#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
KIF1B	23095	hgsc.bcm.edu	37	1	10338126	10338126	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:10338126G>T	ENST00000377086.1	+	13	1322	c.1120G>T	c.(1120-1122)Gag>Tag	p.E374*	KIF1B_ENST00000377081.1_Nonsense_Mutation_p.E374*|KIF1B_ENST00000263934.6_Nonsense_Mutation_p.E368*|KIF1B_ENST00000377083.1_Nonsense_Mutation_p.E368*|KIF1B_ENST00000377093.4_Nonsense_Mutation_p.E368*			O60333	KIF1B_HUMAN	kinesin family member 1B	374					anterograde axon cargo transport (GO:0008089)|apoptotic process (GO:0006915)|cytoskeleton-dependent intracellular transport (GO:0030705)|microtubule-based movement (GO:0007018)|mitochondrion transport along microtubule (GO:0047497)|neuromuscular synaptic transmission (GO:0007274)|neuron-neuron synaptic transmission (GO:0007270)|vesicle-mediated transport (GO:0016192)	cytoplasmic vesicle (GO:0031410)|cytoplasmic vesicle membrane (GO:0030659)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|kinesin binding (GO:0019894)|microtubule motor activity (GO:0003777)|plus-end-directed microtubule motor activity (GO:0008574)			breast(2)|endometrium(7)|kidney(8)|large_intestine(9)|lung(29)|ovary(3)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(2)	71	Ovarian(185;0.203)	all_lung(284;1.31e-05)|Lung NSC(185;2.2e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00205)|Hepatocellular(190;0.00913)|Ovarian(437;0.0228)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0259)|Colorectal(212;9.79e-07)|COAD - Colon adenocarcinoma(227;0.000143)|BRCA - Breast invasive adenocarcinoma(304;0.000413)|Kidney(185;0.00134)|KIRC - Kidney renal clear cell carcinoma(229;0.0037)|STAD - Stomach adenocarcinoma(132;0.0113)|READ - Rectum adenocarcinoma(331;0.0642)		TGAATTAAAGGAGGAGGTGAC	0.398																																					p.E368X		Atlas-SNP	.											.	KIF1B	242	.	0			c.G1102T						PASS	.						109.0	96.0	100.0					1																	10338126		2203	4300	6503	SO:0001587	stop_gained	23095	exon12			TTAAAGGAGGAGG	AF257176	CCDS111.1, CCDS112.1	1p36.22	2014-09-17			ENSG00000054523	ENSG00000054523		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	16636	protein-coding gene	gene with protein product		605995		CMT2A, CMT2		11389829, 10762626	Standard	NM_015074		Approved	KIAA0591, KLP, HMSNII	uc001aqw.4	O60333	OTTHUMG00000001817	ENST00000377086.1:c.1120G>T	chr1.hg19:g.10338126G>T	ENSP00000366290:p.Glu374*	104.0	0.0	.		76.0	28.0	.	NM_183416	A6NFS8|A6NKQ4|Q4VXC3|Q4VXC4|Q4VXC5|Q4VXC6|Q96Q94|Q9BV80|Q9P280	Nonsense_Mutation	SNP	ENST00000377086.1	hg19		.	.	.	.	.	.	.	.	.	.	G	39	7.518828	0.98332	.	.	ENSG00000054523	ENST00000355249;ENST00000263934;ENST00000377093;ENST00000377086;ENST00000377083;ENST00000377081	.	.	.	5.25	5.25	0.73442	.	0.050900	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.87932	D	0	.	19.2117	0.93758	0.0:0.0:1.0:0.0	.	.	.	.	X	374;368;368;374;368;374	.	ENSP00000263934:E368X	E	+	1	0	KIF1B	10260713	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.813000	0.99286	2.611000	0.88343	0.591000	0.81541	GAG	.	.	.	none		0.398	KIF1B-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000005102.1		
LDLRAP1	26119	hgsc.bcm.edu	37	1	25889207	25889207	+	Splice_Site	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:25889207G>A	ENST00000374338.4	+	5	651	c.532G>A	c.(532-534)Gag>Aag	p.E178K	LDLRAP1_ENST00000488127.1_3'UTR	NM_015627.2	NP_056442.2	Q5SW96	ARH_HUMAN	low density lipoprotein receptor adaptor protein 1	178	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				amyloid precursor protein metabolic process (GO:0042982)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|positive regulation of cholesterol metabolic process (GO:0090205)|positive regulation of receptor-mediated endocytosis (GO:0048260)|positive regulation of signal transduction (GO:0009967)|receptor internalization (GO:0031623)|receptor-mediated endocytosis (GO:0006898)|receptor-mediated endocytosis of low-density lipoprotein particle involved in cholesterol transport (GO:0090118)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|regulation of protein binding (GO:0043393)|transport (GO:0006810)	axon (GO:0030424)|basal plasma membrane (GO:0009925)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|early endosome (GO:0005769)|neurofilament (GO:0005883)|recycling endosome (GO:0055037)	AP-2 adaptor complex binding (GO:0035612)|beta-amyloid binding (GO:0001540)|clathrin adaptor activity (GO:0035615)|clathrin binding (GO:0030276)|low-density lipoprotein particle receptor binding (GO:0050750)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphotyrosine binding (GO:0001784)|receptor signaling complex scaffold activity (GO:0030159)|signaling adaptor activity (GO:0035591)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)|urinary_tract(1)	9		Colorectal(325;3.46e-05)|Lung NSC(340;0.000245)|all_lung(284;0.000335)|Renal(390;0.0007)|Ovarian(437;0.00473)|Breast(348;0.0155)|Myeloproliferative disorder(586;0.0255)|all_neural(195;0.0936)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0416)|OV - Ovarian serous cystadenocarcinoma(117;1.63e-26)|Colorectal(126;2.96e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.000728)|STAD - Stomach adenocarcinoma(196;0.000766)|BRCA - Breast invasive adenocarcinoma(304;0.000969)|GBM - Glioblastoma multiforme(114;0.00914)|READ - Rectum adenocarcinoma(331;0.0649)		GTCCAAGGAAGGTGAGACTTT	0.572																																					p.E178K		Atlas-SNP	.											.	LDLRAP1	28	.	0			c.G532A						PASS	.						133.0	119.0	124.0					1																	25889207		2203	4300	6503	SO:0001630	splice_region_variant	26119	exon5			AAGGAAGGTGAGA	BC029770	CCDS30639.1	1p36-p35	2014-09-17			ENSG00000157978	ENSG00000157978			18640	protein-coding gene	gene with protein product		605747					Standard	NM_015627		Approved	ARH, ARH2, FHCB1, FHCB2, MGC34705, DKFZp586D0624	uc001bkl.4	Q5SW96	OTTHUMG00000007386	ENST00000374338.4:c.532+1G>A	chr1.hg19:g.25889207G>A		107.0	0.0	.		84.0	28.0	.	NM_015627	A2BHI5|Q6TQS9|Q8N2Y0|Q9UFI9	Missense_Mutation	SNP	ENST00000374338.4	hg19	CCDS30639.1	.	.	.	.	.	.	.	.	.	.	G	16.81	3.226311	0.58668	.	.	ENSG00000157978	ENST00000374338	T	0.64991	-0.13	5.56	5.56	0.83823	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);	0.265161	0.43579	D	0.000547	T	0.57460	0.2055	M	0.67953	2.075	0.80722	D	1	B	0.10296	0.003	B	0.14578	0.011	T	0.51926	-0.8643	10	0.15499	T	0.54	-18.0094	11.9152	0.52761	0.0794:0.0:0.9206:0.0	.	178	Q5SW96	ARH_HUMAN	K	178	ENSP00000363458:E178K	ENSP00000363458:E178K	E	+	1	0	LDLRAP1	25761794	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.534000	0.82004	2.620000	0.88729	0.555000	0.69702	GAG	.	.	.	none		0.572	LDLRAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000019350.3	NM_015627	Missense_Mutation
RNF19B	127544	hgsc.bcm.edu	37	1	33402549	33402549	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:33402549C>G	ENST00000373456.7	-	9	2056	c.2057G>C	c.(2056-2058)gGc>gCc	p.G686A	RNF19B_ENST00000235150.4_Missense_Mutation_p.G685A|RNF19B_ENST00000356990.5_3'UTR	NM_153341.2	NP_699172.2	Q6ZMZ0	RN19B_HUMAN	ring finger protein 19B	686					interferon-gamma secretion (GO:0072643)|natural killer cell mediated cytotoxicity (GO:0042267)|protein ubiquitination (GO:0016567)	cytolytic granule (GO:0044194)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13		Myeloproliferative disorder(586;0.0393)|all_neural(195;0.186)				GCGGGGGGAGCCACACTCATC	0.612																																					p.G686A		Atlas-SNP	.											.	RNF19B	43	.	0			c.G2057C						PASS	.						91.0	91.0	91.0					1																	33402549		2203	4300	6503	SO:0001583	missense	127544	exon9			GGGGAGCCACACT	AK074486	CCDS372.2, CCDS44107.1, CCDS72754.1	1p35.1	2010-05-11	2007-08-20	2007-08-20	ENSG00000116514	ENSG00000116514		"""RING-type (C3HC4) zinc fingers"""	26886	protein-coding gene	gene with protein product		610872	"""IBR domain containing 3"""	IBRDC3		12477932	Standard	XM_006710356		Approved	FLJ90005	uc010oho.2	Q6ZMZ0	OTTHUMG00000004013	ENST00000373456.7:c.2057G>C	chr1.hg19:g.33402549C>G	ENSP00000362555:p.Gly686Ala	60.0	0.0	.		42.0	19.0	.	NM_153341	B7ZLB2|E9PAW6|G3XA82|Q0VG77|Q5TH44|Q5TH45|Q6P6A4|Q8N2S8|Q8WUF3	Missense_Mutation	SNP	ENST00000373456.7	hg19	CCDS372.2	.	.	.	.	.	.	.	.	.	.	C	12.90	2.077464	0.36662	.	.	ENSG00000116514	ENST00000373456;ENST00000235150	T;T	0.30448	1.53;1.54	5.12	5.12	0.69794	.	0.160327	0.56097	D	0.000036	T	0.19127	0.0459	N	0.19112	0.55	0.35754	D	0.819621	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.12426	-1.0548	10	0.36615	T	0.2	.	9.4831	0.38913	0.0:0.7744:0.1461:0.0795	.	685;686	G3XA82;Q6ZMZ0	.;RN19B_HUMAN	A	686;685	ENSP00000362555:G686A;ENSP00000235150:G685A	ENSP00000235150:G685A	G	-	2	0	RNF19B	33175136	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	3.052000	0.49893	2.565000	0.86533	0.585000	0.79938	GGC	.	.	.	none		0.612	RNF19B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011465.3	NM_153341	
EPHA10	284656	hgsc.bcm.edu	37	1	38192854	38192854	+	Silent	SNP	G	G	C	rs544755981		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:38192854G>C	ENST00000373048.4	-	8	1691	c.1692C>G	c.(1690-1692)ccC>ccG	p.P564P	EPHA10_ENST00000427468.2_Silent_p.P564P|EPHA10_ENST00000446149.2_5'UTR|EPHA10_ENST00000330210.7_Silent_p.P59P|EPHA10_ENST00000540011.1_Silent_p.P59P	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	564					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)			NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CGACAATGGCGGGGCTCTGGT	0.647																																					p.P564P		Atlas-SNP	.											.	EPHA10	120	.	0			c.C1692G						PASS	.						48.0	63.0	58.0					1																	38192854		2041	4187	6228	SO:0001819	synonymous_variant	284656	exon8			AATGGCGGGGCTC	AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.1692C>G	chr1.hg19:g.38192854G>C		124.0	0.0	.		113.0	39.0	.	NM_001099439	A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	hg19	CCDS41305.1																																																																																			.	.	.	none		0.647	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2	NM_173641	
PDE4B	5142	hgsc.bcm.edu	37	1	66798100	66798100	+	Intron	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:66798100A>C	ENST00000329654.4	+	8	821				PDE4B_ENST00000423207.2_Intron|PDE4B_ENST00000371049.3_Intron|PDE4B_ENST00000371045.5_Missense_Mutation_p.S10R	NM_001037341.1	NP_001032418.1	Q07343	PDE4B_HUMAN	phosphodiesterase 4B, cAMP-specific						cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|cellular response to epinephrine stimulus (GO:0071872)|cellular response to lipopolysaccharide (GO:0071222)|leukocyte migration (GO:0050900)|negative regulation of relaxation of cardiac muscle (GO:1901898)|neutrophil chemotaxis (GO:0030593)|neutrophil homeostasis (GO:0001780)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-2 production (GO:0032743)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of high voltage-gated calcium channel activity (GO:1901841)|T cell receptor signaling pathway (GO:0050852)	cell periphery (GO:0071944)|cytosol (GO:0005829)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|Z disc (GO:0030018)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|3',5'-cyclic-nucleotide phosphodiesterase activity (GO:0004114)|cAMP binding (GO:0030552)|ion channel binding (GO:0044325)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(14)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)	37					Adenosine monophosphate(DB00131)|Amrinone(DB01427)|Caffeine(DB00201)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Papaverine(DB01113)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theobromine(DB01412)|Theophylline(DB00277)	CACCTTCAGTAGCACCGGAAT	0.547																																					p.S10R		Atlas-SNP	.											.	PDE4B	231	.	0			c.A28C						PASS	.						83.0	83.0	83.0					1																	66798100		2203	4300	6503	SO:0001627	intron_variant	5142	exon1			TTCAGTAGCACCG	L20971	CCDS632.1, CCDS30742.1, CCDS30743.1, CCDS72802.1	1p31	2010-06-24	2010-06-24		ENSG00000184588	ENSG00000184588		"""Phosphodiesterases"""	8781	protein-coding gene	gene with protein product	"""phosphodiesterase E4 dunce homolog (Drosophila)"""	600127	"""phosphodiesterase 4B, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E4)"", ""phosphodiesterase 4B, cAMP-specific (phosphodiesterase E4 dunce homolog, Drosophila)"""	DPDE4			Standard	XM_005270925		Approved		uc001dco.3	Q07343	OTTHUMG00000009088	ENST00000329654.4:c.635-91A>C	chr1.hg19:g.66798100A>C		81.0	0.0	.		88.0	44.0	.	NM_001037339	A5YW33|O15443|Q13945|Q5TEK4|Q5TEK5|Q5TEK6	Missense_Mutation	SNP	ENST00000329654.4	hg19	CCDS632.1	.	.	.	.	.	.	.	.	.	.	A	13.91	2.377873	0.42105	.	.	ENSG00000184588	ENST00000371045	T	0.65178	-0.14	5.27	4.15	0.48705	.	.	.	.	.	T	0.17365	0.0417	N	0.03608	-0.345	0.80722	D	1	B	0.23058	0.079	B	0.18871	0.023	T	0.08046	-1.0741	9	0.20519	T	0.43	.	9.4851	0.38924	0.9147:0.0:0.0853:0.0	.	52	Q13945	.	R	10	ENSP00000360084:S10R	ENSP00000360084:S10R	S	+	1	0	PDE4B	66570688	0.424000	0.25490	0.978000	0.43139	0.741000	0.42261	1.394000	0.34509	1.049000	0.40321	0.459000	0.35465	AGC	.	.	.	none		0.547	PDE4B-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000025188.3	NM_002600	
BCL10	8915	hgsc.bcm.edu	37	1	85741991	85741991	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:85741991T>G	ENST00000370580.1	-	1	782	c.45A>C	c.(43-45)gaA>gaC	p.E15D	RP11-131L23.1_ENST00000427819.1_RNA|RP11-131L23.1_ENST00000426125.1_RNA	NM_003921.4	NP_003912.1	O95999	BCL10_HUMAN	B-cell CLL/lymphoma 10	15	CARD. {ECO:0000255|PROSITE- ProRule:PRU00046}.				adaptive immune response (GO:0002250)|B cell apoptotic process (GO:0001783)|cell death (GO:0008219)|cellular defense response (GO:0006968)|cellular response to mechanical stimulus (GO:0071260)|Fc-epsilon receptor signaling pathway (GO:0038095)|immunoglobulin mediated immune response (GO:0016064)|innate immune response (GO:0045087)|interleukin-6 biosynthetic process (GO:0042226)|lymphotoxin A biosynthetic process (GO:0042109)|negative regulation of mature B cell apoptotic process (GO:0002906)|neural tube closure (GO:0001843)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-8 biosynthetic process (GO:0045416)|positive regulation of mast cell cytokine production (GO:0032765)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell activation (GO:0050870)|positive regulation of transcription, DNA-templated (GO:0045893)|protein homooligomerization (GO:0051260)|protein oligomerization (GO:0051259)|regulation of T cell receptor signaling pathway (GO:0050856)|response to food (GO:0032094)|response to fungus (GO:0009620)|response to molecule of bacterial origin (GO:0002237)|T cell apoptotic process (GO:0070231)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor signaling pathway (GO:0002224)	CBM complex (GO:0032449)|cytoplasm (GO:0005737)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|immunological synapse (GO:0001772)|lysosome (GO:0005764)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme binding (GO:0019899)|kinase binding (GO:0019900)|NF-kappaB binding (GO:0051059)|protease binding (GO:0002020)|protein C-terminus binding (GO:0008022)|protein kinase B binding (GO:0043422)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)			haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	19				all cancers(265;0.0114)|Epithelial(280;0.0311)		CCTTCTTCACTTCAGTGAGGT	0.697			T	IGH@	MALT																																p.E15D	NSCLC(34;993 1034 12176 32621 50182)	Atlas-SNP	.		Dom	yes		1	1p22	8915	B-cell CLL/lymphoma 10		L	.	BCL10	39	.	0			c.A45C						PASS	.						71.0	65.0	67.0					1																	85741991		2203	4300	6503	SO:0001583	missense	8915	exon1			CTTCACTTCAGTG	AJ006288	CCDS704.1	1p22	2008-07-18			ENSG00000142867	ENSG00000142867			989	protein-coding gene	gene with protein product	"""CARD-like apoptotic protein"", ""CARD-containing apoptotic signaling protein"", ""CARD containing molecule enhancing NF-kB"", ""caspase-recruiting domain-containing protein"", ""CARD-containing proapoptotic protein"""	603517				9989495	Standard	NM_003921		Approved	CARMEN, CIPER, mE10, c-E10, CLAP	uc021opd.1	O95999	OTTHUMG00000009965	ENST00000370580.1:c.45A>C	chr1.hg19:g.85741991T>G	ENSP00000359612:p.Glu15Asp	76.0	0.0	.		59.0	34.0	.	NM_003921	Q5VUF1	Missense_Mutation	SNP	ENST00000370580.1	hg19	CCDS704.1	.	.	.	.	.	.	.	.	.	.	T	15.60	2.882269	0.51908	.	.	ENSG00000142867	ENST00000370580;ENST00000271015;ENST00000394761	T	0.51071	0.72	5.23	4.11	0.48088	DEATH-like (2);Caspase Recruitment (1);	0.324282	0.35291	N	0.003301	T	0.08670	0.0215	N	0.04508	-0.205	0.36773	D	0.883901	B	0.02656	0.0	B	0.04013	0.001	T	0.12268	-1.0554	10	0.22706	T	0.39	-20.4797	5.3938	0.16259	0.0:0.1576:0.1505:0.6919	.	15	O95999	BCL10_HUMAN	D	15	ENSP00000359612:E15D	ENSP00000271015:E15D	E	-	3	2	BCL10	85514579	1.000000	0.71417	1.000000	0.80357	0.965000	0.64279	0.650000	0.24858	1.027000	0.39758	0.379000	0.24179	GAA	.	.	.	none		0.697	BCL10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027612.1	NM_003921	
GBP3	2635	hgsc.bcm.edu	37	1	89473418	89473418	+	Silent	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:89473418G>A	ENST00000370481.4	-	11	1997	c.1777C>T	c.(1777-1779)Cta>Tta	p.L593L		NM_018284.2	NP_060754.2	Q8WXF7	ATLA1_HUMAN	guanylate binding protein 3	0					axonogenesis (GO:0007409)|cell death (GO:0008219)|endoplasmic reticulum organization (GO:0007029)|GTP catabolic process (GO:0006184)|protein homooligomerization (GO:0051260)	cell projection (GO:0042995)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|Golgi apparatus (GO:0005794)|Golgi cis cisterna (GO:0000137)|integral component of membrane (GO:0016021)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|identical protein binding (GO:0042802)			breast(3)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|stomach(1)	26		Lung NSC(277;0.123)		all cancers(265;0.0103)|Epithelial(280;0.0293)		TAGATCTTTAGCTTATGCGAC	0.338																																					p.L593L		Atlas-SNP	.											.	GBP3	53	.	0			c.C1777T						PASS	.						261.0	254.0	256.0					1																	89473418		2203	4300	6503	SO:0001819	synonymous_variant	2635	exon11			TCTTTAGCTTATG	BC063819	CCDS717.2	1p22.2	2008-02-05			ENSG00000117226	ENSG00000117226			4184	protein-coding gene	gene with protein product		600413				7518790	Standard	NM_018284		Approved	FLJ10961	uc001dmt.3	Q9H0R5	OTTHUMG00000010616	ENST00000370481.4:c.1777C>T	chr1.hg19:g.89473418G>A		51.0	0.0	.		68.0	25.0	.	NM_018284	A6NND5|A8K2C0|G5E9T1|O95890|Q69YH7|Q96FK0	Silent	SNP	ENST00000370481.4	hg19	CCDS717.2																																																																																			.	.	.	none		0.338	GBP3-008	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313541.3	NM_018284	
ZNF644	84146	hgsc.bcm.edu	37	1	91404516	91404516	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:91404516T>G	ENST00000370440.1	-	3	2612	c.2395A>C	c.(2395-2397)Agc>Cgc	p.S799R	ZNF644_ENST00000337393.5_Missense_Mutation_p.S799R|ZNF644_ENST00000467231.1_Intron|ZNF644_ENST00000361321.5_Intron|ZNF644_ENST00000347275.5_Intron			Q9H582	ZN644_HUMAN	zinc finger protein 644	799					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(4)|endometrium(2)|large_intestine(10)|lung(21)|ovary(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	47		all_lung(203;0.00206)|Lung NSC(277;0.0519)|Lung SC(238;0.101)		all cancers(265;0.00102)|Epithelial(280;0.00766)|KIRC - Kidney renal clear cell carcinoma(1967;0.147)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		TCTTTGAAGCTTTCAGGCCTT	0.378																																					p.S799R		Atlas-SNP	.											.	ZNF644	120	.	0			c.A2395C						PASS	.						68.0	71.0	70.0					1																	91404516		2203	4300	6503	SO:0001583	missense	84146	exon3			TGAAGCTTTCAGG	AB033047	CCDS731.1, CCDS732.1	1p22.2	2008-02-05			ENSG00000122482	ENSG00000122482			29222	protein-coding gene	gene with protein product		614159				10574462	Standard	NM_032186		Approved	KIAA1221, BM-005, MGC60165, MGC70410	uc001dnw.3	Q9H582	OTTHUMG00000010078	ENST00000370440.1:c.2395A>C	chr1.hg19:g.91404516T>G	ENSP00000359469:p.Ser799Arg	42.0	0.0	.		71.0	32.0	.	NM_201269	A2RU71|Q2TAM0|Q5TCC0|Q6BEP7|Q6P446|Q6PI06|Q7LG67|Q9ULJ9	Missense_Mutation	SNP	ENST00000370440.1	hg19	CCDS731.1	.	.	.	.	.	.	.	.	.	.	T	7.752	0.703462	0.15172	.	.	ENSG00000122482	ENST00000370440;ENST00000337393;ENST00000536941	T;T	0.47528	0.84;0.84	5.94	0.94	0.19513	.	1.368040	0.03945	N	0.287532	T	0.10594	0.0259	N	0.08118	0	0.26551	N	0.973916	B	0.02656	0.0	B	0.01281	0.0	T	0.13308	-1.0514	10	0.24483	T	0.36	2.2487	8.3928	0.32540	0.0:0.6073:0.0:0.3927	.	799	Q9H582	ZN644_HUMAN	R	799;799;371	ENSP00000359469:S799R;ENSP00000337008:S799R	ENSP00000337008:S799R	S	-	1	0	ZNF644	91177104	0.847000	0.29606	0.982000	0.44146	0.624000	0.37722	1.199000	0.32235	0.154000	0.19237	0.482000	0.46254	AGC	.	.	.	none		0.378	ZNF644-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027846.2	NM_032186	
SPTA1	6708	hgsc.bcm.edu	37	1	158622405	158622405	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:158622405C>T	ENST00000368147.4	-	23	3407	c.3227G>A	c.(3226-3228)cGt>cAt	p.R1076H		NM_003126.2	NP_003117.2	P02549	SPTA1_HUMAN	spectrin, alpha, erythrocytic 1	1076					actin filament capping (GO:0051693)|actin filament organization (GO:0007015)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|lymphocyte homeostasis (GO:0002260)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)|positive regulation of protein binding (GO:0032092)|positive regulation of T cell proliferation (GO:0042102)|regulation of cell shape (GO:0008360)	actin cytoskeleton (GO:0015629)|cuticular plate (GO:0032437)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin filament binding (GO:0051015)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)			NS(3)|breast(7)|cervix(1)|endometrium(22)|kidney(9)|large_intestine(29)|liver(2)|lung(183)|ovary(5)|prostate(18)|skin(11)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(9)|urinary_tract(6)	307	all_hematologic(112;0.0378)					CAATAGACGACGTCTGCGTTC	0.438																																					p.R1076H		Atlas-SNP	.											.	SPTA1	720	.	0			c.G3227A						PASS	.						110.0	102.0	104.0					1																	158622405		1890	4110	6000	SO:0001583	missense	6708	exon23			AGACGACGTCTGC	M61877	CCDS41423.1	1q21	2014-06-23	2014-06-23		ENSG00000163554	ENSG00000163554		"""EF-hand domain containing"""	11272	protein-coding gene	gene with protein product	"""elliptocytosis 2"""	182860	"""spectrin, alpha, erythrocytic 1 (elliptocytosis 2)"""				Standard	NM_003126		Approved	EL2	uc001fst.1	P02549	OTTHUMG00000019636	ENST00000368147.4:c.3227G>A	chr1.hg19:g.158622405C>T	ENSP00000357129:p.Arg1076His	61.0	0.0	.		84.0	33.0	.	NM_003126	Q15514|Q5VYL1|Q5VYL2|Q6LDY5	Missense_Mutation	SNP	ENST00000368147.4	hg19	CCDS41423.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.872785	0.33069	.	.	ENSG00000163554	ENST00000368148;ENST00000368147	T;T	0.67523	-0.27;-0.27	5.3	4.39	0.52855	.	0.000000	0.32703	N	0.005759	T	0.41949	0.1181	L	0.54323	1.7	0.37353	D	0.910892	P	0.43542	0.81	B	0.34722	0.188	T	0.51764	-0.8664	10	0.52906	T	0.07	.	9.127	0.36821	0.0:0.8351:0.0:0.1649	.	1076	P02549	SPTA1_HUMAN	H	1076	ENSP00000357130:R1076H;ENSP00000357129:R1076H	ENSP00000357129:R1076H	R	-	2	0	SPTA1	156889029	1.000000	0.71417	0.236000	0.24074	0.013000	0.08279	3.123000	0.50453	1.488000	0.48433	-0.136000	0.14681	CGT	.	.	.	none		0.438	SPTA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051851.3	NM_003126	
NCSTN	23385	hgsc.bcm.edu	37	1	160326855	160326855	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:160326855G>C	ENST00000294785.5	+	16	1944	c.1819G>C	c.(1819-1821)Ggc>Cgc	p.G607R	NCSTN_ENST00000368063.1_Missense_Mutation_p.G587R|NCSTN_ENST00000368065.4_Missense_Mutation_p.G349R|NCSTN_ENST00000535857.1_Missense_Mutation_p.G469R|NCSTN_ENST00000392212.4_Missense_Mutation_p.G587R	NM_015331.2	NP_056146.1	Q92542	NICA_HUMAN	nicastrin	607					amyloid precursor protein catabolic process (GO:0042987)|apoptotic signaling pathway (GO:0097190)|beta-amyloid metabolic process (GO:0050435)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|membrane protein ectodomain proteolysis (GO:0006509)|membrane protein intracellular domain proteolysis (GO:0031293)|myeloid cell homeostasis (GO:0002262)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|positive regulation of apoptotic process (GO:0043065)|positive regulation of catalytic activity (GO:0043085)|protein processing (GO:0016485)|proteolysis (GO:0006508)|T cell proliferation (GO:0042098)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	endopeptidase activity (GO:0004175)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(2)	34	all_cancers(52;8.15e-18)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.111)			ATGGGTCCAGGGCCCTTTGCA	0.552																																					p.G607R		Atlas-SNP	.											.	NCSTN	64	.	0			c.G1819C						PASS	.						200.0	168.0	179.0					1																	160326855		2203	4300	6503	SO:0001583	missense	23385	exon16			GTCCAGGGCCCTT	AF240468	CCDS1203.1	1q22-q23	2014-09-17			ENSG00000162736	ENSG00000162736			17091	protein-coding gene	gene with protein product		605254				9039502, 10993067	Standard	XM_005245053		Approved	KIAA0253, APH2	uc001fvx.3	Q92542	OTTHUMG00000033110	ENST00000294785.5:c.1819G>C	chr1.hg19:g.160326855G>C	ENSP00000294785:p.Gly607Arg	93.0	0.0	.		98.0	43.0	.	NM_015331	Q5T207|Q5T208|Q86VV5	Missense_Mutation	SNP	ENST00000294785.5	hg19	CCDS1203.1	.	.	.	.	.	.	.	.	.	.	G	28.7	4.946235	0.92593	.	.	ENSG00000162736	ENST00000294785;ENST00000368063;ENST00000535857;ENST00000392212;ENST00000368065	T;T;T;T	0.81163	-1.46;-1.45;-0.53;-1.45	5.55	5.55	0.83447	.	0.000000	0.85682	D	0.000000	D	0.87585	0.6214	M	0.71206	2.165	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.999;1.0;0.999	D	0.87185	0.2230	10	0.51188	T	0.08	-23.4934	18.0578	0.89368	0.0:0.0:1.0:0.0	.	469;587;607	F6Y097;Q92542-2;Q92542	.;.;NICA_HUMAN	R	607;587;469;587;349	ENSP00000294785:G607R;ENSP00000357042:G587R;ENSP00000442605:G469R;ENSP00000376047:G587R	ENSP00000294785:G607R	G	+	1	0	NCSTN	158593479	1.000000	0.71417	1.000000	0.80357	0.864000	0.49448	8.756000	0.91651	2.606000	0.88127	0.650000	0.86243	GGC	.	.	.	none		0.552	NCSTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080622.1	NM_015331	
AGT	183	hgsc.bcm.edu	37	1	230846200	230846200	+	Missense_Mutation	SNP	C	C	T	rs559327874		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:230846200C>T	ENST00000366667.4	-	2	611	c.397G>A	c.(397-399)Gtc>Atc	p.V133I	RP11-99J16__A.2_ENST00000412344.1_RNA	NM_000029.3	NP_000020.1	P01019	ANGT_HUMAN	angiotensinogen (serpin peptidase inhibitor, clade A, member 8)	133					activation of NF-kappaB-inducing kinase activity (GO:0007250)|activation of phospholipase C activity (GO:0007202)|aging (GO:0007568)|angiotensin maturation (GO:0002003)|angiotensin mediated vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001998)|angiotensin-mediated drinking behavior (GO:0003051)|artery smooth muscle contraction (GO:0014824)|astrocyte activation (GO:0048143)|blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|branching involved in ureteric bud morphogenesis (GO:0001658)|catenin import into nucleus (GO:0035411)|cell growth involved in cardiac muscle cell development (GO:0061049)|cell-cell signaling (GO:0007267)|cell-matrix adhesion (GO:0007160)|cellular lipid metabolic process (GO:0044255)|cellular protein metabolic process (GO:0044267)|cellular response to mechanical stimulus (GO:0071260)|cellular sodium ion homeostasis (GO:0006883)|cytokine secretion (GO:0050663)|ERK1 and ERK2 cascade (GO:0070371)|establishment of blood-nerve barrier (GO:0008065)|excretion (GO:0007588)|extracellular matrix organization (GO:0030198)|fibroblast proliferation (GO:0048144)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway coupled to cGMP nucleotide second messenger (GO:0007199)|kidney development (GO:0001822)|low-density lipoprotein particle remodeling (GO:0034374)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of neurotrophin TRK receptor signaling pathway (GO:0051387)|negative regulation of sodium ion transmembrane transporter activity (GO:2000650)|negative regulation of tissue remodeling (GO:0034104)|nitric oxide mediated signal transduction (GO:0007263)|ovarian follicle rupture (GO:0001543)|peristalsis (GO:0030432)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of activation of JAK2 kinase activity (GO:0010535)|positive regulation of branching involved in ureteric bud morphogenesis (GO:0090190)|positive regulation of cardiac muscle hypertrophy (GO:0010613)|positive regulation of cellular protein metabolic process (GO:0032270)|positive regulation of cholesterol esterification (GO:0010873)|positive regulation of cytokine production (GO:0001819)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of extracellular matrix constituent secretion (GO:0003331)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of fatty acid biosynthetic process (GO:0045723)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of multicellular organism growth (GO:0040018)|positive regulation of NAD(P)H oxidase activity (GO:0033864)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of organ growth (GO:0046622)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of blood vessel size by renin-angiotensin (GO:0002034)|regulation of blood volume by renin-angiotensin (GO:0002016)|regulation of calcium ion transport (GO:0051924)|regulation of cell growth (GO:0001558)|regulation of cell proliferation (GO:0042127)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of norepinephrine secretion (GO:0014061)|regulation of proteolysis (GO:0030162)|regulation of renal output by angiotensin (GO:0002019)|regulation of renal sodium excretion (GO:0035813)|regulation of vasoconstriction (GO:0019229)|renal response to blood flow involved in circulatory renin-angiotensin regulation of systemic arterial blood pressure (GO:0001999)|renal system process (GO:0003014)|renin-angiotensin regulation of aldosterone production (GO:0002018)|response to cold (GO:0009409)|response to muscle activity involved in regulation of muscle adaptation (GO:0014873)|response to salt stress (GO:0009651)|small molecule metabolic process (GO:0044281)|smooth muscle cell differentiation (GO:0051145)|smooth muscle cell proliferation (GO:0048659)|stress-activated MAPK cascade (GO:0051403)|uterine smooth muscle contraction (GO:0070471)|vasodilation (GO:0042311)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	growth factor activity (GO:0008083)|hormone activity (GO:0005179)|serine-type endopeptidase inhibitor activity (GO:0004867)|superoxide-generating NADPH oxidase activator activity (GO:0016176)|type 1 angiotensin receptor binding (GO:0031702)|type 2 angiotensin receptor binding (GO:0031703)			endometrium(5)|kidney(1)|large_intestine(6)|lung(7)|pancreas(1)|prostate(5)	25	Breast(184;0.0735)|Ovarian(103;0.183)	all_cancers(173;4.64e-23)|all_epithelial(177;3.61e-18)|Breast(1374;0.00093)|all_neural(198;0.0604)|Prostate(94;0.167)		GBM - Glioblastoma multiforme(131;4.4e-06)|Colorectal(1306;5.46e-06)|COAD - Colon adenocarcinoma(196;0.000256)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GGGGAGAGGACGGTGGCCCCA	0.592													C|||	1	0.000199681	0.0	0.0	5008	,	,		20155	0.0		0.0	False		,,,				2504	0.001				p.V133I		Atlas-SNP	.											.	AGT	62	.	0			c.G397A						PASS	.						99.0	99.0	99.0					1																	230846200		2203	4300	6503	SO:0001583	missense	183	exon2			AGAGGACGGTGGC	K02215	CCDS1585.1	1q42.2	2014-02-18	2005-08-18	2001-06-29	ENSG00000135744	ENSG00000135744		"""Serine (or cysteine) peptidase inhibitors"", ""Endogenous ligands"""	333	protein-coding gene	gene with protein product	"""alpha-1 antiproteinase, antitrypsin"""	106150		SERPINA8		6089875, 24172014	Standard	NM_000029		Approved		uc001hty.4	P01019	OTTHUMG00000037757	ENST00000366667.4:c.397G>A	chr1.hg19:g.230846200C>T	ENSP00000355627:p.Val133Ile	94.0	0.0	.		74.0	25.0	.	NM_000029	Q16358|Q16359|Q96F91	Missense_Mutation	SNP	ENST00000366667.4	hg19	CCDS1585.1	.	.	.	.	.	.	.	.	.	.	C	0.057	-1.234253	0.01505	.	.	ENSG00000135744	ENST00000366667;ENST00000430091	D	0.84370	-1.84	5.09	-7.39	0.01402	Serpin domain (3);	0.452988	0.23554	N	0.046932	T	0.56232	0.1971	N	0.08118	0	0.09310	N	1	B;B;B	0.12630	0.002;0.006;0.002	B;B;B	0.11329	0.001;0.006;0.001	T	0.59915	-0.7364	10	0.07813	T	0.8	.	5.113	0.14819	0.0807:0.2591:0.1175:0.5427	.	133;133;133	B0ZBE2;B2R5S1;P01019	.;.;ANGT_HUMAN	I	133	ENSP00000355627:V133I	ENSP00000355627:V133I	V	-	1	0	AGT	228912823	0.013000	0.17824	0.000000	0.03702	0.003000	0.03518	-0.338000	0.07842	-0.993000	0.03467	-1.247000	0.01520	GTC	.	.	.	none		0.592	AGT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092102.1	NM_000029	
KIF26B	55083	hgsc.bcm.edu	37	1	245319611	245319611	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:245319611C>T	ENST00000407071.2	+	2	531	c.91C>T	c.(91-93)Ccc>Tcc	p.P31S		NM_018012.3	NP_060482.2	Q2KJY2	KI26B_HUMAN	kinesin family member 26B	31					establishment of cell polarity (GO:0030010)|metabolic process (GO:0008152)|positive regulation of cell-cell adhesion (GO:0022409)|ureteric bud invasion (GO:0072092)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|microtubule motor activity (GO:0003777)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(21)|ovary(4)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	51	all_cancers(71;3.86e-05)|all_epithelial(71;0.000121)|Ovarian(71;0.0412)|all_lung(81;0.0498)|Lung NSC(105;0.0708)|Breast(184;0.127)		OV - Ovarian serous cystadenocarcinoma(106;0.022)			GCCCACCAAGCCCGCAGCGCC	0.701																																					p.P31S		Atlas-SNP	.											.	KIF26B	343	.	0			c.C91T						PASS	.						5.0	7.0	7.0					1																	245319611		1523	3110	4633	SO:0001583	missense	55083	exon2			ACCAAGCCCGCAG	AK001019	CCDS44342.1	1q44	2008-02-05			ENSG00000162849	ENSG00000162849		"""Kinesins"""	25484	protein-coding gene	gene with protein product		614026					Standard	NM_018012		Approved	FLJ10157	uc001ibf.1	Q2KJY2	OTTHUMG00000040079	ENST00000407071.2:c.91C>T	chr1.hg19:g.245319611C>T	ENSP00000385545:p.Pro31Ser	117.0	0.0	.		95.0	50.0	.	NM_018012	Q6ZQR9|Q6ZUZ0|Q8IUN3|Q8IVR1|Q9NWB4	Missense_Mutation	SNP	ENST00000407071.2	hg19	CCDS44342.1	.	.	.	.	.	.	.	.	.	.	C	10.02	1.236563	0.22711	.	.	ENSG00000162849	ENST00000407071	T	0.74315	-0.83	4.77	3.77	0.43336	.	.	.	.	.	T	0.47911	0.1471	N	0.04508	-0.205	0.80722	D	1	B	0.12630	0.006	B	0.10450	0.005	T	0.42068	-0.9473	9	0.15499	T	0.54	.	8.2256	0.31566	0.193:0.715:0.0:0.0919	.	31	Q2KJY2	KI26B_HUMAN	S	31	ENSP00000385545:P31S	ENSP00000385545:P31S	P	+	1	0	KIF26B	243386234	0.999000	0.42202	0.998000	0.56505	0.966000	0.64601	0.589000	0.23939	2.177000	0.69029	0.561000	0.74099	CCC	.	.	.	none		0.701	KIF26B-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381037.1	XM_371354	
LPIN1	23175	hgsc.bcm.edu	37	2	11924034	11924034	+	Silent	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:11924034G>A	ENST00000256720.2	+	8	1329	c.1236G>A	c.(1234-1236)ctG>ctA	p.L412L	LPIN1_ENST00000396098.1_Silent_p.L454L|LPIN1_ENST00000396099.1_Silent_p.L454L|LPIN1_ENST00000449576.2_Silent_p.L497L|LPIN1_ENST00000425416.2_Silent_p.L418L|LPIN1_ENST00000396097.1_Silent_p.L142L	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	412					cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		TGGCGGCCCTGTATTTTCCCA	0.423																																					p.L497L		Atlas-SNP	.											.	LPIN1	99	.	0			c.G1491A						PASS	.						169.0	173.0	172.0					2																	11924034		2203	4300	6503	SO:0001819	synonymous_variant	23175	exon10			GGCCCTGTATTTT	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1236G>A	chr2.hg19:g.11924034G>A		98.0	0.0	.		82.0	35.0	.	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	hg19	CCDS1682.1																																																																																			.	.	.	none		0.423	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
NRXN1	9378	hgsc.bcm.edu	37	2	51255154	51255154	+	Silent	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:51255154G>A	ENST00000406316.2	-	2	1734	c.258C>T	c.(256-258)ggC>ggT	p.G86G	NRXN1_ENST00000406859.3_Silent_p.G86G|NRXN1_ENST00000405472.3_Silent_p.G86G|NRXN1_ENST00000401669.2_Silent_p.G86G|NRXN1_ENST00000402717.3_Silent_p.G86G|NRXN1_ENST00000405581.1_Silent_p.G86G|NRXN1_ENST00000404971.1_Silent_p.G86G	NM_004801.4	NP_004792.1	Q9ULB1	NRX1A_HUMAN	neurexin 1	86	Laminin G-like 1. {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)			GCAGGCGGCCGCCGCGCGTCA	0.662																																					p.G86G		Atlas-SNP	.											.	NRXN1	1118	.	0			c.C258T						PASS	.						13.0	17.0	16.0					2																	51255154		1982	4144	6126	SO:0001819	synonymous_variant	9378	exon2			GCGGCCGCCGCGC	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.258C>T	chr2.hg19:g.51255154G>A		39.0	0.0	.		48.0	19.0	.	NM_004801	A7KRL9|O60323|Q53TJ9|Q53TQ1|Q9C079|Q9C080|Q9C081|Q9H3M2|Q9UDM6	Silent	SNP	ENST00000406316.2	hg19	CCDS54360.1																																																																																			.	.	.	none		0.662	NRXN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000325291.2		
WDPCP	51057	hgsc.bcm.edu	37	2	63380691	63380691	+	Missense_Mutation	SNP	C	C	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:63380691C>G	ENST00000272321.7	-	16	2624	c.2097G>C	c.(2095-2097)agG>agC	p.R699S	WDPCP_ENST00000398544.3_Missense_Mutation_p.R540S|WDPCP_ENST00000409199.1_Missense_Mutation_p.R507S|WDPCP_ENST00000409120.1_Missense_Mutation_p.R507S	NM_015910.5	NP_056994.3	O95876	FRITZ_HUMAN	WD repeat containing planar cell polarity effector	699					auditory receptor cell morphogenesis (GO:0002093)|camera-type eye development (GO:0043010)|cardiovascular system development (GO:0072358)|cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|digestive system development (GO:0055123)|embryonic digit morphogenesis (GO:0042733)|establishment of protein localization (GO:0045184)|glomerular visceral epithelial cell migration (GO:0090521)|kidney development (GO:0001822)|palate development (GO:0060021)|regulation of embryonic cell shape (GO:0016476)|regulation of establishment of cell polarity (GO:2000114)|regulation of fibroblast migration (GO:0010762)|regulation of focal adhesion assembly (GO:0051893)|regulation of protein localization (GO:0032880)|regulation of ruffle assembly (GO:1900027)|respiratory system development (GO:0060541)|septin cytoskeleton organization (GO:0032185)|smoothened signaling pathway (GO:0007224)	axonemal basal plate (GO:0097541)|axoneme (GO:0005930)|cytoskeleton (GO:0005856)|plasma membrane (GO:0005886)		p.R699S(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(9)|lung(19)|ovary(1)|skin(1)	35						CAAGTTCATTCCTTCTGTCAA	0.294																																					p.R699S		Atlas-SNP	.											WDPCP,NS,carcinoma,0,1	WDPCP	79	.	1	Substitution - Missense(1)	lung(1)	c.G2097C						PASS	.						86.0	80.0	82.0					2																	63380691		1798	4058	5856	SO:0001583	missense	51057	exon16			TTCATTCCTTCTG		CCDS42688.1, CCDS46301.1	2p15	2014-04-24	2011-02-01	2011-02-01	ENSG00000143951	ENSG00000143951			28027	protein-coding gene	gene with protein product		613580	"""chromosome 2 open reading frame 86"""	C2orf86		15654087, 20671153	Standard	NM_015910		Approved	hFrtz, fritz, BBS15	uc002sch.3	O95876	OTTHUMG00000152566	ENST00000272321.7:c.2097G>C	chr2.hg19:g.63380691C>G	ENSP00000272321:p.Arg699Ser	50.0	0.0	.		59.0	19.0	.	NM_015910	Q53RW4|Q7Z2Z3	Missense_Mutation	SNP	ENST00000272321.7	hg19	CCDS42688.1	.	.	.	.	.	.	.	.	.	.	C	0.015	-1.562941	0.00903	.	.	ENSG00000143951	ENST00000272321;ENST00000409199;ENST00000409120;ENST00000398544	T;T;T;T	0.72505	-0.66;-0.08;-0.08;-0.08	4.57	-3.39	0.04868	.	.	.	.	.	T	0.49115	0.1538	N	0.14661	0.345	0.09310	N	1	B;B	0.30281	0.18;0.275	B;B	0.25405	0.017;0.06	T	0.26744	-1.0094	9	0.62326	D	0.03	-0.5444	10.4749	0.44659	0.0:0.3924:0.0:0.6076	.	699;540	O95876;O95876-3	FRITZ_HUMAN;.	S	699;507;507;540	ENSP00000272321:R699S;ENSP00000386592:R507S;ENSP00000386769:R507S;ENSP00000381552:R540S	ENSP00000272321:R699S	R	-	3	2	WDPCP	63234195	0.007000	0.16637	0.001000	0.08648	0.161000	0.22273	-0.042000	0.12063	-1.185000	0.02716	-1.124000	0.02001	AGG	.	.	.	none		0.294	WDPCP-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326820.1	NM_015910	
ACTR1B	10120	hgsc.bcm.edu	37	2	98275931	98275931	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:98275931C>T	ENST00000289228.5	-	4	415	c.199G>A	c.(199-201)Ggg>Agg	p.G67R		NM_005735.3	NP_005726.1	P42025	ACTY_HUMAN	ARP1 actin-related protein 1 homolog B, centractin beta (yeast)	67					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dynactin complex (GO:0005869)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	ATP binding (GO:0005524)			endometrium(1)|large_intestine(5)|lung(7)|ovary(1)|skin(1)	15						GTCAGCAGCCCCCGGTGCTCC	0.652																																					p.G67R		Atlas-SNP	.											ACTR1B,colon,carcinoma,0,1	ACTR1B	34	.	0			c.G199A						PASS	.						152.0	150.0	151.0					2																	98275931		2203	4300	6503	SO:0001583	missense	10120	exon4			GCAGCCCCCGGTG	X82207	CCDS2033.1	2q11.1-q11.2	2008-05-20	2001-11-28		ENSG00000115073	ENSG00000115073			168	protein-coding gene	gene with protein product		605144	"""ARP1 (actin-related protein 1, yeast) homolog B (centractin beta)"""	CTRN2		7696711, 10343100	Standard	NM_005735		Approved		uc002syb.2	P42025	OTTHUMG00000130549	ENST00000289228.5:c.199G>A	chr2.hg19:g.98275931C>T	ENSP00000289228:p.Gly67Arg	45.0	0.0	.		34.0	12.0	.	NM_005735	D3DVH2|Q53SK5|Q9BRB7	Missense_Mutation	SNP	ENST00000289228.5	hg19	CCDS2033.1	.	.	.	.	.	.	.	.	.	.	.	33	5.207637	0.95033	.	.	ENSG00000115073	ENST00000289228	D	0.94650	-3.48	5.18	5.18	0.71444	.	0.062472	0.64402	D	0.000005	D	0.97763	0.9266	M	0.92026	3.265	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98725	1.0710	10	0.87932	D	0	.	16.1821	0.81915	0.0:1.0:0.0:0.0	.	67	P42025	ACTY_HUMAN	R	67	ENSP00000289228:G67R	ENSP00000289228:G67R	G	-	1	0	ACTR1B	97642363	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	7.795000	0.85887	2.427000	0.82271	0.555000	0.69702	GGG	.	.	.	none		0.652	ACTR1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252973.1	NM_005735	
