#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
PADI4	23569	hgsc.bcm.edu	37	1	17674521	17674521	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:17674521A>T	ENST00000375448.4	+	10	1159	c.1133A>T	c.(1132-1134)gAg>gTg	p.E378V	AC004824.2_ENST00000602074.1_Intron|PADI4_ENST00000487048.1_3'UTR	NM_012387.2	NP_036519.2	Q9UM07	PADI4_HUMAN	peptidyl arginine deiminase, type IV	378					cellular protein modification process (GO:0006464)|chromatin modification (GO:0016568)|chromatin remodeling (GO:0006338)|histone citrullination (GO:0036414)|histone H3-R26 citrullination (GO:0036413)|innate immune response (GO:0045087)|nucleosome assembly (GO:0006334)|protein citrullination (GO:0018101)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	arginine deiminase activity (GO:0016990)|calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			autonomic_ganglia(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(13)|ovary(2)|skin(2)|urinary_tract(3)	26		Colorectal(325;3.46e-05)|Breast(348;0.000162)|all_lung(284;0.000338)|Lung NSC(340;0.00042)|Renal(390;0.000518)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00537)|BRCA - Breast invasive adenocarcinoma(304;8.54e-06)|COAD - Colon adenocarcinoma(227;1.33e-05)|Kidney(64;0.000223)|KIRC - Kidney renal clear cell carcinoma(64;0.00313)|STAD - Stomach adenocarcinoma(196;0.00707)|READ - Rectum adenocarcinoma(331;0.0689)|Lung(427;0.199)	L-Citrulline(DB00155)	GGCCTGAAGGAGTTTCCCATC	0.567																																					p.E378V		Atlas-SNP	.											.	PADI4	70	.	0			c.A1133T						PASS	.						99.0	89.0	92.0					1																	17674521		2203	4300	6503	SO:0001583	missense	23569	exon10			TGAAGGAGTTTCC	AB017919	CCDS180.1	1p36.13	2014-06-06	2003-02-12		ENSG00000159339	ENSG00000159339	3.5.3.15	"""Peptidyl arginine deiminases"""	18368	protein-coding gene	gene with protein product		605347	"""peptidyl arginine deiminase, type V"""	PADI5		10488123	Standard	NM_012387		Approved	PAD, PDI5, PDI4	uc001baj.2	Q9UM07	OTTHUMG00000002371	ENST00000375448.4:c.1133A>T	chr1.hg19:g.17674521A>T	ENSP00000364597:p.Glu378Val	129.0	0.0	.		83.0	26.0	.	NM_012387	A8K392|B2RBW0|Q5VTZ8|Q70SX4	Missense_Mutation	SNP	ENST00000375448.4	hg19	CCDS180.1	.	.	.	.	.	.	.	.	.	.	-	15.98	2.991445	0.54041	.	.	ENSG00000159339	ENST00000375448	T	0.25414	1.8	4.85	4.85	0.62838	Protein-arginine deiminase, C-terminal (1);	0.357378	0.28883	N	0.013830	T	0.23649	0.0572	N	0.13235	0.315	0.39431	D	0.967088	B;P	0.47191	0.04;0.891	B;P	0.51550	0.091;0.673	T	0.05920	-1.0856	10	0.41790	T	0.15	-11.7468	11.9518	0.52959	1.0:0.0:0.0:0.0	.	378;378	A8K392;Q9UM07	.;PADI4_HUMAN	V	378	ENSP00000364597:E378V	ENSP00000364597:E378V	E	+	2	0	PADI4	17547108	1.000000	0.71417	0.970000	0.41538	0.890000	0.51754	6.131000	0.71670	2.042000	0.60477	0.423000	0.28283	GAG	.	.	.	none		0.567	PADI4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006799.1	NM_012387	
RWDD3	25950	hgsc.bcm.edu	37	1	95710051	95710051	+	Missense_Mutation	SNP	A	A	T	rs138509057		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:95710051A>T	ENST00000370202.4	+	2	446	c.370A>T	c.(370-372)Agt>Tgt	p.S124C	RWDD3_ENST00000263893.6_Missense_Mutation_p.S124C|RWDD3_ENST00000495272.1_3'UTR|RP11-57H12.6_ENST00000604534.1_3'UTR|RP11-57H12.5_ENST00000444665.1_RNA|RWDD3_ENST00000429514.2_Missense_Mutation_p.S109C	NM_001199682.1|NM_015485.4	NP_001186611.1|NP_056300	Q9Y3V2	RWDD3_HUMAN	RWD domain containing 3	124					negative regulation of NF-kappaB transcription factor activity (GO:0032088)|positive regulation of hypoxia-inducible factor-1alpha signaling pathway (GO:1902073)|positive regulation of protein sumoylation (GO:0033235)	cytoplasm (GO:0005737)|nucleus (GO:0005634)		p.S124R(1)		kidney(1)|large_intestine(2)|lung(6)|ovary(1)	10		all_epithelial(167;5.99e-05)|all_lung(203;0.00168)|Lung NSC(277;0.00769)		all cancers(265;0.112)|Epithelial(280;0.229)		TGGCAGTGGCAGTGAAAAGTG	0.438																																					p.S124C		Atlas-SNP	.											RWDD3,rectum,carcinoma,0,1	RWDD3	24	.	1	Substitution - Missense(1)	large_intestine(1)	c.A370T						PASS	.						107.0	102.0	104.0					1																	95710051		1947	4130	6077	SO:0001583	missense	25950	exon2			AGTGGCAGTGAAA	BC010936	CCDS41357.1, CCDS44177.1	1p22.1	2012-12-07			ENSG00000122481	ENSG00000122481			21393	protein-coding gene	gene with protein product		615875				11230166	Standard	NM_015485		Approved	DKFZP566K023	uc009wdu.3	Q9Y3V2	OTTHUMG00000010910	ENST00000370202.4:c.370A>T	chr1.hg19:g.95710051A>T	ENSP00000359221:p.Ser124Cys	133.0	2.0	.		111.0	32.0	.	NM_015485	A6NP44|A8K9F0|C9J9L7|C9JI45|Q08AJ7|Q6FID3|Q9BX35	Missense_Mutation	SNP	ENST00000370202.4	hg19	CCDS41357.1	.	.	.	.	.	.	.	.	.	.	A	3.798	-0.042270	0.07452	.	.	ENSG00000122481	ENST00000370202;ENST00000429514;ENST00000263893	T;T;T	0.34859	1.34;1.38;1.35	5.38	-5.53	0.02552	.	1.677590	0.02325	N	0.073392	T	0.09202	0.0227	L	0.40543	1.245	0.09310	N	1	B;B;B;B;B	0.11235	0.001;0.001;0.0;0.004;0.0	B;B;B;B;B	0.09377	0.001;0.001;0.0;0.004;0.001	T	0.27191	-1.0081	10	0.52906	T	0.07	0.4062	0.9194	0.01311	0.2608:0.2714:0.1228:0.345	.	109;124;124;109;124	E7ES73;Q9Y3V2;D3DT49;Q9Y3V2-3;Q9Y3V2-2	.;RWDD3_HUMAN;.;.;.	C	124;109;124	ENSP00000359221:S124C;ENSP00000397398:S109C;ENSP00000263893:S124C	ENSP00000263893:S124C	S	+	1	0	RWDD3	95482639	0.000000	0.05858	0.000000	0.03702	0.010000	0.07245	-0.566000	0.05922	-0.478000	0.06823	-0.274000	0.10170	AGT	.	.	.	none		0.438	RWDD3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030078.1	NM_015485	
PLPPR4	9890	hgsc.bcm.edu	37	1	99764611	99764611	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:99764611T>C	ENST00000370185.3	+	4	1056	c.559T>C	c.(559-561)Tgc>Cgc	p.C187R	LPPR4_ENST00000370184.1_Missense_Mutation_p.C29R|LPPR4_ENST00000457765.1_Missense_Mutation_p.C187R	NM_014839.4	NP_055654.2	Q7Z2D5	LPPR4_HUMAN		187					axonogenesis (GO:0007409)|inner ear development (GO:0048839)|phospholipid dephosphorylation (GO:0046839)	integral component of plasma membrane (GO:0005887)	lipid phosphatase activity (GO:0042577)|phosphatidate phosphatase activity (GO:0008195)			endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(39)|ovary(3)|prostate(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	72		all_epithelial(167;3.54e-06)|all_lung(203;0.00139)|Lung NSC(277;0.00202)		Epithelial(280;0.0736)|all cancers(265;0.0975)|COAD - Colon adenocarcinoma(174;0.142)|Lung(183;0.201)|Colorectal(170;0.22)		ATTTGGATTATGCTCTACAGC	0.363																																					p.C187R		Atlas-SNP	.											.	LPPR4	143	.	0			c.T559C						PASS	.						150.0	133.0	138.0					1																	99764611		2203	4300	6503	SO:0001583	missense	0	exon4			GGATTATGCTCTA																												ENST00000370185.3:c.559T>C	chr1.hg19:g.99764611T>C	ENSP00000359204:p.Cys187Arg	97.0	0.0	.		103.0	39.0	.	NM_001166252	E7EPS1|O75043|Q5T9R9|Q86XQ5|Q8N3F1|Q96MP0	Missense_Mutation	SNP	ENST00000370185.3	hg19	CCDS757.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.012287	0.75046	.	.	ENSG00000117600	ENST00000370185;ENST00000457765;ENST00000263178;ENST00000370184	T;T;T	0.52057	0.68;0.68;0.68	5.41	5.41	0.78517	Phosphatidic acid phosphatase/chloroperoxidase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.63920	0.2552	M	0.78637	2.42	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.997	T	0.69636	-0.5092	10	0.72032	D	0.01	-30.56	15.7585	0.78058	0.0:0.0:0.0:1.0	.	187;187	E7EPS1;Q7Z2D5	.;LPPR4_HUMAN	R	187;187;187;29	ENSP00000359204:C187R;ENSP00000394913:C187R;ENSP00000359203:C29R	ENSP00000263178:C187R	C	+	1	0	RP4-788L13.1	99537199	1.000000	0.71417	0.955000	0.39395	0.578000	0.36192	6.235000	0.72332	2.191000	0.70037	0.528000	0.53228	TGC	.	.	.	none		0.363	LPPR4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029670.2		
KCNN3	3782	hgsc.bcm.edu	37	1	154842253	154842253	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:154842253G>T	ENST00000271915.4	-	1	503	c.188C>A	c.(187-189)cCt>cAt	p.P63H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	63	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	aagctgcggaggctgaggctg	0.697																																					p.P63H		Atlas-SNP	.											.	KCNN3	141	.	0			c.C188A						PASS	.						6.0	4.0	5.0					1																	154842253		1984	3925	5909	SO:0001583	missense	3782	exon1			TGCGGAGGCTGAG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.188C>A	chr1.hg19:g.154842253G>T	ENSP00000271915:p.Pro63His	81.0	0.0	.		62.0	15.0	.	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	hg19	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	11.14	1.552427	0.27739	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56275	0.47	5.07	3.18	0.36537	.	1.727610	0.03258	N	0.182822	T	0.18551	0.0445	N	0.08118	0	0.80722	D	1	.	.	.	.	.	.	T	0.11372	-1.0590	8	0.33141	T	0.24	-4.1487	6.4327	0.21807	0.0918:0.0:0.7284:0.1798	.	.	.	.	H	63;158	ENSP00000271915:P63H	ENSP00000271915:P63H	P	-	2	0	KCNN3	153108877	0.863000	0.29885	1.000000	0.80357	0.998000	0.95712	1.873000	0.39558	0.823000	0.34589	0.563000	0.77884	CCT	.	.	.	none		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
THBS3	7059	hgsc.bcm.edu	37	1	155172114	155172114	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:155172114G>A	ENST00000368378.3	-	9	1056	c.1036C>T	c.(1036-1038)Cga>Tga	p.R346*	RP11-263K19.4_ENST00000422665.1_RNA|RP11-263K19.4_ENST00000454348.1_RNA|THBS3_ENST00000457183.2_Nonsense_Mutation_p.R226*|RP11-263K19.4_ENST00000430312.1_RNA|RP11-263K19.4_ENST00000447623.1_RNA|RP11-263K19.4_ENST00000436772.1_RNA|RP11-263K19.4_ENST00000453136.1_RNA|THBS3_ENST00000486260.1_5'UTR|THBS3_ENST00000541990.1_5'UTR|THBS3_ENST00000541576.1_5'Flank	NM_001252607.1|NM_007112.4	NP_001239536.1|NP_009043.1	P49746	TSP3_HUMAN	thrombospondin 3	346	EGF-like 1; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				bone trabecula formation (GO:0060346)|cell-matrix adhesion (GO:0007160)|growth plate cartilage development (GO:0003417)|ossification involved in bone maturation (GO:0043931)	extracellular region (GO:0005576)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)|heparin binding (GO:0008201)			breast(6)|endometrium(4)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(4)|urinary_tract(3)	48	all_epithelial(22;5.72e-28)|all_lung(78;2.07e-24)|all_hematologic(923;0.0359)|Hepatocellular(266;0.0877)		Epithelial(20;3.72e-10)|all cancers(21;1.19e-09)|BRCA - Breast invasive adenocarcinoma(34;0.000752)|LUSC - Lung squamous cell carcinoma(543;0.193)			TTGTACCCTCGAGGACAGGCC	0.602																																					p.R346X		Atlas-SNP	.											.	THBS3	70	.	0			c.C1036T						PASS	.						96.0	90.0	92.0					1																	155172114		2203	4300	6503	SO:0001587	stop_gained	7059	exon9			ACCCTCGAGGACA	L38969	CCDS1099.1, CCDS58034.1, CCDS72937.1	1q21	2008-02-05			ENSG00000169231	ENSG00000169231			11787	protein-coding gene	gene with protein product		188062				1601886	Standard	NM_007112		Approved		uc001fix.3	P49746	OTTHUMG00000035710	ENST00000368378.3:c.1036C>T	chr1.hg19:g.155172114G>A	ENSP00000357362:p.Arg346*	193.0	0.0	.		151.0	41.0	.	NM_007112	B1AVR8|B4DQ20|Q8WV34	Nonsense_Mutation	SNP	ENST00000368378.3	hg19	CCDS1099.1	.	.	.	.	.	.	.	.	.	.	G	34	5.316567	0.95655	.	.	ENSG00000169231	ENST00000368378;ENST00000457183;ENST00000428962	.	.	.	5.44	5.44	0.79542	.	0.674441	0.14773	N	0.299266	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.12766	T	0.61	3.2614	16.8112	0.85720	0.0:0.0:1.0:0.0	.	.	.	.	X	346;226;196	.	ENSP00000357362:R346X	R	-	1	2	THBS3	153438738	0.461000	0.25783	0.082000	0.20525	0.937000	0.57800	3.403000	0.52615	2.837000	0.97791	0.655000	0.94253	CGA	.	.	.	none		0.602	THBS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086856.1	NM_007112	
PAPPA2	60676	hgsc.bcm.edu	37	1	176525851	176525851	+	Silent	SNP	G	G	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:176525851G>A	ENST00000367662.3	+	2	1557	c.393G>A	c.(391-393)ggG>ggA	p.G131G	PAPPA2_ENST00000367661.3_Silent_p.G131G	NM_020318.2	NP_064714.2	Q9BXP8	PAPP2_HUMAN	pappalysin 2	131					bone morphogenesis (GO:0060349)|cell differentiation (GO:0030154)|cellular protein metabolic process (GO:0044267)|proteolysis (GO:0006508)|regulation of cell growth (GO:0001558)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|membrane (GO:0016020)	metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			NS(3)|breast(3)|central_nervous_system(7)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(19)|lung(136)|ovary(7)|pancreas(1)|prostate(4)|skin(10)|upper_aerodigestive_tract(8)|urinary_tract(1)	226						CATGGGTAGGGGATAGTCCTA	0.537																																					p.G131G		Atlas-SNP	.											.	PAPPA2	665	.	0			c.G393A						PASS	.						114.0	115.0	114.0					1																	176525851		2073	4228	6301	SO:0001819	synonymous_variant	60676	exon2			GGTAGGGGATAGT	BG354569	CCDS41438.1, CCDS41439.1	1q23-q25	2008-05-23	2004-07-07	2004-07-09	ENSG00000116183	ENSG00000116183			14615	protein-coding gene	gene with protein product			"""placenta-specific 3"""	PLAC3		11018262, 11264294	Standard	NM_021936		Approved	PAPPE, PAPP-A2	uc001gkz.3	Q9BXP8	OTTHUMG00000035025	ENST00000367662.3:c.393G>A	chr1.hg19:g.176525851G>A		148.0	0.0	.		152.0	12.0	.	NM_021936	A9Z1Y8|Q96PH7|Q96PH8|Q9H4C9	Silent	SNP	ENST00000367662.3	hg19	CCDS41438.1																																																																																			.	.	.	none		0.537	PAPPA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084763.1		
AHCTF1	25909	hgsc.bcm.edu	37	1	247053281	247053281	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:247053281C>T	ENST00000391829.2	-	17	2254	c.2131G>A	c.(2131-2133)Gag>Aag	p.E711K	AHCTF1_ENST00000366508.1_Missense_Mutation_p.E746K|AHCTF1_ENST00000326225.3_Missense_Mutation_p.E720K|AHCTF1_ENST00000470300.1_5'UTR			Q8WYP5	ELYS_HUMAN	AT hook containing transcription factor 1	711	Necessary for cytoplasmic localization. {ECO:0000250}.				cytokinesis (GO:0000910)|mitotic cell cycle (GO:0000278)|mRNA transport (GO:0051028)|nuclear pore complex assembly (GO:0051292)|protein transport (GO:0015031)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|kinetochore (GO:0000776)|nuclear matrix (GO:0016363)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.E711Q(1)		NS(1)|breast(6)|cervix(3)|endometrium(8)|kidney(6)|large_intestine(12)|liver(2)|lung(21)|ovary(5)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(2)	74	all_cancers(71;3.05e-05)|all_epithelial(71;6.72e-06)|Ovarian(71;0.0173)|Breast(184;0.0318)|all_lung(81;0.0458)|Lung NSC(105;0.0518)	all_cancers(173;0.0266)	OV - Ovarian serous cystadenocarcinoma(106;0.00271)			GATAAACGCTCAAACTTCTGT	0.338																																					p.E720K	Colon(145;197 1800 4745 15099 26333)	Atlas-SNP	.											AHCTF1,bladder,carcinoma,0,1	AHCTF1	187	.	1	Substitution - Missense(1)	urinary_tract(1)	c.G2158A						PASS	.						114.0	120.0	118.0					1																	247053281		2203	4300	6503	SO:0001583	missense	25909	exon17			AACGCTCAAACTT		CCDS1629.1, CCDS1629.2	1q44	2008-09-09			ENSG00000153207	ENSG00000153207			24618	protein-coding gene	gene with protein product	"""ELYS transcription factor like protein TMBS62"""	610853				11952839	Standard	NM_015446		Approved	ELYS	uc001ibv.2	Q8WYP5	OTTHUMG00000040706	ENST00000391829.2:c.2131G>A	chr1.hg19:g.247053281C>T	ENSP00000375705:p.Glu711Lys	60.0	0.0	.		47.0	13.0	.	NM_015446	A6NGM0|A8MSG9|A8MZ86|Q7Z4E3|Q8IZA4|Q96EH9|Q9Y4Q6	Missense_Mutation	SNP	ENST00000391829.2	hg19		.	.	.	.	.	.	.	.	.	.	C	10.35	1.327003	0.24080	.	.	ENSG00000153207	ENST00000366508;ENST00000326225;ENST00000391829	T;T;T	0.33438	1.41;1.41;1.41	5.61	3.62	0.41486	.	0.132552	0.52532	D	0.000063	T	0.33323	0.0859	M	0.63428	1.95	0.40661	D	0.982126	P;P	0.48503	0.911;0.605	B;B	0.43867	0.434;0.121	T	0.21211	-1.0252	10	0.34782	T	0.22	-9.9643	12.8931	0.58082	0.0:0.8042:0.1258:0.07	.	746;711	Q8WYP5-2;Q8WYP5	.;ELYS_HUMAN	K	746;720;711	ENSP00000355464:E746K;ENSP00000355465:E720K;ENSP00000375705:E711K	ENSP00000355465:E720K	E	-	1	0	AHCTF1	245119904	1.000000	0.71417	0.890000	0.34922	0.002000	0.02628	3.403000	0.52615	1.379000	0.46325	0.579000	0.79373	GAG	.	.	.	none		0.338	AHCTF1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015446	
ZC3H6	376940	hgsc.bcm.edu	37	2	113089251	113089251	+	Missense_Mutation	SNP	G	G	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:113089251G>C	ENST00000409871.1	+	12	3157	c.2756G>C	c.(2755-2757)aGt>aCt	p.S919T	ZC3H6_ENST00000343936.4_Missense_Mutation_p.S919T|AC115115.2_ENST00000607612.1_RNA	NM_198581.2	NP_940983.2	P61129	ZC3H6_HUMAN	zinc finger CCCH-type containing 6	919							metal ion binding (GO:0046872)			central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(9)|lung(12)|ovary(4)|prostate(2)	35						AATACAAAAAGTGATCTTCAT	0.388																																					p.S919T		Atlas-SNP	.											.	ZC3H6	93	.	0			c.G2756C						PASS	.						65.0	59.0	61.0					2																	113089251		1855	4101	5956	SO:0001583	missense	376940	exon12			CAAAAAGTGATCT	AK123404	CCDS46393.1	2q13	2012-07-05	2005-06-02	2005-06-02	ENSG00000188177	ENSG00000188177		"""Zinc fingers, CCCH-type domain containing"""	24762	protein-coding gene	gene with protein product			"""zinc finger CCCH-type domain containing 6"""	ZC3HDC6			Standard	NM_198581		Approved	FLJ41410, FLJ45877, KIAA2035	uc002thq.1	P61129	OTTHUMG00000153286	ENST00000409871.1:c.2756G>C	chr2.hg19:g.113089251G>C	ENSP00000386764:p.Ser919Thr	74.0	0.0	.		74.0	26.0	.	NM_198581	A9JR71|Q6ZW96	Missense_Mutation	SNP	ENST00000409871.1	hg19	CCDS46393.1	.	.	.	.	.	.	.	.	.	.	G	9.984	1.229069	0.22542	.	.	ENSG00000188177	ENST00000409871;ENST00000343936	T;T	0.15487	2.42;2.42	5.94	5.06	0.68205	.	0.469384	0.26776	N	0.022560	T	0.14485	0.0350	L	0.54323	1.7	0.22389	N	0.999144	P	0.35433	0.501	B	0.26770	0.073	T	0.19679	-1.0298	10	0.39692	T	0.17	-2.4342	9.1318	0.36850	0.2286:0.0:0.7714:0.0	.	919	P61129	ZC3H6_HUMAN	T	919	ENSP00000386764:S919T;ENSP00000340298:S919T	ENSP00000340298:S919T	S	+	2	0	ZC3H6	112805722	0.931000	0.31567	0.994000	0.49952	0.985000	0.73830	1.552000	0.36244	1.512000	0.48834	0.591000	0.81541	AGT	.	.	.	none		0.388	ZC3H6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330551.1	NM_198581	
FAP	2191	hgsc.bcm.edu	37	2	163046173	163046173	+	Silent	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:163046173A>G	ENST00000188790.4	-	18	1749	c.1542T>C	c.(1540-1542)gaT>gaC	p.D514D	FAP_ENST00000443424.1_Silent_p.D489D	NM_004460.2	NP_004451.2			fibroblast activation protein, alpha											NS(2)|breast(1)|central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(34)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(4)	63						TACTAATTTCATCTACTTCAA	0.284																																					p.D514D		Atlas-SNP	.											.	FAP	122	.	0			c.T1542C						PASS	.						58.0	59.0	58.0					2																	163046173		2190	4274	6464	SO:0001819	synonymous_variant	2191	exon18			AATTTCATCTACT	U09278	CCDS33311.1	2q23	2008-02-05			ENSG00000078098	ENSG00000078098			3590	protein-coding gene	gene with protein product	"""seprase"""	600403				9247085, 14707457	Standard	NM_004460		Approved	DPPIV	uc002ucd.3	Q12884	OTTHUMG00000153890	ENST00000188790.4:c.1542T>C	chr2.hg19:g.163046173A>G		72.0	0.0	.		84.0	50.0	.	NM_004460		Silent	SNP	ENST00000188790.4	hg19	CCDS33311.1																																																																																			.	.	.	none		0.284	FAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000332852.2		
