#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
KIAA2013	90231	hgsc.bcm.edu	37	1	11983151	11983151	+	Silent	SNP	G	G	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:11983151G>A	ENST00000376572.3	-	2	1614	c.1429C>T	c.(1429-1431)Ctg>Ttg	p.L477L	KIAA2013_ENST00000376576.3_Silent_p.L477L	NM_138346.2	NP_612355.1	Q8IYS2	K2013_HUMAN	KIAA2013	477						integral component of membrane (GO:0016021)|membrane (GO:0016020)				endometrium(1)|lung(3)|ovary(1)|prostate(1)|skin(1)	7	Ovarian(185;0.249)	Renal(390;0.000469)|Lung NSC(185;0.00149)|all_lung(284;0.00189)|Breast(348;0.00586)|Colorectal(325;0.0062)|Myeloproliferative disorder(586;0.0393)|Hepatocellular(190;0.0556)|Ovarian(437;0.0731)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0228)|Colorectal(212;4.88e-06)|COAD - Colon adenocarcinoma(227;0.000241)|BRCA - Breast invasive adenocarcinoma(304;0.000293)|Kidney(185;0.000722)|KIRC - Kidney renal clear cell carcinoma(229;0.00258)|STAD - Stomach adenocarcinoma(313;0.0072)|READ - Rectum adenocarcinoma(331;0.0649)		CTGTTGTGCAGCACGTCGGGG	0.612																																					p.L477L		Atlas-SNP	.											.	KIAA2013	25	.	0			c.C1429T						PASS	.						45.0	42.0	43.0					1																	11983151		2202	4299	6501	SO:0001819	synonymous_variant	90231	exon2			TGTGCAGCACGTC	AB095933	CCDS141.1	1p36.22	2011-02-09			ENSG00000116685	ENSG00000116685			28513	protein-coding gene	gene with protein product						12477932	Standard	NM_138346		Approved	MGC33867, RP5-1077B9.1	uc001atk.3	Q8IYS2	OTTHUMG00000002391	ENST00000376572.3:c.1429C>T	chr1.hg19:g.11983151G>A		180.0	0.0	.		133.0	48.0	.	NM_138346	Q5JXC1|Q8IVF8|Q8NDI7|Q9BSY1	Silent	SNP	ENST00000376572.3	hg19	CCDS141.1																																																																																			.	.	.	none		0.612	KIAA2013-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006858.1	NM_138346	
SPEN	23013	hgsc.bcm.edu	37	1	16257405	16257405	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:16257405C>T	ENST00000375759.3	+	11	4874	c.4670C>T	c.(4669-4671)tCt>tTt	p.S1557F		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1557					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		GACTTCATTTCTGGTAGGATC	0.413																																					p.S1557F		Atlas-SNP	.											.	SPEN	374	.	0			c.C4670T						PASS	.						91.0	94.0	93.0					1																	16257405		2203	4300	6503	SO:0001583	missense	23013	exon11			TCATTTCTGGTAG		CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4670C>T	chr1.hg19:g.16257405C>T	ENSP00000364912:p.Ser1557Phe	184.0	0.0	.		152.0	72.0	.	NM_015001	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	hg19	CCDS164.1	.	.	.	.	.	.	.	.	.	.	C	11.26	1.586812	0.28268	.	.	ENSG00000065526	ENST00000375759	T	0.09163	3.01	5.03	4.1	0.47936	.	.	.	.	.	T	0.08088	0.0202	N	0.19112	0.55	0.09310	N	1	B	0.29716	0.255	B	0.30029	0.11	T	0.28299	-1.0048	9	0.59425	D	0.04	-0.2817	9.0566	0.36410	0.0:0.7735:0.1492:0.0774	.	1557	Q96T58	MINT_HUMAN	F	1557	ENSP00000364912:S1557F	ENSP00000364912:S1557F	S	+	2	0	SPEN	16129992	0.083000	0.21467	0.063000	0.19743	0.447000	0.32167	1.805000	0.38883	1.295000	0.44724	0.563000	0.77884	TCT	.	.	.	none		0.413	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1	NM_015001	
PADI1	29943	hgsc.bcm.edu	37	1	17555524	17555524	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:17555524C>G	ENST00000375471.4	+	8	999	c.907C>G	c.(907-909)Cct>Gct	p.P303A		NM_013358.2	NP_037490.2	Q9ULC6	PADI1_HUMAN	peptidyl arginine deiminase, type I	303					protein citrullination (GO:0018101)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|protein-arginine deiminase activity (GO:0004668)			haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(14)|ovary(1)|prostate(4)|skin(1)|stomach(1)|urinary_tract(1)	28		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00409)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00522)|BRCA - Breast invasive adenocarcinoma(304;1.3e-05)|COAD - Colon adenocarcinoma(227;1.31e-05)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(196;0.0069)|READ - Rectum adenocarcinoma(331;0.0681)|Lung(427;0.197)	L-Citrulline(DB00155)	CACTCAGCCTCCTGAGGAGCT	0.632																																					p.P303A	Esophageal Squamous(80;414 1257 4580 27746 50832)	Atlas-SNP	.											.	PADI1	77	.	0			c.C907G						PASS	.						38.0	29.0	32.0					1																	17555524		2202	4298	6500	SO:0001583	missense	29943	exon8			CAGCCTCCTGAGG	AB033768	CCDS178.1	1p36.13	2008-07-18			ENSG00000142623	ENSG00000142623	3.5.3.15	"""Peptidyl arginine deiminases"""	18367	protein-coding gene	gene with protein product	"""peptidylarginine deiminase type I"", ""protein-arginine deiminase type-1"", ""hPAD-colony 10"""	607934				12416996	Standard	NM_013358		Approved	HPAD10, PDI1, PDI, PAD1	uc001bah.1	Q9ULC6	OTTHUMG00000002294	ENST00000375471.4:c.907C>G	chr1.hg19:g.17555524C>G	ENSP00000364620:p.Pro303Ala	25.0	0.0	.		21.0	9.0	.	NM_013358	A1L4K6|Q70SX6	Missense_Mutation	SNP	ENST00000375471.4	hg19	CCDS178.1	.	.	.	.	.	.	.	.	.	.	C	20.4	3.990531	0.74589	.	.	ENSG00000142623	ENST00000375471	T	0.38560	1.13	4.93	4.93	0.64822	Protein-arginine deiminase, C-terminal (1);	0.000000	0.85682	D	0.000000	T	0.62539	0.2436	M	0.67625	2.065	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.60885	-0.7174	10	0.34782	T	0.22	-26.2146	16.7057	0.85371	0.0:1.0:0.0:0.0	.	303	Q9ULC6	PADI1_HUMAN	A	303	ENSP00000364620:P303A	ENSP00000364620:P303A	P	+	1	0	PADI1	17428111	1.000000	0.71417	0.974000	0.42286	0.908000	0.53690	5.529000	0.67135	2.280000	0.76307	0.555000	0.69702	CCT	.	.	.	none		0.632	PADI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006621.1	NM_013358	
OR10K1	391109	hgsc.bcm.edu	37	1	158436100	158436100	+	Missense_Mutation	SNP	T	T	G	rs202043017		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:158436100T>G	ENST00000289451.2	+	1	829	c.749T>G	c.(748-750)gTt>gGt	p.V250G		NM_001004473.1	NP_001004473.1	Q8NGX5	O10K1_HUMAN	olfactory receptor, family 10, subfamily K, member 1	250						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	27	all_hematologic(112;0.0378)					GTGGTAACTGTTCACTACAGT	0.453																																					p.V250G		Atlas-SNP	.											.	OR10K1	80	.	0			c.T749G						PASS	.						172.0	148.0	156.0					1																	158436100		2203	4300	6503	SO:0001583	missense	391109	exon1			TAACTGTTCACTA	AP002532	CCDS30897.1	1q23.1	2012-08-09			ENSG00000173285	ENSG00000173285		"""GPCR / Class A : Olfactory receptors"""	14693	protein-coding gene	gene with protein product							Standard	NM_001004473		Approved		uc010pij.2	Q8NGX5	OTTHUMG00000017517	ENST00000289451.2:c.749T>G	chr1.hg19:g.158436100T>G	ENSP00000289451:p.Val250Gly	96.0	0.0	.		60.0	28.0	.	NM_001004473	Q6IFS2	Missense_Mutation	SNP	ENST00000289451.2	hg19	CCDS30897.1	.	.	.	.	.	.	.	.	.	.	t	14.94	2.684253	0.47991	.	.	ENSG00000173285	ENST00000289451	T	0.00202	8.56	4.24	4.24	0.50183	GPCR, rhodopsin-like superfamily (1);	0.000000	0.36740	N	0.002436	T	0.00241	0.0007	M	0.75150	2.29	0.42767	D	0.993828	D	0.63880	0.993	D	0.65140	0.932	T	0.73183	-0.4063	10	0.87932	D	0	.	7.3876	0.26891	0.0:0.1011:0.0:0.8989	.	250	Q8NGX5	O10K1_HUMAN	G	250	ENSP00000289451:V250G	ENSP00000289451:V250G	V	+	2	0	OR10K1	156702724	0.016000	0.18221	0.728000	0.30774	0.644000	0.38419	2.073000	0.41519	1.753000	0.51906	0.455000	0.32223	GTT	.	T|1.000;C|0.000	.	alt		0.453	OR10K1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046367.1		
TEX35	84066	hgsc.bcm.edu	37	1	178483864	178483864	+	Missense_Mutation	SNP	A	A	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:178483864A>C	ENST00000319416.2	+	3	232	c.120A>C	c.(118-120)gaA>gaC	p.E40D	TEX35_ENST00000367639.1_Missense_Mutation_p.E48D|TEX35_ENST00000258298.2_5'UTR|TEX35_ENST00000367643.3_Missense_Mutation_p.E40D|TEX35_ENST00000367642.3_Missense_Mutation_p.E76D|TEX35_ENST00000367641.3_Missense_Mutation_p.E40D	NM_032126.4	NP_115502.2			testis expressed 35																		TTAAACAAGAAGGGCGGTTTA	0.473																																					p.E48D		Atlas-SNP	.											.	TEX35	15	.	0			c.A144C						PASS	.						144.0	106.0	119.0					1																	178483864		2203	4300	6503	SO:0001583	missense	84066	exon3			ACAAGAAGGGCGG	AL136694	CCDS1323.1, CCDS53433.1, CCDS53434.1	1q25.2	2014-01-28	2012-06-29	2012-06-29	ENSG00000240021	ENSG00000240021			25366	protein-coding gene	gene with protein product	"""Testis-Specific Conserved gene 24kDa"""		"""chromosome 1 open reading frame 49"""	C1orf49		11230166, 17077512	Standard	NM_032126		Approved	DKFZP564J047, TSC24	uc001glt.2	Q5T0J7	OTTHUMG00000035023	ENST00000319416.2:c.120A>C	chr1.hg19:g.178483864A>C	ENSP00000323795:p.Glu40Asp	135.0	0.0	.		107.0	55.0	.	NM_001170722		Missense_Mutation	SNP	ENST00000319416.2	hg19	CCDS1323.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.643611	0.29246	.	.	ENSG00000240021	ENST00000319416;ENST00000367643;ENST00000367642;ENST00000367641;ENST00000367639	T;T;T;T;T	0.51574	2.1;2.1;0.7;2.1;2.1	3.72	-1.68	0.08212	.	0.176851	0.27397	N	0.019551	T	0.28499	0.0705	L	0.40543	1.245	0.41184	D	0.986258	B;B;B	0.19073	0.033;0.033;0.033	B;B;B	0.19946	0.027;0.018;0.018	T	0.05920	-1.0856	10	0.45353	T	0.12	-12.1642	0.5174	0.00605	0.4397:0.1788:0.2082:0.1732	.	48;40;40	Q5T0J7-2;Q5T0J7-3;Q5T0J7	.;.;CA049_HUMAN	D	40;40;76;40;48	ENSP00000323795:E40D;ENSP00000356615:E40D;ENSP00000356614:E76D;ENSP00000356613:E40D;ENSP00000356611:E48D	ENSP00000323795:E40D	E	+	3	2	C1orf49	176750487	1.000000	0.71417	0.429000	0.26710	0.053000	0.15095	0.445000	0.21677	-0.316000	0.08690	0.459000	0.35465	GAA	.	.	.	none		0.473	TEX35-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084917.1	NM_032126	
HMCN1	83872	hgsc.bcm.edu	37	1	186099715	186099715	+	Silent	SNP	G	G	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:186099715G>A	ENST00000271588.4	+	85	13345	c.13116G>A	c.(13114-13116)gaG>gaA	p.E4372E	HMCN1_ENST00000367492.2_Silent_p.E4372E	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	4372	Ig-like C2-type 43.				response to stimulus (GO:0050896)|visual perception (GO:0007601)	basement membrane (GO:0005604)|cell cortex (GO:0005938)|cell junction (GO:0030054)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			NS(2)|autonomic_ganglia(1)|breast(10)|central_nervous_system(2)|cervix(1)|endometrium(28)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(58)|liver(3)|lung(101)|ovary(23)|pancreas(4)|prostate(20)|skin(8)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(18)	308						TGAATTGTGAGGTGAAAGGAG	0.478																																					p.E4372E		Atlas-SNP	.											.	HMCN1	797	.	0			c.G13116A						PASS	.						110.0	106.0	108.0					1																	186099715		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon85			TTGTGAGGTGAAA	AF156100	CCDS30956.1	1q25.3-q31.1	2013-01-11			ENSG00000143341	ENSG00000143341		"""Fibulins"", ""Immunoglobulin superfamily / I-set domain containing"""	19194	protein-coding gene	gene with protein product	"""fibulin 6"""	608548	"""age-related macular degeneration 1 (senile macular degeneration)"""	ARMD1		11222143	Standard	NM_031935		Approved	FBLN6, FIBL6, FIBL-6	uc001grq.1	Q96RW7	OTTHUMG00000059337	ENST00000271588.4:c.13116G>A	chr1.hg19:g.186099715G>A		147.0	0.0	.		112.0	53.0	.	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	hg19	CCDS30956.1																																																																																			.	.	.	none		0.478	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
PLXNA2	5362	hgsc.bcm.edu	37	1	208215625	208215625	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:208215625G>C	ENST00000367033.3	-	22	4861	c.4104C>G	c.(4102-4104)ttC>ttG	p.F1368L		NM_025179.3	NP_079455.3	O75051	PLXA2_HUMAN	plexin A2	1368					axon guidance (GO:0007411)|centrosome localization (GO:0051642)|cerebellar granule cell precursor tangential migration (GO:0021935)|limb bud formation (GO:0060174)|neural tube development (GO:0021915)|pharyngeal system development (GO:0060037)|regulation of cell migration (GO:0030334)|semaphorin-plexin signaling pathway (GO:0071526)|somitogenesis (GO:0001756)	integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)			NS(1)|breast(3)|central_nervous_system(5)|cervix(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|liver(1)|lung(28)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)	80				OV - Ovarian serous cystadenocarcinoma(81;0.199)		GGGTGCGGATGAAGGTCAGCA	0.612																																					p.F1368L		Atlas-SNP	.											.	PLXNA2	178	.	0			c.C4104G						PASS	.						118.0	117.0	117.0					1																	208215625		2203	4300	6503	SO:0001583	missense	5362	exon22			GCGGATGAAGGTC	X87831	CCDS31013.1	1q32.2	2008-07-18			ENSG00000076356	ENSG00000076356		"""Plexins"""	9100	protein-coding gene	gene with protein product	"""plexin 2"", ""plexin-A2"", ""semaphorin receptor OCT"", ""transmembrane protein OCT"""	601054		PLXN2		8570614	Standard	NM_025179		Approved	OCT, FLJ11751, FLJ30634, KIAA0463	uc001hgz.3	O75051	OTTHUMG00000036564	ENST00000367033.3:c.4104C>G	chr1.hg19:g.208215625G>C	ENSP00000356000:p.Phe1368Leu	101.0	0.0	.		66.0	26.0	.	NM_025179	A2RTX9|B2RMX7|Q6UX61|Q96GN9|Q9BRL1|Q9UIW1	Missense_Mutation	SNP	ENST00000367033.3	hg19	CCDS31013.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.825465	0.90955	.	.	ENSG00000076356	ENST00000367033	T	0.11169	2.8	5.15	4.24	0.50183	Plexin, cytoplasmic RasGAP domain (1);Rho GTPase activation protein (1);	0.000000	0.85682	D	0.000000	T	0.27798	0.0684	M	0.64997	1.995	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.00849	-1.1541	10	0.54805	T	0.06	.	10.7984	0.46474	0.1524:0.0:0.8476:0.0	.	1368	O75051	PLXA2_HUMAN	L	1368	ENSP00000356000:F1368L	ENSP00000356000:F1368L	F	-	3	2	PLXNA2	206282248	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	4.436000	0.59948	1.169000	0.42739	0.455000	0.32223	TTC	.	.	.	none		0.612	PLXNA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000088932.6	NM_025179	
FOSL2	2355	hgsc.bcm.edu	37	2	28634997	28634997	+	Silent	SNP	G	G	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:28634997G>C	ENST00000264716.4	+	4	1526	c.663G>C	c.(661-663)gtG>gtC	p.V221V	FOSL2_ENST00000545753.1_Silent_p.V182V|FOSL2_ENST00000379619.1_Silent_p.V213V	NM_005253.3	NP_005244.1	P15408	FOSL2_HUMAN	FOS-like antigen 2	221					cell death (GO:0008219)|cellular response to hormone stimulus (GO:0032870)|female pregnancy (GO:0007565)|positive regulation of fibroblast proliferation (GO:0048146)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to cAMP (GO:0051591)|response to corticosterone (GO:0051412)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to morphine (GO:0043278)|response to progesterone (GO:0032570)|transcription from RNA polymerase II promoter (GO:0006366)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(1)|large_intestine(3)|lung(1)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	14	Acute lymphoblastic leukemia(172;0.155)					CTGTAGTGGTGAAACAGGAGC	0.682																																					p.V221V		Atlas-SNP	.											.	FOSL2	39	.	0			c.G663C						PASS	.						33.0	37.0	36.0					2																	28634997		2203	4297	6500	SO:0001819	synonymous_variant	2355	exon4			AGTGGTGAAACAG		CCDS1766.1	2p23.3	2013-01-10			ENSG00000075426	ENSG00000075426		"""basic leucine zipper proteins"""	3798	protein-coding gene	gene with protein product		601575					Standard	NM_005253		Approved	FRA2, FLJ23306	uc002rma.3	P15408	OTTHUMG00000097832	ENST00000264716.4:c.663G>C	chr2.hg19:g.28634997G>C		87.0	0.0	.		80.0	28.0	.	NM_005253	B2RD58|B3KP27|B4DYV4|Q6FG46	Silent	SNP	ENST00000264716.4	hg19	CCDS1766.1																																																																																			.	.	.	none		0.682	FOSL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215116.2	NM_005253	
BIRC6	57448	hgsc.bcm.edu	37	2	32824826	32824826	+	Silent	SNP	G	G	T	rs144649481		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:32824826G>T	ENST00000421745.2	+	70	13985	c.13851G>T	c.(13849-13851)gcG>gcT	p.A4617A		NM_016252.3	NP_057336	Q9NR09	BIRC6_HUMAN	baculoviral IAP repeat containing 6	4617	Ubiquitin-conjugating.				apoptotic process (GO:0006915)|labyrinthine layer development (GO:0060711)|mitotic nuclear division (GO:0007067)|negative regulation of apoptotic process (GO:0043066)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|positive regulation of cell proliferation (GO:0008284)|protein phosphorylation (GO:0006468)|protein ubiquitination (GO:0016567)|regulation of cell proliferation (GO:0042127)|regulation of cytokinesis (GO:0032465)|spongiotrophoblast layer development (GO:0060712)	endosome (GO:0005768)|membrane (GO:0016020)|microtubule organizing center (GO:0005815)|midbody (GO:0030496)|spindle pole (GO:0000922)|trans-Golgi network (GO:0005802)	acid-amino acid ligase activity (GO:0016881)|cysteine-type endopeptidase inhibitor activity (GO:0004869)|ubiquitin-protein transferase activity (GO:0004842)			NS(4)|breast(8)|central_nervous_system(3)|endometrium(21)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(31)|lung(65)|ovary(7)|pancreas(1)|prostate(5)|skin(5)|stomach(1)|urinary_tract(5)	172	Acute lymphoblastic leukemia(172;0.155)					CTGGTCCAGCGGACACCCCTT	0.373																																					p.A4617A	Pancreas(94;175 1509 16028 18060 45422)	Atlas-SNP	.											BIRC6_ENST00000421745,colon,carcinoma,0,2	BIRC6	838	.	0			c.G13851T						PASS	.						117.0	113.0	114.0					2																	32824826		2203	4300	6503	SO:0001819	synonymous_variant	57448	exon70			TCCAGCGGACACC	AF265555	CCDS33175.2	2p22.3	2011-01-25	2011-01-25		ENSG00000115760	ENSG00000115760		"""Baculoviral IAP repeat containing"", ""Ubiquitin-conjugating enzymes E2"""	13516	protein-coding gene	gene with protein product	"""apollon"""	605638	"""baculoviral IAP repeat-containing 6"""			10544019	Standard	NM_016252		Approved	BRUCE	uc010ezu.3	Q9NR09	OTTHUMG00000150528	ENST00000421745.2:c.13851G>T	chr2.hg19:g.32824826G>T		71.0	0.0	.		68.0	3.0	.	NM_016252	Q9ULD1	Silent	SNP	ENST00000421745.2	hg19	CCDS33175.2																																																																																			.	G|1.000;A|0.000	.	alt		0.373	BIRC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318769.3	NM_016252	
LHCGR	3973	hgsc.bcm.edu	37	2	48982764	48982764	+	Missense_Mutation	SNP	A	A	T	rs4539842		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:48982764A>T	ENST00000294954.7	-	1	68	c.47T>A	c.(46-48)cTg>cAg	p.L16Q	LHCGR_ENST00000403273.1_Missense_Mutation_p.L16Q|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000405626.1_Missense_Mutation_p.L16Q|LHCGR_ENST00000344775.3_Missense_Mutation_p.L16Q|LHCGR_ENST00000401907.1_Missense_Mutation_p.L16Q	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	16					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	cggctgcagcagcagcagcag	0.721																																					p.L16Q		Atlas-SNP	.											.	LHCGR	154	.	0			c.T47A						PASS	.						1.0	3.0	2.0					2																	48982764		911	1841	2752	SO:0001583	missense	3973	exon1			TGCAGCAGCAGCA		CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.47T>A	chr2.hg19:g.48982764A>T	ENSP00000294954:p.Leu16Gln	54.0	0.0	.		23.0	5.0	.	NM_000233	Q14751|Q15996|Q9UEW9	Missense_Mutation	SNP	ENST00000294954.7	hg19	CCDS1842.1	.	.	.	.	.	.	.	.	.	.	A	16.68	3.191104	0.58017	.	.	ENSG00000138039	ENST00000344775;ENST00000294954;ENST00000405626;ENST00000403273;ENST00000401907	D;D;D;D;D	0.85702	-2.02;-2.02;-2.02;-2.02;-2.02	4.18	4.18	0.49190	.	1.158800	0.06471	N	0.731104	D	0.83594	0.5288	L	0.29908	0.895	0.28253	N	0.925194	D	0.55172	0.97	P	0.51453	0.67	T	0.72527	-0.4266	9	.	.	.	.	9.5009	0.39017	1.0:0.0:0.0:0.0	rs4539842	16	P22888	LSHR_HUMAN	Q	16	ENSP00000344301:L16Q;ENSP00000294954:L16Q;ENSP00000386033:L16Q;ENSP00000385847:L16Q;ENSP00000385406:L16Q	.	L	-	2	0	LHCGR	48836268	0.561000	0.26578	0.862000	0.33874	0.243000	0.25628	1.821000	0.39041	1.736000	0.51660	0.421000	0.28195	CTG	.	.	.	weak		0.721	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251364.4	NM_000233.3	