MERTK	10461	hgsc.bcm.edu	37	2	112705128	112705128	+	Silent	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:112705128C>T	ENST00000295408.4	+	4	998	c.741C>T	c.(739-741)tcC>tcT	p.S247S	MERTK_ENST00000409780.1_Silent_p.S71S|MERTK_ENST00000421804.2_Silent_p.S247S			Q12866	MERTK_HUMAN	MER proto-oncogene, tyrosine kinase	247	Ig-like C2-type 2.			S -> G (in Ref. 1; AAB60430). {ECO:0000305}.	apoptotic cell clearance (GO:0043277)|blood coagulation (GO:0007596)|cell surface receptor signaling pathway (GO:0007166)|cell-cell signaling (GO:0007267)|leukocyte migration (GO:0050900)|natural killer cell differentiation (GO:0001779)|negative regulation of lymphocyte activation (GO:0051250)|peptidyl-tyrosine phosphorylation (GO:0018108)|phagocytosis (GO:0006909)|platelet activation (GO:0030168)|positive regulation of phagocytosis (GO:0050766)|protein kinase B signaling (GO:0043491)|protein phosphorylation (GO:0006468)|retina development in camera-type eye (GO:0060041)|secretion by cell (GO:0032940)|spermatogenesis (GO:0007283)|substrate adhesion-dependent cell spreading (GO:0034446)|vagina development (GO:0060068)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|rhabdomere (GO:0016028)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|endometrium(3)|kidney(2)|large_intestine(6)|liver(1)|lung(18)|pancreas(1)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(10)	46						AATCCCCCTCCGTGCTAACTG	0.507																																					p.S247S		Atlas-SNP	.											.	MERTK	112	.	0			c.C741T						PASS	.						51.0	54.0	53.0					2																	112705128		2203	4300	6503	SO:0001819	synonymous_variant	10461	exon4			CCCCTCCGTGCTA	U08023	CCDS2094.1	2q14.1	2014-06-26	2014-06-26		ENSG00000153208	ENSG00000153208		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	7027	protein-coding gene	gene with protein product		604705	"""c-mer proto-oncogene tyrosine kinase"""			8086340, 10343112	Standard	XM_005263565		Approved	mer, RP38	uc002thk.1	Q12866	OTTHUMG00000131278	ENST00000295408.4:c.741C>T	chr2.hg19:g.112705128C>T		112.0	0.0	.		131.0	50.0	.	NM_006343	Q9HBB4	Silent	SNP	ENST00000295408.4	hg19	CCDS2094.1																																																																																			.	.	.	none		0.507	MERTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254046.2		
STAM2	10254	hgsc.bcm.edu	37	2	152980339	152980339	+	Silent	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:152980339A>C	ENST00000263904.4	-	13	1639	c.1290T>G	c.(1288-1290)tcT>tcG	p.S430S		NM_005843.4	NP_005834.4	O75886	STAM2_HUMAN	signal transducing adaptor molecule (SH3 domain and ITAM motif) 2	430					endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)				endometrium(3)|large_intestine(4)|lung(8)|ovary(1)	16				BRCA - Breast invasive adenocarcinoma(221;0.22)		TTGGAGGCAGAGATCTCAGTG	0.408																																					p.S430S		Atlas-SNP	.											.	STAM2	44	.	0			c.T1290G						PASS	.						125.0	110.0	115.0					2																	152980339		2203	4300	6503	SO:0001819	synonymous_variant	10254	exon13			AGGCAGAGATCTC	AF042274	CCDS2196.1	2q23.3	2009-04-29			ENSG00000115145	ENSG00000115145			11358	protein-coding gene	gene with protein product	"""HSE1 homolog (S. cerevisiae)"""	606244				10899310, 10993906	Standard	NM_005843		Approved	Hbp	uc002tyc.4	O75886	OTTHUMG00000131885	ENST00000263904.4:c.1290T>G	chr2.hg19:g.152980339A>C		68.0	0.0	.		91.0	39.0	.	NM_005843	A8K8A0|D3DPA1|Q7LDQ0|Q9UF58	Silent	SNP	ENST00000263904.4	hg19	CCDS2196.1																																																																																			.	.	.	none		0.408	STAM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254835.2	NM_005843	
UPP2	151531	hgsc.bcm.edu	37	2	158978032	158978032	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:158978032A>G	ENST00000005756.4	+	5	760	c.566A>G	c.(565-567)gAc>gGc	p.D189G	UPP2_ENST00000460456.1_Intron|UPP2_ENST00000409859.4_Missense_Mutation_p.D246G|UPP2_ENST00000605860.1_Missense_Mutation_p.D246G	NM_173355.3	NP_775491.1	O95045	UPP2_HUMAN	uridine phosphorylase 2	189					nucleobase-containing small molecule metabolic process (GO:0055086)|nucleoside metabolic process (GO:0009116)|nucleotide catabolic process (GO:0009166)|pyrimidine nucleobase metabolic process (GO:0006206)|pyrimidine nucleoside catabolic process (GO:0046135)|pyrimidine nucleoside salvage (GO:0043097)|small molecule metabolic process (GO:0044281)|UMP salvage (GO:0044206)|uridine metabolic process (GO:0046108)	cytosol (GO:0005829)|type III intermediate filament (GO:0045098)	uridine phosphorylase activity (GO:0004850)			breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(5)|lung(11)|ovary(1)|prostate(2)|skin(1)|urinary_tract(1)	31					Fluorouracil(DB00544)	ACTGAACTGGACAAAGAACTG	0.423																																					p.D246G		Atlas-SNP	.											.	UPP2	60	.	0			c.A737G						PASS	.						183.0	178.0	180.0					2																	158978032		2203	4299	6502	SO:0001583	missense	151531	exon7			AACTGGACAAAGA	AY225131	CCDS2207.1, CCDS46435.1	2q24.2	2008-02-05			ENSG00000007001	ENSG00000007001			23061	protein-coding gene	gene with protein product						12849978	Standard	NM_173355		Approved	UPASE2, UP2, UDRPASE2	uc002tzo.3	O95045	OTTHUMG00000131969	ENST00000005756.4:c.566A>G	chr2.hg19:g.158978032A>G	ENSP00000005756:p.Asp189Gly	288.0	0.0	.		349.0	67.0	.	NM_001135098	B3KV87	Missense_Mutation	SNP	ENST00000005756.4	hg19	CCDS2207.1	.	.	.	.	.	.	.	.	.	.	A	14.27	2.486167	0.44147	.	.	ENSG00000007001	ENST00000409859;ENST00000005756	D;D	0.90732	-2.72;-2.72	5.75	4.53	0.55603	Nucleoside phosphorylase domain (1);	0.047805	0.85682	D	0.000000	D	0.95085	0.8408	M	0.88704	2.975	0.58432	D	0.999998	D	0.65815	0.995	D	0.66847	0.947	D	0.95272	0.8378	10	0.66056	D	0.02	.	10.8108	0.46547	0.8584:0.0:0.0:0.1416	.	189	O95045	UPP2_HUMAN	G	246;189	ENSP00000387230:D246G;ENSP00000005756:D189G	ENSP00000005756:D189G	D	+	2	0	UPP2	158686278	1.000000	0.71417	1.000000	0.80357	0.034000	0.12701	6.094000	0.71431	2.195000	0.70347	0.533000	0.62120	GAC	.	.	.	none		0.423	UPP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254929.2	NM_173355	
LY75	4065	hgsc.bcm.edu	37	2	160743016	160743016	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:160743016G>C	ENST00000263636.4	-	5	855	c.828C>G	c.(826-828)ttC>ttG	p.F276L	LY75_ENST00000553424.1_Missense_Mutation_p.F276L|LY75-CD302_ENST00000504764.1_Missense_Mutation_p.F276L|LY75-CD302_ENST00000505052.1_Missense_Mutation_p.F276L|LY75_ENST00000554112.1_Missense_Mutation_p.F276L	NM_002349.3	NP_002340.2	O60449	LY75_HUMAN	lymphocyte antigen 75	276	C-type lectin 1. {ECO:0000255|PROSITE- ProRule:PRU00040}.				endocytosis (GO:0006897)|immune response (GO:0006955)|inflammatory response (GO:0006954)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)	carbohydrate binding (GO:0030246)|receptor activity (GO:0004872)			NS(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(9)|lung(22)|prostate(7)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	59				COAD - Colon adenocarcinoma(177;0.132)		AACCAATCCAGAAAATCTTAG	0.338																																					p.F276L		Atlas-SNP	.											.	LY75	151	.	0			c.C828G						PASS	.						103.0	104.0	103.0					2																	160743016		2203	4300	6503	SO:0001583	missense	4065	exon5			AATCCAGAAAATC	AF011333	CCDS2211.1	2q24	2011-08-30			ENSG00000054219	ENSG00000054219		"""CD molecules"", ""C-type lectin domain containing"""	6729	protein-coding gene	gene with protein product		604524				9553150	Standard	NM_002349		Approved	DEC-205, CLEC13B, CD205		O60449	OTTHUMG00000132025	ENST00000263636.4:c.828C>G	chr2.hg19:g.160743016G>C	ENSP00000263636:p.Phe276Leu	21.0	0.0	.		30.0	16.0	.	NM_002349	O75913|Q53R46|Q53TF5|Q7Z575|Q7Z577	Missense_Mutation	SNP	ENST00000263636.4	hg19	CCDS2211.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418920	0.25552	.	.	ENSG00000054219;ENSG00000054219;ENSG00000054219;ENSG00000248672;ENSG00000248672	ENST00000554112;ENST00000553424;ENST00000263636;ENST00000504764;ENST00000505052	T;T;T;T;T	0.20069	2.1;2.1;2.1;2.1;2.1	5.77	3.95	0.45737	C-type lectin fold (1);C-type lectin-like (1);C-type lectin (3);	0.223549	0.22745	N	0.056144	T	0.12689	0.0308	L	0.33753	1.03	0.32662	N	0.517909	B;P;P	0.44309	0.259;0.832;0.763	B;B;B	0.42495	0.082;0.389;0.309	T	0.11616	-1.0580	10	0.02654	T	1	-9.0045	5.7022	0.17889	0.2339:0.1426:0.6235:0.0	.	276;276;276	O60449-3;O60449;O60449-2	.;LY75_HUMAN;.	L	276	ENSP00000451511:F276L;ENSP00000451446:F276L;ENSP00000263636:F276L;ENSP00000423463:F276L;ENSP00000421035:F276L	ENSP00000423463:F276L	F	-	3	2	LY75;LY75-CD302	160451262	1.000000	0.71417	0.993000	0.49108	0.856000	0.48823	0.890000	0.28295	0.755000	0.32990	0.557000	0.71058	TTC	.	.	.	none		0.338	LY75-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000255035.1		
SCN9A	6335	hgsc.bcm.edu	37	2	167142945	167142945	+	Silent	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:167142945C>T	ENST00000409435.1	-	10	1502	c.1503G>A	c.(1501-1503)tcG>tcA	p.S501S	AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000303354.6_Silent_p.S502S|SCN9A_ENST00000409672.1_Silent_p.S501S|SCN9A_ENST00000375387.4_Silent_p.S502S			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	501				S -> P (in Ref. 4; AAT85835). {ECO:0000305}.	behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)	p.S501S(1)		NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	ATTCTGATTTCGACAATTTCT	0.428																																					p.S501S		Atlas-SNP	.											SCN9A,NS,carcinoma,0,1	SCN9A	296	.	1	Substitution - coding silent(1)	prostate(1)	c.G1503A						PASS	.						170.0	161.0	164.0					2																	167142945		1910	4120	6030	SO:0001819	synonymous_variant	6335	exon11			TGATTTCGACAAT	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.1503G>A	chr2.hg19:g.167142945C>T		51.0	0.0	.		53.0	13.0	.	NM_002977	A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Silent	SNP	ENST00000409435.1	hg19	CCDS46441.1																																																																																			.	.	.	none		0.428	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
NYAP2	57624	hgsc.bcm.edu	37	2	226378138	226378138	+	Silent	SNP	T	T	C	rs373061629		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:226378138T>C	ENST00000272907.6	+	3	686	c.273T>C	c.(271-273)caT>caC	p.H91H	NYAP2_ENST00000409269.2_Intron	NM_020864.1	NP_065915.1	Q9P242	NYAP2_HUMAN	neuronal tyrosine-phosphorylated phosphoinositide-3-kinase adaptor 2	91					neuron projection morphogenesis (GO:0048812)|phosphatidylinositol 3-kinase signaling (GO:0014065)												TGGGCAAACATTTCCGCATGG	0.507																																					p.H91H		Atlas-SNP	.											.	.	.	.	0			c.T273C						PASS	.	T		0,4116		0,0,2058	79.0	83.0	82.0		273	-5.2	0.9	2		82	1,8379		0,1,4189	no	coding-synonymous	KIAA1486	NM_020864.1		0,1,6247	CC,CT,TT		0.0119,0.0,0.0080		91/654	226378138	1,12495	2058	4190	6248	SO:0001819	synonymous_variant	57624	exon3			CAAACATTTCCGC	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.273T>C	chr2.hg19:g.226378138T>C		116.0	0.0	.		117.0	52.0	.	NM_020864	A2RRN4|Q96NL2	Silent	SNP	ENST00000272907.6	hg19	CCDS46529.1																																																																																			.	.	.	weak		0.507	NYAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331258.1	NM_020864	
KCNJ13	3769	hgsc.bcm.edu	37	2	233633084	233633084	+	Silent	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:233633084T>C	ENST00000233826.3	-	3	1039	c.900A>G	c.(898-900)gcA>gcG	p.A300A	GIGYF2_ENST00000409480.1_Intron|GIGYF2_ENST00000452341.2_Intron|KCNJ13_ENST00000409779.1_3'UTR|GIGYF2_ENST00000409196.3_Intron|GIGYF2_ENST00000409451.3_Intron|GIGYF2_ENST00000373566.3_Intron|AC064852.4_ENST00000427571.1_RNA|GIGYF2_ENST00000373563.4_Intron|GIGYF2_ENST00000409547.1_Intron|KCNJ13_ENST00000410029.1_Silent_p.A300A	NM_002242.4	NP_002233.2	O60928	KCJ13_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 13	300					potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)	integral component of membrane (GO:0016021)	inward rectifier potassium channel activity (GO:0005242)			endometrium(3)|large_intestine(2)|lung(2)|stomach(1)|urinary_tract(1)	9		Breast(86;0.00279)|all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0306)|Lung NSC(271;0.0908)		Epithelial(121;5.9e-17)|BRCA - Breast invasive adenocarcinoma(100;0.000311)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(119;0.00942)|GBM - Glioblastoma multiforme(43;0.0617)		TCAACAGAGATGCAAAACAGT	0.428																																					p.A300A		Atlas-SNP	.											.	KCNJ13	18	.	0			c.A900G						PASS	.						167.0	160.0	163.0					2																	233633084		2203	4300	6503	SO:0001819	synonymous_variant	3769	exon3			CAGAGATGCAAAA	AJ006128	CCDS2498.1, CCDS54437.1	2q37	2014-01-28			ENSG00000115474	ENSG00000115474		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6259	protein-coding gene	gene with protein product		603208				9878260, 9620703, 16382105	Standard	NM_002242		Approved	Kir7.1, Kir1.4, LCA16	uc002vtp.3	O60928	OTTHUMG00000153292	ENST00000233826.3:c.900A>G	chr2.hg19:g.233633084T>C		131.0	0.0	.		145.0	65.0	.	NM_002242	A0PGH1|O76023|Q53SA1|Q8N3Y4	Silent	SNP	ENST00000233826.3	hg19	CCDS2498.1																																																																																			.	.	.	none		0.428	KCNJ13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257036.1	NM_002242	
TTC21A	199223	hgsc.bcm.edu	37	3	39175775	39175775	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:39175775G>T	ENST00000431162.2	+	21	2973	c.2839G>T	c.(2839-2841)Gcc>Tcc	p.A947S	TTC21A_ENST00000301819.6_Missense_Mutation_p.A948S|TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000440121.1_Missense_Mutation_p.A899S			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	947										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GCAGCACTGTGCCATCCTCCT	0.602																																					p.A947S		Atlas-SNP	.											.	TTC21A	96	.	0			c.G2839T						PASS	.						147.0	155.0	152.0					3																	39175775		2086	4219	6305	SO:0001583	missense	199223	exon21			CACTGTGCCATCC	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.2839G>T	chr3.hg19:g.39175775G>T	ENSP00000398211:p.Ala947Ser	83.0	0.0	.		81.0	36.0	.	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Missense_Mutation	SNP	ENST00000431162.2	hg19	CCDS46800.1	.	.	.	.	.	.	.	.	.	.	G	7.855	0.724787	0.15439	.	.	ENSG00000168026	ENST00000301819;ENST00000424305;ENST00000431162;ENST00000440121	T;T;T	0.36699	1.24;1.24;1.24	4.65	0.648	0.17801	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.519636	0.18015	N	0.154438	T	0.17408	0.0418	N	0.25992	0.78	0.09310	N	1	B;B;B;B	0.26775	0.159;0.003;0.002;0.001	B;B;B;B	0.24848	0.056;0.003;0.007;0.003	T	0.22977	-1.0201	10	0.08599	T	0.76	-4.3657	3.9914	0.09538	0.4069:0.0:0.4332:0.1599	.	68;899;948;947	B4DSJ5;Q8NDW8-6;Q8NDW8-7;Q8NDW8	.;.;.;TT21A_HUMAN	S	948;930;947;899	ENSP00000301819:A948S;ENSP00000398211:A947S;ENSP00000410882:A899S	ENSP00000301819:A948S	A	+	1	0	TTC21A	39150779	0.000000	0.05858	0.076000	0.20297	0.790000	0.44656	0.000000	0.12993	0.182000	0.20032	0.561000	0.74099	GCC	.	.	.	none		0.602	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
TGM4	7047	hgsc.bcm.edu	37	3	44943387	44943387	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:44943387G>A	ENST00000296125.4	+	8	1003	c.935G>A	c.(934-936)gGc>gAc	p.G312D	RP11-272D20.2_ENST00000427258.1_RNA	NM_003241.3	NP_003232.2	P49221	TGM4_HUMAN	transglutaminase 4	312					mating plug formation (GO:0042628)|peptide cross-linking (GO:0018149)	cytoplasm (GO:0005737)|extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)	metal ion binding (GO:0046872)|protein-glutamine gamma-glutamyltransferase activity (GO:0003810)			NS(1)|breast(1)|endometrium(2)|large_intestine(9)|lung(21)|ovary(2)|stomach(1)|upper_aerodigestive_tract(1)	38				BRCA - Breast invasive adenocarcinoma(193;0.00963)|KIRC - Kidney renal clear cell carcinoma(197;0.0546)|Kidney(197;0.0686)	L-Glutamine(DB00130)	AATGAGAATGGCGAGAAAATC	0.502																																					p.G312D		Atlas-SNP	.											.	TGM4	82	.	0			c.G935A						PASS	.						129.0	124.0	125.0					3																	44943387		2203	4300	6503	SO:0001583	missense	7047	exon8			AGAATGGCGAGAA	BC007003	CCDS2723.1	3p22-p21.33	2013-05-02	2013-05-02		ENSG00000163810	ENSG00000163810	2.3.2.13	"""Transglutaminases"""	11780	protein-coding gene	gene with protein product		600585	"""transglutaminase 4 (prostate)"""			7665178, 7916568	Standard	NM_003241		Approved	TGP	uc003coc.4	P49221	OTTHUMG00000133096	ENST00000296125.4:c.935G>A	chr3.hg19:g.44943387G>A	ENSP00000296125:p.Gly312Asp	70.0	0.0	.		74.0	28.0	.	NM_003241	Q16707|Q96QN4	Missense_Mutation	SNP	ENST00000296125.4	hg19	CCDS2723.1	.	.	.	.	.	.	.	.	.	.	G	10.68	1.418147	0.25552	.	.	ENSG00000163810	ENST00000296125	T	0.58652	0.32	2.99	2.09	0.27110	Transglutaminase-like (2);	0.000000	0.44902	U	0.000419	T	0.70219	0.3199	M	0.73217	2.22	0.09310	N	0.999999	D	0.69078	0.997	D	0.70016	0.967	T	0.61163	-0.7118	10	0.72032	D	0.01	.	10.0566	0.42248	0.1074:0.0:0.8926:0.0	.	312	P49221	TGM4_HUMAN	D	312	ENSP00000296125:G312D	ENSP00000296125:G312D	G	+	2	0	TGM4	44918391	0.008000	0.16893	0.002000	0.10522	0.018000	0.09664	0.567000	0.23608	0.541000	0.28827	0.563000	0.77884	GGC	.	.	.	none		0.502	TGM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256755.2	NM_003241	
EPHA6	285220	hgsc.bcm.edu	37	3	96706660	96706660	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:96706660G>T	ENST00000389672.5	+	3	975	c.937G>T	c.(937-939)Gat>Tat	p.D313Y	EPHA6_ENST00000470610.2_Missense_Mutation_p.D313Y|EPHA6_ENST00000542517.1_Missense_Mutation_p.D219Y	NM_001080448.2	NP_001073917.2	Q9UF33	EPHA6_HUMAN	EPH receptor A6	219						integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)	p.D219Y(2)|p.D219H(1)|p.D313Y(1)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(2)|lung(60)|ovary(3)|skin(11)|stomach(5)|upper_aerodigestive_tract(2)	101						CATGTTTCCTGATACCATTCC	0.478																																					p.D313Y		Atlas-SNP	.											EPHA6_ENST00000389672,rectum,carcinoma,-2,4	EPHA6	439	.	4	Substitution - Missense(4)	lung(3)|breast(1)	c.G937T						PASS	.						214.0	217.0	216.0					3																	96706660		1981	4178	6159	SO:0001583	missense	285220	exon3			TTTCCTGATACCA	AK092565	CCDS46876.1, CCDS54616.1, CCDS63697.1	3q12.1	2013-02-11	2004-10-28		ENSG00000080224	ENSG00000080224		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19296	protein-coding gene	gene with protein product		600066				12471243	Standard	NM_001080448		Approved	FLJ35246	uc010how.1	Q9UF33	OTTHUMG00000159208	ENST00000389672.5:c.937G>T	chr3.hg19:g.96706660G>T	ENSP00000374323:p.Asp313Tyr	75.0	0.0	.		74.0	32.0	.	NM_001080448	D6RAL5	Missense_Mutation	SNP	ENST00000389672.5	hg19	CCDS46876.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.4|22.4	4.282417|4.282417	0.80692|0.80692	.|.	.|.	ENSG00000080224|ENSG00000080224	ENST00000470610;ENST00000389672;ENST00000542517|ENST00000506569	T;T;T|.	0.75938|.	4.94;-0.98;4.4|.	5.47|5.47	5.47|5.47	0.80525|0.80525	.|.	0.150900|.	0.41097|.	U|.	0.000948|.	D|.	0.83524|.	0.5273|.	M|M	0.87456|0.87456	2.885|2.885	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.76071|.	0.987;0.982|.	D|.	0.85544|.	0.1217|.	10|.	0.87932|.	D|.	0|.	.|.	18.3228|18.3228	0.90244|0.90244	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	313;313|.	B3KS12;E7EU71|.	.;.|.	Y|L	313;313;219|257	ENSP00000420598:D313Y;ENSP00000374323:D313Y;ENSP00000439758:D219Y|.	ENSP00000374323:D313Y|.	D|X	+|+	1|2	0|2	EPHA6|EPHA6	98189350|98189350	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.869000|9.869000	0.99810|0.99810	2.549000|2.549000	0.85964|0.85964	0.650000|0.650000	0.86243|0.86243	GAT|TGA	.	.	.	none		0.478	EPHA6-002	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353845.3	NM_001080448	
MBD4	8930	hgsc.bcm.edu	37	3	129156116	129156116	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:129156116A>C	ENST00000249910.1	-	3	546	c.371T>G	c.(370-372)cTt>cGt	p.L124R	MBD4_ENST00000507208.1_Missense_Mutation_p.L124R|MBD4_ENST00000429544.2_Missense_Mutation_p.L124R|IFT122_ENST00000504021.1_5'Flank|IFT122_ENST00000507564.1_5'Flank|MBD4_ENST00000503197.1_Missense_Mutation_p.L124R|MBD4_ENST00000509587.1_Intron|IFT122_ENST00000347300.2_5'Flank|IFT122_ENST00000348417.2_5'Flank|IFT122_ENST00000431818.2_5'Flank|MBD4_ENST00000393278.2_Intron|IFT122_ENST00000349441.2_5'Flank|IFT122_ENST00000296266.3_5'Flank	NM_003925.1	NP_003916.1	O95243	MBD4_HUMAN	methyl-CpG binding domain protein 4	124	MBD. {ECO:0000255|PROSITE- ProRule:PRU00338}.				base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depyrimidination (GO:0045008)|DNA catabolic process, endonucleolytic (GO:0000737)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mitotic G2 DNA damage checkpoint (GO:0007095)|response to radiation (GO:0009314)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	endodeoxyribonuclease activity (GO:0004520)|pyrimidine-specific mismatch base pair DNA N-glycosylase activity (GO:0008263)|satellite DNA binding (GO:0003696)			NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(8)|ovary(2)|prostate(1)	22						ATAATTAGCAAGTGAACTTTT	0.338								Base excision repair (BER), DNA glycosylases																													p.L124R		Atlas-SNP	.											.	MBD4	53	.	0			c.T371G						PASS	.						45.0	47.0	46.0					3																	129156116		2202	4298	6500	SO:0001583	missense	8930	exon3			TTAGCAAGTGAAC	AF072250	CCDS3058.1, CCDS63766.1, CCDS63767.1, CCDS63768.1, CCDS63769.1	3q21.3	2004-03-02			ENSG00000129071	ENSG00000129071			6919	protein-coding gene	gene with protein product		603574				9774669, 10097147	Standard	NM_003925		Approved	MED1	uc003emh.2	O95243	OTTHUMG00000159463	ENST00000249910.1:c.371T>G	chr3.hg19:g.129156116A>C	ENSP00000249910:p.Leu124Arg	21.0	0.0	.		33.0	24.0	.	NM_003925	B4DZN2|D3DNC3|D3DNC4|E9PEE4|Q2MD36|Q7Z4T3|Q96F09	Missense_Mutation	SNP	ENST00000249910.1	hg19	CCDS3058.1	.	.	.	.	.	.	.	.	.	.	A	20.2	3.946829	0.73672	.	.	ENSG00000129071	ENST00000429544;ENST00000249910;ENST00000503197;ENST00000507208	D;D;D;D	0.97772	-4.53;-4.53;-4.53;-4.53	5.44	5.44	0.79542	Methyl-CpG DNA binding (4);DNA-binding, integrase-type (1);	0.141330	0.48286	D	0.000200	D	0.98880	0.9621	M	0.90198	3.095	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;0.999;0.999	D;D;D;D	0.87578	0.964;0.983;0.998;0.964	D	0.99780	1.1027	10	0.87932	D	0	-7.3728	15.2347	0.73419	1.0:0.0:0.0:0.0	.	124;124;124;124	E9PEE4;O95243-2;O95243-3;O95243	.;.;.;MBD4_HUMAN	R	124	ENSP00000394080:L124R;ENSP00000249910:L124R;ENSP00000424873:L124R;ENSP00000422327:L124R	ENSP00000249910:L124R	L	-	2	0	MBD4	130638806	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.294000	0.78760	2.090000	0.63153	0.529000	0.55759	CTT	.	.	.	none		0.338	MBD4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000355529.1	NM_003925	
B3GALNT1	8706	hgsc.bcm.edu	37	3	160803876	160803876	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:160803876G>T	ENST00000392781.2	-	8	1414	c.667C>A	c.(667-669)Cat>Aat	p.H223N	B3GALNT1_ENST00000417187.1_Intron|B3GALNT1_ENST00000320474.4_Missense_Mutation_p.H223N|B3GALNT1_ENST00000392780.1_Missense_Mutation_p.H223N|B3GALNT1_ENST00000392779.2_Missense_Mutation_p.H223N|B3GALNT1_ENST00000473285.1_Missense_Mutation_p.H223N|B3GALNT1_ENST00000488170.1_Missense_Mutation_p.H223N	NM_001038628.1	NP_001033717.1	O75752	B3GL1_HUMAN	beta-1,3-N-acetylgalactosaminyltransferase 1 (globoside blood group)	223					oligosaccharide biosynthetic process (GO:0009312)|protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	galactosylgalactosylglucosylceramide beta-D-acetylgalactosaminyltransferase activity (GO:0047273)|UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|large_intestine(4)|lung(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	13			LUSC - Lung squamous cell carcinoma(72;4.41e-05)|Lung(72;4.61e-05)			TAAGAAATATGGGTTTTTTGG	0.358																																					p.H223N		Atlas-SNP	.											.	B3GALNT1	34	.	0			c.C667A						PASS	.						36.0	38.0	37.0					3																	160803876		2201	4295	6496	SO:0001583	missense	8706	exon8			AAATATGGGTTTT	Y15062	CCDS3193.1	3q25	2014-07-18	2006-06-14	2006-05-09	ENSG00000169255	ENSG00000169255	2.4.1.79	"""Blood group antigens"", ""Beta 3-glycosyltransferases"""	918	protein-coding gene	gene with protein product	"""globoside synthase"", ""P antigen synthase"""	603094	"""UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 3 (Globoside blood group)"", ""UDP-GalNAc:betaGlcNAc beta 1,3-galactosaminyltransferase, polypeptide 1 (Globoside blood group)"""	B3GALT3		9582303, 10993897	Standard	XM_005247861		Approved	beta3Gal-T3, galT3, P1, GLOB	uc003fdv.3	O75752	OTTHUMG00000159064	ENST00000392781.2:c.667C>A	chr3.hg19:g.160803876G>T	ENSP00000376532:p.His223Asn	42.0	0.0	.		104.0	65.0	.	NM_001038628	D3DNM4|Q3Y531|Q6IAI5|Q8NFM8|Q8NFM9|Q9HA06	Missense_Mutation	SNP	ENST00000392781.2	hg19	CCDS3193.1	.	.	.	.	.	.	.	.	.	.	G	11.78	1.740650	0.30865	.	.	ENSG00000169255	ENST00000320474;ENST00000392779;ENST00000392780;ENST00000392781;ENST00000473285;ENST00000488170	T;T;T;T;T;T	0.41758	0.99;0.99;0.99;0.99;0.99;0.99	5.94	3.93	0.45458	.	0.169504	0.42420	D	0.000710	T	0.23572	0.0570	N	0.17474	0.49	0.42318	D	0.992247	P	0.48162	0.906	B	0.39562	0.303	T	0.04621	-1.0938	10	0.54805	T	0.06	.	7.1051	0.25358	0.2735:0.0:0.7265:0.0	.	223	O75752	B3GL1_HUMAN	N	223	ENSP00000323479:H223N;ENSP00000376530:H223N;ENSP00000376531:H223N;ENSP00000376532:H223N;ENSP00000418226:H223N;ENSP00000420163:H223N	ENSP00000323479:H223N	H	-	1	0	B3GALNT1	162286570	1.000000	0.71417	0.924000	0.36721	0.783000	0.44284	4.406000	0.59748	1.525000	0.49052	0.561000	0.74099	CAT	.	.	.	none		0.358	B3GALNT1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353125.1	NM_033167	
ALG3	10195	hgsc.bcm.edu	37	3	183957755	183957755	+	IGR	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:183957755G>A	ENST00000397676.3	-	0	1528				MIR1224_ENST00000408193.1_RNA|EIF2B5_ENST00000444495.1_Intron|VWA5B2_ENST00000426955.2_Missense_Mutation_p.A891T|ALG3_ENST00000463495.1_5'Flank|VWA5B2_ENST00000273794.5_Missense_Mutation_p.A673T	NM_005787.5	NP_005778.1	Q92685	ALG3_HUMAN	ALG3, alpha-1,3- mannosyltransferase						cellular protein metabolic process (GO:0044267)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|mannosylation (GO:0097502)|post-translational protein modification (GO:0043687)|protein glycosylation (GO:0006486)|protein N-linked glycosylation via asparagine (GO:0018279)	endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	alpha-1,3-mannosyltransferase activity (GO:0000033)|dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase activity (GO:0052925)			kidney(1)|large_intestine(1)|lung(6)|upper_aerodigestive_tract(1)	9	all_cancers(143;1.39e-10)|Ovarian(172;0.0339)		Epithelial(37;8.28e-34)|OV - Ovarian serous cystadenocarcinoma(80;2.72e-22)			TCGGCTGACAGCAGCCTCTGT	0.622																																					p.A891T		Atlas-SNP	.											.	VWA5B2	47	.	0			c.G2671A						PASS	.						13.0	18.0	17.0					3																	183957755		692	1587	2279	SO:0001628	intergenic_variant	90113	exon15			CTGACAGCAGCCT	BC002839	CCDS46967.1, CCDS46968.1	3q27.3	2013-02-26	2013-02-26		ENSG00000214160	ENSG00000214160	2.4.1.258	"""Dolichyl D-mannosyl phosphate dependent mannosyltransferases"""	23056	protein-coding gene	gene with protein product	"""carbohydrate deficient glycoprotein syndrome type IV"", ""dol-P-Man:Man(5)GlcNAc(2)-PP-Dol alpha-1,3-mannosyltransferase"", ""dol-P-Man dependent alpha-1,3- mannosyltransferase"""	608750	"""asparagine-linked glycosylation 3 homolog (yeast, alpha-1,3-mannosyltransferase)"", ""asparagine-linked glycosylation 3, alpha-1,3- mannosyltransferase homolog (S. cerevisiae)"""			1058125	Standard	NM_005787		Approved	NOT56L, Not56, CDGS4, D16Ertd36e	uc003fne.2	Q92685	OTTHUMG00000156823		chr3.hg19:g.183957755G>A		52.0	0.0	.		97.0	23.0	.	NM_138345	A8JZZ6|Q9BT71	Missense_Mutation	SNP	ENST00000397676.3	hg19	CCDS46968.1	.	.	.	.	.	.	.	.	.	.	G	28.0	4.880320	0.91740	.	.	ENSG00000145198	ENST00000426955;ENST00000273794	T;T	0.78816	-1.21;-1.21	5.14	5.14	0.70334	.	0.000000	0.53938	D	0.000044	D	0.86456	0.5937	L	0.56769	1.78	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.996;0.996;0.996	D	0.87135	0.2199	10	0.87932	D	0	-3.2673	18.1521	0.89677	0.0:0.0:1.0:0.0	.	673;891;902	E9PF42;B9EGN7;Q8N398	.;.;VW5B2_HUMAN	T	891;673	ENSP00000398688:A891T;ENSP00000273794:A673T	ENSP00000273794:A673T	A	+	1	0	VWA5B2	185440449	1.000000	0.71417	0.997000	0.53966	0.996000	0.88848	8.741000	0.91583	2.840000	0.97914	0.655000	0.94253	GCA	.	.	.	none		0.622	ALG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346033.1	NM_005787	
STX18	53407	hgsc.bcm.edu	37	4	4459185	4459185	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:4459185G>A	ENST00000306200.2	-	4	458	c.395C>T	c.(394-396)aCc>aTc	p.T132I	STX18_ENST00000505286.1_Missense_Mutation_p.T132I	NM_016930.2	NP_058626.1	Q9P2W9	STX18_HUMAN	syntaxin 18	132					ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)				large_intestine(1)|lung(3)|upper_aerodigestive_tract(1)	5				UCEC - Uterine corpus endometrioid carcinoma (64;0.0534)		CAAAACAGCGGTCCTGTGCTC	0.363																																					p.T132I		Atlas-SNP	.											.	STX18	16	.	0			c.C395T						PASS	.						78.0	78.0	78.0					4																	4459185		2203	4300	6503	SO:0001583	missense	53407	exon4			ACAGCGGTCCTGT	AB028741	CCDS3377.1	4p16.3-p16.2	2013-09-23			ENSG00000168818	ENSG00000168818			15942	protein-coding gene	gene with protein product		606046				10788491	Standard	NM_016930		Approved	Ufe1	uc003gic.3	Q9P2W9	OTTHUMG00000090331	ENST00000306200.2:c.395C>T	chr4.hg19:g.4459185G>A	ENSP00000305810:p.Thr132Ile	182.0	0.0	.		219.0	85.0	.	NM_016930	Q596L3|Q5TZP5	Missense_Mutation	SNP	ENST00000306200.2	hg19	CCDS3377.1	.	.	.	.	.	.	.	.	.	.	G	10.34	1.323926	0.24080	.	.	ENSG00000168818	ENST00000505286;ENST00000306200;ENST00000512195;ENST00000507908	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	4.97	0.964	0.19655	.	0.463921	0.24001	N	0.042479	T	0.44953	0.1318	M	0.61703	1.905	0.09310	N	1	B	0.17268	0.021	B	0.23018	0.043	T	0.46048	-0.9219	10	0.45353	T	0.12	-9.8899	13.7013	0.62611	0.0:0.1307:0.7212:0.1481	.	132	Q9P2W9	STX18_HUMAN	I	132;132;51;51	ENSP00000426648:T132I;ENSP00000305810:T132I;ENSP00000425483:T51I;ENSP00000422376:T51I	ENSP00000305810:T132I	T	-	2	0	STX18	4510086	0.117000	0.22190	0.182000	0.23118	0.960000	0.62799	0.441000	0.21611	0.225000	0.20959	0.655000	0.94253	ACC	.	.	.	none		0.363	STX18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206696.1		
EVC	2121	hgsc.bcm.edu	37	4	5755635	5755635	+	Missense_Mutation	SNP	C	C	T	rs372893834		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:5755635C>T	ENST00000264956.6	+	10	1623	c.1439C>T	c.(1438-1440)aCt>aTt	p.T480I	EVC_ENST00000509451.1_Missense_Mutation_p.T480I|EVC_ENST00000382674.2_Missense_Mutation_p.T480I	NM_153717.2	NP_714928.1	P57679	EVC_HUMAN	Ellis van Creveld syndrome	480					cartilage development (GO:0051216)|endochondral bone growth (GO:0003416)|muscle organ development (GO:0007517)|positive regulation of smoothened signaling pathway (GO:0045880)|skeletal system development (GO:0001501)|smoothened signaling pathway (GO:0007224)	ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|breast(1)|endometrium(2)|large_intestine(10)|lung(11)|ovary(1)|skin(1)|stomach(1)	28		Myeloproliferative disorder(84;0.117)				GCCCAGCCGACTGCTGACCCG	0.607																																					p.T480I		Atlas-SNP	.											.	EVC	90	.	0			c.C1439T						PASS	.						69.0	65.0	66.0					4																	5755635		2203	4300	6503	SO:0001583	missense	2121	exon10			AGCCGACTGCTGA	AF216184	CCDS3383.1	4p16	2008-07-03			ENSG00000072840	ENSG00000072840			3497	protein-coding gene	gene with protein product		604831				10700184	Standard	NM_153717		Approved	DWF-1	uc003gil.1	P57679	OTTHUMG00000090427	ENST00000264956.6:c.1439C>T	chr4.hg19:g.5755635C>T	ENSP00000264956:p.Thr480Ile	140.0	0.0	.		108.0	59.0	.	NM_153717		Missense_Mutation	SNP	ENST00000264956.6	hg19	CCDS3383.1	.	.	.	.	.	.	.	.	.	.	C	6.430	0.447423	0.12223	.	.	ENSG00000072840	ENST00000264956;ENST00000382674;ENST00000509451	T;T;T	0.52295	0.67;0.67;0.74	5.04	1.76	0.24704	.	1.042050	0.07485	N	0.904571	T	0.37320	0.0999	L	0.48362	1.52	0.09310	N	0.999999	B	0.20780	0.048	B	0.18561	0.022	T	0.28073	-1.0055	10	0.20046	T	0.44	.	5.4056	0.16320	0.1469:0.6168:0.1437:0.0925	.	480	P57679	EVC_HUMAN	I	480	ENSP00000264956:T480I;ENSP00000372120:T480I;ENSP00000426774:T480I	ENSP00000264956:T480I	T	+	2	0	EVC	5806536	0.000000	0.05858	0.001000	0.08648	0.010000	0.07245	-0.097000	0.11042	0.494000	0.27859	0.561000	0.74099	ACT	.	.	.	alt		0.607	EVC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206859.1		
SLIT2	9353	hgsc.bcm.edu	37	4	20493404	20493404	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:20493404C>A	ENST00000504154.1	+	9	1048	c.796C>A	c.(796-798)Cct>Act	p.P266T	SLIT2_ENST00000503837.1_Missense_Mutation_p.P270T|SLIT2_ENST00000503823.1_Missense_Mutation_p.P266T|SLIT2_ENST00000273739.5_Missense_Mutation_p.P270T	NM_004787.1	NP_004778.1	O94813	SLIT2_HUMAN	slit homolog 2 (Drosophila)	266	LRRNT 2.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|branching morphogenesis of an epithelial tube (GO:0048754)|cell migration involved in sprouting angiogenesis (GO:0002042)|cellular response to heparin (GO:0071504)|cellular response to hormone stimulus (GO:0032870)|chemorepulsion involved in postnatal olfactory bulb interneuron migration (GO:0021836)|corticospinal neuron axon guidance through spinal cord (GO:0021972)|dorsal/ventral axon guidance (GO:0033563)|in utero embryonic development (GO:0001701)|induction of negative chemotaxis (GO:0050929)|mammary duct terminal end bud growth (GO:0060763)|metanephros development (GO:0001656)|motor neuron axon guidance (GO:0008045)|negative chemotaxis (GO:0050919)|negative regulation of actin filament polymerization (GO:0030837)|negative regulation of axon extension (GO:0030517)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cellular response to growth factor stimulus (GO:0090288)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of gene expression (GO:0010629)|negative regulation of lamellipodium assembly (GO:0010593)|negative regulation of leukocyte chemotaxis (GO:0002689)|negative regulation of monocyte chemotaxis (GO:0090027)|negative regulation of mononuclear cell migration (GO:0071676)|negative regulation of neutrophil chemotaxis (GO:0090024)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of retinal ganglion cell axon guidance (GO:0090260)|negative regulation of small GTPase mediated signal transduction (GO:0051058)|negative regulation of smooth muscle cell chemotaxis (GO:0071672)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of vascular permeability (GO:0043116)|positive regulation of apoptotic process (GO:0043065)|positive regulation of axonogenesis (GO:0050772)|response to cortisol (GO:0051414)|retinal ganglion cell axon guidance (GO:0031290)|Roundabout signaling pathway (GO:0035385)|single organismal cell-cell adhesion (GO:0016337)|ureteric bud development (GO:0001657)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|chemorepellent activity (GO:0045499)|GTPase inhibitor activity (GO:0005095)|heparin binding (GO:0008201)|identical protein binding (GO:0042802)|laminin-1 binding (GO:0043237)|protein homodimerization activity (GO:0042803)|proteoglycan binding (GO:0043394)|Roundabout binding (GO:0048495)			NS(1)|breast(4)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(7)|large_intestine(17)|lung(60)|ovary(3)|pancreas(1)|prostate(2)|skin(10)|upper_aerodigestive_tract(1)	116						ATTTATGGCTCCTTCTTGTAG	0.408																																					p.P266T		Atlas-SNP	.											.,1	SLIT2	290	.	0			c.C796A						PASS	.						137.0	137.0	137.0					4																	20493404		2203	4300	6503	SO:0001583	missense	9353	exon9			ATGGCTCCTTCTT	AF055585	CCDS3426.1, CCDS75110.1, CCDS75111.1	4p15.2	2008-08-01	2001-11-28		ENSG00000145147	ENSG00000145147			11086	protein-coding gene	gene with protein product		603746	"""slit (Drosophila) homolog 2"""	SLIL3		9813312, 18269211	Standard	XM_005248211		Approved	Slit-2	uc003gpr.1	O94813	OTTHUMG00000128551	ENST00000504154.1:c.796C>A	chr4.hg19:g.20493404C>A	ENSP00000422591:p.Pro266Thr	53.0	0.0	.		65.0	32.0	.	NM_004787	B7ZLR5|O95710|Q17RU3|Q9Y5Q7	Missense_Mutation	SNP	ENST00000504154.1	hg19	CCDS3426.1	.	.	.	.	.	.	.	.	.	.	C	16.48	3.134469	0.56828	.	.	ENSG00000145147	ENST00000503823;ENST00000504154;ENST00000273739;ENST00000382173;ENST00000503837	T;T;T;T	0.81415	-1.48;-1.49;-1.36;-1.41	5.63	5.63	0.86233	.	0.149034	0.64402	D	0.000006	T	0.77618	0.4157	L	0.54323	1.7	0.45108	D	0.998129	B;B	0.11235	0.004;0.002	B;B	0.06405	0.002;0.002	T	0.71220	-0.4657	10	0.15066	T	0.55	.	20.0572	0.97657	0.0:1.0:0.0:0.0	.	266;266	O94813-3;O94813	.;SLIT2_HUMAN	T	266;266;270;270;270	ENSP00000427548:P266T;ENSP00000422591:P266T;ENSP00000273739:P270T;ENSP00000422261:P270T	ENSP00000273739:P270T	P	+	1	0	SLIT2	20102502	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	3.200000	0.51051	2.826000	0.97356	0.655000	0.94253	CCT	.	.	.	none		0.408	SLIT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250396.2		
APBB2	323	hgsc.bcm.edu	37	4	41015837	41015837	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:41015837T>A	ENST00000295974.8	-	6	1227	c.598A>T	c.(598-600)Atc>Ttc	p.I200F	APBB2_ENST00000508593.1_Missense_Mutation_p.I200F|APBB2_ENST00000506352.1_Missense_Mutation_p.I200F|APBB2_ENST00000513140.1_Missense_Mutation_p.I200F	NM_001166050.1|NM_004307.1	NP_001159522.1|NP_004298.1	Q92870	APBB2_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 2	200					axon guidance (GO:0007411)|cell cycle arrest (GO:0007050)|extracellular matrix organization (GO:0030198)|intracellular signal transduction (GO:0035556)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleus (GO:0005634)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|transcription factor binding (GO:0008134)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|skin(2)|urinary_tract(1)	34						TTCCCAATGATGGTGGAGGCC	0.557																																					p.I200F	Ovarian(3;20 75 16686 49997)	Atlas-SNP	.											.	APBB2	61	.	0			c.A598T						PASS	.						265.0	252.0	256.0					4																	41015837		1987	4158	6145	SO:0001583	missense	323	exon6			CAATGATGGTGGA	U62325	CCDS43224.1, CCDS54760.1, CCDS54761.1, CCDS54762.1	4p13	2011-10-10	2008-07-31		ENSG00000163697	ENSG00000163697			582	protein-coding gene	gene with protein product	"""Fe65-like"""	602710				8955346, 9585438	Standard	NM_173075		Approved	FE65L, FE65L1, MGC35575	uc003gvn.3	Q92870	OTTHUMG00000160416	ENST00000295974.8:c.598A>T	chr4.hg19:g.41015837T>A	ENSP00000295974:p.Ile200Phe	66.0	0.0	.		60.0	23.0	.	NM_173075	B4DSL4|E9PG87|Q8IUI6	Missense_Mutation	SNP	ENST00000295974.8	hg19	CCDS54761.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	4.898|4.898	0.166940|0.166940	0.09339|0.09339	.|.	.|.	ENSG00000163697|ENSG00000163697	ENST00000513611|ENST00000295974;ENST00000316212;ENST00000513140;ENST00000508593;ENST00000506352	.|T;T;T;T	.|0.25749	.|1.78;1.78;1.78;1.78	5.8|5.8	-2.84|-2.84	0.05751|0.05751	.|.	.|1.102730	.|0.06664	.|N	.|0.765002	T|T	0.17959|0.17959	0.0431|0.0431	N|N	0.14661|0.14661	0.345|0.345	0.09310|0.09310	N|N	1|1	.|B;B;B;B	.|0.21821	.|0.017;0.037;0.061;0.037	.|B;B;B;B	.|0.24006	.|0.046;0.023;0.05;0.023	T|T	0.33420|0.33420	-0.9869|-0.9869	5|10	.|0.56958	.|D	.|0.05	-3.9618|-3.9618	14.6774|14.6774	0.68989|0.68989	0.0:0.2997:0.0:0.7003|0.0:0.2997:0.0:0.7003	.|.	.|183;200;200;200	.|B4DJ88;E9PG87;Q92870-2;Q92870	.|.;.;.;APBB2_HUMAN	L|F	189|200;199;200;200;200	.|ENSP00000295974:I200F;ENSP00000426018:I200F;ENSP00000427211:I200F;ENSP00000421539:I200F	.|ENSP00000295974:I200F	H|I	-|-	2|1	0|0	APBB2|APBB2	40710594|40710594	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.057000|0.057000	0.15508|0.15508	-4.051000|-4.051000	0.00305|0.00305	-1.047000|-1.047000	0.03242|0.03242	-0.464000|-0.464000	0.05259|0.05259	CAT|ATC	.	.	.	none		0.557	APBB2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000360523.3	NM_173075	
RUFY3	22902	hgsc.bcm.edu	37	4	71639251	71639251	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:71639251G>T	ENST00000226328.4	+	6	1283	c.720G>T	c.(718-720)atG>atT	p.M240I	RUFY3_ENST00000502653.1_Missense_Mutation_p.M187I|RUFY3_ENST00000536664.1_Missense_Mutation_p.M224I|RUFY3_ENST00000417478.2_Missense_Mutation_p.M300I|RUFY3_ENST00000381006.3_Missense_Mutation_p.M240I	NM_014961.3	NP_055776.1	Q7L099	RUFY3_HUMAN	RUN and FYVE domain containing 3	240					negative regulation of axonogenesis (GO:0050771)	filopodium (GO:0030175)|growth cone (GO:0030426)				endometrium(1)|kidney(3)|large_intestine(4)|lung(6)|prostate(1)|stomach(1)	16		all_hematologic(202;0.248)	Lung(101;0.235)			ATTTTTCAATGTATCTCAAGG	0.343																																					p.M300I		Atlas-SNP	.											.	RUFY3	61	.	0			c.G900T						PASS	.						74.0	77.0	76.0					4																	71639251		2203	4299	6502	SO:0001583	missense	22902	exon6			TTCAATGTATCTC	AF112221	CCDS3547.1, CCDS34001.1, CCDS47068.1, CCDS75138.1	4q13.3	2009-05-29			ENSG00000018189	ENSG00000018189		"""Zinc fingers, FYVE domain containing"""	30285	protein-coding gene	gene with protein product	"""single axon-related 1"""	611194				17439943	Standard	NM_001130709		Approved	RIPx, KIAA0871, Singar1	uc003hfr.3	Q7L099	OTTHUMG00000129910	ENST00000226328.4:c.720G>T	chr4.hg19:g.71639251G>T	ENSP00000226328:p.Met240Ile	204.0	0.0	.		176.0	69.0	.	NM_001130709	B3KM25|B4DYW7|D9N163|O94948|Q9UI00	Missense_Mutation	SNP	ENST00000226328.4	hg19	CCDS3547.1	.	.	.	.	.	.	.	.	.	.	G	20.3	3.971077	0.74246	.	.	ENSG00000018189	ENST00000417478;ENST00000381006;ENST00000226328;ENST00000536664;ENST00000513597;ENST00000502653	T;T;T;T;T;T	0.21361	2.71;3.1;2.74;2.74;2.01;3.1	5.62	5.62	0.85841	.	0.000000	0.85682	D	0.000000	T	0.41373	0.1156	L	0.55834	1.745	0.80722	D	1	B;B;P;B	0.45126	0.123;0.335;0.851;0.057	B;B;P;B	0.58391	0.041;0.19;0.838;0.032	T	0.01920	-1.1247	10	0.40728	T	0.16	-25.3268	19.6602	0.95864	0.0:0.0:1.0:0.0	.	224;240;240;300	B4DKC2;Q7L099-3;Q7L099;Q7L099-2	.;.;RUFY3_HUMAN;.	I	300;240;240;224;176;187	ENSP00000399771:M300I;ENSP00000370394:M240I;ENSP00000226328:M240I;ENSP00000443652:M224I;ENSP00000425574:M176I;ENSP00000425400:M187I	ENSP00000226328:M240I	M	+	3	0	RUFY3	71858115	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	9.390000	0.97246	2.638000	0.89438	0.460000	0.39030	ATG	.	.	.	none		0.343	RUFY3-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252161.2	NM_014961	
SLC4A4	8671	hgsc.bcm.edu	37	4	72222802	72222802	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:72222802C>T	ENST00000264485.5	+	6	745	c.628C>T	c.(628-630)Cgg>Tgg	p.R210W	SLC4A4_ENST00000514331.1_3'UTR|SLC4A4_ENST00000340595.3_Missense_Mutation_p.R166W|SLC4A4_ENST00000425175.1_Missense_Mutation_p.R210W|SLC4A4_ENST00000351898.6_Missense_Mutation_p.R210W|SLC4A4_ENST00000512686.1_Missense_Mutation_p.R166W	NM_001098484.2	NP_001091954.1	Q9Y6R1	S4A4_HUMAN	solute carrier family 4 (sodium bicarbonate cotransporter), member 4	210					bicarbonate transport (GO:0015701)|ion transport (GO:0006811)|sodium ion transmembrane transport (GO:0035725)|transmembrane transport (GO:0055085)|transport (GO:0006810)	basolateral plasma membrane (GO:0016323)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inorganic anion exchanger activity (GO:0005452)|sodium:bicarbonate symporter activity (GO:0008510)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(9)|liver(1)|lung(21)|ovary(3)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(1)	58			Lung(101;0.0739)|LUSC - Lung squamous cell carcinoma(112;0.225)		Sodium bicarbonate(DB01390)	TACTTTGCTCCGGAAGCACCG	0.443																																					p.R210W		Atlas-SNP	.											.	SLC4A4	269	.	0			c.C628T						PASS	.						134.0	135.0	134.0					4																	72222802		2203	4300	6503	SO:0001583	missense	8671	exon6			TTGCTCCGGAAGC	AF007216	CCDS3549.1, CCDS43236.1, CCDS47071.1	4q13.3	2013-07-19	2013-07-19		ENSG00000080493	ENSG00000080493		"""Solute carriers"""	11030	protein-coding gene	gene with protein product		603345	"""solute carrier family 4, sodium bicarbonate cotransporter, member 4"""	SLC4A5		9235899, 9651366	Standard	NM_001098484		Approved	NBC1, HNBC1, NBC2, pNBC, hhNMC	uc010iic.3	Q9Y6R1	OTTHUMG00000129907	ENST00000264485.5:c.628C>T	chr4.hg19:g.72222802C>T	ENSP00000264485:p.Arg210Trp	58.0	0.0	.		76.0	23.0	.	NM_001098484	C4B714|O15153|Q8NEJ2|Q9H262|Q9NRZ1|Q9UIC0|Q9UIC1|Q9UP50	Missense_Mutation	SNP	ENST00000264485.5	hg19	CCDS43236.1	.	.	.	.	.	.	.	.	.	.	C	21.7	4.185700	0.78789	.	.	ENSG00000080493	ENST00000264485;ENST00000425175;ENST00000351898;ENST00000512686;ENST00000340595	T;T;T;T;T	0.68765	-0.35;-0.35;-0.35;-0.35;-0.35	5.84	5.84	0.93424	Bicarbonate transporter, cytoplasmic (2);Phosphotransferase/anion transporter (1);	0.000000	0.85682	D	0.000000	D	0.84220	0.5424	M	0.89534	3.04	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	1.0;0.997;1.0;1.0;0.995;1.0	D	0.86729	0.1947	10	0.87932	D	0	.	13.0889	0.59156	0.2651:0.7349:0.0:0.0	.	210;210;166;166;190;210	A5JJ20;Q9Y6R1-4;Q9Y6R1-2;Q9Y6R1-3;Q9Y6R3;Q9Y6R1	.;.;.;.;.;S4A4_HUMAN	W	210;210;210;166;166	ENSP00000264485:R210W;ENSP00000393557:R210W;ENSP00000307349:R210W;ENSP00000422400:R166W;ENSP00000344272:R166W	ENSP00000264485:R210W	R	+	1	2	SLC4A4	72441666	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.075000	0.41538	2.751000	0.94390	0.655000	0.94253	CGG	.	.	.	none		0.443	SLC4A4-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362090.1	NM_003759	