FN1	2335	hgsc.bcm.edu	37	2	216232592	216232592	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:216232592A>G	ENST00000359671.1	-	41	7004	c.6739T>C	c.(6739-6741)Tca>Cca	p.S2247P	FN1_ENST00000357867.4_Missense_Mutation_p.S2037P|FN1_ENST00000346544.3_Intron|FN1_ENST00000421182.1_Missense_Mutation_p.S2101P|FN1_ENST00000345488.5_Missense_Mutation_p.S2045P|FN1_ENST00000446046.1_Missense_Mutation_p.S2191P|FN1_ENST00000356005.4_Missense_Mutation_p.S2157P|FN1_ENST00000443816.1_Missense_Mutation_p.S2126P|FN1_ENST00000354785.4_Missense_Mutation_p.S2338P|FN1_ENST00000357009.2_3'UTR|FN1_ENST00000336916.4_Missense_Mutation_p.S2216P|FN1_ENST00000432072.2_Missense_Mutation_p.S2128P|FN1_ENST00000323926.6_Missense_Mutation_p.S2307P			P02751	FINC_HUMAN	fibronectin 1	2247	Fibrin-binding 2.|Fibronectin type-I 10. {ECO:0000255|PROSITE-ProRule:PRU00478}.				acute-phase response (GO:0006953)|angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|calcium-independent cell-matrix adhesion (GO:0007161)|cell adhesion (GO:0007155)|cell-substrate junction assembly (GO:0007044)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|integrin activation (GO:0033622)|leukocyte migration (GO:0050900)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of axon extension (GO:0045773)|regulation of cell shape (GO:0008360)|response to wounding (GO:0009611)|substrate adhesion-dependent cell spreading (GO:0034446)	apical plasma membrane (GO:0016324)|basal lamina (GO:0005605)|blood microparticle (GO:0072562)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fibrinogen complex (GO:0005577)|platelet alpha granule lumen (GO:0031093)	collagen binding (GO:0005518)|heparin binding (GO:0008201)|integrin binding (GO:0005178)|peptidase activator activity (GO:0016504)|protease binding (GO:0002020)		FN1/ALK(2)	NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(7)|endometrium(9)|kidney(8)|large_intestine(33)|lung(38)|ovary(1)|pancreas(1)|prostate(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	109		Renal(323;0.127)		Epithelial(149;9.59e-07)|all cancers(144;0.000174)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00948)	Ocriplasmin(DB08888)	TCACTAGATGAATCACATCTG	0.458																																					p.S2338P		Atlas-SNP	.											.	FN1	521	.	0			c.T7012C						PASS	.						115.0	90.0	98.0					2																	216232592		2203	4300	6503	SO:0001583	missense	2335	exon42			TAGATGAATCACA		CCDS2399.1, CCDS2400.1, CCDS42813.1, CCDS42814.1, CCDS46510.1, CCDS46512.1	2q34	2014-01-30			ENSG00000115414	ENSG00000115414		"""Fibronectin type III domain containing"", ""Endogenous ligands"""	3778	protein-coding gene	gene with protein product	"""migration-stimulating factor"", ""cold-insoluble globulin"""	135600				2992939, 3003095	Standard	NM_054034		Approved	MSF, CIG, LETS, GFND2, FINC	uc002vfa.3	P02751	OTTHUMG00000133054	ENST00000359671.1:c.6739T>C	chr2.hg19:g.216232592A>G	ENSP00000352696:p.Ser2247Pro	131.0	0.0	.		155.0	50.0	.	NM_212482	B7ZLF0|E9PE77|E9PG29|O95609|O95610|Q14312|Q14325|Q14326|Q17RV7|Q564H7|Q585T2|Q59EH1|Q60FE4|Q68DP8|Q68DP9|Q68DT4|Q6LDP6|Q6MZS0|Q6MZU5|Q6N025|Q6N0A6|Q7Z391|Q86T27|Q8IVI8|Q96KP7|Q96KP8|Q96KP9|Q9H1B8|Q9HAP3|Q9UMK2	Missense_Mutation	SNP	ENST00000359671.1	hg19		.	.	.	.	.	.	.	.	.	.	A	20.4	3.977481	0.74360	.	.	ENSG00000115414	ENST00000421182;ENST00000323926;ENST00000336916;ENST00000357867;ENST00000354785;ENST00000265313;ENST00000359671;ENST00000345488;ENST00000446046;ENST00000443816;ENST00000432072;ENST00000356005;ENST00000456923	T;T;T;T;T;T;T;T;T;T;T;T	0.66638	-0.22;1.16;1.37;-0.05;1.65;1.31;1.1;1.08;0.57;-0.11;0.61;0.54	5.67	5.67	0.87782	Fibronectin, type I (2);Complement control module (1);	0.000000	0.56097	D	0.000034	T	0.79811	0.4510	L	0.61218	1.895	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;0.995;0.992;1.0;0.992;0.995;0.995;0.999;0.999	D;D;D;D;D;D;D;D;D;D;D	0.91635	0.998;0.989;0.998;0.993;0.985;0.999;0.985;0.993;0.993;0.998;0.995	T	0.80269	-0.1453	10	0.49607	T	0.09	.	15.8986	0.79356	1.0:0.0:0.0:0.0	.	2128;2307;2037;2157;2191;2216;2248;2101;2126;2338;2247	P02751-13;P02751-7;P02751-10;P02751-8;E9PE77;P02751-3;E7ERA1;P02751-9;P02751-14;P02751-15;P02751	.;.;.;.;.;.;.;.;.;.;FINC_HUMAN	P	2101;2307;2216;2037;2338;2248;2247;2045;2191;2126;2128;2157;964	ENSP00000394423:S2101P;ENSP00000323534:S2307P;ENSP00000338200:S2216P;ENSP00000350534:S2037P;ENSP00000346839:S2338P;ENSP00000352696:S2247P;ENSP00000273049:S2045P;ENSP00000410422:S2191P;ENSP00000415018:S2126P;ENSP00000399538:S2128P;ENSP00000348285:S2157P;ENSP00000416139:S964P	ENSP00000265313:S2248P	S	-	1	0	FN1	215940837	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.339000	0.96797	2.156000	0.67533	0.477000	0.44152	TCA	.	.	.	none		0.458	FN1-204	KNOWN	basic	protein_coding	protein_coding		NM_212476	
FBXL2	25827	hgsc.bcm.edu	37	3	33415410	33415410	+	Silent	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:33415410C>T	ENST00000484457.1	+	9	745	c.654C>T	c.(652-654)tgC>tgT	p.C218C	FBXL2_ENST00000283627.6_3'UTR|FBXL2_ENST00000538892.1_Silent_p.C150C|FBXL2_ENST00000446237.3_5'UTR|FBXL2_ENST00000507198.1_Silent_p.C150C|FBXL2_ENST00000542085.1_5'UTR|FBXL2_ENST00000538181.1_Silent_p.C134C	NM_012157.3	NP_036289.3			F-box and leucine-rich repeat protein 2											endometrium(2)|kidney(1)|large_intestine(7)|lung(3)|prostate(1)|urinary_tract(1)	15						TGCAGTCCTGCTCAGTAAGTA	0.498																																					p.C218C		Atlas-SNP	.											.	FBXL2	44	.	0			c.C654T						PASS	.						152.0	145.0	147.0					3																	33415410		2203	4300	6503	SO:0001819	synonymous_variant	25827	exon9			GTCCTGCTCAGTA	AF174589	CCDS2658.1, CCDS54560.1	3p22.3	2011-06-09			ENSG00000153558	ENSG00000153558		"""F-boxes / Leucine-rich repeats"""	13598	protein-coding gene	gene with protein product		605652				10508920, 10531035	Standard	NM_012157		Approved	FBL2, FBL3	uc003cfp.3	Q9UKC9	OTTHUMG00000130745	ENST00000484457.1:c.654C>T	chr3.hg19:g.33415410C>T		132.0	0.0	.		139.0	64.0	.	NM_012157		Silent	SNP	ENST00000484457.1	hg19	CCDS2658.1																																																																																			.	.	.	none		0.498	FBXL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253245.2	NM_012157	
PARP14	54625	hgsc.bcm.edu	37	3	122437696	122437696	+	Silent	SNP	A	A	G	rs377210300		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:122437696A>G	ENST00000474629.2	+	14	4964	c.4698A>G	c.(4696-4698)acA>acG	p.T1566T	PARP14_ENST00000475640.1_3'UTR	NM_017554.2	NP_060024.2	Q460N5	PAR14_HUMAN	poly (ADP-ribose) polymerase family, member 14	1566	WWE. {ECO:0000255|PROSITE- ProRule:PRU00248}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	NAD+ ADP-ribosyltransferase activity (GO:0003950)			NS(2)|breast(5)|cervix(2)|endometrium(7)|kidney(5)|large_intestine(8)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	50				GBM - Glioblastoma multiforme(114;0.0531)		AGAAAAAAACAGTTGATGTCA	0.373																																					p.T1566T		Atlas-SNP	.											.	PARP14	242	.	0			c.A4698G						PASS	.	A		0,3790		0,0,1895	88.0	87.0	87.0		4698	-5.7	0.0	3		87	1,8247		0,1,4123	no	coding-synonymous	PARP14	NM_017554.2		0,1,6018	GG,GA,AA		0.0121,0.0,0.0083		1566/1802	122437696	1,12037	1895	4124	6019	SO:0001819	synonymous_variant	54625	exon14			AAAAACAGTTGAT	AB033094	CCDS46894.1	3q21	2010-02-16			ENSG00000173193	ENSG00000173193		"""Poly (ADP-ribose) polymerases"""	29232	protein-coding gene	gene with protein product		610028				15273990	Standard	NM_017554		Approved	KIAA1268, pART8	uc003efq.4	Q460N5	OTTHUMG00000159552	ENST00000474629.2:c.4698A>G	chr3.hg19:g.122437696A>G		99.0	0.0	.		150.0	39.0	.	NM_017554	B4E2H0|Q460N4|Q8J027|Q9H9X9|Q9NV60|Q9ULF2	Silent	SNP	ENST00000474629.2	hg19	CCDS46894.1																																																																																			.	.	.	weak		0.373	PARP14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356173.2	NM_017554	
NDUFB5	4711	hgsc.bcm.edu	37	3	179322636	179322636	+	Silent	SNP	G	G	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:179322636G>A	ENST00000259037.3	+	1	147	c.33G>A	c.(31-33)tcG>tcA	p.S11S	MRPL47_ENST00000259038.2_5'Flank|NDUFB5_ENST00000493866.1_Silent_p.S11S|MRPL47_ENST00000476781.1_5'Flank|MRPL47_ENST00000392659.2_5'Flank|NDUFB5_ENST00000472629.1_Silent_p.S11S	NM_002492.3	NP_002483.1	O43674	NDUB5_HUMAN	NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa	11					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)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			endometrium(1)|lung(6)|skin(1)	8	all_cancers(143;9.62e-16)|Ovarian(172;0.0172)|Breast(254;0.191)		OV - Ovarian serous cystadenocarcinoma(80;5.98e-26)|GBM - Glioblastoma multiforme(14;0.0169)|BRCA - Breast invasive adenocarcinoma(182;0.18)			GGCGGGTTTCGGTTACTGCGG	0.617																																					p.S11S		Atlas-SNP	.											.	NDUFB5	22	.	0			c.G33A						PASS	.						36.0	36.0	36.0					3																	179322636		2203	4300	6503	SO:0001819	synonymous_variant	4711	exon1			GGTTTCGGTTACT	AF047181	CCDS3234.1, CCDS56297.1, CCDS75054.1	3q27.1	2011-07-04	2002-08-29		ENSG00000136521	ENSG00000136521		"""Mitochondrial respiratory chain complex / Complex I"""	7700	protein-coding gene	gene with protein product	"""complex I SGDH subunit"""	603841	"""NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 (16kD, SGDH)"""			9425316	Standard	NM_002492		Approved	SGDH, CI-SGDH, MGC12314	uc003fkc.3	O43674	OTTHUMG00000157480	ENST00000259037.3:c.33G>A	chr3.hg19:g.179322636G>A		125.0	0.0	.		107.0	34.0	.	NM_002492	Q561V6	Silent	SNP	ENST00000259037.3	hg19	CCDS3234.1	.	.	.	.	.	.	.	.	.	.	G	15.68	2.903796	0.52333	.	.	ENSG00000136521	ENST00000482604	.	.	.	5.75	1.95	0.26073	.	.	.	.	.	T	0.56093	0.1962	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.48340	-0.9044	5	0.40728	T	0.16	-3.1698	6.2744	0.20973	0.2212:0.1325:0.6463:0.0	.	.	.	.	Q	8	.	ENSP00000419099:R3Q	R	+	2	0	NDUFB5	180805330	0.998000	0.40836	0.993000	0.49108	0.016000	0.09150	0.145000	0.16157	0.148000	0.19059	-0.133000	0.14855	CGG	.	.	.	none		0.617	NDUFB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348937.2	NM_002492	
KLHL6	89857	hgsc.bcm.edu	37	3	183226047	183226047	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:183226047C>T	ENST00000341319.3	-	3	744	c.709G>A	c.(709-711)Gag>Aag	p.E237K		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	237	BACK.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			ATCACGGTCTCAAACACCTGa	0.547																																					p.E237K		Atlas-SNP	.											.	KLHL6	100	.	0			c.G709A						PASS	.						135.0	114.0	121.0					3																	183226047		2203	4300	6503	SO:0001583	missense	89857	exon3			CGGTCTCAAACAC	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.709G>A	chr3.hg19:g.183226047C>T	ENSP00000341342:p.Glu237Lys	199.0	0.0	.		277.0	69.0	.	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	hg19	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	C	36	5.904004	0.97087	.	.	ENSG00000172578	ENST00000341319	T	0.69685	-0.42	5.87	5.87	0.94306	BTB/Kelch-associated (2);	0.043908	0.85682	D	0.000000	D	0.83083	0.5177	M	0.79343	2.45	0.80722	D	1	D	0.76494	0.999	D	0.73380	0.98	T	0.82400	-0.0476	10	0.54805	T	0.06	.	20.5827	0.99408	0.0:1.0:0.0:0.0	.	237	Q8WZ60	KLHL6_HUMAN	K	237	ENSP00000341342:E237K	ENSP00000341342:E237K	E	-	1	0	KLHL6	184708741	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.445000	0.80570	2.941000	0.99782	0.655000	0.94253	GAG	.	.	.	none		0.547	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
FAM184B	27146	hgsc.bcm.edu	37	4	17710845	17710845	+	Silent	SNP	G	G	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr4:17710845G>T	ENST00000265018.3	-	2	776	c.564C>A	c.(562-564)ggC>ggA	p.G188G		NM_015688.1	NP_056503.1	Q9ULE4	F184B_HUMAN	family with sequence similarity 184, member B	188										NS(1)|central_nervous_system(1)|endometrium(1)|prostate(1)	4						CCGGGCCCTGGCCTGGCTCCG	0.677																																					p.G188G		Atlas-SNP	.											.	FAM184B	38	.	0			c.C564A						PASS	.						20.0	22.0	22.0					4																	17710845		692	1591	2283	SO:0001819	synonymous_variant	27146	exon2			GCCCTGGCCTGGC		CCDS47033.1	4p16	2009-04-22			ENSG00000047662	ENSG00000047662			29235	protein-coding gene	gene with protein product						10574462	Standard	NM_015688		Approved	KIAA1276	uc003gpm.4	Q9ULE4	OTTHUMG00000160287	ENST00000265018.3:c.564C>A	chr4.hg19:g.17710845G>T		92.0	0.0	.		84.0	12.0	.	NM_015688		Silent	SNP	ENST00000265018.3	hg19	CCDS47033.1																																																																																			.	.	.	none		0.677	FAM184B-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360137.1	NM_015688	
TMPRSS11F	389208	hgsc.bcm.edu	37	4	68930403	68930403	+	Splice_Site	SNP	C	C	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr4:68930403C>A	ENST00000356291.2	-	8	1074	c.1015G>T	c.(1015-1017)Gga>Tga	p.G339*	RP11-35D5.1_ENST00000600441.1_RNA|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000499180.2_RNA|UBA6-AS1_ENST00000511571.1_RNA	NM_207407.2	NP_997290.2	Q6ZWK6	TM11F_HUMAN	transmembrane protease, serine 11F	339	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	serine-type endopeptidase activity (GO:0004252)			NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|liver(1)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|urinary_tract(4)	39						AACTGCTCACCATCATCTACA	0.363																																					p.G339X		Atlas-SNP	.											.	TMPRSS11F	79	.	0			c.G1015T						PASS	.						68.0	68.0	68.0					4																	68930403		2203	4300	6503	SO:0001630	splice_region_variant	389208	exon8			GCTCACCATCATC	AK122625	CCDS3520.1	4q13.2	2010-04-13			ENSG00000198092	ENSG00000198092		"""Serine peptidases / Transmembrane"""	29994	protein-coding gene	gene with protein product							Standard	NM_207407		Approved	FLJ16046	uc003hdt.1	Q6ZWK6	OTTHUMG00000129307	ENST00000356291.2:c.1015+1G>T	chr4.hg19:g.68930403C>A		69.0	0.0	.		40.0	14.0	.	NM_207407	A8MXX2	Nonsense_Mutation	SNP	ENST00000356291.2	hg19	CCDS3520.1	.	.	.	.	.	.	.	.	.	.	C	37	6.372005	0.97515	.	.	ENSG00000198092	ENST00000356291	.	.	.	5.92	5.92	0.95590	.	0.000000	0.53938	D	0.000048	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.8344	0.78787	0.0:1.0:0.0:0.0	.	.	.	.	X	339	.	.	G	-	1	0	TMPRSS11F	68612998	1.000000	0.71417	1.000000	0.80357	0.731000	0.41821	4.819000	0.62664	2.822000	0.97130	0.650000	0.86243	GGA	.	.	.	none		0.363	TMPRSS11F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251439.1	NM_207407	Nonsense_Mutation
SLC12A7	10723	hgsc.bcm.edu	37	5	1093744	1093744	+	Silent	SNP	C	C	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:1093744C>A	ENST00000264930.5	-	3	289	c.246G>T	c.(244-246)gtG>gtT	p.V82V		NM_006598.2	NP_006589.2	Q9Y666	S12A7_HUMAN	solute carrier family 12 (potassium/chloride transporter), member 7	82					cell volume homeostasis (GO:0006884)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|ion transport (GO:0006811)|potassium ion transport (GO:0006813)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	potassium:chloride symporter activity (GO:0015379)|protein kinase binding (GO:0019901)			breast(1)|endometrium(3)|kidney(2)|large_intestine(3)|lung(14)|ovary(2)|prostate(1)|skin(4)|urinary_tract(2)	32	Lung NSC(6;2.47e-13)|all_lung(6;1.67e-12)|all_epithelial(6;5.44e-09)		Epithelial(17;0.000497)|OV - Ovarian serous cystadenocarcinoma(19;0.00239)|all cancers(22;0.00241)|Lung(60;0.165)		Potassium Chloride(DB00761)	GCAGCGAGGACACCATGGGGT	0.682																																					p.V82V		Atlas-SNP	.											.	SLC12A7	97	.	0			c.G246T						PASS	.						111.0	75.0	87.0					5																	1093744		2202	4299	6501	SO:0001819	synonymous_variant	10723	exon3			CGAGGACACCATG	AF105365	CCDS34129.1	5p15	2013-07-18	2013-07-18		ENSG00000113504	ENSG00000113504		"""Solute carriers"""	10915	protein-coding gene	gene with protein product		604879				10347194	Standard	NM_006598		Approved	KCC4, DKFZP434F076	uc003jbu.3	Q9Y666	OTTHUMG00000161931	ENST00000264930.5:c.246G>T	chr5.hg19:g.1093744C>A		235.0	0.0	.		163.0	47.0	.	NM_006598	A6NDS8|Q4G0F3|Q96I81|Q9H7I3|Q9H7I7|Q9UFW2	Silent	SNP	ENST00000264930.5	hg19	CCDS34129.1																																																																																			.	.	.	none		0.682	SLC12A7-001	KNOWN	non_canonical_TEC|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366446.2	NM_006598	
PROB1	389333	hgsc.bcm.edu	37	5	138727939	138727939	+	Silent	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:138727939A>G	ENST00000434752.2	-	1	2946	c.2832T>C	c.(2830-2832)taT>taC	p.Y944Y	MZB1_ENST00000412103.2_5'Flank|MZB1_ENST00000302125.8_5'Flank|MZB1_ENST00000457570.2_5'Flank	NM_001161546.1	NP_001155018.1	E7EW31	PROB1_HUMAN	proline-rich basic protein 1	944	Pro-rich.																GTATAGGCCCATAGGCGGGCG	0.736																																					p.Y944Y		Atlas-SNP	.											.	.	.	.	0			c.T2832C						PASS	.						9.0	18.0	15.0					5																	138727939		687	1586	2273	SO:0001819	synonymous_variant	389333	exon1			AGGCCCATAGGCG	AK316483	CCDS54909.1	5q31.2	2012-10-01	2012-10-01	2012-10-01	ENSG00000228672	ENSG00000228672			41906	protein-coding gene	gene with protein product			"""chromosome 5 open reading frame 65"""	C5orf65			Standard	NM_001161546		Approved		uc011czc.1	E7EW31		ENST00000434752.2:c.2832T>C	chr5.hg19:g.138727939A>G		193.0	0.0	.		124.0	27.0	.	NM_001161546	B4E007	Silent	SNP	ENST00000434752.2	hg19	CCDS54909.1																																																																																			.	.	.	none		0.736	PROB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000470735.1	NM_001161546	
NSD1	64324	hgsc.bcm.edu	37	5	176562915	176562915	+	Missense_Mutation	SNP	T	T	G	rs374083142		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr5:176562915T>G	ENST00000439151.2	+	2	856	c.811T>G	c.(811-813)Tta>Gta	p.L271V	NSD1_ENST00000354179.4_Intron|NSD1_ENST00000347982.4_Intron|NSD1_ENST00000361032.4_Missense_Mutation_p.L271V|NSD1_ENST00000511258.1_Intron	NM_022455.4	NP_071900.2	Q96L73	NSD1_HUMAN	nuclear receptor binding SET domain protein 1	271					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)		AGAAGAGCAATTAAACTCAAT	0.383			T	NUP98	AML		Sotos Syndrome		Weaver syndrome;Sotos syndrome;Beckwith-Wiedemann syndrome	HNSCC(47;0.14)																											p.L271V		Atlas-SNP	.		Dom	yes		5	5q35	64324	nuclear receptor binding SET domain protein 1	yes	L	.	NSD1	416	.	0			c.T811G						PASS	.						66.0	67.0	67.0					5																	176562915		2203	4300	6503	SO:0001583	missense	64324	exon2	Familial Cancer Database	Weaver-Smith syndrome;Cerebral Gigantism;BWS, Exomphalos-Macroglossia-Gigantism (EMG) syndrome, Wiedemann-Beckwith syndrome, WBS	GAGCAATTAAACT	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.811T>G	chr5.hg19:g.176562915T>G	ENSP00000395929:p.Leu271Val	105.0	0.0	.		91.0	31.0	.	NM_022455	Q96PD8|Q96RN7	Missense_Mutation	SNP	ENST00000439151.2	hg19	CCDS4412.1	.	.	.	.	.	.	.	.	.	.	T	12.12	1.841288	0.32513	.	.	ENSG00000165671	ENST00000439151;ENST00000361032	D;D	0.94576	-3.23;-3.46	5.19	5.19	0.71726	.	0.186195	0.26485	N	0.024119	D	0.88633	0.6489	N	0.14661	0.345	0.80722	D	1	B;B;B	0.30634	0.288;0.19;0.137	B;B;B	0.30572	0.117;0.055;0.051	D	0.88112	0.2826	10	0.72032	D	0.01	.	12.6728	0.56876	0.0:0.0:0.0:1.0	.	271;271;271	Q96L73-3;Q96L73;Q6PJ64	.;NSD1_HUMAN;.	V	271	ENSP00000395929:L271V;ENSP00000354310:L271V	ENSP00000354310:L271V	L	+	1	2	NSD1	176495521	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.025000	0.57225	2.189000	0.69895	0.533000	0.62120	TTA	.	.	.	alt		0.383	NSD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253412.2	NM_172349	
MRPS10	55173	hgsc.bcm.edu	37	6	42176601	42176601	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:42176601T>A	ENST00000053468.3	-	6	532	c.517A>T	c.(517-519)Aca>Tca	p.T173S		NM_018141.3	NP_060611.2	P82664	RT10_HUMAN	mitochondrial ribosomal protein S10	173						mitochondrion (GO:0005739)|ribosome (GO:0005840)				endometrium(1)|lung(1)	2	Colorectal(47;0.196)		Colorectal(64;0.00062)|COAD - Colon adenocarcinoma(64;0.00152)|Epithelial(12;0.00528)			TATACCTTTGTTACTTCCATG	0.443																																					p.T173S		Atlas-SNP	.											.	MRPS10	9	.	0			c.A517T						PASS	.						103.0	98.0	100.0					6																	42176601		2203	4300	6503	SO:0001583	missense	55173	exon6			CCTTTGTTACTTC		CCDS4866.1	6p21.1	2012-09-13			ENSG00000048544	ENSG00000048544		"""Mitochondrial ribosomal proteins / small subunits"""	14502	protein-coding gene	gene with protein product		611976				11279123	Standard	NM_018141		Approved	FLJ10567	uc003osa.4	P82664	OTTHUMG00000014694	ENST00000053468.3:c.517A>T	chr6.hg19:g.42176601T>A	ENSP00000053468:p.Thr173Ser	178.0	0.0	.		152.0	45.0	.	NM_018141	B2RE89|Q9H3E5|Q9NVR3	Missense_Mutation	SNP	ENST00000053468.3	hg19	CCDS4866.1	.	.	.	.	.	.	.	.	.	.	T	19.87	3.906883	0.72868	.	.	ENSG00000048544	ENST00000053468	.	.	.	5.78	5.78	0.91487	.	0.094475	0.64402	D	0.000001	T	0.49047	0.1534	L	0.41415	1.275	0.46901	D	0.999243	D	0.53462	0.96	P	0.52454	0.699	T	0.46456	-0.9190	9	0.32370	T	0.25	-7.8115	15.0972	0.72244	0.0:0.0:0.0:1.0	.	173	P82664	RT10_HUMAN	S	173	.	ENSP00000053468:T173S	T	-	1	0	MRPS10	42284579	1.000000	0.71417	1.000000	0.80357	0.909000	0.53808	7.043000	0.76572	2.200000	0.70718	0.460000	0.39030	ACA	.	.	.	none		0.443	MRPS10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040547.1		