NRXN1	9378	hgsc.bcm.edu	37	2	50850545	50850545	+	Silent	SNP	T	T	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:50850545T>C	ENST00000406316.2	-	6	2517	c.1041A>G	c.(1039-1041)ggA>ggG	p.G347G	NRXN1_ENST00000402717.3_Silent_p.G347G|NRXN1_ENST00000404971.1_Silent_p.G380G|NRXN1_ENST00000406859.3_Silent_p.G347G|NRXN1_ENST00000401669.2_Silent_p.G347G|NRXN1_ENST00000405472.3_Silent_p.G347G|NRXN1_ENST00000331040.5_5'UTR	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	347	Laminin G-like 2. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|axon guidance (GO:0007411)|calcium-dependent cell-cell adhesion (GO:0016339)|cerebellar granule cell differentiation (GO:0021707)|establishment of protein localization (GO:0045184)|extracellular matrix organization (GO:0030198)|gamma-aminobutyric acid receptor clustering (GO:0097112)|gephyrin clustering (GO:0097116)|guanylate kinase-associated protein clustering (GO:0097117)|heterophilic cell-cell adhesion (GO:0007157)|learning (GO:0007612)|N-methyl-D-aspartate receptor clustering (GO:0097114)|negative regulation of filopodium assembly (GO:0051490)|neuroligin clustering (GO:0097118)|neuromuscular process controlling balance (GO:0050885)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|neurotransmitter secretion (GO:0007269)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of synapse assembly (GO:0051965)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|presynaptic membrane assembly (GO:0097105)|receptor localization to synapse (GO:0097120)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic vesicle clustering (GO:0097091)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	axonal growth cone (GO:0044295)|cell junction (GO:0030054)|cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|presynaptic membrane (GO:0042734)	acetylcholine receptor binding (GO:0033130)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|cell adhesion molecule binding (GO:0050839)|neuroligin family protein binding (GO:0097109)|receptor activity (GO:0004872)			breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(33)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	58		all_hematologic(82;0.152)|Acute lymphoblastic leukemia(82;0.192)	Lung(47;0.0813)|LUSC - Lung squamous cell carcinoma(58;0.116)			AGGCCCCTGATCCCAAATTAA	0.463																																					p.G380G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.A1140G						PASS	.						117.0	111.0	113.0					2																	50850545		1897	4128	6025	SO:0001819	synonymous_variant	9378	exon7			CCCTGATCCCAAA	AB011150	CCDS1845.1, CCDS46282.1, CCDS54360.1	2p16.3	2008-05-15			ENSG00000179915	ENSG00000179915			8008	protein-coding gene	gene with protein product		600565					Standard	NM_001135659		Approved	KIAA0578, Hs.22998	uc021vhj.1	P58400	OTTHUMG00000129263	ENST00000406316.2:c.1041A>G	chr2.hg19:g.50850545T>C		91.0	0.0	.		67.0	25.0	.	NM_001135659	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.	.	none		0.463	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
ALMS1	7840	hgsc.bcm.edu	37	2	73676852	73676852	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:73676852C>G	ENST00000264448.6	+	8	3306	c.3195C>G	c.(3193-3195)gaC>gaG	p.D1065E	ALMS1_ENST00000377715.1_Missense_Mutation_p.D1065E|ALMS1_ENST00000409009.1_Missense_Mutation_p.D1023E	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	1065	34 X 47 AA approximate tandem repeat.				endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGTTATCAGACAGTCATCTAC	0.488																																					p.D1065E		Atlas-SNP	.											.	ALMS1	384	.	0			c.C3195G						PASS	.						122.0	124.0	123.0					2																	73676852		1911	4127	6038	SO:0001583	missense	7840	exon8			ATCAGACAGTCAT	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.3195C>G	chr2.hg19:g.73676852C>G	ENSP00000264448:p.Asp1065Glu	176.0	0.0	.		150.0	48.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1	.	.	.	.	.	.	.	.	.	.	C	13.96	2.393036	0.42410	.	.	ENSG00000116127	ENST00000409009;ENST00000264448;ENST00000377715	T;T;T	0.20200	2.97;2.96;2.09	4.49	-6.07	0.02158	.	0.685138	0.13351	N	0.394421	T	0.31263	0.0791	L	0.52573	1.65	0.09310	N	1	D;P;D	0.76494	0.982;0.566;0.999	P;B;D	0.67548	0.802;0.138;0.952	T	0.10405	-1.0631	10	0.29301	T	0.29	.	13.7332	0.62802	0.0:0.1772:0.0:0.8228	.	1065;1023;1065	Q8TCU4-3;B8ZZJ3;Q8TCU4	.;.;ALMS1_HUMAN	E	1023;1065;1065	ENSP00000386627:D1023E;ENSP00000264448:D1065E;ENSP00000366944:D1065E	ENSP00000264448:D1065E	D	+	3	2	ALMS1	73530360	0.000000	0.05858	0.000000	0.03702	0.037000	0.13140	-3.161000	0.00577	-1.296000	0.02353	0.591000	0.81541	GAC	.	.	.	none		0.488	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
ALMS1	7840	hgsc.bcm.edu	37	2	73680924	73680925	+	Missense_Mutation	DNP	GG	GG	TT			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:73680924_73680925GG>TT	ENST00000264448.6	+	8	7378_7379	c.7267_7268GG>TT	c.(7267-7269)GGt>TTt	p.G2423F	ALMS1-IT1_ENST00000441587.2_RNA|ALMS1_ENST00000377715.1_Missense_Mutation_p.G2423F|ALMS1_ENST00000409009.1_Missense_Mutation_p.G2381F	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2423					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGATGGAAATGGTTCCTGCTCG	0.381																																					p.G2423C|p.G2423V		Atlas-SNP	.											.	ALMS1	384	.	0			c.G7267T|c.G7268T						PASS	.																																			SO:0001583	missense	7840	exon8			GGAAATGGTTCCT|GAAATGGTTCCTG	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	Exception_encountered	chr2.hg19:g.73680924_73680925delinsTT	ENSP00000264448:p.Gly2423Phe	136.0	0.0	.		78.0	30.0	.	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	Missense_Mutation	SNP	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.381	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
POLR1A	25885	hgsc.bcm.edu	37	2	86302371	86302371	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:86302371T>G	ENST00000263857.6	-	12	1771	c.1393A>C	c.(1393-1395)Aaa>Caa	p.K465Q	POLR1A_ENST00000409681.1_Missense_Mutation_p.K465Q			O95602	RPA1_HUMAN	polymerase (RNA) I polypeptide A, 194kDa	465					gene expression (GO:0010467)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription initiation from RNA polymerase I promoter (GO:0006361)	cytoplasm (GO:0005737)|DNA-directed RNA polymerase I complex (GO:0005736)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|zinc ion binding (GO:0008270)			NS(1)|breast(4)|cervix(2)|endometrium(8)|kidney(3)|large_intestine(12)|liver(1)|lung(20)|ovary(3)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	63						TAGGTCAGTTTTGTGGCAAAC	0.493																																					p.K465Q		Atlas-SNP	.											.	POLR1A	137	.	0			c.A1393C						PASS	.						22.0	22.0	22.0					2																	86302371		1939	4127	6066	SO:0001583	missense	25885	exon12			TCAGTTTTGTGGC	AK025568	CCDS42706.1	2p11.2	2013-01-21			ENSG00000068654	ENSG00000068654		"""RNA polymerase subunits"""	17264	protein-coding gene	gene with protein product						9236775	Standard	NM_015425		Approved	DKFZP586M0122, FLJ21915, RPO1-4, RPA1	uc002sqs.3	O95602	OTTHUMG00000153165	ENST00000263857.6:c.1393A>C	chr2.hg19:g.86302371T>G	ENSP00000263857:p.Lys465Gln	74.0	0.0	.		63.0	23.0	.	NM_015425	B7Z7T0|D6W5M0|Q0VG05|Q9UEH0|Q9UFT9	Missense_Mutation	SNP	ENST00000263857.6	hg19	CCDS42706.1	.	.	.	.	.	.	.	.	.	.	T	18.61	3.660500	0.67586	.	.	ENSG00000068654	ENST00000263857;ENST00000409681	T;T	0.69306	-0.39;-0.39	5.01	5.01	0.66863	RNA polymerase, alpha subunit (1);RNA polymerase, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80308	0.4599	M	0.70275	2.135	0.80722	D	1	D	0.89917	1.0	D	0.79784	0.993	T	0.82717	-0.0319	10	0.72032	D	0.01	-24.511	14.5645	0.68165	0.0:0.0:0.0:1.0	.	465	O95602	RPA1_HUMAN	Q	465	ENSP00000263857:K465Q;ENSP00000386300:K465Q	ENSP00000263857:K465Q	K	-	1	0	POLR1A	86155882	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	7.448000	0.80631	2.107000	0.64212	0.533000	0.62120	AAA	.	.	.	none		0.493	POLR1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329830.2	NM_015425	
XIRP2	129446	hgsc.bcm.edu	37	2	168106667	168106667	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:168106667A>G	ENST00000409195.1	+	9	8854	c.8765A>G	c.(8764-8766)cAg>cGg	p.Q2922R	XIRP2_ENST00000409273.1_Missense_Mutation_p.Q2700R|XIRP2_ENST00000409043.1_Intron|XIRP2_ENST00000420519.1_Intron|XIRP2_ENST00000295237.9_Missense_Mutation_p.Q2922R|XIRP2_ENST00000409756.2_Intron|XIRP2_ENST00000409728.1_Intron|XIRP2_ENST00000409605.1_Intron	NM_152381.5	NP_689594.4	A4UGR9	XIRP2_HUMAN	xin actin-binding repeat containing 2	2747					actin cytoskeleton organization (GO:0030036)|cardiac muscle tissue morphogenesis (GO:0055008)|cell-cell junction organization (GO:0045216)|ventricular septum development (GO:0003281)	cell junction (GO:0030054)|Z disc (GO:0030018)				NS(3)|biliary_tract(2)|breast(5)|cervix(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(51)|lung(160)|ovary(7)|pancreas(3)|prostate(11)|skin(14)|stomach(5)|upper_aerodigestive_tract(8)|urinary_tract(7)	315						GAGATTACACAGAACAAATCT	0.373																																					p.Q2922R		Atlas-SNP	.											XIRP2,colon,carcinoma,0,1	XIRP2	914	.	0			c.A8765G						PASS	.						81.0	77.0	78.0					2																	168106667		1824	4081	5905	SO:0001583	missense	129446	exon9			TTACACAGAACAA	AK056582	CCDS42768.1, CCDS42769.1, CCDS56143.1, CCDS56144.1, CCDS56145.1	2q31.1	2013-10-25	2007-06-27	2007-06-27	ENSG00000163092	ENSG00000163092			14303	protein-coding gene	gene with protein product	"""myomaxin"""	609778	"""cardiomyopathy associated 3"""	CMYA3		17046827, 12203715, 15454575	Standard	NM_001079810		Approved		uc002udx.3	A4UGR9	OTTHUMG00000154027	ENST00000409195.1:c.8765A>G	chr2.hg19:g.168106667A>G	ENSP00000386840:p.Gln2922Arg	355.0	0.0	.		254.0	110.0	.	NM_152381	A0PJ94|B2BBS0|B2BBS1|B2BBS4|B3KVH0|J3KNB1|Q53R52|Q5MJ67|Q702N7|Q86T36|Q86T38|Q86T46|Q86T51|Q86T53|Q86T55|Q86T79|Q86TB6|Q8N1M9|Q8N3R5|Q8TBV6	Missense_Mutation	SNP	ENST00000409195.1	hg19	CCDS42769.1	.	.	.	.	.	.	.	.	.	.	A	13.30	2.196928	0.38806	.	.	ENSG00000163092	ENST00000409195;ENST00000295237;ENST00000409273;ENST00000413534	T;T;T	0.02472	4.28;4.28;4.29	6.02	4.86	0.63082	.	0.687182	0.14362	N	0.324364	T	0.05960	0.0155	L	0.60455	1.87	0.32557	N	0.531638	P;P;P	0.46142	0.799;0.873;0.873	B;P;P	0.44990	0.276;0.466;0.466	T	0.19910	-1.0291	10	0.28530	T	0.3	-0.7943	12.6473	0.56742	0.8617:0.1383:0.0:0.0	.	2747;2747;2700	A4UGR9;A4UGR9-3;A4UGR9-2	XIRP2_HUMAN;.;.	R	2922;2922;2700;336	ENSP00000386840:Q2922R;ENSP00000295237:Q2922R;ENSP00000387255:Q2700R	ENSP00000295237:Q2922R	Q	+	2	0	XIRP2	167814913	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.353000	0.59411	1.082000	0.41137	0.533000	0.62120	CAG	.	.	.	none		0.373	XIRP2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333547.1	NM_152381	
SLC40A1	30061	hgsc.bcm.edu	37	2	190439896	190439896	+	Missense_Mutation	SNP	T	T	C	rs387907374		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:190439896T>C	ENST00000261024.2	-	3	688	c.262A>G	c.(262-264)Aga>Gga	p.R88G	SLC40A1_ENST00000418714.1_5'UTR	NM_014585.5	NP_055400.1	Q9NP59	S40A1_HUMAN	solute carrier family 40 (iron-regulated transporter), member 1	88					anatomical structure morphogenesis (GO:0009653)|cellular iron ion homeostasis (GO:0006879)|endothelium development (GO:0003158)|iron ion transmembrane transport (GO:0034755)|lymphocyte homeostasis (GO:0002260)|multicellular organismal iron ion homeostasis (GO:0060586)|negative regulation of apoptotic process (GO:0043066)|regulation of transcription from RNA polymerase II promoter in response to iron (GO:0034395)|spleen trabecula formation (GO:0060345)|transmembrane transport (GO:0055085)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|multivesicular body (GO:0005771)|plasma membrane (GO:0005886)|synaptic vesicle (GO:0008021)	iron ion transmembrane transporter activity (GO:0005381)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(117;0.000917)|Epithelial(96;0.014)|all cancers(119;0.0491)			CCTTTAAGTCTAGCATTCTTG	0.478																																					p.R88G		Atlas-SNP	.											.	SLC40A1	51	.	0			c.A262G	GRCh37	CM076533	SLC40A1	M		PASS	.						258.0	271.0	267.0					2																	190439896		2203	4300	6503	SO:0001583	missense	30061	exon3			TAAGTCTAGCATT	AF215636	CCDS2299.1	2q32	2014-09-17	2003-06-04	2003-06-05	ENSG00000138449	ENSG00000138449		"""Solute carriers"""	10909	protein-coding gene	gene with protein product	"""ferroportin 1"""	604653	"""solute carrier family 11 (proton-coupled divalent metal ion transporters), member 3"""	SLC11A3		10828623	Standard	NM_014585		Approved	MTP1, IREG1, FPN1, HFE4	uc002uqp.4	Q9NP59	OTTHUMG00000132662	ENST00000261024.2:c.262A>G	chr2.hg19:g.190439896T>C	ENSP00000261024:p.Arg88Gly	142.0	0.0	.		113.0	41.0	.	NM_014585	Q6FI62|Q7Z4F8|Q8IVB2|Q9NRL0	Missense_Mutation	SNP	ENST00000261024.2	hg19	CCDS2299.1	.	.	.	.	.	.	.	.	.	.	T	25.3	4.628792	0.87560	.	.	ENSG00000138449	ENST00000261024;ENST00000427241	D;D	0.96041	-3.89;-3.89	5.16	3.95	0.45737	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.97399	0.9149	M	0.82323	2.585	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	D	0.97680	1.0172	10	0.87932	D	0	-28.426	12.2975	0.54857	0.0:0.0:0.141:0.859	.	88;88	A8K7Y1;Q9NP59	.;S40A1_HUMAN	G	88	ENSP00000261024:R88G;ENSP00000390005:R88G	ENSP00000261024:R88G	R	-	1	2	SLC40A1	190148141	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	3.987000	0.56944	2.177000	0.69029	0.533000	0.62120	AGA	.	.	.	none		0.478	SLC40A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255916.2		
BMPR2	659	hgsc.bcm.edu	37	2	203420241	203420241	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:203420241C>T	ENST00000374580.4	+	12	2392	c.1853C>T	c.(1852-1854)aCa>aTa	p.T618I	BMPR2_ENST00000374574.2_Intron	NM_001204.6	NP_001195.2	Q13873	BMPR2_HUMAN	bone morphogenetic protein receptor, type II (serine/threonine kinase)	618	Poly-Thr.				activin receptor signaling pathway (GO:0032924)|anterior/posterior pattern specification (GO:0009952)|artery development (GO:0060840)|blood vessel remodeling (GO:0001974)|BMP signaling pathway (GO:0030509)|brain development (GO:0007420)|cellular response to starvation (GO:0009267)|chondrocyte development (GO:0002063)|limb development (GO:0060173)|lung alveolus development (GO:0048286)|lymphangiogenesis (GO:0001946)|lymphatic endothelial cell differentiation (GO:0060836)|mesoderm formation (GO:0001707)|negative regulation of cell growth (GO:0030308)|negative regulation of chondrocyte proliferation (GO:1902731)|negative regulation of DNA biosynthetic process (GO:2000279)|negative regulation of systemic arterial blood pressure (GO:0003085)|negative regulation of vasoconstriction (GO:0045906)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epithelial cell migration (GO:0010634)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|regulation of cell proliferation (GO:0042127)|regulation of lung blood pressure (GO:0014916)|retina vasculature development in camera-type eye (GO:0061298)|transcription from RNA polymerase II promoter (GO:0006366)|transmembrane receptor protein serine/threonine kinase signaling pathway (GO:0007178)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|venous blood vessel development (GO:0060841)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|caveola (GO:0005901)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|fully spanning plasma membrane (GO:0044214)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	activin receptor activity, type II (GO:0016362)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|receptor signaling protein serine/threonine kinase activity (GO:0004702)|transforming growth factor beta-activated receptor activity (GO:0005024)			autonomic_ganglia(1)|breast(4)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(11)|lung(7)|ovary(4)|pancreas(1)|skin(1)|stomach(1)|urinary_tract(2)	42						ACAAACACCACAGGACTCACG	0.463																																					p.T618I		Atlas-SNP	.											.	BMPR2	142	.	0			c.C1853T						PASS	.						159.0	137.0	144.0					2																	203420241		2203	4300	6503	SO:0001583	missense	659	exon12			ACACCACAGGACT	Z48923	CCDS33361.1	2q33-q34	2014-09-17			ENSG00000204217	ENSG00000204217			1078	protein-coding gene	gene with protein product		600799	"""primary pulmonary hypertension 1"""	PPH1		7791754	Standard	NM_001204		Approved	BRK-3, T-ALK, BMPR3, BMPR-II	uc002uzf.4	Q13873	OTTHUMG00000133617	ENST00000374580.4:c.1853C>T	chr2.hg19:g.203420241C>T	ENSP00000363708:p.Thr618Ile	93.0	0.0	.		95.0	29.0	.	NM_001204	Q13161|Q16569|Q4ZG08|Q53SA5|Q585T8	Missense_Mutation	SNP	ENST00000374580.4	hg19	CCDS33361.1	.	.	.	.	.	.	.	.	.	.	C	14.47	2.545630	0.45280	.	.	ENSG00000204217	ENST00000374580	D	0.81908	-1.55	5.74	5.74	0.90152	.	0.070435	0.64402	D	0.000018	T	0.74711	0.3752	L	0.27053	0.805	0.80722	D	1	P	0.41313	0.745	B	0.34301	0.179	T	0.76195	-0.3048	10	0.44086	T	0.13	.	19.9329	0.97127	0.0:1.0:0.0:0.0	.	618	Q13873	BMPR2_HUMAN	I	618	ENSP00000363708:T618I	ENSP00000363708:T618I	T	+	2	0	BMPR2	203128486	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	4.062000	0.57492	2.714000	0.92807	0.650000	0.86243	ACA	.	.	.	none		0.463	BMPR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257743.1	NM_001204	
CPS1	1373	hgsc.bcm.edu	37	2	211523412	211523412	+	Splice_Site	SNP	G	G	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:211523412G>C	ENST00000233072.5	+	31	3952	c.3756G>C	c.(3754-3756)ttG>ttC	p.L1252F	CPS1_ENST00000430249.2_Splice_Site_p.L1258F|CPS1_ENST00000451903.2_Splice_Site_p.L801F	NM_001875.4	NP_001866.2	P31327	CPSM_HUMAN	carbamoyl-phosphate synthase 1, mitochondrial	1252	ATP-grasp 2.				anion homeostasis (GO:0055081)|carbamoyl phosphate biosynthetic process (GO:0070409)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to cAMP (GO:0071320)|cellular response to fibroblast growth factor stimulus (GO:0044344)|cellular response to glucagon stimulus (GO:0071377)|cellular response to oleic acid (GO:0071400)|citrulline biosynthetic process (GO:0019240)|glutamine catabolic process (GO:0006543)|glycogen catabolic process (GO:0005980)|hepatocyte differentiation (GO:0070365)|homocysteine metabolic process (GO:0050667)|midgut development (GO:0007494)|nitric oxide metabolic process (GO:0046209)|positive regulation of vasodilation (GO:0045909)|response to amine (GO:0014075)|response to amino acid (GO:0043200)|response to dexamethasone (GO:0071548)|response to drug (GO:0042493)|response to food (GO:0032094)|response to growth hormone (GO:0060416)|response to lipopolysaccharide (GO:0032496)|response to starvation (GO:0042594)|response to toxic substance (GO:0009636)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|triglyceride catabolic process (GO:0019433)|urea cycle (GO:0000050)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|nucleus (GO:0005634)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|carbamoyl-phosphate synthase (ammonia) activity (GO:0004087)|endopeptidase activity (GO:0004175)|glutamate binding (GO:0016595)|modified amino acid binding (GO:0072341)|phospholipid binding (GO:0005543)			breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(85)|ovary(8)|pancreas(1)|prostate(6)|skin(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	142				Epithelial(149;0.00697)|Lung(261;0.0521)|LUSC - Lung squamous cell carcinoma(261;0.0544)|all cancers(144;0.0843)	Carglumic Acid(DB06775)	ATGATGTCTTGGTAAGAAATG	0.443																																					p.L1258F		Atlas-SNP	.											.	CPS1	485	.	0			c.G3774C						PASS	.						93.0	85.0	88.0					2																	211523412		2203	4300	6503	SO:0001630	splice_region_variant	1373	exon32			TGTCTTGGTAAGA	AF154830	CCDS2393.1, CCDS46505.1, CCDS46506.1	2p	2014-09-17	2010-05-11		ENSG00000021826	ENSG00000021826	6.3.4.16		2323	protein-coding gene	gene with protein product		608307	"""carbamoyl-phosphate synthetase 1, mitochondrial"""				Standard	NM_001122633		Approved		uc002vee.4	P31327	OTTHUMG00000132994	ENST00000233072.5:c.3756+1G>C	chr2.hg19:g.211523412G>C		53.0	0.0	.		42.0	10.0	.	NM_001122633	B7Z818|J3KQL0|O43774|Q53TL5|Q59HF8|Q7Z5I5	Missense_Mutation	SNP	ENST00000233072.5	hg19	CCDS2393.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.612712	0.87258	.	.	ENSG00000021826	ENST00000430249;ENST00000539150;ENST00000233072;ENST00000451903	D;D;D	0.97256	-4.31;-4.31;-4.31	5.76	5.76	0.90799	ATP-grasp fold (1);ATP-grasp fold, subdomain 2 (1);Carbamoyl-phosphate synthetase, large subunit, ATP-binding (1);	0.056700	0.64402	D	0.000001	D	0.94066	0.8098	N	0.04203	-0.255	0.80722	D	1	P;P	0.41080	0.737;0.737	P;P	0.46144	0.505;0.505	D	0.95123	0.8248	10	0.87932	D	0	-6.542	19.9595	0.97236	0.0:0.0:1.0:0.0	.	1262;1252	Q59HF8;P31327	.;CPSM_HUMAN	F	1258;1260;1252;801	ENSP00000402608:L1258F;ENSP00000233072:L1252F;ENSP00000406136:L801F	ENSP00000233072:L1252F	L	+	3	2	CPS1	211231657	1.000000	0.71417	1.000000	0.80357	0.947000	0.59692	9.118000	0.94355	2.706000	0.92434	0.563000	0.77884	TTG	.	.	.	none		0.443	CPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256569.5		Missense_Mutation