ARHGAP10	79658	hgsc.bcm.edu	37	4	148800473	148800473	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:148800473G>C	ENST00000336498.3	+	9	1162	c.923G>C	c.(922-924)aGa>aCa	p.R308T	ARHGAP10_ENST00000414545.2_5'Flank	NM_024605.3	NP_078881.3	Q5T5U3	RHG21_HUMAN	Rho GTPase activating protein 10	0					establishment of Golgi localization (GO:0051683)|Golgi organization (GO:0007030)|maintenance of Golgi location (GO:0051684)|organelle transport along microtubule (GO:0072384)|signal transduction (GO:0007165)	cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTPase activator activity (GO:0005096)			autonomic_ganglia(2)|endometrium(5)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(1)|pancreas(1)|prostate(1)|skin(2)	33	all_hematologic(180;0.151)	Renal(17;0.0166)		GBM - Glioblastoma multiforme(119;0.0423)		TTTGAGCACAGATCTGGAGGG	0.373																																					p.R308T		Atlas-SNP	.											.	ARHGAP10	92	.	0			c.G923C						PASS	.						134.0	125.0	128.0					4																	148800473		2203	4300	6503	SO:0001583	missense	79658	exon9			AGCACAGATCTGG	BC047914	CCDS34075.1	4q31.23	2013-09-20			ENSG00000071205	ENSG00000071205		"""Rho GTPase activating proteins"""	26099	protein-coding gene	gene with protein product		609746				8288572	Standard	NM_024605		Approved	FLJ20896, FLJ41791, GRAF2	uc003ilf.3	A1A4S6	OTTHUMG00000161460	ENST00000336498.3:c.923G>C	chr4.hg19:g.148800473G>C	ENSP00000336923:p.Arg308Thr	68.0	0.0	.		82.0	26.0	.	NM_024605	Q0VF98|Q7Z3P7|Q8N3A2|Q8NI19|Q8TBV5|Q9P2C3	Missense_Mutation	SNP	ENST00000336498.3	hg19	CCDS34075.1	.	.	.	.	.	.	.	.	.	.	G	17.19	3.327682	0.60743	.	.	ENSG00000071205	ENST00000336498	T	0.42513	0.97	5.1	5.1	0.69264	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.85682	D	0.000000	T	0.44705	0.1306	L	0.27053	0.805	0.80722	D	1	D	0.63880	0.993	P	0.52957	0.714	T	0.39272	-0.9622	10	0.45353	T	0.12	.	18.1426	0.89644	0.0:0.0:1.0:0.0	.	308	A1A4S6	RHG10_HUMAN	T	308	ENSP00000336923:R308T	ENSP00000336923:R308T	R	+	2	0	ARHGAP10	149019923	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.116000	0.57871	2.378000	0.81104	0.561000	0.74099	AGA	.	.	.	none		0.373	ARHGAP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365005.1	NM_024605	
ETFDH	2110	hgsc.bcm.edu	37	4	159629584	159629584	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr4:159629584G>T	ENST00000511912.1	+	13	2091	c.1759G>T	c.(1759-1761)Gta>Tta	p.V587L	ETFDH_ENST00000307738.5_Missense_Mutation_p.V540L	NM_001281738.1|NM_004453.2	NP_001268667.1|NP_004444.2	Q16134	ETFD_HUMAN	electron-transferring-flavoprotein dehydrogenase	587	4Fe-4S ferredoxin-type. {ECO:0000255|PROSITE-ProRule:PRU00711}.				cellular metabolic process (GO:0044237)|electron transport chain (GO:0022900)|fatty acid beta-oxidation using acyl-CoA dehydrogenase (GO:0033539)|respiratory electron transport chain (GO:0022904)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)	integral component of mitochondrial inner membrane (GO:0031305)|mitochondrial matrix (GO:0005759)|mitochondrial membrane (GO:0031966)	4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|electron-transferring-flavoprotein dehydrogenase activity (GO:0004174)|flavin adenine dinucleotide binding (GO:0050660)|metal ion binding (GO:0046872)|oxidoreductase activity (GO:0016491)|oxidoreductase activity, oxidizing metal ions with flavin as acceptor (GO:0043783)|quinone binding (GO:0048038)|ubiquinone binding (GO:0048039)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(13)|prostate(1)|skin(3)	28	all_hematologic(180;0.24)	Renal(120;0.0458)		COAD - Colon adenocarcinoma(41;0.0172)		TCAGAACTGTGTACATTGTAA	0.363																																					p.V587L		Atlas-SNP	.											.	ETFDH	57	.	0			c.G1759T						PASS	.						115.0	112.0	113.0					4																	159629584		2203	4300	6503	SO:0001583	missense	2110	exon13			AACTGTGTACATT	S69232	CCDS3800.1, CCDS64090.1	4q32-q35	2008-08-26			ENSG00000171503	ENSG00000171503			3483	protein-coding gene	gene with protein product		231675					Standard	NM_004453		Approved	ETFQO	uc003iqb.3	Q16134	OTTHUMG00000161684	ENST00000511912.1:c.1759G>T	chr4.hg19:g.159629584G>T	ENSP00000426638:p.Val587Leu	90.0	0.0	.		81.0	34.0	.	NM_004453	B4E3R9|J3KND9|Q7Z347	Missense_Mutation	SNP	ENST00000511912.1	hg19	CCDS3800.1	.	.	.	.	.	.	.	.	.	.	G	19.84	3.902545	0.72754	.	.	ENSG00000171503	ENST00000511912;ENST00000307738	D;D	0.93763	-3.28;-3.28	6.05	5.21	0.72293	4Fe-4S ferredoxin, iron-sulpur binding domain (1);	0.000000	0.85682	D	0.000000	D	0.89143	0.6631	L	0.31804	0.96	0.58432	D	0.999998	B;B;B	0.34264	0.064;0.111;0.446	B;B;B	0.33890	0.122;0.122;0.172	D	0.88267	0.2927	10	0.49607	T	0.09	-21.6302	15.2075	0.73190	0.067:0.0:0.933:0.0	.	540;526;587	B4E3R9;B4DEQ0;Q16134	.;.;ETFD_HUMAN	L	587;540	ENSP00000426638:V587L;ENSP00000303552:V540L	ENSP00000303552:V540L	V	+	1	0	ETFDH	159849034	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	9.864000	0.99589	1.568000	0.49683	0.650000	0.86243	GTA	.	.	.	none		0.363	ETFDH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000365718.2		
PCDHA9	9752	hgsc.bcm.edu	37	5	140230427	140230427	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:140230427A>G	ENST00000532602.1	+	1	3380	c.2347A>G	c.(2347-2349)Aca>Gca	p.T783A	PCDHA7_ENST00000525929.1_Intron|PCDHA9_ENST00000378122.3_Missense_Mutation_p.T783A|PCDHA2_ENST00000526136.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA8_ENST00000531613.1_Intron|PCDHA3_ENST00000522353.2_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA6_ENST00000527624.1_Intron	NM_031857.1	NP_114063.1	Q9Y5H5	PCDA9_HUMAN	protocadherin alpha 9	783	5 X 4 AA repeats of P-X-X-P.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(17)|lung(18)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	59			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TGCTGGATCTACAGAGCGAAC	0.483																																					p.T783A	Melanoma(55;1800 1972 14909)	Atlas-SNP	.											.	PCDHA9	373	.	0			c.A2347G						PASS	.						70.0	74.0	72.0					5																	140230427		2197	4272	6469	SO:0001583	missense	9752	exon1			GGATCTACAGAGC	AF152487	CCDS54920.1	5q31	2010-11-26				ENSG00000204961		"""Cadherins / Protocadherins : Clustered"""	8675	other	complex locus constituent	"""KIAA0345-like 5"""	606315				10380929	Standard	NM_031857		Approved	KIAA0345, PCDH-ALPHA9		Q9Y5H5		ENST00000532602.1:c.2347A>G	chr5.hg19:g.140230427A>G	ENSP00000436042:p.Thr783Ala	208.0	0.0	.		182.0	149.0	.	NM_031857	O15053|Q2M3S5	Missense_Mutation	SNP	ENST00000532602.1	hg19	CCDS54920.1	.	.	.	.	.	.	.	.	.	.	A	1.760	-0.487128	0.04352	.	.	ENSG00000204961	ENST00000532602;ENST00000378122	T;T	0.10860	2.83;2.83	4.24	0.115	0.14643	.	4.198160	0.02428	U	0.083234	T	0.04137	0.0115	N	0.03000	-0.44	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.33137	-0.9880	10	0.07482	T	0.82	.	4.5943	0.12322	0.3795:0.1576:0.4629:0.0	.	783;783	Q9Y5H5;Q9Y5H5-2	PCDA9_HUMAN;.	A	783	ENSP00000436042:T783A;ENSP00000367362:T783A	ENSP00000367362:T783A	T	+	1	0	PCDHA9	140210611	0.000000	0.05858	0.003000	0.11579	0.269000	0.26545	-0.159000	0.10056	0.004000	0.14682	-0.415000	0.06103	ACA	.	.	.	none		0.483	PCDHA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372896.2	NM_031857	
PCDHGC4	56098	hgsc.bcm.edu	37	5	140865167	140865167	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:140865167G>A	ENST00000306593.1	+	1	427	c.427G>A	c.(427-429)Ggg>Agg	p.G143R	PCDHGA11_ENST00000518882.1_Intron|PCDHGB7_ENST00000398594.2_Intron|PCDHGA9_ENST00000573521.1_Intron|PCDHGB6_ENST00000520790.1_Intron|PCDHGA12_ENST00000252085.3_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA11_ENST00000398587.2_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA10_ENST00000398610.2_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGC3_ENST00000308177.3_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018928.2|NM_032406.1	NP_061751.1|NP_115782.1	Q9Y5F7	PCDGL_HUMAN	protocadherin gamma subfamily C, 4	143	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(13)|lung(13)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	42			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CTTGGAAATTGGGGAGGCAGC	0.542																																					p.G143R		Atlas-SNP	.											.	PCDHGC4	91	.	0			c.G427A						PASS	.						62.0	66.0	65.0					5																	140865167		2203	4300	6503	SO:0001583	missense	56098	exon1			GAAATTGGGGAGG	AF152525	CCDS4262.1, CCDS75349.1	5q31	2010-01-26			ENSG00000242419	ENSG00000242419		"""Cadherins / Protocadherins : Clustered"""	8717	other	protocadherin		606305				10380929	Standard	NM_018928		Approved	PCDH-GAMMA-C4		Q9Y5F7	OTTHUMG00000129625	ENST00000306593.1:c.427G>A	chr5.hg19:g.140865167G>A	ENSP00000306918:p.Gly143Arg	49.0	0.0	.		43.0	16.0	.	NM_018928	Q495T2|Q9Y5C3	Missense_Mutation	SNP	ENST00000306593.1	hg19	CCDS4262.1	.	.	.	.	.	.	.	.	.	.	G	15.02	2.710368	0.48517	.	.	ENSG00000242419	ENST00000306593	T	0.49432	0.78	5.0	4.12	0.48240	Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.35711	0.0941	N	0.11341	0.13	0.09310	N	1	D;P	0.54207	0.965;0.951	P;P	0.50659	0.514;0.647	T	0.08066	-1.0740	9	0.27082	T	0.32	.	9.464	0.38802	0.2253:0.0:0.7747:0.0	.	143;143	Q9Y5F7-2;Q9Y5F7	.;PCDGL_HUMAN	R	143	ENSP00000306918:G143R	ENSP00000306918:G143R	G	+	1	0	PCDHGC4	140845351	0.000000	0.05858	1.000000	0.80357	0.991000	0.79684	0.335000	0.19806	1.305000	0.44909	0.561000	0.74099	GGG	.	.	.	none		0.542	PCDHGC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251820.1	NM_018928	
GABRP	2568	hgsc.bcm.edu	37	5	170235705	170235705	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:170235705T>G	ENST00000518525.1	+	9	1245	c.781T>G	c.(781-783)Tgg>Ggg	p.W261G	GABRP_ENST00000519598.1_Missense_Mutation_p.W261G|GABRP_ENST00000519385.1_Missense_Mutation_p.W261G|GABRP_ENST00000265294.4_Missense_Mutation_p.W261G			O00591	GBRP_HUMAN	gamma-aminobutyric acid (GABA) A receptor, pi	261					signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(5)|large_intestine(4)|lung(11)|prostate(1)|skin(3)|upper_aerodigestive_tract(2)	29	Renal(175;0.000159)|Lung NSC(126;0.0122)|all_lung(126;0.0193)	Medulloblastoma(196;0.0109)|all_neural(177;0.0298)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)		Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGTGTTGTCCTGGGTTTCATT	0.428																																					p.W261G		Atlas-SNP	.											.	GABRP	65	.	0			c.T781G						PASS	.						236.0	212.0	220.0					5																	170235705		2203	4300	6503	SO:0001583	missense	2568	exon8			TTGTCCTGGGTTT	U95367	CCDS4375.1, CCDS75368.1	5q35.1	2012-06-22			ENSG00000094755	ENSG00000094755		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4089	protein-coding gene	gene with protein product	"""GABA(A) receptor, pi"""	602729				9182563	Standard	NM_014211		Approved		uc003mau.3	O00591	OTTHUMG00000130443	ENST00000518525.1:c.781T>G	chr5.hg19:g.170235705T>G	ENSP00000430100:p.Trp261Gly	44.0	0.0	.		49.0	23.0	.	NM_014211	A8KA36|D3DQL2|Q32MJ1	Missense_Mutation	SNP	ENST00000518525.1	hg19	CCDS4375.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.193383	0.78902	.	.	ENSG00000094755	ENST00000518525;ENST00000539175;ENST00000265294;ENST00000519385;ENST00000519598	D;D;D;D	0.83755	-1.76;-1.76;-1.76;-1.76	4.94	4.94	0.65067	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.217481	0.51477	D	0.000081	D	0.92325	0.7565	M	0.90082	3.085	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	0.998;1.0	D	0.93898	0.7186	10	0.87932	D	0	.	14.5722	0.68218	0.0:0.0:0.0:1.0	.	261;261	E7EWG0;O00591	.;GBRP_HUMAN	G	261;159;261;261;261	ENSP00000430100:W261G;ENSP00000265294:W261G;ENSP00000430727:W261G;ENSP00000430772:W261G	ENSP00000265294:W261G	W	+	1	0	GABRP	170168283	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.924000	0.87555	1.970000	0.57323	0.533000	0.62120	TGG	.	.	.	none		0.428	GABRP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252834.3	NM_014211	
PFN3	345456	hgsc.bcm.edu	37	5	176827428	176827428	+	Silent	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:176827428C>T	ENST00000358571.2	-	1	209	c.150G>A	c.(148-150)gtG>gtA	p.V50V	F12_ENST00000514943.1_5'Flank	NM_001029886.2	NP_001025057.1	P60673	PROF3_HUMAN	profilin 3	50					actin cytoskeleton organization (GO:0030036)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	lipid binding (GO:0008289)			lung(1)	1	all_cancers(89;2.04e-05)|Renal(175;0.000269)|Lung NSC(126;0.000832)|all_lung(126;0.00152)	all_neural(177;0.00409)|Medulloblastoma(196;0.00498)|all_hematologic(541;0.21)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			GCCCCGTGAGCACGCCCACCT	0.741																																					p.V50V		Atlas-SNP	.											.	PFN3	4	.	0			c.G150A						PASS	.						4.0	5.0	5.0					5																	176827428		1993	3872	5865	SO:0001819	synonymous_variant	345456	exon1			CGTGAGCACGCCC	AC090063	CCDS34301.1	5q35.2	2008-08-26			ENSG00000196570	ENSG00000196570			18627	protein-coding gene	gene with protein product		612812				11867228	Standard	NM_001029886		Approved		uc003mgl.2	P60673	OTTHUMG00000163408	ENST00000358571.2:c.150G>A	chr5.hg19:g.176827428C>T		23.0	0.0	.		17.0	6.0	.	NM_001029886	A2RUL3	Silent	SNP	ENST00000358571.2	hg19	CCDS34301.1																																																																																			.	.	.	none		0.741	PFN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373234.1	NM_001029886	
DSP	1832	hgsc.bcm.edu	37	6	7542208	7542208	+	Silent	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:7542208C>T	ENST00000379802.3	+	1	401	c.60C>T	c.(58-60)gcC>gcT	p.A20A	DSP_ENST00000418664.2_Silent_p.A20A|RP3-512B11.3_ENST00000561592.1_RNA	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	20	Globular 1.|Interacts with plakophilin 1 and junction plakoglobin.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		TGATCCGCGCCGAGTCTGGCC	0.682																																					p.A20A		Atlas-SNP	.											.	DSP	306	.	0			c.C60T						PASS	.						11.0	13.0	12.0					6																	7542208		2191	4284	6475	SO:0001819	synonymous_variant	1832	exon1			CCGCGCCGAGTCT	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.60C>T	chr6.hg19:g.7542208C>T		170.0	0.0	.		148.0	71.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Silent	SNP	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.682	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
DSP	1832	hgsc.bcm.edu	37	6	7584627	7584627	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:7584627A>T	ENST00000379802.3	+	24	7473	c.7132A>T	c.(7132-7134)Att>Ttt	p.I2378F	DSP_ENST00000418664.2_Missense_Mutation_p.I1779F	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2378	4.5 X 38 AA tandem repeats (Domain B).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CGGGGGGATCATTGACCCAAA	0.448																																					p.I2378F		Atlas-SNP	.											.	DSP	306	.	0			c.A7132T						PASS	.						76.0	75.0	75.0					6																	7584627		2203	4300	6503	SO:0001583	missense	1832	exon24			GGGATCATTGACC	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	ENST00000379802.3:c.7132A>T	chr6.hg19:g.7584627A>T	ENSP00000369129:p.Ile2378Phe	73.0	0.0	.		77.0	34.0	.	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Missense_Mutation	SNP	ENST00000379802.3	hg19	CCDS4501.1	.	.	.	.	.	.	.	.	.	.	A	20.4	3.991459	0.74703	.	.	ENSG00000096696	ENST00000379802;ENST00000418664	T;T	0.79749	-1.3;-1.3	5.6	5.6	0.85130	.	0.000000	0.64402	D	0.000005	D	0.89030	0.6599	M	0.87328	2.875	0.41548	D	0.988558	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	D	0.89707	0.3909	10	0.45353	T	0.12	.	15.7802	0.78255	1.0:0.0:0.0:0.0	.	1826;2378	Q4LE79;P15924	.;DESP_HUMAN	F	2378;1779	ENSP00000369129:I2378F;ENSP00000396591:I1779F	ENSP00000369129:I2378F	I	+	1	0	DSP	7529626	1.000000	0.71417	0.998000	0.56505	0.987000	0.75469	9.301000	0.96167	2.127000	0.65507	0.533000	0.62120	ATT	.	.	.	none		0.448	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
GCNT2	2651	hgsc.bcm.edu	37	6	10529857	10529857	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:10529857A>C	ENST00000379597.3	+	1	1269	c.713A>C	c.(712-714)aAc>aCc	p.N238T	GCNT2_ENST00000397423.2_Intron|GCNT2_ENST00000495262.1_Missense_Mutation_p.N238T|GCNT2_ENST00000410107.1_Intron			Q8N0V5	GNT2A_HUMAN	glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (I blood group)	238					maintenance of lens transparency (GO:0036438)|negative regulation of cell-substrate adhesion (GO:0010812)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of protein kinase B signaling (GO:0051897)|posttranscriptional regulation of gene expression (GO:0010608)|protein glycosylation (GO:0006486)|transforming growth factor beta receptor signaling pathway (GO:0007179)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	N-acetyllactosaminide beta-1,6-N-acetylglucosaminyltransferase activity (GO:0008109)			endometrium(2)|kidney(1)|large_intestine(5)|lung(2)|ovary(2)	12	Ovarian(93;0.107)|Breast(50;0.148)	all_hematologic(90;0.107)		KIRC - Kidney renal clear cell carcinoma(1;0.099)|Kidney(1;0.119)		GAACTGTTAAACCACAAAAAT	0.448																																					p.N238T		Atlas-SNP	.											.	GCNT2	123	.	0			c.A713C						PASS	.						75.0	78.0	77.0					6																	10529857		2202	4300	6502	SO:0001583	missense	2651	exon3			TGTTAAACCACAA	L41605	CCDS4512.1, CCDS4513.1, CCDS34338.1	6p24.2	2014-07-18	2006-02-23		ENSG00000111846	ENSG00000111846	2.4.1.150	"""Blood group antigens"", ""Glucosaminyl (N-acetyl) transferase and xylosyltransferase family"""	4204	protein-coding gene	gene with protein product	"""Ii blood group"", ""unassigned linkage group 3"""	600429	"""glucosaminyl (N-acetyl) transferase 5"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme"", ""glucosaminyl (N-acetyl) transferase 2, I-branching enzyme (Ii blood group)"", ""cataract, congenital"""	NACGT1, II, GCNT5, CCAT		8449405, 9915862	Standard	NM_145649		Approved	IGNT, NAGCT1, bA421M1.1, bA360O19.2, ULG3	uc003mze.3	Q06430	OTTHUMG00000014244	ENST00000379597.3:c.713A>C	chr6.hg19:g.10529857A>C	ENSP00000368917:p.Asn238Thr	70.0	0.0	.		53.0	17.0	.	NM_145649		Missense_Mutation	SNP	ENST00000379597.3	hg19	CCDS34338.1	.	.	.	.	.	.	.	.	.	.	A	1.996	-0.430677	0.04669	.	.	ENSG00000111846	ENST00000495262;ENST00000379597	T;T	0.09723	2.95;2.95	5.6	-5.91	0.02269	.	1.868580	0.02099	N	0.053783	T	0.00875	0.0029	N	0.02765	-0.5	0.09310	N	0.999996	B;B	0.06786	0.001;0.001	B;B	0.12156	0.007;0.007	T	0.40961	-0.9535	10	0.10636	T	0.68	-17.1412	3.8801	0.09074	0.5225:0.0949:0.2781:0.1045	.	238;237	Q8N0V5;Q08M29	GNT2A_HUMAN;.	T	238	ENSP00000419411:N238T;ENSP00000368917:N238T	ENSP00000368917:N238T	N	+	2	0	GCNT2	10637843	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	0.109000	0.15417	-0.665000	0.05317	0.519000	0.50382	AAC	.	.	.	none		0.448	GCNT2-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000327912.3	NM_145649	
OR2J3	442186	hgsc.bcm.edu	37	6	29080095	29080095	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:29080095T>G	ENST00000377169.1	+	1	428	c.428T>G	c.(427-429)tTc>tGc	p.F143C		NM_001005216.2	NP_001005216.2	O76001	OR2J3_HUMAN	olfactory receptor, family 2, subfamily J, member 3	143						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(5)|lung(13)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24						CACCCTCGTTTCTGCCACCTG	0.522																																					p.F143C		Atlas-SNP	.											.	OR2J3	53	.	0			c.T428G						PASS	.						370.0	396.0	387.0					6																	29080095		1387	2633	4020	SO:0001583	missense	442186	exon1			CTCGTTTCTGCCA		CCDS43433.1	6p22.2-p21.31	2012-08-09			ENSG00000204701	ENSG00000204701		"""GPCR / Class A : Olfactory receptors"""	8261	protein-coding gene	gene with protein product		615016					Standard	NM_001005216		Approved	OR6-6	uc011dll.2	O76001	OTTHUMG00000031092	ENST00000377169.1:c.428T>G	chr6.hg19:g.29080095T>G	ENSP00000366374:p.Phe143Cys	75.0	0.0	.		114.0	45.0	.	NM_001005216	B0UY52|B9EH11|Q5SUJ7|Q6IF25|Q96R15|Q9GZK5|Q9GZL4|Q9GZL5	Missense_Mutation	SNP	ENST00000377169.1	hg19	CCDS43433.1	.	.	.	.	.	.	.	.	.	.	T	13.69	2.313785	0.40996	.	.	ENSG00000204701	ENST00000377169	T	0.00036	8.86	2.78	2.78	0.32641	GPCR, rhodopsin-like superfamily (1);	.	.	.	.	T	0.00073	0.0002	L	0.37850	1.14	0.21782	N	0.999544	P	0.51933	0.949	P	0.56343	0.796	T	0.04855	-1.0922	9	0.87932	D	0	.	6.8216	0.23861	0.2081:0.0:0.0:0.7919	.	143	O76001	OR2J3_HUMAN	C	143	ENSP00000366374:F143C	ENSP00000366374:F143C	F	+	2	0	OR2J3	29188074	0.000000	0.05858	0.855000	0.33649	0.771000	0.43674	0.608000	0.24223	1.268000	0.44264	0.358000	0.22013	TTC	.	.	.	none		0.522	OR2J3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076132.2		
MDC1	9656	hgsc.bcm.edu	37	6	30680834	30680834	+	Silent	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:30680834A>C	ENST00000376406.3	-	5	1532	c.885T>G	c.(883-885)ccT>ccG	p.P295P	MDC1-AS1_ENST00000442150.1_RNA|MDC1_ENST00000494654.1_5'Flank|MDC1_ENST00000376405.2_Silent_p.P295P	NM_014641.2	NP_055456.2	Q14676	MDC1_HUMAN	mediator of DNA-damage checkpoint 1	295	Required for nuclear localization (NLS1).				DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|intra-S DNA damage checkpoint (GO:0031573)	chromosome (GO:0005694)|focal adhesion (GO:0005925)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	FHA domain binding (GO:0070975)|protein C-terminus binding (GO:0008022)			breast(2)|kidney(1)|ovary(1)	4						TGTCCTCTCCAGGAGGTTGGC	0.542								Other conserved DNA damage response genes																													p.P295P		Atlas-SNP	.											.	MDC1	218	.	0			c.T885G						PASS	.						146.0	124.0	132.0					6																	30680834		1511	2709	4220	SO:0001819	synonymous_variant	9656	exon5			CTCTCCAGGAGGT	D79992	CCDS34384.1	6p21.3	2010-02-17	2009-06-12		ENSG00000137337	ENSG00000137337			21163	protein-coding gene	gene with protein product		607593				10975465, 12607005	Standard	NM_014641		Approved	NFBD1, KIAA0170, Em:AB023051.5	uc003nrg.4	Q14676	OTTHUMG00000031075	ENST00000376406.3:c.885T>G	chr6.hg19:g.30680834A>C		71.0	0.0	.		87.0	38.0	.	NM_014641	A2AB04|A2BF04|A2RRA8|A7YY86|B0S8A2|Q0EFC2|Q2L6H7|Q2TAZ4|Q5JP55|Q5JP56|Q5ST83|Q68CQ3|Q86Z06|Q96QC2	Silent	SNP	ENST00000376406.3	hg19	CCDS34384.1																																																																																			.	.	.	none		0.542	MDC1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000076103.1	NM_014641	
RRP36	88745	hgsc.bcm.edu	37	6	42989441	42989441	+	Nonsense_Mutation	SNP	C	C	T	rs202053592	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:42989441C>T	ENST00000244496.5	+	1	59	c.49C>T	c.(49-51)Cga>Tga	p.R17*		NM_033112.2	NP_149103.1	Q96EU6	RRP36_HUMAN	ribosomal RNA processing 36 homolog (S. cerevisiae)	17					ribosomal small subunit biogenesis (GO:0042274)|rRNA processing (GO:0006364)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(1)|central_nervous_system(1)|large_intestine(5)|lung(1)|ovary(1)|prostate(1)	11						ggccggggcccgacgtccccg	0.776																																					p.R17X		Atlas-SNP	.											.	RRP36	20	.	0			c.C49T						PASS	.						2.0	2.0	2.0					6																	42989441		866	1798	2664	SO:0001587	stop_gained	88745	exon1			GGGGCCCGACGTC	BC011933	CCDS34453.1	6p21.1	2010-07-06	2010-07-06	2010-07-06	ENSG00000124541	ENSG00000124541			21374	protein-coding gene	gene with protein product		613475	"""chromosome 6 open reading frame 153"""	C6orf153		20038530	Standard	NM_033112		Approved	dJ20C7.4	uc003otp.1	Q96EU6	OTTHUMG00000014715	ENST00000244496.5:c.49C>T	chr6.hg19:g.42989441C>T	ENSP00000244496:p.Arg17*	27.0	0.0	.		23.0	10.0	.	NM_033112	Q9BRF6|Q9P0C8	Nonsense_Mutation	SNP	ENST00000244496.5	hg19	CCDS34453.1	.	.	.	.	.	.	.	.	.	.	C	14.13	2.442813	0.43326	.	.	ENSG00000124541	ENST00000244496	.	.	.	3.24	-0.816	0.10839	.	0.576146	0.10077	U	0.718890	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15499	T	0.54	.	2.3532	0.04289	0.1591:0.2847:0.4261:0.13	.	.	.	.	X	17	.	ENSP00000244496:R17X	R	+	1	2	RRP36	43097419	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.257000	0.08745	-0.199000	0.10317	-0.339000	0.08088	CGA	.	.	.	none		0.776	RRP36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040572.1	NM_033112	
PHKG1	5260	hgsc.bcm.edu	37	7	56155338	56155338	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:56155338A>G	ENST00000297373.2	-	3	409	c.215T>C	c.(214-216)cTg>cCg	p.L72P	PHKG1_ENST00000537360.1_Silent_p.A36A|PHKG1_ENST00000452681.2_Missense_Mutation_p.L72P|PHKG1_ENST00000489604.1_5'UTR	NM_001258460.1|NM_006213.4	NP_001245389.1|NP_006204.1	Q16816	PHKG1_HUMAN	phosphorylase kinase, gamma 1 (muscle)	72	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				carbohydrate metabolic process (GO:0005975)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|glycogen catabolic process (GO:0005980)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphorylase kinase complex (GO:0005964)	ATP binding (GO:0005524)|phosphorylase kinase activity (GO:0004689)|tau-protein kinase activity (GO:0050321)			endometrium(1)|large_intestine(1)|lung(5)	7	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			CACCTCCTTCAGCGTGGCTTC	0.647																																					p.L72P	Melanoma(184;580 2064 5329 24177 35303)	Atlas-SNP	.											.	PHKG1	38	.	0			c.T215C						PASS	.						76.0	51.0	60.0					7																	56155338		2203	4300	6503	SO:0001583	missense	5260	exon3			TCCTTCAGCGTGG	X80590	CCDS5525.1, CCDS59057.1	7p11.2	2009-07-10			ENSG00000164776	ENSG00000164776	2.7.11.19		8930	protein-coding gene	gene with protein product		172470		PHKG		8530014	Standard	NM_001258459		Approved		uc011kdb.2	Q16816	OTTHUMG00000023869	ENST00000297373.2:c.215T>C	chr7.hg19:g.56155338A>G	ENSP00000297373:p.Leu72Pro	45.0	0.0	.		83.0	65.0	.	NM_001258459	B7Z1D0|F5H2S1|Q75LP5	Missense_Mutation	SNP	ENST00000297373.2	hg19	CCDS5525.1	.	.	.	.	.	.	.	.	.	.	A	12.96	2.095532	0.36952	.	.	ENSG00000164776	ENST00000452681;ENST00000297373	T;T	0.46063	3.1;0.88	5.42	4.25	0.50352	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.606658	0.14620	N	0.308456	T	0.44307	0.1287	L	0.60957	1.885	0.80722	D	1	B;B;P	0.45827	0.082;0.451;0.867	B;B;P	0.48901	0.287;0.273;0.594	T	0.26360	-1.0105	10	0.36615	T	0.2	-17.4861	5.7614	0.18203	0.7557:0.0:0.086:0.1583	.	72;72;72	B7Z6U2;F5H2S1;Q16816	.;.;PHKG1_HUMAN	P	72	ENSP00000445440:L72P;ENSP00000297373:L72P	ENSP00000297373:L72P	L	-	2	0	PHKG1	56122832	0.997000	0.39634	0.998000	0.56505	0.790000	0.44656	3.544000	0.53640	0.981000	0.38548	0.460000	0.39030	CTG	.	.	.	none		0.647	PHKG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251587.1	NM_006213	
BAZ1B	9031	hgsc.bcm.edu	37	7	72856678	72856678	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:72856678G>C	ENST00000339594.4	-	19	4638	c.4300C>G	c.(4300-4302)Cag>Gag	p.Q1434E	BAZ1B_ENST00000404251.1_Missense_Mutation_p.Q1434E	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1434					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				ACTAGACACTGTTCTGTCTTC	0.493																																					p.Q1434E	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											.	BAZ1B	147	.	0			c.C4300G						PASS	.						139.0	124.0	129.0					7																	72856678		2203	4300	6503	SO:0001583	missense	9031	exon19			GACACTGTTCTGT	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.4300C>G	chr7.hg19:g.72856678G>C	ENSP00000342434:p.Gln1434Glu	78.0	0.0	.		158.0	118.0	.	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Missense_Mutation	SNP	ENST00000339594.4	hg19	CCDS5549.1	.	.	.	.	.	.	.	.	.	.	G	12.75	2.030593	0.35797	.	.	ENSG00000009954	ENST00000339594;ENST00000404251	T;T	0.17213	2.29;2.29	5.54	4.63	0.57726	Bromodomain (3);	0.184208	0.49305	N	0.000149	T	0.14485	0.0350	L	0.29908	0.895	0.41806	D	0.989949	B	0.02656	0.0	B	0.04013	0.001	T	0.03139	-1.1068	10	0.35671	T	0.21	-23.1276	15.2408	0.73468	0.0:0.1411:0.8589:0.0	.	1434	Q9UIG0	BAZ1B_HUMAN	E	1434	ENSP00000342434:Q1434E;ENSP00000385442:Q1434E	ENSP00000342434:Q1434E	Q	-	1	0	BAZ1B	72494614	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	5.883000	0.69721	1.266000	0.44231	0.643000	0.83706	CAG	.	.	.	none		0.493	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
CLIP2	7461	hgsc.bcm.edu	37	7	73752959	73752959	+	Silent	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:73752959G>A	ENST00000395060.1	+	2	303	c.303G>A	c.(301-303)acG>acA	p.T101T	CLIP2_ENST00000223398.6_Silent_p.T101T|CLIP2_ENST00000361545.5_Silent_p.T101T			Q9UDT6	CLIP2_HUMAN	CAP-GLY domain containing linker protein 2	101	CAP-Gly 1. {ECO:0000255|PROSITE- ProRule:PRU00045}.					cytoplasmic microtubule (GO:0005881)|microtubule associated complex (GO:0005875)|microtubule plus-end (GO:0035371)				breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(13)|pancreas(1)|prostate(2)|skin(3)	30						TGGGAGAGACGCAGTTCGCAC	0.687																																					p.T101T		Atlas-SNP	.											.	CLIP2	134	.	0			c.G303A						PASS	.						60.0	47.0	51.0					7																	73752959		2177	4269	6446	SO:0001819	synonymous_variant	7461	exon3			AGAGACGCAGTTC	AB006629	CCDS5569.1, CCDS5570.1	7q11.23	2008-06-12	2007-01-04	2007-01-04	ENSG00000106665	ENSG00000106665			2586	protein-coding gene	gene with protein product		603432	"""cytoplasmic linker 2"", ""Williams-Beuren syndrome chromosome region 3"""	WBSCR4, CYLN2, WBSCR3		8812460, 9799601	Standard	NM_003388		Approved	CLIP-115, KIAA0291, WSCR4, CLIP, WSCR3	uc003uam.3	Q9UDT6	OTTHUMG00000022980	ENST00000395060.1:c.303G>A	chr7.hg19:g.73752959G>A		54.0	0.0	.		102.0	17.0	.	NM_032421	O14527|O43611	Silent	SNP	ENST00000395060.1	hg19	CCDS5569.1																																																																																			.	.	.	none		0.687	CLIP2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252556.1	NM_003388	
AKAP9	10142	hgsc.bcm.edu	37	7	91624968	91624968	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:91624968G>A	ENST00000359028.2	+	8	1045	c.820G>A	c.(820-822)Gac>Aac	p.D274N	AKAP9_ENST00000356239.3_Missense_Mutation_p.D262N|AKAP9_ENST00000358100.2_Missense_Mutation_p.D274N|AKAP9_ENST00000394564.1_Missense_Mutation_p.D262N			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	274	Gln-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)			NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			CACAGCTGCAGACTTACTACA	0.378			T	BRAF	papillary thyroid																																p.D262N		Atlas-SNP	.		Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	.	AKAP9	788	.	0			c.G784A						PASS	.						96.0	86.0	89.0					7																	91624968		2203	4300	6503	SO:0001583	missense	10142	exon7			GCTGCAGACTTAC	AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.820G>A	chr7.hg19:g.91624968G>A	ENSP00000351922:p.Asp274Asn	189.0	0.0	.		430.0	95.0	.	NM_005751	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	hg19		.	.	.	.	.	.	.	.	.	.	G	24.2	4.506910	0.85282	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394565;ENST00000394564;ENST00000438114	T;T;T;T;T	0.34072	1.38;1.38;1.38;1.38;1.38	5.1	5.1	0.69264	.	0.000000	0.43110	D	0.000602	T	0.49525	0.1562	L	0.27053	0.805	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;0.997	D;D;D;D	0.80764	0.994;0.986;0.993;0.942	T	0.53697	-0.8402	10	0.72032	D	0.01	.	18.8833	0.92365	0.0:0.0:1.0:0.0	.	262;262;274;262	Q99996-2;Q99996-3;A4D1E4;Q6PJH3	.;.;.;.	N	262;274;274;274;274;262;213	ENSP00000348573:D262N;ENSP00000351922:D274N;ENSP00000350813:D274N;ENSP00000378065:D262N;ENSP00000391704:D213N	ENSP00000348573:D262N	D	+	1	0	AKAP9	91462904	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	8.602000	0.90868	2.535000	0.85469	0.655000	0.94253	GAC	.	.	.	none		0.378	AKAP9-202	KNOWN	basic	protein_coding	protein_coding		NM_005751	
PEX1	5189	hgsc.bcm.edu	37	7	92147296	92147296	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr7:92147296T>C	ENST00000248633.4	-	5	628	c.533A>G	c.(532-534)cAg>cGg	p.Q178R	PEX1_ENST00000438045.1_Intron|PEX1_ENST00000428214.1_Missense_Mutation_p.Q178R|PEX1_ENST00000541751.1_5'Flank	NM_000466.2	NP_000457.1	O43933	PEX1_HUMAN	peroxisomal biogenesis factor 1	178					ATP catabolic process (GO:0006200)|microtubule-based peroxisome localization (GO:0060152)|peroxisome organization (GO:0007031)|protein import into peroxisome matrix (GO:0016558)|protein targeting to peroxisome (GO:0006625)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled (GO:0042623)|protein C-terminus binding (GO:0008022)|protein complex binding (GO:0032403)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(6)|lung(17)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	41	all_cancers(62;9.35e-11)|all_epithelial(64;4.59e-10)|Breast(17;0.00201)|all_lung(186;0.0438)|Lung NSC(181;0.0592)	Breast(660;0.000932)|all_neural(109;0.00391)|Myeloproliferative disorder(862;0.0122)|Ovarian(593;0.023)|Medulloblastoma(109;0.123)	GBM - Glioblastoma multiforme(5;4.06e-06)|STAD - Stomach adenocarcinoma(4;4.51e-05)|all cancers(6;5.32e-05)|LUSC - Lung squamous cell carcinoma(200;0.225)|Lung(22;0.23)			TGTCTTTGGCTGAATAAGGAG	0.383																																					p.Q178R		Atlas-SNP	.											.	PEX1	102	.	0			c.A533G						PASS	.						53.0	57.0	55.0					7																	92147296		2158	4289	6447	SO:0001583	missense	5189	exon5			TTTGGCTGAATAA	AF026086	CCDS5627.1, CCDS64710.1	7q21.2	2010-04-21	2008-08-26		ENSG00000127980	ENSG00000127980		"""ATPases / AAA-type"""	8850	protein-coding gene	gene with protein product		602136	"""peroxisome biogenesis factor 1"", ""Zellweger syndrome 1"", ""Zellweger syndrome"""	ZWS1, ZWS		9398848	Standard	NM_001282677		Approved		uc003uly.3	O43933	OTTHUMG00000023926	ENST00000248633.4:c.533A>G	chr7.hg19:g.92147296T>C	ENSP00000248633:p.Gln178Arg	60.0	0.0	.		198.0	152.0	.	NM_000466	A4D1G3|A8KA90|B4DIM7|E9PE75|Q96S71|Q96S72|Q96S73|Q99994	Missense_Mutation	SNP	ENST00000248633.4	hg19	CCDS5627.1	.	.	.	.	.	.	.	.	.	.	T	10.98	1.505840	0.26949	.	.	ENSG00000127980	ENST00000248633;ENST00000428214;ENST00000545192	D;D	0.94417	-3.37;-3.42	5.84	0.871	0.19107	Peroxisome biogenesis factor 1, N-terminal (1);	0.673780	0.16046	N	0.232189	D	0.86209	0.5878	L	0.29908	0.895	0.80722	D	1	B	0.06786	0.001	B	0.04013	0.001	T	0.72972	-0.4129	10	0.25751	T	0.34	-2.6037	1.138	0.01759	0.1586:0.3287:0.1645:0.3482	.	178	O43933	PEX1_HUMAN	R	178	ENSP00000248633:Q178R;ENSP00000394413:Q178R	ENSP00000248633:Q178R	Q	-	2	0	PEX1	91985232	1.000000	0.71417	0.999000	0.59377	0.841000	0.47740	1.064000	0.30579	0.122000	0.18314	0.528000	0.53228	CAG	.	.	.	none		0.383	PEX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254066.3	NM_000466	
MTFR1	9650	hgsc.bcm.edu	37	8	66617006	66617006	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr8:66617006T>C	ENST00000262146.4	+	5	485	c.359T>C	c.(358-360)tTa>tCa	p.L120S	MTFR1_ENST00000458689.2_Missense_Mutation_p.L87S|MTFR1_ENST00000517944.1_3'UTR	NM_014637.3	NP_055452.3	Q15390	MTFR1_HUMAN	mitochondrial fission regulator 1	120					aerobic respiration (GO:0009060)|mitochondrial fission (GO:0000266)|mitochondrion organization (GO:0007005)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(1)|pancreas(1)|urinary_tract(1)	11			Epithelial(68;0.0526)|BRCA - Breast invasive adenocarcinoma(89;0.156)|all cancers(69;0.171)|OV - Ovarian serous cystadenocarcinoma(28;0.194)			CAGATTTCCTTACCAGACTTG	0.507																																					p.L120S		Atlas-SNP	.											.	MTFR1	26	.	0			c.T359C						PASS	.						74.0	74.0	74.0					8																	66617006		2203	4300	6503	SO:0001583	missense	9650	exon5			TTTCCTTACCAGA		CCDS6182.1, CCDS55240.1	8q13.1	2012-11-30							29510	protein-coding gene	gene with protein product	"""likely ortholog of chicken chondrocyte protein with a poly proline region"""					7584026, 7584028, 15389597	Standard	NM_014637		Approved	CHPPR, KIAA0009, FAM54A2	uc003xvn.2	Q15390		ENST00000262146.4:c.359T>C	chr8.hg19:g.66617006T>C	ENSP00000262146:p.Leu120Ser	137.0	0.0	.		197.0	67.0	.	NM_014637	E7EP84|Q6IB94|Q7Z669|Q86XH5|Q8IVD7	Missense_Mutation	SNP	ENST00000262146.4	hg19	CCDS6182.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	14.66|14.66	2.602219|2.602219	0.46423|0.46423	.|.	.|.	ENSG00000066855|ENSG00000066855	ENST00000518609;ENST00000262146;ENST00000458689|ENST00000518800	T;T|.	0.46063|.	0.88;0.88|.	5.39|5.39	1.66|1.66	0.24008|0.24008	.|.	0.233115|.	0.35838|.	N|.	0.002944|.	T|T	0.61924|0.61924	0.2386|0.2386	M|M	0.66439|0.66439	2.03|2.03	0.37434|0.37434	D|D	0.914169|0.914169	B;B;P;B|.	0.34977|.	0.097;0.345;0.478;0.095|.	B;B;B;B|.	0.41813|.	0.063;0.367;0.305;0.094|.	T|T	0.60855|0.60855	-0.7180|-0.7180	10|5	0.28530|.	T|.	0.3|.	-0.7048|-0.7048	9.3755|9.3755	0.38281|0.38281	0.0:0.1972:0.0:0.8028|0.0:0.1972:0.0:0.8028	.|.	120;104;87;120|.	B4E3G8;E5RJS5;E7EP84;Q15390|.	.;.;.;MTFR1_HUMAN|.	S|H	104;120;87|78	ENSP00000262146:L120S;ENSP00000391502:L87S|.	ENSP00000262146:L120S|.	L|Y	+|+	2|1	0|0	MTFR1|MTFR1	66779560|66779560	1.000000|1.000000	0.71417|0.71417	0.979000|0.979000	0.43373|0.43373	0.943000|0.943000	0.58893|0.58893	3.364000|3.364000	0.52328|0.52328	0.042000|0.042000	0.15717|0.15717	0.460000|0.460000	0.39030|0.39030	TTA|TAC	.	.	.	none		0.507	MTFR1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000378894.1	NM_014637	
MMP16	4325	hgsc.bcm.edu	37	8	89068476	89068476	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr8:89068476G>A	ENST00000286614.6	-	8	1534	c.1253C>T	c.(1252-1254)aCt>aTt	p.T418I		NM_005941.4	NP_005932.2	P51512	MMP16_HUMAN	matrix metallopeptidase 16 (membrane-inserted)	418					chondrocyte proliferation (GO:0035988)|collagen catabolic process (GO:0030574)|craniofacial suture morphogenesis (GO:0097094)|embryonic cranial skeleton morphogenesis (GO:0048701)|endochondral ossification (GO:0001958)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of catalytic activity (GO:0043085)	Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|enzyme activator activity (GO:0008047)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(5)|liver(1)|lung(51)|ovary(3)|prostate(4)|skin(1)|upper_aerodigestive_tract(5)|urinary_tract(3)	81					Marimastat(DB00786)	AGGTTGAAGAGTTGTATCCTT	0.368																																					p.T418I		Atlas-SNP	.											.	MMP16	176	.	0			c.C1253T						PASS	.						92.0	88.0	90.0					8																	89068476		2203	4300	6503	SO:0001583	missense	4325	exon8			TGAAGAGTTGTAT	D85511	CCDS6246.1	8q21	2009-01-09	2005-08-08		ENSG00000156103	ENSG00000156103			7162	protein-coding gene	gene with protein product		602262	"""matrix metalloproteinase 16 (membrane-inserted)"", ""chromosome 8 open reading frame 57"""	C8orf57		7559440	Standard	NM_005941		Approved	MT3-MMP, DKFZp761D112	uc003yeb.4	P51512	OTTHUMG00000163769	ENST00000286614.6:c.1253C>T	chr8.hg19:g.89068476G>A	ENSP00000286614:p.Thr418Ile	109.0	0.0	.		175.0	101.0	.	NM_005941	B2RAN7|Q14824|Q52H48	Missense_Mutation	SNP	ENST00000286614.6	hg19	CCDS6246.1	.	.	.	.	.	.	.	.	.	.	G	13.92	2.381730	0.42207	.	.	ENSG00000156103	ENST00000286614	T	0.02863	4.13	5.91	5.91	0.95273	Hemopexin/matrixin (2);	0.310233	0.39274	N	0.001410	T	0.04724	0.0128	L	0.33189	0.99	0.58432	D	0.99999	B	0.20052	0.041	B	0.29077	0.098	T	0.53913	-0.8371	10	0.33141	T	0.24	.	20.2985	0.98592	0.0:0.0:1.0:0.0	.	418	P51512	MMP16_HUMAN	I	418	ENSP00000286614:T418I	ENSP00000286614:T418I	T	-	2	0	MMP16	89137592	1.000000	0.71417	0.998000	0.56505	0.998000	0.95712	4.781000	0.62389	2.793000	0.96121	0.655000	0.94253	ACT	.	.	.	none		0.368	MMP16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375304.2	NM_005941	
ZNF517	340385	hgsc.bcm.edu	37	8	146033121	146033121	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr8:146033121T>C	ENST00000531720.1	+	4	865	c.820T>C	c.(820-822)Tcc>Ccc	p.S274P	ZNF517_ENST00000525105.1_Intron|ZNF517_ENST00000526178.1_Intron|ZNF517_ENST00000359971.3_Missense_Mutation_p.S274P			Q6ZMY9	ZN517_HUMAN	zinc finger protein 517	274					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|endometrium(2)|large_intestine(2)|lung(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	13	all_cancers(97;1.03e-11)|all_epithelial(106;6.69e-11)|Lung NSC(106;4.08e-05)|all_lung(105;0.000125)|Ovarian(258;0.0173)|Acute lymphoblastic leukemia(118;0.155)		Epithelial(56;5.47e-39)|OV - Ovarian serous cystadenocarcinoma(54;6.38e-39)|all cancers(56;5.47e-34)|BRCA - Breast invasive adenocarcinoma(115;0.0355)|Colorectal(110;0.055)			CAGCCGCAGCTCCCGGCTGCT	0.692																																					p.S274P		Atlas-SNP	.											.	ZNF517	30	.	0			c.T820C						PASS	.						21.0	23.0	23.0					8																	146033121		2201	4297	6498	SO:0001583	missense	340385	exon5			CGCAGCTCCCGGC	AK096527	CCDS6434.1	8q24.3	2013-01-08				ENSG00000197363		"""Zinc fingers, C2H2-type"", ""-"""	27984	protein-coding gene	gene with protein product							Standard	NM_213605		Approved		uc003zed.1	Q6ZMY9		ENST00000531720.1:c.820T>C	chr8.hg19:g.146033121T>C	ENSP00000436103:p.Ser274Pro	49.0	0.0	.		67.0	37.0	.	NM_213605		Missense_Mutation	SNP	ENST00000531720.1	hg19	CCDS6434.1	.	.	.	.	.	.	.	.	.	.	T	15.77	2.930921	0.52866	.	.	ENSG00000197363	ENST00000359971;ENST00000531720	T;T	0.08102	3.13;3.13	2.08	2.08	0.27032	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.14141	0.0342	M	0.65975	2.015	0.20196	N	0.999927	D	0.61080	0.989	P	0.50590	0.645	T	0.13818	-1.0495	9	0.66056	D	0.02	.	4.8554	0.13557	0.4587:0.0:0.0:0.5413	.	274	Q6ZMY9	ZN517_HUMAN	P	274	ENSP00000353058:S274P;ENSP00000436103:S274P	ENSP00000353058:S274P	S	+	1	0	ZNF517	146003925	0.000000	0.05858	0.981000	0.43875	0.745000	0.42441	-2.135000	0.01306	0.947000	0.37659	0.379000	0.24179	TCC	.	.	.	none		0.692	ZNF517-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382642.1	XM_291261	
