.698433	0.30142	5.22E-4	0.003044	ENSG00000133454	ENST00000543971	.	.	.	4.94	-4.2	0.03823	.	.	.	.	.	T	0.32793	0.0841	.	.	.	0.31759	N	0.633626	.	.	.	.	.	.	T	0.42032	-0.9475	4	.	.	.	.	5.7129	0.17945	0.2701:0.3964:0.3335:0.0	.	.	.	.	H	187	.	.	R	+	2	0	MYO18B	24752651	0.000000	0.05858	0.003000	0.11579	0.699000	0.40488	-2.672000	0.00843	-1.013000	0.03383	0.491000	0.48974	CGC	G|0.993;A|0.007	0.007	strong		0.597	MYO18B-006	NOVEL	non_canonical_conserved|basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000400691.1	NM_032608	
ZNF652	22834	hgsc.bcm.edu	37	17	47394516	47394516	+	Missense_Mutation	SNP	C	C	T	rs368716483		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:47394516C>T	ENST00000362063.2	-	2	890	c.572G>A	c.(571-573)aGa>aAa	p.R191K	ZNF652_ENST00000430262.2_Missense_Mutation_p.R191K	NM_014897.2	NP_055712.1	Q9Y2D9	ZN652_HUMAN	zinc finger protein 652	191					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(3)|kidney(3)|large_intestine(5)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	20	all_cancers(4;6.81e-14)|Breast(4;4.97e-29)|all_epithelial(4;1.53e-17)		BRCA - Breast invasive adenocarcinoma(1;3.1e-14)|Epithelial(5;2.92e-06)|all cancers(6;3.15e-05)			TCTCCTGGTTCTCCTTTGTGT	0.483																																					p.R191K		Atlas-SNP	.											.	ZNF652	54	.	0			c.G572A						PASS	.	C	LYS/ARG,LYS/ARG	0,4406		0,0,2203	91.0	95.0	93.0		572,572	5.2	1.0	17		93	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ZNF652	NM_001145365.1,NM_014897.2	26,26	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign,benign	191/607,191/607	47394516	1,13005	2203	4300	6503	SO:0001583	missense	22834	exon2			CTGGTTCTCCTTT	AB023141	CCDS32677.1	17q21.32	2013-01-08				ENSG00000198740		"""Zinc fingers, C2H2-type"""	29147	protein-coding gene	gene with protein product		613907				10231032	Standard	NM_014897		Approved	KIAA0924	uc002iow.3	Q9Y2D9		ENST00000362063.2:c.572G>A	17.37:g.47394516C>T	ENSP00000354686:p.Arg191Lys	162.0	0.0	0		188.0	93.0	0.494681	NM_001145365	A4QPD9|Q5H9Q0	Missense_Mutation	SNP	ENST00000362063.2	37	CCDS32677.1	.	.	.	.	.	.	.	.	.	.	C	14.71	2.616802	0.46736	0.0	1.16E-4	ENSG00000198740	ENST00000362063;ENST00000430262	T;T	0.07444	3.19;3.19	5.22	5.22	0.72569	.	0.213072	0.50627	D	0.000118	T	0.05777	0.0151	N	0.14661	0.345	0.42015	D	0.990951	B	0.20261	0.043	B	0.22601	0.04	T	0.13872	-1.0493	10	0.02654	T	1	-12.121	18.5632	0.91108	0.0:1.0:0.0:0.0	.	191	Q9Y2D9	ZN652_HUMAN	K	191	ENSP00000354686:R191K;ENSP00000416305:R191K	ENSP00000354686:R191K	R	-	2	0	ZNF652	44749515	1.000000	0.71417	0.969000	0.41365	0.980000	0.70556	3.567000	0.53813	2.715000	0.92844	0.655000	0.94253	AGA	.	.	weak		0.483	ZNF652-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364524.1	NM_014897	
HERC2	8924	hgsc.bcm.edu	37	15	28459095	28459095	+	Silent	SNP	G	G	A	rs191942261		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459095G>A	ENST00000261609.7	-	42	6687	c.6579C>T	c.(6577-6579)ccC>ccT	p.P2193P		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2											NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		TCTCGGAGTCGGGGAAGTAGT	0.587																																					p.P2193P		Atlas-SNP	.											.	HERC2	501	.	0			c.C6579T						PASS	.						34.0	31.0	32.0					15																	28459095		2203	4297	6500	SO:0001819	synonymous_variant	8924	exon42			GGAGTCGGGGAAG	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6579C>T	15.37:g.28459095G>A		214.0	0.0	0		191.0	15.0	0.078534	NM_004667		Silent	SNP	ENST00000261609.7	37	CCDS10021.1																																																																																			G|0.993;A|0.007	0.007	strong		0.587	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
PCDHA8	56140	hgsc.bcm.edu	37	5	140222316	140222316	+	Silent	SNP	G	G	A	rs202126810		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:140222316G>A	ENST00000531613.1	+	1	1410	c.1410G>A	c.(1408-1410)ccG>ccA	p.P470P	PCDHA8_ENST00000378123.3_Silent_p.P470P|PCDHA4_ENST00000530339.1_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA1_ENST00000394633.3_Intron	NM_018911.2	NP_061734.1	Q9Y5H6	PCDA8_HUMAN	protocadherin alpha 8	470	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)			NS(2)|breast(3)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(10)|lung(31)|ovary(2)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(6)	78			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACAACCCGCCGGGCTGCCACA	0.672																																					p.P470P		Atlas-SNP	.											PCDHA8_ENST00000531613,rectum,carcinoma,0,2	PCDHA8	366	2	0			c.G1410A						PASS	.						38.0	43.0	41.0					5																	140222316		2193	4252	6445	SO:0001819	synonymous_variant	56140	exon1			CCCGCCGGGCTGC	AF152486	CCDS54919.1	5q31	2010-11-26				ENSG00000204962		"""Cadherins / Protocadherins : Clustered"""	8674	other	complex locus constituent	"""KIAA0345-like 6"""	606314				10380929	Standard	NM_018911		Approved			Q9Y5H6		ENST00000531613.1:c.1410G>A	5.37:g.140222316G>A		242.0	0.0	0		304.0	152.0	0.5	NM_031856	B9EGT7|O75281	Silent	SNP	ENST00000531613.1	37	CCDS54919.1																																																																																			G|0.999;T|0.001	.	alt		0.672	PCDHA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372830.2	NM_018911	
ITGA11	22801	hgsc.bcm.edu	37	15	68643659	68643659	+	Silent	SNP	G	G	A	rs61729770	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:68643659G>A	ENST00000315757.7	-	8	917	c.831C>T	c.(829-831)agC>agT	p.S277S	ITGA11_ENST00000423218.2_Silent_p.S277S|ITGA11_ENST00000562826.1_5'UTR	NM_001004439.1	NP_001004439.1	Q9UKX5	ITA11_HUMAN	integrin, alpha 11	277	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell-matrix adhesion (GO:0007160)|collagen-activated signaling pathway (GO:0038065)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)|muscle organ development (GO:0007517)|osteoblast differentiation (GO:0001649)|substrate-dependent cell migration (GO:0006929)	focal adhesion (GO:0005925)|integrin alpha11-beta1 complex (GO:0034681)|integrin complex (GO:0008305)|membrane (GO:0016020)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|collagen receptor activity (GO:0038064)|metal ion binding (GO:0046872)			NS(2)|breast(1)|central_nervous_system(1)|endometrium(7)|kidney(6)|large_intestine(6)|lung(22)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	52						CCAGGTCTGGGCTGTCGTGGG	0.567													G|||	13	0.00259585	0.0	0.0043	5008	,	,		20370	0.0		0.0099	False		,,,				2504	0.0				p.S277S		Atlas-SNP	.											.	ITGA11	110	.	0			c.C831T						PASS	.	G		9,4145		0,9,2068	122.0	130.0	127.0		831	4.5	1.0	15	dbSNP_129	127	78,8372		0,78,4147	no	coding-synonymous	ITGA11	NM_001004439.1		0,87,6215	AA,AG,GG		0.9231,0.2167,0.6903		277/1189	68643659	87,12517	2077	4225	6302	SO:0001819	synonymous_variant	22801	exon8			GTCTGGGCTGTCG	AF109681	CCDS45291.1	15q22.3-q23	2010-03-23				ENSG00000137809		"""Integrins"""	6136	protein-coding gene	gene with protein product		604789				10486209	Standard	NM_001004439		Approved	HsT18964	uc002ari.3	Q9UKX5		ENST00000315757.7:c.831C>T	15.37:g.68643659G>A		146.0	0.0	0		152.0	72.0	0.473684	NM_001004439	J3KQM2|Q8WYI8|Q9UKQ1	Silent	SNP	ENST00000315757.7	37	CCDS45291.1																																																																																			G|0.995;A|0.005	0.005	strong		0.567	ITGA11-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_012211	
DDX41	51428	hgsc.bcm.edu	37	5	176943352	176943352	+	Missense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:176943352G>C	ENST00000507955.1	-	3	758	c.235C>G	c.(235-237)Cta>Gta	p.L79V	DDX41_ENST00000506965.1_5'UTR	NM_016222.2	NP_057306.2	Q9UJV9	DDX41_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 41	79					apoptotic process (GO:0006915)|cellular response to interferon-beta (GO:0035458)|defense response to virus (GO:0051607)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|regulation of type I interferon production (GO:0032479)|RNA processing (GO:0006396)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)					all_cancers(89;0.00033)|Renal(175;0.000269)|Lung NSC(126;0.00161)|all_lung(126;0.00286)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)|Epithelial(233;0.191)			TGAGGGCCTAGCGGGATGTCG	0.607																																					p.L79V		Atlas-SNP	.											.	DDX41	49	.	0			c.C235G						PASS	.						133.0	126.0	128.0					5																	176943352		2203	4300	6503	SO:0001583	missense	51428	exon3			GGCCTAGCGGGAT	AF195417	CCDS4427.1	5q35.3	2008-02-05			ENSG00000183258	ENSG00000183258		"""DEAD-boxes"""	18674	protein-coding gene	gene with protein product		608170				10607561	Standard	NM_016222		Approved	ABS, MGC8828	uc003mho.3	Q9UJV9	OTTHUMG00000130858	ENST00000507955.1:c.235C>G	5.37:g.176943352G>C	ENSP00000422753:p.Leu79Val	131.0	0.0	0		126.0	59.0	0.468254	NM_016222	B2RDC8|Q96BK6|Q96K05|Q9NT96|Q9NW04	Missense_Mutation	SNP	ENST00000507955.1	37	CCDS4427.1	.	.	.	.	.	.	.	.	.	.	G	9.895	1.205196	0.22205	.	.	ENSG00000183258	ENST00000330503;ENST00000507955	T;T	0.26810	1.71;1.72	5.38	2.1	0.27182	.	0.377447	0.23291	N	0.049795	T	0.17408	0.0418	L	0.34521	1.04	0.31726	N	0.637673	B	0.14805	0.011	B	0.11329	0.006	T	0.12656	-1.0539	10	0.30078	T	0.28	-7.6704	9.3594	0.38186	0.3981:0.0:0.6019:0.0	.	79	Q9UJV9	DDX41_HUMAN	V	97;79	ENSP00000330349:L97V;ENSP00000422753:L79V	ENSP00000330349:L97V	L	-	1	2	DDX41	176875958	0.121000	0.22262	0.561000	0.28357	0.816000	0.46133	0.337000	0.19841	0.620000	0.30215	0.491000	0.48974	CTA	.	.	none		0.607	DDX41-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253432.2	NM_016222	
ARC	23237	hgsc.bcm.edu	37	8	143694520	143694520	+	Silent	SNP	C	C	T	rs371075422		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:143694520C>T	ENST00000356613.2	-	1	2313	c.1113G>A	c.(1111-1113)ccG>ccA	p.P371P	ARC_ENST00000581404.1_5'Flank	NM_015193.4	NP_056008.1	O60936	NOL3_HUMAN	activity-regulated cytoskeleton-associated protein	122					apoptotic process (GO:0006915)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|regulation of gene expression (GO:0010468)|response to hypoxia (GO:0001666)|response to injury involved in regulation of muscle adaptation (GO:0014876)|RNA splicing (GO:0008380)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|sarcoplasm (GO:0016528)	identical protein binding (GO:0042802)|RNA binding (GO:0003723)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(4)|lung(3)|upper_aerodigestive_tract(1)	13	all_cancers(97;3.55e-12)|all_epithelial(106;1.03e-08)|Lung NSC(106;0.000353)|all_lung(105;0.00092)|Medulloblastoma(13;0.00276)|all_neural(13;0.00559)|Ovarian(258;0.0254)|Acute lymphoblastic leukemia(118;0.155)	Acute lymphoblastic leukemia(644;0.0279)				CATCCTCCACCGGGAGGTGGG	0.726																																					p.P371P		Atlas-SNP	.											ARC,colon,carcinoma,-2,1	ARC	34	1	0			c.G1113A						PASS	.	C		0,4302		0,0,2151	8.0	11.0	10.0		1113	-2.4	0.0	8		10	1,8483		0,1,4241	no	coding-synonymous	ARC	NM_015193.3		0,1,6392	TT,TC,CC		0.0118,0.0,0.0078		371/397	143694520	1,12785	2151	4242	6393	SO:0001819	synonymous_variant	23237	exon1			CTCCACCGGGAGG	AF193421	CCDS34950.1	8q24.3	2008-08-01			ENSG00000198576	ENSG00000198576			648	protein-coding gene	gene with protein product		612461				10970730, 17466953	Standard	NM_015193		Approved	KIAA0278, Arg3.1	uc003ywn.2	Q7LC44	OTTHUMG00000134310	ENST00000356613.2:c.1113G>A	8.37:g.143694520C>T		32.0	0.0	0		53.0	23.0	0.433962	NM_015193	B4DFL0|O60937	Silent	SNP	ENST00000356613.2	37	CCDS34950.1																																																																																			.	.	weak		0.726	ARC-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259274.2		
HRAS	3265	hgsc.bcm.edu	37	11	534242	534242	+	Silent	SNP	A	A	G	rs12628	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:534242A>G	ENST00000451590.1	-	2	268	c.81T>C	c.(79-81)caT>caC	p.H27H	HRAS_ENST00000397596.2_Silent_p.H27H|HRAS_ENST00000311189.7_Silent_p.H27H|HRAS_ENST00000397594.1_Silent_p.H27H|HRAS_ENST00000417302.1_Silent_p.H27H|HRAS_ENST00000468682.2_5'UTR	NM_001130442.1|NM_005343.2	NP_001123914.1|NP_005334.1	P01112	RASH_HUMAN	Harvey rat sarcoma viral oncogene homolog	27					actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular senescence (GO:0090398)|chemotaxis (GO:0006935)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway (GO:0097193)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|mitotic cell cycle checkpoint (GO:0007093)|negative regulation of cell differentiation (GO:0045596)|negative regulation of cell proliferation (GO:0008285)|negative regulation of gene expression (GO:0010629)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of Rho GTPase activity (GO:0034259)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ morphogenesis (GO:0009887)|positive regulation of actin cytoskeleton reorganization (GO:2000251)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of miRNA metabolic process (GO:2000630)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of Rac protein signal transduction (GO:0035022)|positive regulation of ruffle assembly (GO:1900029)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of wound healing (GO:0090303)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|protein C-terminus binding (GO:0008022)	p.H27H(26)		adrenal_gland(1)|bone(3)|breast(7)|cervix(23)|endometrium(4)|haematopoietic_and_lymphoid_tissue(12)|kidney(1)|large_intestine(2)|liver(1)|lung(16)|oesophagus(2)|penis(2)|pituitary(10)|prostate(31)|salivary_gland(24)|skin(184)|soft_tissue(38)|stomach(14)|testis(5)|thymus(1)|thyroid(173)|upper_aerodigestive_tract(122)|urinary_tract(225)	901		all_cancers(49;4.37e-09)|all_epithelial(84;2.09e-06)|Breast(177;0.000162)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.0538)|all_lung(207;0.0713)		all cancers(45;7.63e-28)|Epithelial(43;7.29e-27)|OV - Ovarian serous cystadenocarcinoma(40;7.15e-21)|BRCA - Breast invasive adenocarcinoma(625;3.56e-05)|Lung(200;0.0375)|LUSC - Lung squamous cell carcinoma(625;0.0703)		CGTCCACAAAATGGTTCTGGA	0.642		6	Mis		"""infrequent sarcomas, rare other types"""	"""rhadomyosarcoma, ganglioneuroblastoma, bladder"""			Costello syndrome	HNSCC(11;0.0054)			G|||	1488	0.297125	0.3729	0.3646	5008	,	,		18347	0.1726		0.3121	False		,,,				2504	0.2597				p.H27H		Atlas-SNP	.	yes	Dom	yes	Costello syndrome	11	11p15.5	3265	v-Ha-ras Harvey rat sarcoma viral oncogene homolog		"""E, L, M"""	HRAS,arm,benign_melanocytic_nevus,0,26	HRAS	1232	26	26	Substitution - coding silent(26)	urinary_tract(25)|skin(1)	c.T81C	GRCh37	CM035804	HRAS	M	rs12628	PASS	.	G	,,	1652,2754	653.2+/-399.5	309,1034,860	135.0	123.0	127.0	http://www.ncbi.nlm.nih.gov/sites/varvu?gene	81,81,81	1.0	1.0	11	dbSNP_52	127	2959,5641	665.8+/-402.3	510,1939,1851	no	coding-synonymous,coding-synonymous,coding-synonymous	HRAS	NM_001130442.1,NM_005343.2,NM_176795.3	,,	819,2973,2711	GG,GA,AA		34.407,37.4943,35.4529	,,	27/190,27/190,27/171	534242	4611,8395	2203	4300	6503	SO:0001819	synonymous_variant	3265	exon2	Familial Cancer Database	incl.: Facio-Cutaneous-Skeletal syndrome	CACAAAATGGTTC	AJ437024	CCDS7698.1, CCDS7699.1	11p15.5	2014-09-17	2013-07-08		ENSG00000174775	ENSG00000174775			5173	protein-coding gene	gene with protein product		190020	"""v-Ha-ras Harvey rat sarcoma viral oncogene homolog"""	HRAS1			Standard	NM_176795		Approved		uc010qvx.2	P01112	OTTHUMG00000131919	ENST00000451590.1:c.81T>C	11.37:g.534242A>G		69.0	0.0	0		87.0	40.0	0.45977	NM_001130442	B5BUA0|Q14080|Q6FHV9|Q9BR65|Q9UCE2	Silent	SNP	ENST00000451590.1	37	CCDS7698.1																																																																																			A|0.663;G|0.337	0.337	strong		0.642	HRAS-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259403.2	NM_176795	
NLRC4	58484	hgsc.bcm.edu	37	2	32463365	32463365	+	Missense_Mutation	SNP	C	C	A	rs149451729	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:32463365C>A	ENST00000404025.2	-	7	2845	c.2357G>T	c.(2356-2358)gGc>gTc	p.G786V	NLRC4_ENST00000342905.6_Missense_Mutation_p.G121V|NLRC4_ENST00000402280.1_Missense_Mutation_p.G786V|NLRC4_ENST00000360906.5_Missense_Mutation_p.G786V			Q9NPP4	NLRC4_HUMAN	NLR family, CARD domain containing 4	786					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of innate immune response (GO:0002218)|defense response to bacterium (GO:0042742)|detection of bacterium (GO:0016045)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1 beta secretion (GO:0050702)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of apoptotic process (GO:0043065)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|protein homooligomerization (GO:0051260)|pyroptosis (GO:0070269)	cytosol (GO:0005829)|intracellular (GO:0005622)|IPAF inflammasome complex (GO:0072557)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|magnesium ion binding (GO:0000287)|protein homodimerization activity (GO:0042803)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(1)|ovary(3)|skin(2)|stomach(2)	16	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.208)					GTTTTTCAGGCCTTCAGCTGA	0.358													C|||	3	0.000599042	0.0	0.0043	5008	,	,		19325	0.0		0.0	False		,,,				2504	0.0				p.G786V		Atlas-SNP	.											.	NLRC4	165	.	0			c.G2357T						PASS	.	C	VAL/GLY,VAL/GLY,VAL/GLY	4,4402	8.1+/-20.4	0,4,2199	94.0	93.0	94.0		2357,2357,2357	2.8	0.0	2	dbSNP_134	94	39,8561	25.7+/-73.6	0,39,4261	yes	missense,missense,missense	NLRC4	NM_001199138.1,NM_001199139.1,NM_021209.4	109,109,109	0,43,6460	AA,AC,CC		0.4535,0.0908,0.3306	probably-damaging,probably-damaging,probably-damaging	786/1025,786/1025,786/1025	32463365	43,12963	2203	4300	6503	SO:0001583	missense	58484	exon6			TTCAGGCCTTCAG	AF376061	CCDS33174.1	2p22-p21	2008-08-27	2006-12-08	2006-12-08	ENSG00000091106	ENSG00000091106		"""Nucleotide-binding domain and leucine rich repeat containing"""	16412	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 4"", ""NOD-like receptor C4"""	606831	"""caspase recruitment domain family, member 12"""	CARD12		11374873	Standard	NM_021209		Approved	CLAN1, ipaf, CLANA, CLANB, CLANC, CLAND, CLR2.1, CLAN	uc021vfq.1	Q9NPP4	OTTHUMG00000152107	ENST00000404025.2:c.2357G>T	2.37:g.32463365C>A	ENSP00000385090:p.Gly786Val	102.0	0.0	0		83.0	37.0	0.445783	NM_001199138	A8K9F8|B2RBQ3|B3KTF0|D6W580|Q96J81|Q96J82|Q96J83	Missense_Mutation	SNP	ENST00000404025.2	37	CCDS33174.1	2	9.157509157509158E-4	0	0.0	2	0.0055248618784530384	0	0.0	0	0.0	C	7.093	0.572525	0.13623	9.08E-4	0.004535	ENSG00000091106	ENST00000360906;ENST00000402280;ENST00000342905;ENST00000404025	T;T;T;T	0.53423	0.62;0.62;0.62;0.62	4.63	2.78	0.32641	.	0.000000	0.41294	D	0.000913	T	0.42787	0.1218	L	0.56769	1.78	0.36099	D	0.843987	D;D	0.62365	0.98;0.991	P;P	0.58013	0.693;0.831	T	0.56080	-0.8038	9	0.16420	T	0.52	-8.9282	6.4653	0.21977	0.0:0.7173:0.1834:0.0993	.	121;786	Q9NPP4-2;Q9NPP4	.;NLRC4_HUMAN	V	786;786;121;786	ENSP00000354159:G786V;ENSP00000385428:G786V;ENSP00000339666:G121V;ENSP00000385090:G786V	ENSP00000339666:G121V	G	-	2	0	NLRC4	32316869	0.035000	0.19736	0.016000	0.15963	0.041000	0.13682	0.929000	0.28844	0.663000	0.31027	-0.150000	0.13652	GGC	C|0.997;A|0.003	0.003	strong		0.358	NLRC4-001	KNOWN	non_canonical_other|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325222.2	NM_021209	