EEF1A1	1915	hgsc.bcm.edu	37	6	74227601	74227601	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:74227601C>T	ENST00000316292.9	-	7	2312	c.1321G>A	c.(1321-1323)Gtg>Atg	p.V441M	EEF1A1_ENST00000491404.1_Intron|EEF1A1_ENST00000331523.2_Missense_Mutation_p.V441M|EEF1A1_ENST00000309268.6_Missense_Mutation_p.V441M	NM_001402.5	NP_001393.1	P68104	EF1A1_HUMAN	eukaryotic translation elongation factor 1 alpha 1	441					cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|translation (GO:0006412)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|eukaryotic translation elongation factor 1 complex (GO:0005853)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|translation elongation factor activity (GO:0003746)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(6)|prostate(2)|skin(3)	18						TTCTTGTCCACTGCTTTGATG	0.443											OREG0003893	type=REGULATORY REGION|Gene=BC038897|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.V441M		Atlas-SNP	.											.	EEF1A1	56	.	0			c.G1321A						PASS	.						29.0	30.0	30.0					6																	74227601		2203	4296	6499	SO:0001583	missense	1915	exon8			TGTCCACTGCTTT	BC019669	CCDS4980.1	6q14.1	2010-06-30	2004-11-19		ENSG00000156508	ENSG00000156508			3189	protein-coding gene	gene with protein product		130590	"""leukocyte receptor cluster (LRC) member 7"""	EF1A, EEF1A, LENG7		8812466, 10941842	Standard	NM_001402		Approved	EE1A1	uc003phj.3	P68104	OTTHUMG00000015031	ENST00000316292.9:c.1321G>A	chr6.hg19:g.74227601C>T	ENSP00000339063:p.Val441Met	172.0	0.0	.	1151	101.0	25.0	.	NM_001402	P04719|P04720|Q6IQ15	Missense_Mutation	SNP	ENST00000316292.9	hg19	CCDS4980.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.352587	0.82132	.	.	ENSG00000156508	ENST00000316292;ENST00000309268;ENST00000331523;ENST00000391977	T;T;T	0.52526	0.66;0.66;0.66	4.81	4.81	0.61882	Translation elongation factor EF1A/initiation factor IF2gamma, C-terminal (2);Translation elongation factor EFTu/EF1A, C-terminal (2);	0.072938	0.53938	U	0.000048	T	0.68229	0.2978	H	0.94462	3.54	0.80722	D	1	D;D;D	0.55172	0.97;0.97;0.97	P;P;P	0.54590	0.756;0.756;0.756	T	0.79850	-0.1629	10	0.87932	D	0	.	18.3119	0.90203	0.0:1.0:0.0:0.0	.	441;441;441	P68104;Q6IPS9;Q5VTE0	EF1A1_HUMAN;.;EF1A3_HUMAN	M	441;441;441;420	ENSP00000339063:V441M;ENSP00000339053:V441M;ENSP00000330054:V441M	ENSP00000339053:V441M	V	-	1	0	EEF1A1	74284322	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.405000	0.80007	2.381000	0.81170	0.556000	0.70494	GTG	.	.	.	none		0.443	EEF1A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041210.2	NM_001402	
RIPPLY2	134701	hgsc.bcm.edu	37	6	84563845	84563845	+	Silent	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:84563845C>T	ENST00000369689.1	+	3	355	c.204C>T	c.(202-204)gcC>gcT	p.A68A	RIPPLY2_ENST00000369687.1_Silent_p.A10A	NM_001009994.1	NP_001009994.1	Q5TAB7	RIPP2_HUMAN	ripply transcriptional repressor 2	68					bone morphogenesis (GO:0060349)|determination of left/right symmetry (GO:0007368)|Notch signaling pathway (GO:0007219)|ossification (GO:0001503)|post-anal tail morphogenesis (GO:0036342)|regulation of gene expression (GO:0010468)|somite rostral/caudal axis specification (GO:0032525)|somitogenesis (GO:0001756)	nucleus (GO:0005634)				large_intestine(2)|lung(4)|urinary_tract(1)	7						TGACCGCAGCCTCAGGAAAGC	0.592																																					p.A68A		Atlas-SNP	.											.	RIPPLY2	17	.	0			c.C204T						PASS	.						102.0	96.0	98.0					6																	84563845		2203	4300	6503	SO:0001819	synonymous_variant	134701	exon3			CGCAGCCTCAGGA	BC130460	CCDS34493.1	6q14.2	2013-07-23	2013-07-23	2008-05-07	ENSG00000203877	ENSG00000203877			21390	protein-coding gene	gene with protein product		609891	"""chromosome 6 open reading frame 159"", ""ripply2 homolog (zebrafish)"""	C6orf159			Standard	NM_001009994		Approved	dJ237I15.1	uc003pke.3	Q5TAB7	OTTHUMG00000015117	ENST00000369689.1:c.204C>T	chr6.hg19:g.84563845C>T		163.0	0.0	.		132.0	13.0	.	NM_001009994	Q5TAB6	Silent	SNP	ENST00000369689.1	hg19	CCDS34493.1																																																																																			.	.	.	none		0.592	RIPPLY2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041360.1	NM_001009994	
GATAD1	57798	hgsc.bcm.edu	37	7	92083893	92083893	+	Silent	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:92083893A>G	ENST00000287957.3	+	4	790	c.513A>G	c.(511-513)agA>agG	p.R171R	AC007566.10_ENST00000427458.1_RNA	NM_021167.4	NP_066990.3	Q8WUU5	GATD1_HUMAN	GATA zinc finger domain containing 1	171						nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			endometrium(1)|kidney(2)|lung(3)	6	all_cancers(62;1.63e-10)|all_epithelial(64;8.33e-10)|Breast(17;0.00311)|all_lung(186;0.0498)|Lung NSC(181;0.0676)		STAD - Stomach adenocarcinoma(171;4.51e-05)|GBM - Glioblastoma multiforme(5;8.83e-05)|all cancers(6;0.000136)|Lung(22;0.123)|Epithelial(20;0.179)|LUSC - Lung squamous cell carcinoma(200;0.225)			CTCAAATCAGAGGTTTTATCC	0.458																																					p.R171R		Atlas-SNP	.											.	GATAD1	10	.	0			c.A513G						PASS	.						193.0	183.0	186.0					7																	92083893		2203	4300	6503	SO:0001819	synonymous_variant	57798	exon4			AATCAGAGGTTTT		CCDS5625.1	7q21-q22	2014-09-17			ENSG00000157259	ENSG00000157259		"""GATA zinc finger domain containing"""	29941	protein-coding gene	gene with protein product	"""ocular development associated gene"""	614518				12062807	Standard	NM_021167		Approved	ODAG, RG083M05.2, FLJ22489	uc003ulx.2	Q8WUU5	OTTHUMG00000131201	ENST00000287957.3:c.513A>G	chr7.hg19:g.92083893A>G		148.0	0.0	.		136.0	63.0	.	NM_021167	B2RE37|D6W5Q5|Q8N5Y5|Q99995|Q9H689	Silent	SNP	ENST00000287957.3	hg19	CCDS5625.1																																																																																			.	.	.	none		0.458	GATAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253929.2	NM_021167	
PDK4	5166	hgsc.bcm.edu	37	7	95217131	95217131	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr7:95217131T>C	ENST00000005178.5	-	8	975	c.778A>G	c.(778-780)Atg>Gtg	p.M260V		NM_002612.3	NP_002603.1	Q16654	PDK4_HUMAN	pyruvate dehydrogenase kinase, isozyme 4	260	Histidine kinase. {ECO:0000255|PROSITE- ProRule:PRU00107}.				cellular metabolic process (GO:0044237)|cellular response to fatty acid (GO:0071398)|cellular response to starvation (GO:0009267)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|negative regulation of anoikis (GO:2000811)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|reactive oxygen species metabolic process (GO:0072593)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of bone resorption (GO:0045124)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of fatty acid biosynthetic process (GO:0042304)|regulation of fatty acid oxidation (GO:0046320)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|response to starvation (GO:0042594)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|liver(1)|lung(4)|skin(1)|upper_aerodigestive_tract(1)	15	all_cancers(62;1.06e-10)|all_epithelial(64;1.04e-09)|Lung NSC(181;0.128)|all_lung(186;0.151)		STAD - Stomach adenocarcinoma(171;0.0151)			GTTGCCCGCATTGCATTCTAA	0.363																																					p.M260V		Atlas-SNP	.											.	PDK4	42	.	0			c.A778G						PASS	.						74.0	74.0	74.0					7																	95217131		2203	4300	6503	SO:0001583	missense	5166	exon8			CCCGCATTGCATT	U54617	CCDS5643.1	7q21.3-q22.1	2008-07-18	2005-11-16		ENSG00000004799	ENSG00000004799			8812	protein-coding gene	gene with protein product		602527	"""pyruvate dehydrogenase kinase, isoenzyme 4"""			7499431	Standard	NM_002612		Approved		uc003uoa.3	Q16654	OTTHUMG00000153977	ENST00000005178.5:c.778A>G	chr7.hg19:g.95217131T>C	ENSP00000005178:p.Met260Val	86.0	0.0	.		99.0	4.0	.	NM_002612		Missense_Mutation	SNP	ENST00000005178.5	hg19	CCDS5643.1	.	.	.	.	.	.	.	.	.	.	T	16.21	3.058332	0.55325	.	.	ENSG00000004799	ENST00000005178;ENST00000542888	T	0.46451	0.87	5.34	5.34	0.76211	Signal transduction histidine kinase, core (1);ATPase-like, ATP-binding domain (4);	0.000000	0.85682	D	0.000000	T	0.54431	0.1858	L	0.41027	1.25	0.80722	D	1	D	0.56968	0.978	D	0.64237	0.923	T	0.57705	-0.7765	10	0.87932	D	0	.	15.6388	0.76977	0.0:0.0:0.0:1.0	.	260	Q16654	PDK4_HUMAN	V	260;224	ENSP00000005178:M260V	ENSP00000005178:M260V	M	-	1	0	PDK4	95055067	1.000000	0.71417	1.000000	0.80357	0.357000	0.29423	4.977000	0.63792	2.154000	0.67381	0.482000	0.46254	ATG	.	.	.	none		0.363	PDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333298.1	NM_002612	
WHSC1L1	54904	hgsc.bcm.edu	37	8	38175506	38175506	+	Intron	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:38175506C>T	ENST00000317025.8	-	9	2373				WHSC1L1_ENST00000525081.1_5'UTR|WHSC1L1_ENST00000316985.3_Missense_Mutation_p.V636I|WHSC1L1_ENST00000527502.1_Intron|WHSC1L1_ENST00000433384.2_Intron	NM_023034.1	NP_075447.1	Q9BZ95	NSD3_HUMAN	Wolf-Hirschhorn syndrome candidate 1-like 1						histone lysine methylation (GO:0034968)|histone methylation (GO:0016571)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|endometrium(3)|kidney(3)|large_intestine(2)|lung(10)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	24	Colorectal(12;0.000442)|Esophageal squamous(3;0.0725)	all_lung(54;0.00787)|Lung NSC(58;0.0295)|Hepatocellular(245;0.065)	Epithelial(3;3.12e-43)|all cancers(3;1.72e-38)|BRCA - Breast invasive adenocarcinoma(5;2.84e-27)|LUSC - Lung squamous cell carcinoma(2;2.79e-25)|Lung(2;5.03e-23)|COAD - Colon adenocarcinoma(9;0.0511)			GCTGCGGAGACGGAGCTGTCA	0.537			T	NUP98	AML																																p.V636I		Atlas-SNP	.		Dom	yes		8	8p12	54904	Wolf-Hirschhorn syndrome candidate 1-like 1 (NSD3)		L	.	WHSC1L1	137	.	0			c.G1906A						PASS	.						90.0	82.0	85.0					8																	38175506		2203	4300	6503	SO:0001627	intron_variant	54904	exon10			CGGAGACGGAGCT	AF332469	CCDS6105.1, CCDS43729.1	8p11.2	2013-05-20			ENSG00000147548	ENSG00000147548			12767	protein-coding gene	gene with protein product		607083				10802047, 23269674	Standard	NM_023034		Approved	FLJ20353, NSD3	uc003xli.3	Q9BZ95		ENST00000317025.8:c.1855+906G>A	chr8.hg19:g.38175506C>T		72.0	0.0	.		79.0	28.0	.	NM_017778	B7ZL11|D3DSX1|Q1RMD3|Q3B796|Q6ZSA5|Q9BYU8|Q9BYU9|Q9H2M8|Q9H9W9|Q9NXA6	Missense_Mutation	SNP	ENST00000317025.8	hg19	CCDS43729.1	.	.	.	.	.	.	.	.	.	.	C	15.44	2.835251	0.50951	.	.	ENSG00000147548	ENST00000316985	T	0.64438	-0.1	6.17	5.29	0.74685	.	.	.	.	.	T	0.50752	0.1634	.	.	.	0.21499	N	0.999666	B	0.14805	0.011	B	0.10450	0.005	T	0.33033	-0.9884	8	0.40728	T	0.16	.	11.9912	0.53176	0.0:0.9189:0.0:0.0811	.	636	Q9BZ95-3	.	I	636	ENSP00000313410:V636I	ENSP00000313410:V636I	V	-	1	0	WHSC1L1	38294663	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.355000	0.44107	2.941000	0.99782	0.655000	0.94253	GTC	.	.	.	none		0.537	WHSC1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381924.3	NM_023034	
JAK2	3717	hgsc.bcm.edu	37	9	5126752	5126752	+	Silent	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:5126752T>C	ENST00000381652.3	+	25	3854	c.3360T>C	c.(3358-3360)gcT>gcC	p.A1120A	JAK2_ENST00000544510.1_Silent_p.A971A|JAK2_ENST00000487310.1_3'UTR|JAK2_ENST00000539801.1_Silent_p.A1120A	NM_004972.3	NP_004963.1	O60674	JAK2_HUMAN	Janus kinase 2	1120	Protein kinase 2. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	GGGATCTAGCTCTTCGAGTGG	0.348		1	"""T, Mis, O"""	"""ETV6, PCM1, BCR"""	"""ALL, AML, MPD,  CML"""				Polycythemia Vera, Familial																												p.A1120A		Atlas-SNP	.		Dom	yes		9	9p24	3717	Janus kinase 2		L	.	JAK2	35466	.	0			c.T3360C						PASS	.						79.0	74.0	76.0					9																	5126752		2203	4299	6502	SO:0001819	synonymous_variant	3717	exon25	Familial Cancer Database		TCTAGCTCTTCGA		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.3360T>C	chr9.hg19:g.5126752T>C		76.0	0.0	.		58.0	45.0	.	NM_004972	O14636|O75297	Silent	SNP	ENST00000381652.3	hg19	CCDS6457.1																																																																																			.	.	.	none		0.348	JAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051609.1		
DAPK1	1612	hgsc.bcm.edu	37	9	90321821	90321821	+	Missense_Mutation	SNP	T	T	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:90321821T>G	ENST00000408954.3	+	26	4170	c.3835T>G	c.(3835-3837)Ttc>Gtc	p.F1279V	DAPK1_ENST00000491893.1_Missense_Mutation_p.F1213V|DAPK1_ENST00000358077.5_Missense_Mutation_p.F1279V|DAPK1_ENST00000469640.2_Missense_Mutation_p.F1304V|DAPK1_ENST00000472284.1_Missense_Mutation_p.F1279V	NM_004938.2	NP_004929.2	P53355	DAPK1_HUMAN	death-associated protein kinase 1	1279					apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cellular response to interferon-gamma (GO:0071346)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|negative regulation of translation (GO:0017148)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of autophagy (GO:0010506)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)	ATP binding (GO:0005524)|calmodulin binding (GO:0005516)|calmodulin-dependent protein kinase activity (GO:0004683)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(5)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(27)|liver(2)|lung(17)|ovary(1)|prostate(2)|skin(3)|stomach(1)	72						CAAGGAAAGCTTCAGCAGCAT	0.567									Chronic Lymphocytic Leukemia, Familial Clustering of																												p.F1279V		Atlas-SNP	.											.	DAPK1	329	.	0			c.T3835G						PASS	.						54.0	62.0	60.0					9																	90321821		2131	4237	6368	SO:0001583	missense	1612	exon26	Familial Cancer Database	Familial CLL	GAAAGCTTCAGCA	X76104	CCDS43842.1	9q34.1	2013-01-10			ENSG00000196730	ENSG00000196730		"""Ankyrin repeat domain containing"""	2674	protein-coding gene	gene with protein product		600831				8530096	Standard	XM_005251757		Approved	DAPK	uc004apd.3	P53355	OTTHUMG00000020150	ENST00000408954.3:c.3835T>G	chr9.hg19:g.90321821T>G	ENSP00000386135:p.Phe1279Val	132.0	0.0	.		108.0	79.0	.	NM_004938	B7ZLD2|B7ZLE7|Q14CQ7|Q1W5W0|Q68CP8|Q6ZRZ3|Q9BTL8	Missense_Mutation	SNP	ENST00000408954.3	hg19	CCDS43842.1	.	.	.	.	.	.	.	.	.	.	T	18.91	3.723375	0.68959	.	.	ENSG00000196730	ENST00000358077;ENST00000472284;ENST00000469640;ENST00000408954;ENST00000491893	T;T;T;T;T	0.63255	0.05;0.05;0.03;0.05;-0.03	5.66	5.66	0.87406	.	0.000000	0.56097	D	0.000040	T	0.77552	0.4147	M	0.66939	2.045	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.998	D;D;D	0.83275	0.987;0.996;0.987	T	0.77534	-0.2552	10	0.45353	T	0.12	.	16.2026	0.82095	0.0:0.0:0.0:1.0	.	1213;1279;1279	B7ZLE7;P53355-3;P53355	.;.;DAPK1_HUMAN	V	1279;1279;1304;1279;1213	ENSP00000350785:F1279V;ENSP00000417076:F1279V;ENSP00000418885:F1304V;ENSP00000386135:F1279V;ENSP00000419026:F1213V	ENSP00000350785:F1279V	F	+	1	0	DAPK1	89511641	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.997000	0.88414	2.285000	0.76669	0.533000	0.62120	TTC	.	.	.	none		0.567	DAPK1-010	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356843.1	NM_004938	
RAPGEF1	2889	hgsc.bcm.edu	37	9	134505712	134505712	+	Splice_Site	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr9:134505712C>T	ENST00000372189.3	-	6	724		c.e6-1		RAPGEF1_ENST00000372190.3_Splice_Site|RAPGEF1_ENST00000481260.1_Intron|RAPGEF1_ENST00000372195.1_Splice_Site	NM_005312.2	NP_005303.2	Q13905	RPGF1_HUMAN	Rap guanine nucleotide exchange factor (GEF) 1						activation of MAPKK activity (GO:0000186)|blood vessel development (GO:0001568)|cellular response to cAMP (GO:0071320)|cellular response to nerve growth factor stimulus (GO:1990090)|establishment of endothelial barrier (GO:0061028)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of neural precursor cell proliferation (GO:2000178)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of Ras protein signal transduction (GO:0046580)|nerve growth factor signaling pathway (GO:0038180)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of neuron projection development (GO:0010976)|positive regulation of Rap GTPase activity (GO:0032854)|Rap protein signal transduction (GO:0032486)|regulation of cell junction assembly (GO:1901888)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)	Rap guanyl-nucleotide exchange factor activity (GO:0017034)			NS(2)|breast(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|large_intestine(8)|lung(9)|ovary(2)|prostate(4)|skin(1)|urinary_tract(1)	39		Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.19e-05)|Epithelial(140;0.000364)		TGACCAGCTCCTACCCCCACA	0.592																																					.		Atlas-SNP	.											.	RAPGEF1	126	.	0			c.601-1G>A						PASS	.						57.0	65.0	62.0					9																	134505712		2074	4208	6282	SO:0001630	splice_region_variant	2889	exon7			CAGCTCCTACCCC	BC041710	CCDS48047.1	9q34.3	2008-02-05	2004-03-01	2004-03-02	ENSG00000107263	ENSG00000107263			4568	protein-coding gene	gene with protein product		600303	"""guanine nucleotide-releasing factor 2 (specific for crk proto-oncogene)"""	GRF2		7959692, 7512734	Standard	NM_005312		Approved	C3G	uc022bos.1	Q13905	OTTHUMG00000020829	ENST00000372189.3:c.601-1G>A	chr9.hg19:g.134505712C>T		87.0	0.0	.		97.0	9.0	.	NM_005312	Q5JUE4|Q8IV73	Splice_Site	SNP	ENST00000372189.3	hg19	CCDS48047.1	.	.	.	.	.	.	.	.	.	.	C	20.5	4.006457	0.74932	.	.	ENSG00000107263	ENST00000266110;ENST00000372195;ENST00000429421;ENST00000372189;ENST00000372190;ENST00000411834;ENST00000337036;ENST00000357686	.	.	.	5.45	5.45	0.79879	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0057	0.80362	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RAPGEF1	133495533	1.000000	0.71417	0.996000	0.52242	0.758000	0.43043	6.814000	0.75236	2.549000	0.85964	0.655000	0.94253	.	.	.	.	none		0.592	RAPGEF1-001	KNOWN	non_canonical_U12|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054759.2	NM_005312	Intron
KIN	22944	hgsc.bcm.edu	37	10	7811178	7811178	+	Splice_Site	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:7811178C>T	ENST00000379562.4	-	8	846		c.e8+1		KIN_ENST00000535925.1_Splice_Site|KIN_ENST00000543003.1_Splice_Site|KIN_ENST00000463666.1_5'Flank	NM_012311.3	NP_036443.1			Kin17 DNA and RNA binding protein											endometrium(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|pancreas(1)|skin(2)	19						ATAAACTGTACCTCCATGATT	0.343																																					.		Atlas-SNP	.											.	KIN	39	.	0			c.798+1G>A						PASS	.						99.0	99.0	99.0					10																	7811178		2203	4300	6503	SO:0001630	splice_region_variant	22944	exon9			ACTGTACCTCCAT	AJ005273	CCDS7080.1	10p15-p14	2014-07-15	2014-07-15		ENSG00000151657	ENSG00000151657			6327	protein-coding gene	gene with protein product		601720	"""antigenic determinant of recA protein (mouse) homolog"", ""KIN, antigenic determinant of recA protein homolog (mouse)"""			1923796, 24140279	Standard	NM_012311		Approved	KIN17, Rts2	uc001ijt.3	O60870	OTTHUMG00000017634	ENST00000379562.4:c.798+1G>A	chr10.hg19:g.7811178C>T		21.0	0.0	.		23.0	8.0	.	NM_012311		Splice_Site	SNP	ENST00000379562.4	hg19	CCDS7080.1	.	.	.	.	.	.	.	.	.	.	C	20.2	3.955761	0.73902	.	.	ENSG00000151657	ENST00000535925;ENST00000379562;ENST00000543003	.	.	.	5.12	5.12	0.69794	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.75	0.85483	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	KIN	7851184	1.000000	0.71417	0.995000	0.50966	0.891000	0.51852	5.846000	0.69444	2.363000	0.80096	0.650000	0.86243	.	.	.	.	none		0.343	KIN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046683.2	NM_012311	Intron