PTPN3	5774	hgsc.bcm.edu	37	9	112145801	112145801	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:112145801G>T	ENST00000374541.2	-	23	2388	c.2284C>A	c.(2284-2286)Ccc>Acc	p.P762T	PTPN3_ENST00000262539.3_Missense_Mutation_p.P608T|PTPN3_ENST00000394827.3_Missense_Mutation_p.P230T|PTPN3_ENST00000412145.1_Missense_Mutation_p.P631T|PTPN3_ENST00000446349.1_Missense_Mutation_p.P586T	NM_001145368.1|NM_002829.3	NP_001138840.1|NP_002820.3	P26045	PTN3_HUMAN	protein tyrosine phosphatase, non-receptor type 3	762	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.				negative regulation of membrane protein ectodomain proteolysis (GO:0051045)|negative regulation of mitotic cell cycle (GO:0045930)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of membrane depolarization during action potential (GO:0098902)|regulation of sodium ion transmembrane transporter activity (GO:2000649)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytoskeleton (GO:0005856)	ATPase binding (GO:0051117)|phosphotyrosine binding (GO:0001784)|protein tyrosine phosphatase activity (GO:0004725)|sodium channel regulator activity (GO:0017080)			breast(1)|endometrium(2)|kidney(2)|large_intestine(8)|liver(1)|lung(14)|ovary(4)|prostate(3)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	41						ATGACGTCGGGGGGATCTGGC	0.557																																					p.P762T		Atlas-SNP	.											.	PTPN3	106	.	0			c.C2284A						PASS	.						126.0	118.0	121.0					9																	112145801		2203	4300	6503	SO:0001583	missense	5774	exon23			CGTCGGGGGGATC		CCDS6776.1, CCDS48000.1, CCDS48001.1	9q31	2011-06-09			ENSG00000070159	ENSG00000070159		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9655	protein-coding gene	gene with protein product		176877				1648725	Standard	NM_002829		Approved	PTPH1	uc004bed.2	P26045	OTTHUMG00000020475	ENST00000374541.2:c.2284C>A	chr9.hg19:g.112145801G>T	ENSP00000363667:p.Pro762Thr	112.0	0.0	.		85.0	34.0	.	NM_002829	A0AUW9|E7EN99|E9PGU7	Missense_Mutation	SNP	ENST00000374541.2	hg19	CCDS6776.1	.	.	.	.	.	.	.	.	.	.	G	8.494	0.862742	0.17178	.	.	ENSG00000070159	ENST00000394831;ENST00000412145;ENST00000446349;ENST00000374541;ENST00000394827;ENST00000262539	D;D;D;D;D	0.83075	-1.68;-1.68;-1.68;-1.68;-1.68	4.75	3.82	0.43975	Protein-tyrosine phosphatase, receptor/non-receptor type (3);	0.053687	0.85682	N	0.000000	D	0.82949	0.5148	N	0.21194	0.64	0.58432	D	0.999999	D;B;B	0.89917	1.0;0.057;0.034	D;B;B	0.91635	0.999;0.083;0.032	T	0.77879	-0.2423	10	0.12103	T	0.63	.	14.3098	0.66407	0.0:0.0:0.8503:0.1497	.	608;717;762	B7Z3H5;B7Z9V1;P26045	.;.;PTN3_HUMAN	T	762;631;586;762;230;608	ENSP00000416654:P631T;ENSP00000395384:P586T;ENSP00000363667:P762T;ENSP00000378304:P230T;ENSP00000262539:P608T	ENSP00000262539:P608T	P	-	1	0	PTPN3	111185622	1.000000	0.71417	0.840000	0.33206	0.135000	0.20990	7.828000	0.86729	1.080000	0.41073	0.462000	0.41574	CCC	.	.	.	none		0.557	PTPN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053598.4		
NUP188	23511	hgsc.bcm.edu	37	9	131731688	131731688	+	Silent	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:131731688T>C	ENST00000372577.2	+	10	828	c.807T>C	c.(805-807)agT>agC	p.S269S		NM_015354.1	NP_056169.1	Q5SRE5	NU188_HUMAN	nucleoporin 188kDa	269					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore (GO:0005643)				breast(2)|central_nervous_system(3)|endometrium(6)|kidney(4)|large_intestine(9)|lung(20)|ovary(6)|prostate(4)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(3)	60						GCTACTTCAGTGCCCTCATCC	0.423																																					p.S269S		Atlas-SNP	.											.	NUP188	140	.	0			c.T807C						PASS	.						138.0	115.0	123.0					9																	131731688		2203	4300	6503	SO:0001819	synonymous_variant	23511	exon10			CTTCAGTGCCCTC	D79991	CCDS35156.1	9q34.13	2014-01-28	2004-03-19	2004-03-24	ENSG00000095319	ENSG00000095319			17859	protein-coding gene	gene with protein product		615587	"""KIAA0169"""	KIAA0169		11029043	Standard	NM_015354		Approved		uc004bws.2	Q5SRE5	OTTHUMG00000020768	ENST00000372577.2:c.807T>C	chr9.hg19:g.131731688T>C		73.0	0.0	.		82.0	33.0	.	NM_015354	Q14675|Q2TA87|Q7Z3K8|Q8IWF1	Silent	SNP	ENST00000372577.2	hg19	CCDS35156.1																																																																																			.	.	.	none		0.423	NUP188-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054529.2		
PTPLA	9200	hgsc.bcm.edu	37	10	17645619	17645619	+	Silent	SNP	A	A	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:17645619A>T	ENST00000361271.3	-	4	460	c.423T>A	c.(421-423)acT>acA	p.T141T		NM_014241.3	NP_055056.3	B0YJ81	HACD1_HUMAN	protein tyrosine phosphatase-like (proline instead of catalytic arginine), member A	141					fatty acid biosynthetic process (GO:0006633)|multicellular organismal development (GO:0007275)|myotube differentiation (GO:0014902)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of G1/S transition of mitotic cell cycle (GO:2000045)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	lyase activity (GO:0016829)|protein tyrosine phosphatase activity (GO:0004725)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(2)|lung(6)|skin(1)	13						CTTGGACCCCAGTCACAATCA	0.353																																					p.T141T		Atlas-SNP	.											.	PTPLA	34	.	0			c.T423A						PASS	.						90.0	84.0	86.0					10																	17645619		2203	4300	6503	SO:0001819	synonymous_variant	9200	exon4			GACCCCAGTCACA	AF114494	CCDS7121.1	10p14-p13	2008-08-01	2005-11-11		ENSG00000165996	ENSG00000165996			9639	protein-coding gene	gene with protein product	"""cementum attachment protein"""	610467	"""protein tyrosine phosphatase-like (proline instead of catalytic arginine), member a"""			10644438	Standard	XM_005252641		Approved	CAP	uc001ipg.3	B0YJ81	OTTHUMG00000017750	ENST00000361271.3:c.423T>A	chr10.hg19:g.17645619A>T		210.0	0.0	.		169.0	11.0	.	NM_014241	B0YJ80|Q6JIC5|Q96FW7|Q9HB93|Q9UHX2	Silent	SNP	ENST00000361271.3	hg19	CCDS7121.1																																																																																			.	.	.	none		0.353	PTPLA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047046.1	NM_014241	
OTUD1	220213	hgsc.bcm.edu	37	10	23729477	23729477	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:23729477A>G	ENST00000376495.3	+	1	1280	c.1091A>G	c.(1090-1092)gAg>gGg	p.E364G		NM_001145373.2	NP_001138845.1	Q5VV17	OTUD1_HUMAN	OTU deubiquitinase 1	364	OTU. {ECO:0000255|PROSITE- ProRule:PRU00139}.				protein K63-linked deubiquitination (GO:0070536)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	5						GACGTGGGGGAGTTTATCATC	0.602																																					p.E364G		Atlas-SNP	.											.	OTUD1	9	.	0			c.A1091G						PASS	.						45.0	45.0	45.0					10																	23729477		692	1591	2283	SO:0001583	missense	220213	exon1			TGGGGGAGTTTAT	AK096389	CCDS44366.1	10p12.31	2014-02-24	2014-02-24		ENSG00000165312	ENSG00000165312		"""OTU domain containing"""	27346	protein-coding gene	gene with protein product		612022	"""OTU domain containing 1"""	OTDC1		23827681	Standard	NM_001145373		Approved	DUBA7	uc001irr.2	Q5VV17	OTTHUMG00000017819	ENST00000376495.3:c.1091A>G	chr10.hg19:g.23729477A>G	ENSP00000365678:p.Glu364Gly	62.0	0.0	.		56.0	20.0	.	NM_001145373		Missense_Mutation	SNP	ENST00000376495.3	hg19	CCDS44366.1	.	.	.	.	.	.	.	.	.	.	A	32	5.135688	0.94517	.	.	ENSG00000165312	ENST00000376495	T	0.48522	0.81	5.07	5.07	0.68467	Ovarian tumour, otubain (2);	0.000000	0.64402	U	0.000004	T	0.70037	0.3178	M	0.80508	2.5	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74965	-0.3484	10	0.66056	D	0.02	-8.7509	14.8392	0.70212	1.0:0.0:0.0:0.0	.	364	Q5VV17	OTUD1_HUMAN	G	364	ENSP00000365678:E364G	ENSP00000365678:E364G	E	+	2	0	OTUD1	23769483	1.000000	0.71417	0.998000	0.56505	0.978000	0.69477	9.093000	0.94163	1.895000	0.54865	0.533000	0.62120	GAG	.	.	.	none		0.602	OTUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047215.1	XM_166659	
GBF1	8729	hgsc.bcm.edu	37	10	104018748	104018748	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:104018748G>T	ENST00000369983.3	+	2	313	c.53G>T	c.(52-54)gGg>gTg	p.G18V	AL160011.1_ENST00000516180.2_RNA	NM_001199378.1|NM_001199379.1|NM_004193.2	NP_001186307.1|NP_001186308.1|NP_004184.1	Q92538	GBF1_HUMAN	golgi brefeldin A resistant guanine nucleotide exchange factor 1	18					COPI coating of Golgi vesicle (GO:0048205)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of ARF protein signal transduction (GO:0032012)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|vesicle-mediated transport (GO:0016192)|viral process (GO:0016032)	cis-Golgi network (GO:0005801)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisome (GO:0005777)|trans-Golgi network (GO:0005802)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(14)|kidney(8)|large_intestine(15)|lung(19)|ovary(1)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	71		Colorectal(252;0.0236)		Epithelial(162;5.16e-08)|all cancers(201;1.19e-06)		ATTGTGGTTGGGGCCATCAAA	0.403																																					p.G18V		Atlas-SNP	.											.	GBF1	142	.	0			c.G53T						PASS	.						138.0	147.0	144.0					10																	104018748		2203	4300	6503	SO:0001583	missense	8729	exon2			TGGTTGGGGCCAT	D87435	CCDS7533.1	10q24	2010-02-12	2010-02-12		ENSG00000107862	ENSG00000107862			4181	protein-coding gene	gene with protein product		603698	"""golgi-specific brefeldin A resistance factor 1"""			9828135	Standard	NM_004193		Approved	KIAA0248, ARF1GEF	uc001kux.2	Q92538	OTTHUMG00000018955	ENST00000369983.3:c.53G>T	chr10.hg19:g.104018748G>T	ENSP00000359000:p.Gly18Val	101.0	0.0	.		83.0	39.0	.	NM_001199378	Q5VXX3|Q96CK6|Q96HZ3|Q9H473	Missense_Mutation	SNP	ENST00000369983.3	hg19	CCDS7533.1	.	.	.	.	.	.	.	.	.	.	G	17.66	3.445710	0.63178	.	.	ENSG00000107862	ENST00000369983	T	0.09163	3.01	5.95	5.95	0.96441	.	0.061547	0.64402	D	0.000005	T	0.10078	0.0247	N	0.12182	0.205	0.80722	D	1	P;P;P;P	0.44195	0.756;0.756;0.828;0.617	B;B;B;B	0.42062	0.374;0.283;0.217;0.173	T	0.09640	-1.0665	10	0.66056	D	0.02	-16.8934	20.3931	0.98965	0.0:0.0:1.0:0.0	.	18;18;18;18	Q149P1;Q149P0;Q92538;Q504U7	.;.;GBF1_HUMAN;.	V	18	ENSP00000359000:G18V	ENSP00000359000:G18V	G	+	2	0	GBF1	104008738	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.804000	0.75186	2.824000	0.97209	0.655000	0.94253	GGG	.	.	.	none		0.403	GBF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050051.1		
PTPRE	5791	hgsc.bcm.edu	37	10	129846027	129846027	+	Splice_Site	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:129846027G>C	ENST00000254667.3	+	5	488		c.e5-1		PTPRE_ENST00000419012.2_Splice_Site|PTPRE_ENST00000306042.5_Splice_Site|PTPRE_ENST00000430713.2_Splice_Site|PTPRE_ENST00000471218.1_Splice_Site	NM_006504.4	NP_006495.1	P23469	PTPRE_HUMAN	protein tyrosine phosphatase, receptor type, E						negative regulation of insulin receptor signaling pathway (GO:0046627)|peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|regulation of mast cell activation (GO:0033003)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(1)	22		all_epithelial(44;1.66e-05)|all_lung(145;0.00456)|Lung NSC(174;0.0066)|all_neural(114;0.0936)|Colorectal(57;0.141)|Breast(234;0.166)|Melanoma(40;0.203)			Alendronate(DB00630)	GTGTCTCTAAGGTTCAGGAAG	0.557																																					.	Colon(52;977 1184 20575 41685)	Atlas-SNP	.											.	PTPRE	132	.	0			c.210-1G>C						PASS	.						102.0	98.0	100.0					10																	129846027		2203	4300	6503	SO:0001630	splice_region_variant	5791	exon5			CTCTAAGGTTCAG	AF406557	CCDS7657.1, CCDS7658.1	10q26	2011-06-09			ENSG00000132334	ENSG00000132334		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"""	9669	protein-coding gene	gene with protein product		600926				8595895	Standard	NM_130435		Approved	PTPE	uc001lkb.3	P23469	OTTHUMG00000019254	ENST00000254667.3:c.210-1G>C	chr10.hg19:g.129846027G>C		86.0	0.0	.		94.0	45.0	.	NM_006504	Q13345|Q5VWH3|Q5VWH4|Q96KQ6	Splice_Site	SNP	ENST00000254667.3	hg19	CCDS7657.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.337182	0.81911	.	.	ENSG00000132334	ENST00000254667;ENST00000442830;ENST00000419012;ENST00000430713;ENST00000455661;ENST00000306042	.	.	.	5.05	5.05	0.67936	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	18.4659	0.90755	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	PTPRE	129736017	1.000000	0.71417	0.997000	0.53966	0.947000	0.59692	8.680000	0.91225	2.519000	0.84933	0.650000	0.86243	.	.	.	.	none		0.557	PTPRE-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050990.1		Intron
DNHD1	144132	hgsc.bcm.edu	37	11	6579352	6579352	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:6579352C>A	ENST00000527990.2	+	23	8827	c.8827C>A	c.(8827-8829)Ctg>Atg	p.L2943M	DNHD1_ENST00000254579.6_Missense_Mutation_p.L2943M			Q96M86	DNHD1_HUMAN	dynein heavy chain domain 1	2943					microtubule-based movement (GO:0007018)	dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)	microtubule motor activity (GO:0003777)			NS(1)|autonomic_ganglia(1)|breast(4)|endometrium(13)|kidney(6)|large_intestine(11)|lung(14)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	55		Medulloblastoma(188;0.00776)|all_neural(188;0.0652)|Breast(177;0.171)		Epithelial(150;3.93e-08)|BRCA - Breast invasive adenocarcinoma(625;0.13)		GCCAGTGGCTCTGTTGGTACC	0.547																																					p.L2943M		Atlas-SNP	.											.	DNHD1	198	.	0			c.C8827A						PASS	.						74.0	65.0	68.0					11																	6579352		692	1591	2283	SO:0001583	missense	144132	exon25			GTGGCTCTGTTGG	AK128064	CCDS44532.1, CCDS7767.1	11p15.4	2011-02-10		2005-11-28	ENSG00000179532	ENSG00000179532			26532	protein-coding gene	gene with protein product			"""chromosome 11 open reading frame 47"", ""dynein heavy chain domain 1-like"", ""coiled-coil domain containing 35"""	DHCD1, C11orf47, DNHD1L, CCDC35		12975309	Standard	NM_173589		Approved	FLJ32752, FLJ46184, FLJ35709, DKFZp686J0796	uc001mdw.4	Q96M86	OTTHUMG00000133403	ENST00000527990.2:c.8827C>A	chr11.hg19:g.6579352C>A	ENSP00000436180:p.Leu2943Met	80.0	0.0	.		76.0	30.0	.	NM_144666	Q2NKK8|Q6UWI9|Q8NAA2|Q8TEE6|Q9NSZ9	Missense_Mutation	SNP	ENST00000527990.2	hg19	CCDS44532.1	.	.	.	.	.	.	.	.	.	.	C	1.131	-0.652479	0.03480	.	.	ENSG00000179532	ENST00000254579;ENST00000527990;ENST00000534210;ENST00000524401	T;T	0.32988	1.43;1.43	5.49	3.61	0.41365	.	.	.	.	.	T	0.35537	0.0935	N	0.14661	0.345	0.27084	N	0.963003	D;D	0.89917	1.0;1.0	D;D	0.91635	0.997;0.999	T	0.22173	-1.0224	9	0.29301	T	0.29	.	11.372	0.49704	0.0:0.851:0.0:0.149	.	2943;690	Q96M86;E9PHZ7	DNHD1_HUMAN;.	M	2943;2943;690;8	ENSP00000254579:L2943M;ENSP00000436180:L2943M	ENSP00000254579:L2943M	L	+	1	2	DNHD1	6535928	0.729000	0.28090	0.197000	0.23402	0.007000	0.05969	0.773000	0.26661	0.670000	0.31165	0.650000	0.86243	CTG	.	.	.	none		0.547	DNHD1-007	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384673.2	NM_144666	
PPFIBP2	8495	hgsc.bcm.edu	37	11	7672127	7672127	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:7672127G>T	ENST00000299492.4	+	22	2566	c.2178G>T	c.(2176-2178)tgG>tgT	p.W726C	PPFIBP2_ENST00000533792.1_Missense_Mutation_p.W568C|PPFIBP2_ENST00000530181.1_Missense_Mutation_p.W583C|PPFIBP2_ENST00000528883.1_Missense_Mutation_p.W614C|PPFIBP2_ENST00000530582.1_3'UTR	NM_003621.3	NP_003612	Q8ND30	LIPB2_HUMAN	PTPRF interacting protein, binding protein 2 (liprin beta 2)	726	SAM 3. {ECO:0000255|PROSITE- ProRule:PRU00184}.				cell-matrix adhesion (GO:0007160)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|intracellular (GO:0005622)|presynaptic active zone (GO:0048786)	DNA binding (GO:0003677)|integrase activity (GO:0008907)			breast(8)|cervix(1)|kidney(1)|large_intestine(8)|lung(8)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	32				Epithelial(150;2.01e-07)|BRCA - Breast invasive adenocarcinoma(625;0.236)		TGATGGAGTGGTTACGATCTG	0.532																																					p.W726C		Atlas-SNP	.											.	PPFIBP2	87	.	0			c.G2178T						PASS	.						207.0	179.0	188.0					11																	7672127		2201	4296	6497	SO:0001583	missense	8495	exon22			GGAGTGGTTACGA	AF034803	CCDS31419.1, CCDS58116.1, CCDS58117.1	11p15.4	2013-01-10			ENSG00000166387	ENSG00000166387		"""Sterile alpha motif (SAM) domain containing"""	9250	protein-coding gene	gene with protein product		603142				9624153	Standard	NM_003621		Approved	Cclp1	uc001mfj.5	Q8ND30	OTTHUMG00000165617	ENST00000299492.4:c.2178G>T	chr11.hg19:g.7672127G>T	ENSP00000299492:p.Trp726Cys	101.0	0.0	.		65.0	29.0	.	NM_003621	B7Z433|E9PK77|O75337|Q8WW26	Missense_Mutation	SNP	ENST00000299492.4	hg19	CCDS31419.1	.	.	.	.	.	.	.	.	.	.	G	13.74	2.326893	0.41197	.	.	ENSG00000166387	ENST00000299492;ENST00000537211;ENST00000533792;ENST00000541115;ENST00000528883;ENST00000530181	D;D;D;D	0.92911	-3.13;-3.13;-3.13;-3.13	5.35	4.43	0.53597	Sterile alpha motif domain (2);Sterile alpha motif/pointed domain (2);Sterile alpha motif, type 2 (1);	0.000000	0.64402	D	0.000003	D	0.96836	0.8967	M	0.93898	3.47	0.80722	D	1	D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D	0.97110	0.999;1.0;0.999;0.999;0.998;0.999	D	0.97670	1.0166	10	0.87932	D	0	-9.916	13.4534	0.61184	0.0:0.0:0.842:0.158	.	614;614;649;568;583;726	E9PK77;B7Z433;F5GWB0;E9PP16;E9PMU1;Q8ND30	.;.;.;.;.;LIPB2_HUMAN	C	726;67;568;649;614;583	ENSP00000299492:W726C;ENSP00000436498:W568C;ENSP00000435469:W614C;ENSP00000437321:W583C	ENSP00000299492:W726C	W	+	3	0	PPFIBP2	7628703	1.000000	0.71417	0.998000	0.56505	0.017000	0.09413	9.601000	0.98297	1.607000	0.50170	-0.181000	0.13052	TGG	.	.	.	none		0.532	PPFIBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385345.2	NM_003621	
OR5P2	120065	hgsc.bcm.edu	37	11	7818479	7818479	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:7818479A>C	ENST00000329434.2	-	1	41	c.11T>G	c.(10-12)cTg>cGg	p.L4R	RP11-35J10.5_ENST00000527565.1_lincRNA	NM_153444.1	NP_703145.1	Q8WZ92	OR5P2_HUMAN	olfactory receptor, family 5, subfamily P, member 2	4						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(2)|pancreas(1)|prostate(1)|skin(4)	22				Epithelial(150;8.62e-08)|BRCA - Breast invasive adenocarcinoma(625;0.189)		CCCGTCCTTCAGGGAATTCAT	0.408																																					p.L4R		Atlas-SNP	.											.	OR5P2	68	.	0			c.T11G						PASS	.						47.0	55.0	53.0					11																	7818479		2095	4291	6386	SO:0001583	missense	120065	exon1			TCCTTCAGGGAAT	AF173006	CCDS7782.1	11p15.4	2012-08-09			ENSG00000183303	ENSG00000183303		"""GPCR / Class A : Olfactory receptors"""	14783	protein-coding gene	gene with protein product							Standard	NM_153444		Approved	JCG3	uc001mfp.1	Q8WZ92	OTTHUMG00000165668	ENST00000329434.2:c.11T>G	chr11.hg19:g.7818479A>C	ENSP00000331823:p.Leu4Arg	31.0	0.0	.		41.0	21.0	.	NM_153444	Q3MIS8	Missense_Mutation	SNP	ENST00000329434.2	hg19	CCDS7782.1	.	.	.	.	.	.	.	.	.	.	A	15.97	2.989773	0.54041	.	.	ENSG00000183303	ENST00000329434	T	0.00145	8.67	5.2	-5.77	0.02369	.	0.363029	0.22658	N	0.057223	T	0.00144	0.0004	L	0.39898	1.24	0.19300	N	0.999978	P	0.44776	0.843	P	0.50970	0.655	T	0.52697	-0.8541	10	0.87932	D	0	5.2615	0.7576	0.01001	0.2152:0.2208:0.1453:0.4188	.	4	Q8WZ92	OR5P2_HUMAN	R	4	ENSP00000331823:L4R	ENSP00000331823:L4R	L	-	2	0	OR5P2	7775055	0.001000	0.12720	0.014000	0.15608	0.001000	0.01503	0.470000	0.22084	-0.713000	0.04981	-0.531000	0.04308	CTG	.	.	.	none		0.408	OR5P2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385696.1	NM_153444	
CAT	847	hgsc.bcm.edu	37	11	34475367	34475367	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:34475367A>C	ENST00000241052.4	+	6	694	c.605A>C	c.(604-606)gAt>gCt	p.D202A		NM_001752.3	NP_001743.1	P04040	CATA_HUMAN	catalase	202					aerobic respiration (GO:0009060)|cellular response to growth factor stimulus (GO:0071363)|cholesterol metabolic process (GO:0008203)|hemoglobin metabolic process (GO:0020027)|hydrogen peroxide catabolic process (GO:0042744)|menopause (GO:0042697)|negative regulation of apoptotic process (GO:0043066)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|nucleobase-containing small molecule metabolic process (GO:0055086)|osteoblast differentiation (GO:0001649)|positive regulation of cell division (GO:0051781)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|protein homotetramerization (GO:0051289)|protein tetramerization (GO:0051262)|purine nucleobase metabolic process (GO:0006144)|purine nucleotide catabolic process (GO:0006195)|response to hyperoxia (GO:0055093)|response to hypoxia (GO:0001666)|response to reactive oxygen species (GO:0000302)|response to vitamin E (GO:0033197)|small molecule metabolic process (GO:0044281)|triglyceride metabolic process (GO:0006641)|ureteric bud development (GO:0001657)|UV protection (GO:0009650)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|lysosome (GO:0005764)|membrane (GO:0016020)|mitochondrial intermembrane space (GO:0005758)|peroxisomal matrix (GO:0005782)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)	aminoacylase activity (GO:0004046)|antioxidant activity (GO:0016209)|catalase activity (GO:0004096)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|metal ion binding (GO:0046872)|NADP binding (GO:0050661)|oxidoreductase activity, acting on peroxide as acceptor (GO:0016684)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)			breast(1)|cervix(2)|endometrium(3)|kidney(2)|large_intestine(6)|lung(5)|ovary(2)|pancreas(1)|stomach(1)|urinary_tract(3)	26		Lung NSC(402;2.76e-08)|Acute lymphoblastic leukemia(5;0.00143)|all_hematologic(20;0.0116)|Melanoma(852;0.027)		BRCA - Breast invasive adenocarcinoma(625;0.000995)	Fomepizole(DB01213)	TTGTTCAGTGATCGGGGGATT	0.353																																					p.D202A		Atlas-SNP	.											.	CAT	42	.	0			c.A605C						PASS	.						111.0	105.0	107.0					11																	34475367		2202	4298	6500	SO:0001583	missense	847	exon6			TCAGTGATCGGGG	AY028632	CCDS7891.1	11p13	2012-10-02			ENSG00000121691	ENSG00000121691	1.11.1.6		1516	protein-coding gene	gene with protein product		115500					Standard	NM_001752		Approved		uc001mvm.3	P04040	OTTHUMG00000044353	ENST00000241052.4:c.605A>C	chr11.hg19:g.34475367A>C	ENSP00000241052:p.Asp202Ala	67.0	0.0	.		77.0	34.0	.	NM_001752	A8K6C0|B2RCZ9|D3DR07|Q2M1U4|Q4VXX5|Q9BWT9|Q9UC85	Missense_Mutation	SNP	ENST00000241052.4	hg19	CCDS7891.1	.	.	.	.	.	.	.	.	.	.	A	17.56	3.420175	0.62622	.	.	ENSG00000121691	ENST00000241052	D	0.93426	-3.22	5.84	5.84	0.93424	Catalase domain (1);Catalase, N-terminal (2);	0.046947	0.85682	D	0.000000	D	0.98143	0.9387	H	0.99404	4.55	0.80722	D	1	D	0.63880	0.993	D	0.66351	0.943	D	0.99081	1.0837	10	0.87932	D	0	-36.6195	13.2555	0.60076	0.8681:0.1319:0.0:0.0	.	202	P04040	CATA_HUMAN	A	202	ENSP00000241052:D202A	ENSP00000241052:D202A	D	+	2	0	CAT	34431943	1.000000	0.71417	0.940000	0.37924	0.519000	0.34347	9.339000	0.96797	2.232000	0.73038	0.533000	0.62120	GAT	.	.	.	none		0.353	CAT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000103197.2	NM_001752	
EXT2	2132	hgsc.bcm.edu	37	11	44129381	44129381	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:44129381C>T	ENST00000343631.3	+	2	248	c.119C>T	c.(118-120)aCt>aTt	p.T40I	EXT2_ENST00000533608.1_Missense_Mutation_p.T40I|EXT2_ENST00000358681.4_Missense_Mutation_p.T40I|EXT2_ENST00000395673.3_Missense_Mutation_p.T73I			Q93063	EXT2_HUMAN	exostosin glycosyltransferase 2	40					carbohydrate metabolic process (GO:0005975)|cell differentiation (GO:0030154)|cellular polysaccharide biosynthetic process (GO:0033692)|glycosaminoglycan biosynthetic process (GO:0006024)|glycosaminoglycan metabolic process (GO:0030203)|heparan sulfate proteoglycan biosynthetic process (GO:0015012)|heparan sulfate proteoglycan biosynthetic process, polysaccharide chain biosynthetic process (GO:0015014)|mesoderm formation (GO:0001707)|ossification (GO:0001503)|protein glycosylation (GO:0006486)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|intrinsic component of endoplasmic reticulum membrane (GO:0031227)|membrane (GO:0016020)	glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N-acetylglucosaminyltransferase activity (GO:0050508)|glucuronosyltransferase activity (GO:0015020)|heparan sulfate N-acetylglucosaminyltransferase activity (GO:0042328)|N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase activity (GO:0050509)|protein heterodimerization activity (GO:0046982)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|lung(17)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	32						CTCATTGCCACTGGCATGTTT	0.512			"""Mis, N, F, S"""			"""exostoses, osteosarcoma"""			Hereditary Multiple Exostoses																												p.T73I		Atlas-SNP	.	yes	Rec		Multiple Exostoses Type 2	11	11p12-p11	2132	multiple exostoses type 2 gene		M	.	EXT2	129	.	0			c.C218T						PASS	.						160.0	166.0	164.0					11																	44129381		2203	4300	6503	SO:0001583	missense	2132	exon2	Familial Cancer Database	HME, Hereditary Exostoses, Multiple Osteochondromatosis, Multiple Cartilaginous Exostoses	TTGCCACTGGCAT		CCDS7908.1, CCDS53618.1, CCDS53619.1	11p12-p11	2014-09-17	2013-03-01		ENSG00000151348	ENSG00000151348	2.4.1.224, 2.4.1.225	"""Exostosin glycosyltransferase family"""	3513	protein-coding gene	gene with protein product	"""Glucuronosyl-N-acetylglucosaminyl-proteoglycan 4-alpha-N- acetylglucosaminyltransferase"", ""N-acetylglucosaminyl-proteoglycan 4-beta-glucuronosyltransferase"""	608210	"""exostoses (multiple) 2"", ""exostosin 2"""			8162019, 9576285	Standard	NM_000401		Approved	SOTV	uc001mya.3	Q93063	OTTHUMG00000166498	ENST00000343631.3:c.119C>T	chr11.hg19:g.44129381C>T	ENSP00000342656:p.Thr40Ile	101.0	0.0	.		84.0	32.0	.	NM_000401	B2R5Z6|C9JU51|J3KPT2|O15288	Missense_Mutation	SNP	ENST00000343631.3	hg19	CCDS7908.1	.	.	.	.	.	.	.	.	.	.	C	16.25	3.071234	0.55646	.	.	ENSG00000151348	ENST00000533608;ENST00000532479;ENST00000527014;ENST00000358681;ENST00000395673;ENST00000343631	T;T;T;T;T;T	0.51817	0.69;0.69;0.69;0.69;0.69;0.69	5.45	5.45	0.79879	.	0.000000	0.85682	D	0.000000	T	0.45155	0.1328	L	0.27053	0.805	0.80722	D	1	P;P;D;P;P	0.53885	0.954;0.938;0.963;0.873;0.873	P;B;P;B;B	0.48921	0.541;0.391;0.595;0.293;0.293	T	0.19778	-1.0295	10	0.22706	T	0.39	-1.6238	19.302	0.94148	0.0:1.0:0.0:0.0	.	40;40;40;40;53	Q6NUL1;C9JU51;Q93063-2;Q93063;D3DR24	.;.;.;EXT2_HUMAN;.	I	40;40;40;40;73;40	ENSP00000431173:T40I;ENSP00000433827:T40I;ENSP00000434716:T40I;ENSP00000351509:T40I;ENSP00000379032:T73I;ENSP00000342656:T40I	ENSP00000342656:T40I	T	+	2	0	EXT2	44085957	1.000000	0.71417	0.988000	0.46212	0.988000	0.76386	7.380000	0.79704	2.568000	0.86640	0.650000	0.86243	ACT	.	.	.	none		0.512	EXT2-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390074.1	NM_000401	
ATG13	9776	hgsc.bcm.edu	37	11	46690086	46690086	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:46690086T>A	ENST00000434074.1	+	14	1879	c.1190T>A	c.(1189-1191)tTt>tAt	p.F397Y	ATG13_ENST00000524625.1_Missense_Mutation_p.F360Y|ATG13_ENST00000312040.4_Missense_Mutation_p.F397Y|ATG13_ENST00000528494.1_Missense_Mutation_p.F430Y|ATG13_ENST00000359513.4_Missense_Mutation_p.F397Y|ATG13_ENST00000529655.1_Missense_Mutation_p.F360Y|ATG13_ENST00000526508.1_Missense_Mutation_p.F397Y|ATG13_ENST00000530500.1_Missense_Mutation_p.F281Y|ATG13_ENST00000451945.1_Missense_Mutation_p.F360Y	NM_001205120.1	NP_001192049.1	O75143	ATG13_HUMAN	autophagy related 13	397					autophagic vacuole assembly (GO:0000045)	ATG1/UKL1 signaling complex (GO:0034273)|cytosol (GO:0005829)|pre-autophagosomal structure (GO:0000407)|ULK1-ATG13-FIP200 complex (GO:0070969)	protein kinase binding (GO:0019901)			NS(1)|central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(5)|prostate(1)|skin(1)	15						TTTGCCATGTTTGCTCCCAAG	0.512																																					p.F430Y		Atlas-SNP	.											.	ATG13	60	.	0			c.T1289A						PASS	.						166.0	147.0	153.0					11																	46690086		2201	4299	6500	SO:0001583	missense	9776	exon15			CCATGTTTGCTCC	AB014552	CCDS7921.1, CCDS44582.1, CCDS55760.1, CCDS55761.1	11p11.2	2014-02-12	2012-06-06	2010-06-29	ENSG00000175224	ENSG00000175224			29091	protein-coding gene	gene with protein product		615088	"""KIAA0652"", ""ATG13 autophagy related 13 homolog (S. cerevisiae)"""	KIAA0652		15169610, 18339812, 17204848	Standard	NM_001205120		Approved		uc001nda.3	O75143	OTTHUMG00000166538	ENST00000434074.1:c.1190T>A	chr11.hg19:g.46690086T>A	ENSP00000400642:p.Phe397Tyr	77.0	0.0	.		61.0	33.0	.	NM_001205119	B4DFI4|D3DQQ1|D3DQQ2|E9PQZ8|Q53EN6|Q9BRL3|Q9H8B0	Missense_Mutation	SNP	ENST00000434074.1	hg19	CCDS44582.1	.	.	.	.	.	.	.	.	.	.	T	18.65	3.669804	0.67814	.	.	ENSG00000175224	ENST00000395549;ENST00000434074;ENST00000312040;ENST00000451945;ENST00000529655;ENST00000530500;ENST00000526508;ENST00000524625;ENST00000359513;ENST00000528494;ENST00000525009	.	.	.	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.73009	0.3532	L	0.53249	1.67	0.58432	D	0.999997	D;D;D;D	0.71674	0.995;0.997;0.998;0.997	P;D;D;D	0.78314	0.829;0.977;0.991;0.984	T	0.67573	-0.5636	9	0.11182	T	0.66	-15.6578	16.422	0.83766	0.0:0.0:0.0:1.0	.	281;397;430;360	B4DFI4;O75143;E9PQZ8;O75143-2	.;ATG13_HUMAN;.;.	Y	360;397;397;360;360;281;397;360;397;430;129	.	ENSP00000310321:F397Y	F	+	2	0	ATG13	46646662	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.307000	0.78920	2.270000	0.75569	0.533000	0.62120	TTT	.	.	.	none		0.512	ATG13-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000390300.2	NM_014741	
SYTL2	54843	hgsc.bcm.edu	37	11	85445743	85445743	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:85445743G>T	ENST00000528231.1	-	6	903	c.626C>A	c.(625-627)aCt>aAt	p.T209N	SYTL2_ENST00000527523.1_Missense_Mutation_p.T161N|SYTL2_ENST00000316356.4_Missense_Mutation_p.T210N|SYTL2_ENST00000389960.4_Missense_Mutation_p.T209N|SYTL2_ENST00000524452.1_Missense_Mutation_p.T209N	NM_001162951.1|NM_001162953.1	NP_001156423.1|NP_001156425.1	Q9HCH5	SYTL2_HUMAN	synaptotagmin-like 2	209					exocytosis (GO:0006887)|intracellular protein transport (GO:0006886)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of mucus secretion (GO:0070257)|vesicle docking involved in exocytosis (GO:0006904)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|exocytic vesicle (GO:0070382)|extrinsic component of plasma membrane (GO:0019897)|Golgi apparatus (GO:0005794)|melanosome (GO:0042470)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	neurexin family protein binding (GO:0042043)|phosphatase binding (GO:0019902)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(22)|ovary(2)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	52		Acute lymphoblastic leukemia(157;4.19e-06)|all_hematologic(158;0.0033)		KIRC - Kidney renal clear cell carcinoma(183;0.202)|Kidney(183;0.237)		TTGGATTGAAGTATCTGCGAC	0.358																																					p.T210N		Atlas-SNP	.											.	SYTL2	231	.	0			c.C629A						PASS	.						94.0	93.0	94.0					11																	85445743		2203	4299	6502	SO:0001583	missense	54843	exon6			ATTGAAGTATCTG	AJ303364	CCDS31649.1, CCDS31652.1, CCDS41698.1, CCDS53687.1, CCDS53688.1, CCDS53689.1	11q14.1	2014-06-13			ENSG00000137501	ENSG00000137501			15585	protein-coding gene	gene with protein product	"""chromosome 11 synaptotagmin"", ""breast cancer-associated antigen SGA-72M"", ""protein phosphatase 1, regulatory subunit 151"""	612880				10997877	Standard	XM_005274057		Approved	FLJ20163, FLJ21219, KIAA1597, exophilin-4, CHR11SYT, SLP2, SGA72M, MGC102768, PPP1R151	uc001pbb.3	Q9HCH5	OTTHUMG00000166977	ENST00000528231.1:c.626C>A	chr11.hg19:g.85445743G>T	ENSP00000431701:p.Thr209Asn	79.0	0.0	.		77.0	32.0	.	NM_001162953	B3KRS3|B4DJT5|B4DKW3|B4DQ26|B7SA85|B7ZLX6|B7ZLX7|Q2YDA7|Q6TV07|Q6ZN59|Q6ZVC5|Q8ND34|Q96BJ2|Q9H768|Q9NXM1	Missense_Mutation	SNP	ENST00000528231.1	hg19	CCDS53688.1	.	.	.	.	.	.	.	.	.	.	G	3.458	-0.110581	0.06924	.	.	ENSG00000137501	ENST00000389960;ENST00000316356;ENST00000528231;ENST00000527523;ENST00000524452	T;T;T;T;T	0.26660	1.8;1.82;1.82;1.72;1.8	5.54	-0.768	0.11013	.	.	.	.	.	T	0.08758	0.0217	N	0.08118	0	0.09310	N	0.999999	B;B;B;B;B	0.33477	0.413;0.413;0.138;0.217;0.396	B;B;B;B;B	0.28139	0.071;0.071;0.032;0.071;0.086	T	0.25012	-1.0144	8	.	.	.	.	1.8756	0.03217	0.4894:0.1246:0.2655:0.1205	.	161;209;209;210;67	Q9HCH5-14;Q9HCH5-6;Q9HCH5;Q9HCH5-13;Q9HCH5-15	.;.;SYTL2_HUMAN;.;.	N	209;210;209;161;209	ENSP00000374610:T209N;ENSP00000318803:T210N;ENSP00000431701:T209N;ENSP00000434010:T161N;ENSP00000435238:T209N	.	T	-	2	0	SYTL2	85123391	0.000000	0.05858	0.287000	0.24848	0.027000	0.11550	-0.258000	0.08733	-0.286000	0.09076	-0.806000	0.03193	ACT	.	.	.	none		0.358	SYTL2-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000392192.1	NM_206927	
HTR3A	3359	hgsc.bcm.edu	37	11	113853914	113853914	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:113853914G>T	ENST00000504030.2	+	5	892	c.447G>T	c.(445-447)aaG>aaT	p.K149N	HTR3A_ENST00000355556.2_Missense_Mutation_p.K155N|HTR3A_ENST00000506841.2_Missense_Mutation_p.K149N|HTR3A_ENST00000375498.2_Missense_Mutation_p.K155N|HTR3A_ENST00000535865.1_5'UTR|HTR3A_ENST00000299961.5_Missense_Mutation_p.K134N			P46098	5HT3A_HUMAN	5-hydroxytryptamine (serotonin) receptor 3A, ionotropic	149					cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|cellular response to growth factor stimulus (GO:0071363)|digestion (GO:0007586)|ion transmembrane transport (GO:0034220)|response to cocaine (GO:0042220)|response to ethanol (GO:0045471)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	receptor activity (GO:0004872)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)|serotonin-activated cation-selective channel activity (GO:0005232)|voltage-gated potassium channel activity (GO:0005249)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(14)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	36		all_cancers(61;2.31e-17)|all_epithelial(67;2.1e-10)|all_hematologic(158;4.64e-05)|Melanoma(852;0.000312)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Prostate(24;0.0294)|Medulloblastoma(222;0.0425)		BRCA - Breast invasive adenocarcinoma(274;2.71e-06)|Epithelial(105;2.58e-05)|all cancers(92;0.000238)|OV - Ovarian serous cystadenocarcinoma(223;0.191)	Alosetron(DB00969)|Amoxapine(DB00543)|Aripiprazole(DB01238)|Chloroprocaine(DB01161)|Cisapride(DB00604)|Clozapine(DB00363)|Dolasetron(DB00757)|Ergoloid mesylate(DB01049)|Granisetron(DB00889)|Loxapine(DB00408)|Memantine(DB01043)|Methadone(DB00333)|Metoclopramide(DB01233)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Ondansetron(DB00904)|Palonosetron(DB00377)|Procaine(DB00721)|Quetiapine(DB01224)|Rocuronium(DB00728)|Tapentadol(DB06204)|Trimipramine(DB00726)|Tubocurarine(DB01199)|Ziprasidone(DB00246)	AGAACTACAAGCCCCTTCAGG	0.542																																					p.K155N		Atlas-SNP	.											.	HTR3A	93	.	0			c.G465T						PASS	.						201.0	180.0	187.0					11																	113853914		2201	4296	6497	SO:0001583	missense	3359	exon5			CTACAAGCCCCTT	D49394	CCDS8365.1, CCDS8366.1, CCDS8365.2, CCDS8366.2, CCDS53710.1	11q23.1-q23.2	2012-05-22	2012-02-03					"""5-HT (serotonin) receptors"", ""Ligand-gated ion channels / 5-HT (serotonin) receptors, ionotropic"""	5297	protein-coding gene	gene with protein product		182139	"""5-hydroxytryptamine (serotonin) receptor 3A"""	HTR3		8530095, 12867984	Standard	NM_000869		Approved	5-HT3R, 5-HT3A	uc010rxb.2	P46098		ENST00000504030.2:c.447G>T	chr11.hg19:g.113853914G>T	ENSP00000424189:p.Lys149Asn	97.0	0.0	.		89.0	26.0	.	NM_000869	B4DSY6|G5E986|O60854|Q7KZM7|Q99918|Q9BSZ9	Missense_Mutation	SNP	ENST00000504030.2	hg19		.	.	.	.	.	.	.	.	.	.	G	19.87	3.907299	0.72868	.	.	ENSG00000166736	ENST00000504030;ENST00000355556;ENST00000375498;ENST00000506841;ENST00000299961	T;T;T;T;T	0.79033	-1.23;-1.23;-1.23;-1.23;-1.23	5.39	3.5	0.40072	.	0.000000	0.85682	D	0.000000	D	0.84777	0.5547	M	0.63428	1.95	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.996;1.0	D	0.85804	0.1375	10	0.87932	D	0	-36.4163	11.5276	0.50588	0.2021:0.0:0.7979:0.0	.	134;155;155	B4DSY6;G5E986;Q7KZM7	.;.;.	N	149;155;155;149;134	ENSP00000424189:K149N;ENSP00000347754:K155N;ENSP00000364648:K155N;ENSP00000424776:K149N;ENSP00000299961:K134N	ENSP00000299961:K134N	K	+	3	2	HTR3A	113359124	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	3.295000	0.51794	1.278000	0.44430	0.555000	0.69702	AAG	.	.	.	none		0.542	HTR3A-001	KNOWN	upstream_ATG|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000360822.2	NM_000869	
ABCG4	64137	hgsc.bcm.edu	37	11	119025032	119025032	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:119025032G>T	ENST00000449422.2	+	4	607	c.419G>T	c.(418-420)cGc>cTc	p.R140L	ABCG4_ENST00000531739.1_Missense_Mutation_p.R140L|ABCG4_ENST00000307417.3_Missense_Mutation_p.R140L	NM_001142505.1	NP_001135977.1	Q9H172	ABCG4_HUMAN	ATP-binding cassette, sub-family G (WHITE), member 4	140	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				cholesterol efflux (GO:0033344)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|cholesterol transporter activity (GO:0017127)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.R140H(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(28)|ovary(2)|prostate(1)|skin(1)	44	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		AGGACCTTCCGCAAGATGTCC	0.577																																					p.R140L		Atlas-SNP	.											ABCG4,NS,carcinoma,0,1	ABCG4	77	.	1	Substitution - Missense(1)	endometrium(1)	c.G419T						PASS	.						107.0	89.0	95.0					11																	119025032		2200	4295	6495	SO:0001583	missense	64137	exon4			CCTTCCGCAAGAT	AJ300465	CCDS8415.1	11q23	2012-03-14			ENSG00000172350	ENSG00000172350		"""ATP binding cassette transporters / subfamily G"""	13884	protein-coding gene	gene with protein product	"""putative ABC transporter"", ""ATP-binding cassette, subfamily G, member 4"""	607784				11435397	Standard	NM_022169		Approved	WHITE2	uc001pvs.3	Q9H172	OTTHUMG00000166169	ENST00000449422.2:c.419G>T	chr11.hg19:g.119025032G>T	ENSP00000406874:p.Arg140Leu	73.0	0.0	.		50.0	22.0	.	NM_022169	A8K1B5|Q8WWH0|Q8WWH1|Q8WWH2	Missense_Mutation	SNP	ENST00000449422.2	hg19	CCDS8415.1	.	.	.	.	.	.	.	.	.	.	G	32	5.170473	0.94768	.	.	ENSG00000172350	ENST00000307417;ENST00000524604;ENST00000449422;ENST00000531739	D;D;D;D	0.94793	-3.52;-3.52;-3.52;-3.52	4.89	4.89	0.63831	ATPase, AAA+ type, core (1);ABC transporter-like (2);	0.103879	0.64402	D	0.000012	D	0.94631	0.8269	M	0.78049	2.395	0.58432	D	0.999999	P	0.42296	0.775	B	0.42087	0.375	D	0.95566	0.8634	10	0.87932	D	0	-22.3413	16.9713	0.86301	0.0:0.0:1.0:0.0	.	140	Q9H172	ABCG4_HUMAN	L	140	ENSP00000304111:R140L;ENSP00000431915:R140L;ENSP00000406874:R140L;ENSP00000434318:R140L	ENSP00000304111:R140L	R	+	2	0	ABCG4	118530242	1.000000	0.71417	0.992000	0.48379	0.937000	0.57800	9.246000	0.95438	2.539000	0.85634	0.491000	0.48974	CGC	.	.	.	none		0.577	ABCG4-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000388215.1	NM_022169	
CD163L1	283316	hgsc.bcm.edu	37	12	7528025	7528025	+	Silent	SNP	T	T	C	rs368493737		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:7528025T>C	ENST00000313599.3	-	11	2910	c.2853A>G	c.(2851-2853)ggA>ggG	p.G951G	CD163L1_ENST00000396630.1_Silent_p.G951G|CD163L1_ENST00000544331.1_5'Flank|CD163L1_ENST00000416109.2_Silent_p.G961G			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	951	SRCR 9. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						TATATTTTCCTCCTGTGGTTG	0.493																																					p.G951G		Atlas-SNP	.											.	CD163L1	238	.	0			c.A2853G						PASS	.	T		1,4405	2.1+/-5.4	0,1,2202	88.0	76.0	80.0		2853	-0.0	0.0	12		80	0,8600		0,0,4300	no	coding-synonymous	CD163L1	NM_174941.4		0,1,6502	CC,CT,TT		0.0,0.0227,0.0077		951/1454	7528025	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	283316	exon11			TTTTCCTCCTGTG	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.2853A>G	chr12.hg19:g.7528025T>C		45.0	0.0	.		59.0	23.0	.	NM_174941	B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	hg19	CCDS8577.1																																																																																			.	.	.	weak		0.493	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
SMCO3	440087	hgsc.bcm.edu	37	12	14959531	14959531	+	Silent	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:14959531G>A	ENST00000316048.2	-	2	156	c.84C>T	c.(82-84)tgC>tgT	p.C28C	C12orf60_ENST00000527783.1_Intron|C12orf60_ENST00000330828.2_Intron	NM_001013698.2	NP_001013720.2	A2RU48	SMCO3_HUMAN	single-pass membrane protein with coiled-coil domains 3	28						integral component of membrane (GO:0016021)											TGTCAGATAAGCAATCAAGAA	0.463																																					p.C28C		Atlas-SNP	.											.	.	.	.	0			c.C84T						PASS	.						88.0	85.0	86.0					12																	14959531		1875	4127	6002	SO:0001819	synonymous_variant	0	exon2			AGATAAGCAATCA		CCDS41759.1	12p12.3	2013-03-11	2013-03-11	2013-03-11	ENSG00000179256	ENSG00000179256			34401	protein-coding gene	gene with protein product			"""chromosome 12 open reading frame 69"""	C12orf69			Standard	NM_001013698		Approved	LOC440087	uc001rck.1	A2RU48	OTTHUMG00000167474	ENST00000316048.2:c.84C>T	chr12.hg19:g.14959531G>A		54.0	0.0	.		56.0	29.0	.	NM_001013698	Q8NAI5	Silent	SNP	ENST00000316048.2	hg19	CCDS41759.1																																																																																			.	.	.	none		0.463	SMCO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394738.1	NM_001013698	
EIF4B	1975	hgsc.bcm.edu	37	12	53432173	53432173	+	Silent	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:53432173T>C	ENST00000262056.9	+	12	1880	c.1554T>C	c.(1552-1554)tcT>tcC	p.S518S	EIF4B_ENST00000416762.3_Silent_p.S479S|RP11-983P16.4_ENST00000552905.1_RNA|RP11-983P16.4_ENST00000550601.1_RNA|EIF4B_ENST00000420463.3_Silent_p.S523S|RP11-983P16.4_ENST00000546566.1_RNA	NM_001417.4	NP_001408.2	P23588	IF4B_HUMAN	eukaryotic translation initiation factor 4B	518					cellular protein metabolic process (GO:0044267)|gene expression (GO:0010467)|insulin receptor signaling pathway (GO:0008286)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|regulation of translational initiation (GO:0006446)|RNA metabolic process (GO:0016070)|translation (GO:0006412)|translational initiation (GO:0006413)	cytosol (GO:0005829)|eukaryotic translation initiation factor 4F complex (GO:0016281)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|translation initiation factor activity (GO:0003743)			breast(4)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(10)|stomach(1)|upper_aerodigestive_tract(1)	22						CTCAACCATCTGAGGAAGGAC	0.408																																					p.S518S		Atlas-SNP	.											.	EIF4B	38	.	0			c.T1554C						PASS	.						141.0	138.0	139.0					12																	53432173		1865	4111	5976	SO:0001819	synonymous_variant	1975	exon12			ACCATCTGAGGAA	X55733	CCDS41788.1, CCDS73474.1	12q13.13	2013-02-12			ENSG00000063046	ENSG00000063046		"""RNA binding motif (RRM) containing"""	3285	protein-coding gene	gene with protein product		603928					Standard	XM_005268709		Approved		uc001sbh.4	P23588	OTTHUMG00000169570	ENST00000262056.9:c.1554T>C	chr12.hg19:g.53432173T>C		81.0	0.0	.		82.0	43.0	.	NM_001417	Q4G0E3|Q53HQ2|Q6GPH5|Q6IB46|Q8WYK5	Silent	SNP	ENST00000262056.9	hg19	CCDS41788.1																																																																																			.	.	.	none		0.408	EIF4B-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000404852.2	NM_001417	