HERC2	8924	hgsc.bcm.edu	37	15	28459325	28459325	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:28459325C>T	ENST00000261609.7	-	41	6560	c.6452G>A	c.(6451-6453)cGc>cAc	p.R2151H		NM_004667.5	NP_004658.3			HECT and RLD domain containing E3 ubiquitin protein ligase 2									p.R2151H(2)		NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(3)|cervix(3)|endometrium(20)|kidney(11)|large_intestine(33)|lung(95)|ovary(7)|prostate(8)|skin(7)|upper_aerodigestive_tract(8)|urinary_tract(4)	204		all_lung(180;1.3e-11)|Breast(32;0.000194)|Colorectal(260;0.227)		all cancers(64;3.93e-09)|Epithelial(43;9.99e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0271)|GBM - Glioblastoma multiforme(186;0.0497)|Lung(196;0.199)		GTGCAGCGTGCGCAGCAGTGC	0.637																																					p.R2151H		Atlas-SNP	.											HERC2,NS,carcinoma,0,2	HERC2	501	2	2	Substitution - Missense(2)	prostate(2)	c.G6452A						scavenged	.						60.0	56.0	57.0					15																	28459325		2203	4300	6503	SO:0001583	missense	8924	exon41			AGCGTGCGCAGCA	AF071172	CCDS10021.1	15q13	2012-02-23	2012-02-23		ENSG00000128731	ENSG00000128731			4868	protein-coding gene	gene with protein product		605837	"""hect domain and RLD 2"""			9949213	Standard	NM_004667		Approved	jdf2, p528, D15F37S1	uc001zbj.4	O95714	OTTHUMG00000129251	ENST00000261609.7:c.6452G>A	15.37:g.28459325C>T	ENSP00000261609:p.Arg2151His	90.0	1.0	0.0111111		104.0	5.0	0.0480769	NM_004667		Missense_Mutation	SNP	ENST00000261609.7	37	CCDS10021.1	.	.	.	.	.	.	.	.	.	.	C	18.08	3.544886	0.65198	.	.	ENSG00000128731	ENST00000261609	T	0.61392	0.11	4.75	4.75	0.60458	.	0.057517	0.64402	D	0.000004	T	0.77485	0.4137	M	0.81942	2.565	0.80722	D	1	D	0.71674	0.998	D	0.72075	0.976	T	0.81212	-0.1035	10	0.72032	D	0.01	.	17.9388	0.89021	0.0:1.0:0.0:0.0	.	2151	O95714	HERC2_HUMAN	H	2151	ENSP00000261609:R2151H	ENSP00000261609:R2151H	R	-	2	0	HERC2	26132920	1.000000	0.71417	0.415000	0.26534	0.134000	0.20937	7.305000	0.78891	2.461000	0.83175	0.484000	0.47621	CGC	.	.	none		0.637	HERC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251358.2	NM_004667	
MUC4	4585	hgsc.bcm.edu	37	3	195506693	195506693	+	Missense_Mutation	SNP	G	G	A	rs146525749	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:195506693G>A	ENST00000463781.3	-	2	12217	c.11758C>T	c.(11758-11760)Cgt>Tgt	p.R3920C	MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.R3920C|MUC4_ENST00000346145.4_Intron	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)			NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		ACAGGAAGACGGGTGGTGTCA	0.592													.|||	15	0.00299521	0.0015	0.0029	5008	,	,		10708	0.0		0.0089	False		,,,				2504	0.002				p.R3920C		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,+1,1	MUC4	1505	1	0			c.C11758T						PASS	.						28.0	27.0	27.0					3																	195506693		542	1109	1651	SO:0001583	missense	4585	exon2			GAAGACGGGTGGT	AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.11758C>T	3.37:g.195506693G>A	ENSP00000417498:p.Arg3920Cys	1.0	0.0	0		130.0	129.0	0.992308	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	11	0.005036630036630037	0	0.0	3	0.008287292817679558	0	0.0	8	0.010554089709762533	g	7.530	0.658436	0.14645	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33865	1.4;1.39	.	.	.	.	.	.	.	.	T	0.17789	0.0427	N	0.14661	0.345	0.25472	N	0.987813	D	0.60160	0.987	P	0.49799	0.622	T	0.12066	-1.0562	7	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3792	E7ESK3	.	C	3920	ENSP00000417498:R3920C;ENSP00000420243:R3920C	.	R	-	1	0	MUC4	196991472	.	.	0.011000	0.14972	0.010000	0.07245	.	.	0.064000	0.16427	0.064000	0.15345	CGT	G|0.995;A|0.005	0.005	strong		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643255	1643255	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:1643255G>A	ENST00000399682.1	-	1	113	c.69C>T	c.(67-69)ggC>ggT	p.G23G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)		p.G23G(1)		NS(1)|endometrium(9)|kidney(2)|lung(2)|pancreas(1)|prostate(3)|skin(2)	20		all_epithelial(84;0.00819)|Breast(177;0.00832)|Ovarian(85;0.0256)|Medulloblastoma(188;0.0321)|all_neural(188;0.0762)		BRCA - Breast invasive adenocarcinoma(625;0.000614)|Lung(200;0.0681)|LUSC - Lung squamous cell carcinoma(625;0.082)		cagagccacagcccccacagc	0.687																																					p.G23G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	1	Substitution - coding silent(1)	kidney(1)	c.C69T						scavenged	.						4.0	8.0	7.0					11																	1643255		646	1526	2172	SO:0001819	synonymous_variant	387267	exon1			GCCACAGCCCCCA	AB126073		11p15.5	2012-04-19			ENSG00000241598	ENSG00000241598		"""Keratin associated proteins"""	23599	protein-coding gene	gene with protein product						15144888	Standard	NM_001012709		Approved	KRTAP5.4	uc009ycy.1	Q6L8H1	OTTHUMG00000057553	ENST00000399682.1:c.69C>T	11.37:g.1643255G>A		89.0	1.0	0.011236		154.0	8.0	0.0519481	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
CUL4A	8451	hgsc.bcm.edu	37	13	113882307	113882307	+	Missense_Mutation	SNP	T	T	C	rs113697945	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr13:113882307T>C	ENST00000375440.4	+	4	470	c.386T>C	c.(385-387)gTt>gCt	p.V129A	CUL4A_ENST00000451881.1_Missense_Mutation_p.V29A|CUL4A_ENST00000375441.3_Missense_Mutation_p.V29A|CUL4A_ENST00000463426.1_3'UTR|CUL4A_ENST00000326335.4_Missense_Mutation_p.V29A	NM_001008895.1	NP_001008895.1	Q13619	CUL4A_HUMAN	cullin 4A	129					cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|G1/S transition of mitotic cell cycle (GO:0000082)|hemopoiesis (GO:0030097)|intrinsic apoptotic signaling pathway (GO:0097193)|negative regulation of cell proliferation (GO:0008285)|negative regulation of granulocyte differentiation (GO:0030853)|positive regulation of cell proliferation (GO:0008284)|positive regulation of G1/S transition of mitotic cell cycle (GO:1900087)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein ubiquitination (GO:0016567)|regulation of DNA damage checkpoint (GO:2000001)|regulation of nucleotide-excision repair (GO:2000819)|regulation of protein metabolic process (GO:0051246)|somatic stem cell maintenance (GO:0035019)|viral process (GO:0016032)	Cul4-RING E3 ubiquitin ligase complex (GO:0080008)|Cul4A-RING E3 ubiquitin ligase complex (GO:0031464)				NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(1)|large_intestine(5)|lung(5)|skin(1)	17	Lung NSC(43;0.0161)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0482)|all_epithelial(44;0.0148)|all_lung(25;0.0271)|Lung NSC(25;0.0977)|Breast(118;0.188)	all cancers(43;0.112)			CTAGATAGTGTTTTATTTTTA	0.363													T|||	10	0.00199681	0.0	0.0014	5008	,	,		20658	0.0		0.008	False		,,,				2504	0.001				p.V129A		Atlas-SNP	.											.	CUL4A	50	.	0			c.T386C						PASS	.	T	ALA/VAL,ALA/VAL	9,4397	16.8+/-37.8	0,9,2194	73.0	73.0	73.0		386,86	5.1	0.7	13	dbSNP_132	73	78,8522	45.4+/-104.0	1,76,4223	yes	missense,missense	CUL4A	NM_001008895.1,NM_003589.2	64,64	1,85,6417	CC,CT,TT		0.907,0.2043,0.6689	benign,benign	129/760,29/660	113882307	87,12919	2203	4300	6503	SO:0001583	missense	8451	exon4			ATAGTGTTTTATT	U58090	CCDS9533.1, CCDS41908.1, CCDS73604.1	13q34	2011-05-24			ENSG00000139842	ENSG00000139842			2554	protein-coding gene	gene with protein product		603137				8681378	Standard	NM_001008895		Approved		uc021rmv.1	Q13619	OTTHUMG00000017384	ENST00000375440.4:c.386T>C	13.37:g.113882307T>C	ENSP00000364589:p.Val129Ala	46.0	0.0	0		50.0	37.0	0.74	NM_001008895	A2A2W2|O75834|Q589T6|Q5TC62|Q6UP08|Q9UP17	Missense_Mutation	SNP	ENST00000375440.4	37	CCDS41908.1	8	0.003663003663003663	0	0.0	0	0.0	0	0.0	8	0.010554089709762533	T	11.40	1.626934	0.28978	0.002043	0.00907	ENSG00000139842	ENST00000375441;ENST00000451881;ENST00000326335;ENST00000375440	T;T;T;T	0.76709	-1.04;-1.04;-1.04;-1.04	5.12	5.12	0.69794	Cullin, N-terminal (1);Cullin repeat-like-containing domain (1);	0.413435	0.24245	N	0.040226	T	0.70430	0.3223	M	0.71581	2.175	0.47862	D	0.999532	B	0.09022	0.002	B	0.25506	0.061	T	0.69881	-0.5025	10	0.16420	T	0.52	-22.1362	15.2361	0.73432	0.0:0.0:0.0:1.0	.	129	Q13619	CUL4A_HUMAN	A	29;29;29;129	ENSP00000364590:V29A;ENSP00000389118:V29A;ENSP00000322132:V29A;ENSP00000364589:V129A	ENSP00000322132:V29A	V	+	2	0	CUL4A	112930308	1.000000	0.71417	0.667000	0.29798	0.042000	0.13812	7.791000	0.85805	2.058000	0.61347	0.528000	0.53228	GTT	T|0.995;C|0.005	0.005	strong		0.363	CUL4A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045888.3	NM_003589	
PLCH2	9651	hgsc.bcm.edu	37	1	2436256	2436256	+	Silent	SNP	G	G	A	rs138038983	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:2436256G>A	ENST00000419816.2	+	22	4129	c.3855G>A	c.(3853-3855)ggG>ggA	p.G1285G	PLCH2_ENST00000449969.1_3'UTR|PLCH2_ENST00000378486.3_Silent_p.G1285G|PLCH2_ENST00000378488.3_Silent_p.G1249G			O75038	PLCH2_HUMAN	phospholipase C, eta 2	1285					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|phosphatidylinositol metabolic process (GO:0046488)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|signal transducer activity (GO:0004871)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(3)|skin(1)	20	all_cancers(77;0.000161)|all_epithelial(69;5.98e-05)|all_lung(157;0.016)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;7.32e-16)|all_lung(118;1.15e-06)|Lung NSC(185;6.26e-05)|Renal(390;0.00571)|Breast(487;0.00832)|Hepatocellular(190;0.0268)|Myeloproliferative disorder(586;0.028)|Ovarian(437;0.127)|Medulloblastoma(700;0.151)|Lung SC(97;0.217)		Epithelial(90;1.44e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.78e-23)|GBM - Glioblastoma multiforme(42;2.8e-08)|Colorectal(212;4.19e-05)|COAD - Colon adenocarcinoma(227;0.000195)|Kidney(185;0.00034)|BRCA - Breast invasive adenocarcinoma(365;0.00443)|KIRC - Kidney renal clear cell carcinoma(229;0.00548)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.2)		TCCCGGGAGGGACACGGCGGG	0.662													G|||	53	0.0105831	0.0008	0.0245	5008	,	,		15355	0.0		0.0298	False		,,,				2504	0.0051				p.G1285G		Atlas-SNP	.											.	PLCH2	131	.	0			c.G3855A						PASS	.	G		21,3963		0,21,1971	13.0	16.0	15.0		3855	-0.4	0.0	1	dbSNP_134	15	235,8037		3,229,3904	no	coding-synonymous	PLCH2	NM_014638.2		3,250,5875	AA,AG,GG		2.8409,0.5271,2.0888		1285/1417	2436256	256,12000	1992	4136	6128	SO:0001819	synonymous_variant	9651	exon22			GGGAGGGACACGG	AB007919	CCDS59959.1	1p36.32	2013-01-10	2006-03-16	2006-03-16	ENSG00000149527	ENSG00000149527	3.1.4.11	"""EF-hand domain containing"""	29037	protein-coding gene	gene with protein product		612836	"""phospholipase C-like 4"""	PLCL4		15899900	Standard	XM_006711054		Approved	KIAA0450, PLCeta2, RP3-395M20.1, PLC-eta2	uc001aji.1	O75038	OTTHUMG00000000719	ENST00000419816.2:c.3855G>A	1.37:g.2436256G>A		78.0	0.0	0		110.0	6.0	0.0545455	NM_014638	A2VCM3|B9DI80|Q3LUA8|Q86XJ2|Q86XU1|Q86YU7|Q8TEH5|Q8WUS6	Silent	SNP	ENST00000419816.2	37		30	0.013736263736263736	2	0.0040650406504065045	8	0.022099447513812154	0	0.0	20	0.026385224274406333	G	0.060	-1.225743	0.01530	0.005271	0.028409	ENSG00000149527	ENST00000419816	.	.	.	4.32	-0.385	0.12470	.	2.338380	0.02026	N	0.048201	T	0.09468	0.0233	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.23904	-1.0175	6	0.42905	T	0.14	.	1.6475	0.02764	0.1628:0.1426:0.4036:0.291	.	.	.	.	E	580	.	ENSP00000389803:G580E	G	+	2	0	PLCH2	2426116	0.000000	0.05858	0.001000	0.08648	0.030000	0.12068	-0.414000	0.07114	0.781000	0.33589	0.491000	0.48974	GGA	G|0.983;A|0.017	0.017	strong		0.662	PLCH2-009	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000467514.1	NM_014638	
RRP12	23223	hgsc.bcm.edu	37	10	99126513	99126513	+	Silent	SNP	C	C	T	rs45527941	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:99126513C>T	ENST00000370992.4	-	27	3312	c.3201G>A	c.(3199-3201)caG>caA	p.Q1067Q	RRP12_ENST00000414986.1_Silent_p.Q1006Q|RRP12_ENST00000536831.1_Silent_p.Q785Q|RRP12_ENST00000315563.6_Silent_p.Q967Q|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		38.0	0.0	0		62.0	36.0	0.580645	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	
NOTCH2	4853	hgsc.bcm.edu	37	1	120458161	120458161	+	Nonsense_Mutation	SNP	G	G	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:120458161G>C	ENST00000256646.2	-	34	7403	c.7184C>G	c.(7183-7185)tCa>tGa	p.S2395*		NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	2395					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		AGCAGCATTTGAGGAAGCATA	0.567			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																												p.S2395X		Atlas-SNP	.		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	.	NOTCH2	348	.	0			c.C7184G						PASS	.						123.0	108.0	113.0					1																	120458161		2203	4300	6503	SO:0001587	stop_gained	4853	exon34	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	GCATTTGAGGAAG	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.7184C>G	1.37:g.120458161G>C	ENSP00000256646:p.Ser2395*	104.0	0.0	0		125.0	51.0	0.408	NM_024408	Q5T3X7|Q99734|Q9H240	Nonsense_Mutation	SNP	ENST00000256646.2	37	CCDS908.1	.	.	.	.	.	.	.	.	.	.	G	48	14.309534	0.99789	.	.	ENSG00000134250	ENST00000256646	.	.	.	5.35	5.35	0.76521	.	0.000000	0.30879	U	0.008688	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	16.2129	0.82178	0.0:0.0:1.0:0.0	.	.	.	.	X	2395	.	ENSP00000256646:S2395X	S	-	2	0	NOTCH2	120259684	1.000000	0.71417	0.953000	0.39169	0.975000	0.68041	9.145000	0.94634	2.506000	0.84524	0.591000	0.81541	TCA	.	.	none		0.567	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033679.1	NM_024408	
CIB2	10518	hgsc.bcm.edu	37	15	78398139	78398139	+	Missense_Mutation	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:78398139C>T	ENST00000258930.3	-	5	812	c.484G>A	c.(484-486)Ggc>Agc	p.G162S	CIB2_ENST00000539011.1_Missense_Mutation_p.G119S|CIB2_ENST00000557846.1_Missense_Mutation_p.G113S|CIB2_ENST00000560618.1_Missense_Mutation_p.G119S	NM_006383.2	NP_006374.1	O75838	CIB2_HUMAN	calcium and integrin binding family member 2	162	EF-hand 3. {ECO:0000255|PROSITE- ProRule:PRU00448}.				calcium ion homeostasis (GO:0055074)|photoreceptor cell maintenance (GO:0045494)	blood microparticle (GO:0072562)|muscle tendon junction (GO:0005927)|neuromuscular junction (GO:0031594)|photoreceptor inner segment (GO:0001917)|sarcolemma (GO:0042383)	calcium ion binding (GO:0005509)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(2)|prostate(1)	11						CCCAGCTTGCCGTCACCGTCC	0.617																																					p.G162S		Atlas-SNP	.											.	CIB2	24	.	0			c.G484A						PASS	.						183.0	150.0	161.0					15																	78398139		2196	4293	6489	SO:0001583	missense	10518	exon5			GCTTGCCGTCACC	BC047381	CCDS10296.1, CCDS61722.1, CCDS61723.1	15q24	2013-01-10			ENSG00000136425	ENSG00000136425		"""EF-hand domain containing"""	24579	protein-coding gene	gene with protein product		605564	"""deafness, autosomal recessive 48"", ""Usher syndrome 1J (autosomal recessive)"""	DFNB48, USH1J		9931475, 23023331	Standard	NM_006383		Approved	KIP2	uc002bdb.2	O75838	OTTHUMG00000143731	ENST00000258930.3:c.484G>A	15.37:g.78398139C>T	ENSP00000258930:p.Gly162Ser	66.0	0.0	0		63.0	27.0	0.428571	NM_006383	B4DDF0|H0YM71|Q05BT6	Missense_Mutation	SNP	ENST00000258930.3	37	CCDS10296.1	.	.	.	.	.	.	.	.	.	.	C	17.71	3.457318	0.63401	.	.	ENSG00000136425	ENST00000258930;ENST00000539011	D;D	0.83591	-1.74;-1.74	5.59	5.59	0.84812	EF-hand-like domain (1);	0.239373	0.43110	D	0.000604	D	0.90556	0.7040	M	0.90977	3.165	0.53688	D	0.999973	D;P	0.65815	0.995;0.657	P;B	0.51516	0.672;0.147	D	0.92297	0.5846	10	0.62326	D	0.03	-22.6145	18.5768	0.91158	0.0:1.0:0.0:0.0	.	162;162	B4DDF0;O75838	.;CIB2_HUMAN	S	162;119	ENSP00000258930:G162S;ENSP00000442459:G119S	ENSP00000258930:G162S	G	-	1	0	CIB2	76185194	0.992000	0.36948	0.956000	0.39512	0.792000	0.44763	2.522000	0.45572	2.641000	0.89580	0.591000	0.81541	GGC	.	.	none		0.617	CIB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000289798.1	NM_006383	
TAF3	83860	hgsc.bcm.edu	37	10	8007260	8007260	+	Missense_Mutation	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:8007260A>C	ENST00000344293.5	+	3	1993	c.1787A>C	c.(1786-1788)gAa>gCa	p.E596A		NM_031923.3	NP_114129.1	Q5VWG9	TAF3_HUMAN	TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140kDa	596	Lys-rich.				maintenance of protein location in nucleus (GO:0051457)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	zinc ion binding (GO:0008270)			NS(2)|breast(4)|endometrium(2)|kidney(1)|large_intestine(6)|lung(16)|ovary(3)|prostate(4)|skin(2)	40						AAAGAATTTGAAGATGTTGAT	0.373																																					p.E596A		Atlas-SNP	.											.	TAF3	93	.	0			c.A1787C						PASS	.						78.0	77.0	77.0					10																	8007260		1819	4076	5895	SO:0001583	missense	83860	exon3			AATTTGAAGATGT	AJ292190	CCDS41487.1	10p15.1	2013-01-28	2002-08-29		ENSG00000165632	ENSG00000165632		"""Zinc fingers, PHD-type"""	17303	protein-coding gene	gene with protein product		606576	"""TAF3 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 140 kD"""			11438666, 18549481	Standard	NM_031923		Approved	TAF140, TAFII140	uc010qbd.3	Q5VWG9	OTTHUMG00000017643	ENST00000344293.5:c.1787A>C	10.37:g.8007260A>C	ENSP00000340271:p.Glu596Ala	84.0	0.0	0		74.0	41.0	0.554054	NM_031923	Q05DA0|Q6GMS5|Q6P6B5|Q86VY6|Q9BQS9|Q9UFI8	Missense_Mutation	SNP	ENST00000344293.5	37	CCDS41487.1	.	.	.	.	.	.	.	.	.	.	A	7.734	0.699927	0.15106	.	.	ENSG00000165632	ENST00000344293	T	0.20332	2.08	5.82	5.82	0.92795	.	0.540850	0.18799	N	0.130845	T	0.29158	0.0725	M	0.73962	2.25	0.38863	D	0.956539	B	0.17038	0.02	B	0.15870	0.014	T	0.05903	-1.0857	10	0.39692	T	0.17	-14.8166	15.8582	0.79000	1.0:0.0:0.0:0.0	.	596	Q5VWG9	TAF3_HUMAN	A	596	ENSP00000340271:E596A	ENSP00000340271:E596A	E	+	2	0	TAF3	8047266	0.999000	0.42202	0.941000	0.38009	0.097000	0.18754	3.650000	0.54424	2.232000	0.73038	0.528000	0.53228	GAA	.	.	none		0.373	TAF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046725.1	NM_031923	