MUC2	4583	hgsc.bcm.edu	37	11	1093292	1093292	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:1093292C>T	ENST00000441003.2	+	30	5138	c.5111C>T	c.(5110-5112)aCc>aTc	p.T1704I	MUC2_ENST00000359061.5_Missense_Mutation_p.T1671I|MUC2_ENST00000333592.6_5'Flank|MUC2_ENST00000361558.6_Intron	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	atcaccaccaccactacggtg	0.637																																					p.T1704I		Atlas-SNP	.											.	MUC2	614	.	0			c.C5111T						PASS	.						107.0	156.0	138.0					11																	1093292		1878	3453	5331	SO:0001583	missense	4583	exon30			CCACCACCACTAC	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5111C>T	chr11.hg19:g.1093292C>T	ENSP00000415183:p.Thr1704Ile	97.0	0.0	.		107.0	7.0	.	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	hg19		.	.	.	.	.	.	.	.	.	.	C	2.150	-0.394632	0.04899	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11063	2.81;2.84	1.6	-2.66	0.06077	.	2.760050	0.04005	U	0.297091	T	0.06416	0.0165	.	.	.	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.36286	-0.9754	9	0.36615	T	0.2	.	2.477	0.04578	0.4942:0.3128:0.0:0.1931	.	1704	E7EUV1	.	I	1704;1671	ENSP00000415183:T1704I;ENSP00000351956:T1671I	ENSP00000351956:T1671I	T	+	2	0	MUC2	1083292	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.330000	0.19715	-0.514000	0.06488	0.184000	0.17185	ACC	.	.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
MPEG1	219972	hgsc.bcm.edu	37	11	58978564	58978564	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:58978564C>T	ENST00000361050.3	-	1	1860	c.1775G>A	c.(1774-1776)aGg>aAg	p.R592K		NM_001039396.1	NP_001034485.1	Q2M385	MPEG1_HUMAN	macrophage expressed 1	592						integral component of membrane (GO:0016021)				NS(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(21)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		all_epithelial(135;0.125)				AGGTGGGAGCCTGGCAGGGGG	0.582																																					p.R592K		Atlas-SNP	.											.	MPEG1	72	.	0			c.G1775A						PASS	.						87.0	97.0	93.0					11																	58978564		1945	4123	6068	SO:0001583	missense	219972	exon1			GGGAGCCTGGCAG	AK097211	CCDS41650.1	11q12.1	2013-07-31				ENSG00000197629			29619	protein-coding gene	gene with protein product	"""macrophage expressed gene 1"""	610390				7888681, 23257510	Standard	NM_001039396		Approved	MPG1	uc001nnu.4	Q2M385		ENST00000361050.3:c.1775G>A	chr11.hg19:g.58978564C>T	ENSP00000354335:p.Arg592Lys	96.0	0.0	.		104.0	39.0	.	NM_001039396	Q2M1T6|Q8TEF8	Missense_Mutation	SNP	ENST00000361050.3	hg19	CCDS41650.1	.	.	.	.	.	.	.	.	.	.	C	14.82	2.648686	0.47258	.	.	ENSG00000197629	ENST00000361050	T	0.23147	1.92	5.69	5.69	0.88448	.	0.109255	0.64402	D	0.000015	T	0.42154	0.1190	L	0.61387	1.9	0.34323	D	0.686779	D	0.60575	0.988	P	0.54759	0.76	T	0.52601	-0.8554	10	0.44086	T	0.13	-27.9243	16.7224	0.85413	0.0:1.0:0.0:0.0	.	592	Q2M385	MPEG1_HUMAN	K	592	ENSP00000354335:R592K	ENSP00000354335:R592K	R	-	2	0	MPEG1	58735140	0.678000	0.27586	1.000000	0.80357	0.942000	0.58702	0.292000	0.19011	2.682000	0.91365	0.655000	0.94253	AGG	.	.	.	none		0.582	MPEG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370027.1	NM_001039396	
PYGM	5837	hgsc.bcm.edu	37	11	64517951	64517951	+	Missense_Mutation	SNP	T	T	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:64517951T>A	ENST00000164139.3	-	17	2472	c.2074A>T	c.(2074-2076)Acc>Tcc	p.T692S	PYGM_ENST00000462303.1_5'Flank|PYGM_ENST00000377432.3_Missense_Mutation_p.T604S	NM_005609.2	NP_005600.1	P11217	PYGM_HUMAN	phosphorylase, glycogen, muscle	692					carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen catabolic process (GO:0005980)|glycogen metabolic process (GO:0005977)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glycogen phosphorylase activity (GO:0008184)|nucleotide binding (GO:0000166)|pyridoxal phosphate binding (GO:0030170)			cervix(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(21)|ovary(3)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						CCGTCCATGGTGCCAATGGTC	0.567																																					p.T692S		Atlas-SNP	.											.	PYGM	77	.	0			c.A2074T						PASS	.						167.0	151.0	157.0					11																	64517951		2201	4297	6498	SO:0001583	missense	5837	exon17			CCATGGTGCCAAT		CCDS8079.1, CCDS53659.1	11q12-q13.2	2013-03-01	2008-07-31		ENSG00000068976	ENSG00000068976	2.4.1.1	"""Glycogen phosphorylases"""	9726	protein-coding gene	gene with protein product	"""McArdle syndrome"", ""glycogen storage disease type V"", ""glycogen phosphorylase, muscle form"""	608455	"""phosphorylase, glycogen; muscle"""				Standard	NM_005609		Approved		uc001oax.4	P11217	OTTHUMG00000066835	ENST00000164139.3:c.2074A>T	chr11.hg19:g.64517951T>A	ENSP00000164139:p.Thr692Ser	156.0	0.0	.		114.0	38.0	.	NM_005609	A0AVK1|A6NDY6	Missense_Mutation	SNP	ENST00000164139.3	hg19	CCDS8079.1	.	.	.	.	.	.	.	.	.	.	T	28.2	4.903517	0.92035	.	.	ENSG00000068976	ENST00000377432;ENST00000164139;ENST00000540450	D;D	0.95342	-3.68;-3.68	4.91	4.91	0.64330	.	0.000000	0.52532	D	0.000074	D	0.96895	0.8986	M	0.93854	3.465	0.80722	D	1	P;P	0.48407	0.91;0.91	P;P	0.52386	0.697;0.697	D	0.97609	1.0128	10	0.87932	D	0	-39.6172	12.5412	0.56172	0.0:0.0:0.0:1.0	.	604;692	A6NDY6;P11217	.;PYGM_HUMAN	S	604;692;673	ENSP00000366650:T604S;ENSP00000164139:T692S	ENSP00000164139:T692S	T	-	1	0	PYGM	64274527	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.832000	0.86757	2.073000	0.62155	0.454000	0.30748	ACC	.	.	.	none		0.567	PYGM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143254.2	NM_005609	
COA4	51287	hgsc.bcm.edu	37	11	73584202	73584202	+	Missense_Mutation	SNP	C	C	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:73584202C>A	ENST00000355693.4	-	2	469	c.222G>T	c.(220-222)gaG>gaT	p.E74D	COA4_ENST00000537289.1_Missense_Mutation_p.E74D|COA4_ENST00000541455.1_Missense_Mutation_p.E83D|COA4_ENST00000537581.1_5'Flank|COA4_ENST00000545127.1_Missense_Mutation_p.E74D	NM_016565.2	NP_057649.2	Q9NYJ1	COA4_HUMAN	cytochrome c oxidase assembly factor 4 homolog (S. cerevisiae)	74						mitochondrion (GO:0005739)											TCTGCAGCTCCTCTTGCCGCC	0.612																																					p.E74D		Atlas-SNP	.											.	.	.	.	0			c.G222T						PASS	.						108.0	81.0	90.0					11																	73584202		2200	4293	6493	SO:0001583	missense	51287	exon2			CAGCTCCTCTTGC	AF242180	CCDS8225.1	11q13.4	2013-10-18	2012-10-15	2012-10-15		ENSG00000181924		"""Coiled-coil-helix-coiled-coil-helix domain containing"", ""Mitochondrial respiratory chain complex assembly factors"""	24604	protein-coding gene	gene with protein product		608016	"""coiled-coil-helix-coiled-coil-helix domain containing 8"""	CHCHD8		11085516, 20624914	Standard	NM_016565		Approved	E2IG2, CMC3	uc001ouj.3	Q9NYJ1		ENST00000355693.4:c.222G>T	chr11.hg19:g.73584202C>A	ENSP00000347919:p.Glu74Asp	85.0	0.0	.		77.0	9.0	.	NM_016565	B2RAA0|Q69YU4	Missense_Mutation	SNP	ENST00000355693.4	hg19	CCDS8225.1	.	.	.	.	.	.	.	.	.	.	C	16.99	3.273202	0.59649	.	.	ENSG00000181924	ENST00000355693;ENST00000545127;ENST00000541455;ENST00000537289	.	.	.	6.02	2.73	0.32206	.	0.000000	0.85682	D	0.000000	T	0.34048	0.0884	.	.	.	0.33160	D	0.546821	P	0.39665	0.682	B	0.34038	0.174	T	0.50890	-0.8774	8	0.59425	D	0.04	-24.9482	8.1718	0.31260	0.0:0.6617:0.0:0.3383	.	74	Q9NYJ1	CHCH8_HUMAN	D	74;74;83;74	.	ENSP00000347919:E74D	E	-	3	2	CHCHD8	73261850	0.857000	0.29778	0.996000	0.52242	0.388000	0.30384	0.299000	0.19138	0.879000	0.35944	0.655000	0.94253	GAG	.	.	.	none		0.612	COA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397878.1	NM_016565	
PRCP	5547	hgsc.bcm.edu	37	11	82560214	82560214	+	Silent	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:82560214T>C	ENST00000313010.3	-	6	992	c.798A>G	c.(796-798)ccA>ccG	p.P266P	PRCP_ENST00000393399.2_Silent_p.P287P|PRCP_ENST00000535099.1_Silent_p.P161P	NM_005040.2	NP_005031.1	P42785	PCP_HUMAN	prolylcarboxypeptidase (angiotensinase C)	266	SKS domain.				angiogenesis involved in wound healing (GO:0060055)|blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|energy homeostasis (GO:0097009)|glucose homeostasis (GO:0042593)|negative regulation of systemic arterial blood pressure (GO:0003085)|plasma kallikrein-kinin cascade (GO:0002353)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of reactive oxygen species metabolic process (GO:2000377)|regulation of thyroid hormone mediated signaling pathway (GO:0002155)	basal part of cell (GO:0045178)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|plasma membrane (GO:0005886)	serine-type carboxypeptidase activity (GO:0004185)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(7)|prostate(1)|skin(2)|urinary_tract(1)	17						GAGAAGTTAATGGGCTGCATA	0.443																																					p.P287P		Atlas-SNP	.											.	PRCP	69	.	0			c.A861G						PASS	.						115.0	108.0	110.0					11																	82560214		2203	4300	6503	SO:0001819	synonymous_variant	5547	exon7			AGTTAATGGGCTG	BC001500, BI827978, L13977	CCDS8262.1, CCDS41695.1	11q14	2005-10-04				ENSG00000137509			9344	protein-coding gene	gene with protein product		176785				8344943	Standard	NM_199418		Approved	PCP, HUMPCP	uc001ozr.3	P42785		ENST00000313010.3:c.798A>G	chr11.hg19:g.82560214T>C		82.0	0.0	.		88.0	18.0	.	NM_199418	A8MU24|B2R7B7|B3KRK5|B5BU34	Silent	SNP	ENST00000313010.3	hg19	CCDS8262.1																																																																																			.	.	.	none		0.443	PRCP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391792.1	NM_005040	
DDX10	1662	hgsc.bcm.edu	37	11	108559718	108559718	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:108559718A>G	ENST00000322536.3	+	7	1033	c.904A>G	c.(904-906)Agt>Ggt	p.S302G	DDX10_ENST00000526794.1_Missense_Mutation_p.S302G	NM_004398.2	NP_004389.2	Q13206	DDX10_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10	302	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				metabolic process (GO:0008152)		ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|poly(A) RNA binding (GO:0044822)|RNA helicase activity (GO:0003724)			breast(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(11)|pancreas(1)|prostate(2)	27		all_cancers(61;1.29e-11)|all_epithelial(67;2.96e-07)|Melanoma(852;1.54e-05)|Acute lymphoblastic leukemia(157;4.24e-05)|all_hematologic(158;0.000141)|Breast(348;0.026)|all_neural(223;0.0729)		BRCA - Breast invasive adenocarcinoma(274;2.48e-05)|Epithelial(105;4.35e-05)|all cancers(92;0.000609)|OV - Ovarian serous cystadenocarcinoma(223;0.133)		GCAAAAAATAAGTGTGCTGTA	0.373			T	NUP98	AML*																																p.S302G		Atlas-SNP	.		Dom	yes		11	11q22-q23	1662	DEAD (Asp-Glu-Ala-Asp) box polypeptide 10		L	.	DDX10	70	.	0			c.A904G						PASS	.						194.0	193.0	193.0					11																	108559718		2201	4298	6499	SO:0001583	missense	1662	exon7			AAAATAAGTGTGC	U28042	CCDS8342.1	11q22-q23	2005-10-11	2003-06-13		ENSG00000178105	ENSG00000178105		"""DEAD-boxes"""	2735	protein-coding gene	gene with protein product		601235	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 10 (RNA helicase)"""			8660968	Standard	NM_004398		Approved	HRH-J8	uc001pkm.3	Q13206	OTTHUMG00000166540	ENST00000322536.3:c.904A>G	chr11.hg19:g.108559718A>G	ENSP00000314348:p.Ser302Gly	112.0	0.0	.		79.0	4.0	.	NM_004398	B2RCQ3|Q5BJD8	Missense_Mutation	SNP	ENST00000322536.3	hg19	CCDS8342.1	.	.	.	.	.	.	.	.	.	.	A	8.380	0.837213	0.16891	.	.	ENSG00000178105	ENST00000322536;ENST00000456020;ENST00000526794	T;T	0.04809	3.55;3.55	5.61	5.61	0.85477	Helicase, C-terminal (1);	0.171976	0.64402	D	0.000008	T	0.04092	0.0114	N	0.16130	0.375	0.30844	N	0.735378	B;B	0.20887	0.049;0.049	B;B	0.16722	0.016;0.016	T	0.20505	-1.0273	10	0.27082	T	0.32	-11.3262	15.8096	0.78547	1.0:0.0:0.0:0.0	.	302;302	Q13206;E9PIF2	DDX10_HUMAN;.	G	302;208;302	ENSP00000314348:S302G;ENSP00000432032:S302G	ENSP00000314348:S302G	S	+	1	0	DDX10	108064928	1.000000	0.71417	1.000000	0.80357	0.015000	0.08874	6.272000	0.72575	2.132000	0.65825	0.533000	0.62120	AGT	.	.	.	none		0.373	DDX10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390343.1	NM_004398	
TRAPPC4	51399	hgsc.bcm.edu	37	11	118895661	118895661	+	IGR	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:118895661T>C	ENST00000533632.1	+	0	1759				SLC37A4_ENST00000545985.1_Missense_Mutation_p.I417V|SLC37A4_ENST00000330775.7_Missense_Mutation_p.I438V|SLC37A4_ENST00000538950.1_Missense_Mutation_p.I344V|SLC37A4_ENST00000357590.5_Missense_Mutation_p.I439V|TRAPPC4_ENST00000533058.1_Missense_Mutation_p.C226R|SLC37A4_ENST00000525102.1_5'UTR	NM_016146.4	NP_057230.1	Q9Y296	TPPC4_HUMAN	trafficking protein particle complex 4						dendrite development (GO:0016358)|ER to Golgi vesicle-mediated transport (GO:0006888)|extracellular matrix organization (GO:0030198)	cis-Golgi network (GO:0005801)|dendrite (GO:0030425)|endoplasmic reticulum (GO:0005783)|Golgi stack (GO:0005795)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)|TRAPP complex (GO:0030008)				NS(1)|endometrium(1)|large_intestine(2)|lung(1)	5	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0523)|all_neural(223;0.224)|all_hematologic(192;0.243)		BRCA - Breast invasive adenocarcinoma(274;7.58e-05)		TTGGTGCGGATGTTTCGTAGG	0.597																																					p.I439V		Atlas-SNP	.											.	SLC37A4	19	.	0			c.A1315G						PASS	.						43.0	51.0	48.0					11																	118895661		2020	4175	6195	SO:0001628	intergenic_variant	2542	exon12			TGCGGATGTTTCG	AF078862	CCDS8407.1	11q23.3	2011-10-10				ENSG00000196655		"""Trafficking protein particle complex"""	19943	protein-coding gene	gene with protein product		610971				10810093	Standard	NM_016146		Approved	TRS23, SBDN, PTD009	uc010ryo.2	Q9Y296			chr11.hg19:g.118895661T>C		180.0	0.0	.		125.0	41.0	.	NM_001164278	A8K3A5|B4DME1	Missense_Mutation	SNP	ENST00000533632.1	hg19	CCDS8407.1	.	.	.	.	.	.	.	.	.	.	T	14.52	2.560807	0.45590	.	.	ENSG00000196655	ENST00000533058	T	0.50001	0.76	5.27	5.27	0.74061	.	.	.	.	.	T	0.52370	0.1730	L	0.36672	1.1	0.50171	D	0.999855	.	.	.	.	.	.	T	0.56147	-0.8027	7	0.87932	D	0	-22.4876	15.3661	0.74523	0.0:0.0:0.0:1.0	.	.	.	.	R	226	ENSP00000432920:C226R	ENSP00000432920:C226R	C	+	1	0	TRAPPC4	118400871	1.000000	0.71417	1.000000	0.80357	0.906000	0.53458	7.309000	0.78937	2.226000	0.72624	0.459000	0.35465	TGT	.	.	.	none		0.597	TRAPPC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389332.1	NM_016146	
NCAPD2	9918	hgsc.bcm.edu	37	12	6637492	6637492	+	Silent	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:6637492T>C	ENST00000315579.5	+	25	4096	c.3297T>C	c.(3295-3297)gcT>gcC	p.A1099A	NCAPD2_ENST00000545962.1_Silent_p.A1054A	NM_014865.3	NP_055680.3	Q15021	CND1_HUMAN	non-SMC condensin I complex, subunit D2	1099					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						ATCTGTATGCTCGGTAAGAGA	0.577																																					p.A1099A		Atlas-SNP	.											.	NCAPD2	99	.	0			c.T3297C						PASS	.						139.0	143.0	142.0					12																	6637492		2203	4300	6503	SO:0001819	synonymous_variant	9918	exon25			GTATGCTCGGTAA	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.3297T>C	chr12.hg19:g.6637492T>C		146.0	0.0	.		134.0	31.0	.	NM_014865	D3DUR4|Q8N6U3	Silent	SNP	ENST00000315579.5	hg19	CCDS8548.1																																																																																			.	.	.	none		0.577	NCAPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399964.1	NM_014865	
A2M	2	hgsc.bcm.edu	37	12	9243036	9243036	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:9243036G>T	ENST00000318602.7	-	20	2819	c.2512C>A	c.(2512-2514)Cca>Aca	p.P838T		NM_000014.4	NP_000005	P01023	A2MG_HUMAN	alpha-2-macroglobulin	838					blood coagulation (GO:0007596)|blood coagulation, intrinsic pathway (GO:0007597)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|negative regulation of complement activation, lectin pathway (GO:0001869)|negative regulation of endopeptidase activity (GO:0010951)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|stem cell differentiation (GO:0048863)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|platelet alpha granule lumen (GO:0031093)	calcium-dependent protein binding (GO:0048306)|enzyme binding (GO:0019899)|growth factor binding (GO:0019838)|interleukin-1 binding (GO:0019966)|interleukin-8 binding (GO:0019959)|protease binding (GO:0002020)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|tumor necrosis factor binding (GO:0043120)			breast(1)|central_nervous_system(6)|cervix(1)|endometrium(5)|kidney(6)|large_intestine(17)|lung(30)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(3)	77					Bacitracin(DB00626)|Becaplermin(DB00102)|Ocriplasmin(DB08888)	TTCTCCACTGGGACAGCTAGG	0.537																																					p.P838T		Atlas-SNP	.											.	A2M	180	.	0			c.C2512A						PASS	.						97.0	100.0	99.0					12																	9243036		2130	4272	6402	SO:0001583	missense	2	exon20			CCACTGGGACAGC	BX647329, X68728, M11313	CCDS44827.1	12p13.31	2010-02-24			ENSG00000175899	ENSG00000175899			7	protein-coding gene	gene with protein product		103950					Standard	XM_006719056		Approved	FWP007, S863-7, CPAMD5	uc001qvk.1	P01023	OTTHUMG00000150267	ENST00000318602.7:c.2512C>A	chr12.hg19:g.9243036G>T	ENSP00000323929:p.Pro838Thr	120.0	0.0	.		93.0	4.0	.	NM_000014	Q13677|Q59F47|Q5QTS0|Q68DN2|Q6PIY3|Q6PN97	Missense_Mutation	SNP	ENST00000318602.7	hg19	CCDS44827.1	.	.	.	.	.	.	.	.	.	.	G	12.82	2.053189	0.36181	.	.	ENSG00000175899	ENST00000318602;ENST00000540099	T	0.13778	2.56	5.08	5.08	0.68730	.	0.243635	0.35805	N	0.002961	T	0.41305	0.1153	M	0.87758	2.905	0.41736	D	0.989588	D	0.62365	0.991	D	0.63703	0.917	T	0.38735	-0.9647	10	0.37606	T	0.19	.	17.397	0.87449	0.0:0.0:1.0:0.0	.	838	P01023	A2MG_HUMAN	T	838;853	ENSP00000323929:P838T	ENSP00000323929:P838T	P	-	1	0	A2M	9134303	1.000000	0.71417	0.518000	0.27811	0.038000	0.13279	5.993000	0.70616	2.512000	0.84698	0.655000	0.94253	CCA	.	.	.	none		0.537	A2M-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317233.2	NM_000014	
LARP4	113251	hgsc.bcm.edu	37	12	50847398	50847398	+	Silent	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:50847398T>C	ENST00000398473.2	+	9	1072	c.960T>C	c.(958-960)taT>taC	p.Y320Y	LARP4_ENST00000347328.5_Intron|LARP4_ENST00000518444.1_Silent_p.Y319Y|LARP4_ENST00000293618.8_Silent_p.Y320Y|LARP4_ENST00000518561.1_Silent_p.Y250Y|LARP4_ENST00000429001.3_Silent_p.Y326Y|LARP4_ENST00000522085.1_Silent_p.Y320Y	NM_052879.4|NM_199188.2	NP_443111.4|NP_954658.2	Q71RC2	LARP4_HUMAN	La ribonucleoprotein domain family, member 4	320					cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)			breast(3)|endometrium(3)|kidney(2)|large_intestine(2)|liver(2)|lung(7)|ovary(1)|skin(2)|urinary_tract(1)	23						ACTCGGTCTATAGTATTGTGC	0.373																																					p.Y320Y		Atlas-SNP	.											.	LARP4	58	.	0			c.T960C						PASS	.						208.0	181.0	190.0					12																	50847398		1906	4126	6032	SO:0001819	synonymous_variant	113251	exon9			GGTCTATAGTATT	AY004310	CCDS41782.1, CCDS44879.1, CCDS44880.1, CCDS44879.2, CCDS53789.1, CCDS53790.1	12q13.12	2005-08-09			ENSG00000161813	ENSG00000161813		"""La ribonucleoprotein domain containing"""	24320	protein-coding gene	gene with protein product						12477932	Standard	NM_052879		Approved	PP13296	uc001rwp.2	Q71RC2	OTTHUMG00000163724	ENST00000398473.2:c.960T>C	chr12.hg19:g.50847398T>C		121.0	0.0	.		178.0	44.0	.	NM_001170808	A8K6T1|E9PDG5|G3XAA8|G5E976|Q5CZ97|Q6ZV14|Q96NF9	Silent	SNP	ENST00000398473.2	hg19	CCDS41782.1																																																																																			.	.	.	none		0.373	LARP4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000374981.1	NM_052879	