AVIL	10677	hgsc.bcm.edu	37	12	58201151	58201151	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:58201151A>T	ENST00000257861.3	-	12	1884	c.1454T>A	c.(1453-1455)tTc>tAc	p.F485Y	AVIL_ENST00000550083.1_5'Flank|TSFM_ENST00000548851.1_Intron|AVIL_ENST00000537081.1_Missense_Mutation_p.F478Y|RNU6-1083P_ENST00000384022.1_RNA|RP11-571M6.17_ENST00000602802.1_lincRNA	NM_006576.3	NP_006567.3	O75366	AVIL_HUMAN	advillin	485	Core. {ECO:0000250}.				actin filament capping (GO:0051693)|cilium morphogenesis (GO:0060271)|cytoskeleton organization (GO:0007010)|nervous system development (GO:0007399)|positive regulation of neuron projection development (GO:0010976)	actin cytoskeleton (GO:0015629)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|neuron projection (GO:0043005)	actin binding (GO:0003779)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(9)|ovary(1)|prostate(6)	32	Glioma(12;6.95e-05)|all_neural(12;0.00016)|Melanoma(17;0.122)					GATGGCCATGAAGTGGCGTGG	0.522																																					p.F485Y		Atlas-SNP	.											.	AVIL	60	.	0			c.T1454A						PASS	.						162.0	143.0	149.0					12																	58201151		2203	4300	6503	SO:0001583	missense	10677	exon12			GCCATGAAGTGGC	AF041449	CCDS8959.1	12q13.11	2006-03-30				ENSG00000135407			14188	protein-coding gene	gene with protein product		613397				9664034, 12034507	Standard	NM_006576		Approved	p92, FLJ12386, ADVIL, DOC6	uc001sqj.2	O75366	OTTHUMG00000170461	ENST00000257861.3:c.1454T>A	chr12.hg19:g.58201151A>T	ENSP00000257861:p.Phe485Tyr	79.0	0.0	.		60.0	29.0	.	NM_006576	B2RAU7|Q2NKM9	Missense_Mutation	SNP	ENST00000257861.3	hg19	CCDS8959.1	.	.	.	.	.	.	.	.	.	.	A	28.4	4.914701	0.92178	.	.	ENSG00000135407	ENST00000537081;ENST00000257861	T;T	0.59083	0.29;0.29	4.77	4.77	0.60923	Gelsolin domain (1);	0.000000	0.85682	D	0.000000	D	0.83487	0.5265	H	0.97682	4.055	0.58432	D	0.999999	D;D	0.76494	0.999;0.991	D;D	0.77004	0.989;0.938	D	0.89012	0.3429	10	0.72032	D	0.01	-23.5203	13.6731	0.62438	1.0:0.0:0.0:0.0	.	478;485	O75366-2;O75366	.;AVIL_HUMAN	Y	478;485	ENSP00000443207:F478Y;ENSP00000257861:F485Y	ENSP00000257861:F485Y	F	-	2	0	AVIL	56487418	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	9.010000	0.93611	2.122000	0.65172	0.459000	0.35465	TTC	.	.	.	none		0.522	AVIL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409276.1	NM_006576	
FAM71C	196472	hgsc.bcm.edu	37	12	100042118	100042118	+	Silent	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:100042118A>C	ENST00000324341.1	+	1	588	c.166A>C	c.(166-168)Aga>Cga	p.R56R	ANKS1B_ENST00000547776.2_Intron|ANKS1B_ENST00000329257.7_Intron|ANKS1B_ENST00000547010.1_Intron	NM_153364.3	NP_699195.1	Q8NEG0	FA71C_HUMAN	family with sequence similarity 71, member C	56										breast(1)|endometrium(1)|kidney(2)|large_intestine(4)|lung(8)|upper_aerodigestive_tract(1)|urinary_tract(1)	18				OV - Ovarian serous cystadenocarcinoma(2;0.00733)|Epithelial(2;0.0385)|all cancers(2;0.19)		GATCAGCAAAAGAGGAGAAGT	0.522																																					p.R56R		Atlas-SNP	.											.	FAM71C	48	.	0			c.A166C						PASS	.						147.0	130.0	136.0					12																	100042118		2203	4300	6503	SO:0001819	synonymous_variant	196472	exon1			AGCAAAAGAGGAG		CCDS9072.1	12q23.1	2006-02-03				ENSG00000180219			28594	protein-coding gene	gene with protein product						12477932	Standard	NM_153364		Approved	MGC39520	uc001tgn.3	Q8NEG0		ENST00000324341.1:c.166A>C	chr12.hg19:g.100042118A>C		77.0	0.0	.		65.0	32.0	.	NM_153364	B2R6Y6	Silent	SNP	ENST00000324341.1	hg19	CCDS9072.1																																																																																			.	.	.	none		0.522	FAM71C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000408458.1	NM_153364	
DRAM1	55332	hgsc.bcm.edu	37	12	102271585	102271585	+	Silent	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:102271585G>A	ENST00000258534.8	+	1	457	c.18G>A	c.(16-18)agG>agA	p.R6R	DRAM1_ENST00000544152.1_Silent_p.R6R	NM_018370.2	NP_060840.2	Q8N682	DRAM1_HUMAN	DNA-damage regulated autophagy modulator 1	6					apoptotic process (GO:0006915)|autophagy (GO:0006914)|regulation of autophagy (GO:0010506)	cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|lysosome (GO:0005764)				central_nervous_system(1)|endometrium(2)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(1)	12						GCTTCCTGAGGGGAATGGCTT	0.711																																					p.R6R		Atlas-SNP	.											.	DRAM1	46	.	0			c.G18A						PASS	.						52.0	54.0	53.0					12																	102271585		1844	3904	5748	SO:0001819	synonymous_variant	55332	exon1			CCTGAGGGGAATG	BC018435, DA721965	CCDS41823.1	12q23.2	2014-02-12	2009-06-12		ENSG00000136048	ENSG00000136048			25645	protein-coding gene	gene with protein product	"""damage-regulated autophagy modulator"""	610776				16839881	Standard	NM_018370		Approved	FLJ11259, DRAM	uc001tix.3	Q8N682		ENST00000258534.8:c.18G>A	chr12.hg19:g.102271585G>A		18.0	0.0	.		25.0	8.0	.	NM_018370	B7Z4T0|Q7L3E3|Q9NUN1	Silent	SNP	ENST00000258534.8	hg19	CCDS41823.1																																																																																			.	.	.	none		0.711	DRAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409195.1	NM_018370	
STAB2	55576	hgsc.bcm.edu	37	12	104031881	104031881	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:104031881A>G	ENST00000388887.2	+	8	1001	c.797A>G	c.(796-798)gAa>gGa	p.E266G		NM_017564.9	NP_060034.9			stabilin 2											NS(4)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(15)|kidney(11)|large_intestine(26)|lung(77)|ovary(10)|pancreas(1)|prostate(5)|skin(14)|stomach(2)	174						ACATGCCAAGAAGGCTACCGT	0.493																																					p.E266G		Atlas-SNP	.											.	STAB2	370	.	0			c.A797G						PASS	.						196.0	165.0	176.0					12																	104031881		2203	4300	6503	SO:0001583	missense	55576	exon8			GCCAAGAAGGCTA	AF160476	CCDS31888.1	12q23.3	2007-01-29				ENSG00000136011			18629	protein-coding gene	gene with protein product	"""hyaluronic acid receptor for endocytosis"""	608561				11829752, 12077138	Standard	XR_429107		Approved	DKFZP434E0321, FELL, STAB-2, HARE, FEEL-2	uc001tjw.3	Q8WWQ8	OTTHUMG00000170056	ENST00000388887.2:c.797A>G	chr12.hg19:g.104031881A>G	ENSP00000373539:p.Glu266Gly	77.0	0.0	.		89.0	34.0	.	NM_017564		Missense_Mutation	SNP	ENST00000388887.2	hg19	CCDS31888.1	.	.	.	.	.	.	.	.	.	.	A	18.87	3.715138	0.68844	.	.	ENSG00000136011	ENST00000388887	T	0.06142	3.34	5.34	5.34	0.76211	EGF domain, merozoite surface protein 1-like (1);Epidermal growth factor-like (1);EGF-like region, conserved site (1);Epidermal growth factor-like, type 3 (1);	0.719585	0.13832	N	0.359654	T	0.12475	0.0303	M	0.70842	2.15	0.28806	N	0.898514	P	0.42161	0.772	B	0.44315	0.446	T	0.06409	-1.0828	10	0.37606	T	0.19	.	10.2614	0.43430	0.8523:0.0:0.0:0.1477	.	266	Q8WWQ8	STAB2_HUMAN	G	266	ENSP00000373539:E266G	ENSP00000373539:E266G	E	+	2	0	STAB2	102556011	0.801000	0.28930	0.907000	0.35723	0.972000	0.66771	3.463000	0.53050	2.022000	0.59522	0.459000	0.35465	GAA	.	.	.	none		0.493	STAB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407089.1		
LRRC43	254050	hgsc.bcm.edu	37	12	122674790	122674790	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr12:122674790C>T	ENST00000339777.4	+	5	804	c.776C>T	c.(775-777)cCa>cTa	p.P259L	LRRC43_ENST00000425921.1_Missense_Mutation_p.P74L	NM_152759.4	NP_689972.3	Q8N309	LRC43_HUMAN	leucine rich repeat containing 43	259	LRRCT.									NS(1)|endometrium(1)|large_intestine(4)|lung(10)|skin(1)|upper_aerodigestive_tract(2)	19	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000312)|Epithelial(86;0.000539)|BRCA - Breast invasive adenocarcinoma(302;0.225)		CAGGGAAACCCACTGGCCTTG	0.632																																					p.P259L		Atlas-SNP	.											.	LRRC43	105	.	0			c.C776T						PASS	.						91.0	102.0	98.0					12																	122674790		2161	4261	6422	SO:0001583	missense	254050	exon5			GAAACCCACTGGC	AK124107	CCDS45001.1	12q24.31	2014-09-11			ENSG00000158113	ENSG00000158113			28562	protein-coding gene	gene with protein product						12477932	Standard	NM_152759		Approved	MGC35140	uc009zxm.3	Q8N309	OTTHUMG00000168915	ENST00000339777.4:c.776C>T	chr12.hg19:g.122674790C>T	ENSP00000344233:p.Pro259Leu	82.0	0.0	.		66.0	35.0	.	NM_001098519	Q6ZVT9	Missense_Mutation	SNP	ENST00000339777.4	hg19	CCDS45001.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.938331	0.92526	.	.	ENSG00000158113	ENST00000537729;ENST00000339777;ENST00000289014;ENST00000425921	T;T;T	0.38560	1.13;1.13;1.13	5.22	5.22	0.72569	.	0.000000	0.85682	D	0.000000	T	0.65739	0.2720	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.69335	-0.5172	10	0.87932	D	0	-43.7481	18.3879	0.90472	0.0:1.0:0.0:0.0	.	259	Q8N309	LRC43_HUMAN	L	74;259;130;74	ENSP00000438751:P74L;ENSP00000344233:P259L;ENSP00000416628:P74L	ENSP00000289014:P130L	P	+	2	0	LRRC43	121240743	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	6.184000	0.72008	2.460000	0.83146	0.561000	0.74099	CCA	.	.	.	none		0.632	LRRC43-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401589.1	NM_152759	
PARP4	143	hgsc.bcm.edu	37	13	25026604	25026604	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:25026604A>G	ENST00000381989.3	-	24	3059	c.2954T>C	c.(2953-2955)cTg>cCg	p.L985P		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	985	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		CTGTAATGTCAGGCTCTCATC	0.557																																					p.L985P		Atlas-SNP	.											.	PARP4	142	.	0			c.T2954C						PASS	.						139.0	133.0	135.0					13																	25026604		2203	4300	6503	SO:0001583	missense	143	exon24			AATGTCAGGCTCT	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.2954T>C	chr13.hg19:g.25026604A>G	ENSP00000371419:p.Leu985Pro	81.0	0.0	.		73.0	39.0	.	NM_006437	O75903|Q14682|Q5QNZ9|Q9H1M6	Missense_Mutation	SNP	ENST00000381989.3	hg19	CCDS9307.1	.	.	.	.	.	.	.	.	.	.	A	15.66	2.898475	0.52227	.	.	ENSG00000102699	ENST00000381989	T	0.08193	3.12	5.29	5.29	0.74685	von Willebrand factor, type A (3);	0.158962	0.43110	D	0.000618	T	0.28532	0.0706	M	0.78916	2.43	0.58432	D	0.999999	D	0.89917	1.0	D	0.83275	0.996	T	0.01133	-1.1441	10	0.39692	T	0.17	-12.1098	13.2758	0.60186	1.0:0.0:0.0:0.0	.	985	Q9UKK3	PARP4_HUMAN	P	985	ENSP00000371419:L985P	ENSP00000371419:L985P	L	-	2	0	PARP4	23924604	1.000000	0.71417	0.985000	0.45067	0.099000	0.18886	3.961000	0.56759	2.242000	0.73789	0.519000	0.50382	CTG	.	.	.	none		0.557	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
LECT1	11061	hgsc.bcm.edu	37	13	53298215	53298215	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:53298215C>T	ENST00000377962.3	-	4	463	c.385G>A	c.(385-387)Gag>Aag	p.E129K	LECT1_ENST00000448904.2_Missense_Mutation_p.E129K			O75829	LECT1_HUMAN	leukocyte cell derived chemotaxin 1	129	BRICHOS. {ECO:0000255|PROSITE- ProRule:PRU00255}.				cartilage development (GO:0051216)|endothelial cell morphogenesis (GO:0001886)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030948)|proteoglycan metabolic process (GO:0006029)|skeletal system development (GO:0001501)	integral component of membrane (GO:0016021)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(5)|ovary(2)|skin(1)|urinary_tract(1)	15		Lung NSC(96;0.00212)|Breast(56;0.00235)|Hepatocellular(98;0.065)|Prostate(109;0.0771)|all_neural(104;0.173)		GBM - Glioblastoma multiforme(99;3.38e-08)		TAGCACTTCTCTCCTCCAGCA	0.448																																					p.E129K		Atlas-SNP	.											.	LECT1	44	.	0			c.G385A						PASS	.						148.0	115.0	126.0					13																	53298215		2203	4300	6503	SO:0001583	missense	11061	exon4			ACTTCTCTCCTCC	AB006000	CCDS9437.1, CCDS45051.1	13q14.3	2012-10-10			ENSG00000136110	ENSG00000136110		"""BRICHOS domain containing"""	17005	protein-coding gene	gene with protein product	"""BRICHOS domain containing 3"""	605147	"""multiple myeloma tumor suppressor 1"""	MYETS1		9731231, 10103018	Standard	XM_006719760		Approved	CHM-I, CHM1, chondromodulin, BRICD3	uc001vhf.2	O75829	OTTHUMG00000016980	ENST00000377962.3:c.385G>A	chr13.hg19:g.53298215C>T	ENSP00000367198:p.Glu129Lys	44.0	0.0	.		51.0	27.0	.	NM_007015	Q5TAM4|Q8TAY6|Q9UM18	Missense_Mutation	SNP	ENST00000377962.3	hg19	CCDS9437.1	.	.	.	.	.	.	.	.	.	.	C	32	5.173276	0.94807	.	.	ENSG00000136110	ENST00000448904;ENST00000377962;ENST00000431550	T;T;T	0.78816	-1.21;-1.21;-1.21	5.9	5.06	0.68205	BRICHOS (2);	0.136600	0.64402	N	0.000003	D	0.83538	0.5276	M	0.69823	2.125	0.58432	D	0.999999	D;D	0.56746	0.971;0.977	P;P	0.53988	0.621;0.739	D	0.85425	0.1145	10	0.62326	D	0.03	.	14.9399	0.70986	0.0:0.9316:0.0:0.0684	.	129;129	O75829-2;O75829	.;LECT1_HUMAN	K	129;129;51	ENSP00000388576:E129K;ENSP00000367198:E129K;ENSP00000396035:E51K	ENSP00000367198:E129K	E	-	1	0	LECT1	52196216	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.253000	0.58791	1.495000	0.48549	0.655000	0.94253	GAG	.	.	.	none		0.448	LECT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045110.3		
LMO7	4008	hgsc.bcm.edu	37	13	76195877	76195877	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:76195877G>T	ENST00000341547.4	+	1	1308	c.48G>T	c.(46-48)atG>atT	p.M16I	RP11-173B14.5_ENST00000568302.1_RNA|RP11-173B14.5_ENST00000568735.1_RNA|LMO7_ENST00000377534.3_Missense_Mutation_p.M16I|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.M16I	NM_005358.5	NP_005349.3	Q8WWI1	LMO7_HUMAN	LIM domain 7	16					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		ACAGTTGGATGTCCTATGATG	0.383																																					p.M16I		Atlas-SNP	.											.	LMO7	334	.	0			c.G48T						PASS	.						72.0	70.0	71.0					13																	76195877		2203	4300	6503	SO:0001583	missense	4008	exon1			TTGGATGTCCTAT	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000341547.4:c.48G>T	chr13.hg19:g.76195877G>T	ENSP00000342112:p.Met16Ile	41.0	0.0	.		59.0	14.0	.	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000341547.4	hg19	CCDS9454.1	.	.	.	.	.	.	.	.	.	.	G	9.697	1.153520	0.21371	.	.	ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534	T;T;T	0.52983	0.64;0.64;0.64	3.82	1.3	0.21679	.	.	.	.	.	T	0.32763	0.0840	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.29882	-0.9997	8	0.87932	D	0	.	4.1462	0.10217	0.1966:0.0:0.2294:0.574	.	16	Q8WWI1-3	.	I	16	ENSP00000342112:M16I;ENSP00000349571:M16I;ENSP00000366757:M16I	ENSP00000342112:M16I	M	+	3	0	LMO7	75093878	0.001000	0.12720	0.000000	0.03702	0.011000	0.07611	0.376000	0.20535	0.096000	0.17463	-0.518000	0.04402	ATG	.	.	.	none		0.383	LMO7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045297.1	NM_005358	
LMO7	4008	hgsc.bcm.edu	37	13	76378589	76378589	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:76378589C>A	ENST00000321797.8	+	6	848	c.127C>A	c.(127-129)Ctg>Atg	p.L43M	LMO7_ENST00000526202.1_Missense_Mutation_p.L237M|LMO7_ENST00000341547.4_Missense_Mutation_p.L328M|LMO7_ENST00000465261.2_Missense_Mutation_p.L43M|LMO7_ENST00000377534.3_Missense_Mutation_p.L328M|RP11-29G8.3_ENST00000563635.1_RNA|LMO7_ENST00000357063.3_Missense_Mutation_p.L328M			Q8WWI1	LMO7_HUMAN	LIM domain 7	328					protein ubiquitination (GO:0016567)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)	ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(2)|kidney(2)|large_intestine(20)|lung(15)|ovary(2)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	56		Breast(118;0.0992)		GBM - Glioblastoma multiforme(99;0.0109)		ACCAGCACCTCTGAGAAAGAA	0.443																																					p.L328M		Atlas-SNP	.											.	LMO7	334	.	0			c.C982A						PASS	.						119.0	128.0	125.0					13																	76378589		2203	4300	6503	SO:0001583	missense	4008	exon9			GCACCTCTGAGAA	AF092557	CCDS9454.1, CCDS53876.1	13q22.2	2008-02-05	2004-06-15		ENSG00000136153	ENSG00000136153			6646	protein-coding gene	gene with protein product	"""F-box only protein 20"""	604362	"""LIM domain only 7"""	FBXO20		9826547, 10531035	Standard	NM_005358		Approved	FBX20, KIAA0858	uc021rkq.1	Q8WWI1	OTTHUMG00000017093	ENST00000321797.8:c.127C>A	chr13.hg19:g.76378589C>A	ENSP00000317802:p.Leu43Met	64.0	0.0	.		77.0	30.0	.	NM_005358	E9PLH4|O15462|O95346|Q5TBK6|Q9UKC1|Q9UQM5|Q9Y6A7	Missense_Mutation	SNP	ENST00000321797.8	hg19		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	14.42|14.42	2.530501|2.530501	0.45073|0.45073	.|.	.|.	ENSG00000136153|ENSG00000136153	ENST00000341547;ENST00000357063;ENST00000377534;ENST00000377499;ENST00000321797;ENST00000526202;ENST00000465261;ENST00000497947;ENST00000526371;ENST00000526528;ENST00000489941;ENST00000525373|ENST00000447038	T;T;T;T;T;T;T;T;T;T;T;T|.	0.35789|.	1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29;1.29|.	5.98|5.98	1.59|1.59	0.23543|0.23543	.|.	0.077397|.	0.52532|.	D|.	0.000064|.	T|T	0.57829|0.57829	0.2080|0.2080	M|M	0.77820|0.77820	2.39|2.39	0.28496|0.28496	N|N	0.914238|0.914238	D;D;D;D;D|.	0.89917|.	0.997;0.997;0.998;1.0;0.998|.	D;D;D;D;D|.	0.87578|.	0.988;0.974;0.994;0.998;0.984|.	T|T	0.54689|0.54689	-0.8256|-0.8256	10|5	0.87932|.	D|.	0|.	-10.7237|-10.7237	11.4846|11.4846	0.50346|0.50346	0.0:0.2787:0.0:0.7213|0.0:0.2787:0.0:0.7213	.|.	237;328;328;43;276|.	E9PMS6;Q8WWI1-3;Q8WWI1;E9PLH4;F8J2B5|.	.;.;LMO7_HUMAN;.;.|.	M|Y	328;328;328;276;43;237;43;43;43;43;43;43|45	ENSP00000342112:L328M;ENSP00000349571:L328M;ENSP00000366757:L328M;ENSP00000366719:L276M;ENSP00000317802:L43M;ENSP00000431129:L237M;ENSP00000433352:L43M;ENSP00000431271:L43M;ENSP00000432269:L43M;ENSP00000434201:L43M;ENSP00000431636:L43M;ENSP00000431896:L43M|.	ENSP00000317802:L43M|.	L|S	+|+	1|2	2|0	LMO7|LMO7	75276590|75276590	0.022000|0.022000	0.18835|0.18835	0.976000|0.976000	0.42696|0.42696	0.782000|0.782000	0.44232|0.44232	0.202000|0.202000	0.17295|0.17295	0.426000|0.426000	0.26116|0.26116	-0.918000|-0.918000	0.02743|0.02743	CTG|TCT	.	.	.	none		0.443	LMO7-005	PUTATIVE	alternative_5_UTR|not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000045301.3	NM_005358	
TEP1	7011	hgsc.bcm.edu	37	14	20846278	20846278	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:20846278G>A	ENST00000262715.5	-	39	5666	c.5626C>T	c.(5626-5628)Cgg>Tgg	p.R1876W	TEP1_ENST00000545983.1_Missense_Mutation_p.R214W|TEP1_ENST00000556935.1_Missense_Mutation_p.R1768W	NM_007110.4	NP_009041.2	Q99973	TEP1_HUMAN	telomerase-associated protein 1	1876					RNA-dependent DNA replication (GO:0006278)|telomere maintenance via recombination (GO:0000722)	chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|ribonucleoprotein complex (GO:0030529)|telomerase holoenzyme complex (GO:0005697)	ATP binding (GO:0005524)|RNA binding (GO:0003723)			NS(4)|breast(1)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(48)|ovary(7)|pancreas(1)|prostate(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	96	all_cancers(95;0.00123)	all_lung(585;0.235)	Epithelial(56;7.42e-08)|all cancers(55;6.46e-07)	GBM - Glioblastoma multiforme(265;0.028)|READ - Rectum adenocarcinoma(17;0.233)		GCAGCCAGCCGTGCCCCTTCT	0.627																																					p.R1876W		Atlas-SNP	.											.	TEP1	224	.	0			c.C5626T						PASS	.						84.0	82.0	83.0					14																	20846278		2203	4300	6503	SO:0001583	missense	7011	exon39			CCAGCCGTGCCCC		CCDS9548.1	14q11.2	2013-01-10			ENSG00000129566	ENSG00000129566		"""WD repeat domain containing"""	11726	protein-coding gene	gene with protein product	"""TROVE domain family, member 1"""	601686				9403057	Standard	NM_007110		Approved	TP1, TLP1, VAULT2, p240, TROVE1	uc001vxe.3	Q99973	OTTHUMG00000029515	ENST00000262715.5:c.5626C>T	chr14.hg19:g.20846278G>A	ENSP00000262715:p.Arg1876Trp	79.0	0.0	.		68.0	40.0	.	NM_007110	A0AUV9	Missense_Mutation	SNP	ENST00000262715.5	hg19	CCDS9548.1	.	.	.	.	.	.	.	.	.	.	G	13.30	2.195644	0.38806	.	.	ENSG00000129566	ENST00000262715;ENST00000359243;ENST00000556935;ENST00000545983	T;T;T	0.51817	0.69;1.55;1.55	5.48	3.57	0.40892	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.353602	0.31897	N	0.006884	T	0.54663	0.1872	L	0.51422	1.61	0.09310	N	1	D;D;D;D	0.76494	0.998;0.997;0.999;0.997	P;P;P;P	0.56916	0.761;0.653;0.809;0.765	T	0.48779	-0.9005	10	0.59425	D	0.04	-11.432	11.9525	0.52962	0.0:0.0:0.5654:0.4346	.	214;1768;1219;1876	B4E0B6;G3V5X7;G3V2A4;Q99973	.;.;.;TEP1_HUMAN	W	1876;1876;1768;214	ENSP00000262715:R1876W;ENSP00000452574:R1768W;ENSP00000438849:R214W	ENSP00000262715:R1876W	R	-	1	2	TEP1	19916118	0.002000	0.14202	0.040000	0.18447	0.215000	0.24574	1.163000	0.31798	1.306000	0.44926	0.557000	0.71058	CGG	.	.	.	none		0.627	TEP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073563.2	NM_007110	
PRMT5	10419	hgsc.bcm.edu	37	14	23393872	23393872	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:23393872T>C	ENST00000324366.8	-	9	1209	c.986A>G	c.(985-987)aAg>aGg	p.K329R	PRMT5-AS1_ENST00000599580.2_RNA|PRMT5_ENST00000553897.1_Missense_Mutation_p.K285R|PRMT5-AS1_ENST00000424245.2_RNA|PRMT5_ENST00000216350.8_Missense_Mutation_p.K268R|PRMT5-AS1_ENST00000590290.1_RNA|PRMT5_ENST00000397441.2_Missense_Mutation_p.K312R|PRMT5_ENST00000553641.1_5'Flank|PRMT5-AS1_ENST00000587245.2_RNA|PRMT5-AS1_ENST00000595662.1_RNA|PRMT5_ENST00000538452.1_Missense_Mutation_p.K223R|PRMT5-AS1_ENST00000609885.1_RNA|PRMT5_ENST00000397440.4_Missense_Mutation_p.K158R|PRMT5-AS1_ENST00000457443.2_RNA	NM_006109.3	NP_006100.2	O14744	ANM5_HUMAN	protein arginine methyltransferase 5	329	SAM-dependent MTase PRMT-type. {ECO:0000255|PROSITE-ProRule:PRU01015}.				cell proliferation (GO:0008283)|circadian regulation of gene expression (GO:0032922)|endothelial cell activation (GO:0042118)|gene expression (GO:0010467)|histone H4-R3 methylation (GO:0043985)|ncRNA metabolic process (GO:0034660)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-arginine methylation (GO:0018216)|peptidyl-arginine methylation, to symmetrical-dimethyl arginine (GO:0019918)|peptidyl-arginine N-methylation (GO:0035246)|regulation of mitosis (GO:0007088)|regulation of transcription, DNA-templated (GO:0006355)|RNA metabolic process (GO:0016070)|spliceosomal snRNP assembly (GO:0000387)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|methylosome (GO:0034709)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|core promoter sequence-specific DNA binding (GO:0001046)|histone-arginine N-methyltransferase activity (GO:0008469)|methyltransferase activity (GO:0008168)|protein-arginine omega-N symmetric methyltransferase activity (GO:0035243)|ribonucleoprotein complex binding (GO:0043021)|transcription corepressor activity (GO:0003714)			endometrium(4)|kidney(3)|large_intestine(3)|lung(9)|ovary(1)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	25	all_cancers(95;2.76e-05)			GBM - Glioblastoma multiforme(265;0.0126)		GATGGGGTCCTTTTCAAACAC	0.488																																					p.K329R		Atlas-SNP	.											.	PRMT5	101	.	0			c.A986G						PASS	.						107.0	96.0	100.0					14																	23393872		2203	4300	6503	SO:0001583	missense	10419	exon9			GGGTCCTTTTCAA	AF015913	CCDS9579.1, CCDS41922.1, CCDS61394.1, CCDS61395.1, CCDS61396.1	14q11.2	2014-06-12	2006-02-16	2006-02-16	ENSG00000100462	ENSG00000100462	2.1.1.125	"""Protein arginine methyltransferases"""	10894	protein-coding gene	gene with protein product		604045	"""skb1 (S. pombe) homolog"", ""SKB1 homolog (S. pombe)"""	HRMT1L5, SKB1		9843966	Standard	NM_001282955		Approved	SKB1Hs	uc001whm.1	O14744	OTTHUMG00000028709	ENST00000324366.8:c.986A>G	chr14.hg19:g.23393872T>C	ENSP00000319169:p.Lys329Arg	77.0	0.0	.		67.0	4.0	.	NM_006109	A8MTP3|A8MZ91|B4DX49|B4DY30|B5BU10|D3DS33|E2QRE7|Q6IBR1|Q9UKH1	Missense_Mutation	SNP	ENST00000324366.8	hg19	CCDS9579.1	.	.	.	.	.	.	.	.	.	.	T	23.6	4.435772	0.83885	.	.	ENSG00000100462	ENST00000324366;ENST00000397441;ENST00000397440;ENST00000216350;ENST00000538452;ENST00000553897;ENST00000553502;ENST00000555530;ENST00000556043;ENST00000553550	T;T;T;T;T;T	0.21932	1.98;1.98;1.98;1.98;1.98;1.98	5.92	5.92	0.95590	.	0.088928	0.85682	D	0.000000	T	0.30885	0.0779	L	0.43701	1.375	0.80722	D	1	P;B;B;P;P	0.52692	0.778;0.363;0.333;0.955;0.516	B;B;B;P;B	0.54060	0.398;0.38;0.208;0.741;0.313	T	0.01143	-1.1438	10	0.28530	T	0.3	-21.0851	15.346	0.74337	0.0:0.0:0.0:1.0	.	285;268;158;329;312	G3V5W5;B4DX49;A8MTP3;O14744;A8MZ91	.;.;.;ANM5_HUMAN;.	R	329;312;158;268;223;285;72;224;81;175	ENSP00000319169:K329R;ENSP00000380583:K312R;ENSP00000380582:K158R;ENSP00000216350:K268R;ENSP00000444915:K223R;ENSP00000452555:K285R	ENSP00000216350:K268R	K	-	2	0	PRMT5	22463712	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.970000	0.76099	2.270000	0.75569	0.459000	0.35465	AAG	.	.	.	none		0.488	PRMT5-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000071674.3		
RALGAPA1	253959	hgsc.bcm.edu	37	14	36103901	36103901	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:36103901G>C	ENST00000389698.3	-	32	4746	c.4356C>G	c.(4354-4356)agC>agG	p.S1452R	RALGAPA1_ENST00000382366.3_Missense_Mutation_p.S1465R|RALGAPA1_ENST00000307138.6_Missense_Mutation_p.S1452R|RALGAPA1_ENST00000258840.6_Missense_Mutation_p.S1499R	NM_014990.1	NP_055805.1	Q6GYQ0	RGPA1_HUMAN	Ral GTPase activating protein, alpha subunit 1 (catalytic)	1452	Minimal domain that binds to TCF3/E12. {ECO:0000250}.				activation of Ral GTPase activity (GO:0032859)|regulation of transcription, DNA-templated (GO:0006355)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein heterodimerization activity (GO:0046982)|Ral GTPase activator activity (GO:0017123)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(7)|kidney(7)|large_intestine(14)|lung(21)|ovary(3)|prostate(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	67						AATCAGAGAGGCTCATGGGAA	0.413																																					p.S1452R		Atlas-SNP	.											.	RALGAPA1	289	.	0			c.C4356G						PASS	.						48.0	45.0	46.0					14																	36103901		2203	4297	6500	SO:0001583	missense	253959	exon32			AGAGAGGCTCATG	AK126975	CCDS32064.1, CCDS32065.1, CCDS61439.1	14q13.2	2012-01-26	2009-09-09	2009-09-09	ENSG00000174373	ENSG00000174373			17770	protein-coding gene	gene with protein product	"""tuberin-like protein 1"", ""GAP-related interacting protein to E12"""	608884	"""GTPase activating RANGAP domain-like 1"", ""GTPase activating Rap/RanGAP domain-like 1"""	GARNL1		19520869	Standard	NM_014990		Approved	GRIPE, DKFZp667F074, KIAA0884, Tulip1, RalGAPalpha1	uc001wtj.3	Q6GYQ0	OTTHUMG00000170619	ENST00000389698.3:c.4356C>G	chr14.hg19:g.36103901G>C	ENSP00000374348:p.Ser1452Arg	125.0	0.0	.		124.0	52.0	.	NM_194301	A6NMA4|B9EK38|C5NU19|O94960|Q6GYP9|Q6ZT23|Q86YF3|Q86YF5|Q8ND69	Missense_Mutation	SNP	ENST00000389698.3	hg19	CCDS32065.1	.	.	.	.	.	.	.	.	.	.	G	14.17	2.455222	0.43634	.	.	ENSG00000174373	ENST00000389698;ENST00000307138;ENST00000335518;ENST00000258840;ENST00000554259;ENST00000382366;ENST00000553892	T;T;T;T;T;T	0.29655	1.56;1.56;1.56;1.56;1.56;1.56	5.38	-0.0408	0.13870	.	0.096424	0.85682	D	0.000000	T	0.27278	0.0669	L	0.59436	1.845	0.32562	N	0.531019	P;B;P;B	0.43826	0.818;0.399;0.666;0.399	B;B;B;B	0.39840	0.311;0.266;0.23;0.147	T	0.38802	-0.9644	10	0.48119	T	0.1	-9.7139	10.9048	0.47073	0.4098:0.0:0.5902:0.0	.	1499;1465;1452;1452	Q6GYQ0-6;B9EK38;Q6GYQ0-2;Q6GYQ0	.;.;.;RGPA1_HUMAN	R	1452;1452;1452;1499;90;1465;1499	ENSP00000374348:S1452R;ENSP00000302647:S1452R;ENSP00000258840:S1499R;ENSP00000451133:S90R;ENSP00000371803:S1465R;ENSP00000451877:S1499R	ENSP00000258840:S1499R	S	-	3	2	RALGAPA1	35173652	1.000000	0.71417	0.982000	0.44146	0.971000	0.66376	0.968000	0.29357	-0.201000	0.10284	-0.142000	0.14014	AGC	.	.	.	none		0.413	RALGAPA1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000409829.1	XM_210022	
BMP4	652	hgsc.bcm.edu	37	14	54417256	54417256	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:54417256G>T	ENST00000245451.4	-	4	1114	c.721C>A	c.(721-723)Ctc>Atc	p.L241I	BMP4_ENST00000417573.1_Missense_Mutation_p.L241I|MIR5580_ENST00000580850.1_RNA|BMP4_ENST00000558984.1_Missense_Mutation_p.L241I|BMP4_ENST00000559087.1_Missense_Mutation_p.L241I	NM_001202.3	NP_001193.2	P12644	BMP4_HUMAN	bone morphogenetic protein 4	241					activation of MAPKK activity (GO:0000186)|anterior/posterior axis specification (GO:0009948)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|BMP signaling pathway (GO:0030509)|BMP signaling pathway involved in heart induction (GO:0003130)|BMP signaling pathway involved in nephric duct formation (GO:0071893)|BMP signaling pathway involved in renal system segmentation (GO:0061151)|BMP signaling pathway involved in ureter morphogenesis (GO:0061149)|branching involved in prostate gland morphogenesis (GO:0060442)|branching involved in ureteric bud morphogenesis (GO:0001658)|branching morphogenesis of an epithelial tube (GO:0048754)|bronchus development (GO:0060433)|bud dilation involved in lung branching (GO:0060503)|bud elongation involved in lung branching (GO:0060449)|cardiac septum development (GO:0003279)|cellular response to growth factor stimulus (GO:0071363)|chondrocyte differentiation (GO:0002062)|cloacal septation (GO:0060197)|common-partner SMAD protein phosphorylation (GO:0007182)|cranial suture morphogenesis (GO:0060363)|deltoid tuberosity development (GO:0035993)|dorsal/ventral neural tube patterning (GO:0021904)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digit morphogenesis (GO:0042733)|embryonic hindlimb morphogenesis (GO:0035116)|embryonic skeletal joint morphogenesis (GO:0060272)|endocardial cushion development (GO:0003197)|endochondral ossification (GO:0001958)|epithelial cell proliferation involved in lung morphogenesis (GO:0060502)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|epithelial-mesenchymal cell signaling (GO:0060684)|erythrocyte differentiation (GO:0030218)|extracellular matrix organization (GO:0030198)|germ cell development (GO:0007281)|glomerular capillary formation (GO:0072104)|glomerular visceral epithelial cell development (GO:0072015)|hematopoietic progenitor cell differentiation (GO:0002244)|inner ear receptor cell differentiation (GO:0060113)|intermediate mesodermal cell differentiation (GO:0048392)|kidney development (GO:0001822)|lens induction in camera-type eye (GO:0060235)|lung alveolus development (GO:0048286)|lung morphogenesis (GO:0060425)|lymphoid progenitor cell differentiation (GO:0002320)|macrophage differentiation (GO:0030225)|mammary gland formation (GO:0060592)|mesenchymal cell differentiation involved in kidney development (GO:0072161)|mesenchymal cell proliferation involved in ureter development (GO:0072198)|mesenchymal cell proliferation involved in ureteric bud development (GO:0072138)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|mesodermal cell fate determination (GO:0007500)|mesonephros development (GO:0001823)|metanephric collecting duct development (GO:0072205)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of branch elongation involved in ureteric bud branching by BMP signaling pathway (GO:0072097)|negative regulation of branching involved in ureteric bud morphogenesis (GO:0090191)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell proliferation involved in heart morphogenesis (GO:2000137)|negative regulation of chondrocyte differentiation (GO:0032331)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of glomerulus development (GO:0090194)|negative regulation of immature T cell proliferation in thymus (GO:0033088)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell proliferation involved in ureter development (GO:0072200)|negative regulation of metanephric comma-shaped body morphogenesis (GO:2000007)|negative regulation of metanephric S-shaped body morphogenesis (GO:2000005)|negative regulation of mitosis (GO:0045839)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle tissue development (GO:0045843)|negative regulation of T cell differentiation in thymus (GO:0033085)|negative regulation of thymocyte apoptotic process (GO:0070244)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|neuron fate commitment (GO:0048663)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive chemotaxis (GO:0050918)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of bone mineralization (GO:0030501)|positive regulation of branching involved in lung morphogenesis (GO:0061047)|positive regulation of cardiac muscle fiber development (GO:0055020)|positive regulation of cartilage development (GO:0061036)|positive regulation of cell death (GO:0010942)|positive regulation of collagen biosynthetic process (GO:0032967)|positive regulation of DNA-dependent DNA replication (GO:2000105)|positive regulation of endothelial cell differentiation (GO:0045603)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of epidermal cell differentiation (GO:0045606)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of kidney development (GO:0090184)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of ossification (GO:0045778)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of protein binding (GO:0032092)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of SMAD protein import into nucleus (GO:0060391)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|post-embryonic development (GO:0009791)|protein localization to nucleus (GO:0034504)|pulmonary artery endothelial tube morphogenesis (GO:0061155)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of cell fate commitment (GO:0010453)|regulation of odontogenesis of dentin-containing tooth (GO:0042487)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of smooth muscle cell differentiation (GO:0051150)|renal system development (GO:0072001)|renal system process (GO:0003014)|secondary heart field specification (GO:0003139)|SMAD protein signal transduction (GO:0060395)|smooth muscle tissue development (GO:0048745)|smoothened signaling pathway (GO:0007224)|specification of organ position (GO:0010159)|specification of ureteric bud anterior/posterior symmetry by BMP signaling pathway (GO:0072101)|steroid hormone mediated signaling pathway (GO:0043401)|telencephalon development (GO:0021537)|telencephalon regionalization (GO:0021978)|tendon cell differentiation (GO:0035990)|trachea development (GO:0060438)|trachea formation (GO:0060440)|type B pancreatic cell development (GO:0003323)|ureter epithelial cell differentiation (GO:0072192)|ureter smooth muscle cell differentiation (GO:0072193)|ureteric bud development (GO:0001657)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	BMP receptor binding (GO:0070700)|chemoattractant activity (GO:0042056)|cytokine activity (GO:0005125)|heparin binding (GO:0008201)			breast(1)|endometrium(3)|large_intestine(2)|lung(9)|prostate(3)|urinary_tract(1)	19						GTCTGATGGAGGTGAGTCACC	0.592																																					p.L241I		Atlas-SNP	.											.	BMP4	45	.	0			c.C721A						PASS	.						103.0	84.0	90.0					14																	54417256		2203	4300	6503	SO:0001583	missense	652	exon4			GATGGAGGTGAGT	AF035427	CCDS9715.1	14q22-q23	2014-01-30			ENSG00000125378	ENSG00000125378		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1071	protein-coding gene	gene with protein product		112262		BMP2B		7558046, 7579580	Standard	NM_001202		Approved		uc010aoh.3	P12644	OTTHUMG00000140303	ENST00000245451.4:c.721C>A	chr14.hg19:g.54417256G>T	ENSP00000245451:p.Leu241Ile	141.0	0.0	.		107.0	44.0	.	NM_130851	Q9UM80	Missense_Mutation	SNP	ENST00000245451.4	hg19	CCDS9715.1	.	.	.	.	.	.	.	.	.	.	G	13.02	2.113400	0.37339	.	.	ENSG00000125378	ENST00000245451;ENST00000417573	T;T	0.66638	-0.22;-0.22	5.09	5.09	0.68999	Transforming growth factor-beta, N-terminal (1);	0.131959	0.52532	D	0.000066	T	0.71239	0.3316	M	0.72118	2.19	0.54753	D	0.999984	B	0.24092	0.097	B	0.36030	0.216	T	0.67377	-0.5686	10	0.30078	T	0.28	.	17.6566	0.88179	0.0:0.0:1.0:0.0	.	241	P12644	BMP4_HUMAN	I	241	ENSP00000245451:L241I;ENSP00000394165:L241I	ENSP00000245451:L241I	L	-	1	0	BMP4	53487006	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	6.385000	0.73182	2.647000	0.89833	0.655000	0.94253	CTC	.	.	.	none		0.592	BMP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276894.2	NM_001202	
SYT16	83851	hgsc.bcm.edu	37	14	62536436	62536436	+	Silent	SNP	T	T	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:62536436T>G	ENST00000430451.2	+	2	836	c.639T>G	c.(637-639)tcT>tcG	p.S213S	SYT16_ENST00000446982.2_Silent_p.S213S|RP11-355I22.5_ENST00000553990.1_lincRNA	NM_031914.2	NP_114120.2	Q17RD7	SYT16_HUMAN	synaptotagmin XVI	213					exocytosis (GO:0006887)					central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(11)|lung(12)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	35				OV - Ovarian serous cystadenocarcinoma(108;0.0438)|BRCA - Breast invasive adenocarcinoma(234;0.118)		CAGTGACATCTGAGAAAGGAA	0.483																																					p.S213S		Atlas-SNP	.											.	SYT16	144	.	0			c.T639G						PASS	.						142.0	137.0	139.0					14																	62536436		1933	4132	6065	SO:0001819	synonymous_variant	83851	exon2			GACATCTGAGAAA	BC040924	CCDS45121.1	14q23.2	2014-07-02	2005-07-15	2005-07-15	ENSG00000139973	ENSG00000139973		"""Synaptotagmins"""	23142	protein-coding gene	gene with protein product	"""synaptotagmin XIV-related"", "" chr14 synaptotagmin"""	610950	"""synaptotagmin XIV-like"""	SYT14L		11543631	Standard	NM_031914		Approved	yt14r, CHR14SYT, Strep14	uc001xfu.1	Q17RD7	OTTHUMG00000171106	ENST00000430451.2:c.639T>G	chr14.hg19:g.62536436T>G		115.0	0.0	.		102.0	43.0	.	NM_031914	B4DZH2|B7ZL60|C9J8I3|Q707N2|Q7Z441|Q8IUU0|Q9BQR8	Silent	SNP	ENST00000430451.2	hg19	CCDS45121.1																																																																																			.	.	.	none		0.483	SYT16-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000411700.1	NM_031914	
SYNE2	23224	hgsc.bcm.edu	37	14	64548159	64548159	+	Splice_Site	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:64548159A>G	ENST00000344113.4	+	57	11558		c.e57-1		SYNE2_ENST00000555002.1_Splice_Site|SYNE2_ENST00000357395.3_Splice_Site|SYNE2_ENST00000358025.3_Splice_Site|SYNE2_ENST00000394768.2_Splice_Site|SYNE2_ENST00000554584.1_Splice_Site	NM_015180.4	NP_055995.4	Q8WXH0	SYNE2_HUMAN	spectrin repeat containing, nuclear envelope 2						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)		TCTCTTTCCCAGGCCACAGTT	0.463																																					.		Atlas-SNP	.											.	SYNE2	577	.	0			c.11347-2A>G						PASS	.						86.0	84.0	85.0					14																	64548159		2203	4300	6503	SO:0001630	splice_region_variant	23224	exon57			TTTCCCAGGCCAC	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.11347-1A>G	chr14.hg19:g.64548159A>G		76.0	0.0	.		67.0	28.0	.	NM_182914	Q540G1|Q8N1S3|Q8NF49|Q8TER7|Q8WWW3|Q8WWW4|Q8WWW5|Q8WXH1|Q9NU50|Q9UFQ4|Q9Y2L4|Q9Y4R1	Splice_Site	SNP	ENST00000344113.4	hg19	CCDS41963.1	.	.	.	.	.	.	.	.	.	.	A	12.28	1.889919	0.33348	.	.	ENSG00000054654	ENST00000358025;ENST00000357395;ENST00000344113;ENST00000554584;ENST00000261678;ENST00000555002;ENST00000394768	.	.	.	5.6	5.6	0.85130	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.653	0.68811	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SYNE2	63617912	1.000000	0.71417	0.993000	0.49108	0.227000	0.25037	5.959000	0.70339	2.257000	0.74773	0.533000	0.62120	.	.	.	.	none		0.463	SYNE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276994.2	NM_182914	Intron
RDH12	145226	hgsc.bcm.edu	37	14	68195931	68195931	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:68195931G>T	ENST00000551171.1	+	8	1006	c.682G>T	c.(682-684)Gtg>Ttg	p.V228L	RDH12_ENST00000267502.3_Missense_Mutation_p.V228L|RDH12_ENST00000539142.1_Missense_Mutation_p.V228L	NM_152443.2	NP_689656.2	Q96NR8	RDH12_HUMAN	retinol dehydrogenase 12 (all-trans/9-cis/11-cis)	228					photoreceptor cell maintenance (GO:0045494)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|retinol metabolic process (GO:0042572)|visual perception (GO:0007601)	intracellular (GO:0005622)|photoreceptor inner segment membrane (GO:0060342)	retinol dehydrogenase activity (GO:0004745)			large_intestine(3)|lung(3)|ovary(1)|prostate(1)|skin(4)	12				all cancers(60;0.000704)|OV - Ovarian serous cystadenocarcinoma(108;0.00161)|BRCA - Breast invasive adenocarcinoma(234;0.00953)	Vitamin A(DB00162)	CACCTACGCAGTGCACCCAGG	0.607																																					p.V228L		Atlas-SNP	.											.	RDH12	43	.	0			c.G682T						PASS	.						105.0	105.0	105.0					14																	68195931		2203	4300	6503	SO:0001583	missense	145226	exon8			TACGCAGTGCACC	AK054835	CCDS9787.1	14q24.1	2013-02-14	2006-05-09		ENSG00000139988	ENSG00000139988	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	19977	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 7C, member 2"""	608830	"""retinol dehydrogenase 12 (all-trans and 9-cis)"""			12226107, 19027726	Standard	NM_152443		Approved	FLJ30273, SDR7C2, LCA13, RP53	uc001xjz.4	Q96NR8		ENST00000551171.1:c.682G>T	chr14.hg19:g.68195931G>T	ENSP00000449079:p.Val228Leu	774.0	1.0	.		594.0	249.0	.	NM_152443	B2RDA2|Q8TAW6	Missense_Mutation	SNP	ENST00000551171.1	hg19	CCDS9787.1	.	.	.	.	.	.	.	.	.	.	G	8.284	0.816291	0.16607	.	.	ENSG00000139988	ENST00000551171;ENST00000267502;ENST00000539142	D;D;D	0.85629	-2.01;-2.01;-2.01	5.74	4.8	0.61643	NAD(P)-binding domain (1);	0.124014	0.53938	D	0.000046	T	0.65176	0.2666	N	0.04994	-0.135	0.80722	D	1	B	0.20988	0.05	B	0.23574	0.047	T	0.61446	-0.7061	10	0.02654	T	1	.	9.6167	0.39696	0.0:0.3024:0.5731:0.1245	.	228	Q96NR8	RDH12_HUMAN	L	228	ENSP00000449079:V228L;ENSP00000267502:V228L;ENSP00000438715:V228L	ENSP00000267502:V228L	V	+	1	0	RDH12	67265684	0.998000	0.40836	0.958000	0.39756	0.104000	0.19210	2.905000	0.48727	2.703000	0.92315	0.655000	0.94253	GTG	.	.	.	none		0.607	RDH12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406918.1		
TTLL5	23093	hgsc.bcm.edu	37	14	76173407	76173407	+	Missense_Mutation	SNP	T	T	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:76173407T>G	ENST00000298832.9	+	8	837	c.632T>G	c.(631-633)aTt>aGt	p.I211S	TTLL5_ENST00000286650.5_Missense_Mutation_p.I211S|TTLL5_ENST00000557636.1_Missense_Mutation_p.I211S|TTLL5_ENST00000555422.1_3'UTR	NM_015072.4	NP_055887.3	Q6EMB2	TTLL5_HUMAN	tubulin tyrosine ligase-like family, member 5	211	TTL. {ECO:0000255|PROSITE- ProRule:PRU00568}.				fertilization (GO:0009566)|protein polyglutamylation (GO:0018095)|sperm axoneme assembly (GO:0007288)|sperm motility (GO:0030317)|transcription, DNA-templated (GO:0006351)	centrosome (GO:0005813)|cilium (GO:0005929)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)			NS(2)|breast(2)|central_nervous_system(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(3)|lung(22)|ovary(2)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(2)	50				BRCA - Breast invasive adenocarcinoma(234;0.029)		TCCCGTTACATTAACAACCCC	0.393																																					p.I211S		Atlas-SNP	.											.	TTLL5	102	.	0			c.T632G						PASS	.						131.0	126.0	128.0					14																	76173407		2203	4300	6503	SO:0001583	missense	23093	exon8			GTTACATTAACAA	AF107885	CCDS32124.1	14q24.3	2014-09-09	2005-07-29	2005-07-29	ENSG00000119685	ENSG00000119685		"""Tubulin tyrosine ligase-like family"""	19963	protein-coding gene	gene with protein product		612268	"""KIAA0998"""	KIAA0998		15890843	Standard	NM_015072		Approved		uc001xrx.3	Q6EMB2	OTTHUMG00000171611	ENST00000298832.9:c.632T>G	chr14.hg19:g.76173407T>G	ENSP00000298832:p.Ile211Ser	91.0	0.0	.		81.0	26.0	.	NM_015072	B9EGH8|B9EGH9|Q9BUB0|Q9H0G4|Q9H7W2|Q9P1V5|Q9UPZ4	Missense_Mutation	SNP	ENST00000298832.9	hg19	CCDS32124.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.515506	0.85389	.	.	ENSG00000119685	ENST00000557636;ENST00000286650;ENST00000298832	T;T;T	0.12984	2.63;2.63;2.63	5.41	5.41	0.78517	.	0.000000	0.85682	D	0.000000	T	0.53417	0.1795	H	0.97465	4.01	0.80722	D	1	D;D;D	0.76494	0.998;0.999;0.999	D;D;D	0.79108	0.976;0.992;0.992	T	0.71606	-0.4542	10	0.87932	D	0	.	15.3992	0.74823	0.0:0.0:0.0:1.0	.	211;211;211	G3V2J9;Q6EMB2;Q6EMB2-3	.;TTLL5_HUMAN;.	S	211	ENSP00000450713:I211S;ENSP00000286650:I211S;ENSP00000298832:I211S	ENSP00000286650:I211S	I	+	2	0	TTLL5	75243160	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	7.303000	0.78871	2.178000	0.69098	0.533000	0.62120	ATT	.	.	.	none		0.393	TTLL5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414453.1	NM_015072	