OR5B21	219968	hgsc.bcm.edu	37	11	58275303	58275303	+	Silent	SNP	G	G	A	rs146345059	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr11:58275303G>A	ENST00000360374.2	-	1	275	c.276C>T	c.(274-276)taC>taT	p.Y92Y		NM_001005218.1	NP_001005218.1	A6NL26	OR5BL_HUMAN	olfactory receptor, family 5, subfamily B, member 21	92						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(16)|ovary(3)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29	Esophageal squamous(5;0.0027)	Breast(21;0.0778)				CACATCCATCGTAGGAGATGG	0.532													G|||	4	0.000798722	0.0	0.0058	5008	,	,		21630	0.0		0.0	False		,,,				2504	0.0				p.Y92Y		Atlas-SNP	.											OR5B21,rectum,NS,0,1	OR5B21	59	1	0			c.C276T						scavenged	.	G		0,4402		0,0,2201	122.0	96.0	105.0		276	2.2	0.5	11	dbSNP_134	105	8,8582	6.4+/-24.3	0,8,4287	no	coding-synonymous	OR5B21	NM_001005218.1		0,8,6488	AA,AG,GG		0.0931,0.0,0.0616		92/310	58275303	8,12984	2201	4295	6496	SO:0001819	synonymous_variant	219968	exon1			TCCATCGTAGGAG		CCDS31552.1	11q12.1	2012-08-09			ENSG00000198283	ENSG00000198283		"""GPCR / Class A : Olfactory receptors"""	19616	protein-coding gene	gene with protein product							Standard	NM_001005218		Approved		uc010rki.2	A6NL26	OTTHUMG00000167519	ENST00000360374.2:c.276C>T	11.37:g.58275303G>A		134.0	1.0	0.00746269		118.0	54.0	0.457627	NM_001005218		Silent	SNP	ENST00000360374.2	37	CCDS31552.1																																																																																			G|0.999;A|0.001	0.001	strong		0.532	OR5B21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394891.1	NM_001005218	
SERTAD4	56256	hgsc.bcm.edu	37	1	210415626	210415626	+	Missense_Mutation	SNP	A	A	C	rs559261349		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:210415626A>C	ENST00000367012.3	+	4	1245	c.1015A>C	c.(1015-1017)Aag>Cag	p.K339Q		NM_019605.3	NP_062551.1	Q9NUC0	SRTD4_HUMAN	SERTA domain containing 4	339						nucleus (GO:0005634)				endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0237)|all cancers(67;0.127)		CTTACGGAAAAAGGAGGCTTC	0.388													A|||	1	0.000199681	0.0	0.0	5008	,	,		20269	0.0		0.001	False		,,,				2504	0.0				p.K339Q		Atlas-SNP	.											.	SERTAD4	53	.	0			c.A1015C						PASS	.						54.0	55.0	54.0					1																	210415626		2202	4300	6502	SO:0001583	missense	56256	exon4			CGGAAAAAGGAGG	BC012083	CCDS1494.1	1q32.1-q41	2008-02-05			ENSG00000082497	ENSG00000082497			25236	protein-coding gene	gene with protein product						12477932	Standard	NM_019605		Approved	DJ667H12.2	uc001hhy.3	Q9NUC0	OTTHUMG00000036391	ENST00000367012.3:c.1015A>C	1.37:g.210415626A>C	ENSP00000355979:p.Lys339Gln	66.0	0.0	0		90.0	34.0	0.377778	NM_019605	B2RD32	Missense_Mutation	SNP	ENST00000367012.3	37	CCDS1494.1	.	.	.	.	.	.	.	.	.	.	A	17.59	3.427383	0.62733	.	.	ENSG00000082497	ENST00000367012	.	.	.	5.84	5.84	0.93424	.	0.000000	0.64402	D	0.000001	T	0.56077	0.1961	L	0.29908	0.895	0.34642	D	0.720729	D	0.60160	0.987	P	0.54544	0.755	T	0.69094	-0.5236	9	0.72032	D	0.01	-2.7444	16.2108	0.82158	1.0:0.0:0.0:0.0	.	339	Q9NUC0	SRTD4_HUMAN	Q	339	.	ENSP00000355979:K339Q	K	+	1	0	SERTAD4	208482249	1.000000	0.71417	1.000000	0.80357	0.952000	0.60782	6.336000	0.72954	2.232000	0.73038	0.533000	0.62120	AAG	.	.	none		0.388	SERTAD4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088577.1	NM_019605	
BRINP1	1620	hgsc.bcm.edu	37	9	121929932	121929932	+	Silent	SNP	C	C	T	rs147029533	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:121929932C>T	ENST00000265922.3	-	8	2177	c.1716G>A	c.(1714-1716)tcG>tcA	p.S572S	BRINP1_ENST00000482797.1_Intron	NM_014618.2	NP_055433.2	O60477	BRNP1_HUMAN	bone morphogenetic protein/retinoic acid inducible neural-specific 1	572					cell cycle arrest (GO:0007050)|cell death (GO:0008219)|cellular response to retinoic acid (GO:0071300)|negative regulation of cell cycle (GO:0045786)|negative regulation of mitotic cell cycle (GO:0045930)|positive regulation of neuron differentiation (GO:0045666)	cytoplasm (GO:0005737)											TCCAGCCCTCCGAATGGCTCC	0.557													C|||	10	0.00199681	0.0	0.0043	5008	,	,		19432	0.0		0.007	False		,,,				2504	0.0				p.S572S		Atlas-SNP	.											DBC1,NS,carcinoma,-2,1	DBC1	194	1	0			c.G1716A						PASS	.	C		5,4401		0,5,2198	43.0	44.0	44.0		1716	-11.3	0.3	9	dbSNP_134	44	70,8524		1,68,4228	no	coding-synonymous	DBC1	NM_014618.2		1,73,6426	TT,TC,CC		0.8145,0.1135,0.5769		572/762	121929932	75,12925	2203	4297	6500	SO:0001819	synonymous_variant	1620	exon8			GCCCTCCGAATGG	AF027734	CCDS6822.1	9q32-q33	2013-08-06	2013-08-06	2013-07-31	ENSG00000078725	ENSG00000078725			2687	protein-coding gene	gene with protein product		602865	"""deleted in bladder cancer chromosome region candidate 1"", ""deleted in bladder cancer 1"""	DBCCR1, DBC1		9175739, 10444335, 15193422	Standard	NM_014618		Approved	FAM5A	uc004bkc.2	O60477	OTTHUMG00000021020	ENST00000265922.3:c.1716G>A	9.37:g.121929932C>T		87.0	0.0	0		86.0	41.0	0.476744	NM_014618	Q6IPV6|Q6P1A0|Q8WU22	Silent	SNP	ENST00000265922.3	37	CCDS6822.1																																																																																			C|0.994;T|0.006	0.006	strong		0.557	BRINP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055440.2	NM_014618	
C16orf70	80262	hgsc.bcm.edu	37	16	67166731	67166731	+	Missense_Mutation	SNP	G	G	A	rs34017457	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr16:67166731G>A	ENST00000219139.3	+	6	555	c.367G>A	c.(367-369)Gct>Act	p.A123T	C16orf70_ENST00000569683.1_3'UTR|C16orf70_ENST00000569600.1_Missense_Mutation_p.A123T	NM_025187.3	NP_079463.2	Q9BSU1	CP070_HUMAN	chromosome 16 open reading frame 70	123										cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|skin(1)	17		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0017)|Epithelial(162;0.00655)|all cancers(182;0.0579)		GTACAACTCCGCTGAGCAGCT	0.483													G|||	14	0.00279553	0.0	0.0014	5008	,	,		23042	0.0		0.0119	False		,,,				2504	0.001				p.A123T		Atlas-SNP	.											.	C16orf70	38	.	0			c.G367A						PASS	.	G	THR/ALA	12,4388	17.9+/-39.9	0,12,2188	129.0	119.0	122.0		367	4.1	1.0	16	dbSNP_126	122	81,8519	47.6+/-106.9	1,79,4220	yes	missense	C16orf70	NM_025187.3	58	1,91,6408	AA,AG,GG		0.9419,0.2727,0.7154	possibly-damaging	123/423	67166731	93,12907	2200	4300	6500	SO:0001583	missense	80262	exon6			AACTCCGCTGAGC	AK022138	CCDS10828.1	16q22.1	2011-01-25	2006-04-12	2006-04-12	ENSG00000125149	ENSG00000125149			29564	protein-coding gene	gene with protein product			"""chromosome 16 open reading frame 6"""	C16orf6, LIN10		12477932	Standard	NM_025187		Approved	lin-10, FLJ12076	uc002erd.3	Q9BSU1	OTTHUMG00000137510	ENST00000219139.3:c.367G>A	16.37:g.67166731G>A	ENSP00000219139:p.Ala123Thr	190.0	0.0	0		134.0	60.0	0.447761	NM_025187	Q9HA86	Missense_Mutation	SNP	ENST00000219139.3	37	CCDS10828.1	9	0.004120879120879121	0	0.0	1	0.0027624309392265192	0	0.0	8	0.010554089709762533	G	15.47	2.842233	0.51057	0.002727	0.009419	ENSG00000125149	ENST00000219139	.	.	.	6.05	4.08	0.47627	.	0.051952	0.85682	N	0.000000	T	0.42877	0.1222	L	0.52759	1.655	0.58432	D	0.999998	B;D	0.56521	0.295;0.976	B;P	0.49451	0.089;0.611	T	0.35201	-0.9798	9	0.17832	T	0.49	-11.1355	11.3429	0.49543	0.1492:0.0:0.8508:0.0	rs34017457	198;123	Q9BSU1-2;Q9BSU1	.;CP070_HUMAN	T	123	.	ENSP00000219139:A123T	A	+	1	0	C16orf70	65724232	1.000000	0.71417	0.963000	0.40424	0.990000	0.78478	6.526000	0.73799	0.871000	0.35750	-0.142000	0.14014	GCT	G|0.994;A|0.006	0.006	strong		0.483	C16orf70-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268829.2	NM_025187	
MRPL4	51073	hgsc.bcm.edu	37	19	10370310	10370310	+	Missense_Mutation	SNP	A	A	G	rs77884668	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:10370310A>G	ENST00000253099.6	+	9	1044	c.757A>G	c.(757-759)Atg>Gtg	p.M253V	MRPL4_ENST00000393733.2_3'UTR|CTD-2369P2.4_ENST00000587088.1_RNA|CTD-2369P2.5_ENST00000592893.1_RNA|MRPL4_ENST00000307422.5_Missense_Mutation_p.M253V	NM_015956.2|NM_146388.1	NP_057040.2|NP_666500.1	Q9BYD3	RM04_HUMAN	mitochondrial ribosomal protein L4	253					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	poly(A) RNA binding (GO:0044822)|structural constituent of ribosome (GO:0003735)			breast(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	11		Renal(1328;0.0112)	OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;1.99e-06)|all cancers(31;4.81e-06)	Lung(535;0.00705)		TGTGCACAGCATGCTCAAGCA	0.677													A|||	73	0.0145767	0.0537	0.0029	5008	,	,		6135	0.0		0.0	False		,,,				2504	0.0				p.M253V		Atlas-SNP	.											.	MRPL4	22	.	0			c.A757G						PASS	.	A	VAL/MET,VAL/MET,	184,4222	109.5+/-147.8	2,180,2021	38.0	29.0	32.0		757,757,	2.9	1.0	19	dbSNP_131	32	1,8599	1.2+/-3.3	0,1,4299	yes	missense,missense,utr-3	MRPL4	NM_015956.2,NM_146387.1,NM_146388.1	21,21,	2,181,6320	GG,GA,AA		0.0116,4.1761,1.4224	possibly-damaging,possibly-damaging,	253/312,253/312,	10370310	185,12821	2203	4300	6503	SO:0001583	missense	51073	exon10			CACAGCATGCTCA	AB049635	CCDS12230.1, CCDS42499.1	19p13.2	2012-11-14			ENSG00000105364	ENSG00000105364		"""Mitochondrial ribosomal proteins / large subunits"""	14276	protein-coding gene	gene with protein product		611823					Standard	NM_015956		Approved	CGI-28	uc002mnn.3	Q9BYD3	OTTHUMG00000180400	ENST00000253099.6:c.757A>G	19.37:g.10370310A>G	ENSP00000253099:p.Met253Val	71.0	0.0	0		74.0	40.0	0.540541	NM_146387	A6NNV7|Q9BW07|Q9H4N2|Q9Y317	Missense_Mutation	SNP	ENST00000253099.6	37	CCDS12230.1	31	0.014194139194139194	29	0.05894308943089431	2	0.0055248618784530384	0	0.0	0	0.0	a	14.63	2.592614	0.46214	0.041761	1.16E-4	ENSG00000105364	ENST00000253099;ENST00000307422	.	.	.	5.1	2.89	0.33648	Ribosomal protein L4 domain (2);	0.224207	0.50627	D	0.000113	T	0.12860	0.0312	L	0.32530	0.975	0.39810	D	0.972685	P	0.37955	0.612	P	0.51055	0.657	T	0.20338	-1.0278	9	0.44086	T	0.13	-21.9678	10.159	0.42840	0.678:0.322:0.0:0.0	.	253	Q9BYD3	RM04_HUMAN	V	253	.	ENSP00000253099:M253V	M	+	1	0	MRPL4	10231310	1.000000	0.71417	1.000000	0.80357	0.649000	0.38597	1.695000	0.37763	0.232000	0.21100	0.449000	0.29647	ATG	A|0.984;G|0.016	0.016	strong		0.677	MRPL4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451197.1		
CAD	790	hgsc.bcm.edu	37	2	27447310	27447310	+	Silent	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:27447310G>A	ENST00000403525.1	+	9	1350	c.1206G>A	c.(1204-1206)ggG>ggA	p.G402G	CAD_ENST00000264705.4_Silent_p.G402G			O76075	DFFB_HUMAN	carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase	0					apoptotic chromosome condensation (GO:0030263)|apoptotic DNA fragmentation (GO:0006309)|apoptotic process (GO:0006915)|brain development (GO:0007420)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cytosol (GO:0005829)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)			NS(1)|breast(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(40)|ovary(6)|pancreas(2)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	92	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGGCTCAGGGGGCCTCTCCA	0.597																																					p.G402G		Atlas-SNP	.											CAD,NS,carcinoma,+2,1	CAD	199	1	0			c.G1206A						PASS	.						67.0	72.0	70.0					2																	27447310		2203	4300	6503	SO:0001819	synonymous_variant	790	exon9			CTCAGGGGGCCTC	D78586	CCDS1742.1	2p22-p21	2012-10-02			ENSG00000084774	ENSG00000084774	2.1.3.2, 3.5.2.-		1424	protein-coding gene	gene with protein product		114010				8619816, 2565865	Standard	NM_004341		Approved		uc002rji.3	P27708	OTTHUMG00000097070	ENST00000403525.1:c.1206G>A	2.37:g.27447310G>A		88.0	0.0	0		90.0	40.0	0.444444	NM_004341	O60521|Q5SR22|Q9BYI4|Q9BYI5|Q9BYI6	Silent	SNP	ENST00000403525.1	37																																																																																				.	.	none		0.597	CAD-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000324970.1		
AGPS	8540	hgsc.bcm.edu	37	2	178364363	178364363	+	Silent	SNP	A	A	C	rs148418568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:178364363A>C	ENST00000264167.4	+	14	1526	c.1380A>C	c.(1378-1380)ccA>ccC	p.P460P	AGPS_ENST00000409888.1_Intron	NM_003659.3	NP_003650.1	O00116	ADAS_HUMAN	alkylglycerone phosphate synthase	460					cellular lipid metabolic process (GO:0044255)|ether lipid biosynthetic process (GO:0008611)|lipid biosynthetic process (GO:0008610)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	alkylglycerone-phosphate synthase activity (GO:0008609)|FAD binding (GO:0071949)|UDP-N-acetylmuramate dehydrogenase activity (GO:0008762)			breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(8)|lung(12)|ovary(2)|skin(1)	32			OV - Ovarian serous cystadenocarcinoma(117;0.0018)|Epithelial(96;0.00919)|all cancers(119;0.0358)			GATTTGACCCAAATCAGCTAA	0.308													A|||	2	0.000399361	0.0	0.0029	5008	,	,		14276	0.0		0.0	False		,,,				2504	0.0				p.P460P		Atlas-SNP	.											.	AGPS	56	.	0			c.A1380C						PASS	.	A		0,4406		0,0,2203	94.0	90.0	91.0		1380	1.5	1.0	2	dbSNP_134	91	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	AGPS	NM_003659.3		0,1,6502	CC,CA,AA		0.0116,0.0,0.0077		460/659	178364363	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	8540	exon14			TGACCCAAATCAG	Y09443	CCDS2275.1	2q	2008-02-05			ENSG00000018510	ENSG00000018510	2.5.1.26		327	protein-coding gene	gene with protein product		603051				9187299, 9553082	Standard	NM_003659		Approved	ADHAPS, ADAS, ALDHPSY, ADPS, ADAP-S	uc002ull.2	O00116	OTTHUMG00000132530	ENST00000264167.4:c.1380A>C	2.37:g.178364363A>C		32.0	0.0	0		23.0	6.0	0.26087	NM_003659	A5D8U9|Q2TU35	Silent	SNP	ENST00000264167.4	37	CCDS2275.1																																																																																			A|1.000;C|0.000	0.000	strong		0.308	AGPS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255730.2		
CFAP46	54777	hgsc.bcm.edu	37	10	134682833	134682833	+	Missense_Mutation	SNP	C	C	T	rs149742494	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134682833C>T	ENST00000368586.5	-	33	4655	c.4555G>A	c.(4555-4557)Gcg>Acg	p.A1519T		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TCATGGCGCGCGGCTGCTTCT	0.677													C|||	52	0.0103834	0.0045	0.0072	5008	,	,		15122	0.002		0.0129	False		,,,				2504	0.0266				p.A1519T		Atlas-SNP	.											.	TTC40	100	.	0			c.G4555A						PASS	.																																			SO:0001583	missense	54777	exon33			GGCGCGCGGCTGC																												ENST00000368586.5:c.4555G>A	10.37:g.134682833C>T	ENSP00000357575:p.Ala1519Thr	34.0	0.0	0		57.0	34.0	0.596491	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	12	0.005494505494505495	2	0.0040650406504065045	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	10.60	1.395276	0.25205	.	.	ENSG00000171811	ENST00000368586	T	0.09817	2.94	4.81	-5.4	0.02656	.	.	.	.	.	T	0.03095	0.0091	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.43228	-0.9404	6	0.15952	T	0.53	.	5.1632	0.15071	0.3408:0.1599:0.0:0.4993	.	.	.	.	T	1519	ENSP00000357575:A1519T	ENSP00000357575:A1519T	A	-	1	0	C10orf93	134532823	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.298000	0.01140	-1.398000	0.02066	-0.218000	0.12543	GCG	C|0.994;T|0.006	0.006	strong		0.677	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
SAMD9	54809	hgsc.bcm.edu	37	7	92730687	92730687	+	Missense_Mutation	SNP	C	C	T	rs148724199	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:92730687C>T	ENST00000379958.2	-	3	4993	c.4724G>A	c.(4723-4725)gGa>gAa	p.G1575E		NM_001193307.1|NM_017654.3	NP_001180236.1|NP_060124.2	Q5K651	SAMD9_HUMAN	sterile alpha motif domain containing 9	1575						cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)				NS(1)|breast(4)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(20)|lung(32)|ovary(4)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(2)	88	all_cancers(62;5.71e-11)|all_epithelial(64;3.25e-10)|Breast(17;0.000675)|Lung NSC(181;0.0969)|all_lung(186;0.125)		STAD - Stomach adenocarcinoma(171;0.000302)			AATGGAAAATCCCAGGTAAAA	0.368																																					p.G1575E		Atlas-SNP	.											.	SAMD9	239	.	0			c.G4724A						PASS	.	C	GLU/GLY,GLU/GLY	1,4405	2.1+/-5.4	0,1,2202	126.0	133.0	131.0		4724,4724	4.4	1.0	7	dbSNP_134	131	7,8591	5.7+/-21.5	0,7,4292	yes	missense,missense	SAMD9	NM_001193307.1,NM_017654.3	98,98	0,8,6494	TT,TC,CC		0.0814,0.0227,0.0615	probably-damaging,probably-damaging	1575/1590,1575/1590	92730687	8,12996	2203	4299	6502	SO:0001583	missense	54809	exon2			GAAAATCCCAGGT	AB095925	CCDS34680.1	7q21.2	2013-01-10	2004-07-15	2004-07-16	ENSG00000205413	ENSG00000205413		"""Sterile alpha motif (SAM) domain containing"""	1348	protein-coding gene	gene with protein product		610456	"""chromosome 7 open reading frame 5"""	C7orf5			Standard	NM_017654		Approved	KIAA2004, FLJ20073	uc003umg.3	Q5K651	OTTHUMG00000155809	ENST00000379958.2:c.4724G>A	7.37:g.92730687C>T	ENSP00000369292:p.Gly1575Glu	66.0	0.0	0		64.0	28.0	0.4375	NM_001193307	A2RU68|Q5K649|Q6P080|Q75N21|Q8IVG6|Q9NXS8	Missense_Mutation	SNP	ENST00000379958.2	37	CCDS34680.1	.	.	.	.	.	.	.	.	.	.	C	21.2	4.106178	0.77096	2.27E-4	8.14E-4	ENSG00000205413	ENST00000379958	T	0.77750	-1.12	4.44	4.44	0.53790	.	0.000000	0.64402	U	0.000003	D	0.86176	0.5870	M	0.62723	1.935	0.51482	D	0.999924	D	0.89917	1.0	D	0.91635	0.999	D	0.87750	0.2591	10	0.87932	D	0	.	16.1321	0.81446	0.0:1.0:0.0:0.0	.	1575	Q5K651	SAMD9_HUMAN	E	1575	ENSP00000369292:G1575E	ENSP00000369292:G1575E	G	-	2	0	SAMD9	92568623	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.170000	0.77587	2.478000	0.83669	0.609000	0.83330	GGA	C|0.999;T|0.001	0.001	strong		0.368	SAMD9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341761.1	NM_017654	