NPFF	8620	hgsc.bcm.edu	37	12	53900627	53900627	+	Missense_Mutation	SNP	C	C	T	rs199569723		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:53900627C>T	ENST00000267017.3	-	3	438	c.275G>A	c.(274-276)cGg>cAg	p.R92Q	RP11-793H13.10_ENST00000591834.1_3'UTR|NPFF_ENST00000609999.1_Missense_Mutation_p.R95Q	NM_003717.2	NP_003708.1	O15130	NPFF_HUMAN	neuropeptide FF-amide peptide precursor	92					acute inflammatory response to antigenic stimulus (GO:0002438)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of appetite (GO:0032099)|negative regulation of heart rate (GO:0010459)|negative regulation of insulin secretion (GO:0046676)|neuropeptide signaling pathway (GO:0007218)|positive regulation of blood pressure (GO:0045777)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of membrane depolarization (GO:0003254)|regulation of sensory perception of pain (GO:0051930)|response to drug (GO:0042493)|response to morphine (GO:0043278)|somatostatin secretion (GO:0070253)|spinal cord development (GO:0021510)|synaptic transmission (GO:0007268)|vasopressin secretion (GO:0030103)	axon terminus (GO:0043679)|dendrite (GO:0030425)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|perikaryon (GO:0043204)|vesicle (GO:0031982)	receptor binding (GO:0005102)			haematopoietic_and_lymphoid_tissue(1)|prostate(1)|urinary_tract(1)	3						CTCTCCAGCCCGGGGACTCAG	0.552																																					p.R92Q		Atlas-SNP	.											.	NPFF	9	.	0			c.G275A						PASS	.						111.0	114.0	113.0					12																	53900627		2203	4300	6503	SO:0001583	missense	8620	exon3			CCAGCCCGGGGAC	AF005271	CCDS8862.1	12q13.13	2013-02-26			ENSG00000139574	ENSG00000139574		"""Endogenous ligands"""	7901	protein-coding gene	gene with protein product		604643				9224703	Standard	NM_003717		Approved	FMRFAL	uc001sdw.1	O15130	OTTHUMG00000169856	ENST00000267017.3:c.275G>A	chr12.hg19:g.53900627C>T	ENSP00000267017:p.Arg92Gln	58.0	0.0	.		76.0	10.0	.	NM_003717	Q3SXL4	Missense_Mutation	SNP	ENST00000267017.3	hg19	CCDS8862.1	.	.	.	.	.	.	.	.	.	.	C	10.28	1.306772	0.23821	.	.	ENSG00000139574	ENST00000267017	T	0.54279	0.58	4.52	-1.46	0.08800	.	0.173981	0.36555	N	0.002528	T	0.36441	0.0967	L	0.49126	1.545	0.09310	N	1	B	0.23490	0.086	B	0.17722	0.019	T	0.13737	-1.0498	10	0.38643	T	0.18	-7.5784	3.979	0.09487	0.3493:0.371:0.0:0.2797	.	92	O15130	NPFF_HUMAN	Q	92	ENSP00000267017:R92Q	ENSP00000267017:R92Q	R	-	2	0	NPFF	52186894	0.048000	0.20356	0.008000	0.14137	0.980000	0.70556	0.139000	0.16036	-0.071000	0.12886	0.491000	0.48974	CGG	.	.	.	weak		0.552	NPFF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406301.1	NM_003717	
ATP5G2	517	hgsc.bcm.edu	37	12	54062935	54062935	+	Missense_Mutation	SNP	G	G	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:54062935G>T	ENST00000549164.1	-	4	495	c.308C>A	c.(307-309)gCc>gAc	p.A103D	ATP5G2_ENST00000602871.1_Missense_Mutation_p.A103D|ATP5G2_ENST00000338662.5_Missense_Mutation_p.A119D|ATP5G2_ENST00000394349.3_Missense_Mutation_p.A160D|ATP5G2_ENST00000550241.1_5'UTR			Q06055	AT5G2_HUMAN	ATP synthase, H+ transporting, mitochondrial Fo complex, subunit C2 (subunit 9)	103					ATP hydrolysis coupled proton transport (GO:0015991)|ATP synthesis coupled proton transport (GO:0015986)|response to ethanol (GO:0045471)	integral component of membrane (GO:0016021)|mitochondrial proton-transporting ATP synthase complex (GO:0005753)|proton-transporting ATP synthase complex, coupling factor F(o) (GO:0045263)	hydrogen ion transmembrane transporter activity (GO:0015078)|lipid binding (GO:0008289)|transporter activity (GO:0005215)			kidney(1)|large_intestine(1)|lung(2)|ovary(1)|prostate(1)	6						ATCTTACCTGGCATAACCAAT	0.498																																					p.A160D		Atlas-SNP	.											.	ATP5G2	16	.	0			c.C479A						PASS	.						81.0	79.0	80.0					12																	54062935		2203	4300	6503	SO:0001583	missense	517	exon4			TACCTGGCATAAC	X69908	CCDS8863.2, CCDS31812.1	12q13.13	2012-10-12	2010-06-11		ENSG00000135390	ENSG00000135390		"""Mitochondrial respiratory chain complex / Complex V"", ""ATPases / F-type"""	842	protein-coding gene	gene with protein product		603193	"""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2"", ""ATP synthase, H+ transporting, mitochondrial F0 complex, subunit C2 (subunit 9)"""			8328972	Standard	NM_005176		Approved		uc001sec.3	Q06055	OTTHUMG00000133442	ENST00000549164.1:c.308C>A	chr12.hg19:g.54062935G>T	ENSP00000447317:p.Ala103Asp	65.0	0.0	.		89.0	4.0	.	NM_005176	B3KQQ6	Missense_Mutation	SNP	ENST00000549164.1	hg19		.	.	.	.	.	.	.	.	.	.	G	34	5.341976	0.95783	.	.	ENSG00000135390	ENST00000394349;ENST00000549164;ENST00000338662	T;T;T	0.57752	0.38;0.38;0.38	5.14	5.14	0.70334	ATPase, F0/V0 complex, subunit C (3);	0.000000	0.85682	D	0.000000	D	0.83454	0.5258	H	0.98682	4.3	0.80722	D	1	D;D;D	0.76494	0.998;0.995;0.999	D;D;D	0.75020	0.971;0.964;0.985	D	0.89594	0.3830	10	0.87932	D	0	.	17.9104	0.88932	0.0:0.0:1.0:0.0	.	103;119;160	Q06055;Q06055-3;Q06055-2	AT5G2_HUMAN;.;.	D	160;103;119	ENSP00000377878:A160D;ENSP00000447317:A103D;ENSP00000340315:A119D	ENSP00000340315:A119D	A	-	2	0	ATP5G2	52349202	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.496000	0.97967	2.847000	0.97988	0.655000	0.94253	GCC	.	.	.	none		0.498	ATP5G2-006	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000407403.1	NM_005176	
CEP290	80184	hgsc.bcm.edu	37	12	88514780	88514780	+	Nonsense_Mutation	SNP	A	A	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:88514780A>C	ENST00000552810.1	-	14	1696	c.1353T>G	c.(1351-1353)taT>taG	p.Y451*	CEP290_ENST00000309041.7_Nonsense_Mutation_p.Y451*|CEP290_ENST00000397838.3_5'UTR	NM_025114.3	NP_079390.3	O15078	CE290_HUMAN	centrosomal protein 290kDa	451					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|establishment or maintenance of cell polarity (GO:0007163)|eye photoreceptor cell development (GO:0042462)|G2/M transition of mitotic cell cycle (GO:0000086)|hindbrain development (GO:0030902)|mitotic cell cycle (GO:0000278)|otic vesicle formation (GO:0030916)|positive regulation of intracellular protein transport (GO:0090316)|positive regulation of transcription, DNA-templated (GO:0045893)|pronephros development (GO:0048793)|protein transport (GO:0015031)|regulation of cAMP metabolic process (GO:0030814)|regulation of establishment of protein localization (GO:0070201)|retina development in camera-type eye (GO:0060041)	centriolar satellite (GO:0034451)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleus (GO:0005634)|photoreceptor connecting cilium (GO:0032391)|protein complex (GO:0043234)|TCTN-B9D complex (GO:0036038)				breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(20)|liver(1)|lung(18)|ovary(5)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)	73						ATACCGATTCATAATCTTTTA	0.363																																					p.Y451X		Atlas-SNP	.											.	CEP290	195	.	0			c.T1353G						PASS	.						89.0	86.0	87.0					12																	88514780		1837	4077	5914	SO:0001587	stop_gained	80184	exon14			CGATTCATAATCT	AB002371	CCDS55858.1	12q21.33	2014-09-17				ENSG00000198707			29021	protein-coding gene	gene with protein product	"""Joubert syndrome 5"", ""nephrocystin-6"", ""cancer/testis antigen 87"", ""POC3 centriolar protein homolog (Chlamydomonas)"", ""Meckel syndrome, type 4"""	610142				15474516, 16682973, 16632484	Standard	NM_025114		Approved	KIAA0373, FLJ13615, 3H11Ag, rd16, NPHP6, JBTS5, SLSN6, LCA10, MKS4, BBS14, CT87, POC3	uc001tar.3	O15078		ENST00000552810.1:c.1353T>G	chr12.hg19:g.88514780A>C	ENSP00000448012:p.Tyr451*	12.0	0.0	.		18.0	10.0	.	NM_025114	Q1PSK5|Q66GS8|Q9H2G6|Q9H6Q7|Q9H8I0	Nonsense_Mutation	SNP	ENST00000552810.1	hg19	CCDS55858.1	.	.	.	.	.	.	.	.	.	.	A	41	8.542306	0.98857	.	.	ENSG00000198707	ENST00000552810;ENST00000309041;ENST00000536998;ENST00000545139	.	.	.	5.61	4.42	0.53409	.	0.147782	0.46758	D	0.000264	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	5.4776	0.16704	0.7324:0.0:0.1371:0.1305	.	.	.	.	X	451;451;451;353	.	ENSP00000308021:Y451X	Y	-	3	2	CEP290	87038911	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	4.199000	0.58426	2.137000	0.66172	0.482000	0.46254	TAT	.	.	.	none		0.363	CEP290-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000406344.1	NM_025114	
ANKS1B	56899	hgsc.bcm.edu	37	12	99640158	99640158	+	Silent	SNP	G	G	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr12:99640158G>A	ENST00000547776.2	-	13	2240	c.2241C>T	c.(2239-2241)tcC>tcT	p.S747S	ANKS1B_ENST00000329257.7_Silent_p.S747S|ANKS1B_ENST00000550833.1_5'Flank|ANKS1B_ENST00000547010.1_Silent_p.S327S	NM_152788.4	NP_690001.3	Q7Z6G8	ANS1B_HUMAN	ankyrin repeat and sterile alpha motif domain containing 1B	747						cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ephrin receptor binding (GO:0046875)			NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(15)|lung(38)|pancreas(1)|prostate(2)|skin(1)	70		all_cancers(3;0.0197)|all_epithelial(3;0.0101)|Esophageal squamous(3;0.0559)|Breast(359;0.209)		OV - Ovarian serous cystadenocarcinoma(2;2.89e-08)|Epithelial(2;6.12e-08)|all cancers(2;4.07e-06)		TTTTCTCATTGGAAGGATAGG	0.413																																					p.S747S		Atlas-SNP	.											.	ANKS1B	180	.	0			c.C2241T						PASS	.						92.0	87.0	89.0					12																	99640158		1912	4102	6014	SO:0001819	synonymous_variant	56899	exon13			CTCATTGGAAGGA	AF145204	CCDS55864.1, CCDS55865.1, CCDS55866.1, CCDS55867.1, CCDS55868.1, CCDS55869.1, CCDS55870.1, CCDS55871.1, CCDS55872.1	12q23.1	2013-01-10						"""Sterile alpha motif (SAM) domain containing"", ""Ankyrin repeat domain containing"""	24600	protein-coding gene	gene with protein product		607815				10490826, 12415113	Standard	NM_020140		Approved	EB-1, AIDA-1, cajalin-2, ANKS2	uc001tge.2	Q7Z6G8		ENST00000547776.2:c.2241C>T	chr12.hg19:g.99640158G>A		198.0	0.0	.		231.0	112.0	.	NM_152788	A5PKY5|A7E259|A8K153|A8MSN4|B4DFP6|B4DH98|F8VPM3|F8VZR9|F8WC27|Q5XLJ0|Q6IVB5|Q6NUS4|Q7Z6G6|Q7Z6G7|Q8TAP3|Q9NRX7|Q9Y5K9	Silent	SNP	ENST00000547776.2	hg19	CCDS55872.1	.	.	.	.	.	.	.	.	.	.	G	7.433	0.639208	0.14386	.	.	ENSG00000185046	ENST00000550778	.	.	.	5.21	-7.15	0.01521	.	.	.	.	.	T	0.38401	0.1039	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.45977	-0.9224	4	.	.	.	-6.1946	3.8547	0.08970	0.0906:0.3375:0.3258:0.2461	.	.	.	.	L	19	.	.	P	-	2	0	ANKS1B	98164289	0.194000	0.23325	0.127000	0.21898	0.969000	0.65631	-1.051000	0.03507	-0.833000	0.04245	0.462000	0.41574	CCA	.	.	.	none		0.413	ANKS1B-003	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000408421.3	NM_020140	
FAM161B	145483	hgsc.bcm.edu	37	14	74409353	74409353	+	Missense_Mutation	SNP	A	A	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr14:74409353A>T	ENST00000534936.1	-	4	1096	c.991T>A	c.(991-993)Tcc>Acc	p.S331T	FAM161B_ENST00000286544.3_Missense_Mutation_p.S394T			Q96MY7	F161B_HUMAN	family with sequence similarity 161, member B	331										breast(3)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(5)|ovary(1)|prostate(2)|skin(2)	21						GCGATAGGGGAAGAGGCCATC	0.532																																					p.S394T		Atlas-SNP	.											.	FAM161B	67	.	0			c.T1180A						PASS	.						88.0	96.0	94.0					14																	74409353		2203	4300	6503	SO:0001583	missense	145483	exon4			TAGGGGAAGAGGC	AA356453	CCDS9822.1, CCDS9822.2	14q24.2	2008-06-05	2008-06-05	2008-06-05		ENSG00000156050			19854	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 44"""	C14orf44			Standard	NM_152445		Approved	FLJ31697	uc001xpd.3	Q96MY7		ENST00000534936.1:c.991T>A	chr14.hg19:g.74409353A>T	ENSP00000445326:p.Ser331Thr	114.0	0.0	.		72.0	18.0	.	NM_152445	B7Z882|J3KNA2	Missense_Mutation	SNP	ENST00000534936.1	hg19		.	.	.	.	.	.	.	.	.	.	A	16.34	3.096005	0.56075	.	.	ENSG00000156050	ENST00000286544;ENST00000534936	T;T	0.21361	2.01;2.01	5.5	4.34	0.51931	.	0.392302	0.25786	N	0.028306	T	0.38719	0.1051	M	0.79475	2.455	0.29528	N	0.852984	D	0.61697	0.99	P	0.61722	0.893	T	0.35475	-0.9787	10	0.09843	T	0.71	-10.2675	12.0316	0.53401	0.5426:0.4574:0.0:0.0	.	331	Q96MY7	F161B_HUMAN	T	394;331	ENSP00000286544:S394T;ENSP00000445326:S331T	ENSP00000286544:S394T	S	-	1	0	FAM161B	73479106	0.652000	0.27349	1.000000	0.80357	0.874000	0.50279	1.334000	0.33827	1.081000	0.41110	0.533000	0.62120	TCC	.	.	.	none		0.532	FAM161B-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_152445	
SYNE3	161176	hgsc.bcm.edu	37	14	95906070	95906070	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr14:95906070C>T	ENST00000334258.5	-	12	2139	c.2125G>A	c.(2125-2127)Gcg>Acg	p.A709T	SYNE3_ENST00000554873.1_Missense_Mutation_p.A466T|SYNE3_ENST00000557275.1_Missense_Mutation_p.A709T	NM_152592.3	NP_689805.3	Q6ZMZ3	SYNE3_HUMAN	spectrin repeat containing, nuclear envelope family member 3	709					cytoskeletal anchoring at nuclear membrane (GO:0090286)|cytoskeleton organization (GO:0007010)|establishment of protein localization to membrane (GO:0090150)|regulation of cell shape (GO:0008360)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear outer membrane (GO:0005640)|SUN-KASH complex (GO:0034993)	actin filament binding (GO:0051015)			breast(1)|endometrium(2)|lung(25)	28						CAGCCCTGCGCTTCCACCAGG	0.637																																					p.A709T		Atlas-SNP	.											.	SYNE3	130	.	0			c.G2125A						PASS	.						44.0	47.0	46.0					14																	95906070		2203	4300	6503	SO:0001583	missense	161176	exon12			CCTGCGCTTCCAC	AK098471	CCDS9935.1	14q32.13	2012-05-31	2012-05-31	2012-05-31	ENSG00000176438	ENSG00000176438			19861	protein-coding gene	gene with protein product		610861	"""chromosome 14 open reading frame 49"""	C14orf49			Standard	NM_152592		Approved	FLJ25605, NET53, Nesprin-3, Nesp3	uc001yei.4	Q6ZMZ3	OTTHUMG00000171632	ENST00000334258.5:c.2125G>A	chr14.hg19:g.95906070C>T	ENSP00000334308:p.Ala709Thr	181.0	0.0	.		137.0	7.0	.	NM_152592	A6H8H3|Q86SX5|Q8N7G8	Missense_Mutation	SNP	ENST00000334258.5	hg19	CCDS9935.1	.	.	.	.	.	.	.	.	.	.	C	14.87	2.663059	0.47572	.	.	ENSG00000176438	ENST00000334258;ENST00000554873;ENST00000557275	T;T;T	0.52295	0.67;0.67;0.67	5.34	5.34	0.76211	.	0.171047	0.27932	N	0.017272	T	0.46034	0.1372	L	0.50333	1.59	0.80722	D	1	P;P	0.50369	0.919;0.934	P;P	0.48598	0.447;0.583	T	0.26573	-1.0099	10	0.12430	T	0.62	-23.2732	11.6332	0.51187	0.1774:0.8226:0.0:0.0	.	709;709	Q6ZMZ3-2;Q6ZMZ3	.;SYNE3_HUMAN	T	709;466;709	ENSP00000334308:A709T;ENSP00000452154:A466T;ENSP00000450562:A709T	ENSP00000334308:A709T	A	-	1	0	C14orf49	94975823	0.218000	0.23608	0.039000	0.18376	0.023000	0.10783	1.454000	0.35178	2.507000	0.84556	0.561000	0.74099	GCG	.	.	.	none		0.637	SYNE3-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000420529.2	NM_152592	
TBC1D24	57465	hgsc.bcm.edu	37	16	2550436	2550436	+	Silent	SNP	G	G	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr16:2550436G>T	ENST00000293970.5	+	7	1603	c.1470G>T	c.(1468-1470)ctG>ctT	p.L490L	TBC1D24_ENST00000567020.1_Silent_p.L484L|TBC1D24_ENST00000434757.2_Silent_p.L490L|RP11-20I23.1_ENST00000564543.1_Intron	NM_001199107.1	NP_001186036.1	Q9ULP9	TBC24_HUMAN	TBC1 domain family, member 24	490	TLD.				neuron projection development (GO:0031175)	cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|terminal bouton (GO:0043195)	Rab GTPase activator activity (GO:0005097)			endometrium(2)|kidney(4)|large_intestine(3)|lung(4)	13						ACTTCAACCTGCCCTCCAAGA	0.692																																					p.L490L		Atlas-SNP	.											.	TBC1D24	35	.	0			c.G1470T						PASS	.						12.0	17.0	15.0					16																	2550436		2057	4196	6253	SO:0001819	synonymous_variant	57465	exon7			CAACCTGCCCTCC	AB032997	CCDS42107.1, CCDS55980.1	16p13.3	2014-05-07				ENSG00000162065			29203	protein-coding gene	gene with protein product	"""TBC/LysM-associated domain containing 6"""	613577	"""deafness, autosomal recessive 86"""	DFNB86		10574461, 24387994, 24729539	Standard	NM_001199107		Approved	KIAA1171, TLDC6, DFNA65	uc002cql.3	Q9ULP9		ENST00000293970.5:c.1470G>T	chr16.hg19:g.2550436G>T		314.0	0.0	.		269.0	58.0	.	NM_001199107	A0JNW3|B9A6M6|Q2KJ08	Silent	SNP	ENST00000293970.5	hg19	CCDS55980.1																																																																																			.	.	.	none		0.692	TBC1D24-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000435637.1	NM_020705	
TCAP	8557	hgsc.bcm.edu	37	17	37821723	37821723	+	Splice_Site	SNP	G	G	A	rs113187448		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:37821723G>A	ENST00000309889.2	+	1	1283		c.e1+1		PNMT_ENST00000394246.1_5'Flank|TCAP_ENST00000578283.1_Splice_Site|PNMT_ENST00000269582.2_5'Flank|PNMT_ENST00000581428.1_5'Flank			O15273	TELT_HUMAN	titin-cap						adult heart development (GO:0007512)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle hypertrophy in response to stress (GO:0014898)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of mechanical stimulus (GO:0050982)|detection of muscle stretch (GO:0035995)|muscle filament sliding (GO:0030049)|otic vesicle formation (GO:0030916)|protein complex assembly (GO:0006461)|response to muscle stretch (GO:0035994)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle contraction (GO:0003009)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)	cytosol (GO:0005829)|I band (GO:0031674)|Z disc (GO:0030018)	FATZ binding (GO:0051373)|ion channel binding (GO:0044325)|protein binding, bridging (GO:0030674)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)|titin Z domain binding (GO:0070080)			kidney(1)|lung(1)	2	all_cancers(6;6.59e-85)|all_epithelial(6;2.89e-103)|Breast(7;1.05e-86)|Lung NSC(9;1.15e-09)|all_lung(9;6.24e-09)|Colorectal(19;0.000442)|Esophageal squamous(10;0.052)		UCEC - Uterine corpus endometrioid carcinoma (11;0.000126)|BRCA - Breast invasive adenocarcinoma(8;3.87e-45)|Lung(15;0.00193)|LUAD - Lung adenocarcinoma(14;0.0664)|LUSC - Lung squamous cell carcinoma(15;0.171)			CCGAGGAGGGGTGAGTGTGGG	0.627																																					.		Atlas-SNP	.											.	TCAP	12	.	0			c.110+1G>A						PASS	.						67.0	64.0	65.0					17																	37821723		2203	4300	6503	SO:0001630	splice_region_variant	8557	exon1			GGAGGGGTGAGTG	AJ000491	CCDS11342.1	17q12	2014-09-17	2012-09-20		ENSG00000173991	ENSG00000173991			11610	protein-coding gene	gene with protein product	"""19 kDa sarcomeric protein"""	604488	"""limb girdle muscular dystrophy 2G (autosomal recessive)"", ""titin-cap (telethonin)"""	LGMD2G		9350988, 9817758	Standard	NM_003673		Approved	T-cap, TELE, telethonin, CMD1N	uc002hsh.3	O15273	OTTHUMG00000133215	ENST00000309889.2:c.110+1G>A	chr17.hg19:g.37821723G>A		87.0	0.0	.		134.0	32.0	.	NM_003673	Q96L27	Splice_Site	SNP	ENST00000309889.2	hg19	CCDS11342.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.194985	0.38806	.	.	ENSG00000173991	ENST00000309889	.	.	.	5.74	5.74	0.90152	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.5082	0.95130	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	TCAP	35075249	1.000000	0.71417	1.000000	0.80357	0.117000	0.20001	7.443000	0.80521	2.710000	0.92621	0.563000	0.77884	.	.	.	.	alt		0.627	TCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256942.1	NM_003673	Intron
RPTOR	57521	hgsc.bcm.edu	37	17	78811724	78811724	+	Missense_Mutation	SNP	A	A	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr17:78811724A>C	ENST00000306801.3	+	10	1501	c.1139A>C	c.(1138-1140)cAa>cCa	p.Q380P	RPTOR_ENST00000544334.2_Missense_Mutation_p.Q380P|RPTOR_ENST00000537330.1_Missense_Mutation_p.Q195P|RPTOR_ENST00000575542.1_3'UTR	NM_020761.2	NP_065812.1	Q8N122	RPTOR_HUMAN	regulatory associated protein of MTOR, complex 1	380					cell cycle arrest (GO:0007050)|cell growth (GO:0016049)|cellular response to amino acid stimulus (GO:0071230)|cellular response to nutrient levels (GO:0031669)|insulin receptor signaling pathway (GO:0008286)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of TOR signaling (GO:0032008)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|regulation of cell size (GO:0008361)|TOR signaling (GO:0031929)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|TORC1 complex (GO:0031931)	14-3-3 protein binding (GO:0071889)|protein complex binding (GO:0032403)|protein kinase binding (GO:0019901)|RNA polymerase III type 1 promoter DNA binding (GO:0001030)|RNA polymerase III type 2 promoter DNA binding (GO:0001031)|RNA polymerase III type 3 promoter DNA binding (GO:0001032)|TFIIIC-class transcription factor binding (GO:0001156)			breast(1)|endometrium(4)|kidney(1)|large_intestine(12)|lung(17)|ovary(3)|prostate(1)|skin(1)|stomach(1)|urinary_tract(3)	44						CTCCGCAGGCAAGCCTGGGAC	0.612																																					p.Q380P		Atlas-SNP	.											.	RPTOR	122	.	0			c.A1139C						PASS	.						111.0	77.0	89.0					17																	78811724		2203	4300	6503	SO:0001583	missense	57521	exon10			GCAGGCAAGCCTG		CCDS11773.1, CCDS54175.1	17q25.3	2013-01-10				ENSG00000141564		"""WD repeat domain containing"""	30287	protein-coding gene	gene with protein product	"""regulatory associated protein of mTOR"""	607130				10718198, 12150926	Standard	NM_001163034		Approved	KOG1, Mip1, KIAA1303, raptor	uc002jyt.1	Q8N122		ENST00000306801.3:c.1139A>C	chr17.hg19:g.78811724A>C	ENSP00000307272:p.Gln380Pro	108.0	0.0	.		174.0	36.0	.	NM_001163034	B2RN36|C6KEF2|F5H7J5|Q8N4V9|Q8TB32|Q9P2P3	Missense_Mutation	SNP	ENST00000306801.3	hg19	CCDS11773.1	.	.	.	.	.	.	.	.	.	.	A	16.94	3.260139	0.59321	.	.	ENSG00000141564	ENST00000537330;ENST00000306801;ENST00000544334	T;T	0.46819	0.86;0.86	5.27	5.27	0.74061	.	0.000000	0.85682	D	0.000000	T	0.66218	0.2767	M	0.79475	2.455	0.80722	D	1	D;B;D	0.56521	0.96;0.168;0.976	D;B;B	0.64237	0.923;0.086;0.438	T	0.68526	-0.5385	10	0.46703	T	0.11	.	13.1464	0.59463	1.0:0.0:0.0:0.0	.	380;195;380	F5H7J5;F5GXV9;Q8N122	.;.;RPTOR_HUMAN	P	195;380;380	ENSP00000307272:Q380P;ENSP00000442479:Q380P	ENSP00000307272:Q380P	Q	+	2	0	RPTOR	76426319	1.000000	0.71417	1.000000	0.80357	0.877000	0.50540	8.087000	0.89521	1.990000	0.58119	0.455000	0.32223	CAA	.	.	.	none		0.612	RPTOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438125.1	NM_020761	