ITPK1	3705	hgsc.bcm.edu	37	14	93429129	93429129	+	Missense_Mutation	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr14:93429129G>T	ENST00000267615.6	-	6	603	c.430C>A	c.(430-432)Ctg>Atg	p.L144M	ITPK1_ENST00000555495.1_Missense_Mutation_p.L25M|ITPK1_ENST00000556603.2_Missense_Mutation_p.L144M|ITPK1_ENST00000354313.3_Missense_Mutation_p.L144M|ITPK1_ENST00000556954.1_5'UTR			Q13572	ITPK1_HUMAN	inositol-tetrakisphosphate 1-kinase	144	ATP-grasp. {ECO:0000255|PROSITE- ProRule:PRU00409}.				blood coagulation (GO:0007596)|dephosphorylation (GO:0016311)|inositol phosphate metabolic process (GO:0043647)|inositol trisphosphate metabolic process (GO:0032957)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)	ATP binding (GO:0005524)|catalytic activity (GO:0003824)|inositol tetrakisphosphate 1-kinase activity (GO:0047325)|inositol-1,3,4,5,6-pentakisphosphate 1-phosphatase activity (GO:0052825)|inositol-1,3,4,6-tetrakisphosphate 1-phosphatase activity (GO:0052831)|inositol-1,3,4,6-tetrakisphosphate 6-phosphatase activity (GO:0052830)|inositol-1,3,4-trisphosphate 5-kinase activity (GO:0052726)|inositol-1,3,4-trisphosphate 6-kinase activity (GO:0052725)|inositol-3,4,6-trisphosphate 1-kinase activity (GO:0052835)|isomerase activity (GO:0016853)|magnesium ion binding (GO:0000287)			endometrium(1)|large_intestine(3)|lung(6)|ovary(1)	11		all_cancers(154;0.077)|all_epithelial(191;0.247)		Epithelial(152;0.124)|all cancers(159;0.169)		TTCTCCAGCAGCCGCATGGTG	0.632																																					p.L144M		Atlas-SNP	.											.	ITPK1	53	.	0			c.C430A						PASS	.						139.0	101.0	114.0					14																	93429129		2203	4300	6503	SO:0001583	missense	3705	exon6			CCAGCAGCCGCAT	U51336	CCDS9907.1, CCDS45157.1	14q32.12	2012-08-16	2011-04-28		ENSG00000100605	ENSG00000100605	2.7.1.134		6177	protein-coding gene	gene with protein product		601838	"""inositol 1,3,4-triphosphate 5/6 kinase"""			8662638, 11042108	Standard	NM_014216		Approved		uc001ybh.3	Q13572	OTTHUMG00000171226	ENST00000267615.6:c.430C>A	chr14.hg19:g.93429129G>T	ENSP00000267615:p.Leu144Met	57.0	0.0	.		40.0	11.0	.	NM_001142593	Q9BTL6|Q9H2E7	Missense_Mutation	SNP	ENST00000267615.6	hg19	CCDS9907.1	.	.	.	.	.	.	.	.	.	.	G	15.85	2.954724	0.53293	.	.	ENSG00000100605	ENST00000354313;ENST00000405174;ENST00000556603;ENST00000555495;ENST00000267615;ENST00000311458;ENST00000554999;ENST00000556185;ENST00000555553;ENST00000553452;ENST00000557309	T	0.08720	3.06	5.51	5.51	0.81932	ATP-grasp fold (1);	0.311884	0.33959	N	0.004388	T	0.15003	0.0362	L	0.52011	1.625	0.38708	D	0.953155	B;B	0.31256	0.316;0.084	B;B	0.42555	0.391;0.139	T	0.04128	-1.0975	10	0.45353	T	0.12	-9.5343	14.2724	0.66159	0.0:0.0:0.8512:0.1488	.	144;144	Q13572;Q13572-2	ITPK1_HUMAN;.	M	144;174;144;25;144;144;102;162;150;144;144	ENSP00000346272:L144M	ENSP00000267615:L144M	L	-	1	2	ITPK1	92498882	1.000000	0.71417	0.990000	0.47175	0.917000	0.54804	3.936000	0.56568	2.570000	0.86706	0.549000	0.68633	CTG	.	.	.	none		0.632	ITPK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412421.2	NM_014216	
SPTBN5	51332	hgsc.bcm.edu	37	15	42163671	42163671	+	Silent	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:42163671G>C	ENST00000320955.6	-	29	5576	c.5349C>G	c.(5347-5349)ggC>ggG	p.G1783G		NM_016642.2	NP_057726.4	Q9NRC6	SPTN5_HUMAN	spectrin, beta, non-erythrocytic 5	1783					actin cytoskeleton organization (GO:0030036)|actin filament capping (GO:0051693)|axon guidance (GO:0007411)|Golgi organization (GO:0007030)|lysosomal transport (GO:0007041)|protein homooligomerization (GO:0051260)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|photoreceptor connecting cilium (GO:0032391)|photoreceptor disc membrane (GO:0097381)|spectrin (GO:0008091)	actin binding (GO:0003779)|dynactin binding (GO:0034452)|dynein intermediate chain binding (GO:0045505)|kinesin binding (GO:0019894)|myosin tail binding (GO:0032029)|protein self-association (GO:0043621)|spectrin binding (GO:0030507)			NS(1)|breast(1)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(6)|lung(18)|ovary(5)|prostate(8)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	62		all_cancers(109;1.84e-17)|all_epithelial(112;1.12e-15)|Lung NSC(122;7.6e-10)|all_lung(180;4.15e-09)|Melanoma(134;0.0179)|Ovarian(310;0.143)|Colorectal(260;0.173)		all cancers(2;4.33e-34)|Epithelial(2;1.72e-25)|OV - Ovarian serous cystadenocarcinoma(18;8.32e-20)|GBM - Glioblastoma multiforme(94;4.69e-07)|Colorectal(2;0.00104)|COAD - Colon adenocarcinoma(120;0.0405)|READ - Rectum adenocarcinoma(92;0.0908)		CCCGCTGGCTGCCCATCTCCA	0.637																																					p.G1748G		Atlas-SNP	.											.	SPTBN5	171	.	0			c.C5244G						PASS	.						21.0	25.0	24.0					15																	42163671		1840	3839	5679	SO:0001819	synonymous_variant	51332	exon29			CTGGCTGCCCATC	AF233523	CCDS61599.1	15q21	2010-08-17			ENSG00000137877	ENSG00000137877			15680	protein-coding gene	gene with protein product	"""beta V spectrin"""	605916				10764729	Standard	NM_016642		Approved	HUSPECV, BSPECV, HUBSPECV	uc001zos.4	Q9NRC6		ENST00000320955.6:c.5349C>G	chr15.hg19:g.42163671G>C		166.0	0.0	.		127.0	51.0	.	NM_016642		Silent	SNP	ENST00000320955.6	hg19																																																																																				.	.	.	none		0.637	SPTBN5-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000420237.1	NM_016642	
MAP1A	4130	hgsc.bcm.edu	37	15	43815125	43815125	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:43815125A>G	ENST00000300231.5	+	4	1904	c.1454A>G	c.(1453-1455)aAa>aGa	p.K485R	MAP1A_ENST00000399453.1_Missense_Mutation_p.K485R|MAP1A_ENST00000382031.1_Missense_Mutation_p.K723R			P78559	MAP1A_HUMAN	microtubule-associated protein 1A	485	9 X 3 AA repeats of K-K-[DE].|Lys-rich (basic).		K -> Q (in dbSNP:rs2584715).		microtubule cytoskeleton organization (GO:0000226)|sensory perception of sound (GO:0007605)	cytosol (GO:0005829)|microtubule (GO:0005874)|microtubule associated complex (GO:0005875)	structural molecule activity (GO:0005198)			breast(5)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(11)|liver(2)|lung(19)|ovary(5)|pancreas(3)|prostate(2)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	66		all_cancers(109;1.03e-14)|all_epithelial(112;2.23e-12)|Lung NSC(122;2.76e-08)|all_lung(180;3.1e-07)|Melanoma(134;0.0476)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;3.05e-06)	Estramustine(DB01196)	GGAAGAGTCAAAATAGACAGG	0.527																																					p.K485R		Atlas-SNP	.											.	MAP1A	189	.	0			c.A1454G						PASS	.						31.0	31.0	31.0					15																	43815125		1903	4110	6013	SO:0001583	missense	4130	exon4			GAGTCAAAATAGA	U38292	CCDS42031.1	15q15.3	2006-06-15			ENSG00000166963	ENSG00000166963			6835	protein-coding gene	gene with protein product		600178		MAP1L		7806212, 7629894	Standard	XM_005254385		Approved		uc001zrt.3	P78559	OTTHUMG00000059756	ENST00000300231.5:c.1454A>G	chr15.hg19:g.43815125A>G	ENSP00000300231:p.Lys485Arg	134.0	0.0	.		115.0	57.0	.	NM_002373	O95643|Q12973|Q15882|Q9UJT4	Missense_Mutation	SNP	ENST00000300231.5	hg19	CCDS42031.1	.	.	.	.	.	.	.	.	.	.	A	12.79	2.044131	0.36085	.	.	ENSG00000166963	ENST00000382031;ENST00000399453;ENST00000300231;ENST00000442025	T;T;T	0.50813	0.73;0.73;0.73	5.39	5.39	0.77823	.	0.000000	0.33670	N	0.004672	T	0.56819	0.2011	M	0.78637	2.42	0.47441	D	0.999427	P	0.50528	0.936	P	0.46320	0.512	T	0.64943	-0.6288	10	0.66056	D	0.02	-21.4983	15.5825	0.76455	1.0:0.0:0.0:0.0	.	485	P78559	MAP1A_HUMAN	R	723;485;485;485	ENSP00000371462:K723R;ENSP00000382380:K485R;ENSP00000300231:K485R	ENSP00000300231:K485R	K	+	2	0	MAP1A	41602417	1.000000	0.71417	0.982000	0.44146	0.961000	0.63080	5.234000	0.65343	2.263000	0.75096	0.533000	0.62120	AAA	.	.	.	none		0.527	MAP1A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000132894.5	NM_002373	
DMXL2	23312	hgsc.bcm.edu	37	15	51749533	51749533	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:51749533C>A	ENST00000251076.5	-	36	8550	c.8263G>T	c.(8263-8265)Gct>Tct	p.A2755S	RP11-707P17.2_ENST00000559977.1_RNA|DMXL2_ENST00000543779.2_Missense_Mutation_p.A2756S|DMXL2_ENST00000449909.3_Missense_Mutation_p.A2119S|RP11-707P17.2_ENST00000559173.1_RNA|RP11-707P17.1_ENST00000561007.1_RNA|RP11-707P17.2_ENST00000560727.1_RNA	NM_001174116.1|NM_015263.3	NP_001167587.1|NP_056078.2	Q8TDJ6	DMXL2_HUMAN	Dmx-like 2	2755						cell junction (GO:0030054)|extracellular space (GO:0005615)|membrane (GO:0016020)|synaptic vesicle (GO:0008021)	Rab GTPase binding (GO:0017137)			breast(4)|central_nervous_system(1)|cervix(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(26)|liver(1)|lung(28)|ovary(7)|prostate(7)|skin(4)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	101				all cancers(107;0.00494)		ACCACACTAGCTCCAGTGCTA	0.418																																					p.A2756S		Atlas-SNP	.											.	DMXL2	262	.	0			c.G8266T						PASS	.						105.0	93.0	97.0					15																	51749533		2196	4293	6489	SO:0001583	missense	23312	exon36			CACTAGCTCCAGT	AB020663	CCDS10141.1, CCDS53945.1, CCDS53946.1	15q21.2	2013-01-10			ENSG00000104093	ENSG00000104093		"""WD repeat domain containing"""	2938	protein-coding gene	gene with protein product	"""rabconnectin 3"""	612186					Standard	NM_001174116		Approved	RC3, KIAA0856	uc010ufy.2	Q8TDJ6	OTTHUMG00000131749	ENST00000251076.5:c.8263G>T	chr15.hg19:g.51749533C>A	ENSP00000251076:p.Ala2755Ser	48.0	0.0	.		60.0	28.0	.	NM_001174116	B2RTR3|B7ZMH3|F5GWF1|O94938	Missense_Mutation	SNP	ENST00000251076.5	hg19	CCDS10141.1	.	.	.	.	.	.	.	.	.	.	C	31	5.092771	0.94149	.	.	ENSG00000104093	ENST00000251076;ENST00000543779;ENST00000449909;ENST00000436119	T;T;T	0.25912	1.91;1.91;1.77	5.78	5.78	0.91487	.	0.000000	0.85682	D	0.000000	T	0.28532	0.0706	L	0.47716	1.5	0.80722	D	1	B;D;B;B	0.53151	0.019;0.958;0.376;0.135	B;B;B;B	0.41202	0.014;0.35;0.062;0.061	T	0.01894	-1.1252	10	0.46703	T	0.11	.	20.3754	0.98918	0.0:1.0:0.0:0.0	.	2756;2119;2755;2756	F5GWF1;B2RTR3;Q8TDJ6;B7ZMH3	.;.;DMXL2_HUMAN;.	S	2755;2756;2119;321	ENSP00000251076:A2755S;ENSP00000441858:A2756S;ENSP00000400855:A2119S	ENSP00000251076:A2755S	A	-	1	0	DMXL2	49536825	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	6.944000	0.75940	2.894000	0.99253	0.591000	0.81541	GCT	.	.	.	none		0.418	DMXL2-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254671.2	NM_015263	
KIAA1024	23251	hgsc.bcm.edu	37	15	79760702	79760702	+	Silent	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:79760702G>T	ENST00000305428.3	+	4	2802	c.2727G>T	c.(2725-2727)gtG>gtT	p.V909V		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	909						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						TTATTGTCGTGCCCATCTGCA	0.468																																					p.V909V		Atlas-SNP	.											.	KIAA1024	146	.	0			c.G2727T						PASS	.						79.0	68.0	72.0					15																	79760702		2196	4293	6489	SO:0001819	synonymous_variant	23251	exon4			TGTCGTGCCCATC	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.2727G>T	chr15.hg19:g.79760702G>T		31.0	0.0	.		57.0	5.0	.	NM_015206	A7MD43	Silent	SNP	ENST00000305428.3	hg19	CCDS32306.1																																																																																			.	.	.	none		0.468	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
NR2F2	7026	hgsc.bcm.edu	37	15	96875731	96875731	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:96875731T>C	ENST00000394166.3	+	1	1786	c.397T>C	c.(397-399)Tac>Cac	p.Y133H	NR2F2_ENST00000394171.2_5'Flank|NR2F2_ENST00000421109.2_Intron|NR2F2_ENST00000453270.2_5'Flank|MIR1469_ENST00000410719.1_RNA	NM_021005.3	NP_066285.1	P24468	COT2_HUMAN	nuclear receptor subfamily 2, group F, member 2	133	Interaction with ZFPM2. {ECO:0000250}.				anterior/posterior pattern specification (GO:0009952)|blood vessel morphogenesis (GO:0048514)|fertilization (GO:0009566)|forebrain development (GO:0030900)|intracellular receptor signaling pathway (GO:0030522)|limb development (GO:0060173)|lipid metabolic process (GO:0006629)|maternal placenta development (GO:0001893)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron migration (GO:0001764)|placenta blood vessel development (GO:0060674)|positive regulation of transcription, DNA-templated (GO:0045893)|radial pattern formation (GO:0009956)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription involved in lymphatic endothelial cell fate commitment (GO:0060849)|response to estradiol (GO:0032355)|signal transduction (GO:0007165)|skeletal muscle tissue development (GO:0007519)|trophoblast giant cell differentiation (GO:0060707)	nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein homodimerization activity (GO:0042803)|retinoic acid binding (GO:0001972)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			breast(1)|endometrium(1)|kidney(1)|large_intestine(6)|liver(2)|lung(3)|ovary(2)|urinary_tract(1)	17	Lung NSC(78;0.0186)|Melanoma(26;0.0195)|all_lung(78;0.0297)		OV - Ovarian serous cystadenocarcinoma(32;0.0856)			CCAGTGCCAGTACTGCCGCCT	0.607																																					p.Y133H		Atlas-SNP	.											.	NR2F2	35	.	0			c.T397C						PASS	.						78.0	71.0	74.0					15																	96875731		2197	4298	6495	SO:0001583	missense	7026	exon1			TGCCAGTACTGCC	M64497	CCDS10375.1, CCDS45358.1, CCDS45359.1	15q26	2013-01-16			ENSG00000185551	ENSG00000185551		"""Nuclear hormone receptors"""	7976	protein-coding gene	gene with protein product		107773		ARP1, TFCOUP2		8530078, 11544252	Standard	NM_021005		Approved	COUP-TFII, COUPTFB, SVP40, NF-E3	uc010uri.2	P24468	OTTHUMG00000149848	ENST00000394166.3:c.397T>C	chr15.hg19:g.96875731T>C	ENSP00000377721:p.Tyr133His	111.0	0.0	.		76.0	35.0	.	NM_021005	B4DQJ2|B6ZGU1|Q03754|Q3KQR7	Missense_Mutation	SNP	ENST00000394166.3	hg19	CCDS10375.1	.	.	.	.	.	.	.	.	.	.	T	21.6	4.179895	0.78564	.	.	ENSG00000185551	ENST00000394166	D	0.97303	-4.33	4.92	4.92	0.64577	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.64402	D	0.000005	D	0.97754	0.9263	L	0.61387	1.9	0.80722	D	1	D	0.76494	0.999	D	0.72338	0.977	D	0.98274	1.0505	10	0.62326	D	0.03	.	13.4089	0.60931	0.0:0.0:0.0:1.0	.	133	P24468	COT2_HUMAN	H	133	ENSP00000377721:Y133H	ENSP00000377721:Y133H	Y	+	1	0	NR2F2	94676735	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.990000	0.88215	1.843000	0.53566	0.459000	0.35465	TAC	.	.	.	none		0.607	NR2F2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313534.1		
IL32	9235	hgsc.bcm.edu	37	16	3119208	3119208	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:3119208C>A	ENST00000534507.1	+	6	768	c.557C>A	c.(556-558)gCa>gAa	p.A186E	RNU1-125P_ENST00000516752.1_RNA|IL32_ENST00000548652.1_Missense_Mutation_p.A131E|IL32_ENST00000530538.2_Missense_Mutation_p.A140E|IL32_ENST00000552356.1_Missense_Mutation_p.A120E|IL32_ENST00000525643.2_Missense_Mutation_p.A140E|IL32_ENST00000548476.1_Missense_Mutation_p.A186E|IL32_ENST00000533097.2_Missense_Mutation_p.A140E|IL32_ENST00000528163.2_Missense_Mutation_p.A140E|IL32_ENST00000529699.1_Missense_Mutation_p.A120E|IL32_ENST00000551122.1_Intron|IL32_ENST00000444393.3_Missense_Mutation_p.A140E|IL32_ENST00000530890.1_Missense_Mutation_p.A120E|IL32_ENST00000440815.3_Missense_Mutation_p.A140E|IL32_ENST00000552936.1_Missense_Mutation_p.A164E|IL32_ENST00000008180.9_Missense_Mutation_p.A120E|IL32_ENST00000396887.3_Intron|IL32_ENST00000549213.1_Intron|IL32_ENST00000529550.1_Missense_Mutation_p.A140E|IL32_ENST00000551513.1_Missense_Mutation_p.A177E|IL32_ENST00000531965.1_Missense_Mutation_p.A130E|IL32_ENST00000526464.2_Missense_Mutation_p.A140E|IL32_ENST00000548246.1_Missense_Mutation_p.A100E|IL32_ENST00000382213.3_Missense_Mutation_p.A131E|IL32_ENST00000325568.5_Missense_Mutation_p.A140E|IL32_ENST00000552664.1_Missense_Mutation_p.A140E|IL32_ENST00000396890.2_Missense_Mutation_p.A186E			P24001	IL32_HUMAN	interleukin 32	186					cell adhesion (GO:0007155)|defense response (GO:0006952)|immune response (GO:0006955)	extracellular space (GO:0005615)|membrane (GO:0016020)				breast(1)|endometrium(1)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	15						CTGGTCCATGCAGTGCAGGCC	0.602																																					p.A140E		Atlas-SNP	.											.	IL32	32	.	0			c.C419A						PASS	.						49.0	57.0	54.0					16																	3119208		2197	4298	6495	SO:0001583	missense	9235	exon7			TCCATGCAGTGCA	M59807	CCDS32377.1, CCDS32378.1, CCDS32379.1, CCDS45394.1	16p13.3	2011-07-21			ENSG00000008517	ENSG00000008517		"""Interleukins and interleukin receptors"""	16830	protein-coding gene	gene with protein product	"""natural killer cell transcript 4"""	606001				1729377, 9653642	Standard	XM_005255686		Approved	NK4, TAIF, TAIFb, TAIFd	uc002ctn.3	P24001	OTTHUMG00000167498	ENST00000534507.1:c.557C>A	chr16.hg19:g.3119208C>A	ENSP00000431775:p.Ala186Glu	220.0	0.0	.		210.0	41.0	.	NM_004221	A6NNM0|A8MPX0|B4DJM1|B8Q191|D3DUB0|D3DUB2|Q5VFH7|Q5VFH8|Q8WV38|Q96GK9	Missense_Mutation	SNP	ENST00000534507.1	hg19		.	.	.	.	.	.	.	.	.	.	c	7.440	0.640466	0.14386	.	.	ENSG00000008517	ENST00000325568;ENST00000534507;ENST00000531965;ENST00000529699;ENST00000526464;ENST00000440815;ENST00000529550;ENST00000525643;ENST00000548807;ENST00000528163;ENST00000530890;ENST00000444393;ENST00000533097;ENST00000008180;ENST00000396890;ENST00000525228;ENST00000548652;ENST00000530538;ENST00000552936;ENST00000548476;ENST00000552664;ENST00000552356;ENST00000551513;ENST00000382213;ENST00000548246	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.57752	0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38;0.38	1.89	-0.329	0.12686	.	.	.	.	.	T	0.33789	0.0875	N	0.19112	0.55	0.09310	N	1	B;B;B;B;B;B	0.18166	0.007;0.026;0.026;0.026;0.007;0.026	B;B;B;B;B;B	0.10450	0.003;0.005;0.005;0.005;0.003;0.005	T	0.17018	-1.0383	9	0.38643	T	0.18	.	8.4032	0.32599	0.3619:0.6381:0.0:0.0	.	100;120;131;120;186;140	B8Q191;C6GKH1;A6NNM0;A8MPX0;P24001;P24001-2	.;.;.;.;IL32_HUMAN;.	E	140;186;130;120;140;140;140;140;186;140;120;140;140;120;186;111;131;140;164;186;140;120;177;131;100	ENSP00000324742:A140E;ENSP00000431775:A186E;ENSP00000433177:A130E;ENSP00000436937:A120E;ENSP00000450364:A140E;ENSP00000405063:A140E;ENSP00000437020:A140E;ENSP00000432218:A140E;ENSP00000448354:A186E;ENSP00000432850:A140E;ENSP00000433747:A120E;ENSP00000411958:A140E;ENSP00000432917:A140E;ENSP00000008180:A120E;ENSP00000380099:A186E;ENSP00000431740:A111E;ENSP00000446624:A131E;ENSP00000436929:A140E;ENSP00000447033:A164E;ENSP00000449483:A186E;ENSP00000448683:A140E;ENSP00000446978:A120E;ENSP00000449147:A177E;ENSP00000371648:A131E;ENSP00000447979:A100E	ENSP00000008180:A120E	A	+	2	0	IL32	3059209	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.401000	0.02502	-0.380000	0.07894	-2.641000	0.00151	GCA	.	.	.	none		0.602	IL32-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000394812.2	NM_004221	
SALL1	6299	hgsc.bcm.edu	37	16	51171131	51171131	+	Silent	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:51171131C>T	ENST00000251020.4	-	3	3900	c.3867G>A	c.(3865-3867)gaG>gaA	p.E1289E	SALL1_ENST00000440970.1_Silent_p.E1192E|SALL1_ENST00000566102.1_3'UTR|SALL1_ENST00000541611.1_Silent_p.E112E	NM_002968.2	NP_002959.2	Q9NSC2	SALL1_HUMAN	spalt-like transcription factor 1	1289					adrenal gland development (GO:0030325)|branching involved in ureteric bud morphogenesis (GO:0001658)|embryonic digestive tract development (GO:0048566)|embryonic digit morphogenesis (GO:0042733)|forelimb morphogenesis (GO:0035136)|gonad development (GO:0008406)|heart development (GO:0007507)|hindlimb morphogenesis (GO:0035137)|histone deacetylation (GO:0016575)|inductive cell-cell signaling (GO:0031129)|kidney development (GO:0001822)|kidney epithelium development (GO:0072073)|limb development (GO:0060173)|mesenchymal to epithelial transition involved in metanephros morphogenesis (GO:0003337)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube closure (GO:0001843)|olfactory bulb interneuron differentiation (GO:0021889)|olfactory bulb mitral cell layer development (GO:0061034)|olfactory nerve development (GO:0021553)|outer ear morphogenesis (GO:0042473)|pituitary gland development (GO:0021983)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of Wnt signaling pathway (GO:0030177)|regulation of neural precursor cell proliferation (GO:2000177)|transcription, DNA-templated (GO:0006351)|ureteric bud development (GO:0001657)|ureteric bud invasion (GO:0072092)|ventricular septum development (GO:0003281)	chromocenter (GO:0010369)|cytoplasm (GO:0005737)|heterochromatin (GO:0000792)|nucleus (GO:0005634)|NuRD complex (GO:0016581)	beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(4)|breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(25)|lung(61)|ovary(3)|prostate(6)|skin(12)|upper_aerodigestive_tract(3)	126		all_cancers(37;0.0322)	COAD - Colon adenocarcinoma(2;0.24)			GAGCATTGGGCTCTGAGTTCT	0.587																																					p.E1289E	GBM(103;1352 1446 1855 4775 8890)	Atlas-SNP	.											.	SALL1	301	.	0			c.G3867A						PASS	.						72.0	68.0	69.0					16																	51171131		2198	4300	6498	SO:0001819	synonymous_variant	6299	exon3			ATTGGGCTCTGAG	X98833	CCDS10747.1, CCDS45483.1	16q12.1	2014-09-17	2013-10-17		ENSG00000103449	ENSG00000103449		"""Zinc fingers, C2H2-type"""	10524	protein-coding gene	gene with protein product		602218	"""sal (Drosophila)-like 1"", ""sal-like 1 (Drosophila)"""	TBS		9425907	Standard	NM_002968		Approved	Hsal1, ZNF794	uc021tie.1	Q9NSC2	OTTHUMG00000133176	ENST00000251020.4:c.3867G>A	chr16.hg19:g.51171131C>T		98.0	0.0	.		132.0	38.0	.	NM_002968	Q99881|Q9NSC3|Q9P1R0	Silent	SNP	ENST00000251020.4	hg19	CCDS10747.1																																																																																			.	.	.	none		0.587	SALL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256883.2	NM_002968	
PDPR	55066	hgsc.bcm.edu	37	16	70170204	70170204	+	Missense_Mutation	SNP	A	A	G	rs541394087		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:70170204A>G	ENST00000288050.4	+	10	2062	c.1105A>G	c.(1105-1107)Atg>Gtg	p.M369V	PDPR_ENST00000398122.3_Missense_Mutation_p.M269V|PDPR_ENST00000562100.1_3'UTR|PDPR_ENST00000568530.1_Missense_Mutation_p.M369V	NM_017990.3	NP_060460.4	Q8NCN5	PDPR_HUMAN	pyruvate dehydrogenase phosphatase regulatory subunit	369					cellular metabolic process (GO:0044237)|glycine catabolic process (GO:0006546)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)	aminomethyltransferase activity (GO:0004047)|oxidoreductase activity (GO:0016491)			breast(1)|central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|skin(2)|stomach(3)	33				BRCA - Breast invasive adenocarcinoma(221;0.124)		GAGGTGCATCATGGGCGAGTC	0.517													.|||	1	0.000199681	0.0	0.0	5008	,	,		26659	0.001		0.0	False		,,,				2504	0.0				p.M369V		Atlas-SNP	.											.	PDPR	66	.	0			c.A1105G						PASS	.						78.0	81.0	80.0					16																	70170204		1977	4175	6152	SO:0001583	missense	55066	exon10			TGCATCATGGGCG		CCDS45520.1	16q22.1	2010-08-24			ENSG00000090857	ENSG00000090857			30264	protein-coding gene	gene with protein product						9395502	Standard	NM_017990		Approved	PDP3	uc002eyf.1	Q8NCN5		ENST00000288050.4:c.1105A>G	chr16.hg19:g.70170204A>G	ENSP00000288050:p.Met369Val	73.0	0.0	.		99.0	15.0	.	NM_017990	A7E298|A8K8Y7|B3KSE1|Q6AI20|Q6AWC9	Missense_Mutation	SNP	ENST00000288050.4	hg19	CCDS45520.1	.	.	.	.	.	.	.	.	.	.	A	12.62	1.993038	0.35131	.	.	ENSG00000090857	ENST00000288050;ENST00000398122;ENST00000205055	T;T	0.79749	-1.3;-1.3	4.42	3.31	0.37934	FAD dependent oxidoreductase (1);	0.040270	0.85682	D	0.000000	T	0.62036	0.2395	N	0.04387	-0.21	0.80722	D	1	B;B	0.33448	0.412;0.002	B;B	0.40982	0.345;0.007	T	0.52472	-0.8571	10	0.09843	T	0.71	.	10.3359	0.43850	0.8344:0.1656:0.0:0.0	.	97;369	Q9NWE6;Q8NCN5	.;PDPR_HUMAN	V	369;269;97	ENSP00000288050:M369V;ENSP00000381190:M269V	ENSP00000205055:M97V	M	+	1	0	PDPR	68727705	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.221000	0.65272	0.526000	0.28541	0.374000	0.22700	ATG	.	.	.	none		0.517	PDPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000434502.1	NM_017990	
SLC43A2	124935	hgsc.bcm.edu	37	17	1486541	1486541	+	Missense_Mutation	SNP	A	A	G			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:1486541A>G	ENST00000301335.5	-	11	1395	c.1307T>C	c.(1306-1308)gTg>gCg	p.V436A	SLC43A2_ENST00000571650.1_Missense_Mutation_p.V440A|SLC43A2_ENST00000382147.4_Missense_Mutation_p.V440A|SLC43A2_ENST00000412517.3_Missense_Mutation_p.V299A	NM_001284498.1|NM_001284499.1	NP_001271427.1|NP_001271428.1	Q8N370	LAT4_HUMAN	solute carrier family 43 (amino acid system L transporter), member 2	436					amino acid transport (GO:0006865)|ion transport (GO:0006811)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	L-amino acid transmembrane transporter activity (GO:0015179)			endometrium(4)|large_intestine(4)|liver(1)|lung(2)|upper_aerodigestive_tract(1)	12				UCEC - Uterine corpus endometrioid carcinoma (25;0.0883)		CCCAAAGCCCACGAGCAGCAG	0.597																																					p.V436A		Atlas-SNP	.											.	SLC43A2	37	.	0			c.T1307C						PASS	.						101.0	101.0	101.0					17																	1486541		2203	4300	6503	SO:0001583	missense	124935	exon11			AAGCCCACGAGCA	BC027923	CCDS11006.1, CCDS67107.1, CCDS67108.1	17p13.3	2013-07-17	2013-07-17		ENSG00000167703	ENSG00000167703		"""Solute carriers"""	23087	protein-coding gene	gene with protein product		610791				23268354	Standard	NM_001284498		Approved	MGC34680	uc002fsv.3	Q8N370	OTTHUMG00000090345	ENST00000301335.5:c.1307T>C	chr17.hg19:g.1486541A>G	ENSP00000301335:p.Val436Ala	68.0	0.0	.		113.0	25.0	.	NM_152346	B7Z6X9|C9JNU8|D3DTH9|Q5CD75|Q6IPM1|Q8NBX1|Q8NC21|Q8WZ00	Missense_Mutation	SNP	ENST00000301335.5	hg19	CCDS11006.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.176893	0.78564	.	.	ENSG00000167703	ENST00000301335;ENST00000382147;ENST00000412517	D;D;D	0.81579	-1.51;-1.51;-1.51	5.67	5.67	0.87782	Major facilitator superfamily domain, general substrate transporter (1);	0.000000	0.85682	D	0.000000	D	0.86443	0.5934	M	0.85373	2.75	0.58432	D	0.999998	B;P	0.45283	0.257;0.855	B;P	0.49561	0.083;0.615	D	0.85660	0.1288	10	0.28530	T	0.3	-17.3303	16.2045	0.82114	1.0:0.0:0.0:0.0	.	436;440	Q8N370;Q8N370-3	LAT4_HUMAN;.	A	436;440;299	ENSP00000301335:V436A;ENSP00000371582:V440A;ENSP00000408284:V299A	ENSP00000301335:V436A	V	-	2	0	SLC43A2	1433291	1.000000	0.71417	0.998000	0.56505	0.991000	0.79684	9.287000	0.95975	2.288000	0.76882	0.533000	0.62120	GTG	.	.	.	none		0.597	SLC43A2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000206717.4	NM_152346	
NCOR1	9611	hgsc.bcm.edu	37	17	16004686	16004686	+	Missense_Mutation	SNP	T	T	A	rs201420293		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:16004686T>A	ENST00000268712.3	-	20	2825	c.2568A>T	c.(2566-2568)agA>agT	p.R856S	NCOR1_ENST00000395851.1_Missense_Mutation_p.R872S|NCOR1_ENST00000395848.1_Missense_Mutation_p.R763S|RNU6-314P_ENST00000516574.1_RNA|NCOR1_ENST00000583226.1_5'Flank	NM_006311.3	NP_006302.2	O75376	NCOR1_HUMAN	nuclear receptor corepressor 1	856					CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation (GO:0002361)|cellular lipid metabolic process (GO:0044255)|cholesterol homeostasis (GO:0042632)|chromatin modification (GO:0016568)|circadian regulation of gene expression (GO:0032922)|definitive erythrocyte differentiation (GO:0060318)|gene expression (GO:0010467)|negative regulation of JNK cascade (GO:0046329)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|positive regulation of histone deacetylation (GO:0031065)|regulation of fatty acid transport (GO:2000191)|regulation of glycolytic process by negative regulation of transcription from RNA polymerase II promoter (GO:0072362)|regulation of lipid transport by negative regulation of transcription from RNA polymerase II promoter (GO:0072368)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|spindle assembly (GO:0051225)|thalamus development (GO:0021794)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle microtubule (GO:0005876)|transcription factor complex (GO:0005667)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|histone deacetylase binding (GO:0042826)|histone deacetylase regulator activity (GO:0035033)|nuclear hormone receptor binding (GO:0035257)|RNA polymerase II activating transcription factor binding (GO:0001102)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription corepressor activity (GO:0003714)|transcription regulatory region DNA binding (GO:0044212)			NS(2)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(17)|lung(26)|ovary(1)|prostate(7)|skin(2)|upper_aerodigestive_tract(6)|urinary_tract(10)	107				UCEC - Uterine corpus endometrioid carcinoma (92;0.101)		AATCTTCATCTCTAGGTTCCA	0.483																																					p.R872S		Atlas-SNP	.											.	NCOR1	240	.	0			c.A2616T						PASS	.						190.0	177.0	181.0					17																	16004686		2203	4300	6503	SO:0001583	missense	9611	exon19			TTCATCTCTAGGT	AF044209	CCDS11175.1, CCDS54094.1, CCDS54095.1	17p11.2	2014-06-12	2010-06-10		ENSG00000141027	ENSG00000141027			7672	protein-coding gene	gene with protein product	"""thyroid hormone- and retinoic acid receptor-associated corepressor 1"", ""protein phosphatase 1, regulatory subunit 109"""	600849	"""nuclear receptor co-repressor 1"""			7566114, 9724795	Standard	NM_006311		Approved	N-CoR, hCIT529I10, TRAC1, hN-CoR, KIAA1047, MGC104216, PPP1R109	uc002gpo.3	O75376	OTTHUMG00000059309	ENST00000268712.3:c.2568A>T	chr17.hg19:g.16004686T>A	ENSP00000268712:p.Arg856Ser	46.0	0.0	.		80.0	47.0	.	NM_001190440	B3DLF8|E9PGV6|Q86YY0|Q9UPV5|Q9UQ18	Missense_Mutation	SNP	ENST00000268712.3	hg19	CCDS11175.1	.	.	.	.	.	.	.	.	.	.	T	2.512	-0.312814	0.05422	.	.	ENSG00000141027	ENST00000268712;ENST00000395851;ENST00000395849;ENST00000395848	T;T;T;T	0.45668	3.41;1.54;0.89;1.54	5.76	-0.452	0.12205	.	0.776473	0.13041	N	0.418546	T	0.22126	0.0533	L	0.29908	0.895	0.46774	D	0.999197	B;B;B	0.21309	0.054;0.0;0.0	B;B;B	0.21360	0.034;0.0;0.0	T	0.15178	-1.0446	10	0.18710	T	0.47	-1.0053	0.985	0.01444	0.2157:0.2558:0.1112:0.4173	.	763;856;872	E9PGV6;O75376;O75376-2	.;NCOR1_HUMAN;.	S	856;872;763;763	ENSP00000268712:R856S;ENSP00000379192:R872S;ENSP00000379190:R763S;ENSP00000379189:R763S	ENSP00000268712:R856S	R	-	3	2	NCOR1	15945411	0.001000	0.12720	0.350000	0.25708	0.105000	0.19272	-0.318000	0.08050	-0.108000	0.12066	-1.109000	0.02080	AGA	.	T|0.999;C|0.001	.	alt		0.483	NCOR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131751.5	NM_006311	
ARHGAP23	57636	hgsc.bcm.edu	37	17	36636124	36636124	+	Splice_Site	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:36636124G>C	ENST00000431231.2	+	14	2697	c.2629G>C	c.(2629-2631)Gat>Cat	p.D877H	ARHGAP23_ENST00000443378.1_Splice_Site_p.D783H|ARHGAP23_ENST00000437668.3_Splice_Site_p.D877H	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	877					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)			breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						AGGGAGCAAGGGTAGGAAGGT	0.662																																					p.D877H		Atlas-SNP	.											.	ARHGAP23	48	.	0			c.G2629C						PASS	.						6.0	5.0	5.0					17																	36636124		686	1545	2231	SO:0001630	splice_region_variant	57636	exon14			AGCAAGGGTAGGA	AB040934	CCDS56027.1	17q12	2014-05-06			ENSG00000225485	ENSG00000275832		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	29293	protein-coding gene	gene with protein product		610590				10819331, 15254754	Standard	NM_001199417		Approved	KIAA1501	uc021twd.1	Q9P227	OTTHUMG00000188547	ENST00000431231.2:c.2629+1G>C	chr17.hg19:g.36636124G>C		135.0	0.0	.		136.0	42.0	.	NM_001199417		Missense_Mutation	SNP	ENST00000431231.2	hg19	CCDS56027.1	.	.	.	.	.	.	.	.	.	.	G	16.35	3.097795	0.56075	.	.	ENSG00000225485	ENST00000437668;ENST00000431231;ENST00000443378	T;T;T	0.17528	2.27;2.66;2.61	4.75	4.75	0.60458	.	0.700803	0.13825	N	0.360123	T	0.18087	0.0434	L	0.38175	1.15	0.34434	D	0.698836	P;B	0.44478	0.836;0.115	B;B	0.42882	0.401;0.134	T	0.19549	-1.0302	10	0.72032	D	0.01	.	13.1086	0.59261	0.0:0.0:1.0:0.0	.	877;877	Q9P227;Q9P227-2	RHG23_HUMAN;.	H	877;877;783	ENSP00000394153:D877H;ENSP00000393539:D877H;ENSP00000407333:D783H	ENSP00000393539:D877H	D	+	1	0	ARHGAP23	33889650	1.000000	0.71417	1.000000	0.80357	0.896000	0.52359	5.846000	0.69444	2.475000	0.83589	0.555000	0.69702	GAT	.	.	.	none		0.662	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1	XM_290799	Missense_Mutation
FAM20A	54757	hgsc.bcm.edu	37	17	66538847	66538847	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:66538847A>C	ENST00000592554.1	-	6	1638	c.916T>G	c.(916-918)Ttt>Gtt	p.F306V	AC079210.1_ENST00000600820.1_5'Flank|FAM20A_ENST00000226094.5_5'UTR|PRKAR1A_ENST00000588188.2_Intron	NM_001243746.1|NM_017565.3	NP_001230675.1|NP_060035.2	Q96MK3	FA20A_HUMAN	family with sequence similarity 20, member A	306					calcium ion homeostasis (GO:0055074)|enamel mineralization (GO:0070166)|tooth eruption (GO:0044691)	cell (GO:0005623)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)				cervix(1)|endometrium(1)|large_intestine(3)|lung(2)|prostate(1)|stomach(1)	9	Breast(10;1.64e-13)					GGAGAGACAAAGAAAACACTC	0.522																																					p.F306V		Atlas-SNP	.											.	FAM20A	35	.	0			c.T916G						PASS	.						107.0	107.0	107.0					17																	66538847		2203	4300	6503	SO:0001583	missense	54757	exon6			AGACAAAGAAAAC	AK056789	CCDS11679.1	17q24.2	2014-02-07			ENSG00000108950	ENSG00000108950			23015	protein-coding gene	gene with protein product		611062					Standard	NM_017565		Approved	DKFZp434F2322	uc002jho.3	Q96MK3	OTTHUMG00000180152	ENST00000592554.1:c.916T>G	chr17.hg19:g.66538847A>C	ENSP00000468308:p.Phe306Val	57.0	0.0	.		85.0	21.0	.	NM_017565	B2RN47|B2RN49|Q9UF95	Missense_Mutation	SNP	ENST00000592554.1	hg19	CCDS11679.1	.	.	.	.	.	.	.	.	.	.	A	32	5.105452	0.94245	.	.	ENSG00000108950	ENST00000226094	.	.	.	6.04	6.04	0.98038	.	0.087086	0.85682	D	0.000000	T	0.77398	0.4124	M	0.89414	3.03	0.80722	D	1	P	0.47034	0.889	P	0.50825	0.651	T	0.81820	-0.0757	9	0.66056	D	0.02	-17.9903	16.5763	0.84648	1.0:0.0:0.0:0.0	.	306	Q96MK3	FA20A_HUMAN	V	306	.	ENSP00000226094:F306V	F	-	1	0	FAM20A	64050442	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	8.962000	0.93254	2.317000	0.78254	0.459000	0.35465	TTT	.	.	.	none		0.522	FAM20A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450029.2	NM_017565	
UBE2O	63893	hgsc.bcm.edu	37	17	74391896	74391896	+	Silent	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:74391896C>T	ENST00000319380.7	-	15	2920	c.2856G>A	c.(2854-2856)aaG>aaA	p.K952K	UBE2O_ENST00000587581.1_5'Flank	NM_022066.3	NP_071349.3	Q9C0C9	UBE2O_HUMAN	ubiquitin-conjugating enzyme E2O	952					positive regulation of BMP signaling pathway (GO:0030513)|protein K63-linked ubiquitination (GO:0070534)|protein monoubiquitination (GO:0006513)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|ubiquitin-protein transferase activity (GO:0004842)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	36						TGAAGAACTTCTTGGCTTCTG	0.502																																					p.K952K		Atlas-SNP	.											.	UBE2O	207	.	0			c.G2856A						PASS	.						124.0	116.0	119.0					17																	74391896		2203	4300	6503	SO:0001819	synonymous_variant	63893	exon15			GAACTTCTTGGCT	AB051521	CCDS32742.1	17q25.1	2013-10-09			ENSG00000175931	ENSG00000175931			29554	protein-coding gene	gene with protein product						11311559, 11214970	Standard	NM_022066		Approved	E2-230K	uc002jrm.4	Q9C0C9	OTTHUMG00000180178	ENST00000319380.7:c.2856G>A	chr17.hg19:g.74391896C>T		41.0	0.0	.		51.0	17.0	.	NM_022066	A6NDU5|Q69YP4|Q6PIZ2|Q86UA4|Q8N425|Q8TBN1|Q9BSW1|Q9H6E6|Q9H7E4|Q9H9B2	Silent	SNP	ENST00000319380.7	hg19	CCDS32742.1																																																																																			.	.	.	none		0.502	UBE2O-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450123.1	NM_022066	
FOXK2	3607	hgsc.bcm.edu	37	17	80477826	80477826	+	Missense_Mutation	SNP	G	G	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						PASS	.						1.0	1.0	1.0					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	0.0	0.0	.		4.0	2.0	.	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.	.	none		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
APCDD1	147495	hgsc.bcm.edu	37	18	10487720	10487720	+	Nonsense_Mutation	SNP	C	C	A	rs139112764		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr18:10487720C>A	ENST00000355285.5	+	5	1584	c.1230C>A	c.(1228-1230)tgC>tgA	p.C410*		NM_153000.4	NP_694545.1			adenomatosis polyposis coli down-regulated 1											NS(1)|breast(1)|endometrium(3)|large_intestine(5)|lung(7)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22				READ - Rectum adenocarcinoma(15;0.08)		CCAATGGCTGCGTGGCCCTGG	0.602																																					p.C410X		Atlas-SNP	.											APCDD1,caecum,carcinoma,0,1	APCDD1	57	.	0			c.C1230A						PASS	.						77.0	68.0	71.0					18																	10487720		2203	4300	6503	SO:0001587	stop_gained	147495	exon5			TGGCTGCGTGGCC	AB056722	CCDS11849.1	18p11.21	2006-07-07			ENSG00000154856	ENSG00000154856			15718	protein-coding gene	gene with protein product		607479				12384519	Standard	NM_153000		Approved	B7323	uc002kom.4	Q8J025	OTTHUMG00000131635	ENST00000355285.5:c.1230C>A	chr18.hg19:g.10487720C>A	ENSP00000347433:p.Cys410*	67.0	0.0	.		101.0	46.0	.	NM_153000		Nonsense_Mutation	SNP	ENST00000355285.5	hg19	CCDS11849.1	.	.	.	.	.	.	.	.	.	.	C	38	6.674971	0.97755	.	.	ENSG00000154856	ENST00000355285;ENST00000423585	.	.	.	5.07	-4.6	0.03390	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-34.3709	13.6645	0.62387	0.0:0.3885:0.0:0.6115	.	.	.	.	X	410;461	.	ENSP00000347433:C410X	C	+	3	2	APCDD1	10477720	0.361000	0.24972	0.907000	0.35723	0.991000	0.79684	-0.250000	0.08830	-1.024000	0.03338	-0.251000	0.11542	TGC	.	C|1.000;T|0.000	.	alt		0.602	APCDD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254529.2	NM_153000	
TCF4	6925	hgsc.bcm.edu	37	18	53018225	53018225	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr18:53018225G>A	ENST00000356073.4	-	7	990	c.379C>T	c.(379-381)Ctt>Ttt	p.L127F	TCF4_ENST00000567880.1_Intron|TCF4_ENST00000564403.2_Missense_Mutation_p.L127F|TCF4_ENST00000537578.1_Missense_Mutation_p.L103F|TCF4_ENST00000564228.1_Missense_Mutation_p.L56F|TCF4_ENST00000570177.2_5'UTR|TCF4_ENST00000561992.1_5'UTR|TCF4_ENST00000568673.1_Missense_Mutation_p.L103F|TCF4_ENST00000566279.1_Intron|TCF4_ENST00000566286.1_Missense_Mutation_p.L125F|TCF4_ENST00000354452.3_Missense_Mutation_p.L127F|TCF4_ENST00000543082.1_Missense_Mutation_p.L85F|TCF4_ENST00000544241.2_Missense_Mutation_p.L56F|TCF4_ENST00000537856.3_5'UTR|TCF4_ENST00000398339.1_Missense_Mutation_p.L229F|TCF4_ENST00000564999.1_Missense_Mutation_p.L127F|TCF4_ENST00000568740.1_Missense_Mutation_p.L102F|TCF4_ENST00000540999.1_Missense_Mutation_p.L103F|TCF4_ENST00000565018.2_Missense_Mutation_p.L127F	NM_003199.2	NP_003190.1	P15884	ITF2_HUMAN	transcription factor 4	127					DNA-templated transcription, initiation (GO:0006352)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein-DNA complex assembly (GO:0065004)|transcription initiation from RNA polymerase II promoter (GO:0006367)	nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein C-terminus binding (GO:0008022)|protein heterodimerization activity (GO:0046982)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|sequence-specific DNA binding RNA polymerase recruiting transcription factor activity (GO:0001011)|sequence-specific DNA binding transcription factor activity (GO:0003700)|TFIIB-class binding transcription factor activity (GO:0001087)|TFIIB-class transcription factor binding (GO:0001093)			breast(1)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(15)|ovary(1)|prostate(1)|skin(5)|urinary_tract(1)	41				Colorectal(16;0.00108)|READ - Rectum adenocarcinoma(59;0.0649)|COAD - Colon adenocarcinoma(17;0.0718)		TCACCTCCAAGGAGACTCTGC	0.428																																					p.L229F		Atlas-SNP	.											.	TCF4	178	.	0			c.C685T						PASS	.						91.0	88.0	89.0					18																	53018225		2203	4300	6503	SO:0001583	missense	6925	exon8			CTCCAAGGAGACT	M74719	CCDS11960.1, CCDS42438.1, CCDS58623.1, CCDS58624.1, CCDS58625.1, CCDS58626.1, CCDS58627.1, CCDS58628.1, CCDS58629.1, CCDS58630.1, CCDS58631.1, CCDS59321.1	18q21.1	2013-05-21			ENSG00000196628	ENSG00000196628		"""Basic helix-loop-helix proteins"""	11634	protein-coding gene	gene with protein product		602272				9302263, 2308860	Standard	NM_001083962		Approved	SEF2-1B, ITF2, bHLHb19, E2-2	uc002lga.3	P15884	OTTHUMG00000132713	ENST00000356073.4:c.379C>T	chr18.hg19:g.53018225G>A	ENSP00000348374:p.Leu127Phe	66.0	0.0	.		107.0	47.0	.	NM_001243226	B3KT62|B3KUC0|B4DT37|B4DUG3|B7Z5M6|B7Z6Y1|G0LNT9|G0LNU0|G0LNU1|G0LNU2|G0LNU4|G0LNU5|G0LNU8|G0LNU9|G0LNV0|G0LNV1|G0LNV2|H3BPQ1|Q08AP2|Q08AP3|Q15439|Q15440|Q15441	Missense_Mutation	SNP	ENST00000356073.4	hg19	CCDS11960.1	.	.	.	.	.	.	.	.	.	.	G	15.75	2.926592	0.52759	.	.	ENSG00000196628	ENST00000354452;ENST00000356073;ENST00000543082;ENST00000540999;ENST00000537578;ENST00000544241;ENST00000398339	T;T;T;T;T;T;T	0.73897	-0.79;-0.79;-0.79;-0.79;-0.79;-0.79;-0.79	5.57	5.57	0.84162	.	0.162083	0.42682	D	0.000670	T	0.82038	0.4950	L	0.59436	1.845	0.58432	D	0.999994	D;B;D;D;P;P;D	0.69078	0.957;0.418;0.975;0.997;0.947;0.913;0.957	P;B;P;P;P;P;P	0.59221	0.729;0.267;0.835;0.854;0.568;0.66;0.729	D	0.83433	0.0039	10	0.87932	D	0	-25.4497	16.8254	0.85929	0.0:0.0:1.0:0.0	.	103;127;103;229;127;85;56	B7Z5M6;G0LNT9;B7Z6Y1;E9PH57;P15884;B3KUC0;B3KT62	.;.;.;.;ITF2_HUMAN;.;.	F	127;127;85;103;103;56;229	ENSP00000346440:L127F;ENSP00000348374:L127F;ENSP00000439656:L85F;ENSP00000445202:L103F;ENSP00000440731:L103F;ENSP00000441562:L56F;ENSP00000381382:L229F	ENSP00000346440:L127F	L	-	1	0	TCF4	51169223	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.547000	0.60712	2.781000	0.95711	0.655000	0.94253	CTT	.	.	.	none		0.428	TCF4-002	KNOWN	upstream_uORF|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256014.1	NM_003199	