NYAP2	57624	hgsc.bcm.edu	37	2	226491661	226491661	+	Missense_Mutation	SNP	C	C	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:226491661C>A	ENST00000272907.6	+	5	2060	c.1647C>A	c.(1645-1647)agC>agA	p.S549R	NYAP2_ENST00000409269.2_Missense_Mutation_p.P84T	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	549					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												AAGTCCGAAGCCACAGCACGG	0.433																																					p.S549R		Atlas-SNP	.											.	.	.	.	0			c.C1647A						PASS	.						26.0	28.0	27.0					2																	226491661		1893	4105	5998	SO:0001583	missense	57624	exon5			CCGAAGCCACAGC	AB040919	CCDS46529.1	2q36.3	2011-11-30	2011-11-30	2011-11-30	ENSG00000144460	ENSG00000144460			29291	protein-coding gene	gene with protein product		615478	"""KIAA1486"""	KIAA1486		10819331, 21946561	Standard	NM_020864		Approved		uc002voe.2	Q9P242	OTTHUMG00000153450	ENST00000272907.6:c.1647C>A	chr2.hg19:g.226491661C>A	ENSP00000272907:p.Ser549Arg	335.0	0.0	.		221.0	96.0	.	NM_020864	A2RRN4|Q96NL2	Missense_Mutation	SNP	ENST00000272907.6	hg19	CCDS46529.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.16|13.16	2.155070|2.155070	0.38021|0.38021	.|.	.|.	ENSG00000144460|ENSG00000144460	ENST00000409269|ENST00000272907	.|T	.|0.33438	.|1.41	5.78|5.78	2.04|2.04	0.26737|0.26737	.|.	.|0.224065	.|0.48286	.|D	.|0.000186	T|T	0.42040|0.42040	0.1185|0.1185	L|L	0.40543|0.40543	1.245|1.245	0.24652|0.24652	N|N	0.993512|0.993512	P|D;P	0.39326|0.71674	0.668|0.998;0.822	B|D;B	0.43867|0.76575	0.434|0.988;0.359	T|T	0.23013|0.23013	-1.0200|-1.0200	8|10	0.21014|0.66056	T|D	0.42|0.02	-24.7943|-24.7943	9.9677|9.9677	0.41734|0.41734	0.0:0.6438:0.0:0.3562|0.0:0.6438:0.0:0.3562	.|.	84|63;549	Q9P242-2|Q9P242-3;Q9P242	.|.;K1486_HUMAN	T|R	84|549	.|ENSP00000272907:S549R	ENSP00000386437:P84T|ENSP00000272907:S549R	P|S	+|+	1|3	0|2	KIAA1486|KIAA1486	226199905|226199905	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.995000|0.995000	0.86356|0.86356	0.765000|0.765000	0.26546|0.26546	0.095000|0.095000	0.17434|0.17434	-0.136000|-0.136000	0.14681|0.14681	CCA|AGC	.	.	.	none		0.433	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
PID1	55022	hgsc.bcm.edu	37	2	229890502	229890502	+	Missense_Mutation	SNP	A	A	T			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:229890502A>T	ENST00000354069.6	-	3	629	c.599T>A	c.(598-600)gTg>gAg	p.V200E	PID1_ENST00000392054.3_Missense_Mutation_p.V198E|PID1_ENST00000392055.3_Missense_Mutation_p.V167E|PID1_ENST00000482518.2_Intron|PID1_ENST00000409462.1_Missense_Mutation_p.V118E			Q7Z2X4	PCLI1_HUMAN	phosphotyrosine interaction domain containing 1	200	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				cellular response to cytokine stimulus (GO:0071345)|cellular response to fatty acid (GO:0071398)|cellular response to interleukin-6 (GO:0071354)|cellular response to leptin stimulus (GO:0044320)|cellular response to tumor necrosis factor (GO:0071356)|energy reserve metabolic process (GO:0006112)|mitochondrion morphogenesis (GO:0070584)|negative regulation of ATP biosynthetic process (GO:2001170)|negative regulation of establishment of protein localization to plasma membrane (GO:0090005)|negative regulation of glucose import in response to insulin stimulus (GO:2001274)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of mitochondrial DNA replication (GO:0090298)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of ATP biosynthetic process (GO:2001171)|positive regulation of fat cell proliferation (GO:0070346)|positive regulation of gene expression (GO:0010628)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of mitochondrial fusion (GO:0010635)|regulation of mitochondrial membrane potential (GO:0051881)|regulation of reactive oxygen species metabolic process (GO:2000377)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				breast(4)|endometrium(3)|large_intestine(5)|lung(8)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	26		Renal(207;0.0112)|all_lung(227;0.0191)|Lung NSC(271;0.0851)|all_hematologic(139;0.104)|Acute lymphoblastic leukemia(138;0.171)		Epithelial(121;3.08e-11)|all cancers(144;2.28e-08)|LUSC - Lung squamous cell carcinoma(224;0.0145)|Lung(261;0.0189)		CTCGCACTCCACGGCGTGGCA	0.592																																					p.V198E		Atlas-SNP	.											.	PID1	43	.	0			c.T593A						PASS	.						132.0	115.0	121.0					2																	229890502		2203	4300	6503	SO:0001583	missense	55022	exon4			CACTCCACGGCGT	AK096636	CCDS2471.1, CCDS42830.1	2q36.3	2007-02-02			ENSG00000153823	ENSG00000153823			26084	protein-coding gene	gene with protein product		612930				17124247, 16815647, 15221005	Standard	NM_001100818		Approved	NYGGF4, FLJ20701	uc002vps.4	Q7Z2X4	OTTHUMG00000133191	ENST00000354069.6:c.599T>A	chr2.hg19:g.229890502A>T	ENSP00000283937:p.Val200Glu	108.0	0.0	.		82.0	30.0	.	NM_017933	B3KU82|Q68CJ2|Q6ZUS3|Q8IXL0|Q9NWP6	Missense_Mutation	SNP	ENST00000354069.6	hg19		.	.	.	.	.	.	.	.	.	.	A	25.7	4.667104	0.88251	.	.	ENSG00000153823	ENST00000392054;ENST00000409462;ENST00000392055;ENST00000542363;ENST00000354069	.	.	.	6.07	6.07	0.98685	Phosphotyrosine interaction domain (2);Pleckstrin homology-type (1);	0.000000	0.85682	D	0.000000	T	0.78266	0.4256	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.89917	0.999;0.999;1.0;1.0	D;D;D;D	0.87578	0.991;0.991;0.998;0.998	T	0.78183	-0.2303	8	.	.	.	-38.6448	15.8218	0.78654	1.0:0.0:0.0:0.0	.	118;167;198;200	Q7Z2X4-3;Q7Z2X4-4;Q7Z2X4-2;Q7Z2X4	.;.;.;PCLI1_HUMAN	E	198;118;167;200;200	.	.	V	-	2	0	PID1	229598746	1.000000	0.71417	0.906000	0.35671	0.997000	0.91878	8.854000	0.92228	2.326000	0.78906	0.533000	0.62120	GTG	.	.	.	none		0.592	PID1-005	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000331810.2	NM_017933	
FAM107A	11170	hgsc.bcm.edu	37	3	58555533	58555533	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:58555533G>C	ENST00000394481.1	-	3	613	c.55C>G	c.(55-57)Cca>Gca	p.P19A	FAM107A_ENST00000360997.2_Missense_Mutation_p.P19A|FAM107A_ENST00000464064.1_Missense_Mutation_p.P19A|RP11-475O23.2_ENST00000472513.1_RNA|FAM107A_ENST00000447756.2_Missense_Mutation_p.P47A|FAM107A_ENST00000474531.1_Missense_Mutation_p.P50A	NM_001282713.1|NM_007177.2	NP_001269642.1|NP_009108.1	O95990	F107A_HUMAN	family with sequence similarity 107, member A	19			P -> L (in renal cell carcinoma cell line). {ECO:0000269|PubMed:10564580}.		regulation of cell growth (GO:0001558)	neuron projection (GO:0043005)|nucleus (GO:0005634)				breast(1)|endometrium(2)|large_intestine(2)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(55;0.000189)|Kidney(10;0.000536)|KIRC - Kidney renal clear cell carcinoma(10;0.000716)|OV - Ovarian serous cystadenocarcinoma(275;0.154)		CTGTATTCTGGCCGGGCCATC	0.607																																					p.P19A		Atlas-SNP	.											.	FAM107A	33	.	0			c.C55G						PASS	.						69.0	73.0	72.0					3																	58555533		2203	4300	6503	SO:0001583	missense	11170	exon2			ATTCTGGCCGGGC	AF089854	CCDS2892.1, CCDS63672.1, CCDS63673.1	3p14.2	2006-02-03			ENSG00000168309	ENSG00000168309			30827	protein-coding gene	gene with protein product		608295				10564580, 10702698	Standard	XM_005264835		Approved	DRR1, TU3A	uc003dkn.3	O95990	OTTHUMG00000159159	ENST00000394481.1:c.55C>G	chr3.hg19:g.58555533G>C	ENSP00000377991:p.Pro19Ala	48.0	0.0	.		42.0	12.0	.	NM_001076778	B3KNQ4|B7ZAY5|J3KR61|Q96NH4	Missense_Mutation	SNP	ENST00000394481.1	hg19	CCDS2892.1	.	.	.	.	.	.	.	.	.	.	G	21.2	4.112146	0.77210	.	.	ENSG00000168309	ENST00000360997;ENST00000394481;ENST00000464064;ENST00000474531;ENST00000447756;ENST00000465970	T;T;T;T;T;T	0.47869	0.83;0.83;0.83;0.83;0.83;0.83	4.68	2.87	0.33458	.	0.000000	0.85682	D	0.000000	T	0.67173	0.2865	M	0.80028	2.48	0.53688	D	0.999974	P;D;B;D	0.89917	0.477;1.0;0.262;0.999	B;D;B;D	0.87578	0.187;0.987;0.135;0.998	T	0.68891	-0.5289	10	0.72032	D	0.01	-5.4675	10.9672	0.47418	0.1515:0.0:0.8485:0.0	.	47;19;50;19	B7ZAY5;O95990-2;B3KNQ4;O95990	.;.;.;F107A_HUMAN	A	19;19;19;50;47;19	ENSP00000354270:P19A;ENSP00000377991:P19A;ENSP00000419529:P19A;ENSP00000419124:P50A;ENSP00000400858:P47A;ENSP00000418038:P19A	ENSP00000354270:P19A	P	-	1	0	FAM107A	58530573	1.000000	0.71417	0.989000	0.46669	0.992000	0.81027	7.884000	0.87274	0.517000	0.28361	0.655000	0.94253	CCA	.	.	.	none		0.607	FAM107A-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353585.1	NM_007177	
MAGEF1	64110	hgsc.bcm.edu	37	3	184429221	184429221	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:184429221C>T	ENST00000317897.3	-	1	615	c.389G>A	c.(388-390)gGt>gAt	p.G130D		NM_022149.4	NP_071432.2	Q9HAY2	MAGF1_HUMAN	melanoma antigen family F, 1	130	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.					extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|large_intestine(1)|lung(5)|ovary(2)|urinary_tract(1)	11	all_cancers(143;4.61e-11)|Ovarian(172;0.0339)|Breast(254;0.247)		Epithelial(37;5.64e-35)|OV - Ovarian serous cystadenocarcinoma(80;2.56e-22)			CAGCTCAAAACCAAAGACATA	0.493																																					p.G130D		Atlas-SNP	.											.	MAGEF1	27	.	0			c.G389A						PASS	.						114.0	120.0	118.0					3																	184429221		2203	4300	6503	SO:0001583	missense	64110	exon1			TCAAAACCAAAGA	AF295378	CCDS3269.1	3q13	2008-02-05			ENSG00000177383	ENSG00000177383			29639	protein-coding gene	gene with protein product		609267				11313144	Standard	NM_022149		Approved		uc003fpa.3	Q9HAY2	OTTHUMG00000156712	ENST00000317897.3:c.389G>A	chr3.hg19:g.184429221C>T	ENSP00000315064:p.Gly130Asp	76.0	0.0	.		80.0	24.0	.	NM_022149	Q9H215	Missense_Mutation	SNP	ENST00000317897.3	hg19	CCDS3269.1	.	.	.	.	.	.	.	.	.	.	C	17.53	3.411928	0.62511	.	.	ENSG00000177383	ENST00000317897	T	0.24151	1.87	4.62	1.74	0.24563	.	0.119020	0.56097	D	0.000024	T	0.53867	0.1823	H	0.94771	3.58	0.09310	N	0.999993	D	0.89917	1.0	D	0.80764	0.994	T	0.47509	-0.9112	10	0.87932	D	0	.	4.5619	0.12165	0.0:0.6151:0.1833:0.2016	.	130	Q9HAY2	MAGF1_HUMAN	D	130	ENSP00000315064:G130D	ENSP00000315064:G130D	G	-	2	0	MAGEF1	185911915	0.491000	0.26019	0.110000	0.21437	0.956000	0.61745	0.575000	0.23729	0.259000	0.21709	0.655000	0.94253	GGT	.	.	.	none		0.493	MAGEF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000345417.1	NM_022149	
SLC2A9	56606	hgsc.bcm.edu	37	4	10020642	10020642	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr4:10020642A>G	ENST00000264784.3	-	2	259	c.206T>C	c.(205-207)tTc>tCc	p.F69S	SLC2A9_ENST00000506583.1_Missense_Mutation_p.F40S|SLC2A9_ENST00000309065.3_Missense_Mutation_p.F40S	NM_020041.2	NP_064425.2	Q9NRM0	GTR9_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 9	69					glucose transport (GO:0015758)|proton transport (GO:0015992)|transmembrane transport (GO:0055085)|urate metabolic process (GO:0046415)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|nuclear envelope (GO:0005635)|plasma membrane (GO:0005886)	glucose transmembrane transporter activity (GO:0005355)|sugar:proton symporter activity (GO:0005351)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(12)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(1)	35					Losartan(DB00678)|Probenecid(DB01032)	GCCGTAGAGGAAGGAGGAGCC	0.706																																					p.F69S		Atlas-SNP	.											.	SLC2A9	158	.	0			c.T206C						PASS	.						16.0	17.0	17.0					4																	10020642		1947	3904	5851	SO:0001583	missense	56606	exon2			TAGAGGAAGGAGG	AF210317	CCDS3406.1, CCDS3407.1	4p16.1	2013-05-22			ENSG00000109667	ENSG00000109667		"""Solute carriers"""	13446	protein-coding gene	gene with protein product	"""urate voltage-driven efflux transporter 1"""	606142				10860667, 17710649	Standard	NM_020041		Approved	Glut9, GLUTX, URATv1	uc003gmc.3	Q9NRM0	OTTHUMG00000044263	ENST00000264784.3:c.206T>C	chr4.hg19:g.10020642A>G	ENSP00000264784:p.Phe69Ser	266.0	0.0	.		188.0	60.0	.	NM_020041	Q0VGC4|Q4W5D1|Q8WV30|Q96P00	Missense_Mutation	SNP	ENST00000264784.3	hg19	CCDS3407.1	.	.	.	.	.	.	.	.	.	.	a	19.38	3.816535	0.70912	.	.	ENSG00000109667	ENST00000506583;ENST00000264784;ENST00000309065;ENST00000513129	T;T;T;D	0.83914	-0.01;-1.06;-0.01;-1.78	4.89	4.89	0.63831	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.000000	0.85682	D	0.000000	D	0.91496	0.7315	M	0.89715	3.055	0.34693	D	0.725902	D;D	0.76494	0.996;0.999	D;D	0.74023	0.969;0.982	D	0.95063	0.8197	9	.	.	.	.	10.8133	0.46559	1.0:0.0:0.0:0.0	.	40;69	Q9NRM0-2;Q9NRM0	.;GTR9_HUMAN	S	40;69;40;40	ENSP00000422209:F40S;ENSP00000264784:F69S;ENSP00000311383:F40S;ENSP00000426800:F40S	.	F	-	2	0	SLC2A9	9629740	1.000000	0.71417	1.000000	0.80357	0.458000	0.32498	3.598000	0.54038	2.068000	0.61886	0.454000	0.30748	TTC	.	.	.	none		0.706	SLC2A9-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000207055.1		
SDAD1	55153	hgsc.bcm.edu	37	4	76896925	76896925	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr4:76896925T>G	ENST00000356260.5	-	6	668	c.550A>C	c.(550-552)Atg>Ctg	p.M184L	SDAD1_ENST00000513089.1_5'Flank|SDAD1_ENST00000395711.4_Missense_Mutation_p.M147L	NM_018115.2	NP_060585.2	Q9NVU7	SDA1_HUMAN	SDA1 domain containing 1	184					actin cytoskeleton organization (GO:0030036)|protein transport (GO:0015031)|ribosomal large subunit biogenesis (GO:0042273)|ribosomal large subunit export from nucleus (GO:0000055)	nucleolus (GO:0005730)				breast(2)|endometrium(2)|kidney(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)	19			Lung(101;0.0809)|LUSC - Lung squamous cell carcinoma(112;0.0934)			AGTTCAATCATTACATCTAAA	0.348																																					p.M184L		Atlas-SNP	.											.	SDAD1	47	.	0			c.A550C						PASS	.						123.0	118.0	120.0					4																	76896925		2203	4300	6503	SO:0001583	missense	55153	exon6			CAATCATTACATC	AF132198	CCDS3573.2, CCDS75147.1	4q21.21	2010-11-24			ENSG00000198301	ENSG00000198301			25537	protein-coding gene	gene with protein product						11483580	Standard	NM_001288984		Approved	FLJ10498	uc003hje.4	Q9NVU7	OTTHUMG00000130111	ENST00000356260.5:c.550A>C	chr4.hg19:g.76896925T>G	ENSP00000348596:p.Met184Leu	140.0	0.0	.		93.0	42.0	.	NM_018115	Q32Q11|Q68D52|Q7Z5U4|Q9H831|Q9H9P6	Missense_Mutation	SNP	ENST00000356260.5	hg19	CCDS3573.2	.	.	.	.	.	.	.	.	.	.	T	15.91	2.972226	0.53614	.	.	ENSG00000198301	ENST00000356260;ENST00000395711	T;T	0.04862	3.71;3.54	5.2	5.2	0.72013	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.08802	0.0218	L	0.51853	1.615	0.58432	D	0.999995	B;P	0.42337	0.075;0.776	B;P	0.44518	0.081;0.452	T	0.25984	-1.0116	10	0.09084	T	0.74	-17.1439	13.2882	0.60255	0.0:0.0:0.0:1.0	.	147;184	E7EW05;Q9NVU7	.;SDA1_HUMAN	L	184;147	ENSP00000348596:M184L;ENSP00000379061:M147L	ENSP00000348596:M184L	M	-	1	0	SDAD1	77115949	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	7.665000	0.83852	2.081000	0.62600	0.533000	0.62120	ATG	.	.	.	none		0.348	SDAD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252418.3	NM_018115	
IL2	3558	hgsc.bcm.edu	37	4	123377451	123377451	+	Missense_Mutation	SNP	T	T	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr4:123377451T>A	ENST00000226730.4	-	1	429	c.145A>T	c.(145-147)Aat>Tat	p.N49Y		NM_000586.3	NP_000577.2	P60568	IL2_HUMAN	interleukin 2	49					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|immune response (GO:0006955)|natural killer cell activation (GO:0030101)|negative regulation of apoptotic process (GO:0043066)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of heart contraction (GO:0045822)|negative regulation of inflammatory response (GO:0050728)|negative regulation of lymphocyte proliferation (GO:0050672)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell growth (GO:0030307)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of dendritic spine development (GO:0060999)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of isotype switching to IgG isotypes (GO:0048304)|positive regulation of regulatory T cell differentiation (GO:0045591)|positive regulation of tissue remodeling (GO:0034105)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|regulation of T cell homeostatic proliferation (GO:0046013)|T cell differentiation (GO:0030217)	extracellular region (GO:0005576)|extracellular space (GO:0005615)	carbohydrate binding (GO:0030246)|cytokine activity (GO:0005125)|glycosphingolipid binding (GO:0043208)|growth factor activity (GO:0008083)|interleukin-2 receptor binding (GO:0005134)|kinase activator activity (GO:0019209)			endometrium(2)|large_intestine(4)|lung(6)|skin(1)	13				LUSC - Lung squamous cell carcinoma(721;0.185)	Pseudoephedrine(DB00852)	ATACTTACATTAATTCCATTC	0.299			T	TNFRSF17	intestinal T-cell lymphoma																																p.N49Y		Atlas-SNP	.		Dom	yes		4	4q26-q27	3558	interleukin 2		L	.	IL2	23	.	0			c.A145T						PASS	.						86.0	83.0	84.0					4																	123377451		2203	4299	6502	SO:0001583	missense	3558	exon1			TTACATTAATTCC	U25676	CCDS3726.1	4q26-q27	2011-07-14			ENSG00000109471	ENSG00000109471		"""Interleukins and interleukin receptors"""	6001	protein-coding gene	gene with protein product	"""T cell growth factor"""	147680				3260003	Standard	NM_000586		Approved	IL-2, TCGF	uc003ier.3	P60568	OTTHUMG00000133075	ENST00000226730.4:c.145A>T	chr4.hg19:g.123377451T>A	ENSP00000226730:p.Asn49Tyr	178.0	0.0	.		99.0	38.0	.	NM_000586	P01585	Missense_Mutation	SNP	ENST00000226730.4	hg19	CCDS3726.1	.	.	.	.	.	.	.	.	.	.	T	25.4	4.634791	0.87760	.	.	ENSG00000109471	ENST00000226730	.	.	.	6.17	2.06	0.26882	Four-helical cytokine-like, core (1);Four-helical cytokine, core (1);	1.224380	0.05498	N	0.557971	T	0.56978	0.2022	M	0.71036	2.16	0.09310	N	1	D	0.65815	0.995	P	0.60012	0.867	T	0.28106	-1.0054	9	0.72032	D	0.01	0.0199	3.7496	0.08561	0.0:0.2335:0.1858:0.5806	.	49	P60568	IL2_HUMAN	Y	49	.	ENSP00000226730:N49Y	N	-	1	0	IL2	123596901	0.001000	0.12720	0.012000	0.15200	0.964000	0.63967	0.806000	0.27126	0.478000	0.27488	0.533000	0.62120	AAT	.	.	.	none		0.299	IL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256715.2		