RTTN	25914	hgsc.bcm.edu	37	18	67863855	67863855	+	Missense_Mutation	SNP	A	A	T	rs2365902		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr18:67863855A>T	ENST00000255674.6	-	7	1009	c.723T>A	c.(721-723)ttT>ttA	p.F241L	RTTN_ENST00000437017.1_Missense_Mutation_p.F241L|RTTN_ENST00000454359.1_Missense_Mutation_p.F241L	NM_173630.3	NP_775901.3	Q86VV8	RTTN_HUMAN	rotatin	241				F -> FG (in Ref. 1; AK096404 and 3; CAH18659). {ECO:0000305}.	determination of left/right symmetry (GO:0007368)	ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(9)|lung(35)|ovary(4)|pancreas(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Esophageal squamous(42;0.129)				TTCCATCTCCAAAGGCCAGTT	0.448																																					p.F241L		Atlas-SNP	.											.,1	RTTN	184	.	0			c.T723A						PASS	.						69.0	66.0	67.0					18																	67863855		1859	4099	5958	SO:0001583	missense	25914	exon7			ATCTCCAAAGGCC	AL117635	CCDS42443.1	18q22.1	2008-08-01				ENSG00000176225			18654	protein-coding gene	gene with protein product		610436				11900971	Standard	NM_173630		Approved	DKFZP434G145	uc002lkp.2	Q86VV8		ENST00000255674.6:c.723T>A	chr18.hg19:g.67863855A>T	ENSP00000255674:p.Phe241Leu	110.0	1.0	.		81.0	7.0	.	NM_173630	Q68CS9|Q6ZRL8|Q6ZTK3|Q86TG4|Q8N8N8|Q8TBQ4|Q96IN9|Q9UFJ4	Missense_Mutation	SNP	ENST00000255674.6	hg19	CCDS42443.1	.	.	.	.	.	.	.	.	.	.	A	14.03	2.412496	0.42817	.	.	ENSG00000176225	ENST00000255674;ENST00000454359;ENST00000437017	T;T;T	0.62364	3.75;0.03;0.03	5.21	-1.64	0.08318	Armadillo-like helical (1);Armadillo-type fold (2);	0.168056	0.41396	D	0.000882	T	0.45256	0.1333	L	0.57536	1.79	0.28531	N	0.912606	B;B	0.11235	0.003;0.004	B;B	0.13407	0.004;0.009	T	0.40098	-0.9581	10	0.06625	T	0.88	.	5.9129	0.19039	0.4745:0.0:0.3977:0.1277	.	241;241	Q86VV8-2;Q86VV8	.;RTTN_HUMAN	L	241	ENSP00000255674:F241L;ENSP00000402352:F241L;ENSP00000399520:F241L	ENSP00000255674:F241L	F	-	3	2	RTTN	66014835	0.504000	0.26123	0.928000	0.36995	0.995000	0.86356	-0.014000	0.12656	-0.284000	0.09102	0.528000	0.53228	TTT	.	.	.	weak		0.448	RTTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442988.1	NM_173630	
PRKCSH	5589	hgsc.bcm.edu	37	19	11558370	11558370	+	Silent	SNP	G	G	A	rs77563879		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:11558370G>A	ENST00000589838.1	+	10	966	c.966G>A	c.(964-966)gaG>gaA	p.E322E	PRKCSH_ENST00000587327.1_Silent_p.E322E|PRKCSH_ENST00000591462.1_Silent_p.E322E|PRKCSH_ENST00000592741.1_Silent_p.E322E|PRKCSH_ENST00000252455.2_Silent_p.E322E|PRKCSH_ENST00000412601.1_Silent_p.E322E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	322	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaagaagagg	0.632																																					p.E322E		Atlas-SNP	.											PRKCSH,caecum,carcinoma,0,1	PRKCSH	55	.	1	Deletion - In frame(1)	central_nervous_system(1)	c.G966A						PASS	.						27.0	27.0	27.0					19																	11558370		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAAGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.966G>A	chr19.hg19:g.11558370G>A		203.0	0.0	.		115.0	6.0	.	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	hg19	CCDS32911.1																																																																																			.	.	.	weak		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
ZNF615	284370	hgsc.bcm.edu	37	19	52496371	52496372	+	Missense_Mutation	DNP	GC	GC	AT			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G|C	G|C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:52496371_52496372GC>AT	ENST00000602063.1	-	6	2306_2307	c.1957_1958GC>AT	c.(1957-1959)GCa>ATa	p.A653I	ZNF615_ENST00000391795.3_Missense_Mutation_p.A658I|ZNF615_ENST00000594083.1_Missense_Mutation_p.A664I|ZNF615_ENST00000598071.1_Missense_Mutation_p.A664I|ZNF615_ENST00000376716.5_Missense_Mutation_p.A653I			Q8N8J6	ZN615_HUMAN	zinc finger protein 615	653					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)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(12)|ovary(5)|prostate(1)|skin(1)|stomach(3)|upper_aerodigestive_tract(2)	42		all_neural(266;0.117)		GBM - Glioblastoma multiforme(134;0.00142)|OV - Ovarian serous cystadenocarcinoma(262;0.019)		TTCAGTACATGCAAAGGAAGTC	0.406																																					p.A664V|p.A664T		Atlas-SNP	.											.	ZNF615	111	.	0			c.C1991T|c.G1990A						PASS	.																																			SO:0001583	missense	284370	exon7			GTACATGCAAAGG|TACATGCAAAGGA	AK096691	CCDS12846.1, CCDS59418.1	19q13.41	2013-01-08						"""Zinc fingers, C2H2-type"", ""-"""	24740	protein-coding gene	gene with protein product						12477932	Standard	NM_001199324		Approved	FLJ33710	uc002pyf.2	Q8N8J6		ENST00000602063.1:c.1957_1958delinsAT	chr19.hg19:g.52496371_52496372delinsAT	ENSP00000473089:p.Ala653Ile	144.0	0.0	.		132.0|134.0	40.0|41.0	.	NM_001199324	B7ZKW9|Q2M2Y6|Q5CZB0|Q6ZMT7|Q6ZRB3	Missense_Mutation	SNP	ENST00000602063.1	hg19	CCDS12846.1																																																																																			.	.	.	none		0.406	ZNF615-009	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462391.1	NM_198480	
ZNF160	90338	hgsc.bcm.edu	37	19	53572249	53572249	+	Missense_Mutation	SNP	T	T	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:53572249T>C	ENST00000429604.1	-	7	1953	c.1538A>G	c.(1537-1539)gAg>gGg	p.E513G	ZNF160_ENST00000599056.1_Missense_Mutation_p.E513G|ZNF160_ENST00000418871.1_Missense_Mutation_p.E513G|ZNF160_ENST00000601421.1_Missense_Mutation_p.E477G	NM_001102603.1|NM_198893.2	NP_001096073.1|NP_942596.1	Q9HCG1	ZN160_HUMAN	zinc finger protein 160	513					hemopoiesis (GO:0030097)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(8)|lung(10)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	35				GBM - Glioblastoma multiforme(134;0.02)		TTTCCCACACTCATTACACTT	0.403																																					p.E513G		Atlas-SNP	.											.	ZNF160	75	.	0			c.A1538G						PASS	.						103.0	103.0	103.0					19																	53572249		2203	4300	6503	SO:0001583	missense	90338	exon7			CCACACTCATTAC	X78928	CCDS12859.1	19q13.42	2013-01-08				ENSG00000170949		"""Zinc fingers, C2H2-type"", ""-"""	12948	protein-coding gene	gene with protein product		600398				7774943, 7865130	Standard	NM_198893		Approved	HZF5, F11, KR18, HKr18, FLJ00032, KIAA1611	uc002qar.4	Q9HCG1		ENST00000429604.1:c.1538A>G	chr19.hg19:g.53572249T>C	ENSP00000406201:p.Glu513Gly	51.0	0.0	.		49.0	16.0	.	NM_001102603	Q14589|Q504Q8|Q96JC5|Q9BVY9|Q9H7N6	Missense_Mutation	SNP	ENST00000429604.1	hg19	CCDS12859.1	.	.	.	.	.	.	.	.	.	.	T	11.15	1.552720	0.27739	.	.	ENSG00000170949	ENST00000429604;ENST00000418871	T;T	0.07444	3.19;3.19	2.47	0.0174	0.14112	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.20780	0.0500	M	0.64080	1.96	0.09310	N	1	D	0.89917	1.0	D	0.76575	0.988	T	0.07908	-1.0748	9	0.87932	D	0	.	6.7782	0.23630	0.363:0.0:0.0:0.637	.	513	Q9HCG1	ZN160_HUMAN	G	513	ENSP00000406201:E513G;ENSP00000409597:E513G	ENSP00000409597:E513G	E	-	2	0	ZNF160	58264061	0.000000	0.05858	0.002000	0.10522	0.354000	0.29330	0.114000	0.15520	-0.237000	0.09739	0.459000	0.35465	GAG	.	.	.	none		0.403	ZNF160-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463994.2	NM_033288	
TMEM230	29058	hgsc.bcm.edu	37	20	5086868	5086868	+	Missense_Mutation	SNP	C	C	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:5086868C>T	ENST00000379286.2	-	4	608	c.188G>A	c.(187-189)gGc>gAc	p.G63D	TMEM230_ENST00000379279.2_Missense_Mutation_p.G63D|TMEM230_ENST00000379283.2_Missense_Mutation_p.G63D|TMEM230_ENST00000342308.5_Missense_Mutation_p.G126D|TMEM230_ENST00000202834.7_Missense_Mutation_p.G63D|TMEM230_ENST00000492419.1_5'UTR|TMEM230_ENST00000379277.2_Missense_Mutation_p.G63D	NM_001009924.1	NP_001009924.1	Q96A57	TM230_HUMAN	transmembrane protein 230	63						integral component of membrane (GO:0016021)											CAGGAGGGAGCCTATAATAAT	0.453																																					p.G126D		Atlas-SNP	.											.	.	.	.	0			c.G377A						PASS	.						66.0	66.0	66.0					20																	5086868		2203	4300	6503	SO:0001583	missense	29058	exon4			AGGGAGCCTATAA	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.188G>A	chr20.hg19:g.5086868C>T	ENSP00000368588:p.Gly63Asp	178.0	0.0	.		93.0	6.0	.	NM_001009923	B2RDM8|D3DVZ9|Q0VGC8|Q5TDS5|Q96ES2|Q9P0A7	Missense_Mutation	SNP	ENST00000379286.2	hg19	CCDS13086.1	.	.	.	.	.	.	.	.	.	.	C	23.2	4.392086	0.83011	.	.	ENSG00000089063	ENST00000379283;ENST00000342308;ENST00000379299;ENST00000202834;ENST00000379286;ENST00000379279;ENST00000379277;ENST00000379276	T	0.60299	0.2	5.2	5.2	0.72013	.	0.000000	0.85682	D	0.000000	T	0.80879	0.4708	M	0.90145	3.09	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.81914	0.964;0.995;0.993	D	0.84375	0.0546	10	0.87932	D	0	-27.0491	17.8394	0.88711	0.0:1.0:0.0:0.0	.	63;63;126	Q5JWB9;Q96A57;Q96A57-2	.;CT030_HUMAN;.	D	63;126;63;63;63;63;63;63	ENSP00000341364:G126D	ENSP00000202834:G63D	G	-	2	0	C20orf30	5034868	1.000000	0.71417	1.000000	0.80357	0.471000	0.32888	7.104000	0.77024	2.854000	0.98071	0.655000	0.94253	GGC	.	.	.	none		0.453	TMEM230-007	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077846.1		
PLCB4	5332	hgsc.bcm.edu	37	20	9440354	9440354	+	Missense_Mutation	SNP	G	G	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:9440354G>A	ENST00000378493.1	+	31	3124	c.3109G>A	c.(3109-3111)Gaa>Aaa	p.E1037K	PLCB4_ENST00000278655.4_Missense_Mutation_p.E1037K|PLCB4_ENST00000378501.2_Missense_Mutation_p.E1037K|PLCB4_ENST00000334005.3_Missense_Mutation_p.E1037K|PLCB4_ENST00000414679.2_Missense_Mutation_p.E1049K|PLCB4_ENST00000378473.3_Missense_Mutation_p.E1049K|PLCB4_ENST00000492632.1_Intron			Q15147	PLCB4_HUMAN	phospholipase C, beta 4	1037					inositol phosphate metabolic process (GO:0043647)|intracellular signal transduction (GO:0035556)|lipid catabolic process (GO:0016042)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|dendrite (GO:0030425)|nucleus (GO:0005634)|postsynaptic density (GO:0014069)|smooth endoplasmic reticulum (GO:0005790)	calcium ion binding (GO:0005509)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|signal transducer activity (GO:0004871)			NS(2)|breast(4)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(11)|liver(4)|lung(34)|ovary(3)|pancreas(1)|prostate(1)|skin(19)|upper_aerodigestive_tract(1)	87						TGAGGAGCAAGAAATCCGAGA	0.502																																					p.E1049K		Atlas-SNP	.											.	PLCB4	204	.	0			c.G3145A						PASS	.						64.0	53.0	57.0					20																	9440354		2203	4300	6503	SO:0001583	missense	5332	exon34			GAGCAAGAAATCC		CCDS13104.1, CCDS13105.1, CCDS54447.1	20p12	2008-03-18			ENSG00000101333	ENSG00000101333	3.1.4.11		9059	protein-coding gene	gene with protein product		600810				8530101	Standard	NM_000933		Approved		uc021wam.1	Q15147	OTTHUMG00000031853	ENST00000378493.1:c.3109G>A	chr20.hg19:g.9440354G>A	ENSP00000367754:p.Glu1037Lys	72.0	0.0	.		71.0	23.0	.	NM_001172646	B7ZLK6|E2QRH8|Q17R56|Q5JYS8|Q5JYS9|Q5JYT0|Q5JYT3|Q5JYT4|Q9BQW5|Q9BQW6|Q9BQW8|Q9UJQ2	Missense_Mutation	SNP	ENST00000378493.1	hg19	CCDS13105.1	.	.	.	.	.	.	.	.	.	.	G	18.17	3.565149	0.65651	.	.	ENSG00000101333	ENST00000334005;ENST00000378473;ENST00000278655;ENST00000378493;ENST00000378501;ENST00000414679	T;T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96;0.96	5.51	5.51	0.81932	.	0.055638	0.64402	D	0.000001	T	0.44829	0.1312	L	0.50333	1.59	0.53688	D	0.999974	B;B;B;P	0.37824	0.042;0.021;0.083;0.609	B;B;B;P	0.44860	0.013;0.014;0.011;0.462	T	0.29027	-1.0025	10	0.35671	T	0.21	.	12.7258	0.57170	0.0753:0.0:0.9247:0.0	.	1049;884;1037;1037	E2QRH8;Q15147-2;Q15147;Q15147-4	.;.;PLCB4_HUMAN;.	K	1037;1049;1037;1037;1037;885	ENSP00000334105:E1037K;ENSP00000367734:E1049K;ENSP00000278655:E1037K;ENSP00000367754:E1037K;ENSP00000367762:E1037K;ENSP00000390616:E885K	ENSP00000278655:E1037K	E	+	1	0	PLCB4	9388354	1.000000	0.71417	0.997000	0.53966	0.965000	0.64279	7.421000	0.80204	2.578000	0.87016	0.561000	0.74099	GAA	.	.	.	none		0.502	PLCB4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077948.2		
APP	351	hgsc.bcm.edu	37	21	27328004	27328004	+	Silent	SNP	G	G	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr21:27328004G>C	ENST00000346798.3	-	12	1557	c.1524C>G	c.(1522-1524)acC>acG	p.T508T	APP_ENST00000357903.3_Silent_p.T489T|APP_ENST00000358918.3_Silent_p.T508T|APP_ENST00000359726.3_Silent_p.T452T|APP_ENST00000439274.2_Silent_p.T452T|APP_ENST00000348990.5_Silent_p.T433T|APP_ENST00000354192.3_Silent_p.T377T|APP_ENST00000440126.3_Silent_p.T484T|APP_ENST00000448388.2_Silent_p.T398T	NM_000484.3	NP_000475.1	P05067	A4_HUMAN	amyloid beta (A4) precursor protein	508	Heparin-binding.				adult locomotory behavior (GO:0008344)|axon cargo transport (GO:0008088)|axon midline choice point recognition (GO:0016199)|axonogenesis (GO:0007409)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular copper ion homeostasis (GO:0006878)|cholesterol metabolic process (GO:0008203)|collateral sprouting in absence of injury (GO:0048669)|dendrite development (GO:0016358)|endocytosis (GO:0006897)|extracellular matrix organization (GO:0030198)|forebrain development (GO:0030900)|innate immune response (GO:0045087)|ionotropic glutamate receptor signaling pathway (GO:0035235)|locomotory behavior (GO:0007626)|mating behavior (GO:0007617)|mRNA polyadenylation (GO:0006378)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron differentiation (GO:0045665)|neuromuscular process controlling balance (GO:0050885)|neuron apoptotic process (GO:0051402)|neuron projection development (GO:0031175)|neuron remodeling (GO:0016322)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of epidermal growth factor-activated receptor activity (GO:0007176)|regulation of multicellular organism growth (GO:0040014)|regulation of protein binding (GO:0043393)|regulation of synapse structure and activity (GO:0050803)|regulation of translation (GO:0006417)|response to oxidative stress (GO:0006979)|smooth endoplasmic reticulum calcium ion homeostasis (GO:0051563)|suckling behavior (GO:0001967)|synaptic growth at neuromuscular junction (GO:0051124)|visual learning (GO:0008542)	apical part of cell (GO:0045177)|axon (GO:0030424)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|ciliary rootlet (GO:0035253)|coated pit (GO:0005905)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|endosome (GO:0005768)|ER to Golgi transport vesicle (GO:0030134)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular membrane-bounded organelle (GO:0043231)|membrane raft (GO:0045121)|neuromuscular junction (GO:0031594)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|receptor complex (GO:0043235)|spindle midzone (GO:0051233)|synapse (GO:0045202)	acetylcholine receptor binding (GO:0033130)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|peptidase activator activity (GO:0016504)|PTB domain binding (GO:0051425)|receptor binding (GO:0005102)|serine-type endopeptidase inhibitor activity (GO:0004867)|transition metal ion binding (GO:0046914)			endometrium(5)|large_intestine(3)|lung(11)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	22		Breast(209;0.00295)				AATGCTTTAGGGTGTGCTGTC	0.483																																					p.T508T		Atlas-SNP	.											.	APP	90	.	0			c.C1524G						PASS	.						229.0	180.0	196.0					21																	27328004		2203	4300	6503	SO:0001819	synonymous_variant	351	exon12			CTTTAGGGTGTGC	M15533	CCDS13576.1, CCDS13577.1, CCDS33523.1, CCDS46638.1, CCDS46639.1, CCDS56211.1, CCDS56212.1, CCDS56213.1	21q21.2	2014-01-30	2008-07-31		ENSG00000142192	ENSG00000142192		"""Endogenous ligands"""	620	protein-coding gene	gene with protein product	"""peptidase nexin-II"""	104760	"""Alzheimer disease"""	AD1		1679289	Standard	NM_001136130		Approved		uc002ylz.3	P05067	OTTHUMG00000078438	ENST00000346798.3:c.1524C>G	chr21.hg19:g.27328004G>C		202.0	0.0	.		168.0	43.0	.	NM_000484	B2R5V1|B4DII8|D3DSD1|D3DSD2|D3DSD3|P09000|P78438|Q13764|Q13778|Q13793|Q16011|Q16014|Q16019|Q16020|Q6GSC0|Q8WZ99|Q9BT38|Q9UC33|Q9UCA9|Q9UCB6|Q9UCC8|Q9UCD1|Q9UQ58	Silent	SNP	ENST00000346798.3	hg19	CCDS13576.1	.	.	.	.	.	.	.	.	.	.	G	8.763	0.923954	0.18056	.	.	ENSG00000142192	ENST00000448850	.	.	.	5.45	3.65	0.41850	.	.	.	.	.	T	0.55970	0.1954	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.50816	-0.8783	4	.	.	.	-24.9633	7.0758	0.25203	0.3229:0.0:0.6771:0.0	.	.	.	.	A	411	.	.	P	-	1	0	APP	26249875	0.782000	0.28689	0.975000	0.42487	0.811000	0.45836	-0.105000	0.10907	0.869000	0.35703	0.655000	0.94253	CCT	.	.	.	none		0.483	APP-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000171340.1	NM_000484	
ARVCF	421	hgsc.bcm.edu	37	22	19967613	19967613	+	Missense_Mutation	SNP	C	C	A	rs376884775		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:19967613C>A	ENST00000263207.3	-	6	1340	c.1049G>T	c.(1048-1050)cGc>cTc	p.R350L	ARVCF_ENST00000344269.3_Missense_Mutation_p.R287L|ARVCF_ENST00000406259.1_Missense_Mutation_p.R350L|ARVCF_ENST00000401994.1_Missense_Mutation_p.R287L|ARVCF_ENST00000487793.1_5'Flank|ARVCF_ENST00000406522.1_Missense_Mutation_p.R287L	NM_001670.2	NP_001661.1	O00192	ARVC_HUMAN	armadillo repeat gene deleted in velocardiofacial syndrome	350					calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|multicellular organismal development (GO:0007275)|single organismal cell-cell adhesion (GO:0016337)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|cervix(1)|endometrium(3)|liver(1)|lung(4)|prostate(1)|urinary_tract(2)	13	Colorectal(54;0.0993)					CGGCTCCTTGCGGGCGCTATC	0.726																																					p.R350L		Atlas-SNP	.											.	ARVCF	54	.	0			c.G1049T						PASS	.						5.0	7.0	6.0					22																	19967613		2043	3993	6036	SO:0001583	missense	421	exon6			TCCTTGCGGGCGC		CCDS13771.1	22q11.21	2013-02-14	2010-04-28		ENSG00000099889	ENSG00000099889		"""Armadillo repeat containing"""	728	protein-coding gene	gene with protein product		602269				9126485, 15456900	Standard	NM_001670		Approved		uc002zqz.3	O00192	OTTHUMG00000030426	ENST00000263207.3:c.1049G>T	chr22.hg19:g.19967613C>A	ENSP00000263207:p.Arg350Leu	51.0	0.0	.		34.0	14.0	.	NM_001670	B7WNV2	Missense_Mutation	SNP	ENST00000263207.3	hg19	CCDS13771.1	.	.	.	.	.	.	.	.	.	.	C	32	5.120544	0.94385	.	.	ENSG00000099889	ENST00000263207;ENST00000344269;ENST00000401994;ENST00000406522;ENST00000406259	T;T;T;T;T	0.69435	-0.4;-0.34;-0.34;-0.34;-0.4	5.35	4.33	0.51752	Armadillo-like helical (1);	0.049736	0.85682	D	0.000000	T	0.61788	0.2375	L	0.38838	1.175	0.80722	D	1	P	0.49090	0.919	P	0.46850	0.529	T	0.60747	-0.7202	9	.	.	.	-18.2472	14.2537	0.66038	0.0:0.9281:0.0:0.0719	.	350	O00192	ARVC_HUMAN	L	350;287;287;287;350	ENSP00000263207:R350L;ENSP00000342042:R287L;ENSP00000384341:R287L;ENSP00000384732:R287L;ENSP00000385444:R350L	.	R	-	2	0	ARVCF	18347613	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	5.598000	0.67585	1.406000	0.46857	0.655000	0.94253	CGC	.	.	.	alt		0.726	ARVCF-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000075314.5	NM_001670	