TRMU	55687	hgsc.bcm.edu	37	22	46733831	46733831	+	Missense_Mutation	SNP	G	G	A	rs55952751	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr22:46733831G>A	ENST00000290846.4	+	2	578	c.238G>A	c.(238-240)Gat>Aat	p.D80N	TRMU_ENST00000424260.2_Missense_Mutation_p.D45N|TRMU_ENST00000381019.3_Missense_Mutation_p.D80N	NM_018006.4	NP_060476.2	O75648	MTU1_HUMAN	tRNA 5-methylaminomethyl-2-thiouridylate methyltransferase	80					tRNA processing (GO:0008033)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)|sulfurtransferase activity (GO:0016783)|tRNA binding (GO:0000049)			NS(2)|cervix(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(2)|ovary(1)	10		Ovarian(80;0.00965)|Breast(42;0.0194)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00449)|LUAD - Lung adenocarcinoma(64;0.248)		GTATTGGAATGATGTGTTCAG	0.502													G|||	5	0.000998403	0.0	0.0	5008	,	,		23073	0.0		0.005	False		,,,				2504	0.0				p.D80N		Atlas-SNP	.											.	TRMU	23	.	0			c.G238A						PASS	.	G	ASN/ASP	0,4406	2.1+/-5.4	0,0,2203	188.0	159.0	169.0		238	2.5	0.1	22	dbSNP_129	169	9,8591	7.1+/-27.0	0,9,4291	yes	missense	TRMU	NM_018006.4	23	0,9,6494	AA,AG,GG		0.1047,0.0,0.0692	possibly-damaging	80/422	46733831	9,12997	2203	4300	6503	SO:0001583	missense	55687	exon2			TGGAATGATGTGT	AY062123	CCDS14075.1, CCDS63510.1	22q13	2005-08-11	2005-08-11	2005-08-11	ENSG00000100416	ENSG00000100416	2.1.1.61		25481	protein-coding gene	gene with protein product		610230	"""tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase """	TRMT		14746906	Standard	XM_005261678		Approved	FLJ10140, MTO2	uc003bhp.3	O75648	OTTHUMG00000150424	ENST00000290846.4:c.238G>A	22.37:g.46733831G>A	ENSP00000290846:p.Asp80Asn	124.0	0.0	0		92.0	32.0	0.347826	NM_018006	A8K3U7|Q05C99|Q5W9C8|Q66K31|Q6ICC3|Q9NWC1	Missense_Mutation	SNP	ENST00000290846.4	37	CCDS14075.1	4	0.0018315018315018315	0	0.0	0	0.0	0	0.0	4	0.005277044854881266	G	9.359	1.067422	0.20067	0.0	0.001047	ENSG00000100416	ENST00000290846;ENST00000381019;ENST00000424260	T;T;T	0.72282	-0.64;-0.64;-0.64	4.8	2.45	0.29901	Rossmann-like alpha/beta/alpha sandwich fold (1);	0.550552	0.19343	N	0.116585	T	0.36276	0.0961	N	0.12527	0.23	0.33732	D	0.618343	P;B;B	0.39920	0.695;0.435;0.005	B;B;B	0.34452	0.183;0.085;0.019	T	0.55366	-0.8152	10	0.02654	T	1	-12.8828	14.316	0.66452	0.0:0.2562:0.7438:0.0	rs55952751	80;80;80	B4DHM1;O75648-2;O75648	.;.;MTU1_HUMAN	N	80;80;45	ENSP00000290846:D80N;ENSP00000370407:D80N;ENSP00000406038:D45N	ENSP00000290846:D80N	D	+	1	0	TRMU	45112495	1.000000	0.71417	0.071000	0.20095	0.176000	0.22953	3.992000	0.56980	2.197000	0.70478	0.557000	0.71058	GAT	G|0.999;A|0.001	0.001	strong		0.502	TRMU-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318042.2	NM_018006	
KCTD2	23510	hgsc.bcm.edu	37	17	73058249	73058249	+	Missense_Mutation	SNP	A	A	G	rs61750318	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr17:73058249A>G	ENST00000322444.6	+	5	677	c.671A>G	c.(670-672)aAt>aGt	p.N224S	KCTD2_ENST00000581589.1_Missense_Mutation_p.N25S	NM_015353.1	NP_056168.1	Q14681	KCTD2_HUMAN	potassium channel tetramerization domain containing 2	224					protein homooligomerization (GO:0051260)		protein complex binding (GO:0032403)			kidney(1)|lung(2)	3	all_lung(278;0.226)					AACTACGGCAATGAGGATCAG	0.438													A|||	4	0.000798722	0.0	0.0014	5008	,	,		20398	0.001		0.002	False		,,,				2504	0.0				p.N224S		Atlas-SNP	.											.	KCTD2	15	.	0			c.A671G						PASS	.	A	SER/ASN	1,4405	2.1+/-5.4	0,1,2202	147.0	130.0	135.0		671	4.5	1.0	17	dbSNP_129	135	3,8597	3.0+/-9.4	0,3,4297	yes	missense	KCTD2	NM_015353.1	46	0,4,6499	GG,GA,AA		0.0349,0.0227,0.0308	benign	224/264	73058249	4,13002	2203	4300	6503	SO:0001583	missense	23510	exon5			ACGGCAATGAGGA	BC033329	CCDS32728.1	17q25.2	2013-06-20	2013-06-20			ENSG00000180901			21294	protein-coding gene	gene with protein product		613422	"""potassium channel tetramerisation domain containing 2"""			12620391	Standard	XR_248405		Approved	KIAA0176	uc002jmp.3	Q14681		ENST00000322444.6:c.671A>G	17.37:g.73058249A>G	ENSP00000312814:p.Asn224Ser	195.0	0.0	0		239.0	95.0	0.39749	NM_015353		Missense_Mutation	SNP	ENST00000322444.6	37	CCDS32728.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	A	12.24	1.879309	0.33162	2.27E-4	3.49E-4	ENSG00000180901	ENST00000322444;ENST00000375286	T	0.75821	-0.97	5.55	4.48	0.54585	.	0.045672	0.85682	D	0.000000	T	0.55130	0.1901	N	0.16743	0.435	0.52501	D	0.999952	B	0.10296	0.003	B	0.06405	0.002	T	0.50311	-0.8843	10	0.14656	T	0.56	-8.6415	10.8859	0.46965	0.9267:0.0:0.0733:0.0	rs61750318	224	Q14681	KCTD2_HUMAN	S	224;206	ENSP00000312814:N224S	ENSP00000312814:N224S	N	+	2	0	KCTD2	70569844	1.000000	0.71417	0.994000	0.49952	0.986000	0.74619	6.366000	0.73095	2.110000	0.64415	0.460000	0.39030	AAT	A|0.999;G|0.001	0.001	strong		0.438	KCTD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445538.1		
SLC12A8	84561	hgsc.bcm.edu	37	3	124829057	124829057	+	Silent	SNP	A	A	G	rs11714448	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:124829057A>G	ENST00000393469.4	-	8	1084	c.1035T>C	c.(1033-1035)ccT>ccC	p.P345P	SLC12A8_ENST00000465475.1_5'UTR|SLC12A8_ENST00000430155.2_Silent_p.P146P|SLC12A8_ENST00000423114.2_Silent_p.P374P|SLC12A8_ENST00000469902.1_Silent_p.P345P|SLC12A8_ENST00000314584.7_Silent_p.P98P	NM_001195483.1	NP_001182412	A0AV02	S12A8_HUMAN	solute carrier family 12, member 8	345					potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	symporter activity (GO:0015293)			endometrium(2)|kidney(2)|lung(12)	16						AGGCAAGTGCAGGGATCACTT	0.493													A|||	56	0.0111821	0.0015	0.0173	5008	,	,		19172	0.0		0.0219	False		,,,				2504	0.0204				p.P345P		Atlas-SNP	.											.	SLC12A8	81	.	0			c.T1035C						PASS	.	A	,	20,3788		0,20,1884	89.0	90.0	89.0		1035,1035	-6.4	0.9	3	dbSNP_120	89	255,7991		3,249,3871	no	coding-synonymous,coding-synonymous	SLC12A8	NM_001195483.1,NM_024628.5	,	3,269,5755	GG,GA,AA		3.0924,0.5252,2.2814	,	345/715,345/715	124829057	275,11779	1904	4123	6027	SO:0001819	synonymous_variant	84561	exon9			AAGTGCAGGGATC		CCDS43143.1	3q21.2	2013-07-18	2013-07-18		ENSG00000221955	ENSG00000221955		"""Solute carriers"""	15595	protein-coding gene	gene with protein product	"""solute carrier family 12 (sodium/potassium/chloride transporters), member 8"", ""cation-chloride cotransporter 9"""	611316				11863360	Standard	NM_024628		Approved	CCC9	uc003ehv.4	A0AV02	OTTHUMG00000159483	ENST00000393469.4:c.1035T>C	3.37:g.124829057A>G		67.0	0.0	0		72.0	24.0	0.333333	NM_024628	C9JJJ2|Q68D04|Q6I9Z2|Q6P4C0|Q7Z3A6|Q86WK0|Q8NFX9|Q8WUI3|Q96RF9|Q9H5P9	Silent	SNP	ENST00000393469.4	37	CCDS43143.1																																																																																			A|0.986;G|0.013	0.013	strong		0.493	SLC12A8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355711.4	NM_024628	
ANAPC16	119504	hgsc.bcm.edu	37	10	73992862	73992862	+	Silent	SNP	C	C	G	rs9275	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:73992862C>G	ENST00000299381.4	+	4	439	c.321C>G	c.(319-321)ccC>ccG	p.P107P	ANAPC16_ENST00000470481.2_3'UTR	NM_001242546.1|NM_001242547.1|NM_001242548.1|NM_173473.3	NP_001229475.1|NP_001229476.1|NP_001229477.1|NP_775744.1	Q96DE5	APC16_HUMAN	anaphase promoting complex subunit 16	107					mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	anaphase-promoting complex (GO:0005680)|cytoplasm (GO:0005737)				large_intestine(1)|ovary(1)	2						GATTCACCCCCTCTTCAGGTT	0.542													C|||	364	0.0726837	0.2595	0.0274	5008	,	,		14954	0.0		0.002	False		,,,				2504	0.0				p.P107P		Atlas-SNP	.											.	ANAPC16	10	.	0			c.C321G						PASS	.	C	,,,	919,3487	344.1+/-307.9	90,739,1374	66.0	64.0	65.0		321,321,246,321	-0.3	1.0	10	dbSNP_52	65	13,8587	9.1+/-34.3	0,13,4287	yes	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	ANAPC16	NM_001242546.1,NM_001242547.1,NM_001242548.1,NM_173473.3	,,,	90,752,5661	GG,GC,CC		0.1512,20.8579,7.1659	,,,	107/111,107/111,82/86,107/111	73992862	932,12074	2203	4300	6503	SO:0001819	synonymous_variant	119504	exon5			CACCCCCTCTTCA	BC009530	CCDS7314.1, CCDS73147.1	10q22.2	2011-08-12	2010-04-06	2010-04-06	ENSG00000166295	ENSG00000166295		"""Anaphase promoting complex subunits"""	26976	protein-coding gene	gene with protein product	"""centromere protein 27"""	613427	"""chromosome 10 open reading frame 104"""	C10orf104		14702039, 20360068	Standard	NM_001242546		Approved	bA570G20.3, FLJ33728, APC16, CENP-27	uc021psp.1	Q96DE5	OTTHUMG00000018433	ENST00000299381.4:c.321C>G	10.37:g.73992862C>G		39.0	0.0	0		40.0	24.0	0.6	NM_001242546		Silent	SNP	ENST00000299381.4	37	CCDS7314.1																																																																																			G|0.064;C|0.936	0.064	strong		0.542	ANAPC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048565.2	NM_173473	
SCN8A	6334	hgsc.bcm.edu	37	12	52200499	52200499	+	Silent	SNP	C	C	A	rs370268493		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:52200499C>A	ENST00000354534.6	+	27	5407	c.5229C>A	c.(5227-5229)atC>atA	p.I1743I	SCN8A_ENST00000545061.1_Silent_p.I1702I|RP11-923I11.3_ENST00000565518.1_lincRNA	NM_001177984.2|NM_014191.3	NP_001171455.1|NP_055006.1	Q9UQD0	SCN8A_HUMAN	sodium channel, voltage gated, type VIII, alpha subunit	1743					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|membrane depolarization during action potential (GO:0086010)|muscle organ development (GO:0007517)|myelination (GO:0042552)|nervous system development (GO:0007399)|neuromuscular process (GO:0050905)|neuronal action potential (GO:0019228)|peripheral nervous system development (GO:0007422)|response to toxic substance (GO:0009636)|sensory perception of sound (GO:0007605)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|cytoplasmic vesicle (GO:0031410)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	ATP binding (GO:0005524)|voltage-gated sodium channel activity (GO:0005248)			breast(2)|central_nervous_system(1)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(7)|lung(19)|ovary(8)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	55				BRCA - Breast invasive adenocarcinoma(357;0.181)	Valproic Acid(DB00313)	CAGTGGGCATCTTCTTCTTTG	0.498																																					p.I1743I		Atlas-SNP	.											.	SCN8A	331	.	0			c.C5229A						PASS	.	C	,	1,4343		0,1,2171	81.0	89.0	87.0		5106,5229	5.3	1.0	12		87	3,8567		0,3,4282	no	coding-synonymous,coding-synonymous	SCN8A	NM_001177984.1,NM_014191.2	,	0,4,6453	AA,AC,CC		0.035,0.023,0.031	,	1702/1940,1743/1981	52200499	4,12910	2172	4285	6457	SO:0001819	synonymous_variant	6334	exon27			GGGCATCTTCTTC	AB027567	CCDS44891.1, CCDS53794.1	12q13.1	2012-02-26	2007-01-23			ENSG00000196876		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10596	protein-coding gene	gene with protein product		600702	"""sodium channel, voltage gated, type VIII, alpha polypeptide"""	MED		7670495, 9828131, 16382098	Standard	NM_014191		Approved	Nav1.6, NaCh6, PN4, CerIII	uc001ryw.4	Q9UQD0		ENST00000354534.6:c.5229C>A	12.37:g.52200499C>A		177.0	0.0	0		163.0	96.0	0.588957	NM_014191	B9VWG8|O95788|Q9NYX2|Q9UPB2	Silent	SNP	ENST00000354534.6	37	CCDS44891.1																																																																																			.	.	weak		0.498	SCN8A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404372.3	NM_014191	
GALNT4	8693	hgsc.bcm.edu	37	12	89917349	89917349	+	Silent	SNP	C	C	T	rs200228838	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr12:89917349C>T	ENST00000529983.2	-	1	1234	c.978G>A	c.(976-978)acG>acA	p.T326T	POC1B-GALNT4_ENST00000547474.1_3'UTR|POC1B_ENST00000549504.1_Intron|POC1B_ENST00000549035.1_Intron|RP11-734K2.4_ENST00000605233.1_RNA|POC1B_ENST00000393179.4_Intron|GALNT4_ENST00000413530.1_Silent_p.T154T|POC1B_ENST00000313546.3_Intron|POC1B-GALNT4_ENST00000548729.1_Silent_p.T323T|POC1B_ENST00000541909.1_Intron	NM_003774.4	NP_003765.2	Q8N4A0	GALT4_HUMAN	polypeptide N-acetylgalactosaminyltransferase 4	326	Catalytic subdomain B.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			endometrium(4)|kidney(2)|lung(5)|prostate(2)|upper_aerodigestive_tract(1)	14						CTGTGTCATACGTTCCAAGGT	0.493													C|||	2	0.000399361	0.0	0.0	5008	,	,		19273	0.0		0.002	False		,,,				2504	0.0				p.T326T		Atlas-SNP	.											.	GALNT4	38	.	0			c.G978A						PASS	.	C	,,,,	0,4026		0,0,2013	182.0	183.0	182.0		,969,462,978,	-11.7	0.0	12		182	15,8367		0,15,4176	no	intron,coding-synonymous,coding-synonymous,coding-synonymous,intron	GALNT4,POC1B,POC1B-GALNT4	NM_001199777.1,NM_001199781.1,NM_001199782.1,NM_003774.4,NM_172240.2	,,,,	0,15,6189	TT,TC,CC		0.179,0.0,0.1209	,,,,	,323/576,154/407,326/579,	89917349	15,12393	2013	4191	6204	SO:0001819	synonymous_variant	8693	exon1			GTCATACGTTCCA	Y08564	CCDS53817.1	12q21.33	2014-03-13	2014-03-13		ENSG00000257594	ENSG00000257594	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4126	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 4"""	603565	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 4 (GalNAc-T4)"""			9804815	Standard	NM_003774		Approved	GalNAc-T4	uc001tbd.3	Q8N4A0	OTTHUMG00000166292	ENST00000529983.2:c.978G>A	12.37:g.89917349C>T		275.0	0.0	0		290.0	141.0	0.486207	NM_003774	B2R775|B4DMX6|O00208	Silent	SNP	ENST00000529983.2	37	CCDS53817.1																																																																																			C|0.996;T|0.004	0.004	strong		0.493	GALNT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388973.2	NM_003774	
BRAF	673	hgsc.bcm.edu	37	7	140477811	140477811	+	Missense_Mutation	SNP	T	T	A	rs397507476		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:140477811T>A	ENST00000288602.6	-	12	1557	c.1497A>T	c.(1495-1497)aaA>aaT	p.K499N		NM_004333.4	NP_004324.2	P15056	BRAF_HUMAN	B-Raf proto-oncogene, serine/threonine kinase	499	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		K -> E (in CFC1). {ECO:0000269|PubMed:16439621, ECO:0000269|PubMed:16474404, ECO:0000269|PubMed:18042262}.|K -> N (in CFC1). {ECO:0000269|PubMed:18042262, ECO:0000269|PubMed:19206169}.		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)	CTACTTCATTTTTGAAGGCTT	0.393		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.K499N	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.A1497T	GRCh37	CM080110	BRAF	M		PASS	.						108.0	97.0	101.0					7																	140477811		2203	4300	6503	SO:0001583	missense	673	exon12	Familial Cancer Database	CFC, CFCS	TTCATTTTTGAAG	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.1497A>T	7.37:g.140477811T>A	ENSP00000288602:p.Lys499Asn	54.0	0.0	0		70.0	26.0	0.371429	NM_004333	A4D1T4|B6HY61|B6HY62|B6HY63|B6HY64|B6HY65|B6HY66|Q13878|Q3MIN6|Q9UDP8|Q9Y6T3	Missense_Mutation	SNP	ENST00000288602.6	37	CCDS5863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	23.5|23.5	4.427562|4.427562	0.83667|0.83667	.|.	.|.	ENSG00000157764|ENSG00000157764	ENST00000496384|ENST00000288602	D|D	0.81739|0.82619	-1.53|-1.63	4.96|4.96	4.96|4.96	0.65561|0.65561	.|Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.82742|0.82742	0.5103|0.5103	L|L	0.35793|0.35793	1.09|1.09	0.80722|0.80722	D|D	1|1	.|P	.|0.51653	.|0.947	.|P	.|0.52031	.|0.688	D|D	0.85140|0.85140	0.0980|0.0980	8|10	0.87932|0.87932	D|D	0|0	.|.	14.3436|14.3436	0.66643|0.66643	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|499	.|P15056	.|BRAF_HUMAN	I|N	107|499	ENSP00000419060:K107I|ENSP00000288602:K499N	ENSP00000419060:K107I|ENSP00000288602:K499N	K|K	-|-	2|3	0|2	BRAF|BRAF	140124280|140124280	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	3.114000|3.114000	0.50383|0.50383	1.853000|1.853000	0.53794|0.53794	0.472000|0.472000	0.43445|0.43445	AAA|AAA	.	.	none		0.393	BRAF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348886.1	NM_004333	
FAM126B	285172	hgsc.bcm.edu	37	2	201846180	201846180	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:201846180A>G	ENST00000418596.3	-	12	1593	c.1406T>C	c.(1405-1407)aTt>aCt	p.I469T	AC005037.3_ENST00000413848.1_RNA|AC005037.3_ENST00000332935.6_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	469						intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						GCCAACCCCAATGCTGGTACT	0.463																																					p.I469T		Atlas-SNP	.											FAM126B,NS,carcinoma,-1,1	FAM126B	34	1	0			c.T1406C						PASS	.						107.0	83.0	91.0					2																	201846180		2203	4300	6503	SO:0001583	missense	285172	exon12			ACCCCAATGCTGG	BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744			28593	protein-coding gene	gene with protein product						12477932	Standard	NM_173822		Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.1406T>C	2.37:g.201846180A>G	ENSP00000393667:p.Ile469Thr	127.0	0.0	0		132.0	63.0	0.477273	NM_173822	B2RCG7|Q4ZG87|Q53TX6	Missense_Mutation	SNP	ENST00000418596.3	37	CCDS2335.1	.	.	.	.	.	.	.	.	.	.	A	1.870	-0.460559	0.04508	.	.	ENSG00000155744	ENST00000418596	T	0.76578	-1.03	5.72	5.72	0.89469	.	0.413650	0.27773	N	0.017905	T	0.63331	0.2502	N	0.22421	0.69	0.29765	N	0.835254	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.0	T	0.54662	-0.8260	10	0.16896	T	0.51	-6.7283	11.9287	0.52835	0.8549:0.1451:0.0:0.0	.	275;469	B3KUG1;Q8IXS8	.;F126B_HUMAN	T	469	ENSP00000393667:I469T	ENSP00000393667:I469T	I	-	2	0	FAM126B	201554425	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.848000	0.48278	2.177000	0.69029	0.533000	0.62120	ATT	.	.	none		0.463	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256285.3	NM_173822	