PNPLA6	10908	hgsc.bcm.edu	37	19	7619899	7619899	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:7619899T>C	ENST00000221249.6	+	25	3072	c.2641T>C	c.(2641-2643)Tcg>Ccg	p.S881P	PNPLA6_ENST00000600737.1_Missense_Mutation_p.S919P|PNPLA6_ENST00000545201.2_Missense_Mutation_p.S854P|PNPLA6_ENST00000450331.3_Missense_Mutation_p.S881P|PNPLA6_ENST00000414982.3_Missense_Mutation_p.S929P	NM_006702.4	NP_006693.3	Q8IY17	PLPL6_HUMAN	patatin-like phospholipase domain containing 6	920					angiogenesis (GO:0001525)|cell death (GO:0008219)|lipid catabolic process (GO:0016042)|organ morphogenesis (GO:0009887)|phosphatidylcholine metabolic process (GO:0046470)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|membrane (GO:0016020)	lysophospholipase activity (GO:0004622)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(14)|ovary(3)|stomach(1)|upper_aerodigestive_tract(1)	35						CAGCTGGTGCTCGGGGCACCT	0.711																																					p.S929P		Atlas-SNP	.											.	PNPLA6	163	.	0			c.T2785C						PASS	.						12.0	13.0	12.0					19																	7619899		2199	4290	6489	SO:0001583	missense	10908	exon24			TGGTGCTCGGGGC	AJ004832	CCDS32891.1, CCDS54206.1, CCDS54207.1, CCDS59343.1	19p13.2	2013-09-11						"""Patatin-like phospholipase domain containing"""	16268	protein-coding gene	gene with protein product	"""neuropathy target esterase"""	603197				9576844, 16799181, 19029121	Standard	NM_006702		Approved	NTE, sws, iPLA2delta, SPG39	uc010xjq.2	Q8IY17		ENST00000221249.6:c.2641T>C	chr19.hg19:g.7619899T>C	ENSP00000221249:p.Ser881Pro	12.0	0.0	.		35.0	13.0	.	NM_001166111	A6NGQ0|B4DFB9|B7Z7T2|F5H5K9|J3KQS3|O60859|Q86W58|Q9UG58	Missense_Mutation	SNP	ENST00000221249.6	hg19	CCDS32891.1	.	.	.	.	.	.	.	.	.	.	t	28.6	4.930713	0.92389	.	.	ENSG00000032444	ENST00000221249;ENST00000545201;ENST00000414982;ENST00000450331	T;T;T;T	0.26957	1.7;1.7;1.7;1.7	5.35	5.35	0.76521	.	0.140180	0.50627	D	0.000120	T	0.56746	0.2006	M	0.90082	3.085	0.58432	D	0.999999	D;B;D;D	0.65815	0.992;0.149;0.995;0.987	D;B;D;D	0.68765	0.912;0.162;0.96;0.937	T	0.66101	-0.6007	10	0.72032	D	0.01	.	13.3305	0.60483	0.0:0.0:0.0:1.0	.	920;854;919;881	Q8IY17;F5H5K9;Q8IY17-3;Q8IY17-2	PLPL6_HUMAN;.;.;.	P	881;854;929;881	ENSP00000221249:S881P;ENSP00000443323:S854P;ENSP00000407509:S929P;ENSP00000394348:S881P	ENSP00000221249:S881P	S	+	1	0	PNPLA6	7525899	1.000000	0.71417	0.996000	0.52242	0.748000	0.42578	7.996000	0.88334	2.040000	0.60383	0.454000	0.30748	TCG	.	.	.	none		0.711	PNPLA6-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459275.1	NM_006702	
ZNF627	199692	hgsc.bcm.edu	37	19	11727866	11727866	+	Missense_Mutation	SNP	G	G	A	rs200860012		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:11727866G>A	ENST00000361113.5	+	4	756	c.548G>A	c.(547-549)cGa>cAa	p.R183Q	ZNF627_ENST00000588174.1_3'UTR	NM_145295.3	NP_660338.1	Q7L945	ZN627_HUMAN	zinc finger protein 627	183					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.R183Q(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(6)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	14						GTAAGCATTCGAAGACACATG	0.403													G|||	1	0.000199681	0.0	0.0	5008	,	,		24586	0.0		0.0	False		,,,				2504	0.001				p.R183Q	Melanoma(112;173 1614 10731 17751 23322)	Atlas-SNP	.											ZNF627,caecum,carcinoma,0,2	ZNF627	43	.	1	Substitution - Missense(1)	central_nervous_system(1)	c.G548A						PASS	.	G	GLN/ARG	0,4336		0,0,2168	84.0	85.0	85.0		548	-2.7	0.0	19		85	1,8559		0,1,4279	yes	missense	ZNF627	NM_145295.3	43	0,1,6447	AA,AG,GG		0.0117,0.0,0.0078	possibly-damaging	183/462	11727866	1,12895	2168	4280	6448	SO:0001583	missense	199692	exon4			GCATTCGAAGACA	AK074846	CCDS42502.1	19p13.2	2013-01-08				ENSG00000198551		"""Zinc fingers, C2H2-type"", ""-"""	30570	protein-coding gene	gene with protein product		612248				12477932	Standard	NM_145295		Approved	FLJ90365	uc002msk.2	Q7L945		ENST00000361113.5:c.548G>A	chr19.hg19:g.11727866G>A	ENSP00000354414:p.Arg183Gln	69.0	0.0	.		99.0	48.0	.	NM_145295	O14846|Q4KMP9|Q6NT81|Q9BRG4	Missense_Mutation	SNP	ENST00000361113.5	hg19	CCDS42502.1	.	.	.	.	.	.	.	.	.	.	g	7.616	0.675785	0.14841	0.0	1.17E-4	ENSG00000198551	ENST00000361113	T	0.36520	1.25	1.36	-2.73	0.05950	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.19046	0.0457	L	0.33189	0.99	0.18873	N	0.999989	P	0.42584	0.784	B	0.38616	0.277	T	0.22173	-1.0224	9	0.07030	T	0.85	.	6.5443	0.22397	0.6527:0.0:0.3473:0.0	.	183	Q7L945	ZN627_HUMAN	Q	183	ENSP00000354414:R183Q	ENSP00000354414:R183Q	R	+	2	0	ZNF627	11588866	0.000000	0.05858	0.001000	0.08648	0.966000	0.64601	-1.336000	0.02660	-0.762000	0.04664	0.313000	0.20887	CGA	.	.	.	weak		0.403	ZNF627-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458875.1	NM_145295	
FBXW9	84261	hgsc.bcm.edu	37	19	12805491	12805491	+	Missense_Mutation	SNP	A	A	T	rs201026853	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:12805491A>T	ENST00000380339.3	-	3	631	c.595T>A	c.(595-597)Ttg>Atg	p.L199M	FBXW9_ENST00000544494.1_De_novo_Start_OutOfFrame|FBXW9_ENST00000393261.3_Missense_Mutation_p.L199M|FBXW9_ENST00000587955.1_Missense_Mutation_p.L189M			Q5XUX1	FBXW9_HUMAN	F-box and WD repeat domain containing 9	199					SCF-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031146)					cervix(1)|lung(4)|ovary(1)|prostate(1)	7						AGGTCCCACAAGTTGACGTTG	0.602																																					p.L199M		Atlas-SNP	.											.	FBXW9	30	.	0			c.T595A						PASS	.						60.0	67.0	65.0					19																	12805491		2043	4197	6240	SO:0001583	missense	84261	exon3			CCCACAAGTTGAC	BC004290	CCDS12278.2	19p13.2	2013-01-09	2007-02-08		ENSG00000132004	ENSG00000132004		"""F-boxes / WD-40 domains"", ""WD repeat domain containing"""	28136	protein-coding gene	gene with protein product		609074	"""F-box and WD-40 domain protein 9"""			12477932	Standard	NM_032301		Approved	MGC10870, Fbw9	uc002mum.1	Q5XUX1	OTTHUMG00000150152	ENST00000380339.3:c.595T>A	chr19.hg19:g.12805491A>T	ENSP00000369696:p.Leu199Met	87.0	0.0	.		92.0	36.0	.	NM_032301	B3KVP7|Q9BT89	Missense_Mutation	SNP	ENST00000380339.3	hg19		.	.	.	.	.	.	.	.	.	.	A	17.06	3.292183	0.59976	.	.	ENSG00000132004	ENST00000393261;ENST00000380339	T;T	0.66638	-0.22;-0.22	4.24	-0.503	0.12000	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40 repeat, conserved site (1);WD40-repeat-containing domain (1);	0.000000	0.64402	D	0.000003	T	0.77745	0.4176	M	0.82132	2.575	0.80722	D	1	D;P;D	0.89917	0.992;0.955;1.0	P;D;D	0.91635	0.899;0.93;0.999	T	0.75825	-0.3181	10	0.56958	D	0.05	-18.2074	8.7017	0.34329	0.4517:0.0:0.5483:0.0	.	189;199;199	Q5XUX1-2;Q5XUX1;Q5XUX1-3	.;FBXW9_HUMAN;.	M	199	ENSP00000376945:L199M;ENSP00000369696:L199M	ENSP00000369696:L199M	L	-	1	2	FBXW9	12666491	1.000000	0.71417	1.000000	0.80357	0.885000	0.51271	0.885000	0.28227	0.106000	0.17784	-0.486000	0.04755	TTG	.	A|0.999;G|0.001	.	alt		0.602	FBXW9-201	KNOWN	basic	protein_coding	protein_coding		NM_032301	
UNC13A	23025	hgsc.bcm.edu	37	19	17751432	17751432	+	Missense_Mutation	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:17751432C>T	ENST00000519716.2	-	22	2674	c.2675G>A	c.(2674-2676)gGg>gAg	p.G892E	UNC13A_ENST00000550896.1_Missense_Mutation_p.G890E|UNC13A_ENST00000551649.1_Missense_Mutation_p.G892E|UNC13A_ENST00000428389.2_Missense_Mutation_p.G980E|UNC13A_ENST00000252773.7_Missense_Mutation_p.G892E|UNC13A_ENST00000552293.1_Missense_Mutation_p.G892E	NM_001080421.2	NP_001073890.2	Q9UPW8	UN13A_HUMAN	unc-13 homolog A (C. elegans)	892					beta-amyloid metabolic process (GO:0050435)|innervation (GO:0060384)|intracellular signal transduction (GO:0035556)|neuromuscular junction development (GO:0007528)|neurotransmitter secretion (GO:0007269)|positive regulation of neurotransmitter secretion (GO:0001956)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission, glutamatergic (GO:0051966)|synaptic transmission, glutamatergic (GO:0035249)|synaptic vesicle docking involved in exocytosis (GO:0016081)|synaptic vesicle maturation (GO:0016188)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|neuromuscular junction (GO:0031594)|neuron projection (GO:0043005)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)	diacylglycerol binding (GO:0019992)|metal ion binding (GO:0046872)|protein N-terminus binding (GO:0047485)|syntaxin-1 binding (GO:0017075)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(11)|lung(31)|ovary(5)|prostate(2)	61						GGCAGGCACCCCTGGGCACAT	0.637																																					p.G892E		Atlas-SNP	.											.	UNC13A	299	.	0			c.G2675A						PASS	.						59.0	69.0	65.0					19																	17751432		2187	4272	6459	SO:0001583	missense	23025	exon21			GGCACCCCTGGGC	AB028955	CCDS46013.1, CCDS46013.2	19p13.12	2008-02-05				ENSG00000130477			23150	protein-coding gene	gene with protein product		609894					Standard	NM_001080421		Approved	KIAA1032, Munc13-1	uc031rjv.1	Q9UPW8		ENST00000519716.2:c.2675G>A	chr19.hg19:g.17751432C>T	ENSP00000429562:p.Gly892Glu	85.0	0.0	.		66.0	29.0	.	NM_001080421	E5RHY9	Missense_Mutation	SNP	ENST00000519716.2	hg19	CCDS46013.2	.	.	.	.	.	.	.	.	.	.	C	17.10	3.303018	0.60195	.	.	ENSG00000130477	ENST00000519716;ENST00000428389;ENST00000252773;ENST00000551649;ENST00000552293;ENST00000550896	D;D;D;D;D;D	0.83837	-1.75;-1.69;-1.75;-1.61;-1.63;-1.77	3.28	3.28	0.37604	.	0.149281	0.45867	U	0.000325	D	0.90092	0.6905	M	0.80746	2.51	0.58432	D	0.999999	D	0.89917	1.0	D	0.79108	0.992	D	0.91311	0.5074	10	0.87932	D	0	-25.1003	12.4632	0.55743	0.0:1.0:0.0:0.0	.	892	Q9UPW8	UN13A_HUMAN	E	892;980;892;892;892;890	ENSP00000429562:G892E;ENSP00000400409:G980E;ENSP00000252773:G892E;ENSP00000447236:G892E;ENSP00000447572:G892E;ENSP00000446831:G890E	ENSP00000252773:G892E	G	-	2	0	UNC13A	17612432	1.000000	0.71417	0.985000	0.45067	0.602000	0.36980	7.340000	0.79292	1.842000	0.53543	0.186000	0.17326	GGG	.	.	.	none		0.637	UNC13A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000376169.2	XM_038604	
ZNF229	7772	hgsc.bcm.edu	37	19	44932512	44932512	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:44932512T>A	ENST00000588931.1	-	6	2877	c.2444A>T	c.(2443-2445)cAa>cTa	p.Q815L	ZNF229_ENST00000291187.4_Missense_Mutation_p.Q809L|ZNF229_ENST00000591289.1_Intron|CTC-512J12.4_ENST00000588655.1_RNA	NM_014518.2	NP_055333.2	Q9UJW7	ZN229_HUMAN	zinc finger protein 229	815					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(5)|central_nervous_system(2)|endometrium(6)|large_intestine(3)|lung(18)|ovary(1)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)	45		Prostate(69;0.0352)				ATGCACTCTTTGGTGGTTCCG	0.473																																					p.Q815L		Atlas-SNP	.											.	ZNF229	123	.	0			c.A2444T						PASS	.						89.0	96.0	94.0					19																	44932512		2150	4282	6432	SO:0001583	missense	7772	exon6			ACTCTTTGGTGGT	AF192979	CCDS42574.1, CCDS62706.1	19q13.2	2013-01-08				ENSG00000278318		"""Zinc fingers, C2H2-type"", ""-"""	13022	protein-coding gene	gene with protein product							Standard	XM_006723372		Approved		uc002oze.1	Q9UJW7		ENST00000588931.1:c.2444A>T	chr19.hg19:g.44932512T>A	ENSP00000466519:p.Gln815Leu	66.0	0.0	.		92.0	45.0	.	NM_014518	B2RWN3|Q59FV2|Q86WL9	Missense_Mutation	SNP	ENST00000588931.1	hg19	CCDS42574.1	.	.	.	.	.	.	.	.	.	.	T	15.55	2.866557	0.51588	.	.	ENSG00000167383	ENST00000291187	.	.	.	3.62	3.62	0.41486	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.25457	0.0619	L	0.35793	1.09	0.27093	N	0.962818	P	0.37997	0.614	B	0.26202	0.067	T	0.13495	-1.0507	8	0.62326	D	0.03	.	11.3701	0.49694	0.0:0.0:0.0:1.0	.	815	Q9UJW7	ZN229_HUMAN	L	815	.	ENSP00000291187:Q815L	Q	-	2	0	ZNF229	49624352	0.430000	0.25538	0.055000	0.19348	0.371000	0.29859	0.889000	0.28282	1.509000	0.48786	0.491000	0.48974	CAA	.	.	.	none		0.473	ZNF229-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000460833.1	NM_014518	
GRIN2D	2906	hgsc.bcm.edu	37	19	48918125	48918125	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:48918125C>A	ENST00000263269.3	+	6	1505	c.1417C>A	c.(1417-1419)Cca>Aca	p.P473T		NM_000836.2	NP_000827.2	O15399	NMDE4_HUMAN	glutamate receptor, ionotropic, N-methyl D-aspartate 2D	473					adult locomotory behavior (GO:0008344)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|regulation of sensory perception of pain (GO:0051930)|signal transduction (GO:0007165)|startle response (GO:0001964)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)			autonomic_ganglia(1)|breast(6)|endometrium(2)|large_intestine(9)|lung(12)|ovary(5)|pancreas(1)|prostate(1)	37		all_epithelial(76;1.11e-06)|all_lung(116;5.79e-06)|Lung NSC(112;1.18e-05)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		all cancers(93;0.00014)|OV - Ovarian serous cystadenocarcinoma(262;0.000233)|Epithelial(262;0.0112)|GBM - Glioblastoma multiforme(486;0.0161)	Acamprosate(DB00659)|Acetylcysteine(DB06151)|Atomoxetine(DB00289)|Gabapentin(DB00996)|Ketobemidone(DB06738)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Pethidine(DB00454)|Phenobarbital(DB01174)|Secobarbital(DB00418)	CCGCAGCCCTCCACCGGATGC	0.597																																					p.P473T		Atlas-SNP	.											.	GRIN2D	76	.	0			c.C1417A						PASS	.						42.0	49.0	46.0					19																	48918125		2203	4300	6503	SO:0001583	missense	2906	exon6			AGCCCTCCACCGG	U77783	CCDS12719.1	19q13.33	2012-08-29			ENSG00000105464	ENSG00000105464		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4588	protein-coding gene	gene with protein product	"""N-methyl-d-aspartate receptor subunit 2D"""	602717		NMDAR2D		9480759, 9418891	Standard	NM_000836		Approved	GluN2D, EB11, NR2D	uc002pjc.4	O15399		ENST00000263269.3:c.1417C>A	chr19.hg19:g.48918125C>A	ENSP00000263269:p.Pro473Thr	103.0	0.0	.		88.0	39.0	.	NM_000836		Missense_Mutation	SNP	ENST00000263269.3	hg19	CCDS12719.1	.	.	.	.	.	.	.	.	.	.	C	12.48	1.952119	0.34471	.	.	ENSG00000105464	ENST00000263269	T	0.11277	2.79	4.36	4.36	0.52297	Ionotropic glutamate receptor (1);	0.596252	0.16331	N	0.219129	T	0.08179	0.0204	N	0.14661	0.345	0.28778	N	0.900003	P	0.42757	0.789	P	0.46110	0.504	T	0.12656	-1.0539	10	0.14656	T	0.56	.	9.899	0.41335	0.0:0.9037:0.0:0.0963	.	473	O15399	NMDE4_HUMAN	T	473	ENSP00000263269:P473T	ENSP00000263269:P473T	P	+	1	0	GRIN2D	53609937	0.913000	0.31002	0.994000	0.49952	0.917000	0.54804	1.202000	0.32271	2.445000	0.82738	0.655000	0.94253	CCA	.	.	.	none		0.597	GRIN2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466121.1		
PLEKHA4	57664	hgsc.bcm.edu	37	19	49341323	49341323	+	Silent	SNP	G	G	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:49341323G>T	ENST00000263265.6	-	19	2583	c.2028C>A	c.(2026-2028)ctC>ctA	p.L676L	HSD17B14_ENST00000599157.1_5'Flank|PLEKHA4_ENST00000355496.5_Missense_Mutation_p.L578I|HSD17B14_ENST00000263278.4_5'Flank	NM_020904.2	NP_065955.2	Q9H4M7	PKHA4_HUMAN	pleckstrin homology domain containing, family A (phosphoinositide binding specific) member 4	676						cytoplasm (GO:0005737)|membrane (GO:0016020)	1-phosphatidylinositol binding (GO:0005545)			NS(1)|breast(5)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(3)|skin(2)|urinary_tract(2)	30		all_lung(116;4.89e-05)|Lung NSC(112;8.3e-05)|all_epithelial(76;0.000108)|all_neural(266;0.0506)|Ovarian(192;0.113)		OV - Ovarian serous cystadenocarcinoma(262;0.00027)|all cancers(93;0.00084)|GBM - Glioblastoma multiforme(486;0.0244)|Epithelial(262;0.0364)		GGGCTTGGGAGAGGCTGAGAA	0.562																																					p.L578I		Atlas-SNP	.											.	PLEKHA4	70	.	0			c.C1732A						PASS	.						78.0	82.0	81.0					19																	49341323		2203	4300	6503	SO:0001819	synonymous_variant	57664	exon16			TTGGGAGAGGCTG	AY007233	CCDS12737.1, CCDS54291.1	19q13.33	2013-01-10	2002-01-14			ENSG00000105559		"""Pleckstrin homology (PH) domain containing"""	14339	protein-coding gene	gene with protein product		607769	"""pleckstrin homology domain-containing, family A (phosphoinositide binding specific) member 4"""			11001876	Standard	NM_020904		Approved	PEPP1	uc002pkx.3	Q9H4M7		ENST00000263265.6:c.2028C>A	chr19.hg19:g.49341323G>T		184.0	0.0	.		142.0	69.0	.	NM_001161354	Q8N4M8|Q8N658	Missense_Mutation	SNP	ENST00000263265.6	hg19	CCDS12737.1	.	.	.	.	.	.	.	.	.	.	g	18.76	3.692992	0.68271	.	.	ENSG00000105559	ENST00000355496	T	0.19105	2.17	3.97	0.263	0.15602	.	1.342660	0.05462	N	0.551512	T	0.13286	0.0322	.	.	.	0.22266	N	0.999243	B	0.21309	0.054	B	0.22152	0.038	T	0.34030	-0.9845	9	0.29301	T	0.29	.	5.5324	0.16993	0.1144:0.4003:0.4854:0.0	.	578	Q9H4M7-2	.	I	578	ENSP00000347683:L578I	ENSP00000347683:L578I	L	-	1	0	PLEKHA4	54033135	1.000000	0.71417	1.000000	0.80357	0.942000	0.58702	1.127000	0.31357	0.452000	0.26830	0.546000	0.68486	CTC	.	.	.	none		0.562	PLEKHA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466216.1		
ZNF471	57573	hgsc.bcm.edu	37	19	57035735	57035735	+	Missense_Mutation	SNP	A	A	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:57035735A>C	ENST00000308031.5	+	5	432	c.299A>C	c.(298-300)cAg>cCg	p.Q100P	ZNF471_ENST00000593197.1_Intron|ZNF471_ENST00000591537.1_Intron	NM_020813.2	NP_065864.2	Q9BX82	ZN471_HUMAN	zinc finger protein 471	100					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(2)|lung(8)|ovary(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Colorectal(82;5.46e-05)|Ovarian(87;0.0822)|Renal(1328;0.157)		GBM - Glioblastoma multiforme(193;0.0307)		CCTCTGAAGCAGTTCATGTAT	0.368																																					p.Q100P	Colon(65;957 1402 6678 10163)|Esophageal Squamous(159;2295 2541 15408 21211)	Atlas-SNP	.											.	ZNF471	99	.	0			c.A299C						PASS	.						87.0	84.0	85.0					19																	57035735		2203	4300	6503	SO:0001583	missense	57573	exon5			TGAAGCAGTTCAT	AB037817	CCDS12945.1	19q13.43	2013-01-08				ENSG00000196263		"""Zinc fingers, C2H2-type"", ""-"""	23226	protein-coding gene	gene with protein product						10718198	Standard	NM_020813		Approved	KIAA1396, Z1971	uc002qnh.3	Q9BX82		ENST00000308031.5:c.299A>C	chr19.hg19:g.57035735A>C	ENSP00000309161:p.Gln100Pro	76.0	0.0	.		66.0	32.0	.	NM_020813	B4DF32|O75260|Q08AD6|Q08AD7|Q8N3V1|Q9P2F1	Missense_Mutation	SNP	ENST00000308031.5	hg19	CCDS12945.1	.	.	.	.	.	.	.	.	.	.	A	6.621	0.483070	0.12581	.	.	ENSG00000196263	ENST00000308031	T	0.05649	3.41	3.56	1.43	0.22495	.	.	.	.	.	T	0.06371	0.0164	L	0.31476	0.935	0.09310	N	0.999998	D	0.57257	0.979	P	0.49012	0.598	T	0.34254	-0.9836	9	0.36615	T	0.2	.	3.613	0.08067	0.6493:0.2294:0.1213:0.0	.	100	Q9BX82	ZN471_HUMAN	P	100	ENSP00000309161:Q100P	ENSP00000309161:Q100P	Q	+	2	0	ZNF471	61727547	0.000000	0.05858	0.004000	0.12327	0.558000	0.35554	0.340000	0.19892	0.234000	0.21139	0.460000	0.39030	CAG	.	.	.	none		0.368	ZNF471-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458405.1	NM_020813	
ZNF814	730051	hgsc.bcm.edu	37	19	58385869	58385869	+	Nonsense_Mutation	SNP	C	C	A	rs199684163|rs10687775|rs55789144|rs66767659	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:58385869C>A	ENST00000435989.2	-	3	1123	c.889G>T	c.(889-891)Gaa>Taa	p.E297*	ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron|ZNF814_ENST00000597342.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	297					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						TCTCCACATTCATGTTTTTTT	0.363																																					p.E297X		Atlas-SNP	.											ZNF814,NS,carcinoma,0,6	ZNF814	93	.	0			c.G889T						PASS	.						5.0	4.0	5.0					19																	58385869		591	1308	1899	SO:0001587	stop_gained	730051	exon3			CACATTCATGTTT		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.889G>T	chr19.hg19:g.58385869C>A	ENSP00000410545:p.Glu297*	19.0	1.0	.		15.0	6.0	.	NM_001144989	A6NF35	Nonsense_Mutation	SNP	ENST00000435989.2	hg19	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	27.5	4.839119	0.91117	.	.	ENSG00000204514	ENST00000435989	.	.	.	1.93	-3.87	0.04218	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	0.6944	0.00896	0.1754:0.2303:0.1739:0.4204	.	.	.	.	X	297	.	ENSP00000410545:E297X	E	-	1	0	ZNF814	63077681	0.000000	0.05858	0.000000	0.03702	0.378000	0.30076	-0.792000	0.04594	-0.856000	0.04120	0.121000	0.15741	GAA	.	.	.	weak		0.363	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708	
CST2	1470	hgsc.bcm.edu	37	20	23805942	23805942	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr20:23805942A>T	ENST00000304725.2	-	2	317	c.247T>A	c.(247-249)Tac>Aac	p.Y83N		NM_001322.2	NP_001313.1	P09228	CYTT_HUMAN	cystatin SA	83					detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|negative regulation of endopeptidase activity (GO:0010951)	extracellular space (GO:0005615)	cysteine-type endopeptidase inhibitor activity (GO:0004869)	p.Y83D(1)		breast(1)|cervix(1)|large_intestine(1)|liver(1)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	10						TCGAAGAAGTAATTCACCCCG	0.537																																					p.Y83N	Pancreas(193;496 3017 22514 29918)	Atlas-SNP	.											CST2,face,carcinoma,0,1	CST2	39	.	1	Substitution - Missense(1)	skin(1)	c.T247A						PASS	.						274.0	212.0	233.0					20																	23805942		2203	4300	6503	SO:0001583	missense	1470	exon2			AGAAGTAATTCAC	M19671	CCDS13161.1	20p11.2	2007-11-29			ENSG00000170369	ENSG00000170369			2474	protein-coding gene	gene with protein product	"""cystatin 2"""	123856					Standard	NM_001322		Approved		uc002wtq.1	P09228	OTTHUMG00000032086	ENST00000304725.2:c.247T>A	chr20.hg19:g.23805942A>T	ENSP00000307540:p.Tyr83Asn	58.0	0.0	.		58.0	24.0	.	NM_001322	Q9UCQ7	Missense_Mutation	SNP	ENST00000304725.2	hg19	CCDS13161.1	.	.	.	.	.	.	.	.	.	.	A	12.88	2.069071	0.36470	.	.	ENSG00000170369	ENST00000304725	T	0.43688	0.94	2.36	2.36	0.29203	Proteinase inhibitor I25, cystatin, conserved site (1);Proteinase inhibitor I25, cystatin (2);	0.075028	0.56097	U	0.000033	T	0.69744	0.3145	H	0.95982	3.75	0.09310	N	0.999996	D	0.89917	1.0	D	0.91635	0.999	T	0.60591	-0.7233	10	0.87932	D	0	.	6.5923	0.22654	1.0:0.0:0.0:0.0	.	83	P09228	CYTT_HUMAN	N	83	ENSP00000307540:Y83N	ENSP00000307540:Y83N	Y	-	1	0	CST2	23753942	0.227000	0.23707	0.027000	0.17364	0.002000	0.02628	2.917000	0.48821	1.087000	0.41251	0.254000	0.18369	TAC	.	.	.	none		0.537	CST2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078352.2		
RNF114	55905	hgsc.bcm.edu	37	20	48562762	48562762	+	Missense_Mutation	SNP	T	T	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr20:48562762T>A	ENST00000244061.2	+	4	490	c.488T>A	c.(487-489)tTc>tAc	p.F163Y		NM_018683.3	NP_061153.1	Q9Y508	RN114_HUMAN	ring finger protein 114	163					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|protein ubiquitination (GO:0016567)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ligase activity (GO:0016874)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(1)|lung(1)|ovary(1)	5						TGCAAATTATTCCATAGCACG	0.393																																					p.F163Y		Atlas-SNP	.											.	RNF114	9	.	0			c.T488A						PASS	.						96.0	81.0	86.0					20																	48562762		2203	4300	6503	SO:0001583	missense	55905	exon4			AATTATTCCATAG	AF265215	CCDS33482.1	20q13	2013-01-09	2008-06-16	2008-06-16	ENSG00000124226	ENSG00000124226		"""RING-type (C3HC4) zinc fingers"""	13094	protein-coding gene	gene with protein product		612451	"""zinc finger protein 313"""	ZNF313		18364390	Standard	NM_018683		Approved	PSORS12	uc002xux.3	Q9Y508	OTTHUMG00000032709	ENST00000244061.2:c.488T>A	chr20.hg19:g.48562762T>A	ENSP00000244061:p.Phe163Tyr	98.0	0.0	.		110.0	29.0	.	NM_018683	B2RDQ9|B4DWY5|E1P627|Q6N0B0	Missense_Mutation	SNP	ENST00000244061.2	hg19	CCDS33482.1	.	.	.	.	.	.	.	.	.	.	T	2.824	-0.244101	0.05906	.	.	ENSG00000124226	ENST00000449816;ENST00000244061	T	0.79352	-1.26	5.97	-0.203	0.13204	Zinc finger, C2H2-like (1);Drought induced 19/ RING finger protein 114 (1);	1.127120	0.06197	N	0.682425	T	0.50888	0.1642	N	0.11789	0.175	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.42498	-0.9448	10	0.02654	T	1	4.9286	0.9014	0.01275	0.2089:0.2819:0.1149:0.3943	.	163;163	Q9Y508-2;Q9Y508	.;RN114_HUMAN	Y	163	ENSP00000244061:F163Y	ENSP00000244061:F163Y	F	+	2	0	RNF114	47996169	0.000000	0.05858	0.011000	0.14972	0.973000	0.67179	0.164000	0.16542	0.061000	0.16311	-0.242000	0.12053	TTC	.	.	.	none		0.393	RNF114-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079663.1	NM_018683	
IFNAR1	3454	hgsc.bcm.edu	37	21	34707892	34707892	+	Silent	SNP	C	C	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr21:34707892C>T	ENST00000270139.3	+	2	291	c.139C>T	c.(139-141)Ctg>Ttg	p.L47L	IFNAR1_ENST00000442357.2_Silent_p.L47L|IFNAR1_ENST00000493503.1_3'UTR|IFNAR1_ENST00000416947.2_5'UTR	NM_000629.2	NP_000620.2	P17181	INAR1_HUMAN	interferon (alpha, beta and omega) receptor 1	47	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|JAK-STAT cascade (GO:0007259)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-1 beta secretion (GO:0050718)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|response to virus (GO:0009615)|T cell activation (GO:0042110)|type I interferon biosynthetic process (GO:0045351)|type I interferon signaling pathway (GO:0060337)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	type I interferon receptor activity (GO:0004905)			breast(2)|central_nervous_system(1)|cervix(1)|kidney(2)|large_intestine(3)|liver(1)|lung(2)|skin(2)	14					"""""""Interferon Alfa-2a(DB00034)|""""Interferon Alfa-2b(DB00105)|Interferon alfa-n1(DB00011)|Interferon alfa-n3(DB00018)|Interferon alfacon-1(DB00069)|Interferon beta-1a(DB00060)|Interferon beta-1b(DB00068)|Natural alpha interferon(DB05258)|Peginterferon alfa-2a(DB00008)|Peginterferon alfa-2b(DB00022)"""	CAACTTTATCCTGAGGTGGAA	0.353																																					p.L47L	Esophageal Squamous(73;817 1211 32990 35667 42746)	Atlas-SNP	.											.	IFNAR1	44	.	0			c.C139T						PASS	.						135.0	122.0	126.0					21																	34707892		2203	4300	6503	SO:0001819	synonymous_variant	3454	exon2			TTTATCCTGAGGT		CCDS13624.1	21q22.1	2008-05-02			ENSG00000142166	ENSG00000142166		"""Interferons"""	5432	protein-coding gene	gene with protein product		107450		IFNAR		8181059	Standard	NM_000629		Approved	IFRC	uc002yrn.3	P17181	OTTHUMG00000065126	ENST00000270139.3:c.139C>T	chr21.hg19:g.34707892C>T		111.0	0.0	.		112.0	45.0	.	NM_000629	B2R6L9|B4DNT3|D3DSF0|Q53GW9|Q53H11|Q6PKD7|Q7M4L2|Q8WTZ2	Silent	SNP	ENST00000270139.3	hg19	CCDS13624.1																																																																																			.	.	.	none		0.353	IFNAR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139823.4		
DYRK1A	1859	hgsc.bcm.edu	37	21	38865374	38865374	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr21:38865374T>C	ENST00000398960.2	+	7	1082	c.1007T>C	c.(1006-1008)aTg>aCg	p.M336T	DYRK1A_ENST00000338785.3_Missense_Mutation_p.M336T|DYRK1A_ENST00000321219.8_Missense_Mutation_p.M336T|DYRK1A_ENST00000339659.4_Missense_Mutation_p.M327T|DYRK1A_ENST00000455387.2_Missense_Mutation_p.M108T|DYRK1A_ENST00000451934.1_Missense_Mutation_p.M336T|DYRK1A_ENST00000398956.2_Missense_Mutation_p.M336T	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	336	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)			breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CTACTGGGAATGCCTTATGAC	0.398																																					p.M336T	Melanoma(114;464 1602 31203 43785 45765)	Atlas-SNP	.											.	DYRK1A	85	.	0			c.T1007C						PASS	.						171.0	157.0	161.0					21																	38865374		2203	4300	6503	SO:0001583	missense	1859	exon7			TGGGAATGCCTTA	U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.1007T>C	chr21.hg19:g.38865374T>C	ENSP00000381932:p.Met336Thr	65.0	0.0	.		83.0	34.0	.	NM_001396	O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	hg19	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	T	15.65	2.895956	0.52121	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	T;T;T;T;T;T;T	0.63580	-0.05;-0.05;-0.05;-0.05;-0.05;-0.05;-0.05	5.76	5.76	0.90799	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.48892	0.1525	N	0.20766	0.605	0.80722	D	1	B;B;B;B;B	0.18166	0.026;0.026;0.0;0.0;0.026	B;B;B;B;B	0.21360	0.034;0.034;0.003;0.002;0.034	T	0.40156	-0.9578	10	0.24483	T	0.36	.	16.3786	0.83431	0.0:0.0:0.0:1.0	.	336;336;336;327;336	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	T	336;327;336;336;336;336;108	ENSP00000342690:M336T;ENSP00000340373:M327T;ENSP00000319032:M336T;ENSP00000416089:M336T;ENSP00000381932:M336T;ENSP00000381929:M336T;ENSP00000407854:M108T	ENSP00000319032:M336T	M	+	2	0	DYRK1A	37787244	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.997000	0.88414	2.323000	0.78572	0.528000	0.53228	ATG	.	.	.	none		0.398	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1	NM_001396	
MORC2	22880	hgsc.bcm.edu	37	22	31331124	31331124	+	Missense_Mutation	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr22:31331124G>A	ENST00000397641.3	-	19	2245	c.1837C>T	c.(1837-1839)Cct>Tct	p.P613S	MORC2-AS1_ENST00000441558.1_RNA|MORC2_ENST00000469915.1_5'Flank|MORC2_ENST00000215862.4_Missense_Mutation_p.P551S			Q9Y6X9	MORC2_HUMAN	MORC family CW-type zinc finger 2	613						cytoplasm (GO:0005737)|nucleus (GO:0005634)	zinc ion binding (GO:0008270)			breast(2)|kidney(2)|large_intestine(5)|lung(4)|ovary(2)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	21						GGCGACCGAGGACGCTGAGGT	0.587																																					p.P551S		Atlas-SNP	.											.	MORC2	78	.	0			c.C1651T						PASS	.						33.0	35.0	34.0					22																	31331124		2203	4300	6503	SO:0001583	missense	22880	exon20			ACCGAGGACGCTG	AB020659	CCDS33636.1	22q12.2	2005-06-15	2005-06-15	2005-06-15	ENSG00000133422	ENSG00000133422			23573	protein-coding gene	gene with protein product			"""zinc finger, CW-type with coiled-coil domain 1"", ""zinc finger, CW type with coiled-coil domain 1"""	ZCWCC1		14607086	Standard	XM_005261391		Approved	ZCW3, KIAA0852, AC004542.C22.1	uc003aje.1	Q9Y6X9	OTTHUMG00000151193	ENST00000397641.3:c.1837C>T	chr22.hg19:g.31331124G>A	ENSP00000380763:p.Pro613Ser	98.0	0.0	.		90.0	43.0	.	NM_014941	B2RNB1|Q9UF28|Q9Y6V2	Missense_Mutation	SNP	ENST00000397641.3	hg19		.	.	.	.	.	.	.	.	.	.	G	22.1	4.246432	0.80024	.	.	ENSG00000133422	ENST00000397641;ENST00000215862	T;T	0.13657	2.58;2.57	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.36963	0.0986	M	0.68952	2.095	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00870	-1.1533	10	0.32370	T	0.25	.	18.1401	0.89637	0.0:0.0:1.0:0.0	.	613	Q9Y6X9	MORC2_HUMAN	S	613;551	ENSP00000380763:P613S;ENSP00000215862:P551S	ENSP00000215862:P551S	P	-	1	0	MORC2	29661124	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.984000	0.88150	2.726000	0.93360	0.655000	0.94253	CCT	.	.	.	none		0.587	MORC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000321710.2	NM_014941	
OFD1	8481	hgsc.bcm.edu	37	X	13779314	13779314	+	Missense_Mutation	SNP	C	C	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chrX:13779314C>A	ENST00000340096.6	+	17	2698	c.2371C>A	c.(2371-2373)Ccg>Acg	p.P791T	OFD1_ENST00000380567.1_Missense_Mutation_p.P651T|OFD1_ENST00000490265.1_3'UTR|OFD1_ENST00000380550.3_Missense_Mutation_p.P751T	NM_003611.2	NP_003602.1	O75665	OFD1_HUMAN	oral-facial-digital syndrome 1	791	Mediates the interaction with SDCCAG8.				axoneme assembly (GO:0035082)|cilium morphogenesis (GO:0060271)|embryonic body morphogenesis (GO:0010172)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|negative regulation of fibroblast growth factor receptor signaling pathway involved in neural plate anterior/posterior pattern formation (GO:2000314)	centriolar satellite (GO:0034451)|centriole (GO:0005814)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cilium (GO:0005929)|cytosol (GO:0005829)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	alpha-tubulin binding (GO:0043014)|gamma-tubulin binding (GO:0043015)			breast(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(7)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	25						CTCCAGCCCTCCGGAGCAGAA	0.488																																					p.P791T		Atlas-SNP	.											.	OFD1	109	.	0			c.C2371A						PASS	.						105.0	81.0	89.0					X																	13779314		2203	4300	6503	SO:0001583	missense	8481	exon17			AGCCCTCCGGAGC	Y15164	CCDS14157.1	Xp22	2014-06-18			ENSG00000046651	ENSG00000046651			2567	protein-coding gene	gene with protein product		300170	"""retinitis pigmentosa 23 (X-linked recessive)"""	CXorf5, RP23		9722947, 9215688, 22619378	Standard	NM_003611		Approved	71-7A, JBTS10	uc004cvp.4	O75665	OTTHUMG00000021159	ENST00000340096.6:c.2371C>A	chrX.hg19:g.13779314C>A	ENSP00000344314:p.Pro791Thr	29.0	0.0	.		44.0	40.0	.	NM_003611	B9ZVU5|O75666|Q4VAK4	Missense_Mutation	SNP	ENST00000340096.6	hg19	CCDS14157.1	.	.	.	.	.	.	.	.	.	.	C	0.006	-2.112891	0.00353	.	.	ENSG00000046651	ENST00000380550;ENST00000340096;ENST00000380567	D;D;D	0.95622	-3.76;-3.76;-1.63	5.03	-1.66	0.08265	.	0.918676	0.09274	N	0.824684	D	0.90463	0.7013	L	0.56769	1.78	0.09310	N	1	B;P;B;B;B	0.38370	0.004;0.628;0.021;0.007;0.004	B;B;B;B;B	0.34489	0.005;0.184;0.009;0.009;0.005	T	0.79300	-0.1860	10	0.13853	T	0.58	4.1682	4.147	0.10220	0.3081:0.4058:0.2115:0.0746	.	791;751;459;651;791	A8K2T9;O75665-3;B4DLQ3;A6NF31;O75665	.;.;.;.;OFD1_HUMAN	T	751;791;651	ENSP00000369923:P751T;ENSP00000344314:P791T;ENSP00000369941:P651T	ENSP00000344314:P791T	P	+	1	0	OFD1	13689235	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.462000	0.06704	-1.265000	0.02449	-2.646000	0.00150	CCG	.	.	.	none		0.488	OFD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055808.1	NM_003611	
AR	367	hgsc.bcm.edu	37	X	66765164	66765164	+	Missense_Mutation	SNP	A	A	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chrX:66765164A>T	ENST00000374690.3	+	1	700	c.176A>T	c.(175-177)cAg>cTg	p.Q59L	AR_ENST00000504326.1_Missense_Mutation_p.Q59L|AR_ENST00000513847.1_3'UTR|AR_ENST00000396044.3_Missense_Mutation_p.Q59L	NM_000044.3	NP_000035.2	P10275	ANDR_HUMAN	androgen receptor	59	Gln-rich.|Modulating.|Poly-Gln.				androgen receptor signaling pathway (GO:0030521)|cell death (GO:0008219)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of integrin biosynthetic process (GO:0045720)|positive regulation of cell proliferation (GO:0008284)|positive regulation of integrin biosynthetic process (GO:0045726)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of phosphorylation (GO:0042327)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland development (GO:0030850)|protein oligomerization (GO:0051259)|regulation of establishment of protein localization to plasma membrane (GO:0090003)|sex differentiation (GO:0007548)|signal transduction (GO:0007165)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transport (GO:0006810)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	androgen binding (GO:0005497)|androgen receptor activity (GO:0004882)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein dimerization activity (GO:0046983)|receptor binding (GO:0005102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription factor binding (GO:0001085)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)			breast(4)|central_nervous_system(2)|cervix(1)|endometrium(8)|kidney(1)|large_intestine(12)|lung(20)|ovary(3)|prostate(11)|stomach(2)|upper_aerodigestive_tract(3)	67	all_cancers(1;0.173)|Prostate(1;2.27e-16)|all_epithelial(1;0.102)	all_lung(315;1.3e-11)			Bicalutamide(DB01128)|Cyproterone acetate(DB04839)|Danazol(DB01406)|Drospirenone(DB01395)|Drostanolone(DB00858)|Enzalutamide(DB08899)|Fludrocortisone(DB00687)|Fluoxymesterone(DB01185)|Flutamide(DB00499)|Ketoconazole(DB01026)|Levonorgestrel(DB00367)|Methyltestosterone(DB06710)|Nandrolone decanoate(DB08804)|Nandrolone phenpropionate(DB00984)|Nilutamide(DB00665)|Oxandrolone(DB00621)|Spironolactone(DB00421)|Testosterone Propionate(DB01420)|Testosterone(DB00624)	CTGCTgcagcagcagcagcag	0.677									Androgen Insensitivity Syndrome																												p.Q59L		Atlas-SNP	.											.	AR	249	.	0			c.A176T						PASS	.						7.0	10.0	9.0					X																	66765164		2055	4063	6118	SO:0001583	missense	367	exon1	Familial Cancer Database	CAIS, Testicular Feminisation, AIS, Morris syndrome; incl. Reifenstein Syndrome	TGCAGCAGCAGCA	M20132	CCDS14387.1, CCDS43965.1	Xq12	2013-01-16	2008-08-07		ENSG00000169083	ENSG00000169083		"""Nuclear hormone receptors"""	644	protein-coding gene	gene with protein product	"""testicular feminization"", ""Kennedy disease"""	313700	"""dihydrotestosterone receptor"", ""spinal and bulbar muscular atrophy"""	DHTR, SBMA		3353726, 3377788	Standard	NM_000044		Approved	AIS, NR3C4, SMAX1, HUMARA	uc004dwu.2	P10275	OTTHUMG00000021740	ENST00000374690.3:c.176A>T	chrX.hg19:g.66765164A>T	ENSP00000363822:p.Gln59Leu	73.0	0.0	.		69.0	8.0	.	NM_000044	A2RUN2|B1AKD7|Q9UD95	Missense_Mutation	SNP	ENST00000374690.3	hg19	CCDS14387.1	.	.	.	.	.	.	.	.	.	.	a	12.32	1.901651	0.33535	.	.	ENSG00000169083	ENST00000374690;ENST00000504326;ENST00000396044;ENST00000538891	T;T;T	0.69175	-0.38;-0.38;-0.38	.	.	.	.	1.117170	0.06949	N	0.814177	T	0.47060	0.1425	N	0.19112	0.55	0.09310	N	0.999999	B;B	0.34313	0.448;0.448	B;B	0.36534	0.227;0.227	T	0.31724	-0.9933	8	0.13108	T	0.6	.	.	.	.	.	59;59	E7EVX6;D3YPQ2	.;.	L	59	ENSP00000363822:Q59L;ENSP00000421155:Q59L;ENSP00000379359:Q59L	ENSP00000363822:Q59L	Q	+	2	0	AR	66681889	0.995000	0.38212	0.864000	0.33941	0.503000	0.33858	0.245000	0.18142	0.000000	0.14550	0.000000	0.15137	CAG	.	.	.	none		0.677	AR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057007.1	NM_000044	
MT-CO3	4514	hgsc.bcm.edu	37	M	9447	9447	+	Missense_Mutation	SNP	T	T	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chrM:9447T>C	ENST00000362079.2	+	1	241	c.241T>C	c.(241-243)Tac>Cac	p.Y81H	MT-ND4_ENST00000361381.2_5'Flank|MT-TH_ENST00000387441.1_RNA|MT-TS2_ENST00000387449.1_RNA|MT-TL2_ENST00000387456.1_RNA|MT-TD_ENST00000387419.1_RNA|MT-TK_ENST00000387421.1_RNA|MT-ND5_ENST00000361567.2_5'Flank|MT-ND3_ENST00000361227.2_5'Flank|MT-TG_ENST00000387429.1_RNA|MT-ND4L_ENST00000361335.1_5'Flank|MT-TS1_ENST00000387416.2_RNA|MT-TR_ENST00000387439.1_RNA			P00414	COX3_HUMAN	mitochondrially encoded cytochrome c oxidase III	81					aerobic electron transport chain (GO:0019646)|cellular metabolic process (GO:0044237)|respiratory chain complex IV assembly (GO:0008535)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|respiratory chain complex IV (GO:0045277)	cytochrome-c oxidase activity (GO:0004129)			breast(1)|endometrium(10)|kidney(14)|lung(1)|urinary_tract(1)	27						AAGGCCTTCGATACGGGATAA	0.468																																					p.Y81H		Atlas-SNP	.											.	.	.	.	0			c.T241C						PASS	.																																			SO:0001583	missense	5742	exon1			CTTCGATACGGGA			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198938	ENSG00000198938		"""Mitochondrial respiratory chain complex / Complex IV"""	7422	protein-coding gene	gene with protein product		516050	"""cytochrome c oxidase III"""	MTCO3			Standard			Approved	COX3, COIII, CO3		P00414		ENST00000362079.2:c.241T>C	chrM.hg19:g.9447T>C	ENSP00000354982:p.Tyr81His	2.0	0.0	.		26.0	8.0	.	ENST00000362079	Q14Y83	Missense_Mutation	SNP	ENST00000362079.2	hg19																																																																																				.	.	.	none		0.468	MT-CO3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024032	
MT-CYB	4519	hgsc.bcm.edu	37	M	15756	15756	+	Silent	SNP	G	G	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chrM:15756G>A	ENST00000361789.2	+	1	1010	c.1010G>A	c.(1009-1011)tGa>tAa	p.*337*	MT-ND6_ENST00000361681.2_5'Flank|MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-TP_ENST00000387461.2_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	337					cellular metabolic process (GO:0044237)|hydrogen ion transmembrane transport (GO:1902600)|mitochondrial electron transport, ubiquinol to cytochrome c (GO:0006122)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|ubiquinol-cytochrome-c reductase activity (GO:0008121)			breast(6)|endometrium(25)|kidney(33)|prostate(1)	65						CATTCTAACCTGAATCGGAGG	0.418																																					p.W337X		Atlas-SNP	.											.	.	.	.	0			c.G1010A						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			TAACCTGAATCGG			mitochondria	2012-11-16	2005-02-15	2005-02-16	ENSG00000198727	ENSG00000198727		"""Cytochrome b genes"", ""Mitochondrial respiratory chain complex / Complex III"""	7427	protein-coding gene	gene with protein product		516020	"""cytochrome b"""	MTCYB			Standard			Approved	COB, CYTB, UQCR3		P00156		ENST00000361789.2:c.1010G>A	chrM.hg19:g.15756G>A		3.0	0.0	.		29.0	8.0	.	ENST00000361789	Q34786|Q8HBR6|Q8HNQ0|Q8HNQ1|Q8HNQ9|Q8HNR4|Q8HNR7|Q8W7V8|Q8WCV9|Q8WCY2|Q8WCY7|Q8WCY8|Q9B1A6|Q9B1B6|Q9B1B8|Q9B1D4|Q9B1X6|Q9B2V0|Q9B2V8|Q9B2W0|Q9B2W3|Q9B2W8|Q9B2X1|Q9B2X7|Q9B2X9|Q9B2Y3|Q9B2Z0|Q9B2Z4|Q9T6H6|Q9T9Y0|Q9TEH4	Nonsense_Mutation	SNP	ENST00000361789.2	hg19																																																																																				.	.	.	none		0.418	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
PYROXD2	84795	hgsc.bcm.edu	37	10	100147000	100147001	+	Frame_Shift_Del	DEL	GA	GA	-	rs376868556		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	GA	GA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:100147000_100147001delGA	ENST00000370575.4	-	14	1559_1560	c.1511_1512delTC	c.(1510-1512)ctcfs	p.L504fs	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	504							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						CTGGTGGTGTGAGGATGTCTCT	0.52																																					p.504_505del		Atlas-Indel,Pindel	.											.	PYROXD2	43	.	0			c.1512_1513del						PASS	.																																			SO:0001589	frameshift_variant	84795	exon14			.	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1511_1512delTC	chr10.hg19:g.100147000_100147001delGA	ENSP00000359607:p.Leu504fs	120.0	0.0	0		96.0	46.0	0.479167	NM_032709	D3DR61|Q5TAA9|Q9BRQ1	Frame_Shift_Del	DEL	ENST00000370575.4	hg19	CCDS7474.1																																																																																			.	.	.	none		0.520	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709	
RARS	5917	hgsc.bcm.edu	37	5	167944991	167944992	+	Frame_Shift_Ins	INS	-	-	TA			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr5:167944991_167944992insTA	ENST00000231572.3	+	14	1851_1852	c.1797_1798insTA	c.(1798-1800)tatfs	p.Y600fs	RARS_ENST00000538719.1_Frame_Shift_Ins_p.Y394fs	NM_002887.3	NP_002878.2	P54136	SYRC_HUMAN	arginyl-tRNA synthetase	600					arginyl-tRNA aminoacylation (GO:0006420)|gene expression (GO:0010467)|tRNA aminoacylation for protein translation (GO:0006418)	aminoacyl-tRNA synthetase multienzyme complex (GO:0017101)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	arginine binding (GO:0034618)|arginine-tRNA ligase activity (GO:0004814)|ATP binding (GO:0005524)|tRNA binding (GO:0000049)			breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|stomach(1)	22	Renal(175;0.000159)|Lung NSC(126;0.0875)|all_lung(126;0.166)	Medulloblastoma(196;0.0208)|all_neural(177;0.0227)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0693)|Epithelial(171;0.131)|OV - Ovarian serous cystadenocarcinoma(192;0.156)		CTCTCTGTGATTATATATATGA	0.386																																					p.D599fs		Atlas-Indel,Pindel	.											.	RARS	58	.	0			c.1797_1798insTA						PASS	.																																			SO:0001589	frameshift_variant	5917	exon14			.	BC000528	CCDS4367.1	5q35.1	2011-07-01			ENSG00000113643	ENSG00000113643	6.1.1.19	"""Aminoacyl tRNA synthetases / Class I"""	9870	protein-coding gene	gene with protein product	"""arginine tRNA ligase 1, cytoplasmic"""	107820				7590355	Standard	NM_002887		Approved	DALRD1	uc003lzx.3	P54136	OTTHUMG00000130411	ENST00000231572.3:c.1804_1805dupTA	chr5.hg19:g.167944998_167944999dupTA	ENSP00000231572:p.Tyr600fs	63.0	0.0	0		77.0	30.0	0.38961	NM_002887	B2RBS9|Q53GY4|Q9BWA1	Frame_Shift_Ins	INS	ENST00000231572.3	hg19	CCDS4367.1																																																																																			.	.	.	none		0.386	RARS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252794.2	NM_002887	
SORCS3	22986	hgsc.bcm.edu	37	10	107016678	107016678	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:107016678delA	ENST00000369701.3	+	25	3666	c.3439delA	c.(3439-3441)aaafs	p.K1147fs		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	1147					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CTACAAGTTTAAAAGGTATGT	0.413																																					p.F1146fs	NSCLC(116;1497 1690 7108 13108 14106)	Atlas-Indel,Pindel	.											.	SORCS3	282	.	0			c.3438delT						PASS	.						145.0	124.0	131.0					10																	107016678		2203	4300	6503	SO:0001589	frameshift_variant	22986	exon25			.	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.3439delA	chr10.hg19:g.107016678delA	ENSP00000358715:p.Lys1147fs	51.0	0.0	0		38.0	15.0	0.394737	NM_014978	Q5VXF9|Q9NQJ2	Frame_Shift_Del	DEL	ENST00000369701.3	hg19	CCDS7558.1																																																																																			.	.	.	none		0.413	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