ITPR3	3710	hgsc.bcm.edu	37	6	33632875	33632875	+	Missense_Mutation	SNP	G	G	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr6:33632875G>A	ENST00000374316.5	+	14	2354	c.1294G>A	c.(1294-1296)Gtg>Atg	p.V432M	ITPR3_ENST00000605930.1_Missense_Mutation_p.V432M			Q14573	ITPR3_HUMAN	inositol 1,4,5-trisphosphate receptor, type 3	432	MIR 5. {ECO:0000255|PROSITE- ProRule:PRU00131}.				activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport into cytosol (GO:0060402)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G-protein coupled receptor signaling pathway (GO:0007186)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|long-term synaptic potentiation (GO:0060291)|memory (GO:0007613)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|response to calcium ion (GO:0051592)|sensory perception of bitter taste (GO:0050913)|sensory perception of sweet taste (GO:0050916)|sensory perception of umami taste (GO:0050917)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	apical part of cell (GO:0045177)|brush border (GO:0005903)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nuclear outer membrane (GO:0005640)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|receptor complex (GO:0043235)	inositol 1,3,4,5 tetrakisphosphate binding (GO:0043533)|inositol 1,4,5 trisphosphate binding (GO:0070679)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|inositol hexakisphosphate binding (GO:0000822)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|breast(6)|central_nervous_system(5)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(18)|liver(1)|lung(24)|ovary(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	85					Caffeine(DB00201)	CTTTGCCATCGTGTCAGTGCC	0.627																																					p.V432M		Atlas-SNP	.											ITPR3_ENST00000374316,colon,carcinoma,0,2	ITPR3	409	.	0			c.G1294A						PASS	.						88.0	84.0	85.0					6																	33632875		2203	4300	6503	SO:0001583	missense	3710	exon13			GCCATCGTGTCAG	D26351	CCDS4783.1	6p21.31	2011-11-24	2011-04-28		ENSG00000096433	ENSG00000096433		"""Ion channels / Inositol triphosphate receptors"""	6182	protein-coding gene	gene with protein product		147267	"""inositol 1,4,5-triphosphate receptor, type 3"""			8081734, 8288584	Standard	NM_002224		Approved	IP3R3	uc021ywr.1	Q14573	OTTHUMG00000014532	ENST00000374316.5:c.1294G>A	chr6.hg19:g.33632875G>A	ENSP00000363435:p.Val432Met	52.0	0.0	.		46.0	34.0	.	NM_002224	Q14649|Q5TAQ2	Missense_Mutation	SNP	ENST00000374316.5	hg19	CCDS4783.1	.	.	.	.	.	.	.	.	.	.	G	17.11	3.305299	0.60305	.	.	ENSG00000096433	ENST00000374316	D	0.91894	-2.93	4.89	4.89	0.63831	MIR motif (1);MIR (1);	0.068603	0.64402	N	0.000018	D	0.96071	0.8720	M	0.84511	2.7	0.58432	D	0.999999	D	0.89917	1.0	D	0.78314	0.991	D	0.96757	0.9558	10	0.87932	D	0	-22.0431	18.0608	0.89377	0.0:0.0:1.0:0.0	.	432	Q14573	ITPR3_HUMAN	M	432	ENSP00000363435:V432M	ENSP00000363435:V432M	V	+	1	0	ITPR3	33740853	1.000000	0.71417	0.964000	0.40570	0.004000	0.04260	9.735000	0.98825	2.260000	0.74910	0.557000	0.71058	GTG	.	.	.	none		0.627	ITPR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040204.2	NM_002224	
FOXP4	116113	hgsc.bcm.edu	37	6	41555205	41555205	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr6:41555205C>G	ENST00000307972.4	+	6	839	c.827C>G	c.(826-828)aCc>aGc	p.T276S	FOXP4_ENST00000409208.1_Missense_Mutation_p.T276S|FOXP4_ENST00000373063.3_Missense_Mutation_p.T275S|FOXP4_ENST00000373057.3_Missense_Mutation_p.T274S|FOXP4_ENST00000373060.1_Missense_Mutation_p.T276S			Q8IVH2	FOXP4_HUMAN	forkhead box P4	276					embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	nucleus (GO:0005634)	metal ion binding (GO:0046872)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					TCCCACCATACCCTGCCCAAC	0.662											OREG0004065	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.T276S		Atlas-SNP	.											.	FOXP4	83	.	0			c.C827G						PASS	.						68.0	73.0	71.0					6																	41555205		2203	4300	6503	SO:0001583	missense	116113	exon7			ACCATACCCTGCC	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.827C>G	chr6.hg19:g.41555205C>G	ENSP00000309823:p.Thr276Ser	171.0	0.0	.	902	137.0	114.0	.	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	hg19	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	C	0.010	-1.757679	0.00657	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;D;T;T;T	0.88431	1.09;-2.38;1.39;1.09;1.09	4.83	3.96	0.45880	.	0.359243	0.29383	N	0.012302	T	0.43743	0.1261	N	0.00841	-1.15	0.22629	N	0.998918	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.04013	0.0;0.0;0.001	T	0.43048	-0.9415	10	0.02654	T	1	.	12.8987	0.58113	0.0:0.9209:0.0:0.0791	.	275;274;276	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	S	276;275;276;274;276	ENSP00000362151:T276S;ENSP00000362154:T275S;ENSP00000386958:T276S;ENSP00000362148:T274S;ENSP00000309823:T276S	ENSP00000309823:T276S	T	+	2	0	FOXP4	41663183	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	3.485000	0.53208	1.241000	0.43820	0.591000	0.81541	ACC	.	.	.	none		0.662	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457	
PCLO	27445	hgsc.bcm.edu	37	7	82508768	82508768	+	Missense_Mutation	SNP	T	T	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr7:82508768T>G	ENST00000333891.9	-	10	13876	c.13539A>C	c.(13537-13539)ttA>ttC	p.L4513F	PCLO_ENST00000423517.2_Missense_Mutation_p.L4513F|PCLO_ENST00000426442.2_5'UTR	NM_033026.5	NP_149015.2			piccolo presynaptic cytomatrix protein											breast(3)|central_nervous_system(3)|cervix(5)|endometrium(19)|haematopoietic_and_lymphoid_tissue(3)|kidney(19)|large_intestine(35)|lung(145)|ovary(7)|prostate(4)|upper_aerodigestive_tract(14)|urinary_tract(2)	259						TTCTAATTCCTAATCCATTAC	0.393																																					p.L4513F		Atlas-SNP	.											.	PCLO	1506	.	0			c.A13539C						PASS	.						71.0	61.0	64.0					7																	82508768		1808	4075	5883	SO:0001583	missense	27445	exon10			AATTCCTAATCCA	AB011131	CCDS47630.1, CCDS47631.1	7q11.23-q21.3	2013-01-07	2013-01-07		ENSG00000186472	ENSG00000186472			13406	protein-coding gene	gene with protein product	"""aczonin"""	604918	"""piccolo (presynaptic cytomatrix protein)"""			8900486, 9628581	Standard	NM_014510		Approved	KIAA0559, DKFZp779G1236, ACZ	uc003uhx.2	Q9Y6V0	OTTHUMG00000154853	ENST00000333891.9:c.13539A>C	chr7.hg19:g.82508768T>G	ENSP00000334319:p.Leu4513Phe	165.0	0.0	.		210.0	51.0	.	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	hg19	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	10.10	1.256665	0.22965	.	.	ENSG00000186472	ENST00000333891;ENST00000423517;ENST00000380195	T;T	0.35973	1.28;1.28	4.91	4.91	0.64330	.	.	.	.	.	T	0.34978	0.0916	L	0.48986	1.54	0.80722	D	1	B;B	0.32350	0.366;0.366	B;B	0.40329	0.191;0.326	T	0.39440	-0.9614	9	0.87932	D	0	.	4.3636	0.11213	0.2927:0.0856:0.0:0.6217	.	4513;4513	Q9Y6V0-5;Q9Y6V0-6	.;.	F	4513;4513;9	ENSP00000334319:L4513F;ENSP00000388393:L4513F	ENSP00000334319:L4513F	L	-	3	2	PCLO	82346704	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	0.672000	0.25187	1.961000	0.56991	0.482000	0.46254	TTA	.	.	.	none		0.393	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
AP4M1	9179	hgsc.bcm.edu	37	7	99703890	99703890	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr7:99703890T>C	ENST00000359593.4	+	13	1159	c.1001T>C	c.(1000-1002)cTc>cCc	p.L334P	AP4M1_ENST00000429084.1_Missense_Mutation_p.L341P|AP4M1_ENST00000421755.1_Missense_Mutation_p.L334P|AP4M1_ENST00000422582.1_Missense_Mutation_p.L206P	NM_004722.3	NP_004713.2	O00189	AP4M1_HUMAN	adaptor-related protein complex 4, mu 1 subunit	334	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				Golgi to endosome transport (GO:0006895)|intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	AP-type membrane coat adaptor complex (GO:0030119)|clathrin adaptor complex (GO:0030131)|coated pit (GO:0005905)|extracellular vesicular exosome (GO:0070062)|Golgi trans cisterna (GO:0000138)|trans-Golgi network (GO:0005802)	transporter activity (GO:0005215)			breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)	17	Lung NSC(181;0.0181)|all_lung(186;0.0284)|Esophageal squamous(72;0.0439)					AGGCTGCACCTCCCCCTGCCT	0.587																																					p.L334P	Pancreas(174;1182 2812 29595 49511)	Atlas-SNP	.											.	AP4M1	39	.	0			c.T1001C						PASS	.						74.0	56.0	62.0					7																	99703890		2203	4300	6503	SO:0001583	missense	9179	exon13			TGCACCTCCCCCT	Y08387	CCDS5685.1	7q22.1	2012-06-29			ENSG00000221838	ENSG00000221838			574	protein-coding gene	gene with protein product	"""mu-adaptin-related protein-2"", ""mu subunit of AP-4"", ""AP-4 adapter complex mu subunit"", ""adaptor-related protein complex AP-4 mu4 subunit"""	602296				9013859, 10066790, 21620353	Standard	NM_004722		Approved	MU-ARP2, MU-4, SPG50	uc003utb.4	O00189	OTTHUMG00000154722	ENST00000359593.4:c.1001T>C	chr7.hg19:g.99703890T>C	ENSP00000352603:p.Leu334Pro	52.0	0.0	.		77.0	4.0	.	NM_004722	D6W5U1|Q8WV65|Q9UHK9	Missense_Mutation	SNP	ENST00000359593.4	hg19	CCDS5685.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	19.53|19.53	3.845106|3.845106	0.71603|0.71603	.|.	.|.	ENSG00000221838|ENSG00000221838	ENST00000438383;ENST00000429084;ENST00000359593;ENST00000421755;ENST00000422582;ENST00000450807|ENST00000445295	T;T;T;T;T;T|.	0.21543|.	2.0;2.0;2.0;2.0;2.0;2.0|.	4.96|4.96	4.96|4.96	0.65561|0.65561	Clathrin adaptor, mu subunit, C-terminal (3);|.	0.195814|.	0.43747|.	D|.	0.000522|.	T|T	0.60235|0.60235	0.2253|0.2253	L|L	0.48642|0.48642	1.525|1.525	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;1.0;1.0|.	D;D;D|.	0.87578|.	0.997;0.998;0.998|.	T|T	0.58160|0.58160	-0.7685|-0.7685	10|5	0.87932|.	D|.	0|.	-12.5702|-12.5702	12.6235|12.6235	0.56616|0.56616	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	286;341;334|.	B4DKN7;C9JC87;O00189|.	.;.;AP4M1_HUMAN|.	P|P	266;341;334;334;206;86|60	ENSP00000401613:L266P;ENSP00000403663:L341P;ENSP00000352603:L334P;ENSP00000412185:L334P;ENSP00000406676:L206P;ENSP00000391585:L86P|.	ENSP00000352603:L334P|.	L|S	+|+	2|1	0|0	AP4M1|AP4M1	99541826|99541826	0.998000|0.998000	0.40836|0.40836	0.995000|0.995000	0.50966|0.50966	0.650000|0.650000	0.38633|0.38633	3.616000|3.616000	0.54174|0.54174	2.079000|2.079000	0.62486|0.62486	0.459000|0.459000	0.35465|0.35465	CTC|TCC	.	.	.	none		0.587	AP4M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336772.4	NM_004722	
POT1	25913	hgsc.bcm.edu	37	7	124493170	124493170	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr7:124493170T>C	ENST00000357628.3	-	10	1323	c.725A>G	c.(724-726)tAt>tGt	p.Y242C	POT1_ENST00000393329.1_Missense_Mutation_p.Y111C	NM_015450.2	NP_056265.2	Q9NUX5	POTE1_HUMAN	protection of telomeres 1	242					DNA duplex unwinding (GO:0032508)|negative regulation of telomerase activity (GO:0051974)|negative regulation of telomere maintenance via telomerase (GO:0032211)|positive regulation of DNA strand elongation (GO:0060383)|positive regulation of helicase activity (GO:0051096)|positive regulation of telomerase activity (GO:0051973)|positive regulation of telomere maintenance via telomerase (GO:0032212)|telomere capping (GO:0016233)|telomere formation via telomerase (GO:0032203)|telomere maintenance (GO:0000723)|telomere maintenance via telomerase (GO:0007004)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear telomere cap complex (GO:0000783)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DEAD/H-box RNA helicase binding (GO:0017151)|single-stranded telomeric DNA binding (GO:0043047)|telomerase inhibitor activity (GO:0010521)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(4)|liver(1)|lung(23)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47						ATGAAGGCTATAGATTCTAAG	0.313																																					p.Y242C	Esophageal Squamous(149;1032 1141 16047 36610 40540 42429 44687 51642)	Atlas-SNP	.											POT1_ENST00000357628,NS,NS,0,2	POT1	186	.	0			c.A725G						PASS	.						63.0	60.0	61.0					7																	124493170		2203	4300	6503	SO:0001583	missense	25913	exon10			AGGCTATAGATTC	AK022580	CCDS5793.1	7q31.33	2013-01-21	2013-01-21		ENSG00000128513	ENSG00000128513			17284	protein-coding gene	gene with protein product		606478	"""protection of telomeres 1 homolog (S. pombe)"""			11349150, 12391173	Standard	NR_003102		Approved	hPot1, DKFZp586D211	uc003vlm.3	Q9NUX5	OTTHUMG00000157194	ENST00000357628.3:c.725A>G	chr7.hg19:g.124493170T>C	ENSP00000350249:p.Tyr242Cys	133.0	0.0	.		131.0	83.0	.	NM_015450	O95018|Q5MJ36|Q9H662|Q9NW19|Q9UG95	Missense_Mutation	SNP	ENST00000357628.3	hg19	CCDS5793.1	.	.	.	.	.	.	.	.	.	.	T	20.9	4.073572	0.76415	.	.	ENSG00000128513	ENST00000357628;ENST00000393329;ENST00000451720;ENST00000440969;ENST00000393326;ENST00000265391	T;T	0.49720	0.78;0.77	6.07	6.07	0.98685	Nucleic acid-binding, OB-fold-like (1);	0.178639	0.50627	D	0.000103	T	0.68384	0.2995	M	0.76002	2.32	0.48696	D	0.999696	D	0.89917	1.0	D	0.87578	0.998	T	0.69537	-0.5119	10	0.48119	T	0.1	-0.6297	14.5927	0.68378	0.0:0.0:0.0:1.0	.	242	Q9NUX5	POTE1_HUMAN	C	242;111;242;242;242;241	ENSP00000350249:Y242C;ENSP00000377002:Y111C	ENSP00000265391:Y241C	Y	-	2	0	POT1	124280406	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	3.512000	0.53407	2.326000	0.78906	0.533000	0.62120	TAT	.	.	.	none		0.313	POT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347861.1		
PTPRD	5789	hgsc.bcm.edu	37	9	8460470	8460470	+	Silent	SNP	A	A	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr9:8460470A>G	ENST00000381196.4	-	30	4359	c.3816T>C	c.(3814-3816)ggT>ggC	p.G1272G	PTPRD_ENST00000360074.4_Silent_p.G1259G|PTPRD_ENST00000397617.3_Silent_p.G851G|PTPRD_ENST00000358503.5_Silent_p.G1250G|PTPRD_ENST00000355233.5_Silent_p.G861G|PTPRD_ENST00000486161.1_Silent_p.G861G|PTPRD_ENST00000540109.1_Silent_p.G1272G|PTPRD_ENST00000397606.3_Silent_p.G851G|PTPRD_ENST00000356435.5_Silent_p.G1272G|PTPRD_ENST00000397611.3_Silent_p.G858G|PTPRD_ENST00000537002.1_Silent_p.G858G	NM_002839.3	NP_002830.1	P23468	PTPRD_HUMAN	protein tyrosine phosphatase, receptor type, D	1272					heterophilic cell-cell adhesion (GO:0007157)|neuron differentiation (GO:0030182)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphate-containing compound metabolic process (GO:0006796)|positive regulation of dendrite morphogenesis (GO:0050775)|presynaptic membrane assembly (GO:0097105)|protein dephosphorylation (GO:0006470)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	cell adhesion molecule binding (GO:0050839)|receptor binding (GO:0005102)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			NS(1)|breast(7)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(22)|liver(1)|lung(83)|ovary(4)|pancreas(1)|prostate(7)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(1)	168		all_cancers(3;3.38e-95)|all_epithelial(3;2.84e-91)|all_lung(3;7.3e-56)|Lung NSC(3;1.82e-52)|Renal(3;3.42e-19)|all_hematologic(3;0.000134)|all_neural(3;0.00409)|Acute lymphoblastic leukemia(23;0.0069)|Melanoma(3;0.0121)|Myeloproliferative disorder(4;0.0122)|Medulloblastoma(3;0.0144)|Lung SC(3;0.0301)|Ovarian(56;0.0694)|Hepatocellular(3;0.0824)		all cancers(1;3.38e-12)|Epithelial(1;2.12e-09)|STAD - Stomach adenocarcinoma(1;1.29e-07)|KIRC - Kidney renal clear cell carcinoma(3;5.49e-07)|Kidney(3;6.36e-07)|GBM - Glioblastoma multiforme(50;9.05e-05)|Lung(1;0.000189)|BRCA - Breast invasive adenocarcinoma(1;0.00178)|LUSC - Lung squamous cell carcinoma(1;0.0115)|LUAD - Lung adenocarcinoma(58;0.119)		CAAGGACAGGACCTACAACCC	0.458										TSP Lung(15;0.13)																											p.G1272G		Atlas-SNP	.											.	PTPRD	1348	.	0			c.T3816C						PASS	.						180.0	158.0	165.0					9																	8460470		2203	4300	6503	SO:0001819	synonymous_variant	5789	exon33			GACAGGACCTACA	X54133	CCDS6472.1, CCDS43786.1, CCDS6472.2, CCDS55288.1, CCDS55289.1, CCDS55290.1, CCDS75813.1	9p24.1-p23	2013-02-11			ENSG00000153707	ENSG00000153707		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	9668	protein-coding gene	gene with protein product		601598				7896816, 8355697	Standard	NM_002839		Approved	PTPD, HPTP	uc003zkk.3	P23468	OTTHUMG00000021005	ENST00000381196.4:c.3816T>C	chr9.hg19:g.8460470A>G		99.0	0.0	.		90.0	28.0	.	NM_002839	B1ALA0|F5GWT7|Q3KPJ0|Q3KPJ1|Q3KPJ2	Silent	SNP	ENST00000381196.4	hg19	CCDS43786.1																																																																																			.	.	.	none		0.458	PTPRD-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055395.3		
BAAT	570	hgsc.bcm.edu	37	9	104130573	104130573	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr9:104130573C>G	ENST00000395051.3	-	2	568	c.498G>C	c.(496-498)ttG>ttC	p.L166F	BAAT_ENST00000259407.2_Missense_Mutation_p.L166F			Q14032	BAAT_HUMAN	bile acid CoA:amino acid N-acyltransferase	166					acyl-CoA metabolic process (GO:0006637)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid conjugation (GO:0002152)|bile acid metabolic process (GO:0008206)|fatty acid metabolic process (GO:0006631)|glycine metabolic process (GO:0006544)|liver development (GO:0001889)|organ regeneration (GO:0031100)|small molecule metabolic process (GO:0044281)|taurine metabolic process (GO:0019530)	cytosol (GO:0005829)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	carboxylic ester hydrolase activity (GO:0052689)|glycine N-choloyltransferase activity (GO:0047963)|long-chain acyl-CoA hydrolase activity (GO:0052816)|medium-chain acyl-CoA hydrolase activity (GO:0052815)|N-acyltransferase activity (GO:0016410)|palmitoyl-CoA hydrolase activity (GO:0016290)|receptor binding (GO:0005102)|very long chain acyl-CoA hydrolase activity (GO:0052817)			breast(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|skin(1)	23		Acute lymphoblastic leukemia(62;0.0559)			Glycine(DB00145)	AACCACCAAACAAATCAATTA	0.458																																					p.L166F		Atlas-SNP	.											.	BAAT	52	.	0			c.G498C						PASS	.						55.0	50.0	51.0					9																	104130573		2203	4300	6503	SO:0001583	missense	570	exon3			ACCAAACAAATCA	L34081	CCDS6752.1	9q22.3	2014-06-24	2014-06-24		ENSG00000136881	ENSG00000136881	2.3.1.65		932	protein-coding gene	gene with protein product	"""glycine N-choloyltransferase"""	602938	"""bile acid Coenzyme A:amino acid N-acyltransferase (glycine N-choloyltransferase)"", ""bile acid CoA: amino acid N-acyltransferase (glycine N-choloyltransferase)"""				Standard	NM_001701		Approved	BAT	uc010mtd.3	Q14032	OTTHUMG00000020377	ENST00000395051.3:c.498G>C	chr9.hg19:g.104130573C>G	ENSP00000378491:p.Leu166Phe	213.0	0.0	.		157.0	64.0	.	NM_001127610	Q3B7W9|Q96L31	Missense_Mutation	SNP	ENST00000395051.3	hg19	CCDS6752.1	.	.	.	.	.	.	.	.	.	.	C	15.55	2.865397	0.51588	.	.	ENSG00000136881	ENST00000259407;ENST00000395051	T;T	0.52754	0.65;0.65	4.76	2.76	0.32466	.	0.343871	0.22294	N	0.061953	T	0.67683	0.2919	M	0.89353	3.025	0.33048	D	0.532319	D	0.65815	0.995	D	0.65443	0.935	T	0.76710	-0.2859	10	0.87932	D	0	-8.5624	8.4628	0.32938	0.0:0.795:0.0:0.205	.	166	Q14032	BAAT_HUMAN	F	166	ENSP00000259407:L166F;ENSP00000378491:L166F	ENSP00000259407:L166F	L	-	3	2	BAAT	103170394	0.998000	0.40836	0.976000	0.42696	0.449000	0.32228	0.773000	0.26661	1.235000	0.43724	0.655000	0.94253	TTG	.	.	.	none		0.458	BAAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053433.1		