CNTNAP3	79937	hgsc.bcm.edu	37	9	39149904	39149904	+	Silent	SNP	G	G	A	rs200999166	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:39149904G>A	ENST00000297668.6	-	10	1621	c.1548C>T	c.(1546-1548)ctC>ctT	p.L516L	CNTNAP3_ENST00000323947.7_Intron|CNTNAP3_ENST00000377656.2_Silent_p.L516L|CNTNAP3_ENST00000358144.2_Silent_p.L428L|CNTNAP3_ENST00000377659.1_Silent_p.L516L	NM_033655.3	NP_387504.2	Q9BZ76	CNTP3_HUMAN	contactin associated protein-like 3	516	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				cell adhesion (GO:0007155)|cell recognition (GO:0008037)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(8)|ovary(1)|upper_aerodigestive_tract(2)	24				GBM - Glioblastoma multiforme(29;0.02)|Lung(182;0.0681)		CAATGGTGATGAGCCTTAGGC	0.532													.|||	3	0.000599042	0.0	0.0014	5008	,	,		14869	0.0		0.002	False		,,,				2504	0.0				p.L516L		Atlas-SNP	.											.	CNTNAP3	82	.	0			c.C1548T						PASS	.	G		0,4292		0,0,2146	10.0	11.0	11.0		1548	1.2	1.0	9		11	6,8376		0,6,4185	no	coding-synonymous	CNTNAP3	NM_033655.3		0,6,6331	AA,AG,GG		0.0716,0.0,0.0473		516/1289	39149904	6,12668	2146	4191	6337	SO:0001819	synonymous_variant	79937	exon10			GGTGATGAGCCTT	AF333769	CCDS6616.1	9q12	2008-02-05			ENSG00000106714	ENSG00000106714			13834	protein-coding gene	gene with protein product	"""cell recognition molecule CASPR3 (FLJ14195, KIAA1714)"""	610517				12093160	Standard	NM_033655		Approved	CASPR3, KIAA1714, FLJ14195, CNTNAP3A	uc004abi.3	Q9BZ76	OTTHUMG00000019954	ENST00000297668.6:c.1548C>T	9.37:g.39149904G>A		816.0	0.0	0		1008.0	254.0	0.251984	NM_033655	B1AMA0|Q9C0E9	Silent	SNP	ENST00000297668.6	37	CCDS6616.1																																																																																			G|0.999;A|0.001	0.001	weak		0.532	CNTNAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052511.1	NM_033655	
TYRO3	7301	hgsc.bcm.edu	37	15	41862356	41862356	+	Splice_Site	SNP	T	T	C	rs149022093		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:41862356T>C	ENST00000263798.3	+	10	1606		c.e10+2		TYRO3_ENST00000559066.1_Splice_Site	NM_006293.3	NP_006284.2	Q06418	TYRO3_HUMAN	TYRO3 protein tyrosine kinase						apoptotic cell clearance (GO:0043277)|cell adhesion (GO:0007155)|forebrain cell migration (GO:0021885)|natural killer cell differentiation (GO:0001779)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of lymphocyte activation (GO:0051250)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|neuron cellular homeostasis (GO:0070050)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol 3-kinase signaling (GO:0014065)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|protein autophosphorylation (GO:0046777)|protein kinase B signaling (GO:0043491)|secretion by cell (GO:0032940)|signal transduction (GO:0007165)|signal transduction by phosphorylation (GO:0023014)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)	ATP binding (GO:0005524)|phosphatidylinositol 3-kinase binding (GO:0043548)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(26)|ovary(3)|prostate(1)	43		all_cancers(109;7.33e-15)|all_epithelial(112;2.8e-12)|Lung NSC(122;3.48e-08)|all_lung(180;1.71e-07)|Melanoma(134;0.0262)		OV - Ovarian serous cystadenocarcinoma(18;3.31e-18)|GBM - Glioblastoma multiforme(113;9.31e-07)|BRCA - Breast invasive adenocarcinoma(123;0.117)		GCGGTTTGGGTAAGGGGATGG	0.567																																					.		Atlas-SNP	.											TYRO3_ENST00000263798,NS,carcinoma,0,2	TYRO3	169	2	0			c.1382+2T>C						PASS	.						76.0	75.0	75.0					15																	41862356		2203	4300	6503	SO:0001630	splice_region_variant	7301	exon10			TTTGGGTAAGGGG	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.1382+2T>C	15.37:g.41862356T>C		110.0	0.0	0		119.0	8.0	0.0672269	NM_006293	O14953|Q86VR3	Splice_Site	SNP	ENST00000263798.3	37	CCDS10080.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.181954	0.78677	.	.	ENSG00000092445	ENST00000540218;ENST00000263798	.	.	.	5.26	5.26	0.73747	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3401	0.74290	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	TYRO3	39649648	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	6.789000	0.75110	2.208000	0.71279	0.533000	0.62120	.	.	.	weak		0.567	TYRO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252693.2		Intron
CFAP46	54777	hgsc.bcm.edu	37	10	134680995	134680995	+	Missense_Mutation	SNP	C	C	T	rs150661681	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134680995C>T	ENST00000368586.5	-	34	4727	c.4627G>A	c.(4627-4629)Gcg>Acg	p.A1543T		NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						TTTTTCAACGCGATCTCTTTT	0.458													C|||	46	0.0091853	0.0	0.0072	5008	,	,		16700	0.002		0.0129	False		,,,				2504	0.0266				p.A1543T		Atlas-SNP	.											.	TTC40	100	.	0			c.G4627A						PASS	.																																			SO:0001583	missense	54777	exon34			TCAACGCGATCTC																												ENST00000368586.5:c.4627G>A	10.37:g.134680995C>T	ENSP00000357575:p.Ala1543Thr	128.0	0.0	0		123.0	55.0	0.447154	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	10	0.004578754578754579	0	0.0	3	0.008287292817679558	0	0.0	7	0.009234828496042216	C	2.465	-0.323251	0.05350	.	.	ENSG00000171811	ENST00000368586	T	0.10960	2.82	4.08	2.18	0.27775	.	.	.	.	.	T	0.07863	0.0197	.	.	.	0.09310	N	0.999998	.	.	.	.	.	.	T	0.24297	-1.0164	6	0.54805	T	0.06	.	5.1014	0.14762	0.0:0.6678:0.216:0.1161	.	.	.	.	T	1543	ENSP00000357575:A1543T	ENSP00000357575:A1543T	A	-	1	0	C10orf93	134530985	0.010000	0.17322	0.186000	0.23195	0.034000	0.12701	0.119000	0.15626	1.044000	0.40200	0.585000	0.79938	GCG	C|0.993;T|0.007	0.007	strong		0.458	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
FCHSD1	89848	hgsc.bcm.edu	37	5	141021108	141021108	+	Missense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:141021108G>A	ENST00000435817.2	-	20	2080	c.2030C>T	c.(2029-2031)cCg>cTg	p.P677L	FCHSD1_ENST00000522126.1_3'UTR|FCHSD1_ENST00000522783.1_3'UTR|FCHSD1_ENST00000523856.1_5'UTR	NM_033449.2	NP_258260.1	Q86WN1	FCSD1_HUMAN	FCH and double SH3 domains 1	677	Pro-rich.								FCHSD1/BRAF(2)	central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(8)|lung(5)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GGCTTTAGCCGGCGGGGGAGG	0.587																																					p.P677L		Atlas-SNP	.											.	FCHSD1	51	.	0			c.C2030T						PASS	.						37.0	45.0	42.0					5																	141021108		1941	4133	6074	SO:0001583	missense	89848	exon20			TTAGCCGGCGGGG	AK027281	CCDS47295.1	5q31.3	2008-02-05			ENSG00000197948	ENSG00000197948			25463	protein-coding gene	gene with protein product						11214971, 15067381	Standard	NM_033449		Approved	FLJ00007	uc003llk.3	Q86WN1	OTTHUMG00000163762	ENST00000435817.2:c.2030C>T	5.37:g.141021108G>A	ENSP00000399259:p.Pro677Leu	90.0	0.0	0		112.0	62.0	0.553571	NM_033449	Q6UX75|Q86Y77|Q9NXX8	Missense_Mutation	SNP	ENST00000435817.2	37	CCDS47295.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.401255	0.62288	.	.	ENSG00000197948	ENST00000435817	T	0.28454	1.61	5.25	5.25	0.73442	.	0.143676	0.48286	D	0.000182	T	0.44787	0.1310	L	0.32530	0.975	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.997	T	0.31475	-0.9942	10	0.72032	D	0.01	-9.0948	14.5305	0.67923	0.0:0.0:1.0:0.0	.	357;677	Q86WN1-2;Q86WN1	.;FCSD1_HUMAN	L	677	ENSP00000399259:P677L	ENSP00000399259:P677L	P	-	2	0	FCHSD1	141001292	0.998000	0.40836	0.831000	0.32960	0.910000	0.53928	4.883000	0.63128	2.885000	0.99019	0.655000	0.94253	CCG	.	.	none		0.587	FCHSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375282.2	NM_033449	
GALNT3	2591	hgsc.bcm.edu	37	2	166621413	166621413	+	Silent	SNP	C	C	T	rs13423840	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:166621413C>T	ENST00000392701.3	-	3	1444	c.669G>A	c.(667-669)gtG>gtA	p.V223V	GALNT3_ENST00000409882.1_5'Flank	NM_004482.3	NP_004473.2	Q14435	GALT3_HUMAN	polypeptide N-acetylgalactosaminyltransferase 3	223	Catalytic subdomain A.				carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(1)|central_nervous_system(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(3)|skin(1)	20						TAGCATCATCCACCAAAATGA	0.393													t|||	50	0.00998403	0.034	0.0072	5008	,	,		17855	0.0		0.0	False		,,,				2504	0.0				p.V223V		Atlas-SNP	.											.	GALNT3	65	.	0			c.G669A						PASS	.	T		126,4280	92.0+/-130.7	1,124,2078	177.0	165.0	169.0		669	2.8	1.0	2	dbSNP_121	169	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	GALNT3	NM_004482.3		1,125,6377	TT,TC,CC		0.0116,2.8597,0.9765		223/634	166621413	127,12879	2203	4300	6503	SO:0001819	synonymous_variant	2591	exon3			ATCATCCACCAAA		CCDS2226.1	2q24-q31	2014-03-13	2014-03-13		ENSG00000115339	ENSG00000115339	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4125	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 3"""	601756	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 3 (GalNAc-T3)"""			9592121, 15133511	Standard	NM_004482		Approved	GalNAc-T3, HHS, HFTC	uc010fph.1	Q14435	OTTHUMG00000132157	ENST00000392701.3:c.669G>A	2.37:g.166621413C>T		232.0	1.0	0.00431034		269.0	117.0	0.434944	NM_004482	Q53TG9|Q7Z476	Silent	SNP	ENST00000392701.3	37	CCDS2226.1																																																																																			C|0.987;T|0.013	0.013	strong		0.393	GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255205.2	NM_004482	
KCNQ4	9132	hgsc.bcm.edu	37	1	41289831	41289831	+	Missense_Mutation	SNP	A	A	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:41289831A>G	ENST00000347132.5	+	9	1275	c.1193A>G	c.(1192-1194)gAg>gGg	p.E398G	KCNQ4_ENST00000506017.1_3'UTR|KCNQ4_ENST00000509682.2_Intron	NM_004700.3|NM_172163.2	NP_004691.2|NP_751895.1	P56696	KCNQ4_HUMAN	potassium voltage-gated channel, KQT-like subfamily, member 4	398					inner ear morphogenesis (GO:0042472)|potassium ion transport (GO:0006813)|sensory perception of sound (GO:0007605)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel activity (GO:0005267)			central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(8)|lung(13)|skin(1)	26	Ovarian(52;0.00769)|all_hematologic(146;0.0977)|Acute lymphoblastic leukemia(166;0.155)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;1.38e-17)		Ezogabine(DB04953)	CGGCCCCTGGAGGTGCGGCGG	0.706																																					p.E398G		Atlas-SNP	.											.	KCNQ4	58	.	0			c.A1193G						PASS	.						6.0	7.0	7.0					1																	41289831		2093	4057	6150	SO:0001583	missense	9132	exon9			CCCTGGAGGTGCG	AF105202	CCDS456.1	1p34	2012-07-05			ENSG00000117013	ENSG00000117013		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6298	protein-coding gene	gene with protein product		603537		DFNA2		10025409, 16382104	Standard	NM_004700		Approved	Kv7.4	uc001cgh.2	P56696	OTTHUMG00000007730	ENST00000347132.5:c.1193A>G	1.37:g.41289831A>G	ENSP00000262916:p.Glu398Gly	45.0	0.0	0		44.0	39.0	0.886364	NM_004700	O96025	Missense_Mutation	SNP	ENST00000347132.5	37	CCDS456.1	.	.	.	.	.	.	.	.	.	.	A	14.89	2.669119	0.47677	.	.	ENSG00000117013	ENST00000347132	D	0.98947	-5.26	5.74	5.74	0.90152	.	0.381642	0.26255	N	0.025436	D	0.96281	0.8787	N	0.08118	0	0.80722	D	1	D	0.58268	0.982	P	0.53006	0.715	D	0.95540	0.8611	10	0.30078	T	0.28	-19.2463	12.4719	0.55792	1.0:0.0:0.0:0.0	.	398	P56696	KCNQ4_HUMAN	G	398	ENSP00000262916:E398G	ENSP00000262916:E398G	E	+	2	0	KCNQ4	41062418	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.349000	0.59385	2.201000	0.70794	0.477000	0.44152	GAG	.	.	none		0.706	KCNQ4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000020812.1	NM_004700	
GBGT1	26301	hgsc.bcm.edu	37	9	136029645	136029645	+	Nonsense_Mutation	SNP	G	G	T	rs35898523	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136029645G>T	ENST00000372040.3	-	7	674	c.363C>A	c.(361-363)taC>taA	p.Y121*	RALGDS_ENST00000542690.1_Intron|GBGT1_ENST00000540636.1_Nonsense_Mutation_p.Y104*|GBGT1_ENST00000372043.3_Intron|GBGT1_ENST00000472281.1_5'UTR|GBGT1_ENST00000372038.3_Missense_Mutation_p.H134N	NM_001282629.1	NP_001269558.1	Q8N5D6	GBGT1_HUMAN	globoside alpha-1,3-N-acetylgalactosaminyltransferase 1	121					glycolipid biosynthetic process (GO:0009247)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	globoside alpha-N-acetylgalactosaminyltransferase activity (GO:0047277)|metal ion binding (GO:0046872)			breast(2)|endometrium(1)|kidney(4)|lung(2)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;3.49e-06)|Epithelial(140;2.59e-05)		TGAAATGAGTGTACCTAGTGA	0.587													G|||	215	0.0429313	0.034	0.0418	5008	,	,		18455	0.002		0.0815	False		,,,				2504	0.0583				p.Y121X		Atlas-SNP	.											GBGT1,NS,carcinoma,-2,1	GBGT1	25	1	0			c.C363A						PASS	.	G	stop/TYR	199,4207	121.7+/-159.2	8,183,2012	39.0	40.0	39.0		363	1.5	0.9	9	dbSNP_126	39	629,7971	155.7+/-209.7	18,593,3689	yes	stop-gained	GBGT1	NM_021996.4		26,776,5701	TT,TG,GG		7.314,4.5166,6.3663		121/348	136029645	828,12178	2203	4300	6503	SO:0001587	stop_gained	26301	exon7			ATGAGTGTACCTA	AY358175	CCDS6960.1, CCDS65175.1, CCDS65176.1	9q34.13-q34.3	2014-07-18			ENSG00000148288	ENSG00000148288		"""Glycosyltransferase family 6 domain containing"""	20460	protein-coding gene	gene with protein product	"""Forssman glycolipid synthetase (FS)"", ""Forssman synthetase"""	606074				10506200, 8855242	Standard	NM_021996		Approved	UDP-GalNAc, A3GALNT, MGC44848, FS		Q8N5D6	OTTHUMG00000020853	ENST00000372040.3:c.363C>A	9.37:g.136029645G>T	ENSP00000361110:p.Tyr121*	20.0	0.0	0		28.0	13.0	0.464286	NM_021996	A8K633|B2RA95|B7Z8S5|Q45F07|Q5T7U9|Q5T7V1|Q8N2K4|Q9UKI5	Nonsense_Mutation	SNP	ENST00000372040.3	37	CCDS6960.1	108|108	0.04945054945054945|0.04945054945054945	23|23	0.046747967479674794|0.046747967479674794	16|16	0.04419889502762431|0.04419889502762431	2|2	0.0034965034965034965|0.0034965034965034965	67|67	0.08839050131926121|0.08839050131926121	G|G	17.35|17.35	3.367115|3.367115	0.61513|0.61513	0.045166|0.045166	0.07314|0.07314	ENSG00000148288|ENSG00000148288	ENST00000372038|ENST00000372040;ENST00000540636	T|.	0.36157|.	1.27|.	5.38|5.38	1.47|1.47	0.22746|0.22746	.|.	.|0.137701	.|0.50627	.|D	.|0.000106	T|.	0.01156|.	0.0038|.	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	T|.	0.02358|.	-1.1171|.	6|.	0.05833|0.07813	T|T	0.94|0.8	-15.2709|-15.2709	6.0904|6.0904	0.19991|0.19991	0.2143:0.0:0.6535:0.1322|0.2143:0.0:0.6535:0.1322	rs35898523;rs62638704|rs35898523;rs62638704	.|.	.|.	.|.	N|X	134|121;104	ENSP00000361108:H134N|.	ENSP00000361108:H134N|ENSP00000361110:Y121X	H|Y	-|-	1|3	0|2	GBGT1|GBGT1	135019466|135019466	0.883000|0.883000	0.30277|0.30277	0.900000|0.900000	0.35374|0.35374	0.243000|0.243000	0.25628|0.25628	0.687000|0.687000	0.25407|0.25407	0.008000|0.008000	0.14787|0.14787	0.491000|0.491000	0.48974|0.48974	CAC|TAC	G|0.941;T|0.059	0.059	strong		0.587	GBGT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054815.1	NM_021996	
ARSE	415	hgsc.bcm.edu	37	X	2852957	2852957	+	Silent	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chrX:2852957C>G	ENST00000381134.3	-	11	1752	c.1686G>C	c.(1684-1686)ctG>ctC	p.L562L	ARSE_ENST00000540563.1_Silent_p.L517L|ARSE_ENST00000545496.1_Silent_p.L587L	NM_000047.2	NP_000038.2	P51690	ARSE_HUMAN	arylsulfatase E (chondrodysplasia punctata 1)	562					cellular protein metabolic process (GO:0044267)|glycosphingolipid metabolic process (GO:0006687)|post-translational protein modification (GO:0043687)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	arylsulfatase activity (GO:0004065)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	17		all_cancers(21;4.28e-07)|all_epithelial(21;2.07e-08)|all_lung(23;2.81e-05)|Lung NSC(23;0.000693)|Lung SC(21;0.122)				AGATGTTGCCCAGCCTGTCCA	0.592																																					p.L562L		Atlas-SNP	.											.	ARSE	43	.	0			c.G1686C						PASS	.						43.0	32.0	36.0					X																	2852957		2203	4296	6499	SO:0001819	synonymous_variant	415	exon11			GTTGCCCAGCCTG	X83573	CCDS14122.1, CCDS75948.1, CCDS75949.1	Xp22.33	2013-02-14			ENSG00000157399	ENSG00000157399		"""Arylsulfatase family"""	719	protein-coding gene	gene with protein product		300180		CDPX, CDPX1		7720070	Standard	NM_000047		Approved		uc004crc.4	P51690	OTTHUMG00000137358	ENST00000381134.3:c.1686G>C	X.37:g.2852957C>G		138.0	0.0	0		144.0	143.0	0.993056	NM_000047	Q53FT2|Q53FU8	Silent	SNP	ENST00000381134.3	37	CCDS14122.1																																																																																			.	.	none		0.592	ARSE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055643.1	NM_000047	
SLC2A6	11182	hgsc.bcm.edu	37	9	136341407	136341407	+	Missense_Mutation	SNP	T	T	C	rs147872568	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:136341407T>C	ENST00000371899.4	-	4	591	c.514A>G	c.(514-516)Aca>Gca	p.T172A	SLC2A6_ENST00000485978.1_5'UTR|SLC2A6_ENST00000371897.4_Missense_Mutation_p.T172A	NM_017585.3	NP_060055.2	Q9UGQ3	GTR6_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 6	172					glucose transport (GO:0015758)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)			cervix(1)|endometrium(1)|large_intestine(1)|lung(3)|prostate(3)|skin(1)	10				OV - Ovarian serous cystadenocarcinoma(145;8.47e-08)|Epithelial(140;9.37e-07)|all cancers(34;1.03e-05)		AGCTGGGGTGTGGCCCCCAGA	0.627													T|||	2	0.000399361	0.0	0.0	5008	,	,		16727	0.0		0.0	False		,,,				2504	0.002				p.T172A		Atlas-SNP	.											.	SLC2A6	31	.	0			c.A514G						PASS	.	T	ALA/THR,ALA/THR	0,4404		0,0,2202	85.0	66.0	72.0		514,514	5.0	1.0	9	dbSNP_134	72	3,8597	3.0+/-9.4	0,3,4297	yes	missense,missense	SLC2A6	NM_001145099.1,NM_017585.3	58,58	0,3,6499	CC,CT,TT		0.0349,0.0,0.0231	benign,benign	172/446,172/508	136341407	3,13001	2202	4300	6502	SO:0001583	missense	11182	exon4			GGGGTGTGGCCCC	AJ011372	CCDS6975.1, CCDS48052.1	9q34	2013-05-22			ENSG00000160326	ENSG00000160326		"""Solute carriers"""	11011	protein-coding gene	gene with protein product		606813				10970791	Standard	NM_001145099		Approved	GLUT9, GLUT6, HSA011372	uc004cee.3	Q9UGQ3	OTTHUMG00000020874	ENST00000371899.4:c.514A>G	9.37:g.136341407T>C	ENSP00000360966:p.Thr172Ala	50.0	0.0	0		69.0	30.0	0.434783	NM_017585	A6NNU6|Q5SXD7|Q8NCC2	Missense_Mutation	SNP	ENST00000371899.4	37	CCDS6975.1	.	.	.	.	.	.	.	.	.	.	T	12.05	1.820748	0.32145	0.0	3.49E-4	ENSG00000160326	ENST00000371897;ENST00000371899;ENST00000432868;ENST00000414172	T;T;T	0.58506	0.33;0.33;0.33	4.98	4.98	0.66077	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.098719	0.64402	D	0.000002	T	0.39489	0.1080	N	0.17723	0.515	0.32320	N	0.562593	B;B;P;P	0.42556	0.012;0.024;0.783;0.679	B;B;B;B	0.40636	0.05;0.089;0.287;0.335	T	0.48703	-0.9012	10	0.22706	T	0.39	.	8.2846	0.31922	0.2861:0.0:0.0:0.7139	.	172;172;172;172	B4DH85;F2Z2F6;Q9UGQ3-2;Q9UGQ3	.;.;.;GTR6_HUMAN	A	172;172;172;99	ENSP00000360964:T172A;ENSP00000360966:T172A;ENSP00000405124:T172A	ENSP00000360964:T172A	T	-	1	0	SLC2A6	135331228	1.000000	0.71417	0.999000	0.59377	0.930000	0.56654	6.118000	0.71583	1.853000	0.53794	0.533000	0.62120	ACA	T|1.000;C|0.000	0.000	strong		0.627	SLC2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054909.1	NM_017585	