CACNA1I	8911	hgsc.bcm.edu	37	22	40055466	40055466	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:40055466A>G	ENST00000402142.3	+	13	2359	c.2359A>G	c.(2359-2361)Aag>Gag	p.K787E	CACNA1I_ENST00000407673.1_Missense_Mutation_p.K752E|CACNA1I_ENST00000400164.3_Missense_Mutation_p.K752E|CACNA1I_ENST00000404898.1_Missense_Mutation_p.K752E|CACNA1I_ENST00000336649.4_Missense_Mutation_p.K793E|CACNA1I_ENST00000401624.1_Missense_Mutation_p.K787E	NM_021096.3	NP_066919.2	Q9P0X4	CAC1I_HUMAN	calcium channel, voltage-dependent, T type, alpha 1I subunit	787					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|signal transduction (GO:0007165)|sleep (GO:0030431)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)			breast(2)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|liver(2)|lung(27)|ovary(1)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	60	Melanoma(58;0.0749)				Cinnarizine(DB00568)|Flunarizine(DB04841)|Paramethadione(DB00617)|Spironolactone(DB00421)|Verapamil(DB00661)|Zonisamide(DB00909)	TTTTGGCTGCAAGTTCAGCCT	0.552																																					p.K787E		Atlas-SNP	.											.	CACNA1I	264	.	0			c.A2359G						PASS	.						51.0	52.0	52.0					22																	40055466		2095	4208	6303	SO:0001583	missense	8911	exon13			GGCTGCAAGTTCA	AF129133	CCDS46710.1, CCDS46711.1	22q13.1	2012-03-07	2007-02-16		ENSG00000100346	ENSG00000100346		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1396	protein-coding gene	gene with protein product		608230				10454147, 16382099	Standard	NM_021096		Approved	Cav3.3	uc003ayd.3	Q9P0X4	OTTHUMG00000151096	ENST00000402142.3:c.2359A>G	chr22.hg19:g.40055466A>G	ENSP00000385019:p.Lys787Glu	222.0	0.0	.		179.0	64.0	.	NM_021096	B0QY12|B0QY13|B0QY14|O95504|Q5JZ88|Q7Z6S9|Q8NFX6|Q9NZC8|Q9UH15|Q9UH30|Q9ULU9|Q9UNE6	Missense_Mutation	SNP	ENST00000402142.3	hg19	CCDS46710.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.813895	0.90790	.	.	ENSG00000100346	ENST00000402142;ENST00000404898;ENST00000401624;ENST00000407673;ENST00000336649;ENST00000400164	D;D;D;D;D;D	0.98400	-4.91;-4.91;-4.91;-4.91;-4.91;-4.91	4.3	4.3	0.51218	Ion transport (1);	0.048588	0.85682	D	0.000000	D	0.98544	0.9514	M	0.69185	2.1	0.58432	D	0.999994	D;D;D;D	0.76494	0.999;0.998;0.999;0.999	D;D;D;D	0.85130	0.995;0.948;0.997;0.996	D	0.99593	1.0976	10	0.87932	D	0	.	13.8843	0.63699	1.0:0.0:0.0:0.0	.	752;787;752;787	Q9P0X4-3;Q9P0X4-2;Q9P0X4-4;Q9P0X4	.;.;.;CAC1I_HUMAN	E	787;752;787;752;793;752	ENSP00000385019:K787E;ENSP00000384093:K752E;ENSP00000383887:K787E;ENSP00000385680:K752E;ENSP00000337829:K793E;ENSP00000383028:K752E	ENSP00000337829:K793E	K	+	1	0	CACNA1I	38385412	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.849000	0.92178	1.920000	0.55613	0.459000	0.35465	AAG	.	.	.	none		0.552	CACNA1I-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000321290.1	NM_001003406	
PKDREJ	10343	hgsc.bcm.edu	37	22	46654194	46654194	+	Nonsense_Mutation	SNP	G	G	A			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46654194G>A	ENST00000253255.5	-	1	5025	c.5026C>T	c.(5026-5028)Cag>Tag	p.Q1676*		NM_006071.1	NP_006062.1	Q9NTG1	PKDRE_HUMAN	polycystin (PKD) family receptor for egg jelly	1676					acrosome reaction (GO:0007340)|calcium ion transmembrane transport (GO:0070588)|detection of mechanical stimulus (GO:0050982)|neuropeptide signaling pathway (GO:0007218)|regulation of acrosome reaction (GO:0060046)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium channel activity (GO:0005262)|calcium ion binding (GO:0005509)			NS(2)|breast(7)|central_nervous_system(1)|cervix(3)|endometrium(4)|kidney(5)|large_intestine(21)|lung(16)|ovary(2)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	73		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00459)		CGGACGATCTGGTCATGTATC	0.418																																					p.Q1676X		Atlas-SNP	.											.	PKDREJ	195	.	0			c.C5026T						PASS	.						200.0	166.0	178.0					22																	46654194		2203	4300	6503	SO:0001587	stop_gained	10343	exon1			CGATCTGGTCATG	AF116458	CCDS14073.1	22q13.31	2013-07-31	2013-07-31		ENSG00000130943	ENSG00000130943			9015	protein-coding gene	gene with protein product		604670	"""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly, sea urchin homolog)-like"", ""polycystic kidney disease (polycystin) and REJ (sperm receptor for egg jelly homolog, sea urchin)-like"", ""polycystic kidney disease (polycystin) and REJ homolog (sperm receptor for egg jelly homolog, sea urchin)"""			9949214, 10591208	Standard	NM_006071		Approved		uc003bhh.3	Q9NTG1	OTTHUMG00000150493	ENST00000253255.5:c.5026C>T	chr22.hg19:g.46654194G>A	ENSP00000253255:p.Gln1676*	68.0	0.0	.		66.0	27.0	.	NM_006071	B1AJY3|O95850	Nonsense_Mutation	SNP	ENST00000253255.5	hg19	CCDS14073.1	.	.	.	.	.	.	.	.	.	.	g	42	9.331670	0.99138	.	.	ENSG00000130943	ENST00000253255	.	.	.	4.95	-3.76	0.04359	.	1.756340	0.02965	N	0.143633	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11794	T	0.64	-0.9396	3.1764	0.06570	0.1516:0.388:0.2844:0.1761	.	.	.	.	X	1676	.	ENSP00000253255:Q1676X	Q	-	1	0	PKDREJ	45032858	0.000000	0.05858	0.000000	0.03702	0.449000	0.32228	0.053000	0.14184	-0.308000	0.08792	0.298000	0.19748	CAG	.	.	.	none		0.418	PKDREJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318466.1	NM_006071	
TTC38	55020	hgsc.bcm.edu	37	22	46677589	46677589	+	Missense_Mutation	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46677589A>G	ENST00000381031.3	+	7	785	c.709A>G	c.(709-711)Atg>Gtg	p.M237V	TTC38_ENST00000445282.2_Missense_Mutation_p.M179V	NM_017931.2	NP_060401	Q5R3I4	TTC38_HUMAN	tetratricopeptide repeat domain 38	237						extracellular vesicular exosome (GO:0070062)				endometrium(4)|large_intestine(3)|lung(4)|ovary(1)	12						GTTGGAATTCATGCAGCACTC	0.512																																					p.M237V		Atlas-SNP	.											.	TTC38	40	.	0			c.A709G						PASS	.						125.0	128.0	127.0					22																	46677589		2092	4220	6312	SO:0001583	missense	55020	exon7			GAATTCATGCAGC		CCDS43030.1	22q13	2013-01-11			ENSG00000075234	ENSG00000075234		"""Tetratricopeptide (TTC) repeat domain containing"""	26082	protein-coding gene	gene with protein product							Standard	NM_017931		Approved	FLJ20699	uc003bhi.3	Q5R3I4	OTTHUMG00000150494	ENST00000381031.3:c.709A>G	chr22.hg19:g.46677589A>G	ENSP00000370419:p.Met237Val	116.0	0.0	.		88.0	31.0	.	NM_017931	Q8WV27|Q9NWP8	Missense_Mutation	SNP	ENST00000381031.3	hg19	CCDS43030.1	.	.	.	.	.	.	.	.	.	.	A	21.0	4.079821	0.76528	.	.	ENSG00000075234	ENST00000381031;ENST00000445282	T;T	0.75704	1.62;-0.96	5.79	5.79	0.91817	Tetratricopeptide-like helical (1);	0.072520	0.85682	D	0.000000	D	0.84320	0.5446	M	0.79693	2.465	0.58432	D	0.999992	D;D	0.62365	0.991;0.962	P;P	0.59171	0.853;0.523	D	0.84956	0.0874	10	0.42905	T	0.14	-12.5636	15.3166	0.74085	1.0:0.0:0.0:0.0	.	179;237	E7ES35;Q5R3I4	.;TTC38_HUMAN	V	237;179	ENSP00000370419:M237V;ENSP00000393960:M179V	ENSP00000370419:M237V	M	+	1	0	TTC38	45056253	1.000000	0.71417	1.000000	0.80357	0.785000	0.44390	4.319000	0.59197	2.207000	0.71202	0.533000	0.62120	ATG	.	.	.	none		0.512	TTC38-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000318469.1	NM_017931	
WWC3	55841	hgsc.bcm.edu	37	X	10062249	10062249	+	Silent	SNP	A	A	T			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chrX:10062249A>T	ENST00000380861.4	+	7	976	c.585A>T	c.(583-585)gtA>gtT	p.V195V	WWC3_ENST00000454666.1_Silent_p.V195V	NM_015691.3	NP_056506.2	Q9ULE0	WWC3_HUMAN	WWC family member 3	195					negative regulation of hippo signaling (GO:0035331)|negative regulation of organ growth (GO:0046621)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	cytosol (GO:0005829)	kinase binding (GO:0019900)|protein complex scaffold (GO:0032947)			NS(1)|breast(3)|endometrium(10)|kidney(1)|large_intestine(11)|lung(17)|ovary(5)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	52						CTCACCATGTAGGCGTGCCTG	0.577																																					p.V195V		Atlas-SNP	.											.	WWC3	142	.	0			c.A585T						PASS	.						144.0	125.0	132.0					X																	10062249		2203	4300	6503	SO:0001819	synonymous_variant	55841	exon7			CCATGTAGGCGTG	AK091936	CCDS14136.1	Xp22.32	2008-02-05			ENSG00000047644	ENSG00000047644		"""WW, C2 and coiled-coil domain containing"""	29237	protein-coding gene	gene with protein product						10574462	Standard	NM_015691		Approved	KIAA1280, BM042	uc004csx.4	Q9ULE0	OTTHUMG00000021123	ENST00000380861.4:c.585A>T	chrX.hg19:g.10062249A>T		92.0	0.0	.		80.0	8.0	.	NM_015691	A8KA96|Q659C1|Q9BTQ1	Silent	SNP	ENST00000380861.4	hg19	CCDS14136.1																																																																																			.	.	.	none		0.577	WWC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055725.1	NM_015691	
HUWE1	10075	hgsc.bcm.edu	37	X	53584383	53584383	+	Silent	SNP	A	A	G			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chrX:53584383A>G	ENST00000342160.3	-	59	8623	c.8166T>C	c.(8164-8166)acT>acC	p.T2722T	MIR98_ENST00000606724.1_RNA|MIRLET7F2_ENST00000385277.1_RNA|HUWE1_ENST00000262854.6_Silent_p.T2722T			Q7Z6Z7	HUWE1_HUMAN	HECT, UBA and WWE domain containing 1, E3 ubiquitin protein ligase	2722					base-excision repair (GO:0006284)|cell differentiation (GO:0030154)|histone ubiquitination (GO:0016574)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligase activity (GO:0016874)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			NS(1)|breast(15)|central_nervous_system(1)|cervix(1)|endometrium(17)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(29)|liver(2)|lung(52)|ovary(11)|prostate(2)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(2)	153						ACTTAGATGCAGTACACTGCA	0.428																																					p.T2722T		Atlas-SNP	.											.	HUWE1	724	.	0			c.T8166C						PASS	.						137.0	122.0	127.0					X																	53584383		2203	4300	6503	SO:0001819	synonymous_variant	10075	exon60			AGATGCAGTACAC	AB071605	CCDS35301.1	Xp11.22	2014-06-09	2012-02-23		ENSG00000086758	ENSG00000086758			30892	protein-coding gene	gene with protein product		300697	"""HECT, UBA and WWE domain containing 1"""			9205841, 10998601	Standard	NM_031407		Approved	Ib772, KIAA0312, UREB1	uc004dsp.4	Q7Z6Z7	OTTHUMG00000021617	ENST00000342160.3:c.8166T>C	chrX.hg19:g.53584383A>G		53.0	0.0	.		41.0	31.0	.	NM_031407	O15029|Q4G2Z2|Q5H961|Q6P4D0|Q8NG67|Q9BUI0|Q9HCJ4|Q9NSL6|Q9P0A9	Silent	SNP	ENST00000342160.3	hg19	CCDS35301.1	.	.	.	.	.	.	.	.	.	.	A	8.337	0.827732	0.16749	.	.	ENSG00000086758	ENST00000427052	.	.	.	5.64	0.708	0.18144	.	.	.	.	.	T	0.22126	0.0533	.	.	.	0.09310	N	1	.	.	.	.	.	.	T	0.22695	-1.0209	4	.	.	.	.	3.0889	0.06286	0.3857:0.0:0.3048:0.3095	.	.	.	.	R	1756	.	.	C	-	1	0	HUWE1	53601108	0.001000	0.12720	0.177000	0.23020	0.915000	0.54546	0.717000	0.25851	0.266000	0.21894	0.486000	0.48141	TGC	.	.	.	none		0.428	HUWE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056766.1	XM_497119	
CNTN4	152330	hgsc.bcm.edu	37	3	3080674	3080675	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr3:3080674_3080675insTA	ENST00000397461.1	+	18	2534_2535	c.2150_2151insTA	c.(2149-2154)gttatafs	p.VI717fs	CNTN4_ENST00000427331.1_Frame_Shift_Ins_p.VI717fs|CNTN4_ENST00000418658.1_Frame_Shift_Ins_p.VI717fs|CNTN4_ENST00000358480.3_Frame_Shift_Ins_p.VI498fs|CNTN4-AS1_ENST00000442749.2_RNA|CNTN4_ENST00000397459.2_Frame_Shift_Ins_p.VI389fs|CNTN4_ENST00000448906.2_Frame_Shift_Ins_p.VI389fs	NM_001206955.1	NP_001193884.1	Q8IWV2	CNTN4_HUMAN	contactin 4	717	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis (GO:0007409)|brain development (GO:0007420)|negative regulation of neuron differentiation (GO:0045665)|nervous system development (GO:0007399)|neuron cell-cell adhesion (GO:0007158)|neuron projection development (GO:0031175)|regulation of synaptic plasticity (GO:0048167)	anchored component of membrane (GO:0031225)|axon (GO:0030424)|extracellular region (GO:0005576)|plasma membrane (GO:0005886)				NS(1)|breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(14)|lung(19)|ovary(2)|pancreas(4)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Ovarian(110;0.156)		Epithelial(13;0.000695)|all cancers(10;0.0047)|OV - Ovarian serous cystadenocarcinoma(96;0.01)		TCTGAACTGGTTATAACCTGGG	0.45																																					p.V717fs		Atlas-Indel,Pindel	.											.	CNTN4	335	.	0			c.2150_2151insTA						PASS	.																																			SO:0001589	frameshift_variant	152330	exon19			.	AW665944	CCDS2558.1, CCDS43041.1	3p26.3	2013-02-11			ENSG00000144619	ENSG00000144619		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2174	protein-coding gene	gene with protein product		607280				8586965, 12202991	Standard	NM_175607		Approved	BIG-2	uc003bpc.3	Q8IWV2	OTTHUMG00000119031	ENST00000397461.1:c.2153_2154dupTA	chr3.hg19:g.3080677_3080678dupTA	ENSP00000380602:p.Val717fs	153.0	0.0	0		158.0	10.0	0.0632911	NM_175607	B2RAX3|Q8IX14|Q8TC35	Frame_Shift_Ins	INS	ENST00000397461.1	hg19	CCDS43041.1																																																																																			.	.	.	none		0.450	CNTN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239236.2		
EFHD1	80303	hgsc.bcm.edu	37	2	233498655	233498656	+	Frame_Shift_Ins	INS	-	-	AC			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:233498655_233498656insAC	ENST00000264059.3	+	1	718_719	c.241_242insAC	c.(241-243)tacfs	p.Y81fs	EFHD1_ENST00000409613.1_Intron	NM_025202.3	NP_079478.1	Q9BUP0	EFHD1_HUMAN	EF-hand domain family, member D1	81					neuron projection development (GO:0031175)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|large_intestine(2)|lung(3)	7		all_hematologic(139;0.0123)|Acute lymphoblastic leukemia(138;0.0182)|Breast(86;0.0199)|Renal(207;0.025)		Epithelial(121;2.08e-16)|BRCA - Breast invasive adenocarcinoma(100;0.000383)|LUSC - Lung squamous cell carcinoma(224;0.00825)|Lung(119;0.0101)		CTTCAACCCCTACACGGAGTTC	0.708																																					p.Y81fs		Atlas-Indel,Pindel	.											.	EFHD1	28	.	0			c.241_242insAC						PASS	.																																			SO:0001589	frameshift_variant	80303	exon1			.		CCDS2497.1, CCDS58755.1	2q37.1	2014-07-01	2005-01-25		ENSG00000115468	ENSG00000115468		"""EF-hand domain containing"""	29556	protein-coding gene	gene with protein product	"""swiprosin-2"""	611617	"""EF hand domain containing 1"""			21244694	Standard	NM_025202		Approved	FLJ13612	uc002vtc.3	Q9BUP0	OTTHUMG00000133263	ENST00000264059.3:c.244_245dupAC	chr2.hg19:g.233498658_233498659dupAC	ENSP00000264059:p.Tyr81fs	22.0	0.0	0		28.0	13.0	0.464286	NM_025202	B2RD83|E9PFH3|Q9BTF8|Q9H8I2|Q9HBQ0	Frame_Shift_Ins	INS	ENST00000264059.3	hg19	CCDS2497.1																																																																																			.	.	.	none		0.708	EFHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257040.2	NM_025202	
NUMA1	4926	hgsc.bcm.edu	37	11	71733436	71733436	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr11:71733436delG	ENST00000393695.3	-	7	652	c.321delC	c.(319-321)accfs	p.T107fs	RP11-849H4.4_ENST00000502284.1_RNA|NUMA1_ENST00000351960.6_Frame_Shift_Del_p.T107fs|NUMA1_ENST00000358965.6_Frame_Shift_Del_p.T107fs	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						TGGAGCTCATGGTAGAGTGGT	0.517			T	RARA	APL																																p.M108X		Atlas-Indel,Pindel	.		Dom	yes		11	11q13	4926	nuclear mitotic apparatus protein 1		L	.	NUMA1	142	.	0			c.322delA						PASS	.						155.0	158.0	157.0					11																	71733436		2200	4293	6493	SO:0001589	frameshift_variant	4926	exon7			.	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.321delC	chr11.hg19:g.71733436delG	ENSP00000377298:p.Thr107fs	85.0	0.0	0		68.0	21.0	0.308824	NM_006185		Frame_Shift_Del	DEL	ENST00000393695.3	hg19	CCDS31633.1																																																																																			.	.	.	none		0.517	NUMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395769.1		
SYT2	127833	hgsc.bcm.edu	37	1	202566051	202566052	+	Frame_Shift_Del	DEL	AG	AG	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	AG	AG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:202566051_202566052delAG	ENST00000367267.1	-	9	1285_1286	c.1093_1094delCT	c.(1093-1095)ctgfs	p.L365fs	SYT2_ENST00000367268.4_Frame_Shift_Del_p.L365fs	NM_001136504.1	NP_001129976.1	Q8N9I0	SYT2_HUMAN	synaptotagmin II	365	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.|Phospholipid binding. {ECO:0000250}.				neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|endocytic vesicle membrane (GO:0030666)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|transporter activity (GO:0005215)			NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(5)|liver(1)|lung(9)|ovary(2)|skin(2)|urinary_tract(1)	29			BRCA - Breast invasive adenocarcinoma(75;0.169)		Botulinum Toxin Type B(DB00042)	GTTCTTGCCCAGCTTGTCATAG	0.584																																					p.365_365del		Atlas-Indel,Pindel	.											.	SYT2	51	.	0			c.1094_1095del						PASS	.																																			SO:0001589	frameshift_variant	127833	exon9			.	AK090672	CCDS1427.1	1q32.1	2013-01-21			ENSG00000143858	ENSG00000143858		"""Synaptotagmins"""	11510	protein-coding gene	gene with protein product		600104				7749232	Standard	NM_177402		Approved		uc010pqb.2	Q8N9I0	OTTHUMG00000041388	ENST00000367267.1:c.1093_1094delCT	chr1.hg19:g.202566051_202566052delAG	ENSP00000356236:p.Leu365fs	134.0	0.0	0		122.0	32.0	0.262295	NM_001136504	Q496K5|Q8NBE5	Frame_Shift_Del	DEL	ENST00000367267.1	hg19	CCDS1427.1																																																																																			.	.	.	none		0.584	SYT2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000099157.1	NM_177402	
WNT7B	7477	hgsc.bcm.edu	37	22	46319111	46319112	+	Frame_Shift_Ins	INS	-	-	C			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr22:46319111_46319112insC	ENST00000339464.4	-	4	1048_1049	c.674_675insG	c.(673-675)ggcfs	p.G225fs	WNT7B_ENST00000409496.3_Frame_Shift_Ins_p.G229fs|WNT7B_ENST00000410089.1_Frame_Shift_Ins_p.G209fs	NM_058238.2	NP_478679.1	P56706	WNT7B_HUMAN	wingless-type MMTV integration site family, member 7B	225					activation of JUN kinase activity (GO:0007257)|anatomical structure regression (GO:0060033)|apoptotic process involved in patterning of blood vessels (GO:1902262)|canonical Wnt signaling pathway (GO:0060070)|cell fate commitment (GO:0045165)|cellular metabolic process (GO:0044237)|cellular response to retinoic acid (GO:0071300)|central nervous system vasculogenesis (GO:0022009)|chorio-allantoic fusion (GO:0060710)|developmental growth involved in morphogenesis (GO:0060560)|embryonic organ development (GO:0048568)|embryonic placenta morphogenesis (GO:0060669)|establishment or maintenance of polarity of embryonic epithelium (GO:0016332)|fibroblast proliferation (GO:0048144)|forebrain regionalization (GO:0021871)|homeostatic process (GO:0042592)|in utero embryonic development (GO:0001701)|inner medullary collecting duct development (GO:0072061)|lens fiber cell development (GO:0070307)|lobar bronchus development (GO:0060482)|lung development (GO:0030324)|lung epithelium development (GO:0060428)|lung morphogenesis (GO:0060425)|lung-associated mesenchyme development (GO:0060484)|mammary gland epithelium development (GO:0061180)|metanephric collecting duct development (GO:0072205)|metanephric epithelium development (GO:0072207)|metanephric loop of Henle development (GO:0072236)|metanephros morphogenesis (GO:0003338)|negative regulation of smoothened signaling pathway (GO:0045879)|neuron differentiation (GO:0030182)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|outer medullary collecting duct development (GO:0072060)|oxygen homeostasis (GO:0032364)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of JNK cascade (GO:0046330)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of cell projection size (GO:0032536)|renal inner medulla development (GO:0072053)|renal outer medulla development (GO:0072054)|response to glucocorticoid (GO:0051384)|smooth muscle cell differentiation (GO:0051145)|stem cell proliferation (GO:0072089)|synapse organization (GO:0050808)|trachea cartilage morphogenesis (GO:0060535)|Wnt signaling pathway (GO:0016055)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)			endometrium(1)|kidney(1)|large_intestine(3)|lung(8)|ovary(2)|skin(3)|upper_aerodigestive_tract(1)	19		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)|LUAD - Lung adenocarcinoma(64;0.247)		TCAGCAGGTGGCCCACCTCTCG	0.649																																					p.G225fs		Atlas-INDEL	.											.	WNT7B	45	.	0			c.675_676insG						PASS	.																																			SO:0001589	frameshift_variant	7477	exon4			.	AF416743	CCDS33667.1	22q13	2013-02-28			ENSG00000188064	ENSG00000188064		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12787	protein-coding gene	gene with protein product		601967				8168088, 9284940, 11562755	Standard	NM_058238		Approved		uc003bgo.2	P56706	OTTHUMG00000154636	ENST00000339464.4:c.675dupG	chr22.hg19:g.46319114_46319114dupC	ENSP00000341032:p.Gly225fs	164.0	0.0	0		184.0	14.0	0.076087	NM_058238	B8A596|Q96Q12	Frame_Shift_Ins	INS	ENST00000339464.4	hg19	CCDS33667.1																																																																																			.	.	.	none		0.649	WNT7B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336418.1	NM_058238	