UVRAG	7405	hgsc.bcm.edu	37	11	75826995	75826995	+	Missense_Mutation	SNP	C	C	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr11:75826995C>A	ENST00000356136.3	+	14	1574	c.1333C>A	c.(1333-1335)Cca>Aca	p.P445T	UVRAG_ENST00000533454.1_Missense_Mutation_p.P73T|UVRAG_ENST00000538870.1_5'UTR|UVRAG_ENST00000532130.1_Missense_Mutation_p.P73T|UVRAG_ENST00000528420.1_Missense_Mutation_p.P344T|UVRAG_ENST00000539288.1_Missense_Mutation_p.P73T|UVRAG_ENST00000531818.1_Missense_Mutation_p.P73T	NM_003369.3	NP_003360.2	Q9P2Y5	UVRAG_HUMAN	UV radiation resistance associated	445					DNA repair (GO:0006281)|positive regulation of autophagy (GO:0010508)|SNARE complex assembly (GO:0035493)|viral entry into host cell (GO:0046718)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|late endosome (GO:0005770)|lysosome (GO:0005764)|phagocytic vesicle (GO:0045335)|protein complex (GO:0043234)				central_nervous_system(1)|cervix(3)|endometrium(3)|kidney(1)|large_intestine(2)|lung(15)|skin(5)|urinary_tract(2)	32						ACTAGGGACTCCAGACTTGCG	0.393																																					p.P445T		Atlas-SNP	.											.	UVRAG	69	.	0			c.C1333A						PASS	.						93.0	81.0	85.0					11																	75826995		2200	4293	6493	SO:0001583	missense	7405	exon14			GGGACTCCAGACT	X99050, AB012958	CCDS8241.1	11q13	2012-11-15	2012-11-15		ENSG00000198382	ENSG00000198382			12640	protein-coding gene	gene with protein product	"""beclin 1 binding protein"""	602493	"""UV radiation resistance associated gene"""			9169138, 16799551, 18843052	Standard	NM_003369		Approved	VPS38	uc001oxc.3	Q9P2Y5	OTTHUMG00000165319	ENST00000356136.3:c.1333C>A	chr11.hg19:g.75826995C>A	ENSP00000348455:p.Pro445Thr	94.0	0.0	.		69.0	22.0	.	NM_003369	B3KTC1|O00392	Missense_Mutation	SNP	ENST00000356136.3	hg19	CCDS8241.1	.	.	.	.	.	.	.	.	.	.	C	18.00	3.524781	0.64747	.	.	ENSG00000198382	ENST00000356136;ENST00000528420;ENST00000533454;ENST00000531818;ENST00000532130;ENST00000539288	T;T	0.32023	1.47;1.47	5.69	5.69	0.88448	.	0.099426	0.64402	D	0.000001	T	0.24967	0.0606	L	0.41573	1.285	0.80722	D	1	B	0.32324	0.364	B	0.31016	0.123	T	0.03608	-1.1020	10	0.06891	T	0.86	-9.8812	17.6702	0.88214	0.0:1.0:0.0:0.0	.	445	Q9P2Y5	UVRAG_HUMAN	T	445;344;73;73;73;73	ENSP00000348455:P445T;ENSP00000436039:P344T	ENSP00000348455:P445T	P	+	1	0	UVRAG	75504643	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	6.753000	0.74904	2.840000	0.97914	0.655000	0.94253	CCA	.	.	.	none		0.393	UVRAG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383430.1	NM_003369	
CALCOCO1	57658	hgsc.bcm.edu	37	12	54115291	54115291	+	Missense_Mutation	SNP	T	T	C	rs545468025		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr12:54115291T>C	ENST00000550804.1	-	6	778	c.718A>G	c.(718-720)Atc>Gtc	p.I240V	CALCOCO1_ENST00000430117.2_Missense_Mutation_p.I207V|CALCOCO1_ENST00000262059.4_Missense_Mutation_p.I240V|CALCOCO1_ENST00000548263.1_Missense_Mutation_p.I240V|CALCOCO1_ENST00000547885.1_5'Flank			Q9P1Z2	CACO1_HUMAN	calcium binding and coiled-coil domain 1	240					intracellular steroid hormone receptor signaling pathway (GO:0030518)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|ligand-dependent nuclear receptor transcription coactivator activity (GO:0030374)|protein C-terminus binding (GO:0008022)|sequence-specific DNA binding (GO:0043565)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	28						TTCTCACTGATGGTCTGGATG	0.597																																					p.I240V		Atlas-SNP	.											.	CALCOCO1	50	.	0			c.A718G						PASS	.						336.0	283.0	301.0					12																	54115291		2203	4300	6503	SO:0001583	missense	57658	exon6			CACTGATGGTCTG	AL136895	CCDS8864.1, CCDS44908.1	12q13.13	2014-01-02			ENSG00000012822	ENSG00000012822			29306	protein-coding gene	gene with protein product	"""coiled-coil leucine zipper coactivator 1"", ""inorganic pyrophosphatase activator"""					10819331, 11230166	Standard	NM_020898		Approved	KIAA1536, calphoglin, Cocoa	uc001sef.3	Q9P1Z2	OTTHUMG00000170095	ENST00000550804.1:c.718A>G	chr12.hg19:g.54115291T>C	ENSP00000449960:p.Ile240Val	79.0	0.0	.		63.0	25.0	.	NM_020898	B3KVA8|Q6FI59|Q71RC3|Q86WF8|Q96JU3|Q9H090	Missense_Mutation	SNP	ENST00000550804.1	hg19	CCDS8864.1	.	.	.	.	.	.	.	.	.	.	T	13.89	2.373295	0.42105	.	.	ENSG00000012822	ENST00000430117;ENST00000262059;ENST00000413257;ENST00000548263;ENST00000550804;ENST00000549935;ENST00000454332	T;T;T;T	0.10573	2.86;2.86;2.86;2.86	5.0	5.0	0.66597	.	0.157519	0.30201	N	0.010164	T	0.04272	0.0118	N	0.01761	-0.735	0.24470	N	0.994392	B;B;B;B;B;B	0.15930	0.008;0.007;0.007;0.015;0.007;0.008	B;B;B;B;B;B	0.22152	0.038;0.018;0.023;0.023;0.026;0.038	T	0.39251	-0.9623	10	0.10377	T	0.69	-7.9671	12.5553	0.56250	0.0:0.0:0.0:1.0	.	233;207;240;240;207;240	B4DG60;E9PAU0;Q9P1Z2-3;Q9P1Z2-2;E7EPK7;Q9P1Z2	.;.;.;.;.;CACO1_HUMAN	V	207;240;178;240;240;233;117	ENSP00000397189:I207V;ENSP00000262059:I240V;ENSP00000447647:I240V;ENSP00000449960:I240V	ENSP00000262059:I240V	I	-	1	0	CALCOCO1	52401558	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.902000	0.39848	2.009000	0.58944	0.460000	0.39030	ATC	.	.	.	none		0.597	CALCOCO1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000407233.2	NM_020898	
CDK4	1019	hgsc.bcm.edu	37	12	58145350	58145350	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr12:58145350T>C	ENST00000257904.6	-	2	516	c.151A>G	c.(151-153)Atc>Gtc	p.I51V	CDK4_ENST00000312990.6_Missense_Mutation_p.I51V|CDK4_ENST00000540325.1_5'UTR|CDK4_ENST00000549606.1_Intron|CDK4_ENST00000551888.1_5'UTR	NM_000075.3	NP_000066.1	P11802	CDK4_HUMAN	cyclin-dependent kinase 4	51	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.|Required for binding D-type cyclins.				cell division (GO:0051301)|circadian rhythm (GO:0007623)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic cell cycle (GO:0000278)|negative regulation of cell cycle arrest (GO:0071157)|organ regeneration (GO:0031100)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell size (GO:0045793)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of G2/M transition of mitotic cell cycle (GO:0010971)|positive regulation of translation (GO:0045727)|protein phosphorylation (GO:0006468)|regulation of gene expression (GO:0010468)|response to drug (GO:0042493)|response to hyperoxia (GO:0055093)|response to lead ion (GO:0010288)|response to testosterone (GO:0033574)|response to toxic substance (GO:0009636)|signal transduction (GO:0007165)	chromatin (GO:0000785)|cyclin-dependent protein kinase holoenzyme complex (GO:0000307)|cytosol (GO:0005829)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|tight junction (GO:0005923)|transcription factor complex (GO:0005667)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)			breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(6)|prostate(1)|skin(2)	21	all_cancers(7;4.96e-69)|Lung NSC(6;5.5e-25)|all_lung(6;3.87e-23)|all_epithelial(6;1.66e-15)|Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)		GBM - Glioblastoma multiforme(5;4.21e-120)|all cancers(5;3.75e-83)|BRCA - Breast invasive adenocarcinoma(9;0.0294)			ACTGTGCTGATGGGAAGGCCT	0.592			Mis			melanoma			Hereditary Melanoma																												p.I51V		Atlas-SNP	.	yes	Dom		Familial malignant melanoma	12	12q14	1019	cyclin-dependent kinase 4		E	.	CDK4	36	.	0			c.A151G						PASS	.						113.0	98.0	103.0					12																	58145350		2203	4300	6503	SO:0001583	missense	1019	exon2	Familial Cancer Database	Familial Atypical Multiple Mole Melanoma sydrome, FAMMM, Familial Dysplastic Nevus syndrome	TGCTGATGGGAAG	M14505	CCDS8953.1	12q13	2014-09-17				ENSG00000135446		"""Cyclin-dependent kinases"""	1773	protein-coding gene	gene with protein product		123829				8275715	Standard	NM_000075		Approved	PSK-J3	uc001spv.3	P11802		ENST00000257904.6:c.151A>G	chr12.hg19:g.58145350T>C	ENSP00000257904:p.Ile51Val	120.0	0.0	.		96.0	34.0	.	NM_000075	B2R9A0|B4DNF9|O00576|Q6FG61	Missense_Mutation	SNP	ENST00000257904.6	hg19	CCDS8953.1	.	.	.	.	.	.	.	.	.	.	T	0.310	-0.968185	0.02232	.	.	ENSG00000135446	ENST00000257904;ENST00000312990;ENST00000552254;ENST00000552388;ENST00000552862	T;T;T;T;T	0.65549	-0.16;-0.16;-0.16;-0.16;-0.16	5.23	-0.832	0.10785	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.292238	0.33144	N	0.005225	T	0.39489	0.1080	N	0.20685	0.6	0.28252	N	0.925209	B	0.02656	0.0	B	0.01281	0.0	T	0.19679	-1.0298	10	0.45353	T	0.12	.	6.7259	0.23357	0.0:0.3783:0.1311:0.4906	.	51	P11802	CDK4_HUMAN	V	51	ENSP00000257904:I51V;ENSP00000316889:I51V;ENSP00000449179:I51V;ENSP00000448963:I51V;ENSP00000446763:I51V	ENSP00000257904:I51V	I	-	1	0	CDK4	56431617	0.979000	0.34478	0.997000	0.53966	0.730000	0.41778	0.454000	0.21827	-0.025000	0.13918	-0.993000	0.02533	ATC	.	.	.	none		0.592	CDK4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408790.2	NM_000075	
FLT1	2321	hgsc.bcm.edu	37	13	28880844	28880844	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr13:28880844G>C	ENST00000282397.4	-	29	4037	c.3786C>G	c.(3784-3786)gaC>gaG	p.D1262E	FLT1_ENST00000543394.1_Missense_Mutation_p.D285E|FLT1_ENST00000540678.1_Missense_Mutation_p.D480E	NM_002019.4	NP_002010.2	P17948	VGFR1_HUMAN	fms-related tyrosine kinase 1	1262					blood vessel morphogenesis (GO:0048514)|cell differentiation (GO:0030154)|cell migration (GO:0016477)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|embryonic morphogenesis (GO:0048598)|monocyte chemotaxis (GO:0002548)|patterning of blood vessels (GO:0001569)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor receptor-1 signaling pathway (GO:0036323)|vascular endothelial growth factor signaling pathway (GO:0038084)	endosome (GO:0005768)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|placental growth factor-activated receptor activity (GO:0036332)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)|VEGF-A-activated receptor activity (GO:0036326)|VEGF-B-activated receptor activity (GO:0036327)			NS(1)|breast(2)|central_nervous_system(5)|endometrium(8)|kidney(3)|large_intestine(20)|lung(55)|ovary(3)|prostate(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	115	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0262)|Breast(139;0.188)	Colorectal(13;0.000674)	all cancers(112;0.0301)|Epithelial(112;0.155)|GBM - Glioblastoma multiforme(144;0.184)|OV - Ovarian serous cystadenocarcinoma(117;0.205)|Lung(94;0.207)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	TGGGTTTGCTGTCAGTCCAGG	0.537																																					p.D1262E		Atlas-SNP	.											.	FLT1	393	.	0			c.C3786G						PASS	.						98.0	91.0	93.0					13																	28880844		2203	4300	6503	SO:0001583	missense	2321	exon29			TTTGCTGTCAGTC	AF063657	CCDS9330.1, CCDS53860.1, CCDS53861.1, CCDS73556.1	13q12	2014-09-17	2012-11-19		ENSG00000102755	ENSG00000102755	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3763	protein-coding gene	gene with protein product	"""vascular endothelial growth factor receptor 1"", ""vascular permeability factor receptor"""	165070	"""fms-related tyrosine kinase 1 (vascular endothelial growth factor/vascular permeability factor receptor)"""	FLT		2158038	Standard	NM_001159920		Approved	VEGFR1	uc001usb.3	P17948	OTTHUMG00000016648	ENST00000282397.4:c.3786C>G	chr13.hg19:g.28880844G>C	ENSP00000282397:p.Asp1262Glu	67.0	0.0	.		59.0	29.0	.	NM_002019	A3E342|A3E344|A8KA71|B0LPF1|B2BF46|B2BF47|B2BF48|B3FR89|B5A923|F5H5L6|O60722|P16057|Q12954	Missense_Mutation	SNP	ENST00000282397.4	hg19	CCDS9330.1	.	.	.	.	.	.	.	.	.	.	G	2.348	-0.349552	0.05173	.	.	ENSG00000102755	ENST00000282397;ENST00000543394;ENST00000540678	T;T;T	0.75938	-0.74;-0.94;-0.98	5.23	-0.809	0.10864	.	0.437579	0.23416	N	0.048409	T	0.28532	0.0706	N	0.00377	-1.585	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42882	-0.9425	10	0.02654	T	1	.	5.9864	0.19436	0.0:0.2813:0.2785:0.4402	.	1262	P17948	VGFR1_HUMAN	E	1262;285;480	ENSP00000282397:D1262E;ENSP00000437841:D285E;ENSP00000443311:D480E	ENSP00000282397:D1262E	D	-	3	2	FLT1	27778844	0.303000	0.24463	0.975000	0.42487	0.967000	0.64934	-0.392000	0.07314	-0.200000	0.10300	-0.219000	0.12488	GAC	.	.	.	none		0.537	FLT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044322.1		
SETDB2	83852	hgsc.bcm.edu	37	13	50041999	50041999	+	Splice_Site	SNP	G	G	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr13:50041999G>A	ENST00000317257.8	+	6	1069		c.e6-1		SETDB2_ENST00000354234.4_Splice_Site|SETDB2_ENST00000258672.5_Splice_Site	NM_031915.2	NP_114121.2	Q96T68	SETB2_HUMAN	SET domain, bifurcated 2						chromosome segregation (GO:0007059)|heart looping (GO:0001947)|histone H3-K9 methylation (GO:0051567)|left/right axis specification (GO:0070986)|mitotic nuclear division (GO:0007067)|negative regulation of transcription, DNA-templated (GO:0045892)	chromosome (GO:0005694)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K9 specific) (GO:0046974)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)	15		Lung NSC(96;0.000408)|Breast(56;0.00131)|Prostate(109;0.00446)|Hepatocellular(98;0.0556)|Glioma(44;0.236)	KIRC - Kidney renal clear cell carcinoma(9;0.206)	GBM - Glioblastoma multiforme(99;3.1e-09)		TTTTTGTGTAGATCCTATGCC	0.363																																					.		Atlas-SNP	.											.	SETDB2	48	.	0			c.245-1G>A						PASS	.						82.0	76.0	78.0					13																	50041999		2203	4298	6501	SO:0001630	splice_region_variant	83852	exon6			TGTGTAGATCCTA	AF334407	CCDS9417.1, CCDS53868.1	13q14	2011-07-01	2003-05-06	2003-05-09	ENSG00000136169	ENSG00000136169		"""Chromatin-modifying enzymes / K-methyltransferases"""	20263	protein-coding gene	gene with protein product		607865	"""chromosome 13 open reading frame 4"""	C13orf4		11306461	Standard	NM_031915		Approved	CLLD8, CLLL8, KMT1F	uc001vda.3	Q96T68	OTTHUMG00000016918	ENST00000317257.8:c.245-1G>A	chr13.hg19:g.50041999G>A		32.0	0.0	.		35.0	17.0	.	NM_031915	Q5TC65|Q5TC66|Q5W0A7|Q659A7|Q86UD6|Q96AI6	Splice_Site	SNP	ENST00000317257.8	hg19	CCDS9417.1	.	.	.	.	.	.	.	.	.	.	G	14.14	2.446781	0.43429	.	.	ENSG00000136169	ENST00000354234;ENST00000317257;ENST00000258672	.	.	.	4.96	4.96	0.65561	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	13.8987	0.63790	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SETDB2	48940000	1.000000	0.71417	0.787000	0.31911	0.547000	0.35210	4.071000	0.57556	2.707000	0.92482	0.655000	0.94253	.	.	.	.	none		0.363	SETDB2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000044925.1	NM_031915	Intron
SYNE2	23224	hgsc.bcm.edu	37	14	64669618	64669618	+	Silent	SNP	C	C	T			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr14:64669618C>T	ENST00000344113.4	+	100	18350	c.18138C>T	c.(18136-18138)tcC>tcT	p.S6046S	ESR2_ENST00000542956.1_Intron|SYNE2_ENST00000555002.1_Silent_p.S2680S|SYNE2_ENST00000358025.3_Silent_p.S6046S|SYNE2_ENST00000357395.3_Silent_p.S2431S|SYNE2_ENST00000394768.2_Silent_p.S2431S|SYNE2_ENST00000555022.1_5'Flank|SYNE2_ENST00000554584.1_Silent_p.S6008S	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	6046					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		CTGAGCTTTCCAAGCCTGTTG	0.483																																					p.S6046S		Atlas-SNP	.											.	SYNE2	577	.	0			c.C18138T						PASS	.						142.0	124.0	130.0					14																	64669618		2203	4300	6503	SO:0001819	synonymous_variant	23224	exon100			GCTTTCCAAGCCT	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.18138C>T	chr14.hg19:g.64669618C>T		87.0	0.0	.		65.0	31.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Silent	SNP	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.	.	none		0.483	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
SNW1	22938	hgsc.bcm.edu	37	14	78203382	78203382	+	Silent	SNP	A	A	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr14:78203382A>G	ENST00000261531.7	-	6	632	c.570T>C	c.(568-570)tcT>tcC	p.S190S	SNW1_ENST00000554775.1_Silent_p.S28S|SLIRP_ENST00000557431.1_Intron|SNW1_ENST00000555761.1_Silent_p.S190S	NM_012245.2	NP_036377.1	Q13573	SNW1_HUMAN	SNW domain containing 1	190	SNW.				cellular response to retinoic acid (GO:0071300)|gene expression (GO:0010467)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation by host of viral transcription (GO:0043923)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of mRNA splicing, via spliceosome (GO:0048026)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|positive regulation of vitamin D receptor signaling pathway (GO:0070564)|regulation of retinoic acid receptor signaling pathway (GO:0048385)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of vitamin D receptor signaling pathway (GO:0070562)|retinoic acid receptor signaling pathway (GO:0048384)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	catalytic step 2 spliceosome (GO:0071013)|chromatin (GO:0000785)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	Notch binding (GO:0005112)|nuclear hormone receptor binding (GO:0035257)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)|SMAD binding (GO:0046332)|transcription coactivator activity (GO:0003713)|transcription corepressor activity (GO:0003714)|vitamin D receptor binding (GO:0042809)			NS(1)|endometrium(3)|kidney(3)|large_intestine(6)|lung(6)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	24			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0291)		GTTTAGCTCCAGAGTTGAATG	0.398																																					p.S190S		Atlas-SNP	.											.	SNW1	44	.	0			c.T570C						PASS	.						156.0	140.0	145.0					14																	78203382		2203	4300	6503	SO:0001819	synonymous_variant	22938	exon6			AGCTCCAGAGTTG	AF045184	CCDS9867.1	14q22.1-q22.3	2005-09-13	2005-09-13	2005-09-13		ENSG00000100603			16696	protein-coding gene	gene with protein product		603055	"""SKI interacting protein"""	SKIIP		8973337, 9632709	Standard	NM_012245		Approved	NCoA-62, SKIP, Prp45, PRPF45, Bx42	uc001xuf.3	Q13573		ENST00000261531.7:c.570T>C	chr14.hg19:g.78203382A>G		24.0	0.0	.		22.0	13.0	.	NM_012245	A8K8A9|Q13483|Q32N03|Q5D0D6	Silent	SNP	ENST00000261531.7	hg19	CCDS9867.1																																																																																			.	.	.	none		0.398	SNW1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413912.1	NM_012245	
ZWILCH	55055	hgsc.bcm.edu	37	15	66838985	66838985	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr15:66838985A>G	ENST00000307897.5	+	18	2124	c.1744A>G	c.(1744-1746)Atg>Gtg	p.M582V	ZWILCH_ENST00000446801.2_Missense_Mutation_p.M468V|ZWILCH_ENST00000535141.2_Missense_Mutation_p.M468V|ZWILCH_ENST00000565627.1_Missense_Mutation_p.M468V	NM_017975.3	NP_060445.3	Q9H900	ZWILC_HUMAN	zwilch kinetochore protein	582					mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)	cytosol (GO:0005829)|kinetochore (GO:0000776)				breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(4)|liver(1)|lung(6)|ovary(1)	18						CTTTACTAACATGGTTACCTG	0.368																																					p.M582V		Atlas-SNP	.											.	ZWILCH	46	.	0			c.A1744G						PASS	.						108.0	105.0	106.0					15																	66838985		2201	4299	6500	SO:0001583	missense	55055	exon18			ACTAACATGGTTA	AK023175	CCDS10219.1, CCDS73746.1	15q22.31	2013-01-17	2012-12-13		ENSG00000174442	ENSG00000174442			25468	protein-coding gene	gene with protein product		609984	"""Zwilch, kinetochore associated, homolog (Drosophila)"""			12686595	Standard	NM_017975		Approved	FLJ10036, KNTC1AP	uc002aqb.3	Q9H900	OTTHUMG00000133194	ENST00000307897.5:c.1744A>G	chr15.hg19:g.66838985A>G	ENSP00000311429:p.Met582Val	76.0	0.0	.		50.0	21.0	.	NM_017975	B3KVB8|Q6N049|Q8N404|Q96SY7|Q9NWG7	Missense_Mutation	SNP	ENST00000307897.5	hg19	CCDS10219.1	.	.	.	.	.	.	.	.	.	.	A	15.98	2.993504	0.54041	.	.	ENSG00000174442	ENST00000307897;ENST00000446801;ENST00000535141	T;T;T	0.40756	1.02;1.02;1.02	5.63	-7.38	0.01407	.	0.476664	0.26539	N	0.023813	T	0.28699	0.0711	M	0.64997	1.995	0.09310	N	1	B	0.25809	0.135	B	0.23852	0.049	T	0.09574	-1.0668	10	0.62326	D	0.03	-4.3179	4.9984	0.14251	0.2239:0.5001:0.1786:0.0973	.	582	Q9H900	ZWILC_HUMAN	V	582;468;468	ENSP00000311429:M582V;ENSP00000402217:M468V;ENSP00000437749:M468V	ENSP00000311429:M582V	M	+	1	0	ZWILCH	64626039	0.001000	0.12720	0.000000	0.03702	0.948000	0.59901	-0.202000	0.09451	-1.637000	0.01531	-1.883000	0.00544	ATG	.	.	.	none		0.368	ZWILCH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256904.4	NM_017975	