PGC	5225	hgsc.bcm.edu	37	6	41704716	41704716	+	Silent	SNP	G	G	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:41704716G>T	ENST00000373025.3	-	9	1103	c.1041C>A	c.(1039-1041)gtC>gtA	p.V347V	TFEB_ENST00000358871.2_5'Flank|TFEB_ENST00000230323.4_5'Flank|TFEB_ENST00000373033.1_5'Flank|TFEB_ENST00000403298.4_5'Flank|TFEB_ENST00000420312.1_5'Flank|RP11-298J23.5_ENST00000438967.1_RNA	NM_002630.3	NP_002621.1	P20142	PEPC_HUMAN	progastricsin (pepsinogen C)	347					digestion (GO:0007586)|proteolysis (GO:0006508)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(3)|kidney(1)|large_intestine(5)|lung(6)|skin(1)	16	Ovarian(28;0.0355)|Colorectal(47;0.121)		Epithelial(12;0.000132)|STAD - Stomach adenocarcinoma(11;0.000204)|Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00507)			AGGTGGGCTCGACTCCCACGG	0.572																																					p.V347V		Atlas-SNP	.											.	PGC	56	.	0			c.C1041A						PASS	.						69.0	64.0	66.0					6																	41704716		2203	4300	6503	SO:0001819	synonymous_variant	5225	exon9			GGGCTCGACTCCC		CCDS4859.1, CCDS55000.1	6p21.1	2012-10-02			ENSG00000096088	ENSG00000096088	3.4.23.3		8890	protein-coding gene	gene with protein product		169740					Standard	NM_002630		Approved		uc003ora.2	P20142	OTTHUMG00000014683	ENST00000373025.3:c.1041C>A	6.37:g.41704716G>T		118.0	0.0	0		104.0	53.0	0.509615	NM_002630	B4DVZ3|Q5T3D7|Q5T3D8	Silent	SNP	ENST00000373025.3	37	CCDS4859.1																																																																																			.	.	none		0.572	PGC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040521.2		
ERCC6	2074	hgsc.bcm.edu	37	10	50678544	50678544	+	Silent	SNP	A	A	C			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:50678544A>C	ENST00000355832.5	-	18	3540	c.3462T>G	c.(3460-3462)tcT>tcG	p.S1154S	ERCC6_ENST00000542458.1_Silent_p.S524S|RP11-123B3.2_ENST00000423283.1_RNA|ERCC6_ENST00000465653.1_5'Flank	NM_000124.2	NP_000115.1	Q03468	ERCC6_HUMAN	excision repair cross-complementation group 6	1154					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|ATP catabolic process (GO:0006200)|base-excision repair (GO:0006284)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|multicellular organism growth (GO:0035264)|nucleotide-excision repair (GO:0006289)|photoreceptor cell maintenance (GO:0045494)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of protein tyrosine kinase activity (GO:0061098)|pyrimidine dimer repair (GO:0006290)|regulation of DNA-templated transcription, elongation (GO:0032784)|response to gamma radiation (GO:0010332)|response to oxidative stress (GO:0006979)|response to superoxide (GO:0000303)|response to toxic substance (GO:0009636)|response to UV (GO:0009411)|response to UV-B (GO:0010224)|response to X-ray (GO:0010165)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase II promoter (GO:0006366)|transcription-coupled nucleotide-excision repair (GO:0006283)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription elongation factor complex (GO:0008023)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|DNA-dependent ATPase activity (GO:0008094)|helicase activity (GO:0004386)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)|protein N-terminus binding (GO:0047485)|protein tyrosine kinase activator activity (GO:0030296)			breast(5)|central_nervous_system(1)|endometrium(6)|kidney(5)|large_intestine(15)|lung(19)|ovary(3)|pancreas(1)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	64						CTCTTTTGTAAGAAAGACCTA	0.358								Direct reversal of damage;Nucleotide excision repair (NER)																													p.A1154A		Atlas-SNP	.											ERCC6,NS,haematopoietic_neoplasm,-1,1	ERCC6	162	1	0			c.C3462G						scavenged	.						75.0	74.0	74.0					10																	50678544		2203	4300	6503	SO:0001819	synonymous_variant	2074	exon18			TTTGTAAGAAAGA	L04791	CCDS7229.1	10q11	2014-09-17	2014-03-07		ENSG00000225830	ENSG00000225830			3438	protein-coding gene	gene with protein product	"""Cockayne syndrome B protein"""	609413	"""excision repair cross-complementing rodent repair deficiency, complementation group 6"""	CKN2		1339317, 19179336	Standard	NM_000124		Approved	CSB, RAD26, ARMD5	uc001jhs.5	Q03468	OTTHUMG00000018195	ENST00000355832.5:c.3462T>G	10.37:g.50678544A>C		142.0	1.0	0.00704225		156.0	58.0	0.371795	NM_000124	D3DX94|Q5W0L9	Silent	SNP	ENST00000355832.5	37	CCDS7229.1																																																																																			.	.	none		0.358	ERCC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047990.1	NM_000124	
ADAMTSL3	57188	hgsc.bcm.edu	37	15	84611805	84611805	+	Missense_Mutation	SNP	C	C	T	rs61752778	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr15:84611805C>T	ENST00000286744.5	+	19	2685	c.2461C>T	c.(2461-2463)Cca>Tca	p.P821S	ADAMTSL3_ENST00000567476.1_Missense_Mutation_p.P821S	NM_207517.2	NP_997400.2	P82987	ATL3_HUMAN	ADAMTS-like 3	821	TSP type-1 7. {ECO:0000255|PROSITE- ProRule:PRU00210}.					proteinaceous extracellular matrix (GO:0005578)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(2)|breast(7)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(24)|lung(51)|ovary(7)|pancreas(2)|prostate(2)|skin(8)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	130			BRCA - Breast invasive adenocarcinoma(143;0.211)			AGACTGTCCTCCACATTTAGC	0.493													C|||	66	0.0131789	0.0008	0.0101	5008	,	,		21353	0.0		0.0288	False		,,,				2504	0.0297				p.P821S		Atlas-SNP	.											.	ADAMTSL3	290	.	0			c.C2461T						PASS	.	C	SER/PRO	11,4395	17.9+/-39.9	0,11,2192	66.0	58.0	60.0		2461	5.1	0.5	15	dbSNP_129	60	160,8440	75.7+/-138.4	1,158,4141	yes	missense	ADAMTSL3	NM_207517.2	74	1,169,6333	TT,TC,CC		1.8605,0.2497,1.3148	probably-damaging	821/1692	84611805	171,12835	2203	4300	6503	SO:0001583	missense	57188	exon19			TGTCCTCCACATT	AF237652	CCDS10326.1, CCDS73773.1	15q25.2	2013-01-29			ENSG00000156218	ENSG00000156218		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	14633	protein-coding gene	gene with protein product		609199				9628581, 10574462	Standard	NM_207517		Approved	KIAA1233, punctin-2	uc002bjz.4	P82987	OTTHUMG00000147363	ENST00000286744.5:c.2461C>T	15.37:g.84611805C>T	ENSP00000286744:p.Pro821Ser	91.0	0.0	0		65.0	33.0	0.507692	NM_207517	A1A566|A1A567|Q9ULI7	Missense_Mutation	SNP	ENST00000286744.5	37	CCDS10326.1	28	0.01282051282051282	0	0.0	4	0.011049723756906077	0	0.0	24	0.0316622691292876	C	14.08	2.428426	0.43122	0.002497	0.018605	ENSG00000156218	ENST00000286744	T	0.60797	0.16	5.08	5.08	0.68730	.	0.450530	0.16546	N	0.209689	T	0.47857	0.1468	L	0.53671	1.685	0.54753	D	0.999986	P;D	0.89917	0.754;1.0	P;D	0.85130	0.45;0.997	T	0.57242	-0.7845	10	0.11794	T	0.64	.	18.0594	0.89372	0.0:1.0:0.0:0.0	rs61752778	821;821	P82987-2;P82987	.;ATL3_HUMAN	S	821	ENSP00000286744:P821S	ENSP00000286744:P821S	P	+	1	0	ADAMTSL3	82402809	0.994000	0.37717	0.490000	0.27465	0.988000	0.76386	4.535000	0.60629	2.358000	0.79984	0.655000	0.94253	CCA	C|0.988;T|0.012	0.012	strong		0.493	ADAMTSL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000304007.2	NM_207517	
ADRA2C	152	hgsc.bcm.edu	37	4	3769573	3769573	+	Missense_Mutation	SNP	G	G	C	rs370580020		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:3769573G>C	ENST00000330055.5	+	1	1449	c.1240G>C	c.(1240-1242)Gtg>Ctg	p.V414L	ADRA2C_ENST00000509482.1_Intron	NM_000683.3	NP_000674.2	P18825	ADA2C_HUMAN	adrenoceptor alpha 2C	414					activation of MAPK activity by adrenergic receptor signaling pathway (GO:0071883)|activation of protein kinase B activity (GO:0032148)|blood coagulation (GO:0007596)|cell-cell signaling (GO:0007267)|energy reserve metabolic process (GO:0006112)|epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway (GO:0035625)|female pregnancy (GO:0007565)|G-protein coupled receptor signaling pathway (GO:0007186)|negative regulation of epinephrine secretion (GO:0032811)|negative regulation of norepinephrine secretion (GO:0010700)|negative regulation of uterine smooth muscle contraction (GO:0070473)|platelet activation (GO:0030168)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of vasoconstriction (GO:0045907)|regulation of insulin secretion (GO:0050796)|regulation of sensory perception of pain (GO:0051930)|small molecule metabolic process (GO:0044281)	axon terminus (GO:0043679)|cytoplasm (GO:0005737)|endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alpha-2A adrenergic receptor binding (GO:0031694)|alpha2-adrenergic receptor activity (GO:0004938)|epinephrine binding (GO:0051379)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)			endometrium(2)|kidney(1)|large_intestine(1)|lung(4)	8				UCEC - Uterine corpus endometrioid carcinoma (64;0.163)	Amoxapine(DB00543)|Amphetamine(DB00182)|Apomorphine(DB00714)|Aripiprazole(DB01238)|Asenapine(DB06216)|Bethanidine(DB00217)|Brimonidine(DB00484)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Clonidine(DB00575)|Clozapine(DB00363)|Desipramine(DB01151)|Doxepin(DB01142)|Dronedarone(DB04855)|Droxidopa(DB06262)|Ephedra(DB01363)|Epinephrine(DB00668)|Ergoloid mesylate(DB01049)|Fenoldopam(DB00800)|Iloperidone(DB04946)|Lisuride(DB00589)|Loxapine(DB00408)|Lurasidone(DB08815)|Maprotiline(DB00934)|Mephentermine(DB01365)|Methamphetamine(DB01577)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Norepinephrine(DB00368)|Nortriptyline(DB00540)|Olanzapine(DB00334)|Oxymetazoline(DB00935)|Paliperidone(DB01267)|Pergolide(DB01186)|Phenoxybenzamine(DB00925)|Pramipexole(DB00413)|Quetiapine(DB01224)|Risperidone(DB00734)|Ropinirole(DB00268)|Tizanidine(DB00697)|Tolazoline(DB00797)|Xylometazoline(DB06694)|Yohimbine(DB01392)|Ziprasidone(DB00246)	GGCCTGCCAGGTGCCCGGCCC	0.592																																					p.V414L	Esophageal Squamous(12;454 628 4517 14479)	Atlas-SNP	.											.	ADRA2C	24	.	0			c.G1240C						PASS	.						34.0	40.0	38.0					4																	3769573		2195	4299	6494	SO:0001583	missense	152	exon1			TGCCAGGTGCCCG	AY455666	CCDS47004.1	4p16.3	2013-10-22	2012-05-09		ENSG00000184160	ENSG00000184160		"""GPCR / Class A : Adrenoceptors : alpha"""	283	protein-coding gene	gene with protein product		104250	"""adrenergic, alpha-2C-, receptor"""	ADRA2L2, ADRA2RL2		1849485	Standard	NM_000683		Approved	ADRARL2	uc003ghm.3	P18825	OTTHUMG00000159830	ENST00000330055.5:c.1240G>C	4.37:g.3769573G>C	ENSP00000386069:p.Val414Leu	72.0	0.0	0		77.0	35.0	0.454545	NM_000683	P35369|Q9HB49	Missense_Mutation	SNP	ENST00000330055.5	37	CCDS47004.1	.	.	.	.	.	.	.	.	.	.	G	15.87	2.960398	0.53400	.	.	ENSG00000184160	ENST00000330055	T	0.72394	-0.65	3.66	1.85	0.25348	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.60830	0.2299	L	0.39692	1.235	0.24721	N	0.993141	P	0.38551	0.636	B	0.40602	0.334	T	0.47548	-0.9109	9	0.33940	T	0.23	.	8.0626	0.30642	0.0:0.2357:0.6079:0.1563	.	414	P18825	ADA2C_HUMAN	L	414	ENSP00000386069:V414L	ENSP00000386069:V414L	V	+	1	0	ADRA2C	3739371	0.246000	0.23909	0.999000	0.59377	0.985000	0.73830	0.541000	0.23207	0.202000	0.20498	0.603000	0.83216	GTG	.	.	alt		0.592	ADRA2C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357607.1	NM_000683	
PRPF18	8559	hgsc.bcm.edu	37	10	13642257	13642257	+	Missense_Mutation	SNP	A	A	G	rs142307573	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:13642257A>G	ENST00000378572.3	+	3	318	c.158A>G	c.(157-159)gAg>gGg	p.E53G		NM_003675.3	NP_003666.1	Q99633	PRP18_HUMAN	pre-mRNA processing factor 18	53					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						CAGCCAAAAGAGGAGGACCAG	0.333													A|||	11	0.00219649	0.0	0.0043	5008	,	,		18338	0.0		0.008	False		,,,				2504	0.0				p.E53G		Atlas-SNP	.											.	PRPF18	32	.	0			c.A158G						PASS	.	A	GLY/GLU	0,4406		0,0,2203	93.0	93.0	93.0		158	5.8	1.0	10	dbSNP_134	93	26,8574	15.3+/-51.7	0,26,4274	yes	missense	PRPF18	NM_003675.3	98	0,26,6477	GG,GA,AA		0.3023,0.0,0.1999	benign	53/343	13642257	26,12980	2203	4300	6503	SO:0001583	missense	8559	exon3			CAAAAGAGGAGGA	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.158A>G	10.37:g.13642257A>G	ENSP00000367835:p.Glu53Gly	65.0	0.0	0		53.0	22.0	0.415094	NM_003675	Q5T9P9|Q9BUI9	Missense_Mutation	SNP	ENST00000378572.3	37	CCDS7100.1	5	0.0022893772893772895	0	0.0	1	0.0027624309392265192	0	0.0	4	0.005277044854881266	A	15.59	2.878789	0.51801	0.0	0.003023	ENSG00000165630	ENST00000378572;ENST00000417658;ENST00000320054;ENST00000378544	.	.	.	5.76	5.76	0.90799	.	0.242726	0.48286	D	0.000184	T	0.42245	0.1194	L	0.31207	0.915	0.52501	D	0.999951	B	0.02656	0.0	B	0.04013	0.001	T	0.37709	-0.9694	9	0.23302	T	0.38	-18.2333	14.9492	0.71057	1.0:0.0:0.0:0.0	.	53	Q99633	PRP18_HUMAN	G	53;47;38;47	.	ENSP00000367824:E38G	E	+	2	0	PRPF18	13682263	1.000000	0.71417	0.995000	0.50966	0.978000	0.69477	5.371000	0.66150	2.323000	0.78572	0.528000	0.53228	GAG	A|0.998;G|0.002	0.002	strong		0.333	PRPF18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046879.1		
PHC2	1912	hgsc.bcm.edu	37	1	33820515	33820515	+	Missense_Mutation	SNP	C	C	G			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr1:33820515C>G	ENST00000257118.5	-	7	1369	c.1316G>C	c.(1315-1317)gGc>gCc	p.G439A	PHC2_ENST00000373422.3_Missense_Mutation_p.G44A|PHC2_ENST00000431992.1_Missense_Mutation_p.G410A|PHC2_ENST00000419414.2_Missense_Mutation_p.G439A|PHC2_ENST00000373416.1_5'UTR|RP11-415J8.5_ENST00000432703.1_RNA	NM_198040.2	NP_932157.1	Q8IXK0	PHC2_HUMAN	polyhomeotic homolog 2 (Drosophila)	439					multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	heterochromatin (GO:0000792)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PcG protein complex (GO:0031519)|PRC1 complex (GO:0035102)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(8)|liver(1)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	31		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.211)				GTGGGGCACGCCCTCGGGATG	0.607																																					p.G439A		Atlas-SNP	.											.	PHC2	78	.	0			c.G1316C						PASS	.						75.0	70.0	72.0					1																	33820515		2203	4300	6503	SO:0001583	missense	1912	exon7			GGCACGCCCTCGG	AJ419231	CCDS378.1, CCDS379.1	1p34.3	2013-01-10	2006-09-12	2002-11-15	ENSG00000134686	ENSG00000134686		"""Sterile alpha motif (SAM) domain containing"""	3183	protein-coding gene	gene with protein product		602979	"""early development regulator 2 (homolog of polyhomeotic 2)"", ""polyhomeotic-like 2 (Drosophila)"""	EDR2		9121482, 12384788	Standard	NM_198040		Approved	HPH2	uc001bxg.1	Q8IXK0	OTTHUMG00000004133	ENST00000257118.5:c.1316G>C	1.37:g.33820515C>G	ENSP00000257118:p.Gly439Ala	72.0	0.0	0		98.0	93.0	0.94898	NM_198040	A1L4Q1|A8KA40|D3DPR2|Q2TAL3|Q5T0C1|Q6NUJ6|Q6ZQR1|Q8N306|Q8TAG8|Q96BL4|Q9Y4Y7	Missense_Mutation	SNP	ENST00000257118.5	37	CCDS378.1	.	.	.	.	.	.	.	.	.	.	C	0.732	-0.779508	0.02929	.	.	ENSG00000134686	ENST00000431992;ENST00000257118;ENST00000373422;ENST00000419414	T;T;T;T	0.39997	2.06;1.68;1.05;2.1	5.86	2.88	0.33553	.	0.800952	0.11105	N	0.599163	T	0.29684	0.0741	L	0.56769	1.78	0.54753	D	0.999989	P;P;P	0.40050	0.7;0.7;0.7	B;B;B	0.36092	0.217;0.217;0.217	T	0.36335	-0.9752	10	0.02654	T	1	-2.4586	4.4467	0.11600	0.1605:0.6014:0.1549:0.0832	.	439;410;439	A8KA40;B7ZLY0;Q8IXK0	.;.;PHC2_HUMAN	A	410;439;44;439	ENSP00000389436:G410A;ENSP00000257118:G439A;ENSP00000362521:G44A;ENSP00000391440:G439A	ENSP00000257118:G439A	G	-	2	0	PHC2	33593102	0.989000	0.36119	0.212000	0.23672	0.034000	0.12701	1.042000	0.30303	0.339000	0.23719	0.591000	0.81541	GGC	.	.	none		0.607	PHC2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000011895.1	NM_198040	
NPR2	4882	hgsc.bcm.edu	37	9	35806500	35806500	+	Silent	SNP	C	C	T			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr9:35806500C>T	ENST00000342694.2	+	16	2739	c.2484C>T	c.(2482-2484)cgC>cgT	p.R828R		NM_003995.3	NP_003986.2	P20594	ANPRB_HUMAN	natriuretic peptide receptor 2	828					bone development (GO:0060348)|cell surface receptor signaling pathway (GO:0007166)|cellular response to granulocyte macrophage colony-stimulating factor stimulus (GO:0097011)|cGMP biosynthetic process (GO:0006182)|intracellular signal transduction (GO:0035556)|negative regulation of meiotic cell cycle (GO:0051447)|negative regulation of oocyte maturation (GO:1900194)|ossification (GO:0001503)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|signal transduction (GO:0007165)|single organism reproductive process (GO:0044702)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(14)|ovary(2)|prostate(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	45	all_epithelial(49;0.161)		LUSC - Lung squamous cell carcinoma(32;0.00521)|Lung(28;0.00697)|STAD - Stomach adenocarcinoma(86;0.194)		Erythrityl Tetranitrate(DB01613)|Nesiritide(DB04899)	AGGAAAAACGCAAGGCTGAAG	0.512																																					p.R828R		Atlas-SNP	.											.	NPR2	162	.	0			c.C2484T						PASS	.						119.0	106.0	110.0					9																	35806500		2203	4300	6503	SO:0001819	synonymous_variant	4882	exon16			AAAACGCAAGGCT	AJ005282	CCDS6590.1	9p21-p12	2014-03-03	2014-03-03		ENSG00000159899	ENSG00000159899			7944	protein-coding gene	gene with protein product	"""guanylate cyclase B"""	108961	"""acromesomelic dysplasia, Maroteaux type"", ""atrionatriuretic peptide receptor B"", ""natriuretic peptide receptor B"""	ANPRB, NPRB, AMDM		9634515, 15146390	Standard	XM_005251478		Approved	GUCY2B, ANPb	uc003zyd.3	P20594	OTTHUMG00000019871	ENST00000342694.2:c.2484C>T	9.37:g.35806500C>T		99.0	0.0	0		102.0	54.0	0.529412	NM_003995	B0ZBF2|B0ZBF3|D3DRP3|D3DRP4|O60871|Q4VAK7|Q5TCV2|Q8TA93|Q9UQ50	Silent	SNP	ENST00000342694.2	37	CCDS6590.1	.	.	.	.	.	.	.	.	.	.	C	6.453	0.451797	0.12283	.	.	ENSG00000159899	ENST00000421267	.	.	.	6.17	5.26	0.73747	.	.	.	.	.	T	0.72787	0.3504	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.72561	-0.4256	4	.	.	.	.	16.1789	0.81887	0.0:0.8665:0.1335:0.0	.	.	.	.	V	175	.	.	A	+	2	0	NPR2	35796500	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	1.000000	0.29770	1.587000	0.49959	0.655000	0.94253	GCA	.	.	none		0.512	NPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052345.1		