DNMT3A	1788	hgsc.bcm.edu	37	2	25505312	25505312	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:25505312delG	ENST00000264709.3	-	4	783	c.446delC	c.(445-447)gcgfs	p.A149fs	DNMT3A_ENST00000406659.3_Frame_Shift_Del_p.A149fs|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.A149fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	149					C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					GGACTCACCCGCTTCTGCAGG	0.637			"""Mis, F, N, S"""		AML																																p.A149fs		Atlas-Indel,Pindel	.		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	.	DNMT3A	1807	.	0			c.447delG						PASS	.						14.0	17.0	16.0					2																	25505312		2202	4299	6501	SO:0001589	frameshift_variant	1788	exon4			.		CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.446delC	chr2.hg19:g.25505312delG	ENSP00000264709:p.Ala149fs	115.0	0.0	0		146.0	67.0	0.458904	NM_175630	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	ENST00000264709.3	hg19	CCDS33157.1																																																																																			.	.	.	none		0.637	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000211587.1	NM_022552	
KIF13B	23303	hgsc.bcm.edu	37	8	28984648	28984650	+	In_Frame_Del	DEL	CTC	CTC	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	CTC	CTC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:28984648_28984650delCTC	ENST00000524189.1	-	25	3249_3251	c.3211_3213delGAG	c.(3211-3213)gagdel	p.E1071del	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1071					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CATGGAAGGTCTCATGTGTTCTG	0.424																																					p.1071_1072del		Atlas-INDEL	.											.	KIF13B	192	.	0			c.3212_3214del						PASS	.																																			SO:0001651	inframe_deletion	23303	exon25			.	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3211_3213delGAG	chr8.hg19:g.28984648_28984650delCTC	ENSP00000427900:p.Glu1071del	128.0	0.0	0		97.0	10.0	0.103093	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	In_Frame_Del	DEL	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.	.	none		0.424	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
OAT	4942	hgsc.bcm.edu	37	10	126100644	126100644	+	Frame_Shift_Del	DEL	T	T	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr10:126100644delT	ENST00000368845.5	-	2	189	c.97delA	c.(97-99)acafs	p.T33fs	OAT_ENST00000539214.1_Intron	NM_000274.3	NP_000265.1	P04181	OAT_HUMAN	ornithine aminotransferase	33					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|L-proline biosynthetic process (GO:0055129)|protein hexamerization (GO:0034214)|small molecule metabolic process (GO:0044281)|visual perception (GO:0007601)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ornithine-oxo-acid transaminase activity (GO:0004587)|pyridoxal phosphate binding (GO:0030170)			endometrium(2)|large_intestine(1)|lung(2)	5		all_lung(145;0.0271)|Lung NSC(174;0.0436)|Colorectal(57;0.102)|all_neural(114;0.116)			L-Ornithine(DB00129)	CCTTGGACTGTTTTTTTAGTT	0.433																																					p.T33fs		Atlas-Indel,Pindel	.											.	OAT	25	.	0			c.98delC						PASS	.						88.0	81.0	83.0					10																	126100644		2203	4300	6503	SO:0001589	frameshift_variant	4942	exon2			.	BC016928	CCDS7639.1, CCDS53586.1	10q26	2014-09-17	2010-01-20		ENSG00000065154	ENSG00000065154	2.6.1.13		8091	protein-coding gene	gene with protein product	"""Ornithine aminotransferase"", ""ornithine aminotransferase precursor"", ""gyrate atrophy"""	613349				1682785	Standard	NM_000274		Approved	HOGA	uc001lhp.3	P04181	OTTHUMG00000019213	ENST00000368845.5:c.97delA	chr10.hg19:g.126100644delT	ENSP00000357838:p.Thr33fs	99.0	0.0	0		96.0	27.0	0.28125	NM_000274	D3DRF0|Q16068|Q16069|Q68CS0|Q6IAV9|Q9UD03	Frame_Shift_Del	DEL	ENST00000368845.5	hg19	CCDS7639.1																																																																																			.	.	.	none		0.433	OAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050863.1	NM_000274	
NUP210L	91181	hgsc.bcm.edu	37	1	154033038	154033049	+	In_Frame_Del	DEL	ATGTAAGTGATG	ATGTAAGTGATG	-	rs368673993		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	ATGTAAGTGATG	ATGTAAGTGATG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:154033038_154033049delATGTAAGTGATG	ENST00000368559.3	-	20	2888_2899	c.2817_2828delCATCACTTACAT	c.(2815-2829)accatcacttacatg>acg	p.ITYM940del	NUP210L_ENST00000271854.3_In_Frame_Del_p.ITYM940del	NM_207308.2	NP_997191.2	Q5VU65	P210L_HUMAN	nucleoporin 210kDa-like	940					Sertoli cell development (GO:0060009)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)				NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(12)|lung(34)|ovary(4)|pancreas(1)|prostate(2)|skin(6)|urinary_tract(2)	80	all_lung(78;9.35e-31)|Lung NSC(65;1.33e-28)|Hepatocellular(266;0.0877)|Melanoma(130;0.128)		LUSC - Lung squamous cell carcinoma(543;0.151)|Colorectal(543;0.198)			TTCTGCTTCCATGTAAGTGATGGTGACAACAC	0.415																																					p.940_943del		Atlas-Indel,Pindel	.											.	NUP210L	181	.	0			c.2818_2829del						PASS	.																																			SO:0001651	inframe_deletion	91181	exon20			.	AK125924	CCDS41399.1, CCDS53370.1	1q21.3	2008-02-05			ENSG00000143552	ENSG00000143552			29915	protein-coding gene	gene with protein product							Standard	NM_207308		Approved		uc001fdw.3	Q5VU65	OTTHUMG00000035852	ENST00000368559.3:c.2817_2828delCATCACTTACAT	chr1.hg19:g.154033038_154033049delATGTAAGTGATG	ENSP00000357547:p.Ile940_Met943del	99.0	0.0	0		64.0	14.0	0.21875	NM_207308	E7EP56|Q5T4L7|Q6ZRN1|Q6ZRT4|Q6ZU81|Q8NDI6|Q9UF31	In_Frame_Del	DEL	ENST00000368559.3	hg19	CCDS41399.1																																																																																			.	.	.	none		0.415	NUP210L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087270.3	NM_207308	
KIF13B	23303	hgsc.bcm.edu	37	8	28984652	28984654	+	In_Frame_Del	DEL	TGT	TGT	-	rs536929811		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TGT	TGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:28984652_28984654delTGT	ENST00000524189.1	-	25	3245_3247	c.3207_3209delACA	c.(3205-3210)acacat>act	p.H1070del	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1070					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		GAAGGTCTCATGTGTTCTGGGGG	0.429																																					p.1070_1070del		Atlas-INDEL	.											.	KIF13B	192	.	0			c.3208_3210del						PASS	.																																			SO:0001651	inframe_deletion	23303	exon25			.	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3207_3209delACA	chr8.hg19:g.28984652_28984654delTGT	ENSP00000427900:p.His1070del	126.0	0.0	0		99.0	10.0	0.10101	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	In_Frame_Del	DEL	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.	.	none		0.429	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
LRP2	4036	hgsc.bcm.edu	37	2	170096143	170096143	+	Frame_Shift_Del	DEL	A	A	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr2:170096143delA	ENST00000263816.3	-	26	4473	c.4188delT	c.(4186-4188)attfs	p.I1396fs		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	1396	EGF-like 6; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)			biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AAGAGCCTAGAATATCACATT	0.438																																					p.L1397X		Atlas-Indel,Pindel	.											.	LRP2	751	.	0			c.4189delC						PASS	.						145.0	138.0	141.0					2																	170096143		2203	4300	6503	SO:0001589	frameshift_variant	4036	exon26			.		CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.4188delT	chr2.hg19:g.170096143delA	ENSP00000263816:p.Ile1396fs	196.0	0.0	0		211.0	15.0	0.0710901	NM_004525	O00711|Q16215	Frame_Shift_Del	DEL	ENST00000263816.3	hg19	CCDS2232.1																																																																																			.	.	.	none		0.438	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2	NM_004525	
MYH7B	57644	hgsc.bcm.edu	37	20	33567508	33567512	+	Frame_Shift_Del	DEL	TCGCT	TCGCT	-	rs539864476|rs572570454	byFrequency	TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TCGCT	TCGCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr20:33567508_33567512delTCGCT	ENST00000262873.7	+	5	461_465	c.369_373delTCGCT	c.(367-375)cctcgcttcfs	p.RF124fs		NM_020884.3	NP_065935.2	A7E2Y1	MYH7B_HUMAN	myosin, heavy chain 7B, cardiac muscle, beta	82	Myosin motor.					membrane (GO:0016020)|myosin filament (GO:0032982)	ATP binding (GO:0005524)|motor activity (GO:0003774)			NS(2)|breast(5)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(19)|ovary(5)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	54			BRCA - Breast invasive adenocarcinoma(18;0.00691)			TGAACCCGCCTCGCTTCGACTTACT	0.629																																					p.123_124del		Atlas-Indel,Pindel	.											.	MYH7B	145	.	0			c.368_372del						PASS	.																																			SO:0001589	frameshift_variant	57644	exon7			.	AB040945	CCDS42869.1	20q11	2011-09-27	2006-09-29		ENSG00000078814	ENSG00000078814		"""Myosins / Myosin superfamily : Class II"""	15906	protein-coding gene	gene with protein product		609928	"""myosin, heavy polypeptide 7B, cardiac muscle, beta"""			11919279, 15014174	Standard	XM_006723839		Approved	KIAA1512, dJ756N5.1, MYH14, MHC14	uc002xbi.2	A7E2Y1	OTTHUMG00000032320	ENST00000262873.7:c.369_373delTCGCT	chr20.hg19:g.33567508_33567512delTCGCT	ENSP00000262873:p.Arg124fs	81.0	0.0	0		76.0	29.0	0.381579	NM_020884	Q5JVW7|Q6NT44|Q6NT57|Q6WG75|Q96I57|Q9NWE2|Q9P216	Frame_Shift_Del	DEL	ENST00000262873.7	hg19	CCDS42869.1																																																																																			.	.	.	none		0.629	MYH7B-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000078833.2	NM_020884	
KIF13B	23303	hgsc.bcm.edu	37	8	28984648	28984654	+	Frame_Shift_Del	DEL	CTCATGT	CTCATGT	-	rs536929811		TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	CTCATGT	CTCATGT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr8:28984648_28984654delCTCATGT	ENST00000524189.1	-	25	3245_3251	c.3207_3213delACATGAG	c.(3205-3213)acacatgagfs	p.THE1069fs	CTD-2647L4.1_ENST00000523661.1_RNA	NM_015254.3	NP_056069.2	Q9NQT8	KI13B_HUMAN	kinesin family member 13B	1069					metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|protein targeting (GO:0006605)|regulation of axonogenesis (GO:0050770)|signal transduction (GO:0007165)|T cell activation (GO:0042110)	axon (GO:0030424)|cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)|protein kinase binding (GO:0019901)			endometrium(6)|kidney(1)|lung(20)|urinary_tract(1)	28		Ovarian(32;0.000536)		KIRC - Kidney renal clear cell carcinoma(542;0.152)|Kidney(114;0.181)		CATGGAAGGTCTCATGTGTTCTGGGGG	0.425																																					p.1070_1072del		Pindel	.											.	KIF13B	192	.	0			c.3208_3214del						PASS	.																																			SO:0001589	frameshift_variant	23303	exon25			.	AB014539	CCDS55217.1	8p21	2008-07-30				ENSG00000197892		"""Kinesins"""	14405	protein-coding gene	gene with protein product		607350				9734811, 10859302, 16864656	Standard	NM_015254		Approved	GAKIN, KIAA0639	uc003xhh.4	Q9NQT8		ENST00000524189.1:c.3207_3213delACATGAG	chr8.hg19:g.28984648_28984654delCTCATGT	ENSP00000427900:p.Thr1069fs	134.0	0.0	.		102.0	13.0	0.127	NM_015254	B4DGY5|B5MC45|F8VPJ2|O75134|Q9BYJ6	Frame_Shift_Del	DEL	ENST00000524189.1	hg19	CCDS55217.1																																																																																			.	.	.	none		0.425	KIF13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376878.1		
DIP2A	23181	hgsc.bcm.edu	37	21	47985760	47985761	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TG	TG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr21:47985760_47985761delTG	ENST00000417564.2	+	36	4320_4321	c.4299_4300delTG	c.(4297-4302)cttggcfs	p.G1434fs	DIP2A_ENST00000400274.1_Frame_Shift_Del_p.G1430fs|DIP2A_ENST00000318711.7_Frame_Shift_Del_p.G1435fs|DIP2A_ENST00000479654.1_3'UTR			Q14689	DIP2A_HUMAN	DIP2 disco-interacting protein 2 homolog A (Drosophila)	1434					multicellular organismal development (GO:0007275)|negative regulation of gene expression (GO:0010629)|regulation of apoptotic process (GO:0042981)	cell surface (GO:0009986)|nucleus (GO:0005634)	catalytic activity (GO:0003824)			cervix(1)|endometrium(7)|kidney(2)|large_intestine(6)|lung(22)|ovary(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Breast(49;0.0933)			Epithelial(3;3.12e-06)|OV - Ovarian serous cystadenocarcinoma(3;5.68e-06)|all cancers(3;4.08e-05)|Colorectal(79;0.0129)|COAD - Colon adenocarcinoma(84;0.0824)		CCGGCTACCTTGGCTTCCTTCG	0.614																																					p.1433_1433del		Pindel	.											.	DIP2A	332	.	0			c.4298_4299del						PASS	.																																			SO:0001589	frameshift_variant	23181	exon36			.	AF490768	CCDS46655.1, CCDS46656.1, CCDS46657.1, CCDS54490.1, CCDS54491.1	21q22.3	2010-08-20	2006-01-13	2006-01-13	ENSG00000160305	ENSG00000160305			17217	protein-coding gene	gene with protein product		607711	"""chromosome 21 open reading frame 106"""	C21orf106			Standard	NM_015151		Approved	Dip2, KIAA0184	uc002zjo.2	Q14689	OTTHUMG00000090717	ENST00000417564.2:c.4299_4300delTG	chr21.hg19:g.47985760_47985761delTG	ENSP00000392066:p.Gly1434fs	139.0	0.0	.		117.0	27.0	0.231	NM_015151	A6P4T3|B4E0F0|E7EMA5|Q8IVA3|Q8N4S2|Q8TD89|Q96ML9	Frame_Shift_Del	DEL	ENST00000417564.2	hg19	CCDS46655.1																																																																																			.	.	.	none		0.614	DIP2A-012	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000376736.1	NM_015151	
GRWD1	83743	hgsc.bcm.edu	37	19	48953775	48953775	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr19:48953775delG	ENST00000253237.5	+	4	907	c.674delG	c.(673-675)cggfs	p.R225fs		NM_031485.3	NP_113673.3	Q9BQ67	GRWD1_HUMAN	glutamate-rich WD repeat containing 1	225						cytoplasm (GO:0005737)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|stomach(1)	19		all_lung(116;0.000147)|Lung NSC(112;0.000251)|all_epithelial(76;0.000326)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.000206)|all cancers(93;0.000207)|Epithelial(262;0.0125)|GBM - Glioblastoma multiforme(486;0.0222)		TGGTCCCCCCGGGTGACCGGT	0.667																																					p.R225fs		Pindel	.											.	GRWD1	41	.	0			c.673delC						PASS	.						34.0	37.0	36.0					19																	48953775		2203	4300	6503	SO:0001589	frameshift_variant	83743	exon4			.	AF337808	CCDS12720.1	19q13.33	2013-05-21				ENSG00000105447		"""WD repeat domain containing"""	21270	protein-coding gene	gene with protein product	regulator of ribosome biogenesis 1 homolog (S. cerevisiae)	610597				15885502	Standard	NM_031485		Approved	WDR28, GRWD, RRB1	uc002pjd.2	Q9BQ67		ENST00000253237.5:c.674delG	chr19.hg19:g.48953775delG	ENSP00000253237:p.Arg225fs	51.0	0.0	.		54.0	12.0	0.222	NM_031485	Q8TF59	Frame_Shift_Del	DEL	ENST00000253237.5	hg19	CCDS12720.1																																																																																			.	.	.	none		0.667	GRWD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466122.1	NM_031485	
IGF2R	3482	hgsc.bcm.edu	37	6	160494272	160494272	+	Frame_Shift_Del	DEL	G	G	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr6:160494272delG	ENST00000356956.1	+	34	4866	c.4718delG	c.(4717-4719)agcfs	p.S1573fs		NM_000876.2	NP_000867	P11717	MPRI_HUMAN	insulin-like growth factor 2 receptor	1573					insulin-like growth factor receptor signaling pathway (GO:0048009)|liver development (GO:0001889)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|response to retinoic acid (GO:0032526)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|clathrin coat (GO:0030118)|endocytic vesicle (GO:0030139)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|late endosome (GO:0005770)|lysosome (GO:0005764)|membrane (GO:0016020)|nuclear envelope lumen (GO:0005641)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network transport vesicle (GO:0030140)	G-protein coupled receptor activity (GO:0004930)|glycoprotein binding (GO:0001948)|identical protein binding (GO:0042802)|insulin-like growth factor-activated receptor activity (GO:0005010)|mannose binding (GO:0005537)|phosphoprotein binding (GO:0051219)|receptor activity (GO:0004872)|retinoic acid binding (GO:0001972)|transporter activity (GO:0005215)			breast(2)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(27)|lung(31)|ovary(3)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	95		Breast(66;0.000777)|Ovarian(120;0.0305)		OV - Ovarian serous cystadenocarcinoma(65;2.45e-17)|BRCA - Breast invasive adenocarcinoma(81;1.09e-05)	Mecasermin(DB01277)	ACCAGGATTAGCGTGGGCAAG	0.547																																					p.S1573fs		Pindel	.											.	IGF2R	251	.	0			c.4717delA						PASS	.						146.0	128.0	134.0					6																	160494272		2203	4300	6503	SO:0001589	frameshift_variant	3482	exon34			.	J03528	CCDS5273.1	6q25.3	2014-09-16			ENSG00000197081	ENSG00000197081		"""CD molecules"""	5467	protein-coding gene	gene with protein product	"""cation-independent mannose-6 phosphate receptor"""	147280					Standard	NM_000876		Approved	CD222, MPRI, MPR1, CIMPR, M6P-R	uc003qta.3	P11717	OTTHUMG00000015945	ENST00000356956.1:c.4718delG	chr6.hg19:g.160494272delG	ENSP00000349437:p.Ser1573fs	248.0	0.0	.		226.0	54.0	0.239	NM_000876	Q7Z7G9|Q96PT5	Frame_Shift_Del	DEL	ENST00000356956.1	hg19	CCDS5273.1																																																																																			.	.	.	none		0.547	IGF2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042931.1	NM_000876	
RGSL1	353299	hgsc.bcm.edu	37	1	182462175	182462194	+	Frame_Shift_Del	DEL	TTGAGGAGCTTTGCTACAAG	TTGAGGAGCTTTGCTACAAG	-			TCGA-GL-A59T-01A-21D-A28G-10	TCGA-GL-A59T-10A-01D-A28G-10	TTGAGGAGCTTTGCTACAAG	TTGAGGAGCTTTGCTACAAG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	c895d83d-e672-4e7a-bcd6-d068d309c625	ac797190-ad63-4351-9d7b-129d999487c2	g.chr1:182462175_182462194delTTGAGGAGCTTTGCTACAAG	ENST00000294854.8	+	9	1756_1775	c.1736_1755delTTGAGGAGCTTTGCTACAAG	c.(1735-1755)tttgaggagctttgctacaagfs	p.FEELCYK579fs	RGSL1_ENST00000542961.1_Frame_Shift_Del_p.FEELCYK614fs	NM_001137669.1	NP_001131141.1	A5PLK6	RGSL_HUMAN	regulator of G-protein signaling like 1	579					termination of G-protein coupled receptor signaling pathway (GO:0038032)	integral component of membrane (GO:0016021)				central_nervous_system(2)|skin(4)	6						AAAATGTCCTTTGAGGAGCTTTGCTACAAGAACCCAAAGA	0.368																																					p.579_585del	Ovarian(71;11 616 11292 12944 18021 32289 33994 41738 46526)	Pindel	.											.	RGSL1	111	.	0			c.1735_1754del						PASS	.																																			SO:0001589	frameshift_variant	353299	exon9			.	AF510428	CCDS58049.1	1q25	2013-04-02	2007-08-14		ENSG00000121446	ENSG00000121446			18636	protein-coding gene	gene with protein product		611012	"""regulator of G-protein signalling like 1"", ""regulator of G-protein signaling like 2"", ""regulator of G-protein signalling like 2"""	RGSL2		12801632	Standard	NM_001137669		Approved		uc009wxw.3	A5PLK6	OTTHUMG00000035217	ENST00000294854.8:c.1736_1755delTTGAGGAGCTTTGCTACAAG	chr1.hg19:g.182462175_182462194delTTGAGGAGCTTTGCTACAAG	ENSP00000457748:p.Phe579fs	84.0	0.0	.		45.0	11.0	0.244	NM_001137669	A2A2Z0|A6PVM2|A6PVM3|Q0VAJ4|Q0VAJ5|Q6ZRL0|Q86UV0|Q9H084	Frame_Shift_Del	DEL	ENST00000294854.8	hg19	CCDS58049.1																																																																																			.	.	.	none		0.368	RGSL1-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320710.3	NM_181572	