CYP1A2	1544	hgsc.bcm.edu	37	15	75042609	75042609	+	Missense_Mutation	SNP	A	A	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr15:75042609A>C	ENST00000343932.4	+	2	593	c.530A>C	c.(529-531)cAg>cCg	p.Q177P		NM_000761.3	NP_000752.2	P05177	CP1A2_HUMAN	cytochrome P450, family 1, subfamily A, polypeptide 2	177					alkaloid metabolic process (GO:0009820)|arachidonic acid metabolic process (GO:0019369)|cellular respiration (GO:0045333)|cellular response to cadmium ion (GO:0071276)|dibenzo-p-dioxin metabolic process (GO:0018894)|drug catabolic process (GO:0042737)|drug metabolic process (GO:0017144)|epoxygenase P450 pathway (GO:0019373)|exogenous drug catabolic process (GO:0042738)|heterocycle metabolic process (GO:0046483)|hydrogen peroxide biosynthetic process (GO:0050665)|lung development (GO:0030324)|methylation (GO:0032259)|monocarboxylic acid metabolic process (GO:0032787)|monoterpenoid metabolic process (GO:0016098)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|oxidative deethylation (GO:0071615)|oxidative demethylation (GO:0070989)|porphyrin-containing compound metabolic process (GO:0006778)|post-embryonic development (GO:0009791)|regulation of gene expression (GO:0010468)|response to estradiol (GO:0032355)|response to lipopolysaccharide (GO:0032496)|small molecule metabolic process (GO:0044281)|steroid catabolic process (GO:0006706)|toxin biosynthetic process (GO:0009403)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|intracellular membrane-bounded organelle (GO:0043231)	aromatase activity (GO:0070330)|caffeine oxidase activity (GO:0034875)|demethylase activity (GO:0032451)|electron carrier activity (GO:0009055)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|monooxygenase activity (GO:0004497)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen (GO:0016712)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|lung(7)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	33					"""""""Insulin(DB00071)|Acenocoumarol(DB01418)|Acetaminophen(DB00316)|Agomelatine(DB06594)|Albendazole(DB00518)|Alitretinoin(DB00523)|Almotriptan(DB00918)|Alosetron(DB00969)|Aminoglutethimide(DB00357)|Aminophenazone(DB01424)|Aminophylline(DB01223)|Amiodarone(DB01118)|Amitriptyline(DB00321)|Amlodipine(DB00381)|Anagrelide(DB00261)|Anastrozole(DB01217)|Antipyrine(DB01435)|Apixaban(DB06605)|Aprepitant(DB00673)|Asenapine(DB06216)|Atropine(DB00572)|Axitinib(DB06626)|Azelastine(DB00972)|Azithromycin(DB00207)|Benzyl alcohol(DB06770)|Betaxolol(DB00195)|Bortezomib(DB00188)|Bromazepam(DB01558)|Bromocriptine(DB01200)|Bupivacaine(DB00297)|Buprenorphine(DB00921)|Bupropion(DB01156)|Caffeine(DB00201)|Carbamazepine(DB00564)|Carmustine(DB00262)|Carvedilol(DB01136)|Chlorpromazine(DB00477)|Chlorzoxazone(DB00356)|Cilostazol(DB01166)|Cimetidine(DB00501)|Cinacalcet(DB01012)|Cinnarizine(DB00568)|Ciprofloxacin(DB00537)|Cisapride(DB00604)|Citalopram(DB00215)|Clarithromycin(DB01211)|Clenbuterol(DB01407)|Clevidipine(DB04920)|Clobetasol propionate(DB01013)|Clomifene(DB00882)|Clomipramine(DB01242)|Clonidine(DB00575)|Clopidogrel(DB00758)|Clotrimazole(DB00257)|Clozapine(DB00363)|Conjugated Estrogens(DB00286)|Cyclobenzaprine(DB00924)|Dacarbazine(DB00851)|Dapagliflozin(DB06292)|Dasatinib(DB01254)|Daunorubicin(DB00694)|Delavirdine(DB00705)|Desipramine(DB01151)|Desloratadine(DB00967)|Dexfenfluramine(DB01191)|Dexmedetomidine(DB00633)|Diazepam(DB00829)|Diclofenac(DB00586)|Dinoprostone(DB00917)|Diphenhydramine(DB01075)|Domperidone(DB01184)|Dopamine(DB00988)|Doxepin(DB01142)|Duloxetine(DB00476)|Edetic Acid(DB00974)|Efavirenz(DB00625)|Eltrombopag(DB06210)|Enoxacin(DB00467)|Epinephrine(DB00668)|Ergotamine(DB00696)|Erlotinib(DB00530)|Erythromycin(DB00199)|Estradiol(DB00783)|Estrone(DB00655)|Estropipate(DB04574)|Ethanol(DB00898)|Etoposide(DB00773)|Etoricoxib(DB01628)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Fluoxetine(DB00472)|Fluphenazine(DB00623)|Flutamide(DB00499)|Fluvastatin(DB01095)|Fluvoxamine(DB00176)|Frovatriptan(DB00998)|Gemfibrozil(DB01241)|Griseofulvin(DB00400)|Guanabenz(DB00629)|Haloperidol(DB00502)|Hesperetin(DB01094)|Hexobarbital(DB01355)|Iloperidone(DB04946)|Imatinib(DB00619)|Imipramine(DB00458)|Imiquimod(DB00724)|inhaled insulin(DB05278)|Insulin Aspart(DB01306)|Insulin Detemir(DB01307)|Insulin Glargine(DB00047)|Insulin Glulisine(DB01309)|Insulin Lispro(DB00046)|Insulin Regular(DB00030)|Irbesartan(DB01029)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Lansoprazole(DB00448)|Leflunomide(DB01097)|Levobupivacaine(DB01002)|Levofloxacin(DB01137)|Lidocaine(DB00281)|Lomefloxacin(DB00978)|Lopinavir(DB01601)|Lorcaserin(DB04871)|Losartan(DB00678)|Lumiracoxib(DB01283)|Malathion(DB00772)|Maprotiline(DB00934)|Meclizine(DB00737)|Melatonin(DB01065)|Menadione(DB00170)|Methadone(DB00333)|Methimazole(DB00763)|Methotrimeprazine(DB01403)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Mexiletine(DB00379)|Mianserin(DB06148)|Miconazole(DB01110)|Mirtazapine(DB00370)|Moclobemide(DB01171)|Modafinil(DB00745)|Nabumetone(DB00461)|Nafcillin(DB00607)|Naproxen(DB00788)|Nelfinavir(DB00220)|Nevirapine(DB00238)|Niclosamide(DB06803)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nisoldipine(DB00401)|Nitric Oxide(DB00435)|Nitroprusside(DB00325)|Norepinephrine(DB00368)|Norfloxacin(DB01059)|Nortriptyline(DB00540)|Ofloxacin(DB01165)|Olanzapine(DB00334)|Omeprazole(DB00338)|Ondansetron(DB00904)|Oxaliplatin(DB00526)|Oxtriphylline(DB01303)|Palonosetron(DB00377)|Pantoprazole(DB00213)|Pazopanib(DB06589)|Pefloxacin(DB00487)|Pentamidine(DB00738)|Pentoxifylline(DB00806)|Perphenazine(DB00850)|Phenobarbital(DB01174)|Phentermine(DB00191)|Phenylephrine(DB00388)|Phenylpropanolamine(DB00397)|Pimozide(DB01100)|Pipotiazine(DB01621)|Pomalidomide(DB08910)|Praziquantel(DB01058)|Primaquine(DB01087)|Primidone(DB00794)|Progesterone(DB00396)|Proguanil(DB01131)|Promazine(DB00420)|Propafenone(DB01182)|Propofol(DB00818)|Propranolol(DB00571)|Pyrazinamide(DB00339)|Quinidine(DB00908)|Quinine(DB00468)|Rabeprazole(DB01129)|Ramelteon(DB00980)|Ranitidine(DB00863)|Rasagiline(DB01367)|Rifabutin(DB00615)|Rifampicin(DB01045)|Rilpivirine(DB08864)|Riluzole(DB00740)|Ritonavir(DB00503)|Rizatriptan(DB00953)|Ropinirole(DB00268)|Ropivacaine(DB00296)|Rosiglitazone(DB00412)|Rotigotine(DB05271)|Roxithromycin(DB00778)|Secobarbital(DB00418)|Selegiline(DB01037)|Sertraline(DB01104)|SIMEPREVIR(DB06290)|Sorafenib(DB00398)|Streptozocin(DB00428)|Sulindac(DB00605)|Tamoxifen(DB00675)|Telithromycin(DB00976)|Tenofovir(DB00300)|Terbinafine(DB00857)|Thalidomide(DB01041)|Theobromine(DB01412)|Theophylline(DB00277)|Thiabendazole(DB00730)|Thioridazine(DB00679)|Thiothixene(DB01623)|Ticlopidine(DB00208)|Tioconazole(DB01007)|Tizanidine(DB00697)|Tocainide(DB01056)|Toremifene(DB00539)|Tranylcypromine(DB00752)|Triamterene(DB00384)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)|Vemurafenib(DB08881)|Verapamil(DB00661)|Warfarin(DB00682)|Zafirlukast(DB00549)|Zileuton(DB00744)|Ziprasidone(DB00246)|Zolmitriptan(DB00315)|Zolpidem(DB00425)"""	AGCAGGTTGCAGGAGCTGATG	0.582																																					p.Q177P		Atlas-SNP	.											.	CYP1A2	70	.	0			c.A530C						PASS	.						157.0	129.0	138.0					15																	75042609		2197	4296	6493	SO:0001583	missense	1544	exon2			GGTTGCAGGAGCT	AF182274	CCDS32293.1	15q24.1	2013-11-11	2003-01-14		ENSG00000140505	ENSG00000140505	1.14.14.1	"""Cytochrome P450s"""	2596	protein-coding gene	gene with protein product		124060	"""cytochrome P450, subfamily I (aromatic compound-inducible), polypeptide 2"""			15128046	Standard	NM_000761		Approved	P3-450, CP12	uc002ayr.1	P05177	OTTHUMG00000172901	ENST00000343932.4:c.530A>C	chr15.hg19:g.75042609A>C	ENSP00000342007:p.Gln177Pro	53.0	0.0	.		58.0	22.0	.	NM_000761	Q16754|Q6NWU5|Q9BXX7|Q9UK49	Missense_Mutation	SNP	ENST00000343932.4	hg19	CCDS32293.1	.	.	.	.	.	.	.	.	.	.	A	13.97	2.395368	0.42512	.	.	ENSG00000140505	ENST00000343932	T	0.70045	-0.45	4.98	3.82	0.43975	.	0.467933	0.25916	N	0.027474	D	0.82586	0.5069	M	0.92649	3.33	0.30278	N	0.791562	D	0.69078	0.997	D	0.70227	0.968	T	0.79804	-0.1649	10	0.30854	T	0.27	.	9.8555	0.41084	0.7119:0.0:0.0:0.2881	.	177	P05177-2	.	P	177	ENSP00000342007:Q177P	ENSP00000342007:Q177P	Q	+	2	0	CYP1A2	72829662	0.026000	0.19158	0.926000	0.36857	0.943000	0.58893	1.348000	0.33987	0.879000	0.35944	0.459000	0.35465	CAG	.	.	.	none		0.582	CYP1A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421263.2	NM_000761	
IL16	3603	hgsc.bcm.edu	37	15	81598444	81598444	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr15:81598444C>G	ENST00000302987.4	+	16	3616	c.3616C>G	c.(3616-3618)Ctc>Gtc	p.L1206V	RP11-761I4.4_ENST00000607019.1_RNA|IL16_ENST00000394660.2_Missense_Mutation_p.L1206V|IL16_ENST00000394652.2_Missense_Mutation_p.L505V			Q14005	IL16_HUMAN	interleukin 16	1206					immune response (GO:0006955)|induction of positive chemotaxis (GO:0050930)|leukocyte chemotaxis (GO:0030595)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				NS(1)|autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(3)|skin(3)|stomach(1)|urinary_tract(1)	57						CATGCCCGACCTCAACTCCTC	0.567																																					p.L1206V		Atlas-SNP	.											.	IL16	254	.	0			c.C3616G						PASS	.						89.0	92.0	91.0					15																	81598444		2203	4300	6503	SO:0001583	missense	3603	exon17			CCCGACCTCAACT	U82972	CCDS10317.1, CCDS42069.1, CCDS53966.1	15q26.3	2011-07-14	2011-07-14		ENSG00000172349	ENSG00000172349		"""Interleukins and interleukin receptors"""	5980	protein-coding gene	gene with protein product	"""prointerleukin 16"", ""lymphocyte chemoattractant factor"""	603035	"""interleukin 16 (lymphocyte chemoattractant factor)"""			9144227	Standard	NM_004513		Approved	LCF, IL-16, prIL-16, HsT19289, FLJ42735, FLJ16806	uc021ssh.1	Q14005	OTTHUMG00000144186	ENST00000302987.4:c.3616C>G	chr15.hg19:g.81598444C>G	ENSP00000302935:p.Leu1206Val	43.0	0.0	.		32.0	10.0	.	NM_001172128	A6NM20|A8MU65|B5TY35|B9EGR6|H3BVH5|Q16435|Q6VVE6|Q6ZMQ7|Q9UP18	Missense_Mutation	SNP	ENST00000302987.4	hg19	CCDS42069.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	13.66|13.66	2.303149|2.303149	0.40795|0.40795	.|.	.|.	ENSG00000172349|ENSG00000172349	ENST00000394660;ENST00000355368;ENST00000302987;ENST00000394653;ENST00000394652;ENST00000394656|ENST00000329842	T;T;T|.	0.39229|.	2.64;1.09;1.09|.	5.03|5.03	3.04|3.04	0.35103|0.35103	PDZ/DHR/GLGF (2);|.	0.206204|.	0.24341|.	N|.	0.039367|.	T|T	0.55955|0.55955	0.1953|0.1953	M|M	0.75447|0.75447	2.3|2.3	0.09310|0.09310	N|N	1|1	D;P;P;P;B|.	0.57571|.	0.98;0.601;0.843;0.601;0.029|.	P;B;D;B;B|.	0.68192|.	0.815;0.425;0.956;0.242;0.099|.	T|T	0.50259|0.50259	-0.8849|-0.8849	10|6	0.29301|0.72032	T|D	0.29|0.01	.|.	8.2659|8.2659	0.31813|0.31813	0.152:0.7674:0.0:0.0806|0.152:0.7674:0.0:0.0806	.|.	1038;699;596;1206;1206|.	F8W7Z5;Q6ZTT5;B3KY62;Q14005;Q14005-2|.	.;.;.;IL16_HUMAN;.|.	V|R	1206;1038;1206;596;505;505|716	ENSP00000378155:L1206V;ENSP00000302935:L1206V;ENSP00000378147:L505V|.	ENSP00000302935:L1206V|ENSP00000329317:P716R	L|P	+|+	1|2	0|0	IL16|IL16	79385499|79385499	0.766000|0.766000	0.28496|0.28496	0.148000|0.148000	0.22405|0.22405	0.023000|0.023000	0.10783|0.10783	1.183000|1.183000	0.32041|0.32041	1.027000|1.027000	0.39758|0.39758	0.561000|0.561000	0.74099|0.74099	CTC|CCT	.	.	.	none		0.567	IL16-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000303952.1	NM_172217	
NLRP1	22861	hgsc.bcm.edu	37	17	5445303	5445303	+	Missense_Mutation	SNP	G	G	T			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:5445303G>T	ENST00000572272.1	-	6	2572	c.2573C>A	c.(2572-2574)gCc>gAc	p.A858D	NLRP1_ENST00000345221.3_Missense_Mutation_p.A858D|NLRP1_ENST00000577119.1_Missense_Mutation_p.A858D|NLRP1_ENST00000354411.3_Missense_Mutation_p.A858D|NLRP1_ENST00000269280.4_Missense_Mutation_p.A858D|NLRP1_ENST00000262467.5_Missense_Mutation_p.A858D|NLRP1_ENST00000571307.1_5'UTR			Q9C000	NALP1_HUMAN	NLR family, pyrin domain containing 1	858					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|apoptotic process (GO:0006915)|defense response to bacterium (GO:0042742)|innate immune response (GO:0045087)|neuron apoptotic process (GO:0051402)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of inflammatory response (GO:0050727)|response to muramyl dipeptide (GO:0032495)	cytosol (GO:0005829)|intracellular (GO:0005622)|NLRP1 inflammasome complex (GO:0072558)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|enzyme binding (GO:0019899)|protein domain specific binding (GO:0019904)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(17)|liver(5)|lung(17)|ovary(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	65		Colorectal(1115;3.48e-05)				CAGCCCAAAGGCAAGGTCCTT	0.557																																					p.A858D		Atlas-SNP	.											.	NLRP1	358	.	0			c.C2573A						PASS	.						81.0	62.0	68.0					17																	5445303		2203	4300	6503	SO:0001583	missense	22861	exon6			CCAAAGGCAAGGT	AB023143	CCDS32537.1, CCDS42244.1, CCDS42245.1, CCDS42246.1, CCDS58508.1	17p13	2014-01-29	2006-12-08	2006-12-08	ENSG00000091592	ENSG00000091592		"""Nucleotide-binding domain and leucine rich repeat containing"""	14374	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and pyrin domain containing 1"""	606636	"""NACHT, leucine rich repeat and PYD (pyrin domain) containing 1"", ""systemic lupus erythematosus, vitiligo-related 1"""	NALP1, SLEV1		8781126, 12563287, 17377159	Standard	NM_033006		Approved	KIAA0926, DKFZp586O1822, CARD7, NAC, CLR17.1, DEFCAP, VAMAS1	uc002gci.3	Q9C000		ENST00000572272.1:c.2573C>A	chr17.hg19:g.5445303G>T	ENSP00000460475:p.Ala858Asp	50.0	0.0	.		51.0	17.0	.	NM_033007	E9PE50|I6L9D9|Q9BZZ8|Q9BZZ9|Q9H5Z7|Q9H5Z8|Q9HAV8|Q9UFT4|Q9Y2E0	Missense_Mutation	SNP	ENST00000572272.1	hg19	CCDS42246.1	.	.	.	.	.	.	.	.	.	.	G	12.85	2.061098	0.36373	.	.	ENSG00000091592	ENST00000544378;ENST00000262467;ENST00000269280;ENST00000354411;ENST00000345221;ENST00000537069	T;T;T;T;T	0.42900	0.96;0.96;0.96;0.96;0.96	2.13	1.13	0.20643	.	0.496363	0.15148	N	0.277896	T	0.65015	0.2651	M	0.93638	3.44	0.09310	N	1	D;D;D;D;D;D	0.76494	0.999;0.998;0.998;0.998;0.999;0.997	D;D;D;P;D;D	0.66351	0.929;0.943;0.943;0.852;0.929;0.925	T	0.53493	-0.8431	10	0.66056	D	0.02	.	4.7785	0.13190	0.1885:0.0:0.8115:0.0	.	124;858;858;858;858;858	F5H042;Q9C000-3;Q9C000-4;Q9C000;Q9C000-2;E9PE50	.;.;.;NALP1_HUMAN;.;.	D	858;858;858;858;858;124	ENSP00000442029:A858D;ENSP00000262467:A858D;ENSP00000269280:A858D;ENSP00000346390:A858D;ENSP00000324366:A858D	ENSP00000262467:A858D	A	-	2	0	NLRP1	5386027	0.049000	0.20398	0.014000	0.15608	0.010000	0.07245	2.010000	0.40913	0.494000	0.27859	-0.266000	0.10368	GCC	.	.	.	none		0.557	NLRP1-011	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000439517.1	NM_033004	
SENP3	26168	hgsc.bcm.edu	37	17	7474735	7474735	+	Silent	SNP	G	G	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:7474735G>A	ENST00000429205.2	+	12	1708	c.1659G>A	c.(1657-1659)caG>caA	p.Q553Q	SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Silent_p.Q552Q|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000582746.1_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|EIF4A1_ENST00000293831.8_5'Flank|EIF4A1_ENST00000577269.1_5'Flank			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	553						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				GCTTCACCCAGCAGGACATGC	0.547																																					p.Q553Q		Atlas-SNP	.											.	SENP3	18	.	0			c.G1659A						PASS	.						102.0	101.0	102.0					17																	7474735		1987	4188	6175	SO:0001819	synonymous_variant	26168	exon12			CACCCAGCAGGAC	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		ENST00000429205.2:c.1659G>A	chr17.hg19:g.7474735G>A		69.0	0.0	.		52.0	9.0	.	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Silent	SNP	ENST00000429205.2	hg19																																																																																				.	.	.	none		0.547	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	
MAPT	4137	hgsc.bcm.edu	37	17	44073780	44073780	+	Nonsense_Mutation	SNP	C	C	A			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:44073780C>A	ENST00000571987.1	+	9	1523	c.1523C>A	c.(1522-1524)tCa>tAa	p.S508*	MAPT_ENST00000431008.3_Nonsense_Mutation_p.S191*|MAPT_ENST00000446361.3_Nonsense_Mutation_p.S133*|MAPT_ENST00000420682.2_Nonsense_Mutation_p.S162*|MAPT_ENST00000347967.5_Nonsense_Mutation_p.S97*|MAPT_ENST00000334239.8_Nonsense_Mutation_p.S133*|STH_ENST00000537309.1_5'Flank|MAPT_ENST00000262410.5_Nonsense_Mutation_p.S508*|MAPT_ENST00000344290.5_Nonsense_Mutation_p.S526*|MAPT_ENST00000351559.5_Nonsense_Mutation_p.S191*|MAPT_ENST00000570299.1_3'UTR|MAPT_ENST00000574436.1_Nonsense_Mutation_p.S191*|MAPT_ENST00000535772.1_Nonsense_Mutation_p.S191*|MAPT_ENST00000576518.1_Nonsense_Mutation_p.S122*|MAPT_ENST00000340799.5_Nonsense_Mutation_p.S162*|MAPT_ENST00000415613.2_Nonsense_Mutation_p.S526*			P10636	TAU_HUMAN	microtubule-associated protein tau	508					adult walking behavior (GO:0007628)|apoptotic process (GO:0006915)|axon cargo transport (GO:0008088)|axon extension (GO:0048675)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|generation of neurons (GO:0048699)|microtubule cytoskeleton organization (GO:0000226)|mitochondrion transport along microtubule (GO:0047497)|negative regulation of intracellular transport (GO:0032387)|neuron migration (GO:0001764)|positive regulation of axon extension (GO:0045773)|positive regulation of microtubule polymerization (GO:0031116)|regulation of autophagy (GO:0010506)|regulation of microtubule polymerization (GO:0031113)|regulation of microtubule-based movement (GO:0060632)	axon (GO:0030424)|axoneme (GO:0005930)|cytoplasmic ribonucleoprotein granule (GO:0036464)|cytosol (GO:0005829)|growth cone (GO:0030426)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|nuclear periphery (GO:0034399)|plasma membrane (GO:0005886)|tubulin complex (GO:0045298)	apolipoprotein binding (GO:0034185)|enzyme binding (GO:0019899)|lipoprotein particle binding (GO:0071813)|microtubule binding (GO:0008017)|SH3 domain binding (GO:0017124)|structural constituent of cytoskeleton (GO:0005200)			breast(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(14)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	38		Melanoma(429;0.216)			Docetaxel(DB01248)|Paclitaxel(DB01229)	CCTCCAAAATCAGGGGATCGC	0.682																																					p.S526X		Atlas-SNP	.											.	MAPT	135	.	0			c.C1577A						PASS	.						18.0	23.0	21.0					17																	44073780		2179	4264	6443	SO:0001587	stop_gained	4137	exon11			CAAAATCAGGGGA	J03778	CCDS11499.1, CCDS11500.1, CCDS11501.1, CCDS11502.1, CCDS45715.1, CCDS45716.1, CCDS56033.1	17q21	2014-09-17			ENSG00000186868	ENSG00000186868			6893	protein-coding gene	gene with protein product	"""G protein beta1/gamma2 subunit-interacting factor 1"", ""microtubule-associated protein tau, isoform 4"", ""protein phosphatase 1, regulatory subunit 103"""	157140		DDPAC, MAPTL		7936241, 3131773	Standard	NM_001123067		Approved	MTBT1, tau, PPND, FTDP-17, TAU, MSTD, MTBT2, FLJ31424, MGC138549, PPP1R103	uc010dau.3	P10636	OTTHUMG00000168833	ENST00000571987.1:c.1523C>A	chr17.hg19:g.44073780C>A	ENSP00000458742:p.Ser508*	56.0	0.0	.		59.0	32.0	.	NM_001123066	P18518|Q14799|Q15549|Q15550|Q15551|Q1RMF6|Q53YB1|Q5CZI7|Q5XWF0|Q6QT54|Q9UDJ3|Q9UMH0|Q9UQ96	Nonsense_Mutation	SNP	ENST00000571987.1	hg19	CCDS11501.1	.	.	.	.	.	.	.	.	.	.	C	36	5.672474	0.96754	.	.	ENSG00000186868	ENST00000344290;ENST00000262410;ENST00000351559;ENST00000340799;ENST00000535772;ENST00000347967;ENST00000354326;ENST00000446361;ENST00000334239;ENST00000420682;ENST00000415613;ENST00000431008	.	.	.	5.62	5.62	0.85841	.	0.000000	0.39985	N	0.001217	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-12.1915	18.2196	0.89897	0.0:1.0:0.0:0.0	.	.	.	.	X	526;508;191;162;191;97;140;133;133;162;526;45	.	ENSP00000262410:S508X	S	+	2	0	MAPT	41429617	1.000000	0.71417	0.996000	0.52242	0.796000	0.44982	5.434000	0.66526	2.651000	0.90000	0.561000	0.74099	TCA	.	.	.	none		0.682	MAPT-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000440133.1	NM_016835	