ZHX2	22882	hgsc.bcm.edu	37	8	123964819	123964819	+	Missense_Mutation	SNP	G	G	A	rs9649951	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	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	121.0	0.0	0		130.0	56.0	0.430769	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	
TRAPPC12	51112	hgsc.bcm.edu	37	2	3392021	3392021	+	Silent	SNP	C	C	T	rs140551015	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:3392021C>T	ENST00000324266.5	+	2	822	c.627C>T	c.(625-627)ttC>ttT	p.F209F	TRAPPC12_ENST00000382110.2_Silent_p.F209F	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	209					vesicle-mediated transport (GO:0016192)												TCAGCACGTTCTTCGGAGACA	0.672													C|||	12	0.00239617	0.0008	0.0014	5008	,	,		7296	0.0		0.0099	False		,,,				2504	0.0				p.F209F		Atlas-SNP	.											.	.	.	.	0			c.C627T						PASS	.	C		16,4390	19.1+/-41.9	0,16,2187	32.0	39.0	37.0		627	-2.8	0.6	2	dbSNP_134	37	122,8478	57.2+/-118.5	0,122,4178	no	coding-synonymous	TTC15	NM_016030.5		0,138,6365	TT,TC,CC		1.4186,0.3631,1.061		209/736	3392021	138,12868	2203	4300	6503	SO:0001819	synonymous_variant	51112	exon2			CACGTTCTTCGGA	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.627C>T	2.37:g.3392021C>T		11.0	0.0	0		58.0	24.0	0.413793	NM_016030	B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	CCDS1652.1																																																																																			C|0.991;T|0.009	0.009	strong		0.672	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
ABCA7	10347	hgsc.bcm.edu	37	19	1054267	1054267	+	Missense_Mutation	SNP	G	G	A	rs534172941		TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:1054267G>A	ENST00000263094.6	+	27	3884	c.3653G>A	c.(3652-3654)cGc>cAc	p.R1218H	ABCA7_ENST00000433129.1_Missense_Mutation_p.R1218H|ABCA7_ENST00000435683.2_Missense_Mutation_p.R1080H	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	1218					apolipoprotein A-I-mediated signaling pathway (GO:0038027)|ATP catabolic process (GO:0006200)|cholesterol efflux (GO:0033344)|high-density lipoprotein particle assembly (GO:0034380)|memory (GO:0007613)|negative regulation of amyloid precursor protein biosynthetic process (GO:0042985)|negative regulation of ATPase activity (GO:0032780)|negative regulation of beta-amyloid formation (GO:1902430)|peptide cross-linking (GO:0018149)|phagocytosis (GO:0006909)|phospholipid efflux (GO:0033700)|phospholipid scrambling (GO:0017121)|positive regulation of ATPase activity (GO:0032781)|positive regulation of beta-amyloid clearance (GO:1900223)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of engulfment of apoptotic cell (GO:1901076)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phospholipid efflux (GO:1902995)|protein localization to nucleus (GO:0034504)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|ATP-binding cassette (ABC) transporter complex (GO:0043190)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|phagocytic cup (GO:0001891)|plasma membrane (GO:0005886)|ruffle membrane (GO:0032587)	apolipoprotein A-I receptor activity (GO:0034188)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|phospholipid transporter activity (GO:0005548)|transporter activity (GO:0005215)			NS(1)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(7)|lung(22)|ovary(1)|pancreas(7)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	65		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;1.04e-05)|all_lung(49;1.53e-05)|Breast(49;9.42e-05)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCACTGACCCGCCAGCAGCTC	0.697													G|||	1	0.000199681	0.0	0.0	5008	,	,		14782	0.0		0.0	False		,,,				2504	0.001				p.R1218H		Atlas-SNP	.											.	ABCA7	174	.	0			c.G3653A						PASS	.						12.0	16.0	15.0					19																	1054267		2185	4270	6455	SO:0001583	missense	10347	exon27			TGACCCGCCAGCA	AF328787	CCDS12055.1	19p13.3	2012-03-14			ENSG00000064687	ENSG00000064687		"""ATP binding cassette transporters / subfamily A"""	37	protein-coding gene	gene with protein product		605414					Standard	NM_019112		Approved	ABCX	uc002lqw.4	Q8IZY2	OTTHUMG00000167547	ENST00000263094.6:c.3653G>A	19.37:g.1054267G>A	ENSP00000263094:p.Arg1218His	26.0	0.0	0		25.0	13.0	0.52	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	g	11.52	1.664688	0.29604	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	D;D	0.86865	-2.18;-2.18	3.54	-5.43	0.02632	.	.	.	.	.	T	0.74068	0.3668	L	0.42529	1.33	0.09310	N	1	B;B	0.24426	0.103;0.007	B;B	0.23852	0.049;0.004	T	0.59958	-0.7356	9	0.17369	T	0.5	.	0.5118	0.00597	0.3927:0.134:0.2029:0.2704	.	1080;1218	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	H	1218	ENSP00000263094:R1218H;ENSP00000414062:R1218H	ENSP00000263094:R1218H	R	+	2	0	ABCA7	1005267	0.000000	0.05858	0.002000	0.10522	0.778000	0.44026	-1.209000	0.03002	-1.417000	0.02017	-0.649000	0.03915	CGC	.	.	none		0.697	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
LETM1	3954	hgsc.bcm.edu	37	4	1824020	1824020	+	Missense_Mutation	SNP	C	C	T	rs28681468	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:1824020C>T	ENST00000302787.2	-	10	1792	c.1496G>A	c.(1495-1497)cGt>cAt	p.R499H		NM_012318.2	NP_036450.1	O95202	LETM1_HUMAN	leucine zipper-EF-hand containing transmembrane protein 1	499					cristae formation (GO:0042407)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)			breast(3)|central_nervous_system(2)|large_intestine(3)|lung(3)|prostate(1)|urinary_tract(1)	13			all cancers(2;0.00756)|OV - Ovarian serous cystadenocarcinoma(23;0.00989)|Epithelial(3;0.0141)			AGCTACCACACGTTCGGGCTC	0.592													c|||	59	0.0117812	0.0091	0.0173	5008	,	,		18177	0.0		0.0268	False		,,,				2504	0.0082				p.R499H		Atlas-SNP	.											.	LETM1	48	.	0			c.G1496A						PASS	.	C	HIS/ARG	52,4354	50.9+/-86.3	0,52,2151	59.0	53.0	55.0		1496	-0.7	0.0	4	dbSNP_125	55	266,8334	102.3+/-163.5	3,260,4037	yes	missense	LETM1	NM_012318.2	29	3,312,6188	TT,TC,CC		3.093,1.1802,2.445	benign	499/740	1824020	318,12688	2203	4300	6503	SO:0001583	missense	3954	exon10			ACCACACGTTCGG	AF061025	CCDS3355.1	4p16.3	2013-01-10			ENSG00000168924	ENSG00000168924		"""EF-hand domain containing"""	6556	protein-coding gene	gene with protein product	"""Mdm38 homolog (yeast)"""	604407				10486213	Standard	NM_012318		Approved		uc003gdv.3	O95202	OTTHUMG00000121149	ENST00000302787.2:c.1496G>A	4.37:g.1824020C>T	ENSP00000305653:p.Arg499His	129.0	0.0	0		110.0	53.0	0.481818	NM_012318	B4DED2|Q9UF65	Missense_Mutation	SNP	ENST00000302787.2	37	CCDS3355.1	24	0.01098901098901099	2	0.0040650406504065045	5	0.013812154696132596	0	0.0	17	0.022427440633245383	C	11.17	1.560042	0.27827	0.011802	0.03093	ENSG00000168924	ENST00000302787	.	.	.	4.65	-0.707	0.11245	.	0.970810	0.08436	N	0.946208	T	0.05456	0.0144	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.18745	-1.0327	9	0.45353	T	0.12	-2.8575	3.2806	0.06913	0.6202:0.1675:0.0962:0.1161	rs28681468;rs28681468	499	O95202	LETM1_HUMAN	H	499	.	ENSP00000305653:R499H	R	-	2	0	LETM1	1793818	0.001000	0.12720	0.002000	0.10522	0.002000	0.02628	0.573000	0.23699	-0.059000	0.13154	0.456000	0.33151	CGT	C|0.980;T|0.020	0.020	strong		0.592	LETM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241634.1		
LOXHD1	125336	hgsc.bcm.edu	37	18	44157764	44157764	+	Missense_Mutation	SNP	C	C	A	rs34589386	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr18:44157764C>A	ENST00000398722.4	-	7	1041	c.1042G>T	c.(1042-1044)Ggc>Tgc	p.G348C	LOXHD1_ENST00000536736.1_Missense_Mutation_p.G626C|LOXHD1_ENST00000441551.2_Missense_Mutation_p.G626C			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	348	PLAT 3. {ECO:0000255|PROSITE- ProRule:PRU00152}.		G -> C (in dbSNP:rs34589386).		calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|sensory perception of sound (GO:0007605)	membrane (GO:0016020)|stereocilium (GO:0032420)	calcium channel activity (GO:0005262)			NS(3)|autonomic_ganglia(1)|breast(4)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(2)|pancreas(1)|prostate(4)|skin(4)|stomach(1)	36						GAGCCTTTGCCATCGTGTCTG	0.582													C|||	64	0.0127796	0.0121	0.0144	5008	,	,		19545	0.0		0.0129	False		,,,				2504	0.0256				p.G626C		Atlas-SNP	.											.	LOXHD1	367	.	0			c.G1876T						PASS	.	C	CYS/GLY	21,1363		0,21,671	51.0	61.0	58.0		1876	5.7	1.0	18	dbSNP_126	58	45,3137		0,45,1546	yes	missense	LOXHD1	NM_144612.6	159	0,66,2217	AA,AC,CC		1.4142,1.5173,1.4455	probably-damaging	626/2212	44157764	66,4500	692	1591	2283	SO:0001583	missense	125336	exon14			CTTTGCCATCGTG	AK057232	CCDS45861.1, CCDS45862.1, CCDS54184.1	18q21.1	2009-09-11			ENSG00000167210	ENSG00000167210			26521	protein-coding gene	gene with protein product		613072	"""deafness, autosomal recessive 77"""	DFNB77		19732867	Standard	NM_144612		Approved	FLJ32670, LH2D1	uc010xcw.1	Q8IVV2	OTTHUMG00000132644	ENST00000398722.4:c.1042G>T	18.37:g.44157764C>A	ENSP00000381707:p.Gly348Cys	76.0	0.0	0		73.0	39.0	0.534247	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		29|29	0.013278388278388278|0.013278388278388278	13|13	0.026422764227642278|0.026422764227642278	5|5	0.013812154696132596|0.013812154696132596	0|0	0.0|0.0	11|11	0.014511873350923483|0.014511873350923483	C|C	16.20|16.20	3.055236|3.055236	0.55325|0.55325	0.015173|0.015173	0.014142|0.014142	ENSG00000167210|ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000335730|ENST00000441551	T;T|.	0.25414|.	1.8;1.8|.	5.66|5.66	5.66|5.66	0.87406|0.87406	.|.	0.162693|.	0.53938|.	D|.	0.000050|.	T|T	0.70518|0.70518	0.3233|0.3233	M|M	0.89840|0.89840	3.065|3.065	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.97110|.	1.0;1.0|.	T|T	0.82157|0.82157	-0.0596|-0.0596	10|5	0.66056|.	D|.	0.02|.	.|.	19.7398|19.7398	0.96223|0.96223	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs34589386|rs34589386	626;348|.	F5GZB4;Q8IVV2-2|.	.;.|.	C|L	348;626;348|606	ENSP00000381707:G348C;ENSP00000444586:G626C|.	ENSP00000338222:G348C|.	G|W	-|-	1|2	0|0	LOXHD1|LOXHD1	42411762|42411762	1.000000|1.000000	0.71417|0.71417	0.964000|0.964000	0.40570|0.40570	0.900000|0.900000	0.52787|0.52787	7.701000|7.701000	0.84566|0.84566	2.665000|2.665000	0.90641|0.90641	0.561000|0.561000	0.74099|0.74099	GGC|TGG	C|0.983;A|0.017	0.017	strong		0.582	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
HIST1H1B	3009	hgsc.bcm.edu	37	6	27835055	27835055	+	Silent	SNP	G	G	A	rs116008322	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr6:27835055G>A	ENST00000331442.3	-	1	304	c.253C>T	c.(253-255)Ctg>Ttg	p.L85L		NM_005322.2	NP_005313.1	P16401	H15_HUMAN	histone cluster 1, H1b	85	H15. {ECO:0000255|PROSITE- ProRule:PRU00837}.				chromatin organization (GO:0006325)|establishment of protein localization to chromatin (GO:0071169)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nucleosome assembly (GO:0006334)|positive regulation of cell growth (GO:0030307)|positive regulation of histone H3-K9 methylation (GO:0051574)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|nuclear chromatin (GO:0000790)|nuclear heterochromatin (GO:0005720)|nucleosome (GO:0000786)	chromatin DNA binding (GO:0031490)|histone deacetylase binding (GO:0042826)|poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(12)|prostate(2)|upper_aerodigestive_tract(2)	24						TTGAGGCCCAGCTTAATGCGG	0.577													G|||	45	0.00898562	0.0038	0.0101	5008	,	,		16701	0.004		0.0278	False		,,,				2504	0.001				p.L85L		Atlas-SNP	.											.	HIST1H1B	54	.	0			c.C253T						PASS	.	G		40,4366	43.8+/-77.6	0,40,2163	124.0	135.0	131.0		253	3.7	1.0	6	dbSNP_132	131	238,8362	96.6+/-158.3	4,230,4066	no	coding-synonymous	HIST1H1B	NM_005322.2		4,270,6229	AA,AG,GG		2.7674,0.9079,2.1375		85/227	27835055	278,12728	2203	4300	6503	SO:0001819	synonymous_variant	3009	exon1			GGCCCAGCTTAAT	AF531304	CCDS4635.1	6p22.1	2012-05-04	2006-10-11	2003-02-14	ENSG00000184357	ENSG00000184357		"""Histones / Replication-dependent"""	4719	protein-coding gene	gene with protein product		142711	"""H1 histone family, member 5"", ""histone 1, H1b"""	H1F5		9031620, 9119399, 12408966	Standard	NM_005322		Approved	H1.5, H1b, H1s-3	uc003njx.3	P16401	OTTHUMG00000016139	ENST00000331442.3:c.253C>T	6.37:g.27835055G>A		152.0	0.0	0		157.0	82.0	0.522293	NM_005322	Q14529|Q3MJ42	Silent	SNP	ENST00000331442.3	37	CCDS4635.1																																																																																			G|0.982;A|0.018	0.018	strong		0.577	HIST1H1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043371.1	NM_005322	
CFAP46	54777	hgsc.bcm.edu	37	10	134671148	134671148	+	Missense_Mutation	SNP	C	C	T	rs144154094	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr10:134671148C>T	ENST00000368586.5	-	39	5620	c.5520G>A	c.(5518-5520)atG>atA	p.M1840I	TTC40_ENST00000263170.5_Start_Codon_SNP_p.M1I	NM_001200049.2	NP_001186978.2														breast(1)|endometrium(5)|lung(19)|urinary_tract(3)	28						CTTCCTCAGCCATGGCGCCCT	0.592													C|||	46	0.0091853	0.0	0.0072	5008	,	,		16347	0.002		0.0129	False		,,,				2504	0.0266				p.M1840I		Atlas-SNP	.											.	TTC40	100	.	0			c.G5520A						PASS	.	C	ILE/MET	5,4401	6.2+/-15.9	0,5,2198	140.0	92.0	108.0		456	-0.1	0.0	10	dbSNP_134	108	58,8542	21.0+/-64.5	0,58,4242	yes	missense	C10orf92	NM_001200049.1	10	0,63,6440	TT,TC,CC		0.6744,0.1135,0.4844	benign	152/1028	134671148	63,12943	2203	4300	6503	SO:0001583	missense	54777	exon39			CTCAGCCATGGCG																												ENST00000368586.5:c.5520G>A	10.37:g.134671148C>T	ENSP00000357575:p.Met1840Ile	127.0	0.0	0		123.0	55.0	0.447154	NM_001200049		Missense_Mutation	SNP	ENST00000368586.5	37	CCDS58101.1	38	0.0173992673992674	8	0.016260162601626018	6	0.016574585635359115	7	0.012237762237762238	17	0.022427440633245383	C	4.658	0.122270	0.08931	0.001135	0.006744	ENSG00000171811	ENST00000368586;ENST00000263170	T;T	0.12465	3.01;2.68	0.924	-0.142	0.13448	.	.	.	.	.	T	0.02342	0.0072	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42103	-0.9471	9	0.23302	T	0.38	.	3.2464	0.06798	0.0:0.6673:0.0:0.3327	.	1	Q8IYW2	CJ092_HUMAN	I	1840;1	ENSP00000357575:M1840I;ENSP00000263170:M1I	ENSP00000263170:M1I	M	-	3	0	C10orf93	134521138	0.031000	0.19500	0.005000	0.12908	0.041000	0.13682	-0.661000	0.05311	-0.024000	0.13941	0.064000	0.15345	ATG	C|0.988;T|0.012	0.012	strong		0.592	TTC40-001	PUTATIVE	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000051095.3		
SNX25	83891	hgsc.bcm.edu	37	4	186283092	186283092	+	Missense_Mutation	SNP	C	C	T	rs34120554	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr4:186283092C>T	ENST00000504273.1	+	17	2468	c.2174C>T	c.(2173-2175)aCa>aTa	p.T725I	SNX25_ENST00000512853.1_3'UTR|SNX25_ENST00000264694.8_Missense_Mutation_p.T725I			Q9H3E2	SNX25_HUMAN	sorting nexin 25	725			T -> I (in dbSNP:rs34120554).		negative regulation of pathway-restricted SMAD protein phosphorylation (GO:0060394)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|protein transport (GO:0015031)|receptor catabolic process (GO:0032801)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	endosome (GO:0005768)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			NS(1)|breast(4)|endometrium(2)|kidney(4)|large_intestine(8)|lung(13)|ovary(2)|pancreas(2)|prostate(2)|urinary_tract(2)	40		all_lung(41;1.03e-13)|Lung NSC(41;2.5e-13)|Hepatocellular(41;0.00826)|Colorectal(36;0.00886)|Renal(120;0.00988)|Prostate(90;0.0235)|all_hematologic(60;0.0592)|all_neural(102;0.243)		all cancers(43;2.13e-24)|Epithelial(43;6.15e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.6e-11)|BRCA - Breast invasive adenocarcinoma(30;0.00013)|Colorectal(24;0.000165)|GBM - Glioblastoma multiforme(59;0.000357)|COAD - Colon adenocarcinoma(29;0.000887)|STAD - Stomach adenocarcinoma(60;0.00118)|LUSC - Lung squamous cell carcinoma(40;0.0129)|READ - Rectum adenocarcinoma(43;0.228)		ATCCGGGACACAGTCAGCTGG	0.383													C|||	17	0.00339457	0.0008	0.0058	5008	,	,		15815	0.0		0.0099	False		,,,				2504	0.002				p.T725I		Atlas-SNP	.											.	SNX25	100	.	0			c.C2174T						PASS	.	C	ILE/THR	9,4397	16.8+/-37.8	0,9,2194	83.0	86.0	85.0		2174	4.3	1.0	4	dbSNP_126	85	105,8495	57.2+/-118.5	0,105,4195	yes	missense	SNX25	NM_031953.2	89	0,114,6389	TT,TC,CC		1.2209,0.2043,0.8765	probably-damaging	725/841	186283092	114,12892	2203	4300	6503	SO:0001583	missense	83891	exon17			GGGACACAGTCAG	AF113223	CCDS34116.1	4q35.1	2011-05-03			ENSG00000109762	ENSG00000109762		"""Sorting nexins"""	21883	protein-coding gene	gene with protein product						12461558	Standard	NM_031953		Approved	SBBI31	uc003ixh.3	Q9H3E2	OTTHUMG00000160475	ENST00000504273.1:c.2174C>T	4.37:g.186283092C>T	ENSP00000426255:p.Thr725Ile	47.0	0.0	0		30.0	13.0	0.433333	NM_031953	Q3ZT30|Q8N6K3	Missense_Mutation	SNP	ENST00000504273.1	37	CCDS34116.1	11	0.005036630036630037	0	0.0	2	0.0055248618784530384	0	0.0	9	0.011873350923482849	C	21.1	4.091462	0.76756	0.002043	0.012209	ENSG00000109762	ENST00000504273;ENST00000264694;ENST00000264693	T;T	0.30714	1.52;1.52	5.15	4.3	0.51218	Sorting nexin, C-terminal (1);	0.053228	0.85682	D	0.000000	T	0.35335	0.0928	L	0.41573	1.285	0.50313	D	0.99986	D;P;D	0.89917	0.999;0.728;1.0	D;B;D	0.91635	0.995;0.299;0.999	T	0.09818	-1.0657	10	0.21540	T	0.41	-3.1783	13.6912	0.62547	0.0:0.9249:0.0:0.0751	rs34120554	441;258;725	Q8N6K3;Q9H5Q8;Q9H3E2	.;.;SNX25_HUMAN	I	725;725;258	ENSP00000426255:T725I;ENSP00000264694:T725I	ENSP00000264693:T258I	T	+	2	0	SNX25	186520086	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.732000	0.68563	1.300000	0.44818	0.542000	0.68232	ACA	C|0.993;T|0.007	0.007	strong		0.383	SNX25-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360756.1	NM_031953	