PDS5B	23047	hgsc.bcm.edu	37	13	33332296	33332298	+	In_Frame_Del	DEL	TGG	TGG	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TGG	TGG	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr13:33332296_33332298delTGG	ENST00000315596.10	+	27	3314_3316	c.3128_3130delTGG	c.(3127-3132)atggta>ata	p.1043_1044MV>I		NM_015032.3	NP_055847.1	Q9NTI5	PDS5B_HUMAN	PDS5, regulator of cohesion maintenance, homolog B (S. cerevisiae)	1043					cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic sister chromatid cohesion (GO:0007064)|negative regulation of cell proliferation (GO:0008285)|regulation of cell proliferation (GO:0042127)	chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(4)|kidney(5)|large_intestine(14)|lung(14)|ovary(5)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	62		Lung SC(185;0.0367)		all cancers(112;5.55e-06)|Epithelial(112;2.7e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00303)|BRCA - Breast invasive adenocarcinoma(63;0.0204)		ATCAGAAAGATGGTAGAAAATAT	0.266																																					p.1043_1043del		Atlas-Indel,Pindel	.											.	PDS5B	141	.	0			c.3127_3129del						PASS	.																																			SO:0001651	inframe_deletion	23047	exon27			.	AB023196	CCDS41878.1	13q12.3	2008-02-05	2007-07-18	2007-07-18	ENSG00000083642	ENSG00000083642			20418	protein-coding gene	gene with protein product		605333	"""androgen-induced proliferation inhibitor"""	APRIN		8812419, 10215036	Standard	NM_015032		Approved	AS3, KIAA0979, FLJ23236, CG008	uc010abf.3	Q9NTI5	OTTHUMG00000016704	ENST00000315596.10:c.3128_3130delTGG	chr13.hg19:g.33332296_33332298delTGG	ENSP00000313851:p.Met1043_Val1044delinsIle	335.0	0.0	0		351.0	137.0	0.390313	NM_015032	Q5R3S3|Q5W0K8|Q6NSC3|Q8IXT6|Q9H5N8|Q9Y2I5|Q9Y451	In_Frame_Del	DEL	ENST00000315596.10	hg19	CCDS41878.1																																																																																			.	.	.	none		0.266	PDS5B-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044428.3	NM_015032	
XRN1	54464	hgsc.bcm.edu	37	3	142141761	142141764	+	Splice_Site	DEL	TACC	TACC	-	rs183730909|rs370828065|rs146086047	byFrequency	TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TACC	TACC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:142141761_142141764delTACC	ENST00000264951.4	-	7	828_831	c.711_714delGGTA	c.(709-714)cgggta>cg	p.RV237fs	XRN1_ENST00000392981.2_Splice_Site_p.RV237fs|RNU1-100P_ENST00000365255.1_RNA|XRN1_ENST00000544157.1_Splice_Site_p.RV27fs|XRN1_ENST00000463916.1_Splice_Site_p.RV237fs	NM_019001.3	NP_061874.3	Q8IZH2	XRN1_HUMAN	5'-3' exoribonuclease 1	237					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|nuclear mRNA surveillance (GO:0071028)|nuclear-transcribed mRNA catabolic process (GO:0000956)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|rRNA catabolic process (GO:0016075)	cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|membrane (GO:0016020)	5'-3' exonuclease activity (GO:0008409)|DNA binding (GO:0003677)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(6)|kidney(12)|large_intestine(11)|liver(1)|lung(17)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	61						CTGGAGCACATACCCTGGAATTAG	0.304																																					p.238_239del		Atlas-Indel,Pindel	.											.	XRN1	138	.	0			c.712_715del						PASS	.																																			SO:0001630	splice_region_variant	54464	exon7			.	AY137776	CCDS3123.1, CCDS63801.1, CCDS75028.1	3q23	2008-02-05			ENSG00000114127	ENSG00000114127			30654	protein-coding gene	gene with protein product		607994				12515382	Standard	XM_005247544		Approved	SEP1	uc003eus.3	Q8IZH2	OTTHUMG00000159251	ENST00000264951.4:c.711-1GGTA>-	chr3.hg19:g.142141761_142141764delTACC		156.0	0.0	0		361.0	59.0	0.163435	NM_001042604	Q4G0S3|Q68D88|Q6AI24|Q6MZS8|Q86WS7|Q8N8U4|Q9UF39	Frame_Shift_Del	DEL	ENST00000264951.4	hg19	CCDS3123.1																																																																																			.	.	.	none		0.304	XRN1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000354087.2	NM_019001	Frame_Shift_Del
DCLRE1B	64858	hgsc.bcm.edu	37	1	114450642	114450643	+	Frame_Shift_Ins	INS	-	-	A			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:114450642_114450643insA	ENST00000369563.3	+	3	813_814	c.367_368insA	c.(367-369)tacfs	p.Y123fs	AP4B1_ENST00000256658.4_5'Flank|DCLRE1B_ENST00000466480.1_3'UTR	NM_022836.3	NP_073747.1	Q9H816	DCR1B_HUMAN	DNA cross-link repair 1B	123					cell cycle checkpoint (GO:0000075)|DNA repair (GO:0006281)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|protection from non-homologous end joining at telomere (GO:0031848)|telomere maintenance (GO:0000723)|telomeric 3' overhang formation (GO:0031860)|telomeric loop formation (GO:0031627)	centrosome (GO:0005813)|chromosome, telomeric region (GO:0000781)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	5'-3' exonuclease activity (GO:0008409)			breast(1)|endometrium(4)|kidney(2)|large_intestine(2)|liver(2)|lung(6)|stomach(1)	18	Lung SC(450;0.184)	all_cancers(81;1.46e-05)|all_epithelial(167;2.42e-05)|all_lung(203;0.000353)|Lung NSC(69;0.000518)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TGATTTTCGATACACACCATCC	0.47								Other identified genes with known or suspected DNA repair function																													p.Y123_T124delinsX		Atlas-Indel,Pindel	.											.	DCLRE1B	36	.	0			c.367_368insA						PASS	.																																			SO:0001589	frameshift_variant	64858	exon3			.	BC029687	CCDS866.1	1p11.1	2010-06-24	2010-06-24		ENSG00000118655	ENSG00000118655			17641	protein-coding gene	gene with protein product	"""APOLLO"", ""PSO2 homolog (S. cerevisiae)"""	609683	"""DNA cross-link repair 1B (PSO2 homolog, S. cerevisiae)"""				Standard	NM_022836		Approved	SNM1B, FLJ12810, FLJ13998	uc001eeg.3	Q9H816	OTTHUMG00000011937	ENST00000369563.3:c.368dupA	chr1.hg19:g.114450643_114450643dupA	ENSP00000358576:p.Tyr123fs	68.0	0.0	0		57.0	26.0	0.45614	NM_022836	Q9H9E5	Frame_Shift_Ins	INS	ENST00000369563.3	hg19	CCDS866.1																																																																																			.	.	.	none		0.470	DCLRE1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033020.2	NM_022836	
RPS6KC1	26750	hgsc.bcm.edu	37	1	213302993	213302993	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:213302993delC	ENST00000366960.3	+	6	746	c.596delC	c.(595-597)tcgfs	p.S199fs	RPS6KC1_ENST00000366959.3_Frame_Shift_Del_p.S187fs|RPS6KC1_ENST00000490299.1_3'UTR|RPS6KC1_ENST00000543470.1_Frame_Shift_Del_p.S18fs|RPS6KC1_ENST00000543354.1_Intron	NM_012424.3	NP_036556.2	Q96S38	KS6C1_HUMAN	ribosomal protein S6 kinase, 52kDa, polypeptide 1	199					signal transduction (GO:0007165)	cytoplasm (GO:0005737)|early endosome (GO:0005769)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|endometrium(6)|kidney(4)|large_intestine(8)|liver(2)|lung(15)|ovary(3)|prostate(1)|urinary_tract(3)	43				OV - Ovarian serous cystadenocarcinoma(81;0.00705)|all cancers(67;0.016)|GBM - Glioblastoma multiforme(131;0.0663)|Epithelial(68;0.145)		AATCTTTCTTCGGATTCTTCA	0.433																																					p.S199fs		Atlas-Indel,Pindel	.											.	RPS6KC1	114	.	0			c.595delT						PASS	.						96.0	95.0	96.0					1																	213302993		2203	4300	6503	SO:0001589	frameshift_variant	26750	exon6			.	AF037447	CCDS1513.1, CCDS44317.1, CCDS73028.1, CCDS73029.1, CCDS73030.1	1q41	2011-04-05	2002-08-29		ENSG00000136643	ENSG00000136643			10439	protein-coding gene	gene with protein product			"""ribosomal protein S6 kinase, 52kD, polypeptide 1"""			10552933	Standard	XM_005273095		Approved	humS6PKh1	uc010ptr.2	Q96S38	OTTHUMG00000036926	ENST00000366960.3:c.596delC	chr1.hg19:g.213302993delC	ENSP00000355927:p.Ser199fs	42.0	0.0	0		71.0	23.0	0.323944	NM_012424	B1APS8|B3KVM4|D3DTA4|Q8TDD3|Q9NSF4|Q9UL66	Frame_Shift_Del	DEL	ENST00000366960.3	hg19	CCDS1513.1																																																																																			.	.	.	none		0.433	RPS6KC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000089690.3	NM_012424	
NUP214	8021	hgsc.bcm.edu	37	9	134073449	134073453	+	Frame_Shift_Del	DEL	CAGCC	CAGCC	-	rs368154028		TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	CAGCC	CAGCC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:134073449_134073453delCAGCC	ENST00000359428.5	+	29	4712_4716	c.4568_4572delCAGCC	c.(4567-4572)tcagccfs	p.SA1523fs	NUP214_ENST00000451030.1_Frame_Shift_Del_p.SA1524fs|NUP214_ENST00000411637.2_Frame_Shift_Del_p.SA1513fs|NUP214_ENST00000483497.2_Frame_Shift_Del_p.SA349fs			P35658	NU214_HUMAN	nucleoporin 214kDa	1523	11 X 3 AA approximate repeats.|11 X 5 AA approximate repeats.|18 X 4 AA approximate repeats.|Pro/Ser/Thr-rich.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|gene expression (GO:0010467)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|regulation of cell cycle (GO:0051726)|regulation of glucose transport (GO:0010827)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytosol (GO:0005829)|focal adhesion (GO:0005925)|intracellular membrane-bounded organelle (GO:0043231)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	nucleocytoplasmic transporter activity (GO:0005487)|transporter activity (GO:0005215)			NS(1)|breast(9)|central_nervous_system(3)|endometrium(13)|kidney(2)|large_intestine(9)|liver(2)|lung(29)|ovary(2)|prostate(3)|skin(7)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	86	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;3.42e-05)|Epithelial(140;0.000256)		GAGCAACAGTCAGCCCAGCTTCCCC	0.537			T	"""DEK, SET, ABL1"""	"""AML, T-ALL"""																																p.1523_1524del	Pancreas(4;24 48 25510 30394 32571)	Atlas-Indel,Pindel	.		Dom	yes		9	9q34.1	8021	nucleoporin 214kDa (CAN)		L	.	NUP214	166	.	0			c.4567_4571del						PASS	.																																			SO:0001589	frameshift_variant	8021	exon29			.	X64228	CCDS6940.1	9q34	2008-07-21	2002-08-29		ENSG00000126883	ENSG00000126883			8064	protein-coding gene	gene with protein product	"""nuclear pore complex protein Nup214"", ""CAN protein, putative oncogene"""	114350	"""nucleoporin 214kD (CAIN)"""			8108440, 2370860	Standard	NM_005085		Approved	CAIN, CAN, D9S46E, N214	uc004cag.3	P35658	OTTHUMG00000020816	ENST00000359428.5:c.4568_4572delCAGCC	chr9.hg19:g.134073449_134073453delCAGCC	ENSP00000352400:p.Ser1523fs	88.0	0.0	0		76.0	34.0	0.447368	NM_005085	A6NFQ0|Q15010|Q3KQZ0|Q5JUP7|Q75R47|Q86XD3	Frame_Shift_Del	DEL	ENST00000359428.5	hg19	CCDS6940.1																																																																																			.	.	.	none		0.537	NUP214-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000054694.2	NM_005085	
UQCRC2	7385	hgsc.bcm.edu	37	16	21974207	21974208	+	Splice_Site	INS	-	-	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr16:21974207_21974208insT	ENST00000268379.4	+	6	1278		c.e6+1		UQCRC2_ENST00000561553.1_Splice_Site	NM_003366.2	NP_003357.2	P22695	QCR2_HUMAN	ubiquinol-cytochrome c reductase core protein II						aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|oxidative phosphorylation (GO:0006119)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex III (GO:0005750)|mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			breast(1)|cervix(1)|endometrium(2)|large_intestine(5)|lung(4)|prostate(1)|skin(1)	15				GBM - Glioblastoma multiforme(48;0.0264)		CCGCAGACTCGTAAGTACATTT	0.361																																					.	Colon(123;450 1645 12841 25393 45623)	Atlas-Indel,Pindel	.											.	UQCRC2	46	.	0			c.514+1->T						PASS	.																																			SO:0001630	splice_region_variant	7385	exon6			.	J04973	CCDS10601.1	16p12	2011-07-04			ENSG00000140740	ENSG00000140740	1.10.2.2	"""Mitochondrial respiratory chain complex / Complex III"""	12586	protein-coding gene	gene with protein product		191329				8288258, 2547763	Standard	NM_003366		Approved	QCR2, UQCR2	uc002djx.3	P22695	OTTHUMG00000131585	ENST00000268379.4:c.514+1->T	chr16.hg19:g.21974208_21974208dupT		53.0	0.0	0		62.0	34.0	0.548387	NM_003366	B3KSN4|Q9BQ05	Splice_Site	INS	ENST00000268379.4	hg19	CCDS10601.1																																																																																			.	.	.	none		0.361	UQCRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254466.1	NM_003366	Intron
DSP	1832	hgsc.bcm.edu	37	6	7584626	7584627	+	Frame_Shift_Ins	INS	-	-	T			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:7584626_7584627insT	ENST00000379802.3	+	24	7472_7473	c.7131_7132insT	c.(7132-7134)attfs	p.I2378fs	DSP_ENST00000418664.2_Frame_Shift_Ins_p.I1779fs	NM_004415.2	NP_004406.2	P15924	DESP_HUMAN	desmoplakin	2378	4.5 X 38 AA tandem repeats (Domain B).|Globular 2.				adherens junction organization (GO:0034332)|apoptotic process (GO:0006915)|bundle of His cell to Purkinje myocyte communication (GO:0086069)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|desmosome organization (GO:0002934)|epidermis development (GO:0008544)|intermediate filament organization (GO:0045109)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)|protein localization to adherens junction (GO:0071896)|regulation of heart rate by cardiac conduction (GO:0086091)|single organismal cell-cell adhesion (GO:0016337)|ventricular cardiac muscle cell action potential (GO:0086005)|ventricular compact myocardium morphogenesis (GO:0003223)|wound healing (GO:0042060)	basolateral plasma membrane (GO:0016323)|cornified envelope (GO:0001533)|desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intercalated disc (GO:0014704)|intermediate filament (GO:0005882)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	poly(A) RNA binding (GO:0044822)|protein binding, bridging (GO:0030674)|protein kinase C binding (GO:0005080)|scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			biliary_tract(1)|breast(6)|central_nervous_system(7)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(16)|liver(2)|lung(27)|ovary(4)|prostate(1)|skin(8)|stomach(3)|upper_aerodigestive_tract(7)|urinary_tract(5)	101	Ovarian(93;0.0584)	all_hematologic(90;0.236)		OV - Ovarian serous cystadenocarcinoma(45;0.000508)		CCGGGGGGATCATTGACCCAAA	0.45																																					p.I2377fs		Atlas-INDEL	.											.	DSP	306	.	0			c.7131_7132insT						PASS	.																																			SO:0001589	frameshift_variant	1832	exon24			.	J05211	CCDS4501.1, CCDS47368.1	6p24.3	2014-09-17	2003-05-20		ENSG00000096696	ENSG00000096696			3052	protein-coding gene	gene with protein product		125647	"""desmoplakin (DPI, DPII)"""			1889810	Standard	NM_004415		Approved	KPPS2, PPKS2, DPI, DPII	uc003mxp.1	P15924	OTTHUMG00000014212	Exception_encountered	chr6.hg19:g.7584626_7584627insT	ENSP00000369129:p.Ile2378fs	75.0	0.0	0		74.0	32.0	0.432432	NM_004415	B2RTT2|D7RX09|O75993|Q14189|Q9UHN4	Frame_Shift_Ins	INS	ENST00000379802.3	hg19	CCDS4501.1																																																																																			.	.	.	none		0.450	DSP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039786.2	NM_004415	
DDX58	23586	hgsc.bcm.edu	37	9	32466289	32466289	+	Splice_Site	DEL	T	T	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr9:32466289delT	ENST00000379883.2	-	16	2493	c.2336delA	c.(2335-2337)aag>ag	p.K779fs	DDX58_ENST00000379882.1_Splice_Site_p.K734fs|DDX58_ENST00000379868.1_Splice_Site_p.K576fs|DDX58_ENST00000542096.1_Splice_Site_p.K708fs	NM_014314.3	NP_055129.2	O95786	DDX58_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 58	779	Interaction with ZC3HAV1.|Repressor domain.				cytoplasmic pattern recognition receptor signaling pathway in response to virus (GO:0039528)|detection of virus (GO:0009597)|innate immune response (GO:0045087)|negative regulation of type I interferon production (GO:0032480)|positive regulation of defense response to virus by host (GO:0002230)|positive regulation of interferon-alpha production (GO:0032727)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription factor import into nucleus (GO:0042993)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell migration (GO:0030334)|regulation of type III interferon production (GO:0034344)|response to exogenous dsRNA (GO:0043330)|response to virus (GO:0009615)|RIG-I signaling pathway (GO:0039529)|viral process (GO:0016032)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|ruffle membrane (GO:0032587)|tight junction (GO:0005923)	ATP binding (GO:0005524)|double-stranded DNA binding (GO:0003690)|double-stranded RNA binding (GO:0003725)|helicase activity (GO:0004386)|identical protein binding (GO:0042802)|single-stranded RNA binding (GO:0003727)|zinc ion binding (GO:0008270)			autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|liver(1)|lung(9)|ovary(2)|pancreas(1)|prostate(1)	27			LUSC - Lung squamous cell carcinoma(29;0.00813)	GBM - Glioblastoma multiforme(74;0.00056)		TAGACTTACCTTTTCCCTAAA	0.348																																					p.K779fs		Atlas-Indel,Pindel	.											.	DDX58	82	.	0			c.2337delG						PASS	.						194.0	182.0	186.0					9																	32466289		2203	4300	6503	SO:0001630	splice_region_variant	23586	exon16			.	AF038963	CCDS6526.1	9p12	2011-08-05			ENSG00000107201	ENSG00000107201		"""DEAD-boxes"""	19102	protein-coding gene	gene with protein product	"""RNA helicase RIG-I"", ""retinoic acid inducible gene I"""	609631				21690088	Standard	NM_014314		Approved	RIG-I, FLJ13599, DKFZp434J1111	uc003zra.3	O95786	OTTHUMG00000019746	ENST00000379883.2:c.2337+1A>-	chr9.hg19:g.32466289delT		39.0	0.0	0		32.0	13.0	0.40625	NM_014314	A2RU81|Q5HYE1|Q5VYT1|Q9NT04	Frame_Shift_Del	DEL	ENST00000379883.2	hg19	CCDS6526.1																																																																																			.	.	.	none		0.348	DDX58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052011.1	NM_014314	Frame_Shift_Del
OGDHL	55753	hgsc.bcm.edu	37	10	50944091	50944100	+	Frame_Shift_Del	DEL	GGATGGTCAT	GGATGGTCAT	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	GGATGGTCAT	GGATGGTCAT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr10:50944091_50944100delGGATGGTCAT	ENST00000374103.4	-	22	2963_2972	c.2878_2887delATGACCATCC	c.(2878-2889)atgaccatcctgfs	p.MTIL960fs	OGDHL_ENST00000419399.1_Frame_Shift_Del_p.MTIL903fs|OGDHL_ENST00000432695.1_Frame_Shift_Del_p.MTIL751fs|OGDHL_ENST00000490844.1_5'UTR	NM_018245.2	NP_060715.2	Q9ULD0	OGDHL_HUMAN	oxoglutarate dehydrogenase-like	960					glycolytic process (GO:0006096)|tricarboxylic acid cycle (GO:0006099)	mitochondrion (GO:0005739)	metal ion binding (GO:0046872)|oxoglutarate dehydrogenase (succinyl-transferring) activity (GO:0004591)|thiamine pyrophosphate binding (GO:0030976)			central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(2)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|soft_tissue(1)|upper_aerodigestive_tract(1)	61						GCGCGCCTCAGGATGGTCATGAAGCGTGGG	0.605																																					p.960_963del		Atlas-Indel,Pindel	.											.	OGDHL	149	.	0			c.2879_2888del						PASS	.																																			SO:0001589	frameshift_variant	55753	exon22			.	AK001713	CCDS7234.1, CCDS44390.1, CCDS44391.1	10q11.23	2013-09-20			ENSG00000197444	ENSG00000197444			25590	protein-coding gene	gene with protein product						10574462	Standard	NM_018245		Approved	FLJ10851	uc001jie.3	Q9ULD0	OTTHUMG00000018200	ENST00000374103.4:c.2878_2887delATGACCATCC	chr10.hg19:g.50944091_50944100delGGATGGTCAT	ENSP00000363216:p.Met960fs	28.0	0.0	0		32.0	13.0	0.40625	NM_018245	A8K2G1|B4DKG2|B4E193|Q8TAN9|Q9NVA0	Frame_Shift_Del	DEL	ENST00000374103.4	hg19	CCDS7234.1																																																																																			.	.	.	none		0.605	OGDHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048007.1	NM_018245	
OR5W2	390148	hgsc.bcm.edu	37	11	55682005	55682005	+	Frame_Shift_Del	DEL	G	G	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr11:55682005delG	ENST00000344514.1	-	1	53	c.54delC	c.(52-54)accfs	p.T18fs		NM_001001960.1	NP_001001960.1	Q8NH69	OR5W2_HUMAN	olfactory receptor, family 5, subfamily W, member 2	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(7)|lung(28)|ovary(1)|pancreas(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	49						CTGGGTTATTGGTAATTCCCA	0.343																																					p.N19fs	Melanoma(48;171 1190 15239 43886 49348)	Atlas-Indel,Pindel	.											.	OR5W2	112	.	0			c.55delA						PASS	.						49.0	52.0	51.0					11																	55682005		2201	4296	6497	SO:0001589	frameshift_variant	390148	exon1			.	BK004398	CCDS31513.1	11q11	2012-08-09		2004-03-10	ENSG00000187612	ENSG00000187612		"""GPCR / Class A : Olfactory receptors"""	15299	protein-coding gene	gene with protein product				OR5W2P, OR5W3P			Standard	NM_001001960		Approved		uc010rir.2	Q8NH69	OTTHUMG00000166818	ENST00000344514.1:c.54delC	chr11.hg19:g.55682005delG	ENSP00000342448:p.Thr18fs	82.0	0.0	0		81.0	33.0	0.407407	NM_001001960		Frame_Shift_Del	DEL	ENST00000344514.1	hg19	CCDS31513.1																																																																																			.	.	.	none		0.343	OR5W2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391523.1	NM_001001960	
HIVEP2	3097	hgsc.bcm.edu	37	6	143094459	143094459	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:143094459delC	ENST00000367604.1	-	4	2056	c.1417delG	c.(1417-1419)gatfs	p.D473fs	HIVEP2_ENST00000012134.2_Frame_Shift_Del_p.D473fs|HIVEP2_ENST00000367603.2_Frame_Shift_Del_p.D473fs			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GAAACAGGATCTTCAAACATC	0.483																																					p.D473fs	Esophageal Squamous(107;843 1510 13293 16805 42198)	Atlas-INDEL	.											.	HIVEP2	225	.	0			c.1418delA						PASS	.						138.0	135.0	136.0					6																	143094459		2033	4190	6223	SO:0001589	frameshift_variant	3097	exon5			.	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.1417delG	chr6.hg19:g.143094459delC	ENSP00000356576:p.Asp473fs	75.0	0.0	0		61.0	24.0	0.393443	NM_006734	Q02646|Q5THT5|Q9NS05	Frame_Shift_Del	DEL	ENST00000367604.1	hg19	CCDS43510.1																																																																																			.	.	.	none		0.483	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
MYH9	4627	hgsc.bcm.edu	37	22	36702564	36702570	+	Frame_Shift_Del	DEL	TGCGGAA	TGCGGAA	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TGCGGAA	TGCGGAA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr22:36702564_36702570delTGCGGAA	ENST00000216181.5	-	16	2157_2163	c.1927_1933delTTCCGCA	c.(1927-1935)ttccgcactfs	p.FRT643fs		NM_002473.4	NP_002464.1	P35579	MYH9_HUMAN	myosin, heavy chain 9, non-muscle	643	Myosin motor.				actin cytoskeleton reorganization (GO:0031532)|actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|angiogenesis (GO:0001525)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|blood vessel endothelial cell migration (GO:0043534)|cytokinesis (GO:0000910)|establishment of meiotic spindle localization (GO:0051295)|establishment of T cell polarity (GO:0001768)|in utero embryonic development (GO:0001701)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|meiotic spindle organization (GO:0000212)|membrane protein ectodomain proteolysis (GO:0006509)|monocyte differentiation (GO:0030224)|myoblast fusion (GO:0007520)|platelet aggregation (GO:0070527)|platelet formation (GO:0030220)|protein transport (GO:0015031)|regulation of cell shape (GO:0008360)|termination of G-protein coupled receptor signaling pathway (GO:0038032)|uropod organization (GO:0032796)	actin cytoskeleton (GO:0015629)|actomyosin (GO:0042641)|actomyosin contractile ring (GO:0005826)|cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|cleavage furrow (GO:0032154)|cortical cytoskeleton (GO:0030863)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|ruffle (GO:0001726)|spindle (GO:0005819)|stress fiber (GO:0001725)|uropod (GO:0001931)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|actin-dependent ATPase activity (GO:0030898)|ADP binding (GO:0043531)|ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microfilament motor activity (GO:0000146)|motor activity (GO:0003774)|poly(A) RNA binding (GO:0044822)|protein anchor (GO:0043495)|protein homodimerization activity (GO:0042803)			NS(1)|breast(8)|central_nervous_system(3)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(16)|lung(29)|ovary(4)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(3)	86						TGCCCCACAGTGCGGAACATGCCCTTC	0.618			T	ALK	ALCL		"""Deafness, autosomal dominant 17, Epstein syndrome, Fechtner syndrome, May-Hegglin anomaly, Sebastian syndrome"""		Hereditary Macrothrombocytopenia, MYH9-associated																												p.643_645del		Atlas-Indel,Pindel	.		Dom	yes		22	22q13.1	4627	"""myosin, heavy polypeptide 9, non-muscle"""	yes	L	.	MYH9	225	.	0			c.1928_1934del						PASS	.																																			SO:0001589	frameshift_variant	4627	exon16	Familial Cancer Database	MYHIIA syndrome, incl. Fechtner Syndrome, FTNS, and May-Hegglin Anomaly, MHA	.		CCDS13927.1	22q13.1	2014-09-17	2006-09-29		ENSG00000100345	ENSG00000100345		"""Myosins / Myosin superfamily : Class II"""	7579	protein-coding gene	gene with protein product	"""nonmuscle myosin heavy chain II-A"""	160775	"""myosin, heavy polypeptide 9, non-muscle"""	DFNA17		1860190, 11023810	Standard	NM_002473		Approved	NMMHCA, NMHC-II-A, MHA, FTNS, EPSTS	uc003apg.3	P35579	OTTHUMG00000030429	ENST00000216181.5:c.1927_1933delTTCCGCA	chr22.hg19:g.36702564_36702570delTGCGGAA	ENSP00000216181:p.Phe643fs	89.0	0.0	0		57.0	17.0	0.298246	NM_002473	A8K6E4|O60805|Q60FE2|Q86T83	Frame_Shift_Del	DEL	ENST00000216181.5	hg19	CCDS13927.1																																																																																			.	.	.	none		0.618	MYH9-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000259110.3	NM_002473	
FAM98B	283742	hgsc.bcm.edu	37	15	38776684	38776685	+	IGR	INS	-	-	GGG			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr15:38776684_38776685insGGG	ENST00000491535.1	+	0	3111				FAM98B_ENST00000397609.2_In_Frame_Ins_p.383_384insG	NM_001042429.1	NP_001035894.1	Q52LJ0	FA98B_HUMAN	family with sequence similarity 98, member B							cytoplasm (GO:0005737)|nucleus (GO:0005634)|tRNA-splicing ligase complex (GO:0072669)	poly(A) RNA binding (GO:0044822)			endometrium(2)|large_intestine(3)|lung(1)|ovary(1)|skin(1)	8		all_cancers(109;3.11e-17)|all_epithelial(112;2.64e-15)|Lung NSC(122;2.11e-11)|all_lung(180;5.61e-10)|Melanoma(134;0.0574)		GBM - Glioblastoma multiforme(113;9e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0209)		gggaggagggtgggggGGAGGA	0.658																																					p.W376delinsWG		Atlas-INDEL	.											.	FAM98B	53	.	0			c.1126_1127insGGG						PASS	.																																			SO:0001628	intergenic_variant	283742	exon8			.		CCDS10047.2	15q14	2006-11-29		2005-11-20	ENSG00000171262	ENSG00000171262			26773	protein-coding gene	gene with protein product						12477932	Standard	NM_173611		Approved	FLJ38426	uc001zkc.3	Q52LJ0	OTTHUMG00000129831		chr15.hg19:g.38776688_38776690dupGGG		47.0	0.0	0		41.0	14.0	0.341463	NM_173611	A8MUW5|Q8N935	In_Frame_Ins	INS	ENST00000491535.1	hg19	CCDS42015.1																																																																																			.	.	.	none		0.658	FAM98B-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252071.2	NM_173611	
IGFN1	91156	hgsc.bcm.edu	37	1	201174369	201174369	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr1:201174369delC	ENST00000335211.4	+	11	1206	c.1076delC	c.(1075-1077)tccfs	p.S359fs	IGFN1_ENST00000295591.8_5'UTR|IGFN1_ENST00000451870.2_Frame_Shift_Del_p.S359fs	NM_001164586.1	NP_001158058.1	Q86VF2	IGFN1_HUMAN	immunoglobulin-like and fibronectin type III domain containing 1	359	Ig-like 2.					nucleus (GO:0005634)|Z disc (GO:0030018)				autonomic_ganglia(2)|cervix(1)|endometrium(3)|kidney(1)|large_intestine(6)|lung(21)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	45						GTGTATGTGTCCCCTGACGGG	0.617																																					p.S359fs		Atlas-Indel,Pindel	.											.	IGFN1	220	.	0			c.1075delT						PASS	.						33.0	32.0	32.0					1																	201174369		692	1591	2283	SO:0001589	frameshift_variant	91156	exon11			.	AY245430	CCDS53455.1	1q32.1	2013-02-11			ENSG00000163395	ENSG00000163395		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	24607	protein-coding gene	gene with protein product							Standard	NM_001164586		Approved	DKFZp434B1231, EEF1A2BP1	uc001gwc.3	Q86VF2	OTTHUMG00000035728	ENST00000335211.4:c.1076delC	chr1.hg19:g.201174369delC	ENSP00000334714:p.Ser359fs	122.0	0.0	0		122.0	46.0	0.377049	NM_001164586	F8WAI1|Q9NT72	Frame_Shift_Del	DEL	ENST00000335211.4	hg19	CCDS53455.1																																																																																			.	.	.	none		0.617	IGFN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_178275	
HSD17B14	51171	hgsc.bcm.edu	37	19	49316501	49316502	+	Frame_Shift_Ins	INS	-	-	C			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr19:49316501_49316502insC	ENST00000263278.4	-	9	1009_1010	c.743_744insG	c.(742-744)ggtfs	p.G248fs	HSD17B14_ENST00000599157.1_Frame_Shift_Ins_p.G224fs|BCAT2_ENST00000316273.6_5'Flank|BCAT2_ENST00000599246.1_5'Flank|BCAT2_ENST00000598162.1_5'Flank|BCAT2_ENST00000597011.1_5'Flank|BCAT2_ENST00000545387.2_5'Flank|BCAT2_ENST00000601496.1_5'Flank|BCAT2_ENST00000402551.1_5'Flank	NM_016246.2	NP_057330.2	Q9BPX1	DHB14_HUMAN	hydroxysteroid (17-beta) dehydrogenase 14	248					steroid catabolic process (GO:0006706)	cytosol (GO:0005829)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|testosterone 17-beta-dehydrogenase (NADP+) activity (GO:0047045)			large_intestine(3)|lung(1)|skin(1)	5		all_epithelial(76;7e-07)|all_lung(116;1.7e-06)|Lung NSC(112;3.55e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)		OV - Ovarian serous cystadenocarcinoma(262;0.000341)|all cancers(93;0.000764)|GBM - Glioblastoma multiforme(486;0.0233)|Epithelial(262;0.0346)		CCAGCTCTGCACCCCCCGTCAC	0.658																																					p.G248fs		Atlas-Indel,Pindel	.											.	HSD17B14	25	.	0			c.744_745insG						PASS	.			2,4256		0,2,2127						-5.4	0.5			23	5,8237		0,5,4116	no	frameshift	HSD17B14	NM_016246.2		0,7,6243	A1A1,A1R,RR		0.0607,0.047,0.056				7,12493				SO:0001589	frameshift_variant	51171	exon9			.	AF126781	CCDS12736.1	19q13.33	2011-09-14	2006-11-22	2006-11-22		ENSG00000087076		"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 1"""	23238	protein-coding gene	gene with protein product	"""retinal short-chain dehydrogenase/reductase 3"", ""short chain dehydrogenase/reductase family 47C, member 1"""	612832	"""dehydrogenase/reductase (SDR family) member 10"""	DHRS10		10800688, 17067289, 19027726	Standard	XM_005258969		Approved	retSDR3, SDR47C1	uc002pkv.1	Q9BPX1		ENST00000263278.4:c.744dupG	chr19.hg19:g.49316507_49316507dupC	ENSP00000263278:p.Gly248fs	140.0	0.0	0		126.0	51.0	0.404762	NM_016246	Q9UKU3	Frame_Shift_Ins	INS	ENST00000263278.4	hg19	CCDS12736.1																																																																																			.	.	.	none		0.658	HSD17B14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466212.1	NM_016246	
TTC21A	199223	hgsc.bcm.edu	37	3	39175774	39175775	+	Frame_Shift_Ins	INS	-	-	TCCA			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:39175774_39175775insTCCA	ENST00000431162.2	+	21	2972_2973	c.2838_2839insTCCA	c.(2839-2841)gccfs	p.A947fs	TTC21A_ENST00000301819.6_Frame_Shift_Ins_p.A948fs|TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000440121.1_Frame_Shift_Ins_p.A899fs			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A	947										NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		AGCAGCACTGTGCCATCCTCCT	0.599																																					p.C946fs		Atlas-INDEL	.											.	TTC21A	96	.	0			c.2838_2839insTCCA						PASS	.																																			SO:0001589	frameshift_variant	199223	exon21			.	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	Exception_encountered	chr3.hg19:g.39175774_39175775insTCCA	ENSP00000398211:p.Ala947fs	84.0	0.0	0		82.0	36.0	0.439024	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Frame_Shift_Ins	INS	ENST00000431162.2	hg19	CCDS46800.1																																																																																			.	.	.	none		0.599	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
ENOSF1	55556	hgsc.bcm.edu	37	18	677380	677380	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr18:677380delA	ENST00000251101.7	-	14	1201	c.1113delT	c.(1111-1113)tttfs	p.F371fs	ENOSF1_ENST00000583973.1_5'UTR|ENOSF1_ENST00000319815.6_Frame_Shift_Del_p.F141fs|ENOSF1_ENST00000340116.7_Frame_Shift_Del_p.F378fs|ENOSF1_ENST00000383578.3_Frame_Shift_Del_p.F289fs|ENOSF1_ENST00000580982.1_Frame_Shift_Del_p.F295fs	NM_017512.5	NP_059982.2	Q7L5Y1	ENOF1_HUMAN	enolase superfamily member 1	371					cellular amino acid catabolic process (GO:0009063)|cellular carbohydrate catabolic process (GO:0044275)	mitochondrion (GO:0005739)	isomerase activity (GO:0016853)|L-fuconate dehydratase activity (GO:0050023)|magnesium ion binding (GO:0000287)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(3)|ovary(1)|prostate(1)	10						ATATGTAGTCAAATATAATCA	0.423																																					p.D379fs		Atlas-Indel,Pindel	.											ENOSF1,NS,lymphoid_neoplasm,0,1	ENOSF1	44	.	0			c.1135delG						PASS	.						84.0	86.0	85.0					18																	677380		2203	4300	6503	SO:0001589	frameshift_variant	55556	exon13			.	X67098	CCDS11822.1, CCDS11823.1, CCDS45821.1	18p11.32	2005-01-26			ENSG00000132199	ENSG00000132199			30365	protein-coding gene	gene with protein product		607427				14508106	Standard	NM_001126123		Approved	HSRTSBETA, rTS, TYMSAS	uc002kku.4	Q7L5Y1	OTTHUMG00000131470	ENST00000251101.7:c.1113delT	chr18.hg19:g.677380delA	ENSP00000251101:p.Phe371fs	132.0	0.0	0		123.0	56.0	0.455285	NM_202758	A6NMP3|A8K9R5|B3KSL6|B3KXE4|D3DUH0|Q15407|Q15594|Q15595|Q6ZS08|Q9HAS5|Q9HAS6	Frame_Shift_Del	DEL	ENST00000251101.7	hg19	CCDS11822.1																																																																																			.	.	.	none		0.423	ENOSF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254312.2	NM_017512	
DLK2	65989	hgsc.bcm.edu	37	6	43418926	43418926	+	Frame_Shift_Del	DEL	C	C	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:43418926delC	ENST00000357338.3	-	6	1203	c.503delG	c.(502-504)ggtfs	p.G168fs	DLK2_ENST00000372488.3_Frame_Shift_Del_p.G168fs|DLK2_ENST00000372485.1_Frame_Shift_Del_p.G162fs|DLK2_ENST00000414245.1_Frame_Shift_Del_p.G162fs	NM_206539.1	NP_996262.1	Q6UY11	DLK2_HUMAN	delta-like 2 homolog (Drosophila)	168	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				negative regulation of Notch signaling pathway (GO:0045746)|regulation of fat cell differentiation (GO:0045598)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)	p.G168D(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(1)|upper_aerodigestive_tract(1)	7	all_lung(25;0.00536)		Colorectal(64;0.00245)|COAD - Colon adenocarcinoma(64;0.00536)|all cancers(41;0.0152)|OV - Ovarian serous cystadenocarcinoma(102;0.0804)			ACAGCGGGCACCCACAAAGCC	0.612																																					p.G168fs		Atlas-Indel,Pindel	.											.	DLK2	22	.	1	Substitution - Missense(1)	upper_aerodigestive_tract(1)	c.504delT						PASS	.						80.0	57.0	65.0					6																	43418926		2203	4300	6503	SO:0001589	frameshift_variant	65989	exon6			.	AK055380	CCDS4897.1, CCDS75461.1	6p21.1	2008-02-05	2007-07-05	2007-07-05	ENSG00000171462	ENSG00000171462			21113	protein-coding gene	gene with protein product			"""EGF-like-domain, multiple 9"""	EGFL9			Standard	NM_001286656		Approved	MGC2487	uc003ovb.3	Q6UY11	OTTHUMG00000014735	ENST00000357338.3:c.503delG	chr6.hg19:g.43418926delC	ENSP00000349893:p.Gly168fs	137.0	0.0	0		110.0	51.0	0.463636	NM_206539	B3KNZ7|Q5T3T8|Q9BQ54	Frame_Shift_Del	DEL	ENST00000357338.3	hg19	CCDS4897.1																																																																																			.	.	.	none		0.612	DLK2-003	KNOWN	alternative_5_UTR|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040618.1	NM_023932	
PARD3B	117583	hgsc.bcm.edu	37	2	205550903	205550903	+	Splice_Site	DEL	G	G	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:205550903delG	ENST00000406610.2	+	2	327		c.e2-1		PARD3B_ENST00000358768.2_Splice_Site|PARD3B_ENST00000351153.1_Splice_Site|PARD3B_ENST00000462231.1_Splice_Site|PARD3B_ENST00000349953.3_Splice_Site	NM_057177.6|NM_152526.5|NM_205863.3	NP_476518.4|NP_689739.4|NP_995585.2	Q8TEW8	PAR3L_HUMAN	par-3 family cell polarity regulator beta						cell cycle (GO:0007049)|cell division (GO:0051301)	membrane (GO:0016020)|tight junction (GO:0005923)				breast(1)|endometrium(9)|kidney(2)|large_intestine(6)|liver(4)|lung(33)|ovary(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	65		all_cancers(1;2.88e-06)|all_epithelial(1;3.23e-06)		Epithelial(149;0.0739)		TTCTACTATAGGGTCCTGGTT	0.328																																					.		Atlas-Indel,Pindel	.											.	PARD3B	314	.	0			c.121-2G>-						PASS	.						127.0	114.0	118.0					2																	205550903		1830	4085	5915	SO:0001630	splice_region_variant	117583	exon2			.	AB053321	CCDS42804.1, CCDS42805.1, CCDS42806.1	2q33.3	2013-08-28	2013-08-28	2006-09-28	ENSG00000116117	ENSG00000116117			14446	protein-coding gene	gene with protein product			"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 19"", ""par-3 partitioning defective 3 homolog B (C. elegans)"""	ALS2CR19		11586298, 12459187	Standard	NM_057177		Approved	Par3L, PAR3beta	uc002vap.2	Q8TEW8	OTTHUMG00000154562	ENST00000406610.2:c.121-1G>-	chr2.hg19:g.205550903delG		58.0	0.0	0		103.0	25.0	0.242718	NM_057177	E9PE87|Q8IUC7|Q8IUC9|Q96DK9|Q96N09|Q96NX6|Q96NX7|Q96Q29	Splice_Site	DEL	ENST00000406610.2	hg19																																																																																				.	.	.	none		0.328	PARD3B-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000335992.1	NM_057177	Intron
DYSF	8291	hgsc.bcm.edu	37	2	71740432	71740437	+	Intron	DEL	TACTCT	TACTCT	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	TACTCT	TACTCT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr2:71740432_71740437delTACTCT	ENST00000258104.3	+	6	734				DYSF_ENST00000409366.1_Intron|DYSF_ENST00000394120.2_Intron|DYSF_ENST00000409762.1_In_Frame_Del_p.YS174del|DYSF_ENST00000409651.1_In_Frame_Del_p.YS175del|DYSF_ENST00000410020.3_In_Frame_Del_p.YS175del|DYSF_ENST00000410041.1_In_Frame_Del_p.YS175del|DYSF_ENST00000413539.2_In_Frame_Del_p.YS174del|DYSF_ENST00000409744.1_Intron|DYSF_ENST00000409582.3_In_Frame_Del_p.YS174del|DYSF_ENST00000429174.2_Intron	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin						plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GGACACGAGATACTCTGGAAAGAAGT	0.636																																					p.174_176del		Atlas-Indel,Pindel	.											.	DYSF	536	.	0			c.522_527del						PASS	.																																			SO:0001627	intron_variant	8291	exon6			.	AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.458-409TACTCT>-	chr2.hg19:g.71740432_71740437delTACTCT		206.0	0.0	0		156.0	38.0	0.24359	NM_001130987	A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	In_Frame_Del	DEL	ENST00000258104.3	hg19	CCDS1918.1																																																																																			.	.	.	none		0.636	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3	NM_003494	
TTC21A	199223	hgsc.bcm.edu	37	3	39175775	39175776	+	Frame_Shift_Ins	INS	-	-	CCAT			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	-	-	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr3:39175775_39175776insCCAT	ENST00000431162.2	+	21	2973_2974	c.2839_2840insCCAT	c.(2839-2841)gccfs	p.-948fs	TTC21A_ENST00000301819.6_Frame_Shift_Ins_p.-949fs|TTC21A_ENST00000493856.1_3'UTR|TTC21A_ENST00000440121.1_Frame_Shift_Ins_p.-900fs			Q8NDW8	TT21A_HUMAN	tetratricopeptide repeat domain 21A											NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(23)|ovary(1)|prostate(1)|skin(3)	50				KIRC - Kidney renal clear cell carcinoma(284;0.0588)|Kidney(284;0.0738)		GCAGCACTGTGCCATCCTCCTG	0.599																																					p.A947fs		Pindel	.											.	TTC21A	96	.	0			c.2839_2840insCCAT						PASS	.																																			SO:0001589	frameshift_variant	199223	exon21			.	AJ487015	CCDS43068.1, CCDS46800.1, CCDS43068.2	3p22.2	2014-09-04			ENSG00000168026	ENSG00000168026		"""Tetratricopeptide (TTC) repeat domain containing"""	30761	protein-coding gene	gene with protein product		611430					Standard	NM_145755		Approved	STI2	uc003cjc.2	Q8NDW8	OTTHUMG00000155973	ENST00000431162.2:c.2840_2843dupCCAT	chr3.hg19:g.39175776_39175779dupCCAT	ENSP00000398211:p.Ile948fs	84.0	0.0	.		81.0	25.0	0.309	NM_145755	A1L388|B4DYF6|B4DYJ3|D3YTE7|D4PHA5|Q6P5W8|Q8N7G5|Q8NA02	Frame_Shift_Ins	INS	ENST00000431162.2	hg19	CCDS46800.1																																																																																			.	.	.	none		0.599	TTC21A-021	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000377829.1	NM_145755	
HIVEP2	3097	hgsc.bcm.edu	37	6	143094459	143094460	+	Frame_Shift_Del	DEL	CT	CT	-			TCGA-2Z-A9J3-01A-12D-A382-10	TCGA-2Z-A9J3-10A-01D-A385-10	CT	CT	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	32cc4455-b4d6-47b7-8121-6a41d2f6aec3	72bef80f-14ac-48e0-b629-117038e12a5c	g.chr6:143094459_143094460delCT	ENST00000367604.1	-	4	2055_2056	c.1416_1417delAG	c.(1414-1419)gaagatfs	p.D473fs	HIVEP2_ENST00000012134.2_Frame_Shift_Del_p.D473fs|HIVEP2_ENST00000367603.2_Frame_Shift_Del_p.D473fs			P31629	ZEP2_HUMAN	human immunodeficiency virus type I enhancer binding protein 2	473					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(2)|breast(4)|central_nervous_system(6)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(19)|lung(35)|ovary(4)|prostate(6)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	100				OV - Ovarian serous cystadenocarcinoma(155;1.61e-05)|GBM - Glioblastoma multiforme(68;0.0102)		GAAACAGGATCTTCAAACATCT	0.485																																					p.473_473del	Esophageal Squamous(107;843 1510 13293 16805 42198)	Pindel	.											.	HIVEP2	225	.	0			c.1417_1418del						PASS	.																																			SO:0001589	frameshift_variant	3097	exon5			.	M60119	CCDS43510.1	6q23-q24	2013-01-08	2001-11-28		ENSG00000010818	ENSG00000010818		"""Zinc fingers, C2H2-type"""	4921	protein-coding gene	gene with protein product	"""c-myc intron binding protein 1"""	143054	"""human immunodeficiency virus type I enhancer-binding protein 2"""			1733857, 2022670	Standard	NM_006734		Approved	MBP-2, HIV-EP2, MIBP1, ZAS2, Schnurri-2, ZNF40B	uc003qjd.3	P31629	OTTHUMG00000015713	ENST00000367604.1:c.1416_1417delAG	chr6.hg19:g.143094459_143094460delCT	ENSP00000356576:p.Asp473fs	76.0	0.0	.		62.0	14.0	0.226	NM_006734	Q02646|Q5THT5|Q9NS05	Frame_Shift_Del	DEL	ENST00000367604.1	hg19	CCDS43510.1																																																																																			.	.	.	none		0.485	HIVEP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042495.1		