BZRAP1	9256	hgsc.bcm.edu	37	17	56405116	56405116	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:56405116T>C	ENST00000343736.4	-	1	329	c.166A>G	c.(166-168)Agg>Ggg	p.R56G	BZRAP1-AS1_ENST00000579527.1_RNA|BZRAP1_ENST00000355701.3_Missense_Mutation_p.R56G|BZRAP1_ENST00000268893.6_Missense_Mutation_p.R56G|BZRAP1-AS1_ENST00000580515.1_RNA|BZRAP1-AS1_ENST00000578334.1_RNA|BZRAP1-AS1_ENST00000580633.1_RNA			O95153	RIMB1_HUMAN	benzodiazepine receptor (peripheral) associated protein 1	56						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	benzodiazepine receptor binding (GO:0030156)			cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|liver(2)|lung(16)|ovary(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	54	Medulloblastoma(34;0.127)|all_neural(34;0.237)					TCCTCAGACCTCAGTTCTTGA	0.622																																					p.R56G		Atlas-SNP	.											.	BZRAP1	287	.	0			c.A166G						PASS	.						72.0	65.0	67.0					17																	56405116		2203	4300	6503	SO:0001583	missense	9256	exon1			CAGACCTCAGTTC	AB014512	CCDS11605.1, CCDS45742.1	17q22-q23	2014-01-09	2014-01-09						16831	protein-coding gene	gene with protein product		610764				9734811, 9915832	Standard	NM_004758		Approved	PRAX-1, KIAA0612, RIM-BP1, RIMBP1	uc002ivx.5	O95153		ENST00000343736.4:c.166A>G	chr17.hg19:g.56405116T>C	ENSP00000345824:p.Arg56Gly	50.0	0.0	.		59.0	16.0	.	NM_024418	O75111|Q8N5W3	Missense_Mutation	SNP	ENST00000343736.4	hg19	CCDS11605.1	.	.	.	.	.	.	.	.	.	.	T	9.117	1.008075	0.19199	.	.	ENSG00000005379	ENST00000355701;ENST00000343736;ENST00000268893	T;T;T	0.05447	3.57;3.57;3.44	4.87	0.943	0.19531	.	0.624206	0.15757	N	0.246132	T	0.03827	0.0108	L	0.31294	0.92	0.09310	N	1	B;B;B	0.06786	0.0;0.0;0.001	B;B;B	0.08055	0.0;0.001;0.003	T	0.47156	-0.9139	10	0.09084	T	0.74	.	6.0457	0.19758	0.0:0.3872:0.0:0.6128	.	56;56;56	B7ZVZ7;O95153-2;O95153	.;.;RIMB1_HUMAN	G	56	ENSP00000347929:R56G;ENSP00000345824:R56G;ENSP00000268893:R56G	ENSP00000268893:R56G	R	-	1	2	BZRAP1	53760115	0.001000	0.12720	0.004000	0.12327	0.106000	0.19336	0.525000	0.22956	0.299000	0.22661	0.379000	0.24179	AGG	.	.	.	none		0.622	BZRAP1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000443980.1	NM_004758	
CLUL1	27098	hgsc.bcm.edu	37	18	619309	619309	+	Missense_Mutation	SNP	A	A	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr18:619309A>G	ENST00000400606.2	+	3	348	c.203A>G	c.(202-204)aAg>aGg	p.K68R	CLUL1_ENST00000579494.1_Missense_Mutation_p.K68R|CLUL1_ENST00000338387.7_Missense_Mutation_p.K68R|CLUL1_ENST00000580436.1_3'UTR|CLUL1_ENST00000540035.1_Missense_Mutation_p.K120R|CLUL1_ENST00000581619.1_Missense_Mutation_p.K93R	NM_014410.4	NP_055225.1	Q15846	CLUL1_HUMAN	clusterin-like 1 (retinal)	68					cell death (GO:0008219)	extracellular region (GO:0005576)				NS(1)|breast(1)|endometrium(5)|large_intestine(5)|liver(2)|lung(7)|ovary(2)|skin(1)	24						AGAAAAGAGAAGGAACACACC	0.398																																					p.K68R		Atlas-SNP	.											.	CLUL1	57	.	0			c.A203G						PASS	.						143.0	133.0	136.0					18																	619309		1903	4129	6032	SO:0001583	missense	27098	exon3			AAGAGAAGGAACA	D63813	CCDS42405.1, CCDS74187.1	18p11.32	2008-07-28				ENSG00000079101			2096	protein-coding gene	gene with protein product						10675623, 14507903	Standard	NM_199167		Approved		uc002kkq.3	Q15846		ENST00000400606.2:c.203A>G	chr18.hg19:g.619309A>G	ENSP00000383449:p.Lys68Arg	215.0	0.0	.		146.0	59.0	.	NM_199167	A0FDN7	Missense_Mutation	SNP	ENST00000400606.2	hg19	CCDS42405.1	.	.	.	.	.	.	.	.	.	.	A	12.97	2.096911	0.37048	.	.	ENSG00000079101	ENST00000400606;ENST00000540035;ENST00000338387	T;T;T	0.24151	1.87;1.87;1.87	5.26	3.97	0.46021	Clusterin, N-terminal (1);	0.286892	0.38663	N	0.001609	T	0.17789	0.0427	N	0.22421	0.69	0.21325	N	0.999722	B;B	0.30973	0.257;0.302	B;B	0.30855	0.074;0.121	T	0.19484	-1.0304	10	0.54805	T	0.06	-9.7385	11.7298	0.51730	0.8008:0.0:0.0:0.1991	.	120;68	F5GWQ8;Q15846	.;CLUL1_HUMAN	R	68;120;68	ENSP00000383449:K68R;ENSP00000441726:K120R;ENSP00000341128:K68R	ENSP00000341128:K68R	K	+	2	0	CLUL1	609309	1.000000	0.71417	1.000000	0.80357	0.794000	0.44872	3.195000	0.51013	1.989000	0.58080	0.528000	0.53228	AAG	.	.	.	none		0.398	CLUL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441183.1		
CLIP3	25999	hgsc.bcm.edu	37	19	36510103	36510103	+	Missense_Mutation	SNP	C	C	T			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:36510103C>T	ENST00000360535.4	-	8	1251	c.1024G>A	c.(1024-1026)Gtt>Att	p.V342I	AC002116.7_ENST00000586962.1_RNA|CLIP3_ENST00000593074.1_Missense_Mutation_p.V342I	NM_015526.2	NP_056341.1	Q96DZ5	CLIP3_HUMAN	CAP-GLY domain containing linker protein 3	342	CAP-Gly 1. {ECO:0000255|PROSITE- ProRule:PRU00045}.				chaperone-mediated protein transport (GO:0072321)|fat cell differentiation (GO:0045444)|membrane biogenesis (GO:0044091)|negative regulation of microtubule polymerization (GO:0031115)|peptidyl-L-cysteine S-palmitoylation (GO:0018230)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endocytosis (GO:0045807)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose transport (GO:0010828)|positive regulation of protein phosphorylation (GO:0001934)	early endosome membrane (GO:0031901)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)|trans-Golgi network (GO:0005802)|trans-Golgi network membrane (GO:0032588)	ganglioside binding (GO:0035594)|microtubule binding (GO:0008017)			cervix(1)|endometrium(6)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(2)	23	Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.06)			AAGTACCGAACGCCCCCAACG	0.637																																					p.V342I		Atlas-SNP	.											.	CLIP3	53	.	0			c.G1024A						PASS	.						109.0	92.0	98.0					19																	36510103		2203	4300	6503	SO:0001583	missense	25999	exon7			ACCGAACGCCCCC	AJ427922	CCDS12486.1	19q13.12	2014-08-12			ENSG00000105270	ENSG00000105270		"""Ankyrin repeat domain containing"""	24314	protein-coding gene	gene with protein product	"""CLIP-170-related"", ""restin-like 1"""	607382				11854307	Standard	NM_015526		Approved	CLIPR-59, RSNL1	uc002ocz.2	Q96DZ5	OTTHUMG00000181747	ENST00000360535.4:c.1024G>A	chr19.hg19:g.36510103C>T	ENSP00000353732:p.Val342Ile	35.0	0.0	.		26.0	11.0	.	NM_001199570	A8K0E4|Q8WWL1|Q96C99|Q9UFT7	Missense_Mutation	SNP	ENST00000360535.4	hg19	CCDS12486.1	.	.	.	.	.	.	.	.	.	.	c	13.77	2.336043	0.41398	.	.	ENSG00000105270	ENST00000360535;ENST00000544037;ENST00000534959	T	0.75477	-0.94	5.25	4.21	0.49690	Cytoskeleton-associated protein, Gly-rich domain (4);Cytoskeleton-associated protein, Gly-rich conserved site (1);	0.158804	0.47852	D	0.000220	T	0.55705	0.1937	N	0.25060	0.705	0.32427	N	0.548523	B	0.14805	0.011	B	0.12837	0.008	T	0.55528	-0.8127	10	0.23891	T	0.37	-29.9258	7.0873	0.25264	0.0:0.8131:0.0:0.1869	.	342	Q96DZ5	CLIP3_HUMAN	I	342;224;318	ENSP00000353732:V342I	ENSP00000353732:V342I	V	-	1	0	CLIP3	41201943	0.638000	0.27225	0.983000	0.44433	0.899000	0.52679	1.249000	0.32839	2.478000	0.83669	0.580000	0.79431	GTT	.	.	.	none		0.637	CLIP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457426.1	NM_015526	
PRR12	57479	hgsc.bcm.edu	37	19	50105116	50105116	+	Missense_Mutation	SNP	G	G	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:50105116G>C	ENST00000418929.2	+	6	4726	c.4714G>C	c.(4714-4716)Ggc>Cgc	p.G1572R		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	751							DNA binding (GO:0003677)			NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		TGGCGGAGAGGGCATCTTCCG	0.642																																					p.G1572R		Atlas-SNP	.											.	PRR12	157	.	0			c.G4714C						PASS	.						23.0	32.0	29.0					19																	50105116		2055	4175	6230	SO:0001583	missense	57479	exon6			GGAGAGGGCATCT	AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4714G>C	chr19.hg19:g.50105116G>C	ENSP00000394510:p.Gly1572Arg	122.0	0.0	.		69.0	27.0	.	NM_020719	E9PB06|Q8N4J6	Missense_Mutation	SNP	ENST00000418929.2	hg19	CCDS46143.1	.	.	.	.	.	.	.	.	.	.	G	8.279	0.815113	0.16607	.	.	ENSG00000126464	ENST00000418929;ENST00000246798;ENST00000314734	.	.	.	3.72	3.72	0.42706	.	0.200317	0.24566	N	0.037429	T	0.68897	0.3051	L	0.48642	1.525	0.47407	D	0.999416	D	0.89917	1.0	D	0.76575	0.988	T	0.73094	-0.4091	9	0.87932	D	0	-14.9557	14.4198	0.67175	0.0:0.0:1.0:0.0	.	1572	Q9ULL5-3	.	R	1572;752;752	.	ENSP00000246798:G752R	G	+	1	0	PRR12	54796928	1.000000	0.71417	1.000000	0.80357	0.369000	0.29798	7.892000	0.87324	1.902000	0.55061	0.305000	0.20034	GGC	.	.	.	none		0.642	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1	NM_020719	
ZNF616	90317	hgsc.bcm.edu	37	19	52618903	52618903	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:52618903T>C	ENST00000600228.1	-	4	1775	c.1514A>G	c.(1513-1515)cAt>cGt	p.H505R	ZNF616_ENST00000330123.5_3'UTR	NM_178523.3	NP_848618.2	Q08AN1	ZN616_HUMAN	zinc finger protein 616	505					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(4)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	48				GBM - Glioblastoma multiforme(134;0.00392)|OV - Ovarian serous cystadenocarcinoma(262;0.0189)		AAGACGTGAATGTTGACTGAA	0.423																																					p.H505R		Atlas-SNP	.											.	ZNF616	109	.	0			c.A1514G						PASS	.						114.0	106.0	109.0					19																	52618903		2203	4300	6503	SO:0001583	missense	90317	exon4			CGTGAATGTTGAC	AK092266	CCDS33090.1	19q13.41	2013-01-08				ENSG00000204611		"""Zinc fingers, C2H2-type"", ""-"""	28062	protein-coding gene	gene with protein product							Standard	NM_178523		Approved	MGC45556	uc002pym.3	Q08AN1		ENST00000600228.1:c.1514A>G	chr19.hg19:g.52618903T>C	ENSP00000471000:p.His505Arg	57.0	0.0	.		55.0	21.0	.	NM_178523	B3KRV1|Q0P658|Q658V7	Missense_Mutation	SNP	ENST00000600228.1	hg19	CCDS33090.1	.	.	.	.	.	.	.	.	.	.	T	0.097	-1.157827	0.01686	.	.	ENSG00000204611	ENST00000330123	.	.	.	1.08	-1.23	0.09465	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.08313	0.0207	N	0.00980	-1.08	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.37150	-0.9718	8	0.14252	T	0.57	.	6.2605	0.20897	0.0:0.5161:0.0:0.4839	.	505	Q08AN1	ZN616_HUMAN	R	505	.	ENSP00000328722:H505R	H	-	2	0	ZNF616	57310715	0.000000	0.05858	0.000000	0.03702	0.130000	0.20726	-4.154000	0.00284	-0.563000	0.06078	0.254000	0.18369	CAT	.	.	.	none		0.423	ZNF616-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000462451.1	XM_030892	
NPEPL1	79716	hgsc.bcm.edu	37	20	57268881	57268881	+	Missense_Mutation	SNP	C	C	G			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268881C>G	ENST00000356091.6	+	2	527	c.239C>G	c.(238-240)cCc>cGc	p.P80R	NPEPL1_ENST00000525817.1_Missense_Mutation_p.P32R|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Missense_Mutation_p.P52R	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	80						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			GCTGCCCTGCCCTGCAGGGTG	0.677																																					p.P80R		Atlas-SNP	.											.	NPEPL1	36	.	0			c.C239G						PASS	.						32.0	39.0	37.0					20																	57268881		2084	4196	6280	SO:0001583	missense	79716	exon2			CCCTGCCCTGCAG	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.239C>G	chr20.hg19:g.57268881C>G	ENSP00000348395:p.Pro80Arg	166.0	0.0	.		97.0	25.0	.	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Missense_Mutation	SNP	ENST00000356091.6	hg19	CCDS46621.1	.	.	.	.	.	.	.	.	.	.	C	29.1	4.976448	0.92982	.	.	ENSG00000215440	ENST00000525967;ENST00000525817;ENST00000356091	T;T;T	0.39592	1.13;1.15;1.07	4.97	4.97	0.65823	.	0.000000	0.85682	D	0.000000	T	0.68044	0.2958	M	0.83384	2.64	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.79784	0.984;0.993;0.984	T	0.74003	-0.3804	10	0.72032	D	0.01	-36.5305	17.2194	0.86953	0.0:1.0:0.0:0.0	.	80;32;52	Q8NDH3;G5EA34;E9PN47	PEPL1_HUMAN;.;.	R	52;32;80	ENSP00000434810:P52R;ENSP00000437112:P32R;ENSP00000348395:P80R	ENSP00000348395:P80R	P	+	2	0	NPEPL1	56702288	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	5.622000	0.67750	2.304000	0.77564	0.505000	0.49811	CCC	.	.	.	none		0.677	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
MT-ND5	4540	hgsc.bcm.edu	37	M	13286	13286	+	Missense_Mutation	SNP	T	T	C			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chrM:13286T>C	ENST00000361567.2	+	1	950	c.950T>C	c.(949-951)aTc>aCc	p.I317T	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA|MT-TR_ENST00000387439.1_RNA|MT-TH_ENST00000387441.1_RNA|MT-CYB_ENST00000361789.2_5'Flank|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA			P03915	NU5M_HUMAN	mitochondrially encoded NADH dehydrogenase 5	317					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			breast(4)|endometrium(29)|kidney(33)|pancreas(1)|prostate(7)	74						AATAGTTACAATCGGCATCAA	0.463																																					p.I317T		Atlas-SNP	.											.	.	.	.	0			c.T950C						PASS	.																																			SO:0001583	missense	0	exon1			TTACAATCGGCAT			mitochondria	2011-07-04	2005-02-15	2005-02-16	ENSG00000198786	ENSG00000198786	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7461	protein-coding gene	gene with protein product	"""complex I ND5 subunit"", ""NADH-ubiquinone oxidoreductase chain 5"""	516005	"""NADH dehydrogenase 5"""	MTND5			Standard			Approved	ND5, NAD5		P03915		ENST00000361567.2:c.950T>C	chrM.hg19:g.13286T>C	ENSP00000354813:p.Ile317Thr	22.0	0.0	.		11.0	6.0	.	ENST00000361567	Q34773|Q8WCY3	Missense_Mutation	SNP	ENST00000361567.2	hg19																																																																																				.	.	.	none		0.463	MT-ND5-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024036	
ZNF256	10172	hgsc.bcm.edu	37	19	58452978	58452978	+	Frame_Shift_Del	DEL	G	G	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr19:58452978delG	ENST00000282308.3	-	3	1394	c.1198delC	c.(1198-1200)cttfs	p.L400fs	ZNF256_ENST00000598928.1_3'UTR	NM_005773.2	NP_005764.2	Q9Y2P7	ZN256_HUMAN	zinc finger protein 256	400					multicellular organismal development (GO:0007275)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	19		Colorectal(82;5.46e-05)|all_neural(62;0.0218)|Breast(46;0.0389)|Ovarian(87;0.0443)|Renal(1328;0.157)		UCEC - Uterine corpus endometrioid carcinoma (67;0.168)|GBM - Glioblastoma multiforme(193;0.0155)		CCAATGTGAAGTCTCCGGTGT	0.428																																					p.L400fs	NSCLC(55;1313 1552 8040 11996)	Atlas-Indel,Pindel	.											.	ZNF256	117	.	0			c.1199delT						PASS	.						71.0	68.0	69.0					19																	58452978		2203	4300	6503	SO:0001589	frameshift_variant	10172	exon3			.	AF067165	CCDS12966.1	19q13	2013-01-08				ENSG00000152454		"""Zinc fingers, C2H2-type"", ""-"""	13049	protein-coding gene	gene with protein product		606956					Standard	NM_005773		Approved	BMZF-3	uc002qqu.3	Q9Y2P7		ENST00000282308.3:c.1198delC	chr19.hg19:g.58452978delG	ENSP00000282308:p.Leu400fs	66.0	0.0	0		61.0	27.0	0.442623	NM_005773	B2RA92|Q53Y85|Q9BV71	Frame_Shift_Del	DEL	ENST00000282308.3	hg19	CCDS12966.1																																																																																			.	.	.	none		0.428	ZNF256-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466702.1		
OBSCN	84033	hgsc.bcm.edu	37	1	228404296	228404297	+	Frame_Shift_Ins	INS	-	-	A	rs116554705	byFrequency	TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:228404296_228404297insA	ENST00000422127.1	+	7	2314_2315	c.2270_2271insA	c.(2269-2274)tcggccfs	p.A758fs	OBSCN_ENST00000366707.4_5'UTR|OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000284548.11_Frame_Shift_Ins_p.A758fs|C1orf145_ENST00000295012.5_5'Flank|OBSCN_ENST00000570156.2_Frame_Shift_Ins_p.A758fs	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	758	Ig-like 7.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)			NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GTGCAGGCATCGGCCGGGCGGC	0.683																																					p.S757fs		Atlas-Indel,Pindel	.											.	OBSCN	2142	.	0			c.2270_2271insA						PASS	.																																			SO:0001589	frameshift_variant	84033	exon7			.	AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	Exception_encountered	chr1.hg19:g.228404296_228404297insA	ENSP00000409493:p.Ala758fs	151.0	0.0	0		127.0	52.0	0.409449	NM_001098623	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Frame_Shift_Ins	INS	ENST00000422127.1	hg19	CCDS58065.1																																																																																			.	.	.	none		0.683	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_052843	
ALMS1	7840	hgsc.bcm.edu	37	2	73680903	73680911	+	In_Frame_Del	DEL	AGTGATGCC	AGTGATGCC	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	AGTGATGCC	AGTGATGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr2:73680903_73680911delAGTGATGCC	ENST00000264448.6	+	8	7357_7365	c.7246_7254delAGTGATGCC	c.(7246-7254)agtgatgccdel	p.SDA2416del	ALMS1-IT1_ENST00000441587.2_RNA|ALMS1_ENST00000377715.1_In_Frame_Del_p.SDA2416del|ALMS1_ENST00000409009.1_In_Frame_Del_p.SDA2374del	NM_015120.4	NP_055935	Q8TCU4	ALMS1_HUMAN	Alstrom syndrome 1	2416					endosomal transport (GO:0016197)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|regulation of stress fiber assembly (GO:0051492)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|cytosol (GO:0005829)				breast(4)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(31)|lung(68)|ovary(4)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)|urinary_tract(2)	147						TGATTCAAGTAGTGATGCCAGTGATGGAA	0.392																																					p.2415_2418del		Atlas-Indel,Pindel	.											.	ALMS1	384	.	0			c.7245_7253del						PASS	.																																			SO:0001651	inframe_deletion	7840	exon8			.	AB002326	CCDS42697.1	2p13.1	2014-09-17			ENSG00000116127	ENSG00000116127			428	protein-coding gene	gene with protein product		606844				9063741	Standard	NM_015120		Approved	KIAA0328	uc002sje.1	Q8TCU4	OTTHUMG00000152812	ENST00000264448.6:c.7246_7254delAGTGATGCC	chr2.hg19:g.73680903_73680911delAGTGATGCC	ENSP00000264448:p.Ser2416_Ala2418del	122.0	0.0	0		77.0	23.0	0.298701	NM_015120	Q53S05|Q580Q8|Q86VP9|Q9Y4G4	In_Frame_Del	DEL	ENST00000264448.6	hg19	CCDS42697.1																																																																																			.	.	.	none		0.392	ALMS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327776.1	NM_015120	
SENP3	26168	hgsc.bcm.edu	37	17	7474732	7474733	+	In_Frame_Ins	INS	-	-	CAA			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:7474732_7474733insCAA	ENST00000429205.2	+	12	1705_1706	c.1656_1657insCAA	c.(1657-1659)cag>CAAcag	p.553_553Q>QQ	SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_In_Frame_Ins_p.552_552Q>QQ|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000582746.1_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|EIF4A1_ENST00000293831.8_5'Flank|EIF4A1_ENST00000577269.1_5'Flank			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	553						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				TCAGCTTCACCCAGCAGGACAT	0.54																																					p.T552delinsTQ		Atlas-INDEL	.											.	SENP3	18	.	0			c.1656_1657insCAA						PASS	.																																			SO:0001652	inframe_insertion	26168	exon12			.	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		Exception_encountered	chr17.hg19:g.7474732_7474733insCAA	ENSP00000403712:p.Gln554dup	70.0	0.0	0		52.0	18.0	0.346154	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	In_Frame_Ins	INS	ENST00000429205.2	hg19																																																																																				.	.	.	none		0.540	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	