ACAD11	84129	hgsc.bcm.edu	37	3	132337477	132337477	+	Splice_Site	SNP	C	C	A	rs41272317	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr3:132337477C>A	ENST00000264990.6	-	11	2386		c.e11+1		ACAD11_ENST00000545291.1_Intron|ACAD11_ENST00000481970.2_Missense_Mutation_p.G472V|ACAD11_ENST00000355458.3_Splice_Site	NM_032169.4	NP_115545	Q709F0	ACD11_HUMAN	acyl-CoA dehydrogenase family, member 11						fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)	mitochondrial membrane (GO:0031966)|nucleus (GO:0005634)|peroxisome (GO:0005777)	flavin adenine dinucleotide binding (GO:0050660)|long-chain-acyl-CoA dehydrogenase activity (GO:0004466)|medium-chain-acyl-CoA dehydrogenase activity (GO:0070991)|transferase activity, transferring phosphorus-containing groups (GO:0016772)|very-long-chain-acyl-CoA dehydrogenase activity (GO:0017099)	p.?(1)		breast(2)|endometrium(6)|kidney(2)|large_intestine(8)|lung(10)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(1)	36						AATGTAGTAACCTGGTGCTTG	0.338													C|||	212	0.0423323	0.0333	0.0029	5008	,	,		15862	0.0704		0.0159	False		,,,				2504	0.0808				.		Atlas-SNP	.											ACAD11,NS,carcinoma,0,1	ACAD11	78	1	1	Unknown(1)	stomach(1)	c.1414+1G>T						scavenged	.	C		114,4292	76.2+/-114.5	1,112,2090	65.0	66.0	66.0			5.5	1.0	3	dbSNP_127	66	133,8465	63.9+/-126.0	1,131,4167	yes	splice-5	ACAD11	NM_032169.4		2,243,6257	AA,AC,CC		1.5469,2.5874,1.8994			132337477	247,12757	2203	4299	6502	SO:0001630	splice_region_variant	84129	exon12			TAGTAACCTGGTG	BC019607	CCDS3074.1	3q22.1	2010-04-30	2010-04-30		ENSG00000240303	ENSG00000240303			30211	protein-coding gene	gene with protein product		614288	"""acyl-Coenzyme A dehydrogenase family, member 11"""				Standard	NM_032169		Approved	FLJ12592		Q709F0	OTTHUMG00000159780	ENST00000264990.6:c.1414+1G>T	3.37:g.132337477C>A		136.0	2.0	0.0147059		153.0	66.0	0.431373	NM_032169	Q08AF0|Q658N9|Q658Y2|Q6ZND2|Q8WUT6|Q9H9R3	Splice_Site	SNP	ENST00000264990.6	37	CCDS3074.1	78|78	0.03571428571428571|0.03571428571428571	22|22	0.044715447154471545|0.044715447154471545	2|2	0.0055248618784530384|0.0055248618784530384	42|42	0.07342657342657342|0.07342657342657342	12|12	0.0158311345646438|0.0158311345646438	C|C	18.10|18.10	3.548345|3.548345	0.65311|0.65311	0.025874|0.025874	0.015469|0.015469	ENSG00000240303|ENSG00000240303	ENST00000355458;ENST00000264990|ENST00000481970	.|T	.|0.22134	.|1.97	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	.|.	.|.	.|.	.|.	.|T	.|0.06872	.|0.0175	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.91635	.|0.999	.|T	.|0.03473	.|-1.1033	.|8	.|0.87932	.|D	.|0	.|.	19.3995|19.3995	0.94621|0.94621	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	rs41272317|rs41272317	.|472	.|D6RDI8	.|.	.|V	-1|472	.|ENSP00000420907:G472V	.|ENSP00000420907:G472V	.|G	-|-	.|2	.|0	ACAD11|ACAD11	133820167|133820167	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.712000|0.712000	0.41017|0.41017	7.426000|7.426000	0.80270|0.80270	2.754000|2.754000	0.94517|0.94517	0.650000|0.650000	0.86243|0.86243	.|GGT	A|0.027;C|0.973;T|0.000	0.027	strong		0.338	ACAD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357279.2	NM_032169	Intron
WIPI2	26100	hgsc.bcm.edu	37	7	5257639	5257639	+	Silent	SNP	G	G	A	rs147063855	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:5257639G>A	ENST00000288828.4	+	7	895	c.663G>A	c.(661-663)tcG>tcA	p.S221S	WIPI2_ENST00000404704.3_Silent_p.S221S|WIPI2_ENST00000382384.2_Silent_p.S203S|WIPI2_ENST00000401525.3_Silent_p.S203S|WIPI2_ENST00000484262.1_Silent_p.S162S	NM_001033518.1|NM_001278299.1|NM_015610.3	NP_001028690.1|NP_001265228.1|NP_056425.1	Q9Y4P8	WIPI2_HUMAN	WD repeat domain, phosphoinositide interacting 2	221					autophagic vacuole assembly (GO:0000045)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|protein complex (GO:0043234)	phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)			NS(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)	16		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0925)|OV - Ovarian serous cystadenocarcinoma(56;2.59e-14)		CCACGGCTTCGGAGAAGGTGA	0.537																																					p.S221S		Atlas-SNP	.											WIPI2,NS,carcinoma,+1,1	WIPI2	41	1	0			c.G663A						PASS	.	G	,,,,	0,4406		0,0,2203	125.0	116.0	119.0		663,609,486,663,609	-11.6	0.1	7	dbSNP_134	119	15,8585	11.2+/-40.8	0,15,4285	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	WIPI2	NM_001033518.1,NM_001033519.1,NM_001033520.1,NM_015610.3,NM_016003.3	,,,,	0,15,6488	AA,AG,GG		0.1744,0.0,0.1153	,,,,	221/444,203/426,162/385,221/455,203/437	5257639	15,12991	2203	4300	6503	SO:0001819	synonymous_variant	26100	exon7			GGCTTCGGAGAAG		CCDS5339.1, CCDS34593.1, CCDS47531.1, CCDS47532.1, CCDS47533.1	7p22.1	2014-02-12			ENSG00000157954	ENSG00000157954		"""WD repeat domain containing"""	32225	protein-coding gene	gene with protein product		609225				15602573	Standard	NM_001278299		Approved	Atg21, CGI-50, FLJ12979, FLJ14217, FLJ42984, DKFZP434J154, DKFZp686P02188, ATG18B	uc003snv.3	Q9Y4P8	OTTHUMG00000121179	ENST00000288828.4:c.663G>A	7.37:g.5257639G>A		130.0	0.0	0		171.0	84.0	0.491228	NM_015610	B3KNC2|Q5MNZ8|Q6FI96|Q75L50|Q96IE4|Q9Y364	Silent	SNP	ENST00000288828.4	37	CCDS5339.1																																																																																			G|0.999;A|0.001	0.001	strong		0.537	WIPI2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241669.2	NM_015610	
TTN	7273	hgsc.bcm.edu	37	2	179447755	179447755	+	Silent	SNP	G	G	A	rs72646867	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:179447755G>A	ENST00000591111.1	-	263	61076	c.60852C>T	c.(60850-60852)agC>agT	p.S20284S	TTN_ENST00000589042.1_Silent_p.S21925S|TTN_ENST00000342992.6_Silent_p.S19357S|TTN-AS1_ENST00000456053.1_RNA|RP11-171I2.2_ENST00000603521.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Silent_p.S13052S|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000590743.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000589907.1_RNA|TTN-AS1_ENST00000590932.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000438095.1_RNA|TTN_ENST00000359218.5_Silent_p.S12985S|TTN_ENST00000460472.2_Silent_p.S12860S|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000586452.1_RNA			Q8WZ42	TITIN_HUMAN	titin	20284	Ig-like 111.				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)			TCCGGTTCACGCTGAATAGCT	0.428													G|||	8	0.00159744	0.0	0.0014	5008	,	,		18214	0.0		0.003	False		,,,				2504	0.0041				p.S21925S		Atlas-SNP	.											.	TTN	18412	.	0			c.C65775T						PASS	.	G	,,,	1,3963		0,1,1981	89.0	87.0	87.0		38580,58071,38955,39156	-10.5	0.7	2	dbSNP_130	87	14,8306		0,14,4146	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	TTN	NM_003319.4,NM_133378.4,NM_133432.3,NM_133437.3	,,,	0,15,6127	AA,AG,GG		0.1683,0.0252,0.1221	,,,	12860/26927,19357/33424,12985/27052,13052/27119	179447755	15,12269	1982	4160	6142	SO:0001819	synonymous_variant	7273	exon313			GTTCACGCTGAAT	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.60852C>T	2.37:g.179447755G>A		159.0	0.0	0		187.0	84.0	0.449198	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	Silent	SNP	ENST00000591111.1	37																																																																																				G|0.999;A|0.001	0.001	weak		0.428	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
SPATC1	375686	hgsc.bcm.edu	37	8	145095328	145095328	+	Missense_Mutation	SNP	T	T	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr8:145095328T>A	ENST00000377470.3	+	2	832	c.730T>A	c.(730-732)Tcc>Acc	p.S244T	SPATC1_ENST00000447830.2_Missense_Mutation_p.S244T	NM_198572.2	NP_940974.2	Q76KD6	SPERI_HUMAN	spermatogenesis and centriole associated 1	244						centrosome (GO:0005813)|cytoplasm (GO:0005737)				NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	15	all_cancers(97;8.2e-11)|all_epithelial(106;1.1e-09)|Lung NSC(106;5.89e-05)|all_lung(105;0.000174)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		OV - Ovarian serous cystadenocarcinoma(54;6.79e-41)|Epithelial(56;1.02e-39)|all cancers(56;3.67e-35)|Colorectal(110;0.055)|BRCA - Breast invasive adenocarcinoma(115;0.105)			TGGGCCCCAGTCCCCAGCTTG	0.677																																					p.S244T		Atlas-SNP	.											.	SPATC1	77	.	0			c.T730A						PASS	.						14.0	16.0	16.0					8																	145095328		2198	4293	6491	SO:0001583	missense	375686	exon2			CCCCAGTCCCCAG	BC053547	CCDS6413.2, CCDS47937.1	8q24.3	2005-01-11			ENSG00000186583	ENSG00000186583			30510	protein-coding gene	gene with protein product		610874				15280373	Standard	NM_198572		Approved	MGC61633, SPATA15, SPERIOLIN	uc011lkw.2	Q76KD6	OTTHUMG00000156976	ENST00000377470.3:c.730T>A	8.37:g.145095328T>A	ENSP00000366690:p.Ser244Thr	69.0	0.0	0		90.0	53.0	0.588889	NM_001134374	B4DWW9|Q5U5I8|Q7Z6L7	Missense_Mutation	SNP	ENST00000377470.3	37	CCDS6413.2	.	.	.	.	.	.	.	.	.	.	T	5.096	0.203364	0.09704	.	.	ENSG00000186583	ENST00000377470;ENST00000447830	T	0.44083	0.93	3.69	-3.7	0.04437	.	1.671390	0.03864	N	0.274514	T	0.23094	0.0558	L	0.36672	1.1	0.09310	N	1	B;B	0.14012	0.009;0.003	B;B	0.16289	0.015;0.006	T	0.16541	-1.0399	10	0.02654	T	1	-2.9873	0.8322	0.01132	0.172:0.1768:0.344:0.3072	.	244;244	B4DWW9;Q76KD6	.;SPERI_HUMAN	T	244	ENSP00000366690:S244T	ENSP00000366690:S244T	S	+	1	0	SPATC1	145167316	0.000000	0.05858	0.000000	0.03702	0.028000	0.11728	-1.964000	0.01512	-0.526000	0.06383	0.260000	0.18958	TCC	.	.	none		0.677	SPATC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000346926.1	NM_198572	
POU4F3	5459	hgsc.bcm.edu	37	5	145719368	145719368	+	Silent	SNP	G	G	A	rs113137300	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr5:145719368G>A	ENST00000230732.4	+	2	467	c.378G>A	c.(376-378)acG>acA	p.T126T	CTC-359M8.1_ENST00000515598.1_RNA	NM_002700.2	NP_002691.1	Q15319	PO4F3_HUMAN	POU class 4 homeobox 3	126					auditory receptor cell differentiation (GO:0042491)|axon extension (GO:0048675)|inner ear morphogenesis (GO:0042472)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|retinal ganglion cell axon guidance (GO:0031290)|sensory perception of sound (GO:0007605)|vestibulocochlear nerve development (GO:0021562)|visual perception (GO:0007601)	nucleus (GO:0005634)	RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|endometrium(4)|kidney(1)|large_intestine(6)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	17			KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			TCTCGCCCACGCTGAGTGTGA	0.687													G|||	14	0.00279553	0.0091	0.0029	5008	,	,		13001	0.0		0.0	False		,,,				2504	0.0				p.T126T		Atlas-SNP	.											.	POU4F3	47	.	0			c.G378A						PASS	.	G		34,4372	39.2+/-71.8	0,34,2169	76.0	71.0	73.0		378	1.8	1.0	5	dbSNP_132	73	0,8598		0,0,4299	no	coding-synonymous	POU4F3	NM_002700.2		0,34,6468	AA,AG,GG		0.0,0.7717,0.2615		126/339	145719368	34,12970	2203	4299	6502	SO:0001819	synonymous_variant	5459	exon2			GCCCACGCTGAGT	U10060	CCDS4281.1	5q32	2011-06-20	2007-07-13		ENSG00000091010	ENSG00000091010		"""Homeoboxes / POU class"""	9220	protein-coding gene	gene with protein product		602460	"""POU domain class 4, transcription factor 3"""	DFNA15		9506947	Standard	NM_002700		Approved	BRN3C	uc003loa.2	Q15319	OTTHUMG00000129684	ENST00000230732.4:c.378G>A	5.37:g.145719368G>A		44.0	0.0	0		59.0	29.0	0.491525	NM_002700	O60557|Q2M3F8	Silent	SNP	ENST00000230732.4	37	CCDS4281.1																																																																																			G|0.997;A|0.003	0.003	strong		0.687	POU4F3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251887.2	NM_002700	
CCDC74A	90557	hgsc.bcm.edu	37	2	132290912	132290912	+	Missense_Mutation	SNP	G	G	A	rs140033985	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr2:132290912G>A	ENST00000295171.6	+	8	1216	c.1078G>A	c.(1078-1080)Gag>Aag	p.E360K	CCDC74A_ENST00000409856.3_Missense_Mutation_p.E294K|CCDC74A_ENST00000467992.2_3'UTR	NM_001258304.1|NM_001258305.1|NM_138770.2	NP_001245233.1|NP_001245234.1|NP_620125.1	Q96AQ1	CC74A_HUMAN	coiled-coil domain containing 74A	360										endometrium(4)|large_intestine(3)|lung(9)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	19						CAACTTTGCCGAGAGGCAGAA	0.632													g|||	28	0.00559105	0.0	0.0058	5008	,	,		18487	0.0		0.0179	False		,,,				2504	0.0061				p.E360K		Atlas-SNP	.											.	CCDC74A	44	.	0			c.G1078A						PASS	.	G	LYS/GLU	11,4395		0,11,2192	44.0	42.0	43.0		1078	3.1	0.8	2	dbSNP_134	43	139,8455		2,135,4160	no	missense	CCDC74A	NM_138770.1	56	2,146,6352	AA,AG,GG		1.6174,0.2497,1.1538	probably-damaging	360/379	132290912	150,12850	2203	4297	6500	SO:0001583	missense	90557	exon8			TTTGCCGAGAGGC		CCDS2167.1, CCDS58732.1, CCDS74578.1	2q21.1	2008-02-05		2006-02-16	ENSG00000163040	ENSG00000163040			25197	protein-coding gene	gene with protein product						12477932	Standard	NM_138770		Approved	FLJ40345	uc002ttb.4	Q96AQ1	OTTHUMG00000131667	ENST00000295171.6:c.1078G>A	2.37:g.132290912G>A	ENSP00000295171:p.Glu360Lys	272.0	1.0	0.00367647		255.0	118.0	0.462745	NM_138770	Q6P4I5	Missense_Mutation	SNP	ENST00000295171.6	37	CCDS2167.1	16	0.007326007326007326	0	0.0	3	0.008287292817679558	0	0.0	13	0.017150395778364115	.	15.00	2.701859	0.48307	0.002497	0.016174	ENSG00000163040	ENST00000295171;ENST00000409856	T;T	0.36878	1.23;1.23	3.07	3.07	0.35406	.	0.000000	0.33235	U	0.005125	T	0.36248	0.0960	M	0.69823	2.125	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.925	T	0.46775	-0.9167	10	0.72032	D	0.01	.	6.44	0.21845	0.1445:0.0:0.8555:0.0	.	294;360	Q96AQ1-2;Q96AQ1	.;CC74A_HUMAN	K	360;294	ENSP00000295171:E360K;ENSP00000387009:E294K	ENSP00000295171:E360K	E	+	1	0	CCDC74A	132007382	1.000000	0.71417	0.764000	0.31436	0.199000	0.23934	4.182000	0.58310	1.436000	0.47453	0.430000	0.28490	GAG	G|0.991;A|0.009	0.009	strong		0.632	CCDC74A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254570.2	NM_138770	
RANBP3	8498	hgsc.bcm.edu	37	19	5914470	5914470	+	IGR	SNP	G	G	A	rs143117009	byFrequency	TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr19:5914470G>A	ENST00000340578.6	-	0	3233				AC104532.4_ENST00000591109.1_RNA|CAPS_ENST00000588776.1_Missense_Mutation_p.R104H|AC104532.2_ENST00000588891.1_3'UTR|CAPS_ENST00000222125.5_Missense_Mutation_p.R18H|CAPS_ENST00000452990.2_Missense_Mutation_p.R18H	NM_003624.2|NM_007320.2|NM_007322.2	NP_003615.2|NP_015559.2|NP_015561.1	Q9H6Z4	RANB3_HUMAN	RAN binding protein 3						intracellular transport (GO:0046907)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	R-SMAD binding (GO:0070412)|Ran GTPase binding (GO:0008536)			breast(1)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(3)|upper_aerodigestive_tract(1)	18						TGCCTGTCCCGCGGGGCCTCG	0.672													G|||	17	0.00339457	0.0	0.0029	5008	,	,		15870	0.0		0.0129	False		,,,				2504	0.002				p.R18H		Atlas-SNP	.											.	CAPS	14	.	0			c.G53A						PASS	.	G	HIS/ARG,HIS/ARG	12,4394	19.1+/-41.9	0,12,2191	43.0	47.0	45.0		53,53	5.0	1.0	19	dbSNP_134	45	130,8470	64.6+/-126.8	1,128,4171	yes	missense,missense	CAPS	NM_004058.3,NM_080590.2	29,29	1,140,6362	AA,AG,GG		1.5116,0.2724,1.0918	probably-damaging,probably-damaging	18/190,18/163	5914470	142,12864	2203	4300	6503	SO:0001628	intergenic_variant	828	exon2			TGTCCCGCGGGGC	Y08698	CCDS42477.1, CCDS42478.1, CCDS45935.1, CCDS74268.1	19p13.3	2008-02-05							9850	protein-coding gene	gene with protein product		603327				9637251	Standard	NM_007322		Approved		uc002mdw.3	Q9H6Z4			19.37:g.5914470G>A		112.0	0.0	0		104.0	52.0	0.5	NM_080590	B2RAT8|O60405|O75759|O75760|Q9BT47|Q9UG74	Missense_Mutation	SNP	ENST00000340578.6	37	CCDS42478.1	13	0.005952380952380952	0	0.0	2	0.0055248618784530384	0	0.0	11	0.014511873350923483	G	25.1	4.602108	0.87055	0.002724	0.015116	ENSG00000105519	ENST00000394521;ENST00000222125;ENST00000452990	T;T	0.57273	0.41;0.79	4.98	4.98	0.66077	.	0.000000	0.64402	D	0.000017	T	0.46288	0.1385	M	0.80332	2.49	0.20403	N	0.999902	D;P	0.65815	0.995;0.877	P;B	0.47402	0.546;0.097	T	0.58578	-0.7612	10	0.59425	D	0.04	-10.7081	15.7308	0.77804	0.0:0.0:1.0:0.0	.	151;18	Q8NF12;Q13938	.;CAYP1_HUMAN	H	151;18;18	ENSP00000222125:R18H;ENSP00000403263:R18H	ENSP00000222125:R18H	R	+	2	0	CAPS	5865470	0.867000	0.29959	0.990000	0.47175	0.760000	0.43138	5.362000	0.66098	2.307000	0.77673	0.561000	0.74099	CGC	G|0.988;A|0.012	0.012	strong		0.672	RANBP3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000452304.1	NM_007322	
ZC3HC1	51530	hgsc.bcm.edu	37	7	129663533	129663533	+	Nonsense_Mutation	SNP	G	G	A			TCGA-G8-6906-01A-11D-2210-10	TCGA-G8-6906-14A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina HiSeq	3d6aae99-3cf5-4e45-b65e-409ed0ddf21b	36d604db-0d58-48bc-af48-e938df529253	g.chr7:129663533G>A	ENST00000358303.4	-	8	1135	c.1051C>T	c.(1051-1053)Cga>Tga	p.R351*	RP11-306G20.1_ENST00000587038.1_RNA|ZC3HC1_ENST00000311873.5_Nonsense_Mutation_p.R330*|ZC3HC1_ENST00000360708.5_Intron|ZC3HC1_ENST00000481503.1_Nonsense_Mutation_p.R308*|RP11-306G20.1_ENST00000480018.1_RNA	NM_016478.3	NP_057562.3	Q86WB0	NIPA_HUMAN	zinc finger, C3HC-type containing 1	351					mitotic nuclear division (GO:0007067)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|protein ubiquitination (GO:0016567)	nuclear membrane (GO:0031965)|nucleus (GO:0005634)	protein kinase binding (GO:0019901)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(6)|large_intestine(10)|lung(2)|prostate(1)|urinary_tract(1)	22	Melanoma(18;0.0435)					CTCCGAGTTCGAGAGACAATG	0.512																																					p.R351X	Melanoma(115;540 1606 16325 28853 48167)	Atlas-SNP	.											ZC3HC1,NS,carcinoma,0,1	ZC3HC1	45	1	0			c.C1051T						PASS	.						67.0	62.0	64.0					7																	129663533		2203	4300	6503	SO:0001587	stop_gained	51530	exon8			GAGTTCGAGAGAC	AF151050	CCDS34753.1, CCDS64767.1, CCDS75659.1	7q32.2	2013-01-17			ENSG00000091732	ENSG00000091732		"""Zinc fingers, C3HC-type"""	29913	protein-coding gene	gene with protein product	"""nuclear interaction partner of ALK"""					11042152	Standard	XM_005250403		Approved	NIPA	uc003vpi.3	Q86WB0	OTTHUMG00000157648	ENST00000358303.4:c.1051C>T	7.37:g.129663533G>A	ENSP00000351052:p.Arg351*	63.0	0.0	0		74.0	27.0	0.364865	NM_016478	A6NH66|Q75MF3|Q75MF4|Q8N330|Q96F75|Q9HA34|Q9NVX4|Q9P0R0	Nonsense_Mutation	SNP	ENST00000358303.4	37	CCDS34753.1	.	.	.	.	.	.	.	.	.	.	G	22.6	4.305782	0.81247	.	.	ENSG00000091732	ENST00000358303;ENST00000311873;ENST00000481503	.	.	.	5.49	3.59	0.41128	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-8.802	12.559	0.56271	0.0:0.0:0.5483:0.4517	.	.	.	.	X	351;330;308	.	ENSP00000309301:R330X	R	-	1	2	ZC3HC1	129450769	0.997000	0.39634	0.999000	0.59377	0.984000	0.73092	2.978000	0.49305	1.297000	0.44761	0.563000	0.77884	CGA	.	.	none		0.512	ZC3HC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349316.1	NM_016478	