NAA50	80218	hgsc.bcm.edu	37	3	113441795	113441795	+	Frame_Shift_Del	DEL	A	A	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:113441795delA	ENST00000240922.3	-	4	614	c.290delT	c.(289-291)ttafs	p.L97fs	NAA50_ENST00000497525.1_Frame_Shift_Del_p.L23fs|NAA50_ENST00000497255.1_Intron|NAA50_ENST00000477813.1_Frame_Shift_Del_p.L57fs|NAA50_ENST00000467022.1_5'Flank|NAA50_ENST00000493454.1_Frame_Shift_Del_p.L23fs|NAA50_ENST00000493900.1_Frame_Shift_Del_p.L96fs	NM_025146.2	NP_079422.1	Q9GZZ1	NAA50_HUMAN	N(alpha)-acetyltransferase 50, NatE catalytic subunit	97	N-acetyltransferase. {ECO:0000255|PROSITE-ProRule:PRU00532}.				histone H4 acetylation (GO:0043967)|mitotic sister chromatid cohesion, centromeric (GO:0071962)|N-terminal protein amino acid acetylation (GO:0006474)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)	H4 histone acetyltransferase activity (GO:0010485)|peptide alpha-N-acetyltransferase activity (GO:0004596)|peptidyl-lysine N-acetyltransferase activity, acting on acetyl phosphate as donor (GO:0052858)			large_intestine(2)|lung(2)|skin(1)	5						ACAGATGTTTAAGACATGATT	0.274																																					p.L97fs		Atlas-Indel,Pindel	.											.	NAA50	10	.	0			c.291delA						PASS	.						21.0	20.0	20.0					3																	113441795		2154	4192	6346	SO:0001589	frameshift_variant	80218	exon4			.	AK023256	CCDS2975.1	3q13.31	2010-05-07	2010-01-14	2010-01-14	ENSG00000121579	ENSG00000121579	2.3.1.-	"""N(alpha)-acetyltransferase subunits"""	29533	protein-coding gene	gene with protein product		610834	"""Mak3 homolog (S. cerevisiae)"", ""N-acetyltransferase 13"", ""N-acetyltransferase 13 (GCN5-related)"""	MAK3, NAT13		16507339, 17502424, 19660095	Standard	NM_025146		Approved	FLJ13194, NAT5, San	uc003ean.2	Q9GZZ1	OTTHUMG00000159294	ENST00000240922.3:c.290delT	chr3.hg19:g.113441795delA	ENSP00000240922:p.Leu97fs	536.0	0.0	0		522.0	145.0	0.277778	NM_025146	D3DN74|Q68DQ1	Frame_Shift_Del	DEL	ENST00000240922.3	hg19	CCDS2975.1																																																																																			.	.	.	none		0.274	NAA50-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000354446.2	NM_025146	
SYNE2	23224	hgsc.bcm.edu	37	14	64519388	64519388	+	Frame_Shift_Del	DEL	T	T	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr14:64519388delT	ENST00000344113.4	+	48	8969	c.8757delT	c.(8755-8757)aatfs	p.N2919fs	SYNE2_ENST00000358025.3_Frame_Shift_Del_p.N2919fs|SYNE2_ENST00000357395.3_5'UTR|SYNE2_ENST00000554584.1_Frame_Shift_Del_p.N2952fs	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2	2919					centrosome localization (GO:0051642)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment or maintenance of cell polarity (GO:0007163)|fibroblast migration (GO:0010761)|nuclear envelope organization (GO:0006998)|nuclear migration (GO:0007097)|nuclear migration along microfilament (GO:0031022)|positive regulation of cell migration (GO:0030335)|protein localization to nucleus (GO:0034504)	aggresome (GO:0016235)|cytoplasm (GO:0005737)|filopodium membrane (GO:0031527)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intermediate filament cytoskeleton (GO:0045111)|lamellipodium membrane (GO:0031258)|mitochondrion (GO:0005739)|nuclear envelope (GO:0005635)|nuclear lumen (GO:0031981)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum (GO:0016529)|SUN-KASH complex (GO:0034993)|Z disc (GO:0030018)	actin binding (GO:0003779)			NS(5)|breast(17)|central_nervous_system(3)|cervix(8)|endometrium(17)|haematopoietic_and_lymphoid_tissue(2)|kidney(21)|large_intestine(34)|lung(75)|ovary(10)|pancreas(2)|prostate(8)|skin(8)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(4)	224				all cancers(60;0.00153)|OV - Ovarian serous cystadenocarcinoma(108;0.00444)|BRCA - Breast invasive adenocarcinoma(234;0.0681)		AGTTGAAAAATCTTAAGATTA	0.328																																					p.N2919fs		Atlas-Indel,Pindel	.											.	SYNE2	577	.	0			c.8756delA						PASS	.						31.0	29.0	30.0					14																	64519388		1834	4083	5917	SO:0001589	frameshift_variant	23224	exon48			.	AB023228	CCDS9761.2, CCDS41963.1, CCDS45124.1, CCDS45125.1	14q22.1-q22.3	2014-09-17			ENSG00000054654	ENSG00000054654			17084	protein-coding gene	gene with protein product	"""nuclear envelope spectrin repeat-2"", ""nucleus and actin connecting element"""	608442				10231032, 10878022	Standard	NM_182910		Approved	SYNE-2, DKFZP434H2235, Nesprin-2, NUANCE, NUA, KIAA1011, Nesp2	uc001xgl.3	Q8WXH0	OTTHUMG00000140349	ENST00000344113.4:c.8757delT	chr14.hg19:g.64519388delT	ENSP00000341781:p.Asn2919fs	146.0	0.0	0		120.0	52.0	0.433333	NM_015180	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Frame_Shift_Del	DEL	ENST00000344113.4	hg19	CCDS41963.1																																																																																			.	.	.	none		0.328	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	
NPEPL1	79716	hgsc.bcm.edu	37	20	57268883	57268883	+	Frame_Shift_Del	DEL	T	T	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268883delT	ENST00000356091.6	+	2	529	c.241delT	c.(241-243)tgcfs	p.C81fs	NPEPL1_ENST00000525817.1_Frame_Shift_Del_p.C33fs|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Frame_Shift_Del_p.C53fs	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	81						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			TGCCCTGCCCTGCAGGGTGAG	0.677																																					p.P80fs		Atlas-INDEL	.											.	NPEPL1	36	.	0			c.240delC						PASS	.						31.0	38.0	36.0					20																	57268883		2083	4195	6278	SO:0001589	frameshift_variant	79716	exon2			.	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.241delT	chr20.hg19:g.57268883delT	ENSP00000348395:p.Cys81fs	166.0	0.0	0		96.0	26.0	0.270833	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Frame_Shift_Del	DEL	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.	.	none		0.677	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
DHX30	22907	hgsc.bcm.edu	37	3	47891247	47891253	+	Frame_Shift_Del	DEL	GTGCACA	GTGCACA	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	GTGCACA	GTGCACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr3:47891247_47891253delGTGCACA	ENST00000445061.1	+	21	3726_3732	c.3319_3325delGTGCACA	c.(3319-3327)gtgcacatcfs	p.VHI1107fs	MIR1226_ENST00000408658.1_RNA|DHX30_ENST00000348968.4_Frame_Shift_Del_p.VHI1079fs|DHX30_ENST00000457607.1_Frame_Shift_Del_p.VHI1135fs|DHX30_ENST00000446256.2_Frame_Shift_Del_p.VHI1068fs	NM_138615.2	NP_619520.1	Q7L2E3	DHX30_HUMAN	DEAH (Asp-Glu-Ala-His) box helicase 30	1107						cytoplasm (GO:0005737)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|ATP-dependent helicase activity (GO:0008026)|chromatin binding (GO:0003682)|double-stranded RNA binding (GO:0003725)|poly(A) RNA binding (GO:0044822)			endometrium(3)|kidney(1)|large_intestine(11)|lung(13)|ovary(4)|pancreas(1)|prostate(1)|skin(3)	37				BRCA - Breast invasive adenocarcinoma(193;0.000696)|KIRC - Kidney renal clear cell carcinoma(197;0.00609)|Kidney(197;0.007)		CGACGGGGACGTGCACATCCGTGGTGG	0.643											OREG0015550	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.1106_1108del		Atlas-Indel,Pindel	.											.	DHX30	101	.	0			c.3318_3324del						PASS	.																																			SO:0001589	frameshift_variant	22907	exon21			.	AB020697	CCDS2759.1	3p24.3-p22.1	2013-07-16	2013-07-16	2003-06-13	ENSG00000132153	ENSG00000132153		"""DEAH-boxes"""	16716	protein-coding gene	gene with protein product			"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 30"", ""DEAH (Asp-Glu-Ala-His) box polypeptide 30"""	DDX30		10048485, 18022663	Standard	NM_138615		Approved	KIAA0890, FLJ11214	uc003cru.3	Q7L2E3	OTTHUMG00000133522	ENST00000445061.1:c.3319_3325delGTGCACA	chr3.hg19:g.47891247_47891253delGTGCACA	ENSP00000405620:p.Val1107fs	80.0	0.0	0	950	62.0	27.0	0.435484	NM_138615	A8K5F1|O94965|Q7Z753|Q96CH4|Q9NUQ0	Frame_Shift_Del	DEL	ENST00000445061.1	hg19	CCDS2759.1																																																																																			.	.	.	none		0.643	DHX30-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257495.2	NM_138615	
NPEPL1	79716	hgsc.bcm.edu	37	20	57268875	57268875	+	Frame_Shift_Del	DEL	C	C	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268875delC	ENST00000356091.6	+	2	521	c.233delC	c.(232-234)gccfs	p.A78fs	NPEPL1_ENST00000525817.1_Frame_Shift_Del_p.A30fs|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Frame_Shift_Del_p.A50fs	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	78						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			ACCGTGGCTGCCCTGCCCTGC	0.677																																					p.A78fs		Atlas-INDEL	.											.	NPEPL1	36	.	0			c.232delG						PASS	.						36.0	44.0	41.0					20																	57268875		2088	4197	6285	SO:0001589	frameshift_variant	79716	exon2			.	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.233delC	chr20.hg19:g.57268875delC	ENSP00000348395:p.Ala78fs	174.0	0.0	0		107.0	23.0	0.214953	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Frame_Shift_Del	DEL	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.	.	none		0.677	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
NBEA	26960	hgsc.bcm.edu	37	13	35644191	35644191	+	Frame_Shift_Del	DEL	A	A	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr13:35644191delA	ENST00000400445.3	+	9	1920	c.1386delA	c.(1384-1386)ccafs	p.P462fs	NBEA_ENST00000540320.1_Frame_Shift_Del_p.P462fs|NBEA_ENST00000379939.2_Frame_Shift_Del_p.P462fs|NBEA_ENST00000310336.4_Frame_Shift_Del_p.P462fs	NM_015678.4	NP_056493.3	Q8NFP9	NBEA_HUMAN	neurobeachin	462					protein localization (GO:0008104)	cytosol (GO:0005829)|endomembrane system (GO:0012505)|plasma membrane (GO:0005886)|trans-Golgi network (GO:0005802)				NS(1)|breast(1)|endometrium(14)|kidney(4)|large_intestine(29)|lung(40)|ovary(9)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	108		Breast(139;0.0141)|Lung SC(185;0.0548)|Prostate(109;0.207)		all cancers(112;1.93e-08)|Epithelial(112;1.62e-07)|BRCA - Breast invasive adenocarcinoma(63;0.00033)|OV - Ovarian serous cystadenocarcinoma(117;0.00109)|KIRC - Kidney renal clear cell carcinoma(186;0.00575)|Kidney(163;0.00656)|GBM - Glioblastoma multiforme(144;0.191)|Lung(94;0.199)		AATCATCACCAAAAGAGAATG	0.408																																					p.P462fs		Atlas-Indel,Pindel	.											.	NBEA	340	.	0			c.1385delC						PASS	.						50.0	44.0	46.0					13																	35644191		1908	4132	6040	SO:0001589	frameshift_variant	26960	exon9			.	AF467288	CCDS45026.1, CCDS55894.1	13q13	2014-09-17			ENSG00000172915	ENSG00000172915		"""A-kinase anchor proteins"", ""WD repeat domain containing"""	7648	protein-coding gene	gene with protein product		604889				10501977	Standard	NM_015678		Approved	KIAA1544, BCL8B, FLJ10197	uc021ric.1	Q8NFP9	OTTHUMG00000016724	ENST00000400445.3:c.1386delA	chr13.hg19:g.35644191delA	ENSP00000383295:p.Pro462fs	133.0	0.0	0		96.0	40.0	0.416667	NM_015678	B7Z2H9|Q5T320|Q9HCM8|Q9NSU1|Q9NW98|Q9Y6J1	Frame_Shift_Del	DEL	ENST00000400445.3	hg19	CCDS45026.1																																																																																			.	.	.	none		0.408	NBEA-202	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_015678	
POLR3H	171568	hgsc.bcm.edu	37	22	41926870	41926871	+	Frame_Shift_Del	DEL	CC	CC	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	CC	CC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr22:41926870_41926871delCC	ENST00000355209.4	-	5	724_725	c.381_382delGG	c.(379-384)tgggtgfs	p.WV127fs	POLR3H_ENST00000396504.2_Frame_Shift_Del_p.WV127fs|POLR3H_ENST00000337566.5_Frame_Shift_Del_p.WV98fs|POLR3H_ENST00000407461.1_Frame_Shift_Del_p.WV127fs|POLR3H_ENST00000420561.1_5'Flank	NM_001018050.2	NP_001018060.1	Q9Y535	RPC8_HUMAN	polymerase (RNA) III (DNA directed) polypeptide H (22.9kD)	127					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|nucleobase-containing compound metabolic process (GO:0006139)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase III promoter (GO:0006384)	centrosome (GO:0005813)|cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)			breast(1)|lung(5)|skin(1)|urinary_tract(1)	8						TACTCCCACACCCACACCTGCT	0.639																																					p.128_128del		Atlas-Indel,Pindel	.											.	POLR3H	30	.	0			c.382_383del						PASS	.																																			SO:0001589	frameshift_variant	171568	exon5			.	AB051452	CCDS14018.1, CCDS33651.1	22q13	2013-01-21			ENSG00000100413	ENSG00000100413		"""RNA polymerase subunits"""	30349	protein-coding gene	gene with protein product						11258795, 12391170	Standard	XR_244356		Approved	RPC8, KIAA1665	uc003baf.3	Q9Y535	OTTHUMG00000150971	ENST00000355209.4:c.381_382delGG	chr22.hg19:g.41926870_41926871delCC	ENSP00000347345:p.Trp127fs	84.0	0.0	0		69.0	34.0	0.492754	NM_001018050	B0QYH9|Q5M7Y8|Q96AE3|Q9BY95	Frame_Shift_Del	DEL	ENST00000355209.4	hg19	CCDS14018.1																																																																																			.	.	.	none		0.639	POLR3H-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320701.1	NM_138338	
CACNA1H	8912	hgsc.bcm.edu	37	16	1270632	1270632	+	Frame_Shift_Del	DEL	C	C	-	rs532352517		TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr16:1270632delC	ENST00000348261.5	+	35	6948	c.6700delC	c.(6700-6702)cccfs	p.P2234fs	CACNA1H_ENST00000565831.1_Frame_Shift_Del_p.P2228fs|CACNA1H_ENST00000358590.4_Frame_Shift_Del_p.P2228fs	NM_021098.2	NP_066921.2	O95180	CAC1H_HUMAN	calcium channel, voltage-dependent, T type, alpha 1H subunit	2234					aldosterone biosynthetic process (GO:0032342)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|cellular response to hormone stimulus (GO:0032870)|cellular response to potassium ion (GO:0035865)|cortisol biosynthetic process (GO:0034651)|membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|muscle organ development (GO:0007517)|myoblast fusion (GO:0007520)|positive regulation of acrosome reaction (GO:2000344)|regulation of heart contraction (GO:0008016)|regulation of membrane potential (GO:0042391)|transport (GO:0006810)	caveola (GO:0005901)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|metal ion binding (GO:0046872)|scaffold protein binding (GO:0097110)			breast(4)|endometrium(5)|kidney(2)|lung(23)	34		Hepatocellular(780;0.00369)			Amiodarone(DB01118)|Bepridil(DB01244)|Cinnarizine(DB00568)|Felodipine(DB01023)|Flunarizine(DB04841)|Isradipine(DB00270)|Nifedipine(DB01115)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Zonisamide(DB00909)	CTCCCTGGAGCCCACAGAGGG	0.746																																					p.E2233fs		Atlas-Indel,Pindel	.											.	CACNA1H	317	.	0			c.6699delG						PASS	.						7.0	8.0	8.0					16																	1270632		1700	3835	5535	SO:0001589	frameshift_variant	8912	exon35			.	AL031703	CCDS45375.1, CCDS45376.1	16p13.3	2012-03-07	2007-02-16					"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1395	protein-coding gene	gene with protein product		607904				9670923, 16382099	Standard	NM_021098		Approved	Cav3.2	uc002cks.3	O95180		ENST00000348261.5:c.6700delC	chr16.hg19:g.1270632delC	ENSP00000334198:p.Pro2234fs	52.0	0.0	0		74.0	21.0	0.283784	NM_021098	B5ME00|F8WFD1|O95802|Q8WWI6|Q96QI6|Q96RZ9|Q9NYY4|Q9NYY5	Frame_Shift_Del	DEL	ENST00000348261.5	hg19	CCDS45375.1																																																																																			.	.	.	none		0.746	CACNA1H-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000421601.1	NM_001005407	
LCE4A	199834	hgsc.bcm.edu	37	1	152681648	152681648	+	Frame_Shift_Del	DEL	T	T	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr1:152681648delT	ENST00000368777.1	+	2	353	c.97delT	c.(97-99)tgcfs	p.C33fs	LCE4A_ENST00000335535.3_Frame_Shift_Del_p.C33fs			Q5TA78	LCE4A_HUMAN	late cornified envelope 4A	33	Cys-rich.				keratinization (GO:0031424)					endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|skin(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.116)			TGCATCCTCATGCCCACCTCC	0.592																																					p.S32fs		Atlas-Indel,Pindel	.											.	LCE4A	37	.	0			c.96delA						PASS	.						121.0	135.0	130.0					1																	152681648		2203	4300	6503	SO:0001589	frameshift_variant	199834	exon1			.	BI670517	CCDS1022.1	1q22	2008-02-05	2004-10-11	2004-10-15	ENSG00000187170	ENSG00000187170		"""Late cornified envelopes"""	16613	protein-coding gene	gene with protein product		612618	"""small proline rich-like (epidermal differentiation complex) 4A"""	SPRL4A		11698679	Standard	NM_178356		Approved	LEP8	uc001fak.2	Q5TA78	OTTHUMG00000014394	ENST00000368777.1:c.97delT	chr1.hg19:g.152681648delT	ENSP00000357766:p.Cys33fs	250.0	0.0	0		168.0	81.0	0.482143	NM_178356	Q14D97	Frame_Shift_Del	DEL	ENST00000368777.1	hg19	CCDS1022.1																																																																																			.	.	.	none		0.592	LCE4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040048.1	NM_178356	
SENP3	26168	hgsc.bcm.edu	37	17	7474735	7474736	+	Frame_Shift_Ins	INS	-	-	GA			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr17:7474735_7474736insGA	ENST00000429205.2	+	12	1708_1709	c.1659_1660insGA	c.(1660-1662)cagfs	p.Q554fs	SENP3_ENST00000578868.1_3'UTR|SENP3_ENST00000321337.7_Frame_Shift_Ins_p.Q553fs|SENP3-EIF4A1_ENST00000579777.1_RNA|EIF4A1_ENST00000582746.1_5'Flank|EIF4A1_ENST00000380512.5_5'Flank|EIF4A1_ENST00000293831.8_5'Flank|EIF4A1_ENST00000577269.1_5'Flank			Q9H4L4	SENP3_HUMAN	SUMO1/sentrin/SMT3 specific peptidase 3	554						cytoplasm (GO:0005737)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)	cysteine-type peptidase activity (GO:0008234)			central_nervous_system(1)|ovary(1)	2		Prostate(122;0.157)				GCTTCACCCAGCAGGACATGCC	0.545																																					p.Q553fs		Atlas-Indel,Pindel	.											.	SENP3	18	.	0			c.1659_1660insGA						PASS	.																																			SO:0001589	frameshift_variant	26168	exon12			.	AK000923	CCDS73958.1	17p13	2012-05-02	2005-08-17			ENSG00000161956			17862	protein-coding gene	gene with protein product		612844	"""SUMO1/sentrin/SMT3 specific protease 3"""			10806345, 11230166	Standard	NM_015670		Approved	DKFZP586K0919, SSP3, DKFZp762A152, SMT3IP1, Ulp1	uc002ghm.3	Q9H4L4		Exception_encountered	chr17.hg19:g.7474735_7474736insGA	ENSP00000403712:p.Gln554fs	69.0	0.0	0		52.0	18.0	0.346154	NM_015670	Q66K15|Q86VS7|Q96PS4|Q9Y3W9	Frame_Shift_Ins	INS	ENST00000429205.2	hg19																																																																																				.	.	.	none		0.545	SENP3-202	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding		NM_015670	
NPEPL1	79716	hgsc.bcm.edu	37	20	57268877	57268883	+	Frame_Shift_Del	DEL	CTGCCCT	CTGCCCT	-			TCGA-UZ-A9PU-01A-11D-A42J-10	TCGA-UZ-A9PU-10A-01D-A42M-10	CTGCCCT	CTGCCCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	3dc9ae4b-b140-4e01-9339-de952605d9eb	b843c2a5-db31-4152-b8d4-7ad08f849f7e	g.chr20:57268877_57268883delCTGCCCT	ENST00000356091.6	+	2	523_529	c.235_241delCTGCCCT	c.(235-243)ctgccctgcfs	p.LPC79fs	NPEPL1_ENST00000525817.1_Frame_Shift_Del_p.LPC31fs|STX16-NPEPL1_ENST00000530122.1_3'UTR|NPEPL1_ENST00000525967.1_Frame_Shift_Del_p.LPC51fs	NM_024663.3	NP_078939.3	Q8NDH3	PEPL1_HUMAN	aminopeptidase-like 1	79						cytoplasm (GO:0005737)|nucleus (GO:0005634)	aminopeptidase activity (GO:0004177)|manganese ion binding (GO:0030145)|metalloexopeptidase activity (GO:0008235)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|prostate(1)	14	all_lung(29;0.0175)		BRCA - Breast invasive adenocarcinoma(13;2.88e-09)|Colorectal(105;0.109)			CGTGGCTGCCCTGCCCTGCAGGGTGAG	0.676																																					p.78_80del		Pindel	.											.	NPEPL1	36	.	0			c.234_240del						PASS	.																																			SO:0001589	frameshift_variant	79716	exon2			.	AK021645	CCDS46621.1, CCDS56200.1, CCDS56201.1	20q13.32	2008-07-02			ENSG00000215440	ENSG00000215440			16244	protein-coding gene	gene with protein product						14702039	Standard	NM_001204872		Approved	FLJ11583, bA261P9.2	uc010zzs.1	Q8NDH3	OTTHUMG00000033060	ENST00000356091.6:c.235_241delCTGCCCT	chr20.hg19:g.57268877_57268883delCTGCCCT	ENSP00000348395:p.Leu79fs	171.0	0.0	.		106.0	19.0	0.179	NM_024663	A6NGZ0|B4DMW7|B7ZBN0|E9PN47|G5EA34|Q53G37|Q5W083|Q8TF28|Q8WUI2|Q9H1T6|Q9HAI5	Frame_Shift_Del	DEL	ENST00000356091.6	hg19	CCDS46621.1																																																																																			.	.	.	none		0.676	NPEPL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080402.6	NM_024663	
